Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 7 of 32
Found at i:792611 original size:19 final size:19
Alignment explanation
Indices: 792566--792617 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
792556 TTATTATTTT
792566 ATAAT-TAAAAATTATTTAA
1 ATAATATAAAAA-TATTTAA
** *
792585 ATTTTATATAAATATTTAA
1 ATAATATAAAAATATTTAA
792604 ATAATATAAAAATA
1 ATAATATAAAAATA
792618 ATTTTTCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATATAAAAATATTTAA
Found at i:796712 original size:22 final size:20
Alignment explanation
Indices: 796664--796714 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
796654 TTATTTATAT
*
796664 TTTTAAACTTAATAAAATAAA
1 TTTTAAA-TCAATAAAATAAA
*
796685 TATTAAATCAATAAAAATCAAA
1 TTTTAAATCAAT-AAAAT-AAA
796707 TTTTAAAT
1 TTTTAAAT
796715 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTTAAATCAATAAAATAAA
Found at i:796840 original size:31 final size:32
Alignment explanation
Indices: 796805--796864 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
796795 ATTAAAAATT
796805 TATATTTTAA-ATTAA-ATTAAATTTAAATAAA
1 TATA-TTTAATATTAATATTAAATTTAAATAAA
*
796836 TATATTTAATATTAATATTATATTTAAAT
1 TATATTTAATATTAATATTAAATTTAAAT
796865 TTAACCTAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTAATATTAATATTAAATTTAAATAAA
Found at i:811376 original size:13 final size:13
Alignment explanation
Indices: 811354--811397 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
811344 ATAATTCGTA
811354 TATT-TTTATATT
1 TATTATTTATATT
811366 TATTATTTATATTT
1 TATTATTTATA-TT
811380 TATTATTT-TATAT
1 TATTATTTATAT-T
811393 TATTA
1 TATTA
811398 AAATAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.17
13 14 0.48
14 10 0.34
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTATTTATATT
Found at i:811406 original size:22 final size:22
Alignment explanation
Indices: 811381--811447 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
811371 TTTATATTTT
811381 ATTATTTTATATTATTAAAATA
1 ATTATTTTATATTATTAAAATA
*
811403 ATTATTTAATA-TATTAATAATAA
1 ATTATTTTATATTATTAA-AAT-A
*
811426 ATTTTTTTA-ATT-TTATAAATA
1 ATTATTTTATATTATTA-AAATA
811447 A
1 A
811448 AATTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.21
22 20 0.53
23 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATTTTATATTATTAAAATA
Found at i:812123 original size:25 final size:25
Alignment explanation
Indices: 812095--812206 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
812085 ATGATACGAG
812095 TATAATATTTATAAAATATAAAATA
1 TATAATATTTATAAAATATAAAATA
* *
812120 TATAATA-TAATATAAATAT-ATATA
1 TATAATATTTATA-AAATATAAAATA
* *
812144 T-TAAAATTTATATAATATAAAAT-
1 TATAATATTTATAAAATATAAAATA
**
812167 TACTAATATATTA-AAGTTATATAAATA
1 TA-TAATAT-TTATAAAATATA-AAATA
812194 TA-AATATTT-TAAA
1 TATAATATTTATAAA
812207 CATAATTATA
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
23 10 0.15
24 20 0.30
25 28 0.42
26 7 0.10
27 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
TATAATATTTATAAAATATAAAATA
Found at i:812126 original size:14 final size:14
Alignment explanation
Indices: 812104--812176 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 14
812094 GTATAATATT
*
812104 TATAAAATATAAAA
1 TATATAATATAAAA
812118 TATATAATATAATATA
1 TATATAATATAA-A-A
*
812134 AATATATATATTAAAA
1 TATATA-ATA-TAAAA
812150 TTTATATAATATAAAA
1 --TATATAATATAAAA
812166 T-TACTAATATA
1 TATA-TAATATA
812177 TTAAAGTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
13 2 0.04
14 19 0.39
15 1 0.02
16 12 0.24
17 7 0.14
18 8 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATAATATAAAA
Found at i:812133 original size:19 final size:19
Alignment explanation
Indices: 812109--812242 Score: 62
Period size: 19 Copynumber: 7.4 Consensus size: 19
812099 ATATTTATAA
812109 AATATAAAATATATAATAT
1 AATATAAAATATATAATAT
812128 AATAT--AA-ATAT-ATAT
1 AATATAAAATATATAATAT
812143 -AT-TAAAAT-T-T-ATAT
1 AATATAAAATATATAATAT
812157 AATATAAAAT-TACTAATAT
1 AATATAAAATATA-TAATAT
*
812176 -AT-TAAAGTTATATAAATAT
1 AATATAAA-ATATAT-AATAT
* * *
812195 AAATATTTTAAACATA-ATTAT
1 -AATA--TAAAATATATAATAT
*
812216 AATATAAAA-AAATAAATAT
1 AATATAAAATATAT-AATAT
812235 AATATAAA
1 AATATAAA
812243 TTATTAAATT
Statistics
Matches: 89, Mismatches: 8, Indels: 36
0.67 0.06 0.27
Matches are distributed among these distances:
13 1 0.01
14 7 0.08
15 9 0.10
16 11 0.12
17 8 0.09
18 9 0.10
19 28 0.31
20 4 0.04
21 6 0.07
23 3 0.03
24 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AATATAAAATATATAATAT
Found at i:812424 original size:34 final size:34
Alignment explanation
Indices: 812371--812585 Score: 245
Period size: 34 Copynumber: 6.4 Consensus size: 34
812361 GGGAATACTG
*
812371 TTGATTAAAT-GGTGATTTGGTAGTTTATCATTA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
* * *
812404 TTGATTAAATGGGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
* * * *
812438 TTGACTAAATAGGAGATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
* ** *
812472 TTGATTAAATGAGAAATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
* *
812506 TTGATTAAATGGGTGATTTGGTGGTTTACCATTG
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
* * * *
812540 TTGACTAAAT-GGTAGATTTGGTAGGTTGCCATTG
1 TTGATTAAATGGGT-GATTTGGTAGTTTACCATTA
812574 TTGATTAAATGG
1 TTGATTAAATGG
812586 TAGTTTTTAC
Statistics
Matches: 153, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 13 0.08
34 139 0.91
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
TTGATTAAATGGGTGATTTGGTAGTTTACCATTA
Found at i:812510 original size:102 final size:101
Alignment explanation
Indices: 812371--812585 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 101
812361 GGGAATACTG
** * * *
812371 TTGATTAAATGGTGATTTGGTAGTTTATCATTATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACCAT
812436 TGTTGACTAAATAGG-AGATTTGGTAGCTTACCATTA
66 TGTTGACTAAAT-GGTAGATTTGGTAGCTTACCATTA
812472 TTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACCA
* * *
812537 TTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTG
65 TTGTTGACTAAATGGTAGATTTGGTAGCTTACCATTA
812574 TTGATTAAATGG
1 TTGATTAAATGG
812586 TAGTTTTTAC
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 14 0.13
102 90 0.87
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (101 bp):
TTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACCAT
TGTTGACTAAATGGTAGATTTGGTAGCTTACCATTA
Found at i:814085 original size:35 final size:33
Alignment explanation
Indices: 814041--814137 Score: 92
Period size: 35 Copynumber: 2.9 Consensus size: 33
814031 AAAGTAAATT
*
814041 TAAATTATTATTAATAATAAAATAAATTTTTATAA
1 TAAAATATTATTAATAATAAAATAAATTTTT-T-A
* *
814076 TAAAATATTAATAA-ATATATAAAT-AATATTTTA
1 TAAAATATTATTAATA-ATA-AAATAAATTTTTTA
* *
814109 -AAAATATAATAAATAATAAAATAAATTTT
1 TAAAATATTATTAATAATAAAATAAATTTT
814138 AAAATCAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
31 4 0.08
32 18 0.35
33 2 0.04
34 2 0.04
35 21 0.41
36 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAATATTATTAATAATAAAATAAATTTTTTA
Found at i:814089 original size:32 final size:32
Alignment explanation
Indices: 814049--814141 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 32
814039 TTTAAATTAT
* *
814049 TATTAATAATAAAATAAATTTTTATAATAAAA
1 TATTAATAATAAAATAAATTTTAAAAATAAAA
*
814081 TATTAATAAATATATAAATAATATTTTAAAAATATAA
1 TATTAAT--A-ATA-AAATAA-ATTTTAAAAATAAAA
814118 TA--AATAATAAAATAAATTTTAAAA
1 TATTAATAATAAAATAAATTTTAAAA
814142 TCAAATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
30 9 0.17
31 6 0.11
32 10 0.19
33 1 0.02
34 1 0.02
35 6 0.11
36 6 0.11
37 14 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
TATTAATAATAAAATAAATTTTAAAAATAAAA
Found at i:814119 original size:31 final size:31
Alignment explanation
Indices: 814029--814141 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 31
814019 ATAAATTTAG
* * *
814029 ATAAAGTAAA-TTT-AAATTATT-ATTAATA
1 ATAAAATAAATTTTAAAAATATTAATAAATA
814057 ATAAAATAAATTTTTATAATAAAATATTAATAAAT-
1 ATAAAATAAA--TTT-T-A-AAAATATTAATAAATA
814092 ATATAAATAATATTTTAAAAATA-TAATAAATA
1 ATA-AAATAA-ATTTTAAAAATATTAATAAATA
814124 ATAAAATAAATTTTAAAA
1 ATAAAATAAATTTTAAAA
814142 TCAAATTTAA
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
28 9 0.13
30 9 0.13
31 16 0.23
32 10 0.14
33 1 0.01
34 1 0.01
35 13 0.18
36 11 0.15
37 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
ATAAAATAAATTTTAAAAATATTAATAAATA
Found at i:814125 original size:23 final size:23
Alignment explanation
Indices: 814074--814126 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
814064 AAATTTTTAT
*
814074 AATAAAATATTAATAAATATATA
1 AATAATATATTAATAAATATATA
*
814097 AATAATATTTTAA-AAATATAATA
1 AATAATATATTAATAAATAT-ATA
814120 AATAATA
1 AATAATA
814127 AAATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAATATATTAATAAATATATA
Found at i:814133 original size:23 final size:22
Alignment explanation
Indices: 814053--814133 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 22
814043 AATTATTATT
** *
814053 AATAATAAAATAAATTTTTAT-
1 AATAATAAAATAAAAATATATA
*
814074 AATAA-AATATTAATAAATATATA
1 AATAATAA-AATAA-AAATATATA
***
814097 AATAATATTTTAAAAATATAATA
1 AATAATAAAATAAAAATAT-ATA
814120 AATAATAAAATAAA
1 AATAATAAAATAAA
814134 TTTTAAAATC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.04
21 9 0.20
22 11 0.24
23 23 0.50
24 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAATAAAATAAAAATATATA
Found at i:814153 original size:31 final size:30
Alignment explanation
Indices: 814053--814155 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 30
814043 AATTATTATT
*
814053 AATAATAAAATAAATTTTTATAATAAAATATTA
1 AATAATAAAATAAA-TTTTAAAAT-AAAT-TTA
*
814086 ATAAATATATAAATAATATTTTAAAAATATAA--TA
1 A-ATA-ATA-AAATAA-ATTTT-AAAATA-AATTTA
814120 AATAATAAAATAAATTTTAAAATCAAATTTA
1 AATAATAAAATAAATTTTAAAAT-AAATTTA
814151 AATAA
1 AATAA
814156 AACTAATTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
29 7 0.12
30 6 0.10
31 13 0.22
32 3 0.05
33 3 0.05
34 5 0.09
35 3 0.05
36 11 0.19
37 7 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
AATAATAAAATAAATTTTAAAATAAATTTA
Found at i:815389 original size:2 final size:2
Alignment explanation
Indices: 815382--815427 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
815372 CATGTATAAA
* *
815382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815424 AT AT
1 AT AT
815428 TTTTTTTGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:819374 original size:27 final size:27
Alignment explanation
Indices: 819343--819397 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
819333 AAAACATTTG
819343 ATGCAAGAAAGAGGAAATACCAAAGTC
1 ATGCAAGAAAGAGGAAATACCAAAGTC
* * *
819370 ATGCATGAAAGAGGAGATAGCAAAGTC
1 ATGCAAGAAAGAGGAAATACCAAAGTC
819397 A
1 A
819398 ACCCTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.25, T:0.13
Consensus pattern (27 bp):
ATGCAAGAAAGAGGAAATACCAAAGTC
Found at i:821778 original size:34 final size:31
Alignment explanation
Indices: 821734--821800 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
821724 AATATAATTT
*
821734 TATAAAATAATATATTAAGTAAATATTATTAAAA
1 TATAAAATAATA-ATTAA--AAATAATATTAAAA
* *
821768 TATAATATAATAGTTAAAAATAATATTAAAA
1 TATAAAATAATAATTAAAAATAATATTAAAA
821799 TA
1 TA
821801 ATTTAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 15 0.50
33 4 0.13
34 11 0.37
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (31 bp):
TATAAAATAATAATTAAAAATAATATTAAAA
Found at i:821785 original size:29 final size:30
Alignment explanation
Indices: 821727--821800 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
821717 TAAATTTAAT
* *
821727 ATAATTTTATAAA-ATAATATATTAAGT-AA
1 ATAATATTA-AAATATAATATAATAAGTAAA
*
821756 ATATTATTAAAATATAATATAAT-AGTTAAAA
1 ATAATATTAAAATATAATATAATAAG-T-AAA
821787 ATAATATTAAAATA
1 ATAATATTAAAATA
821801 ATTTAAATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 5 0.14
29 17 0.46
31 15 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
ATAATATTAAAATATAATATAATAAGTAAA
Found at i:821801 original size:29 final size:29
Alignment explanation
Indices: 821754--821823 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
821744 TATATTAAGT
*
821754 AAATATTATTAAAATATAATAT-AATAGTTAA
1 AAATAATATT-AAATATAATATAAAT-GTT-A
*
821785 AAATAATATTAAA-ATAATTTAAATGTTA
1 AAATAATATTAAATATAATATAAATGTTA
821813 AAAT-ATATTAA
1 AAATAATATTAA
821824 TATTTATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 7 0.19
28 5 0.14
29 9 0.25
30 6 0.17
31 9 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATAATATTAAATATAATATAAATGTTA
Found at i:821855 original size:16 final size:16
Alignment explanation
Indices: 821833--821879 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
821823 ATATTTATAC
821833 AATTAAATTATTAATA
1 AATTAAATTATTAATA
*
821849 TATTAAATT-TTATATA
1 AATTAAATTATTA-ATA
*
821865 AATAAAATATATTAA
1 AATTAAAT-TATTAA
821880 ATTTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 2 0.08
18 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAAATTATTAATA
Found at i:821873 original size:25 final size:22
Alignment explanation
Indices: 821845--821906 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
821835 TTAAATTATT
821845 AATATATTAAATTTTATATAAATAA
1 AATATATTAAATTTTATAT---TAA
821870 AATATATTAAA-TTTA-ATTAA
1 AATATATTAAATTTTATATTAA
*
821890 AATATATAAAATTTTAT
1 AATATATTAAATTTTAT
821907 GAAAGGATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 13 0.38
21 4 0.12
23 2 0.06
24 4 0.12
25 11 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATATTAAATTTTATATTAA
Found at i:822179 original size:13 final size:14
Alignment explanation
Indices: 822149--822178 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
822139 TGTCAACCTC
822149 AAATATTGATAAAA
1 AAATATTGATAAAA
*
822163 AAATATTTATAAAA
1 AAATATTGATAAAA
822177 AA
1 AA
822179 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAATATTGATAAAA
Found at i:823213 original size:3 final size:3
Alignment explanation
Indices: 823205--823254 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
823195 ACACAGCGGC
823205 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
823253 AG
1 AG
823255 CCAGAAAGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:824776 original size:2 final size:2
Alignment explanation
Indices: 824769--824797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
824759 AGTAGAATGC
824769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
824798 CAGCATCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:825284 original size:13 final size:13
Alignment explanation
Indices: 825266--825290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
825256 TGTTTCAAAA
825266 TTTATATAATATC
1 TTTATATAATATC
825279 TTTATATAATAT
1 TTTATATAATAT
825291 GAATTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATATAATATC
Found at i:825653 original size:2 final size:2
Alignment explanation
Indices: 825646--825675 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
825636 ATCAGCATTC
*
825646 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
825676 CACACACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:828510 original size:24 final size:26
Alignment explanation
Indices: 828470--828517 Score: 57
Period size: 24 Copynumber: 1.9 Consensus size: 26
828460 GATTCATTTT
*
828470 ATAATTATATAATTTATGTTATTTTT
1 ATAATTATATAATTTATGTAATTTTT
828496 AT-ATT-TAT-ATGTTATGTAATTT
1 ATAATTATATAAT-TTATGTAATTT
828518 ATATCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
23 2 0.10
24 13 0.65
25 3 0.15
26 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATAATTATATAATTTATGTAATTTTT
Found at i:829573 original size:24 final size:25
Alignment explanation
Indices: 829546--829592 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
829536 CAATTACCAC
*
829546 AGTCAC-CATAACCTTTATCTCCTT
1 AGTCACTCACAACCTTTATCTCCTT
*
829570 AGTCACTTACAACCTTTATCTCC
1 AGTCACTCACAACCTTTATCTCC
829593 ACTAATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (25 bp):
AGTCACTCACAACCTTTATCTCCTT
Found at i:829849 original size:12 final size:12
Alignment explanation
Indices: 829827--829858 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
829817 ATATCACAAA
829827 AAAATTAAAATAT
1 AAAA-TAAAATAT
829840 AAAATAAAATAT
1 AAAATAAAATAT
829852 AAAATAA
1 AAAATAA
829859 TATGAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:832731 original size:21 final size:22
Alignment explanation
Indices: 832707--832766 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
832697 ACATCACGTA
832707 AATT-AAATTTAATATAAAAAT
1 AATTAAAATTTAATATAAAAAT
* * *
832728 AATTAAAATATATTATAAATAT
1 AATTAAAATTTAATATAAAAAT
832750 -ATTAAAATTT-ATATAAA
1 AATTAAAATTTAATATAAA
832767 TATATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 6 0.18
21 13 0.39
22 14 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTAAAATTTAATATAAAAAT
Found at i:832737 original size:9 final size:10
Alignment explanation
Indices: 832718--832781 Score: 69
Period size: 10 Copynumber: 6.3 Consensus size: 10
832708 ATTAAATTTA
*
832718 ATATAAAAAT
1 ATATTAAAAT
832728 A-ATTAAAAT
1 ATATTAAAAT
832737 ATATTATAAAT
1 ATATTA-AAAT
832748 ATATTAAAAT
1 ATATTAAAAT
*
832758 TTA-TATAAAT
1 ATATTA-AAAT
832768 ATATATAAAAT
1 ATAT-TAAAAT
832779 ATA
1 ATA
832782 AAATTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 10 0.22
10 17 0.37
11 17 0.37
12 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATTAAAAT
Found at i:832768 original size:31 final size:29
Alignment explanation
Indices: 832717--832809 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
832707 AATTAAATTT
*
832717 AATATA-AAAATAAT-TAAAATATATTATA
1 AATATATAAAATTATAT-AAATATATTATA
832745 AATATATTAAAATTTATATAAATATA-TATA
1 AATATA-TAAAA-TTATATAAATATATTATA
* *
832775 AA-ATATAAAATTATATATATATATACATA
1 AATATATAAAATTATATAAATATAT-TATA
832804 AATATA
1 AATATA
832810 ATATAAACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 12 0.22
28 11 0.20
29 8 0.15
30 13 0.24
31 10 0.18
32 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
AATATATAAAATTATATAAATATATTATA
Found at i:832776 original size:21 final size:21
Alignment explanation
Indices: 832718--832816 Score: 93
Period size: 20 Copynumber: 4.9 Consensus size: 21
832708 ATTAAATTTA
*
832718 ATATAAAAATA-AT-TAAAAT
1 ATATATAAATATATATAAAAT
832737 ATATTATAAATATAT-TAAAAT
1 ATA-TATAAATATATATAAAAT
*
832758 TTATATAAATATATATAAAAT
1 ATATATAAATATATATAAAAT
* *
832779 ATA-A-AATTATATAT-ATAT
1 ATATATAAATATATATAAAAT
*
832797 ATACATAAATATAATATAAA
1 ATATATAAATAT-ATATAAA
832817 CATAAAATGA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.09
19 13 0.20
20 24 0.36
21 22 0.33
22 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATAAATATATATAAAAT
Found at i:832790 original size:10 final size:9
Alignment explanation
Indices: 832717--832791 Score: 57
Period size: 10 Copynumber: 7.9 Consensus size: 9
832707 AATTAAATTT
832717 AATATA-AA
1 AATATATAA
832725 AATA-ATTAA
1 AATATA-TAA
832734 AATATATTATA
1 AATATA-TA-A
832745 AATATATTAA
1 AATATA-TAA
832755 AATTTATATAA
1 AA--TATATAA
832766 ATATATATAA
1 A-ATATATAA
832776 AATATA-AA
1 AATATATAA
*
832784 ATTATATA
1 AATATATA
832792 TATATATACA
Statistics
Matches: 58, Mismatches: 1, Indels: 15
0.78 0.01 0.20
Matches are distributed among these distances:
7 1 0.02
8 11 0.19
9 12 0.21
10 15 0.26
11 14 0.24
12 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATATATAA
Found at i:832819 original size:17 final size:17
Alignment explanation
Indices: 832760--832822 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
832750 ATTAAAATTT
* * *
832760 ATATAAATATATATAAA
1 ATATAAACATAAATATA
*
832777 ATATAAA-AT-TATATA
1 ATATAAACATAAATATA
*
832792 TATATATACATAAATATA
1 -ATATAAACATAAATATA
832810 ATATAAACATAAA
1 ATATAAACATAAA
832823 ATGAATTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 8 0.21
17 21 0.54
18 5 0.13
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAAACATAAATATA
Found at i:833041 original size:14 final size:14
Alignment explanation
Indices: 833019--833070 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
833009 TAATTATATT
*
833019 TTTAAATATTTTTA
1 TTTATATATTTTTA
833033 TTTATATATTTTTA
1 TTTATATATTTTTA
* *
833047 TATATTTATAATTTTA
1 T-T-TATATATTTTTA
*
833063 ATTATATA
1 TTTATATA
833071 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 19 0.61
15 2 0.06
16 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATATATTTTTA
Found at i:833048 original size:8 final size:8
Alignment explanation
Indices: 833012--833137 Score: 53
Period size: 8 Copynumber: 15.1 Consensus size: 8
833002 ATGTATTTAA
833012 TTATATTT
1 TTATATTT
*
833020 TTAAATATT
1 TTATAT-TT
833029 TT-TATTT
1 TTATATTT
*
833036 ATATATTT
1 TTATATTT
*
833044 TTATATAT
1 TTATATTT
*
833052 TTATAATT
1 TTATATTT
833060 TTA-ATTAT
1 TTATATT-T
* *
833068 ATAAATTT
1 TTATATTT
*
833076 TAAAATATTT
1 T--TATATTT
* *
833086 ATATATTA
1 TTATATTT
*
833094 TTATCA-TA
1 TTAT-ATTT
833102 TTATATCATT
1 TTATAT--TT
833112 TTAT-TTT
1 TTATATTT
833119 TTATATAATT
1 TTATAT--TT
833129 TTATATTT
1 TTATATTT
833137 T
1 T
833138 ACGTAATATT
Statistics
Matches: 88, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
7 12 0.14
8 49 0.56
9 9 0.10
10 18 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATATTT
Found at i:833054 original size:22 final size:22
Alignment explanation
Indices: 833005--833055 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
832995 TGGGAGTATG
*
833005 TATTTAATTATATTTTTAAATA
1 TATTTATTTATATTTTTAAATA
* *
833027 TTTTTATTTATATATTTT-TATA
1 TATTTATTTATAT-TTTTAAATA
833049 TATTTAT
1 TATTTAT
833056 AATTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTATTTATATTTTTAAATA
Found at i:833061 original size:16 final size:16
Alignment explanation
Indices: 833031--833138 Score: 69
Period size: 18 Copynumber: 6.4 Consensus size: 16
833021 TAAATATTTT
833031 TATTTATATATTTTTATA
1 TATTTATA-A-TTTTATA
833049 TATTTATAATTTTA-A
1 TATTTATAATTTTATA
* *
833064 T-TATATAAATTTTAAAA
1 TATTTAT-AATTTT-ATA
833081 TATTTATATATTATTATCA
1 TATTTATA-ATT-TTAT-A
* *
833100 TATTATATCATTTTATT
1 TATT-TATAATTTTATA
*
833117 TTTTATATAATTTTATA
1 TATT-TATAATTTTATA
833134 T-TTTA
1 TATTTA
833139 CGTAATATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
14 4 0.05
15 10 0.14
16 8 0.11
17 19 0.26
18 20 0.27
19 10 0.14
20 3 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATAATTTTATA
Found at i:833084 original size:32 final size:31
Alignment explanation
Indices: 833026--833088 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
833016 ATTTTTAAAT
* * * *
833026 ATTTTTATTTATATATTTTTATATATTTATA
1 ATTTTAATTTATAAATTTTAAAATATTTATA
833057 ATTTTAATTATATAAATTTTAAAATATTTATA
1 ATTTTAATT-TATAAATTTTAAAATATTTATA
833089 TATTATTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTTTAATTTATAAATTTTAAAATATTTATA
Found at i:833124 original size:17 final size:17
Alignment explanation
Indices: 833012--833138 Score: 88
Period size: 17 Copynumber: 7.6 Consensus size: 17
833002 ATGTATTTAA
833012 TTATATTTT-TA-AATAT
1 TTATATTTTATATAAT-T
* *
833028 TTTTA-TTTATATATTT
1 TTATATTTTATATAATT
*
833044 TTATATATT-TATAATT
1 TTATATTTTATATAATT
*
833060 TTA-ATTATATA-AATT
1 TTATATTTTATATAATT
*
833075 TTAAAATATTTATAT-ATT
1 TT-ATAT-TTTATATAATT
* *
833093 ATTATCATATTATATCATT
1 -TTAT-ATTTTATATAATT
*
833112 TTATTTTTTATATAATT
1 TTATATTTTATATAATT
833129 TTATATTTTA
1 TTATATTTTA
833139 CGTAATATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
15 12 0.14
16 23 0.27
17 25 0.29
18 19 0.22
19 7 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTTATATAATT
Found at i:833678 original size:27 final size:26
Alignment explanation
Indices: 833639--833694 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 26
833629 TGATGATCCG
833639 ATATGAATATAATATAAAAATAATTAAC
1 ATATGAATATAATATAAAAA-AA-TAAC
833667 ATATG-ATATAATATAAAAAAATAAC
1 ATATGAATATAATATAAAAAAATAAC
833692 ATA
1 ATA
833695 AACACTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.25
26 2 0.07
27 14 0.50
28 5 0.18
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (26 bp):
ATATGAATATAATATAAAAAAATAAC
Found at i:833762 original size:18 final size:17
Alignment explanation
Indices: 833736--833787 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
833726 TCTATATAAA
833736 ATAAATTATTAATATAT
1 ATAAATTATTAATATAT
*
833753 TTAAATTTATATAA-ATAT
1 ATAAA-TTAT-TAATATAT
*
833771 ATAAAATTATAAATATA
1 AT-AAATTATTAATATA
833788 AATATAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 6 0.21
18 16 0.57
19 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATTATTAATATAT
Found at i:833770 original size:6 final size:6
Alignment explanation
Indices: 833761--833974 Score: 81
Period size: 6 Copynumber: 35.2 Consensus size: 6
833751 ATTTAAATTT
*
833761 ATATAA ATAT-- ATA-AA ATTATAA ATATAA ATATAA CATA-AA AAAT-A
1 ATATAA ATATAA ATATAA A-TATAA ATATAA ATATAA -ATATAA ATATAA
* * * * * * *
833806 ATACAA ATATAA ATAT-A ATATCACGTG ATATAA ATTTAA AAATTA TTAAATA
1 ATATAA ATATAA ATATAA ATAT-A---A ATATAA ATATAA ATATAA ATATA-A
* * * *
833858 ATATAA AT-TAA ACTTTATA ATTTCAA CTAT-A ATATAA TTATATA ATATAA
1 ATATAA ATATAA A-TATA-A ATAT-AA ATATAA ATATAA ATATA-A ATATAA
* *
833908 ATATAA TATAATAA AAATAA TTA-AA ATATAA ATATAA A-A-AA ATATAA
1 ATATAA -AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* *
833955 ATATAA CTTAAAA ATATAA A
1 ATATAA -ATATAA ATATAA A
833975 ATATCGAAAT
Statistics
Matches: 154, Mismatches: 29, Indels: 50
0.66 0.12 0.21
Matches are distributed among these distances:
4 6 0.04
5 25 0.16
6 81 0.53
7 30 0.19
8 7 0.05
9 1 0.01
10 4 0.03
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:833903 original size:13 final size:12
Alignment explanation
Indices: 833885--833960 Score: 67
Period size: 11 Copynumber: 6.8 Consensus size: 12
833875 TAATTTCAAC
833885 TATAATATAATTA
1 TATAATATAA-TA
833898 TATAATATAA-A
1 TATAATATAATA
833909 TATAATATAATA
1 TATAATATAATA
833921 -A-AA-ATAAT-
1 TATAATATAATA
*
833929 TAAAATATAA-A
1 TATAATATAATA
* *
833940 TATAAAAAAATA
1 TATAATATAATA
833952 TA-AATATAA
1 TATAATATAA
833961 CTTAAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
9 6 0.12
10 4 0.08
11 28 0.54
12 4 0.08
13 10 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAATATAATA
Found at i:833918 original size:16 final size:16
Alignment explanation
Indices: 833885--833960 Score: 81
Period size: 16 Copynumber: 5.0 Consensus size: 16
833875 TAATTTCAAC
833885 TATAATAT-AAT-T-A
1 TATAATATAAATATAA
833898 TATAATATAAATATAA
1 TATAATATAAATATAA
833914 TATAATA-AAA-ATAA
1 TATAATATAAATATAA
*
833928 TTAAAATATAAATATAA
1 -TATAATATAAATATAA
* *
833945 AAAAATATAAATATAA
1 TATAATATAAATATAA
833961 CTTAAAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.15
14 7 0.13
15 10 0.18
16 26 0.47
17 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATAATATAAATATAA
Found at i:833935 original size:20 final size:19
Alignment explanation
Indices: 833907--833978 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 19
833897 ATATAATATA
*
833907 AATATAATATAATAAAAAT
1 AATAAAATATAATAAAAAT
*
833926 AATTAAAATATAAATATAAAAA
1 AA-TAAAATAT-AATA-AAAAT
833948 AATATAAATATAACTTAAAAAT
1 AATA-AAATATAA--TAAAAAT
833970 -ATAAAATAT
1 AATAAAATAT
833979 CGAAATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 11 0.25
22 16 0.36
23 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAAATATAATAAAAAT
Found at i:833958 original size:42 final size:42
Alignment explanation
Indices: 833888--833978 Score: 107
Period size: 42 Copynumber: 2.1 Consensus size: 42
833878 TTTCAACTAT
*
833888 AATATAATTATATAATATAAATATAATATAA-TAAAAATAATTAA
1 AATATAA-TATATAATAAAAATATAATATAACTAAAAAT-A-TAA
833932 AATATAA-ATATAA-AAAAATATAAATATAACTTAAAAATATAA
1 AATATAATATATAATAAAAATAT-AATATAAC-TAAAAATATAA
833974 AATAT
1 AATAT
833979 CGAAATTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
41 7 0.16
42 21 0.49
43 1 0.02
44 14 0.33
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (42 bp):
AATATAATATATAATAAAAATATAATATAACTAAAAATATAA
Found at i:834339 original size:16 final size:16
Alignment explanation
Indices: 834329--834361 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
834319 TTATTTTTAT
834329 ATTTATATATTATATA
1 ATTTATATATTATATA
834345 ATTTATAT-TATATATA
1 ATTTATATAT-TATATA
834361 A
1 A
834362 AATAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTATATATTATATA
Found at i:834349 original size:22 final size:23
Alignment explanation
Indices: 834324--834374 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
834314 TGATATTATT
* *
834324 TTTATATTTATATATTATAT-AA
1 TTTATATTTATATATAAAATAAA
834346 TTTATA-TTATATATAAAATAAA
1 TTTATATTTATATATAAAATAAA
834368 TTTATAT
1 TTTATAT
834375 AAAATTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATATTTATATATAAAATAAA
Found at i:834433 original size:15 final size:17
Alignment explanation
Indices: 834413--834444 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
834403 TATTAAATTA
834413 TTTATAT-TTTA-AAAT
1 TTTATATATTTATAAAT
834428 TTTATATATTTATAAAT
1 TTTATATATTTATAAAT
834445 ATAATTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATATTTATAAAT
Found at i:834439 original size:16 final size:17
Alignment explanation
Indices: 834400--834446 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
834390 ATATTAAAAA
*
834400 ATATA-TTAAATTATTT
1 ATATATTTAAAATATTT
834416 ATAT-TTTAAAAT-TTT
1 ATATATTTAAAATATTT
834431 ATATATTTATAAATAT
1 ATATATTTA-AAATAT
834447 AATTAGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 7 0.27
16 14 0.54
17 4 0.15
18 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTTAAAATATTT
Found at i:834499 original size:16 final size:16
Alignment explanation
Indices: 834478--834510 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
834468 AAATTTATTT
834478 TTTAAATTAAAT-TAAA
1 TTTAAA-TAAATATAAA
834494 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
834510 T
1 T
834511 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:835596 original size:14 final size:14
Alignment explanation
Indices: 835562--835597 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
835552 ATGATTTAGA
*
835562 ATGGAAAGGAATAG
1 ATGGAATGGAATAG
835576 ATGGAATGGAATAG
1 ATGGAATGGAATAG
835590 ATGGAATG
1 ATGGAATG
835598 AAAATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.19
Consensus pattern (14 bp):
ATGGAATGGAATAG
Found at i:836518 original size:442 final size:442
Alignment explanation
Indices: 835694--836580 Score: 1738
Period size: 442 Copynumber: 2.0 Consensus size: 442
835684 AAGCATAATA
835694 ACATTTGGTTATTAAAAGTTGTATTTTTTTCATCCAAAAAATGCATTATTTTATCTAACCAATTC
1 ACATTTGGTTATTAAAAGTTGTATTTTTTTCATCCAAAAAATGCATTATTTTATCTAACCAATTC
835759 ATTATTTCCTTCAAATATACCTTTTCGAAAGATGGTGTCTATACACCATTTCATCCAAGGTGATT
66 ATTATTTCCTTCAAATATACCTTTTCGAAAGATGGTGTCTATACACCATTTCATCCAAGGTGATT
835824 ATTGGATGATTATAAATTTGTAATCTACCACTTGGTAAAATTACAACAATCCCCCACTAGATTAC
131 ATTGGATGATTATAAATTTGTAATCTACCACTTGGTAAAATTACAACAATCCCCCACTAGATTAC
*
835889 AAATTCCAAAATATAATAAAGTATATAGTTATGTATAAAGGAAATGTATCATTAGATTTAAACCT
196 AAATTCCAAAATATAATAAAGTATATAGTTATGCATAAAGGAAATGTATCATTAGATTTAAACCT
835954 TCCATTAGTGTAAACGTATCAAAATTCCAACAAAGTAATTGGTGGCTAGTCGCTTAAACCATTAC
261 TCCATTAGTGTAAACGTATCAAAATTCCAACAAAGTAATTGGTGGCTAGTCGCTTAAACCATTAC
836019 TCTTGAGTTAGAATCGGATAAATCACACATATAACTATATTTAAAGAAAGAATAAGAATTTTTAT
326 TCTTGAGTTAGAATCGGATAAATCACACATATAACTATATTTAAAGAAAGAATAAGAATTTTTAT
* *
836084 ATTGCTTTAGCACTATTATGGCCATGTGCTCATCCTGGTTTCATGAATATTT
391 ATTACTTTAGCACTATTATGGCCATGTGCTCATCCTGATTTCATGAATATTT
836136 ACATTTGGTTATTAAAAGTTGTATTTTTTTCATCCAAAAAATGCATTATTTTATCTAACCAATTC
1 ACATTTGGTTATTAAAAGTTGTATTTTTTTCATCCAAAAAATGCATTATTTTATCTAACCAATTC
836201 ATTATTTCCTTCAAATATACCTTTTCGAAAGATGGTGTCTATACACCATTTCATCCAAGGTGATT
66 ATTATTTCCTTCAAATATACCTTTTCGAAAGATGGTGTCTATACACCATTTCATCCAAGGTGATT
*
836266 ATTGGATGATTATAAATTTGTAATCTACCACTTGGTAAAATTACAACAATTCCCCACTAGATTAC
131 ATTGGATGATTATAAATTTGTAATCTACCACTTGGTAAAATTACAACAATCCCCCACTAGATTAC
836331 AAATTCCAAAATATAATAAAGTATATAGTTATGCATAAAGGAAATGTATCATTAGATTTAAACCT
196 AAATTCCAAAATATAATAAAGTATATAGTTATGCATAAAGGAAATGTATCATTAGATTTAAACCT
836396 TCCATTAGTGTAAACGTATCAAAATTCCAACAAAGTAATTGGTGGCTAGTCGCTTAAACCATTAC
261 TCCATTAGTGTAAACGTATCAAAATTCCAACAAAGTAATTGGTGGCTAGTCGCTTAAACCATTAC
836461 TCTTGAGTTAGAATCGGATAAATCACACATATAACTATATTTAAAGAAAGAATAAGAATTTTTAT
326 TCTTGAGTTAGAATCGGATAAATCACACATATAACTATATTTAAAGAAAGAATAAGAATTTTTAT
836526 ATTACTTTAGCACTATTATGGCCATGTGCTCATCCTGATTTCATGAATATTT
391 ATTACTTTAGCACTATTATGGCCATGTGCTCATCCTGATTTCATGAATATTT
836578 ACA
1 ACA
836581 AAAGTAAAAC
Statistics
Matches: 441, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
442 441 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (442 bp):
ACATTTGGTTATTAAAAGTTGTATTTTTTTCATCCAAAAAATGCATTATTTTATCTAACCAATTC
ATTATTTCCTTCAAATATACCTTTTCGAAAGATGGTGTCTATACACCATTTCATCCAAGGTGATT
ATTGGATGATTATAAATTTGTAATCTACCACTTGGTAAAATTACAACAATCCCCCACTAGATTAC
AAATTCCAAAATATAATAAAGTATATAGTTATGCATAAAGGAAATGTATCATTAGATTTAAACCT
TCCATTAGTGTAAACGTATCAAAATTCCAACAAAGTAATTGGTGGCTAGTCGCTTAAACCATTAC
TCTTGAGTTAGAATCGGATAAATCACACATATAACTATATTTAAAGAAAGAATAAGAATTTTTAT
ATTACTTTAGCACTATTATGGCCATGTGCTCATCCTGATTTCATGAATATTT
Found at i:839927 original size:12 final size:12
Alignment explanation
Indices: 839903--839936 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
839893 TACACCATTA
839903 AAAAAATTAAAAT
1 AAAAAA-TAAAAT
*
839916 ATAAAATAAAAT
1 AAAAAATAAAAT
839928 AAAAAATAA
1 AAAAAATAA
839937 CATGAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:842562 original size:24 final size:26
Alignment explanation
Indices: 842522--842569 Score: 57
Period size: 24 Copynumber: 1.9 Consensus size: 26
842512 GATTCATTTT
*
842522 ATAATTATATAATTTATGTTATTTTT
1 ATAATTATATAATTTATGTAATTTTT
842548 AT-ATT-TAT-ATGTTATGTAATTT
1 ATAATTATATAAT-TTATGTAATTT
842570 ATATCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
23 2 0.10
24 13 0.65
25 3 0.15
26 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATAATTATATAATTTATGTAATTTTT
Found at i:843625 original size:24 final size:25
Alignment explanation
Indices: 843598--843644 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
843588 CAATTACCAC
*
843598 AGTCAC-CATAACCTTTATCTCCTT
1 AGTCACTCACAACCTTTATCTCCTT
*
843622 AGTCACTTACAACCTTTATCTCC
1 AGTCACTCACAACCTTTATCTCC
843645 ACTAATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (25 bp):
AGTCACTCACAACCTTTATCTCCTT
Found at i:843901 original size:12 final size:12
Alignment explanation
Indices: 843879--843910 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
843869 ATATCACAAA
843879 AAAATTAAAATAT
1 AAAA-TAAAATAT
843892 AAAATAAAATAT
1 AAAATAAAATAT
843904 AAAATAA
1 AAAATAA
843911 TATGAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:846138 original size:10 final size:10
Alignment explanation
Indices: 846123--846153 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
846113 AAAATATTAA
846123 ATTTTAATAT
1 ATTTTAATAT
846133 ATTTTAATAT
1 ATTTTAATAT
*
846143 ATTATAATAT
1 ATTTTAATAT
846153 A
1 A
846154 AATATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:849593 original size:34 final size:34
Alignment explanation
Indices: 849533--849599 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
849523 ATGTGTTACT
* * *
849533 TTTTAAATTTTTTTATTTTATATTTAAATTAAAA
1 TTTTAAATTTTATTAATTAATATTTAAATTAAAA
849567 TTTTAAATTATTATTAATTAAT-TTTAAATTAAA
1 TTTTAAATT-TTATTAATTAATATTTAAATTAAA
849600 TGTCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 20 0.69
35 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTTTAAATTTTATTAATTAATATTTAAATTAAAA
Found at i:849743 original size:16 final size:17
Alignment explanation
Indices: 849722--849754 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
849712 AAATATTAAT
849722 ATTTATGATT-TTTTTA
1 ATTTATGATTATTTTTA
*
849738 ATTTATTATTATTTTTA
1 ATTTATGATTATTTTTA
849755 TTGAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATGATTATTTTTA
Found at i:850318 original size:9 final size:10
Alignment explanation
Indices: 850304--850338 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 10
850294 ATATAACATA
850304 AAAATA-ATT
1 AAAATATATT
850313 AAAATATATT
1 AAAATATATT
850323 ATAAATATATT
1 A-AAATATATT
850334 AAAAT
1 AAAAT
850339 TTACATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 6 0.25
10 8 0.33
11 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATATATT
Found at i:850320 original size:22 final size:22
Alignment explanation
Indices: 850283--850356 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
850273 AATTAAATTT
*
850283 AATAATTTTAAATATAACATAAA
1 AATAA-TTAAAATATAACATAAA
**
850306 AATAATTAAAATATATTATAAA
1 AATAATTAAAATATAACATAAA
* *
850328 TAT-ATTAAAAT-TTACATAAA
1 AATAATTAAAATATAACATAAA
*
850348 TATATATTA
1 AATA-ATTA
850357 TATATAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 9 0.21
21 8 0.19
22 20 0.48
23 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAATTAAAATATAACATAAA
Found at i:850328 original size:11 final size:10
Alignment explanation
Indices: 850314--850379 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
850304 AAAATAATTA
850314 AAATATATTAT
1 AAATATA-TAT
850325 AAATATAT-T
1 AAATATATAT
* *
850334 AAAATTTACAT
1 -AAATATATAT
850345 AAATATATAT
1 AAATATATAT
850355 ---TATATAT
1 AAATATATAT
850362 AAATATGATAT
1 AAATAT-ATAT
850373 AAATATA
1 AAATATA
850380 ATTACGAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 7 0.16
9 1 0.02
10 19 0.42
11 18 0.40
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (10 bp):
AAATATATAT
Found at i:850346 original size:20 final size:20
Alignment explanation
Indices: 850292--850352 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
850282 TAATAATTTT
*
850292 AAATATAACATAAAAATAATTA
1 AAATAT-ACATAAATAT-ATTA
*
850314 AAATATATTATAAATATATTA
1 AAATATA-CATAAATATATTA
*
850335 AAATTTACATAAATATAT
1 AAATATACATAAATATAT
850353 ATTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.29
21 11 0.32
22 13 0.38
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATACATAAATATATTA
Found at i:850378 original size:17 final size:17
Alignment explanation
Indices: 850343--850380 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
850333 TAAAATTTAC
*
850343 ATAAATATATATTATAT
1 ATAAATATATATTAAAT
850360 ATAAATATGATA-TAAAT
1 ATAAATAT-ATATTAAAT
850377 ATAA
1 ATAA
850381 TTACGAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAAATATATATTAAAT
Found at i:850605 original size:18 final size:18
Alignment explanation
Indices: 850578--850621 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
850568 GTATTTAATA
850578 TTTATATTTAAAGATATT
1 TTTATATTTAAAGATATT
* * *
850596 TTTATTTTTATATATATT
1 TTTATATTTAAAGATATT
850614 TATTATAT
1 T-TTATAT
850622 ATTTTATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTATATTTAAAGATATT
Found at i:850640 original size:21 final size:22
Alignment explanation
Indices: 850601--850683 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 22
850591 ATATTTTTAT
850601 TTTTATATATATT-TATTATATA
1 TTTTATA-ATATTATATTATATA
850623 TTTTATAAT-TTATATTATATAAA
1 TTTTATAATATTATATTATAT--A
850646 TTTTA-AA-A-TAT-TTATATA
1 TTTTATAATATTATATTATATA
*
850664 TTATTATAATATCATATTAT
1 TT-TTATAATATTATATTAT
850684 TTTATATCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
18 3 0.06
19 3 0.06
20 10 0.20
21 14 0.27
22 11 0.22
23 10 0.20
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATATTATATTATATA
Found at i:851291 original size:26 final size:25
Alignment explanation
Indices: 851262--851337 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 25
851252 TCTATATAAA
851262 ATAAATTAT-TAATGAGTTTAAATTAT
1 ATAAATTATATAAT-A-TTTAAATTAT
*
851288 ATAAATATATAATATTTATTTAAATTAT
1 ATAAAT-TAT-ATA-ATATTTAAATTAT
851316 ATAAA-TATATAATATTTTAAAT
1 ATAAATTATATAATA-TTTAAAT
851338 ATGATTATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
24 2 0.05
25 10 0.23
26 9 0.21
27 3 0.07
28 15 0.35
29 3 0.07
30 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
ATAAATTATATAATATTTAAATTAT
Found at i:851298 original size:8 final size:9
Alignment explanation
Indices: 851280--851327 Score: 55
Period size: 8 Copynumber: 5.3 Consensus size: 9
851270 TTAATGAGTT
851280 TAAATTATA
1 TAAATTATA
851289 TAAA-TATA
1 TAAATTATA
*
851297 TAATATTTATT
1 TAA-A-TTATA
851308 TAAATTATA
1 TAAATTATA
851317 TAAA-TATA
1 TAAATTATA
851325 TAA
1 TAA
851328 TATTTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 14 0.41
9 13 0.38
10 1 0.03
11 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAAATTATA
Found at i:851315 original size:28 final size:28
Alignment explanation
Indices: 851278--851332 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
851268 TATTAATGAG
851278 TTTAAATTATATAAATATATAATATTTA
1 TTTAAATTATATAAATATATAATATTTA
851306 TTTAAATTATATAAATATATAATATTT
1 TTTAAATTATATAAATATATAATATTT
851333 TAAATATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAAATTATATAAATATATAATATTTA
Found at i:851346 original size:30 final size:28
Alignment explanation
Indices: 851280--851338 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
851270 TTAATGAGTT
**
851280 TAAATTATATAAATATATAATATTTATT
1 TAAATTATATAAATATATAATATTTAAA
851308 TAAATTATATAAATATATAATATTTTAAA
1 TAAATTATATAAATATATAATA-TTTAAA
851337 TA
1 TA
851339 TGATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATTATATAAATATATAATATTTAAA
Found at i:851488 original size:19 final size:18
Alignment explanation
Indices: 851466--851510 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
851456 ATATAAATAT
851466 AATATGATAAAATAATTAA
1 AATAT-ATAAAATAATTAA
* *
851485 AATATA-AATATAATTTA
1 AATATATAAAATAATTAA
851502 AATATATAA
1 AATATATAA
851511 TTATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 15 0.65
18 3 0.13
19 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATATATAAAATAATTAA
Found at i:851524 original size:30 final size:31
Alignment explanation
Indices: 851442--851525 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
851432 TTTTAAACAT
851442 AATATAATTACATGATATAAATATAATATGATA
1 AATATAATTA-AT-ATATAAATATAATATGATA
* *
851475 AA-ATAATTAAAATATAAATATAAT-TTA-A
1 AATATAATTAATATATAAATATAATATGATA
851503 ATATATAATT-ATATATAAA-ATAA
1 A-ATATAATTAATATATAAATATAA
851526 ATCATTAGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 6 0.13
29 11 0.24
30 19 0.41
31 1 0.02
32 7 0.15
33 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (31 bp):
AATATAATTAATATATAAATATAATATGATA
Found at i:851883 original size:21 final size:20
Alignment explanation
Indices: 851857--851902 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
851847 TTTTTATCAT
851857 ATATAAAATAAACATATAAAA
1 ATATAAAATAAACAT-TAAAA
* **
851878 TTATAACGTAAACATTAAAA
1 ATATAAAATAAACATTAAAA
851898 ATATA
1 ATATA
851903 TTAAATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (20 bp):
ATATAAAATAAACATTAAAA
Found at i:851916 original size:34 final size:35
Alignment explanation
Indices: 851878--851947 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 35
851868 ACATATAAAA
*
851878 TTATAACGTAAACA-TTAAAAATA-TATTAAATTAT
1 TTATAACGTAAA-ATTTAAAAAAATTATTAAATTAT
***
851912 TTATATTTTAAAATTTAAAAAAATTATTAAATTAT
1 TTATAACGTAAAATTTAAAAAAATTATTAAATTAT
851947 T
1 T
851948 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
33 1 0.03
34 17 0.57
35 12 0.40
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (35 bp):
TTATAACGTAAAATTTAAAAAAATTATTAAATTAT
Found at i:851935 original size:27 final size:27
Alignment explanation
Indices: 851905--851957 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
851895 AAAATATATT
* *
851905 AAATTATTTATATT-TTAAAATTTAAAA
1 AAATTA-TTAAATTATTAAAAATTAAAA
851932 AAATTATTAAATTATTAAAAATTAAA
1 AAATTATTAAATTATTAAAAATTAAA
851958 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATTATTAAATTATTAAAAATTAAAA
Found at i:851990 original size:21 final size:19
Alignment explanation
Indices: 851953--851989 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
851943 TTATTAAAAA
851953 TTAAATTAAAAAATATATT
1 TTAAATTAAAAAATATATT
851972 TTAAATATAAAAAA-ATAT
1 TTAAAT-TAAAAAATATAT
851990 AAACAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAAAATATATT
Found at i:854372 original size:8 final size:9
Alignment explanation
Indices: 854353--854386 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
854343 AATATTTAAA
854353 TTTTAAATT
1 TTTTAAATT
854362 TTTTAAATT
1 TTTTAAATT
854371 TTTTAAATT
1 TTTTAAATT
854380 TTTTAAA
1 TTTTAAA
854387 AAAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTAAATT
Found at i:855092 original size:22 final size:21
Alignment explanation
Indices: 855060--855111 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
855050 TAAATTTTAA
* *
855060 ATTTTAATATTCATAATAATTT
1 ATTTTATTATTAATAAT-ATTT
*
855082 ATTTTATTATTAATTATATTT
1 ATTTTATTATTAATAATATTT
855103 -TTTTATTAT
1 ATTTTATTAT
855112 AAATTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 4 0.15
22 14 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTATTATTAATAATATTT
Found at i:855101 original size:17 final size:16
Alignment explanation
Indices: 855076--855110 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
855066 ATATTCATAA
855076 TAATTTATTTTATTAT
1 TAATTTATTTTATTAT
*
855092 TAATTATATTTTTTTAT
1 TAATT-TATTTTATTAT
855109 TA
1 TA
855111 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTATTTTATTAT
Found at i:855108 original size:20 final size:21
Alignment explanation
Indices: 855078--855116 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
855068 ATTCATAATA
*
855078 ATTTATTTTATTATTAATTAT
1 ATTTATTTTATTATAAATTAT
855099 ATTT-TTTTATTATAAATT
1 ATTTATTTTATTATAAATT
855117 TTTTGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTATTTTATTATAAATTAT
Found at i:855185 original size:23 final size:23
Alignment explanation
Indices: 855157--855205 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
855147 AATTAATTTT
855157 TTTATTTTGTTAATTA-AAGTTAA
1 TTTATTTT-TTAATTAGAAGTTAA
* *
855180 TTTATTTTTTTATTAGAAGTTCA
1 TTTATTTTTTAATTAGAAGTTAA
855203 TTT
1 TTT
855206 GGATGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (23 bp):
TTTATTTTTTAATTAGAAGTTAA
Found at i:855425 original size:2 final size:2
Alignment explanation
Indices: 855418--855449 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
855408 ACACCCACAA
855418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
855450 CACTTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:855564 original size:23 final size:23
Alignment explanation
Indices: 855517--855585 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
855507 AAATAAGTTT
* * *
855517 AATAATTTTAGATATATTATAAAA
1 AATAATTATA-ATATAATATTAAA
855541 AATAATTATAATATAATATTAAA
1 AATAATTATAATATAATATTAAA
855564 AATTATATTATAA-A-AATATTAA
1 AA-TA-ATTATAATATAATATTAA
855586 TATATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 21 0.52
24 12 0.30
25 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
AATAATTATAATATAATATTAAA
Found at i:855593 original size:31 final size:31
Alignment explanation
Indices: 855556--855650 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 31
855546 TTATAATATA
855556 ATATTAAAAATTATATTATAAAAATATTAAT
1 ATATTAAAAATTATATTATAAAAATATTAAT
*
855587 ATATT-AAAATT-TA-TATAAATATA-TAAT
1 ATATTAAAAATTATATTATAAAAATATTAAT
* * * *
855614 ATTTTAAATATAATTATAATAAAAATATATAAAT
1 ATATTAAAAATTA-TATTATAAAAATAT-T-AAT
855648 ATA
1 ATA
855651 ACATAAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
27 8 0.16
28 13 0.26
29 2 0.04
30 8 0.16
31 13 0.26
33 1 0.02
34 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATATTAAAAATTATATTATAAAAATATTAAT
Found at i:855595 original size:16 final size:15
Alignment explanation
Indices: 855556--855641 Score: 56
Period size: 16 Copynumber: 5.8 Consensus size: 15
855546 TTATAATATA
855556 ATATTAAAA-ATTAT
1 ATATTAAAATATTAT
*
855570 ATTATAAAAATATTAAT
1 A-TATTAAAATATT-AT
855587 ATATTAAAAT-TTAT
1 ATATTAAAATATTAT
* *
855601 ATA--AATATATAAT
1 ATATTAAAATATTAT
*
855614 ATTTTAAATATAATTAT
1 ATATTAAA-AT-ATTAT
*
855631 A-ATAAAAATAT
1 ATATTAAAATAT
855642 ATAAATATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 4 0.07
13 5 0.09
14 8 0.15
15 13 0.24
16 17 0.31
17 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAAAATATTAT
Found at i:855607 original size:20 final size:19
Alignment explanation
Indices: 855579--855650 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
855569 TATTATAAAA
*
855579 ATATTAATATATTAAAATTT
1 ATATAAATATA-TAAAATTT
*
855599 ATATAAATATATAATATTTT
1 ATATAAATATATAA-AATTT
* *
855619 AAATATAATTATAATAAAA-AT
1 --ATATAAATAT-ATAAAATTT
855640 ATATAAATATA
1 ATATAAATATA
855651 ACATAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
20 14 0.33
21 1 0.02
22 10 0.24
23 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAATATATAAAATTT
Found at i:855607 original size:26 final size:27
Alignment explanation
Indices: 855571--855621 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
855561 AAAAATTATA
855571 TTATAAAAATAT-TAATATATTAAAAT
1 TTATAAAAATATATAATATATTAAAAT
* *
855597 TTATATAAATATATAATATTTTAAA
1 TTATAAAAATATATAATATATTAAA
855622 TATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTATAAAAATATATAATATATTAAAAT
Found at i:855645 original size:19 final size:19
Alignment explanation
Indices: 855621--855669 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
855611 AATATTTTAA
*
855621 ATATAATTATAATAAAAAT
1 ATATAATTATAACAAAAAT
* *
855640 ATATAAATATAACATAAAT
1 ATATAATTATAACAAAAAT
*
855659 ATATATTTATA
1 ATATAATTATA
855670 TGTCTCTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAATTATAACAAAAAT
Found at i:856803 original size:18 final size:19
Alignment explanation
Indices: 856770--856805 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
856760 TTATTTATTT
*
856770 AATTTTTATAATTAATATA
1 AATTGTTATAATTAATATA
856789 AATTGTTAT-ATTAATAT
1 AATTGTTATAATTAATAT
856806 TAAAAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTGTTATAATTAATATA
Found at i:856809 original size:19 final size:20
Alignment explanation
Indices: 856765--856809 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
856755 ATTTTTTATT
* *
856765 TATTTAATTTTTATAATTAA
1 TATTAAATTGTTATAATTAA
856785 TA-TAAATTGTTAT-ATTAA
1 TATTAAATTGTTATAATTAA
856803 TATTAAA
1 TATTAAA
856810 AATACTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 13 0.59
20 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTAAATTGTTATAATTAA
Found at i:856842 original size:14 final size:14
Alignment explanation
Indices: 856823--856849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
856813 ACTTAATAAT
856823 AATTTCTATTTTTA
1 AATTTCTATTTTTA
856837 AATTTCTATTTTT
1 AATTTCTATTTTT
856850 TCCTCTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTCTATTTTTA
Found at i:857194 original size:14 final size:14
Alignment explanation
Indices: 857171--857204 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
857161 GATTAATCAG
*
857171 TTTAATTAAAAATT
1 TTTAAATAAAAATT
*
857185 TTTAAATAAAATTT
1 TTTAAATAAAAATT
857199 TTTAAA
1 TTTAAA
857205 ATTTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATAAAAATT
Found at i:857947 original size:17 final size:17
Alignment explanation
Indices: 857919--857978 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
857909 TAACAGGTCC
857919 ATTTTAATTTTTAAATAA
1 ATTTT-ATTTTTAAATAA
* *
857937 ATTTTATTTTT-ATTTA
1 ATTTTATTTTTAAATAA
857953 A-TTT-TTTTTAAATTAA
1 ATTTTATTTTTAAA-TAA
857969 TATTTTATTT
1 -ATTTTATTT
857979 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 6 0.18
17 7 0.21
18 8 0.24
19 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATTTTTAAATAA
Found at i:857979 original size:17 final size:17
Alignment explanation
Indices: 857928--857981 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
857918 CATTTTAATT
857928 TTTAAA-TAA-ATTTTA
1 TTTAAATTAATATTTTA
* *
857943 TTTTTATTTAAT-TTTT-
1 -TTTAAATTAATATTTTA
857959 TTTAAATTAATATTTTA
1 TTTAAATTAATATTTTA
857976 TTTAAA
1 TTTAAA
857982 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.30
16 8 0.27
17 13 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAAATTAATATTTTA
Found at i:858305 original size:15 final size:15
Alignment explanation
Indices: 858285--858314 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
858275 AATAAATATT
*
858285 AATAAATAGTATTTA
1 AATAAATACTATTTA
858300 AATAAATACTATTTA
1 AATAAATACTATTTA
858315 TAAATCGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
AATAAATACTATTTA
Found at i:860182 original size:3 final size:3
Alignment explanation
Indices: 860176--860211 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
860166 AATCACATTG
860176 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
860212 GCTAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:860606 original size:17 final size:18
Alignment explanation
Indices: 860584--860627 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
860574 TTCATTTATT
860584 TTAATTTTAAT-AATAAA
1 TTAATTTTAATAAATAAA
860601 TTAATTTT-ATAAATAAA
1 TTAATTTTAATAAATAAA
*
860618 ATAATTTTAA
1 TTAATTTTAA
860628 GTATTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTTTAATAAATAAA
Found at i:861729 original size:16 final size:16
Alignment explanation
Indices: 861704--861735 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
861694 CTTTATGCAC
861704 ATTTAAATAAGTCTAG
1 ATTTAAATAAGTCTAG
*
861720 ATTTAGATAAGTCTAG
1 ATTTAAATAAGTCTAG
861736 GTAGTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
ATTTAAATAAGTCTAG
Found at i:863180 original size:2 final size:2
Alignment explanation
Indices: 863173--863206 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
863163 AGTGTTACCA
863173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
863207 GTAAGCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:863489 original size:22 final size:23
Alignment explanation
Indices: 863446--863494 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
863436 AAGAACCTTC
* *
863446 AATAATTTTAAAAATTACA-TTT
1 AATAAATTTAAAAATTAAATTTT
**
863468 AATAAATTTAAATTTTAAATTTT
1 AATAAATTTAAAAATTAAATTTT
863491 AATA
1 AATA
863495 TTAATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAAATTTAAAAATTAAATTTT
Found at i:864208 original size:21 final size:21
Alignment explanation
Indices: 864148--864214 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
864138 TATTTTTATT
*
864148 TAATATATTAA-AAATCATAAA
1 TAATATATTAATTAAT-ATAAA
* *
864169 CAA-A-ATTAATTACTATAAA
1 TAATATATTAATTAATATAAA
* *
864188 TGATATATTAATTAATTTAAA
1 TAATATATTAATTAATATAAA
864209 TAATAT
1 TAATAT
864215 TCGAACTTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 11 0.31
20 4 0.11
21 20 0.57
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (21 bp):
TAATATATTAATTAATATAAA
Found at i:864670 original size:2 final size:2
Alignment explanation
Indices: 864665--864690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
864655 ATCAATTAGC
864665 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
864691 TTGATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:865096 original size:25 final size:24
Alignment explanation
Indices: 865057--865111 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
865047 GTTAAATTGA
* *
865057 TTTTAAAATTTTTTATTATTTTAAC
1 TTTTAAAAATATTTATT-TTTTAAC
*
865082 TTTTAAAAATATTTATTTTTTGAC
1 TTTTAAAAATATTTATTTTTTAAC
*
865106 TATTAA
1 TTTTAA
865112 TATTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTAAAAATATTTATTTTTTAAC
Found at i:865680 original size:32 final size:31
Alignment explanation
Indices: 865614--865675 Score: 79
Period size: 34 Copynumber: 1.9 Consensus size: 31
865604 TAAAATATTT
*
865614 TTATATAAATTTTAATAATTAATATTTTATG
1 TTATATAAATTTAAATAATTAATATTTTATG
*
865645 TTATATAAAATTTAACATATATTTATATTTT
1 TTATAT-AAATTTAA-ATA-ATTAATATTTT
865676 GTTATGTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 7 0.27
33 3 0.12
34 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TTATATAAATTTAAATAATTAATATTTTATG
Found at i:866101 original size:15 final size:18
Alignment explanation
Indices: 866066--866102 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
866056 CTCAAAAGAC
866066 TATTAATTTTAATATAAA
1 TATTAATTTTAATATAAA
866084 TATT-ATTTTAA-A-AAA
1 TATTAATTTTAATATAAA
866099 TATT
1 TATT
866103 TTAATAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 7 0.37
18 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAATTTTAATATAAA
Found at i:866470 original size:20 final size:21
Alignment explanation
Indices: 866431--866470 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
866421 AAATATTAAA
* *
866431 ATTTATAACAATATATAATAT
1 ATTTATAACAAAAAATAATAT
866452 ATTTATAA-AAAAAATAATA
1 ATTTATAACAAAAAATAATA
866471 CAAAACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTTATAACAAAAAATAATAT
Found at i:868070 original size:29 final size:28
Alignment explanation
Indices: 868028--868083 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
868018 TTTCTCTTTA
868028 TTTTTTCTTATTATTATTTT-AATTTAAG
1 TTTTTTCTTATTATT-TTTTGAATTTAAG
*
868056 TTTTTTCCTTTTTATTTTTTGAATTTAA
1 TTTTTT-CTTATTATTTTTTGAATTTAA
868084 CCGTTTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (28 bp):
TTTTTTCTTATTATTTTTTGAATTTAAG
Found at i:870889 original size:21 final size:21
Alignment explanation
Indices: 870865--870904 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
870855 CAAAACAAGA
* *
870865 TAATATATAATTAAATAAATT
1 TAATATAAAATAAAATAAATT
870886 TAATATAAAATAAAATAAA
1 TAATATAAAATAAAATAAA
870905 ATATAAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATATAAAATAAAATAAATT
Found at i:871981 original size:17 final size:18
Alignment explanation
Indices: 871948--871980 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
871938 AAAAACTGTT
871948 ATCTGTTCTTTTCTTTTA
1 ATCTGTTCTTTTCTTTTA
871966 ATCT-TTCTTTT-TTTT
1 ATCTGTTCTTTTCTTTT
871981 TTTTTAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (18 bp):
ATCTGTTCTTTTCTTTTA
Found at i:880446 original size:7 final size:7
Alignment explanation
Indices: 880434--880459 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
880424 TTATTATAAT
880434 AATTTTA
1 AATTTTA
880441 AATTTTA
1 AATTTTA
880448 AATTTTA
1 AATTTTA
880455 AATTT
1 AATTT
880460 ATTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:880487 original size:17 final size:17
Alignment explanation
Indices: 880456--880488 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
880446 TAAATTTTAA
880456 ATTTATTAAATATTATT
1 ATTTATTAAATATTATT
880473 ATTT-TTAAATAATTAT
1 ATTTATTAAAT-ATTAT
880489 GTAAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTATTAAATATTATT
Found at i:882298 original size:3 final size:3
Alignment explanation
Indices: 882292--882326 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
882282 TGTATTTATT
882292 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
882327 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:882331 original size:3 final size:3
Alignment explanation
Indices: 882325--882355 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
882315 AATAATAATA
882325 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
882356 CCTATCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:882541 original size:13 final size:14
Alignment explanation
Indices: 882513--882604 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
882503 AAAGAAAAAA
882513 TATATATTTATATT
1 TATATATTTATATT
*
882527 TATAT-TTTTTATT
1 TATATATTTATATT
* *
882540 TATAAAATTATATT
1 TATATATTTATATT
* * **
882554 TTTGTATAAATATTT
1 TATATATTTATA-TT
* *
882569 TATATATTAATAAT
1 TATATATTTATATT
*
882583 T-TAT-TTTATTTTT
1 TATATATTTA-TATT
882596 TATATATTT
1 TATATATTT
882605 TTATACGTAC
Statistics
Matches: 56, Mismatches: 17, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
12 3 0.05
13 17 0.30
14 22 0.39
15 14 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
TATATATTTATATT
Found at i:882541 original size:19 final size:19
Alignment explanation
Indices: 882517--882609 Score: 55
Period size: 21 Copynumber: 4.7 Consensus size: 19
882507 AAAAAATATA
882517 TATTTATATTTATATTTTT
1 TATTTATATTTATATTTTT
*
882536 TATTTATAAAATTATATTTTT
1 TATTTAT--ATTTATATTTTT
** **
882557 GTATAAATATTTTATATATTAA
1 -TATTTATA-TTTATAT-TTTT
*
882579 TAATT-TATTT-TATTTTT
1 TATTTATATTTATATTTTT
* *
882596 TATATATTTTTATA
1 TATTTATATTTATA
882610 CGTACTTATA
Statistics
Matches: 53, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
17 5 0.09
18 7 0.13
19 12 0.23
20 3 0.06
21 19 0.36
22 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (19 bp):
TATTTATATTTATATTTTT
Done.