Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 135 of 170
Found at i:40925283 original size:2 final size:2
Alignment explanation
Indices: 40925278--40925322 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40925268 AAAAAAGAAA
40925278 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40925320 AG A
1 AG A
40925323 CCTCTGAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40935051 original size:18 final size:18
Alignment explanation
Indices: 40935022--40935090 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
40935012 AAGGGGATCA
* *
40935022 CATATTAGAACTCCATAT
1 CATATCAGAACTCCACAT
* *
40935040 AATATCATAACTCCACAT
1 CATATCAGAACTCCACAT
40935058 CATATCAGAACTCCACAT
1 CATATCAGAACTCCACAT
*
40935076 CATATTAGAACTCCA
1 CATATCAGAACTCCA
40935091 TACTAAATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.28
Consensus pattern (18 bp):
CATATCAGAACTCCACAT
Found at i:40936250 original size:44 final size:44
Alignment explanation
Indices: 40936213--40937183 Score: 589
Period size: 44 Copynumber: 22.3 Consensus size: 44
40936203 ACTACTGCTT
* * *
40936213 AGGGAGATAGGATTTACAATCTTCAACCTATTCCACTACTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * *
40936257 AGGGAGATAGGACATACAATCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
40936301 AGGGAGATAAGACTTACAATCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
40936345 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
40936389 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
40936433 AGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * **
40936477 AAGGAGATAGGA-TT----T-GT-AA-CT-TGT--A--GCTTCTC
1 AGGGAGATAGGACTTACAATCTTCAACCTAT-TCCACTGCTGGTC
** * ** * * * * * ** ***
40936509 AAAAGA-ACAAAATTTGCTATCTTTAGCCTGCTCCACTGCAACTTC
1 -AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGC-TGGTC
* ** * * * ** *** *
40936554 -GGAGAGATAAGACTT-GTAGCTTCAACTTGTTCTGCTGCAACTTT
1 AGG-GAGATAGGACTTACAATCTTCAACCTATTCCACTGC-TGGTC
* * * * * * * * *
40936598 A--AAGATAAGTCTGATGCGATC-T--ACTCTATTGCAACTCCAGAG-A
1 AGGGAGATAGGACT--TACAATCTTCAAC-CTATT-CCACTGCTG-GTC
*** ** * *** * * * *
40936641 AATAAGATTTG-TTGTTGTAGCTTCAATCTATTCGACTGCAAT-GTT
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGC--TGGTC
* * * ** * ** * * *
40936686 GGGGA-AGTAAGA-TTCGCCGTCTTCAATCTGCTCCACTAC-AGCC
1 AGGGAGA-TAGGACTT-ACAATCTTCAACCTATTCCACTGCTGGTC
* * * * *
40936729 TAGGGAGACA-GAATCTACCATCTTCAACCTATTCCACTGTTGTTC
1 -AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGGTC
* * *
40936774 AGGGAGATAGGACATACAATCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * *
40936818 AGGGAGATAGGACTTACAATCTTCCACATATTCCACTGTTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
40936862 AAGGAGATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * * * * *
40936906 AGAGAGATAGGACTTGCAAACTTTAACCTATTTCACTGCTGGTT
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
40936950 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
40936994 AGGGAGATAGGACTTGCAATC--GAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
40937036 AGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* ** * * *
40937080 AGGGAGATAGGATTTGTAATCTTCAACCTATTACAACTGTTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATT-CCACTGCTGGTC
* ** * *
40937125 AGGGAGATAGGAATTGTAATCTTCAACCTATTCCACTACTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
40937169 AGGGAGATAGGACTT
1 AGGGAGATAGGACTT
40937184 GTGGTTTCAC
Statistics
Matches: 742, Mismatches: 139, Indels: 92
0.76 0.14 0.09
Matches are distributed among these distances:
32 8 0.01
33 6 0.01
34 1 0.00
35 1 0.00
36 3 0.00
37 3 0.00
38 2 0.00
39 2 0.00
40 3 0.00
42 52 0.07
43 13 0.02
44 563 0.76
45 84 0.11
46 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
Found at i:40936936 original size:517 final size:517
Alignment explanation
Indices: 40935962--40937005 Score: 1732
Period size: 517 Copynumber: 2.0 Consensus size: 517
40935952 GCAATGTCGG
*
40935962 GGAGATAGGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCCA
1 GGAGATAGGATTTGTAACTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCCA
*
40936027 CTGCAACTTTAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGTC
66 CTGCAACTTGAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGTC
* *
40936092 TGATGCAATCTGCTCTACTGCAACTCCAGAGAAATAAGATTCGCTTTTGTAGCTTCAACCTATTT
131 TGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCGCTTTTGTAGCTTCAACCTATTC
* * * * *
40936157 GACTACAACGTTGGGGAAGTAAGATTCGCTGTCTCCGATCTGCTCCACTACTGCTTAGGGAGATA
196 GACTACAACGTTGGGGAAGTAAGATTCGCCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGACA
* *
40936222 GGATTTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACCTA
261 GAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACCTA
* *
40936287 TTCCACTGCTGTTCAGGGAGATAAGACTTACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGA
326 TTCCACTGCTGTTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGAGA
* * * *
40936352 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGCAATCTTCAACC
391 TAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGAGAGATAGGACTTGCAAACTTCAACC
*
40936417 TATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTCAA
456 TATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAA
40936479 GGAGATAGGATTTGTAACTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCCA
1 GGAGATAGGATTTGTAACTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCCA
*
40936544 CTGCAACTTCGGA-GAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGT
66 CTGCAACTT-GAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGT
* * * *
40936608 CTGATGCGATCTACTCTATTGCAACTCCAGAGAAATAAGATTTG-TTGTTGTAGCTTCAATCTAT
130 CTGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCGCTT-TTGTAGCTTCAACCTAT
* * *
40936672 TCGACTGCAATGTTGGGGAAGTAAGATTCGCCGTCTTCAATCTGCTCCACTACAGCCTAGGGAGA
194 TCGACTACAACGTTGGGGAAGTAAGATTCGCCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGA
* **
40936737 CAGAATCTACCATCTTCAACCTATTCCACTGTTGTTCAGGGAGATAGGACATACAATCTTCCACC
259 CAGAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACC
* *
40936802 TATTCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACATATTCCACTGTTGGTCAAGGA
324 TATTCCACTGCTGTTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGA
*
40936867 GATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGAGAGATAGGACTTGCAAACTTTAA
389 GATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGAGAGATAGGACTTGCAAACTTCAA
* * * *
40936932 CCTATTTCACTGCTGGTTAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAG
454 CCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAA
40936996 GGAGATAGGA
1 GGAGATAGGA
40937006 CTTGCAATCG
Statistics
Matches: 489, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
516 2 0.00
517 486 0.99
518 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (517 bp):
GGAGATAGGATTTGTAACTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCCA
CTGCAACTTGAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGTC
TGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCGCTTTTGTAGCTTCAACCTATTC
GACTACAACGTTGGGGAAGTAAGATTCGCCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGACA
GAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACCTA
TTCCACTGCTGTTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGAGA
TAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGAGAGATAGGACTTGCAAACTTCAACC
TATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAA
Found at i:40938143 original size:28 final size:28
Alignment explanation
Indices: 40938111--40938166 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
40938101 ATAAATAGTA
* *
40938111 TGAAAATTGGGTGTCCTATATATCGCAG
1 TGAAAATTGGGTGTCCCAGATATCGCAG
40938139 TGAAAATTGGGTGTCCCAGATATCGCAG
1 TGAAAATTGGGTGTCCCAGATATCGCAG
40938167 CTTGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
TGAAAATTGGGTGTCCCAGATATCGCAG
Found at i:40939408 original size:22 final size:23
Alignment explanation
Indices: 40939383--40939438 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
40939373 TTTTCTTTTC
*
40939383 TTTTTCTTTTTCA-TTTCATCAT
1 TTTTTCTTTTTCATTTTAATCAT
* *
40939405 TTTTT-ATTTTCATTTTAATTAT
1 TTTTTCTTTTTCATTTTAATCAT
40939427 TTTTTCTCTTTT
1 TTTTTCT-TTTT
40939439 TTTTTGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
24 4 0.15
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTCTTTTTCATTTTAATCAT
Found at i:40939419 original size:13 final size:13
Alignment explanation
Indices: 40939401--40939476 Score: 52
Period size: 13 Copynumber: 5.7 Consensus size: 13
40939391 TTTCATTTCA
40939401 TCATTTTTTATTT
1 TCATTTTTTATTT
40939414 TCATTTTAATTATTTTT
1 TCATTTT--TTA--TTT
40939431 TC-TCTTTTT-TTT
1 TCAT-TTTTTATTT
*
40939443 TGATTTTTTATTT
1 TCATTTTTTATTT
*
40939456 TGATTTCTTT-TTT
1 TCATTT-TTTATTT
40939469 TC-TTTTTT
1 TCATTTTTT
40939477 TTATTGAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
11 3 0.06
12 12 0.23
13 21 0.40
14 3 0.06
15 5 0.09
16 1 0.02
17 8 0.15
ACGTcount: A:0.12, C:0.08, G:0.03, T:0.78
Consensus pattern (13 bp):
TCATTTTTTATTT
Found at i:40944004 original size:3 final size:3
Alignment explanation
Indices: 40943996--40944045 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
40943986 ATAATCAAAT
* *
40943996 ATA ATA ATA ATA ATA ACA ATA ATAA ATA GTA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
40944041 ATA AT
1 ATA AT
40944046 TAAGTGATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:40944023 original size:27 final size:28
Alignment explanation
Indices: 40943986--40944045 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
40943976 ATAGCTAAAT
40943986 ATAATCAAATA-TAATAATAATAATAACA
1 ATAATCAAATAGTAA-AATAATAATAACA
*
40944014 ATAAT-AAATAGTAAAATAATAATAATA
1 ATAATCAAATAGTAAAATAATAATAACA
40944041 ATAAT
1 ATAAT
40944046 TAAGTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAATCAAATAGTAAAATAATAATAACA
Found at i:40944424 original size:33 final size:33
Alignment explanation
Indices: 40944382--40944460 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
40944372 GAGGCTTCTG
40944382 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
1 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
*
40944415 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAG
1 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
40944448 AACGGCGTCGTTT
1 AACGGCGTCGTTT
40944461 CCTTCACATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (33 bp):
AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
Found at i:40947836 original size:24 final size:24
Alignment explanation
Indices: 40947809--40947860 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40947799 AAGTAATCAT
* * *
40947809 ATTTTAATTGGAAAAAGATAGTAG
1 ATTTTAACTGGAAAAAGAAACTAG
*
40947833 ATTTTAACTGGGAAAAGAAACTAG
1 ATTTTAACTGGAAAAAGAAACTAG
40947857 ATTT
1 ATTT
40947861 ATGTGGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (24 bp):
ATTTTAACTGGAAAAAGAAACTAG
Found at i:40950133 original size:17 final size:17
Alignment explanation
Indices: 40950111--40950144 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40950101 TGGCTGCAGC
40950111 CTACATGAATTGATAAG
1 CTACATGAATTGATAAG
*
40950128 CTACATGAATTTATAAG
1 CTACATGAATTGATAAG
40950145 TTCGTTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
CTACATGAATTGATAAG
Found at i:40962989 original size:20 final size:19
Alignment explanation
Indices: 40962954--40963016 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
40962944 AAAATTATTA
*
40962954 AAAAAATATATAAAAAAGTT
1 AAAAATTAT-TAAAAAAGTT
*
40962974 AATAATTATTTAAAAAAGTAT
1 AAAAATTA-TTAAAAAAGT-T
*
40962995 AAAAATTATTAAAAAATTT
1 AAAAATTATTAAAAAAGTT
40963014 AAA
1 AAA
40963017 TATGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.11
20 24 0.65
21 9 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATTATTAAAAAAGTT
Found at i:40962989 original size:31 final size:30
Alignment explanation
Indices: 40962938--40962999 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
40962928 CATTTTAGGT
40962938 AAGTGTAAAATTATTAAAAAAATATATAAAA
1 AAGTGTAAAATTATTAAAAAAA-ATATAAAA
* *
40962969 AAGT-TAATAATTATTTAAAAAAGTATAAAA
1 AAGTGTAA-AATTATTAAAAAAAATATAAAA
40962999 A
1 A
40963000 TTATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (30 bp):
AAGTGTAAAATTATTAAAAAAAATATAAAA
Found at i:40969470 original size:17 final size:17
Alignment explanation
Indices: 40969448--40969508 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
40969438 AAAAATATAT
40969448 TTAAAAATATAAAAATA
1 TTAAAAATATAAAAATA
* **
40969465 TTAAAAAAATTCAAATA
1 TTAAAAATATAAAAATA
*
40969482 GTAAATAATTATAAAAAATA
1 TTAAA-AA-TAT-AAAAATA
*
40969502 ATAAAAA
1 TTAAAAA
40969509 ATAGCACATC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 4 0.12
20 9 0.27
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
TTAAAAATATAAAAATA
Found at i:40969481 original size:25 final size:26
Alignment explanation
Indices: 40969452--40969500 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40969442 ATATATTTAA
40969452 AAATA-TAAAAATATTA-AAAAAATTC
1 AAATAGTAAAAA-ATTATAAAAAATTC
*
40969477 AAATAGTAAATAATTATAAAAAAT
1 AAATAGTAAAAAATTATAAAAAAT
40969501 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAGTAAAAAATTATAAAAAATTC
Found at i:40979303 original size:33 final size:33
Alignment explanation
Indices: 40979266--40979329 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40979256 TTGCAGCAGA
*
40979266 CTTGCGACGTGGCTGT-ATCACACAGCTAATAGG
1 CTTGCAACGTGGCTGTGAT-ACACAGCTAATAGG
* *
40979299 CTTGCAATGTGGCTGTGATATACAGCTAATA
1 CTTGCAACGTGGCTGTGATACACAGCTAATA
40979330 TTTGCTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (33 bp):
CTTGCAACGTGGCTGTGATACACAGCTAATAGG
Found at i:40983383 original size:43 final size:43
Alignment explanation
Indices: 40983331--40983579 Score: 369
Period size: 43 Copynumber: 5.8 Consensus size: 43
40983321 TTTTAGAAAT
* *
40983331 AAACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
40983374 AAATGCCGCTATAGATCAGGACCTTTAGCGGCGCTTCTT-CCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT-TTCCCAC
* *
40983417 AAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTT-GCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
40983459 AAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
40983502 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
40983545 AAACGCCGATATAGAACAA-ACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
40983580 CTCACAAAAA
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
42 55 0.29
43 130 0.70
44 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:40983503 original size:85 final size:86
Alignment explanation
Indices: 40983331--40983581 Score: 382
Period size: 85 Copynumber: 2.9 Consensus size: 86
40983321 TTTTAGAAAT
* * * *
40983331 AAACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCATAAATGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
40983396 CTTTAGCGGCGCTTCTTCCAC
66 CTTTAGCGACGCTTCTTCCAC
* * *
40983417 AAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTT-GCACAAACGCCGCTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
40983481 CTTTAGCGACGCTT-TTCCCAC
66 CTTTAGCGACGCTTCTT-CCAC
* *
40983502 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGATATAGAACAA-AC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
40983566 CTTTAGCGACGCTTCT
66 CTTTAGCGACGCTTCT
40983582 CACAAAAACG
Statistics
Matches: 149, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
84 2 0.01
85 91 0.61
86 56 0.38
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGACGCTTCTTCCAC
Found at i:40983591 original size:128 final size:128
Alignment explanation
Indices: 40983331--40983587 Score: 385
Period size: 128 Copynumber: 2.0 Consensus size: 128
40983321 TTTTAGAAAT
* * * * *
40983331 AAACACCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCATAAATGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
* * * * *
40983396 CTTTAGCGGCGCTTCTTCCACAAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTTGCAC
66 CTTTAGCGGCGCTTCTTCCACAAACGCCGATATAGAACAAGACCTTTAGCGACGCTTCTGCAC
*
40983459 AAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
40983524 CTTTAGCGGCGCTT-TTCCCACAAACGCCGATATAGAACAA-ACCTTTAGCGACGCTTCT-CAC
66 CTTTAGCGGCGCTTCTT-CCACAAACGCCGATATAGAACAAGACCTTTAGCGACGCTTCTGCAC
40983585 AAA
1 AAA
40983588 AACGGCACTA
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 6 0.05
127 18 0.15
128 93 0.79
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (128 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCTTCTTCCACAAACGCCGATATAGAACAAGACCTTTAGCGACGCTTCTGCAC
Found at i:40988011 original size:11 final size:12
Alignment explanation
Indices: 40987982--40988014 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40987972 TTCAGCTTGG
*
40987982 ATGCTGGTCTGC
1 ATGCTGGTTTGC
40987994 ATGCTGGTTTGC
1 ATGCTGGTTTGC
40988006 -TGCTGGTTT
1 ATGCTGGTTT
40988015 CCTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:40992072 original size:20 final size:20
Alignment explanation
Indices: 40992047--40992085 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40992037 AAATTTATAG
40992047 TTTTTAAAAAATTATAAAAT
1 TTTTTAAAAAATTATAAAAT
*
40992067 TTTTTAAAAAATTCTAAAA
1 TTTTTAAAAAATTATAAAA
40992086 AATATATAAA
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:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAAATTATAAAAT
Found at i:40994408 original size:26 final size:28
Alignment explanation
Indices: 40994359--40994413 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
40994349 ATATTTCTAT
*
40994359 TTTTTTAATGAATATTTTTCTATATTTA
1 TTTTTAAATGAATATTTTTCTATATTTA
40994387 TTTTTAAATGAATA-TTTT-TATATTTA
1 TTTTTAAATGAATATTTTTCTATATTTA
40994413 T
1 T
40994414 ACGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 9 0.35
27 4 0.15
28 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTTTAAATGAATATTTTTCTATATTTA
Found at i:41006714 original size:44 final size:43
Alignment explanation
Indices: 41006584--41007647 Score: 525
Period size: 44 Copynumber: 24.6 Consensus size: 43
41006574 CCAATAATCC
* * *
41006584 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCT
* * * * * * *
41006628 CATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
41006668 TATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
41006712 TATC-CTCCTAAAGTTGCAGT-GAGACAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGAG-CAGACT-AAGA-AGCAAGTCT
* * * * *
41006757 TATCTCTCTGAAGTTGCATTGGAGCAGA-TTA-AAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * * * *
41006801 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAA-AACCTTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
41006845 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
41006885 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * *
41006929 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGAAAAATTT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGAAG-CAAGTCT
* ** *
41006974 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCTGATAAACC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC--A-AGTCT
* * * *
41007018 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAA-AATTTC-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA--GCAAG-TCT
* * * * * * * *
41007062 CATCACTCTGAAGTTGCAG-AGAGCAGA-TCA-CATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
41007102 TATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * * *
41007146 TATC-CTCCTAAAGTTACAGT-GAGGCAGACTGAAGATGGAAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * * *
41007191 TATCTCCCTGAAGTTGCATTGGAGCAGA-TTA-AAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * * *
41007235 TATCTCCCTGAAGTCGCAGTAGAGCGGATTAA-AA-CATTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA--AG-TCT
* * * * * *
41007279 TATCTCTCTGAAGTTGCAG-AGAGCA-A-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
41007318 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * *
41007362 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAAAATTT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * **
41007407 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
41007451 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* *
41007491 TATCTACTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
41007535 TATC-CTCCTAAAGTTGCAGT-AAGGCAGACTGAAGAAAGTAAGTCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAG-AAGCAAGTCT
* * * * * * *
41007580 TATCCCCCTAAAATTGTAGTGGGGCAGACTAAATGAA-CAAATCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AA-GAAGCAAGTCT
* * *
41007624 TGTCTCCCTAAAGTTGTAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
41007648 TGGATTAGAG
Statistics
Matches: 785, Mismatches: 158, Indels: 154
0.72 0.14 0.14
Matches are distributed among these distances:
39 21 0.03
40 87 0.11
41 41 0.05
42 27 0.03
43 60 0.08
44 362 0.46
45 171 0.22
46 15 0.02
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:41006726 original size:84 final size:85
Alignment explanation
Indices: 41006584--41006739 Score: 194
Period size: 84 Copynumber: 1.8 Consensus size: 85
41006574 CCAATAATCC
* * * * *
41006584 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTCATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTACAGTGGAGCAGACTAAAAGCACAGATCTCATCTCTCTAAAGTTGCAGAG
41006649 AG-CAGATCGCATCTAGTCT
66 AGACAGATCGCATCTAGTCT
*
41006668 TATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA-AG-TCTTATC-CTCCTAAAGTTGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGACTAA--AAGCACAGATCTCATCTCT-CTAAAGTTGCA
*
41006730 GTGAGACAGA
63 GAGAGACAGA
41006740 CTGAAGATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
83 2 0.03
84 49 0.80
85 6 0.10
86 4 0.07
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (85 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGACTAAAAGCACAGATCTCATCTCTCTAAAGTTGCAGAG
AGACAGATCGCATCTAGTCT
Found at i:41006959 original size:217 final size:217
Alignment explanation
Indices: 41006577--41007439 Score: 1451
Period size: 217 Copynumber: 4.0 Consensus size: 217
41006567 TCAGTGGCCA
* * **
41006577 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTCATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
*
41006642 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * *
41006707 AGTCTTATCCTCCTAAAGTTGCAGTGAGACAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
*
41006772 GCATTGGAGCAGATTAAAGCCG
196 GCAGTGGAGCAGATTAAAGCCG
*
41006794 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
41006859 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * *
41006924 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGAAAAATTTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
*
41006989 GCAGTGGAGCAGATTAAAGCTG
196 GCAGTGGAGCAGATTAAAGCCG
* * * * *
41007011 ATAAACCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA-TTTCAGATCTCATCACTCTGAAG
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTT-AGATCTCATCTCTCTGAAG
* *
41007075 TTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGC
65 TTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
*
41007140 AAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGT
130 AAGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGT
*
41007205 TGCATTGGAGCAGATTAAAGCCG
195 TGCAGTGGAGCAGATTAAAGCCG
* * *
41007228 ATAATCCTATCTCCCTGAAGTCGCAGTAGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
41007293 TGCAGAGAGCA-ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
41007357 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATTTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
41007422 GCAGTGGAGCAGATTAAA
196 GCAGTGGAGCAGATTAAA
41007440 ACCTTGGATC
Statistics
Matches: 603, Mismatches: 41, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
216 132 0.22
217 469 0.78
218 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCG
Found at i:41007532 original size:173 final size:172
Alignment explanation
Indices: 41007235--41007569 Score: 580
Period size: 173 Copynumber: 1.9 Consensus size: 172
41007225 CCGATAATCC
*
41007235 TATCTCCCTGAAGTCGCAGTAGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTCGCAGTAGAGCAGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
*
41007300 AGCAATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTAT
66 AGCAATCGCATCTAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTAT
* *
41007365 CCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATTT
131 CCTCCTAAAGTTGCAGTAAGGCAGACTGAAGATGGAAAATTT
* * * *
41007407 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTCGCAGTAGAGCAGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
*
41007472 AGCAGATCGCATCTAGTCTTATCTACTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCA-ATCGCATCTAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
41007537 TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGA
130 TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGA
41007570 AAGTAAGTCT
Statistics
Matches: 153, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
172 64 0.42
173 89 0.58
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (172 bp):
TATCTCCCTGAAGTCGCAGTAGAGCAGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
AGCAATCGCATCTAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTAT
CCTCCTAAAGTTGCAGTAAGGCAGACTGAAGATGGAAAATTT
Found at i:41007607 original size:89 final size:88
Alignment explanation
Indices: 41006880--41007611 Score: 350
Period size: 89 Copynumber: 8.4 Consensus size: 88
41006870 GATCGCATCT
41006880 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
41006945 CAGTGAGGCAGACTGAAGATGAA--A
66 CAGT-AGGCAGACTGAAGA--AAGTA
* * * * * * *
41006969 AATTTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGA-TAA-ACCTAT-CTCCCTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAGTCTTATCCT-CCTGAAG
* * * * ** *
41007031 TTGTAGTGGAGCGGA-TTAA-AATTTC
63 TTGCAGTAG-GCAGACTGAAGAAAGTA
* * * * * * * *
41007056 AGATCTCATCACTCTGAAGTTGCAG-AGAGCAGA-TCA--CATCTAGTCTTAT-CTCCCTGAAGT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCT-CCTGAAGT
* * * *
41007116 TGCAGTGGAGTAGACT-AAGTAAGCA
64 TGCAGTAG-GCAGACTGAAGAAAGTA
* * * * *
41007141 AGTCTTATC-CTCCTAAAGTTACAGT-GAGGCAGACTGAAG-ATGGAAAATCTTAT-CTCCCTGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAGTCTTATCCT-CCTGA
* * * * **
41007202 AGTTGCATTGGAGCAGATTAAAG-CCGATA
61 AGTTGCAGTAG-GCAGACTGAAGAAAG-TA
* * * * *
41007231 A-TCCTATCTCCCTGAAGTCGCAGTAGAGCGGATTAA--AA-CATTAGATCTTAT-CTCTCTGAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA--AG-TCTTATCCTC-CTGAA
* * **
41007291 GTTGCAG-AGAGCA-A-T--CGCATCT-
62 GTTGCAGTAG-GCAGACTGAAGAAAGTA
41007313 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
** *
41007378 CAGTGAGGCAGACTGAAGATGGAA
66 CAGT-AGGCAGACTGAAGAAAGTA
* * * * **
41007402 AATTTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCTTGGATCTTAT-CTCTCTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAG-TCTTATCCTC-CTGAAG
* * **
41007464 TTGCAG-AGAGCAGA-T--CGCATCT-
63 TTGCAGTAG-GCAGACTGAAGAAAGTA
* * *
41007486 AGTCTTATCTACTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTAAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
41007551 CAGTAAGGCAGACTGAAGAAAGTA
66 CAGT-AGGCAGACTGAAGAAAGTA
* * * * *
41007575 AGTCTTATCCCCCTAAAATTGTAGTGGGGCAGACTAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
41007612 ATGAACAAAT
Statistics
Matches: 483, Mismatches: 108, Indels: 104
0.69 0.16 0.15
Matches are distributed among these distances:
82 2 0.00
83 52 0.11
84 103 0.21
85 28 0.06
86 12 0.02
87 24 0.05
88 58 0.12
89 189 0.39
90 13 0.03
91 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
CAGTAGGCAGACTGAAGAAAGTA
Found at i:41009164 original size:19 final size:19
Alignment explanation
Indices: 41009140--41009179 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
41009130 TTAATTGATA
41009140 ATGTAATTATTTTATATAT
1 ATGTAATTATTTTATATAT
*
41009159 ATGTAATTATTTTATCTAT
1 ATGTAATTATTTTATATAT
41009178 AT
1 AT
41009180 ATGCATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
ATGTAATTATTTTATATAT
Found at i:41009192 original size:23 final size:19
Alignment explanation
Indices: 41009144--41009194 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
41009134 TTGATAATGT
*
41009144 AATTATTTTATATATATGT
1 AATTATTTTATATATATGC
41009163 AATTATTTTATCTATATATGC
1 AATTATTTTA--TATATATGC
41009184 ATATATATTTT
1 A-AT-TATTTT
41009195 TGTTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
21 9 0.33
22 2 0.07
23 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTATTTTATATATATGC
Found at i:41009236 original size:29 final size:27
Alignment explanation
Indices: 41009197--41009253 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 27
41009187 TATATTTTTG
*
41009197 TTTTTTTAATGAATATTTTTCTATATTTA
1 TTTTTTAAATGAATA-TTTT-TATATTTA
41009226 TTTTTTAAATGAATATTTTTATATTTA
1 TTTTTTAAATGAATATTTTTATATTTA
41009253 T
1 T
41009254 ACGTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.33
28 4 0.15
29 14 0.52
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTTAAATGAATATTTTTATATTTA
Found at i:41009625 original size:15 final size:15
Alignment explanation
Indices: 41009605--41009639 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41009595 TTTCTATGCC
41009605 ATTGTTATATTTATT
1 ATTGTTATATTTATT
*
41009620 ATTGTTGTATTTATT
1 ATTGTTATATTTATT
41009635 ATTGT
1 ATTGT
41009640 GGCATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
ATTGTTATATTTATT
Found at i:41011042 original size:98 final size:98
Alignment explanation
Indices: 41010818--41011042 Score: 299
Period size: 98 Copynumber: 2.3 Consensus size: 98
41010808 TTCAATGTAT
* * * * * *
41010818 TACCATCCCAGATGGCCCGAAAACAATGGCTTCCACACTTTACCTATACTATCATCTCGAATGGC
1 TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
*
41010883 TCGACAATTATAACATTCATGATCAATTCATTC
66 TCGACAATGATAACATTCATGATCAATTCATTC
* * * * *
41010916 TATCATTCCGGATGGCTCAACGACGATGGCTTCCACACTTTACCTATATTACCATCCCGAATGGC
1 TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
*
41010981 TCTACAATGATGAA-ATTCATGATCAATTCATTC
66 TCGACAATGAT-AACATTCATGATCAATTCATTC
* *
41011014 TACCATTTCGGATGGCCCGACAATGATGG
1 TACCATTCCGGATGGCCCGACAACGATGG
41011043 TTTTCACTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
98 105 0.98
99 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (98 bp):
TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
TCGACAATGATAACATTCATGATCAATTCATTC
Found at i:41011067 original size:98 final size:98
Alignment explanation
Indices: 41010818--41011069 Score: 267
Period size: 98 Copynumber: 2.6 Consensus size: 98
41010808 TTCAATGTAT
* * * * * * *
41010818 TACCATCCCAGATGGCCCGAA-AACAATGGCTTCCACACTTTACCTATACTATCATCTCGAATGG
1 TACCATTCCGGATGGCCC-AACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGG
*
41010882 CTCGACAATTATAACATTCATGATCAATTCATTC
65 CTCGACAATGATAACATTCATGATCAATTCATTC
* * * * * *
41010916 TATCATTCCGGATGGCTCAACGACGATGGCTTCCACACTTTACCTATATTACCATCCCGAATGGC
1 TACCATTCCGGATGGCCCAACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGGC
*
41010981 TCTACAATGATGAA-ATTCATGATCAATTCATTC
66 TCGACAATGAT-AACATTCATGATCAATTCATTC
* * * * * *
41011014 TACCATTTCGGATGGCCCGACAATGATGGTTTTCACTA-TATACATATCCTACCATC
1 TACCATTCCGGATGGCCCAACAACGATGGCTTCCAC-ACTATACATATACTACCATC
41011070 ACGGTTGGCC
Statistics
Matches: 128, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
97 2 0.02
98 123 0.96
99 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (98 bp):
TACCATTCCGGATGGCCCAACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGGC
TCGACAATGATAACATTCATGATCAATTCATTC
Found at i:41021871 original size:22 final size:21
Alignment explanation
Indices: 41021843--41021889 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41021833 ATTAAATTTT
*
41021843 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAA-ATAAAAATAA
* *
41021865 AAAATTTTAAAATTAAAATAA
1 AAAATTTGAAAATAAAAATAA
41021886 AAAA
1 AAAA
41021890 AGGGAGGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATTTGAAAATAAAAATAA
Found at i:41021882 original size:21 final size:21
Alignment explanation
Indices: 41021828--41021889 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
41021818 ATACTAATAA
* *
41021828 TTAAAATTAAATTTTAAAATT
1 TTAAAATTAAAATTAAAAATT
* *
41021849 TGAAATATAAAAATTAAAAATT
1 TTAAA-ATTAAAATTAAAAATT
*
41021871 TTAAAATTAAAATAAAAAA
1 TTAAAATTAAAATTAAAAA
41021890 AGGGAGGAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TTAAAATTAAAATTAAAAATT
Found at i:41023950 original size:16 final size:16
Alignment explanation
Indices: 41023929--41023967 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41023919 GTTTAGTTCA
*
41023929 CTGTAATGGAATAGAG
1 CTGTAATGGAATAAAG
*
41023945 CTGTAATGGACTAAAG
1 CTGTAATGGAATAAAG
41023961 CTGTAAT
1 CTGTAAT
41023968 TAGTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:41024142 original size:12 final size:12
Alignment explanation
Indices: 41024125--41024149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41024115 AATTTAATAA
41024125 AATTATTATTAT
1 AATTATTATTAT
41024137 AATTATTATTAT
1 AATTATTATTAT
41024149 A
1 A
41024150 TGAATTAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTATTATTAT
Found at i:41030962 original size:11 final size:11
Alignment explanation
Indices: 41030932--41030966 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
41030922 ATCAAAAGGC
41030932 CTCTCTATTTT
1 CTCTCTATTTT
41030943 CTGTCTCTATTTT
1 C--TCTCTATTTT
41030956 CTCTCTATTTT
1 CTCTCTATTTT
41030967 GTCAAAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.09, C:0.26, G:0.03, T:0.63
Consensus pattern (11 bp):
CTCTCTATTTT
Found at i:41035017 original size:35 final size:35
Alignment explanation
Indices: 41034974--41035148 Score: 248
Period size: 35 Copynumber: 5.0 Consensus size: 35
41034964 TTGCAGAATA
*
41034974 TTTGTTGCAGGGAGTCTCTTCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
*
41035009 TTTGTTGCAGGGAATCTCTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
41035044 TTTGTTGCAGGGAATCT-TTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTT-CTGTTCACGCATTAT
* * *
41035079 TTTGTTGCAAGGAATCT-TTCCTGTTCACACATCA-
1 TTTGTTGCAGGGAATCTCTT-CTGTTCACGCATTAT
* *
41035113 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
41035148 T
1 T
41035149 AGGAGAAAGA
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
34 28 0.22
35 98 0.78
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
Found at i:41036756 original size:20 final size:23
Alignment explanation
Indices: 41036726--41036770 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
41036716 AGAAAAAGAG
41036726 AAATACAAAAAAGAA-TAG-ATC
1 AAATACAAAAAAGAAGTAGAATC
41036747 AAAT-CAAAAAAGAAGTAGAATC
1 AAATACAAAAAAGAAGTAGAATC
41036769 AA
1 AA
41036771 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 7 0.32
22 5 0.23
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAGTAGAATC
Found at i:41039660 original size:35 final size:35
Alignment explanation
Indices: 41039571--41039781 Score: 311
Period size: 35 Copynumber: 6.1 Consensus size: 35
41039561 GTCCAAAAAG
*
41039571 AAATAATGCGTGAACA-GAAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAA-AGATTCCCTGCAACA
* * *
41039605 AAATGATGTGTGAACAGGAAAGATTCCTTGCAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
*
41039640 AAATAATGCGTGAACAGGAAAGATTCCCTGTAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
*
41039675 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
* *
41039710 AAATAATGCGTGAACAGGAGAGATTCCCTGCGACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
41039745 AAATAATGCGTGAACA-GAAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAA-AGATTCCCTGCAACA
41039780 AA
1 AA
41039782 TATTCCCTGC
Statistics
Matches: 161, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
34 28 0.17
35 133 0.83
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
Found at i:41041286 original size:13 final size:13
Alignment explanation
Indices: 41041268--41041292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41041258 ACGAACTATT
41041268 TTTTAAAAATAAA
1 TTTTAAAAATAAA
41041281 TTTTAAAAATAA
1 TTTTAAAAATAA
41041293 TCTCGGGATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTTAAAAATAAA
Found at i:41052839 original size:24 final size:24
Alignment explanation
Indices: 41052807--41052864 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
41052797 ATGTCCCAAA
41052807 ATTACAGTGGATTAAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
*
41052831 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
41052855 ATTACAGTGG
1 ATTACAGTGG
41052865 GGGCAATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGATTAAACCTTGAAG
Found at i:41053180 original size:51 final size:49
Alignment explanation
Indices: 41053120--41053319 Score: 214
Period size: 46 Copynumber: 4.1 Consensus size: 49
41053110 TGAAACCACA
* * *
41053120 AATCTTATTTCCTTGGTGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGT--AGTAGATTAAAGCTGAAGGCAGCG
* **
41053171 AATCTTATTTCCCTAGCGTT---GTAGTAGATTAAAGCTGAAGGCAGTA
1 AATCTTATTTCCCTGGCGTTGCAGTAGTAGATTAAAGCTGAAGGCAGCG
* * * *
41053217 AATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAACGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGT--AGTAGATTAAAGCTGAAGGCAGCG
* *
41053268 AATCTTATTTCCCTGGCGTTGCA--A-TAAATTAAAGCTGAAGGCAGCT
1 AATCTTATTTCCCTGGCGTTGCAGTAGTAGATTAAAGCTGAAGGCAGCG
41053314 AATCTT
1 AATCTT
41053320 TTTTGCAGTA
Statistics
Matches: 126, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
46 63 0.50
47 1 0.01
48 2 0.02
49 2 0.02
51 58 0.46
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (49 bp):
AATCTTATTTCCCTGGCGTTGCAGTAGTAGATTAAAGCTGAAGGCAGCG
Found at i:41053221 original size:46 final size:46
Alignment explanation
Indices: 41053150--41053559 Score: 324
Period size: 46 Copynumber: 9.0 Consensus size: 46
41053140 GCAGTGGAGC
* * *
41053150 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
** *
41053196 AGATTAAAGCTGAAGGCAGTAAATCTTATTTCCTTGGCGTTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGC-----AAT
* *
41053247 AGATTAAAGCTAAACGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
41053293 AAATTAAAGCTGAAGGCAGCTAATC---TTT---T----TTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * **
41053329 AGGTTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGACGTTGCCGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* ** * * ** ** *
41053375 GGA--GCAGCTGAAGGCAACAAATCTTATTTCTTTGGCGTTATAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * *
41053419 AGATCAAAGCTGAGGGTAGCGAATCTTATTTCCTCGGTGTTGCAG-TGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCC-C--TG--GC-GTTGCAAT
* *
41053470 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCCGACGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* *
41053516 AGATTAAGGCTGAAGGCAGCGAATCTTATTTCTCTGGCGTTGCA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCA
41053560 GTGGAATAGA
Statistics
Matches: 287, Mismatches: 53, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
36 28 0.10
39 3 0.01
40 1 0.00
42 1 0.00
43 3 0.01
44 34 0.12
45 1 0.00
46 136 0.47
48 1 0.00
49 2 0.01
50 1 0.00
51 75 0.26
52 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
Found at i:41053287 original size:97 final size:98
Alignment explanation
Indices: 41053119--41053319 Score: 307
Period size: 97 Copynumber: 2.1 Consensus size: 98
41053109 GTGAAACCAC
* * * *
41053119 AAATCTTATTTCCTTGGTGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCC
1 AAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTAAACGCAGCGAATCTTATTTCCC
* * *
41053184 TAGCGTTGTAGTAGATTAAAGCTGAAGGCAG-T
66 TAGCGTTGCAATAAATTAAAGCTGAAGGCAGCT
*
41053216 AAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAACGCAGCGAATCTTATTTCCC
1 AAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTAAACGCAGCGAATCTTATTTCCC
*
41053281 TGGCGTTGCAATAAATTAAAGCTGAAGGCAGCT
66 TAGCGTTGCAATAAATTAAAGCTGAAGGCAGCT
41053314 -AATCTT
1 AAATCTT
41053320 TTTTGCAGTA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
97 93 0.99
98 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (98 bp):
AAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTAAACGCAGCGAATCTTATTTCCC
TAGCGTTGCAATAAATTAAAGCTGAAGGCAGCT
Found at i:41053494 original size:51 final size:51
Alignment explanation
Indices: 41053418--41053577 Score: 197
Period size: 51 Copynumber: 3.2 Consensus size: 51
41053408 GGCGTTATAG
* * * *
41053418 TAGATCAAAGCTGAGGGTAGCGAATCTTATTTCCTCGGTGTTGCAGTGGAA
1 TAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCGGCGTTGCAGTGGAA
* *
41053469 TAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCCGACGTTGC-----AA
1 TAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCGGCGTTGCAGTGGAA
*
41053515 TAGATTAAGGCTGAAGGCAGCGAATCTTATTT-CTCTGGCGTTGCAGTGGAA
1 TAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTC-GGCGTTGCAGTGGAA
*
41053566 TAGATTGAAGCT
1 TAGATTAAAGCT
41053578 ACTAATCCTA
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.02
46 40 0.43
51 50 0.54
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (51 bp):
TAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCGGCGTTGCAGTGGAA
Found at i:41060915 original size:15 final size:15
Alignment explanation
Indices: 41060895--41060927 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41060885 GTAAGGTTTG
41060895 CTTAATT-TTTCTTTT
1 CTTAATTGTTT-TTTT
41060910 CTTAATTGTTTTTTT
1 CTTAATTGTTTTTTT
41060925 CTT
1 CTT
41060928 TTCAGGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.73
Consensus pattern (15 bp):
CTTAATTGTTTTTTT
Found at i:41067191 original size:14 final size:15
Alignment explanation
Indices: 41067169--41067245 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
41067159 CAATCAAACA
41067169 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
41067183 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
41067198 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
41067218 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
41067232 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
41067246 ACTAGCAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.43
15 15 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:41067210 original size:20 final size:20
Alignment explanation
Indices: 41067185--41067224 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41067175 AATATTTTCC
*
41067185 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41067205 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41067225 TCATTTTCCG
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:41072199 original size:45 final size:44
Alignment explanation
Indices: 41072122--41072223 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 44
41072112 AATGGTAGCA
* * *
41072122 GTAACAGTAACAGTAATAGTATTCAACGCACAAAGTG-CTGAATC
1 GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAATC
* *
41072166 TGTAATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATC
1 -GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
41072211 GATAATAGTAACA
1 G-TAATAGTAACA
41072224 ATAGTCAGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 1 0.02
45 47 0.96
46 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (44 bp):
GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
Found at i:41072470 original size:40 final size:40
Alignment explanation
Indices: 41072426--41072512 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
41072416 AGTTCATTAC
* *
41072426 TTTAGTAA-TCTCACAGTTCAATGCAATACACATAACAATA
1 TTTAGTAACT-TCACAATTCAATGCAATACACAAAACAATA
* * *
41072466 TTTAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
*
41072506 TTCAGTA
1 TTTAGTA
41072513 TTCCATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (40 bp):
TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:41073186 original size:25 final size:23
Alignment explanation
Indices: 41073142--41073202 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
41073132 ATTTTGATTT
*
41073142 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
41073166 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
41073190 ATATAAATTATAT
1 AT-TTAATTATAT
41073203 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:41073205 original size:35 final size:35
Alignment explanation
Indices: 41073150--41073218 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
41073140 TTATTTAATA
* *
41073150 ATATAATATCATTATAATTTAATTATCATAAATTC
1 ATATAATATAATTATAATTTAAATATCATAAATTC
*
41073185 ATATAATATAAATTAT-ATTTAAATATCATTAATT
1 ATATAATAT-AATTATAATTTAAATATCATAAATT
41073219 AAATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (35 bp):
ATATAATATAATTATAATTTAAATATCATAAATTC
Found at i:41078856 original size:35 final size:35
Alignment explanation
Indices: 41078801--41078880 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
41078791 TTATTTAATA
* *
41078801 ATATAATAT-CATTATAATTTAATTATCACAAATT
1 ATATAATATAAATTATAATTTAAATATCACAAATT
**
41078835 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCACAAATT
41078870 ATATAAT-TAAA
1 ATATAATATAAA
41078881 ACAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 24 0.60
36 5 0.12
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCACAAATT
Found at i:41080882 original size:17 final size:17
Alignment explanation
Indices: 41080860--41080893 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41080850 TTATTTTTTA
41080860 ATTTAT-ATTTCTTATTT
1 ATTTATGATTT-TTATTT
41080877 ATTTATGATTTTTATTT
1 ATTTATGATTTTTATTT
41080894 GTTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATGATTTTTATTT
Found at i:41082056 original size:6 final size:6
Alignment explanation
Indices: 41082045--41082078 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41082035 GTAGGTTTCC
* *
41082045 AAAATG AAAATG GAAATG GAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
41082079 CGATTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:41082253 original size:26 final size:26
Alignment explanation
Indices: 41082224--41082300 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
41082214 AACATATTTC
*
41082224 TCAAAATTTTAATAGGGGTAAAATTA
1 TCAAAATTTTACTAGGGGTAAAATTA
* * *
41082250 TCAAAAAATTTACCAGGGGTAAAATTG
1 TC-AAAATTTTACTAGGGGTAAAATTA
*
41082277 TTAAAATTTTACT-GAGGGTAAAAT
1 TCAAAATTTTACTAG-GGGTAAAAT
41082301 AGAGATGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 20 0.48
27 21 0.50
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATTA
Found at i:41087815 original size:24 final size:24
Alignment explanation
Indices: 41087787--41087835 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41087777 TATCTTGAAA
41087787 AGAAGATAAAGTAAACGGACTGAC
1 AGAAGATAAAGTAAACGGACTGAC
41087811 AGAAGATAAAGTAAACGGACTGAC
1 AGAAGATAAAGTAAACGGACTGAC
41087835 A
1 A
41087836 TTTTTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (24 bp):
AGAAGATAAAGTAAACGGACTGAC
Found at i:41089036 original size:47 final size:47
Alignment explanation
Indices: 41088982--41089076 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
41088972 TAGTGCCTAG
* * *
41088982 TGATTGAAATAAAAACTTCTAAATAGTTGAGTGACTTGATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
*
41089029 TGATTGAAATAAAAACTTCTAAATAATTTAGTGAATTAATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
41089076 T
1 T
41089077 TCGAATAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (47 bp):
TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
Found at i:41094581 original size:17 final size:17
Alignment explanation
Indices: 41094559--41094645 Score: 59
Period size: 17 Copynumber: 4.8 Consensus size: 17
41094549 ATATATAGAG
41094559 AGAGAAAAGAAAGAAAA
1 AGAGAAAAGAAAGAAAA
* *
41094576 AGAGAAATGAAACGAACA
1 AGAGAAAAGAAA-GAAAA
* * *
41094594 TGA-AAAATATAATATATAGA
1 AGAGAAAAGA-AAGA-A-A-A
41094614 GAGAGAAAAGAAAGAAAA
1 -AGAGAAAAGAAAGAAAA
*
41094632 AGAGAAATGAAAGA
1 AGAGAAAAGAAAGA
41094646 GATGAAATCA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
17 29 0.56
18 10 0.19
19 1 0.02
20 2 0.04
21 5 0.10
22 5 0.10
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (17 bp):
AGAGAAAAGAAAGAAAA
Found at i:41094652 original size:54 final size:56
Alignment explanation
Indices: 41094529--41094643 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
41094519 ATAAACTATA
41094529 AAACGAACATGAAAAATATAATATATAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
1 AAACGAACATGAAAAATATAATATATAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
41094585 AAACGAACATGAAAAATATAATATATAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
1 AAACGAACATGAAAAATATAATATATAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
41094641 AAA
1 AAA
41094644 GAGATGAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.65, C:0.03, G:0.19, T:0.12
Consensus pattern (56 bp):
AAACGAACATGAAAAATATAATATATAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
Found at i:41099685 original size:41 final size:41
Alignment explanation
Indices: 41099628--41099709 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
41099618 AAAATGGTGT
41099628 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
1 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
41099669 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
1 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
41099710 CACTTTTGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
Found at i:41103482 original size:18 final size:17
Alignment explanation
Indices: 41103449--41103482 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41103439 GCAATTAATA
*
41103449 TAAAAAATAAAGATATT
1 TAAAAAATAAAAATATT
41103466 TAAAAAATATAAAATAT
1 TAAAAAATA-AAAATAT
41103483 AGCCTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAATAAAAATATT
Found at i:41110021 original size:17 final size:18
Alignment explanation
Indices: 41109989--41110022 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41109979 AGTCAACAAA
*
41109989 ATAATAACAGTAAAATAC
1 ATAATAACAATAAAATAC
41110007 ATAATAA-AATAAAATA
1 ATAATAACAATAAAATA
41110023 AAACATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAATAACAATAAAATAC
Found at i:41110207 original size:3 final size:3
Alignment explanation
Indices: 41110199--41110261 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
41110189 TAAAAATGGA
** *
41110199 AAT AAT AAT AAT AAT GGT AAT AAT AAC AAT -AT AAT AA- AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
41110243 -AT AAT AAT AAAT AA- AAT AA
1 AAT AAT AAT -AAT AAT AAT AA
41110262 ACAAAAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.17
3 35 0.73
4 5 0.10
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41110214 original size:18 final size:18
Alignment explanation
Indices: 41110187--41110229 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41110177 AACTTAGCAG
*
41110187 AATAAAAATGGAAATAAT
1 AATAATAATGGAAATAAT
*
41110205 AATAATAATGGTAATAAT
1 AATAATAATGGAAATAAT
*
41110223 AACAATA
1 AATAATA
41110230 TAATAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (18 bp):
AATAATAATGGAAATAAT
Found at i:41111942 original size:29 final size:30
Alignment explanation
Indices: 41111883--41111940 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41111873 TCCGAGCCTT
*
41111883 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
41111913 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
41111941 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:41112170 original size:13 final size:13
Alignment explanation
Indices: 41112152--41112183 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41112142 TTTCCAGCAA
41112152 TTATGAATTTATT
1 TTATGAATTTATT
41112165 TTATGAATTTATT
1 TTATGAATTTATT
*
41112178 TGATGA
1 TTATGA
41112184 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41112391 original size:50 final size:50
Alignment explanation
Indices: 41112278--41112519 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
41112268 ATTTGGGTAA
* * *
41112278 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
41112334 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41112384 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41112434 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
41112484 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41112520 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:41112467 original size:100 final size:103
Alignment explanation
Indices: 41112278--41112527 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
41112268 ATTTGGGTAA
41112278 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
41112343 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
41112384 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
41112446 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
41112484 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41112528 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:41119532 original size:29 final size:30
Alignment explanation
Indices: 41119473--41119530 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41119463 TCCGAGCCTT
*
41119473 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
41119503 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
41119531 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:41119760 original size:13 final size:13
Alignment explanation
Indices: 41119742--41119773 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41119732 TTTCCAGCAA
41119742 TTATGAATTTATT
1 TTATGAATTTATT
41119755 TTATGAATTTATT
1 TTATGAATTTATT
*
41119768 TGATGA
1 TTATGA
41119774 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:41119981 original size:50 final size:50
Alignment explanation
Indices: 41119868--41120109 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
41119858 ATTTGGGTAA
* * *
41119868 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
41119924 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41119974 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
41120024 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
41120074 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
41120110 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:41120057 original size:100 final size:103
Alignment explanation
Indices: 41119868--41120117 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
41119858 ATTTGGGTAA
41119868 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
41119933 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
41119974 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
41120036 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
41120074 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41120118 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:41134838 original size:19 final size:19
Alignment explanation
Indices: 41134814--41134854 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
41134804 CCCCCTTTTT
* *
41134814 TTTATTTTAATGCAATTTA
1 TTTATTTTAATACAATATA
*
41134833 TTTATTTTTATACAATATA
1 TTTATTTTAATACAATATA
41134852 TTT
1 TTT
41134855 TTTCTTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATTTTAATACAATATA
Found at i:41144801 original size:227 final size:227
Alignment explanation
Indices: 41144398--41144843 Score: 741
Period size: 227 Copynumber: 2.0 Consensus size: 227
41144388 TCATTGGTTG
*
41144398 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGGTGGAATACATTAACT
1 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
* * *
41144463 TTTGTTGTGCCAAAAGAGAGGATTGCTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATATAT
66 TCTGTTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATACAT
* * * *
41144528 CAGTCAGAGGTTTCTCGACCAGAAACGTAAAGAATTTTTAGAGCTTAAATAGGGTCATATGACAA
131 CAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACAA
*
41144593 TGTCCGAATATGAATTAGAATTTGTTCGGCTA
196 TGTCCGAATATGAACTAGAATTTGTTCGGCTA
* *
41144625 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAATATTCAGCTTACCAGTGATGGAATACATTAACT
1 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
* * *
41144690 TCTGTTGTGCCGAAAGAGAGGATTACTTGGGAATTCTTTCAAATTGAG-TTCTGAAAGAAATACA
66 TCTGTTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTC-AAAAGAAATACA
*
41144754 TCAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTGGAGCTTAAACAGGGTCATATGACA
130 TCAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACA
41144819 ATGTCCGAATATGAACTAGAATTTG
195 ATGTCCGAATATGAACTAGAATTTG
41144844 CTCGATTGAG
Statistics
Matches: 203, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
226 3 0.01
227 200 0.99
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (227 bp):
AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
TCTGTTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATACAT
CAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACAA
TGTCCGAATATGAACTAGAATTTGTTCGGCTA
Found at i:41149689 original size:25 final size:24
Alignment explanation
Indices: 41149661--41149741 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
41149651 GACACACCAC
*
41149661 AGCTCGTATGAGCTTCCCATTATAT
1 AGCTCGCATGAGCTTCCCATTAT-T
*
41149686 AGCTCACATGAGCTT-CCAGTTACTT
1 AGCTCGCATGAGCTTCCCA-TTA-TT
* *
41149711 AGCTCGCATAAGCTTCCCTTTATT
1 AGCTCGCATGAGCTTCCCATTATT
41149735 CAGCTCG
1 -AGCTCG
41149742 GAGAAGCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 5 0.11
25 39 0.83
26 3 0.06
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.33
Consensus pattern (24 bp):
AGCTCGCATGAGCTTCCCATTATT
Found at i:41156546 original size:24 final size:21
Alignment explanation
Indices: 41156493--41156536 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41156483 ATATGGTCTT
41156493 TTGTTTTGCATGAGGCACATG
1 TTGTTTTGCATGAGGCACATG
41156514 TTGTTTTGCATGAGGCACATG
1 TTGTTTTGCATGAGGCACATG
41156535 TT
1 TT
41156537 CTTGTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (21 bp):
TTGTTTTGCATGAGGCACATG
Found at i:41158667 original size:14 final size:14
Alignment explanation
Indices: 41158650--41158678 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41158640 TATAATACTA
41158650 GTTTTATGTCATGT
1 GTTTTATGTCATGT
41158664 GTTTTATGTCATGT
1 GTTTTATGTCATGT
41158678 G
1 G
41158679 CTCAGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (14 bp):
GTTTTATGTCATGT
Found at i:41159860 original size:22 final size:23
Alignment explanation
Indices: 41159834--41159882 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
41159824 AAATATAAAC
41159834 TTTATTATTCTATTATTA-ATTA
1 TTTATTATTCTATTATTACATTA
* *
41159856 TTTATTTTTGTATTATTACTATTA
1 TTTATTATTCTATTATTAC-ATTA
41159880 TTT
1 TTT
41159883 TGTCTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
24 7 0.30
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTATTCTATTATTACATTA
Found at i:41160303 original size:30 final size:30
Alignment explanation
Indices: 41160240--41160303 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
41160230 AGTCTATATC
** *
41160240 TTTATAATTTTTAAAGGGTTAAATCAAATT
1 TTTATAATTTTTAAAGGGCCAAATCAAAAT
*
41160270 TTTATAATTTTTAGAGGGCCAAAGT-AAAAT
1 TTTATAATTTTTAAAGGGCCAAA-TCAAAAT
41160300 TTTA
1 TTTA
41160304 CCTTCACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGGCCAAATCAAAAT
Found at i:41163372 original size:32 final size:32
Alignment explanation
Indices: 41163307--41163382 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
41163297 CATAGAGGGA
*
41163307 TTAATTAATTTTT--TATTATTTTATAAGGAC
1 TTAATTAATTTTTAAAATTATTTTATAAGGAC
* *
41163337 TTAATTGATTTTTAAAATTATTTTA-AGAGGTC
1 TTAATTAATTTTTAAAATTATTTTATA-AGGAC
41163369 TTAATTAATTTTTA
1 TTAATTAATTTTTA
41163383 GGGATTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.31
31 1 0.03
32 26 0.67
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (32 bp):
TTAATTAATTTTTAAAATTATTTTATAAGGAC
Found at i:41163958 original size:19 final size:20
Alignment explanation
Indices: 41163912--41163960 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
41163902 TAATATTTTC
41163912 ATTTTTAATAACATATTAATA
1 ATTTTT-ATAACATATTAATA
*
41163933 ATATTTTATAATAT-TTAATA
1 AT-TTTTATAACATATTAATA
*
41163953 GTTTTTAT
1 ATTTTTAT
41163961 TTTTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 7 0.28
21 8 0.32
22 4 0.16
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTTTTATAACATATTAATA
Found at i:41164032 original size:20 final size:19
Alignment explanation
Indices: 41164009--41164049 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41163999 ATTTTAAAAT
41164009 AATTTAAAAAATTAATTAAA
1 AATTTAAAAAA-TAATTAAA
**
41164029 AATTTGTAAAATAATTAAA
1 AATTTAAAAAATAATTAAA
41164048 AA
1 AA
41164050 AATCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTTAAAAAATAATTAAA
Found at i:41164324 original size:20 final size:20
Alignment explanation
Indices: 41164301--41164345 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41164291 ATTTAGTTAT
*
41164301 TAAAATGATAATTTTATAAA
1 TAAAATGATAATATTATAAA
*
41164321 TAAAATTATAATATTATAAA
1 TAAAATGATAATATTATAAA
41164341 TAAAA
1 TAAAA
41164346 CAATTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAATGATAATATTATAAA
Found at i:41164848 original size:15 final size:14
Alignment explanation
Indices: 41164821--41164860 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
41164811 GTTTGTGGGT
41164821 TTTTAAAAA-ATTA
1 TTTTAAAAATATTA
41164834 TTTATAAAAATATTA
1 TTT-TAAAAATATTA
41164849 TTTTAATAAATA
1 TTTTAA-AAATA
41164861 AACTTCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTAAAAATATTA
Found at i:41170401 original size:17 final size:18
Alignment explanation
Indices: 41170369--41170416 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
41170359 ATTAAAAATA
*
41170369 AAAATTTTAAAAATATGG
1 AAAATTTTAAAAATATAG
*
41170387 AAAATTTT-CAAATATAG
1 AAAATTTTAAAAATATAG
41170404 AAAATTATTAAAA
1 AAAATT-TTAAAA
41170417 TTATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 13 0.52
18 10 0.40
19 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAAATATAG
Found at i:41170436 original size:9 final size:9
Alignment explanation
Indices: 41170404--41170437 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
41170394 TCAAATATAG
41170404 AAAATTATT
1 AAAATTATT
41170413 AAAATTATT
1 AAAATTATT
*
41170422 AAAAATATAT
1 AAAATTAT-T
41170432 AAAATT
1 AAAATT
41170438 GTAAATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATTATT
Found at i:41170538 original size:20 final size:21
Alignment explanation
Indices: 41170510--41170558 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
41170500 CAAAGTAACT
*
41170510 CAAATAAATAATA-AAAAATA
1 CAAAAAAATAATATAAAAATA
* *
41170530 CAAAAAAATGATATAAAATTA
1 CAAAAAAATAATATAAAAATA
41170551 CAAAAAAA
1 CAAAAAAA
41170559 AAAATTACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
CAAAAAAATAATATAAAAATA
Found at i:41170906 original size:18 final size:19
Alignment explanation
Indices: 41170885--41170954 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
41170875 ATTCATGTAA
41170885 TTTTATA-ATTTTTTACAC
1 TTTTATATATTTTTTACAC
* * * *
41170903 TTTTTTATATTTTATAATAT
1 TTTTATATATTTT-TTACAC
*
41170923 TTTTA-AT-TATTTTTGCAC
1 TTTTATATAT-TTTTTACAC
41170941 TTTTATATATTTTT
1 TTTTATATATTTTT
41170955 ATAGTTTTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
18 14 0.37
19 16 0.42
20 8 0.21
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTATATATTTTTTACAC
Found at i:41170989 original size:27 final size:27
Alignment explanation
Indices: 41170880--41170990 Score: 77
Period size: 27 Copynumber: 4.0 Consensus size: 27
41170870 TCATAATTCA
*
41170880 TGTAATTTTATAAT-TTTTTACACTTTTT
1 TGTAA-TTTATAATATTTTTATA-TTTTT
* *
41170908 TATATTTTATAATATTTTTA-ATTATTTT
1 TGTAATTTATAATATTTTTATA-T-TTTT
* * *
41170936 TGCACTTT-TATATATTTTTATAGTTTT
1 TGTAATTTATA-ATATTTTTATATTTTT
*
41170963 TGTAATTTGTAAT-TTTTTATTATTTTT
1 TGTAATTTATAATATTTTTA-TATTTTT
41170990 T
1 T
41170991 AAAATATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
26 6 0.09
27 31 0.46
28 29 0.43
29 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.67
Consensus pattern (27 bp):
TGTAATTTATAATATTTTTATATTTTT
Found at i:41177718 original size:16 final size:16
Alignment explanation
Indices: 41177697--41177737 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41177687 GATAATGAAT
*
41177697 TTTAATTTTT-TTTATA
1 TTTAATTTTTATTT-GA
41177713 TTTAATTTTTATTTGA
1 TTTAATTTTTATTTGA
41177729 TTTAATTTT
1 TTTAATTTT
41177738 CACAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTAATTTTTATTTGA
Found at i:41186108 original size:45 final size:45
Alignment explanation
Indices: 41186031--41186146 Score: 108
Period size: 45 Copynumber: 2.6 Consensus size: 45
41186021 GTGCTTTCAT
* * ** *
41186031 ATGATACCATAGCATCTTTCA-ATCATGGTCTTACTAATTCCCGTC
1 ATGATGCCATAGCATCTTTCAGCT-ATAATCTTACTAATTCCCATC
* * * ***
41186076 ATGATGCTATAGCGTCTTTCAGCTATAATCTTACTCATTTTTATC
1 ATGATGCCATAGCATCTTTCAGCTATAATCTTACTAATTCCCATC
*
41186121 CTGATGCCATAGCATCTTTCAGCTAT
1 ATGATGCCATAGCATCTTTCAGCTAT
41186147 GGTTTTGCTC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (45 bp):
ATGATGCCATAGCATCTTTCAGCTATAATCTTACTAATTCCCATC
Found at i:41189325 original size:85 final size:84
Alignment explanation
Indices: 41189222--41189380 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 84
41189212 GAAATTAAAA
* * * * *
41189222 TTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGATTAACAAGATTTTATTCGATTTTAATTTT
1 TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAAAAAGATTTTATTCAATATTAA-TTT
41189287 ATTTCCAAATTAGAATTAAT
65 ATTTCCAAATTAGAATTAAT
* * * *
41189307 TTAAATAAAATCTATTTCGAGATTTATTCTCGTCGTTTAAAAAGATTTTATTCAATATTAATTTG
1 TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAAAAAGATTTTATTCAATATTAATTTA
41189372 TTTCCAAAT
66 TTTCCAAAT
41189381 GAAGACTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 12 0.18
85 53 0.82
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (84 bp):
TTAAATAAAATCTATTTCGAGATTTATTCCCGCCGATTAAAAAGATTTTATTCAATATTAATTTA
TTTCCAAATTAGAATTAAT
Found at i:41194313 original size:14 final size:14
Alignment explanation
Indices: 41194292--41194328 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
41194282 TAAATCATTC
41194292 TATTTATATA-TTT
1 TATTTATATATTTT
41194305 TATTTTATATATTTT
1 TA-TTTATATATTTT
41194320 TATTTATAT
1 TATTTATAT
41194329 TTATTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.68
15 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:41194315 original size:16 final size:15
Alignment explanation
Indices: 41194296--41194333 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
41194286 TCATTCTATT
41194296 TATATATTTTATTT-
1 TATATATTTTATTTA
41194310 TATATATTTTTATTTA
1 TATATA-TTTTATTTA
*
41194326 TATTTATT
1 TATATATT
41194334 CATTTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 10 0.48
16 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATATATTTTATTTA
Found at i:41198299 original size:104 final size:104
Alignment explanation
Indices: 41198119--41198328 Score: 420
Period size: 104 Copynumber: 2.0 Consensus size: 104
41198109 TGTAGATTAG
41198119 GCAACAAGTATGTGGTTGACCTCCTCAACTGCTCCTGTTCATGTAGAAAATGGGATTTGTCAGGA
1 GCAACAAGTATGTGGTTGACCTCCTCAACTGCTCCTGTTCATGTAGAAAATGGGATTTGTCAGGA
41198184 ATCCCATGTAAGCATGCTGTTTCTTGCATGCAATTACTT
66 ATCCCATGTAAGCATGCTGTTTCTTGCATGCAATTACTT
41198223 GCAACAAGTATGTGGTTGACCTCCTCAACTGCTCCTGTTCATGTAGAAAATGGGATTTGTCAGGA
1 GCAACAAGTATGTGGTTGACCTCCTCAACTGCTCCTGTTCATGTAGAAAATGGGATTTGTCAGGA
41198288 ATCCCATGTAAGCATGCTGTTTCTTGCATGCAATTACTT
66 ATCCCATGTAAGCATGCTGTTTCTTGCATGCAATTACTT
41198327 GC
1 GC
41198329 TGTGAGCCCT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (104 bp):
GCAACAAGTATGTGGTTGACCTCCTCAACTGCTCCTGTTCATGTAGAAAATGGGATTTGTCAGGA
ATCCCATGTAAGCATGCTGTTTCTTGCATGCAATTACTT
Found at i:41203500 original size:2 final size:2
Alignment explanation
Indices: 41203495--41203554 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
41203485 AAAAAAAGAA
41203495 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41203537 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
41203555 GGGCAAAGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41204489 original size:21 final size:21
Alignment explanation
Indices: 41204449--41204489 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41204439 AAACAAATCA
*
41204449 ATAATAATTTTTATTTTTTGT
1 ATAATAATTTTTATTATTTGT
41204470 ATAA-AATTTTTATTAATTTG
1 ATAATAATTTTTATT-ATTTG
41204490 AACTACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATAATAATTTTTATTATTTGT
Found at i:41205050 original size:3 final size:3
Alignment explanation
Indices: 41205042--41205067 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41205032 TTTGAAATAT
41205042 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41205068 TTACAAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41211139 original size:90 final size:90
Alignment explanation
Indices: 41210899--41211142 Score: 317
Period size: 90 Copynumber: 2.7 Consensus size: 90
41210889 CGTCCATAGA
* *
41210899 TTTCTGACAGCTCTTATCTGCAAATATGTTATGCATTCACAACCATCTGGCAGCGTATTAACCTG
1 TTTCTGGCAGCTCTTATATGCAAATATGTTATGCATTCACAACCATCTGGCAGCGTATTAACCTG
*
41210964 CAACACTGGTGGTTCATCAACCCAT
66 CAACACTGGTGGTTCACCAACCCAT
* * * * * * * *
41210989 TTTTTTGCAGCTCTTATGTGTAAATATGTTCTGCATTCACAACCATCTGACAACGTATTAATCTG
1 TTTCTGGCAGCTCTTATATGCAAATATGTTATGCATTCACAACCATCTGGCAGCGTATTAACCTG
* *
41211054 CAACACTGGTGGTTCACCCATCCAT
66 CAACACTGGTGGTTCACCAACCCAT
* * * * * *
41211079 TTTCTGGCAGCTCTCATATACAAATATGTTGTGCATTCACAACCGTTTGGCAGCGAATTAACCT
1 TTTCTGGCAGCTCTTATATGCAAATATGTTATGCATTCACAACCATCTGGCAGCGTATTAACCT
41211143 ACAAAATTTT
Statistics
Matches: 129, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 129 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (90 bp):
TTTCTGGCAGCTCTTATATGCAAATATGTTATGCATTCACAACCATCTGGCAGCGTATTAACCTG
CAACACTGGTGGTTCACCAACCCAT
Found at i:41212002 original size:21 final size:21
Alignment explanation
Indices: 41211976--41212023 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41211966 TGAGACAAGA
*
41211976 CACATGGTCGTGT-GAGTGGGT
1 CACATGGTCATGTGGA-TGGGT
*
41211997 CACATGGTCATGTGGATTGGT
1 CACATGGTCATGTGGATGGGT
41212018 CACATG
1 CACATG
41212024 ACCGTGTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (21 bp):
CACATGGTCATGTGGATGGGT
Found at i:41214202 original size:14 final size:14
Alignment explanation
Indices: 41214180--41214219 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
41214170 CATTGATCTA
41214180 TAAAATAATTAAAT
1 TAAAATAATTAAAT
*
41214194 TAAATTAATTAAAT
1 TAAAATAATTAAAT
41214208 TAAAATATATTA
1 TAAAATA-ATTA
41214220 TCATATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATAATTAAAT
Found at i:41215913 original size:17 final size:18
Alignment explanation
Indices: 41215880--41215913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41215870 TACTTCTTAT
41215880 GTATACAAAACTTAAGTA
1 GTATACAAAACTTAAGTA
*
41215898 GTATATAAAA-TTAAGT
1 GTATACAAAACTTAAGT
41215914 TTTGTCTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (18 bp):
GTATACAAAACTTAAGTA
Found at i:41216654 original size:16 final size:18
Alignment explanation
Indices: 41216625--41216669 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
41216615 TAAAAATTAT
41216625 AAATTAA-A-TTTTATT-
1 AAATTAATATTTTTATTC
41216640 AAA-TAATATTTTTATTC
1 AAATTAATATTTTTATTC
41216657 AAATTAATATTTT
1 AAATTAATATTTT
41216670 GAAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 7 0.27
17 3 0.12
18 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTAATATTTTTATTC
Found at i:41217793 original size:17 final size:16
Alignment explanation
Indices: 41217767--41217798 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41217757 GTGCTTTTCT
41217767 AAAACACTTCTGAAAG
1 AAAACACTTCTGAAAG
41217783 AAAAGCACTTCTGAAA
1 AAAA-CACTTCTGAAA
41217799 AGGAGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAACACTTCTGAAAG
Found at i:41218284 original size:13 final size:13
Alignment explanation
Indices: 41218268--41218320 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
41218258 TTTAAACCAA
41218268 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
41218281 ACTTTTCCACAAC
1 ACTTTTCAAAAAC
*
41218294 ACTTTTCAAAAAT
1 ACTTTTCAAAAAC
41218307 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
41218320 A
1 A
41218321 ATGAAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:41221995 original size:46 final size:45
Alignment explanation
Indices: 41221928--41222299 Score: 460
Period size: 46 Copynumber: 8.6 Consensus size: 45
41221918 TTTGAGTACT
*
41221928 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
41221974 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
41222020 TCTGATCAAGTGAAAAAGTGATAA---GT-G--T---TACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
41222056 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
41222102 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
41222138 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
41222184 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
41222230 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
41222275 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
41222300 ATCATATGTA
Statistics
Matches: 289, Mismatches: 17, Indels: 43
0.83 0.05 0.12
Matches are distributed among these distances:
36 57 0.20
38 1 0.00
39 4 0.01
40 4 0.01
41 1 0.00
42 5 0.02
43 17 0.06
44 6 0.02
45 19 0.07
46 175 0.61
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:41222058 original size:36 final size:36
Alignment explanation
Indices: 41222012--41222167 Score: 168
Period size: 36 Copynumber: 4.1 Consensus size: 36
41222002 TAGCATTAGC
41222012 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* * *
41222048 TACATTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAA---GT-G---T
*
41222091 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
1 ---TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
* *
41222130 TATACTTATCTGATCAAGTGACAAAGTGATAAGTGT
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
41222166 TA
1 TA
41222168 GCCTTAGCTA
Statistics
Matches: 100, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
36 64 0.64
39 2 0.02
40 1 0.01
42 1 0.01
43 3 0.03
46 29 0.29
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGT
Found at i:41222064 original size:82 final size:81
Alignment explanation
Indices: 41221966--41222299 Score: 447
Period size: 82 Copynumber: 4.0 Consensus size: 81
41221956 TAGCATTAGC
*
41221966 TACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGT
41222031 GAAAAAGTGATAAGTGT
65 GAAAAAGTGATAAGTGT
* *
41222048 TACATTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGT
*
41222113 GAAAAAGTGATAAGTGC
65 GAAAAAGTGATAAGTGT
* *
41222130 TATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGT
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGT
*
41222195 GAGAAAGTGATAAGTGGTAGCCT
65 GAAAAAGTGATAA---GT-G--T
*
41222218 TAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-
1 TA-C-A--CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCA
* *
41222282 AG-GGACAAGTGATAAGTG
62 AGTGAAAAAGTGATAAGTG
41222300 ATCATATGTA
Statistics
Matches: 224, Mismatches: 17, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
82 148 0.66
83 1 0.00
85 3 0.01
86 3 0.01
88 2 0.01
89 10 0.04
90 3 0.01
91 20 0.09
92 34 0.15
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (81 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTG
AAAAAGTGATAAGTGT
Found at i:41222292 original size:128 final size:126
Alignment explanation
Indices: 41221928--41222299 Score: 431
Period size: 128 Copynumber: 2.9 Consensus size: 126
41221918 TTTGAGTACT
* *
41221928 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
* * *
41221993 GATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTACATTTA
66 GATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GGAAAAGTGATAAGTGCTACACTTA
* *
41222056 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
41222121 GATAA---GT-GC-TA--T--ACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCT
66 GATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGA-AAAGTGAT-A-----AG---T-GCT
41222177 ACACTTA
120 ACACTTA
* * * *
41222184 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACTCTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
41222249 GATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGACAAGTGATAAGTG
66 GATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGATAAGTG
41222300 ATCATATGTA
Statistics
Matches: 209, Mismatches: 15, Indels: 43
0.78 0.06 0.16
Matches are distributed among these distances:
117 1 0.00
118 23 0.11
119 1 0.00
120 1 0.00
122 2 0.01
124 4 0.02
125 3 0.01
126 1 0.00
127 1 0.00
128 139 0.67
129 2 0.01
131 2 0.01
132 2 0.01
133 2 0.01
134 1 0.00
135 8 0.04
136 4 0.02
137 12 0.06
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (126 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGATAAGTGCTACACTTA
Found at i:41225229 original size:19 final size:20
Alignment explanation
Indices: 41225201--41225239 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
41225191 GCTCATTTCA
*
41225201 ATGCATATTTCGT-AAAACG
1 ATGCAGATTTCGTGAAAACG
*
41225220 ATGCAGATTTTGTGAAAACG
1 ATGCAGATTTCGTGAAAACG
41225240 GTCTTACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGCAGATTTCGTGAAAACG
Found at i:41238966 original size:37 final size:37
Alignment explanation
Indices: 41238913--41238988 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
41238903 AGATTATCAC
*
41238913 TTTAATATTAAATTAATA-AAATACTATTAAGATAAGTA
1 TTTAATATTAAATTAATATAAA-ACTATTAAAATAA-TA
* *
41238951 TTTAAT-TTAATTTAATATTAAACTATTAAAATAATA
1 TTTAATATTAAATTAATATAAAACTATTAAAATAATA
41238987 TT
1 TT
41238989 ATTTCTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.12
37 22 0.65
38 8 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTAATATTAAATTAATATAAAACTATTAAAATAATA
Found at i:41240623 original size:16 final size:16
Alignment explanation
Indices: 41240602--41240632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41240592 CTATGAGTGC
*
41240602 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
41240618 AAAATACAAAAGACA
1 AAAATACAAAAGACA
41240633 TAATAATGAA
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:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:41241879 original size:23 final size:24
Alignment explanation
Indices: 41241803--41241878 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
41241793 TTATAAGATT
* ***
41241803 AAAAAATTTAGTAATCAAT-CCCC
1 AAAAAATTTATTAATCAATATATC
* *
41241826 AAAAAAATTGTTAATCAATATATC
1 AAAAAATTTATTAATCAATATATC
*
41241850 AAAAAATTTATTAATCAATATATG
1 AAAAAATTTATTAATCAATATATC
41241874 AAAAA
1 AAAAA
41241879 TTGATTTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 16 0.37
24 27 0.63
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAAATTTATTAATCAATATATC
Found at i:41244954 original size:22 final size:22
Alignment explanation
Indices: 41244929--41245020 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
41244919 AAATTCAATA
* *
41244929 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
41244951 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
*
41244973 TCAATTCCCTTCAAAATTTC-C
1 TCAATTCCCTTCAAAAATTCTC
* *
41244994 ATCAATTTCCTTCCAAAATTCTC
1 -TCAATTCCCTTCAAAAATTCTC
41245017 TCAA
1 TCAA
41245021 ACTATCAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.02
22 60 0.97
23 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:41244986 original size:44 final size:44
Alignment explanation
Indices: 41244929--41245020 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
41244919 AAATTCAATA
* * *
41244929 TCAATTTCTTTCAAAAATTCTC-TCAA-TTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTC-CATCAATTTCCTTCCAAAA-TTCTC
*
41244973 TCAATTCCCTTCAAAATTTCCATCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
41245017 TCAA
1 TCAA
41245021 ACTATCAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (44 bp):
TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
Found at i:41245034 original size:30 final size:30
Alignment explanation
Indices: 41244994--41245050 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
41244984 CAAAATTTCC
* *
41244994 ATCAATTTCCTTCCAAAATTCTCTCAAACT
1 ATCAAATTCCTTCCAAAATCCTCTCAAACT
41245024 ATCAAATTCCTTCCAAAATCCTCTCAA
1 ATCAAATTCCTTCCAAAATCCTCTCAA
41245051 TTTCCTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.33
Consensus pattern (30 bp):
ATCAAATTCCTTCCAAAATCCTCTCAAACT
Done.