Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 27
Found at i:344214 original size:23 final size:23
Alignment explanation
Indices: 344161--344221 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
344151 CTCATATAAA
*
344161 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
344184 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
344207 TGCACCGTGGTGCCA
1 TGCACCGTAGTGCCA
344222 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:344408 original size:103 final size:103
Alignment explanation
Indices: 344237--344454 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
344227 TAATGTCCAT
* *
344237 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTATGGATCAATTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
344302 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
344340 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
344405 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
344443 AAGGACCACATA
1 AAGGACCACATA
344455 GACCCGACTC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:345661 original size:21 final size:21
Alignment explanation
Indices: 345623--345667 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
345613 TTTTATTCGT
* *
345623 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCAATTCCCC
* *
345644 TTGAATGGGTACCAATTCCTC
1 TTGAAGGGGTACCAATTCCCC
345665 TTG
1 TTG
345668 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCAATTCCCC
Found at i:349982 original size:44 final size:44
Alignment explanation
Indices: 349897--349993 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
349887 TTGTGCCTTA
* * *
349897 TGCATCGATACACTTAACAGTGCATCGATGCATCTCTTTGAATG
1 TGCATCGATACACTTAACAGTGCACCGATGCATCGCCTTGAATG
*
349941 TGCATCGATACACTATGAA-GGTGCACCGATGCA-CGCCTTGAATG
1 TGCATCGATACACT-T-AACAGTGCACCGATGCATCGCCTTGAATG
349985 TGCATCGAT
1 TGCATCGAT
349994 GCACAAGGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 32 0.68
45 13 0.28
46 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTTAACAGTGCACCGATGCATCGCCTTGAATG
Found at i:352377 original size:65 final size:63
Alignment explanation
Indices: 352265--352464 Score: 210
Period size: 65 Copynumber: 3.1 Consensus size: 63
352255 TGATGAACCA
* **
352265 ATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCAT
1 ATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATTTCATGCAT
352328 CG
62 CG
* ** *
352330 ATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATTAATTTGATGCAT
1 ATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTCATGCAT
352393 CG
62 CG
* *
352395 ATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTCATGCATCG
1 ATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATCG
352459 ATGCAC
1 ATGCAC
352465 TAAGGATCCA
Statistics
Matches: 114, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 47 0.41
65 57 0.50
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATCG
Found at i:355358 original size:27 final size:27
Alignment explanation
Indices: 355327--355380 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
355317 TTTTTACAAC
355327 ATAAGAGT-ATTTTCGTAAATTTT-TCAT
1 ATAAG-GTAATTTTCGT-AATTTTATCAT
*
355354 ATAAGGTAATTTTTGTAATTTTATCAT
1 ATAAGGTAATTTTCGTAATTTTATCAT
355381 CCAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (27 bp):
ATAAGGTAATTTTCGTAATTTTATCAT
Found at i:356002 original size:15 final size:15
Alignment explanation
Indices: 355982--356010 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
355972 CATATTTGTT
355982 GAGTTGACTCAGTGC
1 GAGTTGACTCAGTGC
355997 GAGTTGACTCAGTG
1 GAGTTGACTCAGTG
356011 GGCTGATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (15 bp):
GAGTTGACTCAGTGC
Found at i:357518 original size:17 final size:17
Alignment explanation
Indices: 357496--357529 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
357486 CATTTTTGTA
*
357496 ATTAATGGCATTATTTT
1 ATTAATGACATTATTTT
*
357513 ATTAATGATATTATTTT
1 ATTAATGACATTATTTT
357530 TAATAATATA
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:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTAATGACATTATTTT
Found at i:359059 original size:9 final size:9
Alignment explanation
Indices: 359040--359084 Score: 65
Period size: 9 Copynumber: 4.9 Consensus size: 9
359030 AAGAATAACC
359040 AAAACAAAAG
1 AAAA-AAAAG
359050 AAAAAAAAG
1 AAAAAAAAG
359059 -AAAAAAAG
1 AAAAAAAAG
359067 AAAAAAAAAG
1 -AAAAAAAAG
359077 AAAAAAAA
1 AAAAAAAA
359085 AACTTCACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.24
9 13 0.39
10 12 0.36
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:359063 original size:10 final size:10
Alignment explanation
Indices: 359040--359085 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
359030 AAGAATAACC
*
359040 AAAACAAAAG
1 AAAAAAAAAG
359050 -AAAAAAAAG
1 AAAAAAAAAG
359059 --AAAAAAAG
1 AAAAAAAAAG
359067 AAAAAAAAAG
1 AAAAAAAAAG
359077 AAAAAAAAA
1 AAAAAAAAA
359086 ACTTCACCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 8 0.24
9 8 0.24
10 17 0.52
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:364319 original size:18 final size:19
Alignment explanation
Indices: 364296--364376 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
364286 GATGTCATCT
*
364296 AAAATATTTAA-AAGTAAA
1 AAAATATTTAATAAATAAA
364314 AAAATATTATAAATAAATAAAA
1 AAAATATT-T-AATAAAT-AAA
* *
364336 ATAAATATTT-A-AGATTAA
1 A-AAATATTTAATAAATAAA
*
364354 AAAATATTAAATAAATAAA
1 AAAATATTTAATAAATAAA
364373 AAAA
1 AAAA
364377 GTACCTTGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.14
18 12 0.24
19 13 0.26
20 3 0.06
21 3 0.06
22 5 0.10
23 7 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATTTAATAAATAAA
Found at i:364355 original size:41 final size:38
Alignment explanation
Indices: 364297--364374 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
364287 ATGTCATCTA
364297 AAATATTTAAAAGTAAAAAAATATTATAAATAAATAAAAAT
1 AAATATTTAAAAGT-AAAAAATA-T-TAAATAAATAAAAAT
* *
364338 AAATATTTAAGATTAAAAAATATTAAATAAATAAAAA
1 AAATATTTAAAAGTAAAAAATATTAAATAAATAAAAA
364375 AAGTACCTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 14 0.40
39 1 0.03
40 8 0.23
41 12 0.34
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (38 bp):
AAATATTTAAAAGTAAAAAATATTAAATAAATAAAAAT
Found at i:366730 original size:36 final size:36
Alignment explanation
Indices: 366677--366768 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
366667 ATTTCGTAAA
* *
366677 CCATCCGTTCTAGTTGAATCGGAAGTG-CGAATGCTT
1 CCATCCGTTCGACTTGAATCGGAAGTGTCG-ATGCTT
*
366713 CCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTT
1 CCATCCGTTCGACTTGAATCGGAAGTGTCGATGCTT
366749 CCATCCGTTCGACTTGAATC
1 CCATCCGTTCGACTTGAATC
366769 CATGCAAACT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 49 0.96
37 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (36 bp):
CCATCCGTTCGACTTGAATCGGAAGTGTCGATGCTT
Found at i:371286 original size:186 final size:187
Alignment explanation
Indices: 371075--371418 Score: 521
Period size: 186 Copynumber: 1.8 Consensus size: 187
371065 AAAGATAATT
* * *
371075 TTTAATTTGAATATTAGTAGGATAATTACTCTTTTAACAAGTCAATTTAAAAAAGTATTTGTTAT
1 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAACAAGTCAA-TTAAAAAAGTATTTATTAC
* *
371140 C-TTTTTAATTTTGAATATTAAA-AAAATTATATACTTTTTTATATTTCAAATTAAAATAATATA
65 CTTTTTTAACTTTGAATATTAAAGAAAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
* *
371203 TGTTAAAGTTTGAATAGTAAAAAGAGTTTATTTTGACCATTGTAAATTAAATATATTA
130 TATTAAAGTTTAAATAGTAAAAAGAGTTTATTTTGACCATTGTAAATTAAATATATTA
* * *
371261 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATATGTCAATTAAAAAGGTATTTATTACC
1 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAACAAGTCAATTAAAAAAGTATTTATTACC
* * *
371326 TTTTTTAACTTTGAATATTAAAGATAATTATATACTTTTGTATATTTTAAATTAAAATAATATCT
66 TTTTTTAACTTTGAATATTAAAGAAAATTATATACTTTTGTATATTTCAAATTAAAATAATATAT
* * *
371391 ATTTAAGTTTAAATGGTAAAATGAGTTT
131 ATTAAAGTTTAAATAGTAAAAAGAGTTT
371419 TATCTTTTGA
Statistics
Matches: 140, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
185 17 0.12
186 62 0.44
187 61 0.44
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (187 bp):
TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAACAAGTCAATTAAAAAAGTATTTATTACC
TTTTTTAACTTTGAATATTAAAGAAAATTATATACTTTTGTATATTTCAAATTAAAATAATATAT
ATTAAAGTTTAAATAGTAAAAAGAGTTTATTTTGACCATTGTAAATTAAATATATTA
Found at i:371497 original size:187 final size:184
Alignment explanation
Indices: 371059--371453 Score: 443
Period size: 186 Copynumber: 2.1 Consensus size: 184
371049 TGACTATTAC
* * * * * *
371059 AAATTAAAAGATAATT-TTTAATTTGAATATTAGTAGGATAATTACTCTTTTAACAAGTCAATTT
1 AAATT-AAAGAT-ATTATTTAATTTGAATATTAATAGGATAAATACTATTTGAATATG-CAA-TT
* * * *
371123 AAAAAAGTATTTGTTATCTTTTTAATTTTGAATATTAAAAAAATTATATACTTTTTTATATTTCA
62 AAAAAAGTATTTATTACCTTTTTAACTTTGAATATTAAAAAAATTATATACTTTTGTATATTTCA
* * *
371188 AATTAAAATAATATATGTTAAAGTTTGAATAGTAAAAAGAGTTTATTTTGACCATTGT
127 AATTAAAATAATATATATTAAAGTTTAAATAGTAAAAAGAGTTTATTTTGAACATTGT
* * * *
371246 AAATTAAATATATTATTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATATGTCAATTAAA
1 AAATTAAAGATATTATTTAATTTGAATATTAATAGGATAAATACTATTTGAATATG-CAATTAAA
* * *
371311 AAGGTATTTATTACCTTTTTTAACTTTGAATATTAAAGATAATTATATACTTTTGTATATTTTAA
65 AAAGTATTTATTACC-TTTTTAACTTTGAATATTAAA-AAAATTATATACTTTTGTATATTTCAA
* * * * *
371376 ATTAAAATAATATCTATTTAAGTTTAAATGGTAAAATGAGTTTTATCTTTTGAATATT-T
128 ATTAAAATAATATATATTAAAGTTTAAATAGTAAAAAGAG-TTTA--TTTTGAACATTGT
371435 CAAATTAAAAGATATTATT
1 -AAATT-AAAGATATTATT
371454 ATATTCTTAA
Statistics
Matches: 180, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
185 20 0.11
186 67 0.37
187 63 0.35
188 4 0.02
189 1 0.01
190 14 0.08
191 11 0.06
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (184 bp):
AAATTAAAGATATTATTTAATTTGAATATTAATAGGATAAATACTATTTGAATATGCAATTAAAA
AAGTATTTATTACCTTTTTAACTTTGAATATTAAAAAAATTATATACTTTTGTATATTTCAAATT
AAAATAATATATATTAAAGTTTAAATAGTAAAAAGAGTTTATTTTGAACATTGT
Found at i:371985 original size:17 final size:17
Alignment explanation
Indices: 371963--372011 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
371953 ATTTCCTTTA
*
371963 ATTTTATAATGA-TATTT
1 ATTTTATAATCATTA-TT
*
371980 ATTTTATTATCATTATT
1 ATTTTATAATCATTATT
371997 ATTTTATATATCATT
1 ATTTTATA-ATCATT
372012 CTCGGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTATAATCATTATT
Found at i:371996 original size:18 final size:18
Alignment explanation
Indices: 371978--372011 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
371968 ATAATGATAT
371978 TTATTTTAT-TATCATTA
1 TTATTTTATATATCATTA
371995 TTATTTTATATATCATT
1 TTATTTTATATATCATT
372012 CTCGGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTATATATCATTA
Found at i:375072 original size:194 final size:190
Alignment explanation
Indices: 374742--375093 Score: 483
Period size: 194 Copynumber: 1.8 Consensus size: 190
374732 AAGTAATTAA
* *
374742 AATATAAACGTATTAAATGAACTCAATAATTAAAAGGAATTTTTTTGAGGTTTTGAGTTGAGCAG
1 AATATAAACGTATTAAATGAACTCAATAATTAAAAGGAATTTTTTT---GTTTCGAGTTGAACAG
* * *
374807 TTACATCTGTATGGTGTGTGTTTATGGTCAATGATTATGAAAAATTAGAAGCATATACTACCTTG
63 TTACATCTGTATGGTATGTGTTTATGGTCAATGATTATAAAAAATTAGAAACATATACTACCTTG
*
374872 TAATCACTTCAGAC-TATTCAAAAAAAATAATATATCTTTTCTAATTTGAAATTAATCGACCTC
128 TAATCACTCCAGACTTATT-AAAAAAAATAATATATCTTTTCTAATTTGAAATTAATCGACCTC
* * *
374935 AATATAAACGTATTAAATGATCTCAATAGTTAAAGGGAAATATTATTTT-TTCTCGAGTTTGAAC
1 AATATAAACGTATTAAATGAACTCAATAATTAAAAGG-AAT-TT-TTTTGTT-TCGAG-TTGAAC
* * *
374999 AGTTGCGTCTGTATGGTATGTGTTTATGGTCAATGATTATAAAAAATTAGAAACATATATTACCT
61 AGTTACATCTGTATGGTATGTGTTTATGGTCAATGATTATAAAAAATTAGAAACATATACTACCT
* *
375064 TTTAATCACTCCAGACTTATTAAAAGAAAT
126 TGTAATCACTCCAGACTTATTAAAAAAAAT
375094 TGAAATTAAT
Statistics
Matches: 139, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
192 2 0.01
193 38 0.27
194 89 0.64
195 6 0.04
196 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (190 bp):
AATATAAACGTATTAAATGAACTCAATAATTAAAAGGAATTTTTTTGTTTCGAGTTGAACAGTTA
CATCTGTATGGTATGTGTTTATGGTCAATGATTATAAAAAATTAGAAACATATACTACCTTGTAA
TCACTCCAGACTTATTAAAAAAAATAATATATCTTTTCTAATTTGAAATTAATCGACCTC
Found at i:375470 original size:22 final size:22
Alignment explanation
Indices: 375429--375470 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
375419 AAAATCATAT
*
375429 AAAATTTACTAATATTATATAA
1 AAAATTTACCAATATTATATAA
375451 AAAATTTACCAA-ATTGATAT
1 AAAATTTACCAATATT-ATAT
375471 GTCTAATTTT
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:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATTTACCAATATTATATAA
Found at i:381121 original size:31 final size:32
Alignment explanation
Indices: 381086--381153 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 32
381076 TATTATTCTC
381086 ATTTTAATAAATA-ATAAT-TTATAATAATTTT
1 ATTTTAATAAA-ACATAATATTATAATAATTTT
* *
381117 ATTTTAATAAAACATAATAATTGTAATATTTTT
1 ATTTTAATAAAACATAAT-ATTATAATAATTTT
381150 ATTT
1 ATTT
381154 ATAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 16 0.50
33 15 0.47
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
ATTTTAATAAAACATAATATTATAATAATTTT
Found at i:381248 original size:24 final size:25
Alignment explanation
Indices: 381204--381274 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
381194 CAAATAATAT
381204 TAAATAA-ATTATT-TTTATATTTAA
1 TAAATAATATTATTATTT-TATTTAA
*
381228 -AAATATTATTATTATTTTA-TTAA
1 TAAATAATATTATTATTTTATTTAA
* *
381251 TAGATAATATTATTCATTGTATTT
1 TAAATAATATTATT-ATTTTATTT
381275 GATGATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 9 0.24
24 19 0.50
25 8 0.21
26 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (25 bp):
TAAATAATATTATTATTTTATTTAA
Found at i:381370 original size:14 final size:15
Alignment explanation
Indices: 381351--381381 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
381341 CAAACACCGT
381351 AAAATGTTTTC-AAG
1 AAAATGTTTTCTAAG
381365 AAAATGTTTTCTAAG
1 AAAATGTTTTCTAAG
381380 AA
1 AA
381382 TTGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
AAAATGTTTTCTAAG
Found at i:385893 original size:37 final size:37
Alignment explanation
Indices: 385820--385894 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
385810 GTTGAAAAAT
* *
385820 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
385857 ATTTATATAATTTT-TGTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCT-TTAAAAAATTGAAAATCATAAA
385894 A
1 A
385895 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:386581 original size:27 final size:27
Alignment explanation
Indices: 386551--386635 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
386541 CTTTATTTGT
386551 ATAAAAATAAATTTTAAAATATTTAAA
1 ATAAAAATAAATTTTAAAATATTTAAA
* * * *
386578 ATAATAATAAA-TTTAATATGTATAAAA
1 ATAAAAATAAATTTTAAAATAT-TTAAA
*
386605 ATAAAATTAATATTTTTAAAATAATTTAAA
1 ATAAAAATAA-A-TTTTAAAAT-ATTTAAA
386635 A
1 A
386636 ATTAATTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
26 8 0.18
27 22 0.50
28 1 0.02
30 12 0.27
31 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
ATAAAAATAAATTTTAAAATATTTAAA
Found at i:386607 original size:21 final size:20
Alignment explanation
Indices: 386578--386633 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
386568 AATATTTAAA
*
386578 ATAATAATAAATTTAATATGT
1 ATAAAAATAAATTTAATAT-T
*
386599 ATAAAAATAAAATTAATATT
1 ATAAAAATAAATTTAATATT
* *
386619 TTTAAAAT-AATTTAA
1 ATAAAAATAAATTTAA
386634 AAATTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 17 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAAAAATAAATTTAATATT
Found at i:386790 original size:23 final size:24
Alignment explanation
Indices: 386737--386854 Score: 105
Period size: 23 Copynumber: 4.8 Consensus size: 24
386727 ATATATATAT
* * *
386737 ATAATTATTAAATAAAATTAAACTTA
1 ATAATTA-TATATAAAAAT-AATTTA
*
386763 TTAATTATAT-TAAAAATAATTTA
1 ATAATTATATATAAAAATAATTTA
* * *
386786 ATAATTATATGTACAAATTTAAATTA
1 ATAATTATATATA-AAA-ATAATTTA
* *
386812 TTTATTATAT-TAAAAATAATTTA
1 ATAATTATATATAAAAATAATTTA
386835 ATAATTATATATAAAAATAA
1 ATAATTATATATAAAAATAA
386855 AGATAGTTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
23 28 0.37
24 20 0.27
25 7 0.09
26 20 0.27
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAATTATATATAAAAATAATTTA
Found at i:386791 original size:49 final size:47
Alignment explanation
Indices: 386737--386855 Score: 166
Period size: 49 Copynumber: 2.4 Consensus size: 47
386727 ATATATATAT
*
386737 ATAATTATTAAATAAAATTAAACTTATTAATTATATTAAAAATAATTTA
1 ATAATTA-TATATAAAATTAAA-TTATTAATTATATTAAAAATAATTTA
* *
386786 ATAATTATATGTACAAATTTAAATTATTTATTATATTAAAAATAATTTA
1 ATAATTATATATA-AAA-TTAAATTATTAATTATATTAAAAATAATTTA
*
386835 ATAATTATATATAAAAATAAA
1 ATAATTATATATAAAATTAAA
386856 GATAGTTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
47 4 0.06
48 7 0.11
49 47 0.75
50 5 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (47 bp):
ATAATTATATATAAAATTAAATTATTAATTATATTAAAAATAATTTA
Found at i:386842 original size:26 final size:25
Alignment explanation
Indices: 386768--386854 Score: 92
Period size: 24 Copynumber: 3.6 Consensus size: 25
386758 ACTTATTAAT
386768 TATATTAAAAATAATTTAATAATTA
1 TATATTAAAAATAATTTAATAATTA
* * * *
386793 TAT-GTACAAAT--TTAAATTATTTA
1 TATATTAAAAATAATTTAA-TAATTA
386816 TTATATTAAAAATAATTTAATAATTA
1 -TATATTAAAAATAATTTAATAATTA
386842 TATA-TAAAAATAA
1 TATATTAAAAATAA
386855 AGATAGTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
22 4 0.08
23 5 0.10
24 18 0.37
25 13 0.27
26 5 0.10
27 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
TATATTAAAAATAATTTAATAATTA
Found at i:386875 original size:49 final size:49
Alignment explanation
Indices: 386769--386877 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 49
386759 CTTATTAATT
* * * **
386769 ATATTAAAAATAATTTAATAATTATATGTACAAATTTAAATTATTTATT
1 ATATTAAAAATAATTTAATAATTATATATACAAATATAAAATATTTAAA
386818 ATATTAAAAATAATTTAATAATTATATATA-AAA-ATAAAGATAGTTTGAAA
1 ATATTAAAAATAATTTAATAATTATATATACAAATATAAA-ATA-TTT-AAA
386868 ATA-TAAAAAT
1 ATATTAAAAAT
386878 CTAAATTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
47 4 0.08
48 5 0.10
49 39 0.75
50 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (49 bp):
ATATTAAAAATAATTTAATAATTATATATACAAATATAAAATATTTAAA
Found at i:387732 original size:13 final size:13
Alignment explanation
Indices: 387714--387747 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
387704 CTTTGTATGC
*
387714 TATATGTAAATTA
1 TATATGTAAAATA
*
387727 TATATGAAAAATA
1 TATATGTAAAATA
387740 TATATGTA
1 TATATGTA
387748 TTGTATATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
TATATGTAAAATA
Found at i:398218 original size:5 final size:5
Alignment explanation
Indices: 398208--398247 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
398198 TTAAAACCAT
398208 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
398248 AGATTGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:403036 original size:36 final size:36
Alignment explanation
Indices: 402989--403059 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
402979 CCTTCCCACA
402989 ATGTCTTGCCCTCAATCAAAACGACATGAATTAACC
1 ATGTCTTGCCCTCAATCAAAACGACATGAATTAACC
*
403025 ATGTCTTGCCCTCAATCAAGACGACATGAATTAAC
1 ATGTCTTGCCCTCAATCAAAACGACATGAATTAAC
403060 TATATAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (36 bp):
ATGTCTTGCCCTCAATCAAAACGACATGAATTAACC
Found at i:404689 original size:24 final size:24
Alignment explanation
Indices: 404660--404706 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
404650 AGTTAGTAAA
*
404660 ATATAAAATCAAAATTTTAAAATG
1 ATATAAAAACAAAATTTTAAAATG
* *
404684 ATATAAAAAGAATATTTTAAAAT
1 ATATAAAAACAAAATTTTAAAAT
404707 AATTATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATAAAAACAAAATTTTAAAATG
Found at i:408231 original size:30 final size:31
Alignment explanation
Indices: 408180--408328 Score: 201
Period size: 29 Copynumber: 5.1 Consensus size: 31
408170 GGTCACAATA
408180 TAAACTGTTC--ATGTGCCTTT-AACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
408208 TAGACTGCTCATATGTTCCTTTAAACATA--
1 TAAACTGTTCATATGTGCCTTTAAACATATG
408237 TAAACTGTTCATATGTGCCTTTAAAC-TA-G
1 TAAACTGTTCATATGTGCCTTTAAACATATG
408266 TAAA-TG-TCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
408295 TAAACTGTTCATATGTG-CTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
408325 TAAA
1 TAAA
408329 ATTGCCTTTA
Statistics
Matches: 107, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.17
28 14 0.13
29 32 0.30
30 28 0.26
31 15 0.14
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:411699 original size:65 final size:65
Alignment explanation
Indices: 411584--411734 Score: 191
Period size: 65 Copynumber: 2.3 Consensus size: 65
411574 GCACTAAGAG
*
411584 TGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAAAGTGCATCGATGCAT-G-ACTGGTGCATC
1 TGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGTA-T-GTGCATC
411646 GA
64 GA
* * * ** *
411648 TGCATCAAATACATTCGATGTTTTCATAATATCCTCAGTGCATCGGTGCATGGTATGTGCATCGA
1 TGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGTATGTGCATCGA
*
411713 TGCATGAAATGCATTCGATGTT
1 TGCATCAAATGCATTCGATGTT
411735 CAATTTAATT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 18 0.24
65 54 0.72
66 2 0.03
67 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
TGCATCAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGTATGTGCATCGA
Found at i:411773 original size:65 final size:65
Alignment explanation
Indices: 411584--411784 Score: 182
Period size: 65 Copynumber: 3.1 Consensus size: 65
411574 GCACTAAGAG
* * * * * * *
411584 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCA-AAGTGCATCGATGCAT-GACTGGTGCATCG
1 TGCATCAAATACATTCGATGTTTTATAATA-TCATCAGTGCATCGATGCATGGATTGGTGCATCG
411647 A
65 A
* *
411648 TGCATCAAATACATTCGATGTTTTCATAATATCCTCAGTGCATCGGTGCATGG-TAT-GTGCATC
1 TGCATCAAATACATTCGATGTTTT-ATAATATCATCAGTGCATCGATGCATGGAT-TGGTGCATC
411711 GA
64 GA
* * *
411713 TGCATGAAATGCATTCGATGTTCAATT-TAAT-TCAT-GGTGCATCGATGCATGGATTGGTGCAT
1 TGCATCAAATACATTCGATGTT---TTATAATATCATCAGTGCATCGATGCATGGATTGGTGCAT
*
411775 CGG
63 CGA
411778 TGCATCA
1 TGCATCA
411785 CTCTGAAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
64 38 0.34
65 66 0.59
66 6 0.05
68 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
TGCATCAAATACATTCGATGTTTTATAATATCATCAGTGCATCGATGCATGGATTGGTGCATCGA
Found at i:413414 original size:24 final size:23
Alignment explanation
Indices: 413340--413420 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
413330 CATAATCCCG
413340 TGCATCGATGCACATTCAAGGCG-
1 TGCATCGATGCACATTCAAGG-GA
* *
413363 TGCATCGGTGCATCA-TC-A-TGA
1 TGCATCGATGCA-CATTCAAGGGA
*
413384 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
413408 TGCATCGATGCAC
1 TGCATCGATGCAC
413421 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 1 0.02
23 14 0.30
24 16 0.35
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:417283 original size:22 final size:21
Alignment explanation
Indices: 417241--417280 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
417231 GAGTTTATTT
*
417241 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
417262 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
417281 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:421789 original size:24 final size:24
Alignment explanation
Indices: 421761--421808 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
421751 TAGCTATAAT
421761 TACAAGTGTAGTTTAAAACAAAGA
1 TACAAGTGTAGTTTAAAACAAAGA
421785 TACAAGTGTAGTTTAAAACAAAGA
1 TACAAGTGTAGTTTAAAACAAAGA
421809 ACAGAAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (24 bp):
TACAAGTGTAGTTTAAAACAAAGA
Found at i:429322 original size:60 final size:60
Alignment explanation
Indices: 429245--429601 Score: 527
Period size: 60 Copynumber: 6.0 Consensus size: 60
429235 AATCACCAAA
* *
429245 GAAAGAAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTAT-GAAAGGCCTTCTAGC
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCT-TCGAAAGGCCTTCTAAC
* * *
429305 GAAATCAGCAATCAACATAATATAGTTATTGCAGCCGAAGGCTTCGAAAGGCCTTCTAGC
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCTAAC
* * * * *
429365 AAAATCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCATCGAAAGGCCTTTTAAT
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCTAAC
* * *
429425 GAAAGCAGCAATCAACATAATATAGTTATTGCACCCGAGGACTTCGAAATGCCTTCTAAC
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCTAAC
* * * *
429485 GAAAGCAGCAATCAACATAATATAGTTATTGCAGTCGAGGGCTTCGAAATGCCGTCTAAT
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCTAAC
* *
429545 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTTGAATGGCCTTCT
1 GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCT
429602 TACTTAGAGT
Statistics
Matches: 269, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 1 0.00
60 268 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
GAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTCGAAAGGCCTTCTAAC
Found at i:430542 original size:533 final size:528
Alignment explanation
Indices: 429542--430596 Score: 1700
Period size: 533 Copynumber: 2.0 Consensus size: 528
429532 AATGCCGTCT
* *
429542 AATGAAAGCAGCAATCAACATAATATAGTTATTGCAGCCGAGGGCTTTGAATGGCCTTCTTACTT
1 AATGAAAGCAGCAATCAACATAATATAGTTATTGCAGCCAAGGGCTTTGAAGGGCCTTCTTACTT
* * *
429607 AGAGTATCTTGCCGAAGAGGACATTTTTCCAACTGTAAACTCTCTCTCTCTTAATCAGTTATTGA
66 AGAGTATCATGCCGAAGAGGACATTATTCCAACAGTAAACTCTCTCTCTCTTAATCAGTTATTGA
*
429672 TGAAGAATGTAAAACTGAAGGAAAGAACTAATCTGTTTTATTGTCCATGTTTCAGGAACCGTTAT
131 TGAAGAATGTAAAACTGAAGGAAAGAACTAATATGTTTTATTGTCCATGTTTCAGGAACCGTTAT
* * * *
429737 ATAATGATGGATTATATAACATATTATCATCACTTTATGTGTTATTAGAAGCGCCAGGACCAACT
196 ATAATGATGGATTATATAACAAATTATCACCACTTGATGGGTTATTAGAAGCGCCAGGACCAACT
* *
429802 AATAACTCGAATTGGATTCAAGATCAATATATCATCAACAAAGAACATGATCAGTTCTTGAATTC
261 AATAACTCGAATTGGATTCAAGATCAATATATCACCAACAAAGAACATGATCAGCTCTTGAATTC
*
429867 AACTTTTGCTGATACAAATCAAGCTTACCTTCAAGAAGGAAACATGCAACAATGCTTGGCAGCTG
326 AACTTTTGCTGATAAAAATCAAGCTTACCTTCAAGAAGGAAACATGCAACAATGCTTGGCAGCTG
* * * * *
429932 ACAATGAAGGTTTCGGCTTGCCCTGCATAAGGTTGATGCTGGAATCATCAAATTGGATGGAGAAA
391 AAAATGAAGGTTTCCGCTTGCCCTGCATAAGCTCGATGCCGGAATCATCAAATTGGATGGAGAAA
429997 TCTAGGAAAAGAAAAGAGC-ATGTCGAATATAATGAGCCATCTATAGAAAC-TGAGGCTCAACAT
456 TCTAGGAAAAGAAAAGAGCGAT-TCGAATATAATGAGCCATCTATAGAAACTTGAGGCTCAACAT
430060 CTGCCTTCA
520 CTGCCTTCA
* *
430069 AATGAAAGTAGCAATGAACATAATATAGTTATTGCAGCCAAGGGCTTTGAAGGGCCTTCTTACTT
1 AATGAAAGCAGCAATCAACATAATATAGTTATTGCAGCCAAGGGCTTTGAAGGGCCTTCTTACTT
* * *
430134 AGAGTATCATGTCGAAGAGGACATTATTCCAGCAGTAAACTCTCTCTCTCTCTCTTTTAATCATT
66 AGAGTATCATGCCGAAGAGGACATTATTCCAACAGTAAA----CTCTCTCTCTC--TTAATCAGT
* *
430199 TATTGATGCAGAATGTAAAACTGAAGGAAATAACTAATATGTTTTATTGTCCATGTTTCAGGAAC
125 TATTGATGAAGAATGTAAAACTGAAGGAAAGAACTAATATGTTTTATTGTCCATGTTTCAGGAAC
* *
430264 TGTTATATAATGATGGATTATCTAACAAATTATCACCACTTGATGGGTTATTAGAAGCGCCAGGA
190 CGTTATATAATGATGGATTATATAACAAATTATCACCACTTGATGGGTTATTAGAAGCGCCAGGA
* * *
430329 GCAACTAATAACTCGAATTGGATTCAAGATCAATATATCACCAACAAAGAACATGGTGAGCTCTT
255 CCAACTAATAACTCGAATTGGATTCAAGATCAATATATCACCAACAAAGAACATGATCAGCTCTT
*
430394 GAATTCAACTTTTGCTGATAAAAATGAAGCTTACCTTCAAGAAGGAAACATGCAACAATGCTTGG
320 GAATTCAACTTTTGCTGATAAAAATCAAGCTTACCTTCAAGAAGGAAACATGCAACAATGCTTGG
430459 CAGCTGAAAATGAAGGTTTCCGCTTGCCCTGCATAAGCTCGATGCCGGAATCATCAAATTGGATG
385 CAGCTGAAAATGAAGGTTTCCGCTTGCCCTGCATAAGCTCGATGCCGGAATCATCAAATTGGATG
* * * *
430524 GAGAAATCTAGGAAAAGAAAAGAGCGATTCGAATATGATGAGTCGTTTATAGAAACTGTTGAGGC
450 GAGAAATCTAGGAAAAGAAAAGAGCGATTCGAATATAATGAGCCATCTATAGAAAC--TTGAGGC
430589 TCAACATC
513 TCAACATC
430597 GGGGGAGAAT
Statistics
Matches: 483, Mismatches: 35, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
527 95 0.20
531 11 0.02
533 361 0.75
534 2 0.00
536 14 0.03
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (528 bp):
AATGAAAGCAGCAATCAACATAATATAGTTATTGCAGCCAAGGGCTTTGAAGGGCCTTCTTACTT
AGAGTATCATGCCGAAGAGGACATTATTCCAACAGTAAACTCTCTCTCTCTTAATCAGTTATTGA
TGAAGAATGTAAAACTGAAGGAAAGAACTAATATGTTTTATTGTCCATGTTTCAGGAACCGTTAT
ATAATGATGGATTATATAACAAATTATCACCACTTGATGGGTTATTAGAAGCGCCAGGACCAACT
AATAACTCGAATTGGATTCAAGATCAATATATCACCAACAAAGAACATGATCAGCTCTTGAATTC
AACTTTTGCTGATAAAAATCAAGCTTACCTTCAAGAAGGAAACATGCAACAATGCTTGGCAGCTG
AAAATGAAGGTTTCCGCTTGCCCTGCATAAGCTCGATGCCGGAATCATCAAATTGGATGGAGAAA
TCTAGGAAAAGAAAAGAGCGATTCGAATATAATGAGCCATCTATAGAAACTTGAGGCTCAACATC
TGCCTTCA
Found at i:430766 original size:20 final size:21
Alignment explanation
Indices: 430743--430783 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
430733 AATAGATTCC
430743 TAAATTAGA-AAGATTATGTA
1 TAAATTAGATAAGATTATGTA
*
430763 TAAATTAGATAGGATTATGTA
1 TAAATTAGATAAGATTATGTA
430784 AATATCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
TAAATTAGATAAGATTATGTA
Found at i:434154 original size:22 final size:21
Alignment explanation
Indices: 434114--434158 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
434104 ATTAATCTGG
434114 TTAAATATGATGCAATATTTAT
1 TTAAATATGATGCAATA-TTAT
**
434136 TTAAATATGATGCTTTATTAT
1 TTAAATATGATGCAATATTAT
434157 TT
1 TT
434159 GAGATATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (21 bp):
TTAAATATGATGCAATATTAT
Found at i:435077 original size:23 final size:22
Alignment explanation
Indices: 435050--435094 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
435040 CAAATATAAT
*
435050 AAATAATATTATTTATTATAAAA
1 AAATAATAATA-TTATTATAAAA
*
435073 AAATAATAATATTATTTTAAAA
1 AAATAATAATATTATTATAAAA
435095 TATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATAATATTATTATAAAA
Found at i:441516 original size:2 final size:2
Alignment explanation
Indices: 441509--441536 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
441499 TTATAAGATA
441509 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
441537 GAAAATATCG
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:451874 original size:12 final size:12
Alignment explanation
Indices: 451857--451885 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
451847 TCTTTGTTGG
451857 TATTTCTATATC
1 TATTTCTATATC
451869 TATTTCTATATC
1 TATTTCTATATC
451881 TATTT
1 TATTT
451886 ATCGGGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTCTATATC
Found at i:454104 original size:20 final size:20
Alignment explanation
Indices: 454081--454131 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
454071 CACGGAATGT
454081 AAGATTACCAGT-AGGAATAA
1 AAGATTACCAGTGA-GAATAA
454101 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
454121 AAGATTACCAG
1 AAGATTACCAG
454132 GGAATAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:454304 original size:15 final size:15
Alignment explanation
Indices: 454286--454318 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
454276 AAATTCTAAA
454286 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
454301 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
454316 TAT
1 TAT
454319 ATCTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:458183 original size:21 final size:21
Alignment explanation
Indices: 458143--458189 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
458133 TCTTCAATAA
458143 CTTTTTTTTCTTTATAGCATG
1 CTTTTTTTTCTTTATAGCATG
* *
458164 -TTTTCTTTTCTTTTTGGCATG
1 CTTTT-TTTTCTTTATAGCATG
458185 CTTTT
1 CTTTT
458190 GGTCTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.66
Consensus pattern (21 bp):
CTTTTTTTTCTTTATAGCATG
Found at i:461320 original size:24 final size:23
Alignment explanation
Indices: 461278--461323 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
461268 TGTAGTAGAG
461278 AAAAATAAATGTATTTAAAAGAT
1 AAAAATAAATGTATTTAAAAGAT
461301 AAAAATAAAT-TATTAATAAAAGA
1 AAAAATAAATGTATT--TAAAAGA
461324 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (23 bp):
AAAAATAAATGTATTTAAAAGAT
Found at i:474604 original size:18 final size:18
Alignment explanation
Indices: 474581--474650 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
474571 CCGTAGAATT
474581 TGTCCCGTAA-GACCACTA
1 TGTCCCG-AAGGACCACTA
474599 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
474617 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
474635 TGTCCCAAAGGACCAC
1 TGTCCCGAAGGACCAC
474651 ATAGACCCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 2 0.04
18 48 0.96
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:484152 original size:3 final size:3
Alignment explanation
Indices: 484146--484175 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
484136 AAAGTACTTA
484146 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
484176 GAGAATGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:485544 original size:2 final size:2
Alignment explanation
Indices: 485537--485602 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
485527 ATGAGAAGGA
485537 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
485579 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
485603 GTTTGGCTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493878 original size:2 final size:2
Alignment explanation
Indices: 493873--493904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
493863 AAGTTCACTA
493873 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
493905 CTGTATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:494207 original size:6 final size:6
Alignment explanation
Indices: 494196--494220 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
494186 AAATCTACTG
494196 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
494221 CATGTTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:496039 original size:29 final size:30
Alignment explanation
Indices: 496002--496066 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
495992 TACATTTTAG
*
496002 TTTT-TTTTAATATTTAAA-ATATA-TTATA
1 TTTTATTTTAA-AATTAAATATATATTTATA
496030 TTTTATTTTAAAATTAAATATATATTTATA
1 TTTTATTTTAAAATTAAATATATATTTATA
496060 TATTTAT
1 T-TTTAT
496067 ATCCTATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 10 0.31
29 11 0.34
30 6 0.19
31 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTATTTTAAAATTAAATATATATTTATA
Found at i:496454 original size:2 final size:2
Alignment explanation
Indices: 496447--496474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
496437 TGTAAATTAA
496447 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
496475 GAGAGGTGGT
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:501287 original size:21 final size:21
Alignment explanation
Indices: 501263--501303 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
501253 CGAAAATATT
*
501263 TAAAAATATTAATATTTTAAG
1 TAAAAATAATAATATTTTAAG
501284 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
501304 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:504745 original size:14 final size:13
Alignment explanation
Indices: 504722--504759 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
504712 TAATAATACT
*
504722 TATATAATATATA
1 TATAAAATATATA
504735 TAT-AAATATATAA
1 TATAAAATATAT-A
504748 TATAAAATATAT
1 TATAAAATATAT
504760 GTTTTTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 7 0.32
14 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAAAATATATA
Found at i:505210 original size:105 final size:105
Alignment explanation
Indices: 505017--506209 Score: 2149
Period size: 105 Copynumber: 11.4 Consensus size: 105
505007 GTATTGTCCC
* *** * * *
505017 GAGTCCAATATCCTCCACCGTGAAGTTGAAACTAGCTCT-AAATTGAG-AATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
* * *
505080 CAGTGGTCCCTTCGTCGTGAGGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505120 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
505185 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505225 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
* *
505290 CAGCGGT-CCTTCGTCGTGAAGCTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
505329 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
505394 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* * *
505434 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGATAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
505499 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505539 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
505604 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505644 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
* *
505709 CAGCGGTCCCTTCGTCGTGAAGCTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505749 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
505814 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
505854 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
505919 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
505959 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
506024 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
506064 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
506129 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
506169 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
506210 GTAAAACCTG
Statistics
Matches: 1057, Mismatches: 30, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
103 33 0.03
104 109 0.10
105 915 0.87
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:517827 original size:21 final size:21
Alignment explanation
Indices: 517797--517841 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
517787 ATAATAATAG
*
517797 TAAAAGTAAAAGGGGAAATAAA
1 TAAAAGTAAAAAGGG-AATAAA
*
517819 TAAAA-TAAAAATGGAATAAA
1 TAAAAGTAAAAAGGGAATAAA
517839 TAA
1 TAA
517842 TTAATGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.18
Consensus pattern (21 bp):
TAAAAGTAAAAAGGGAATAAA
Found at i:517921 original size:2 final size:2
Alignment explanation
Indices: 517914--517957 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
517904 GGTAAAATGA
* *
517914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
517956 AT
1 AT
517958 GTAAATACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:519156 original size:2 final size:2
Alignment explanation
Indices: 519145--519188 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
519135 TAATAATACT
*
519145 TA TA TA -A TA TA TA TA TA TA TA -A TA TA TA -A TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519184 TA TA T
1 TA TA T
519189 GTTTTTTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:519165 original size:15 final size:15
Alignment explanation
Indices: 519145--519188 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
519135 TAATAATACT
519145 TATATAATATATATA
1 TATATAATATATATA
519160 TATATAATATATA-A
1 TATATAATATATATA
519174 TATATAA-ATATATA
1 TATATAATATATATA
519188 T
1 T
519189 GTTTTTTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.18
14 10 0.36
15 13 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAATATATATA
Found at i:519170 original size:22 final size:22
Alignment explanation
Indices: 519145--519187 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
519135 TAATAATACT
*
519145 TATATAATATATATATATATAA
1 TATATAATATATAAATATATAA
519167 TATATAATATATAAATATATA
1 TATATAATATATAAATATATA
519188 TGTTTTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATAATATATAAATATATAA
Found at i:519883 original size:13 final size:13
Alignment explanation
Indices: 519865--519892 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
519855 GTTATATTGA
519865 TTTTTCCCTCAAT
1 TTTTTCCCTCAAT
519878 TTTTTCCCTCAAT
1 TTTTTCCCTCAAT
519891 TT
1 TT
519893 AAGGGTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTCCCTCAAT
Found at i:522693 original size:17 final size:17
Alignment explanation
Indices: 522671--522704 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
522661 TTAAATAATC
522671 CACGTAATATAGATTTT
1 CACGTAATATAGATTTT
522688 CACGTAATATAGATTTT
1 CACGTAATATAGATTTT
522705 AAACATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
CACGTAATATAGATTTT
Found at i:533017 original size:23 final size:24
Alignment explanation
Indices: 532960--533024 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
532950 GATCATTCAG
*
532960 TTTT-AAATTTAAATATTTAATATA
1 TTTTAAAATTTTAATA-TTAATATA
532984 TTTTAAAATTTTAATATTAATA-A
1 TTTTAAAATTTTAATATTAATATA
533007 -TTTAAACATTTTAATATT
1 TTTTAAA-ATTTTAATATT
533025 TTACCTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 10 0.26
25 10 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAAATTTTAATATTAATATA
Found at i:533026 original size:8 final size:8
Alignment explanation
Indices: 532960--533027 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
532950 GATCATTCAG
532960 TTTTAA-A
1 TTTTAATA
*
532967 TTTAAATA
1 TTTTAATA
*
532975 TTTAATATA
1 TTTTA-ATA
*
532984 TTTTAAAA
1 TTTTAATA
532992 TTTTAATA
1 TTTTAATA
533000 --TTAATAA
1 TTTTAAT-A
* *
533007 TTTAAACA
1 TTTTAATA
533015 TTTTAATA
1 TTTTAATA
533023 TTTTA
1 TTTTA
533028 CCTTTTGACT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
6 5 0.10
7 6 0.12
8 27 0.56
9 10 0.21
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAATA
Found at i:535686 original size:16 final size:16
Alignment explanation
Indices: 535663--535710 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
535653 AGTTGCTTTT
*
535663 GATTCAGATTATTTTC
1 GATTCAGATTAATTTC
*
535679 GGTTCAGATTAATTTC
1 GATTCAGATTAATTTC
535695 GATTCA-AGTTAATTTC
1 GATTCAGA-TTAATTTC
535711 ATTTCGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (16 bp):
GATTCAGATTAATTTC
Found at i:539319 original size:20 final size:19
Alignment explanation
Indices: 539282--539323 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
539272 TTGACATGAT
*
539282 AAAAAAACCTTAAATTCTTA
1 AAAAAAACCTAAAATTC-TA
539302 AAAAAAACC-AAAATTTCTA
1 AAAAAAACCTAAAA-TTCTA
539321 AAA
1 AAA
539324 TTGCCCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAAACCTAAAATTCTA
Found at i:539921 original size:25 final size:25
Alignment explanation
Indices: 539887--539935 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
539877 GTCGCGCCAA
539887 AACGACCTCATTTTGGTGAGACATG
1 AACGACCTCATTTTGGTGAGACATG
539912 AACGACCTCATTTTGGTGAGACAT
1 AACGACCTCATTTTGGTGAGACAT
539936 CCATGTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (25 bp):
AACGACCTCATTTTGGTGAGACATG
Found at i:545862 original size:23 final size:23
Alignment explanation
Indices: 545836--545882 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
545826 TCCCTCGTCA
545836 TTTATCTTTCATGATTATATTAG
1 TTTATCTTTCATGATTATATTAG
545859 TTTATCTTTCATGATTATATTAG
1 TTTATCTTTCATGATTATATTAG
545882 T
1 T
545883 GTCAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTATCTTTCATGATTATATTAG
Found at i:547597 original size:22 final size:22
Alignment explanation
Indices: 547572--547620 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
547562 CCAAATAACA
*
547572 AAAAAATGTCA-AAAAACATAAT
1 AAAAAATGCCATAAAAACAT-AT
* *
547594 AAAATATGCCATAAAAGCATAT
1 AAAAAATGCCATAAAAACATAT
547616 AAAAA
1 AAAAA
547621 CGTGTCATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAATGCCATAAAAACATAT
Found at i:553708 original size:10 final size:9
Alignment explanation
Indices: 553690--553729 Score: 57
Period size: 8 Copynumber: 4.7 Consensus size: 9
553680 TTGATTTTCA
553690 ATAATATAT
1 ATAATATAT
553699 AT-ATATAT
1 ATAATATAT
553707 ATAATA-AT
1 ATAATATAT
*
553715 ATAAAATAT
1 ATAATATAT
553724 ATAATA
1 ATAATA
553730 ATTTAATCAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAATATAT
Found at i:553714 original size:20 final size:17
Alignment explanation
Indices: 553690--553731 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
553680 TTGATTTTCA
*
553690 ATAAT-ATATATATATAT
1 ATAATAATATA-AAATAT
553707 ATAATAATATAAAATAT
1 ATAATAATATAAAATAT
553724 ATAATAAT
1 ATAATAAT
553732 TTAATCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAATATAAAATAT
Found at i:554161 original size:24 final size:24
Alignment explanation
Indices: 554133--554178 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
554123 TTGTAACGAT
*
554133 TTTTCTTTACTCTTGTGGCACGCG
1 TTTTCTCTACTCTTGTGGCACGCG
* *
554157 TTTTCTCTGCTCTTGTTGCACG
1 TTTTCTCTACTCTTGTGGCACG
554179 ATCCTCACGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.07, C:0.26, G:0.20, T:0.48
Consensus pattern (24 bp):
TTTTCTCTACTCTTGTGGCACGCG
Found at i:556467 original size:155 final size:157
Alignment explanation
Indices: 556184--556495 Score: 562
Period size: 155 Copynumber: 2.0 Consensus size: 157
556174 TTGATCGACC
556184 AAGGAAGGTGATTTTAAAGAGATATTTTATAGTAGAAAAGTATAATATGAGCTTAAGGAAAGAAA
1 AAGGAAGGTGATTTTAAAGAGATATTTTATAGTAGAAAAGTATAATATGAGCTTAAGGAAAGAAA
556249 GGTGTGATGAAAAAAGAGAAAAAAGGTTGACATGTTAGCACTTAACAGACCATGCAAGTTTCGGT
66 GGTGTGATGAAAAAAGAGAAAAAAGGTTGACATGTTAGCACTTAACAGACCATGCAAGTTTCGGT
556314 CA-CC-CGTTAATGGCGAGTGACTGTTT
131 CACCCACGTT-ATGGCGAGTGACTGTTT
556340 AAGGAAGAG-GATTTTAAAGAGATA-TTTATAGTAGAAAAAGTATAATATGAGCTTAAGGAAAGA
1 AAGGAAG-GTGATTTTAAAGAGATATTTTATAGTAG-AAAAGTATAATATGAGCTTAAGGAAAGA
556403 AA-GTGTGATGAAAAAAGAGAAAAAAGGTTGACATGTTAGCACTTAACAGACCATGCAAGTTTCG
64 AAGGTGTGATGAAAAAAGAGAAAAAAGGTTGACATGTTAGCACTTAACAGACCATGCAAGTTTCG
556467 GTCACCCACGTTATGGCGAGTGACTGTTT
129 GTCACCCACGTTATGGCGAGTGACTGTTT
556496 TGTTACAAAT
Statistics
Matches: 152, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
155 76 0.50
156 71 0.47
157 5 0.03
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.26
Consensus pattern (157 bp):
AAGGAAGGTGATTTTAAAGAGATATTTTATAGTAGAAAAGTATAATATGAGCTTAAGGAAAGAAA
GGTGTGATGAAAAAAGAGAAAAAAGGTTGACATGTTAGCACTTAACAGACCATGCAAGTTTCGGT
CACCCACGTTATGGCGAGTGACTGTTT
Found at i:559123 original size:65 final size:64
Alignment explanation
Indices: 559020--559148 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 64
559010 TGAGTCGCTT
559020 GTCTAATTATAGACAAAAGAAAAGAATGGGACCCAGAACCAGAAAAAGAATTAATTGGGTCCTC
1 GTCTAATTATAGACAAAAGAAAAGAATGGGACCCAGAACCAGAAAAAGAATTAATTGGGTCCTC
559084 GTCTAATTATTAGACAAAAGAAAAGAATGGGACCCAGAACCAGAAAAAGAATTAATTGGGTCCTC
1 GTCTAATTA-TAGACAAAAGAAAAGAATGGGACCCAGAACCAGAAAAAGAATTAATTGGGTCCTC
559149 AAGCGCCACC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 9 0.14
65 55 0.86
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (64 bp):
GTCTAATTATAGACAAAAGAAAAGAATGGGACCCAGAACCAGAAAAAGAATTAATTGGGTCCTC
Found at i:560385 original size:18 final size:18
Alignment explanation
Indices: 560362--560399 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
560352 ATAAAACAAA
560362 AAAGGTGATATTAATCTT
1 AAAGGTGATATTAATCTT
560380 AAAGGTGATATTAATCTT
1 AAAGGTGATATTAATCTT
560398 AA
1 AA
560400 TACTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (18 bp):
AAAGGTGATATTAATCTT
Found at i:571670 original size:105 final size:105
Alignment explanation
Indices: 571488--571700 Score: 399
Period size: 105 Copynumber: 2.0 Consensus size: 105
571478 ATCCAATAAG
*
571488 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAATGG
1 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
571553 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
66 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
* *
571593 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGAGGAATTTTTTGTACAACGG
1 CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
571658 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
66 AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
571698 CAT
1 CAT
571701 TGAATCAAAG
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (105 bp):
CATGGCAAAGAATTTACCTACACAAACTTCTCTTTGACATCATTGACGAAATTTTTGTACAACGG
AATAACATATAAATCTGATACCTGTACAGCTTACAAAGAA
Found at i:572020 original size:27 final size:28
Alignment explanation
Indices: 571972--572024 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
571962 ACACCATAAA
571972 ATCCTAAGAACACAACTTTAATCAATGC
1 ATCCTAAGAACACAACTTTAATCAATGC
*
572000 ATCCTAAG-ACATAACTTTAATCAAT
1 ATCCTAAGAACACAACTTTAATCAAT
572025 TACTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (28 bp):
ATCCTAAGAACACAACTTTAATCAATGC
Found at i:575608 original size:30 final size:30
Alignment explanation
Indices: 575561--575725 Score: 188
Period size: 30 Copynumber: 5.5 Consensus size: 30
575551 GAAAGGGATA
* * *
575561 TAATTCCATGCAAATGTCAAAATGGGGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* *
575591 TAA-CTCTATGCAGATGTCAAAGCGGGGAAT
1 TAATC-CCATGCAGATGTCAAAACGGGGAAT
*
575621 TAATCCCATGCAGATGTCAAAACGGGAAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* *
575651 CAATCCCATGCAGATGTCAGAACGGGGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
* * * * *
575681 TAATCTCATGCAGACGTCAGAACAGAGAAT
1 TAATCCCATGCAGATGTCAAAACGGGGAAT
*
575711 TAATCCCATACAGAT
1 TAATCCCATGCAGAT
575726 CGAAAATACA
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
30 113 0.99
31 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (30 bp):
TAATCCCATGCAGATGTCAAAACGGGGAAT
Found at i:581731 original size:9 final size:9
Alignment explanation
Indices: 581719--581795 Score: 64
Period size: 9 Copynumber: 8.4 Consensus size: 9
581709 GACGACAACA
*
581719 AAGAAAAAG
1 AAGAAGAAG
581728 AAGAAGAAG
1 AAGAAGAAG
581737 AAGAAGAAG
1 AAGAAGAAG
* *
581746 AGGAAGAGG
1 AAGAAGAAG
*
581755 AAGAGGAAG
1 AAGAAGAAG
* *
581764 AGGGAAGAGG
1 A-AGAAGAAG
*
581774 AAGAGGAAG
1 AAGAAGAAG
* *
581783 AGGAAGAGG
1 AAGAAGAAG
581792 AAGA
1 AAGA
581796 GAGTGTTGTA
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
9 45 0.88
10 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (9 bp):
AAGAAGAAG
Found at i:581777 original size:31 final size:31
Alignment explanation
Indices: 581736--581796 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
581726 AGAAGAAGAA
581736 GAAGAAGAAGAGGAAGAGGAAGAGGAAGAGG
1 GAAGAAGAAGAGGAAGAGGAAGAGGAAGAGG
*
581767 GAAGAGGAAGAGGAAGAGGAAGAGGAAGAG
1 GAAGAAGAAGAGGAAGAGGAAGAGGAAGAG
581797 AGTGTTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (31 bp):
GAAGAAGAAGAGGAAGAGGAAGAGGAAGAGG
Found at i:581796 original size:6 final size:6
Alignment explanation
Indices: 581725--581796 Score: 108
Period size: 6 Copynumber: 11.8 Consensus size: 6
581715 AACAAAGAAA
* * *
581725 AAGAAG AAGAAG AAGAAG AAGAGG AAGAGG AAGAGG AAGAGGG AAGAGG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGA-GG AAGAGG
581774 AAGAGG AAGAGG AAGAGG AAGAG
1 AAGAGG AAGAGG AAGAGG AAGAG
581797 AGTGTTGTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
6 58 0.91
7 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:585252 original size:3 final size:3
Alignment explanation
Indices: 585244--585272 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
585234 GGCACTTATA
585244 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
585273 AGCTTACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:591743 original size:19 final size:19
Alignment explanation
Indices: 591707--591744 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
591697 TCAAAATAAA
*
591707 AAATATTTCAAGTTACAAT
1 AAATATTTCAAGTCACAAT
591726 AAATATTTACAA-TCACAAT
1 AAATATTT-CAAGTCACAAT
591745 TGTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (19 bp):
AAATATTTCAAGTCACAAT
Found at i:593612 original size:2 final size:2
Alignment explanation
Indices: 593607--593638 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
593597 TTAAAAAATA
593607 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
593639 TAATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:599139 original size:4 final size:4
Alignment explanation
Indices: 599132--599172 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
599122 TTTGTATTTC
*
599132 TATG TATG TAGG TATG TATG TA-G TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
599173 CGTGGAGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:599159 original size:19 final size:19
Alignment explanation
Indices: 599135--599172 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
599125 GTATTTCTAT
599135 GTATGTAGGTATGTATGTA
1 GTATGTAGGTATGTATGTA
*
599154 GTATGTATGTATGTATGTA
1 GTATGTAGGTATGTATGTA
599173 CGTGGAGTTG
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:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (19 bp):
GTATGTAGGTATGTATGTA
Found at i:600233 original size:46 final size:46
Alignment explanation
Indices: 600180--600289 Score: 211
Period size: 46 Copynumber: 2.4 Consensus size: 46
600170 ATGCAATTTG
*
600180 ACCATTTAAATTAAAACAAAATTATTGGGGTGGGTAGTGTATTTTA
1 ACCATTTATATTAAAACAAAATTATTGGGGTGGGTAGTGTATTTTA
600226 ACCATTTATATTAAAACAAAATTATTGGGGTGGGTAGTGTATTTTA
1 ACCATTTATATTAAAACAAAATTATTGGGGTGGGTAGTGTATTTTA
600272 ACCATTTATATTAAAACA
1 ACCATTTATATTAAAACA
600290 GAAAGGTACT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (46 bp):
ACCATTTATATTAAAACAAAATTATTGGGGTGGGTAGTGTATTTTA
Found at i:601337 original size:21 final size:21
Alignment explanation
Indices: 601289--601338 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
601279 GTTTCCAGAT
*
601289 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
601310 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
601331 TCGCAATG
1 TCGCAATG
601339 TGAATATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:601514 original size:21 final size:21
Alignment explanation
Indices: 601470--601543 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
601460 GCGAATTTAA
601470 ATCGCAATGCGAACTTCG-CT
1 ATCGCAATGCGAACTTCGACT
* *
601490 ATCGTAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
601511 ATCGCAAAGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
601532 ATCGCATTGCGA
1 ATCGCAATGCGA
601544 TTTACATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:601582 original size:21 final size:21
Alignment explanation
Indices: 601556--601626 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
601546 TACATATTCA
601556 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
601577 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
* *
601598 AATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
601619 CGTTGCGA
1 CATTGCGA
601627 ATCTGAAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:614436 original size:20 final size:20
Alignment explanation
Indices: 614397--614436 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
614387 TTGTATTTTT
*
614397 TTATATTTTTTAATATAAAA
1 TTATATTTTTTAATAGAAAA
614417 TTATATTTTATTAA-AGAAAA
1 TTATATTTT-TTAATAGAAAA
614437 AAAGACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATATTTTTTAATAGAAAA
Found at i:615235 original size:38 final size:38
Alignment explanation
Indices: 615184--615257 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
615174 TACTAATTGG
615184 GGTCTAGTTTGTATATGTTTGTGCAAACATGTTTATTT
1 GGTCTAGTTTGTATATGTTTGTGCAAACATGTTTATTT
615222 GGTCTAGTTTGTATATGTTTGTGCAAACATGTTTAT
1 GGTCTAGTTTGTATATGTTTGTGCAAACATGTTTAT
615258 CTAACATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (38 bp):
GGTCTAGTTTGTATATGTTTGTGCAAACATGTTTATTT
Found at i:615383 original size:19 final size:20
Alignment explanation
Indices: 615340--615393 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
615330 TTTCATCCTA
615340 TTTTTAAAAT-TTCTTATCAT
1 TTTTTAAAATATT-TTATCAT
615360 TTTTTAAAATATTTTATC-T
1 TTTTTAAAATATTTTATCAT
**
615379 TTTTTGTAATATTTT
1 TTTTTAAAATATTTT
615394 GTACGTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 14 0.45
20 15 0.48
21 2 0.06
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTAAAATATTTTATCAT
Found at i:616272 original size:22 final size:20
Alignment explanation
Indices: 616228--616272 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
616218 TCGAAATTTA
*
616228 ATTTAAAATTTAATTTTATT
1 ATTTAAAATTTAATTTTAAT
*
616248 ATTTAAAATATGTTATTTTAAT
1 ATTTAAAAT-T-TAATTTTAAT
616270 ATT
1 ATT
616273 GATTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 1 0.05
22 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTAAAATTTAATTTTAAT
Found at i:624622 original size:24 final size:25
Alignment explanation
Indices: 624595--624658 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
624585 TAAATAAGCG
624595 CACATTAACGAATATAAATGAAC-A
1 CACATTAACGAATATAAATGAACGA
*
624619 CACATTAACGAACATAAATGAACGA
1 CACATTAACGAATATAAATGAACGA
* *
624644 -ACATAAATGAATATA
1 CACATTAACGAATATA
624659 TTACCAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (25 bp):
CACATTAACGAATATAAATGAACGA
Found at i:624642 original size:14 final size:14
Alignment explanation
Indices: 624625--624654 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
624615 AACACACATT
624625 AACGAACATAAATG
1 AACGAACATAAATG
624639 AACGAACATAAATG
1 AACGAACATAAATG
624653 AA
1 AA
624655 TATATTACCA
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:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:626525 original size:32 final size:30
Alignment explanation
Indices: 626483--626545 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
626473 GGATATCAAC
* *
626483 ATAAATTATAAGTTAATCATAGAAAATGAGAT
1 ATAAAATATAA-TTAATCATAAAAAAT-AGAT
*
626515 ATAAAATATAATTAATTATAAAAAATAGAT
1 ATAAAATATAATTAATCATAAAAAATAGAT
626545 A
1 A
626546 ATATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 13 0.46
32 10 0.36
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (30 bp):
ATAAAATATAATTAATCATAAAAAATAGAT
Found at i:631227 original size:22 final size:22
Alignment explanation
Indices: 631202--631243 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
631192 AGCATCTTCG
631202 TTAAATATTAACGATCAATGGT
1 TTAAATATTAACGATCAATGGT
631224 TTAAATATTAACGATCAATG
1 TTAAATATTAACGATCAATG
631244 ATTTGATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTAAATATTAACGATCAATGGT
Found at i:642446 original size:79 final size:80
Alignment explanation
Indices: 642338--642495 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
642328 TACTATTTTT
* * *
642338 TTTAACATTTTCGGTAAAACGCTATCTAAAACATTA-TTTTTTCTACAGGAAATGTTAATATTGG
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTTCTACAGGAAATATTAATATTGG
642402 GCACTACCTAAAATA
66 GCACTACCTAAAATA
* *
642417 TTTAACATTTCCGGTAAAACTCTACCTAAAACATTATTTTTTTCTACCGGAAATATTAATATTGG
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTTCTACAGGAAATATTAATATTGG
*
642482 GCGCTACCTAAAAT
66 GCACTACCTAAAAT
642496 GTTATTTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 33 0.46
80 39 0.54
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (80 bp):
TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTTCTACAGGAAATATTAATATTGG
GCACTACCTAAAATA
Found at i:642558 original size:20 final size:21
Alignment explanation
Indices: 642517--642564 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
642507 CTACAGGAAA
*
642517 TTAGGTAACAAAATTAACATT
1 TTAGGTAACAAAAATAACATT
*
642538 TTAGGTAA-AAAAATAATATT
1 TTAGGTAACAAAAATAACATT
642558 TTAGGTA
1 TTAGGTA
642565 GCGCTTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (21 bp):
TTAGGTAACAAAAATAACATT
Found at i:643116 original size:21 final size:22
Alignment explanation
Indices: 643077--643118 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
643067 TTTATATTAT
*
643077 AAGAAATTAAATTATATTTAAC
1 AAGAAATTAAAGTATATTTAAC
*
643099 AAGAATTTAAAGTA-ATTTAA
1 AAGAAATTAAAGTATATTTAA
643119 TTTGTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
AAGAAATTAAAGTATATTTAAC
Found at i:651194 original size:31 final size:31
Alignment explanation
Indices: 651151--651225 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
651141 TTAAAACTTA
* * * *
651151 CAATAT-AGTCCCCTAACATTTATTCTATTTT
1 CAATATGA-TCCCCCAACATTTAGTCCATTTG
651182 CAATATGATCCCCCAACATTTAGTCCATTTG
1 CAATATGATCCCCCAACATTTAGTCCATTTG
*
651213 CAATATGGTCCCC
1 CAATATGATCCCC
651226 GATGTAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (31 bp):
CAATATGATCCCCCAACATTTAGTCCATTTG
Found at i:651320 original size:29 final size:29
Alignment explanation
Indices: 651261--651320 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
651251 GCAAACGGAC
* * * *
651261 TAAATGTTGGGGGACCATATTGCAAGTTT
1 TAAAAGTTGGGGGACCATAATGAAAGCTT
651290 TAAAAGTTGGGGGACC-TAAATGAAAGCTT
1 TAAAAGTTGGGGGACCAT-AATGAAAGCTT
651319 TA
1 TA
651321 GAAAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (29 bp):
TAAAAGTTGGGGGACCATAATGAAAGCTT
Found at i:651448 original size:13 final size:13
Alignment explanation
Indices: 651417--651441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
651407 TAAAGCATAT
651417 TATATATATATAA
1 TATATATATATAA
651430 TATATATATATA
1 TATATATATATA
651442 CATTATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:655612 original size:2 final size:2
Alignment explanation
Indices: 655605--655642 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
655595 TTAAATTAGA
655605 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
655643 TAAAGAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:657157 original size:4 final size:4
Alignment explanation
Indices: 657150--657177 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
657140 TTTGGTTTTT
657150 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
657178 AGGGTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:672032 original size:90 final size:90
Alignment explanation
Indices: 671842--672037 Score: 211
Period size: 90 Copynumber: 2.2 Consensus size: 90
671832 TTTGACTCTG
* * * * *
671842 AGTTTTTATGCTTACCAAGCCAACCTAAAATGTTATATATACCGGTAAAAATTTTAGGTTGAAAA
1 AGTTTTGATGCTTATCAAGCCAACCTAAAATATTATATATACCGGTAAAAATTTTAGGCTCAAAA
671907 AATAAATATCAAAGCTCAGAGAATA
66 AATAAATATCAAAGCTCAGAGAATA
* * * * *
671932 AATTTCGATGCTTATCAATCCAACCTAAAATATTATATATATCGGT-AACATTTTAGGCTCAAAA
1 AGTTTTGATGCTTATCAAGCCAACCTAAAATATTATATATACCGGTAAAAATTTTAGGCTCAAAA
** *
671996 TGGTAAGTATCGAAA-CT-ATGAGCAA-A
66 -AATAAATATC-AAAGCTCA-GAG-AATA
672022 AGTTTTGATGCTTATC
1 AGTTTTGATGCTTATC
672038 GTGAAATATA
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
89 16 0.18
90 66 0.76
91 5 0.06
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (90 bp):
AGTTTTGATGCTTATCAAGCCAACCTAAAATATTATATATACCGGTAAAAATTTTAGGCTCAAAA
AATAAATATCAAAGCTCAGAGAATA
Found at i:672178 original size:38 final size:39
Alignment explanation
Indices: 672095--672178 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
672085 TATTTTTTAA
672095 CTAAAATGTTATATATTTAGAAACATTTCTAGTTGTAAC
1 CTAAAATGTTATATATTTAGAAACATTTCTAGTTGTAAC
* *
672134 CTAAAATGTTATATAATTT-GAAACATTTTTA-TTGTAGC
1 CTAAAATGTTATAT-ATTTAGAAACATTTCTAGTTGTAAC
672172 CTAAAAT
1 CTAAAAT
672179 ATTTTTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
38 13 0.31
39 25 0.60
40 4 0.10
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (39 bp):
CTAAAATGTTATATATTTAGAAACATTTCTAGTTGTAAC
Found at i:677909 original size:29 final size:30
Alignment explanation
Indices: 677867--677934 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
677857 CCATTCTAAA
*
677867 TTAATCCTCGAAAC-TTTTAAACATTTCAAT
1 TTAATCC-CCAAACATTTTAAACATTTCAAT
* *
677897 TTAATCCCCAAACATTTTGAACGTTTCAAT
1 TTAATCCCCAAACATTTTAAACATTTCAAT
*
677927 TTTATCCC
1 TTAATCCC
677935 AAATTATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAATCCCCAAACATTTTAAACATTTCAAT
Found at i:681624 original size:63 final size:63
Alignment explanation
Indices: 681545--681670 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
681535 GACGAAAGAC
* * *
681545 GAGGATTGTTATAGAGGAAAGAGGATGAGAAATTTGGGGTTTTATCCAAATTGTTGATCAGTT
1 GAGGATTGCTATAGAGGAAAGAGGACGAGAAATTTGGGGTTTTATCCAAATTGTTGATAAGTT
681608 GAGGATTGCTATAGAGGAAAGAGGACGAGAAATTTGGGGTTTTATCCAAATTGTTGATAAGTT
1 GAGGATTGCTATAGAGGAAAGAGGACGAGAAATTTGGGGTTTTATCCAAATTGTTGATAAGTT
681671 ATTTTGAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.32
Consensus pattern (63 bp):
GAGGATTGCTATAGAGGAAAGAGGACGAGAAATTTGGGGTTTTATCCAAATTGTTGATAAGTT
Found at i:691367 original size:21 final size:21
Alignment explanation
Indices: 691330--691369 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
691320 GATTCTACTG
*
691330 AAAACAACGAAATTGAGATAA
1 AAAACAACGAAACTGAGATAA
691351 AAAACAAC-AGAACTGAGAT
1 AAAACAACGA-AACTGAGAT
691370 TAACTTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.60, C:0.12, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAACAACGAAACTGAGATAA
Found at i:692382 original size:20 final size:20
Alignment explanation
Indices: 692344--692382 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
692334 AGTAAGATTC
* *
692344 GTGTTGCGAATTATAAATTT
1 GTGTCGCGAATTAGAAATTT
*
692364 GTGTCGCGAATTAGGAATT
1 GTGTCGCGAATTAGAAATT
692383 AGCGAATTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (20 bp):
GTGTCGCGAATTAGAAATTT
Found at i:692988 original size:14 final size:15
Alignment explanation
Indices: 692971--693008 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
692961 ATTTATAATT
692971 AAATTTAAAT-AAAA
1 AAATTTAAATCAAAA
*
692985 AAA-TTAACTCAAAA
1 AAATTTAAATCAAAA
692999 AAATTTAAAT
1 AAATTTAAAT
693009 TATAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTTAAATCAAAA
Found at i:694114 original size:13 final size:13
Alignment explanation
Indices: 694080--694106 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
694070 CACGGGATCT
694080 AAATAATGAATAA
1 AAATAATGAATAA
694093 AAATAATGAATAA
1 AAATAATGAATAA
694106 A
1 A
694107 CTATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AAATAATGAATAA
Found at i:694803 original size:130 final size:130
Alignment explanation
Indices: 694585--694839 Score: 483
Period size: 130 Copynumber: 2.0 Consensus size: 130
694575 TTACTTACTC
694585 AACTTTACTCTCTCTCCTATTACACTCATCGTACTTTCAGTTTTTTCAATTTGCTCACTAAACTT
1 AACTTTACTCTCTCTCCTATTACACTCATCGTACTTTCAGTTTTTTCAATTTGCTCACTAAACTT
694650 TAAACATTAAATTTTTTTGATCACTCGATCATTAATTTTATAACATCGTTATGACATGGTCATTG
66 TAAACATTAAATTTTTTTGATCACTCGATCATTAATTTTATAACATCGTTATGACATGGTCATTG
694715 AACTTTACTCTCTCTCCTATTACACTCATCGTACTTTCAGTTTTTTCAATTTGCTCACTAAACTT
1 AACTTTACTCTCTCTCCTATTACACTCATCGTACTTTCAGTTTTTTCAATTTGCTCACTAAACTT
* * *
694780 TAGATATTAAATTTTTTTTATCACTCGATCATTAATTTTATAACATCGTTATGACATGGT
66 TAAACATTAAATTTTTTTGATCACTCGATCATTAATTTTATAACATCGTTATGACATGGT
694840 TTATTTTAAT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 122 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (130 bp):
AACTTTACTCTCTCTCCTATTACACTCATCGTACTTTCAGTTTTTTCAATTTGCTCACTAAACTT
TAAACATTAAATTTTTTTGATCACTCGATCATTAATTTTATAACATCGTTATGACATGGTCATTG
Done.