Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015382.1 Kokia drynarioides strain JFW-HI SEQ_130429, 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: 764726
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 399 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:11315 original size:32 final size:30
Alignment explanation
Indices: 11260--11343 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
11250 TTTTTTTATG
* *
11260 TATCATTATAAT-AATTTTTAAATA-AATT
1 TATCATTATATTAAATTTTTAAAAATAATT
11288 TATCATTATATTAAATTATTTAAAAATAATT
1 TATCATTATATTAAATT-TTTAAAAATAATT
* *
11319 TATTATTATATTTAAAATTTTAAAA
1 TATCATTATA-TTAAATTTTTAAAA
11344 TATACAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 11 0.23
29 4 0.08
30 7 0.15
31 20 0.42
32 6 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TATCATTATATTAAATTTTTAAAAATAATT
Found at i:14959 original size:27 final size:27
Alignment explanation
Indices: 14908--14959 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
14898 CCAGTAAGGT
* **
14908 AGTCCATTCATAGTACGCCACAAAGAC
1 AGTCCATTCAAAGTAAACCACAAAGAC
*
14935 AGTCCATTCAAAGTAAACCATAAAG
1 AGTCCATTCAAAGTAAACCACAAAG
14960 GCTTTCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.19
Consensus pattern (27 bp):
AGTCCATTCAAAGTAAACCACAAAGAC
Found at i:20035 original size:21 final size:20
Alignment explanation
Indices: 20004--20045 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
19994 CTAAACCTAA
20004 TTAATTAACTA-ATTATAAAC
1 TTAATTAACTATA-TATAAAC
20024 TTAATCTAACTATATATAAAC
1 TTAAT-TAACTATATATAAAC
20045 T
1 T
20046 AGTGGATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 14 0.70
22 1 0.05
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATTAACTATATATAAAC
Found at i:21035 original size:79 final size:79
Alignment explanation
Indices: 20912--21069 Score: 201
Period size: 79 Copynumber: 2.0 Consensus size: 79
20902 TACGTTCGAC
* * *** *
20912 GATGCACTTACGTGCCTTTATATTTACTTCGGCATGTTTGATGATGCACTTACATTCCAATATAT
1 GATGCACTTACGTGCCTGTATATTTACTTCGACATGTCCAATGATGCACTTACATGCCAATATAT
20977 TAACTTCGATATAT
66 TAACTTCGATATAT
* ** *
20991 GATGCACTTACGTG-CTAGTATATTTACTTCGATATGTCCAATGATGCACTTATGTGCCAGTATA
1 GATGCACTTACGTGCCT-GTATATTTACTTCGACATGTCCAATGATGCACTTACATGCCAATATA
*
21055 TTTACTTCGATATAT
65 TTAACTTCGATATAT
21070 CTAATGATGC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
78 2 0.03
79 65 0.97
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (79 bp):
GATGCACTTACGTGCCTGTATATTTACTTCGACATGTCCAATGATGCACTTACATGCCAATATAT
TAACTTCGATATAT
Found at i:21082 original size:121 final size:124
Alignment explanation
Indices: 20868--21138 Score: 309
Period size: 121 Copynumber: 2.2 Consensus size: 124
20858 GGTATATCTG
* * * **
20868 ATGATGCACTTATGTG-TAAGTATATTTACTTCGATACGTTCGACGATGCACTTACGTGCCTTTA
1 ATGATGCACTTACGTGCT-AGTATATTTACTTCGATACGTCCAACGATGCACTTACGTGCCAGTA
* * * * *
20932 TATTTACTTCGGCATGTTTGATGATGCACTTACATTCCAATATATTAAC-TTCG-A-TAT
65 TATTTACTTCGACATATCTAATGATGCACTTACATGCCAATATATTAACTTTCGTATTAT
* * *
20989 ATGATGCACTTACGTGCTAGTATATTTACTTCGATATGTCCAATGATGCACTTATGTGCCAGTAT
1 ATGATGCACTTACGTGCTAGTATATTTACTTCGATACGTCCAACGATGCACTTACGTGCCAGTAT
* ** * *
21054 ATTTACTTCGATATATCTAATGATGCACTTATGTGCCAATATATTTACTTTGGTATATTAT
66 ATTTACTTCGACATATCTAATGATGCACTTACATGCCAATATATTAACTTTCG--TATTAT
21115 ATGATGCACTTACGTGGC-AGTATA
1 ATGATGCACTTACGT-GCTAGTATA
21139 ATTGCTTTGG
Statistics
Matches: 125, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
121 94 0.75
122 4 0.03
125 1 0.01
126 24 0.19
127 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (124 bp):
ATGATGCACTTACGTGCTAGTATATTTACTTCGATACGTCCAACGATGCACTTACGTGCCAGTAT
ATTTACTTCGACATATCTAATGATGCACTTACATGCCAATATATTAACTTTCGTATTAT
Found at i:21149 original size:42 final size:42
Alignment explanation
Indices: 20852--21138 Score: 248
Period size: 42 Copynumber: 7.0 Consensus size: 42
20842 TACAGGTTTA
* * * **
20852 TACTTCGGTATATCTGATGATGCACTTATGTGTAAGTATATT
1 TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
* * **
20894 TACTTCGATACGT-TC-GACGATGCACTTACGTGCCTTTATATT
1 TACTTCGATA--TATCTAATGATGCACTTACGTGCCAGTATATT
** * * * * * *
20936 TACTTCGGCATGTTTGATGATGCACTTACATTCCAATATATT
1 TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
* *
20978 AACTTCG--ATA--T-ATGATGCACTTACGTGCTAGTATATT
1 TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
* * *
21015 TACTTCGATATGTCCAATGATGCACTTATGTGCCAGTATATT
1 TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
* *
21057 TACTTCGATATATCTAATGATGCACTTATGTGCCAATATATT
1 TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
* * *
21099 TACTTTGGTATAT-TATATGATGCACTTACGTGGCAGTATA
1 TACTTCGATATATCTA-ATGATGCACTTACGTGCCAGTATA
21139 ATTGCTTTGG
Statistics
Matches: 201, Mismatches: 34, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
37 28 0.14
38 1 0.00
39 2 0.01
40 3 0.01
41 3 0.01
42 161 0.80
43 2 0.01
44 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (42 bp):
TACTTCGATATATCTAATGATGCACTTACGTGCCAGTATATT
Found at i:21161 original size:42 final size:42
Alignment explanation
Indices: 20989--21190 Score: 178
Period size: 42 Copynumber: 4.8 Consensus size: 42
20979 ACTTCGATAT
* * * * *
20989 ATGATGCACTTACGTGCTAGTATATTTACTTCGATATGTCCA
1 ATGATGCACTTACGTGCCAGTATAATTACTTTGGTATATCCA
* * * * *
21031 ATGATGCACTTATGTGCCAGTATATTTACTTCGATATATCTA
1 ATGATGCACTTACGTGCCAGTATAATTACTTTGGTATATCCA
* * * *
21073 ATGATGCACTTATGTGCCAATATATTTACTTTGGTATAT-TA
1 ATGATGCACTTACGTGCCAGTATAATTACTTTGGTATATCCA
* *
21114 TATGATGCACTTACGTGGCAGTATAATTGCTTTGGT-TCATCCA
1 -ATGATGCACTTACGTGCCAGTATAATTACTTTGGTAT-ATCCA
* *
21157 ATGATGCACCT-CGTGTTCC-GTATAATTGCTTTGG
1 ATGATGCACTTACGTG--CCAGTATAATTACTTTGG
21191 CTTGCCCAAT
Statistics
Matches: 140, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
41 7 0.05
42 131 0.94
43 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (42 bp):
ATGATGCACTTACGTGCCAGTATAATTACTTTGGTATATCCA
Found at i:24576 original size:65 final size:65
Alignment explanation
Indices: 24470--24601 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
24460 TGAAATAATC
24470 AAAATTCGCATTCAAGTCTTCAACTAATTTTACTTTCGAGTTCGATTCATAAACAATCATCTACT
1 AAAATTCGCATTCAAGTCTTCAACTAATTTTACTTTCGAGTTCGATTCATAAACAATCATCTACT
*
24535 AAAATTCGCATTCAAGTCTTCAACTAATTTTACTTTTGAGTTCGATTCATAAACAATCATCTACT
1 AAAATTCGCATTCAAGTCTTCAACTAATTTTACTTTCGAGTTCGATTCATAAACAATCATCTACT
24600 AA
1 AA
24602 GAAAAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (65 bp):
AAAATTCGCATTCAAGTCTTCAACTAATTTTACTTTCGAGTTCGATTCATAAACAATCATCTACT
Found at i:25650 original size:17 final size:19
Alignment explanation
Indices: 25617--25651 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
25607 AAATCACGGA
25617 TTTAAAATATAAATATATG
1 TTTAAAATATAAATATATG
25636 TTTAAAA-AT-AATATAT
1 TTTAAAATATAAATATAT
25652 AATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTAAAATATAAATATATG
Found at i:26849 original size:17 final size:17
Alignment explanation
Indices: 26811--26852 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
26801 TTCATTAATT
* * *
26811 TATTTTGATTTTTTATA
1 TATTTTTATTTTTAAAA
26828 T-TTTTTATTTTTAAAA
1 TATTTTTATTTTTAAAA
26844 TATTTTTAT
1 TATTTTTAT
26853 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TATTTTTATTTTTAAAA
Found at i:26859 original size:20 final size:18
Alignment explanation
Indices: 26825--26868 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
26815 TTGATTTTTT
26825 ATATTTTTTATTTTTAAA
1 ATATTTTTTATTTTTAAA
26843 ATATTTTTATAATTTTTAAA
1 ATATTTTT-T-ATTTTTAAA
*
26863 TTATTT
1 ATATTT
26869 ATTGACGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTTTTATTTTTAAA
Found at i:36367 original size:30 final size:30
Alignment explanation
Indices: 36323--36387 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
36313 ATTGAATGAT
*
36323 TTTTTAATCTATTTGATAAATTA-TTTAATA
1 TTTTAAATCTATTTGAT-AATTATTTTAATA
* *
36353 TTTTAAATGTATTTGATAATTATTTTAATT
1 TTTTAAATCTATTTGATAATTATTTTAATA
36383 TTTTA
1 TTTTA
36388 TATACTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTAAATCTATTTGATAATTATTTTAATA
Found at i:36659 original size:29 final size:29
Alignment explanation
Indices: 36627--36721 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 29
36617 AATATAAATA
36627 AATAAAAGTTATAAAAATTATTTAAATTT
1 AATAAAAGTTATAAAAATTATTTAAATTT
*
36656 AATAAAA--TATTTAAAATATATTATAAA-TT
1 AATAAAAGTTA-TAAAAAT-TATT-TAAATTT
*
36685 AGGA-AAAAGATTATAAAAATTA-TAAAATTT
1 A--ATAAAAG-TTATAAAAATTATTTAAATTT
*
36715 TATAAAA
1 AATAAAA
36722 TCAAGCAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
27 2 0.04
28 7 0.13
29 21 0.40
30 11 0.21
31 3 0.06
32 6 0.12
33 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (29 bp):
AATAAAAGTTATAAAAATTATTTAAATTT
Found at i:36722 original size:10 final size:10
Alignment explanation
Indices: 36635--36722 Score: 51
Period size: 10 Copynumber: 8.9 Consensus size: 10
36625 TAAATAAAAG
36635 TTATAAAA-A
1 TTATAAAATA
*
36644 TTATTTAAAT-
1 TTA-TAAAATA
36654 TTAATAAAATA
1 TT-ATAAAATA
36665 TT-TAAAATATA
1 TTAT-AAA-ATA
*
36676 TTATAAATTA
1 TTATAAAATA
** *
36686 GGA-AAAAGA
1 TTATAAAATA
36695 TTATAAAA-A
1 TTATAAAATA
*
36704 TTATAAAATT
1 TTATAAAATA
36714 TTATAAAAT
1 TTATAAAAT
36723 CAAGCAATCC
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
9 18 0.30
10 30 0.50
11 11 0.18
12 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
TTATAAAATA
Found at i:43412 original size:2 final size:2
Alignment explanation
Indices: 43407--43431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43397 TAAAAAAAAA
43407 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43432 AAACTTTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62224 original size:5 final size:5
Alignment explanation
Indices: 62216--62241 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
62206 GTTTTACTTA
62216 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
62242 TTATTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:63708 original size:225 final size:225
Alignment explanation
Indices: 63317--63776 Score: 776
Period size: 225 Copynumber: 2.0 Consensus size: 225
63307 TGAATTATAC
*
63317 GAAAAATCACACCCAGCACATTAGGGCATAATTCTTCGAAGTTTTCACACGAAGGGATATTGCCT
1 GAAAAATCACACCCAGCACATTAGAGCATAATTCTTCGAAGTTTTCACACGAAGGGATATTGCCT
* *
63382 CGATTTTGAAATTTTAAGGCACTCGGTTATTTCGAGTCAAAGAGGAAGAAACACGCCCAGTAAGT
66 CGATTTTGAAATTTTAAGGCACTCGATTATTTCGAGTCAAAGAGGAAGAAACACGCCCAGTAAAT
*
63447 TAAGGCATGAGTTTCTCAAATTCTCGTAAATAACGAGCATTCCTTCATTGTCGATTTCGAAACTT
131 TAAGGCATGAGTTTCTCAAATTCTCGTAAATAACGAGCATTCCTTCATTGTCGATTTCAAAACTT
*
63512 TAAAAGGGTATTCGATTATTTCGGTTTGAA
196 TAAAAGGGTATTCGATTATTCCGGTTTGAA
* * *
63542 GAAAAATCGCGCCCAGCACATTAGAGCATAATTCTTCGAAGTTTTCACACGAAGGGATATTGTCT
1 GAAAAATCACACCCAGCACATTAGAGCATAATTCTTCGAAGTTTTCACACGAAGGGATATTGCCT
* * *
63607 TGATTTTGAAATTTTAAGGCACTCGATTATTTCGAGTCGAAGAGGAAGAAACACGCTCAGTAAAT
66 CGATTTTGAAATTTTAAGGCACTCGATTATTTCGAGTCAAAGAGGAAGAAACACGCCCAGTAAAT
* * * *
63672 TAAGGCATGAGTTTCTCAAATTCTCGTAAATAACGAGCTTTTCTTCTTTGTCGATTTTAAAACTT
131 TAAGGCATGAGTTTCTCAAATTCTCGTAAATAACGAGCATTCCTTCATTGTCGATTTCAAAACTT
*
63737 TATAAGGGTATTCGATTATTCCGGTTTGAA
196 TAAAAGGGTATTCGATTATTCCGGTTTGAA
63767 GAAAAATCAC
1 GAAAAATCAC
63777 GCGTAGTAAA
Statistics
Matches: 218, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
225 218 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (225 bp):
GAAAAATCACACCCAGCACATTAGAGCATAATTCTTCGAAGTTTTCACACGAAGGGATATTGCCT
CGATTTTGAAATTTTAAGGCACTCGATTATTTCGAGTCAAAGAGGAAGAAACACGCCCAGTAAAT
TAAGGCATGAGTTTCTCAAATTCTCGTAAATAACGAGCATTCCTTCATTGTCGATTTCAAAACTT
TAAAAGGGTATTCGATTATTCCGGTTTGAA
Found at i:64815 original size:21 final size:21
Alignment explanation
Indices: 64789--64839 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
64779 GAGACAATAT
64789 TACCGATACAAGT-ATGACTTC
1 TACCGATACAAGTCATG-CTTC
* *
64810 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
64831 TACCGATAC
1 TACCGATAC
64840 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:67024 original size:19 final size:19
Alignment explanation
Indices: 67002--67040 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
66992 CCACTTATAC
67002 TAAA-TTTTAATTCAATAAT
1 TAAATTTTTAATTCAA-AAT
67021 TAAATTTTTAATTCAAAAT
1 TAAATTTTTAATTCAAAAT
67040 T
1 T
67041 TCATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTTTAATTCAAAAT
Found at i:67336 original size:21 final size:21
Alignment explanation
Indices: 67312--67373 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
67302 AAATAAAACT
* *
67312 AACAATTTATATATATAAT-TA
1 AACAATATAAATATA-AATATA
67333 AACAATATAAATATAAATATA
1 AACAATATAAATATAAATATA
* *
67354 AATAA-ATAAATATATATATA
1 AACAATATAAATATAAATATA
67374 TATATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AACAATATAAATATAAATATA
Found at i:67345 original size:6 final size:6
Alignment explanation
Indices: 67337--67421 Score: 125
Period size: 6 Copynumber: 14.2 Consensus size: 6
67327 TAATTAAACA
* * * * *
67337 ATATAA ATATAA ATATAA ATAAAT AAATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
67385 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A
67422 CCTTGAGAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:67360 original size:10 final size:10
Alignment explanation
Indices: 67337--67421 Score: 125
Period size: 10 Copynumber: 8.5 Consensus size: 10
67327 TAATTAAACA
*
67337 ATATAAATAT
1 ATATATATAT
* *
67347 AAATATAAAT
1 ATATATATAT
* *
67357 AAATAAATAT
1 ATATATATAT
67367 ATATATATAT
1 ATATATATAT
67377 ATATATATAT
1 ATATATATAT
67387 ATATATATAT
1 ATATATATAT
67397 ATATATATAT
1 ATATATATAT
67407 ATATATATAT
1 ATATATATAT
67417 ATATA
1 ATATA
67422 CCTTGAGAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 68 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:67370 original size:4 final size:4
Alignment explanation
Indices: 67337--67421 Score: 125
Period size: 4 Copynumber: 21.2 Consensus size: 4
67327 TAATTAAACA
* * * * *
67337 ATAT AAAT ATAA ATAT AAAT AAAT AAAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
67385 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
67422 CCTTGAGAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:77988 original size:20 final size:21
Alignment explanation
Indices: 77954--77992 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
77944 TCAGATTTTT
77954 TTTGGGGGTGAAAATTTTGGA
1 TTTGGGGGTGAAAATTTTGGA
*
77975 TTTGGGGTTG-AAATTTTG
1 TTTGGGGGTGAAAATTTTG
77993 ATCCATGAGT
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:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (21 bp):
TTTGGGGGTGAAAATTTTGGA
Found at i:85672 original size:2 final size:2
Alignment explanation
Indices: 85665--85695 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
85655 AATGATGATG
85665 GA GA GA GA GA GA GA 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 G
85696 CAGTGGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:86331 original size:33 final size:32
Alignment explanation
Indices: 86288--86357 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
86278 TTAAAGTATT
* *
86288 AAAT-TTTTATT-TTTAATAATTAAATTTAAATA
1 AAATATTTTATTATTAAATAA-T-AATTCAAATA
86320 AAATATTTTATTAATTAAATAATAATTCAAATA
1 AAATATTTTATT-ATTAAATAATAATTCAAATA
86353 AAATA
1 AAATA
86358 AATCTACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 4 0.12
33 21 0.64
34 1 0.03
35 7 0.21
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
AAATATTTTATTATTAAATAATAATTCAAATA
Found at i:95165 original size:14 final size:14
Alignment explanation
Indices: 95146--95218 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 14
95136 ATGGTGTGGA
95146 TTTAATTTTTATAT
1 TTTAATTTTTATAT
95160 TTTAA--TTTAGTAT
1 TTTAATTTTTA-TAT
* *
95173 TTTAGTTTTTGTATT
1 TTTAATTTTTATA-T
** *
95188 TTTAATGGGTCA-AT
1 TTTAAT-TTTTATAT
95202 TTTAATTTTTATAT
1 TTTAATTTTTATAT
95216 TTT
1 TTT
95219 TCGAATTTTG
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
12 4 0.09
13 9 0.21
14 19 0.44
15 10 0.23
16 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.08, T:0.66
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:104846 original size:11 final size:11
Alignment explanation
Indices: 104830--104869 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
104820 GCTCAGATAA
104830 GTTGTTTTGTT
1 GTTGTTTTGTT
*
104841 GTTGTTTCGTT
1 GTTGTTTTGTT
*
104852 GTTATTTTGTT
1 GTTGTTTTGTT
104863 GTTGTTT
1 GTTGTTT
104870 CGCTATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.03, C:0.03, G:0.25, T:0.70
Consensus pattern (11 bp):
GTTGTTTTGTT
Found at i:104878 original size:22 final size:22
Alignment explanation
Indices: 104834--104878 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
104824 AGATAAGTTG
* *
104834 TTTTGTTGTTGTTTCGTTGTTA
1 TTTTGTTGTTGTTTCGCTATTA
104856 TTTTGTTGTTGTTTCGCTATTA
1 TTTTGTTGTTGTTTCGCTATTA
104878 T
1 T
104879 ATGGCTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (22 bp):
TTTTGTTGTTGTTTCGCTATTA
Found at i:119224 original size:8 final size:8
Alignment explanation
Indices: 119211--119236 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
119201 AATGATCACC
119211 CAATTATT
1 CAATTATT
119219 CAATTATT
1 CAATTATT
119227 CAATTATT
1 CAATTATT
119235 CA
1 CA
119237 TGAAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (8 bp):
CAATTATT
Found at i:124284 original size:12 final size:12
Alignment explanation
Indices: 124267--124291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
124257 TGAATTAACG
124267 AAAATAATCAAT
1 AAAATAATCAAT
124279 AAAATAATCAAT
1 AAAATAATCAAT
124291 A
1 A
124292 CATGATCAAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATCAAT
Found at i:125222 original size:61 final size:60
Alignment explanation
Indices: 125140--125263 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 60
125130 TGACACTTAA
* * ** *
125140 CAAGTTTAGGCACCAAATTGAACCTAAAAAATTTTAGGTACCAAATTAGAAAAAAAAATGT
1 CAAGTTCAGGCACCAAATTGAACCCAAAAAAAGTTAGGCACCAAATTA-AAAAAAAAATGT
* * * *
125201 CAAGTTCAGGTACCAATTTGAACCCAAAAAAAGTTAGGCACTAAATTAATAAAAAAATGT
1 CAAGTTCAGGCACCAAATTGAACCCAAAAAAAGTTAGGCACCAAATTAAAAAAAAAATGT
125261 CAA
1 CAA
125264 ATTTAGATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 14 0.26
61 40 0.74
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (60 bp):
CAAGTTCAGGCACCAAATTGAACCCAAAAAAAGTTAGGCACCAAATTAAAAAAAAAATGT
Found at i:131606 original size:23 final size:23
Alignment explanation
Indices: 131577--131620 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
131567 CGGTAAAGCT
131577 TTTTACCAAATTAAGCTGATAGC
1 TTTTACCAAATTAAGCTGATAGC
131600 TTTTACCAAATTAAGCTGATA
1 TTTTACCAAATTAAGCTGATA
131621 ACAATAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (23 bp):
TTTTACCAAATTAAGCTGATAGC
Found at i:137490 original size:37 final size:37
Alignment explanation
Indices: 137449--137522 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
137439 CATGTATAGC
137449 TAAAATGAAATTTCCAAATTGTGGACTTCCATGCTCT
1 TAAAATGAAATTTCCAAATTGTGGACTTCCATGCTCT
137486 TAAAATGAAATTTCCAAATTGTGGACTTCCATGCTCT
1 TAAAATGAAATTTCCAAATTGTGGACTTCCATGCTCT
137523 AATTACTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (37 bp):
TAAAATGAAATTTCCAAATTGTGGACTTCCATGCTCT
Found at i:137703 original size:18 final size:19
Alignment explanation
Indices: 137673--137710 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
137663 TTGAATCGAA
137673 TTTTATAATTTTA-TTAAT
1 TTTTATAATTTTATTTAAT
137691 TTTTAATAA-TTTATTTAAT
1 TTTT-ATAATTTTATTTAAT
137710 T
1 T
137711 AAAAGTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTATTTAAT
Found at i:140016 original size:2 final size:2
Alignment explanation
Indices: 140009--140054 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
139999 ACATAGAAGA
140009 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
140050 AT AT A
1 AT AT A
140055 ACATTTCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:140702 original size:23 final size:24
Alignment explanation
Indices: 140658--140702 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
140648 TCTTCCTTTC
* * *
140658 CTTTCTTTTTTATTCTTTTAATTT
1 CTTTCTTTATTATTATTATAATTT
140682 CTTTC-TTATTATTATTATAAT
1 CTTTCTTTATTATTATTATAAT
140703 CTCTAAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (24 bp):
CTTTCTTTATTATTATTATAATTT
Found at i:143343 original size:2 final size:2
Alignment explanation
Indices: 143336--143367 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
143326 GAGGGCGGGA
143336 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
143368 TTAAGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:145537 original size:125 final size:125
Alignment explanation
Indices: 145325--145577 Score: 488
Period size: 125 Copynumber: 2.0 Consensus size: 125
145315 TAATGGAGGG
145325 CATTAATTTCAACATTGAACACATGGCCACTTGCACTTGGTTCAATCTTCAAGGACAAAACAAGC
1 CATTAATTTCAACATTGAACACATGGCCACTTGCACTTGGTTCAATCTTCAAGGACAAAACAAGC
*
145390 AACTTAATTAATAACTAATGCATATGGGTTGGATTTAATCCATATTCCATTAATGGCTGC
66 AACTTAATTAATAACTAATGCATATGGGTTAGATTTAATCCATATTCCATTAATGGCTGC
*
145450 CATTAATTTCAACATTGAACACATGGCCACTTGCACTTGGTTCAATCTTCAAGGACAAGACAAGC
1 CATTAATTTCAACATTGAACACATGGCCACTTGCACTTGGTTCAATCTTCAAGGACAAAACAAGC
145515 AACTTAATTAATAACTAATGCATATGGGTTAGATTTAATCCATATTCCATTAATGGCTGC
66 AACTTAATTAATAACTAATGCATATGGGTTAGATTTAATCCATATTCCATTAATGGCTGC
145575 CAT
1 CAT
145578 CCTTTGTTTT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (125 bp):
CATTAATTTCAACATTGAACACATGGCCACTTGCACTTGGTTCAATCTTCAAGGACAAAACAAGC
AACTTAATTAATAACTAATGCATATGGGTTAGATTTAATCCATATTCCATTAATGGCTGC
Found at i:145757 original size:28 final size:31
Alignment explanation
Indices: 145726--145797 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 31
145716 GAAGGCCATT
145726 TAAAATTATTAAAATTATTT-TTT-AAAT-A
1 TAAAATTATTAAAATTATTTGTTTGAAATAA
145754 TAAAATTATTAAAATTATTTGTTTGAAATAA
1 TAAAATTATTAAAATTATTTGTTTGAAATAA
*
145785 TAAAATCATTAAA
1 TAAAATTATTAAA
145798 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 20 0.50
29 3 0.08
30 4 0.10
31 13 0.32
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTGTTTGAAATAA
Found at i:146882 original size:9 final size:9
Alignment explanation
Indices: 146846--146916 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
146836 ATTAAAATTA
146846 TTTAATAAT
1 TTTAATAAT
* *
146855 TTTATTATT
1 TTTAATAAT
146864 TTTAAAAATAAT
1 TTT---AATAAT
146876 TTTAATAAT
1 TTTAATAAT
146885 TTTAAAATAAT
1 TTT--AATAAT
*
146896 TTTAACAAT
1 TTTAATAAT
146905 TTT-AT-AT
1 TTTAATAAT
146912 TTTAA
1 TTTAA
146917 AAAATTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 27 0.54
11 9 0.18
12 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTAATAAT
Found at i:146893 original size:20 final size:20
Alignment explanation
Indices: 146849--146908 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
146839 AAAATTATTT
* *
146849 AATAATTTTATTATTTTTAAA
1 AATAATTTTAATAATTTT-AA
146870 AATAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
*
146890 AATAATTTTAACAATTTTA
1 AATAATTTTAATAATTTTA
146909 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:146895 original size:11 final size:11
Alignment explanation
Indices: 146863--146900 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
146853 ATTTTATTAT
146863 TTTTAAAAATAA
1 TTTT-AAAATAA
146875 TTTT--AATAA
1 TTTTAAAATAA
146884 TTTTAAAATAA
1 TTTTAAAATAA
146895 TTTTAA
1 TTTTAA
146901 CAATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.38
11 11 0.46
12 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTAAAATAA
Found at i:150106 original size:5 final size:5
Alignment explanation
Indices: 150096--150120 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
150086 CGCAATTTTA
150096 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
150121 GGATATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:150534 original size:27 final size:27
Alignment explanation
Indices: 150466--150535 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
150456 TAAAAATGAG
**
150466 TCAATTGATTTTTTTTTTCATTGAATGC
1 TCAATTGA-TTTTTTTTTCATAAAATGC
* * ***
150494 TTAGTTGGCATTTTTTTCATAAAATGC
1 TCAATTGATTTTTTTTTCATAAAATGC
150521 TCAATTGATTTTTTT
1 TCAATTGATTTTTTT
150536 ATTTTTTTTA
Statistics
Matches: 30, Mismatches: 12, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (27 bp):
TCAATTGATTTTTTTTTCATAAAATGC
Found at i:151092 original size:18 final size:17
Alignment explanation
Indices: 151069--151102 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
151059 AATAATATGT
151069 ATTATATAAAATGTAAAA
1 ATTATATAAAAT-TAAAA
151087 ATTATATAAAATTAAA
1 ATTATATAAAATTAAA
151103 GTTCTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTATATAAAATTAAAA
Found at i:151400 original size:91 final size:91
Alignment explanation
Indices: 151287--151496 Score: 327
Period size: 91 Copynumber: 2.3 Consensus size: 91
151277 ATCAATGTAA
* *
151287 TACTTGAACTATTAATTTGTGTATTATTT-GATATTTGTACTTTCATAAGA-TGTCCAATGTGGT
1 TACTTGAACTATCAATTTGTGTATTATTTAG-TACTTGTACTTTCATAA-ATTGTCCAATGTGGT
151350 ACTTATACTTTGAAAATGTTCAAAAT-G
64 ACTTATACTTTGAAAATGTTCAAAATAG
*
151377 ATATTTGAACTATCAATTTGTGTATTATTTAGTACTTGTACTTTCATAAATTGTCCAATGTGGTA
1 -TACTTGAACTATCAATTTGTGTATTATTTAGTACTTGTACTTTCATAAATTGTCCAATGTGGTA
*
151442 CTTATACTTTGAAAATGTTCAATATAG
65 CTTATACTTTGAAAATGTTCAAAATAG
*
151469 TACTTGAATTATCAATTTGTGTATTATT
1 TACTTGAACTATCAATTTGTGTATTATT
151497 ATGGTATCTA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
90 1 0.01
91 107 0.97
92 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (91 bp):
TACTTGAACTATCAATTTGTGTATTATTTAGTACTTGTACTTTCATAAATTGTCCAATGTGGTAC
TTATACTTTGAAAATGTTCAAAATAG
Found at i:151768 original size:31 final size:32
Alignment explanation
Indices: 151731--151793 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
151721 AAAAATTTTG
151731 GAATGTTTAGGGTTTTT-AAAAAAATTGAAGT
1 GAATGTTTAGGGTTTTTAAAAAAAATTGAAGT
151762 GAATGTTTAGGGTTTTTAAAAAAAATTGAAGT
1 GAATGTTTAGGGTTTTTAAAAAAAATTGAAGT
151794 AATCTTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (32 bp):
GAATGTTTAGGGTTTTTAAAAAAAATTGAAGT
Found at i:151860 original size:21 final size:21
Alignment explanation
Indices: 151836--151876 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
151826 GTTAAACTTA
**
151836 TGTTGTTTAGGTTTAATTATT
1 TGTTGTTTAAATTTAATTATT
*
151857 TGTTTTTTAAATTTAATTAT
1 TGTTGTTTAAATTTAATTAT
151877 ATTAATTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (21 bp):
TGTTGTTTAAATTTAATTATT
Found at i:152360 original size:30 final size:31
Alignment explanation
Indices: 152326--152384 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
152316 TTTTAAAAAT
* *
152326 TTTAAAGAAA-TTTCACCAACTTTTAAGGGA
1 TTTAAAAAAATTTTCACCAACATTTAAGGGA
*
152356 TTTAAAAAAATTTTCTCCAACATTTAAGG
1 TTTAAAAAAATTTTCACCAACATTTAAGG
152385 AGTCTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (31 bp):
TTTAAAAAAATTTTCACCAACATTTAAGGGA
Found at i:152393 original size:31 final size:30
Alignment explanation
Indices: 152328--152393 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
152318 TTAAAAATTT
* * *
152328 TAAAGAAATTTCACCAACTTTTAAGGGATT
1 TAAAAAAATTTCACCAACATTTAAGGGATC
*
152358 TAAAAAAATTTTCTCCAACATTTAA-GGAGTC
1 TAAAAAAA-TTTCACCAACATTTAAGGGA-TC
152389 TAAAA
1 TAAAA
152394 CCCATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (30 bp):
TAAAAAAATTTCACCAACATTTAAGGGATC
Found at i:155792 original size:3 final size:3
Alignment explanation
Indices: 155784--155821 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
155774 TCGTTATCAT
155784 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
155822 TTAAACTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:156346 original size:2 final size:2
Alignment explanation
Indices: 156339--156369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
156329 TAAGTTCTTT
156339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
156370 TGTATGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:168109 original size:18 final size:18
Alignment explanation
Indices: 168064--168111 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
168054 TCCAACAATC
* *
168064 TCCTTTTGAAGAGTAGTT
1 TCCTTTTGAACAGTAGCT
***
168082 TCCCCCTGAACAGTAGCT
1 TCCTTTTGAACAGTAGCT
168100 TCCTTTTGAACA
1 TCCTTTTGAACA
168112 ATGGTGCTTT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (18 bp):
TCCTTTTGAACAGTAGCT
Found at i:177899 original size:15 final size:15
Alignment explanation
Indices: 177879--177925 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
177869 AAATTCGATT
177879 AATTCGATCAATACA
1 AATTCGATCAATACA
177894 AATTCGAT---T---
1 AATTCGATCAATACA
177903 AATTCGATCAATACA
1 AATTCGATCAATACA
177918 AATTCGAT
1 AATTCGAT
177926 TAACAGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 8 0.31
12 2 0.08
15 16 0.62
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (15 bp):
AATTCGATCAATACA
Found at i:177899 original size:24 final size:24
Alignment explanation
Indices: 177869--177928 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
177859 AAAAATTAAA
177869 AAATTCGATTAATTCGATCAATAC
1 AAATTCGATTAATTCGATCAATAC
177893 AAATTCGATTAATTCGATCAATAC
1 AAATTCGATTAATTCGATCAATAC
177917 AAATTCGATTAA
1 AAATTCGATTAA
177929 CAGTTTGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATTCGATTAATTCGATCAATAC
Found at i:191898 original size:19 final size:21
Alignment explanation
Indices: 191874--191915 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
191864 AAGTTGATCA
191874 ATATTTTTA-AA-TTTTAAAT
1 ATATTTTTACAACTTTTAAAT
191893 ATATTTTTACAACTTTTAAAT
1 ATATTTTTACAACTTTTAAAT
191914 AT
1 AT
191916 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 10 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTTACAACTTTTAAAT
Found at i:191916 original size:19 final size:18
Alignment explanation
Indices: 191873--191925 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
191863 CAAGTTGATC
191873 AATATTTTTAAATTTTAA
1 AATATTTTTAAATTTTAA
191891 ATATATTTTTACAACTTTT-A
1 A-ATATTTTTA-AA-TTTTAA
191911 AATA-TTTTAAATTTT
1 AATATTTTTAAATTTT
191926 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 6 0.19
19 12 0.38
20 4 0.12
21 4 0.12
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTTTTAAATTTTAA
Found at i:201053 original size:73 final size:75
Alignment explanation
Indices: 200936--201106 Score: 190
Period size: 73 Copynumber: 2.3 Consensus size: 75
200926 GGTTATTTTT
** *
200936 TTTATATATAGTATG-TATATATTCACCACATACATTCTGTTTCCTT-AACTT-TA-ATATATTA
1 TTTATATATAGTATGATATATATTCACCACATACACCCTGCTTCCTTGAA-TTATATATATA-TA
* *
200997 TATGGTTTATTA
64 TATAGCTTATTA
* ** *
201009 TTTATATATAATATGAT-TATATTTGCCACATACACCCTGCTTCCTTGAATTATGTATATATATA
1 TTTATATATAGTATGATATATATTCACCACATACACCCTGCTTCCTTGAATTATATATATATATA
*
201073 TAGCTTATTG
66 TAGCTTATTA
201083 TTTATATATAGTATGTATATATAT
1 TTTATATATAGTATG-ATATATAT
201107 ATTATTCTGT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
73 40 0.49
74 29 0.36
75 7 0.09
76 5 0.06
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (75 bp):
TTTATATATAGTATGATATATATTCACCACATACACCCTGCTTCCTTGAATTATATATATATATA
TAGCTTATTA
Found at i:202556 original size:6 final size:6
Alignment explanation
Indices: 202545--202630 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
202535 GGCCCAATAG
* * *
202545 AATTTA AATTT- ATTTTA AAATTA AGTTT- -ATTATA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA
*
202590 -ATTTGA AATTTG AATTT- -ATTATA AATTTA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
202631 TTTAAATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
4 9 0.14
5 6 0.10
6 38 0.60
7 10 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:202573 original size:17 final size:17
Alignment explanation
Indices: 202545--202624 Score: 108
Period size: 17 Copynumber: 4.7 Consensus size: 17
202535 GGCCCAATAG
*
202545 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* *
202562 AAATTAAGTTTATTATA
1 AATTTAAATTTATTATA
202579 AATTTAAATTTATT-TGA
1 AATTTAAATTTATTAT-A
*
202596 AATTTGAATTTATTATA
1 AATTTAAATTTATTATA
202613 AATTTAAATTTA
1 AATTTAAATTTA
202625 AATTTATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 1 0.02
17 52 0.96
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:202588 original size:34 final size:34
Alignment explanation
Indices: 202545--202624 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
202535 GGCCCAATAG
*
202545 AATTTAAATTTATTTTAAAATT-AAGTTTATTATA
1 AATTTAAATTTATTTGAAAATTGAA-TTTATTATA
*
202579 AATTTAAATTTATTTGAAATTTGAATTTATTATA
1 AATTTAAATTTATTTGAAAATTGAATTTATTATA
202613 AATTTAAATTTA
1 AATTTAAATTTA
202625 AATTTATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 41 0.95
35 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (34 bp):
AATTTAAATTTATTTGAAAATTGAATTTATTATA
Found at i:202598 original size:11 final size:10
Alignment explanation
Indices: 202580--202637 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
202570 TTTATTATAA
202580 ATTTAAATTT
1 ATTTAAATTT
*
202590 ATTTGAA---
1 ATTTAAATTT
*
202597 ATTTGAATTT
1 ATTTAAATTT
202607 ATTATAAATTT
1 ATT-TAAATTT
202618 AAATTTAAATTT
1 --ATTTAAATTT
202630 ATTTAAAT
1 ATTTAAAT
202638 AATGTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 7 0.17
10 17 0.43
11 6 0.15
12 7 0.17
13 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:202605 original size:23 final size:22
Alignment explanation
Indices: 202590--202637 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
202580 ATTTAAATTT
*
202590 ATTTGAAATTTGAATTTATTATAA
1 ATTT-AAATTTAAATTTATT-TAA
202614 ATTTAAATTTAAATTTATTTAA
1 ATTTAAATTTAAATTTATTTAA
202636 AT
1 AT
202638 AATGTCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTAAATTTAAATTTATTTAA
Found at i:204582 original size:59 final size:59
Alignment explanation
Indices: 204429--204952 Score: 396
Period size: 59 Copynumber: 8.9 Consensus size: 59
204419 CCCTAAATTA
* * * * ***
204429 TTCC-AAAATCCCATTTTTACCCCCGAACTTCCAAAAATTACATTTTTGACCTTGAAAC
1 TTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAAC
* *
204487 TTCTC-AAAATACCA-TTTTA-CCCTCGAACTTCCAAAAATGCCATTTTTAACCCCAAAAC
1 TTC-CAAAAATTCCATTTTTACCCCT-GAACTTCCAAAAATTCCATTTTTAACCCCAAAAC
* * * ** *
204545 TTCCAAAAATTCCAATTTTACCCCTAAACTTTCAAAAATTATATTTTTTACCCTC-AAAC
1 TTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCC-CAAAAC
* * * * * * *
204604 TTCTAAAAATGCTATTTTTA-ACCTCGAAACTTCCAAAAATTTCATTTTTGACCTCAAAAC
1 TTCCAAAAATTCCATTTTTACCCCT-G-AACTTCCAAAAATTCCATTTTTAACCCCAAAAC
* * *
204664 TTCTAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTCTTGACCCCAAAAC
1 TTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAAC
* * * *
204723 TTGCAAAAATTCCATTATTA-CCTTCGAACTTCCAAAAATTCCATTTTTAACCCTAAAAC
1 TTCCAAAAATTCCATTTTTACCCCT-GAACTTCCAAAAATTCCATTTTTAACCCCAAAAC
* ** * **
204782 TTCCAAAAGTTCCATTTTTACCCCAAAACCTCC-AAAATTCCCATTTTTGAA-CCTGAAAC
1 TTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATT-CCATTTTT-AACCCCAAAAC
** * * * * ***
204841 TTTTAGAAATTACTATTTTT-CTCCC-GAA-TGTCCAAAAACTCCATTTTCAACCTTGAAAC
1 TTCCAAAAATT-CCATTTTTAC-CCCTGAACT-TCCAAAAATTCCATTTTTAACCCCAAAAC
* *
204900 -TCTC-AAAATTACC-CTTTTACCCCTGAA-TATCTAAAAATTCCATTTTTAACCCC
1 TTC-CAAAAATT-CCATTTTTACCCCTGAACT-TCCAAAAATTCCATTTTTAACCCC
204953 GAACTTTTCC
Statistics
Matches: 376, Mismatches: 68, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
57 11 0.03
58 93 0.25
59 200 0.53
60 69 0.18
61 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
TTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAAC
Found at i:204612 original size:89 final size:89
Alignment explanation
Indices: 204429--204828 Score: 349
Period size: 89 Copynumber: 4.6 Consensus size: 89
204419 CCCTAAATTA
* ** * * *
204429 TTCC-AAAATCCCATTTTT-ACCCCCGAACTTCCAAAAATTACATTTTTGA-CCTTGAAACTTCT
1 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTT-ACCCCT-AAACTT-T
* *
204491 C-AAAATACCA--TTTTACCCTCGAAC
63 CAAAAATTCCATTTTTTACCCTCAAAC
204515 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCTAAACTTTCAA
1 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCTAAACTTTCAA
**
204580 AAATTATATTTTTTACCCTCAAAC
66 AAATTCCATTTTTTACCCTCAAAC
* * * * * * * *
204604 TTCTAAAAATGCTATTTTTAACCTCGAAACTTCCAAAAATTTCATTTTTGACCTCAAAAC-TTCT
1 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTT-ACCCCTAAACTTTC-
*
204668 AAAAATTCCA-TTTTTACCC-CTGAAC
64 AAAAATTCCATTTTTTACCCTC-AAAC
* * * * * * *
204693 TTCCAAAAATTCCATTCTTGACCCCAAAACTTGCAAAAATTCC-ATTATTA-CCTTCGAACTTCC
1 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATT-TTACCCCT-AAACTTTC
* *
204756 AAAAATTCCATTTTTAACCCTAAAAC
64 AAAAATTCCATTTTTTACCCTCAAAC
* * * *
204782 TTCCAAAAGTTCCATTTTT-ACCCCAAAACCTCC-AAAATTCCCATTTT
1 TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTT
204829 TGAACCTGAA
Statistics
Matches: 256, Mismatches: 43, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
86 6 0.02
87 37 0.14
88 60 0.23
89 137 0.54
90 16 0.06
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (89 bp):
TTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCTAAACTTTCAA
AAATTCCATTTTTTACCCTCAAAC
Found at i:204809 original size:29 final size:29
Alignment explanation
Indices: 204429--204829 Score: 348
Period size: 30 Copynumber: 13.7 Consensus size: 29
204419 CCCTAAATTA
* **
204429 TTCC-AAAATCCCATTTTTACCCCCGAAC
1 TTCCAAAAATTCCATTTTTACCCCAAAAC
* ***
204457 TTCCAAAAATTACATTTTTGACCTTGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCAAAAC
* *
204487 TTCTC-AAAATACCA-TTTTACCCTC-GAAC
1 TTC-CAAAAATTCCATTTTTACCC-CAAAAC
*
204515 TTCCAAAAATGCCATTTTTAACCCCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCAAAAC
* *
204545 TTCCAAAAATTCCAATTTTACCCCTAAAC
1 TTCCAAAAATTCCATTTTTACCCCAAAAC
* **
204574 TTTCAAAAATTATATTTTTTACCCTC-AAAC
1 TTCCAAAAATTCCA-TTTTTACCC-CAAAAC
* * * * *
204604 TTCTAAAAATGCTATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCAAAAC
* *
204634 TTCCAAAAATTTCATTTTTGACCTCAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCAAAAC
* **
204664 TTCTAAAAATTCCATTTTTACCCCTGAAC
1 TTCCAAAAATTCCATTTTTACCCCAAAAC
*
204693 TTCCAAAAATTCCATTCTTGACCCCAAAAC
1 TTCCAAAAATTCCATT-TTTACCCCAAAAC
* * * *
204723 TTGCAAAAATTCCATTATTACCTTC-GAAC
1 TTCCAAAAATTCCATTTTTACC-CCAAAAC
*
204752 TTCCAAAAATTCCATTTTTAACCCTAAAAC
1 TTCCAAAAATTCCATTTTT-ACCCCAAAAC
*
204782 TTCCAAAAGTTCCATTTTTACCCCAAAAC
1 TTCCAAAAATTCCATTTTTACCCCAAAAC
*
204811 CTCC-AAAATTCCCATTTTT
1 TTCCAAAAATT-CCATTTTT
204830 GAACCTGAAA
Statistics
Matches: 302, Mismatches: 54, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.00
28 26 0.09
29 113 0.37
30 160 0.53
31 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTTACCCCAAAAC
Found at i:204946 original size:29 final size:29
Alignment explanation
Indices: 204665--204952 Score: 82
Period size: 29 Copynumber: 9.8 Consensus size: 29
204655 CCTCAAAACT
204665 TCTAAAAATTCCATTTTTACCCCTGAACT-
1 TCTAAAAATTCCATTTTTACCCCTGAA-TA
* * **
204694 TCCAAAAATTCCATTCTTGACCCCAAAACT-
1 TCTAAAAATTCCATT-TTTACCCCTGAA-TA
* *
204724 TGC-AAAAATTCCATTATTA-CCTTCGAACT-
1 T-CTAAAAATTCCATTTTTACCCCT-GAA-TA
* * *
204753 TCCAAAAATTCCATTTTTAACCCT-AAAA
1 TCTAAAAATTCCATTTTTACCCCTGAATA
* * *
204781 CTTCCAAAAGTTCCATTTTTACCCC--AAAA
1 --TCTAAAAATTCCATTTTTACCCCTGAATA
* * *
204810 CCTCCAAAATTCCCATTTTTGA-ACCTGAA-A
1 TCT-AAAAATT-CCATTTTT-ACCCCTGAATA
* * * *
204840 CTTTTAGAAATTACTATTTTT-CTCCC-GAATG
1 --TCTAAAAATT-CCATTTTTAC-CCCTGAATA
* * * * *
204871 TCCAAAAACTCCATTTTCAACCTTGAA-A
1 TCTAAAAATTCCATTTTTACCCCTGAATA
* *
204899 CTCTCAAAATTACC-CTTTTACCCCTGAATA
1 -TCTAAAAATT-CCATTTTTACCCCTGAATA
204929 TCTAAAAATTCCATTTTTAACCCC
1 TCTAAAAATTCCATTTTT-ACCCC
204953 GAACTTTTCC
Statistics
Matches: 189, Mismatches: 45, Indels: 49
0.67 0.16 0.17
Matches are distributed among these distances:
27 1 0.01
28 20 0.11
29 89 0.47
30 61 0.32
31 17 0.09
32 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TCTAAAAATTCCATTTTTACCCCTGAATA
Found at i:217630 original size:40 final size:39
Alignment explanation
Indices: 217569--217657 Score: 151
Period size: 40 Copynumber: 2.3 Consensus size: 39
217559 CATACACCTA
*
217569 AATCCGATCTCTTATCCCGACCATGGGACAGATTGAAGAC
1 AATCCAATCTCTTATCCCGACCATGGGACAGATTGAAG-C
*
217609 CATCCAATCTCTTATCCCGACCATGGGACAGATTGAAGC
1 AATCCAATCTCTTATCCCGACCATGGGACAGATTGAAGC
217648 AATCCAATCT
1 AATCCAATCT
217658 TTTACCCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 10 0.22
40 36 0.78
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (39 bp):
AATCCAATCTCTTATCCCGACCATGGGACAGATTGAAGC
Found at i:218302 original size:20 final size:20
Alignment explanation
Indices: 218264--218302 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
218254 TAATATTATA
* **
218264 TATATATTTTAAATTAAATT
1 TATATAATTTAAAAAAAATT
218284 TATATAATTTAAAAAAAAT
1 TATATAATTTAAAAAAAAT
218303 GTTAAATACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATAATTTAAAAAAAATT
Found at i:234155 original size:121 final size:121
Alignment explanation
Indices: 234004--234248 Score: 429
Period size: 121 Copynumber: 2.0 Consensus size: 121
233994 TTTAACTGAA
*
234004 ACAAATTACATTTCACCACCACAGTTTTTTTTTTCCTTTAAAAATGGTTAATAACTTTGATTAAC
1 ACAAATTACATTTCACCACCACAGTGTTTTTTTTCCTTTAAAAATGGTTAATAACTTTGATTAAC
234069 ATATTCAACTTTTTACTTTTTGGAGTTAATGAAAGGTCAGGTTAGTATAGATTAAT
66 ATATTCAACTTTTTACTTTTTGGAGTTAATGAAAGGTCAGGTTAGTATAGATTAAT
* *
234125 ACAAATTACATTTCACCCACCAGAG-GTTTTTTTTCCTTTAAAAGTGGTTAATAACTTTGATTAA
1 ACAAATTACATTTCA-CCACCACAGTGTTTTTTTTCCTTTAAAAATGGTTAATAACTTTGATTAA
* *
234189 CATATTTAACTTTTTATTTTTTGGAGTTAATGAAAGGTCAGGTTAGTATAGATTAAT
65 CATATTCAACTTTTTACTTTTTGGAGTTAATGAAAGGTCAGGTTAGTATAGATTAAT
234246 ACA
1 ACA
234249 GTGATACATA
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
121 110 0.93
122 8 0.07
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (121 bp):
ACAAATTACATTTCACCACCACAGTGTTTTTTTTCCTTTAAAAATGGTTAATAACTTTGATTAAC
ATATTCAACTTTTTACTTTTTGGAGTTAATGAAAGGTCAGGTTAGTATAGATTAAT
Found at i:239351 original size:25 final size:23
Alignment explanation
Indices: 239323--239368 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
239313 GTTGGATCCA
239323 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
239348 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
239369 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:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:239455 original size:13 final size:13
Alignment explanation
Indices: 239434--239467 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
239424 ACAATATAAT
239434 AATAATAATCCTA
1 AATAATAATCCTA
*
239447 AATATTAATCCTA
1 AATAATAATCCTA
*
239460 AAAAATAA
1 AATAATAA
239468 AGTCTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:242124 original size:23 final size:24
Alignment explanation
Indices: 242080--242124 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
242070 CAAAATCTAG
* *
242080 TATTTTTAATCGTTATTTATATAA
1 TATTTTTAATCGTAATTGATATAA
*
242104 TATTTTTAATTG-AATTGATAT
1 TATTTTTAATCGTAATTGATAT
242125 CACAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (24 bp):
TATTTTTAATCGTAATTGATATAA
Found at i:243672 original size:18 final size:17
Alignment explanation
Indices: 243637--243679 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
243627 CTTCATTTAT
243637 TTCCCCTTTTCTTCTTC
1 TTCCCCTTTTCTTCTTC
*
243654 TTCCCC-TTTCATC-TC
1 TTCCCCTTTTCTTCTTC
243669 TTCTCCCTTTT
1 TTC-CCCTTTT
243680 TCTTTCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCCCCTTTTCTTCTTC
Found at i:247592 original size:26 final size:26
Alignment explanation
Indices: 247543--247592 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
247533 TATTAAGATA
* *
247543 AATAATATTTATCTTTATGTTAATTG
1 AATAAGATTTATCTTTATGATAATTG
247569 AATAAGATTTAT-TTTCATGATAAT
1 AATAAGATTTATCTTT-ATGATAAT
247593 AGCATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (26 bp):
AATAAGATTTATCTTTATGATAATTG
Found at i:249013 original size:22 final size:23
Alignment explanation
Indices: 248972--249019 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
248962 GAACGCTAGC
248972 GTGCTTACTGATCAGCACTGTGT
1 GTGCTTACTGATCAGCACTGTGT
* *
248995 GTGCTT-CTTATCAGTACTGTGT
1 GTGCTTACTGATCAGCACTGTGT
249017 GTG
1 GTG
249020 ATATCTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.40
Consensus pattern (23 bp):
GTGCTTACTGATCAGCACTGTGT
Found at i:249049 original size:23 final size:22
Alignment explanation
Indices: 249023--249111 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 22
249013 GTGTGTGATA
249023 TCTGTTCAGCACGTTTCGTG-CCC
1 TCTGTTCAGCAC-TTT-GTGACCC
*
249046 TCTGATCAGCACTTTGTGTACCC
1 TCTGTTCAGCACTTTGTG-ACCC
*
249069 TCTGTTATTAGCACTTCGTGTG-CCC
1 TCTG-T-TCAGCACTT--TGTGACCC
249094 TCTGATT-AGCACTTTGTG
1 TCTG-TTCAGCACTTTGTG
249112 TGCCCTTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
21 7 0.12
22 3 0.05
23 25 0.45
24 1 0.02
25 16 0.29
27 4 0.07
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.38
Consensus pattern (22 bp):
TCTGTTCAGCACTTTGTGACCC
Found at i:249084 original size:25 final size:25
Alignment explanation
Indices: 249040--249148 Score: 113
Period size: 23 Copynumber: 4.5 Consensus size: 25
249030 AGCACGTTTC
*
249040 GTGCCCTCTG--ATCAGCACTTTGT
1 GTGCCCTCTGTTATTAGCACTTTGT
* *
249063 GTACCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTGTTATTAGCACTTTGT
249088 GTGCCCTCTG--ATTAGCACTTTGT
1 GTGCCCTCTGTTATTAGCACTTTGT
* *
249111 GTGCCCTTTGTTACCTAGCACTTATGT
1 GTGCCCTCTGTTA-TTAGCACTT-TGT
249138 GT--CCTCTGTTA
1 GTGCCCTCTGTTA
249149 AGTACTTCGG
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
23 30 0.42
25 29 0.40
26 8 0.11
27 5 0.07
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (25 bp):
GTGCCCTCTGTTATTAGCACTTTGT
Found at i:249092 original size:48 final size:49
Alignment explanation
Indices: 249040--249133 Score: 145
Period size: 48 Copynumber: 1.9 Consensus size: 49
249030 AGCACGTTTC
*
249040 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTA-TTAGCACTTCGT
1 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTACCTAGCACTTCGT
* * *
249088 GTGCCCTCTGATTAGCACTTTGTGTGCCCTTTGTTACCTAGCACTT
1 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTACCTAGCACTT
249134 ATGTGTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 33 0.80
49 8 0.20
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (49 bp):
GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTACCTAGCACTTCGT
Found at i:249144 original size:48 final size:48
Alignment explanation
Indices: 249040--249145 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
249030 AGCACGTTTC
* *
249040 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTACTAGCACTTCAT
* * *
249088 GTGCCCTCTGATTAGCACTTTGTGTGCCCTTTGTTACCTAGCACTT-AT
1 GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTA-CTAGCACTTCAT
*
249136 GTGTCCTCTG
1 GTGCCCTCTG
249146 TTAAGTACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
48 43 0.84
49 8 0.16
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (48 bp):
GTGCCCTCTGATCAGCACTTTGTGTACCCTCTGTTACTAGCACTTCAT
Found at i:250868 original size:22 final size:22
Alignment explanation
Indices: 250843--250886 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
250833 TATCACTTTC
*
250843 AATTCCAATTTCACTTTTACTT
1 AATTCCAATTTCACTTTCACTT
* * *
250865 AATTTCACTTTTACTTTCACTT
1 AATTCCAATTTCACTTTCACTT
250887 TCACTTTCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTCCAATTTCACTTTCACTT
Found at i:250870 original size:16 final size:16
Alignment explanation
Indices: 250849--250880 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
250839 TTTCAATTCC
250849 AATTTCACTTTTACTT
1 AATTTCACTTTTACTT
250865 AATTTCACTTTTACTT
1 AATTTCACTTTTACTT
250881 TCACTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTCACTTTTACTT
Found at i:250880 original size:6 final size:6
Alignment explanation
Indices: 250835--250895 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
250825 ACAATTCATA
* * * * * *
250835 TCACTT TCAATT CCAATT TCACTT TTAC-T T-AATT TCACTT TTACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
250881 TCACTT TCACTT TCA
1 TCACTT TCACTT TCA
250896 ATTTTGATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 1 0.02
5 4 0.09
6 39 0.89
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:250884 original size:12 final size:12
Alignment explanation
Indices: 250867--250900 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
250857 TTTTACTTAA
250867 TTTCACTTTTAC
1 TTTCACTTTTAC
*
250879 TTTCACTTTCAC
1 TTTCACTTTTAC
*
250891 TTTCAATTTT
1 TTTCACTTTT
250901 GATCACAAAT
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:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTCACTTTTAC
Found at i:255863 original size:34 final size:33
Alignment explanation
Indices: 255806--255983 Score: 142
Period size: 34 Copynumber: 5.0 Consensus size: 33
255796 GTTAAATTCT
* *
255806 AAACCCTAAACCTTAGAGCTAAACCTTAAACCTA
1 AAACCCTAAACCTTA-AGTTAAACCCTAAACCTA
* *
255840 AAACCCTAAATCTTAAGTTTAAACCCTAAACATA
1 AAACCCTAAACCTTAAG-TTAAACCCTAAACCTA
*
255874 AAACCTTAAACCTTAAAGTTAAACCCTAAACCCT-
1 AAACCCTAAACCTT-AAGTTAAACCCTAAA-CCTA
** * *
255908 AAACTTTAAACCCTAAACTTTAAACCCTAAACCATA
1 AAACCCTAAA-CCTTAA-GTTAAACCCTAAACC-TA
*
255944 GAATTTACCCTAAACCTTAGGGTTAAACCCTAAATCCTA
1 -AA---ACCCTAAACCTTA-AGTTAAACCCTAAA-CCTA
255983 A
1 A
255984 GGTTAAACTC
Statistics
Matches: 116, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
33 2 0.02
34 64 0.55
35 21 0.18
37 2 0.02
38 1 0.01
39 18 0.16
40 8 0.07
ACGTcount: A:0.44, C:0.27, G:0.04, T:0.25
Consensus pattern (33 bp):
AAACCCTAAACCTTAAGTTAAACCCTAAACCTA
Found at i:255870 original size:27 final size:26
Alignment explanation
Indices: 255780--255925 Score: 77
Period size: 27 Copynumber: 5.4 Consensus size: 26
255770 TAAAACCATA
*
255780 AAACCCTAAACCCT-AAGTTAAATTCT
1 AAACCCTAAACCCTAAACTTAAATT-T
* * *
255806 AAACCCTAAACCTTAGAGC-TAAACCTT
1 AAACCCTAAACCCTA-AACTTAAA-TTT
*
255833 AAA-CCTAAAACCCTAAATCTTAAGTTT
1 AAACCCT-AAACCCTAAA-CTTAAATTT
* *
255860 AAACCCTAAA-CATAAAACCTTAAACCTT
1 AAACCCTAAACCCT-AAA-CTTAAA-TTT
** *
255888 AAA-GTTAAACCCTAAACCCTAAACTTT
1 AAACCCTAAACCCTAAA-CTTAAA-TTT
255915 AAACCCTAAAC
1 AAACCCTAAAC
255926 TTTAAACCCT
Statistics
Matches: 90, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
26 19 0.21
27 51 0.57
28 20 0.22
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.24
Consensus pattern (26 bp):
AAACCCTAAACCCTAAACTTAAATTT
Found at i:255884 original size:7 final size:7
Alignment explanation
Indices: 255805--255940 Score: 89
Period size: 7 Copynumber: 19.9 Consensus size: 7
255795 AGTTAAATTC
*
255805 TAAACCC
1 TAAACCT
255812 TAAACCT
1 TAAACCT
* *
255819 TAGAGC-
1 TAAACCT
255825 TAAACCT
1 TAAACCT
255832 TAAACCT
1 TAAACCT
* *
255839 AAAACCC
1 TAAACCT
*
255846 TAAATCT
1 TAAACCT
**
255853 T-AAGTT
1 TAAACCT
*
255859 TAAACCC
1 TAAACCT
*
255866 TAAACAT
1 TAAACCT
*
255873 AAAACCT
1 TAAACCT
255880 TAAACCT
1 TAAACCT
*
255887 TAAA-GT
1 TAAACCT
*
255893 TAAACCC
1 TAAACCT
*
255900 TAAACCC
1 TAAACCT
*
255907 TAAACTT
1 TAAACCT
*
255914 TAAACCC
1 TAAACCT
*
255921 TAAACTT
1 TAAACCT
*
255928 TAAACCC
1 TAAACCT
255935 TAAACC
1 TAAACC
255941 ATAGAATTTA
Statistics
Matches: 95, Mismatches: 31, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
6 13 0.14
7 82 0.86
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (7 bp):
TAAACCT
Found at i:255903 original size:20 final size:19
Alignment explanation
Indices: 255874--256004 Score: 78
Period size: 20 Copynumber: 6.8 Consensus size: 19
255864 CCTAAACATA
*
255874 AAACCTTAAACCTTAAAGTT
1 AAACCCTAAACC-TAAAGTT
*
255894 AAACCCTAAACCCTAAACTTT
1 AAACCCTAAA-CCTAAA-GTT
255915 AAACCCTAAA-CT----TT
1 AAACCCTAAACCTAAAGTT
255929 AAACCCTAAACCATAGAA-TT
1 AAACCCTAAACC-TA-AAGTT
* **
255949 -TACCCTAAACCTTAGGGTT
1 AAACCCTAAACC-TAAAGTT
*
255968 AAACCCTAAATCCTAAGGTT
1 AAACCCTAAA-CCTAAAGTT
*
255988 AAACTCTAAACCCTAAA
1 AAACCCTAAA-CCTAAA
256005 CACTAAACCT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
14 12 0.13
15 1 0.01
16 1 0.01
19 16 0.18
20 43 0.48
21 16 0.18
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (19 bp):
AAACCCTAAACCTAAAGTT
Found at i:255938 original size:21 final size:21
Alignment explanation
Indices: 255893--256005 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 21
255883 ACCTTAAAGT
** **
255893 TAAACCCTAAACCCTAAACTT
1 TAAACCCTAAACGTTAAACCC
*
255914 TAAACCCTAAACTTTAAACCC
1 TAAACCCTAAACGTTAAACCC
* *
255935 TAAACCATAGAA--TT-TACCC
1 TAAACCCTA-AACGTTAAACCC
* **
255954 TAAA-CCTTAGGGTTAAACCC
1 TAAACCCTAAACGTTAAACCC
* * *
255974 TAAATCCT-AAGGTTAAACTC
1 TAAACCCTAAACGTTAAACCC
255994 TAAACCCTAAAC
1 TAAACCCTAAAC
256006 ACTAAACCTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
17 1 0.01
18 2 0.03
19 10 0.14
20 27 0.38
21 30 0.42
22 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACGTTAAACCC
Found at i:256005 original size:34 final size:34
Alignment explanation
Indices: 255967--256047 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
255957 ACCTTAGGGT
* *
255967 TAAACCCTAAATCCTAAG-GTTAAACTCTAAACCC
1 TAAACACTAAA-CCTAAGAGTTAAACACTAAACCC
**
256001 TAAACACTAAACCTTCGAGTTAAACACTAAACCC
1 TAAACACTAAACCTAAGAGTTAAACACTAAACCC
256035 TAAA-ACATAAACC
1 TAAACAC-TAAACC
256048 CTAAACCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.15
34 35 0.85
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (34 bp):
TAAACACTAAACCTAAGAGTTAAACACTAAACCC
Found at i:256010 original size:14 final size:14
Alignment explanation
Indices: 255987--256060 Score: 60
Period size: 14 Copynumber: 4.9 Consensus size: 14
255977 ATCCTAAGGT
*
255987 TAAACTCTAAACCC
1 TAAACACTAAACCC
256001 TAAACACTAAACCTTC
1 TAAACACTAAACC--C
256017 GAGTTAAACACTAAACCC
1 ----TAAACACTAAACCC
256035 TAAA-ACATAAACCC
1 TAAACAC-TAAACCC
*
256049 TAAACCCTAAAC
1 TAAACACTAAAC
256061 AAATGAACAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
13 2 0.04
14 32 0.64
15 1 0.02
16 1 0.02
18 1 0.02
20 13 0.26
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (14 bp):
TAAACACTAAACCC
Found at i:257906 original size:24 final size:22
Alignment explanation
Indices: 257879--257938 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
257869 AAATTGAAAG
* *
257879 TGAAAGTGAAAATGAAATTTGAAT
1 TGAAATTGAAAATG--ATATGAAT
*
257903 TGAAATTGAAAGTGATATGAAT
1 TGAAATTGAAAATGATATGAAT
257925 TGTAAATTGAAAAT
1 TG-AAATTGAAAAT
257939 CCCTATTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 9 0.29
23 10 0.32
24 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (22 bp):
TGAAATTGAAAATGATATGAAT
Found at i:258112 original size:37 final size:38
Alignment explanation
Indices: 258017--258123 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 38
258007 CTTCGACCTC
** *
258017 GAGTCGATGAGACACTAGTTGTCATTATTTTACTTCGGATA
1 GAGTCGATGAGACACTAG--GT-ACCACTTTACTTCGGATA
* ** *
258058 GATTCGATGAGGTACTAGGTACCACTTTACTTTGGATA
1 GAGTCGATGAGACACTAGGTACCACTTTACTTCGGATA
**
258096 G-GTCGATGAGACACTAGGTGTCACTTTA
1 GAGTCGATGAGACACTAGGTACCACTTTA
258124 TTTCTTCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 22 0.41
38 15 0.28
39 2 0.04
41 15 0.28
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (38 bp):
GAGTCGATGAGACACTAGGTACCACTTTACTTCGGATA
Found at i:262882 original size:22 final size:22
Alignment explanation
Indices: 262857--262909 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
262847 TGAAATCTAT
262857 GTCTCGAGACATGGTTTCTCAA
1 GTCTCGAGACATGGTTTCTCAA
262879 GTCTCGAGACATGGTTTCTCAA
1 GTCTCGAGACATGGTTTCTCAA
262901 GTCTCGAGA
1 GTCTCGAGA
262910 TAGGCCTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
GTCTCGAGACATGGTTTCTCAA
Found at i:263516 original size:41 final size:41
Alignment explanation
Indices: 263456--263841 Score: 411
Period size: 41 Copynumber: 9.4 Consensus size: 41
263446 AAACGCCGCA
*
263456 AAAGGT-AGAGCAATAGCGGCACTTATGGGAAAGCGCTGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
* * * * * *
263496 AAAGGTTAAAGCAATTGCGGCGCTTATCGAAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
* **
263537 AAAGGTCAGAGCAATAGCGTCGCTTATGGTCAAGCGCTGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
* *
263578 AAAGGTCAGAGCAATAGCGGCGTTTATGGGCAAGCG-TCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCT-GCT
*
263619 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGTG-TCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCT-GCT
** * **
263660 AAAGGTCAGAGCAATAGCGATGCTTATAGGG-AAGCACCACT
1 AAAGGTCAGAGCAATAGCGGCGCTTAT-GGGAAAGCGCTGCT
* * * *
263701 AAAGGTCCGAGCAATAACGGCGCTTATGGGCAAGCGCCACCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG---CTGCT
* * * *
263745 AAATGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGTT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
* ** * *
263786 AAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAATGCCGCA
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
263827 AAAGGTCAGAGCAAT
1 AAAGGTCAGAGCAAT
263842 GGGTAAGCGT
Statistics
Matches: 295, Mismatches: 43, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
40 10 0.03
41 245 0.83
42 3 0.01
44 37 0.13
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCT
Found at i:263560 original size:24 final size:24
Alignment explanation
Indices: 263528--263596 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
263518 CTTATCGAAA
*
263528 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGTCGCTAAAGGTCAGAGCAAT
* *
263552 AGCGTCGCTTATGGTCA-AGC---
1 AGCGTCGCTAAAGGTCAGAGCAAT
263572 -GC-T-GCTAAAGGTCAGAGCAAT
1 AGCGTCGCTAAAGGTCAGAGCAAT
263593 AGCG
1 AGCG
263597 GCGTTTATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 13
0.65 0.10 0.25
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 2 0.06
22 2 0.06
23 3 0.09
24 14 0.41
ACGTcount: A:0.29, C:0.23, G:0.30, T:0.17
Consensus pattern (24 bp):
AGCGTCGCTAAAGGTCAGAGCAAT
Found at i:263572 original size:82 final size:82
Alignment explanation
Indices: 263449--263841 Score: 459
Period size: 82 Copynumber: 4.8 Consensus size: 82
263439 TCTACATAAA
* * * * *
263449 CGCCGCAAAAGGT-AGAGCAATAGCGGCACTTATGGGAAAGCGCTGCTAAAGGTTAAAGCAATTG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCTAAAGGTCAGAGCAATAG
* **
263513 CGGCGCTTATCGAAAAG
66 CGGCGCTTATGGGCAAG
* **
263530 CGCCGCTAAAGGTCAGAGCAATAGCGTCGCTTATGGTCAAGCGCTGCTAAAGGTCAGAGCAATAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCTAAAGGTCAGAGCAATAG
*
263595 CGGCGTTTATGGGCAAG
66 CGGCGCTTATGGGCAAG
* *
263612 CGTCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGTG-TCGCTAAAGGTCAGAGCAATA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCT-GCTAAAGGTCAGAGCAATA
**
263676 GCGATGCTTATAGGG-AAG
65 GCGGCGCTTAT-GGGCAAG
* * * * * * *
263694 CACCACTAAAGGTCCGAGCAATAACGGCGCTTATGGGCAAGCGCCACCGCTAAATGTCAGAGCAA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG---CTGCTAAAGGTCAGAGCAA
263759 TAGCGGCGCTTATGGGCAAG
63 TAGCGGCGCTTATGGGCAAG
* * ** * *
263779 CGCCGTTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAATGCCGCAAAAGGTCAGAGCAAT
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCTAAAGGTCAGAGCAAT
263842 GGGTAAGCGT
Statistics
Matches: 262, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
81 13 0.05
82 179 0.68
83 3 0.01
84 3 0.01
85 64 0.24
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.18
Consensus pattern (82 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCTGCTAAAGGTCAGAGCAATAG
CGGCGCTTATGGGCAAG
Found at i:263605 original size:123 final size:121
Alignment explanation
Indices: 263449--263841 Score: 457
Period size: 123 Copynumber: 3.2 Consensus size: 121
263439 TCTACATAAA
* * * * * *
263449 CGCCGCAAAAGGT-AGAGCAATAGCGGCACTTATGGGAAAGCGCTGCTAAAGGTTAAAGCAATTG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAG
* * *
263513 CGGCGCTTATCGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGTCGCTTATGGTCAAG
66 CGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGT-GCTTATGG-AAAG
* *
263571 CGCTGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGCAAGCG-TCGCTAAAGGTCAGAGCAATA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCT-GCTAAAGGTCAGAGCAATA
* * *
263635 GCGGCGCTTATGGGAAAGTGTCGCTAAAGGTCAGAGCAATAGCGATGCTTATAGGGAAG
65 GCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCG-TGCTTAT-GGAAAG
* * * * * *
263694 CACCACTAAAGGTCCGAGCAATAACGGCGCTTATGGGCAAGCGCCACCGCTAAATGTCAGAGCAA
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG---CTGCTAAAGGTCAGAGCAA
* * *
263759 TAGCGGCGCTTATGGGCAAGCGCCGTTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAA
63 TAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGC-GTGCTTAT-GGAAAG
* *
263820 TGCCGCAAAAGGTCAGAGCAAT
1 CGCCGCTAAAGGTCAGAGCAAT
263842 GGGTAAGCGT
Statistics
Matches: 229, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
122 12 0.05
123 128 0.56
124 3 0.01
126 85 0.37
127 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.18
Consensus pattern (121 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAATAG
CGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGTGCTTATGGAAAG
Found at i:263883 original size:70 final size:70
Alignment explanation
Indices: 263770--263909 Score: 181
Period size: 70 Copynumber: 2.0 Consensus size: 70
263760 AGCGGCGCTT
* * ** *
263770 ATGGGCAAGCGCCGTTAAAGGTCAGAGCAATAGCGGTGCTTATGGGAAAATGCCGCAAAAGGTCA
1 ATGGGCAAGCGCCGCTAAAGATCAGAGCAATAGCGACGCTTATGGGAAAATGCCGCAAAAGATCA
263835 GAGCA
66 GAGCA
* * * * **
263840 ATGGGTAAGCGTCGCTAAAGATCAGAGCAATAGCGACGCTTATGGGCAAGTGCCGTTAAAGATCA
1 ATGGGCAAGCGCCGCTAAAGATCAGAGCAATAGCGACGCTTATGGGAAAATGCCGCAAAAGATCA
263905 GAGCA
66 GAGCA
263910 TTAGCGGCGC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (70 bp):
ATGGGCAAGCGCCGCTAAAGATCAGAGCAATAGCGACGCTTATGGGAAAATGCCGCAAAAGATCA
GAGCA
Found at i:269222 original size:31 final size:29
Alignment explanation
Indices: 269180--269243 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
269170 ATTTTTCTAA
* * *
269180 ATGTTTACAATTGAATCGAAATCAATATTTT
1 ATGTGTACAATTGAAAC-AAATCAA-AGTTT
269211 ATGTGTACAATTGAAACAAATCAAAGTTT
1 ATGTGTACAATTGAAACAAATCAAAGTTT
269240 ATGT
1 ATGT
269244 ATCATATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 7 0.23
31 15 0.50
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (29 bp):
ATGTGTACAATTGAAACAAATCAAAGTTT
Found at i:269836 original size:3 final size:3
Alignment explanation
Indices: 269828--269857 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
269818 TTTCGGATTT
269828 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
269858 AGTGTTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:271888 original size:41 final size:41
Alignment explanation
Indices: 271831--271909 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
271821 GAAATACTAT
271831 CAAAATAAAAACAAATTAAGAAGTTGACAAAGAGCCACCCA
1 CAAAATAAAAACAAATTAAGAAGTTGACAAAGAGCCACCCA
*
271872 CAAAATAGAAACAAATTAAGAAGTTGACAAAGAGCCAC
1 CAAAATAAAAACAAATTAAGAAGTTGACAAAGAGCCAC
271910 TCACTTTCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.13
Consensus pattern (41 bp):
CAAAATAAAAACAAATTAAGAAGTTGACAAAGAGCCACCCA
Found at i:287929 original size:12 final size:12
Alignment explanation
Indices: 287914--287955 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
287904 AATAACAACC
*
287914 AAAACAGCAGCA
1 AAAACAACAGCA
*
287926 AAAATAACAGC-
1 AAAACAACAGCA
*
287937 AAAACAACAACA
1 AAAACAACAGCA
287949 AAAACAA
1 AAAACAA
287956 TAAATAAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.69, C:0.21, G:0.07, T:0.02
Consensus pattern (12 bp):
AAAACAACAGCA
Found at i:287939 original size:23 final size:24
Alignment explanation
Indices: 287896--287952 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
287886 TAACATCCAG
*
287896 ACAACCAAAATAACAACCAAAACA
1 ACAACAAAAATAACAACCAAAACA
* * *
287920 GCAGCAAAAATAAC-AGCAAAACA
1 ACAACAAAAATAACAACCAAAACA
287943 ACAACAAAAA
1 ACAACAAAAA
287953 CAATAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.67, C:0.25, G:0.05, T:0.04
Consensus pattern (24 bp):
ACAACAAAAATAACAACCAAAACA
Found at i:287970 original size:21 final size:21
Alignment explanation
Indices: 287944--287995 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
287934 AGCAAAACAA
287944 CAACAAAAACAATAAATAA-AG
1 CAACAAAAACAATAAA-AATAG
*
287965 CAACAAATACAATAAAAATAG
1 CAACAAAAACAATAAAAATAG
*
287986 CAGCAAAAAC
1 CAACAAAAAC
287996 TGCAACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (21 bp):
CAACAAAAACAATAAAAATAG
Found at i:287990 original size:24 final size:24
Alignment explanation
Indices: 287896--288038 Score: 94
Period size: 24 Copynumber: 5.8 Consensus size: 24
287886 TAACATCCAG
* * *
287896 ACAACCAAAATAACAACCAAAAC-
1 ACAACAAAAATAACAGCAAAAACT
* *
287919 AGCAGCAAAAATAACAGCAAAACAACA
1 A-CAACAAAAATAACAGC-AAA-AACT
287946 ACAAAAACAATAAATAA-AGCAACAAA-T
1 AC---AACAA-AAATAACAGCAA-AAACT
* *
287973 ACAATAAAAATAGCAGCAAAAACT
1 ACAACAAAAATAACAGCAAAAACT
* * *
287997 GCAACAAAAATAATAGCAAAAACA
1 ACAACAAAAATAACAGCAAAAACT
*
288021 ATAACAAAAATAACAGCA
1 ACAACAAAAATAACAGCA
288039 TCAAAACAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
23 9 0.10
24 57 0.61
25 2 0.02
26 4 0.04
27 3 0.03
28 4 0.04
29 8 0.09
30 6 0.06
ACGTcount: A:0.66, C:0.20, G:0.06, T:0.08
Consensus pattern (24 bp):
ACAACAAAAATAACAGCAAAAACT
Found at i:288053 original size:24 final size:24
Alignment explanation
Indices: 287978--288057 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
287968 CAAATACAAT
* ***
287978 AAAAATAGCAGCAAAAACTGCAAC
1 AAAAATAACAGCAAAAACAATAAC
*
288002 AAAAATAATAGCAAAAACAATAAC
1 AAAAATAACAGCAAAAACAATAAC
288026 AAAAATAACAGCATCAAAACAATAA-
1 AAAAATAACAGCA--AAAACAATAAC
288051 AAAAATA
1 AAAAATA
288058 TCAAATAGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 31 0.65
25 7 0.15
26 10 0.21
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.11
Consensus pattern (24 bp):
AAAAATAACAGCAAAAACAATAAC
Found at i:288055 original size:26 final size:24
Alignment explanation
Indices: 287925--288055 Score: 77
Period size: 24 Copynumber: 5.2 Consensus size: 24
287915 AAACAGCAGC
*
287925 AAAAATAACAGCAAAACAACAACAAA
1 AAAAATAACAGC-AAA-AACAATAAA
* *
287951 AACAATAA-A-TAAAGCAACAAATACAA
1 AAAAATAACAGCAAA--AAC-AATA-AA
* *** *
287977 TAAAAATAGCAGCAAAAACTGCAAC
1 -AAAAATAACAGCAAAAACAATAAA
* *
288002 AAAAATAATAGCAAAAACAATAAC
1 AAAAATAACAGCAAAAACAATAAA
288026 AAAAATAACAGCATCAAAACAATAAA
1 AAAAATAACAGCA--AAAACAATAAA
288052 AAAA
1 AAAA
288056 TATCAAATAG
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
23 3 0.04
24 35 0.44
25 5 0.06
26 24 0.30
27 9 0.11
28 1 0.01
29 3 0.04
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (24 bp):
AAAAATAACAGCAAAAACAATAAA
Found at i:288103 original size:18 final size:17
Alignment explanation
Indices: 288070--288102 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
288060 AAATAGCAAC
288070 CAAAACAGTAAAAAAAT
1 CAAAACAGTAAAAAAAT
*
288087 CAAAATAGTAAAAAAA
1 CAAAACAGTAAAAAAA
288103 AGCAACCAAA
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:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (17 bp):
CAAAACAGTAAAAAAAT
Found at i:288118 original size:22 final size:22
Alignment explanation
Indices: 288064--288121 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
288054 AATATCAAAT
288064 AGCAACCAAAACAGT---AAAA
1 AGCAACCAAAACAGTAAAAAAA
* *
288083 A--AATCAAAATAGTAAAAAAA
1 AGCAACCAAAACAGTAAAAAAA
288103 AGCAACCAAAACAGTAAAA
1 AGCAACCAAAACAGTAAAA
288122 CGAACAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 10 0.33
19 1 0.03
20 5 0.17
22 14 0.47
ACGTcount: A:0.67, C:0.16, G:0.09, T:0.09
Consensus pattern (22 bp):
AGCAACCAAAACAGTAAAAAAA
Found at i:288234 original size:110 final size:111
Alignment explanation
Indices: 288112--288331 Score: 406
Period size: 111 Copynumber: 2.0 Consensus size: 111
288102 AAGCAACCAA
*
288112 AACAGTAAAACGAACAGCACTAAAATAATAATATAA-TGTTTTTATTAAAAATGGTTAATTTATT
1 AACAGTAAAACGAACAGCACTAAAATAATAATATAATTGTTTTTATTAAAAATGATTAATTTATT
*
288176 CGGGTCAGGTCGGACTCGGCTCGAGCCAAAAAACTCTTACCCGAGC
66 CGGGTCAGGTCGGACTCGACTCGAGCCAAAAAACTCTTACCCGAGC
*
288222 AACAGTAAAACGAACAGCACTAAAATAATAATATAATTTTTTTTATTAAAAATGATTAATTTATT
1 AACAGTAAAACGAACAGCACTAAAATAATAATATAATTGTTTTTATTAAAAATGATTAATTTATT
288287 CGGGTCAGGTCGGACTCGACTCGAGCCAAAAAACTCTTACCCGAG
66 CGGGTCAGGTCGGACTCGACTCGAGCCAAAAAACTCTTACCCGAG
288332 GCTCGATGGG
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 36 0.34
111 70 0.66
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (111 bp):
AACAGTAAAACGAACAGCACTAAAATAATAATATAATTGTTTTTATTAAAAATGATTAATTTATT
CGGGTCAGGTCGGACTCGACTCGAGCCAAAAAACTCTTACCCGAGC
Found at i:291733 original size:11 final size:12
Alignment explanation
Indices: 291712--291803 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 12
291702 GATTTATTTC
*
291712 TAAAATTAAATT
1 TAAATTTAAATT
*
291724 T-ACTTTAAATT
1 TAAATTTAAATT
291735 TAAATTTAAA-T
1 TAAATTTAAATT
*
291746 TAATTTTTTAAATT
1 TAA--ATTTAAATT
*
291760 TAAATTT-AGTT
1 TAAATTTAAATT
291771 TAAATTTGAAA--
1 TAAATTT-AAATT
* *
291782 TAATTTTAAACT
1 TAAATTTAAATT
291794 TAAATTTAAA
1 TAAATTTAAA
291804 ATCAATTACA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.05
11 29 0.46
12 20 0.32
13 7 0.11
14 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:291736 original size:6 final size:6
Alignment explanation
Indices: 291712--291803 Score: 68
Period size: 6 Copynumber: 15.7 Consensus size: 6
291702 GATTTATTTC
* * *
291712 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAA-T TAATTTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAA--ATT TAAATT
* * *
291760 TAAATT T-AGTT TAAATT TGAAA-- TAATTT TAAACT TAAATT TAAA
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAA
291804 ATCAATTACA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 45 0.67
7 3 0.04
8 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:291737 original size:17 final size:16
Alignment explanation
Indices: 291698--291801 Score: 62
Period size: 17 Copynumber: 6.6 Consensus size: 16
291688 TTAGATGGGT
*
291698 TTTAGATTTATTTCTAAA
1 TTTAAATTTA-TT-TAAA
*
291716 ATTAAATTTACTTTAAA
1 TTTAAATTTA-TTTAAA
291733 TTT-AA---ATTTAAA
1 TTTAAATTTATTTAAA
291745 -TT-AATTT-TTTAAA
1 TTTAAATTTATTTAAA
291758 TTTAAATTTAGTTTAAA
1 TTTAAATTTA-TTTAAA
*
291775 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTA-TTTAAA
*
291792 CTTAAATTTA
1 TTTAAATTTA
291802 AAATCAATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
13 7 0.10
14 2 0.03
15 5 0.07
16 5 0.07
17 27 0.39
18 13 0.19
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:291757 original size:36 final size:36
Alignment explanation
Indices: 291717--291802 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
291707 ATTTCTAAAA
*
291717 TTAAATTT-ACTTTAAATTTAAATTT-AAATTAATTTT
1 TTAAATTTAAATTT-AATTTAAATTTGAAA-TAATTTT
*
291753 TTAAATTTAAATTTAGTTTAAATTTGAAATAA--TT
1 TTAAATTTAAATTTAATTTAAATTTGAAATAATTTT
*
291787 TTAAACTTAAATTTAA
1 TTAAATTTAAATTTAA
291803 AATCAATTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
34 16 0.36
36 21 0.48
37 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (36 bp):
TTAAATTTAAATTTAATTTAAATTTGAAATAATTTT
Found at i:292550 original size:13 final size:13
Alignment explanation
Indices: 292532--292564 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
292522 TTTAATGCTG
292532 TTAATAAATATTA
1 TTAATAAATATTA
292545 TTAATAAATATTA
1 TTAATAAATATTA
*
292558 ATAATAA
1 TTAATAA
292565 TAATAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAATAAATATTA
Found at i:292783 original size:17 final size:18
Alignment explanation
Indices: 292746--292780 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
292736 CGATTAATAA
292746 TAAAATAAAAACAGTTTT
1 TAAAATAAAAACAGTTTT
292764 TAAAA-AAAAA-AGTTTT
1 TAAAATAAAAACAGTTTT
292780 T
1 T
292781 TAAGAATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAAATAAAAACAGTTTT
Found at i:293672 original size:59 final size:59
Alignment explanation
Indices: 293571--293887 Score: 406
Period size: 59 Copynumber: 5.4 Consensus size: 59
293561 GGAGGTCCCT
* * * * *
293571 AAACTGTCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * * *
293631 AAACCTCTAAAAATTCCATTTTCACCCTCAAACTTCCAAAAAGCTCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
293690 AAACTTCCAAAAATTCCATTTTTACCCTCAAAATTCCAAAAATCCCATTTTTGATCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
293749 AAACTTCCAAAAATTCAATTTTTA-CC-CGAACTTCC-AAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
293805 AAACTTCCAAAAATTCTATTTTTACCCTCAAAATTCTAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
293864 AAACTTCCAAAAATTCCCTTTTTA
1 AAACTTCCAAAAATTCCATTTTTA
293888 AACCCGAATT
Statistics
Matches: 224, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
56 41 0.18
57 9 0.04
58 8 0.04
59 162 0.72
60 4 0.02
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:293885 original size:29 final size:29
Alignment explanation
Indices: 293571--293885 Score: 259
Period size: 30 Copynumber: 10.8 Consensus size: 29
293561 GGAGGTCCCT
* *
293571 AAACTGTCCAAAAATTCCATTTTCACCCCC
1 AAACT-TCCAAAAATTCCATTTTGACCCCA
* *
293601 GAACTTCCAAAAA-TCTCATTTTTAACCCCA
1 AAACTTCCAAAAATTC-CA-TTTTGACCCCA
* * *
293631 AAACCTCTAAAAATTCCATTTTCACCCTC-
1 AAACTTCCAAAAATTCCATTTTGACCC-CA
* *
293660 AAACTTCCAAAAA-GCTCATTTTTGACCTCA
1 AAACTTCCAAAAATTC-CA-TTTTGACCCCA
*
293690 AAACTTCCAAAAATTCCATTTTTACCCTCA
1 AAACTTCCAAAAATTCCATTTTGACCC-CA
* * *
293720 AAA-TTCCAAAAATCCCATTTTTGATCCTA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCA
* *
293749 AAACTTCCAAAAATTCAATTTTTA-CCC-
1 AAACTTCCAAAAATTCCATTTTGACCCCA
* * *
293776 GAACTTCC-AAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCA
* *
293805 AAACTTCCAAAAATTCTATTTTTACCCTCA
1 AAACTTCCAAAAATTCCATTTTGACCC-CA
* * *
293835 AAA-TTCTAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCA
*
293864 AAACTTCCAAAAATTCCCTTTT
1 AAACTTCCAAAAATTCCATTTT
293886 TAAACCCGAA
Statistics
Matches: 226, Mismatches: 41, Indels: 37
0.74 0.13 0.12
Matches are distributed among these distances:
26 7 0.03
27 12 0.05
28 7 0.03
29 94 0.42
30 103 0.46
31 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCCA
Done.