Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006500.1 Hibiscus syriacus cultivar Beakdansim tig00015816_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: 60687
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2973 original size:54 final size:54
Alignment explanation
Indices: 2883--3487 Score: 601
Period size: 54 Copynumber: 11.2 Consensus size: 54
2873 GGGAAGGAAA
* ** *
2883 AGAAGATTGTTCGAGTTC-TACTCCCTGAAACAAGAGGGAGATAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* *
2936 AGAAGATCGTTCGAGTTCTTACTCCCTGAAGCAAGAGGTAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
2990 AGAACATCGTTCAAGTT-TCTACTCCCTGAAGCAAGAGGGAGTGAACTCGTAGGC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * *
3044 ATAAGATTATTCGAGTTCCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
3098 AGAAGATTGTTTGAGTTCTTATTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
3152 AGAAGATTGTTTGAGTTCCTACTCCTTGAACCAAGAGGAAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* ** * * * * * *
3206 AGAAGATTGTTCGAGTTCCTACAACCTAAAGAAAGAAGGAGC-AATCCGTTGGT
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* ** * *
3259 AGAATATCATTCGAGTTC-TACTCCCTGAATCAAGAGGGAGCAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * *
3312 AGAAGATTGTTCGAGTTATACACTCCTTGAAGCAAGAGAGAGCGAACCCGTTGAC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * ***
3367 ATAAGATTATTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCGTTCAC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
3422 AGAAGA-TGTTTGAGTTTCATACTCCCTGAAGAAAGAGGGATCGAACCCGCTAGTC
1 AGAAGATTGTTCGAG-TTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGC
*
3477 -GAATATTGTTC
1 AGAAGATTGTTC
3488 AAAGAAGAGG
Statistics
Matches: 451, Mismatches: 92, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
52 17 0.04
53 63 0.14
54 284 0.63
55 87 0.19
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (54 bp):
AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
Found at i:3661 original size:3 final size:3
Alignment explanation
Indices: 3653--3687 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3643 ATATTAAATA
3653 TAT TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
3688 CATAATGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:8784 original size:26 final size:26
Alignment explanation
Indices: 8755--8806 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
8745 CAAGTTCCGA
8755 ATCTCAGAATGTCCGGACTCGGCATT
1 ATCTCAGAATGTCCGGACTCGGCATT
8781 ATCTCAGAATGTCCGGACTCGGCATT
1 ATCTCAGAATGTCCGGACTCGGCATT
8807 CTTGATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (26 bp):
ATCTCAGAATGTCCGGACTCGGCATT
Found at i:12558 original size:31 final size:31
Alignment explanation
Indices: 12520--12592 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
12510 TCAACGTTGT
12520 TTTGTTGAGT-ATTCTGACTATAAGGCGATGC
1 TTTGTTGAGTCATTC-GACTATAAGGCGATGC
* *
12551 TTTGTTGAGTCATTCGACTATAAGGTGTTGC
1 TTTGTTGAGTCATTCGACTATAAGGCGATGC
12582 TTTGTTGAGTC
1 TTTGTTGAGTC
12593 CCCGACTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.42
Consensus pattern (31 bp):
TTTGTTGAGTCATTCGACTATAAGGCGATGC
Found at i:12601 original size:30 final size:31
Alignment explanation
Indices: 12535--12601 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
12525 TGAGTATTCT
**
12535 GACTATAAGGCGATGCTTTGTTGAGTCATTC
1 GACTATAAGGCGATGCTTTGTTGAGTCACCC
* *
12566 GACTATAAGGTGTTGCTTTGTTGAGTC-CCC
1 GACTATAAGGCGATGCTTTGTTGAGTCACCC
12596 GACTAT
1 GACTAT
12602 TAAAAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (31 bp):
GACTATAAGGCGATGCTTTGTTGAGTCACCC
Found at i:15284 original size:18 final size:18
Alignment explanation
Indices: 15261--15318 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
15251 GTGGTGGTGG
15261 TGGTGGTGGAGATGGAGA
1 TGGTGGTGGAGATGGAGA
*
15279 TGGTGGTGGAGATGTAGA
1 TGGTGGTGGAGATGGAGA
*
15297 ---TGATGGAGATGGAGA
1 TGGTGGTGGAGATGGAGA
*
15312 TGTTGGT
1 TGGTGGT
15319 AGTGATGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.39
18 20 0.61
ACGTcount: A:0.22, C:0.00, G:0.50, T:0.28
Consensus pattern (18 bp):
TGGTGGTGGAGATGGAGA
Found at i:15301 original size:21 final size:19
Alignment explanation
Indices: 15261--15314 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
15251 GTGGTGGTGG
15261 TGGTGGTGGAGATG-GAGA
1 TGGTGGTGGAGATGTGAGA
15279 TGGTGGTGGAGATGTAGATGA
1 TGGTGGTGGAGATGT-GA-GA
* *
15300 TGGAGATGGAGATGT
1 TGGTGGTGGAGATGT
15315 TGGTAGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.24, C:0.00, G:0.50, T:0.26
Consensus pattern (19 bp):
TGGTGGTGGAGATGTGAGA
Found at i:15306 original size:33 final size:33
Alignment explanation
Indices: 15267--15454 Score: 262
Period size: 33 Copynumber: 5.9 Consensus size: 33
15257 GTGGTGGTGG
* * *
15267 TGGAGATGGAGATGGTGGTGGAGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
* *
15300 TGGAGATGGAGATGTTGGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
15333 T---G--G-AGATGGTGGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
* *
15360 TGGAGATGAAAATGGTTGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
15393 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
*
15426 TGGAGATGAAGATGGTTGTAGTGATGTAG
1 TGGAGATGAAGATGGTGGTAGTGATGTAG
15455 TAGTTGTGAA
Statistics
Matches: 140, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
27 24 0.17
28 1 0.01
30 2 0.01
32 1 0.01
33 112 0.80
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (33 bp):
TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
Found at i:15360 original size:60 final size:60
Alignment explanation
Indices: 15271--15454 Score: 262
Period size: 60 Copynumber: 3.0 Consensus size: 60
15261 TGGTGGTGGA
* * *
15271 GATGGAGATGGTGGTGGAGATGTAGATGATGGAGATGGAGAT-GTTGGTAGTGATGTAGAT
1 GATGGAGATGGTGGTAGTGATGTAGATGATGGAGATGAAGATGGTT-GTAGTGATGTAGAT
*
15331 GATGGAGATGGTGGTAGTGATGTAGATGATGGAGATGAAAATGGTTGTAGTGATGTAGAT
1 GATGGAGATGGTGGTAGTGATGTAGATGATGGAGATGAAGATGGTTGTAGTGATGTAGAT
15391 GATGGAGATGAAGATGGTGGTAGTGATGTAGATGATGGAGATGAAGATGGTTGTAGTGATGTAG
1 GAT---G--G-AGATGGTGGTAGTGATGTAGATGATGGAGATGAAGATGGTTGTAGTGATGTAG
15455 TAGTTGTGAA
Statistics
Matches: 112, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
60 55 0.49
61 3 0.03
63 1 0.01
65 1 0.01
66 52 0.46
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (60 bp):
GATGGAGATGGTGGTAGTGATGTAGATGATGGAGATGAAGATGGTTGTAGTGATGTAGAT
Found at i:16441 original size:35 final size:36
Alignment explanation
Indices: 16401--16477 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 36
16391 TGAGCATCAG
16401 TAAAAGCATCATATTACCTAAACCCATTAGAGTA-A
1 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
16436 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
1 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
16472 TAAAAG
1 TAAAAG
16478 AAGGGCCCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 34 0.83
36 7 0.17
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (36 bp):
TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
Found at i:16475 original size:18 final size:18
Alignment explanation
Indices: 16419--16475 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
16409 TCATATTACC
16419 TAAACCCATTAGAGTA-A
1 TAAACCCATTAGAGTACA
** * * * *
16436 TAAAAGCATCATATTACC
1 TAAACCCATTAGAGTACA
16454 TAAACCCATTAGAGTACA
1 TAAACCCATTAGAGTACA
16472 TAAA
1 TAAA
16476 AGAAGGGCCC
Statistics
Matches: 27, Mismatches: 12, Indels: 1
0.68 0.30 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (18 bp):
TAAACCCATTAGAGTACA
Found at i:16779 original size:15 final size:15
Alignment explanation
Indices: 16757--16893 Score: 166
Period size: 15 Copynumber: 9.1 Consensus size: 15
16747 GCACTATCAA
16757 TACAAGCAGAATTAT
1 TACAAGCAGAATTAT
* *
16772 TACGAGCAGAATTAA
1 TACAAGCAGAATTAT
**
16787 TACGTGCAGAATTAT
1 TACAAGCAGAATTAT
* *
16802 TACAAGCATAATTAG
1 TACAAGCAGAATTAT
**
16817 TATGAGCAGAATTAT
1 TACAAGCAGAATTAT
*
16832 TACAAGCAGAATTAA
1 TACAAGCAGAATTAT
16847 TACAAGCAGAATTAT
1 TACAAGCAGAATTAT
*
16862 CACAAGCAGAATTAT
1 TACAAGCAGAATTAT
* *
16877 CACAAGTAGAATTAT
1 TACAAGCAGAATTAT
16892 TA
1 TA
16894 ATATGCAGAC
Statistics
Matches: 103, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 103 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (15 bp):
TACAAGCAGAATTAT
Found at i:21815 original size:53 final size:53
Alignment explanation
Indices: 21758--21860 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 53
21748 TTTTAATTTA
* * *
21758 CAATAT-AATATCTAAAATTTTCATT-TTATCTTTTTAAAATTATTTTTTAGCAT
1 CAATATAAATAT-TAAAATTTTCATTGTAAT-TTTTAAAAAATATTTTTTAGCAT
*
21811 CAATATCAAATATTTAAATTTTCATTGTAATTTTTAAAAAATATTTTTTA
1 CAATAT-AAATATTAAAATTTTCATTGTAATTTTTAAAAAATATTTTTTA
21861 CTACATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
53 6 0.14
54 29 0.67
55 8 0.19
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (53 bp):
CAATATAAATATTAAAATTTTCATTGTAATTTTTAAAAAATATTTTTTAGCAT
Found at i:23917 original size:11 final size:11
Alignment explanation
Indices: 23901--23928 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
23891 TCCTACTTGA
23901 CATTTTCTTAC
1 CATTTTCTTAC
23912 CATTTTCTTAC
1 CATTTTCTTAC
23923 CATTTT
1 CATTTT
23929 TACTTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (11 bp):
CATTTTCTTAC
Found at i:30227 original size:29 final size:29
Alignment explanation
Indices: 30185--30271 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
30175 ATACTGATGT
30185 TACTGATGTTACACTCAAATAAGCCCTTA
1 TACTGATGTTACACTCAAATAAGCCCTTA
30214 TACTGATGTTACACTCAAATAAGCCCTTA
1 TACTGATGTTACACTCAAATAAGCCCTTA
30243 TACTGATGTTACACTCAAATAAGCCCTTA
1 TACTGATGTTACACTCAAATAAGCCCTTA
30272 AGGCTTAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (29 bp):
TACTGATGTTACACTCAAATAAGCCCTTA
Found at i:43491 original size:30 final size:29
Alignment explanation
Indices: 43420--43493 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
43410 TAACAGTAGA
*
43420 AAACA-TCATGTATGAAATGAGAATTTTT
1 AAACATTCATGTATGAAATGAGAATTTGT
*
43448 AAACATT-ATGTATGAAACTTAGAATTGTGT
1 AAACATTCATGTATGAAA-TGAGAATT-TGT
*
43478 ATAC-TTCATGTATGAA
1 AAACATTCATGTATGAA
43494 TAGGGTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 15 0.38
29 10 0.26
30 14 0.36
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (29 bp):
AAACATTCATGTATGAAATGAGAATTTGT
Found at i:45935 original size:17 final size:18
Alignment explanation
Indices: 45913--45947 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45903 ATGTCGTGTT
45913 CGAATCA-AAATCTCAAG
1 CGAATCAGAAATCTCAAG
*
45930 CGAATCAGGAATCTCAAG
1 CGAATCAGAAATCTCAAG
45948 GGACAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (18 bp):
CGAATCAGAAATCTCAAG
Found at i:47538 original size:4 final size:4
Alignment explanation
Indices: 47529--48077 Score: 959
Period size: 4 Copynumber: 141.0 Consensus size: 4
47519 TAAATGATCC
47529 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
47576 CATA CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
47624 CATA CATA CATA CATA CATA CATTA CATG CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA
47673 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47720 C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47766 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47814 C-TA CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47860 CAT- CATA CATA CATA C-TA CATA C-TA -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47904 CATA CATA CATA CAT- -ATA CATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47948 CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
47994 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
48042 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
48078 TTGTTTATAA
Statistics
Matches: 524, Mismatches: 4, Indels: 34
0.93 0.01 0.06
Matches are distributed among these distances:
2 6 0.01
3 28 0.05
4 486 0.93
5 4 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:54186 original size:105 final size:105
Alignment explanation
Indices: 53914--55581 Score: 2826
Period size: 105 Copynumber: 16.0 Consensus size: 105
53904 GGGTCGCTCA
* *
53914 AGACAACGCAGGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
* * *
53979 AGAGCCAATTTCAACTTCTCAACGAAGGATCTT-GACTCT
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
54018 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCCCAATTT
*
54083 CAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
54124 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
54189 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
54229 AGACAACGCAAGTTCAACTTCACGACGAAGGGA-C-CTGGTTGTCAATAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
54292 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
54332 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
*
54397 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
54437 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCCCAATTT
*
54502 CAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
54543 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
54608 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
54648 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
54713 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
54753 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
*
54818 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
54858 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
*
54923 AGAGCCAATTTCGACTTCACAACGAAGG--ATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
54961 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
55026 AGAG-CAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
55065 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
**
55130 AGAGCCAATTTTGACTTCACAACGAAGGATA-TGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
55169 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
*
55233 AGAGCCAATTTCGACTTCACAACGAAGGATA-TGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
55272 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
*
55337 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
55377 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCCCAATTT
* * * * *
55442 CAAAGCCAATTTCAACTTCTCAACGAATGATCTT-GAATCC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * * *
55482 AAGACAACACAAGCTCAACTTCATGACGAAGGGGCGGCTGATTGTCAACAAA-ATTT--C-A-TT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
* * * *
55542 CAGAGTCAATTCCAACTTCACAGCGGAGGATATTGGACTC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
55582 GGAACAATGC
Statistics
Matches: 1495, Mismatches: 56, Indels: 29
0.95 0.04 0.02
Matches are distributed among these distances:
100 28 0.02
101 5 0.00
102 23 0.02
103 279 0.19
104 236 0.16
105 683 0.46
106 241 0.16
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:55938 original size:33 final size:32
Alignment explanation
Indices: 55896--55997 Score: 118
Period size: 31 Copynumber: 3.2 Consensus size: 32
55886 ATCTGTCAAC
*
55896 AACCTTTGAAATTGTTTCTCTTGAAACATAAAA
1 AACCTTTGAAATTATTTCTCTTGAAACA-AAAA
* * *
55929 AACCTTTGAACTCATTTCTCCTGAAAC-AAAA
1 AACCTTTGAAATTATTTCTCTTGAAACAAAAA
*
55960 AACCTTTGAGAA-TATTTCTCTTGAAACACAAA
1 AACCTTTGA-AATTATTTCTCTTGAAACAAAAA
*
55992 GACCTT
1 AACCTT
55998 CGAGTTCGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 26 0.45
32 9 0.16
33 23 0.40
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (32 bp):
AACCTTTGAAATTATTTCTCTTGAAACAAAAA
Found at i:59469 original size:23 final size:23
Alignment explanation
Indices: 59435--59478 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
59425 TTTATATATA
59435 AAATATTCTTTT-ATCCAATATCT
1 AAATATTCTTTTGAT-CAATATCT
59458 AAATATAT-TTTTGATCAATAT
1 AAATAT-TCTTTTGATCAATAT
59479 AATATATCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATATTCTTTTGATCAATATCT
Done.