Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001802.1 Hibiscus syriacus cultivar Beakdansim tig00003644_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: 65073
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1054 original size:52 final size:52
Alignment explanation
Indices: 976--1092 Score: 234
Period size: 52 Copynumber: 2.2 Consensus size: 52
966 GCACTCTTAG
976 TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTACACTTGA
1 TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTACACTTGA
1028 TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTACACTTGA
1 TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTACACTTGA
1080 TGCACCGATGCAC
1 TGCACCGATGCAC
1093 CTTGGGTATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (52 bp):
TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTACACTTGA
Found at i:8387 original size:28 final size:28
Alignment explanation
Indices: 8333--8411 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
8323 TTGGATTGAT
*
8333 TTTGATG-TTTCTGGATGTTT-AA---A
1 TTTGATGCTTTATGGATGTTTGAACTTA
*
8356 TTTGATGGTTGT-TGGATGTTTGAACTTA
1 TTTGATGCTT-TATGGATGTTTGAACTTA
* *
8384 TTTGTTGCTTTATGGATTTTTGAACTTA
1 TTTGATGCTTTATGGATGTTTGAACTTA
8412 ATATATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 7 0.15
24 11 0.24
25 3 0.07
27 1 0.02
28 24 0.52
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (28 bp):
TTTGATGCTTTATGGATGTTTGAACTTA
Found at i:9958 original size:61 final size:61
Alignment explanation
Indices: 9824--9949 Score: 191
Period size: 61 Copynumber: 2.1 Consensus size: 61
9814 ACGTGTTAGA
* * *
9824 AACCCTGCGAATGCGCGGATCACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
1 AACCCCGCGAAGGCGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
* *
9885 AACCCCGCGAAGGCGCGGATGACGATCCGCGCCTTTCCTTACGTGATGCCAGCTT-GGACAG
1 AACCCCGCGAAGGCGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAG-TTCGGACAG
9946 AACC
1 AACC
9950 TCTTGAAGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 57 0.97
62 2 0.03
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.19
Consensus pattern (61 bp):
AACCCCGCGAAGGCGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
Found at i:9964 original size:61 final size:61
Alignment explanation
Indices: 9824--9966 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 61
9814 ACGTGTTAGA
* * * *
9824 AACCCTGCGAATGCGCGGATCACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
1 AACCCCGCGAAGGAGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
* * *
9885 AACCCCGCGAAGGCGCGGATGACGATCCGCGCCTTTCCTTACGTGATGCCAGCTT-GGACAG
1 AACCCCGCGAAGGAGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAG-TTCGGACAG
* **
9946 AACCTCTTGAAGGAGCGGATG
1 AACCCCGCGAAGGAGCGGATG
9967 GTGATCAACG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 70 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (61 bp):
AACCCCGCGAAGGAGCGGATGACCATCCGCACCTTTCCTTACGTGATGCCAGTTCGGACAG
Found at i:12796 original size:216 final size:215
Alignment explanation
Indices: 12374--12980 Score: 913
Period size: 216 Copynumber: 2.8 Consensus size: 215
12364 CTTATTCATA
* * *
12374 TATTGAATAAAAAT-ATTTTTTATTATTTCAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* * *
12438 CGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTC--G-G-GTCG
66 CGGATGAAACTTTATTTTGTTCGGGTCGGGTC-GGTTTTTTTAAGTGTGATATTCGGGTGAGTCG
* * **
12499 GGTTGGGTTCGGGTTTATGGTGAAAAAAAATGGACCGACCCGAAAATATATATAATCCAGGTCGG
130 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATCCAGGTCGG
12564 GTCGGATTAAGTCACTGTTTT
195 GTCGGATTAAGTCACTGTTTT
**
12585 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTTAGATTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
*
12650 CGGATGAAACTTTATTTTGTTCGGGTCGGGTCGAG-TTTTTTAAGTATGATATTCGGGTCGAGTC
66 CGGATGAAACTTTATTTTGTTCGGGTCGGGTCG-GTTTTTTTAAGTGTGATATTCGGGT-GAGTC
* *
12714 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCG
129 GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATCCAGGTCG
12779 GGTCGGATTAAGTCACTGTTTT
194 GGTCGGATTAAGTCACTGTTTT
*
12801 TATTAAATAAGAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCAGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTC--G-
* * *
12866 CGAGTCGGATGAAACTTTATTTTATTCGGGTCGAGTCGGTTTTTTTAAGTGTGATATTCGGGTTA
63 -G-GTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTGA
12931 GGTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCGGACCGACCCGAAAA
126 -GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAA
12981 AAATAAATAA
Statistics
Matches: 360, Mismatches: 22, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
211 32 0.09
212 76 0.21
213 1 0.00
215 1 0.00
216 142 0.39
218 1 0.00
220 26 0.07
221 81 0.22
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (215 bp):
TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
CGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTGAGTCGG
GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATCCAGGTCGGG
TCGGATTAAGTCACTGTTTT
Found at i:13558 original size:18 final size:17
Alignment explanation
Indices: 13522--13567 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
13512 TATGGAATTG
13522 GATTCTAATT-CTTACA
1 GATTCTAATTCCTTACA
13538 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTT-ACA
*
13556 GATTCCAATTCC
1 GATTCTAATTCC
13568 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 14 0.52
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (17 bp):
GATTCTAATTCCTTACA
Found at i:13615 original size:12 final size:12
Alignment explanation
Indices: 13600--13624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13590 AAACGCCACC
13600 TCAAAGTTTACT
1 TCAAAGTTTACT
13612 TCAAAGTTTACT
1 TCAAAGTTTACT
13624 T
1 T
13625 GAGAAAAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCAAAGTTTACT
Found at i:14776 original size:13 final size:13
Alignment explanation
Indices: 14755--14785 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14745 TTTCCGACCA
*
14755 CGACCACTGCCAC
1 CGACAACTGCCAC
14768 CGACAACTGCCAC
1 CGACAACTGCCAC
14781 CGACA
1 CGACA
14786 TAGTTTCTAC
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:0.29, C:0.48, G:0.16, T:0.06
Consensus pattern (13 bp):
CGACAACTGCCAC
Found at i:26823 original size:8 final size:8
Alignment explanation
Indices: 26810--26837 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
26800 AGATTCTCCC
26810 ATATGTAT
1 ATATGTAT
26818 ATATGTAT
1 ATATGTAT
26826 ATATGTAT
1 ATATGTAT
26834 ATAT
1 ATAT
26838 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:30368 original size:9 final size:9
Alignment explanation
Indices: 30354--30382 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
30344 AGTGAAAATG
30354 AAAAATAAA
1 AAAAATAAA
30363 AAAAAT-AA
1 AAAAATAAA
30371 AAAAATAAA
1 AAAAATAAA
30380 AAA
1 AAA
30383 TGAAAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:31412 original size:53 final size:55
Alignment explanation
Indices: 31331--31487 Score: 210
Period size: 53 Copynumber: 2.9 Consensus size: 55
31321 CAACAATTAT
** *
31331 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGTAATTGA
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATCGA
* * * * * *
31386 TGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGT
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATCGA
*
31439 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATACAC
1 TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACAC
31488 GATTGTTGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 43 0.50
54 2 0.02
55 41 0.48
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACAATCGA
Found at i:31477 original size:55 final size:55
Alignment explanation
Indices: 31330--31508 Score: 238
Period size: 55 Copynumber: 3.3 Consensus size: 55
31320 CCAACAATTA
***
31330 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACGTAATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * * *
31385 ATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
31438 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
31493 TTGAAGA-TATTCGAGT
1 TTGAAGATTGTTCGAGT
31509 TCTATTCTCC
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
53 43 0.41
54 10 0.10
55 52 0.50
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:31681 original size:156 final size:156
Alignment explanation
Indices: 31492--31909 Score: 567
Period size: 156 Copynumber: 2.7 Consensus size: 156
31482 ATACACGATT
* *
31492 GTTGAAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATTT
1 GTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATTT
*
31556 CTAAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTGT-GAAGATATCCGAGTTCCATA
66 -TAAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATA
*
31619 CTCCTTAAAGAAAGAAGGGAGCGAACCC-
129 CTCCGTAAAGAAA-AAGGGAGCGAACCCA
* * * * **
31647 GTTGGAAGATGTTCGAGCTCTATACTCTTTAAAGAGAGAAAGAGCGAACCCGTAAGAAGAAGATT
1 GTT-GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGA-T
* * * * *
31712 TTTGAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCC-TGTCGAAGATGTTCGAGTTCTATA
64 TTTAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATA
31776 CTCCGTAAAGAAAAAGGGAGCGAACCCA
129 CTCCGTAAAGAAAAAGGGAGCGAACCCA
* * * * *
31804 GTTGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGTTTGCAGAAGATTT
1 GTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATTT
31869 TCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
66 T-AAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
31910 AGGCAAAAGA
Statistics
Matches: 227, Mismatches: 28, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
155 7 0.03
156 147 0.65
157 69 0.30
158 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (156 bp):
GTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAAGATTT
TAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTGTCGAAGATATCCGAGTTCCATACT
CCGTAAAGAAAAAGGGAGCGAACCCA
Found at i:31787 original size:51 final size:51
Alignment explanation
Indices: 31495--31907 Score: 345
Period size: 51 Copynumber: 7.9 Consensus size: 51
31485 CACGATTGTT
* * * *
31495 GAAGATATTCGAGTTCTATTCTCCTTAAAGAAAGAA-GGAGCGAACCC-GTTT
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAA-AAGGGAGCGAACCCTG-TC
* * * *
31546 GAAGA-GATTTCTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT-
1 GAAGATG--TTC-GAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCC-TGTC
* * * * *
31599 GAAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGGAGCGAACCC-GTTG
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAA-AAGGGAGCGAACCCTG-TC
* ** **
31651 GAAGATGTTCGAGCTCTATACTCTTTAAAGAGAGAAA--GAGCGAACCCGTAAGAA
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGA-A-AAAGGGAGCGAACCC-T--GTC
* * *
31705 GAAGATTTTTGAGTTCTATACTCCCTGAAGAAAAAGGGAGCGAACCCTGTC
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCTGTC
* * *
31756 GAAGATGTTCGAGTTCTATACTCCGTAAAGAAAAAGGGAGCGAACCCAGTT
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCTGTC
* * * *
31807 GAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCCGTTTGC
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCC-TGT-C
* * * *
31860 AGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
1 -GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCC
31908 GTAGGCAAAA
Statistics
Matches: 297, Mismatches: 44, Indels: 39
0.78 0.12 0.10
Matches are distributed among these distances:
50 1 0.00
51 125 0.42
52 49 0.16
53 39 0.13
54 81 0.27
55 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (51 bp):
GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCTGTC
Found at i:35046 original size:46 final size:45
Alignment explanation
Indices: 34962--35048 Score: 104
Period size: 46 Copynumber: 1.9 Consensus size: 45
34952 TATTTATCTC
* *
34962 TATTTTTTTTTTTGTGTTTTTGAAGCTCTCCTTTTAAAAATGGTT
1 TATTTTTTTTTTTGTGTTTTTGAAGATCTCCTTATAAAAATGGTT
* **
35007 TATTTTTTCTTTTTGTTTTTTTGTCGATC-CTCTTATAAAAAT
1 TATTTTTT-TTTTTGTGTTTTTGAAGATCTC-CTTATAAAAAT
35049 TATTGTGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
45 9 0.26
46 26 0.74
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (45 bp):
TATTTTTTTTTTTGTGTTTTTGAAGATCTCCTTATAAAAATGGTT
Found at i:47161 original size:14 final size:14
Alignment explanation
Indices: 47142--47170 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47132 TTACTATTAA
47142 ATCTGGAAAGTAAT
1 ATCTGGAAAGTAAT
47156 ATCTGGAAAGTAAT
1 ATCTGGAAAGTAAT
47170 A
1 A
47171 CCATGCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
ATCTGGAAAGTAAT
Found at i:56211 original size:19 final size:19
Alignment explanation
Indices: 56187--56224 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56177 TCAATGCACC
56187 TACTCGCATGATGTTGGAT
1 TACTCGCATGATGTTGGAT
56206 TACTCGCATGATGTTGGAT
1 TACTCGCATGATGTTGGAT
56225 GCCTCAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
TACTCGCATGATGTTGGAT
Found at i:58184 original size:23 final size:24
Alignment explanation
Indices: 58147--58216 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
58137 GTTGAGGGTT
58147 CTATGTGCTCATTTGGGA-AAAAC
1 CTATGTGCTCATTTGGGACAAAAC
* *
58170 CTATGTGGTCCTTTGGGACAAAAC
1 CTATGTGCTCATTTGGGACAAAAC
* * *
58194 ATATGTGTTCATTCGGGACAAAA
1 CTATGTGCTCATTTGGGACAAAA
58217 ATATATGGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (24 bp):
CTATGTGCTCATTTGGGACAAAAC
Found at i:58198 original size:24 final size:24
Alignment explanation
Indices: 58148--58234 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 24
58138 TTGAGGGTTC
* *
58148 TATGTGCTCATTTGGGA-AAAACC
1 TATGTGGTCATTTGGGACAAAACA
*
58171 TATGTGGTCCTTTGGGACAAAACA
1 TATGTGGTCATTTGGGACAAAACA
* *
58195 TATGTGTTCATTCGGGACAAAA-A
1 TATGTGGTCATTTGGGACAAAACA
* *
58218 TATATGGTCATTCGGGA
1 TATGTGGTCATTTGGGA
58235 TAAATATGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 31 0.56
24 24 0.44
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (24 bp):
TATGTGGTCATTTGGGACAAAACA
Found at i:65006 original size:24 final size:24
Alignment explanation
Indices: 64970--65015 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
64960 GTCGAGGGTT
* * *
64970 CTATGTGCTCCTTTGGGCAAAAAC
1 CTATGTGCACCTTCGGACAAAAAC
*
64994 CTATGTGGACCTTCGGACAAAA
1 CTATGTGCACCTTCGGACAAAA
65016 CTATGAGGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (24 bp):
CTATGTGCACCTTCGGACAAAAAC
Found at i:65028 original size:22 final size:24
Alignment explanation
Indices: 64989--65037 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
64979 CCTTTGGGCA
*
64989 AAAACCTATGTGGACCTTC-GGAC
1 AAAACCTATGAGGACCTTCGGGAC
*
65012 AAAA-CTATGAGGTCCTTCGGGAC
1 AAAACCTATGAGGACCTTCGGGAC
65035 AAA
1 AAA
65038 TATGTCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (24 bp):
AAAACCTATGAGGACCTTCGGGAC
Done.