Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 159 of 279
Found at i:52345453 original size:14 final size:14
Alignment explanation
Indices: 52345434--52345469 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52345424 CCCTAACTTG
*
52345434 ACCCTTAACCCCTA
1 ACCCTTAACCCATA
52345448 ACCCTTAACCCATA
1 ACCCTTAACCCATA
*
52345462 AACCTTAA
1 ACCCTTAA
52345470 ATCACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (14 bp):
ACCCTTAACCCATA
Found at i:52345511 original size:14 final size:15
Alignment explanation
Indices: 52345492--52345524 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
52345482 CTTAAATCAG
52345492 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
52345506 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
52345521 AATC
1 AATC
52345525 TATAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:52346243 original size:145 final size:146
Alignment explanation
Indices: 52346091--52346388 Score: 526
Period size: 145 Copynumber: 2.0 Consensus size: 146
52346081 ATTTAGGAAA
*
52346091 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
1 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGAAAACGCCGCTATTGCTTACCTTT
* * *
52346156 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCATTCTGCTA
52346221 TTCT-AATTTTTTATT
131 TTCTAAATTTTTTATT
*
52346236 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGCCGCTATTGCTTACCTTT
1 TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGAAAACGCCGCTATTGCTTACCTTT
52346301 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCATTCTGCTA
66 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCATTCTGCTA
52346366 TTCTAACAATTTTTTATT
131 TTCT-A-AATTTTTTATT
52346384 TTTTT
1 TTTTT
52346389 ATACGCTTTG
Statistics
Matches: 145, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
145 129 0.89
148 16 0.11
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (146 bp):
TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGAAAACGCCGCTATTGCTTACCTTT
AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAACGACGCCATTCTGCTA
TTCTAAATTTTTTATT
Found at i:52346425 original size:181 final size:179
Alignment explanation
Indices: 52346214--52346571 Score: 621
Period size: 181 Copynumber: 2.0 Consensus size: 179
52346204 ACGACGCCGT
52346214 TTTGCTATTCTAATTTTTTATTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGA
1 TTTGCTATTCTAATTTTTTA-TTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGA
*
52346279 AACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGA
65 AACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGA
52346344 AAAAAACGACGCC-ATTCTGCTATTCTAACAATTTTTTATTTTTTTATACGC
130 AAAAAACGACGCCGATT-TGCTATTCTAA-AATTTTTTATTTTTTTATACGC
*
52346395 TTTGCTATTCTAAAATTTTTTA-TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGG
1 TTTGCTATTCT--AATTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGG
52346459 AAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTG
64 AAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTG
* *
52346524 AACAAAACGACGCCGCTTTGCTATTCTAAAATTTTTTATTTTTTTATA
129 AAAAAAACGACGCCGATTTGCTATTCTAAAATTTTTTATTTTTTTATA
52346572 AATTGATTTA
Statistics
Matches: 170, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
180 19 0.11
181 140 0.82
182 2 0.01
183 9 0.05
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (179 bp):
TTTGCTATTCTAATTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAA
ACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAA
AAAAACGACGCCGATTTGCTATTCTAAAATTTTTTATTTTTTTATACGC
Found at i:52346693 original size:326 final size:324
Alignment explanation
Indices: 52346090--52346716 Score: 1132
Period size: 326 Copynumber: 1.9 Consensus size: 324
52346080 AATTTAGGAA
52346090 ATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTT
1 ATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTT
* *
52346155 TAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTGCT
66 TAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCT
52346220 ATTCTAATTTTTTATTTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGCC
131 ATTCTAATTTTTTA-TTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGCC
*
52346285 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAA
195 GCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAA
52346350 CGACGCCATTCTGCTATTCTAACAATTTTTTATTTTTTTATACGCTTTGCTATTCTAAAATTTTT
260 CGACGCCATTCTGCTATTCTAA-AATTTTTTATTTTTTTATACGCTTTGCTATTCTAAAATTTTT
52346415 T
324 T
*
52346416 ATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGCCGCTATTGCTTACCTT
1 ATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTT
52346481 TAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCT
66 TAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCT
*
52346546 ATTCTAAAATTTTTTA-TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGGAAACGC
131 ATTCT--AATTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGC
*
52346610 CGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAA
194 CGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAA
*
52346675 ACGACGCCGCTT-TGCTATTCTAAAATTTTTTATTTTTTTATA
259 ACGACGCC-ATTCTGCTATTCTAAAATTTTTTATTTTTTTATA
52346717 AATTGATTTA
Statistics
Matches: 291, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
325 19 0.07
326 261 0.90
327 2 0.01
328 9 0.03
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (324 bp):
ATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTT
TAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGCTTTGCT
ATTCTAATTTTTTATTTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTATATAGGAAACGCCG
CTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTTTGAAAAAAAC
GACGCCATTCTGCTATTCTAAAATTTTTTATTTTTTTATACGCTTTGCTATTCTAAAATTTTTT
Found at i:52346796 original size:145 final size:145
Alignment explanation
Indices: 52346392--52346781 Score: 771
Period size: 145 Copynumber: 2.7 Consensus size: 145
52346382 TTTTTTTATA
52346392 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
1 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
52346457 GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTT
66 GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTT
52346522 TGAACAAAACGACGC
131 TGAACAAAACGACGC
52346537 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
1 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
52346602 GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTT
66 GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTT
52346667 TGAACAAAACGACGC
131 TGAACAAAACGACGC
52346682 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
1 CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
*
52346747 GGAAACGCCGCTATTGCTTACCTTTAGCGACGCTT
66 GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTT
52346782 TACAAAAAAC
Statistics
Matches: 244, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 244 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (145 bp):
CGCTTTGCTATTCTAAAATTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATA
GGAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCATATAAAGCGCCGCAAAATTTTTTCATTT
TGAACAAAACGACGC
Found at i:52346864 original size:73 final size:72
Alignment explanation
Indices: 52346777--52346945 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 72
52346767 CCTTTAGCGA
* * * * *
52346777 CGCTTTACAAAAAACGCCGCTAAATCTCTGAAAGTTCAGAAAACGGCATCGTTGGGCTTGGGTTT
1 CGCTTTACCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG-TT
*
52346842 TTTTGCGG
65 ATTTGCGG
* *
52346850 CGCTTTACCAAAAACGTCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTA
1 CGCTTTACCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTA
52346915 TTTGCGG
66 TTTGCGG
*
52346922 CGCTTTGCTCAAAAACGCCGCTAA
1 CGCTTTAC-CAAAAACGCCGCTAA
52346946 TGCTTTTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 16 0.19
73 69 0.81
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (72 bp):
CGCTTTACCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTA
TTTGCGG
Found at i:52347029 original size:12 final size:12
Alignment explanation
Indices: 52347012--52347037 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52347002 TTTTTTATCC
52347012 AAACGCCGCTAA
1 AAACGCCGCTAA
52347024 AAACGCCGCTAA
1 AAACGCCGCTAA
52347036 AA
1 AA
52347038 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:52352014 original size:21 final size:21
Alignment explanation
Indices: 52351989--52352032 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
52351979 GAACAATCAG
52351989 TTGTTTGAATTAAATACTAGT
1 TTGTTTGAATTAAATACTAGT
52352010 TTGTTTGAATTAAATACTAGT
1 TTGTTTGAATTAAATACTAGT
52352031 TT
1 TT
52352033 TTGTTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (21 bp):
TTGTTTGAATTAAATACTAGT
Found at i:52400646 original size:58 final size:58
Alignment explanation
Indices: 52400575--52400686 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 58
52400565 CATAATTGAC
*
52400575 ATGAAGAAGATGATTGAC-GGGTATTTAATAATTGTTTACTCCTAATTTGGTTATGATT
1 ATGAACAAGATGATTGACGGGGTATTTAATAATTGTTTACTCCTAA-TTGGTTATGATT
52400633 ATGAACAAGATGATTGACGGGGTATTTAATAATTGTTTACTCCTAATTGGTTAT
1 ATGAACAAGATGATTGACGGGGTATTTAATAATTGTTTACTCCTAATTGGTTAT
52400687 AGAAAATCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
58 25 0.48
59 27 0.52
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (58 bp):
ATGAACAAGATGATTGACGGGGTATTTAATAATTGTTTACTCCTAATTGGTTATGATT
Found at i:52401131 original size:21 final size:19
Alignment explanation
Indices: 52401095--52401133 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
52401085 ATAAAAATAG
52401095 TTAAAAACATTATTTATTA
1 TTAAAAACATTATTTATTA
*
52401114 TTAAAAGATCATTTTTTATT
1 TTAAAA-A-CATTATTTATT
52401134 CATATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAAAAACATTATTTATTA
Found at i:52410669 original size:4 final size:4
Alignment explanation
Indices: 52410660--52410689 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
52410650 TTGCTTTGAT
52410660 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
52410690 CAATTGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:52430344 original size:96 final size:96
Alignment explanation
Indices: 52430175--52430367 Score: 305
Period size: 96 Copynumber: 2.0 Consensus size: 96
52430165 ATGAGCCAAG
* * *
52430175 ATTACCAGGAATATAACTTCCCTGTCGCCTAGGTTGGACTATAAGATACCCTTCCTTTTCAATGA
1 ATTACCAGGAATATAACTTCCCTGTCGACTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
* *
52430240 CCGATGGTTCCATTGCAAAGTTTTCATCTTC
66 CCGATGGTTCCATAGCAAAGTTTTCACCTTC
* *
52430271 ATTATCAGGAATGTAACTTCCCTGTCGACTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
1 ATTACCAGGAATATAACTTCCCTGTCGACTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
* *
52430336 CTGATGGTTCCATAGCTAAGTTTTCACCTTC
66 CCGATGGTTCCATAGCAAAGTTTTCACCTTC
52430367 A
1 A
52430368 CTAAACTTGA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (96 bp):
ATTACCAGGAATATAACTTCCCTGTCGACTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
CCGATGGTTCCATAGCAAAGTTTTCACCTTC
Found at i:52458459 original size:36 final size:36
Alignment explanation
Indices: 52458412--52458485 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
52458402 TGTTTTGTTT
52458412 CTCTGACCCTTTTAGCTACCATATATACGTTGATTA
1 CTCTGACCCTTTTAGCTACCATATATACGTTGATTA
52458448 CTCTGACCCTTTTAGCTACCATATATACGTTGATTA
1 CTCTGACCCTTTTAGCTACCATATATACGTTGATTA
52458484 CT
1 CT
52458486 ACTGTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (36 bp):
CTCTGACCCTTTTAGCTACCATATATACGTTGATTA
Found at i:52470775 original size:16 final size:15
Alignment explanation
Indices: 52470750--52470783 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
52470740 GTTAAAAATT
*
52470750 TATATGTTATATTATA
1 TATATATTATATT-TA
52470766 TATATATTATATTTA
1 TATATATTATATTTA
52470781 TAT
1 TAT
52470784 GTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATATATTATATTTA
Found at i:52474798 original size:31 final size:31
Alignment explanation
Indices: 52474763--52474832 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
52474753 CTTGTCACTT
* * *
52474763 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * *
52474794 GTAGCCGGAGCTACCATTTTTCACTAATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
52474825 GTAGCCGA
1 GTAGCCGA
52474833 TGATCAGGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:52474854 original size:46 final size:46
Alignment explanation
Indices: 52474787--52474878 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
52474777 CACTATTCAC
* *
52474787 TGATCAGGTAGCCGGAGCTACCATTTTTCACTAATCAAGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
* * *
52474833 TGATCAGGTAGCCGAAGCTACCACTTTTCATTGATCAGGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
52474879 AGCTACCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (46 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
Found at i:52474871 original size:31 final size:31
Alignment explanation
Indices: 52474833--52474891 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
52474823 AAGTAGCCGA
52474833 TGATCAGGTAGCCGAAGCTACCACTTTTCAT
1 TGATCAGGTAGCCGAAGCTACCACTTTTCAT
52474864 TGATCAGGTAGCCGAAGCTACCACTTTT
1 TGATCAGGTAGCCGAAGCTACCACTTTT
52474892 TACTTGCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (31 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCAT
Found at i:52474970 original size:50 final size:51
Alignment explanation
Indices: 52474871--52474998 Score: 195
Period size: 50 Copynumber: 2.5 Consensus size: 51
52474861 CATTGATCAG
* * * * *
52474871 GTAGCCGAAGCTACCACTTTTTACTTGCCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGCCACTTGTCATTGATCAGATAAGT
*
52474922 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGCCACTTGTCATTGATCAGATAAGT
52474972 GTAGCCGAAGCTATCACTTATCACTTG
1 GTAGCCGAAGCTATCACTTATCACTTG
52474999 TTGCCATGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 47 0.67
51 23 0.33
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGCCACTTGTCATTGATCAGATAAGT
Found at i:52476086 original size:16 final size:18
Alignment explanation
Indices: 52476055--52476089 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
52476045 CAATTAACCC
52476055 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
52476073 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
52476089 C
1 C
52476090 CTAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:52486291 original size:6 final size:6
Alignment explanation
Indices: 52486280--52486307 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52486270 TATGACTGAC
52486280 AAGAGA AAGAGA AAGAGA AAGAGA AAGA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGA
52486308 CTAAGACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:52496356 original size:20 final size:19
Alignment explanation
Indices: 52496327--52496379 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
52496317 AGATGGTATG
52496327 TCAT-TATATGTTGGCAATA
1 TCATGTATATGTTGG-AATA
*
52496346 TCATGTATATGATTTGAATA
1 TCATGTATATG-TTGGAATA
*
52496366 T-ATGTATAAGTTGG
1 TCATGTATATGTTGG
52496380 TTTGAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 11 0.38
21 3 0.10
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (19 bp):
TCATGTATATGTTGGAATA
Found at i:52507601 original size:61 final size:61
Alignment explanation
Indices: 52507506--52507627 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
52507496 CATTCTAGGC
52507506 ACATCATCATCACTATCAAAACCTTCCAAAAATTGGACATATGTAATGCCAAACCAAAAAT
1 ACATCATCATCACTATCAAAACCTTCCAAAAATTGGACATATGTAATGCCAAACCAAAAAT
52507567 ACATCATCATCACTATCAAAACCTTCCAAAAATTGGACATATGTAATGCCAAACCAAAAAT
1 ACATCATCATCACTATCAAAACCTTCCAAAAATTGGACATATGTAATGCCAAACCAAAAAT
52507628 TAAAAATTCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.23
Consensus pattern (61 bp):
ACATCATCATCACTATCAAAACCTTCCAAAAATTGGACATATGTAATGCCAAACCAAAAAT
Found at i:52509391 original size:16 final size:16
Alignment explanation
Indices: 52509370--52509422 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
52509360 AATAGATGAA
52509370 ATTTTTTTATTTTTCT
1 ATTTTTTTATTTTTCT
* **
52509386 ATTTTTTAACCTTTC-
1 ATTTTTTTATTTTTCT
*
52509401 AATTTTTTATTTTTCT
1 ATTTTTTTATTTTTCT
52509417 AATTTT
1 -ATTTT
52509423 ATTTCACTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
15 11 0.41
16 12 0.44
17 4 0.15
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTTATTTTTCT
Found at i:52511487 original size:19 final size:20
Alignment explanation
Indices: 52511463--52511502 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52511453 TTTTAAAAAA
*
52511463 TTATAAA-AATTTGAAATTT
1 TTATAAATAATTTAAAATTT
*
52511482 TTATAAATACTTTAAAATTT
1 TTATAAATAATTTAAAATTT
52511502 T
1 T
52511503 ATATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATAAATAATTTAAAATTT
Found at i:52511561 original size:16 final size:16
Alignment explanation
Indices: 52511523--52511573 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
52511513 TATTGAGAAA
52511523 AATTAATTTA-TATTT
1 AATTAATTTATTATTT
*
52511538 ATACTAATTTATTATTT
1 A-ATTAATTTATTATTT
*
52511555 AATTAATTGAATTATTT
1 AATTAATT-TATTATTT
52511572 AA
1 AA
52511574 ATTGTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 14 0.47
17 15 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTAATTTATTATTT
Found at i:52516771 original size:39 final size:40
Alignment explanation
Indices: 52516663--52516774 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 40
52516653 CGACCTCGAG
* *
52516663 TCGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCAAC--TATTACTTCGGATAGAC
** * ** * *
52516704 TCGATGAGGTACCGGGTACCAACT-TTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
52516743 T-GATGAGACACTGGGTGTCAACTATTACTTCG
1 TCGATGAGACACTGGGTGTCAACTATTACTTCG
52516775 AACTATCCGA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
38 17 0.31
39 20 0.36
40 1 0.02
41 15 0.27
42 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
Found at i:52524477 original size:76 final size:76
Alignment explanation
Indices: 52524385--52524535 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
52524375 AAAATTCTAC
*
52524385 ATTACCCTCTCAGGGATACATATATTCAGCTGATCTGTCAAATGAAAACTCTGTACCTACTGAAA
1 ATTACCCTCTCAGGGATACATATACTCAGCTGATCTGTCAAATGAAAACTCTGTACCTACTGAAA
52524450 TGATCATACAA
66 TGATCATACAA
*
52524461 ATTACCCTCTCAGGGATTCATATACTCAGCTGATCTGTCAAATGAAAACTCTGTACCTACTGAAA
1 ATTACCCTCTCAGGGATACATATACTCAGCTGATCTGTCAAATGAAAACTCTGTACCTACTGAAA
52524526 TGATCATACA
66 TGATCATACA
52524536 GATCTTTCTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.29
Consensus pattern (76 bp):
ATTACCCTCTCAGGGATACATATACTCAGCTGATCTGTCAAATGAAAACTCTGTACCTACTGAAA
TGATCATACAA
Found at i:52526538 original size:23 final size:22
Alignment explanation
Indices: 52526477--52526542 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
52526467 ACCTGATCAG
52526477 AATACGACACATAAGTGCCTG-
1 AATACGACACATAAGTGCCTGA
* *
52526498 AA-ACGACACACGAGGTGCCTGA
1 AATACGACACA-TAAGTGCCTGA
52526520 AATACGACACATAAAGTGCCTGA
1 AATACGACACAT-AAGTGCCTGA
52526543 TCAGTAAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 8 0.22
21 10 0.27
22 2 0.05
23 17 0.46
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (22 bp):
AATACGACACATAAGTGCCTGA
Found at i:52526854 original size:98 final size:98
Alignment explanation
Indices: 52526685--52526880 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
52526675 CAAGACTCGG
52526685 ACTTTGGCGGATACACGGATTCCATCCAAACACACCAAAATGTCCAACCAAAACACACCAGTATA
1 ACTTTGGCGGATACACGGATTCCATCCAAACACACCAAAATGTCCAACCAAAACACACCAGTATA
*
52526750 ATCCTCCAAAACACACTAGTATCATATAATCCT
66 ATCCTCCAAAACACACCAGTATCATATAATCCT
52526783 ACTTTGGCGGATACACGGATTCCATCCAAACACACCAAAATGTCCAACCAAAACACACCAGTATA
1 ACTTTGGCGGATACACGGATTCCATCCAAACACACCAAAATGTCCAACCAAAACACACCAGTATA
*
52526848 ATCCTCCAAAACACACCAGTATCGTATAATCCT
66 ATCCTCCAAAACACACCAGTATCATATAATCCT
52526881 TCCAGACACA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (98 bp):
ACTTTGGCGGATACACGGATTCCATCCAAACACACCAAAATGTCCAACCAAAACACACCAGTATA
ATCCTCCAAAACACACCAGTATCATATAATCCT
Found at i:52526875 original size:28 final size:29
Alignment explanation
Indices: 52526842--52526928 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 29
52526832 AAAACACACC
*
52526842 AGTATAATCC-TCCAAAACACACCAGTAT
1 AGTATAATCCATCCAAAACACACCAGAAT
* * *
52526870 CGTATAATCCTTCC-AGACACACCAGAAT
1 AGTATAATCCATCCAAAACACACCAGAAT
*
52526898 AATATAATCCATCCAAAACACACCAGAAT
1 AGTATAATCCATCCAAAACACACCAGAAT
52526927 AG
1 AG
52526929 CACAAAGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.44, C:0.29, G:0.08, T:0.20
Consensus pattern (29 bp):
AGTATAATCCATCCAAAACACACCAGAAT
Found at i:52529399 original size:25 final size:25
Alignment explanation
Indices: 52529365--52529414 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
52529355 TTTGATTATC
52529365 ATATTAATTTTTCTTAAATTTTGTT
1 ATATTAATTTTTCTTAAATTTTGTT
52529390 ATATTAATTTTTCTTAAATTTTGTT
1 ATATTAATTTTTCTTAAATTTTGTT
52529415 CTACATCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (25 bp):
ATATTAATTTTTCTTAAATTTTGTT
Found at i:52530301 original size:31 final size:30
Alignment explanation
Indices: 52530245--52530302 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
52530235 AAAAAAGATG
* **
52530245 TTTTTTTTACTATTTTGCTGTTATTTTCTT
1 TTTTTTTTACTATTTTACTACTATTTTCTT
52530275 TTTTTTTTCACTATTTTACTACTATTTT
1 TTTTTTTT-ACTATTTTACTACTATTTT
52530303 ATTATTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.14, C:0.12, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTTTTTTACTATTTTACTACTATTTTCTT
Found at i:52530302 original size:22 final size:22
Alignment explanation
Indices: 52530284--52530327 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52530274 TTTTTTTTTC
*
52530284 ACTATTTTACTACTATTTTATT
1 ACTATGTTACTACTATTTTATT
* *
52530306 ATTATGTTGCTACTATTTTATT
1 ACTATGTTACTACTATTTTATT
52530328 GTCATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (22 bp):
ACTATGTTACTACTATTTTATT
Found at i:52536000 original size:28 final size:28
Alignment explanation
Indices: 52535969--52536024 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
52535959 AGCTAGGAGT
* *
52535969 AAATTGATAGATTTTGTAAATGTTGAGG
1 AAATTGACAAATTTTGTAAATGTTGAGG
52535997 AAATTGACAAATTTTGTAAATGTTGAGG
1 AAATTGACAAATTTTGTAAATGTTGAGG
52536025 GTAGGGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (28 bp):
AAATTGACAAATTTTGTAAATGTTGAGG
Found at i:52545798 original size:10 final size:10
Alignment explanation
Indices: 52545785--52545841 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 10
52545775 ATTCAAAAAA
52545785 ATTAAAAATT
1 ATTAAAAATT
52545795 ATT-AAAATT
1 ATTAAAAATT
52545804 ATTTAAAAA-T
1 A-TTAAAAATT
*
52545814 ATGAAAATATT
1 ATTAAAA-ATT
*
52545825 TTTAAAAATT
1 ATTAAAAATT
52545835 AATTAAA
1 -ATTAAA
52545842 CGTTAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 12 0.32
10 11 0.29
11 15 0.39
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:52545811 original size:20 final size:21
Alignment explanation
Indices: 52545786--52545841 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
52545776 TTCAAAAAAA
52545786 TTAAAAATTATTAAAAT-TAT
1 TTAAAAATTATTAAAATATAT
* *
52545806 TTAAAAA-TATGAAAATATTT
1 TTAAAAATTATTAAAATATAT
52545826 TTAAAAATTAATTAAA
1 TTAAAAATT-ATTAAA
52545842 CGTTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 8 0.27
20 16 0.53
21 1 0.03
22 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAAATTATTAAAATATAT
Found at i:52547834 original size:29 final size:30
Alignment explanation
Indices: 52547797--52547875 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
52547787 AAATTTTAAA
*
52547797 TTAATAATAATAAAATTATAATTTAAT-TT
1 TTAAAAATAATAAAATTATAATTTAATATT
*
52547826 TTAAAAATAATAAAATTTTAATTTAATATT
1 TTAAAAATAATAAAATTATAATTTAATATT
*
52547856 ATAAAAACT-ATAAAA-TATAA
1 TTAAAAA-TAATAAAATTATAA
52547876 ACTATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 29 0.66
30 14 0.32
31 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATATT
Found at i:52547886 original size:15 final size:15
Alignment explanation
Indices: 52547856--52547892 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
52547846 ATTTAATATT
52547856 ATAA-AAACTATAAA
1 ATAATAAACTATAAA
52547870 AT-ATAAACTATTAAA
1 ATAATAAACTA-TAAA
52547885 ATAATAAA
1 ATAATAAA
52547893 ATTATATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 8 0.40
15 6 0.30
16 5 0.25
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAATAAACTATAAA
Found at i:52552062 original size:12 final size:12
Alignment explanation
Indices: 52552045--52552070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52552035 GTTATAAAAT
52552045 ATAATAATATTA
1 ATAATAATATTA
52552057 ATAATAATATTA
1 ATAATAATATTA
52552069 AT
1 AT
52552071 TGTGACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATAATATTA
Found at i:52558124 original size:10 final size:11
Alignment explanation
Indices: 52558100--52558128 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
52558090 CTGTCCTTAT
52558100 TCTGTTTTGGC
1 TCTGTTTTGGC
52558111 TCTGTTTT-GC
1 TCTGTTTTGGC
52558121 TCTGTTTT
1 TCTGTTTT
52558129 CATGTATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.17, G:0.21, T:0.62
Consensus pattern (11 bp):
TCTGTTTTGGC
Found at i:52562029 original size:13 final size:14
Alignment explanation
Indices: 52562002--52562031 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
52561992 ATCATTTCAA
52562002 ATTTTATATAAATG
1 ATTTTATATAAATG
52562016 ATTTTATA-AAATG
1 ATTTTATATAAATG
52562029 ATT
1 ATT
52562032 GTAATTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTTATATAAATG
Found at i:52563366 original size:21 final size:22
Alignment explanation
Indices: 52563334--52563374 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
52563324 AAATGACGTA
52563334 ATTTTGTGTTTTAA-TTTAATG
1 ATTTTGTGTTTTAACTTTAATG
52563355 ATTTTGAT-TTTTAACTTTAA
1 ATTTTG-TGTTTTAACTTTAA
52563375 AAATGGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTTTGTGTTTTAACTTTAATG
Found at i:52565059 original size:4 final size:4
Alignment explanation
Indices: 52565050--52565074 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52565040 TACTGATAAA
52565050 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
52565075 TTGTAGGTAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:52573189 original size:15 final size:15
Alignment explanation
Indices: 52573169--52573198 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52573159 TATTCACTTG
52573169 ATTACTTAATTTCAC
1 ATTACTTAATTTCAC
52573184 ATTACTTAATTTCAC
1 ATTACTTAATTTCAC
52573199 CATGAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTACTTAATTTCAC
Found at i:52584300 original size:9 final size:8
Alignment explanation
Indices: 52584284--52584308 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52584274 TACGAATAAC
52584284 TCTTTTTT
1 TCTTTTTT
52584292 TCTTTTTT
1 TCTTTTTT
52584300 TCTTTTTT
1 TCTTTTTT
52584308 T
1 T
52584309 GCTTAAAGAA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TCTTTTTT
Found at i:52589933 original size:690 final size:690
Alignment explanation
Indices: 52588612--52589996 Score: 2770
Period size: 690 Copynumber: 2.0 Consensus size: 690
52588602 AGGCTGTTAG
52588612 GTTGCAACGGAGTGAAGAGGACTGTGTAGTTGATATGTGCACACAGATAGAGGCTGGAAAATCAA
1 GTTGCAACGGAGTGAAGAGGACTGTGTAGTTGATATGTGCACACAGATAGAGGCTGGAAAATCAA
52588677 AGGAAATTTTGAGTGAAGGAATGGAAAAGGCACCTTCAGAGCACTCGAGTCTGGTAGGTCTTAAT
66 AGGAAATTTTGAGTGAAGGAATGGAAAAGGCACCTTCAGAGCACTCGAGTCTGGTAGGTCTTAAT
52588742 GATGCTGCCGATGAATTCTTTGATGTTCCAGAACCAACAGACTATGATCAATCAACAGATGGGTG
131 GATGCTGCCGATGAATTCTTTGATGTTCCAGAACCAACAGACTATGATCAATCAACAGATGGGTG
52588807 GGATTCTGACTATGCTCCTGAAGTATACTCTCAGGTATAAGTCAAAGTAATTTATCATTGATTCT
196 GGATTCTGACTATGCTCCTGAAGTATACTCTCAGGTATAAGTCAAAGTAATTTATCATTGATTCT
52588872 TACATGCAAACTAAGTTGCAGTTAGTGGTGCTTCATATCTCAGAGGATGTGACCAACTATAGAGT
261 TACATGCAAACTAAGTTGCAGTTAGTGGTGCTTCATATCTCAGAGGATGTGACCAACTATAGAGT
52588937 CTCTATTTTTCCTATTATGTTTCTTAGTATGGCTGTATTACTCTAGAGTTTTTCTCCCCTAAAGG
326 CTCTATTTTTCCTATTATGTTTCTTAGTATGGCTGTATTACTCTAGAGTTTTTCTCCCCTAAAGG
52589002 TTTTGTGTGTGTATGTTTTGCTCGAAGTTTCTCACATGACATCTATGTGACTGAAATTTACAGGA
391 TTTTGTGTGTGTATGTTTTGCTCGAAGTTTCTCACATGACATCTATGTGACTGAAATTTACAGGA
52589067 TACACGCCAAACAAAGTTATCAACTGCTGCTGTTTTTGTGAAAAAGTTACATGATCTTGCAGGTG
456 TACACGCCAAACAAAGTTATCAACTGCTGCTGTTTTTGTGAAAAAGTTACATGATCTTGCAGGTG
52589132 GTTCCTATTTGGATGATCAGTATTCCTTTCTATAATATAGAAACAAAGAATTTTCTTTTCAATAG
521 GTTCCTATTTGGATGATCAGTATTCCTTTCTATAATATAGAAACAAAGAATTTTCTTTTCAATAG
52589197 AATTTTTAGAAAGATAATTGCTGATGGCTTCCAATTCCTTGTATGTTGCAGTCCAGAAAAGGGGC
586 AATTTTTAGAAAGATAATTGCTGATGGCTTCCAATTCCTTGTATGTTGCAGTCCAGAAAAGGGGC
52589262 TACATGGACTTACAAGACATGACGAAGGAAGATGGCATAT
651 TACATGGACTTACAAGACATGACGAAGGAAGATGGCATAT
52589302 GTTGCAACGGAGTGAAGAGGACTGTGTAGTTGATATGTGCACACAGATAGAGGCTGGAAAATCAA
1 GTTGCAACGGAGTGAAGAGGACTGTGTAGTTGATATGTGCACACAGATAGAGGCTGGAAAATCAA
52589367 AGGAAATTTTGAGTGAAGGAATGGAAAAGGCACCTTCAGAGCACTCGAGTCTGGTAGGTCTTAAT
66 AGGAAATTTTGAGTGAAGGAATGGAAAAGGCACCTTCAGAGCACTCGAGTCTGGTAGGTCTTAAT
52589432 GATGCTGCCGATGAATTCTTTGATGTTCCAGAACCAACAGACTATGATCAATCAACAGATGGGTG
131 GATGCTGCCGATGAATTCTTTGATGTTCCAGAACCAACAGACTATGATCAATCAACAGATGGGTG
52589497 GGATTCTGACTATGCTCCTGAAGTATACTCTCAGGTATAAGTCAAAGTAATTTATCATTGATTCT
196 GGATTCTGACTATGCTCCTGAAGTATACTCTCAGGTATAAGTCAAAGTAATTTATCATTGATTCT
52589562 TACATGCAAACTAAGTTGCAGTTAGTGGTGCTTCATATCTCAGAGGATGTGACCAACTATAGAGT
261 TACATGCAAACTAAGTTGCAGTTAGTGGTGCTTCATATCTCAGAGGATGTGACCAACTATAGAGT
52589627 CTCTATTTTTCCTATTATGTTTCTTAGTATGGCTGTATTACTCTAGAGTTTTTCTCCCCTAAAGG
326 CTCTATTTTTCCTATTATGTTTCTTAGTATGGCTGTATTACTCTAGAGTTTTTCTCCCCTAAAGG
52589692 TTTTGTGTGTGTATGTTTTGCTCGAAGTTTCTCACATGACATCTATGTGACTGAAATTTACAGGA
391 TTTTGTGTGTGTATGTTTTGCTCGAAGTTTCTCACATGACATCTATGTGACTGAAATTTACAGGA
52589757 TACACGCCAAACAAAGTTATCAACTGCTGCTGTTTTTGTGAAAAAGTTACATGATCTTGCAGGTG
456 TACACGCCAAACAAAGTTATCAACTGCTGCTGTTTTTGTGAAAAAGTTACATGATCTTGCAGGTG
52589822 GTTCCTATTTGGATGATCAGTATTCCTTTCTATAATATAGAAACAAAGAATTTTCTTTTCAATAG
521 GTTCCTATTTGGATGATCAGTATTCCTTTCTATAATATAGAAACAAAGAATTTTCTTTTCAATAG
52589887 AATTTTTAGAAAGATAATTGCTGATGGCTTCCAATTCCTTGTATGTTGCAGTCCAGAAAAGGGGC
586 AATTTTTAGAAAGATAATTGCTGATGGCTTCCAATTCCTTGTATGTTGCAGTCCAGAAAAGGGGC
52589952 TACATGGACTTACAAGACATGACGAAGGAAGATGGCATAT
651 TACATGGACTTACAAGACATGACGAAGGAAGATGGCATAT
52589992 GTTGC
1 GTTGC
52589997 TCCTATGGAA
Statistics
Matches: 695, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
690 695 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (690 bp):
GTTGCAACGGAGTGAAGAGGACTGTGTAGTTGATATGTGCACACAGATAGAGGCTGGAAAATCAA
AGGAAATTTTGAGTGAAGGAATGGAAAAGGCACCTTCAGAGCACTCGAGTCTGGTAGGTCTTAAT
GATGCTGCCGATGAATTCTTTGATGTTCCAGAACCAACAGACTATGATCAATCAACAGATGGGTG
GGATTCTGACTATGCTCCTGAAGTATACTCTCAGGTATAAGTCAAAGTAATTTATCATTGATTCT
TACATGCAAACTAAGTTGCAGTTAGTGGTGCTTCATATCTCAGAGGATGTGACCAACTATAGAGT
CTCTATTTTTCCTATTATGTTTCTTAGTATGGCTGTATTACTCTAGAGTTTTTCTCCCCTAAAGG
TTTTGTGTGTGTATGTTTTGCTCGAAGTTTCTCACATGACATCTATGTGACTGAAATTTACAGGA
TACACGCCAAACAAAGTTATCAACTGCTGCTGTTTTTGTGAAAAAGTTACATGATCTTGCAGGTG
GTTCCTATTTGGATGATCAGTATTCCTTTCTATAATATAGAAACAAAGAATTTTCTTTTCAATAG
AATTTTTAGAAAGATAATTGCTGATGGCTTCCAATTCCTTGTATGTTGCAGTCCAGAAAAGGGGC
TACATGGACTTACAAGACATGACGAAGGAAGATGGCATAT
Found at i:52602283 original size:9 final size:10
Alignment explanation
Indices: 52602264--52602296 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
52602254 TCAATTATCA
52602264 TTTCTTTTTT
1 TTTCTTTTTT
52602274 TTTCTTTTTT
1 TTTCTTTTTT
52602284 TTTCTTTTTT
1 TTTCTTTTTT
52602294 TTT
1 TTT
52602297 TGTTTGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:52608769 original size:25 final size:25
Alignment explanation
Indices: 52608741--52608791 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52608731 AGAAAGAAGT
52608741 CTAGTTCCTGATTTTATGAAAATGA
1 CTAGTTCCTGATTTTATGAAAATGA
52608766 CTAGTTCCTGATTTTATGAAAATGA
1 CTAGTTCCTGATTTTATGAAAATGA
52608791 C
1 C
52608792 ATACTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (25 bp):
CTAGTTCCTGATTTTATGAAAATGA
Found at i:52610522 original size:15 final size:15
Alignment explanation
Indices: 52610466--52610516 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
52610456 TTAAGCTAAT
52610466 AAAA-AAATAATTATA
1 AAAATAAATAA-TATA
* *
52610481 AAAAT-AATTATGTTA
1 AAAATAAATAAT-ATA
52610496 AAAATAAATAATATA
1 AAAATAAATAATATA
52610511 AAAATA
1 AAAATA
52610517 TTTAATGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 23 0.79
16 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAATAAATAATATA
Found at i:52622670 original size:18 final size:18
Alignment explanation
Indices: 52622635--52622672 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
52622625 AGCCAAGTGG
*
52622635 GTGGTGTTTTTTTTTTTT
1 GTGGTGTTTTTTTCTTTT
52622653 GTGG-GTTTTTTGTCTTTT
1 GTGGTGTTTTTT-TCTTTT
52622671 GT
1 GT
52622673 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.03, G:0.26, T:0.71
Consensus pattern (18 bp):
GTGGTGTTTTTTTCTTTT
Found at i:52629527 original size:37 final size:37
Alignment explanation
Indices: 52629486--52629604 Score: 104
Period size: 37 Copynumber: 3.3 Consensus size: 37
52629476 AAAAAAAAAC
52629486 TATAATAAAAAAATAACCTGTAATACCCTAAAATCAA
1 TATAATAAAAAAATAACCTGTAATACCCTAAAATCAA
* * ** * * *
52629523 TATAATATAAAAAT-A---GTATTA-AATTAAATGATG
1 TATAATAAAAAAATAACCTGTAATACCCTAAAATCA-A
* *
52629556 TATAATAAGAAAATAACCTCTAATACCCTAAAATCAA
1 TATAATAAAAAAATAACCTGTAATACCCTAAAATCAA
*
52629593 TATAATATAAAA
1 TATAATAAAAAA
52629605 TAGTATTAAA
Statistics
Matches: 58, Mismatches: 18, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
32 6 0.10
33 17 0.29
34 1 0.02
36 1 0.02
37 27 0.47
38 6 0.10
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (37 bp):
TATAATAAAAAAATAACCTGTAATACCCTAAAATCAA
Found at i:52629560 original size:70 final size:69
Alignment explanation
Indices: 52629486--52629630 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 69
52629476 AAAAAAAAAC
*
52629486 TATAATAAAAAAATAACCTGTAATACCCTAAAATCAATATAATATAAAAATAGTATTAAATTAAA
1 TATAATAAAAAAATAACCTCTAATACCCTAAAATCAATATAATAT-AAAATAGTATTAAATTAAA
52629551 TGATG
65 TGATG
* *
52629556 TATAATAAGAAAATAACCTCTAATACCCTAAAATCAATATAATATAAAATAGTATTAAATTGAAT
1 TATAATAAAAAAATAACCTCTAATACCCTAAAATCAATATAATATAAAATAGTATTAAATTAAAT
52629621 GATG
66 GATG
52629625 TATAAT
1 TATAAT
52629631 TGATTTTTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 29 0.40
70 43 0.60
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (69 bp):
TATAATAAAAAAATAACCTCTAATACCCTAAAATCAATATAATATAAAATAGTATTAAATTAAAT
GATG
Found at i:52630332 original size:30 final size:30
Alignment explanation
Indices: 52630306--52630368 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
52630296 TATTGTTTTT
* *
52630306 TTTCTTGTTATTTTTTACTATTTTGTTGCTA
1 TTTCTTATT-TTTTTCACTATTTTGTTGCTA
*
52630337 TTTCTTATTTTTTTCACTATTTTGTTGTTA
1 TTTCTTATTTTTTTCACTATTTTGTTGCTA
52630367 TT
1 TT
52630369 GTTTAGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.70
Consensus pattern (30 bp):
TTTCTTATTTTTTTCACTATTTTGTTGCTA
Found at i:52630350 original size:21 final size:21
Alignment explanation
Indices: 52630302--52630351 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
52630292 AATTTATTGT
* *
52630302 TTTTTTTCTTGTTATTTTTTA
1 TTTTTTTCTTGCTATTTCTTA
* * *
52630323 CTATTTTGTTGCTATTTCTTA
1 TTTTTTTCTTGCTATTTCTTA
52630344 TTTTTTTC
1 TTTTTTTC
52630352 ACTATTTTGT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTTTTCTTGCTATTTCTTA
Found at i:52630816 original size:2 final size:2
Alignment explanation
Indices: 52630809--52630835 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52630799 AACCCCACTT
52630809 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
52630836 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52633332 original size:14 final size:14
Alignment explanation
Indices: 52633310--52633353 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
52633300 TAATTCAAGT
*
52633310 TATTTATTTTTAAG
1 TATTTATTTTAAAG
* *
52633324 TATTAATTTTAAAT
1 TATTTATTTTAAAG
*
52633338 TATTTATTTTATAG
1 TATTTATTTTAAAG
52633352 TA
1 TA
52633354 ATTCAATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
TATTTATTTTAAAG
Found at i:52645425 original size:17 final size:17
Alignment explanation
Indices: 52645403--52645436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52645393 ATCCACTAAT
*
52645403 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
52645420 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
52645437 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:52650064 original size:17 final size:17
Alignment explanation
Indices: 52650042--52650075 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52650032 ATCCACTAAT
*
52650042 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
52650059 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
52650076 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:52651621 original size:195 final size:196
Alignment explanation
Indices: 52651258--52651648 Score: 660
Period size: 195 Copynumber: 2.0 Consensus size: 196
52651248 TCTTAACTAC
* * * *
52651258 AATAATTGATCTAAAAAGATTCCTATAGAATTTCACTCTAATAAAACTCCACCTTAAATTTTATT
1 AATAATTGATCTAAAAAGATTCCTACAGAATTTCACTATAACAAAACTCCACCTTAAATATTATT
52651323 TGTTCCCTTAAAAAAATTTGTCACTCATTACTATATTATTAGATTGTTTTAAAAGCCTTTTAGTA
66 TGTTCCCTTAAAAAAATTTGTCACTCATTACTATATTATTAGATTGTTTTAAAAGCCTTTTAGTA
*
52651388 TACAATAATGACATTAAACTTCAATTAAATTCTAAATTGAGTGAAATCTTAACTCTAAACATAAT
131 TACAATAATAACATTAAACTTCAATTAAATTCTAAATTGAGTGAAATC-TAACTCTAAACATAAT
52651453 TT
195 TT
*
52651455 AATAATTGATCTAAAAA-ATT-CTACAGAATTTCACTATAACAAAACTCTACCTTAAATATTATT
1 AATAATTGATCTAAAAAGATTCCTACAGAATTTCACTATAACAAAACTCCACCTTAAATATTATT
* * *
52651518 TGTTCCCTTAAAAAAATTTGTCACTCGTTACTATATTATTAGATTTTTTTAAAAGCCTTTTGGTA
66 TGTTCCCTTAAAAAAATTTGTCACTCATTACTATATTATTAGATTGTTTTAAAAGCCTTTTAGTA
* *
52651583 TACAATAATAACATTAAACTTCAATTAAATTTTAAATTGAGTGAAATCTAACTTTAAACATAATT
131 TACAATAATAACATTAAACTTCAATTAAATTCTAAATTGAGTGAAATCTAACTCTAAACATAATT
52651648 T
196 T
52651649 GTTTCTCCAT
Statistics
Matches: 183, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
194 17 0.09
195 146 0.80
196 3 0.02
197 17 0.09
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.39
Consensus pattern (196 bp):
AATAATTGATCTAAAAAGATTCCTACAGAATTTCACTATAACAAAACTCCACCTTAAATATTATT
TGTTCCCTTAAAAAAATTTGTCACTCATTACTATATTATTAGATTGTTTTAAAAGCCTTTTAGTA
TACAATAATAACATTAAACTTCAATTAAATTCTAAATTGAGTGAAATCTAACTCTAAACATAATT
T
Found at i:52653581 original size:24 final size:24
Alignment explanation
Indices: 52653549--52653598 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
52653539 TGAATTACAA
52653549 TTGCAGCATTGTGCATAAGGTGTT
1 TTGCAGCATTGTGCATAAGGTGTT
52653573 TTGCAGCATTGTGCATAAGGTGTT
1 TTGCAGCATTGTGCATAAGGTGTT
52653597 TT
1 TT
52653599 CTGCCTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (24 bp):
TTGCAGCATTGTGCATAAGGTGTT
Found at i:52660214 original size:54 final size:54
Alignment explanation
Indices: 52660155--52660264 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
52660145 CCCAAAAGAA
*
52660155 TTAATTAGCTCATTAGATAATGATGTCACATAAGAGATTAGATGAGTTAGGAAT
1 TTAATTAGCTCATTAGATAATGATGTCACAAAAGAGATTAGATGAGTTAGGAAT
52660209 TTAATTAGCTCATTAGATAATGATGTCACAAAAGAGATTAGATGAGTTAGGAAT
1 TTAATTAGCTCATTAGATAATGATGTCACAAAAGAGATTAGATGAGTTAGGAAT
52660263 TT
1 TT
52660265 GTGGCGGTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (54 bp):
TTAATTAGCTCATTAGATAATGATGTCACAAAAGAGATTAGATGAGTTAGGAAT
Found at i:52662364 original size:13 final size:14
Alignment explanation
Indices: 52662340--52662368 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
52662330 AGGGAAATCT
52662340 TAAATACATGTGAG
1 TAAATACATGTGAG
52662354 TAAAT-CATGTGAG
1 TAAATACATGTGAG
52662367 TA
1 TA
52662369 GAGTAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (14 bp):
TAAATACATGTGAG
Found at i:52667529 original size:18 final size:19
Alignment explanation
Indices: 52667506--52667544 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52667496 TTGCTGTTTT
*
52667506 TTTTACT-TTTTTTCATTA
1 TTTTACTATTGTTTCATTA
*
52667524 TTTTACTATTGTTTCGTTA
1 TTTTACTATTGTTTCATTA
52667543 TT
1 TT
52667545 ATATTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTACTATTGTTTCATTA
Found at i:52678932 original size:34 final size:33
Alignment explanation
Indices: 52678894--52678968 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 33
52678884 TAGATACAAC
52678894 TTAACAAGTAAATGCCTCTAAAAT-AATAAAAAAA
1 TTAACAAG-AAATGCCT-TAAAATAAATAAAAAAA
*
52678928 TTAAC---AAATGCCTTTAAATAAATAAAAAAA
1 TTAACAAGAAATGCCTTAAAATAAATAAAAAAA
52678958 TTAACAAGAAA
1 TTAACAAGAAA
52678969 ATAAATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 5 0.14
30 23 0.64
33 3 0.08
34 5 0.14
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (33 bp):
TTAACAAGAAATGCCTTAAAATAAATAAAAAAA
Found at i:52678956 original size:29 final size:30
Alignment explanation
Indices: 52678903--52678964 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
52678893 CTTAACAAGT
52678903 AAATGCCTCTAAAATAATAAAAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAATTAAC
*
52678933 AAATGCCT-TTAAATAAATAAAAAAATTAAC
1 AAATGCCTCTAAAAT-AATAAAAAAATTAAC
52678963 AA
1 AA
52678965 GAAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAAC
Found at i:52679019 original size:11 final size:11
Alignment explanation
Indices: 52679001--52679040 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
52678991 ACAATAACAA
52679001 CAAAATAATAG
1 CAAAATAATAG
*
52679012 CAATATAATAG
1 CAAAATAATAG
* *
52679023 TAAAATAGTAG
1 CAAAATAATAG
52679034 CAAAATA
1 CAAAATA
52679041 TGGAGAAAAC
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:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:52687387 original size:17 final size:18
Alignment explanation
Indices: 52687347--52687386 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52687337 ATTTTATTTA
*
52687347 TTTTTCTTGGAATTTAAC
1 TTTTTCTTGGAAGTTAAC
52687365 TTTTTCTTGGAGAGTT-AC
1 TTTTTCTTGGA-AGTTAAC
52687383 TTTT
1 TTTT
52687387 CCATAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.57
Consensus pattern (18 bp):
TTTTTCTTGGAAGTTAAC
Found at i:52688562 original size:2 final size:2
Alignment explanation
Indices: 52688555--52688605 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
52688545 TCACTTGTTT
52688555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
52688597 TC TC TC TC T
1 TC TC TC TC T
52688606 TTTCCACTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:52705522 original size:22 final size:19
Alignment explanation
Indices: 52705475--52705531 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 19
52705465 CAAATTATTC
52705475 AAAAATTATAAAAATAAAA
1 AAAAATTATAAAAATAAAA
*
52705494 AACAAATTAATCAAAATTAAAA
1 AA-AAATT-AT-AAAAATAAAA
52705516 TAAAAATATATAAAAA
1 -AAAAAT-TATAAAAA
52705532 GTTCATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 6 0.19
22 15 0.48
23 3 0.10
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATTATAAAAATAAAA
Found at i:52705693 original size:31 final size:32
Alignment explanation
Indices: 52705629--52705694 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
52705619 GTATTATCAT
*
52705629 TTTGGCTCTTTTTCAAAAGATTAATAGTCAAA
1 TTTGACTCTTTTTCAAAAGATTAATAGTCAAA
52705661 TTTGACTCTTTTT-AAGAAG-TTAATGAGT-AAA
1 TTTGACTCTTTTTCAA-AAGATTAAT-AGTCAAA
52705692 TTT
1 TTT
52705695 AGCTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (32 bp):
TTTGACTCTTTTTCAAAAGATTAATAGTCAAA
Found at i:52706785 original size:21 final size:23
Alignment explanation
Indices: 52706738--52706791 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
52706728 CATTCAAGAT
**
52706738 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
52706761 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
52706782 AAAAT-ATATA
1 AAAATAATATA
52706792 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:52706917 original size:4 final size:4
Alignment explanation
Indices: 52706908--52706932 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52706898 AAAAAATGTA
52706908 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
52706933 GAATGTTAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:52707040 original size:23 final size:24
Alignment explanation
Indices: 52706973--52707087 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 24
52706963 ATAAGAAAAA
*
52706973 AGTAAT-AAT-GAAA-ATAATATT
1 AGTAATAAATAGAAATATAATAAT
52706994 AGTATATAAATAGAAATA-AA-AAT
1 AGTA-ATAAATAGAAATATAATAAT
52707017 A-TAATAAATAGAAATATAATAAT
1 AGTAATAAATAGAAATATAATAAT
* * *
52707040 AGT-AGAAATATAAATA-GATAA-
1 AGTAATAAATAGAAATATAATAAT
52707061 A-TAA-AAATTAGATAA-ATAATAAT
1 AGTAATAAA-TAGA-AATATAATAAT
52707084 AGTA
1 AGTA
52707088 TTAGAATAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
20 4 0.05
21 23 0.31
22 16 0.21
23 22 0.29
24 9 0.12
25 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (24 bp):
AGTAATAAATAGAAATATAATAAT
Found at i:52707055 original size:44 final size:44
Alignment explanation
Indices: 52707001--52707087 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
52706991 ATTAGTATAT
52707001 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGTAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGTAG
* *
52707045 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATAGTA
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTA
52707088 TTAGAATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 28 0.74
45 5 0.13
46 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
Found at i:52707072 original size:15 final size:14
Alignment explanation
Indices: 52706999--52707127 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 14
52706989 ATATTAGTAT
*
52706999 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
52707012 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
52707028 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
52707042 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
52707057 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
52707072 ATAAATAATAATAG
1 ATAAATAAAAATAG
*
52707086 TATTAGAATAACAA-A-
1 -A-TA-AATAAAAATAG
*
52707101 ATAAATATAAATAG
1 ATAAATAAAAATAG
52707115 A-AACATAAAAATA
1 ATAA-ATAAAAATA
52707128 ATAGGAATAA
Statistics
Matches: 92, Mismatches: 12, Indels: 23
0.72 0.09 0.18
Matches are distributed among these distances:
12 6 0.07
13 8 0.09
14 30 0.33
15 35 0.38
16 6 0.07
17 7 0.08
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:52707077 original size:29 final size:28
Alignment explanation
Indices: 52707020--52707127 Score: 73
Period size: 29 Copynumber: 3.8 Consensus size: 28
52707010 TAAAAATATA
* * *
52707020 ATAAATAGAAATATAATAATAGTAGAAAT
1 ATAAATAGAAACATAAAAATAG-ATAAAT
52707049 ATAAATAGATAA-ATAAAAATTAGATAAAT
1 ATAAATAGA-AACATAAAAA-TAGATAAAT
*
52707078 A-ATAATAGTATTAGA-ATAACAA-A-ATAAAT
1 ATA-AATAG-A--A-ACATAAAAATAGATAAAT
52707107 ATAAATAGAAACATAAAAATA
1 ATAAATAGAAACATAAAAATA
52707128 ATAGGAATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
25 1 0.02
26 7 0.11
27 1 0.02
28 2 0.03
29 38 0.58
30 8 0.12
31 2 0.03
32 7 0.11
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (28 bp):
ATAAATAGAAACATAAAAATAGATAAAT
Found at i:52708091 original size:7 final size:7
Alignment explanation
Indices: 52708079--52708142 Score: 51
Period size: 7 Copynumber: 8.4 Consensus size: 7
52708069 GATATCAAAA
52708079 TATATAT
1 TATATAT
52708086 TATATAT
1 TATATAT
52708093 TATATTAACT
1 TATA-T-A-T
52708103 TA-ATAT
1 TATATAT
52708109 T-TAAGTAT
1 TAT-A-TAT
52708117 TAATATAT
1 T-ATATAT
52708125 TATATAT
1 TATATAT
52708132 TATATTAT
1 TATA-TAT
52708140 TAT
1 TAT
52708143 CACTGTTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
6 2 0.04
7 23 0.48
8 16 0.33
9 3 0.06
10 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:52711298 original size:22 final size:22
Alignment explanation
Indices: 52711269--52711325 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
52711259 TAGCACGTTA
52711269 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
52711292 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
52711313 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
52711326 CGTTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:52731249 original size:12 final size:12
Alignment explanation
Indices: 52731232--52731309 Score: 84
Period size: 12 Copynumber: 6.5 Consensus size: 12
52731222 CAGAAACTAC
52731232 AGGAAGTGGAAG
1 AGGAAGTGGAAG
*
52731244 AGGAAGTAGAAG
1 AGGAAGTGGAAG
* *
52731256 AGGAGGTTGAAG
1 AGGAAGTGGAAG
* *
52731268 AAGAAGAGGAAG
1 AGGAAGTGGAAG
* *
52731280 TGGAACTGGAAG
1 AGGAAGTGGAAG
*
52731292 AGGAAGAGGAAG
1 AGGAAGTGGAAG
52731304 AGGAAG
1 AGGAAG
52731310 AGGAGGAAGA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.45, C:0.01, G:0.46, T:0.08
Consensus pattern (12 bp):
AGGAAGTGGAAG
Found at i:52731322 original size:6 final size:6
Alignment explanation
Indices: 52731232--52731313 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
52731222 CAGAAACTAC
* * ** *
52731232 AGGAAG TGGAAG AGGAAG TA-GAAG AGGAGG TTGAAG AAGAAG AGGAAG
1 AGGAAG AGGAAG AGGAAG -AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG
* * *
52731280 TGGAAC TGGAAG AGGAAG AGGAAG AGGAAG AGGA
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGA
52731314 GGAAGAGGAG
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 1 0.02
6 59 0.97
7 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.46, T:0.07
Consensus pattern (6 bp):
AGGAAG
Found at i:52732317 original size:27 final size:27
Alignment explanation
Indices: 52732287--52732341 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
52732277 AGTGGGAGTG
*
52732287 GGGTTCAACCCTGGAGTTGCTGCTGCT
1 GGGTTCAACCCTGGAGTGGCTGCTGCT
* *
52732314 GGGTTTAACCCTGGGGTGGCTGCTGCT
1 GGGTTCAACCCTGGAGTGGCTGCTGCT
52732341 G
1 G
52732342 CACCAGCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.24, G:0.38, T:0.29
Consensus pattern (27 bp):
GGGTTCAACCCTGGAGTGGCTGCTGCT
Found at i:52734526 original size:41 final size:41
Alignment explanation
Indices: 52734481--52734560 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
52734471 TTTATTTTGA
* *
52734481 AGTTTGAGATTCATTCATTTGAGGTTAACGGAAAAAAAAGT
1 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAAGT
52734522 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAA
1 AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAA
52734561 ATTAACTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.30
Consensus pattern (41 bp):
AGTTTGAGATTCATTCATTCGAGGTTAAAGGAAAAAAAAGT
Found at i:52751233 original size:2 final size:2
Alignment explanation
Indices: 52751226--52751251 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52751216 CAGAAGTACT
52751226 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
52751252 AGATTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52753327 original size:12 final size:12
Alignment explanation
Indices: 52753312--52753337 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52753302 AAAAAAAAGC
52753312 AACCAAAATAAA
1 AACCAAAATAAA
52753324 AACCAAAATAAA
1 AACCAAAATAAA
52753336 AA
1 AA
52753338 GGTTTCGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (12 bp):
AACCAAAATAAA
Found at i:52755403 original size:29 final size:30
Alignment explanation
Indices: 52755348--52755427 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
52755338 AATTTTAAAA
* *
52755348 TTATACGTGAACTTTGATTTAATGTGTAATT
1 TTATACATGAACTTTAATTT-ATGTGTAATT
52755379 TTATACATGAACTTTAATTT-TGTGTAATT
1 TTATACATGAACTTTAATTTATGTGTAATT
* * *
52755408 ATACACATGAAACTCTAATT
1 TTATACATG-AACTTTAATT
52755428 GTGGCTCAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.37
30 9 0.21
31 18 0.42
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (30 bp):
TTATACATGAACTTTAATTTATGTGTAATT
Found at i:52757604 original size:46 final size:45
Alignment explanation
Indices: 52757554--52757729 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
52757544 TGGTTGAGCA
52757554 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
52757600 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
52757647 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
52757693 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52757730 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:52757710 original size:93 final size:93
Alignment explanation
Indices: 52757551--52757721 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
52757541 GGATGGTTGA
* *
52757551 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52757616 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
52757644 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52757709 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
52757722 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:52759195 original size:42 final size:42
Alignment explanation
Indices: 52759130--52759291 Score: 146
Period size: 42 Copynumber: 3.7 Consensus size: 42
52759120 TCATTTTCTC
** * * *
52759130 GATGCCATAGTTCAACTACGGTCTTACACA-ACTTCACATAAT
1 GATGCCATAGCCCAGCTATGGTCTTACACATA-TTCACACAAT
* * * *
52759172 GATGTCATAGCCCAGTTATGGTCTTACACATATTCATACATT
1 GATGCCATAGCCCAGCTATGGTCTTACACATATTCACACAAT
*
52759214 GATGCCATAGCCCAGCTATGGTCTTACACATAATCACATGTCACATAT
1 GATGCCATAGCCCAGCTATGGTCTTACACAT-AT-TCA---CACA-AT
*
52759262 CGATGCCATAACCCAGCTATGGTCTTACAC
1 -GATGCCATAGCCCAGCTATGGTCTTACAC
52759292 GAATCACATA
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
42 60 0.62
43 3 0.03
44 2 0.02
47 3 0.03
48 1 0.01
49 28 0.29
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATATTCACACAAT
Found at i:52759441 original size:31 final size:31
Alignment explanation
Indices: 52759403--52759492 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
52759393 CTTGTCACTT
* *
52759403 GTAGCCGAAGCTACCACTATTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
52759434 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
52759465 GTAGCTGGAGCTACCACTTTTCACTGAT
1 GTAGCCGAAGCTACCACTTTTCACTGAT
52759493 AAATTATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:52760127 original size:16 final size:18
Alignment explanation
Indices: 52760096--52760130 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
52760086 CAATTAACCC
52760096 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
52760114 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
52760130 C
1 C
52760131 CTAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:52763702 original size:8 final size:8
Alignment explanation
Indices: 52763689--52763714 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
52763679 TCTCATGTTA
52763689 AAAAAAAG
1 AAAAAAAG
52763697 AAAAAAAG
1 AAAAAAAG
52763705 AAAAAAAG
1 AAAAAAAG
52763713 AA
1 AA
52763715 GAAGCAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:52770955 original size:52 final size:49
Alignment explanation
Indices: 52770772--52770964 Score: 200
Period size: 47 Copynumber: 4.0 Consensus size: 49
52770762 TGCACATAGT
* ** * *
52770772 CACATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
52770820 CACATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
52770867 CACATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
52770914 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
52770965 ATCACATTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
46 25 0.20
47 54 0.44
48 11 0.09
49 1 0.01
52 31 0.25
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:52773338 original size:10 final size:9
Alignment explanation
Indices: 52773325--52773396 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
52773315 TATTTTAGAA
52773325 TATAATTTTT
1 TATAA-TTTT
*
52773335 TATACTTTT
1 TATAATTTT
*
52773344 TA-AGAATTT
1 TATA-ATTTT
* *
52773353 TATAAGCTTG
1 TATAA-TTTT
52773363 TATGAATTTT
1 TAT-AATTTT
52773373 TATAATTTT
1 TATAATTTT
52773382 ATATAATTTT
1 -TATAATTTT
52773392 TATAA
1 TATAA
52773397 GCTGTTTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.02
9 23 0.46
10 24 0.48
11 2 0.04
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (9 bp):
TATAATTTT
Found at i:52773369 original size:19 final size:20
Alignment explanation
Indices: 52773350--52773399 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
52773340 TTTTTAAGAA
*
52773350 TTTTATAAGCTTGTATGAAT
1 TTTTATAAGCTTATATGAAT
**
52773370 TTTTATAATTTTATAT-AAT
1 TTTTATAAGCTTATATGAAT
52773389 TTTTATAAGCT
1 TTTTATAAGCT
52773400 GTTTCAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTTATAAGCTTATATGAAT
Found at i:52778554 original size:14 final size:14
Alignment explanation
Indices: 52778512--52778547 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52778502 GTGTAGAAGA
*
52778512 ATATATGAATATAT
1 ATATATGTATATAT
*
52778526 ATATTTGTATATAT
1 ATATATGTATATAT
52778540 ATATATGT
1 ATATATGT
52778548 GTGTATAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:52778554 original size:16 final size:16
Alignment explanation
Indices: 52778520--52778554 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52778510 GAATATATGA
*
52778520 ATATATATATTTGTAT
1 ATATATATATGTGTAT
*
52778536 ATATATATATGTGTGT
1 ATATATATATGTGTAT
52778552 ATA
1 ATA
52778555 ACATGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
ATATATATATGTGTAT
Found at i:52782049 original size:53 final size:53
Alignment explanation
Indices: 52781893--52782058 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
52781883 GACGAAAAAT
* **
52781893 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
52781945 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
52781998 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
52782052 TATGTGA
1 -ATGTGA
52782059 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:52789567 original size:53 final size:53
Alignment explanation
Indices: 52789411--52789576 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
52789401 GACGAAAAAT
* **
52789411 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
52789463 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
52789516 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
52789570 TATGTGA
1 -ATGTGA
52789577 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:52791060 original size:21 final size:21
Alignment explanation
Indices: 52791034--52791078 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52791024 GTATATATAT
*
52791034 GTTCATGGTCTAGGTTTTAGG
1 GTTCATGGTCTAGGATTTAGG
* *
52791055 GTTCATGGTTTAGGATTTGGG
1 GTTCATGGTCTAGGATTTAGG
52791076 GTT
1 GTT
52791079 TAATTATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.07, G:0.36, T:0.44
Consensus pattern (21 bp):
GTTCATGGTCTAGGATTTAGG
Found at i:52791481 original size:22 final size:21
Alignment explanation
Indices: 52791448--52791489 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
52791438 AAATCTTCAA
* *
52791448 AAAAAATTAAAATTTAAAAAT
1 AAAAAATAAAAACTTAAAAAT
52791469 AAAAAATAAAAAACTTAAAAA
1 AAAAAAT-AAAAACTTAAAAA
52791490 CTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATAAAAACTTAAAAAT
Found at i:52795596 original size:25 final size:25
Alignment explanation
Indices: 52795568--52795616 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
52795558 TCATCTATAG
* *
52795568 CGGCATTTTTTGCGGCGCTTAAAAA
1 CGGCATTTTTTGCGACACTTAAAAA
*
52795593 CGGCGTTTTTTGCGACACTTAAAA
1 CGGCATTTTTTGCGACACTTAAAA
52795617 GCGCCGCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
CGGCATTTTTTGCGACACTTAAAAA
Found at i:52810536 original size:21 final size:22
Alignment explanation
Indices: 52810510--52810560 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
52810500 AATTTTCAAA
52810510 AAAAAATTAAGTCATTC-T-TTT
1 AAAAAATTAAGT-ATTCATATTT
**
52810531 AAAAAAACAAGTATTCATATTT
1 AAAAAATTAAGTATTCATATTT
52810553 AAAAAATT
1 AAAAAATT
52810561 TCATTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 9 0.38
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAAATTAAGTATTCATATTT
Found at i:52825148 original size:21 final size:22
Alignment explanation
Indices: 52825124--52825171 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
52825114 TGATACAAAA
*
52825124 AAATATTGTGTC-AAGAAAATT
1 AAATATTGTGTCAAAAAAAATT
52825145 AAATATTGTGTCATAAAAAAATT
1 AAATATTGTGTCA-AAAAAAATT
52825168 AAAT
1 AAAT
52825172 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
23 12 0.50
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATATTGTGTCAAAAAAAATT
Found at i:52832319 original size:22 final size:22
Alignment explanation
Indices: 52832291--52832333 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
52832281 GAATAAAGCA
52832291 TTTGCCAATAATGAACTTAGGC
1 TTTGCCAATAATGAACTTAGGC
52832313 TTTGCCAATAATGAACTTAGG
1 TTTGCCAATAATGAACTTAGG
52832334 ACAGCCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (22 bp):
TTTGCCAATAATGAACTTAGGC
Found at i:52837622 original size:25 final size:28
Alignment explanation
Indices: 52837594--52837644 Score: 81
Period size: 25 Copynumber: 1.9 Consensus size: 28
52837584 AATGATAATT
52837594 CAAATATA-ATT-TAATTG-TAAAATAA
1 CAAATATATATTATAATTGTTAAAATAA
52837619 CAAATATATATTATAATTGTTAAAAT
1 CAAATATATATTATAATTGTTAAAAT
52837645 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 3 0.13
27 6 0.26
28 6 0.26
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
CAAATATATATTATAATTGTTAAAATAA
Found at i:52839153 original size:20 final size:20
Alignment explanation
Indices: 52839117--52839175 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
52839107 AAAAAATTCA
52839117 AAAAATATATATAAATATTTTT
1 AAAAATATA-AT-AATATTTTT
*
52839139 AAAAATATAATAATA-ATTT
1 AAAAATATAATAATATTTTT
**
52839158 AAATTGTATAATAATATT
1 AAA-AATATAATAATATT
52839176 AATATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 14 0.45
21 2 0.06
22 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAATATAATAATATTTTT
Found at i:52839763 original size:21 final size:20
Alignment explanation
Indices: 52839739--52839800 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
52839729 TTTTATTTTA
52839739 TTTAATATTATTATTATATAT
1 TTTAA-ATTATTATTATATAT
52839760 TTTAAATTTATTATTATAT-T
1 TTTAAA-TTATTATTATATAT
*
52839780 TTTAAAATA-T-TTATATAT
1 TTTAAATTATTATTATATAT
52839798 TTT
1 TTT
52839801 TTAAAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 6 0.16
18 5 0.13
19 2 0.05
20 8 0.21
21 17 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAAATTATTATTATATAT
Found at i:52839793 original size:20 final size:21
Alignment explanation
Indices: 52839742--52839807 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
52839732 TATTTTATTT
52839742 AATATTATTATTATATATTTT-A
1 AATA-TATTATTATAT-TTTTAA
*
52839764 AATTTATTATTATATTTTTAA
1 AATATATTATTATATTTTTAA
52839785 AATAT-TTA-TATATTTTTTAA
1 AATATATTATTATA-TTTTTAA
52839805 AAT
1 AAT
52839808 TAAAATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.10
20 17 0.43
21 16 0.40
22 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATATATTATTATATTTTTAA
Found at i:52839823 original size:26 final size:27
Alignment explanation
Indices: 52839781--52839835 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
52839771 TATTATATTT
*
52839781 TTAAAATATTTATATATT-TTTTAAAA
1 TTAAAATAATTATATATTATTTTAAAA
*
52839807 TTAAAATAAATTA-ATATTATTTTTAAA
1 TTAAAAT-AATTATATATTATTTTAAAA
52839834 TT
1 TT
52839836 TTGAGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAAATAATTATATATTATTTTAAAA
Found at i:52840392 original size:18 final size:18
Alignment explanation
Indices: 52840364--52840402 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52840354 TAAAAAAAAC
52840364 TAAATTTATTAAATTATTA
1 TAAATTTATTAAATTA-TA
52840383 TAAA-TTATTAAATTATA
1 TAAATTTATTAAATTATA
52840400 TAA
1 TAA
52840403 TAAAATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTTATTAAATTATA
Found at i:52845250 original size:25 final size:21
Alignment explanation
Indices: 52845205--52845254 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
52845195 TTAATAGTTA
*
52845205 AAAAAATAATATTTTAAATTTT
1 AAAAAATAATA-TTTAAAATTT
52845227 AAAAAATAATATTATAAAACATTT
1 AAAAAATAATATT-T-AAA-ATTT
52845251 AAAA
1 AAAA
52845255 TGTACATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 12 0.50
23 3 0.12
24 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATAATATTTAAAATTT
Found at i:52845968 original size:24 final size:24
Alignment explanation
Indices: 52845936--52845985 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
52845926 TCTAGAGCTT
52845936 TTCGTTTTGTTTAGTTGTAAACTG
1 TTCGTTTTGTTTAGTTGTAAACTG
52845960 TTCGTTTTGTTTAGTTGTAAACTG
1 TTCGTTTTGTTTAGTTGTAAACTG
52845984 TT
1 TT
52845986 TTTAGGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (24 bp):
TTCGTTTTGTTTAGTTGTAAACTG
Found at i:52846117 original size:19 final size:19
Alignment explanation
Indices: 52846072--52846109 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
52846062 TATTAAATTT
52846072 ATTAAA-ATT-AAGATTAA
1 ATTAAATATTGAAGATTAA
52846089 ATTAAATATTGAAGATTAA
1 ATTAAATATTGAAGATTAA
52846108 AT
1 AT
52846110 ATATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
ATTAAATATTGAAGATTAA
Found at i:52847664 original size:15 final size:16
Alignment explanation
Indices: 52847638--52847671 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52847628 TATTTTATTT
52847638 TTTAATATTAATATAA
1 TTTAATATTAATATAA
*
52847654 TTTAATA-TAATATGA
1 TTTAATATTAATATAA
52847669 TTT
1 TTT
52847672 GATTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAATATTAATATAA
Found at i:52850874 original size:20 final size:20
Alignment explanation
Indices: 52850849--52850892 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
52850839 CTTAGTCAAA
52850849 TTTTGAATTAAGGTATCGAT
1 TTTTGAATTAAGGTATCGAT
52850869 TTTTGAATTAAGGTATCGAT
1 TTTTGAATTAAGGTATCGAT
52850889 TTTT
1 TTTT
52850893 TTCCTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTTGAATTAAGGTATCGAT
Found at i:52859272 original size:25 final size:25
Alignment explanation
Indices: 52859197--52859360 Score: 144
Period size: 27 Copynumber: 6.6 Consensus size: 25
52859187 AACAATACAT
*
52859197 AAATATATACGT-ATATA-TATT-A
1 AAATATATACATAATATAGTATTAA
* *
52859219 AAATATATACGTAATAATAAG-AATAA
1 AAATATATACATAAT-AT-AGTATTAA
*
52859245 AAAGTATATACATAATATAGTGTTAA
1 AAA-TATATACATAATATAGTATTAA
*
52859271 AAATACATACATAATATAGTTATTAAA
1 AAATATATACATAATATAG-TATT-AA
* * **
52859298 AAATATATACATAAGATAATA-TGC
1 AAATATATACATAATATAGTATTAA
52859322 AAATATAT--ATAATATAGTATTAA
1 AAATATATACATAATATAGTATTAA
*
52859345 AGATATATACATAATA
1 AAATATATACATAATA
52859361 CATATAAAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
22 21 0.18
23 10 0.09
24 10 0.09
25 27 0.24
26 17 0.15
27 29 0.25
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (25 bp):
AAATATATACATAATATAGTATTAA
Found at i:52859379 original size:47 final size:49
Alignment explanation
Indices: 52859242--52859379 Score: 122
Period size: 52 Copynumber: 2.8 Consensus size: 49
52859232 ATAATAAGAA
* * * * *
52859242 TAAAAAGTATATACATAATATAGTGTTAAAAATACATACATAATATAGTTAT
1 TAAAAAATATATACATAAGATAAT-ATAAAAA-A-ATATATAATATAGTTAT
** *
52859294 TAAAAAATATATACATAAGATAATATGCAAATATATATAATATAG-TAT
1 TAAAAAATATATACATAAGATAATATAAAAAAATATATAATATAGTTAT
*
52859342 T-AAAGATATATACAT-A-ATACATATAAAAAAATCATATA
1 TAAAAAATATATACATAAGATA-ATATAAAAAAAT-ATATA
52859380 TACATGATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.04
46 10 0.14
47 18 0.25
48 4 0.06
49 12 0.17
51 4 0.06
52 21 0.29
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (49 bp):
TAAAAAATATATACATAAGATAATATAAAAAAATATATAATATAGTTAT
Found at i:52859379 original size:49 final size:50
Alignment explanation
Indices: 52859269--52859381 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 50
52859259 ATATAGTGTT
* * *
52859269 AAAAATACATACATAATATAGTTATTAAAAAATATATACATAAGATAATAT
1 AAAAAT-CATATATAATATAGTTATTAAAAAATATATACATAAGACAATAA
** * *
52859320 GCAAAT-ATATATAATATAG-TATT-AAAGATATATACATAATACATATAA
1 AAAAATCATATATAATATAGTTATTAAAAAATATATACATAAGACA-ATAA
52859368 AAAAATCATATATA
1 AAAAATCATATATA
52859382 CATGATATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
47 17 0.33
48 11 0.22
49 19 0.37
51 4 0.08
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (50 bp):
AAAAATCATATATAATATAGTTATTAAAAAATATATACATAAGACAATAA
Found at i:52859522 original size:25 final size:26
Alignment explanation
Indices: 52859457--52859608 Score: 128
Period size: 25 Copynumber: 6.1 Consensus size: 26
52859447 ACGTATGTAT
* *
52859457 ATATATAAATAATAATGGTATTAG-A
1 ATATATACATAATAATAGTATTAGAA
*
52859482 A-ATATACAAAAT-ATAGTATTAGAA
1 ATATATACATAATAATAGTATTAGAA
52859506 ATATATACATAA-AATAGTA-TA-AA
1 ATATATACATAATAATAGTATTAGAA
*
52859529 A-A-ATATATAACTAAT-GATATTA-AA
1 ATATATACATAA-TAATAG-TATTAGAA
* *
52859553 ATATATACATAATAATA-TATAAAAA
1 ATATATACATAATAATAGTATTAGAA
*
52859578 ATATATACATAATATATACATATTAGAA
1 ATATATACATAATA-ATA-GTATTAGAA
52859606 ATA
1 ATA
52859609 AAAAACGACT
Statistics
Matches: 104, Mismatches: 9, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
21 7 0.07
22 2 0.02
23 17 0.16
24 22 0.21
25 37 0.36
26 10 0.10
28 9 0.09
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATATACATAATAATAGTATTAGAA
Done.