Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001693.1 Hibiscus syriacus cultivar Beakdansim tig00003382_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: 52484
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3739 original size:3 final size:3
Alignment explanation
Indices: 3725--3755 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3715 GGGGGCAAAT
*
3725 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3756 ATATATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4188 original size:26 final size:25
Alignment explanation
Indices: 4159--4233 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 25
4149 TAAAATAGAG
*
4159 AGAAGGAAAAAATATATAGAAAA-AAA
1 AGAA-GAAAAAATAGATA-AAAAGAAA
4185 AGAA-AAAAAATAGATAAAAAGAAA
1 AGAAGAAAAAATAGATAAAAAGAAA
*
4209 A-AAGAAAAAATAAGA-AAGAAGAAA
1 AGAAGAAAAAAT-AGATAAAAAGAAA
4233 A
1 A
4234 TAGACGGATC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 6 0.14
24 31 0.70
25 3 0.07
26 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (25 bp):
AGAAGAAAAAATAGATAAAAAGAAA
Found at i:4192 original size:22 final size:19
Alignment explanation
Indices: 4150--4211 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
4140 TCAAGTTGAT
* * *
4150 AAAATAGAGAGAAGGAAAA
1 AAAATAGAAAAAAAGAAAA
4169 AATATATAGAAAAAAAAGAAAA
1 AA-A-ATAG-AAAAAAAGAAAA
*
4191 AAAATAGATAAAAAGAAAA
1 AAAATAGAAAAAAAGAAAA
4210 AA
1 AA
4212 GAAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 15 0.42
20 5 0.14
21 5 0.14
22 11 0.31
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATAGAAAAAAAGAAAA
Found at i:4856 original size:15 final size:16
Alignment explanation
Indices: 4828--4861 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4818 CTGCTTCATC
*
4828 GAATCAATGAACGCCA
1 GAATCAATGAACGCAA
4844 GAATCAA-GAACGCAA
1 GAATCAATGAACGCAA
4859 GAA
1 GAA
4862 GCTAGCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (16 bp):
GAATCAATGAACGCAA
Found at i:6290 original size:44 final size:43
Alignment explanation
Indices: 6225--6400 Score: 262
Period size: 44 Copynumber: 4.0 Consensus size: 43
6215 ATAAGAAACT
* *
6225 AAGCTTGAGTGACCAATGTGATATATAGGGGTTCCTTGATGAC
1 AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
* *
6268 AAGCTTGAAGTGACCAACGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTG-AGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
* * *
6312 AAGCTGGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGAT
1 AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
*
6355 AAGGCTTGAGGGACCAACGTGATATATAGAGGTTCCTTGATGAC
1 AA-GCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
6399 AA
1 AA
6401 CTAAGAAACT
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
43 43 0.35
44 79 0.65
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (43 bp):
AAGCTTGAGGGACCAACGTGATATATAGGGGTTCCTTGATGAC
Found at i:6371 original size:87 final size:87
Alignment explanation
Indices: 6225--6400 Score: 264
Period size: 87 Copynumber: 2.0 Consensus size: 87
6215 ATAAGAAACT
* * * *
6225 AAGCTTGAGTGACCAATGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGTGACCAACGTGA
1 AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGGACCAACGTGA
* *
6290 TATGTAGGGGTTCCTTGATGAC
66 TATATAGAGGTTCCTTGATGAC
* *
6312 AAGCTGGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGATAAGGCTTG-AGGGACCAACGTG
1 AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAA-GCTTGAAGGGACCAACGTG
6376 ATATATAGAGGTTCCTTGATGAC
65 ATATATAGAGGTTCCTTGATGAC
6399 AA
1 AA
6401 CTAAGAAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 75 0.94
88 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (87 bp):
AAGCTGGAGGGACCAACGTGATATATAGGGGTTCCTTGATGACAAGCTTGAAGGGACCAACGTGA
TATATAGAGGTTCCTTGATGAC
Found at i:6776 original size:38 final size:36
Alignment explanation
Indices: 6687--6812 Score: 126
Period size: 36 Copynumber: 3.4 Consensus size: 36
6677 TCTGTTTCTT
* * * **
6687 TTGAAACAAAGTTTGTCTCTTTTGAGACGGTTTCTA
1 TTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCC
* *
6723 TTGAAGCAAATTTTGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCC
* * *
6759 TTGAAACAGAAGATTTGTCTCGCTTGCGCCAGTTTCCC
1 TTGAAACA-AA-ATTTGTCTCTCTTGAGACAGTTTCCC
6797 TTGAAACTAGAAATTT
1 TTGAAAC-A-AAATTT
6813 TATCTTACTT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
36 37 0.49
37 2 0.03
38 33 0.43
39 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (36 bp):
TTGAAACAAAATTTGTCTCTCTTGAGACAGTTTCCC
Found at i:7664 original size:133 final size:133
Alignment explanation
Indices: 7270--8235 Score: 1277
Period size: 133 Copynumber: 7.3 Consensus size: 133
7260 TTCAACTTTT
* *
7270 GTTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTCGT-TCAAATCCATCGCAGAA
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTC-TCTCAAATCCATCGCAGAA
* * * *
7334 GGAGTTGGATCAGTGTCAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACACTGACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
7399 TCTC
130 TCTC
* * * * *
7403 GTTCGATTTCATCAAATAAGGAGGTGGATCGAC--TTTTATTTT-GCTCAAATCCATCGTAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
* * * * *
7465 GAGTTGGATCAACGTTAACTTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACA
66 GAGTTGGATCAGCGTCAAC-TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
*
7530 TCTT
130 TCTC
* *
7534 GTTCGATTCTATCACAGAAGAAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
* * *
7599 GAGTTGGATCAACGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACAT
7664 CTC
131 CTC
* * * *
7667 ATTTGATTTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAA
1 GTTCGA-TTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAA
* *
7732 GGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
7797 TCTC
130 TCTC
* * * *
7801 ATTTGATTCCATCACAGAAGGAGGTTGATCGACATTTTTATTTT-TGCTCAAATTCATCGCAGAA
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCT-CTCAAATCCATCGCAGAA
* * * *
7865 GGAGTTGGATCAGCGTCAACTTTTAGCTTGATTCTAGCACAGAAGAAGGTAGATCAACACCGACA
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACA
7930 TCTC
130 TCTC
* * * *
7934 ATTCGATTCCATCACAGAAGGAGGTGGATCGACA--TTTA-CTTCGCTCAAATCCATCGCAAAAG
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
* * * * * *
7996 AAGTTGGATCAGCATAAACTTTTAGCTCGATTCTATCGCAGAAGGAGGTAGATCAGCAACAACAT
66 GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACAT
8061 CTC
131 CTC
* * * *
8064 GTTTGATTCTATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGT-TCAAATACATTGCAGAA
1 GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTC-TCTCAAATCCATCGCAGAA
* * *
8128 GGAGTTGGATCAGCGCCAACTTTTAGCTCAATTCTATCACAGAAGGAGGTAGATTAGCACAC-AC
65 GGAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCAC-CGAC
* *
8192 ACCTT
129 ATCTC
* * *
8197 GTTTTGATTCCATCACAGAAAGAGGTGGATCAACATTTT
1 G-TTCGATTCCATCACAGAAGGAGGTGGATCGACATTTT
8236 CATTCATCAC
Statistics
Matches: 736, Mismatches: 83, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
130 141 0.19
131 85 0.12
132 4 0.01
133 309 0.42
134 197 0.27
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (133 bp):
GTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGCAGAAG
GAGTTGGATCAGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACAT
CTC
Found at i:7896 original size:89 final size:87
Alignment explanation
Indices: 7261--7923 Score: 267
Period size: 89 Copynumber: 7.5 Consensus size: 87
7251 AAAAACTTGT
* * *
7261 TCAACTTTTG-TTCGATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTCGTTCAAATCC
1 TCAACTTTTGCTT-GATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTTGCTC-AATTC
* * *
7325 ATCGCAGAAGGAGTTGGATCAGTG
64 ATCACAGAAGGAGGTGGATCAGCG
* * *** * * * *
7349 TCAACTTTTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACACTGACA-TCTCGTTCGATTTC
1 TCAACTTTT-GCTTGATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTTGCTC-AATTC
* * *
7413 ATCAAATAAGGAGGTGGATC-GACT
64 ATCACAGAAGGAGGTGGATCAG-CG
** ** * ** * * * ** *
7437 TTTA-TTTTGCTCAAATCCATCGTAGAAGGAGTTGGATCAACGTTAACT-TTTTTGCTCGATTCT
1 TCAACTTTTGCTTGATTCCATCACAGAAGGAGGTAGATCAACATT-TTTATTTTTGCTCAATTC-
* * *
7500 ATCACAGAAGGAGGTAGATCAACA
64 ATCACAGAAGGAGGTGGATCAGCG
* * * * * *
7524 TCGACATCTTG-TTCGATTCTATCACAGAAGAAGGTGGATCGACATTTTTATTTTCT-CTCAAAT
1 TCAAC-TTTTGCTT-GATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTT-TGCTC-AAT
* * * *
7587 CCATCGCAGAAGGAGTTGGATCAACG
62 TCATCACAGAAGGAGGTGGATCAGCG
* * * ***** *
7613 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCATTTG---ATT
1 TCAAC-TTTTGCTTGATTCCATCACAGAAGGAGGTAGATCAACATTTTTAT-T--TTTGCTCAAT
*
7675 TCCATCACAGAAGGAGGTGGATC-GACATT
62 T-CATCACAGAAGGAGGTGGATCAG-C--G
** ** * ** * * * * ** *
7704 TTTA-TTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGC--GTCAACTTTTTGCTCGATTC
1 TCAACTTTT-GCTTGATTCCATCACAGAAGGAGGTAGATCAACATTTTTA-TTTTTGCTCAATTC
* *
7766 TATCACAGAAGGAGGTAGATCAGCA
64 -ATCACAGAAGGAGGTGGATCAGCG
* * * * *
7791 TCGACATCT-CATTTGATTCCATCACAGAAGGAGGTTGATCGACATTTTTATTTTTGCTCAAATT
1 TCAACTTTTGC--TTGATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTTGCTC-AATT
* *
7855 CATCGCAGAAGGAGTTGGATCAGCG
63 CATCACAGAAGGAGGTGGATCAGCG
* * *
7880 TCAACTTTTAGCTTGATTCTAGCACAGAAGAAGGTAGATCAACA
1 TCAACTTTT-GCTTGATTCCATCACAGAAGGAGGTAGATCAACA
7924 CCGACATCTC
Statistics
Matches: 412, Mismatches: 126, Indels: 73
0.67 0.21 0.12
Matches are distributed among these distances:
86 34 0.08
87 32 0.08
88 68 0.17
89 231 0.56
90 41 0.10
91 4 0.01
92 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (87 bp):
TCAACTTTTGCTTGATTCCATCACAGAAGGAGGTAGATCAACATTTTTATTTTTGCTCAATTCAT
CACAGAAGGAGGTGGATCAGCG
Found at i:8714 original size:14 final size:14
Alignment explanation
Indices: 8695--8729 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
8685 TCTTCGGCTC
8695 TCTTTCTCTATCTT
1 TCTTTCTCTATCTT
8709 TCTTTCTCTATCTT
1 TCTTTCTCTATCTT
8723 TCTTTCT
1 TCTTTCT
8730 ATGCATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTTTCTCTATCTT
Found at i:12008 original size:2 final size:2
Alignment explanation
Indices: 12001--12103 Score: 185
Period size: 2 Copynumber: 53.0 Consensus size: 2
11991 TCCAACGTTA
12001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12042 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
12084 AT A- AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
12104 TTAATAAGTT
Statistics
Matches: 98, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
1 3 0.03
2 95 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16433 original size:116 final size:116
Alignment explanation
Indices: 16233--16641 Score: 389
Period size: 116 Copynumber: 3.5 Consensus size: 116
16223 TGTGGAATGA
* * * * *
16233 TTCATAATGAGAAGAACTCGTCCGATGA-GGAGAAGAAATTTCTAATGAGAATAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAAC
* ** * *
16297 CTTGACTCACCCATCGTAGAATG-AGGTGGACCAATATTTACTGTGGAAGGG
66 CTTGAATCGTCCATCATAGAATGAAGGTGGACCAATATTT-CTATGGAAGGG
* * * *
16348 TTCATAATGAAAAGAACTCGTCCGATGAGGGAGAAGAAGTCCCTAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAAC
* * * *** *
16413 CTTGAATCGTCTATCATAGAA-GAAGATGGACCAAAATTTCTAACAAAACGG
66 CTTGAATCGTCCATCATAGAATGAAGGTGGACCAATATTTCT-ATGGAAGGG
* * * ** * *
16464 TTTATAATGAGATGAGCTCATCCAATGAATGAGATA-AAGTTCCTAATAAGAAGAACTTGTTCCA
1 TTCATAATGAGAAGAACTCATCCAATGAGGGAGA-AGAAGTTCCTAATGAGAAGAACTTGTTCAA
** * * * *
16528 CCTTGGTTCGATTCCATCATAG-ATGAAGGAGGATCAATATTTCTAT-TAGAGAG
65 CCTTGAATCG--TCCATCATAGAATGAAGGTGGACCAATATTTCTATGGA-AGGG
* * *
16581 TTCATAATGAGAATAATTCATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 TTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAGAAGAACTTGTT
16642 TAAATCTCAG
Statistics
Matches: 237, Mismatches: 48, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
115 30 0.13
116 127 0.54
117 55 0.23
118 25 0.11
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (116 bp):
TTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAGAAGAACTTGTTCAAC
CTTGAATCGTCCATCATAGAATGAAGGTGGACCAATATTTCTATGGAAGGG
Found at i:17304 original size:3 final size:3
Alignment explanation
Indices: 17298--17332 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17288 GTTGTTGTTG
*
17298 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17333 TACTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:38750 original size:5 final size:5
Alignment explanation
Indices: 38740--38839 Score: 67
Period size: 5 Copynumber: 18.8 Consensus size: 5
38730 TGTTCACAGA
** * *
38740 AAAAT AAAAT AAAAT AAAAT AAAGCAT ATGAT ACAAT AAAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT AAA--AT AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
38792 GAAAT AAATT AAAAAT GAAAT AAAGTAT ACAAA- AAAAT AATAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAA--AT A-AAAT AAAAT AA-AAT AAAA
38840 AATGAAAATG
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
4 3 0.04
5 55 0.72
6 10 0.13
7 6 0.08
8 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:38799 original size:20 final size:21
Alignment explanation
Indices: 38774--38812 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38764 CATATGATAC
38774 AATAAAAT-AAAATGAAATGA
1 AATAAAATAAAAATGAAATGA
*
38794 AATAAATTAAAAATGAAAT
1 AATAAAATAAAAATGAAAT
38813 AAAGTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAAAATAAAAATGAAATGA
Found at i:51896 original size:180 final size:181
Alignment explanation
Indices: 50946--51898 Score: 1231
Period size: 180 Copynumber: 5.3 Consensus size: 181
50936 AAATATAAAT
* * * *
50946 ATGACAAAATCGGTAAAGCGCTACTAAATATATTGAAAGTGTTC-ATACTTTAATACAAATATCG
1 ATGACAAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTG-TCGATACTTTAATATAAATATCG
* * * *
51010 ACAC-TTTAGAATATAAAAGAGAAACAGT-ATAGCGTCTA-AAA-TGTCGATACATTATAAAAAT
65 ACACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAA-
51071 GTATCGATCCAT---AATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
129 GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * *
51121 ATGACAAAACCAGTAAAGTGCTAC-GGATATGTTGAAAGTGTCGATACTTTAATATAAATATCGA
1 ATGACAAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTCGATACTTTAATATAAATATCGA
* * *
51185 CACTTTTGGAATTTTAAAATAGAAGCAATAATAGCGCCTATAAAGTGTCGATACTTTTATAAAAA
66 CACTTTTAGAA-TTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAC-TTTATAAAAA
* * * * * *
51250 TGTATTGACCCATAACAATATAACAAGTAAAAATATGACAAAATCGATCTTGAA
129 -GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * *
51304 ATGACAAAACCGGTAAAACGCTACCGAATATGTTAAAAGTGTCGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTCGATACTTTAATATAAATATCGA
* *
51369 CACTTTTAGAATTTAAAAGAGAAGCAATAATAGCGCTTATAAAGTGTC--TACTTTATAAAAATG
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAA-G
* * *
51432 TATCGATCCATAATAATATAATATGTAAAATTATGA-AAAACCGGTCTCGAA
130 TATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
* * * * * *
51483 ATGACAAAACCAGTAAAAC-ATA-TCGGATATGTTGAAAGTGTCGATATTTTAATATAAGTATCG
1 ATGACAAAACCGGTAAAGCGCTACT-GAATATGTTGAAAGTGTCGATACTTTAATATAAATATCG
* *
51546 ACACTTTTAGAATTTAAAAGAGAAGCAGTAATATCGCCTATAAAGTGTTGATACTTTATAAAAAT
65 ACACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAA-
*
51611 GTATCGATCCATAACAATATAACATGT-AAAATATAACAAAACCGGTCTCGAAA
129 GTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCG-AA
* * * *
51664 ATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAATATTGA
1 ATGACAAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTCGATACTTTAATATAAATATCGA
* *
51729 CACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATAC-TAAT-AAAA-T
66 CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAAGT
* * *
51791 ATCGATCCATAACAATATAAACAGGTAAAAATATGATAAAACCGGTCTCTAA
131 ATCGATCCATAACAATAT-AACATGTAAAAATATGACAAAACCGGTCTCGAA
* * *
51843 ATGACAAAAACCGGTAAAGCACTGCTGAATATGTTGAAAGTGTTGATACTTTAATA
1 ATGAC-AAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTCGATACTTTAATA
51899 AGAGTAAAAT
Statistics
Matches: 683, Mismatches: 74, Indels: 37
0.86 0.09 0.05
Matches are distributed among these distances:
173 2 0.00
174 36 0.05
175 27 0.04
176 13 0.02
177 9 0.01
178 105 0.15
179 59 0.09
180 182 0.27
181 24 0.04
182 89 0.13
183 90 0.13
184 47 0.07
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (181 bp):
ATGACAAAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTCGATACTTTAATATAAATATCGA
CACTTTTAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAAGT
ATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
Done.