Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007731.1 Hibiscus syriacus cultivar Beakdansim tig00109983_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: 835416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:10645 original size:16 final size:17
Alignment explanation
Indices: 10624--10659 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
10614 CAAGCCGAGC
10624 CGCTGACCG-CGTTGAT
1 CGCTGACCGACGTTGAT
*
10640 CGCTGACCGATGTTGAT
1 CGCTGACCGACGTTGAT
10657 CGC
1 CGC
10660 CGTTGACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.25
Consensus pattern (17 bp):
CGCTGACCGACGTTGAT
Found at i:12143 original size:24 final size:24
Alignment explanation
Indices: 12115--12180 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
12105 GTTTTATCTT
*
12115 ATTTCCTATTTGAATTCTATTCTG
1 ATTTCCTATCTGAATTCTATTCTG
* *
12139 ATTTCTTATCTGAATTCTGTTCTG
1 ATTTCCTATCTGAATTCTATTCTG
** *
12163 ATTTTTTATCTGGATTCT
1 ATTTCCTATCTGAATTCT
12181 GTTATGATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (24 bp):
ATTTCCTATCTGAATTCTATTCTG
Found at i:12181 original size:24 final size:24
Alignment explanation
Indices: 12125--12213 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 24
12115 ATTTCCTATT
* *
12125 TGAATTCTATTCTGATTTCTTATC
1 TGAATTCTGTTCTGATTTTTTATC
12149 TGAATTCTGTTCTGATTTTTTATC
1 TGAATTCTGTTCTGATTTTTTATC
* * * *
12173 TGGATTCTGTTATGATATTTGATC
1 TGAATTCTGTTCTGATTTTTTATC
* *
12197 TAAATTCT-TTTTGATTT
1 TGAATTCTGTTCTGATTT
12214 CAGATATCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 7 0.13
24 48 0.87
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.56
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTTTTATC
Found at i:14369 original size:11 final size:10
Alignment explanation
Indices: 14342--14371 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
14332 GATGTTGATT
14342 GCCGTTGACC
1 GCCGTTGACC
14352 GCCGTTGACC
1 GCCGTTGACC
14362 GACCGTTGAC
1 G-CCGTTGAC
14372 TTTTTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.13, C:0.37, G:0.30, T:0.20
Consensus pattern (10 bp):
GCCGTTGACC
Found at i:15902 original size:24 final size:24
Alignment explanation
Indices: 15836--15937 Score: 93
Period size: 24 Copynumber: 4.3 Consensus size: 24
15826 TTTATCTAAT
* * *
15836 TTTC-GATTTGAATTATGTTCTAA
1 TTTCTGATCTGAATTCTGTTCTGA
* *
15859 TTTCTTATCTGAATTTTGTTCTGA
1 TTTCTGATCTGAATTCTGTTCTGA
*
15883 TTTCTGATCT-AGATTCTGTTATGA
1 TTTCTGATCTGA-ATTCTGTTCTGA
* * *
15907 TATCTAATCTGAATTCTATT-TGA
1 TTTCTGATCTGAATTCTGTTCTGA
15930 TTTCTGAT
1 TTTCTGAT
15938 ATCTCGTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 14 0.22
24 49 0.77
25 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (24 bp):
TTTCTGATCTGAATTCTGTTCTGA
Found at i:22629 original size:16 final size:16
Alignment explanation
Indices: 22610--22649 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
22600 CGTTATTAAA
*
22610 CTGAATTGATATTTAT
1 CTGAATTGATATTTAC
*
22626 CTGACTTGATATTTAC
1 CTGAATTGATATTTAC
22642 CTGAATTG
1 CTGAATTG
22650 TAAGTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (16 bp):
CTGAATTGATATTTAC
Found at i:23707 original size:57 final size:58
Alignment explanation
Indices: 23598--23710 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
23588 CATTTATATG
* * *
23598 CTTGTTGAAATTTATGAAAATTTAATAAAAAAACAGCAAATGTAAAATCAGTAGCATA
1 CTTGCTGAAATTCATGAAAATTTAATAAAAAAACAGCAAATGTAAAAGCAGTAGCATA
*
23656 CTTGCTGAAATTCATGAAAA-TTAA-AGAAAAAACAGTAAATGTAAAAGCAGTAGCA
1 CTTGCTGAAATTCATGAAAATTTAATA-AAAAAACAGCAAATGTAAAAGCAGTAGCA
23711 CCCTACAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.02
57 31 0.62
58 18 0.36
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (58 bp):
CTTGCTGAAATTCATGAAAATTTAATAAAAAAACAGCAAATGTAAAAGCAGTAGCATA
Found at i:33971 original size:14 final size:14
Alignment explanation
Indices: 33952--33984 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33942 TAGAATTACA
33952 AAAATAAAATAATT
1 AAAATAAAATAATT
33966 AAAATAAAATAATT
1 AAAATAAAATAATT
33980 AAAAT
1 AAAAT
33985 TATAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATAAAATAATT
Found at i:35442 original size:107 final size:101
Alignment explanation
Indices: 35313--35508 Score: 250
Period size: 100 Copynumber: 1.9 Consensus size: 101
35303 AACATACTAC
35313 TAAAAAACAGAACAAAACAGAATATAAAAACAGACAATAAAAATAATAACAAAAACATATACAAA
1 TAAAAAACAGAACAAAACAGAATAT-AAAACAG-CAA-AAAAA-AAT-A-AAAAA-ATATACAAA
* *
35378 ACAAATAATAAATAACATATAACATATAACACTATATAAATAA
59 ACAAATAATAAATAACATAAAACATAAAACACTATATAAATAA
* ** * * *
35421 TAAAAAA-AGAACAAAATAGAATATAAAATTGTAACAAAAAATAATAAAATATACAAAACAAATA
1 TAAAAAACAGAACAAAACAGAATATAAAACAGCAAAAAAAAATAAAAAAATATACAAAACAAATA
35485 ATAAATAACATAAAACATAAAACA
66 ATAAATAACATAAAACATAAAACA
35509 AAACATACTA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
100 38 0.47
101 4 0.05
102 1 0.01
103 3 0.04
104 4 0.05
105 2 0.03
106 5 0.06
107 16 0.20
108 7 0.09
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (101 bp):
TAAAAAACAGAACAAAACAGAATATAAAACAGCAAAAAAAAATAAAAAAATATACAAAACAAATA
ATAAATAACATAAAACATAAAACACTATATAAATAA
Found at i:35571 original size:100 final size:100
Alignment explanation
Indices: 35360--35585 Score: 239
Period size: 100 Copynumber: 2.2 Consensus size: 100
35350 TAAAAATAAT
* * ** *
35360 AACAA-AAACATATACAAAACAAATAATAAATAACATATAACATATAACACTATATAAATAATAA
1 AACAATAAA-ATATACAAAACAAATAATAAATAACATAAAACATAAAACAAAACATAAATAATAA
**
35424 AAAAAGAACAAAATAGAATATAAAATTGTAACAAAA
65 AAAAAGAACAAAATAGAATATAAAATAATAACAAAA
* * *
35460 AATAATAAAATATACAAAACAAATAATAAATAACATAAAACATAAAACAAAACAT-ACTATTAAA
1 AACAATAAAATATACAAAACAAATAATAAATAACATAAAACATAAAACAAAACATAAATAATAAA
*
35524 AAACAGATAACGAAAATA-AA-A-AAACTAAT-ACAAAA
66 AAA-AG--AAC-AAAATAGAATATAAAATAATAACAAAA
*
35559 CACAATATAAATAATACAAAACAAATA
1 AACAATA-AAAT-ATACAAAACAAATA
35586 CAAAACAGAG
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
99 21 0.20
100 56 0.53
101 18 0.17
102 5 0.05
103 6 0.06
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (100 bp):
AACAATAAAATATACAAAACAAATAATAAATAACATAAAACATAAAACAAAACATAAATAATAAA
AAAAGAACAAAATAGAATATAAAATAATAACAAAA
Found at i:35580 original size:32 final size:31
Alignment explanation
Indices: 35537--35613 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
35527 CAGATAACGA
*
35537 AAATAA-AAAAACTAATACAAAACACAATAT
1 AAATAATAAAAACAAATACAAAACACAATAT
* *
35567 AAATAATACAAAACAAATACAAAACAGAGTAT
1 AAATAATA-AAAACAAATACAAAACACAATAT
35599 AAA-AATAAAAA-AAAT
1 AAATAATAAAAACAAAT
35614 TATAAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.10
30 10 0.24
31 5 0.12
32 23 0.55
ACGTcount: A:0.71, C:0.10, G:0.03, T:0.16
Consensus pattern (31 bp):
AAATAATAAAAACAAATACAAAACACAATAT
Found at i:35652 original size:51 final size:50
Alignment explanation
Indices: 35564--35671 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
35554 CAAAACACAA
* * * ** *
35564 TATAAATAATACAAAACAAATACAAAACAGAGTATAAAAATAAAAAAAAT
1 TATAAAAAAAACAAAACAAATAAAAAACAGAAAATAAAAACAAAAAAAAT
* * *
35614 TATAAAAAAAACAAAAGCACATAAAAAACAGAAAATAAAACCAAATAAAAT
1 TATAAAAAAAACAAAA-CAAATAAAAAACAGAAAATAAAAACAAAAAAAAT
35665 TATAAAA
1 TATAAAA
35672 CACTGATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 14 0.29
51 34 0.71
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (50 bp):
TATAAAAAAAACAAAACAAATAAAAAACAGAAAATAAAAACAAAAAAAAT
Found at i:35783 original size:12 final size:12
Alignment explanation
Indices: 35766--35798 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
35756 AGAACCCTAA
35766 AAAAGAAAAAAG
1 AAAAGAAAAAAG
35778 AAAAGAAAAAAG
1 AAAAGAAAAAAG
35790 AAAA-AAAAA
1 AAAAGAAAAA
35799 CATCTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:35796 original size:8 final size:7
Alignment explanation
Indices: 35764--35795 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
35754 TTAGAACCCT
35764 AAAAAAG
1 AAAAAAG
35771 AAAAAAG
1 AAAAAAG
35778 --AAAAG
1 AAAAAAG
35783 AAAAAAG
1 AAAAAAG
35790 AAAAAA
1 AAAAAA
35796 AAACATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.22
7 18 0.78
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35910 original size:21 final size:21
Alignment explanation
Indices: 35885--35953 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
35875 AAAAATGAGT
35885 AGTCACGAACAGTAGGTAAAG
1 AGTCACGAACAGTAGGTAAAG
* * *
35906 AGTCAAGAAGATTA-GT----
1 AGTCACGAACAGTAGGTAAAG
*
35922 AGTCACAAACAGTAGGTAAAG
1 AGTCACGAACAGTAGGTAAAG
*
35943 AGTTACGAACA
1 AGTCACGAACA
35954 AATTTTTTCG
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
20 2 0.06
21 20 0.59
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.17
Consensus pattern (21 bp):
AGTCACGAACAGTAGGTAAAG
Found at i:36559 original size:2 final size:2
Alignment explanation
Indices: 36552--36928 Score: 226
Period size: 2 Copynumber: 192.5 Consensus size: 2
36542 GTCCTACGTG
36552 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
* *
36594 TA TA TA TA T- TA TA CTT TA TA CTT TA TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
36638 -A TA T- TA TA CTT TA -A TA CTT TA TA AA T- TT TA TA TA T- TT TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
36677 TA CT- TA TT TA -A TT TA AA TA TA TA TA TA TA TA TA TA CT- TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
36718 TA TA TA TA TA TA TA CA TA TA CT- TA TA TA TA TA TA TA TA CA CT-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
36760 TA TA GTG TA T- TG TT TA TA TA -A GTT TA CA TA TA TA TA CA -A TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
36801 TA TA TA CA TT TA -A AA TA TA TA TA CT- TA TA T- TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
*
36841 TA TA -A GTA TA -A TG TA TA CT- TA TA T- 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
* *
36881 TA TA TA TA TA T- TA TA AA TA TA AA CTA TA -A 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
36922 TA TA TA T
1 TA TA TA T
36929 TAATTGTTTC
Statistics
Matches: 293, Mismatches: 42, Indels: 80
0.71 0.10 0.19
Matches are distributed among these distances:
1 24 0.08
2 254 0.87
3 15 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:36842 original size:21 final size:20
Alignment explanation
Indices: 36818--36895 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 20
36808 ATTTAAAATA
36818 TATATACTTATATTATATACT
1 TATATA-TTATATTATATACT
* * *
36839 TATATAAGTATAATGTATAC-
1 TATAT-ATTATATTATATACT
36859 T-TATATTATATATATATA-T
1 TATATATTATAT-TATATACT
36878 ATATATATATATATTATA
1 -TATATAT-TATATTATA
36896 AATATAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.11
19 8 0.18
20 2 0.04
21 24 0.53
22 6 0.13
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (20 bp):
TATATATTATATTATATACT
Found at i:37521 original size:15 final size:16
Alignment explanation
Indices: 37495--37524 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37485 GTGTTTAACT
37495 GTTTTAGACCTGAACC
1 GTTTTAGACCTGAACC
37511 GTTTT-GACCTGAAC
1 GTTTTAGACCTGAAC
37525 TGACATCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (16 bp):
GTTTTAGACCTGAACC
Found at i:45025 original size:2 final size:2
Alignment explanation
Indices: 45018--45103 Score: 76
Period size: 2 Copynumber: 46.0 Consensus size: 2
45008 TCGGGCCGGG
* * *
45018 TA TA TA TA TA TA TT TA AA T- TA AA 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
* * *
45059 TA T- TA AA T- TA AA TT TA T- TA -A TA T- 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
45096 TA TA TA TA
1 TA TA TA TA
45104 ATAATTATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
1 6 0.09
2 60 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46157 original size:60 final size:60
Alignment explanation
Indices: 46014--46157 Score: 189
Period size: 60 Copynumber: 2.4 Consensus size: 60
46004 ATTAAGTCTT
* * *
46014 TCAACTATTAAAAATTATAAAATAATTCTTCAATTATAGGGCATTATTTTGTTAAATTCC
1 TCAACTATTAAAAATTATAAAATGATCCTTCAACTATAGGGCATTATTTTGTTAAATTCC
* ** * * *
46074 TCAATTATTAAAAATTATAAAATGATCCTTCAACTATAGGGTGTTATTTTGTTGAGTTTC
1 TCAACTATTAAAAATTATAAAATGATCCTTCAACTATAGGGCATTATTTTGTTAAATTCC
* *
46134 TCAACTATTAAAAGTTACAAAATG
1 TCAACTATTAAAAATTATAAAATG
46158 GTCACATGAC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (60 bp):
TCAACTATTAAAAATTATAAAATGATCCTTCAACTATAGGGCATTATTTTGTTAAATTCC
Found at i:49630 original size:21 final size:21
Alignment explanation
Indices: 49600--49647 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
49590 GCAGGGGTAC
* *
49600 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
49621 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
49642 ATGCCA
1 ATGCCA
49648 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:49677 original size:21 final size:21
Alignment explanation
Indices: 49651--49723 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
49641 TATGCCATCT
*
49651 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
49672 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
49693 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
49714 CCGCAGGGTT
1 CCGCAGGGTT
49724 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:50295 original size:34 final size:34
Alignment explanation
Indices: 50243--50349 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
50233 ATAAATGTTT
*
50243 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
50277 TTAAAATAAAAATAATATTATTCGAAATTTAAAT
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
50311 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
50345 TTAAA
1 TTAAA
50350 TTTCAACTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:51400 original size:128 final size:128
Alignment explanation
Indices: 51241--52125 Score: 1547
Period size: 128 Copynumber: 6.9 Consensus size: 128
51231 TTACCTGATT
51241 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
51306 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* * *
51369 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGTAATAATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
51434 TGACAAAATAATGGAAGGCGCGCCCCCAGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
51497 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
51562 TGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
51625 TATTGATATATCTAGTGTCCCCTAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
51690 TGACAAAATAATGGAAGGCGCGCCCCCTGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
51753 TACTAATATATCTAGAGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
51818 TGACAAAATAATAGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
51881 TATTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
51946 TGACAAAATAATGGAAAGCGCGATCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCG-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* * *
52010 TACTGATATAACTAGTGTCCCCAAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCT-
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
52074 TGACAAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
52126 ACTCTGATTA
Statistics
Matches: 717, Mismatches: 39, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
127 27 0.04
128 592 0.83
129 98 0.14
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:52209 original size:8 final size:8
Alignment explanation
Indices: 52196--52236 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
52186 TCACAAGCTT
52196 TCAAATTC
1 TCAAATTC
52204 TCAAATTC
1 TCAAATTC
* *
52212 CCAAACTC
1 TCAAATTC
52220 T-AAATTC
1 TCAAATTC
52227 TCAAATTC
1 TCAAATTC
52235 TC
1 TC
52237 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:56749 original size:6 final size:6
Alignment explanation
Indices: 56738--56816 Score: 113
Period size: 6 Copynumber: 13.2 Consensus size: 6
56728 TCGGCTCGGC
* * * *
56738 TCGTGG TCGTGG TCGTGG TCGTGG TCATGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
56786 TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
56817 AATACGTGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.06, C:0.16, G:0.48, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:57116 original size:22 final size:22
Alignment explanation
Indices: 57091--57145 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
57081 TCAGGAGTTA
* *
57091 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
57113 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
57135 CGGGAGTTATA
1 CAGGAGTTATA
57146 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:62686 original size:5 final size:5
Alignment explanation
Indices: 62667--62715 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
62657 GTCTGTTCGT
* * * * *
62667 CTCGT CTCGT CTCGG CTCGG CACGG CACAG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
62716 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.06, C:0.41, G:0.33, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:62724 original size:6 final size:6
Alignment explanation
Indices: 62713--62773 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
62703 TCGGCTCGGC
* * * * *
62713 TCGTGG TCGTGG TCGTGG TCGTGG TCATGG TTGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
62761 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
62774 AATACGTGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.07, C:0.15, G:0.48, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:62757 original size:30 final size:30
Alignment explanation
Indices: 62717--62773 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
62707 CTCGGCTCGT
* *
62717 GGTCGTGGTCGTGGTCGTGGTCATGGTTGA
1 GGTCGAGGTCGAGGTCGTGGTCATGGTTGA
*
62747 GGTCGAGGTCGAGGTCGTGGTCGTGGT
1 GGTCGAGGTCGAGGTCGTGGTCATGGT
62774 AATACGTGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.07, C:0.14, G:0.49, T:0.30
Consensus pattern (30 bp):
GGTCGAGGTCGAGGTCGTGGTCATGGTTGA
Found at i:64053 original size:16 final size:15
Alignment explanation
Indices: 64026--64063 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
64016 TACGATTAAA
64026 AAATAGTGATTGATT
1 AAATAGTGATTGATT
64041 AAATAGATGATTGATT
1 AAATAG-TGATTGATT
64057 AAA-AGTG
1 AAATAGTG
64064 TTACTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 8 0.36
16 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (15 bp):
AAATAGTGATTGATT
Found at i:64630 original size:108 final size:107
Alignment explanation
Indices: 64259--64619 Score: 408
Period size: 108 Copynumber: 3.4 Consensus size: 107
64249 AGAAATCGAT
* *
64259 GATAA-AAAATAAGTTAATTACTTATTTTGTTATTAATATTATCAACATATTAGGGA-GCGCCTA
1 GATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTA-GGATGAGCCTA
* * * *
64322 AAATATTACTAAAGTTTAAGCTGATAGAATCTTATAAATCCAAC
65 AAATATTACTAAAGTTTAAGCTGAT-GAGTTTTAGAAATCCTAC
* * * * ** *
64366 GATAACAAAATATGTCAATTGCTTATTTTGTTATTAATATTATCATTATATTA-GATAATGCCTA
1 GATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGATGA-GCCTA
* * *
64430 AAATGTTACTAAAGTTTAAGCTGATGGGCTTTAGAAAT-CTCAC
65 AAATATTACTAAAGTTTAAGCTGATGAGTTTTAGAAATCCT-AC
* * *
64473 AATAACAAAAAAAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTGAGCCTA
1 GATAAC-AAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGATGAGCCTA
* * *
64538 ATATATTA-TCGAAGTTTAAGCTGATGAGTTTTCGAAATCCTAC
65 AAATATTACT-AAAGTTTAAGCTGATGAGTTTTAGAAATCCTAC
* * *
64581 GACAACAAAATAGGTTAAATACTTATTTTGTTATAAATA
1 GATAACAAAATAAGTTAATTACTTATTTTGTTATAAATA
64620 AATATTAACA
Statistics
Matches: 211, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
106 3 0.01
107 51 0.24
108 152 0.72
109 5 0.02
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (107 bp):
GATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGATGAGCCTAA
AATATTACTAAAGTTTAAGCTGATGAGTTTTAGAAATCCTAC
Found at i:65269 original size:50 final size:50
Alignment explanation
Indices: 65196--65297 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
65186 AGATGTATGG
*
65196 AAATTATTAATACCAATAATTAGTGTATAAGTATCGATACGTATTCAGGA
1 AAATTATTAATACCAATAATTAGTGTATAAGTATCGATACATATTCAGGA
* * * * *
65246 AAATTATTAATATCACTACTTAGTGTATATGTATCGATACATATTCATGA
1 AAATTATTAATACCAATAATTAGTGTATAAGTATCGATACATATTCAGGA
65296 AA
1 AA
65298 TATATCGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (50 bp):
AAATTATTAATACCAATAATTAGTGTATAAGTATCGATACATATTCAGGA
Found at i:65664 original size:99 final size:98
Alignment explanation
Indices: 65493--65786 Score: 453
Period size: 99 Copynumber: 3.0 Consensus size: 98
65483 TTTCAAACGA
* * * *
65493 TTAAGTTCTAAATATTTTACCGTTTACATTATTGTTATACCTTTAAACAAACCGATAGATAGTTT
1 TTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACCGGTAGATAG-TT
65558 AACGTAATAGATAGCGCCTATTTTATTTTAATGG
65 AACGTAATAGATAGCGCCTATTTTATTTTAATGG
* *
65592 TTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAACAAACAGGTAGATAGTCT
1 TTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACCGGTAGATAGT-T
* *
65657 AACGTAATAGATAGCGCATATTTTATTTTAAAGG
65 AACGTAATAGATAGCGCCTATTTTATTTTAATGG
*
65691 TTAAGCTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACCGGTAGATAGTTA
1 TTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACCGGTAGATAGTTA
* * **
65756 ATGTAATAGGTAATGCCTATTTTATTTTAAT
66 ACGTAATAGATAGCGCCTATTTTATTTTAAT
65787 CGATTACATT
Statistics
Matches: 177, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
98 28 0.16
99 149 0.84
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (98 bp):
TTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACCGGTAGATAGTTA
ACGTAATAGATAGCGCCTATTTTATTTTAATGG
Found at i:65824 original size:76 final size:77
Alignment explanation
Indices: 65714--65862 Score: 192
Period size: 76 Copynumber: 1.9 Consensus size: 77
65704 ATTTTACCGT
* * *
65714 TTACATTAATATTATACCTTTAAACAAACCGGTAGAT-AGTTAATGTAATAGGTAATGCCTATTT
1 TTACATTAATATTATACCTTCAAACAAACCGGTAGATAAGTTAAAGTAATAGGTAACGCCTATTT
65778 TATTTTAATCGA
66 TATTTTAATCGA
* * * * * * **
65790 TTACATTACTATTATATCTTCAAATAAACTGGTAGCTAATTTAAAGTAATAGGTTGCGCCTATTT
1 TTACATTAATATTATACCTTCAAACAAACCGGTAGATAAGTTAAAGTAATAGGTAACGCCTATTT
65855 TATTTTAA
66 TATTTTAA
65863 CCGGTTAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 31 0.51
77 30 0.49
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (77 bp):
TTACATTAATATTATACCTTCAAACAAACCGGTAGATAAGTTAAAGTAATAGGTAACGCCTATTT
TATTTTAATCGA
Found at i:65841 original size:175 final size:174
Alignment explanation
Indices: 65615--65997 Score: 438
Period size: 175 Copynumber: 2.2 Consensus size: 174
65605 ATTTTACCGT
* * *
65615 TTACATTAATATTATACATTTAAACAAACAGGTAGATAGTCTAACGTAATAGATAGCGCATATTT
1 TTACATTAATATTATACATTCAAACAAACAGGTAGATAATCTAAAGTAATAGATAGCGCATATTT
65680 TATTTTAA-AGGTTAAGCTGTAAATATTTTACCGTTTACATTAATATTATACCTTTAAACAAACC
66 TATTTTAACAGGTTAAGCTGTAAATATTTTACCGTTTACA-T--TATTATACCTTTAAACAAACC
* *
65744 GGTAGA-TAG-TTAATGTAATAGGTAATGCCTATTTTATTTTAATCGA
128 AGTA-ACTAGTTTAACGTAATAGGTAATGCCTATTTTATTTTAATCGA
* * * * * * * *
65790 TTACATTACTATTATATC-TTCAAATAAACTGGTAGCTAATTTAAAGTAATAGGTTGCGCCTATT
1 TTACATTAATATTATA-CATTCAAACAAACAGGTAGATAATCTAAAGTAATAGATAGCGCATATT
* * *
65854 TTATTTTAACCGGTTAAGTTGTAAATATTTTACCGTTTACATTATTATACCTTTGAACAAACCAG
65 TTATTTTAACAGGTTAAGCTGTAAATATTTTACCGTTTACATTATTATACCTTTAAACAAACCAG
* * * *
65919 TAACTAGTTTAACGTAATAGG-AA-GCGGTTATTTTGTTTT-ACCGT
130 TAACTAGTTTAACGTAATAGGTAATGC--CTATTTTATTTTAATCGA
* * * *
65963 TTACATTATTATTATACTTTTAAACAAACATGTAG
1 TTACATTAATATTATACATTCAAACAAACAGGTAG
65998 CTAGTTTACC
Statistics
Matches: 176, Mismatches: 25, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
172 4 0.02
173 59 0.34
174 22 0.12
175 61 0.35
176 30 0.17
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (174 bp):
TTACATTAATATTATACATTCAAACAAACAGGTAGATAATCTAAAGTAATAGATAGCGCATATTT
TATTTTAACAGGTTAAGCTGTAAATATTTTACCGTTTACATTATTATACCTTTAAACAAACCAGT
AACTAGTTTAACGTAATAGGTAATGCCTATTTTATTTTAATCGA
Found at i:65978 original size:173 final size:173
Alignment explanation
Indices: 65604--66034 Score: 500
Period size: 173 Copynumber: 2.5 Consensus size: 173
65594 AAGTTGTAAA
* * * *
65604 TATTTTACCGTTTACATTAATATTATACATTTAAACAAACAGGTAGATAGTCTAACGTAATAGAT
1 TATTTTACCGTTTACATTAATATTATACATTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGT
* *
65669 AGCGCATATTTTATTTTAAAGGTTAAGCTGTAAATATTTTACCGTTTACATTAATATTATACCTT
66 TGCGCCTATTTTATTTTAAAGGTTAAGCTGTAAATATTTTACCGTTTACATT-ATATTATACCTT
* *
65734 TAAACAAACCGGTAGATAGTTAATGTAATAGGTAATGCCTATTT
130 TAAACAAACCAGTAGATAGTTAACGTAATAGGTAATGCCTATTT
* * * * * * *
65778 TATTTTAATCGATTACATTACTATTATATC-TTCAAATAAACTGGTAGCTAATTTAAAGTAATAG
1 TATTTT-ACCGTTTACATTAATATTATA-CATTTAAACAAACTGGTAGCTAGTTTAACGTAATAG
* *
65842 GTTGCGCCTATTTTATTTTAACCGGTTAAGTTGTAAATATTTTACCGTTTACA-T-TATTATACC
64 GTTGCGCCTATTTTATTTTAA-AGGTTAAGCTGTAAATATTTTACCGTTTACATTATATTATACC
* *
65905 TTTGAACAAACCAGTA-ACTAGTTTAACGTAATAGG-AA-GCGGTTATTT
128 TTTAAACAAACCAGTAGA-TAG-TTAACGTAATAGGTAATGC--CTATTT
* * * *
65952 TGTTTTACCGTTTACATTATTATTATACTTTTAAACAAACAT-GTAGCTAGTTTACCGTAATAGG
1 TATTTTACCGTTTACATTAATATTATACATTTAAACAAAC-TGGTAGCTAGTTTAACGTAATAGG
*
66016 TTGC-ACTAATTTTATTTTA
65 TTGCGCCT-ATTTTATTTTA
66035 CGTTTACATT
Statistics
Matches: 218, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
172 6 0.03
173 89 0.41
174 29 0.13
175 64 0.29
176 30 0.14
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (173 bp):
TATTTTACCGTTTACATTAATATTATACATTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGT
TGCGCCTATTTTATTTTAAAGGTTAAGCTGTAAATATTTTACCGTTTACATTATATTATACCTTT
AAACAAACCAGTAGATAGTTAACGTAATAGGTAATGCCTATTT
Found at i:66072 original size:72 final size:73
Alignment explanation
Indices: 65879--66085 Score: 265
Period size: 76 Copynumber: 2.8 Consensus size: 73
65869 AAGTTGTAAA
* *
65879 TATTTTACCGTTTACATTATTATACCTTTGAACAAACCAGTAACTAGTTTAACGTAATAGGAAGC
1 TATTTTACCGTTTACATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGAAGC
** *
65944 GGTTATTT
66 ACTAATTT
* * *
65952 TGTTTTACCGTTTACATTATTATTATACTTTTAAACAAA-CATGTAGCTAGTTTACCGTAATAGG
1 TATTTTACCGTTTAC---ATTATTATACCTTTAAACAAACCA-GTAGCTAGTTTAACGTAATAGG
**
66016 TTGCACTAATTT
62 AAGCACTAATTT
*
66028 TATTTTA-CGTTTACATTATTATACCTTTAAACAAACCAGTAGCTAATTTAACGTAATA
1 TATTTTACCGTTTACATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATA
66086 TTTGCTTCTA
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
72 38 0.33
73 16 0.14
75 9 0.08
76 52 0.45
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (73 bp):
TATTTTACCGTTTACATTATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGAAGC
ACTAATTT
Found at i:66158 original size:171 final size:170
Alignment explanation
Indices: 65954--66277 Score: 460
Period size: 171 Copynumber: 1.9 Consensus size: 170
65944 GGTTATTTTG
* * * *
65954 TTTTACCGTTTACATTATTATTATACTTTTAAACAAACAT-GTAGCTAGTTTACCGTAATAGGTT
1 TTTTACCATTTACATTATTATTATACCTTTAAACAAAC-TGGTAGCTAGTTTAACGTAATAGATT
66018 GC-ACTAATTTTATTTTA-CGTTTAC-ATTATTATACCTTTAAACAAACCAGTAGCTAATTTAAC
65 GCGACT-ATTTTA-TTTACCGTTTACTATTATTATACCTTTAAACAAACC-GTAGCTAATTTAAC
*
66080 GTAATAT-TTGCTTCTATTTTATTTTAATCGGTTAAGTTGTAAATA
127 GTAATATGTTGC--ATATTTTATTTTAATCGGTTAAGTTGTAAATA
* *
66125 TTTTACCATTTACATTTTTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATATATTG
1 TTTTACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGATTG
* *
66190 CGCCTATTTTATTTACCGTTTACATTATTATTATACCTTTAAACAAACCGTAGCTAGTTTAACGT
66 CGACTATTTTATTTACCGTTTAC--TATTATTATACCTTTAAACAAACCGTAGCTAATTTAACGT
66255 AATATGTTGCATATTTTATTTTA
129 AATATGTTGCATATTTTATTTTA
66278 CTGTTTACAT
Statistics
Matches: 137, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
170 5 0.04
171 71 0.52
172 14 0.10
173 20 0.15
174 27 0.20
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (170 bp):
TTTTACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGATTG
CGACTATTTTATTTACCGTTTACTATTATTATACCTTTAAACAAACCGTAGCTAATTTAACGTAA
TATGTTGCATATTTTATTTTAATCGGTTAAGTTGTAAATA
Found at i:66221 original size:75 final size:75
Alignment explanation
Indices: 66123--66574 Score: 555
Period size: 75 Copynumber: 6.1 Consensus size: 75
66113 AAGTTGTAAA
* * * *
66123 TATTTTACCATTTACATTTTTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATATAT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
66188 TGCGCCTATTT
66 TG-GCCTATTT
66199 TA-TTTACCGTTTACATTATTATTATACCTTTAAACAAACC-GTAGCTAGTTTAACGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
*
66262 T-GCATATTT
66 TGGCCTATTT
* * * * *
66271 TATTTTACTGTTTACATTATTATTATACCTTTAAATAAACTGGTAACTAGTTTAACTTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
**
66336 T---C-A-AA
66 TGGCCTATTT
* * *
66341 TATTTTACCGTTTATATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAATGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
* *
66406 AGTG-TTATTT
66 TG-GCCTATTT
* * * * *
66416 TATTTTACCGTTTACATTATTATTTTACCTTTAAATATACCAGTAACTAGTTTAACGTAATA-GA
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATG-
66480 TTGTGCCTATTT
65 TTG-GCCTATTT
* *
66492 TATTTTACCGTTTACATTATTATTATATCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
**
66557 TGCGTTTATTT
66 TG-GCCTATTT
66568 TATTTTA
1 TATTTTA
66575 ACCGATTAAG
Statistics
Matches: 322, Mismatches: 44, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
70 57 0.18
71 1 0.00
72 9 0.03
73 35 0.11
74 47 0.15
75 93 0.29
76 79 0.25
77 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (75 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATATGT
TGGCCTATTT
Found at i:66513 original size:218 final size:216
Alignment explanation
Indices: 66120--66553 Score: 584
Period size: 218 Copynumber: 2.0 Consensus size: 216
66110 GTTAAGTTGT
* * *
66120 AAATATTTTACCATTTACATTTTTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATA
1 AAATATTTTACCATTTACATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAACGTAATA
* *
66185 TATTGCGCCTATTTTATTTACCGTTTACATTATTATTATACCTTTAAACAAACCGTAGCTAGTTT
66 TATAGCGCCTATTTTATTTACCGTTTACATTATTATTATACCTTTAAACAAACCGTAACTAGTTT
* * *
66250 AACGTAATATGTTGCATATTTTATTTTACTGTTTACATTATTATTATACCTTTAAATAAACTGGT
131 AACGTAATATGTTGCATATTTTATTTTACCGTTTAC--TATTATTATACCTTTAAACAAACCGGT
*
66315 AACTAGTTTAACTTAATATGTTC
194 AACTAGTTTAACGTAATATGTTC
* * *
66338 AAATATTTTACCGTTTATATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAATGTAATA
1 AAATATTTTACCATTTACATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAACGTAATA
* * * * * *
66403 TGTAGTG-TTATTTTATTTTACCGTTTACATTATTATTTTACCTTTAAATATACCAGTAACTAGT
66 TATAGCGCCTATTTTA-TTTACCGTTTACATTATTATTATACCTTTAAACAAACC-GTAACTAGT
* *
66467 TTAACGTAATA-GATTGTGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTAAACAAA
129 TTAACGTAATATG--T-TGCATATTTTATTTTACCGTTTAC--TATTATTATACCTTTAAACAAA
*
66531 CCGGTAGCTAGTTTAACGTAATA
189 CCGGTAACTAGTTTAACGTAATA
66554 GGTTGCGTTT
Statistics
Matches: 190, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
217 7 0.04
218 99 0.52
219 19 0.10
220 1 0.01
221 64 0.34
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (216 bp):
AAATATTTTACCATTTACATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAACGTAATA
TATAGCGCCTATTTTATTTACCGTTTACATTATTATTATACCTTTAAACAAACCGTAACTAGTTT
AACGTAATATGTTGCATATTTTATTTTACCGTTTACTATTATTATACCTTTAAACAAACCGGTAA
CTAGTTTAACGTAATATGTTC
Found at i:66604 original size:100 final size:100
Alignment explanation
Indices: 66492--66674 Score: 294
Period size: 100 Copynumber: 1.8 Consensus size: 100
66482 GTGCCTATTT
* * *
66492 TATTTTACCGTTTACATTATTATTATATCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAACGTAATAGGT
* * *
66557 TGCGTTTATTTTATTTTAACCGATTAAGTTGTAAA
66 CGCATCTATTTTATTTTAACCGATTAAGTTGTAAA
* *
66592 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAATGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAACGTAATAGGT
66657 CGCATCTATTTTATTTTA
66 CGCATCTATTTTATTTTA
66675 CTGTTTACAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (100 bp):
TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAACGTAATAGGT
CGCATCTATTTTATTTTAACCGATTAAGTTGTAAA
Found at i:66692 original size:76 final size:76
Alignment explanation
Indices: 66592--66769 Score: 284
Period size: 76 Copynumber: 2.3 Consensus size: 76
66582 AAGTTGTAAA
* *
66592 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAATGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACATATAAACAAACCGATAGCTAGTTTAACGTAATATGT
*
66657 CGCATCTATTT
66 CGCACCTATTT
* * *
66668 TATTTTACTGTTTACATTATTATTATACATTTAAACAAACCGATAGCTATTTTAACGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACATATAAACAAACCGATAGCTAGTTTAACGTAATATGT
* *
66733 TGCGCCTATTT
66 CGCACCTATTT
66744 TATTTTACCGTTTACATTATTATTAT
1 TATTTTACCGTTTACATTATTATTAT
66770 TATACTTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 93 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (76 bp):
TATTTTACCGTTTACATTATTATTATACATATAAACAAACCGATAGCTAGTTTAACGTAATATGT
CGCACCTATTT
Found at i:66724 original size:176 final size:175
Alignment explanation
Indices: 66416--66750 Score: 480
Period size: 176 Copynumber: 1.9 Consensus size: 175
66406 AGTGTTATTT
* * * *
66416 TATTTTACCGTTTACATTATTATTTTACCTTTAAATATACCAGTAACTAGTTTAACGTAATAGAT
1 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCAGTAACTAGTTTAACGTAATA-AT
*
66481 TGTGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTAAACAAACCGGTAGCTAGTTTA
65 TGTGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTAAACAAACCGATAGCTAGTTTA
**
66546 ACGTAATAGGTTGCGTTTATTTTATTTTAACCGATTAAGTTGTAAA
130 ACGTAATAGGTTGCGCCTATTTTATTTTAACCGATTAAGTTGTAAA
* *
66592 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACC-GATAGCTAGTTTAATGTAAT-A-
1 TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCAG-TAACTAGTTTAACGTAATAAT
* *
66654 TGTCGCATCTATTTTATTTTACTGTTTACATTATTATTATA-CATTTAAACAAACCGATAGCTAT
65 TGT-GC--CTATTTTATTTTACCGTTTACATTATTATTATATC-TTTAAACAAACCGATAGCTAG
*
66718 TTTAACGTAATATGTTGCGCCTATTTTATTTTA
126 TTTAACGTAATAGGTTGCGCCTATTTTATTTTA
66751 CCGTTTACAT
Statistics
Matches: 142, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
173 3 0.02
174 3 0.02
175 2 0.01
176 134 0.94
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (175 bp):
TATTTTACCGTTTACATTATTATTATACCTATAAACAAACCAGTAACTAGTTTAACGTAATAATT
GTGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTAAACAAACCGATAGCTAGTTTAA
CGTAATAGGTTGCGCCTATTTTATTTTAACCGATTAAGTTGTAAA
Found at i:66888 original size:242 final size:244
Alignment explanation
Indices: 66338--66916 Score: 785
Period size: 242 Copynumber: 2.4 Consensus size: 244
66328 TAATATGTTC
* *
66338 AAATATTTTACCGTTTATATTATTATTATACATTTAAACAAACCGGTAGCTAGTTTAATGTAATA
1 AAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATA
* * * * *
66403 TGTAGTGT-TATTTTATTTTACCGTTTACATTATTATTTTACCTTTAAATATACCAGTAACTAGT
66 TGTAGCGTCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAACTAGT
*
66467 TTAACGTAATAGATTGTGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTAAACAAAC
131 TTAACGTAATAGATTGCGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTT--ACAAA-
* *
66532 CGGTAGCTAGTTTAACGTAATAGGTTGCGTTTATTTTATTTTAACCGATTAAGTTGT
193 C---A-CTAGTTTAACGTAATAGGTTACG-CTATTTTATTTTAACCGATTAAGTTGT
* *
66589 AAATATTTTACCGTTTACATTATTATTATACCTATAAACAAACCGATAGCTAGTTTAATGTAATA
1 AAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATA
* * * * *
66654 TGTCGCATCTATTTTATTTTACTGTTTACATTATTATTATACATTTAAACAAACC-GATAGCTAT
66 TGTAGCGTCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAG-TAACTAG
*
66718 TTTAACGTAATATG-TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATTATACTTT-TAA
130 TTTAACGTAATA-GATTGCGCCTATTTTATTTTACCGTTTACATTATTATTA-TAT-CTTTACAA
*
66781 A-A-TAGTTTAACGTAATAGGTTAC-CTATTTTATTTTAACCGGTTAAGTTGT
192 ACACTAGTTTAACGTAATAGGTTACGCTATTTTATTTTAACCGATTAAGTTGT
* *
66831 AAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGGTAGTTAGTTTAATGTAATA
1 AAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATA
* * *
66896 GGTTGCGCCTATTTTATTTTA
66 TGTAGCGTCTATTTTATTTTA
66917 ACCGGTTAAA
Statistics
Matches: 296, Mismatches: 27, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
242 103 0.35
244 20 0.07
246 1 0.00
251 70 0.24
252 94 0.32
253 4 0.01
254 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (244 bp):
AAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAATGTAATA
TGTAGCGTCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAACTAGT
TTAACGTAATAGATTGCGCCTATTTTATTTTACCGTTTACATTATTATTATATCTTTACAAACAC
TAGTTTAACGTAATAGGTTACGCTATTTTATTTTAACCGATTAAGTTGT
Found at i:67316 original size:73 final size:70
Alignment explanation
Indices: 67178--67363 Score: 198
Period size: 73 Copynumber: 2.6 Consensus size: 70
67168 AATTTAATAT
*
67178 TTTGCAGCCTTCTCATTTTCTATTTTTTTAAAATTCGAAAGTATAGATATTTTTGAAAAAATATT
1 TTTGCAGCCTTCTCATTTTCTATTTTTTTAAAATTCGAAAGTATAGATATTTTAGAAAAAATATT
67243 GAAAC
66 GAAAC
* * *
67248 TTTGCGGCCTTCTCATTTTCCATGTTTTTTTTTAAATTCGAAAGTAT-GAATATTTGTAG-AAAA
1 TTTGCAGCCTTCTCATTTT-C-T-ATTTTTTTAAAATTCGAAAGTATAG-ATATTT-TAGAAAAA
* *
67311 GTATTGATAC
61 ATATTGAAAC
* * * * * *
67321 TTTTCAACATTTTCATTTTTTATTTTTTT-AAATTTGAAAGTAT
1 TTTGCAGCCTTCTCATTTTCTATTTTTTTAAAATTCGAAAGTAT
67364 CTATACTTGT
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
69 13 0.13
70 25 0.26
71 2 0.02
72 2 0.02
73 53 0.55
74 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (70 bp):
TTTGCAGCCTTCTCATTTTCTATTTTTTTAAAATTCGAAAGTATAGATATTTTAGAAAAAATATT
GAAAC
Found at i:68358 original size:22 final size:22
Alignment explanation
Indices: 68324--68378 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
68314 TGCAAAGATA
* * * *
68324 CATGATCTGCATTTTTTTAATG
1 CATGATTTACATTGTTTGAATG
68346 CATGATTTACATTGTTTGAATG
1 CATGATTTACATTGTTTGAATG
* *
68368 CCTAATTTACA
1 CATGATTTACA
68379 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (22 bp):
CATGATTTACATTGTTTGAATG
Found at i:81204 original size:20 final size:20
Alignment explanation
Indices: 81175--81213 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
81165 AAGGCCCATA
*
81175 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
81195 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
81214 GTGGTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:85643 original size:28 final size:28
Alignment explanation
Indices: 85600--85658 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
85590 TGAACTTATT
85600 CATGCATTTACCAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
* *
85628 CATGTATTTACGAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
85656 CAT
1 CAT
85659 AAAGCATACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (28 bp):
CATGCATTTACCAACTATCAATGTGTAC
Found at i:90559 original size:22 final size:22
Alignment explanation
Indices: 90518--90583 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
90508 AACCGACCAC
* **
90518 CGTCGGTCACTATTTTGGCCAT
1 CGTCGATCACTATTCCGGCCAT
*
90540 CGTCGATCACTATTCCGGCCAC
1 CGTCGATCACTATTCCGGCCAT
*
90562 CGTC-AGTTACTATTCCGGCCAT
1 CGTCGA-TCACTATTCCGGCCAT
90584 ACTATTCCAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.17, C:0.33, G:0.20, T:0.30
Consensus pattern (22 bp):
CGTCGATCACTATTCCGGCCAT
Found at i:91078 original size:25 final size:25
Alignment explanation
Indices: 91044--91094 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
91034 TTTACTGGAA
91044 GCTACTGGAATTTCAACATGTAGGG
1 GCTACTGGAATTTCAACATGTAGGG
*
91069 GCTACTGGAATTTCAACGTGTAGGG
1 GCTACTGGAATTTCAACATGTAGGG
91094 G
1 G
91095 TGCTGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (25 bp):
GCTACTGGAATTTCAACATGTAGGG
Found at i:92000 original size:177 final size:176
Alignment explanation
Indices: 91703--92056 Score: 642
Period size: 177 Copynumber: 2.0 Consensus size: 176
91693 GCATAAAAAT
91703 CATCTGTAAAATTAAAACTCAAAGGCTAATAATCATCTGATGCATAATGACCAAAAAATCTGCTA
1 CATCTGTAAAATTAAAACTCAAAGGCTAATAATCATCTGATGCATAATGACCAAAAAATCTGCTA
91768 TGATATTTCCTTTTTGCTTTTCATTTGACATATATGATATCAAACTCTGATAATAACATCTTCCA
66 TGATATTTCCTTTTTGCTTTTCATTTGACA-ATATGATATCAAACTCTGATAATAACATCTTCCA
91833 TCTAGCCATTTTTCCTGTCAAAGCTGGTGATTAAATTAAGAAGGGATC
130 TCTAGCCA-TTTTCCTGTCAAAGCTGGTGATTAAATTAAGAAGGGATC
91881 CATCTGTAAAATT-AAACTCAAAGGCTAATAATCATCTGATGCATAACTGACCAAAAAATCTGCT
1 CATCTGTAAAATTAAAACTCAAAGGCTAATAATCATCTGATGCATAA-TGACCAAAAAATCTGCT
91945 ATGAT-TTTCCTTTTATTGCTTTTCATTTGAC-ATATGATATCAAACTCTGATAATAACATCTTC
65 ATGATATTTCC-TTT-TTGCTTTTCATTTGACAATATGATATCAAACTCTGATAATAACATCTTC
92008 CATCTAGCCATTTTCCTGTCAAAGCTGGTGATTAAATTAAGAAGGGATC
128 CATCTAGCCATTTTCCTGTCAAAGCTGGTGATTAAATTAAGAAGGGATC
92057 AAGTCTGGAT
Statistics
Matches: 173, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
176 39 0.23
177 80 0.46
178 38 0.22
179 16 0.09
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (176 bp):
CATCTGTAAAATTAAAACTCAAAGGCTAATAATCATCTGATGCATAATGACCAAAAAATCTGCTA
TGATATTTCCTTTTTGCTTTTCATTTGACAATATGATATCAAACTCTGATAATAACATCTTCCAT
CTAGCCATTTTCCTGTCAAAGCTGGTGATTAAATTAAGAAGGGATC
Found at i:95413 original size:11 final size:12
Alignment explanation
Indices: 95397--95425 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
95387 ATATAAGGAT
95397 ATAAAAT-AAAA
1 ATAAAATAAAAA
95408 ATAAAATAAAAA
1 ATAAAATAAAAA
95420 ATAAAA
1 ATAAAA
95426 GAATTGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:96042 original size:25 final size:28
Alignment explanation
Indices: 96013--96073 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
96003 TTTCCGACTG
96013 AAATAATAAG-A-A-AAACTCTTACCAA
1 AAATAATAAGAATAGAAACTCTTACCAA
96038 AAATAATAAGAATATGAAACTCTTACCAA
1 AAATAATAAGAATA-GAAACTCTTACCAA
*
96067 GAATAAT
1 AAATAAT
96074 TTGATATAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 10 0.32
26 1 0.03
27 1 0.03
29 19 0.61
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (28 bp):
AAATAATAAGAATAGAAACTCTTACCAA
Found at i:96264 original size:2 final size:2
Alignment explanation
Indices: 96257--96290 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
96247 TTAACCTTTC
96257 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96291 ATGTGACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107260 original size:20 final size:20
Alignment explanation
Indices: 107227--107266 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
107217 ATAATCATAT
*
107227 TCACTAATAATCTTTTATTC
1 TCACTAATAATCTTATATTC
* *
107247 TCACTGATATTCTTATATTC
1 TCACTAATAATCTTATATTC
107267 CATGAACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.50
Consensus pattern (20 bp):
TCACTAATAATCTTATATTC
Found at i:107553 original size:31 final size:31
Alignment explanation
Indices: 107490--107582 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
107480 GATGTTATAC
* * *
107490 ATACCACGTCATT-TTTTAATAATATGATAT
1 ATACAACGTCATTATTTTAATAATGTGACAT
*
107520 ATACAACGTCATTATTTTAATGATGTGACAT
1 ATACAACGTCATTATTTTAATAATGTGACAT
* ** *
107551 ATATAATATCATCATTTTTAATAATGTGACAT
1 ATACAACGTCATTA-TTTTAATAATGTGACAT
107583 TTTCTTGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.23
31 24 0.46
32 16 0.31
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (31 bp):
ATACAACGTCATTATTTTAATAATGTGACAT
Found at i:108631 original size:24 final size:24
Alignment explanation
Indices: 108585--108636 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
108575 AACAAACTCG
**
108585 TTTAACTACTCGTTTATTGGCTCC
1 TTTAACTACTCGTTTATAAGCTCC
* *
108609 TTTAACTATTCGTTTATAAGCTCG
1 TTTAACTACTCGTTTATAAGCTCC
108633 TTTA
1 TTTA
108637 CCCTGTTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTAACTACTCGTTTATAAGCTCC
Found at i:108959 original size:135 final size:135
Alignment explanation
Indices: 108769--109036 Score: 479
Period size: 135 Copynumber: 2.0 Consensus size: 135
108759 TATTATTTTT
108769 CTGAACATATAAACATTCTTGAATGTTAACGAATCGAACACGAACCAGGAATGAACACCTT-AAA
1 CTGAACATATAAACATTCTTGAATGTTAACGAATCGAACACGAACCAGGAATGAACACCTTAAAA
108833 AAAAACAAACAAACATGAATGTAACCTTATTCGTTCAAGTTTGGTTCA-T-TACCCCTATTAAAC
66 AAAAACAAACAAACATGAATGT-ACCTTATTCG-TCAAGTTTGGTTCATTATACCCCTATTAAAC
108896 CTCAACC
129 CTCAACC
108903 CTGAACATATAAACATTCTTGAATGTTAAACGAATCGAACACGAACCAGGAATGAACACCTTAAA
1 CTGAACATATAAACATTCTTGAATGTT-AACGAATCGAACACGAACCAGGAATGAACACCTTAAA
108968 AAAAAACAAACAAACATGAATGTACCTTATTCGTCAAGTTTGGTTCATTTATACCCCTATTAAAC
65 AAAAAACAAACAAACATGAATGTACCTTATTCGTCAAGTTTGGTTCA-TTATACCCCTATTAAAC
109033 CTCA
129 CTCA
109037 CCCATAGACA
Statistics
Matches: 129, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
134 41 0.32
135 44 0.34
136 26 0.20
137 18 0.14
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (135 bp):
CTGAACATATAAACATTCTTGAATGTTAACGAATCGAACACGAACCAGGAATGAACACCTTAAAA
AAAAACAAACAAACATGAATGTACCTTATTCGTCAAGTTTGGTTCATTATACCCCTATTAAACCT
CAACC
Found at i:118068 original size:59 final size:60
Alignment explanation
Indices: 118000--118117 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 60
117990 ACATTTTCTC
* * * * * *
118000 AAATTATGACCT-TCATTTTAAGTTGGTCCTTAA-ATTTTAAATATTTCAATTTCATCCCT
1 AAATTATGA-CTATCATTCTAAATTAGTCCTCAACATTTTAAACATTCCAATTTCATCCCT
* *
118059 AAATTATGACTATCATTCTAAATTAGTCCTCAACCTTTTGAACATTCCAATTTCATCCC
1 AAATTATGACTATCATTCTAAATTAGTCCTCAACATTTTAAACATTCCAATTTCATCCC
118118 AAACTATACA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 2 0.04
59 26 0.53
60 21 0.43
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (60 bp):
AAATTATGACTATCATTCTAAATTAGTCCTCAACATTTTAAACATTCCAATTTCATCCCT
Found at i:120381 original size:85 final size:86
Alignment explanation
Indices: 120265--120421 Score: 237
Period size: 85 Copynumber: 1.8 Consensus size: 86
120255 TCTTTTGACT
* * * *
120265 GTCTTCTATATTCATATATATTGTTGGAGTTGCCTAATTAATACATATGGCACTAGTGAAATCTC
1 GTCTTCTACATTCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAAGTGAAATATC
120330 -AATTTGGCATTTTTATGGCA
66 TAATTTGGCATTTTTATGGCA
* *
120350 GTCTTCTACATGT-ATATATATTGTTAGAGTTGCCTGATTAATCCATATGGCACAAGTGAAATAT
1 GTCTTCTACAT-TCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAAGTGAAATAT
120414 CTAATTTG
65 CTAATTTG
120422 ACATAATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
85 57 0.89
86 7 0.11
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (86 bp):
GTCTTCTACATTCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAAGTGAAATATC
TAATTTGGCATTTTTATGGCA
Found at i:125060 original size:22 final size:22
Alignment explanation
Indices: 125030--125071 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
125020 TAATTAAAAA
125030 TGTTAATGAACAATTAAAATCT
1 TGTTAATGAACAATTAAAATCT
* *
125052 TGTTTATGAACATTTAAAAT
1 TGTTAATGAACAATTAAAAT
125072 ACAAAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
TGTTAATGAACAATTAAAATCT
Found at i:137931 original size:29 final size:29
Alignment explanation
Indices: 137880--137979 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 29
137870 CATTTTACAC
* *
137880 AAATAGCA-CTTTTTT-AAATAATTACCA
1 AAATAGCACCTTTTTTGAATTAATTCCCA
137907 AAATAGCACCTTTTTTGAATTAATTCCCA
1 AAATAGCACCTTTTTTGAATTAATTCCCA
* ** *
137936 TAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCTTTTTTGAATTAATTCCCA
* *
137965 GAATATCACCTTTTT
1 AAATAGCACCTTTTT
137980 CAAAAAAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
27 8 0.13
28 7 0.11
29 46 0.75
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (29 bp):
AAATAGCACCTTTTTTGAATTAATTCCCA
Found at i:137980 original size:29 final size:29
Alignment explanation
Indices: 137898--138031 Score: 124
Period size: 29 Copynumber: 4.6 Consensus size: 29
137888 CTTTTTTAAA
* * * *
137898 TAATTACCAAAATAGCACCTTTTTTGAAT
1 TAATTCCCAGAATAGCACCTATTTCGAAT
* *
137927 TAATTCCCATAATAGCACCAATTTCGAAT
1 TAATTCCCAGAATAGCACCTATTTCGAAT
* * * *
137956 TAATTCCCAGAATATCACCTTTTTCAAAA
1 TAATTCCCAGAATAGCACCTATTTCGAAT
* * * *
137985 AAATTACCGGAAATAGCACCCATTTCGAAT
1 TAATTCCCAG-AATAGCACCTATTTCGAAT
*
138015 TAATTCCCCGAATAGCA
1 TAATTCCCAGAATAGCA
138032 ATAAACCGAA
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
29 61 0.74
30 21 0.26
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (29 bp):
TAATTCCCAGAATAGCACCTATTTCGAAT
Found at i:138125 original size:10 final size:10
Alignment explanation
Indices: 138105--138140 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
138095 ACGGGTCGTG
138105 ACCGGTC-AA
1 ACCGGTCAAA
138114 ACCGGTCAAA
1 ACCGGTCAAA
138124 ACCGGTTCAAA
1 ACCGG-TCAAA
138135 ACCGGT
1 ACCGGT
138141 TTCCAGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:145237 original size:29 final size:29
Alignment explanation
Indices: 145205--145309 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
145195 CTTTTTTAAA
145205 TAATTACC-AAAATAGCACACTTTTCGAAT
1 TAATT-CCTAAAATAGCACACTTTTCGAAT
*
145234 TAATTCCTAAAATAGCACCCTTTTCGAAT
1 TAATTCCTAAAATAGCACACTTTTCGAAT
* * * * *
145263 TAATTCCTAGAATATCACATTTTTCAAAA
1 TAATTCCTAAAATAGCACACTTTTCGAAT
*
145292 AAATTACC-AAAATAGCAC
1 TAATT-CCTAAAATAGCAC
145310 CCATTTTAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.94
30 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (29 bp):
TAATTCCTAAAATAGCACACTTTTCGAAT
Found at i:145393 original size:13 final size:13
Alignment explanation
Indices: 145375--145404 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
145365 ACCGGTCAAC
145375 GGTCAACGGGTCG
1 GGTCAACGGGTCG
145388 GGTCAACGGGTCG
1 GGTCAACGGGTCG
145401 GGTC
1 GGTC
145405 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:145404 original size:18 final size:17
Alignment explanation
Indices: 145381--145421 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
145371 CAACGGTCAA
145381 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAAC-GGT
145399 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
145416 CGGGTC
1 CGGGTC
145422 AACGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.10, C:0.24, G:0.49, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:145418 original size:12 final size:12
Alignment explanation
Indices: 145401--145426 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
145391 CAACGGGTCG
145401 GGTCGGGTCAAC
1 GGTCGGGTCAAC
145413 GGTCGGGTCAAC
1 GGTCGGGTCAAC
145425 GG
1 GG
145427 GTAAACGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:154605 original size:25 final size:24
Alignment explanation
Indices: 154563--154624 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 24
154553 ATCCTCTATG
* *
154563 TTCCTTTTTCCTT-ATTTTCTTTTTC
1 TTCCTTTTT-CTTCCTTTT-TTCTTC
154588 TTCCTTTTTCTTCC-TTTTTCTTC
1 TTCCTTTTTCTTCCTTTTTTCTTC
154611 -TCCTTTTTC-TCCTT
1 TTCCTTTTTCTTCCTT
154625 GTTATTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 3 0.09
22 10 0.30
23 5 0.15
24 6 0.18
25 9 0.27
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCCTTTTTCTTCCTTTTTTCTTC
Found at i:154620 original size:9 final size:10
Alignment explanation
Indices: 154581--154624 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
154571 TCCTTATTTT
154581 CTTTTTCTTC
1 CTTTTTCTTC
154591 CTTTTTCTTC
1 CTTTTTCTTC
154601 CTTTTTCTTCTC
1 CTTTTTC-T-TC
154613 CTTTTTC-TC
1 CTTTTTCTTC
154622 CTT
1 CTT
154625 GTTATTTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.16
10 17 0.53
11 1 0.03
12 9 0.28
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTTTCTTC
Found at i:154635 original size:21 final size:22
Alignment explanation
Indices: 154588--154636 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
154578 TTTCTTTTTC
* *
154588 TTCCTTTTTCTTCCTTTTTCTT
1 TTCCTTTTTCTTCCTTGTTATT
*
154610 CTCCTTTTTC-TCCTTGTTATT
1 TTCCTTTTTCTTCCTTGTTATT
154631 TTCCTT
1 TTCCTT
154637 GTCGTCGTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCCTTTTTCTTCCTTGTTATT
Found at i:156001 original size:27 final size:29
Alignment explanation
Indices: 155955--156008 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
155945 AACATATTTA
155955 TTGAGTATTTAAACTATTATTTTTTTATT
1 TTGAGTATTTAAACTATTATTTTTTTATT
*
155984 TTGA-TATTTAAA-TTTTATTTTTTTA
1 TTGAGTATTTAAACTATTATTTTTTTA
156009 AATCATACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
28 8 0.33
29 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (29 bp):
TTGAGTATTTAAACTATTATTTTTTTATT
Found at i:156236 original size:25 final size:26
Alignment explanation
Indices: 156208--156256 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
156198 TAATTTTGAA
*
156208 AAAAATAA-AATTTAGGTACCAAAAC
1 AAAAATAATAATTTAGATACCAAAAC
* *
156233 AAAAGTAATATTTTAGATACCAAA
1 AAAAATAATAATTTAGATACCAAA
156257 TGTGTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.24
Consensus pattern (26 bp):
AAAAATAATAATTTAGATACCAAAAC
Found at i:156587 original size:31 final size:31
Alignment explanation
Indices: 156523--156599 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
156513 ACGATTTAAC
** *
156523 AGTTCAGTGGTATAATTGAAATGGAAATCAA
1 AGTTCAGTGGTATAATTGAAATAAAAATAAA
*
156554 AGTTCAGTGCTATAATTGAAA-AAAAACTAAA
1 AGTTCAGTGGTATAATTGAAATAAAAA-TAAA
*
156585 AGTTTAGTGGTATAA
1 AGTTCAGTGGTATAA
156600 ACGATACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.30
Consensus pattern (31 bp):
AGTTCAGTGGTATAATTGAAATAAAAATAAA
Found at i:161665 original size:16 final size:18
Alignment explanation
Indices: 161644--161676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
161634 AATAACACAC
161644 ATAAA-TAT-TAAAATAA
1 ATAAATTATATAAAATAA
161660 ATAAATTATATAAAATA
1 ATAAATTATATAAAATA
161677 TCCAACTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAATTATATAAAATAA
Found at i:161831 original size:14 final size:14
Alignment explanation
Indices: 161814--161840 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
161804 TTTCTATTCA
161814 TCTAAACCCTAAAC
1 TCTAAACCCTAAAC
161828 TCTAAACCCTAAA
1 TCTAAACCCTAAA
161841 AAAAACCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TCTAAACCCTAAAC
Found at i:164885 original size:33 final size:34
Alignment explanation
Indices: 164816--164885 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
164806 ACTTAAAGTA
* *
164816 TTTTTTTGGTCAAAATAAGTATCTAAAGTTACTT
1 TTTTTTTGGTCAAAATAAGCACCTAAAGTTACTT
*
164850 TTTTTTTTGTCAAAATAAGCACCTAAA-TTA-TT
1 TTTTTTTGGTCAAAATAAGCACCTAAAGTTACTT
164882 TTTT
1 TTTT
164886 ATCAAATAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 6 0.18
33 3 0.09
34 24 0.73
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (34 bp):
TTTTTTTGGTCAAAATAAGCACCTAAAGTTACTT
Found at i:164892 original size:27 final size:28
Alignment explanation
Indices: 164852--164908 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
164842 AGTTACTTTT
* *
164852 TTTTTTGTCAAAATAAGCACCTAAATTA
1 TTTTTTATCAAAATAAGCACCTAAAGTA
* *
164880 TTTTTTATC-AAATAGGTACCTAAAGTA
1 TTTTTTATCAAAATAAGCACCTAAAGTA
164907 TT
1 TT
164909 CAAACTTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (28 bp):
TTTTTTATCAAAATAAGCACCTAAAGTA
Found at i:165028 original size:29 final size:30
Alignment explanation
Indices: 164992--165077 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 30
164982 ATTGAATATG
*
164992 TTAGGTACATATTTTGACTAAAAAAT-ACT
1 TTAGGTACTTATTTTGACTAAAAAATAACT
* *
165021 TTAGGTACTTATTTTAACAAAAAAAATATAACT
1 TTAGGTACTTATTTTGAC--TAAAAA-ATAACT
165054 TTAGGTACTTATTTTGA-TAAAAAA
1 TTAGGTACTTATTTTGACTAAAAAA
165078 AATACCTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 17 0.35
30 5 0.10
31 5 0.10
32 2 0.04
33 19 0.40
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.38
Consensus pattern (30 bp):
TTAGGTACTTATTTTGACTAAAAAATAACT
Found at i:165060 original size:33 final size:32
Alignment explanation
Indices: 165011--165081 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 32
165001 TATTTTGACT
165011 AAAAA-ATACTTTAGGTACTTATTTTAACAAA
1 AAAAATATACTTTAGGTACTTATTTTAACAAA
* *
165042 AAAAATATAACTTTAGGTACTTATTTTGATAAA
1 AAAAATAT-ACTTTAGGTACTTATTTTAACAAA
165075 AAAAATA
1 AAAAATA
165082 CCTTAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 5 0.14
32 2 0.06
33 29 0.81
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (32 bp):
AAAAATATACTTTAGGTACTTATTTTAACAAA
Found at i:167406 original size:31 final size:31
Alignment explanation
Indices: 167368--167498 Score: 151
Period size: 31 Copynumber: 4.3 Consensus size: 31
167358 GAGTTGAGGG
* * *
167368 TTACCTATGTCTTTCGAGACATATGTACATA
1 TTACCTATGTCTTTCGAGATATATGGACAAA
167399 TTACCTATGTCTTTCGAGATATATGGACAAA
1 TTACCTATGTCTTTCGAGATATATGGACAAA
****
167430 TTACCTATGTCTTTCGAGATATATGGATGGT
1 TTACCTATGTCTTTCGAGATATATGGACAAA
* * *
167461 TTACCTATGTCCTTAG-GACATATGGAC-AA
1 TTACCTATGTCTTTCGAGATATATGGACAAA
167490 TTA-CTATGT
1 TTACCTATGT
167499 TCTTCGGAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.07
29 3 0.03
30 9 0.10
31 69 0.79
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (31 bp):
TTACCTATGTCTTTCGAGATATATGGACAAA
Found at i:167516 original size:59 final size:62
Alignment explanation
Indices: 167368--167516 Score: 166
Period size: 62 Copynumber: 2.5 Consensus size: 62
167358 GAGTTGAGGG
* ** * * *
167368 TTACCTATGTCTTTCGAGACATATGTA-CATATTACCTATGTCTTTCGAGATATATGGACAAA
1 TTACCTATGTCTTTCGAGACATATGGATGGT-TTACCTATGTCCTTAGAGACATATGGACAAA
*
167430 TTACCTATGTCTTTCGAGATATATGGATGGTTTACCTATGTCCTTAG-GACATATGGAC-AA
1 TTACCTATGTCTTTCGAGACATATGGATGGTTTACCTATGTCCTTAGAGACATATGGACAAA
167490 TTA-CTATGT-TCTTCG-GAACATATGGAT
1 TTACCTATGTCT-TTCGAG-ACATATGGAT
167517 AGTGGTCATT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 2 0.03
59 19 0.25
60 5 0.07
61 10 0.13
62 39 0.51
63 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (62 bp):
TTACCTATGTCTTTCGAGACATATGGATGGTTTACCTATGTCCTTAGAGACATATGGACAAA
Found at i:176770 original size:23 final size:21
Alignment explanation
Indices: 176716--176777 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
176706 TTTTGGTGCA
176716 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
176736 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
176757 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
176778 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:183537 original size:13 final size:14
Alignment explanation
Indices: 183519--183550 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
183509 CATATCTATG
183519 CAAAGGA-GGGATT
1 CAAAGGAGGGGATT
183532 CAAAGGAGGGGATT
1 CAAAGGAGGGGATT
183546 CAAAG
1 CAAAG
183551 AAGGATCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.41, C:0.09, G:0.38, T:0.12
Consensus pattern (14 bp):
CAAAGGAGGGGATT
Found at i:186603 original size:22 final size:22
Alignment explanation
Indices: 186575--186653 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
186565 GAGGGTTTAT
*
186575 AGTGGTCCTTCGGGATATATCC
1 AGTGGTCCTTCGGGACATATCC
*
186597 AGTGGTCTTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
186619 AGTGGTCCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACATATCC
186638 A-TGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
186654 AATATTCACT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.26
19 1 0.02
22 36 0.72
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:188784 original size:40 final size:40
Alignment explanation
Indices: 188725--188808 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
188715 CCATTAGATT
188725 TAAG-AATGGGTTTTAACGAGGCTTTGATCTCTGCTACTA
1 TAAGTAATGGGTTTTAACGAGGCTTTGATCTCTGCTACTA
*
188764 TAAGTAATGGTTTTTAACGAGGCTTTGATCTCTGCTACTA
1 TAAGTAATGGGTTTTAACGAGGCTTTGATCTCTGCTACTA
188804 TAAGT
1 TAAGT
188809 TTTCCCAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (40 bp):
TAAGTAATGGGTTTTAACGAGGCTTTGATCTCTGCTACTA
Found at i:190444 original size:99 final size:100
Alignment explanation
Indices: 190309--190508 Score: 242
Period size: 99 Copynumber: 2.0 Consensus size: 100
190299 TATCGTAATA
* ** * * *
190309 TGATAAATTTTGATATTCTATAAATTCGTTTTATTATAAAGTATTTTATGAGACCTCGTTTT-AA
1 TGATAAA-TTTGATATTCTATAAATTCATTCGATTATAAAATATTTT-TGAGACATCATTTTAAA
* * *
190373 ATGTAGCACACGACCTCTAAATCTATTGGGACGAACC
64 ATGTAGCACACAACCTCCAAATCTATTGGGACAAACC
* * *
190410 TGATAAA-TTGATATTTTATAATTTCATTCGATTATAAAATATTTTTGAGATATCATTTTAAAAT
1 TGATAAATTTGATATTCTATAAATTCATTCGATTATAAAATATTTTTGAGACATCATTTTAAAAT
* *
190474 GTAGCACATAACCTCCAAATTTATTGGGACAAACC
66 GTAGCACACAACCTCCAAATCTATTGGGACAAACC
190509 AGATCTTTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
98 11 0.13
99 66 0.79
101 7 0.08
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (100 bp):
TGATAAATTTGATATTCTATAAATTCATTCGATTATAAAATATTTTTGAGACATCATTTTAAAAT
GTAGCACACAACCTCCAAATCTATTGGGACAAACC
Found at i:191616 original size:65 final size:65
Alignment explanation
Indices: 191423--191619 Score: 309
Period size: 61 Copynumber: 3.1 Consensus size: 65
191413 ACACCCCATT
191423 TCGAATGCATTTTATGCACCGATGCACAG-CCATGCATCGATGCACTCTGGATTTTATTGAAACA
1 TCGAATGCATTTTATGCACCGATGCACAGACCATGCATCGATGCACTCTGGATTTTATTGAAACA
191487 TCGAATGCATTTTATGCACCGATG--C--ACCATGCATCGATGCACTCTGGATTTTATTGAAACA
1 TCGAATGCATTTTATGCACCGATGCACAGACCATGCATCGATGCACTCTGGATTTTATTGAAACA
* *
191548 TCGAATGCATTTTATGCACCGATGCACAGACCATACATCGATGCACTCCTCG-TTTGT-TTGAAA
1 TCGAATGCATTTTATGCACCGATGCACAGACCATGCATCGATGCACT-CTGGATTT-TATTGAAA
191611 CA
64 CA
191613 TCGAATG
1 TCGAATG
191620 TAATTAGTGT
Statistics
Matches: 124, Mismatches: 2, Indels: 13
0.89 0.01 0.09
Matches are distributed among these distances:
61 59 0.48
62 1 0.01
63 1 0.01
64 24 0.19
65 35 0.28
66 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (65 bp):
TCGAATGCATTTTATGCACCGATGCACAGACCATGCATCGATGCACTCTGGATTTTATTGAAACA
Found at i:199701 original size:28 final size:28
Alignment explanation
Indices: 199657--199715 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
199647 AACGGGATAG
*
199657 AATATAGTAAGGGGGAGTAATTTTACAA
1 AATATAGTAAGGAGGAGTAATTTTACAA
199685 AATATAGTAAGGAGGAGTAATTTTACAA
1 AATATAGTAAGGAGGAGTAATTTTACAA
199713 AAT
1 AAT
199716 CAAAATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (28 bp):
AATATAGTAAGGAGGAGTAATTTTACAA
Found at i:200211 original size:65 final size:64
Alignment explanation
Indices: 200088--200220 Score: 189
Period size: 65 Copynumber: 2.1 Consensus size: 64
200078 TCCCATTTCG
* * *
200088 AATGCATTTTATGCGCCGATGCACAGCCATACATCGATGCACTCTGGATTTTATTGAAACATCA
1 AATGCATTTTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
200152 AATGCATTTTATGCACCGATGCACAAACCATACATCGATGCACTCCT-GACTTGT-TTGAAACAT
1 AATGCATTTTATGCACCGATGCAC-AACCATACATCGATGCACT-CTGGA-TTGTATTGAAACAT
*
200215 CG
63 CA
200217 AATG
1 AATG
200221 TAATTAGTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
64 23 0.37
65 34 0.55
66 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AATGCATTTTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
Found at i:200235 original size:65 final size:64
Alignment explanation
Indices: 200088--200240 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 64
200078 TCCCATTTCG
* * * *
200088 AATGCATTTTATGCGCCGATGCACAGCCATACATCGATGCACTCTGGATTTTATTGAAACATCA
1 AATGCATATTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
*
200152 AATGCATTTTATGCACCGATGCACAAACCATACATCGATGCACTCCT-GACTTGT-TTGAAACAT
1 AATGCATATTATGCACCGATGCAC-AACCATACATCGATGCACT-CTGGA-TTGTATTGAAACAT
*
200215 CG
63 CA
* *
200217 AATGTA-ATTAGTGTACCGATGCAC
1 AATGCATATTA-TGCACCGATGCAC
200241 GAAGTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
64 26 0.33
65 47 0.60
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AATGCATATTATGCACCGATGCACAACCATACATCGATGCACTCTGGATTGTATTGAAACATCA
Found at i:202094 original size:16 final size:16
Alignment explanation
Indices: 202069--202104 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
202059 AGCTTAAAAT
*
202069 ATATATTTAATATATA
1 ATATAGTTAATATATA
*
202085 ATATAGTTAATATTTA
1 ATATAGTTAATATATA
202101 ATAT
1 ATAT
202105 TTTTAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATATAGTTAATATATA
Found at i:234631 original size:60 final size:59
Alignment explanation
Indices: 234558--234674 Score: 180
Period size: 60 Copynumber: 2.0 Consensus size: 59
234548 GACATAATAA
* * *
234558 TTAGTCGGGTGACCATTTTGTAACTTTTAATAGTTGGTGGACTCAACAAAGCAACACCCT
1 TTAGTCGGATGACCATTTTGTAACTTTTAATAGTCGATGGACTCAA-AAAGCAACACCCT
* *
234618 TTAGTCGGATGACCATTTTGTAACTTTTAATAGTCGATGGACTTAAAAAGCATCACC
1 TTAGTCGGATGACCATTTTGTAACTTTTAATAGTCGATGGACTCAAAAAGCAACACC
234675 TTATAGTTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
59 10 0.19
60 42 0.81
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (59 bp):
TTAGTCGGATGACCATTTTGTAACTTTTAATAGTCGATGGACTCAAAAAGCAACACCCT
Found at i:234703 original size:59 final size:60
Alignment explanation
Indices: 234568--234703 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
234558 TTAGTCGGGT
* * * *
234568 GACCATTTTGTAACTTTTAATAGTTGGTGGACTCAACAAAGCAACACCCTTTAGTCGGAT
1 GACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACCCTTTAGTAGGAG
* *
234628 GACCATTTTGTAACTTTTAATAGTCGATGGACTTAA-AAAGCATCA-CCTTATAGTTAGG-G
1 GACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACCCTT-TAG-TAGGAG
234687 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
234704 ACCATAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
58 4 0.06
59 24 0.36
60 39 0.58
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACCCTTTAGTAGGAG
Found at i:236051 original size:18 final size:18
Alignment explanation
Indices: 235999--236052 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
235989 ATTGCCATCA
* *
235999 AATTAAAATATATAATTT
1 AATTAAATTATTTAATTT
*
236017 AATTAAATTATTAAATTT
1 AATTAAATTATTTAATTT
*
236035 -ATTTAATTATCTTAATTT
1 AATTAAATTAT-TTAATTT
236053 TTTCATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 9 0.30
18 21 0.70
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAAATTATTTAATTT
Found at i:240955 original size:2 final size:2
Alignment explanation
Indices: 240948--241004 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
240938 CAGGCGCCGT
240948 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
240990 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
241005 GAGTATAGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:241579 original size:64 final size:64
Alignment explanation
Indices: 241436--241558 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
241426 TTTTAAAGGG
* *
241436 ATGCACCGATGCACTCGGGTTTTAATGAAAACATCGAATGCATTTTATGCATCGATGCACACACC
1 ATGCACCGATGCACTCGGGTTTT-ATCAAAACATCGAATGCAATTTATGCATCGATGCACACACC
* * * *
241501 ATGTATCGATGCACTTGGGCTTTT-TCAAAACATTGAATGCAATTTATGCATCGATGCA
1 ATGCACCGATGCACTCGGG-TTTTATCAAAACATCGAATGCAATTTATGCATCGATGCA
241559 TGCTTAGTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 31 0.61
65 16 0.31
66 4 0.08
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCACCGATGCACTCGGGTTTTATCAAAACATCGAATGCAATTTATGCATCGATGCACACACC
Found at i:245874 original size:64 final size:64
Alignment explanation
Indices: 245724--245883 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
245714 TTGTTGAAGG
* *
245724 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTAATGAACATCAAATGCCATTGA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACTCA-TTAAAATAATAAACATCAAATGCCATTGA
* * *
245789 TGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAAT-ATAAACATCGAATGCCTTTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCA-CT-CATTAAAATAATAAACATCAAATGCCATTG
245852 A
64 A
*
245853 TGCA-CTGATGCATAAGTAGTGCATCGATGCA
1 TGCATC-GATGCATAAGGAGTGCATCGATGCA
245884 TACCTTCATT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 1 0.01
64 45 0.52
65 37 0.43
66 2 0.02
67 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTAAAATAATAAACATCAAATGCCATTGA
Found at i:246434 original size:22 final size:22
Alignment explanation
Indices: 246390--246491 Score: 152
Period size: 22 Copynumber: 4.7 Consensus size: 22
246380 GGGTATATTA
246390 GTCCTTCGGGACGTAT-CAGTG
1 GTCCTTCGGGACGTATCCAGTG
** *
246411 GTCCTTTAGGACATATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
246433 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
246455 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
**
246477 GTGTTTCGGGACGTA
1 GTCCTTCGGGACGTA
246492 GTGGTCCTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
21 13 0.18
22 59 0.82
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:246472 original size:44 final size:43
Alignment explanation
Indices: 246390--246510 Score: 151
Period size: 44 Copynumber: 2.9 Consensus size: 43
246380 GGGTATATTA
*
246390 GTCCTTCGGGACGTATCAGTGGTCCTTTAGGACATATCCAGTG
1 GTCCTTCGGGACGTATCAGTGGTCCTTCAGGACATATCCAGTG
* *
246433 GTCCTTCGGGACGTATCCAGTGGTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTAT-CAGTGGTCCTTCAGGACATATCCAGTG
**
246477 GTGTTTCGGGACG--T-AGTGGTCCTTC-GAGACATAT
1 GTCCTTCGGGACGTATCAGTGGTCCTTCAG-GACATAT
246511 ATAGTAGTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
39 1 0.01
40 17 0.24
42 1 0.01
43 16 0.23
44 35 0.50
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.30
Consensus pattern (43 bp):
GTCCTTCGGGACGTATCAGTGGTCCTTCAGGACATATCCAGTG
Found at i:246532 original size:18 final size:18
Alignment explanation
Indices: 246509--246563 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
246499 TTCGAGACAT
* *
246509 ATATAGTAGTTCTTCGGG
1 ATATAGAAGTCCTTCGGG
246527 ATATAGAAGTCCTTCGGG
1 ATATAGAAGTCCTTCGGG
*
246545 ATATAGCAGTCCTTCGGG
1 ATATAGAAGTCCTTCGGG
246563 A
1 A
246564 CGAATACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (18 bp):
ATATAGAAGTCCTTCGGG
Found at i:252870 original size:64 final size:64
Alignment explanation
Indices: 252716--252875 Score: 216
Period size: 64 Copynumber: 2.5 Consensus size: 64
252706 TTGTTGAAGG
* *
252716 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTAATGAACATCGAATGCCATTAA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACTCA-TTAAAATAATAAACATCGAATGCCATTAA
* *
252781 TGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAAT-ATAAACATCGAATGCCTTTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCA-CT-CATTAAAATAATAAACATCGAATGCCATTA
252844 A
64 A
* * *
252845 TGCACCGATGCATAAGTAGTACATCGATGCA
1 TGCATCGATGCATAAGGAGTGCATCGATGCA
252876 TACCTTCATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 46 0.53
65 37 0.43
66 2 0.02
67 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTAAAATAATAAACATCGAATGCCATTAA
Found at i:253408 original size:22 final size:22
Alignment explanation
Indices: 253383--253463 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
253373 GGGTATATTA
253383 GTCATTCGGGACGTATCCAGTG
1 GTCATTCGGGACGTATCCAGTG
*
253405 GTCATTCGGGACATATCCAGTG
1 GTCATTCGGGACGTATCCAGTG
* *
253427 GTCCTTCGTGACGTATCCAGTG
1 GTCATTCGGGACGTATCCAGTG
* *
253449 GTCCTTCAGGACGTA
1 GTCATTCGGGACGTA
253464 GTGCTCCTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (22 bp):
GTCATTCGGGACGTATCCAGTG
Found at i:253493 original size:22 final size:22
Alignment explanation
Indices: 253387--253503 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
253377 ATATTAGTCA
* * *
253387 TTCGGGACGTATCCAGTGGTCA
1 TTCGAGACATATCCAGTGGTCC
*
253409 TTCGGGACATATCCAGTGGTCC
1 TTCGAGACATATCCAGTGGTCC
* *
253431 TTCGTGACGTATCCAGTGGTCC
1 TTCGAGACATATCCAGTGGTCC
* *
253453 TTC-AGGAC--GT--AGTGCTCC
1 TTCGA-GACATATCCAGTGGTCC
*
253471 TTCGAGACATATACAGTGGTCC
1 TTCGAGACATATCCAGTGGTCC
*
253493 TTCGGGACATA
1 TTCGAGACATA
253504 GCAGTCCTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.16
19 1 0.01
20 2 0.03
22 63 0.80
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (22 bp):
TTCGAGACATATCCAGTGGTCC
Found at i:253512 original size:40 final size:40
Alignment explanation
Indices: 253382--253519 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
253372 AGGGTATATT
* * * *
253382 AGTCATTCGGGACGTATCCAGTGGTCATTCGGGACATATCC
1 AGTCCTTCGAGACGTATCCAGTGGTCCTTCGGGACATA-GC
* * *
253423 AGTGGTCCTTCGTGACGTATCCAGTGGTCCTTCAGGACGTAG-
1 A---GTCCTTCGAGACGTATCCAGTGGTCCTTCGGGACATAGC
* * *
253465 TGCTCCTTCGAGACATATACAGTGGTCCTTCGGGACATAGC
1 AG-TCCTTCGAGACGTATCCAGTGGTCCTTCGGGACATAGC
*
253506 AGTCCTTCGGGACG
1 AGTCCTTCGAGACG
253520 AATACTGAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 42 0.55
41 2 0.03
44 32 0.42
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (40 bp):
AGTCCTTCGAGACGTATCCAGTGGTCCTTCGGGACATAGC
Found at i:256636 original size:23 final size:22
Alignment explanation
Indices: 256564--256645 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 22
256554 GCACTTAACA
256564 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* *
256588 GTGCATCGATACA-CCATGAA-
1 GTGCATCGATGCACCCTTGAAT
*
256608 GCTGCACCGATGCACGCCTTGAAT
1 G-TGCATCGATGCAC-CCTTGAAT
256632 GTGCATCGATGCAC
1 GTGCATCGATGCAC
256646 ACTGCCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 2 0.04
23 18 0.38
24 13 0.27
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:259346 original size:20 final size:20
Alignment explanation
Indices: 259317--259354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
259307 TTTCAAAGGG
259317 ATGCACCGATGCACCAATCT
1 ATGCACCGATGCACCAATCT
*
259337 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
259355 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCT
Found at i:259511 original size:64 final size:64
Alignment explanation
Indices: 259365--259523 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 64
259355 GAATAAATTG
* * * * ** *
259365 AACATCGAATGCAATTAATGCACCGATGCACTCTTCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGGTTTT-ATGAA
* ** *
259430 AACATCGAATGCATTTTATTCATCGATGCACACACCATACATCGATGCACTTGGGCTTTT-TTAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGG-TTTTATGAA
259494 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTTATGCATCGATGCA
259524 TGCTTAGTGC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
64 32 0.40
65 45 0.56
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATACATCGATGCACTCAGGTTTTATGAA
Found at i:262136 original size:40 final size:40
Alignment explanation
Indices: 262074--262178 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
262064 GTGAAAAGTT
* **
262074 AGGGACCATATTGCAAATGTACTAATGACAGTTTAATGGAG
1 AGGG-CCATATTGCAAACGTACTAATGACAGTGCAATGGAG
*
262115 GGGGCCATATTGCAAACGTACTAATGACAGTGCAATGGAG
1 AGGGCCATATTGCAAACGTACTAATGACAGTGCAATGGAG
* *
262155 AGGGACATATTGCAAACGGACTAA
1 AGGGCCATATTGCAAACGTACTAA
262179 ATGTTTGAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 54 0.95
41 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (40 bp):
AGGGCCATATTGCAAACGTACTAATGACAGTGCAATGGAG
Found at i:262275 original size:2 final size:2
Alignment explanation
Indices: 262268--262317 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
262258 ATACTTTACC
262268 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
262310 AT AT AT AT
1 AT AT AT AT
262318 CACTCTATGT
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:262528 original size:15 final size:15
Alignment explanation
Indices: 262492--262530 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
262482 TAATTGTAAC
262492 TAAATTTTAAAATAT
1 TAAATTTTAAAATAT
**
262507 TTTATTTTAAAATAT
1 TAAATTTTAAAATAT
262522 TAAATTTTA
1 TAAATTTTA
262531 GATTTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTTTAAAATAT
Found at i:263942 original size:2 final size:2
Alignment explanation
Indices: 263935--263961 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
263925 TGAATTTTGT
263935 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 T
263962 GACACCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:265444 original size:24 final size:24
Alignment explanation
Indices: 265417--265489 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
265407 GTAAACGGAG
*
265417 ATATTAGAAATCAAAACAGAATTC
1 ATATAAGAAATCAAAACAGAATTC
* * * *
265441 ATATCAGATATCAGAACAGAATCC
1 ATATAAGAAATCAAAACAGAATTC
* *
265465 AGATAAGAAATCATAACAGAATTC
1 ATATAAGAAATCAAAACAGAATTC
265489 A
1 A
265490 GGTAATGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (24 bp):
ATATAAGAAATCAAAACAGAATTC
Found at i:270508 original size:24 final size:24
Alignment explanation
Indices: 270481--270552 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
270471 AAACGGAGAT
270481 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
270505 ATCAGATATCACAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
270529 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
270553 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:270510 original size:12 final size:12
Alignment explanation
Indices: 270483--270552 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
270473 ACGGAGATAT
* *
270483 CAGAAATCAAAA
1 CAGAATTCAGAA
*
270495 CAGAATTCAGAT
1 CAGAATTCAGAA
*
270507 CAG-ATATCACAA
1 CAGAAT-TCAGAA
* *
270519 CAGAATCCAGAT
1 CAGAATTCAGAA
*
270531 CAGAAATCAGAA
1 CAGAATTCAGAA
270543 CAGAATTCAG
1 CAGAATTCAG
270553 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:270563 original size:48 final size:47
Alignment explanation
Indices: 270481--270589 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
270471 AAACGGAGAT
* *
270481 ATCAGAAATCAAAACAGAATTCAGATCAGATATCACAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCACAACAGAATCCA
* * * *
270528 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAATAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCACAACAGAATCCA
270576 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
270590 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCACAACAGAATCCA
Found at i:270587 original size:24 final size:25
Alignment explanation
Indices: 270481--270589 Score: 102
Period size: 24 Copynumber: 4.5 Consensus size: 25
270471 AAACGGAGAT
*
270481 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
270505 ATCAGATATCACAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
270529 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * *
270553 GTAATG-TATCAGAATAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
270578 -TCAGAAATCAGA
1 ATCAGAAATCAGA
270590 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.04
24 62 0.89
25 5 0.07
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:279234 original size:226 final size:226
Alignment explanation
Indices: 278861--279273 Score: 553
Period size: 226 Copynumber: 1.8 Consensus size: 226
278851 GGGGCTTTGG
* * *
278861 AAATCCAACGATGACATAATCGGTTAATTATTGGAAACATTACCAAGCATAATAACATATTAGGT
1 AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAACATAATAACATATTAGGT
** * * * ** * *
278926 AGTCCTTATATAACGTAAATATGTAGCACCTTTTTAAGCTGATAGGGTTTTGGAAATTCGACAAT
66 AGTCCTTATATAACGTAAATAAATAACACATTTTAAAGCTGATAGGGCCTTAGAAATCCGACAAT
* * * * *
278991 AACAAATTATGTTAATTACTTAATTTGTTATTAGTATTATCAATATATTAGGTAACGCCTAAAAT
131 AAAAAAATATGTTAATTACTTAATTTATTATTAGTATCATCAATATATTAGGCAACGCCTAAAAT
279056 GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
196 GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
* * * *
279087 AAATCCGACGATAACATACTCGGTTAATTACTGGAAACATTATCAAACATACTAACATATTAGGT
1 AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAACATAATAACATATTAGGT
* * * *
279152 AG-CGCTTATGTAACGT-AATAAATAACACATTATTAAATCTGATGGGGCCTTAGAAATCCGACG
66 AGTC-CTTATATAACGTAAATAAATAACACATT-TTAAAGCTGATAGGGCCTTAGAAATCCGACA
279215 ATAAAAAAATA-GTTTAATTACTTAATTTATTATTAGTATCATCAATATATTAGGCAACG
129 ATAAAAAAATATG-TTAATTACTTAATTTATTATTAGTATCATCAATATATTAGGCAACG
279274 TACTCTATTG
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
225 13 0.08
226 146 0.92
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (226 bp):
AAATCCAACGATAACATAATCGGTTAATTACTGGAAACATTACCAAACATAATAACATATTAGGT
AGTCCTTATATAACGTAAATAAATAACACATTTTAAAGCTGATAGGGCCTTAGAAATCCGACAAT
AAAAAAATATGTTAATTACTTAATTTATTATTAGTATCATCAATATATTAGGCAACGCCTAAAAT
GTTACCAAAGTTTAAGCTGATAGAGCCTTAA
Found at i:288341 original size:20 final size:20
Alignment explanation
Indices: 288316--288399 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
288306 TTTTGGTGCA
*
288316 GAGGGAATCGATCCCCCCCT
1 GAGGGAACCGATCCCCCCCT
* *
288336 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCCT
*
288356 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGA-TCCCCCC-CT
* *
288380 G-GGGAATCGATACCCCCCT
1 GAGGGAACCGATCCCCCCCT
288399 G
1 G
288400 GGGTTCTGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.04
20 24 0.47
21 9 0.18
22 9 0.18
23 6 0.12
24 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCCT
Done.