Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015179.1 Kokia drynarioides strain JFW-HI SEQ_130223, 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: 658618
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 95 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:404368 original size:24 final size:24
Alignment explanation
Indices: 404338--404550 Score: 295
Period size: 24 Copynumber: 8.9 Consensus size: 24
404328 CGTTATTCTA
* *
404338 ATTCTGGGCTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
*
404362 ATTCTGGGCTTGTAGGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
* *
404386 ATTCTGGGTTTGTAGGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
*
404410 ATTCTGGGCTTGTAGGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
* *
404434 ATTCTGGGCTTGTAAGAGC-AACC
1 ATTCTGGGCTCGTAGGAGCTAACC
*
404457 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
* *
404481 GTTATGGGCTCGTAGGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
*
404505 GTTCTGGGCTCGTAGGAGCTAACC
1 ATTCTGGGCTCGTAGGAGCTAACC
404529 ATTCTGGGCTCGTATGG-GCTAA
1 ATTCTGGGCTCGTA-GGAGCTAA
404551 ATATTGTCTA
Statistics
Matches: 175, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
23 22 0.13
24 151 0.86
25 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (24 bp):
ATTCTGGGCTCGTAGGAGCTAACC
Found at i:404478 original size:95 final size:96
Alignment explanation
Indices: 404338--404539 Score: 307
Period size: 95 Copynumber: 2.1 Consensus size: 96
404328 CGTTATTCTA
* * * * *
404338 ATTCTGGGCTCATAAGAGCTAACCATTCTGGGCTTGTAGGAGCTAACCATTCTGGGTTTGTAGGA
1 ATTCTGGGCTCATAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAACCATTATGGGCTCGTAGGA
*
404403 GCTAACCATTCTGGGCTTGTAGGAGCTAACC
66 GCTAACCATTCTGGGCTCGTAGGAGCTAACC
** *
404434 ATTCTGGGCTTGTAAGAGC-AACCATTCTGGGCTCGTAAGAGCTAACCGTTATGGGCTCGTAGGA
1 ATTCTGGGCTCATAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAACCATTATGGGCTCGTAGGA
*
404498 GCTAACCGTTCTGGGCTCGTAGGAGCTAACC
66 GCTAACCATTCTGGGCTCGTAGGAGCTAACC
404529 ATTCTGGGCTC
1 ATTCTGGGCTC
404540 GTATGGGCTA
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 78 0.82
96 17 0.18
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (96 bp):
ATTCTGGGCTCATAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAACCATTATGGGCTCGTAGGA
GCTAACCATTCTGGGCTCGTAGGAGCTAACC
Found at i:406887 original size:18 final size:19
Alignment explanation
Indices: 406859--406902 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
406849 TCTTGTTTAT
*
406859 TTGTTTTATT-AATTTATAA
1 TTGTATTATTAAATTTA-AA
406878 TT-TATTATTAAATTTAAA
1 TTGTATTATTAAATTTAAA
406896 TTGTATT
1 TTGTATT
406903 TATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTGTATTATTAAATTTAAA
Found at i:407607 original size:17 final size:17
Alignment explanation
Indices: 407587--407619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
407577 TTTTTTCATT
*
407587 TTTTATTTTTATTAATA
1 TTTTATTTTAATTAATA
407604 TTTTATTTTAATTAAT
1 TTTTATTTTAATTAAT
407620 TTAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTTAATTAATA
Found at i:408201 original size:10 final size:10
Alignment explanation
Indices: 408188--408248 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
408178 ATTATTTAAA
408188 ATTTAAATTT
1 ATTTAAATTT
* *
408198 ATTTGATCATTA
1 ATTT-A-AATTT
*
408210 AATTAAATTT
1 ATTTAAATTT
*
408220 ATTTTAATTT
1 ATTTAAATTT
*
408230 ATTTTAATTT
1 ATTTAAATTT
408240 ATTTTAAAT
1 A-TTTAAAT
408249 CATTTCACAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
10 26 0.65
11 8 0.20
12 6 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:408253 original size:10 final size:10
Alignment explanation
Indices: 408215--408246 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
408205 CATTAAATTA
408215 AATTTATTTT
1 AATTTATTTT
408225 AATTTATTTT
1 AATTTATTTT
408235 AATTTATTTT
1 AATTTATTTT
408245 AA
1 AA
408247 ATCATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTTATTTT
Found at i:408253 original size:20 final size:20
Alignment explanation
Indices: 408215--408253 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
408205 CATTAAATTA
* *
408215 AATTTATTTTAATTTATTTT
1 AATTTATTTTAAATCATTTT
408235 AATTTATTTTAAATCATTT
1 AATTTATTTTAAATCATTT
408254 CACAATCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTATTTTAAATCATTTT
Found at i:408451 original size:19 final size:22
Alignment explanation
Indices: 408397--408451 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 22
408387 CTTCCATTAG
*
408397 ATTTTAATAATATTCATAATGT
1 ATTTTAATAATATTCATAATGC
* **
408419 ATTTTTATGTTATT-A-AAT-C
1 ATTTTAATAATATTCATAATGC
408438 ATTTTAATAATATT
1 ATTTTAATAATATT
408452 TCTTTTTTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 1 0.04
22 11 0.42
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTTAATAATATTCATAATGC
Found at i:409006 original size:24 final size:24
Alignment explanation
Indices: 408974--409019 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
408964 TATTTGTTTC
*
408974 TTATTTGTTTCAATTAAACTCTAT
1 TTATTTGTTTCAATCAAACTCTAT
*
408998 TTATTTGTTTCAGTCAAACTCT
1 TTATTTGTTTCAATCAAACTCT
409020 TATTAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (24 bp):
TTATTTGTTTCAATCAAACTCTAT
Found at i:416636 original size:26 final size:26
Alignment explanation
Indices: 416593--416686 Score: 86
Period size: 26 Copynumber: 3.6 Consensus size: 26
416583 GACATGCTTA
* *
416593 TACAGCTACAACTCTGAACATA-TTCAC
1 TACAGCGACAATTCTGAACA-AGTTC-C
* *
416620 -ACAGCGATAATTTTGAACAAGTTCC
1 TACAGCGACAATTCTGAACAAGTTCC
*
416645 TACAGCGACAATTCTGAACAAGTTCT
1 TACAGCGACAATTCTGAACAAGTTCC
*
416671 TGCAG-GAACAATTCTG
1 TACAGCG-ACAATTCTG
416687 GGCGCAATGC
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
25 3 0.05
26 53 0.95
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (26 bp):
TACAGCGACAATTCTGAACAAGTTCC
Found at i:417124 original size:17 final size:17
Alignment explanation
Indices: 417104--417137 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
417094 TTTAAGGACT
417104 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
417121 TTTTATTTTAGTTTAAG
1 TTTTATTTTAGTTTAAG
417138 AAGTGTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:417398 original size:50 final size:50
Alignment explanation
Indices: 417331--417452 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 50
417321 TTACATCCAT
* * *
417331 TAACTCTCATGATTAGTTAAGTTTGCAGCATAAATAATGA-CATGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCAGCATAAATAAT-ATCATGCATTAAG
* * * ** *
417382 TAACTTACATGTTAGTTAAATATGCATCATTAATCCTATCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCAGCATAAATAATATCATGCATTAAG
*
417432 TAACTCCCATGTTAGTTAAAT
1 TAACTCACATGTTAGTTAAAT
417453 GCATCATTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.02
50 49 0.83
51 9 0.15
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCAGCATAAATAATATCATGCATTAAG
Found at i:419378 original size:17 final size:17
Alignment explanation
Indices: 419345--419389 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
419335 CATTAAATTA
*
419345 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
419363 CAATGACAATGCAAATG
1 CAATGACAATGCAAATG
*
419380 CAGTGACAAT
1 CAATGACAAT
419390 TAGAATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:427119 original size:51 final size:51
Alignment explanation
Indices: 427036--427278 Score: 339
Period size: 51 Copynumber: 4.8 Consensus size: 51
427026 GAGCTAACGA
*
427036 AAAGGTCTGATGACTAAGTGTC-ATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCAAT-GTGAGTAAATGAATCCTTTACGGATT
* *
427087 AAAGGTCCGATGACTAAGTGTCAATGTAAGTAAATGAATCCTTTACGAATT
1 AAAGGTCCGATGACTAAGTGTCAATGTGAGTAAATGAATCCTTTACGGATT
** *
427138 AAAGGTTTGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCAATGTGAGTAAATGAATCCTTTACGGATT
* * *
427189 AAAGGTCCGATGACTAAGAGTC-ATCATGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCAAT-GTGAGTAAATGAATCCTTTACGGATT
* *
427240 AAAGGTTCGATGACTAAGTGTC-ATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCAAT-GTGAGTAAATGAAT
427279 TCCTATATAG
Statistics
Matches: 172, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
50 1 0.01
51 169 0.98
52 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCAATGTGAGTAAATGAATCCTTTACGGATT
Found at i:427160 original size:102 final size:101
Alignment explanation
Indices: 427036--427278 Score: 389
Period size: 102 Copynumber: 2.4 Consensus size: 101
427026 GAGCTAACGA
*
427036 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
1 AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
*
427101 TAAGTGTCA-ATGTAAGTAAATGAATCCTTTACGAATT
66 TAAGAGTCACATG--AGTAAATGAATCCTTTACGAATT
*
427138 AAAGGTTTGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
1 AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
* *
427203 TAAGAGTCATCATGAGTAAATGAATCCTTTATGGATT
66 TAAGAGTCA-CATGAGTAAATGAATCCTTTACGAATT
* *
427240 AAAGGTTCGATGACTAAGTGTCATCGTGAGTATATGAAT
1 AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAAT
427279 TCCTATATAG
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
102 128 0.98
104 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (101 bp):
AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
TAAGAGTCACATGAGTAAATGAATCCTTTACGAATT
Found at i:428071 original size:21 final size:22
Alignment explanation
Indices: 428044--428103 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
428034 TAGATGTATG
*
428044 ACATGTATCGGTAGAAATTA-T
1 ACATGTACCGGTAGAAATTAGT
* *
428065 ACTTGTACCGATAG-AATTAGT
1 ACATGTACCGGTAGAAATTAGT
*
428086 ACAGGTACCGGTAGAAAT
1 ACATGTACCGGTAGAAAT
428104 CTGCACCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.74
22 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (22 bp):
ACATGTACCGGTAGAAATTAGT
Found at i:430932 original size:26 final size:26
Alignment explanation
Indices: 430877--430932 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
430867 ACACAGCGAT
* *
430877 AATTTTGAACAAGTTCCTGCAACGAT
1 AATTTTGAACAAGTTCCTGCAACAAC
** *
430903 AATTTTGAACAAGTTTTTGCAGCAAC
1 AATTTTGAACAAGTTCCTGCAACAAC
430929 AATT
1 AATT
430933 CTGGGCGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (26 bp):
AATTTTGAACAAGTTCCTGCAACAAC
Found at i:434730 original size:11 final size:11
Alignment explanation
Indices: 434699--434723 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
434689 AAATAGAGGT
434699 TTTTATTTTTC
1 TTTTATTTTTC
434710 TTTTATTTTTC
1 TTTTATTTTTC
434721 TTT
1 TTT
434724 CTTTTTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:434795 original size:3 final size:3
Alignment explanation
Indices: 434769--434821 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
434759 ATCATCATCA
* *
434769 TTC TTA TTC TTA TTC -TC ATTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
434814 TTC TTC TT
1 TTC TTC TT
434822 ATTATTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:434826 original size:3 final size:3
Alignment explanation
Indices: 434820--434882 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
434810 CTTCTTCTTC
434820 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
434868 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
434883 GGGTTTCATG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:435518 original size:115 final size:115
Alignment explanation
Indices: 435293--435504 Score: 297
Period size: 115 Copynumber: 1.8 Consensus size: 115
435283 TTTTAAAATA
* *
435293 AAAGTTTTGATTTTAGAGTAAAATAGTGATTTTCTTTAAAAATAGAAAGTTTATATTTTTAAAAA
1 AAAGTTTGGATTTTAGAGTAAAATAGTGATTTTCTTTAAAAAGAGAAAGTTTATATTTTTAAAAA
* * * *
435358 TAAAAATATGTTTTTTAGTTATTTTAAAGAAAATATTTAAATTTTTAAAC
66 TAAAAATATGCTATTTAATGATTTTAAAGAAAATATTTAAATTTTTAAAC
435408 AAAGTTTGGATTTTTA-AGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTATATTTTTAA
1 AAAGTTTGGA-TTTTAGAGTAAAATAGTGATTTTCTTT--AAAAAGAGAAAGTTTATATTTTTAA
*
435472 AAA-ATAAACT-T-CTATTTAATGATTTTAAAGAAA
63 AAATA-AAAATATGCTATTTAATGATTTTAAAGAAA
435505 GTTTTGATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
115 48 0.56
116 7 0.08
117 31 0.36
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (115 bp):
AAAGTTTGGATTTTAGAGTAAAATAGTGATTTTCTTTAAAAAGAGAAAGTTTATATTTTTAAAAA
TAAAAATATGCTATTTAATGATTTTAAAGAAAATATTTAAATTTTTAAAC
Found at i:437409 original size:21 final size:21
Alignment explanation
Indices: 437383--437462 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
437373 GCCTAGAGCT
437383 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGTTTGAAAAAC
** * **
437404 ATTTTGAAGTGTTAGAATGAC
1 ATTTTGACTTGTTTGAAAAAC
*
437425 --TTTGACTTGTTT-AAAATC
1 ATTTTGACTTGTTTGAAAAAC
* *
437443 ATTTTAACTTGATTTTAAAA
1 ATTTTGACTTG-TTTGAAAA
437463 TTGTTTCAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
18 3 0.07
19 9 0.21
20 8 0.19
21 19 0.44
22 4 0.09
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (21 bp):
ATTTTGACTTGTTTGAAAAAC
Found at i:438024 original size:30 final size:29
Alignment explanation
Indices: 437990--438046 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
437980 GTAAAAGAGT
437990 AAAAGGTGAAGGATTAAATTATAAATATTC
1 AAAAGGTGAAGGATTAAATTA-AAATATTC
* * *
438020 AAAAGTTGAGGGGTTAAATTAAAATAT
1 AAAAGGTGAAGGATTAAATTAAAATAT
438047 GAAAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (29 bp):
AAAAGGTGAAGGATTAAATTAAAATATTC
Found at i:438373 original size:3 final size:3
Alignment explanation
Indices: 438365--438402 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
438355 ATGTTGGGAT
* *
438365 TTA TTA TTA TTA TTA TTA TTA TT- TTA ATA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
438403 AAGGAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:440475 original size:75 final size:75
Alignment explanation
Indices: 440389--440678 Score: 334
Period size: 75 Copynumber: 3.9 Consensus size: 75
440379 TAGAAATTAA
* * * *
440389 AATTGAATAATTTTGTTTC-GAGATTTATTCATGTCGTTCAACAGAATTCATTCGATTTTTTTCT
1 AATTAAATAATTCTGTTTCAG-GATTTATTCATGTCGTTCAACAGAATTTATTCGATTTTTTTCA
*
440453 AGACAAGAATT
65 AAACAAGAATT
* * * * * *
440464 AATTAAATAATTTTGTTTCAAGATTTATTCCTGCCATTCAATAGAATTTATT-GTATTTTTTTCA
1 AATTAAATAATTCTGTTTCAGGATTTATTCATGTCGTTCAACAGAATTTATTCG-ATTTTTTTCA
*
440528 AAATAAGAATT
65 AAACAAGAATT
* * * *
440539 AATTAAATAATTCTGTTTTAGGATTTATTCATATCGTTCAACAGAATTTATTCTATTTTTTTCCA
1 AATTAAATAATTCTGTTTCAGGATTTATTCATGTCGTTCAACAGAATTTATTCGATTTTTTTCAA
440604 AACAAGAATT
66 AACAAGAATT
* * * * *
440614 AATTAAATAATTCTGTTTCAGGATTTATTCCT-ACTGTTCAACAGAACTGATTTTGATTTTTTTC
1 AATTAAATAATTCTGTTTCAGGATTTATTCATGTC-GTTCAACAGAATTTA-TTCGATTTTTTTC
440678 A
64 A
440679 GAATTTTAAT
Statistics
Matches: 181, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
74 2 0.01
75 168 0.93
76 11 0.06
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.46
Consensus pattern (75 bp):
AATTAAATAATTCTGTTTCAGGATTTATTCATGTCGTTCAACAGAATTTATTCGATTTTTTTCAA
AACAAGAATT
Found at i:452087 original size:49 final size:48
Alignment explanation
Indices: 452034--452183 Score: 192
Period size: 49 Copynumber: 3.1 Consensus size: 48
452024 AGCTTTTTCG
452034 AGCCTAGATAGAATTAGCTCTTACGAGCCTAGATAAGTTAGCTCTTACA
1 AGCCTAGATAG-ATTAGCTCTTACGAGCCTAGATAAGTTAGCTCTTACA
* * * *
452083 AGCCTAGATAGGTTAGCTGTAACGAGCCTAGATAAAATTAGCTCTTACA
1 AGCCTAGATAGATTAGCTCTTACGAGCCTAGAT-AAGTTAGCTCTTACA
* * * * * *
452132 AGCCTAGATAGGTAAGCTCTTACAAGCCCAGATAAGTTAGCTTTTACG
1 AGCCTAGATAGATTAGCTCTTACGAGCCTAGATAAGTTAGCTCTTACA
452180 AGCC
1 AGCC
452184 CAAATAGAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
48 35 0.40
49 53 0.60
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (48 bp):
AGCCTAGATAGATTAGCTCTTACGAGCCTAGATAAGTTAGCTCTTACA
Found at i:452141 original size:73 final size:73
Alignment explanation
Indices: 452032--452183 Score: 232
Period size: 73 Copynumber: 2.1 Consensus size: 73
452022 TTAGCTTTTT
* * * * *
452032 CGAGCCTAGATAGAATTAGCTCTTACGAGCCTAGATAAGTTAGCTCTTACAAGCCTAGATAGGTT
1 CGAGCCTAGATAAAATTAGCTCTTACAAGCCTAGATAAGTAAGCTCTTACAAGCCCAGATAAGTT
452097 AGCTGTAA
66 AGCTGTAA
*
452105 CGAGCCTAGATAAAATTAGCTCTTACAAGCCTAGATAGGTAAGCTCTTACAAGCCCAGATAAGTT
1 CGAGCCTAGATAAAATTAGCTCTTACAAGCCTAGATAAGTAAGCTCTTACAAGCCCAGATAAGTT
* *
452170 AGCTTTTA
66 AGCTGTAA
452178 CGAGCC
1 CGAGCC
452184 CAAATAGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (73 bp):
CGAGCCTAGATAAAATTAGCTCTTACAAGCCTAGATAAGTAAGCTCTTACAAGCCCAGATAAGTT
AGCTGTAA
Found at i:452185 original size:24 final size:24
Alignment explanation
Indices: 452022--452183 Score: 180
Period size: 24 Copynumber: 6.7 Consensus size: 24
452012 CTCCAAATAT
* * *
452022 TTAGCTTTTTCGAGCCTAGATAGAA
1 TTAGCTCTTACGAGCCTAGATA-AG
452047 TTAGCTCTTACGAGCCTAGATAAG
1 TTAGCTCTTACGAGCCTAGATAAG
* *
452071 TTAGCTCTTACAAGCCTAGATAGG
1 TTAGCTCTTACGAGCCTAGATAAG
* * *
452095 TTAGCTGTAACGAGCCTAGATAAAA
1 TTAGCTCTTACGAGCCTAGAT-AAG
* *
452120 TTAGCTCTTACAAGCCTAGATAGG
1 TTAGCTCTTACGAGCCTAGATAAG
* * *
452144 TAAGCTCTTACAAGCCCAGATAAG
1 TTAGCTCTTACGAGCCTAGATAAG
*
452168 TTAGCTTTTACGAGCC
1 TTAGCTCTTACGAGCC
452184 CAAATAGAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
24 76 0.66
25 39 0.34
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCTAGATAAG
Found at i:456073 original size:18 final size:19
Alignment explanation
Indices: 456050--456088 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
456040 TCATTTGTTT
456050 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTGTA
456068 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
456087 TT
1 TT
456089 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:461772 original size:37 final size:37
Alignment explanation
Indices: 461717--461794 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
461707 CCTTTGCTTA
* *
461717 CTTTGTTTTGTACGGGTGCCTTTGGATATCAAATATT
1 CTTTGTTTTGTAAGGGTGCCTTTGAATATCAAATATT
*
461754 CTTTGTTTTGTAATGGTGCCTTTGAATATCAAATATT
1 CTTTGTTTTGTAAGGGTGCCTTTGAATATCAAATATT
461791 CTTT
1 CTTT
461795 AAGTCTGGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (37 bp):
CTTTGTTTTGTAAGGGTGCCTTTGAATATCAAATATT
Found at i:470610 original size:29 final size:30
Alignment explanation
Indices: 470567--470869 Score: 186
Period size: 30 Copynumber: 10.1 Consensus size: 30
470557 TTGTTTTTTG
* * *
470567 ACCCTTAAATTTTTCAAAAATTCAAATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
*
470597 ACACCC-AAACTTTCCAAAAATTCAAATTTG
1 AC-CCCTAAACTTTCCAAAAATTCAAATTTA
** * *
470627 ACCCCTAAACTTTTTAGAAAA-TCTAATTTG
1 ACCCCTAAACTTTCCA-AAAATTCAAATTTA
** ** **
470657 ACCTTTAAACTTTATAAAAATTTGAATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* ** * ** *
470687 ACCCTTAAACTTTTTAGAAATTTGAATTTG
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* * *
470717 A-CCCTCGAAC-TTCCAAAAATACAAATTTG
1 ACCCCT-AAACTTTCCAAAAATTCAAATTTA
* *
470746 A-CCCTTAACTTTCCAAAAAATTCAAATTTG
1 ACCCCTAAACTTTCC-AAAAATTCAAATTTA
* * *
470776 ACCCCTGAACTTTCCAAAAATGT-GAATTTG
1 ACCCCTAAACTTTCCAAAAAT-TCAAATTTA
* * * **
470806 ACCCTTGAATTTTCCAAAAATTCCGATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* * *
470836 ACCCCTAAAGTTTCCATAAATTCAAATTTG
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
470866 ACCC
1 ACCC
470870 AATTTTAATG
Statistics
Matches: 222, Mismatches: 41, Indels: 20
0.78 0.14 0.07
Matches are distributed among these distances:
28 3 0.01
29 33 0.15
30 167 0.75
31 19 0.09
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34
Consensus pattern (30 bp):
ACCCCTAAACTTTCCAAAAATTCAAATTTA
Found at i:470627 original size:60 final size:59
Alignment explanation
Indices: 470563--470869 Score: 248
Period size: 60 Copynumber: 5.1 Consensus size: 59
470553 AAAATTGTTT
*
470563 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTAACACCCAAACTTTCCAAAAATTCAAA
1 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGAC-CCCAAACTTTCCAAAAATTCAAA
* * ** ** **
470623 TTTGACCCCTAAACTTTTT-AGAAAA-TCTAATTTGACCTTTAAACTTTATAAAAATTTGAA
1 TTTGACCCTTAAA-TTTTTCA-AAAATTCAAATTTGACC-CCAAACTTTCCAAAAATTCAAA
* * ** * *
470683 TTTAACCCTTAAACTTTTT-AGAAATTTGAATTTGACCCTCGAAC-TTCCAAAAATACAAA
1 TTTGACCCTTAAA-TTTTTCAAAAATTCAAATTTGACCC-CAAACTTTCCAAAAATTCAAA
* * * *
470742 TTTGACCCTT-AACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCAAAAATGT-GAA
1 TTTGACCCTTAAATTTTTC-AAAAATTCAAATTTGACCCC-AAACTTTCCAAAAAT-TCAAA
* * ** * * *
470802 TTTGACCCTTGAATTTTCCAAAAATTCCGATTTAACCCCTAAAGTTTCCATAAATTCAAA
1 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGACCCC-AAACTTTCCAAAAATTCAAA
470862 TTTGACCC
1 TTTGACCC
470870 AATTTTAATG
Statistics
Matches: 197, Mismatches: 38, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
57 3 0.02
58 3 0.02
59 44 0.22
60 131 0.66
61 16 0.08
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (59 bp):
TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGACCCCAAACTTTCCAAAAATTCAAA
Found at i:470788 original size:89 final size:90
Alignment explanation
Indices: 470563--470869 Score: 227
Period size: 90 Copynumber: 3.4 Consensus size: 90
470553 AAAATTGTTT
* * * *
470563 TTTGACCCTTAAATTTTTC-AAAAATTCAAATTTAACACCC-AAACTTTCCAAAAAT-TCAAATT
1 TTTGACCCTT-AACTTTCCAAAAAATTCAAATTTGAC-CCCTAAACTTTCCAAAAATGT-GAATT
* * ** *
470625 TGACCC-CTAAACTTTTTAGAAAAT-CTAA
63 TGACCCTCGAATC-TTCCA-AAAATACAAA
* ** * * ** * *
470653 TTTGACCTTTAAACTTT--ATAAAAATTTGAATTTAACCCTTAAACTTTTTAGAAATTTGAATTT
1 TTTGACCCTT-AACTTTCCA-AAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTT
470716 GACCCTCGAA-CTTCCAAAAATACAAA
64 GACCCTCGAATCTTCCAAAAATACAAA
*
470742 TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCAAAAATGTGAATTTGA
1 TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTTGA
* * * **
470807 CCCTTGAATTTTCCAAAAATTCCGA
66 CCCTCGAATCTTCCAAAAATACAAA
* * * *
470832 TTTAACCCCTAAAGTTTCC-ATAAATTCAAATTTGACCC
1 TTTGA-CCCTTAACTTTCCAAAAAATTCAAATTTGACCC
470870 AATTTTAATG
Statistics
Matches: 175, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
88 11 0.06
89 61 0.35
90 88 0.50
91 15 0.09
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (90 bp):
TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTTGA
CCCTCGAATCTTCCAAAAATACAAA
Found at i:470857 original size:149 final size:149
Alignment explanation
Indices: 470581--470869 Score: 341
Period size: 149 Copynumber: 1.9 Consensus size: 149
470571 TTAAATTTTT
* **
470581 CAAAAATTCAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTTTAGAA
1 CAAAAATACAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCCAGAA
* * * * ** **
470646 AATCTAATTTGACCTTTAAACTTTATAAAAATTTGAATTTAACCCTTAAACTTTTTAGAAATTTG
66 AATCTAATTTGACCCTTAAACTTTACAAAAATTCGAATTTAACCCCTAAACTTTCCAGAAATTCA
470711 AATTTGACCCTCGAACTTC
131 AATTTGACCCTCGAACTTC
* ** *
470730 CAAAAATACAAATTTGAC-CCTTAACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCA-A
1 CAAAAATACAAATTTAACACCCAAACTTTCC-AAAAATTCAAATTTGACCCCTAAACTTTCCAGA
* * * * * *
470793 AAATGTGAATTTGACCCTTGAATTTTCCAAAAATTCCG-ATTTAACCCCTAAAGTTTCCATAAAT
65 AAATCT-AATTTGACCCTTAAACTTTACAAAAATT-CGAATTTAACCCCTAAACTTTCCAGAAAT
470857 TCAAATTTGACCC
128 TCAAATTTGACCC
470870 AATTTTAATG
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
148 16 0.14
149 99 0.85
150 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (149 bp):
CAAAAATACAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCCAGAA
AATCTAATTTGACCCTTAAACTTTACAAAAATTCGAATTTAACCCCTAAACTTTCCAGAAATTCA
AATTTGACCCTCGAACTTC
Found at i:474385 original size:26 final size:25
Alignment explanation
Indices: 474356--474440 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
474346 ACATAGTACT
* *
474356 TGCTAAACATTCATCGGCTTAAAGCC
1 TGCTATACATTCA-CGGCTTAAGGCC
* * *
474382 TGCTATATATTCACGTGCTCAAGGTC
1 TGCTATACATTCACG-GCTTAAGGCC
*
474408 TGCTATACATTCACCAGCTTAAGGCC
1 TGCTATACATTCA-CGGCTTAAGGCC
474434 TGCTATA
1 TGCTATA
474441 TATATATTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
25 2 0.04
26 45 0.94
27 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (25 bp):
TGCTATACATTCACGGCTTAAGGCC
Found at i:477291 original size:59 final size:58
Alignment explanation
Indices: 477200--477312 Score: 208
Period size: 59 Copynumber: 1.9 Consensus size: 58
477190 TGCATTGATG
*
477200 TTATTTTGAATATTTTGTACACATTATTTTTATATTGTATGATTTAATAAAATAGAAA
1 TTATTTTGAATATTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAAA
477258 TTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATA
1 TTATTTTGAATA-TTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATA
477313 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 12 0.23
59 41 0.77
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (58 bp):
TTATTTTGAATATTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAAA
Found at i:482709 original size:29 final size:30
Alignment explanation
Indices: 482666--482968 Score: 186
Period size: 30 Copynumber: 10.1 Consensus size: 30
482656 TTGTTTTTTG
* * *
482666 ACCCTTAAATTTTTCAAAAATTCAAATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
*
482696 ACACCC-AAACTTTCCAAAAATTCAAATTTG
1 AC-CCCTAAACTTTCCAAAAATTCAAATTTA
** * *
482726 ACCCCTAAACTTTTTAGAAAA-TCTAATTTG
1 ACCCCTAAACTTTCCA-AAAATTCAAATTTA
** ** **
482756 ACCTTTAAACTTTATAAAAATTTGAATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* ** * ** *
482786 ACCCTTAAACTTTTTAGAAATTTGAATTTG
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* * *
482816 A-CCCTCGAAC-TTCCAAAAATACAAATTTG
1 ACCCCT-AAACTTTCCAAAAATTCAAATTTA
* *
482845 A-CCCTTAACTTTCCAAAAAATTCAAATTTG
1 ACCCCTAAACTTTCC-AAAAATTCAAATTTA
* * *
482875 ACCCCTGAACTTTCCAAAAATGT-GAATTTG
1 ACCCCTAAACTTTCCAAAAAT-TCAAATTTA
* * * **
482905 ACCCTTGAATTTTCCAAAAATTCCGATTTA
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
* * *
482935 ACCCCTAAAGTTTCCATAAATTCAAATTTG
1 ACCCCTAAACTTTCCAAAAATTCAAATTTA
482965 ACCC
1 ACCC
482969 AATTTTAATG
Statistics
Matches: 222, Mismatches: 41, Indels: 20
0.78 0.14 0.07
Matches are distributed among these distances:
28 3 0.01
29 33 0.15
30 167 0.75
31 19 0.09
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.34
Consensus pattern (30 bp):
ACCCCTAAACTTTCCAAAAATTCAAATTTA
Found at i:482726 original size:60 final size:59
Alignment explanation
Indices: 482662--482968 Score: 248
Period size: 60 Copynumber: 5.1 Consensus size: 59
482652 AAAATTGTTT
*
482662 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTAACACCCAAACTTTCCAAAAATTCAAA
1 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGAC-CCCAAACTTTCCAAAAATTCAAA
* * ** ** **
482722 TTTGACCCCTAAACTTTTT-AGAAAA-TCTAATTTGACCTTTAAACTTTATAAAAATTTGAA
1 TTTGACCCTTAAA-TTTTTCA-AAAATTCAAATTTGACC-CCAAACTTTCCAAAAATTCAAA
* * ** * *
482782 TTTAACCCTTAAACTTTTT-AGAAATTTGAATTTGACCCTCGAAC-TTCCAAAAATACAAA
1 TTTGACCCTTAAA-TTTTTCAAAAATTCAAATTTGACCC-CAAACTTTCCAAAAATTCAAA
* * * *
482841 TTTGACCCTT-AACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCAAAAATGT-GAA
1 TTTGACCCTTAAATTTTTC-AAAAATTCAAATTTGACCCC-AAACTTTCCAAAAAT-TCAAA
* * ** * * *
482901 TTTGACCCTTGAATTTTCCAAAAATTCCGATTTAACCCCTAAAGTTTCCATAAATTCAAA
1 TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGACCCC-AAACTTTCCAAAAATTCAAA
482961 TTTGACCC
1 TTTGACCC
482969 AATTTTAATG
Statistics
Matches: 197, Mismatches: 38, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
57 3 0.02
58 3 0.02
59 44 0.22
60 131 0.66
61 16 0.08
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (59 bp):
TTTGACCCTTAAATTTTTCAAAAATTCAAATTTGACCCCAAACTTTCCAAAAATTCAAA
Found at i:482887 original size:89 final size:90
Alignment explanation
Indices: 482662--482968 Score: 227
Period size: 90 Copynumber: 3.4 Consensus size: 90
482652 AAAATTGTTT
* * * *
482662 TTTGACCCTTAAATTTTTC-AAAAATTCAAATTTAACACCC-AAACTTTCCAAAAAT-TCAAATT
1 TTTGACCCTT-AACTTTCCAAAAAATTCAAATTTGAC-CCCTAAACTTTCCAAAAATGT-GAATT
* * ** *
482724 TGACCC-CTAAACTTTTTAGAAAAT-CTAA
63 TGACCCTCGAATC-TTCCA-AAAATACAAA
* ** * * ** * *
482752 TTTGACCTTTAAACTTT--ATAAAAATTTGAATTTAACCCTTAAACTTTTTAGAAATTTGAATTT
1 TTTGACCCTT-AACTTTCCA-AAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTT
482815 GACCCTCGAA-CTTCCAAAAATACAAA
64 GACCCTCGAATCTTCCAAAAATACAAA
*
482841 TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCAAAAATGTGAATTTGA
1 TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTTGA
* * * **
482906 CCCTTGAATTTTCCAAAAATTCCGA
66 CCCTCGAATCTTCCAAAAATACAAA
* * * *
482931 TTTAACCCCTAAAGTTTCC-ATAAATTCAAATTTGACCC
1 TTTGA-CCCTTAACTTTCCAAAAAATTCAAATTTGACCC
482969 AATTTTAATG
Statistics
Matches: 175, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
88 11 0.06
89 61 0.35
90 88 0.50
91 15 0.09
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (90 bp):
TTTGACCCTTAACTTTCCAAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATGTGAATTTGA
CCCTCGAATCTTCCAAAAATACAAA
Found at i:482956 original size:149 final size:149
Alignment explanation
Indices: 482680--482968 Score: 341
Period size: 149 Copynumber: 1.9 Consensus size: 149
482670 TTAAATTTTT
* **
482680 CAAAAATTCAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTTTAGAA
1 CAAAAATACAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCCAGAA
* * * * ** **
482745 AATCTAATTTGACCTTTAAACTTTATAAAAATTTGAATTTAACCCTTAAACTTTTTAGAAATTTG
66 AATCTAATTTGACCCTTAAACTTTACAAAAATTCGAATTTAACCCCTAAACTTTCCAGAAATTCA
482810 AATTTGACCCTCGAACTTC
131 AATTTGACCCTCGAACTTC
* ** *
482829 CAAAAATACAAATTTGAC-CCTTAACTTTCCAAAAAATTCAAATTTGACCCCTGAACTTTCCA-A
1 CAAAAATACAAATTTAACACCCAAACTTTCC-AAAAATTCAAATTTGACCCCTAAACTTTCCAGA
* * * * * *
482892 AAATGTGAATTTGACCCTTGAATTTTCCAAAAATTCCG-ATTTAACCCCTAAAGTTTCCATAAAT
65 AAATCT-AATTTGACCCTTAAACTTTACAAAAATT-CGAATTTAACCCCTAAACTTTCCAGAAAT
482956 TCAAATTTGACCC
128 TCAAATTTGACCC
482969 AATTTTAATG
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
148 16 0.14
149 99 0.85
150 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (149 bp):
CAAAAATACAAATTTAACACCCAAACTTTCCAAAAATTCAAATTTGACCCCTAAACTTTCCAGAA
AATCTAATTTGACCCTTAAACTTTACAAAAATTCGAATTTAACCCCTAAACTTTCCAGAAATTCA
AATTTGACCCTCGAACTTC
Found at i:486484 original size:26 final size:25
Alignment explanation
Indices: 486455--486539 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
486445 ACATAGTACT
* *
486455 TGCTAAACATTCATCGGCTTAAAGCC
1 TGCTATACATTCA-CGGCTTAAGGCC
* * *
486481 TGCTATATATTCACGTGCTCAAGGTC
1 TGCTATACATTCACG-GCTTAAGGCC
*
486507 TGCTATACATTCACCAGCTTAAGGCC
1 TGCTATACATTCA-CGGCTTAAGGCC
486533 TGCTATA
1 TGCTATA
486540 TATATATTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
25 2 0.04
26 45 0.94
27 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (25 bp):
TGCTATACATTCACGGCTTAAGGCC
Found at i:489390 original size:59 final size:59
Alignment explanation
Indices: 489298--489657 Score: 623
Period size: 59 Copynumber: 6.1 Consensus size: 59
489288 ATGCATTGAT
*
489298 GTTATTTTGAATA-TTTTGTACACATTATTTTTATATTGTATGATTTAATAAAATAGAA
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
*
489356 ATTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
489415 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
* * *
489474 GTTCTTTTGAATATTTTTGTACACATTATTTTTATATTGTATGATTTAATAAAATAGAG
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
* *
489533 GTTCTTTTGAATATTTTTGTTCACATTATTTTTATATTGTATCATTTAATAAAATAGAA
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
* *
489592 GTTCTTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAAAA
1 GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
*
489651 GTCATTT
1 GTTATTT
489658 AATTGAGAAC
Statistics
Matches: 288, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
58 12 0.04
59 276 0.96
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (59 bp):
GTTATTTTGAATATTTTTGTACACATTATTTTTATATTGTATCATTTAATAAAATAGAA
Found at i:493625 original size:194 final size:196
Alignment explanation
Indices: 493367--493727 Score: 501
Period size: 194 Copynumber: 1.9 Consensus size: 196
493357 ATAAACTATC
* * * * *
493367 CCCTAACGATGTTGCTTACACGAGCTGTCGAGAATATGCATTTAAGCATAAAATCCAACCATCTT
1 CCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCACTTAAGCATAAAATCCAACCATCTT
* *
493432 AGGGCCTATAATCCATT-TAGGATTCATATCTCTTTTC-TGATTCACGATGCTACTCACACGAGC
66 AGGGCCTATAATCCATTCTAGGATTCATATCTCATTTCTTGACTCACGATGCTACTCACACGAGC
* * *
493495 TATCGAGGACTCGCAATATATGTGGTACCTCAGCCATTGATACGGTATCTGTGCATATAATTATT
131 TATCGAGGACTCGCAACATATGCGGTACCTCAACCATTGATACGGTATCTGTGCATATAATTATT
493560 T
196 T
* * * * * * *
493561 CCCTAACAATGCTGCTCACACGAGCTTTTAAGAATATGCACTTATGTATAAATTCTAGCCATCTT
1 CCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCACTTAAGCATAAAATCCAACCATCTT
* * * *
493626 AGGGCCTGTAATCCATTCTTGGATTCATTTCTCATTTCTTGACTCATGATGCTACTCACACGAGC
66 AGGGCCTATAATCCATTCTAGGATTCATATCTCATTTCTTGACTCACGATGCTACTCACACGAGC
* *
493691 TGTCGAGGACTCGTAACATATGCGGTACCTCAACCAT
131 TATCGAGGACTCGCAACATATGCGGTACCTCAACCAT
493728 CGCGTCAGTT
Statistics
Matches: 142, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
194 69 0.49
195 17 0.12
196 56 0.39
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (196 bp):
CCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCACTTAAGCATAAAATCCAACCATCTT
AGGGCCTATAATCCATTCTAGGATTCATATCTCATTTCTTGACTCACGATGCTACTCACACGAGC
TATCGAGGACTCGCAACATATGCGGTACCTCAACCATTGATACGGTATCTGTGCATATAATTATT
T
Found at i:502824 original size:10 final size:10
Alignment explanation
Indices: 502809--502844 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
502799 TGAAAAATAT
502809 TTTTAATTAA
1 TTTTAATTAA
502819 TTTTAATTAA
1 TTTTAATTAA
*
502829 TTTT-ATTTA
1 TTTTAATTAA
502838 TTTTAAT
1 TTTTAAT
502845 ATTATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAATTAA
Found at i:503362 original size:17 final size:18
Alignment explanation
Indices: 503330--503364 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
503320 CATTTAAAAA
*
503330 AAATATCATTTTTTTTAT
1 AAATATCATTTCTTTTAT
503348 AAATAT-ATTTCTTTTAT
1 AAATATCATTTCTTTTAT
503365 TTTTTCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATATCATTTCTTTTAT
Found at i:504535 original size:12 final size:12
Alignment explanation
Indices: 504518--504548 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
504508 CTAAGGTAGA
504518 ATTTTTTAAATT
1 ATTTTTTAAATT
504530 A-TTTTTAAATT
1 ATTTTTTAAATT
504541 ATTTTTTA
1 ATTTTTTA
504549 GCATTATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTTAAATT
Found at i:504841 original size:13 final size:13
Alignment explanation
Indices: 504825--504858 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
504815 TCAAGATTTA
504825 AAGTTCGGGGTTC
1 AAGTTCGGGGTTC
*
504838 AAGTTTGGGGTTC
1 AAGTTCGGGGTTC
504851 AATGTTCG
1 AA-GTTCG
504859 AGTTCGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.18, C:0.12, G:0.35, T:0.35
Consensus pattern (13 bp):
AAGTTCGGGGTTC
Found at i:507896 original size:105 final size:102
Alignment explanation
Indices: 507703--507982 Score: 280
Period size: 102 Copynumber: 2.7 Consensus size: 102
507693 TTAACATGTG
* * * * * *
507703 TCTTTTTTTAATATATTGCTATAACCTTATATGATACTTGTCAACCTCCTGATTTTACTTGTGGA
1 TCTTTTTTTAATATTTTACTAT-ACCTTATAGGACACTTGTCAACCTCCTAATTCTACTTGTGGA
* * * *
507768 GTTTAAAATCTCCATTGGTAATGTATCAAATAATTTTTTT
65 GTTTAAAATCTCCACTCGCAATGTACCAAATAA--TTTTT
* *
507808 TCCTTTTTTTAATATTTTACTATACCTCTATAGGACATTTGTCAA-CTCTTAATTCTACTTGTGG
1 T-CTTTTTTTAATATTTTACTATACCT-TATAGGACACTTGTCAACCTCCTAATTCTACTTGTGG
* *
507872 AGTTTAAAATCTTCGCTCGCAATGTACCAAATAATTTTT
64 AGTTTAAAATCTCCACTCGCAATGTACCAAATAATTTTT
* * * * * *
507911 TATTTTTTAAATATTTTACTATACCTTAAAAGG-CACTTATCAATCC-CTTAACTCTACTTGT-G
1 TCTTTTTTTAATATTTTACTATACCTT-ATAGGACACTTGTCAA-CCTCCTAATTCTACTTGTGG
507973 ATGTTTAAAA
64 A-GTTTAAAA
507983 ACTCTACTGA
Statistics
Matches: 149, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
101 11 0.07
102 49 0.33
103 7 0.05
105 49 0.33
106 33 0.22
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (102 bp):
TCTTTTTTTAATATTTTACTATACCTTATAGGACACTTGTCAACCTCCTAATTCTACTTGTGGAG
TTTAAAATCTCCACTCGCAATGTACCAAATAATTTTT
Found at i:509135 original size:30 final size:31
Alignment explanation
Indices: 509095--509157 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
509085 TATTTATATC
*
509095 TTTATAATTTTTAAAAAATTAAATTA-AATT
1 TTTATAATTTTTAAAAAATTAAAGTATAATT
* * *
509125 TTTATTATTTTTAAGAAGTTAAAGTATAATT
1 TTTATAATTTTTAAAAAATTAAAGTATAATT
509156 TT
1 TT
509158 ATTTTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTATAATTTTTAAAAAATTAAAGTATAATT
Found at i:512687 original size:20 final size:21
Alignment explanation
Indices: 512662--512700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
512652 TTTAGTTACA
512662 AATAATTA-AATATAAATATT
1 AATAATTATAATATAAATATT
*
512682 AATAATTATATTATAAATA
1 AATAATTATAATATAAATA
512701 AAATAAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTATAATATAAATATT
Found at i:512705 original size:20 final size:20
Alignment explanation
Indices: 512661--512706 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
512651 TTTTAGTTAC
512661 AAATAATTAAATATAAATAT
1 AAATAATTAAATATAAATAT
* *
512681 TAATAATTATATTATAAATA-
1 AAATAATTA-AATATAAATAT
512701 AAATAA
1 AAATAA
512707 GTACACACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATTAAATATAAATAT
Found at i:515090 original size:21 final size:21
Alignment explanation
Indices: 515062--515121 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
515052 TCTTTTCAAT
* *
515062 TTAA-ACTCAATTCTTAATTC
1 TTAATACTCAATTCTCAATTA
*
515082 TTAATACTCAATTATCAATTA
1 TTAATACTCAATTCTCAATTA
* *
515103 TTTATTCTCAATTCTCAAT
1 TTAATACTCAATTCTCAAT
515122 CCTCTCGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATACTCAATTCTCAATTA
Found at i:515099 original size:28 final size:28
Alignment explanation
Indices: 515068--515121 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
515058 CAATTTAAAC
* *
515068 TCAATTCTTAATTCTTAATACTCAATTA
1 TCAATTATTAATTCTCAATACTCAATTA
* *
515096 TCAATTATTTATTCTCAATTCTCAAT
1 TCAATTATTAATTCTCAATACTCAAT
515122 CCTCTCGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (28 bp):
TCAATTATTAATTCTCAATACTCAATTA
Found at i:521077 original size:15 final size:15
Alignment explanation
Indices: 521057--521087 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
521047 TTTAAACTCT
*
521057 AAAAGATAAATCTAA
1 AAAAGATAAATATAA
521072 AAAAGATAAATATAA
1 AAAAGATAAATATAA
521087 A
1 A
521088 TTAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAGATAAATATAA
Found at i:523562 original size:3 final size:3
Alignment explanation
Indices: 523554--523585 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
523544 AACATGAAAA
523554 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
523586 ACGACAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:524129 original size:33 final size:33
Alignment explanation
Indices: 524036--524220 Score: 124
Period size: 33 Copynumber: 5.6 Consensus size: 33
524026 ATGAGTGAAG
* * * *
524036 GGTGGTAATAGGCTGGAGGAAGTAGAGTACTGC
1 GGTGGTAATGGGCTGAAAGAAGTGGAGTACTGC
* * ** * *
524069 GGTGTTAATGGACCAAAATG-AGCGGAGTACTGT
1 GGTGGTAATGGGCTGAAA-GAAGTGGAGTACTGC
*
524102 GGTGGTAATGGGCTGAAAGAAGTGGAGTATTGC
1 GGTGGTAATGGGCTGAAAGAAGTGGAGTACTGC
** * * * **
524135 GGTATTAATGGTCCAGAATG-AGTGGAGTACAAC
1 GGTGGTAATGG-GCTGAAAGAAGTGGAGTACTGC
* * * *
524168 AGTGGTAATGGGCTCAAAAAGAGTGGAGTACTAC
1 GGTGGTAATGGGCTGAAAGA-AGTGGAGTACTGC
524202 GGTGGTAATGGGCT-AAAGA
1 GGTGGTAATGGGCTGAAAGA
524221 TATCAAATGT
Statistics
Matches: 111, Mismatches: 36, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
32 4 0.04
33 76 0.68
34 31 0.28
ACGTcount: A:0.31, C:0.10, G:0.37, T:0.23
Consensus pattern (33 bp):
GGTGGTAATGGGCTGAAAGAAGTGGAGTACTGC
Found at i:524173 original size:66 final size:66
Alignment explanation
Indices: 524037--524204 Score: 183
Period size: 66 Copynumber: 2.5 Consensus size: 66
524027 TGAGTGAAGG
* * * * * ***
524037 GTGGTAATAGGCTGGAGGAAGTAGAGTACTGCGGTGTTAATGGACCAAAATGAGCGGAGTACTGT
1 GTGGTAATGGGCTGAAAGAAGTGGAGTACTGCGGTATTAATGGACCAAAATGAGCGGAGTACAAC
*
524102 G
66 A
* * * *
524103 GTGGTAATGGGCTGAAAGAAGTGGAGTATTGCGGTATTAATGGTCCAGAATGAGTGGAGTACAAC
1 GTGGTAATGGGCTGAAAGAAGTGGAGTACTGCGGTATTAATGGACCAAAATGAGCGGAGTACAAC
524168 A
66 A
* * *
524169 GTGGTAATGGGCTCAAAAAGAGTGGAGTACTACGGT
1 GTGGTAATGGGCTGAAAGA-AGTGGAGTACTGCGGT
524205 GGTAATGGGC
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
66 70 0.83
67 14 0.17
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.23
Consensus pattern (66 bp):
GTGGTAATGGGCTGAAAGAAGTGGAGTACTGCGGTATTAATGGACCAAAATGAGCGGAGTACAAC
A
Found at i:526254 original size:25 final size:23
Alignment explanation
Indices: 526225--526270 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
526215 GTTGGATCCA
526225 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
526250 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
526271 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:527348 original size:21 final size:21
Alignment explanation
Indices: 527318--527368 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
527308 TGTCTTCTTT
*
527318 TTTTTCTTTTTCTTTTCTCAA
1 TTTTTCTTTTTTTTTTCTCAA
*
527339 -TTTTCTTTTTTTTTTTTCAA
1 TTTTTCTTTTTTTTTTCTCAA
527359 TTTTTCTTTT
1 TTTTTCTTTT
527369 CGACTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTTTTTTTTCTCAA
Found at i:527363 original size:35 final size:35
Alignment explanation
Indices: 527315--527392 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
527305 TTTTGTCTTC
*
527315 TTTTTTTTCTTTTTCTTTTC-TCAATTTTCTTT-T
1 TTTTTTTTCTTTTTCTTTTCGACAATTTTCTTTCT
* *
527348 TTTTTTTTCAATTTTTCTTTTCGACTATTTTTTTTCT
1 TTTTTTTTC--TTTTTCTTTTCGACAATTTTCTTTCT
527385 TTTTTTTT
1 TTTTTTTT
527393 TCTAAACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 9 0.24
35 11 0.29
36 9 0.24
37 9 0.24
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (35 bp):
TTTTTTTTCTTTTTCTTTTCGACAATTTTCTTTCT
Found at i:528341 original size:6 final size:6
Alignment explanation
Indices: 528322--528381 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
528312 TTGCATAATT
* *
528322 AAAATA AAACTA AAAAT- AAAAT- AAAATA AAACTA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
528368 AATATG AAAATA AA
1 AAAATA AAAATA AA
528382 TATACTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
5 10 0.22
6 35 0.78
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:528346 original size:22 final size:23
Alignment explanation
Indices: 528321--528369 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
528311 ATTGCATAAT
528321 TAAAATAAAACTAAAAAT-AAAA
1 TAAAATAAAACTAAAAATAAAAA
528343 TAAAATAAAACTAAAAATAAAAA
1 TAAAATAAAACTAAAAATAAAAA
528366 TAAA
1 TAAA
528370 TATGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (23 bp):
TAAAATAAAACTAAAAATAAAAA
Found at i:532395 original size:25 final size:23
Alignment explanation
Indices: 532366--532411 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
532356 GTTGAATCCA
532366 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
532391 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
532412 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:534470 original size:29 final size:28
Alignment explanation
Indices: 534401--534470 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
534391 AGGTTTTTGG
* *
534401 ATTTGGGGATTTTGGTTTAGGTTGTCGA
1 ATTTGGGGATTTTGGTTCAGGTTCTCGA
534429 ATTTGGGGATTTTGTGTTCATGGTTCT-GA
1 ATTTGGGGATTTTG-GTTCA-GGTTCTCGA
*
534458 TTTTGGGGATTTT
1 ATTTGGGGATTTT
534471 TTTGGGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.38
29 18 0.49
30 5 0.14
ACGTcount: A:0.13, C:0.04, G:0.33, T:0.50
Consensus pattern (28 bp):
ATTTGGGGATTTTGGTTCAGGTTCTCGA
Found at i:534490 original size:15 final size:15
Alignment explanation
Indices: 534470--534521 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
534460 TTGGGGATTT
534470 TTTTGGGTTTTTTGA
1 TTTTGGGTTTTTTGA
*
534485 TTTTGGGGATTTTTG-
1 TTTT-GGGTTTTTTGA
*
534500 TTTAGGGTTTTTTGA
1 TTTTGGGTTTTTTGA
534515 TTTTGGG
1 TTTTGGG
534522 GATTTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 13 0.42
16 9 0.29
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (15 bp):
TTTTGGGTTTTTTGA
Found at i:534510 original size:30 final size:30
Alignment explanation
Indices: 534392--534541 Score: 145
Period size: 30 Copynumber: 5.2 Consensus size: 30
534382 TAATGTCTAA
* *
534392 GGTTTTTGGA-TTTGGGGATTTTGGTTTA-
1 GGTTTTTTGATTTTGGGGATTTTTGTTTAG
* * * * *
534420 GG-TTGTCGAATTTGGGGATTTTGTGTTCAT
1 GGTTTTTTGATTTTGGGGATTTT-TGTTTAG
*
534450 GG--TTCTGATTTTGGGGA-TTTT-TTT-G
1 GGTTTTTTGATTTTGGGGATTTTTGTTTAG
534475 GGTTTTTTGATTTTGGGGATTTTTGTTTAG
1 GGTTTTTTGATTTTGGGGATTTTTGTTTAG
* *
534505 GGTTTTTTGATTTTGGGGATTTTTATTTAA
1 GGTTTTTTGATTTTGGGGATTTTTGTTTAG
534535 GGTTTTT
1 GGTTTTT
534542 GAGTTTTTGA
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
25 2 0.02
26 2 0.02
27 20 0.20
28 21 0.21
29 18 0.18
30 38 0.38
ACGTcount: A:0.11, C:0.02, G:0.31, T:0.56
Consensus pattern (30 bp):
GGTTTTTTGATTTTGGGGATTTTTGTTTAG
Found at i:535518 original size:81 final size:79
Alignment explanation
Indices: 535299--535524 Score: 258
Period size: 80 Copynumber: 2.8 Consensus size: 79
535289 AGGGTGAGGA
* * *
535299 TGAGGGTGGTAAAGGTTTAGGTGGGAAGGGTGTTGAGGTTTGTTGGCAGTAAAGGTGGTGAA-AG
1 TGAGGGTGCTGAAGGTTTAGGTGGGAA--GTGTTGAGG-TTGTTGGCAGTAAAGGTGGT-AAGGG
* *
535363 CTTAGGTGGGGAGGATGG
62 TTTAGGTGGGAAGGATGG
* * * *
535381 TGAGGGTGGTGAAGGTTTAGGTGGGAGGGTGTTGAGATTGTTGTCAGTAAAGGTGGTAAGGGTTT
1 TGAGGGTGCTGAAGGTTTAGGTGGGA-AGTGTTGAGGTTGTTGGCAGTAAAGGTGGTAAGGGTTT
*
535446 GGGTGGTGAAGG-TGG
65 AGGTGG-GAAGGATGG
* *
535461 TGAGGTTGCTGAAGGTTTAGGTGAGGATAGTGTTGAGGTTGTTGGCAGTAAAGGTGGTGAGGGT
1 TGAGGGTGCTGAAGGTTTAGGTG-GGA-AGTGTTGAGGTTGTTGGCAGTAAAGGTGGTAAGGGT
535525 GAGGAAGATT
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
79 2 0.02
80 51 0.41
81 47 0.38
82 25 0.20
ACGTcount: A:0.20, C:0.02, G:0.48, T:0.29
Consensus pattern (79 bp):
TGAGGGTGCTGAAGGTTTAGGTGGGAAGTGTTGAGGTTGTTGGCAGTAAAGGTGGTAAGGGTTTA
GGTGGGAAGGATGG
Found at i:536871 original size:31 final size:31
Alignment explanation
Indices: 536817--536877 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
536807 GTAAATAATA
** * *
536817 CTATTAATTTTGCATTAATTTATTATTGATT
1 CTATTAATTTTGCACCAAATTATTACTGATT
*
536848 CTATTTATTTTGCACCAAATTATTACTGAT
1 CTATTAATTTTGCACCAAATTATTACTGAT
536878 GTTTTGTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (31 bp):
CTATTAATTTTGCACCAAATTATTACTGATT
Found at i:539279 original size:182 final size:181
Alignment explanation
Indices: 538972--539324 Score: 564
Period size: 182 Copynumber: 1.9 Consensus size: 181
538962 CCTACAATTC
* * *
538972 ACACAAAAAAAATTGACTTTTTATTATATAAACCTTACAATTCACTCAAAAATCTACTGCTATGA
1 ACACAAAAAAAATTCACTTTTTATTATATAAACCCTACAATTCACTCAAAAATCTAATGCTATGA
* * *
539037 CGAATTGTAGCACCAATTTAGTCCAATCGACACAATAATCAAAAAATAAAAAAATCCCCAATTTC
66 CGAACTGTAGCACCAATTTAATCCAATCGACACAATAATAAAAAAATAAAAAAATCCCCAATTTC
* * *
539102 TCATGAATCCTAAAATAAATC-AGCTAAATATATGTTTACCCAAATACAAAT
131 TCATGAACCCTAAAACAAATCGA-CTAAATATATGCTTACCCAAATACAAAT
539153 ACACAAAAAAAATTCAGCTTTTTATTATATAAACCCTACAATTCACTCAAAAATCTAATGCTATG
1 ACACAAAAAAAATTCA-CTTTTTATTATATAAACCCTACAATTCACTCAAAAATCTAATGCTATG
* * *
539218 ACGAACTGTAGCATCAATTTAATCCAATTGACACAATAATAAAAAAATAAAAAATTCCCCAATTT
65 ACGAACTGTAGCACCAATTTAATCCAATCGACACAATAATAAAAAAATAAAAAAATCCCCAATTT
*
539283 CTTATGAACCCTAAAACAAATCGACTAAATATATGCTTACCC
130 CTCATGAACCCTAAAACAAATCGACTAAATATATGCTTACCC
539325 GAAAATCTGA
Statistics
Matches: 157, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
181 15 0.10
182 141 0.90
183 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (181 bp):
ACACAAAAAAAATTCACTTTTTATTATATAAACCCTACAATTCACTCAAAAATCTAATGCTATGA
CGAACTGTAGCACCAATTTAATCCAATCGACACAATAATAAAAAAATAAAAAAATCCCCAATTTC
TCATGAACCCTAAAACAAATCGACTAAATATATGCTTACCCAAATACAAAT
Found at i:540248 original size:27 final size:25
Alignment explanation
Indices: 540193--540249 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
540183 ATATTAAACT
* *
540193 AAAC-AAATAATTTATAATAATTAC
1 AAACAAAATAATTTAAAATAATTAA
*
540217 TAACAAAATAACTTTAAAATAAATTAA
1 AAACAAAATAA-TTTAAAAT-AATTAA
540244 AAACAA
1 AAACAA
540250 CAAAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 6 0.23
26 7 0.27
27 10 0.38
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (25 bp):
AAACAAAATAATTTAAAATAATTAA
Found at i:540481 original size:17 final size:17
Alignment explanation
Indices: 540459--540493 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
540449 TAAAATTTTT
540459 TCCTTCTACCT-TTCTTC
1 TCCTTCT-CCTCTTCTTC
540476 TCCTTCTCCTCTTCTTC
1 TCCTTCTCCTCTTCTTC
540493 T
1 T
540494 ACTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (17 bp):
TCCTTCTCCTCTTCTTC
Found at i:549622 original size:30 final size:30
Alignment explanation
Indices: 549466--549653 Score: 168
Period size: 30 Copynumber: 6.3 Consensus size: 30
549456 CATTAAAATT
* *
549466 GGGTCAAATTGGAATTTTT-GAAAACTTTAA
1 GGGTCAAATTTGAATTTTTAGAAAA-TTTGA
* *
549496 GGGTTAAATTTGAATTTTTGGAAAATTTG-
1 GGGTCAAATTTGAATTTTTAGAAAATTTGA
* * * *
549525 GGAATTAAATTTGATTTTTTGGAAAATTTG-
1 GG-GTCAAATTTGAATTTTTAGAAAATTTGA
* * * *
549555 GGGTTAAATTTGGA-TTTTAGAAAGTTTAGGG
1 GGGTCAAATTTGAATTTTTAGAAAATTT--GA
**
549586 GGGTCAAATTCAAATTTTTAGAAAATTTGA
1 GGGTCAAATTTGAATTTTTAGAAAATTTGA
* *
549616 GGGTCAAATTTAAATTTTTAGAAAGTTTGA
1 GGGTCAAATTTGAATTTTTAGAAAATTTGA
549646 GGGTCAAA
1 GGGTCAAA
549654 AAACAATTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.08
29 11 0.08
30 85 0.63
31 15 0.11
32 12 0.09
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTAGAAAATTTGA
Found at i:549662 original size:30 final size:30
Alignment explanation
Indices: 549586--549663 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
549576 AAGTTTAGGG
**
549586 GGGTCAAATTCAAATTTTTAGAAAATTTGA
1 GGGTCAAATAAAAATTTTTAGAAAATTTGA
** *
549616 GGGTCAAATTTAAATTTTTAGAAAGTTTGA
1 GGGTCAAATAAAAATTTTTAGAAAATTTGA
549646 GGGTCAAA-AAACAATTTT
1 GGGTCAAATAAA-AATTTT
549664 AAAATAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (30 bp):
GGGTCAAATAAAAATTTTTAGAAAATTTGA
Found at i:551409 original size:39 final size:40
Alignment explanation
Indices: 551229--551415 Score: 152
Period size: 40 Copynumber: 4.7 Consensus size: 40
551219 AACTTTAAGT
* * *
551229 GTAAAAGATTGAATTGT-TTCAATCTGCCCCATGATC-GAG
1 GTAAAAGATAGAATGGTCTTCAATCTGCCCTATGATCAG-G
* * * * *
551268 GTAAGAGATTGAATGATCTTCAATCTGCCCTCTGATTAGG
1 GTAAAAGATAGAATGGTCTTCAATCTGCCCTATGATCAGG
* * * * *
551308 GTAAAAGATTGAATGGTCTTTAAGT-TACCCTTTGATTAGG
1 GTAAAAGATAGAATGGTCTTCAA-TCTGCCCTATGATCAGG
* *
551348 GTAAAAGATTAG-ATAGTTTTCAATCTGCCC-ATGATCAGG
1 GTAAAAGA-TAGAATGGTCTTCAATCTGCCCTATGATCAGG
*
551387 GTAAGAGATCAG-ATGGTCTTCAATCTGCC
1 GTAAAAGAT-AGAATGGTCTTCAATCTGCC
551416 TTCTAGTTAG
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
38 1 0.01
39 46 0.38
40 70 0.58
41 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (40 bp):
GTAAAAGATAGAATGGTCTTCAATCTGCCCTATGATCAGG
Found at i:551614 original size:50 final size:50
Alignment explanation
Indices: 551479--551638 Score: 142
Period size: 50 Copynumber: 3.2 Consensus size: 50
551469 AGAGTATAAG
* * * * ** *
551479 ATTTGTCCTTGTGACTTCAATCTTCCCCTTTACAGCTTTAGGTGAATGAT
1 ATTTGTCATTGCGACTTCAATCTGCACCTCCACAGCTTTAGGTGTATGAT
* * * * * * *
551529 ATTGGCCTTTGCGACTTCATTTTGCCCCTCTACAGCTTTAGGTGTATGAT
1 ATTTGTCATTGCGACTTCAATCTGCACCTCCACAGCTTTAGGTGTATGAT
* * **
551579 ATTTGTCATTGC-AGTTTCAATCTGCACCTCCACAGCTTTAGGGGTAAAAT
1 ATTTGTCATTGCGA-CTTCAATCTGCACCTCCACAGCTTTAGGTGTATGAT
551629 ATTTGTCATT
1 ATTTGTCATT
551639 CTATCACCAT
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 1 0.01
50 88 0.99
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (50 bp):
ATTTGTCATTGCGACTTCAATCTGCACCTCCACAGCTTTAGGTGTATGAT
Found at i:563297 original size:58 final size:57
Alignment explanation
Indices: 563207--563374 Score: 158
Period size: 59 Copynumber: 2.9 Consensus size: 57
563197 TAAAATTGAG
* *
563207 TCAAATTGGAATTTTTGAAAACTTTAGGGGTCAAATTTGAATTTTTGGAAA-TTCGGAGA
1 TCAAATTCGAATTTTTGAAAA-TTT-GGGGTCAAATTTGAATTTTTGGAAATTTAGG-GA
* * * * * * *
563266 TCAAATTTGATTTTTTGGAAAATTTGGGGTCAAATTCGTATTTTAGAAAATTTAGGGG
1 TCAAATTCGAATTTTT-GAAAATTTGGGGTCAAATTTGAATTTTTGGAAATTTAGGGA
* * * *
563324 TCAAATTCAAAATTTTAGAAAATTTGAGGGTCAAATTTCATTTTTTGGAAA
1 TCAAATTC-GAATTTTTGAAAATTTG-GGGTCAAATTTGAATTTTTGGAAA
563375 ATTTGACAGT
Statistics
Matches: 87, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
58 38 0.44
59 44 0.51
60 5 0.06
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (57 bp):
TCAAATTCGAATTTTTGAAAATTTGGGGTCAAATTTGAATTTTTGGAAATTTAGGGA
Found at i:563298 original size:29 final size:29
Alignment explanation
Indices: 563206--563379 Score: 165
Period size: 30 Copynumber: 5.9 Consensus size: 29
563196 TTAAAATTGA
*
563206 GTCAAATTGGAATTTTT-GAAAACTTTAGGG
1 GTCAAATTTGAATTTTTGGAAAA-TTT-GGG
*
563236 GTCAAATTTGAATTTTTGG-AAATTCGGAG
1 GTCAAATTTGAATTTTTGGAAAATTTGG-G
* *
563265 ATCAAATTTGATTTTTTGGAAAATTTGGG
1 GTCAAATTTGAATTTTTGGAAAATTTGGG
* * *
563294 GTCAAATTCGTA-TTTTAGAAAATTTAGGG
1 GTCAAATTTGAATTTTTGGAAAATTT-GGG
** * *
563323 GTCAAATTCAAAATTTTAGAAAATTTGAGG
1 GTCAAATTTGAATTTTTGGAAAATTTG-GG
* *
563353 GTCAAATTTCATTTTTTGGAAAATTTG
1 GTCAAATTTGAATTTTTGGAAAATTTG
563380 ACAGTCAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.12
29 43 0.36
30 63 0.52
31 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (29 bp):
GTCAAATTTGAATTTTTGGAAAATTTGGG
Found at i:563358 original size:88 final size:88
Alignment explanation
Indices: 563206--563379 Score: 226
Period size: 88 Copynumber: 2.0 Consensus size: 88
563196 TTAAAATTGA
* * ** * *
563206 GTCAAATTGGAATTTTTGAAAACTTTAGGGGTCAAATTTGAATTTTTGGAAATTCGGAGATCAAA
1 GTCAAATTCGAATTTTAGAAAACTTTAGGGGTCAAATTAAAATTTTAGAAAATTCGGAGATCAAA
*
563271 TTTGATTTTTTGGAAAATTTGGG
66 TTTCATTTTTTGGAAAATTTGGG
* * *
563294 GTCAAATTCGTATTTTAGAAAA-TTTAGGGGTCAAATTCAAAATTTTAGAAAATT-TGAGGGTCA
1 GTCAAATTCGAATTTTAGAAAACTTTAGGGGTCAAATT-AAAATTTTAGAAAATTCGGA-GATCA
563357 AATTTCATTTTTTGGAAAATTTG
64 AATTTCATTTTTTGGAAAATTTG
563380 ACAGTCAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 17 0.23
88 57 0.77
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (88 bp):
GTCAAATTCGAATTTTAGAAAACTTTAGGGGTCAAATTAAAATTTTAGAAAATTCGGAGATCAAA
TTTCATTTTTTGGAAAATTTGGG
Found at i:565668 original size:2 final size:2
Alignment explanation
Indices: 565661--565686 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
565651 ATACAACCTA
565661 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
565687 TAACGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571857 original size:6 final size:6
Alignment explanation
Indices: 571846--571879 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
571836 AAAATCATTC
*
571846 ATAAAT ATAAAT ATAAAT ATAAAT TTAAAGT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA-T ATA
571880 TAAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 22 0.88
7 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:577784 original size:20 final size:20
Alignment explanation
Indices: 577727--577784 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
577717 CACTTTAGCA
**
577727 ACTTTTGATTAATGTTTGCT
1 ACTTTTGACCAATGTTTGCT
**
577747 ACTTTTGACCAACATTTGCT
1 ACTTTTGACCAATGTTTGCT
*
577767 ATTTTTGACCAATGTTTG
1 ACTTTTGACCAATGTTTG
577785 TAATCTTTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (20 bp):
ACTTTTGACCAATGTTTGCT
Found at i:579213 original size:15 final size:16
Alignment explanation
Indices: 579187--579217 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
579177 AAATTAAAAA
579187 ATAAACAAAACCCTAG
1 ATAAACAAAACCCTAG
579203 ATAAA-AAAACCCTAG
1 ATAAACAAAACCCTAG
579218 CTGTCGCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.23, G:0.06, T:0.13
Consensus pattern (16 bp):
ATAAACAAAACCCTAG
Found at i:585137 original size:20 final size:20
Alignment explanation
Indices: 585112--585151 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
585102 TGGTAACCTA
585112 CTCAAGTCCATAGCAATGGT
1 CTCAAGTCCATAGCAATGGT
585132 CTCAAGTCCATAGCAATGGT
1 CTCAAGTCCATAGCAATGGT
585152 GGGGAATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
CTCAAGTCCATAGCAATGGT
Found at i:585420 original size:18 final size:18
Alignment explanation
Indices: 585385--585419 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
585375 AATTTTTGTA
585385 AATGAACATGGACATTTT
1 AATGAACATGGACATTTT
*
585403 AATGAA-ATGGATATTTT
1 AATGAACATGGACATTTT
585420 TTTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (18 bp):
AATGAACATGGACATTTT
Found at i:585452 original size:20 final size:19
Alignment explanation
Indices: 585414--585453 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
585404 ATGAAATGGA
**
585414 TATTTTTTTGTTTTTATTT
1 TATTTTTTTGTTTGGATTT
585433 TATTTTGTTTGTTTGGATTT
1 TATTTT-TTTGTTTGGATTT
585453 T
1 T
585454 GTTGGACCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (19 bp):
TATTTTTTTGTTTGGATTT
Found at i:588132 original size:18 final size:18
Alignment explanation
Indices: 588109--588151 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
588099 GAATAAACTT
588109 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
588127 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
588145 TTAATTA
1 TTAATTA
588152 CAACAGAAAA
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:588418 original size:29 final size:27
Alignment explanation
Indices: 588364--588419 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
588354 AATCATACAT
*
588364 ATTTTAAAAAATAAATACATTAATTTA
1 ATTTTAAAAAATAAATAAATTAATTTA
588391 ATTTTATAATAAATAAATATAATT-ATTTA
1 ATTTTA-AA-AAATAAATA-AATTAATTTA
588420 TGAATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 2 0.08
29 14 0.56
30 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTTTAAAAAATAAATAAATTAATTTA
Found at i:588451 original size:31 final size:29
Alignment explanation
Indices: 588395--588456 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
588385 AATTTAATTT
* * *
588395 TATAATAAATAAATATAATTATTTATGAA
1 TATAATAAATAAAAATAAATATTTATAAA
*
588424 TATAATATATAAAAATAAAATATTTTATAAA
1 TATAATAAATAAAAAT-AAATA-TTTATAAA
588455 TA
1 TA
588457 ATTGTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 4 0.15
31 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TATAATAAATAAAAATAAATATTTATAAA
Found at i:591407 original size:23 final size:23
Alignment explanation
Indices: 591374--591425 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
591364 AATATTTTTA
591374 ATTATATGTTTATGAACATGTTTG
1 ATTA-ATGTTTATGAACATGTTTG
* * *
591398 TTTAATGTTTGTGAATATGTTTG
1 ATTAATGTTTATGAACATGTTTG
591421 ATTAA
1 ATTAA
591426 GTTAAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (23 bp):
ATTAATGTTTATGAACATGTTTG
Found at i:591505 original size:28 final size:28
Alignment explanation
Indices: 591450--591511 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
591440 TTCGTGAACA
* *
591450 TTAAATAAATAAACATAAATATATAATT
1 TTAAATAAATAAACATAAATAAAAAATT
* *
591478 TTAAATAAATGAACATGAATAAAAAATT
1 TTAAATAAATAAACATAAATAAAAAATT
*
591506 TAAAAT
1 TTAAAT
591512 TTTTAATACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
TTAAATAAATAAACATAAATAAAAAATT
Found at i:592067 original size:20 final size:20
Alignment explanation
Indices: 592042--592081 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
592032 CCTCATCACA
592042 TGTCATCTAAAATCAGTTTT
1 TGTCATCTAAAATCAGTTTT
592062 TGTCATCTAAAATCAGTTTT
1 TGTCATCTAAAATCAGTTTT
592082 ACCTTGCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
TGTCATCTAAAATCAGTTTT
Found at i:592582 original size:158 final size:159
Alignment explanation
Indices: 592283--592605 Score: 531
Period size: 158 Copynumber: 2.0 Consensus size: 159
592273 AATATTAAAA
* *
592283 TTATATATCAACTTTGATTTAATGTGTAATTGTATATATATGAACTTTAATTTGGAACAATTATG
1 TTATACATCAACTTTGATTTAATGTGCAATTG-ATATATATGAACTTTAATTTGGAACAATTATG
* *
592348 CACGTGAAACTTTAATTATGGCTCAAATGTATACTTGAAACTTTAATTTTGATTTAATCATACAT
65 CACGTGAAACTTTAATTATAGCTCAAATGTATACTTGAAACTTTAATTTTGATTTAATCATACAC
592413 ATTTAAAGACATAAATACATCAATTTATTT
130 ATTTAAAGACATAAATACATCAATTTATTT
* * *
592443 TTATACATGAACTTTGATTTAATGTGCAATTG-TATATATGAACTTTAGTTTGGTACAATTATGC
1 TTATACATCAACTTTGATTTAATGTGCAATTGATATATATGAACTTTAATTTGGAACAATTATGC
* * **
592507 TCGTGAAACTTTAATTATAGTTCGGATGTATACTTGAAACTTTAATTTTGATTTAATCATACACA
66 ACGTGAAACTTTAATTATAGCTCAAATGTATACTTGAAACTTTAATTTTGATTTAATCATACACA
592572 TTTAAAGACATAAATACATCAATTTATTT
131 TTTAAAGACATAAATACATCAATTTATTT
592601 TTATA
1 TTATA
592606 TTAAATAAAT
Statistics
Matches: 152, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
158 123 0.81
160 29 0.19
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (159 bp):
TTATACATCAACTTTGATTTAATGTGCAATTGATATATATGAACTTTAATTTGGAACAATTATGC
ACGTGAAACTTTAATTATAGCTCAAATGTATACTTGAAACTTTAATTTTGATTTAATCATACACA
TTTAAAGACATAAATACATCAATTTATTT
Found at i:594502 original size:4 final size:4
Alignment explanation
Indices: 594493--594518 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
594483 AGTATATGAC
594493 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
594519 CAGTCTCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:599034 original size:33 final size:33
Alignment explanation
Indices: 598992--599057 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
598982 CCTTTACTTT
598992 CTCTTCTAGCTATTTGTATATGTCCTCTAGCTA
1 CTCTTCTAGCTATTTGTATATGTCCTCTAGCTA
599025 CTCTTCTAGCTATTTGTATATGTCCTCTAGCTA
1 CTCTTCTAGCTATTTGTATATGTCCTCTAGCTA
599058 TTTAGAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (33 bp):
CTCTTCTAGCTATTTGTATATGTCCTCTAGCTA
Found at i:603127 original size:220 final size:219
Alignment explanation
Indices: 602736--603168 Score: 575
Period size: 220 Copynumber: 2.0 Consensus size: 219
602726 CGAACTTTGC
* *
602736 GAGGAAGACTCGTCATTTTGAAAATTGAGAAAGGAAGTCGGGTCCAAAAAGTTAAGGCGCGACAC
1 GAGGAAGACTCGTCATTTTGAAAATCGAGAAAGGAAGTCGGGTCCAAAAAGTTAAGGCACGACAC
* * * * * *
602801 CTCACGTTTTCAAAATCACAAACATTCCTATTTTTTAAATCTCTTGTTTGCTTATTTTTTAGAGA
66 CTCACGTTTTAAAAATAACAAACATTCCTATTTCTCAAATCTCATGTTTGATTATTTTTTAGAGA
** * * *
602866 GAAAATTATTTTAATATTTCAATTCGAAAAAAAATCGCACCTAGTAAGTTAAGACTTGACTTTTC
131 GAAAAGCATTTGAATATTTCAATTCGAAAAAAAATCGCACCTAATAAGTTAAGACTCGACTTTTC
602931 AAATCACGAAATAACGAACTGTAT
196 AAATCACGAAATAACGAACTGTAT
* * *
602955 GAGGAAGACTCGTTATTTTGAAAAATCGAGAAAGGAAGTCGGGTCCAATAAGTTAGGGCACGACG
1 GAGGAAGACTCGTCATTTTG-AAAATCGAGAAAGGAAGTCGGGTCCAAAAAGTTAAGGCACGAC-
* * * *
603020 A-CTCATGTTTTAAAAAATAACAAGCATTCC-ATATTCTCAAATTTCATGTTTTATTATTTTTTA
64 ACCTCACGTTTT-AAAAATAACAAACATTCCTAT-TTCTCAAATCTCATGTTTGATTATTTTTTA
* * * * *
603083 GAGAGGAAAGCATTTGAATTTTTCGATTCGAAGAAAAA-CGCACCTAATAAGTTAAGGCTCGACT
127 GAGAGAAAAGCATTTGAATATTTCAATTCGAAAAAAAATCGCACCTAATAAGTTAAGACTCGACT
*
603147 TTTCACATCACGAAATAACGAA
192 TTTCAAATCACGAAATAACGAA
603169 TTTTACCTCA
Statistics
Matches: 184, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
219 19 0.10
220 94 0.51
221 71 0.39
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (219 bp):
GAGGAAGACTCGTCATTTTGAAAATCGAGAAAGGAAGTCGGGTCCAAAAAGTTAAGGCACGACAC
CTCACGTTTTAAAAATAACAAACATTCCTATTTCTCAAATCTCATGTTTGATTATTTTTTAGAGA
GAAAAGCATTTGAATATTTCAATTCGAAAAAAAATCGCACCTAATAAGTTAAGACTCGACTTTTC
AAATCACGAAATAACGAACTGTAT
Found at i:606058 original size:59 final size:59
Alignment explanation
Indices: 605894--606068 Score: 235
Period size: 61 Copynumber: 2.9 Consensus size: 59
605884 TCAACTGCCT
* * * * *
605894 ATGTTGGCTTTCGATTCTGAACTACCTGTTAAAAGATATTTTGCACGATTGGACCGCTC
1 ATGTTCGCTTTCAATTCTGAACTGCCTGTTAAAAGATCTTTTGCACAATTGGACCGCTC
* *
605953 ATGTTCAG-TTTCACATTTCTGAACTGCCTGTTAGAAGATCTTTTGCACAATTGGACTGCTC
1 ATGTTC-GCTTTCA-A-TTCTGAACTGCCTGTTAAAAGATCTTTTGCACAATTGGACCGCTC
606014 ATGTTCGCTTTCAATTCTGAACTGCCTGTTAAAAGATCTTTTGCACGATATTGGA
1 ATGTTCGCTTTCAATTCTGAACTGCCTGTTAAAAGATCTTTTGCAC-A-ATTGGA
606069 TCGGACAGGA
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
59 40 0.39
60 5 0.05
61 57 0.56
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (59 bp):
ATGTTCGCTTTCAATTCTGAACTGCCTGTTAAAAGATCTTTTGCACAATTGGACCGCTC
Found at i:622918 original size:154 final size:154
Alignment explanation
Indices: 622638--622945 Score: 415
Period size: 154 Copynumber: 2.0 Consensus size: 154
622628 CATCATATCA
* *
622638 TGTAATGCTCACACAAGCTGTGAAATGGGGCTGCTTACACGAGCTCTAGGTCGAGATGTTGAGCT
1 TGTAATGCTCACACAAGCTGTGAAATGGGGCTGCTCACACGAGCTATAGGTCGAGATGTTGAGCT
* * ** * *
622703 ACATGATGCTGTTCACACGAGCTATGGAGAATCCGCAATAATTTATGGATCACAGCCATCGGTAG
66 ACACGATGATACTCACACGAGCTATGGAGAATCCGCAATAATTTACGGATCACAGCCATCGGTAA
622768 GACATCTAAGACCAACACCCATAT
131 GACATCTAAGACCAACACCCATAT
* * * *
622792 TGTAATGCTCACACGAGTTGTGAAAT-GGGCTTGCTCACACGAGCTATGGGTTGAGATGTTGAGC
1 TGTAATGCTCACACAAGCTGTGAAATGGGGC-TGCTCACACGAGCTATAGGTCGAGATGTTGAGC
* *
622856 TACACGATGATACTCACACGAGCTGTGGAGAATCCGCAATAATTGT-CGGAT-ATCAGCTATCGG
65 TACACGATGATACTCACACGAGCTATGGAGAATCCGCAATAATT-TACGGATCA-CAGCCATCGG
* * *
622919 TAAGACATTTAAGACTAGCACCCATAT
128 TAAGACATCTAAGACCAACACCCATAT
622946 AACTTGTAAT
Statistics
Matches: 134, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
153 5 0.04
154 128 0.96
155 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (154 bp):
TGTAATGCTCACACAAGCTGTGAAATGGGGCTGCTCACACGAGCTATAGGTCGAGATGTTGAGCT
ACACGATGATACTCACACGAGCTATGGAGAATCCGCAATAATTTACGGATCACAGCCATCGGTAA
GACATCTAAGACCAACACCCATAT
Found at i:627331 original size:46 final size:46
Alignment explanation
Indices: 627264--627353 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
627254 CATAAAGAAG
*
627264 ACCAATTGAGGCTTATACAACCTCAACATGTGCCAAAGTCCTCGCA
1 ACCAACTGAGGCTTATACAACCTCAACATGTGCCAAAGTCCTCGCA
*
627310 ACCAACTGAGGCTTATTCAACCTCAACATGTGCCAAAGTCCTCG
1 ACCAACTGAGGCTTATACAACCTCAACATGTGCCAAAGTCCTCG
627354 TAGCACCCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (46 bp):
ACCAACTGAGGCTTATACAACCTCAACATGTGCCAAAGTCCTCGCA
Found at i:629234 original size:16 final size:16
Alignment explanation
Indices: 629213--629243 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
629203 TGAATTACTA
629213 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
629229 ATTACAGTTCTATTC
1 ATTACAGTTCTATTC
629244 TATTTATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:632903 original size:28 final size:30
Alignment explanation
Indices: 632869--632931 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
632859 ACTTATTTTA
632869 TTGTTAA-TTT-TTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAGAGGTAT
632897 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAGAGGTAT
632927 TTGTT
1 TTGTT
632932 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 7 0.21
29 3 0.09
30 23 0.70
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGGTAT
Found at i:633768 original size:14 final size:14
Alignment explanation
Indices: 633749--633788 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
633739 AAATCAAATT
633749 TTAAATTAATTTAC
1 TTAAATTAATTTAC
* *
633763 TTAAATTAATTAAT
1 TTAAATTAATTTAC
*
633777 TTATATTAATTT
1 TTAAATTAATTT
633789 TTAAATCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATTAATTTAC
Found at i:634205 original size:27 final size:27
Alignment explanation
Indices: 634146--634205 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
634136 ATGATTTTAA
* *
634146 AAAAAATTTAAAAAACGATTATCATTT
1 AAAAAATTAAAAAAACGATTATAATTT
* *
634173 ATAAAATTAAAAAAATGA-TATAATATT
1 AAAAAATTAAAAAAACGATTATAAT-TT
634200 AAAAAA
1 AAAAAA
634206 AATAAAATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAAAATTAAAAAAACGATTATAATTT
Found at i:636564 original size:24 final size:24
Alignment explanation
Indices: 636536--636594 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
636526 TAGACTAATA
* *
636536 AGAGTTCGACTCAAATAAATAAAC
1 AGAGTTCAACTCAAACAAATAAAC
* * *
636560 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTCAACTCAAACAAATAAAC
*
636584 AGAGTTTAACT
1 AGAGTTCAACT
636595 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTCAACTCAAACAAATAAAC
Found at i:636597 original size:24 final size:24
Alignment explanation
Indices: 636552--636598 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
636542 CGACTCAAAT
*
636552 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAACTGAAAC
636576 AAATAAACAGAGTTTAACTGAAA
1 AAATAAACAGAGTTTAACTGAAA
636599 GATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (24 bp):
AAATAAACAGAGTTTAACTGAAAC
Found at i:638542 original size:24 final size:24
Alignment explanation
Indices: 638515--638565 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
638505 AGTTTGACTC
*
638515 AAACAAATAAACATAGTTTAATAG
1 AAACAAATAAACAGAGTTTAATAG
* *
638539 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATAG
638563 AAA
1 AAA
638566 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATAG
Found at i:638955 original size:16 final size:17
Alignment explanation
Indices: 638934--638977 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
638924 ATATCAAATT
638934 TATTTTTTTTAATTT-A
1 TATTTTTTTTAATTTAA
* *
638950 TATTTTTATCAATTTAA
1 TATTTTTTTTAATTTAA
638967 TATTTATTTTT
1 TATTT-TTTTT
638978 TAGTTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 6 0.27
18 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTTTTAATTTAA
Found at i:638969 original size:17 final size:16
Alignment explanation
Indices: 638925--638971 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
638915 TTAGGTATAA
638925 TATCAAATTTAT-TTTT
1 TATC-AATTTATATTTT
*
638941 T-TTAATTTATATTTT
1 TATCAATTTATATTTT
638956 TATCAATTTAATATTT
1 TATCAATTT-ATATTT
638972 ATTTTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 7 0.27
17 6 0.23
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCAATTTATATTTT
Found at i:648839 original size:18 final size:18
Alignment explanation
Indices: 648816--648852 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
648806 TTTGTGATTA
648816 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
648834 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
648852 A
1 A
648853 TGTGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:657054 original size:21 final size:21
Alignment explanation
Indices: 657030--657071 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
657020 CTAGAGTATA
657030 ACTTTCGATCTCATTAGAATC
1 ACTTTCGATCTCATTAGAATC
657051 ACTTTCGATCTCATTAGAATC
1 ACTTTCGATCTCATTAGAATC
657072 TGCTTGATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
ACTTTCGATCTCATTAGAATC
Found at i:658168 original size:21 final size:21
Alignment explanation
Indices: 658142--658193 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
658132 GCCTGCTAGG
*
658142 CACAAAGCCTGAATACACCGA
1 CACAAAGCCTGAAAACACCGA
* * *
658163 CACAAAGCTTGAAAACATCGG
1 CACAAAGCCTGAAAACACCGA
*
658184 CACGAAGCCT
1 CACAAAGCCT
658194 ACTAGGCACA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.31, G:0.17, T:0.12
Consensus pattern (21 bp):
CACAAAGCCTGAAAACACCGA
Found at i:658204 original size:37 final size:37
Alignment explanation
Indices: 658163--658281 Score: 193
Period size: 37 Copynumber: 3.2 Consensus size: 37
658153 AATACACCGA
*
658163 CACAAAGCTTGAAAACATCGGCACGAAGCCTACTAGG
1 CACAAAGCTTGAAAACACCGGCACGAAGCCTACTAGG
* * *
658200 CACAATGCCTGAAAACACCAGCACGAAGCCTACTAGG
1 CACAAAGCTTGAAAACACCGGCACGAAGCCTACTAGG
*
658237 CACAAAGCTTGAAAACACCGACACGAAGCCTACTAGG
1 CACAAAGCTTGAAAACACCGGCACGAAGCCTACTAGG
658274 CACAAAGC
1 CACAAAGC
658282 CTAAAAATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.39, C:0.30, G:0.19, T:0.11
Consensus pattern (37 bp):
CACAAAGCTTGAAAACACCGGCACGAAGCCTACTAGG
Done.