Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001712.1 Hibiscus syriacus cultivar Beakdansim tig00003459_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: 77821
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:6310 original size:19 final size:19
Alignment explanation
Indices: 6288--6336 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
6278 TTTACCCTAA
6288 TTTCTTAATTTTTTTTGTC
1 TTTCTTAATTTTTTTTGTC
* * *
6307 TTTCTGTATTTTTTTTTTTG
1 TTTCT-TAATTTTTTTTGTC
6327 TTT-TTAATTT
1 TTTCTTAATTT
6337 GATAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 5 0.20
19 6 0.24
20 14 0.56
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTCTTAATTTTTTTTGTC
Found at i:9635 original size:105 final size:104
Alignment explanation
Indices: 9393--9688 Score: 418
Period size: 105 Copynumber: 2.8 Consensus size: 104
9383 CAGGATGCTA
*
9393 GCCTTTGCTAACTTGCCAGCCCA-GATGCTAGCCTCTTCC-TTACTTCCCTCAACTCTTGTTCAA
1 GCCTCTGCTAACTTGCCAG-CCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAA
* * *
9456 TCTGTATCTTGGTAGTCTGACAACAATCATAGTTGCTTGG
65 TCTGTATCTTGGAAGTCTGACAATAATCATAGTCGCTTGG
* * * *
9496 GCTTCTGCTAACTTGCCAACCAGGATGCTAGCCTCTTCCTTTACTT-TCTGCAACTCTTGTTCAG
1 GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCT-CAACTCTTGTTCAA
* *
9560 TCTGTGTCTTAGAAGTCTGACAATAATCAATAGTCGCTTGG
65 TCTGTATCTTGGAAGTCTGACAATAATC-ATAGTCGCTTGG
* * *
9601 GCCTCTGCTAACTTTCCAGCCAGGGTGCTAGCCTCTTCTTTTACTTCCCTCAACTCTTGTTCAAT
1 GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAAT
*
9666 CCGTATCTTGGAAGTCTGACAAT
66 CTGTATCTTGGAAGTCTGACAAT
9689 CATCGATATA
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
102 3 0.02
103 34 0.20
104 43 0.26
105 86 0.51
106 2 0.01
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (104 bp):
GCCTCTGCTAACTTGCCAGCCAGGATGCTAGCCTCTTCCTTTACTTCCCTCAACTCTTGTTCAAT
CTGTATCTTGGAAGTCTGACAATAATCATAGTCGCTTGG
Found at i:14951 original size:20 final size:21
Alignment explanation
Indices: 14923--14961 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14913 ATAATAATTG
*
14923 TATTTTTTTATAAT-TTTAAT
1 TATTATTTTATAATATTTAAT
14943 TATTATTTTATAATATTTA
1 TATTATTTTATAATATTTA
14962 GATACTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTTTATAATATTTAAT
Found at i:14970 original size:21 final size:21
Alignment explanation
Indices: 14928--14981 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
14918 AATTGTATTT
*
14928 TTTTATAAT-TTTAATTATTA
1 TTTTATAATATTTAATTACTA
14948 TTTTATAATATTTAGA-TACTA
1 TTTTATAATATTTA-ATTACTA
* *
14969 TTTAATACTATTT
1 TTTTATAATATTT
14982 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 19 0.66
22 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATAATATTTAATTACTA
Found at i:16190 original size:3 final size:3
Alignment explanation
Indices: 16182--16253 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
16172 ATTCTCTTAC
16182 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16230 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
16254 GGAAGGGAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17254 original size:18 final size:17
Alignment explanation
Indices: 17214--17254 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
17204 TCTTTTCATC
*
17214 ATTCTGGTTCTACTGAA
1 ATTCTGGTACTACTGAA
17231 AGTTCTGGTACTACTGCAA
1 A-TTCTGGTACTACTG-AA
17250 ATTCT
1 ATTCT
17255 AATGATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (17 bp):
ATTCTGGTACTACTGAA
Found at i:17463 original size:193 final size:193
Alignment explanation
Indices: 17103--17463 Score: 521
Period size: 193 Copynumber: 1.9 Consensus size: 193
17093 TCCGATTCTT
* * *
17103 CAAATCAAGGTGGTGTTATGGGTCATAGCTCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
* *
17168 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTCATCATTCTGGTTCTACTGAAAG
66 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTACTGAAAG
* **
17233 TTCTGGTACTACTGCAAATTCTAATGATTCTAAGGTTCTGGTGATCATCAATATCTAGTTCAG
131 TTCTGGAACTACAACAAATTCTAATGATTCTAAGGTTCTGGTGATCATCAATATCTAGTTCAG
* * *
17296 CAAATCAAGGTGGTATTACGGGTCATGGCTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGC
1 CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
* * * *
17361 TCATCCTTACATTCCGGTTCAGCTTCACATTCTGCTTC-TTTAATCACTCTGGTTCTA-TTAAAG
66 TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTACTGAAA-
* *
17424 GTTCTGGAACTACAACGAATGT-TGATGATTCTAAAGGTTC
130 GTTCTGGAACTACAACAAAT-TCTAATGATTCT-AAGGTTC
17464 AGGCTCTACT
Statistics
Matches: 148, Mismatches: 17, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
191 4 0.03
192 42 0.28
193 102 0.69
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (193 bp):
CAAATCAAGGTGGTATTACGGGTCATAGCTCTGCATCTTTCTCACATGCAAGTTCAGCTTCTAGC
TCATCCTCACATTCCAGTTCAGCTTCACATTCCGCTTCTTTTAATCACTCTGGTTCTACTGAAAG
TTCTGGAACTACAACAAATTCTAATGATTCTAAGGTTCTGGTGATCATCAATATCTAGTTCAG
Found at i:18908 original size:489 final size:489
Alignment explanation
Indices: 16937--19710 Score: 4918
Period size: 489 Copynumber: 5.7 Consensus size: 489
16927 GATTTCTAAG
*
16937 GGTTCTGGAACTACAACGGATGTTGATAACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
* *
17002 TTCATCAGGTTCCGGGGGTTCCGGTTCCACTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
* * * *
17067 TTAAGGGTTCTGACAACTCCTCACAATCCGATTCTTCAAATCAAGGTGGTGTTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
* *
17132 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCTCATCCTCACATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
*
17197 TTCCGCTTCTTTTCATCATTCTGGTTCTACTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
17262 CT-AAGGTTCTGGTG-ATCATCA-ATATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGG
326 CTAAAGGTTCTGGTGAATCATCACA-ATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGG
*
17324 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTACATTCCGGTTCAGCTTCAC
390 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCAC
17389 ATTCTGCTTC-TTTAATCACTCTGGTTCTATTAAA
455 ATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
* * * * **
17423 GGTTCTGGAACTACAACGAATGTTGATGATTCTAAAGGTTCAGGCTCTACTGCAACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
*
17488 TTCATCAGGTTCCGGGGCTTCCGGTTCCACTACAAGTTCTGGTTCTTCATCAGGTTAT-GGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
*
17552 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGTGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
* *
17617 TCTGCATCTTTCTCCCATGCAGGTTCAGCTTCTAGCGCATCCTCCCATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
* *
17682 TTCCGCTTCTTTTCATCACTCTGGTTCTATTGAAAGTTATGGTACTACTGC-AATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
*
17746 CTAAAGGTTCTGGTGAATCATCACAATTTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
* *
17811 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCACATCCTTGCATTCCGGTTCAGATTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
17876 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
*
17910 GGTTCTGGAACTACAACGGATGTTGATAACTCT-AAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
* *
17974 TTCATCAGGTTCC-GGGCTTCCGGTTCCTCTACAAGTTCGGGTTCTTCACCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGG-TT
*
18038 TCTAAGGGTTCTGACAATTCCTCACAATCTGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAG
130 TCTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAG
*
18103 CTCTGTATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCAC
195 CTCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCAC
18168 ATTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGAT
260 ATTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGAT
* *
18233 TCTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTAC-GGTCAAGG
325 TCTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGG
18297 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCAC
390 CTCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCAC
18362 ATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
455 ATTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
18397 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
*
18462 TTCATCAGGTTCCGGGACTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
*
18527 CTAAGGGTTCTGACAATTCCTCACAATCTGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
*
18592 TCTGTATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
18657 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
* *
18722 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGCATTACGGGTCAAGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
18787 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
18852 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
18886 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
* *
18951 TTCATCAGGTTCCGGGACTTCCGGTTCCTCAACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
19016 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
* * *
19081 TCTGCATCTTTCTCCCATGCAGGTTCAGCTTCTAGCGCATCCCCGCATTCCAGTTCAGTTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
* * *
19146 TTCCGCTTCGTTTCATCATTCTGGTTCTATTGAAATTTCTGGCACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
* * *
19211 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTTAGCAAATCAAGGTGGTATTTCAGGTCATGGC
326 CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
*
19276 TCTTCATCTTTCTCACATTCGAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
391 TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
19341 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
456 TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
* *
19375 GGTTCTGGAACTACAACGGACGTTGATGACTCTAAAGGTTCCGGTTCTGCTGTGACTTCTAACTC
1 GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
*
19440 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTAATGGGGTTT
66 TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
* * *
19505 CTAAGAGTTCTAACAATTCCTCACAATCTGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
131 CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
*
19570 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCACATTCCAGTTCAGCTTCACA
196 TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
* * *
19635 TTCAGCTTCTTTTCATCATTCTGGTTCTATTGAAGGTTCTGGCACTACTGCAAATTCTAATGATT
261 TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
*
19700 TTAAAGGTTCT
326 CTAAAGGTTCT
19711 AGTTCAACAA
Statistics
Matches: 2199, Mismatches: 79, Indels: 17
0.96 0.03 0.01
Matches are distributed among these distances:
484 15 0.01
485 231 0.11
486 275 0.13
487 369 0.17
488 363 0.17
489 946 0.43
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (489 bp):
GGTTCTGGAACTACAACGGATGTTGATGACTCTAAAGGTTCCGGTTCTACTGTGACTTCTAACTC
TTCATCAGGTTCCGGGGCTTCCGGTTCCTCTACAAGTTCTGGTTCTTCATCAGGTTATGGGGTTT
CTAAGGGTTCTGACAATTCCTCACAATCCGATTCTTCAAATCAAGGAGGTGCTATGGGTCATAGC
TCTGCATCTTTCTCACATGCAGGTTCAGCTTCTAGCGCATCCTCGCATTCCAGTTCAGCTTCACA
TTCCGCTTCTTTTCATCATTCTGGTTCTATTGAAAGTTCTGGTACTACTGCAAATTCTAATGATT
CTAAAGGTTCTGGTGAATCATCACAATCTAGTTCAGCAAATCAAGGTGGTATTACGGGTCATGGC
TCTTCATCTTTCTCACATTCAAGTTCAGCTTCTAGCTCATCCTTGCATTCCGGTTCAGCTTCACA
TTCTGCTTCTTTTAATCACTCTGGTTCTATTAAA
Found at i:20329 original size:30 final size:30
Alignment explanation
Indices: 20295--20363 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
20285 CTTCATCTTT
*
20295 CTCACATTCAAGTGCAGCTTCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
20325 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
20355 CTCACATTC
1 CTCACATTC
20364 CGGTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:20617 original size:30 final size:30
Alignment explanation
Indices: 20583--20651 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
20573 CTTCATCTTT
*
20583 CTCACATTCAAGTGCAGCTTCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
20613 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
20643 CTCACATTC
1 CTCACATTC
20652 CGGTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:20938 original size:30 final size:30
Alignment explanation
Indices: 20876--20941 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
20866 ATCTTTCTCA
* *
20876 ACATTCAAGTGCAGCTTCTGGATCATCCTC
1 ACATTCAAGTGCAGCTGCCGGATCATCCTC
* **
20906 ACATTCAAGTGCAGCTGCCGGTTCATTTTC
1 ACATTCAAGTGCAGCTGCCGGATCATCCTC
20936 ACATTC
1 ACATTC
20942 TACTTCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (30 bp):
ACATTCAAGTGCAGCTGCCGGATCATCCTC
Found at i:21190 original size:30 final size:30
Alignment explanation
Indices: 21156--21224 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
21146 CTTCATCTTT
*
21156 CTCACATTCAAGTGCAGCTTCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21186 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21216 CTCACATTC
1 CTCACATTC
21225 CGGTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:21419 original size:291 final size:293
Alignment explanation
Indices: 20923--22673 Score: 3084
Period size: 291 Copynumber: 5.9 Consensus size: 293
20913 AGTGCAGCTG
*
20923 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCCTTCGTAGATTCGAAC-AATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
*
20987 GATTCTGGTTCTGCTACGACTTATCACTCTTCATCAGGTTCTGGGCTTCAAGTTCCTCTTCAAGT
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGG-----AG----TCTTCAAGT
*
21052 TCTGGTTCTTCATCAGGTTCTAGAGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTAC
122 TCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTAC
21117 GAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGAT
187 GAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGAT
21182 CATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATT
252 CATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATT
*
21224 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCACTTTCGTAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
*
21289 GATTCTGGTTCTGCTACGACTTATCACTCTTCATCAGGTTCTGGG-G-CTTCAAGTTCTGGTTCT
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGGAGTCTTCAAGTTCTGGTTCT
21352 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
131 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
21417 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
196 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
21482 ATTCAAGTGCAGCTGCTGGATCATCCTCACATT
261 ATTCAAGTGCAGCTGCTGGATCATCCTCACATT
21515 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
* *
21580 GATTCTGGTTCTGCTACGACTGCTCACTCTTTATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCT-GGG-----AG----TCTTCAAG
21645 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
121 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
*
21710 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
186 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGA
21775 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATT
251 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATT
21818 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
21883 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGG-G-CTTCAAGTTCTGGTTCT
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGGAGTCTTCAAGTTCTGGTTCT
21946 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
131 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
22011 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
196 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
22076 ATTCAAGTGCAGCTGCTGGATCATCCTCACATT
261 ATTCAAGTGCAGCTGCTGGATCATCCTCACATT
*
22109 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGCAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
*
22174 GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCT-GGG-----AG----TCTTCAAG
22239 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
121 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
*
22304 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
186 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGA
*
22369 TCATCCTCACGTTCAAGTGCAGCTGCTGGATCATCCTCACATT
251 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATT
22412 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
22477 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGG-G-CTTCAAGTTCTGGTTCT
66 GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGGAGTCTTCAAGTTCTGGTTCT
22540 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
131 TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
22605 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
196 TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
22670 ATTC
261 ATTC
22674 CACTTCATTT
Statistics
Matches: 1406, Mismatches: 19, Indels: 60
0.95 0.01 0.04
Matches are distributed among these distances:
291 715 0.51
292 6 0.00
296 3 0.00
298 2 0.00
301 54 0.04
302 59 0.04
303 567 0.40
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (293 bp):
CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
GATTCTGGTTCTGCTACGACTTCTCACTCTTCATCAGGTTCTGGGAGTCTTCAAGTTCTGGTTCT
TCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAG
TGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCAC
ATTCAAGTGCAGCTGCTGGATCATCCTCACATT
Found at i:21481 original size:30 final size:30
Alignment explanation
Indices: 21447--21515 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
21437 CTTCATCTTT
*
21447 CTCACATTCAAGTGCAGCTTCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21477 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21507 CTCACATTC
1 CTCACATTC
21516 CGGTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:21720 original size:594 final size:594
Alignment explanation
Indices: 20923--22673 Score: 3398
Period size: 594 Copynumber: 3.0 Consensus size: 594
20913 AGTGCAGCTG
*
20923 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCCTTCGTAGATTCGAAC-AATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
**
20987 GATTCTGGTTCTGCTACGACTTATCACTCTTCATCAGGTTCT-GGGCTTCAAGTTCCTCTTCAAG
66 GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
*
21051 TTCTGGTTCTTCATCAGGTTCTAGAGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
131 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
*
21116 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGA
196 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
21181 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
261 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
*
21246 TTCTAAAGGTTCTGGCACTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
326 TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
*
21311 ATCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
391 CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
21376 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
456 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
21441 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTCAAGTGCAGCTGCTGGATCAT
521 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTCAAGTGCAGCTGCTGGATCAT
21506 CCTCACATT
586 CCTCACATT
21515 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
*
21580 GATTCTGGTTCTGCTACGACTGCTCACTCTTTATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
66 GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
21645 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
131 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
21710 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
196 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
21775 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
261 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
21840 TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
326 TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
21905 CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
391 CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
21970 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
456 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
22035 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTCAAGTGCAGCTGCTGGATCAT
521 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTCAAGTGCAGCTGCTGGATCAT
22100 CCTCACATT
586 CCTCACATT
*
22109 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGCAGATTCGAACAAATCTAAG
1 CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
22174 GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
66 GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
22239 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
131 TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
22304 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
196 CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
*
22369 TCATCCTCACGTTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
261 TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
22434 TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
326 TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
22499 CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
391 CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
22564 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
456 GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
22629 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTC
521 ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTC
22674 CACTTCATTT
Statistics
Matches: 1146, Mismatches: 11, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
592 55 0.05
593 47 0.04
594 1044 0.91
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (594 bp):
CCGGTTCATTTTCACATTCTACTTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAG
GATTCTGGTTCTGCTACGACTGCTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCCTCTTCAAG
TTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAGGGTTCTGGCTCGTCTTCACATTCTGGTTCTA
CGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTCATCTTTCTCACATTCAAGTGCAGCTTCTGGT
TCATCCTCACATTCAAGTGCAGCTGCTGGATCATCCTCACATTCCGGTTCATTTTCACATTCTAC
TTCTAAAGGTTCTGGCTCTTTCGTAGATTCGAACAAATCTAAGGATTCTGGTTCTGCTACGACTT
CTCACTCTTCATCAGGTTCTGGGGCTTCAAGTTCTGGTTCTTCATCAGGTTCTAGCGATTCTAAG
GGTTCTGGCTCGTCTTCACATTCTGGTTCTACGAGTCACAGTGTTGCTGCAGGTCATGGTTCTTC
ATCTTTCTCACATTCAAGTGCAGCTTCTGGATCATCCTCACATTCAAGTGCAGCTGCTGGATCAT
CCTCACATT
Found at i:21785 original size:30 final size:30
Alignment explanation
Indices: 21750--21818 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
21740 CTTCATCTTT
* *
21750 CTCACATTCAAGTGCAGCTTCTGGTTCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21780 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
21810 CTCACATTC
1 CTCACATTC
21819 CGGTTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:22075 original size:30 final size:30
Alignment explanation
Indices: 22041--22109 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
22031 CTTCATCTTT
*
22041 CTCACATTCAAGTGCAGCTTCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
22071 CTCACATTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
22101 CTCACATTC
1 CTCACATTC
22110 CGGTTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:22384 original size:30 final size:30
Alignment explanation
Indices: 22344--22412 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
22334 CTTCATCTTT
* *
22344 CTCACATTCAAGTGCAGCTTCTGGTTCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
*
22374 CTCACGTTCAAGTGCAGCTGCTGGATCATC
1 CTCACATTCAAGTGCAGCTGCTGGATCATC
22404 CTCACATTC
1 CTCACATTC
22413 CGGTTCATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.30
Consensus pattern (30 bp):
CTCACATTCAAGTGCAGCTGCTGGATCATC
Found at i:23229 original size:33 final size:33
Alignment explanation
Indices: 23192--23262 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
23182 TGTACATCAG
* *
23192 GTTCCGGTGATTCAAGCTCTTCCGCAAGTTCAA
1 GTTCCGGTGATTCAACCTCTTCCACAAGTTCAA
*
23225 GTTCCGGTGATTCAACCTCTTCCACAGGTTCAA
1 GTTCCGGTGATTCAACCTCTTCCACAAGTTCAA
23258 GTTCC
1 GTTCC
23263 AACAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (33 bp):
GTTCCGGTGATTCAACCTCTTCCACAAGTTCAA
Found at i:23607 original size:39 final size:39
Alignment explanation
Indices: 23425--23626 Score: 185
Period size: 39 Copynumber: 5.2 Consensus size: 39
23415 CCCACACATT
* * *
23425 GGTTCTTCTGCAACATCTAGTCACTCTACGGCACAAAGC
1 GGTTCTTCTGCAACATCTAGTCACTCTGCGGCACACACC
* * * * *
23464 GGTTCTTTTGCGAGATCTAGTCACTCTGCGGCACAGATC
1 GGTTCTTCTGCAACATCTAGTCACTCTGCGGCACACACC
** * * *
23503 GGTTCTTCTGTTATATCTAGTCACTCTGTC-ACACACAGC
1 GGTTCTTCTGCAACATCTAGTCACTCTG-CGGCACACACC
23542 GGTTCTTCTGCAACATCTAG-CAACTCTGCGGCACACACC
1 GGTTCTTCTGCAACATCTAGTC-ACTCTGCGGCACACACC
* * * * * *
23581 GGTTCTTTTGCGACATCTGGAT-ACTCTGTGGTACACACT
1 GGTTCTTCTGCAACATCTAG-TCACTCTGCGGCACACACC
23620 GGTTCTT
1 GGTTCTT
23627 TGAGAGGCAC
Statistics
Matches: 134, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.01
39 131 0.98
40 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (39 bp):
GGTTCTTCTGCAACATCTAGTCACTCTGCGGCACACACC
Found at i:37925 original size:2 final size:2
Alignment explanation
Indices: 37918--37943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37908 AATTTTGTAA
37918 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
37944 GAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41469 original size:17 final size:17
Alignment explanation
Indices: 41447--41503 Score: 114
Period size: 17 Copynumber: 3.4 Consensus size: 17
41437 TAGTCACTTT
41447 CTTATTATAATACTATC
1 CTTATTATAATACTATC
41464 CTTATTATAATACTATC
1 CTTATTATAATACTATC
41481 CTTATTATAATACTATC
1 CTTATTATAATACTATC
41498 CTTATT
1 CTTATT
41504 TCGTTGAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (17 bp):
CTTATTATAATACTATC
Found at i:46876 original size:123 final size:123
Alignment explanation
Indices: 46657--46907 Score: 353
Period size: 123 Copynumber: 2.0 Consensus size: 123
46647 ACCACCCATG
46657 TCTTCAAGTATGTACCGTTTGAATCTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
1 TCTTCAAGTATGTACCGTTTGAATCTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
* * * ** *
46722 CTGTTTCTTGCTTCTCTTCAACTTGGATTTCAGTTCACTTCCTCGTTCTCTATCACCA
66 CTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
* * * * *
46780 TCTTCAAGTATGTGCCGTTTGAATGTGTCCGGTATGTCGGGTGTTGGGATT-GAGGATTG-GGGT
1 TCTTCAAGTATGTACCGTTTGAATCTGTCCGGCACGTCGGGTGTTGGGATTGGA-GA-AGAGGGT
* *
46843 TTCTGTTTCTTGGGTCTCTTCAACTTGGGTTTCAGTCCACTTCCCCAATCTCCATCACCA
64 TTCTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
46903 TCTTC
1 TCTTC
46908 TTCTTTCAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
122 2 0.02
123 110 0.97
124 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (123 bp):
TCTTCAAGTATGTACCGTTTGAATCTGTCCGGCACGTCGGGTGTTGGGATTGGAGAAGAGGGTTT
CTGTTTCTTGCGTCTCTTCAACTTGGATTTCAGTCCACTTCCCCAATCTCCATCACCA
Found at i:47302 original size:23 final size:24
Alignment explanation
Indices: 47262--47315 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
47252 GAAAAAAACC
**
47262 TTTCTTGAGTTAAAAGTA-ATTTG
1 TTTCTTGAGAGAAAAGTATATTTG
* *
47285 TTTCTTGAGAGAAGAGTATTTTTG
1 TTTCTTGAGAGAAAAGTATATTTG
47309 TTT-TTGA
1 TTTCTTGA
47316 ATTATGAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (24 bp):
TTTCTTGAGAGAAAAGTATATTTG
Found at i:48487 original size:10 final size:10
Alignment explanation
Indices: 48472--48498 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
48462 TTCTATTGAT
48472 TAATTTAAAA
1 TAATTTAAAA
48482 TAATTTAAAA
1 TAATTTAAAA
48492 TAATTTA
1 TAATTTA
48499 TTGAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATTTAAAA
Found at i:48783 original size:15 final size:16
Alignment explanation
Indices: 48763--48795 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
48753 AGTGAAATTT
48763 AAATGTA-TATATGAA
1 AAATGTACTATATGAA
48778 AAATGTATCTATATGAA
1 AAATGTA-CTATATGAA
48795 A
1 A
48796 GTTGCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (16 bp):
AAATGTACTATATGAA
Found at i:54965 original size:41 final size:42
Alignment explanation
Indices: 54882--54976 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 42
54872 CAAAATAACG
* * *
54882 AAGGGATTAATCATTTTTTCCCGAGAGATCGATCTTTTTGAA
1 AAGGGATTGATCATTTTCTCCCGAGAGATCGATCCTTTTGAA
* * *
54924 AATGGATTGATCA-TTTCTCTCGAGGGATCGATCCTTTTGAA
1 AAGGGATTGATCATTTTCTCCCGAGAGATCGATCCTTTTGAA
*
54965 AAGGGATCGATC
1 AAGGGATTGATC
54977 CATTGCACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 34 0.76
42 11 0.24
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (42 bp):
AAGGGATTGATCATTTTCTCCCGAGAGATCGATCCTTTTGAA
Found at i:62398 original size:185 final size:183
Alignment explanation
Indices: 62004--62387 Score: 634
Period size: 184 Copynumber: 2.1 Consensus size: 183
61994 TTTTCTAATT
* * *
62004 TATATAA-AAATTAAATGTTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
*
62068 ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAATG
66 ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAATA
* *
62133 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
131 GATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
62186 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATT-AAAAAA-AGTTTATAATTAATTTAAATAATATATAA
* * *
62251 TTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
64 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAA
62315 TAGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATG-T-
129 TAGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
62368 TATATAATATA-TTAATATTT
1 TATATAATATATTTAATATTT
62388 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
181 9 0.05
182 18 0.09
183 18 0.09
184 96 0.51
185 49 0.26
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAATA
GATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
Found at i:66885 original size:18 final size:18
Alignment explanation
Indices: 66862--66900 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
66852 ATCTTTCATG
66862 GAAGACTCCCACTTGACT
1 GAAGACTCCCACTTGACT
66880 GAAGACTCCCACTTGACT
1 GAAGACTCCCACTTGACT
66898 GAA
1 GAA
66901 TCCTCTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (18 bp):
GAAGACTCCCACTTGACT
Found at i:70958 original size:90 final size:89
Alignment explanation
Indices: 70822--70994 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
70812 TAACACACCC
* * * *
70822 TTTTATAGCCAAGTTACCCTAGTCCTATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATGAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
*
70887 TTAATTAATTAGAATTTAATAATCA
66 TTAATTAATT-GAAATTAATAATCA
*
70912 TTTTATATCCAAGTTACCCTAATCATATGAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATGAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
70977 TTAATTAATTGAAATTAA
66 TTAATTAATTGAAATTAA
70995 ATATTCAAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATGAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATCA
Found at i:75374 original size:7 final size:7
Alignment explanation
Indices: 75352--75387 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
75342 CCGAAATTTA
*
75352 TAAATAA
1 TAAATAT
*
75359 TATATAT
1 TAAATAT
75366 TAAATAT
1 TAAATAT
75373 TAAATAT
1 TAAATAT
75380 TAAATAT
1 TAAATAT
75387 T
1 T
75388 TTTTGATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATAT
Done.