Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, whole genome shotgun sequence
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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 30
Found at i:6199914 original size:15 final size:15
Alignment explanation
Indices: 6199894--6199943 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
6199884 TATTATTATT
6199894 AAATCATTAAATATC
1 AAATCATTAAATATC
*
6199909 AAATCATTAGAT-T-
1 AAATCATTAAATATC
*
6199922 -AAT-AGTAAATATC
1 AAATCATTAAATATC
6199935 AAATCATTA
1 AAATCATTA
6199944 GATTAATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
14 4 0.15
15 14 0.52
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:6199917 original size:26 final size:25
Alignment explanation
Indices: 6199901--6199969 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 25
6199891 ATTAAATCAT
6199901 TAAATATCAAATCATTAGATTAATAG
1 TAAATATCAAATCATTA-ATTAATAG
6199927 TAAATATCAAATCATTAGATTAATAG
1 TAAATATCAAATCATTA-ATTAATAG
*
6199953 TAATTATCAAATCATTA
1 TAAATATCAAATCATTA
6199970 TTAGGTTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (25 bp):
TAAATATCAAATCATTAATTAATAG
Found at i:6202880 original size:26 final size:26
Alignment explanation
Indices: 6202851--6203276 Score: 334
Period size: 26 Copynumber: 17.2 Consensus size: 26
6202841 TTTGATGATT
6202851 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6202877 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
6202903 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
6202929 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
6202951 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
6202975 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6203001 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
6203027 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
6203053 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
6203075 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
6203099 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6203125 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
6203151 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
6203177 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * *
6203199 TA--AAT-ATTAATGAT-TTGATGATT-
1 TAGTAATGATT--TGATAATAATCATTA
6203222 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
6203248 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
6203273 TAGT
1 TAGT
6203277 TATTATTAGT
Statistics
Matches: 339, Mismatches: 30, Indels: 63
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.01
20 14 0.04
22 9 0.03
23 41 0.12
24 23 0.07
25 33 0.10
26 204 0.60
27 12 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:6203016 original size:124 final size:124
Alignment explanation
Indices: 6202796--6203311 Score: 925
Period size: 124 Copynumber: 4.2 Consensus size: 124
6202786 ATGTATTTAT
6202796 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
6202861 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
6202920 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
6202985 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
6203044 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
6203109 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
6203168 TAATCATTATAAAAATGATTTAATAATGATTTAAATA-TTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
6203232 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTA-TTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
6203289 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
6203312 CTAATGATTT
Statistics
Matches: 384, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
119 18 0.05
121 10 0.03
122 6 0.02
123 65 0.17
124 285 0.74
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:6203034 original size:150 final size:145
Alignment explanation
Indices: 6202851--6203194 Score: 412
Period size: 150 Copynumber: 2.3 Consensus size: 145
6202841 TTTGATGATT
* *
6202851 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT-
* * *
6202916 GTAATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AAT-ATTTAATGATTTGATGATT-T
63 -TAATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATGATTTAAT-A-ATAATCATTAT
6202976 AGTAATGATTTGATAATAATCATTA
121 AGTAATGATTTGATAATAATCATTA
6203001 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* *
6203066 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATCATTTAAATATTTAATGA--T-ATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
6203131 TGATTTGATAATAATCATTA
126 TGATTTGATAATAATCATTA
* *
6203151 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
6203195 GATTTAAATA
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
143 7 0.04
144 5 0.03
146 1 0.01
147 10 0.06
148 8 0.05
149 10 0.06
150 125 0.72
151 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (145 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATCATTTAAATATTTAATGATATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATT
TGATAATAATCATTA
Found at i:6203304 original size:48 final size:48
Alignment explanation
Indices: 6203245--6203337 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
6203235 ATAATAATCA
* * * * *
6203245 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTAGTAATTAT
1 TTATAATAATGATTTAATAATAATGATTTAATAATTATTACTAATTAT
*
6203293 TTATAATAATGATTTAATACTAATGATTTAATAATTATTACTAAT
1 TTATAATAATGATTTAATAATAATGATTTAATAATTATTACTAAT
6203338 AATTATAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (48 bp):
TTATAATAATGATTTAATAATAATGATTTAATAATTATTACTAATTAT
Found at i:6203559 original size:17 final size:17
Alignment explanation
Indices: 6203534--6203566 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6203524 ACTAAATATT
*
6203534 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
6203551 TAATGATTTGATACTA
1 TAATGATTTGATACTA
6203567 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:6203559 original size:25 final size:23
Alignment explanation
Indices: 6203480--6203559 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
6203470 GATTTATTGT
6203480 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
6203501 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
6203528 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
6203550 GTAATGATTT
1 -TAAT-ATTT
6203560 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:6205740 original size:15 final size:14
Alignment explanation
Indices: 6205717--6205747 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
6205707 TACAACACTA
6205717 AACTTTAATATAAT
1 AACTTTAATATAAT
6205731 AACTTATAATATAAT
1 AACTT-TAATATAAT
6205746 AA
1 AA
6205748 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:6205755 original size:16 final size:16
Alignment explanation
Indices: 6205722--6205768 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6205712 CACTAAACTT
*
6205722 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
6205737 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
6205753 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
6205769 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:6206007 original size:45 final size:45
Alignment explanation
Indices: 6205930--6206062 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
6205920 TCAACAAACA
*
6205930 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
6205978 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
6206022 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
6206063 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:6206090 original size:41 final size:40
Alignment explanation
Indices: 6206002--6206090 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
6205992 TTAACAAAAC
* *
6206002 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
6206043 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
6206084 AAACTAA
1 AAACTAA
6206091 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:6206255 original size:21 final size:21
Alignment explanation
Indices: 6206225--6206277 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6206215 CCCTTTCTTC
*
6206225 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
6206246 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
6206267 TTCTTTCTTTC
1 TTCTTTCTTTC
6206278 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:6206268 original size:17 final size:16
Alignment explanation
Indices: 6206248--6206279 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
6206238 TTCTCCCTTT
6206248 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
6206265 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
6206280 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:6206312 original size:23 final size:23
Alignment explanation
Indices: 6206282--6206327 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6206272 TCTTTCTCGG
6206282 CTGCAATCTCTTCTAACTTTCTT
1 CTGCAATCTCTTCTAACTTTCTT
**
6206305 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTAACTTTCTT
6206328 TCTTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.35, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTAACTTTCTT
Found at i:6206610 original size:29 final size:29
Alignment explanation
Indices: 6206586--6206686 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
6206576 GGCGCCGGGA
*
6206586 CTACATGGCGACCTACAAGGTCGCC-GGG
1 CTACATGGCGACCTACAAGGTCGCCTAGG
*
6206614 ACTACACGGCGACCTACAAGGTCGCCTAGG
1 -CTACATGGCGACCTACAAGGTCGCCTAGG
*
6206644 CTGCATGGCGACCTACAAGGTCGCCTAGG
1 CTACATGGCGACCTACAAGGTCGCCTAGG
*
6206673 CTGCATGGCGACCT
1 CTACATGGCGACCT
6206687 CTCTATTCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 65 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.16
Consensus pattern (29 bp):
CTACATGGCGACCTACAAGGTCGCCTAGG
Found at i:6206772 original size:12 final size:12
Alignment explanation
Indices: 6206755--6206798 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
6206745 TCGTATGGCT
6206755 CGTATGTCACCC
1 CGTATGTCACCC
6206767 CGTATGTCACCC
1 CGTATGTCACCC
6206779 CGTATGTCACCC
1 CGTATGTCACCC
6206791 CGTATGTC
1 CGTATGTC
6206799 GCCTGGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.16, C:0.39, G:0.18, T:0.27
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:6212410 original size:54 final size:54
Alignment explanation
Indices: 6212346--6212455 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
6212336 TATTTCCCCC
6212346 CTTAATTTTATAAATTACCCTAGAATAAAATCTTACGTCCGTCCCTGCACATAG
1 CTTAATTTTATAAATTACCCTAGAATAAAATCTTACGTCCGTCCCTGCACATAG
6212400 CTTAATTTTATAAATTACCCTAGAATAAAATCTTACGTCCGTCCCTGCACATAG
1 CTTAATTTTATAAATTACCCTAGAATAAAATCTTACGTCCGTCCCTGCACATAG
6212454 CT
1 CT
6212456 AATATTTCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.34
Consensus pattern (54 bp):
CTTAATTTTATAAATTACCCTAGAATAAAATCTTACGTCCGTCCCTGCACATAG
Found at i:6217532 original size:18 final size:18
Alignment explanation
Indices: 6217509--6217554 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
6217499 CTATAATTTT
6217509 AATTCGTCCCTAAGTTTA
1 AATTCGTCCCTAAGTTTA
6217527 AATTCGTCCCTAAGTTTA
1 AATTCGTCCCTAAGTTTA
6217545 AATTCGTCCC
1 AATTCGTCCC
6217555 CTACATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (18 bp):
AATTCGTCCCTAAGTTTA
Found at i:6219814 original size:21 final size:21
Alignment explanation
Indices: 6219790--6219830 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6219780 AAATGTTAAA
*
6219790 AAATATTAATATTTTATGTAT
1 AAATAATAATATTTTATGTAT
6219811 AAATAATAATATTTTATGTA
1 AAATAATAATATTTTATGTA
6219831 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATAATAATATTTTATGTAT
Found at i:6222401 original size:25 final size:23
Alignment explanation
Indices: 6222364--6222410 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
6222354 GTTTTGCTTA
6222364 TATTTTTGAACTCCCTTAAATTTTT
1 TATTTTTGAACT-CCTT-AATTTTT
**
6222389 TATTTTTTCACTCCTTAATTTT
1 TATTTTTGAACTCCTTAATTTT
6222411 CTAATGTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.21, C:0.17, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTTTTGAACTCCTTAATTTTT
Found at i:6226284 original size:15 final size:15
Alignment explanation
Indices: 6226264--6226304 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
6226254 TTAAAATTAT
6226264 TTTATATTTTAAATA
1 TTTATATTTTAAATA
* *
6226279 TTTATATATTAATTA
1 TTTATATTTTAAATA
6226294 TTTATAATTTT
1 TTTAT-ATTTT
6226305 TCGAGGTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTTTAAATA
Found at i:6227585 original size:24 final size:25
Alignment explanation
Indices: 6227558--6227607 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
6227548 AATAAATTTT
*
6227558 AACATATAAAT-ATATTTTTAAATG
1 AACATAAAAATAATATTTTTAAATG
6227582 AACATAAAAATAAAATATTTTTAAAT
1 AACATAAAAAT--AATATTTTTAAAT
6227608 TAAGTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
27 12 0.55
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
AACATAAAAATAATATTTTTAAATG
Found at i:6233940 original size:38 final size:38
Alignment explanation
Indices: 6233889--6233966 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
6233879 AATGGTGAAT
6233889 AAGAGTCCTTTAATGGCTTGTCACTTGGCTGAGGTTGA
1 AAGAGTCCTTTAATGGCTTGTCACTTGGCTGAGGTTGA
6233927 AAGAGTCCTTTAATGGCTTGTCACTTGGCTGAGGTTGA
1 AAGAGTCCTTTAATGGCTTGTCACTTGGCTGAGGTTGA
6233965 AA
1 AA
6233967 AGACTCTCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (38 bp):
AAGAGTCCTTTAATGGCTTGTCACTTGGCTGAGGTTGA
Found at i:6233982 original size:38 final size:37
Alignment explanation
Indices: 6233901--6233982 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
6233891 GAGTCCTTTA
* **
6233901 ATGGCTTGTCACTTGGCTGAGGTTGAAAGAGTCCTTT
1 ATGGCTTGTCACTTGGCTGAGGTTGAAAGACTCCCCT
6233938 AATGGCTTGTCACTTGGCTGAGGTTGAAAAGACTCTCCCT
1 -ATGGCTTGTCACTTGGCTGAGGTTG-AAAGACTC-CCCT
6233978 -TGGCT
1 ATGGCT
6233983 CAAACTCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 30 0.77
39 7 0.18
40 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (37 bp):
ATGGCTTGTCACTTGGCTGAGGTTGAAAGACTCCCCT
Found at i:6234093 original size:17 final size:17
Alignment explanation
Indices: 6234071--6234132 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
6234061 ATCTCAAGCA
6234071 TAAATGAACTACTTCCC
1 TAAATGAACTACTTCCC
* **** *
6234088 TAAATGATCTAAAGGCA
1 TAAATGAACTACTTCCC
6234105 TAAATGAACTACTTCCC
1 TAAATGAACTACTTCCC
6234122 TAAATGAACTA
1 TAAATGAACTA
6234133 GATGAACTAG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (17 bp):
TAAATGAACTACTTCCC
Found at i:6234139 original size:9 final size:9
Alignment explanation
Indices: 6234125--6234206 Score: 60
Period size: 9 Copynumber: 9.3 Consensus size: 9
6234115 ACTTCCCTAA
6234125 ATGAACTAG
1 ATGAACTAG
6234134 ATGAACTAG
1 ATGAACTAG
* *
6234143 ATGATCTAA
1 ATGAACTAG
* * *
6234152 AGGCA-TAA
1 ATGAACTAG
6234160 ATGAACTAG
1 ATGAACTAG
* *
6234169 ATGATCTAA
1 ATGAACTAG
* * *
6234178 AGGCA-TAA
1 ATGAACTAG
6234186 ATGAACTAG
1 ATGAACTAG
6234195 ATGAACTAG
1 ATGAACTAG
6234204 ATG
1 ATG
6234207 CATGAATGAA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
8 12 0.22
9 43 0.78
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (9 bp):
ATGAACTAG
Found at i:6234168 original size:35 final size:34
Alignment explanation
Indices: 6234121--6234206 Score: 107
Period size: 26 Copynumber: 2.7 Consensus size: 34
6234111 AACTACTTCC
6234121 CTAAATGAACTAGATGAACTAGATGATCTAAAGG
1 CTAAATGAACTAGATGAACTAGATGATCTAAAGG
6234155 C---AT--A--A-ATGAACTAGATGATCTAAAGG
1 CTAAATGAACTAGATGAACTAGATGATCTAAAGG
6234181 CATAAATGAACTAGATGAACTAGATG
1 C-TAAATGAACTAGATGAACTAGATG
6234207 CATGAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
26 22 0.51
27 1 0.02
29 1 0.02
30 2 0.05
31 2 0.05
32 1 0.02
34 2 0.05
35 12 0.28
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (34 bp):
CTAAATGAACTAGATGAACTAGATGATCTAAAGG
Found at i:6234190 original size:52 final size:52
Alignment explanation
Indices: 6234091--6234216 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 52
6234081 ACTTCCCTAA
* ** * *
6234091 ATGATCTAAAGGCATAAATGAACTACTTCCCTAAATGAACTAGATGAACTAG
1 ATGATCTAAAGGCATAAATGAACTAATGACCTAAAGGAACTAAATGAACTAG
* *
6234143 ATGATCTAAAGGCATAAATGAACTAGATGATCTAAAGGCA-TAAATGAACTAG
1 ATGATCTAAAGGCATAAATGAACTA-ATGACCTAAAGGAACTAAATGAACTAG
* * * *
6234195 ATGAACTAGATGCATGAATGAA
1 ATGATCTAAAGGCATAAATGAA
6234217 GTAGCTTACT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
52 54 0.87
53 8 0.13
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (52 bp):
ATGATCTAAAGGCATAAATGAACTAATGACCTAAAGGAACTAAATGAACTAG
Found at i:6235514 original size:14 final size:14
Alignment explanation
Indices: 6235495--6235537 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
6235485 TTTTAATTGT
6235495 ATTTTCATTTTAAA
1 ATTTTCATTTTAAA
6235509 ATTTTCATTTTATAA
1 ATTTTCATTTTA-AA
*
6235524 ATATT--TTTTAAA
1 ATTTTCATTTTAAA
6235536 AT
1 AT
6235538 AATTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 4 0.15
13 5 0.19
14 12 0.44
15 6 0.22
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTTCATTTTAAA
Found at i:6238259 original size:305 final size:305
Alignment explanation
Indices: 6237717--6238290 Score: 911
Period size: 305 Copynumber: 1.9 Consensus size: 305
6237707 TAGACCATAC
* * *
6237717 AAGAAGAAGCGTTTATCTCTTTAGAGTAATCTTACTGTTGTTTCAAGACCGGCTAGTACCCCTTG
1 AAGAAGAAGCGTTTATCTCTATAGAGTAATCTTACTGCTGTTGCAAGACCGGCTAGTACCCCTTG
*
6237782 GTTATGATGGGTGATTTTAATGCCATCTTTCACGTACTGAGAAGTCGGGTGGAGTTCAACGTGGC
66 GTTATGACGGGTGATTTTAATGCCATCTTTCACGTACTGAGAAGTCGGGTGGAGTTCAACGTGGC
* * *
6237847 AAAGGTTTCCCTATGTTCCAGAGTTTTATGGACTATCATAATCTTATGGACCTTGGATTCAAAGG
131 AAAGGTTGCCCTATGTTCCAGAGCTTTATGGACTATCATAATCTTATGCACCTTGGATTCAAAGG
* * * *
6237912 TCCGCAGTTTACTTGGTATCTTGGGGGTATCTCGAGAAGGCTGGATCGGATGGTTGTTAATAAAG
196 TCCGCAGTTTACTTGGTATCGTGGAGGTATCTCGAAAAGGCTGGATCGAATGGTTGTTAATAAAG
6237977 ATTGCAATCATATGGTTGTTAATGGTTGTATATGGTAGCCCGGAT
261 ATTGCAATCATATGGTTGTTAATGGTTGTATATGGTAGCCCGGAT
* *
6238022 AAGAAGAAGCGTTTATCTCTATGGAGTAATCTTAGTGCTGTTGCAAGACCGGCTAGTACCCCTTG
1 AAGAAGAAGCGTTTATCTCTATAGAGTAATCTTACTGCTGTTGCAAGACCGGCTAGTACCCCTT-
* * *
6238087 GGTTATGGCGGGTGATTTTAATGCCATTCTTTCGA-GTACTGAGAAGTCGGGTGGATTTTAACGT
65 GGTTATGACGGGTGATTTTAATGCCA-TCTTTC-ACGTACTGAGAAGTCGGGTGGAGTTCAACGT
* *
6238151 GGCAAAGG-TGCTCTATG-TCCAGAGCTTTATGGACTATCGTAATCTTATGCACCTTGGATTCAA
128 GGCAAAGGTTGCCCTATGTTCCAGAGCTTTATGGACTATCATAATCTTATGCACCTTGGATTCAA
* *
6238214 AGGTCCGCAGTTTACTTGGTCTCGTGGAGGTATCTCGAAAAGGCTGGATCGAATGGTTGTTAATG
193 AGGTCCGCAGTTTACTTGGTATCGTGGAGGTATCTCGAAAAGGCTGGATCGAATGGTTGTTAATA
*
6238279 AAGATTGGAATC
258 AAGATTGCAATC
6238291 GTCTATTTCC
Statistics
Matches: 245, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
305 172 0.70
306 31 0.13
307 41 0.17
308 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (305 bp):
AAGAAGAAGCGTTTATCTCTATAGAGTAATCTTACTGCTGTTGCAAGACCGGCTAGTACCCCTTG
GTTATGACGGGTGATTTTAATGCCATCTTTCACGTACTGAGAAGTCGGGTGGAGTTCAACGTGGC
AAAGGTTGCCCTATGTTCCAGAGCTTTATGGACTATCATAATCTTATGCACCTTGGATTCAAAGG
TCCGCAGTTTACTTGGTATCGTGGAGGTATCTCGAAAAGGCTGGATCGAATGGTTGTTAATAAAG
ATTGCAATCATATGGTTGTTAATGGTTGTATATGGTAGCCCGGAT
Found at i:6238934 original size:20 final size:20
Alignment explanation
Indices: 6238884--6238926 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6238874 TCTAATTTTC
*
6238884 AAACCATAAATTATAAACTTT
1 AAACCATAAA-AATAAACTTT
*
6238905 AAACCCTAAAAATAAACTTT
1 AAACCATAAAAATAAACTTT
6238925 AA
1 AA
6238927 GACATAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (20 bp):
AAACCATAAAAATAAACTTT
Found at i:6241699 original size:3 final size:3
Alignment explanation
Indices: 6241693--6241730 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
6241683 ATGAGAAAAA
6241693 AAT AAT AA- AA- AAT AAT AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6241731 ATGAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6241719 original size:21 final size:21
Alignment explanation
Indices: 6241693--6241759 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 21
6241683 ATGAGAAAAA
6241693 AATAATAAAAAATAATAATAT
1 AATAATAAAAAATAATAATAT
*
6241714 AATAAT-AATAATAATAA-AT
1 AATAATAAAAAATAATAATAT
*
6241733 GA-AATAAATAAATAAATAAATAT
1 AATAATAAA-AAAT-AAT-AATAT
6241756 AATA
1 AATA
6241760 TAACAATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
18 3 0.08
19 5 0.14
20 13 0.36
21 9 0.25
22 2 0.06
23 3 0.08
24 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (21 bp):
AATAATAAAAAATAATAATAT
Found at i:6241785 original size:47 final size:46
Alignment explanation
Indices: 6241688--6241782 Score: 106
Period size: 47 Copynumber: 2.1 Consensus size: 46
6241678 TAAACATGAG
* * *
6241688 AAAA-AAATAATAAAAAATAATAATATAATAATAATAATAATAAAT
1 AAAATAAATAATAAAAAATAATAATATAACAATAATAAAAAGAAAT
* *
6241733 GAAATAAATAAATAAATAAAT-ATAATATAACAAT-GTAAAAAGAAAT
1 AAAATAAAT-AATAAA-AAATAATAATATAACAATAATAAAAAGAAAT
6241779 AAAA
1 AAAA
6241783 ATATTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
45 3 0.07
46 16 0.39
47 18 0.44
48 4 0.10
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (46 bp):
AAAATAAATAATAAAAAATAATAATATAACAATAATAAAAAGAAAT
Found at i:6241845 original size:11 final size:11
Alignment explanation
Indices: 6241689--6241846 Score: 53
Period size: 13 Copynumber: 13.5 Consensus size: 11
6241679 AAACATGAGA
6241689 AAAAAAT-AAT
1 AAAAAATAAAT
6241699 AAAAAAT-AAT
1 AAAAAATAAAT
*
6241709 AATATAAT-AAT
1 AA-AAAATAAAT
6241720 AATAATAATAAAT
1 AA-AA-AATAAAT
6241733 GAAATAAATAAAT
1 -AAA-AAATAAAT
6241746 AAATAAATATAAT
1 AAA-AAATA-AAT
* *
6241759 ATAACAAT--GT
1 A-AAAAATAAAT
*
6241769 -AAAAAGAAAT
1 AAAAAATAAAT
6241779 AAAAATATTAAAATT
1 AAAAA-A-T-AAA-T
6241794 AGGAGAAAAT-AA-
1 A--A-AAAATAAAT
*
6241806 AAAAAATATAT
1 AAAAAATAAAT
6241817 AAAGTAAATAAAT
1 AAA--AAATAAAT
6241830 AAAAAATGAAAT
1 AAAAAAT-AAAT
6241842 AAAAA
1 AAAAA
6241847 GAATAAGTCA
Statistics
Matches: 116, Mismatches: 10, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
8 4 0.03
9 5 0.04
10 16 0.14
11 22 0.19
12 23 0.20
13 28 0.24
14 10 0.09
15 2 0.02
16 1 0.01
17 2 0.02
18 3 0.03
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:6242153 original size:33 final size:34
Alignment explanation
Indices: 6242116--6242196 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
6242106 GTCCTACTTG
* *
6242116 GACTCAAAATGC-TTCGGTTTTAG-GTTTCAATAT
1 GACTCAAAATACGTT-GGTTTTAGTGTTTCAATAA
6242149 GACTC-AAATACGTTGGTTTTAGTGTTTCAATAA
1 GACTCAAAATACGTTGGTTTTAGTGTTTCAATAA
6242182 GACTC-AAATACGTTG
1 GACTCAAAATACGTTG
6242197 ATTTATTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 13 0.30
33 31 0.70
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (34 bp):
GACTCAAAATACGTTGGTTTTAGTGTTTCAATAA
Found at i:6242170 original size:32 final size:33
Alignment explanation
Indices: 6242131--6242196 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
6242121 AAAATGCTTC
*
6242131 GGTTTTAG-GTTTCAATATGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
6242163 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
6242196 G
1 G
6242197 ATTTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
Found at i:6243950 original size:29 final size:29
Alignment explanation
Indices: 6243907--6243989 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
6243897 CTCACCTAAC
*
6243907 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
6243937 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
6243966 TAAATGATGTAAGTAATGAAATCA
1 TAAATGATGTAAGCAATGACATCA
6243990 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:6247373 original size:15 final size:15
Alignment explanation
Indices: 6247353--6247382 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6247343 CTTTCTCATA
6247353 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
6247368 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
6247383 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:6248704 original size:29 final size:29
Alignment explanation
Indices: 6248658--6248740 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
6248648 ATTACCTAAC
* *
6248658 TAAATTGATGTAAACAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
6248688 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
6248717 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
6248741 ATTTACTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:6250714 original size:21 final size:20
Alignment explanation
Indices: 6250690--6250753 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
6250680 AACTTTGAAA
6250690 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
6250711 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
6250725 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
6250746 AAATGTTT
1 AAATGTTT
6250754 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:6250728 original size:35 final size:36
Alignment explanation
Indices: 6250655--6250803 Score: 182
Period size: 35 Copynumber: 4.2 Consensus size: 36
6250645 TGAAAGTATT
***
6250655 AAAATGATTTTC-AAGTTTGGT-AAT-CAACTTTGAA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG-A
6250689 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
*
6250724 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
6250760 AAAATTATTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAATGA-TTTTCAAAGTTTGGTAAATGTTTCTTTGA
6250796 AAAATGAT
1 AAAATGAT
6250804 AATGGGATAA
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
34 12 0.12
35 44 0.44
36 18 0.18
37 27 0.27
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (36 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:6255344 original size:37 final size:38
Alignment explanation
Indices: 6255289--6255372 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
6255279 TGGTAACCAA
*
6255289 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
* *
6255326 CTTTGAAAAATA-GTTTTTCAAAGTTTAGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
*
6255363 -GTTGAAAAAT
1 CTTTGAAAAAT
6255373 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
Found at i:6261057 original size:6 final size:6
Alignment explanation
Indices: 6261043--6261077 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6261033 GAGGCACACA
* *
6261043 GGCACG GGTACG GGTACG GGCACG GGCACG GGCAC
1 GGCACG GGCACG GGCACG GGCACG GGCACG GGCAC
6261078 ATGCTGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.29, G:0.49, T:0.06
Consensus pattern (6 bp):
GGCACG
Found at i:6261615 original size:30 final size:29
Alignment explanation
Indices: 6261581--6261642 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
6261571 AAGGGTAAAG
* *
6261581 TGTATAAATGGTTTCTTGACTATATAATAT
1 TGTATAAATGCTCTCTTGA-TATATAATAT
* *
6261611 TGTATAAATGCTCTCTTGATTTATGATAT
1 TGTATAAATGCTCTCTTGATATATAATAT
6261640 TGT
1 TGT
6261643 TTTATTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (29 bp):
TGTATAAATGCTCTCTTGATATATAATAT
Found at i:6271044 original size:19 final size:20
Alignment explanation
Indices: 6271020--6271087 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
6271010 AACCCGACTC
6271020 AAAATAATATATTTATT-AA
1 AAAATAATATATTTATTCAA
* *
6271039 AAAATATTATTTTTATTCAA
1 AAAATAATATATTTATTCAA
* *
6271059 TAAAAT-ATAAATTTAATTGAA
1 -AAAATAATATATTT-ATTCAA
*
6271080 CAAATAAT
1 AAAATAAT
6271088 TAGAGTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 15 0.39
20 11 0.29
21 12 0.32
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
AAAATAATATATTTATTCAA
Found at i:6271462 original size:39 final size:40
Alignment explanation
Indices: 6271419--6271537 Score: 108
Period size: 39 Copynumber: 3.1 Consensus size: 40
6271409 AAGTTAAAAC
*
6271419 AATTTATAATGTTAATGTGAAATAATTTAAGAAATTATG-
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTATGA
* * *
6271458 AATTTCGAATATT-ATGGTGACAA-AATTTAATAAATTA-GA
1 AATTTAGAATGTTAAT-GTGA-AATAATTTAAGAAATTATGA
* *
6271497 AATTTAGAACGTTAGA-GTGAAATAATTTGAG-AATTAT-A
1 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAAATTATGA
6271535 AAT
1 AAT
6271538 AAAAATTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
38 14 0.22
39 47 0.73
40 2 0.03
41 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (40 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTATGA
Found at i:6273675 original size:23 final size:23
Alignment explanation
Indices: 6273656--6273700 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6273646 AATAATATTT
6273656 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
6273679 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
6273701 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:6274753 original size:20 final size:20
Alignment explanation
Indices: 6274706--6274753 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
6274696 ATCTTATTCC
*
6274706 CTAATAATATTTTATTCTCA
1 CTAATAATATTTTATTCTAA
**
6274726 CTGGTAATATTTTATTCTAA
1 CTAATAATATTTTATTCTAA
6274746 CTAATAAT
1 CTAATAAT
6274754 CTTACATTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.48
Consensus pattern (20 bp):
CTAATAATATTTTATTCTAA
Found at i:6275769 original size:35 final size:35
Alignment explanation
Indices: 6275722--6275807 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
6275712 AAAACAGTCA
* * *
6275722 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
6275757 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
6275792 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
6275808 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:6275801 original size:21 final size:21
Alignment explanation
Indices: 6275776--6275818 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6275766 TTCTAAACCC
6275776 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
6275797 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
6275818 T
1 T
6275819 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:6275973 original size:16 final size:18
Alignment explanation
Indices: 6275941--6275974 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
6275931 TATTAATGTA
6275941 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
6275959 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
6275975 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:6276642 original size:130 final size:130
Alignment explanation
Indices: 6276439--6276686 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
6276429 AATTTTCTTC
* * *
6276439 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
6276504 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
6276569 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
6276634 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
6276687 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:6277787 original size:30 final size:31
Alignment explanation
Indices: 6277752--6277825 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
6277742 AAAACCGAAT
*
6277752 TAAATGGGGACGGGGAAAAATC-GTTTATGC
1 TAAATGGGGACGGGGAAAAAACTGTTTATGC
* *
6277782 TAAATGGGGAC-GAGAAAAAACTGTTTATGT
1 TAAATGGGGACGGGGAAAAAACTGTTTATGC
*
6277812 TAAACGGGGACGGG
1 TAAATGGGGACGGG
6277826 TTTGGTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.22
30 28 0.76
31 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.34, T:0.22
Consensus pattern (31 bp):
TAAATGGGGACGGGGAAAAAACTGTTTATGC
Found at i:6277893 original size:4 final size:4
Alignment explanation
Indices: 6277884--6277973 Score: 52
Period size: 4 Copynumber: 24.5 Consensus size: 4
6277874 TAAAAATAAT
* * * *
6277884 TATA TATA TATA TATA TATA -ATA T-TA -ATA AATT TA-A TTTA AAT-
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
6277927 TA-A TATA TATA TATA TA-A TATT TATA TATT TA-A TTTA AATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
6277972 TA
1 TA
6277974 CCCGACCCGA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
3 15 0.24
4 48 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:6277895 original size:6 final size:6
Alignment explanation
Indices: 6277884--6277973 Score: 52
Period size: 6 Copynumber: 16.3 Consensus size: 6
6277874 TAAAAATAAT
* * * *
6277884 TATATA TATATA TATATA TA-ATA T-TA-A TAAATT TA-ATT TAAAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
6277927 TA-ATA TATATA TATATA -ATATT TATATA TTTA-A TTTAAA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
6277972 TA
1 TA
6277974 CCCGACCCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.06
5 24 0.35
6 41 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:6277944 original size:40 final size:38
Alignment explanation
Indices: 6277887--6277973 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 38
6277877 AAATAATTAT
6277887 ATATATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATATATAATATTAATAAATTTAATTTAA
* *
6277925 ATTAATATATATATATATAATATTTATATATTTAATTTAA
1 A-T-ATATATATATATATAATATTAATAAATTTAATTTAA
6277965 ATATATATA
1 ATATATATA
6277974 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 8 0.18
39 2 0.04
40 35 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
ATATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:6278505 original size:26 final size:26
Alignment explanation
Indices: 6278456--6278508 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6278446 ATTTTACTCG
*
6278456 AAACTTACGAATTTTAGTCTTATCCA
1 AAACTTACGAATTTTAGTCCTATCCA
*
6278482 AAACTTGCGAATTTT-GATCCTATCCA
1 AAACTTACGAATTTTAG-TCCTATCCA
6278508 A
1 A
6278509 TCTGATGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (26 bp):
AAACTTACGAATTTTAGTCCTATCCA
Found at i:6279529 original size:3 final size:3
Alignment explanation
Indices: 6279521--6279553 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
6279511 GCACAAACAA
6279521 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6279554 TAAAACAATT
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):
AAT
Found at i:6280407 original size:29 final size:29
Alignment explanation
Indices: 6280308--6280442 Score: 108
Period size: 29 Copynumber: 4.5 Consensus size: 29
6280298 GGACGCCGGC
* * *
6280308 GTGCATGGCGACCTATAAGGTCGTTGGGC
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
* * *
6280337 GTACATGGCGACCTACCATCTTGGTCGCCGGGA
1 GTGCATGGCGACCTA-CA---AGGTCGCTGGGA
* * *
6280370 TTGCTTGGCGACCTACAAGGTCGCTAGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*** *
6280399 GTGCATGGCGACCTTGTAGGTCGCTTGGA
1 GTGCATGGCGACCTACAAGGTCGCTGGGA
*
6280428 GTGCTTGGCGACCTA
1 GTGCATGGCGACCTA
6280443 TGGTTGGGTT
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 59 0.72
30 1 0.01
32 2 0.02
33 20 0.24
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (29 bp):
GTGCATGGCGACCTACAAGGTCGCTGGGA
Found at i:6281090 original size:30 final size:30
Alignment explanation
Indices: 6281049--6281122 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
6281039 AAAACCGAAT
*
6281049 TAAATGGGGACGGGAAAAAA-TCGTTTATGC
1 TAAACGGGGACGGGAAAAAACT-GTTTATGC
*
6281079 TAAACGGGGACGGGAAAAAACTGTTTATGT
1 TAAACGGGGACGGGAAAAAACTGTTTATGC
6281109 TAAACGGGGACGGG
1 TAAACGGGGACGGG
6281123 GACGGGTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAAACTGTTTATGC
Found at i:6281229 original size:19 final size:19
Alignment explanation
Indices: 6281205--6281263 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
6281195 TATATATAAT
*
6281205 ATTAATAAATTTAATTTAA
1 ATTAATATATTTAATTTAA
* *
6281224 ATTAATATATAT-ATATAA
1 ATTAATATATTTAATTTAA
*
6281242 TATTTATATATTTAATTTAA
1 -ATTAATATATTTAATTTAA
6281262 AT
1 AT
6281264 ATATATACCC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.16
19 22 0.69
20 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAATATATTTAATTTAA
Found at i:6281241 original size:38 final size:38
Alignment explanation
Indices: 6281184--6281270 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
6281174 TATTAAAAAT
6281184 AATTATATATATATATATAATATTAATAAATTTAATTTA
1 AATTA-ATATATATATATAATATTAATAAATTTAATTTA
* *
6281223 AATTAATATATATATATAATATTTATATATTTAATTTA
1 AATTAATATATATATATAATATTAATAAATTTAATTTA
6281261 AA-T-ATATATA
1 AATTAATATATA
6281271 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 7 0.15
37 1 0.02
38 33 0.72
39 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
AATTAATATATATATATAATATTAATAAATTTAATTTA
Found at i:6281243 original size:32 final size:34
Alignment explanation
Indices: 6281194--6281270 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
6281184 AATTATATAT
6281194 ATATATATAATATTAATAAATT-TA-ATTTAAATTA
1 ATATATAT-ATATTAAT-AATTATATATTTAAATTA
* *
6281228 ATATATATATA-TAATATTTATATATTTAATTTA
1 ATATATATATATTAATAATTATATATTTAAATTA
6281261 A-ATATATATA
1 ATATATATATA
6281271 CCCGACCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 13 0.33
34 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATATATATATATTAATAATTATATATTTAAATTA
Found at i:6281802 original size:26 final size:26
Alignment explanation
Indices: 6281753--6281805 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6281743 ATTTTACTCG
*
6281753 AAACTTACGAATTTTAGTCTTATCCA
1 AAACTTACGAATTTTAGTCCTATCCA
*
6281779 AAACTTGCGAATTTT-GATCCTATCCA
1 AAACTTACGAATTTTAG-TCCTATCCA
6281805 A
1 A
6281806 TCTGATGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (26 bp):
AAACTTACGAATTTTAGTCCTATCCA
Found at i:6282237 original size:2 final size:2
Alignment explanation
Indices: 6282230--6282266 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6282220 TACATTTATT
6282230 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
6282267 TAATATTACA
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:6282817 original size:5 final size:5
Alignment explanation
Indices: 6282807--6282967 Score: 235
Period size: 5 Copynumber: 32.4 Consensus size: 5
6282797 ATTCCCTCAC
6282807 ATTAT ATTAT ATTAT ATTAT A-TATT ATATAT ATTATAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTA-T AT-TAT A-T-TAT ATTAT ATTAT
6282855 ATTAT A-TAT A-TAT ATTAT A-TAT ATTAT ATTAT ATTAT A-TAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
6282901 ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT ATTAT ATATAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT ATTAT
6282951 ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT AT
6282968 GTAAGTATTC
Statistics
Matches: 147, Mismatches: 0, Indels: 18
0.89 0.00 0.11
Matches are distributed among these distances:
4 22 0.15
5 109 0.74
6 8 0.05
7 8 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:6282831 original size:7 final size:7
Alignment explanation
Indices: 6282819--6282967 Score: 116
Period size: 7 Copynumber: 20.4 Consensus size: 7
6282809 TATATTATAT
6282819 TATATTA
1 TATATTA
6282826 TATATTATA
1 TATA-T-TA
6282835 TATATTA
1 TATATTA
6282842 TATATTA
1 TATATTA
6282849 TAT-TATA
1 TATAT-TA
6282856 TTATATATA
1 -TATAT-TA
6282865 TATATTA
1 TATATTA
6282872 TATA-TA
1 TATATTA
6282878 T-TA-TA
1 TATATTA
6282883 TTATATTA
1 -TATATTA
6282891 TATA-TA
1 TATATTA
6282897 TTATATTA
1 -TATATTA
6282905 TAT-TATA
1 TATAT-TA
6282912 TTATATTA
1 -TATATTA
6282920 TAT-TATA
1 TATAT-TA
6282927 TATATTA
1 TATATTA
6282934 TATATATA
1 TATAT-TA
6282942 TTATATTA
1 -TATATTA
6282950 TAT-TATA
1 TATAT-TA
6282957 TTATATTA
1 -TATATTA
6282965 TAT
1 TAT
6282968 GTAAGTATTC
Statistics
Matches: 122, Mismatches: 0, Indels: 40
0.75 0.00 0.25
Matches are distributed among these distances:
5 4 0.03
6 10 0.08
7 62 0.51
8 29 0.24
9 17 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:6282836 original size:2 final size:2
Alignment explanation
Indices: 6282809--6282967 Score: 150
Period size: 2 Copynumber: 91.5 Consensus size: 2
6282799 TCCCTCACAT
6282809 TA TA T- TA TA T- TA TA T- TA TA TA T- TA TA TA TA T- 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
6282846 T- TA TA T- TA TA T- TA TA TA TA TA TA T- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6282883 T- TA TA T- TA TA TA TA T- TA TA T- TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6282918 TA TA T- TA TA TA TA T- TA TA TA TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6282955 TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA T
6282968 GTAAGTATTC
Statistics
Matches: 133, Mismatches: 0, Indels: 48
0.73 0.00 0.27
Matches are distributed among these distances:
1 24 0.18
2 109 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:6284574 original size:2 final size:2
Alignment explanation
Indices: 6284567--6284602 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6284557 CAATGTTAAT
6284567 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
6284603 ACTATAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6286049 original size:95 final size:94
Alignment explanation
Indices: 6285927--6286243 Score: 504
Period size: 88 Copynumber: 3.4 Consensus size: 94
6285917 TTTCTTTAAT
*
6285927 CGTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTCT
1 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAA-TTTTTTTCT
* * * *
6285992 TTAACAATAATCAAACTGAAATTATTTGAT
65 TTAACATTAATCGAACTAAAATTATTTGAC
6286022 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCG-A----TTT-TT
1 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTT
6286081 TAACATTAATCGAACTAAAATTATTTGAC
66 TAACATTAATCGAACTAAAATTATTTGAC
*
6286110 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGAATTTTTTTCTT
1 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTT
*
6286175 TAACATTAATCGAACCAAAATTATTTGAC
66 TAACATTAATCGAACTAAAATTATTTGAC
*
6286204 CGTTAATCGAACC-AAAATTATTTGAAAATTATTAACCGAA
1 CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
6286244 TTTTTTTCTT
Statistics
Matches: 208, Mismatches: 8, Indels: 14
0.90 0.03 0.06
Matches are distributed among these distances:
88 79 0.38
89 4 0.02
93 29 0.14
94 44 0.21
95 52 0.25
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (94 bp):
CGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTCTT
TAACATTAATCGAACTAAAATTATTTGAC
Found at i:6286091 original size:88 final size:88
Alignment explanation
Indices: 6285987--6286373 Score: 443
Period size: 88 Copynumber: 4.4 Consensus size: 88
6285977 CCGAATTTTT
* * ** *
6285987 TTTCTTTAACAATAATCAAACTGAAATTATTTGATCGTTAATCGAACCGAAATTTATTTGAAAAT
1 TTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAAT
6286052 TATTAACCGAACCAAATTAACCGA
66 TATTAACCGAACCAAATTAA-CGA
*
6286076 TTT-TTTAACATTAATCGAACTAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAAT
1 TTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAAT
6286140 TATTAACCGAACCAAATTAATCGAA
66 TATTAACCGAACCAAATTAA-CG-A
*
6286165 TTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACC-AAAATTATTTGA
1 ----TTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGA
**
6286229 AAATTATTAACCG-----AATT---TT
62 AAATTATTAACCGAACCAAATTAACGA
* *
6286248 TTTCTTTAACCATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTTGAAAA
1 TTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAA
** * **
6286313 TTATTAACCGAATAAAATAAATTA
65 TTATTAACCGAACCAAATTAACGA
* *
6286337 TTTTCTTTAACCTTTAATCGAACCGAAATTTATTTGA
1 -TTTCTTTAA-CATTAATCGAACC-AAAATTATTTGA
6286374 AAATTATTAA
Statistics
Matches: 264, Mismatches: 16, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
79 9 0.03
80 38 0.14
81 24 0.09
86 3 0.01
88 83 0.31
89 5 0.02
90 21 0.08
91 11 0.04
93 27 0.10
94 43 0.16
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (88 bp):
TTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAAT
TATTAACCGAACCAAATTAACGA
Found at i:6286216 original size:26 final size:26
Alignment explanation
Indices: 6286178--6286309 Score: 106
Period size: 26 Copynumber: 5.0 Consensus size: 26
6286168 TTTTCTTTAA
6286178 CATTAATCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAAATTATTTGAC
* *
6286204 CGTTAATCGAACCAAAATTATTTGAA
1 CATTAATCGAACCAAAATTATTTGAC
* * ** * *
6286230 AATT-AT-TAACCGAATTTTTTTCTTTAAC
1 CATTAATCGAACC-AA---AATTATTTGAC
*
6286258 CATTAACCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAAATTATTTGAC
* *
6286284 CGTTAATCGAACCCAAATTTATTTGA
1 CATTAATCGAA-CCAAAATTATTTGA
6286310 AAATTATTAA
Statistics
Matches: 79, Mismatches: 20, Indels: 13
0.71 0.18 0.12
Matches are distributed among these distances:
24 4 0.05
25 4 0.05
26 42 0.53
27 13 0.16
28 9 0.11
29 3 0.04
30 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (26 bp):
CATTAATCGAACCAAAATTATTTGAC
Found at i:6286275 original size:80 final size:80
Alignment explanation
Indices: 6286155--6286325 Score: 299
Period size: 80 Copynumber: 2.1 Consensus size: 80
6286145 ACCGAACCAA
* *
6286155 ATTAATCGAATTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAA-CCAA
1 ATTAACCGAATTTTTTTCTTTAACATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCAA
6286219 AATTATTTGAAAATT
66 AATTATTTGAAAATT
6286234 ATTAACCGAATTTTTTTCTTTAACCATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCGAATTTTTTTCTTTAA-CATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCA
*
6286299 AATTTATTTGAAAATT
65 AAATTATTTGAAAATT
6286315 ATTAACCGAAT
1 ATTAACCGAAT
6286326 AAAATAAATT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
79 22 0.25
80 36 0.41
81 29 0.33
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (80 bp):
ATTAACCGAATTTTTTTCTTTAACATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCAA
AATTATTTGAAAATT
Found at i:6286358 original size:64 final size:67
Alignment explanation
Indices: 6286286--6286441 Score: 221
Period size: 64 Copynumber: 2.4 Consensus size: 67
6286276 TATTTGACCG
* *
6286286 TTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAAT-AA-ATT-ATTTTCTTTAAC
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAACATTGATTTTCTTTAAC
*
6286348 CT
66 CA
* *
6286350 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTGTTTTTCTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAA-C-ATTGATTTTCTTTA
6286415 ACCA
64 ACCA
6286419 TTAATCGAACCGAAA-TTATTTGA
1 TTAATCGAACCGAAATTTATTTGA
6286442 CCATTAATCG
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
64 42 0.51
65 2 0.02
68 11 0.13
69 27 0.33
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (67 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAACATTGATTTTCTTTAAC
CA
Found at i:6286445 original size:26 final size:27
Alignment explanation
Indices: 6286415--6286468 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
6286405 TTTTTCTTTA
6286415 ACCATTAATCGAACCGAAA-TTATTTG
1 ACCATTAATCGAACCGAAATTTATTTG
*
6286441 ACCATTAATCGAATCGAAATTTATTTG
1 ACCATTAATCGAACCGAAATTTATTTG
6286468 A
1 A
6286469 AAATTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (27 bp):
ACCATTAATCGAACCGAAATTTATTTG
Found at i:6286449 original size:95 final size:93
Alignment explanation
Indices: 6286350--6286534 Score: 257
Period size: 95 Copynumber: 2.0 Consensus size: 93
6286340 TCTTTAACCT
* *
6286350 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATT-GTTTTTCTTT
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAAT-AA---ATTAGTTTTTCCTT
*
6286414 AACCATTAATCGAACCGAAA-TTATTTGACCA
62 AACCATTAATCGAACCAAAATTTATTTGACCA
* * *
6286445 TTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACC
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATAAATTAGTTTTTCCTTAACC
*
6286510 GTTAATCGAACCAAAATTTATTTGA
66 ATTAATCGAACCAAAATTTATTTGA
6286535 AAATTATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
91 3 0.04
92 26 0.32
93 8 0.10
94 2 0.02
95 42 0.52
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (93 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATAAATTAGTTTTTCCTTAACC
ATTAATCGAACCAAAATTTATTTGACCA
Found at i:6286474 original size:27 final size:26
Alignment explanation
Indices: 6286418--6286474 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
6286408 TTCTTTAACC
**
6286418 ATTAATCGAACCGAAATTATTTGACC
1 ATTAATCGAACCGAAATTATTTGAAA
*
6286444 ATTAATCGAATCGAAATTTATTTGAAA
1 ATTAATCGAACCGAAA-TTATTTGAAA
6286471 ATTA
1 ATTA
6286475 TTAACCGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (26 bp):
ATTAATCGAACCGAAATTATTTGAAA
Found at i:6286640 original size:160 final size:159
Alignment explanation
Indices: 6286234--6286643 Score: 655
Period size: 159 Copynumber: 2.6 Consensus size: 159
6286224 TTTGAAAATT
* * *
6286234 ATTAACCGA-ATTTTTTTCTTTAACCATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCC
1 ATTAACCGATA-TTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCA
* * *
6286298 AAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTCTTTAACCTTTAATCGAACCGA
65 AAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTCCTTAACCGTTAATCGAACCAA
6286363 AATTTATTTGAAAATTATTAACCGAACCAA
130 AATTTATTTGAAAATTATTAACCGAACCAA
* * * *
6286393 ATCAACCGAT-TGTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCGAATCG
1 ATTAACCGATAT-TTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCA
6286457 AAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACC
65 AAATTTATTTGAAAATTATTAACCGAATAAAATAAATTA--TTTTCCTTAACCGTTAATCGAACC
*
6286522 AAAATTTATTTGAAAATTATTAACCGAACCCA
128 AAAATTTATTTGAAAATTATTAACCGAACCAA
*
6286554 ATTAACCGATATTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGACTGTTAATCGAACCAA
1 ATTAACCGATATTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAA
6286618 AATTTATTTGAAAATTATTAACCGAA
66 AATTTATTTGAAAATTATTAACCGAA
6286644 CCAAATTAAC
Statistics
Matches: 231, Mismatches: 15, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
158 1 0.00
159 94 0.41
160 63 0.27
161 72 0.31
162 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (159 bp):
ATTAACCGATATTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAA
AATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTCCTTAACCGTTAATCGAACCAAA
ATTTATTTGAAAATTATTAACCGAACCAA
Found at i:6286693 original size:160 final size:160
Alignment explanation
Indices: 6286024--6286694 Score: 760
Period size: 161 Copynumber: 4.2 Consensus size: 160
6286014 TATTTGATCG
6286024 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCG--A---TTT-TTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATATTTTTTCTTTA
** *
6286083 A-CATTAATCGAACTAAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAAC
66 ACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAAC
* *
6286147 CGAACCAAATTAATCGAATTTTTTTCTTTAA-CA
131 CGAA-TAAAATAA---AATTTTTTTCTTTAACCA
* *** * * **
6286180 TTAATCGAACC-AAAATTATTTGACCGTTAATCGAACCAAAATTATTTGAAAATTATTAACCGA-
1 TTAATCGAACCGAAATTTATTTGAAAATT-AT-TAACC--GA--A----CCAA--ATTAACCGAT
* * *
6286243 ATTTTTTTCTTTAACCATTAACCGAACCAAAATTATTTGACCGTTAATCGAACCCAAATTTATTT
54 A-TTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTT
* *
6286308 GAAAATTATTAACCGAATAAAAT-AAATTATTTTCTTTAACCT
118 GAAAATTATTAACCGAATAAAATAAAATTTTTTTCTTTAACCA
*
6286350 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGAT-TGTTTTTCTTT
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATAT-TTTTTCTTT
* * *
6286414 AACCATTAATCGAACCGAAATTATTTGACCATTAATCGAATCGAAATTTATTTGAAAATTATTAA
65 AACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAA
* * *
6286479 CCGAATAAAATAAATTATTTTTTCCTTAACCG
130 CCGAATAAAATAAAAT-TTTTTTCTTTAACCA
* *
6286511 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCCAATTAACCGATATTTTTTCTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATATTTTTTCTTTA
*
6286576 A-CATTAATCGAACCGAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGAAAATTATTAAC
66 ACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAAC
* *
6286640 CGAACCAAATTAACCAATTTTTTTCTTTAA-CA
131 CGAA-TAAAATAA--AATTTTTTTCTTTAACCA
*
6286672 TTAATCGAATCGAAA-TTATTTGA
1 TTAATCGAACCGAAATTTATTTGA
6286695 TCGTTATCAA
Statistics
Matches: 439, Mismatches: 47, Indels: 54
0.81 0.09 0.10
Matches are distributed among these distances:
155 13 0.03
156 13 0.03
157 4 0.01
158 1 0.00
159 89 0.20
160 74 0.17
161 96 0.22
162 12 0.03
163 2 0.00
165 3 0.01
167 9 0.02
168 1 0.00
169 18 0.04
170 14 0.03
171 13 0.03
172 4 0.01
173 9 0.02
174 64 0.15
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (160 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATATTTTTTCTTTA
ACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAAC
CGAATAAAATAAAATTTTTTTCTTTAACCA
Found at i:6286732 original size:92 final size:93
Alignment explanation
Indices: 6286509--6286732 Score: 371
Period size: 94 Copynumber: 2.4 Consensus size: 93
6286499 TTTCCTTAAC
* *
6286509 CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCCAATTAACCGATATTTTTTCTT
1 CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAATATTTTTTCTT
6286574 TAACATTAATCGAACCGAAATTATTTGA
66 TAACATTAATCGAACCGAAATTATTTGA
6286602 CTGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAAT-TTTTTTCT
1 C-GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAATATTTTTTCT
*
6286666 TTAACATTAATCGAATCGAAATTATTTGA
65 TTAACATTAATCGAACCGAAATTATTTGA
* *
6286695 TCGTT-ATCAAACCAAAATTTATTTGATAATTATTAACC
1 -CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
6286733 AACAGTTAAT
Statistics
Matches: 124, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
92 31 0.25
93 40 0.32
94 53 0.43
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (93 bp):
CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCAATATTTTTTCTT
TAACATTAATCGAACCGAAATTATTTGA
Found at i:6287916 original size:19 final size:19
Alignment explanation
Indices: 6287892--6287943 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
6287882 AATAGCCAGA
6287892 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
6287911 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
6287930 GTGCATCGATGCAT
1 GTGCATCGATGCAT
6287944 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:6287980 original size:65 final size:62
Alignment explanation
Indices: 6287910--6288075 Score: 183
Period size: 65 Copynumber: 2.6 Consensus size: 62
6287900 ATGCATGGCT
6287910 GGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCT
1 GGTGCATCGATGCATGG-TGGTGCATCGATGCATCAAATGCATTCGATG--TTCAATAAAAT--T
6287974 CA
61 CA
* * * **
6287976 -GTGCATCGGTGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTCAATTTAATTCA
1 GGTGCATCGATGCATGGT-GGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCA
*
6288038 TGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 -GGTGCATCGATGCATGG--TGGTGCATCGATGCATCA
6288076 CTCTGAAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.25
65 57 0.67
66 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (62 bp):
GGTGCATCGATGCATGGTGGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCA
Found at i:6288005 original size:84 final size:85
Alignment explanation
Indices: 6287827--6288009 Score: 239
Period size: 84 Copynumber: 2.2 Consensus size: 85
6287817 AAGCGTCTCA
* *
6287827 TGCATCGATGCATACCCTAGGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGA
1 TGCATCGATGCATACCCTAGGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACA
6287892 GTGCATCGATGCATGGCTGG
66 GTGCATCGATGCATGGCTGG
** * *
6287912 TGCATCGATGCAT-GGCT-GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT
1 TGCATCGATGCATACCCTAGGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCA
* *
6287974 CAGTGCATCGGTGCATGG-TATG
64 CAGTGCATCGATGCATGGCT-GG
6287996 TGCATCGATGCATA
1 TGCATCGATGCATA
6288010 AAATGCATTC
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
83 30 0.35
84 40 0.47
85 16 0.19
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (85 bp):
TGCATCGATGCATACCCTAGGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACA
GTGCATCGATGCATGGCTGG
Found at i:6288317 original size:20 final size:21
Alignment explanation
Indices: 6288280--6288319 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6288270 AAATTAAGTT
6288280 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
6288301 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
6288320 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:6288605 original size:65 final size:63
Alignment explanation
Indices: 6288489--6288695 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 63
6288479 ATTTGAGGTG
* * * * *
6288489 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
6288553 C
63 C
* *
6288554 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
6288619 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
6288683 ATGCATCGATGCA
1 ATGCACCGATGCA
6288696 CACTTGGTGC
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 84 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:6288714 original size:64 final size:65
Alignment explanation
Indices: 6288536--6288699 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
6288526 GAATTAATTG
* * ** *
6288536 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
6288601 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
6288665 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
6288700 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:6290401 original size:15 final size:16
Alignment explanation
Indices: 6290383--6290413 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6290373 CATAGACCAT
6290383 TATCACATAA-ATGTA
1 TATCACATAACATGTA
6290398 TATCACATAACATGTA
1 TATCACATAACATGTA
6290414 ATACAAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (16 bp):
TATCACATAACATGTA
Found at i:6290977 original size:55 final size:53
Alignment explanation
Indices: 6290892--6291034 Score: 180
Period size: 55 Copynumber: 2.6 Consensus size: 53
6290882 CTACTTGGGA
* * *
6290892 GTATCAATACACTCCCCAGTGTACCGATACACAAATTGTAC-TCGATGTTTTGAAT
1 GTATCGATACACTCCTCAGTGTACCGATACACAAA-TG-ACATCGATGTTTTG-AG
* *
6290947 GTATCGATACACTACTCAGTGTACCAATACACAAATGACATTCGATGTTTTGAG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATGACA-TCGATGTTTTGAG
*
6291001 GATATCGATACACTCCTCAGCGTACCGATACACA
1 G-TATCGATACACTCCTCAGTGTACCGATACACA
6291035 CTCATACAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
53 2 0.03
54 4 0.05
55 71 0.92
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (53 bp):
GTATCGATACACTCCTCAGTGTACCGATACACAAATGACATCGATGTTTTGAG
Found at i:6298403 original size:17 final size:17
Alignment explanation
Indices: 6298383--6298417 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6298373 ACAAACTAGG
6298383 CCTTAAAATGAACTAAA
1 CCTTAAAATGAACTAAA
6298400 CCTTAAAATGAACTAAA
1 CCTTAAAATGAACTAAA
6298417 C
1 C
6298418 GTTCATGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (17 bp):
CCTTAAAATGAACTAAA
Found at i:6304992 original size:30 final size:30
Alignment explanation
Indices: 6304947--6305021 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
6304937 AATATTATAA
6304947 TTGAAAAAGCTGGAAATCACATGCA-AAGCAG
1 TTGAAAAA-CTGGAAATCACATGCAGAA-CAG
*
6304978 TTGAAAAACTGGAAATCACATGCAGAACTG
1 TTGAAAAACTGGAAATCACATGCAGAACAG
*
6305008 TTGAAAAGCTGGAA
1 TTGAAAAACTGGAA
6305022 CAATAGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 31 0.76
31 10 0.24
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (30 bp):
TTGAAAAACTGGAAATCACATGCAGAACAG
Found at i:6324962 original size:17 final size:18
Alignment explanation
Indices: 6324926--6324960 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6324916 TATTTTTATG
6324926 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
6324944 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
6324961 AAAAAGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:6326127 original size:156 final size:152
Alignment explanation
Indices: 6325676--6326171 Score: 559
Period size: 156 Copynumber: 3.2 Consensus size: 152
6325666 TGTGGTATAT
6325676 GAGCATGTGGTTCAAATTTGGTAAAAAAAAATGGACTTGAAATAAAGGATGAATTGAAGAAATAA
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAAATGGACTTGAAATAAAGGATGAATTGAAGAAATAA
** ** * **
6325741 GAAAATTACGA-AAAATTGATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
66 GAAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
*
6325805 ATATGTATTAGACA-ATGGTTTAG
131 ATATGTATTATA-AGAT-GTTTAG
*
6325828 GAGCATGTGGTTCAAATTTTGT-AAAAAAAATGGACTTGAAATAAAGGATG-ATTGAAGAAATAC
1 GAGCATGTGGTTCAAATTTGGTAAAAAAAAATGGACTTGAAATAAAGGATGAATTGAAGAAAT--
** * * * * *
6325891 GGAAATTATGAAAAAAAATAAGGGACTAAATTGAAAAAAAGAAAATTTGTTATCATAAAGGGGCA
64 ----A--A-GAAAATTAAT-AGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAA
* *
6325956 TTGAAAGCACATATGTATTTTAAGATAGTTTAG
121 TTGAAAGTACATATGTATTATAAGAT-GTTTAG
* * *
6325989 GAGCATGTAGTTCAAATTTGGTAAAAAAAAATAATAGACTTGAAATAAAGGAGGAATTGAAGAAA
1 GAGCATGTGGTTCAAATTTGGT--AAAAAAA-AATGGACTTGAAATAAAGGATGAATTGAAGAAA
* * ***
6326054 TAAGTAAATTAATAGGGACTAAATTGAAAAATTGAAAAAAAATTATCAAAAAGAGGAATTGAAAG
63 TAAGAAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAG
*
6326119 TACATATGTATTCTAAGATGATTTAG
128 TACATATGTATTATAAGATG-TTTAG
*
6326145 GAGCATGTGGTTTAAATTTGGTAAAAA
1 GAGCATGTGGTTCAAATTTGGTAAAAA
6326172 TTATACTTAA
Statistics
Matches: 287, Mismatches: 39, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
150 11 0.04
151 28 0.10
152 21 0.07
154 5 0.02
155 1 0.00
156 86 0.30
157 7 0.02
158 2 0.01
159 6 0.02
160 3 0.01
161 80 0.28
164 6 0.02
165 20 0.07
166 11 0.04
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (152 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAAAATGGACTTGAAATAAAGGATGAATTGAAGAAATAA
GAAAATTAATAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAAGTAC
ATATGTATTATAAGATGTTTAG
Found at i:6326651 original size:26 final size:26
Alignment explanation
Indices: 6326621--6326685 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
6326611 ACATATGTAT
*
6326621 TAAATTATTAAAATAAAT-CTCATAAA
1 TAAATTATTAAAA-AAATACTAATAAA
***
6326647 TAAATTATTAAAAGCGTACTAATAAA
1 TAAATTATTAAAAAAATACTAATAAA
6326673 TAAATTATTAAAA
1 TAAATTATTAAAA
6326686 GCGTACTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAATTATTAAAAAAATACTAATAAA
Found at i:6326703 original size:26 final size:26
Alignment explanation
Indices: 6326642--6326695 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
6326632 AATAAATCTC
6326642 ATAAATAAATTATTAAAAGCGTACTA
1 ATAAATAAATTATTAAAAGCGTACTA
6326668 ATAAATAAATTATTAAAAGCGTACTA
1 ATAAATAAATTATTAAAAGCGTACTA
6326694 AT
1 AT
6326696 TATGAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.31
Consensus pattern (26 bp):
ATAAATAAATTATTAAAAGCGTACTA
Found at i:6326957 original size:26 final size:25
Alignment explanation
Indices: 6326928--6327040 Score: 106
Period size: 25 Copynumber: 4.4 Consensus size: 25
6326918 CAATTTAGTT
6326928 ATATTTTTAATAAATTAAAATAAATTA
1 ATATTTTTAATAAATTAAAATAAA--A
*
6326955 TATATTTTTAAATGAA--AAAAT-AAA
1 -ATATTTTT-AATAAATTAAAATAAAA
*
6326979 ATATTTTTAAATAACTTAATAATAAAA
1 ATATTTTT-AATAAATTAA-AATAAAA
* * *
6327006 ATATATTTAATAAGTTAATATAAAA
1 ATATTTTTAATAAATTAAAATAAAA
6327031 ATATTTTTAA
1 ATATTTTTAA
6327041 GTTAATATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
23 13 0.18
24 1 0.01
25 17 0.23
26 14 0.19
27 15 0.21
28 8 0.11
29 5 0.07
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATTTTTAATAAATTAAAATAAAA
Found at i:6327034 original size:25 final size:24
Alignment explanation
Indices: 6326976--6327049 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 24
6326966 ATGAAAAAAT
*
6326976 AAAATATTTTTAAATAACTTAATAATA
1 AAAATA-TTTT-AATAAGTTAAT-ATA
6327003 AAAATATATTTAATAAGTTAATATA
1 AAAATAT-TTTAATAAGTTAATATA
6327028 AAAATATTTT--TAAGTTAATATA
1 AAAATATTTTAATAAGTTAATATA
6327050 TATAAAATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
22 12 0.27
24 3 0.07
25 10 0.22
26 11 0.24
27 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
AAAATATTTTAATAAGTTAATATA
Found at i:6327056 original size:25 final size:26
Alignment explanation
Indices: 6326989--6327068 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 26
6326979 ATATTTTTAA
*
6326989 ATAACTTAATA-ATAAAAATATATTT
1 ATAAGTTAATATATAAAAATATATTT
6327014 AATAAGTT-A-ATATAAAAATAT-TTT
1 -ATAAGTTAATATATAAAAATATATTT
6327038 -TAAGTTAATATATATAAAATTATATTAT
1 ATAAGTTAATATATA-AAAA-TATATT-T
6327066 ATA
1 ATA
6327069 TAATCTGAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
22 6 0.13
23 1 0.02
24 9 0.20
25 15 0.33
26 9 0.20
27 2 0.04
28 1 0.02
29 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAAGTTAATATATAAAAATATATTT
Found at i:6327274 original size:22 final size:22
Alignment explanation
Indices: 6327225--6327276 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
6327215 TTAAAAATTC
*
6327225 AAATTAAATAAATAAAATAAAT
1 AAATTAAAAAAATAAAATAAAT
**
6327247 TTATTAAAAAAATAAAATAAAT
1 AAATTAAAAAAATAAAATAAAT
6327269 AAATTAAA
1 AAATTAAA
6327277 TTAAATTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTAAAAAAATAAAATAAAT
Found at i:6327463 original size:13 final size:13
Alignment explanation
Indices: 6327447--6327477 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6327437 ATAAAAATTT
6327447 AATATAAAATAAA
1 AATATAAAATAAA
*
6327460 AATAAAAAATAAA
1 AATATAAAATAAA
6327473 AATAT
1 AATAT
6327478 GTATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATAAAATAAA
Found at i:6327899 original size:31 final size:31
Alignment explanation
Indices: 6327830--6327902 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
6327820 ACTTGGGGTG
* * *
6327830 ATCACATCTTAAATAAATAAAAACGAAAGTG
1 ATCATATCTTAAATAAATAAAAACAAAAGTA
* *
6327861 GTCATATCTTAATTAAATAAAAACAAAAGTA
1 ATCATATCTTAAATAAATAAAAACAAAAGTA
*
6327892 ATTATATCTTA
1 ATCATATCTTA
6327903 TGTTTTTTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (31 bp):
ATCATATCTTAAATAAATAAAAACAAAAGTA
Found at i:6329801 original size:24 final size:25
Alignment explanation
Indices: 6329765--6329812 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6329755 TTCTCCTTGT
*
6329765 AAATTTTAAATATAAATA-ATATAA
1 AAATATTAAATATAAATATATATAA
* *
6329789 AAATATTATATATATATATATATA
1 AAATATTAAATATAAATATATATA
6329813 TAATACACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATTAAATATAAATATATATAA
Found at i:6335621 original size:24 final size:25
Alignment explanation
Indices: 6335582--6335630 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6335572 GATCCCAAAC
*
6335582 TTTTAATTCACTTTTTCTCTATCAT
1 TTTTAATTCACTTTTTCTATATCAT
*
6335607 TTTTTATTCACTTTTT-TATATCAT
1 TTTTAATTCACTTTTTCTATATCAT
6335631 GAATGCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTAATTCACTTTTTCTATATCAT
Found at i:6336572 original size:59 final size:58
Alignment explanation
Indices: 6336478--6336603 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 58
6336468 AAGGGTCAAG
* * * ** * *
6336478 TACACAAATGGTCCCAACTATAGGATAATGTTTTATCGAGTCCCTTGATTATTAAATGT
1 TACA-AAATGATCCCAACTATAGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGT
* *
6336537 TACAAAATGATCCCAAACTATAAGGAT-TTGCTTTATTGAATCCCTCAACTATTAAAAGT
1 TACAAAATGATCCC-AACTAT-AGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGT
6336596 TACAAAAT
1 TACAAAAT
6336604 AGTCACTCGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 9 0.16
59 42 0.75
60 5 0.09
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (58 bp):
TACAAAATGATCCCAACTATAGGATAATGCTTTATCGAATCCCTCAACTATTAAAAGT
Found at i:6337187 original size:25 final size:25
Alignment explanation
Indices: 6337159--6337206 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
6337149 AAAAGCTACT
*
6337159 CCATATCAAAATTTCATTTCTAAAC
1 CCATATCAAAATTTCATCTCTAAAC
* * *
6337184 CCATTTTACAATTTCATCTCTAA
1 CCATATCAAAATTTCATCTCTAA
6337207 TTTATTTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
CCATATCAAAATTTCATCTCTAAAC
Found at i:6339079 original size:31 final size:31
Alignment explanation
Indices: 6339041--6339196 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
6339031 CCCGAAGGAC
* * *
6339041 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
6339072 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
6339103 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6339134 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6339165 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6339196 C
1 C
6339197 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:6339438 original size:23 final size:24
Alignment explanation
Indices: 6339412--6339458 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
6339402 ATATACTTGT
*
6339412 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
6339435 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
6339459 CATGTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:6340119 original size:21 final size:21
Alignment explanation
Indices: 6340089--6340133 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6340079 ATTCTGTCGT
* *
6340089 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
6340110 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
6340131 TTG
1 TTG
6340134 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:6343127 original size:31 final size:31
Alignment explanation
Indices: 6343089--6343244 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
6343079 CCCGAAGGAC
* * *
6343089 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
6343120 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
6343151 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6343182 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6343213 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
6343244 C
1 C
6343245 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:6343483 original size:23 final size:24
Alignment explanation
Indices: 6343457--6343503 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
6343447 ATATACTTGT
*
6343457 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
6343480 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
6343504 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:6344170 original size:21 final size:20
Alignment explanation
Indices: 6344127--6344166 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6344117 ATTCTGTCGT
* *
6344127 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
6344147 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
6344167 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:6351052 original size:140 final size:140
Alignment explanation
Indices: 6350797--6351086 Score: 526
Period size: 140 Copynumber: 2.1 Consensus size: 140
6350787 AATAGAAAAT
* *
6350797 TATTTAAAATTAATATTAATTTATTCAATTTAATAGTATAAAGTTAAGATAATTTTTAATATAAT
1 TATTTAAAATAAATATTAATTTATTCAATTTAATAGTATAAAGTTAAGATAATTATTAATATAAT
6350862 AATATATTTTAATATATGAATGGATCGAGGAGGGACAATGGGCGACAATCACTCATCTTAACTGT
66 AATATATTTTAATATATGAATGGATCGAGGAGGGACAATGGGCGACAATCACTCATCTTAACTGT
*
6350927 TTAGATTACC
131 TTAGATTACA
6350937 TATTTAAAATAAATATTAATTTATTCAATTTAATAGTATAAAGTTAAGATAATTATTAATATAAT
1 TATTTAAAATAAATATTAATTTATTCAATTTAATAGTATAAAGTTAAGATAATTATTAATATAAT
* *
6351002 AATATATTTTAATATATGAATGGATCGAGGAGGGACGATGGGCGATAATCACTCATCTTAACTGT
66 AATATATTTTAATATATGAATGGATCGAGGAGGGACAATGGGCGACAATCACTCATCTTAACTGT
6351067 TTAGATTACA
131 TTAGATTACA
*
6351077 TATTTTAAAT
1 TATTTAAAAT
6351087 TTTTTTATAT
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 144 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (140 bp):
TATTTAAAATAAATATTAATTTATTCAATTTAATAGTATAAAGTTAAGATAATTATTAATATAAT
AATATATTTTAATATATGAATGGATCGAGGAGGGACAATGGGCGACAATCACTCATCTTAACTGT
TTAGATTACA
Found at i:6358641 original size:20 final size:20
Alignment explanation
Indices: 6358611--6358677 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
6358601 AATTTTAATT
6358611 TTTATATTATTAAATATATTA
1 TTTA-ATTATTAAATATATTA
**
6358632 TTTAATTATTAAATATAAAA
1 TTTAATTATTAAATATATTA
*
6358652 TATT-ATTATAAAATATATTAA
1 T-TTAATTATTAAATATATT-A
6358673 TTTAA
1 TTTAA
6358678 CCGTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 29 0.76
21 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAATTATTAAATATATTA
Found at i:6358663 original size:13 final size:13
Alignment explanation
Indices: 6358614--6358671 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
6358604 TTTAATTTTT
*
6358614 ATATTATTA-AAT
1 ATATTATTATAAA
6358626 ATATTATT-T-AA
1 ATATTATTATAAA
* *
6358637 TTATTAAATATAAA
1 ATATT-ATTATAAA
6358651 ATATTATTATAAA
1 ATATTATTATAAA
6358664 ATA-TATTA
1 ATATTATTA
6358672 ATTTAACCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 5 0.14
12 15 0.41
13 11 0.30
14 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTATTATAAA
Found at i:6358719 original size:20 final size:20
Alignment explanation
Indices: 6358612--6358719 Score: 57
Period size: 20 Copynumber: 5.3 Consensus size: 20
6358602 ATTTTAATTT
6358612 TTAT-ATTATTAAATATATTA
1 TTATAATTA-TAAATATATTA
*
6358632 TT-TAATTATTAAATATA-AA
1 TTATAATTA-TAAATATATTA
* *
6358651 ATATTATTATAAAATATATTAA
1 TTATAATTAT-AAATATATT-A
*
6358673 TT-TAACCGTT-TAAA-ATATAA
1 TTATAA---TTATAAATATATTA
*
6358693 TAAATAATTATAAATATATTA
1 T-TATAATTATAAATATATTA
6358714 TTATAA
1 TTATAA
6358720 AATATATGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
19 6 0.09
20 37 0.56
21 12 0.18
22 8 0.12
23 1 0.02
24 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (20 bp):
TTATAATTATAAATATATTA
Found at i:6358724 original size:15 final size:14
Alignment explanation
Indices: 6358615--6358726 Score: 56
Period size: 14 Copynumber: 8.0 Consensus size: 14
6358605 TTAATTTTTA
6358615 TATTATTAAATATAT
1 TATTA-TAAATATAT
6358630 TATT-T-AAT-TAT
1 TATTATAAATATAT
*
6358641 TAAATATAAA-ATAT
1 T-ATTATAAATATAT
6358655 TATTATAAAATATAT
1 TATTAT-AAATATAT
***
6358670 TAATT-TAACCGT-T
1 T-ATTATAAATATAT
** *
6358683 TAAAATATAATAAAT
1 TATTATA-AATATAT
*
6358698 AATTATAAATATAT
1 TATTATAAATATAT
6358712 TATTATAAAATATAT
1 TATTAT-AAATATAT
6358727 GTTTTGAATT
Statistics
Matches: 70, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
13 10 0.14
14 24 0.34
15 23 0.33
16 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (14 bp):
TATTATAAATATAT
Found at i:6362633 original size:2 final size:2
Alignment explanation
Indices: 6362626--6362651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6362616 GAAGAAACAC
6362626 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
6362652 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6362656 original size:2 final size:2
Alignment explanation
Indices: 6362651--6362679 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6362641 TCTCTCTCTC
6362651 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 T
6362680 TGGTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6364124 original size:18 final size:17
Alignment explanation
Indices: 6364091--6364124 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6364081 GAATAATTAA
6364091 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
6364108 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
6364125 AAACAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Done.