Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold95
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: 582947
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:191287 original size:15 final size:15
Alignment explanation
Indices: 191269--191298 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
191259 TAAACCTTAA
191269 AAATTTAAAAAAATT
1 AAATTTAAAAAAATT
191284 AAATTTAAAAAAATT
1 AAATTTAAAAAAATT
191299 TCAAACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTAAAAAAATT
Found at i:192079 original size:21 final size:20
Alignment explanation
Indices: 192046--192084 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
192036 TTATGGATGT
192046 ATTTTAAAATTTTTACTTTTA
1 ATTTTAAAATTTTT-CTTTTA
* *
192067 ATTTTGAACTTTTTCTTT
1 ATTTTAAAATTTTTCTTT
192085 CATTCCACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTTAAAATTTTTCTTTTA
Found at i:194283 original size:21 final size:22
Alignment explanation
Indices: 194241--194283 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
194231 TTAAATTAAT
* *
194241 TTTTTTGTCTTAATCATTTTTA
1 TTTTTTGTCATAATCATATTTA
*
194263 TTTTTT-TCATAATTATATTTA
1 TTTTTTGTCATAATCATATTTA
194284 AGAATAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTGTCATAATCATATTTA
Found at i:194856 original size:19 final size:18
Alignment explanation
Indices: 194832--194867 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
194822 TGGACCCAAA
194832 TAAAAATAAAATTAAAAAT
1 TAAAAATAAAA-TAAAAAT
*
194851 TAAAAATATAATAAAAA
1 TAAAAATAAAATAAAAA
194868 GCAGCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAATAAAATAAAAAT
Found at i:198026 original size:23 final size:24
Alignment explanation
Indices: 197989--198042 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
197979 CTCATATCAT
* * *
197989 TTATTTGAATATATTTTTTATTAAA
1 TTATTTG-TTATATTTTATATAAAA
198014 -TATTTGTTATATTTTATATAAAA
1 TTATTTGTTATATTTTATATAAAA
198037 TTATTT
1 TTATTT
198043 ACTTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTATTTGTTATATTTTATATAAAA
Found at i:198899 original size:2 final size:2
Alignment explanation
Indices: 198892--198919 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
198882 GGCCATTTAC
198892 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
198920 TTGTTTTTAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:200907 original size:2 final size:2
Alignment explanation
Indices: 200900--200942 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
200890 TATTTAAAAC
200900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
200942 T
1 T
200943 TTCAAAGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:203856 original size:2 final size:2
Alignment explanation
Indices: 203849--203876 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
203839 AAATAAAATA
203849 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
203877 TCAACCATTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204351 original size:30 final size:30
Alignment explanation
Indices: 204298--204374 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
204288 TGACCTTTAA
* * *
204298 TTATATTTATTTTGTATTCAAATAAGTTTT
1 TTATATTTAATTTATATTCAAATAAATTTT
* *
204328 TTATTTTTAATTTATATTTAAATAAATTTT
1 TTATATTTAATTTATATTCAAATAAATTTT
**
204358 TTACCTTTAATTTATAT
1 TTATATTTAATTTATAT
204375 CCATATAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (30 bp):
TTATATTTAATTTATATTCAAATAAATTTT
Found at i:204443 original size:30 final size:29
Alignment explanation
Indices: 204333--204448 Score: 83
Period size: 30 Copynumber: 3.9 Consensus size: 29
204323 GTTTTTTATT
* * *
204333 TTTAATTTATATTTAAATAA-ATTTTTTACC
1 TTTAATTTATATCTAAATAAGA--CTTTAAC
* * *
204363 TTTAATTTATATCCATATAAGTCTTTAAC
1 TTTAATTTATATCTAAATAAGACTTTAAC
* *
204392 GTTTAATTTACA-CTAACATAAGACATTAATC
1 -TTTAATTTATATCTAA-ATAAGACTTTAA-C
*
204423 TTTAATTTATATTTAAATAAGTACTT
1 TTTAATTTATATCTAAATAAG-ACTT
204449 AGTATAAATC
Statistics
Matches: 66, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
29 7 0.11
30 52 0.79
31 7 0.11
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAATTTATATCTAAATAAGACTTTAAC
Found at i:206362 original size:22 final size:23
Alignment explanation
Indices: 206307--206364 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
206297 TTGAAATTGA
*
206307 AATTAAAATTTTATTTTTATTTT
1 AATTAAAATTTTATTTTTATTAT
* *
206330 TATTAATATTTCTA-TTTT-TTAT
1 AATTAAAATTT-TATTTTTATTAT
206352 AATTAAAATTTTA
1 AATTAAAATTTTA
206365 AAAATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.07
22 12 0.41
23 13 0.45
24 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTAAAATTTTATTTTTATTAT
Found at i:206610 original size:15 final size:15
Alignment explanation
Indices: 206590--206635 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
206580 ATTATAAAAA
206590 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
*
206605 TAATTTAAATCAAA-
1 TAATTTAAATTAAAT
*
206619 TAATTAAAATTTAAAT
1 TAATTTAAA-TTAAAT
206635 T
1 T
206636 TAAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 8 0.31
15 17 0.65
16 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:207602 original size:16 final size:17
Alignment explanation
Indices: 207562--207610 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
207552 TATTTAAGAT
* *
207562 ATTTTATATTTATATTA
1 ATTTTATATATATAGTA
207579 ATTTT-TATATATTAGTA
1 ATTTTATATATA-TAGTA
207596 ATTTTATATTATATA
1 ATTTTATA-TATATA
207611 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 14 0.52
18 4 0.15
19 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTATATATATAGTA
Found at i:207614 original size:16 final size:16
Alignment explanation
Indices: 207562--207617 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
207552 TATTTAAGAT
*
207562 ATTTTATATTTATATTA
1 ATTTTATA-TTATATAA
207579 ATTTT-TA-TATATTAGTA
1 ATTTTATATTATA-TA--A
207596 ATTTTATATTATATAA
1 ATTTTATATTATATAA
207612 ATTTTA
1 ATTTTA
207618 AAATATGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 9 0.27
17 11 0.33
18 4 0.12
19 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:208086 original size:36 final size:32
Alignment explanation
Indices: 208052--208113 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
208042 ATTATTTTTC
208052 TTTTAA-AAAAGAATATTCATTTATTAATAAT
1 TTTTAATAAAAGAATATTCATTTATTAATAAT
208083 TTTTAATAAAAGAATATTCATTTATTAATAA
1 TTTTAATAAAAGAATATTCATTTATTAATAA
208114 ACAATCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (32 bp):
TTTTAATAAAAGAATATTCATTTATTAATAAT
Found at i:208390 original size:32 final size:33
Alignment explanation
Indices: 208354--208424 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
208344 ATATTATAAT
** *
208354 TTATATATTTTTTAATAAATTAATA-ATTTATA
1 TTATATAAATTTTAACAAATTAATATATTTATA
* *
208386 TTATATAAATTTTAACATATTAATATATTTATC
1 TTATATAAATTTTAACAAATTAATATATTTATA
208419 TTATAT
1 TTATAT
208425 TTATATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (33 bp):
TTATATAAATTTTAACAAATTAATATATTTATA
Found at i:208424 original size:19 final size:17
Alignment explanation
Indices: 208402--208458 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 17
208392 AAATTTTAAC
208402 ATATTAATATATTTATCTT
1 ATATTAATATATTT-T-TT
*
208421 ATATTTATATTATTTTTT
1 ATATTAATA-TATTTTTT
208439 ATATCATAATATATTTTTT
1 ATAT--TAATATATTTTTT
208458 A
1 A
208459 ACGGATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 6 0.18
19 18 0.55
20 9 0.27
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTAATATATTTTTT
Found at i:208736 original size:19 final size:19
Alignment explanation
Indices: 208714--208767 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
208704 AAAAATTTTT
* *
208714 TAATTAATTATATATTATA
1 TAATTAATTATAAATTAAA
208733 TAATTAAATT-TAAATTAAA
1 TAATT-AATTATAAATTAAA
*
208752 AAATTAATTAATAAAT
1 TAATTAATT-ATAAAT
208768 AGTTATCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 16 0.55
20 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTAATTATAAATTAAA
Found at i:209516 original size:14 final size:14
Alignment explanation
Indices: 209499--209543 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
209489 TTTAAAAAAA
*
209499 TATATTTTAATATT
1 TATATTTAAATATT
209513 TATATTTAAATATAT
1 TATATTTAAATAT-T
* *
209528 CATATATAAATATT
1 TATATTTAAATATT
209542 TA
1 TA
209544 ATATAAGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATTTAAATATT
Found at i:209547 original size:15 final size:14
Alignment explanation
Indices: 209507--209555 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
209497 AATATATTTT
*
209507 AATATTTATATTTA
1 AATATTTATATATA
*
209521 AATATATCATATATA
1 AATAT-TTATATATA
209536 AATATTTA-ATATA
1 AATATTTATATATA
*
209549 AGTATTT
1 AATATTT
209556 TCAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 7 0.23
15 12 0.40
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
AATATTTATATATA
Found at i:211286 original size:23 final size:22
Alignment explanation
Indices: 211247--211292 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
211237 AAAAATTAAA
*
211247 ATATTATTTTTATATTAATATTT
1 ATATTATTTTTAAATTAA-ATTT
211270 ATATT-TTTTTAAAATTAAATTT
1 ATATTATTTTT-AAATTAAATTT
211292 A
1 A
211293 AATAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATTTTTAAATTAAATTT
Found at i:212798 original size:23 final size:25
Alignment explanation
Indices: 212763--212817 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
212753 AGCACGAAAA
212763 ATAAT-TACAGTATAATATAAAT-T
1 ATAATATACAGTATAATATAAATAT
* *
212786 ATAATATA-AGTATGATATGAATAT
1 ATAATATACAGTATAATATAAATAT
212810 ATGAATAT
1 AT-AATAT
212818 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 17 0.63
24 5 0.19
25 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (25 bp):
ATAATATACAGTATAATATAAATAT
Found at i:213100 original size:9 final size:9
Alignment explanation
Indices: 213086--213110 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
213076 TTTTTTAAAT
213086 ATTTAAAAA
1 ATTTAAAAA
213095 ATTTAAAAA
1 ATTTAAAAA
213104 ATTTAAA
1 ATTTAAA
213111 TTAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:213174 original size:20 final size:20
Alignment explanation
Indices: 213133--213170 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
213123 TAAATTTTAT
213133 TTAATATTAATTATAAAATA
1 TTAATATTAATTATAAAATA
213153 TTAATATTAA-TATAAAAT
1 TTAATATTAATTATAAAAT
213171 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATATTAATTATAAAATA
Found at i:213588 original size:22 final size:22
Alignment explanation
Indices: 213563--213607 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
213553 TCATTATTAT
* * *
213563 ATATACACATTTTAATTTAAAA
1 ATATACAAATATTAATATAAAA
*
213585 ATATATAAATATTAATATAAAA
1 ATATACAAATATTAATATAAAA
213607 A
1 A
213608 ATATTTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATACAAATATTAATATAAAA
Found at i:213852 original size:21 final size:19
Alignment explanation
Indices: 213823--213863 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
213813 TAATATTATT
*
213823 TAAATTTAATTTAAAATATA
1 TAAATTTAATATAAAA-ATA
213843 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
213863 T
1 T
213864 TTAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:215676 original size:30 final size:29
Alignment explanation
Indices: 215640--215739 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 29
215630 ATATTAAGGA
215640 TTTATTTAAAAATAAATTAAAGTTTAAAAG
1 TTTATTTAAAAATAAATTAAA-TTTAAAAG
* * *
215670 TTTATTTAAGTACT-AATTAAAAATTAAAAG
1 TTTATTTAA-AAATAAATT-AAATTTAAAAG
* * *
215700 TTTATTTGAGAGTAAATTAAATATTAAAAG
1 TTTATTTAAAAATAAATTAAAT-TTAAAAG
*
215730 ATTATTTAAA
1 TTTATTTAAA
215740 TATCATAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
29 5 0.09
30 46 0.82
31 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTATTTAAAAATAAATTAAATTTAAAAG
Found at i:215778 original size:30 final size:30
Alignment explanation
Indices: 215718--215779 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
215708 AGAGTAAATT
* * *
215718 AAATATTAAAAGATTATTTAAATATCATAA
1 AAATATTAAAAAATTATTAAAAAATCATAA
*
215748 AAATA-TAAAAAATTAATTAAAAAATTATAA
1 AAATATTAAAAAATT-ATTAAAAAATCATAA
215778 AA
1 AA
215780 TTTAATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATATTAAAAAATTATTAAAAAATCATAA
Found at i:215779 original size:20 final size:22
Alignment explanation
Indices: 215746--215787 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
215736 TAAATATCAT
215746 AAAAATATAAAAAA-TTAATTA
1 AAAAATATAAAAAATTTAATTA
*
215767 AAAAAT-TATAAAATTTAATTA
1 AAAAATATAAAAAATTTAATTA
215788 CTTTTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATATAAAAAATTTAATTA
Found at i:216159 original size:2 final size:2
Alignment explanation
Indices: 216152--216176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
216142 TAATATTACT
216152 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
216177 GAAGATCCAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:216564 original size:2 final size:2
Alignment explanation
Indices: 216557--216603 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
216547 TAAATCTCTT
216557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
216599 TA TA T
1 TA TA T
216604 GGATGGCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:218623 original size:21 final size:21
Alignment explanation
Indices: 218597--218646 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
218587 ATCGAATTTG
218597 TTGTTCAAGATTTTCATACTA
1 TTGTTCAAGATTTTCATACTA
*
218618 TTGTTCAAGATTTTCATATTA
1 TTGTTCAAGATTTTCATACTA
218639 TTGTTCAA
1 TTGTTCAA
218647 AAATGTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
TTGTTCAAGATTTTCATACTA
Found at i:221385 original size:4 final size:4
Alignment explanation
Indices: 221378--221441 Score: 92
Period size: 4 Copynumber: 16.0 Consensus size: 4
221368 ATATATATGT
* * * *
221378 ATAC ATAC ATTC ATAT GTAC ATAC ATAC CTAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
221426 ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC
221442 GGGTGTATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:222507 original size:20 final size:21
Alignment explanation
Indices: 222472--222511 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
222462 AACTCAAACC
*
222472 ATAAATATATAATTGAAAAAT
1 ATAAATATAGAATTGAAAAAT
222493 ATAAATAT-GAATTGAAAAA
1 ATAAATATAGAATTGAAAAA
222512 GGGATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAAATATAGAATTGAAAAAT
Found at i:230256 original size:6 final size:6
Alignment explanation
Indices: 230245--230275 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
230235 TTTAAGGTAT
230245 TTTATA TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA T
230276 AATTTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:230597 original size:14 final size:14
Alignment explanation
Indices: 230576--230610 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
230566 TATCATATTT
230576 TAATTA-TTTTATA
1 TAATTATTTTTATA
230589 TATATTATTTTTATA
1 TA-ATTATTTTTATA
230604 TAATTAT
1 TAATTAT
230611 ATATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 9 0.45
15 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTATTTTTATA
Found at i:231001 original size:22 final size:22
Alignment explanation
Indices: 230970--231115 Score: 75
Period size: 22 Copynumber: 6.4 Consensus size: 22
230960 GTATTGATAT
230970 TTTTTATATTTATATTATATTTA
1 TTTTT-TATTTATATTATATTTA
* *
230993 TTTTTTATTAAAATTATATTTA
1 TTTTTTATTTATATTATATTTA
**
231015 AATTTTA--TATATTAATAATTTA
1 TTTTTTATTTATATT-AT-ATTTA
* *
231037 TATTATATAAATTT-TAATATATTTA
1 T-TT-T-T-TATTTATATTATATTTA
* * *
231062 TATATTTATGTTATATTAAAATTA
1 T-TTTTTAT-TTATATTATATTTA
* *
231086 -TTTTTATATTATATTTTAATTA
1 TTTTTTAT-TTATATTATATTTA
231108 TTTTTTAT
1 TTTTTTAT
231116 ATAATATATC
Statistics
Matches: 93, Mismatches: 19, Indels: 22
0.69 0.14 0.16
Matches are distributed among these distances:
20 4 0.04
21 2 0.02
22 45 0.48
23 16 0.17
24 10 0.11
25 9 0.10
26 3 0.03
27 3 0.03
28 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
TTTTTTATTTATATTATATTTA
Found at i:231042 original size:33 final size:35
Alignment explanation
Indices: 231005--231108 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 35
230995 TTTTATTAAA
231005 ATTATATTTAAATTTT-ATATATTAATA-ATTTAT
1 ATTATATTTAAATTTTAATATATTAATATATTTAT
*
231038 ATTATA--TAAATTTTAATATATTTATATATTTAT
1 ATTATATTTAAATTTTAATATATTAATATATTTAT
* * **
231071 GTTATATTAAAATTATTTTTATATT-ATAT-TTTA-
1 ATTATATTTAAATT-TTAATATATTAATATATTTAT
231104 ATTAT
1 ATTAT
231109 TTTTTATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
31 8 0.13
32 10 0.17
33 21 0.35
34 4 0.07
35 9 0.15
36 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
ATTATATTTAAATTTTAATATATTAATATATTTAT
Found at i:231116 original size:23 final size:22
Alignment explanation
Indices: 231066--231122 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
231056 TATTTATATA
*
231066 TTTATGTTATATTAAAATTATT
1 TTTATATTATATTAAAATTATT
**
231088 TTTATATTATATTTTAATTATTT
1 TTTATATTATATTAAAATTA-TT
*
231111 TTTATATAATAT
1 TTTATATTATAT
231123 ATCTTCACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATATTATATTAAAATTATT
Found at i:233875 original size:2 final size:2
Alignment explanation
Indices: 233868--233895 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
233858 TAAGTATTAG
233868 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
233896 CTAACATGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238543 original size:12 final size:12
Alignment explanation
Indices: 238522--238555 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
238512 AAAATTGGAA
*
238522 CTTTCCCTCTCT
1 CTTTCTCTCTCT
238534 CTTTCTCTCTCT
1 CTTTCTCTCTCT
*
238546 CTCTCTCTCT
1 CTTTCTCTCT
238556 TTCAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (12 bp):
CTTTCTCTCTCT
Found at i:238820 original size:17 final size:18
Alignment explanation
Indices: 238798--238831 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
238788 TTATTTAAAT
238798 ATTTAAAAAAT-ATTTTA
1 ATTTAAAAAATAATTTTA
*
238815 ATTTAAATAATAATTTT
1 ATTTAAAAAATAATTTT
238832 TACTATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAAAAATAATTTTA
Found at i:239768 original size:22 final size:21
Alignment explanation
Indices: 239743--239811 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
239733 AATAAAAAAT
239743 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAA-ATTTATA
* *
239765 TATTTTCATAATTAAATTTAAA
1 TATTTTTAT-ATTAAATTTATA
*
239787 TAATTTTT-TAATATACATTTATA
1 T-ATTTTTAT-AT-TAAATTTATA
239810 TA
1 TA
239812 AAAAGTAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTATATTAAATTTATA
Found at i:240143 original size:17 final size:16
Alignment explanation
Indices: 240102--240144 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
240092 AAATATAAAA
240102 ATAATAA-ATATATTT
1 ATAATAATATATATTT
*
240117 ATATTAAATATATATTT
1 ATAAT-AATATATATTT
240134 ATAAATAATAT
1 AT-AATAATAT
240145 TCACATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.17
16 2 0.09
17 15 0.65
18 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATAATATATATTT
Found at i:240696 original size:22 final size:20
Alignment explanation
Indices: 240666--240708 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
240656 AATATTTAAA
*
240666 ATATCTTTTTATATTAATATTT
1 ATATATTTTTA-ATTAA-ATTT
240688 ATATATTTTTAATTAAATTT
1 ATATATTTTTAATTAAATTT
240708 A
1 A
240709 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTTTAATTAAATTT
Found at i:241491 original size:16 final size:16
Alignment explanation
Indices: 241472--241521 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
241462 GAGATTATAT
241472 ATTTATATAAATTTTG
1 ATTTATATAAATTTTG
* *
241488 ATTTAT-TAATAATTCG
1 ATTTATATAA-ATTTTG
241504 -TGTTATATAAATTTTG
1 AT-TTATATAAATTTTG
241520 AT
1 AT
241522 ATATTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (16 bp):
ATTTATATAAATTTTG
Found at i:242293 original size:2 final size:2
Alignment explanation
Indices: 242288--242333 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
242278 ACACACTAAG
*
242288 AT AT AT AT GT 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 AT AT AT AT
242330 AT AT
1 AT AT
242334 CCTTATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244077 original size:29 final size:28
Alignment explanation
Indices: 244045--244140 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 28
244035 ATAATTTATT
*
244045 TATTTATATTATATTTATATATTTTGTTA
1 TATTTATATTATATTTATATATTAT-TTA
*
244074 TA-TTATAATTATATTTA-A-AATATTTA
1 TATTTAT-ATTATATTTATATATTATTTA
* * *
244100 TATTTATATAATTATTAATATATTA-ATA
1 TATTTATATTA-TATTTATATATTATTTA
244128 -ATTTATATTATAT
1 TATTTATATTATAT
244141 ATTTATAAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
26 11 0.20
27 21 0.38
28 8 0.15
29 15 0.27
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TATTTATATTATATTTATATATTATTTA
Found at i:244421 original size:22 final size:23
Alignment explanation
Indices: 244396--244453 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
244386 ATACATACGA
244396 AAAAATAAT-TAAAATATAATA-T
1 AAAAATAATAT-AAATATAATATT
*
244418 AAAATTAATATAAATATAATATT
1 AAAAATAATATAAATATAATATT
244441 AATAAATAA-ATAA
1 AA-AAATAATATAA
244454 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 18 0.58
23 8 0.26
24 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAATAATATAAATATAATATT
Found at i:244438 original size:11 final size:11
Alignment explanation
Indices: 244407--244542 Score: 79
Period size: 11 Copynumber: 12.5 Consensus size: 11
244397 AAAATAATTA
244407 AAATATAATAT
1 AAATATAATAT
244418 AAA-ATTAATAT
1 AAATA-TAATAT
244429 AAATATAATAT
1 AAATATAATAT
* *
244440 TAATA-AATAA
1 AAATATAATAT
* *
244450 ATAATTTAAAAT
1 A-AATATAATAT
**
244462 TTATATAATAT
1 AAATATAATAT
*
244473 AAAT-TATTTAT
1 AAATATA-ATAT
* * *
244484 ATATTAAAATTT
1 A-AATATAATAT
244496 AAATA-AATAT
1 AAATATAATAT
*
244506 AAA-ATAATTT
1 AAATATAATAT
244516 AAATATAAT-T
1 AAATATAATAT
244526 ATAATATAATA-
1 A-AATATAATAT
244537 AAATAT
1 AAATAT
244543 TTAAATACAA
Statistics
Matches: 94, Mismatches: 20, Indels: 23
0.69 0.15 0.17
Matches are distributed among these distances:
9 1 0.01
10 28 0.30
11 55 0.59
12 9 0.10
13 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATAATAT
Found at i:244443 original size:6 final size:5
Alignment explanation
Indices: 244408--244542 Score: 57
Period size: 5 Copynumber: 27.0 Consensus size: 5
244398 AAATAATTAA
* * *
244408 AATAT AATAT AAAATT AATAT AAATAT AATAT TA-AT AA-AT AA-AT AATTT
1 AATAT AATAT AATA-T AATAT -AATAT AATAT AATAT AATAT AATAT AATAT
* * * * * * *
244457 AAAATT TATAT AATAT AA-AT TAT-T TATAT ATTAA AATTT AA-AT AAATAT
1 AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT
* * *
244506 AAAAT AATTT AAATAT AATTAT AATAT AATAA AATAT
1 AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
244543 TTAAATACAA
Statistics
Matches: 96, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
4 19 0.20
5 54 0.56
6 23 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:244505 original size:20 final size:20
Alignment explanation
Indices: 244491--244535 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
244481 TATATATTAA
244491 AATTTAAATAAATATAAAAT
1 AATTTAAATAAATATAAAAT
*
244511 AATTTAAATATAATTATAATAT
1 AATTTAAATA-AA-TATAAAAT
244533 AAT
1 AAT
244536 AAAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTAAATAAATATAAAAT
Found at i:244947 original size:3 final size:3
Alignment explanation
Indices: 244939--244981 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
244929 CTTTAGTATG
244939 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
244982 GCCTTGTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:245138 original size:24 final size:24
Alignment explanation
Indices: 245111--245156 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
245101 TTTAATTAAT
245111 AATTT-TTATTTAAATTTATTTTTA
1 AATTTATT-TTTAAATTTATTTTTA
245135 AATTTATTTTTAAATTTATTTT
1 AATTTATTTTTAAATTTATTTT
245157 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
AATTTATTTTTAAATTTATTTTTA
Found at i:245159 original size:11 final size:12
Alignment explanation
Indices: 245119--245156 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
245109 ATAATTTTTA
245119 TTTAAATTTATT
1 TTTAAATTTATT
245131 TTTAAATTTATT
1 TTTAAATTTATT
245143 TTTAAATTTATT
1 TTTAAATTTATT
245155 TT
1 TT
245157 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:248224 original size:6 final size:6
Alignment explanation
Indices: 248184--248209 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
248174 TGAAGTTTCA
248184 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
248210 AGTATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:248456 original size:44 final size:44
Alignment explanation
Indices: 248393--248480 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
248383 TCTCTCTCTC
248393 TCTTTTAATTCAATATGAAAACAAATTGCAAGAGGAAAAAATAT
1 TCTTTTAATTCAATATGAAAACAAATTGCAAGAGGAAAAAATAT
248437 TCTTTTAATTCAATATGAAAACAAATTGCAAGAGGAAAAAATAT
1 TCTTTTAATTCAATATGAAAACAAATTGCAAGAGGAAAAAATAT
248481 ATATATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (44 bp):
TCTTTTAATTCAATATGAAAACAAATTGCAAGAGGAAAAAATAT
Found at i:249699 original size:22 final size:22
Alignment explanation
Indices: 249671--249726 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
249661 CATCAAAAAC
*
249671 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTAAA
249693 TATTTTTATAATTAAATTTAAA
1 TATTTTTATAATTAAATTTAAA
249715 TAATTTTT-TAAT
1 T-ATTTTTATAAT
249727 ATAGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTAAA
Found at i:250703 original size:18 final size:21
Alignment explanation
Indices: 250682--250727 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
250672 ATTTAAATAC
250682 TTAAA-ATAT-TATTTTTT-A
1 TTAAATATATATATTTTTTAA
*
250700 TTAATATTTATATATTTTTTAA
1 TTAA-ATATATATATTTTTTAA
250722 TTAAAT
1 TTAAAT
250728 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 1 0.04
20 3 0.13
21 10 0.43
22 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATATATATATTTTTTAA
Found at i:250715 original size:21 final size:21
Alignment explanation
Indices: 250691--250730 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
250681 CTTAAAATAT
250691 TATTTTTT-ATTAATATTTATA
1 TATTTTTTAATTAA-ATTTATA
250712 TATTTTTTAATTAAATTTA
1 TATTTTTTAATTAAATTTA
250731 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTTTAATTAAATTTATA
Found at i:251501 original size:25 final size:25
Alignment explanation
Indices: 251476--251524 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
251466 ATTATGATAT
*
251476 ATTTATATATCTATATCGTATTTATA
1 ATTT-TATATCTATATCATATTTATA
* *
251502 ATTTTTTATTTATATCATATTTA
1 ATTTTATATCTATATCATATTTA
251525 CGTGAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTTATATCTATATCATATTTATA
Found at i:252448 original size:29 final size:29
Alignment explanation
Indices: 252373--252449 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
252363 AAATAAAACT
* *
252373 TTAAAATTAAAAAAATTTATTAAAATCATA
1 TTAAAATTTAAAATA-TTATTAAAATCATA
** *
252403 TTAAAATTTAATTTATTATTAATAATCGTA
1 TTAAAATTTAAAATATTATTAA-AATCATA
*
252433 TTCAAA-TTAAAATATTA
1 TTAAAATTTAAAATATTA
252450 ATATGATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (29 bp):
TTAAAATTTAAAATATTATTAAAATCATA
Found at i:253755 original size:2 final size:2
Alignment explanation
Indices: 253750--253813 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
253740 AATTATTTTT
* * *
253750 TA TA TA T- TA TA TT TA TA TA -A T- TA TA TT TA -A AA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
253786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
253814 AAGGTTGTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
1 6 0.12
2 45 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:253758 original size:14 final size:15
Alignment explanation
Indices: 253739--253814 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 15
253729 TAAACATATT
*
253739 TAATTATTTTTTATA
1 TAATTATTATTTATA
253754 T-ATTA-TATTTATA
1 TAATTATTATTTATA
253767 TAATTA-TATTTA-A
1 TAATTATTATTTATA
*
253780 -AATTATTATATATA
1 TAATTATTATTTATA
*
253794 TATATATATATATATATA
1 TA-AT-TAT-TATTTATA
253812 TAA
1 TAA
253815 AGGTTGTACC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.10
13 14 0.27
14 15 0.29
15 2 0.04
16 2 0.04
17 4 0.08
18 10 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTATTTATA
Found at i:253785 original size:12 final size:14
Alignment explanation
Indices: 253739--253814 Score: 64
Period size: 15 Copynumber: 5.2 Consensus size: 14
253729 TAAACATATT
*
253739 TAATTAT-TTTTTA
1 TAATTATATTTATA
253752 TATATTATATTTATA
1 TA-ATTATATTTATA
*
253767 TAATTATATTTAAAA
1 TAATTATATTT-ATA
* *
253782 TTATTATATATATA
1 TAATTATATTTATA
*
253796 TATATATATATATATA
1 TA-AT-TATATTTATA
253812 TAA
1 TAA
253815 AGGTTGTACC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.04
14 17 0.33
15 21 0.40
16 12 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:254027 original size:21 final size:20
Alignment explanation
Indices: 254002--254119 Score: 85
Period size: 22 Copynumber: 5.5 Consensus size: 20
253992 GTCAACATAT
254002 TATAATATGAAAAAAATAAAA
1 TATAATAT-AAAAAAATAAAA
*
254023 TATAATATAAAATTAATATAAA
1 TATAATATAAAA-AAATA-AAA
* *
254045 TATAATATTAATAAAT-AAA
1 TATAATATAAAAAAATAAAA
* ** *
254064 TATAAAATAATTTAAATATAAT
1 TATAATATAA-AAAAATA-AAA
*
254086 TATAATATAATAAAATATTTAAA
1 TATAATATAA-AAAA-A-TAAAA
254109 TATAATATAAA
1 TATAATATAAA
254120 TATATAAATA
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
19 11 0.14
20 9 0.12
21 15 0.19
22 28 0.36
23 13 0.17
24 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
TATAATATAAAAAAATAAAA
Found at i:254041 original size:11 final size:12
Alignment explanation
Indices: 254017--254126 Score: 75
Period size: 11 Copynumber: 9.9 Consensus size: 12
254007 TATGAAAAAA
254017 ATAAAATATAAT
1 ATAAAATATAAT
254029 ATAAAAT-TAAT
1 ATAAAATATAAT
254040 AT-AAATATAAT
1 ATAAAATATAAT
254051 ATTAATAA-ATAA-
1 A-TAA-AATATAAT
254063 ATATAAA-ATAAT
1 ATA-AAATATAAT
*
254075 -TTAAATATAAT
1 ATAAAATATAAT
*
254086 -TATAATAT-A-
1 ATAAAATATAAT
254095 ATAAAATAT--T
1 ATAAAATATAAT
254105 -T-AAATATAAT
1 ATAAAATATAAT
254115 ATAAATATATAA
1 ATAAA-ATATAA
254127 ATAGTTAAGT
Statistics
Matches: 80, Mismatches: 4, Indels: 27
0.72 0.04 0.24
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
10 16 0.20
11 32 0.40
12 12 0.15
13 11 0.14
14 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:254085 original size:35 final size:35
Alignment explanation
Indices: 254020--254129 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 35
254010 GAAAAAAATA
*
254020 AAATATAATATAAAATTAATATAAATATAATATTAAT
1 AAATA-AATATAAAA-TAATTTAAATATAATATTAAT
254057 AAATAAATATAAAATAATTTAAATAT-A-ATT-AT
1 AAATAAATATAAAATAATTTAAATATAATATTAAT
* *
254089 -AATATA-ATAAAAT-ATTTAAATATAATATAAAT
1 AAATAAATATAAAATAATTTAAATATAATATTAAT
*
254121 ATATAAATA
1 AAATAAATA
254130 GTTAAGTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
29 10 0.16
30 8 0.13
31 7 0.11
32 4 0.06
33 7 0.11
34 2 0.03
35 11 0.17
36 9 0.14
37 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (35 bp):
AAATAAATATAAAATAATTTAAATATAATATTAAT
Found at i:254096 original size:5 final size:5
Alignment explanation
Indices: 254002--254126 Score: 82
Period size: 5 Copynumber: 25.0 Consensus size: 5
253992 GTCAACATAT
* * * *
254002 TATAA TATGAA AAAAA TAAAA TATAA TATAA AATTAA TATAAA TATAA
1 TATAA TAT-AA TATAA TATAA TATAA TATAA TA-TAA TAT-AA TATAA
* *
254050 TATTAA TA-AA TA-AA TATAA AATAA TTTAAA TATAA TTATAA TATAA
1 TA-TAA TATAA TATAA TATAA TATAA TAT-AA TATAA -TATAA TATAA
* *
254096 TAAAA TAT-T TA-AA TATAA TATAA -AT-A TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
254127 ATAGTTAAGT
Statistics
Matches: 95, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
3 1 0.01
4 16 0.17
5 52 0.55
6 26 0.27
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:254121 original size:29 final size:29
Alignment explanation
Indices: 254020--254127 Score: 104
Period size: 29 Copynumber: 3.8 Consensus size: 29
254010 GAAAAAAATA
254020 AAATATAATATAAA-ATTAATATAAATA--T
1 AAATATAATATAAATA-TAATA-AAATATTT
* *
254048 -AATATTA-ATAAATAAATATAAAATAATTT
1 AAATATAATATAAATATA-ATAAAAT-ATTT
254077 AAATATAAT-TATAATATAATAAAATATTT
1 AAATATAATATA-AATATAATAAAATATTT
254106 AAATATAATATAAATAT-ATAAA
1 AAATATAATATAAATATAATAAA
254128 TAGTTAAGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
26 10 0.15
27 11 0.16
28 5 0.07
29 19 0.28
30 17 0.25
31 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATATAATATAAATATAATAAAATATTT
Found at i:254391 original size:3 final size:3
Alignment explanation
Indices: 254383--254415 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
254373 TAATCTACCC
254383 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
254416 GGAAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:254530 original size:3 final size:3
Alignment explanation
Indices: 254522--254558 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
254512 GTTTAGTATG
254522 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
254559 GCCTTGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:257613 original size:4 final size:4
Alignment explanation
Indices: 257604--257646 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
257594 TTACACTTCA
* *
257604 AAAT AAAT AAAT AGAT TAAT AAAT AAAT -AAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
257647 TTGTTCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:258303 original size:20 final size:20
Alignment explanation
Indices: 258280--258337 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
258270 TACAAGTATG
258280 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
258300 AATGTATTGATACATTCTTC
1 AATGTATCGATACATTCTTC
258320 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
258338 ATCTTTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:258352 original size:91 final size:89
Alignment explanation
Indices: 258185--258385 Score: 278
Period size: 91 Copynumber: 2.2 Consensus size: 89
258175 ATCACATTTT
* * * *
258185 TATTCAGATGTATCGATATATTTTTCAATGTATCGATACATGTAAATGTATCGATACATTTTATT
1 TATTCA-ATGTATCGATACATTCTTCAATGTATCGATACATGTAAATGTATCGATACATTCTATC
258250 TTTTTACCCAGATGTATCGATACAAG
65 TTTTTACCCAGATGTATCGATAC-AG
* * * *
258276 TA-TGAATGTATCGATACATTCTTCAATGTATTGATACATTCTTCAATGTATCGATACATTCTAT
1 TATTCAATGTATCGATACATTCTTCAATGTATCGATACA-T-GTAAATGTATCGATACATTCTAT
*
258340 CTTTTTACCCAGATGTATCGATACAT
64 CTTTTTACCCAGATGTATCGATACAG
258366 TATTCAATGTATCGATACAT
1 TATTCAATGTATCGATACAT
258386 CTAGTTAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
89 30 0.31
90 6 0.06
91 61 0.63
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (89 bp):
TATTCAATGTATCGATACATTCTTCAATGTATCGATACATGTAAATGTATCGATACATTCTATCT
TTTTACCCAGATGTATCGATACAG
Found at i:260032 original size:10 final size:11
Alignment explanation
Indices: 260017--260045 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
260007 ACAATAGATG
260017 ATTTTTCAAA-
1 ATTTTTCAAAC
260027 ATTTTTCAAAC
1 ATTTTTCAAAC
260038 ATTTTTCA
1 ATTTTTCA
260046 TTAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:270865 original size:21 final size:22
Alignment explanation
Indices: 270821--270867 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
270811 ATAATTATAA
*
270821 AAAATTATTTAAATTTAATCAT
1 AAAATTATATAAATTTAATCAT
270843 AAAA-TATATAAATATTAAT-AT
1 AAAATTATATAAAT-TTAATCAT
270864 AAAA
1 AAAA
270868 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTATATAAATTTAATCAT
Found at i:270868 original size:22 final size:22
Alignment explanation
Indices: 270820--270870 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
270810 AATAATTATA
*
270820 AAAAATTATTTAAATTTAATCAT
1 AAAAA-TATATAAATTTAATCAT
270843 -AAAATATATAAATATTAAT-AT
1 AAAAATATATAAAT-TTAATCAT
270864 AAAAATA
1 AAAAATA
270871 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATATATAAATTTAATCAT
Found at i:271437 original size:18 final size:18
Alignment explanation
Indices: 271416--271452 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
271406 GATACAATGC
271416 AAATATAACACATTTAAT
1 AAATATAACACATTTAAT
*
271434 AAATATAACACTTTTAAT
1 AAATATAACACATTTAAT
271452 A
1 A
271453 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATAACACATTTAAT
Found at i:271460 original size:9 final size:9
Alignment explanation
Indices: 271446--271479 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
271436 ATATAACACT
271446 TTTAATATA
1 TTTAATATA
271455 TTTAATATA
1 TTTAATATA
*
271464 TTATATTATA
1 TT-TAATATA
271474 TTTAAT
1 TTTAAT
271480 TTATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAATATA
Found at i:274614 original size:19 final size:18
Alignment explanation
Indices: 274592--274633 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
274582 AAATTTATTT
274592 AATTAATATAATATTTAAA
1 AATT-ATATAATATTTAAA
* *
274611 AATT-TTTATTATTTAAA
1 AATTATATAATATTTAAA
274628 AATTAT
1 AATTAT
274634 TTATTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.75
18 1 0.05
19 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTATATAATATTTAAA
Found at i:274625 original size:17 final size:18
Alignment explanation
Indices: 274603--274645 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
274593 ATTAATATAA
274603 TATTTAAAAATT-TTTAT
1 TATTTAAAAATTATTTAT
274620 TATTTAAAAATTATTTAT
1 TATTTAAAAATTATTTAT
*
274638 TAATTAAA
1 TATTTAAA
274646 TTTATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTAAAAATTATTTAT
Found at i:274690 original size:26 final size:25
Alignment explanation
Indices: 274643--274715 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
274633 TTTATTAATT
*
274643 AAATTT-ATATTTT-ATTTAATTAGTA
1 AAATTTAAAATTTTAATTTAATTA--A
*
274668 ATATTTAAAATTTTAATTT-ATTAA
1 AAATTTAAAATTTTAATTTAATTAA
*
274692 AAATTTAAAATTATTAAATTAATT
1 AAATTTAAAATT-TTAATTTAATT
274716 TTTAAAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 12 0.30
25 11 0.28
26 13 0.32
27 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
AAATTTAAAATTTTAATTTAATTAA
Found at i:274698 original size:16 final size:17
Alignment explanation
Indices: 274669--274709 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
274659 TAATTAGTAA
* * *
274669 TATTTAAAATTTTAATT
1 TATTAAAAATTTAAAAT
274686 TATTAAAAATTTAAAAT
1 TATTAAAAATTTAAAAT
274703 TATTAAA
1 TATTAAA
274710 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTAAAAATTTAAAAT
Found at i:274728 original size:28 final size:29
Alignment explanation
Indices: 274680--274738 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 29
274670 ATTTAAAATT
* *
274680 TTAATTTATTAAAAATTTAAAATTATTAAA
1 TTAATTTATTAAAAA-TTAAAAATATGAAA
274710 TTAATTT-TTAAAAGA-TAAAAATATGAAA
1 TTAATTTATTAAAA-ATTAAAAATATGAAA
274738 T
1 T
274739 AAAATATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 12 0.46
29 6 0.23
30 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
TTAATTTATTAAAAATTAAAAATATGAAA
Found at i:275128 original size:14 final size:14
Alignment explanation
Indices: 275111--275140 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
275101 TTAAAATACG
275111 TAATAAAAAAATAT
1 TAATAAAAAAATAT
*
275125 TAATATAAAAATAT
1 TAATAAAAAAATAT
275139 TA
1 TA
275141 TTAATACACG
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:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAAAAAATAT
Found at i:275142 original size:17 final size:16
Alignment explanation
Indices: 275113--275146 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
275103 AAAATACGTA
275113 ATAAAAAAATATTAAT
1 ATAAAAAAATATTAAT
*
275129 ATAAAAATATTATTAAT
1 ATAAAAA-AATATTAAT
275146 A
1 A
275147 CACGAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAAAAATATTAAT
Found at i:275320 original size:15 final size:14
Alignment explanation
Indices: 275296--275337 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
275286 AAATTATTTT
275296 TATATTAATAATTA
1 TATATTAATAATTA
275310 TATATTTAATAATTA
1 TATA-TTAATAATTA
*
275325 -A-ATTAAAAATTA
1 TATATTAATAATTA
275337 T
1 T
275338 TTTTTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 5 0.20
15 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATTAATAATTA
Found at i:275350 original size:26 final size:27
Alignment explanation
Indices: 275299--275354 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
275289 TTATTTTTAT
*
275299 ATTAATAATTATATATTTAATAATTAA
1 ATTAAAAATTATATATTTAATAATTAA
* *
275326 ATTAAAAATTAT-TTTTTAATTATTAA
1 ATTAAAAATTATATATTTAATAATTAA
275352 ATT
1 ATT
275355 TTAGCTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAAAAATTATATATTTAATAATTAA
Found at i:279462 original size:21 final size:20
Alignment explanation
Indices: 279425--279463 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
279415 TATTTTTATT
* *
279425 TAAATTTAATTATAAATATA
1 TAAATTTAATAAAAAATATA
279445 TAAATATTAATAAAAAATA
1 TAAAT-TTAATAAAAAATA
279464 ATTTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATAAAAAATATA
Found at i:279791 original size:11 final size:12
Alignment explanation
Indices: 279761--279807 Score: 71
Period size: 11 Copynumber: 4.0 Consensus size: 12
279751 TTATTCAATG
279761 AAAATATAATAT
1 AAAATATAATAT
279773 AAAA-ATAAT-T
1 AAAATATAATAT
279783 AAAATATAATAT
1 AAAATATAATAT
279795 AAATATATAATAT
1 AAA-ATATAATAT
279808 GATATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.16
11 10 0.31
12 8 0.25
13 9 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:279812 original size:18 final size:16
Alignment explanation
Indices: 279785--279825 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
279775 AAATAATTAA
279785 AATATAATATAAATATAT
1 AATATAATATAAA-A-AT
*
279803 AATATGATATAAAAAT
1 AATATAATATAAAAAT
279819 AATATAA
1 AATATAA
279826 ATTTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:279825 original size:11 final size:11
Alignment explanation
Indices: 279761--279826 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
279751 TTATTCAATG
279761 AAAATATAATAT
1 AAAA-ATAATAT
279773 AAAAATAAT-T
1 AAAAATAATAT
279783 AAAATATAATAT
1 AAAA-ATAATAT
279795 --AAAT-ATAT
1 AAAAATAATAT
* *
279803 -AATATGATAT
1 AAAAATAATAT
279813 AAAAATAATAT
1 AAAAATAATAT
279824 AAA
1 AAA
279827 TTTATAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.09
9 5 0.11
10 11 0.24
11 21 0.46
12 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:280413 original size:16 final size:16
Alignment explanation
Indices: 280394--280445 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
280384 TATAAGAACA
*
280394 ATAATTAAAACATAAT
1 ATAAATAAAACATAAT
*
280410 ATAAATAAAAGATAA-
1 ATAAATAAAACATAAT
*
280425 ATACA-AAAA-ATAAT
1 ATAAATAAAACATAAT
280439 ATAAATA
1 ATAAATA
280446 TATAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 5 0.17
16 13 0.43
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (16 bp):
ATAAATAAAACATAAT
Found at i:282009 original size:3 final size:3
Alignment explanation
Indices: 282001--282048 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
281991 TTAATTTTTA
282001 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
282049 TTTTTGCAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:284384 original size:2 final size:2
Alignment explanation
Indices: 284377--284420 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
284367 CTATATTCTT
284377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
284419 TA
1 TA
284421 ATTTTACACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:287890 original size:234 final size:234
Alignment explanation
Indices: 287474--287925 Score: 823
Period size: 234 Copynumber: 1.9 Consensus size: 234
287464 GAAATTGGCA
* * *
287474 TTTGGCTGTCCTTATAAACGTGCACATCCAAGCATCTGCGTCGTTTACTTTGATTGTAATATCTA
1 TTTGGCTGTCCTTATAAACGTGCACATCCAAGCATCTGCGTCGTCTACTTCGATTGTAATATCAA
*
287539 CTTTTATCTTCGTAACAATTTACAGGTTTGGTTTTTCATTTTTGTTGCAGATGATTTACATCACG
66 CTTTTATCTTCCTAACAATTTACAGGTTTGGTTTTTCATTTTTGTTGCAGATGATTTACATCACG
*
287604 GCACCACTTCCATCTGTTCTTCAAACGCGGGAAGAGGTCAACAGCTCAGGGGAATCCATGGTGAT
131 GCACCACTTCCATCTGTTCTTCAAACGCGGGAAGAGGTCAACAGCCCAGGGGAATCCATGGTGAT
287669 CAGCTCGGGTAATTGAGAGAAGAGCGCACATTTTACAGG
196 CAGCTCGGGTAATTGAGAGAAGAGCGCACATTTTACAGG
* *
287708 TTTGGCTTTCCTTATAAACGTGCACATCCAAGCATCTGCGTTGTCTACTTCGATTGTAATATCAA
1 TTTGGCTGTCCTTATAAACGTGCACATCCAAGCATCTGCGTCGTCTACTTCGATTGTAATATCAA
287773 CTTTTATCTTCCTAACAATTTACAGGTTTGGTTTTTCATTTTTGTTGCAGATGATTTACATCACG
66 CTTTTATCTTCCTAACAATTTACAGGTTTGGTTTTTCATTTTTGTTGCAGATGATTTACATCACG
**
287838 GCACCACTTCCATCTGTTCTTTGAACGCGGGAAGAGGTCAACAGCCCAGGGGAATCCATGGTGAT
131 GCACCACTTCCATCTGTTCTTCAAACGCGGGAAGAGGTCAACAGCCCAGGGGAATCCATGGTGAT
287903 CAGCTCGGGTAATTGAGAGAAGA
196 CAGCTCGGGTAATTGAGAGAAGA
287926 ACACTCATTT
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
234 209 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (234 bp):
TTTGGCTGTCCTTATAAACGTGCACATCCAAGCATCTGCGTCGTCTACTTCGATTGTAATATCAA
CTTTTATCTTCCTAACAATTTACAGGTTTGGTTTTTCATTTTTGTTGCAGATGATTTACATCACG
GCACCACTTCCATCTGTTCTTCAAACGCGGGAAGAGGTCAACAGCCCAGGGGAATCCATGGTGAT
CAGCTCGGGTAATTGAGAGAAGAGCGCACATTTTACAGG
Found at i:288930 original size:2 final size:2
Alignment explanation
Indices: 288923--288959 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
288913 AGCATCCATT
288923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
288960 TCTATGTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:291004 original size:22 final size:22
Alignment explanation
Indices: 290970--291017 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
290960 TTTGACGTTA
*
290970 TAAATATTAAAATTTTAATTT-T
1 TAAATATTAAAATATT-ATTTAT
290992 TAAATTATT-AAATATTATTTAT
1 TAAA-TATTAAAATATTATTTAT
291014 TAAA
1 TAAA
291018 AGTGATCGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATATTAAAATATTATTTAT
Found at i:292925 original size:17 final size:17
Alignment explanation
Indices: 292880--292917 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
292870 TTAATATTCA
*
292880 AATAATTAAATCTTTGT
1 AATAATTAAATATTTGT
292897 AATAATTAAATATTTGT
1 AATAATTAAATATTTGT
292914 AATA
1 AATA
292918 TTTGAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
AATAATTAAATATTTGT
Found at i:293188 original size:32 final size:29
Alignment explanation
Indices: 293152--293222 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
293142 TGCCAATTCA
* **
293152 TTTATATATTTTTATATATTATAATTATATTT
1 TTTATATAATTTTA-ATAAAATAA-TA-ATTT
293184 TTTATATAAATTTTAATAAAATAATAATTT
1 TTTATAT-AATTTTAATAAAATAATAATTT
293214 TTTATATAA
1 TTTATATAA
293223 ATATTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 11 0.31
31 2 0.06
32 14 0.40
33 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATATAATTTTAATAAAATAATAATTT
Found at i:293224 original size:19 final size:19
Alignment explanation
Indices: 293189--293240 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
293179 TATTTTTTAT
* *
293189 ATAAATTTTAATA-AAATA
1 ATAATTTTTTATATAAATA
293207 ATAATTTTTTATATAAATA
1 ATAATTTTTTATATAAATA
* *
293226 TTATTTTTTTATATA
1 ATAATTTTTTATATA
293241 TTTATATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAATTTTTTATATAAATA
Found at i:293271 original size:11 final size:11
Alignment explanation
Indices: 293257--293283 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
293247 TCATATTTAA
293257 ATATTAATTTT
1 ATATTAATTTT
293268 ATATTAATTTT
1 ATATTAATTTT
293279 ATATT
1 ATATT
293284 TTATAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:293271 original size:19 final size:19
Alignment explanation
Indices: 293202--293272 Score: 51
Period size: 19 Copynumber: 3.9 Consensus size: 19
293192 AATTTTAATA
* * *
293202 AAATAATAATTTTTTATAT
1 AAATATTAATTTTATATTT
293221 AAATATT-A-TTT-T-TTT
1 AAATATTAATTTTATATTT
* * * *
293236 ATATATTTATATCATATTT
1 AAATATTAATTTTATATTT
293255 AAATATTAATTTTATATT
1 AAATATTAATTTTATATT
293273 AATTTTATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
15 8 0.21
16 2 0.05
17 4 0.10
18 2 0.05
19 23 0.59
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
AAATATTAATTTTATATTT
Found at i:295075 original size:22 final size:23
Alignment explanation
Indices: 295030--295080 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
295020 TTTTAAATTT
**
295030 TTTTATATATTTAAATTATCATA
1 TTTTATATATTTAAATTAAAATA
*
295053 TTTT-TATATTTATATTAAAATA
1 TTTTATATATTTAAATTAAAATA
*
295075 TGTTAT
1 TTTTAT
295081 GATACGTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATATATTTAAATTAAAATA
Found at i:295334 original size:22 final size:22
Alignment explanation
Indices: 295309--295352 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
295299 CAAAATTTAT
*
295309 AGGAGATTAGATTCGAACTTAA
1 AGGAGATGAGATTCGAACTTAA
*
295331 AGGAGATGAGGTTCGAACTTAA
1 AGGAGATGAGATTCGAACTTAA
295353 GATCTAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (22 bp):
AGGAGATGAGATTCGAACTTAA
Found at i:297024 original size:19 final size:20
Alignment explanation
Indices: 297000--297037 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
296990 CTAGTTTAGA
297000 ATAATAT-TTTTTAATTAAT
1 ATAATATATTTTTAATTAAT
*
297019 ATAATATATTTTTATTTAA
1 ATAATATATTTTTAATTAA
297038 ATTTAATTAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATATATTTTTAATTAAT
Found at i:297718 original size:3 final size:3
Alignment explanation
Indices: 297705--297754 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
297695 AACAGAAAAG
297705 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
297751 ATA A
1 ATA A
297755 AAGAAAAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:298075 original size:22 final size:22
Alignment explanation
Indices: 298036--298077 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
298026 TATTTATAAT
***
298036 ATCTTTTTTATTTTAAATTATG
1 ATCTTTTTTATAAAAAATTATG
298058 ATCTTTTTTATAAAAAATTA
1 ATCTTTTTTATAAAAAATTA
298078 CTTTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
ATCTTTTTTATAAAAAATTATG
Found at i:301976 original size:17 final size:17
Alignment explanation
Indices: 301934--301979 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
301924 ATATCACTAA
* *
301934 TATATTCATAATATTTTT
1 TATA-TCATATTATATTT
301952 TCATATCATATTATATTT
1 T-ATATCATATTATATTT
301970 TATATCATAT
1 TATATCATAT
301980 ATTAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 13 0.52
19 3 0.12
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATCATATTATATTT
Found at i:303286 original size:17 final size:17
Alignment explanation
Indices: 303255--303297 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
303245 TTAATAAAAA
303255 AATT-AATTT-TTTTAT
1 AATTAAATTTATTTTAT
303270 -ATTAATATTTATTTTAT
1 AATTAA-ATTTATTTTAT
303287 AATTAAATTTA
1 AATTAAATTTA
303298 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.12
15 1 0.04
16 4 0.17
17 11 0.46
18 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTAAATTTATTTTAT
Found at i:304243 original size:21 final size:21
Alignment explanation
Indices: 304206--304245 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
304196 TATTTTTATT
*
304206 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAAAAAATATA
304227 TAAATATTAA-TAAAAAATA
1 TAAAT-TTAATTAAAAAATA
304246 AAATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTAAAAAATATA
Found at i:305270 original size:20 final size:19
Alignment explanation
Indices: 305221--305275 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
305211 TGATGTTTAA
*
305221 AATATTATATATTTATATC
1 AATATTATATATTTAGATC
*
305240 AATTTTAATATATTAATAGAT-
1 AATATT-ATATATT--TAGATC
305261 AATATTATATATTTA
1 AATATTATATATTTA
305276 AATTTATTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 14 0.47
21 5 0.17
22 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATTATATATTTAGATC
Found at i:305328 original size:32 final size:32
Alignment explanation
Indices: 305286--305361 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
305276 AATTTATTCG
* *
305286 TATAT-TTATATTGTATTTATATTATTAATTT
1 TATATATTATATTGTATTCATATTATTAATAT
* * * *
305317 TTTATATTATATTTTATTCATTTTATTTATAT
1 TATATATTATATTGTATTCATATTATTAATAT
305349 TATATAATTATAT
1 TATAT-ATTATAT
305362 AATGTTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 4 0.11
32 25 0.69
33 7 0.19
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
TATATATTATATTGTATTCATATTATTAATAT
Found at i:305652 original size:17 final size:17
Alignment explanation
Indices: 305632--305702 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 17
305622 ATAAATTATT
305632 TATATATAAAAATAAAA
1 TATATATAAAAATAAAA
*
305649 TATAT-TAAAAATAATTA
1 TATATATAAAAATAA-AA
*
305666 TGACATATAAAATACTTAGAAA
1 T-ATATATAAAA-A--TA-AAA
305688 TATA-ATAAAAATAAA
1 TATATATAAAAATAAA
305703 GTAATTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
16 11 0.26
17 9 0.21
18 3 0.07
19 6 0.14
20 7 0.16
21 2 0.05
22 4 0.09
23 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TATATATAAAAATAAAA
Found at i:305662 original size:22 final size:22
Alignment explanation
Indices: 305581--305662 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
305571 AATTTTATAA
*
305581 AAAATA-ATT-AAAAT-ATAAT
1 AAAATATATTAAAAATAAAAAT
**
305600 AAAATATATATAAATTTAAAATAT
1 AAAATATAT-TAAAAATAAAA-AT
* * *
305624 AAATTAT-TTATATATAAAAAT
1 AAAATATATTAAAAATAAAAAT
305645 AAAATATATTAAAAATAA
1 AAAATATATTAAAAATAA
305663 TTATGACATA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
19 6 0.12
20 2 0.04
21 9 0.19
22 20 0.42
23 3 0.06
24 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATATATTAAAAATAAAAAT
Found at i:305755 original size:21 final size:22
Alignment explanation
Indices: 305731--305781 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
305721 ACTCATTCTG
* *
305731 TTAATTTTAAATTATTATTTA-
1 TTAATTTAAAATAATTATTTAT
*
305752 TTAA-TTAAAATAATTTTTTAT
1 TTAATTTAAAATAATTATTTAT
305773 TTAATTTAA
1 TTAATTTAA
305782 TTATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.52
21 8 0.32
22 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAATTTAAAATAATTATTTAT
Found at i:305821 original size:22 final size:22
Alignment explanation
Indices: 305772--305823 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
305762 TAATTTTTTA
305772 TTTAAT-TTAATTATAAAATAT
1 TTTAATATTAATTATAAAATAT
* *
305793 ATAAATATTAATTA-AAAATATT
1 TTTAATATTAATTATAAAATA-T
305815 TTTAATATT
1 TTTAATATT
305824 TTATTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATATTAATTATAAAATAT
Found at i:305854 original size:27 final size:28
Alignment explanation
Indices: 305824--305892 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
305814 TTTTAATATT
305824 TTATTATATTTTAAATAATAAT-T-TAAA
1 TTATTATATTTTAAATAA-AATATATAAA
*
305851 TTATTAAATAAATTTAAATAAAATATATAAA
1 TTATT--AT-ATTTTAAATAAAATATATAAA
*
305882 TTATTAAATTT
1 TTATTATATTT
305893 ATCTTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 6 0.18
30 11 0.32
31 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATTATATTTTAAATAAAATATATAAA
Found at i:305885 original size:31 final size:30
Alignment explanation
Indices: 305833--305890 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
305823 TTTATTATAT
305833 TTTAAATAATAATTTAAATTATTAAATAAA
1 TTTAAATAATAATTTAAATTATTAAATAAA
305863 TTTAAATAA-AATATATAAATTATTAAAT
1 TTTAAATAATAAT-T-TAAATTATTAAAT
305891 TTATCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 3 0.12
30 10 0.38
31 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAAATAATAATTTAAATTATTAAATAAA
Done.