Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 18 of 147
Found at i:3904915 original size:26 final size:26
Alignment explanation
Indices: 3904879--3904953 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
3904869 GTCAAGCCCT
*
3904879 AAACCTAAAACTCAAAACCAAACCCC
1 AAACCTTAAACTCAAAACCAAACCCC
* * *
3904905 AAACCTTAAAC-CTAACCCTAAACCCT
1 AAACCTTAAACTCAAAACC-AAACCCC
*
3904931 AAACCTTAAACCTTAAAACCAAA
1 AAACCTTAAA-CTCAAAACCAAA
3904954 ACCTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 5 0.13
26 26 0.67
27 4 0.10
28 4 0.10
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.15
Consensus pattern (26 bp):
AAACCTTAAACTCAAAACCAAACCCC
Found at i:3912947 original size:160 final size:159
Alignment explanation
Indices: 3912622--3913470 Score: 667
Period size: 160 Copynumber: 5.3 Consensus size: 159
3912612 CCATTCATAC
* * * * * * *
3912622 ATATCAATCATAAAAATCAAATTCAATCATTTGGACAAGTTTAATATCATATATTGAAGCTATCT
1 ATATCAATTATGAAAA-CAAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGAAGCTATCC
* ** * * * * * *
3912687 AAACTGTT--AA-AACATGATGAATAGCAACTTTGTATTTTTACCTTTTAACAGCAAAAAAAGTC
65 AAACTGTTAAAATAAAACAAT-AACAGTAAATTTGTATTTTTATCTTTTAACGGCCAAAAAA-TC
* * *
3912749 TTAAACAGAGGTAAACAACAACTTTGTCACAT
128 CTAAACAGACGTAAACAACAACTTTTTCACAT
** *
3912781 ATATCAATTATGAAAACAAGTTCAATCATTCAAAAAAGTTTAATATCATATATTGAAGCTATCCA
1 ATATCAATTATGAAAACAAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGAAGCTATCCA
*
3912846 AACTGCTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTTTTAACGGCCTAAAAAATCCT
66 AACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTTTTAACGGCC-AAAAAATCCT
* * *
3912911 AAACAGAGGTAAACAGCAACTATTTCACAT
130 AAACAGACGTAAACAACAACTTTTTCACAT
* * * * *
3912941 ATATCAATTACGGAAACCAAGTTTAATCATTC-AAAAACTTTAATATCATGTATTGAAG-TCATC
1 ATATCAATTA-TGAAAACAAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGAAGCT-ATC
* * * * * *
3913004 CAAACTGTTAAAATAGAATAATAATAGTAAATTTATATTTTTATATTTTAAC-GACAAAAATATC
64 CAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTTTTAACGGCCAAAAA-ATC
* * ** *
3913068 CTAAATATACGTAAATGATAACTTTTTCACAT
128 CTAAACAGACGTAAACAACAACTTTTTCACAT
* * * *
3913100 ATATCAACTGTGGAAACCAAGTTCAATCATTCGGATAAGTTTAATATCATGTATT-ATAGCTATC
1 ATATCAATTAT-GAAAACAAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGA-AGCTATC
* * * * * * *
3913164 TAAACTATTAAAATAGAACAATAACA-AAAATTTGTATTATTA-CTTGTTAATGGCACAAAAAGT
64 CAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTT-TTAACGGC-CAAAAAAT
* * * * *
3913227 CCTAAATAAACGTAAACAATAACTTTTTCATAC
127 CCTAAACAGACGTAAACAACAACTTTTTCACAT
* * * * * * *
3913260 ATATCAACTGTGAAAACTAAGTTCAATGATTTGGATAAGTTTAATATTATGTATTGAAACTAT-C
1 ATATCAATTATGAAAAC-AAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGAAGCTATCC
* * * * * * * * ** * * *
3913324 AAAATATTAAAATAGAATAATAACTA-TAACTTTGCATTTTTACCTTGTAATAGCACGAAAAGTT
65 AAACTGTTAAAATAAAACAATAAC-AGTAAATTTGTATTTTTATCTTTTAACGGC-CAAAAAATC
* * * ** * ***
3913388 GTAAATAGACATAAATTACAAATTACGACACAT
128 CTAAACAGACGTAAACAACAACTT-TTTCACAT
* * *
3913421 ATATCAATAACGAAAATCAAGTTCAATCATTCGAAAAAGTTTAATATCAT
1 ATATCAATTATGAAAA-CAAGTTCAATCATTCGGAAAAGTTTAATATCAT
3913471 AAACTTACTA
Statistics
Matches: 568, Mismatches: 102, Indels: 38
0.80 0.14 0.05
Matches are distributed among these distances:
158 56 0.10
159 116 0.20
160 313 0.55
161 82 0.14
162 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (159 bp):
ATATCAATTATGAAAACAAGTTCAATCATTCGGAAAAGTTTAATATCATGTATTGAAGCTATCCA
AACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTTTTAACGGCCAAAAAATCCTA
AACAGACGTAAACAACAACTTTTTCACAT
Found at i:3913305 original size:320 final size:321
Alignment explanation
Indices: 3912634--3913471 Score: 768
Period size: 319 Copynumber: 2.6 Consensus size: 321
3912624 ATCAATCATA
* * * * *
3912634 AAAATCAAATTCAATCATTTGGACAAGTTTAATATCATATATTGAAGCTATCTAAACTGTTAAAA
1 AAAACCAAGTTCAATCATTTGGAAAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAA
* * * * * * *
3912699 CATG-AT--GAATAGCAACTTTGTATTTTTACCTTTTAACAGCAAAAAAAGTCTTAAACAGAGGT
66 TA-GAATAATAATAGCAAATTTATATTTTTACATTTTAACAGCAAAAAAAGTCCTAAACAGACGT
*
3912761 AAACAACAACTTTGTCACATATATCAATTATGAAAACAAGTTCAATCATTCAAAAAAGTTTAATA
130 AAACAACAACTTTGTCACATATATCAACTATGAAAACAAGTTCAATCATTCAAAAAAGTTTAATA
* * *
3912826 TCATATATTGAAGCTATCCAAACTGCTAAAATAAAACAATAACAGTAAATTTGTATTTTTATCTT
195 TCATATATTGAAGCTATCCAAACTACTAAAATAAAACAATAACAGAAAATTTGTATTATTATCTT
* * * * *
3912891 TTAACGGCCTAAAAAATCCTAAACAGAGGTAAACAGCAACTATTTCACATATATCAATTACG
260 TTAACGGCCTAAAAAATCCTAAACAAACGTAAACAACAACTATTTCACACATATCAACTACG
* * ** *
3912953 GAAACCAAGTTTAATCA-TTCAAAAACTTTAATATCATGTATTGAAG-TCATCCAAACTGTTAAA
1 AAAACCAAGTTCAATCATTTGGAAAAGTTTAATATCATGTATTGAAGCT-ATCCAAACTGTTAAA
* * * * *
3913016 ATAGAATAATAATAGTAAATTTATATTTTTATATTTTAAC-GACAAAAATA-TCCTAAATATACG
65 ATAGAATAATAATAGCAAATTTATATTTTTACATTTTAACAG-CAAAAAAAGTCCTAAACAGACG
** * * * * ** *
3913079 TAAATGATAACTTTTTCACATATATCAACTGTGGAAACCAAGTTCAATCATTCGGATAAGTTTAA
129 TAAACAACAACTTTGTCACATATATCAACTAT-GAAAACAAGTTCAATCATTCAAAAAAGTTTAA
* * * *
3913144 TATCATGTATT-ATAGCTATCTAAACTATTAAAATAGAACAATAACA-AAAATTTGTATTATTA-
193 TATCATATATTGA-AGCTATCCAAACTACTAAAATAAAACAATAACAGAAAATTTGTATTATTAT
* * * * * * *
3913206 CTTGTTAATGGCAC-AAAAAGTCCTAAATAAACGTAAACAATAACTTTTTCATACATATCAACTG
257 CTT-TTAACGGC-CTAAAAAATCCTAAACAAACGTAAACAACAACTATTTCACACATATCAACTA
*
3913270 TG
320 CG
* * * * * * *
3913272 AAAACTAAGTTCAATGATTTGGATAAGTTTAATATTATGTATTGAAACTAT-CAAAATATTAAAA
1 AAAACCAAGTTCAATCATTTGGAAAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAA
* * ** * * * ** ** * *
3913336 TAGAATAATAACTA-TAACTTTGCATTTTTACCTTGTAATAGCACGAAAAGTTGTAAATAGACAT
66 TAGAATAATAA-TAGCAAATTTATATTTTTACATTTTAACAGCAAAAAAAGTCCTAAACAGACGT
** * * * * *
3913400 AAATTACAAATTACGACACATATATCAA-TAACGAAAATCAAGTTCAATCATTCGAAAAAGTTTA
130 AAACAACAACTT-TGTCACATATATCAACT-ATGAAAA-CAAGTTCAATCATTCAAAAAAGTTTA
3913464 ATATCATA
192 ATATCATA
3913472 AACTTACTAT
Statistics
Matches: 412, Mismatches: 90, Indels: 32
0.77 0.17 0.06
Matches are distributed among these distances:
317 2 0.00
318 45 0.11
319 169 0.41
320 152 0.37
321 44 0.11
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (321 bp):
AAAACCAAGTTCAATCATTTGGAAAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAA
TAGAATAATAATAGCAAATTTATATTTTTACATTTTAACAGCAAAAAAAGTCCTAAACAGACGTA
AACAACAACTTTGTCACATATATCAACTATGAAAACAAGTTCAATCATTCAAAAAAGTTTAATAT
CATATATTGAAGCTATCCAAACTACTAAAATAAAACAATAACAGAAAATTTGTATTATTATCTTT
TAACGGCCTAAAAAATCCTAAACAAACGTAAACAACAACTATTTCACACATATCAACTACG
Found at i:3913954 original size:18 final size:18
Alignment explanation
Indices: 3913931--3913969 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3913921 CATGCGGAGA
*
3913931 CATGAAATCTCATGAAGG
1 CATGAAATCTCACGAAGG
3913949 CATGAAATCTCACGAAGG
1 CATGAAATCTCACGAAGG
3913967 CAT
1 CAT
3913970 AGATACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (18 bp):
CATGAAATCTCACGAAGG
Found at i:3915646 original size:52 final size:51
Alignment explanation
Indices: 3915514--3915660 Score: 170
Period size: 51 Copynumber: 2.9 Consensus size: 51
3915504 TTTATTTTTG
*
3915514 TTTTAATGAGAATTGATTCTAAAATCAAATCCCAAAAATCTCTCCCTATCA
1 TTTTAATGAGAATTGATTCTAAAATTAAATCCCAAAAATCTCTCCCTATCA
* * * * * * *
3915565 TTGTAATGTGAATTGTTTATGAAATTAAATCCCGACAATCTCTCCAC-ATCA
1 TTTTAATGAGAATTGATTCTAAAATTAAATCCCAAAAATCTCTCC-CTATCA
** *
3915616 TTTTTAATGCCAATTGATTCTAAAATTAAATTCCAAAAATCTCTC
1 -TTTTAATGAGAATTGATTCTAAAATTAAATCCCAAAAATCTCTC
3915661 AATTGAAGCT
Statistics
Matches: 77, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
51 41 0.53
52 36 0.47
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (51 bp):
TTTTAATGAGAATTGATTCTAAAATTAAATCCCAAAAATCTCTCCCTATCA
Found at i:3915751 original size:9 final size:9
Alignment explanation
Indices: 3915730--3915779 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
3915720 TAAAAGTGAA
3915730 AATAAAAA-
1 AATAAAAAT
*
3915738 GATAAAAAT
1 AATAAAAAT
*
3915747 AATAATAAT
1 AATAAAAAT
3915756 AATAAAAAT
1 AATAAAAAT
3915765 AAT-AAAAT
1 AATAAAAAT
3915773 -ATAAAAA
1 AATAAAAA
3915780 ATCAAGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 2 0.06
8 16 0.44
9 18 0.50
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (9 bp):
AATAAAAAT
Found at i:3916128 original size:37 final size:34
Alignment explanation
Indices: 3916082--3916154 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
3916072 TATAAATATA
* *
3916082 TATATATCTTTACACTCACCAAATACAAGTTTTTTAT
1 TATACATCTTT-CACT-A-CAAATACAAGCTTTTTAT
* *
3916119 TATACATCTTTCTCTACAAATACAGGCTTTTTAT
1 TATACATCTTTCACTACAAATACAAGCTTTTTAT
3916153 TA
1 TA
3916155 AACCTCTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 18 0.56
35 1 0.03
36 3 0.09
37 10 0.31
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (34 bp):
TATACATCTTTCACTACAAATACAAGCTTTTTAT
Found at i:3916167 original size:34 final size:34
Alignment explanation
Indices: 3916101--3916167 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
3916091 TTACACTCAC
* * *
3916101 CAAATACAAGTTTTTTATTATACATCTTTCTCTA
1 CAAATACAAGCTTTTTATTAAACATCTATCTCTA
* *
3916135 CAAATACAGGCTTTTTATTAAACCTCTATCTCT
1 CAAATACAAGCTTTTTATTAAACATCTATCTCT
3916168 CTAAAAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (34 bp):
CAAATACAAGCTTTTTATTAAACATCTATCTCTA
Found at i:3917264 original size:26 final size:26
Alignment explanation
Indices: 3917234--3917346 Score: 88
Period size: 26 Copynumber: 4.3 Consensus size: 26
3917224 CTAATCTTAT
*
3917234 CCTAAACCATAAACCAAATCCCAAAC
1 CCTAAACCATAAACCAAATCCTAAAC
* * *
3917260 CCTAAACCCTAAATTCTAGA-CCTTAAA-
1 CCTAAACCATAAA--CCAAATCC-TAAAC
* * *
3917287 CAT-AACCCTAAACCAAATCCTAAAA
1 CCTAAACCATAAACCAAATCCTAAAC
* * *
3917312 CCTAAACCTTCAACTAAATCCTAAAC
1 CCTAAACCATAAACCAAATCCTAAAC
3917338 CCTAAACCA
1 CCTAAACCA
3917347 AACCCTAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
24 7 0.10
25 4 0.06
26 47 0.69
27 4 0.06
28 6 0.09
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.19
Consensus pattern (26 bp):
CCTAAACCATAAACCAAATCCTAAAC
Found at i:3917266 original size:7 final size:7
Alignment explanation
Indices: 3917234--3917356 Score: 61
Period size: 7 Copynumber: 19.0 Consensus size: 7
3917224 CTAATCTTAT
3917234 CCTAAAC
1 CCTAAAC
*
3917241 CATAAA-
1 CCTAAAC
3917247 CC-AAATC
1 CCTAAA-C
3917254 CC-AAAC
1 CCTAAAC
3917260 CCTAAAC
1 CCTAAAC
*
3917267 CCTAAAT
1 CCTAAAC
* *
3917274 TCTAGAC
1 CCTAAAC
*
3917281 CTTAAA-
1 CCTAAAC
*
3917287 CAT-AAC
1 CCTAAAC
3917293 CCTAAA-
1 CCTAAAC
*
3917299 CC-AAAT
1 CCTAAAC
*
3917305 CCTAAAA
1 CCTAAAC
3917312 CCTAAAC
1 CCTAAAC
* *
3917319 CTTCAA-
1 CCTAAAC
*
3917325 -CTAAAT
1 CCTAAAC
3917331 CCTAAAC
1 CCTAAAC
3917338 CCTAAA-
1 CCTAAAC
3917344 CC-AAAC
1 CCTAAAC
3917350 CCTAAAC
1 CCTAAAC
3917357 TAAGAACCTA
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
5 14 0.16
6 16 0.18
7 57 0.66
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.18
Consensus pattern (7 bp):
CCTAAAC
Found at i:3917353 original size:19 final size:19
Alignment explanation
Indices: 3917234--3917356 Score: 74
Period size: 19 Copynumber: 6.4 Consensus size: 19
3917224 CTAATCTTAT
*
3917234 CCTAAACCATAAACCAAATC
1 CCTAAACCCTAAACCAAA-C
*
3917254 CC-AAACCCTAAACCCTAAAT
1 CCTAAACCCTAAA-CC-AAAC
* * *
3917274 TCTAGACCTTAAA-CATAAC
1 CCTAAACCCTAAACCA-AAC
*
3917293 CCTAAA-CC-AAATCCTAAAA
1 CCTAAACCCTAAA-CC-AAAC
* * * *
3917312 CCTAAACCTTCAACTAAAT
1 CCTAAACCCTAAACCAAAC
3917331 CCTAAACCCTAAACCAAAC
1 CCTAAACCCTAAACCAAAC
3917350 CCTAAAC
1 CCTAAAC
3917357 TAAGAACCTA
Statistics
Matches: 76, Mismatches: 18, Indels: 19
0.67 0.16 0.17
Matches are distributed among these distances:
17 3 0.04
18 2 0.03
19 50 0.66
20 8 0.11
21 13 0.17
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.18
Consensus pattern (19 bp):
CCTAAACCCTAAACCAAAC
Found at i:3917448 original size:18 final size:19
Alignment explanation
Indices: 3917425--3917460 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3917415 TTCATTTTGA
*
3917425 TAAATTGTTA-TGCATTCC
1 TAAATTGTCATTGCATTCC
3917443 TAAATTGTCATTGCATTC
1 TAAATTGTCATTGCATTC
3917461 ATGCATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTGTCATTGCATTCC
Found at i:3918170 original size:42 final size:42
Alignment explanation
Indices: 3918109--3918229 Score: 215
Period size: 42 Copynumber: 2.9 Consensus size: 42
3918099 TCTATTAAAA
*
3918109 AGATAAATATTTTAGATGGCCAATTGCACTTTTAAAAATAAG
1 AGATAAATATTTTAAATGGCCAATTGCACTTTTAAAAATAAG
3918151 AGATAAATATTTTAAATGGCCAATTGCACTTTTAAAAATAAG
1 AGATAAATATTTTAAATGGCCAATTGCACTTTTAAAAATAAG
* *
3918193 AGATAAACATTTTAAATGGCCAATTGCACCTTTAAAA
1 AGATAAATATTTTAAATGGCCAATTGCACTTTTAAAA
3918230 GAAAATTAGT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (42 bp):
AGATAAATATTTTAAATGGCCAATTGCACTTTTAAAAATAAG
Found at i:3918755 original size:26 final size:26
Alignment explanation
Indices: 3918726--3918807 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 26
3918716 TTGTGTTTGA
*
3918726 GCCCATTTAGGCCTATTAGTGTCCGG
1 GCCCAATTAGGCCTATTAGTGTCCGG
* *
3918752 GCCCAATTAGACACCTATTTGTGTCCGG
1 GCCCAATTAG--GCCTATTAGTGTCCGG
* *
3918780 GTCCAATTAGG-CTGATTGGTGTCCGG
1 GCCCAATTAGGCCT-ATTAGTGTCCGG
3918806 GC
1 GC
3918808 TTAGCTAGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.04
26 21 0.46
28 23 0.50
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (26 bp):
GCCCAATTAGGCCTATTAGTGTCCGG
Found at i:3918790 original size:54 final size:54
Alignment explanation
Indices: 3918705--3918807 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
3918695 AAAAGGATTG
** *
3918705 TAGACACCCATTTGTGTTTGAGCCCATTTAGGCCT-ATTAGTGTCCGGGCCCAAT
1 TAGACACCCATTTGTGTCCGAGCCCAATTAGG-CTGATTAGTGTCCGGGCCCAAT
* * * *
3918759 TAGACACCTATTTGTGTCCGGGTCCAATTAGGCTGATTGGTGTCCGGGC
1 TAGACACCCATTTGTGTCCGAGCCCAATTAGGCTGATTAGTGTCCGGGC
3918808 TTAGCTAGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.05
54 39 0.95
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.31
Consensus pattern (54 bp):
TAGACACCCATTTGTGTCCGAGCCCAATTAGGCTGATTAGTGTCCGGGCCCAAT
Found at i:3926296 original size:69 final size:70
Alignment explanation
Indices: 3926184--3926325 Score: 205
Period size: 69 Copynumber: 2.0 Consensus size: 70
3926174 GATCTATCGG
* * * * *
3926184 TGACTCAACTCATAAATGCCTTATATATAAAAGTAGTAGAAAAATAATTAAAATGTTGTTACAGA
1 TGACTCAACCCATAAATGCCCTATATATAAAAGTAGCAAAAAAATAATTAAAATATTGTTACAGA
3926249 TCTTT
66 TCTTT
* * *
3926254 TGACTCAACCCAT-AATGCCCTATATATAGAAGTAGCAAAAAAATCATTAAAATATTTTTACAGA
1 TGACTCAACCCATAAATGCCCTATATATAAAAGTAGCAAAAAAATAATTAAAATATTGTTACAGA
3926318 TCTTT
66 TCTTT
3926323 TGA
1 TGA
3926326 ACTAGTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 52 0.81
70 12 0.19
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (70 bp):
TGACTCAACCCATAAATGCCCTATATATAAAAGTAGCAAAAAAATAATTAAAATATTGTTACAGA
TCTTT
Found at i:3937385 original size:11 final size:11
Alignment explanation
Indices: 3937369--3937412 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3937359 ATATGATGAT
*
3937369 ATAATATGAAA
1 ATAATATAAAA
3937380 ATAATATAAATAA
1 ATAATAT-AA-AA
*
3937393 AAAATATAAAA
1 ATAATATAAAA
3937404 ATAATATAA
1 ATAATATAA
3937413 CTTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 17 0.61
12 3 0.11
13 8 0.29
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3938887 original size:7 final size:7
Alignment explanation
Indices: 3938875--3938903 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3938865 AATGCCTTTG
3938875 CTTTTTT
1 CTTTTTT
3938882 CTTTTTT
1 CTTTTTT
3938889 CTTTTTT
1 CTTTTTT
3938896 -TTTTTT
1 CTTTTTT
3938902 CT
1 CT
3938904 CTCCACGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
CTTTTTT
Found at i:3938899 original size:13 final size:14
Alignment explanation
Indices: 3938875--3938903 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3938865 AATGCCTTTG
3938875 CTTTTTTCTTTTTT
1 CTTTTTTCTTTTTT
3938889 CTTTTTT-TTTTTT
1 CTTTTTTCTTTTTT
3938902 CT
1 CT
3938904 CTCCACGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTTTCTTTTTT
Found at i:3939191 original size:24 final size:23
Alignment explanation
Indices: 3939164--3939210 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3939154 AAAAATTTTT
3939164 ATTATA-ATATTATTTTTAAGTAAA
1 ATTATATA-ATTATTTTTAA-TAAA
*
3939188 ATTATTTAATTATTTTTAATAAA
1 ATTATATAATTATTTTTAATAAA
3939211 TTACATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 16 0.76
25 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTATATAATTATTTTTAATAAA
Found at i:3942153 original size:20 final size:20
Alignment explanation
Indices: 3942105--3942154 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3942095 TATTAGTCTA
* *
3942105 TTTTATAATCATTATATATT
1 TTTTATTATTATTATATATT
3942125 TTTTATTATTATTAT-TATT
1 TTTTATTATTATTATATATT
*
3942144 TATTTTTTATT
1 T-TTTATTATT
3942155 TAACACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTATTATTATATATT
Found at i:3942188 original size:2 final size:2
Alignment explanation
Indices: 3942181--3942205 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3942171 ATTCTTTTAA
3942181 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 A
3942206 CACACATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3942581 original size:10 final size:10
Alignment explanation
Indices: 3942566--3942590 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3942556 ATCGGTTCGA
3942566 CGGTTTGATT
1 CGGTTTGATT
3942576 CGGTTTGATT
1 CGGTTTGATT
3942586 CGGTT
1 CGGTT
3942591 CAACTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.32, T:0.48
Consensus pattern (10 bp):
CGGTTTGATT
Found at i:3944025 original size:37 final size:36
Alignment explanation
Indices: 3943887--3944085 Score: 130
Period size: 38 Copynumber: 5.4 Consensus size: 36
3943877 TCACAAGTAG
* * * *
3943887 AAAAATAAAGAGTCGATCGAGACAATACCGTAAGTCA
1 AAAAATAAAGAAT-GATTGGGACAACACCGTAAGTCA
* ** * ** *
3943924 AAAAATAAAAAAAATGATCAGGACAACATCACAAGTCG
1 AAAAAT--AAAGAATGATTGGGACAACACCGTAAGTCA
* ** * *
3943962 AATAATAAAGAACAACCT-GGACAACACCGTAAATCA
1 AAAAATAAAGAATGA-TTGGGACAACACCGTAAGTCA
*
3943998 AAAAATAAAGAATCGATTGGGACAACACCGTAAGTCG
1 AAAAATAAAGAAT-GATTGGGACAACACCGTAAGTCA
* * * * *
3944035 AATATTAAAGAAAATGATTGGGATAACACCATAAGTTA
1 AAAAATAAAG--AATGATTGGGACAACACCGTAAGTCA
3944073 AAAAATAAAGAAT
1 AAAAATAAAGAAT
3944086 TAACTAAGAC
Statistics
Matches: 121, Mismatches: 34, Indels: 15
0.71 0.20 0.09
Matches are distributed among these distances:
36 34 0.28
37 31 0.26
38 48 0.40
39 8 0.07
ACGTcount: A:0.53, C:0.15, G:0.16, T:0.17
Consensus pattern (36 bp):
AAAAATAAAGAATGATTGGGACAACACCGTAAGTCA
Found at i:3944044 original size:73 final size:73
Alignment explanation
Indices: 3943907--3944046 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
3943897 AGTCGATCGA
* * *
3943907 GACAATACCGTAAGTCAAAAAATAAAAAAAATGATCAGGACAACATCACAAGTCGAATAATAAAG
1 GACAACACCGTAAATCAAAAAAT-AAAAAAATGATCAGGACAACACCACAAGTCGAATAATAAAG
3943972 AACAACCTG
65 AACAACCTG
* ** ** *
3943981 GACAACACCGTAAATCAAAAAAT-AAAGAATCGATTGGGACAACACCGTAAGTCGAATATTAAAG
1 GACAACACCGTAAATCAAAAAATAAAAAAAT-GATCAGGACAACACCACAAGTCGAATAATAAAG
3944045 AA
65 AA
3944047 AATGATTGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
72 6 0.11
73 29 0.52
74 21 0.38
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.16
Consensus pattern (73 bp):
GACAACACCGTAAATCAAAAAATAAAAAAATGATCAGGACAACACCACAAGTCGAATAATAAAGA
ACAACCTG
Found at i:3944266 original size:33 final size:33
Alignment explanation
Indices: 3944208--3944289 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
3944198 GAGGGTTAGC
3944208 TAAATTGGGCTTTAAAATTTCATTGAATG-CTAGA
1 TAAATTGGGC-TTAAAATTTCATTGAATGTC-AGA
* * *
3944242 TAAATTGGGCTTAAAGCTTT-ATTGAGTGTCAGC
1 TAAATTGGGCTTAAA-ATTTCATTGAATGTCAGA
*
3944275 TAATTTGGGCTTAAA
1 TAAATTGGGCTTAAA
3944290 TCTCTCTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 28 0.67
34 14 0.33
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (33 bp):
TAAATTGGGCTTAAAATTTCATTGAATGTCAGA
Found at i:3944377 original size:33 final size:33
Alignment explanation
Indices: 3944302--3944427 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 33
3944292 TCTCTTTGGT
* * *
3944302 GCCAAATAAACTTGGCTTCAA-TTTCATTGAG-
1 GCCAAATAAACTGGGCTTAAACTTTCATTAAGA
* *
3944333 GACCAACTAAACCGGGCTTAAACTTTCATTAAGA
1 G-CCAAATAAACTGGGCTTAAACTTTCATTAAGA
* * *
3944367 GCCAGATAAACTGGGCTTAAAATTTTCATTAAGG
1 GCCAAATAAACTGGGCTT-AAACTTTCATTAAGA
* *
3944401 GCCAAATAAACTAGGCTTAAAGTTTCA
1 GCCAAATAAACTGGGCTTAAACTTTCA
3944428 CTGAGAGCTA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
31 1 0.01
32 16 0.21
33 31 0.40
34 30 0.38
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (33 bp):
GCCAAATAAACTGGGCTTAAACTTTCATTAAGA
Found at i:3944399 original size:34 final size:34
Alignment explanation
Indices: 3944347--3944527 Score: 129
Period size: 34 Copynumber: 5.4 Consensus size: 34
3944337 AACTAAACCG
* *
3944347 GGCTT-AAACTTTCATTAAGAGCCAGATAAACTG
1 GGCTTAAAATTTTCATTAAGAGCCAGATAAACTA
* *
3944380 GGCTTAAAATTTTCATTAAGGGCCAAATAAACTA
1 GGCTTAAAATTTTCATTAAGAGCCAGATAAACTA
* * * * * *
3944414 GGCTT-AAAGTTTCACTGAGAGCTAGCTAAGCTA
1 GGCTTAAAATTTTCATTAAGAGCCAGATAAACTA
* * * *
3944447 GACTTAAAATTTTCACT-AGTGCCAGGTAAACT-
1 GGCTTAAAATTTTCATTAAGAGCCAGATAAACTA
* * *
3944479 GGACTTTAAAAATCTTTC-TTTAGTGCCAGATAAATTA
1 GG-C-TT-AAAAT-TTTCATTAAGAGCCAGATAAACTA
*
3944516 GGCTTGAAATTT
1 GGCTTAAAATTT
3944528 CATGTAGATT
Statistics
Matches: 117, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
32 1 0.01
33 43 0.37
34 45 0.38
35 8 0.07
36 18 0.15
37 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (34 bp):
GGCTTAAAATTTTCATTAAGAGCCAGATAAACTA
Found at i:3944419 original size:67 final size:67
Alignment explanation
Indices: 3944302--3944461 Score: 162
Period size: 67 Copynumber: 2.4 Consensus size: 67
3944292 TCTCTTTGGT
* * * * * * *
3944302 GCCAAATAAACTTGGCTT-CAA-TTTCATTGAGGACCAACTAAACCGGGCTTAAACTTTCATTAA
1 GCCAGATAAACTAGGCTTAAAATTTTCATTAAGGACCAAATAAACCAGGCTTAAACTTTCACTAA
3944365 GA
66 GA
* * * * *
3944367 GCCAGATAAACTGGGCTTAAAATTTTCATTAAGGGCCAAATAAACTAGGCTTAAAGTTTCACTGA
1 GCCAGATAAACTAGGCTTAAAATTTTCATTAAGGACCAAATAAACCAGGCTTAAACTTTCACTAA
3944432 GA
66 GA
* * * *
3944434 GCTAGCTAAGCTAGACTTAAAATTTTCA
1 GCCAGATAAACTAGGCTTAAAATTTTCA
3944462 CTAGTGCCAG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 16 0.21
66 2 0.03
67 59 0.77
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (67 bp):
GCCAGATAAACTAGGCTTAAAATTTTCATTAAGGACCAAATAAACCAGGCTTAAACTTTCACTAA
GA
Found at i:3944484 original size:33 final size:34
Alignment explanation
Indices: 3944356--3944512 Score: 106
Period size: 33 Copynumber: 4.6 Consensus size: 34
3944346 GGGCTTAAAC
* * *
3944356 TTTCATTAAGAGCCAGATAAACTGGGCTTAAAAT
1 TTTCACTAAGTGCCAGATAAACTGGACTTAAAAT
* * * *
3944390 TTTCATTAAGGGCCAAATAAACTAGG-CTT-AAAG
1 TTTCACTAAGTGCCAGATAAACT-GGACTTAAAAT
* * * * * *
3944423 TTTCACTGAGAGCTAGCTAAGCTAGACTTAAAAT
1 TTTCACTAAGTGCCAGATAAACTGGACTTAAAAT
*
3944457 TTTCACT-AGTGCCAGGTAAACTGGACTTTAAAAAT
1 TTTCACTAAGTGCCAGATAAACTGGAC-TT-AAAAT
* *
3944492 CTTTC-TTTAGTGCCAGATAAA
1 -TTTCACTAAGTGCCAGATAAA
3944513 TTAGGCTTGA
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
32 1 0.01
33 36 0.37
34 36 0.37
35 8 0.08
36 16 0.16
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (34 bp):
TTTCACTAAGTGCCAGATAAACTGGACTTAAAAT
Found at i:3946414 original size:18 final size:18
Alignment explanation
Indices: 3946393--3946427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3946383 CCATTTTTCA
3946393 TTTTTTCTCTTTTTTTAC
1 TTTTTTCTCTTTTTTTAC
* *
3946411 TTTTTTGTTTTTTTTTA
1 TTTTTTCTCTTTTTTTA
3946428 TTTACATGCC
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:0.06, C:0.09, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTAC
Found at i:3947075 original size:7 final size:7
Alignment explanation
Indices: 3947053--3947101 Score: 73
Period size: 7 Copynumber: 7.1 Consensus size: 7
3947043 CAAAACTTTC
3947053 TTTATTT
1 TTTATTT
*
3947060 TTT-TGT
1 TTTATTT
*
3947066 TTTGTTT
1 TTTATTT
3947073 TTTATTT
1 TTTATTT
3947080 TTTATTT
1 TTTATTT
3947087 TTTATTT
1 TTTATTT
3947094 TTTATTT
1 TTTATTT
3947101 T
1 T
3947102 GCTTTTTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.10, C:0.00, G:0.04, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:3948791 original size:4 final size:4
Alignment explanation
Indices: 3948765--3948810 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
3948755 TGCATTATTT
* *
3948765 TGAA TGAA T-ACA TAAA TGGA TGAA TGAA TGAA TGAA TGAA TGAA TG
1 TGAA TGAA TGA-A TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TG
3948811 CACAAATGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 1 0.03
4 35 0.95
5 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (4 bp):
TGAA
Found at i:3952316 original size:14 final size:14
Alignment explanation
Indices: 3952297--3952326 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3952287 GGATTTCACT
3952297 TTAGGGTTTTAAGA
1 TTAGGGTTTTAAGA
*
3952311 TTAGGGTTTTGAGA
1 TTAGGGTTTTAAGA
3952325 TT
1 TT
3952327 TTAAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTTAAGA
Found at i:3952350 original size:15 final size:15
Alignment explanation
Indices: 3952311--3952411 Score: 68
Period size: 15 Copynumber: 6.7 Consensus size: 15
3952301 GGTTTTAAGA
3952311 TTAGGGTTTTGAGATT
1 TTAGGGTTTTG-GATT
**
3952327 TTAAAGTTTTGGATT
1 TTAGGGTTTTGGATT
3952342 TTAGGGTTTTGG--T
1 TTAGGGTTTTGGATT
* *
3952355 TT-GAGTTTTAAGGGTT
1 TTAGGGTTTT--GGATT
3952371 TTAGGG-TTTGGAAGGTT
1 TTAGGGTTTTGG-A--TT
*
3952388 TTAGGG-CTTGGATT
1 TTAGGGTTTTGGATT
3952402 TTAGGGTTTT
1 TTAGGGTTTT
3952412 AAAGATTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
12 6 0.09
13 3 0.04
14 12 0.18
15 16 0.24
16 16 0.24
17 14 0.21
ACGTcount: A:0.17, C:0.01, G:0.33, T:0.50
Consensus pattern (15 bp):
TTAGGGTTTTGGATT
Found at i:3952387 original size:17 final size:16
Alignment explanation
Indices: 3952367--3952410 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
3952357 GAGTTTTAAG
3952367 GGTTTTAGGGTTTGGAA
1 GGTTTTAGGGTTTGG-A
*
3952384 GGTTTTAGGGCTTGGA
1 GGTTTTAGGGTTTGGA
3952400 --TTTTAGGGTTT
1 GGTTTTAGGGTTT
3952411 TAAAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.40
16 1 0.04
17 14 0.56
ACGTcount: A:0.14, C:0.02, G:0.39, T:0.45
Consensus pattern (16 bp):
GGTTTTAGGGTTTGGA
Found at i:3952485 original size:30 final size:27
Alignment explanation
Indices: 3952436--3952500 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 27
3952426 TTTGAAATTA
3952436 AAGGTTTAGGTTTGAATTTTAGGGTTT
1 AAGGTTTAGGTTTGAATTTTAGGGTTT
3952463 GGAAGGTTTAGGGTTTCG-ATTTTAGGGTTT
1 --AAGGTTTA-GGTTT-GAATTTTAGGGTTT
3952493 AAGGTTTA
1 AAGGTTTA
3952501 ATGTTTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.24
29 8 0.24
30 17 0.50
31 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.45
Consensus pattern (27 bp):
AAGGTTTAGGTTTGAATTTTAGGGTTT
Found at i:3952500 original size:14 final size:15
Alignment explanation
Indices: 3952436--3952500 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
3952426 TTTGAAATTA
3952436 AAGGTTTA-GGTTTG
1 AAGGTTTAGGGTTTG
*
3952450 AA-TTTTAGGGTTTGG
1 AAGGTTTAGGGTTT-G
3952465 AAGGTTTAGGGTTTCG
1 AAGGTTTAGGGTTT-G
*
3952481 -A-TTTTAGGGTTT-
1 AAGGTTTAGGGTTTG
3952493 AAGGTTTA
1 AAGGTTTA
3952501 ATGTTTTAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 21 0.51
15 4 0.10
16 11 0.27
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.45
Consensus pattern (15 bp):
AAGGTTTAGGGTTTG
Found at i:3952537 original size:16 final size:16
Alignment explanation
Indices: 3952518--3952552 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3952508 AGTTTTAAGA
3952518 TTTTAAAAGTTTAGGG
1 TTTTAAAAGTTTAGGG
*
3952534 TTTTAAAGGTTTAGGG
1 TTTTAAAAGTTTAGGG
3952550 TTT
1 TTT
3952553 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (16 bp):
TTTTAAAAGTTTAGGG
Found at i:3952839 original size:22 final size:21
Alignment explanation
Indices: 3952814--3952862 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3952804 AAAATCTTTT
*
3952814 TTATTAGTTTATTTTATAATCA
1 TTATTA-TATATTTTATAATCA
* *
3952836 TTATATATATATTTTATTATTA
1 TTAT-TATATATTTTATAATCA
3952858 TTATT
1 TTATT
3952863 TTTGTTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTATATATTTTATAATCA
Found at i:3953095 original size:3 final size:3
Alignment explanation
Indices: 3953087--3953139 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
3953077 TTTTGTTTGG
3953087 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
3953133 TTA TTA T
1 TTA TTA T
3953140 AAAATAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3956309 original size:5 final size:4
Alignment explanation
Indices: 3956286--3956319 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
3956276 ATTTACGGAA
*
3956286 ATTT ATTT ATTT ATTT ATTTT ATTT TTTT ATTT A
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT A
3956320 AGGCTTGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:3956309 original size:17 final size:17
Alignment explanation
Indices: 3956287--3956319 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3956277 TTTACGGAAA
3956287 TTTATTTATTTATTTAT
1 TTTATTTATTTATTTAT
*
3956304 TTTATTTTTTTATTTA
1 TTTATTTATTTATTTA
3956320 AGGCTTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTATTTAT
Found at i:3957646 original size:224 final size:223
Alignment explanation
Indices: 3957244--3957690 Score: 732
Period size: 224 Copynumber: 2.0 Consensus size: 223
3957234 TTAATTAAAA
* *
3957244 AGAAATGAGAGATAGAAAAGAATAATTCAAAAATGAATTGGATTTTAAAATAAACTCATATTAAT
1 AGAAATAAGAGATAAAAAAGAATAATTCAAAAATGAATTGGATTTTAAAATAAACTCATATTAAT
*
3957309 CTTTATTTATAGAGAATGAATCATAAAATTATGACTCTTTGATTGTATTATTTCAATCAAAAATA
66 CTTTATTTATAGAGAATGAATCATAAAATTATGACTCTTTGATTGTATTATTTCAATAAAAAATA
*
3957374 ATTTTCTTTTAGTTACAAATATATCCCTTTAAAAGACTACAGATATATTTGTTCATTTGAATAAT
131 ATTTTCTTTTAGTTACAAATATATCCCTTTAAAAGACTACAAATATATTTGTTCATTTGAATAAT
*
3957439 TAAATTTTTCATACAAAAAGAAACAATTT
196 TAAA-CTTTCATACAAAAAGAAACAATTT
*
3957468 AGAAATAAGAGATAAAAAAGAATAATTCAAAAATGAATTGGATTTTAAAATGAACTCATATTAAT
1 AGAAATAAGAGATAAAAAAGAATAATTCAAAAATGAATTGGATTTTAAAATAAACTCATATTAAT
* *
3957533 CTTTATTTATAGAGATTGAATCATAAAATTGTGACTCTTTGATTGTATTATTTCAATAAAAAATA
66 CTTTATTTATAGAGAATGAATCATAAAATTATGACTCTTTGATTGTATTATTTCAATAAAAAATA
* * ** * *
3957598 ATTTTTTTTTAGTTATAAATATATCTTTTTGAAAGACTACAAATATATTTGTTCATTTGCATAAT
131 ATTTTCTTTTAGTTACAAATATATCCCTTTAAAAGACTACAAATATATTTGTTCATTTGAATAAT
* * *
3957663 TAAACTTTCATATAAAAATAAATAATTT
196 TAAACTTTCATACAAAAAGAAACAATTT
3957691 TTCACGTTTT
Statistics
Matches: 206, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
223 20 0.10
224 186 0.90
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (223 bp):
AGAAATAAGAGATAAAAAAGAATAATTCAAAAATGAATTGGATTTTAAAATAAACTCATATTAAT
CTTTATTTATAGAGAATGAATCATAAAATTATGACTCTTTGATTGTATTATTTCAATAAAAAATA
ATTTTCTTTTAGTTACAAATATATCCCTTTAAAAGACTACAAATATATTTGTTCATTTGAATAAT
TAAACTTTCATACAAAAAGAAACAATTT
Found at i:3958202 original size:34 final size:34
Alignment explanation
Indices: 3958164--3958229 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
3958154 GTCCGGAAGC
3958164 TTTT-AAGAACTTTTGGAAATGGATTTTCAAAATT
1 TTTTAAAG-ACTTTTGGAAATGGATTTTCAAAATT
* * **
3958198 TTTTAAAGGCTTTTGGACATTTATTTTCAAAA
1 TTTTAAAGACTTTTGGAAATGGATTTTCAAAA
3958230 ATCTTTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (34 bp):
TTTTAAAGACTTTTGGAAATGGATTTTCAAAATT
Found at i:3958257 original size:34 final size:34
Alignment explanation
Indices: 3958186--3958257 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
3958176 TTGGAAATGG
* * * **
3958186 ATTTTCAAAATTTTTTAAAGGCTTTTGGACATTT
1 ATTTTCAAAAATCTTTAAAGGCTTTTGGAAACCT
**
3958220 ATTTTCAAAAATCTTTAACTGCTTTTGGAAACCT
1 ATTTTCAAAAATCTTTAAAGGCTTTTGGAAACCT
3958254 ATTT
1 ATTT
3958258 CTAGTAGGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
ATTTTCAAAAATCTTTAAAGGCTTTTGGAAACCT
Found at i:3959106 original size:3 final size:3
Alignment explanation
Indices: 3959098--3959133 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3959088 TGTAACAAAA
3959098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3959134 CAAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3959487 original size:3 final size:3
Alignment explanation
Indices: 3959479--3959515 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3959469 TTAGTCGGAC
3959479 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3959516 GAGGAAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3961248 original size:30 final size:30
Alignment explanation
Indices: 3961195--3961268 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
3961185 ATTGAAACTT
* *
3961195 TTTTTTTTTAATTACATTCATTAAACAAAA
1 TTTTTGTTTAATTACATTAATTAAACAAAA
3961225 TTTTTGTTTACATT-CATTAATTAAACAAAA
1 TTTTTGTTTA-ATTACATTAATTAAACAAAA
*
3961255 CTTTTGTTTTAATT
1 TTTTTG-TTTAATT
3961269 GATCAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 32 0.82
31 7 0.18
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTTGTTTAATTACATTAATTAAACAAAA
Found at i:3965182 original size:18 final size:17
Alignment explanation
Indices: 3965156--3965195 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3965146 TTTAGTGGTC
*
3965156 TTTTATTACTCTTTTTAT
1 TTTTATTACTATTTTT-T
*
3965174 TTTTTTTACTATTTTTT
1 TTTTATTACTATTTTTT
3965191 TTTTA
1 TTTTA
3965196 GCTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTACTATTTTTT
Found at i:3965192 original size:14 final size:15
Alignment explanation
Indices: 3965173--3965201 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3965163 ACTCTTTTTA
3965173 TTTTTTTTA-CTATT
1 TTTTTTTTAGCTATT
3965187 TTTTTTTTAGCTATT
1 TTTTTTTTAGCTATT
3965202 GATTAGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTTAGCTATT
Found at i:3967169 original size:14 final size:13
Alignment explanation
Indices: 3967152--3967191 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
3967142 AAAATTAATA
3967152 AAAAATAACAACAT
1 AAAAATAA-AACAT
*
3967166 AAAAATAAATCAT
1 AAAAATAAAACAT
3967179 AAAAATTAAAACA
1 AAAAA-TAAAACA
3967192 AGTACATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAACAT
Found at i:3967179 original size:13 final size:14
Alignment explanation
Indices: 3967152--3967184 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3967142 AAAATTAATA
3967152 AAAAATAACAACAT
1 AAAAATAACAACAT
*
3967166 AAAAATAA-ATCAT
1 AAAAATAACAACAT
3967179 AAAAAT
1 AAAAAT
3967185 TAAAACAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAACAACAT
Found at i:3967626 original size:31 final size:31
Alignment explanation
Indices: 3967590--3967664 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
3967580 TTAAAACTCT
* *
3967590 TTTTGTTTTAATTACATTCATTAAA-CAAAAC
1 TTTTGTTTTAATT-CATTAATTAAATAAAAAC
3967621 TTTTG-TTTACATTCATTAATTAAATAAAAAC
1 TTTTGTTTTA-ATTCATTAATTAAATAAAAAC
3967652 TTTTGTTTTAATT
1 TTTTGTTTTAATT
3967665 GATCAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 14 0.36
31 21 0.54
32 4 0.10
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (31 bp):
TTTTGTTTTAATTCATTAATTAAATAAAAAC
Found at i:3969231 original size:2 final size:2
Alignment explanation
Indices: 3969224--3969252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3969214 TAAATAAGCA
3969224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3969253 AATTAACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3970725 original size:1 final size:1
Alignment explanation
Indices: 3970684--3970713 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
3970674 GATCCACGTT
*
3970684 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3970714 CTCTTCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:3976354 original size:95 final size:95
Alignment explanation
Indices: 3976191--3976372 Score: 265
Period size: 95 Copynumber: 1.9 Consensus size: 95
3976181 TATGTTAGAA
* * * ** * * *
3976191 ATAAGGCGCATCTAGAAAGATCAACTGCTGAGGCATTTGTTGTGCAAGAATGCATGTATTTTTGT
1 ATAAGGCACATCTAGAAAGATCAACTGCTAAAGCATTTGTCATACAAGAATGCAAGCATTTTTGT
3976256 TCAAGATATTTACATGAAACTGTTACTAAG
66 TCAAGATATTTACATGAAACTGTTACTAAG
* * *
3976286 ATAAGGCATATCTAGAAAGATTAATTGCTAAAGCATTTGTCATACAAGAATGCAAGCATTTTTGT
1 ATAAGGCACATCTAGAAAGATCAACTGCTAAAGCATTTGTCATACAAGAATGCAAGCATTTTTGT
3976351 TCAAGATATTTACATGAAACTG
66 TCAAGATATTTACATGAAACTG
3976373 ATATGAAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
95 76 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (95 bp):
ATAAGGCACATCTAGAAAGATCAACTGCTAAAGCATTTGTCATACAAGAATGCAAGCATTTTTGT
TCAAGATATTTACATGAAACTGTTACTAAG
Found at i:3982650 original size:33 final size:33
Alignment explanation
Indices: 3982613--3982715 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
3982603 AATTATTTTA
3982613 TGAAATTTATTTAGGTTTTGGTTTTATGTTTGT
1 TGAAATTTATTTAGGTTTTGGTTTTATGTTTGT
3982646 TGAAA-TT-TTT--G--TTGG-TTTATGTTTGT
1 TGAAATTTATTTAGGTTTTGGTTTTATGTTTGT
* * * *
3982672 TGAAATTTGTTTAGGTTTTGGTTATATATTAGT
1 TGAAATTTATTTAGGTTTTGGTTTTATGTTTGT
*
3982705 TAAAATTTATT
1 TGAAATTTATT
3982716 GGTGATATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
26 16 0.28
27 6 0.10
28 3 0.05
29 1 0.02
30 1 0.02
31 3 0.05
32 6 0.10
33 22 0.38
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58
Consensus pattern (33 bp):
TGAAATTTATTTAGGTTTTGGTTTTATGTTTGT
Found at i:3982688 original size:26 final size:26
Alignment explanation
Indices: 3982635--3982689 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
3982625 AGGTTTTGGT
*
3982635 TTTATGTTTGTTGAAATTTTTGTTGG
1 TTTATGTTTGTTGAAATTTTTGTAGG
3982661 TTTATGTTTGTTGAAATTTGTT-TAGG
1 TTTATGTTTGTTGAAATTT-TTGTAGG
3982687 TTT
1 TTT
3982690 TGGTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (26 bp):
TTTATGTTTGTTGAAATTTTTGTAGG
Found at i:3984020 original size:16 final size:16
Alignment explanation
Indices: 3983992--3984025 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3983982 TATGGTCAAT
3983992 CAATAAAAGGGTTTAA
1 CAATAAAAGGGTTTAA
3984008 CAATACAAA-GGTTTAA
1 CAATA-AAAGGGTTTAA
3984024 CA
1 CA
3984026 CTTTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
CAATAAAAGGGTTTAA
Found at i:3987716 original size:15 final size:16
Alignment explanation
Indices: 3987696--3987727 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3987686 CAAGCTGAAG
3987696 AAGAAGAAGAAA-AAA
1 AAGAAGAAGAAATAAA
3987711 AAGAAGAAGAAATAAA
1 AAGAAGAAGAAATAAA
3987727 A
1 A
3987728 TGATGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAGAAGAAGAAATAAA
Found at i:3987733 original size:3 final size:3
Alignment explanation
Indices: 3987727--3987768 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
3987717 AAGAAATAAA
* *
3987727 ATG ATG ATG ATG ATG ACG ATG ATG ATA ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3987769 GTGAAACACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:3988285 original size:21 final size:21
Alignment explanation
Indices: 3988240--3988285 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3988230 TTTCTTTAAG
*
3988240 ATTTTATCTGATCTATATGAG
1 ATTTTATCTGATCTATATGAA
3988261 ATTTTATCTGATCTAT-TAGAA
1 ATTTTATCTGATCTATAT-GAA
3988282 ATTT
1 ATTT
3988286 GTATATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (21 bp):
ATTTTATCTGATCTATATGAA
Found at i:4001694 original size:66 final size:66
Alignment explanation
Indices: 4001588--4001719 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
4001578 AAAGATTATA
*
4001588 ATATATACAATTAAATAATATCTATCTAAATCAAATATTTGATTTGTTAAAATCTTTTATATTAC
1 ATATATACAATTAAATAATATCTATCTAAATCAAATATTTGATTTGTTAAAATCTTTCATATTAC
4001653 T
66 T
* * * * *
4001654 ATATATACAATTAAATGATGTCT-CCTTAAATCAAATATTTGATTTGTTAGAATCTTTCCTATTA
1 ATATATACAATTAAATAATATCTATC-TAAATCAAATATTTGATTTGTTAAAATCTTTCATATTA
4001718 CT
65 CT
4001720 TTTAAACTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 58 0.98
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (66 bp):
ATATATACAATTAAATAATATCTATCTAAATCAAATATTTGATTTGTTAAAATCTTTCATATTAC
T
Found at i:4005469 original size:4 final size:4
Alignment explanation
Indices: 4005460--4005563 Score: 52
Period size: 4 Copynumber: 25.2 Consensus size: 4
4005450 TATGTATATC
* * * *
4005460 TTTA TTTA TTTA TTTA TTTA TTT- TTTG TTAATA TCTA TATA TATA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA -TTTA
** * * *
4005510 TTTA CCTA GTTA TATA TTTA -TTA TTATAA TTTA TTTA -TTA TTATT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-T-A TTTA TTTA TTTA TT-TA TTTA
4005559 TTTA T
1 TTTA T
4005564 CTTGTAGTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
3 9 0.12
4 56 0.72
5 8 0.10
6 5 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4005546 original size:17 final size:16
Alignment explanation
Indices: 4005412--4005563 Score: 68
Period size: 17 Copynumber: 9.3 Consensus size: 16
4005402 TTTTTTGTAT
4005412 TTTATGTATT-TA-TTA
1 TTTAT-TATTATATTTA
* *
4005427 TTTATTATTACCATGTA
1 TTTATTATTA-TATTTA
*
4005444 TTAATATATGTATATCTTTA
1 TTTAT-TAT-TATA--TTTA
4005464 TTTATTTATT-TATTTA
1 TTTA-TTATTATATTTA
* * *
4005480 TTTTTTGTTAATATCTA
1 TTTATTATT-ATATTTA
*
4005497 TATA-TA-TAT-TTTA
1 TTTATTATTATATTTA
*
4005510 TTTACCTAGTTATA--TA
1 TTTA-TTA-TTATATTTA
4005526 TTTATTATTATAATTTA
1 TTTATTATTAT-ATTTA
*
4005543 TTTATTATTATTTTTA
1 TTTATTATTATATTTA
4005559 TTTAT
1 TTTAT
4005564 CTTGTAGTAT
Statistics
Matches: 103, Mismatches: 16, Indels: 35
0.67 0.10 0.23
Matches are distributed among these distances:
13 6 0.06
14 10 0.10
15 15 0.15
16 24 0.23
17 29 0.28
18 6 0.06
19 3 0.03
20 9 0.09
21 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATTATTATATTTA
Found at i:4005547 original size:14 final size:13
Alignment explanation
Indices: 4005519--4005560 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
4005509 ATTTACCTAG
4005519 TTATATATTTATTA
1 TTATA-ATTTATTA
4005533 TTATAATTTATTTA
1 TTATAATTTA-TTA
*
4005547 TTATTATTT-TTA
1 TTATAATTTATTA
4005559 TT
1 TT
4005561 TATCTTGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 16 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATAATTTATTA
Found at i:4005605 original size:21 final size:21
Alignment explanation
Indices: 4005527--4005607 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
4005517 AGTTATATAT
*
4005527 TTATTA-TTATAATTTAT-TTA
1 TTATTATTTTTAA-TTATCTTA
*
4005547 TTATTATTTTTATTTATCTT-
1 TTATTATTTTTAATTATCTTA
* * *
4005567 GTAGTATTTGTTATTTATCTTA
1 TTATTATTT-TTAATTATCTTA
4005589 TTATTATTTTTAATTATCT
1 TTATTATTTTTAATTATCT
4005608 ATTTTTCTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.34
21 26 0.52
22 7 0.14
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTATTTTTAATTATCTTA
Found at i:4005654 original size:21 final size:21
Alignment explanation
Indices: 4005621--4005672 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
4005611 TTTCTTTTTT
*
4005621 TTTCTTTTTTCGTTTATCTGA
1 TTTCTTTTTTCGTTTATCAGA
4005642 TTT-TTTTTCTCGTTTATCAGA
1 TTTCTTTTT-TCGTTTATCAGA
4005663 TTTCTTTTTT
1 TTTCTTTTTT
4005673 TTTCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.18
21 18 0.64
22 5 0.18
ACGTcount: A:0.10, C:0.13, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTCTTTTTTCGTTTATCAGA
Found at i:4006557 original size:4 final size:4
Alignment explanation
Indices: 4006515--4006541 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4006505 TTTTTTCTAA
4006515 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
4006542 AGATTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:4006590 original size:7 final size:6
Alignment explanation
Indices: 4006564--4006627 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
4006554 TTTAATATTC
* * * *
4006564 TTTTAT CTTTA- TTTTAT TTTTAC TTTT-G TTTTAC TTTTA- -TTT-T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
4006607 TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTT
4006628 GTTTTATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 11 0.23
6 34 0.71
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:4006614 original size:37 final size:39
Alignment explanation
Indices: 4006554--4006650 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 39
4006544 ATTAGGTTTA
* *
4006554 TTTAATATTCT-TTTATCTTTA-TTTTATTTTTACTTTTGT
1 TTTACTATTCTATTT-TTTTTATTTTTATTTTTA-TTTTGT
4006593 TTTACT-TT-TATTTTTTTTATTTTTATTTTTATTTTGT
1 TTTACTATTCTATTTTTTTTATTTTTATTTTTATTTTGT
*
4006630 TTTATTATTCTATTTTTTTTA
1 TTTACTATTCTATTTTTTTTA
4006651 AATAAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 17 0.33
38 18 0.35
39 16 0.31
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (39 bp):
TTTACTATTCTATTTTTTTTATTTTTATTTTTATTTTGT
Found at i:4006632 original size:11 final size:11
Alignment explanation
Indices: 4006564--4006649 Score: 65
Period size: 11 Copynumber: 7.8 Consensus size: 11
4006554 TTTAATATTC
*
4006564 TTTTATCTTTA
1 TTTTATTTTTA
4006575 TTTTATTTTTA
1 TTTTATTTTTA
*
4006586 CTTTT-GTTTTA
1 -TTTTATTTTTA
4006597 CTTTTA-TTTT-
1 -TTTTATTTTTA
4006607 TTTTATTTTTA
1 TTTTATTTTTA
*
4006618 TTTT-TATTTTG
1 TTTTAT-TTTTA
4006629 TTTTATTATTCTA
1 TTTTATT-TT-TA
4006642 TTTT-TTTT
1 TTTTATTTT
4006650 AAATAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
9 5 0.08
10 5 0.08
11 39 0.62
12 9 0.14
13 5 0.08
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:4006648 original size:16 final size:15
Alignment explanation
Indices: 4006564--4006635 Score: 74
Period size: 17 Copynumber: 4.5 Consensus size: 15
4006554 TTTAATATTC
4006564 TTTTATCTTTATTTTAT
1 TTTTAT-TTT-TTTTAT
*
4006581 TTTTACTTTTGTTTTAC
1 TTTTA-TTTT-TTTTAT
4006598 TTTTATTTTTTTTAT
1 TTTTATTTTTTTTAT
4006613 TTTTATTTTTATTT-T
1 TTTTATTTTT-TTTAT
4006628 GTTTTATT
1 -TTTTATT
4006636 ATTCTATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 16 0.33
16 14 0.29
17 18 0.37
18 1 0.02
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTTTAT
Found at i:4006648 original size:32 final size:36
Alignment explanation
Indices: 4006575--4006650 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 36
4006565 TTTATCTTTA
* *
4006575 TTTTATTTTTACTTTTGTTTTACTTTTATTTTTTTTAT
1 TTTTATTTTTACTTTTGTTTTA--TTTATTTCTATTAT
*
4006613 TTTTATTTTTA-TTTTGTTTTA-TTA-TTCTATTTT
1 TTTTATTTTTACTTTTGTTTTATTTATTTCTATTAT
4006646 TTTTA
1 TTTTA
4006651 AATAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 11 0.31
34 3 0.09
37 10 0.29
38 11 0.31
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.79
Consensus pattern (36 bp):
TTTTATTTTTACTTTTGTTTTATTTATTTCTATTAT
Found at i:4006816 original size:60 final size:57
Alignment explanation
Indices: 4006661--4007055 Score: 459
Period size: 58 Copynumber: 6.7 Consensus size: 57
4006651 AATAAAAATA
* *
4006661 AAAAAATATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAA-ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* * * *
4006720 AAAAAAGGGT-TTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAA--ATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTC
* * * *
4006779 AAAAAAAACATTTTTTGGGAAAAGTCGAAAGTGTCAATTTTTCTTAAAAATAAAATTTC
1 -AAAAAAATA-TTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* * * * *
4006838 ATAAAAATATTCTTGAGGAAAAGTGGAAAGTGTCAATTTTTCTTAAAAATAAAATTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* * * *
4006896 ATAAAAATATTCTTGAGGAAAAGTGGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
* *
4006954 AAAAAATTCAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAGTTTCC
1 AAAAAAAT--ATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAA-TTT-C
4007016 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTT
4007056 TCCTGCACAA
Statistics
Matches: 297, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
57 5 0.02
58 141 0.47
59 27 0.09
60 113 0.38
61 3 0.01
62 8 0.03
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (57 bp):
AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
Found at i:4006978 original size:176 final size:177
Alignment explanation
Indices: 4006661--4007057 Score: 523
Period size: 176 Copynumber: 2.2 Consensus size: 177
4006651 AATAAAAATA
* * *
4006661 AAAAAATATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
1 AAAAAA-ATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAA
* * * * * *
4006726 GGGTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAACATT
64 GGATTCTTGAGGAAAAGTGGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAAACAAT
* *
4006791 TTTTGGGAAAAGTCGAAAGTGTCAATTTTTCTTAAAAATAAAA-TTT-C
129 TTTTGGGAAAAGTCGAAAGTATCAATTTTCCTTAAAAATAAAAGTTTCC
* * * *
4006838 ATAAAAATATTCTTGAGGAAAAGTGGAAAGTGTCAATTTTTCTTAAAAATAAAATTTCATAAAAA
1 AAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCA-AAAAA
* * **
4006903 -TATTCTTGAGGAAAAGTGGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTCAAAAAATTCAAT
64 GGATTCTTGAGGAAAAGTGGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAAACAAT
* *
4006966 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAGTTTCC
129 TTTTG-GGAAAAGTCGAAAGTATCAATTTTCCTTAAAAATAAAAGTTTCC
4007016 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTC
1 AAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTC
4007058 CTGCACAAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
175 22 0.12
176 116 0.61
177 15 0.08
178 36 0.19
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (177 bp):
AAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGG
ATTCTTGAGGAAAAGTGGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAAACAATTT
TTGGGAAAAGTCGAAAGTATCAATTTTCCTTAAAAATAAAAGTTTCC
Found at i:4017639 original size:177 final size:174
Alignment explanation
Indices: 4017343--4017697 Score: 471
Period size: 177 Copynumber: 2.0 Consensus size: 174
4017333 CACTGGCAGT
* * *
4017343 AGTGAATGGTCTCACGCTCGACTTCGTGGACTTTTTAGTTGACCGAACGATTACCTTGCAAACGC
1 AGTGAATGGTCTCACGCTCGACTCCGTGGACTTTTTAGTTGACCGAACGATAACCTTACAAACGC
* ** * * * *
4017408 GTTTCCTGAATTTCAACGCAATAACCGCTACTTTTACTTCCCGGCAGCTCTTGTAAAGGTGTTTT
66 GTTTCCTGAACTTCAACAAAAGAACCCCTAC--TTACCTCCCGGCAGCTCTTGTAAAGGTGTTTG
*
4017473 TCTTTTATGAATGTTTCGTGGAAAGACCCTCTTTGGCCTTTGCCAGG
129 TCTTTTATGAATGTTTCGTGGAAAGACCCTC-TCGGCCTTTGCCAGG
* * * *
4017520 AGTGAATGGTCTGACGCTCGACTCCGTTGACTTTTTTTAGTTGATCGAACGATAATCTTAC-AAC
1 AGTGAATGGTCTCACGCTCGACTCCGTGGAC--TTTTTAGTTGACCGAACGATAACCTTACAAAC
* * *
4017584 TGCGTTTGCTTAACTTCAACAAAAGAACCCCTAC-TACCTCGCCGTCAGCTCTTGTAAAGGTGTT
64 -GCGTTTCCTGAACTTCAACAAAAGAACCCCTACTTACCTC-CCGGCAGCTCTTGTAAAGGTGTT
4017648 TGTCTTTTATGAATGTTTCGTGGAAAGACCCTCTCGGCCTTTGCCAGG
127 TGTCTTTTATGAATGTTTCGTGGAAAGACCCTCTCGGCCTTTGCCAGG
4017696 AG
1 AG
4017698 GTTCCAATAG
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
176 21 0.13
177 82 0.53
178 3 0.02
179 50 0.32
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (174 bp):
AGTGAATGGTCTCACGCTCGACTCCGTGGACTTTTTAGTTGACCGAACGATAACCTTACAAACGC
GTTTCCTGAACTTCAACAAAAGAACCCCTACTTACCTCCCGGCAGCTCTTGTAAAGGTGTTTGTC
TTTTATGAATGTTTCGTGGAAAGACCCTCTCGGCCTTTGCCAGG
Found at i:4018789 original size:2 final size:2
Alignment explanation
Indices: 4018782--4018822 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4018772 GATAAAAGCG
4018782 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4018823 TGTTTTGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4025319 original size:20 final size:20
Alignment explanation
Indices: 4025294--4025331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4025284 GAATGCAACA
* *
4025294 AATTAAATAATGCAAATGCC
1 AATTAAAAAATACAAATGCC
4025314 AATTAAAAAATACAAATG
1 AATTAAAAAATACAAATG
4025332 AATACAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
AATTAAAAAATACAAATGCC
Found at i:4025334 original size:47 final size:47
Alignment explanation
Indices: 4025273--4025368 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
4025263 ATAAAATAAT
* * *
4025273 AAAATGCATATGAATGCAACAAATTAAATAATGCAAATGCCAATTAA
1 AAAATACAAATGAATACAACAAATTAAATAATGCAAATGCCAATTAA
* * *
4025320 AAAATACAAATGAATACAATAAATTAAATAATGTAAATGGCAATTAA
1 AAAATACAAATGAATACAACAAATTAAATAATGCAAATGCCAATTAA
4025367 AA
1 AA
4025369 TGCACATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (47 bp):
AAAATACAAATGAATACAACAAATTAAATAATGCAAATGCCAATTAA
Found at i:4029800 original size:54 final size:52
Alignment explanation
Indices: 4029737--4029943 Score: 170
Period size: 54 Copynumber: 3.8 Consensus size: 52
4029727 CATTTTAAAG
* *
4029737 TTTTCTTTTTTATATTTTTAAGAATAAATTTATACTTTCAACTTTTCCTC-AAA
1 TTTT-TTTTTTTTATTTTTAAGAA-AAATTGATACTTTCAACTTTTCCTCAAAA
* * * * * *
4029790 -GTTTTTTTTTT-TTTTCAAGAAAAATTGAAACTTTTAATTTTTCCTTAAAA
1 TTTTTTTTTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA
* * *
4029840 TTTTTTTTTACTTTACTTTTAAGAAAAATTGGTA-TTTCCAACTTTTCTTCAAAA
1 TTTTTTTTT--TTTATTTTTAAGAAAAATTGATACTTT-CAACTTTTCCTCAAAA
* *
4029894 TATTTTTTTGGAAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTT
1 T-TTTTTTT-----TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTT
4029944 TCACAAAAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
49 20 0.17
50 12 0.10
51 14 0.12
52 2 0.02
53 6 0.05
54 28 0.23
55 7 0.06
58 27 0.22
59 3 0.03
60 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.53
Consensus pattern (52 bp):
TTTTTTTTTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA
Found at i:4029815 original size:49 final size:49
Alignment explanation
Indices: 4029742--4029848 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 49
4029732 TAAAGTTTTC
* * * * *
4029742 TTTTTTATATTTTTAAGAATAAATTTATACTTTCAACTTTTCCTCAAAG
1 TTTTTTTTTTTTTTAAGAATAAATTGAAACTTTCAACTTTTCCTCAAAA
* * *
4029791 TTTTTTTTTTTTTTCAAGAA-AAATTGAAACTTTTAATTTTTCCTTAAAA
1 TTTTTTTTTTTTTT-AAGAATAAATTGAAACTTTCAACTTTTCCTCAAAA
4029840 TTTTTTTTT
1 TTTTTTTTT
4029849 ACTTTACTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 44 0.90
50 5 0.10
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (49 bp):
TTTTTTTTTTTTTTAAGAATAAATTGAAACTTTCAACTTTTCCTCAAAA
Found at i:4029845 original size:50 final size:53
Alignment explanation
Indices: 4029731--4029943 Score: 129
Period size: 58 Copynumber: 4.0 Consensus size: 53
4029721 TTAAAGCATT
* * * *
4029731 TTAAAGTTTTCTTTTTTATATTTTTAAGAATAAATTTATACTTTCAACTTTTCC
1 TTAAAATTTT-TTTTTTATATTTTCAAGAATAAATTGAAACTTTCAACTTTTCC
* * * *
4029785 -TCAAAGTTTTTTTTT-T-TTTTCAAGAA-AAATTGAAACTTTTAATTTTTCC
1 TTAAAATTTTTTTTTTATATTTTCAAGAATAAATTGAAACTTTCAACTTTTCC
* **
4029834 TTAAAATTTTTTTTTACTTTACTTTT-AAGAA-AAATTGGTA-TTTCCAACTTTT-C
1 TTAAAATTTTTTTTT--TATA-TTTTCAAGAATAAATTGAAACTTT-CAACTTTTCC
* * *
4029887 TTCAAAATATTTTTTTGGAAATTTTATTTTCAAGAA-AAATTGATACTTTCAAATTTT
1 TT-AAAAT-TTTTTTT-----TTATATTTTCAAGAATAAATTGAAACTTTCAACTTTT
4029944 TCACAAAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 28
0.74 0.09 0.16
Matches are distributed among these distances:
49 19 0.15
50 21 0.17
51 1 0.01
52 7 0.06
53 13 0.10
54 23 0.18
55 11 0.09
57 4 0.03
58 24 0.19
59 3 0.02
60 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.53
Consensus pattern (53 bp):
TTAAAATTTTTTTTTTATATTTTCAAGAATAAATTGAAACTTTCAACTTTTCC
Found at i:4029966 original size:58 final size:55
Alignment explanation
Indices: 4029796--4029967 Score: 138
Period size: 58 Copynumber: 3.0 Consensus size: 55
4029786 CAAAGTTTTT
* * * **
4029796 TTTTTTTTTCAAGAAAAATTGAAACTTT-TAATTTTTCCTTAAAAT-TTTTTT-TTA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCC--AAAATATTTTTTGAAA
* * * *
4029850 CTTTACTTTT-AAGAAAAATTGGTA-TTTCCAACTTTTCTTCAAAATATTTTTTTGGAAA
1 TTTTA-TTTTCAAGAAAAATTGATACTTT-CAAATTTT-TCCAAAATA-TTTTTT-GAAA
4029908 TTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATATTTTTTAGAAA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTC-C-AAAATATTTTTT-GAAA
4029966 TT
1 TT
4029968 GAAAATATTT
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
53 3 0.03
54 20 0.22
55 9 0.10
56 8 0.09
57 5 0.05
58 38 0.41
59 9 0.10
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (55 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCCAAAATATTTTTTGAAA
Found at i:4030029 original size:78 final size:81
Alignment explanation
Indices: 4029890--4030047 Score: 234
Period size: 79 Copynumber: 2.0 Consensus size: 81
4029880 ACTTTTCTTC
*
4029890 AAAATATTTTTTTGGAAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCAC-AAAA-A
1 AAAATATTTTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATA
4029953 TATTTTTTAGAAATTG
66 TATTTTTTAGAAATTG
* * **
4029969 AAAATATTTTTTTATAAATTTTATTTT-AATG-AAAATTGATACTTTCAACTTTTTTTCAAAAAT
1 AAAATATTTTTTTAGAAATTTTATTTTCAA-GAAAAATTGATACTTTCAAATTTTTCACAAAAAT
4030032 ATATTTTTTAGAAATT
65 ATATTTTTTAGAAATT
4030048 TTTATTTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
78 25 0.35
79 30 0.42
80 16 0.23
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (81 bp):
AAAATATTTTTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATA
TATTTTTTAGAAATTG
Found at i:4030066 original size:78 final size:77
Alignment explanation
Indices: 4029905--4030066 Score: 179
Period size: 78 Copynumber: 2.1 Consensus size: 77
4029895 ATTTTTTTGG
4029905 AAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATATTTTTTAGAAATTGA
1 AAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATATTTTTTAGAAATT--
** *
4029970 AAATATTTTTTTAT
64 AAATATTTTTAGAA
*
4029984 AAATTTTATTTT-AATG-AAAATTGATACTTTCAACTTTTTTTCA-AAAATATATTTTTTAGAAA
1 AAATTTTATTTTCAA-GAAAAATTGATACTTTCAA--ATTTTTCACAAAA-ATATTTTTTAGAAA
**
4030046 TT-TTTATTTTTAAGAA
62 TTAAATATTTTT-AGAA
4030062 AAATT
1 AAATT
4030067 GATACTTTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
77 7 0.10
78 25 0.35
79 17 0.24
80 23 0.32
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (77 bp):
AAATTTTATTTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATATTTTTTAGAAATTAA
ATATTTTTAGAA
Found at i:4030066 original size:139 final size:137
Alignment explanation
Indices: 4029851--4030179 Score: 407
Period size: 139 Copynumber: 2.4 Consensus size: 137
4029841 TTTTTTTTAC
* *
4029851 TTTACTTTTAAGAAAAATTGGTA-TTTCCAACTTTTCTTC-AAAATATTTTTTTGGAAATTTTAT
1 TTTACTTTTAAG-AAAATTGATACTTT-CAACTTTTCTTCAAAAATATTTTTTTAGAAATTTTAT
*
4029914 TTTCAAGAAAAATTGATACTTTCAAATTTTTCACAAAAATA-TTTTTTAGAAATTGAAAATATTT
64 TTTCAAGAAAAATTGATACTTTCAAATTTTCCACAAAAATATTTTTTTAGAAATT-AAAAT-TTT
*
4029978 TTTTATAAA-T
127 TTTTAGAAATT
*
4029988 TTTA-TTTTAATGAAAATTGATACTTTCAACTTTTTTTCAAAAATATATTTTTTAGAAATTTTTA
1 TTTACTTTTAA-GAAAATTGATACTTTCAACTTTTCTTCAAAAATAT-TTTTTTAGAAA-TTTTA
* * ** * ***
4030052 TTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAGATATTTTTATTTTT
63 TTTTCAAGAAAAATTGATACTTTCAAATTTTCCACAAAAATATTTTTTTAGAAATTAAAATTTTT
4030117 TTTAGAAATT
128 TTTAGAAATT
* * *
4030127 TTTATTTTTAAGGAAGATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 TTTACTTTTAA-GAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTT
4030180 TTTTGAAAAT
Statistics
Matches: 167, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
136 26 0.16
137 15 0.09
138 21 0.13
139 55 0.33
140 50 0.30
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (137 bp):
TTTACTTTTAAGAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTTAGAAATTTTATTT
TCAAGAAAAATTGATACTTTCAAATTTTCCACAAAAATATTTTTTTAGAAATTAAAATTTTTTTT
AGAAATT
Found at i:4030070 original size:61 final size:60
Alignment explanation
Indices: 4029969--4030116 Score: 214
Period size: 61 Copynumber: 2.5 Consensus size: 60
4029959 TTAGAAATTG
* *
4029969 AAAATATTTTTTTATAAA-TTTTA-TTTTAATGAAAATTGATACTTTCAACTTTT-TTTCA
1 AAAATATTTTTTTAGAAATTTTTATTTTTAATGAAAATTGATACTTTCAACTTTTCCTT-A
4030027 AAAATATATTTTTTAGAAATTTTTATTTTTAA-GAAAAATTGATACTTTCAACTTTTCCTTA
1 AAAATAT-TTTTTTAGAAATTTTTATTTTTAATG-AAAATTGATACTTTCAACTTTTCCTTA
*
4030088 AAAATATTTTTTTAGATATTTTTATTTTT
1 AAAATATTTTTTTAGAAATTTTTATTTTT
4030117 TTTAGAAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
58 7 0.09
59 10 0.12
60 27 0.33
61 36 0.44
62 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (60 bp):
AAAATATTTTTTTAGAAATTTTTATTTTTAATGAAAATTGATACTTTCAACTTTTCCTTA
Found at i:4030118 original size:19 final size:19
Alignment explanation
Indices: 4030094--4030135 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4030084 CTTAAAAATA
*
4030094 TTTTTTTAGATATTTTTAT
1 TTTTTTTAGAAATTTTTAT
4030113 TTTTTTTAGAAATTTTTAT
1 TTTTTTTAGAAATTTTTAT
4030132 TTTT
1 TTTT
4030136 AAGGAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTTAGAAATTTTTAT
Found at i:4030284 original size:3 final size:3
Alignment explanation
Indices: 4030278--4030331 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
4030268 AGTAAAAAAA
* *
4030278 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAC AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
4030324 AAAT AAT A
1 -AAT AAT A
4030332 TTGACATGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.85
4 7 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4030603 original size:13 final size:13
Alignment explanation
Indices: 4030585--4030609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4030575 TTTCCCTTTC
4030585 TTTTTTTCTCTCA
1 TTTTTTTCTCTCA
4030598 TTTTTTTCTCTC
1 TTTTTTTCTCTC
4030610 CCCCTCTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTCTCTCA
Found at i:4034486 original size:4 final size:4
Alignment explanation
Indices: 4034477--4034507 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4034467 CAAATGATGC
*
4034477 TTTA TTTA TTCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4034508 GTTACTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4038279 original size:3 final size:3
Alignment explanation
Indices: 4038271--4038295 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4038261 TATACACTAT
4038271 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4038296 ATTTAGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4038395 original size:2 final size:2
Alignment explanation
Indices: 4038383--4038420 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
4038373 TCTTAACGAG
*
4038383 TA TA TA CTA TA TA TA TA TA TA TA TA GA 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
4038421 CGGAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4041579 original size:20 final size:20
Alignment explanation
Indices: 4041550--4041588 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4041540 AATTTTCATT
4041550 AATTGGTTGATCATAGGTAA
1 AATTGGTTGATCATAGGTAA
*
4041570 AATTGTTTGATCATAGGTA
1 AATTGGTTGATCATAGGTA
4041589 TTTAATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (20 bp):
AATTGGTTGATCATAGGTAA
Found at i:4043185 original size:9 final size:9
Alignment explanation
Indices: 4043171--4043196 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4043161 TCTGAAGAAA
4043171 GTATGTCTG
1 GTATGTCTG
4043180 GTATGTCTG
1 GTATGTCTG
4043189 GTATGTCT
1 GTATGTCT
4043197 ATGCCTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.46
Consensus pattern (9 bp):
GTATGTCTG
Found at i:4049553 original size:16 final size:16
Alignment explanation
Indices: 4049532--4049565 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4049522 AAATAAAAAA
*
4049532 TAAAATGATTCGAATT
1 TAAAATGATTCAAATT
4049548 TAAAATGATTCAAATT
1 TAAAATGATTCAAATT
4049564 TA
1 TA
4049566 TAAAAGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAAATGATTCAAATT
Found at i:4050619 original size:37 final size:37
Alignment explanation
Indices: 4050567--4050641 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
4050557 CAAAAGCTAA
4050567 AAGATAAACCATTAATCCAAAATCCTTTCTAAACCTT
1 AAGATAAACCATTAATCCAAAATCCTTTCTAAACCTT
* *
4050604 AAGATAAACCGTTAATCCAAAATCCTTTCTAGACCTT
1 AAGATAAACCATTAATCCAAAATCCTTTCTAAACCTT
4050641 A
1 A
4050642 CTTATAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (37 bp):
AAGATAAACCATTAATCCAAAATCCTTTCTAAACCTT
Found at i:4053820 original size:20 final size:20
Alignment explanation
Indices: 4053795--4053834 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4053785 AATTTAACTT
4053795 TCTTGCTTTAATTTTCAGTG
1 TCTTGCTTTAATTTTCAGTG
4053815 TCTTGCTTTAATTTTCAGTG
1 TCTTGCTTTAATTTTCAGTG
4053835 CACTTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (20 bp):
TCTTGCTTTAATTTTCAGTG
Found at i:4058034 original size:2 final size:2
Alignment explanation
Indices: 4058027--4058056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4058017 TAACCCTAGA
4058027 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
4058057 TAACAAAATC
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:4061737 original size:2 final size:2
Alignment explanation
Indices: 4061730--4061766 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4061720 TTTCCTAATC
4061730 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4061767 CCCCCCCCCA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4064919 original size:29 final size:29
Alignment explanation
Indices: 4064886--4064943 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4064876 CAAACAAAAA
*
4064886 TAAAACAAAATAACATTGTATCTAACTAT
1 TAAAACAAAATAACATTGTATCAAACTAT
4064915 TAAAACAAAATAACATTGTATCAAACTAT
1 TAAAACAAAATAACATTGTATCAAACTAT
4064944 ATCAATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.29
Consensus pattern (29 bp):
TAAAACAAAATAACATTGTATCAAACTAT
Found at i:4066532 original size:31 final size:31
Alignment explanation
Indices: 4066478--4066538 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
4066468 TTCATATTTA
*
4066478 CTATTCTATTTTTTATAAAATTTTA-TCATC
1 CTATTATATTTTTTATAAAATTTTAGTCATC
* *
4066508 CTATTATATTTTTTGATTATATTTTAGTCAT
1 CTATTATATTTTTT-ATAAAATTTTAGTCAT
4066539 AGATGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 9 0.35
32 4 0.15
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (31 bp):
CTATTATATTTTTTATAAAATTTTAGTCATC
Found at i:4066846 original size:19 final size:21
Alignment explanation
Indices: 4066818--4066862 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
4066808 ATTTTTTAAA
*
4066818 ATTTTAATTATTTTTATT-TT
1 ATTTTAATTATTTATATTATT
4066838 ATTTT-ATTATTTATATTATT
1 ATTTTAATTATTTATATTATT
4066858 ATTTT
1 ATTTT
4066863 TGTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTAATTATTTATATTATT
Found at i:4068587 original size:14 final size:14
Alignment explanation
Indices: 4068568--4068600 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4068558 AAAAATCATT
*
4068568 TCTTTATTTTTTTC
1 TCTTTATTTTATTC
4068582 TCTTTATTTTATTC
1 TCTTTATTTTATTC
4068596 T-TTTA
1 TCTTTA
4068601 CCCTTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TCTTTATTTTATTC
Found at i:4087494 original size:21 final size:21
Alignment explanation
Indices: 4087468--4087522 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
4087458 GCAGCAGCTA
*
4087468 ATTGTGTTCACATTATAGGTT
1 ATTGTGTTCACATTACAGGTT
* *
4087489 ATTGTGTTCACACTACAGTTT
1 ATTGTGTTCACATTACAGGTT
4087510 ATTGTGTTCACAT
1 ATTGTGTTCACAT
4087523 GCGAATCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (21 bp):
ATTGTGTTCACATTACAGGTT
Found at i:4088023 original size:234 final size:234
Alignment explanation
Indices: 4087587--4088031 Score: 698
Period size: 235 Copynumber: 1.9 Consensus size: 234
4087577 CAATCCCATC
* * * *
4087587 AATTCAGCAACCCAAGAAAAAGGCAGTATTTGAAATTTCTATGCTTGGAGAGATGTTCCAAGCCT
1 AATTCAGCAACCCAAGAAAAAAGCAATATTTGAAATTACCATGCTTGGAGAGATGTTCCAAGCCT
* *
4087652 ATTTATTTTTAGTTATTGCTGTATTAGGCAGAGTAGAGTTTATTTAACCTTAAGTAATCTTTTAG
66 ATTTATTTTCAGTTATTGCTGTATTAGGCAGAGTAGAGTTTATTTAACCTTAAGCAATCTTTTAG
*
4087717 ATTGTTCTCAAGTTCTGTATCTCTCTGGTGAATTTCTTAGAGTGAACTTCTATAGTTATGTATCT
131 ATTGTTCTCAAGTTCTGTATCTCTCAGGTGAATTTCTTAGAGTGAACTTCTATAGTTATGTATCT
*
4087782 TTGATTAGAGTTCTTAGGATGATGTTTTTGTATCCAATG
196 CTGATTAGAGTTCTTAGGATGATGTTTTTGTATCCAATG
* * *
4087821 AATTCAGCAACCTAAGAAAAAAGCAATTTTTGAAATTACCATGCTTGTAGAGATGTTCCAAGCCT
1 AATTCAGCAACCCAAGAAAAAAGCAATATTTGAAATTACCATGCTTGGAGAGATGTTCCAAGCCT
* *
4087886 ATTTATTTTCAGTTATTGCTTGTATTAGGGAGAGTAGAGTTTGTTTAACCTTAAGCAATCTTTTA
66 ATTTATTTTCAGTTATTGC-TGTATTAGGCAGAGTAGAGTTTATTTAACCTTAAGCAATCTTTTA
* * *
4087951 GATTGTTCTCAAGTTCTGTATCTCAT-AGGTGGATTT-TCTAGAGTGAACTTGTATAGTTTTGTA
130 GATTGTTCTCAAGTTCTGTATCTC-TCAGGTGAATTTCT-TAGAGTGAACTTCTATAGTTATGTA
4088014 TC-CTGATTAGAGTTCTTA
193 TCTCTGATTAGAGTTCTTA
4088032 AGGTGGTGTT
Statistics
Matches: 192, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
234 92 0.48
235 99 0.52
236 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (234 bp):
AATTCAGCAACCCAAGAAAAAAGCAATATTTGAAATTACCATGCTTGGAGAGATGTTCCAAGCCT
ATTTATTTTCAGTTATTGCTGTATTAGGCAGAGTAGAGTTTATTTAACCTTAAGCAATCTTTTAG
ATTGTTCTCAAGTTCTGTATCTCTCAGGTGAATTTCTTAGAGTGAACTTCTATAGTTATGTATCT
CTGATTAGAGTTCTTAGGATGATGTTTTTGTATCCAATG
Found at i:4090498 original size:22 final size:22
Alignment explanation
Indices: 4090470--4090513 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4090460 CTAAATCTTC
* *
4090470 CTTAATTTTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
4090492 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
4090514 TAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:4090525 original size:22 final size:22
Alignment explanation
Indices: 4090473--4090525 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4090463 AATCTTCCTT
* * *
4090473 AATTTTAGGGATACAAATACTT
1 AATTATAGAGATACAAATACTA
*
4090495 AATTCTAGAGATACAAATA-TA
1 AATTATAGAGATACAAATACTA
4090516 AATATATAGA
1 AAT-TATAGA
4090526 TTACAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (22 bp):
AATTATAGAGATACAAATACTA
Found at i:4094107 original size:22 final size:23
Alignment explanation
Indices: 4094074--4094121 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
4094064 TAATATATTA
4094074 AAATAGGAATTT-GTATAATGTG
1 AAATAGGAATTTAGTATAATGTG
* *
4094096 AAATATGG-ATTTAGTATGATTTG
1 AAATA-GGAATTTAGTATAATGTG
4094119 AAA
1 AAA
4094122 CGTCTGTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.38
Consensus pattern (23 bp):
AAATAGGAATTTAGTATAATGTG
Found at i:4096058 original size:30 final size:30
Alignment explanation
Indices: 4096016--4096077 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4096006 GTCAATGTTT
4096016 ATGTAAGGTGTTCAACTTAGACTAGCATAC
1 ATGTAAGGTGTTCAACTTAGACTAGCATAC
*
4096046 ATGT-AGGATGTTCAACTTGGACTAGCATAC
1 ATGTAAGG-TGTTCAACTTAGACTAGCATAC
4096076 AT
1 AT
4096078 ATACACATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (30 bp):
ATGTAAGGTGTTCAACTTAGACTAGCATAC
Found at i:4096468 original size:34 final size:34
Alignment explanation
Indices: 4096400--4096469 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
4096390 ATCAAGTTTA
**
4096400 TCAAAAATAGATATATGAGAATCTTTGAGACTTT
1 TCAAAAATAGATATATGAGAATCTTAAAGACTTT
* *
4096434 TCAAAAATAGTTATTTGAGAATTCTTAAAG-CTTT
1 TCAAAAATAGATATATGAGAA-TCTTAAAGACTTT
4096468 TC
1 TC
4096470 GGATATCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (34 bp):
TCAAAAATAGATATATGAGAATCTTAAAGACTTT
Found at i:4098824 original size:17 final size:17
Alignment explanation
Indices: 4098804--4098836 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4098794 ATTTGTATTC
4098804 TCTTTACATGTATACCT
1 TCTTTACATGTATACCT
4098821 TCTTTACATGTATACC
1 TCTTTACATGTATACC
4098837 GTTATCAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TCTTTACATGTATACCT
Found at i:4100607 original size:102 final size:104
Alignment explanation
Indices: 4100431--4100621 Score: 235
Period size: 102 Copynumber: 1.9 Consensus size: 104
4100421 CATTAATTGA
* * * * *
4100431 CAAGGCTTTCATTTCCTTCATTTCATTTTTATACTCCTTTAAGTAGGTAGTTCTAACAACTTTTC
1 CAAGGCTTTCATTTCCTTCATTGCATATTCATACTCCATTAAATAGGTAGTTCTAACAACTTTTC
*
4100496 ACAAAAAAT-CTTTCA-ATTTTTTATACTCTTTTATTTG
66 ACAAAAAATCCTTTAACATTTTTTATACTCTTTTATTTG
* * * * **
4100533 CAAGGTTTTCATTTCTTTCATTGCATATTCATATTCCATTAAATAGGTAGCTT-TAGCAGTTTTT
1 CAAGGCTTTCATTTCCTTCATTGCATATTCATACTCCATTAAATAGGTAG-TTCTAACAACTTTT
*
4100597 CATAAAAAATCCTTTAACATTTTTT
65 CACAAAAAATCCTTTAACATTTTTT
4100622 TTTATTTGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
102 59 0.81
103 7 0.10
104 7 0.10
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (104 bp):
CAAGGCTTTCATTTCCTTCATTGCATATTCATACTCCATTAAATAGGTAGTTCTAACAACTTTTC
ACAAAAAATCCTTTAACATTTTTTATACTCTTTTATTTG
Found at i:4102437 original size:17 final size:17
Alignment explanation
Indices: 4102397--4102438 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4102387 TTTTAATCTT
* *
4102397 TAATAAAATATATCATA
1 TAATAATATATATAATA
4102414 -AACTAATATATATAATA
1 TAA-TAATATATATAATA
4102431 TAATAATA
1 TAATAATA
4102439 ACCTTCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATAATATATATAATA
Found at i:4102661 original size:75 final size:78
Alignment explanation
Indices: 4102568--4102716 Score: 187
Period size: 79 Copynumber: 1.9 Consensus size: 78
4102558 ATGACTTGGC
* *
4102568 AGAAGAAGGTATCCATAAC-A-ATA-ATAAAAAATAAAACAAAACCAGTTTATTCATATATAGGC
1 AGAAAAAGGTATCCATAACAACATATATAAAAAATAAAACAAAACCAGTTCATTCATATATAGGC
*
4102630 AGAAACAACTACA
66 AAAAACAACTACA
* * * ** *
4102643 AGAAAAAGGTATCTATAACAACCATATTTAATACTTAAAACAAAACCAGTTCATTCATGTATAGG
1 AGAAAAAGGTATCCATAACAA-CATATATAAAAAATAAAACAAAACCAGTTCATTCATATATAGG
4102708 CAAAAACAA
65 CAAAAACAA
4102717 AACTAGTGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
75 17 0.28
76 1 0.02
78 3 0.05
79 40 0.66
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.22
Consensus pattern (78 bp):
AGAAAAAGGTATCCATAACAACATATATAAAAAATAAAACAAAACCAGTTCATTCATATATAGGC
AAAAACAACTACA
Found at i:4102730 original size:31 final size:31
Alignment explanation
Indices: 4102679--4102744 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
4102669 TTTAATACTT
* *
4102679 AAAACAAAACCAGTTCATTCATGTATAGG-CA
1 AAAACAAAACCAGTGCATTCACGTAT-GGCCA
* *
4102710 AAAACAAAACTAGTGGATTCACGTATGGCCA
1 AAAACAAAACCAGTGCATTCACGTATGGCCA
4102741 AAAA
1 AAAA
4102745 GGGAAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (31 bp):
AAAACAAAACCAGTGCATTCACGTATGGCCA
Found at i:4103952 original size:11 final size:11
Alignment explanation
Indices: 4103915--4103970 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
4103905 TATGAAATAA
*
4103915 AAAAAATAATAC
1 AAAAAATAA-AG
**
4103927 AAAAAGGAAA-
1 AAAAAATAAAG
4103937 AAAAAGATAAAG
1 AAAAA-ATAAAG
4103949 AAAAAATAAAG
1 AAAAAATAAAG
4103960 AAAAAAATAAA
1 -AAAAAATAAA
4103971 AGGGTAAGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 5 0.14
11 10 0.27
12 22 0.59
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAAATAAAG
Found at i:4103964 original size:12 final size:12
Alignment explanation
Indices: 4103936--4103970 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
4103926 CAAAAAGGAA
4103936 AAAAAAGATAAAG
1 AAAAAA-ATAAAG
4103949 -AAAAAATAAAG
1 AAAAAAATAAAG
4103960 AAAAAAATAAA
1 AAAAAAATAAA
4103971 AGGGTAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAATAAAG
Done.