Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 119 of 167
Found at i:39842731 original size:25 final size:25
Alignment explanation
Indices: 39842681--39842731 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
39842671 ATAATATTAC
*
39842681 TTATTAAAATATTATTTTAAATAAA
1 TTATTAAAATATTATTTTAAAAAAA
* *
39842706 TTATTAAATTTTTA-TTTAATAAAAA
1 TTATTAAAATATTATTTTAA-AAAAA
39842731 T
1 T
39842732 ATCATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTATTAAAATATTATTTTAAAAAAA
Found at i:39846748 original size:13 final size:13
Alignment explanation
Indices: 39846730--39846761 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39846720 GATAGTTATA
*
39846730 AGTTAAATGAATT
1 AGTTAAATGAAAT
39846743 AGTTAAATGAAAT
1 AGTTAAATGAAAT
39846756 AGTTAA
1 AGTTAA
39846762 TTAAGGTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (13 bp):
AGTTAAATGAAAT
Found at i:39848203 original size:25 final size:25
Alignment explanation
Indices: 39848162--39848233 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
39848152 TTGTGGATTC
*
39848162 TCTGAAGCTAGTATTAGTAGCATCG-
1 TCTGAAGCTAGTGTTAGTAGCAT-GA
* *
39848187 TACT-AAGCTAGTGTTAGCAACCATGA
1 T-CTGAAGCTAGTGTTAG-TAGCATGA
39848213 TCTGAAGCTAGTGTTAGTAGC
1 TCTGAAGCTAGTGTTAGTAGC
39848234 TCGAATATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (25 bp):
TCTGAAGCTAGTGTTAGTAGCATGA
Found at i:39856712 original size:39 final size:39
Alignment explanation
Indices: 39856687--39856761 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
39856677 ATCGGACGAC
39856687 CTGACCCAAAATCCTACACGCTCGTGTAGCACACACGGA
1 CTGACCCAAAATCCTACACGCTCGTGTAGCACACACGGA
*
39856726 CTGACCCAAAATCCTACACGCTCGTGTAGCCCACAC
1 CTGACCCAAAATCCTACACGCTCGTGTAGCACACAC
39856762 AGCCTAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.39, G:0.16, T:0.16
Consensus pattern (39 bp):
CTGACCCAAAATCCTACACGCTCGTGTAGCACACACGGA
Found at i:39858166 original size:54 final size:55
Alignment explanation
Indices: 39858062--39858190 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 55
39858052 AATCATAATA
* * * *
39858062 CATAGTCTAAAGGAATCAAATTGACCAAATGTATTAGTTGGTAGTTTAAGTTATC
1 CATAGTCTAAAGGAATCAAATTGACCAAATATATTAGTAGGTAATATAAGTTATC
* ** * * *
39858117 CATAGTCT-AAGGAGTCAAATTGAGTAATTATATTGGTAGGTAATATAAGTTCTC
1 CATAGTCTAAAGGAATCAAATTGACCAAATATATTAGTAGGTAATATAAGTTATC
39858171 CATAGTCTAAAGGAATCAAA
1 CATAGTCTAAAGGAATCAAA
39858191 CTAAACAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
54 44 0.71
55 18 0.29
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (55 bp):
CATAGTCTAAAGGAATCAAATTGACCAAATATATTAGTAGGTAATATAAGTTATC
Found at i:39859081 original size:36 final size:37
Alignment explanation
Indices: 39859006--39859082 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
39858996 TGTTTCAACA
* * *
39859006 TTTACAAAACAACCCCTATACCTCAAAAATTATAGTT
1 TTTACAAAACAACCCCTATAACTCAAAAATTACAATT
* **
39859043 TTTACAAAACAACCCCTA-AATTCAAATTTTACAATT
1 TTTACAAAACAACCCCTATAACTCAAAAATTACAATT
39859079 TTTA
1 TTTA
39859083 TTATTTAGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (37 bp):
TTTACAAAACAACCCCTATAACTCAAAAATTACAATT
Found at i:39864800 original size:57 final size:58
Alignment explanation
Indices: 39864688--39864806 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 58
39864678 GGTTATGAAC
*
39864688 TTCTCCAAACTGAGACTATTTCTTTTTTTCTCTCTTTTATAAGGAAAGCTAAGACTAT
1 TTCTCCAAACTGACACTATTTCTTTTTTTCTCTCTTTTATAAGGAAAGCTAAGACTAT
*
39864746 TTCTCCAAACTGACACTATTTCTTTTTTT-TCTCTTTTATAAGGAAAGCTGAGACTAT
1 TTCTCCAAACTGACACTATTTCTTTTTTTCTCTCTTTTATAAGGAAAGCTAAGACTAT
39864803 TTCT
1 TTCT
39864807 TTCTTCCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 31 0.53
58 28 0.47
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (58 bp):
TTCTCCAAACTGACACTATTTCTTTTTTTCTCTCTTTTATAAGGAAAGCTAAGACTAT
Found at i:39870396 original size:27 final size:27
Alignment explanation
Indices: 39870348--39870452 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
39870338 GCGAGGCTGC
* *
39870348 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
39870375 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
39870401 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
39870428 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
39870453 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 8 0.11
27 60 0.85
28 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:39872074 original size:26 final size:26
Alignment explanation
Indices: 39872038--39872119 Score: 119
Period size: 26 Copynumber: 3.2 Consensus size: 26
39872028 TGAAATGCCC
*
39872038 ATCATGGAACATTTACCTAAACTATT
1 ATCATGGAACATTTACCTAAACCATT
*
39872064 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* * *
39872090 CTCATGGAACATTTACCTAACCCTTT
1 ATCATGGAACATTTACCTAAACCATT
39872116 ATCA
1 ATCA
39872120 ATTTGTACCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:39876810 original size:31 final size:30
Alignment explanation
Indices: 39876775--39876833 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
39876765 CACCCTTAAA
*
39876775 ATATTTGCACTATTAA-CCCTTCAAATTTTTC
1 ATATTTACACT-TTAATCCCTT-AAATTTTTC
39876806 ATATTTACACTTTAATCCCTTAAATTTT
1 ATATTTACACTTTAATCCCTTAAATTTT
39876834 GAGTATATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (30 bp):
ATATTTACACTTTAATCCCTTAAATTTTTC
Found at i:39886198 original size:40 final size:40
Alignment explanation
Indices: 39886146--39886289 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 40
39886136 AACGTTTTAC
*
39886146 GCCCAGCGCTAGTCGGATAAACCGACAATATCAAATGTGT
1 GCCCAGCACTAGTCGGATAAACCGACAATATCAAATGTGT
* * * * *
39886186 ACCCAGCACTAGTCGTATAAA---ACAATA--ATTAGGTCT
1 GCCCAGCACTAGTCGGATAAACCGACAATATCA-AATGTGT
* *
39886222 GCCCAACACTAGTCAGATAAACCGA-AGATATCAAATGTGT
1 GCCCAGCACTAGTCGGATAAACCGACA-ATATCAAATGTGT
* *
39886262 GCCCAGCACTAATCGGATAAACTGACAA
1 GCCCAGCACTAGTCGGATAAACCGACAA
39886290 ATACATATGT
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
35 1 0.01
36 21 0.27
37 6 0.08
38 1 0.01
39 4 0.05
40 44 0.56
41 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
GCCCAGCACTAGTCGGATAAACCGACAATATCAAATGTGT
Found at i:39891602 original size:27 final size:26
Alignment explanation
Indices: 39891554--39891766 Score: 225
Period size: 27 Copynumber: 7.9 Consensus size: 26
39891544 GCGAGGCTGC
* *
39891554 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
*
39891580 ACAGATATTGTGGCAGAGCCACCAGAA
1 -CAGATATTGTGGCAGAGCCACCAGAT
*
39891607 CAGATATATGTGGCAGAGCCATCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
39891634 CAGATAATTGTGGCATAGCCACCAGGA-
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
*
39891661 CAGATATATGTGGTAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
39891688 CAGATAATTGTGGCATAGCAACCAGGAT
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
*
39891716 -AGATATATGTGGCAGAGCCACCATAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
*
39891742 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
39891767 GACGCTTCCT
Statistics
Matches: 158, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
26 15 0.09
27 131 0.83
28 12 0.08
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:39891647 original size:54 final size:54
Alignment explanation
Indices: 39891572--39891769 Score: 317
Period size: 54 Copynumber: 3.7 Consensus size: 54
39891562 GTGACGAAGT
* *
39891572 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
* *
39891626 CATCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGTAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
* *
39891680 CACCAGATCAGATAATTGTGGCATAGCAACCAGGATAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
39891734 CACCATATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
39891770 GCTTCCTCCA
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 5 0.04
54 127 0.96
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:39897849 original size:8 final size:8
Alignment explanation
Indices: 39897826--39897862 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
39897816 TTCAGTTTTA
*
39897826 TTTATTTT
1 TTTATTTC
39897834 TTTATTTC
1 TTTATTTC
39897842 TTTATTTC
1 TTTATTTC
39897850 -TTATTTC
1 TTTATTTC
39897857 -TTATTT
1 TTTATTT
39897863 GTTATTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
7 13 0.46
8 15 0.54
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATTTC
Found at i:39897855 original size:7 final size:7
Alignment explanation
Indices: 39897823--39897868 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
39897813 TATTTCAGTT
*
39897823 TTATTTA
1 TTATTTC
39897830 TT-TTT-
1 TTATTTC
39897835 TTATTTC
1 TTATTTC
39897842 TTTATTTC
1 -TTATTTC
39897850 TTATTTC
1 TTATTTC
*
39897857 TTATTTG
1 TTATTTC
39897864 TTATT
1 TTATT
39897869 CTATTTTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
5 2 0.06
6 6 0.17
7 20 0.57
8 7 0.20
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (7 bp):
TTATTTC
Found at i:39899439 original size:6 final size:6
Alignment explanation
Indices: 39899428--39899490 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
39899418 TTGAGTCCGA
* * * *
39899428 TTATCT TTATCT TTATCT TTATCT TTATTT TTATTT TTATTT TTATGT
1 TTATCT TTATCT TTATCT TTATCT TTATCT TTATCT TTATCT TTATCT
*
39899476 TTAT-T TTGTCT TTAT
1 TTATCT TTATCT TTAT
39899491 ATTTTGAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.08
6 48 0.92
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (6 bp):
TTATCT
Found at i:39900536 original size:11 final size:11
Alignment explanation
Indices: 39900522--39900561 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
39900512 TATTTTCTCC
39900522 CTATTTTACTA
1 CTATTTTACTA
39900533 CTATTTTACTA
1 CTATTTTACTA
* * *
39900544 TTATGTTGCTA
1 CTATTTTACTA
39900555 CTATTTT
1 CTATTTT
39900562 GTTATTATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (11 bp):
CTATTTTACTA
Found at i:39900652 original size:28 final size:27
Alignment explanation
Indices: 39900599--39900653 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
39900589 GCTTATTTTA
39900599 TTGTTAATTTTTATTATTTTAAAGAAAT
1 TTGTTAATTTTTATTATTTT-AAGAAAT
39900627 TTGTTAATTTTGTTATTATTTT-AGAAA
1 TTGTTAA-TTT-TTATTATTTTAAGAAA
39900654 CATTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 12 0.48
29 3 0.12
30 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (27 bp):
TTGTTAATTTTTATTATTTTAAGAAAT
Found at i:39900811 original size:12 final size:12
Alignment explanation
Indices: 39900781--39900813 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
39900771 TATATATTTT
39900781 AAAATT-ATATA
1 AAAATTAATATA
39900792 AAAA-TAATATA
1 AAAATTAATATA
39900803 AAAATTAATAT
1 AAAATTAATAT
39900814 GGGCGGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:39907398 original size:245 final size:245
Alignment explanation
Indices: 39906968--39907461 Score: 988
Period size: 245 Copynumber: 2.0 Consensus size: 245
39906958 TATTTACTCA
39906968 TTTTCTTCCCCAAAAATACAAGGAAGCCCTAGGAGAGAGAGAAGAAACTTTCATGGCTTAATTGG
1 TTTTCTTCCCCAAAAATACAAGGAAGCCCTAGGAGAGAGAGAAGAAACTTTCATGGCTTAATTGG
39907033 GTAAGTTTCCTATTCCCGTTTTTAGTAATTTCGATATTTTTGAAACCGGGATAACTTAATCTATC
66 GTAAGTTTCCTATTCCCGTTTTTAGTAATTTCGATATTTTTGAAACCGGGATAACTTAATCTATC
39907098 TATTTGGGGGATCAATTTGAAGAGTTATCAAAGTATGGAAATTATTTCATGGATGTATATATTGA
131 TATTTGGGGGATCAATTTGAAGAGTTATCAAAGTATGGAAATTATTTCATGGATGTATATATTGA
39907163 AAATTAGAAATTTATGGTAGAAAATGAAAGGTTGTTGATAGATAAACAAC
196 AAATTAGAAATTTATGGTAGAAAATGAAAGGTTGTTGATAGATAAACAAC
39907213 TTTTCTTCCCCAAAAATACAAGGAAGCCCTAGGAGAGAGAGAAGAAACTTTCATGGCTTAATTGG
1 TTTTCTTCCCCAAAAATACAAGGAAGCCCTAGGAGAGAGAGAAGAAACTTTCATGGCTTAATTGG
39907278 GTAAGTTTCCTATTCCCGTTTTTAGTAATTTCGATATTTTTGAAACCGGGATAACTTAATCTATC
66 GTAAGTTTCCTATTCCCGTTTTTAGTAATTTCGATATTTTTGAAACCGGGATAACTTAATCTATC
39907343 TATTTGGGGGATCAATTTGAAGAGTTATCAAAGTATGGAAATTATTTCATGGATGTATATATTGA
131 TATTTGGGGGATCAATTTGAAGAGTTATCAAAGTATGGAAATTATTTCATGGATGTATATATTGA
39907408 AAATTAGAAATTTATGGTAGAAAATGAAAGGTTGTTGATAGATAAACAAC
196 AAATTAGAAATTTATGGTAGAAAATGAAAGGTTGTTGATAGATAAACAAC
39907458 TTTT
1 TTTT
39907462 ACAAAGTGAT
Statistics
Matches: 249, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
245 249 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (245 bp):
TTTTCTTCCCCAAAAATACAAGGAAGCCCTAGGAGAGAGAGAAGAAACTTTCATGGCTTAATTGG
GTAAGTTTCCTATTCCCGTTTTTAGTAATTTCGATATTTTTGAAACCGGGATAACTTAATCTATC
TATTTGGGGGATCAATTTGAAGAGTTATCAAAGTATGGAAATTATTTCATGGATGTATATATTGA
AAATTAGAAATTTATGGTAGAAAATGAAAGGTTGTTGATAGATAAACAAC
Found at i:39911643 original size:27 final size:26
Alignment explanation
Indices: 39911604--39911656 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
39911594 TCCAATGCCT
*
39911604 TTAAAAAGACCTTGAAAAGCTTATTTAA
1 TTAAAAAGACCTTAAAAAG--TATTTAA
39911632 TTAAAAAG-CCTTAAAAAGTATTTAA
1 TTAAAAAGACCTTAAAAAGTATTTAA
39911657 AATAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
27 9 0.38
28 8 0.33
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (26 bp):
TTAAAAAGACCTTAAAAAGTATTTAA
Found at i:39912852 original size:59 final size:59
Alignment explanation
Indices: 39912769--39912894 Score: 191
Period size: 59 Copynumber: 2.1 Consensus size: 59
39912759 TTAATTATAA
* * * *
39912769 AATTAATTGATCCCATTGTTAAAAAGTGCAATCAATTAAACATTTAATCGAAAGTTAGC
1 AATTAATTGAGCCCATTGTCAAAAAATGCAATCAATTAAACATTTAATAGAAAGTTAGC
*
39912828 AATTAATTGAGCCTC-TTGTCAAAAAATGCAATCAATTAAACCTTTAATAGAAAGTTAGC
1 AATTAATTGAGCC-CATTGTCAAAAAATGCAATCAATTAAACATTTAATAGAAAGTTAGC
39912887 AATTAATT
1 AATTAATT
39912895 AAATCATGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 60 0.98
60 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (59 bp):
AATTAATTGAGCCCATTGTCAAAAAATGCAATCAATTAAACATTTAATAGAAAGTTAGC
Found at i:39912895 original size:30 final size:30
Alignment explanation
Indices: 39912796--39912897 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
39912786 GTTAAAAAGT
* *
39912796 GCAATCAATTAAACATTTAATCGAAAGTTA
1 GCAATCAATTAAACCTTTAATAGAAAGTTA
* * * * **
39912826 GCAATTAATTGAGCCTCTT-GTCA-AAAAAT-
1 GCAATCAATTAAACCT-TTAAT-AGAAAGTTA
39912855 GCAATCAATTAAACCTTTAATAGAAAGTTA
1 GCAATCAATTAAACCTTTAATAGAAAGTTA
*
39912885 GCAATTAATTAAA
1 GCAATCAATTAAA
39912898 TCATGTAATA
Statistics
Matches: 52, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
28 3 0.06
29 18 0.35
30 29 0.56
31 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (30 bp):
GCAATCAATTAAACCTTTAATAGAAAGTTA
Found at i:39913166 original size:17 final size:18
Alignment explanation
Indices: 39913144--39913190 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
39913134 ATAATAGAAT
*
39913144 TTTAATTTTTT-GTAACA
1 TTTAATTTTTTAATAACA
39913161 TTTAATAGTTTTTAATAACA
1 TTTAAT--TTTTTAATAACA
*
39913181 TATAATTTTT
1 TTTAATTTTT
39913191 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 5 0.20
20 10 0.40
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTAATTTTTTAATAACA
Found at i:39913444 original size:19 final size:18
Alignment explanation
Indices: 39913399--39913449 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
39913389 CCCTTGTTTG
*
39913399 ATTTAAT-AATATTTAAT
1 ATTTAATAAAAATTTAAT
**
39913416 ATTTTTTAAAAATTCTAAT
1 ATTTAATAAAAATT-TAAT
39913435 ATTTAAT-AAAATTTA
1 ATTTAATAAAAATTTA
39913450 TAGTTTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 7 0.26
18 11 0.41
19 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAATAAAAATTTAAT
Found at i:39913468 original size:9 final size:9
Alignment explanation
Indices: 39913454--39913487 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
39913444 AATTTATAGT
39913454 TTTTTATAA
1 TTTTTATAA
39913463 TTTTTATAA
1 TTTTTATAA
39913472 TATTTTAATAA
1 T-TTTT-ATAA
39913483 TTTTT
1 TTTTT
39913488 TAGCTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 10 0.43
10 8 0.35
11 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:39913487 original size:10 final size:10
Alignment explanation
Indices: 39913400--39913487 Score: 53
Period size: 10 Copynumber: 9.3 Consensus size: 10
39913390 CCTTGTTTGA
*
39913400 TTTAATAATA
1 TTTAATAATT
*
39913410 TTTAATATTT
1 TTTAATAATT
*
39913420 TTTAA-AAAT
1 TTTAATAATT
*
39913429 TCTAAT-A--
1 TTTAATAATT
**
39913436 TTTAATAAAA
1 TTTAATAATT
*
39913446 TTT-ATAGTT
1 TTTAATAATT
*
39913455 TTTTATAATT
1 TTTAATAATT
39913465 TTT-ATAATAT
1 TTTAATAAT-T
39913475 TTTAATAATT
1 TTTAATAATT
39913485 TTT
1 TTT
39913488 TAGCTTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
7 5 0.08
8 1 0.02
9 18 0.30
10 32 0.52
11 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTAATAATT
Found at i:39924850 original size:27 final size:27
Alignment explanation
Indices: 39924812--39924868 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
39924802 AAAGATGAAG
39924812 ATAAAGAAGCAAATTCAAGGGAAATTA
1 ATAAAGAAGCAAATTCAAGGGAAATTA
39924839 ATAAAGAAGCAAATTCAAGGGAAATTA
1 ATAAAGAAGCAAATTCAAGGGAAATTA
39924866 ATA
1 ATA
39924869 CCATGATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.19
Consensus pattern (27 bp):
ATAAAGAAGCAAATTCAAGGGAAATTA
Found at i:39927942 original size:14 final size:14
Alignment explanation
Indices: 39927923--39927951 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39927913 TTTTTAAAGG
39927923 AAATAAAAATAAAA
1 AAATAAAAATAAAA
39927937 AAATAAAAATAAAA
1 AAATAAAAATAAAA
39927951 A
1 A
39927952 TTTTTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:39928784 original size:21 final size:21
Alignment explanation
Indices: 39928745--39928790 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39928735 TAGTATATGT
* * *
39928745 TTTATTATATATGCATATATC
1 TTTAATATATATACATATATA
*
39928766 TTTAATATATATACGTATATA
1 TTTAATATATATACATATATA
39928787 TTTA
1 TTTA
39928791 GGTAGTATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTAATATATATACATATATA
Found at i:39928964 original size:23 final size:21
Alignment explanation
Indices: 39928920--39928971 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
39928910 TTTTAATATC
*
39928920 ATATTTTTATATATTATGTAT
1 ATATTTTTAAATATTATGTAT
39928941 AT-TTTTTAAATATTATTAGTTAT
1 ATATTTTTAAATATTA-T-G-TAT
39928964 ATATTTTT
1 ATATTTTT
39928972 TATACTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.46
21 3 0.12
22 1 0.04
23 5 0.19
24 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
ATATTTTTAAATATTATGTAT
Found at i:39928974 original size:11 final size:11
Alignment explanation
Indices: 39928876--39928981 Score: 54
Period size: 13 Copynumber: 8.8 Consensus size: 11
39928866 CTATTTTATA
39928876 TATATATATTTT
1 TATATAT-TTTT
* *
39928888 CATATATGTTATG
1 TATATAT-TT-TT
39928901 TATATATGTTTT
1 TATATAT-TTTT
39928913 TAATATCATATTTT
1 T-ATAT-AT-TTTT
*
39928927 TATATA--TTA
1 TATATATTTTT
*
39928936 TGTATATTTTT
1 TATATATTTTT
*
39928947 TAAATATTATTAGT
1 TATATATT-TT--T
39928961 TATATATTTTT
1 TATATATTTTT
39928972 TATACTATTT
1 TATA-TATTT
39928982 CAGGTATATA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
9 7 0.10
11 13 0.18
12 18 0.25
13 20 0.27
14 15 0.21
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTT
Found at i:39928980 original size:23 final size:23
Alignment explanation
Indices: 39928920--39929004 Score: 70
Period size: 25 Copynumber: 3.7 Consensus size: 23
39928910 TTTTAATATC
39928920 ATATTTTT-ATA-TATTA-TGTAT
1 ATATTTTTAATACTATTAGT-TAT
*
39928941 AT-TTTTTAAATATTATTAGTTAT
1 ATATTTTT-AATACTATTAGTTAT
* *
39928964 ATATTTTTTATACTATTTCAGGTAT
1 ATATTTTTAATACTA-TT-AGTTAT
*
39928989 ATATTTCTAATACTAT
1 ATATTTTTAATACTAT
39929005 ATTACATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 5 0.10
21 2 0.04
22 3 0.06
23 15 0.29
24 9 0.17
25 18 0.35
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (23 bp):
ATATTTTTAATACTATTAGTTAT
Found at i:39928989 original size:25 final size:26
Alignment explanation
Indices: 39928938--39929004 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 26
39928928 ATATATTATG
* * *
39928938 TATATTTTTTA-AATATTATTAGTTA
1 TATATTTTTTATACTATTATCAGGTA
39928963 TATATTTTTTATACTATT-TCAGGTA
1 TATATTTTTTATACTATTATCAGGTA
* *
39928988 TATATTTCTAATACTAT
1 TATATTTTTTATACTAT
39929005 ATTACATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (26 bp):
TATATTTTTTATACTATTATCAGGTA
Found at i:39929134 original size:20 final size:22
Alignment explanation
Indices: 39929077--39929135 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
39929067 TTTTTAACAC
39929077 TATTATGTACATACTTTCAATAT
1 TATTATGTACATA-TTTCAATAT
** *
39929100 TATTATGTATTTATTTTAATA-
1 TATTATGTACATATTTCAATAT
39929121 TA-TATGTACATATTT
1 TATTATGTACATATTT
39929136 ATGTAGCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.35
21 2 0.06
22 7 0.23
23 11 0.35
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (22 bp):
TATTATGTACATATTTCAATAT
Found at i:39941389 original size:73 final size:73
Alignment explanation
Indices: 39941291--39941720 Score: 381
Period size: 73 Copynumber: 5.7 Consensus size: 73
39941281 TGATGTTTTT
* * * * *
39941291 ATTTCTAT-TTTCAGAAATTAACTCATATTGCGAGAGTTGAGTTGATCTTCAAGACACGTTGAGG
1 ATTTCTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGG
39941355 TATTTTCA
66 TATTTTCA
* * * * *
39941363 ATTTCTATCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACACTGATG
1 ATTTCTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGG
*
39941428 TATTCTCA
66 TATTTTCA
* * *
39941436 A-TT-AATGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTATGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAG
39941499 GTATTTTCAA
65 GTATTTTC-A
* *
39941509 ATTCTGTTTTTCAATTTTTGTTTCAAAAATCAACTCATATTGGGAGAGGTGAGTTGAGCTTCAA-
1 A-------TTTC----TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAG
39941573 ATCACGCACTGAGGTATTTTCA
55 A-CACG--CTGAGGTATTTTCA
*
39941595 A-TT-TATGATTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-AGATCATACACT
1 ATTTCTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGA-C--ACGCT
*
39941656 GAGGTATTACTTTA
62 GAGGTATT--TTCA
* * * *
39941670 ATTTATGTTTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 ATTTCTATGTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
39941721 CTTGGGTAAC
Statistics
Matches: 298, Mismatches: 29, Indels: 54
0.78 0.08 0.14
Matches are distributed among these distances:
71 6 0.02
72 65 0.22
73 110 0.37
74 3 0.01
75 6 0.02
76 5 0.02
77 2 0.01
78 2 0.01
80 34 0.11
81 2 0.01
84 1 0.00
85 41 0.14
86 8 0.03
87 13 0.04
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (73 bp):
ATTTCTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAAGACACGCTGAGG
TATTTTCA
Found at i:39941493 original size:145 final size:144
Alignment explanation
Indices: 39941305--39941722 Score: 426
Period size: 145 Copynumber: 2.7 Consensus size: 144
39941295 CTATTTTCAG
* * * *
39941305 AAATTAACTCATATTGCGAGAGTTGAGTTGATCTTCAAGACACGTTGAGGTATTTTCAATTTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-AGACACGCTGAGGTATTTTCAATTTCTA
* *
39941370 TCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCA-CACTGATGTATTCT
65 TCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACCACTGAGGTATTCT
39941434 CAATTAATG-TTTCAAA
130 CAATTAATGATTT--AA
*
39941450 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCA-GACACGCTGAGGTATTTTC-AA-----
* * * *
39941515 TTTTTCAATTTTTGTTTCAAAAATCAACTCATATTGGGAGAGGTGAGTTGAGCTTCAAATCACGC
59 --TTTC----TATCTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCAC-C
* *
39941580 ACTGAGGTATTTTCAATTTATGATTTAA
117 ACTGAGGTATTCTCAATTAATGATTTAA
* *
39941608 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCATACACTGAGGTATTACTTTAATT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA-C--ACGCTGAGGTATT--TTCAATT
* * * *
39941673 TATGTTTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
61 TCTATCTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
39941723 TGGGTAACAT
Statistics
Matches: 227, Mismatches: 22, Indels: 40
0.79 0.08 0.14
Matches are distributed among these distances:
144 1 0.00
145 50 0.22
146 2 0.01
150 6 0.03
153 38 0.17
154 3 0.01
157 49 0.22
158 39 0.17
159 20 0.09
160 15 0.07
161 2 0.01
162 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (144 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGACACGCTGAGGTATTTTCAATTTCTAT
CTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACCACTGAGGTATTCTC
AATTAATGATTTAA
Found at i:39941847 original size:88 final size:86
Alignment explanation
Indices: 39941686--39941896 Score: 246
Period size: 88 Copynumber: 2.4 Consensus size: 86
39941676 GTTTTTCAAA
* *
39941686 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTAACATGTCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCT-ACATGTCGAGCTATTTTCAAAA
* *
39941751 TCTATTTTTCAAAT-TTTGTTTTC
65 TCTATTTTT--AATGTCTATTTTC
* * *
39941774 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT-CATGTGCTGAGCTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTACATGT-C-GAGCTATTTTCAAA
* * *
39941838 TTCTGTTTTTAATGTCTATTTTT
64 ATCTATTTTTAATGTCTATTTTC
* *
39941861 AAAGAGTCAACTCATATTGCGAGAAATGAGTTGAGC
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGC
39941897 TCAGGATTAC
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
86 8 0.08
87 10 0.10
88 87 0.83
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (86 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTACATGTCGAGCTATTTTCAAAAT
CTATTTTTAATGTCTATTTTC
Found at i:39943783 original size:21 final size:21
Alignment explanation
Indices: 39943744--39943789 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39943734 TAGTATATGT
* * *
39943744 TTTATTATATATGCATATATC
1 TTTAATATATATACATATATA
*
39943765 TTTAATATATATACGTATATA
1 TTTAATATATATACATATATA
39943786 TTTA
1 TTTA
39943790 GGTAGTATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTAATATATATACATATATA
Found at i:39943954 original size:23 final size:22
Alignment explanation
Indices: 39943910--39943970 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
39943900 TTTTAATATC
39943910 ATATTTTTATATATTA-TGTAT
1 ATATTTTTATATATTATTGTAT
*
39943931 AT-TTTTTAAATATTATTAGTTAT
1 ATATTTTTATATATTATT-G-TAT
39943954 ATATTTTT-TATATTATT
1 ATATTTTTATATATTATT
39943971 TCAGGTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.35
21 3 0.09
22 1 0.03
23 13 0.38
24 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (22 bp):
ATATTTTTATATATTATTGTAT
Found at i:39943962 original size:25 final size:25
Alignment explanation
Indices: 39943928--39943984 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
39943918 ATATATTATG
*
39943928 TATATTTTTTAAATATTA-TT-AGTTA
1 TATATTTTTT--ATATTATTTCAGGTA
39943953 TATATTTTTTATATTATTTCAGGTA
1 TATATTTTTTATATTATTTCAGGTA
39943978 TATATTT
1 TATATTT
39943985 CTAATACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 2 0.07
25 21 0.72
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (25 bp):
TATATTTTTTATATTATTTCAGGTA
Found at i:39943964 original size:11 final size:11
Alignment explanation
Indices: 39943872--39943971 Score: 51
Period size: 13 Copynumber: 8.3 Consensus size: 11
39943862 ATACTATTTT
39943872 TTTTTTCATATA
1 TTTTTT-ATATA
*
39943884 TGTTATGTATATA
1 T-TT-TTTATATA
39943897 TGTTTTTAATATCA
1 T-TTTTT-ATAT-A
39943911 TATTTTTATATA
1 T-TTTTTATATA
* *
39943923 --TTATGTATA
1 TTTTTTATATA
*
39943932 TTTTTTAAATA
1 TTTTTTATATA
39943943 TTATTAGTTATATA
1 TT-TT--TTATATA
39943957 TTTTTTATATTA
1 TTTTTTATA-TA
39943969 TTT
1 TTT
39943972 CAGGTATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
9 7 0.10
11 13 0.19
12 11 0.16
13 21 0.30
14 17 0.25
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (11 bp):
TTTTTTATATA
Found at i:39944070 original size:23 final size:23
Alignment explanation
Indices: 39944044--39944106 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
39944034 TTAATAGCTA
*
39944044 TATTATGTATATATTTTTAACAC
1 TATTATGTATATATTTTCAACAC
* * * *
39944067 TATTATGTACATACTTTCAATAT
1 TATTATGTATATATTTTCAACAC
*
39944090 TATTATGTATTTATTTT
1 TATTATGTATATATTTT
39944107 AATATATATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.56
Consensus pattern (23 bp):
TATTATGTATATATTTTCAACAC
Found at i:39944129 original size:32 final size:32
Alignment explanation
Indices: 39944092--39944163 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
39944082 TTCAATATTA
*
39944092 TTATGTATTTATT-TTAATATATATGTACATAT
1 TTATGTATTTATTATTAATATATATATACAT-T
** *
39944124 TTATGTA-GCATTATTAATATATATATATATT
1 TTATGTATTTATTATTAATATATATATACATT
39944155 TTA-GTATTT
1 TTATGTATTT
39944164 CTAATATATG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
30 3 0.09
31 7 0.22
32 22 0.69
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.56
Consensus pattern (32 bp):
TTATGTATTTATTATTAATATATATATACATT
Found at i:39952061 original size:44 final size:46
Alignment explanation
Indices: 39951962--39952078 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 46
39951952 GTCAGGGAGG
* * * *
39951962 TAAAATCTGCCATCTTCGATCTGCTTCTCTGCCAAATACAGGAAGG
1 TAAAATCTGCAATCTTCGATCTACTTCACTGCCAAATACAGGAAGA
* * * *
39952008 CAAGATCTGCAATCTTCGATCTACTTCAC-G-CTAATACATGAAGA
1 TAAAATCTGCAATCTTCGATCTACTTCACTGCCAAATACAGGAAGA
**
39952052 TAAAATCTGCTTTCTTCGATCTACTTC
1 TAAAATCTGCAATCTTCGATCTACTTC
39952079 GCCACCAGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 34 0.58
45 1 0.02
46 24 0.41
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (46 bp):
TAAAATCTGCAATCTTCGATCTACTTCACTGCCAAATACAGGAAGA
Found at i:39953211 original size:7 final size:7
Alignment explanation
Indices: 39953195--39953244 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
39953185 TGGCCTCTCC
39953195 TTTTTC-
1 TTTTTCT
39953201 TTTTTCT
1 TTTTTCT
39953208 TTTTTC-
1 TTTTTCT
39953214 -TTTTCT
1 TTTTTCT
39953220 TTTTTCAT
1 TTTTTC-T
*
39953228 TTTTTCA
1 TTTTTCT
39953235 TTTTTCT
1 TTTTTCT
39953242 TTT
1 TTT
39953245 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.13
6 6 0.16
7 20 0.53
8 7 0.18
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:39953251 original size:7 final size:6
Alignment explanation
Indices: 39953194--39953256 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
39953184 TTGGCCTCTC
39953194 CTTTTT CTTTTT CTTTTT -TCTTTT CTTTTTT CATTTTTT CATTTTT C-TTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT C-TTTTT C--TTTTT C-TTTTT CTTTTT
*
39953245 CGTTTT -TTTTT C
1 CTTTTT CTTTTT C
39953257 AAGTGAAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 10 0.20
6 20 0.41
7 11 0.22
8 8 0.16
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:39953734 original size:11 final size:12
Alignment explanation
Indices: 39953717--39953746 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
39953707 TTTTTTTACC
39953717 TTTTTTTGT-CT
1 TTTTTTTGTCCT
39953728 TTTTTTTGTCCT
1 TTTTTTTGTCCT
39953740 TTTTTTT
1 TTTTTTT
39953747 TGCCTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTCCT
Found at i:39955134 original size:62 final size:62
Alignment explanation
Indices: 39955032--39955156 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
39955022 CTAAACTCGA
* *
39955032 CGTACTTTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAGTGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
* * * *
39955094 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
39955156 C
1 C
39955157 AAAAAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (62 bp):
CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
Found at i:39957086 original size:15 final size:15
Alignment explanation
Indices: 39957062--39957095 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39957052 AACAATTACG
* *
39957062 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
39957077 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
39957092 ATAA
1 ATAA
39957096 CAAAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:39961179 original size:58 final size:58
Alignment explanation
Indices: 39961109--39961248 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
39961099 TTTTTAATTC
* * * *
39961109 ATTTAATAATAATTATATTAAGAATGTTATTAAATTATATT-TTA-TTTTATTAAACTAT
1 ATTTAATAATAATTATATTAA-AATATGATTAAATTAT-TTATTATTTTTAATAAAATAT
* *
39961167 ATTTAATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTAATAAAATAT
1 ATTTAATAATAATTATATTAAAATATGATTAAATTATTTATTATTTTTAATAAAATAT
* *
39961225 ATTTAACAATAATTTTATTAAAAT
1 ATTTAATAATAATTATATTAAAAT
39961249 TTAATAACAA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
56 2 0.03
57 16 0.23
58 53 0.75
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (58 bp):
ATTTAATAATAATTATATTAAAATATGATTAAATTATTTATTATTTTTAATAAAATAT
Found at i:39961246 original size:26 final size:25
Alignment explanation
Indices: 39961211--39961261 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
39961201 TATTTATTAT
*
39961211 TTTTAATAAAATATATTTAACAATAA
1 TTTTAATAAAATATA-ATAACAATAA
* *
39961237 TTTTATTAAAATTTAATAACAATAA
1 TTTTAATAAAATATAATAACAATAA
39961262 CAATAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTAATAAAATATAATAACAATAA
Found at i:39961394 original size:16 final size:16
Alignment explanation
Indices: 39961373--39961411 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39961363 TGAATTATTG
*
39961373 ATTACAGCTCTATTCA
1 ATTACAGCCCTATTCA
* *
39961389 ATTACAACCCTATTCC
1 ATTACAGCCCTATTCA
39961405 ATTACAG
1 ATTACAG
39961412 TGAACCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (16 bp):
ATTACAGCCCTATTCA
Found at i:39963026 original size:39 final size:39
Alignment explanation
Indices: 39962972--39963060 Score: 178
Period size: 39 Copynumber: 2.3 Consensus size: 39
39962962 AGATTTATGG
39962972 ATGTCTCTTCTAATAATATCGTCATTAAAGTTTAAACAT
1 ATGTCTCTTCTAATAATATCGTCATTAAAGTTTAAACAT
39963011 ATGTCTCTTCTAATAATATCGTCATTAAAGTTTAAACAT
1 ATGTCTCTTCTAATAATATCGTCATTAAAGTTTAAACAT
39963050 ATGTCTCTTCT
1 ATGTCTCTTCT
39963061 TATATTATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.43
Consensus pattern (39 bp):
ATGTCTCTTCTAATAATATCGTCATTAAAGTTTAAACAT
Found at i:39965131 original size:19 final size:19
Alignment explanation
Indices: 39965099--39965147 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
39965089 TATAAAAAAG
* *
39965099 TAAAAATCAATAAACGTTT-
1 TAAAAATTATTAAAC-TTTA
39965118 TAAAAATTATTAAACTTTAA
1 TAAAAATTATTAAACTTT-A
39965138 TAAAAATTAT
1 TAAAAATTAT
39965148 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 13 0.50
20 10 0.38
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAAATTATTAAACTTTA
Found at i:39965150 original size:29 final size:30
Alignment explanation
Indices: 39965118--39965245 Score: 90
Period size: 29 Copynumber: 4.4 Consensus size: 30
39965108 ATAAACGTTT
*
39965118 TAAAAATTAT-TAAACTTTAATAAAAATTA
1 TAAAAATTATATAAAATTTAATAAAAATTA
*
39965147 TAAAAA-TATTTAAAATTTACA-AAAAATTA
1 TAAAAATTATATAAAATTTA-ATAAAAATTA
* * * *
39965176 GAAATA-TATATATAAA--TAGTAAAAAATA
1 TAAAAATTATATA-AAATTTAATAAAAATTA
* * *
39965204 TAAAAAATT-TGTAAAATTTTATAAAAATCA
1 T-AAAAATTATATAAAATTTAATAAAAATTA
39965234 TAAGAAATTATA
1 TAA-AAATTATA
39965246 AAATGCATAA
Statistics
Matches: 75, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
28 15 0.20
29 40 0.53
30 19 0.25
31 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
TAAAAATTATATAAAATTTAATAAAAATTA
Found at i:39965219 original size:10 final size:10
Alignment explanation
Indices: 39965118--39965248 Score: 53
Period size: 10 Copynumber: 13.5 Consensus size: 10
39965108 ATAAACGTTT
39965118 TAAAAA-TTA
1 TAAAAATTTA
* *
39965127 TTAAACTTTAA
1 TAAAAATTT-A
39965138 TAAAAA-TTA
1 TAAAAATTTA
39965147 TAAAAATATT-
1 TAAAAAT-TTA
39965157 T-AAAATTTA
1 TAAAAATTTA
* *
39965166 CAAAAAATTA
1 TAAAAATTTA
* * *
39965176 GAAATATATA
1 TAAAAATTTA
* *
39965186 TATAAATAGTA
1 TAAAAAT-TTA
*
39965197 -AAAAATATA
1 TAAAAATTTA
*
39965206 -AAAAATTTG
1 TAAAAATTTA
*
39965215 TAAAATTTTA
1 TAAAAATTTA
*
39965225 TAAAAA-TCA
1 TAAAAATTTA
39965234 TAAGAAA-TTA
1 TAA-AAATTTA
39965244 TAAAA
1 TAAAA
39965249 TGCATAAAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 18
0.69 0.18 0.14
Matches are distributed among these distances:
8 2 0.02
9 32 0.36
10 47 0.52
11 9 0.10
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:39965541 original size:20 final size:20
Alignment explanation
Indices: 39965516--39965560 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39965506 TTTCTATATA
* *
39965516 TTTTATATTTTTTTTACAAT
1 TTTTATAGTCTTTTTACAAT
*
39965536 TTTTATAGTCTTTTTCCAAT
1 TTTTATAGTCTTTTTACAAT
39965556 TTTTA
1 TTTTA
39965561 ATTAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATAGTCTTTTTACAAT
Found at i:39965583 original size:26 final size:26
Alignment explanation
Indices: 39965554--39965607 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39965544 TCTTTTTCCA
39965554 ATTTTTAATT-AAATTAAATATTTCTT
1 ATTTTT-ATTAAAATTAAATATTTCTT
* *
39965580 ATTTTTATTAAAATTTAATATTTTTT
1 ATTTTTATTAAAATTAAATATTTCTT
39965606 AT
1 AT
39965608 AACTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTTATTAAAATTAAATATTTCTT
Found at i:39967960 original size:43 final size:43
Alignment explanation
Indices: 39967891--39968052 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 43
39967881 AAAATAGGTT
39967891 TTTAGCGGCGCTTTTC-C-C--A-GCCGCTATAGAACGTGACC
1 TTTAGCGGCGCTTTTCTCACAAATGCCGCTATAGAACGTGACC
* * * *
39967929 TTTAGCGGCGCTTTTTTCAGAAATGCCGCTATATAACGTGATCTT
1 TTTAGCGGCGCTTTTCTCACAAATGCCGCTATAGAACGTGA-C-C
** * *
39967974 TAGTATAGCGGCGCTTTTCTCACAAATGTTGCTATAGAATGTGGCC
1 T--T-TAGCGGCGCTTTTCTCACAAATGCCGCTATAGAACGTGACC
* * *
39968020 TTTAGCGGTGCTTTTACT-GCAAACGCCGCTATA
1 TTTAGCGGCGCTTTT-CTCACAAATGCCGCTATA
39968053 AAACTTGGTT
Statistics
Matches: 96, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
38 15 0.16
39 1 0.01
42 1 0.01
43 39 0.41
44 4 0.04
45 1 0.01
46 1 0.01
47 2 0.02
48 32 0.33
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCTCACAAATGCCGCTATAGAACGTGACC
Found at i:39968023 original size:48 final size:48
Alignment explanation
Indices: 39967910--39968024 Score: 123
Period size: 48 Copynumber: 2.5 Consensus size: 48
39967900 GCTTTTCCCA
* *
39967910 GCCGCTATAGAACGTGACC--T--T-TAGCGGCGCTTTTTTCAGAAAT
1 GCCGCTATAGAACGTGACCTTTAGTATAGCGGCGCTTTTCTCACAAAT
* *
39967953 GCCGCTATATAACGTGATCTTTAGTATAGCGGCGCTTTTCTCACAAAT
1 GCCGCTATAGAACGTGACCTTTAGTATAGCGGCGCTTTTCTCACAAAT
** * *
39968001 GTTGCTATAGAATGTGGCCTTTAG
1 GCCGCTATAGAACGTGACCTTTAG
39968025 CGGTGCTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
43 17 0.30
45 1 0.02
47 1 0.02
48 38 0.67
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (48 bp):
GCCGCTATAGAACGTGACCTTTAGTATAGCGGCGCTTTTCTCACAAAT
Found at i:39968901 original size:13 final size:14
Alignment explanation
Indices: 39968875--39968903 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39968865 ACAAACGATG
39968875 AATTAAACCATTAT
1 AATTAAACCATTAT
39968889 AATTAAA-CATTAT
1 AATTAAACCATTAT
39968902 AA
1 AA
39968904 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:39970402 original size:7 final size:7
Alignment explanation
Indices: 39970390--39970414 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39970380 AGGGTTTTAT
39970390 GGTTCAA
1 GGTTCAA
39970397 GGTTCAA
1 GGTTCAA
39970404 GGTTCAA
1 GGTTCAA
39970411 GGTT
1 GGTT
39970415 TAGGGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (7 bp):
GGTTCAA
Found at i:39970421 original size:7 final size:7
Alignment explanation
Indices: 39970411--39970531 Score: 53
Period size: 7 Copynumber: 17.3 Consensus size: 7
39970401 CAAGGTTCAA
39970411 GGTTTAG
1 GGTTTAG
39970418 GGTTTAG
1 GGTTTAG
*
39970425 GGTTTAA
1 GGTTTAG
*
39970432 GGTTTAT
1 GGTTTAG
*** * *
39970439 AAATGAT
1 GGTTTAG
*
39970446 GGTTTAT
1 GGTTTAG
*
39970453 AGTTTAG
1 GGTTTAG
39970460 GGTTTAG
1 GGTTTAG
* * *
39970467 TGTATAT
1 GGTTTAG
*
39970474 AGTTTAG
1 GGTTTAG
*
39970481 GGTTTAA
1 GGTTTAG
*
39970488 GGTTTAA
1 GGTTTAG
* *
39970495 AGTTTTG
1 GGTTTAG
** *
39970502 TATTTAT
1 GGTTTAG
*
39970509 AGTTTAG
1 GGTTTAG
39970516 GGTTTAG
1 GGTTTAG
39970523 GGTTTAG
1 GGTTTAG
39970530 GG
1 GG
39970532 ATAAATAGAT
Statistics
Matches: 82, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
7 82 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:39970421 original size:21 final size:21
Alignment explanation
Indices: 39970397--39970437 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39970387 TATGGTTCAA
39970397 GGTTCAAGGTTCAAGGTTTAG
1 GGTTCAAGGTTCAAGGTTTAG
* * *
39970418 GGTTTAGGGTTTAAGGTTTA
1 GGTTCAAGGTTCAAGGTTTA
39970438 TAAATGATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.05, G:0.34, T:0.39
Consensus pattern (21 bp):
GGTTCAAGGTTCAAGGTTTAG
Found at i:39970436 original size:14 final size:14
Alignment explanation
Indices: 39970326--39970437 Score: 57
Period size: 14 Copynumber: 7.8 Consensus size: 14
39970316 GGTTTGGAGT
* *
39970326 TTTAAGATTTAGGA
1 TTTAAGGTTTAGGG
39970340 TTTAAGGATTTAAGGGG
1 TTTAAGG-TTT-A-GGG
* *
39970357 TTCAAGGCTTTAGTG
1 TTTAAGG-TTTAGGG
*
39970372 TCTAA-G-TTAGGG
1 TTTAAGGTTTAGGG
* * *
39970384 TTTTATGGTTCAAGG
1 -TTTAAGGTTTAGGG
* * *
39970399 TTCAAGGTTCAAGG
1 TTTAAGGTTTAGGG
*
39970413 TTTAGGGTTTAGGG
1 TTTAAGGTTTAGGG
39970427 TTTAAGGTTTA
1 TTTAAGGTTTA
39970438 TAAATGATGG
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
12 5 0.07
13 3 0.04
14 40 0.55
15 12 0.16
16 2 0.03
17 11 0.15
ACGTcount: A:0.25, C:0.05, G:0.29, T:0.40
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:39970449 original size:28 final size:28
Alignment explanation
Indices: 39970418--39970493 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
39970408 CAAGGTTTAG
39970418 GGTTTAGGGTTTAAGGTTTA-TAAATGAT
1 GGTTTAGGGTTTAAGGTTTAGTAAAT-AT
** * **
39970446 GGTTTATAGTTTAGGGTTTAGTGTATAT
1 GGTTTAGGGTTTAAGGTTTAGTAAATAT
*
39970474 AGTTTAGGGTTTAAGGTTTA
1 GGTTTAGGGTTTAAGGTTTA
39970494 AAGTTTTGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (28 bp):
GGTTTAGGGTTTAAGGTTTAGTAAATAT
Found at i:39970485 original size:35 final size:34
Alignment explanation
Indices: 39970446--39970531 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 34
39970436 TATAAATGAT
*
39970446 GGTTTATAGTTTAGGGTTTAGTGTATATAGTTTAG
1 GGTTTA-AGTTTAGGGTTTAGTATATATAGTTTAG
** * *
39970481 GGTTTAAGGTTTAAAGTTTTGTATTTATAGTTTAG
1 GGTTTAA-GTTTAGGGTTTAGTATATATAGTTTAG
*
39970516 GGTTTAGGGTTTAGGG
1 GGTTTA-AGTTTAGGG
39970532 ATAAATAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
34 1 0.02
35 40 0.98
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (34 bp):
GGTTTAAGTTTAGGGTTTAGTATATATAGTTTAG
Found at i:39970498 original size:21 final size:20
Alignment explanation
Indices: 39970446--39970499 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
39970436 TATAAATGAT
39970446 GGTTTATAGTTTAGGGTTTA
1 GGTTTATAGTTTAGGGTTTA
*
39970466 GTGTATATAGTTTAGGGTTTAA
1 G-GTTTATAGTTTAGGGTTT-A
*
39970488 GGTTTAAAGTTT
1 GGTTTATAGTTT
39970500 TGTATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (20 bp):
GGTTTATAGTTTAGGGTTTA
Found at i:39979077 original size:41 final size:41
Alignment explanation
Indices: 39978899--39979099 Score: 210
Period size: 41 Copynumber: 5.0 Consensus size: 41
39978889 TTGTAAAATG
*** *
39978899 CAGAGCAATAGCGGCG-TTTTACCAAAAACACCGCTAAAAA-
1 CAGAGCAATAGCGGCGCTTTT-GGTAAAACGCCGCTAAAAAC
* * *
39978939 CAAAGCAATAGCGACGCTTTTGGTAAAACGCCACTAAAAAC
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* * *
39978980 CAGAGCATTAGTGGCACTTTTGGT-AAACGCCGCTAAAAAC
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* * *
39979020 TAGAGCATTAGTGGCGCTTTTGGTAAAACGCCGCTAAAAAC
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* *** *
39979061 CAGAGTAATAGCGGCGCTTTCAATAAAATGCCGCTAAAA
1 CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
39979100 GTTATATAAC
Statistics
Matches: 135, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 65 0.48
41 70 0.52
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
Found at i:39979371 original size:15 final size:15
Alignment explanation
Indices: 39979332--39979382 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
39979322 TATTTTTGGG
*
39979332 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* * *
39979346 TCTATGATTTAGGGT
1 TTTATGGTTTAAGGT
39979361 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
39979376 TTAATGG
1 TTTATGG
39979383 CCATGGGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:39979984 original size:7 final size:7
Alignment explanation
Indices: 39979961--39980078 Score: 112
Period size: 8 Copynumber: 15.9 Consensus size: 7
39979951 ACATTAAATC
39979961 AAAA-TA
1 AAAATTA
*
39979967 AAAATAAA
1 AAAAT-TA
39979975 AAAATTA
1 AAAATTA
*
39979982 AAATTTA
1 AAAATTA
*
39979989 AAATTTA
1 AAAATTA
39979996 AAAATTTA
1 AAAA-TTA
39980004 AAAATTTA
1 AAAA-TTA
39980012 AAAATTTA
1 AAAA-TTA
39980020 AAAATTAA
1 AAAATT-A
39980028 AAAATTAA
1 AAAATT-A
39980036 AAAATTA
1 AAAATTA
39980043 AAAACTTA
1 AAAA-TTA
39980051 AAAACTTA
1 AAAA-TTA
*
39980059 AAAATTT
1 AAAATTA
*
39980066 AAAATTT
1 AAAATTA
39980073 AAAATT
1 AAAATT
39980079 TTAGTCCATG
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
6 4 0.04
7 39 0.38
8 59 0.58
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (7 bp):
AAAATTA
Found at i:39979990 original size:16 final size:16
Alignment explanation
Indices: 39979961--39980069 Score: 129
Period size: 16 Copynumber: 7.1 Consensus size: 16
39979951 ACATTAAATC
*
39979961 AAAA-TAAAAA-TAAA
1 AAAATTAAAAATTTAA
39979975 AAAATT-AAAATTT-A
1 AAAATTAAAAATTTAA
*
39979989 AAATTTAAAAATTTAA
1 AAAATTAAAAATTTAA
*
39980005 AAATTTAAAAATTT-A
1 AAAATTAAAAATTTAA
*
39980020 AAAATTAAAAAATTAA
1 AAAATTAAAAATTTAA
*
39980036 AAAATTAAAAACTTAA
1 AAAATTAAAAATTTAA
*
39980052 AAACTTAAAAATTTAA
1 AAAATTAAAAATTTAA
39980068 AA
1 AA
39980070 TTTAAAATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
14 14 0.17
15 22 0.27
16 47 0.57
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTAAAAATTTAA
Found at i:39980016 original size:31 final size:31
Alignment explanation
Indices: 39979981--39980081 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
39979971 TAAAAAAATT
39979981 AAAATTT-AAAATTTAAAAATTTAAAAATTTA
1 AAAATTTAAAAATTTAAAAATTT-AAAATTTA
* * *
39980012 AAAATTTAAAAATTAAAAAATTAAAAAATTA
1 AAAATTTAAAAATTTAAAAATTTAAAATTTA
* *
39980043 AAAACTTAAAAACTTAAAAATTTAAAATTTA
1 AAAATTTAAAAATTTAAAAATTTAAAATTTA
*
39980074 AAATTTTA
1 AAAATTTA
39980082 GTCCATGTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 46 0.78
32 13 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATTTAAAAATTTAAAAATTTAAAATTTA
Found at i:39980051 original size:8 final size:8
Alignment explanation
Indices: 39979981--39980081 Score: 136
Period size: 8 Copynumber: 13.0 Consensus size: 8
39979971 TAAAAAAATT
39979981 AAAATTT-
1 AAAATTTA
39979988 AAAATTTA
1 AAAATTTA
39979996 AAAATTTA
1 AAAATTTA
39980004 AAAATTTA
1 AAAATTTA
39980012 AAAATTTA
1 AAAATTTA
39980020 AAAA-TTA
1 AAAATTTA
*
39980027 AAAAATTA
1 AAAATTTA
*
39980035 AAAAATTA
1 AAAATTTA
*
39980043 AAAACTTA
1 AAAATTTA
*
39980051 AAAACTTA
1 AAAATTTA
39980059 AAAATTT-
1 AAAATTTA
39980066 AAAATTTA
1 AAAATTTA
*
39980074 AAATTTTA
1 AAAATTTA
39980082 GTCCATGTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
7 21 0.24
8 67 0.76
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTTA
Found at i:39980182 original size:21 final size:19
Alignment explanation
Indices: 39980158--39980250 Score: 66
Period size: 21 Copynumber: 4.7 Consensus size: 19
39980148 TTTGAAAGAA
39980158 AAAAATAAAAAAATATATGTT
1 AAAAATAAAAAAA-A-ATGTT
*
39980179 AAAAATGAAAAAAAA--TT
1 AAAAATAAAAAAAAATGTT
* **
39980196 AAAATTAAACAATAAAA-GAAA
1 AAAAATAAA-AA-AAAATG-TT
*
39980217 AAAAATAAAAAATATATGTT
1 AAAAATAAAAAA-AAATGTT
39980237 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
39980251 TAAAAACAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 9 0.16
18 2 0.04
19 7 0.12
20 17 0.30
21 21 0.38
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAAATAAAAAAAAATGTT
Found at i:39980199 original size:29 final size:29
Alignment explanation
Indices: 39980155--39980256 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 29
39980145 AAATTTGAAA
*
39980155 GAAAAAAATAAAAAAATATATGTTAAAAAT
1 GAAAAAAA-ATAAAAATATATGTTAAAAAT
* *** *
39980185 GAAAAAAAATTAAAAT-TA-AACAATAAAA
1 GAAAAAAAATAAAAATATATGTTAA-AAAT
39980213 GAAAAAAAATAAAAAATATATGTTAAAAAT
1 GAAAAAAAAT-AAAAATATATGTTAAAAAT
39980243 -AAAAAAAATAAAAA
1 GAAAAAAAATAAAAA
39980257 CAAAAGATTG
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
27 2 0.04
28 20 0.35
29 20 0.35
30 13 0.23
31 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.20
Consensus pattern (29 bp):
GAAAAAAAATAAAAATATATGTTAAAAAT
Found at i:39983437 original size:19 final size:19
Alignment explanation
Indices: 39983415--39983455 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39983405 TTTATTGATA
39983415 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
39983433 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
39983452 TTTT
1 TTTT
39983456 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:39994284 original size:19 final size:19
Alignment explanation
Indices: 39994262--39994308 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39994252 CTTCCTTTCT
39994262 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTCCA-ACA
* *
39994281 TTTGTATTACATTGCAACA
1 TTTGCATTACATTCCAACA
39994300 TTTGCATTA
1 TTTGCATTA
39994309 AACTTTCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTCCAACA
Found at i:39997109 original size:6 final size:6
Alignment explanation
Indices: 39997098--39997127 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
39997088 GGAGTTATAT
39997098 GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA
1 GGCAAA GGCAAA GGCAAA GGCAAA GGCAAA
39997128 AAAAACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (6 bp):
GGCAAA
Found at i:40001390 original size:20 final size:21
Alignment explanation
Indices: 40001361--40001400 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40001351 ATTGACTTAA
*
40001361 TTTAATATATATTT-TAATTG
1 TTTAAAATATATTTATAATTG
40001381 TTTAAAATATATTTATAATT
1 TTTAAAATATATTTATAATT
40001401 TATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAAAATATATTTATAATTG
Found at i:40004648 original size:35 final size:35
Alignment explanation
Indices: 40004562--40004846 Score: 412
Period size: 35 Copynumber: 8.2 Consensus size: 35
40004552 TTCAAATGAT
* *
40004562 TTTCACAACTCGGTATGGAAAATGCCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
** *
40004597 -TTCTTAACTCAGTATGGATAATACCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
*
40004631 TTTCACAACTCGGTATGGATGATACCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
* * *
40004666 TATCACAACTCAGTATGGTTAATACCATACCTAC-
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
*
40004700 TTTCACAACTCGGTATGGATGATACCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
* *
40004735 TTTCACAACTCGGTATGGTTAATACCATACTTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
* *
40004770 TTTCACAACTCGGTATGGATGATATCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
* *
40004805 TTTCACAACTCAGTATGGATGATACCATACCTACG
1 TTTCACAACTCGGTATGGATAATACCATACCTACG
40004840 TTTCACA
1 TTTCACA
40004847 CTTTGCCATA
Statistics
Matches: 222, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
34 59 0.27
35 163 0.73
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTCACAACTCGGTATGGATAATACCATACCTACG
Found at i:40004866 original size:104 final size:105
Alignment explanation
Indices: 40004562--40004846 Score: 430
Period size: 104 Copynumber: 2.7 Consensus size: 105
40004552 TTCAAATGAT
* * ** *
40004562 TTTCACAACTCGGTATGGAAAATGCCATACCTACG-TTCTTAACTCAGTATGGATAATACCATAC
1 TTTCACAACTCGGTATGGATAATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATAC
*
40004626 CTACGTTTCACAACTCGGTATGGATGATACCATACCTACG
66 CTACGTTTCACAACTCGGTATGGATAATACCATACCTACG
* * * *
40004666 TATCACAACTCAGTATGGTTAATACCATACCTAC-TTTCACAACTCGGTATGGATGATACCATAC
1 TTTCACAACTCGGTATGGATAATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATAC
* *
40004730 CTACGTTTCACAACTCGGTATGGTTAATACCATACTTACG
66 CTACGTTTCACAACTCGGTATGGATAATACCATACCTACG
* *
40004770 TTTCACAACTCGGTATGGATGATATCATACCTACGTTTCACAACTCAGTATGGATGATACCATAC
1 TTTCACAACTCGGTATGGATAATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATAC
40004835 CTACGTTTCACA
66 CTACGTTTCACA
40004847 CTTTGCCATA
Statistics
Matches: 161, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
104 120 0.75
105 41 0.25
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (105 bp):
TTTCACAACTCGGTATGGATAATACCATACCTACGTTTCACAACTCAGTATGGATGATACCATAC
CTACGTTTCACAACTCGGTATGGATAATACCATACCTACG
Found at i:40004866 original size:139 final size:138
Alignment explanation
Indices: 40004586--40004866 Score: 395
Period size: 139 Copynumber: 2.0 Consensus size: 138
40004576 ATGGAAAATG
**
40004586 CCATACCTACGTTCTTAACTCAGTATGGATAATACCATACCTACGTTTCACAACTCGGTATGGAT
1 CCATACCTACGTTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTCGGTATGGAT
* **
40004651 GATACCATACCTACGTATCACAACTCAGTATGGTTAATACCATACCTACTTTCACAACTCGGTAT
66 GATACCATACCTACGTATCACAACTCAGTATGGATAATACCATACCTACTTTCACAACTCGCCAT
* *
40004716 GGATGATA
131 AGATCATA
* * *
40004724 CCATACCTACGTTTCACAACTCGGTATGGTTAATACCATACTTACGTTTCACAACTCGGTATGGA
1 CCATACCTACG-TTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTCGGTATGGA
* * * *
40004789 TGATATCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCAC-ACTTTGC
65 TGATACCATACCTACGTATCACAACTCAGTATGGATAATACCATACCTAC-TTTCACAAC-TCGC
40004853 CATAGATCA-A
128 CATAGATCATA
40004863 CCAT
1 CCAT
40004867 TGTCTTTTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
138 11 0.09
139 101 0.80
140 14 0.11
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (138 bp):
CCATACCTACGTTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTCGGTATGGAT
GATACCATACCTACGTATCACAACTCAGTATGGATAATACCATACCTACTTTCACAACTCGCCAT
AGATCATA
Found at i:40009783 original size:35 final size:35
Alignment explanation
Indices: 40009757--40010110 Score: 439
Period size: 35 Copynumber: 10.2 Consensus size: 35
40009747 CATGGCAAAG
* *
40009757 TGTGAAACGTACGTATGGTATCATCCATACGGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
40009792 TGTGAAATGTAGGTATGGTATTAACCATA-TCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACT-GAGT
*
40009827 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
40009862 TGTGAAACGTAGGTATGGTATCATTCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
40009897 TG-GAAA-GTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
40009930 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
40009965 TGTGAAACGTAGTTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* * *
40010000 TGTGAAATGTAGGTATGGTATCATCCATACCGGGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
* *
40010035 TATGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
** * * * *
40010070 TAAG-AATGTAGGTATGGCAT-TTCTCATACCGAGT
1 TGTGAAACGTAGGTATGGTATCATC-CATACTGAGT
40010104 TGTGAAA
1 TGTGAAA
40010111 TGTAAATAAA
Statistics
Matches: 276, Mismatches: 37, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
33 27 0.10
34 33 0.12
35 216 0.78
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATCATCCATACTGAGT
Found at i:40010046 original size:173 final size:174
Alignment explanation
Indices: 40009757--40010110 Score: 534
Period size: 173 Copynumber: 2.0 Consensus size: 174
40009747 CATGGCAAAG
*
40009757 TGTGAAACGTACGTATGGTATCATCCATACGGAGTTGTGAAATGTAGGTATGGTATTAACCATAT
1 TGTGAAACGTACGTATGGTATCATCCATACGGAGTTGTGAAACGTAGGTATGGTATTAACCATAT
* *
40009822 CGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATT
66 CGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATCATC
* * *
40009887 CATACCGAGTT-GGAAAGTAGGTATGGTATTAAC-CATACTGAGT
131 CATACCGAGTTAAGAAAGTAGGTATGGCATT-ACTCATACCGAGT
* * *
40009930 TGTGAAACGTAGGTATGGTATCATCCATACTGAGTTGTGAAACGTAGTTATGGTATTAACCATA-
1 TGTGAAACGTACGTATGGTATCATCCATACGGAGTTGTGAAACGTAGGTATGGTATTAACCATAT
* * *
40009994 CTGAGTTGTGAAATGTAGGTATGGTATCATCCATACCGGGTTATGAAACGTAGGTATGGTATTAT
66 C-GAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATCAT
* * *
40010059 CCATACTGAGTTAAGAATGTAGGTATGGCATTTCTCATACCGAGT
130 CCATACCGAGTTAAGAAAGTAGGTATGGCATTACTCATACCGAGT
40010104 TGTGAAA
1 TGTGAAA
40010111 TGTAAATAAA
Statistics
Matches: 163, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
172 1 0.01
173 130 0.80
174 32 0.20
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (174 bp):
TGTGAAACGTACGTATGGTATCATCCATACGGAGTTGTGAAACGTAGGTATGGTATTAACCATAT
CGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGTTATGAAACGTAGGTATGGTATCATC
CATACCGAGTTAAGAAAGTAGGTATGGCATTACTCATACCGAGT
Found at i:40011530 original size:10 final size:10
Alignment explanation
Indices: 40011515--40011561 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
40011505 GCGACCTCTC
40011515 AAATTAAACT
1 AAATTAAACT
40011525 AAATTAAACT
1 AAATTAAACT
*
40011535 AAGATTAATCT
1 AA-ATTAAACT
40011546 -AATT-AACT
1 AAATTAAACT
40011554 AAGATTAA
1 AA-ATTAA
40011562 TTATAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
10 16 0.52
11 8 0.26
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (10 bp):
AAATTAAACT
Found at i:40014222 original size:12 final size:12
Alignment explanation
Indices: 40014207--40014237 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40014197 TTCTCTTTTA
40014207 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
40014219 TTTTTCTTTCTC
1 TTTTTCTTTCCC
40014231 TTTTTCT
1 TTTTTCT
40014238 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:40014338 original size:16 final size:16
Alignment explanation
Indices: 40014317--40014347 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40014307 TTTATTATTT
40014317 TATTAACATAATATAA
1 TATTAACATAATATAA
*
40014333 TATTAATATAATATA
1 TATTAACATAATATA
40014348 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:40020057 original size:8 final size:8
Alignment explanation
Indices: 40020044--40020068 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40020034 GTATTCCAAT
40020044 TTTTTTTA
1 TTTTTTTA
40020052 TTTTTTTA
1 TTTTTTTA
40020060 TTTTTTTA
1 TTTTTTTA
40020068 T
1 T
40020069 AAAAATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:40020823 original size:22 final size:22
Alignment explanation
Indices: 40020793--40020871 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 22
40020783 GTACGCGGAT
*
40020793 TCCATCCAAACACACCAGAATG
1 TCCAACCAAACACACCAGAATG
* *
40020815 TCCAACC-AATACA-C-GGAT-
1 TCCAACCAAACACACCAGAATG
** *
40020833 TTTATCCAAACACACCAGAATG
1 TCCAACCAAACACACCAGAATG
40020855 TCCAACCCAAACACACC
1 TCCAA-CCAAACACACC
40020872 CGGAATATTG
Statistics
Matches: 41, Mismatches: 11, Indels: 9
0.67 0.18 0.15
Matches are distributed among these distances:
18 4 0.10
19 8 0.20
20 2 0.05
21 8 0.20
22 8 0.20
23 11 0.27
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.15
Consensus pattern (22 bp):
TCCAACCAAACACACCAGAATG
Found at i:40021635 original size:31 final size:31
Alignment explanation
Indices: 40021597--40021660 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40021587 CCTTTTCATA
*
40021597 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
** *
40021628 TTTCATATTTCATATTACTAGGCTGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
40021659 TT
1 TT
40021661 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:40021972 original size:50 final size:48
Alignment explanation
Indices: 40021880--40022072 Score: 287
Period size: 50 Copynumber: 3.9 Consensus size: 48
40021870 CCTCTTTTAG
* * *
40021880 TAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTTATCG
1 TAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTATCA
*
40021929 TAACTGGGGCATAAGCCCTTCATCATAACTGGGGCATAAGCCCTTTATCA
1 TAACTGGGGCATAAGCCCTT--TAATAACTGGGGCATAAGCCCTTTATCA
* *
40021979 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTCCTTTAA
1 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTT--TATCA
40022029 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTT
1 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTT
40022073 TGCACTTCCT
Statistics
Matches: 134, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
48 25 0.19
49 17 0.13
50 92 0.69
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (48 bp):
TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTATCA
Found at i:40022008 original size:23 final size:23
Alignment explanation
Indices: 40021875--40022072 Score: 252
Period size: 25 Copynumber: 8.1 Consensus size: 23
40021865 CCTAGCCTCT
* *
40021875 TTTAGTAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
40021898 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
40021922 TTTATCGTAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
*
40021947 TTCATCATAACTGGGGCATAAGCCC
1 TT--TAATAACTGGGGCATAAGCCC
40021972 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
40021997 TTTAATAACTGGGGCATAAGCCCTTCC
1 TTTAATAACTGGGGCATAAG--C--CC
40022024 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
40022047 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
40022070 TTT
1 TTT
40022073 TGCACTTCCT
Statistics
Matches: 156, Mismatches: 8, Indels: 21
0.84 0.04 0.11
Matches are distributed among these distances:
23 48 0.31
24 20 0.13
25 65 0.42
27 23 0.15
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:40022145 original size:9 final size:9
Alignment explanation
Indices: 40022131--40022187 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40022121 ATCTCATGTG
40022131 CATATCATA
1 CATATCATA
*
40022140 CATATCATGTG
1 CATATCA--TA
40022151 CATATCATA
1 CATATCATA
* *
40022160 CATGTCATGTG
1 CATATCA--TA
40022171 CATATCATA
1 CATATCATA
40022180 CATATCAT
1 CATATCAT
40022188 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40022147 original size:20 final size:20
Alignment explanation
Indices: 40022119--40022189 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
40022109 GCATTTATGA
*
40022119 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40022139 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
40022159 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
40022179 ACATATCATGT
1 ACATATCATGT
40022190 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:40022154 original size:11 final size:11
Alignment explanation
Indices: 40022124--40022178 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
40022114 TATGAACATC
40022124 TCATGTGCATA
1 TCATGTGCATA
*
40022135 TCA--TACATA
1 TCATGTGCATA
40022144 TCATGTGCATA
1 TCATGTGCATA
* *
40022155 TCA--TACATG
1 TCATGTGCATA
40022164 TCATGTGCATA
1 TCATGTGCATA
40022175 TCAT
1 TCAT
40022179 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:40023024 original size:18 final size:17
Alignment explanation
Indices: 40022998--40023031 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40022988 TTTAATCCTC
*
40022998 ACTAGCACCAACAAACCA
1 ACTAACACCAA-AAACCA
40023016 ACTAACACCAAAAACC
1 ACTAACACCAAAAACC
40023032 CTTTTAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.38, G:0.03, T:0.06
Consensus pattern (17 bp):
ACTAACACCAAAAACCA
Found at i:40023530 original size:27 final size:27
Alignment explanation
Indices: 40023430--40023513 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
40023420 GGGCATATTC
* * *
40023430 GTCATTTTACCATACAGGGG-TATTACT
1 GTCACTTTACCCTACAGGGGCT-TTACG
*
40023457 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40023484 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
40023511 GTC
1 GTC
40023514 TTTTTACCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:40023759 original size:81 final size:81
Alignment explanation
Indices: 40023663--40023843 Score: 251
Period size: 81 Copynumber: 2.2 Consensus size: 81
40023653 TTTGTAAATC
40023663 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTA-TTTCGATAATTTCACAAACC-AGTGGTATT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTTCG-TAATTTCACAAACCAAG-GGTATT
* *
40023726 TTGGTAATTTTACAAACT
64 TTAGCAATTTTACAAACT
* * *
40023744 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTTGTAATTTTACAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTTCGTAATTTCACAAACCAAGGGTATTTT
*
40023809 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
* *
40023825 A-GGGTATTCTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
40023844 GTAAATCGAG
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
80 16 0.18
81 68 0.76
82 6 0.07
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTTCGTAATTTCACAAACCAAGGGTATTTT
AGCAATTTTACAAACT
Found at i:40023815 original size:27 final size:27
Alignment explanation
Indices: 40023552--40023843 Score: 194
Period size: 27 Copynumber: 10.8 Consensus size: 27
40023542 TTTCATCCTA
* * *
40023552 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** **
40023579 CAAAGGTATTCCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** * *
40023606 CAATGGTATTTCCATAATTTTTAAAAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAA-C
* ** *
40023635 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAC
* *
40023662 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * * *
40023689 TAAGGGTATTTCGATAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
40023716 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* * *
40023743 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
** *
40023770 TGAGGGTATTTTTGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * *
40023797 CAAGGGTATTTTAGCAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * *
40023823 CTAGGGTATTCTAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
40023844 GTAAATCGAG
Statistics
Matches: 208, Mismatches: 51, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
26 21 0.10
27 160 0.77
28 14 0.07
29 13 0.06
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:40023865 original size:27 final size:27
Alignment explanation
Indices: 40023836--40023992 Score: 206
Period size: 27 Copynumber: 5.8 Consensus size: 27
40023826 GGGTATTCTA
* *
40023836 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
40023863 GTAATTCTATAAATCAAAGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40023890 GTACTTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40023917 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
40023944 GTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40023971 GTAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40023993 CTTTGGTAAT
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:40024019 original size:27 final size:26
Alignment explanation
Indices: 40023989--40024087 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 26
40023979 GTAAATCGGG
* *
40023989 GGTACTTTGGTAATTTTACAAGTCGAA
1 GGTA-TTTAGTAATTTTACAAATCGAA
*
40024016 GGTATTTTAGTAATTTTACAAATCGAG
1 GGTA-TTTAGTAATTTTACAAATCGAA
* *
40024043 GGTATTTCAGTATTTTTACAAA-CTAA
1 GGTATTT-AGTAATTTTACAAATCGAA
*
40024069 GCGTATTTCGGTAATTTTA
1 G-GTATTT-AGTAATTTTA
40024088 GTAAACTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
26 6 0.10
27 55 0.90
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (26 bp):
GGTATTTAGTAATTTTACAAATCGAA
Found at i:40024101 original size:27 final size:27
Alignment explanation
Indices: 40023998--40024102 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
40023988 GGGTACTTTG
* * *
40023998 GTAATTTTACAAGTCGAAG-GTATTTTA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
40024025 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
40024052 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
40024079 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
40024103 CTAAACAGGG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.03
27 53 0.84
28 8 0.13
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:40027520 original size:146 final size:147
Alignment explanation
Indices: 40027249--40027530 Score: 469
Period size: 146 Copynumber: 1.9 Consensus size: 147
40027239 TGATATAAAA
* * *
40027249 TGCTATTTTGATCATCAATTGAAATGGTGTAAAAGTATGATATTTGAGTATTGAATATGCAAATT
1 TGCTAGTTTAATCATCAATTGAAATAGTGTAAAAGTATGATATTTGAGTATTGAATATGCAAATT
*
40027314 GATCTAGTTGAATTGTGGCATATATTGATTGAATTTCTATATTAAGTATGCTCACTTGTGACTTG
66 GATCTAGTTGAATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTCACTTGTGACTTG
40027379 AATCATAAACGCACCAC
131 AATCATAAACGCACCAC
40027396 TGCTAGTTTAATCATCAATTGAAATAGTGTAAAAGTA-GATATTTGAGTATTGAATATGCAAATT
1 TGCTAGTTTAATCATCAATTGAAATAGTGTAAAAGTATGATATTTGAGTATTGAATATGCAAATT
* * * *
40027460 TATTTGGTTGAATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTA-TCTGTGACTT
66 GATCTAGTTGAATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTCACT-TGTGACTT
40027524 GAATCAT
130 GAATCAT
40027531 GAAAGTACCA
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
145 1 0.01
146 91 0.72
147 34 0.27
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (147 bp):
TGCTAGTTTAATCATCAATTGAAATAGTGTAAAAGTATGATATTTGAGTATTGAATATGCAAATT
GATCTAGTTGAATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTCACTTGTGACTTG
AATCATAAACGCACCAC
Found at i:40031533 original size:20 final size:20
Alignment explanation
Indices: 40031504--40031592 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
40031494 TACAATATCT
*
40031504 TAAAAAAAAATTAATAACTA
1 TAAAATAAAATTAATAACTA
40031524 TAAAATAAAATT-A-AACTA
1 TAAAATAAAATTAATAACTA
* * *
40031542 TAAACT----TTAAAACACAA
1 TAAAATAAAATTAATA-ACTA
*
40031559 TAAAAACAAAATTAATAACTA
1 T-AAAATAAAATTAATAACTA
40031580 TAAAATAAAATTA
1 TAAAATAAAATTA
40031593 CAATCTAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 1 0.02
17 4 0.08
18 13 0.25
19 1 0.02
20 22 0.42
21 4 0.08
22 5 0.09
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAAAATTAATAACTA
Found at i:40031585 original size:56 final size:56
Alignment explanation
Indices: 40031504--40031623 Score: 208
Period size: 56 Copynumber: 2.2 Consensus size: 56
40031494 TACAATATCT
40031504 TAAAAA-AAAATTAATAACTATAAAATAAAATTA-AACTATAAACTTTAAAACACAA
1 TAAAAACAAAATTAATAACTATAAAATAAAATTACAA-TATAAACTTTAAAACACAA
*
40031559 TAAAAACAAAATTAATAACTATAAAATAAAATTACAATCTAAACTTTAAAACACAA
1 TAAAAACAAAATTAATAACTATAAAATAAAATTACAATATAAACTTTAAAACACAA
40031615 TAAAAACAA
1 TAAAAACAA
40031624 TTGTAAAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
55 6 0.10
56 54 0.87
57 2 0.03
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (56 bp):
TAAAAACAAAATTAATAACTATAAAATAAAATTACAATATAAACTTTAAAACACAA
Found at i:40043403 original size:23 final size:22
Alignment explanation
Indices: 40043360--40043406 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
40043350 AATGCTCTAA
*
40043360 TTTTCCTTTTTATTTCTTTTTC
1 TTTTCCTTTTTATTTCATTTTC
40043382 TTTTCTCTTTTT-TCTTCATTTTC
1 TTTTC-CTTTTTAT-TTCATTTTC
40043405 TT
1 TT
40043407 ATTTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTCCTTTTTATTTCATTTTC
Found at i:40043412 original size:20 final size:21
Alignment explanation
Indices: 40043389--40043427 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
40043379 TTCTTTTCTC
40043389 TTTTTTC-TTCAT-TTTCTTA
1 TTTTTTCATTCATCTTTCTTA
40043408 TTTTTTCATTCATCTTTCTT
1 TTTTTTCATTCATCTTTCTT
40043428 TCTATTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTCATTCATCTTTCTTA
Found at i:40043415 original size:16 final size:17
Alignment explanation
Indices: 40043376--40043417 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40043366 TTTTTATTTC
*
40043376 TTTTTC-TTTTCTCTTT
1 TTTTTCATTTTCTCTAT
40043392 TTTCTTCATTTTCT-TAT
1 TTT-TTCATTTTCTCTAT
40043409 TTTTTCATT
1 TTTTTCATT
40043418 CATCTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTTCTCTAT
Found at i:40043425 original size:21 final size:19
Alignment explanation
Indices: 40043369--40043427 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
40043359 ATTTTCCTTT
40043369 TTATTTCTTT-TTC-TTTTC
1 TTATTT-TTTCTTCATTTTC
*
40043387 -TCTTTTTTCTTCATTTTC
1 TTATTTTTTCTTCATTTTC
40043405 TTATTTTTTCATTCATCTTTC
1 TTATTTTTTC-TTCAT-TTTC
40043426 TT
1 TT
40043428 TCTATTCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 7 0.21
18 5 0.15
19 8 0.24
20 5 0.15
21 6 0.18
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTTTTCTTCATTTTC
Found at i:40044708 original size:7 final size:7
Alignment explanation
Indices: 40044673--40044790 Score: 55
Period size: 7 Copynumber: 16.7 Consensus size: 7
40044663 AACATAAATA
40044673 ATATAAT
1 ATATAAT
*
40044680 AGATAAT
1 ATATAAT
*
40044687 ATACGATAT
1 ATA-TA-AT
*
40044696 ACATAAT
1 ATATAAT
40044703 ATATAAT
1 ATATAAT
* *
40044710 AAAAAAT
1 ATATAAT
40044717 ATATAAT
1 ATATAAT
40044724 A-AGTAAT
1 ATA-TAAT
40044731 ATATAAT
1 ATATAAT
*
40044738 A-AAAAT
1 ATATAAT
* *
40044744 AAAAAAT
1 ATATAAT
40044751 ATAATAA-
1 AT-ATAAT
* *
40044758 ATGTTAT
1 ATATAAT
*
40044765 ATAATAAA
1 AT-ATAAT
*
40044773 ATCTAAT
1 ATATAAT
40044780 ATA-AAT
1 ATATAAT
40044786 ATATA
1 ATATA
40044791 GGAAAATAAT
Statistics
Matches: 81, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
6 14 0.17
7 53 0.65
8 10 0.12
9 4 0.05
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (7 bp):
ATATAAT
Found at i:40044766 original size:32 final size:33
Alignment explanation
Indices: 40044693--40044773 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
40044683 TAATATACGA
* *
40044693 TATACATAATATATAATAAAAAATATATAATAAG
1 TATATATAATA-AAAATAAAAAATATATAATAAG
*
40044727 TAATATATAATAAAAATAAAAAATATAATAA-ATG
1 T-ATATATAATAAAAATAAAAAATAT-ATAATAAG
40044761 T-TATATAATAAAA
1 TATATATAATAAAA
40044774 TCTAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.29
34 17 0.40
35 13 0.31
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (33 bp):
TATATATAATAAAAATAAAAAATATATAATAAG
Found at i:40044813 original size:14 final size:14
Alignment explanation
Indices: 40044673--40044813 Score: 83
Period size: 14 Copynumber: 9.9 Consensus size: 14
40044663 AACATAAATA
*
40044673 ATATAATAGATAAT
1 ATATAATAAATAAT
* *
40044687 ATACGATATACATAAT
1 ATA-TA-ATAAATAAT
*
40044703 ATATAATAAAAAAT
1 ATATAATAAATAAT
*
40044717 ATATAATAAGTAAT
1 ATATAATAAATAAT
40044731 ATATAATAAA-AAT
1 ATATAATAAATAAT
* *
40044744 AAAAAATATAATAA-
1 ATATAATA-AATAAT
* * *
40044758 ATGTTATATAATAAA
1 ATATAATA-AATAAT
* *
40044773 ATCTAATATA-AAT
1 ATATAATAAATAAT
40044786 ATATAGGA-AAATAAT
1 ATATA--ATAAATAAT
*
40044801 ATATGATAAATAA
1 ATATAATAAATAA
40044814 ATTTTTTTAT
Statistics
Matches: 97, Mismatches: 21, Indels: 18
0.71 0.15 0.13
Matches are distributed among these distances:
13 16 0.16
14 52 0.54
15 18 0.19
16 11 0.11
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (14 bp):
ATATAATAAATAAT
Found at i:40048446 original size:20 final size:20
Alignment explanation
Indices: 40048410--40048461 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40048400 CTGAGGTGTT
40048410 ATACAGGGCA-CGAAAATGC
1 ATACAGGGCACCGAAAATGC
40048429 ATACAGGAGCACCG-AAATGC
1 ATACAGG-GCACCGAAAATGC
*
40048449 TTATCAGGGCACC
1 ATA-CAGGGCACC
40048462 AGAGTGCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.24
20 16 0.55
21 6 0.21
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.13
Consensus pattern (20 bp):
ATACAGGGCACCGAAAATGC
Found at i:40057500 original size:45 final size:45
Alignment explanation
Indices: 40057451--40057563 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
40057441 GTCATAGCGC
* *
40057451 CTTTCAGCTATGGTCTTACTCAT-TTCTATCATGATGCCATAACAT
1 CTTTCAACTATGGTCTTACTCATCTT-AATCATGATGCCATAACAT
* * ***
40057496 CTTTCAACTATGGTTTTACTTATCTTAATCATGATGCCATAGTGT
1 CTTTCAACTATGGTCTTACTCATCTTAATCATGATGCCATAACAT
*
40057541 CTTTTAACTA-GGTTCTTACTCAT
1 CTTTCAACTATGG-TCTTACTCAT
40057564 TTTAGGCGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
44 2 0.04
45 52 0.93
46 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (45 bp):
CTTTCAACTATGGTCTTACTCATCTTAATCATGATGCCATAACAT
Found at i:40058545 original size:15 final size:15
Alignment explanation
Indices: 40058525--40058574 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
40058515 TACAATGATC
*
40058525 CCTAATGTAATTTAT
1 CCTAATGCAATTTAT
*
40058540 CCTAATGCAA-TGAT
1 CCTAATGCAATTTAT
40058554 CCCTAATGCAATTTAT
1 -CCTAATGCAATTTAT
40058570 CCTAA
1 CCTAA
40058575 GTATGCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 24 0.80
16 3 0.10
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (15 bp):
CCTAATGCAATTTAT
Found at i:40058553 original size:30 final size:30
Alignment explanation
Indices: 40058517--40058574 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
40058507 AAACTAAATA
*
40058517 CAATGATCCCTAATGTAATTTATCCTAATG
1 CAATGATCCCTAATGCAATTTATCCTAATG
40058547 CAATGATCCCTAATGCAATTTATCCTAA
1 CAATGATCCCTAATGCAATTTATCCTAA
40058575 GTATGCAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (30 bp):
CAATGATCCCTAATGCAATTTATCCTAATG
Found at i:40071710 original size:34 final size:35
Alignment explanation
Indices: 40071633--40071732 Score: 107
Period size: 34 Copynumber: 2.9 Consensus size: 35
40071623 ATGCTTTGTT
*
40071633 TGCATACTG-TATTGAAATGGGCTAAGGCCCAGAC
1 TGCATACTGTTACTGAAATGGGCTAAGGCCCAGAC
* * *
40071667 TGCCT-CTGTTACTGAAATGGGCTTAGGCCCATAC
1 TGCATACTGTTACTGAAATGGGCTAAGGCCCAGAC
* *
40071701 TG-ATACTGTTACTAAAAAAGGGGCTAAGGCCC
1 TGCATACTGTTACT--GAAATGGGCTAAGGCCC
40071733 TAACCCGAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 4 0.07
34 36 0.67
36 14 0.26
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (35 bp):
TGCATACTGTTACTGAAATGGGCTAAGGCCCAGAC
Found at i:40073896 original size:15 final size:15
Alignment explanation
Indices: 40073876--40073904 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40073866 CTTTTAATGT
40073876 ATATGGAGTATTTAA
1 ATATGGAGTATTTAA
40073891 ATATGGAGTATTTA
1 ATATGGAGTATTTA
40073905 TGTTGCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
ATATGGAGTATTTAA
Done.