Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 19
Found at i:160343 original size:15 final size:15
Alignment explanation
Indices: 160323--160371 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
160313 ATTTTAAAAA
160323 ATTAAAAATATTTAT
1 ATTAAAAATATTTAT
160338 ATTAAAAAAATATTTAT
1 ATT--AAAAATATTTAT
* *
160355 -TTTAAATTATTTAT
1 ATTAAAAATATTTAT
160369 ATT
1 ATT
160372 TAAATCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 10 0.34
15 5 0.17
16 2 0.07
17 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAAAAATATTTAT
Found at i:160346 original size:17 final size:17
Alignment explanation
Indices: 160326--160360 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
160316 TTAAAAAATT
160326 AAAAATATTTATATTAA
1 AAAAATATTTATATTAA
*
160343 AAAAATATTTATTTTAA
1 AAAAATATTTATATTAA
160360 A
1 A
160361 TTATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATATTTATATTAA
Found at i:160367 original size:14 final size:15
Alignment explanation
Indices: 160348--160376 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
160338 ATTAAAAAAA
160348 TATTTAT-TTTAAAT
1 TATTTATATTTAAAT
160362 TATTTATATTTAAAT
1 TATTTATATTTAAAT
160377 CTGAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTATATTTAAAT
Found at i:164397 original size:4 final size:4
Alignment explanation
Indices: 164388--164414 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
164378 TTGAAGAACC
164388 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
164415 AACCAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:169780 original size:12 final size:13
Alignment explanation
Indices: 169757--169787 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
169747 ATTTTCATGC
169757 TTTCTCTTTTTTT
1 TTTCTCTTTTTTT
169770 TTTCT-TTTTTTT
1 TTTCTCTTTTTTT
169782 TTTCTC
1 TTTCTC
169788 GCAATTGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:170473 original size:19 final size:19
Alignment explanation
Indices: 170451--170491 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
170441 ATAATAATAA
*
170451 TATTAAAATATATATTTTT
1 TATTAAAATATATATATTT
* *
170470 TATTAATATTTATATATTT
1 TATTAAAATATATATATTT
170489 TAT
1 TAT
170492 AATTAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTAAAATATATATATTT
Found at i:170483 original size:21 final size:21
Alignment explanation
Indices: 170459--170502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
170449 AATATTAAAA
*
170459 TATATATTTT-TTATTAATATT
1 TATATATTTTATAATTAA-ATT
170480 TATATATTTTATAATTAAATT
1 TATATATTTTATAATTAAATT
170501 TA
1 TA
170503 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATATTTTATAATTAAATT
Found at i:170528 original size:29 final size:30
Alignment explanation
Indices: 170481--170562 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
170471 ATTAATATTT
*
170481 ATATATTTTATAATT-AAATTTAA-ATAAAA
1 ATAT-TTTTATTATTAAAATTTAATATAAAA
* *
170510 ATATTTTTATTATTAAAATAATAATTTAAAA
1 ATATTTTTATTATTAAAAT-TTAATATAAAA
*
170541 ATAATTATTATTATTAAAATTT
1 AT-ATTTTTATTATTAAAATTT
170563 TGTTTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 9 0.20
29 8 0.18
30 3 0.07
31 8 0.18
32 16 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATTTTTATTATTAAAATTTAATATAAAA
Found at i:170961 original size:32 final size:29
Alignment explanation
Indices: 170900--170961 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
170890 TTATATATAA
**
170900 ATTTAAATTATATTTAAAATAATTTAAAT
1 ATTTAAATTATATTTAAAATAATAAAAAT
170929 ATTTAAATTATTATTTATAAATTAATAAAAAT
1 ATTTAAATTA-TATTTA-AAA-TAATAAAAAT
170961 A
1 A
170962 AAAAAGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 6 0.21
31 3 0.11
32 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAAATTATATTTAAAATAATAAAAAT
Found at i:172138 original size:12 final size:11
Alignment explanation
Indices: 172121--172146 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
172111 CTTGAAGTGG
172121 AAAAAAAAATT
1 AAAAAAAAATT
172132 AAAAAAAAATT
1 AAAAAAAAATT
172143 AAAA
1 AAAA
172147 GACTTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:173113 original size:2 final size:2
Alignment explanation
Indices: 173106--173135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
173096 TTAATCGTCT
173106 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
173136 CCCTAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:174963 original size:34 final size:34
Alignment explanation
Indices: 174907--175122 Score: 274
Period size: 34 Copynumber: 6.4 Consensus size: 34
174897 TCGTATTTAA
174907 TGTTGATTAAATG-GTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
* *
174940 TGTTGATTAAATGAGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
* * *
174974 TGTTGACTAAATGAGAGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
** *
175008 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
* * * *
175042 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
* * *
175076 TGTTGACTAAATG-GTAGATTTGGTAGGTTATCAT
1 TGTTGATTAAATGAGT-GATTTGGTAGTTTACCAT
175110 TGTTGATTAAATG
1 TGTTGATTAAATG
175123 GTGGTTTTTA
Statistics
Matches: 159, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 144 0.91
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.42
Consensus pattern (34 bp):
TGTTGATTAAATGAGTGATTTGGTAGTTTACCAT
Found at i:175099 original size:102 final size:101
Alignment explanation
Indices: 174907--175123 Score: 337
Period size: 102 Copynumber: 2.1 Consensus size: 101
174897 TCGTATTTAA
** * * * *
174907 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGAGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACC
*
174972 ATTGTTGACTAAATGAGAGATTTGGTAGTTTATCAT
66 ATTGTTGACTAAATGAGAGATTTGGTAGGTTATCAT
*
175008 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTAC
175073 CATTGTTGACTAAATG-GTAGATTTGGTAGGTTATCAT
65 CATTGTTGACTAAATGAG-AGATTTGGTAGGTTATCAT
175110 TGTTGATTAAATGG
1 TGTTGATTAAATGG
175124 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.42
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGAGAGATTTGGTAGGTTATCAT
Found at i:179601 original size:34 final size:33
Alignment explanation
Indices: 179532--179752 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 33
179522 AAGTGGGAGA
*
179532 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
* * *
179565 ATTGTTGATTAAATGGCTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGG-TGATTTGGTAGCTTACC
* *
179599 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* **
179633 ATTGTTAATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* *
179667 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* * *
179701 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGCTTACC
179735 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
179753 GTTTTTACCA
Statistics
Matches: 162, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
33 21 0.13
34 138 0.85
35 3 0.02
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
Found at i:179675 original size:102 final size:101
Alignment explanation
Indices: 179532--179750 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
179522 AAGTGGGAGA
** * * * *
179532 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGCTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGCTGATTTGGTGGCTTA
179597 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
179633 ATTGTTAATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGCTGATTTGGTGGCTT
* * *
179698 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
179735 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
179751 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGCTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:184071 original size:27 final size:27
Alignment explanation
Indices: 183993--184073 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
183983 GACAAATAAT
* *
183993 AAACCACAATTTTTGACAAATAAAAAG
1 AAACCACCATTTTTGACAAATACAAAG
* * *
184020 TAACTACCATTTTTTACAAATACAAAG
1 AAACCACCATTTTTGACAAATACAAAG
*
184047 AAACCACCATTTTTGACAAACACAAAG
1 AAACCACCATTTTTGACAAATACAAAG
184074 GGTGGCTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (27 bp):
AAACCACCATTTTTGACAAATACAAAG
Found at i:189702 original size:2 final size:2
Alignment explanation
Indices: 189697--189724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
189687 TTTTTTTTTG
189697 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
189725 AAAGAGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:189892 original size:15 final size:14
Alignment explanation
Indices: 189866--189896 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
189856 TTAATTCATC
189866 AATTTTTTAATTTT
1 AATTTTTTAATTTT
189880 AATTTTATTAATTTT
1 AATTTT-TTAATTTT
189895 AA
1 AA
189897 AATAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTTTTAATTTT
Found at i:190010 original size:104 final size:104
Alignment explanation
Indices: 189887--190111 Score: 443
Period size: 104 Copynumber: 2.2 Consensus size: 104
189877 TTTAATTTTA
189887 TTAATTT-TAAAATAAAATATTTATTTTATATTATAAAAAATTTAACATTAATTAAAAATAAATA
1 TTAATTTATAAAATAAAATATTTATTTTATATTATAAAAAATTTAACATTAATTAAAAATAAATA
189951 AAAAATAACATCTAATTCATTTTGATTAACTGTCGTCTT
66 AAAAATAACATCTAATTCATTTTGATTAACTGTCGTCTT
189990 TTAATTTATAAAATAAAATATTTATTTTATATTATAAAAAATTTAACATTAATTAAAAATAAATA
1 TTAATTTATAAAATAAAATATTTATTTTATATTATAAAAAATTTAACATTAATTAAAAATAAATA
190055 AAAAATAACATCTAATTCATTTTGATTAACTGTCGTCTT
66 AAAAATAACATCTAATTCATTTTGATTAACTGTCGTCTT
190094 TTAATTTATAAAATAAAA
1 TTAATTTATAAAATAAAA
190112 ATCAAACTAA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 7 0.06
104 114 0.94
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (104 bp):
TTAATTTATAAAATAAAATATTTATTTTATATTATAAAAAATTTAACATTAATTAAAAATAAATA
AAAAATAACATCTAATTCATTTTGATTAACTGTCGTCTT
Found at i:190013 original size:21 final size:21
Alignment explanation
Indices: 189989--190035 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
189979 ACTGTCGTCT
*
189989 TTTAATTTATAAAATAAAATA
1 TTTAATTTATAAAATAAAAAA
* **
190010 TTTATTTTATATTATAAAAAA
1 TTTAATTTATAAAATAAAAAA
190031 TTTAA
1 TTTAA
190036 CATTAATTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATTTATAAAATAAAAAA
Found at i:191809 original size:27 final size:28
Alignment explanation
Indices: 191778--191838 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
191768 ATTTATGCAG
191778 AAAAATTGAAT-AAATTAAATAAATT-TT
1 AAAAATT-AATCAAATTAAATAAATTATT
* *
191805 AAAAATTAATCGAATTAAATTAATTAATT
1 AAAAATTAATCAAATTAAATAAATT-ATT
191834 AAAAA
1 AAAAA
191839 ATAAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 19 0.66
29 7 0.24
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATTAATCAAATTAAATAAATTATT
Found at i:191907 original size:25 final size:25
Alignment explanation
Indices: 191874--191938 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
191864 TTTATTCACT
191874 TTTA-ATTATT-TACAAAATAAATTA
1 TTTATATTATTATACAAAA-AAATTA
* *
191898 TTTATATTATTATATAAAAAACTTA
1 TTTATATTATTATACAAAAAAATTA
191923 TTATATATATATTATA
1 TT-TATAT-TATTATA
191939 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.11
25 13 0.37
26 11 0.31
27 7 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTATATTATTATACAAAAAAATTA
Found at i:192118 original size:19 final size:19
Alignment explanation
Indices: 192090--192126 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
192080 AAAACTAATT
192090 TTAAAATAAAATAATTAAG
1 TTAAAATAAAATAATTAAG
* *
192109 TTAAACTAAATTAATTAA
1 TTAAAATAAAATAATTAA
192127 ATTTAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
TTAAAATAAAATAATTAAG
Found at i:193172 original size:38 final size:38
Alignment explanation
Indices: 193130--193206 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
193120 TAACTAGTTT
* *
193130 AATTACATAAAAAATAAATTA-TTTATATTATTATATAA
1 AATTA-ATAAAAAATAAATAATTTTAAATTATTATATAA
* * *
193168 AATTATTAAAAATTATATAATTTTAAATTATTATATAA
1 AATTAATAAAAAATAAATAATTTTAAATTATTATATAA
193206 A
1 A
193207 TATATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (38 bp):
AATTAATAAAAAATAAATAATTTTAAATTATTATATAA
Found at i:193200 original size:18 final size:18
Alignment explanation
Indices: 193151--193205 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
193141 AAATAAATTA
*
193151 TTTATATTATTATATAAAAT
1 TTTAAATTATTATAT--AAT
*
193171 TATTAAA-AATTATATAAT
1 T-TTAAATTATTATATAAT
193189 TTTAAATTATTATATAA
1 TTTAAATTATTATATAA
193206 ATATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 5 0.17
18 13 0.43
20 8 0.27
21 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATTATTATATAAT
Found at i:194942 original size:4 final size:4
Alignment explanation
Indices: 194933--194966 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
194923 CGTCTTGATC
194933 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
194967 CCCGCGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:195616 original size:22 final size:22
Alignment explanation
Indices: 195580--195625 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
195570 AAATGATTTT
*
195580 AATATATATAATATAATACTAAA
1 AATATATAAAATATAATA-TAAA
195603 AATATA-AAAATATAATATAAA
1 AATATATAAAATATAATATAAA
195624 AA
1 AA
195626 CAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATATAAAATATAATATAAA
Found at i:197928 original size:3 final size:3
Alignment explanation
Indices: 197920--197962 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
197910 TAGCATAGAG
* *
197920 TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
197963 ATAGTACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:201122 original size:38 final size:38
Alignment explanation
Indices: 201080--201155 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
201070 ATATTTTGGG
* *
201080 TTTGAGTTTTATTTTTAGAATCT-TCGATTTAAATAAAA
1 TTTGAGTTTTATTTTAAAAATCTCT-GATTTAAATAAAA
*
201118 TTTGATTTTTATTTTAAAAATCTCTGATTTAAATAAAA
1 TTTGAGTTTTATTTTAAAAATCTCTGATTTAAATAAAA
201156 GGTTAACGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (38 bp):
TTTGAGTTTTATTTTAAAAATCTCTGATTTAAATAAAA
Found at i:201552 original size:24 final size:25
Alignment explanation
Indices: 201501--201554 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
201491 TTAAATATTT
* **
201501 TTTAAAATAAATATAAATAATTTTA
1 TTTATAATAAATATAAATAATTAAA
*
201526 TTTATAATAAA-ATAAATTATTAAA
1 TTTATAATAAATATAAATAATTAAA
201550 TTTAT
1 TTTAT
201555 TGACTACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTATAATAAATATAAATAATTAAA
Found at i:201957 original size:20 final size:20
Alignment explanation
Indices: 201932--201982 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
201922 AATTAAGTTA
201932 AATTTAAATATAATATT-TTT
1 AATTTAAATATAAT-TTATTT
201952 AATTTAAAT-TAATTTGATTT
1 AATTTAAATATAATTT-ATTT
201972 AATTTAAATAT
1 AATTTAAATAT
201983 TAAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 21 0.75
21 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTTAAATATAATTTATTT
Found at i:202011 original size:46 final size:46
Alignment explanation
Indices: 201917--202012 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
201907 AGTTTATTTG
* * *
201917 ATTTGAATTAAGTTAAATTTAAATATAATATTTTTAATTTAAATTA
1 ATTTGAATTAAGTTAAATTTAAATATAATATTATTAATATAAAATA
* * *
201963 ATTTGATTTAATTTAAATATTAAATTATAA-A-TATTGATATAAAATA
1 ATTTGAATTAAGTTAAAT-TTAAA-TATAATATTATTAATATAAAATA
202009 ATTT
1 ATTT
202013 TTTAAATTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
46 31 0.74
47 6 0.14
48 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (46 bp):
ATTTGAATTAAGTTAAATTTAAATATAATATTATTAATATAAAATA
Found at i:202265 original size:19 final size:18
Alignment explanation
Indices: 202231--202274 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
202221 ATAAATACTA
202231 AATTATTATTTATTATAT
1 AATTATTATTTATTATAT
202249 AATTAATTATATT-TTATAT
1 AATT-ATTAT-TTATTATAT
*
202268 ATTTATT
1 AATTATT
202275 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTATTATTTATTATAT
Found at i:204965 original size:31 final size:30
Alignment explanation
Indices: 204927--205013 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
204917 TAATTACATT
*
204927 TAAATAAATTTTTAACTTTTTAATTTGTAAC
1 TAAATAAATTTTTAA-TTTTTAATTTATAAC
** *
204958 TAAATAAATCATTAATATTTTAATTTATACC
1 TAAATAAATTTTTAAT-TTTTAATTTATAAC
* *
204989 TAAATAAACTTTTAATCTTTAATTT
1 TAAATAAATTTTTAATTTTTAATTT
205014 TTACTTACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 9 0.19
31 38 0.81
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (30 bp):
TAAATAAATTTTTAATTTTTAATTTATAAC
Found at i:205012 original size:30 final size:30
Alignment explanation
Indices: 204927--205030 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
204917 TAATTACATT
* * *
204927 TAAATAAATTTTTAACTTTTTAATTTGTAAC
1 TAAATAAACTTTTAA-TTTTTAATTTATACC
*
204958 TAAATAAA-TCATTAATATTTTAATTTATACC
1 TAAATAAACT-TTTAAT-TTTTAATTTATACC
* * *
204989 TAAATAAACTTTTAATCTTTAATTTTTACT
1 TAAATAAACTTTTAATTTTTAATTTATACC
205019 TACAA-AAACTTT
1 TA-AATAAACTTT
205031 CACGTTATGC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
30 22 0.35
31 39 0.63
32 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (30 bp):
TAAATAAACTTTTAATTTTTAATTTATACC
Found at i:208535 original size:25 final size:25
Alignment explanation
Indices: 208507--208571 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
208497 ATACGTATTA
208507 TTATATTAAAATAATATTAA-AAAAT
1 TTATATTAAAATAATA-TAATAAAAT
* *
208532 TTATATTAATAT-ATATAATTAAAT
1 TTATATTAAAATAATATAATAAAAT
*
208556 TTAAATTAAAACTAAT
1 TTATATTAAAA-TAAT
208572 TTTAGGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 3 0.09
24 16 0.48
25 12 0.36
26 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATATTAAAATAATATAATAAAAT
Found at i:211812 original size:27 final size:29
Alignment explanation
Indices: 211758--211815 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
211748 AAAATAAAAA
211758 TATTTTTATTATTTATTAATTATTAAATAT
1 TATTTTTATTATTTATTAATTA-TAAATAT
*
211788 TATTTTTATTATTT-TTACTTA-AAATAT
1 TATTTTTATTATTTATTAATTATAAATAT
211815 T
1 T
211816 TTTAATTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
29 6 0.22
30 14 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TATTTTTATTATTTATTAATTATAAATAT
Found at i:211947 original size:17 final size:16
Alignment explanation
Indices: 211923--211957 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
211913 AAATATTTTA
211923 AATTTATTTTAAATTT
1 AATTTATTTTAAATTT
*
211939 AATTATATTTTAACTTT
1 AATT-TATTTTAAATTT
211956 AA
1 AA
211958 AATTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTATTTTAAATTT
Found at i:211965 original size:28 final size:26
Alignment explanation
Indices: 211915--211999 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 26
211905 TGTATATTAA
**
211915 ATATTTTAAATTTATTTTAAATTTAATT
1 ATATTTT-AATTTAAATT-AATTTAATT
211943 ATATTTTAACTTTAAAATTAATTT-ATT
1 ATATTTTAA-TTT-AAATTAATTTAATT
*
211970 AAAATATTTTTATTTAAATTAA-TTAATT
1 ---ATATTTTAATTTAAATTAATTTAATT
211998 AT
1 AT
212000 TATTATTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
25 2 0.04
27 7 0.15
28 25 0.52
29 6 0.12
30 8 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATTTTAATTTAAATTAATTTAATT
Found at i:211986 original size:23 final size:22
Alignment explanation
Indices: 211960--212008 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
211950 AACTTTAAAA
* *
211960 TTAATTTATTAAAATATTTTTAT
1 TTAATTAATT-AAATATTATTAT
*
211983 TTAAATTAATTAATTATTATTAT
1 TT-AATTAATTAAATATTATTAT
212006 TTA
1 TTA
212009 TAAATTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAATTAATTAAATATTATTAT
Found at i:212485 original size:17 final size:17
Alignment explanation
Indices: 212463--212496 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
212453 AACTTTATAG
212463 TAATTAAAAAAATTTTA
1 TAATTAAAAAAATTTTA
*
212480 TAATTAAAAATATTTTA
1 TAATTAAAAAAATTTTA
212497 AGTAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTAAAAAAATTTTA
Found at i:222873 original size:18 final size:17
Alignment explanation
Indices: 222818--222873 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
222808 ACTATATTTT
222818 TAAATTATTATT-ATATA
1 TAAATT-TTATTAATATA
*
222835 TAAATTTTATTATTATGA
1 TAAATTTTATTAATAT-A
222853 TAACA-TTTATTCAATATA
1 TAA-ATTTTATT-AATATA
222871 TAA
1 TAA
222874 GCCAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 14 0.42
19 5 0.15
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAATTTTATTAATATA
Found at i:231601 original size:29 final size:30
Alignment explanation
Indices: 231569--231633 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
231559 ATTTTTAAAT
* *
231569 TTTTTATTAATTTAAAAA-TAAAGT-ATTTA
1 TTTTTA-TAATTTAAAAATTAAAATAATTAA
*
231598 TTTTTATATTTTAAAAATTAAAATAATTAA
1 TTTTTATAATTTAAAAATTAAAATAATTAA
231628 TTTTTA
1 TTTTTA
231634 AAAAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.32
29 11 0.35
30 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTTATAATTTAAAAATTAAAATAATTAA
Found at i:231915 original size:7 final size:7
Alignment explanation
Indices: 231899--231940 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
231889 CGGACGGAGG
231899 AAAA-AA
1 AAAAGAA
231905 AAAAGAA
1 AAAAGAA
231912 AAAAGAA
1 AAAAGAA
231919 AAAAGAGA
1 AAAAGA-A
231927 AAAGAGAA
1 AAA-AGAA
231935 AAAAGA
1 AAAAGA
231941 GCAAGGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 4 0.12
7 18 0.55
8 8 0.24
9 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:231939 original size:16 final size:16
Alignment explanation
Indices: 231901--231941 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
231891 GACGGAGGAA
*
231901 AAAAAAAAGAAAAAAG
1 AAAAAAGAGAAAAAAG
*
231917 AAAAAAGAGAAAAGAG
1 AAAAAAGAGAAAAAAG
231933 AAAAAAGAG
1 AAAAAAGAG
231942 CAAGGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAG
Found at i:233355 original size:2 final size:2
Alignment explanation
Indices: 233348--233372 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
233338 AAAGTAGAAC
233348 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 A
233373 ATTACCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:233744 original size:55 final size:55
Alignment explanation
Indices: 233670--233793 Score: 171
Period size: 55 Copynumber: 2.3 Consensus size: 55
233660 CTAAATAAAA
**
233670 TTTAT-TAGTTTTGGTATTTAGAATTAATTCCA-TTAATTCAAGCAGAAGTGATAT
1 TTTATATAGTTTTGAAATTTAGAATTAATTCCAGTT-ATTCAAGCAGAAGTGATAT
* * *
233724 TTTATATAGTTTTGAAATTTAGATTTAATTCCAGTTGTTCAAGCAGGAGTGATAT
1 TTTATATAGTTTTGAAATTTAGAATTAATTCCAGTTATTCAAGCAGAAGTGATAT
*
233779 TTTATATAGATTTGA
1 TTTATATAGTTTTGA
233794 GTACAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
54 5 0.08
55 55 0.89
56 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (55 bp):
TTTATATAGTTTTGAAATTTAGAATTAATTCCAGTTATTCAAGCAGAAGTGATAT
Found at i:235786 original size:10 final size:10
Alignment explanation
Indices: 235703--235787 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 10
235693 TTTAAAATAT
*
235703 TATATTTTTA
1 TATATATTTA
*
235713 TATAAATTT-
1 TATATATTTA
235722 TGATATATTTA
1 T-ATATATTTA
235733 TA-A-ATTTA
1 TATATATTTA
235741 T-TCATATTTA
1 TAT-ATATTTA
* *
235751 TGTTATTTTTA
1 T-ATATATTTA
235762 TATCATAATTTTA
1 TAT-AT-A-TTTA
235775 TATATATTTA
1 TATATATTTA
235785 TAT
1 TAT
235788 TTTTTTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
8 6 0.10
9 3 0.05
10 29 0.49
11 11 0.19
12 3 0.05
13 7 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:236010 original size:20 final size:21
Alignment explanation
Indices: 235972--236010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
235962 TTTTGAATAC
*
235972 AAAATTATTATATAATATAAA
1 AAAATTAATATATAATATAAA
235993 AAAATTAATATA-AATATA
1 AAAATTAATATATAATATA
236011 TAAATATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTAATATATAATATAAA
Found at i:236013 original size:8 final size:8
Alignment explanation
Indices: 236000--236253 Score: 56
Period size: 8 Copynumber: 29.5 Consensus size: 8
235990 AAAAAAATTA
236000 ATATAAAT
1 ATATAAAT
236008 ATATAAAT
1 ATATAAAT
236016 ATATCAAAATT
1 ATAT--AAA-T
236027 ATATAATTTAT
1 ATATAA---AT
*
236038 TTATAAAT
1 ATATAAAT
236046 ATATTAAA-
1 ATA-TAAAT
* *
236054 ATTTATAT
1 ATATAAAT
*
236062 TTAT-AAT
1 ATATAAAT
*
236069 ATTTTAAAT
1 A-TATAAAT
*
236078 ATATTAAT
1 ATATAAAT
236086 AATATAAAT
1 -ATATAAAT
236095 ATAATATAATT
1 AT-ATA-AA-T
236106 ATATAAATTT
1 ATATAAA--T
236116 ATATTAAAT
1 ATA-TAAAT
* *
236125 AT-TTATT
1 ATATAAAT
*
236132 A-AAAAAT
1 ATATAAAT
*
236139 TTATAAAT
1 ATATAAAT
*
236147 ATGACGTAATT
1 AT-A--TAAAT
236158 ATATAAAT
1 ATATAAAT
236166 ATATCAAA-
1 ATAT-AAAT
* *
236174 ATTTATAT
1 ATATAAAT
236182 ATCATAAAT
1 AT-ATAAAT
*
236191 -TTTAAAT
1 ATATAAAT
236198 CA-ATTAAAATTT
1 -ATA-T-AAA--T
236210 ATATAAAT
1 ATATAAAT
236218 ATAT-AAT
1 ATATAAAT
*
236225 ATTTTAAAT
1 A-TATAAAT
* *
236234 ATAAAAAA
1 ATATAAAT
*
236242 ATATAAAA
1 ATATAAAT
236250 ATAT
1 ATAT
236254 TATTATAAAT
Statistics
Matches: 180, Mismatches: 33, Indels: 66
0.65 0.12 0.24
Matches are distributed among these distances:
7 22 0.12
8 71 0.39
9 38 0.21
10 20 0.11
11 26 0.14
12 3 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:236045 original size:30 final size:28
Alignment explanation
Indices: 236009--236065 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
235999 AATATAAATA
236009 TATAAATATATCAAAATTATATAATTTATT
1 TATAAATATATCAAAATT-TAT-ATTTATT
*
236039 TATAAATATATTAAAATTTATATTTAT
1 TATAAATATATCAAAATTTATATTTAT
236066 AATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.23
29 3 0.12
30 17 0.65
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAAATATATCAAAATTTATATTTATT
Found at i:236059 original size:22 final size:23
Alignment explanation
Indices: 236035--236091 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
236025 TTATATAATT
236035 TATTTATAAATATATTAAAATTTA
1 TATTTAT-AATATATTAAAATTTA
*
236059 TATTTATAATAT-TTTAAA--TA
1 TATTTATAATATATTAAAATTTA
*
236079 TATTAATAATATA
1 TATTTATAATATA
236092 AATATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
22 5 0.17
23 5 0.17
24 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTATAATATATTAAAATTTA
Found at i:236183 original size:14 final size:15
Alignment explanation
Indices: 236164--236214 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
236154 AATTATATAA
236164 ATATATCA-AAATTT
1 ATATATCATAAATTT
236178 ATATATCATAAATTT
1 ATATATCATAAATTT
*
236193 -TAAATCAATTAAAATTT
1 ATATATC-A-T-AAATTT
236210 ATATA
1 ATATA
236215 AATATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 13 0.43
15 7 0.23
16 1 0.03
17 6 0.20
18 3 0.10
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATCATAAATTT
Found at i:236683 original size:28 final size:28
Alignment explanation
Indices: 236601--236689 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
236591 TTAATATATA
*
236601 AATTTAATTTA--AAATAAAAATAAAATT
1 AATTTAATTTATTTAATAAAAAT-AAATT
* * * * *
236628 ATTTTAATTTATTTGATTAAATTTAATT
1 AATTTAATTTATTTAATAAAAATAAATT
236656 AAATTT-ATTTATTTAATAAAAATAAATTT
1 -AATTTAATTTATTTAATAAAAATAAA-TT
236685 AATTT
1 AATTT
236690 TTATACATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
27 10 0.21
28 25 0.53
29 12 0.26
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AATTTAATTTATTTAATAAAAATAAATT
Found at i:236777 original size:19 final size:19
Alignment explanation
Indices: 236755--236792 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
236745 TGAAATTTTT
*
236755 AATTTTTATTAAAAATAAA
1 AATTTATATTAAAAATAAA
236774 AATTTATATTAAAAATAAA
1 AATTTATATTAAAAATAAA
236793 TAAAGCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTATATTAAAAATAAA
Found at i:238252 original size:17 final size:18
Alignment explanation
Indices: 238223--238257 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
238213 GCCCATTGAT
238223 TATATATATTATACTCTC
1 TATATATATTATACTCTC
238241 TATATA-ATTATACTCTC
1 TATATATATTATACTCTC
238258 CTCTGTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATATTATACTCTC
Found at i:238486 original size:22 final size:23
Alignment explanation
Indices: 238461--238508 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
238451 TTATTTAATA
*
238461 TAATTAT-AAAATTTATAATTTT
1 TAATTATAAAAATATATAATTTT
*
238483 TAA-TATAAAAATATATATTTTT
1 TAATTATAAAAATATATAATTTT
238505 TAAT
1 TAAT
238509 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATAAAAATATATAATTTT
Found at i:238509 original size:22 final size:22
Alignment explanation
Indices: 238468--238510 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
238458 ATATAATTAT
*
238468 AAAATTTATAATTTTTAATATA
1 AAAATATATAATTTTTAATATA
*
238490 AAAATATATATTTTTTAATAT
1 AAAATATATAATTTTTAATAT
238511 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATATAATTTTTAATATA
Found at i:238519 original size:29 final size:29
Alignment explanation
Indices: 238449--238539 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
238439 ATAATAAAAA
* * *
238449 AATTATTTAATATAAT--TATAAAATTTAT
1 AATT-TTTAATATAATAAAATAAATTTTTT
*
238477 AATTTTTAATATAA-AAATATATATTTTTT
1 AATTTTTAATATAATAAA-ATAAATTTTTT
*
238506 AATATTTTAA-ATAATAAAATAAATTTTTA
1 AAT-TTTTAATATAATAAAATAAATTTTTT
238535 AATTT
1 AATTT
238540 AATTTAATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
27 10 0.19
28 6 0.12
29 27 0.52
30 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AATTTTTAATATAATAAAATAAATTTTTT
Found at i:238690 original size:17 final size:18
Alignment explanation
Indices: 238668--238721 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 18
238658 AAATAATTTT
238668 TATAATTAAT-AATTAAA
1 TATAATTAATAAATTAAA
238685 TATAA-TAATAAATTAAA
1 TATAATTAATAAATTAAA
238702 T-TAATTTAATTTAAATTAAA
1 TATAA-TTAA--TAAATTAAA
238722 AAATTTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.22
17 13 0.41
18 3 0.09
20 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAATTAATAAATTAAA
Found at i:238984 original size:25 final size:26
Alignment explanation
Indices: 238930--238991 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
238920 TTATGTATAC
238930 TAAAA-AAATATAAAATATAATAATA
1 TAAAATAAATATAAAATATAATAATA
* *
238955 TAAAATTAATAT-AAATATAAT-ATT
1 TAAAATAAATATAAAATATAATAATA
238979 TAAAAATAAATAT
1 T-AAAATAAATAT
238992 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 3 0.09
25 24 0.75
26 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAAATAAATATAAAATATAATAATA
Found at i:238995 original size:15 final size:15
Alignment explanation
Indices: 238933--238999 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
238923 TGTATACTAA
* *
238933 AAAAATATAAAATAT
1 AAAAATATAATATTT
* *
238948 AATAATATAAAATTAAT
1 AAAAATATAATATT--T
*
238965 ATAAATATAATATTT
1 AAAAATATAATATTT
238980 AAAAATA-AATATTT
1 AAAAATATAATATTT
*
238994 TAAAAT
1 AAAAAT
239000 TTATATTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
14 12 0.28
15 19 0.44
17 12 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATATAATATTT
Found at i:239006 original size:28 final size:28
Alignment explanation
Indices: 238974--239057 Score: 73
Period size: 32 Copynumber: 2.9 Consensus size: 28
238964 TATAAATATA
238974 ATATTTAAAAATAAATATTTTAAAATTT
1 ATATTTAAAAATAAATATTTTAAAATTT
*
239002 ATATTATATAAATTATTAAT-TTATTAAAATTT
1 ATATT-TA-AAA--ATAAATATT-TTAAAATTT
* *
239034 A-ATATAAATATAAAATATTTTAAA
1 ATATTTAAAAAT-AAATATTTTAAA
239058 CATATTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
27 2 0.04
28 13 0.29
29 6 0.13
30 5 0.11
31 4 0.09
32 15 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTTAAAAATAAATATTTTAAAATTT
Found at i:239802 original size:23 final size:22
Alignment explanation
Indices: 239740--239824 Score: 63
Period size: 23 Copynumber: 4.0 Consensus size: 22
239730 ATTAACAAGT
*
239740 TTATAAATT-TATA-TATTAAA
1 TTATAATTTATATATTATTAAA
* * *
239760 -TATAATTT-TTTAATAATAAA
1 TTATAATTTATATATTATTAAA
*
239780 CTTAT-ATTTAATATATTCTTAAA
1 -TTATAATTT-ATATATTATTAAA
239803 TTATAAATTTATATATTATTAA
1 TTAT-AATTTATATATTATTAA
239825 TAAATTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 10 0.20
20 6 0.12
21 4 0.08
22 7 0.14
23 19 0.38
24 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAATTTATATATTATTAAA
Found at i:239815 original size:30 final size:33
Alignment explanation
Indices: 239740--239820 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 33
239730 ATTAACAAGT
* *
239740 TTATAAATTTATATATTAAATATAATTTTTTAA
1 TTATAAATTTATATATTAAATATAATTCTTAAA
* *
239773 TAATAAACTTATAT-TT-AATAT-ATTCTTAAA
1 TTATAAATTTATATATTAAATATAATTCTTAAA
239803 TTATAAATTTATATATTA
1 TTATAAATTTATATATTA
239821 TTAATAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 19 0.47
31 7 0.17
32 2 0.05
33 12 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
TTATAAATTTATATATTAAATATAATTCTTAAA
Found at i:239840 original size:18 final size:19
Alignment explanation
Indices: 239805--239843 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
239795 TTCTTAAATT
239805 ATAAATTTATATATTATTA
1 ATAAATTTATATATTATTA
239824 ATAAATTATATTATATTATT
1 ATAAATT-TA-TATATTATT
239844 TTATTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAAATTTATATATTATTA
Found at i:240078 original size:21 final size:22
Alignment explanation
Indices: 240052--240095 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
240042 ATGTCGAGGT
*
240052 TTAAATTTTATTTTTA-TTAAA
1 TTAAATTTTATTTTAATTTAAA
240073 TTAAATTTTATTTTAATTTAAA
1 TTAAATTTTATTTTAATTTAAA
240095 T
1 T
240096 AATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAAATTTTATTTTAATTTAAA
Found at i:246385 original size:28 final size:27
Alignment explanation
Indices: 246354--246419 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
246344 TTTTAAATCG
246354 ATTTAAATTATTATTTAATAATAAAAAT
1 ATTTAAATTATTATTTAATAAT-AAAAT
* * * *
246382 ATTTTATTTAAT-TTTAATTATAAAAT
1 ATTTAAATTATTATTTAATAATAAAAT
*
246408 ATATAAA-TATTA
1 ATTTAAATTATTA
246420 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
25 3 0.10
26 9 0.31
27 8 0.28
28 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTAAATTATTATTTAATAATAAAAT
Found at i:247115 original size:50 final size:50
Alignment explanation
Indices: 247018--247117 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
247008 TTTATTAAAT
* * *
247018 ATTATTTTTTAAAAATAATTATTACTAATTAAATCATATTTAGAATTCAA
1 ATTACTTTTTAAAAATAATTATTACCAATTAAATCAAATTTAGAATTCAA
* *
247068 ATTACTTTTTAAAAATGATTGTTACCAATTAAA-CTAAATTTCA-AATTCAA
1 ATTACTTTTTAAAAATAATTATTACCAATTAAATC-AAATTT-AGAATTCAA
247118 CCTCCAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 41 0.95
51 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (50 bp):
ATTACTTTTTAAAAATAATTATTACCAATTAAATCAAATTTAGAATTCAA
Found at i:247554 original size:22 final size:22
Alignment explanation
Indices: 247522--247567 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
247512 CACCGAGTTA
*
247522 AATATGGTTCACATTTAGTAGC
1 AATATGATTCACATTTAGTAGC
247544 AATATGATTCACATTTAGTAGC
1 AATATGATTCACATTTAGTAGC
247566 AA
1 AA
247568 AATAGATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
AATATGATTCACATTTAGTAGC
Found at i:251801 original size:22 final size:22
Alignment explanation
Indices: 251769--251834 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
251759 TAATACTTAT
251769 AATAT-TTTAATATATAAATTA
1 AATATATTTAATATATAAATTA
* *
251790 AATATATTTAAT-TATTATTTA
1 AATATATTTAATATATAAATTA
*
251811 AATTAAATTTAATA-A-AAATTA
1 AA-TATATTTAATATATAAATTA
251832 AAT
1 AAT
251835 TAAAATCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.03
21 20 0.54
22 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATTTAATATATAAATTA
Found at i:252550 original size:2 final size:2
Alignment explanation
Indices: 252543--252574 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
252533 GCAATACTTC
252543 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
252575 GTACATGTTT
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:254802 original size:5 final size:5
Alignment explanation
Indices: 254803--254847 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
254793 GAAGGGAAGG
* * * *
254803 GGGGA GGGGA TGGGA TGGGA TGGGA TGGGA GGGGA GGGGA GGGGA
1 GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA GGGGA
254848 TTTTTCATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.71, T:0.09
Consensus pattern (5 bp):
GGGGA
Found at i:254827 original size:15 final size:15
Alignment explanation
Indices: 254804--254848 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
254794 AAGGGAAGGG
254804 GGGAGGGGATGGGAT
1 GGGAGGGGATGGGAT
* *
254819 GGGATGGGATGGGAG
1 GGGAGGGGATGGGAT
*
254834 GGGAGGGGAGGGGAT
1 GGGAGGGGATGGGAT
254849 TTTTCATCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.69, T:0.11
Consensus pattern (15 bp):
GGGAGGGGATGGGAT
Found at i:267298 original size:20 final size:19
Alignment explanation
Indices: 267273--267310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
267263 TATTAAAAAT
*
267273 TATTAAAATATTATTTATTA
1 TATTAAAAT-TTATATATTA
267293 TATTAAAATTTATATATT
1 TATTAAAATTTATATATT
267311 TTTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTAAAATTTATATATTA
Found at i:267323 original size:22 final size:23
Alignment explanation
Indices: 267273--267326 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
267263 TATTAAAAAT
267273 TATTAAAA--TAT-TATTTATTA
1 TATTAAAATTTATATATTTATTA
267293 TATTAAAATTTATATATTT-TTA
1 TATTAAAATTTATATATTTATTA
267315 TAATT-AAATTTA
1 T-ATTAAAATTTA
267327 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.27
22 14 0.47
23 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAAAATTTATATATTTATTA
Found at i:271549 original size:16 final size:16
Alignment explanation
Indices: 271528--271642 Score: 52
Period size: 16 Copynumber: 7.6 Consensus size: 16
271518 TCACAAACTA
271528 ATTATATAATATAAAT
1 ATTATATAATATAAAT
*
271544 ATTATATAAAATATAATT
1 ATTATAT--AATATAAAT
** *
271562 AAAATACAATATAAAAT
1 ATTATATAATAT-AAAT
* *
271579 ATAATA-AATATCAA-
1 ATTATATAATATAAAT
*
271593 A-TA-ATAACAT-AA-
1 ATTATATAATATAAAT
271605 A-TATATAATATAAAT
1 ATTATATAATATAAAT
*
271620 ATGTA-AAAATATAAA-
1 AT-TATATAATATAAAT
271635 ATT-TATAA
1 ATTATATAA
271643 AACATAAATG
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
12 6 0.08
13 11 0.14
14 7 0.09
15 5 0.06
16 26 0.34
17 10 0.13
18 12 0.16
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (16 bp):
ATTATATAATATAAAT
Found at i:271550 original size:11 final size:11
Alignment explanation
Indices: 271531--271621 Score: 61
Period size: 11 Copynumber: 8.4 Consensus size: 11
271521 CAAACTAATT
271531 ATATAATATAA
1 ATATAATATAA
*
271542 ATATTATATAAA
1 ATATAATAT-AA
271554 ATATAAT-TAAA
1 ATATAATAT-AA
*
271565 ATACAATATAA
1 ATATAATATAA
271576 A-AT-ATAATAA
1 ATATAAT-ATAA
271586 ATATCAA-AT-A
1 ATAT-AATATAA
271596 ATA-ACATA-AA
1 ATATA-ATATAA
271606 TATATAATATAA
1 -ATATAATATAA
271618 ATAT
1 ATAT
271622 GTAAAAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
8 1 0.02
9 3 0.05
10 12 0.19
11 35 0.55
12 12 0.19
13 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:271566 original size:23 final size:24
Alignment explanation
Indices: 271531--271583 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
271521 CAAACTAATT
**
271531 ATATAA-TATAAATATTATATAAA
1 ATATAATTATAAATACAATATAAA
271554 ATATAATTA-AAATACAATATAAA
1 ATATAATTATAAATACAATATAAA
271577 ATATAAT
1 ATATAAT
271584 AAATATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAATTATAAATACAATATAAA
Found at i:271595 original size:23 final size:22
Alignment explanation
Indices: 271538--271621 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 22
271528 ATTATATAAT
*
271538 ATAAATAT-TATATAAAATATA
1 ATAAATATAAATATAAAATATA
271559 ATTAAA-ATACAATATAAAATATA
1 A-TAAATATA-AATATAAAATATA
* *
271582 ATAAATATCAAATAATAACATAAA
1 ATAAATAT-AAAT-ATAAAATATA
271606 TATATAATATAAATAT
1 -ATA-AATATAAATAT
271622 GTAAAAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
21 3 0.06
22 8 0.15
23 18 0.35
24 11 0.21
25 7 0.13
26 5 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATATAAATATAAAATATA
Found at i:271614 original size:19 final size:19
Alignment explanation
Indices: 271535--271614 Score: 52
Period size: 19 Copynumber: 4.6 Consensus size: 19
271525 CTAATTATAT
*
271535 AATATA-AATATTAT-ATA
1 AATATATAATAATATAATA
*
271552 AA-ATATAAT--TAAAATA
1 AATATATAATAATATAATA
*
271568 CA-ATATAA-AATATAATA
1 AATATATAATAATATAATA
271585 AATATCA-AATAATA-ACATA
1 AATAT-ATAATAATATA-ATA
271604 AATATATAATA
1 AATATATAATA
271615 TAAATATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
15 2 0.04
16 13 0.26
17 12 0.24
18 6 0.12
19 17 0.34
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATATAATAATATAATA
Found at i:271644 original size:16 final size:17
Alignment explanation
Indices: 271606--271651 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
271596 ATAACATAAA
*
271606 TATATAATATAAATATG
1 TATAAAATATAAATATG
*
271623 TA-AAAATATAAA-ATT
1 TATAAAATATAAATATG
*
271638 TATAAAACATAAAT
1 TATAAAATATAAAT
271652 GATCAAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 18 0.75
17 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
TATAAAATATAAATATG
Found at i:271977 original size:19 final size:19
Alignment explanation
Indices: 271955--271991 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
271945 ATAATATGAT
*
271955 TATATAATATAAAAAATAA
1 TATAAAATATAAAAAATAA
*
271974 TATAAAATATAAATAATA
1 TATAAAATATAAAAAATA
271992 TGAAAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAATATAAAAAATAA
Found at i:274363 original size:15 final size:17
Alignment explanation
Indices: 274343--274374 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
274333 AAAAAAATTG
274343 AACATAT-CC-ATGTCC
1 AACATATACCTATGTCC
274358 AACATATACCTATGTCC
1 AACATATACCTATGTCC
274375 GACACTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.28
Consensus pattern (17 bp):
AACATATACCTATGTCC
Found at i:279130 original size:28 final size:29
Alignment explanation
Indices: 279082--279190 Score: 80
Period size: 30 Copynumber: 3.7 Consensus size: 29
279072 TATTAATTAA
* *
279082 ATATTAAAAAAATTATCTAAATAAATATTT
1 ATATTATAAATATTAT-TAAATAAATATTT
279112 ATATTATAAAT-TTATTAAATTCATAAATATTT
1 ATATTATAAATATTATT-AA---ATAAATATTT
* * *
279144 -TA-TATTAATATCATTAAATAAATATTA
1 ATATTATAAATATTATTAAATAAATATTT
* *
279171 ATATAATAATTAATTATTAA
1 ATATTATAAAT-ATTATTAA
279191 CACAATTACA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
27 9 0.15
28 3 0.05
29 10 0.16
30 24 0.39
31 6 0.10
32 10 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTATAAATATTATTAAATAAATATTT
Found at i:279625 original size:19 final size:20
Alignment explanation
Indices: 279592--279640 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
279582 ACAAATTGGG
279592 AAACAAAAATGAAAAAA-AGGAA
1 AAACAAAAA--AAAAAACA-GAA
279614 AAA-AAAAAAAAAAACAGAA
1 AAACAAAAAAAAAAACAGAA
279633 AAACAAAA
1 AAACAAAA
279641 CTTGTTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.48
20 5 0.20
21 5 0.20
22 3 0.12
ACGTcount: A:0.84, C:0.06, G:0.08, T:0.02
Consensus pattern (20 bp):
AAACAAAAAAAAAAACAGAA
Found at i:282277 original size:30 final size:30
Alignment explanation
Indices: 282243--282306 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
282233 TGATAAAATG
282243 AGAATATTTTCTTGGAATAATTCACGAAGA
1 AGAATATTTTCTTGGAATAATTCACGAAGA
282273 AGAATATTTTCTTGGAATAATTCACGAAGA
1 AGAATATTTTCTTGGAATAATTCACGAAGA
282303 AGAA
1 AGAA
282307 GAAAAATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (30 bp):
AGAATATTTTCTTGGAATAATTCACGAAGA
Found at i:290189 original size:14 final size:14
Alignment explanation
Indices: 290172--290205 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
290162 ATTTTTATTT
290172 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
290186 AAATATTAATATAA
1 AAATATTAATATAA
290200 AAATAT
1 AAATAT
290206 ATCTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:290977 original size:94 final size:94
Alignment explanation
Indices: 290816--290999 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 94
290806 AAGGTAGTCG
** * * *
290816 AATTCCTCTCCCGTGTCTTTAAATTTTCACCCTCAACATTGATTATTTTACTTACATTTTCGTTT
1 AATTCCTCTCCCGTGTCCATAAATTTTCACCCTCAACATTGATTATTTTACTTAAATCTCCGTTT
*
290881 AATAATTTCATTTTTAACAGATAGAAGAT
66 AATAATCTCATTTTTAACAGATAGAAGAT
290910 AATTCCTCTCCCGTGTCCATAAATTTTCACCCTCAACATTGATTATTTTACTTAAATCTCCGTTT
1 AATTCCTCTCCCGTGTCCATAAATTTTCACCCTCAACATTGATTATTTTACTTAAATCTCCGTTT
290975 AATAATCTCATTTTTAACAGATAGA
66 AATAATCTCATTTTTAACAGATAGA
291000 GGATTTGATG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.42
Consensus pattern (94 bp):
AATTCCTCTCCCGTGTCCATAAATTTTCACCCTCAACATTGATTATTTTACTTAAATCTCCGTTT
AATAATCTCATTTTTAACAGATAGAAGAT
Found at i:292354 original size:29 final size:29
Alignment explanation
Indices: 292311--292369 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
292301 AGATGATCAT
* *
292311 AAATATATGTCAGATGTGATTACTTTTGA
1 AAATATATATAAGATGTGATTACTTTTGA
292340 AAATATATATAAGATGTGATTACTTTTGA
1 AAATATATATAAGATGTGATTACTTTTGA
292369 A
1 A
292370 CAAAATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (29 bp):
AAATATATATAAGATGTGATTACTTTTGA
Found at i:294941 original size:111 final size:117
Alignment explanation
Indices: 294740--294957 Score: 306
Period size: 111 Copynumber: 1.9 Consensus size: 117
294730 GGAGAAAAAA
294740 AATCTATAAGCAAATTCGGAGAATAGATGGAGAAGAAAGGTCAAAGCAAAAGCATTGCTTGAAGC
1 AATCTATAAGCAAATTCGGAGAATAGATGGAGAAGAAAGG-CAAAGCAAAAGCATTGCTTGAAGC
294805 AGAATCAAACAAGCCATAGCCATATGTTAAGAAGTATTTCTTAAGGGCCAAAC
65 AGAATCAAACAAGCCATAGCCATATGTTAAGAAGTATTTCTTAAGGGCCAAAC
* * *
294858 AATCTATAAGCAAATTTGGAGAATATAT-G-G-AG-AA-G-AAAGCAAAAGGATTGCTTG-AGAC
1 AATCTATAAGCAAATTCGGAGAATAGATGGAGAAGAAAGGCAAAGCAAAAGCATTGCTTGAAG-C
* * * *
294916 GGAATCAAGCAAGCCATAGCTATATGTTAAGAAGTCTTTCTT
65 AGAATCAAACAAGCCATAGCCATATGTTAAGAAGTATTTCTT
294958 CTCTAAAGTA
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
110 2 0.02
111 57 0.62
113 1 0.01
114 2 0.02
115 2 0.02
116 1 0.01
117 1 0.01
118 26 0.28
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (117 bp):
AATCTATAAGCAAATTCGGAGAATAGATGGAGAAGAAAGGCAAAGCAAAAGCATTGCTTGAAGCA
GAATCAAACAAGCCATAGCCATATGTTAAGAAGTATTTCTTAAGGGCCAAAC
Found at i:300719 original size:24 final size:23
Alignment explanation
Indices: 300662--300722 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
300652 TTATGGGGTA
**
300662 GGGTTTTGATTT-TTTAGGTTAT
1 GGGTTTTGATTTGTTCGGGTTAT
300684 GGGTTTTGATTTGTTCGGGTTAT
1 GGGTTTTGATTTGTTCGGGTTAT
* *
300707 GGATTTTTTATTTGTT
1 GG-GTTTTGATTTGTT
300723 GGTTTGTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 12 0.36
23 10 0.30
24 11 0.33
ACGTcount: A:0.11, C:0.02, G:0.28, T:0.59
Consensus pattern (23 bp):
GGGTTTTGATTTGTTCGGGTTAT
Found at i:302460 original size:2 final size:2
Alignment explanation
Indices: 302453--302485 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
302443 AAAAGCAGAA
302453 AT AT 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 AT AT A
302486 AAAGAGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:305035 original size:98 final size:98
Alignment explanation
Indices: 304920--305118 Score: 373
Period size: 98 Copynumber: 2.0 Consensus size: 98
304910 AAAATTTAAT
*
304920 TATAGTAAAATAATCAATTTAGCCGAA-ATTAAAATTAACAAAAAATTAATTTTTCGTTATTTAT
1 TATAGTAAAATAATCAATTTAGCC-AAGATTAAAATTAACAAAAAATTAATTTTTCATTATTTAT
304984 TTAAGATATTATTTATATTTAATTTATAAATAAA
65 TTAAGATATTATTTATATTTAATTTATAAATAAA
305018 TATAGTAAAATAATCAATTTAGCCAAGATTAAAATTAACAAAAAATTAATTTTTCATTATTTATT
1 TATAGTAAAATAATCAATTTAGCCAAGATTAAAATTAACAAAAAATTAATTTTTCATTATTTATT
305083 TAAGATATTATTTATATTTAATTTATAAATAAA
66 TAAGATATTATTTATATTTAATTTATAAATAAA
305116 TAT
1 TAT
305119 TCAAACAATA
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
97 2 0.02
98 97 0.98
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (98 bp):
TATAGTAAAATAATCAATTTAGCCAAGATTAAAATTAACAAAAAATTAATTTTTCATTATTTATT
TAAGATATTATTTATATTTAATTTATAAATAAA
Found at i:305181 original size:98 final size:95
Alignment explanation
Indices: 304920--305183 Score: 241
Period size: 98 Copynumber: 2.7 Consensus size: 95
304910 AAAATTTAAT
* * *** * *
304920 TATAGTAAAATAATCAATTTAGCCGAAATTAAAATTAACAAAAAATTAATTTTTCGTTATTTATT
1 TATA-TAAAACAATCAATTTAG-C-AGATTAAAATTAACAAAAAATTAATTAACCATTATCTATT
304985 TAAGATATTATTTATATTTAATTTATAAATAAA
63 TAAGATATTATTTATATTTAATTTATAAATAAA
* *** *
305018 TATAGTAAAATAATCAATTTAGCCAAGATTAAAATTAACAAAAAATTAATTTTTCATTATTTATT
1 TATA-TAAAACAATCAATTTAG-C-AGATTAAAATTAACAAAAAATTAATTAACCATTATCTATT
305083 TAAGATATTATTTATATTTAATTTATAAATAAA
63 TAAGATATTATTTATATTTAATTTATAAATAAA
* *
305116 TAT-TCAAACAAT-ATTATTTAG-ATATTAAATCAATT-ACATAAATAATTAATTAAACCA-TAT
1 TATATAAAACAATCA--ATTTAGCAGATT-AA--AATTAACA-AAA-AATTAATT-AACCATTAT
305176 CTATTTAA
58 CTATTTAA
305184 TTTAAAATTA
Statistics
Matches: 148, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
94 4 0.03
95 3 0.02
96 10 0.07
97 13 0.09
98 116 0.78
99 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (95 bp):
TATATAAAACAATCAATTTAGCAGATTAAAATTAACAAAAAATTAATTAACCATTATCTATTTAA
GATATTATTTATATTTAATTTATAAATAAA
Found at i:307434 original size:34 final size:34
Alignment explanation
Indices: 307391--307458 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
307381 ATTTTTAATG
*
307391 ATTAAGAATGATAGAGCAGATTAAGAACTATGTT
1 ATTAAGAATGACAGAGCAGATTAAGAACTATGTT
307425 ATTAAGAATGACAGAGCAGATTAAGAACTATGTT
1 ATTAAGAATGACAGAGCAGATTAAGAACTATGTT
307459 CAACAATGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (34 bp):
ATTAAGAATGACAGAGCAGATTAAGAACTATGTT
Found at i:307694 original size:20 final size:20
Alignment explanation
Indices: 307669--307710 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
307659 TGTTCAATTA
307669 ATTCAATTTTAAGAGTTTTT
1 ATTCAATTTTAAGAGTTTTT
307689 ATTCAATTTTAAGAGTTTTT
1 ATTCAATTTTAAGAGTTTTT
307709 AT
1 AT
307711 CCGGCAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTCAATTTTAAGAGTTTTT
Found at i:312800 original size:18 final size:18
Alignment explanation
Indices: 312767--312825 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
312757 TTAATTTTTT
*
312767 AATTTATATT-TAAATAA
1 AATTTTTATTATAAATAA
**
312784 TTTTTTTATTATAAATAA
1 AATTTTTATTATAAATAA
312802 AATTTTTACTTA-AAATAA
1 AATTTTTA-TTATAAATAA
312820 ATATTT
1 A-ATTT
312826 ATTTAAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.21
18 20 0.59
19 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTATTATAAATAA
Found at i:312802 original size:22 final size:23
Alignment explanation
Indices: 312758--312842 Score: 60
Period size: 22 Copynumber: 4.0 Consensus size: 23
312748 AATAAGTGTT
* **
312758 TAATTTTTTAATTTATATTTAAA
1 TAATTTTTTAACTTATAAATAAA
*
312781 TAATTTTTTTA-TTATAAAT-AA
1 TAATTTTTTAACTTATAAATAAA
312802 -AA-TTTTT-ACTTA-AAATAAA
1 TAATTTTTTAACTTATAAATAAA
*
312821 T-ATTTATTTAA-GTATAAATAAA
1 TAATTT-TTTAACTTATAAATAAA
312843 AAATATGAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 4 0.08
21 7 0.14
22 14 0.27
23 10 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
TAATTTTTTAACTTATAAATAAA
Found at i:313382 original size:30 final size:28
Alignment explanation
Indices: 313297--313407 Score: 107
Period size: 30 Copynumber: 3.8 Consensus size: 28
313287 ATTGGCTTAT
*
313297 ATTAAAAATTTATTT-AGGTATAAATTAA
1 ATTAAAAGTTTATTTGA-GTATAAATTAA
* * * *
313325 ATTAATAGCTTATTTGAATACAAATTAA
1 ATTAAAAGTTTATTTGAGTATAAATTAA
*
313353 ATGTTAAAAGTTTATATGAGTATAAATTAAAA
1 A--TTAAAAGTTTATTTGAGTATAAATT--AA
*
313385 ATTAAAAATTTATTTGAGTATAA
1 ATTAAAAGTTTATTTGAGTATAA
313408 TAAAAGAATG
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
28 22 0.33
29 1 0.02
30 40 0.61
32 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.41
Consensus pattern (28 bp):
ATTAAAAGTTTATTTGAGTATAAATTAA
Found at i:317518 original size:14 final size:15
Alignment explanation
Indices: 317499--317532 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
317489 CATATTGAAC
*
317499 TTATTTTTAATAT-T
1 TTATTTTTAAAATAT
317513 TTATTTTTAAAATAT
1 TTATTTTTAAAATAT
317528 TTATT
1 TTATT
317533 ATATTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTTAAAATAT
Found at i:317585 original size:20 final size:19
Alignment explanation
Indices: 317560--317597 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
317550 AATAGACCAC
317560 TAAATATGTATATATATTTT
1 TAAATATGTAT-TATATTTT
*
317580 TAAATATTTATTATATTT
1 TAAATATGTATTATATTT
317598 AATACTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TAAATATGTATTATATTTT
Found at i:317640 original size:20 final size:20
Alignment explanation
Indices: 317577--317640 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
317567 GTATATATAT
*
317577 TTTTAAATATTTA-TT-ATA
1 TTTTAATTATTTATTTAATA
* *
317595 -TTTAA-TACTTATATAATA
1 TTTTAATTATTTATTTAATA
**
317613 TTAAAATTATTTATTTAATA
1 TTTTAATTATTTATTTAATA
317633 TTTTAATT
1 TTTTAATT
317641 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 3 0.09
19 3 0.09
20 17 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATTATTTATTTAATA
Found at i:318512 original size:23 final size:23
Alignment explanation
Indices: 318486--318589 Score: 77
Period size: 23 Copynumber: 4.3 Consensus size: 23
318476 AATCAACAAG
318486 AATATAATTAAAAAATAATAATA
1 AATATAATTAAAAAATAATAATA
* *** *
318509 AATATTAA-CAAATTTTAATAATT
1 AATA-TAATTAAAAAATAATAATA
*
318532 AATATAATAAAAAAATAATTAAAATAA
1 AATATAATTAAAAAATAA-T--AAT-A
*
318559 AATATAATATAAAAAATAAT-ACA
1 AATATAAT-TAAAAAATAATAATA
318582 AATATAAT
1 AATATAAT
318590 ATGAATACAT
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
22 3 0.05
23 33 0.53
24 5 0.08
26 3 0.05
27 9 0.15
28 9 0.15
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATAATTAAAAAATAATAATA
Found at i:318553 original size:27 final size:28
Alignment explanation
Indices: 318532--318596 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
318522 TTTAATAATT
318532 AATATAATA-AAAAAATAATTAAAATAA
1 AATATAATATAAAAAATAATTAAAATAA
*
318559 AATATAATATAAAAAATAA-TACAAATAT
1 AATATAATATAAAAAATAATTA-AAATAA
318587 AATATGAATA
1 AATAT-AATA
318597 CATAAATATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.32
28 19 0.56
29 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (28 bp):
AATATAATATAAAAAATAATTAAAATAA
Found at i:318560 original size:16 final size:17
Alignment explanation
Indices: 318531--318572 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
318521 TTTTAATAAT
*
318531 TAATATAATA-AAAAAA
1 TAATATAAAATAAAAAA
*
318547 TAAT-TAAAATAAAATA
1 TAATATAAAATAAAAAA
318563 TAATATAAAA
1 TAATATAAAA
318573 AATAATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAATATAAAATAAAAAA
Found at i:322546 original size:11 final size:11
Alignment explanation
Indices: 322532--322557 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
322522 TGTCTGTTCA
322532 ATTTTTTATTT
1 ATTTTTTATTT
322543 ATTTTTTATTT
1 ATTTTTTATTT
322554 ATTT
1 ATTT
322558 GGAAGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:324242 original size:19 final size:20
Alignment explanation
Indices: 324213--324250 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
324203 TAAAATAAAA
324213 TATTAAATTAATATTAATTT
1 TATTAAATTAATATTAATTT
324233 TATT-AATTAATATTAATT
1 TATTAAATTAATATTAATT
324251 GATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAAATTAATATTAATTT
Found at i:324257 original size:53 final size:50
Alignment explanation
Indices: 324180--324279 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 50
324170 ACAGCGGTTA
* * * *
324180 TATTTATTAGTATTTATTGGTTTTAAAATAAAATATTAAATTAATATTAATTT
1 TATTAATTAATATTAATTGATTTTAAAATAAAATA--AAATT-ATATTAATTT
324233 TATTAATTAATATTAATTGATTTTAAAATAAAATAAAATTATATTAA
1 TATTAATTAATATTAATTGATTTTAAAATAAAATAAAATTATATTAA
324280 CATTAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 7 0.16
51 5 0.12
53 31 0.72
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (50 bp):
TATTAATTAATATTAATTGATTTTAAAATAAAATAAAATTATATTAATTT
Found at i:324258 original size:10 final size:10
Alignment explanation
Indices: 324211--324250 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
324201 TTTAAAATAA
324211 AATATTAAATT
1 AATATT-AATT
324222 AATATTAATT
1 AATATTAATT
*
324232 -TTATTAATT
1 AATATTAATT
324241 AATATTAATT
1 AATATTAATT
324251 GATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 12 0.46
11 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATTAATT
Found at i:327888 original size:21 final size:17
Alignment explanation
Indices: 327862--327904 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 17
327852 AAACTGTTAT
327862 TAATATTTATTATTATTTAAA
1 TAATATTT-TTA--ATTT-AA
327883 TAATATTTTTAATTTAA
1 TAATATTTTTAATTTAA
327900 TAATA
1 TAATA
327905 ATTCATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
20 3 0.14
21 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATTTTTAATTTAA
Found at i:329559 original size:19 final size:18
Alignment explanation
Indices: 329537--329582 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
329527 TTAAAGTTTG
*
329537 TATTTTAAATGAATCTAAT
1 TATTTTAAATAAAT-TAAT
*
329556 TATTTTAAATAAATTTAT
1 TATTTTAAATAAATTAAT
329574 T-TTTTAAAT
1 TATTTTAAAT
329583 TTAATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTTTAAATAAATTAAT
Found at i:329594 original size:19 final size:17
Alignment explanation
Indices: 329539--329596 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
329529 AAAGTTTGTA
* *
329539 TTTTAAATGAATCTAATT
1 TTTTAAATAAAT-TTATT
329557 ATTTTAAATAAATTTATT
1 -TTTTAAATAAATTTATT
*
329575 TTTTAAATTTAATATTATT
1 TTTTAAA-TAAAT-TTATT
329594 TTT
1 TTT
329597 CAATTTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 19 0.56
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTAAATAAATTTATT
Found at i:330846 original size:16 final size:16
Alignment explanation
Indices: 330825--330906 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
330815 ATTTCGAATG
330825 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
* * *
330841 ATTTTAAAGTTGAATC
1 ATTTTAAATTTAAATT
330857 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
* * *
330873 TTTTTAGATATAAATT
1 ATTTTAAATTTAAATT
*
330889 GA--TTAATTTTAAATT
1 -ATTTTAAATTTAAATT
330904 ATT
1 ATT
330907 AATTTTTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
16 39 0.78
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:330902 original size:37 final size:36
Alignment explanation
Indices: 330825--330962 Score: 108
Period size: 37 Copynumber: 3.9 Consensus size: 36
330815 ATTTCGAATG
* * * *
330825 ATTTTAAATTTAAATTATTTT-A--AAGTTGAA-TC
1 ATTTTAAATTTAAATTTTTTTAATTAAATTAAATTA
*
330857 ATTTTAAATTTAAATTTTTTTAGATATAAATT-GATTA
1 ATTTTAAATTTAAATTTTTTTA-AT-TAAATTAAATTA
* *
330894 ATTTTAAATTATTAATTTTTTTACTTAAATTAAATTA
1 ATTTTAAATT-TAAATTTTTTTAATTAAATTAAATTA
* * *
330931 AATTTAAATTTAAA-TATATTAATTAAAATTAA
1 ATTTTAAATTTAAATTTTTTTAATT-AAATTAA
330963 TATATATAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
32 20 0.24
34 1 0.01
35 7 0.08
36 17 0.20
37 29 0.34
38 11 0.13
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (36 bp):
ATTTTAAATTTAAATTTTTTTAATTAAATTAAATTA
Found at i:330913 original size:15 final size:15
Alignment explanation
Indices: 330883--330912 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
330873 TTTTTAGATA
330883 TAAATTGATTAATTT
1 TAAATTGATTAATTT
330898 TAAATT-ATTAATTT
1 TAAATTGATTAATTT
330912 T
1 T
330913 TTTACTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TAAATTGATTAATTT
Found at i:330954 original size:20 final size:20
Alignment explanation
Indices: 330920--330976 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
330910 TTTTTTACTT
330920 AAATTAA-AT-TA-AATTTA
1 AAATTAATATATATAATTTA
*
330937 AATTTAA-ATATATTAA-TTA
1 AAATTAATATATA-TAATTTA
330956 AAATTAATATATATAATTTA
1 AAATTAATATATATAATTTA
330976 A
1 A
330977 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 8 0.24
18 2 0.06
19 12 0.36
20 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTAATATATATAATTTA
Found at i:334062 original size:21 final size:21
Alignment explanation
Indices: 334033--334077 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
334023 AACTTTAAGC
*
334033 ATGAGTTTATTTAAATATGTA
1 ATGAATTTATTTAAATATGTA
334054 ATGAATTTATTTAAATATGTA
1 ATGAATTTATTTAAATATGTA
334075 ATG
1 ATG
334078 TAACACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (21 bp):
ATGAATTTATTTAAATATGTA
Found at i:341652 original size:28 final size:27
Alignment explanation
Indices: 341587--341653 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
341577 TAATATTTAA
* *
341587 AATTTAAAATTTGATTTAATTAATTTAT
1 AATTT-AAATTTGATTTAATAAATCTAT
* *
341615 ATAGTT-AATTTATATTTAATAAATCTAT
1 A-ATTTAAATTT-GATTTAATAAATCTAT
341643 AATTTAAATTT
1 AATTTAAATTT
341654 TAATATCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 8 0.26
28 20 0.65
29 3 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (27 bp):
AATTTAAATTTGATTTAATAAATCTAT
Found at i:341663 original size:21 final size:21
Alignment explanation
Indices: 341620--341666 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
341610 TTTATATAGT
*
341620 TAATTTATATTTAATAAATCTA
1 TAATTTAAATTTAAT-AATCTA
341642 TAATTTAAATTTTAAT-ATCTA
1 TAATTTAAA-TTTAATAATCTA
341663 TAAT
1 TAAT
341667 CTTTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 8 0.35
23 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTAAATTTAATAATCTA
Done.