Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005373.1 Hibiscus syriacus cultivar Beakdansim tig00012233_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: 312417
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:234775 original size:3 final size:3
Alignment explanation
Indices: 234765--234801 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
234755 GTAATAATTT
234765 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
234802 TATGAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:235151 original size:123 final size:121
Alignment explanation
Indices: 235017--235681 Score: 548
Period size: 113 Copynumber: 5.7 Consensus size: 121
235007 TGGGATAAAA
* * * * *
235017 TCATGCAAAGGTTGAACAAGTTTTTTTGCATTATGAACTTCTTTTTCTTCTTCAGATGAA-TTCT
1 TCATGCAAAGGTTGAACAAGCTCTTCT-CATTATGAACTTCTTCTTCCTCTTCAGAT-AAGTTCT
* * *
235081 TCTTATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTTCTGTGATAGAG
64 TCTCATTATGAACTCTTCTGGAAAAGTTGATG-TGATCTATCTCATTTCTGTGATAGAG
235140 TCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
1 TCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
* * *
235205 TCATTATGAACTTTCTCTGGAAAAGTTGA--TG--C-ATC-GA-----GTGAT-GAAT
66 TCATTATGAACTCT-TCTGGAAAAGTTGATGTGATCTATCTCATTTCTGTGATAG-AG
* * * * *
235251 TCAAGAAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT-AGATGAGTTCT
1 TCATG-CAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
* * *
235315 TCTCATTATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTCTTTTCTGTAATAGAG
64 TCTCATTATGAAC-TCTTCTGGAAAAGTTGATG-TGATCTATCTCATTTCTGTGATAGAG
* *
235375 TTATGCAGAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
1 TCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
* * *
235440 TCATTATGAACT-TTCTTTGGAAACGTTGA--TG--C-ATC-GA-----GTGAT-GAAT
66 TCATTATGAACTCTTC--TGGAAAAGTTGATGTGATCTATCTCATTTCTGTGATAG-AG
* * * *
235486 TCGA-GAAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TC-ATG-CAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTC
* * * *
235550 TTCTCATTATGAACTTCCTCTGGAAAA---G-T-TGATCCA--TCA----AGTGAT-GAAT
63 TTCTCATTATGAAC-TCTTCTGGAAAAGTTGATGTGATCTATCTCATTTCTGTGATAG-AG
* * * *
235599 TCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
235664 TCTCATTATGAACT-TTCT
64 TCTCATTATGAACTCTTCT
235682 CTAGAAAATT
Statistics
Matches: 460, Mismatches: 46, Indels: 84
0.78 0.08 0.14
Matches are distributed among these distances:
110 5 0.01
111 20 0.04
112 119 0.26
113 123 0.27
114 1 0.00
115 4 0.01
116 1 0.00
117 7 0.02
118 5 0.01
120 4 0.01
121 4 0.01
122 49 0.11
123 109 0.24
124 8 0.02
125 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (121 bp):
TCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTC
TCATTATGAACTCTTCTGGAAAAGTTGATGTGATCTATCTCATTTCTGTGATAGAG
Found at i:235434 original size:235 final size:235
Alignment explanation
Indices: 235023--235789 Score: 1105
Period size: 235 Copynumber: 3.3 Consensus size: 235
235013 AAAATCATGC
* * * * * *
235023 AAAGGTTGAACAAGTTTTTTTGCATTATGAACTTCTT-TTTCTTCTTCAGATGAATTCTTCTTAT
1 AAAGGTTAAACAAGTTCTTCT-CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
235087 TATGAAC-ACTTCTGGAAATGTTGATGTTGATCTATCTCATTTCTGTGATAGAGTCATGCAAAGG
65 TATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTC-TTTCTGTGATAGAGTTATGCAAAGG
235151 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
129 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
235216 TTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCAAGAA
194 TTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCAAGAA
235258 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT-AGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
235322 ATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTCTTTTCTGTAATAGAGTTATGCAGAGGT
66 ATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTC-TTTCTGTGATAGAGTTATGCAAAGGT
235387 TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
130 TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
* * *
235452 TTCTTTGGAAACGTTGATGCATCGAGTGATGAATTCGAGAA
195 TTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCAAGAA
235493 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * *
235558 ATGAACTTCCTCTGGAAAAGTTGAT-C----C-A--TC---AAGTGAT-GAATTCAAGCAAAAGG
66 ATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAGTT-ATGC-AAAGG
* * *
235611 TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
129 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAA
* * * * *
235676 CTTTCTCTAGAAAATTTGATCCATCAAGTGATGAATACAAGAA
193 CTTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCAAGAA
* *
235719 AAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
235784 ATGAAC
66 ATGAAC
235790 CCTACCTGGC
Statistics
Matches: 490, Mismatches: 36, Indels: 21
0.90 0.07 0.04
Matches are distributed among these distances:
223 4 0.01
224 7 0.01
225 38 0.08
226 131 0.27
228 2 0.00
230 1 0.00
231 1 0.00
234 37 0.08
235 226 0.46
236 43 0.09
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (235 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAGTTATGCAAAGGTT
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
TCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCAAGAA
Found at i:235581 original size:113 final size:113
Alignment explanation
Indices: 235383--235789 Score: 663
Period size: 113 Copynumber: 3.6 Consensus size: 113
235373 AGTTATGCAG
* * *
235383 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTAT
1 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
235447 GAACTTTCTTTGGAAACGTTGATGCATCGAGTGATGAATTCGAGAAAA
66 GAACTTTCTCTGGAAAAGTTGATGCATCAAGTGATGAATTCAAGAAAA
235495 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
235560 GAACTTCCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCAAA
66 GAACTTTCTCTGGAAAAGTTGATGCATCAAGTGATGAATTCAAGAAAA
235608 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
235673 GAACTTTCTCTAGAAAATTTGATCCATCAAGTGATGAATACAAGAAAA
66 GAACTTTCTCTGGAAAAGTTGATGCATCAAGTGATGAATTCAAGAAAA
* *
235721 AGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTAT
1 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
235786 GAAC
66 GAAC
235790 CCTACCTGGC
Statistics
Matches: 277, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 37 0.13
113 240 0.87
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGCATCAAGTGATGAATTCAAGAAAA
Found at i:239898 original size:19 final size:20
Alignment explanation
Indices: 239857--239907 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
239847 GAAACCCCTT
*
239857 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
239877 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
239896 TGAAGATACATG
1 TGAAAATACATG
239908 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:241941 original size:24 final size:24
Alignment explanation
Indices: 241908--241991 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
241898 TGTAATGAAC
*
241908 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
241932 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* * *
241956 TTTGAACTTCAAGTGGCATAACTG
1 TTGGAACTTCAAGTGACATAACTT
*
241980 TTGGAACGTCAA
1 TTGGAACTTCAA
241992 AGGACATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
24 46 0.94
25 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:243254 original size:25 final size:24
Alignment explanation
Indices: 243226--243288 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
243216 TTTTCTTGGC
* *
243226 TTTTCTTCTTTTTGAAATTCTTCT
1 TTTTTTTCTTTTTGAAATTCTTAT
***
243250 TTTTTTTCTTTTCTTCTATTCTTAT
1 TTTTTTTCTTTT-TGAAATTCTTAT
243275 TTTTTTTCTTTTTG
1 TTTTTTTCTTTTTG
243289 TCTTTTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.75
Consensus pattern (24 bp):
TTTTTTTCTTTTTGAAATTCTTAT
Found at i:243263 original size:17 final size:17
Alignment explanation
Indices: 243243--243304 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
243233 CTTTTTGAAA
243243 TTCTTCTTTTTTTTCTT
1 TTCTTCTTTTTTTTCTT
*
243260 TTCTTCTATTCTTATT-TT
1 TTCTTCT-TT-TTTTTCTT
*
243278 TT-TTC-TTTTTGTCTT
1 TTCTTCTTTTTTTTCTT
243293 TTCTTTCTTTTT
1 TTC-TTCTTTTT
243305 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
14 3 0.08
15 6 0.17
17 13 0.36
18 10 0.28
19 4 0.11
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (17 bp):
TTCTTCTTTTTTTTCTT
Found at i:243595 original size:19 final size:20
Alignment explanation
Indices: 243558--243598 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
243548 GGGGTAATAA
243558 AATAAGTAAGGAAAAGAAAT
1 AATAAGTAAGGAAAAGAAAT
* *
243578 AATAAG-AATGAAATGAAAT
1 AATAAGTAAGGAAAAGAAAT
243597 AA
1 AA
243599 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (20 bp):
AATAAGTAAGGAAAAGAAAT
Found at i:244052 original size:19 final size:20
Alignment explanation
Indices: 244011--244061 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
244001 GAAACCCCTT
*
244011 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
244031 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
244050 TGAAGATACATG
1 TGAAAATACATG
244062 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:254138 original size:27 final size:25
Alignment explanation
Indices: 254082--254139 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
254072 AAAATAAAAC
* *
254082 TAAAAAATAATATATATTAATATAT
1 TAAAAAATAATATATATAAAAATAT
* *
254107 GAAAATAATAAGTATATATAAAAATTT
1 TAAAA-AATAA-TATATATAAAAATAT
254134 TAAAAA
1 TAAAAA
254140 GAATTATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 4 0.15
26 6 0.23
27 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
TAAAAAATAATATATATAAAAATAT
Found at i:254992 original size:3 final size:3
Alignment explanation
Indices: 254984--255010 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
254974 TACATGACTA
254984 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
255011 TAAATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:256394 original size:3 final size:3
Alignment explanation
Indices: 256388--256425 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
256378 AATAATAATA
256388 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
256426 GAAATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:273899 original size:20 final size:20
Alignment explanation
Indices: 273874--273917 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
273864 TCTAAGGCAT
273874 GATCATTGCAACTATACACA
1 GATCATTGCAACTATACACA
273894 GATCATTGCAACTATACACA
1 GATCATTGCAACTATACACA
273914 GATC
1 GATC
273918 CTCTTGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (20 bp):
GATCATTGCAACTATACACA
Found at i:276966 original size:16 final size:16
Alignment explanation
Indices: 276945--276982 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
276935 GTATTACCCA
276945 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
*
276961 ACCTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
276977 ACCTGT
1 ACCTGT
276983 AAATGATCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.39
Consensus pattern (16 bp):
ACCTGTTTTCAACCTG
Found at i:277023 original size:16 final size:15
Alignment explanation
Indices: 277004--277054 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 15
276994 CTTGTTAATG
277004 ACCTGATCTGATATTT
1 ACCTGA-CTGATATTT
277020 ACCTGACTTGATATTT
1 ACCTGAC-TGATATTT
*
277036 ACCTGACTTATATATT
1 ACCTGACTGATAT-TT
277052 ACC
1 ACC
277055 ATGATCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 6 0.19
16 26 0.81
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (15 bp):
ACCTGACTGATATTT
Found at i:277040 original size:32 final size:32
Alignment explanation
Indices: 276990--277054 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
276980 TGTAAATGAT
*
276990 CTGACTTGTTAATGACCTGATCTGATAT-TTAC
1 CTGACTTGATAATGACCTGA-CTGATATATTAC
* * *
277022 CTGACTTGATATTTACCTGACTTATATATTAC
1 CTGACTTGATAATGACCTGACTGATATATTAC
277054 C
1 C
277055 ATGATCGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (32 bp):
CTGACTTGATAATGACCTGACTGATATATTAC
Found at i:277560 original size:7 final size:7
Alignment explanation
Indices: 277527--277571 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
277517 GGTTTTAATA
*
277527 TTTAGTG
1 TTTAGGG
*
277534 TTTATGG
1 TTTAGGG
*
277541 TTTAGAG
1 TTTAGGG
277548 TTTAGGG
1 TTTAGGG
*
277555 TTTAGGA
1 TTTAGGG
277562 TTTAGGG
1 TTTAGGG
277569 TTT
1 TTT
277572 CTATAAACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:277660 original size:2 final size:2
Alignment explanation
Indices: 277655--277709 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
277645 TTATATAGTC
** **
277655 TA TA TA TA TA TA TA TA TA GC T- TA TA TA TA TA TA TA TA -A CC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
277695 TA TA TA TA TA CTA TA
1 TA TA TA TA TA -TA TA
277710 CATGGTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:277672 original size:21 final size:20
Alignment explanation
Indices: 277646--277709 Score: 85
Period size: 19 Copynumber: 3.1 Consensus size: 20
277636 TAATTTACTT
277646 TATATAGTCTATATATATATA
1 TATATAG-CTATATATATATA
277667 TATATAGCT-TATATATATA
1 TATATAGCTATATATATATA
*
277686 TATATAACCTATATATATACTA
1 TATAT-AGCTATATATATA-TA
277708 TA
1 TA
277710 CATGGTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 15 0.38
20 5 0.13
21 15 0.38
22 4 0.10
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATAGCTATATATATATA
Found at i:278835 original size:20 final size:20
Alignment explanation
Indices: 278810--278859 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
278800 ATTTATTCAA
278810 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
278830 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
278850 TGGTGCATCG
1 TGGTGCATCG
278860 GTGTATTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:281553 original size:23 final size:22
Alignment explanation
Indices: 281523--281604 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
281513 GCATGGCTTT
281523 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
281545 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
281567 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
281590 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
281605 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:281615 original size:44 final size:42
Alignment explanation
Indices: 281501--281623 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 42
281491 AAAACCCGAC
* *
281501 GGATGCATCGATGCA-TGGCTT-TGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-G-TTAAGTGTATCGATGCACATTCAA
* * *
281543 GGAGTGCATCGGTGCACCT-TCATGGTGTATCGATGCACATTCAAA
1 GGA-TGCATCGATGCA-CTGTTA-AGTGTATCGATGCACATTC-AA
281588 GGGATGCATCGATGCACTGTTAAGTGTATCGATGCA
1 -GGATGCATCGATGCACTGTTAAGTGTATCGATGCA
281624 TTAAGCACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
42 4 0.06
43 11 0.17
44 32 0.48
45 16 0.24
46 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTTAAGTGTATCGATGCACATTCAA
Found at i:285643 original size:117 final size:117
Alignment explanation
Indices: 285423--285643 Score: 286
Period size: 117 Copynumber: 1.9 Consensus size: 117
285413 CTTTCAAATC
* *
285423 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
* *
285488 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
* * * *
285540 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAAAAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAAAAT
* * * *
285603 TTCTTTTTGATTTTCTAAATCTAGTTTGGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCAGTTTCG-TTTCTAAAAGAA
285644 TATAATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 83 0.93
118 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:287021 original size:64 final size:64
Alignment explanation
Indices: 286951--287130 Score: 229
Period size: 65 Copynumber: 2.8 Consensus size: 64
286941 TGGAACACTT
* * * * *
286951 AGTGCATTGGTGCACTAAGTGTGCATCGATGCATAAAAGGCATTCGATGTTTTGAAT-AAGCCTA
1 AGTGCATCGATGCA-TAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
* * *
287015 AGTGCATCGATGCATGATGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCAT-AAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
*
287080 AGTGCATCGATGCAT-GGTATGTGCATCGATGCATAAAATGCATTCGATGTT
1 AGTGCATCGATGCATAAG--TGTGCATCGATGCATAAAATGCATTCGATGTT
287131 CAATTTATTC
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
63 2 0.02
64 49 0.48
65 52 0.50
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
Found at i:287116 original size:65 final size:64
Alignment explanation
Indices: 286970--287130 Score: 250
Period size: 65 Copynumber: 2.5 Consensus size: 64
286960 GTGCACTAAG
* * * *
286970 TGTGCATCGATGCATAAAAGGCATTCGATGTTTTGAATAAGCCTAAGTGCATCGATGCATGATG
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATGATA
* * *
287034 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATGGTA
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAT-AAACCTAAGTGCATCGATGCATGATA
287099 TGTGCATCGATGCATAAAATGCATTCGATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
287131 CAATTTATTC
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 35 0.39
65 54 0.61
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATGATA
Found at i:287525 original size:21 final size:21
Alignment explanation
Indices: 287496--287538 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
287486 TCCATTTACA
287496 TTAAGGTTT-GTGATTTAGGGT
1 TTAAGGTTTAG-GATTTAGGGT
* *
287517 TTAATGTTTAGGGTTTAGGGT
1 TTAAGGTTTAGGATTTAGGGT
287538 T
1 T
287539 ACAATTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.49
Consensus pattern (21 bp):
TTAAGGTTTAGGATTTAGGGT
Found at i:288641 original size:7 final size:7
Alignment explanation
Indices: 288601--288644 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
288591 TCCATTTATA
288601 TTAGGGT
1 TTAGGGT
* *
288608 TTATGAT
1 TTAGGGT
*
288615 TTAGGAT
1 TTAGGGT
*
288622 TTAAGGT
1 TTAGGGT
288629 TTAGGGT
1 TTAGGGT
288636 TTAGGGT
1 TTAGGGT
288643 TT
1 TT
288645 CTATAAACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:288951 original size:2 final size:2
Alignment explanation
Indices: 288944--288987 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
288934 TCATAGTTTT
**
288944 TA TA TA TA GG TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
288986 TA
1 TA
288988 CATGGTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:289098 original size:2 final size:2
Alignment explanation
Indices: 289091--289278 Score: 176
Period size: 2 Copynumber: 95.0 Consensus size: 2
289081 TTCTATAAAC
289091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
289133 TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA AA T- TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
289173 T- TA GT- TA TA CA TA TA TA TA TA CA CTA TA T- TA TA TA AA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
289213 TA -A TT TA TA AA CTA TA TA GTT TA TA CA TA TA TA GTT TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
289255 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
289279 AATAATTAAA
Statistics
Matches: 152, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
1 8 0.05
2 138 0.91
3 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:289530 original size:19 final size:20
Alignment explanation
Indices: 289490--289568 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 20
289480 AAATTTTCTA
289490 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
*
289510 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCCCAAT
289529 TTCCCTATACTCTTAAAATTTCCCAAT
1 TT-CC----CTC-T-AAATTTCCCAAT
289556 TTCCCTCTAAATT
1 TTCCCTCTAAATT
289569 CACAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 9 0.18
20 18 0.37
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 5 0.10
27 9 0.18
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:289712 original size:2 final size:2
Alignment explanation
Indices: 289646--289702 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
289636 ACTTTGAATA
*
289646 AT AT AT AT AT GT 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
289688 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
289703 AAAGTATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290182 original size:15 final size:14
Alignment explanation
Indices: 290162--290264 Score: 81
Period size: 13 Copynumber: 7.1 Consensus size: 14
290152 GTGAATATTT
290162 TATAGTTTATACATA
1 TATAGTTTATA-ATA
*
290177 TATAGTTTA-GATA
1 TATAGTTTATAATA
290190 TATAGTTTAT-ATA
1 TATAGTTTATAATA
290203 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
*
290218 CATTA-TTTAT-ATA
1 TA-TAGTTTATAATA
290231 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
290249 TATAGTTTATAATA
1 TATAGTTTATAATA
290263 TA
1 TA
290265 AATATAGTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 25
0.72 0.03 0.25
Matches are distributed among these distances:
12 3 0.04
13 27 0.37
14 6 0.08
15 21 0.29
16 6 0.08
17 3 0.04
18 7 0.10
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:290269 original size:18 final size:18
Alignment explanation
Indices: 290225--290283 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
290215 AAACATTATT
* *
290225 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
290243 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
290261 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
290278 TATAAA
1 TATAAA
290284 CTTATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 28 0.76
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:304505 original size:17 final size:17
Alignment explanation
Indices: 304483--304525 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
304473 TGATGAAAAG
304483 GGATAGACACTTGAGTA
1 GGATAGACACTTGAGTA
**
304500 GGATAGATGCTTGAGTA
1 GGATAGACACTTGAGTA
304517 GGATAGACA
1 GGATAGACA
304526 AAGATTACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (17 bp):
GGATAGACACTTGAGTA
Found at i:305416 original size:22 final size:22
Alignment explanation
Indices: 305389--305430 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
305379 AAACCATTCA
305389 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
305411 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
305431 GAGCAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:305797 original size:16 final size:16
Alignment explanation
Indices: 305776--305808 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
305766 CCCATTTATC
305776 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
305792 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
305808 A
1 A
305809 AAACCACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:308085 original size:21 final size:21
Alignment explanation
Indices: 308059--308098 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
308049 CAGAACCCCA
*
308059 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
308080 GGGGGGAATCGTTTCCCCT
1 GGGGGGAATCGATTCCCCT
308099 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:308127 original size:20 final size:20
Alignment explanation
Indices: 308081--308140 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
308071 TTCCCCTGTG
*
308081 GGGGGAATCGTTTCCCCTTCAA
1 GGGGGAATCGATT-CCC-TCAA
*
308103 AGGGGAATCTG-TTCCCTCAA
1 GGGGGAATC-GATTCCCTCAA
*
308123 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
308141 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.03
20 18 0.55
21 3 0.09
22 10 0.30
23 1 0.03
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:311193 original size:12 final size:13
Alignment explanation
Indices: 311168--311197 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
311158 AAAGGGATGT
311168 AACCAACGATATG
1 AACCAACGATATG
311181 AACCAAC-ATATG
1 AACCAACGATATG
311193 AACCA
1 AACCA
311198 GAGAGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.50, C:0.27, G:0.10, T:0.13
Consensus pattern (13 bp):
AACCAACGATATG
Found at i:312207 original size:20 final size:20
Alignment explanation
Indices: 312182--312219 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
312172 TAATTTTTCA
*
312182 ATATATTATTATTATTATAT
1 ATATATTATTAATATTATAT
312202 ATATATTATTAATATTAT
1 ATATATTATTAATATTAT
312220 TAAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTATTAATATTATAT
Found at i:312222 original size:9 final size:9
Alignment explanation
Indices: 312184--312226 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
312174 ATTTTTCAAT
312184 ATATTATTA
1 ATATTATTA
*
312193 TTATTATATA
1 ATATTAT-TA
312203 TATATTATTA
1 -ATATTATTA
312213 ATATTATTA
1 ATATTATTA
312222 A-ATTA
1 ATATTA
312227 ATATTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 4 0.13
9 16 0.53
10 4 0.13
11 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTATTA
Found at i:312230 original size:23 final size:22
Alignment explanation
Indices: 312181--312233 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
312171 TTAATTTTTC
* *
312181 AATA-TATTATTATTATTATAT
1 AATATTATTAATATTATTAAAT
312202 ATATATTATTAATATTATTAAATT
1 A-ATATTATTAATATTATTAAA-T
312226 AATATTAT
1 AATATTAT
312234 AAAACCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 21 0.78
24 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTATTAATATTATTAAAT
Done.