Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000891.1 Hibiscus syriacus cultivar Beakdansim tig00001743_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: 36672
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5872 original size:34 final size:35
Alignment explanation
Indices: 5828--5905 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
5818 CTTAAAATTT
* *
5828 TAATACATGCATCAT-ACATACATAT-ATACATACA
1 TAATATATGCAT-ATAACATACATATCATACACACA
**
5862 TAATATATGCATATAACATATGTATCATACACACA
1 TAATATATGCATATAACATACATATCATACACACA
5897 TCAATATAT
1 T-AATATAT
5906 TTTTATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 19 0.51
35 9 0.24
36 7 0.19
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (35 bp):
TAATATATGCATATAACATACATATCATACACACA
Found at i:7253 original size:28 final size:28
Alignment explanation
Indices: 7213--7266 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
7203 TCACTCTGAT
7213 TTGTTTTTTATTTGTGTTGATTTTGTGG
1 TTGTTTTTTATTTGTGTTGATTTTGTGG
7241 TTGTTTTTTATTTGTGTTGATTTTGT
1 TTGTTTTTTATTTGTGTTGATTTTGT
7267 TCAATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.07, C:0.00, G:0.22, T:0.70
Consensus pattern (28 bp):
TTGTTTTTTATTTGTGTTGATTTTGTGG
Found at i:7970 original size:24 final size:24
Alignment explanation
Indices: 7934--7981 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
7924 ACAAAGGAAA
7934 AAACACATATTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
* *
7958 AAACGCATGTTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
7982 TCCACACACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
AAACACATATTTCCTTCTTATTAT
Found at i:8333 original size:28 final size:28
Alignment explanation
Indices: 8292--8345 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
8282 TCACTCTGAT
8292 TTGTTTTTTATTTGTGTTGATTTTGTGG
1 TTGTTTTTTATTTGTGTTGATTTTGTGG
8320 TTGTTTTTGT-TTTGTGTTGATTTTGT
1 TTGTTTTT-TATTTGTGTTGATTTTGT
8346 TCAATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.06, C:0.00, G:0.24, T:0.70
Consensus pattern (28 bp):
TTGTTTTTTATTTGTGTTGATTTTGTGG
Found at i:14021 original size:15 final size:16
Alignment explanation
Indices: 14001--14030 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13991 AGTCTATGTA
14001 ATGCATGCAT-CATAC
1 ATGCATGCATACATAC
14016 ATGCATGCATACATA
1 ATGCATGCATACATA
14031 TCATAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (16 bp):
ATGCATGCATACATAC
Found at i:14191 original size:14 final size:13
Alignment explanation
Indices: 14137--14193 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
14127 GCATGTAATA
14137 TATATATTAGGGTT
1 TATAT-TTAGGGTT
*
14151 TATGTTTAGGGTT
1 TATATTTAGGGTT
*
14164 TAGTATTTATGGTT
1 TA-TATTTAGGGTT
*
14178 TAAATTGTAGGGTT
1 TATATT-TAGGGTT
14192 TA
1 TA
14194 GGGTTTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 13 0.36
14 23 0.64
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (13 bp):
TATATTTAGGGTT
Found at i:14293 original size:15 final size:15
Alignment explanation
Indices: 14273--14326 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 15
14263 TAATTTACTT
14273 TATATAGTTTATATA
1 TATATAGTTTATATA
14288 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
14305 TATATAGTTTATATA
1 TATATAGTTTATATA
14320 TACTATA
1 TA-TATA
14327 CATGGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.39
16 10 0.28
17 12 0.33
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:14302 original size:17 final size:17
Alignment explanation
Indices: 14273--14326 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
14263 TAATTTACTT
14273 TATATA-GTT-TATATA
1 TATATAGGTTATATATA
14288 TATATAGGTTATATATA
1 TATATAGGTTATATATA
*
14305 TATATAGTTTATATATA
1 TATATAGGTTATATATA
14322 CTATA
1 -TATA
14327 CATGGTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 6 0.17
16 3 0.09
17 22 0.63
18 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGGTTATATATA
Found at i:14334 original size:20 final size:20
Alignment explanation
Indices: 14297--14342 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14287 ATATATAGGT
*
14297 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
14316 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
14336 TACATAC
1 TATATAC
14343 ATATTATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:14566 original size:21 final size:21
Alignment explanation
Indices: 14517--14567 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
14507 ATTTTGCATG
*
14517 TTAGGGTTTAGGGTTAAGGAT
1 TTAGGGTTTAGGGTTAACGAT
* * *
14538 TAAAGGTTTAGGGTTCACGAT
1 TTAGGGTTTAGGGTTAACGAT
14559 TTAGGGTTT
1 TTAGGGTTT
14568 TTATACACTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.33, T:0.39
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTAACGAT
Found at i:14905 original size:19 final size:20
Alignment explanation
Indices: 14869--14906 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14859 AAATTTTTTA
*
14869 TTCCCTCTAAATTTCCCAAT
1 TTCCCTATAAATTTCCCAAT
14889 TTCCCTATAAA-TTCCCAA
1 TTCCCTATAAATTTCCCAA
14907 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (20 bp):
TTCCCTATAAATTTCCCAAT
Found at i:15096 original size:11 final size:13
Alignment explanation
Indices: 15050--15090 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
15040 TTATAGTTTA
15050 TACATATATAGTT
1 TACATATATAGTT
15063 TACATATATATAGTT
1 TAC--ATATATAGTT
15078 TACATATATAGTT
1 TACATATATAGTT
15091 CATATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
TACATATATAGTT
Found at i:15107 original size:28 final size:28
Alignment explanation
Indices: 15050--15115 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
15040 TTATAGTTTA
* * * *
15050 TACATATATAGTTTACATATATATAGTT
1 TACATATATAGTTCACATAAACATAATT
*
15078 TACATATATAGTTCATATAAACATAATT
1 TACATATATAGTTCACATAAACATAATT
*
15106 TATATATATA
1 TACATATATA
15116 ACTTATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (28 bp):
TACATATATAGTTCACATAAACATAATT
Found at i:15150 original size:18 final size:19
Alignment explanation
Indices: 15129--15164 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
15119 TATAATAATT
*
15129 ATATAGTTTATA-ATATAA
1 ATATAGGTTATATATATAA
15147 ATATAGGTTATATATATA
1 ATATAGGTTATATATATA
15165 GTTTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
ATATAGGTTATATATATAA
Found at i:15163 original size:13 final size:13
Alignment explanation
Indices: 15142--15175 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15132 TAGTTTATAA
*
15142 TATAAATATAGGT
1 TATATATATAGGT
*
15155 TATATATATAGTT
1 TATATATATAGGT
15168 TATATATA
1 TATATATA
15176 AACTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (13 bp):
TATATATATAGGT
Found at i:15174 original size:15 final size:15
Alignment explanation
Indices: 15041--15175 Score: 93
Period size: 15 Copynumber: 9.0 Consensus size: 15
15031 ATATACTTTT
*
15041 TATAGTTTATACATA
1 TATAGTTTATATATA
*
15056 TATAGTTTACATATA
1 TATAGTTTATATATA
*
15071 TATAG-TT-TACATA
1 TATAGTTTATATATA
* *
15084 TATAGTTCATATAAA
1 TATAGTTTATATATA
* *
15099 CATAATTTATATATA
1 TATAGTTTATATATA
*
15114 TA-A-CTTATAATAATTA
1 TATAGTTTAT-AT-A-TA
15130 TATAGTTTATAATATAAA
1 TATAGTTTAT-ATAT--A
*
15148 TATAG-GT-TATATA
1 TATAGTTTATATATA
15161 TATAGTTTATATATA
1 TATAGTTTATATATA
15176 AACTTATATT
Statistics
Matches: 93, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
13 19 0.20
14 7 0.08
15 45 0.48
16 6 0.06
17 3 0.03
18 13 0.14
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (15 bp):
TATAGTTTATATATA
Found at i:15175 original size:30 final size:30
Alignment explanation
Indices: 15128--15193 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
15118 TTATAATAAT
15128 TATATAGTTTATAATATAAA-TATAGGTTATA
1 TATATAGTTTATAATATAAACTATA--TTATA
15159 TATATAGTTTAT-ATATAAACTTATATTATA
1 TATATAGTTTATAATATAAAC-TATATTATA
15189 TATAT
1 TATAT
15194 TATATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
30 17 0.52
31 12 0.36
32 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (30 bp):
TATATAGTTTATAATATAAACTATATTATA
Found at i:16177 original size:42 final size:41
Alignment explanation
Indices: 16092--16421 Score: 464
Period size: 42 Copynumber: 7.8 Consensus size: 41
16082 TATACACCAA
* * *
16092 TAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTG
1 TAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACTG
* * * *
16136 TAAGGTTTATCCTTGCACACAGTAAAGGGACATGGTAAACTG
1 TAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACTG
16178 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACTG
16220 TAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACTG
*
16262 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTG
1 TAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACTG
16304 TAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTG
1 TAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACTG
* *
16346 TAAGGCTTACCCTTGCACATAGCAAAGGGACCTGGTAAACTG
1 TAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACTG
16388 TAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 TAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
16422 ATAATACTTC
Statistics
Matches: 263, Mismatches: 16, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
41 12 0.05
42 217 0.83
43 21 0.08
44 13 0.05
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (41 bp):
TAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACTG
Found at i:16238 original size:84 final size:84
Alignment explanation
Indices: 16092--16421 Score: 520
Period size: 84 Copynumber: 3.9 Consensus size: 84
16082 TATACACCAA
* * * * *
16092 TAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCACA
1 TAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCACA
* * *
16155 CAGTAAAGGGACATGGTAAACTG
62 CAGCAAAGGGACCTGGGAAACTG
*
16178 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTCGCACACAGC
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
16243 AAAGGGACCTGGGAAACTG
66 AAAGGGACCTGGGAAACTG
16262 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
16327 AAAGGGACCTGGGAAACTG
66 AAAGGGACCTGGGAAACTG
*
16346 TAAGGCTTACCCTTGCACATAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
16411 AAAGGGACCTG
66 AAAGGGACCTG
16422 ATAATACTTC
Statistics
Matches: 232, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
83 4 0.02
84 199 0.86
85 14 0.06
86 15 0.06
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (84 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAGC
AAAGGGACCTGGGAAACTG
Found at i:17328 original size:29 final size:30
Alignment explanation
Indices: 17296--17431 Score: 104
Period size: 29 Copynumber: 4.6 Consensus size: 30
17286 CTTTTTAAAA
17296 TAATTACCAAAATAGCACC-CTTTTCGAAT
1 TAATTACCAAAATAGCACCTCTTTTCGAAT
* **
17325 TAATTCCCAAAATAGCACCAATTTT-GAAT
1 TAATTACCAAAATAGCACCTCTTTTCGAAT
* * * *
17354 TGATT-CTC-AAATATCACCTTTTTTTCGAAA
1 TAATTAC-CAAAATAGCACC-TCTTTTCGAAT
* * *
17384 AAATTACCAAAATAACACC-CATTTCGAAT
1 TAATTACCAAAATAGCACCTCTTTTCGAAT
*
17413 TAA-TACCCAGAATAGCACC
1 TAATTA-CCAAAATAGCACC
17432 AAAATCAAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
28 12 0.14
29 51 0.61
30 11 0.13
31 10 0.12
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.30
Consensus pattern (30 bp):
TAATTACCAAAATAGCACCTCTTTTCGAAT
Found at i:17377 original size:28 final size:29
Alignment explanation
Indices: 17277--17432 Score: 102
Period size: 29 Copynumber: 5.4 Consensus size: 29
17267 CATTTTACAC
* * * *
17277 AAATAGTACC-TTTTTAAAATAATTACCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* *
17305 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCATTTTTGAATTAATTCCCA
* * *
17334 AAATAGCACCAATTTTGAATTGATTCTC-
1 AAATAGCACCATTTTTGAATTAATTCCCA
* * ** *
17362 AAATATCACCTTTTTTTCGAAAAAATTACCA
1 AAATAGCACC-ATTTTT-GAATTAATTCCCA
* * *
17393 AAATAACACCCA-TTTCGAATTAATACCCA
1 AAATAGCA-CCATTTTTGAATTAATTCCCA
*
17422 GAATAGCACCA
1 AAATAGCACCA
17433 AAATCAAATA
Statistics
Matches: 96, Mismatches: 27, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
28 21 0.22
29 56 0.58
30 10 0.10
31 7 0.07
32 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCATTTTTGAATTAATTCCCA
Found at i:17484 original size:5 final size:5
Alignment explanation
Indices: 17474--17513 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
17464 CAACGCTAAA
17474 CGGGT CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CG
1 CGGGT CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT CG
17514 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 27 0.84
8 5 0.16
ACGTcount: A:0.05, C:0.23, G:0.55, T:0.17
Consensus pattern (5 bp):
CGGGT
Found at i:22195 original size:174 final size:176
Alignment explanation
Indices: 21905--22254 Score: 686
Period size: 174 Copynumber: 2.0 Consensus size: 176
21895 TACCAGAAAT
21905 TGATTGCCACCATCTGAAGCTCTATTTCTTCAACATAGTTAGGGCCCCTTCAACTTCTGCTCAGG
1 TGATTGCCACCATCTGAAGCTCTATTTCTTCAACATAGTTAGGGCCCCTTCAACTTCTGCTCAGG
21970 TCTGAGGTCCATCTCATCCATAATCCTCTCTGTGTCCTCCAGCCAATACTCAACGTCTGTCGGAG
66 TCTGAGGTCCATCTCATCCATAATCCTCTCTGTGTCCTCCAGCCAATACTCAACGTCTGTCGGAG
22035 GTGCACCAGTAATA-CC-CGAATGGAATTACACCAGCAGCGACCAA
131 GTGCACCAGTAATACCCTCGAATGGAATTACACCAGCAGCGACCAA
22079 TGATTGCCACCATCTGAAGCTCTATTTCTTCAACATAGTTAGGGCCCCTTCAACTTCTGCTCAGG
1 TGATTGCCACCATCTGAAGCTCTATTTCTTCAACATAGTTAGGGCCCCTTCAACTTCTGCTCAGG
22144 TCTGAGGTCCATCTCATCCATAATCCTCTCTGTGTCCTCCAGCCAATACTCAACGTCTGTCGGAG
66 TCTGAGGTCCATCTCATCCATAATCCTCTCTGTGTCCTCCAGCCAATACTCAACGTCTGTCGGAG
22209 GTGCACCAGTAATACCCTCGAATGGAATTACACCAGCAGCGACCAA
131 GTGCACCAGTAATACCCTCGAATGGAATTACACCAGCAGCGACCAA
22255 AGAATTTGAA
Statistics
Matches: 174, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
174 144 0.83
175 2 0.01
176 28 0.16
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (176 bp):
TGATTGCCACCATCTGAAGCTCTATTTCTTCAACATAGTTAGGGCCCCTTCAACTTCTGCTCAGG
TCTGAGGTCCATCTCATCCATAATCCTCTCTGTGTCCTCCAGCCAATACTCAACGTCTGTCGGAG
GTGCACCAGTAATACCCTCGAATGGAATTACACCAGCAGCGACCAA
Found at i:23255 original size:42 final size:41
Alignment explanation
Indices: 23164--23494 Score: 457
Period size: 42 Copynumber: 7.8 Consensus size: 41
23154 CTATACACCA
* * *
23164 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* *
23208 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
23250 ATAAGGCTTACCCTTGCACACAGCAAAGGGACTTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
23292 GTAAGGCTTACCTTCGTACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
23334 GTAAGGCTTACCCTTACACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
23376 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
23418 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
23460 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
23495 ATAATACTTC
Statistics
Matches: 262, Mismatches: 18, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
41 12 0.05
42 213 0.81
43 23 0.09
44 14 0.05
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:23313 original size:84 final size:84
Alignment explanation
Indices: 23164--23494 Score: 513
Period size: 84 Copynumber: 3.9 Consensus size: 84
23154 CTATACACCA
* * * * *
23164 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
*
23227 ACAGCAAAGGGACCTGGTAAACT
62 ACAGCAAAGGGACCTGGGAAACT
* * * *
23250 ATAAGGCTTACCCTTGCACACAGCAAAGGGACTTGGGAAACTGTAAGGCTTACCTTCGTACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
23315 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
23334 GTAAGGCTTACCCTTACACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
23399 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
23418 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
23483 CAAAGGGACCTG
66 CAAAGGGACCTG
23495 ATAATACTTC
Statistics
Matches: 228, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
83 4 0.02
84 196 0.86
85 13 0.06
86 15 0.07
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:24370 original size:29 final size:29
Alignment explanation
Indices: 24334--24463 Score: 93
Period size: 29 Copynumber: 4.4 Consensus size: 29
24324 CATTTTACAC
24334 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
** *
24363 AAATAGCACCCTTTTCGAATTAATT-CCAA
1 AAATAGCACCCTTTTTAAAATAATTACC-A
** * * *
24392 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * * *
24421 GAATATCA-CTTTTTTGAAAAAAAAAATTACCA
1 AAATAGCACCCTTTTT----AAAATAATTACCA
24453 AAATAGCACCC
1 AAATAGCACCC
24464 ATTTCGAATT
Statistics
Matches: 77, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
28 7 0.09
29 52 0.68
30 2 0.03
32 15 0.19
33 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:24391 original size:28 final size:28
Alignment explanation
Indices: 24334--24418 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 28
24324 CATTTTACAC
* *
24334 AAATAGCACCCTTTTTAAAATAATTACC-A
1 AAATAGCACCC-TTTTGAATTAATT-CCAA
24363 AAATAGCACCCTTTTCGAATTAATTCCAA
1 AAATAGCACCCTTTT-GAATTAATTCCAA
*
24392 AAATAGCACCAATTTTGAATTAATTCC
1 AAATAGCACC-CTTTTGAATTAATTCC
24419 CAGAATATCA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.12
29 40 0.80
30 4 0.08
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (28 bp):
AAATAGCACCCTTTTGAATTAATTCCAA
Found at i:24462 original size:90 final size:90
Alignment explanation
Indices: 24350--24515 Score: 244
Period size: 90 Copynumber: 1.8 Consensus size: 90
24340 CACCCTTTTT
* * * * * * *
24350 AAAATAATTACCAAAATAGCACCCTTTTCGAATTAATTC-CAAAAATAGCACCAATTTTGAATTA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCTC-AAAATAACACAAATATCGAATAA
24414 ATTCCCAGAATATCACTTTTTTGAAA
65 ATTCCCAGAATATCACTTTTTTGAAA
*
24440 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCTCATAATAACACAAATATCGAATAAA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCTCAAAATAACACAAATATCGAATAAA
24505 TTCCCAGAATA
66 TTCCCAGAATA
24516 GCACCAGGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
90 66 0.99
91 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (90 bp):
AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCTCAAAATAACACAAATATCGAATAAA
TTCCCAGAATATCACTTTTTTGAAA
Found at i:24548 original size:13 final size:13
Alignment explanation
Indices: 24548--24584 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
24538 GTCAACGGGT
24548 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
24561 CGGTTCGGGTCAA
1 CGGGTCGGGTCAA
24574 CGGGTCGGGTC
1 CGGGTCGGGTC
24585 GTGACCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:24548 original size:18 final size:18
Alignment explanation
Indices: 24525--24585 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
24515 AGCACCAGGT
24525 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
24543 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
24561 C-GGT----TCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
24574 CGGGTCGGGTCG
1 CGGGTCGGGTCG
24586 TGACCGGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.26
14 3 0.08
17 3 0.08
18 22 0.58
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:25830 original size:30 final size:30
Alignment explanation
Indices: 25794--25861 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
25784 AGCAGACTTG
*
25794 TATCGCTCGTTCTACCATGAAGTCAGAGTT
1 TATCGCTCGTTATACCATGAAGTCAGAGTT
25824 TATCGCTCGTTATACCATGAAGTCAGAGTT
1 TATCGCTCGTTATACCATGAAGTCAGAGTT
25854 TATCGCTC
1 TATCGCTC
25862 TTGACTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (30 bp):
TATCGCTCGTTATACCATGAAGTCAGAGTT
Found at i:26274 original size:13 final size:13
Alignment explanation
Indices: 26256--26284 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26246 AGACTCATAG
26256 TGTATATTTTACC
1 TGTATATTTTACC
26269 TGTATATTTTACC
1 TGTATATTTTACC
26282 TGT
1 TGT
26285 CTATCCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (13 bp):
TGTATATTTTACC
Found at i:28110 original size:2 final size:2
Alignment explanation
Indices: 28103--28143 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28093 GGAAAAAGGG
28103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28144 ATGCAAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31568 original size:2 final size:2
Alignment explanation
Indices: 31561--31590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31551 GTAAACAGAA
31561 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
31591 TCATAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32506 original size:21 final size:21
Alignment explanation
Indices: 32482--32539 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
32472 GAAAATATTG
* **
32482 TTAATGTTGATGATTCTAATA
1 TTAATATTGATGATAATAATA
* *
32503 TTAATATCGATGATAATAATG
1 TTAATATTGATGATAATAATA
*
32524 TTAATATTGATCATAA
1 TTAATATTGATGATAA
32540 CGTGCATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (21 bp):
TTAATATTGATGATAATAATA
Found at i:34415 original size:18 final size:17
Alignment explanation
Indices: 34394--34437 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
34384 TATTTTTGTG
*
34394 TTTTTTGTATTTTTCTTC
1 TTTTTTGTAGTTTT-TTC
*
34412 TTTTTTCTAGTTTTTTC
1 TTTTTTGTAGTTTTTTC
34429 TTTTGTTGT
1 TTTT-TTGT
34438 TTTCTACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTTTGTAGTTTTTTC
Found at i:34429 original size:17 final size:18
Alignment explanation
Indices: 34394--34432 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34384 TATTTTTGTG
* *
34394 TTTTTTGTATTTTTCTTC
1 TTTTTTCTAGTTTTCTTC
34412 TTTTTTCTAGTTTT-TTC
1 TTTTTTCTAGTTTTCTTC
34429 TTTT
1 TTTT
34433 GTTGTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTCTAGTTTTCTTC
Done.