Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004473.1 Hibiscus syriacus cultivar Beakdansim tig00009861_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: 75836
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1002 original size:21 final size:21
Alignment explanation
Indices: 976--1015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
966 ATTAGACATA
*
976 ATTGAA-TTGAGAGTCTTGAGG
1 ATTGAAGTTG-GAATCTTGAGG
997 ATTGAAGTTGGAATCTTGA
1 ATTGAAGTTGGAATCTTGA
1016 ACATTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGAAGTTGGAATCTTGAGG
Found at i:6023 original size:12 final size:12
Alignment explanation
Indices: 6008--6047 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5998 CGTATGTATA
*
6008 TATGTGTATCTG
1 TATGCGTATCTG
*
6020 TATGCGTATTTG
1 TATGCGTATCTG
*
6032 TATGCGTATGTG
1 TATGCGTATCTG
6044 TATG
1 TATG
6048 AGTTGCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.47
Consensus pattern (12 bp):
TATGCGTATCTG
Found at i:10806 original size:14 final size:13
Alignment explanation
Indices: 10787--10830 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 13
10777 GATATAGTAT
10787 TAAATAAGTAAAAA
1 TAAATAA-TAAAAA
10801 TAAATAAT-AAAA
1 TAAATAATAAAAA
10813 TAAATACATATAAAA
1 TAAATA-ATA-AAAA
10828 TAA
1 TAA
10831 TAGGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.37
13 3 0.11
14 7 0.26
15 7 0.26
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:10814 original size:12 final size:14
Alignment explanation
Indices: 10787--10840 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
10777 GATATAGTAT
10787 TAAATAAGTAAAAA
1 TAAATAAGTAAAAA
10801 TAAATAA-T-AAAA
1 TAAATAAGTAAAAA
10813 TAAATACA-TATAAAA
1 TAAATA-AGTA-AAAA
*
10828 T-AATAGGTAAAAA
1 TAAATAAGTAAAAA
10841 CAAAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 10 0.29
13 7 0.20
14 13 0.37
15 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (14 bp):
TAAATAAGTAAAAA
Found at i:11115 original size:23 final size:23
Alignment explanation
Indices: 11089--11134 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11079 TATAAAATAA
**
11089 TAAAAACAAACCAAGAAAAAAAT
1 TAAAAACAAAAAAAGAAAAAAAT
* *
11112 TAAATATAAAAAAAGAAAAAAAT
1 TAAAAACAAAAAAAGAAAAAAAT
11135 AATATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (23 bp):
TAAAAACAAAAAAAGAAAAAAAT
Found at i:13125 original size:85 final size:84
Alignment explanation
Indices: 12902--14297 Score: 1775
Period size: 85 Copynumber: 16.4 Consensus size: 84
12892 CTCGACAGTT
**** * * * * ** *
12902 TTTGTTGACAGATAGTTTTTCTCGACTTAAGCTATGATGTAAATTGGATATGTATTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATT-GATATGCCTTTGAGCTGAG
*
12967 TGTAATCGAACTCGAATGTC
65 TGTAATCGAACTCGAAGGTC
* * *
12987 TTTTGTTGACGGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATATGCATTTGAGCTGA
1 -TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA-TTGATATGCCTTTGAGCTGA
*
13052 ATGTAATCGAACTCGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* * * * * * *
13073 TTGGTTAACAGATAACTCTTCTCTCCTTTAGTTATGCTGTAAATTGAATATGCCTTTGAACTAAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTG-ATATGCCTTTGAGCTGAG
*
13138 TGTAATCGAACTCGAAGGTTT
65 TGTAATCGAACTCGAAGG-TC
* * * * *
13159 TTTGTTGACAGATAGCCCTTCTCGCCTTGAATTATGCTGTAAATTTATGTGCCTTTGAGCTGAAT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
*
13224 GTAATCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
13243 TTGGTTGACAGATAACCCTTATCGCCTTGAGTTATGCTGTAAATTGGATATGTCTTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATT-GATATGCCTTTGAGCTGAG
13308 TGTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * *
13328 TTTGTTGACAGATAATCCTTCTCGCCTTGAGCTATGATGTAAATTTGATGTGCCTTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA-TTGATATGCCTTTGAGCTGAG
13393 TGTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
13413 TTGGTTGACAGATAACCCTTCTCTCATTGAGTTATACTGTAAATTTGGTATGCCTTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA-TTGATATGCCTTTGAGCTGAG
*
13478 TGTAATCAAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * *
13498 TTGGTTGACAGATAACCCTTCTTGCCTTGAGTTATGTTGTAATTTGATATGCCTTTGAGCTGAGT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
*
13563 GTAATTGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
13582 TTGGTTGACAGATAACCATTCTCGCCTTGAGTTATACTATAAATCGATATGCCTTTGAGCTGAGT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
13647 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
13666 CTTGTTGACAGATAACCTTTCTCGCCTTGAGTTATGTTGTAAATTGGATATTCCATTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATT-GATATGCCTTTGAGCTGAG
13731 TGTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
** * * *
13751 TTTTGTTGACAGATAGTCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTTA
1 -TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA-TTGATATGCCTTTGAGCTGA
*
13816 GTGTAATCGAACTTGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* ** * * * * *
13837 TTTGTCGACAGATTGCCCTTCTCTCCTTGAGCTATGTTATAAATTTGATGTGCCTTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA-TTGATATGCCTTTGAGCTGAG
13902 TGTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* *
13922 TTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
13987 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* ** * ** *
14006 TTTGTCGACAGATAGTCCTTCTCGCCTTGAGCTATGCTGCGAATTGGATATACCTTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATT-GATATGCCTTTGAGCTGAG
*
14071 TGTAATCGAACTCGAAGGTTT
65 TGTAATCGAACTCGAAGG-TC
* *
14092 TTTGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTATATGCCTTTGAGCTGAGT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
14157 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * ** * *** * *
14176 TTTATCGACAGATAGTCCTTCTCGCCTTGAGCTATGCTACGAATCAGATATGCCTTTGAGTTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT-TGATATGCCTTTGAGCTGAG
*
14241 TATAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* *
14261 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 -TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
14298 TTGCAAATAG
Statistics
Matches: 1145, Mismatches: 153, Indels: 24
0.87 0.12 0.02
Matches are distributed among these distances:
84 310 0.27
85 577 0.50
86 254 0.22
87 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (84 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGATATGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:15620 original size:95 final size:95
Alignment explanation
Indices: 15437--15687 Score: 369
Period size: 95 Copynumber: 2.6 Consensus size: 95
15427 TCCATAAGTT
* * *
15437 GGGGCGTTTAACTAATTGCTCTAGAGGGACAACTCAA-TATCATTGTATAGATATTATAATCACC
1 GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGT-T--TTAT-TATATATTATAATCACC
15501 TTTATCAGGCTAACTGAATATTATCCATAAACCC
62 TTTATCAGGCTAACTGAATATTATCCATAAACCC
15535 GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTATATATTATAATCACCTTTA
1 GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTATATATTATAATCACCTTTA
* * *
15600 TCAGGCTAGCTGAATCTTATCCATAAAGCC
66 TCAGGCTAACTGAATATTATCCATAAACCC
* * *
15630 GGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATAAT
1 GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTATATAT-TATAAT
15688 ATTATAATCT
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
95 95 0.67
96 9 0.06
98 37 0.26
99 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTATATATTATAATCACCTTTA
TCAGGCTAACTGAATATTATCCATAAACCC
Found at i:19583 original size:14 final size:14
Alignment explanation
Indices: 19564--19652 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
19554 TAAATTACGG
19564 AAATAAATAAAATA
1 AAATAAATAAAATA
*
19578 AAATAAAGAAAA-A
1 AAATAAATAAAATA
* *
19591 AAAGAAATAAAAAGA
1 AAATAAAT-AAAATA
* *
19606 AAAAACAATAAATAAA
1 AAATA-AATAAA-ATA
* *
19622 AAACAAAAAAAATA
1 AAATAAATAAAATA
19636 ATAATAAA-AAAATA
1 A-AATAAATAAAATA
19650 AAA
1 AAA
19653 ATATATAACT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
13 9 0.15
14 25 0.41
15 18 0.30
16 9 0.15
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.12
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:19630 original size:22 final size:20
Alignment explanation
Indices: 19568--19660 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
19558 TTACGGAAAT
19568 AAATAAAATAAAATAAAGAAAAA
1 AAAT-AAATAAAA-AAA-AAAAA
* *
19591 AAAGAAATAAAAAGAAAAAA
1 AAATAAATAAAAAAAAAAAA
* *
19611 CAATAAATAAAAAACAAAAA
1 AAATAAATAAAAAAAAAAAA
*
19631 AAAT-AATAATAAAAAAATAA
1 AAATAAATAA-AAAAAAAAAA
*
19651 AAATATATAA
1 AAATAAATAA
19661 CTATTAGGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.09
20 36 0.62
21 6 0.10
22 8 0.14
23 3 0.05
ACGTcount: A:0.81, C:0.02, G:0.03, T:0.14
Consensus pattern (20 bp):
AAATAAATAAAAAAAAAAAA
Found at i:19653 original size:23 final size:21
Alignment explanation
Indices: 19572--19647 Score: 57
Period size: 22 Copynumber: 3.6 Consensus size: 21
19562 GGAAATAAAT
* *
19572 AAAATAAAATAAAGAAAAAAA
1 AAAATAAAAAAAACAAAAAAA
* *
19593 AGAAATAAAAAGAA-AAAACAA
1 A-AAATAAAAAAAACAAAAAAA
*
19614 TAAATAAAAAACAA-AAAAAATA
1 AAAATAAAAAA-AACAAAAAA-A
*
19636 ATAATAAAAAAA
1 AAAATAAAAAAA
19648 TAAAAATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.20
21 15 0.34
22 20 0.45
ACGTcount: A:0.83, C:0.03, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAATAAAAAAAACAAAAAAA
Found at i:20099 original size:4 final size:4
Alignment explanation
Indices: 20090--20269 Score: 67
Period size: 4 Copynumber: 44.5 Consensus size: 4
20080 AATTAGAAAA
20090 AAAT AAAT AAA- AAAT AAGAT AAAT AAAT AAAATT AAAT -AA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT -AAA-T AAAT AAAT AAAT AAAT
* * ** *
20138 -AAC AAA- AAAT AAAT AATAC AAAT AAAT -AAT AAA- AACC AAAC AAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
20183 AAAA AAAT AGAACTT AAAT AAAAT AAAA AGAAG AAAA AAAT ATATAT AAAT
1 AAAT AAAT A-AA--T AAAT -AAAT AAAT A-AAT AAAT AAAT A-A-AT AAAT
* *
20234 --AT AAAT -AA- AAAT AAAA AAAT ACATAT ATAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AA
20270 TGTTATGTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 48
0.68 0.08 0.24
Matches are distributed among these distances:
2 2 0.01
3 21 0.15
4 77 0.57
5 25 0.18
6 9 0.07
7 2 0.01
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:20101 original size:10 final size:10
Alignment explanation
Indices: 20088--20252 Score: 89
Period size: 10 Copynumber: 16.4 Consensus size: 10
20078 AAAATTAGAA
20088 AAAAATAAAT
1 AAAAATAAAT
20098 AAAAAATAAGAT
1 -AAAAATAA-AT
20110 --AAATAAAT
1 AAAAATAAAT
*
20118 AAAATTAAAT
1 AAAAATAAAT
20128 AAAAATAAAT
1 AAAAATAAAT
20138 AACAAA-AAAT
1 AA-AAATAAAT
20148 AAATAATACAAAT
1 AAA-AAT--AAAT
20161 AAATAATAAA-
1 AAA-AATAAAT
*
20171 AACCAAACAAAT
1 AA--AAATAAAT
20183 -AAAA-AAAT
1 AAAAATAAAT
**
20191 AGAACTTAAAT
1 A-AAAATAAAT
20202 -AAAATAAA-
1 AAAAATAAAT
* *
20210 AAGAAGAAA-
1 AAAAATAAAT
*
20219 AAAATATATAT
1 AAAA-ATAAAT
*
20230 AAATATAAAT
1 AAAAATAAAT
20240 AAAAATAAA-
1 AAAAATAAAT
20249 AAAA
1 AAAA
20253 TACATATATA
Statistics
Matches: 122, Mismatches: 15, Indels: 36
0.71 0.09 0.21
Matches are distributed among these distances:
8 6 0.05
9 29 0.24
10 46 0.38
11 27 0.22
12 3 0.02
13 11 0.09
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:20117 original size:24 final size:24
Alignment explanation
Indices: 20076--20172 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 24
20066 TAAACGTATA
*
20076 AAAAAATTAGA-AAA-AAATAAAT
1 AAAAAATAAGATAAATAAATAAAT
20098 AAAAAATAAGATAAATAAATAAAATT
1 AAAAAATAAGATAAATAAAT-AAA-T
*
20124 AAATAA-AA-ATAAATAACA-AAA-
1 AAAAAATAAGATAAATAA-ATAAAT
* * *
20145 AATAAATAATACAAATAAAT-AAT
1 AAAAAATAAGATAAATAAATAAAT
20168 AAAAA
1 AAAAA
20173 CCAAACAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
21 4 0.07
22 15 0.25
23 17 0.28
24 12 0.20
25 6 0.10
26 6 0.10
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAAATAAGATAAATAAATAAAT
Found at i:20182 original size:18 final size:17
Alignment explanation
Indices: 20156--20189 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20146 ATAAATAATA
*
20156 CAAATAAATAATAAAAAC
1 CAAACAAATAA-AAAAAC
20174 CAAACAAATAAAAAAA
1 CAAACAAATAAAAAAA
20190 TAGAACTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAACAAATAAAAAAAC
Found at i:20232 original size:28 final size:30
Alignment explanation
Indices: 20200--20269 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
20190 TAGAACTTAA
*
20200 ATAAAATAAA-AAGAAGAAAAAAAT-ATAT
1 ATAAAATAAATAAAAAGAAAAAAATAATAT
*
20228 ATAAATATAAATAAAAATAAAAAAATACATAT
1 ATAAA-ATAAATAAAAAGAAAAAAATA-ATAT
20260 ATATAAATAA
1 ATA-AAATAA
20270 TGTTATGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 5 0.14
30 12 0.34
32 11 0.31
33 2 0.06
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (30 bp):
ATAAAATAAATAAAAAGAAAAAAATAATAT
Found at i:20238 original size:34 final size:34
Alignment explanation
Indices: 20197--20268 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
20187 AAATAGAACT
20197 TAAATA-AAATAAAAAGAAGAAAAA-A-ATATATA
1 TAAATATAAATAAAAAGAA-AAAAATACATATATA
*
20229 TAAATATAAATAAAAATAAAAAAATACATATATA
1 TAAATATAAATAAAAAGAAAAAAATACATATATA
20263 TAAATA
1 TAAATA
20269 ATGTTATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 11 0.31
33 12 0.33
34 13 0.36
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (34 bp):
TAAATATAAATAAAAAGAAAAAAATACATATATA
Found at i:22198 original size:2 final size:2
Alignment explanation
Indices: 22191--22232 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
22181 GTTTTAATTA
*
22191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
22233 TAGTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23232 original size:21 final size:21
Alignment explanation
Indices: 23206--23247 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23196 CCAGAATGGG
*
23206 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
23227 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
23248 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:23377 original size:19 final size:19
Alignment explanation
Indices: 23353--23419 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
23343 GAGCCTCGGG
*
23353 TTACTGTTCAAATAGTGAT
1 TTACTGTTCAAATAGTAAT
23372 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAT
*
23391 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAT
*
23410 TTACTATTCA
1 TTACTGTTCA
23420 TAAAAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:23531 original size:30 final size:31
Alignment explanation
Indices: 23484--23574 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
23474 AAATTTTGAA
23484 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
23513 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
23544 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
23575 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:24937 original size:44 final size:43
Alignment explanation
Indices: 24722--25064 Score: 187
Period size: 43 Copynumber: 8.0 Consensus size: 43
24712 GAAGTCCCTA
* *
24722 TTTTTATCTTTATAATT-AGG-TCTTTATATTTTTTGAATCTTA-T
1 TTTTTA-CTTTATAATTGAGGCTC-CTA-ATTTTTTCAATCTTACT
* * * *
24765 ATTTTACTTTTATAATTGATG-TCCTAATATTATACAATCTTAC-
1 TTTTTAC-TTTATAATTGAGGCTCCTAAT-TTTTTCAATCTTACT
* * *
24808 TTTTTATTTTTATAATTGAAG-TCTCT-ATTTTTTCAATC--CCT
1 TTTTTA-CTTTATAATTGAGGCTC-CTAATTTTTTCAATCTTACT
* * *
24849 TTTTGTACCTTTATAATTGA-GCCCCTAATTTTAT-AATCTCACT
1 TTTT-TA-CTTTATAATTGAGGCTCCTAATTTTTTCAATCTTACT
**
24892 TTTTTACTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTTAC-
1 TTTTTACTTTATAATTGAGGCTCCTAA-TTTTTTCAATCTTACT
* * **
24935 TTTCTACATTT-TCAATTGAGGCACCTAAGTTTTTT-AATCCAACT
1 TTTTTAC-TTTAT-AATTGAGGCTCCTAA-TTTTTTCAATCTTACT
** *
24979 TTTTTAACTTTATAATTGATAC-CCTTAAGTTTTTT-AATCTCACT
1 TTTTT-ACTTTATAATTGAGGCTCC-TAA-TTTTTTCAATCTTACT
* * * * *
25023 TTCTAACTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCTTA
1 TTTTTACTTTATAATTGAGGCTCCTAA-TTTTTTCAATCTTA
25065 ATTATACCTT
Statistics
Matches: 237, Mismatches: 40, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
40 1 0.00
41 23 0.10
42 38 0.16
43 96 0.41
44 76 0.32
45 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (43 bp):
TTTTTACTTTATAATTGAGGCTCCTAATTTTTTCAATCTTACT
Found at i:25024 original size:87 final size:87
Alignment explanation
Indices: 24857--25056 Score: 257
Period size: 87 Copynumber: 2.3 Consensus size: 87
24847 CTTTTTGTAC
* * * **
24857 CTTTATAATTGA-GCCCCTAA-TTTTATAATCTCACTTTTTTACTTTATAATTGAGGCTTTTAAG
1 CTTTCTAATTGAGGCCCCTAAGTTTTTTAATCTCACTTTTTTACTTTATAATTGAGACCCTTAAG
*
24920 TTTTTTCAATCTTACTTTCTACA
66 TTTTTTCAATCTCACTTTCTA-A
* * *
24943 TTTTC-AATTGAGGCACCTAAGTTTTTTAATC-CAACTTTTTTAACTTTATAATTGATACCCTTA
1 CTTTCTAATTGAGGCCCCTAAGTTTTTTAATCTC-ACTTTTTT-ACTTTATAATTGAGACCCTTA
25006 AGTTTTTT-AATCTCACTTTCTAA
64 AGTTTTTTCAATCTCACTTTCTAA
25029 CTTTCTAATTGAGGCCCCTAAGTTTTTT
1 CTTTCTAATTGAGGCCCCTAAGTTTTTT
25057 CGATCTTAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
85 6 0.06
86 16 0.16
87 51 0.52
88 25 0.26
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (87 bp):
CTTTCTAATTGAGGCCCCTAAGTTTTTTAATCTCACTTTTTTACTTTATAATTGAGACCCTTAAG
TTTTTTCAATCTCACTTTCTAA
Found at i:25031 original size:43 final size:43
Alignment explanation
Indices: 24857--25056 Score: 203
Period size: 44 Copynumber: 4.7 Consensus size: 43
24847 CTTTTTGTAC
* * *
24857 CTTTATAATTGA-GCCCCTAA-TTTTATAATCTCACTTTTTTA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACTTTCTAA
*** *
24898 CTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTTACTTTCT-A
1 CTTTATAATTGAGGCCCCTAAGTTTTTT-AATCTCACTTTCTAA
* *
24941 CATTT-TCAATTGAGGCACCTAAGTTTTTTAATC-CAACTTTTTTAA
1 C-TTTAT-AATTGAGGCCCCTAAGTTTTTTAATCTC-AC-TTTCTAA
** *
24986 CTTTATAATTGATACCCTTAAGTTTTTTAATCTCACTTTCTAA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACTTTCTAA
*
25029 CTTTCTAATTGAGGCCCCTAAGTTTTTT
1 CTTTATAATTGAGGCCCCTAAGTTTTTT
25057 CGATCTTAAT
Statistics
Matches: 129, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
41 12 0.09
42 5 0.04
43 44 0.34
44 64 0.50
45 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (43 bp):
CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACTTTCTAA
Found at i:25081 original size:43 final size:43
Alignment explanation
Indices: 24857--25084 Score: 171
Period size: 44 Copynumber: 5.3 Consensus size: 43
24847 CTTTTTGTAC
* * * *
24857 CTTTATAATTGA-GCCCCTAA-TTTTATAATCTCACTTTTTTA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACATTCTAA
*** * *
24898 CTTTATAATTGAGGCTTTTAAGTTTTTTCAATCTTACTTTCT-A
1 CTTTATAATTGAGGCCCCTAAGTTTTTT-AATCTCACATTCTAA
* * *
24941 CATTT-TCAATTGAGGCACCTAAGTTTTTTAATC-CAACTTTTTTAA
1 C-TTTAT-AATTGAGGCCCCTAAGTTTTTTAATCTC-AC-ATTCTAA
** * *
24986 CTTTATAATTGATACCCTTAAGTTTTTTAATCTCACTTTCTAA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACATTCTAA
* * * * *
25029 CTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCTTA-ATTATAC
1 CTTTATAATTGAGGCCCCTAAGTTTTTT-AATCTCACATTCTAA
25072 CTTTATAATTGAG
1 CTTTATAATTGAG
25085 ACCTCTTGTA
Statistics
Matches: 150, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
41 12 0.08
42 5 0.03
43 60 0.40
44 69 0.46
45 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (43 bp):
CTTTATAATTGAGGCCCCTAAGTTTTTTAATCTCACATTCTAA
Found at i:26928 original size:21 final size:21
Alignment explanation
Indices: 26832--26929 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
26822 AGTCGAGGGT
* * * *
26832 TATACGTGGTCCTTCGGGATA
1 TATATGTGGTCCTTTGGAACA
**
26853 TATATGTAATCCTTTGGAACA
1 TATATGTGGTCCTTTGGAACA
** *
26874 TATATACGGTTCTTTGAGACACA
1 TATATGTGGTCCTTTG-GA-ACA
*
26897 TAT-T-TGGTCCTTTGGAATA
1 TATATGTGGTCCTTTGGAACA
*
26916 TATATGTGATCCTT
1 TATATGTGGTCCTT
26930 AAGGAGTGGT
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
19 5 0.09
20 3 0.05
21 41 0.71
22 3 0.05
23 6 0.10
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (21 bp):
TATATGTGGTCCTTTGGAACA
Found at i:26989 original size:23 final size:21
Alignment explanation
Indices: 26935--26994 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
26925 TCCTTAAGGA
*
26935 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAC
*
26956 GTGGTCCTTCGGGACATTTCTAC
1 GTGGTCCTTCGGGACA--TATAC
*
26979 GTTGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
26995 AATTCTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 16 0.47
23 18 0.53
ACGTcount: A:0.15, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAC
Found at i:38982 original size:31 final size:31
Alignment explanation
Indices: 38947--39067 Score: 118
Period size: 31 Copynumber: 3.9 Consensus size: 31
38937 TTTTAAAATC
*
38947 ATAAAATGATTATTAAATTTATCAAATAATT
1 ATAAAATGATCATTAAATTTATCAAATAATT
* * *
38978 ATAAAATAATCATTAAATTTATTAAATTATT
1 ATAAAATGATCATTAAATTTATCAAATAATT
** * **
39009 GCAAAAT-AGTCATTAAATTTATCAAGTTGTT
1 ATAAAATGA-TCATTAAATTTATCAAATAATT
* * *
39040 ATAAAATGATCGTTAAACTCATCAAATA
1 ATAAAATGATCATTAAATTTATCAAATA
39068 TTTTACAAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
30 1 0.01
31 70 0.97
32 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (31 bp):
ATAAAATGATCATTAAATTTATCAAATAATT
Found at i:40845 original size:119 final size:119
Alignment explanation
Indices: 40634--40871 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
40624 TTTTTTGAAA
40634 CCATACCTAACGTTTAGTTTTTGTTTCATCTTAATACTTTGTCGTTAAAAACTTAACGGACGGAC
1 CCATACCTAACGTTTAGTTTTTGTTTCATCTTAATACTTTGTCGTTAAAAACTTAACGGACGGAC
40699 TAACAAGACATAGCTCCTGTGGACAAATGACCAATCCAAATAATGGATCGCGAG
66 TAACAAGACATAGCTCCTGTGGACAAATGACCAATCCAAATAATGGATCGCGAG
40753 CCATACCTAACGTTTAGTTTTTGTTTCATCTTAATACTTTGTCGTTAAAAACTTAACGGACGGAC
1 CCATACCTAACGTTTAGTTTTTGTTTCATCTTAATACTTTGTCGTTAAAAACTTAACGGACGGAC
40818 TAACAAGACATAGCTCCTGTGGACAAATGACCAATCCAAATAATGGATCGCGAG
66 TAACAAGACATAGCTCCTGTGGACAAATGACCAATCCAAATAATGGATCGCGAG
40872 AGAACGACGA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (119 bp):
CCATACCTAACGTTTAGTTTTTGTTTCATCTTAATACTTTGTCGTTAAAAACTTAACGGACGGAC
TAACAAGACATAGCTCCTGTGGACAAATGACCAATCCAAATAATGGATCGCGAG
Found at i:58124 original size:18 final size:17
Alignment explanation
Indices: 58084--58128 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
58074 GAAAATATTC
58084 TTTTTACTTTATTCATT
1 TTTTTACTTTATTCATT
* *
58101 TCTTTTATTTTATTTCCTT
1 T-TTTTACTTTA-TTCATT
58120 TTTTTACTT
1 TTTTTACTT
58129 CTCTCTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTACTTTATTCATT
Found at i:60322 original size:54 final size:53
Alignment explanation
Indices: 60213--60440 Score: 323
Period size: 54 Copynumber: 4.3 Consensus size: 53
60203 TAGTGCCAAT
*
60213 ACTGTGTG-ACAACTTAAGAAGTTCATAATAAGTTTATGAATTTCGTATTGGC
1 ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTTCATATTGGC
* *
60265 ACTGTGTGTACAACTTAAGAAGTTTATATTAAGTTTATGAATTTCCATATTGGC
1 ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTT-CATATTGGC
*
60319 ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTTTAGTATTGGC
1 ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTTCA-TATTGGC
* * * * *
60373 ACTATGTGTTCAACCTAAGAAATTCATAATAAGTTTATAAATTTCTATATTGGC
1 ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTTC-ATATTGGC
* *
60427 ACTATGTGTGCAAC
1 ACTGTGTGTACAAC
60441 CCCACGTAAT
Statistics
Matches: 159, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
52 8 0.05
53 34 0.21
54 116 0.73
55 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (53 bp):
ACTGTGTGTACAACTTAAGAAGTTCATAATAAGTTTATGAATTTCATATTGGC
Found at i:60484 original size:55 final size:53
Alignment explanation
Indices: 60236--60485 Score: 212
Period size: 54 Copynumber: 4.6 Consensus size: 53
60226 TTAAGAAGTT
* * * ** * *
60236 CATAATAAGTTTATGAATTTCGTATTGGCACTGTGTGTACAACTTAAGAAGTT
1 CATAATAAGTTTATGAATTTTGTATTGGCACTATGTGTGCAACCCAAGAAATC
* * ** * * ** * *
60289 TATATTAAGTTTATGAATTTCCATATTGGCACTGTGTGTACAACTTAAGAAGTT
1 CATAATAAGTTTATGAATTT-TGTATTGGCACTATGTGTGCAACCCAAGAAATC
* * *
60343 CATAATAAGTTTATGAATTTTAGTATTGGCACTATGTGTTCAACCTAAGAAATT
1 CATAATAAGTTTATGAATTTT-GTATTGGCACTATGTGTGCAACCCAAGAAATC
* * * *
60397 CATAATAAGTTTATAAATTTCTATATTGGCACTATGTGTGCAACCCCACGTAATC
1 CATAATAAGTTTATGAATTT-TGTATTGGCACTATGTGTGCAA-CCCAAGAAATC
* * *
60452 CATAATGAGTTTGTGAATTATTGTATCGGCACTA
1 CATAATAAGTTTATGAATT-TTGTATTGGCACTA
60486 CATGTCTAAA
Statistics
Matches: 169, Mismatches: 23, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
53 18 0.11
54 115 0.68
55 35 0.21
56 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (53 bp):
CATAATAAGTTTATGAATTTTGTATTGGCACTATGTGTGCAACCCAAGAAATC
Found at i:67801 original size:82 final size:83
Alignment explanation
Indices: 67608--67906 Score: 247
Period size: 82 Copynumber: 3.6 Consensus size: 83
67598 TGCCGACAAG
* * * * *
67608 GAAAGACACGTTCTGGGGGATACATTTTTCAATTATTATTAAGAGAATCT-CTATATTATAATAG
1 GAAAGACACGTTATGGGGAAAACATTTTTCCATTATTATTAAGAGAATCTATTA-ATTATAATAG
67672 TGA-TCATCCCATCTGAAAT
65 TGATTCATCCCATC-GAAAT
*** ** * * *
67691 GAAATG-TGTGTTACAGGG-AAGCTTTTTTCCATTATTATTAAGAGAATATATTAATTATAATAG
1 GAAA-GACACGTTATGGGGAAAACATTTTTCCATTATTATTAAGAGAATCTATTAATTATAATAG
67754 TGATTCATCCCATCGAAAT
65 TGATTCATCCCATCGAAAT
* ** * * *
67773 GAAAGACACGTT-TGGGGAAAATCA-TTTTCCATTATTATTCAGAGAATCTATGCCA-TGTCAGA
1 GAAAGACACGTTATGGGGAAAA-CATTTTTCCATTATTATTAAGAGAATCTAT-TAATTATAATA
*
67835 GTG-TTCCATCCCATCCGAAAC
64 GTGATT-CATCCCAT-CGAAAT
* * *
67856 GAAAGGCACGTT-TCGGGGAAAACATTTTTTTCATTATTATTCAGAGAATCT
1 GAAAGACACGTTAT-GGGGAAAACA-TTTTTCCATTATTATTAAGAGAATCT
67907 CTACCATGTC
Statistics
Matches: 175, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
81 6 0.03
82 93 0.53
83 43 0.25
84 9 0.05
85 24 0.14
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (83 bp):
GAAAGACACGTTATGGGGAAAACATTTTTCCATTATTATTAAGAGAATCTATTAATTATAATAGT
GATTCATCCCATCGAAAT
Found at i:67914 original size:85 final size:85
Alignment explanation
Indices: 67759--68159 Score: 405
Period size: 85 Copynumber: 4.8 Consensus size: 85
67749 AATAGTGATT
*
67759 CATCCCAT-CGAAATGAAAGACACGTTT-GGGGAAAATCA--TTTTCCATTATTATTCAGAGAAT
1 CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAA-CATGTTTTCCATTATTATTCAGAGAAT
* *
67820 CTATGCCATGTCAGAGTGTTC
65 CTCTACCATGTCAGAGTGTTC
* * *
67841 CATCCCATCCGAAACGAAAGGCACGTTTCGGGGAAAACATTTTTTTCATTATTATTCAGAGAATC
1 CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAACATGTTTTCCATTATTATTCAGAGAATC
67906 TCTACCATGTCAGAGTGTTC
66 TCTACCATGTCAGAGTGTTC
* * * * * * * * *
67926 CATTCCATCTGAAACGAAAGGCGCATTTC-GGGTAAA-GTGTTTTGCATTATTATTTAGAGAATC
1 CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAACATGTTTTCCATTATTATTCAGAGAATC
**
67989 TCTGTCA--TCAGAGTGTTC
66 TCTACCATGTCAGAGTGTTC
* * * * * * *
68007 CATCCCATCTGAAATGAAAGGCGCATTTCGGGGAAAGCTTTTTTTTCATTATTATTCAGAGAATC
1 CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAACATGTTTTCCATTATTATTCAGAGAATC
* *
68072 TCTACCATATCATAGTG-TC
66 TCTACCATGTCAGAGTGTTC
* * * * * *
68091 TTATCCCATCCAAAATGAAAGGTATGGTT--GGG-AAA-GTGTTTTCCATTATTATTCAGAGAAT
1 -CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAACATGTTTTCCATTATTATTCAGAGAAT
68152 CTCTACCA
65 CTCTACCA
68160 CTTGACATAA
Statistics
Matches: 271, Mismatches: 39, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
81 69 0.25
82 15 0.06
83 78 0.29
84 16 0.06
85 93 0.34
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (85 bp):
CATCCCATCCGAAATGAAAGGCACGTTTCGGGGAAAACATGTTTTCCATTATTATTCAGAGAATC
TCTACCATGTCAGAGTGTTC
Found at i:68276 original size:16 final size:17
Alignment explanation
Indices: 68236--68278 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
68226 AGTAACTTTG
68236 AACTCTCAAACATTCAA
1 AACTCTCAAACATTCAA
* *
68253 AACT-TCAAACCTT-GA
1 AACTCTCAAACATTCAA
68268 AACTCTCAAAC
1 AACTCTCAAAC
68279 TACGAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.23
Consensus pattern (17 bp):
AACTCTCAAACATTCAA
Found at i:73895 original size:18 final size:19
Alignment explanation
Indices: 73861--73920 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
73851 ATGAATTATT
*
73861 AGAATCGAAATACATGCTTC
1 AGAATC-AAATATATGCTTC
73881 AGAA-CAAATATATGCTTC
1 AGAATCAAATATATGCTTC
* *
73899 -GAATTAAATATATGCTTT
1 AGAATCAAATATATGCTTC
73917 AGAA
1 AGAA
73921 ATATTATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 3 0.09
18 24 0.69
19 4 0.11
20 4 0.11
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
AGAATCAAATATATGCTTC
Done.