Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004469.1 Hibiscus syriacus cultivar Beakdansim tig00009851_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: 63225
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:20117 original size:33 final size:33
Alignment explanation
Indices: 20050--20148 Score: 141
Period size: 33 Copynumber: 3.1 Consensus size: 33
20040 AAAGATGAAA
20050 AATAAGTTGGCCACCT-ACCAA-A-GAATTTTCC
1 AATAAGTTGGCCA-CTAACCAAGATGAATTTTCC
*
20081 AATAAGTTGGCCACTAACCAAGATGAATTTTTC
1 AATAAGTTGGCCACTAACCAAGATGAATTTTCC
* *
20114 AATAAGTTGGCCACCAACCAAGATGAAATTTCC
1 AATAAGTTGGCCACTAACCAAGATGAATTTTCC
20147 AA
1 AA
20149 CTTGCCAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.03
31 18 0.30
32 1 0.02
33 40 0.66
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (33 bp):
AATAAGTTGGCCACTAACCAAGATGAATTTTCC
Found at i:24815 original size:33 final size:33
Alignment explanation
Indices: 24748--24846 Score: 157
Period size: 33 Copynumber: 3.1 Consensus size: 33
24738 AAAGATGAAA
*
24748 AATAAGTTGGCCACCTACCAA-A-GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
24779 AATAAGTTGGCCACCAACCAAGATGAATTTTTC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
24812 AATAAGTTGGCCACCAACCAAGATGAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
24845 AA
1 AA
24847 CTTCCAAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 20 0.32
32 1 0.02
33 41 0.66
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:26868 original size:7 final size:7
Alignment explanation
Indices: 26856--26930 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
26846 TTAATATAAA
26856 AAAATAT
1 AAAATAT
26863 AAAATAT
1 AAAATAT
* *
26870 TATATAT
1 AAAATAT
*
26877 ATAAT-T
1 AAAATAT
* *
26883 AATATAAA
1 AAAAT-AT
26891 AAAATAT
1 AAAATAT
26898 AAAATAT
1 AAAATAT
* *
26905 TATATAT
1 AAAATAT
26912 AATTAATAT
1 AA--AATAT
26921 AAAATAT
1 AAAATAT
26928 AAA
1 AAA
26931 CTATTATATA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
6 4 0.08
7 36 0.72
8 4 0.08
9 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATAT
Found at i:26874 original size:35 final size:35
Alignment explanation
Indices: 26828--26944 Score: 190
Period size: 35 Copynumber: 3.5 Consensus size: 35
26818 CCCGAATCCG
26828 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
26863 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
26898 AAAATA-T-TATATATAATTAATAT---AAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
*
26928 AAACTATTATATATATA
1 AAAATATTATATATATA
26945 TATAATCGGG
Statistics
Matches: 79, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
30 12 0.15
31 1 0.01
32 8 0.10
33 16 0.20
34 1 0.01
35 41 0.52
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAAAAATAT
Found at i:32353 original size:145 final size:140
Alignment explanation
Indices: 32031--32354 Score: 486
Period size: 140 Copynumber: 2.3 Consensus size: 140
32021 AAGGCTTAAA
*
32031 ATGGCCCGAAGGACTTATCATTTTACTCGAAAGACATACAAATGACCCGAAGAATTTCACCATCA
1 ATGGCCCGAAGGACTTATCATTTTACTCGAAAGACTTACAAATGACCCGAAGAATTTCACCATCA
* *
32096 TGCTTGAAAGTCTTACTGATGGCCCGCAGGACTTACTATTTTTTTGTGAAAACATCCTACCCGAA
66 TGCTCGAAAGTCTTACTGATGGCCCGCAAGACTTACTATTTTTTTGTGAAAACATCCTACCCGAA
32161 GGTCTTATAG
131 GGTCTTATAG
* * *
32171 ATGGCCCAAAGGACTTATCATTTTTCTCGAAAGACTTACAAATGACCCGAAGGATTTCACCATCA
1 ATGGCCCGAAGGACTTATCATTTTACTCGAAAGACTTACAAATGACCCGAAGAATTTCACCATCA
* * *
32236 TGCTCGAAAGTCTTATTGATGGCCCGCAAGACTTACTAAATATTTTTTGTGTGAAGATATCCTAC
66 TGCTCGAAAGTCTTACTGATGGCCCGCAAGACTTAC----TATTTTTT-TGTGAAAACATCCTAC
*
32301 CCGAAGGTCTTATGG
126 CCGAAGGTCTTATAG
* * *
32316 ATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
1 ATGGCCCGAAGGACTTATCATTTTACTCGAAAGACTTAC
32355 TGATGTATTT
Statistics
Matches: 165, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
140 94 0.57
144 8 0.05
145 63 0.38
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (140 bp):
ATGGCCCGAAGGACTTATCATTTTACTCGAAAGACTTACAAATGACCCGAAGAATTTCACCATCA
TGCTCGAAAGTCTTACTGATGGCCCGCAAGACTTACTATTTTTTTGTGAAAACATCCTACCCGAA
GGTCTTATAG
Found at i:32470 original size:20 final size:20
Alignment explanation
Indices: 32423--32471 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
32413 TCATCATGCT
*
32423 CGAAAGACTTACTGATGGCC
1 CGAAAGATTTACTGATGGCC
32443 CGAAAGATTTACTGATGGCC
1 CGAAAGATTTACTGATGGCC
32463 CGAAAGATT
1 CGAAAGATT
32472 CTTAATCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (20 bp):
CGAAAGATTTACTGATGGCC
Found at i:33294 original size:215 final size:215
Alignment explanation
Indices: 32473--33827 Score: 1666
Period size: 225 Copynumber: 6.2 Consensus size: 215
32463 CGAAAGATTC
* * **
32473 TTAATCATCATGCTCGAAAGGCTTGTTGATGGCCCGAAGGACTTATAAAATGTGAAATGTT-GAA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT-AAATGTGAAATGTTGGAA
* * * *
32537 ATCGCATTCTTACTTTTCAAATATCTCATTTTCTTAAAACATCAC-TT-TCATTTTTCAAATTCA
65 ATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTTTTCAAATTCA
* * * * * *
32600 TGTCAAAACGTCTTACCCGAAGGTTTTATGGATGACCC-AAAGGACTTATCATATTGCTCTAAAG
130 TGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAA-GACTTATCATCTTGCTCAAAAG
*
32664 CCTTACAGATGACCCGAAGGAT
194 GCTTACAGATGACCCGAAGGAT
* * *
32686 TTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACTAAGTGTGAAATTTTGGAA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TAAATGTGAAATGTTGGAA
* * * *
32751 ACCGCCTTCTTAGTTTTCAAA-ATTTCATCTTCTTAAAACATTATTTTCTCA-TTTTCAAATTCA
65 ATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTTTTCAAATTCA
* * *
32814 CGTGAAAACATCTTACCCGAAGGTTTTATGGATGGCCCGAAAGACTTATAATCTTGCTCAAAAGG
130 TGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCAAAAGG
32879 CTTACAGATGACCCGAAGGAT
195 CTTACAGATGACCCGAAGGAT
* * * *
32900 TTAAGTATCATGCTCGAAAGACTTACTGATGGCTCGACGGACTTATAAATTTTGAAAATAGTTTA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA-TGTG-AAAT-G--T-
* * *
32965 CTAGGTAAGAAT-TCTTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCCTTT
60 -T-GG--A-AATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTT
* **
33029 TTCAAATTCATGTGAAAACATCTTACCCGAAGTTCTTATATATGGCCCGAAAGACTTATCATCTT
120 TTCAAATTCATGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTT
** *
33094 GCTTTAAAGGCTTACAGATAACCCGAAGGAT
185 GCTCAAAAGGCTTACAGATGACCCGAAGGAT
* * * *
33125 TTAAGCATCATGCTCGAAAGACTTACTGACGGCCTGAAGGACTTACTAAATGCGAAATGTT-GAG
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TAAATGTGAAATGTTGGAA
* *
33189 ATCGCCTTCTTACCTTTCAAAGATTTCATTTTCTTAAAACATAACTTTCTCATTTTTCAAATTCA
65 ATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTTTTCAAATTCA
* * * * * *
33254 TTTGAAAACATATTACCCGAAGGTATTATGGATGGCCCGAATGACTTATCGTCTTGCTCTAAAGG
130 TGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCAAAAGG
33319 CTTACAGATGACCCGAAGGAT
195 CTTACAGATGACCCGAAGGAT
* * * *
33340 TTAAGCATCATGCTCGAAAGACTTATTGATGGTCCGAAGGACTTACTAAGTGTGAAATTTTGGAA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA-TAAATGTGAAATGTTGGAA
* * * * * * * * *
33405 ATCGCCTTATTAGTTTTAAAAAATTTCCTCTTCTTAAAACATCATTTTCTCATTTTTCAAATTCT
65 ATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTTTTCAAATTCA
* * * *
33470 TGTGAAAACATCGTACCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTTAAAAGG
130 TGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCAAAAGG
* *
33535 CTTACAGATGGCCCGAATGAT
195 CTTACAGATGACCCGAAGGAT
* *
33556 TTAAACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA-TGT-GAAAT-G--T-
* * *
33621 CTAGGTCAGAAACG-TTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCAATT
60 -T-GG--A-AATCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTT
* * * *
33685 TTCAAATTCATGTGAAGACATCCTACCCGAAGGTCTTATGGATGGACCGAAGGACTTATCATCTT
120 TTCAAATTCATGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTT
*
33750 GCTCAAAAGGCTTATAGATGACCCGAAGGATTT
185 GCTCAAAAGGCTTACAGATGACCCGAAGGA--T
*
33783 TTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
1 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
33828 ACTTGTTAAC
Statistics
Matches: 986, Mismatches: 122, Indels: 54
0.85 0.10 0.05
Matches are distributed among these distances:
213 76 0.08
214 156 0.16
215 201 0.20
216 176 0.18
217 6 0.01
218 1 0.00
219 1 0.00
220 2 0.00
221 3 0.00
222 1 0.00
223 19 0.02
224 33 0.03
225 258 0.26
226 8 0.01
227 45 0.05
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (215 bp):
TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATGTGAAATGTTGGAAA
TCGCCTTCTTACTTTTCAAAGATTTCATTTTCTTAAAACATTACTTTCTCATTTTTCAAATTCAT
GTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCAAAAGGC
TTACAGATGACCCGAAGGAT
Found at i:33776 original size:41 final size:40
Alignment explanation
Indices: 33714--33827 Score: 104
Period size: 44 Copynumber: 2.7 Consensus size: 40
33704 ATCCTACCCG
*
33714 AAGGTCTTATGGATGGA-CCGAAGGACTTATCATCTTGCTCAA
1 AAGG-CTTAT-GAT-GACCCGAAGGACTTATCATCATGCTCAA
* *
33756 AAGGCTTATAGATGACCCGAAGGATTTTTAATCATCATGCTCGA
1 AAGGCTTAT-GATGACCCGAAGGA--CTT-ATCATCATGCTCAA
* *
33800 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTA-TGATGACCCGAAGGACTTA
33828 ACTTGTTAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
40 2 0.03
41 17 0.28
42 6 0.10
43 2 0.03
44 32 0.53
45 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (40 bp):
AAGGCTTATGATGACCCGAAGGACTTATCATCATGCTCAA
Found at i:35331 original size:125 final size:125
Alignment explanation
Indices: 35104--35359 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 125
35094 TCACTAGTGC
* * * *
35104 CCCCAACATTATCTTATACTAGTACGAGCCTTCAAAACGCCCCAACACCTCAAATTGTAAGGCTC
1 CCCCAACATTATCCTATACTAGTACGAGCCTTCAAAACACCCCAACACCACAAATTATAAGGCTC
** *
35169 ATTCTCAATGCATTCTTGGTCTGAATCTTGTCATCTCAACATGACGTGGGTTCAGTCGTA
66 ATTCTCAATGCATTCTTGGTCTGAATCTTGAAATCTCAACATGACATGGGTTCAGTCGTA
* * * * *
35229 CCCCTACATTATCCTATACTGGTACGGGCCTTCAAAATACCCCAATACCACAAATTATAAGGCTC
1 CCCCAACATTATCCTATACTAGTACGAGCCTTCAAAACACCCCAACACCACAAATTATAAGGCTC
* * * *
35294 ATTCTCAATGCCTTCTTGGTTTGAATCTTGAAATCTCAACATGATATGGGTTCAGTCGTG
66 ATTCTCAATGCATTCTTGGTCTGAATCTTGAAATCTCAACATGACATGGGTTCAGTCGTA
35354 CCCCAA
1 CCCCAA
35360 TGTGTATTCT
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
125 114 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (125 bp):
CCCCAACATTATCCTATACTAGTACGAGCCTTCAAAACACCCCAACACCACAAATTATAAGGCTC
ATTCTCAATGCATTCTTGGTCTGAATCTTGAAATCTCAACATGACATGGGTTCAGTCGTA
Found at i:38716 original size:13 final size:13
Alignment explanation
Indices: 38696--38733 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
38686 AAATGAATAC
38696 ATGC-AATGCAAA
1 ATGCAAATGCAAA
*
38708 ATGCAAATGCTAA
1 ATGCAAATGCAAA
38721 ATGCAAATGCAAA
1 ATGCAAATGCAAA
38734 GGGTGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (13 bp):
ATGCAAATGCAAA
Found at i:38717 original size:6 final size:6
Alignment explanation
Indices: 38696--38733 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
38686 AAATGAATAC
38696 ATGC-A ATGCAAA ATGCAA ATGCTAA ATGCAA ATGCAA A
1 ATGCAA ATGC-AA ATGCAA ATGC-AA ATGCAA ATGCAA A
38734 GGGTGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 15 0.50
7 11 0.37
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:39248 original size:177 final size:178
Alignment explanation
Indices: 38914--39280 Score: 485
Period size: 177 Copynumber: 2.1 Consensus size: 178
38904 TTTGATGATG
* *
38914 TCGGATGTCCTTAAATTGATTCTTGAAGTCTTCATTCTTACCTTCAATGCTAAGTGGTCTTCATG
1 TCGGATGTCCTTAAATTGATTCTTGAAGTCTCCATTCTTACCTTCAATGCTAAGTGGTATTCATG
* * ***
38979 TTTTTATGAAGGGTCTTCTCGTCCTTGGTATGGGTATATCTATCTTCTGAGTCAACATCTTGGCC
66 TCTCTATGAAGGGTCTTCTCGTCCTTGGTATGACCATATCTATCTTCTGAGTCAACATCTTGGCC
* * ** * *
39044 TTTGCACTTTTAAAGGAATTCTTCAATAGCTTCATATTTCTTCATTCA
131 TTTACACCTTTAAAAAAATTATTCAATAGCTTCAGATTTCTTCATTCA
*
39092 TCGGATGTCCTTAGATTG-TATCTTG-AGATC-CCATTCTTACC-TCAAATG-TGAAGTGGTATT
1 TCGGATGTCCTTAAATTGAT-TCTTGAAG-TCTCCATTCTTACCTTC-AATGCT-AAGTGGTATT
* * *
39152 CATGTCTCTATGAAGGGTCTTTTCGTCCTTGGTATGACCGTATCTATC-TCTTTAGTCAACATCT
62 CATGTCTCTATGAAGGGTCTTCTCGTCCTTGGTATGACCATATCTATCTTC-TGAGTCAACATCT
39216 TGGCCTTTACACCTTTAAAAAAATTATTCAATAGCTTCAGATTTCTTCATTCA
126 TGGCCTTTACACCTTTAAAAAAATTATTCAATAGCTTCAGATTTCTTCATTCA
*
39269 TCAGATGTCCTT
1 TCGGATGTCCTT
39281 CTCCATGGAT
Statistics
Matches: 166, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
176 5 0.03
177 137 0.83
178 24 0.14
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (178 bp):
TCGGATGTCCTTAAATTGATTCTTGAAGTCTCCATTCTTACCTTCAATGCTAAGTGGTATTCATG
TCTCTATGAAGGGTCTTCTCGTCCTTGGTATGACCATATCTATCTTCTGAGTCAACATCTTGGCC
TTTACACCTTTAAAAAAATTATTCAATAGCTTCAGATTTCTTCATTCA
Found at i:50202 original size:18 final size:19
Alignment explanation
Indices: 50167--50203 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
50157 CACGGAATGT
50167 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
50187 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
50204 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:52201 original size:12 final size:11
Alignment explanation
Indices: 52175--52218 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
52165 AATGAAGAAT
52175 AAAAATAAAAA
1 AAAAATAAAAA
*
52186 AAAAATAAAAGG
1 AAAAATAAAA-A
52198 AAAAATAAATAA
1 AAAAATAAA-AA
*
52210 ATAAATAAA
1 AAAAATAAA
52219 TGAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.36
12 17 0.61
13 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:52300 original size:5 final size:5
Alignment explanation
Indices: 52274--52311 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
52264 CATAACAATA
52274 ATAAT AGTAAT ATAA- A-AAT ATAAT ATAAT ATAAT ATAA
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
52312 AAAAACCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 21 0.70
6 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:52304 original size:18 final size:19
Alignment explanation
Indices: 52259--52306 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
52249 ATAAAAAATA
*
52259 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
52279 AGTAATATAAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
52298 ATAATATAA
1 ATAATATAA
52307 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
20 8 0.31
21 4 0.15
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:52599 original size:23 final size:24
Alignment explanation
Indices: 52568--52616 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
52558 ACCAAATGAA
52568 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
52591 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
52615 TA
1 TA
52617 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:53119 original size:37 final size:36
Alignment explanation
Indices: 53078--53182 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 36
53068 GTGCTTGTGG
* *
53078 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
53115 ATCCTATTTTAAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTT-AGGAGTTTGAATCCTAGTAGAACTCT
53152 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
53183 GACGAAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 3 0.05
37 52 0.88
38 4 0.07
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:54221 original size:106 final size:107
Alignment explanation
Indices: 53910--55598 Score: 2422
Period size: 106 Copynumber: 16.0 Consensus size: 107
53900 GCATTGTTCT
* * * ** * * *
53910 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTTTGGAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * * * *
53974 ACCAGCCGTCCCTTCATTGTAAAGTTGAACTTGTGTTGTC-TC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
54016 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
54075 TCAGTC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* *
54117 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54181 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * *
54222 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
54287 CCAGTGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
54328 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54393 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
54434 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54499 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
54540 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
54605 CTAGCGATACCTTCAG-CGTGAAGTTGAACTTGCATTGTC-TG
66 CCAGCGGTCCCTTC-GTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
54646 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG-TGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54710 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* *
54751 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54816 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * *
54857 GAGTCCAATATCCTACGCTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
54922 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * * *
54963 GAGTCTAATAT-CTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
55027 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTC-TA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
*
55068 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
55133 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
*
55174 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
55239 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * * *
55280 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
55345 CCAGCGGTCCCTTCGTTGTTAATTTGAACTTGCATTG-CCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
55386 GAGTCCAATAGCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
55451 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
* * * *
55492 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
55557 CTAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
55599 AGTGGCACGA
Statistics
Matches: 1432, Mismatches: 126, Indels: 49
0.89 0.08 0.03
Matches are distributed among these distances:
100 76 0.05
101 6 0.00
102 4 0.00
104 4 0.00
105 198 0.14
106 1136 0.79
107 8 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (107 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
Found at i:56416 original size:21 final size:22
Alignment explanation
Indices: 56375--56443 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
56365 TTATGTTTGG
56375 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
56397 TCAAAGGTTTGGCA-TTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
56418 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
56440 TCAA
1 TCAA
56444 CGATTTGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.45
22 24 0.55
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:60741 original size:19 final size:19
Alignment explanation
Indices: 60708--60744 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
60698 TGCAGATGAT
60708 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
60727 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
60745 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:61849 original size:12 final size:12
Alignment explanation
Indices: 61832--61886 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
61822 AATGAAGAAT
*
61832 AAAAATAAGTAA
1 AAAAATAAATAA
*
61844 AAAAATAAA-AGG
1 AAAAATAAATA-A
61856 AAAAATAAATAA
1 AAAAATAAATAA
*
61868 ATAAATAAATAA
1 AAAAATAAATAA
*
61880 ATAAATA
1 AAAAATA
61887 TATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 1 0.03
12 35 0.95
13 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:61867 original size:4 final size:4
Alignment explanation
Indices: 61858--61886 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
61848 ATAAAAGGAA
61858 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
61887 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:62017 original size:29 final size:30
Alignment explanation
Indices: 61949--62033 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 30
61939 TAATAATAGT
61949 AATATGAAAATATAAATAATATAAAAAACCA
1 AATAT-AAAATATAAATAATATAAAAAACCA
* *
61980 AA-ACCAAAA-ATAAATAA-ATATATAAACCA
1 AATA-TAAAATATAAATAATATA-AAAAACCA
*
62009 AATATAAAAGTATATATAATGATAA
1 AATATAAAA-TATAAATAAT-ATAA
62034 TTGGCTTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
28 3 0.07
29 21 0.49
30 6 0.14
31 9 0.21
32 1 0.02
33 3 0.07
ACGTcount: A:0.66, C:0.07, G:0.04, T:0.24
Consensus pattern (30 bp):
AATATAAAATATAAATAATATAAAAAACCA
Found at i:62258 original size:23 final size:24
Alignment explanation
Indices: 62227--62275 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
62217 AACCAATGAA
62227 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
62250 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
62274 TA
1 TA
62276 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:62778 original size:37 final size:36
Alignment explanation
Indices: 62737--62840 Score: 120
Period size: 36 Copynumber: 2.8 Consensus size: 36
62727 GTGCTTGTGG
* *
62737 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
62774 ATCCTATTTAAGGAGTTTGAATCCTA-TCAAAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGT-AGAACTCT
*
62810 ATCTTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
62841 GACGAAAGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.02
36 27 0.48
37 27 0.48
38 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTCT
Done.