Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 68 of 93
Found at i:9577794 original size:15 final size:15
Alignment explanation
Indices: 9577774--9577814 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
9577764 TTTATTATTA
* *
9577774 TTATTATTTAATCTT
1 TTATTATTTAATATG
9577789 TTATTA-TT-ATATG
1 TTATTATTTAATATG
9577802 TTATTATTTAATA
1 TTATTATTTAATA
9577815 ATTTTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTATTTAATATG
Found at i:9580066 original size:36 final size:35
Alignment explanation
Indices: 9579966--9580109 Score: 96
Period size: 36 Copynumber: 4.1 Consensus size: 35
9579956 AAGATGACTT
* * *
9579966 GGACAATAGCGTAAGTTG-AAAAATAAAAATGATG
1 GGACAACACCGTAAGTAGAAAAAATAAAAATGATG
* * * * *
9580000 GAGACAACACTGCAAGTCA-AAGAAACAAATATGATTG
1 G-GACAACACCGTAAGT-AGAAAAAATAAAAATGA-TG
* * **
9580037 GGACAACACCGTAAGTAGAAAAAATAAATACGACC
1 GGACAACACCGTAAGTAGAAAAAATAAAAATGATG
* * *
9580072 GGACAACATCGTAACT-TAAAAAATAAAAATGACTG
1 GGACAACACCGTAAGTAGAAAAAATAAAAATGA-TG
9580107 GGA
1 GGA
9580110 TAATACCACA
Statistics
Matches: 82, Mismatches: 22, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
34 14 0.17
35 29 0.35
36 36 0.44
37 3 0.04
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (35 bp):
GGACAACACCGTAAGTAGAAAAAATAAAAATGATG
Found at i:9580221 original size:35 final size:35
Alignment explanation
Indices: 9580124--9580312 Score: 121
Period size: 36 Copynumber: 5.3 Consensus size: 35
9580114 ACCACAGGCT
**
9580124 GAAAAATAAAAATAACTAAGACAACACTATAAGT-A
1 GAAAAAT-AAAATAACTAAGACAACACCGTAAGTCA
* * *
9580159 GGAAAGATAAATATGACCAAGACAACACCGTAAGTCA
1 -GAAAAATAAA-ATAACTAAGACAACACCGTAAGTCA
* *
9580196 -AAAAATAAAAGTAACTAAGATAACACCGTAGGTCA
1 GAAAAATAAAA-TAACTAAGACAACACCGTAAGTCA
* *** * *
9580231 GAAATATAAAGATGGTTAGGACAACACCGTAGGTCA
1 GAAAAATAAA-ATAACTAAGACAACACCGTAAGTCA
* * * * ** *
9580267 AAAAAACAAATATGACTAAGATAACATTGTAGGTCA
1 GAAAAATAAA-ATAACTAAGACAACACCGTAAGTCA
*
9580303 AAAAAATAAA
1 GAAAAATAAA
9580313 GATGATCAGG
Statistics
Matches: 121, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
34 1 0.01
35 31 0.26
36 87 0.72
37 2 0.02
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.17
Consensus pattern (35 bp):
GAAAAATAAAATAACTAAGACAACACCGTAAGTCA
Found at i:9580240 original size:71 final size:70
Alignment explanation
Indices: 9580125--9580326 Score: 210
Period size: 71 Copynumber: 2.8 Consensus size: 70
9580115 CCACAGGCTG
* * * * * * *
9580125 AAAAATAAAAATAACTAAGACAACACTATAAGT-AGGAAAGATAAATATGACCAAGACAACACCG
1 AAAAAT-AAAATAACTAAGATAACACTGTAGGTCA-GAAAAATAAAGATGATCAGGACAACACCG
9580189 TAAGTCA
64 TAAGTCA
* * * *
9580196 AAAAATAAAAGTAACTAAGATAACACCGTAGGTCAGAAATATAAAGATGGTTAGGACAACACCGT
1 AAAAATAAAA-TAACTAAGATAACACTGTAGGTCAGAAAAATAAAGATGATCAGGACAACACCGT
*
9580261 AGGTCA
65 AAGTCA
* *
9580267 AAAAA-ACAAATATGACTAAGATAACATTGTAGGTCAAAAAAATAAAGATGATCAGGACAA
1 AAAAATA-AAATA--ACTAAGATAACACTGTAGGTCAGAAAAATAAAGATGATCAGGACAA
9580327 TACCAACAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
70 7 0.06
71 61 0.56
72 41 0.38
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.17
Consensus pattern (70 bp):
AAAAATAAAATAACTAAGATAACACTGTAGGTCAGAAAAATAAAGATGATCAGGACAACACCGTA
AGTCA
Found at i:9580355 original size:36 final size:36
Alignment explanation
Indices: 9580308--9580386 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
9580298 GGTCAAAAAA
*
9580308 ATAAAGATGATCAGGACAATACCAACAATCAAGAAG
1 ATAAAGATGATCAGGACAACACCAACAATCAAGAAG
** *
9580344 ATAAAGATGATCAGGACAACACCAACGGTCAGGAAG
1 ATAAAGATGATCAGGACAACACCAACAATCAAGAAG
9580380 ATAAAGA
1 ATAAAGA
9580387 ATAAAGTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.13
Consensus pattern (36 bp):
ATAAAGATGATCAGGACAACACCAACAATCAAGAAG
Found at i:9580726 original size:26 final size:26
Alignment explanation
Indices: 9580673--9580726 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
9580663 TGTGGATGTA
*
9580673 ATAATGCAAATGTAAATGCCCTTTTT
1 ATAATGCAAATGTAAATGCCCTTGTT
* *
9580699 ATAATGCAAGTGTGAATG-CCTTGGTT
1 ATAATGCAAATGTAAATGCCCTT-GTT
9580725 AT
1 AT
9580727 GATACAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (26 bp):
ATAATGCAAATGTAAATGCCCTTGTT
Found at i:9581482 original size:83 final size:82
Alignment explanation
Indices: 9581347--9581508 Score: 209
Period size: 83 Copynumber: 2.0 Consensus size: 82
9581337 CTCTTACAAA
* * *
9581347 TTAATGACCACTATTTGGAAGGCGTGTGGATGGTGTGCTTGACAATTTAATTTTTTCACTAGTGG
1 TTAATGACCACTATTTAGAAGGCGTGTGGATGGTGTGATTGACAATTCAA-TTTTTCACTAGTGG
9581412 GCATATTTCAAGGAAGGC
65 GCATATTTCAAGGAAGGC
** * * * * *
9581430 TTAATGATTACTATTTAGAATGCTTGTGGATGAG-GTGATTGTCAATTCAATTTTTCATTGGTGG
1 TTAATGACCACTATTTAGAAGGCGTGTGGATG-GTGTGATTGACAATTCAATTTTTCACTAGTGG
9581494 GCATATTTCAAGGAA
65 GCATATTTCAAGGAA
9581509 AGATTGATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 27 0.40
83 40 0.59
84 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (82 bp):
TTAATGACCACTATTTAGAAGGCGTGTGGATGGTGTGATTGACAATTCAATTTTTCACTAGTGGG
CATATTTCAAGGAAGGC
Found at i:9582751 original size:433 final size:428
Alignment explanation
Indices: 9582136--9582946 Score: 1078
Period size: 433 Copynumber: 1.9 Consensus size: 428
9582126 GCATTCTTTT
* **
9582136 TTATTGAATTCTATCTCCTTTTTTACTTGGAACTAAAGCCTTATTCACTTTTTACCTTGAACTCT
1 TTATTGAATTCTATCTCCTTTTTTACTTGGAACTAAAGCCTTATTCACTTTTCACCTCAAACTCT
* * * * * * *
9582201 CATCTTTGAGGTGCATGTCTTTCTTTCTTTATTCTTTTCTTTTTATTTTTTTAATGAATGAATCG
66 CATCTCTAAGGTGCATATCTTTCTTTCTCTATTCTTTTATTTATATTTTTTTAATGAACGAATCG
* * * * *
9582266 TATTTATATAGTAAAAAATTAGATAATCATGAACAACATTCCAAAATTCTTTCTCTTAAAAACTT
131 TATTTAGACAATAAAAAATTAGAAAATCATGAACAAAATTCCAAAATTCTTTCTCTTAAAAACTT
* * * * * *
9582331 ATT-TCATTTATGCCTTTGATCTTTTTAAGTTCATTGTACTGGGCATTA-CCTCCCATAAATTGG
196 ATTCT-ATTAATGCCCTTCATCCTTTCAAGTTCATTCTACTGGGCATTACCCT-CCATAAATTGG
* * *
9582394 TATTCCTTTGCATTTAAGATGCCTTTTTAAGTTTTCAACTTAGAT-ATTTCCTTTGACTCAAACT
259 TATTCCTTTGCATCTAAGATACCTTTTCAAGTTTTCAACTTAGATCATTT-CTTTGACTCAAACT
* * *
9582458 GCCATTTTTGGGTTTTTAGTCATGAGTCCTCCTTTATTTCTTATTCATCTTTTTTTCTCTTTTTT
323 GCCATTTTTGGATTTTCAATCATGAGTCCTCCTTTATTTCTTATTCATCTTTTTTTCTCTTTTTT
9582523 TCTTCTTTTTCTTTTGAGAAATATTTGGCATCAACTTTAAC
388 TCTTCTTTTTCTTTTGAGAAATATTTGGCATCAACTTTAAC
*
9582564 TTATTGAATTCTATCTCCTTTTTTTACTTGGGATTTTAACTATAA-CCTTATTCACTTTTCATCT
1 TTATTGAATTCTATCTCC-TTTTTTACTT-GG-----AACTA-AAGCCTTATTCACTTTTCACCT
*
9582628 CAAACTCTCATCTCTAATGTGCATATCTTTCTTTCTCTATTC-TTTATTTAT-TTTTTTTAATGA
58 CAAACTCTCATCTCTAAGGTGCATATCTTTCTTTCTCTATTCTTTTATTTATATTTTTTTAATGA
* * * * *
9582691 ACGAATTGTATTTAGACAAT-GAATATTCAGAAAATCATGAACAAAATTTCAAAATTCTTTCTTT
123 ACGAATCGTATTTAGACAATAAAAAATT-AGAAAATCATGAACAAAATTCCAAAATTCTTTCTCT
* * * *
9582755 TGAAAACTTATTCTATTAATGCCCTTCATCCTTTCGAGTTCATTCTACTGGGCATTGCCCTCTAT
187 TAAAAACTTATTCTATTAATGCCCTTCATCCTTTCAAGTTCATTCTACTGGGCATTACCCTCCAT
* * *
9582820 AAATTGGTATTCTTTTGCATCTAAGTTACCTTTTCAAGTTTTCAACTTAGATCCTTTCTTTGACT
252 AAATTGGTATTCCTTTGCATCTAAGATACCTTTTCAAGTTTTCAACTTAGATCATTTCTTTGACT
* *
9582885 CAAACTGCCCTTTTTGGATTTTCAATCATGAGTCCTCCTTTATTTTTTATTCATCTTTTTTT
317 CAAACTGCCATTTTTGGATTTTCAATCATGAGTCCTCCTTTATTTCTTATTCATCTTTTTTT
9582947 TTTTAGAAAT
Statistics
Matches: 328, Mismatches: 43, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
428 18 0.05
429 10 0.03
430 2 0.01
432 5 0.02
433 220 0.67
434 14 0.04
435 57 0.17
436 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (428 bp):
TTATTGAATTCTATCTCCTTTTTTACTTGGAACTAAAGCCTTATTCACTTTTCACCTCAAACTCT
CATCTCTAAGGTGCATATCTTTCTTTCTCTATTCTTTTATTTATATTTTTTTAATGAACGAATCG
TATTTAGACAATAAAAAATTAGAAAATCATGAACAAAATTCCAAAATTCTTTCTCTTAAAAACTT
ATTCTATTAATGCCCTTCATCCTTTCAAGTTCATTCTACTGGGCATTACCCTCCATAAATTGGTA
TTCCTTTGCATCTAAGATACCTTTTCAAGTTTTCAACTTAGATCATTTCTTTGACTCAAACTGCC
ATTTTTGGATTTTCAATCATGAGTCCTCCTTTATTTCTTATTCATCTTTTTTTCTCTTTTTTTCT
TCTTTTTCTTTTGAGAAATATTTGGCATCAACTTTAAC
Found at i:9587026 original size:4 final size:4
Alignment explanation
Indices: 9587013--9587050 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
9587003 TCAATAATGT
* *
9587013 TAAA -AAA TAAA TAAA CAAA CAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
9587051 TCAAGCATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (4 bp):
TAAA
Found at i:9589643 original size:21 final size:21
Alignment explanation
Indices: 9589613--9589653 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9589603 TGGTATTTTA
*
9589613 TTTTTCTATTTTTTTACTAGC
1 TTTTTATATTTTTTTACTAGC
*
9589634 TTTTTATATTTTTTTTCTAG
1 TTTTTATATTTTTTTACTAG
9589654 TTTCTCCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTTTTACTAGC
Found at i:9590294 original size:144 final size:137
Alignment explanation
Indices: 9590010--9590353 Score: 327
Period size: 144 Copynumber: 2.5 Consensus size: 137
9590000 ATTATTCAAG
* * * * * *
9590010 ATTTTAAA-GCACCAAAAATCATAAAATATTAT-AAAATTAGATCTAAAAATTTTCGTCAAAATT
1 ATTTCAAATGCACCAAAAATCAT-AAATATTATGAAAATAAGATCTAAAAAATTTCATAAAAATC
** ** * *
9590073 CAAGCTCAAGAGGTTAAATTATGAAAATACCCCTAAAGTTTAGTAATTTCATACCTTCCGAGGTA
65 CAAGCTCAAGAGGCCAAATTACAAAAATACCCCTAAAGTTTAGTAATTTCACACCTACCGAGGTA
* *
9590138 TTGTAATG
130 CTGTAATA
* * *
9590146 ATTTCAAATGCACCAAAAATCATGAAATATTATGAAAGTAAGATCTAAAAAGTTTCATGAAAATC
1 ATTTCAAATGCACCAAAAATCAT-AAATATTATGAAAATAAGATCTAAAAAATTTCATAAAAATC
* *
9590211 CAAGCTCATGAAGGCCAAATTACAAAAATACCCCTAAGGGGTATTTTCA-TAATTTCACACCTAC
65 CAAGCTCAAG-AGGCCAAATTACAAAAATACCCCTAA-----AGTTT-AGTAATTTCACACCTAC
* *
9590275 TGAGGTACTGCT-GTA
123 CGAGGTACTG-TAATA
* * * * *
9590290 ATTTCAAATGCTCTAAAAATCATAAACTATTATGAAATTAAAACCTAAAAAATTTCATAAAAAT
1 ATTTCAAATGCACCAAAAATCATAAA-TATTATGAAAATAAGATCTAAAAAATTTCATAAAAAT
9590354 TTAGGCTTGA
Statistics
Matches: 170, Mismatches: 27, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
136 7 0.04
137 23 0.14
138 34 0.20
139 22 0.13
143 3 0.02
144 79 0.46
145 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (137 bp):
ATTTCAAATGCACCAAAAATCATAAATATTATGAAAATAAGATCTAAAAAATTTCATAAAAATCC
AAGCTCAAGAGGCCAAATTACAAAAATACCCCTAAAGTTTAGTAATTTCACACCTACCGAGGTAC
TGTAATA
Found at i:9592837 original size:39 final size:40
Alignment explanation
Indices: 9592756--9592887 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
9592746 TTTTTCAAAA
* ** *
9592756 TTTTGAAAGATTTTCAAAACCTCC-GAGCAAAATTTTA-AA
1 TTTTGAAAGATTTTCAAGACCTCCAG-GCAAACCTTTAGAC
* *
9592795 TTTTGAAAGA-TTTCTAAGACTTCCAGGCAAACCTTTAGAT
1 TTTTGAAAGATTTTC-AAGACCTCCAGGCAAACCTTTAGAC
* * * * *
9592835 TTTTGAATGATTTTCAAGGCCTCTAGGTAAACCCTTAGAC
1 TTTTGAAAGATTTTCAAGACCTCCAGGCAAACCTTTAGAC
*
9592875 TTTTGAATGATTT
1 TTTTGAAAGATTT
9592888 CCAAAGCCTT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
38 4 0.05
39 26 0.34
40 43 0.56
41 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (40 bp):
TTTTGAAAGATTTTCAAGACCTCCAGGCAAACCTTTAGAC
Found at i:9593318 original size:15 final size:15
Alignment explanation
Indices: 9593282--9593324 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9593272 CAAAACCAAA
*
9593282 AAAAAAAAGAA-AAG
1 AAAAAAAACAACAAG
* *
9593296 AAAGAAAACAACAAT
1 AAAAAAAACAACAAG
9593311 AAAAAAAACAACAA
1 AAAAAAAACAACAA
9593325 CAACAGCCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.81, C:0.09, G:0.07, T:0.02
Consensus pattern (15 bp):
AAAAAAAACAACAAG
Found at i:9595653 original size:19 final size:19
Alignment explanation
Indices: 9595589--9595666 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
9595579 CATGCATTTT
* *
9595589 CCATGAAACTCTTAACCAC
1 CCATGAAACCCTAAACCAC
* * *
9595608 TCAT-AAACCCTAAAGCAT
1 CCATGAAACCCTAAACCAC
*
9595626 CC-TCCAAACCCTAAACCAC
1 CCAT-GAAACCCTAAACCAC
*
9595645 CCATGAAACCCTATACCAC
1 CCATGAAACCCTAAACCAC
9595664 CCA
1 CCA
9595667 CACAGCCCTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 1 0.02
18 11 0.24
19 33 0.72
20 1 0.02
ACGTcount: A:0.38, C:0.41, G:0.04, T:0.17
Consensus pattern (19 bp):
CCATGAAACCCTAAACCAC
Found at i:9595792 original size:27 final size:27
Alignment explanation
Indices: 9595743--9595854 Score: 106
Period size: 27 Copynumber: 4.2 Consensus size: 27
9595733 CCTTAAACCT
**
9595743 TAAACCTTAAACTATAAAC-CTAAACTC
1 TAAACCTTAAAC-CCAAACTCTAAACTC
* *
9595770 TAAACCTTATACCCAAACTCTAAACCC
1 TAAACCTTAAACCCAAACTCTAAACTC
9595797 TAAATCC-TAAACCCAAACTCTAAAC-C
1 TAAA-CCTTAAACCCAAACTCTAAACTC
** *
9595823 TAAATGTTAAACCCAAAACCCTAAACT-
1 TAAACCTTAAACCC-AAACTCTAAACTC
9595850 TAAAC
1 TAAAC
9595855 TAAATCTCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
26 16 0.23
27 53 0.75
28 2 0.03
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.22
Consensus pattern (27 bp):
TAAACCTTAAACCCAAACTCTAAACTC
Found at i:9595796 original size:13 final size:13
Alignment explanation
Indices: 9595780--9595822 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
9595770 TAAACCTTAT
9595780 ACCCAAACTCTAA
1 ACCCAAACTCTAA
9595793 ACCCTAAA-TCCTAA
1 ACCC-AAACT-CTAA
9595807 ACCCAAACTCTAA
1 ACCCAAACTCTAA
9595820 ACC
1 ACC
9595823 TAAATGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCCAAACTCTAA
Found at i:9595799 original size:7 final size:7
Alignment explanation
Indices: 9595705--9595848 Score: 80
Period size: 7 Copynumber: 20.6 Consensus size: 7
9595695 ATCACCTATG
9595705 AAACCCT
1 AAACCCT
9595712 AAACCACT
1 AAACC-CT
*
9595720 AAAGAACCTT
1 --A-AACCCT
*
9595730 AAACCTT
1 AAACCCT
*
9595737 AAACCTT
1 AAACCCT
*
9595744 AAACCTT
1 AAACCCT
**
9595751 AAACTAT
1 AAACCCT
9595758 AAA-CCT
1 AAACCCT
*
9595764 AAACTCT
1 AAACCCT
*
9595771 AAACCTT
1 AAACCCT
*
9595778 ATACCC-
1 AAACCCT
*
9595784 AAACTCT
1 AAACCCT
9595791 AAACCCT
1 AAACCCT
*
9595798 AAATCCT
1 AAACCCT
9595805 AAACCC-
1 AAACCCT
*
9595811 AAACTCT
1 AAACCCT
9595818 AAA-CCT
1 AAACCCT
***
9595824 AAATGTT
1 AAACCCT
*
9595831 AAACCCA
1 AAACCCT
9595838 AAACCCT
1 AAACCCT
9595845 AAAC
1 AAAC
9595849 TTAAACTAAA
Statistics
Matches: 105, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
6 18 0.17
7 78 0.74
8 3 0.03
10 2 0.02
11 4 0.04
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:9595852 original size:20 final size:20
Alignment explanation
Indices: 9595727--9595854 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 20
9595717 ACTAAAGAAC
* *
9595727 CTTAAACCTTAAACCTTAAA
1 CTTAAACCCTAAACCCTAAA
**
9595747 CCTTAAACTATAAA-CCTAAA
1 -CTTAAACCCTAAACCCTAAA
* *
9595767 CTCTAAACCTTATACCC-AAA
1 CT-TAAACCCTAAACCCTAAA
*
9595787 CTCTAAACCCTAAATCCTAAA
1 CT-TAAACCCTAAACCCTAAA
** *
9595808 CCCAAACTCTAAA-CCTAAA
1 CTTAAACCCTAAACCCTAAA
* *
9595827 TGTTAAACCCAAAACCCTAAA
1 -CTTAAACCCTAAACCCTAAA
9595848 CTTAAAC
1 CTTAAAC
9595855 TAAATCTCAA
Statistics
Matches: 84, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
19 8 0.10
20 53 0.63
21 23 0.27
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (20 bp):
CTTAAACCCTAAACCCTAAA
Found at i:9598154 original size:52 final size:52
Alignment explanation
Indices: 9598074--9598178 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
9598064 TGGATAAGAA
*
9598074 GACTTACAAAAAAAGAATTCTAAGAGAAAAACGATTCTTAATAGGCAAGTTT
1 GACTTACAAAAAAAGAATTCTAAAAGAAAAACGATTCTTAATAGGCAAGTTT
* * **
9598126 GACTTGCAAAAGAAGAATTCTAAAAGAAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTACAAAAAAAGAATTCTAAAAGAAAAACGATTCTTAATAGGCAAGTTT
9598178 G
1 G
9598179 TATGCTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (52 bp):
GACTTACAAAAAAAGAATTCTAAAAGAAAAACGATTCTTAATAGGCAAGTTT
Found at i:9598731 original size:25 final size:25
Alignment explanation
Indices: 9598694--9598746 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
9598684 AAGTGGTAGT
*
9598694 AAAGCTAAAGGTTTAAGACGTGAGA
1 AAAGCTAAAGGTTTAAGACATGAGA
* * * *
9598719 AAAGCTGATGGTTTGAGACATGGGA
1 AAAGCTAAAGGTTTAAGACATGAGA
9598744 AAA
1 AAA
9598747 AGTAAGTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.30, T:0.21
Consensus pattern (25 bp):
AAAGCTAAAGGTTTAAGACATGAGA
Found at i:9599853 original size:29 final size:29
Alignment explanation
Indices: 9599811--9599870 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
9599801 TCACTCTTAG
* **
9599811 ATTCTTCTTTCCAAATGTGGTAGTATTAA
1 ATTCTTCTTTCCAAACGTAATAGTATTAA
9599840 ATTCTTCTTTCCAAACGTAATAGTATTAA
1 ATTCTTCTTTCCAAACGTAATAGTATTAA
9599869 AT
1 AT
9599871 GAAATGTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
ATTCTTCTTTCCAAACGTAATAGTATTAA
Found at i:9601442 original size:14 final size:14
Alignment explanation
Indices: 9601425--9601451 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9601415 ATAAGTCATT
9601425 TAAAAAATTTTAAC
1 TAAAAAATTTTAAC
9601439 TAAAAAATTTTAA
1 TAAAAAATTTTAA
9601452 AAGTGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAAATTTTAAC
Found at i:9603262 original size:24 final size:24
Alignment explanation
Indices: 9603207--9603268 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
9603197 AATGTCATTC
* *
9603207 AAATATAATATTA-ATCATTCAAT
1 AAATATAATATCATATCATGCAAT
* *
9603230 AACACATAATATCATATTATGCAAT
1 AA-ATATAATATCATATCATGCAAT
*
9603255 AAATATAAAATCAT
1 AAATATAATATCAT
9603269 GCAATAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.06
24 19 0.61
25 10 0.32
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:9603368 original size:20 final size:19
Alignment explanation
Indices: 9603334--9603378 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
9603324 CATACAAACA
* *
9603334 AATTAATTAATAATCATGT
1 AATTAAATAATAATCATGC
9603353 AATTAAATATATAATCATGC
1 AATTAAATA-ATAATCATGC
9603373 AATTAA
1 AATTAA
9603379 CAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTAAATAATAATCATGC
Found at i:9603494 original size:20 final size:20
Alignment explanation
Indices: 9603471--9603577 Score: 79
Period size: 22 Copynumber: 5.0 Consensus size: 20
9603461 AAATAAAGTA
*
9603471 ATAATCAGGCAATTAAATAT
1 ATAATCATGCAATTAAATAT
* *
9603491 ATAATTATGCAAATAATAATATT
1 ATAATCATGC-AATTA-AATA-T
* *
9603514 AATAATCATGTAATTAAATAC
1 -ATAATCATGCAATTAAATAT
* *
9603535 CTAATCATGCAAATAAAAATAT
1 ATAATCATGC-AAT-TAAATAT
*
9603557 ATAAACCATGCAATTAAATAT
1 AT-AATCATGCAATTAAATAT
9603578 GCAATAAATA
Statistics
Matches: 66, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
20 16 0.24
21 13 0.20
22 17 0.26
23 12 0.18
24 8 0.12
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
ATAATCATGCAATTAAATAT
Found at i:9603518 original size:44 final size:43
Alignment explanation
Indices: 9603469--9603577 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 43
9603459 AGAAATAAAG
* * *
9603469 TAATAATCAGGCAATTAAATATATAATTATGCAAATAATAATA
1 TAATAATCATGCAATTAAATATATAATCATGCAAATAAAAATA
* **
9603512 TTAATAATCATGTAATTAAATACCTAATCATGCAAATAAAAATA
1 -TAATAATCATGCAATTAAATATATAATCATGCAAATAAAAATA
*
9603556 T-ATAAACCATGCAATTAAATAT
1 TAAT-AATCATGCAATTAAATAT
9603578 GCAATAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 2 0.04
43 16 0.29
44 37 0.67
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (43 bp):
TAATAATCATGCAATTAAATATATAATCATGCAAATAAAAATA
Found at i:9603638 original size:54 final size:53
Alignment explanation
Indices: 9603536--9603642 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 53
9603526 ATTAAATACC
* **
9603536 TAATCATGCAAATAAAAATATATAAACCATGCAATTAAATATGCAATAAATATA
1 TAATCATGCAAATAAAAATATATAAACCATGCAATCAAATAAACAAT-AATATA
* * ** *
9603590 TAATCATGCAAATAATAATATATAAATCATGCAATCATGTAAATAATAATATA
1 TAATCATGCAAATAAAAATATATAAACCATGCAATCAAATAAACAATAATATA
9603643 CAAACCATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 6 0.13
54 39 0.87
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (53 bp):
TAATCATGCAAATAAAAATATATAAACCATGCAATCAAATAAACAATAATATA
Found at i:9603772 original size:24 final size:24
Alignment explanation
Indices: 9603690--9603780 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
9603680 GCCAAAAAGT
* *
9603690 TATTAATAATCA-AGCAATTAAACA
1 TATTAATAATCATA-CAAATAAATA
*
9603714 TATTAATAATCATGC-AATCAAAT-
1 TATTAATAATCATACAAAT-AAATA
*
9603737 TA-AATATAATCATACAAATAAATA
1 TATTA-ATAATCATACAAATAAATA
*
9603761 TATTAATAATCATGCAAATA
1 TATTAATAATCATACAAATA
9603781 TATTAATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 17 0.31
24 35 0.65
25 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (24 bp):
TATTAATAATCATACAAATAAATA
Found at i:9603786 original size:47 final size:46
Alignment explanation
Indices: 9603695--9603831 Score: 138
Period size: 47 Copynumber: 2.9 Consensus size: 46
9603685 AAAGTTATTA
* *
9603695 ATAATCAAGCAATTAAACATATTAATAATCATGC-AATCAAATTAAAT
1 ATAATCAA-CAAATAAACATATTAATAATCATGCAAAT-ATATTAAAT
*
9603742 ATAATCATACAAATAAATATATTAATAATCATGCAAATATATT-AAT
1 ATAATCA-ACAAATAAACATATTAATAATCATGCAAATATATTAAAT
* **
9603788 A-AATC-ACATTAATAAACATATTAATCATGCAAACAAATATATTA
1 ATAATCAACA--AATAAACATATTAATAAT-CATGCAAATATATTA
9603832 GGCAAATAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
43 3 0.04
45 20 0.26
46 16 0.21
47 34 0.44
48 4 0.05
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (46 bp):
ATAATCAACAAATAAACATATTAATAATCATGCAAATATATTAAAT
Found at i:9603854 original size:16 final size:16
Alignment explanation
Indices: 9603811--9603861 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
9603801 AAACATATTA
*
9603811 ATCATGCAAACAAATAT
1 ATCATGCAAATAAAT-T
* *
9603828 ATTAGGCAAATAAATT
1 ATCATGCAAATAAATT
*
9603844 ATCATGCAAATATATT
1 ATCATGCAAATAAATT
9603860 AT
1 AT
9603862 TAGTCATGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (16 bp):
ATCATGCAAATAAATT
Found at i:9604534 original size:12 final size:12
Alignment explanation
Indices: 9604502--9604554 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
9604492 TTTGACTTAA
9604502 AAAATAAAAATT
1 AAAATAAAAATT
**
9604514 AAACCAAAAATT
1 AAAATAAAAATT
9604526 AAAATAAAAAATT
1 AAAAT-AAAAATT
*
9604539 AAAATATAAA-T
1 AAAATAAAAATT
9604550 AAAAT
1 AAAAT
9604555 TTAAGGCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 6 0.17
12 17 0.49
13 12 0.34
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:9604535 original size:13 final size:13
Alignment explanation
Indices: 9604502--9604544 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
9604492 TTTGACTTAA
9604502 AAAAT-AAAAATT
1 AAAATAAAAAATT
**
9604514 -AAACCAAAAATT
1 AAAATAAAAAATT
9604526 AAAATAAAAAATT
1 AAAATAAAAAATT
9604539 AAAATA
1 AAAATA
9604545 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 3 0.12
12 7 0.27
13 16 0.62
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:9605885 original size:9 final size:9
Alignment explanation
Indices: 9605871--9605909 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
9605861 AATACACAAT
*
9605871 TAGTAGTTG
1 TAGTAGTTA
9605880 TAGTAGTTA
1 TAGTAGTTA
9605889 TAGTAGTTAA
1 TAGTAGTT-A
*
9605899 AAGTAGTTA
1 TAGTAGTTA
9605908 TA
1 TA
9605910 TGAGTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (9 bp):
TAGTAGTTA
Found at i:9605905 original size:19 final size:19
Alignment explanation
Indices: 9605881--9605918 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
9605871 TAGTAGTTGT
9605881 AGTAGTTATA-GTAGTTAAA
1 AGTAGTTATATG-AGTTAAA
9605900 AGTAGTTATATGAGTTAAA
1 AGTAGTTATATGAGTTAAA
9605919 TTTCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AGTAGTTATATGAGTTAAA
Found at i:9618788 original size:54 final size:54
Alignment explanation
Indices: 9618723--9618939 Score: 199
Period size: 54 Copynumber: 4.0 Consensus size: 54
9618713 AAAAAAAAAA
*
9618723 TTTCAATCAAAGACTATC-TATCAACTTTCATAAATATATTCTTTATAAATTTTT
1 TTTCAATCAAAGACTA-CGTATCAACTTTCACAAATATATTCTTTATAAATTTTT
* * * * * * * *
9618777 TTTCAACCAAAGACTATGTTTCTACTTTTAAAAAATATAGTCTTTGTAAATTTTT
1 TTTCAATCAAAGACTACGTATCAAC-TTTCACAAATATATTCTTTATAAATTTTT
* * * ** *
9618832 TTT-AATAAAAAATTACGTATCAACTTTTGCAAACATAGTT-TTGTA-AAATTTTT
1 TTTCAATCAAAGACTACGTATCAACTTTCACAAATATA-TTCTT-TATAAATTTTT
* * * *
9618885 TTTCAATCAAATACTACGTATCAACTTTCACAAATGTAATCTTTGTAAATTTTT
1 TTTCAATCAAAGACTACGTATCAACTTTCACAAATATATTCTTTATAAATTTTT
9618939 T
1 T
9618940 CAATTACTTT
Statistics
Matches: 126, Mismatches: 30, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
53 24 0.19
54 74 0.59
55 28 0.22
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (54 bp):
TTTCAATCAAAGACTACGTATCAACTTTCACAAATATATTCTTTATAAATTTTT
Found at i:9618855 original size:108 final size:107
Alignment explanation
Indices: 9618741--9618939 Score: 240
Period size: 108 Copynumber: 1.9 Consensus size: 107
9618731 AAAGACTATC
* * * * *
9618741 TATCAACTTTCATAAATATA-TTCTT-TATAAATTTTTTTTCAACCAAAGACTATGTTTCTACTT
1 TATCAACTTTCACAAACATAGTT-TTGTA-AAATTTTTTTTCAACCAAAGACTACGTATCAAC-T
*
9618804 TTAAAAAATATAGTCTTTGTAAATTTTTTTTAATAAAAAATTACG
63 TTAAAAAATATAATCTTTGTAAATTTTTTTTAATAAAAAATTACG
** * * *
9618849 TATCAACTTTTGCAAACATAGTTTTGTAAAATTTTTTTTCAATCAAATACTACGTATCAACTTTC
1 TATCAACTTTCACAAACATAGTTTTGTAAAATTTTTTTTCAACCAAAGACTACGTATCAACTTTA
* *
9618914 ACAAATGTAATCTTTGTAAATTTTTT
66 AAAAATATAATCTTTGTAAATTTTTT
9618940 CAATTACTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 26 0.34
108 46 0.61
109 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (107 bp):
TATCAACTTTCACAAACATAGTTTTGTAAAATTTTTTTTCAACCAAAGACTACGTATCAACTTTA
AAAAATATAATCTTTGTAAATTTTTTTTAATAAAAAATTACG
Found at i:9620552 original size:42 final size:42
Alignment explanation
Indices: 9620491--9620572 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
9620481 AATGTTACCT
*
9620491 GATATATATTATGATCCCACTGTTATT-ATTCCATATAACAAG
1 GATATATATTATGACCCCACTGTTATTGATTCCAT-TAACAAG
*
9620533 GATATATATTATGGCCCCACTGTTATTGATTCCATTAACA
1 GATATATATTATGACCCCACTGTTATTGATTCCATTAACA
9620573 CTTGTTATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 30 0.81
43 7 0.19
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (42 bp):
GATATATATTATGACCCCACTGTTATTGATTCCATTAACAAG
Found at i:9620815 original size:30 final size:29
Alignment explanation
Indices: 9620752--9620885 Score: 92
Period size: 30 Copynumber: 4.5 Consensus size: 29
9620742 CATTTTGTTT
* *
9620752 AAATAAATTTTTATATTTTTA-TTATACAT-
1 AAATAAGTTTTTA-ATTTTAATTTATAC-TC
9620781 AAATAAGTTTTTGAATTTTAATTTATACTC
1 AAATAAGTTTTT-AATTTTAATTTATACTC
** *
9620811 AAATAAGTCATTAATCTTTAATTTATATTC
1 AAATAAGTTTTTAAT-TTTAATTTATACTC
* **** * *
9620841 AAAGAAACCATTAGGTTTTAATTTATACTT
1 AAATAAGTTTTTA-ATTTTAATTTATACTC
*
9620871 AAATAAGTATTTAAT
1 AAATAAGTTTTTAAT
9620886 ATAAATTAAT
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
29 22 0.27
30 60 0.72
31 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATAAGTTTTTAATTTTAATTTATACTC
Found at i:9620942 original size:31 final size:29
Alignment explanation
Indices: 9620906--9620984 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
9620896 TTTTTATTTG
9620906 AAATAAAGACTTATTTAAATATAAATTAAAA
1 AAATAAAGACTTATTTAAATA-AAA-TAAAA
* * * *
9620937 AAATAAAGGCTTATCTAGATACAATAAAA
1 AAATAAAGACTTATTTAAATAAAATAAAA
*
9620966 ATATAAAAGA-TTATTTAAA
1 AAAT-AAAGACTTATTTAAA
9620985 AATATGAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 15 0.38
30 6 0.15
31 18 0.46
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAAAGACTTATTTAAATAAAATAAAA
Found at i:9621696 original size:1 final size:1
Alignment explanation
Indices: 9621690--9621716 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
9621680 CTAAAACAAA
9621690 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
9621717 AGCGCCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:9622871 original size:16 final size:17
Alignment explanation
Indices: 9622846--9622880 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9622836 ATTGAATTTA
9622846 ATAAAAAAATATT-ATT
1 ATAAAAAAATATTAATT
*
9622862 ATAAATAAATATTAATT
1 ATAAAAAAATATTAATT
9622879 AT
1 AT
9622881 CATTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAAAAATATTAATT
Found at i:9624069 original size:52 final size:53
Alignment explanation
Indices: 9623935--9624414 Score: 401
Period size: 52 Copynumber: 8.9 Consensus size: 53
9623925 TTTTAATGAA
* * * * * **
9623935 AAAAAAAATTACATTCACTATGTTTATGAAAATAGAAACACACTCTTCTTTGATT-
1 AAAAAAATTTACAATCACTACGTTTATGAAAGTAG-AA-AC-GTAGTCTTTGATTG
* * * * * *
9623990 AAAAAAATGTTACAATCACTACATTTATCAAAGTACAAACATAATATTTGATTG
1 AAAAAAAT-TTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
* * * * * * *
9624044 AACAAAA-TTAAAATCACTATGTTTATGAAAGTAAAAACGTAGTTTTTTATTA
1 AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
* * * * *
9624096 AAAAAAATTTTACAATCACTACATTTATAAAAATAGAAATGTAGCCTTTGATTGGG
1 AAAAAAA-TTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATT--G
** *
9624152 AAAAAAAATTTACAATCACTATATTTATGAAAGTAGAAACATAGTCTTTGATTG
1 -AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
* * * * *
9624206 AAAAAAAAATTTTACAATCACTATGTTTATGAAAGTAGAAAGGTAGTGTTTTATTTT
1 --AAAAAAA-TTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGA-TTG
* * * * *
9624263 TAAAAAATTTACAATCATTACGTTTATAAAAGTAGAAACGTAATCTTTAATTG
1 AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
* * * ** *
9624316 AAAAAAA-TTATAATCACTACGTTTATAAAAATAGAAATATAATCTTTGATT-
1 AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
* * *
9624367 AAAAAAATTTACAATCATTATGTTTATGAAAGTAGAAACTTAGTCTTT
1 AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTT
9624415 TGTTATTGTT
Statistics
Matches: 344, Mismatches: 70, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
51 7 0.02
52 111 0.32
53 17 0.05
54 79 0.23
55 23 0.07
56 98 0.28
57 9 0.03
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (53 bp):
AAAAAAATTTACAATCACTACGTTTATGAAAGTAGAAACGTAGTCTTTGATTG
Found at i:9624291 original size:166 final size:160
Alignment explanation
Indices: 9623982--9624415 Score: 509
Period size: 162 Copynumber: 2.7 Consensus size: 160
9623972 ACACACTCTT
* * * *
9623982 CTTTGATT-AAAAAAATGTTACAATCACTACATTTATCAAAGTACAAACATAATATTTGATTGAA
1 CTTTAATTGAAAAAAAT-TTACAATCACTACATTTATAAAAGTAGAAACATAATCTTTGATTGAA
* * * *
9624046 CAAAA-TTAAAATCACTATGTTTATGAAAGTAAAAACGTAGTTTTTTATTAAAAAAAATTTTACA
65 AAAAATTTACAATCACTATGTTTATGAAAGTAGAAACGTAGTGTTTTATTAAAAAAAATTTTACA
* *
9624110 ATCACTACATTTATAAAAATAGAAATGTAGC
130 ATCACTACATTTATAAAAATAGAAACGTAAC
* * * *
9624141 CTTTGATTGGGAAAAAAAATTTACAATCACTATATTTATGAAAGTAGAAACATAGTCTTTGATTG
1 CTTTAATT--G-AAAAAAATTTACAATCACTACATTTATAAAAGTAGAAACATAATCTTTGATTG
* **
9624206 AAAAAAAAATTTTACAATCACTATGTTTATGAAAGTAGAAAGGTAGTGTTTTATTTTTAAAAAA-
63 --AAAAAAA-TTTACAATCACTATGTTTATGAAAGTAGAAACGTAGTGTTTTA-TTAAAAAAAAT
* * * *
9624270 TTTACAATCATTACGTTTATAAAAGTAGAAACGTAAT
124 TTTACAATCACTACATTTATAAAAATAGAAACGTAAC
* * * *
9624307 CTTTAATTGAAAAAAA-TTATAATCACTACGTTTATAAAAATAGAAATATAATCTTTGATT-AAA
1 CTTTAATTGAAAAAAATTTACAATCACTACATTTATAAAAGTAGAAACATAATCTTTGATTGAAA
* * *
9624370 AAAATTTACAATCATTATGTTTATGAAAGTAGAAACTTAGTCTTTT
66 AAAATTTACAATCACTATGTTTATGAAAGTAGAAACGTAGTGTTTT
9624416 GTTATTGTTT
Statistics
Matches: 236, Mismatches: 30, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
158 38 0.16
159 15 0.06
162 77 0.33
163 15 0.06
164 7 0.03
166 76 0.32
167 8 0.03
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (160 bp):
CTTTAATTGAAAAAAATTTACAATCACTACATTTATAAAAGTAGAAACATAATCTTTGATTGAAA
AAAATTTACAATCACTATGTTTATGAAAGTAGAAACGTAGTGTTTTATTAAAAAAAATTTTACAA
TCACTACATTTATAAAAATAGAAACGTAAC
Found at i:9624333 original size:218 final size:213
Alignment explanation
Indices: 9623934--9624415 Score: 540
Period size: 218 Copynumber: 2.2 Consensus size: 213
9623924 TTTTTAATGA
* * * * * *
9623934 AAAAAAAAATTACATTCACTATGTTTATGAAAATAGAAACACACTCTTCTTTGATTAAAAAAATG
1 AAAAAAAATTTACAATCACTATGTTTATGAAAGTAGAAACATAGTCTT-TTTGATAAAAAAAATG
*
9623999 TTACAATCACTACATTTATCAAAGTACAAACATAATATTTGATTGAACAAAATTAAAATCACTAT
65 TTACAATCACTACATTTATCAAAGTACAAACATAATATTTGATTGAACAAAATTAAAATCACTAC
* * * *
9624064 GTTTATGAAAGTAAAAACGTAGTTTTTTATTAAAAAAAATTTTACAATCACTACATTTATAAAAA
130 GTTTATAAAAGTAAAAACGTAATCTTTAATTAAAAAAAA-TTTACAATCACTACATTTATAAAAA
* *
9624129 TAGAAATGTAGCCTTTGATT
194 TAGAAATATAACCTTTGATT
*
9624149 GGGAAAAAAAATTTACAATCACTATATTTATGAAAGTAGAAACATAGTCTTTGATTGA-AAAAAA
1 ---AAAAAAAATTTACAATCACTATGTTTATGAAAGTAGAAACATAGTCTTT--TTGATAAAAAA
* ** * * ** * * * * *
9624213 AATTTTACAATCACTATGTTTATGAAAGTAGAAAGGTAGTGTTTTATTTTTAA-AAAATTTACAA
61 AATGTTACAATCACTACATTTATCAAAGTACAAACATAATATTTGA--TTGAACAAAA-TTAAAA
* * * * *
9624277 TCATTACGTTTATAAAAGTAGAAACGTAATCTTTAATTGAAAAAAA-TTATAATCACTACGTTTA
123 TCACTACGTTTATAAAAGTAAAAACGTAATCTTTAATTAAAAAAAATTTACAATCACTACATTTA
*
9624341 TAAAAATAGAAATATAATCTTTGATT
188 TAAAAATAGAAATATAACCTTTGATT
* *
9624367 -AAAAAAATTTACAATCATTATGTTTATGAAAGTAGAAACTTAGTCTTTT
1 AAAAAAAATTTACAATCACTATGTTTATGAAAGTAGAAACATAGTCTTTT
9624416 GTTATTGTTT
Statistics
Matches: 224, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
212 1 0.00
214 45 0.20
217 1 0.00
218 122 0.54
219 8 0.04
220 47 0.21
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (213 bp):
AAAAAAAATTTACAATCACTATGTTTATGAAAGTAGAAACATAGTCTTTTTGATAAAAAAAATGT
TACAATCACTACATTTATCAAAGTACAAACATAATATTTGATTGAACAAAATTAAAATCACTACG
TTTATAAAAGTAAAAACGTAATCTTTAATTAAAAAAAATTTACAATCACTACATTTATAAAAATA
GAAATATAACCTTTGATT
Found at i:9627378 original size:48 final size:48
Alignment explanation
Indices: 9627326--9627419 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
9627316 CAATGTAAAT
* *
9627326 AATTTTTTCATTTATACAACTCCAAAATTTATGATTAATACAAGTCCA
1 AATTTTTTAATTTAAACAACTCCAAAATTTATGATTAATACAAGTCCA
** * *
9627374 AATTTTTTAATTTAAACATGTCCAAAATTTATTATTTATACAAGTC
1 AATTTTTTAATTTAAACAACTCCAAAATTTATGATTAATACAAGTC
9627420 AGTTATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (48 bp):
AATTTTTTAATTTAAACAACTCCAAAATTTATGATTAATACAAGTCCA
Found at i:9627401 original size:25 final size:24
Alignment explanation
Indices: 9627326--9627419 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 24
9627316 CAATGTAAAT
* *
9627326 AATTTTTTCATTTATACAACTCCAA
1 AATTTTTT-ATTTAAACAAGTCCAA
* *
9627351 AATTTATGA-TTAATACAAGTCC-A
1 AATTTTTTATTTAA-ACAAGTCCAA
*
9627374 AATTTTTTAATTTAAACATGTCCAA
1 AATTTTTT-ATTTAAACAAGTCCAA
* *
9627399 AATTTATTATTTATACAAGTC
1 AATTTTTTATTTAAACAAGTC
9627420 AGTTATAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 10 0.18
24 27 0.49
25 18 0.33
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (24 bp):
AATTTTTTATTTAAACAAGTCCAA
Found at i:9627936 original size:35 final size:34
Alignment explanation
Indices: 9627888--9627994 Score: 91
Period size: 35 Copynumber: 3.3 Consensus size: 34
9627878 CAAGCATGCA
9627888 AAGATATCATGCAAATAAGCATCATGCAATAATAT
1 AAGATATCATGCAAA-AAGCATCATGCAATAATAT
* * **
9627923 AAGATTTCTTGCAAAAATTATCATGCAAT-A-A-
1 AAGATATCATGCAAAAAGCATCATGCAATAATAT
* * *
9627954 AAG-CATCATGCAAAAA-TATCATGTAATAATAT
1 AAGATATCATGCAAAAAGCATCATGCAATAATAT
9627986 ATA-ATATCA
1 A-AGATATCA
9627995 AGCCAAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
29 10 0.17
30 11 0.19
31 4 0.07
32 2 0.03
33 6 0.10
34 12 0.21
35 13 0.22
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (34 bp):
AAGATATCATGCAAAAAGCATCATGCAATAATAT
Found at i:9628317 original size:15 final size:14
Alignment explanation
Indices: 9628297--9628348 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
9628287 TCAATTAACA
9628297 AAAAAAAATCAAAAT
1 AAAAAAAA-CAAAAT
*
9628312 AAAAAATAGCAAAAT
1 AAAAAA-AACAAAAT
*
9628327 AAAAGTCAAACAAAAT
1 AAAA--AAAACAAAAT
9628343 AAAAAA
1 AAAAAA
9628349 TCAAAACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 12 0.40
17 1 0.03
ACGTcount: A:0.77, C:0.08, G:0.04, T:0.12
Consensus pattern (14 bp):
AAAAAAAACAAAAT
Found at i:9628317 original size:16 final size:15
Alignment explanation
Indices: 9628296--9628348 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
9628286 TTCAATTAAC
9628296 AAAAAAAAATCAAAAT
1 AAAAAAAAA-CAAAAT
* *
9628312 AAAAAATAGCAAAAT
1 AAAAAAAAACAAAAT
**
9628327 AAAAGTCAAACAAAAT
1 AAAA-AAAAACAAAAT
9628343 AAAAAA
1 AAAAAA
9628349 TCAAAACCCA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.77, C:0.08, G:0.04, T:0.11
Consensus pattern (15 bp):
AAAAAAAAACAAAAT
Found at i:9629483 original size:12 final size:12
Alignment explanation
Indices: 9629457--9629497 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
9629447 ATAAATTTTA
* *
9629457 GAATCCAAAATT
1 GAATCTAAAACT
*
9629469 GAATCTAACACT
1 GAATCTAAAACT
9629481 GAATCTAAAACT
1 GAATCTAAAACT
9629493 GAATC
1 GAATC
9629498 CAAGATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (12 bp):
GAATCTAAAACT
Found at i:9629581 original size:20 final size:21
Alignment explanation
Indices: 9629546--9629585 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9629536 TTTTTTTATC
9629546 TTTTTTTTACCCTTTTGACTT
1 TTTTTTTTACCCTTTTGACTT
*
9629567 TTTTTTTTA-CTTTTTGACT
1 TTTTTTTTACCCTTTTGACT
9629586 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTTTTACCCTTTTGACTT
Found at i:9629594 original size:6 final size:6
Alignment explanation
Indices: 9629585--9629686 Score: 82
Period size: 6 Copynumber: 17.2 Consensus size: 6
9629575 ACTTTTTGAC
* * * *
9629585 TAAAAA TAAAAT TAAACA- AAAAAT T-AAAT TAAAAT CAAAAT CAAAAT
1 TAAAAT TAAAAT TAAA-AT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* * * * * * *
9629632 CAAAAT TAACAT TAACAT TAAAAT CAAAAT GAAAAT TACAAT AAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
9629680 TAAAAT T
1 TAAAAT T
9629687 TTTGGCTTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
5 6 0.08
6 72 0.91
7 1 0.01
ACGTcount: A:0.66, C:0.08, G:0.01, T:0.25
Consensus pattern (6 bp):
TAAAAT
Found at i:9630033 original size:82 final size:82
Alignment explanation
Indices: 9629933--9630104 Score: 220
Period size: 82 Copynumber: 2.1 Consensus size: 82
9629923 AAAGGCTTTG
* * * *
9629933 AAACTTTTTGAAATAAAATGGT-CCCCACAACTGAGGCATTGAAATTTTTGAAAAATAAAATGCT
1 AAAC-TTTTGAAAAAAAATGCTCCCCCACAACTGAGGC-TTGAAACTTTTGAAAAATAAAATACT
*
9629997 TTTCCAAAACTGAGGCTTA
64 TTCCCAAAACTGAGGCTTA
* * *
9630016 AAACTTTTGAAAAAAAATGCTCCCCCATAATTGAGGCTTGAAACTTTTGAAAACTAAAATACTTT
1 AAACTTTTGAAAAAAAATGCTCCCCCACAACTGAGGCTTGAAACTTTTGAAAAATAAAATACTTT
* * *
9630081 CCCATAACTGAGGGTTG
66 CCCAAAACTGAGGCTTA
9630098 AAACTTT
1 AAACTTT
9630105 AAATAAAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 60 0.78
83 17 0.22
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (82 bp):
AAACTTTTGAAAAAAAATGCTCCCCCACAACTGAGGCTTGAAACTTTTGAAAAATAAAATACTTT
CCCAAAACTGAGGCTTA
Found at i:9630093 original size:42 final size:41
Alignment explanation
Indices: 9629925--9630104 Score: 186
Period size: 42 Copynumber: 4.3 Consensus size: 41
9629915 TCCTCAATAA
* * *
9629925 AGGCTTTGAAACTTTTTG-AAATAAAATG-GTCCCCACAACTG
1 AGGC-TTGAAAC-TTTTGAAAATAAAATGCTTTCCCATAACTG
* * *
9629966 AGGCATTGAAATTTTTGAAAAATAAAATGCTTTTCCAAAACTG
1 AGGC-TTGAAACTTTTG-AAAATAAAATGCTTTCCCATAACTG
* ** *
9630009 AGGCTTAAAACTTTTGAAAA-AAAATGCTCCCCCATAATTG
1 AGGCTTGAAACTTTTGAAAATAAAATGCTTTCCCATAACTG
*
9630049 AGGCTTGAAACTTTTGAAAACTAAAATACTTTCCCATAACTG
1 AGGCTTGAAACTTTTGAAAA-TAAAATGCTTTCCCATAACTG
*
9630091 AGGGTTGAAACTTT
1 AGGCTTGAAACTTT
9630105 AAATAAAATA
Statistics
Matches: 115, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
40 39 0.34
41 14 0.12
42 49 0.43
43 13 0.11
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (41 bp):
AGGCTTGAAACTTTTGAAAATAAAATGCTTTCCCATAACTG
Found at i:9633033 original size:15 final size:16
Alignment explanation
Indices: 9633010--9633047 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9633000 ACAAAATTAC
9633010 AATATACAATTGAAAA
1 AATATACAATTGAAAA
*
9633026 AATA-ACAATTTAAAA
1 AATATACAATTGAAAA
9633041 ATATATA
1 A-ATATA
9633048 TATAGAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 7 0.37
17 1 0.05
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (16 bp):
AATATACAATTGAAAA
Found at i:9633955 original size:4 final size:4
Alignment explanation
Indices: 9633931--9634012 Score: 56
Period size: 4 Copynumber: 19.8 Consensus size: 4
9633921 ATCTTTGTAT
* * * *
9633931 TTTA TTATA ATTA TCTA TTTA TTTA TTTA TTTTG TTTA TTTG TTTA TTTTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA -TTTA
** * * *
9633982 TTTA TTTA ACTA TCTA TGTG TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
9634013 GTAAATATTT
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
4 50 0.83
5 10 0.17
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:9633968 original size:13 final size:13
Alignment explanation
Indices: 9633941--9633989 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
9633931 TTTATTATAA
*
9633941 TTATCTATTTA-T
1 TTATTTATTTATT
9633953 TTATTTATTT-TGT
1 TTATTTATTTAT-T
*
9633966 TTATTTGTTTATT
1 TTATTTATTTATT
9633979 TTATTTATTTA
1 TTATTTATTTA
9633990 ACTATCTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 9 0.29
13 21 0.68
14 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:9633968 original size:17 final size:17
Alignment explanation
Indices: 9633948--9634012 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
9633938 TAATTATCTA
9633948 TTTATTTATTTATTTTG
1 TTTATTTATTTATTTTG
* *
9633965 TTTATTTGTTTATTTTA
1 TTTATTTATTTATTTTG
**
9633982 TTTATTTAACTATCTATGTG
1 TTTATTTATTTAT-T-T-TG
9634002 TTTATTTATTT
1 TTTATTTATTT
9634013 GTAAATATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 25 0.68
18 1 0.03
19 1 0.03
20 10 0.27
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATTTATTTATTTTG
Found at i:9633970 original size:9 final size:9
Alignment explanation
Indices: 9633956--9633988 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9633946 TATTTATTTA
9633956 TTTATTTTG
1 TTTATTTTG
9633965 TTTA-TTTG
1 TTTATTTTG
*
9633973 TTTATTTTA
1 TTTATTTTG
9633982 TTTATTT
1 TTTATTT
9633989 AACTATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (9 bp):
TTTATTTTG
Found at i:9634459 original size:35 final size:36
Alignment explanation
Indices: 9634419--9634493 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 36
9634409 TAGAAAAGAA
* *
9634419 ATAATTTC-CATAAAATCCTACCAACATCTTGGAGG
1 ATAATTTCACAAAAAATCCTACCAACATATTGGAGG
*
9634454 ATAATTTCTAGCAAAAAATCTTACCAACATATTGGAGG
1 ATAATTTC-A-CAAAAAATCCTACCAACATATTGGAGG
9634492 AT
1 AT
9634494 TTTTTTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
38 26 0.76
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (36 bp):
ATAATTTCACAAAAAATCCTACCAACATATTGGAGG
Found at i:9638787 original size:10 final size:11
Alignment explanation
Indices: 9638738--9638828 Score: 66
Period size: 11 Copynumber: 8.3 Consensus size: 11
9638728 ATGAATGAAG
9638738 TGAAAAAGAAA
1 TGAAAAAGAAA
*
9638749 TGAAAAAAAAA
1 TGAAAAAGAAA
9638760 TTGAAAAA-ATAA
1 -TGAAAAAGA-AA
9638772 -GAAAAAGAAA
1 TGAAAAAGAAA
*
9638782 TGAAAAGGACAA
1 TGAAAAAGA-AA
*
9638794 --AAATGAGAAA
1 TGAAA-AAGAAA
*
9638804 TGAGAAAA-ATA
1 TGA-AAAAGAAA
9638815 TGAAAAAGAAA
1 TGAAAAAGAAA
9638826 TGA
1 TGA
9638829 GGAAAAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
10 17 0.27
11 31 0.49
12 13 0.21
13 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.12
Consensus pattern (11 bp):
TGAAAAAGAAA
Found at i:9639633 original size:15 final size:15
Alignment explanation
Indices: 9639622--9639681 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
9639612 ACAATTAGAG
9639622 TTGCATTCATTAACA
1 TTGCATTCATTAACA
*
9639637 TTGCATTCATAAACA
1 TTGCATTCATTAACA
* *
9639652 TTGCTTTCA-T-GCA
1 TTGCATTCATTAACA
*
9639665 TTGCATTCATAAACA
1 TTGCATTCATTAACA
9639680 TT
1 TT
9639682 ACACTCATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 10 0.28
15 26 0.72
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (15 bp):
TTGCATTCATTAACA
Found at i:9639689 original size:28 final size:28
Alignment explanation
Indices: 9639635--9639690 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
9639625 CATTCATTAA
* **
9639635 CATTGCATTCATAAACATTGCTTTCATG
1 CATTGCATTCATAAACATTACACTCATG
9639663 CATTGCATTCATAAACATTACACTCATG
1 CATTGCATTCATAAACATTACACTCATG
9639691 TAATTTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (28 bp):
CATTGCATTCATAAACATTACACTCATG
Found at i:9652214 original size:6 final size:6
Alignment explanation
Indices: 9652199--9652315 Score: 55
Period size: 6 Copynumber: 20.2 Consensus size: 6
9652189 CTCTTTTGAC
* * * * *
9652199 TAAAAA TAAAAT T-AAAC TAAAAG T-AAAT T-AAAT T-AAAT CAACAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
* * * * * * *
9652243 CAAAAT CAAAAT CAAATT TAACAT TAAAAT CAAAA- TACAAAT CAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TA-AAAT TAAAAT
* * *
9652291 CAAAAT TACAAT CAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
9652316 TTGGCTTTCA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
5 18 0.21
6 68 0.78
7 1 0.01
ACGTcount: A:0.62, C:0.11, G:0.01, T:0.26
Consensus pattern (6 bp):
TAAAAT
Found at i:9652226 original size:16 final size:17
Alignment explanation
Indices: 9652197--9652235 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
9652187 TACTCTTTTG
9652197 ACTAAAAATAAAATTAA
1 ACTAAAAATAAAATTAA
*
9652214 ACTAAAAGT-AAATTAA
1 ACTAAAAATAAAATTAA
*
9652230 ATTAAA
1 ACTAAA
9652236 TCAACATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
ACTAAAAATAAAATTAA
Found at i:9652250 original size:12 final size:12
Alignment explanation
Indices: 9652233--9652314 Score: 76
Period size: 12 Copynumber: 6.8 Consensus size: 12
9652223 AAATTAAATT
*
9652233 AAATCAACATCA
1 AAATCAAAATCA
9652245 AAATCAAAATCA
1 AAATCAAAATCA
* * * *
9652257 AATTTAACATTA
1 AAATCAAAATCA
9652269 AAATCAAAAT-A
1 AAATCAAAATCA
9652280 CAAATCAAAATCA
1 -AAATCAAAATCA
* *
9652293 AAATTACAATCA
1 AAATCAAAATCA
*
9652305 AAATTAAAAT
1 AAATCAAAAT
9652315 TTTGGCTTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 1 0.02
12 55 0.96
13 1 0.02
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATCAAAATCA
Found at i:9652256 original size:18 final size:18
Alignment explanation
Indices: 9652233--9652314 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
9652223 AAATTAAATT
* *
9652233 AAATCAACATCAAAATCA
1 AAATCAAAATCAACATCA
* * *
9652251 AAATCAAATTTAACATTA
1 AAATCAAAATCAACATCA
9652269 AAATCAAAATACAA-ATCA
1 AAATCAAAAT-CAACATCA
*
9652287 AAATCAAAAT-TACAATCA
1 AAATCAAAATCAAC-ATCA
*
9652305 AAATTAAAAT
1 AAATCAAAAT
9652315 TTTGGCTTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.02
18 48 0.94
19 2 0.04
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATCAAAATCAACATCA
Found at i:9652315 original size:18 final size:18
Alignment explanation
Indices: 9652246--9652315 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
9652236 TCAACATCAA
*
9652246 AATCAAAATCAAATTTA-
1 AATCAAAATCAAAATTAC
*
9652263 ACATTAAAATCAAAA-TAC
1 A-ATCAAAATCAAAATTAC
9652281 AAATCAAAATCAAAATTAC
1 -AATCAAAATCAAAATTAC
*
9652300 AATCAAAATTAAAATT
1 AATCAAAATCAAAATT
9652316 TTGGCTTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
17 3 0.07
18 38 0.84
19 4 0.09
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (18 bp):
AATCAAAATCAAAATTAC
Found at i:9665214 original size:31 final size:32
Alignment explanation
Indices: 9665158--9665217 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
9665148 AAATTTTTGC
9665158 TATTTTATTTTATTCTTGTAGTTTTATATATT
1 TATTTTATTTTATTCTTGTAGTTTTATATATT
*
9665190 TATTTTAGTTTT-TT-TTGTATTTTTATAT
1 TATTTTA-TTTTATTCTTGTAGTTTTATAT
9665218 GATTAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.50
32 9 0.35
33 4 0.15
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (32 bp):
TATTTTATTTTATTCTTGTAGTTTTATATATT
Found at i:9669408 original size:11 final size:11
Alignment explanation
Indices: 9669374--9669427 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
9669364 GATAGAAAGC
9669374 AAAAAAAAA--
1 AAAAAAAAATG
* *
9669383 AAAAGAAAATC
1 AAAAAAAAATG
*
9669394 AAAATAAAA-G
1 AAAAAAAAATG
9669404 AAAAAAAAATG
1 AAAAAAAAATG
*
9669415 AAAGAAAAATG
1 AAAAAAAAATG
9669426 AA
1 AA
9669428 TGCCATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 8 0.22
10 8 0.22
11 21 0.57
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:9669412 original size:15 final size:15
Alignment explanation
Indices: 9669369--9669423 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
9669359 TCAAAGATAG
9669369 AAAGCAAAAAAAAA-A
1 AAAG-AAAAAAAAATA
*
9669384 AAAGAAAATCAAAATA
1 AAAGAAAA-AAAAATA
*
9669400 AAAGAAAAAAAAATG
1 AAAGAAAAAAAAATA
9669415 AAAGAAAAA
1 AAAGAAAAA
9669424 TGAATGCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.11
15 22 0.63
16 9 0.26
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.05
Consensus pattern (15 bp):
AAAGAAAAAAAAATA
Found at i:9669412 original size:31 final size:33
Alignment explanation
Indices: 9669359--9669422 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
9669349 ATAAAAGGTT
*
9669359 TCAAAGATAGAAAGCAAAAAAAAAAAAAGAAAA
1 TCAAAGATAGAAAGAAAAAAAAAAAAAAGAAAA
**
9669392 TCAAA-ATA-AAAGAAAAAAAAATGAAAGAAAA
1 TCAAAGATAGAAAGAAAAAAAAAAAAAAGAAAA
9669423 ATGAATGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 20 0.71
32 3 0.11
33 5 0.18
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.08
Consensus pattern (33 bp):
TCAAAGATAGAAAGAAAAAAAAAAAAAAGAAAA
Found at i:9669814 original size:14 final size:14
Alignment explanation
Indices: 9669777--9669835 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 14
9669767 TAATGGGTAA
9669777 AAAAATGAAAGAAAG
1 AAAAATGAAA-AAAG
*
9669792 AAAAA--AAAAGAG
1 AAAAATGAAAAAAG
*
9669804 AAAAATGAAAAATG
1 AAAAATGAAAAAAG
9669818 -AAAATGAGAGAAAAG
1 AAAAATGA-A-AAAAG
9669833 AAA
1 AAA
9669836 GACTCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
12 8 0.23
13 10 0.29
14 6 0.17
15 9 0.26
16 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAAATGAAAAAAG
Found at i:9671020 original size:29 final size:30
Alignment explanation
Indices: 9670983--9671048 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
9670973 CTTTTGATGA
*
9670983 GAATCTTTGAAAT-TCAAATGAGAATCTTT
1 GAATTTTTGAAATCTCAAATGAGAATCTTT
**
9671012 GAATTTTTGAGTTCTCAAATGAGAATCTTT
1 GAATTTTTGAAATCTCAAATGAGAATCTTT
9671042 GAATTTT
1 GAATTTT
9671049 CAAATAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (30 bp):
GAATTTTTGAAATCTCAAATGAGAATCTTT
Found at i:9671042 original size:22 final size:21
Alignment explanation
Indices: 9671012--9671076 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
9671002 GAGAATCTTT
*
9671012 GAATTTTTGAGTTCTCAAATGA
1 GAATCTTTGAGTT-TCAAATGA
* *
9671034 GAATCTTTGAATTTTCAAATAA
1 GAATCTTTG-AGTTTCAAATGA
*
9671056 GAATCTTCGAGTTTCAAATGA
1 GAATCTTTGAGTTTCAAATGA
9671077 TGATCATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 10 0.28
22 23 0.64
23 3 0.08
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
GAATCTTTGAGTTTCAAATGA
Found at i:9671224 original size:20 final size:20
Alignment explanation
Indices: 9671199--9671237 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9671189 TTAAGATTTG
9671199 TCAAAT-ATGAACCTTTGAAC
1 TCAAATGAT-AACCTTTGAAC
*
9671219 TCAAATGATAAGCTTTGAA
1 TCAAATGATAACCTTTGAA
9671238 ATTTTGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
TCAAATGATAACCTTTGAAC
Found at i:9671686 original size:40 final size:40
Alignment explanation
Indices: 9671577--9671884 Score: 314
Period size: 40 Copynumber: 7.6 Consensus size: 40
9671567 CATGATTGTT
** *
9671577 GAGGAG-CTTTATTTTTCAAAGTCATTGAGCCTCTATTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* *
9671616 AAGGAGCCTTATTTTATTTTTTAAAGTTGTTGAGCCTCTACTTA
1 GAGGAGCC----TTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* *
9671660 GATGAGCCTTTATTTTTCAAATTTGTTGAGCCTCTACTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* * * * *
9671700 GAGGAGCATTTA-TTTTCAAAGTTGTTAAGTCACTGCTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* * * *
9671739 GAAGAGCCTTTATTTTTCAAAGTTGTTGAGCTTTTGCTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* * * *
9671779 GAGGAACCTTTGTTTTTTAAAGTCGTTGAGCCTCTACTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
* * * *
9671819 GAGGAGCCTTTATTTTCCAAAGTCGTTGAGCCTTTATTTA
1 GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
*
9671859 GAGGACCCTTGTTTATTTTTCAAAGT
1 GAGGAGCC---TTTATTTTTCAAAGT
9671885 CATTGGGCCT
Statistics
Matches: 221, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
39 37 0.17
40 136 0.62
43 14 0.06
44 34 0.15
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (40 bp):
GAGGAGCCTTTATTTTTCAAAGTTGTTGAGCCTCTACTTA
Found at i:9671895 original size:43 final size:42
Alignment explanation
Indices: 9671584--9671927 Score: 269
Period size: 40 Copynumber: 8.3 Consensus size: 42
9671574 GTTGAGGAGC
* * * *
9671584 TTTATTTTTCAAAGTCATTGAGCCTCTATTTAAAGGAGCCTTAT
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCC-T-T
* * * *
9671628 TTTATTTTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCC--
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* * * *
9671668 TTTATTTTTCAAATTTGTTGAGCCTCTACTTAGAGGAG-C-A
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* * * ** * *
9671708 TTTA-TTTTCAAAGTTGTTAAGTCACTGCTTAGAAGAGCC--
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* * * *
9671747 TTTATTTTTCAAAGTTGTTGAGCTTTTGCTTAGAGGAACCTT
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* *
9671789 TGT-TTTTT-AAAGTCGTTGAGCCTCTACTTAGAGGAGCC--
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* * *
9671827 TTTATTTTCCAAAGTCGTTGAGCCTTTATTTAGAGGACCCTT
1 TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
* * ** *
9671869 GTTTATTTTTCAAAGTCATTGGGCCTTTGTTTAGATGAGCCTT
1 -TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
9671912 GTTTATTTTTCCAAAG
1 -TTTATTTTT-CAAAG
9671928 GTGCTTAGAA
Statistics
Matches: 250, Mismatches: 39, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.01
39 36 0.14
40 120 0.48
41 5 0.02
42 2 0.01
43 46 0.18
44 39 0.16
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.43
Consensus pattern (42 bp):
TTTATTTTTCAAAGTCGTTGAGCCTTTACTTAGAGGAGCCTT
Found at i:9672150 original size:20 final size:20
Alignment explanation
Indices: 9672108--9672150 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9672098 GGTCCAAGTT
*
9672108 CAAGCCCATTAGGCCTGGTC
1 CAAGCCCATTAGGCCTGGCC
*
9672128 CAAGCCCATTAGGCTTGGCC
1 CAAGCCCATTAGGCCTGGCC
9672148 CAA
1 CAA
9672151 AAGTGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (20 bp):
CAAGCCCATTAGGCCTGGCC
Found at i:9672190 original size:5 final size:5
Alignment explanation
Indices: 9672180--9672259 Score: 55
Period size: 5 Copynumber: 16.6 Consensus size: 5
9672170 CCAATTACTC
* * *
9672180 TTTAT TTTAT TTTAT ATTA- TTTA- TTTA- TTTAT TTAAG TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
*
9672226 TATT-T AGTTAT TTTAT TTTA- TTTAT CTTTAT TTT
1 T-TTAT -TTTAT TTTAT TTTAT TTTAT -TTTAT TTT
9672260 CTAGTTGATT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
4 18 0.30
5 34 0.57
6 8 0.13
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:9672205 original size:4 final size:4
Alignment explanation
Indices: 9672180--9672250 Score: 54
Period size: 4 Copynumber: 16.2 Consensus size: 4
9672170 CCAATTACTC
*
9672180 TTTA TTTTA TTTTA TATTA TTTA TTTA TTTA TTTAA GTTTT TTTA -TTA
1 TTTA -TTTA -TTTA T-TTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA
*
9672228 TTTA GTTA TTTTA TTTTA TTTA T
1 TTTA TTTA -TTTA -TTTA TTTA T
9672251 CTTTATTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.05
4 29 0.51
5 22 0.39
6 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:9673198 original size:22 final size:22
Alignment explanation
Indices: 9673150--9673198 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
9673140 TGGTATTTTA
* *
9673150 TTTTATTTTTGTATTTTTATGT
1 TTTTATTTTAGTATTTTTATAT
*
9673172 ATTTA-TTTAGTATTTTTAATAT
1 TTTTATTTTAGTATTTTT-ATAT
9673194 TTTTA
1 TTTTA
9673199 CATGATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTATTTTAGTATTTTTATAT
Found at i:9678335 original size:223 final size:223
Alignment explanation
Indices: 9677941--9678388 Score: 806
Period size: 223 Copynumber: 2.0 Consensus size: 223
9677931 TACTGGAATA
*
9677941 ACTCCTAGTATTTTCATGATTACTTTGGGATCTTTAATTTCTTCTGAAAGAAATCAAATATTCAT
1 ACTCCCAGTATTTTCATGATTACTTTGGGATCTTTAATTTCTTCTGAAAGAAATCAAATATTCAT
* * *
9678006 TGTTCTTGGTTTCCATTTATTTAGCATATGTTAGATGGTCATATCCTACATGAATTGAACTTGGG
66 TCTTCTTGGTTTCCATTTATTTAGCATACGTTAAATGGTCATATCCTACATGAATTGAACTTGGG
*
9678071 GTTTTTGTACTCGACAAGATAGGCTGATATGTCTAAGTTGTTCTATTAGGCTACACCCGAGGGAG
131 GTTTTTGTACTCGACAAGATAGGCTGATATGTCTAAGTTGTTCTATTAGGCTACACCCAAGGGAG
9678136 AATGGTAAGTGGTAATATGTCCTATATC
196 AATGGTAAGTGGTAATATGTCCTATATC
* * *
9678164 ACTCCCAGTATTTTCATGATTATTTTGGGATCTTTCATTTCTTCTGAAAGAAATCAAATATTCGT
1 ACTCCCAGTATTTTCATGATTACTTTGGGATCTTTAATTTCTTCTGAAAGAAATCAAATATTCAT
9678229 TCTTCTTGGTTTCCATTTATTTAGCATACGTTAAATGGTCATATCCTACATGAATTGAACTTGGG
66 TCTTCTTGGTTTCCATTTATTTAGCATACGTTAAATGGTCATATCCTACATGAATTGAACTTGGG
*
9678294 GTTTTTGTACTTGACAAGATAGGCTGATATGTCTAAGTTGTTCTATTAGGCTACACCCAAGGGAG
131 GTTTTTGTACTCGACAAGATAGGCTGATATGTCTAAGTTGTTCTATTAGGCTACACCCAAGGGAG
*
9678359 AATGGTAAGTGGTATTATGTCCTATATC
196 AATGGTAAGTGGTAATATGTCCTATATC
9678387 AC
1 AC
9678389 AGTTTTCAGT
Statistics
Matches: 215, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
223 215 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (223 bp):
ACTCCCAGTATTTTCATGATTACTTTGGGATCTTTAATTTCTTCTGAAAGAAATCAAATATTCAT
TCTTCTTGGTTTCCATTTATTTAGCATACGTTAAATGGTCATATCCTACATGAATTGAACTTGGG
GTTTTTGTACTCGACAAGATAGGCTGATATGTCTAAGTTGTTCTATTAGGCTACACCCAAGGGAG
AATGGTAAGTGGTAATATGTCCTATATC
Found at i:9678705 original size:99 final size:98
Alignment explanation
Indices: 9678571--9678762 Score: 305
Period size: 99 Copynumber: 1.9 Consensus size: 98
9678561 TTATGATTTC
* * **
9678571 TTTCTACATAATTATGGTGAATTGATGATGGTTAGCTTATTATCTGATTATGAGAGGGGTACAAA
1 TTTCTACATAATTATGATGAATTGATGATGGTTAGCTTACTATCTGATTACAAGAGGGGTACAAA
* *
9678636 ATTGTATCCTCCCTTTCTCTCTCTCTCTCTCTT
66 ATTGTATCCACCCTCTCTCTCTCTCTCTCTCTT
9678669 TTTCTATCTATAATTATGATGAA-TGATGATGGTTAGCTTACTATCTGATTACAAGAGGGGTACA
1 TTTCTA-C-ATAATTATGATGAATTGATGATGGTTAGCTTACTATCTGATTACAAGAGGGGTACA
9678733 AAATTGTATCCACCCTCTCTCTCTCTCTCT
64 AAATTGTATCCACCCTCTCTCTCTCTCTCT
9678763 ATATATATAT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 6 0.07
99 67 0.78
100 13 0.15
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (98 bp):
TTTCTACATAATTATGATGAATTGATGATGGTTAGCTTACTATCTGATTACAAGAGGGGTACAAA
ATTGTATCCACCCTCTCTCTCTCTCTCTCTCTT
Found at i:9678767 original size:2 final size:2
Alignment explanation
Indices: 9678762--9678791 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9678752 TCTCTCTCTC
9678762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9678792 AGAAACACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9682534 original size:3 final size:3
Alignment explanation
Indices: 9682528--9682571 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9682518 TTTTTATCTG
*
9682528 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9682572 GTTTGGTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9695061 original size:2 final size:2
Alignment explanation
Indices: 9695051--9695083 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9695041 ATATGTTTTA
*
9695051 AT AT A- AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9695084 GATTTTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9695555 original size:2 final size:2
Alignment explanation
Indices: 9695550--9695583 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9695540 AAAATGAGGG
9695550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9695584 ATTTTCAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9695816 original size:15 final size:15
Alignment explanation
Indices: 9695796--9695851 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
9695786 ATCATAAACT
9695796 TTTTCAAAAAATAAA
1 TTTTCAAAAAATAAA
9695811 TTTTCAAAAATCATAAAA
1 TTTTCAAAAA--AT-AAA
** *
9695829 TTTTTTAAAAATAGA
1 TTTTCAAAAAATAAA
9695844 TTTTCAAA
1 TTTTCAAA
9695852 TAATTATAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 18 0.55
16 2 0.06
17 2 0.06
18 11 0.33
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (15 bp):
TTTTCAAAAAATAAA
Found at i:9695820 original size:34 final size:34
Alignment explanation
Indices: 9695775--9695872 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 34
9695765 TTAATTATGC
9695775 ATTTTCCAAAAATCATAAACTTTTTCAAAAAATAA
1 ATTTT-CAAAAATCATAAACTTTTTCAAAAAATAA
* * *
9695810 ATTTTCAAAAATCATAAAATTTTT-TAAAAATAG
1 ATTTTCAAAAATCATAAACTTTTTCAAAAAATAA
* * *
9695843 ATTTTCAAATAATTATAGACCTTTTCAAAA
1 ATTTTCAAA-AATCATAAACTTTTTCAAAA
9695873 TTTGATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
33 16 0.30
34 29 0.55
35 8 0.15
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (34 bp):
ATTTTCAAAAATCATAAACTTTTTCAAAAAATAA
Found at i:9695826 original size:17 final size:17
Alignment explanation
Indices: 9695775--9695832 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 17
9695765 TTAATTATGC
9695775 ATTTTCCAAAAATCATAA
1 ATTTT-CAAAAATCATAA
9695793 ACTTTTTCAAAAA--ATAA
1 A--TTTTCAAAAATCATAA
9695810 ATTTTCAAAAATCATAAA
1 ATTTTCAAAAATCAT-AA
9695828 ATTTT
1 ATTTT
9695833 TTAAAAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.29
17 7 0.20
18 8 0.23
19 6 0.17
20 4 0.11
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTTCAAAAATCATAA
Found at i:9695901 original size:50 final size:51
Alignment explanation
Indices: 9695843--9695938 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
9695833 TTAAAAATAG
9695843 ATTTTC-AAATAATTATA-GACCTTTTCAAAATTTGATTTTTGAAAAGCTAA
1 ATTTTCAAAATAATTATATGA-CTTTTCAAAATTTGATTTTTGAAAAGCTAA
* * *
9695893 ATTTTCAAAATGATTTTATGACTTTTCAAAATTTTATTTTTGAAAA
1 ATTTTCAAAATAATTATATGACTTTTCAAAATTTGATTTTTGAAAA
9695939 ATTATATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
50 6 0.15
51 33 0.80
52 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (51 bp):
ATTTTCAAAATAATTATATGACTTTTCAAAATTTGATTTTTGAAAAGCTAA
Found at i:9695928 original size:517 final size:498
Alignment explanation
Indices: 9695051--9696016 Score: 1216
Period size: 517 Copynumber: 1.9 Consensus size: 498
9695041 ATATGTTTTA
* * *
9695051 ATATAATATATACATATATATATATATATATATGATTTTCAAGTTTCAAGTGTTAATCGGAAAAG
1 ATATAATATATACATATATATATATATATATATAATTTTCAAGCTTCAAGTGTTAATCAGAAAAG
* * * * *
9695116 ATAGAGGTGCATTGGAAAATTTAATAGGTGCAAGCCGTAAGAATGGATACGAGTGATGCGAAATG
66 ATAGAGGTACATCGGAAAATTTAATAGGTGCAAGCCATAAGAATGAATAAGAGTGATGCGAAATG
*
9695181 CATTTTAAGCTTTTCTCTTCGCACTCTAATTTTTTTTAATTTTTTAAAATAAAGTTATTTAATTA
131 CATTTCAAGCTTTTCTCTTCGCACTCTAATTTTTTTTAATTTTTTAAAATAAAGTTATTTAATTA
* *** *
9695246 TTTTTTTCACACAAGTTTTGAAAAATCATAAATTTTTTTGAAAATAGATTTCCGAAAAACCATAT
196 TTTTTTTCACACAAGTTTTCAAAAATCATAAATTTTTCAAAAAATAAATTTCCGAAAAACCATAT
9695311 AAATTTTCTAAAATAAAGTTTCAAAAAATTATAAACCTTTTCAAAAATTTTTTTTGAAAAGAAAA
261 AAATTTTCTAAAATAAAGTTTCAAAAAATTATAAACCTTTTCAAAAATTTTTTTTGAAAAGAAAA
* * * * *
9695376 ATTTTCAAAAAGATTTTGTGACTTTTTAAAATTTTATTTTTGAAAATTTATATAATTTTTTGAAA
326 ATTTTCAAAAAGATTTTATGACTTTTCAAAATTTTATTTTTGAAAAATTATATAA-CTTCTG--A
*
9695441 ATTTATTTT-T-AAAAATTATAAAACTTTATAAAATTACGAGAACAGTAATTAAATAATTTTTTA
388 ATTT-TTTTATAAAAAATTATAAAAATTTATAAAATTACGAGAACAGTAATTAAATAATTTTTTA
9695504 AAAAATAACCTAAATAAAATTAAGGTATAAAGAAAAAAAATGAGGGT
452 AAAAATAACCTAAATAAAATTAAGGTATAAAGAAAAAAAATGAGGGT
* *
9695551 ATAT-ATATATATATATATATATATATATATATAATTTTCAAGCTTCGAGTGTTAATCAGAAAAG
1 ATATAATATATACATATATATATATATATATATAATTTTCAAGCTTCAAGTGTTAATCAGAAAAG
* * * *
9695615 AT-GATGGTACATC-GAGAAATTTAATAGGTGTAAGTCATAAGAGTGAATAAAGAGTGATAG-TA
66 ATAGA-GGTACATCGGA-AAATTTAATAGGTGCAAGCCATAAGAATGAAT-AAGAGTGAT-GCGA
*
9695677 AATGCATTTCAAGCTTTTCTCTTCGCACTCTAA-TTTTTTT-ATTTTTTAAAATGAAGTTATTTA
127 AATGCATTTCAAGCTTTTCTCTTCGCACTCTAATTTTTTTTAATTTTTTAAAATAAAGTTATTTA
9695740 ATTATCTTTTTTTTCACACTAATTTTTAATTATGCATTTTCCAAAAATCATAAACTTTTTCAAAA
192 ATTA---TTTTTTTCACAC---------A--A-G--TTTT-CAAAAATCATAAA-TTTTTCAAAA
* * * * * * *
9695805 AATAAATTTTC-AAAAATCATA-AAATTTTTTAAAAATAGATTTTCAAATAATTATAGACCTTTT
238 AATAAATTTCCGAAAAACCATATAAATTTTCT-AAAATAAAGTTTCAAAAAATTATAAACCTTTT
** *
9695868 C-AAAATTTGATTTTTGAAAAGCTAAATTTTCAAAATGATTTTATGACTTTTCAAAATTTTATTT
302 CAAAAATTT--TTTTTGAAAAGAAAAATTTTCAAAAAGATTTTATGACTTTTCAAAATTTTATTT
*
9695932 TTGAAAAATTATATAACTTCTGAATTTTTTTATAAAAAAAATTATAAAAATTTATAAAATTATGA
365 TTGAAAAATTATATAACTTCTGAATTTTTTTAT--AAAAAATTATAAAAATTTATAAAATTACGA
*
9695997 GAGCAGTAATTAAATAATTT
428 GAACAGTAATTAAATAATTT
9696017 AAAAAAATTG
Statistics
Matches: 397, Mismatches: 39, Indels: 43
0.83 0.08 0.09
Matches are distributed among these distances:
498 30 0.08
499 97 0.24
500 45 0.11
501 13 0.03
510 1 0.00
512 1 0.00
513 5 0.01
514 6 0.02
515 19 0.05
516 54 0.14
517 126 0.32
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (498 bp):
ATATAATATATACATATATATATATATATATATAATTTTCAAGCTTCAAGTGTTAATCAGAAAAG
ATAGAGGTACATCGGAAAATTTAATAGGTGCAAGCCATAAGAATGAATAAGAGTGATGCGAAATG
CATTTCAAGCTTTTCTCTTCGCACTCTAATTTTTTTTAATTTTTTAAAATAAAGTTATTTAATTA
TTTTTTTCACACAAGTTTTCAAAAATCATAAATTTTTCAAAAAATAAATTTCCGAAAAACCATAT
AAATTTTCTAAAATAAAGTTTCAAAAAATTATAAACCTTTTCAAAAATTTTTTTTGAAAAGAAAA
ATTTTCAAAAAGATTTTATGACTTTTCAAAATTTTATTTTTGAAAAATTATATAACTTCTGAATT
TTTTTATAAAAAATTATAAAAATTTATAAAATTACGAGAACAGTAATTAAATAATTTTTTAAAAA
ATAACCTAAATAAAATTAAGGTATAAAGAAAAAAAATGAGGGT
Found at i:9696301 original size:2 final size:2
Alignment explanation
Indices: 9696296--9696327 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9696286 AATCTCTCCA
9696296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9696328 TCACAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9701311 original size:29 final size:30
Alignment explanation
Indices: 9701227--9701314 Score: 126
Period size: 29 Copynumber: 3.0 Consensus size: 30
9701217 ATATCCAAAC
* *
9701227 AATAAAAAATAAATAATAAAATTATATTAA
1 AATAATAAATAAATAATAAAATTATATTCA
9701257 AATAATAAATAAA-AATAAAATTATATTCA
1 AATAATAAATAAATAATAAAATTATATTCA
* *
9701286 AATAATAAA-AAATAATAAAGTAATATTCA
1 AATAATAAATAAATAATAAAATTATATTCA
9701315 CACAATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 3 0.06
29 38 0.72
30 12 0.23
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (30 bp):
AATAATAAATAAATAATAAAATTATATTCA
Found at i:9702082 original size:21 final size:21
Alignment explanation
Indices: 9702056--9702208 Score: 152
Period size: 21 Copynumber: 7.3 Consensus size: 21
9702046 AAGAAAAAAC
* *
9702056 CTGCTGAAGGAAACCAGTAGT
1 CTGCTGCAGGAAACCAGCAGT
9702077 CTGCTGCAGGAAACCAGCAGT
1 CTGCTGCAGGAAACCAGCAGT
*
9702098 CTGCTGCAGGAAACCAGCAATCT
1 CTGCTGCAGGAAACCAGC-A-GT
* *
9702121 GCTGCTGCAGGAAACCAGTAAT
1 -CTGCTGCAGGAAACCAGCAGT
* *
9702143 CTGCTACAGGAAACCAGCAGA
1 CTGCTGCAGGAAACCAGCAGT
*
9702164 C--AT--AGGAAACCAGCAGT
1 CTGCTGCAGGAAACCAGCAGT
* *
9702181 CTGCTGCAGGAAACTAGTAGT
1 CTGCTGCAGGAAACCAGCAGT
*
9702202 TTGCTGC
1 CTGCTGC
9702209 TGTCTTTGCT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
17 14 0.13
19 2 0.02
21 73 0.66
22 2 0.02
23 2 0.02
24 17 0.15
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (21 bp):
CTGCTGCAGGAAACCAGCAGT
Found at i:9706953 original size:25 final size:25
Alignment explanation
Indices: 9706923--9706990 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
9706913 TATTAGTATA
9706923 ATTATTAAA-ATATTAAAAAATATTT
1 ATTATTAAAGATATT-AAAAATATTT
* *
9706948 ATTATTAAAGTATATTGAAATTATTT
1 ATTATTAAAG-ATATTAAAAATATTT
* *
9706974 ATGATTAAAGTTATTAA
1 ATTATTAAAGATATTAA
9706991 TATTCAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 14 0.39
26 17 0.47
27 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
ATTATTAAAGATATTAAAAATATTT
Found at i:9707140 original size:43 final size:44
Alignment explanation
Indices: 9707093--9707177 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 44
9707083 TATATTAATA
* * * *
9707093 TTTTA-AAATATTTTAAATAGTATTAT-TATTCTTACAATATTCT
1 TTTTATAAATA-TTAAAATAGTAATATGTATTATTAAAATATTCT
*
9707136 TTTTATTAATATTAAAATAGTAATATGTATTATTAAAATATT
1 TTTTATAAATATTAAAATAGTAATATGTATTATTAAAATATT
9707178 TATACTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 18 0.51
44 17 0.49
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (44 bp):
TTTTATAAATATTAAAATAGTAATATGTATTATTAAAATATTCT
Found at i:9707188 original size:17 final size:17
Alignment explanation
Indices: 9707166--9707198 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9707156 TAATATGTAT
9707166 TATTAAAATATTTATAC
1 TATTAAAATATTTATAC
9707183 TATTAAAATATTTATA
1 TATTAAAATATTTATA
9707199 TTTTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAATATTTATAC
Found at i:9707338 original size:11 final size:11
Alignment explanation
Indices: 9707322--9707346 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9707312 ATTTTAAACT
9707322 AAAAATATTTA
1 AAAAATATTTA
9707333 AAAAATATTTA
1 AAAAATATTTA
9707344 AAA
1 AAA
9707347 TATTCATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATATTTA
Found at i:9707424 original size:10 final size:10
Alignment explanation
Indices: 9707409--9707436 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9707399 ATAATAAAAT
9707409 TATTATTATA
1 TATTATTATA
9707419 TATTATTATA
1 TATTATTATA
9707429 TATTATTA
1 TATTATTA
9707437 AAATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTATTATA
Found at i:9707433 original size:37 final size:36
Alignment explanation
Indices: 9707352--9707463 Score: 88
Period size: 37 Copynumber: 3.0 Consensus size: 36
9707342 TAAAATATTC
* *
9707352 ATATTA-AGAAAATAATATTATTATATTATTTAACATTA-
1 ATATTATA-AAAATAAAATTATTATACTATTT---ATTAT
9707390 ATTATTA-AAATAATAAAATTATTATTA-TATATTATTAT
1 A-TATTATAAA-AATAAAATTATTA-TACTAT-TTATTAT
* *
9707428 ATATTATTAAAATAATATTATTATACTATTTATTAT
1 ATATTATAAAAATAAAATTATTATACTATTTATTAT
9707464 TGAAATACTA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
36 9 0.14
37 24 0.38
38 6 0.09
39 21 0.33
40 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (36 bp):
ATATTATAAAAATAAAATTATTATACTATTTATTAT
Found at i:9707476 original size:37 final size:35
Alignment explanation
Indices: 9707373--9707481 Score: 88
Period size: 34 Copynumber: 3.2 Consensus size: 35
9707363 ATAATATTAT
*
9707373 TATATTATT-TAAC-ATTAATTATTAAAATAATAAAA
1 TATATTATTAT-ACTATTTATTATT-AAATAATAAAA
* *
9707408 T-TATTATTATA-TA-TTATTA-TATATTATTAAAA
1 TATATTATTATACTATTTATTATTA-AATAATAAAA
*
9707440 TAATATTATTATACTATTTATTATTGAAATACTAAAA
1 T-ATATTATTATACTATTTATTATT-AAATAATAAAA
9707477 -ATATT
1 TATATT
9707482 TATATTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
31 1 0.02
32 10 0.17
33 5 0.08
34 19 0.32
35 9 0.15
36 6 0.10
37 9 0.15
38 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TATATTATTATACTATTTATTATTAAATAATAAAA
Found at i:9713422 original size:11 final size:11
Alignment explanation
Indices: 9713406--9713440 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9713396 ATATTCGTTT
9713406 GAGATTTGTTA
1 GAGATTTGTTA
*
9713417 GAGATTTGTTT
1 GAGATTTGTTA
*
9713428 GGGATTTGTTA
1 GAGATTTGTTA
9713439 GA
1 GA
9713441 TATTGCTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (11 bp):
GAGATTTGTTA
Found at i:9714356 original size:11 final size:11
Alignment explanation
Indices: 9714340--9714372 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9714330 ATTCATTTGG
9714340 GATTTGTTAGA
1 GATTTGTTAGA
9714351 GATTTGTTTAG-
1 GATTTG-TTAGA
9714362 GATTTGTTAGA
1 GATTTGTTAGA
9714373 TATTGCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.20
11 12 0.60
12 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (11 bp):
GATTTGTTAGA
Found at i:9715167 original size:924 final size:924
Alignment explanation
Indices: 9713366--9715873 Score: 3218
Period size: 924 Copynumber: 2.7 Consensus size: 924
9713356 TGTTCCAAAG
* * *
9713366 TGTTAAGAATAATGACTTAAATCCCATAAGATATTCGTTTGAGATTTGTTAGAGATTTGTTTGGG
1 TGTTAGGAATAATGACTCAAATCCCATAAGATATTCGTTTGGGATTTGTTAGAGATTTGTTT-GG
* * * *
9713431 ATTTGTTAGATATTGCTTGATGGACAAGAAAACTTACAAAAAAAAAATTTTGAAAGGAAAAAAGA
65 ATTTGTTAGATATTGCTTGATGGACAAGAAGACTTGC-AAAAAAAAATTTTAAAAGG-AAAATGA
*
9713496 TACTTAATAGGCAAGTTTGACTTGAAGGAGAAGAATTCTAAGAGGAAAGGGATTGTTAATAGGCA
128 TTCTTAATAGGCAAGTTTGACTT-AAGGAGAAGAATTCT-A-A-GAAA-GGA---TTAATAGGCA
* * * * *
9713561 AGTTTATAT-G-TATAAATAGATGGAGTCTCTCCAGGATTAGATATGAGAAAAATATGTAAAAAA
185 AGTTTGTATGGTTATAAATAGATGAAGTCTCTCCAAGATTAGGTATGAGAAAAATATGTAAAAGA
* * * ** *
9713624 ATTGTAGGGTTTTATGGGATAAACA-CCTAGAAGGAGTACT-GAGGCTTTATGTTTTATAGGTAT
250 ATTGTAAGGTTTTATAGGATAAACACCCTA-TAGGAGTACTAG-GGCTTTACATTTTATGGGTAT
* * * * *
9713687 GTTTGTTTGTTTGTGAGTGGACTAGAGAAA-ACTAAGAGGGTCCACATAGATGTGATGTATGGGT
313 GTATGTTTGTTTGTGAATGGACTAGA-AAAGATTGAGAGGGTCCACATAGATGTGATGTATGGGC
* * *
9713751 GCATATGAGTACATGTTTGGTTATGTTGAAATGGTGCATATGGATATGTATTTGTTTGGATT-AA
377 GTATATGAGTATATGTTTGGTTGTGTTGAAATGGTGCATATGGATATGTATTTGTTTGGATTGAA
* *
9713815 GAATATTCAATA-GACTAGAGGAGATTAAGAGGGTCTATGGGTATTGATTGTTGAGTGGTTGATA
442 -AATACTCAATAGGACTAGAGGAGATTAAGAGGGTCTATGAGTATTGATTGTTGAGTGGTTGATA
* * * *
9713879 CCTTTTGATGCATGTTTGTAATTCTCTATAACTAGTGAATCTTGTTTCTCATCCGTGAACGTAGG
506 CATTTTGATGTATGTTTGTAATTCTCTATAACTAGTGAATCTTGTTTCTCATCCGTGGACATAGG
* *
9713944 TCAGTTAGATTGAACCACATTAAATTGTTGTCTCTTATATGTTTGATTAATTATTTGATTATGCT
571 TCAGTTAGATCGAACCACATTAAATTGTTGTCTCTTATGTGTTTGATTAATTATTTGATTATGCT
** ** * * *** * *
9714009 TCTGCTGGTGTGATTGGAAAGGGGTTTTTTTGCCCAACAAGTGGTATTAGAGCTACGGTATCCCT
636 TCCACTGGCATGATTGGAAAGGGATTTTTTTACCCAACAAGTAACATCAGAGCTACGGTATCCCC
* * **
9714074 AACAAGTGGTATCAGAGCATGGTTTAAGTCATAGGAAAAAGTAAGTCCAAAGGAGCTCGATTCAA
701 AACAAGTGGTATCAGAGCATGGTTCAAGCCATAGGAAAAAACAAGTCCAAAGGAGCTCGATTCAA
* * * *
9714139 GAGAAGAGTTTGAGTTCAAGTTTTGAGGATTGAAGATTGATTTGCATGAAGCGTGAAGACACATA
766 GAGAAGAATTTAAGTTCAAGTTTTGAGGATTGAAGATTGATTTACATGAAGCATGAAGACACATA
* * * * *
9714204 AGAGAAGATGATTATAAGACTTTCATTATAAGTGGAGCCAAGCATGTCTAGCATGAAGACAGATG
831 AAAGAAGATGATTATAAGACTTTCATTACAAGTGGAGCCAAGCATATCTAGCATAAAAACAGATG
9714269 ATTGATGAAATTTGAGTCAAAGTAAAGAT
896 ATTGATGAAATTTGAGTCAAAGTAAAGAT
*
9714298 TGTTAGGAATAATGACTCAAATCCCATAAGATATTCATTTGGGATTTGTTAGAGATTTGTTTAGG
1 TGTTAGGAATAATGACTCAAATCCCATAAGATATTCGTTTGGGATTTGTTAGAGATTTGTTT-GG
* *
9714363 ATTTGTTAGATATTGCTTGATAGACAAGAAGACTTGCAAAAAAAGAATTCTAAAAGGAAAATGGA
65 ATTTGTTAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAA-AATTTTAAAAGGAAAAT-GA
* *
9714428 TTCTTAATAGGTAAGTTTGACTTATAGGAGAAGAATTCT-A-ATAGGA-TAATAGGCAAGTTTGT
128 TTCTTAATAGGCAAGTTTGACTTA-AGGAGAAGAATTCTAAGAAAGGATTAATAGGCAAGTTTGT
* * * *
9714490 ATGGTTATAAATAGATGAAGTCTCTCCAAGATTAGGTATGAAAAAAATATATAAGAGACTTGTAA
192 ATGGTTATAAATAGATGAAGTCTCTCCAAGATTAGGTATGAGAAAAATATGTAAAAGAATTGTAA
* * * * * *
9714555 GGTTTTGTAGGATAGACACCCCATAGGAGTACTAGGGCTTTACATTTTATGGGTGTGTATATTTA
257 GGTTTTATAGGATAAACACCCTATAGGAGTACTAGGGCTTTACATTTTATGGGTATGTATGTTTG
* * * *
9714620 TTT-TCGAACGGACTA-AAAGAGATTGAGAGGGTCCACATAGATATGATGTATGGGCATATATAA
322 TTTGT-GAATGGACTAGAAA-AGATTGAGAGGGTCCACATAGATGTGATGTATGGGCGTATATGA
* * *
9714683 G-ATATGTTTGGTTGTGTTGAAATGGTGCATATAGATATGTATTTATTTGGATTGAAAATACTCT
385 GTATATGTTTGGTTGTGTTGAAATGGTGCATATGGATATGTATTTGTTTGGATTGAAAATACTCA
* * * * * *
9714747 ATAGGATTAGAAGAGATTAAGAGGGTCTATGAGTGTTGATTATTGAGTGATTGATACGTTTTGAT
450 ATAGGACTAGAGGAGATTAAGAGGGTCTATGAGTATTGATTGTTGAGTGGTTGATACATTTTGAT
* * *
9714812 GTATGTTTGTAATTCTCTATAACTAGT-AGATCTTGTTTCTCATCCATGGACATAAGTTAGTTA-
515 GTATGTTTGTAATTCTCTATAACTAGTGA-ATCTTGTTTCTCATCCGTGGACATAGGTCAGTTAG
* * *
9714875 ATCGAACCACATTAAATTATTGTCTCTTATGTATTTAATTAATTATTTGATTATGCTTCCACTGG
579 ATCGAACCACATTAAATTGTTGTCTCTTATGTGTTTGATTAATTATTTGATTATGCTTCCACTGG
* *
9714940 CATGATTGGAAAGGGATTTTTTTACCCAATAAGTAACATCAGAGCTATGGTGATCCCCAACAAGT
644 CATGATTGGAAAGGGATTTTTTTACCCAACAAGTAACATCAGAGCTACGGT-ATCCCCAACAAGT
* * *
9715005 GGTATCAGAGCATGGTTCAAGCCAT-GAGAAAAAACAAGTCCAAATGAGCTCGATTTAATAGAAG
708 GGTATCAGAGCATGGTTCAAGCCATAG-GAAAAAACAAGTCCAAAGGAGCTCGATTCAAGAGAAG
* ** *
9715069 AATTTAAGTTCAAGTTTTGAGGATTGAGGATTGATTTATGTGAAGCATGAAGATACATAAAAGAA
772 AATTTAAGTTCAAGTTTTGAGGATTGAAGATTGATTTACATGAAGCATGAAGACACATAAAAGAA
* * * *
9715134 TATGATTGTAAGACTTTTATTACAGGTGGAGCCAAGCATATCTAGCATAAAAACAGATGATTGAT
837 GATGATTATAAGACTTTCATTACAAGTGGAGCCAAGCATATCTAGCATAAAAACAGATGATTGAT
* *
9715199 GGAATTTGAGTCAAGGTAAAGAT
902 GAAATTTGAGTCAAAGTAAAGAT
* * *
9715222 TGTTAGGAATAATGACTCAAATCCTATAAGATATTCGTTTGGAATTTGTTAGAGATTTATTTGAG
1 TGTTAGGAATAATGACTCAAATCCCATAAGATATTCGTTTGGGATTTGTTAGAGATTTGTTTG-G
* * * *
9715287 ATTTGTTAGATATTACTTGATGGACAAAAAGAATTGCAAAAGAAAAATTTTAAAAAGAAAAATGA
65 ATTTGTTAGATATTGCTTGATGGACAAGAAGACTTGCAAAA-AAAAATTTT-AAAAGGAAAATGA
*
9715352 TTCTTAATAGGCAAGTTT-AGCTTACAGGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGAC
128 TTCTTAATAGGCAAGTTTGA-CTTA-AGGAGAAGAATTCT-A-A-GAAAG-GA---TTAATAGGC
* * *
9715416 AAGTTTGTATGGTTATACATAGATGGAA-TCTCTCTAAGATTAGGTATGAGAAAAAGATGTAAAA
184 AAGTTTGTATGGTTATAAATAGAT-GAAGTCTCTCCAAGATTAGGTATGAGAAAAATATGTAAAA
* ** * * * *
9715480 GAGTTGTAAAATTTTATAGGATACACACCTTATAGGAGTACTAAGGCTTTACATATTATGGGTAT
248 GAATTGTAAGGTTTTATAGGATAAACACCCTATAGGAGTACTAGGGCTTTACATTTTATGGGTAT
* * * * *
9715545 GTACGTTTGTTTGTAAATAGATTAGAAAAGATTGAGAGGATCCACATAGATGTGATGTATGGGCG
313 GTATGTTTGTTTGTGAATGGACTAGAAAAGATTGAGAGGGTCCACATAGATGTGATGTATGGGCG
* * * * *
9715610 TATATGAGTATGTGTTTGGTTGTGTTGAAATTGTGCATATGGATATGTGTTTGTTTGAATTGAGA
378 TATATGAGTATATGTTTGGTTGTGTTGAAATGGTGCATATGGATATGTATTTGTTTGGATTGAAA
* * *
9715675 ATACTCCATAGGACTAGAGGAGATTAAAAGGATCTATGAGTATTGATTGTTGAGTGGTTGATACA
443 ATACTCAATAGGACTAGAGGAGATTAAGAGGGTCTATGAGTATTGATTGTTGAGTGGTTGATACA
* * *
9715740 TTTTGATGTATGTTTGTAATTCTCTACAACTAGTGAATTTTGTTTCTCATCCGTAGG-TATAGGT
508 TTTTGATGTATGTTTGTAATTCTCTATAACTAGTGAATCTTGTTTCTCATCCGT-GGACATAGGT
* * * * *
9715804 CAGTTAGACCAAATCACATTAAATTGTTGTTTCTTATGTGTTTGATTAATTATTTGATTATACTT
572 CAGTTAGATCGAACCACATTAAATTGTTGTCTCTTATGTGTTTGATTAATTATTTGATTATGCTT
9715869 CCACT
637 CCACT
9715874 AACGTGATTG
Statistics
Matches: 1361, Mismatches: 179, Indels: 68
0.85 0.11 0.04
Matches are distributed among these distances:
922 19 0.01
923 164 0.12
924 595 0.44
925 17 0.01
926 3 0.00
927 3 0.00
929 4 0.00
930 2 0.00
931 12 0.01
932 141 0.10
934 172 0.13
935 171 0.13
936 58 0.04
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (924 bp):
TGTTAGGAATAATGACTCAAATCCCATAAGATATTCGTTTGGGATTTGTTAGAGATTTGTTTGGA
TTTGTTAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAAATTTTAAAAGGAAAATGATTC
TTAATAGGCAAGTTTGACTTAAGGAGAAGAATTCTAAGAAAGGATTAATAGGCAAGTTTGTATGG
TTATAAATAGATGAAGTCTCTCCAAGATTAGGTATGAGAAAAATATGTAAAAGAATTGTAAGGTT
TTATAGGATAAACACCCTATAGGAGTACTAGGGCTTTACATTTTATGGGTATGTATGTTTGTTTG
TGAATGGACTAGAAAAGATTGAGAGGGTCCACATAGATGTGATGTATGGGCGTATATGAGTATAT
GTTTGGTTGTGTTGAAATGGTGCATATGGATATGTATTTGTTTGGATTGAAAATACTCAATAGGA
CTAGAGGAGATTAAGAGGGTCTATGAGTATTGATTGTTGAGTGGTTGATACATTTTGATGTATGT
TTGTAATTCTCTATAACTAGTGAATCTTGTTTCTCATCCGTGGACATAGGTCAGTTAGATCGAAC
CACATTAAATTGTTGTCTCTTATGTGTTTGATTAATTATTTGATTATGCTTCCACTGGCATGATT
GGAAAGGGATTTTTTTACCCAACAAGTAACATCAGAGCTACGGTATCCCCAACAAGTGGTATCAG
AGCATGGTTCAAGCCATAGGAAAAAACAAGTCCAAAGGAGCTCGATTCAAGAGAAGAATTTAAGT
TCAAGTTTTGAGGATTGAAGATTGATTTACATGAAGCATGAAGACACATAAAAGAAGATGATTAT
AAGACTTTCATTACAAGTGGAGCCAAGCATATCTAGCATAAAAACAGATGATTGATGAAATTTGA
GTCAAAGTAAAGAT
Found at i:9718917 original size:17 final size:17
Alignment explanation
Indices: 9718895--9718927 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9718885 ATTACGAAGG
*
9718895 TGTACCAATAACCATCA
1 TGTACCAAAAACCATCA
9718912 TGTACCAAAAACCATC
1 TGTACCAAAAACCATC
9718928 GTATGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.21
Consensus pattern (17 bp):
TGTACCAAAAACCATCA
Found at i:9721057 original size:18 final size:18
Alignment explanation
Indices: 9721034--9721076 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9721024 TTTCTCATTT
*
9721034 TTTATTACTT-ATTCTTAA
1 TTTATTAATTAATT-TTAA
*
9721052 TTTATTAATTAATTTTTA
1 TTTATTAATTAATTTTAA
9721070 TTTATTA
1 TTTATTA
9721077 TTTTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAATTTTAA
Found at i:9723855 original size:18 final size:19
Alignment explanation
Indices: 9723819--9723866 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
9723809 CCATCAGACC
*
9723819 CTTTTATTTTTTACCTTTT
1 CTTTTATTTTTTACATTTT
9723838 -TTTTATTTTTT-CTATTTT
1 CTTTTATTTTTTAC-ATTTT
9723856 CTTTGTATTTT
1 CTTT-TATTTT
9723867 GTATATTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
19 3 0.12
20 6 0.24
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.77
Consensus pattern (19 bp):
CTTTTATTTTTTACATTTT
Found at i:9724367 original size:50 final size:51
Alignment explanation
Indices: 9724298--9724901 Score: 457
Period size: 48 Copynumber: 11.8 Consensus size: 51
9724288 ATTTAAAATC
* * *
9724298 TGAAAAAGGTTCCTCTCAGCAAAGGCTCAACAACTTTAAAAA-TCT-ATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* * * * *
9724347 TGAAAAAAAGCTCCTCTCAGCAAAAGCTTAACAACTTAAAGAAATTCTTATCT
1 TG-AAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAA-AAATTCTCATCT
*
9724400 TG-AAAAAGCTCCTCTCAGCAAAGGCTCAACAACTTTAAAAAAATTCTCATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATTCTCATCT
* * * *
9724452 T-AAAAAAGCTTCTCTTAGCAGAGGTTCAATAACTTTAAAAA-TCTCATC-
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* * * * * *
9724500 TG-GAAAAGCTCCTCTAAGCAGAGGTTCAATAACTTT-AAAATACTAATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* ** * *
9724549 TAAAAAAAGCTTATCTCAGTAGAGGTTCAACAACTTTAAAAA-TCT-ATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* ** * * * *
9724598 TG-AAAAAGTTTATCTCAGCAGAAGCTTAACAACTTTAAAAATT-TTATTT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* * * *
9724647 TG-AAAAAGCTCATTTCAGTAGAGGCTCAACAACTTCAAAGAAATTCTCATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTT-TAA-AAATTCTCATCT
* * * * ** *
9724699 TGAAAAAGGATTCTCTCAGTAGAAACTTAACAACTTTAAAAAAATTCTCATCT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATTCTCATCT
* * * * * *
9724752 TAAAAAAGCTATAAGCTCCTCTTAACAGAGGCTTAACAACTTTAAAAAAATTTTGATCT
1 T--GAAA---A-AAGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATTCTCATCT
* * * *
9724811 TG-AAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTT--AAAGTCTTATAT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
* * *
9724859 TGAAAAAAGCTCATCTTAACAGAGGCTCAACAACTTTAAAAAT
1 TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAT
9724902 CTAATATGTT
Statistics
Matches: 449, Mismatches: 77, Indels: 56
0.77 0.13 0.10
Matches are distributed among these distances:
47 4 0.01
48 82 0.18
49 78 0.17
50 69 0.15
51 46 0.10
52 77 0.17
53 47 0.10
54 2 0.00
55 3 0.01
56 2 0.00
58 1 0.00
59 38 0.08
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (51 bp):
TGAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCT
Found at i:9724678 original size:49 final size:49
Alignment explanation
Indices: 9724267--9724901 Score: 386
Period size: 49 Copynumber: 12.4 Consensus size: 49
9724257 TGTCTCACTT
* * * * *
9724267 GAGGCTCGACAACTTTTGAAAATTTAAAATC-TGAAAAAGGTTCCTCTCAGCA
1 GAGGCTCAACAAC-TTTAAAAATTT--TATCTTGAAAAA-GCTCATCTCAGCA
* * *
9724319 AAGGCTCAACAACTTTAAAAA-TCTATCTTGAAAAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTG--AAAAAGCTCATCTCAGCA
* * * * *
9724369 AAAGCTTAACAACTTAAAGAAATTCTTATCTTGAAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTAA-AAATT-TTATCTTGAAAAAGCTCATCTCAGCA
* * * *
9724420 AAGGCTCAACAACTTTAAAAAAATTCTCATCTTAAAAAAGCTTC-TCTTAGCA
1 GAGGCTCAACAACTTT--AAAAATT-TTATCTTGAAAAAGC-TCATCTCAGCA
* * * * * * *
9724472 GAGGTTCAATAACTTTAAAAATCTCATC-TGGAAAAGCTCCTCTAAGCA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCATCTCAGCA
* * * * * * *
9724520 GAGGTTCAATAACTTT-AAAATACTAATCTTAAAAAAAGCTTATCTCAGTA
1 GAGGCTCAACAACTTTAAAAAT-TTTATCTT-GAAAAAGCTCATCTCAGCA
* * * *
9724570 GAGGTTCAACAACTTTAAAAA-TCTATCTTGAAAAAGTTTATCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCATCTCAGCA
* * * * *
9724618 GAAGCTTAACAACTTTAAAAATTTTATTTTGAAAAAGCTCATTTCAGTA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCATCTCAGCA
* * * *
9724667 GAGGCTCAACAACTTCAAAGAAATTCTCATCTTGAAAAAGGATTC-TCTCAGTA
1 GAGGCTCAACAACTT-TAA-AAATT-TTATCTTGAAAAA-G-CTCATCTCAGCA
** * * * * *
9724720 GAAACTTAACAACTTTAAAAAAATTCTCATCTTAAAAAAGCTATAAGCTCCTCTTAACA
1 GAGGCTCAACAACTTT--AAAAATT-TTATCTTGAAAAAGC--TCA--T-CTC--AGCA
* *
9724779 GAGGCTTAACAACTTTAAAAAAATTTTGATCTTGAAAAAGCTCCTCTCAGCA
1 GAGGCTCAACAACTTT--AAAAATTTT-ATCTTGAAAAAGCTCATCTCAGCA
* * * * * *
9724831 GAGGTTCAACAACTTT-AAAGTCTTATATTGAAAAAAGCTCATCTTAACA
1 GAGGCTCAACAACTTTAAAAATTTTATCTTG-AAAAAGCTCATCTCAGCA
9724880 GAGGCTCAACAACTTTAAAAAT
1 GAGGCTCAACAACTTTAAAAAT
9724902 CTAATATGTT
Statistics
Matches: 471, Mismatches: 79, Indels: 68
0.76 0.13 0.11
Matches are distributed among these distances:
47 7 0.01
48 77 0.16
49 83 0.18
50 68 0.14
51 55 0.12
52 80 0.17
53 50 0.11
54 7 0.01
55 1 0.00
56 1 0.00
57 4 0.01
58 1 0.00
59 37 0.08
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (49 bp):
GAGGCTCAACAACTTTAAAAATTTTATCTTGAAAAAGCTCATCTCAGCA
Found at i:9736975 original size:18 final size:18
Alignment explanation
Indices: 9736954--9736996 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9736944 TTTCTCATTT
*
9736954 TTTATTACTT-ATTCTTAA
1 TTTATTAATTAATT-TTAA
*
9736972 TTTATTAATTAATTTTTA
1 TTTATTAATTAATTTTAA
9736990 TTTATTA
1 TTTATTA
9736997 TTTTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAATTTTAA
Found at i:9738212 original size:18 final size:18
Alignment explanation
Indices: 9738189--9738231 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9738179 TTTCTCATTT
*
9738189 TTTATTACTT-ATTCTTAA
1 TTTATTAATTAATT-TTAA
*
9738207 TTTATTAATTAATTTTTA
1 TTTATTAATTAATTTTAA
9738225 TTTATTA
1 TTTATTA
9738232 TTTTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAATTTTAA
Found at i:9739326 original size:274 final size:265
Alignment explanation
Indices: 9738839--9739385 Score: 686
Period size: 274 Copynumber: 2.0 Consensus size: 265
9738829 TAAAATGACA
*
9738839 TCGTTTTAGTGTTTAAATGAAACAACGTCGTTTTGGCTATTGGCAGTTTATAGAAAAGCCAAAAA
1 TCGTTTTAGTGTTTAAATGAAACAACGTCATTTTGGCTATTGGCAGTTTATAGAAAAGCC-AAAA
9738904 AAAAAATTTTACTTCATTTCTCCCCTCTCCCCGAAAAAAATCTCTCTCTTTTTTTTTAGATCGAT
65 AAAAAATTTTACTTCATTTCTCCCCTCTCCCCGAAAAAAATCTCTCTCTTTTTTTTTAGATCGAT
* * **
9738969 CTGGGGCTGGTGACCGTCGGTCGTGACGACCGCCGTGGTCCTCGCACTTAAAGGGTTCCAACCGC
130 CTGGGGCTAGTGACCGTCGGTCGTGACGACCACCGTGGTCCTCGCACGCAAAGGGTTCCAACCGC
* *
9739034 TGTCGTCGATGTTGAAAAATTTTAAAAAATACCCACAAACTCCTCTCGACCTCATGAATACAGAT
195 TGTCGTCGATGTTGAAAAATTTTAAAAAACACCCACAAACTCCTCTCGACCTCATGAACACAGAT
9739099 TCGACC
260 TCGACC
* * *
9739105 TCGTTTTGGTGTTTAAATGAAACAACGTCATTTTGGTTATTGGCAGTTTATAGAAAAGTC-AAAA
1 TCGTTTTAGTGTTTAAATGAAACAACGTCATTTTGGCTATTGGCAGTTTATAGAAAAGCCAAAAA
* * * * *
9739169 AAAATTTTTACTTTATTTTTCCCCTTCTCTCTGAAAAAAATCTCTCTCTCTCTCTCCTCTTTTTT
66 AAAAATTTTACTTCATTTCTCCCC-TCTCCCCGAAAAAAA------TCTCTCTCT--T-TTTTTT
* ** * * * *** *
9739234 TAGATCGATTTGGGG-TAAGTGAGTGTCGGTTGTGACGACCATCGTGGTCGTCGTTGGCAACGGG
121 TAGATCGATCTGGGGCT-AGTGACCGTCGGTCGTGACGACCACCGTGGTCCTCGCACGCAAAGGG
* * *
9739298 TTCCAACCG-TCGTTGTCGATGTTGAAAAATTTTAAAAAACACCCACAAACTCCTCTCGATCTCT
185 TTCCAACCGCT-GTCGTCGATGTTGAAAAATTTTAAAAAACACCCACAAACTCCTCTCGACCTCA
*
9739362 TGAACACAGATTTGACC
249 TGAACACAGATTCGACC
*
9739379 TCTTTTT
1 TCGTTTT
9739386 TACCAAAAAA
Statistics
Matches: 239, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
264 25 0.10
265 13 0.05
266 56 0.23
271 9 0.04
273 3 0.01
274 133 0.56
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (265 bp):
TCGTTTTAGTGTTTAAATGAAACAACGTCATTTTGGCTATTGGCAGTTTATAGAAAAGCCAAAAA
AAAAATTTTACTTCATTTCTCCCCTCTCCCCGAAAAAAATCTCTCTCTTTTTTTTTAGATCGATC
TGGGGCTAGTGACCGTCGGTCGTGACGACCACCGTGGTCCTCGCACGCAAAGGGTTCCAACCGCT
GTCGTCGATGTTGAAAAATTTTAAAAAACACCCACAAACTCCTCTCGACCTCATGAACACAGATT
CGACC
Found at i:9740089 original size:18 final size:18
Alignment explanation
Indices: 9740066--9740107 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
9740056 CATCAGACCC
*
9740066 TTTTGTTTTTTTCTTTTT
1 TTTTGTTTTTTTCTATTT
9740084 TTTTGTTTTTTTCTATTT
1 TTTTGTTTTTTTCTATTT
9740102 TTTTGT
1 TTTTGT
9740108 ATTTGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (18 bp):
TTTTGTTTTTTTCTATTT
Found at i:9740122 original size:14 final size:15
Alignment explanation
Indices: 9740103--9740136 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9740093 TTTCTATTTT
9740103 TTTGTA-TTTGTATC
1 TTTGTATTTTGTATC
*
9740117 TTTGTATTTTGTATT
1 TTTGTATTTTGTATC
9740132 TTTGT
1 TTTGT
9740137 TTAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (15 bp):
TTTGTATTTTGTATC
Found at i:9741590 original size:19 final size:18
Alignment explanation
Indices: 9741559--9741598 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
9741549 TAATAACACA
9741559 TATTTTATTTTTTTGAAT
1 TATTTTATTTTTTTGAAT
* *
9741577 TATTTTTTTATTTTTTAAT
1 TATTTTATT-TTTTTGAAT
9741596 TAT
1 TAT
9741599 ATACTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TATTTTATTTTTTTGAAT
Found at i:9742225 original size:26 final size:26
Alignment explanation
Indices: 9742177--9742226 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9742167 AAAATTATAT
**
9742177 TTTATATTTTAATAGTTAGAATAATA
1 TTTATATTTTAATAAATAGAATAATA
*
9742203 TTTATATTTTAATAAATATAATAA
1 TTTATATTTTAATAAATAGAATAA
9742227 ATAATAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TTTATATTTTAATAAATAGAATAATA
Found at i:9743561 original size:17 final size:18
Alignment explanation
Indices: 9743528--9743561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9743518 AATTTAACAG
9743528 TTAACAATTTAATTAAAT
1 TTAACAATTTAATTAAAT
*
9743546 TTAATAATTT-ATTAAA
1 TTAACAATTTAATTAAA
9743562 AAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAACAATTTAATTAAAT
Found at i:9744413 original size:24 final size:25
Alignment explanation
Indices: 9744386--9744436 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
9744376 TCGATTTTAT
* *
9744386 ATTTGATGTATTGTTAATAAA-TAA
1 ATTTGATATATTATTAATAAATTAA
*
9744410 ATTTTATATATTATTAATAAATTAA
1 ATTTGATATATTATTAATAAATTAA
9744435 AT
1 AT
9744437 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTGATATATTATTAATAAATTAA
Done.