Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015216.1 Kokia drynarioides strain JFW-HI SEQ_130260, 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: 531577
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 459 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:247992 original size:281 final size:282
Alignment explanation
Indices: 247495--248066 Score: 776
Period size: 281 Copynumber: 2.0 Consensus size: 282
247485 TTGATATTTA
* * * * * *
247495 TATTATTGTAAATACAGTAAGATGTGGGTTCAAGTGCGTTGAAGTACATTATCATCTTATTTATG
1 TATTATTGTCAATATAATAAGATGTGGGTTCAAGTGAGTTGAAATACATTATCATCCTATTTATG
* *
247560 AGTCAAAGAGAGATTATGAGTAATTTTAAACATTATGTAAAAAAAACAAATATGATCAGAATTTA
66 AGTCAAAGAGAGATTATGAGTAATTTTAAACATTATGTAAAAAAAACAAATATAATCAGAACTTA
* * * * * *
247625 TAATAATATTGTTAGCTTTTAGAGATAGTGCATATATTTTTTAACTCAAAATTTTCTGCAGGTGA
131 TAATAAAATTGTTAACTTTTAAAGAGAGTGCACACATTTTTTAACTCAAAATTTTCTGCAGGTGA
** * *
247690 TCCATCAAATTTTCCTACACCATTTGTAAAGAGCTTGTATTTCAAGTATCAATTTT-TCGATTGA
196 TCCATCAAATCGTCCTACACCATTTGTAAAGAGCTTGGATTTAAAGTATCAATTTTGTCGATTGA
* *
247754 GTTTTAGCTCGATTGGCATGGT
261 GTTTTAACTCGATTGGCATGAT
* * *
247776 TATTGTTGTCAATATAATAAGATGTGGGTTTAAGTGAGTTGAAATGCATTAT-ACTCCTATTTAT
1 TATTATTGTCAATATAATAAGATGTGGGTTCAAGTGAGTTGAAATACATTATCA-TCCTATTTAT
* * ** ** * *
247840 GGGTTAGGGAGAGATTATGAGTAATTTTAAGTATTATGTCAAAAAGAGCAAATATAATCAGAACT
65 GAGTCAAAGAGAGATTATGAGTAATTTTAAACATTATGT-AAAAAAAACAAATATAATCAGAACT
*
247905 TATAATAAAATTGTTAACTTTTAAAGAGAGTGTACACATTTTTTAACTCAAAA-TTTCTTGC-GA
129 TATAATAAAATTGTTAACTTTTAAAGAGAGTGCACACATTTTTTAACTCAAAATTTTC-TGCAG-
*
247968 GTGATCCATCAAA-CGTCTTACACCATTTGTAAAGAGCTTGGATTTAAAGTATCAATTTTGTCGA
192 GTGATCCATCAAATCGTCCTACACCATTTGTAAAGAGCTTGGATTTAAAGTATCAATTTTGTCGA
248032 TTGAGTTTTAACTCGATTGGCATGAT
257 TTGAGTTTTAACTCGATTGGCATGAT
248058 TATTATTGT
1 TATTATTGT
248067 TAATGTAACA
Statistics
Matches: 252, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
280 1 0.00
281 132 0.52
282 119 0.47
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (282 bp):
TATTATTGTCAATATAATAAGATGTGGGTTCAAGTGAGTTGAAATACATTATCATCCTATTTATG
AGTCAAAGAGAGATTATGAGTAATTTTAAACATTATGTAAAAAAAACAAATATAATCAGAACTTA
TAATAAAATTGTTAACTTTTAAAGAGAGTGCACACATTTTTTAACTCAAAATTTTCTGCAGGTGA
TCCATCAAATCGTCCTACACCATTTGTAAAGAGCTTGGATTTAAAGTATCAATTTTGTCGATTGA
GTTTTAACTCGATTGGCATGAT
Found at i:249409 original size:40 final size:41
Alignment explanation
Indices: 249338--249440 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 41
249328 TTGGAAACGA
* *
249338 TTTCATCTAATTTGCAAAAAAACACTCCTATTT-AAAATCAT
1 TTTCAACTGATTTGCAAAAAAACACTCCTATTTGAAAAT-AT
* *
249379 TTTCAACTGATTTGCAAAAAAACACT-CTATTTGAAAGTGT
1 TTTCAACTGATTTGCAAAAAAACACTCCTATTTGAAAATAT
* *
249419 TTTCAACTGAGTTGTAAAAAAA
1 TTTCAACTGATTTGCAAAAAAA
249441 ACTTTAAGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 27 0.49
41 28 0.51
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.35
Consensus pattern (41 bp):
TTTCAACTGATTTGCAAAAAAACACTCCTATTTGAAAATAT
Found at i:253916 original size:42 final size:42
Alignment explanation
Indices: 253868--253952 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
253858 GTGGTGCGTT
* *
253868 CTAATAATATCATGTGGAAGGTCAACAATTGGTCAATAGTTG
1 CTAATAATATCATGTGAAAGGTCAACAATTGGTCAACAGTTG
*
253910 CTAATAATGTCATGTGAAAGGTCAACAATTGGTCAACAGTTG
1 CTAATAATATCATGTGAAAGGTCAACAATTGGTCAACAGTTG
253952 C
1 C
253953 CAATGTCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (42 bp):
CTAATAATATCATGTGAAAGGTCAACAATTGGTCAACAGTTG
Found at i:258154 original size:22 final size:22
Alignment explanation
Indices: 258124--258166 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
258114 TTTGCTACTA
*
258124 TTTTGTTGTCAATTCACTGTTG
1 TTTTATTGTCAATTCACTGTTG
* *
258146 TTTTATTGTCATTTCGCTGTT
1 TTTTATTGTCAATTCACTGTT
258167 ATATTGTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (22 bp):
TTTTATTGTCAATTCACTGTTG
Found at i:260048 original size:5 final size:5
Alignment explanation
Indices: 260035--260076 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
260025 AACTCGATTT
* * *
260035 GAATC GAGTC GAGTC GAGTC GAATC GAATC GAATC GAATC GA
1 GAATC GAATC GAATC GAATC GAATC GAATC GAATC GAATC GA
260077 GTTAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (5 bp):
GAATC
Found at i:260315 original size:37 final size:39
Alignment explanation
Indices: 260274--260395 Score: 96
Period size: 39 Copynumber: 3.2 Consensus size: 39
260264 ATTTTAGAAA
* *
260274 ATTTTTA-AAATTTT-AACTTTCTTT-ATATATATTTTAG
1 ATTTTTATAAATTTTAAAATTT-TTTAATATAAATTTTAG
*
260311 A-TTTTATAATTTTTAAAATTTTTTAAATATAAATTTTAG
1 ATTTTTATAAATTTTAAAATTTTTT-AATATAAATTTTAG
** * *
260350 ATTTTTTATAAATATTTTGAA-TTTTAAATAT-TATTTT-G
1 A-TTTTTATAAAT-TTTAAAATTTTTTAATATAAATTTTAG
260388 ATTTTTAT
1 ATTTTTAT
260396 TTTATTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
36 5 0.07
37 17 0.24
38 7 0.10
39 18 0.26
40 5 0.07
41 13 0.19
42 5 0.07
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (39 bp):
ATTTTTATAAATTTTAAAATTTTTTAATATAAATTTTAG
Found at i:260316 original size:18 final size:18
Alignment explanation
Indices: 260295--260392 Score: 51
Period size: 18 Copynumber: 5.2 Consensus size: 18
260285 TTTAACTTTC
260295 TTTATATATATTTTAGAT
1 TTTATATATATTTTAGAT
*
260313 TTTATA-AT-TTTTAAAATTT
1 TTTATATATATTTT-AGA--T
*
260332 TTTAAATATAAATTTTAGATTT
1 TTT--ATATATATTTTAGA--T
*
260354 TTTATAAATATTTT-GAAT
1 TTTATATATATTTTAG-AT
*
260372 TTTAAATATTATTTT-GAT
1 TTTATATA-TATTTTAGAT
260390 TTT
1 TTT
260393 TATTTTATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
16 4 0.06
17 4 0.06
18 18 0.28
19 12 0.19
20 10 0.16
21 3 0.05
22 9 0.14
23 4 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTATATATATTTTAGAT
Found at i:260345 original size:24 final size:24
Alignment explanation
Indices: 260315--260364 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
260305 TTTTAGATTT
*
260315 TATAATTTTTAAAATTTTT-TAAA
1 TATAAATTTTAAAATTTTTATAAA
* *
260338 TATAAATTTTAGATTTTTTATAAA
1 TATAAATTTTAAAATTTTTATAAA
260362 TAT
1 TAT
260365 TTTGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATAAATTTTAAAATTTTTATAAA
Found at i:273228 original size:3 final size:3
Alignment explanation
Indices: 273220--273245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
273210 GTAAAGAACG
273220 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
273246 ATGGCTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:277117 original size:29 final size:29
Alignment explanation
Indices: 277048--277107 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
277038 TATCTGATTT
* * *
277048 AAATTAATTAAATTATTAAAAAATTATAA
1 AAATAAATTAAAATATTAAAAAAATATAA
*
277077 AAATAAAATAAAATATTAAAAAAATATAA
1 AAATAAATTAAAATATTAAAAAAATATAA
277106 AA
1 AA
277108 TCTGATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (29 bp):
AAATAAATTAAAATATTAAAAAAATATAA
Found at i:278634 original size:39 final size:39
Alignment explanation
Indices: 278553--278645 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
278543 AAACCATGAG
* **
278553 TAAAACACCATACCAAACTGAAATCAGCAGAACAGATGA
1 TAAAACACCATACCAAACTGAAATCAGCAGAAAAGACCA
* * *
278592 TAAAACCCCATACCAGACTGAAAGT-AGCATAAAAGACCA
1 TAAAACACCATACCAAACTGAAA-TCAGCAGAAAAGACCA
* *
278631 TAAATCACCGTACCA
1 TAAAACACCATACCA
278646 GAATCCACCG
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
39 43 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (39 bp):
TAAAACACCATACCAAACTGAAATCAGCAGAAAAGACCA
Found at i:281783 original size:15 final size:15
Alignment explanation
Indices: 281734--281784 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
281724 TTGTCTCGTA
* *
281734 TTACATTTTAATCAT
1 TTACGTTTTAATAAT
*
281749 TTACG-TTTGA-AAT
1 TTACGTTTTAATAAT
281762 ATTACGTTTTAATAAT
1 -TTACGTTTTAATAAT
281778 TTACGTT
1 TTACGTT
281785 AGTGTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 15 0.52
16 3 0.10
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (15 bp):
TTACGTTTTAATAAT
Found at i:283838 original size:3 final size:3
Alignment explanation
Indices: 283832--283865 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
283822 TATCTCGAAT
283832 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
283866 CTATCATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:285069 original size:157 final size:158
Alignment explanation
Indices: 284773--285168 Score: 471
Period size: 157 Copynumber: 2.5 Consensus size: 158
284763 TTTCATCTGG
** * * * *
284773 TTCATAAATCAATATGTTGATTGGGGTTATGTTTTTCGACTTTAACAGTTTAATTATTTTACGGA
1 TTCATAAATCAATATGTTGATTGAAGTTTTGTTTTTAGACTTT-ACAATTTAATTATTTTACTGA
* * * * * *
284838 ATG-AAAGTGATTTTGAATTATTTAAATAACCCATATGTTATAGTTAATGTTATAGGTAATGAAT
65 AAGAAAAGTGATTTCGAATTATTGAAATAACCCATATGTTATAATTAATATTATAGCTAATGAAT
* * * *
284902 TCATCTTGTTGATTGATGTGATTTTATTA
130 TCATCCTGTTGATTAAGGTGATTTTACTA
* * *
284931 TTCATAAATCAATATGTTGATTGAAATTTTATTTTTTGACTTTACAATTTAATTATTTTA-TGAA
1 TTCATAAATCAATATGTTGATTGAAGTTTTGTTTTTAGACTTTACAATTTAATTATTTTACTGAA
* * *
284995 AGAAAAGTG-TCTTCGAGTGT-TTGAAATAATCTATATGTTATAATTAATATTATAGCTAAT-AA
66 AGAAAAGTGAT-TTCGAAT-TATTGAAATAACCCATATGTTATAATTAATATTATAGCTAATGAA
* *
285057 GTTGATCCTGTTGATTAAGGTGATTTTACTG
129 -TTCATCCTGTTGATTAAGGTGATTTTACTA
* *
285088 TTTATAAATCAATATGTTGATTGAAGTTTTGTTTTTAGACTTTACAACTTAATTATTTTACTGGA
1 TTCATAAATCAATATGTTGATTGAAGTTTTGTTTTTAGACTTTACAATTTAATTATTTTACT-GA
285153 AAG-AAAGTGATTTCGA
65 AAGAAAAGTGATTTCGA
285169 CTAGTTGAAA
Statistics
Matches: 203, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
156 7 0.03
157 140 0.69
158 50 0.25
159 6 0.03
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (158 bp):
TTCATAAATCAATATGTTGATTGAAGTTTTGTTTTTAGACTTTACAATTTAATTATTTTACTGAA
AGAAAAGTGATTTCGAATTATTGAAATAACCCATATGTTATAATTAATATTATAGCTAATGAATT
CATCCTGTTGATTAAGGTGATTTTACTA
Found at i:286464 original size:156 final size:155
Alignment explanation
Indices: 286195--286970 Score: 975
Period size: 156 Copynumber: 5.0 Consensus size: 155
286185 CTACAAGCAT
* * *
286195 CCTTTTCAGGAAATTGTATC---GAAGCCATCTGAGGAATTACTCTCCAAGGAGAAAATGGTATG
1 CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGTATG
* ** * * * *
286257 TTCTTGTGTACATGTTTATATCTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAATGTCA
66 TTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCA
*
286322 AATCAAGGATAACGAACTACGAACA
131 AATCAAGGATAATGAACTACGAACA
* * **
286347 CCTTTTTCAGGAAATTGAATCGAGGAAGCCATCTGAGAAATTACTCAACAAGGAGAAAATGGTAT
1 CC-TTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGTAT
* * *
286412 GTTCTCGTGCATTTATTTATATTTTGAGTTGTGTGTTAGAGGATGGAGATAGGAACATAAAAGTC
65 GTTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTC
* *
286477 AAATCAAGGAAAATGAACTAGGAACA
130 AAATCAAGGATAATGAACTACGAACA
*
286503 CCCTTTTCAGGAAACTGTATCGCGGAAGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGG
1 -CCTTTTCAGGAAACTGTAT--C-GAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGG
* * * *
286568 TATGTTCTTGTGC-TTGAATTTATATTTTGAGTTGTGTGTTTTAGGATGGAGAT----A-AGAAC
62 TATGTTCTTGTGCATT-TATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAA
* *
286627 GGTCAAAT-AGAGGATGATGAACTA-GAAACA
126 AGTCAAATCA-AGGATAATGAACTACG-AACA
* *
286657 CCCTTTCAGGAAACTGTATCGAGGAAGAAGCCATCTGAGAAGTTACTCCCCAAGGAGAAAATGGT
1 CCTTTTCAGGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGT
* *
286722 AAGTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
63 ATGTTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
*
286787 TCAAATCAAGGATAATGAACTAC-AAGCGT
128 TCAAATCAAGGATAATGAACTACGAA-C-A
* * * *
286816 CCTTTTCAGGAAACTATATCAAGGAAGCCATCTGAGAAATTACTCCCCAAGGAAAAAATGGTATT
1 CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGTATG
* * *
286881 TTCTTGTGC-TTGTATTTATATTTTGAGTCGTGTGTTTGAGGATGGATATAGGGATATAAAAGTC
66 TTCTTGTGCATT-TATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTC
*
286945 AAATCAAGGATAATGAACTATGAACA
130 AAATCAAGGATAATGAACTACGAACA
286971 TTTCTTTTGT
Statistics
Matches: 542, Mismatches: 56, Indels: 49
0.84 0.09 0.08
Matches are distributed among these distances:
150 2 0.00
151 1 0.00
152 2 0.00
153 121 0.22
154 27 0.05
155 2 0.00
156 248 0.46
157 7 0.01
158 28 0.05
159 104 0.19
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (155 bp):
CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGTATG
TTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCA
AATCAAGGATAATGAACTACGAACA
Found at i:288910 original size:22 final size:22
Alignment explanation
Indices: 288878--288925 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
288868 ATTTTGATCT
288878 AGCTCAAGCCAAAATTAAAAGG
1 AGCTCAAGCCAAAATTAAAAGG
*
288900 AGCTCATGCCAAAATTAAAAGG
1 AGCTCAAGCCAAAATTAAAAGG
288922 AGCT
1 AGCT
288926 AGCACCACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (22 bp):
AGCTCAAGCCAAAATTAAAAGG
Found at i:298471 original size:23 final size:22
Alignment explanation
Indices: 298439--298518 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
298429 GCTGGGGAAA
*
298439 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
298461 CTAGTAGGCACACACAGTGCAAT
1 C-AGTAGGCACACACAGTGCAAT
** * **
298484 CAGTAGGTGCACATAACGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
298507 CAGTAGGCACAC
1 CAGTAGGCACAC
298519 GAGGTGCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 14 0.29
23 34 0.71
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:298582 original size:23 final size:23
Alignment explanation
Indices: 298507--298583 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
298497 TAACGCAAAT
* * *
298507 CAGTAGGCACACGAGGTGCAAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
298530 TAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
298553 CAATAAGCACAC-ACAGTGCTG-AA
1 CAGTAAGCACACGA-AGTGC-GAAA
298576 CAGTAAGC
1 CAGTAAGC
298584 GCGCTAGCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:301566 original size:2 final size:2
Alignment explanation
Indices: 301559--301587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
301549 TTTATATGTC
301559 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
301588 TCTAGAAGCC
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:303141 original size:3 final size:3
Alignment explanation
Indices: 303133--303160 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
303123 TTATATATTT
303133 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
303161 CATTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:303231 original size:24 final size:25
Alignment explanation
Indices: 303204--303253 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
303194 TTTTTAAAGA
*
303204 ATTAAATTAA-TTTTTACAATTTTT
1 ATTAAATTAAGTTTTTACAAATTTT
* *
303228 ATTAATTTAAGTTTTTATAAATTTT
1 ATTAAATTAAGTTTTTACAAATTTT
303253 A
1 A
303254 AAGATGCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTAAATTAAGTTTTTACAAATTTT
Found at i:310666 original size:11 final size:11
Alignment explanation
Indices: 310645--310678 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
310635 GTTTATACAA
310645 TTTTA-ATTTT
1 TTTTATATTTT
310655 TTTTATATTTT
1 TTTTATATTTT
*
310666 TTTAATATTTT
1 TTTTATATTTT
310677 TT
1 TT
310679 AAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATATTTT
Found at i:310668 original size:20 final size:20
Alignment explanation
Indices: 310645--310684 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
310635 GTTTATACAA
* *
310645 TTTTAATTTTTTTTATATTT
1 TTTTAATATTTTTTAAATTT
310665 TTTTAATATTTTTTAAATTT
1 TTTTAATATTTTTTAAATTT
310685 CAAACACCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTAATATTTTTTAAATTT
Found at i:315602 original size:15 final size:16
Alignment explanation
Indices: 315582--315616 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
315572 GATATCGATT
315582 TTCATAGTTGTTACA-
1 TTCATAGTTGTTACAG
*
315597 TTCATATTTGTTACAG
1 TTCATAGTTGTTACAG
315613 TTCA
1 TTCA
315617 ATGAGCGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (16 bp):
TTCATAGTTGTTACAG
Found at i:323743 original size:17 final size:17
Alignment explanation
Indices: 323721--323762 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
323711 TCACAAAAAA
**
323721 AAAATTAACAATACATT
1 AAAATTAACAATACACG
323738 AAAATTAACAATACACG
1 AAAATTAACAATACACG
323755 AAAATTAA
1 AAAATTAA
323763 ACATTTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAATTAACAATACACG
Found at i:331356 original size:23 final size:22
Alignment explanation
Indices: 331301--331417 Score: 103
Period size: 23 Copynumber: 5.2 Consensus size: 22
331291 CTAGCGCGCT
* * *
331301 TACTGTTTCGCACTTTGTGTGCT
1 TACTGATT-GCACTATGTGTGCC
* *
331324 TACTGTTTTGCACTTTGTGTGCC
1 TACTG-ATTGCACTATGTGTGCC
* * *
331347 TACTAATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTATGTGTGCC
*
331370 TACTGATTGCACTATGTGTGTC
1 TACTGATTGCACTATGTGTGCC
331392 TACTGGATTGCAC--TGTGTGCC
1 TACT-GATTGCACTATGTGTGCC
331413 TACTG
1 TACTG
331418 TTTCCCCAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.01
21 11 0.14
22 17 0.21
23 48 0.60
24 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (22 bp):
TACTGATTGCACTATGTGTGCC
Found at i:336064 original size:31 final size:31
Alignment explanation
Indices: 336028--336086 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
336018 AAAACCTTAA
336028 AGTTCAAG-CTCCAATATGAAAATAATTGTTT
1 AGTTCAAGTC-CCAATATGAAAATAATTGTTT
* *
336059 AGTTCAAGTCCCAATATGAGAGTAATTG
1 AGTTCAAGTCCCAATATGAAAATAATTG
336087 CAAAGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (31 bp):
AGTTCAAGTCCCAATATGAAAATAATTGTTT
Found at i:336094 original size:31 final size:31
Alignment explanation
Indices: 336026--336097 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
336016 TAAAAACCTT
*
336026 AAAGTTCAAGCTCCAATATGAAAATAATTGT
1 AAAGTTCAAGCTCCAATATGAAAATAATTGC
** * *
336057 TTAGTTCAAG-TCCCAATATGAGAGTAATTGC
1 AAAGTTCAAGCT-CCAATATGAAAATAATTGC
336088 AAAGTTCAAG
1 AAAGTTCAAG
336098 GACTAACTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAGTTCAAGCTCCAATATGAAAATAATTGC
Found at i:338027 original size:2 final size:2
Alignment explanation
Indices: 338022--338057 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
338012 ACACACACAG
338022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
338058 CCTCCCTCAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:347669 original size:14 final size:15
Alignment explanation
Indices: 347637--347674 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
347627 TGGTCTCGAG
*
347637 TTTAGAATTTCAAGA
1 TTTAGGATTTCAAGA
347652 -TTAGGATTT-AAGA
1 TTTAGGATTTCAAGA
347665 TTTAGGATTT
1 TTTAGGATTT
347675 TGAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
TTTAGGATTTCAAGA
Found at i:348939 original size:141 final size:141
Alignment explanation
Indices: 348685--348947 Score: 305
Period size: 141 Copynumber: 1.9 Consensus size: 141
348675 GGTTGAAAAA
* *** *
348685 TTTTAAGGCTTAATATATATATTGGCCCCTAAACTTGGTAATTTTTTCAAATTAGCCCCTAAACT
1 TTTTAAGGCTTAATATATAGATTGGCCCCTAAACTTACAAATTTTCTCAAATTAGCCCCTAAACT
* *** * * *
348750 TTTTTCTTGGATCACATTAGTCCCTAAGGTTAACATTCTTTCACAAATTGGTCCCTATGGTTAAC
66 TTTTTCTTAGATCACATTAGTCCCTAAAACTAACATCCTTACACAAATTGATCCCTATGGTTAAC
348815 ATTGTTAGTTC
131 ATTGTTAGTTC
* * * * * *
348826 TTTTAAGGCTTAATATATAGATTGGTCCTTGAACTTCACAAATTTTCTCACATTGGCCCTTAAA-
1 TTTTAAGGCTTAATATATAGATTGGCCCCTAAACTT-ACAAATTTTCTCAAATTAGCCCCTAAAC
* * *
348890 TTTTTT-TTAGATCATATTGGTCCCTAAAACTGACATCCATTACACAAATTGATCCCTA
65 TTTTTTCTTAGATCACATTAGTCCCTAAAACTAACATCC-TTACACAAATTGATCCCTA
348948 CATTGACATA
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
140 24 0.24
141 55 0.56
142 20 0.20
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (141 bp):
TTTTAAGGCTTAATATATAGATTGGCCCCTAAACTTACAAATTTTCTCAAATTAGCCCCTAAACT
TTTTTCTTAGATCACATTAGTCCCTAAAACTAACATCCTTACACAAATTGATCCCTATGGTTAAC
ATTGTTAGTTC
Found at i:350297 original size:16 final size:15
Alignment explanation
Indices: 350276--350327 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
350266 GTGATTTGTG
*
350276 AAAATTGAATCAAATC
1 AAAATTGCAT-AAATC
* *
350292 AAAATTTCATACAT-
1 AAAATTGCATAAATC
350306 AAAATTGCATAAAATC
1 AAAATTGCAT-AAATC
350322 AAAATT
1 AAAATT
350328 CAAGTGTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.29
Consensus pattern (15 bp):
AAAATTGCATAAATC
Found at i:358203 original size:18 final size:19
Alignment explanation
Indices: 358165--358225 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
358155 AGATTCATTT
358165 TAAAATTATAAAAAAAATA
1 TAAAATTATAAAAAAAATA
* *
358184 TAAAATTAT-TAAAAACTA
1 TAAAATTATAAAAAAAATA
* * *
358202 TAAAAATAGAAAAAAATTA
1 TAAAATTATAAAAAAAATA
358221 TAAAA
1 TAAAA
358226 AATATTAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 14 0.40
19 21 0.60
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAATTATAAAAAAAATA
Found at i:358228 original size:10 final size:10
Alignment explanation
Indices: 358166--358228 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
358156 GATTCATTTT
358166 AAAATTATAA
1 AAAATTATAA
* *
358176 AAAA-AATAT
1 AAAATTATAA
*
358185 AAAATTATTA
1 AAAATTATAA
*
358195 AAAACTAT-A
1 AAAATTATAA
*
358204 AAAA-TAGAAA
1 AAAATTA-TAA
358214 AAAATTATAA
1 AAAATTATAA
358224 AAAAT
1 AAAAT
358229 ATTAGAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 2 0.05
9 12 0.29
10 25 0.61
11 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAATTATAA
Found at i:361594 original size:25 final size:25
Alignment explanation
Indices: 361535--361615 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
361525 AATATCGTCA
** * *
361535 TTTTAATAATTTATATATTTATAATT
1 TTTTAATAATAAAT-TATTTTTTATT
361561 TTTTAAATAATAAATTATTTTTTATT
1 TTTT-AATAATAAATTATTTTTTATT
* * *
361587 TTTTAATATTAAAATATAATTTTATT
1 TTTTAATAATAAATTAT-TTTTTATT
361613 TTT
1 TTT
361616 ATTAATTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 11 0.24
26 27 0.59
27 8 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTAATAATAAATTATTTTTTATT
Found at i:361601 original size:26 final size:28
Alignment explanation
Indices: 361552--361629 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 28
361542 AATTTATATA
* *
361552 TTTATAATTTTTTAA-ATAATAAATT-AT
1 TTTATTATTTTTTAATATTA-AAATTAAT
361579 TTT-TTATTTTTTAATATTAAAATATAAT
1 TTTATTATTTTTTAATATTAAAAT-TAAT
*
361607 TTTATT-TTTATTAAT-TTAAAATT
1 TTTATTATTTTTTAATATTAAAATT
361630 TTATAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 15 0.34
27 14 0.32
28 13 0.30
29 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTATTATTTTTTAATATTAAAATTAAT
Found at i:361631 original size:16 final size:17
Alignment explanation
Indices: 361612--361644 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
361602 ATAATTTTAT
*
361612 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
361628 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
361645 AATTCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:370918 original size:18 final size:19
Alignment explanation
Indices: 370886--370928 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
370876 AAGATTAGAA
370886 TTTTTTAATTATTAA-A-T
1 TTTTTTAATTATTAACACT
*
370903 TTTTTTATATTTTTAACACT
1 TTTTTTA-ATTATTAACACT
370923 TTTTTT
1 TTTTTT
370929 TTTTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 1 0.05
20 7 0.32
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTAATTATTAACACT
Found at i:373674 original size:3 final size:3
Alignment explanation
Indices: 373668--373730 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
373658 TTTAAGCTTA
373668 AAT AAT AAT AAT 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 AAT AAT AAT AAT
373716 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
373731 CACTCTTCCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:386123 original size:86 final size:86
Alignment explanation
Indices: 385978--386151 Score: 312
Period size: 86 Copynumber: 2.0 Consensus size: 86
385968 TCGGAAATCC
* *
385978 AACAAACTACACGAACCAACATGCTTTTACTTGCACCCATGTTTTTGCATTGTATTCAATTACCT
1 AACAAACTACACGAACCAACATGCTTTTACTTGCACCCATGTTTTCGCATTGTATTCAATTACCA
386043 AAAATAAAAATATATGAAAGA
66 AAAATAAAAATATATGAAAGA
*
386064 AACAAACTACATGAACCAACATGCTTTTACTTGCACCCATGTTTTCGCATTGTATTCAATTACCA
1 AACAAACTACACGAACCAACATGCTTTTACTTGCACCCATGTTTTCGCATTGTATTCAATTACCA
*
386129 AAAATAAAAATATATGTAAGA
66 AAAATAAAAATATATGAAAGA
386150 AA
1 AA
386152 AAAAGAAGTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (86 bp):
AACAAACTACACGAACCAACATGCTTTTACTTGCACCCATGTTTTCGCATTGTATTCAATTACCA
AAAATAAAAATATATGAAAGA
Found at i:387928 original size:6 final size:6
Alignment explanation
Indices: 387917--387947 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
387907 GGAAGATCAA
387917 CTTCGG CTTCGG CTTCGG CTTCGG CTTCGG C
1 CTTCGG CTTCGG CTTCGG CTTCGG CTTCGG C
387948 ATCGAAGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.32, T:0.32
Consensus pattern (6 bp):
CTTCGG
Found at i:390318 original size:17 final size:16
Alignment explanation
Indices: 390274--390318 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
390264 CATTAAAAAA
390274 ATAAACATATATTAAAT
1 ATAAACAT-TATTAAAT
*
390291 ATATAATATTATTATAAT
1 ATA-AACATTATTA-AAT
390309 ATAAACATTA
1 ATAAACATTA
390319 AAAAATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAACATTATTAAAT
Found at i:395805 original size:11 final size:11
Alignment explanation
Indices: 395789--395840 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
395779 TATGACCATA
395789 TTTTAAATTAT
1 TTTTAAATTAT
395800 TTTT-AA--A-
1 TTTTAAATTAT
395807 TTTTAAATTA-
1 TTTTAAATTAT
*
395817 TTTTAATTATAT
1 TTTTAAAT-TAT
395829 TTTTAAATTAT
1 TTTTAAATTAT
395840 T
1 T
395841 GAGATTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.12
8 3 0.09
10 10 0.29
11 10 0.29
12 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAAATTAT
Found at i:395847 original size:22 final size:22
Alignment explanation
Indices: 395807--395848 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
395797 TATTTTTAAA
*
395807 TTTTAAATTATTTTAATTATAT
1 TTTTAAATTATTTGAATTATAT
395829 TTTTAAATTA-TTGAGATTAT
1 TTTTAAATTATTTGA-ATTAT
395849 GTTAATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTAAATTATTTGAATTATAT
Found at i:395854 original size:31 final size:29
Alignment explanation
Indices: 395797--395856 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
395787 TATTTTAAAT
*
395797 TATTTTTAAATTTTAAATTATTTTAATTA
1 TATTTTTAAATTTTAAATTATGTTAATTA
*
395826 TATTTTTAAATTATTGAGATTATGTTAATTA
1 TATTTTTAAATT-TT-AAATTATGTTAATTA
395857 GGTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 2 0.07
31 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (29 bp):
TATTTTTAAATTTTAAATTATGTTAATTA
Found at i:395863 original size:31 final size:29
Alignment explanation
Indices: 395798--395864 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
395788 ATTTTAAATT
* *
395798 ATTTTTAAATTTTAAATTATTTTAATTAT
1 ATTTTTAAATTTTAAATTATGTTAATTAG
*
395827 ATTTTTAAATTATTGAGATTATGTTAATTAG
1 ATTTTTAAATT-TT-AAATTATGTTAATTAG
*
395858 GTTTTTA
1 ATTTTTA
395865 TTACTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.34
30 2 0.06
31 19 0.59
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.58
Consensus pattern (29 bp):
ATTTTTAAATTTTAAATTATGTTAATTAG
Found at i:395973 original size:14 final size:15
Alignment explanation
Indices: 395940--395976 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
395930 ATTTTAAGAA
395940 AAAAATAAATATTGT
1 AAAAATAAATATTGT
395955 AAAAATAAATATAT-T
1 AAAAATAAATAT-TGT
395970 AAAAATA
1 AAAAATA
395977 TTAATATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:400063 original size:17 final size:17
Alignment explanation
Indices: 400031--400063 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
400021 TCCAGTTTAG
400031 ATTGGTTTTGATAATTC
1 ATTGGTTTTGATAATTC
400048 ATTGGATTTTGA-AATT
1 ATTGG-TTTTGATAATT
400064 TTTATCGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
ATTGGTTTTGATAATTC
Found at i:400444 original size:27 final size:27
Alignment explanation
Indices: 400396--400447 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
400386 ATATTTGTAA
* *
400396 AAAATTATATATAATTTTAATAAAATG
1 AAAATTATATATAAGTTAAATAAAATG
400423 AAAATTATAT-TATAGTTAAATAAAA
1 AAAATTATATATA-AGTTAAATAAAA
400448 ACGATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATTATATATAAGTTAAATAAAATG
Found at i:402958 original size:23 final size:25
Alignment explanation
Indices: 402927--402974 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
402917 TATAAAAATT
402927 TTTAATAAATA-AAAAT-ATATAAA
1 TTTAATAAATATAAAATAATATAAA
*
402950 TTTATTAAATATTAAAATAATATAA
1 TTTAATAAATA-TAAAATAATATAA
402975 TATAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTAATAAATATAAAATAATATAAA
Found at i:402966 original size:25 final size:25
Alignment explanation
Indices: 402916--402974 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
402906 AAAAATATTT
*
402916 ATATAAAAATTTTTAATAAATAAAA
1 ATATATAAATTTTTAATAAATAAAA
* *
402941 ATATATAAATTTATTAA-ATATTAAA
1 ATATATAAATTT-TTAATAAATAAAA
402966 ATAATATAA
1 AT-ATATAA
402975 TATAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATATAAATTTTTAATAAATAAAA
Found at i:407556 original size:32 final size:32
Alignment explanation
Indices: 407473--407586 Score: 81
Period size: 32 Copynumber: 3.7 Consensus size: 32
407463 GGGTTATTGG
* * *
407473 ATTTAGGG-ATTT-TGG-TTTAGGTTTAAAAA
1 ATTTAGGGAATTTCGGGATTTAGATTTCAAAA
* * * *
407502 ATGTGGGGTATTTCGGGTTTTAGATTTCAAAA
1 ATTTAGGGAATTTCGGGATTTAGATTTCAAAA
* * * * *
407534 TTTTTGGGAATTTGGGGATTTAGGTTTTAAAA
1 ATTTAGGGAATTTCGGGATTTAGATTTCAAAA
* *
407566 ATTTAGGGATTTTCGAGATTT
1 ATTTAGGGAATTTCGGGATTT
407587 TTAGGATTGT
Statistics
Matches: 64, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 6 0.09
30 4 0.06
31 2 0.03
32 52 0.81
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (32 bp):
ATTTAGGGAATTTCGGGATTTAGATTTCAAAA
Found at i:407664 original size:62 final size:62
Alignment explanation
Indices: 407552--407707 Score: 226
Period size: 62 Copynumber: 2.5 Consensus size: 62
407542 AATTTGGGGA
* * *
407552 TTTAGGTTTTAAAAATTTAGGGATTTTCGAGATTTTTAGGATTGTTGGGTTTGGGGAATTTGG
1 TTTAGG-TTTAAAAATTTGGGGATTTTAGAGATTTTTAGGATTGATGGGTTTGGGGAATTTGG
*
407615 TTTAGGTTTAAGAAATTTGGGGATTTT-GAGATTTTTGAGG-TTGATGGGTTTGGGGATTTTGG
1 TTTAGGTTTAA-AAATTTGGGGATTTTAGAGATTTTT-AGGATTGATGGGTTTGGGGAATTTGG
*
407677 TTTAAGTTTAAAAATTTGGGGATTTTAGAGA
1 TTTAGGTTTAAAAATTTGGGGATTTTAGAGA
407708 CTTAGGTTTC
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
61 15 0.17
62 48 0.56
63 23 0.27
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (62 bp):
TTTAGGTTTAAAAATTTGGGGATTTTAGAGATTTTTAGGATTGATGGGTTTGGGGAATTTGG
Found at i:412616 original size:27 final size:27
Alignment explanation
Indices: 412578--412632 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
412568 TCCAATATGA
412578 ATGTTACTTTTCTTCAATAGCCATTCT
1 ATGTTACTTTTCTTCAATAGCCATTCT
412605 ATGTTACTTTTCTTCAATAGCCATTCT
1 ATGTTACTTTTCTTCAATAGCCATTCT
412632 A
1 A
412633 GAGGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (27 bp):
ATGTTACTTTTCTTCAATAGCCATTCT
Found at i:420231 original size:36 final size:35
Alignment explanation
Indices: 420191--420293 Score: 116
Period size: 36 Copynumber: 2.9 Consensus size: 35
420181 CATAAGAAGA
* * * * *
420191 ATCATGTCAACATATAATAAAACATAGATGACGTGG
1 ATCATGTCAAC-TAAAATAAAACAAAAAAGAAGTGG
* *
420227 ATCATGTTGATCTAAAATAAAACAAAAAAGAAGTGG
1 ATCATG-TCAACTAAAATAAAACAAAAAAGAAGTGG
420263 ATCATGTCAATCTAAAATAAAACAAAAAAGA
1 ATCATGTCAA-CTAAAATAAAACAAAAAAGA
420294 TGTCGCCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 2 0.04
36 51 0.91
37 3 0.05
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (35 bp):
ATCATGTCAACTAAAATAAAACAAAAAAGAAGTGG
Found at i:422725 original size:20 final size:20
Alignment explanation
Indices: 422702--422744 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
422692 TTATTATTTG
*
422702 AAAA-AAAATGATATTTGAAT
1 AAAAGAAAATGA-ATTTAAAT
*
422722 AAAAGAAAATTAATTTAAAT
1 AAAAGAAAATGAATTTAAAT
422742 AAA
1 AAA
422745 TGTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAGAAAATGAATTTAAAT
Found at i:434197 original size:30 final size:29
Alignment explanation
Indices: 434144--434211 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
434134 CAAAGCGTTT
* *
434144 TTATT-TTTTTTATATATTAATATATTTA
1 TTATTATTTATTACATATTAATATATTTA
*
434172 CTTATTATTTATTACATATTTATATATTTA
1 -TTATTATTTATTACATATTAATATATTTA
434202 TTAATTATTT
1 TT-ATTATTT
434212 TCTACGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTATTTATTACATATTAATATATTTA
Found at i:435329 original size:60 final size:60
Alignment explanation
Indices: 435265--435441 Score: 193
Period size: 59 Copynumber: 3.0 Consensus size: 60
435255 CTCAAAAATC
* * *
435265 ATATTTTAACCCCTAAACTTTTCAAAAAGTTACATTTTGACCCCAATCTTTTCTAATATT-
1 ATATTTTAACCCCTAAACTTTTCAAAAA-TTACATTTTGACCCAAATCTTTTCCAAAATTG
* * * *
435325 ATATTTTAACCCCTAAACTATTCTAAAATTACATTTTTACCCTAAAT-ATTTCCAAAATTG
1 ATATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCC-AAATCTTTTCCAAAATTG
* *
435385 A-ATTTTTA-CCCTCAAACTTTTCCAAAATTACATTTTGATCCCTAAA-CTTTTCCAAAA
1 ATATTTTAACCCCT-AAACTTTTCAAAAATTACATTTTGA-CCC-AAATCTTTTCCAAAA
435442 ATCACGTTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.04
59 50 0.50
60 46 0.46
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (60 bp):
ATATTTTAACCCCTAAACTTTTCAAAAATTACATTTTGACCCAAATCTTTTCCAAAATTG
Found at i:435361 original size:30 final size:30
Alignment explanation
Indices: 435215--435441 Score: 171
Period size: 30 Copynumber: 7.6 Consensus size: 30
435205 CTCAAAATGT
* * * * *
435215 CCCC-AAACTTATCAAAAATCATATTTTAG
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * * *
435244 CCTCC-AAACTTCTCAAAAATCATATTTTAA
1 CC-CCTAAACTTTTCCAAAATTACATTTTAA
* *
435274 CCCCTAAACTTTTCAAAAAGTTACATTTTGA
1 CCCCTAAACTTTTCCAAAA-TTACATTTTAA
* * * *
435305 CCCC-AATCTTTTCTAATATTATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
435334 CCCCTAAACTATTCTAAAATTACATTTTTA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
*
435364 -CCCTAAA-TATTTCCAAAATTGA-ATTTTTA
1 CCCCTAAACT-TTTCCAAAATT-ACATTTTAA
*
435393 -CCCTCAAACTTTTCCAAAATTACATTTTGA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
*
435423 TCCCTAAACTTTTCCAAAA
1 CCCCTAAACTTTTCCAAAA
435442 ATCACGTTTT
Statistics
Matches: 169, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.01
29 45 0.27
30 106 0.63
31 17 0.10
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:450877 original size:21 final size:20
Alignment explanation
Indices: 450853--450892 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
450843 CATTATTATT
*
450853 AATAATATTCCTTAATTAAAA
1 AATAATA-TCCATAATTAAAA
*
450874 AATAGTATCCATAATTAAA
1 AATAATATCCATAATTAAA
450893 CACGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAATATCCATAATTAAAA
Found at i:457383 original size:36 final size:36
Alignment explanation
Indices: 457343--457436 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
457333 GAATAAGATG
457343 GATCTGATGCAATAAACAATCTAACATTATGTGACT
1 GATCTGATGCAATAAACAATCTAACATTATGTGACT
*
457379 GATCTGATGCAATAAACAATCTAACATTCTGTGACT
1 GATCTGATGCAATAAACAATCTAACATTATGTGACT
* *
457415 AATCTGAAGCAATAAAC-ATCTA
1 GATCTGATGCAATAAACAATCTA
457437 CTGATCTAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 5 0.09
36 50 0.91
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (36 bp):
GATCTGATGCAATAAACAATCTAACATTATGTGACT
Found at i:461296 original size:60 final size:60
Alignment explanation
Indices: 461230--461374 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
461220 ATTAAACATA
* * ** *
461230 ATGATAAATCTAGCACATAGAGTAA-GAAAAGACATATTGCAACACGTCAAAAGCAATTAC
1 ATGATAAATCTAGCACATAGAGTAACAAAAAG-CAGATTGCAACAAATCAAAAGCAATCAC
* *
461290 ATGATAAGTCTGGCACATAGAGTAACAAAAAGCAGATTGCAACAAATCAAAAGCAATCAC
1 ATGATAAATCTAGCACATAGAGTAACAAAAAGCAGATTGCAACAAATCAAAAGCAATCAC
* * *
461350 ATAATAAACCTAGCACATAGGGTAA
1 ATGATAAATCTAGCACATAGAGTAA
461375 TAACAAAAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 67 0.93
61 5 0.07
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (60 bp):
ATGATAAATCTAGCACATAGAGTAACAAAAAGCAGATTGCAACAAATCAAAAGCAATCAC
Found at i:462560 original size:3 final size:3
Alignment explanation
Indices: 462549--462582 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
462539 GGCGGTGGGA
*
462549 GTG GGG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
462583 CGGAGGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (3 bp):
GTG
Found at i:470251 original size:30 final size:31
Alignment explanation
Indices: 470215--470272 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
470205 GACAATCCAA
*
470215 TGACTTAAAT-AAAACTTTCGAATAGTTTAG
1 TGACTTAAATGAAAACTTTCAAATAGTTTAG
*
470245 TGACTTAAATGAAAACTTTTAAATAGTT
1 TGACTTAAATGAAAACTTTCAAATAGTT
470273 CAATGTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTTAG
Found at i:473989 original size:15 final size:15
Alignment explanation
Indices: 473947--473990 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
473937 ACAAATGAAT
473947 TTAAAATTATTAAAA
1 TTAAAATTATTAAAA
* ** *
473962 TTTATTTTTTTAAAA
1 TTAAAATTATTAAAA
473977 TTAAAATTATTAAA
1 TTAAAATTATTAAA
473991 TAATTTTAAT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAATTATTAAAA
Found at i:474434 original size:29 final size:30
Alignment explanation
Indices: 474409--474481 Score: 121
Period size: 29 Copynumber: 2.4 Consensus size: 30
474399 ATTAAAATTA
474409 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
*
474440 TTTAATAATTTTATATTT-TAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
474469 TTTAATAATTTTA
1 TTTAATAATTTTA
474482 AAATAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:474468 original size:20 final size:22
Alignment explanation
Indices: 474443--474484 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
474433 AAATAATTTT
474443 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
474463 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
474485 TAATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:474485 original size:20 final size:20
Alignment explanation
Indices: 474434--474490 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
474424 ATTTCAAAAA
474434 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
474452 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
474472 AATAATTTTAAAATAATTT
1 AATAATTTTAAAATAATTT
474491 GTTGACGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
20 19 0.58
21 2 0.06
22 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:481568 original size:7 final size:7
Alignment explanation
Indices: 481552--481591 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
481542 TGTTAGGTCA
481552 CTAACCT
1 CTAACCT
*
481559 CTAACTT
1 CTAACCT
481566 CTAACCT
1 CTAACCT
*
481573 CTAACGT
1 CTAACCT
*
481580 CTAACCC
1 CTAACCT
481587 CTAAC
1 CTAAC
481592 TCTTTGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.30, C:0.40, G:0.03, T:0.28
Consensus pattern (7 bp):
CTAACCT
Found at i:481571 original size:14 final size:14
Alignment explanation
Indices: 481552--481592 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
481542 TGTTAGGTCA
481552 CTAACCTCTAACTT
1 CTAACCTCTAACTT
*
481566 CTAACCTCTAACGT
1 CTAACCTCTAACTT
*
481580 CTAACCCCTAACT
1 CTAACCTCTAACT
481593 CTTTGTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.39, G:0.02, T:0.29
Consensus pattern (14 bp):
CTAACCTCTAACTT
Found at i:481732 original size:209 final size:205
Alignment explanation
Indices: 481364--481983 Score: 845
Period size: 209 Copynumber: 3.0 Consensus size: 205
481354 TGTTAGGTTA
* * *
481364 CTAACCTCTAACCCCTAGCTCTTTGTAATAGCCTCTTGTCTAATGGACGACTTGTACGATGAGAA
1 CTAACCTCTAACCCCTAACTCTTTGTAATAGCCTCTTATCTAATGGATGACTTGTACGATGAGAA
* **
481429 AGCACACTCATTAGTTAGTACTATACAGGACTATGACATTAGAACAAGATAACCTACGACACAAA
66 AGCACACTCATTAGTTGGTACTGCACAGGACTATGACATTAGAACAAGATAACCTACGACACAAA
* *
481494 CATGATCACATGGGATGTACCACAACACCAACCTATGTTGGCAATGCCTGTTAGGTCACTAACCT
131 CATGATCACATGGGATGTACCATAACACCAACCTATGTTGGCAGTGCCTGTTAGGTCACTAACCT
481559 CTAACTTCTAACCT
196 CTAACTTCT----T
* * * * *
481573 CTAACGTCTAACCCCTAACTCTTTGTAATAACCTCTTCTCTAACGAATGACTTGTACGATGAGAA
1 CTAACCTCTAACCCCTAACTCTTTGTAATAGCCTCTTATCTAATGGATGACTTGTACGATGAGAA
*
481638 AGCACACTCATTAGTTGGTACTGCAC-GAGACTATGACATTAGAACAAGATAGCCTACGACACAA
66 AGCACACTCATTAGTTGGTACTGCACAG-GACTATGACATTAGAACAAGATAACCTACGACACAA
* * *
481702 ACATGATCACATGGGACGTACCATAACACCAACCAACCTATGTTGGTAGTACCTGTTAGGTCACT
130 ACATGATCACATGGGATGTACCAT-A-A-C-ACCAACCTATGTTGGCAGTGCCTGTTAGGTCACT
481767 AACCTCTAA--TCTT
191 AACCTCTAACTTCTT
* *
481780 -TAACCTCTAACCCCTAACTCTTTGTAATAGCCTTTTATCTAATGGATGACTTATACGATGAGAA
1 CTAACCTCTAACCCCTAACTCTTTGTAATAGCCTCTTATCTAATGGATGACTTGTACGATGAGAA
* * *
481844 AGCACACTCATTAGTTGGTATTGCACAGGAGTATGACATTAGAACAAGATAACCTACGGCACAAA
66 AGCACACTCATTAGTTGGTACTGCACAGGACTATGACATTAGAACAAGATAACCTACGACACAAA
* * * * *
481909 CATGATCACATGGGATGTACTACATGTTA-AGCAACCTATGTTGGCAGTGCTTGTTTGGTCACTG
131 CATGATCACATGGGATGTAC--CA--TAACACCAACCTATGTTGGCAGTGCCTGTTAGGTCACTA
481973 ACCTCTAACTT
192 ACCTCTAACTT
481984 GTCAATACAA
Statistics
Matches: 364, Mismatches: 35, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
205 37 0.10
206 135 0.37
207 3 0.01
208 4 0.01
209 138 0.38
210 2 0.01
211 4 0.01
212 1 0.00
213 40 0.11
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (205 bp):
CTAACCTCTAACCCCTAACTCTTTGTAATAGCCTCTTATCTAATGGATGACTTGTACGATGAGAA
AGCACACTCATTAGTTGGTACTGCACAGGACTATGACATTAGAACAAGATAACCTACGACACAAA
CATGATCACATGGGATGTACCATAACACCAACCTATGTTGGCAGTGCCTGTTAGGTCACTAACCT
CTAACTTCTT
Found at i:485246 original size:16 final size:16
Alignment explanation
Indices: 485214--485251 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
485204 AATTATTTAA
485214 AAATT-TTAAAGATAT
1 AAATTATTAAAGATAT
485229 AAATTATTAAA-ATAAT
1 AAATTATTAAAGAT-AT
485245 AAATTAT
1 AAATTAT
485252 ATTTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATTATTAAAGATAT
Found at i:485321 original size:2 final size:2
Alignment explanation
Indices: 485316--485353 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
485306 ATTTCAACCC
*
485316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
485354 TTGATTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:485951 original size:17 final size:17
Alignment explanation
Indices: 485924--485957 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
485914 CTTATCCAAA
485924 AAATTATATAT-TTTTT
1 AAATTATATATATTTTT
485940 AAATTAATATATATTTTT
1 AAATT-ATATATATTTTT
485958 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATTATATATATTTTT
Found at i:486532 original size:7 final size:7
Alignment explanation
Indices: 486517--486560 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
486507 TTGAATCATT
486517 AATTTTA
1 AATTTTA
*
486524 AATTATA
1 AATTTTA
486531 AATTTTA
1 AATTTTA
* *
486538 AATCTCA
1 AATTTTA
486545 AATTTTA
1 AATTTTA
*
486552 ATTTTTA
1 AATTTTA
486559 AA
1 AA
486561 CTCTGAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (7 bp):
AATTTTA
Found at i:486547 original size:21 final size:22
Alignment explanation
Indices: 486523--486571 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
486513 CATTAATTTT
486523 AAATTATAAATTTTAAA-TCTC
1 AAATTATAAATTTTAAACTCTC
* * *
486544 AAATTTTAATTTTTAAACTCTG
1 AAATTATAAATTTTAAACTCTC
486566 AAATTA
1 AAATTA
486572 AGTTTAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATTATAAATTTTAAACTCTC
Found at i:487387 original size:21 final size:20
Alignment explanation
Indices: 487362--487433 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
487352 AAGTTTTAGC
487362 ATTTATTTATAATTAATTATT
1 ATTTATTTATAATT-ATTATT
** * *
487383 ATTTAAATAAAATTATTAAT
1 ATTTATTTATAATTATTATT
487403 ATTTATTTATAAATTTATTATT
1 ATTTATTTAT-AA-TTATTATT
487425 A-TTATTTAT
1 ATTTATTTAT
487434 TTTATTTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 12 0.29
21 21 0.51
22 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATTTATAATTATTATT
Found at i:493027 original size:3 final size:3
Alignment explanation
Indices: 493019--493092 Score: 50
Period size: 3 Copynumber: 25.7 Consensus size: 3
493009 AATATTTTAA
* * *
493019 AAT AAT AAT AA- AATT AAT AAT AA- AAT AAA AAT CAT -AT AAT ATT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
493062 TA- AAT AAT AAT AAC AA- AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
493093 CGTAATAGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
2 9 0.16
3 42 0.75
4 5 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:493035 original size:17 final size:17
Alignment explanation
Indices: 493015--493092 Score: 56
Period size: 17 Copynumber: 4.6 Consensus size: 17
493005 AATAAATATT
493015 TTAA-AATAATAATAAAA
1 TTAATAATAA-AATAAAA
493032 TTAATAATAAAATAAAA
1 TTAATAATAAAATAAAA
* * * *
493049 ATCAT-ATAATATTTAAA
1 TTAATAATAA-AATAAAA
493066 -TAATAATAACAA-AATAA
1 TTAATAATAA-AATAA-AA
493083 TTAATAATAA
1 TTAATAATAA
493093 CGTAATAGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.17
17 26 0.54
18 14 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAATAATAAAATAAAA
Found at i:493038 original size:12 final size:12
Alignment explanation
Indices: 493016--493044 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
493006 ATAAATATTT
493016 TAAAA-TAATAA
1 TAAAATTAATAA
493027 TAAAATTAATAA
1 TAAAATTAATAA
493039 TAAAAT
1 TAAAAT
493045 AAAAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:494750 original size:27 final size:27
Alignment explanation
Indices: 494720--494809 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
494710 AAATATTTGG
494720 AAATAAAGAAACTTATTTAAGTAAATA
1 AAATAAAGAAACTTATTTAAGTAAATA
** * *
494747 AAATAAAGGGTAAAC-TATAAAAAT-GATA
1 AAATAAA--G-AAACTTATTTAAGTAAATA
494775 AAATAAAGAAACTTATTTAAGTAAATA
1 AAATAAAGAAACTTATTTAAGTAAATA
494802 AAATAAAG
1 AAATAAAG
494810 GGTAAACTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 18 0.36
28 10 0.20
29 7 0.14
30 4 0.08
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (27 bp):
AAATAAAGAAACTTATTTAAGTAAATA
Found at i:494779 original size:28 final size:28
Alignment explanation
Indices: 494744--494828 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
494734 ATTTAAGTAA
494744 ATAAAATAAAGGGTAAACTATAAAAATG
1 ATAAAATAAAGGGTAAACTATAAAAATG
** * *
494772 ATAAAATAAA--G-AAACTTATTTAAGTAA
1 ATAAAATAAAGGGTAAAC-TATAAAAAT-G
494799 ATAAAATAAAGGGTAAACTATAAAAATG
1 ATAAAATAAAGGGTAAACTATAAAAATG
494827 AT
1 AT
494829 CATTTTTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
25 4 0.09
26 7 0.16
27 10 0.23
28 12 0.27
29 7 0.16
30 4 0.09
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.25
Consensus pattern (28 bp):
ATAAAATAAAGGGTAAACTATAAAAATG
Found at i:494795 original size:55 final size:55
Alignment explanation
Indices: 494720--494828 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
494710 AAATATTTGG
494720 AAATAAAGAAACTTATTTAAGTAAATAAAATAAAGGGTAAACTATAAAAATGATA
1 AAATAAAGAAACTTATTTAAGTAAATAAAATAAAGGGTAAACTATAAAAATGATA
494775 AAATAAAGAAACTTATTTAAGTAAATAAAATAAAGGGTAAACTATAAAAATGAT
1 AAATAAAGAAACTTATTTAAGTAAATAAAATAAAGGGTAAACTATAAAAATGAT
494829 CATTTTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.26
Consensus pattern (55 bp):
AAATAAAGAAACTTATTTAAGTAAATAAAATAAAGGGTAAACTATAAAAATGATA
Found at i:495051 original size:18 final size:18
Alignment explanation
Indices: 495028--495070 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
495018 AATTGATTTT
495028 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
495046 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
495064 TTAATTA
1 TTAATTA
495071 CAGGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:495069 original size:22 final size:23
Alignment explanation
Indices: 495037--495084 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
495027 TTTAATTAAA
*
495037 TAAATTTAATTA-ATTGAAAATTT
1 TAAATTTAATTACA-GGAAAATTT
495060 TAAA-TTAATTACAGGAAAATTT
1 TAAATTTAATTACAGGAAAATTT
495082 TAA
1 TAA
495085 TTTGGTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (23 bp):
TAAATTTAATTACAGGAAAATTT
Found at i:502283 original size:19 final size:18
Alignment explanation
Indices: 502259--502309 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
502249 TTTATGAGTT
502259 AAAAAATAATTATAAAAGA
1 AAAAAATAATTATAAAA-A
* **
502278 AAAAAATAATAATATCAA
1 AAAAAATAATTATAAAAA
502296 AAAAAATAA-TATAA
1 AAAAAATAATTATAA
502310 GCATATGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 14 0.52
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAATAATTATAAAAA
Found at i:502303 original size:15 final size:16
Alignment explanation
Indices: 502278--502307 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
502268 TTATAAAAGA
502278 AAAAAATAATAATATC
1 AAAAAATAATAATATC
502294 AAAAAA-AATAATAT
1 AAAAAATAATAATAT
502308 AAGCATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATAATAATATC
Found at i:503722 original size:28 final size:23
Alignment explanation
Indices: 503690--503754 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
503680 TTTGATAATT
*
503690 ATCGAATCGAACTCGAGCTATTG
1 ATCGAATCGAATTCGAGCTATTG
503713 ATCGAATCGAATTCGAGCTATTG
1 ATCGAATCGAATTCGAGCTATTG
503736 ATCGAATCGAATTCGAGCT
1 ATCGAATCGAATTCGAGCT
503755 TAGTACTACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
ATCGAATCGAATTCGAGCTATTG
Found at i:507944 original size:24 final size:24
Alignment explanation
Indices: 507908--507959 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
507898 ACTCGAATAT
* *
507908 AATACATTTAAAAATATTAGCAAA
1 AATACATTCAAAAAAATTAGCAAA
* *
507932 AATATATTCAAAAAAATTAGCGAA
1 AATACATTCAAAAAAATTAGCAAA
507956 AATA
1 AATA
507960 ATTATATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.27
Consensus pattern (24 bp):
AATACATTCAAAAAAATTAGCAAA
Found at i:508003 original size:23 final size:23
Alignment explanation
Indices: 507959--508003 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
507949 TAGCGAAAAT
*
507959 AATTATATAATAAATTTATTAAA
1 AATTAAATAATAAATTTATTAAA
*
507982 AATTAAAT-ATAATTTTAGTTAA
1 AATTAAATAATAAATTTA-TTAA
508004 TATGATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTAAATAATAAATTTATTAAA
Found at i:508974 original size:19 final size:19
Alignment explanation
Indices: 508950--508987 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
508940 CAATGCATAG
508950 AACTACACATAACTCCTCC
1 AACTACACATAACTCCTCC
*
508969 AACTACACATAGCTCCTCC
1 AACTACACATAACTCCTCC
508988 CCAACCCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.42, G:0.03, T:0.21
Consensus pattern (19 bp):
AACTACACATAACTCCTCC
Found at i:513457 original size:21 final size:23
Alignment explanation
Indices: 513423--513470 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
513413 TCAAAAATTC
513423 AAAATATTTATAAAAAAT-TATA
1 AAAATATTTATAAAAAATATATA
* *
513445 AAAAT-TTTCTAAAGAATATATA
1 AAAATATTTATAAAAAATATATA
513467 AAAA
1 AAAA
513471 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATATTTATAAAAAATATATA
Found at i:515193 original size:21 final size:20
Alignment explanation
Indices: 515169--515215 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
515159 TATTATACAC
515169 TCATTTTAATCATTAAATTTT
1 TCATTTTAATCATT-AATTTT
* *
515190 TCATTTTGATCATTTATTTT
1 TCATTTTAATCATTAATTTT
515210 T-ATTTT
1 TCATTTT
515216 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
21 13 0.54
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (20 bp):
TCATTTTAATCATTAATTTT
Found at i:515826 original size:58 final size:56
Alignment explanation
Indices: 515708--515827 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 56
515698 GAATTTATCA
* *
515708 TTTTTTTAATTTGATACCTAAATTTTTTTATCCAATTTGATATCTAAACTTGATAC
1 TTTTTTTAATTTGATACCTAAATTTTTTTAGCCAATTTGATATCTAAACTTGACAC
* * * * *
515764 TTTTTTATAATTTGGTGCCTAAATTTTTTTGAGCCAATTTGATATTTGAAC-TGACAT
1 TTTTTT-TAATTTGATACCTAAATTTTTTT-AGCCAATTTGATATCTAAACTTGACAC
515821 TTTTTTT
1 TTTTTTT
515828 CCTAATTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 7 0.13
57 31 0.56
58 17 0.31
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (56 bp):
TTTTTTTAATTTGATACCTAAATTTTTTTAGCCAATTTGATATCTAAACTTGACAC
Found at i:524366 original size:12 final size:12
Alignment explanation
Indices: 524349--524454 Score: 56
Period size: 12 Copynumber: 9.1 Consensus size: 12
524339 AAAACATTCA
*
524349 AACAACAAAAAT
1 AACAACAAAAAC
*
524361 AACAACCAAAAC
1 AACAACAAAAAC
* * *
524373 AGCAGCAAAAAT
1 AACAACAAAAAC
* *
524385 AACAA-GAAGAC
1 AACAACAAAAAC
524396 AACAACAAAAAC
1 AACAACAAAAAC
* * *
524408 AGCAATAAAAAT
1 AACAACAAAAAC
**
524420 AACAGTAAAAAC
1 AACAACAAAAAC
* *
524432 AGC-ACCAAAAC
1 AACAACAAAAAC
*
524443 AATAA-AAAAAC
1 AACAACAAAAAC
524454 A
1 A
524455 GCTCAAAACA
Statistics
Matches: 66, Mismatches: 26, Indels: 5
0.68 0.27 0.05
Matches are distributed among these distances:
11 20 0.30
12 46 0.70
ACGTcount: A:0.68, C:0.20, G:0.07, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:524406 original size:24 final size:24
Alignment explanation
Indices: 524349--524406 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
524339 AAAACATTCA
524349 AACAACAAAAATAACAACCAAAAC
1 AACAACAAAAATAACAACCAAAAC
* * * *
524373 AGCAGCAAAAATAACAA-GAAGAC
1 AACAACAAAAATAACAACCAAAAC
524396 AACAACAAAAA
1 AACAACAAAAA
524407 CAGCAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.69, C:0.21, G:0.07, T:0.03
Consensus pattern (24 bp):
AACAACAAAAATAACAACCAAAAC
Found at i:524442 original size:35 final size:34
Alignment explanation
Indices: 524361--524484 Score: 84
Period size: 35 Copynumber: 3.7 Consensus size: 34
524351 CAACAAAAAT
**
524361 AACA-ACCAAAACAGCAGCAAAAATAACAAG-AAGA
1 AACACACCAAAACAGCAATAAAAATAAC-AGTAA-A
*
524395 CAACA-ACAAAAACAGCAATAAAAATAACAGTAAA
1 -AACACACCAAAACAGCAATAAAAATAACAGTAAA
*
524429 AACAGCACC-AAA-A-CAATAAAAA-AACAGCTCAA
1 AACA-CACCAAAACAGCAATAAAAATAACAG-TAAA
*
524461 AACATCAATCAAAACAGCAA-AAAA
1 AACA-C-ACCAAAACAGCAATAAAA
524485 TAGCAATCAT
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
31 5 0.07
32 17 0.23
33 7 0.09
34 9 0.12
35 33 0.45
36 3 0.04
ACGTcount: A:0.65, C:0.21, G:0.07, T:0.06
Consensus pattern (34 bp):
AACACACCAAAACAGCAATAAAAATAACAGTAAA
Found at i:524484 original size:22 final size:22
Alignment explanation
Indices: 524449--524499 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
524439 AAACAATAAA
** *
524449 AAAACAGCTCAAAACATCAATC
1 AAAACAGCAAAAAACAGCAATC
*
524471 AAAACAGCAAAAAATAGCAATC
1 AAAACAGCAAAAAACAGCAATC
*
524493 ATAACAG
1 AAAACAG
524500 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.22, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAACAGCAAAAAACAGCAATC
Found at i:524512 original size:23 final size:22
Alignment explanation
Indices: 524466--524520 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
524456 CTCAAAACAT
*
524466 CAATCAAAACAGCAAAAAATAG
1 CAATCAAAACAGCAAAAAAAAG
* *
524488 CAATCATAACAGTTAAAAAAAAG
1 CAATCAAAACAG-CAAAAAAAAG
*
524511 C-ACCAAAACA
1 CAATCAAAACA
524521 ATAATATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.62, C:0.20, G:0.07, T:0.11
Consensus pattern (22 bp):
CAATCAAAACAGCAAAAAAAAG
Found at i:529337 original size:35 final size:35
Alignment explanation
Indices: 529291--529371 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
529281 TAGATTGAAG
529291 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
529326 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
529361 TGGTTGGTGAG
1 TGGTTGGTGAG
529372 ATGGTGGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.36, C:0.00, G:0.42, T:0.22
Consensus pattern (35 bp):
TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
Done.