Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006249.1 Hibiscus syriacus cultivar Beakdansim tig00014894_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: 69479
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:17471 original size:24 final size:24
Alignment explanation
Indices: 17439--17488 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
17429 ATGTCCCACG
17439 CTCAACCAATTGTGTA-GCACATAC
1 CTCAACCAATTGTGTAGGC-CATAC
17463 CTCAACCAATTGTGTAGGCCATAC
1 CTCAACCAATTGTGTAGGCCATAC
17487 CT
1 CT
17489 TGGAGACGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (24 bp):
CTCAACCAATTGTGTAGGCCATAC
Found at i:21800 original size:43 final size:43
Alignment explanation
Indices: 21739--21827 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
21729 ACTAGTACAC
*
21739 TTTAAAGACTTAGGATCTAACTTGGACTTATTAGGAGCAATGT
1 TTTAAAGACTTAGGATCTAACTTGGACTTATTAAGAGCAATGT
21782 TTTAAAGACTTAGGATCTAACTTGGACTTATTAAGAGCAATGT
1 TTTAAAGACTTAGGATCTAACTTGGACTTATTAAGAGCAATGT
21825 TTT
1 TTT
21828 GGATAAAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (43 bp):
TTTAAAGACTTAGGATCTAACTTGGACTTATTAAGAGCAATGT
Found at i:27689 original size:25 final size:24
Alignment explanation
Indices: 27661--27731 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
27651 ACTCAAAAAA
* *
27661 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
27686 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
27710 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATTGAAGC
27732 GAAAGAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 36 0.84
25 7 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:27705 original size:24 final size:24
Alignment explanation
Indices: 27676--27731 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
27666 TAGAAGTTCG
27676 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
27700 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
27724 ATTGAAGC
1 ATTGAAGC
27732 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:28781 original size:80 final size:79
Alignment explanation
Indices: 28678--28885 Score: 274
Period size: 80 Copynumber: 2.6 Consensus size: 79
28668 AAAATAAAAT
* * *
28678 TTAGGTACCAAAAT-AGAACAAAAATAATAATTTAGATACTAAATATTTAATTTATCCTAGCTTT
1 TTAGGTACCAAAATGA-AACAAAAATAATAATTTA-ATACTAAATATGTAATTCATCCTAGATTT
28742 TTTTACATGGTAATTA
64 TTTTACATGGTAATTA
* *
28758 TTAGGTACCGAAATGAAATAAAAATAATAATTTAAATACTAAATATGTAATTCATCCTAGATTTT
1 TTAGGTACCAAAATGAAACAAAAATAATAATTT-AATACTAAATATGTAATTCATCCTAGATTTT
* *
28823 TTTGCTTGGTAATTA
65 TTTACATGGTAATTA
** * * *
28838 TTAAATACCAAAATGGAACAAAAATACTAAATTAATACTAAATATGTA
1 TTAGGTACCAAAATGAAACAAAAATAATAATTTAATACTAAATATGTA
28886 GTTTTTCACC
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 15 0.13
80 95 0.85
81 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (79 bp):
TTAGGTACCAAAATGAAACAAAAATAATAATTTAATACTAAATATGTAATTCATCCTAGATTTTT
TTACATGGTAATTA
Found at i:29131 original size:11 final size:10
Alignment explanation
Indices: 29117--29202 Score: 50
Period size: 11 Copynumber: 8.2 Consensus size: 10
29107 CATTAATTAA
29117 AATTTAATTCT
1 AATTTAATT-T
*
29128 AATTTTAATAT
1 AA-TTTAATTT
29139 AATTATAATTT
1 AATT-TAATTT
*
29150 AATTATATTTT
1 AATT-TAATTT
* * *
29161 TATTAAATAT
1 AATTTAATTT
*
29171 AATAATTAATGT
1 AAT--TTAATTT
29183 AATTT-ATTT
1 AATTTAATTT
29192 AATTT-ATTT
1 AATTTAATTT
29201 AA
1 AA
29203 AATTAAGATT
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 14 0.23
10 9 0.15
11 23 0.38
12 14 0.23
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
AATTTAATTT
Found at i:29153 original size:5 final size:5
Alignment explanation
Indices: 29117--29202 Score: 50
Period size: 5 Copynumber: 16.4 Consensus size: 5
29107 CATTAATTAA
* * * *
29117 AATTT AATTCT AATTTT AATAT AATTAT AATTT AATTAT ATTTT TATTA
1 AATTT AATT-T AA-TTT AATTT AATT-T AATTT AATT-T AATTT AATTT
* *
29166 AATAT AATAATT AATGT AATTT -ATTT AATTT -ATTT AA
1 AATTT AAT--TT AATTT AATTT AATTT AATTT AATTT AA
29203 AATTAAGATT
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
4 8 0.13
5 32 0.52
6 15 0.25
7 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:29156 original size:17 final size:18
Alignment explanation
Indices: 29117--29156 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
29107 CATTAATTAA
*
29117 AATT-TAATTCTAATTTT
1 AATTATAATTATAATTTT
29134 AA-TATAATTATAA-TTT
1 AATTATAATTATAATTTT
29150 AATTATA
1 AATTATA
29157 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATAATTATAATTTT
Found at i:30090 original size:21 final size:21
Alignment explanation
Indices: 30064--30180 Score: 141
Period size: 21 Copynumber: 5.6 Consensus size: 21
30054 GTTTCCAGAT
* *
30064 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
30085 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
30106 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
30127 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
30147 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
30168 TCGCAATGCGAAC
1 TCGCAATGCGAAC
30181 AATGCGAATA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.19
21 68 0.81
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:30229 original size:21 final size:21
Alignment explanation
Indices: 30203--30256 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
30193 TAAATTGCAA
30203 TGCGATAGTCGAAGTTCACAT
1 TGCGATAGTCGAAGTTCACAT
* *
30224 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCGAAGTTCACAT
*
30245 TACGATAGTCGA
1 TGCGATAGTCGA
30257 CTATCGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCACAT
Found at i:30986 original size:5 final size:5
Alignment explanation
Indices: 30972--31005 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
30962 CCGCCGCCGC
30972 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
31006 TGGGTCGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.00, C:0.41, G:0.21, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:31040 original size:12 final size:11
Alignment explanation
Indices: 31008--31043 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
30998 TCTCGTCTTG
31008 GGTCGGGTCG-
1 GGTCGGGTCGT
31018 GGTCGGGTCGT
1 GGTCGGGTCGT
31029 GGTCGTGGTCGT
1 GGTCG-GGTCGT
31041 GGT
1 GGT
31044 AATACGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:31093 original size:19 final size:19
Alignment explanation
Indices: 31069--31106 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31059 CACGTCCGCG
*
31069 CGAACTTGGATTATCGCAA
1 CGAACTTGGACTATCGCAA
31088 CGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
31107 TGCGAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:35165 original size:17 final size:17
Alignment explanation
Indices: 35140--35182 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
35130 TTCACCTCAT
* *
35140 TCTTTTTCTTGTTATTC
1 TCTTATTCTTCTTATTC
*
35157 TCTTATTCTTCTTCTTC
1 TCTTATTCTTCTTATTC
35174 -CTTATTCTT
1 TCTTATTCTT
35183 TTGGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (17 bp):
TCTTATTCTTCTTATTC
Found at i:35693 original size:20 final size:21
Alignment explanation
Indices: 35670--35726 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
35660 CAAACCTAGT
35670 GGGGGTATCGATTCCCT-AAA
1 GGGGGTATCGATTCCCTGAAA
* * *
35690 GGGGGAATCGGTTCCCCTGTAA
1 GGGGGTATCGATT-CCCTGAAA
35712 GGGGGTATCGATTCC
1 GGGGGTATCGATTCC
35727 TCCTGCACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.37
21 6 0.20
22 13 0.43
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTGAAA
Found at i:35716 original size:22 final size:23
Alignment explanation
Indices: 35688--35731 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
35678 CGATTCCCTA
*
35688 AAGGGGGAATCGGTTCC-CCTGT
1 AAGGGGGAATCGATTCCTCCTGT
*
35710 AAGGGGGTATCGATTCCTCCTG
1 AAGGGGGAATCGATTCCTCCTG
35732 CACTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.18, C:0.23, G:0.34, T:0.25
Consensus pattern (23 bp):
AAGGGGGAATCGATTCCTCCTGT
Found at i:43445 original size:18 final size:18
Alignment explanation
Indices: 43419--43453 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43409 TATCATTATT
*
43419 AAATTAAAAAATAATTAG
1 AAATAAAAAAATAATTAG
43437 AAATAAAAAAATAATTA
1 AAATAAAAAAATAATTA
43454 AATAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATAAAAAAATAATTAG
Found at i:43456 original size:16 final size:16
Alignment explanation
Indices: 43416--43458 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
43406 TTGTATCATT
*
43416 ATTAAATTAAAAAATA
1 ATTAAATAAAAAAATA
43432 ATTAGAAATAAAAAAATA
1 ATT--AAATAAAAAAATA
43450 ATTAAATAA
1 ATTAAATAA
43459 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
18 15 0.62
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATTAAATAAAAAAATA
Found at i:43696 original size:20 final size:19
Alignment explanation
Indices: 43665--43702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
43655 AATTTAAATT
43665 ATTTAAAATTAAATAGATA
1 ATTTAAAATTAAATAGATA
*
43684 ATTTAATAATTAATTAGAT
1 ATTTAA-AATTAAATAGAT
43703 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTAAAATTAAATAGATA
Found at i:43792 original size:29 final size:30
Alignment explanation
Indices: 43760--43821 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
43750 TTTTATAATT
* *
43760 ATTTCATATAATTTTTAT-AAAATATATGA
1 ATTTCATATAATTTTAATAAAAATATAAGA
43789 ATTTCATATAATTTTAATAAAAATATAAGA
1 ATTTCATATAATTTTAATAAAAATATAAGA
43819 ATT
1 ATT
43822 ATTTAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTTCATATAATTTTAATAAAAATATAAGA
Found at i:47924 original size:78 final size:79
Alignment explanation
Indices: 47770--47925 Score: 235
Period size: 78 Copynumber: 2.0 Consensus size: 79
47760 TTAATATTTT
* * *
47770 TTTAACATTTTCGGTAAAGCTCTACCTAGAACAATATTTTTTATACCGGAAATGTTAATATTGAG
1 TTTAACATTTTCGGTAAAGCTCTACCTAAAACAATATTTTTTATACAGGAAATATTAATATTGAG
47835 CGCTACCTAAAATG
66 CGCTACCTAAAATG
* * *
47849 TTTAACATTTTCGGTAAAG-TGCTACCTAAAACATTA-TTTTTCTACAGGAAATATTAATATTGG
1 TTTAACATTTTCGGTAAAGCT-CTACCTAAAACAATATTTTTTATACAGGAAATATTAATATTGA
47912 GCGCTACCTAAAAT
65 GCGCTACCTAAAAT
47926 ATTATTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
78 38 0.54
79 32 0.46
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTAACATTTTCGGTAAAGCTCTACCTAAAACAATATTTTTTATACAGGAAATATTAATATTGAG
CGCTACCTAAAATG
Found at i:49223 original size:182 final size:182
Alignment explanation
Indices: 48910--49359 Score: 735
Period size: 182 Copynumber: 2.5 Consensus size: 182
48900 ATTTTTTTAC
* * *
48910 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
48975 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTTTTTTCTTTTAAATTTCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTTCAAAAG
* *
49040 TGTCGATACTTATAATAAAGTATCGACACTATCAACATAT-TCGGTAGCTCTT
131 TGTCGATACATATAATAAAGTATCGACACTATCAACATATCT-GGTAGCGCTT
49092 TACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
49157 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAA-TTCTAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTTC-AAAA
49221 GTGTCGATACATATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
130 GTGTCGATACATATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
* ** *
49274 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCAT-TTTTTGACCTGTTTTATTGTTATGGATCG
1 TACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTT-ACCTGTTATATTGTTATGGATCG
*
49338 ATACATTTTTATAAAGTTTCGA
65 ATACATTTTTATAAAGTATCGA
49360 AACTATCAAC
Statistics
Matches: 252, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
181 8 0.03
182 243 0.96
183 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
TACCAGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTTCAAAAG
TGTCGATACATATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
Found at i:49322 original size:20 final size:20
Alignment explanation
Indices: 49275--49323 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
49265 GTAGCGCTTT
49275 ACCTGTTTTGTCATTTATAG
1 ACCTGTTTTGTCATTTATAG
* * *
49295 ACCGGTTTTGTCATTTTTTG
1 ACCTGTTTTGTCATTTATAG
49315 ACCTGTTTT
1 ACCTGTTTT
49324 ATTGTTATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.53
Consensus pattern (20 bp):
ACCTGTTTTGTCATTTATAG
Found at i:52461 original size:199 final size:199
Alignment explanation
Indices: 52114--52545 Score: 677
Period size: 199 Copynumber: 2.2 Consensus size: 199
52104 GGTTATAATT
* * * *
52114 ATTATGTTTTTCGATGTTTTTGGGATCGAAAATTGTTATAAATGTATCGAAACTTTGTTGCGCAC
1 ATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGAAACTTTGTTGCGCAC
52179 TTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTTT
66 TTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTTT
* * *
52244 GTACACATGTTTTCTCAAAAACCGATACATTTAGACCTGTTATATTGTTAATTTACCTATTACAT
131 GAACACATGTTTTCTCAAAAACCGATACATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
52309 TATA
196 TATA
* *
52313 ATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGATACTTT-TTAGGGCA
1 ATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGAAACTTTGTT-GCGCA
* * *
52377 CTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTT
65 CTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTT
* * * * *
52442 TGAACACCTGTTTTCTCAAAACCCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTATA
130 TGAACACATGTTTTCTCAAAAACCGATACATTTAGACCGGTTATATTGCTAATTTACCTATTACA
52507 TTATA
195 TTATA
* *
52512 ATTATGGTTTTTGATGTTTTTGGGATCGACACTT
1 ATTATGATTTTCGATGTTTTTGGGATCGACACTT
52546 TTTAGGGCAC
Statistics
Matches: 213, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
198 2 0.01
199 211 0.99
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
ATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGAAACTTTGTTGCGCAC
TTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTTT
GAACACATGTTTTCTCAAAAACCGATACATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
TATA
Found at i:53157 original size:199 final size:198
Alignment explanation
Indices: 52536--54334 Score: 3100
Period size: 199 Copynumber: 9.1 Consensus size: 198
52526 TGTTTTTGGG
52536 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* * *
52601 TATTTGTGTCGATACTTTTTGTACACCTG-TTTCTCAAAAACCGGCATATTTAGACCGGTTATAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-
*
52665 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGAATCGACACTTGTTACAA
130 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
52730 ATGT
195 ATGT
*
52734 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCAACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
52799 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTC-AAAACCGGTATATTTAGACCGTTTACAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACAT
* * * *
52863 GAATAATTTACCTATTACATTATAATTATAGTTTTTGATGATTTTGGGATCGACACTTGTTACAA
131 G-CTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
52928 ATGT
195 ATGT
*
52932 ATCGACACTTTTTAGGGCACTTGTTTTTTAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* * *
52997 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGATATATTTAGACTGTTTACAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACAT
* *
53062 GAATAATTTACCTATTACATTATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAA
131 G-CTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
53127 ATGT
195 ATGT
*
53131 ATCGACACTTTTTAGGGCATTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* * *
53196 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGGTTATAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-
53261 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
130 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
53326 ATGT
195 ATGT
53330 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* * *
53395 TATTTGTGTCGATACTTTTTGTACACATGTTTTCTCAAAAATCGGTATATTTATACCGTTTACAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACAT
* *
53460 GAATAATTTACCTATTACATTATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAA
131 G-CTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
53525 ATGT
195 ATGT
*
53529 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGAAAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* * * *
53594 TATTTGTGTCGATACTTTTTGTACACATGTTTCCTCAAAAACCGGTATATTTAGACCGATTATAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-
53659 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
130 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
53724 ATGT
195 ATGT
* *
53728 ATCGACACTTTTTAGGGTACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTATTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
* *
53793 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-
53858 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
130 TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
53923 ATGT
195 ATGT
*
53927 ATCGACACTTTTTAGGGGACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
*
53992 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCAGATATAC
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACC-G-TTTAC
*
54057 -TGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCTACACTTGTTACA
129 ATGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
54121 AATGT
194 AATGT
* *
54126 ATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTTTGGACAAAAAGTATCGACACTTGTTC
1 ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
*
54191 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGTTTACAT
66 TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACAT
* * * *
54256 GAATAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTATGGGATCAACACTTGTTATAA
131 G-CTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAA
54321 ATGT
195 ATGT
54325 ATCGACACTT
1 ATCGACACTT
54335 AAGTTTACCT
Statistics
Matches: 1527, Mismatches: 64, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
197 6 0.00
198 283 0.19
199 1231 0.81
200 5 0.00
201 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (198 bp):
ATCGACACTTTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTC
TATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACAT
GCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAA
TGT
Found at i:53435 original size:398 final size:397
Alignment explanation
Indices: 52114--54334 Score: 3594
Period size: 398 Copynumber: 5.6 Consensus size: 397
52104 GGTTATAATT
* * * * * *
52114 ATTATGTTTTTCGATGTTTTTGGGATCGAAAATTGTTATAAATGTATCGAAACTTTGTT-GCGCA
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT-TTAGGGCA
* * * *
52178 CTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTT
65 CTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTT
* * * * *
52243 TGTACACATGTTTTCTCAAAAACCGATACATTTAGACCTGTTATA-TTGTTAATTTACCTATTAC
130 TGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACC-GTT-TACATGATAATTTACCTATTAC
* *
52307 ATTATAATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGATACTTTTTA
193 ATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTA
*
52372 GGGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
258 GGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
* *
52437 CTTTTTGAACACCTGTTTTCTCAAAACCCGGTATATTTAGACCGGTTATATTGCTAATTTACCTA
323 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTA
*
52502 TTATATTATA
388 TTACATTATA
*
52512 ATTATGGTTTTTGATG-TTTT----T-G------G--------G-ATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
52556 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * * *
52621 GTACACCTG-TTTCTCAAAAACCGGCATATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
131 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGATAATTTACCTATTACAT
*
52685 TATAATTATGGTTTTCGATGTTTTTGGAATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
195 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
*
52750 GCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCAACACTTGTTCTATTTGTGTCGATACT
260 GCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
* * *
52815 TTTTGTACACCTGTTTTCTC-AAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACCTAT
325 TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTG-CTAATTTACCTAT
52878 TACATTATA
389 TACATTATA
* * *
52887 ATTATAGTTTTTGATGATTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
*
52952 TTGTTTTTTAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * *
53017 GTACACCTGTTTTCTCAAAAACTGATATATTTAGACTGTTTACATGAATAATTTACCTATTACAT
131 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCTATTACAT
*
53082 TATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
195 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
*
53147 GCATTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
260 GCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
*
53212 TTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGCTAATTTACCTATT
325 TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATT
53277 ACATTATA
390 ACATTATA
53285 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
53350 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * *
53415 GTACACATGTTTTCTCAAAAATCGGTATATTTATACCGTTTACATGAATAATTTACCTATTACAT
131 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCTATTACAT
*
53480 TATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
195 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
*
53545 GCACTTGTTTTTGAAATACATTCTGGAAAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
260 GCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
* * *
53610 TTTTGTACACATGTTTCCTCAAAAACCGGTATATTTAGACCGATTATATTGCTAATTTACCTATT
325 TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATT
53675 ACATTATA
390 ACATTATA
*
53683 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGTAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
*
53748 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTATTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * *
53813 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
131 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGATAATTTACCTATTACAT
53878 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
195 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
*
53943 GGACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
260 GCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
* * *
54008 TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCAGATATACTGCTAATTTACCTATT
325 TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATT
54073 ACATTATA
390 ACATTATA
*
54081 ATTATGGTTTTCGATGTTTTTGGGATCTACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
* *
54146 TTGGTTTTGAAATACATTTTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
*
54211 GTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGTTTACATGAATAATTTACCTATTACAT
131 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATG-ATAATTTACCTATTACAT
* * *
54276 TATAATTATGGTTTTCGATGTTTATGGGATCAACACTTGTTATAAATGTATCGACACTT
195 TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTT
54335 AAGTTTACCT
Statistics
Matches: 1704, Mismatches: 88, Indels: 62
0.92 0.05 0.03
Matches are distributed among these distances:
374 4 0.00
375 61 0.04
376 193 0.11
377 84 0.05
378 1 0.00
380 1 0.00
381 1 0.00
386 1 0.00
387 1 0.00
392 1 0.00
393 1 0.00
395 1 0.00
396 95 0.06
397 197 0.12
398 1058 0.62
399 4 0.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (397 bp):
ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGATAATTTACCTATTACATT
ATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGG
CACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTT
TTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTA
CATTATA
Found at i:53677 original size:597 final size:597
Alignment explanation
Indices: 52114--54334 Score: 3620
Period size: 597 Copynumber: 3.8 Consensus size: 597
52104 GGTTATAATT
* * * * * *
52114 ATTATGTTTTTCGATGTTTTTGGGATCGAAAATTGTTATAAATGTATCGAAACTTTGTT-GCGCA
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT-TTAGGGCA
* * * *
52178 CTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCCATTTGTGTCGATACTGTT
65 CTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTT
* * * * *
52243 TGTACACATGTTTTCTCAAAAACCGATACATTTAGACCTGTTATA-TTGTTAATTTACCTATTAC
130 TGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCAGTT-TACATGATAATTTACCTATTAC
* *
52307 ATTATAATTATGATTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGATACTTTTTA
194 ATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTA
52372 GGGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
259 GGGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
* * * * *
52437 CTTTTTGAACACCTGTTTTCTCAAAACCCGGTATATTTAGACCGGTTATATTG-CTAATTTACCT
324 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACCT
* *
52501 ATTATATTATAATTATGGTTTTTGATG-TTTT----T-G------G--------G-ATCGACACT
388 ATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACT
52545 TTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGT
453 TTTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGT
*
52610 CGATACTTTTTGTACACCTG-TTTCTCAAAAACCGGCATATTTAGACCGGTTATATTGCTAATTT
518 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTT
52674 ACCTATTACATTATA
583 ACCTATTACATTATA
*
52689 ATTATGGTTTTCGATGTTTTTGGAATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
*
52754 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCAACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
*
52819 GTACACCTGTTTTCTC-AAAACCGGTATATTTAGACC-GTTTACATGAATAATTTACCTATTACA
131 GTACACATGTTTTCTCAAAAACCGGTATATTTAGACCAGTTTACATG-ATAATTTACCTATTACA
* * *
52882 TTATAATTATAGTTTTTGATGATTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAG
195 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAG
* *
52947 GGCACTTGTTTTTTAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
260 GGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
* * *
53012 TTTTTGTACACCTGTTTTCTCAAAAACTGATATATTTAGACTGTTTACATGAATAATTTACCTAT
325 TTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
*
53077 TACATTATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
390 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
*
53142 TTAGGGCATTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCG
455 TTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCG
*
53207 ATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGCTAATTTAC
520 ATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTAC
53272 CTATTACATTATA
585 CTATTACATTATA
53285 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
53350 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* *
53415 GTACACATGTTTTCTCAAAAATCGGTATATTTATACC-GTTTACATGAATAATTTACCTATTACA
131 GTACACATGTTTTCTCAAAAACCGGTATATTTAGACCAGTTTACATG-ATAATTTACCTATTACA
*
53479 TTATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAG
195 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAG
* *
53544 GGCACTTGTTTTTGAAATACATTCTGGAAAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
260 GGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
* * * * *
53609 TTTTTGTACACATGTTTCCTCAAAAACCGGTATATTTAGACCGATTATATTG-CTAATTTACCTA
325 TTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACCTA
53673 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTT
389 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTT
* *
53738 TTTAGGGTACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTATTCTATTTGTGTC
454 TTTAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTC
53803 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTA
519 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTA
53868 CCTATTACATTATA
584 CCTATTACATTATA
*
53882 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGGAC
1 ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
53947 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
66 TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
* * *
54012 GTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCAGATATAC-TGCTAATTTACCTATTACA
131 GTACACATGTTTTCTCAAAAACCGGTATATTTAGACCAG-TTTACATGATAATTTACCTATTACA
*
54076 TTATAATTATGGTTTTCGATGTTTTTGGGATCTACACTTGTTACAAATGTATCGACACTTTTTAG
195 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAG
*
54141 GGCACTTGGTTTTGAAATACATTTTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
260 GGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
*
54206 TTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
325 TTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
* * *
54271 TACATTATAATTATGGTTTTCGATGTTTATGGGATCAACACTTGTTATAAATGTATCGACACTT
390 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTT
54335 AAGTTTACCT
Statistics
Matches: 1533, Mismatches: 82, Indels: 40
0.93 0.05 0.02
Matches are distributed among these distances:
572 2 0.00
573 7 0.00
574 235 0.15
575 134 0.09
579 1 0.00
580 1 0.00
586 1 0.00
594 1 0.00
595 93 0.06
596 202 0.13
597 847 0.55
598 5 0.00
599 4 0.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (597 bp):
ATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCAC
TTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACTTTTT
GTACACATGTTTTCTCAAAAACCGGTATATTTAGACCAGTTTACATGATAATTTACCTATTACAT
TATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGG
GCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTATT
ACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTT
TAGGGCACTTGTTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGA
TACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACC
TATTACATTATA
Found at i:54725 original size:18 final size:19
Alignment explanation
Indices: 54677--54726 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
54667 ATTACATTCA
*
54677 TATACAAAATTATAAATCG
1 TATACAAAATTAAAAATCG
*
54696 TATACAAAATTAAAAATCT
1 TATACAAAATTAAAAATCG
54715 TATAC-AAATTAA
1 TATACAAAATTAA
54727 CCATGCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (19 bp):
TATACAAAATTAAAAATCG
Found at i:56231 original size:21 final size:18
Alignment explanation
Indices: 56193--56231 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
56183 TTCTCCTCAT
56193 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
56211 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
56229 TTC
1 TTC
56232 AAAATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:56929 original size:22 final size:23
Alignment explanation
Indices: 56901--56950 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
56891 AACCTGCATT
56901 TATAATAAA-AGT-TATCATTTTA
1 TATAATAAATA-TATATCATTTTA
56923 TATAATAAATATACTATCATTTTA
1 TATAATAAATATA-TATCATTTTA
56947 TATA
1 TATA
56951 GAAAAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 14 0.56
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAATAAATATATATCATTTTA
Found at i:57935 original size:18 final size:18
Alignment explanation
Indices: 57912--57950 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
57902 TACTGTCAAC
57912 ATTTAAAATTTGTAAT-CA
1 ATTTAAAATTT-TAATCCA
57930 ATTTAAAATTTTAATCCA
1 ATTTAAAATTTTAATCCA
57948 ATT
1 ATT
57951 ACCATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:58067 original size:21 final size:21
Alignment explanation
Indices: 58019--58068 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
58009 CTTTGGTTGC
*
58019 TTTCCTCCCATTGACTTCATT
1 TTTCCTTCCATTGACTTCATT
58040 TTTCCTTCCATTGACTTCATT
1 TTTCCTTCCATTGACTTCATT
58061 TTTCCTTC
1 TTTCCTTC
58069 ATATATCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.12, C:0.32, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTCCTTCCATTGACTTCATT
Found at i:58269 original size:19 final size:20
Alignment explanation
Indices: 58222--58270 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
58212 TATTTATATA
58222 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
58241 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
58259 ACCTATAAATAT
1 ACCTATAAATAT
58271 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:59167 original size:182 final size:180
Alignment explanation
Indices: 58653--59296 Score: 864
Period size: 182 Copynumber: 3.5 Consensus size: 180
58643 TACGCGTACT
* *
58653 TATTAAAGTATCGACACTTTCAACATATACGGT-ATCTATTTACCGGTTTTGTCATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAT-T-TTT-CCGGTTTTGTCATTTTGAGACC
* *
58717 GGTTTTATCATATTTTTACCTGTTATATTGTTTTGGATCGATACATTTTCATAAAGTGTCGACAC
63 GGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACAC
* *
58782 TTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTAAGAAAGTGTCGATACTTA
128 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
58835 TATTAAATTATCGACACTTTTAACATATCTGGTAACTTTTT-CGGTTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAA-TTTTTCCGGTTTTGTCA-TTTTGAGACCG
* *
58899 GTTTTATCATATTTTTACCTGTTATATTGGTAAGGATCAATACATTTTCATAAAGTGTCGACACT
64 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACT
*
58964 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTAA
129 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * *
59016 TATTAAATTATTGACACTTTCAATATATCCGATAATGTTTTCCGGTTTTGTCACTTATGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAT-TTTTCCGGTTTTGTCA-TTTTGAGACCG
* * ** *
59081 GTTTTATCATATTTTTACCTGTTATATTGTTGTGGATCAATATATTTTTTTAAAGTATCGACACT
64 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACT
* * * * *
59146 TTATAGGCACTATAGCTTCTTCTCTTTTAAATTCAGAAAGTTTTGATACTTA
129 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
59198 TATTAAATTATCGACACTTTCAATATATCCAGTAGCATTTTACCGG--TTGTCATTTTGGGATCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTA--ATTTTTCCGGTTTTGTCATTTTGAGACCG
* * * *
59261 GTTTTGTCATATTTGTACCTGTAATATTGCTATGGA
64 GTTTTATCATATTTTTACCTGTTATATTGTTATGGA
59297 GCGATCCATT
Statistics
Matches: 410, Mismatches: 45, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
180 51 0.12
181 160 0.39
182 187 0.46
183 9 0.02
184 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (180 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAATTTTTCCGGTTTTGTCATTTTGAGACCGGT
TTTATCATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTCATAAAGTGTCGACACTTT
TTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:59508 original size:2 final size:2
Alignment explanation
Indices: 59501--59533 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59491 TAATCCCTAT
59501 TA 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 TA T
59534 CATTTCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59854 original size:31 final size:31
Alignment explanation
Indices: 59811--59876 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
59801 ATTTAGTCTG
*
59811 TTTGTAATATGGTCCCCGACATAACCGGCCA
1 TTTGCAATATGGTCCCCGACATAACCGGCCA
** *
59842 TTTGCAATATGGTCCCCGATGTAACCGGCCG
1 TTTGCAATATGGTCCCCGACATAACCGGCCA
59873 TTTG
1 TTTG
59877 ACGTCGTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (31 bp):
TTTGCAATATGGTCCCCGACATAACCGGCCA
Found at i:61919 original size:13 final size:13
Alignment explanation
Indices: 61879--61938 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
61869 AAATGAACAT
*
61879 AAACGAACATGAAC
1 AAAC-AACATAAAC
*
61893 GAACGAACATAAAC
1 AAAC-AACATAAAC
61907 AAAC-ACAATAAAC
1 AAACAAC-ATAAAC
* *
61920 GAACAACACAAAC
1 AAACAACATAAAC
61933 AAACAA
1 AAACAA
61939 AAAACTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 2 0.05
13 19 0.50
14 17 0.45
ACGTcount: A:0.63, C:0.23, G:0.08, T:0.05
Consensus pattern (13 bp):
AAACAACATAAAC
Found at i:62205 original size:14 final size:14
Alignment explanation
Indices: 62186--62227 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
62176 CCTCTAATCG
62186 AACATAAATGAACA
1 AACATAAATGAACA
*
62200 AACATAAATGAACG
1 AACATAAATGAACA
*
62214 AACATAAACGAACA
1 AACATAAATGAACA
62228 TATAATCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:62540 original size:30 final size:30
Alignment explanation
Indices: 62504--62560 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
62494 TCGGGGACCA
** *
62504 TATTGCAAATGGACTAAATGTTGGGGGTTG
1 TATTGCAAACAGACTAAATGTTAGGGGTTG
62534 TATTGCAAACAGACTAAATGTTAGGGG
1 TATTGCAAACAGACTAAATGTTAGGGG
62561 ACTGTATTAT
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:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (30 bp):
TATTGCAAACAGACTAAATGTTAGGGGTTG
Done.