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 149 of 214
Found at i:44430043 original size:96 final size:93
Alignment explanation
Indices: 44429768--44430067 Score: 339
Period size: 96 Copynumber: 3.2 Consensus size: 93
44429758 TGTAATCCTA
* * *
44429768 AACCCCAAACCCTAATTTATTTGAGTTTTTTCTTAAAAACCCTAAACATTAAACCCTAATCTATT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTTTTAAAAACCCTAAACACTAAACCCTAATCTATT
*** * *
44429833 TTTTTAATTTATAATTAATTTACTCAAGT
65 TTAAAAATTTTTAATTAATTTACTTAAGT
* * * * *
44429862 AATCTTAAACCCTAATTTATTTGATTTTTCTTTAAAAACCCTTAACACTAAACCCTAATATGATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTTTTAAAAACCCTAAACACTAAACCCTAATCT-ATT
*
44429927 TTAAAATTTTTTTAATTAATTTACTTAAGT
65 TTAAAA-ATTTTTAATTAATTTACTTAAGT
* ** * *
44429957 AACCCTAAACCCTAATTTAATTGATTTTTTATTTAAAAACTATAAATACAAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTT-TTTAAAAACCCTAAACACTAAACCCTAATCT-AT
* * *
44430022 TTTGAAAAATTTTTAATTAATTTAATTGAGA
64 TTT-AAAAATTTTTAATTAATTTACTTAAGT
*
44430053 AACCTTAAACCCTAA
1 AACCCTAAACCCTAA
44430068 ACCATAATCC
Statistics
Matches: 172, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
93 32 0.19
94 27 0.16
95 46 0.27
96 63 0.37
97 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.41
Consensus pattern (93 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTTTTAAAAACCCTAAACACTAAACCCTAATCTATTT
TAAAAATTTTTAATTAATTTACTTAAGT
Found at i:44430158 original size:27 final size:30
Alignment explanation
Indices: 44430108--44430162 Score: 89
Period size: 27 Copynumber: 1.9 Consensus size: 30
44430098 TTTAAAATCT
44430108 TAAACCTAAAAACCCTCAAAACCCTAACCC
1 TAAACCTAAAAACCCTCAAAACCCTAACCC
44430138 TAAACC-AAAAA-CC-CAAAACCCTAAC
1 TAAACCTAAAAACCCTCAAAACCCTAAC
44430163 AACAGGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 12 0.48
28 2 0.08
29 5 0.20
30 6 0.24
ACGTcount: A:0.51, C:0.38, G:0.00, T:0.11
Consensus pattern (30 bp):
TAAACCTAAAAACCCTCAAAACCCTAACCC
Found at i:44430397 original size:23 final size:23
Alignment explanation
Indices: 44430348--44430397 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
44430338 GATTTTTCCT
**
44430348 AAATATTATCACTAAATAATTTT
1 AAATATTATCACTAAATAATTCA
*
44430371 AAATATTATCACTAAATAGTTCA
1 AAATATTATCACTAAATAATTCA
44430394 AAAT
1 AAAT
44430398 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:44430822 original size:39 final size:41
Alignment explanation
Indices: 44430743--44430832 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 41
44430733 TAAAAAATAT
*
44430743 TTATATTAAAAAACACTATTATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
*
44430784 TTATATTAAAAAACAC-A-AATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
*
44430823 TTGTATTAAA
1 TTATATTAAA
44430833 TATAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 29 0.63
40 1 0.02
41 16 0.35
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
Found at i:44431421 original size:21 final size:20
Alignment explanation
Indices: 44431367--44431422 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
44431357 CTAAAGTTAG
*
44431367 GATTTCTCTCTTTATCCTTTT
1 GATTTCT-TCTTTTTCCTTTT
44431388 GA--TCTTCAATTTTTCCCTTTT
1 GATTTCTTC--TTTTT-CCTTTT
44431409 GATTTCTTCTTTTT
1 GATTTCTTCTTTTT
44431423 GTATTCAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 4 0.14
21 15 0.52
23 5 0.17
ACGTcount: A:0.11, C:0.21, G:0.05, T:0.62
Consensus pattern (20 bp):
GATTTCTTCTTTTTCCTTTT
Found at i:44448546 original size:135 final size:137
Alignment explanation
Indices: 44448303--44448621 Score: 463
Period size: 135 Copynumber: 2.3 Consensus size: 137
44448293 CGGGACACGG
* ***
44448303 TATTTAACTCCGATT---ACACTCTCTAAATCAAATTCAAAATTAAGTTAATATTTTTTTTCAAA
1 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATA-TTTTTAAAAAA
* *
44448365 GTTACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCGGCACAAAAGAAACTAAAATCAAATTC
65 GATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACT-AAATCAAATTC
*
44448430 AAATTTTGA
129 AAAATTTGA
44448439 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATT-A-A-TTTTAAAAAAG
1 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATATTTTTAAAAAAG
*
44448501 ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAGCTAAATCAAATTCAA
66 ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACTAAATCAAATTCAA
44448566 AATTTGA
131 AATTTGA
*
44448573 TATTTTAACTCCGATTGCAACACGT-TATAAATCAAATATCAAAATTAAA
1 TA-TTTAACTCCGATTGCAACAC-TCTCTAAATCAAAT-TCAAAATTAAA
44448622 ACTTTTTAAG
Statistics
Matches: 168, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
134 21 0.12
135 88 0.52
136 27 0.16
137 1 0.01
138 1 0.01
139 30 0.18
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (137 bp):
TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATATTTTTAAAAAAG
ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACTAAATCAAATTCAA
AATTTGA
Found at i:44456695 original size:21 final size:21
Alignment explanation
Indices: 44456669--44456724 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
44456659 AATAGCGGTG
*
44456669 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
44456690 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
44456711 GCAGTGCGATTAGA
1 GCGGTGAGATTAGA
44456725 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:44458558 original size:4 final size:4
Alignment explanation
Indices: 44458549--44458611 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
44458539 TGCAAAAGGA
44458549 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
44458597 TATG TATG TATG TAT
1 TATG TATG TATG TAT
44458612 ATAAATATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:44459059 original size:3 final size:3
Alignment explanation
Indices: 44458982--44459040 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
44458972 AAATGGAAAT
* * * * * *
44458982 ATA ATG ATA ATA ACA ATA ATA TTA ATA ATA ATA CTA ATA ATG ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44459030 ATA ATA ATA AT
1 ATA ATA ATA AT
44459041 TTATTAATTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44461036 original size:12 final size:12
Alignment explanation
Indices: 44461019--44461050 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
44461009 TTATTTATTG
44461019 TTATTATTAATA
1 TTATTATTAATA
*
44461031 TTATTATTACTA
1 TTATTATTAATA
44461043 TTATTATT
1 TTATTATT
44461051 CCATTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:44474811 original size:18 final size:18
Alignment explanation
Indices: 44474777--44474817 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
44474767 TAAAATTATT
*
44474777 TTATAAATTTCTAATTTA
1 TTATAAACTTCTAATTTA
44474795 CTTATAAACTT-TAATTTA
1 -TTATAAACTTCTAATTTA
44474813 TTATA
1 TTATA
44474818 CGATTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAAACTTCTAATTTA
Found at i:44476322 original size:254 final size:245
Alignment explanation
Indices: 44475679--44476672 Score: 696
Period size: 251 Copynumber: 3.9 Consensus size: 245
44475669 TTTTAAGGCG
* * * *
44475679 AGTGGAATCTAGTTTTACAATTGATCTTCGGA-TCAAAATCGAATATAATTTTATATTTTTTGTT
1 AGTGAAATCTAGTTTTTCAATTGA---TC-GACTCAAAATCAAATATAA-CTT-TA-TTTTTGTT
* * * * * * ** *
44475743 GGATTCAAGGTAAGTATATTAATATATAATTTTAGGCGGGTGGAATCTAGTTTTTCAATTGGTGG
59 GGATTCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAGT-GAATTTAATTTTTCAATTCATCG
* * * * * *
44475808 GGTTAAAAATATGCATATCATGTTAAAATCGTTGGTAGCATTGGATATTGTTAC-ATAT-G--AC
123 GATAAAAAATATGCCTAGCAAGTTAAAATCGTTGGTAGCATTGGATATTG-TACGA-ATGGCAAA
* * ** * * * * * *
44475869 A-AAAAAAAAAACTCAAAC-CTAGTA-AGCGGTTAGGTTTTTTAAAAAGTCAAAATTTGAGA-CG
186 AGAAAAAAAAAACTCAAACTC-AATAGA-CAGTTAAATTTTTT-TAAA-TCGAGA-TTCAAACCA
* * * * * *
44475930 AGTGAAATCTAGTTTTTCTATTGATCAAATCAAAAAT-AAATTTAGCTTTGTTTTCTTTTCGTTG
1 AGTGAAATCTAGTTTTTCAATTGATCGACTC-AAAATCAAATATAAC--T-TTAT-TTTT-GTTG
* *
44475994 GATTCAAGGTAAGTAAATTAATGTTTACTTTTAGGCAAGTGGAATTT-ATATTTTCAA-TCGATC
60 GATTCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAGT-GAATTTAAT-TTTTCAATTC-ATC
* * * * *
44476057 GAATAAAAAATATGCCAAACACGTTAAAATCGTTGGTAGCATTGGATACTGCTACGAATGGCAAA
122 GGATAAAAAATATGCCTAGCAAGTTAAAATCGTTGGTAGCATTGGATATTG-TACGAATGGCAAA
* *
44476122 AGAAAAAAAAAATTCGAA-TCCAATAGACAGTTAAATTCTTTTTAAAAGAAATC-AGATTTCAAA
186 AGAAAAAAAAAACTCAAACT-CAATAGACAGTTAAATT-TTTTT-----AAATCGAGA-TTCAAA
44476185 CCA
243 CCA
* * ** *
44476188 AGTGGAATCTAG-TTTTCAATTGATTGGAC-CAAAAT-GGATATAAC-TTATTTTTGTTGGATTT
1 AGTGAAATCTAGTTTTTCAATTGA-TCGACTCAAAATCAAATATAACTTTATTTTTGTTGGATTC
* * *
44476249 AGGGTAAAGAAATTAATTAATATTTACTTTTAGGCGAGTGAAATTTAATTTTTCAATTCATTGGA
65 AAGGT-AAG---TAAATTAATATTTACTTTTAGGCGAGTG-AATTTAATTTTTCAATTCATCGGA
* * * ** * *
44476314 TCAAAAATATGCCTAGCATGTTAAAATTGTTGACAACATTGGATTTTGTCACGAATGGCAAAAGA
125 TAAAAAATATGCCTAGCAAGTTAAAATCGTTGGTAGCATTGGATATTGT-ACGAATGGCAAAAGA
* * * * ****
44476379 GAAATAAAAACTCAAACTCAATAGACGGTTAGATTTTTTTAAATCGGGATTCAAGGTG
189 -AAAAAAAAACTCAAACTCAATAGACAGTTAAATTTTTTTAAATCGAGATTCAAACCA
44476437 AGTGAAATCTAGTTTTTCAATTGATCGACTCAAAATCAAATATAACTTTATTATTTTTGTTGGAT
1 AGTGAAATCTAGTTTTTCAATTGATCGACTCAAAATCAAATATAAC--T-TTATTTTTGTTGGAT
* * * *
44476502 TCAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTGGATTCTAATTTTTTAATTGATCGGATA
63 TCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAGTGAATT-TAATTTTTCAATTCATCGGAT-
* * * * *
44476567 AAAAAATATACCTAGCAAGTT-AAATCGTTAGTAGCATTGGATATTGTTACAAATAGCAAAAAAA
126 AAAAAATATGCCTAGCAAGTTAAAATCGTTGGTAGCATTGGATATTG-TACGAATGGC-AAAAGA
* *
44476631 AAAAAAAAACTCAAAC-CTAATAGGCAGTTAGATTTTGTTTAA
189 AAAAAAAAACTCAAACTC-AATAGACAGTTAAATTTT-TTTAA
44476673 TTGGATTTTG
Statistics
Matches: 589, Mismatches: 105, Indels: 97
0.74 0.13 0.12
Matches are distributed among these distances:
247 1 0.00
248 10 0.02
249 38 0.06
250 136 0.23
251 138 0.23
252 32 0.05
253 4 0.01
254 125 0.21
255 57 0.10
256 11 0.02
257 18 0.03
258 16 0.03
259 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (245 bp):
AGTGAAATCTAGTTTTTCAATTGATCGACTCAAAATCAAATATAACTTTATTTTTGTTGGATTCA
AGGTAAGTAAATTAATATTTACTTTTAGGCGAGTGAATTTAATTTTTCAATTCATCGGATAAAAA
ATATGCCTAGCAAGTTAAAATCGTTGGTAGCATTGGATATTGTACGAATGGCAAAAGAAAAAAAA
AACTCAAACTCAATAGACAGTTAAATTTTTTTAAATCGAGATTCAAACCA
Found at i:44476607 original size:251 final size:248
Alignment explanation
Indices: 44475587--44476672 Score: 871
Period size: 250 Copynumber: 4.3 Consensus size: 248
44475577 ATAGCTCTTG
* * *
44475587 GCATTGGATATTGTTATGGATGGCAAAAAGAAAGAAAGAAAAACTCATACCCAATA-AGCGGTTA
1 GCATTGGATATTGTTACGAATGGC-AAAAG-AA-AAA-AAAAACTCA-AACCAATAGA-CGGTTA
* * * * * *
44475651 GATTATTTTTAAACCGGGTTTTAAGGCGAGTGGAATCTAGTTTTACAATTGATCTTCGGA-TCAA
60 GATT-TTTTTAAATCGAGATTCAAGGCGAGTGAAATCTAGTTTTTCAATTGA--TTC-GACTCAA
* * * * *
44475715 AATCGAATATAATTTTA-TATTTTTTGTTGGATTCAAGGTAAGTATATTAATATATAATTTTAGG
121 AAT-AAATATAACTTTATTA-TTTTTGTTGGATTCAAGGTAAGTAAATTAATATTTACTTTTAGG
* * * * * * * * *
44475779 CGGGTGGAATCTAGTTTTTCAATTGGTGGGGTTAAAAATATGCATATCATGTTAAAATCGTTGGT
184 CGAGTGG-ATTTAATTTTTCAATTGATCGGATAAAAAATATGCCTAGCATGTTAAAATCGTTGGT
44475844 A
248 A
* * *
44475845 GCATTGGATATTGTTAC-ATAT-G--ACA-AAAAAAAAAACTCAAACCTAGTA-AGCGGTTAGGT
1 GCATTGGATATTGTTACGA-ATGGCAAAAGAAAAAAAAAACTCAAACC-AATAGA-CGGTTAGAT
* * * ** * * * *
44475904 TTTTTAAAAAGTCAAAATTTGAGACGAGTGAAATCTAGTTTTTCTATTGA-TCAAATCAAAAATA
63 TTTTT-TAAA-TCGAGATTCAAGGCGAGTGAAATCTAGTTTTTCAATTGATTCGACTC-AAAATA
* * * * * *
44475968 AATTTAGCTTTGTTTTCTTTTCGTTGGATTCAAGGTAAGTAAATTAATGTTTACTTTTAGGCAAG
125 AATATAACTTTATTAT-TTTT-GTTGGATTCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAG
* * * * *
44476033 TGGAATTT-ATATTTTCAATCGATCGAATAAAAAATATGCCAAACACGTTAAAATCGTTGGTA
188 TGG-ATTTAAT-TTTTCAATTGATCGGATAAAAAATATGCCTAGCATGTTAAAATCGTTGGTA
* * * * * *
44476095 GCATTGGATACTGCTACGAATGGCAAAAGAAAAAAAAAATTCGAATCCAATAGACAGTTAAATTC
1 GCATTGGATATTGTTACGAATGGCAAAAGAAAAAAAAAACTC-AAACCAATAGACGGTTAGATT-
** * * *
44476160 TTTTTAAAAGAAATC-AGATTTCAAACCAAGTGGAATCTAG-TTTTCAATTGATTGGAC-CAAAA
64 TTTTT-----AAATCGAGA-TTCAAGGCGAGTGAAATCTAGTTTTTCAATTGATTCGACTCAAAA
** * * *
44476222 TGGATATAAC----TTATTTTTGTTGGATTTAGGGTAAAGAAATTAATTAATATTTACTTTTAGG
123 TAAATATAACTTTATTATTTTTGTTGGATTCAAGGT-AAG---TAAATTAATATTTACTTTTAGG
* * * * * **
44476283 CGAGTGAAATTTAATTTTTCAATTCATTGGATCAAAAATATGCCTAGCATGTTAAAATTGTTGAC
184 CGAGTG-GATTTAATTTTTCAATTGATCGGATAAAAAATATGCCTAGCATGTTAAAATCGTTGGT
44476348 A
248 A
* * * *
44476349 ACATTGGATTTTGTCACGAATGGCAAAAGAGAAATAAAAACTCAAACTCAATAGACGGTTAGATT
1 GCATTGGATATTGTTACGAATGGCAAAAGA-AAAAAAAAACTCAAAC-CAATAGACGGTTAGATT
* *
44476414 TTTTTAAATCGGGATTCAAGGTGAGTGAAATCTAGTTTTTCAATTGA-TCGACTCAAAATCAAAT
64 TTTTTAAATCGAGATTCAAGGCGAGTGAAATCTAGTTTTTCAATTGATTCGACTCAAAAT-AAAT
*
44476478 ATAACTTTATTATTTTTGTTGGATTCAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTGGAT
128 ATAACTTTATTATTTTTGTTGGATTCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAGTGGAT
* * * *
44476543 TCTAATTTTTTAATTGATCGGATAAAAAAATATACCTAGCAAGTT-AAATCGTTAGTA
193 T-TAATTTTTCAATTGATCGGAT-AAAAAATATGCCTAGCATGTTAAAATCGTTGGTA
* * * * *
44476600 GCATTGGATATTGTTACAAATAGCAAAAAAAAAAAAAAAACTCAAACCTAATAGGCAGTTAGATT
1 GCATTGGATATTGTTACGAATGGC-AAAAGAAAAAAAAAACTCAAACC-AATAGACGGTTAGATT
44476665 TTGTTTAA
64 TT-TTTAA
44476673 TTGGATTTTG
Statistics
Matches: 654, Mismatches: 128, Indels: 98
0.74 0.15 0.11
Matches are distributed among these distances:
247 1 0.00
248 13 0.02
249 43 0.07
250 163 0.25
251 150 0.23
252 33 0.05
253 2 0.00
254 129 0.20
255 56 0.09
256 10 0.02
257 14 0.02
258 37 0.06
259 3 0.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (248 bp):
GCATTGGATATTGTTACGAATGGCAAAAGAAAAAAAAAACTCAAACCAATAGACGGTTAGATTTT
TTTAAATCGAGATTCAAGGCGAGTGAAATCTAGTTTTTCAATTGATTCGACTCAAAATAAATATA
ACTTTATTATTTTTGTTGGATTCAAGGTAAGTAAATTAATATTTACTTTTAGGCGAGTGGATTTA
ATTTTTCAATTGATCGGATAAAAAATATGCCTAGCATGTTAAAATCGTTGGTA
Found at i:44476710 original size:251 final size:252
Alignment explanation
Indices: 44475932--44476783 Score: 550
Period size: 251 Copynumber: 3.4 Consensus size: 252
44475922 TTGAGACGAG
* * * * * * * *
44475932 TGAAATCTAGTTTTTCTATTGATCAAATCAAAAAT-AAATTTAGCTTTGTTTTCTTTTC-GTTGG
1 TGAAATCTAATTTCTCAATTGATCAGATC-AAAATCAAATATAACTTT-ATTTC-TTTCAATTGG
* * * *
44475995 ATTCAAGGTAAGTAAATTAATGTTTACTTTTAGGCAAGTGGAATTT-ATATTTTCAA-TCGATCG
63 ATTCAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTGAAATTTAAT-TTTTCAATTC-ATCG
* * * * * ** * * * *
44476058 AATAAAAAATATGCCAAACACGTTAAAATCGTTGGTAGCATTGGATACTG-CTACGAATGGC-AA
126 GATAAAAAATATACCTAGCAAGTTAAAATCGTTGACAACATTGGATATTGTC-ACAAATAGCAAA
* * * * *
44476121 AAGAAAAAAAAAATTCGAA-TCCAATAGACAGTTAAATTCTTTTTAAAAGAAATC-AGATTTCAA
190 AAAAAAAAAAAAACTCAAACT-CAATAGACAGTTAGATT-TTTTT-----AAATCGGGA-TTCAA
*
44476184 --ACCAA
247 GGA-GAA
* * ** * ** *
44476189 GTGGAATCTAGTTT-TCAATTGATTGGACCAAAAT-GGATATAAC-TTA-TT-TTT--GTTGGAT
1 -TGAAATCTAATTTCTCAATTGATCAGATCAAAATCAAATATAACTTTATTTCTTTCAATTGGAT
* * * * *
44476247 TTAGGGTAAAGAAATTAATTAATATTTACTTTTAGGCGAGTGAAATTTAATTTTTCAATTCATTG
65 TCAAGGT-AAG---TAAATTAATATTTACTTTTAGACGAGTGAAATTTAATTTTTCAATTCATCG
* * * * * * *
44476312 GATCAAAAATATGCCTAGCATGTTAAAATTGTTGACAACATTGGATTTTGTCACGAATGGCAAAA
126 GATAAAAAATATACCTAGCAAGTTAAAATCGTTGACAACATTGGATATTGTCACAAATAGCAAAA
* * * * * *
44476377 GAGAAATAAAAACTCAAACTCAATAGACGGTTAGATTTTTTTAAATCGGGATTCAAGGTGAG
191 AAAAAAAAAAAACTCAAACTCAATAGACAGTTAGATTTTTTTAAATCGGGATTCAAGGAGAA
* * **
44476439 TGAAATCTAGTTTTTCAATTGATC-GACTCAAAATCAAATATAACTTTATTAT-TTT-TGTTGGA
1 TGAAATCTAATTTCTCAATTGATCAGA-TCAAAATCAAATATAACTTTATT-TCTTTCAATTGGA
* * *
44476501 TTCAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTG-GATTCTAATTTTTTAATTGATCGGA
64 TTCAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTGAAATT-TAATTTTTCAATTCATCGGA
* * *
44476565 TAAAAAAATATACCTAGCAAGTT-AAATCGTT-AGTAGCATTGGATATTGTTACAAATAGCAAAA
128 T-AAAAAATATACCTAGCAAGTTAAAATCGTTGA-CAACATTGGATATTGTCACAAATAGCAAAA
* * **
44476628 AAAAAAAAAAAACTCAAAC-CTAATAGGCAGTTAGATTTTGTTT-AAT-TGGATTTTGAGGAGAA
191 AAAAAAAAAAAACTCAAACTC-AATAGACAGTTAGATTTT-TTTAAATCGGGA-TTCAAGGAGAA
** * * * ** *
44476690 TTTAATTTAATTTCTCAATTGGTCAGATCAAAATCAGATATAGTTTTGTTTCTTTCAATTGGATT
1 TGAAATCTAATTTCTCAATTGATCAGATCAAAATCAAATATAACTTTATTTCTTTCAATTGGATT
** *
44476755 CGTGGTAAGTAAATTAATGTTTACTTTTA
66 CAAGGTAAGTAAATTAATATTTACTTTTA
44476784 AGTAACTGAA
Statistics
Matches: 477, Mismatches: 89, Indels: 62
0.76 0.14 0.10
Matches are distributed among these distances:
249 24 0.05
250 39 0.08
251 170 0.36
252 59 0.12
253 3 0.01
254 100 0.21
255 49 0.10
256 11 0.02
257 10 0.02
258 12 0.03
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (252 bp):
TGAAATCTAATTTCTCAATTGATCAGATCAAAATCAAATATAACTTTATTTCTTTCAATTGGATT
CAAGGTAAGTAAATTAATATTTACTTTTAGACGAGTGAAATTTAATTTTTCAATTCATCGGATAA
AAAATATACCTAGCAAGTTAAAATCGTTGACAACATTGGATATTGTCACAAATAGCAAAAAAAAA
AAAAAAACTCAAACTCAATAGACAGTTAGATTTTTTTAAATCGGGATTCAAGGAGAA
Found at i:44479504 original size:22 final size:19
Alignment explanation
Indices: 44479471--44479516 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
44479461 TAGTTGTTTC
*
44479471 TAAATTATTTTTAGGGCTCCG
1 TAAATTAATTTTA-GGC-CCG
44479492 TAAACTTAATTTTAGGCCCG
1 TAAA-TTAATTTTAGGCCCG
44479512 TAAAT
1 TAAAT
44479517 GTATTTATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 7 0.30
22 8 0.35
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (19 bp):
TAAATTAATTTTAGGCCCG
Found at i:44482119 original size:2 final size:2
Alignment explanation
Indices: 44482112--44482191 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
44482102 CCCAAATTAA
44482112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
44482154 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
44482192 TTTTGAAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44483297 original size:26 final size:26
Alignment explanation
Indices: 44483237--44483298 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
44483227 ACAAAGAAAT
*
44483237 AAAAAGAAAAAACTAATATTGTTCAA
1 AAAAATAAAAAACTAATATTGTTCAA
44483263 AAAAATAAAAAACTAATATTGTTCAA
1 AAAAATAAAAAACTAATATTGTTCAA
*
44483289 AAAATTAAAA
1 AAAAATAAAA
44483299 GTATAGAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.65, C:0.06, G:0.05, T:0.24
Consensus pattern (26 bp):
AAAAATAAAAAACTAATATTGTTCAA
Found at i:44500578 original size:12 final size:12
Alignment explanation
Indices: 44500563--44500591 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44500553 ATTTAACAGC
44500563 ATTGCTCAATAT
1 ATTGCTCAATAT
44500575 ATTGCTCAATAT
1 ATTGCTCAATAT
44500587 -TTGCT
1 ATTGCT
44500592 TGAGTTTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (12 bp):
ATTGCTCAATAT
Found at i:44512041 original size:105 final size:105
Alignment explanation
Indices: 44511850--44512058 Score: 337
Period size: 105 Copynumber: 2.0 Consensus size: 105
44511840 ATATGGTAGA
* *
44511850 CGCCACTAGTAGAGGAGCATTGGTCAACATGACTTCCCAACAAGCAAGAGACTTGATCTCCGCGA
1 CGCCACTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGCAAGAGACTTGATCTCCACGA
* * *
44511915 TGGTTGCAAATTCTTAGCAGTTCCGAGCCAATACTGAACT
66 TGGCTGCAAATTCTCAACAGTTCCGAGCCAATACTGAACT
* **
44511955 CGCCGCTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGTGAGAGACTTGATCTCCACGA
1 CGCCACTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGCAAGAGACTTGATCTCCACGA
*
44512020 TGGCTGTAAATTCTCAACAGTTCCGAGCCAATACTGAAC
66 TGGCTGCAAATTCTCAACAGTTCCGAGCCAATACTGAAC
44512059 CCCCTAGAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (105 bp):
CGCCACTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGCAAGAGACTTGATCTCCACGA
TGGCTGCAAATTCTCAACAGTTCCGAGCCAATACTGAACT
Found at i:44516510 original size:4 final size:4
Alignment explanation
Indices: 44516501--44516580 Score: 62
Period size: 4 Copynumber: 19.5 Consensus size: 4
44516491 CAACTCAATT
44516501 TTTA TTTA -TTA TTTA TTTA TTTA -TTA TTTTA TTT- TATTA TTTTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA -TTTA -TTTA
44516550 TTTA -TTA CTTTA TTTTA TTT- TATTA TTTA TT
1 TTTA TTTA -TTTA -TTTA TTTA T-TTA TTTA TT
44516581 ACTTATTTGG
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
3 11 0.17
4 34 0.53
5 18 0.28
6 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:44516534 original size:5 final size:5
Alignment explanation
Indices: 44516524--44516573 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
44516514 TATTTATTTA
* *
44516524 TTATT TTATT TTA-- TTATT TTACT TTATTT ATTACT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT -TTATT TTATT TTATT TTATT
44516574 ATTTATTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.08
5 29 0.78
6 2 0.05
7 3 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:44516563 original size:35 final size:33
Alignment explanation
Indices: 44516500--44516577 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 33
44516490 GCAACTCAAT
*
44516500 TTTTATT-TATTATTTATTTATTTATTATTTTA
1 TTTTATTATTTTATTTATTTATTTATTATTTTA
44516532 TTTTATTATTTTACTTTATTTA-TTACTTTATTTTA
1 TTTTATTATTTTA-TTTATTTATTTA--TTATTTTA
44516567 TTTTATTATTT
1 TTTTATTATTT
44516578 ATTACTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 7 0.17
33 7 0.17
34 8 0.20
35 19 0.46
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTATTATTTTATTTATTTATTTATTATTTTA
Found at i:44517953 original size:24 final size:23
Alignment explanation
Indices: 44517904--44517953 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
44517894 TAAAAAATAT
* *
44517904 AAATAATAAATAAATCAAAATCA
1 AAATAATAAAAAAATCAAAAACA
* *
44517927 AAATAAGTAAAAAAATGAAAAAGA
1 AAATAA-TAAAAAAATCAAAAACA
44517951 AAA
1 AAA
44517954 AAAAATAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (23 bp):
AAATAATAAAAAAATCAAAAACA
Found at i:44518560 original size:18 final size:18
Alignment explanation
Indices: 44518539--44518580 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
44518529 AATATTAAAA
44518539 TAATTATTA-AATTTTATT
1 TAATT-TTAGAATTTTATT
*
44518557 TAATTTTAGGATTTTATT
1 TAATTTTAGAATTTTATT
*
44518575 TTATTT
1 TAATTT
44518581 ATCTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TAATTTTAGAATTTTATT
Found at i:44520360 original size:46 final size:46
Alignment explanation
Indices: 44520255--44520461 Score: 350
Period size: 46 Copynumber: 4.6 Consensus size: 46
44520245 TATGTATGAT
* *
44520255 CACTAATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
44520298 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
44520344 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
44520390 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
44520436 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
44520462 AGTACTCAAA
Statistics
Matches: 155, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
43 9 0.06
44 5 0.03
45 29 0.19
46 112 0.72
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:44528063 original size:25 final size:24
Alignment explanation
Indices: 44528035--44528131 Score: 68
Period size: 25 Copynumber: 3.9 Consensus size: 24
44528025 AAGCTCTTCC
* *
44528035 GAGCCATGTAACATGAAGCTCATGT
1 GAGCCAT-TAACAGGAAGCTCATAT
* * *
44528060 GAGCTATATAACGGGAAGCTCTTAT
1 GAGCCAT-TAACAGGAAGCTCATAT
* *
44528085 GAGCCAATTATCAGGAAGCTCATAC
1 GAGCC-ATTAACAGGAAGCTCATAT
* * *
44528110 CAGCCATATATCAGGAAACTCA
1 GAGCCAT-TAACAGGAAGCTCA
44528132 AGAGAGCTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 2 0.04
25 53 0.93
26 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (24 bp):
GAGCCATTAACAGGAAGCTCATAT
Found at i:44528119 original size:50 final size:50
Alignment explanation
Indices: 44528021--44528119 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
44528011 AGCATGTAAT
* * *** *
44528021 CGGGAAGCTCTTCCGAGCCATGTAACATGAAGCTCATGTGAGCTATATAA
1 CGGGAAGCTCTTACGAGCCATGTAACAGGAAGCTCATACCAGCCATATAA
* *
44528071 CGGGAAGCTCTTATGAGCCAAT-TATCAGGAAGCTCATACCAGCCATATA
1 CGGGAAGCTCTTACGAGCC-ATGTAACAGGAAGCTCATACCAGCCATATA
44528120 TCAGGAAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 38 0.95
51 2 0.05
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (50 bp):
CGGGAAGCTCTTACGAGCCATGTAACAGGAAGCTCATACCAGCCATATAA
Found at i:44530423 original size:32 final size:32
Alignment explanation
Indices: 44530382--44530446 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
44530372 TACAAGTTAG
44530382 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
1 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
44530414 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
1 AATTTTATTTTAAGACAAACTCAAAAAGGCGT
44530446 A
1 A
44530447 TTCAAGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (32 bp):
AATTTTATTTTAAGACAAACTCAAAAAGGCGT
Found at i:44531449 original size:27 final size:27
Alignment explanation
Indices: 44531377--44531450 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
44531367 CTAACAGAAC
* *
44531377 ACGCCACAAAGGC-AACCATATAGAGT
1 ACGCCACAAAGGCTAATCTTATAGAGT
* * *
44531403 ACGCCACAAAGGTTATTCTTCTAGAGT
1 ACGCCACAAAGGCTAATCTTATAGAGT
*
44531430 TCGCCACAAAGGCTAATCTTA
1 ACGCCACAAAGGCTAATCTTA
44531451 GCTGTCGTGC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 12 0.32
27 26 0.68
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (27 bp):
ACGCCACAAAGGCTAATCTTATAGAGT
Found at i:44534896 original size:16 final size:16
Alignment explanation
Indices: 44534877--44534912 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
44534867 TATTTGATTA
44534877 AATATATGATACTACT
1 AATATATGATACTACT
44534893 AATATATGATACTACT
1 AATATATGATACTACT
44534909 AATA
1 AATA
44534913 AAGAATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (16 bp):
AATATATGATACTACT
Found at i:44551823 original size:31 final size:30
Alignment explanation
Indices: 44551761--44551826 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
44551751 TTTAGTCATA
*
44551761 TAATAAATTATTAATATAATTTATTATTTT
1 TAATAAATTATTAATATAAATTATTATTTT
44551791 TAATAAATTATTTAATATTTAAATT-TTA-TTT
1 TAATAAATTA-TTAATA--TAAATTATTATTTT
44551822 TAATA
1 TAATA
44551827 GTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 14 0.44
32 3 0.09
33 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATAAATTATTAATATAAATTATTATTTT
Found at i:44553085 original size:22 final size:23
Alignment explanation
Indices: 44553047--44553102 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
44553037 CAAACGTGGG
*
44553047 TTTAAAAGTAAATAATAAAATATATAA
1 TTTAAAA--AAATAA-AAAATA-AAAA
44553074 TTTAAAAAAATAAAAAATAAAAA
1 TTTAAAAAAATAAAAAATAAAAA
44553097 TTTAAA
1 TTTAAA
44553103 TTATGAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.32
24 6 0.21
25 6 0.21
27 7 0.25
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
TTTAAAAAAATAAAAAATAAAAA
Found at i:44559961 original size:14 final size:14
Alignment explanation
Indices: 44559955--44559984 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44559945 TTAATGATTA
44559955 ATGATTAATTAATT
1 ATGATTAATTAATT
44559969 ATGATTAAGTTAATT
1 ATGATTAA-TTAATT
44559984 A
1 A
44559985 ATTAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATGATTAATTAATT
Found at i:44559995 original size:14 final size:13
Alignment explanation
Indices: 44559958--44559999 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
44559948 ATGATTAATG
44559958 ATTAA-TTAATTA
1 ATTAAGTTAATTA
44559970 TGATTAAGTTAATTA
1 --ATTAAGTTAATTA
44559985 ATTAAGTTTAATTA
1 ATTAAG-TTAATTA
44559999 A
1 A
44560000 AACTAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.23
14 13 0.50
15 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
ATTAAGTTAATTA
Found at i:44559995 original size:19 final size:18
Alignment explanation
Indices: 44559958--44559999 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
44559948 ATGATTAATG
*
44559958 ATTAATTAATTATGATTA
1 ATTAATTAATTAAGATTA
*
44559976 AGTTAATTAATTAAGTTTA
1 A-TTAATTAATTAAGATTA
44559995 ATTAA
1 ATTAA
44560000 AACTAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
ATTAATTAATTAAGATTA
Found at i:44573109 original size:47 final size:47
Alignment explanation
Indices: 44572977--44573338 Score: 553
Period size: 47 Copynumber: 7.6 Consensus size: 47
44572967 TATTTGAATA
* *
44572977 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44573026 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATG
44573075 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
44573122 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATG
* *
44573171 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44573218 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
* * * * *
44573265 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
* *
44573312 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
44573339 TCCCGAAGGG
Statistics
Matches: 296, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 189 0.64
49 107 0.36
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATG
Found at i:44573110 original size:96 final size:96
Alignment explanation
Indices: 44572977--44573338 Score: 570
Period size: 96 Copynumber: 3.8 Consensus size: 96
44572967 TATTTGAATA
*
44572977 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
44573042 TATATGTGATAAGGCCGAATGGCCAATGTGATG
64 TATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44573075 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
44573140 TATGTGATAAGGCCGAATGGCCGATGTGATG
66 TATGTGATAAGGCCGAATGGCCGATGTGATG
* * *
44573171 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
44573234 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCGAATGGCCGATGTGATG
* * * * *
44573265 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
44573329 -ATGTGATAAG
66 TATGTGATAAG
44573339 TCCCGAAGGG
Statistics
Matches: 248, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
94 95 0.38
95 1 0.00
96 140 0.56
98 12 0.05
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.28
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCGAATGGCCGATGTGATG
Found at i:44575625 original size:40 final size:40
Alignment explanation
Indices: 44575568--44575924 Score: 518
Period size: 40 Copynumber: 8.9 Consensus size: 40
44575558 CTCGACAATG
44575568 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
44575608 ACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
44575648 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
44575688 ACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
44575728 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
44575768 ATCCGGACTAAGTCTCGAAAAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
44575808 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * * * *
44575848 ATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCC-CGAAGAGCATTCATGCTAGTGATGT
* * *
44575888 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
44575925 CGTGTATTCG
Statistics
Matches: 285, Mismatches: 30, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
39 1 0.00
40 282 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:44579235 original size:40 final size:41
Alignment explanation
Indices: 44579188--44579377 Score: 130
Period size: 49 Copynumber: 4.1 Consensus size: 41
44579178 ATATTTGAAT
*
44579188 AAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC
1 AAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
44579229 AATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
1 ------A--AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
* * *
44579278 -AATGTGATGAATGTGAAAGTGTATATTGTGATAAGGCCGAATGACC
1 AAATGTGA--AA-GTG-TA-TATATA-TGTGATAAGGCCGAATGGCC
44579324 GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
1 ------A--AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
*
44579373 GAATG
1 AAATG
44579378 GCCAATGTGA
Statistics
Matches: 118, Mismatches: 8, Indels: 40
0.71 0.05 0.24
Matches are distributed among these distances:
40 7 0.06
41 4 0.03
42 2 0.02
43 3 0.03
44 1 0.01
45 5 0.04
46 19 0.16
47 1 0.01
49 58 0.49
50 5 0.04
51 1 0.01
52 3 0.03
53 2 0.02
55 7 0.06
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (41 bp):
AAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC
Found at i:44579245 original size:49 final size:49
Alignment explanation
Indices: 44579189--44579701 Score: 730
Period size: 47 Copynumber: 10.6 Consensus size: 49
44579179 TATTTGAATA
* *
44579189 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44579238 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44579287 AATGTGAAAGTG--TATAT-TGTGATAAGGCCGAATGACCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
44579333 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCC-----G---ATGTGATG
44579390 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
44579437 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44579486 AATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
* *
44579534 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44579581 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
* * * * *
44579628 AATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
*
44579675 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
44579702 TCCCGAAGGG
Statistics
Matches: 432, Mismatches: 16, Indels: 34
0.90 0.03 0.07
Matches are distributed among these distances:
46 53 0.12
47 150 0.35
48 37 0.09
49 144 0.33
50 1 0.00
54 1 0.00
55 26 0.06
57 20 0.05
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATG
Found at i:44579552 original size:199 final size:192
Alignment explanation
Indices: 44579189--44579701 Score: 754
Period size: 199 Copynumber: 2.7 Consensus size: 192
44579179 TATTTGAATA
*
44579189 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
44579254 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATAT-TGTGATAAGGCC
64 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCC
*
44579316 GAATGACCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGAATGGCC
128 GAATGACCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCC---T-----AATAGCC
44579381 AATGTGATG
184 AATGTGATG
*
44579390 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
44579455 TATGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGCCTAA
66 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGCCGAA
* *
44579520 TGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATAGCCGATGTGATG
131 TGACCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAGCCAATGTGATG
44579581 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * *
44579644 TATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
66 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
44579702 TCCCGAAGGG
Statistics
Matches: 295, Mismatches: 14, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
187 10 0.03
188 1 0.00
189 45 0.15
191 72 0.24
196 1 0.00
199 111 0.38
201 47 0.16
202 8 0.03
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (192 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGCCGAA
TGACCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATAGCCAATGTGATG
Found at i:44590965 original size:21 final size:21
Alignment explanation
Indices: 44590939--44590979 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44590929 ATCTGCTCAA
* *
44590939 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
44590960 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
44590980 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:44598970 original size:26 final size:26
Alignment explanation
Indices: 44598922--44598980 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
44598912 TTAATACTGT
*
44598922 TTATTAGTATTATTATTACTATATTA
1 TTATTAGTATTATTATTACTATATCA
* *
44598948 TTATTAGT-TTTTTATTTATTATATCA
1 TTATTAGTATTATTA-TTACTATATCA
44598974 TATATTA
1 T-TATTA
44598981 TTATACCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTAGTATTATTATTACTATATCA
Found at i:44599132 original size:7 final size:7
Alignment explanation
Indices: 44599107--44599166 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
44599097 ATAGTTTTTA
44599107 TATATTT
1 TATATTT
44599114 TATATACATT
1 TATAT---TT
44599124 TATATTT
1 TATATTT
44599131 TATACTATT
1 TATA-T-TT
44599140 TATATTT
1 TATATTT
44599147 TCATATTT
1 T-ATATTT
*
44599155 TATAATT
1 TATATTT
44599162 TATAT
1 TATAT
44599167 ATGTTTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 23 0.51
8 9 0.20
9 6 0.13
10 7 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTT
Found at i:44599139 original size:10 final size:9
Alignment explanation
Indices: 44599070--44599175 Score: 63
Period size: 8 Copynumber: 12.4 Consensus size: 9
44599060 GCATATTATG
44599070 TATATATTT
1 TATATATTT
44599079 TAT-TATTAT
1 TATATATT-T
44599088 T-T-TATTT
1 TATATATTT
44599095 TCATAGT-TTT
1 T-ATA-TATTT
44599105 TATATATTT
1 TATATATTT
**
44599114 TATATACAT
1 TATATATTT
44599123 T-TATATTT
1 TATATATTT
44599131 TATACTA--T
1 TATA-TATTT
44599139 T-TATATTT
1 TATATATTT
*
44599147 T-CATATTT
1 TATATATTT
44599155 TATA-A-TT
1 TATATATTT
44599162 TATATATGTT
1 TATATAT-TT
44599172 TATA
1 TATA
44599176 CATTCTTTGT
Statistics
Matches: 77, Mismatches: 6, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
6 2 0.03
7 10 0.13
8 29 0.38
9 23 0.30
10 12 0.16
11 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TATATATTT
Found at i:44599142 original size:35 final size:36
Alignment explanation
Indices: 44599061--44599152 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
44599051 AATACATATG
* * *
44599061 CATATTATGTATATATTTTAT-TATTATTTTATTTT
1 CATACTATTTATATATTTTATATATCATTTTATTTT
* *
44599096 CATAGTTTTTATATATTTTATATA-CATTTATATTTT
1 CATACTATTTATATATTTTATATATCATTT-TATTTT
*
44599132 -ATACTATTTATAT-TTTCATAT
1 CATACTATTTATATATTTTATAT
44599153 TTTATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.15
35 33 0.69
36 8 0.17
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (36 bp):
CATACTATTTATATATTTTATATATCATTTTATTTT
Found at i:44599146 original size:52 final size:50
Alignment explanation
Indices: 44599072--44599168 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 50
44599062 ATATTATGTA
*
44599072 TATATTTTATTATTATTTTATTTTCATAGTTTTTATATATTT-TATATACATT
1 TATATTTTATTACTATTTTATTTTCATA--TTTTATA-ATTTATATATACATT
44599124 TATATTTTA-TACTATTTATATTTTCATATTTTATAATTTATATAT
1 TATATTTTATTACTATTT-TATTTTCATATTTTATAATTTATATAT
44599169 GTTTATACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
49 4 0.10
50 12 0.29
51 7 0.17
52 19 0.45
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (50 bp):
TATATTTTATTACTATTTTATTTTCATATTTTATAATTTATATATACATT
Found at i:44599162 original size:22 final size:23
Alignment explanation
Indices: 44599073--44599166 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 23
44599063 TATTATGTAT
44599073 ATATTTTATTATTATTT-TATTTTC
1 ATATTTTA-TA-TATTTATATTTTC
44599097 ATAGTTTTTATATATTTTATATACATTT-
1 ATA--TTTTATATA-TTTATAT---TTTC
44599125 ATATTTTATACTATTTATATTTTC
1 ATATTTTATA-TATTTATATTTTC
44599149 ATATTTTATA-ATTTATAT
1 ATATTTTATATATTTATAT
44599167 ATGTTTATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.13
23 3 0.05
24 15 0.25
25 5 0.08
26 22 0.36
27 2 0.03
28 3 0.05
29 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATATATTTATATTTTC
Found at i:44603980 original size:23 final size:23
Alignment explanation
Indices: 44603954--44603999 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44603944 CAAAATATAA
44603954 AAAAAAACAAAAAAAATAGAGAG
1 AAAAAAACAAAAAAAATAGAGAG
* * * *
44603977 AAAAGAAGAAAGAAAATGGAGAG
1 AAAAAAACAAAAAAAATAGAGAG
44604000 GCCAAGATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (23 bp):
AAAAAAACAAAAAAAATAGAGAG
Found at i:44604135 original size:42 final size:42
Alignment explanation
Indices: 44604067--44604147 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
44604057 CCCGAAAAGG
*
44604067 GCAGCTCAAATATTGATTAGAATGGGGCATGA-GATGATCAGA
1 GCAGCTCAAATATTGATCAGAATGGGGCAT-ATGATGATCAGA
* * *
44604109 GCAGTTCAAATTTTGATCAGATTGGGGCATATGATGATC
1 GCAGCTCAAATATTGATCAGAATGGGGCATATGATGATC
44604148 TTGAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (42 bp):
GCAGCTCAAATATTGATCAGAATGGGGCATATGATGATCAGA
Found at i:44605735 original size:7 final size:7
Alignment explanation
Indices: 44605723--44605782 Score: 66
Period size: 7 Copynumber: 8.3 Consensus size: 7
44605713 GTTTTGGGGT
44605723 TTTAAGG
1 TTTAAGG
44605730 TTTAAGG
1 TTTAAGG
**
44605737 TTTTAACC
1 -TTTAAGG
44605745 TTTAAGG
1 TTTAAGG
44605752 TTTAAGG
1 TTTAAGG
44605759 TTTTAAGG
1 -TTTAAGG
*
44605767 TTTAGGG
1 TTTAAGG
*
44605774 TTTATGG
1 TTTAAGG
44605781 TT
1 TT
44605783 AAAAATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
7 33 0.73
8 12 0.27
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:44605740 original size:15 final size:15
Alignment explanation
Indices: 44605720--44605782 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
44605710 CCTGTTTTGG
44605720 GGTTTTAAGGTTTAA
1 GGTTTTAAGGTTTAA
**
44605735 GGTTTTAACCTTTAA
1 GGTTTTAAGGTTTAA
44605750 GG-TTTAAGGTTTTAA
1 GGTTTTAAGG-TTTAA
* *
44605765 GG-TTTAGGGTTTAT
1 GGTTTTAAGGTTTAA
44605779 GGTT
1 GGTT
44605783 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 11 0.28
15 29 0.73
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (15 bp):
GGTTTTAAGGTTTAA
Found at i:44605749 original size:22 final size:22
Alignment explanation
Indices: 44605723--44605782 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
44605713 GTTTTGGGGT
44605723 TTTAAGGTTTAAGGTTTTAACC
1 TTTAAGGTTTAAGGTTTTAACC
**
44605745 TTTAAGGTTTAAGGTTTTAAGG
1 TTTAAGGTTTAAGGTTTTAACC
* *
44605767 TTTAGGGTTTATGGTT
1 TTTAAGGTTTAAGGTT
44605783 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.48
Consensus pattern (22 bp):
TTTAAGGTTTAAGGTTTTAACC
Found at i:44606597 original size:6 final size:6
Alignment explanation
Indices: 44606588--44606637 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
44606578 AAAAATTAGA
* * *
44606588 TTAGGG TTAGGG TTAGGG TTAAGG TTAAGG TTAGGG TTAAGGT TTAGGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT-AGGG TTAGGG
44606637 T
1 T
44606638 GTTTTTAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (6 bp):
TTAGGG
Found at i:44606619 original size:18 final size:18
Alignment explanation
Indices: 44606592--44606631 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
44606582 ATTAGATTAG
*
44606592 GGTTAGGGTTAGGGTTAA
1 GGTTAAGGTTAGGGTTAA
44606610 GGTTAAGGTTAGGGTTAA
1 GGTTAAGGTTAGGGTTAA
44606628 GGTT
1 GGTT
44606632 TAGGGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (18 bp):
GGTTAAGGTTAGGGTTAA
Found at i:44606818 original size:245 final size:243
Alignment explanation
Indices: 44606376--44606852 Score: 780
Period size: 246 Copynumber: 2.0 Consensus size: 243
44606366 AAAAATTAGA
* * *
44606376 TTAGGGTTAGGGTTTAGGGTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAATCAAATAAATTAGTG
1 TTAGGGTTAAGGTTTAGGGTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAATCAAACAAATTAGAG
* *
44606441 TTTAGAGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTTGTG
66 TTTAGAGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTCCAAAATTGGATTAGTTTTCGTG
*
44606506 TTTATTATCTTTTATGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAATAATTTAATTAA
131 TTTATTATCTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAATAATTTAATTAA
**
44606571 AAAA-ATTAAAAATTAGATTAGGGTTAGGGTTAGGGTTAAGGTTAAGG
196 AAAATATTAAAAATTAGATTAGAATTAGGGTTAGGGTTAAGGTTAAGG
44606618 TTAGGGTTAAGGTTTAGGGTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAAT-AAACAAATTAGAG
1 TTAGGGTTAAGGTTTAGGGTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAATCAAACAAATTAGAG
*
44606682 TTTAGAGTTTATGGTTTGTCAATTAAATTATTTATAAATATTCGTAGCCAAAATTGGATTAGTTT
66 TTTAGAGTTTAGGGTTTGTCAATTAAATTATTTATAAAT-TT--T--CCAAAATTGGATTAGTTT
* *
44606747 TCGTGTTTATTATTTTTTAAG-AAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTA
126 TCGTGTTTATTATCTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAATAATTTA
*
44606811 ATTAAAAAATTTTAAAAATTAGATTAGAATTAGGGTTAGGGT
191 ATTAAAAAATATTAAAAATTAGATTAGAATTAGGGTTAGGGT
44606853 CAGGGTTTAG
Statistics
Matches: 217, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
241 49 0.23
242 52 0.24
244 1 0.00
245 51 0.24
246 64 0.29
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (243 bp):
TTAGGGTTAAGGTTTAGGGTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAATCAAACAAATTAGAG
TTTAGAGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTCCAAAATTGGATTAGTTTTCGTG
TTTATTATCTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAATAATTTAATTAA
AAAATATTAAAAATTAGATTAGAATTAGGGTTAGGGTTAAGGTTAAGG
Found at i:44611030 original size:49 final size:51
Alignment explanation
Indices: 44610971--44611068 Score: 139
Period size: 49 Copynumber: 2.0 Consensus size: 51
44610961 AATAATTAAA
*
44610971 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATT-A-AGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGGA-AGCAAATTGAGAGCAAATTGAGATT
* *
44611020 AAATATGGATTTGAGAGAAATTTGGAAGCAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTGGAAGCAAATTGAGAGCAAATTGAGA
44611069 GGAAATTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 28 0.65
50 3 0.07
51 12 0.28
ACGTcount: A:0.46, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTGGAAGCAAATTGAGAGCAAATTGAGATT
Found at i:44611042 original size:11 final size:12
Alignment explanation
Indices: 44611028--44611075 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
44611018 TTAAATATGG
44611028 ATTTGAGAG-AA
1 ATTTGAGAGCAA
44611039 ATTTG-GAAGCAA
1 ATTTGAG-AGCAA
44611051 A-TTGAGAGCAA
1 ATTTGAGAGCAA
*
44611062 A-TTGAGAGGAA
1 ATTTGAGAGCAA
44611073 ATT
1 ATT
44611076 AAGATGTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 1 0.03
11 26 0.81
12 5 0.16
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (12 bp):
ATTTGAGAGCAA
Found at i:44611730 original size:23 final size:22
Alignment explanation
Indices: 44611694--44611744 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
44611684 TGCTCTTATT
44611694 AAAAATTAGAAAAATTATTAAATA
1 AAAAATTAGAAAAATT-TTAAA-A
* *
44611718 AAAAATT-GTAAAATTTTATAA
1 AAAAATTAGAAAAATTTTAAAA
44611739 AAAAAT
1 AAAAAT
44611745 CATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 4 0.16
23 7 0.28
24 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAAATTAGAAAAATTTTAAAA
Found at i:44611947 original size:20 final size:19
Alignment explanation
Indices: 44611919--44612057 Score: 60
Period size: 19 Copynumber: 7.2 Consensus size: 19
44611909 GAAAATTATA
44611919 TTTCTTTACATTTTGTATAAT
1 TTTC-TTACATTTT-TATAAT
* *
44611940 TTTCTTACGACTTTATAAAAT
1 TTTCTTAC-A-TTTTTATAAT
* *
44611961 TTTATAAC-TTTTTAT-A-
1 TTTCTTACATTTTTATAAT
*
44611977 TTTCTATA-TTTTTTATAAT
1 TTTCT-TACATTTTTATAAT
*
44611996 TTT-TTACGATTTTTATAAA
1 TTTCTTAC-ATTTTTATAAT
*
44612015 ATT-TTACAATTTTT-TATAT
1 TTTCTTAC-ATTTTTATA-AT
44612034 TTT-TTAACGATTTTTATATAT
1 TTTCTT-AC-ATTTTTATA-AT
44612055 TTT
1 TTT
44612058 TCTAGTTTTT
Statistics
Matches: 92, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
16 4 0.04
17 11 0.12
18 9 0.10
19 29 0.32
20 12 0.13
21 24 0.26
22 3 0.03
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTCTTACATTTTTATAAT
Found at i:44611973 original size:10 final size:9
Alignment explanation
Indices: 44611960--44612079 Score: 66
Period size: 10 Copynumber: 12.6 Consensus size: 9
44611950 CTTTATAAAA
44611960 TTTTATAACT
1 TTTTATAA-T
44611970 TTTTAT-AT
1 TTTTATAAT
* *
44611978 TTCTATATT
1 TTTTATAAT
44611987 TTTTATAAT
1 TTTTATAAT
44611996 TTTT-TACGAT
1 TTTTATA--AT
*
44612006 TTTTATAAAA
1 TTTTAT-AAT
*
44612016 TTTTACAATT
1 TTTTATAA-T
*
44612026 TTTTATATT
1 TTTTATAAT
44612035 TTTTA-ACGAT
1 TTTTATA--AT
44612045 TTTTATATAT
1 TTTTATA-AT
* *
44612055 TTTTCTAGT
1 TTTTATAAT
44612064 TTTTAATAACT
1 TTTT-ATAA-T
44612075 TTTTA
1 TTTTA
44612080 ATATTTGAAT
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
8 9 0.11
9 26 0.31
10 41 0.49
11 7 0.08
12 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:44611994 original size:56 final size:57
Alignment explanation
Indices: 44611914--44612058 Score: 170
Period size: 56 Copynumber: 2.5 Consensus size: 57
44611904 ATTACGAAAA
*
44611914 TTATATTTCTTTACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTATAACTTT
1 TTATATTTC-TTACATTTTGTATAATTTT-TTACGATCTTTATAAAATTTTACAACTTT
* * * *
44611972 TTATATTTC-TATATTTTTTATAATTTTTTACGATTTTTATAAAATTTTACAATTTT
1 TTATATTTCTTACATTTTGTATAATTTTTTACGATCTTTATAAAATTTTACAACTTT
*
44612028 TTATATTTTTTAACGATTTT-TATATATTTTT
1 TTATATTTCTT-AC-ATTTTGTATA-ATTTTT
44612059 CTAGTTTTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
55 6 0.08
56 43 0.57
57 1 0.01
58 14 0.19
59 11 0.15
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (57 bp):
TTATATTTCTTACATTTTGTATAATTTTTTACGATCTTTATAAAATTTTACAACTTT
Found at i:44612010 original size:19 final size:19
Alignment explanation
Indices: 44611986--44612079 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
44611976 ATTTCTATAT
44611986 TTTTTATAATTTTTTACGA
1 TTTTTATAATTTTTTACGA
** *
44612005 TTTTTATAAAATTTTACAA
1 TTTTTATAATTTTTTACGA
44612024 TTTTT-TATATTTTTTAACGA
1 TTTTTATA-ATTTTTT-ACGA
44612044 TTTTTATATATTTTTCTA-G-
1 TTTTTATA-ATTTTT-TACGA
*
44612063 TTTTTAATAACTTTTTA
1 TTTTT-ATAATTTTTTA
44612080 ATATTTGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
18 4 0.06
19 36 0.57
20 12 0.19
21 10 0.16
22 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTTTTTACGA
Found at i:44612067 original size:39 final size:38
Alignment explanation
Indices: 44611969--44612079 Score: 118
Period size: 39 Copynumber: 2.9 Consensus size: 38
44611959 ATTTTATAAC
* *
44611969 TTTT-TATATTTCTATATTTTTTATAATTTTTTACGAT
1 TTTTATATATTTTTCTATTTTTTATAATTTTTTACGAT
* * *
44612006 TTTTATAAAATTTTACAATTTTTTAT-ATTTTTTAACGAT
1 TTTTAT-ATATTTTTCTATTTTTTATAATTTTTT-ACGAT
* *
44612045 TTTTATATATTTTTCTAGTTTTTAATAACTTTTTA
1 TTTTATATATTTTTCTA-TTTTTTATAATTTTTTA
44612080 ATATTTGAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 4 0.07
38 16 0.27
39 33 0.56
40 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (38 bp):
TTTTATATATTTTTCTATTTTTTATAATTTTTTACGAT
Found at i:44612347 original size:90 final size:90
Alignment explanation
Indices: 44612176--44612350 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 90
44612166 ATAAAAGCAT
* * *
44612176 GGGCTTAATTGCTTTTTTTGAAAAACTTTGAGGGTCTTTTTGATGCATTTTGAAAATTGAAGGAC
1 GGGCCTAATTGCTTTTTTTGAAAAACTTTGAGAGTCTTTTTGATGCATTTTGAAAATTCAAGGAC
* * *
44612241 CCAATTGAGTGCAAAAAAAAACTAG
66 CAAAATGAATGCAAAAAAAAACTAG
* * * *
44612266 GGGCCTAATTG-TTTTTTTTAAAAAGGTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
1 GGGCCTAATTGCTTTTTTTGAAAAA-CTTTGAGAGTCTTTTTGATGCATTTTGAAAATTCAAGGA
*
44612330 CCAAAATGAATGTAAAAAAAA
65 CCAAAATGAATGCAAAAAAAA
44612351 GGGCTTATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 12 0.16
90 61 0.84
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (90 bp):
GGGCCTAATTGCTTTTTTTGAAAAACTTTGAGAGTCTTTTTGATGCATTTTGAAAATTCAAGGAC
CAAAATGAATGCAAAAAAAAACTAG
Found at i:44612475 original size:21 final size:23
Alignment explanation
Indices: 44612451--44612502 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44612441 AGGTCTATAC
44612451 ATATATATT-T-TAATTTTTAAA
1 ATATATATTATATAATTTTTAAA
*
44612472 ATATATATTATATTATTTTTAAA
1 ATATATATTATATAATTTTTAAA
*
44612495 TTATATAT
1 ATATATAT
44612503 ATTCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.33
22 1 0.04
23 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATATATTATATAATTTTTAAA
Found at i:44614190 original size:37 final size:36
Alignment explanation
Indices: 44614126--44614199 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
44614116 CCGAATATAA
*
44614126 TAAAATATTTTTTATTTTTTAATTTTAAAATACTTT
1 TAAAATATTTTTTATTTTTTAATTTTAAAATAATTT
*
44614162 TAAAAT-TTTTTTATTTTTTTTATTTTTAAAATAATTT
1 TAAAATATTTTTTA--TTTTTTAATTTTAAAATAATTT
44614199 T
1 T
44614200 TTAATGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 6 0.18
37 21 0.62
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (36 bp):
TAAAATATTTTTTATTTTTTAATTTTAAAATAATTT
Found at i:44614979 original size:10 final size:10
Alignment explanation
Indices: 44614964--44614998 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
44614954 TTATATTTTT
44614964 TAAAAAATTA
1 TAAAAAATTA
44614974 T-AAAAATTA
1 TAAAAAATTA
44614983 TAAAAAA-TA
1 TAAAAAATTA
44614992 TAAAAAA
1 TAAAAAA
44614999 AATTGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:44614998 original size:19 final size:19
Alignment explanation
Indices: 44614964--44615020 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
44614954 TTATATTTTT
**
44614964 TAAAAAATTATAAAAATTA
1 TAAAAAATTATAAAAAAAA
44614983 TAAAAAA-TATAAAAAAAA
1 TAAAAAATTATAAAAAAAA
** *
44615001 TTGAAAATTTTAAAAAAAA
1 TAAAAAATTATAAAAAAAA
44615020 T
1 T
44615021 TCTAAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
TAAAAAATTATAAAAAAAA
Found at i:44615219 original size:19 final size:19
Alignment explanation
Indices: 44615195--44615286 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
44615185 AATTTTTGAG
44615195 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
44615214 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
44615233 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
44615252 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44615271 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
44615287 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:44615516 original size:19 final size:19
Alignment explanation
Indices: 44615479--44615517 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44615469 GGTGGCTTAC
*
44615479 TATTTTTTTTTCTTCCGAT
1 TATTTTTTTTTCTTACGAT
44615498 TATTTTTTTTAT-TTACGAT
1 TATTTTTTTT-TCTTACGAT
44615517 T
1 T
44615518 TTAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTTTTTTCTTACGAT
Found at i:44616461 original size:98 final size:98
Alignment explanation
Indices: 44616338--44616532 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
44616328 AAAAATCATG
*
44616338 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
44616403 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
44616436 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
44616501 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
44616533 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:44620073 original size:6 final size:6
Alignment explanation
Indices: 44620057--44620086 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
44620047 TTCAGATAAA
44620057 AAAAAC AAAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC -AAAAAC AAAAAC AAAAAC AAAAA
44620087 AATGAAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:44621577 original size:132 final size:132
Alignment explanation
Indices: 44621337--44621992 Score: 996
Period size: 132 Copynumber: 5.0 Consensus size: 132
44621327 TTCCTCGTTT
* *
44621337 GTAGTCGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
*
44621402 CAGTAATTCTACTTCCCTGGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
44621467 CA
131 CA
*
44621469 GTAGTGGAGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* * * ** ** *
44621534 TAGTAATTCTACTTCCCTGGGCAGTAGTGGAATAGATTAAAGATAGCAGATCTTGCCTTCCT--G
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
44621597 CA
131 CA
* * * *
44621599 TTGACAGCGAAACAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGA
1 --G-TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGA
* *
44621664 AGCCAATAATTCTACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT
63 AGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT
44621729 AAGCA
128 AAGCA
*
44621734 GTAGTGGAGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* *
44621799 CAGTAATTCTACTTCCTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
66 CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
44621864 CA
131 CA
* * *
44621866 GTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGT
1 GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
* * *
44621931 CAGTAATTCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
66 CAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
44621993 GCAGTTGCAG
Statistics
Matches: 472, Mismatches: 45, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
130 3 0.01
131 1 0.00
132 350 0.74
133 115 0.24
135 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (132 bp):
GTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGC
CAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG
CA
Found at i:44621830 original size:265 final size:263
Alignment explanation
Indices: 44621346--44621992 Score: 987
Period size: 265 Copynumber: 2.4 Consensus size: 263
44621336 TGTAGTCGAG
44621346 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
* *
44621411 TACTTCCCTGGGCAGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
44621476 AGTAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCTAGTAAT
131 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
** * *
44621541 TCTACTTCCCTGGGCAGTAGTGGAATAGATTAAAGATAGCAGATCTTGCCTTCCT-GCATTGACA
196 TCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACCTCCCTAGCA--G-CA
44621605 GCGAAA
258 GCGAAA
* *
44621611 CAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
44621676 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
66 TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
44621741 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
131 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* * ** * * *
44621806 TCTACTTCCTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
196 TCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACCTCCCT-AGCAGCAGC
* *
44621871 GGAG
260 GAAA
* *
44621875 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATTC
1 CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
* *
44621940 TA-TCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
66 TACT-TCCCTGGGT-AGCAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
44621993 GCAGTTGCAG
Statistics
Matches: 351, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
263 4 0.01
264 106 0.30
265 238 0.68
267 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (263 bp):
CAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
TACTTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATAGCAGATCTTACCTCCCTAGCAGCAGCG
AAA
Found at i:44621971 original size:43 final size:44
Alignment explanation
Indices: 44621823--44622017 Score: 114
Period size: 44 Copynumber: 4.4 Consensus size: 44
44621813 CCTTGGGCAA
* * * *
44621823 CAGTGGAATAGATTGAAGAT-TTCAGATCTTATCTCCCTAAGCAG
1 CAGTGGAATAGATTGAAGATAGTAAG-TCTTATCTCCCTGAGTAG
* ** * * * * * *
44621867 TAGTGGAGCAGATCGAAGATGGT-GGATTTTACCTCCCTGTGGTTA-
1 CAGTGGAATAGATTGAAGATAGTAAG-TCTTATCTCCCTG-AG-TAG
* * *
44621912 CAGTGGAGTACATTGAAG-TCAGTAATTC-TATCTCCCTG-GTCAG
1 CAGTGGAATAGATTGAAGAT-AGTAAGTCTTATCTCCCTGAGT-AG
* * *
44621955 CAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTGCAGTTG
1 CAGTGGAATAGATTGAAGATAGTAAGTCTTATCTCCCTG-AGTAG
44622000 CAGTGGAATAGATTGAAG
1 CAGTGGAATAGATTGAAG
44622018 CACTAGCTCC
Statistics
Matches: 113, Mismatches: 27, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 21 0.19
44 49 0.43
45 37 0.33
46 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
CAGTGGAATAGATTGAAGATAGTAAGTCTTATCTCCCTGAGTAG
Found at i:44622244 original size:19 final size:19
Alignment explanation
Indices: 44622220--44622292 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
44622210 AATTTTTGAG
44622220 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44622239 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
44622258 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44622277 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
44622293 ATATATGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:44623471 original size:98 final size:98
Alignment explanation
Indices: 44623348--44623542 Score: 320
Period size: 98 Copynumber: 2.0 Consensus size: 98
44623338 AAAAATCATG
* **
44623348 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACATATTGGGTGTGATTTCTT
1 AAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCATGCCCTAACATATTGGGTGTGATTTCTT
44623413 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
44623446 AAGGAAATATTCCAAGTTT-AGGATTCTAAAGGGATCATGCCCTAACGTATTGGGTGTGATTTCT
1 AAGGAAATATTCCAAGTTTGA-GATTCTAAAGGAATCATGCCCTAACATATTGGGTGTGATTTCT
*
44623510 TAAATCTTGGATGAGTGGATGTTCTTTTAAAGT
65 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGT
44623543 TTTATTGTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
97 1 0.01
98 89 0.99
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCAAGTTTGAGATTCTAAAGGAATCATGCCCTAACATATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:44634786 original size:22 final size:24
Alignment explanation
Indices: 44634742--44634787 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44634732 TTTTGAGCAC
* *
44634742 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAACTTTTTTCTTTTACGTTCT
44634766 TTTAACTTTTTT-TTTT-CGTTCT
1 TTTAACTTTTTTCTTTTACGTTCT
44634788 CTTCTGCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTAACTTTTTTCTTTTACGTTCT
Found at i:44658897 original size:35 final size:35
Alignment explanation
Indices: 44658858--44658930 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
44658848 CATCTACCAT
44658858 ATTTTAAAAATACCAATTTTGGTATCTAAAGTTTC
1 ATTTTAAAAATACCAATTTTGGTATCTAAAGTTTC
44658893 ATTTTAAAAATACCAATTTTGGTATCTAAAGTTTC
1 ATTTTAAAAATACCAATTTTGGTATCTAAAGTTTC
44658928 ATT
1 ATT
44658931 CCTTCCACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (35 bp):
ATTTTAAAAATACCAATTTTGGTATCTAAAGTTTC
Found at i:44663240 original size:20 final size:22
Alignment explanation
Indices: 44663215--44663289 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 22
44663205 TAAATCTATT
44663215 AATATATTAT-TTA-ATTATAA
1 AATATATTATATTATATTATAA
44663235 AATATATTATATTATATTAT--
1 AATATATTATATTATATTATAA
*
44663255 ATTATATTATATTATATTAT--
1 AATATATTATATTATATTATAA
*
44663275 ATTATATTATATTAT
1 AATATATTATATTAT
44663290 TATGTAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
20 44 0.85
21 3 0.06
22 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATATTATATTATATTATAA
Found at i:44663247 original size:5 final size:5
Alignment explanation
Indices: 44663237--44663289 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
44663227 AATTATAAAA
44663237 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
44663287 TAT
1 TAT
44663290 TATGTAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:44663532 original size:16 final size:17
Alignment explanation
Indices: 44663511--44663542 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44663501 CAGGGGAGAA
44663511 AGAAAGAAA-GAAAAAG
1 AGAAAGAAAGGAAAAAG
44663527 AGAAAGAAAGGAAAAA
1 AGAAAGAAAGGAAAAA
44663543 CTAGGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAAAAAG
Found at i:44664600 original size:45 final size:45
Alignment explanation
Indices: 44664535--44664639 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
44664525 ATGTGCCGAC
* * * *
44664535 TACTGTTGCTGTTACTGATTC-GATACTTTATGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCAG-CACTTTATGTGTCGAATACTGT
* *
44664580 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTATGTGTCGAATACTGT
*
44664625 TCCTGTTACTGTTAC
1 TACTGTTACTGTTAC
44664640 TGTTGCTGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTATGTGTCGAATACTGT
Found at i:44664636 original size:6 final size:6
Alignment explanation
Indices: 44664619--44664666 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
44664609 GTGTGTTGAA
* * * *
44664619 TACTGT TCCTGT TACTGT TACTGT TGCTGC TACCGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
44664667 ATCAGGTACT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:44676707 original size:126 final size:126
Alignment explanation
Indices: 44676494--44676735 Score: 371
Period size: 126 Copynumber: 1.9 Consensus size: 126
44676484 GCTAATTGGT
* * * *
44676494 TTTGTCACTGATTTACCATTTCCTCCTTCAACCACATCCAAGTTAAAAGGGATGTGGACATTGTC
1 TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGGATGTGGACATTATC
44676559 CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
66 CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
* * * *
44676620 TTTGTCACTGATTCATCATTTCCACCTTCAAGCACGTCCAACTTAGAAGGGCTATG-GGA-ATTA
1 TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGG--ATGTGGACATTA
*
44676683 TCCTTCCCCAGCTTTCTATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATT
64 TCCTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATT
44676736 CTGCAGCTCA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 99 0.94
127 3 0.03
128 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (126 bp):
TTTGTCACTGATTCACCATTTCCACCTTCAACCACATCCAACTTAAAAGGGATGTGGACATTATC
CTTCCCCAGCTTTCCATCAAGTGAAGGAACCTGAACATCTTGCTGCTTATTGCTAACTGAG
Found at i:44683916 original size:21 final size:23
Alignment explanation
Indices: 44683891--44683950 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
44683881 TTATTTCTCA
44683891 ATTTAATTTAATTTTTG-ATTT-
1 ATTTAATTTAATTTTTGTATTTG
*
44683912 ATTTAATTGTTTATTTTTGTTATTTG
1 ATTTAA-T-TTAATTTTTG-TATTTG
44683938 ATTT-ATTTAATTT
1 ATTTAATTTAATTT
44683951 CTAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 15 0.47
24 1 0.03
25 5 0.16
26 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTAATTTAATTTTTGTATTTG
Found at i:44685417 original size:41 final size:43
Alignment explanation
Indices: 44685343--44685422 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
44685333 AGCGCCACTA
* * *
44685343 TAGATCAAGACCTTTAGCGGCGCTTTTATC-AAAACGCCGCTT
1 TAGAACAAGACCTTTAGCGACGCTTTTAGCAAAAACGCCGCTT
44685385 TAGAACAA-ACCTTTAGCGACGCTTCTT-GCAAAAACGCC
1 TAGAACAAGACCTTTAGCGACGCTT-TTAGCAAAAACGCC
44685423 ACTAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 16 0.48
42 17 0.52
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
TAGAACAAGACCTTTAGCGACGCTTTTAGCAAAAACGCCGCTT
Found at i:44688852 original size:73 final size:72
Alignment explanation
Indices: 44688751--44688922 Score: 238
Period size: 73 Copynumber: 2.4 Consensus size: 72
44688741 CTGAGCATTA
* ** * *
44688751 GCGGCGCTTTCTTATTAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTAG
44688816 GTTTTTTT
66 G-TTTTTT
* * * *
44688824 GCGGTGCTTTC-CGAAAAACGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGTCCTTGGGCTTA
1 GCGGCGCTTTCTC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTA
44688888 GGTTTTTT
65 GGTTTTTT
44688896 GCGGCGCTTTCTCAAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
44688923 TGCTTATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 30 0.34
73 57 0.66
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCCTTGGGCTTAG
GTTTTTT
Found at i:44690825 original size:3 final size:3
Alignment explanation
Indices: 44690819--44690849 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
44690809 TTATTTAAGT
*
44690819 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44690850 ACTAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:44714151 original size:16 final size:16
Alignment explanation
Indices: 44714087--44714154 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
44714077 GAAGTAATAT
* *
44714087 TATTTTAATAGTTTAA
1 TATTTTATTAATTTAA
*
44714103 TATTTAATTTAATTTAA
1 TATTTTA-TTAATTTAA
* *
44714120 TA-TTTATCTAA-ATAG
1 TATTTTAT-TAATTTAA
*
44714135 TATTTTATTAATTTAG
1 TATTTTATTAATTTAA
44714151 TATT
1 TATT
44714155 AAAGTGATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
15 8 0.20
16 24 0.59
17 9 0.22
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:44714220 original size:16 final size:16
Alignment explanation
Indices: 44714098--44714223 Score: 55
Period size: 16 Copynumber: 7.6 Consensus size: 16
44714088 ATTTTAATAG
44714098 TTTAATATT-TAATTTAA
1 TTTAATATTAT-A-TTAA
44714115 TTTAATATT-TATCTAA
1 TTTAATATTATAT-TAA
* * *
44714131 -ATAGTATTTTATTAA
1 TTTAATATTATATTAA
*
44714146 TTTAGTATTAAAGTGATT-A
1 TTTAATATT--A-T-ATTAA
*
44714165 TCTTAATATTAAATTAA
1 T-TTAATATTATATTAA
* *
44714182 TCTAATATT-TATCAA
1 TTTAATATTATATTAA
* *
44714197 GATAAATATTATATTAA
1 -TTTAATATTATATTAA
44714214 TTTAATATTA
1 TTTAATATTA
44714224 AAGTGATTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
15 14 0.17
16 38 0.46
17 17 0.20
18 1 0.01
19 3 0.04
20 10 0.12
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (16 bp):
TTTAATATTATATTAA
Found at i:44714223 original size:68 final size:68
Alignment explanation
Indices: 44714099--44714232 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
44714089 TTTTAATAGT
* * * * *
44714099 TTAATATTTAATTTAATTTAATATTTATCTAAATAGTATTTTATTAATTTAGTATTAAAGTGATT
1 TTAATATTTAAATTAATCTAATATTTATCTAAATAATATTATATTAATTTAATATTAAAGTGATT
44714164 ATC
66 ATC
44714167 TTAATA-TTAAATTAATCTAATATTTATC-AAGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTAATATTTAAATTAATCTAATATTTATCTAA-AT-AATATTATATTAATTTAATATTAAAGTGA
44714230 TTA
64 TTA
44714233 AGTTTAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 2 0.03
67 22 0.37
68 35 0.59
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (68 bp):
TTAATATTTAAATTAATCTAATATTTATCTAAATAATATTATATTAATTTAATATTAAAGTGATT
ATC
Found at i:44717594 original size:33 final size:33
Alignment explanation
Indices: 44717557--44717619 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
44717547 ATCACTGCCC
*
44717557 CATCCACACCACAACC-CTAGGTGTCTCTCTCAA
1 CATCCACACCACAACCTC-AGGTGTCCCTCTCAA
44717590 CATCCACACCACAACCTCAGGTGTCCCTCT
1 CATCCACACCACAACCTCAGGTGTCCCTCT
44717620 GACTCTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (33 bp):
CATCCACACCACAACCTCAGGTGTCCCTCTCAA
Found at i:44719469 original size:15 final size:17
Alignment explanation
Indices: 44719431--44719471 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
44719421 TTACATAATA
44719431 AAAATAATATTGATATT
1 AAAATAATATTGATATT
*
44719448 AAAATAAT-TTTATATT
1 AAAATAATATTGATATT
44719464 -AAATAATA
1 AAAATAATA
44719472 ATTTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATAATATTGATATT
Found at i:44719473 original size:18 final size:17
Alignment explanation
Indices: 44719429--44719480 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
44719419 TCTTACATAA
*
44719429 TAAAAATAATATTGATAT
1 TAAAAATAAT-TTTATAT
44719447 T-AAAATAATTTTATAT
1 TAAAAATAATTTTATAT
44719463 TAAATAATAATTTTATAT
1 TAAA-AATAATTTTATAT
44719481 ATTTATTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 7 0.23
17 10 0.32
18 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TAAAAATAATTTTATAT
Found at i:44721303 original size:19 final size:19
Alignment explanation
Indices: 44721281--44721318 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44721271 AATTTTTGGA
44721281 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
44721300 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
44721319 TGTTTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:44731723 original size:35 final size:34
Alignment explanation
Indices: 44731684--44731750 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
44731674 TAAAATGCGC
*
44731684 ATATAAATACATACATGTAT-TAAAATATATAAAAA
1 ATATAAACACATACATGTATGT-AAATAT-TAAAAA
* *
44731719 ATATAAACATATATATGTATGTAAATATTAAA
1 ATATAAACACATACATGTATGTAAATATTAAA
44731751 TATGTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 23 0.82
36 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (34 bp):
ATATAAACACATACATGTATGTAAATATTAAAAA
Found at i:44733742 original size:19 final size:19
Alignment explanation
Indices: 44733718--44733754 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44733708 TTAATGTGCG
*
44733718 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
44733737 AATATATATATATGTGTG
1 AATATATATATATGTGTG
44733755 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:44734028 original size:41 final size:41
Alignment explanation
Indices: 44733966--44734141 Score: 280
Period size: 41 Copynumber: 4.3 Consensus size: 41
44733956 GTTTGGAATT
* *
44733966 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
44734007 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
44734048 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
44734089 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
44734130 GGTGATCCGAAT
1 GGTGATCTGAAT
44734142 ATGATGAATT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:44734103 original size:82 final size:82
Alignment explanation
Indices: 44733966--44734135 Score: 331
Period size: 82 Copynumber: 2.1 Consensus size: 82
44733956 GTTTGGAATT
44733966 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
44734031 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
44734048 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
44734113 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
44734130 GGTGAT
1 GGTGAT
44734136 CCGAATATGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:44741383 original size:19 final size:19
Alignment explanation
Indices: 44741359--44741395 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44741349 TTAATGTGCG
*
44741359 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
44741378 AATATATATATATGTGTG
1 AATATATATATATGTGTG
44741396 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:44741669 original size:41 final size:41
Alignment explanation
Indices: 44741607--44741782 Score: 280
Period size: 41 Copynumber: 4.3 Consensus size: 41
44741597 GTTTGGAATT
* *
44741607 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
44741648 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
44741689 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
44741730 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
44741771 GGTGATCCGAAT
1 GGTGATCTGAAT
44741783 ATGATGAATT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:44741744 original size:82 final size:82
Alignment explanation
Indices: 44741607--44741776 Score: 331
Period size: 82 Copynumber: 2.1 Consensus size: 82
44741597 GTTTGGAATT
44741607 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
44741672 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
44741689 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
44741754 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
44741771 GGTGAT
1 GGTGAT
44741777 CCGAATATGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:44755668 original size:24 final size:24
Alignment explanation
Indices: 44755641--44755688 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44755631 TGTTCGATTG
44755641 AGCTCAACTTGAGTATCAAAACCT
1 AGCTCAACTTGAGTATCAAAACCT
44755665 AGCTCAACTTGAGTATCAAAACCT
1 AGCTCAACTTGAGTATCAAAACCT
44755689 TGAGTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (24 bp):
AGCTCAACTTGAGTATCAAAACCT
Found at i:44758547 original size:32 final size:31
Alignment explanation
Indices: 44758492--44758551 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
44758482 GTTTATAAAA
44758492 TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
1 TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
*
44758523 TTAA-GTTTAGGGTTTTATTTATTTTTAGG
1 TTAAGGTTTA-GGATTT-TTTATTTTTAGG
44758552 GTTTAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 9 0.35
32 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (31 bp):
TTAAGGTTTAGGATTTTTTATTTTTAGGTGG
Found at i:44762285 original size:43 final size:43
Alignment explanation
Indices: 44762224--44762361 Score: 206
Period size: 43 Copynumber: 3.2 Consensus size: 43
44762214 TATAAACAAT
*
44762224 GCCGCTATAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
44762267 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
* * * *
44762310 GCTGCTAAAGGACATGACCTTTAGCGGCGCTTTTA-TCACAAAC
1 GCCGCTAAAGAACATGGCCTTTAGCGGCGC-TTTACCCACAAAC
*
44762353 GTCGCTAAA
1 GCCGCTAAA
44762362 AGTACCGTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 83 0.95
44 4 0.05
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGCCTTTAGCGGCGCTTTACCCACAAAC
Found at i:44765157 original size:106 final size:105
Alignment explanation
Indices: 44764905--44765210 Score: 461
Period size: 106 Copynumber: 2.9 Consensus size: 105
44764895 CGAGAAAAGT
* *
44764905 AAAATTTTTTTTTTTGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTTAATTTTTTTTTTACTT
1 AAAAATTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACC-TTTTAATTTTTTTTTTACTT
* *
44764970 TTTTCGTGTCAGATAAGATATCAGTATACGAAAAAAGTAAA
65 TTTTCATGTCAGATAAGCTATCAGTATACGAAAAAAGTAAA
** * *
44765011 AAAAA-TAATTTTTGGTGGTGGCCTAGCAATGGCCGGCACCACCTTTTAAATTTTTTTTTACTTT
1 AAAAATTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAATTTTTTTTTTACTTT
* **
44765075 TTTCTTGTCAGATAAGCTATCAGTATACGAAAAGGGTAAAA
66 TTTCATGTCAGATAAGCTATCAGTATACGAAAAAAGT-AAA
* * *
44765116 AAAAATTTTTTTTTGGTGGTGGCCTGGTAATGGCCGACACCACCTTTTAATTTTTTTTTTACCTT
1 AAAAATTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAATTTTTTTTTTACTTT
44765181 TTTCATGTCAGATAAGCTATCAGTATACGA
66 TTTCATGTCAGATAAGCTATCAGTATACGA
44765211 GCATGCGCAC
Statistics
Matches: 180, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
104 53 0.29
105 42 0.23
106 85 0.47
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (105 bp):
AAAAATTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTTAATTTTTTTTTTACTTT
TTTCATGTCAGATAAGCTATCAGTATACGAAAAAAGTAAA
Found at i:44765236 original size:21 final size:21
Alignment explanation
Indices: 44765212--44765264 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
44765202 AGTATACGAG
*
44765212 CATGCGCACACGCTGTATGAA
1 CATGCGCACACGCTGCATGAA
*
44765233 CATGCACACACGCTGCATGAA
1 CATGCGCACACGCTGCATGAA
44765254 CATGCGCACAC
1 CATGCGCACAC
44765265 AATATCGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (21 bp):
CATGCGCACACGCTGCATGAA
Found at i:44765999 original size:102 final size:101
Alignment explanation
Indices: 44765717--44766049 Score: 447
Period size: 101 Copynumber: 3.2 Consensus size: 101
44765707 TAAAGATTAC
* * *
44765717 ATCTGACACGAAATAATTAAAATTTTTTTTTAAAAAGGTGGAGCGGGCCATTGCCAGGCCACCAC
1 ATCTGACACGAAAAAAGTAAAA-TTTTTTTTAAAAAGGTGGTGC-GGCCATTGCCAGGCCACCAC
*** * *
44765782 CAAAAAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTT
64 C-----AATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
* *
44765825 ATCTGACACGAAAAAAGTAAATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCATGCCACCA
1 ATCTGACACGAAAAAAGTAAAATTTTTTTT--AAAAAGGTGGTG-CGGCCATTGCCAGGCCACCA
44765890 CC-A-TTTTTTTTTTACTTTTTT-GTATATTGATATCTT
63 CCAATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
*
44765926 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTGTCGGCCATTGCTAGGCCACCACC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTG-CGGCCATTGCCAGGCCACCACC
44765991 AATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
65 AATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
44766028 ATCTGACACGAAAAAAGTAAAA
1 ATCTGACACGAAAAAAGTAAAA
44766050 CAATTTTTTT
Statistics
Matches: 205, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
99 32 0.16
100 1 0.00
101 60 0.29
102 52 0.25
103 1 0.00
107 8 0.04
108 19 0.09
109 31 0.15
110 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (101 bp):
ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAGGTGGTGCGGCCATTGCCAGGCCACCACCA
ATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
Found at i:44766057 original size:102 final size:101
Alignment explanation
Indices: 44765717--44766098 Score: 462
Period size: 109 Copynumber: 3.6 Consensus size: 101
44765707 TAAAGATTAC
* * * * *
44765717 ATCTGACACGAAATAATTAAAATTTTTTTTTAAAAAGGTGGAGCGGGCCATTGCCAGGCCACCAC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC
** * *
44765782 CAAAAAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTT
66 C------AT-TTTTTTTTTACTTTTTTCGTATATTGATATCTT
* *
44765825 ATCTGACACGAAAAAAGTAAATTTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCATGCCACCA
1 ATCTGACACGAAAAAAGTAAAATTTTTTTT-AAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCA
44765890 CCATTTTTTTTTTACTTTTTT-GTATATTGATATCTT
65 CCATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
* *
44765926 ATCTGACACGAAAAAAGTAAAATTTTTTTT-AAAAAGGTGGTGTCGGCCATTGCTAGGCCACCAC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC
44765990 CAATTTTTTTTTTTACTTTTTTCGTATATTGATATCTT
66 C-A-TTTTTTTTTTACTTTTTTCGTATATTGATATCTT
* * *
44766028 ATCTGACACGAAAAAAGTAAAACAATTTTTTTTTAAAAAAAAGATGGTGCCGACCATTGTCAGGC
1 ATCTGACACGAAAAAAGT--AA-AA-TTTTTTTT--AAAAAAGGTGGTGCCGGCCATTGCCAGGC
44766093 CACCAC
60 CACCAC
44766099 AATATATATA
Statistics
Matches: 243, Mismatches: 20, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
99 32 0.13
100 1 0.00
101 60 0.25
102 48 0.20
103 2 0.01
104 2 0.01
105 2 0.01
106 8 0.03
108 27 0.11
109 61 0.25
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (101 bp):
ATCTGACACGAAAAAAGTAAAATTTTTTTTAAAAAAGGTGGTGCCGGCCATTGCCAGGCCACCAC
CATTTTTTTTTTACTTTTTTCGTATATTGATATCTT
Found at i:44766078 original size:208 final size:205
Alignment explanation
Indices: 44765717--44766098 Score: 536
Period size: 208 Copynumber: 1.8 Consensus size: 205
44765707 TAAAGATTAC
* *
44765717 ATCTGACACGAAATAATTAAAATTTTTTTTTAAAAAGGTGGAGCGGGCCATTGCCAGGCCACCAC
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAGGTGGAGCGGGCCATTGCCAGGCCACCAC
44765782 CAAAAAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTTATCTGACACGAAAAAAGTAAAT
66 C----AAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTTATCTGACACGAAAAAAGTAAAT
* * *
44765847 TTTTTTTTAAAAAAAGGTGGTGCCGGCCATTGCCATGCCACCACCATTTTTTTTTTACTTTTTTG
127 TTTTTTTTAAAAAAAGATGGTGCCGACCATTGCCAGGCCACCACCATTTTTTTTTTACTTTTTTG
44765912 TATATTGATATCTT
192 TATATTGATATCTT
* *
44765926 ATCTGACACGAAAAAAGTAAAA-TTTTTTTTAAAAAGGTGGTGTC-GGCCATTGCTAGGCCACCA
1 ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAGGTGGAG-CGGGCCATTGCCAGGCCACCA
*** * *
44765989 CC-AATTTTTTTTTTTACTTTTTTCGTATATTGATATCTTATCTGACACGAAAAAAGTAAAACAA
65 CCAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTTATCTGACACGAAAAAAGT---A-AA
*
44766053 TTTTTTTTTAAAAAAAAGATGGTGCCGACCATTGTCAGGCCACCAC
126 TTTTTTTTT-AAAAAAAGATGGTGCCGACCATTGCCAGGCCACCAC
44766099 AATATATATA
Statistics
Matches: 154, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
203 50 0.32
206 1 0.01
207 11 0.07
208 71 0.46
209 21 0.14
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (205 bp):
ATCTGACACGAAAAAAGTAAAATTTTTTTTTAAAAAGGTGGAGCGGGCCATTGCCAGGCCACCAC
CAAATAAATTTTTTTACTTTTTTCGTATACTGATAGCTTATCTGACACGAAAAAAGTAAATTTTT
TTTTAAAAAAAGATGGTGCCGACCATTGCCAGGCCACCACCATTTTTTTTTTACTTTTTTGTATA
TTGATATCTT
Found at i:44771873 original size:5 final size:5
Alignment explanation
Indices: 44771859--44771917 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
44771849 AAAACAAACA
* *
44771859 AAAAG AAAAAG AAAAG AAAA- AAGAA- AAAAG AAAAG AAAGGAA AAAAT
1 AAAAG -AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAA--AG AAAAG
44771906 AAAAG AAAAG AA
1 AAAAG AAAAG AA
44771918 GAAAGAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.09
5 33 0.72
6 5 0.11
7 4 0.09
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:44771873 original size:12 final size:12
Alignment explanation
Indices: 44771858--44771935 Score: 67
Period size: 12 Copynumber: 6.5 Consensus size: 12
44771848 AAAAACAAAC
44771858 AAAAAGAAAAAG
1 AAAAAGAAAAAG
44771870 -AAAAGAAAAAAG
1 AAAAAG-AAAAAG
44771882 AAAAA-AGAAAAG
1 AAAAAGA-AAAAG
*
44771894 -AAAGGAAAAA-
1 AAAAAGAAAAAG
44771904 ATAAAAG-AAAAG
1 A-AAAAGAAAAAG
44771916 AAGAAAGAAGAAAG
1 AA-AAAGAA-AAAG
44771930 AAAAAG
1 AAAAAG
44771936 GAGAGGCCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
11 18 0.33
12 21 0.39
13 9 0.17
14 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:44771880 original size:7 final size:7
Alignment explanation
Indices: 44771858--44771928 Score: 60
Period size: 7 Copynumber: 10.3 Consensus size: 7
44771848 AAAAACAAAC
44771858 AAAAAG-
1 AAAAAGA
44771864 AAAAAG-
1 AAAAAGA
44771870 -AAAAGA
1 AAAAAGA
44771876 AAAAAGA
1 AAAAAGA
44771883 AAAAAGAA
1 AAAAAG-A
*
44771891 AAGAAAGG
1 AA-AAAGA
44771899 AAAAA-A
1 AAAAAGA
*
44771905 TAAAAGA
1 AAAAAGA
44771912 AAAGAAGA
1 AAA-AAGA
*
44771920 AAGAAGA
1 AAAAAGA
44771927 AA
1 AA
44771929 GAAAAAGGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 5 0.09
6 10 0.19
7 24 0.44
8 11 0.20
9 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:44772379 original size:103 final size:103
Alignment explanation
Indices: 44772259--44772561 Score: 419
Period size: 103 Copynumber: 2.9 Consensus size: 103
44772249 TTATTCTCAT
*
44772259 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTC
1 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
44772324 CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
66 CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
*
44772362 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGCTCTCAATAAAATTC
1 TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
* * * * * *
44772427 TATCTTATCCATTGTCATAATACTTTTCATCTTATTCAG
66 CATATTGTCCATTGTGATAAT-CTTTTTATCTTATTCAA
* * *
44772466 TTCT-TATCTTAGCAAAATTTGCTATATTGATTAACTTATTCATTTTGAGCCTTATTCTCAATAA
1 TT-TGTATCTTAGCAAAATTTGCTATCTTGA-T---TTATTCATTTCGAGCCTTGTTCTCAATAA
* * *
44772530 AATTCCATTTTGTCCATTTTGATCATCTTTTT
61 AATTCCATATTGTCCATTGTGATAATCTTTTT
44772562 CAAGCATTTT
Statistics
Matches: 175, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
103 80 0.46
104 42 0.24
105 2 0.01
107 5 0.03
108 46 0.26
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (103 bp):
TTTGTATCTTAGCAAAATTTGCTATCTTGATTTATTCATTTCGAGCCTTGTTCTCAATAAAATTC
CATATTGTCCATTGTGATAATCTTTTTATCTTATTCAA
Found at i:44773525 original size:46 final size:46
Alignment explanation
Indices: 44773456--44773869 Score: 612
Period size: 46 Copynumber: 9.0 Consensus size: 46
44773446 GACTAAAAGC
* * *
44773456 AGCAGATCTTGTCTTCCTATATTTGGCAGTGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* * *
44773502 AGCAGATCTTGTCTTTCTGTATTTGGCAGCGGAGTAGATCGAGGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
44773548 AGCAGATCTTGTCTTTCTGTATTTGGCAGCAGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
44773594 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *
44773640 AGCAGATCTTGCCTTTCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* * *
44773686 AGCAGATATTGTCTTACTGTATTTGGCAGCAGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
44773732 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
* *** *
44773778 AGCAGATCTTGTCTTCCTGTATTTGGCAACGGAAAAGATTGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
** * * *
44773824 AGCAGATTCTTGTCTTCCTGTATCCGGCAGTGAAGTAGATCGAAGA
1 AGCAGA-TCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGA
44773870 CACAAGCCTG
Statistics
Matches: 336, Mismatches: 31, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
46 305 0.91
47 31 0.09
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTGGATCGAAGAT
Found at i:44774025 original size:44 final size:44
Alignment explanation
Indices: 44773966--44774132 Score: 160
Period size: 44 Copynumber: 3.8 Consensus size: 44
44773956 TCAAATTTTG
* *
44773966 TCTCTCTGAAGTTGCAGTAGAGCAGGTTGAA-ATAGCAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAACCTTA
* * * **
44774010 TC-CCCATGAAGTTGCAATGGGGCAAGTTGAAGATACAAGTCTTA
1 TCTCCC-TGAAGTTGCAGTGGAGCAGGTTGAAGATACAAACCTTA
* * **
44774054 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCC-TA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAC-AAACCTTA
* * *
44774098 TCTCCCTGAAGTTGCAGTGGGGCAAGTCGAAGATA
1 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA
44774133 ACAAGTCTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 2 0.02
44 89 0.90
45 8 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAACCTTA
Found at i:44774254 original size:44 final size:44
Alignment explanation
Indices: 44774153--44774242 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
44774143 TGGAAGCTAT
* ** *
44774153 AAATTACAAACCTTACCTCTCTGAAGTTGCAGTAGAGTAGGTTG
1 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
44774197 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
1 AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
44774241 AA
1 AA
44774243 GTCACTAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
AAATAACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTG
Found at i:44774268 original size:44 final size:44
Alignment explanation
Indices: 44774158--44774313 Score: 129
Period size: 44 Copynumber: 3.5 Consensus size: 44
44774148 GCTATAAATT
* * * * *
44774158 ACAAACCTTA-CCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAATA
1 ACAAACCTTATCC-CCCTAAAGTTGCAGTAGAGCAGGTTGAAGTC
* * * *
44774202 ACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGTC
1 ACAAACCTTATCCCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTC
* * * * **
44774246 ACTAACCTTATCCCCCTAAAGTTACAGTGGGGCAAATTGAAG-C
1 ACAAACCTTATCCCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTC
44774289 TACAAACCTTATCTCCCC-AAAGTTG
1 -ACAAACCTTATC-CCCCTAAAGTTG
44774314 TAGTGGAGTG
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 1 0.01
44 86 0.93
45 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (44 bp):
ACAAACCTTATCCCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTC
Done.