Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004593.1 Hibiscus syriacus cultivar Beakdansim tig00010263_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: 1592963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:184217 original size:2 final size:2
Alignment explanation
Indices: 184210--184243 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
184200 TATCTAAGCA
184210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184244 GTGATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:186449 original size:37 final size:40
Alignment explanation
Indices: 186408--186494 Score: 110
Period size: 37 Copynumber: 2.3 Consensus size: 40
186398 GGATAAAGAT
*
186408 AAAAAGAAAATAG-ATAAATAAATGAGTAAAAT-A-AATA
1 AAAAAGAAAATAGCATAAATAAATAAGTAAAATAATAATA
* * *
186445 AAAAAGTAAA-AGCATATATATATAAGTAAAATAATAATA
1 AAAAAGAAAATAGCATAAATAAATAAGTAAAATAATAATA
186484 AAAAAGAAAAT
1 AAAAAGAAAAT
186495 CAAAAGTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 2 0.05
37 25 0.61
38 1 0.02
39 13 0.32
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.21
Consensus pattern (40 bp):
AAAAAGAAAATAGCATAAATAAATAAGTAAAATAATAATA
Found at i:186452 original size:17 final size:17
Alignment explanation
Indices: 186421--186455 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
186411 AAGAAAATAG
**
186421 ATAAATAAATGAGTAAA
1 ATAAATAAAAAAGTAAA
186438 ATAAATAAAAAAGTAAA
1 ATAAATAAAAAAGTAAA
186455 A
1 A
186456 GCATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (17 bp):
ATAAATAAAAAAGTAAA
Found at i:187064 original size:37 final size:37
Alignment explanation
Indices: 186974--187066 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
186964 GAATCATATC
* * * *
186974 TTTAAGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTATT
* *
187011 TTTAGGAGTTTGAATCCTAGTAAAATTCTATCTTATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTATT
187048 TTTAGGAGTTTGAATCCTA
1 TTTAGGAGTTTGAATCCTA
187067 ATAGGACGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAAAACTCTATCCTATT
Found at i:187982 original size:106 final size:106
Alignment explanation
Indices: 187801--188851 Score: 1823
Period size: 106 Copynumber: 9.9 Consensus size: 106
187791 GCGTTGTTCC
* * * * *
187801 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
187866 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
187907 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
187972 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
188013 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
188078 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
188119 GAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
188184 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
188225 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
188290 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
188331 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
188396 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
188437 GAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
188502 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
188543 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
188608 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTCGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
188649 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
188714 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
188755 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
188820 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
188852 ACTATAAAAG
Statistics
Matches: 904, Mismatches: 41, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 904 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:189472 original size:22 final size:21
Alignment explanation
Indices: 189447--189523 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 21
189437 TTATGTTTGG
189447 TCAAGGGTTTGGCATTTGATGC
1 TCAA-GGTTTGGCATTTGATGC
189469 TCAAAGGTTTGGCATTTGATGC
1 TC-AAGGTTTGGCATTTGATGC
189491 TCATAGGTTTGGCATTTGATGC
1 TCA-AGGTTTGGCATTTGATGC
189513 TCAATGGTTTG
1 TCAA-GGTTTG
189524 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.04
22 48 0.92
23 2 0.04
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (21 bp):
TCAAGGTTTGGCATTTGATGC
Found at i:190176 original size:17 final size:18
Alignment explanation
Indices: 190150--190219 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 18
190140 ATTTTTGTTC
190150 TTTCTT-TTTTTCTTTTG
1 TTTCTTCTTTTTCTTTTG
*
190167 TTTC-TCTTTTTTCTTTCTT
1 TTTCTTC-TTTTTCTTT-TG
* *
190186 TTTCTTCTTTTGCTTCT-
1 TTTCTTCTTTTTCTTTTG
190203 TTTCTTCTTTTT-TTTTG
1 TTTCTTCTTTTTCTTTTG
190220 ATTGGATCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.09
17 15 0.35
18 10 0.23
19 12 0.28
20 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTCTTCTTTTTCTTTTG
Found at i:190179 original size:9 final size:8
Alignment explanation
Indices: 190150--190218 Score: 59
Period size: 9 Copynumber: 8.0 Consensus size: 8
190140 ATTTTTGTTC
190150 TTTCTTTT
1 TTTCTTTT
190158 TTTCTTTT
1 TTTCTTTT
190166 GTTTCTCTTT
1 -TTTCT-TTT
190176 TTTCTTTCTT
1 TTTC-TT-TT
190186 TTTCTTCTT
1 TTTCTT-TT
* *
190195 TTGCTTCT
1 TTTCTTTT
190203 TTTCTTCTT
1 TTTCTT-TT
190212 TTT-TTTT
1 TTTCTTTT
190219 GATTGGATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 2 0.04
8 16 0.31
9 24 0.46
10 10 0.19
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:190179 original size:26 final size:27
Alignment explanation
Indices: 190150--190216 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
190140 ATTTTTGTTC
*
190150 TTTCTTTTTTTCTT-TTGTTTC-TCTTT
1 TTTCTTTTTTTCTTCTT-TTGCTTCTTT
190176 TTTCTTTCTTTTTCTTCTTTTGCTTCTTT
1 TTTC-TT-TTTTTCTTCTTTTGCTTCTTT
190205 TCTTCTTTTTTT
1 T-TTCTTTTTTT
190217 TTGATTGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.11
27 2 0.06
28 16 0.46
29 10 0.29
30 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (27 bp):
TTTCTTTTTTTCTTCTTTTGCTTCTTT
Found at i:190183 original size:13 final size:12
Alignment explanation
Indices: 190150--190216 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 12
190140 ATTTTTGTTC
*
190150 TTTCTTTTTTTCT
1 TTTCTTTCTTT-T
*
190163 TTTGTTTCTCTTT
1 TTTCTTTCT-TTT
190176 TTTCTTTCTTTT
1 TTTCTTTCTTTT
*
190188 TCTTCTTTTGCTTCT
1 T-TTC-TTT-CTTTT
190203 TTTC-TTCTTTT
1 TTTCTTTCTTTT
190214 TTT
1 TTT
190217 TTGATTGGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 7 0.16
12 6 0.13
13 19 0.42
14 8 0.18
15 5 0.11
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:190183 original size:30 final size:29
Alignment explanation
Indices: 190141--190218 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
190131 TTCTTTTTGA
*
190141 TTTTTGTTCTTTCTTTTTTTCTTTTGTTTC
1 TTTTT-TTCTTTCTTTTTTTCTTTTGCTTC
190171 TCTTTTTTCTTTCTTTTTCTTCTTTTGCTTC
1 T-TTTTTTCTTTCTTTTT-TTCTTTTGCTTC
*
190202 TTTTCTTCTTT-TTTTTT
1 TTTTTTTCTTTCTTTTTT
190219 GATTGGATCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
28 1 0.02
29 5 0.11
30 22 0.50
31 16 0.36
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTTTTTCTTTCTTTTTTTCTTTTGCTTC
Found at i:190548 original size:14 final size:14
Alignment explanation
Indices: 190529--190561 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
190519 ATGCATGATA
*
190529 GAATTATTTCGGAT
1 GAATTATTTCAGAT
190543 GAATTATTTCAGAT
1 GAATTATTTCAGAT
190557 GAATT
1 GAATT
190562 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (14 bp):
GAATTATTTCAGAT
Found at i:191392 original size:8 final size:8
Alignment explanation
Indices: 191379--191414 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
191369 GTAGACGAAG
191379 ATGCAAAA
1 ATGCAAAA
191387 ATGCAAAA
1 ATGCAAAA
191395 ATGC-AAA
1 ATGCAAAA
*
191402 ATGCAAGA
1 ATGCAAAA
191410 ATGCA
1 ATGCA
191415 TGAAATGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (8 bp):
ATGCAAAA
Found at i:191404 original size:15 final size:15
Alignment explanation
Indices: 191379--191414 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
191369 GTAGACGAAG
191379 ATGCAAAAATGCAAAA
1 ATGC-AAAATGCAAAA
*
191395 ATGCAAAATGCAAGA
1 ATGCAAAATGCAAAA
191410 ATGCA
1 ATGCA
191415 TGAAATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:194939 original size:20 final size:20
Alignment explanation
Indices: 194914--194951 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
194904 AATGAGTAAA
194914 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
194934 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
194952 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:195054 original size:2 final size:2
Alignment explanation
Indices: 195002--195034 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
194992 AAAATAAGAA
195002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
195035 ACACTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196291 original size:12 final size:12
Alignment explanation
Indices: 196274--196303 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
196264 CTTTAACATA
196274 GTTTATACTTTT
1 GTTTATACTTTT
196286 GTTTATACTTTT
1 GTTTATACTTTT
*
196298 GCTTAT
1 GTTTAT
196304 CAAACTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (12 bp):
GTTTATACTTTT
Found at i:214542 original size:45 final size:45
Alignment explanation
Indices: 214478--214622 Score: 263
Period size: 45 Copynumber: 3.2 Consensus size: 45
214468 GTTAACCAAA
* *
214478 AGGAACTCAACATAGTAAATAGGATGAGAATCATACCCATCTAAG
1 AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCAACTAAG
*
214523 AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCACCTAAG
1 AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCAACTAAG
214568 AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCAACTAAG
1 AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCAACTAAG
214613 AGGAACCCAA
1 AGGAACCCAA
214623 GACTTCTATA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.16
Consensus pattern (45 bp):
AGGAACCCAACATAGTAAATAGGATGAGAATCATACCCAACTAAG
Found at i:217715 original size:18 final size:18
Alignment explanation
Indices: 217674--217721 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
217664 TTTAATCCTT
* * *
217674 TCATTCAATTCAATCTTT
1 TCATTTAATTCAAACTTG
*
217692 TTATTTAATTCAAACTTG
1 TCATTTAATTCAAACTTG
*
217710 TCATTTATTTCA
1 TCATTTAATTCA
217722 GTCATTTCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (18 bp):
TCATTTAATTCAAACTTG
Found at i:222592 original size:19 final size:19
Alignment explanation
Indices: 222568--222621 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 19
222558 CATTAAGCGG
222568 AGATATCAGAATTCAGAAC
1 AGATATCAGAATTCAGAAC
222587 AGATATCAGAACAGAATTCAGAAC
1 AGATAT-----CAGAATTCAGAAC
222611 AGATATCAGAA
1 AGATATCAGAA
222622 CAGAATCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
19 11 0.37
24 19 0.63
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (19 bp):
AGATATCAGAATTCAGAAC
Found at i:222595 original size:12 final size:11
Alignment explanation
Indices: 222574--222629 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 11
222564 GCGGAGATAT
222574 CAGAATTCAGAA
1 CAGAA-TCAGAA
222586 CAGATATCAGAA
1 CAGA-ATCAGAA
222598 CAGAATTCAGAA
1 CAGAA-TCAGAA
222610 CAGATATCAGAA
1 CAGA-ATCAGAA
222622 CAGAATCA
1 CAGAATCA
222630 AGATCATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.12
12 34 0.83
13 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (11 bp):
CAGAATCAGAA
Found at i:222606 original size:24 final size:24
Alignment explanation
Indices: 222574--222655 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
222564 GCGGAGATAT
222574 CAGAATTCAGAACAGATATCAGAA
1 CAGAATTCAGAACAGATATCAGAA
222598 CAGAATTCAGAACAGATATCAGAA
1 CAGAATTCAGAACAGATATCAGAA
* * * *
222622 CAGAA-TCAAGATCATAAATCAAAA
1 CAGAATTC-AGAACAGATATCAGAA
222646 CAGAATTCAG
1 CAGAATTCAG
222656 GTCATATATC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.04
24 48 0.92
25 2 0.04
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
CAGAATTCAGAACAGATATCAGAA
Found at i:222620 original size:7 final size:6
Alignment explanation
Indices: 222572--222629 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 6
222562 AAGCGGAGAT
222572 ATCAGA ATTCAGA A-CAGA TATCAGA A-CAGA ATTCAGA A-CAGA TATCAGA
1 ATCAGA A-TCAGA ATCAGA -ATCAGA ATCAGA A-TCAGA ATCAGA -ATCAGA
222621 A-CAGA ATCA
1 ATCAGA ATCA
222630 AGATCATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
5 18 0.41
6 7 0.16
7 19 0.43
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:222633 original size:19 final size:19
Alignment explanation
Indices: 222568--222633 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 19
222558 CATTAAGCGG
222568 AGATATCAGAATTCAGAA-C-
1 AGATATCAGAA--CAGAATCA
222587 AGATATCAGAACAGAATTCAGAA
1 AGATATCAGAACAGAA-TC---A
222610 CAGATATCAGAACAGAATCA
1 -AGATATCAGAACAGAATCA
222630 AGAT
1 AGAT
222634 CATAAATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 5 0.12
19 16 0.40
20 1 0.03
23 2 0.05
24 16 0.40
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (19 bp):
AGATATCAGAACAGAATCA
Found at i:222648 original size:36 final size:36
Alignment explanation
Indices: 222580--222649 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
222570 ATATCAGAAT
* *
222580 TCAGAACAGATATCAGAACAGAATTCAGAACAGATA
1 TCAGAACAGATATCAGAACAGAAATCAAAACAGATA
* *
222616 TCAGAACAGA-ATCAAGATCATAAATCAAAACAGA
1 TCAGAACAGATATC-AGAACAGAAATCAAAACAGA
222650 ATTCAGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 26 0.90
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (36 bp):
TCAGAACAGATATCAGAACAGAAATCAAAACAGATA
Found at i:222660 original size:24 final size:24
Alignment explanation
Indices: 222574--222666 Score: 107
Period size: 24 Copynumber: 3.9 Consensus size: 24
222564 GCGGAGATAT
* *
222574 CAGAATTCAGAACAGATATCAGAA
1 CAGAATTCAGATCATATATCAGAA
* *
222598 CAGAATTCAGAACAGATATCAGAA
1 CAGAATTCAGATCATATATCAGAA
* *
222622 CAGAA-TCAAGATCATAAATCAAAA
1 CAGAATTC-AGATCATATATCAGAA
*
222646 CAGAATTCAGGTCATATATCA
1 CAGAATTCAGATCATATATCA
222667 TAATAAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 2 0.03
24 57 0.93
25 2 0.03
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
CAGAATTCAGATCATATATCAGAA
Found at i:229566 original size:123 final size:124
Alignment explanation
Indices: 229432--229684 Score: 490
Period size: 123 Copynumber: 2.0 Consensus size: 124
229422 CATTTGTTTT
229432 TAATTTTTTTCCTACTGTGATACTAATTTAGTGTTGGTCCCCAACATCGGTGGTTTTTCTTATTC
1 TAATTTTTTTCCTACTGTGATACTAATTTAGTGTTGGTCCCCAACATCGGTGGTTTTTCTTATTC
229497 CCTTTTTTCCTCTTTATATC-TTTTTTTAATAATTTATCCTGTTTTATTTTTACATATC
66 CCTTTTTTCCTCTTTATATCTTTTTTTTAATAATTTATCCTGTTTTATTTTTACATATC
229555 TAATTTTTTTCCTACTGTGATACTAATTTAGTGTTGGTCCCCAACATCGGTGGTTTTTCTTATTC
1 TAATTTTTTTCCTACTGTGATACTAATTTAGTGTTGGTCCCCAACATCGGTGGTTTTTCTTATTC
*
229620 CCTTTTTTCCTCTTTATATCTTTTTTTTAATAATTTATCGTGTTTTATTTTTACATATC
66 CCTTTTTTCCTCTTTATATCTTTTTTTTAATAATTTATCCTGTTTTATTTTTACATATC
229679 TAATTT
1 TAATTT
229685 ATGTTGTTTA
Statistics
Matches: 128, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 85 0.66
124 43 0.34
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (124 bp):
TAATTTTTTTCCTACTGTGATACTAATTTAGTGTTGGTCCCCAACATCGGTGGTTTTTCTTATTC
CCTTTTTTCCTCTTTATATCTTTTTTTTAATAATTTATCCTGTTTTATTTTTACATATC
Found at i:230539 original size:2 final size:2
Alignment explanation
Indices: 230534--230561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
230524 ATAAACAAAC
230534 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
230562 TACTTAAATA
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:231620 original size:2 final size:2
Alignment explanation
Indices: 231613--231665 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
231603 ATATCAAATA
231613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
231655 AT AT AT AT AT A
1 AT AT AT AT AT A
231666 AAAGAACTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:233814 original size:136 final size:135
Alignment explanation
Indices: 233438--233928 Score: 777
Period size: 136 Copynumber: 3.6 Consensus size: 135
233428 TTGTTAGATT
* * * * *
233438 GAACAAGTTCTTCGCATTATGAAATTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * **
233502 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATGTTGTGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
233567 AGGTC
131 AGGTC
*
233572 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
233637 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
233702 AGGTC
131 AGGTC
*
233707 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
233772 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
233837 TAGGTC
130 TAGGTC
*
233843 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACT
*
233908 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
233929 ACCTATTTTT
Statistics
Matches: 328, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
134 31 0.09
135 127 0.39
136 169 0.52
137 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:234913 original size:14 final size:13
Alignment explanation
Indices: 234894--234941 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
234884 TCCTTCTTCA
*
234894 TTTTTTCTTTCTT
1 TTTTTTTTTTCTT
234907 TTTTTTTTCTTCTT
1 TTTTTTTT-TTCTT
* *
234921 TTTATTTTTTCAT
1 TTTTTTTTTTCTT
234934 TTTTTTTT
1 TTTTTTTT
234942 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:234946 original size:14 final size:14
Alignment explanation
Indices: 234887--234946 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
234877 CGAACCCTCC
234887 TTCTTCATTTTTTCT
1 TTCTTCATTTTTT-T
234902 TTC-T--TTTTTTT
1 TTCTTCATTTTTTT
234913 TTCTTC-TTTTTATT
1 TTCTTCATTTTT-TT
234927 TT-TTCATTTTTTT
1 TTCTTCATTTTTTT
234940 TTCTTCA
1 TTCTTCA
234947 AGCATAGTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
13 12 0.30
14 14 0.35
15 3 0.08
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTCATTTTTTT
Found at i:252617 original size:21 final size:21
Alignment explanation
Indices: 252592--252631 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
252582 TCAGCGAACC
252592 GTTCAAGAACCGTACGGCGAA
1 GTTCAAGAACCGTACGGCGAA
252613 GTTCAAGAACCGTACGGCG
1 GTTCAAGAACCGTACGGCG
252632 GGAAGTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.15
Consensus pattern (21 bp):
GTTCAAGAACCGTACGGCGAA
Found at i:252765 original size:10 final size:10
Alignment explanation
Indices: 252766--252799 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
252756 GGTTATGTTC
252766 GTTCGGTTAT
1 GTTCGGTTAT
252776 GTTCGGTTAT
1 GTTCGGTTAT
*
252786 GTTCGTTTAT
1 GTTCGGTTAT
252796 GTTC
1 GTTC
252800 ATTCGGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (10 bp):
GTTCGGTTAT
Found at i:252768 original size:24 final size:24
Alignment explanation
Indices: 252741--252792 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
252731 CATTCATTTA
252741 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* *
252765 CGTTCGGTTATGTTCGGTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
252789 CGTT
1 CGTT
252793 TATGTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:252790 original size:34 final size:34
Alignment explanation
Indices: 252752--252823 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
252742 GTTCGTGAAC
* *
252752 GTTCGGTTATGTTCGTTCGGTTATGTTCGGTTAT
1 GTTCGGTTATGTTCATTCGGTTATATTCGGTTAT
* *
252786 GTTCGTTTATGTTCATTCGGTTATATTCGTTTAT
1 GTTCGGTTATGTTCATTCGGTTATATTCGGTTAT
252820 GTTC
1 GTTC
252824 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.11, C:0.12, G:0.24, T:0.53
Consensus pattern (34 bp):
GTTCGGTTATGTTCATTCGGTTATATTCGGTTAT
Found at i:252804 original size:24 final size:24
Alignment explanation
Indices: 252777--252836 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
252767 TTCGGTTATG
252777 TTCGGTTATGTTCGTTTATGTTCA
1 TTCGGTTATGTTCGTTTATGTTCA
*
252801 TTCGGTTATATTCGTTTATGTTCA
1 TTCGGTTATGTTCGTTTATGTTCA
**
252825 TTCATTTATGTT
1 TTCGGTTATGTT
252837 TAACTCAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.57
Consensus pattern (24 bp):
TTCGGTTATGTTCGTTTATGTTCA
Found at i:252809 original size:14 final size:14
Alignment explanation
Indices: 252751--252780 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
252741 CGTTCGTGAA
252751 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
252765 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
252779 CG
1 CG
252781 GTTATGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.30, T:0.47
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:252827 original size:14 final size:14
Alignment explanation
Indices: 252787--252836 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
252777 TTCGGTTATG
252787 TTCGTTTATGTTCA
1 TTCGTTTATGTTCA
*
252801 TTCGGTTA---T-A
1 TTCGTTTATGTTCA
252811 TTCGTTTATGTTCA
1 TTCGTTTATGTTCA
*
252825 TTCATTTATGTT
1 TTCGTTTATGTT
252837 TAACTCAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
13 1 0.03
14 19 0.66
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (14 bp):
TTCGTTTATGTTCA
Found at i:253949 original size:16 final size:16
Alignment explanation
Indices: 253910--253950 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
253900 GGGTCTCCAA
*
253910 CGTTTATGTTCGTGTT
1 CGTTTATTTTCGTGTT
253926 CGTTTATTTTCGTGTT
1 CGTTTATTTTCGTGTT
253942 CGTTTATTT
1 CGTTTATTT
253951 ATTAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.12, G:0.20, T:0.61
Consensus pattern (16 bp):
CGTTTATTTTCGTGTT
Found at i:263766 original size:42 final size:42
Alignment explanation
Indices: 263574--263782 Score: 197
Period size: 43 Copynumber: 4.9 Consensus size: 42
263564 TTAAACAAAA
* * * *
263574 AAACGCCGCAATAGATATTGATATTTAGCGGCGTTTGTGT-GAC
1 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTT-T-TCCAC
* ** *
263617 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTATTTTAGAT
1 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGT-TTTTCCAC
* *
263660 AAACGCCGCAATAGGT-TATGATGTTTAGCGGCGTTTTTCTATA
1 AAACGCCGCAATAGGTGT-TGATGTTTAGCGGCGTTTTTCCA-C
* * * * *
263703 AAACGTCGCAGTAAGTATTGATGTTTTGCGGCGTTTTTCCAC
1 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTTCCAC
* * *
263745 AAACGTCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTT
1 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTT
263783 GCTAAAAACG
Statistics
Matches: 146, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
42 43 0.29
43 100 0.68
44 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTTCCAC
Found at i:263861 original size:44 final size:44
Alignment explanation
Indices: 263806--263889 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
263796 GTAAAGGTCT
263806 GTATATAGCGGCATTTCTAGGATACAAACGCCGCTAAATATATG
1 GTATATAGCGGCATTTCTAGGATACAAACGCCGCTAAATATATG
* * * ** *
263850 GTATATTGCGGCGTTTTTTTGTTACAAACGCCGCTAAATA
1 GTATATAGCGGCATTTCTAGGATACAAACGCCGCTAAATA
263890 ACACAGAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (44 bp):
GTATATAGCGGCATTTCTAGGATACAAACGCCGCTAAATATATG
Found at i:264952 original size:41 final size:41
Alignment explanation
Indices: 264755--264954 Score: 305
Period size: 41 Copynumber: 4.9 Consensus size: 41
264745 TTTATACAAA
* * *
264755 AAAAATGCCACTATTGATT-ACACTATTGTGGCATTTGT-T
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * *
264794 AAAAATGCCACTATTGATTAACACTATTGTGGCATTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
264835 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
264876 AAAAACGCCACCATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* *
264917 AAAAACGCCACTATTGATTATCACTATTGCCGCGTTTG
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTG
264955 AGGAATAAAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
39 19 0.12
40 19 0.12
41 114 0.75
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:265916 original size:37 final size:36
Alignment explanation
Indices: 265845--265916 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
265835 TTCGGGTCGG
*
265845 GTTTTTTAAGATTGATATTCGGGTCGGGCCGGGTCA
1 GTTTTTTAAGATTGATATTCGGGTCGGGCAGGGTCA
*
265881 GTTTTTTAAG-TGTGATATTCGGGTTCGGGTAGGGTC
1 GTTTTTTAAGAT-TGATATTCGGG-TCGGGCAGGGTC
265917 GGGTCAGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 21 0.66
37 10 0.31
ACGTcount: A:0.15, C:0.11, G:0.35, T:0.39
Consensus pattern (36 bp):
GTTTTTTAAGATTGATATTCGGGTCGGGCAGGGTCA
Found at i:265919 original size:47 final size:48
Alignment explanation
Indices: 265865--265958 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 48
265855 ATTGATATTC
*
265865 GGGTCGGGCCGGGTCA-G-TTTTTTAAGTGTGATATTCGGGTTCGGGTA
1 GGGTCGGGCCAGGTCAGGTTTTTTTAAGTGTGATATTCGGG-TCGGGTA
* *
265912 GGGTCGGGTCAGGTCAGGTTTTTTTAAGTTTGATATTCGGGTCGGGT
1 GGGTCGGGCCAGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGT
265959 CAGGTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 14 0.33
48 7 0.17
49 21 0.50
ACGTcount: A:0.13, C:0.12, G:0.39, T:0.36
Consensus pattern (48 bp):
GGGTCGGGCCAGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTA
Found at i:265919 original size:85 final size:81
Alignment explanation
Indices: 265830--265991 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 81
265820 TTTAAAAAAA
* *
265830 TCGGGTTCGGGTC-GGGTTTTTTAAGATTGATATTCGGGTCGGGCCGGGTCAGTTTTTTAAGTGT
1 TCGGG-TCAGGTCAGGGTTTTTTAAGATTGATATTCGGGTCGGGCCAGGT---TTTTTTAAGTGT
265894 GATATTCGGGTTCGGGTAGGG
62 GATATTCGGG-TCGGGTAGGG
* * *
265915 TCGGGTCAGGTCAGGTTTTTTTAAGTTTGATATTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATA
1 TCGGGTCAGGTCAGGGTTTTTTAAGATTGATATTCGGGTCGGGCCAGGTTTTTTTAAGTGTGATA
265980 TTCGGGTCGGGT
66 TTCGGGTCGGGT
265992 CGAGTTCAGG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
81 6 0.08
82 22 0.31
84 6 0.08
85 37 0.52
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (81 bp):
TCGGGTCAGGTCAGGGTTTTTTAAGATTGATATTCGGGTCGGGCCAGGTTTTTTTAAGTGTGATA
TTCGGGTCGGGTAGGG
Found at i:265952 original size:33 final size:33
Alignment explanation
Indices: 265915--265992 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
265905 TCGGGTAGGG
* *
265915 TCGGGTCAGGTCAGGTTTTTTTAAGTTTGATAT
1 TCGGGTCGGGTCAGGTTTTTTTAAGTGTGATAT
265948 TCGGGTCGGGTCAGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCAGGTTTTTTTAAGTGTGATAT
265981 TCGGGTCGGGTC
1 TCGGGTCGGGTC
265993 GAGTTCAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.41
Consensus pattern (33 bp):
TCGGGTCGGGTCAGGTTTTTTTAAGTGTGATAT
Found at i:265957 original size:38 final size:38
Alignment explanation
Indices: 265912--266004 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 38
265902 GGTTCGGGTA
*
265912 GGGTCGGGTCAGGTCAGGTTTTTTTAAGTTTGATATTC
1 GGGTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATATTC
265950 GGGTC--G---GGTCAGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATATTC
*
265983 GGGTCGGGTCGAGTTCAGGTTT
1 GGGTCGGGTC-AGGTCAGGTTT
266005 ATGGTGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
33 31 0.66
35 1 0.02
36 1 0.02
38 5 0.11
39 9 0.19
ACGTcount: A:0.14, C:0.11, G:0.35, T:0.40
Consensus pattern (38 bp):
GGGTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATATTC
Found at i:266567 original size:16 final size:17
Alignment explanation
Indices: 266546--266593 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
266536 GTTTCAGATT
266546 CAGATTCCAATTCCT-A
1 CAGATTCCAATTCCTCA
*
266562 CAGATTCCAATTCTTTCA
1 CAGATTCCAATTC-CTCA
*
266580 CAGATTTCAATTCC
1 CAGATTCCAATTCC
266594 CTCATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 1 0.04
18 13 0.48
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:266664 original size:2 final size:2
Alignment explanation
Indices: 266657--266772 Score: 232
Period size: 2 Copynumber: 58.0 Consensus size: 2
266647 AATTGAATCC
266657 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
266699 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
266741 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
266773 AGACTTGACA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 114 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:267518 original size:5 final size:5
Alignment explanation
Indices: 267508--267544 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
267498 CCTTTGATTG
267508 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CT
267545 ACTGTTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTCT
Found at i:269329 original size:65 final size:64
Alignment explanation
Indices: 269257--269415 Score: 232
Period size: 65 Copynumber: 2.5 Consensus size: 64
269247 ATAAATTGAG
*
269257 CATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATGAA
1 CATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-T-AA
269320 AA
63 AA
* * *
269322 TATCGAATGCATTTAATACATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAA
1 CATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAA
269386 CATCGAATGCATTTTATGCATCCGATGCAC
1 CATCGAATGCATTTTATGCAT-CGATGCAC
269416 TAAGGGTCCA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
64 23 0.27
65 57 0.68
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
CATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAA
Found at i:280211 original size:32 final size:33
Alignment explanation
Indices: 280139--280329 Score: 279
Period size: 32 Copynumber: 6.0 Consensus size: 33
280129 TATAATAATT
280139 TGTCCATATGTCCCGAAGA-ACATAGGTAATA-
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
*
280170 TGTCAATATGTCCCGAAGA-ACATAGGTAATAC
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
*
280202 TGTCAATATGTCCCGAAGA-ACATAGGTAATAC
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
* *
280234 TGTCCATATGTCCCGAA-AGACATATGTAATAT
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
*
280266 TGTCCATATGTCCC-AAAAGACATAGGTAATAC
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
*
280298 TGTCCATATATCCCGAA-AGACATAGGTAATAC
1 TGTCCATATGTCCCGAAGAGACATAGGTAATAC
280330 CTCAACTCTT
Statistics
Matches: 149, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
31 33 0.22
32 114 0.77
33 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (33 bp):
TGTCCATATGTCCCGAAGAGACATAGGTAATAC
Found at i:283688 original size:23 final size:23
Alignment explanation
Indices: 283653--283700 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
283643 ATCAAGTACA
*
283653 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* * *
283676 ATAATGTAATAGGTAGCGTTTAT
1 ATAATATAATAGGTAACGCTTAT
283699 AT
1 AT
283701 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:284639 original size:182 final size:181
Alignment explanation
Indices: 284321--284773 Score: 701
Period size: 182 Copynumber: 2.5 Consensus size: 181
284311 ACTATTTTAC
284321 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACC-GTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
284386 TACATTTTTATAAAGTATAGACACTTTATTGGCGCTATAACTTATTTTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAG
* * * *
284451 TGTCGATACTTATAATAAAGTTTCAACACTATCAACATATCTGGTAGCTCTT
130 TGTCGATACTTATAATAAAGTATCAACACTATCAACATATCCGATAGCGCTT
* * *
284503 TACCGATTTTATCATTTCGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1 TACCG-TTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
284568 TACAATTTTATAAAGTATCGACATTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAG
* *
284633 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGATTGCGCTT
130 TGTCGATACTTATAATAAAGTATCAACACTATCAACATATCCGATAGCGCTT
** * *
284685 TACCTGTTTTGTCATTTATAGACCGATTTTGTCAT-TTTTTACCTGTTTTATTGTTATGGATCGA
1 TACC-GTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
284749 TACATTTTTATAAAGTATCGACACT
65 TACATTTTTATAAAGTATCGACACT
284774 ATCATCATAT
Statistics
Matches: 245, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 51 0.21
182 193 0.79
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
TACCGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAAGTATCAACACTATCAACATATCCGATAGCGCTT
Found at i:284988 original size:112 final size:112
Alignment explanation
Indices: 284647--285219 Score: 945
Period size: 112 Copynumber: 5.1 Consensus size: 112
284637 GATACTTATA
* * * * *
284647 ATAAAGTATCGACACTATCAACATATCCGATTGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
284712 TTTGTCA-TTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
284758 ATAAAGTATCGACACTATC-ATCATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC-G
1 ATAAAGTATCGACACTTTCAAT-ATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
284821 TTTTGTTATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
284869 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
284934 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCTATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
284981 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
285046 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
285093 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
285158 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
285205 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
285220 AAACCGACAA
Statistics
Matches: 433, Mismatches: 25, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
110 8 0.02
111 152 0.35
112 273 0.63
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:289549 original size:46 final size:46
Alignment explanation
Indices: 289482--289574 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
289472 TTCTGTCTAT
289482 CAAAAGAAGCTTTCAAATGATCATGAATCAGAACAATTTTATGTTC
1 CAAAAGAAGCTTTCAAATGATCATGAATCAGAACAATTTTATGTTC
289528 CAAAAGAAGCTTTCAAATGATCATGAATCAGAACAATTTTATGTTC
1 CAAAAGAAGCTTTCAAATGATCATGAATCAGAACAATTTTATGTTC
289574 C
1 C
289575 GTTTCATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (46 bp):
CAAAAGAAGCTTTCAAATGATCATGAATCAGAACAATTTTATGTTC
Found at i:291468 original size:20 final size:21
Alignment explanation
Indices: 291423--291469 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
291413 TTCGCAACTC
*
291423 AATTTCAAATTCGCAACATAG
1 AATTTCAAATTCACAACATAG
* *
291444 -TTTTCGAATTCACAACA-AG
1 AATTTCAAATTCACAACATAG
291463 AATTTCA
1 AATTTCA
291470 TTTCGCAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
AATTTCAAATTCACAACATAG
Found at i:291559 original size:22 final size:22
Alignment explanation
Indices: 291531--291590 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
291521 TCAAATTCGG
*
291531 ATTTCGCAACTTGAATTCGCCA
1 ATTTCGCAACTCGAATTCGCCA
*
291553 ATTTCGCAACTCGAATTCGTCA
1 ATTTCGCAACTCGAATTCGCCA
291575 ATTTCGCAACTC-AATT
1 ATTTCGCAACTCGAATT
291591 TTACCGCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (22 bp):
ATTTCGCAACTCGAATTCGCCA
Found at i:292414 original size:22 final size:22
Alignment explanation
Indices: 292385--292506 Score: 112
Period size: 22 Copynumber: 5.8 Consensus size: 22
292375 AACTCGGTAA
292385 AATT-GAGTTGCGAAATTGGAG
1 AATTCGAGTTGCGAAATTGGAG
*
292406 AATTCGAGTTGTGAAATTGGAG
1 AATTCGAGTTGCGAAATTGGAG
**
292428 AATTCGAGTTGCGAAA-T-CCG
1 AATTCGAGTTGCGAAATTGGAG
* *
292448 AATTCGAGTTGCG-AATTTGAA
1 AATTCGAGTTGCGAAATTGGAG
* * *
292469 AACT-GAGTTACGAATTTGGCA-
1 AATTCGAGTTGCGAAATTGG-AG
*
292490 AATTCGTGTTGCGAAAT
1 AATTCGAGTTGCGAAAT
292507 GTAAATTCTT
Statistics
Matches: 80, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
19 2 0.03
20 22 0.28
21 15 0.19
22 41 0.51
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (22 bp):
AATTCGAGTTGCGAAATTGGAG
Found at i:292494 original size:62 final size:62
Alignment explanation
Indices: 292428--292550 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
292418 GAAATTGGAG
* *
292428 AATTCGAGTTGCGAAATCCGAATTCGAGTTGCGAATTTGAAAACTGAGTTACGAATTTGGCA
1 AATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTCGAAAACTGAGTTACGAATTTGGCA
* ** ** * * *
292490 AATTCGTGTTGCGAAATGTAAATTCTTGTTGCGAATTCGAAAATTGTGTTGCGAATTTGGC
1 AATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTCGAAAACTGAGTTACGAATTTGGC
292551 TTTCGTGTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (62 bp):
AATTCGAGTTGCGAAATCCAAATTCGAGTTGCGAATTCGAAAACTGAGTTACGAATTTGGCA
Found at i:292545 original size:20 final size:20
Alignment explanation
Indices: 292448--292546 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
292438 GCGAAATCCG
*
292448 AATTCGAGTTGCGAATTTGAA
1 AATTCGTGTTGCGAA-TTGAA
* * * *
292469 AACT-GAGTTACGAATTTGGCA
1 AATTCGTGTTGCGAA-TT-GAA
* *
292490 AATTCGTGTTGCGAAATGTA
1 AATTCGTGTTGCGAATTGAA
*
292510 AATTCTTGTTGCGAATTCGAA
1 AATTCGTGTTGCGAATT-GAA
292531 AATT-GTGTTGCGAATT
1 AATTCGTGTTGCGAATT
292547 TGGCTTTCGT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 40 0.63
21 15 0.24
22 8 0.13
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (20 bp):
AATTCGTGTTGCGAATTGAA
Found at i:294718 original size:3 final size:3
Alignment explanation
Indices: 294710--294745 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
294700 CCTAAACATG
294710 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
294746 CCTATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:296022 original size:24 final size:24
Alignment explanation
Indices: 295989--296044 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
295979 CTAAAGTCAT
*
295989 ATATATGTCCATGTGATTCCTTTA
1 ATATAGGTCCATGTGATTCCTTTA
296013 ATATAGGTCCATGTGATTCCTTTA
1 ATATAGGTCCATGTGATTCCTTTA
296037 ATATAGGT
1 ATATAGGT
296045 TGAGATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (24 bp):
ATATAGGTCCATGTGATTCCTTTA
Found at i:301597 original size:30 final size:30
Alignment explanation
Indices: 301563--301653 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
301553 CAAGAAAGGC
*
301563 TAAATGGTGAATGATTGCCCTCTAAAACAG
1 TAAATGGTGAATGATTGCCTTCTAAAACAG
* *
301593 TAAATGGTGAATTATTGCCTTCTAAATCAG
1 TAAATGGTGAATGATTGCCTTCTAAAACAG
301623 TAAATGGTGAATGATTGCCTTCTAAAACAG
1 TAAATGGTGAATGATTGCCTTCTAAAACAG
301653 T
1 T
301654 GACATAGCAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (30 bp):
TAAATGGTGAATGATTGCCTTCTAAAACAG
Found at i:304923 original size:2 final size:2
Alignment explanation
Indices: 304916--304978 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
304906 GTACTATGTT
304916 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
304958 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
304979 CCAAGACATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:309092 original size:18 final size:18
Alignment explanation
Indices: 309069--309190 Score: 108
Period size: 18 Copynumber: 6.8 Consensus size: 18
309059 GTAATCTACG
309069 TCTGATAACTGTAAAATA
1 TCTGATAACTGTAAAATA
309087 TCTGATAACTG-AAAATCA
1 TCTGATAACTGTAAAAT-A
*
309105 TCTGATAACTAT-AAATA
1 TCTGATAACTGTAAAATA
* **
309122 TCTAATAACTG-GCAATCA
1 TCTGATAACTGTAAAAT-A
309140 TCTGATAACTGT-AAATA
1 TCTGATAACTGTAAAATA
* * * *
309157 TCTAATAACTTTGAAATTG
1 TCTGATAACTGT-AAAATA
*
309176 TCTGATAAATGTAAA
1 TCTGATAACTGTAAA
309191 CATTTAGAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
17 29 0.35
18 43 0.51
19 12 0.14
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (18 bp):
TCTGATAACTGTAAAATA
Found at i:309130 original size:35 final size:35
Alignment explanation
Indices: 309069--309166 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
309059 GTAATCTACG
*
309069 TCTGATAACTGTAAAATATCTGATAACTGAAAATCA
1 TCTGATAACTGT-AAATATCTAATAACTGAAAATCA
* **
309105 TCTGATAACTATAAATATCTAATAACTGGCAATCA
1 TCTGATAACTGTAAATATCTAATAACTGAAAATCA
309140 TCTGATAACTGTAAATATCTAATAACT
1 TCTGATAACTGTAAATATCTAATAACT
309167 TTGAAATTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 46 0.81
36 11 0.19
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (35 bp):
TCTGATAACTGTAAATATCTAATAACTGAAAATCA
Found at i:310777 original size:22 final size:22
Alignment explanation
Indices: 310752--310797 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
310742 TCCGATCAAC
*
310752 TTTCTAA-CTTAAAATTCCAGCA
1 TTTCTAATATTAAAATT-CAGCA
310774 TTTCTAATATTAAAATTCAGCA
1 TTTCTAATATTAAAATTCAGCA
310796 TT
1 TT
310798 AACACTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTCTAATATTAAAATTCAGCA
Found at i:316313 original size:15 final size:15
Alignment explanation
Indices: 316293--316324 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
316283 ACACTAAACA
*
316293 GACATGTTTATGAAT
1 GACATGTTCATGAAT
316308 GACATGTTCATGAAT
1 GACATGTTCATGAAT
316323 GA
1 GA
316325 TAAATGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (15 bp):
GACATGTTCATGAAT
Found at i:316358 original size:23 final size:23
Alignment explanation
Indices: 316314--316358 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
316304 GAATGACATG
* *
316314 TTCATGAATGATAAATGAATATA
1 TTCATGAACGATAAACGAATATA
* *
316337 TTCATGAACGTTAAACGTATAT
1 TTCATGAACGATAAACGAATAT
316359 GTTAGCAAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
TTCATGAACGATAAACGAATATA
Found at i:319175 original size:21 final size:21
Alignment explanation
Indices: 319151--319329 Score: 83
Period size: 21 Copynumber: 8.9 Consensus size: 21
319141 ACTTACACAC
319151 TAAACCCTAAACCCTAAACTA
1 TAAACCCTAAACCCTAAACTA
* * * * *
319172 TAAACCTTATATCATATCAC-A
1 TAAACCCTAAACCCTA-AACTA
* * *
319193 TAAACTCTAAACCTTAAACTT
1 TAAACCCTAAACCCTAAACTA
* * *
319214 TAAACTCTAAACTCTAAACTC
1 TAAACCCTAAACCCTAAACTA
*
319235 T-AACCC---A---TAACCTA
1 TAAACCCTAAACCCTAAACTA
*
319249 TAAACCCTAAACCCTAATA-TC
1 TAAACCCTAAACCCTAA-ACTA
* * *
319270 TAAACCTTAAATCCTATCAC-A
1 TAAACCCTAAACCCTA-AACTA
319291 TAAACCCTAAACCCTAAACCT-
1 TAAACCCTAAACCCTAAA-CTA
* *
319312 TAAACCTTAAACCTTAAA
1 TAAACCCTAAACCCTAAA
319330 TCTTAAATCA
Statistics
Matches: 115, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
14 6 0.05
15 5 0.04
17 1 0.01
18 1 0.01
20 7 0.06
21 93 0.81
22 2 0.02
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACTA
Found at i:319203 original size:49 final size:49
Alignment explanation
Indices: 319150--319366 Score: 199
Period size: 49 Copynumber: 4.3 Consensus size: 49
319140 AACTTACACA
* * *
319150 CTAAACCCTAAACCCTAAACTATAAACCTTATATCATATCACATAAACT
1 CTAAACCCTAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACC
* ** * *
319199 CTAAACCTTAAACTTTAAACTCTAAA-CTCTAAACTC-TAACCCAT-AACC
1 CTAAACCCTAAACCCTAAACTCTAAACCT-TAAA-TCATATCACATAAACC
* *
319247 TATAAACCCTAAACCCTAATA-TCTAAACCTTAAATCCTATCACATAAACC
1 -CTAAACCCTAAACCCTAA-ACTCTAAACCTTAAATCATATCACATAAACC
* *
319297 CTAAACCCTAAACCTTAAACCTTAAACCTTAAATCTTAAATCATATCACATAAACC
1 CTAAACCCTAAACCCTAAA-C-T----C-TAAACCTTAAATCATATCACATAAACC
319353 CTAAACCCTAAACC
1 CTAAACCCTAAACC
319367 TTAACGCATA
Statistics
Matches: 135, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
48 8 0.06
49 77 0.57
50 9 0.07
51 1 0.01
55 1 0.01
56 39 0.29
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (49 bp):
CTAAACCCTAAACCCTAAACTCTAAACCTTAAATCATATCACATAAACC
Found at i:319259 original size:7 final size:7
Alignment explanation
Indices: 319193--319366 Score: 70
Period size: 7 Copynumber: 24.9 Consensus size: 7
319183 TCATATCACA
*
319193 TAAACTC
1 TAAACCC
*
319200 TAAACCT
1 TAAACCC
**
319207 TAAACTT
1 TAAACCC
*
319214 TAAACTC
1 TAAACCC
*
319221 TAAACTC
1 TAAACCC
*
319228 TAAACTC
1 TAAACCC
319235 T-AACCC
1 TAAACCC
*
319241 -ATAACCTA
1 TA-AACC-C
319249 TAAACCC
1 TAAACCC
319256 TAAACCC
1 TAAACCC
*
319263 TAATA-TC
1 TAA-ACCC
*
319270 TAAACCT
1 TAAACCC
*
319277 TAAATCC
1 TAAACCC
* *
319284 T-ATCACA
1 TAAAC-CC
319291 TAAACCC
1 TAAACCC
319298 TAAACCC
1 TAAACCC
*
319305 TAAACCT
1 TAAACCC
*
319312 TAAACCT
1 TAAACCC
*
319319 TAAACCT
1 TAAACCC
* *
319326 TAAATCT
1 TAAACCC
* *
319333 TAAATCA
1 TAAACCC
* *
319340 T-ATCACA
1 TAAAC-CC
319347 TAAACCC
1 TAAACCC
319354 TAAACCC
1 TAAACCC
319361 TAAACC
1 TAAACC
319367 TTAACGCATA
Statistics
Matches: 133, Mismatches: 24, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
6 7 0.05
7 116 0.87
8 9 0.07
9 1 0.01
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAACCC
Found at i:319309 original size:56 final size:56
Alignment explanation
Indices: 319249--319366 Score: 175
Period size: 56 Copynumber: 2.1 Consensus size: 56
319239 CCATAACCTA
* *
319249 TAAACCCTAAACCCTAATATC-TAAACCTTAAATCCTATCACATAAACCCTAAACCC
1 TAAACCCTAAACCCTAA-ACCTTAAACCTTAAATCATATCACATAAACCCTAAACCC
* * *
319305 TAAACCTTAAACCTTAAACCTTAAATCTTAAATCATATCACATAAACCCTAAACCC
1 TAAACCCTAAACCCTAAACCTTAAACCTTAAATCATATCACATAAACCCTAAACCC
319361 TAAACC
1 TAAACC
319367 TTAACGCATA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 2 0.04
56 54 0.96
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (56 bp):
TAAACCCTAAACCCTAAACCTTAAACCTTAAATCATATCACATAAACCCTAAACCC
Found at i:319775 original size:14 final size:14
Alignment explanation
Indices: 319758--319798 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
319748 TTTATTCATC
319758 AATAATGTATTTTT
1 AATAATGTATTTTT
319772 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
319783 AATAATGTAATTTT
1 AATAATGTATTTTT
319797 AA
1 AA
319799 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:321169 original size:18 final size:18
Alignment explanation
Indices: 321146--321180 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
321136 CTACCGGTTC
*
321146 ACCGGTTCAACCGGTCGA
1 ACCGGTCCAACCGGTCGA
*
321164 ACCGGTCCGACCGGTCG
1 ACCGGTCCAACCGGTCG
321181 GAAGAATATT
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:0.17, C:0.37, G:0.31, T:0.14
Consensus pattern (18 bp):
ACCGGTCCAACCGGTCGA
Found at i:325885 original size:17 final size:17
Alignment explanation
Indices: 325845--325904 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
325835 ATTTTTAATT
*
325845 ATTA-AAAAAGTTAAAA
1 ATTATAAAAATTTAAAA
* *
325861 ATCCATAAAAATTTATAA
1 AT-TATAAAAATTTAAAA
325879 ATTATAAAAATTTAAAA
1 ATTATAAAAATTTAAAA
325896 ATTATAAAA
1 ATTATAAAA
325905 TCTAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.05
17 23 0.62
18 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (17 bp):
ATTATAAAAATTTAAAA
Found at i:325889 original size:9 final size:9
Alignment explanation
Indices: 325865--325904 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
325855 TTAAAAATCC
325865 ATAAAAATT
1 ATAAAAATT
*
325874 -TATAAATT
1 ATAAAAATT
325882 ATAAAAATT
1 ATAAAAATT
325891 -TAAAAATT
1 ATAAAAATT
325899 ATAAAA
1 ATAAAA
325905 TCTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.56
9 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:325912 original size:17 final size:17
Alignment explanation
Indices: 325877--325924 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
325867 AAAAATTTAT
*
325877 AAATTATAAAAAT-TTAA
1 AAATTAT-AAAATCTAAA
325894 AAATTATAAAATCTAAA
1 AAATTATAAAATCTAAA
* *
325911 AAAATCTAAAATCT
1 AAATTATAAAATCT
325925 CTTTCAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTATAAAATCTAAA
Found at i:333806 original size:272 final size:275
Alignment explanation
Indices: 333292--333827 Score: 871
Period size: 272 Copynumber: 2.0 Consensus size: 275
333282 AAGACTTGTA
* *
333292 CTTTGATACCATTGGATTTCTGTTTATTCATTTGGATAGTACTTAATGTTATTATTATGTCATAA
1 CTTTGATACCATTGGATTGCTGTTTATTCAATTGGATAGTACTTAATGTTATTATTATGTCATAA
*
333357 AGAGAAAAAATACTCTCCTTGGCATTACTCAGCCATATCTATGGTTGGATTTATTGGTGTTCTCA
66 AGAG-AAAAATACTCTCCTTGGCATTACTCAGCCATATCTATGGTTGGATTTATTGATGTTCTCA
* * * * *
333422 AGCTGTGAATCTAGGTGTGCCTACGCCTTAGTGCTAGGCAACTAAAGCACCTTAGACCCTTTCAG
130 AGCAGTGAACCTAGGTGTGCCTACACCTTAGTGCCAGGCAACAAAAGCACCTTAGACCCTTTCAG
**
333487 GCAAGTCACATATGGTCAGGAACATGCCCAGCGTACCTTGCACATGAGGCAGTATAAAGGTTCTA
195 GCAAGTCACATATGACCAGGAACATGCCCAGCGTACCTTGCACATGAGGCAGTATAAAGGTTCTA
333552 GCACCTACAGTGCACC
260 GCACCTACAGTGCACC
* *
333568 CTTTGATATCATTGGATTGCTGTTTATTCAATTGGATAGTACTTAATGTTATTCTTATGTCATAA
1 CTTTGATACCATTGGATTGCTGTTTATTCAATTGGATAGTACTTAATGTTATTATTATGTCATAA
*
333633 AGAG-AAAATACTCTCCTTGGCATTACTCAGCCATATCTGTGGTTGGATTTATTGATGTTCTCAA
66 AGAGAAAAATACTCTCCTTGGCATTACTCAGCCATATCTATGGTTGGATTTATTGATGTTCTCAA
333697 G-AGTGAACCTAGGTGTGCCT-CACCTTAGTGCCAGGCAACAAAAGCACCTTAGACCCTTTCAGG
131 GCAGTGAACCTAGGTGTGCCTACACCTTAGTGCCAGGCAACAAAAGCACCTTAGACCCTTTCAGG
* * * * * *
333760 CGAGTCACATATGACCAGGAACGTGCCCAGTGTGCCTTGTACATGAGGCAGTGTAAAGGTTCTAG
196 CAAGTCACATATGACCAGGAACATGCCCAGCGTACCTTGCACATGAGGCAGTATAAAGGTTCTAG
333825 CAC
261 CAC
333828 GGTAGCACCT
Statistics
Matches: 241, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
272 100 0.41
273 17 0.07
274 59 0.24
276 65 0.27
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (275 bp):
CTTTGATACCATTGGATTGCTGTTTATTCAATTGGATAGTACTTAATGTTATTATTATGTCATAA
AGAGAAAAATACTCTCCTTGGCATTACTCAGCCATATCTATGGTTGGATTTATTGATGTTCTCAA
GCAGTGAACCTAGGTGTGCCTACACCTTAGTGCCAGGCAACAAAAGCACCTTAGACCCTTTCAGG
CAAGTCACATATGACCAGGAACATGCCCAGCGTACCTTGCACATGAGGCAGTATAAAGGTTCTAG
CACCTACAGTGCACC
Found at i:334920 original size:156 final size:156
Alignment explanation
Indices: 334635--335101 Score: 835
Period size: 156 Copynumber: 3.0 Consensus size: 156
334625 TGTGATATTG
* *
334635 GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCCTTTTTTTTTCCTTGTAAACTCATTCCTATAG
1 GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCC-TTTTTTTCCCTTGTAAACTCATTCCTAGAG
*
334700 TTTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATTTCATAATATTAGATTTAG
65 TTTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGATTTAG
*
334765 GGGCTGGCAGTTAGCCTGCGGTATAAA
130 GGGCTGGCAGTTAGCCTGCGATATAAA
* *
334792 GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCCTTTTTTCCCCTTTTAAACTCATTCCTAGAGT
1 GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCCTTTTTTTCCCTTGTAAACTCATTCCTAGAGT
*
334857 TTAAGATTTCTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGATTTAGG
66 TTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGATTTAGG
334922 GGCTGGCAGTTAGCCTGCGATATAAA
131 GGCTGGCAGTTAGCCTGCGATATAAA
* *
334948 GTTATGAACGATTTTTGGGCCCTGATGTTTGTCCTTTTTTTCCCTTGTAAATTCATTCCTAGAGT
1 GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCCTTTTTTTCCCTTGTAAACTCATTCCTAGAGT
*
335013 TTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGTTTTAGG
66 TTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGATTTAGG
335078 GGCTGGCAGTTAGCCTGCGATATA
131 GGCTGGCAGTTAGCCTGCGATATA
335102 CATTTATATA
Statistics
Matches: 297, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
156 263 0.89
157 34 0.11
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (156 bp):
GTTATGAACGATTTTTGGGCCCTGAGGTTTGTCCTTTTTTTCCCTTGTAAACTCATTCCTAGAGT
TTAAGATTACTGGAAGTATTCCTTTATATTAGTGTATATATAAATCTCATAATATTAGATTTAGG
GGCTGGCAGTTAGCCTGCGATATAAA
Found at i:339648 original size:34 final size:31
Alignment explanation
Indices: 339610--339681 Score: 74
Period size: 34 Copynumber: 2.2 Consensus size: 31
339600 TAAAAGAATG
**
339610 ATAAAAAAGTATTTTTTATTAATATATAAATATT
1 ATAAAAAA-TATTTCAT-TTAATA-ATAAATATT
*
339644 ATAAAATAATATTTCATTTGATAATAAATATT
1 ATAAAA-AATATTTCATTTAATAATAAATATT
339676 -TAAAAA
1 ATAAAAA
339682 CAACTCGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.03
31 5 0.15
32 9 0.26
33 5 0.15
34 12 0.35
35 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (31 bp):
ATAAAAAATATTTCATTTAATAATAAATATT
Found at i:350617 original size:23 final size:25
Alignment explanation
Indices: 350567--350641 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 25
350557 AAAAATGTAC
* * * *
350567 ATAAGAAAAATATATATAATATAAT
1 ATAATAAAAATAAAAATAAGATAAT
350592 ATAAT-AAAATAAAAAT-AGATAAT
1 ATAATAAAAATAAAAATAAGATAAT
* *
350615 AT-ATAAAAATAATAATAAGATAGT
1 ATAATAAAAATAAAAATAAGATAAT
350639 ATA
1 ATA
350642 GCGTAAAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.05
23 18 0.44
24 17 0.41
25 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAATAAAAATAAAAATAAGATAAT
Found at i:350622 original size:17 final size:16
Alignment explanation
Indices: 350494--350631 Score: 66
Period size: 15 Copynumber: 8.9 Consensus size: 16
350484 GTTATAATGG
*
350494 TAAACATAATAATA-A
1 TAAAAATAATAATATA
*
350509 T-AAAATAATAAT-GA
1 TAAAAATAATAATATA
*
350523 TGAAAATAAT-A-A-A
1 TAAAAATAATAATATA
350536 TAAAAAT-ATATATCCATA
1 TAAAAATAATA-AT--ATA
* *
350554 TAAAAA-AAT-GTACA
1 TAAAAATAATAATATA
350568 TAAGAAA-AAT-ATATA
1 TAA-AAATAATAATATA
*
350583 TAATATAAT-ATAATAAAA
1 TAA-A-AATAATAAT-ATA
350601 TAAAAATAGATAATATA
1 TAAAAATA-ATAATATA
350618 TAAAAATAATAATA
1 TAAAAATAATAATA
350632 AGATAGTATA
Statistics
Matches: 97, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
12 2 0.02
13 7 0.07
14 19 0.20
15 22 0.23
16 14 0.14
17 14 0.14
18 19 0.20
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (16 bp):
TAAAAATAATAATATA
Found at i:351723 original size:2 final size:2
Alignment explanation
Indices: 351718--351757 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
351708 CAAATAAAAA
351718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
351758 GTAAATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351770 original size:10 final size:11
Alignment explanation
Indices: 351717--351779 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 11
351707 TCAAATAAAA
*
351717 AATATATATAT
1 AATATATGTAT
*
351728 -ATATATATAT
1 AATATATGTAT
*
351738 ATATATATATAT
1 A-ATATATGTAT
351750 ATATATATGTA-
1 A-ATATATGTAT
*
351761 AATATGTGTAT
1 AATATATGTAT
351772 AATATATG
1 AATATATG
351780 CGTAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
10 18 0.39
11 8 0.17
12 20 0.43
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (11 bp):
AATATATGTAT
Found at i:352495 original size:32 final size:32
Alignment explanation
Indices: 352449--352526 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
352439 CGATTCCATT
*
352449 CGTCTTGAAGTTGAAACCGCGCGTGGCCCCTC
1 CGTCGTGAAGTTGAAACCGCGCGTGGCCCCTC
* *
352481 CGTCGTGAAGTTGAAACCGTGGGTGGCCCCTC
1 CGTCGTGAAGTTGAAACCGCGCGTGGCCCCTC
352513 CGTCGTGAAGTTGA
1 CGTCGTGAAGTTGA
352527 GCCTGGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.17, C:0.28, G:0.32, T:0.23
Consensus pattern (32 bp):
CGTCGTGAAGTTGAAACCGCGCGTGGCCCCTC
Found at i:352777 original size:106 final size:105
Alignment explanation
Indices: 352586--352942 Score: 439
Period size: 106 Copynumber: 3.5 Consensus size: 105
352576 GTATTGCTCC
* * * *
352586 GAGTCCAATATCC-TCCTCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGT-CGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-TTTGTTGACA
* * * *
352650 GTCAGCCACCCCTTCGTTGTGAAGTAGAGCTTGTGTTGTCTT
64 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
352692 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-TTTGTTGACAG
*
352757 TCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCTT
65 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
352798 GAGTCTAATATCCTTCGTCGTGAAATTGAAATTGACTCTG-AA-T--G-AA----T-TTGACAAT
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTGTTGACAGT
*
352853 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
66 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * *
352893 GAGTCCAATATCCTTCGTTGCGAAGTTGAAATTAGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
352943 GCCCCTTCAT
Statistics
Matches: 220, Mismatches: 25, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
95 79 0.36
96 3 0.01
97 1 0.00
99 1 0.00
100 1 0.00
101 2 0.01
102 1 0.00
104 1 0.00
105 2 0.01
106 126 0.57
107 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTGTTGACAGT
CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:352922 original size:95 final size:95
Alignment explanation
Indices: 352750--352934 Score: 291
Period size: 95 Copynumber: 1.9 Consensus size: 95
352740 AAATTGTTTG
* * *
352750 TTGACAGTCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCTAATATCCTTCG
1 TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
*
352815 TCGTGAAATTGAAATT-GACTCTGAATGAAT
66 TCGCGAAATTGAAATTAG-CTCTGAATGAAT
*
352845 TTGACAATCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
1 TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
* *
352910 TTGCGAAGTTGAAATTAGCTCTGAA
66 TCGCGAAATTGAAATTAGCTCTGAA
352935 ATTGGGAAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 81 0.99
96 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (95 bp):
TTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCG
TCGCGAAATTGAAATTAGCTCTGAATGAAT
Found at i:354035 original size:6 final size:6
Alignment explanation
Indices: 354024--354068 Score: 54
Period size: 6 Copynumber: 6.8 Consensus size: 6
354014 ACCCACCTTA
354024 TTTTTC TTTTTC TTTTTC TTTTTTC TTCTGTTC TTTTTC TCTTTT
1 TTTTTC TTTTTC TTTTTC -TTTTTC TT-T-TTC TTTTTC T-TTTT
354069 TTCAATTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 18 0.51
7 12 0.34
8 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:354059 original size:21 final size:20
Alignment explanation
Indices: 354024--354069 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
354014 ACCCACCTTA
354024 TTTTTCTTTTTCTTTTTCT-
1 TTTTTCTTTTTCTTTTTCTC
354043 TTTTTCTTCTGTTCTTTTTCTC
1 TTTTTCTT-T-TTCTTTTTCTC
354065 TTTTT
1 TTTTT
354070 TCAATTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 1 0.04
21 10 0.42
22 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTCTC
Found at i:354061 original size:16 final size:13
Alignment explanation
Indices: 354024--354069 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 13
354014 ACCCACCTTA
354024 TTTTTC-TTTTTC
1 TTTTTCTTTTTTC
354036 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
354049 TTCTGTTCTTTTTCTC
1 TT-T-TTCTTTTT-TC
354065 TTTTT
1 TTTTT
354070 TCAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.20
13 8 0.27
14 3 0.10
15 9 0.30
16 4 0.13
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:364679 original size:2 final size:2
Alignment explanation
Indices: 364674--364720 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
364664 AAAATGAGTA
364674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
364716 AT AT A
1 AT AT A
364721 ATGAAAATAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:364755 original size:3 final size:3
Alignment explanation
Indices: 364747--364882 Score: 51
Period size: 3 Copynumber: 46.3 Consensus size: 3
364737 TAATGGTAAA
* * *
364747 AAT AAT AAT AAT AA- AAT AAT GAT GAT GAA- AAT AAT AAAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT
* * *
364792 -AT ATAT GCAT -AT AA- AA- AAT -AT ACAT AAG AAA AAT -AT ATAT AAT
1 AAT A-AT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT
* *
364835 -AT AAT -AT AAT AA- AAT AAA AAT AGAT AAT ATAT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT
364879 AAT A
1 AAT A
364883 TAGTATAGCG
Statistics
Matches: 103, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
2 22 0.21
3 61 0.59
4 20 0.19
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:364761 original size:15 final size:15
Alignment explanation
Indices: 364743--364882 Score: 96
Period size: 15 Copynumber: 9.1 Consensus size: 15
364733 GTTATAATGG
364743 TAAAAATAATAATAA
1 TAAAAATAATAATAA
* *
364758 T-AAAATAATGATGA
1 TAAAAATAATAATAA
*
364772 TGAAAATAAT-A-AA
1 TAAAAATAATAATAA
364785 TAAAAAT-ATATATGCATA
1 TAAAAATAATA-AT--A-A
364803 TAAAAA-ATATACATAA
1 TAAAAATA-ATA-ATAA
*
364819 GAAAAAT-ATATATAA
1 TAAAAATAATA-ATAA
*
364834 TATAATATAATAA-AA
1 TA-AAAATAATAATAA
364849 TAAAAATAGATAATATA
1 TAAAAATA-ATAATA-A
364866 TAAAAATAATAATAA
1 TAAAAATAATAATAA
364881 TA
1 TA
364883 TAGTATAGCG
Statistics
Matches: 100, Mismatches: 10, Indels: 30
0.71 0.07 0.21
Matches are distributed among these distances:
12 2 0.02
13 7 0.07
14 19 0.19
15 28 0.28
16 18 0.18
17 14 0.14
18 7 0.07
19 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (15 bp):
TAAAAATAATAATAA
Found at i:364865 original size:23 final size:23
Alignment explanation
Indices: 364835--364879 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
364825 TATATATAAT
364835 ATAATATA-ATAAAATAAAAATAG
1 ATAATATATA-AAAATAAAAATAG
*
364858 ATAATATATAAAAATAATAATA
1 ATAATATATAAAAATAAAAATA
364880 ATATAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAATATATAAAAATAAAAATAG
Found at i:364870 original size:17 final size:17
Alignment explanation
Indices: 364743--364884 Score: 69
Period size: 17 Copynumber: 8.1 Consensus size: 17
364733 GTTATAATGG
364743 TAAAAATAATAATAATA
1 TAAAAATAATAATAATA
* * *
364760 -AAATAATGATGATGAAAA
1 TAAA-AATAATAAT-AATA
*
364778 TAATAAATAAAAATATATA
1 TAA-AAATAATAATA-ATA
** *
364797 TGCATATAA-AA-AATA
1 TAAAAATAATAATAATA
* * *
364812 TACATAAGAAAAATATATA
1 TA-AAAATAATAATA-ATA
*
364831 TAATATAAT-ATAATAAAA
1 TAA-A-AATAATAATAATA
364849 TAAAAATAGATAAT-ATA
1 TAAAAATA-ATAATAATA
364866 TAAAAATAATAATAATA
1 TAAAAATAATAATAATA
364883 TA
1 TA
364885 GTATAGCGTA
Statistics
Matches: 91, Mismatches: 20, Indels: 28
0.65 0.14 0.20
Matches are distributed among these distances:
15 4 0.04
16 15 0.16
17 27 0.30
18 21 0.23
19 21 0.23
20 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (17 bp):
TAAAAATAATAATAATA
Found at i:364873 original size:28 final size:31
Alignment explanation
Indices: 364776--364882 Score: 83
Period size: 34 Copynumber: 3.3 Consensus size: 31
364766 TGATGATGAA
* * * *
364776 AATAATAAATAAAAATATATATGCATATAAAAA
1 AATAAT-AATAAAAATAGATAT-AATATAATAT
* *
364809 ATATACATAAGAAAAATATATATAATATAATAT
1 A-ATA-ATAATAAAAATAGATATAATATAATAT
*
364842 AATAA-AATAAAAATAGATA-ATATATAAAAAT
1 AATAATAATAAAAATAGATATA-ATAT-AATAT
364873 AATAATAATA
1 AATAATAATA
364883 TAGTATAGCG
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
29 1 0.02
30 16 0.26
31 10 0.16
32 7 0.11
33 9 0.15
34 17 0.27
35 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (31 bp):
AATAATAATAAAAATAGATATAATATAATAT
Found at i:364885 original size:28 final size:29
Alignment explanation
Indices: 364808--364885 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
364798 GCATATAAAA
* *
364808 AATATACATAAGA-AAAATATATATAATAT
1 AATATA-ATAAAATAAAATATAGATAATAT
364837 AATATAATAAAATAAAA-ATAGATAATAT
1 AATATAATAAAATAAAATATAGATAATAT
364865 -ATA-AA-AATAATAATAATATAG
1 AATATAATAA-AATAA-AATATAG
364886 TATAGCGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 7 0.16
27 5 0.12
28 19 0.44
29 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (29 bp):
AATATAATAAAATAAAATATAGATAATAT
Found at i:364925 original size:2 final size:2
Alignment explanation
Indices: 364915--364950 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
364905 AAAAGGAAAA
364915 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
364951 AAGGGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:366904 original size:17 final size:17
Alignment explanation
Indices: 366871--366904 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
366861 TTTAACCATA
*
366871 AAGTTTAAAGTTTTACG
1 AAGTTTAAAGTTCTACG
*
366888 AAGTTTAATGTTCTACG
1 AAGTTTAAAGTTCTACG
366905 TTCAGATTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (17 bp):
AAGTTTAAAGTTCTACG
Found at i:367324 original size:15 final size:15
Alignment explanation
Indices: 367304--367333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
367294 TAATAATATG
367304 TTATGATAAAATTAA
1 TTATGATAAAATTAA
*
367319 TTATGATTAAATTAA
1 TTATGATAAAATTAA
367334 AATTGAATTT
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:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TTATGATAAAATTAA
Found at i:373185 original size:60 final size:60
Alignment explanation
Indices: 373112--373255 Score: 209
Period size: 60 Copynumber: 2.4 Consensus size: 60
373102 GAGGGGTGTG
* * * * *
373112 CCCTCAGCCCCATAAGGACTTACCCAAGGCACACAGCAGAGGAGTCACCCTAATGGATTA
1 CCCTCAGCTCCATAAGGACTTACCCAAGGCACACAACAGAGGAGCCACCCTAAGGGAGTA
373172 CCCTCAGCTCCATAAGGACTTACCCAAGGCACACAACAGAGGAGCCACCCTAAGGGAGTA
1 CCCTCAGCTCCATAAGGACTTACCCAAGGCACACAACAGAGGAGCCACCCTAAGGGAGTA
* *
373232 -CCTCAGGGTCCATAAGGTCTTACC
1 CCCTCA-GCTCCATAAGGACTTACC
373256 ACTAGGCCCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 5 0.07
60 71 0.93
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (60 bp):
CCCTCAGCTCCATAAGGACTTACCCAAGGCACACAACAGAGGAGCCACCCTAAGGGAGTA
Found at i:380070 original size:2 final size:2
Alignment explanation
Indices: 380063--380089 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
380053 AGTTAGAAAA
380063 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
380090 ATAACTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:383228 original size:6 final size:6
Alignment explanation
Indices: 383217--383243 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
383207 GTCAAGGAAA
383217 GGAGAT GGAGAT GGAGAT GGAGAT GGA
1 GGAGAT GGAGAT GGAGAT GGAGAT GGA
383244 ACGAGAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GGAGAT
Found at i:390876 original size:30 final size:30
Alignment explanation
Indices: 390841--390914 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
390831 CATCTCACCA
390841 AAAATTAACAGAATCAACTGTTAATTAAGC
1 AAAATTAACAGAATCAACTGTTAATTAAGC
390871 AAAATTAACAGAATCAACTGTTAATTAAGC
1 AAAATTAACAGAATCAACTGTTAATTAAGC
390901 AAAATTAACAGAAT
1 AAAATTAACAGAAT
390915 TTAACAAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (30 bp):
AAAATTAACAGAATCAACTGTTAATTAAGC
Found at i:394927 original size:22 final size:21
Alignment explanation
Indices: 394872--394928 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
394862 AGTCAATTCG
* *
394872 TTGACTTTGACTAATGTTGACT
1 TTGACTTTGAC-CATGATGACT
*
394894 TTGACCTTGACCATCGATGACT
1 TTGACTTTGACCAT-GATGACT
394916 TTGACTTTGACCA
1 TTGACTTTGACCA
394929 AAAAGTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGACTTTGACCATGATGACT
Found at i:398164 original size:25 final size:28
Alignment explanation
Indices: 398135--398194 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
398125 TTTATATACC
*
398135 TATTTTAAT-AAAAA-AATAT-TTTAAA
1 TATTTAAATAAAAAACAATATATTTAAA
398160 TATTTAAATAAAAAACAATATACTTTAAA
1 TATTTAAATAAAAAACAATATA-TTTAAA
398189 TATTTA
1 TATTTA
398195 TTTCTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.27
26 5 0.17
27 5 0.17
29 12 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
TATTTAAATAAAAAACAATATATTTAAA
Found at i:406164 original size:2 final size:2
Alignment explanation
Indices: 406157--406182 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
406147 TCGGTGATTA
406157 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
406183 TCGTAGCAAC
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:408866 original size:17 final size:17
Alignment explanation
Indices: 408846--408878 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
408836 ATATTTATTT
*
408846 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
408863 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
408879 GATGATCTCG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:408942 original size:21 final size:21
Alignment explanation
Indices: 408918--408957 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
408908 TTTCAATGTA
*
408918 TAAAATTCATTTTTAATAAAT
1 TAAAATTCATTTTAAATAAAT
*
408939 TAAAATTTATTTTAAATAA
1 TAAAATTCATTTTAAATAA
408958 TATCATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTCATTTTAAATAAAT
Found at i:408973 original size:17 final size:16
Alignment explanation
Indices: 408948--408982 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
408938 TTAAAATTTA
408948 TTTTAAATAATATCAT
1 TTTTAAATAATATCAT
408964 TTTTACAATAATATCAT
1 TTTTA-AATAATATCAT
408981 TT
1 TT
408983 GTCACCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAATAATATCAT
Found at i:414383 original size:22 final size:21
Alignment explanation
Indices: 414331--414383 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
414321 TAATTATGAT
* *
414331 ATTTAAATAAAATATTTTATA
1 ATTTAAATAAAAAATTTAATA
*
414352 ATCTATAATAAAAAATTTCAATA
1 ATTTA-AATAAAAAATTT-AATA
414375 ATTTAAATA
1 ATTTAAATA
414384 GATGTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAAATAAAAAATTTAATA
Found at i:424953 original size:111 final size:111
Alignment explanation
Indices: 424756--425299 Score: 487
Period size: 111 Copynumber: 4.9 Consensus size: 111
424746 TTGCCCTCTG
* * *
424756 ACCCCAAGAATCCTGTAAC-TAGTCCCATGGCTAAAGTTGCATCCTT-GGAGACGAGTCTTACCA
1 ACCCCAAGAATCCTGTAACTTA-T-CC-T-GCTAAAGTTGCAT-CTTCAGAGACAAGTGTTACCA
* * * *
424819 TTCCAATATATACGAACTTAGACCATGTAAAAGATACAGATTTGTCCTCCA
61 TTCCAGTAGATAAGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCA
* * * * *
424870 ACCCCGAGAATCCTGTAACTTATCCTGCTGAAGTTGCATCTTTAGAAACAAGTGTTACCATTTCA
1 ACCCCAAGAATCCTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACAAGTGTTACCATTCCA
* * *
424935 GTAGATAAGAGCTTAGACCACGTAAAAGATAAAGATTTGTCTTCCA
66 GTAGATAAGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCA
* * *
424981 ACCCCAAGAATCCTCTAACTTATCCGGCTAAAGTTGCATCTTCAGAGACAAGTGTTACTATTCCA
1 ACCCCAAGAATCCTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACAAGTGTTACCATTCCA
* * * * *
425046 GTTGATATGAACTTAGACAATGTAAAAGA-AACAGATCTGGCCTCCA
66 GTAGATAAGAACTTAGACCATGTAAAAGATAA-AGATTTGTCCTCCA
* * * * * * ** *
425092 ACCTCAAGAATCATGTAACTTATCCAGCTGAATTTGCACCTTCAGAGACGGGTGTTTCCATTCCA
1 ACCCCAAGAATCCTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACAAGTGTTACCATTCCA
* * * * **
425157 GTTGATACA-AGCTTATACCATGTAAAAGATAAATATTTGTCCTTGA
66 GTAGATA-AGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCA
* * * ** * * * *
425203 A-CCC----TTCAT-TAGCTTATCCTATGGCTAAAGTCACATCCTCAGAGGCGAGTTTTACCATT
1 ACCCCAAGAATCCTGTAACTTATCC--T-GCTAAAGTTGCATCTTCAGAGACAAGTGTTACCATT
* *
425262 CCAGTAGATATGAACTTAGACCATGTAAAAGTTAAAGA
63 CCAGTAGATAAGAACTTAGACCATGTAAAAGATAAAGA
425300 CTCCCATACC
Statistics
Matches: 351, Mismatches: 70, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
105 9 0.03
106 4 0.01
108 57 0.16
110 7 0.02
111 248 0.71
112 3 0.01
113 2 0.01
114 19 0.05
115 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (111 bp):
ACCCCAAGAATCCTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACAAGTGTTACCATTCCA
GTAGATAAGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCA
Found at i:425184 original size:222 final size:224
Alignment explanation
Indices: 424756--425197 Score: 554
Period size: 222 Copynumber: 2.0 Consensus size: 224
424746 TTGCCCTCTG
* * *
424756 ACCCCAAGAATCCTGTAACTAGTCCCATGGCTAAAGTTGCATCCTTGGAGACGAGTCTTACCATT
1 ACCCCAAGAATCCTCTAACTAGTCCCA-GGCTAAAGTTGCATCCTTAGAGACAAGTCTTACCATT
* * * * * *
424821 CCAATATATACGAACTTAGACCATGTAAAAGATACAGATTTGTCCTCCAACCCCGAGAATCCTGT
65 CCAATATATACGAACTTAGACAATGTAAAAGAAACAGATCTGGCCTCCAACCCCAAGAATCATGT
* * * *
424886 AACTTATCCTGCTGAAGTTGCATCTTTAGAAACAAGTGTTACCATTTCAGTAGATAAGAGCTTAG
130 AACTTATCCAGCTGAAGTTGCACCTTCAGAAACAAGTGTTACCATTCCAGTAGATAAGAGCTTAG
424951 ACCACGTAAAAGATAAAGATTTGTCTTCCA
195 ACCACGTAAAAGATAAAGATTTGTCTTCCA
* *
424981 ACCCCAAGAATCCTCTAACTTA-T-CC-GGCTAAAGTTGCAT-CTTCAGAGACAAGTGTTACTAT
1 ACCCCAAGAATCCTCTAAC-TAGTCCCAGGCTAAAGTTGCATCCTT-AGAGACAAGTCTTACCAT
* * *
425042 TCCAGT-TGATATGAACTTAGACAATGTAAAAGAAACAGATCTGGCCTCCAACCTCAAGAATCAT
64 TCCAATAT-ATACGAACTTAGACAATGTAAAAGAAACAGATCTGGCCTCCAACCCCAAGAATCAT
* * ** * *
425106 GTAACTTATCCAGCTGAATTTGCACCTTCAGAGACGGGTGTTTCCATTCCAGTTGATACA-AGCT
128 GTAACTTATCCAGCTGAAGTTGCACCTTCAGAAACAAGTGTTACCATTCCAGTAGATA-AGAGCT
* * *
425170 TATACCATGTAAAAGATAAATATTTGTC
192 TAGACCACGTAAAAGATAAAGATTTGTC
425198 CTTGAACCCT
Statistics
Matches: 186, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
221 4 0.02
222 158 0.85
223 1 0.01
224 2 0.01
225 19 0.10
226 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (224 bp):
ACCCCAAGAATCCTCTAACTAGTCCCAGGCTAAAGTTGCATCCTTAGAGACAAGTCTTACCATTC
CAATATATACGAACTTAGACAATGTAAAAGAAACAGATCTGGCCTCCAACCCCAAGAATCATGTA
ACTTATCCAGCTGAAGTTGCACCTTCAGAAACAAGTGTTACCATTCCAGTAGATAAGAGCTTAGA
CCACGTAAAAGATAAAGATTTGTCTTCCA
Found at i:436781 original size:2 final size:2
Alignment explanation
Indices: 436774--436811 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
436764 AACATGAATA
436774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
436812 ATGATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:437402 original size:5 final size:5
Alignment explanation
Indices: 437380--437468 Score: 56
Period size: 5 Copynumber: 16.6 Consensus size: 5
437370 AGTAAACAAG
* * *
437380 TAAAA TCAAAA GTAAAA TAAAA TTAAA CAAATA TAAAA GAAAAA TAAGAA
1 TAAAA T-AAAA -TAAAA TAAAA TAAAA TAAA-A TAAAA -TAAAA TAA-AA
*
437430 TAAAGA -AAAA TAAAAA TGAAA TGAAAA -AAAA TAAAA TAA
1 TAAA-A TAAAA T-AAAA TAAAA T-AAAA TAAAA TAAAA TAA
437469 TAAAAGGCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
4 5 0.08
5 30 0.45
6 30 0.45
7 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:437417 original size:27 final size:27
Alignment explanation
Indices: 437381--437444 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
437371 GTAAACAAGT
*
437381 AAAATCAAAAGTAAAATAA-AATTAAACA
1 AAAAT-AAAAGAAAAATAAGAA-TAAACA
* *
437409 AATATAAAAGAAAAATAAGAATAAAGA
1 AAAATAAAAGAAAAATAAGAATAAACA
437436 AAAATAAAA
1 AAAATAAAA
437445 ATGAAATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (27 bp):
AAAATAAAAGAAAAATAAGAATAAACA
Found at i:437434 original size:16 final size:17
Alignment explanation
Indices: 437415--437457 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
437405 AACAAATATA
*
437415 AAAGAAAAATAAGAAT-
1 AAAGAAAAATAAAAATG
437431 AAAGAAAAATAAAAATG
1 AAAGAAAAATAAAAATG
437448 AAATGAAAAA
1 AAA-GAAAAA
437458 AAATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 3 0.12
18 6 0.25
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAGAAAAATAAAAATG
Done.