Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003165.1 Hibiscus syriacus cultivar Beakdansim tig00006660_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: 47626
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2246 original size:6 final size:6
Alignment explanation
Indices: 2235--2271 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2225 GACACGTATT
*
2235 ACCACG ACCACG ACCATG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2272 GCCGAGCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.46, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:11777 original size:11 final size:11
Alignment explanation
Indices: 11761--11823 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
11751 AAAATTACAT
11761 TATTAAAAATA
1 TATTAAAAATA
11772 TATTAAAAATA
1 TATTAAAAATA
* * ***
11783 CACTATTGATA
1 TATTAAAAATA
11794 -ATTATAAAAT-
1 TATTA-AAAATA
11804 T-TTAAAAATA
1 TATTAAAAATA
11814 TATTAAAAAT
1 TATTAAAAAT
11824 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:12364 original size:21 final size:22
Alignment explanation
Indices: 12318--12370 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
12308 TCTTTGTAAT
* *
12318 GAACCTTGAATCCTAAACTTTA
1 GAACCTTAAACCCTAAACTTTA
12340 -AACCTTAAACCCTAAAC-TTA
1 GAACCTTAAACCCTAAACTTTA
*
12360 GAACCCTAAAC
1 GAACCTTAAAC
12371 TTTGTAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.42, C:0.28, G:0.06, T:0.25
Consensus pattern (22 bp):
GAACCTTAAACCCTAAACTTTA
Found at i:12371 original size:14 final size:13
Alignment explanation
Indices: 12338--12372 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
12328 TCCTAAACTT
12338 TAAACCTTAAACCC
1 TAAA-CTTAAACCC
12352 TAAACTTAGAACCC
1 TAAACTTA-AACCC
12366 TAAACTT
1 TAAACTT
12373 TGTAACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.43, C:0.29, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAACTTAAACCC
Found at i:13454 original size:29 final size:28
Alignment explanation
Indices: 13389--13454 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
13379 TAAAAAATAA
*
13389 AGATAAGAAATAAAAGTAAAAATGAAAT
1 AGATAAAAAATAAAAGTAAAAATGAAAT
* *
13417 AGAGGAAAAAATAAAAAGGTAAATA-GAAAT
1 AGA-TAAAAAAT-AAAA-GTAAAAATGAAAT
13447 AGATAAAA
1 AGATAAAA
13455 TAGAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.10
29 10 0.32
30 12 0.39
31 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (28 bp):
AGATAAAAAATAAAAGTAAAAATGAAAT
Found at i:13811 original size:23 final size:23
Alignment explanation
Indices: 13710--13815 Score: 58
Period size: 23 Copynumber: 4.6 Consensus size: 23
13700 AAAATGTTTT
*
13710 AAAAATAATAATAAATTTAAAAAAGA
1 AAAAATAATAAT-AA--TAATAAAGA
*
13736 TAAAAA-AATAA-AACATATAAA-A
1 -AAAAATAATAATAATA-ATAAAGA
* * * *
13758 GATAATAATAATAATAATGAAGT
1 AAAAATAATAATAATAATAAAGA
* * *
13781 ATATATAATAATAATAGTAAAGA
1 AAAAATAATAATAATAATAAAGA
13804 AAAAATAA-AATA
1 AAAAATAATAATA
13816 TAAAAATTTT
Statistics
Matches: 59, Mismatches: 16, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
21 3 0.05
22 15 0.25
23 29 0.49
24 2 0.03
26 5 0.08
27 5 0.08
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.25
Consensus pattern (23 bp):
AAAAATAATAATAATAATAAAGA
Found at i:14265 original size:37 final size:37
Alignment explanation
Indices: 14159--14266 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
14149 TTATGGATCA
* *
14159 TATTTTTAGGAGTTTGAATCTTAGTAAAACTCCATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
14196 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
14233 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
14267 ACGTTATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
Found at i:15039 original size:84 final size:83
Alignment explanation
Indices: 14926--15501 Score: 600
Period size: 83 Copynumber: 6.9 Consensus size: 83
14916 GGTTTCCTCT
* * *
14926 AAGCTGAGTGTAATCGAACTCTAAGGTCTTTGGTTGGTAGATAACCATTCTAGCCTTGAGTTATG
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* *
14991 CTACAAATGATGTGCCTTG
65 TTGCAAATGATGTGCCTTG
* * * * * * * * *
15010 AAGCTGAGCGTAGTCGAACGCGAAGGTCTTTGGTTGGCAGATAGCCCTTATCGACTTAAGCTATG
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
15075 TTGCAAATGATGTGCCTATG
65 TTGCAAATGATGTGCCT-TG
* * *
15095 -AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAAACCTTCTAGCCTTGAGTTATGC
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGT
* *
15159 TGTAAATGATGCGCCTTG
66 TGCAAATGATGTGCCTTG
* ** * * * * * * * * * *
15177 GAGCTGAGCATAATCAAACTCGAAGGTATTTAGTTGTCAAATAGCCTTTCTCGACTTAAGCTATG
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* *
15242 CTGCAAATGATGTTCCTTTG
65 TTGCAAATGATGTGCC-TTG
* * * *
15262 AA-CTGAGTGTAATTGAACTTGAAGGTCTTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATGT
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGT
*
15326 TGTAAATGATGTGCCTTG
66 TGCAAATGATGTGCCTTG
* * * * * *
15344 CAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTTTGGCAGATAAACCTTCTAGCCTTGAGTTATGT
1 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGT
*
15409 TGTAAATGATGTGCCTT-
66 TGCAAATGATGTGCCTTG
* * * * * *
15426 AGAGCTGAGTGTAGTCGAACTCGAAGGTATTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTAT
1 A-AGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
15491 GTTGCAAATGA
64 GTTGCAAATGA
15502 ACACGATATC
Statistics
Matches: 405, Mismatches: 80, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
82 6 0.01
83 199 0.49
84 194 0.48
85 6 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (83 bp):
AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGT
TGCAAATGATGTGCCTTG
Found at i:15233 original size:167 final size:164
Alignment explanation
Indices: 14927--15501 Score: 668
Period size: 167 Copynumber: 3.4 Consensus size: 164
14917 GTTTCCTCTA
* ** *
14927 AGCTGAGTGTAATCGAACTCTAAGGTCTTTGGTTGGTAGAT-AACCATTCTAGCCTTGAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGACAAATAAACC-TTCTAGCCTTGAGTTATG
* * *
14991 CTACAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACGCGAAGGTCTTTGGTTGGCAGATAGCC
64 CTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT-TTTAGTTGGCAGATAG-C
*
15056 CTTATCGACTTAAGCTATGTTGCAAATGATGTGCCTATG
127 CTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCT-TG
*
15095 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAAACCTTCTAGCCTTGAGTTATGCT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAAACCTTCTAGCCTTGAGTTATGCT
* * * * * * * *
15160 GTAAATGATGCGCCTTGGAGCTGAGCATAATCAAACTCGAAGGTATTTAGTTGTCAAATAGCCTT
66 GCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT-TTTAGTTGGCAGATAGCC-T
* *
15225 TCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTTG
129 TCTCGACTTAAGCTATGTTGCAAATGATGTGCC-TTG
* * * * *
15262 AACTGAGTGTAATTGAACTTGAAGGTCTTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATGTT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAAACCTTCTAGCCTTGAGTTATGCT
* * ** *
15327 GTAAATGATGTGCCTTGCAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTTTGGCAGATAAACCTT
66 GCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTTTTAGTTGGCAGAT-AGCCTT
* * * * *
15392 CTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTAG
130 CTCGACTTAAGCTATGTTGCAAATGATGTGCCTT-G
* * * * *
15428 AGCTGAGTGTAGTCGAACTCGAAGGTATTTTGTTGGA-AAATAACCCTTCTTGCCTTGAGCTATG
1 AGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTT-GACAAATAAACCTTCTAGCCTTGAGTTATG
*
15492 TTGCAAATGA
64 CTGCAAATGA
15502 ACACGATATC
Statistics
Matches: 351, Mismatches: 49, Indels: 15
0.85 0.12 0.04
Matches are distributed among these distances:
165 2 0.01
166 62 0.18
167 251 0.72
168 36 0.10
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (164 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAAATAAACCTTCTAGCCTTGAGTTATGCT
GCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTTTTAGTTGGCAGATAGCCTTC
TCGACTTAAGCTATGTTGCAAATGATGTGCCTTG
Found at i:15363 original size:250 final size:251
Alignment explanation
Indices: 14876--15501 Score: 668
Period size: 250 Copynumber: 2.5 Consensus size: 251
14866 AATTTTATTA
* * * * * **
14876 ACAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAAT-TTGGGTTTCCTCTA-AGCTGAGTGTAA
1 ACAGATAAACCTTCTAGCCTTGAGTTATGCTGTAAATGATGCG---CCT-TAGAGCTGAGCATAA
* * * * * * * * * * * *
14939 TCGAACTCTAAGGTCTTTGGTTGGTAGATAACCATTCTAGCCTTGAGTTATGCTACAAATGATGT
62 TCAAACTCGAAGGTATTTAGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * * *
15004 GCCTTGAAGCTGAGCGTAGTCGAACGCGAAGGTCTTTGGTTGGCAGATAGCCCTTATCGACTTAA
127 GCCTTGAAGCTGAGCGTAATCGAACGCGAAGGTCTTTGGTTGACAAATAACCCTTATAGACTTAA
*
15069 GCTATGTTGCAAATGATGTGCCTATGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG
192 GCTATGTTGCAAATGATGTGCCTATGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTG
*
15129 ACAGATAAACCTTCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTGGAGCTGAGCATAATCAA
1 ACAGATAAACCTTCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTAGAGCTGAGCATAATCAA
** * * *
15194 ACTCGAAGGTATTTAGTTGTCAAATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCT
66 ACTCGAAGGTATTTAGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-
* * ** * * * *
15259 TTGAA-CTGAGTGTAATTGAACTTGAAGGTCTTT-GTTGACAAATAACCCTTCTAGCCTTGAGTT
130 TTGAAGCTGAGCGTAATCGAACGCGAAGGTCTTTGGTTGACAAATAACCCTTATAGACTTAAGCT
* * * *
15322 ATGTTGTAAATGATGTGCCT-TGCAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTTTG
195 ATGTTGCAAATGATGTGCCTATG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTG
* * * ** * *
15379 GCAGATAAACCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTAGAGCTGAGTGTAGTCGA
1 ACAGATAAACCTTCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTAGAGCTGAGCATAATCAA
* * * * *
15444 ACTCGAAGGTATTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
66 ACTCGAAGGTATTTAGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
15502 ACACGATATC
Statistics
Matches: 311, Mismatches: 58, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
249 2 0.01
250 178 0.57
251 89 0.29
252 5 0.02
253 34 0.11
254 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (251 bp):
ACAGATAAACCTTCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTAGAGCTGAGCATAATCAA
ACTCGAAGGTATTTAGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
TGAAGCTGAGCGTAATCGAACGCGAAGGTCTTTGGTTGACAAATAACCCTTATAGACTTAAGCTA
TGTTGCAAATGATGTGCCTATGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTG
Found at i:15712 original size:124 final size:124
Alignment explanation
Indices: 15503--15976 Score: 666
Period size: 124 Copynumber: 3.8 Consensus size: 124
15493 TGCAAATGAA
* * * *
15503 CACGATAT-CCTTCATGGTGAAGTTGAAATCGTGGAGGGCCCATTCGTTTTGAAGTTGAGCCTTG
1 CACGAT-TCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTT-
* * * * * * *
15567 AA-TTGGATATCATTCGCCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGCTGGTGGG
64 AACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGAGAG
* * * *
15627 TATGATTCCCTTCATCATGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTAA
1 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA
* *
15692 CTTTG-ATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGACGATTGTTACTGGAGAG
66 C-TTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGAGAG
** * * *
15751 CACGATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGTCTTAA
1 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA
*
15816 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGCTACTGGAGAG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGAGAG
* *
15875 CACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTAA
1 CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA
*
15940 CTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCT
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT
15977 TGTATTGTTT
Statistics
Matches: 314, Mismatches: 32, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
123 6 0.02
124 305 0.97
125 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (124 bp):
CACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAA
CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTGAAGATGAATGTTACTGGAGAG
Found at i:18039 original size:35 final size:36
Alignment explanation
Indices: 17993--18060 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
17983 ATGTCCTTAT
*
17993 AAAAAGAAATATGTCAAAGTTC-AAAAACAAGTTAC
1 AAAAAGAAATATGACAAAGTTCAAAAAACAAGTTAC
* *
18028 AAAAAGAAATATGAGAATGTTCAAAAAACAAGT
1 AAAAAGAAATATGACAAAGTTCAAAAAACAAGT
18061 CTAAACAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (36 bp):
AAAAAGAAATATGACAAAGTTCAAAAAACAAGTTAC
Found at i:22276 original size:16 final size:16
Alignment explanation
Indices: 22246--22306 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
22236 TACGTTTTTT
* *
22246 ATTTTAATAAAATTAA
1 ATTTTAATTATATTAA
22262 ATTTTAATTATATTAA
1 ATTTTAATTATATTAA
22278 A----ACATT-TATTAA
1 ATTTTA-ATTATATTAA
22290 ATTTTAATTATATTAA
1 ATTTTAATTATATTAA
22306 A
1 A
22307 ACAACATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
15 3 0.08
16 23 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAATTATATTAA
Found at i:23882 original size:20 final size:20
Alignment explanation
Indices: 23859--23897 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
23849 TTTGAAACTT
*
23859 AAATTCGCAATACGAAAATG
1 AAATTCGCAACACGAAAATG
23879 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
23898 CGCAACCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:23900 original size:14 final size:14
Alignment explanation
Indices: 23878--23911 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23868 ATACGAAAAT
*
23878 GAAATTCGCAACAC
1 GAAAATCGCAACAC
*
23892 GAAAATCGCAACCC
1 GAAAATCGCAACAC
23906 GAAAAT
1 GAAAAT
23912 GAAAATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:23943 original size:14 final size:14
Alignment explanation
Indices: 23924--23955 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
23914 AAATCACAAC
23924 GCGATTTTTGCGTT
1 GCGATTTTTGCGTT
23938 GCGATTTTTGCGTT
1 GCGATTTTTGCGTT
23952 GCGA
1 GCGA
23956 ATTCAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.16, G:0.31, T:0.44
Consensus pattern (14 bp):
GCGATTTTTGCGTT
Found at i:25265 original size:42 final size:42
Alignment explanation
Indices: 25176--25271 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
25166 CCCCCACTTC
* * * **
25176 GAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACC
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAA
*
25218 CAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAA
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAA
25260 GAGAGCCATCAC
1 GAGAGCCATCAC
25272 ATATTCTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (42 bp):
GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAA
Found at i:25412 original size:21 final size:21
Alignment explanation
Indices: 25388--25437 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
25378 GTTAGGCGAG
*
25388 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
25409 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
25430 TTACGTGA
1 TTACGTGA
25438 CGACAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:25877 original size:21 final size:21
Alignment explanation
Indices: 25849--25965 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
25839 TTCACCTGTC
25849 ATCGTTCAAGAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
25870 ATCATTCAAGAGG-CCCTTCT
1 ATCGTTCAAGAGGCCCCTCCT
*
25890 CATCGTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
25912 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* *
25932 CATCGTTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
25954 ATCGTTCAAGAG
1 ATCGTTCAAGAG
25966 CCCGATTCAC
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.08
21 69 0.86
22 5 0.06
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:25894 original size:42 final size:42
Alignment explanation
Indices: 25847--25965 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
25837 GATTCACCTG
* * *
25847 TCATCGTTCAAGAGGCCCCTCCTATCATTCAAGAGGCCCTTC
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
* *
25889 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
*
25931 TCATCGTTCAAGAGGTCCCTCCCATCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAG
25966 CCCGATTCAC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
Found at i:27454 original size:207 final size:206
Alignment explanation
Indices: 27068--27470 Score: 607
Period size: 207 Copynumber: 1.9 Consensus size: 206
27058 GTACTGAAAG
27068 TGTGCATAAAAAACCATTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACTCTTTG
1 TGTGCATAAAAAACCATTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATAC-CTTTG
27133 TTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTATCTGTTGGTTTAAGATG
65 TTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTATCTGTTGGTTTAAGATG
** * *
27198 TGTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTCTACAGGTAAATCCTGAAGTGAGCTGTGTGA
130 TGTAGAAAGTGTCATTTGAACAAATGTTTGGTTTCTACAGGTAAATCCTGAAGTGAGCTGCGTGA
27263 AATTGATGTATT
195 AATTGATGTATT
* * *
27275 TGTGTATAAACAACCAGTTT-TTATTGGTAAGTTT-ATGCAAGTGTTGTTAACTGTTATATA-C-
1 TGTGCATAAAAAACCA-TTTGTTATTGGTAAGTTTGA-GCAAGTGTTGTTAAC--ATATATACCT
* * *
27336 TTGTTGGTTTGAAAATGTTTGGTTTAAGTACCTAGAATTCAATAATTTGTTGTTTGTTGGTTTTA
62 TTGTTGGTTTGAAAATGTTTGG-TTAAGTACCTAGAATTCAATAATTTGTTATCTGTTGGTTTAA
* * *
27401 GATGTGTAGAAAGTGTCATTTGAACAAATGTTTGGTTTCTGCAGGTTAATCCTGAAGTGAGTTGC
126 GATGTGTAGAAAGTGTCATTTGAACAAATGTTTGGTTTCTACAGGTAAATCCTGAAGTGAGCTGC
27466 GTGAA
191 GTGAA
27471 TGTAAGCTCC
Statistics
Matches: 178, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
206 23 0.13
207 146 0.82
208 3 0.02
209 6 0.03
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (206 bp):
TGTGCATAAAAAACCATTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACCTTTGT
TGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTATCTGTTGGTTTAAGATGT
GTAGAAAGTGTCATTTGAACAAATGTTTGGTTTCTACAGGTAAATCCTGAAGTGAGCTGCGTGAA
ATTGATGTATT
Found at i:27712 original size:19 final size:20
Alignment explanation
Indices: 27675--27732 Score: 100
Period size: 19 Copynumber: 3.0 Consensus size: 20
27665 GTACACTTTC
27675 GCAACGCGAAAGTCAAATTT
1 GCAACGCGAAAGTCAAATTT
*
27695 GCAACGCGGAAG-CAAATTT
1 GCAACGCGAAAGTCAAATTT
27714 GCAACGCGAAAGTCAAATT
1 GCAACGCGAAAGTCAAATT
27733 CACGTTGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTT
Found at i:30379 original size:24 final size:24
Alignment explanation
Indices: 30328--30379 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
30318 ATCCGAGTAT
** *
30328 TGACCAAGATCAAAGTCTGGGTAT
1 TGACCAAGATCAAAGTCTGAATAC
* *
30352 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTCTGAATAC
30376 TGAC
1 TGAC
30380 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCTGAATAC
Found at i:31582 original size:22 final size:22
Alignment explanation
Indices: 31557--31598 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
31547 CAATTCATTT
31557 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
31579 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
31599 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:31962 original size:18 final size:18
Alignment explanation
Indices: 31917--31955 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
31907 TATTTTTTTC
31917 AAAAA-AAAAAAAAACAA
1 AAAAACAAAAAAAAACAA
31934 AAAAACAAAAAAAAACAA
1 AAAAACAAAAAAAAACAA
31952 AAAA
1 AAAA
31956 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAAAAACAA
Found at i:31974 original size:1 final size:1
Alignment explanation
Indices: 31917--31955 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
31907 TATTTTTTTC
* * *
31917 AAAAAAAAAAAAAACAAAAAAACAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31956 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38238 original size:22 final size:22
Alignment explanation
Indices: 38213--38254 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
38203 CAATTCATTT
38213 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
38235 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
38255 CTAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:39132 original size:40 final size:40
Alignment explanation
Indices: 39088--39205 Score: 141
Period size: 40 Copynumber: 2.9 Consensus size: 40
39078 AATAAAACCC
*
39088 GTTGCGAAATTAAAATTCGTGTTGCAAATTC-GAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAG-AAATCGA
** *
39128 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGA
* *
39168 GTTGC-AAATTTGAAATTCAGTGTTGCGAATTTAGAAAT
1 GTTGCGAAA-TTAAAATTC-GTGTTGCGAATTCAGAAAT
39206 TGCGTTGTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
39 3 0.05
40 45 0.68
41 18 0.27
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCAGAAATCGA
Found at i:39172 original size:60 final size:59
Alignment explanation
Indices: 39070--39196 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 59
39060 AAATATTTGT
* *
39070 GTTGCGAAAATAAAACCCGTTGCGAAATTAAAATTCGTGTTGCAAATTCGAAAATC-GA
1 GTTGCGAAAACAAAACCCGTTGCGAAATTAAAATTCGAGTTGCAAATTCGAAAATCAGA
* * * *
39128 GTTGCGAAAACAAAATTCGCGTTGCG-AATTCAGAAA-TCGAGTTGCAAATTTGAAATTCAGT
1 GTTGCGAAAACAAAA--CCCGTTGCGAAATT-A-AAATTCGAGTTGCAAATTCGAAAATCAGA
39189 GTTGCGAA
1 GTTGCGAA
39197 TTTAGAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
58 14 0.24
59 4 0.07
60 28 0.48
61 12 0.21
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (59 bp):
GTTGCGAAAACAAAACCCGTTGCGAAATTAAAATTCGAGTTGCAAATTCGAAAATCAGA
Found at i:39217 original size:20 final size:21
Alignment explanation
Indices: 39087--39219 Score: 89
Period size: 20 Copynumber: 6.6 Consensus size: 21
39077 AAATAAAACC
*
39087 CGTTGCGAAATTA-AAATTCG
1 CGTTGCGAATTTAGAAATTCG
* * * *
39107 TGTTGC-AAATTCGAAAATCG
1 CGTTGCGAATTTAGAAATTCG
* ***
39127 AGTTGCGAAAACA-AAATTCG
1 CGTTGCGAATTTAGAAATTCG
*
39147 CGTTGCGAATTCAGAAA-TCG
1 CGTTGCGAATTTAGAAATTCG
* *
39167 AGTTGCAAATTT-GAAATTCAG
1 CGTTGCGAATTTAGAAATTC-G
*
39188 TGTTGCGAATTTAGAAATT-G
1 CGTTGCGAATTTAGAAATTCG
*
39208 CGTTGTGAATTT
1 CGTTGCGAATTT
39220 GTTGGTCATT
Statistics
Matches: 89, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.10
20 57 0.64
21 17 0.19
22 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (21 bp):
CGTTGCGAATTTAGAAATTCG
Found at i:43196 original size:22 final size:22
Alignment explanation
Indices: 43168--43213 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
43158 ATGGAGTGTT
43168 AATGCT-GAATTTTAATATTAGA
1 AATGCTGGAATTTTAA-ATTAGA
*
43190 AATGCTGGAATTTTAAGTTAGA
1 AATGCTGGAATTTTAAATTAGA
43212 AA
1 AA
43214 GTTGATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (22 bp):
AATGCTGGAATTTTAAATTAGA
Done.