Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 35 of 153
Found at i:12084829 original size:18 final size:18
Alignment explanation
Indices: 12084808--12084847 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12084798 GAAATATTTA
*
12084808 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
12084826 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
12084844 TTTT
1 TTTT
12084848 TAAAATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:12085335 original size:24 final size:23
Alignment explanation
Indices: 12085308--12085358 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
12085298 ATTTTTACTG
12085308 TTAACAAAATTAATCTATTTATCT
1 TTAACAAAATTAATCTATTTAT-T
* *
12085332 TTAATAATATTAATCTATTTATT
1 TTAACAAAATTAATCTATTTATT
12085355 TTAA
1 TTAA
12085359 ATTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAACAAAATTAATCTATTTATT
Found at i:12085421 original size:21 final size:22
Alignment explanation
Indices: 12085397--12085446 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
12085387 ATCGAAAATA
*
12085397 AATTTAAAATA-T-TTTATATGT
1 AATTTAAAATAGTATTTA-AAGT
*
12085418 AATTTTAAATAGTATTTAAAGT
1 AATTTAAAATAGTATTTAAAGT
12085440 AATTTAA
1 AATTTAA
12085447 TATTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 10 0.42
23 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
AATTTAAAATAGTATTTAAAGT
Found at i:12085867 original size:21 final size:21
Alignment explanation
Indices: 12085841--12085895 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
12085831 AATAGCAGTG
*
12085841 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
12085862 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
12085883 GCGGTGAGATTAG
1 GCGGTGAGATTAG
12085896 AAACAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:12086209 original size:22 final size:22
Alignment explanation
Indices: 12086158--12086209 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
12086148 TTTTATAGTT
*
12086158 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
12086181 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
12086203 ATAATAA
1 ATAATAA
12086210 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:12089563 original size:64 final size:64
Alignment explanation
Indices: 12089462--12089608 Score: 285
Period size: 64 Copynumber: 2.3 Consensus size: 64
12089452 ATGTTATATT
12089462 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
*
12089526 AGTTCGAATCCTTTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
12089590 AGTTCGAATCCTCTAATTT
1 AGTTCGAATCCTCTAATTT
12089609 AAATACTATA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (64 bp):
AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
Found at i:12090261 original size:15 final size:15
Alignment explanation
Indices: 12090241--12090272 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12090231 TGTAAGTTTC
12090241 TTAGAAATAAAATGA
1 TTAGAAATAAAATGA
*
12090256 TTAGAAATAAGATGA
1 TTAGAAATAAAATGA
12090271 TT
1 TT
12090273 GGGGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
TTAGAAATAAAATGA
Found at i:12090955 original size:379 final size:379
Alignment explanation
Indices: 12090256--12091000 Score: 1481
Period size: 379 Copynumber: 2.0 Consensus size: 379
12090246 AATAAAATGA
12090256 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
12090321 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
12090386 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
12090451 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
12090516 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
*
12090581 CAATTGTGTGTTCATCTCTTGTTTTCATTATAATTTATTGCATTTGTAAGTTTC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
12090635 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
1 TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
12090700 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
66 GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
12090765 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
131 GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
12090830 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
196 TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
12090895 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
261 TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
12090960 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
326 CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGC
12091001 TATTGAATGC
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
379 365 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (379 bp):
TTAGAAATAAGATGATTGGGGAAATTTGGGTCAAAATTGAGGAAAAAGCAGTGAAGATAATCCTG
GGAAGTGAATGGGAAACTTCCCAATCCAGGTGTTGAATGCAACAGTTTTTTCCTTTGAAATGAAC
GACCGAAAGAGTGAGCTCTTTTTTTTCCTTCTTGTTGTTGATTTAATTTGTGCTTTCTTTGCTTC
TTTTCATTTGGTTAACGAATCTCTGAATCTTTTCATTTGATTTAATTTGTGCTTTCTTCGCTTTT
TTTCATTTGGTTTGATTTATCCTCTCCCTCTCTCTTTGTCTCACACATATGCACATCAACAGACG
CAATTGTGTGTTCATCTCTTGTTCTCATTATAATTTATTGCATTTGTAAGTTTC
Found at i:12093324 original size:21 final size:21
Alignment explanation
Indices: 12093298--12093341 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12093288 AAATAGAGCT
12093298 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
12093319 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
12093340 TC
1 TC
12093342 AATTGAAGAG
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:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (21 bp):
TCTTTGAGTCTGCTGTGAGTG
Found at i:12095372 original size:30 final size:31
Alignment explanation
Indices: 12095325--12095391 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
12095315 TGGTATCTTA
12095325 TTTTAATTTCTTCAATTTCAATCATT-TACT
1 TTTTAATTTCTTCAATTTCAATCATTATACT
* * * *
12095355 TTTTAATTTGGTT-AATTTTAATCTTTATATT
1 TTTTAATTT-CTTCAATTTCAATCATTATACT
12095386 TTTTAA
1 TTTTAA
12095392 AATTTAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTTAATTTCTTCAATTTCAATCATTATACT
Found at i:12096853 original size:19 final size:18
Alignment explanation
Indices: 12096829--12096865 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12096819 AGTGTTGGAT
*
12096829 ATAAAATAATAATAAAATA
1 ATAAAATAACAA-AAAATA
12096848 ATAAAATAACAAAAAATA
1 ATAAAATAACAAAAAATA
12096866 GGCAAAGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAATAACAAAAAATA
Found at i:12098498 original size:94 final size:94
Alignment explanation
Indices: 12098362--12098565 Score: 327
Period size: 94 Copynumber: 2.2 Consensus size: 94
12098352 CATTTCAACA
12098362 TTAAGGAGATAAGATTTGTTGTTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATAGAATAT
1 TTAAGGAGATAAGATTTGTTGTTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATAGAATAT
* * ** *
12098427 TTTTAGTTTCATTTTTTTTCACTGCATCC
66 TTGTAGCTTCATTTTGCTCCACTGCATCC
* * * *
12098456 TTAGGGAGATAAGATTTGTTGTTGTAGTTTCAATCCATTCTACTGCAATTTTAGGGATATAATAT
1 TTAAGGAGATAAGATTTGTTGTTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATAGAATAT
12098521 TTGTAGCTTCATTTTGCTCCACTGCATCC
66 TTGTAGCTTCATTTTGCTCCACTGCATCC
12098550 TTAAGGAGATAAGATT
1 TTAAGGAGATAAGATT
12098566 CGCCATGGTA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 100 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (94 bp):
TTAAGGAGATAAGATTTGTTGTTATAGTTTCAATCCATTCTACTGCAATTTCAGGGATAGAATAT
TTGTAGCTTCATTTTGCTCCACTGCATCC
Found at i:12098510 original size:50 final size:49
Alignment explanation
Indices: 12098366--12098524 Score: 143
Period size: 50 Copynumber: 3.3 Consensus size: 49
12098356 TCAACATTAA
*
12098366 GGAGATAAGATTTGTTGTTATAGTTTCAATCCATTCTACTGCAATTTCA-
1 GGAGATAAGATTTGTTGTT-TAGTTTCAATCCATTCTACTGCAATTTTAG
* * *** * *
12098415 GG-GAT-AGA-ATATT-TTTAGTTTC-ATTTTTTTTCACTGC-ATCCTTAG
1 GGAGATAAGATTTGTTGTTTAGTTTCAATCCATTCT-ACTGCAAT-TTTAG
12098460 GGAGATAAGATTTGTTGTTGTAGTTTCAATCCATTCTACTGCAATTTTAG
1 GGAGATAAGATTTGTTGTT-TAGTTTCAATCCATTCTACTGCAATTTTAG
* *
12098510 GGATATAATATTTGT
1 GGAGATAAGATTTGT
12098525 AGCTTCATTT
Statistics
Matches: 83, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
43 7 0.08
44 14 0.17
45 4 0.05
46 6 0.07
47 6 0.07
48 6 0.07
49 4 0.05
50 29 0.35
51 7 0.08
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (49 bp):
GGAGATAAGATTTGTTGTTTAGTTTCAATCCATTCTACTGCAATTTTAG
Found at i:12098714 original size:94 final size:93
Alignment explanation
Indices: 12098538--12098753 Score: 227
Period size: 94 Copynumber: 2.3 Consensus size: 93
12098528 TTCATTTTGC
* * * * * *
12098538 TCCACTGCATCCTTAAGGAGATAAGATTCGCCATGGTAGTTTCAATCTAACCCACTGTAACTTTA
1 TCCACTGCA-ACTTAAGGAGATAAGATTCACCATGATAATTTCAATCTAACCCACTGCAACTTCA
* * * * * *
12098603 TGGGTATTGGATTTGTATCTTT-ATCTTGT
65 AGGGTATAGGAATTGTATATTTAATC-CGA
* * * *
12098632 TCCACTGCAACTTCAGGAAGATAAGATTCACCATTATAATTTCATTCTGACCCACTGCAACTTCA
1 TCCACTGCAACTTAAGG-AGATAAGATTCACCATGATAATTTCAATCTAACCCACTGCAACTTCA
12098697 AGGGTATAGGAATTGTATATTTAATCCGA
65 AGGGTATAGGAATTGTATATTTAATCCGA
* *
12098726 TCCACTGCAACTTTAAGGATATAGGATT
1 TCCACTGCAAC-TTAAGGAGATAAGATT
12098754 TGTAGCTTCA
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
93 6 0.06
94 86 0.86
95 8 0.08
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (93 bp):
TCCACTGCAACTTAAGGAGATAAGATTCACCATGATAATTTCAATCTAACCCACTGCAACTTCAA
GGGTATAGGAATTGTATATTTAATCCGA
Found at i:12098749 original size:44 final size:43
Alignment explanation
Indices: 12098683--12099060 Score: 188
Period size: 44 Copynumber: 8.3 Consensus size: 43
12098673 TCATTCTGAC
*
12098683 CCACTGCAACTTCAAGGGTATAGGAATTGTATATTTAATCCGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTA-ATTTAATCCGAT
* * * * * *
12098727 CCACTGCAACTTTAAGGATATAGGATTTGTAGCTTCATAT-TGCT
1 CCACTGCAACTTCAAGGATATAGGAATTGTA-ATTTA-ATCCGAT
* * * * *
12098771 CCACTGCAACTTTCGA-GAGATAGGATTCACCATTGTAATTTCATTCCAAC
1 CCACTGCAAC-TTCAAGGATATAGG----A--ATTGTAATTT-AATCCGAT
* * * * *
12098821 CCATTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCTGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTA-ATTTAATCCGAT
* ** * **
12098865 CCACTGCAACTTCAAGGATATAGGATTTGTAGCTTCATCTTATT
1 CCACTGCAACTTCAAGGATATAGGAATTGTAATTTAATCCGA-T
* * * * *
12098909 CCACTGCAACTTCAAGGAAATAAGATTTGCCATTGTAATTTCATTCAGAC
1 CCACTGCAACTTCAAGGATAT-AG----G-AATTGTAATTT-AATCCGAT
* * * *
12098959 CCACTGCAACTTCAGGGGTATAAGAATTGT-ATCTTCAATTCGAT
1 CCACTGCAACTTCAAGGATATAGGAATTGTAAT-TT-AATCCGAT
* * * *
12099003 CCACTGCAACTTCAAGGATATA-GAATTTGTAGTTTCATCTTGCT
1 CCACTGCAACTTCAAGGATATAGGAA-TTGTAATTTAATC-CGAT
12099047 CCACTGCAACTTCA
1 CCACTGCAACTTCA
12099061 GTAAGATAAG
Statistics
Matches: 247, Mismatches: 63, Indels: 48
0.69 0.18 0.13
Matches are distributed among these distances:
43 14 0.06
44 162 0.66
45 12 0.05
46 1 0.00
48 1 0.00
49 8 0.03
50 46 0.19
51 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (43 bp):
CCACTGCAACTTCAAGGATATAGGAATTGTAATTTAATCCGAT
Found at i:12098840 original size:138 final size:137
Alignment explanation
Indices: 12098611--12099074 Score: 644
Period size: 138 Copynumber: 3.4 Consensus size: 137
12098601 TATGGGTATT
* * * *
12098611 GGATTTGTATCTTTATCTTGTTCCACTGCAACTTCAGGAAGATAAGATTCACCATTATAATTTCA
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGG-AGATAAGATTCACCATTGTAATTTCA
** * * *
12098676 TTCTGACCCACTGCAACTTCAAGGGTATAGGAATTGTATATTTAATCCGATCCACTGCAACTTTA
65 TTCCAACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTCA
12098741 AGGATATA
130 AGGATATA
* *
12098749 GGATTTGTAGCTTCATATTGCTCCACTGCAACTTTC-GAGAGATAGGATTCACCATTGTAATTTC
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAAC-TTCAG-GAGATAAGATTCACCATTGTAATTTC
* *
12098813 ATTCCAACCCATTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCTGATCCACTGCAACTTC
64 ATTCCAACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTC
12098878 AAGGATATA
129 AAGGATATA
** * **
12098887 GGATTTGTAGCTTCATCTTATTCCACTGCAACTTCAAGGAAATAAGATTTGCCATTGTAATTTCA
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTC-AGGAGATAAGATTCACCATTGTAATTTCA
* * *
12098952 TT-CAGACCCACTGCAACTTCAGGGGTATAAGAATTGTATCTTCAATTCGATCCACTGCAACTTC
65 TTCCA-ACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTC
12099016 AAGGATATA
129 AAGGATATA
* * *
12099025 GAATTTGTAGTTTCATCTTGCTCCACTGCAACTTCAGTAAGATAAGATTC
1 GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAG-GAGATAAGATTC
12099075 GTTATAGTAA
Statistics
Matches: 288, Mismatches: 32, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
137 7 0.02
138 276 0.96
139 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (137 bp):
GGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGAGATAAGATTCACCATTGTAATTTCAT
TCCAACCCACTGCAACTTCAGGGGTATAGGAATTGTATCTTTAATCCGATCCACTGCAACTTCAA
GGATATA
Found at i:12099900 original size:117 final size:117
Alignment explanation
Indices: 12099692--12099902 Score: 332
Period size: 117 Copynumber: 1.8 Consensus size: 117
12099682 TTTGATTTGT
* *
12099692 TGGTTATTTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTTT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTGT
* *
12099757 GATGCGATAGTAATCCCGATGCTGTTGATAAAACTATTGTCAAAATTGTAGA
66 GATGCGACAGTAATCCCGATGATGTTGATAAAACTATTGTCAAAATTGTAGA
* **
12099809 TGGTTAATTGTGATTTATTATTGCAATTTTAGTGCCACAATGTAGGGTTTGTTTTGTTGATTTGT
1 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTGT
** *
12099874 GATGCGACAGTGGTCCCGGTGATGTTGAT
66 GATGCGACAGTAATCCCGATGATGTTGAT
12099903 TTCTGTTACC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 84 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (117 bp):
TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCAATTTGT
GATGCGACAGTAATCCCGATGATGTTGATAAAACTATTGTCAAAATTGTAGA
Found at i:12100585 original size:33 final size:33
Alignment explanation
Indices: 12100515--12100586 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
12100505 TACTAAGGAG
* * *
12100515 GGTGATGCTGAAGGGGTAGAAGTTGATGGGGAG
1 GGTGATGATGAAGGGGTAGAAGTTGATAGGGAA
*
12100548 GGTGATGATGAAGGGGTAGAA-TCTGATAGTGAA
1 GGTGATGATGAAGGGGTAGAAGT-TGATAGGGAA
12100581 GGTGAT
1 GGTGAT
12100587 CTGGAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.28, C:0.03, G:0.46, T:0.24
Consensus pattern (33 bp):
GGTGATGATGAAGGGGTAGAAGTTGATAGGGAA
Found at i:12100835 original size:51 final size:51
Alignment explanation
Indices: 12100757--12100857 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
12100747 AAGTTGCTGC
*
12100757 TGATGAATATGTTGGTGATTTTCCAACATCAGATGGAGTGGATAATGTTGT
1 TGATGAATATGTTGGTGATTTTCCAACATCAGATGGACTGGATAATGTTGT
*
12100808 TGATGAATATGTTGGTGATTTTGCAACATCAGATGGACTGGATAATGTTG
1 TGATGAATATGTTGGTGATTTTCCAACATCAGATGGACTGGATAATGTTG
12100858 CTGCTGCACG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.37
Consensus pattern (51 bp):
TGATGAATATGTTGGTGATTTTCCAACATCAGATGGACTGGATAATGTTGT
Found at i:12101167 original size:9 final size:9
Alignment explanation
Indices: 12101156--12101224 Score: 77
Period size: 9 Copynumber: 7.7 Consensus size: 9
12101146 TTTGGTTAAA
*
12101156 AATTAACCA
1 AATTAACCG
*
12101165 AATTAACTG
1 AATTAACCG
12101174 AATTAACCG
1 AATTAACCG
*
12101183 AATTACCCG
1 AATTAACCG
12101192 AATT-ACCTG
1 AATTAACC-G
* *
12101201 AATTACCCA
1 AATTAACCG
12101210 AATTAACCG
1 AATTAACCG
12101219 AATTAA
1 AATTAA
12101225 ATCACTACAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
8 2 0.04
9 45 0.92
10 2 0.04
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:12101187 original size:27 final size:27
Alignment explanation
Indices: 12101155--12101224 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
12101145 TTTTGGTTAA
*
12101155 AAATTAACCAAATTAACTGAATTAACC
1 AAATTAACCGAATTAACTGAATTAACC
* * * *
12101182 GAATTACCCGAATTACCTGAATTACCC
1 AAATTAACCGAATTAACTGAATTAACC
12101209 AAATTAACCGAATTAA
1 AAATTAACCGAATTAA
12101225 ATCACTACAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATTAACCGAATTAACTGAATTAACC
Found at i:12101397 original size:18 final size:18
Alignment explanation
Indices: 12101374--12101426 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
12101364 TATGATTGGG
12101374 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGGGTAA
* *
12101392 TTGGGTTGGGTTGGATAC
1 TTGGGTTGGGTTGGGTAA
*
12101410 TTGGGTTTGGATTGGGT
1 TTGGG-TTGGGTTGGGT
12101427 TTAGGTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.09, C:0.02, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGGGTAA
Found at i:12108464 original size:32 final size:33
Alignment explanation
Indices: 12108421--12108562 Score: 161
Period size: 32 Copynumber: 4.4 Consensus size: 33
12108411 TCACAATTTG
*
12108421 GTTTTAAGGGATTTC-ATGATTTTATTCT-TAATA
1 GTTTT-AGGGATTTCAATGATTTGATT-TGTAATA
12108454 GTTTTAGGGA-TTCAATGATTTGATTTGTAA-A
1 GTTTTAGGGATTTCAATGATTTGATTTGTAATA
* * *
12108485 ATTGTTAGGGATTTC-ATGATTTCATTTTTAATA
1 GTT-TTAGGGATTTCAATGATTTGATTTGTAATA
*
12108518 GTTTTAGGGA-TTCAATGATTTGATTTGTAAAA
1 GTTTTAGGGATTTCAATGATTTGATTTGTAATA
*
12108550 TTTTTAGGGATTT
1 GTTTTAGGGATTT
12108563 TAAGAATATT
Statistics
Matches: 93, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
31 10 0.11
32 70 0.75
33 13 0.14
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.49
Consensus pattern (33 bp):
GTTTTAGGGATTTCAATGATTTGATTTGTAATA
Found at i:12108528 original size:64 final size:64
Alignment explanation
Indices: 12108427--12108562 Score: 245
Period size: 64 Copynumber: 2.1 Consensus size: 64
12108417 TTTGGTTTTA
*
12108427 AGGGATTTCATGATTTTATTCTTAATAGTTTTAGGGATTCAATGATTTGATTTGTAAAATTGTT
1 AGGGATTTCATGATTTCATTCTTAATAGTTTTAGGGATTCAATGATTTGATTTGTAAAATTGTT
* *
12108491 AGGGATTTCATGATTTCATTTTTAATAGTTTTAGGGATTCAATGATTTGATTTGTAAAATTTTT
1 AGGGATTTCATGATTTCATTCTTAATAGTTTTAGGGATTCAATGATTTGATTTGTAAAATTGTT
12108555 AGGGATTT
1 AGGGATTT
12108563 TAAGAATATT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (64 bp):
AGGGATTTCATGATTTCATTCTTAATAGTTTTAGGGATTCAATGATTTGATTTGTAAAATTGTT
Found at i:12108629 original size:17 final size:16
Alignment explanation
Indices: 12108587--12108630 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
12108577 AATGCTAATG
*
12108587 TTTTAGGGATTTTAAA
1 TTTTAGGGATTTGAAA
* *
12108603 ATTTAAGGATTTGAAGA
1 TTTTAGGGATTTGAA-A
12108620 TTTTAGGGATT
1 TTTTAGGGATT
12108631 CAATAAAGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (16 bp):
TTTTAGGGATTTGAAA
Found at i:12109105 original size:94 final size:93
Alignment explanation
Indices: 12108931--12109199 Score: 337
Period size: 94 Copynumber: 2.9 Consensus size: 93
12108921 AAATTATGCC
* * * * *
12108931 TAACTTCAATCCGACCCACTGCAACTTTAAGGGTATTGGATTTGTAACTTTATCTTTCTCCACTG
1 TAACTTCAATCCGACCCACTGCAAC-TTCAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
* *
12108996 -TAACTTCAGGAAGATAAGGCTCGCTATGG
65 CT-ACTTTAGGAAGATAAGACTCGCTATGG
12109025 TAACTTCAATCCGACCCACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTG
1 TAACTTCAATCCGACCCACTGCAACTTCAGGG-TATAGGATTTGTAGCTTCATCTTGCTCCACTG
**
12109090 CTACTTTAAGG-AGATAAGACTTTCTATGG
65 CTACTTT-AGGAAGATAAGACTCGCTATGG
* * * * *
12109119 TAAATTCAATCCAACCCTCTGCAACTTCAGGGGTATAAGATTTGTAGCTTCAT-ATGCTCCACTG
1 TAACTTCAATCCGACCCACTGCAACTTCA-GGGTATAGGATTTGTAGCTTCATCTTGCTCCACTG
*
12109183 CAACTTTAGGAAGATAA
65 CTACTTTAGGAAGATAA
12109200 AATTTGAGGT
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
92 3 0.02
93 28 0.18
94 117 0.75
95 7 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (93 bp):
TAACTTCAATCCGACCCACTGCAACTTCAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGC
TACTTTAGGAAGATAAGACTCGCTATGG
Found at i:12111875 original size:9 final size:9
Alignment explanation
Indices: 12111861--12111936 Score: 80
Period size: 9 Copynumber: 8.4 Consensus size: 9
12111851 TTTGGTTAAA
12111861 AATTAACCG
1 AATTAACCG
*
12111870 AATTAACCA
1 AATTAACCG
*
12111879 AATTACCCG
1 AATTAACCG
*
12111888 AATTAACTG
1 AATTAACCG
* *
12111897 AATTACCCA
1 AATTAACCG
* *
12111906 AATTACCCT
1 AATTAACCG
*
12111915 AATTAATCG
1 AATTAACCG
12111924 AATTAACCG
1 AATTAACCG
12111933 AATT
1 AATT
12111937 GAATCACTAC
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:12111899 original size:27 final size:27
Alignment explanation
Indices: 12111861--12111936 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
12111851 TTTGGTTAAA
*
12111861 AATTAACCGAATTAACCAAATTACCCG
1 AATTAACTGAATTAACCAAATTACCCG
* *
12111888 AATTAACTGAATTACCCAAATTACCCT
1 AATTAACTGAATTAACCAAATTACCCG
*
12111915 AATTAA-TCGAATTAACCGAATT
1 AATTAACT-GAATTAACCAAATT
12111937 GAATCACTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTAACTGAATTAACCAAATTACCCG
Found at i:12114737 original size:57 final size:57
Alignment explanation
Indices: 12114575--12114861 Score: 282
Period size: 56 Copynumber: 5.1 Consensus size: 57
12114565 ATTTTTCAAT
* * * * * * * *
12114575 AGCAT-AATAATGCTTACTTTGAGACACTGAAGCAAC-ACTGTAATTTAATTTAGGAC
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGAC
* * * * *
12114631 AGCAT-AATAATACTCAATTTGGAACA-TTAAACAACAGC-TTAATTTAATTTAAGAC
1 AGCATGAA-AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGAC
* * * *
12114686 AACATGAAAATGCTCAATTTGATACACTAAAACACCAACTTTAATTCAATTTATGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGAC
* ** * *
12114743 AGCATGAAAATGCTCAATTTGAAACACGAAAACAGTAGC-TTGATTCAATTTAAGAC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGAC
* *
12114799 AGTATGAAAATGCTCAATTTGAAACACTCAAACAACAACTTTAATTCAATTTATA-AC
1 AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTA-AGAC
12114856 AGCATG
1 AGCATG
12114862 CAAACAGTAA
Statistics
Matches: 190, Mismatches: 35, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
55 41 0.22
56 81 0.43
57 67 0.35
58 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (57 bp):
AGCATGAAAATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGAC
Found at i:12114808 original size:113 final size:113
Alignment explanation
Indices: 12114583--12114861 Score: 330
Period size: 113 Copynumber: 2.5 Consensus size: 113
12114573 ATAGCATAAT
* * * * * * * *
12114583 AATGCTTACTTTGAGACACTGAAGCAAC-ACTGTAATTTAATTTAGGACAGCAT-AATAATACTC
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
* ** *
12114646 AATTTGGAACATTAAACAACAGCTTAATTTAATTTAAGACAACATGAA
66 AATTTGAAACAGAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
* * *
12114694 AATGCTCAATTTGATACACTAAAACACCAACTTTAATTCAATTTATGACAGCATGAA-AATGCTC
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
** * **
12114758 AATTTGAAACACGAAAACAGTAGCTTGATTCAATTTAAGACAGTATGAA
66 AATTTGAAACA-GAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
* *
12114807 AATGCTCAATTTGAAACACTCAAACAACAACTTTAATTCAATTTATAACAGCATG
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATG
12114862 CAAACAGTAA
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
111 22 0.15
112 38 0.27
113 82 0.58
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (113 bp):
AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTATGACAGCATGAATAATACTC
AATTTGAAACAGAAAACAACAGCTTAATTCAATTTAAGACAACATGAA
Found at i:12114812 original size:56 final size:56
Alignment explanation
Indices: 12114615--12114861 Score: 248
Period size: 57 Copynumber: 4.4 Consensus size: 56
12114605 AGCAACACTG
* * * * ** *
12114615 TAATTTAATTTAGGACAGCAT-AATAATACTCAATTTGGAACA-TTAAACAACAGCT
1 TAATTCAATTTAAGACAGCATGAA-AATGCTCAATTTGAAACACGAAAACACCAGCT
* * * * *
12114670 TAATTTAATTTAAGACAACATGAAAATGCTCAATTTGATACACTAAAACACCAACTT
1 TAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACGAAAACACCAGC-T
* **
12114727 TAATTCAATTTATGACAGCATGAAAATGCTCAATTTGAAACACGAAAACAGTAGCT
1 TAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACGAAAACACCAGCT
* * ** * *
12114783 TGATTCAATTTAAGACAGTATGAAAATGCTCAATTTGAAACACTCAAACAACAACTT
1 TAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACGAAAACACCAGC-T
12114840 TAATTCAATTTATA-ACAGCATG
1 TAATTCAATTTA-AGACAGCATG
12114862 CAAACAGTAA
Statistics
Matches: 161, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
55 34 0.21
56 59 0.37
57 67 0.42
58 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (56 bp):
TAATTCAATTTAAGACAGCATGAAAATGCTCAATTTGAAACACGAAAACACCAGCT
Found at i:12114970 original size:33 final size:33
Alignment explanation
Indices: 12114928--12114996 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12114918 AACAAGGGAG
12114928 TATGTATGCTAATTTTCCAGCATTTGGTCAACA
1 TATGTATGCTAATTTTCCAGCATTTGGTCAACA
12114961 TATGTATGCTAATTTTCCAGCATTTGGTCAACA
1 TATGTATGCTAATTTTCCAGCATTTGGTCAACA
12114994 TAT
1 TAT
12114997 AAACTTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (33 bp):
TATGTATGCTAATTTTCCAGCATTTGGTCAACA
Found at i:12115719 original size:18 final size:18
Alignment explanation
Indices: 12115696--12115739 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
12115686 AATTTTTATG
*
12115696 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
12115714 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
12115732 CTTGGGTT
1 ATTGGGTT
12115740 TGGATTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.02, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:12116181 original size:14 final size:16
Alignment explanation
Indices: 12116155--12116186 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12116145 GAAAATTCAC
12116155 TATTGCACTTCTA-TT
1 TATTGCACTTCTAGTT
12116170 TATTGC-CTTCTAGTT
1 TATTGCACTTCTAGTT
12116185 TA
1 TA
12116187 CATAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (16 bp):
TATTGCACTTCTAGTT
Found at i:12127595 original size:19 final size:18
Alignment explanation
Indices: 12127574--12127631 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
12127564 TTTTAATTTT
*
12127574 TTTTTAAAATTTTTTAAA
1 TTTTTAAAATTTTTTGAA
*
12127592 TTTTTATAAATATTTTGAA
1 TTTTTA-AAATTTTTTGAA
*
12127611 TTTTAAAAATTATTTTGAA
1 TTTTTAAAATT-TTTTGAA
12127630 TT
1 TT
12127632 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.29
19 24 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTAAAATTTTTTGAA
Found at i:12132781 original size:23 final size:23
Alignment explanation
Indices: 12132755--12132805 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
12132745 CAAGTTAGCT
12132755 TGTAAAA-TCCCGAAAATTACTAC
1 TGTAAAACT-CCGAAAATTACTAC
* *
12132778 TGTAATACTCTGAAAATTACTAC
1 TGTAAAACTCCGAAAATTACTAC
*
12132801 AGTAA
1 TGTAA
12132806 GAAAATAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAAAACTCCGAAAATTACTAC
Found at i:12135936 original size:17 final size:17
Alignment explanation
Indices: 12135914--12135952 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12135904 TGAGCATTTT
12135914 GGGAACAAC-TCTATGTC
1 GGGAACAACATC-ATGTC
*
12135931 GGGAACAACATCATGTT
1 GGGAACAACATCATGTC
12135948 GGGAA
1 GGGAA
12135953 TGACTAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (17 bp):
GGGAACAACATCATGTC
Found at i:12138590 original size:15 final size:16
Alignment explanation
Indices: 12138570--12138599 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12138560 AATAGCATGA
12138570 TTTAATTTT-TATTCG
1 TTTAATTTTATATTCG
12138585 TTTAATTTTATATTC
1 TTTAATTTTATATTC
12138600 ATATTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTAATTTTATATTCG
Found at i:12167235 original size:11 final size:10
Alignment explanation
Indices: 12167168--12167246 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 10
12167158 AAAATATAGA
12167168 AAAAAATATAT
1 AAAAAAT-TAT
* * *
12167179 ATAAAGTCAT
1 AAAAAATTAT
12167189 AAGAAAATTAT
1 AA-AAAATTAT
12167200 AAAAAATGTA-
1 AAAAAAT-TAT
*
12167210 AAGAAA-TAT
1 AAAAAATTAT
12167219 --AAAATTCAT
1 AAAAAATT-AT
12167228 AAAAAATTAT
1 AAAAAATTAT
12167238 -AAAAATTAT
1 AAAAAATTAT
12167247 CGTAATGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
7 3 0.06
8 3 0.06
9 11 0.21
10 15 0.28
11 21 0.40
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:12169405 original size:30 final size:30
Alignment explanation
Indices: 12169361--12169432 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
12169351 TAGCAATTAA
12169361 TTATTTTT-AAAAATAT-TTTTTATAATCT
1 TTATTTTTAAAAAATATATTTTTATAATCT
* *
12169389 TTAGTTTTTAAAAAATATATTTTTATATTTT
1 TTA-TTTTTAAAAAATATATTTTTATAATCT
12169420 TTATTTTTAAAAA
1 TTATTTTTAAAAA
12169433 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 3 0.08
29 5 0.13
30 18 0.46
31 13 0.33
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (30 bp):
TTATTTTTAAAAAATATATTTTTATAATCT
Found at i:12172943 original size:17 final size:17
Alignment explanation
Indices: 12172907--12172940 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
12172897 TTGCATATTG
12172907 TGTAATTTGGTCTTTTT
1 TGTAATTTGGTCTTTTT
12172924 TGTAATTT-GTCTTTTT
1 TGTAATTTGGTCTTTTT
12172940 T
1 T
12172941 TGTGACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (17 bp):
TGTAATTTGGTCTTTTT
Found at i:12184389 original size:7 final size:7
Alignment explanation
Indices: 12184379--12184404 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12184369 GTTGTAAAAT
12184379 ATAGGGG
1 ATAGGGG
12184386 ATAGGGG
1 ATAGGGG
12184393 ATAGGGG
1 ATAGGGG
12184400 ATAGG
1 ATAGG
12184405 AAATAGCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
ATAGGGG
Found at i:12187256 original size:26 final size:26
Alignment explanation
Indices: 12187204--12187257 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
12187194 ATGCATATAC
12187204 ATTTTATAATACATGTACACTTTCTAT
1 ATTTTATAATACA-GTACACTTTCTAT
12187231 ATTTTATATATACA-TACA-TTTCCTAT
1 ATTTTATA-ATACAGTACACTTT-CTAT
12187257 A
1 A
12187258 ATATATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 3 0.12
26 9 0.36
27 8 0.32
28 5 0.20
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTTTATAATACAGTACACTTTCTAT
Found at i:12187847 original size:30 final size:30
Alignment explanation
Indices: 12187809--12187880 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
12187799 GGGTGTGATG
* *
12187809 TTTAAATTCTTTGAA-ATAAGAACGTTTTAT
1 TTTAAATTCTTTCAAGATAA-AAAGTTTTAT
* *
12187839 TTTTAATTCATTCAAGATAAAAAGTTTTAT
1 TTTAAATTCTTTCAAGATAAAAAGTTTTAT
*
12187869 TTTAAAATCTTT
1 TTTAAATTCTTT
12187881 TCAAATTTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTAAATTCTTTCAAGATAAAAAGTTTTAT
Found at i:12197474 original size:13 final size:14
Alignment explanation
Indices: 12197456--12197484 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12197446 CACCAAATCA
12197456 TTTTCTTTT-CTTC
1 TTTTCTTTTCCTTC
12197469 TTTTCTTTTCCTTC
1 TTTTCTTTTCCTTC
12197483 TT
1 TT
12197485 ATACACCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTCCTTC
Found at i:12200713 original size:26 final size:25
Alignment explanation
Indices: 12200668--12200729 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 25
12200658 GAAAGCAGAA
12200668 TAATTAT-TTTCTATTATTAA-ATAAT
1 TAATTATATTTC-ATTATTAATAT-AT
12200693 CTAATTATATTTC-TTACTTAATATAT
1 -TAATTATATTTCATTA-TTAATATAT
*
12200719 TAAATATATTT
1 TAATTATATTT
12200730 TATAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 13 0.41
26 13 0.41
27 6 0.19
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTATATTTCATTATTAATATAT
Found at i:12202346 original size:50 final size:50
Alignment explanation
Indices: 12202241--12202365 Score: 115
Period size: 50 Copynumber: 2.5 Consensus size: 50
12202231 TCATTGAGGT
** *** *
12202241 TATGAGAGGTCCCATGTAAGACCATGTCTGCGACATGGTGTTGACACCGA
1 TATGAGAGGTCCCACATAAGACCATGTCTGCGACATGACATGGACACCGA
* * * * *
12202291 GATGAGAGGTCCCCCATAAGACCATGTCTGGGACATGACATGGGCACTGA
1 TATGAGAGGTCCCACATAAGACCATGTCTGCGACATGACATGGACACCGA
** **
12202341 TATGAGAACTCCCATGTAAGACCAT
1 TATGAGAGGTCCCACATAAGACCAT
12202366 ATTTGGGATA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCACATAAGACCATGTCTGCGACATGACATGGACACCGA
Found at i:12202373 original size:50 final size:49
Alignment explanation
Indices: 12202307--12202426 Score: 134
Period size: 49 Copynumber: 2.4 Consensus size: 49
12202297 AGGTCCCCCA
* *
12202307 TAAGACCATGTCTGGGACATGACATGGGCACTGATATGAGAAC-TCCCATG
1 TAAGACCATGTCTGGGACATGACATGGGCACT-ACAAGA-AACATCCCATG
* * * * * * *
12202357 TAAGACCATATTTGGGATATGGCATTGTCAGTACAAGAAACATCCCATG
1 TAAGACCATGTCTGGGACATGACATGGGCACTACAAGAAACATCCCATG
12202406 TAAGACCATGTCTGGGACATG
1 TAAGACCATGTCTGGGACATG
12202427 GTTTTGACAT
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.05
49 29 0.51
50 25 0.44
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (49 bp):
TAAGACCATGTCTGGGACATGACATGGGCACTACAAGAAACATCCCATG
Found at i:12205591 original size:12 final size:12
Alignment explanation
Indices: 12205574--12205599 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12205564 AACATTTATA
12205574 ACGCCACCACTT
1 ACGCCACCACTT
12205586 ACGCCACCACTT
1 ACGCCACCACTT
12205598 AC
1 AC
12205600 AACCGAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.50, G:0.08, T:0.15
Consensus pattern (12 bp):
ACGCCACCACTT
Found at i:12207055 original size:21 final size:21
Alignment explanation
Indices: 12207026--12207126 Score: 51
Period size: 21 Copynumber: 4.8 Consensus size: 21
12207016 ACTTATATGA
*
12207026 GTTTTAGTTTAACCCTTCTAG
1 GTTTCAGTTTAACCCTTCTAG
* * * *
12207047 GTTTCAGTTCAGCTCTT-TTG
1 GTTTCAGTTTAACCCTTCTAG
* ** *
12207067 AGATTCAGTTTAACCCTAATGG
1 -GTTTCAGTTTAACCCTTCTAG
* * * *
12207089 GTTTCATTTTAGCTCTTCTAA
1 GTTTCAGTTTAACCCTTCTAG
* *
12207110 GCTTCAGATTAACCCTT
1 GTTTCAGTTTAACCCTT
12207127 ATGGGTTTTC
Statistics
Matches: 54, Mismatches: 24, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTCTAG
Found at i:12207078 original size:42 final size:42
Alignment explanation
Indices: 12207031--12207142 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
12207021 TATGAGTTTT
* * *
12207031 AGTTTAACCCTTCTAGGTTTCAGTTCAGCTCTTTTGAGATTC
1 AGTTTAACCCTTATAGGTTTCAGTTCAGCTCTTCTAAGATTC
* * * * *
12207073 AGTTTAACCCTAATGGGTTTCATTTTAGCTCTTCTAAGCTTC
1 AGTTTAACCCTTATAGGTTTCAGTTCAGCTCTTCTAAGATTC
* *
12207115 AGATTAACCCTTATGGGTTTTC-GTTCAG
1 AGTTTAACCCTTATAGG-TTTCAGTTCAG
12207143 TTCCTATGAG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 53 0.93
43 4 0.07
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (42 bp):
AGTTTAACCCTTATAGGTTTCAGTTCAGCTCTTCTAAGATTC
Found at i:12211736 original size:13 final size:13
Alignment explanation
Indices: 12211718--12211750 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12211708 CAAACAGATT
*
12211718 GAAAAAGGAAAAA
1 GAAAAAAGAAAAA
12211731 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
12211744 GAAAAAA
1 GAAAAAA
12211751 AACCAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:12225832 original size:16 final size:15
Alignment explanation
Indices: 12225796--12225835 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
12225786 TTCTAAAAAA
12225796 TCAAAAATAATAAAT
1 TCAAAAATAATAAAT
* *
12225811 TAAAAAATAATGAACT
1 TCAAAAATAAT-AAAT
12225827 TCAAAAATA
1 TCAAAAATA
12225836 GAAAAGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (15 bp):
TCAAAAATAATAAAT
Found at i:12225903 original size:22 final size:21
Alignment explanation
Indices: 12225860--12225911 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12225850 AATAAATTTT
* *
12225860 TTTTATAAAAATGCACACAAA
1 TTTTATAAAAATACACAAAAA
*
12225881 TTTTATAAAAATATACATAAAA
1 TTTTATAAAAATACACA-AAAA
12225903 TTTTA-AAAA
1 TTTTATAAAA
12225912 TAATTTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (21 bp):
TTTTATAAAAATACACAAAAA
Found at i:12226300 original size:33 final size:34
Alignment explanation
Indices: 12226262--12226346 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
12226252 ATGGTTATAT
12226262 TTAAATATTTAAAATATAGTT-TATATATT-CTTA
1 TTAAATATTTAAAATATA-TTATATATATTGCTTA
*
12226295 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTA
1 TTAAATATTTA-AAATATATT-ATATATATTGCTTA
*
12226329 -AAAATATTTAAAATATAT
1 TTAAATATTTAAAATATAT
12226347 ATTTCATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
31 2 0.05
32 5 0.11
33 27 0.61
34 10 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (34 bp):
TTAAATATTTAAAATATATTATATATATTGCTTA
Found at i:12228973 original size:20 final size:20
Alignment explanation
Indices: 12228950--12228988 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12228940 AAGAAAATAA
12228950 AAGAGAGAAAACAAAAAAAG
1 AAGAGAGAAAACAAAAAAAG
* *
12228970 AAGAGAGAAGAGAAAAAAA
1 AAGAGAGAAAACAAAAAAA
12228989 ATCATCCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (20 bp):
AAGAGAGAAAACAAAAAAAG
Found at i:12230336 original size:19 final size:19
Alignment explanation
Indices: 12230302--12230339 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12230292 TAGTTTTTTT
*
12230302 GTTAATTAAATATAATTAA
1 GTTAATTAAACATAATTAA
*
12230321 GTTAATTAAACCTAATTAA
1 GTTAATTAAACATAATTAA
12230340 CTAATCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
GTTAATTAAACATAATTAA
Found at i:12237698 original size:19 final size:20
Alignment explanation
Indices: 12237669--12237710 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12237659 CAATCTCGGG
* *
12237669 TTTTGATTCTCGGGTTCAAT
1 TTTTGATTCTCGAGTCCAAT
12237689 TTTTGA-TCTCGAGTCCAAT
1 TTTTGATTCTCGAGTCCAAT
12237708 TTT
1 TTT
12237711 CAAGTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTGATTCTCGAGTCCAAT
Found at i:12240546 original size:13 final size:13
Alignment explanation
Indices: 12240528--12240552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12240518 TATTTTAATA
12240528 TTATTTTGTGTGT
1 TTATTTTGTGTGT
12240541 TTATTTTGTGTG
1 TTATTTTGTGTG
12240553 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:12242477 original size:41 final size:41
Alignment explanation
Indices: 12242428--12242536 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
12242418 GACTTTAAGT
*
12242428 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
**
12242469 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
12242510 CTAGCAGGCTATGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
12242537 TTTAAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
41 57 0.92
42 5 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:12243371 original size:27 final size:27
Alignment explanation
Indices: 12243333--12243384 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
12243323 AAATAGTAGC
12243333 ATCTTGAATGGAAAGCAAGGATCATGT
1 ATCTTGAATGGAAAGCAAGGATCATGT
12243360 ATCTTGAATGGAAAGCAAGGATCAT
1 ATCTTGAATGGAAAGCAAGGATCAT
12243385 CTTTATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
ATCTTGAATGGAAAGCAAGGATCATGT
Found at i:12257356 original size:18 final size:18
Alignment explanation
Indices: 12257333--12257384 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
12257323 AACCCCGGGC
*
12257333 CCCTTATATGTATCCTAG
1 CCCTTATATGTATCCTAA
12257351 CCCTTATATGTATCCTAA
1 CCCTTATATGTATCCTAA
* *
12257369 CCCCTATATGTTTCCT
1 CCCTTATATGTATCCT
12257385 TTGCCTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (18 bp):
CCCTTATATGTATCCTAA
Found at i:12257799 original size:24 final size:23
Alignment explanation
Indices: 12257772--12257828 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
12257762 CATTTAATAA
12257772 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAA-TTGTTTTTATAT-TTTT
12257796 AATAGTAAATTGTTTTTATATTTTT
1 AATA--AAATTGTTTTTATATTTTT
12257821 AATAAAAT
1 AATAAAAT
12257829 AGAAGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 17 0.57
26 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
AATAAAATTGTTTTTATATTTTT
Found at i:12259577 original size:125 final size:125
Alignment explanation
Indices: 12259377--12259776 Score: 527
Period size: 126 Copynumber: 3.2 Consensus size: 125
12259367 GGCCAAACAG
** * * *
12259377 GAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGTTTTTTTTCCA-TCAATTTTGCTGATAGTGC
1 GAACTACTGTAGAAAAAAAACGTCCACATGGGAG-CTTTTTT-CAGT-AATTTTGCTGACAGTGC
** * * *
12259441 ATCCTGCTTGAAGTATTTTTGACACCATTTGTTCAGAACCATTTTCTCAAAATTATTTTTTAA
63 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTAA
* *
12259504 GAACTACTGTAGAAAAAAAACGTCCACATGAGAGCTTTTTTCAGTATTTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAAAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
12259569 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTT-AA
* * * **
12259630 GAACTACTGTAGAAAACAAGCTTTTACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAAAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * *
12259695 CTGCTTGAAGCGTTTTTGACATTATCTT-TTCAGAACCGTCTTCCCAAAATTAATTTTTCTGA
66 CTGCTTGAAGCGTTTTTGACACTAT-TTGTTCAGAACCGTCTTCTCAAAATT-ATTTTT-TAA
*
12259757 -AACTAATGTAGAAAAAAAAC
1 GAACTACTGTAGAAAAAAAAC
12259777 AAAATCCTTA
Statistics
Matches: 243, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
125 73 0.30
126 130 0.53
127 39 0.16
128 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAAAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTAA
Found at i:12259885 original size:34 final size:33
Alignment explanation
Indices: 12259833--12259962 Score: 136
Period size: 34 Copynumber: 3.8 Consensus size: 33
12259823 CACAAAATCA
*
12259833 TTTAAAAA-ACTAAACCCTAATTTAATTAATTT
1 TTTAAAAACTCTAAACCCTAATTTAATTAATTT
*
12259865 TCTTAAAAACTCTAAACCCTAATTTTATTTATTTATTT
1 T-TTAAAAACTCTAAACCCTAA-TTTA---ATTAATTT
* * *
12259903 ATTTAAAACCCCTAAAACCTAATTTAATTAATTT
1 -TTTAAAAACTCTAAACCCTAATTTAATTAATTT
*
12259937 TTAAAAAAACTCTAAACCCTAATTTA
1 TT-TAAAAACTCTAAACCCTAATTTA
12259963 TTTTTTAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
32 1 0.01
33 9 0.11
34 37 0.46
35 4 0.05
37 4 0.05
38 24 0.30
39 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (33 bp):
TTTAAAAACTCTAAACCCTAATTTAATTAATTT
Found at i:12259927 original size:29 final size:28
Alignment explanation
Indices: 12259895--12259972 Score: 66
Period size: 34 Copynumber: 2.5 Consensus size: 28
12259885 AATTTTATTT
*
12259895 ATTTATTTATTTAAAACCCCTAAAACCTA
1 ATTTATTT-TTTAAAAACCCTAAAACCTA
* *
12259924 ATTTAATTAATTTTTAAAAAAACTCTAAACCCTA
1 ATTT-A-T--TTTTT--AAAAACCCTAAAACCTA
12259958 ATTTATTTTTTAAAA
1 ATTTATTTTTTAAAA
12259973 TTCTTAAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
28 4 0.10
29 4 0.10
30 6 0.15
31 1 0.03
32 4 0.10
33 3 0.08
34 18 0.45
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTATTTTTTAAAAACCCTAAAACCTA
Found at i:12260026 original size:28 final size:27
Alignment explanation
Indices: 12259987--12260056 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
12259977 TAAACCGTAC
* *
12259987 ACCCTAAACCTAAATTATTTTAACAAA
1 ACCCTAACCCTAAACTATTTTAACAAA
12260014 ACCCTATACCCTAAACTATTTTAACAAA
1 ACCCTA-ACCCTAAACTATTTTAACAAA
12260042 ACCCTAAACCCTAAA
1 ACCCT-AACCCTAAA
12260057 ATCCCTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 6 0.15
28 32 0.82
29 1 0.03
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (27 bp):
ACCCTAACCCTAAACTATTTTAACAAA
Found at i:12260073 original size:16 final size:16
Alignment explanation
Indices: 12260039--12260076 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12260029 CTATTTTAAC
**
12260039 AAAA-CCCTAAACCCT
1 AAAATCCCTAAACCAA
12260054 AAAATCCCTAAACCAA
1 AAAATCCCTAAACCAA
12260070 AAAATCC
1 AAAATCC
12260077 TAAGGACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATCCCTAAACCAA
Found at i:12260276 original size:43 final size:43
Alignment explanation
Indices: 12260215--12260437 Score: 295
Period size: 43 Copynumber: 5.2 Consensus size: 43
12260205 AAAAGTATTT
*
12260215 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
* * * *
12260258 GCGGCGCTTTTCTCACAAACGCCACTATAGGCCATGACCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
* * *
12260301 GTGACGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
* * *
12260344 GCGGCGTTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
* * * *
12260387 GCGGCGCTTTTCCCACAAATGCCGCTATAGATCA-AACCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
*
12260429 GCGACGCTT
1 GCGGCGCTT
12260438 CTCGCAAAAA
Statistics
Matches: 156, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 15 0.10
43 141 0.90
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (43 bp):
GCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTA
Found at i:12260364 original size:86 final size:86
Alignment explanation
Indices: 12260219--12260413 Score: 336
Period size: 86 Copynumber: 2.3 Consensus size: 86
12260209 GTATTTGCGG
*
12260219 CGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCTCACAAACGCCACT
1 CGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACT
*
12260284 ATAGGCCATGACCTTTAGTGA
66 ATAGGCCATGACCTTTAGCGA
* *
12260305 CGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGTTTTTCCCACAAACGCCGCT
1 CGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACT
*
12260370 ATAGGCCATGACCTTTAGCGG
66 ATAGGCCATGACCTTTAGCGA
*
12260391 CGCTTTTCCCACAAATGCCGCTA
1 CGCTTTTCCCACAAACGCCGCTA
12260414 TAGATCAAAC
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 103 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (86 bp):
CGCTTTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACT
ATAGGCCATGACCTTTAGCGA
Found at i:12262798 original size:3 final size:3
Alignment explanation
Indices: 12262790--12262938 Score: 298
Period size: 3 Copynumber: 49.7 Consensus size: 3
12262780 ATGAGCGAAG
12262790 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12262838 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12262886 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12262934 AAT AA
1 AAT AA
12262939 CAGCTCAATG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 146 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12264792 original size:41 final size:41
Alignment explanation
Indices: 12264743--12264979 Score: 357
Period size: 41 Copynumber: 5.8 Consensus size: 41
12264733 AAATGTTTTT
*
12264743 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
12264784 GCGTCGCTTTTCCAAAAACGCCGCTAAAGCCTTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
12264825 GCAGCGCTTATTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
12264866 GCGGCGCTTATTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
12264907 GCGGCACTTCTCCAAAAATGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
12264948 GCGGCGCTTTTTTAAAAACGCCACTAAAGCCC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
12264980 CGAAAGGTCC
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 176 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:12265064 original size:40 final size:40
Alignment explanation
Indices: 12265014--12265167 Score: 186
Period size: 40 Copynumber: 3.8 Consensus size: 40
12265004 TGGGCTTAGG
*
12265014 TTTTTTGCGGCGTTTTTTGTAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTTTGT-AAAACGCCGCTAATGCTCGA
* * *
12265054 TTTTTAGCGGCGCTTTCTTG-ATAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCG-TTTTTTGTAAAACGCCGCTAATGCTCGA
* * *
12265094 TCTTTAGCGGCGTTTTGTGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGTAAAACGCCGCTAATGCTCGA
* *
12265134 TTTTTAGCGGCGTTTTTTGTCCAAACGCCACTAA
1 TTTTTAGCGGCGTTTTTTGT-AAAACGCCGCTAA
12265168 AAATGCCGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 21 0.22
40 60 0.62
41 16 0.16
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTGTAAAACGCCGCTAATGCTCGA
Found at i:12266511 original size:30 final size:31
Alignment explanation
Indices: 12266465--12266543 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
12266455 CAAAATTTTT
12266465 TTTAGAAAATTAAAAAAAGTATTTTAAAA-ATAC
1 TTTA-AAAA-TAAAAAAAGTATTTTAAAATAT-C
*
12266498 TTTAAAAATAAAAAAAGTATTTTAAAATATT
1 TTTAAAAATAAAAAAAGTATTTTAAAATATC
12266529 TTTAAAAATAAAAAA
1 TTTAAAAATAAAAAA
12266544 TATATATTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 34 0.77
32 6 0.14
33 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (31 bp):
TTTAAAAATAAAAAAAGTATTTTAAAATATC
Found at i:12272689 original size:112 final size:112
Alignment explanation
Indices: 12272492--12272718 Score: 445
Period size: 112 Copynumber: 2.0 Consensus size: 112
12272482 AATCCAAACA
*
12272492 CTAGTGGATGTTCGTATAATACCCCAGACTCGTGTCCTCGTCTAGAGATCCATCCAGAGGTGTTG
1 CTAGTGGATGTTCGTATAACACCCCAGACTCGTGTCCTCGTCTAGAGATCCATCCAGAGGTGTTG
12272557 GCCACTACGGAAGATAGTGATGAAGGGTCCGATAATGATGATCAGTC
66 GCCACTACGGAAGATAGTGATGAAGGGTCCGATAATGATGATCAGTC
12272604 CTAGTGGATGTTCGTATAACACCCCAGACTCGTGTCCTCGTCTAGAGATCCATCCAGAGGTGTTG
1 CTAGTGGATGTTCGTATAACACCCCAGACTCGTGTCCTCGTCTAGAGATCCATCCAGAGGTGTTG
12272669 GCCACTACGGAAGATAGTGATGAAGGGTCCGATAATGATGATCAGTC
66 GCCACTACGGAAGATAGTGATGAAGGGTCCGATAATGATGATCAGTC
12272716 CTA
1 CTA
12272719 CCGTGATGTC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (112 bp):
CTAGTGGATGTTCGTATAACACCCCAGACTCGTGTCCTCGTCTAGAGATCCATCCAGAGGTGTTG
GCCACTACGGAAGATAGTGATGAAGGGTCCGATAATGATGATCAGTC
Found at i:12275011 original size:21 final size:23
Alignment explanation
Indices: 12274990--12275033 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12274980 GTAAATTAAA
12274990 TTTAAATGAAATGAGG-GAAAAT
1 TTTAAATGAAATGAGGAGAAAAT
* *
12275012 TTTAATTTAAATGAGGAGAAAA
1 TTTAAATGAAATGAGGAGAAAA
12275034 AAAATTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (23 bp):
TTTAAATGAAATGAGGAGAAAAT
Found at i:12275095 original size:49 final size:49
Alignment explanation
Indices: 12275027--12275169 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 49
12275017 TTTAAATGAG
* *
12275027 GAGAAAAAAAATTGAATTGAAAATAGAAAATTTAAATATAAAATGAAAT
1 GAGAAAAAAATTTGCATTGAAAATAGAAAATTTAAATATAAAATGAAAT
*
12275076 GAGAAAAAAATTTGCATTGAAAATAGAAATTTTAAATATAAAATGAAAT
1 GAGAAAAAAATTTGCATTGAAAATAGAAAATTTAAATATAAAATGAAAT
12275125 GAGAAAAAAATAAATTTGCATTGAAAATAGAAAATTTAAAT-TAAA
1 GAG---AAAA-AAATTTGCATTGAAAATAGAAAATTTAAATATAAA
12275170 TTAGAATGAA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
49 49 0.57
52 8 0.09
53 29 0.34
ACGTcount: A:0.60, C:0.01, G:0.12, T:0.27
Consensus pattern (49 bp):
GAGAAAAAAATTTGCATTGAAAATAGAAAATTTAAATATAAAATGAAAT
Found at i:12275223 original size:16 final size:17
Alignment explanation
Indices: 12275202--12275233 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12275192 AATGGTAATG
12275202 GAAATGAAAT-AAAAAT
1 GAAATGAAATGAAAAAT
12275218 GAAATGAAATGAAAAA
1 GAAATGAAATGAAAAA
12275234 AAAAGGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (17 bp):
GAAATGAAATGAAAAAT
Found at i:12275286 original size:41 final size:40
Alignment explanation
Indices: 12275214--12275298 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 40
12275204 AATGAAATAA
*
12275214 AAATGAAATGAAATGAAAAAAAAAGGATGTGAGGCCTTTT
1 AAATGAAATGAAATGAAAAAAAAAGGATGTGAGGCCTTTG
*
12275254 AAATGAAAT-AAATGAAAAAAAAAAAGGGTGTGAGGCCTTTG
1 AAATGAAATGAAATG--AAAAAAAAAGGATGTGAGGCCTTTG
12275295 AAAT
1 AAAT
12275299 TTGCATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 5 0.12
40 9 0.22
41 27 0.66
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (40 bp):
AAATGAAATGAAATGAAAAAAAAAGGATGTGAGGCCTTTG
Found at i:12275591 original size:22 final size:20
Alignment explanation
Indices: 12275553--12275608 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 20
12275543 GCATAAAATT
12275553 TAAATTTAAATT-AAAAATAATA
1 TAAA-TTAAATTGAAAAA-AA-A
12275575 TAAA-TAAATTGAGAAAAAAA
1 TAAATTAAATTGA-AAAAAAA
12275595 TAAATTGAAATTGA
1 TAAATT-AAATTGA
12275609 CAGGCCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 11 0.37
21 4 0.13
22 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
TAAATTAAATTGAAAAAAAA
Found at i:12276286 original size:3 final size:3
Alignment explanation
Indices: 12276261--12276325 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
12276251 CAGCCCAGCT
* * * ** *
12276261 GAA GGA GAA GGA GAA GGA GAA GAA GAA GAA GAGA GCT GAA GAA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
12276307 GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G
12276326 GTGGCGCAGG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.42, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:12277786 original size:20 final size:20
Alignment explanation
Indices: 12277763--12277800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12277753 AAATATATAT
*
12277763 ATAGAAATTATAAAATATGG
1 ATAGAAAGTATAAAATATGG
*
12277783 ATAGAAAGTATAATATAT
1 ATAGAAAGTATAAAATAT
12277801 ATACGTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
ATAGAAAGTATAAAATATGG
Found at i:12277873 original size:100 final size:101
Alignment explanation
Indices: 12277755--12277965 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 101
12277745 ATAAAGAAAA
12277755 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTAC-ATATATATAA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACAATATATATAA
* * * * *
12277819 GTTAATAAATATATAGATCATAAAGATAATGATAAT
66 GGTAATAAATATATAAATCATAAAAATAATAATAAC
*
12277855 ATATATATATAGAAATTATAAAATATGTATAGAAAGTATAATATATATACGTACATATATATATA
1 ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACA-ATATATATA
*
12277920 AGGTAATAAATATATAAATCATAAAAATAATAATTAC
65 AGGTAATAAATATATAAATCATAAAAATAATAATAAC
12277957 ATATATATA
1 ATATATATA
12277966 AGGTAATAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 53 0.52
102 49 0.48
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (101 bp):
ATATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATACGTACAATATATATAA
GGTAATAAATATATAAATCATAAAAATAATAATAAC
Found at i:12277885 original size:20 final size:20
Alignment explanation
Indices: 12277857--12277903 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12277847 ATGATAATAT
*
12277857 ATATATATAGAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
12277877 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
12277897 ATATATA
1 ATATATA
12277904 CGTACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:12277932 original size:16 final size:15
Alignment explanation
Indices: 12277888--12277982 Score: 63
Period size: 16 Copynumber: 6.1 Consensus size: 15
12277878 TATGTATAGA
12277888 AAGT-ATAATATATAT
1 AAGTAATAA-ATATAT
* *
12277903 ACGTACATATATATAT
1 AAGTA-ATAAATATAT
12277919 AAGGTAATAAATATAT
1 AA-GTAATAAATATAT
* *
12277935 AAATCATAAA-A-AT
1 AAGTAATAAATATAT
12277948 AA-TAATTACATATATAT
1 AAGTAA-TA-A-ATATAT
12277965 AAGGTAATAAATATAT
1 AA-GTAATAAATATAT
12277981 AA
1 AA
12277983 ATCATAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.03
13 6 0.10
14 2 0.03
15 10 0.16
16 27 0.43
17 11 0.17
18 2 0.03
19 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (15 bp):
AAGTAATAAATATAT
Found at i:12277975 original size:46 final size:45
Alignment explanation
Indices: 12277911--12278008 Score: 178
Period size: 46 Copynumber: 2.2 Consensus size: 45
12277901 ATACGTACAT
12277911 ATATATATAAGGTAATAAATATATAAATCATAAAAATAATAATTAC
1 ATATATATAAGGTAATAAATATATAAATCAT-AAAATAATAATTAC
12277957 ATATATATAAGGTAATAAATATATAAATCATAAAATAATAATTAC
1 ATATATATAAGGTAATAAATATATAAATCATAAAATAATAATTAC
*
12278002 ATGTATA
1 ATATATA
12278009 AACTTAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 20 0.39
46 31 0.61
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (45 bp):
ATATATATAAGGTAATAAATATATAAATCATAAAATAATAATTAC
Found at i:12277997 original size:48 final size:48
Alignment explanation
Indices: 12277806--12277998 Score: 180
Period size: 46 Copynumber: 4.0 Consensus size: 48
12277796 TATATATACG
* * *
12277806 TACATATATATAAGTTAATAAATATATAGATCATAAAGATAATGATAA
1 TACATATATATAAGGTAATAAATATATAAATCATAAAGATAATAATAA
* ** * ** *
12277854 TATATATATATAGAAATTATAAA-ATATGTAT-AGAAAGTATAATATATATA
1 TACATATATATA-AGGTAATAAATATATAAATCATAAAG-ATAATA-ATA-A
*
12277904 CGTACATATATATATAAGGTAATAAATATATAAATCATAAAAATAATAAT--
1 --TAC--ATATATATAAGGTAATAAATATATAAATCATAAAGATAATAATAA
12277954 TACATATATATAAGGTAATAAATATATAAATCATAAA-ATAATAAT
1 TACATATATATAAGGTAATAAATATATAAATCATAAAGATAATAAT
12277999 TACATGTATA
Statistics
Matches: 119, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
45 8 0.07
46 34 0.29
47 5 0.04
48 25 0.21
49 10 0.08
50 1 0.01
52 2 0.02
53 9 0.08
54 21 0.18
55 4 0.03
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (48 bp):
TACATATATATAAGGTAATAAATATATAAATCATAAAGATAATAATAA
Found at i:12278973 original size:22 final size:22
Alignment explanation
Indices: 12278948--12279004 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
12278938 TACAAATTAA
12278948 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTACAAAATCAT
* *
12278970 ATCTTCTAAAATTAC-ATATCAT
1 ATC-TCTAAGATTACAAAATCAT
12278992 A--TCTAAGATTACA
1 ATCTCTAAGATTACA
12279005 TATCCTCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.33
22 10 0.33
23 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (22 bp):
ATCTCTAAGATTACAAAATCAT
Found at i:12278983 original size:23 final size:22
Alignment explanation
Indices: 12278938--12278995 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
12278928 AAAGGGTATC
* * *
12278938 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAAAT
12278959 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATCTTCTAAAAT
*
12278982 TACATATCATATCT
1 TACAAATCATATCT
12278996 AAGATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAAAT
Found at i:12279250 original size:8 final size:8
Alignment explanation
Indices: 12279222--12279263 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
12279212 GAGCTTATGC
*
12279222 TGTAAAGT
1 TGTAATGT
*
12279230 TGTTATG-
1 TGTAATGT
12279237 TGTAATGT
1 TGTAATGT
12279245 TGTAATGT
1 TGTAATGT
*
12279253 TGCAATGT
1 TGTAATGT
12279261 TGT
1 TGT
12279264 GGTAACACCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (8 bp):
TGTAATGT
Found at i:12281811 original size:156 final size:154
Alignment explanation
Indices: 12281524--12281976 Score: 630
Period size: 153 Copynumber: 2.9 Consensus size: 154
12281514 CTGCAACTTC
* * *
12281524 AAAACAAATTTAGTAAAAAATCCTTATTTCAGCCCTTTGTTCATA-TTTTTCCCCAATTTTATTA
1 AAAATAAATTTAGTAAAAAACCCTTATTTCAGCCCTTTGTTCATATTTTTTCCCGAATTTTATTA
* * *
12281588 CTTT-AAAAAAATATACTATTTTC-TGATTTTCTGATTTTACATTATTTTAGTACATTATA-TTT
66 CTTTCAAAAAAATATATTATTTTCGT-ATTTTATAATTTTACATTATTTTAGTACATTA-AGTTT
12281650 GAAATGTATTAATTTAGTGTGTTTTTT
129 GAAATGTATTAATTTAGTGT-TTTTTT
* * *
12281677 TAAATAAATTTAGTAAAAAACCCTTATTTCGGCCCTTTATTCATATTTTTTCCCGAATTTTATTA
1 AAAATAAATTTAGTAAAAAACCCTTATTTCAGCCCTTTGTTCATATTTTTTCCCGAATTTTATTA
* *
12281742 CTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTAAGTTTA
66 CTTTCAA-AAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTTAGTACATTAAGTTTG
12281807 AAATGTATTAATTTAGTGTTTTTTT
130 AAATGTATTAATTTAGTGTTTTTTT
* * * * ** *
12281832 AAAATAAATTTAGTAAAAAACCATTATTTTAGCCCTTTGTTCGTATTTTTTACCGAAGCCTCATT
1 AAAATAAATTTAGTAAAAAACCCTTATTTCAGCCCTTTGTTCATATTTTTTCCCGAA-TTTTATT
* * *
12281897 -GTTTC-AAAAAATATATTATTTTCGTATTTTATAATTTTACGTTATTTTAGTACATTATGTTTG
65 ACTTTCAAAAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTTAGTACATTAAGTTTG
12281960 AAATGTATTAATTTAGT
130 AAATGTATTAATTTAGT
12281977 AAAAAACCCT
Statistics
Matches: 269, Mismatches: 25, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
153 110 0.41
154 23 0.09
155 63 0.23
156 72 0.27
157 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (154 bp):
AAAATAAATTTAGTAAAAAACCCTTATTTCAGCCCTTTGTTCATATTTTTTCCCGAATTTTATTA
CTTTCAAAAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTTAGTACATTAAGTTTGA
AATGTATTAATTTAGTGTTTTTTT
Found at i:12282089 original size:131 final size:131
Alignment explanation
Indices: 12281838--12282075 Score: 343
Period size: 131 Copynumber: 1.8 Consensus size: 131
12281828 TTTTAAAATA
* *
12281838 AATTTAGTAAAAAACCATTATTTTAGCCCTTTGTTCGTATTTTTTACCGAAGCCTCATTGTTTCA
1 AATTTAGTAAAAAACCATTATTTTAGCCCTTTATTCGTATTTTTTACCGAAGCCTCATTCTTTCA
*
12281903 AAAAATATATTATTTTCGTATTTTATAATTTTACGTTATTTTAGTACATTATGTTTGAAATGTAT
66 AAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
12281968 T
131 T
* * * * ** *
12281969 AATTTAGTAAAAAACCCTTATTTTGGCCCTTTATTCGTATTTTTTTCCGGA-TTTTATTACTTTC
1 AATTTAGTAAAAAACCATTATTTTAGCCCTTTATTCGTATTTTTTACCGAAGCCTCATT-CTTTC
* * *
12282033 AAAAAATATTTTATTTTCGTATTTTATTATTTTACATTCTTTT
65 AAAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTT
12282076 CATATTTTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 4 0.04
131 89 0.96
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (131 bp):
AATTTAGTAAAAAACCATTATTTTAGCCCTTTATTCGTATTTTTTACCGAAGCCTCATTCTTTCA
AAAAATATATTATTTTCGTATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
T
Found at i:12282272 original size:26 final size:27
Alignment explanation
Indices: 12282218--12282272 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
12282208 GGGTTTTTTC
* * * *
12282218 ATGCTAAATAAATTTCATAAAATATAT
1 ATGCTAAATAAATATAATAAAACACAT
12282245 ATGCTAAATAAA-ATAATAAAACACAT
1 ATGCTAAATAAATATAATAAAACACAT
12282271 AT
1 AT
12282273 AATGTATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (27 bp):
ATGCTAAATAAATATAATAAAACACAT
Found at i:12282377 original size:10 final size:10
Alignment explanation
Indices: 12282362--12282448 Score: 58
Period size: 10 Copynumber: 9.1 Consensus size: 10
12282352 CTCCCTCTTC
12282362 TTCTTCTCCT
1 TTCTTCTCCT
*
12282372 TTCTTCTCCG
1 TTCTTCTCCT
* *
12282382 TTCTTTTTCT
1 TTCTTCTCCT
* *
12282392 TTCTTTTTCT
1 TTCTTCTCCT
*
12282402 TTCTTCTTCT
1 TTCTTCTCCT
12282412 TTCCTT-TCCT
1 TT-CTTCTCCT
12282422 TT-TT-T--T
1 TTCTTCTCCT
* *
12282428 TTCTTTTTCT
1 TTCTTCTCCT
12282438 TTCTTCTCCT
1 TTCTTCTCCT
12282448 T
1 T
12282449 CTTTCTTCTC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
6 3 0.05
7 2 0.03
8 4 0.06
10 52 0.81
11 3 0.05
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
TTCTTCTCCT
Found at i:12282393 original size:20 final size:20
Alignment explanation
Indices: 12282362--12282457 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
12282352 CTCCCTCTTC
* * *
12282362 TTCTTCTCCTTTCTTCTCCG
1 TTCTTCTCCTTTCTTTTTCT
* *
12282382 TTCTTTTTCTTTCTTTTTCT
1 TTCTTCTCCTTTCTTTTTCT
* * *
12282402 TTCTTCTTCTTTCCTTTCCT
1 TTCTTCTCCTTTCTTTTTCT
12282422 TT-TT-T--TTTCTTTTTCT
1 TTCTTCTCCTTTCTTTTTCT
12282438 TTCTTCTCC-TTCTTTCTTCT
1 TTCTTCTCCTTTCTTT-TTCT
12282458 CTCCAGCCGG
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
16 11 0.18
17 2 0.03
18 2 0.03
19 8 0.13
20 38 0.62
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (20 bp):
TTCTTCTCCTTTCTTTTTCT
Found at i:12282412 original size:36 final size:37
Alignment explanation
Indices: 12282372--12282450 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 37
12282362 TTCTTCTCCT
12282372 TTCTTCTCCGTT-CTTTTTCTTTCTTTTTCTTTCTTC
1 TTCTTCTCCGTTCCTTTTTCTTTCTTTTTCTTTCTTC
* *
12282408 TTCTT-TCCTTTCCTTTTTTTTTCTTTTTCTTTCTTC
1 TTCTTCTCCGTTCCTTTTTCTTTCTTTTTCTTTCTTC
*
12282444 TCCTTCT
1 TTCTTCT
12282451 TTCTTCTCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 5 0.13
36 32 0.84
37 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (37 bp):
TTCTTCTCCGTTCCTTTTTCTTTCTTTTTCTTTCTTC
Found at i:12282447 original size:26 final size:25
Alignment explanation
Indices: 12282382--12282457 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
12282372 TTCTTCTCCG
*
12282382 TTCTT-TTTCTTT-CTTTTTCTTTC
1 TTCTTCTTTCTTTCCTTTTTTTTTC
12282405 TTCTTCTTTCCTTTCCTTTTTTTTTC
1 TTCTTCTTT-CTTTCCTTTTTTTTTC
* * *
12282431 TTTTTCTTTCTTCTCCTTCTTTCTTC
1 TTCTTCTTTCTT-TCCTTTTTTTTTC
12282457 T
1 T
12282458 CTCCAGCCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 7 0.16
26 30 0.67
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (25 bp):
TTCTTCTTTCTTTCCTTTTTTTTTC
Found at i:12282531 original size:16 final size:16
Alignment explanation
Indices: 12282510--12282546 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
12282500 TTGGTTCGCT
12282510 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
12282526 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
12282542 GTAAT
1 GTAAT
12282547 AGGTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:12282617 original size:39 final size:44
Alignment explanation
Indices: 12282526--12282625 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 44
12282516 GAATAGAGGC
* * *
12282526 GTAATGGAATAGAGGTGTAATAGGTAATTCTTTTGTTTGGTTGACT
1 GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT-A-T
12282572 GTAATAGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
12282612 G-AATAGAATAGAGG
1 GTAATAGAATAGAGG
12282626 TATAATAGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
39 13 0.25
40 2 0.04
43 1 0.02
44 13 0.25
45 3 0.06
46 19 0.37
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (44 bp):
GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:12282622 original size:44 final size:46
Alignment explanation
Indices: 12282526--12282623 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 46
12282516 GAATAGAGGC
* * * *
12282526 GTAATGGAATAGAGGTGTAATAGGTAATTCTTTTGTTTGGTTGACT
1 GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
12282572 GTAATAGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
12282616 AG-AATAGA
1 -GTAATAGA
12282624 GGTATAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 24 0.51
45 4 0.09
46 19 0.40
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.38
Consensus pattern (46 bp):
GTAATAGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:12283770 original size:49 final size:49
Alignment explanation
Indices: 12283698--12283801 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
12283688 GAAAAAAAAC
* * ** * *
12283698 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
12283747 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
12283796 AAATTA
1 AAATTA
12283802 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Found at i:12286136 original size:29 final size:29
Alignment explanation
Indices: 12286044--12286160 Score: 118
Period size: 29 Copynumber: 4.1 Consensus size: 29
12286034 AATATTTTTA
12286044 GATTATTTTGATGTATTTCAATCATTATC
1 GATTATTTTGATGTATTTCAATCATTATC
* ** * *
12286073 GA-T-TTAT-ATAAATTTTAAT-ATT-TT
1 GATTATTTTGATGTATTTCAATCATTATC
*
12286097 AATTTCATTTTGATGTATTTCAATCATTATC
1 GA-TT-ATTTTGATGTATTTCAATCATTATC
*
12286128 GATTATTTTGATGTATTTCGATCATTATC
1 GATTATTTTGATGTATTTCAATCATTATC
12286157 GATT
1 GATT
12286161 TATATAGTCC
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 2 0.03
25 3 0.04
26 10 0.15
27 3 0.04
28 4 0.06
29 39 0.57
30 5 0.07
31 2 0.03
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (29 bp):
GATTATTTTGATGTATTTCAATCATTATC
Found at i:12294456 original size:21 final size:23
Alignment explanation
Indices: 12294417--12294462 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12294407 TAATATATAC
*
12294417 TTAATAAAAATATATCAAT-TTT
1 TTAATAAAAATAGATCAATATTT
*
12294439 TTAATAAAAATCGA-CAATATTT
1 TTAATAAAAATAGATCAATATTT
12294461 TT
1 TT
12294463 TTCTCTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (23 bp):
TTAATAAAAATAGATCAATATTT
Found at i:12295168 original size:16 final size:16
Alignment explanation
Indices: 12295132--12295184 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
12295122 TTGGTTCGCT
*
12295132 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
* *
12295148 ATAATGGAATAGATGC
1 GTAATGGAATAGAGGC
*
12295164 GTAATGAAATAGAGGC
1 GTAATGGAATAGAGGC
12295180 GTAAT
1 GTAAT
12295185 AGGTAATTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.42, C:0.04, G:0.30, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:12295248 original size:44 final size:46
Alignment explanation
Indices: 12295166--12295258 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
12295156 ATAGATGCGT
*
12295166 AATGAAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
*
12295212 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
12295256 AAT
1 AAT
12295259 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:12295254 original size:39 final size:44
Alignment explanation
Indices: 12295166--12295271 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
12295156 ATAGATGCGT
* *
12295166 AATGAAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
12295212 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
12295251 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
12295272 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 19 0.34
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 18 0.32
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:12295443 original size:18 final size:18
Alignment explanation
Indices: 12295420--12295551 Score: 90
Period size: 18 Copynumber: 6.9 Consensus size: 18
12295410 TTATTATTAA
12295420 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
12295438 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
12295455 ATATGAATTTACTAAATCATATT
1 ATAT-AATTTAATAAA--A-A-T
*
12295478 ATATAATACT-ATAAAAAT
1 ATATAAT-TTAATAAAAAT
* * *
12295496 AATTTAAATTAATTATTATTAA-
1 -ATATAATTTAA-TA--A-AAAT
12295518 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
12295536 ATATAATTTGATAAAA
1 ATATAATTTAATAAAA
12295552 TTCTTAGTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
17 11 0.12
18 37 0.42
19 9 0.10
20 5 0.06
21 10 0.11
22 9 0.10
23 8 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:12295611 original size:61 final size:60
Alignment explanation
Indices: 12295454--12295615 Score: 144
Period size: 61 Copynumber: 2.7 Consensus size: 60
12295444 TTTAATAAAA
* *
12295454 TATATGAATTTACT-AAATCATATTATATAATACTATAAAAATAATTTAAATTAATTATTAT
1 TATATGAATTTACTAAAATCATAATATATAATACTAT-AAAAT-ATTTAAATTAAATATTAT
* * * *
12295515 TAAATAT-AATTTA--ATAA--A-AATATATAAT-TTGATAAAAT-TCTTAGTATTAAATATTCT
1 T--ATATGAATTTACTAAAATCATAATATATAATACT-ATAAAATAT-TTA-AATTAAATATTAT
12295572 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATAT
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATAT
12295616 AATTTAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
55 5 0.06
56 9 0.11
57 17 0.22
58 14 0.18
59 1 0.01
60 1 0.01
61 20 0.25
62 8 0.10
63 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (60 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATTTAAATTAAATATTAT
Found at i:12303266 original size:38 final size:38
Alignment explanation
Indices: 12303217--12303291 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
12303207 GTCACTAACA
*
12303217 TTATTGAAAAGTGACAAATCAGTCACCCATTAACATTG
1 TTATCGAAAAGTGACAAATCAGTCACCCATTAACATTG
* * *
12303255 TTATCGAAAAGTTACAAATCAGTTACTCATTAACATT
1 TTATCGAAAAGTGACAAATCAGTCACCCATTAACATT
12303292 TTCCATTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (38 bp):
TTATCGAAAAGTGACAAATCAGTCACCCATTAACATTG
Found at i:12305943 original size:13 final size:13
Alignment explanation
Indices: 12305925--12305949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12305915 AAATTCAATG
12305925 TCAATTTCATATA
1 TCAATTTCATATA
12305938 TCAATTTCATAT
1 TCAATTTCATAT
12305950 CCAAACATGT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:12326602 original size:96 final size:97
Alignment explanation
Indices: 12326486--12326700 Score: 308
Period size: 96 Copynumber: 2.2 Consensus size: 97
12326476 GATTTTAGGG
* * * * *
12326486 TTTTAAGTAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTAT-AATTTTC
1 TTTTAAGGAAAAAATCAAATAAATAAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTA
* * *
12326550 AAAAAATTAGATTAGGGTTTAGTGTTTATGAT
66 AAAAAATTAGACTAGGGTTTAGTATTTAGGAT
** *
12326582 TTTTAAGGAAAAAATCAAATAAATTGGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTA
1 TTTTAAGGAAAAAATCAAATAAATAAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTA
*
12326647 AAAAAATTAGACTGGGGTTTAGTATTTAGGAT
66 AAAAAATTAGACTAGGGTTTAGTATTTAGGAT
12326679 TTTTAAGG-AAAAATCAAATAAA
1 TTTTAAGGAAAAAATCAAATAAA
12326701 GCTAGTTGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 64 0.60
97 42 0.40
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (97 bp):
TTTTAAGGAAAAAATCAAATAAATAAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTA
AAAAAATTAGACTAGGGTTTAGTATTTAGGAT
Found at i:12328356 original size:16 final size:16
Alignment explanation
Indices: 12328316--12328370 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
12328306 TTAATCATAT
*
12328316 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
12328332 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
12328347 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
12328365 -TAAAAT
1 TTAAAAT
12328371 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:12328363 original size:18 final size:17
Alignment explanation
Indices: 12328336--12328370 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12328326 TTTTTATTAA
*
12328336 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12328354 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12328371 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12328543 original size:119 final size:120
Alignment explanation
Indices: 12328319--12328596 Score: 436
Period size: 119 Copynumber: 2.3 Consensus size: 120
12328309 ATCATATTTA
*
12328319 AACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * * *
12328384 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAATT
*
12328439 AACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
* * *
12328502 ATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATAATTT
65 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAATT
*
12328558 AACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATA
12328597 TTTTCAATTA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
118 14 0.10
119 87 0.60
120 45 0.31
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAATT
Found at i:12333226 original size:107 final size:107
Alignment explanation
Indices: 12332936--12333298 Score: 601
Period size: 105 Copynumber: 3.4 Consensus size: 107
12332926 TATAATTATA
* *
12332936 TTTATTTTTTTCGTATACTGAAATCTGATTCTGACACGAAAAAAAAAAAGAATTTTTTTTTTAAA
1 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACG--AAAAAAAAAGAA-ATTTTTTTTAAA
12333001 -TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
63 TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
* *
12333045 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACG-AAAAAAAA-TAATTTTTTTTAATTTG
1 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTG
12333108 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
66 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
12333150 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTG
1 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTG
* *
12333215 TACTGGGTGCCGGCTATTGACAGGCCAGTACCCAAAA--TTT
66 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
*
12333255 TTTATTTTTTTCGTATACTGATATCTTATTCTGACACGAAAAAA
1 TTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAA
12333299 TTTTTTTTCT
Statistics
Matches: 242, Mismatches: 9, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
104 10 0.04
105 129 0.53
106 16 0.07
107 50 0.21
109 37 0.15
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (107 bp):
TTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTG
TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
Found at i:12334097 original size:16 final size:16
Alignment explanation
Indices: 12334076--12334127 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
12334066 TTTGGTTCGC
12334076 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
12334092 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
12334108 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12334124 TGTA
1 TGTA
12334128 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12334383 original size:16 final size:16
Alignment explanation
Indices: 12334343--12334397 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
12334333 TTAATCATAT
*
12334343 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
12334359 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
12334374 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
12334392 -TAAAAT
1 TTAAAAT
12334398 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:12334390 original size:18 final size:17
Alignment explanation
Indices: 12334363--12334397 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12334353 TTTTTATTAA
*
12334363 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12334381 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12334398 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12334510 original size:18 final size:17
Alignment explanation
Indices: 12334483--12334517 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12334473 TTACTATTAA
*
12334483 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12334501 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12334518 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12334563 original size:61 final size:60
Alignment explanation
Indices: 12334378--12334568 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
12334368 TTTTAATTAA
* *
12334378 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
12334439 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
12334497 A
60 T
*
12334498 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
12334559 AATATATAAT
1 AATATATAAT
12334569 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Done.