Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001200.1 Hibiscus syriacus cultivar Beakdansim tig00002374_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: 81998
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:114 original size:33 final size:33
Alignment explanation
Indices: 2--113 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
1 C
*
2 CGAGAGCATCCGAGGCCATCTGAACGAGCTATG
1 CGAGGGCATCCGAGGCCATCTGAACGAGCTATG
*
35 CGA-GGCATCCGA-GCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCATCTGAACGAGCTATG
* * *
66 CGAGGGCATCCGAGGGCAACTGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCATCTGAACGAGCTATG
*
99 CGAGGGAATCCGAGG
1 CGAGGGCATCCGAGG
114 GAAGCCGAGC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
31 21 0.30
32 17 0.24
33 32 0.46
ACGTcount: A:0.26, C:0.27, G:0.35, T:0.12
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCATCTGAACGAGCTATG
Found at i:124 original size:33 final size:32
Alignment explanation
Indices: 26--126 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 32
16 GCCATCTGAA
** * *
26 CGAGCTATGCGA-GGCATCCGAGCCATCCGAA
1 CGAGCTATGCGAGGGCATCCGAGGGAACCGAG
*
57 CGAGCTATGCGAGGGCATCCGAGGGCAACTGAG
1 CGAGCTATGCGAGGGCATCCGAGGG-AACCGAG
*
90 CGAGCTATGCGAGGGAATCCGAGGGAAGCCGAG
1 CGAGCTATGCGAGGGCATCCGAGGGAA-CCGAG
123 CGAG
1 CGAG
127 GGTAGGTCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
31 12 0.20
32 12 0.20
33 36 0.60
ACGTcount: A:0.26, C:0.26, G:0.38, T:0.11
Consensus pattern (32 bp):
CGAGCTATGCGAGGGCATCCGAGGGAACCGAG
Found at i:176 original size:29 final size:29
Alignment explanation
Indices: 130--185 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
120 GAGCGAGGGT
*
130 AGGTCGCCCGGAGTGCATGGAGACCTACA
1 AGGTCGCCCGGAGGGCATGGAGACCTACA
*
159 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGAGACCTA
186 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGAGACCTACA
Found at i:233 original size:14 final size:14
Alignment explanation
Indices: 214--242 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
204 TGCCATGTAA
214 CACGTTCATTCTCT
1 CACGTTCATTCTCT
228 CACGTTCATTCTCT
1 CACGTTCATTCTCT
242 C
1 C
243 TGTTTGAGCA
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:0.14, C:0.38, G:0.07, T:0.41
Consensus pattern (14 bp):
CACGTTCATTCTCT
Found at i:674 original size:23 final size:23
Alignment explanation
Indices: 609--691 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 23
599 CGATAAATTG
* *
609 CACCAAAGTGCCACGTAGAAATTGT
1 CACCGAAGTGCCACGTAGAAA-T-A
* *
634 C-CCGAAG-GACCGCATAGAAATA
1 CACCGAAGTG-CCACGTAGAAATA
* *
656 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAAATA
*
679 CACCGTAGTGCCA
1 CACCGAAGTGCCA
692 TATAAGATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 1 0.02
23 29 0.63
24 15 0.33
25 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAAATA
Found at i:1815 original size:19 final size:19
Alignment explanation
Indices: 1791--1842 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1781 TTTAAGGGGG
1791 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1810 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1829 TGCATCGATGCACT
1 TGCATCGATGCACT
1843 AATTGTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:1951 original size:54 final size:54
Alignment explanation
Indices: 1883--2023 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 54
1873 AGTTTTCTCA
* ** *
1883 TAAGGCGTGAGCACGAATTATTCATTTTGAGCTTTCGTAGAAGAGGTATTTAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTTTCGCAGAAGAGGTATTTAGT
* *
1937 TAAGGCGTGGGCACGGCTTATTCATTTGGAGCTTTCGCAGAAGAGGTCTTTAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTTTCGCAGAAGAGGTATTTAGT
*
1991 TAAGGCGTTGGCACGGCTTATTCATTTTGAGCT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCT
2024 ATTGCATTCG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTTTCGCAGAAGAGGTATTTAGT
Found at i:4965 original size:30 final size:30
Alignment explanation
Indices: 4909--5151 Score: 167
Period size: 30 Copynumber: 8.1 Consensus size: 30
4899 ATATTACTAA
* * *
4909 TAATAATAATTAATTAAAT-ATTAATTAACAC
1 TAATAA-AACTAATTAAATGA-AAATTAATAC
** * **
4940 TAATAAGGCTAATTAGATGGCAATTAATAC
1 TAATAAAACTAATTAAATGAAAATTAATAC
4970 TAATAAAACTAATTAAATGAAAATTAATAC
1 TAATAAAACTAATTAAATGAAAATTAATAC
* * *
5000 TAATAAAACTAATTAAAT-AGTAGTTAATGC
1 TAATAAAACTAATTAAATGA-AAATTAATAC
* *
5030 TAATAAAGCTAATTAAAT-AACAATTACTAC
1 TAATAAAACTAATTAAATGAA-AATTAATAC
* ** * *
5060 TAATAAAACTAATGAAAT-AATTGTTAGTAA
1 TAATAAAACTAATTAAATGAA-AATTAATAC
* *
5090 TAATAAAACTAATTAAAT-AGTAGTTAATAC
1 TAATAAAACTAATTAAATGA-AAATTAATAC
* *
5120 TAAT-AAATTAAATTAAAT-AGTAATTAATAC
1 TAATAAAACT-AATTAAATGA-AAATTAATAC
5150 TA
1 TA
5152 CTAATAATAT
Statistics
Matches: 173, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
29 5 0.03
30 162 0.94
31 6 0.03
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (30 bp):
TAATAAAACTAATTAAATGAAAATTAATAC
Found at i:4982 original size:15 final size:15
Alignment explanation
Indices: 4964--5012 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
4954 AGATGGCAAT
4964 TAATACTAATAAAAC
1 TAATACTAATAAAAC
*
4979 TAAT--TAAATGAAAAT
1 TAATACT-AAT-AAAAC
4994 TAATACTAATAAAAC
1 TAATACTAATAAAAC
5009 TAAT
1 TAAT
5013 TAAATAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.04
14 3 0.11
15 20 0.71
16 3 0.11
17 1 0.04
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (15 bp):
TAATACTAATAAAAC
Found at i:5004 original size:60 final size:59
Alignment explanation
Indices: 4909--5151 Score: 218
Period size: 60 Copynumber: 4.0 Consensus size: 59
4899 ATATTACTAA
* * * ** * *
4909 TAATAATAATTAATTAAATATTAATTAACACTAATAAGGCTAATTAGATGGCAATTAATAC
1 TAATAA-AACTAATTAAATA-AAATTAATACTAATAAAACTAATTAAATAGCAATTAATAC
* * *
4970 TAATAAAACTAATTAAATGAAAATTAATACTAATAAAACTAATTAAATAGTAGTTAATGC
1 TAATAAAACTAATTAAAT-AAAATTAATACTAATAAAACTAATTAAATAGCAATTAATAC
* * * **** * *
5030 TAATAAAGCTAATTAAATAACAATTACTACTAATAAAACTAATGAAATAATTGTTAGTAA
1 TAATAAAACTAATTAAATAA-AATTAATACTAATAAAACTAATTAAATAGCAATTAATAC
* * * *
5090 TAATAAAACTAATTAAATAGTAGTTAATACTAAT-AAATTAAATTAAATAGTAATTAATAC
1 TAATAAAACTAATTAAATA-AAATTAATACTAATAAAACT-AATTAAATAGCAATTAATAC
5150 TA
1 TA
5152 CTAATAATAT
Statistics
Matches: 149, Mismatches: 29, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
59 6 0.04
60 136 0.91
61 7 0.05
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (59 bp):
TAATAAAACTAATTAAATAAAATTAATACTAATAAAACTAATTAAATAGCAATTAATAC
Found at i:5054 original size:90 final size:90
Alignment explanation
Indices: 4897--5151 Score: 300
Period size: 90 Copynumber: 2.8 Consensus size: 90
4887 ATACTAATAT
* * * * * * * *
4897 TAAT-ATTACTAATAATAATAATTAATTAAATATTAATTAACACTAATAAGGCTAATTAGATGGC
1 TAATAATTAATAATAATAA-AACTAATTAAATAGTAGTTAATACTAATAAAGCTAATTAAATAGC
*
4961 AATTAATACTAATAAAACTAATTAAA
65 AATTAATACTAATAAAACTAATGAAA
* * *
4987 TGAA-AATTAATACTAATAAAACTAATTAAATAGTAGTTAATGCTAATAAAGCTAATTAAATAAC
1 T-AATAATTAATAATAATAAAACTAATTAAATAGTAGTTAATACTAATAAAGCTAATTAAATAGC
*
5051 AATTACTACTAATAAAACTAATGAAA
65 AATTAATACTAATAAAACTAATGAAA
** * * *
5077 TAATTGTTAGTAATAATAAAACTAATTAAATAGTAGTTAATACTAATAAA-TTAAATTAAATAGT
1 TAATAATTAATAATAATAAAACTAATTAAATAGTAGTTAATACTAATAAAGCT-AATTAAATAGC
5141 AATTAATACTA
65 AATTAATACTA
5152 CTAATAATAT
Statistics
Matches: 139, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
89 3 0.02
90 122 0.88
91 14 0.10
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (90 bp):
TAATAATTAATAATAATAAAACTAATTAAATAGTAGTTAATACTAATAAAGCTAATTAAATAGCA
ATTAATACTAATAAAACTAATGAAA
Found at i:5167 original size:15 final size:15
Alignment explanation
Indices: 5144--5188 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
5134 AAATAGTAAT
5144 TAATACTACTAATAA
1 TAATACTACTAATAA
*
5159 TATTACTACTAATAA
1 TAATACTACTAATAA
*
5174 TAATA-TAATAATAA
1 TAATACTACTAATAA
5188 T
1 T
5189 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATACTACTAATAA
Found at i:5168 original size:18 final size:18
Alignment explanation
Indices: 5142--5188 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5132 TTAAATAGTA
*
5142 ATTAATACTACTAATAAT
1 ATTAATACTAATAATAAT
*
5160 ATTACTACTAATAATAAT
1 ATTAATACTAATAATAAT
*
5178 A-TAATAATAAT
1 ATTAATACTAAT
5189 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAATACTAATAATAAT
Found at i:9264 original size:19 final size:20
Alignment explanation
Indices: 9227--9264 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9217 GAACTAAAAA
* *
9227 GTTAGAATGCTGAATTTGAT
1 GTTAAAATGCTGAAATTGAT
9247 GTTAAAATG-TGAAATTGA
1 GTTAAAATGCTGAAATTGA
9265 ACTAATTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTAAAATGCTGAAATTGAT
Found at i:14413 original size:28 final size:28
Alignment explanation
Indices: 14381--14436 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
14371 GATTTATATT
* *
14381 CGTGAATCATTTGTATAACATTTGTTTA
1 CGTGAAACATTTGTATAACATTCGTTTA
14409 CGTGAAACATTTGTATAACATTCGTTTA
1 CGTGAAACATTTGTATAACATTCGTTTA
14437 TATTTGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (28 bp):
CGTGAAACATTTGTATAACATTCGTTTA
Found at i:15064 original size:30 final size:26
Alignment explanation
Indices: 14994--15067 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 26
14984 ACACGAACAC
*
14994 ATTAAAAATAAATAAACAAACAAGAT
1 ATTAAAAATAAATAAACAAACAAAAT
*
15020 ATTAAAAATTTAAATGAACACAAATAAAAT
1 ATTAAAAA--TAAAT-AA-ACAAACAAAAT
15050 ACCTTAAAAATAAATAAA
1 A--TTAAAAATAAATAAA
15068 AGAACCCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 8 0.20
28 6 0.15
29 4 0.10
30 15 0.38
32 7 0.17
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.23
Consensus pattern (26 bp):
ATTAAAAATAAATAAACAAACAAAAT
Found at i:27153 original size:55 final size:54
Alignment explanation
Indices: 27096--27566 Score: 664
Period size: 55 Copynumber: 8.7 Consensus size: 54
27086 CGGGTTCGCT
* * * * * *
27096 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTCAATAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTC-AACAATCTTCAACAATCGCGTCTGCC
* *
27151 CCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCC
* *
27204 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCC
* * *
27259 CCCTATTTCTTTAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCC
* *
27312 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCC
*
27367 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCC
*
27422 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCC
* *
27477 CCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATA-AATCGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCA-ACAATCGCGTCTGCC
27530 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCT
27567 CCATCAAACG
Statistics
Matches: 378, Mismatches: 30, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
53 141 0.37
54 7 0.02
55 228 0.60
56 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (54 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCC
Found at i:27250 original size:108 final size:108
Alignment explanation
Indices: 27096--27566 Score: 766
Period size: 108 Copynumber: 4.3 Consensus size: 108
27086 CGGGTTCGCT
* * * *
27096 CCCTCTTTCTTTAGAGAGTAT-AGAACTCG-GACAATCTTCAATAATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAG-CAATCTTCAACAATCGTGTCTGCCCCCTATTT
27159 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
64 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
27204 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
*
27269 TTAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
27312 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* * *
27377 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
66 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
* * *
27422 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* *
27487 TCAGAGAGTATAAGACCCACAATCTTCATAAATCGCGTATGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
27530 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCT
27567 CCATCAAACG
Statistics
Matches: 342, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
108 236 0.69
109 5 0.01
110 101 0.30
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
Found at i:27371 original size:163 final size:163
Alignment explanation
Indices: 27096--27566 Score: 727
Period size: 163 Copynumber: 2.9 Consensus size: 163
27086 CGGGTTCGCT
* * * *
27096 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTCAAT-AATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTTAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGCGTCTGCCCCCTATTT
*
27159 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
64 CTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
* *
27224 TAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
129 TAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
27259 CCCTATTTCTTTAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCT
* *
27322 TCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTA
66 TCAGAGAGTATAAGAC-CCA-CAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
*
27387 TAAGACTCGAACAATCTTCAACAATCGCGTCTGTC
129 TAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
27422 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCT
*
27487 TCAGAGAGTATAAGACCCACAATCTTCATA-AATCGCGTATGCCCCCTATTTCTTCAGAGAGTAT
66 TCAGAGAGTATAAGACCCACAATCTTCA-ACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
27551 AAGACTCGAACAATCT
130 AAGACTCGAACAATCT
27567 CCATCAAACG
Statistics
Matches: 284, Mismatches: 17, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
160 2 0.01
161 46 0.16
162 3 0.01
163 178 0.63
164 6 0.02
165 49 0.17
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (163 bp):
CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:38559 original size:20 final size:20
Alignment explanation
Indices: 38534--38576 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
38524 CCCTCAATCC
38534 TGGCCCATCACAGGCTTTAG
1 TGGCCCATCACAGGCTTTAG
38554 TGGCCCATCACAGGCTTTAG
1 TGGCCCATCACAGGCTTTAG
38574 TGG
1 TGG
38577 ATCGAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (20 bp):
TGGCCCATCACAGGCTTTAG
Found at i:53439 original size:20 final size:21
Alignment explanation
Indices: 53414--53458 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
53404 CATATGCCAA
*
53414 AATATTTATT-TTAACAAAAG
1 AATATTTATTATTAAAAAAAG
*
53434 AATATTTCTTATTAAAAAAAG
1 AATATTTATTATTAAAAAAAG
53455 AATA
1 AATA
53459 ATTGTTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
AATATTTATTATTAAAAAAAG
Found at i:53886 original size:58 final size:57
Alignment explanation
Indices: 53754--53957 Score: 164
Period size: 58 Copynumber: 3.6 Consensus size: 57
53744 GAAAATGATG
* * * *
53754 AGAAATTGAGAA-A-TTTATAAAATTGAAAAAAATTAGGAGCCCTCACTTATAAATGT
1 AGAAAGTGAGAACATTTTATAAAATT-AAAAAAAGTAGGAGCCCTCAATTATAAAGGT
* *
53810 AGAAAGTGAGACCTTTTTATAAAATTAAAAAAAGTAGG-GACCCTCAATTATAAAGGT
1 AGAAAGTGAGAACATTTTATAAAATTAAAAAAAGTAGGAG-CCCTCAATTATAAAGGT
* * * * * * * * *
53867 AGAAAGTGGGAAAGATTTTATAAAACTGAAAAAAA-CAAGAGCCCTTAATAATTAAGAT
1 AGAAAGTGAG-AACATTTTATAAAA-TTAAAAAAAGTAGGAGCCCTCAATTATAAAGGT
* * * *
53925 AGAAAATGGGGACTATTTCATAAAATTAAAAAA
1 AGAAAGTGAGAAC-ATTTTATAAAATTAAAAAA
53958 GTTATAGGCC
Statistics
Matches: 119, Mismatches: 22, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
56 11 0.09
57 43 0.36
58 56 0.47
59 9 0.08
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (57 bp):
AGAAAGTGAGAACATTTTATAAAATTAAAAAAAGTAGGAGCCCTCAATTATAAAGGT
Found at i:53899 original size:57 final size:56
Alignment explanation
Indices: 53754--53899 Score: 136
Period size: 57 Copynumber: 2.6 Consensus size: 56
53744 GAAAATGATG
* * * *
53754 AGAAATTGAGAA-A-TTTATAAAATTGAAAAAAATTAGGAGCCCTCACTTATAAATGT
1 AGAAAGTGAGAACATTTTATAAAATTG--AAAAAGTAGGAGCCCTCAATTATAAAGGT
* * *
53810 AGAAAGTGAGACCTTTTTATAAAATTAAAAAAAGTAGG-GACCCTCAATTATAAAGGT
1 AGAAAGTGAGAACATTTTATAAAATT-GAAAAAGTAGGAG-CCCTCAATTATAAAGGT
* * *
53867 AGAAAGTGGGAAAGATTTTATAAAACTGAAAAA
1 AGAAAGTGAG-AACATTTTATAAAATTGAAAAA
53900 AACAAGAGCC
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
56 11 0.15
57 38 0.53
58 23 0.32
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (56 bp):
AGAAAGTGAGAACATTTTATAAAATTGAAAAAGTAGGAGCCCTCAATTATAAAGGT
Found at i:54211 original size:20 final size:21
Alignment explanation
Indices: 54186--54233 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
54176 CCCAATTCGT
*
54186 AATGCGAA-TAAGTAAATCGC
1 AATGCGAATTAAGAAAATCGC
**
54206 AATGCGAATTTGGAAAATCGC
1 AATGCGAATTAAGAAAATCGC
54227 AATGCGA
1 AATGCGA
54234 TACTGACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
AATGCGAATTAAGAAAATCGC
Found at i:54277 original size:21 final size:20
Alignment explanation
Indices: 54243--54315 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
54233 ATACTGACTA
* *
54243 TCGCAATGCAATTTTCCTATT
1 TCGCAATGCGATTTTCATA-T
* * *
54264 TCGCATTGCGATTTACGTAT
1 TCGCAATGCGATTTTCATAT
**
54284 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCAT-AT
54305 TCGCAATGCGA
1 TCGCAATGCGA
54316 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCAATGCGATTTTCATAT
Found at i:54329 original size:21 final size:21
Alignment explanation
Indices: 54305--54358 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
54295 TTTTCATAAT
*
54305 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
54326 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
54346 TCGCAATGCGAAT
1 TCGCAATGCGAAT
54359 CTTACTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:54933 original size:19 final size:19
Alignment explanation
Indices: 54895--54961 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
54885 TTCGAGAATG
*
54895 AAAATTGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
54915 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
54934 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
54953 AAAATCGCA
1 AAAATCGCA
54962 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:55054 original size:34 final size:33
Alignment explanation
Indices: 54971--55058 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
54961 ATTGCGATTT
* * *
54971 TCATTTCGCGTTTCGATTCTCTCGTTGCGATAG
1 TCATTTCGCATTGCGATTCTCTCGTTGCAATAG
*
55004 TCATTTAGCATTGCGATTCTCTCGTTGCAATAG
1 TCATTTCGCATTGCGATTCTCTCGTTGCAATAG
55037 TCATTTCCGCATTGCGATTCTC
1 TCATTT-CGCATTGCGATTCTC
55059 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (33 bp):
TCATTTCGCATTGCGATTCTCTCGTTGCAATAG
Found at i:57251 original size:21 final size:21
Alignment explanation
Indices: 57227--57293 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
57217 TCATTCCTCG
57227 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
57248 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
57269 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
57290 AGAG
1 AGAG
57294 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:57251 original size:42 final size:42
Alignment explanation
Indices: 57175--57293 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
57165 GACTCGCCTG
* * * * * * *
57175 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
57217 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
57259 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
57294 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 59 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:58670 original size:14 final size:14
Alignment explanation
Indices: 58651--58686 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
58641 ATTGTTTAAT
58651 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
58665 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
58679 TGATTTGT
1 TGATTTGT
58687 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:58877 original size:33 final size:32
Alignment explanation
Indices: 58835--58961 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
58825 ATTAAATTCG
58835 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
58868 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
58901 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
58934 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
58962 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:58911 original size:66 final size:66
Alignment explanation
Indices: 58828--58960 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
58818 ACGAGAAATT
* *
58828 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
58893 G
66 G
* *
58894 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
58959 G
66 G
58960 A
1 A
58961 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:61345 original size:20 final size:20
Alignment explanation
Indices: 61312--61390 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
61302 AATTTGGAAA
* *
61312 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
61332 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
61353 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
61373 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
61391 AAATCGTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:61688 original size:20 final size:20
Alignment explanation
Indices: 61613--61680 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
61603 CAACGGGGAA
61613 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
61633 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
61653 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
61673 ATCGCAAC
1 ATCGCAAC
61681 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:61731 original size:14 final size:14
Alignment explanation
Indices: 61712--61765 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
61702 GAAAACCGCA
61712 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
61726 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
61743 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
61759 TTGCGAT
1 TTGCGAT
61766 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:61731 original size:33 final size:33
Alignment explanation
Indices: 61694--61764 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
61684 AAAATCGCAA
61694 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
** ** ***
61727 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
61760 TGCGA
1 TGCGA
61765 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
Found at i:63736 original size:20 final size:20
Alignment explanation
Indices: 63713--63780 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
63703 GAAACTTAAA
63713 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
63733 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
* **
63753 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
63772 ATCGCAACG
1 ATCGCAACG
63781 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:63788 original size:14 final size:14
Alignment explanation
Indices: 63769--63826 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
63759 ATGCGAAATG
63769 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
63783 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
63799 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
63815 AAAATCGCAACG
1 AAAATCGCAACG
63827 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:63816 original size:32 final size:33
Alignment explanation
Indices: 63753--63831 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
63743 AGAAATGGCT
*
63753 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
63786 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
63818 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
63832 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:63860 original size:19 final size:18
Alignment explanation
Indices: 63838--63934 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
63828 GAAACACAAA
63838 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
63857 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
63873 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
63890 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
63906 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
63923 TCGCATTGCGAT
1 TCGCATTGCGAT
63935 AGCCATTTCC
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
14 12 0.19
15 6 0.09
16 8 0.12
17 8 0.12
18 7 0.11
19 23 0.36
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:63881 original size:14 final size:14
Alignment explanation
Indices: 63862--63918 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
63852 TCATTTCGCA
63862 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
63876 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
63893 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
63909 TTGCGATTTT
1 TTGCGATTTT
63919 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:63887 original size:33 final size:33
Alignment explanation
Indices: 63843--63934 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
63833 ACAAATCGCA
*
63843 TTGCGACTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
63876 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
63909 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
63935 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:63941 original size:19 final size:20
Alignment explanation
Indices: 63919--63962 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
63909 TTGCGATTTT
63919 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
63938 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
63958 CATTT
1 CATTT
63963 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:63970 original size:20 final size:20
Alignment explanation
Indices: 63928--63973 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
63918 TCATTTCGCA
*
63928 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
63948 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
63968 TTGCGA
1 TTGCGA
63974 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:65867 original size:20 final size:20
Alignment explanation
Indices: 65819--65877 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
65809 AATAGTTTCT
** *
65819 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
65839 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
65859 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
65878 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:66167 original size:22 final size:22
Alignment explanation
Indices: 66140--66183 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66130 GATGGAGATA
66140 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
66162 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
66184 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:66456 original size:20 final size:20
Alignment explanation
Indices: 66350--66484 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
66340 CGCTTTGAAA
*
66350 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
66371 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
66391 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
66411 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
*
66432 ATCGCATTACGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
*
66452 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
66472 ATCGCATTGCGAT
1 ATCGCATTGCGAT
66485 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.69
21 22 0.23
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:66456 original size:61 final size:61
Alignment explanation
Indices: 66350--66487 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
66340 CGCTTTGAAA
* * * * *
66350 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
66411 ATCTCGTTGCGATTTTGTATTATCGCATTACGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
66472 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
66488 CCCAATTTGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:67272 original size:6 final size:7
Alignment explanation
Indices: 67202--67273 Score: 56
Period size: 7 Copynumber: 9.7 Consensus size: 7
67192 AAAAAAGGAA
67202 AAAAATT
1 AAAAATT
*
67209 ATAAAATAA
1 A-AAAAT-T
*
67218 AAAAATC
1 AAAAATT
*
67225 AAACATT
1 AAAAATT
*
67232 CAAAA-T
1 AAAAATT
67238 AAAAACTT
1 AAAAA-TT
67246 AAAGAATT
1 AAA-AATT
67254 GAAAAATT
1 -AAAAATT
67262 AAAAATT
1 AAAAATT
67269 AAAAA
1 AAAAA
67274 AAAAGGAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.10
7 21 0.40
8 20 0.38
9 6 0.12
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (7 bp):
AAAAATT
Found at i:67517 original size:29 final size:29
Alignment explanation
Indices: 67475--67531 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
67465 AGTGTTGGTC
*
67475 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGAGCGACCTT
*
67504 GTAGGTCGTCATGCACTCCGAGCGACCT
1 GTAGGTCGCCATGCACTCCGAGCGACCT
67532 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGAGCGACCTT
Found at i:67623 original size:29 final size:29
Alignment explanation
Indices: 67590--67645 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
67580 TCCCAACACA
* *
67590 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
67619 TAGGTCGTCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
67646 ATCCTCGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:67697 original size:23 final size:23
Alignment explanation
Indices: 67663--67715 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
67653 CTCGGCTTCC
67663 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATTCCCTCGCATAGCTCG
67686 CTCGG-TTGCCCTCGCATAGCTCG
1 CTCGGATT-CCCTCGCATAGCTCG
*
67709 TTCGGAT
1 CTCGGAT
67716 AGCCTCGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.11, C:0.36, G:0.25, T:0.28
Consensus pattern (23 bp):
CTCGGATTCCCTCGCATAGCTCG
Found at i:67817 original size:29 final size:29
Alignment explanation
Indices: 67780--67837 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
67770 GCAATCTCTT
*
67780 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
67809 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
67838 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:79791 original size:29 final size:29
Alignment explanation
Indices: 79758--79814 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
79748 ATGTTAAAAA
*
79758 GTAAAGG-AAAAGGCTTGGATTGTTCATTG
1 GTAAAGGTAAAA-GCTTGGAATGTTCATTG
*
79787 GTAAAGGTAAAATCTTGGAATGTTCATT
1 GTAAAGGTAAAAGCTTGGAATGTTCATT
79815 TCAAAAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (29 bp):
GTAAAGGTAAAAGCTTGGAATGTTCATTG
Done.