Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 187 of 214
Found at i:54818387 original size:66 final size:66
Alignment explanation
Indices: 54818281--54818413 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
54818271 TTATGTATTT
* * * *
54818281 ACTTTAATTTAATCTTAATATAAATTGAGCTTGAATTATACCAGCATCACTTAGTATTCATTACT
1 ACTTTAATTTAATCCTAATATAAATTGAACTTGAATTATACCAGCATCACTTAATATTCAATACT
54818346 C
66 C
* *
54818347 ACTTTAATTTAATCCTAATATAACTTGAACTTGAATTATACTAGCATCACTTAATATTCAATACT
1 ACTTTAATTTAATCCTAATATAAATTGAACTTGAATTATACCAGCATCACTTAATATTCAATACT
54818412 C
66 C
54818413 A
1 A
54818414 GTGTATGATT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (66 bp):
ACTTTAATTTAATCCTAATATAAATTGAACTTGAATTATACCAGCATCACTTAATATTCAATACT
C
Found at i:54828692 original size:36 final size:37
Alignment explanation
Indices: 54828647--54828768 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 37
54828637 TGGTAGTATG
* *
54828647 AAACA-TAAGAATTGTATATTATTTGTTGGCGATATA
1 AAACAGTAAGAAATGTGTATTATTTGTTGGCGATATA
* * * * **
54828683 AAA-TGTAAGAAATGTGTATTGTCTATTGGTAATATA
1 AAACAGTAAGAAATGTGTATTATTTGTTGGCGATATA
* *
54828719 AAACAG-AAGAAATGTGTATCATTCGTTGGCGATATA
1 AAACAGTAAGAAATGTGTATTATTTGTTGGCGATATA
*
54828755 ATACA-TAAGAAATG
1 AAACAGTAAGAAATG
54828769 CATAAGGCCC
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
36 65 0.98
37 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (37 bp):
AAACAGTAAGAAATGTGTATTATTTGTTGGCGATATA
Found at i:54829229 original size:49 final size:49
Alignment explanation
Indices: 54829168--54829417 Score: 177
Period size: 49 Copynumber: 5.1 Consensus size: 49
54829158 TTGCAATAAA
* ** *
54829168 TAATAAAATGACCTTACTCCCAGACGCATGGAGGAAGGCTTACAGAAGG
1 TAATAAAGTGACCTTACTCCCAGACATATGGAGGAAGGCTTATAGAAGG
* * * *
54829217 TAATAAAGTGACCTTGCTCCCTA-ACATATGGGGGAAGGCTTATGGAAAG
1 TAATAAAGTGACCTTACTCCC-AGACATATGGAGGAAGGCTTATAGAAGG
* * * * *
54829266 CAATAAACCG-GACC-TACTCCCAGACTTATGGGGGGACGCTTATAGAAGG
1 TAATAAA--GTGACCTTACTCCCAGACATATGGAGGAAGGCTTATAGAAGG
* * * * * *
54829315 TAATAAAGTGACCTTGCTTCCAAACACAT-GAGGGAAGGCTTATGGAAAG
1 TAATAAAGTGACCTTACTCCCAGACATATGGA-GGAAGGCTTATAGAAGG
* * * * * * * *
54829364 CAATAAATTGGCCCTACTCCTAGACGTATGG-GGGAGGCTTACAGAAGG
1 TAATAAAGTGACCTTACTCCCAGACATATGGAGGAAGGCTTATAGAAGG
*
54829412 TGATAA
1 TAATAA
54829418 TGTGGCCCTA
Statistics
Matches: 151, Mismatches: 42, Indels: 17
0.72 0.20 0.08
Matches are distributed among these distances:
47 1 0.01
48 23 0.15
49 120 0.79
50 6 0.04
51 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (49 bp):
TAATAAAGTGACCTTACTCCCAGACATATGGAGGAAGGCTTATAGAAGG
Found at i:54829321 original size:98 final size:98
Alignment explanation
Indices: 54829177--54829417 Score: 331
Period size: 98 Copynumber: 2.5 Consensus size: 98
54829167 ATAATAAAAT
* * * *
54829177 GACCTTACTCCCAGACGCATGGAGGAAGGCTTACAGAAGGTAATAAAGTGACCTTGCTCCCTAAC
1 GACC-TACTCCCAGACGTATGGGGGGAGGCTTACAGAAGGTAATAAAGTGACCTTGCTCCCAAAC
* *
54829242 ATATGGGGGAAGGCTTATGGAAAGCAATAAACCG
65 ACATGAGGGAAGGCTTATGGAAAGCAATAAACCG
* * * *
54829276 GACCTACTCCCAGACTTATGGGGGGACGCTTATAGAAGGTAATAAAGTGACCTTGCTTCCAAACA
1 GACCTACTCCCAGACGTATGGGGGGAGGCTTACAGAAGGTAATAAAGTGACCTTGCTCCCAAACA
**
54829341 CATGAGGGAAGGCTTATGGAAAGCAATAAATTG
66 CATGAGGGAAGGCTTATGGAAAGCAATAAACCG
* * *
54829374 GCCCTACTCCTAGACGTAT-GGGGGAGGCTTACAGAAGGTGATAA
1 GACCTACTCCCAGACGTATGGGGGGAGGCTTACAGAAGGTAATAA
54829418 TGTGGCCCTA
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
97 22 0.18
98 98 0.79
99 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (98 bp):
GACCTACTCCCAGACGTATGGGGGGAGGCTTACAGAAGGTAATAAAGTGACCTTGCTCCCAAACA
CATGAGGGAAGGCTTATGGAAAGCAATAAACCG
Found at i:54829673 original size:53 final size:53
Alignment explanation
Indices: 54829542--54829714 Score: 143
Period size: 53 Copynumber: 3.2 Consensus size: 53
54829532 TGATGCACGA
* ** ** * *
54829542 GGGAGGCTTAAGGGCAAGGTTTAATGATAATATCTC-CACTCCCAAACACATAGG
1 GGGAGGCTTACGAACAAGGTTTAACAATAATATC-CATACTCTCAAACACAT-GG
* * *** * *
54829596 GGTAGGCTTACGGATGGGGTTTAACAATAATGTCCTTACTCTCAAACACATGG
1 GGGAGGCTTACGAACAAGGTTTAACAATAATATCCATACTCTCAAACACATGG
* *
54829649 GGGAGGCTTACGAACAAGGTTTAACAATAATATCCATGCT-TCCAAACGCATGG
1 GGGAGGCTTACGAACAAGGTTTAACAATAATATCCATACTCT-CAAACACATGG
*
54829702 GGGAAGACTTACG
1 GGG-AGGCTTACG
54829715 GTAAGAAATC
Statistics
Matches: 95, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
52 1 0.01
53 48 0.51
54 46 0.48
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (53 bp):
GGGAGGCTTACGAACAAGGTTTAACAATAATATCCATACTCTCAAACACATGG
Found at i:54846755 original size:7 final size:7
Alignment explanation
Indices: 54846743--54846768 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54846733 TGCAAGCCTT
54846743 TAACCTG
1 TAACCTG
54846750 TAACCTG
1 TAACCTG
54846757 TAACCTG
1 TAACCTG
54846764 TAACC
1 TAACC
54846769 AAATAAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (7 bp):
TAACCTG
Found at i:54848240 original size:20 final size:20
Alignment explanation
Indices: 54848194--54848243 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
54848184 ATGACAAAAT
54848194 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
*
54848214 AACTCAAAAT-ATTTAT-AAA
1 AATTCAAAATAATTT-TCAAA
54848233 AATTTCAAAAT
1 AA-TTCAAAAT
54848244 TTGTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:54848250 original size:24 final size:25
Alignment explanation
Indices: 54848223--54848269 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
54848213 AAACTCAAAA
*
54848223 TATTTATAAAAATT-TCAAAATTTG
1 TATTTATAAAAATTATAAAAATTTG
*
54848247 TATTTTTAAAAATTATAAAAATT
1 TATTTATAAAAATTATAAAAATT
54848270 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTTATAAAAATTATAAAAATTTG
Found at i:54849472 original size:19 final size:19
Alignment explanation
Indices: 54849450--54849489 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54849440 AAAATTGTAG
*
54849450 AAAATTACAAA-AATATATA
1 AAAATAACAAACAAT-TATA
54849469 AAAATAACAAACAATTATA
1 AAAATAACAAACAATTATA
54849488 AA
1 AA
54849490 CATGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATAACAAACAATTATA
Found at i:54852665 original size:5 final size:5
Alignment explanation
Indices: 54852657--54852681 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54852647 ATAATATAAT
54852657 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
54852682 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:54858317 original size:4 final size:4
Alignment explanation
Indices: 54858308--54858332 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54858298 AATCGAGTAG
54858308 AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT A
54858333 CCTTAGGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:54870414 original size:35 final size:35
Alignment explanation
Indices: 54870368--54870439 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
54870358 ATTCGACTCA
54870368 CCTTTCATTATTTTATTTGGGTATTTCTCCTAAAC
1 CCTTTCATTATTTTATTTGGGTATTTCTCCTAAAC
*
54870403 CCTTTCATTATTTTGTTTGGGTATTTCTCCTAAAC
1 CCTTTCATTATTTTATTTGGGTATTTCTCCTAAAC
54870438 CC
1 CC
54870440 AAATTTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.18, C:0.22, G:0.10, T:0.50
Consensus pattern (35 bp):
CCTTTCATTATTTTATTTGGGTATTTCTCCTAAAC
Found at i:54875464 original size:3 final size:3
Alignment explanation
Indices: 54875443--54875478 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
54875433 AGCCTCAGAG
* *
54875443 GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
54875479 AGCGAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:54885695 original size:16 final size:16
Alignment explanation
Indices: 54885674--54885724 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
54885664 CTTTGAAACA
54885674 AAACTATTATTAATTT
1 AAACTATTATTAATTT
* ***
54885690 AAACTATCCA-TAAAAA
1 AAACTAT-TATTAATTT
54885706 AAACTATTATTAATTT
1 AAACTATTATTAATTT
54885722 AAA
1 AAA
54885725 AGATAAATAT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
AAACTATTATTAATTT
Found at i:54885747 original size:15 final size:16
Alignment explanation
Indices: 54885727--54885761 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
54885717 AATTTAAAAG
*
54885727 ATAAATATATTTTT-T
1 ATAAATACATTTTTAT
54885742 ATAAATACATTTTTAT
1 ATAAATACATTTTTAT
54885758 ATAA
1 ATAA
54885762 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAATACATTTTTAT
Found at i:54888340 original size:17 final size:17
Alignment explanation
Indices: 54888306--54888348 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54888296 AAATAAGATT
*
54888306 ATTTAAATTTAATATAA
1 ATTTAAAATTAATATAA
* *
54888323 ATTTAAAATTATTTTAA
1 ATTTAAAATTAATATAA
*
54888340 ATTAAAAAT
1 ATTTAAAAT
54888349 AAAAAATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAAATTAATATAA
Found at i:54888740 original size:24 final size:21
Alignment explanation
Indices: 54888698--54888740 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
54888688 TTTTTTATTT
54888698 TTAATTTAATTTAATATTTAC
1 TTAATTTAATTTAATATTTAC
54888719 TTAATATTAATTTTAAATATTT
1 TTAAT-TTAA-TTT-AATATTT
54888741 TATTTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 3 0.16
24 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATTTAATTTAATATTTAC
Found at i:54889319 original size:30 final size:31
Alignment explanation
Indices: 54889269--54889333 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
54889259 TTAGTAATTA
* *
54889269 ATAAAAATTAAATTAAATT-AAAATTTCATAT
1 ATAAAAATGAAATAAAATTAAAAATTT-ATAT
54889300 ATAAAAATGAAA-AAAATTAAAAATTTATAT
1 ATAAAAATGAAATAAAATTAAAAATTTATAT
54889330 ATAA
1 ATAA
54889334 TATTACACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (31 bp):
ATAAAAATGAAATAAAATTAAAAATTTATAT
Found at i:54908959 original size:15 final size:15
Alignment explanation
Indices: 54908941--54908981 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54908931 AAGTTTTTTA
* *
54908941 AATTATTATTTAATT
1 AATTATAATTAAATT
54908956 AATTATAATTAAATT
1 AATTATAATTAAATT
54908971 AATTAGTAATT
1 AATTA-TAATT
54908982 GTGAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATTATAATTAAATT
Found at i:54923187 original size:21 final size:21
Alignment explanation
Indices: 54923161--54923201 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54923151 ATCTGCTCAA
* *
54923161 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54923182 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54923202 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54926400 original size:104 final size:104
Alignment explanation
Indices: 54926274--54926500 Score: 377
Period size: 104 Copynumber: 2.2 Consensus size: 104
54926264 TACAATGGAT
54926274 ATCA-CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
1 ATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* *
54926338 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGA
66 TGGTGGATCA-CGCACATAGCACCACCAATAAACCGGGGA
54926377 ATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
1 ATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* *
54926442 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGA
66 TGGTGGATCACGCACATAGCACCACCAATAAACCGGGGA
**
54926481 ATCAGCACACAGCAACCCCT
1 ATCAGCACTTAGCAACCCCT
54926501 TTTATATACA
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 4 0.03
104 111 0.96
105 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
ATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
TGGTGGATCACGCACATAGCACCACCAATAAACCGGGGA
Found at i:54926862 original size:29 final size:29
Alignment explanation
Indices: 54926829--54926892 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
54926819 TAATCCACCA
54926829 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
54926858 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
54926888 CCCAA
1 CCCAA
54926893 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:54926866 original size:30 final size:30
Alignment explanation
Indices: 54926836--54926892 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54926826 CCACCCAACT
54926836 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
54926865 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
54926893 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:54933779 original size:27 final size:27
Alignment explanation
Indices: 54933744--54933795 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
54933734 CCACTGAATC
* *
54933744 GGGGAATCATCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
54933771 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
54933796 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:54944091 original size:17 final size:18
Alignment explanation
Indices: 54944069--54944114 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
54944059 ATTTATTTAT
54944069 ATCATATTATATA-ATGC
1 ATCATATTATATATATGC
54944086 ATCATA-TATGATATATGC
1 ATCATATTAT-ATATATGC
*
54944104 AT-ACATTATAT
1 ATCATATTATAT
54944115 TTGCGACGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 13 0.52
18 9 0.36
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (18 bp):
ATCATATTATATATATGC
Found at i:54947092 original size:31 final size:31
Alignment explanation
Indices: 54947030--54947093 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
54947020 TTGAAATGTT
* *
54947030 ACATTTTAGTCACTTACGTTAATACGTTGTA
1 ACATTTTAGTCACTAACGTTAACACGTTGTA
54947061 ACATTTTAGTCACTGAATCGTTAACA-G-TGTA
1 ACATTTTAGTCACT-AA-CGTTAACACGTTGTA
54947092 AC
1 AC
54947094 GGTAAGCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 20 0.69
32 2 0.07
33 7 0.24
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (31 bp):
ACATTTTAGTCACTAACGTTAACACGTTGTA
Found at i:54949111 original size:21 final size:22
Alignment explanation
Indices: 54949085--54949125 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
54949075 AATTTACAGA
*
54949085 AGAAGAAGATAG-AAAGAAAGG
1 AGAAGAAGAAAGAAAAGAAAGG
54949106 AGAAGAAGAAAGAAAAGAAA
1 AGAAGAAGAAAGAAAAGAAA
54949126 AAGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (22 bp):
AGAAGAAGAAAGAAAAGAAAGG
Found at i:54955779 original size:146 final size:146
Alignment explanation
Indices: 54955467--54955910 Score: 650
Period size: 149 Copynumber: 3.0 Consensus size: 146
54955457 TTTGATATTT
* *
54955467 ATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTATTTTAGTACATAATATT
1 ATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTATTTTAGTACATAATATT
* *
54955532 TCAAATGTATTATTTTTATATATTTTTT-TACTAATTTAGTAAAAAACTCTGATTTTTGCCGTTT
66 TCAAATGTATTA-TTTTA-AT-TTTTTTATATTAATTTAGTAAAAAACTCTGA-TTTTGGCGTTT
54955596 GTTTTTTTATTTTATTTTCGG
127 G-TTTTTTATTTTATTTTCGG
* *
54955617 ATTTTATTTTTTAAAATATACTATTTTTGTAATTTA-TTTTTATATTATTTTAGTACATAATGTT
1 ATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTATTTTAGTACATAATATT
54955681 TCAAATGTATTATTTTAATTTTTTTATATTAATTTAGTAAAAAACTCTGATTTTGGCAGTTTGTT
66 TCAAATGTATTATTTTAATTTTTTTATATTAATTTAGTAAAAAACTCTGATTTTGGC-GTTTGTT
54955746 TTTTATTTTATTTTCGG
130 TTTTATTTTATTTTCGG
* *
54955763 ATTTTATTTTTCAAAATATACTATTTTTTCTATTTTATTTTTTTATATTATTTTAGTACATAATA
1 ATTTTATTTTTTAAAATATACTA-TTTTTGTATTTTA-TTTTTTATATTATTTTAGTACATAATA
* * * * *
54955828 TTTCATATGTATTATTTTAGTATATTTATATTAATTTAGTAAAAAACT-TGATTTTGGC----CT
64 TTTCAAATGTATTATTTTAATTTTTTTATATTAATTTAGTAAAAAACTCTGATTTTGGCGTTTGT
54955888 TTTTTATTTTATTTTCGG
129 TTTTTATTTTATTTTCGG
54955906 ATTTT
1 ATTTT
54955911 TTAAAATATA
Statistics
Matches: 274, Mismatches: 15, Indels: 17
0.90 0.05 0.06
Matches are distributed among these distances:
143 24 0.09
146 53 0.19
147 41 0.15
148 15 0.05
149 108 0.39
150 33 0.12
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (146 bp):
ATTTTATTTTTTAAAATATACTATTTTTGTATTTTATTTTTTATATTATTTTAGTACATAATATT
TCAAATGTATTATTTTAATTTTTTTATATTAATTTAGTAAAAAACTCTGATTTTGGCGTTTGTTT
TTTATTTTATTTTCGG
Found at i:54955813 original size:13 final size:14
Alignment explanation
Indices: 54955779--54955816 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
54955769 TTTTTCAAAA
*
54955779 TATACTATTTTTTC
1 TATATTATTTTTTC
*
54955793 TATTTTATTTTTT-
1 TATATTATTTTTTC
54955806 TATATTATTTT
1 TATATTATTTT
54955817 AGTACATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TATATTATTTTTTC
Found at i:54955923 original size:14 final size:14
Alignment explanation
Indices: 54955906--54955934 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54955896 TTATTTTCGG
54955906 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
54955920 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
54955934 A
1 A
54955935 CTATTAAGCT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:54963547 original size:23 final size:23
Alignment explanation
Indices: 54963508--54963569 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
54963498 GAATAATATT
* *
54963508 ATAAT-AATAAATTAATT-GAAA
1 ATAATAAATAAATAAATTAAAAA
54963529 ATAAATAAATAAATAAATTAAAAA
1 AT-AATAAATAAATAAATTAAAAA
*
54963553 ATAATAAAGAAATAAAT
1 ATAATAAATAAATAAAT
54963570 ATTATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 25 0.71
24 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (23 bp):
ATAATAAATAAATAAATTAAAAA
Found at i:54963582 original size:4 final size:4
Alignment explanation
Indices: 54963527--54963570 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
54963517 AATTAATTGA
*
54963527 AAAT AAAT AAAT AAAT AAATT AAA- AAAT -AAT AAAG AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT A
54963571 TTATATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 6 0.17
4 25 0.71
5 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:54964398 original size:201 final size:202
Alignment explanation
Indices: 54964052--54964462 Score: 815
Period size: 201 Copynumber: 2.0 Consensus size: 202
54964042 GAAATATATG
54964052 TTTTTAAATTATAATTAATATTATTATGATGACACTTTTACTTTTTCATATTTTTATATCATATT
1 TTTTTAAATTATAATTAATATTATTATGATGACACTTTTACTTTTTCATATTTTTATATCATATT
54964117 TAAATAAAACAATTAAAGATCACAAATCTAAGGATCAAACACGTGTTTGATAGTATTAAAATACA
66 TAAATAAAACAATTAAAGATCACAAATCTAAGGATCAAACACGTGTTTGATAGTATTAAAATACA
54964182 AGTTCATTACCACTCCACTTATATTCATTATTGTATAAATTTTAAAATGACAAAATTTAATAATT
131 AGTTCATTACCACTCCACTTATATTCATTATTGTATAAATTTTAAAATGACAAAATTTAATAATT
54964247 TAATAAT
196 TAATAAT
54964254 TTTTTAAATTATAATTAATATTATTATGATGACACTTTTACTTTTT-ATATTTTTATATCATATT
1 TTTTTAAATTATAATTAATATTATTATGATGACACTTTTACTTTTTCATATTTTTATATCATATT
54964318 TAAATAAAACAATTAAAGATCACAAATCTAAGGATCAAACACGTGTTTGATAGTATTAAAATACA
66 TAAATAAAACAATTAAAGATCACAAATCTAAGGATCAAACACGTGTTTGATAGTATTAAAATACA
54964383 AGTTCATTACCACTCCACTTATATTCATTATTGTATAAATTTTAAAATGACAAAATTTAATAATT
131 AGTTCATTACCACTCCACTTATATTCATTATTGTATAAATTTTAAAATGACAAAATTTAATAATT
54964448 TAATAAT
196 TAATAAT
54964455 TTTTTAAA
1 TTTTTAAA
54964463 GGAATAATTT
Statistics
Matches: 209, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 163 0.78
202 46 0.22
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (202 bp):
TTTTTAAATTATAATTAATATTATTATGATGACACTTTTACTTTTTCATATTTTTATATCATATT
TAAATAAAACAATTAAAGATCACAAATCTAAGGATCAAACACGTGTTTGATAGTATTAAAATACA
AGTTCATTACCACTCCACTTATATTCATTATTGTATAAATTTTAAAATGACAAAATTTAATAATT
TAATAAT
Found at i:54990750 original size:27 final size:27
Alignment explanation
Indices: 54990715--54990781 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
54990705 TTTCTATTGT
*
54990715 TTTTTTGCTTATTTAAGTTAGTTTTTG
1 TTTTTTGCTTATTTAAGTTAATTTTTG
54990742 TTTTTTGCTTATTTAAGTTAATTTTTG
1 TTTTTTGCTTATTTAAGTTAATTTTTG
54990769 TTGTTTTAGCTTA
1 TT-TTTT-GCTTA
54990782 CTGATTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 28 0.76
28 4 0.11
29 5 0.14
ACGTcount: A:0.16, C:0.04, G:0.13, T:0.66
Consensus pattern (27 bp):
TTTTTTGCTTATTTAAGTTAATTTTTG
Found at i:54991215 original size:17 final size:17
Alignment explanation
Indices: 54991193--54991234 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
54991183 TTGGTTAAAA
*
54991193 ATTAACCGACTTAACTG
1 ATTAACCGACTTAACCG
54991210 ATTAACCGACTTAACCG
1 ATTAACCGACTTAACCG
54991227 ATTTAACC
1 A-TTAACC
54991235 AAATTGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (17 bp):
ATTAACCGACTTAACCG
Found at i:54991223 original size:9 final size:9
Alignment explanation
Indices: 54991194--54991234 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
54991184 TGGTTAAAAA
54991194 TTAACCGAC
1 TTAACCGAC
*
54991203 TTAACTGA-
1 TTAACCGAC
54991211 TTAACCGAC
1 TTAACCGAC
*
54991220 TTAACCGAT
1 TTAACCGAC
54991229 TTAACC
1 TTAACC
54991235 AAATTGAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (9 bp):
TTAACCGAC
Found at i:54991302 original size:17 final size:17
Alignment explanation
Indices: 54991280--54991340 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
54991270 TTTGAATCAC
54991280 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
54991297 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
54991317 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
54991334 TACATAA
1 TACATAA
54991341 AAATGAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 20 0.61
20 13 0.39
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:54991313 original size:37 final size:37
Alignment explanation
Indices: 54991238--54991340 Score: 178
Period size: 37 Copynumber: 2.9 Consensus size: 37
54991228 TTTAACCAAA
54991238 TTGAATCACTACATAATTAAAAA-A--A-ATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
54991271 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
54991308 TTGAATCACTACATAATTAAAAACATTACATAA
1 TTGAATCACTACATAATTAAAAACATTACATAA
54991341 AAATGAAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 23 0.35
34 1 0.02
36 1 0.02
37 41 0.62
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.31
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:54991322 original size:20 final size:20
Alignment explanation
Indices: 54991263--54991323 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
54991253 ATTAAAAAAA
54991263 ATAAGTCTTTGAATCACTAC
1 ATAAGTCTTTGAATCACTAC
** * *
54991283 ATAA---TTAAAAACATTAC
1 ATAAGTCTTTGAATCACTAC
54991300 ATAAGTCTTTGAATCACTAC
1 ATAAGTCTTTGAATCACTAC
54991320 ATAA
1 ATAA
54991324 TTAAAAACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 13 0.43
20 17 0.57
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (20 bp):
ATAAGTCTTTGAATCACTAC
Found at i:54998433 original size:24 final size:27
Alignment explanation
Indices: 54998382--54998440 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
54998372 CATATAACTC
*
54998382 CAATTCAATCATAATTTCTCACATTTT
1 CAATTCAATCATAATTTCTCACACTTT
*
54998409 CAATTCAATCAT-TTTTC-CAC-CTTT
1 CAATTCAATCATAATTTCTCACACTTT
54998433 CAA-TCAAT
1 CAATTCAAT
54998441 AATTAATCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 6 0.20
25 3 0.10
26 4 0.13
27 12 0.40
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.42
Consensus pattern (27 bp):
CAATTCAATCATAATTTCTCACACTTT
Found at i:54998450 original size:23 final size:24
Alignment explanation
Indices: 54998406--54998451 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
54998396 TTTCTCACAT
* **
54998406 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
54998430 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
54998452 AAATTCACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:54999266 original size:14 final size:14
Alignment explanation
Indices: 54999246--54999282 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54999236 CTAGTTTTTC
54999246 CTTTCTTTCTCTTT
1 CTTTCTTTCTCTTT
* *
54999260 TTTTCTTTTTCTTT
1 CTTTCTTTCTCTTT
54999274 CTTTCTTTC
1 CTTTCTTTC
54999283 GCCCCTGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTCTTTCTCTTT
Found at i:55001144 original size:134 final size:133
Alignment explanation
Indices: 55000931--55001182 Score: 450
Period size: 134 Copynumber: 1.9 Consensus size: 133
55000921 AGAAGCACAG
* **
55000931 CAAAGTCAAAGCACAAATACTTTAAATTTCTGGCTGTTAAAGTAAAAATTCAAAGTGATCAGGTG
1 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAACTG
*
55000996 TTTATAAAACATATTGGGACAAACTCTATGATTGCAGATTCGTTTATTAAGGGAATAATAGGAGC
66 TTTATAAAACATATTGGGACAAA-TCTATGATTGCAGATCCGTTTATTAAGGGAATAATAGGAGC
55001061 AAAT
130 AAAT
*
55001065 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAACGTGATCAACTG
1 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAACTG
55001130 TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGTTTATTAAGGGA
66 TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGTTTATTAAGGGA
55001183 TTACCACCCA
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
133 29 0.26
134 84 0.74
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (133 bp):
CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAACTG
TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGTTTATTAAGGGAATAATAGGAGCA
AAT
Found at i:55001990 original size:14 final size:14
Alignment explanation
Indices: 55001971--55002000 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
55001961 ATGATTCAGC
55001971 TACGCTTCTATATT
1 TACGCTTCTATATT
55001985 TACGCTTCTATATT
1 TACGCTTCTATATT
55001999 TA
1 TA
55002001 GTTTGCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (14 bp):
TACGCTTCTATATT
Found at i:55007930 original size:13 final size:13
Alignment explanation
Indices: 55007898--55007936 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55007888 GCGCAAATGC
55007898 ATATGAATAT-TAT
1 ATAT-AATATATAT
55007911 ATA-AATATATAT
1 ATATAATATATAT
55007923 ATATAATATATAT
1 ATATAATATATAT
55007936 A
1 A
55007937 AAAATGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:55008205 original size:15 final size:13
Alignment explanation
Indices: 55008141--55008215 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
55008131 CTAAACTATC
55008141 ATATAATAATAAT
1 ATATAATAATAAT
*
55008154 ATGATGAATAAAAAT
1 AT-AT-AATAATAAT
55008169 GATATAAATAATAAT
1 -ATAT-AATAATAAT
*
55008184 AGA-AATAATAAT
1 ATATAATAATAAT
*
55008196 -CATAATAATAA-
1 ATATAATAATAAT
55008207 ATGATAATA
1 AT-ATAATA
55008216 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 1 0.02
12 17 0.34
13 8 0.16
14 4 0.08
15 18 0.36
16 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:55009898 original size:87 final size:87
Alignment explanation
Indices: 55009634--55009937 Score: 296
Period size: 87 Copynumber: 3.5 Consensus size: 87
55009624 AGACCTGATG
* * *
55009634 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGTAACTT
*
55009699 -AGGGAGATAGGATTATATCTT
66 CAGGGAGATAGGATTATGTCTT
* * * * * ** ** *
55009720 TGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCGCTGTAAC
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATT-TT-AATCCGCTCCACTGTAAC
* * * *
55009785 CTCAGGGGGATAAGGCCTGATG----
64 TTCAGGGAGAT-AGG-ATTATGTCTT
* * *
55009807 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGAT-CTGTAATTTTAATCCGCTCCACTGTAACT
55009871 TCAGGGAGATAGGATTATGTCTT
65 TCAGGGAGATAGGATTATGTCTT
* * * *
55009894 CGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTT
1 CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTT
55009938 CCAACCTATT
Statistics
Matches: 165, Mismatches: 42, Indels: 21
0.72 0.18 0.09
Matches are distributed among these distances:
83 4 0.02
84 3 0.02
85 22 0.13
86 39 0.24
87 68 0.41
88 16 0.10
89 7 0.04
90 3 0.02
91 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (87 bp):
CGATCTACTCCACTGTAACCTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATTATGTCTT
Found at i:55010191 original size:85 final size:85
Alignment explanation
Indices: 55010096--55010494 Score: 694
Period size: 85 Copynumber: 4.7 Consensus size: 85
55010086 GTAAGAAGAT
55010096 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
*
55010161 CGTTGTTAACGTTGGAAGGC
66 CGTTGTTAACGCTGGAAGGC
* * * * *
55010181 AAGATCTGCTTCTTTAACCAACTCCATTGTAACCAATGAAGGCAAGGTTTTGTTTTCGA--TGTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-CTTGTTTTCGATCTGCT
*
55010244 TCGTTGTTAACGTTGGAAGGC
65 TCGTTGTTAACGCTGGAAGGC
55010265 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
55010330 CGTTGTTAACGCTGGAAGGC
66 CGTTGTTAACGCTGGAAGGC
55010350 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
55010415 CGTTGTTAACGCTGGAAGGC
66 CGTTGTTAACGCTGGAAGGC
*
55010435 AAGATCTGCTTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGAT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGC-TTGTTTTCGAT
55010495 GTTCACTGAT
Statistics
Matches: 298, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
83 10 0.03
84 68 0.23
85 199 0.67
86 21 0.07
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (85 bp):
AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
CGTTGTTAACGCTGGAAGGC
Found at i:55010352 original size:42 final size:42
Alignment explanation
Indices: 55010302--55010437 Score: 118
Period size: 42 Copynumber: 3.2 Consensus size: 42
55010292 TGCAACCAAT
55010302 GAAGGCAAGGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTG
1 GAAGGCAAGGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTG
* ** * * * ** *
55010344 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT-
1 GAAGGCAAGGCT-TG-TT-TTCGATCTGCTTCGTTGTTAACGC--TG
55010387 GAAGGCAAGGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTG
1 GAAGGCAAGGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTG
55010429 GAAGGCAAG
1 GAAGGCAAG
55010438 ATCTGCTTCT
Statistics
Matches: 67, Mismatches: 18, Indels: 18
0.65 0.17 0.17
Matches are distributed among these distances:
41 13 0.19
42 25 0.37
43 16 0.24
44 13 0.19
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (42 bp):
GAAGGCAAGGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTG
Found at i:55010386 original size:169 final size:169
Alignment explanation
Indices: 55010096--55010494 Score: 692
Period size: 169 Copynumber: 2.3 Consensus size: 169
55010086 GTAAGAAGAT
55010096 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
* * *
55010161 CGTTGTTAACGTTGGAAGGCAAGATCTGCTTCTTTAACCAACTCCATTGTAACCAATGAAGGCAA
66 CGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCCACTGCAACCAATGAAGGCAA
* * *
55010226 GGTTTTGTTTTCGA-TGTTTCGTTGTTAACGTTGGAAGGC
131 GG-CTTGTTTTCGACTGCTTCGTTGTTAACGCTGGAAGGC
55010265 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
*
55010330 CGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAA
66 CGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCCACTGCAACCAATGAAGGCAA
55010395 GGCTTGTTTTCGATCTGCTTCGTTGTTAACGCTGGAAGGC
131 GGCTTGTTTTCGA-CTGCTTCGTTGTTAACGCTGGAAGGC
*
55010435 AAGATCTGCTTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGAT
1 AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGC-TTGTTTTCGAT
55010495 GTTCACTGAT
Statistics
Matches: 219, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
168 10 0.05
169 128 0.58
170 70 0.32
171 11 0.05
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (169 bp):
AAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTT
CGTTGTTAACGCTGGAAGGCAAGATCTGCTTCTTTAACCAACTCCACTGCAACCAATGAAGGCAA
GGCTTGTTTTCGACTGCTTCGTTGTTAACGCTGGAAGGC
Found at i:55012716 original size:17 final size:18
Alignment explanation
Indices: 55012690--55012725 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
55012680 TTGATCTTGA
*
55012690 TTTTGATTTTTTTCTTCT
1 TTTTGATTTTTTTATTCT
55012708 TTTTG-TTTTTTTATTCT
1 TTTTGATTTTTTTATTCT
55012725 T
1 T
55012726 AAGCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTGATTTTTTTATTCT
Found at i:55015164 original size:19 final size:19
Alignment explanation
Indices: 55015140--55015182 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
55015130 GTGAAAATCT
* *
55015140 AATGCATATG-ATGCAATG
1 AATGCAAATGCATGAAATG
55015158 CAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
55015178 AATGC
1 AATGC
55015183 CTAAAGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:55017093 original size:13 final size:13
Alignment explanation
Indices: 55017061--55017099 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55017051 GCGCAAATGC
55017061 ATATGAATAT-TAT
1 ATAT-AATATATAT
55017074 ATA-AATATATAT
1 ATATAATATATAT
55017086 ATATAATATATAT
1 ATATAATATATAT
55017099 A
1 A
55017100 AAAATGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:55017369 original size:15 final size:13
Alignment explanation
Indices: 55017305--55017379 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
55017295 CTAAACTATC
55017305 ATATAATAATAAT
1 ATATAATAATAAT
*
55017318 ATGATGAATAAAAAT
1 AT-AT-AATAATAAT
55017333 GATATAAATAATAAT
1 -ATAT-AATAATAAT
*
55017348 AGA-AATAATAAT
1 ATATAATAATAAT
*
55017360 -CATAATAATAA-
1 ATATAATAATAAT
55017371 ATGATAATA
1 AT-ATAATA
55017380 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 1 0.02
12 17 0.34
13 8 0.16
14 4 0.08
15 18 0.36
16 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:55025398 original size:29 final size:29
Alignment explanation
Indices: 55025346--55025423 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
55025336 CAGATTTAGT
55025346 TATATATATACATAAATACATTTTCATAA-
1 TATATATATACATAAATACATTTT-ATAAC
* * **
55025375 TATATATGTACATATATATTTTTTATAAC
1 TATATATATACATAAATACATTTTATAAC
* *
55025404 T-TATATATATATACATACAT
1 TATATATATACATAAATACAT
55025424 ACATACATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (29 bp):
TATATATATACATAAATACATTTTATAAC
Found at i:55025497 original size:47 final size:47
Alignment explanation
Indices: 55025445--55025535 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
55025435 TACGTACTCA
* * *
55025445 TATATATATTTTATATATTT-TGTAATTTATATACATGTTTATATATC
1 TATATATATTTTATATTTTTATG-AATATATATACATGCTTATATATC
*
55025492 TATATATATTTTCTATTTTTATGAATATATATACATGCTTATAT
1 TATATATATTTTATATTTTTATGAATATATATACATGCTTATAT
55025536 TTTTTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 37 0.95
48 2 0.05
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (47 bp):
TATATATATTTTATATTTTTATGAATATATATACATGCTTATATATC
Found at i:55026215 original size:108 final size:108
Alignment explanation
Indices: 55025936--55026251 Score: 492
Period size: 109 Copynumber: 2.9 Consensus size: 108
55025926 AAAGAAAATT
* * *
55025936 TTTCAAAGTAAGGCAATATTTTGTGTTTGGAAATTTGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
55026001 CGATCTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
66 CGAT-TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
* *
55026045 TTCCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
55026110 CGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAA-AA
66 CGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
* * * **
55026153 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCAAGAAAACGTGCTTTAATGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
55026218 CGA-TTTCTCATTGGACCAAATAGCCAAATATCCT
66 CGATTTTCTCGTTCGACCAAATAGCCAAATATCCT
55026252 CTTATATCTT
Statistics
Matches: 192, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
106 29 0.15
108 63 0.33
109 99 0.52
110 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (108 bp):
TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
Found at i:55029937 original size:3 final size:3
Alignment explanation
Indices: 55029931--55029980 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
55029921 AAAAAATAAG
*
55029931 GAA GAA GAA GAA -AA -AA GAAA GAA GAA GAA GAA -AA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA
55029974 -AA GAA GA
1 GAA GAA GA
55029981 GGCTAAGGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55029938 original size:20 final size:20
Alignment explanation
Indices: 55029921--55029980 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
55029911 AAAAAAGAGA
* *
55029921 AAAAAATAAGGAAGAAGAAG
1 AAAAAAGAAAGAAGAAGAAG
55029941 AAAAAAGAAAGAAGAAGAAG
1 AAAAAAGAAAGAAGAAGAAG
55029961 AAAAGAA-AAAGAA-AAGAAG
1 AAAA-AAGAAAGAAGAAGAAG
55029980 A
1 A
55029981 GGCTAAGGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAAGAAGAAGAAG
Found at i:55029952 original size:17 final size:17
Alignment explanation
Indices: 55029910--55029973 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
55029900 AAAAACATTT
*
55029910 AAAA-AAAG-AGAAAAA
1 AAAAGAAAGAAGAAGAA
*
55029925 AATAAGGAAGAAGAAGAA
1 AA-AAGAAAGAAGAAGAA
55029943 AAAAGAAAGAAGAAGAA
1 AAAAGAAAGAAGAAGAA
55029960 GAAAAGAAA-AAGAA
1 -AAAAGAAAGAAGAA
55029974 AAGAAGAGGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 22 0.52
18 16 0.38
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAGAAGAA
Found at i:55029954 original size:14 final size:13
Alignment explanation
Indices: 55029935--55029980 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
55029925 AATAAGGAAG
55029935 AAGAAGAAAAAAGA
1 AAGAAG-AAAAAGA
*
55029949 AAGAAGAAGAAG-
1 AAGAAGAAAAAGA
55029961 AA-AAGAAAAAGAA
1 AAGAAGAAAAAG-A
55029974 AAGAAGA
1 AAGAAGA
55029981 GGCTAAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 7 0.26
14 10 0.37
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:55031369 original size:89 final size:89
Alignment explanation
Indices: 55031218--55031530 Score: 435
Period size: 89 Copynumber: 3.6 Consensus size: 89
55031208 CAGATCAGTC
*
55031218 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTTC
* * *
55031283 CTGTACTGACAGTGGAGCAAACTT
66 CTGTACTGACAGCGGAGCAGACTG
* * * *
55031307 AAGATAGCAGATCTTGCCTTCTTGTACTGACGGCGAAGCAGATCGAAAACACCAACCTTGCCTTT
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTTC
55031372 CTGTACTGACAGCGGAGCAGACTG
66 CTGTACTGACAGCGGAGCAGACTG
* * * *
55031396 AGGATAGTAGATCTTGCCTT-C---AC-G---GTGAAGCAGATCGAAGACACCATCCTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTTC
55031453 CTGTACTGACAGCGGAGCAGACTG
66 CTGTACTGACAGCGGAGCAGACTG
* * *
55031477 AAGATAGCAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATTGAAGACACCA
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
55031531 TAGTTTGCAG
Statistics
Matches: 198, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
81 71 0.36
82 1 0.01
84 1 0.01
85 4 0.02
86 1 0.01
89 120 0.61
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (89 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTTC
CTGTACTGACAGCGGAGCAGACTG
Found at i:55031461 original size:81 final size:81
Alignment explanation
Indices: 55031336--55031497 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 81
55031326 TCTTGTACTG
* *
55031336 ACGGCGAAGCAGATCGAAAACACCAACCTTGCCTTTCTGTACTGACAGCGGAGCAGACTGAGGAT
1 ACGGCGAAGCAGATCGAAAACACCAACCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGAT
*
55031401 AGTAGATCTTGCCTTC
66 AGCAGATCTTGCCTTC
* * *
55031417 ACGGTGAAGCAGATCGAAGACACCATCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGAT
1 ACGGCGAAGCAGATCGAAAACACCAACCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGAT
55031482 AGCAGATCTTGCCTTC
66 AGCAGATCTTGCCTTC
55031498 CTATACTGAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.21
Consensus pattern (81 bp):
ACGGCGAAGCAGATCGAAAACACCAACCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGAT
AGCAGATCTTGCCTTC
Found at i:55031610 original size:44 final size:44
Alignment explanation
Indices: 55031544--55031899 Score: 182
Period size: 44 Copynumber: 8.1 Consensus size: 44
55031534 TTTGCAGCAA
* * *
55031544 AGCAGATTAAAGATAACA-AATCTTATCTCCCTAAGCAGTAGTGG
1 AGCAGATTGAAGAT-GCAGAATCCTATCTCCCTAAGCAGTAGTGG
* * * * * * *
55031588 AGCAGATCGAAGATGAAGAATCTTATCTTCCC-AAGTTAGTGGAGA
1 AGCAGATTGAAGATGCAGAATCCTATC-TCCCTAAG-CAGTAGTGG
* * * * *
55031633 AGCAGATTTAAGCAAT-TAG--TCCTATCTCCCGAAACAGTGGTGG
1 AGCAGATTGAAG--ATGCAGAATCCTATCTCCCTAAGCAGTAGTGG
* *
55031676 AGTAGGTTGAAGATTGCAG-ATCCTATCTCCCTAAGCAGTAGTGG
1 AGCAGATTGAAGA-TGCAGAATCCTATCTCCCTAAGCAGTAGTGG
* ** * *
55031720 AGCAGATCGAAGATGGTGAATCTTATTTTCCC-AAG-A-TAGTGG
1 AGCAGATTGAAGATGCAGAATCCTA-TCTCCCTAAGCAGTAGTGG
* * *
55031762 AGAAACAGATTTAAGCCAT-TAG--CCCTATCTCCCTAAGCAGTAGTGG
1 AG---CAGATTGAAG--ATGCAGAATCCTATCTCCCTAAGCAGTAGTGG
* * * *
55031808 AGTAGGTTGAAGATTGCAG-ATTCTGTCTCCCTAAGCAGTAGTGG
1 AGCAGATTGAAGA-TGCAGAATCCTATCTCCCTAAGCAGTAGTGG
** * * *
55031852 AATAGGTTGAAGATTGCAG-ATTCTGTCTCCCTAAGCAGTAGTGG
1 AGCAGATTGAAGA-TGCAGAATCCTATCTCCCTAAGCAGTAGTGG
55031896 AGCA
1 AGCA
55031900 AATCAAAGAC
Statistics
Matches: 243, Mismatches: 47, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
41 2 0.01
42 10 0.04
43 40 0.16
44 143 0.59
45 33 0.14
46 11 0.05
47 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
AGCAGATTGAAGATGCAGAATCCTATCTCCCTAAGCAGTAGTGG
Found at i:55031865 original size:132 final size:132
Alignment explanation
Indices: 55031567--55031852 Score: 464
Period size: 132 Copynumber: 2.2 Consensus size: 132
55031557 TAACAAATCT
*
55031567 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGAATCTTATCTTCCCAAGTTAGTGGAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGAATCTTATCTTCCCAAGATAGTGGAG
* * *
55031632 AAGCAGATTTAAGCAATTAGTCCTATCTCCCGAAACAGTGGTGGAGTAGGTTGAAGATTGCAGAT
66 AAACAGATTTAAGCAATTAGCCCTATCTCCCGAAACAGTAGTGGAGTAGGTTGAAGATTGCAGAT
55031697 CC
131 CC
** *
55031699 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATTTTCCCAAGATAGTGGAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGAATCTTATCTTCCCAAGATAGTGGAG
* * *
55031764 AAACAGATTTAAGCCATTAGCCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGAT
66 AAACAGATTTAAGCAATTAGCCCTATCTCCCGAAACAGTAGTGGAGTAGGTTGAAGATTGCAGAT
*
55031829 TC
131 CC
*
55031831 TGTCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGA
55031853 ATAGGTTGAA
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 142 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAAGAATCTTATCTTCCCAAGATAGTGGAG
AAACAGATTTAAGCAATTAGCCCTATCTCCCGAAACAGTAGTGGAGTAGGTTGAAGATTGCAGAT
CC
Found at i:55031967 original size:50 final size:50
Alignment explanation
Indices: 55031912--55032057 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 50
55031902 TCAAAGACAG
* *
55031912 TGAATCATACTTCCCTTGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
1 TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
* * * ** * ** * * *
55031962 TGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCTGCAACGG
1 TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
* * *
55032012 TGAATTTTACTTCCCTAGCGGTGTAGTGGGGACAGATTGAAGCTAC
1 TGAATCTTACTTCCCTAGCGGTGCAGT-GGAACAGATTGAAGCTAC
55032058 GACAGCGAAT
Statistics
Matches: 69, Mismatches: 26, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
50 56 0.81
51 13 0.19
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (50 bp):
TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
Found at i:55032085 original size:101 final size:100
Alignment explanation
Indices: 55031919--55032104 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 100
55031909 CAGTGAATCA
* *
55031919 TACTTCCCTTGCGGTGCAGTGGAACAGATTGAAGCTACAACGATGAATCTTGCTTCCCCAACATT
1 TACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCCCCAACATT
55031984 GCAATTAAAAAGATTGAAGCTGCAACGGTGAATTT
66 GCAATTAAAAAGATTGAAGCTGCAACGGTGAATTT
* * * *
55032019 TACTTCCCTAGCGGTGTAGTGGGGACAGATTGAAGCTACGAC-AGCGAATCTTGCTTCCCCGACA
1 TACTTCCCTAGCGGTGCAGT-GGAACAGATTGAAGCTACAACGA-CGAATCTTGCTTCCCCAACA
* *
55032083 TTGTAGTTAAAAAGATTGAAGC
64 TTGCAATTAAAAAGATTGAAGC
55032105 CATACATTAC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 19 0.25
101 57 0.75
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
TACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCCCCAACATT
GCAATTAAAAAGATTGAAGCTGCAACGGTGAATTT
Found at i:55032254 original size:44 final size:43
Alignment explanation
Indices: 55032159--55032493 Score: 205
Period size: 44 Copynumber: 7.8 Consensus size: 43
55032149 TCGCGTCCAG
* * ** *
55032159 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGACGAAAGA-AACTAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA-ATCAC-AA
* * *
55032203 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACA-A
** ** * ***
55032247 TCTTATCTATCTAAAGTTGCAGTATAGTAGA-TCGCATC-CAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAA
* * * ** *
55032288 TTTTATCTTCCTGAAGTTGCAGTGGAGCAGACAGAAGAAGC-CAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAA-AATCACAA
* * * *
55032332 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCATAGA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACA-A
** * * *** *
55032376 TCTTATCTTTCTGAAGTTGCAGTTGAGCAGA-TCGCATC-CAG
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAA
* * * *
55032417 TCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTGAAGATAACAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAATCACAA
* *
55032461 TCTTATCTCCCTAAAGTTACAGTGGAGAAGATT
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT
55032494 GAAGCTGTTA
Statistics
Matches: 216, Mismatches: 65, Indels: 20
0.72 0.22 0.07
Matches are distributed among these distances:
41 50 0.23
42 7 0.03
43 14 0.06
44 145 0.67
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAA
Found at i:55032343 original size:129 final size:127
Alignment explanation
Indices: 55032113--55032487 Score: 473
Period size: 129 Copynumber: 2.9 Consensus size: 127
55032103 GCCATACATT
* * * * *
55032113 ACAGATCTTATTTCTCTGAAGTTACAGTAGAGCAGATCGCGTCCAGTCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTATCTGAAGTTGCAGTATAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
* * * *
55032178 CAGTGGAGAAGACGAAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC
66 CAGTGGAGCAGACG-AAG-AACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
* * * * *
55032242 ACAGATCTTATCTATCTAAAGTTGCAGTATAGTAGATCGCATCCAATTTTATCTTCCTGAAGTTG
1 ACAGATCTTATCTATCTGAAGTTGCAGTATAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
55032307 CAGTGGAGCAGACAGAAGAAGCCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
66 CAGTGGAGCAGAC-GAAGAA-CCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
* * *
55032371 ATAGATCTTATCTTTCTGAAGTTGCAGT-TGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTT
1 ACAGATCTTATCTATCTGAAGTTGCAGTAT-AGCAGATCGCATCCAGTCTTATCTCCCTGAAGTT
* ** * * *
55032435 GTAGTGGAGCAGGTTGAAGATAACAATCTTATCTCCCTAAAGTTACAGTGGAG
65 GCAGTGGAGCA-GACGAAGA-ACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
55032488 AAGATTGAAG
Statistics
Matches: 213, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
128 3 0.01
129 207 0.97
130 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (127 bp):
ACAGATCTTATCTATCTGAAGTTGCAGTATAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
CAGTGGAGCAGACGAAGAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
Found at i:55032464 original size:85 final size:85
Alignment explanation
Indices: 55032117--55032492 Score: 239
Period size: 85 Copynumber: 4.4 Consensus size: 85
55032107 TACATTACAG
* * ** *
55032117 ATCTTAT-TTCTCTGAAGTTACAGTAGAGCAGATCGCGTCCAGTCTTATCTCCCTGAAGTTGCAG
1 ATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGATCGAATCCAGTCTTATCTCCCTAAAGTTGCAG
* *
55032181 TGGAG-AAGACGAAAGA-AACTA
65 TGGAGCAGGTCG-AAGATAAC-A
* * * ** **
55032202 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTATCTAAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TCGAATC-CAG-TCTTATCTCCCTAAAGTTGC
** * * * *
55032267 AGTATAGTAGATCG--CAT-CCA
63 AGTGGAGCAGGTCGAAGATAACA
* * * *
55032287 ATTTTATCTTCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAGCCAATCCTATCTCCCTAAAGTTG
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATC----GAATCCAGTCTTATCTCCCTAAAGTTG
* * ** *
55032351 CAGTGGAGC-GGAT-TAAAACCATA
62 CAGTGGAGCAGG-TCGAAGATAACA
* * * *
55032374 GATCTTATCTTTCTGAAGTTGCAGTTGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGTAG
1 -ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATCGAATCCAGTCTTATCTCCCTAAAGTTGCAG
*
55032439 TGGAGCAGGTTGAAGATAACA
65 TGGAGCAGGTCGAAGATAACA
* * * *
55032460 ATCTTATCTCCCTAAAGTTACAGTGGAGAAGAT
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
55032493 TGAAGCTGTT
Statistics
Matches: 215, Mismatches: 58, Indels: 36
0.70 0.19 0.12
Matches are distributed among these distances:
84 1 0.00
85 135 0.63
86 17 0.08
87 7 0.03
88 51 0.24
89 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (85 bp):
ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATCGAATCCAGTCTTATCTCCCTAAAGTTGCAGT
GGAGCAGGTCGAAGATAACA
Found at i:55034230 original size:47 final size:47
Alignment explanation
Indices: 55034152--55034242 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
55034142 TACGTACTCG
* *
55034152 TATATATATTTTATATATTTTGTAATTTATATACATGTTTATATATC
1 TATATATATTTTATATATTTTGTAATATATATACATGCTTATATATC
* *
55034199 TATATATATTTTCTAT-TTTTATGAATATATATACATGCTTATAT
1 TATATATATTTTATATATTTTGT-AATATATATACATGCTTATAT
55034243 TTTTTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 5 0.13
47 34 0.87
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (47 bp):
TATATATATTTTATATATTTTGTAATATATATACATGCTTATATATC
Found at i:55034844 original size:109 final size:107
Alignment explanation
Indices: 55034653--55034964 Score: 475
Period size: 109 Copynumber: 2.9 Consensus size: 107
55034643 GAAAAATTTT
*
55034653 CAAAGTAAGGCAATATTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA
1 CAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA
** *
55034718 TCTTTCTATTTCGACCAAATAGCTAAATATCCTTTTAATAATTC
66 T-TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAA-AATTC
* * *
55034762 CAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGTTGGGTTTCGA
1 CAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA
*
55034827 TTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTT
66 -TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTC
* * *
55034870 CAAAATAAGGCAATGTTTTGTGTTTGGAAATTCAAGAAAA-GTGCTCTAATGTGCTGGGTTTCGA
1 CAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA
*
55034934 -TTTCTCGTTGGACCAAATAGCCAAATATCCT
66 TTTTCTCGTTCGACCAAATAGCCAAATATCCT
55034965 CTTATATCTT
Statistics
Matches: 187, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
105 30 0.16
107 21 0.11
108 41 0.22
109 94 0.50
110 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (107 bp):
CAAAGTAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA
TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTC
Found at i:55036778 original size:29 final size:29
Alignment explanation
Indices: 55036727--55036786 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
55036717 TCTTTATAAA
*
55036727 TTTAAAGGATTAAATTAATATTTTATTAT
1 TTTAAAGGATTAAAATAATATTTTATTAT
*
55036756 TTTAAAGTATTAAAAT-ATAATTTTATTAT
1 TTTAAAGGATTAAAATAAT-ATTTTATTAT
55036785 TT
1 TT
55036787 ATTAACTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTAAAGGATTAAAATAATATTTTATTAT
Found at i:55043321 original size:50 final size:50
Alignment explanation
Indices: 55043253--55043353 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
55043243 AAATGACTAA
55043253 TACAATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACT
1 TACAATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACT
*
55043303 TACAATTATGTTTAACCATATATACCATGTAACCAAGTAATCAACTAACT
1 TACAATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACT
55043353 T
1 T
55043354 TTATGTCTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (50 bp):
TACAATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACT
Found at i:55045120 original size:22 final size:22
Alignment explanation
Indices: 55045080--55045122 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55045070 GCACTAATGA
**
55045080 ACAGAGAGCACTGAAGTGCTAT
1 ACAGAGAGCAAAGAAGTGCTAT
*
55045102 ACAGAGAGCAAAGATGTGCTA
1 ACAGAGAGCAAAGAAGTGCTA
55045123 AATGGAGAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCAAAGAAGTGCTAT
Found at i:55046128 original size:5 final size:5
Alignment explanation
Indices: 55046114--55046166 Score: 79
Period size: 5 Copynumber: 10.2 Consensus size: 5
55046104 TTTACTTTAT
*
55046114 ATATA TATATA ATATA ATATA ATATA ATATA ATATT ATAATA ATATA ATATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
55046166 A
1 A
55046167 CAACATACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 35 0.80
6 9 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:55046156 original size:26 final size:26
Alignment explanation
Indices: 55046114--55046166 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
55046104 TTTACTTTAT
55046114 ATATATATATAATATAATATAATATA
1 ATATATATATAATATAATATAATATA
*
55046140 ATATA-ATATTATAATAATATAATATA
1 ATATATATATAAT-ATAATATAATATA
55046166 A
1 A
55046167 CAACATACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATATATATAATATAATATAATATA
Found at i:55048418 original size:11 final size:11
Alignment explanation
Indices: 55048400--55048437 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55048390 AGAAACTTTC
55048400 TAATTTCACTTT
1 TAATTTCA-TTT
55048412 T-ATTTCATTT
1 TAATTTCATTT
*
55048422 TAATTTCAATT
1 TAATTTCATTT
55048433 TAATT
1 TAATT
55048438 ACAATTTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 19 0.79
12 1 0.04
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (11 bp):
TAATTTCATTT
Found at i:55050606 original size:24 final size:20
Alignment explanation
Indices: 55050551--55050589 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55050541 CAGGAAAACT
55050551 TGAAAAATTGTAGTTATGAG
1 TGAAAAATTGTAGTTATGAG
55050571 TGAAAAATTGTAGTTATGA
1 TGAAAAATTGTAGTTATGA
55050590 AGATAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (20 bp):
TGAAAAATTGTAGTTATGAG
Found at i:55053989 original size:18 final size:15
Alignment explanation
Indices: 55053944--55053977 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
55053934 ATTCTTCCAG
*
55053944 TTTTCTTCTTCTTCT
1 TTTTCTTTTTCTTCT
55053959 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
55053974 TTTT
1 TTTT
55053978 GCTGATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:55054815 original size:3 final size:3
Alignment explanation
Indices: 55054807--55054833 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55054797 ATAGTATATG
55054807 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT
55054834 ATTAAGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:55060886 original size:30 final size:30
Alignment explanation
Indices: 55060818--55060887 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
55060808 AGAAAAGGAG
**
55060818 GAAAAATGACAGCTCCGTTAAGTCTGTAAC
1 GAAAAATGGTAGCTCCGTTAAGTCTGTAAC
* * *
55060848 GAAAAATGGTAGCTCCGTTATGTTTGTAAT
1 GAAAAATGGTAGCTCCGTTAAGTCTGTAAC
*
55060878 GGAAAATGGT
1 GAAAAATGGT
55060888 TAATGGTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (30 bp):
GAAAAATGGTAGCTCCGTTAAGTCTGTAAC
Found at i:55071273 original size:29 final size:29
Alignment explanation
Indices: 55071231--55071290 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
55071221 TGAATTTCTC
55071231 AAAAATACAAGAGCCCAATGGATCTTGAT
1 AAAAATACAAGAGCCCAATGGATCTTGAT
55071260 AAAAATACAAGAGCCCAATGGATCTTGAT
1 AAAAATACAAGAGCCCAATGGATCTTGAT
55071289 AA
1 AA
55071291 TTTTTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (29 bp):
AAAAATACAAGAGCCCAATGGATCTTGAT
Found at i:55075206 original size:9 final size:9
Alignment explanation
Indices: 55075192--55075285 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
55075182 TTTGGTTAAA
55075192 AATTAACCG
1 AATTAACCG
55075201 AATTAACCG
1 AATTAACCG
*
55075210 AATTACCCG
1 AATTAACCG
55075219 AATTAACCG
1 AATTAACCG
*
55075228 AATTACCCG
1 AATTAACCG
**
55075237 AATTAATTG
1 AATTAACCG
55075246 AATTAACCG
1 AATTAACCG
*
55075255 AATTACCCG
1 AATTAACCG
55075264 AATTAACCG
1 AATTAACCG
*
55075273 AATTAACCT
1 AATTAACCG
55075282 AATT
1 AATT
55075286 GAATCATACA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:55084816 original size:19 final size:18
Alignment explanation
Indices: 55084764--55084817 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
55084754 TAACAAGTTG
55084764 AATTAGTTTATTAATTTTTT
1 AATTA-TTTATTAA-TTTTT
55084784 ATATT-TTTATTAATTTTT
1 A-ATTATTTATTAATTTTT
55084802 AATTATTTATATAATT
1 AATTATTTAT-TAATT
55084818 ATTGTTGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.10
18 11 0.35
19 13 0.42
20 1 0.03
21 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTATTTATTAATTTTT
Found at i:55084819 original size:26 final size:27
Alignment explanation
Indices: 55084765--55084820 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
55084755 AACAAGTTGA
* * **
55084765 ATTAGTTTATTAATTTTTTATATTTTT
1 ATTAATTTATTAATTATTTATATAATT
55084792 ATTAATTT-TTAATTATTTATATAATT
1 ATTAATTTATTAATTATTTATATAATT
55084818 ATT
1 ATT
55084821 GTTGATCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTAATTTATTAATTATTTATATAATT
Found at i:55086585 original size:3 final size:3
Alignment explanation
Indices: 55086577--55086624 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
55086567 AAGAGCAATT
* * *
55086577 ATA ATA ATA ATG ATA ACA ATA ATA ACA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55086624 A
1 A
55086625 AATTTGCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:55101462 original size:31 final size:29
Alignment explanation
Indices: 55101409--55101466 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
55101399 ACATGTGTAT
*
55101409 AATTACACTAAATCAAAGTTTATATATCA
1 AATTACACTAAATCAAAATTTATATATCA
*
55101438 AATTACACAGTAAATTAAAATTTATATAT
1 AATTACAC--TAAATCAAAATTTATATAT
55101467 AATTTTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.36
Consensus pattern (29 bp):
AATTACACTAAATCAAAATTTATATATCA
Found at i:55101470 original size:29 final size:27
Alignment explanation
Indices: 55101406--55101470 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
55101396 GTAACATGTG
*
55101406 TATAATTACACTAAATCAAAGTTTATA
1 TATAATTACACTAAATCAAAATTTATA
*
55101433 TATCAAATTACACAGTAAATTAAAATTTATA
1 TAT--AATTACAC--TAAATCAAAATTTATA
55101464 TATAATT
1 TATAATT
55101471 TTGATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
29 12 0.38
31 17 0.53
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (27 bp):
TATAATTACACTAAATCAAAATTTATA
Found at i:55103188 original size:20 final size:21
Alignment explanation
Indices: 55103152--55103190 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55103142 TAGGCGCCAA
55103152 TGAATAAAATAATAATTTTTT
1 TGAATAAAATAATAATTTTTT
55103173 TGAATAAAAT-ATAATTTT
1 TGAATAAAATAATAATTTT
55103191 ATACTTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TGAATAAAATAATAATTTTTT
Found at i:55103399 original size:22 final size:21
Alignment explanation
Indices: 55103345--55103398 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
55103335 AAAACAGAAG
*
55103345 AAAGAAGAAAAGGAGGAAGGA
1 AAAGAAGAAAAGAAGGAAGGA
*
55103366 AGCAGAAGAAAAGAAGGAAGGA
1 A-AAGAAGAAAAGAAGGAAGGA
55103388 AAAGAAGAAAA
1 AAAGAAGAAAA
55103399 AAATTAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAAGAAGGAAGGA
Found at i:55106772 original size:16 final size:15
Alignment explanation
Indices: 55106741--55106782 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
55106731 ACAAAATCAA
*
55106741 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
55106756 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
55106772 ATAAAAATTAA
1 ATAAAAGTTAA
55106783 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:55107210 original size:22 final size:22
Alignment explanation
Indices: 55107185--55107519 Score: 160
Period size: 22 Copynumber: 15.0 Consensus size: 22
55107175 ACAAAATTAC
55107185 AAAATTACAATATTCATATAAA
1 AAAATTACAATATTCATATAAA
** *
55107207 AAAATTGTAATATTCATACAAAA
1 AAAATTACAATATTCATA-TAAA
*
55107230 TTATAATATTACAATATTCATACAAA
1 --A-AA-ATTACAATATTCATATAAA
*
55107256 AAAA-TATAATATTCATATAAAATTA
1 AAAATTACAATATTCATAT--AA--A
*
55107281 CAAAATTACAATATTCATACAAA
1 -AAAATTACAATATTCATATAAA
* *
55107304 AAAATTGCAATATTCATACAAAA
1 AAAATTACAATATTCATA-TAAA
*
55107327 CTATAATATTACAATATTCATACAAA
1 --A-AA-ATTACAATATTCATATAAA
* * *
55107353 AAATTTATAATATTC--AT-AC
1 AAAATTACAATATTCATATAAA
* *
55107372 AAAATTATAATATTCATA-CAA
1 AAAATTACAATATTCATATAAA
* *
55107393 AAAATTACTA-ATCCA-A-AACTA
1 AAAATTACAATATTCATATAA--A
* *
55107414 TAAA-TACAA-ATTTAATTATAAA
1 AAAATTACAATA-TTCA-TATAAA
* *
55107436 ATAATTACAATATTC--AT-AC
1 AAAATTACAATATTCATATAAA
*
55107455 AACATTACAATATTC--ATAAA
1 AAAATTACAATATTCATATAAA
* *
55107475 AAAATTATAATATTCATACAAA
1 AAAATTACAATATTCATATAAA
* * *
55107497 AAATTTAAAATATTCATACAAA
1 AAAATTACAATATTCATATAAA
55107519 A
1 A
55107520 TTCTAATCTA
Statistics
Matches: 243, Mismatches: 40, Indels: 60
0.71 0.12 0.17
Matches are distributed among these distances:
19 33 0.14
20 26 0.11
21 28 0.12
22 72 0.30
23 21 0.09
24 5 0.02
25 5 0.02
26 14 0.06
27 39 0.16
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.33
Consensus pattern (22 bp):
AAAATTACAATATTCATATAAA
Found at i:55107282 original size:97 final size:98
Alignment explanation
Indices: 55107163--55107378 Score: 380
Period size: 97 Copynumber: 2.2 Consensus size: 98
55107153 ATCCCCACAT
* *
55107163 TATAATATTCATACAAAATTACAAAATTACAATATTCATATAAAAAAATTGTAATATTCATACAA
1 TATAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAA
*
55107228 AATTATAATATTACAATATTCATACAAAAAA-A
66 AACTATAATATTACAATATTCATACAAAAAATA
*
55107260 TATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAA
1 TATAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAA
*
55107325 AACTATAATATTACAATATTCATACAAAAAATT
66 AACTATAATATTACAATATTCATACAAAAAATA
55107358 TATAATATTCATACAAAATTA
1 TATAATATTCATACAAAATTA
55107379 TAATATTCAT
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 92 0.82
98 20 0.18
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (98 bp):
TATAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATACAA
AACTATAATATTACAATATTCATACAAAAAATA
Found at i:55107364 original size:30 final size:27
Alignment explanation
Indices: 55107161--55107385 Score: 170
Period size: 27 Copynumber: 9.1 Consensus size: 27
55107151 ATATCCCCAC
* * * *
55107161 ATTATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAACTATAAT
*
55107188 ATTACAATATTCATATAAAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
*
55107212 -TGT--AATATTCATACAAAATTATAAT
1 AT-TACAATATTCATACAAAACTATAAT
55107237 ATTACAATATTCATACAAAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
* * * *
55107261 A-T--AATATTCATATAAAATTACAAA
1 ATTACAATATTCATACAAAACTATAAT
55107285 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAACTATAAT
*
55107307 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAACTATAAT
55107334 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAACTATAAT
* *
55107357 -TTATAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAACTATAAT
55107383 ATT
1 ATT
55107386 CATACAAAAA
Statistics
Matches: 165, Mismatches: 10, Indels: 46
0.75 0.05 0.21
Matches are distributed among these distances:
21 14 0.08
22 43 0.26
23 14 0.08
24 13 0.08
25 9 0.05
26 12 0.07
27 60 0.36
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAACTATAAT
Found at i:55107381 original size:49 final size:49
Alignment explanation
Indices: 55107161--55107385 Score: 344
Period size: 49 Copynumber: 4.6 Consensus size: 49
55107151 ATATCCCCAC
* * *
55107161 ATTATAATATTCATACAAAATTACAAAATTACAATATTCATATAAAAAA
1 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
*
55107210 ATTGTAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
1 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
* * *
55107259 A-TATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAAAA
1 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
** *
55107307 ATTGCAATATTCATACAAAACTATAATATTACAATATTCATACAAAAAA
1 ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
*
55107356 TTTATAATATTCATACAAAATTATAATATT
1 ATTATAATATTCATACAAAATTATAATATT
55107386 CATACAAAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 44 0.28
49 113 0.72
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (49 bp):
ATTATAATATTCATACAAAATTATAATATTACAATATTCATACAAAAAA
Found at i:55107699 original size:3 final size:3
Alignment explanation
Indices: 55107693--55107722 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
55107683 TTTTCTTTCT
55107693 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
55107723 CCTCCTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:55107702 original size:14 final size:15
Alignment explanation
Indices: 55107685--55107723 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
55107675 ACCTTTTTTT
55107685 TTCTTTCTT-TCTTC
1 TTCTTTCTTCTCTTC
55107699 TTC-TTCTTCTCTTC
1 TTCTTTCTTCTCTTC
55107713 TTC-TTCTTCTC
1 TTCTTTCTTCTC
55107724 CTCCTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTTCTTCTCTTC
Found at i:55107713 original size:17 final size:17
Alignment explanation
Indices: 55107689--55107733 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
55107679 TTTTTTTTCT
55107689 TTCT-TTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
55107705 TTCTCTTCTTCTTCTTC
1 TTCTCTTCTTCTTCTTC
* *
55107722 TCCTCCTCTTCT
1 TTCTCTTCTTCT
55107734 CCTCCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTCTTCTTCTTCTTC
Found at i:55107731 original size:14 final size:14
Alignment explanation
Indices: 55107700--55107739 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55107690 TCTTTCTTCT
* *
55107700 TCTTCTTCTCTTCT
1 TCTTCTTCTCCTCC
55107714 TCTTCTTCTCCTCC
1 TCTTCTTCTCCTCC
*
55107728 TCTTCTCCTCCT
1 TCTTCTTCTCCT
55107740 TTCTCTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTCTTCTCCTCC
Found at i:55107747 original size:17 final size:16
Alignment explanation
Indices: 55107691--55107748 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
55107681 TTTTTTCTTT
*
55107691 CTTTCTTCTTCTTCTT
1 CTTTCTTCTTCTTCTC
55107707 CTCTTCTTCTTCTTCTC
1 CT-TTCTTCTTCTTCTC
* *
55107724 C--TCCTCTTCTCCTC
1 CTTTCTTCTTCTTCTC
55107738 CTTTCTCTCTT
1 CTTTCT-TCTT
55107749 TTTTTTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 12 0.35
16 4 0.12
17 18 0.53
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (16 bp):
CTTTCTTCTTCTTCTC
Found at i:55115524 original size:42 final size:42
Alignment explanation
Indices: 55115353--55115535 Score: 206
Period size: 42 Copynumber: 4.4 Consensus size: 42
55115343 AAAGCTCATG
** * *
55115353 AGAGCTAAACAAAAACCCATAAGGGTTGAACAGAAGCTTGTAA
1 AGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTT-AAA
* * *
55115396 A-AGCTGAACGAAAACCCATAAGGGTTAAATAGAAGCTTAAA
1 AGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTTAAA
* *
55115437 AGAGCTGAACGGAAACCCATAAGGGTTAAACAGAAGCTCAAA
1 AGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTTAAA
* * * * **
55115479 AGAGCTAAACGGAAACTCATATGAGTTAAACAGAATCTTGTA
1 AGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTTAAA
*
55115521 AGAGCTAAACAGAAA
1 AGAGCTAAACGGAAA
55115536 GTAAAACATG
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
41 3 0.02
42 118 0.97
43 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (42 bp):
AGAGCTAAACGGAAACCCATAAGGGTTAAACAGAAGCTTAAA
Found at i:55115529 original size:21 final size:21
Alignment explanation
Indices: 55115347--55115535 Score: 83
Period size: 21 Copynumber: 9.0 Consensus size: 21
55115337 TGAATAAAAG
* *
55115347 CTCATGAGAGCTAAACAAAAA
1 CTCATAAGAGCTAAACAGAAA
* * * * *
55115368 CCCATAAGGGTTGAACAGAAG
1 CTCATAAGAGCTAAACAGAAA
** * *
55115389 CTTGTAAAAGCTGAAC-GAAAA
1 CTCATAAGAGCTAAACAG-AAA
* * * * *
55115410 CCCATAAGGGTTAAATAGAAG
1 CTCATAAGAGCTAAACAGAAA
* * * *
55115431 CTTAAAAGAGCTGAACGGAAA
1 CTCATAAGAGCTAAACAGAAA
* * * *
55115452 CCCATAAGGGTTAAACAGAAG
1 CTCATAAGAGCTAAACAGAAA
* *
55115473 CTCAAAAGAGCTAAACGGAAA
1 CTCATAAGAGCTAAACAGAAA
* * *
55115494 CTCATATGAGTTAAACAGAAT
1 CTCATAAGAGCTAAACAGAAA
**
55115515 CTTGTAAGAGCTAAACAGAAA
1 CTCATAAGAGCTAAACAGAAA
55115536 GTAAAACATG
Statistics
Matches: 110, Mismatches: 56, Indels: 4
0.65 0.33 0.02
Matches are distributed among these distances:
20 1 0.01
21 108 0.98
22 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
CTCATAAGAGCTAAACAGAAA
Found at i:55124071 original size:2 final size:2
Alignment explanation
Indices: 55124064--55124091 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55124054 TAATATCATT
55124064 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
55124092 TATATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:55129260 original size:29 final size:28
Alignment explanation
Indices: 55129227--55129306 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
55129217 TTTTTAAAAA
55129227 AAATATTTATATTATTTGAATTTAATATT
1 AAATATTTATATTATTT-AATTTAATATT
55129256 AAATAATTTA-A-TA-TT--TTT-A-ATT
1 AAAT-ATTTATATTATTTAATTTAATATT
*
55129278 AAAAATTTATATATATTTAATTTAATATT
1 AAATATTTATAT-TATTTAATTTAATATT
55129307 TTTTAATGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 18
0.68 0.02 0.30
Matches are distributed among these distances:
21 5 0.12
22 7 0.17
23 1 0.02
24 5 0.12
25 2 0.05
27 5 0.12
28 3 0.07
29 8 0.20
30 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
AAATATTTATATTATTTAATTTAATATT
Found at i:55129278 original size:22 final size:23
Alignment explanation
Indices: 55129253--55129304 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
55129243 TGAATTTAAT
*
55129253 ATTAAATAATTTA-ATATTTTTA
1 ATTAAATAATTTATATATATTTA
55129275 ATTAAA-AATTTATATATATTTA
1 ATTAAATAATTTATATATATTTA
*
55129297 ATTTAATA
1 ATTAAATA
55129305 TTTTTTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 19 0.73
23 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTAAATAATTTATATATATTTA
Found at i:55129400 original size:15 final size:17
Alignment explanation
Indices: 55129368--55129407 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
55129358 TATGTGTTAT
55129368 AAATTACATAATATATA
1 AAATTACATAATATATA
*
55129385 AAATTACATAATATAAA
1 AAATTACATAATATATA
55129402 AAATTA
1 AAATTA
55129408 TAAACTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTACATAATATATA
Found at i:55137441 original size:28 final size:30
Alignment explanation
Indices: 55137410--55137503 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 30
55137400 TTGTATTTAG
55137410 AATAAAAATTTAAATTATATTTATATTAAAT
1 AATAAAAATTTAAATTATATTTATATT-AAT
*
55137441 AATAAAATATATTTAAATTAT-TTTGTATT-A-
1 AAT-AAA-A-ATTTAAATTATATTTATATTAAT
* **
55137471 AA-AAAAATTTAAAATATATTTATGCTAAT
1 AATAAAAATTTAAATTATATTTATATTAAT
55137500 AATA
1 AATA
55137504 TTTTTCTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
26 10 0.20
27 6 0.12
28 4 0.08
29 2 0.04
30 3 0.06
31 4 0.08
32 3 0.06
33 8 0.16
34 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (30 bp):
AATAAAAATTTAAATTATATTTATATTAAT
Found at i:55137553 original size:20 final size:18
Alignment explanation
Indices: 55137529--55137564 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55137519 ATTATATAAT
55137529 ATTTTTTAAATATATTTA
1 ATTTTTTAAATATATTTA
55137547 ATTTTTTAAATATATTTA
1 ATTTTTTAAATATATTTA
55137565 TATCATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTAAATATATTTA
Found at i:55141028 original size:20 final size:20
Alignment explanation
Indices: 55141005--55141056 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
55140995 AACATTTCCT
55141005 TTAATTAATTTAAAAAAAAA
1 TTAATTAATTTAAAAAAAAA
* **
55141025 TTAATTCATTTAATTAAAAA
1 TTAATTAATTTAAAAAAAAA
**
55141045 CCAATTAATTTA
1 TTAATTAATTTA
55141057 CTTGGCTGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATTAATTTAAAAAAAAA
Found at i:55145996 original size:24 final size:24
Alignment explanation
Indices: 55145961--55146014 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
55145951 ATAAAGTTAC
* *
55145961 AATTGCCA-ATTGAGTTTCAGCTT
1 AATTGGCAGATTGAGTTTCAACTT
*
55145984 GATTGGCAGATTGAGTTTCAACTT
1 AATTGGCAGATTGAGTTTCAACTT
55146008 AATTGGC
1 AATTGGC
55146015 TTGGACATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (24 bp):
AATTGGCAGATTGAGTTTCAACTT
Found at i:55147468 original size:32 final size:32
Alignment explanation
Indices: 55147431--55147586 Score: 177
Period size: 32 Copynumber: 4.9 Consensus size: 32
55147421 CATGTTTTAT
* *
55147431 ATATTGCTGAATTGAATTGTATAGGTATAGAC
1 ATATTGCTGAATTGAATTGTATATGTATACAC
* * *
55147463 CTATTGTTGAATTGAATTGTATATATATACAC
1 ATATTGCTGAATTGAATTGTATATGTATACAC
* * ***
55147495 CTATTGCTGAAATGAATTGTATATGTATATTT
1 ATATTGCTGAATTGAATTGTATATGTATACAC
* * *
55147527 ATATTGCCGAATTTAATTGTATAGGTATACAC
1 ATATTGCTGAATTGAATTGTATATGTATACAC
* *
55147559 ATATTGCCGAATTGATTTGTATATGTAT
1 ATATTGCTGAATTGAATTGTATATGTAT
55147587 TTATGTATTG
Statistics
Matches: 102, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (32 bp):
ATATTGCTGAATTGAATTGTATATGTATACAC
Found at i:55147596 original size:32 final size:32
Alignment explanation
Indices: 55147417--55147597 Score: 132
Period size: 32 Copynumber: 5.7 Consensus size: 32
55147407 TAAATTTAAA
* *
55147417 TGTACATGT-TTTATATATTGCTGAATTGAAT
1 TGTATATGTATTTATATATTGCCGAATTGAAT
* ** ** **
55147448 TGTATAGGTATAGACCTATTGTTGAATTGAAT
1 TGTATATGTATTTATATATTGCCGAATTGAAT
* ** ** * *
55147480 TGTATATATATACACCTATTGCTGAAATGAAT
1 TGTATATGTATTTATATATTGCCGAATTGAAT
*
55147512 TGTATATGTATATT-TATATTGCCGAATTTAAT
1 TGTATATGTAT-TTATATATTGCCGAATTGAAT
* ** * *
55147544 TGTATAGGTATACACATATTGCCGAATTGATT
1 TGTATATGTATTTATATATTGCCGAATTGAAT
*
55147576 TGTATATGTATTTATGTATTGC
1 TGTATATGTATTTATATATTGC
55147598 TGATTTGATT
Statistics
Matches: 116, Mismatches: 31, Indels: 5
0.76 0.20 0.03
Matches are distributed among these distances:
31 7 0.06
32 109 0.94
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (32 bp):
TGTATATGTATTTATATATTGCCGAATTGAAT
Found at i:55150682 original size:20 final size:19
Alignment explanation
Indices: 55150653--55150694 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55150643 CCTTTTCAGA
55150653 ATATTGTATTAGAATTATAT
1 ATATTGTATTAGAATTA-AT
* *
55150673 ATATTTTATTAGTATTAAT
1 ATATTGTATTAGAATTAAT
55150692 ATA
1 ATA
55150695 CAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
ATATTGTATTAGAATTAAT
Found at i:55154093 original size:17 final size:17
Alignment explanation
Indices: 55154067--55154112 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
55154057 AATTTTGGAA
*
55154067 TTTT-ATTTTTATTATT
1 TTTTAATTTTTATAATT
55154083 TTTTAATTTTT-TAATT
1 TTTTAATTTTTATAATT
55154099 TTTCTAGATTTTTA
1 TTT-TA-ATTTTTA
55154113 AATGAGGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.44
17 8 0.32
18 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTAATTTTTATAATT
Found at i:55154301 original size:23 final size:23
Alignment explanation
Indices: 55154273--55154317 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
55154263 ATCTTTAAAA
*
55154273 TTTATACATATTTGATAAAAGAG
1 TTTATACATATTTAATAAAAGAG
*
55154296 TTTATATATATTTAATAAAAGA
1 TTTATACATATTTAATAAAAGA
55154318 ACATGTCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (23 bp):
TTTATACATATTTAATAAAAGAG
Found at i:55165006 original size:43 final size:43
Alignment explanation
Indices: 55164896--55165059 Score: 154
Period size: 43 Copynumber: 3.8 Consensus size: 43
55164886 TTTCTGATAA
* * *
55164896 GTATTTTCATGTAAGACCACGTCTGGGATGATGGAATTGATTT
1 GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
* ** *
55164939 ATATTTTTGTGTAAAACCACGTCTGGGACGATGGCATCGATTT
1 GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
** *
55164982 GTATTTTCGA-GTAAGACCTTGTCTGGGA-TAGTGGCATCGATTT
1 GTATTTTC-ATGTAAGACCACGTCTGGGACGA-TGGCATCGATTT
* * * *
55165025 GCGA-TTACATGTAAGACCATGTCTAGGACGATGGC
1 G-TATTTTCATGTAAGACCACGTCTGGGACGATGGC
55165060 GTTGTATGAA
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 2 0.02
43 93 0.96
44 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
Found at i:55170885 original size:18 final size:18
Alignment explanation
Indices: 55170864--55170906 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
55170854 CATTCTTCTC
* *
55170864 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTACCCCTT
55170882 CCCTTTCCCCTACCCCTT
1 CCCTTTCCCCTACCCCTT
55170900 CCCTTTC
1 CCCTTTC
55170907 TCGTTTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40
Consensus pattern (18 bp):
CCCTTTCCCCTACCCCTT
Found at i:55171392 original size:25 final size:25
Alignment explanation
Indices: 55171355--55171409 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
55171345 TTTCTGAATA
55171355 TGTTTAAGGGCCAAAGTCACTTCTT
1 TGTTTAAGGGCCAAAGTCACTTCTT
*
55171380 TGTTTAAGTGCCAAAGTCACTTCTT
1 TGTTTAAGGGCCAAAGTCACTTCTT
55171405 TGTTT
1 TGTTT
55171410 GTACATTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (25 bp):
TGTTTAAGGGCCAAAGTCACTTCTT
Found at i:55173421 original size:20 final size:20
Alignment explanation
Indices: 55173396--55173435 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55173386 AATATTTTCC
*
55173396 AGTAAACCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
* *
55173416 AGTAAAATATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55173436 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Done.