Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007409.1 Hibiscus syriacus cultivar Beakdansim tig00020017_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: 62262
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:256 original size:26 final size:26
Alignment explanation
Indices: 196--258 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 26
186 GATAAAATAA
196 GAATAATATTGATGAGATCAAAAAGG
1 GAATAATATTGATGAGATCAAAAAGG
222 GAATGAATATTGATGAGATCAAAAAGG
1 GAAT-AATATTGATGAGATCAAAAAGG
**
249 GCCTAATATT
1 GAATAATATT
259 AAAATGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.25
Consensus pattern (26 bp):
GAATAATATTGATGAGATCAAAAAGG
Found at i:581 original size:26 final size:27
Alignment explanation
Indices: 545--602 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
535 AAAATGAGGA
* *
545 GTTACATGAGATGT-AACTAGTCAAGT
1 GTTACATGAGATATAAACCAGTCAAGT
571 GTTACATGAGATATAAACCAGTCAAGT
1 GTTACATGAGATATAAACCAGTCAAGT
598 GTTAC
1 GTTAC
603 TTACCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (27 bp):
GTTACATGAGATATAAACCAGTCAAGT
Found at i:3136 original size:31 final size:31
Alignment explanation
Indices: 3098--3177 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
3088 AATTGATTTG
3098 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
3129 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
3160 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
3178 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:15878 original size:18 final size:18
Alignment explanation
Indices: 15844--15878 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15834 TGCAAATATG
*
15844 GTATCGATACTGAAGGAA
1 GTATCGATACCGAAGGAA
*
15862 GTATCGATACCGTAGGA
1 GTATCGATACCGAAGGA
15879 GGAGTACCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (18 bp):
GTATCGATACCGAAGGAA
Found at i:17748 original size:24 final size:24
Alignment explanation
Indices: 17721--17790 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
17711 TATATCAAAA
17721 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
17745 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
17769 ATCATATCAGAATCCAAGTCAA
1 ATCAAAACAAAATCCAGGTCAA
17791 TTATTAGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.08
24 36 0.92
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:17815 original size:12 final size:13
Alignment explanation
Indices: 17798--17853 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 13
17788 CAATTATTAG
*
17798 ATCAGAAT-TTAT
1 ATCAGAATATCAT
*
17810 ATCAG-ATATCAG
1 ATCAGAATATCAT
*
17822 ATCAGAATCT-AT
1 ATCAGAATATCAT
17834 ATCAG-ATATCAT
1 ATCAGAATATCAT
17846 ATCAGAAT
1 ATCAGAAT
17854 CCATGTCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.14
12 25 0.71
13 5 0.14
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (13 bp):
ATCAGAATATCAT
Found at i:17823 original size:24 final size:24
Alignment explanation
Indices: 17796--17877 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
17786 GTCAATTATT
*
17796 AGATCAGAATTTATATCAGATATC
1 AGATCAGAATCTATATCAGATATC
17820 AGATCAGAATCTATATCAGATATC
1 AGATCAGAATCTATATCAGATATC
* * * *
17844 ATATCAGAATCCATGTCA-AGTGTC
1 AGATCAGAATCTATATCAGA-TATC
17868 AGATCAGAAT
1 AGATCAGAAT
17878 TCAAATCGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 1 0.02
24 50 0.98
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (24 bp):
AGATCAGAATCTATATCAGATATC
Found at i:21935 original size:24 final size:24
Alignment explanation
Indices: 21908--21983 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
21898 TATATCAAAA
21908 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
21932 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
21956 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
21980 ATCA
1 ATCA
21984 GATCAGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:21984 original size:24 final size:24
Alignment explanation
Indices: 21925--22040 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
21915 CATAAATCAG
* *
21925 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
*
21949 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
***
21973 GTCAAGTATCAGATCAGAAAATAT
1 GTCAAGTATCAGATCAGAATCCAT
*
21997 GTC-AGATATCAGATTAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
22021 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
22041 TCAAATCCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 2 0.03
24 71 0.92
25 4 0.05
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:24428 original size:13 final size:13
Alignment explanation
Indices: 24410--24449 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
24400 GGTCAACGGA
24410 TCAACGGGTCGGG
1 TCAACGGGTCGGG
24423 TCAACGGGTC-GG
1 TCAACGGGTCGGG
*
24435 TCAACAGGTCGGG
1 TCAACGGGTCGGG
24448 TC
1 TC
24450 GGGTAAACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:24438 original size:12 final size:12
Alignment explanation
Indices: 24410--24446 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
24400 GGTCAACGGA
24410 TCAACGGGTCGGG
1 TCAACGGGTC-GG
24423 TCAACGGGTCGG
1 TCAACGGGTCGG
*
24435 TCAACAGGTCGG
1 TCAACGGGTCGG
24447 GTCGGGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.24, G:0.41, T:0.16
Consensus pattern (12 bp):
TCAACGGGTCGG
Found at i:32330 original size:258 final size:256
Alignment explanation
Indices: 31860--32468 Score: 728
Period size: 258 Copynumber: 2.4 Consensus size: 256
31850 AGTTATTTTG
* * * * ** *
31860 AAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTCAAAATGAATTTTTTGAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTT-ATTATTTTCAGAAAAT-AAATTTTTG-AA
* * * * *
31925 AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTGGTATGTCCTTC
63 AAGTAAGAAAGTGATTTCCAAAG-TTCTTACCCAATAAACTATTTCCAAAATTGGGAAGTCATTC
* *
31990 GGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATTCTTAGGGTCATCTGTAAGTCTTTCAAG
127 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAAGTCTTTCAAG
* * * * * * *
32055 AAAGATGATATGTCCTTCGGTCCAACCGTAATACCTTCGGGTATTATATTTTCACA-TGATTTTC
192 AAAGATGATAAGTCCTTCGGACCAACCATAAGACCTTCAGGCATGATATTTTCACACT-ATTTTC
32119 A
256 A
* *
32120 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAGAAAATTATATTTTTGAAGA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAGAAAA-TAAATTTTTGAAAA
32185 GTAAGAAAGTGATTTCCAAAGCTTCTTACCCAATAAACTATTTCCAAAATTGGGAAGTCATTCGG
65 GTAAGAAAGTGATTTCCAAAG-TTCTTACCCAATAAACTATTTCCAAAATTGGGAAGTCATTCGG
* * * * *
32250 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGTGTCATCTGTTAGTCTTTCGAGCA
129 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAAGTCTTTCAAGAA
* * * * *
32315 AGAAT-ATAAGTCCTTCGGACCATCTATAAGATCTTCAGGCATGATGTTTTCTCACTATTTTCA
194 AG-ATGATAAGTCCTTCGGACCAACCATAAGACCTTCAGGCATGATATTTTCACACTATTTTCA
* * *
32378 AAAAA-GATGAGAA--TATTTTCAAAGTTTC-CCTTTATTGTTTTCAGAAAATAAAATTTTT-AA
1 AAAAATGA-GA-AAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAGAAAAT-AAATTTTTGAA
*
32438 AAGTAAGAAAGCGATTTCCAAAGTTCCTTAC
63 AAGTAAGAAAGTGATTTCCAAAGTT-CTTAC
32469 TAGTAAATTA
Statistics
Matches: 302, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
254 2 0.01
255 29 0.10
256 25 0.08
257 16 0.05
258 173 0.57
259 23 0.08
260 34 0.11
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (256 bp):
AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAGAAAATAAATTTTTGAAAAG
TAAGAAAGTGATTTCCAAAGTTCTTACCCAATAAACTATTTCCAAAATTGGGAAGTCATTCGGGC
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAAGTCTTTCAAGAAAG
ATGATAAGTCCTTCGGACCAACCATAAGACCTTCAGGCATGATATTTTCACACTATTTTCA
Found at i:32711 original size:44 final size:43
Alignment explanation
Indices: 32658--32928 Score: 188
Period size: 44 Copynumber: 6.1 Consensus size: 43
32648 TGAAAGAGGT
*
32658 GTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCTTGAAGATGA
1 GTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCTTGAAGA-GA
* * * *
32702 GTCAATCTTTAGTGTTATTATTCTTGACTTTCTCATGAAGAGGT
1 GTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCTTGAAGA-GA
* * *
32746 GTCAATCTTTAGT-TATTTTATTCTTGACTTTCTCATGAAGAGAA
1 GTCAATCTTTAGTGT-TGTCATTCTTGACTTTCTCTTGAAGAG-A
* ** ** * * *
32790 GTCAACCTTTTAGTGGAGTTGTTCTTGACTTTTTAGTTG-AGAAA
1 GTCAATC-TTTAGTGTTGTCATTCTTGACTTTCT-CTTGAAGAGA
* * * * *
32834 GTCAACCTTTTAGTGATGTCATTCTTGAATTTTTCTTGAAGAAAA
1 GTCAATC-TTTAGTGTTGTCATTCTTGACTTTCTCTTGAAG-AGA
* * * * **
32879 ATCAATATTTCAGTATTGTCA-ACTTGACTTTCTCGCGAAGAGGA
1 GTCAATCTTT-AGTGTTGTCATTCTTGACTTTCTCTTGAAGA-GA
32923 GTCAAT
1 GTCAAT
32929 ATTGTTTTCC
Statistics
Matches: 183, Mismatches: 35, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
43 6 0.03
44 137 0.75
45 38 0.21
46 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (43 bp):
GTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCTTGAAGAGA
Found at i:33165 original size:89 final size:89
Alignment explanation
Indices: 33009--33186 Score: 252
Period size: 89 Copynumber: 2.0 Consensus size: 89
32999 GACCTAACAC
* *
33009 ATCCTTTTAAATCGAGCTACCCTAATCACATTAGGGATTTCATTATTTCAAATTAATTAAATTTA
1 ATCCTTTTAAATCAAGCTACCCTAATCACATTAGGGATTTCATTATTTCAAATTAATTAAATCTA
*
33074 TATTTAATTAATTAGAATTTAATA
66 TATTTAATTAATTAGAATTAAATA
* * *
33098 ATCCTTTTATATCCAAGTTACCCTAATCATATTA-GGATTTTC-TTATTTCAAATTAATTAAATC
1 ATCCTTTTAAAT-CAAGCTACCCTAATCACATTAGGGA-TTTCATTATTTCAAATTAATTAAATC
* *
33161 TATATTTAATTAGTTGGAATTAAATA
64 TATATTTAATTAATTAGAATTAAATA
33187 TTAGGGATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
89 57 0.72
90 22 0.28
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (89 bp):
ATCCTTTTAAATCAAGCTACCCTAATCACATTAGGGATTTCATTATTTCAAATTAATTAAATCTA
TATTTAATTAATTAGAATTAAATA
Found at i:37793 original size:16 final size:15
Alignment explanation
Indices: 37761--37796 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
37751 TAAAAAAGGA
37761 AAATAATATAATAAT
1 AAATAATATAATAAT
*
37776 AAATAATAATAGTAAT
1 AAATAAT-ATAATAAT
37792 AAATA
1 AAATA
37797 TGAAAGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATAATATAATAAT
Found at i:38620 original size:70 final size:65
Alignment explanation
Indices: 38464--38631 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
38454 TAAAACATCT
* * *
38464 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAAATAATATAATATT
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTCAACTAAAATACCTAAAAAAATAAAATAATATC
38528 C
65 C
38529 TAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCTAAAACAAAGATAAAAAATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCT-AAA-AAA-AT--AAAATAA
38594 TATCC
61 TATCC
* *
38599 TCAAA-CCTAATTAAAATACTAAAAACATATTTC
1 T-AAATCCTAATTAAAACACT-AAAACCTATTTC
38632 CAGAATCTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
64 5 0.06
65 38 0.42
66 3 0.03
67 3 0.03
68 2 0.02
70 25 0.28
71 14 0.16
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.28
Consensus pattern (65 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTCAACTAAAATACCTAAAAAAATAAAATAATATCC
Found at i:40240 original size:16 final size:17
Alignment explanation
Indices: 40219--40256 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
40209 GTTCACTAAG
40219 AAAAATAAAAT-AAAAC
1 AAAAATAAAATGAAAAC
*
40235 AAAAATAAAATGAAAAT
1 AAAAATAAAATGAAAAC
40252 AAAAA
1 AAAAA
40257 CAAAGATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (17 bp):
AAAAATAAAATGAAAAC
Found at i:40272 original size:23 final size:22
Alignment explanation
Indices: 40225--40272 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
40215 TAAGAAAAAT
*
40225 AAAATAAAACAAAAATAAAATG
1 AAAATAAAACAAAAATAAAACG
* *
40247 AAAATAAAAACAAAGATATAACG
1 AAAAT-AAAACAAAAATAAAACG
40270 AAA
1 AAA
40273 TTGGTTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (22 bp):
AAAATAAAACAAAAATAAAACG
Found at i:42873 original size:21 final size:22
Alignment explanation
Indices: 42849--42891 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
42839 AGTAAGGGAA
42849 AATAAATGAAAT-AATAAAGAT
1 AATAAATGAAATAAATAAAGAT
42870 AATAAATGAAATGAAATAAAGA
1 AATAAATGAAAT-AAATAAAGA
42892 AAGGATAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (22 bp):
AATAAATGAAATAAATAAAGAT
Found at i:44828 original size:10 final size:10
Alignment explanation
Indices: 44776--44831 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
44766 AGATATATTA
44776 AAATAAT-AT
1 AAATAATAAT
*
44785 AAATAATAAA
1 AAATAATAAT
* *
44795 AAAGGAAAAAT
1 AAA-TAATAAT
44806 AATATAATAAT
1 AA-ATAATAAT
*
44817 AAATAGTAAT
1 AAATAATAAT
44827 AAATA
1 AAATA
44832 TAAAAGGGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.19
10 16 0.43
11 13 0.35
12 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (10 bp):
AAATAATAAT
Found at i:45572 original size:65 final size:69
Alignment explanation
Indices: 45487--45673 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 69
45477 AAAACAAGCT
* * * **
45487 AAAACATCTTAAATCCTAATTAAAACACTAAAAACTATTTAAACTAAAATACCT-CTA-AAA-AT
1 AAAATATCCTAAATCCTAATTAAAATACTAAAAACTATTTAAACTAAAATACCTAAAACAAAGAT
*
45549 -AAT
66 AAAA
* * *
45552 ATAATATTCTAAATCCTAATTAAAATACT-AAAACTTATTTCAACTAAAATACCTAAAACAAAGA
1 AAAATATCCTAAATCCTAATTAAAATACTAAAAAC-TATTTAAACTAAAATACCTAAAACAAAGA
45616 TAAAA
65 TAAAA
*
45621 AAAATATCCTAAAAT-TTAATTAAAATACTAAAAACCTATTTAAACTAAAATAC
1 AAAATATCCT-AAATCCTAATTAAAATACTAAAAA-CTATTTAAACTAAAATAC
45674 AAAGATAAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
64 5 0.05
65 42 0.42
66 1 0.01
67 3 0.03
68 2 0.02
69 23 0.23
70 24 0.24
71 1 0.01
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.29
Consensus pattern (69 bp):
AAAATATCCTAAATCCTAATTAAAATACTAAAAACTATTTAAACTAAAATACCTAAAACAAAGAT
AAAA
Found at i:52871 original size:54 final size:54
Alignment explanation
Indices: 52106--52855 Score: 922
Period size: 54 Copynumber: 13.9 Consensus size: 54
52096 TATTATCGGG
* * *
52106 ACTAAGTGTGCAACCCACTGAATTCATCATATGTTGATGAACGACTGAATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
*
52160 ACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAATGACCGTATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * * *
52213 ACTAAATGTGCAACCTATATAATTCACCATATGTTGATGAACGACCGTATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * *
52267 AGTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAAAGACTGTATCGGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCGTATCGAC
* * * *
52321 ACTTAGTGTGCAACCCATATAATTCACCATATGTTGATGAACGACCGTATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* *
52375 ACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAACGACTGTATCGGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCGTATCGAC
** * * *
52429 ACTAAGTGTGCAACATA-AGGAATTCATTATATTTTGATGAACGACCCTATCGAC
1 ACTAAGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * * * * * *
52483 GCAAAGTGTGAAACCCATAAAATTCATCATATGTGGATGAATGACCATATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* *
52537 ACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAACTACCGTATTGAC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCGTATCGAC
* * * *
52591 ACTAAGTGTGCAACCCAC-GAAATGCATCATATGTTGATGAATGACTGTATCGGC
1 ACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCGTATCGAC
** *
52645 ACTAAGTGTGCAACCCATGGAATTCATCATATTTTGATGAACGACCGTATCGAC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * * * *
52699 GCTAAATGTGCAACCCACGGAATTCATCATATGTTAATGAATGACTGTATC-AGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGA-C
* * *
52753 CCTAAGTGTGCAACCCACA-AATTCATTATATGTTGATGAACGACCGTATCGGC
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
* *
52806 ACTAAGTGTGCAACCCACAGAATTCATCGTATATTGATGAACGACCGTAT
1 ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTAT
52856 AGGCACTATT
Statistics
Matches: 593, Mismatches: 91, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
53 94 0.16
54 496 0.84
55 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATCGAC
Found at i:59394 original size:54 final size:54
Alignment explanation
Indices: 59306--59578 Score: 379
Period size: 54 Copynumber: 5.1 Consensus size: 54
59296 CTATGTGTAC
*
59306 TATCAGCACTAAGTGTGCAACCCATC-GAATTCATCATATGTTGATGAACGACCG
1 TATCAACACTAAGTGTGCAACCCA-CAGAATTCATCATATGTTGATGAACGACCG
* * *
59360 TATCGACACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACTG
1 TATCAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
59414 TATCAACACTAAGTGTGCAACCCAC-GAAACTCAACATGTGTTGATGAACGACCG
1 TATCAACACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
* * * * * *
59468 TATCGATACTAAGTGTGCAACCCACAAAATTTATCATATGTTGATGAACTACTG
1 TATCAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
59522 TATTAACACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCG
1 TATCAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
59576 TAT
1 TAT
59579 AAGTACTACG
Statistics
Matches: 189, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 188 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCAACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:59586 original size:108 final size:108
Alignment explanation
Indices: 59306--59578 Score: 440
Period size: 108 Copynumber: 2.5 Consensus size: 108
59296 CTATGTGTAC
* *
59306 TATCAGCACTAAGTGTGCAACCCATC-GAATTCATCATATGTTGATGAACGACCGTATCGACACT
1 TATCAACACTAAGTGTGCAACCCA-CGGAATTCATCATATGTTGATGAACGACCGTATCGATACT
*
59370 AAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACTG
65 AAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACTG
* * * *
59414 TATCAACACTAAGTGTGCAACCCACGAAACTCAACATGTGTTGATGAACGACCGTATCGATACTA
1 TATCAACACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGATACTA
* *
59479 AGTGTGCAACCCACAAAATTTATCATATGTTGATGAACTACTG
66 AGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACTG
*
59522 TATTAACACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTAT
1 TATCAACACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTAT
59579 AAGTACTACG
Statistics
Matches: 150, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
107 1 0.01
108 149 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (108 bp):
TATCAACACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGATACTA
AGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACTG
Done.