Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009172.1 Hibiscus syriacus cultivar Beakdansim tig00112730_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: 21639
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:153 original size:18 final size:18
Alignment explanation
Indices: 130--172 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
120 TCTTAGATTA
130 TTTATTTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
148 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
166 TTTATTT
1 TTTATTT
173 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:257 original size:30 final size:34
Alignment explanation
Indices: 221--297 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 34
211 CTACTATTAT
221 TTATTATTTTATTA-TTTTCCCTTTT-ATT-T-A
1 TTATTATTTTATTATTTTTCCCTTTTAATTATAA
* *
251 TTATTATTTTATTATTTTTTCTTTTTAATTATAA
1 TTATTATTTTATTATTTTTCCCTTTTAATTATAA
285 TTATTATTTTATT
1 TTATTATTTTATT
298 TTATTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 14 0.34
31 9 0.22
32 3 0.07
33 1 0.02
34 14 0.34
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (34 bp):
TTATTATTTTATTATTTTTCCCTTTTAATTATAA
Found at i:298 original size:31 final size:32
Alignment explanation
Indices: 221--299 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
211 CTACTATTAT
* *
221 TTATTATTTTATTATTTTCCCTTTTATTTATTA
1 TTATTATTTTATT-TTTTCCCTTTTAATTATAA
*
254 TTATT-TTATTATTTTTT-CTTTTTAATTATAA
1 TTATTATT-TTATTTTTTCCCTTTTAATTATAA
285 TTATTATTTTATTTT
1 TTATTATTTTATTTT
300 ATTATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 23 0.56
32 8 0.20
33 10 0.24
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (32 bp):
TTATTATTTTATTTTTTCCCTTTTAATTATAA
Found at i:8299 original size:221 final size:225
Alignment explanation
Indices: 7618--8329 Score: 1204
Period size: 221 Copynumber: 3.2 Consensus size: 225
7608 GTTATATTGT
*
7618 AAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
7682 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTC---ATAATATTTTATAAAATATC-AAACAAT-AA
*
7747 ATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
126 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
7812 AAAAAAATTGAAACATAAATTACATAACTTTAAAAA
191 AAAAAAATTGAAACATAAATTACATAACTTT-AAAA
*
7848 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
*
7913 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTC---ATAATATTTTATAAAATATCAAACAAT-AAA
*
7978 TAATTTTTTGTGTAAATGAAATT-CTAAA-TAATATTGTAGGTGGAAAACATGAAACACTATTAA
127 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
*
8041 AAAAAATTGAAACATAAATTACATAACTTTTAAA
192 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
8075 AAAGTATATATCATTTTTATAAAAGTG-CCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
*
8139 ATATTTGGTTAATATTGTTAAATTTAAATTC-TAATATTTTATAAAATATCAAA-AAT-AATAAT
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCATAATATTTTATAAAATATCAAACAATAAATAAT
8201 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
131 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
*
8266 ATTTGAAACATAAATTACATAACTTTAAAA
196 AATTGAAACATAAATTACATAACTTTAAAA
8296 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
8330 GTATAAAAGT
Statistics
Matches: 466, Mismatches: 12, Indels: 16
0.94 0.02 0.03
Matches are distributed among these distances:
219 25 0.05
220 4 0.01
221 97 0.21
222 28 0.06
226 65 0.14
227 30 0.06
228 65 0.14
229 4 0.01
230 77 0.17
231 71 0.15
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (225 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCATAATATTTTATAAAATATCAAACAATAAATAAT
TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
AATTGAAACATAAATTACATAACTTTAAAA
Found at i:8402 original size:20 final size:19
Alignment explanation
Indices: 8379--8423 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
8369 GATATACCAT
8379 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
8399 GTAACAAAATGATAAAACCG
1 GTAA-AAAATGATAAAACCG
8419 GTAAA
1 GTAAA
8424 TCGTTACCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:8580 original size:20 final size:19
Alignment explanation
Indices: 8557--8601 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
8547 CGATATAACA
8557 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
8577 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
8597 GGTAA
1 GGTAA
8602 TATGATACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:8608 original size:17 final size:19
Alignment explanation
Indices: 8563--8608 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
8553 AACAGGTAAA
8563 AATATGATAAAACCGGTATC
1 AATATGATAAAACCGG-ATC
*
8583 AAAATGATAAAACCGG-T-
1 AATATGATAAAACCGGATC
8600 AATATGATA
1 AATATGATA
8609 CCGGATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
20 15 0.62
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (19 bp):
AATATGATAAAACCGGATC
Found at i:10840 original size:21 final size:21
Alignment explanation
Indices: 10816--10859 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10806 AAGACAATCA
10816 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
10837 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
10858 AG
1 AG
10860 GCATAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:10933 original size:33 final size:33
Alignment explanation
Indices: 10891--10956 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
10881 AAATAGATGG
*
10891 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
10924 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
10957 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:12162 original size:4 final size:4
Alignment explanation
Indices: 12153--12177 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12143 TAAGAGATTG
12153 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
12178 AAAGGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:12778 original size:19 final size:19
Alignment explanation
Indices: 12754--12802 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12744 AATGTAGGGT
12754 TAATTTTGTATAAGATGTA
1 TAATTTTGTATAAGATGTA
* *
12773 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATGTA
*
12792 TATTTTTGTAT
1 TAATTTTGTAT
12803 GTGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATGTA
Found at i:13691 original size:198 final size:199
Alignment explanation
Indices: 12915--13886 Score: 1681
Period size: 198 Copynumber: 4.9 Consensus size: 199
12905 AATTTACAAT
* * *
12915 ATGGACAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAAC-C
1 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* *
12979 CTAAACCC-AAAGTATAATATAATATGTAATTTTTTCAATCTAACCGGTACAAGTATACCGGTTT
66 C-GAACCCAAAAGTATAATGTAATATGTAA-TTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
13043 TATGAGAGAATATGTCTAACTAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCA
129 TATGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCA
13108 GAATGA
194 GAATGA
13114 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
13179 CGAACCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
*
13244 TGAGAGAATATGTCTAAATAA-GTGTCGACACTTTTTTAG-TTGTGTCGATATTTTTGTTCCAGA
131 TGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGA
13307 ATGA
196 ATGA
*
13311 ATGGAAAACAGGGTGTAACCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAAACAT
1 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
13374 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
* * *
13439 TGAGAGAATATGTCTAAATAATGTGTCGACATTTTTTTAGTTTGTTTCGATATTTTTGTTCCAGA
131 TGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGA
13504 ATGA
196 ATGA
*
13508 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACAT
1 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* * *
13573 CGAACCCAAAAGTATAATGTAATATATAATTTTTCCATCTAACCGGTACAAGTATACCAGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
*
13638 TGAGAGAATA-GTCTAAATAATCTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGA
131 TGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGA
13702 ATGA
196 ATGA
*
13706 ATGGAAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
13771 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
66 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
* *
13836 TGAGAGAATATGTCTAAATAATTTGTCGACAC-GTTTTAGTTTGTGTCGATA
131 TGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
13887 CTAATTTAAA
Statistics
Matches: 738, Mismatches: 28, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
195 91 0.12
196 32 0.04
197 135 0.18
198 238 0.32
199 222 0.30
200 20 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
TGAGAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGA
ATGA
Found at i:15373 original size:24 final size:24
Alignment explanation
Indices: 15345--15415 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
15335 GGTCGCAGAA
15345 GATGAAACTGACGATGAAGATGAC
1 GATGAAACTGACGATGAAGATGAC
* *
15369 GATGATGA-TGACGATGATGATGAC
1 GATGA-AACTGACGATGAAGATGAC
15393 GAT-AAAGCTGACGATGAAGATGA
1 GATGAAA-CTGACGATGAAGATGA
15416 TGACGATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 37 0.93
25 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (24 bp):
GATGAAACTGACGATGAAGATGAC
Found at i:15377 original size:3 final size:3
Alignment explanation
Indices: 15357--15449 Score: 78
Period size: 3 Copynumber: 31.0 Consensus size: 3
15347 TGAAACTGAC
* * * * * * * *
15357 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAT GAT GAC GAT AAA GCT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * *
15405 GAT GAA GAT GAT GAC GAT GAT GAT GAG GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
15450 CCAAACAAGT
Statistics
Matches: 66, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:15426 original size:12 final size:12
Alignment explanation
Indices: 15353--15449 Score: 104
Period size: 12 Copynumber: 8.1 Consensus size: 12
15343 AAGATGAAAC
*
15353 TGACGATGAAGA
1 TGACGATGATGA
15365 TGACGATGATGA
1 TGACGATGATGA
15377 TGACGATGATGA
1 TGACGATGATGA
* * *
15389 TGACGATAAAGC
1 TGACGATGATGA
*
15401 TGACGATGAAGA
1 TGACGATGATGA
* *
15413 TGATGACGATGA
1 TGACGATGATGA
* *
15425 TGATGAGGATGA
1 TGACGATGATGA
*
15437 TGAAGATGATGA
1 TGACGATGATGA
15449 T
1 T
15450 CCAAACAAGT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 73 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:15444 original size:6 final size:6
Alignment explanation
Indices: 15342--15445 Score: 57
Period size: 6 Copynumber: 17.3 Consensus size: 6
15332 AGCGGTCGCA
* * * * *
15342 GAAGAT GAA-ACT GACGAT GAAGAT GACGAT GATGAT GACGAT GATGAT
1 GAAGAT GAAGA-T GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * * * * *
15390 GACGAT AAAGCT GACGAT GAAGAT GATGAC GATGAT GATGAG GATGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
15438 GAAGAT GA
1 GAAGAT GA
15446 TGATCCAAAC
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
5 1 0.01
6 74 0.97
7 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:16655 original size:16 final size:16
Alignment explanation
Indices: 16623--16656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16613 TATCCACAAC
* *
16623 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
16639 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
16655 AA
1 AA
16657 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:19817 original size:25 final size:25
Alignment explanation
Indices: 19789--19848 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
19779 TTATCATTAA
19789 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
19814 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
19839 ATTTAGGTAT
1 ATTTAGGTAT
19849 ACATCTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:20243 original size:22 final size:22
Alignment explanation
Indices: 20194--20265 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
20184 TAATAGTAAA
* *
20194 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTATCG-TT
20217 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
20239 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTA-TCGTT
20262 ATAT
1 ATAT
20266 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 19 0.42
23 26 0.58
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:20577 original size:25 final size:25
Alignment explanation
Indices: 20539--20588 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20529 AAATCAATTA
*
20539 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
20564 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
20589 GAAAAATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:20986 original size:18 final size:18
Alignment explanation
Indices: 20965--21001 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20955 GTAATTGGAG
20965 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
20983 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
21001 T
1 T
21002 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:21009 original size:24 final size:24
Alignment explanation
Indices: 20957--21003 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20947 TTTCATATGT
* *
20957 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
20981 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
21004 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:21306 original size:36 final size:37
Alignment explanation
Indices: 21236--21319 Score: 134
Period size: 36 Copynumber: 2.2 Consensus size: 37
21226 TCCGATGCTC
21236 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATA--GTGCCAAGCAAAAGGAA
*
21275 ATCAAAATCCAAATCTCATA-TGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATAGTGCCAAGCAAAAGGAA
21311 ATCAAAATC
1 ATCAAAATC
21320 TACAACTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 25 0.57
39 19 0.43
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (37 bp):
ATCAAAATCCAAAGCTCATAGTGCCAAGCAAAAGGAA
Done.