Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 86 of 295
Found at i:25316434 original size:11 final size:11
Alignment explanation
Indices: 25316420--25316463 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
25316410 TTATTAAAAC
25316420 TTATAAAATCA
1 TTATAAAATCA
25316431 TTATAAAATCA
1 TTATAAAATCA
25316442 TTAT-AAA--A
1 TTATAAAATCA
25316450 TTATAAAATCA
1 TTATAAAATCA
25316461 TTA
1 TTA
25316464 GAAGTTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.17
9 3 0.10
10 3 0.10
11 19 0.63
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (11 bp):
TTATAAAATCA
Found at i:25316454 original size:19 final size:18
Alignment explanation
Indices: 25316430--25316494 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
25316420 TTATAAAATC
25316430 ATTATAAAATCATTATAAA
1 ATTATAAAATCATTA-AAA
*
25316449 ATTATAAAATCATTAGAA
1 ATTATAAAATCATTAAAA
*
25316467 GTTATAGAAAATCA-TAAAA
1 ATTAT--AAAATCATTAAAA
25316486 ATTATAAAA
1 ATTATAAAA
25316495 ACCATAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.10
18 6 0.15
19 23 0.57
20 7 0.17
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTATAAAATCATTAAAA
Found at i:25320576 original size:27 final size:27
Alignment explanation
Indices: 25320534--25320616 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
25320524 ATAGTGACAA
25320534 TGGCACTTCGATGCAAATCAATGATAG
1 TGGCACTTCGATGCAAATCAATGATAG
* * *
25320561 TGGTACTTCGGTGCAAATC-A-GTTAG
1 TGGCACTTCGATGCAAATCAATGATAG
* * *
25320586 TGGCACCTCGATGCAATTCAGTGATAG
1 TGGCACTTCGATGCAAATCAATGATAG
25320613 TGGC
1 TGGC
25320617 TCATTGGAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
25 19 0.42
26 1 0.02
27 25 0.56
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (27 bp):
TGGCACTTCGATGCAAATCAATGATAG
Found at i:25322040 original size:63 final size:63
Alignment explanation
Indices: 25321962--25322088 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
25321952 TTTTACAAGT
25321962 GTTGTTTCGGCTTTTTTTAAGAATGCTTTGATTCTCTAGTTTCAGAGCTTTGAAGGCTAAAAG
1 GTTGTTTCGGCTTTTTTTAAGAATGCTTTGATTCTCTAGTTTCAGAGCTTTGAAGGCTAAAAG
25322025 GTTGTTTCGGCTTTTTTTAAGAATGCTTTGATTCTCTAGTTTCAGAGCTTTGAAGGCTAAAAG
1 GTTGTTTCGGCTTTTTTTAAGAATGCTTTGATTCTCTAGTTTCAGAGCTTTGAAGGCTAAAAG
25322088 G
1 G
25322089 GAGTGCGATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.43
Consensus pattern (63 bp):
GTTGTTTCGGCTTTTTTTAAGAATGCTTTGATTCTCTAGTTTCAGAGCTTTGAAGGCTAAAAG
Found at i:25322647 original size:182 final size:182
Alignment explanation
Indices: 25322340--25322704 Score: 694
Period size: 182 Copynumber: 2.0 Consensus size: 182
25322330 ACACAGACGT
*
25322340 GTGACTGATTTGGAAATTAAGGATTCCACACGGATGTGTGTTTTGGGACACACGGTCGTGTCTGG
1 GTGACTGATTTGGAAATTAAGGATTCCACACGGACGTGTGTTTTGGGACACACGGTCGTGTCTGG
25322405 TGGCCACACGGGCATGTGAGACCCTCACACGGCCGTGTCTACTCTGCACTTGAGCTTAGTGAAAT
66 TGGCCACACGGGCATGTGAGACCCTCACACGGCCGTGTCTACTCTGCACTTGAGCTTAGTGAAAT
* *
25322470 AGGATAGTGTCTTACACGGCCTGATTACATGGTCGTGCCTCTACACCACACG
131 AGGATAGTGTCTTACACGGCCTGATCACATGGCCGTGCCTCTACACCACACG
*
25322522 GTGACTGATTTGGGAATTAAGGATTCCACACGGACGTGTGTTTTGGGACACACGGTCGTGTCTGG
1 GTGACTGATTTGGAAATTAAGGATTCCACACGGACGTGTGTTTTGGGACACACGGTCGTGTCTGG
25322587 TGGCCACACGGGCATGTGAGACCCTCACACGGCCGTGTCTACTCTGCACTTGAGCTTAGTGAAAT
66 TGGCCACACGGGCATGTGAGACCCTCACACGGCCGTGTCTACTCTGCACTTGAGCTTAGTGAAAT
25322652 AGGATAGTGTCTTACACGGCCTGATCACATGGCCGTGCCTCTACACCACACG
131 AGGATAGTGTCTTACACGGCCTGATCACATGGCCGTGCCTCTACACCACACG
25322704 G
1 G
25322705 GCGTATGTCT
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
182 179 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (182 bp):
GTGACTGATTTGGAAATTAAGGATTCCACACGGACGTGTGTTTTGGGACACACGGTCGTGTCTGG
TGGCCACACGGGCATGTGAGACCCTCACACGGCCGTGTCTACTCTGCACTTGAGCTTAGTGAAAT
AGGATAGTGTCTTACACGGCCTGATCACATGGCCGTGCCTCTACACCACACG
Found at i:25328273 original size:37 final size:37
Alignment explanation
Indices: 25328196--25328281 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
25328186 GATAAGATAA
** *
25328196 TCTGCTGGACTTATCCGTATGTTTCAAGGTAAAACAG
1 TCTGCTGGACTTATCCGTACATTTCAAGCTAAAACAG
* *
25328233 TCTGCTGGACTTATCCTTACATTTCAAGCTAAGATC-G
1 TCTGCTGGACTTATCCGTACATTTCAAGCTAA-AACAG
*
25328270 TCTGTTGGACTT
1 TCTGCTGGACTT
25328282 GTCTCTAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 40 0.95
38 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (37 bp):
TCTGCTGGACTTATCCGTACATTTCAAGCTAAAACAG
Found at i:25328421 original size:28 final size:28
Alignment explanation
Indices: 25328398--25328512 Score: 117
Period size: 28 Copynumber: 4.1 Consensus size: 28
25328388 TGTACATATA
25328398 AATCTGCATATATGATTTCGTA-CATATG
1 AATCTGCATATATGATTTCGTATC-TATG
*
25328426 AAT-TAGCATATAAGATTTCGTATCTATG
1 AATCT-GCATATATGATTTCGTATCTATG
* * *
25328454 AATCTGCCTATGTGATTTTGTATCTATG
1 AATCTGCATATATGATTTCGTATCTATG
* * ** *
25328482 AATCTGCCTATGTGATCACGTTTCTATG
1 AATCTGCATATATGATTTCGTATCTATG
25328510 AAT
1 AAT
25328513 TTCACCTATG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.01
28 72 0.96
29 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (28 bp):
AATCTGCATATATGATTTCGTATCTATG
Found at i:25334932 original size:24 final size:24
Alignment explanation
Indices: 25334905--25334954 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
25334895 GGTTATGAAG
25334905 TTCAACTCCACTTACTTATTTTAT
1 TTCAACTCCACTTACTTATTTTAT
25334929 TTCAACTCCACTTACTTATTTTAT
1 TTCAACTCCACTTACTTATTTTAT
25334953 TT
1 TT
25334955 TCGATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (24 bp):
TTCAACTCCACTTACTTATTTTAT
Found at i:25341999 original size:27 final size:27
Alignment explanation
Indices: 25341980--25342125 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
25341970 ATTACCAAAG
*
25341980 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
25342007 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25342034 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
25342061 TATCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
25342088 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
25342115 TACCCTCGATT
1 TACCCTCGATT
25342126 GTGAAATTAC
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 108 1.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:25342146 original size:27 final size:26
Alignment explanation
Indices: 25342115--25342281 Score: 106
Period size: 27 Copynumber: 6.2 Consensus size: 26
25342105 ATTACCATTT
* *
25342115 TACCCTCGATTGTGAAATTACTGAAA
1 TACCCTAGATTGTGAAATTACCGAAA
* ** *
25342141 TAACCCTATAGGGT-AGAATTACCAAAA
1 T-ACCCTAGATTGTGA-AATTACCGAAA
* *
25342168 TACCCCTAGTTTGTAAAATTACCGAAA
1 TA-CCCTAGATTGTGAAATTACCGAAA
* *
25342195 TACCACTAGTTTGTGAAATTACTGAAA
1 TACC-CTAGATTGTGAAATTACCGAAA
* *
25342222 TACCCTCA-ATTTGTAAAATTACCAAAA
1 TACCCT-AGA-TTGTGAAATTACCGAAA
* * *
25342249 TACCCCT-GATTTATAAAATTACAGAAA
1 TA-CCCTAGA-TTGTGAAATTACCGAAA
25342276 TACCCT
1 TACCCT
25342282 TGACTTTCTA
Statistics
Matches: 112, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
26 11 0.10
27 96 0.86
28 5 0.04
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (26 bp):
TACCCTAGATTGTGAAATTACCGAAA
Found at i:25342242 original size:81 final size:81
Alignment explanation
Indices: 25342124--25342279 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 81
25342114 TTACCCTCGA
* *
25342124 TTGTGAAATTACTGAAATAACCCTATAGGGTAGAATTACCAAAATACCCCT-AGTTTGTAAAATT
1 TTGTGAAATTACTGAAATAACCCTATAGGGTAAAATTACCAAAATACCCCTGA-TTTATAAAATT
*
25342188 ACCGAAATACCACTAGT
65 ACAGAAATACCACTAGT
**
25342205 TTGTGAAATTACTGAAAT-ACCCTCA-ATTTGTAAAATTACCAAAATACCCCTGATTTATAAAAT
1 TTGTGAAATTACTGAAATAACCCT-ATA-GGGTAAAATTACCAAAATACCCCTGATTTATAAAAT
25342268 TACAGAAATACC
64 TACAGAAATACC
25342280 CTTGACTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 6 0.09
81 60 0.90
82 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (81 bp):
TTGTGAAATTACTGAAATAACCCTATAGGGTAAAATTACCAAAATACCCCTGATTTATAAAATTA
CAGAAATACCACTAGT
Found at i:25342268 original size:54 final size:54
Alignment explanation
Indices: 25342177--25342337 Score: 164
Period size: 54 Copynumber: 2.9 Consensus size: 54
25342167 ATACCCCTAG
* * *
25342177 TTTGTAAAATTACCGAAATACCACT-AGTTTGTGAAATTACTGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGA-TTTATAAAATTACTGAAATACCCTCAA
* * * *
25342231 TTTGTAAAATTACCAAAATACCCCTGATTTATAAAATTACAGAAATACCCTTGAC
1 TTTGTAAAATTACCAAAATACCACTGATTTATAAAATTACTGAAATACCC-TCAA
* * * * *
25342286 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 TTTGT-AAAATTACCA-AAATACCACTGATTTATAAAATTACTGAAATACCCT
25342338 TGGTTTGTAG
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
54 43 0.48
55 9 0.10
56 37 0.42
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGATTTATAAAATTACTGAAATACCCTCAA
Found at i:25342303 original size:29 final size:27
Alignment explanation
Indices: 25342157--25342336 Score: 118
Period size: 27 Copynumber: 6.6 Consensus size: 27
25342147 TATAGGGTAG
*
25342157 AATTACCA-AAATACCCCT-AGTTTGTAA
1 AATTA-CAGAAATACCCCTGA-TTTATAA
* * * *
25342184 AATTACCGAAATACCACT-AGTTTGTGA
1 AATTACAGAAATACCCCTGA-TTTATAA
* * *
25342211 AATTACTGAAATA-CCCTCAATTTGTAA
1 AATTACAGAAATACCCCT-GATTTATAA
25342238 AATTACCA-AAATACCCCTGATTTATAA
1 AATTA-CAGAAATACCCCTGATTTATAA
* *
25342265 AATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACAGAAATACCCCTGA-TTTAT-AA
* ** * *
25342294 AATTATAGAAATACCATTGGTTTACAA
1 AATTACAGAAATACCCCTGATTTATAA
*
25342321 AATTACTGAAATACCC
1 AATTACAGAAATACCC
25342337 TTGGTTTGTA
Statistics
Matches: 126, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
26 6 0.05
27 88 0.70
28 13 0.10
29 19 0.15
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACAGAAATACCCCTGATTTATAA
Found at i:25342331 original size:27 final size:27
Alignment explanation
Indices: 25342292--25342343 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
25342282 TGACTTTCTA
25342292 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
25342319 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
25342344 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:25343231 original size:16 final size:16
Alignment explanation
Indices: 25343210--25343240 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25343200 CAAATATGGG
*
25343210 CATGACATTCTGCATA
1 CATGACATGCTGCATA
25343226 CATGACATGCTGCAT
1 CATGACATGCTGCAT
25343241 GGGTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (16 bp):
CATGACATGCTGCATA
Found at i:25343347 original size:24 final size:25
Alignment explanation
Indices: 25343271--25343340 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
25343261 AGGAAGTGCT
* * *
25343271 AAAAGGGATTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
25343296 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
25343321 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
25343341 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:25343353 original size:24 final size:24
Alignment explanation
Indices: 25343270--25343353 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
25343260 GAGGAAGTGC
* *
25343270 TAAAAGGGATTTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
25343295 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
25343319 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
25343343 TAAAAGAGGCT
1 TAAAAG-GGCT
25343354 AAGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 8 0.15
25 39 0.75
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:25343364 original size:50 final size:50
Alignment explanation
Indices: 25343271--25343365 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
25343261 AGGAAGTGCT
**
25343271 AAAAGGGATTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGATTTGCCCCAGTTTACCGAAAAGGGCTAAGCCCCAGTTTATCA
* **
25343321 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAAGCCTCCAGTT
1 AAAAGGGATTTGCCCCAGTTTACCGAAAAG-GGCTAAGCC-CCAGTT
25343366 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.25
Consensus pattern (50 bp):
AAAAGGGATTTGCCCCAGTTTACCGAAAAGGGCTAAGCCCCAGTTTATCA
Found at i:25343547 original size:42 final size:43
Alignment explanation
Indices: 25343488--25343580 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 43
25343478 TAGTCTCCCC
* *
25343488 AAATGGGCTTGCATACATTCATTGGTA-TTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTTAATGTGATATTG
*
25343530 AAATGGGCTTGCATACATTCATTGATATTTTAATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTTAATGTGATATTG
25343573 AAATGGGC
1 AAATGGGC
25343581 CTATGGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 26 0.55
43 21 0.45
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.40
Consensus pattern (43 bp):
AAATGGGCTTGCATACATTCATTGATATTTTAATGTGATATTG
Found at i:25345609 original size:27 final size:27
Alignment explanation
Indices: 25345590--25345735 Score: 166
Period size: 27 Copynumber: 5.4 Consensus size: 27
25345580 ATTACCAAAG
* *
25345590 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
25345617 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
25345644 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * ***
25345671 TATCCTTGATTTACAGAATTATTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * *
25345698 TACCCTTGATTTACACAATTAGCATTT
1 TACCCTCGATTTATAGAATTACCATTT
25345725 TACCCTCGATT
1 TACCCTCGATT
25345736 GTGAAATTAC
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 105 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:25345699 original size:54 final size:54
Alignment explanation
Indices: 25345590--25345735 Score: 184
Period size: 54 Copynumber: 2.7 Consensus size: 54
25345580 ATTACCAAAG
*
25345590 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
* * * * ***
25345644 TACCCTCGATTTATAGAATTATCGTTTTATCCTTGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
* * * *
25345698 TACCCTTGATTTACACAATTAGCATTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
25345736 GTGAAATTAC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
Found at i:25345797 original size:27 final size:27
Alignment explanation
Indices: 25345767--25345889 Score: 106
Period size: 27 Copynumber: 4.6 Consensus size: 27
25345757 TATAGGGTAG
*
25345767 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* * * * ** *
25345794 AATTATC-GAATATCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
* * *
25345820 AATTATCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
**
25345847 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAATTTGTAA
25345874 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
25345890 TTGACTTTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 23 0.30
27 53 0.70
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:25345949 original size:27 final size:27
Alignment explanation
Indices: 25345867--25345952 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
25345857 ATACCCCTAA
* *
25345867 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCCTTG-G
*
25345895 TTT-CTAAAAGTTA-TAGAAATACCATTGG
1 TTTAC-AAAA-TTACT-GAAATACCCTTGG
25345923 TTTACAAAATTACTGAAATACCCTTGG
1 TTTACAAAATTACTGAAATACCCTTGG
25345950 TTT
1 TTT
25345953 GTAGATTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 19 0.39
28 15 0.31
29 15 0.31
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCCTTGG
Found at i:25346985 original size:42 final size:42
Alignment explanation
Indices: 25346926--25347017 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
25346916 TAGTCTCCCC
*
25346926 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
25346968 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
25347010 AAATGGGC
1 AAATGGGC
25347018 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:25349014 original size:26 final size:27
Alignment explanation
Indices: 25348981--25349068 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
25348971 TCAATTTGTA
25348981 AAATTACCAAAGTACCCTCGATTTA-C
1 AAATTACCAAAGTACCCTCGATTTATC
****
25349007 AAATTACCGTTTTACCCTCGATTTATC
1 AAATTACCAAAGTACCCTCGATTTATC
*** *
25349034 AAATTACCATTTTACCTTCGATTTAT-
1 AAATTACCAAAGTACCCTCGATTTATC
25349060 AGAATTACC
1 A-AATTACC
25349069 GTTTTATCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
26 22 0.41
27 32 0.59
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (27 bp):
AAATTACCAAAGTACCCTCGATTTATC
Found at i:25349145 original size:27 final size:26
Alignment explanation
Indices: 25348993--25349137 Score: 182
Period size: 27 Copynumber: 5.4 Consensus size: 26
25348983 ATTACCAAAG
25348993 TACCCTCGATTTACAAATTACCGTTT
1 TACCCTCGATTTACAAATTACCGTTT
*
25349019 TACCCTCGATTTATCAAATTACCATTT
1 TACCCTCGATTTA-CAAATTACCGTTT
* *
25349046 TACCTTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACA-AATTACCGTTT
* * *
25349073 TATCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACA-AATTACCGTTT
* *
25349100 TGCCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTAC-AAATTACCGTTT
25349127 TACCCTCGATT
1 TACCCTCGATT
25349138 GTGAAAATAC
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.14
27 87 0.85
28 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (26 bp):
TACCCTCGATTTACAAATTACCGTTT
Found at i:25349199 original size:27 final size:26
Alignment explanation
Indices: 25349169--25349292 Score: 88
Period size: 27 Copynumber: 4.6 Consensus size: 26
25349159 TATAGGATAG
*
25349169 AATTACCAATATACCCCTAGTTTGTAA
1 AATTACCAA-ATACCCCTAATTTGTAA
* * ** *
25349196 AATTATCTAAATACCACTGGTTTGTGA
1 AATTA-CCAAATACCCCTAATTTGTAA
25349223 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACC-AAATACCCCT-AATTTGTAA
* * **
25349250 AATTAGCAAAATACCTCTAATTTACAA
1 AATTA-CCAAATACCCCTAATTTGTAA
*
25349277 AATTACAAAAATACCC
1 AATTAC-CAAATACCC
25349293 TTGACTTTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
26 5 0.06
27 65 0.84
28 7 0.09
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (26 bp):
AATTACCAAATACCCCTAATTTGTAA
Found at i:25349343 original size:27 final size:27
Alignment explanation
Indices: 25349304--25349355 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
25349294 TGACTTTCTA
25349304 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
25349331 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
25349356 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:25350365 original size:24 final size:25
Alignment explanation
Indices: 25350283--25350376 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
25350273 AGGAAGTGCT
*
25350283 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
25350308 AAAAGGGTTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
25350333 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTACCG
25350357 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
25350377 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
24 20 0.31
25 45 0.69
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:25350389 original size:24 final size:23
Alignment explanation
Indices: 25350283--25350403 Score: 116
Period size: 25 Copynumber: 5.0 Consensus size: 23
25350273 AGGAAGTGCT
* *
25350283 AAAAGGGCTTTGCCCTAGTTTACC
1 AAAAGGGCTTTGCCCCAG-TTATC
* *
25350307 GAAAAGGGTTTTGCCCCAGTTTACC
1 -AAAAGGGCTTTGCCCCAG-TTATC
25350332 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTATC
*
25350357 AAAAGGGCTTTGCCCCAGTTATT
1 AAAAGGGCTTTGCCCCAGTTATC
**
25350380 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTTTGCC-CCAGTTAT
25350404 ATGATAAAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.10
24 25 0.29
25 53 0.61
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCCAGTTATC
Found at i:25350400 original size:49 final size:50
Alignment explanation
Indices: 25350283--25350401 Score: 118
Period size: 49 Copynumber: 2.4 Consensus size: 50
25350273 AGGAAGTGCT
** * *
25350283 AAAAGGGCTTTGCCCTAGTTTACCGAAAAGGGTTTTGCCCCAGTTTACCG
1 AAAAGGGCTAGGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
** * **
25350333 AAAAGGGCTTTGCCCCAGTTTATC-AAAAGGGCTTTGCCCCAG-TTA-TT
1 AAAAGGGCTAGGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
25350380 AAAAGAGGCTAGGCCTCCAGTT
1 AAAAG-GGCTAGGCC-CCAGTT
25350402 ATATGATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 5 0.08
48 10 0.17
49 23 0.38
50 22 0.37
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (50 bp):
AAAAGGGCTAGGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:25350583 original size:42 final size:42
Alignment explanation
Indices: 25350524--25350615 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
25350514 TAGTCTCCCC
**
25350524 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGAAATTTCATGTGATATTG
*
25350566 AAATGGGCTTGCATACATTCATTGAAATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGAAATTTCATGTGATATTG
25350608 AAATGGGC
1 AAATGGGC
25350616 CTATAGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGAAATTTCATGTGATATTG
Found at i:25354754 original size:19 final size:19
Alignment explanation
Indices: 25354716--25354753 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
25354706 TGCAAATGGA
*
25354716 TCATTTCTCATTTTCATTT
1 TCATTTCTCATTTCCATTT
25354735 TCATTTC-CATTTCCATTT
1 TCATTTCTCATTTCCATTT
25354753 T
1 T
25354754 TTATAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (19 bp):
TCATTTCTCATTTCCATTT
Found at i:25356374 original size:48 final size:48
Alignment explanation
Indices: 25356313--25356496 Score: 253
Period size: 48 Copynumber: 3.8 Consensus size: 48
25356303 CATTACGGTT
* *
25356313 ATATAAGATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCG
1 ATATGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTAGCATCG
* *
25356361 ATATGAGATCCCATGTAAGACCATGTTTAGGACATCGCATTAGCATCG
1 ATATGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTAGCATCG
* * *
25356409 ATATGAGATCCCATGTAAGACCATATTTGGGATATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTAGCATCG
** * *
25356457 ATATGTA-ATTTCTTGTAAGACAATGTTTGGGACATGGCAT
1 ATATG-AGATCCCATGTAAGACCATGTTTGGGACATGGCAT
25356497 CGATATGAGA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
48 119 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTAGCATCG
Found at i:25359615 original size:27 final size:27
Alignment explanation
Indices: 25359585--25359851 Score: 115
Period size: 27 Copynumber: 9.9 Consensus size: 27
25359575 ATGGTTCCGA
25359585 CGGACTTCCCACATAAGATAGTCCTTG
1 CGGACTTCCCACATAAGATAGTCCTTG
*
25359612 CGGACTTCCCACATTAGATAGTCCTGATG
1 CGGACTTCCCACATAAGATAGTCCT--TG
* * * *
25359641 -GAATTTTCC-CATTAGATAGTCCTTG
1 CGGACTTCCCACATAAGATAGTCCTTG
* * *
25359666 TGGAC-TCCCATA-ATAGATGGTCCTTG
1 CGGACTTCCCACATA-AGATAGTCCTTG
* * **
25359692 CGGA-TTTCCATA-ATAGATAGTTTTTG
1 CGGACTTCCCACATA-AGATAGTCCTTG
** ** *
25359718 TAGA-TTTTCACA-ATAGATAGTCCCTG
1 CGGACTTCCCACATA-AGATAGTCCTTG
* * * *
25359744 GGGACTTCCCATATAATAAATGATCCTTG
1 CGGACTTCCCACATAAGATA-G-TCCTTG
* * *
25359773 TGGACTTCCCACATAATATAGT-GTTG
1 CGGACTTCCCACATAAGATAGTCCTTG
* *
25359799 ACAGACTTTCCTTA-AT-AGATAGTCCTTG
1 -CGGAC-TTCC-CACATAAGATAGTCCTTG
* *
25359827 CGGACTTCCTATATAAGATAGTCCT
1 CGGACTTCCCACATAAGATAGTCCT
25359852 GACGAACTTT
Statistics
Matches: 184, Mismatches: 40, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
25 7 0.04
26 64 0.35
27 70 0.38
28 18 0.10
29 25 0.14
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (27 bp):
CGGACTTCCCACATAAGATAGTCCTTG
Found at i:25359836 original size:26 final size:26
Alignment explanation
Indices: 25359600--25359851 Score: 106
Period size: 26 Copynumber: 9.4 Consensus size: 26
25359590 TTCCCACATA
* *
25359600 AGATAGTCCTTGCGGACTTCCCACATT
1 AGATAGTCCTTGCGGACTT-CCATAAT
* *
25359627 AGATAGTCCTGATG-GAATTTTCCCAT--T
1 AGATAGTCCT--TGCGGA-CTT-CCATAAT
* *
25359654 AGATAGTCCTTGTGGACTCCCATAAT
1 AGATAGTCCTTGCGGACTTCCATAAT
* *
25359680 AGATGGTCCTTGCGGATTTCCATAAT
1 AGATAGTCCTTGCGGACTTCCATAAT
** ** * * *
25359706 AGATAGTTTTTGTAGATTTTCACAAT
1 AGATAGTCCTTGCGGACTTCCATAAT
* *
25359732 AGATAGTCCCTGGGGACTTCCCATATAAT
1 AGATAGTCCTTGCGGACTT-CC--ATAAT
* *
25359761 AAAT-GATCCTTGTGGACTTCCCACATAAT
1 AGATAG-TCCTTGCGGACTT--C-CATAAT
* * *
25359790 --ATAGT-GTTGACAGACTTTCCTTAAT
1 AGATAGTCCTTG-CGGAC-TTCCATAAT
25359815 AGATAGTCCTTGCGGACTTCC-TATAT
1 AGATAGTCCTTGCGGACTTCCATA-AT
25359841 AAGATAGTCCT
1 -AGATAGTCCT
25359852 GACGAACTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
24 4 0.02
25 10 0.06
26 67 0.39
27 47 0.27
28 9 0.05
29 31 0.18
30 2 0.01
31 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (26 bp):
AGATAGTCCTTGCGGACTTCCATAAT
Found at i:25361843 original size:11 final size:11
Alignment explanation
Indices: 25361827--25361852 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25361817 TTGATTCTGA
25361827 AAAAATATTTT
1 AAAAATATTTT
25361838 AAAAATATTTT
1 AAAAATATTTT
25361849 AAAA
1 AAAA
25361853 TTTTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:25367433 original size:13 final size:15
Alignment explanation
Indices: 25367415--25367446 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25367405 AACACTCCTA
25367415 TGTGTC-CA-GGTCG
1 TGTGTCGCACGGTCG
25367428 TGTGTCGCACGGTCG
1 TGTGTCGCACGGTCG
25367443 TGTG
1 TGTG
25367447 GCTTGAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 2 0.12
15 9 0.53
ACGTcount: A:0.06, C:0.22, G:0.41, T:0.31
Consensus pattern (15 bp):
TGTGTCGCACGGTCG
Found at i:25369737 original size:12 final size:13
Alignment explanation
Indices: 25369701--25369738 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
25369691 AAATATTTGA
25369701 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
25369714 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
25369728 CTTG-TCTTAAT
1 CTTGTTCTTAAT
25369739 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:25383181 original size:18 final size:18
Alignment explanation
Indices: 25383133--25383184 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
25383123 AAAATGTGAG
*
25383133 AAATGATGTTCAAATTTC
1 AAATGATGTTCACATTTC
25383151 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
25383169 AAATTATGTTCACATT
1 AAATGATGTTCACATT
25383185 GATGGAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:25383699 original size:72 final size:72
Alignment explanation
Indices: 25383604--25383868 Score: 390
Period size: 72 Copynumber: 3.7 Consensus size: 72
25383594 CAATGCTAAA
* *
25383604 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGATGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
25383669 GTGTAAT
66 GTGTAAT
* *
25383676 CTAGTTTTATCAATGGATGTTTATGTTTGGTTTTTGGATATTGAATTTATATTCTACTTATTTAT
1 CTAGTTTTATCAATAGATGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
25383741 GTGTAAT
66 GTGTAAT
* * *
25383748 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGGTCTAATTATTTAT
1 CTAGTTTTATCAATAGATGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
25383813 GCT-TAGAG
66 G-TGTA-AT
* * *
25383821 CTAGTTTTATCAATA-ATTTTTTATGTTTGATTTTTGGATATTAAATTT
1 CTAGTTTTATCAATAGA-TGTTTATGTTTGGTTTTTGGATATTGAATTT
25383869 GTAACATCCC
Statistics
Matches: 176, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
72 131 0.74
73 45 0.26
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGATGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:25388103 original size:3 final size:3
Alignment explanation
Indices: 25388095--25388130 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
25388085 GTCAAGAAAG
* *
25388095 TGA TGA TGA TGA TGA CGA TGA TGA TGG TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
25388131 CGGTGAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:25396361 original size:19 final size:18
Alignment explanation
Indices: 25396332--25396369 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
25396322 AAAATTAAAT
25396332 AATTTTAAAATATTTATC
1 AATTTTAAAATATTTATC
25396350 AATTTATAAAATATTTATC
1 AATTT-TAAAATATTTATC
25396369 A
1 A
25396370 TAAATTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTAAAATATTTATC
Found at i:25396444 original size:26 final size:25
Alignment explanation
Indices: 25396408--25396458 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
25396398 AAAAAATCTA
25396408 AAATAAAAAAATTTAT-CACATACATT
1 AAATAAAAAAA-TTATCCA-ATACATT
*
25396434 AAATAATAAAATTATCCAATACATT
1 AAATAAAAAAATTATCCAATACATT
25396459 TAAAGATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAAAAAAATTATCCAATACATT
Found at i:25396462 original size:26 final size:26
Alignment explanation
Indices: 25396408--25396458 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
25396398 AAAAAATCTA
25396408 AAATAAAAAAATTTATCACATACATT
1 AAATAAAAAAATTTATCACATACATT
*
25396434 AAATAATAAAA-TTATC-CAATACATT
1 AAATAAAAAAATTTATCAC-ATACATT
25396459 TAAAGATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 12 0.52
26 10 0.43
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAAAAAAATTTATCACATACATT
Found at i:25400954 original size:21 final size:22
Alignment explanation
Indices: 25400923--25400963 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25400913 GAATGTATTG
*
25400923 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
25400945 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
25400964 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:25403651 original size:27 final size:26
Alignment explanation
Indices: 25403621--25403671 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
25403611 GAGTCCTAAT
25403621 TAGTTTAGGGTTAAA-TTGAAAATAAAC
1 TAGTTTA--GTTAAATTTGAAAATAAAC
*
25403648 TAGTTTAGTTAAATTTTAAAATAA
1 TAGTTTAGTTAAATTTGAAAATAA
25403672 TTGAAGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (26 bp):
TAGTTTAGTTAAATTTGAAAATAAAC
Found at i:25404843 original size:24 final size:25
Alignment explanation
Indices: 25404802--25404848 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
25404792 GCTTTATGCT
25404802 GGTGTTATTTATCAGGCTTTGTGTA
1 GGTGTTATTTATCAGGCTTTGTGTA
**
25404827 GGTG-TATTTATTGGGCTTTGTG
1 GGTGTTATTTATCAGGCTTTGTG
25404849 CCTAGCAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.13, C:0.06, G:0.32, T:0.49
Consensus pattern (25 bp):
GGTGTTATTTATCAGGCTTTGTGTA
Found at i:25404861 original size:40 final size:39
Alignment explanation
Indices: 25404817--25404911 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
25404807 TATTTATCAG
* * *
25404817 GCTTTGTGTAGGTGTATTTATTGGGCTTTGTGCCTAGCAA
1 GCTTTGTGTA-ATGTATTTATCGAGCTTTGTGCCTAGCAA
* *
25404857 GCTTTGTGCTAATGTGTTTATCGAGCTTTGTGCCTAGCAT
1 GCTTTGTG-TAATGTATTTATCGAGCTTTGTGCCTAGCAA
*
25404897 GCCTTGTGTCAATGT
1 GCTTTGTGT-AATGT
25404912 TTTCTATCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 44 0.94
41 2 0.04
ACGTcount: A:0.15, C:0.16, G:0.27, T:0.42
Consensus pattern (39 bp):
GCTTTGTGTAATGTATTTATCGAGCTTTGTGCCTAGCAA
Found at i:25405147 original size:110 final size:107
Alignment explanation
Indices: 25404925--25405148 Score: 261
Period size: 110 Copynumber: 2.1 Consensus size: 107
25404915 CTATCAGGCA
* * * *
25404925 ATGAGCCGGTGATCATTTAGCAGTACTATGTACAGGTGATACAGACAATAGCGATGGCTGAGATC
1 ATGAGCCGGTGATCATTTAACAGTACTATGTACAGATGATACAGACAATAACAATGGCTGAGATC
* **
25404990 CTCATCTGCTGCGGATTTTCTACAGCTTGTGTGAGTAGCATC
66 CTCATCTACTGCGGATTTTCTACAGCTTGTGTGACCAGCATC
** * **
25405032 ATGAGCCGGTGATTTTTTAACAGGTACTATGTACCGATGATACAGACTGTAACAATGGCCTGAGA
1 ATGAGCCGGTGATCATTTAACA-GTACTATGTACAGATGATACAGACAATAACAATGG-CTGAGA
* * *
25405097 TCCTACATCTATTGTGGATTCTT-TACAGCTTGTGTGACCAGTATC
64 TCCT-CATCTACTGCGGATT-TTCTACAGCTTGTGTGACCAGCATC
*
25405142 GTGAGCC
1 ATGAGCC
25405149 AGTCAAAGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
107 19 0.20
108 29 0.30
109 10 0.10
110 37 0.38
111 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (107 bp):
ATGAGCCGGTGATCATTTAACAGTACTATGTACAGATGATACAGACAATAACAATGGCTGAGATC
CTCATCTACTGCGGATTTTCTACAGCTTGTGTGACCAGCATC
Found at i:25406009 original size:128 final size:129
Alignment explanation
Indices: 25405834--25406081 Score: 399
Period size: 128 Copynumber: 1.9 Consensus size: 129
25405824 CTCGCTTTAG
* *
25405834 AAAACACGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCGAAACCCAG
1 AAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCAAAACCCAG
* *
25405899 CACAATAGGGCACTATTCCCCAAATTTCCAGACATCGGATATTGCC-TTGTTTTAGCGTTTGGA
66 CACAATAGGGCACTATTCCCCAAATTTCCAAACATCGAATATTGCCTTTGTTTTAGCGTTTGGA
* * *
25405962 AAAACACGAGTAAAATTCTAAAGTAATATTCGATTATTTTGAACAAACGGGAAATCAAAACCCAG
1 AAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCAAAACCCAG
* * *
25406027 CACGATAGGGCACTATTCCCCGAATTTCTAAACATCGAATATTGCCTTTGTTTTA
66 CACAATAGGGCACTATTCCCCAAATTTCCAAACATCGAATATTGCCTTTGTTTTA
25406082 ATGAATTTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 101 0.93
129 8 0.07
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (129 bp):
AAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATCAAAACCCAG
CACAATAGGGCACTATTCCCCAAATTTCCAAACATCGAATATTGCCTTTGTTTTAGCGTTTGGA
Found at i:25408887 original size:176 final size:176
Alignment explanation
Indices: 25408650--25409105 Score: 507
Period size: 176 Copynumber: 2.6 Consensus size: 176
25408640 AGGATTGTGA
* * * * *
25408650 CTTCGATTTGCTCTATTGCAACTTCAGGGAGATAAGATCT-ACAATTTAGCCTATTACCCTACTA
1 CTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGA-AATTCAGCCTGTTACCCTACTA
* * * *
25408714 CTTAGGAGGTTAAGGCTCAT-C-GTCTTCGATCTGTTCCACT-GTAACTTCAGGGAGACAAGATC
65 CTTAGGGGGTTAAGGCTC-TGCTGTCTTCGATCTGCTCCACTACT-ACTTCAAGGAGACAAGATC
** * * * *
25408776 TATGATCTTTAGCCTGTTACCCTACCACTTAGGGGGTTAAGGCTTGCTTT
128 TACAATCATCAGCCTGTTACCCTACCACTTAGAGGGTTAAGGCCTGC-TT
* **
25408826 CTTTGATCTTTTCCACTGCAACTTCAGGGAGATAAGATCTGAAATTCAGCCTGTTACCCTACTAC
1 CTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGAAATTCAGCCTGTTACCCTACTAC
* * * * * *
25408891 TTAGGGGGTTAAGGC-CTGCTTTTTTCGATTTGCTCCACTACTATTTTAAGGAGACAAGATCTGC
66 TTAGGGGGTTAAGGCTCTGCTGTCTTCGATCTGCTCCACTACTACTTCAAGGAGACAAGATCTAC
*
25408955 AATCATCAGCCTGTTACCCTACTACTTAGAGGGTTAAGGCCTGCTT
131 AATCATCAGCCTGTTACCCTACCACTTAGAGGGTTAAGGCCTGCTT
** * * *
25409001 CTTCGATCTGCTCCACT--ATTTTTTAGGGAGATAAGATTTGCAATCTTCAGCCTGTTACCCTAC
1 CTTCGATCTGCTCCACTGCA-ACTTCAGGGAGATAAGATCTG-AA-ATTCAGCCTGTTACCCTAC
*
25409064 TACTTAGGGGGTTAAGGCT-TGCT-TCTTCGATTTGCTCCACTA
63 TACTTAGGGGGTTAAGGCTCTGCTGTCTTCGATCTGCTCCACTA
25409106 TTGTTTAGGG
Statistics
Matches: 238, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
173 1 0.00
174 18 0.08
175 38 0.16
176 179 0.75
177 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (176 bp):
CTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGAAATTCAGCCTGTTACCCTACTAC
TTAGGGGGTTAAGGCTCTGCTGTCTTCGATCTGCTCCACTACTACTTCAAGGAGACAAGATCTAC
AATCATCAGCCTGTTACCCTACCACTTAGAGGGTTAAGGCCTGCTT
Found at i:25409105 original size:87 final size:87
Alignment explanation
Indices: 25408670--25409127 Score: 480
Period size: 87 Copynumber: 5.2 Consensus size: 87
25408660 CTCTATTGCA
* * * * *
25408670 ACTTCAGGGAGATAAGATCTACAAT-TT-AGCCTATTACCCTACTACTTAGGAGGTTAAGGCTCA
1 ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCT--
* * * *
25408733 T-CGTCTTCGATCTGTTCCACTGT
64 TGCTTCTTCGATTTGCTCCACTAT
* *** * *
25408756 AACTTCAGGGAGACAAGATCTATGATCTTTAGCCTGTTACCCTACCACTTAGGGGGTTAAGGCTT
1 -ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTT
* *
25408821 GCTTTCTTTGATCTT-TTCCACTGCA-
65 GC-TTCTTCGAT-TTGCTCCACT--AT
* * * *
25408846 ACTTCAGGGAGATAAGATCTG-AA-ATTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCCTG
1 ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG
*
25408909 CTTTTTTCGATTTGCTCCACTACT
66 C-TTCTTCGATTTGCTCCACTA-T
* * * * *
25408933 ATTTTAAGGAGACAAGATCTGCAATCATCAGCCTGTTACCCTACTACTTAGAGGGTTAAGGCCTG
1 ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG
*
25408998 CTTCTTCGATCTGCTCCACTAT
66 CTTCTTCGATTTGCTCCACTAT
** * *
25409020 TTTTTAGGGAGATAAGATTTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG
1 ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG
25409085 CTTCTTCGATTTGCTCCACTAT
66 CTTCTTCGATTTGCTCCACTAT
**
25409107 TGTTTAGGGAGACAAGATCTG
1 ACTTTAGGGAGACAAGATCTG
25409128 TGAATTCACT
Statistics
Matches: 319, Mismatches: 40, Indels: 24
0.83 0.10 0.06
Matches are distributed among these distances:
85 1 0.00
86 2 0.01
87 189 0.59
88 24 0.08
89 102 0.32
90 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (87 bp):
ACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTG
CTTCTTCGATTTGCTCCACTAT
Found at i:25417040 original size:21 final size:21
Alignment explanation
Indices: 25417011--25417050 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25417001 TGGGACAATT
25417011 GACTCATCATCT-CTCTTTGG
1 GACTCATCATCTACTCTTTGG
*
25417031 GACTCCATCATTTACTCTTT
1 GACT-CATCATCTACTCTTT
25417051 CATCTCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.42
Consensus pattern (21 bp):
GACTCATCATCTACTCTTTGG
Found at i:25420734 original size:120 final size:124
Alignment explanation
Indices: 25420595--25420900 Score: 368
Period size: 128 Copynumber: 2.5 Consensus size: 124
25420585 AACGAAAACC
* * * *
25420595 CGAAACCCAGCACGGTAGGGCACGATTCATCGAATTTCCAAACATTGAACATTGCC-TC-GC-TT
1 CGAAACCCAGCACGATAGGGCACTATTCCTCGAATTTCCAAACATCGAACATTGCCTTCAGCGTT
* *
25420657 TAG-AAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAGCGGGAAAT
66 TAGAAAAACACGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAAT
* * * * * *
25420715 TGAAACCTAGCACGATAGGGCATTATTCCTCGAATTTCCAGACATCGGATATTGCCTTGTTTCAG
1 CGAAACCCAGCACGATAGGGCACTATTCCTCGAATTTCCAAACATCGAACATTGCC----TTCAG
* * *
25420780 CGTTTGGAAAAACATGAGTAAAATTCTAAAGGAATATTCAATTATTTTGAACAAACGGGAAAT
62 CGTTTAGAAAAACACGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAAT
* * * * *
25420843 CGAAACCCAGCATGATAGGACACTATTCCCCGAATTTCCAAACATCAAATATTGCCTT
1 CGAAACCCAGCACGATAGGGCACTATTCCTCGAATTTCCAAACATCGAACATTGCCTT
25420901 TGTTTTAATG
Statistics
Matches: 154, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
120 46 0.30
124 2 0.01
125 2 0.01
126 2 0.01
127 4 0.03
128 98 0.64
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (124 bp):
CGAAACCCAGCACGATAGGGCACTATTCCTCGAATTTCCAAACATCGAACATTGCCTTCAGCGTT
TAGAAAAACACGAGTAAAATTCCAAAGGAATATTCAATTATTTTGAACAAACGGGAAAT
Found at i:25430655 original size:6 final size:6
Alignment explanation
Indices: 25430641--25430686 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
25430631 TTGAGTCCGA
* *
25430641 TTATCT TTATTT TTATTT TTATTT TTATTT TGTATTT ATATTT TTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT T-TATTT TTATTT TTA
25430687 ACTCTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:25430667 original size:18 final size:19
Alignment explanation
Indices: 25430641--25430686 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
25430631 TTGAGTCCGA
*
25430641 TTATCTTTATTTT-TATTT
1 TTATTTTTATTTTGTATTT
25430659 TTATTTTTATTTTGTATTT
1 TTATTTTTATTTTGTATTT
*
25430678 ATATTTTTA
1 TTATTTTTA
25430687 ACTCTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTATTTTGTATTT
Found at i:25430694 original size:25 final size:25
Alignment explanation
Indices: 25430648--25430696 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
25430638 CGATTATCTT
* ** *
25430648 TATTTTTATTTTTATTTTTATTTTG
1 TATTTATATTTTTAACTCTATTTTG
25430673 TATTTATATTTTTAACTCTATTTT
1 TATTTATATTTTTAACTCTATTTT
25430697 AATTATTATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (25 bp):
TATTTATATTTTTAACTCTATTTTG
Found at i:25445767 original size:116 final size:116
Alignment explanation
Indices: 25445625--25445860 Score: 364
Period size: 116 Copynumber: 2.0 Consensus size: 116
25445615 AATGTGGTAT
** **
25445625 TTGATGAACAATGATTTCTGTCTCTGTTGTTTGCTACGTTGGGGTTTGGTGGTTTGTATGCTATT
1 TTGATGAACAACAATTTCTGTCTCTGTTGTTTGCTACGTCAGGGTTTGGTGGTTTGTATGCTATT
* * * *
25445690 ATAACAACTTGTGTTCCTCTAATTCAAGCAGTTTCTTCTCGATCTACAGAC
66 ATAACAACTTGTGTTACTCCAATTCAAGCAGCTTCTTCTCAATCTACAGAC
25445741 TTGATGAACAACAATTTCTGTCTCTGTTGTTTGCTACGTCAGGGTTTGGTGGTTTGTATGCTATT
1 TTGATGAACAACAATTTCTGTCTCTGTTGTTTGCTACGTCAGGGTTTGGTGGTTTGTATGCTATT
* ** *
25445806 ATACCAACTTGTGTTACTCCGGTTCAAGCAGCTTCTTCTCAATCTACGGAC
66 ATAACAACTTGTGTTACTCCAATTCAAGCAGCTTCTTCTCAATCTACAGAC
25445857 TTGA
1 TTGA
25445861 CACCTGTTAT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (116 bp):
TTGATGAACAACAATTTCTGTCTCTGTTGTTTGCTACGTCAGGGTTTGGTGGTTTGTATGCTATT
ATAACAACTTGTGTTACTCCAATTCAAGCAGCTTCTTCTCAATCTACAGAC
Found at i:25459509 original size:13 final size:14
Alignment explanation
Indices: 25459485--25459513 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25459475 TTGGAAAGTC
25459485 AAAATAAAAATTTG
1 AAAATAAAAATTTG
25459499 AAAAT-AAAATTTG
1 AAAATAAAAATTTG
25459512 AA
1 AA
25459514 GCTTCTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAATAAAAATTTG
Found at i:25461805 original size:11 final size:12
Alignment explanation
Indices: 25461781--25461808 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25461771 ATAAAAACAT
25461781 AAAAATTAGAAA
1 AAAAATTAGAAA
25461793 AAAAATTAGAAA
1 AAAAATTAGAAA
25461805 AAAA
1 AAAA
25461809 GTTATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAATTAGAAA
Found at i:25461843 original size:20 final size:21
Alignment explanation
Indices: 25461793--25461844 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
25461783 AAATTAGAAA
25461793 AAAAAT-TAGAAAAAAAGTTAT
1 AAAAATGTA-AAAAAAAGTTAT
25461814 -AAAATCGTAAAAAAAA-TTAT
1 AAAAAT-GTAAAAAAAAGTTAT
25461834 AAAAATGTAAA
1 AAAAATGTAAA
25461845 GAAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 14 0.50
21 12 0.43
22 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (21 bp):
AAAAATGTAAAAAAAAGTTAT
Found at i:25461919 original size:11 final size:12
Alignment explanation
Indices: 25461895--25461919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25461885 AAAAAAAGAA
25461895 TTTTATAAATTT
1 TTTTATAAATTT
25461907 TTTTATAAATTT
1 TTTTATAAATTT
25461919 T
1 T
25461920 ATTGATTTTT
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):
TTTTATAAATTT
Found at i:25486030 original size:45 final size:45
Alignment explanation
Indices: 25485968--25486058 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
25485958 ATGGTGTATA
25485968 TATATGTTGATAGTGCTATTTCGAAGGCTATATGAAATATACATG
1 TATATGTTGATAGTGCTATTTCGAAGGCTATATGAAATATACATG
25486013 TATATGTTGATAGTGCTATTTCGAAGGCTATATGAAATATACATG
1 TATATGTTGATAGTGCTATTTCGAAGGCTATATGAAATATACATG
25486058 T
1 T
25486059 TATACTCACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (45 bp):
TATATGTTGATAGTGCTATTTCGAAGGCTATATGAAATATACATG
Found at i:25489334 original size:17 final size:17
Alignment explanation
Indices: 25489290--25489323 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25489280 TATTTATTTA
* *
25489290 TAAAATAAACATTAAAT
1 TAAATTAAATATTAAAT
25489307 TAAATTAAATATTAAAT
1 TAAATTAAATATTAAAT
25489324 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATTAAATATTAAAT
Found at i:25499549 original size:5 final size:5
Alignment explanation
Indices: 25499539--25499563 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25499529 TAATAATAAA
25499539 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
25499564 GCAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:25502342 original size:10 final size:10
Alignment explanation
Indices: 25502327--25502370 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
25502317 GCGATTAATC
25502327 CATACCAAAA
1 CATACCAAAA
25502337 CATACCAAAA
1 CATACCAAAA
*
25502347 CATAAGCCAAAGT
1 CAT-A-CCAAA-A
25502360 CATACCAAAA
1 CATACCAAAA
25502370 C
1 C
25502371 CTAAGATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 14 0.48
11 6 0.21
12 6 0.21
13 3 0.10
ACGTcount: A:0.55, C:0.30, G:0.05, T:0.11
Consensus pattern (10 bp):
CATACCAAAA
Found at i:25503217 original size:42 final size:41
Alignment explanation
Indices: 25503126--25503267 Score: 133
Period size: 42 Copynumber: 3.3 Consensus size: 41
25503116 CCCAGATGTT
* * * * *
25503126 GTCTTACACGTAATCAAATATCAATGCCTCTGTCCCAGACAGG
1 GTCTTACACGAAATCAAATA-CGATGCC-ATATCCCAGACATG
*
25503169 GTCTTACACGAAATCAAATACGATGTCGATATCCCAGACATG
1 GTCTTACACGAAATCAAATACGATG-CCATATCCCAGACATG
* * *
25503211 GTCTTACACGTAAATATCAAAT-CGATGCCAAAGTTCCAGACTTG
1 GTCTTACACG--AA-ATCAAATACGATGCCATA-TCCCAGACATG
25503255 GTCTTACACGAAA
1 GTCTTACACGAAA
25503268 ACACATATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.32
43 23 0.27
44 26 0.31
45 7 0.08
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
GTCTTACACGAAATCAAATACGATGCCATATCCCAGACATG
Found at i:25503251 original size:44 final size:42
Alignment explanation
Indices: 25503158--25503267 Score: 125
Period size: 44 Copynumber: 2.6 Consensus size: 42
25503148 AATGCCTCTG
* * *
25503158 TCCCAGACAGGGTCTTACACGAAATCAAATACGATGTCGATA
1 TCCCAGACATGGTCTTACACGAAATCAAATACGATGTCCAAA
25503200 TCCCAGACATGGTCTTACACGTAAATATCAAAT-CGATG-CCAAA
1 TCCCAGACATGGTCTTACACG--AA-ATCAAATACGATGTCCAAA
* *
25503243 GTTCCAGACTTGGTCTTACACGAAA
1 -TCCCAGACATGGTCTTACACGAAA
25503268 ACACATATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
41 1 0.02
42 22 0.37
43 3 0.05
44 26 0.44
45 7 0.12
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCAAATACGATGTCCAAA
Found at i:25510541 original size:2 final size:2
Alignment explanation
Indices: 25510534--25510567 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
25510524 GATCATGATT
*
25510534 CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
25510568 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:25510614 original size:16 final size:18
Alignment explanation
Indices: 25510576--25510619 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
25510566 CATATATATA
*
25510576 TATATCATATCTCATTCT
1 TATATCATATCTCATACT
*
25510594 CATATCA-A-CTCATACT
1 TATATCATATCTCATACT
25510610 TATATCATAT
1 TATATCATAT
25510620 GTTCACAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATCATATCTCATACT
Found at i:25510851 original size:43 final size:41
Alignment explanation
Indices: 25510801--25510899 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 41
25510791 TCCCAAACGT
*
25510801 GGTCTTACATATAATCAAATATCGATGCCT-CTGTCCCAGACAG
1 GGTCTTACA-ATAATCAAATAT-GATG-CTGATGTCCCAGACAG
* *
25510844 GGTCTTACAAGAAATCAAATATGATGCTGATGTCCCAGACAT
1 GGTCTTACAA-TAATCAAATATGATGCTGATGTCCCAGACAG
25510886 GGTCTTACACATAA
1 GGTCTTACA-ATAA
25510900 ATCTCAAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
41 2 0.04
42 27 0.55
43 20 0.41
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (41 bp):
GGTCTTACAATAATCAAATATGATGCTGATGTCCCAGACAG
Found at i:25510883 original size:42 final size:43
Alignment explanation
Indices: 25510813--25510894 Score: 123
Period size: 42 Copynumber: 1.9 Consensus size: 43
25510803 TCTTACATAT
*
25510813 AATCAAATATCGATGCCTCTGTCCCAGACAGGGTCTTACAAGA
1 AATCAAATATCGATGCCTATGTCCCAGACAGGGTCTTACAAGA
*
25510856 AATCAAATAT-GATG-CTGATGTCCCAGACATGGTCTTACA
1 AATCAAATATCGATGCCT-ATGTCCCAGACAGGGTCTTACA
25510895 CATAAATCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 2 0.06
42 24 0.67
43 10 0.28
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (43 bp):
AATCAAATATCGATGCCTATGTCCCAGACAGGGTCTTACAAGA
Found at i:25510902 original size:43 final size:42
Alignment explanation
Indices: 25510790--25510939 Score: 135
Period size: 43 Copynumber: 3.5 Consensus size: 42
25510780 TATTGCCAGC
* * * *
25510790 GTCCCAAACGTGGTCTTACATAT-AATCAAATATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACATAAATCAAATAT-GATG-CTAT
* *
25510833 GTCCCAGACAGGGTCTTACA-AGAAATCAAATATGATGCTGAT
1 GTCCCAGACATGGTCTTACACATAAATCAAATATGATGCT-AT
* *
25510875 GTCCCAGACATGGTCTTACACATAAATCTCAAGT-TGATGCCAAT
1 GTCCCAGACATGGTCTTACACATAAA--TCAAATATGATG-CTAT
* *
25510919 GTCACAGACGTGGTCTTACAC
1 GTCCCAGACATGGTCTTACAC
25510940 GAAAACACAT
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.02
42 25 0.28
43 31 0.34
44 26 0.29
45 6 0.07
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACATAAATCAAATATGATGCTAT
Found at i:25522706 original size:12 final size:12
Alignment explanation
Indices: 25522689--25522714 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25522679 AAAATAGGGC
25522689 TTTAGCGGCGTT
1 TTTAGCGGCGTT
25522701 TTTAGCGGCGTT
1 TTTAGCGGCGTT
25522713 TT
1 TT
25522715 ATCAACAAAC
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:25522814 original size:41 final size:40
Alignment explanation
Indices: 25522738--25522828 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 40
25522728 GCAAAAATTT
* *
25522738 TAAAATACAGAGCAATAGCGGCGTTTTAAGAAAAACGCCGC
1 TAAAA-ACAGAGCAACAGCGGCGTTTTAACAAAAACGCCGC
* * * *
25522779 TAAAAACAGAGCAACAGCGGCATTTTTTACTAAAACGCCTC
1 TAAAAACAGAGCAACAGCGGC-GTTTTAACAAAAACGCCGC
25522820 TAAAAACAG
1 TAAAAACAG
25522829 TTAGCGGCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 15 0.35
41 28 0.65
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (40 bp):
TAAAAACAGAGCAACAGCGGCGTTTTAACAAAAACGCCGC
Found at i:25522888 original size:41 final size:41
Alignment explanation
Indices: 25522829--25523065 Score: 379
Period size: 41 Copynumber: 5.8 Consensus size: 41
25522819 CTAAAAACAG
** *
25522829 TTAGCGGCGCTTTAGGTAAAACGCCGCTAAAAACCAGATCA
1 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
*
25522870 TTAGCGGCGCTTCGGGTAAAATGCCGCTAAAAACCAGAGCA
1 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
*
25522911 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAAACAGAGCA
1 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
*
25522952 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGTA
1 TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
*
25522993 TTAGCGGCGCCTTC-GATAAAACGCCGCTAAAAACCAGAGCA
1 TTAGCGGCG-CTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
25523034 TTAGCGGCGCTTTC-GGTAAAACGCCGCTAAAA
1 TTAGCGGCGC-TTCGGGTAAAACGCCGCTAAAA
25523066 GTCATAGAAC
Statistics
Matches: 183, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.01
41 178 0.97
42 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.17
Consensus pattern (41 bp):
TTAGCGGCGCTTCGGGTAAAACGCCGCTAAAAACCAGAGCA
Found at i:25523314 original size:36 final size:39
Alignment explanation
Indices: 25523244--25523319 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 39
25523234 ATAGTTTAAG
* * *
25523244 ATATATGGTTTAGGGTTTAAGCAGGTTTATGAGTTAACT
1 ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
25523283 ATATATGGTTTAAGATTT-A-C-GGTTTAGGAGTTAACT
1 ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
25523319 A
1 A
25523320 GTAATTGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 1 0.03
38 1 0.03
39 16 0.47
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (39 bp):
ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
Found at i:25527103 original size:21 final size:20
Alignment explanation
Indices: 25527065--25527104 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
25527055 GGTGATTCCA
*
25527065 TTTTGGTTATTTAGATGTTC
1 TTTTGGTTATTTACATGTTC
*
25527085 TTTTGGTCTATTTTCATGTT
1 TTTTGGT-TATTTACATGTT
25527105 TCTATCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.62
Consensus pattern (20 bp):
TTTTGGTTATTTACATGTTC
Found at i:25527309 original size:133 final size:133
Alignment explanation
Indices: 25527064--25527448 Score: 743
Period size: 133 Copynumber: 2.9 Consensus size: 133
25527054 TGGTGATTCC
*
25527064 ATTTTGGTTATTTAGATGTTCTTTTGGTCTATTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
1 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
25527129 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTGT
66 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTGT
25527194 TAT
131 TAT
25527197 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
1 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
* *
25527262 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGTTTACGTTTTATATAATAAAATTGT
66 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTGT
25527327 TAT
131 TAT
25527330 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
1 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
25527395 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATAT
66 TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATAT
25527449 TGTTGAATTC
Statistics
Matches: 247, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 247 1.00
ACGTcount: A:0.20, C:0.10, G:0.18, T:0.52
Consensus pattern (133 bp):
ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTCATGTTTCTATCCAACTTATGTGTTTAGTG
TGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTGT
TAT
Found at i:25529424 original size:21 final size:21
Alignment explanation
Indices: 25529395--25529434 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25529385 GTTTTTATAT
*
25529395 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
25529416 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
25529435 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:25535954 original size:44 final size:43
Alignment explanation
Indices: 25535905--25536151 Score: 255
Period size: 43 Copynumber: 5.7 Consensus size: 43
25535895 CTGGGCAAAT
*
25535905 TAGCGGCGTTTTTTTTAAAAAGCGCCGCTAATGTTCTTGGTCTA
1 TAGCGGCG-TTTTTTTAAAAAGCGCCGCTAAAGTTCTTGGTCTA
*
25535949 TAGCGGCGTTTTTTTACTAAAGCGCCGCTAAAGTTCTTGGTCTA
1 TAGCGGCGTTTTTTTA-AAAAGCGCCGCTAAAGTTCTTGGTCTA
* * * * * *** * *
25535993 TAGCGGCGCTTTTGTAAAAAACGCCGCCAAAG-ACCAAGACTTG
1 TAGCGGCGTTTTTTTAAAAAGCGCCGCTAAAGTTCTTGGTC-TA
*
25536036 TAGCGGCGTTTTTTTATAAAAGCGCCGCTAAAGTTCTTGGTGTA
1 TAGCGGCGTTTTTTTA-AAAAGCGCCGCTAAAGTTCTTGGTCTA
* * *
25536080 TAGCGGCG-TTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTTTTTA-AAAAGCGCCGCTAAAGTTCTTGGTCTA
* * * *
25536123 TAGCTGCGCTTTTATAAAAAACGCCGCTA
1 TAGCGGCGTTTTTTTAAAAAGCGCCGCTA
25536152 TACACCAAGA
Statistics
Matches: 167, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
42 3 0.02
43 86 0.51
44 76 0.46
45 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (43 bp):
TAGCGGCGTTTTTTTAAAAAGCGCCGCTAAAGTTCTTGGTCTA
Found at i:25536040 original size:43 final size:42
Alignment explanation
Indices: 25535993--25536239 Score: 203
Period size: 43 Copynumber: 5.8 Consensus size: 42
25535983 TCTTGGTCTA
* *
25535993 TAGCGGCGCTTTTGTAAAAAACGCCGCCAAAGACCAAGACTT
1 TAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAAGACTT
* * * ** ** *
25536035 GTAGCGGCGTTTTTTTATAAAAGCGCCGCTAAAGTTCTTG-GTGT
1 -TAGCGGCGCTTTTATA-AAAAACGCCGCTAAAGACCAAGACT-T
* * * ** *
25536079 ATAGCGGCG-TTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 -TAGCGGCGCTTTTATA-AAAAACGCCGCTAAA-GACCAAGACTT
* * *
25536123 TAGCTGCGCTTTTATAAAAAACGCCGCTATACACCAAGAACTT
1 TAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAAG-ACTT
* * *
25536166 TAGCGGCGCTTTTATAAAAAACGTCGCTATAGACCAAGAACAT
1 TAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAAG-ACTT
25536209 TAGCGGCGCTTTTAT-AAAAACGCCGCTAAAG
1 TAGCGGCGCTTTTATAAAAAACGCCGCTAAAG
25536240 GTCCTGGTCT
Statistics
Matches: 170, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
42 17 0.10
43 115 0.68
44 37 0.22
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (42 bp):
TAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCAAGACTT
Found at i:25536058 original size:87 final size:87
Alignment explanation
Indices: 25535949--25536111 Score: 258
Period size: 87 Copynumber: 1.9 Consensus size: 87
25535939 TCTTGGTCTA
25535949 TAGCGGCGTTTTTTTACTAAAGCGCCGCTAAAGTTCTTGGTCTATAGCGGCGCTTTTGTA-AAAA
1 TAGCGGCGTTTTTTTACTAAAGCGCCGCTAAAGTTCTTGGTCTATAGCGGCG-TTTTGTATAAAA
25536013 ACGCCGCCAAAGACCAAGACTTG
65 ACGCCGCCAAAGACCAAGACTTG
* *
25536036 TAGCGGCGTTTTTTTA-TAAAAGCGCCGCTAAAGTTCTTGGTGTATAGCGGCGTTTTTTATAAAA
1 TAGCGGCGTTTTTTTACT-AAAGCGCCGCTAAAGTTCTTGGTCTATAGCGGCGTTTTGTATAAAA
* *
25536100 GCGCCGCTAAAG
65 ACGCCGCCAAAG
25536112 GTCCTGGTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
86 7 0.10
87 63 0.90
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (87 bp):
TAGCGGCGTTTTTTTACTAAAGCGCCGCTAAAGTTCTTGGTCTATAGCGGCGTTTTGTATAAAAA
CGCCGCCAAAGACCAAGACTTG
Found at i:25539551 original size:42 final size:44
Alignment explanation
Indices: 25539447--25539583 Score: 145
Period size: 42 Copynumber: 3.2 Consensus size: 44
25539437 TGTTATCGTG
** * * *
25539447 TAAGACCACATCTAGGACATTGGCATCGATTTGTGATTTATGTA
1 TAAGACCATGTCTAGGACATTGGCATCGATATATGATTTACGTA
25539491 TAAGACCATGTCTAGGACATTGGCATCG-TATATGATTT-CGTA
1 TAAGACCATGTCTAGGACATTGGCATCGATATATGATTTACGTA
* * * * * * *
25539533 TAAGGCCTTGTCTGGGACAATGGCATCGATATTTGA-TTACATG
1 TAAGACCATGTCTAGGACATTGGCATCGATATATGATTTACGTA
25539576 TAAGACCA
1 TAAGACCA
25539584 CATCTGAGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 29 0.38
43 22 0.29
44 26 0.34
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (44 bp):
TAAGACCATGTCTAGGACATTGGCATCGATATATGATTTACGTA
Found at i:25539801 original size:19 final size:20
Alignment explanation
Indices: 25539779--25539817 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
25539769 AATGACAACG
25539779 AATGATATGA-ATG-TATATA
1 AATGA-ATGATATGTTATATA
25539798 AATGAATGATATGTTATATA
1 AATGAATGATATGTTATATA
25539818 TGCTCGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
AATGAATGATATGTTATATA
Found at i:25539983 original size:18 final size:18
Alignment explanation
Indices: 25539960--25539996 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25539950 TGAGTTTTCA
25539960 AATTCAAATAACTCGAAT
1 AATTCAAATAACTCGAAT
*
25539978 AATTCAAATAATTCGAAT
1 AATTCAAATAACTCGAAT
25539996 A
1 A
25539997 TCAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:25552429 original size:25 final size:27
Alignment explanation
Indices: 25552401--25552468 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
25552391 AAAATTGGTA
25552401 AGACATTTTCCATTCT-TCTCT-A-AGC
1 AGACATTTTCCATTCTCT-TCTAACAGC
**
25552426 AGACATTTTCTGTTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAA-CAGC
25552454 AGACATTTTCCATTC
1 AGACATTTTCCATTC
25552469 CTCAAAGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 17 0.49
26 2 0.06
28 16 0.46
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAACAGC
Found at i:25554877 original size:15 final size:16
Alignment explanation
Indices: 25554852--25554884 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
25554842 ATTTTTGAAC
25554852 TTTCAATGCTTTCATT
1 TTTCAATGCTTTCATT
25554868 TTTC-ATGCTTTCATT
1 TTTCAATGCTTTCATT
25554883 TT
1 TT
25554885 AAGTGGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTCAATGCTTTCATT
Found at i:25556463 original size:35 final size:36
Alignment explanation
Indices: 25556415--25556483 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
25556405 ATTTGTTAGA
25556415 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
25556451 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
25556484 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:25557547 original size:71 final size:72
Alignment explanation
Indices: 25557428--25557566 Score: 253
Period size: 71 Copynumber: 1.9 Consensus size: 72
25557418 TTGATACATT
*
25557428 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
25557493 TTGGATA
66 TTGGATA
*
25557500 TATGTGGTGTAATATTATGCAC-TAGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
25557564 TTG
66 TTG
25557567 AATAATATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 43 0.66
72 22 0.34
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:25557780 original size:14 final size:14
Alignment explanation
Indices: 25557761--25557788 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25557751 ACAATTTATT
25557761 AATATATATTAATA
1 AATATATATTAATA
25557775 AATATATATTAATA
1 AATATATATTAATA
25557789 TATGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:25557893 original size:14 final size:15
Alignment explanation
Indices: 25557871--25557947 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
25557861 TTACCAAACA
25557871 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
25557885 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
25557900 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
25557920 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
25557934 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
25557948 ACTGTCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:25557912 original size:20 final size:20
Alignment explanation
Indices: 25557887--25557926 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25557877 AATATTTTCC
*
25557887 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25557907 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
25557927 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25557932 original size:34 final size:35
Alignment explanation
Indices: 25557875--25557941 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
25557865 CAAACACCAG
*
25557875 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
25557910 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25557942 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25557948 original size:14 final size:14
Alignment explanation
Indices: 25557910--25557949 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25557900 ACAGAAAAGT
*
25557910 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
25557924 AAATCATTTTACGG
1 AAAACATTTTACAG
25557938 AAAACATTTTAC
1 AAAACATTTTAC
25557950 TGTCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:25574797 original size:22 final size:22
Alignment explanation
Indices: 25574757--25574811 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
25574747 ACTTATCAAA
25574757 TATTATCC-T-AAAATACTACC
1 TATTATCCTTAAAAATACTACC
*
25574777 TATTGATCCTTAAAAAT-CTACT
1 TATT-ATCCTTAAAAATACTACC
*
25574799 TATTATTCTTAAA
1 TATTATCCTTAAA
25574812 GAAACAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 9 0.30
23 5 0.17
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (22 bp):
TATTATCCTTAAAAATACTACC
Found at i:25579550 original size:5 final size:6
Alignment explanation
Indices: 25579516--25579549 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
25579506 AAATTTTGGG
25579516 AAAAAT AAAAAT AAAAAT AGAAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAA
25579550 TCTATTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:25580038 original size:18 final size:17
Alignment explanation
Indices: 25580015--25580054 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
25580005 AAATGAAGTT
*
25580015 TTTTAATATTTTTTAATA
1 TTTTAATA-ATTTTAATA
25580033 TTTTAATAATTTTAATA
1 TTTTAATAATTTTAATA
*
25580050 ATTTA
1 TTTTA
25580055 TTATAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATAATTTTAATA
Found at i:25580050 original size:9 final size:9
Alignment explanation
Indices: 25580015--25580104 Score: 58
Period size: 9 Copynumber: 9.6 Consensus size: 9
25580005 AAATGAAGTT
*
25580015 TTTTAATATT
1 TTTTAATA-A
25580025 TTTTAAT-A
1 TTTTAATAA
25580033 TTTTAATAA
1 TTTTAATAA
25580042 TTTTAATAA
1 TTTTAATAA
*
25580051 TTTATTATAA
1 TTT-TAATAA
25580061 GTTTT-ATAA
1 -TTTTAATAA
*
25580070 GTTTTTATGAA
1 -TTTTAAT-AA
**
25580081 TTTTATATTT
1 TTTTA-ATAA
*
25580091 TTTTTATAA
1 TTTTAATAA
25580100 TTTTA
1 TTTTA
25580105 TTGTTGTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.11
9 28 0.43
10 23 0.35
11 7 0.11
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTAATAA
Found at i:25580060 original size:19 final size:18
Alignment explanation
Indices: 25580025--25580104 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 18
25580015 TTTTAATATT
*
25580025 TTTTAAT-ATTTTAATAA
1 TTTTAATAATTTTTATAA
25580042 TTTTAATAATTTATTATAA
1 TTTTAATAATTT-TTATAA
25580061 GTTTT-ATAAGTTTTTATGAA
1 -TTTTAATAA-TTTTTAT-AA
**
25580081 TTTTATATTTTTTTTATAA
1 TTTTA-ATAATTTTTATAA
25580100 TTTTA
1 TTTTA
25580105 TTGTTGTTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
17 7 0.13
18 4 0.08
19 24 0.45
20 16 0.30
21 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTAATAATTTTTATAA
Found at i:25580083 original size:39 final size:38
Alignment explanation
Indices: 25580033--25580195 Score: 104
Period size: 39 Copynumber: 4.2 Consensus size: 38
25580023 TTTTTTAATA
*
25580033 TTTTAATAATTTTAATAATTTATTATAAGTTTTATAAG
1 TTTTTATAATTTTAATAATTTATTATAAGTTTTATAAG
* * *
25580071 TTTTTATGAATTTT-ATATTTTTTTTATAA-TTTTAT-TG
1 TTTTTAT-AATTTTAATA-ATTTATTATAAGTTTTATAAG
** ** * *
25580108 TTGTTGTAATTTTTTTTGTAATTTATTAT-ATTTTTATGAG
1 TT-TT-T-ATAATTTTAATAATTTATTATAAGTTTTATAAG
*
25580148 TTTTTATAATATTTTATTAATATT-TT-TAAGTTTTATAAG
1 TTTTTAT-A-ATTTTAATAAT-TTATTATAAGTTTTATAAG
*
25580187 TTTATATAA
1 TTTTTATAA
25580196 AATTGAAAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
37 6 0.06
38 21 0.22
39 60 0.62
40 9 0.09
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.63
Consensus pattern (38 bp):
TTTTTATAATTTTAATAATTTATTATAAGTTTTATAAG
Found at i:25580084 original size:10 final size:9
Alignment explanation
Indices: 25580013--25580195 Score: 77
Period size: 10 Copynumber: 19.0 Consensus size: 9
25580003 ATAAATGAAG
25580013 TTTTT-TAA
1 TTTTTATAA
*
25580021 TATTTTTTAA
1 T-TTTTATAA
25580031 TATTTTAATAA
1 T-TTTT-ATAA
*
25580042 TTTTAATAA
1 TTTTTATAA
25580051 TTTATTATAA
1 TTT-TTATAA
*
25580061 GTTTTATAA
1 TTTTTATAA
25580070 GTTTTTATGAA
1 -TTTTTAT-AA
**
25580081 TTTTATATTT
1 TTTT-TATAA
25580091 TTTTTATAA
1 TTTTTATAA
**
25580100 -TTTTATTG
1 TTTTTATAA
**
25580108 TTGTTGTAATTT
1 TT-TT-T-ATAA
*
25580120 TTTTTGTAA
1 TTTTTATAA
25580129 TTTATTAT-A
1 TTT-TTATAA
*
25580138 TTTTTATGAG
1 TTTTTAT-AA
25580148 TTTTTATAA
1 TTTTTATAA
25580157 TATTTTATTAA
1 T-TTTTA-TAA
25580168 TATTTT-TAA
1 T-TTTTATAA
*
25580177 GTTTTATAA
1 TTTTTATAA
*
25580186 GTTTATATAA
1 -TTTTTATAA
25580196 AATTGAAAAT
Statistics
Matches: 136, Mismatches: 21, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
8 15 0.11
9 37 0.27
10 58 0.43
11 21 0.15
12 5 0.04
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:25580383 original size:15 final size:16
Alignment explanation
Indices: 25580363--25580395 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25580353 ATATTTAATT
25580363 ATTCAAATATT-GATA
1 ATTCAAATATTGGATA
*
25580378 ATTCAATTATTGGATA
1 ATTCAAATATTGGATA
25580394 AT
1 AT
25580396 AAAGATAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTCAAATATTGGATA
Found at i:25586629 original size:38 final size:38
Alignment explanation
Indices: 25586575--25586948 Score: 235
Period size: 38 Copynumber: 8.9 Consensus size: 38
25586565 TGGAAAAACA
25586575 TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
1 TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
* * * *
25586613 TGGTGCTAAGTAGATATACCACGATTACACATATTGATACATGTAACA
1 TGGTGCTAAGTGGATATGCCACG---------GTT-ATACATGTAACG
*
25586661 TGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACG
1 TGGTGCTAAGTGGATATGCCACGGTT--ATACA-TG------TAACG
* * * *
25586708 TGGTGCTAAGAGGATATACCACGGTTAAACATGTAATG
1 TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
* * * *
25586746 TTGTGCTAAGTGGATATGCCACGATTACATATATTGATTATTAACA
1 TGGTGCTAAGTGGATATGCCACGGTT--ATACA-TG-----TAACG
* *
25586792 TGGTGCTAAGTGGATATACCACGGTTAAACATGTAACG
1 TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
* *
25586830 TGGTGCTAAGTGGATATGCTACGGTTACATATATTGATTCATTAACG
1 TGGTGCTAAGTGGATATGCCACGGTT--ATACA-TG------TAACG
* * *
25586877 TGGTGCTAAGTGGATATACCACGATTAAACATGTAACG
1 TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
*
25586915 TGGTGCTAAGTGGATATGCCACGATTATACATGT
1 TGGTGCTAAGTGGATATGCCACGGTTATACATGT
25586949 TAATTTGAAA
Statistics
Matches: 261, Mismatches: 40, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
38 112 0.43
39 2 0.01
40 10 0.04
41 6 0.02
43 2 0.01
44 7 0.03
45 6 0.02
46 26 0.10
47 58 0.22
48 32 0.12
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (38 bp):
TGGTGCTAAGTGGATATGCCACGGTTATACATGTAACG
Found at i:25586911 original size:85 final size:85
Alignment explanation
Indices: 25586651--25586937 Score: 495
Period size: 85 Copynumber: 3.4 Consensus size: 85
25586641 ACATATTGAT
*
25586651 ACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
*
25586716 AGAGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
* * * *
25586736 ACATGTAATGTTGTGCTAAGTGGATATGCCACGATTACATATATTGATT-ATTAACATGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
25586800 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
*
25586820 ACATGTAACGTGGTGCTAAGTGGATATGCTACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
*
25586885 AGTGGATATACCACGATTAA
66 AGTGGATATACCACGGTTAA
25586905 ACATGTAACGTGGTGCTAAGTGGATATGCCACG
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACG
25586938 ATTATACATG
Statistics
Matches: 188, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
84 78 0.41
85 110 0.59
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGTGGATATACCACGGTTAA
Found at i:25586971 original size:169 final size:169
Alignment explanation
Indices: 25586651--25586972 Score: 511
Period size: 169 Copynumber: 1.9 Consensus size: 169
25586641 ACATATTGAT
25586651 ACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
* * * *
25586716 AGAGGATATACCACGGTTAAACATGTAATGTTGTGCTAAGTGGATATGCCACGATTACATATATT
66 AGAGGATATACCACGATTAAACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACACATATT
* * * *
25586781 GATTATTAACATGGTGCTAAGTGGATATACCACGGTTAA
131 AATTATGAAAATGGCGCTAAGTGGATATACCACGGTTAA
* *
25586820 ACATGTAACGTGGTGCTAAGTGGATATGCTACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
* * *
25586885 AGTGGATATACCACGATTAAACATGTAACGTGGTGCTAAGTGGATATGCCACGATTATACATGTT
66 AGAGGATATACCACGATTAAACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACACATATT
25586950 AATT-TGAAAATTGGCGCTAAGTG
131 AATTATGAAAA-TGGCGCTAAGTG
25586973 CGTATGCCAC
Statistics
Matches: 139, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
168 4 0.03
169 135 0.97
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (169 bp):
ACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
AGAGGATATACCACGATTAAACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACACATATT
AATTATGAAAATGGCGCTAAGTGGATATACCACGGTTAA
Found at i:25590226 original size:15 final size:15
Alignment explanation
Indices: 25590186--25590226 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25590176 CTGTAAATGA
25590186 GATTTCCTTATCATG
1 GATTTCCTTATCATG
** *
25590201 GATTTTTTTATCTTG
1 GATTTCCTTATCATG
25590216 GATTTCCTTAT
1 GATTTCCTTAT
25590227 TCTGTGCTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (15 bp):
GATTTCCTTATCATG
Found at i:25592220 original size:69 final size:68
Alignment explanation
Indices: 25592080--25592360 Score: 217
Period size: 69 Copynumber: 4.1 Consensus size: 68
25592070 GATTATCAAG
* * * * * **
25592080 AATATGACAGCTGGGAGCTTTGTTCTCACTAACAGTTTTGGAGGTTGCTGCTCTTCGCCTATGAA
1 AATATGACAGCTGGGAGCTTTGCTCTCACTAATA-TTTTGGAGGTTACGGCTCTTTGCCTGCGAA
**
25592145 ATTT
65 CCTT
* * *
25592149 AATATGATAGCTGGGAGCTTTGCTCTCAGTAAGTATTTTGGAGGTTACGGCTCTTTACCTGCGAA
1 AATATGACAGCTGGGAGCTTTGCTCTCACTAA-TATTTTGGAGGTTACGGCTCTTTGCCTGCGAA
25592214 CCTT
65 CCTT
* * * * * *
25592218 AATATGACA-TTTGGAGCATTTGCTCTTC-CTAACTGTTTTGGAGGTTATGGCTCTTTGCTTGCA
1 AATATGACAGCTGGGAGC-TTTGCTC-TCACTAA-TATTTTGGAGGTTACGGCTCTTTGCCTGCG
25592281 AACCTT
63 AACCTT
* * ** * * * * * *
25592287 AATATGACAGCTAGAAG-TTGTGCTCTCGGTAATTGTTTTAGAGGTTGCGGCTCTTCGCTTGTGA
1 AATATGACAGCTGGGAGCTT-TGCTCTCACTAA-TATTTTGGAGGTTACGGCTCTTTGCCTGCGA
*
25592351 ACATT
64 ACCTT
25592356 AATAT
1 AATAT
25592361 CATGTGAACG
Statistics
Matches: 172, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
68 10 0.06
69 155 0.90
70 7 0.04
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (68 bp):
AATATGACAGCTGGGAGCTTTGCTCTCACTAATATTTTGGAGGTTACGGCTCTTTGCCTGCGAAC
CTT
Found at i:25598212 original size:41 final size:41
Alignment explanation
Indices: 25598167--25598297 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
25598157 TGCTTAAACA
* * *
25598167 AGCTGTGGGTTGGGACATTAGCTAACGATGTTGCTCACACG
1 AGCTGTGGGTCGGGACATTAGCTAACAATGCTGCTCACACG
* * *
25598208 AGCTGTGGGTGGGGATATTAACTAACAATGCTGCTCACACG
1 AGCTGTGGGTCGGGACATTAGCTAACAATGCTGCTCACACG
* * * * *
25598249 AGCTGTGGGTCAGGACGTTAGCTAACAATGCTACTCAAACA
1 AGCTGTGGGTCGGGACATTAGCTAACAATGCTGCTCACACG
25598290 AGCTGTGG
1 AGCTGTGG
25598298 AGAATTCACA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (41 bp):
AGCTGTGGGTCGGGACATTAGCTAACAATGCTGCTCACACG
Found at i:25599505 original size:144 final size:144
Alignment explanation
Indices: 25599244--25599534 Score: 537
Period size: 144 Copynumber: 2.0 Consensus size: 144
25599234 TATGAGGAAT
25599244 GAATCGAGAAGGAAAGGTTTGAAAATATACCTTTTGAAATCTAAAAAATATGAAAGAACCATTGC
1 GAATCGAGAAGGAAAGGTTTGAAAATATACCTTTTGAAATCTAAAAAATATGAAAGAACCATTGC
* *
25599309 TGGCTTAATCCCCTTCGCACACTGCCGATCCAAAGCTGCAACAGAATCGTCCTAGCCTCTACGTA
66 TGGCTTAATCCCCTTCGCACAATACCGATCCAAAGCTGCAACAGAATCGTCCTAGCCTCTACGTA
25599374 GTCCGCCCAGTTGC
131 GTCCGCCCAGTTGC
25599388 GAATCGAGAAGGAAAGGTTTGAAAATATACCTTTTGAAATCTAAAAAATATGAAAGAACCATTGC
1 GAATCGAGAAGGAAAGGTTTGAAAATATACCTTTTGAAATCTAAAAAATATGAAAGAACCATTGC
* * *
25599453 TGGCTTAATCCCCTTCGTACAATACCGATCCAAAGCTGCATCAGAATTGTCCTAGCCTCTACGTA
66 TGGCTTAATCCCCTTCGCACAATACCGATCCAAAGCTGCAACAGAATCGTCCTAGCCTCTACGTA
25599518 GTCCGCCCAGTTGC
131 GTCCGCCCAGTTGC
25599532 GAA
1 GAA
25599535 CGAATGAACA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (144 bp):
GAATCGAGAAGGAAAGGTTTGAAAATATACCTTTTGAAATCTAAAAAATATGAAAGAACCATTGC
TGGCTTAATCCCCTTCGCACAATACCGATCCAAAGCTGCAACAGAATCGTCCTAGCCTCTACGTA
GTCCGCCCAGTTGC
Found at i:25604544 original size:39 final size:39
Alignment explanation
Indices: 25604490--25604569 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
25604480 TGTAGGAAAG
25604490 TTTGACATTGGGTTAAATTCATCCAAGATGCAAGTACTT
1 TTTGACATTGGGTTAAATTCATCCAAGATGCAAGTACTT
25604529 TTTGACATTGGGTTAAATTCATCCAAGATGCAAGTACTT
1 TTTGACATTGGGTTAAATTCATCCAAGATGCAAGTACTT
25604568 TT
1 TT
25604570 GGATTTTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (39 bp):
TTTGACATTGGGTTAAATTCATCCAAGATGCAAGTACTT
Found at i:25604977 original size:12 final size:12
Alignment explanation
Indices: 25604960--25604985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25604950 GAATGGGAAT
25604960 ATGTGATTTTGA
1 ATGTGATTTTGA
25604972 ATGTGATTTTGA
1 ATGTGATTTTGA
25604984 AT
1 AT
25604986 ATATATGAAT
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:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
ATGTGATTTTGA
Found at i:25609318 original size:59 final size:57
Alignment explanation
Indices: 25609226--25609337 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 57
25609216 TTTTATTATA
* *
25609226 TATAAATATATAATATATGCATGCTTTGATTGGTTTAGTGCATGTTGTAGTTTTGTATG
1 TATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATG-T-TAGTTTTGTATG
25609285 TATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTAGTTTTG
1 TATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTAGTTTTG
25609338 GAAAATTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
57 8 0.16
58 1 0.02
59 42 0.82
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (57 bp):
TATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTAGTTTTGTATG
Found at i:25609703 original size:17 final size:17
Alignment explanation
Indices: 25609677--25609721 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
25609667 GTCTAAAGAT
*
25609677 TAATTCATTGTTTGACA
1 TAATTTATTGTTTGACA
25609694 TAATTTATTGTTTGACA
1 TAATTTATTGTTTGACA
25609711 TAATTTATTGT
1 TAATTTATTGT
25609722 CAATGTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (17 bp):
TAATTTATTGTTTGACA
Found at i:25614043 original size:33 final size:35
Alignment explanation
Indices: 25613979--25614043 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 35
25613969 AATTGTAATT
* *
25613979 TATTTATCTAATTACTTTTTATTTAAGTAAATAGA
1 TATTTATCTAATTACTTATTATTAAAGTAAATAGA
* *
25614014 TATTTAT-TATTTA-TTATTATTAAATTAAAT
1 TATTTATCTAATTACTTATTATTAAAGTAAAT
25614044 TAAACACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 14 0.54
34 5 0.19
35 7 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
TATTTATCTAATTACTTATTATTAAAGTAAATAGA
Found at i:25614292 original size:23 final size:23
Alignment explanation
Indices: 25614266--25614310 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25614256 TGTATATGTG
25614266 TAGTTAATTGTATA-ATAGATATT
1 TAGTTAATT-TATATATAGATATT
*
25614289 TAGTTAATTTATATATATATAT
1 TAGTTAATTTATATATAGATAT
25614311 ATAAGTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
TAGTTAATTTATATATAGATATT
Found at i:25615874 original size:18 final size:19
Alignment explanation
Indices: 25615851--25615895 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
25615841 TTACTGAATC
* *
25615851 ATATTGATAA-ATTGATTG
1 ATATTGAAAATATTGACTG
25615869 ATATTGAAAAATATTGACTG
1 ATATTG-AAAATATTGACTG
25615889 ATATTGA
1 ATATTGA
25615896 GCTTGGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (19 bp):
ATATTGAAAATATTGACTG
Found at i:25624445 original size:28 final size:28
Alignment explanation
Indices: 25624405--25624461 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25624395 TTGCTCCACC
25624405 CAAAGTAAAAACATTCCTACTTGTAAAG
1 CAAAGTAAAAACATTCCTACTTGTAAAG
25624433 CAAAGTAAAAACATTCCTACTTGTAAAG
1 CAAAGTAAAAACATTCCTACTTGTAAAG
25624461 C
1 C
25624462 TAACTTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.25
Consensus pattern (28 bp):
CAAAGTAAAAACATTCCTACTTGTAAAG
Found at i:25629169 original size:8 final size:8
Alignment explanation
Indices: 25629156--25629185 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
25629146 GAAGCCTGTA
25629156 ACATATGC
1 ACATATGC
*
25629164 ACATATGT
1 ACATATGC
25629172 ACATATGC
1 ACATATGC
25629180 ACATAT
1 ACATAT
25629186 AACATCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (8 bp):
ACATATGC
Done.