Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:2563888 original size:13 final size:13
Alignment explanation
Indices: 2563870--2564284 Score: 208
Period size: 13 Copynumber: 31.6 Consensus size: 13
2563860 TGAAGAGTAG
2563870 TATATGAAATGGT
1 TATATGAAATGGT
* *
2563883 TATATGAATTGAT
1 TATATGAAATGGT
* *
2563896 TATATGGAAATAGA
1 TATAT-GAAATGGT
*
2563910 TAAATGAAATGGT
1 TATATGAAATGGT
*
2563923 TATATG-AATCGAT
1 TATATGAAAT-GGT
***
2563936 TATATG-AATAAA
1 TATATGAAATGGT
*
2563948 TATAAGAAATGGT
1 TATATGAAATGGT
*
2563961 TATATG-AATCGAT
1 TATATGAAAT-GGT
* *
2563974 TATATGGAAATAGA
1 TATAT-GAAATGGT
*
2563988 TAAATGAAATGGT
1 TATATGAAATGGT
**
2564001 TATATG-AATCAAT
1 TATATGAAAT-GGT
* *
2564014 TATATGGAAATAGA
1 TATAT-GAAATGGT
*
2564028 TAAATGAAATGGT
1 TATATGAAATGGT
2564041 TATATG-AATAGGT
1 TATATGAAAT-GGT
* * *
2564054 TATATGGAAGTAGA
1 TATAT-GAAATGGT
*
2564068 TATATAAAATGGT
1 TATATGAAATGGT
*
2564081 TATATG-AATCGTT
1 TATATGAAAT-GGT
* *
2564094 TATATGGAAATAGA
1 TATAT-GAAATGGT
*
2564108 TAAATGAAATGGT
1 TATATGAAATGGT
* *
2564121 TATATG-ATTCAGT
1 TATATGAAAT-GGT
* * *
2564134 TATATGGAAGTAGA
1 TATAT-GAAATGGT
*
2564148 TATATGAAATGAT
1 TATATGAAATGGT
*
2564161 TATATG-AATCAGT
1 TATATGAAAT-GGT
*
2564174 TATATGAAA---A
1 TATATGAAATGGT
*
2564184 TAGATGAAATGGT
1 TATATGAAATGGT
2564197 TATAT-AAATCGGT
1 TATATGAAAT-GGT
* * *
2564210 TATATGGAAGTAGA
1 TATAT-GAAATGGT
*
2564224 TATATGAAATGGA
1 TATATGAAATGGT
2564237 TATATG-AATCGGT
1 TATATGAAAT-GGT
* *
2564250 TATATGGAAATAGA
1 TATAT-GAAATGGT
2564264 TATATGAAATGGT
1 TATATGAAATGGT
2564277 TATATGAA
1 TATATGAA
2564285 TCAAGTACAT
Statistics
Matches: 299, Mismatches: 74, Indels: 58
0.69 0.17 0.13
Matches are distributed among these distances:
10 8 0.03
12 33 0.11
13 185 0.62
14 54 0.18
15 19 0.06
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:2563923 original size:40 final size:40
Alignment explanation
Indices: 2563873--2564322 Score: 576
Period size: 40 Copynumber: 11.4 Consensus size: 40
2563863 AGAGTAGTAT
*
2563873 ATGAAATGGTTATATGAATTGATTATATGGAAATAGATAA
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
*
2563913 ATGAAATGGTTATATGAATCGATTATAT-G-AATAAATATA
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATA-A
2563952 A-GAAATGGTTATATGAATCGATTATATGGAAATAGATAA
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
*
2563991 ATGAAATGGTTATATGAATCAATTATATGGAAATAGATAA
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
* * * *
2564031 ATGAAATGGTTATATGAATAGGTTATATGGAAGTAGATAT
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
* *
2564071 ATAAAATGGTTATATGAATCGTTTATATGGAAATAGATAA
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
* * *
2564111 ATGAAATGGTTATATGATTC-AGTTATATGGAAGTAGATAT
1 ATGAAATGGTTATATGAATCGA-TTATATGGAAATAGATAA
* *
2564151 ATGAAATGATTATATGAATC-AGTTATAT-G-AA-A-ATAG
1 ATGAAATGGTTATATGAATCGA-TTATATGGAAATAGATAA
* * * *
2564187 ATGAAATGGTTATATAAATCGGTTATATGGAAGTAGATAT
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
* * *
2564227 ATGAAATGGATATATGAATCGGTTATATGGAAATAGATAT
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
* * * * *
2564267 ATGAAATGGTTATATGAATCAAGTACATGGAAATTGATAT
1 ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
2564307 ATGAAATGGTTATATG
1 ATGAAATGGTTATATG
2564323 GAAAGAGATG
Statistics
Matches: 363, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
36 27 0.07
37 2 0.01
38 35 0.10
39 8 0.02
40 291 0.80
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.34
Consensus pattern (40 bp):
ATGAAATGGTTATATGAATCGATTATATGGAAATAGATAA
Found at i:2564367 original size:67 final size:68
Alignment explanation
Indices: 2564220--2564367 Score: 153
Period size: 67 Copynumber: 2.2 Consensus size: 68
2564210 TATATGGAAG
* * **
2564220 TAGATATATGAAATGGATATATGAATCGGTTATATGGAAATAGATATATGAAATGGTTATATGAA
1 TAGATATTTGAAATGGATATATGAATCGGTTATATGGAAAGAGATATATGAAATGAATATATGAA
2564285 TCA
66 TCA
* * * *
2564288 -AG-TACATGGAAATTGATATATGAAAT-GGTTATATGGAAAGAGATGTATGAAATGAA-ATATT
1 TAGATA-TTTGAAATGGATATATG-AATCGGTTATATGGAAAGAGATATATGAAATGAATATA-T
*
2564349 GGAT-A
63 GAATCA
2564354 TAGATATTTGAAAT
1 TAGATATTTGAAAT
2564368 AAAATGTGAG
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
66 6 0.09
67 53 0.83
68 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (68 bp):
TAGATATTTGAAATGGATATATGAATCGGTTATATGGAAAGAGATATATGAAATGAATATATGAA
TCA
Found at i:2566674 original size:4 final size:4
Alignment explanation
Indices: 2566665--2566694 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2566655 ATAAACCATT
2566665 CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
2566695 ACGTCCCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:2567900 original size:36 final size:36
Alignment explanation
Indices: 2567853--2567973 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 36
2567843 AATGCAACCA
2567853 AAACACACCAAAAGCTCATAAGAGCTAATCCATCTG
1 AAACACACCAAAAGCTCATAAGAGCTAATCCATCTG
*
2567889 AAACACACCAAATA-CTCATCAGAGCTAATCCAT-TCG
1 AAACACACCAAA-AGCTCATAAGAGCTAATCCATCT-G
** ** * *
2567925 AAACACACCAATGGCTCCGAAGAGCTAGTCCAACCT-
1 AAACACACCAAAAGCTCATAAGAGCTAATCC-ATCTG
2567961 AAACACACCAAAA
1 AAACACACCAAAA
2567974 CAGATAGTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
35 1 0.01
36 66 0.94
37 2 0.03
38 1 0.01
ACGTcount: A:0.44, C:0.31, G:0.11, T:0.15
Consensus pattern (36 bp):
AAACACACCAAAAGCTCATAAGAGCTAATCCATCTG
Found at i:2579040 original size:17 final size:16
Alignment explanation
Indices: 2579018--2579060 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2579008 TAGTTCCTTA
2579018 TCTTTTCTTTTCTTTTT
1 TCTTTTCTTTT-TTTTT
2579035 TCTTTT-TTTTTTTTT
1 TCTTTTCTTTTTTTTT
*
2579050 TGCCTTTCTTT
1 T-CTTTTCTTT
2579061 CGTGGCAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 8 0.35
17 9 0.39
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (16 bp):
TCTTTTCTTTTTTTTT
Found at i:2582751 original size:27 final size:28
Alignment explanation
Indices: 2582710--2582762 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
2582700 AGAAGGCACC
*
2582710 ACCCATACCATCCAAATACCCGTATTTT
1 ACCCATACCACCCAAATACCCGTATTTT
* *
2582738 ACCC-TACCACCCAACTACTCGTATT
1 ACCCATACCACCCAAATACCCGTATT
2582763 GAACCCGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.30, C:0.40, G:0.04, T:0.26
Consensus pattern (28 bp):
ACCCATACCACCCAAATACCCGTATTTT
Found at i:2582768 original size:27 final size:28
Alignment explanation
Indices: 2582710--2582768 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
2582700 AGAAGGCACC
* **
2582710 ACCCATACCATCCAAATACCCGTATTTT
1 ACCCATACCACCCAAATACCCGTATTGA
* *
2582738 ACCC-TACCACCCAACTACTCGTATTGA
1 ACCCATACCACCCAAATACCCGTATTGA
2582765 ACCC
1 ACCC
2582769 GTATACCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.41, G:0.05, T:0.24
Consensus pattern (28 bp):
ACCCATACCACCCAAATACCCGTATTGA
Found at i:2587368 original size:18 final size:19
Alignment explanation
Indices: 2587342--2587380 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2587332 GCAACCATAA
2587342 TTCTAATTT-TATTTTATT
1 TTCTAATTTATATTTTATT
* *
2587360 TTCTTATTTATTTTTTATT
1 TTCTAATTTATATTTTATT
2587379 TT
1 TT
2587381 ATTTTCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTAATTTATATTTTATT
Found at i:2587371 original size:12 final size:13
Alignment explanation
Indices: 2587350--2587388 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
2587340 AATTCTAATT
2587350 TTATTTTATTTTC
1 TTATTTTATTTTC
2587363 TTA-TTTATTTT-
1 TTATTTTATTTTC
2587374 TTATTTTATTTTC
1 TTATTTTATTTTC
2587387 TT
1 TT
2587389 TATCAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 16 0.67
13 5 0.21
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTTC
Found at i:2590584 original size:198 final size:199
Alignment explanation
Indices: 2590241--2590622 Score: 640
Period size: 198 Copynumber: 1.9 Consensus size: 199
2590231 ATGATGAGCC
*
2590241 AACCTCATGAAAAAGTGATGTGTGCGGTGTTTGGGTCACTATAGGCGTGTAACCATAAGGTGCCC
1 AACCTCATGAAAAAGTGATGTGTGCGGTGTTTAGGTCACTATAGGCGTGTAACCATAAGGTGCCC
*
2590306 CAAATATTGGGTACATCAAAACGCTGTCGGGCATCGTCATCATCATCAATTGCTACACAAGCATC
66 CAAATATTGGGTACATCAAAACGCTGTCGGGCATCATCATCATCATCAATTGCTACACAAGCATC
* * * *
2590371 TACATCGGTATCGCCATCGGTGACGGTGCATACCTTGGTGTCTGTCTTGGCATGGGGTTCGGCAT
131 TACAGCGGTATCGCCATCGGTGAAGGTGCATACCTTGGCGTCTGTCCTGGCATGGGGTTCGGCAT
2590436 TAGA
196 TAGA
*
2590440 AACC-CATGAAAAAGTGATGTGTGCGGTGTTTAGGTCACTATAGTCGTGTAACCATAAGGTGCCC
1 AACCTCATGAAAAAGTGATGTGTGCGGTGTTTAGGTCACTATAGGCGTGTAACCATAAGGTGCCC
* * * * *
2590504 CAAATCTTGGGTACATCAGAACGCTGTTGGGCATCATCATCATCATCAATTGTTGCACAAGCATC
66 CAAATATTGGGTACATCAAAACGCTGTCGGGCATCATCATCATCATCAATTGCTACACAAGCATC
*
2590569 TGCAGCGGTATCGCCATCGGTGAAGGTGCATACCTTGGCGTCTGTCCTGGCATG
131 TACAGCGGTATCGCCATCGGTGAAGGTGCATACCTTGGCGTCTGTCCTGGCATG
2590623 AGTTTGGCAT
Statistics
Matches: 170, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
198 166 0.98
199 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (199 bp):
AACCTCATGAAAAAGTGATGTGTGCGGTGTTTAGGTCACTATAGGCGTGTAACCATAAGGTGCCC
CAAATATTGGGTACATCAAAACGCTGTCGGGCATCATCATCATCATCAATTGCTACACAAGCATC
TACAGCGGTATCGCCATCGGTGAAGGTGCATACCTTGGCGTCTGTCCTGGCATGGGGTTCGGCAT
TAGA
Found at i:2591618 original size:2 final size:2
Alignment explanation
Indices: 2591557--2591599 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2591547 TGGTTTAAAG
* * *
2591557 AT AT AT AT AT AT AT AT AT AT AT AC AT GT GT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2591598 AT
1 AT
2591600 GTTAACTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2593824 original size:64 final size:64
Alignment explanation
Indices: 2593754--2593886 Score: 250
Period size: 64 Copynumber: 2.1 Consensus size: 64
2593744 TTTTTTTAAA
*
2593754 ATATATTTATGTACACGTTTTAAAAAAATCATTGTAAACATTTTTTTTACACATTCTATTATTT
1 ATATATTTATGTACACATTTTAAAAAAATCATTGTAAACATTTTTTTTACACATTCTATTATTT
2593818 ATATATTTATGTACACATTTTAAAAAAATCATTGTAAACATTTTTTTTACACATTCTATTATTT
1 ATATATTTATGTACACATTTTAAAAAAATCATTGTAAACATTTTTTTTACACATTCTATTATTT
2593882 -TATAT
1 ATATAT
2593887 GCATATTGTA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 5 0.07
64 63 0.93
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (64 bp):
ATATATTTATGTACACATTTTAAAAAAATCATTGTAAACATTTTTTTTACACATTCTATTATTT
Found at i:2600785 original size:50 final size:50
Alignment explanation
Indices: 2600703--2601220 Score: 333
Period size: 50 Copynumber: 10.4 Consensus size: 50
2600693 GCAGTGGAAT
* *** * *
2600703 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
* * ** ** * *
2600753 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGACGGTGCGGTGGAAC
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
* * * * *** * *
2600803 GGATTGAAGCTACAACGACGGATCTGGTTTCCCTGATACTGCAATTTAAA
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
* * * * *
2600853 AGATTGAAGCCACGACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGA-TAGTGCAATTGAAA
* * ** * * *
2600903 AGATTGAAGCTACGACGGCAGAT-TTGGTTTCCCTGATATTACAATTTAAA
1 AGATTGAAGCCACGACGGCGGATCTT-ACTTCCCTGATAGTGCAATTGAAA
* * * * * * *
2600953 AGATTGAAGCCACAACGGTGGATCTTACTT-CCTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGA-TAGTGCAATTGAAA
* * *** * *
2601003 AGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
* * * * *
2601053 AGATTGAAGCCACGACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGGAAT
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGA-TAGTGCAATTGAAA
* * *** * * *
2601103 AGATTGAAGCTACGATGGCGGATCTGGTTTTCCTGATATTGCAATTAAAA
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
* * * * * * * *
2601153 ATATTGAAGCCACAACGGCGGATCTTACTTCCTTAACAGTGCAGTGGAAT
1 AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
*
2601203 AGATTGAAGCGACGACGG
1 AGATTGAAGCCACGACGG
2601221 TAGATCTGGT
Statistics
Matches: 336, Mismatches: 124, Indels: 16
0.71 0.26 0.03
Matches are distributed among these distances:
49 14 0.04
50 308 0.92
51 14 0.04
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACGACGGCGGATCTTACTTCCCTGATAGTGCAATTGAAA
Found at i:2601261 original size:100 final size:100
Alignment explanation
Indices: 2600677--2601235 Score: 859
Period size: 100 Copynumber: 5.6 Consensus size: 100
2600667 ACCATAGATT
*
2600677 TTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
2600742 TGCAATTAAAAAGATTGAAGCCACAACGGCAGATC
66 TGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
* * * * * *
2600777 TTACTTCCCT-GACGGTGCGGTGGAACGGATTGAAGCTACAACGACGGATCTGGTTTCCCTGATA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
* *
2600841 CTGCAATTTAAAAGATTGAAGCCACGACGGCGGATC
65 TTGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
* *
2600877 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATTTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
2600942 TACAATTTAAAAGATTGAAGCCACAACGGTGGATC
66 TGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
*
2600977 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
2601042 TGCAATTTAAAAGATTGAAGCCACGACGGCGGATC
66 TGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
* * *
2601077 TTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGCTACGATGGCGGATCTGGTTTTCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
2601142 TGCAATTAAAAATATTGAAGCCACAACGGCGGATC
66 TGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
* * * **
2601177 TTACTTCCTTAACAGTGCAGTGGAATAGATTGAAGCGACGACGGTAGATCTGGTTTCCC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
2601236 CGACATTGTA
Statistics
Matches: 415, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 413 1.00
101 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTTAAAAGATTGAAGCCACAACGGCGGATC
Found at i:2602932 original size:2 final size:2
Alignment explanation
Indices: 2602925--2602963 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2602915 CATTCTTGTA
2602925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2602964 AACTTTTNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2604548 original size:18 final size:18
Alignment explanation
Indices: 2604522--2604570 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
2604512 AATGGCAAAG
*
2604522 ATGATAAATGAATACGAA
1 ATGAGAAATGAATACGAA
*
2604540 ATGAGAAATGAAATATGAA
1 ATGAGAAATG-AATACGAA
2604559 ATGGAGAAATGA
1 AT-GAGAAATGA
2604571 GATGTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (18 bp):
ATGAGAAATGAATACGAA
Found at i:2604579 original size:20 final size:19
Alignment explanation
Indices: 2604522--2604570 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2604512 AATGGCAAAG
* *
2604522 ATGATAAATG-AATACGAA
1 ATGAGAAATGAAATATGAA
2604540 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
2604559 ATGGAGAAATGA
1 AT-GAGAAATGA
2604571 GATGTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 9 0.33
19 9 0.33
20 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:2607624 original size:29 final size:29
Alignment explanation
Indices: 2607592--2607648 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2607582 CCTATTTCCC
** *
2607592 TAATTAATTTTAAAACCAACCTAAAGGCT
1 TAATTAATTAAAAAAACAACCTAAAGGCT
*
2607621 TAATTAATTAAAAAAACAACCTATAGGC
1 TAATTAATTAAAAAAACAACCTAAAGGC
2607649 CTTACTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (29 bp):
TAATTAATTAAAAAAACAACCTAAAGGCT
Found at i:2610063 original size:48 final size:48
Alignment explanation
Indices: 2609993--2610181 Score: 272
Period size: 48 Copynumber: 3.9 Consensus size: 48
2609983 GCCATGGCTG
* * * * *
2609993 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAG-AGAAAGCCG
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAG-AAGCCA
* *
2610041 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGTAGAAGAAGTCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
2610089 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
* * *
2610137 ATAAACCGAGAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGGAAG
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAGAAG
2610182 GAAGCGTTAG
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
48 128 0.98
49 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (48 bp):
ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
Found at i:2610585 original size:9 final size:9
Alignment explanation
Indices: 2610573--2610640 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
2610563 CAATTCCAGC
2610573 AGAAGAGAA
1 AGAAGAGAA
*
2610582 AGAAGTGAA
1 AGAAGAGAA
*
2610591 GGAAGTA-AA
1 AGAAG-AGAA
2610600 AGAAGTA-AA
1 AGAAG-AGAA
*
2610609 AGAAGTGAA
1 AGAAGAGAA
*
2610618 ACAAGAGAA
1 AGAAGAGAA
*
2610627 AGAAAAGAA
1 AGAAGAGAA
2610636 AGAAG
1 AGAAG
2610641 TAGCTCTGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.63, C:0.01, G:0.29, T:0.06
Consensus pattern (9 bp):
AGAAGAGAA
Found at i:2610637 original size:27 final size:27
Alignment explanation
Indices: 2610573--2610641 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
2610563 CAATTCCAGC
* **
2610573 AGAAGAGAAAGAAGTGAAGGAAGTAAA
1 AGAAAAGAAAGAAGTGAAACAAGTAAA
*
2610600 AGAAGTA-AAAGAAGTGAAACAAG-AGAA
1 AGAA-AAGAAAGAAGTGAAACAAGTA-AA
2610627 AGAAAAGAAAGAAGT
1 AGAAAAGAAAGAAGT
2610642 AGCTCTGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.06
27 32 0.91
28 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.29, T:0.07
Consensus pattern (27 bp):
AGAAAAGAAAGAAGTGAAACAAGTAAA
Found at i:2611427 original size:1 final size:1
Alignment explanation
Indices: 2611421--2611484 Score: 74
Period size: 1 Copynumber: 64.0 Consensus size: 1
2611411 CTATAAGCTC
** *** *
2611421 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTTTTTTTTAGCTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2611485 ACTTGGGGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.02, C:0.03, G:0.05, T:0.91
Consensus pattern (1 bp):
T
Found at i:2617905 original size:26 final size:26
Alignment explanation
Indices: 2617886--2617938 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2617876 CATATCATTA
2617886 ACATCTCATTTATTTACATATAAATT
1 ACATCTCATTTATTTACATATAAATT
2617912 ACATCTCATTTATTTACATATAAATT
1 ACATCTCATTTATTTACATATAAATT
2617938 A
1 A
2617939 GATAACGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (26 bp):
ACATCTCATTTATTTACATATAAATT
Found at i:2625032 original size:44 final size:42
Alignment explanation
Indices: 2624892--2625049 Score: 133
Period size: 42 Copynumber: 3.7 Consensus size: 42
2624882 AACTCGTACA
* * ** *
2624892 ATGCCAACGTCTCAGGCATGGTCTTACATGT-AATCAATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACATAAATCAA-ATCG
* * * *
2624934 ATGCC-ACTGTCCCAAACAGGGTCTTACA-AGAAATCAAATATG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACATAAATCAAAT-CG
* *
2624976 ATGCCGATGTCCCAGACATGGTCTTACACATAAATCTCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACATAAA--TCAAATCG
**
2625020 ATGCCAACGTCCCAGACGCGGTCTTACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACA
2625050 ATAACACATA
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 4 0.04
42 50 0.54
43 5 0.05
44 27 0.29
45 6 0.07
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATAAATCAAATCG
Found at i:2635497 original size:21 final size:22
Alignment explanation
Indices: 2635473--2635524 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 22
2635463 CCTCTTTTCT
2635473 TTCTTTCTCTTCTTCAGCAAC-
1 TTCTTTCTCTTCTTCAGCAACA
2635494 TTC-TT-T-TTCTTCAGCAACA
1 TTCTTTCTCTTCTTCAGCAACA
*
2635513 AT-TTTCTCTTCT
1 TTCTTTCTCTTCT
2635525 ACAGTAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 3 0.12
21 7 0.27
ACGTcount: A:0.15, C:0.29, G:0.04, T:0.52
Consensus pattern (22 bp):
TTCTTTCTCTTCTTCAGCAACA
Found at i:2663730 original size:15 final size:15
Alignment explanation
Indices: 2663706--2663737 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2663696 ATGCCTCACA
2663706 CACCACGTTATCAAT
1 CACCACGTTATCAAT
*
2663721 CACCATGTTATCAAT
1 CACCACGTTATCAAT
2663736 CA
1 CA
2663738 AAAATAAACC
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:0.34, C:0.31, G:0.06, T:0.28
Consensus pattern (15 bp):
CACCACGTTATCAAT
Found at i:2665074 original size:15 final size:15
Alignment explanation
Indices: 2665050--2665081 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2665040 ATGCCTCACA
2665050 CACCACGTTATCAAT
1 CACCACGTTATCAAT
*
2665065 CACCATGTTATCAAT
1 CACCACGTTATCAAT
2665080 CA
1 CA
2665082 AAAATAAACC
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:0.34, C:0.31, G:0.06, T:0.28
Consensus pattern (15 bp):
CACCACGTTATCAAT
Found at i:2666659 original size:20 final size:20
Alignment explanation
Indices: 2666634--2666674 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2666624 AAATGTCCGT
2666634 AGGTATCGATATTGACATCC
1 AGGTATCGATATTGACATCC
*
2666654 AGGTATCGATATTGATATCC
1 AGGTATCGATATTGACATCC
2666674 A
1 A
2666675 AGTAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (20 bp):
AGGTATCGATATTGACATCC
Found at i:2672150 original size:132 final size:133
Alignment explanation
Indices: 2671991--2672255 Score: 505
Period size: 132 Copynumber: 2.0 Consensus size: 133
2671981 TTACAGCTAT
**
2671991 ATATATATATATATATATTGTGTGTGTGTTTTTGAAAGTGTAAGCTATATTGTTTCTTACCATTC
1 ATATATATATATATATATTGTGTGTGTGTTTTTGAAAGTACAAGCTATATTGTTTCTTACCATTC
2672056 AAACTTTTTTAAAGGAAAAAAATATTTTATTATTATTGTAAAGATTTGATGAAAAAGAATTCAAG
66 AAACTTTTTTAAAGGAAAAAAATATTTTATTATTATTGTAAAGATTTGATGAAAAAGAATTCAAG
2672121 AGG
131 AGG
2672124 ATATATATAT-TATATATTGTGTGTGTGTTTTTGAAAGTACAAGCTATATTGTTTCTTACCATTC
1 ATATATATATATATATATTGTGTGTGTGTTTTTGAAAGTACAAGCTATATTGTTTCTTACCATTC
2672188 AAACTTTTTTAAAGGAAAAAAATATTTTATTATTATTGTAAAGATTTGATGAAAAAGAATTCAAG
66 AAACTTTTTTAAAGGAAAAAAATATTTTATTATTATTGTAAAGATTTGATGAAAAAGAATTCAAG
2672253 AGG
131 AGG
2672256 TAAGGCATTG
Statistics
Matches: 130, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
132 120 0.92
133 10 0.08
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (133 bp):
ATATATATATATATATATTGTGTGTGTGTTTTTGAAAGTACAAGCTATATTGTTTCTTACCATTC
AAACTTTTTTAAAGGAAAAAAATATTTTATTATTATTGTAAAGATTTGATGAAAAAGAATTCAAG
AGG
Found at i:2673574 original size:43 final size:43
Alignment explanation
Indices: 2673526--2673713 Score: 331
Period size: 43 Copynumber: 4.4 Consensus size: 43
2673516 TTTTAGAAAT
2673526 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
2673569 AAACGCCGCTATAGAACAAGACATTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
*
2673612 AAACGCCGCTAAAGAACAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
*
2673655 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
2673698 AAACGCCGCTAAAGAA
1 AAACGCCGCTAAAGAA
2673714 TATGACTTTT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 136 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:2674450 original size:16 final size:15
Alignment explanation
Indices: 2674429--2674460 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2674419 ACATACATAT
2674429 ATATATCTATATCTAA
1 ATATATCTATAT-TAA
2674445 ATATATCTATATTAA
1 ATATATCTATATTAA
2674460 A
1 A
2674461 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATCTATATTAA
Found at i:2678013 original size:115 final size:114
Alignment explanation
Indices: 2677727--2678186 Score: 722
Period size: 114 Copynumber: 4.0 Consensus size: 114
2677717 NNNNNNNNNN
**
2677727 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
1 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACG
*
2677792 GCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTTCTCAAAAACGCCGCT
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
* * **
2677841 AAAGCCTTGAGCATTAGCGGTGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACG
1 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACG
* * * *
2677906 GCGTCGTTCGGATTAGGTTTTTTTACGGTGCTTTCTCAAAAACGCCGCT
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
**
2677955 AAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAAC
1 -AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAAC
* *
2678020 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAATGACGCT
65 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
* * *
2678070 AAAGCCTTGAGCATTAGCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACG
1 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACG
* * *
2678135 ACGTCATTGAGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
2678184 AAA
1 AAA
2678187 TCCCCGAAAG
Statistics
Matches: 314, Mismatches: 31, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
114 212 0.68
115 102 0.32
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACG
GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
Found at i:2678128 original size:229 final size:229
Alignment explanation
Indices: 2677727--2678186 Score: 823
Period size: 229 Copynumber: 2.0 Consensus size: 229
2677717 NNNNNNNNNN
2677727 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
1 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
* *
2677792 GCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTA
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGACGCTAAAGCCTTGAGCATTA
* * *
2677857 GCGGTGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTCG-GATTA
131 GCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATT-GAGATTA
*
2677921 GGTTTTTTTACGGTGCTTTCTCAAAAACGCCGCTA
195 GGTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTA
2677956 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
1 AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
*
2678021 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAATGACGCTAAAGCCTTGAGCATTA
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGACGCTAAAGCCTTGAGCATTA
*
2678086 GCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGCTTAG
131 GCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGATTAG
*
2678151 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTA
196 GTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTA
2678185 AA
1 AA
2678187 TCCCCGAAAG
Statistics
Matches: 221, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 1 0.00
229 220 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (229 bp):
AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACG
GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGACGCTAAAGCCTTGAGCATTA
GCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGATTAG
GTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTA
Found at i:2678202 original size:187 final size:187
Alignment explanation
Indices: 2677972--2678373 Score: 646
Period size: 187 Copynumber: 2.1 Consensus size: 187
2677962 CTGAGCATTA
* * ** *
2677972 GCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACGGCGTCGTTGGGCTT-A
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
* * * *
2678036 GGTTTTTTTGCGGCGCTTTCTCAAAAATGACGCTAAAGCCTTGAGCATTAGCGGTGCTTTCTTAA
66 GGTTTTTTTGCGACGCTTTCTCAAAAACGACGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
2678101 AAACGCCGCTAAATCCCCGA-AAGCTCAGAAAACGACGTCATTGAGCTTAGGTTTTTTT
131 AAACGCCGCTAAATCCCCGATAA-CTCA-AAAACGACGTCATTGAGCTTAGGTTTTTTT
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
*
2678224 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
66 GGTTTTTTTGCGACGCTTTCTCAAAAACGACGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
* * * *
2678289 AAACGCCGCTAAATCCCCGATTACTCAAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
131 AAACGCCGCTAAATCCCCGATAACTCAAAAACGACGTCATTGAGCTTAGGTTTTTTT
2678346 GCGGCGCTTTCTCAAAAACGCCGCTAAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAA
2678374 GCCCTAAGCA
Statistics
Matches: 199, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
187 113 0.57
188 85 0.43
189 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (187 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
GGTTTTTTTGCGACGCTTTCTCAAAAACGACGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
AAACGCCGCTAAATCCCCGATAACTCAAAAACGACGTCATTGAGCTTAGGTTTTTTT
Found at i:2678222 original size:73 final size:74
Alignment explanation
Indices: 2678086--2678260 Score: 282
Period size: 73 Copynumber: 2.4 Consensus size: 74
2678076 TTGAGCATTA
* *
2678086 GCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGCTT-A
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGCTTAA
2678150 GGTTTTTTT
66 GGTTTTTTT
* *
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGT-AGTTGGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCA-TTGAGCTTA
2678223 AGGTTTTTTT
65 AGGTTTTTTT
*
2678233 GCGACGCTTTCTCAAAAACGCCGCTAAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAA
2678261 GCCCTGAGCA
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
72 1 0.01
73 57 0.60
74 37 0.39
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (74 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCATTGAGCTTAA
GGTTTTTTT
Found at i:2678413 original size:301 final size:302
Alignment explanation
Indices: 2677857--2678487 Score: 1032
Period size: 301 Copynumber: 2.1 Consensus size: 302
2677847 TTGAGCATTA
* * *
2677857 GCGGTGCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTCGGATTAG
1 GCGGTGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTCGGATTAG
**
2677922 GTTTTTTTACGGTGCTTTCTCAAAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
66 GTTTTTTTACGACGCTTTCTCAAAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
*
2677987 AAACACCGCTAAATCCCCGACTGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC
131 AAACACCGCTAAATCCCCGACTACTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC
* * * *
2678052 TTTCTCAAAAATGACGCTAAAGCCTTGAGCATTAGCGGTGCTTTCTTAAAAACGCCGCTAAATCC
196 TTTCTCAAAAACGACGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCC
* *
2678117 CCGAAAGCTCAGAAAACGACGTCATTGAGCTTAGGTTTTTTT
261 CAGAAAGCTCAGAAAACGACATCATTGAGCTTAGGTTTTTTT
* * *
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTCGGATT-A
*
2678224 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTTTCTTA
65 GGTTTTTTTACGACGCTTTCTCAAAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTA
* *
2678288 AAAACGCCGCTAAATCCCCGATTACTCA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
130 AAAACACCGCTAAATCCCCGACTACTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
*
2678352 CTTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC
195 CTTTCTCAAAAACGACGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC
* * * *
2678417 CCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
260 CCAGAAAGCTCAGAAAACGACATCATTGAGCTTAGGTTTTTTT
2678460 GCGGTGCTTTCTCAAAAACGCCGCTAAA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAA
2678488 GCCCTGAGCA
Statistics
Matches: 304, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
301 160 0.53
302 112 0.37
303 32 0.11
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (302 bp):
GCGGTGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTCGGATTAG
GTTTTTTTACGACGCTTTCTCAAAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
AAACACCGCTAAATCCCCGACTACTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC
TTTCTCAAAAACGACGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCC
CAGAAAGCTCAGAAAACGACATCATTGAGCTTAGGTTTTTTT
Found at i:2678491 original size:114 final size:114
Alignment explanation
Indices: 2678159--2678599 Score: 724
Period size: 114 Copynumber: 3.9 Consensus size: 114
2678149 AGGTTTTTTT
* * * * *
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTT-A
*
2678224 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
65 GGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
2678274 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGATTACTCA-AAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAG
*
2678338 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
2678387 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAG
*
2678452 GTTTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
2678501 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAATGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAG
**
2678566 G-TTTTTTGCGGCGCTTTCTGGAAAACGCCGCTAA
66 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
2678600 TGCTTATTTT
Statistics
Matches: 308, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
113 118 0.38
114 152 0.49
115 38 0.12
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:2678506 original size:227 final size:228
Alignment explanation
Indices: 2678159--2678599 Score: 733
Period size: 227 Copynumber: 1.9 Consensus size: 228
2678149 AGGTTTTTTT
* *
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAACGGCATAGTTGGGCTTAA
2678224 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
66 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
* * *
2678289 AAACGCCGCTAAATCCCCGATTACTCA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC
131 AAACGCCGCTAAATCCCAGAATACTCAGAAAACGGCATCGTTGGGCTTAGG-TTTTTTGCGGCGC
2678353 TTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
195 TTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * *
2678387 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTT-A
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAACGGCATAGTTGGGCTTAA
**
2678451 GGTTTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
66 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
* *
2678516 AAACGCCGCTAAATCCCAGAATGCTCAGAAAATGGCATCGTTGGGCTTAGGTTTTTTGCGGCGCT
131 AAACGCCGCTAAATCCCAGAATACTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTGCGGCGCT
**
2678581 TTCTGGAAAACGCCGCTAA
196 TTCTCAAAAACGCCGCTAA
2678600 TGCTTATTTT
Statistics
Matches: 198, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
227 119 0.60
228 79 0.40
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (228 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAACGGCATAGTTGGGCTTAA
GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
AAACGCCGCTAAATCCCAGAATACTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTGCGGCGCT
TTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
Found at i:2678514 original size:415 final size:415
Alignment explanation
Indices: 2677743--2678599 Score: 1360
Period size: 415 Copynumber: 2.1 Consensus size: 415
2677733 CTGAGCATTA
* * ** *
2677743 GCGGCGCTTTCTTAAAAACACCGCTAAATCCCCGACTGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAG
** * *
2677808 GTTTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGTGCTTTCTTAAA
66 GTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAA
* *
2677873 AATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTCGGATTAGGTTTTTTTACGGTGCT
131 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTCGGATTAGGTTTTTTTACGGCGCT
*
2677938 TTCTCAAAAACGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCC
196 TTCTCAAAAACGCCGCTAAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCC
* * * *
2678003 CCGACTGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAATGACG
261 CAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGACG
* * *
2678068 CTAAAGCCTTGAGCATTAGCGGTGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
326 CTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAA
*
2678133 CGACGTCATTGAGCTTAGGTTTTTTT
391 CGACATCATTGAGCTTAGG-TTTTTT
2678159 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTT-A
2678224 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
65 GGTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAA
* * * *
2678289 AAACGCCGCTAAATCCCCGATTA-CTCA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
130 AAACGCCGCTAAATCCCCGA-AAGCTCAGAAAACGGCGTCGTTCGGATTAGGTTTTTTTACGGCG
*
2678352 CTTTCTCAAAAACGCCGCT-AAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
194 CTTTCTCAAAAACGCCGCTAAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAAT
* *
2678416 CCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGTGCTTTCTCAAAAACGC
259 CCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGA
*
2678481 CGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAA
324 CGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAAAGCTCAGAA
* * * *
2678546 AATGGCATCGTTGGGCTTAGGTTTTTT
389 AACGACATCATTGAGCTTAGGTTTTTT
**
2678573 GCGGCGCTTTCTGGAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
2678600 TGCTTATTTT
Statistics
Matches: 405, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
414 31 0.08
415 179 0.44
416 109 0.27
417 85 0.21
418 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (415 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTAGTTGGGCTTAG
GTTTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAA
AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTCGGATTAGGTTTTTTTACGGCGCT
TTCTCAAAAACGCCGCTAAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACACCGCTAAATCC
CAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGACG
CTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAA
CGACATCATTGAGCTTAGGTTTTTT
Found at i:2679321 original size:29 final size:30
Alignment explanation
Indices: 2679279--2679338 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2679269 CTAAGAAGTT
2679279 ACAATATTG-TTTTTTTTTTAGAGATACAC
1 ACAATATTGTTTTTTTTTTTAGAGATACAC
2679308 ACAATATTGTTTTTTTTTTTAGAGATACAC
1 ACAATATTGTTTTTTTTTTTAGAGATACAC
2679338 A
1 A
2679339 TGAATTTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
ACAATATTGTTTTTTTTTTTAGAGATACAC
Found at i:2680365 original size:26 final size:24
Alignment explanation
Indices: 2680317--2680367 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
2680307 TTTAAAATAC
* *
2680317 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
2680341 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
2680367 T
1 T
2680368 AAAAGATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:2680779 original size:14 final size:14
Alignment explanation
Indices: 2680760--2680796 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2680750 TCAAGCTACC
2680760 TCCACCTCCACCAA
1 TCCACCTCCACCAA
**
2680774 TCCACCTCCACCGG
1 TCCACCTCCACCAA
2680788 TCCACCTCC
1 TCCACCTCC
2680797 GGTCCTGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.59, G:0.05, T:0.16
Consensus pattern (14 bp):
TCCACCTCCACCAA
Found at i:2682048 original size:25 final size:25
Alignment explanation
Indices: 2682014--2682061 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
2682004 TTAAGATTTG
2682014 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
2682039 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
2682062 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:2682734 original size:17 final size:18
Alignment explanation
Indices: 2682706--2682739 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2682696 TAAGTTAGTG
2682706 AAAATAAAATTAAATATT
1 AAAATAAAATTAAATATT
2682724 AAAAT-AAATTAAATAT
1 AAAATAAAATTAAATAT
2682740 CGACCAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAATTAAATATT
Found at i:2685807 original size:90 final size:91
Alignment explanation
Indices: 2685694--2685874 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 91
2685684 ATATACATGA
2685694 GTAAGAAAAGTTGAAAATCGTAAACTATTCCAAAATGAGGTATTTAGATGGTTTATGAATTATAA
1 GTAAGAAAAGTTGAAAATCGTAAACTATTCCAAAATGAGGTATTTAGATGGTTTATGAATTATAA
2685759 GTTTTAAAATCGTGGTTATCCGAAAC
66 GTTTTAAAATCGTGGTTATCCGAAAC
2685785 GTAAGAAAAG-TGAAAATCGTAAACTATTCCAAAATGAGGTATTTAGATGGTTTATGAATTATAA
1 GTAAGAAAAGTTGAAAATCGTAAACTATTCCAAAATGAGGTATTTAGATGGTTTATGAATTATAA
2685849 GTTTTAAAATCGTGGTTATCCGAAAC
66 GTTTTAAAATCGTGGTTATCCGAAAC
2685875 CAAACCGAAT
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (91 bp):
GTAAGAAAAGTTGAAAATCGTAAACTATTCCAAAATGAGGTATTTAGATGGTTTATGAATTATAA
GTTTTAAAATCGTGGTTATCCGAAAC
Found at i:2685942 original size:21 final size:22
Alignment explanation
Indices: 2685918--2685964 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2685908 TAATTTTAAT
2685918 ATTTTATGATATAAAA-A-TAAA
1 ATTTTAT-ATATAAAATAGTAAA
*
2685939 ATTTTATATTTAAAATAGTAAA
1 ATTTTATATATAAAATAGTAAA
2685961 ATTT
1 ATTT
2685965 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 8 0.35
22 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTTATATATAAAATAGTAAA
Found at i:2687273 original size:14 final size:14
Alignment explanation
Indices: 2687254--2687284 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2687244 AGAAAAAAAA
2687254 TTTAAAACCCCTTG
1 TTTAAAACCCCTTG
2687268 TTTAAAACCCCTTG
1 TTTAAAACCCCTTG
2687282 TTT
1 TTT
2687285 TCTATGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (14 bp):
TTTAAAACCCCTTG
Found at i:2695570 original size:19 final size:19
Alignment explanation
Indices: 2695546--2695584 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2695536 ATTTATTCTT
*
2695546 AGATTTATCTACTTAAATA
1 AGATTTATCTACCTAAATA
2695565 AGATTTATCTACCTAAATA
1 AGATTTATCTACCTAAATA
2695584 A
1 A
2695585 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (19 bp):
AGATTTATCTACCTAAATA
Found at i:2699361 original size:41 final size:41
Alignment explanation
Indices: 2699267--2699362 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
2699257 AACCTAATTG
* **
2699267 AGAAAACAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 AGAAAATAATTCTTTTATTCTAATAAACTACTAAAAGATAA
*
2699308 GGAAAATAATTCTTTTATTCTAATAAACTACTAAAAGATAAA
1 AGAAAATAATTCTTTTATTCTAATAAACTACTAAAAGAT-AA
*
2699350 ATAAAAT-ATTCTT
1 AGAAAATAATTCTT
2699363 AGAATATCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 41 0.85
42 7 0.15
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (41 bp):
AGAAAATAATTCTTTTATTCTAATAAACTACTAAAAGATAA
Found at i:2699410 original size:19 final size:19
Alignment explanation
Indices: 2699386--2699426 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2699376 TGATGTATTC
*
2699386 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACCTAAA
2699405 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
2699424 TAA
1 TAA
2699427 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:2717999 original size:44 final size:44
Alignment explanation
Indices: 2717950--2718427 Score: 643
Period size: 44 Copynumber: 10.9 Consensus size: 44
2717940 CATAGAAACT
* * * * *
2717950 AATCTTCCACCTTTTCCACTGTTGGTTAGGGAGATAGGACTTGT
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* *
2717994 AATCTTCAACCTATTCCACTACTGGTTAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* * *
2718038 AATCTTCAGCCTATTCCAATGTTGGTCAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* * * **
2718082 AATCTTCAACCTATTCTAATGCTGGTCAGGGAGATAGAACTCAC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* *
2718126 AATCTTTAACCTATTCCACTGCTGGTTAGGGAGATAAGG-CTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGAT-AGGACTTGC
* *
2718170 AATCTTCAACCTATCCCACTGCTGGTCAAGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* * * * *
2718214 AATCTTCAACCTATTCCAATGCTTGTTAGGGAGATCGGGCTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
*
2718258 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAAGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
*
2718302 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAAGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
* * * * * * *
2718346 AATCTTCAACCTAATCCACTACTGTTCAGGGAGCTAGAATTTAC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
2718390 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGG
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGG
2718428 GCTTTGTGAT
Statistics
Matches: 379, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
43 3 0.01
44 374 0.99
45 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
Found at i:2719804 original size:49 final size:49
Alignment explanation
Indices: 2719702--2719804 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 49
2719692 CATTTTTCAT
* * *
2719702 TTTTTGGACTCAAAGCGCCCTTTAAGGGTTTTCACATTGGTCTCTTTTT
1 TTTTTAGACTCAAAGCGCCCTTTAAGGGTTTTCACATTGGTCTCTTCTC
** * *
2719751 TTTTTAGACTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTAT-TCTCTC
1 TTTTTAGACTCAAAGCGCCCTTTAAGGGTTTTCACATTGGTCTCT-TCTC
2719800 TTTTT
1 TTTTT
2719805 TATGCGAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
48 1 0.02
49 45 0.98
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (49 bp):
TTTTTAGACTCAAAGCGCCCTTTAAGGGTTTTCACATTGGTCTCTTCTC
Found at i:2725547 original size:15 final size:16
Alignment explanation
Indices: 2725517--2725549 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2725507 TATTAAGTTA
2725517 TTGGGTTTAAAAATTT
1 TTGGGTTTAAAAATTT
*
2725533 TTGGGTTT-TAAATTT
1 TTGGGTTTAAAAATTT
2725548 TT
1 TT
2725550 AATATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTGGGTTTAAAAATTT
Found at i:2726916 original size:31 final size:30
Alignment explanation
Indices: 2726874--2726977 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
2726864 GTACACCATA
2726874 GGTCACCCAACTATGGATCATTTTCTTTTTT
1 GGTCACCCAACTATGGAT-ATTTTCTTTTTT
* **
2726905 GGTCACTCAACTAT-GA-ATTTAT-TTAAATT
1 GGTCACCCAACTATGGATATTT-TCTT-TTTT
*
2726934 GGTCA-CCAACTATGGATTTGTTTCTTTTTT
1 GGTCACCCAACTATGGATAT-TTTCTTTTTT
2726964 GGTCACCCAACTAT
1 GGTCACCCAACTAT
2726978 AAACTTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
28 13 0.22
29 10 0.17
30 11 0.19
31 25 0.42
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.42
Consensus pattern (30 bp):
GGTCACCCAACTATGGATATTTTCTTTTTT
Found at i:2726967 original size:59 final size:59
Alignment explanation
Indices: 2726874--2726999 Score: 175
Period size: 59 Copynumber: 2.1 Consensus size: 59
2726864 GTACACCATA
* * *
2726874 GGTCACCCAACTATGGATCATTTTCTTTTTTGGTCACTCAACTATGAA-TTTATTTAAATT
1 GGTCA-CCAACTATGGATCATTTTCTTTTTTGGTCACCCAACTATAAACTTT-TTAAAATT
*
2726934 GGTCACCAACTATGGAT-TTGTTTCTTTTTTGGTCACCCAACTATAAACTTTTTAAAATT
1 GGTCACCAACTATGGATCAT-TTTCTTTTTTGGTCACCCAACTATAAACTTTTTAAAATT
2726993 GGTCACC
1 GGTCACC
2727000 CTACTAATTG
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
58 1 0.02
59 51 0.85
60 8 0.13
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (59 bp):
GGTCACCAACTATGGATCATTTTCTTTTTTGGTCACCCAACTATAAACTTTTTAAAATT
Found at i:2736207 original size:21 final size:19
Alignment explanation
Indices: 2736183--2736236 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
2736173 TCTTTTTTGC
*
2736183 AAAATCAAAATTTTCTTTTAA
1 AAAATCAAAATTTT-TCTT-A
**
2736204 AAAATCACTATTTTTCTTA
1 AAAATCAAAATTTTTCTTA
*
2736223 AAAATCAAAGTTTT
1 AAAATCAAAATTTT
2736237 ATTTCGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATCAAAATTTTTCTTA
Found at i:2738500 original size:19 final size:22
Alignment explanation
Indices: 2738438--2738487 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2738428 GTTTTCAAGC
*
2738438 TTCCAAGCTCGATAGTAAGTGA
1 TTCCAAGCTCCATAGTAAGTGA
2738460 TTCCAAGCTCCATAGTAAGTGA
1 TTCCAAGCTCCATAGTAAGTGA
2738482 TTCCAA
1 TTCCAA
2738488 CCCTTGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (22 bp):
TTCCAAGCTCCATAGTAAGTGA
Found at i:2743991 original size:17 final size:17
Alignment explanation
Indices: 2743941--2743992 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
2743931 AACTAATGTA
2743941 AAAAATA-ATTAATTAC
1 AAAAATATATTAATTAC
*
2743957 AAAAA-ATA-T-A-T-G
1 AAAAATATATTAATTAC
2743969 AAAAATATATTAATTAC
1 AAAAATATATTAATTAC
2743986 AAAAATA
1 AAAAATA
2743993 AGCATTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
12 5 0.18
13 4 0.14
14 2 0.07
15 3 0.11
16 7 0.25
17 7 0.25
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAAATATATTAATTAC
Found at i:2745040 original size:18 final size:19
Alignment explanation
Indices: 2744993--2745040 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2744983 TGACAAAAAC
*
2744993 TTTTTAAAAAATCATAATT
1 TTTTTAAAAAATCATAAGT
*
2745012 TTTTTTAAAAA-CA-ATAGT
1 TTTTTAAAAAATCATA-AGT
2745030 TTTTTAAAAAA
1 TTTTTAAAAAA
2745041 AACTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
19 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTTTAAAAAATCATAAGT
Found at i:2745040 original size:19 final size:18
Alignment explanation
Indices: 2744993--2745041 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2744983 TGACAAAAAC
*
2744993 TTTTTAAAAAATCATAAT
1 TTTTTAAAAAAACATAAT
** *
2745011 TTTTTTTAAAAACAATAGT
1 TTTTTAAAAAAAC-ATAAT
2745030 TTTTTAAAAAAA
1 TTTTTAAAAAAA
2745042 ACTTTTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAAAACATAAT
Found at i:2748655 original size:23 final size:23
Alignment explanation
Indices: 2748625--2748669 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2748615 CGGAAGTATA
2748625 TCTCTTTCACAACTGAGGTTATG
1 TCTCTTTCACAACTGAGGTTATG
2748648 TCTCTTTCACAACTGAGGTTAT
1 TCTCTTTCACAACTGAGGTTAT
2748670 TGGCAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (23 bp):
TCTCTTTCACAACTGAGGTTATG
Found at i:2751802 original size:29 final size:29
Alignment explanation
Indices: 2751754--2751831 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
2751744 ACCCATCTTG
* * *
2751754 TCAAAATTATTTCTTCAGAACTTATCCCC
1 TCAAAATTATTTTTTTAGAACCTATCCCC
***
2751783 TCAAAATTATTTTTTTAGAACCTATCTTG
1 TCAAAATTATTTTTTTAGAACCTATCCCC
2751812 T-AAAATTTATTTTTTTAGAA
1 TCAAAA-TTATTTTTTTAGAA
2751832 TCCCTAAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (29 bp):
TCAAAATTATTTTTTTAGAACCTATCCCC
Found at i:2751913 original size:19 final size:19
Alignment explanation
Indices: 2751837--2751906 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
2751827 TAGAATCCCT
*
2751837 AAACCCTAAAAATTAAATA
1 AAACCCTAAAAAATAAATA
*
2751856 AAACCCTAAATCCATAATTAAT-
1 AAACCCTAAA---A-AATAAATA
*
2751878 AAACACTAAAAAATAAATA
1 AAACCCTAAAAAATAAATA
2751897 AAACCCTAAA
1 AAACCCTAAA
2751907 CCTTAAACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 6 0.15
19 20 0.49
22 10 0.24
23 5 0.12
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.20
Consensus pattern (19 bp):
AAACCCTAAAAAATAAATA
Found at i:2753980 original size:228 final size:228
Alignment explanation
Indices: 2753583--2754002 Score: 493
Period size: 228 Copynumber: 1.8 Consensus size: 228
2753573 ATTGGTTTGC
** ** * * **
2753583 TTTTATGAGATTTTGGAACTTGAAGGAACCTGAAAACTTGCCCCGAATGAACCAAGTCTTTGCTG
1 TTTTATGAGATTTTGGAACTCAAACAAACCCGAAAACTTGCACCGAATGAACCAAGTCTTTGCCA
* * *
2753648 GGGACTTAGTAGGCTCAAATTGGTATATTTTTCAGTATCAGAACACTTAAGATTCCTAGCTCGAT
66 GGGACTTAGTAGGCTCAAATTGGTATATTTTTCAGCATCAAAACACTTAAGATTCATAGCTCGAT
* * * * * * *
2753713 CTCATTTCTTTTCCTTACTTTTTTAAATTGACTATTAGTAATCTATCATGGGGTTAAATTTGGTT
131 CTCATTTCTTTTCCATACCTTCTTAAAGTGAATATTAGTAAACTATCATGGGATTAAATTTGGTT
2753778 TGTGGTAAAGATATGTATTCCGGAATGTGAATG
196 TGTGGTAAAGATATGTATTCCGGAATGTGAATG
* * * * *
2753811 TTTTATGTGATTTTGGAACTCAAACAAACCCGAAAATTTGCACCTAATGAACGAAGTTTTTGCCA
1 TTTTATGAGATTTTGGAACTCAAACAAACCCGAAAACTTGCACCGAATGAACCAAGTCTTTGCCA
*** * * * * *
2753876 GGGA-TTAAGTAGGCTTGGATTGTTATATTGTTT-AGCATCAAAACACTTAGGATTGATAGTTTG
66 GGGACTT-AGTAGGCTCAAATTGGTATATT-TTTCAGCATCAAAACACTTAAGATTCATAGCTCG
* * * *
2753939 ATTTCGTTTCTTTTCCATACCTTCTTGAAGTGAATATTAGTAAACTATTATGGGATTAAATTTG
129 ATCTCATTTCTTTTCCATACCTTCTTAAAGTGAATATTAGTAAACTATCATGGGATTAAATTTG
2754003 ATTTTAGATT
Statistics
Matches: 155, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
227 2 0.01
228 150 0.97
229 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (228 bp):
TTTTATGAGATTTTGGAACTCAAACAAACCCGAAAACTTGCACCGAATGAACCAAGTCTTTGCCA
GGGACTTAGTAGGCTCAAATTGGTATATTTTTCAGCATCAAAACACTTAAGATTCATAGCTCGAT
CTCATTTCTTTTCCATACCTTCTTAAAGTGAATATTAGTAAACTATCATGGGATTAAATTTGGTT
TGTGGTAAAGATATGTATTCCGGAATGTGAATG
Found at i:2756429 original size:22 final size:23
Alignment explanation
Indices: 2756398--2756440 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2756388 TTTTTAATTT
2756398 TTTTAAGGTTAAGG-TTTTTTAA
1 TTTTAAGGTTAAGGATTTTTTAA
* *
2756420 TTTTAGGGTTTAGGATTTTTT
1 TTTTAAGGTTAAGGATTTTTT
2756441 TGGAAGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (23 bp):
TTTTAAGGTTAAGGATTTTTTAA
Found at i:2758848 original size:13 final size:14
Alignment explanation
Indices: 2758832--2758869 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2758822 AGAGAAAGAG
2758832 AAGAAAGAAAAAA-
1 AAGAAAGAAAAAAT
2758845 AAGAAA-AAAAAAT
1 AAGAAAGAAAAAAT
2758858 AAGGAAAGAAAA
1 AA-GAAAGAAAA
2758870 GTTGGAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 4 0.18
15 4 0.18
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
AAGAAAGAAAAAAT
Found at i:2759483 original size:16 final size:16
Alignment explanation
Indices: 2759462--2759492 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2759452 TGGCACTTTG
2759462 ATAGTGAATTGAAATT
1 ATAGTGAATTGAAATT
*
2759478 ATAGTGGATTGAAAT
1 ATAGTGAATTGAAAT
2759493 GGATTGAATT
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
ATAGTGAATTGAAATT
Found at i:2761104 original size:13 final size:14
Alignment explanation
Indices: 2761086--2761126 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2761076 TTTCCAAAGA
2761086 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
2761099 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
2761113 TACGGTTTA-GACT
1 TATGGTTTAGGACT
2761126 T
1 T
2761127 TAGGGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:2761218 original size:25 final size:26
Alignment explanation
Indices: 2761185--2761236 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
2761175 TTGTTTGTGG
*
2761185 TTTACGGGTTTAATG-TTTATGGTTAA
1 TTTACGGGTTTAA-GATCTATGGTTAA
2761211 TTTA-GGGTTTAAGATCTATGGTTAA
1 TTTACGGGTTTAAGATCTATGGTTAA
2761236 T
1 T
2761237 GTCTACGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 19 0.79
26 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (26 bp):
TTTACGGGTTTAAGATCTATGGTTAA
Found at i:2761344 original size:21 final size:21
Alignment explanation
Indices: 2761310--2761349 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2761300 TGACGTGTTA
*
2761310 GGGTTTAAGTTTTACGGTTTG
1 GGGTTTAAGGTTTACGGTTTG
* *
2761331 GGGTTTGAGGTTTAGGGTT
1 GGGTTTAAGGTTTACGGTT
2761350 AAGGGTATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.40, T:0.45
Consensus pattern (21 bp):
GGGTTTAAGGTTTACGGTTTG
Found at i:2770542 original size:21 final size:20
Alignment explanation
Indices: 2770516--2770584 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
2770506 CAACAACTTA
*
2770516 AAGCAGAGGTGGCAGCGAGAG
1 AAGCAGAGGT-GCAGTGAGAG
*
2770537 AAGCAGAGGCTACAGTGAGAG
1 AAGCAGAGG-TGCAGTGAGAG
* *
2770558 AAGCAAAGGCCGCAGTGAGAG
1 AAGCAGAGG-TGCAGTGAGAG
2770579 AAGCAG
1 AAGCAG
2770585 CGATAGAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.41, T:0.06
Consensus pattern (20 bp):
AAGCAGAGGTGCAGTGAGAG
Found at i:2770579 original size:23 final size:21
Alignment explanation
Indices: 2770532--2770583 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2770522 AGGTGGCAGC
* *
2770532 GAGAGAAGCAGAGGCTACAGT
1 GAGAGAAGCAAAGGCCACAGT
*
2770553 GAGAGAAGCAAAGGCCGCAGT
1 GAGAGAAGCAAAGGCCACAGT
2770574 GAGAGAAGCA
1 GAGAGAAGCA
2770584 GCGATAGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.38, T:0.06
Consensus pattern (21 bp):
GAGAGAAGCAAAGGCCACAGT
Found at i:2771132 original size:43 final size:42
Alignment explanation
Indices: 2771028--2771321 Score: 434
Period size: 42 Copynumber: 7.0 Consensus size: 42
2771018 GTTTGTGAAA
*
2771028 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGACC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCC
* *
2771071 -AAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCC
*
2771113 TAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCC
* * *
2771156 TAAGCGCCACTAAAGAACATGATCTTTAGCGACGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
*
2771198 TAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
2771240 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
2771282 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
2771322 TCTGTAAGCG
Statistics
Matches: 235, Mismatches: 12, Indels: 9
0.92 0.05 0.04
Matches are distributed among these distances:
41 1 0.00
42 158 0.67
43 75 0.32
44 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:2772398 original size:21 final size:21
Alignment explanation
Indices: 2772374--2772419 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2772364 CTAGGATAAT
* *
2772374 TGTTTTAGCATGTTTTGATTA
1 TGTTTGAGCATGTTTTGAATA
* *
2772395 TGTTTGATCGTGTTTTGAATA
1 TGTTTGAGCATGTTTTGAATA
2772416 TGTT
1 TGTT
2772420 AAACGAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.22, T:0.57
Consensus pattern (21 bp):
TGTTTGAGCATGTTTTGAATA
Found at i:2776014 original size:24 final size:24
Alignment explanation
Indices: 2775962--2776022 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
2775952 CATTTGGAGG
*
2775962 TGCAACCGGAGGTACATCTAGAGC
1 TGCAACCGGAGGTACATCCAGAGC
*
2775986 TGCAACCGGAGGTACATCCGGAGAC
1 TGCAACCGGAGGTACATCCAGAG-C
*
2776011 -GCAATCGGAGGT
1 TGCAACCGGAGGT
2776023 GTATCTGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.33, T:0.15
Consensus pattern (24 bp):
TGCAACCGGAGGTACATCCAGAGC
Found at i:2778654 original size:23 final size:23
Alignment explanation
Indices: 2778626--2778683 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
2778616 TTAATAAATT
2778626 ATATATATTATAT-ATACATGCAA
1 ATATAT-TTATATAATACATGCAA
* *
2778649 ATATATTTCA-ATAATTCATGTAA
1 ATATATTT-ATATAATACATGCAA
2778672 ATATATTTATAT
1 ATATATTTATAT
2778684 GTAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (23 bp):
ATATATTTATATAATACATGCAA
Found at i:2796351 original size:24 final size:24
Alignment explanation
Indices: 2796265--2796351 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
2796255 AATTATTTAT
*
2796265 ATTATA-AATATATAAAAAATAATA
1 ATTATATAATATATAAAATAT-ATA
* * *
2796289 TTTATTAAAATATATAAAATCTA-A
1 ATTA-TATAATATATAAAATATATA
*
2796313 ATT-TAATGATAATATAAAATATATA
1 ATTAT-ATAAT-ATATAAAATATATA
2796338 ATTATATAATATAT
1 ATTATATAATATAT
2796352 TAATTTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.02
23 3 0.06
24 21 0.43
25 11 0.22
26 13 0.27
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
ATTATATAATATATAAAATATATA
Found at i:2796362 original size:16 final size:15
Alignment explanation
Indices: 2796321--2796373 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
2796311 AAATTTAATG
*
2796321 ATAA-TATAAAATAT
1 ATAATTATATAATAT
2796335 ATAATTATATAATAT
1 ATAATTATATAATAT
2796350 ATTAATT-TAATAATAT
1 A-TAATTAT-ATAATAT
2796366 GATAATTA
1 -ATAATTA
2796374 GTGTTATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 4 0.12
15 11 0.33
16 17 0.52
17 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATAATTATATAATAT
Found at i:2796370 original size:8 final size:7
Alignment explanation
Indices: 2796262--2796371 Score: 50
Period size: 7 Copynumber: 15.9 Consensus size: 7
2796252 TATAATTATT
*
2796262 TATATTA
1 TATAATA
2796269 TA-AATA
1 TATAATA
*
2796275 TATAAAA
1 TATAATA
*
2796282 AATAATA
1 TATAATA
*
2796289 T-TTAT-
1 TATAATA
*
2796294 TAAAATA
1 TATAATA
*
2796301 TATAAAA
1 TATAATA
*
2796308 TCTAA-A
1 TATAATA
*
2796314 TTTAAT-
1 TATAATA
*
2796320 GATAATA
1 TATAATA
*
2796327 TAAAATA
1 TATAATA
2796334 TATAATTA
1 TATAA-TA
2796342 TATAATA
1 TATAATA
*
2796349 TATTAATT
1 TA-TAATA
2796357 TAATAATA
1 T-ATAATA
2796365 TGATAAT
1 T-ATAAT
2796372 TAGTGTTATA
Statistics
Matches: 75, Mismatches: 20, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
5 1 0.01
6 19 0.25
7 32 0.43
8 22 0.29
9 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:2796764 original size:19 final size:19
Alignment explanation
Indices: 2796724--2796766 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2796714 TCCAAATATT
* *
2796724 ATTATAATATTTTTTTACA
1 ATTATAATATTTTTATAAA
2796743 ATTATAAT-TTTTTCATAAA
1 ATTATAATATTTTT-ATAAA
2796762 ATTAT
1 ATTAT
2796767 TTATAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATAATATTTTTATAAA
Found at i:2797117 original size:26 final size:26
Alignment explanation
Indices: 2797062--2797117 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
2797052 TATTTTAAAT
* ** *
2797062 AAAAAATAAAAAATTTTAAATTTTTC
1 AAAAAATAAAAAATTTGAAATAATTA
2797088 AAAAAATAAAAAATTATGAAA-AATTA
1 AAAAAATAAAAAATT-TGAAATAATTA
2797114 AAAA
1 AAAA
2797118 GCATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAAAATAAAAAATTTGAAATAATTA
Found at i:2797130 original size:46 final size:44
Alignment explanation
Indices: 2797061--2797157 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 44
2797051 ATATTTTAAA
***
2797061 TAAAAAA-TAAAAAATTTTAAATTTTTCAAAAA-ATAAAAAATT
1 TAAAAAATTAAAAAATTTTAAATTTCAAAAAAATATAAAAAATT
*
2797103 ATGAAAAATTAAAAAGCATTTTAAATTTCAAAAAAATATAAAAAATT
1 -TAAAAAATTAAAAA--ATTTTAAATTTCAAAAAAATATAAAAAATT
2797150 TAAAAAAT
1 TAAAAAAT
2797158 ATAGCAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 6 0.13
44 6 0.13
46 23 0.51
47 10 0.22
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (44 bp):
TAAAAAATTAAAAAATTTTAAATTTCAAAAAAATATAAAAAATT
Found at i:2797148 original size:20 final size:21
Alignment explanation
Indices: 2797125--2797175 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2797115 AAAGCATTTT
2797125 AAATTTCAAAAAAATATA-AA
1 AAATTTCAAAAAAATATACAA
2797145 AAATTT--AAAAAATATAGCAA
1 AAATTTCAAAAAAATATA-CAA
*
2797165 AAATTCCAAAA
1 AAATTTCAAAA
2797176 TTCAATGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.38
20 13 0.50
22 3 0.12
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATTTCAAAAAAATATACAA
Found at i:2797418 original size:19 final size:20
Alignment explanation
Indices: 2797383--2797425 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2797373 CAAAGCAAAT
2797383 AAATTATTAAAAATATAAAA
1 AAATTATTAAAAATATAAAA
*
2797403 AAATTA-TAAAATTATAAAA
1 AAATTATTAAAAATATAAAA
2797422 AAAT
1 AAAT
2797426 CAGTTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTATTAAAAATATAAAA
Found at i:2805210 original size:18 final size:18
Alignment explanation
Indices: 2805180--2805231 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
2805170 TAAATGATTT
2805180 TTTTAATTAAGTAATAATA
1 TTTTAA-TAAGTAATAATA
2805199 TTTTAATAAGTAATAATA
1 TTTTAATAAGTAATAATA
* *
2805217 TTTTATTAATTAATA
1 TTTTAATAAGTAATA
2805232 TTATAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.81
19 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTTAATAAGTAATAATA
Found at i:2809987 original size:49 final size:52
Alignment explanation
Indices: 2809930--2810034 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 52
2809920 AAAATGTCAC
2809930 TAAAGTCATTGCTTTCAATC-AA-A-TTCTTTTCTTTTTTTTTACAGGATTT
1 TAAAGTCATTGCTTTCAATCAAATATTTCTTTTCTTTTTTTTTACAGGATTT
2809979 TAAAGTCATTGCTTTCAATCAAATTATTTTCTTTTCTTTTTTTTTACAGGATTT
1 TAAAGTCATTGCTTTCAATCAAA-TA-TTTCTTTTCTTTTTTTTTACAGGATTT
2810033 TA
1 TA
2810035 TGGATTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
49 20 0.39
50 2 0.04
52 1 0.02
54 28 0.55
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (52 bp):
TAAAGTCATTGCTTTCAATCAAATATTTCTTTTCTTTTTTTTTACAGGATTT
Found at i:2811561 original size:3 final size:3
Alignment explanation
Indices: 2811555--2811597 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2811545 GATAAGTAGC
* * *
2811555 AAT AAT ATT AGT AAT AAT AAT AAT AAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
2811598 CGGGGCGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2811592 original size:15 final size:15
Alignment explanation
Indices: 2811536--2811597 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
2811526 AGCTATTATA
2811536 TAATAATATGATAAGTAG
1 TAATAATA--ATAA-TAG
* * * *
2811554 CAATAATATTAGTAA
1 TAATAATAATAATAG
2811569 TAATAATAATAATAG
1 TAATAATAATAATAG
2811584 TAATAATAAATAAT
1 TAATAAT-AATAAT
2811598 CGGGGCGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 20 0.57
16 8 0.23
18 7 0.20
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:2813826 original size:90 final size:91
Alignment explanation
Indices: 2813732--2813925 Score: 252
Period size: 92 Copynumber: 2.2 Consensus size: 91
2813722 AAAAGAGAGT
* * *
2813732 AATTAAGCTCCT-C-TTTTTTTTACACTCAATTAAGCACTTGAACTTTCAAAATGTATCAAAAAG
1 AATTAAGCCCCTGCTTTTTTTTTACACTCAATTAAACACTTGAACTTTCAAAATGCATCAAAAAG
* *
2813795 GCCCTCAAACTTCTTTAAAAAAAAAAC
66 ACCCTCAAAATT-TTTAAAAAAAAAAC
* * *
2813822 AATTAAGCCCCTGCTTTTTTTTTTCACTCAATTAAATACTTGAACTTTCAAAATGCATCAAGAAG
1 AATTAAGCCCCTGCTTTTTTTTTACACTCAATTAAACACTTGAACTTTCAAAATGCATCAAAAAG
* *
2813887 ACCCTCAAAATTTTT--CAAAAAAAT
66 ACCCTCAAAATTTTTAAAAAAAAAAC
*
2813911 AATTAAGCCCATGCT
1 AATTAAGCCCCTGCT
2813926 CTTATTAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
89 21 0.23
90 11 0.12
91 4 0.04
92 55 0.60
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (91 bp):
AATTAAGCCCCTGCTTTTTTTTTACACTCAATTAAACACTTGAACTTTCAAAATGCATCAAAAAG
ACCCTCAAAATTTTTAAAAAAAAAAC
Found at i:2814015 original size:26 final size:28
Alignment explanation
Indices: 2813972--2814023 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
2813962 TAAATTTTAG
2813972 AAAAATTATTAAATTTTAATAAAAATAA
1 AAAAATTATTAAATTTTAATAAAAATAA
*
2814000 AAAAATT-TTAAA-TTTATTAAAAAT
1 AAAAATTATTAAATTTTAATAAAAAT
2814024 TATAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 5 0.22
28 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAAATTATTAAATTTTAATAAAAATAA
Found at i:2814030 original size:17 final size:17
Alignment explanation
Indices: 2814000--2814037 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2813990 ATAAAAATAA
*
2814000 AAAAATTTTAAATTTATT
1 AAAAATTATAAATTT-TT
2814018 AAAAATTAT-AATTTTT
1 AAAAATTATAAATTTTT
2814034 AAAA
1 AAAA
2814038 GAAAATTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAATTATAAATTTTT
Found at i:2814062 original size:20 final size:19
Alignment explanation
Indices: 2814012--2814063 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2814002 AAATTTTAAA
*
2814012 TTTATTAAAAATTATAATT
1 TTTAATAAAAATTATAATT
* *
2814031 TTTAAAAGAAAATTCCTAATT
1 TTTAATA-AAAATT-ATAATT
2814052 TTTAATAAAAAT
1 TTTAATAAAAAT
2814064 AGAGGCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 11 0.41
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTAATAAAAATTATAATT
Found at i:2814206 original size:88 final size:93
Alignment explanation
Indices: 2814058--2814240 Score: 250
Period size: 88 Copynumber: 2.0 Consensus size: 93
2814048 AATTTTTAAT
* **
2814058 AAAAATAGAGGCTTAATTGCTTCTTTTTTTAAAAAAATTTGAGGGTGTTTTTTTAATGCATTTTG
1 AAAAATAGAGGCTTAATTGCTTCTTTTTTAAAAAAAATTTGAGGGTACTTTTTTAATGCATTTTG
* * *
2814123 AAAGTTCAAGTACCCAATTGAGTGCAAA
66 AAAGCTCAAATACCCAAATGAGTGCAAA
*
2814151 AAAAATAGGGGCTTAATTG-TT-TTTTTTAAAAAAAATTT-A-GG-ACTTTTTTAATGCATTTTG
1 AAAAATAGAGGCTTAATTGCTTCTTTTTTAAAAAAAATTTGAGGGTACTTTTTTAATGCATTTTG
* *
2814211 AAAGCTCAAATACCTAAATGGGTGCAAA
66 AAAGCTCAAATACCCAAATGAGTGCAAA
2814239 AA
1 AA
2814241 TAAAAAACAG
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
88 42 0.52
89 2 0.02
90 1 0.01
91 16 0.20
92 2 0.02
93 18 0.22
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (93 bp):
AAAAATAGAGGCTTAATTGCTTCTTTTTTAAAAAAAATTTGAGGGTACTTTTTTAATGCATTTTG
AAAGCTCAAATACCCAAATGAGTGCAAA
Found at i:2815060 original size:274 final size:274
Alignment explanation
Indices: 2814564--2815111 Score: 1087
Period size: 274 Copynumber: 2.0 Consensus size: 274
2814554 GGCAAAATAG
2814564 TTGATGCTTCTATTTTTTAATATTAAATTTAATCCATACTATTATTTAAGCTTTTGATTGAGTTG
1 TTGATGCTTCTATTTTTTAATATTAAATTTAATCCATACTATTATTTAAGCTTTTGATTGAGTTG
2814629 TTATCATGAGCCAATTGTGTATTAACTCATTGAAAAATTACAAAAATACCATTCATTTTACAAAG
66 TTATCATGAGCCAATTGTGTATTAACTCATTGAAAAATTACAAAAATACCATTCATTTTACAAAG
2814694 TAAATTATATTATAATGAGGGTGTTTTTATCTTTTTATAAATAAATAAAAACTTATAGTGGAATT
131 TAAATTATATTATAATGAGGGTGTTTTTATCTTTTTATAAATAAATAAAAACTTATAGTGGAATT
2814759 TGAACCAAAAAAACACTACAAAGCGCTAATAAAGCGGCTCATGCTTTGGCCAGGGAGGCTTTATC
196 TGAACCAAAAAAACACTACAAAGCGCTAATAAAGCGGCTCATGCTTTGGCCAGGGAGGCTTTATC
2814824 TCAAGCGAATTACT
261 TCAAGCGAATTACT
*
2814838 TTGATGTTTCTATTTTTTAATATTAAATTTAATCCATACTATTATTTAAGCTTTTGATTGAGTTG
1 TTGATGCTTCTATTTTTTAATATTAAATTTAATCCATACTATTATTTAAGCTTTTGATTGAGTTG
2814903 TTATCATGAGCCAATTGTGTATTAACTCATTGAAAAATTACAAAAATACCATTCATTTTACAAAG
66 TTATCATGAGCCAATTGTGTATTAACTCATTGAAAAATTACAAAAATACCATTCATTTTACAAAG
2814968 TAAATTATATTATAATGAGGGTGTTTTTATCTTTTTATAAATAAATAAAAACTTATAGTGGAATT
131 TAAATTATATTATAATGAGGGTGTTTTTATCTTTTTATAAATAAATAAAAACTTATAGTGGAATT
2815033 TGAACCAAAAAAACACTACAAAGCGCTAATAAAGCGGCTCATGCTTTGGCCAGGGAGGCTTTATC
196 TGAACCAAAAAAACACTACAAAGCGCTAATAAAGCGGCTCATGCTTTGGCCAGGGAGGCTTTATC
2815098 TCAAGCGAATTACT
261 TCAAGCGAATTACT
2815112 CTGAATATGT
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 273 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (274 bp):
TTGATGCTTCTATTTTTTAATATTAAATTTAATCCATACTATTATTTAAGCTTTTGATTGAGTTG
TTATCATGAGCCAATTGTGTATTAACTCATTGAAAAATTACAAAAATACCATTCATTTTACAAAG
TAAATTATATTATAATGAGGGTGTTTTTATCTTTTTATAAATAAATAAAAACTTATAGTGGAATT
TGAACCAAAAAAACACTACAAAGCGCTAATAAAGCGGCTCATGCTTTGGCCAGGGAGGCTTTATC
TCAAGCGAATTACT
Found at i:2815175 original size:16 final size:16
Alignment explanation
Indices: 2815156--2815186 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2815146 TAATGTTTTT
*
2815156 TTCTCATTGTTCATTG
1 TTCTCATTGCTCATTG
2815172 TTCTCATTGCTCATT
1 TTCTCATTGCTCATT
2815187 TTACTTGGGT
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:0.13, C:0.23, G:0.10, T:0.55
Consensus pattern (16 bp):
TTCTCATTGCTCATTG
Found at i:2817288 original size:19 final size:19
Alignment explanation
Indices: 2817264--2817307 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2817254 GAGAAATTTA
*
2817264 TGCTAAAGCACTTTCCACT
1 TGCTAAAGCACTTCCCACT
2817283 TGCTAAAGCACTTCCCACT
1 TGCTAAAGCACTTCCCACT
2817302 TGCTAA
1 TGCTAA
2817308 GATAGCCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (19 bp):
TGCTAAAGCACTTCCCACT
Found at i:2823267 original size:9 final size:9
Alignment explanation
Indices: 2823255--2823386 Score: 58
Period size: 9 Copynumber: 14.2 Consensus size: 9
2823245 CTTTTCCTTA
2823255 TTATTATTTT
1 TTATTA-TTT
2823265 TATATTTATTT
1 T-TA-TTATTT
*
2823276 ATTATTCTTAT
1 -TTATTATT-T
*
2823287 TTATTATTC
1 TTATTATTT
2823296 TTATTTATTT
1 TTA-TTATTT
* *
2823306 TTATTGTAT
1 TTATTATTT
*
2823315 TTATTATGCT
1 TTATTAT-TT
* *
2823325 TTGTT-TTC
1 TTATTATTT
2823333 TTATTATTCT
1 TTATTATT-T
*
2823343 TT-CTATTTT
1 TTATTA-TTT
*
2823352 TTATTATGT
1 TTATTATTT
*
2823361 TTATTACTT
1 TTATTATTT
2823370 TTA-T-TTT
1 TTATTATTT
2823377 TTATT-TTT
1 TTATTATTT
2823385 TT
1 TT
2823387 GCTTCGCTAT
Statistics
Matches: 92, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.05
8 11 0.12
9 33 0.36
10 31 0.34
11 8 0.09
12 4 0.04
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (9 bp):
TTATTATTT
Found at i:2823279 original size:19 final size:19
Alignment explanation
Indices: 2823255--2823384 Score: 70
Period size: 19 Copynumber: 6.6 Consensus size: 19
2823245 CTTTTCCTTA
2823255 TTATTATTTTTATATTTAT
1 TTATTATTTTTATATTTAT
* *
2823274 TTATTATTCTTATTTATTATT
1 TTATTATTTTTATAT-TTA-T
*
2823295 CTTATTTATTTTTAT-TGTAT
1 -TTA-TTATTTTTATATTTAT
* * *
2823315 TTATTATGCTTTGT-TTT-C
1 TTATTAT-TTTTATATTTAT
*
2823333 TTATTATTCTTTCTATTT-T
1 TTATTATT-TTTATATTTAT
*
2823352 TTATTATGTTTATTACTTTTAT
1 TTATTATTTTTA-TA--TTTAT
*
2823374 TTTTTATTTTT
1 TTATTATTTTT
2823385 TTGCTTCGCT
Statistics
Matches: 85, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
18 18 0.21
19 34 0.40
20 4 0.05
21 6 0.07
22 14 0.16
23 9 0.11
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.72
Consensus pattern (19 bp):
TTATTATTTTTATATTTAT
Found at i:2823286 original size:13 final size:13
Alignment explanation
Indices: 2823252--2823304 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
2823242 ACCCTTTTCC
*
2823252 TTATTATTATTT-
1 TTATTCTTATTTA
2823264 TTATAT-TTATTTA
1 TTAT-TCTTATTTA
2823277 TTATTCTTATTTA
1 TTATTCTTATTTA
2823290 TTATTCTTATTTA
1 TTATTCTTATTTA
2823303 TT
1 TT
2823305 TTTATTGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTCTTATTTA
Found at i:2823582 original size:3 final size:3
Alignment explanation
Indices: 2823574--2823635 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
2823564 AAGTTTTGTT
*
2823574 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
2823620 TAA TTTA TTA TT- TTA T
1 TTA -TTA TTA TTA TTA T
2823636 ATCTTGGTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2825153 original size:17 final size:15
Alignment explanation
Indices: 2825133--2825173 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2825123 TCTTTTTATG
2825133 TTTATTTTTTTCGTTGT
1 TTTATTTTTTTC-TT-T
2825150 TTTA--TTTTTCTTT
1 TTTATTTTTTTCTTT
2825163 TTTATTTTTTT
1 TTTATTTTTTT
2825174 AGACTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.23
14 2 0.09
15 11 0.50
17 4 0.18
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (15 bp):
TTTATTTTTTTCTTT
Found at i:2825164 original size:12 final size:13
Alignment explanation
Indices: 2825101--2825171 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 13
2825091 AGTTTATTTG
*
2825101 TTTTC-TTTTTAG
1 TTTTCTTTTTTAT
*
2825113 TTTTCTTTTTTCT
1 TTTTCTTTTTTAT
*
2825126 TTTTATGTTTATT-T
1 TTTTCT-TTT-TTAT
2825140 TTTTCGTTGTTTTAT
1 TTTTC-TT-TTTTAT
2825155 TTTTCTTTTTTAT
1 TTTTCTTTTTTAT
2825168 TTTT
1 TTTT
2825172 TTAGACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.10
13 20 0.41
14 13 0.27
15 11 0.22
ACGTcount: A:0.07, C:0.07, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTAT
Found at i:2825208 original size:26 final size:23
Alignment explanation
Indices: 2825163--2825209 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
2825153 ATTTTTCTTT
*
2825163 TTTATTTTTTTAGACTTATTTCA
1 TTTATTTTTTTAAACTTATTTCA
2825186 TTTATTATCTTTTAAACTATATTT
1 TTTATT-T-TTTTAAACT-TATTT
2825210 TTATTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 8 0.40
26 5 0.25
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTATTTTTTTAAACTTATTTCA
Found at i:2826125 original size:8 final size:8
Alignment explanation
Indices: 2826112--2826158 Score: 62
Period size: 7 Copynumber: 5.9 Consensus size: 8
2826102 TTGTTCTTGT
2826112 AAAAAAAG
1 AAAAAAAG
2826120 -AAAAAAG
1 AAAAAAAG
2826127 -AAAAAAG
1 AAAAAAAG
2826134 AAAAAAAG
1 AAAAAAAG
2826142 ATCAAAAAAG
1 A--AAAAAAG
2826152 AAAAAAA
1 AAAAAAA
2826159 TATTGATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.39
8 14 0.39
10 8 0.22
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2828910 original size:59 final size:59
Alignment explanation
Indices: 2828841--2828959 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
2828831 GGAAGAATGT
*
2828841 GCAAGAGAAGATAACTTCAGGAGTTAGATTCATGAATTGAAAATAATATGTTGTTTGAG
1 GCAAGAGAAGATAACTTCAGGAGTTAGATTCATGAATTGAAAATAATATATTGTTTGAG
* *
2828900 GCAAGTGAAGATAACTTCAGGAGTTTGATTCATGAATTGAAAATAATATATTGTTTGAG
1 GCAAGAGAAGATAACTTCAGGAGTTAGATTCATGAATTGAAAATAATATATTGTTTGAG
2828959 G
1 G
2828960 GAGAATCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.32
Consensus pattern (59 bp):
GCAAGAGAAGATAACTTCAGGAGTTAGATTCATGAATTGAAAATAATATATTGTTTGAG
Found at i:2853254 original size:21 final size:22
Alignment explanation
Indices: 2853229--2853270 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
2853219 TGAAGAACTC
2853229 AAGTAATGGAAA-GAAAAAAGA
1 AAGTAATGGAAAGGAAAAAAGA
2853250 AAGTAATGGAAATGGAAAAAA
1 AAGTAATGGAAA-GGAAAAAA
2853271 TATAAGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (22 bp):
AAGTAATGGAAAGGAAAAAAGA
Found at i:2855977 original size:2 final size:2
Alignment explanation
Indices: 2855970--2855994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2855960 AAAATTTTGG
2855970 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2855995 GTAACAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2857457 original size:24 final size:24
Alignment explanation
Indices: 2857391--2857530 Score: 128
Period size: 24 Copynumber: 5.7 Consensus size: 24
2857381 TCATTAGGGA
*
2857391 TTACTGATTTCAGCTCG--TGAGAGC
1 TTACCGATTTCAGCTCGAAT-A-AGC
* *
2857415 GTACCAATTCTCAGCTCGAATAAGC
1 TTACCGATT-TCAGCTCGAATAAGC
*
2857440 TTACCGATTTCAGCTCGAATGAGC
1 TTACCGATTTCAGCTCGAATAAGC
2857464 TTACCGATTTCAGCTCG--TGAGAGC
1 TTACCGATTTCAGCTCGAAT-A-AGC
*
2857488 TTACCGATTCTCAGCTC-ATATGAGC
1 TTACCGATT-TCAGCTCGA-ATAAGC
2857513 TTACCGATTTACAGCTCG
1 TTACCGATTT-CAGCTCG
2857531 TGAGAGCATA
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.01
24 50 0.52
25 43 0.44
26 1 0.01
27 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGAATAAGC
Found at i:2857502 original size:49 final size:50
Alignment explanation
Indices: 2857437--2857560 Score: 184
Period size: 50 Copynumber: 2.5 Consensus size: 50
2857427 AGCTCGAATA
2857437 AGCTTACCGATT-TCAGCTCGA-ATGAGCTTACCGATTT-CAGCTCGTGAG
1 AGCTTACCGATTCTCAGCTC-ATATGAGCTTACCGATTTACAGCTCGTGAG
2857485 AGCTTACCGATTCTCAGCTCATATGAGCTTACCGATTTACAGCTCGTGAG
1 AGCTTACCGATTCTCAGCTCATATGAGCTTACCGATTTACAGCTCGTGAG
* *
2857535 AGCATATCGATTCAT-AGCTCATATGA
1 AGCTTACCGATTC-TCAGCTCATATGA
2857561 CCAGACATGT
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
48 13 0.19
49 23 0.33
50 33 0.47
51 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (50 bp):
AGCTTACCGATTCTCAGCTCATATGAGCTTACCGATTTACAGCTCGTGAG
Found at i:2857515 original size:73 final size:74
Alignment explanation
Indices: 2857391--2857530 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 74
2857381 TCATTAGGGA
*
2857391 TTACTGATTTCAGCTCGTGAGAGCGTACCAATTCTCAGCTCGAATAAGCTTACCGATTT-CAGCT
1 TTACCGATTTCAGCTCGTGAGAGCGTACCAATTCTCAGCTCGAATAAGCTTACCGATTTACAGCT
2857455 CGAATGAGC
66 CGAATGAGC
* * *
2857464 TTACCGATTTCAGCTCGTGAGAGCTTACCGATTCTCAGCTC-ATATGAGCTTACCGATTTACAGC
1 TTACCGATTTCAGCTCGTGAGAGCGTACCAATTCTCAGCTCGA-ATAAGCTTACCGATTTACAGC
2857528 TCG
65 TCG
2857531 TGAGAGCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 1 0.02
73 53 0.87
74 7 0.11
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (74 bp):
TTACCGATTTCAGCTCGTGAGAGCGTACCAATTCTCAGCTCGAATAAGCTTACCGATTTACAGCT
CGAATGAGC
Found at i:2857537 original size:25 final size:24
Alignment explanation
Indices: 2857391--2857546 Score: 158
Period size: 25 Copynumber: 6.4 Consensus size: 24
2857381 TCATTAGGGA
*
2857391 TTACTGATTTCAGCTCGTGAGAGC
1 TTACCGATTTCAGCTCGTGAGAGC
* *
2857415 GTACCAATTCTCAGCTCGAAT-A-AGC
1 TTACCGATT-TCAGCTCG--TGAGAGC
*
2857440 TTACCGATTTCAGCTCG-AATGAGC
1 TTACCGATTTCAGCTCGTGA-GAGC
2857464 TTACCGATTTCAGCTCGTGAGAGC
1 TTACCGATTTCAGCTCGTGAGAGC
*
2857488 TTACCGATTCTCAGCTCAT-ATGAGC
1 TTACCGATT-TCAGCTCGTGA-GAGC
2857513 TTACCGATTTACAGCTCGTGAGAGC
1 TTACCGATTT-CAGCTCGTGAGAGC
* *
2857538 ATATCGATT
1 TTACCGATT
2857547 CATAGCTCAT
Statistics
Matches: 111, Mismatches: 10, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.01
24 49 0.44
25 58 0.52
26 2 0.02
27 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGTGAGAGC
Found at i:2860907 original size:15 final size:16
Alignment explanation
Indices: 2860887--2860916 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2860877 TGATGCCTGG
2860887 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
2860902 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
2860917 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:2861110 original size:13 final size:13
Alignment explanation
Indices: 2861100--2861137 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2861090 GGAGTTGATA
2861100 TGGTCATTTGAAG
1 TGGTCATTTGAAG
2861113 TGGTCATTTGAAG
1 TGGTCATTTGAAG
*
2861126 TGGTCTTTTGAA
1 TGGTCATTTGAA
2861138 TAACCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (13 bp):
TGGTCATTTGAAG
Found at i:2862270 original size:9 final size:9
Alignment explanation
Indices: 2862256--2862280 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2862246 AATTAAAAGA
2862256 TTTTAAATC
1 TTTTAAATC
2862265 TTTTAAATC
1 TTTTAAATC
2862274 TTTTAAA
1 TTTTAAA
2862281 CTCGCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTAAATC
Found at i:2862417 original size:2 final size:2
Alignment explanation
Indices: 2862410--2862437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2862400 ACCGCTCTTC
2862410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2862438 TTGCATACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2863654 original size:29 final size:29
Alignment explanation
Indices: 2863600--2863671 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
2863590 AAATAAAAAA
* *
2863600 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATACATATTTTTTAT
*
2863628 TTACCAAAATATATATATATATTTTTTAT
1 TTACCAAAATATATATACATATTTTTTAT
2863657 TTACCAAAATATATA
1 TTACCAAAATATATA
2863672 AAAAAAACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 11 0.28
29 29 0.73
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (29 bp):
TTACCAAAATATATATACATATTTTTTAT
Found at i:2863681 original size:19 final size:18
Alignment explanation
Indices: 2863659--2863696 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2863649 TTTTTTATTT
*
2863659 ACCAAAATATATAAAAAAA
1 ACCAAAA-AAATAAAAAAA
2863678 ACCAAAAAAATAAAAAAA
1 ACCAAAAAAATAAAAAAA
2863696 A
1 A
2863697 TCTGGACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCAAAAAAATAAAAAAA
Found at i:2863766 original size:27 final size:27
Alignment explanation
Indices: 2863736--2863803 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
2863726 AAGGGAACAC
2863736 TGTTGGCGGCACCAAACAAGGAAACCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
**
2863763 TGTTGGCGGCACCAAACAAGGATTCCT
1 TGTTGGCGGCACCAAACAAGGAAACCT
2863790 TGTTGGCGGCACCA
1 TGTTGGCGGCACCA
2863804 CCTTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (27 bp):
TGTTGGCGGCACCAAACAAGGAAACCT
Found at i:2867772 original size:20 final size:18
Alignment explanation
Indices: 2867737--2867775 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2867727 NNNNTTTCTA
*
2867737 TTTTTTTTGTTTTTTTGG
1 TTTTTTTTGTTATTTTGG
2867755 TTTTTTTTGATATATTTTGG
1 TTTTTTTTG-T-TATTTTGG
2867775 T
1 T
2867776 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (18 bp):
TTTTTTTTGTTATTTTGG
Done.