Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008420.1 Hibiscus syriacus cultivar Beakdansim tig00111200_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: 1020524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:332405 original size:18 final size:17
Alignment explanation
Indices: 332382--332424 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
332372 ATATATACAT
332382 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
332400 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
332417 ATAA-AATA
1 ATAATAATA
332425 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:332745 original size:37 final size:38
Alignment explanation
Indices: 332695--332799 Score: 142
Period size: 37 Copynumber: 2.8 Consensus size: 38
332685 GTGCTTGTGG
* * * *
332695 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAAC-TCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
* *
332732 ATCCTATTTTTAGGAGTTTGAATCCTAGCA-AACTTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
332769 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
332800 GACGAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 3 0.05
37 56 0.95
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTCT
Found at i:333013 original size:18 final size:18
Alignment explanation
Indices: 332977--333013 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
332967 TCTGCCTTGA
*
332977 TCATCTTCGTTTTCATCT
1 TCATCTTCGTTTGCATCT
*
332995 TCATCTTCGTTTGCTTCT
1 TCATCTTCGTTTGCATCT
333013 T
1 T
333014 GAAGAGGAGG
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:0.08, C:0.27, G:0.08, T:0.57
Consensus pattern (18 bp):
TCATCTTCGTTTGCATCT
Found at i:334177 original size:16 final size:16
Alignment explanation
Indices: 334156--334216 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
334146 TAATAAATAA
*
334156 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
334172 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
334188 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
334204 ACGAACATAAACG
1 ACGAACATAAACG
334217 TTAGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:334682 original size:24 final size:24
Alignment explanation
Indices: 334642--334703 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
334632 GATTAGATTA
* *
334642 AACATAAAT-GAATGAACATAAACT
1 AACAT-AATCGAACGAACATAAACG
334666 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
334690 AACATAACCGAACG
1 AACATAATCGAACG
334704 TTCACGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:343193 original size:16 final size:17
Alignment explanation
Indices: 343155--343196 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
343145 CGACTTGATC
343155 AAATATTTAATAAATTT
1 AAATATTTAATAAATTT
** *
343172 TTATATTT-TTAAATTT
1 AAATATTTAATAAATTT
343188 AAATATTTA
1 AAATATTTA
343197 TTTTTACATA
Statistics
Matches: 19, Mismatches: 5, Indels: 2
0.73 0.19 0.08
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTTAATAAATTT
Found at i:346581 original size:1 final size:1
Alignment explanation
Indices: 346575--346600 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
346565 TGGACTCCTC
346575 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
346601 CTCACCAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:348625 original size:110 final size:110
Alignment explanation
Indices: 348442--348841 Score: 644
Period size: 110 Copynumber: 3.7 Consensus size: 110
348432 TTGTGTCGCT
* *
348442 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
* * *
348507 TGACAGTCAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
348552 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
*
348617 TGACAGTCAGTCGCCCATTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
348662 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
* * *
348727 TGACAGTTAGTCGCCCCTTCACTGTGAAGTTGAACTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
348772 TCGAGTTCAATATCCTTCGCTGTGACA-TTGAAA--GACTCTGAATGAAACTGAAAAGTTATTTG
1 TCGAGTCCAATATCCTTCGCTGTGA-AGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTG
348834 TTGACAGT
65 TTGACAGT
348842 AAGCTTTTCT
Statistics
Matches: 272, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
108 37 0.14
110 234 0.86
111 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:350551 original size:30 final size:29
Alignment explanation
Indices: 350490--350572 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 29
350480 TTTGCATATA
*
350490 TTGTCTTCTTTTTTCTTCATTTTTTCGTTGTTT
1 TTGT-TTC-TTTTT-TT-ATTTTCTCGTTGTTT
*
350523 TTGTTTCTCTTTTTTATTTTCTCTTTGTTT
1 TTGTTTCT-TTTTTTATTTTCTCGTTGTTT
* *
350553 TTCCTTTGTTTTTTTATTTT
1 TT-GTTTCTTTTTTTATTTT
350573 TTGTTCTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 26 0.59
31 7 0.16
32 7 0.16
33 4 0.09
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (29 bp):
TTGTTTCTTTTTTTATTTTCTCGTTGTTT
Found at i:353812 original size:3 final size:3
Alignment explanation
Indices: 353804--353841 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
353794 AATAAAATAG
*
353804 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
353842 AAACCATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:353924 original size:29 final size:29
Alignment explanation
Indices: 353892--353995 Score: 190
Period size: 29 Copynumber: 3.6 Consensus size: 29
353882 AGGGTATAAG
353892 AATAATAAATAAAATATATTTATATATGT
1 AATAATAAATAAAATATATTTATATATGT
353921 AATAATAAATAAAATATATTTATATATGT
1 AATAATAAATAAAATATATTTATATATGT
353950 AATAATAAATAAAATATATTTATATATGT
1 AATAATAAATAAAATATATTTATATATGT
* *
353979 AATCATAAATATAATAT
1 AATAATAAATAAAATAT
353996 TTGCAACAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
AATAATAAATAAAATATATTTATATATGT
Found at i:353931 original size:58 final size:59
Alignment explanation
Indices: 353869--353989 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 59
353859 TAATAAAAGA
*
353869 AAATAAAAATAGAAGGGTATAAG-AATAATAAATAAAATATATTTATATATGTAATAAT
1 AAATAAAAATAGAAGGATATAAGTAATAATAAATAAAATATATTTATATATGTAATAAT
* *** * *
353927 AAAT-AAAATATATTTATATATGTAATAATAAATAAAATATATTTATATATGTAATCAT
1 AAATAAAAATAGAAGGATATAAGTAATAATAAATAAAATATATTTATATATGTAATAAT
353985 AAATA
1 AAATA
353990 TAATATTTGC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 12 0.22
58 42 0.78
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.36
Consensus pattern (59 bp):
AAATAAAAATAGAAGGATATAAGTAATAATAAATAAAATATATTTATATATGTAATAAT
Found at i:354015 original size:58 final size:58
Alignment explanation
Indices: 353895--354022 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
353885 GTATAAGAAT
* * * * *
353895 AATAAATAAAATATATTTATATATGTAATAATAAATAAAATATATTTATATATGTAAT
1 AATAAATAAAATATATTTATATATGTAATAATAAATAAAATATATTAACAAATGAAAA
* *
353953 AATAAATAAAATATATTTATATATGTAATCATAAATATAATAT-TTGCAACAAAT-AAAA
1 AATAAATAAAATATATTTATATATGTAATAATAAATAAAATATATT--AACAAATGAAAA
354011 AATAAATGAAAA
1 AATAAAT-AAAA
354023 AAATGTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.03
58 50 0.83
59 8 0.13
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (58 bp):
AATAAATAAAATATATTTATATATGTAATAATAAATAAAATATATTAACAAATGAAAA
Found at i:354112 original size:9 final size:10
Alignment explanation
Indices: 354099--354131 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
354089 GATAAAACAA
354099 AATAAAATAT
1 AATAAAATAT
354109 -ATAAAATAT
1 AATAAAATAT
354118 AATAAAA-AT
1 AATAAAATAT
354127 AATAA
1 AATAA
354132 TGAAGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAAAATAT
Found at i:354131 original size:19 final size:18
Alignment explanation
Indices: 354065--354131 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
354055 AGTAATAGAG
354065 AAAAATAATAATAAATTAA-
1 AAAAATAATAA-AAA-TAAT
* *
354084 AAAAA-GATAAAACAAAAT
1 AAAAATAATAAAA-ATAAT
354102 -AAAATATATAAAATATAAT
1 AAAAATA-ATAAAA-ATAAT
354121 AAAAATAATAA
1 AAAAATAATAA
354132 TGAAGTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 8 0.21
18 5 0.13
19 19 0.50
20 6 0.16
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (18 bp):
AAAAATAATAAAAATAAT
Found at i:354560 original size:37 final size:37
Alignment explanation
Indices: 354510--354621 Score: 190
Period size: 37 Copynumber: 3.0 Consensus size: 37
354500 ATGGTTATGG
*
354510 ATCATCTTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
354547 ATCATATTTTTAGGTGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
354584 ATCATATTTTTAGGAGTTTGAATTC-TAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAA-TCATAGTAAAACTCT
354621 A
1 A
354622 ACGTTATGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 69 0.97
38 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:357915 original size:31 final size:30
Alignment explanation
Indices: 357855--357911 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
357845 ATAATTTCAA
* *
357855 AAAATATTAAGTTTTTTTAAAAATAAATTT
1 AAAATATTAAGTGTTTTCAAAAATAAATTT
357885 AAAAT-TTAAGTGTTTTCATAAAATAAA
1 AAAATATTAAGTGTTTTCA-AAAATAAA
357912 ATTTTATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
AAAATATTAAGTGTTTTCAAAAATAAATTT
Found at i:365754 original size:21 final size:21
Alignment explanation
Indices: 365729--365776 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
365719 TGGAGGTTGG
365729 CTAGAACGACTAGAGGAGGCC
1 CTAGAACGACTAGAGGAGGCC
*
365750 CTAGAACGACTAGAGGATGCC
1 CTAGAACGACTAGAGGAGGCC
365771 CTAGAA
1 CTAGAA
365777 TGTTTATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.29, T:0.12
Consensus pattern (21 bp):
CTAGAACGACTAGAGGAGGCC
Found at i:366456 original size:23 final size:23
Alignment explanation
Indices: 366430--366491 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
366420 TAGAACCCTC
366430 AGGGGGTATCGATTCCCCTTCAA
1 AGGGGGTATCGATTCCCCTTCAA
* *
366453 A-GGGGAATCGGTTCCCCTTCAA
1 AGGGGGTATCGATTCCCCTTCAA
*
366475 GGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
366492 TCTGCACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (23 bp):
AGGGGGTATCGATTCCCCTTCAA
Found at i:373111 original size:2 final size:2
Alignment explanation
Indices: 373104--373138 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
373094 GAACAAGGTC
*
373104 GA GA GA GA GA GA GA GA TA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
373139 CATCTATCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:374532 original size:20 final size:20
Alignment explanation
Indices: 374462--374535 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
374452 AATGTTTTTA
* *
374462 TGAATAATATCGATATTGTA
1 TGAATAATACCGATATTGTG
* *
374482 TGAATAGTATCGATATTGTG
1 TGAATAATACCGATATTGTG
*
374502 TTAA-AAGTACCGATATTGTG
1 TGAATAA-TACCGATATTGTG
*
374522 TGAACAATACCGAT
1 TGAATAATACCGAT
374536 GTTAATAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.93
21 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TGAATAATACCGATATTGTG
Found at i:379020 original size:31 final size:31
Alignment explanation
Indices: 378969--379053 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
378959 GAGGTCATAT
* *
378969 AAAGAACTTCGGT-AACTGTCCATAGGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTTCC
*
378999 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTTCC
** *
379030 TTAGAACCTAGGTATACTGTCCAT
1 AAAGAACCTAGGTAAACTGTCCAT
379054 GTCTCGAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 11 0.23
31 37 0.77
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTTCC
Found at i:380163 original size:64 final size:62
Alignment explanation
Indices: 380089--380249 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 62
380079 TCTTTAACAT
* * * *
380089 GTGCATCGATGCACTACCCATACATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGG
* * **
380152 GATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTAAGGG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGG
*
380216 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
380250 CTGAACAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 29 0.35
64 55 0.65
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGG
Found at i:382868 original size:12 final size:12
Alignment explanation
Indices: 382851--382884 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
382841 CAGGCTGACT
382851 TCTTCCTCTACC
1 TCTTCCTCTACC
* *
382863 TCTTCCTCTTCG
1 TCTTCCTCTACC
382875 TCTTCCTCTA
1 TCTTCCTCTA
382885 TGAGATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.44, G:0.03, T:0.47
Consensus pattern (12 bp):
TCTTCCTCTACC
Found at i:384328 original size:20 final size:20
Alignment explanation
Indices: 384303--384344 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
384293 TATTTTTATG
384303 AATAGTATCCATACTGTGTT
1 AATAGTATCCATACTGTGTT
*
384323 AATAGTATCGATACTGTGTT
1 AATAGTATCCATACTGTGTT
384343 AA
1 AA
384345 CAATAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
AATAGTATCCATACTGTGTT
Found at i:384419 original size:19 final size:19
Alignment explanation
Indices: 384395--384443 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
384385 AAATGTATAT
384395 CGATACTACTACAGTGTAC
1 CGATACTACTACAGTGTAC
384414 CGATACTACTACAGTGTAC
1 CGATACTACTACAGTGTAC
384433 CGATAC-ACTAC
1 CGATACTACTAC
384444 TACAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
CGATACTACTACAGTGTAC
Found at i:387684 original size:18 final size:18
Alignment explanation
Indices: 387656--387706 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
387646 TTTTAAAACA
*
387656 ATTTATATTTAATTA-TTT
1 ATTT-TATTTTATTATTTT
387674 ATTTTATTTTATTATTTT
1 ATTTTATTTTATTATTTT
*
387692 ATTTTATTTTTTTAT
1 ATTTTATTTTATTAT
387707 CCTTATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTATTTTATTATTTT
Found at i:387688 original size:13 final size:13
Alignment explanation
Indices: 387672--387706 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
387662 ATTTAATTAT
387672 TTATTTTATTTTA
1 TTATTTTATTTTA
387685 TTATTTTATTTTA
1 TTATTTTATTTTA
*
387698 TTTTTTTAT
1 TTATTTTAT
387707 CCTTATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:387973 original size:42 final size:42
Alignment explanation
Indices: 387867--388077 Score: 158
Period size: 42 Copynumber: 5.0 Consensus size: 42
387857 TTAAGCTCCT
* * * * **
387867 AATTTTTT-AATCTCCCTTTTAACTTTTATAATTGAGACCCTT
1 AATTTTTTCAATC-CACTTTTTACCTTTATAATTGAGGCCCCG
387909 AATTTTTTTCAATCCTACTTTTTACCTTTATAATTGAGGCCTCC-
1 AA-TTTTTTCAATCC-ACTTTTTACCTTTATAATTGAGGCC-CCG
* * **
387953 AATTTTTTCAATCCCCTTTTTACCTTTATAATCGTTGCCCCG
1 AATTTTTTCAATCCACTTTTTACCTTTATAATTGAGGCCCCG
* * * * **
387995 ATTTTTTTCAATATCACTTTCTACCTTTATAATTGAAGCCCTT
1 AATTTTTTCAAT-CCACTTTTTACCTTTATAATTGAGGCCCCG
* * * * *
388038 AATTGTTGC-ATCAAACTTTTTACTTTTATAATTGAAGCCC
1 AATTTTTTCAATC-CACTTTTTACCTTTATAATTGAGGCCC
388078 ATAATTTAAT
Statistics
Matches: 137, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.01
42 60 0.44
43 47 0.34
44 27 0.20
45 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.47
Consensus pattern (42 bp):
AATTTTTTCAATCCACTTTTTACCTTTATAATTGAGGCCCCG
Found at i:393148 original size:2 final size:2
Alignment explanation
Indices: 393141--393203 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
393131 TCTTTCGAAT
393141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
393183 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
393204 TTGAGTATCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:393462 original size:70 final size:70
Alignment explanation
Indices: 393334--393926 Score: 443
Period size: 70 Copynumber: 8.5 Consensus size: 70
393324 AAGTTACCTG
* * ** * * *
393334 AAATTAATTATGATTAGGTGCTCTTGTACGAG-CTACTCTAATATTTCAGAGCTTCTGTACGAGT
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTC-ACTCTAATCCTTCGGGGCTCCTGTACGAGT
*
393398 CACTCA
65 CACCCA
*
393404 AAATTAATTATGATTAGGTTTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
* *
393469 ACTCG
66 ACCCA
* * * * * * * *
393474 GAATTAATTATGATTAGGTATT-C-AT-CAAGCCACTCTAATCCTTTGGGGATCTTGTACGAGTC
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
*
393536 ACCCG
66 ACCCA
* * * * * * *
393541 AAATTAATTATGATTAAGTGCTCCCTTTTA--AGTCACTTTAATCCTCCGGGGCTTCTGTATGAG
1 AAATTAATTATGATTAGGTG-TTCC-TGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAG
393604 TCACTCCA
64 TCAC-CCA
* * * ** ** * *
393612 TAATTAATTCTGATTTGGTGTTCCCATACGAGTCACTCTAATTTTTCGGGACTCCCGTACGAGTC
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
393677 ACCCA
66 ACCCA
* * * * ** * *
393682 TAAA-TAATTATGATTAGGTGCT-CTCATACGAGTCACTTTAATTCTTCAAGGCTCCTGTAAGTG
1 -AAATTAATTATGATTAGGTGTTCCT-GTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAG
*
393745 TCACCCT
64 TCACCCA
** * * *** * * * *
393752 AAATTAATTATGATTAAATGCTCCTTTTTAAGTCACGCTAATCCTTCGGGGTTTCTATACGAGTC
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
*
393817 ACCCT
66 ACCCA
* * * * * * *
393822 TAATTAATTATGAGTAGGTG-TCCCGTACAAGTCACTCTAATCCTTCGAGACTCCCGTACGAGTC
1 AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
393886 ACCCA
66 ACCCA
* *
393891 TAAA-TAATTATAATTAGGTG-CCCTCGTACGAGTCAC
1 -AAATTAATTATGATTAGGTGTTCCT-GTACGAGTCAC
393927 CCTTAATTAA
Statistics
Matches: 409, Mismatches: 99, Indels: 30
0.76 0.18 0.06
Matches are distributed among these distances:
67 53 0.13
68 2 0.00
69 61 0.15
70 240 0.59
71 53 0.13
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (70 bp):
AAATTAATTATGATTAGGTGTTCCTGTACGAGTCACTCTAATCCTTCGGGGCTCCTGTACGAGTC
ACCCA
Found at i:393909 original size:209 final size:209
Alignment explanation
Indices: 393384--393926 Score: 651
Period size: 211 Copynumber: 2.6 Consensus size: 209
393374 ATATTTCAGA
* * * *
393384 GCTTCTGTACGAGTCACTCAAAATTAATTATGATTAGGTTTTCCTGTACGAGTCACTCTAATCCT
1 GCTTCTGTACGAGTCACCCATAATTAATTATGATTAGG-TGTCCCGTACGAGTCACTCTAATCCT
* * * ** * * * *
393449 TCGGGGCTCCTGTACGAGTCACTCGGAATTAATTATGATTAGGT-AT-TCAT-CAAGCCACTCTA
65 TCGGGACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCTA
*** * * *
393511 ATCCTTTGGGGATCTTGTACGAGTCACCCGAAATTAATTATGATTAAGTGCTCCCTTTTAAGTCA
130 ATCCTTCAAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTCA
**
393576 CTTTAATCCTCCGGG
195 CGCTAATCCTCCGGG
* * * * **
393591 GCTTCTGTATGAGTCACTCCATAATTAATTCTGATTTGGTGTTCCCATACGAGTCACTCTAATTT
1 GCTTCTGTACGAGTCAC-CCATAATTAATTATGATTAGGTG-TCCCGTACGAGTCACTCTAATCC
*
393656 TTCGGGACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTTT
64 TTCGGGACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCT
* * * * *
393721 AATTCTTCAAGGCTCCTGTAAGTGTCACCCTAAATTAATTATGATTAAATGCTCCTTTTTAAGTC
129 AATCCTTCAAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTC
*
393786 ACGCTAATCCTTCGGG
194 ACGCTAATCCTCCGGG
* * * * *
393802 GTTTCTATACGAGTCACCCTTAATTAATTATGAGTAGGTGTCCCGTACAAGTCACTCTAATCCTT
1 GCTTCTGTACGAGTCACCCATAATTAATTATGATTAGGTGTCCCGTACGAGTCACTCTAATCCTT
* * * *
393867 CGAGACTCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCGTACGAGTCAC
66 CGGGACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCAC
393927 CCTTAATTAA
Statistics
Matches: 282, Mismatches: 49, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
207 17 0.06
208 75 0.27
209 78 0.28
210 23 0.08
211 89 0.32
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (209 bp):
GCTTCTGTACGAGTCACCCATAATTAATTATGATTAGGTGTCCCGTACGAGTCACTCTAATCCTT
CGGGACTCCCGTACGAGTCACCCATAAATAATTATGATTAGGTGCTCTCATACGAGTCACTCTAA
TCCTTCAAGGATCCTGTAAGAGTCACCCGAAATTAATTATGATTAAATGCTCCCTTTTAAGTCAC
GCTAATCCTCCGGG
Found at i:393937 original size:178 final size:179
Alignment explanation
Indices: 393744--394067 Score: 409
Period size: 178 Copynumber: 1.8 Consensus size: 179
393734 TCCTGTAAGT
** ** * ** * *
393744 GTCACCCTAAATTAATTATGATTAAATGCTCCTTTTTAAGTCACGCTAATCCTTCGGGGTTTCTA
1 GTCACCCTAAATTAATTATGATTAAATGCTCCCGTACAAGTCACGCTAATCCTTCGAGACTCCCA
* * *
393809 TACGAGTCACCCTTAATTAATTATGAGTAGGTGTCC-CGTACAAGTCACTCTAATCCTTCG-AGA
66 TACGAGTCACCCATAAATAATTATAAGTAGGTGTCCTCGTACAAGTCACTCTAATCCTTCGAAG-
*
393872 CTCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCGTACGA
130 CTCCCGTAAGAGTCACCCATAAATAATTATAATTAGGTGCCCTCGTACGA
* ** * * *
393922 GTCACCCTTAATTAATTATGATTAGGTGTTCCCGTACAAGTCACTCTAATCCTTCGAGACTCCCG
1 GTCACCCTAAATTAATTATGATTAAATGCTCCCGTACAAGTCACGCTAATCCTTCGAGACTCCCA
* * * *
393987 TACGAGTCACCCATAAATAATTATAATTAGGTGTCCTCGTACGAGTCACTTTAATTCTTCGAAGC
66 TACGAGTCACCCATAAATAATTATAAGTAGGTGTCCTCGTACAAGTCACTCTAATCCTTCGAAGC
*
394052 TCCCGTAAGTGTCACC
131 TCCCGTAAGAGTCACC
394068 TAGAATTAAT
Statistics
Matches: 120, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
178 82 0.68
179 36 0.30
180 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (179 bp):
GTCACCCTAAATTAATTATGATTAAATGCTCCCGTACAAGTCACGCTAATCCTTCGAGACTCCCA
TACGAGTCACCCATAAATAATTATAAGTAGGTGTCCTCGTACAAGTCACTCTAATCCTTCGAAGC
TCCCGTAAGAGTCACCCATAAATAATTATAATTAGGTGCCCTCGTACGA
Found at i:393958 original size:39 final size:38
Alignment explanation
Indices: 393873--394035 Score: 142
Period size: 39 Copynumber: 4.4 Consensus size: 38
393863 CCTTCGAGAC
393873 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
1 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
* * * *
393911 CCCTCGTACGAGTCACCCTTAATTAATTATGATTAGGTG
1 TCC-CGTACGAGTCACCCATAAATAATTATAATTAGGTG
* * ** ** **
393950 TTCCCGTACAAGTCACTC-T-AAT-CCT-T--CGA-GAC
1 -TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
393982 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
1 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
394020 TCCTCGTACGAGTCAC
1 TCC-CGTACGAGTCAC
394036 TTTAATTCTT
Statistics
Matches: 93, Mismatches: 22, Indels: 19
0.69 0.16 0.14
Matches are distributed among these distances:
31 15 0.16
32 2 0.02
33 4 0.04
34 1 0.01
35 2 0.02
36 1 0.01
37 3 0.03
38 7 0.08
39 56 0.60
40 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (38 bp):
TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTG
Found at i:393999 original size:109 final size:108
Alignment explanation
Indices: 393809--394035 Score: 427
Period size: 109 Copynumber: 2.1 Consensus size: 108
393799 GGGGTTTCTA
393809 TACGAGTCACCCTTAATTAATTATGAGTAGGTGTCCCGTACAAGTCACTCTAATCCTTCGAGACT
1 TACGAGTCACCCTTAATTAATTATGAGTAGGTGTCCCGTACAAGTCACTCTAATCCTTCGAGACT
393874 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
66 CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
*
393917 TACGAGTCACCCTTAATTAATTATGATTAGGTGTTCCCGTACAAGTCACTCTAATCCTTCGAGAC
1 TACGAGTCACCCTTAATTAATTATGAGTAGGTG-TCCCGTACAAGTCACTCTAATCCTTCGAGAC
*
393982 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGTCCTCG
65 TCCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
394026 TACGAGTCAC
1 TACGAGTCAC
394036 TTTAATTCTT
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 32 0.28
109 84 0.72
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (108 bp):
TACGAGTCACCCTTAATTAATTATGAGTAGGTGTCCCGTACAAGTCACTCTAATCCTTCGAGACT
CCCGTACGAGTCACCCATAAATAATTATAATTAGGTGCCCTCG
Found at i:394028 original size:70 final size:70
Alignment explanation
Indices: 393915--394067 Score: 202
Period size: 70 Copynumber: 2.2 Consensus size: 70
393905 TAGGTGCCCT
* * *
393915 CGTACGAGTCACCCTTAATTAATTATGATTAGGTGTTCCCGTACAAGTCACTCTAATCCTTCG-A
1 CGTACGAGTCACCCATAAATAATTATAATTAGGTGTTCCCGTACAAGTCACTCTAATCCTTCGAA
393979 GACTCC
66 G-CTCC
* * *
393985 CGTACGAGTCACCCATAAATAATTATAATTAGGTG-TCCTCGTACGAGTCACTTTAATTCTTCGA
1 CGTACGAGTCACCCATAAATAATTATAATTAGGTGTTCC-CGTACAAGTCACTCTAATCCTTCGA
394049 AGCTCC
65 AGCTCC
* *
394055 CGTAAGTGTCACC
1 CGTACGAGTCACC
394068 TAGAATTAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 3 0.04
70 68 0.93
71 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (70 bp):
CGTACGAGTCACCCATAAATAATTATAATTAGGTGTTCCCGTACAAGTCACTCTAATCCTTCGAA
GCTCC
Found at i:394248 original size:26 final size:26
Alignment explanation
Indices: 394192--394241 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
394182 TCATAATACA
394192 TATTTACACCAATGAAATTTAACACG
1 TATTTACACCAATGAAATTTAACACG
**
394218 TATTTACATTAATGAAA-TTAACAC
1 TATTTACACCAATGAAATTTAACAC
394242 TTAATTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (26 bp):
TATTTACACCAATGAAATTTAACACG
Found at i:394287 original size:51 final size:51
Alignment explanation
Indices: 394229--394554 Score: 291
Period size: 51 Copynumber: 6.4 Consensus size: 51
394219 ATTTACATTA
* * * *
394229 ATGAAATTAACACTTAATTTTAGCAGTAAAACTTAACATAAACTTACAATG
1 ATGAAATTAACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
* * * * *
394280 ATAAAATTAACACTTAATTCTACCAATGAAACTTAATATAGACTTACACCG
1 ATGAAATTAACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
* * * * * * *
394331 GT-AAATTAAACTCTTAATTCCAACAATGGAAGTTAACATAGACTTACACTG
1 ATGAAATT-AACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
* * * *
394382 GTGAAATTAAGACTTAATTCTAGTAGTGAAACTTAACATAGACTTACA-TC
1 ATGAAATTAACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
* ** *** ** *
394432 AGTGAAATTAACACTTAATTATAATAGTGAAACTTGTTATAGGGTTACACTA
1 A-TGAAATTAACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
* *
394484 ATGAAATTAACACTTAATT-TCAGCAGTAAAACTTAACATAGACTTATA-TCG
1 ATGAAATTAACACTTAATTCT-AGCAGTGAAACTTAACATAGACTTACACT-G
* *
394535 GTGAAATTAACACTAAATTC
1 ATGAAATTAACACTTAATTC
394555 CAGTAATGAA
Statistics
Matches: 220, Mismatches: 48, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
50 8 0.04
51 205 0.93
52 7 0.03
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (51 bp):
ATGAAATTAACACTTAATTCTAGCAGTGAAACTTAACATAGACTTACACTG
Found at i:394460 original size:25 final size:25
Alignment explanation
Indices: 394382--394463 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
394372 ACTTACACTG
* * *
394382 GTGAAATTAAGACTTAATTCTAGTA
1 GTGAAATTAACACTTAATTATAATA
*
394407 GTGAAACTTAACA--TAGACTTA-CATCA
1 GTGAAA-TTAACACTTA-A-TTATAAT-A
394433 GTGAAATTAACACTTAATTATAATA
1 GTGAAATTAACACTTAATTATAATA
394458 GTGAAA
1 GTGAAA
394464 CTTGTTATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
24 2 0.04
25 24 0.53
26 17 0.38
27 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (25 bp):
GTGAAATTAACACTTAATTATAATA
Found at i:394480 original size:153 final size:153
Alignment explanation
Indices: 394230--394566 Score: 365
Period size: 153 Copynumber: 2.2 Consensus size: 153
394220 TTTACATTAA
* * * *
394230 TGAAATTAACACTTAATTTTAGCAGTAAAACTTAACATAAACTTACAATGATAAAATTAACACTT
1 TGAAATTAACACTTAATTCTAGTAGTGAAACTTAACATAAACTTACAATCATAAAATTAACACTT
* * ** * *
394295 AATTCTACCAATGAAACTTAATATAGACTTACACCGGT-AAATTAAACTCTTAATTCCAACAATG
66 AATTATAACAATGAAACTTAATATAGACTTACACCAATGAAATT-AACACTTAATTCCAACAATA
* *
394359 GAAGTTAACATAGACTTACA-CTGG
130 AAACTTAACATAGACTTACATC-GG
* * *
394383 TGAAATTAAGACTTAATTCTAGTAGTGAAACTTAACATAGACTTAC-ATCAGTGAAATTAACACT
1 TGAAATTAACACTTAATTCTAGTAGTGAAACTTAACATAAACTTACAATCA-TAAAATTAACACT
* * ** ** * * * *
394447 TAATTATAATAGTGAAACTTGTTATAGGGTTACACTAATGAAATTAACACTTAATTTCAGCAGTA
65 TAATTATAACAATGAAACTTAATATAGACTTACACCAATGAAATTAACACTTAATTCCAACAATA
*
394512 AAACTTAACATAGACTTATATCGG
130 AAACTTAACATAGACTTACATCGG
* * *
394536 TGAAATTAACACTAAATTCCAGTAATGAAAC
1 TGAAATTAACACTTAATTCTAGTAGTGAAAC
394567 GATAAAAATG
Statistics
Matches: 151, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
152 3 0.02
153 142 0.94
154 6 0.04
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (153 bp):
TGAAATTAACACTTAATTCTAGTAGTGAAACTTAACATAAACTTACAATCATAAAATTAACACTT
AATTATAACAATGAAACTTAATATAGACTTACACCAATGAAATTAACACTTAATTCCAACAATAA
AACTTAACATAGACTTACATCGG
Found at i:397997 original size:12 final size:12
Alignment explanation
Indices: 397980--398004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397970 AAGAGTTGAT
397980 AAGTTGAATTTG
1 AAGTTGAATTTG
397992 AAGTTGAATTTG
1 AAGTTGAATTTG
398004 A
1 A
398005 CTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:404258 original size:24 final size:24
Alignment explanation
Indices: 404231--404306 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
404221 TATATCAAAA
404231 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
404255 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
404279 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
404303 ATCA
1 ATCA
404307 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:404307 original size:24 final size:24
Alignment explanation
Indices: 404248--404363 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
404238 CATAAATCAG
* *
404248 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
*
404272 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
404296 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
404320 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
404344 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
404364 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.02
24 77 0.93
25 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:405366 original size:26 final size:26
Alignment explanation
Indices: 405337--405389 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
405327 TCAGTTTTAT
*
405337 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
405363 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
405389 T
1 T
405390 TCTTGGGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:406817 original size:8 final size:8
Alignment explanation
Indices: 406787--406835 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
406777 AGTCAACAGT
406787 GGTCAACG
1 GGTCAACG
406795 CCGGTCAAC-
1 --GGTCAACG
406804 GGTCAACG
1 GGTCAACG
406812 GGTCAACG
1 GGTCAACG
406820 GGT---CG
1 GGTCAACG
406825 GGTCAACG
1 GGTCAACG
406833 GGT
1 GGT
406836 TGGTCAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
7 7 0.20
8 16 0.46
10 7 0.20
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:406817 original size:15 final size:16
Alignment explanation
Indices: 406787--406820 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
406777 AGTCAACAGT
406787 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
406804 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
406819 GG
1 GG
406821 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:406828 original size:13 final size:13
Alignment explanation
Indices: 406810--406853 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
406800 CAACGGTCAA
406810 CGGGTCAACGGGT
1 CGGGTCAACGGGT
406823 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
406836 -TGGTCAACAGGT
1 CGGGTCAACGGGT
*
406848 TGGGTC
1 CGGGTC
406854 GGGTAAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.16, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:406842 original size:12 final size:12
Alignment explanation
Indices: 406812--406850 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
406802 ACGGTCAACG
*
406812 GGTCAACGGGTCG
1 GGTCAACGGGT-T
406825 GGTCAACGGGTT
1 GGTCAACGGGTT
*
406837 GGTCAACAGGTT
1 GGTCAACGGGTT
406849 GG
1 GG
406851 GTCGGGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.21
Consensus pattern (12 bp):
GGTCAACGGGTT
Found at i:415690 original size:28 final size:30
Alignment explanation
Indices: 415657--415720 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
415647 ACTAAAATAT
* *
415657 AAATAATTATAATTTT-AA-GCATAAATTA
1 AAATAATTAGAATTTTAAAGGCAAAAATTA
*
415685 AAATAA-TAGAATTTTAAAGGGAAAAATTA
1 AAATAATTAGAATTTTAAAGGCAAAAATTA
415714 AAATAAT
1 AAATAAT
415721 AGTAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 8 0.27
28 8 0.27
29 14 0.47
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (30 bp):
AAATAATTAGAATTTTAAAGGCAAAAATTA
Found at i:416390 original size:22 final size:22
Alignment explanation
Indices: 416365--416413 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
416355 TAAAAAAATC
416365 TTTTTTTC-CTTTTCCTTCTCAT
1 TTTTTTTCACTTTTCCTT-TCAT
* *
416387 TTTTCTTCATTTTTCCTTTCAT
1 TTTTTTTCACTTTTCCTTTCAT
416409 TTTTT
1 TTTTT
416414 AGAGAGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTCACTTTTCCTTTCAT
Found at i:416398 original size:10 final size:12
Alignment explanation
Indices: 416374--416412 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
416364 CTTTTTTTCC
416374 TTTTCCTTCTCAT
1 TTTTCCTT-TCAT
416387 TTTT-C-TTCAT
1 TTTTCCTTTCAT
416397 TTTTCCTTTCAT
1 TTTTCCTTTCAT
416409 TTTT
1 TTTT
416413 TAGAGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 10 0.42
13 4 0.17
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCCTTTCAT
Found at i:420921 original size:20 final size:20
Alignment explanation
Indices: 420897--420939 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
420887 TGAAGAAATG
*
420897 AAAAAGAAAAAAATAAAAGTT
1 AAAATGAAAAAAA-AAAAGTT
* *
420918 AAAATGAAATAGAAAAAGTT
1 AAAATGAAAAAAAAAAAGTT
420938 AA
1 AA
420940 GGATGAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (20 bp):
AAAATGAAAAAAAAAAAGTT
Found at i:420954 original size:20 final size:20
Alignment explanation
Indices: 420911--420954 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
420901 AGAAAAAAAT
*
420911 AAAAGTTAAAATGAAATAGA
1 AAAAGTTAAAATGAAAGAGA
*
420931 AAAAGTTAAGGATGAAAGAGA
1 AAAAGTTAA-AATGAAAGAGA
420952 AAA
1 AAA
420955 TAAAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAATGAAAGAGA
Found at i:436082 original size:3 final size:3
Alignment explanation
Indices: 436074--436152 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
436064 GATCCATACA
436074 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
436122 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
436153 CTTTTAAACA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:438086 original size:21 final size:22
Alignment explanation
Indices: 438044--438086 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
438034 AATCAGATTG
438044 CCCAGGGGGTACCGATTCCCCC
1 CCCAGGGGGTACCGATTCCCCC
438066 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACCGATTCCCC
438087 TTGTCTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (22 bp):
CCCAGGGGGTACCGATTCCCCC
Found at i:439388 original size:19 final size:20
Alignment explanation
Indices: 439364--439411 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
439354 AACGATTTTC
*
439364 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
439383 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
439403 TTTTGAAAA
1 TTTTGAAAA
439412 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:440803 original size:21 final size:20
Alignment explanation
Indices: 440772--440875 Score: 129
Period size: 21 Copynumber: 5.1 Consensus size: 20
440762 AATCAGATTG
440772 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
440792 CCACAAGGGGTACAGATTCCC
1 CC-CAGGGGGTACAGATTCCC
*
440813 CCCTAGGGGGTACCGATTCCC
1 CCC-AGGGGGTACAGATTCCC
* * *
440834 CCCTGGGGGAACATATTCCC
1 CCCAGGGGGTACAGATTCCC
440854 CCCAGGGGGTATC-GATTCCC
1 CCCAGGGGGTA-CAGATTCCC
440874 CC
1 CC
440876 TGTCTAACGG
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
20 33 0.46
21 38 0.54
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:440870 original size:40 final size:40
Alignment explanation
Indices: 440772--440875 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 40
440762 AATCAGATTG
*
440772 CCCAGGGGGTACAGATTCCCCCACAAGGGGTACAGATTCCC
1 CCCAGGGGGTAC-GATTCCCCCACAAGGGGAACAGATTCCC
** *
440813 CCCTAGGGGGTACCGATTCCCCC-CTGGGGGAACATATTCCC
1 CCC-AGGGGGTA-CGATTCCCCCACAAGGGGAACAGATTCCC
440854 CCCAGGGGGTATCGATTCCCCC
1 CCCAGGGGGTA-CGATTCCCCC
440876 TGTCTAACGG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
40 18 0.32
41 20 0.36
42 17 0.30
43 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (40 bp):
CCCAGGGGGTACGATTCCCCCACAAGGGGAACAGATTCCC
Found at i:444169 original size:13 final size:13
Alignment explanation
Indices: 444151--444176 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444141 ACGCCCAGCG
444151 ACCCGTAGATCGC
1 ACCCGTAGATCGC
444164 ACCCGTAGATCGC
1 ACCCGTAGATCGC
444177 CATGCGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
ACCCGTAGATCGC
Found at i:444492 original size:15 final size:15
Alignment explanation
Indices: 444472--444510 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
444462 TTCGGTTGTA
444472 AGAACAAAGAAAGGG
1 AGAACAAAGAAAGGG
444487 AGAACAAAGAAAGGG
1 AGAACAAAGAAAGGG
*
444502 AGAAGAAAG
1 AGAACAAAG
444511 GAAAAAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAACAAAGAAAGGG
Found at i:444690 original size:10 final size:10
Alignment explanation
Indices: 444675--444703 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
444665 TTGTTTGTTG
444675 AATTATATTA
1 AATTATATTA
444685 AATTATATTA
1 AATTATATTA
444695 AATT-TATTA
1 AATTATATTA
444704 TATGTCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTATATTA
Found at i:444845 original size:33 final size:33
Alignment explanation
Indices: 444808--444875 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
444798 GAAGTTATAA
** * *
444808 TATATATAAAATTTAGTTAATTAGTTTTTTAGT
1 TATATATAAAAAATAATTAATTAGTTTGTTAGT
444841 TATATATAAAAAATAATTAATTAGTTTGTTAGT
1 TATATATAAAAAATAATTAATTAGTTTGTTAGT
444874 TA
1 TA
444876 AATAGTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (33 bp):
TATATATAAAAAATAATTAATTAGTTTGTTAGT
Found at i:444958 original size:36 final size:36
Alignment explanation
Indices: 444906--444983 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
444896 TTTGTTGAAT
* *
444906 TTATATTATATAAAAAATATAGTTTATTAGTTTTAG
1 TTATATTATATAAAAAAAATAGTTTATTAGTTTAAG
444942 TTATATTATA-ATAAAAAAATAGTTTATTAGTTTAAG
1 TTATATTATATA-AAAAAAATAGTTTATTAGTTTAAG
444978 TTATAT
1 TTATAT
444984 GAAAGAATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (36 bp):
TTATATTATATAAAAAAAATAGTTTATTAGTTTAAG
Found at i:445107 original size:27 final size:27
Alignment explanation
Indices: 445072--445123 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
445062 ATATATAAGT
445072 TATTATATAAAAAATTT-GTTGAATTTA
1 TATTATATAAAAAATTTAGTT-AATTTA
445099 TATTATATAAAAAATTTAGTTAATT
1 TATTATATAAAAAATTTAGTTAATT
445124 AGTTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (27 bp):
TATTATATAAAAAATTTAGTTAATTTA
Found at i:445110 original size:70 final size:70
Alignment explanation
Indices: 445028--445158 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
445018 CACGTTTAAG
** *
445028 TTATATTTTAAAAAATTTAGTTTGTTAGTTTATTATATATAAG-T-TATTAT-ATAAAAAATTTG
1 TTATATTTTAAAAAATTTAGTTAATTAGTTAATTA-ATATAAGTTATATTATAATAAAAAATTTG
445090 TTGAAT
65 TTGAAT
*
445096 TTATATTATATAAAAAATTTAGTTAATTAGTTAATTAATTTAAGTTATATTATAATAAAAAAT
1 TTATATT-T-TAAAAAATTTAGTTAATTAGTTAATTAATATAAGTTATATTATAATAAAAAAT
445159 AGTTTATTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
68 7 0.13
69 7 0.13
70 25 0.46
71 6 0.11
72 9 0.17
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (70 bp):
TTATATTTTAAAAAATTTAGTTAATTAGTTAATTAATATAAGTTATATTATAATAAAAAATTTGT
TGAAT
Found at i:447728 original size:22 final size:22
Alignment explanation
Indices: 447703--447744 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
447693 TAAAAAGAAA
447703 AAATTCGACTATTTATAAATAT
1 AAATTCGACTATTTATAAATAT
*
447725 AAATTTGACTATTTATAAAT
1 AAATTCGACTATTTATAAAT
447745 TCAACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTCGACTATTTATAAATAT
Found at i:447852 original size:24 final size:24
Alignment explanation
Indices: 447796--447876 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
447786 TTTGAATATT
*
447796 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATTATTATTAG
*
447820 TAACCATTATTAAATTATTATTAG
1 TAATCATTATTAAATTATTATTAG
* *
447844 TAATTATTA-TAATTTCATTATTAG
1 TAATCATTATTAAATT-ATTATTAG
447868 TAATCATTA
1 TAATCATTA
447877 CCAAATCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.10
24 45 0.90
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
TAATCATTATTAAATTATTATTAG
Found at i:447885 original size:24 final size:24
Alignment explanation
Indices: 447796--447887 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
447786 TTTGAATATT
*
447796 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
447820 TAACCATTATTAAATTATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
447844 TAATTATTA-TAATTTCATTATTAG
1 TAATCATTATTAA-ATCATTATTAG
**
447868 TAATCATTACCAAATCATTA
1 TAATCATTATTAAATCATTA
447888 GTATCAAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.05
24 52 0.91
25 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (24 bp):
TAATCATTATTAAATCATTATTAG
Found at i:448126 original size:16 final size:16
Alignment explanation
Indices: 448105--448144 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
448095 CTTTTAAATG
448105 ATTTAAATATG-TACAA
1 ATTTAAATATGCTA-AA
*
448121 ATTTAAATTTGCTAAA
1 ATTTAAATATGCTAAA
448137 ATTTAAAT
1 ATTTAAAT
448145 GGTTAACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTTAAATATGCTAAA
Found at i:448425 original size:66 final size:61
Alignment explanation
Indices: 448318--448454 Score: 211
Period size: 66 Copynumber: 2.2 Consensus size: 61
448308 GAAAGCTAAA
*
448318 TTGAATGAAACAATGTTTCCTTTATTTTAGGTAGTCAGATGTGATAGATCAGAAATAATTG
1 TTGAATGAAACAATGTTTCCTTTATTTTAGGAAGTCAGATGTGATAGATCAGAAATAATTG
*
448379 TTGAATGAAACAATGTTTGTCGCCCTTTATTTTAGGAAGTCGGATGTGATAGATCAGAAATAATT
1 TTGAATGAAACAATG-TT-T---CCTTTATTTTAGGAAGTCAGATGTGATAGATCAGAAATAATT
448444 G
61 G
448445 TTGAATGAAA
1 TTGAATGAAA
448455 GCCACATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
61 15 0.22
62 2 0.03
63 1 0.01
66 51 0.74
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (61 bp):
TTGAATGAAACAATGTTTCCTTTATTTTAGGAAGTCAGATGTGATAGATCAGAAATAATTG
Found at i:451892 original size:30 final size:30
Alignment explanation
Indices: 451858--451916 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
451848 CTAACTTTTT
*
451858 AAAATTACACTTTTGGTACCTAAACATTTG
1 AAAATTACACTTTTGATACCTAAACATTTG
* * *
451888 AAAATTACCCTTTTGATCCCTAAATATTT
1 AAAATTACACTTTTGATACCTAAACATTT
451917 CCATACATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
AAAATTACACTTTTGATACCTAAACATTTG
Found at i:452767 original size:19 final size:19
Alignment explanation
Indices: 452743--452802 Score: 120
Period size: 19 Copynumber: 3.2 Consensus size: 19
452733 TGAAAATCGT
452743 GATTTTCCAAATTCGTTGC
1 GATTTTCCAAATTCGTTGC
452762 GATTTTCCAAATTCGTTGC
1 GATTTTCCAAATTCGTTGC
452781 GATTTTCCAAATTCGTTGC
1 GATTTTCCAAATTCGTTGC
452800 GAT
1 GAT
452803 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (19 bp):
GATTTTCCAAATTCGTTGC
Found at i:452822 original size:22 final size:22
Alignment explanation
Indices: 452793--452846 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
452783 TTTTCCAAAT
452793 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
452815 TTGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
452837 TCGTTGCGAT
1 TCGTTGCGAT
452847 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:454618 original size:2 final size:2
Alignment explanation
Indices: 454611--454655 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
454601 AACATGCACC
454611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
454653 TA T
1 TA T
454656 TGACAATAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:456266 original size:3 final size:3
Alignment explanation
Indices: 456260--456292 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
456250 TAAGATGACG
456260 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
456293 CGAAAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:456545 original size:40 final size:41
Alignment explanation
Indices: 456489--456808 Score: 183
Period size: 40 Copynumber: 7.5 Consensus size: 41
456479 TATCTATGGT
*
456489 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* *
456529 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * *
456575 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-GGG-
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
456617 TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* *
456657 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * * * * *
456703 TAACACGGTTCCTATGTGATGAGGACG-GCTGGTTATCTA-TGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
*
456746 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* * *
456787 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGA
456809 GGACGACTGG
Statistics
Matches: 214, Mismatches: 43, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
38 3 0.01
39 2 0.01
40 65 0.30
41 20 0.09
42 26 0.12
43 31 0.14
44 2 0.01
46 57 0.27
47 8 0.04
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (41 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGGA
Found at i:456613 original size:46 final size:45
Alignment explanation
Indices: 456449--456778 Score: 164
Period size: 40 Copynumber: 7.7 Consensus size: 45
456439 GTTGGGGACG
* * ** * *
456449 ACACTGCTCGTACGTGATGAAGAG-TTTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
* * * *
456491 ACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
** **
456531 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * *
456577 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-AGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* * *
456619 ACACGGCTCATACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
** **
456659 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * * * *
456705 ACACGGTTCCTATGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
*
456748 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGAGCTGGT
456779 CTGGGGAATG
Statistics
Matches: 227, Mismatches: 36, Indels: 49
0.73 0.12 0.16
Matches are distributed among these distances:
37 4 0.02
38 1 0.00
39 2 0.01
40 63 0.28
41 1 0.00
42 48 0.21
43 34 0.15
44 3 0.01
45 4 0.02
46 59 0.26
47 8 0.04
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (45 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
Found at i:456687 original size:128 final size:129
Alignment explanation
Indices: 456475--456808 Score: 598
Period size: 128 Copynumber: 2.6 Consensus size: 129
456465 ATGAAGAGTT
*
456475 TGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
456540 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
*
456604 TGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
*
456668 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTATGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
*
456732 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGTT
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGGCT
* *
456797 CCTACATGATGA
65 CATACGTGATGA
456809 GGACGACTGG
Statistics
Matches: 196, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
128 125 0.64
129 46 0.23
130 25 0.13
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (129 bp):
TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
Found at i:457249 original size:15 final size:15
Alignment explanation
Indices: 457225--457268 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
457215 AAGATGATCT
*
457225 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
457240 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
457255 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
457269 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:457479 original size:62 final size:60
Alignment explanation
Indices: 457385--457521 Score: 145
Period size: 62 Copynumber: 2.2 Consensus size: 60
457375 AAGGTGGGTA
*
457385 TTTTCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAACCA-ACTCAAAG-ATT
1 TTTTCAAAAGAAATTGTCTCGAGAGACAAAA-TTT-TTTCAAA-GAAA-CAGACTCAAAGAATT
** * *
457447 TTTTCAAAAGAAATTGTCTTTAGGAGA-TAAATTTTTTCAAAGAAATAGACTCAAAGATATT
1 TTTTCAAAAGAAATTGTCTCGA-GAGACAAAATTTTTTCAAAGAAACAGACTCAAAGA-ATT
457508 TGTTTCAAAAGAAA
1 T-TTTCAAAAGAAA
457522 CAACTCAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
58 1 0.02
59 12 0.18
60 7 0.11
61 7 0.11
62 34 0.52
63 4 0.06
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (60 bp):
TTTTCAAAAGAAATTGTCTCGAGAGACAAAATTTTTTCAAAGAAACAGACTCAAAGAATT
Found at i:457527 original size:29 final size:29
Alignment explanation
Indices: 457477--457562 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
457467 TAGGAGATAA
*
457477 ATTTTTTC-AAAGAAATAGACTCAAAGAT
1 ATTTTTTCAAAAGAAACAGACTCAAAGAT
457505 ATTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 ATTT-TTTCAAAAGAAACAGACTCAAAGAT
*
457534 -TTTTATTCAAAAGGAACAGACTCAAAGAT
1 ATTTT-TTCAAAAGAAACAGACTCAAAGAT
457563 TTATCTCAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
27 1 0.02
28 19 0.37
29 24 0.46
30 8 0.15
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (29 bp):
ATTTTTTCAAAAGAAACAGACTCAAAGAT
Found at i:457571 original size:28 final size:27
Alignment explanation
Indices: 457477--457578 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 27
457467 TAGGAGATAA
* *
457477 ATTTTTTC-AAAGAAATAGACTCAAAG
1 ATTTATTCAAAAGAAACAGACTCAAAG
*
457503 ATATTTGTTTCAAAAGAAACA-ACTCAAAG
1 --ATTT-ATTCAAAAGAAACAGACTCAAAG
*
457532 ATTTTTATTCAAAAGGAACAGACTCAAAG
1 A--TTTATTCAAAAGAAACAGACTCAAAG
*
457561 ATTTATCTCAAGAGAAAC
1 ATTTAT-TCAAAAGAAAC
457579 TGTCTCCAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
27 6 0.10
28 25 0.40
29 24 0.38
30 8 0.13
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (27 bp):
ATTTATTCAAAAGAAACAGACTCAAAG
Found at i:458050 original size:104 final size:105
Alignment explanation
Indices: 457899--458094 Score: 290
Period size: 104 Copynumber: 1.9 Consensus size: 105
457889 ACGATCTCAA
* *
457899 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCA
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAAATTGGATCTCAAAGGAAAAAGGTCTCA
457964 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
66 AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
* * *
458004 GTGAGATTAA-TTTGTTTTAA-GTGAATCAAATTC-AAAATTGGTATCTCAAAGGAAAAATGTCT
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCGAAAATTGG-ATCTCAAAGGAAAAAGGTCT
* *
458066 CAAGCGAGACGAAGTTTGTTTTAAGAGAA
64 CAAGCGAGACGAAATTTGTTTTAAAAGAA
458095 TTTGTCTCAA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
103 7 0.09
104 61 0.74
105 14 0.17
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAAATTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
Found at i:458110 original size:36 final size:35
Alignment explanation
Indices: 458061--458162 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 35
458051 AAAGGAAAAA
* * **
458061 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGA-AAGC
* *
458097 TGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAGC
*
458132 TGTCTCAAGCGAGAC-AAA-TTGTTTCAAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAAA
458163 AACACCCTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
33 11 0.19
34 3 0.05
35 16 0.28
36 27 0.47
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAGC
Found at i:458465 original size:4 final size:4
Alignment explanation
Indices: 458449--458516 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
458439 ATGCAAATTT
*
458449 TATG TAT- TATG TATG TATG TAT- TGATG TATG TATG TAT- TGATA TATG
1 TATG TATG TATG TATG TATG TATG T-ATG TATG TATG TATG T-ATG TATG
*
458496 TTTG TAT- TGATG TATG TATG T
1 TATG TATG T-ATG TATG TATG T
458517 TGATTTGTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 6 0.11
4 45 0.83
5 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:458478 original size:16 final size:16
Alignment explanation
Indices: 458449--458516 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
458439 ATGCAAATTT
458449 TATGTATT-ATGTATG
1 TATGTATTGATGTATG
458464 TATGTATTGATGTATG
1 TATGTATTGATGTATG
*
458480 TATGTATTGATATATG
1 TATGTATTGATGTATG
*
458496 TTTGTATTGATGTATG
1 TATGTATTGATGTATG
458512 TATGT
1 TATGT
458517 TGATTTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
15 8 0.17
16 40 0.83
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (16 bp):
TATGTATTGATGTATG
Found at i:464308 original size:2 final size:2
Alignment explanation
Indices: 464301--464325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
464291 AACATGCACC
464301 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
464326 TGACAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:465945 original size:3 final size:3
Alignment explanation
Indices: 465939--465968 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
465929 TAAGATGACG
465939 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
465969 CGAAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:466221 original size:40 final size:41
Alignment explanation
Indices: 466165--466484 Score: 174
Period size: 40 Copynumber: 7.5 Consensus size: 41
466155 TATCTATGGT
*
466165 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* *
466205 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * *
466251 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-GGG-
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
*
466293 TGACACGACTCATACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* *
466333 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * * * * *
466379 TAACACGGTTCCTATGTGATGAGGACG-GCTGGTTATCTA-TGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
*
466422 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* * *
466463 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGA
466485 GGACGACTTG
Statistics
Matches: 212, Mismatches: 45, Indels: 45
0.70 0.15 0.15
Matches are distributed among these distances:
38 3 0.01
39 2 0.01
40 64 0.30
41 20 0.09
42 25 0.12
43 31 0.15
44 2 0.01
46 57 0.27
47 8 0.04
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (41 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGGA
Found at i:466289 original size:46 final size:45
Alignment explanation
Indices: 466125--466454 Score: 155
Period size: 40 Copynumber: 7.7 Consensus size: 45
466115 GTTGGGGACG
* * ** * *
466125 ACACTGCTCGTACGTGATGAAGAG-TTTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
* * * *
466167 ACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
** **
466207 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * *
466253 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-AGG-G-TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* * * *
466295 ACACGACTCATACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
** **
466335 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * * * *
466381 ACACGGTTCCTATGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
*
466424 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGAGCTGGT
466455 CTGGGGAATG
Statistics
Matches: 225, Mismatches: 38, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
37 4 0.02
38 1 0.00
39 2 0.01
40 62 0.28
41 1 0.00
42 47 0.21
43 34 0.15
44 3 0.01
45 4 0.02
46 59 0.26
47 8 0.04
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (45 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
Found at i:466363 original size:128 final size:129
Alignment explanation
Indices: 466151--466484 Score: 589
Period size: 128 Copynumber: 2.6 Consensus size: 129
466141 ATGAAGAGTT
*
466151 TGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
466216 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
* *
466280 TGGTTATCTA-GGGTGACACGACTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
*
466344 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTATGTGATGAGGACGGC
66 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
*
466408 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGTT
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGGCT
* *
466473 CCTACATGATGA
65 CATACGTGATGA
466485 GGACGACTTG
Statistics
Matches: 194, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
128 124 0.64
129 45 0.23
130 25 0.13
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (129 bp):
TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
Found at i:466931 original size:15 final size:15
Alignment explanation
Indices: 466907--466950 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
466897 AAGATGATCT
*
466907 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
466922 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
466937 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
466951 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:467160 original size:62 final size:60
Alignment explanation
Indices: 467066--467202 Score: 145
Period size: 62 Copynumber: 2.2 Consensus size: 60
467056 AAGGTGGGTA
*
467066 TTTTCAAAAGAAGTTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAACCA-ACTCAAAG-ATT
1 TTTTCAAAAGAAATTGTCTCGAGAGACAAAA-TTT-TTTCAAA-GAAA-CAGACTCAAAGAATT
** * *
467128 TTTTCAAAAGAAATTGTCTTTAGGAGA-TAAATTTTTTCAAAGAAATAGACTCAAAGATATT
1 TTTTCAAAAGAAATTGTCTCGA-GAGACAAAATTTTTTCAAAGAAACAGACTCAAAGA-ATT
467189 TGTTTCAAAAGAAA
1 T-TTTCAAAAGAAA
467203 CAACTCAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
58 1 0.02
59 12 0.18
60 7 0.11
61 7 0.11
62 34 0.52
63 4 0.06
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (60 bp):
TTTTCAAAAGAAATTGTCTCGAGAGACAAAATTTTTTCAAAGAAACAGACTCAAAGAATT
Found at i:467236 original size:28 final size:27
Alignment explanation
Indices: 467159--467258 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
467149 AGGAGATAAA
*
467159 TTTTTTCAAAGAAATAGACTCAAAGAT
1 TTTTTTCAAAGAAACAGACTCAAAGAT
467186 ATTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 -TTT-TTTC-AAAGAAACAGACTCAAAGAT
*
467215 TTTTATTCAAAGGAACAGACTCAAAGAT
1 TTTT-TTCAAAGAAACAGACTCAAAGAT
* *
467243 TTATCTCAAGAGAAAC
1 TTTTTTCAA-AGAAAC
467259 TGTCTCCAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
27 13 0.21
28 27 0.44
29 14 0.23
30 8 0.13
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (27 bp):
TTTTTTCAAAGAAACAGACTCAAAGAT
Found at i:480674 original size:24 final size:24
Alignment explanation
Indices: 480620--480674 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
480610 GTAATTATTC
* *
480620 ATTCAAAAGATGTGACTTTAGGAG
1 ATTCAAAAGATGTGACTATAGAAG
**
480644 AAACAAAAGATGTGACTCAT-GAAG
1 ATTCAAAAGATGTGACT-ATAGAAG
480668 ATTCAAA
1 ATTCAAA
480675 GGGTGTTCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (24 bp):
ATTCAAAAGATGTGACTATAGAAG
Found at i:492320 original size:2 final size:2
Alignment explanation
Indices: 492315--492364 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
492305 TTCAGAGAGG
492315 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
492357 AT AT AT AT
1 AT AT AT AT
492365 GGTTCCACGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:497743 original size:21 final size:21
Alignment explanation
Indices: 497719--497807 Score: 135
Period size: 21 Copynumber: 4.2 Consensus size: 21
497709 AATATGTAAA
497719 TCGCATTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCGAAT
*
497740 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCGAAT
*
497761 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCGAAT
*
497782 TCG-AGTTGCGATTTTCTGAAT
1 TCGCA-TTGCGATTTTCCGAAT
497803 TCGCA
1 TCGCA
497808 GCACAGAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
21 62 0.98
22 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCGAAT
Found at i:497775 original size:42 final size:42
Alignment explanation
Indices: 497719--497807 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
497709 AATATGTAAA
*
497719 TCGCATTGCGATTTTCCGAATTCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCGAATTCGAGTTGCGATTTTCCGAAT
* *
497761 TCGCGTTGCGATTTTCCGAATTCGAGTTGCGATTTTCTGAAT
1 TCGCATTGCGATTTTCCGAATTCGAGTTGCGATTTTCCGAAT
497803 TCGCA
1 TCGCA
497808 GCACAGAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (42 bp):
TCGCATTGCGATTTTCCGAATTCGAGTTGCGATTTTCCGAAT
Found at i:497825 original size:20 final size:20
Alignment explanation
Indices: 497800--497870 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
497790 CGATTTTCTG
*
497800 AATTCGCAGCACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
497820 AATTCGCAATACATAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
497840 AATTCGCAACACTGAATTTCA
1 AATTCGCAACACAGAA-GTCA
497861 AATTCGCAAC
1 AATTCGCAAC
497871 GCAAATTTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 30 0.70
21 13 0.30
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.23
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:497914 original size:28 final size:28
Alignment explanation
Indices: 497874--497935 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
497864 TCGCAACGCA
*
497874 AATTTGGAAAATCGTAACTCGATTTTCG
1 AATTTGGAAAATCGCAACTCGATTTTCG
*
497902 AATTTGGAAAATCGCAACTCGATTTTTG
1 AATTTGGAAAATCGCAACTCGATTTTCG
497930 AATTTG
1 AATTTG
497936 CAACACGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (28 bp):
AATTTGGAAAATCGCAACTCGATTTTCG
Found at i:497938 original size:20 final size:21
Alignment explanation
Indices: 497915--497961 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
497905 TTGGAAAATC
*
497915 GCAACTCG-ATTTTTGAA-TTT
1 GCAACACGAATTTTT-AATTTT
497935 GCAACACGAATTTTTAATTTT
1 GCAACACGAATTTTTAATTTT
497956 GCAACA
1 GCAACA
497962 GGTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
GCAACACGAATTTTTAATTTT
Found at i:498961 original size:24 final size:24
Alignment explanation
Indices: 498910--498963 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
498900 GTATTCGAAA
* * *
498910 TTTGGTCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCAGAC
* *
498934 TTTGATCTTGATCAATACTCAGAT
1 TTTGATCTTGATCAATACCCAGAC
498958 TTTGAT
1 TTTGAT
498964 GATTTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCAGAC
Found at i:501246 original size:18 final size:18
Alignment explanation
Indices: 501223--501258 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
501213 AAGTAAAAGG
*
501223 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
501241 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
501259 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:501542 original size:29 final size:29
Alignment explanation
Indices: 501500--501556 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
501490 GTGATTTTTT
*
501500 GTTGCGATTGTTGCGAAAGTCAAATTCGC
1 GTTGCGATTGTTGCGAAAATCAAATTCGC
501529 GTTGCGATTGTTGCGAAAATCAAATTCG
1 GTTGCGATTGTTGCGAAAATCAAATTCG
501557 AAACGCGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (29 bp):
GTTGCGATTGTTGCGAAAATCAAATTCGC
Found at i:501564 original size:29 final size:29
Alignment explanation
Indices: 501503--501564 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
501493 ATTTTTTGTT
* ****
501503 GCGATTGTTGCGAAAGTCAAATTCGCGTT
1 GCGATTGTTGCGAAAATCAAATTCGAAAC
501532 GCGATTGTTGCGAAAATCAAATTCGAAAC
1 GCGATTGTTGCGAAAATCAAATTCGAAAC
501561 GCGA
1 GCGA
501565 AATTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (29 bp):
GCGATTGTTGCGAAAATCAAATTCGAAAC
Found at i:501566 original size:20 final size:20
Alignment explanation
Indices: 501541--501587 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
501531 TGCGATTGTT
*
501541 GCGAAAATCAAATTCGAAAC
1 GCGAAAATAAAATTCGAAAC
* * *
501561 GCGAAATTAAAATTTGCAAC
1 GCGAAAATAAAATTCGAAAC
501581 GCGAAAA
1 GCGAAAA
501588 ATCGCAACGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (20 bp):
GCGAAAATAAAATTCGAAAC
Found at i:503137 original size:21 final size:21
Alignment explanation
Indices: 503111--503205 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
503101 GTGAATTGGA
* *
503111 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
503132 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
503153 CTCTTGAACGGTGGGA-GGGC
1 CTCTTGAACGATGAGAGGGGC
*
503173 CTCTTGAAAGAT-AG-GGGGC
1 CTCTTGAACGATGAGAGGGGC
503192 CTCTTGAACGATGA
1 CTCTTGAACGATGA
503206 CAGGTGAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
19 16 0.25
20 15 0.23
21 33 0.52
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:503170 original size:42 final size:39
Alignment explanation
Indices: 503111--503201 Score: 146
Period size: 42 Copynumber: 2.3 Consensus size: 39
503101 GTGAATTGGA
*
503111 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAAAGAT-AG-GGGGC
503153 CTCTTGAACGGTGGGAGGGCCTCTTGAAAGATAGGGGGC
1 CTCTTGAACGGTGGGAGGGCCTCTTGAAAGATAGGGGGC
503192 CTCTTGAACG
1 CTCTTGAACG
503202 ATGACAGGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 15 0.31
40 2 0.04
41 15 0.31
42 16 0.33
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.21
Consensus pattern (39 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAAAGATAGGGGGC
Found at i:503483 original size:21 final size:21
Alignment explanation
Indices: 503453--503493 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
503443 ACCATTATCG
* *
503453 TCACGTAAAGTACTGACCTCC
1 TCACGCAAAGCACTGACCTCC
503474 TCACGCAAAGCACTGACCTC
1 TCACGCAAAGCACTGACCTC
503494 ATCGCGTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.20
Consensus pattern (21 bp):
TCACGCAAAGCACTGACCTCC
Found at i:503776 original size:16 final size:16
Alignment explanation
Indices: 503755--503797 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
503745 AGTGGCAAGC
503755 TCAGCCTCTGTGGGTG
1 TCAGCCTCTGTGGGTG
503771 TCAGCCTCTGTGGGTG
1 TCAGCCTCTGTGGGTG
503787 TCAGCCTCTGT
1 TCAGCCTCTGT
503798 AATGGATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.28, G:0.33, T:0.33
Consensus pattern (16 bp):
TCAGCCTCTGTGGGTG
Found at i:505745 original size:20 final size:20
Alignment explanation
Indices: 505720--505768 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
505710 TAAACGCGCT
505720 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTAACTTCTGTG
*
505740 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTAACTTCTGTG
*
505760 TTGTGAATT
1 TTGCGAATT
505769 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.12, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTAACTTCTGTG
Found at i:505782 original size:20 final size:20
Alignment explanation
Indices: 505759--505808 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
505749 TGACTTCTGT
*
505759 GTTGTGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
505779 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
505799 GTTGCGAATT
1 GTTGCGAATT
505809 TTTTGGTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:506783 original size:47 final size:45
Alignment explanation
Indices: 506697--506787 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 45
506687 TGAAATATAT
*
506697 GTTTATTTATTTTAATTTTTTATTCATAATATTGAAATTTTATTTTA
1 GTTTATTTATTGTAATTTTTTA-TCATAATATTGAAA-TTTATTTTA
**
506744 GTTTATGTTATTGTAATTTTTTA-CGATAATATTTTAATTTATTT
1 GTTTAT-TTATTGTAATTTTTTATC-ATAATATTGAAATTTATTT
506788 GCACCATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 8 0.21
47 16 0.41
48 15 0.38
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.63
Consensus pattern (45 bp):
GTTTATTTATTGTAATTTTTTATCATAATATTGAAATTTATTTTA
Found at i:506988 original size:25 final size:26
Alignment explanation
Indices: 506942--506993 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
506932 TAGGGATCGA
506942 CACTGTTGGCCTTTTTGTTTCGAGAG
1 CACTGTTGGCCTTTTTGTTTCGAGAG
506968 CACTGTTGGCC-TTTTGTTTCGAGAG
1 CACTGTTGGCCTTTTTGTTTCGAGAG
506993 C
1 C
506994 TATGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (26 bp):
CACTGTTGGCCTTTTTGTTTCGAGAG
Found at i:508244 original size:13 final size:13
Alignment explanation
Indices: 508226--508250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
508216 ATGATGATAT
508226 TGGTGGTGGTGGG
1 TGGTGGTGGTGGG
508239 TGGTGGTGGTGG
1 TGGTGGTGGTGG
508251 TGAAGGTAAT
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:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (13 bp):
TGGTGGTGGTGGG
Found at i:521176 original size:23 final size:23
Alignment explanation
Indices: 521150--521209 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
521140 CATAACAGCT
*
521150 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * *
521173 CGTAGACTTGCACTGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
521196 CGTAGAATTTCACC
1 CGTAGAATTGCACC
521210 ATAGTGTCAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:521326 original size:2 final size:2
Alignment explanation
Indices: 521321--521368 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
521311 GTTCCAAAGA
521321 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
521363 AT AT AT
1 AT AT AT
521369 CCCGAAGGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:522186 original size:23 final size:23
Alignment explanation
Indices: 522133--522187 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
522123 ATAACCTTTT
**
522133 CATATAACCCCATAGATCTTTAA
1 CATATAATTCCATAGATCTTTAA
*
522156 CATATAATTCCATAGATCTTTAG
1 CATATAATTCCATAGATCTTTAA
522179 CATATAATT
1 CATATAATT
522188 TATCATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (23 bp):
CATATAATTCCATAGATCTTTAA
Found at i:527613 original size:12 final size:12
Alignment explanation
Indices: 527596--527620 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
527586 AATATGAAAA
527596 TAAAATAATCAT
1 TAAAATAATCAT
527608 TAAAATAATCAT
1 TAAAATAATCAT
527620 T
1 T
527621 TAAACATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATAATCAT
Found at i:527724 original size:29 final size:30
Alignment explanation
Indices: 527670--527728 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
527660 ATTGCAATTA
527670 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
527700 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
527729 TTACAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Done.