Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005362.1 Hibiscus syriacus cultivar Beakdansim tig00012180_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: 58880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1146 original size:32 final size:32
Alignment explanation
Indices: 1110--1227 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
1100 ATTCTAAGGA
1110 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* ***
1142 ACATATGGACAGTA-TACCTATGTTCTAAGGA-
1 ACATATGGACAGAATTACCTATG-TCTTTCGAG
1173 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
1205 ACATATGGAC--AATATACCTATGT
1 ACATATGGACAGAAT-TACCTATGT
1228 TCTAAGGAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
30 3 0.04
31 35 0.47
32 36 0.49
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:1189 original size:63 final size:63
Alignment explanation
Indices: 1090--1255 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
1080 AGAGTTGAGG
*
1090 GTATACCTATATTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1153 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
1216 ATATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTA
1256 GGTTCTTCGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:1280 original size:31 final size:31
Alignment explanation
Indices: 1093--1280 Score: 182
Period size: 31 Copynumber: 6.0 Consensus size: 31
1083 GTTGAGGGTA
* *
1093 TACCTATATTCTAAGGAACATATGGACAGAAT
1 TACCTATGTTCTAAGGAACATATGGACAG-TT
*** *
1125 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTT
*
1156 TACCTATGTTCTAAGGAACATATGGACAGAAT
1 TACCTATGTTCTAAGGAACATATGGACAG-TT
*** * *
1188 TACCTATG-TCTTTCGAGACATATGGACAATA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTT
1219 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTT
* ** *
1250 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTT
1281 GCCGAGGATC
Statistics
Matches: 125, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
31 77 0.62
32 48 0.38
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTT
Found at i:1318 original size:30 final size:30
Alignment explanation
Indices: 1267--1338 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1257 GTTCTTCGGA
* * *
1267 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
1297 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
1327 ACCTCTGGATAG
1 ACCTCTGGATAG
1339 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:8880 original size:22 final size:20
Alignment explanation
Indices: 8834--8896 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 20
8824 GAAATATTGC
8834 CCAGAGGGTACAGATA-CCCT
1 CCAGAGGGTAC-GATACCCCT
8854 CCAGAGGGTATCGATACCCACT
1 CCAGAGGGTA-CGATACCC-CT
8876 CCAGAGGGTACCGATACCCCT
1 CCAGAGGGTA-CGATACCCCT
8897 ATATGAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 14 0.36
21 5 0.13
22 20 0.51
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (20 bp):
CCAGAGGGTACGATACCCCT
Found at i:29072 original size:21 final size:22
Alignment explanation
Indices: 29043--29084 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29033 AAAAACTAAA
* *
29043 AAACTAAAAATATAAT-AATAG
1 AAACAAAAAAGATAATGAATAG
29064 AAACAAAAAAGATAATGAATA
1 AAACAAAAAAGATAATGAATA
29085 CGGTCAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (22 bp):
AAACAAAAAAGATAATGAATAG
Found at i:31094 original size:23 final size:22
Alignment explanation
Indices: 31015--31094 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
31005 GACGAAACGT
* *
31015 TAAATGAACATGTTGATGAACATA
1 TAAATGAACATGTTCACG-A-ATA
*
31039 TAAATGTAA-ATGTTCGCGAATA
1 TAAATG-AACATGTTCACGAATA
**
31061 TTAAACAAACATGTTCACGAATA
1 -TAAATGAACATGTTCACGAATA
31084 CTAAATGAACA
1 -TAAATGAACA
31095 AAACATAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
22 5 0.11
23 25 0.57
24 12 0.27
25 2 0.05
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (22 bp):
TAAATGAACATGTTCACGAATA
Found at i:31132 original size:30 final size:30
Alignment explanation
Indices: 31096--31154 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
31086 AAATGAACAA
*
31096 AACATAAACAACTTCAAAAATAAACAAACG
1 AACATAAACAACTTCAAAAACAAACAAACG
* * *
31126 AACATAAACCACTTTAAAAGCAAACAAAC
1 AACATAAACAACTTCAAAAACAAACAAAC
31155 TGATACAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.61, C:0.22, G:0.03, T:0.14
Consensus pattern (30 bp):
AACATAAACAACTTCAAAAACAAACAAACG
Found at i:31749 original size:23 final size:23
Alignment explanation
Indices: 31722--31768 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31712 AATTTTCGGA
*
31722 AAGATATATTA-ATATTTATAAAT
1 AAGATAT-TTATATATTTAGAAAT
*
31745 AAGATATTTATTTATTTAGAAAT
1 AAGATATTTATATATTTAGAAAT
31768 A
1 A
31769 TCATAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (23 bp):
AAGATATTTATATATTTAGAAAT
Found at i:32002 original size:29 final size:29
Alignment explanation
Indices: 31970--32025 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
31960 CCTAAAAGTA
31970 ATTTATATAAAATTAAAT-TTATAAATAGG
1 ATTTATATAAAA-TAAATATTATAAATAGG
* **
31999 ATTTTTATTTAATAAATATTATAAATA
1 ATTTATATAAAATAAATATTATAAATA
32026 AATATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTTATATAAAATAAATATTATAAATAGG
Found at i:32027 original size:13 final size:13
Alignment explanation
Indices: 32009--32033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31999 ATTTTTATTT
32009 AATAAATATTATA
1 AATAAATATTATA
32022 AATAAATATTAT
1 AATAAATATTAT
32034 TATATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAAATATTATA
Found at i:32062 original size:3 final size:3
Alignment explanation
Indices: 32054--32080 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32044 TATATGACTA
32054 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
32081 TAAATATATT
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:33468 original size:4 final size:4
Alignment explanation
Indices: 33459--33492 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
33449 TAATAATAAT
33459 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
33493 ATGAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:34056 original size:217 final size:221
Alignment explanation
Indices: 33704--34233 Score: 816
Period size: 217 Copynumber: 2.3 Consensus size: 221
33694 ACAAGATCTA
* *
33704 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTATTCTTCAGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
*
33769 TGAACTCTTCTGGAAATATTGACCATCAAAAGAGGTATTGTTAATTCAACTTCAATATGTGATGA
66 TGAACTCTTCTGGAAATATTGACCATCAAAAGAGGTATTGTTAATTCAACTTCAATATGTGATAA
33834 ATCAAATTAAGGTTG-AA-C-A-AGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGA
131 ATCAAATTAAGGTTGAAATCAAGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGA
33895 TCTATCTCCTTCTGTGATAGAGTCAT
196 TCTATCTCCTTCTGTGATAGAGTCAT
*
33921 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAAATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
*
33986 TGAACTCTTCTGGAAATATTGACCTTCAAAAGAGGTATTGTTAATTCAACTTCAATATGTGATAA
66 TGAACTCTTCTGGAAATATTGACCATCAAAAGAGGTATTGTTAATTCAACTTCAATATGTGATAA
34051 ATCAAATTAAGGTTGAACAAGTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGG
131 ATCAAATTAAGGTTG-A-AA-----------TCA-A-GAGTTCTTCTCATTATGAACACTTCTGG
34116 AAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
181 AAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
*
34157 GCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-T--TCTTCAGATGAGTTCTTCTCA
34222 TTATGAACTCTT
63 TTATGAACTCTT
34234 ATGAAAATGT
Statistics
Matches: 284, Mismatches: 7, Indels: 22
0.91 0.02 0.07
Matches are distributed among these distances:
217 140 0.49
220 2 0.01
232 1 0.00
234 1 0.00
236 107 0.38
237 1 0.00
239 32 0.11
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (221 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCTGGAAATATTGACCATCAAAAGAGGTATTGTTAATTCAACTTCAATATGTGATAA
ATCAAATTAAGGTTGAAATCAAGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGA
TCTATCTCCTTCTGTGATAGAGTCAT
Found at i:34296 original size:122 final size:122
Alignment explanation
Indices: 33853--34491 Score: 816
Period size: 122 Copynumber: 5.3 Consensus size: 122
33843 AGGTTGAACA
* *
33853 AGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
*
33918 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-T--TCTTCAAATG
66 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* * * * ****** * * *
33972 AGTTCTTCTCATTATGAACTCTTCTGGAAATATTGA-CCT--TCAAAAGAGGTAT-TGTTA-ATT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
* * * * *** * * *** *
34032 CAACTTCAATATG-TGATA-AATCAAAT-TAAGGT-TGAACAAGTTCTTCTTCTTCAGATG
66 C-A-TGCAAAAGGTTGA-ACAAGCTCTTCTCA-TTATGAACTTCTTCTTCCTCTTCAGATG
* *
34089 AGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
*
34154 CATGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
66 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* *
34211 AGTTCTTCTCATTATGAACTCTTATGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAAT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
*
34276 CAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
66 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
*
34333 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
* *
34398 CATGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTTAGATG
66 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
34455 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGAT
1 AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGAT
34492 TCATTGAATG
Statistics
Matches: 440, Mismatches: 64, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
114 13 0.03
115 14 0.03
116 12 0.03
117 43 0.10
118 4 0.01
119 34 0.08
120 12 0.03
121 13 0.03
122 295 0.67
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (122 bp):
AGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGT
CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
Found at i:34816 original size:22 final size:22
Alignment explanation
Indices: 34782--34888 Score: 169
Period size: 22 Copynumber: 4.9 Consensus size: 22
34772 AAATCCAATA
* * *
34782 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
34804 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
34826 AATCTATCATCTTTGGAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
34848 AATCTATCATCTTTGGAGAGAG
1 AATCTATCATCTTTGAAGAGAG
34870 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
34889 ATGTATCATC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 80 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:34848 original size:44 final size:43
Alignment explanation
Indices: 34782--34906 Score: 166
Period size: 44 Copynumber: 2.9 Consensus size: 43
34772 AAATCCAATA
* * *
34782 AATCTTTCTTCTTTGAAAAGAGAATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTG-AGAGAGAATCTATCATCTTTGAAGAGAG
*
34826 AATCTATCATCTTTGGAGAGAGAATCTATCATCTTTGGAGAGAG
1 AATCTATCATCTTT-GAGAGAGAATCTATCATCTTTGAAGAGAG
*
34870 AATCTATCATCTTT--GA-AGAATGTATCATCTTTGAAGA
1 AATCTATCATCTTTGAGAGAGAATCTATCATCTTTGAAGA
34907 ATGTAGATGT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
40 19 0.26
41 2 0.03
44 52 0.70
45 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (43 bp):
AATCTATCATCTTTGAGAGAGAATCTATCATCTTTGAAGAGAG
Found at i:34895 original size:18 final size:18
Alignment explanation
Indices: 34868--34911 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
34858 CTTTGGAGAG
*
34868 AGAATCTATCATCTTTGA
1 AGAATGTATCATCTTTGA
34886 AGAATGTATCATCTTTGA
1 AGAATGTATCATCTTTGA
34904 AGAATGTA
1 AGAATGTA
34912 GATGTAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (18 bp):
AGAATGTATCATCTTTGA
Found at i:35724 original size:18 final size:18
Alignment explanation
Indices: 35701--35738 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35691 TATATAAAAG
35701 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCGAA
35719 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCGAA
35737 AA
1 AA
35739 GATAAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCGAA
Found at i:36102 original size:11 final size:11
Alignment explanation
Indices: 36078--36134 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
36068 CATCTTGACC
36078 ATTTT-TTTTCT
1 ATTTTATTTT-T
36089 ATTTTATTTTT
1 ATTTTATTTTT
36100 ATTTTATTTGTT
1 ATTTTATTT-TT
36112 -TTATTATTTTTT
1 ATT-TTA-TTTTT
*
36124 GTTTTATTTTT
1 ATTTTATTTTT
36135 CTTCTTTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
11 22 0.54
12 14 0.34
13 5 0.12
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.81
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:36113 original size:15 final size:14
Alignment explanation
Indices: 36096--36133 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
36086 TCTATTTTAT
36096 TTTTATTTTATTTG
1 TTTTATTTTATTTG
*
36110 TTTTATTATTTTTTG
1 TTTTATT-TTATTTG
36125 TTTTATTTT
1 TTTTATTTT
36134 TCTTCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTTATTTTATTTG
Found at i:38459 original size:295 final size:295
Alignment explanation
Indices: 37929--38506 Score: 1111
Period size: 295 Copynumber: 2.0 Consensus size: 295
37919 ATAACATCTA
*
37929 CCATCTAGCCATTTTGCATGTTAAAGCCGATGATTACATTAAGAACTTTAAAGGATCAAGTCTAG
1 CCATCTAGCCATTTTGCATGTTAAAGCCAATGATTACATTAAGAACTTTAAAGGATCAAGTCTAG
37994 ATATCAGCCAAGTGGTATGATATAACATGTATTGTCTGAGTCTTCGAGTAACCCACACCAAGGTA
66 ATATCAGCCAAGTGGTATGATATAACATGTATTGTCTGAGTCTTCGAGTAACCCACACCAAGGTA
38059 CAACATAATTTTTGTATTAGTGGGTATCGAATTTCACAATCAGTAAACTTCTTACTCATATAATA
131 CAACATAATTTTTGTATTAGTGGGTATCGAATTTCACAATCAGTAAACTTCTTACTCATATAATA
*
38124 AATGGCTTTTTCTTTTCTTCCAGATTCATCATGCTGTCCCAGTACGCATCCCATCGAATTTTCAA
196 AATGGCTTTTTCTTTTCTTCCAGATTCACCATGCTGTCCCAGTACGCATCCCATCGAATTTTCAA
38189 AGACTGTCACGTAAAGAATTAACCCAGTACGCATC
261 AGACTGTCACGTAAAGAATTAACCCAGTACGCATC
*
38224 CCATCTAGCCATTTTGCATGTTAAAGCCAATGATTCCATTAAGAACTTTAAAGGATCAAGTCTAG
1 CCATCTAGCCATTTTGCATGTTAAAGCCAATGATTACATTAAGAACTTTAAAGGATCAAGTCTAG
38289 ATATCAGCCAAGTGGTATGATATAACATGTATTGTCTGAGTCTTCGAGTAACCCACACCAAGGTA
66 ATATCAGCCAAGTGGTATGATATAACATGTATTGTCTGAGTCTTCGAGTAACCCACACCAAGGTA
*
38354 CAACATAATTTTTGTATTGGTGGGTATCGAATTTCACAATCAGTAAACTTCTTACTCATATAATA
131 CAACATAATTTTTGTATTAGTGGGTATCGAATTTCACAATCAGTAAACTTCTTACTCATATAATA
38419 AATGGCTTTTTCTTTTCTTCCAGATTCACCATGCTGTCCCAGTACGCATCCCATCGAATTTTCAA
196 AATGGCTTTTTCTTTTCTTCCAGATTCACCATGCTGTCCCAGTACGCATCCCATCGAATTTTCAA
*
38484 AGACTGTCACGTAAATAATTAAC
261 AGACTGTCACGTAAAGAATTAAC
38507 GGTCTATCAG
Statistics
Matches: 278, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
295 278 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (295 bp):
CCATCTAGCCATTTTGCATGTTAAAGCCAATGATTACATTAAGAACTTTAAAGGATCAAGTCTAG
ATATCAGCCAAGTGGTATGATATAACATGTATTGTCTGAGTCTTCGAGTAACCCACACCAAGGTA
CAACATAATTTTTGTATTAGTGGGTATCGAATTTCACAATCAGTAAACTTCTTACTCATATAATA
AATGGCTTTTTCTTTTCTTCCAGATTCACCATGCTGTCCCAGTACGCATCCCATCGAATTTTCAA
AGACTGTCACGTAAAGAATTAACCCAGTACGCATC
Found at i:47482 original size:23 final size:23
Alignment explanation
Indices: 47455--47501 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
47445 AATTTTCGGA
*
47455 AAGATATATTA-ATATTTATAAAT
1 AAGATAT-TTATATATTTAGAAAT
*
47478 AAGATATTTATTTATTTAGAAAT
1 AAGATATTTATATATTTAGAAAT
47501 A
1 A
47502 TCATAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (23 bp):
AAGATATTTATATATTTAGAAAT
Found at i:47796 original size:3 final size:3
Alignment explanation
Indices: 47788--47826 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
47778 TATATGACTA
47788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47827 TAAATATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58289 original size:2 final size:2
Alignment explanation
Indices: 58282--58314 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
58272 ATTACAATTA
58282 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58315 ATCAAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58298 original size:15 final size:15
Alignment explanation
Indices: 58280--58310 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58270 TAATTACAAT
58280 TAATATATATATATA
1 TAATATATATATATA
58295 TAATATATATATATA
1 TAATATATATATATA
58310 T
1 T
58311 TATAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:58302 original size:13 final size:13
Alignment explanation
Indices: 58284--58314 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58274 TACAATTAAT
58284 ATATATATATATA
1 ATATATATATATA
58297 ATATATATATATA
1 ATATATATATATA
*
58310 TTATA
1 ATATA
58315 ATCAAAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Done.