Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008465.1 Hibiscus syriacus cultivar Beakdansim tig00111278_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: 924357
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 5 of 5
Found at i:813105 original size:27 final size:27
Alignment explanation
Indices: 813007--813110 Score: 65
Period size: 27 Copynumber: 3.9 Consensus size: 27
812997 TTATTATTTT
*
813007 TTGA-TTGTTTAA-TTGATTTGTAAAAG
1 TTGATTTGTTAAAGTTGATTTGT-AAAG
* *
813033 ATGATTTG-TAAATGTTGATTTGTTTAA-
1 TTGATTTGTTAAA-GTTGATTTG-TAAAG
* * *
813060 TTGGTTTGTAAAAGATGATTTGTAAATG
1 TTGATTTGTTAAAGTTGATTTGTAAA-G
* *
813088 TTGATTTGTTTAA-TTGATGTGTA
1 TTGATTTGTTAAAGTTGATTTGTA
813111 CATAATTCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
26 9 0.16
27 25 0.43
28 23 0.40
29 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (27 bp):
TTGATTTGTTAAAGTTGATTTGTAAAG
Found at i:813299 original size:19 final size:19
Alignment explanation
Indices: 813236--813306 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
813226 GCAACGAGAG
813236 AATCGCAATGCGAAA-TGAA
1 AATCGCAATGCGAAACT-AA
*
813255 AATCGCAACGCGAAAAC-ACA
1 AATCGCAATGCG-AAACTA-A
813275 AATCGCAATGCGAAACTAA
1 AATCGCAATGCGAAACTAA
* *
813294 ATTCGCATTGCGA
1 AATCGCAATGCGA
813307 TTCTCTCGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAACTAA
Found at i:813334 original size:53 final size:53
Alignment explanation
Indices: 813277--813379 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
813267 AAAACACAAA
813277 TCGCAATGCGAAACTAAATTCGCATTGCGATTCTCTCGTTGCGATAGTCAGTT
1 TCGCAATGCGAAACTAAATTCGCATTGCGATTCTCTCGTTGCGATAGTCAGTT
* *** * * *
813330 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTTGTTGCGATAGTCA
1 TCGCAATGCGAAACTAAATTCGCATTGCGATTCTCTCGTTGCGATAGTCA
813380 AATTCGCGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (53 bp):
TCGCAATGCGAAACTAAATTCGCATTGCGATTCTCTCGTTGCGATAGTCAGTT
Found at i:813340 original size:20 final size:19
Alignment explanation
Indices: 813313--813459 Score: 126
Period size: 20 Copynumber: 7.7 Consensus size: 19
813303 GCGATTCTCT
813313 CGTTGCGATAGTCAGTTTCG
1 CGTTGCGATAGTCA-TTTCG
* **
813333 CATTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
813352 CATTGCGAT--TC-TCTT--
1 CGTTGCGATAGTCAT-TTCG
*
813367 -GTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
813386 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
813406 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
813426 CGTTGCGATAGTCATTTACT
1 CGTTGCGATAGTCATTT-CG
*
813446 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
813460 AATGAATGTC
Statistics
Matches: 106, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 6 0.06
19 20 0.19
20 67 0.63
21 3 0.03
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:813402 original size:53 final size:53
Alignment explanation
Indices: 813295--813414 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
813285 CGAAACTAAA
** ***
813295 TTCGCATTGCGATTCTCTCGTTGCGATAGTCAGTTTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGCCAT
* *
813348 TTCGCATTGCGATTCTCTTGTTGCGATAGTCAAATTCGCGTTGCGATAGCCAT
1 TTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGCCAT
*
813401 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
813415 AGTCATTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 48 0.83
54 10 0.17
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (53 bp):
TTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGCCAT
Found at i:815747 original size:12 final size:12
Alignment explanation
Indices: 815730--815754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
815720 TCTTCGGGGA
815730 CTTTTTCTTCTT
1 CTTTTTCTTCTT
815742 CTTTTTCTTCTT
1 CTTTTTCTTCTT
815754 C
1 C
815755 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:815963 original size:24 final size:24
Alignment explanation
Indices: 815929--815978 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
815919 CTGAAACATC
815929 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
815953 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
815977 AT
1 AT
815979 GAAATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:816754 original size:20 final size:20
Alignment explanation
Indices: 816729--816797 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
816719 TGTATTATCT
816729 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
816749 CGTTGCGATAGGT-AGAATCG
1 CGTTGCGATA-GTCAGAATCG
* * *
816769 CGTTGCGAAAGTCAGTATTG
1 CGTTGCGATAGTCAGAATCG
*
816789 CATTGCGAT
1 CGTTGCGAT
816798 TTTCCAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 38 0.90
21 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:816815 original size:21 final size:21
Alignment explanation
Indices: 816789--816830 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
816779 GTCAGTATTG
816789 CATTGCGATTTTCCAAATTCA
1 CATTGCGATTTTCCAAATTCA
816810 CATTGCGATTTTCCAAATTCA
1 CATTGCGATTTTCCAAATTCA
816831 AGTGGATCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCA
Found at i:817073 original size:14 final size:14
Alignment explanation
Indices: 817054--817080 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
817044 AAAAAGTTGA
817054 AAATAATAAATAAG
1 AAATAATAAATAAG
817068 AAATAATAAATAA
1 AAATAATAAATAA
817081 ATATTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAAATAAG
Found at i:817081 original size:18 final size:18
Alignment explanation
Indices: 817058--817100 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
817048 AGTTGAAAAT
817058 AATAAATAAGAAATAATA
1 AATAAATAAGAAATAATA
** *
817076 AATAAATATTAAATATTA
1 AATAAATAAGAAATAATA
817094 AATAAAT
1 AATAAAT
817101 CAATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAAATAAGAAATAATA
Found at i:817183 original size:14 final size:14
Alignment explanation
Indices: 817160--817213 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
817150 TGTTAAATTC
*
817160 TAAAAGTAATAAAA
1 TAAAAATAATAAAA
817174 TAAAAATAATAAGAA
1 TAAAAATAATAA-AA
817189 GTAAAAA-ACATAAAA
1 -TAAAAATA-ATAAAA
817204 TAAATAATAA
1 TAAA-AATAA
817214 AAATGCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 15 0.44
15 8 0.24
16 11 0.32
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:817194 original size:30 final size:28
Alignment explanation
Indices: 817159--817238 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 28
817149 ATGTTAAATT
817159 CTAAAAGTAATAAAATAAAAATAATAAGAAG
1 CTAAAA-TAATAAAATAAAAATAA-AA-AAG
* *
817190 -TAAAAAACATAAAATAAATAATAAAAATG
1 CTAAAATA-ATAAAATAAA-AATAAAAAAG
*
817219 CTAAAATTAAAAAAATAAAA
1 CTAAAA-TAATAAAATAAAA
817239 CCAACTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 4 0.10
30 31 0.76
31 6 0.15
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (28 bp):
CTAAAATAATAAAATAAAAATAAAAAAG
Found at i:817900 original size:9 final size:10
Alignment explanation
Indices: 817888--817930 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
817878 TTACAAAAAT
817888 AATAA-AATA
1 AATAATAATA
817897 AATAATAATAA
1 AATAATAAT-A
817908 TAATAATAATA
1 -AATAATAATA
817919 AATAATAATA
1 AATAATAATA
817929 AA
1 AA
817931 ATATTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.16
10 15 0.48
11 2 0.06
12 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAATAATA
Found at i:817901 original size:12 final size:13
Alignment explanation
Indices: 817885--817929 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
817875 GGCTTACAAA
817885 AATAATAAAATAAAT
1 AATAAT-AAAT-AAT
817900 AATAAT-AATAAT
1 AATAATAAATAAT
817912 AATAATAAATAAT
1 AATAATAAATAAT
817925 AATAA
1 AATAA
817930 AATATTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.31
13 14 0.48
15 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:817903 original size:3 final size:3
Alignment explanation
Indices: 817885--817933 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
817875 GGCTTACAAA
817885 AAT AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AA-
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
817930 AAT A
1 AAT A
817934 TTTTTGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:819013 original size:124 final size:124
Alignment explanation
Indices: 818793--819585 Score: 1284
Period size: 124 Copynumber: 6.4 Consensus size: 124
818783 TGCCCCTTTC
** * * *
818793 TTGTGAAGTTGAGATTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTAAAGATGGA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* * * *
818858 TGTTGCTGGTGAGCACGATGTTCTTCGTCGTGAAGTTGAAATCGTGGATGACACATTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
*
818917 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTTAAAGATGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* * *
818982 TGTTTCTAGTGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTC-TTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACC-CATTCG
* * *
819041 TTGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGTTGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* * *
819106 TGTTGCTGGTGGGCACGATATCCGTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
*
819165 TTGTGAAGTTGAGCCTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* *
819230 TGTTGCTGGT-GGCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCCTTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
*
819288 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* *
819353 TGTTGCTGGTGGGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCATTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
* *
819412 TTGTGAAGTTAAGCCTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* * * *
819477 TATTGCTGGTGGGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATGACCCCTTCG
66 TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
819536 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
819586 GTGGATGACC
Statistics
Matches: 617, Mismatches: 49, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
123 117 0.19
124 499 0.81
125 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (124 bp):
TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
TGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCG
Found at i:819208 original size:190 final size:191
Alignment explanation
Indices: 818999--819775 Score: 736
Period size: 190 Copynumber: 4.1 Consensus size: 191
818989 AGTGGGCACA
*
818999 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTATGAAGTTGAGCCTTGAATTG
*
819064 AATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGT-TGAATGTTGCTGGTGGGCACGATATC
66 AATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGTATGAATGTTGCTGGTGGGCACGATATC
* * * *
819128 CGTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTAG
131 CTTCATCGTGAAGTTGAAATCATGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGG
* ** * * * *
819189 ATATCCTTCGTCGTGAAGTTGAAATC---CA--A--TCTAAAG--ATGAATGTTGCTG-GTGGCA
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCT-TCGTTATGAA-GTTG-AGCCTTGAA
* * * * ** *
819244 -CG-ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCCT-TCGTTGTGAA-GTTGAGCCT-
63 TTGAATATCCTTCGTCGTGAAGTTGAAATC---CA--A--TCTAAAG-TATGAATGTT--G-CTG
***** ** * ** *
819304 -TGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGA-TGAAT-GTTGCTG--G-T
117 GTGGGCACGATATCCTTCATCGTGAAGTTGAAAT-C-AT-GGATGACCCATTCGTTG-TGAAGTT
* *
819363 G-G----GCA--CG
178 GAGCCTTGAATTGG
* * * *
819370 ATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCC-CATTCGTTGTGAAGTTAAGCCTTGAATT
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTC-TTCGTTATGAAGTTGAGCCTTGAATT
* * *
819434 GGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAG-ATGAATATTGCTGGTGGGCACGATAT
65 GAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGTATGAATGTTGCTGGTGGGCACGATAT
*
819498 CCTTCATCGTGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGG
130 CCTTCATCGTGAAGTTGAAATCATGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGG
*
819560 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTATGAAGTTGAGCCTTGAATTG
819625 AATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAA-TATGAATGTTGCTGGTGGGCACGATATC
66 AATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGTATGAATGTTGCTGGTGGGCACGATATC
* * * * *
819689 CTTCACCGTGAAGTTAAAATCGTGGATGACTCATTCGTTGTAAAGTTGAGCCTTGAATTGG
131 CTTCATCGTGAAGTTGAAATCATGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGG
819750 ATATCCTTCGTCGTGAAGTTGAAATC
1 ATATCCTTCGTCGTGAAGTTGAAATC
819776 CAATCTAAAG
Statistics
Matches: 459, Mismatches: 78, Indels: 100
0.72 0.12 0.16
Matches are distributed among these distances:
179 3 0.01
180 7 0.02
181 56 0.12
182 38 0.08
183 18 0.04
184 6 0.01
185 2 0.00
186 1 0.00
187 7 0.02
188 17 0.04
189 36 0.08
190 257 0.56
191 9 0.02
192 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (191 bp):
ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTATGAAGTTGAGCCTTGAATTG
AATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGTATGAATGTTGCTGGTGGGCACGATATC
CTTCATCGTGAAGTTGAAATCATGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGG
Found at i:819485 original size:371 final size:372
Alignment explanation
Indices: 818793--819585 Score: 1311
Period size: 371 Copynumber: 2.1 Consensus size: 372
818783 TGCCCCTTTC
** * * *
818793 TTGTGAAGTTGAGATTTGAATTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTAAAGATGGA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* * *
818858 TGTTGCTGGTGAGCACGATGTTCTTCGTCGTGAAGTTGAAATCGTGGATGACACATTCGTTGTGA
66 TGTTGCTGGTGAGCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACACATTCGTTGTGA
* * *
818923 AGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTTAAAGATGAATGTTTC
131 AGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC
* *
818988 TAGTGGGCACAATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCTCTTCGTTGTGAAGTTGA
196 TAGTGGGCACAATATCCTTCGTCATGAAGTTGAAATCGTGGATGACCTCTTCGTTGTGAAGTTAA
* * *
819053 GCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGTTGAATGTTGCTGGTGG
261 GCCTTGAATTGAATATCATTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATATTGCTGGTGG
* *
819118 GCACGATATCCGTCGTCGTGAAGTTGAAATCATGGATGGCCCATTCG
326 GCACGATATCCGTCATCGTGAAGTTGAAATCATGGATGACCCATTCG
*
819165 TTGTGAAGTTGAGCCTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
* *
819230 TGTTGCTGGTG-GCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACCCCTTCGTTGTGA
66 TGTTGCTGGTGAGCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACACATTCGTTGTGA
819294 AGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC
131 AGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC
* * *
819359 TGGTGGGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCC-CATTCGTTGTGAAGTTA
196 TAGTGGGCACAATATCCTTCGTCATGAAGTTGAAATCGTGGATGACCTC-TTCGTTGTGAAGTTA
* *
819423 AGCCTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATATTGCTGGTG
260 AGCCTTGAATTGAATATCATTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATATTGCTGGTG
* *
819488 GGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATGACCCCTTCG
325 GGCACGATATCCGTCATCGTGAAGTTGAAATCATGGATGACCCATTCG
819536 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
1 TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
819586 GTGGATGACC
Statistics
Matches: 391, Mismatches: 29, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
370 1 0.00
371 320 0.82
372 70 0.18
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (372 bp):
TTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAA
TGTTGCTGGTGAGCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGACACATTCGTTGTGA
AGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGC
TAGTGGGCACAATATCCTTCGTCATGAAGTTGAAATCGTGGATGACCTCTTCGTTGTGAAGTTAA
GCCTTGAATTGAATATCATTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATATTGCTGGTGG
GCACGATATCCGTCATCGTGAAGTTGAAATCATGGATGACCCATTCG
Found at i:819542 original size:32 final size:32
Alignment explanation
Indices: 819506--819613 Score: 103
Period size: 32 Copynumber: 3.3 Consensus size: 32
819496 ATCCTTCATC
819506 GTGAAGTTGAAATCATGGATGACCCCTTCGTT
1 GTGAAGTTGAAATCATGGATGACCCCTTCGTT
** * * *
819538 GTGAAGTTGAGCCTTGAATTGGAT-A-TCCTTCGTC
1 GTGAAGTTGA--AAT-CA-TGGATGACCCCTTCGTT
*
819572 GTGAAGTTGAAATCGTGGATGACCCCTTCGTT
1 GTGAAGTTGAAATCATGGATGACCCCTTCGTT
*
819604 ATGAAGTTGA
1 GTGAAGTTGA
819614 GCCTTGAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
30 5 0.09
31 1 0.02
32 27 0.47
34 18 0.31
35 2 0.03
36 5 0.09
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (32 bp):
GTGAAGTTGAAATCATGGATGACCCCTTCGTT
Found at i:819576 original size:34 final size:34
Alignment explanation
Indices: 819530--819647 Score: 118
Period size: 34 Copynumber: 3.5 Consensus size: 34
819520 ATGGATGACC
*
819530 CCTTCGTTGTGAAGTTGAGCCTTGAATTGGATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
** * *
819564 CCTTCGTCGTGAAGTTGA-AATCG---TGGATGACC
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGAT-A-T
** *
819596 CCTTCGTTATGAAGTTGAGCCTTGAATTGAATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
819630 CCTTCGTCGTGAAGTTGA
1 CCTTCGTCGTGAAGTTGA
819648 AATCCAATCT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
30 5 0.08
31 1 0.02
32 16 0.25
33 4 0.06
34 33 0.52
35 1 0.02
36 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (34 bp):
CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
Found at i:819599 original size:66 final size:66
Alignment explanation
Indices: 819493--819651 Score: 282
Period size: 66 Copynumber: 2.4 Consensus size: 66
819483 TGGTGGGCAC
* *
819493 GATATCCTTCATCGTGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATT
819558 G
66 G
*
819559 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATT
819624 G
66 G
*
819625 AATATCCTTCGTCGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
819652 CAATCTAAAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 89 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (66 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATT
G
Found at i:819687 original size:124 final size:124
Alignment explanation
Indices: 819559--819797 Score: 397
Period size: 124 Copynumber: 1.9 Consensus size: 124
819549 CCTTGAATTG
** * * *
819559 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATT
1 GATATCCTTCACCGTGAAGTTAAAATCGTGGATGACCCATTCGTTATAAAGTTGAGCCTTGAATT
*
819624 GAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAATATGAATGTTGCTGGTGGGCAC
66 GAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCAC
* *
819683 GATATCCTTCACCGTGAAGTTAAAATCGTGGATGACTCATTCGTTGTAAAGTTGAGCCTTGAATT
1 GATATCCTTCACCGTGAAGTTAAAATCGTGGATGACCCATTCGTTATAAAGTTGAGCCTTGAATT
*
819748 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
66 GAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
819798 TCGAGTTCAA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 106 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (124 bp):
GATATCCTTCACCGTGAAGTTAAAATCGTGGATGACCCATTCGTTATAAAGTTGAGCCTTGAATT
GAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCAC
Found at i:820552 original size:19 final size:19
Alignment explanation
Indices: 820528--820583 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
820518 GAATGCATTT
*
820528 CATGCACCGATGCACTCTC
1 CATGCATCGATGCACTCTC
820547 CATGCATCGATGCACTCTC
1 CATGCATCGATGCACTCTC
820566 CATGCATCGATGCACTCT
1 CATGCATCGATGCACTCT
820584 GAATATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (19 bp):
CATGCATCGATGCACTCTC
Found at i:820657 original size:64 final size:64
Alignment explanation
Indices: 820548--820688 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 64
820538 TGCACTCTCC
*** *
820548 ATGCATCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTG
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTG
** * *
820612 ATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCATACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCAAACATCGAATGCATTTG
*
820676 ATGCATCAATGCA
1 ATGCATCGATGCA
820689 TCCTTAGTGC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 4 0.06
64 63 0.94
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTG
Found at i:828720 original size:2 final size:2
Alignment explanation
Indices: 828713--828740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
828703 GCAGCTTAAG
828713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
828741 CAATTGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:829368 original size:64 final size:64
Alignment explanation
Indices: 829291--829413 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
829281 GAATGCATTT
*
829291 CATGCACCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTTGATGCATCGATGCACAAGC
1 CATGCACCGATGCAC-CAGAATATTTTTCAAACATCGAATGCATTTGATGCATCGATGCACAAGC
* ** * *
829355 CATGCATCGATGCACCAGGCTATTTTTCATACATCGAATGCATTTTATGCATCGATGCA
1 CATGCACCGATGCACCAGAATATTTTTCAAACATCGAATGCATTTGATGCATCGATGCA
829414 TCCTTAGTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 4 0.08
64 48 0.92
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
CATGCACCGATGCACCAGAATATTTTTCAAACATCGAATGCATTTGATGCATCGATGCACAAGC
Found at i:830973 original size:95 final size:95
Alignment explanation
Indices: 830805--831003 Score: 335
Period size: 95 Copynumber: 2.1 Consensus size: 95
830795 GGACAACTTA
* *
830805 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACATTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
*
830870 GCTCTAGAGGGACAACTCAAGCTTTATTGT
66 GATCTAGAGGGACAACTCAAGCTTTATTGT
* *
830900 ATATTATAATCACATTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATT
1 ATATTATAATCACATTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
*
830965 GATTTAGAGGGACAACTCAAGCTTTATTGT
66 GATCTAGAGGGACAACTCAAGCTTTATTGT
830995 ATATATATA
1 ATAT-TATA
831004 TAATATTATA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 93 0.96
96 4 0.04
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
ATATTATAATCACATTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATT
GATCTAGAGGGACAACTCAAGCTTTATTGT
Found at i:831756 original size:5 final size:5
Alignment explanation
Indices: 831746--831771 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
831736 TGACTTAGAA
831746 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
831772 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:833082 original size:27 final size:27
Alignment explanation
Indices: 833039--833090 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
833029 CACCTCTTTT
* *
833039 AAATGAATGATGAAAAAGATGAAAATA
1 AAATGAAAGATGAAAAAAATGAAAATA
833066 AAATGAAAGA-GAGAAAAAATGAAAA
1 AAATGAAAGATGA-AAAAAATGAAAA
833091 AAGTTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.13
Consensus pattern (27 bp):
AAATGAAAGATGAAAAAAATGAAAATA
Found at i:834162 original size:11 final size:11
Alignment explanation
Indices: 834142--834171 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
834132 GTTAGATAAG
834142 AAATAATAAAT
1 AAATAATAAAT
*
834153 AAATATTAAAT
1 AAATAATAAAT
834164 AAATAATA
1 AAATAATA
834172 TTAAATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:834171 original size:14 final size:15
Alignment explanation
Indices: 834146--834177 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
834136 GATAAGAAAT
834146 AATAAATAAATATTA
1 AATAAATAAATATTA
834161 AATAAAT-AATATTA
1 AATAAATAAATATTA
834175 AAT
1 AAT
834178 GAATCAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATAAATATTA
Found at i:834236 original size:14 final size:14
Alignment explanation
Indices: 834213--834271 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 14
834203 TGTTAAATTC
*
834213 TAAAACTAATAAAA
1 TAAAAATAATAAAA
834227 TAAAAATAATAAGAA
1 TAAAAATAATAA-AA
834242 GTAAAAA-ACATAAAA
1 -TAAAAATA-ATAAAA
834257 TAAATAATAATAAAA
1 TAAA-AATAATAAAA
834272 AATGCTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
14 15 0.38
15 13 0.33
16 11 0.28
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:836055 original size:31 final size:31
Alignment explanation
Indices: 836017--836078 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
836007 CAATAACGAG
836017 ATAGTCTCCTAAATAATTGGAGTGAAATATT
1 ATAGTCTCCTAAATAATTGGAGTGAAATATT
836048 ATAGTCTCCTAAATAATTGGAGTGAAATATT
1 ATAGTCTCCTAAATAATTGGAGTGAAATATT
836079 CGTTAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (31 bp):
ATAGTCTCCTAAATAATTGGAGTGAAATATT
Found at i:838311 original size:24 final size:24
Alignment explanation
Indices: 838278--838353 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
838268 GCGATGGAAG
* * *
838278 TGAAAAAACACTTTCTATTAATCT
1 TGAAAGAACACTTTCTATTGAGCT
838302 TGAAAGAACACTTTCTATTGAGCT
1 TGAAAGAACACTTTCTATTGAGCT
*
838326 TGAGAGAACACTTTCTATTGAGCT
1 TGAAAGAACACTTTCTATTGAGCT
838350 TGAA
1 TGAA
838354 GGACACCGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (24 bp):
TGAAAGAACACTTTCTATTGAGCT
Found at i:839145 original size:24 final size:24
Alignment explanation
Indices: 839092--839137 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
839082 CACTGTTGGT
839092 TGGTTTGATGAATTTATTTTGTCA
1 TGGTTTGATGAATTTATTTTGTCA
839116 TGGTTTGATGAATTTATTTTGT
1 TGGTTTGATGAATTTATTTTGT
839138 TATTGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.57
Consensus pattern (24 bp):
TGGTTTGATGAATTTATTTTGTCA
Found at i:839983 original size:14 final size:14
Alignment explanation
Indices: 839960--839990 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
839950 AGTGCTGGGA
839960 AAGATCGTCTTTTG
1 AAGATCGTCTTTTG
*
839974 AAGATTGTCTTTTG
1 AAGATCGTCTTTTG
839988 AAG
1 AAG
839991 TACTGGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (14 bp):
AAGATCGTCTTTTG
Found at i:842573 original size:3 final size:3
Alignment explanation
Indices: 842565--842595 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
842555 TTTATAATTA
842565 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
842596 ATGTCTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:842782 original size:20 final size:19
Alignment explanation
Indices: 842745--842788 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
842735 TACTATTAAT
842745 AAAAGATGTTTAAATTTTA
1 AAAAGATGTTTAAATTTTA
* * *
842764 AAAAGTTGTCTTAACTTTTC
1 AAAAGATGT-TTAAATTTTA
842784 AAAAG
1 AAAAG
842789 GGAACATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAAGATGTTTAAATTTTA
Found at i:843482 original size:15 final size:15
Alignment explanation
Indices: 843464--843502 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
843454 CTCATATAGC
843464 AAGAAAAAGATATTA
1 AAGAAAAAGATATTA
*
843479 AAGACAAAGATATTA
1 AAGAAAAAGATATTA
843494 AAGACAAAA
1 AAGA-AAAA
843503 TTTGGGTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (15 bp):
AAGAAAAAGATATTA
Found at i:849809 original size:2 final size:2
Alignment explanation
Indices: 849802--849884 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
849792 GAAATAGGGT
849802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
849844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
849885 CTTATTGACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:852138 original size:17 final size:18
Alignment explanation
Indices: 852099--852138 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
852089 AGCTTACATA
*
852099 TCTTTATTTATATTTTTC
1 TCTTTATTTATATTTATC
852117 T-TTTATTT-TATTTATC
1 TCTTTATTTATATTTATC
852133 TCTTTA
1 TCTTTA
852139 GTCATTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 11 0.55
18 1 0.05
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTTTATTTATATTTATC
Found at i:852265 original size:45 final size:45
Alignment explanation
Indices: 852193--852674 Score: 671
Period size: 45 Copynumber: 10.7 Consensus size: 45
852183 TATGCATCAT
* * *
852193 TATGCATTTTCATTTATGGCATTCTTTCATGCCAATAATGCACCCA
1 TATGCA-TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
*
852239 TATGCATTTCAATCATGGCATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
*** * *
852284 TATGCATTTCAATTATTATATCATTTCATGCTGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
*
852329 TATGCATTTCAATTATGACATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
852374 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * **
852419 TATGCATTTTAATTATGACATCAATTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * * *
852464 TATGGATTTTAATTATGTCATCCTTTCATACCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* *
852509 TATGCATTTCAATTATGGCATCATTTCATGACGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * * *
852554 TATGCATTTCAATTATGGCATCATTTTATACCGATAATACA-CCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* *
852598 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATACA-CTA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * *
852642 TTATACATTTCATTTATGGCATCATTTCATGCC
1 -TATGCATTTCAATTATGGCATCCTTTCATGCC
852675 TTTTATACAA
Statistics
Matches: 394, Mismatches: 41, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
44 43 0.11
45 345 0.88
46 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (45 bp):
TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
Found at i:852940 original size:67 final size:67
Alignment explanation
Indices: 852810--853195 Score: 524
Period size: 67 Copynumber: 5.8 Consensus size: 67
852800 AGGTATTTAA
* * * *
852810 CCTTTCATCTAACT-GCATAATTGACACCTTTCTATCAAATG-AGTAGCTAGGTCTCAAAGGCAC
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCA-CAGTTAGGCCTCAAAGGCAC
*
852873 TTAT
64 TTAG
* * ** * *
852877 CATTTCATCTAACTAGCATAATTGACATATTTCTATCAATGCACAGTTAGGCCTCAAAAGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
852942 AG
66 AG
* * *
852944 CCTTTCATCTAACTGACATAATTAACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
853009 AG
66 AG
* ** * *
853011 CCTTTCATCTAACTGGCATAATTGAAATTTTTCTGTCAATGCATAGTTAGGCCTCAAAGGTACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
853076 AG
66 AG
* *
853078 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCATCAAAGTCACTT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
853143 AG
66 AG
* * *
853145 CCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAATACATAGTTAGG
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGG
853196 ACTTAAATAT
Statistics
Matches: 282, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
67 261 0.93
68 21 0.07
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (67 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
AG
Found at i:853468 original size:57 final size:57
Alignment explanation
Indices: 853407--853536 Score: 172
Period size: 57 Copynumber: 2.3 Consensus size: 57
853397 GTTCTTATAC
* * ** *
853407 GGAAATTCATAAACAGATTATGAATTCCTTA-ACTTTTTGCACACTCAGTTCCCATAA
1 GGAAATTCATAAACAAATTACGAATTCCTTATA-TTTTTGCACACAAAGTGCCCATAA
* * *
853464 GGAAATTCATAAATAAATTACGAATTTCTTATATTTTTGCACACAAAGTGCCCATAC
1 GGAAATTCATAAACAAATTACGAATTCCTTATATTTTTGCACACAAAGTGCCCATAA
853521 GGAAATTCATAAACAA
1 GGAAATTCATAAACAA
853537 TGCCTAACTG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 62 0.98
58 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (57 bp):
GGAAATTCATAAACAAATTACGAATTCCTTATATTTTTGCACACAAAGTGCCCATAA
Found at i:853650 original size:67 final size:67
Alignment explanation
Indices: 853538--853737 Score: 303
Period size: 67 Copynumber: 3.0 Consensus size: 67
853528 CATAAACAAT
*
853538 GCCTAACTGTGCATT-AACAAAAAGGTGTCAGTTATGCCAGCTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTGAA-AAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
853602 GAG
65 GAG
* *
853605 GCCTAACTTTGCATTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 GCCTAACTGTGCATTGAAAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
853670 AG
66 AG
** * * * *
853672 ATCTAACTGTGCATTGACAGAAAGGTGTCAGCTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTG
1 GCCTAACTGTGCATTGAAAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
853737 A
66 A
853738 CAGAAAGGTG
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
67 119 0.98
68 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (67 bp):
GCCTAACTGTGCATTGAAAAAAAGGTGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AG
Found at i:853785 original size:49 final size:49
Alignment explanation
Indices: 853685--853786 Score: 150
Period size: 49 Copynumber: 2.1 Consensus size: 49
853675 TAACTGTGCA
* * **
853685 TTGACAGAAAGGTGTCAGCTATGCCAGTTAGATGAAAGGCTAAGTGTCT
1 TTGACAGAAAGGTGTCAACTATGCCAGTTAGATGAAAGGCTAAATACCT
* *
853734 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCT
1 TTGACAGAAAGGTGTCAACTATGCCAGTTAGATGAAAGGCTAAATACCT
853783 TTGA
1 TTGA
853787 GTAAAAGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (49 bp):
TTGACAGAAAGGTGTCAACTATGCCAGTTAGATGAAAGGCTAAATACCT
Found at i:853895 original size:81 final size:80
Alignment explanation
Indices: 853733--853895 Score: 195
Period size: 81 Copynumber: 2.0 Consensus size: 80
853723 GCTAAGTGTC
* * * * *
853733 TTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
1 TTTGACAAAAAGGTGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTGAGTAAAAGACTA
* **
853798 ATGACCTAGCTGTGCA
66 ATGA-CTAACAATGCA
*
853814 TTTGACAAAAAGGTGTCAATCATGCCA-TATATATAAAAAGTTAAATACCTTTGAGTAAAAGACT
1 TTTGACAAAAAGGTGTCAATCATGCCAGT-TAGATAAAAAGTTAAATACCTTTGAGTAAAAGACT
853878 AGATGTA-TAACAATGCA
65 A-ATG-ACTAACAATGCA
853895 T
1 T
853896 AATGTTGTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
80 1 0.01
81 65 0.93
82 3 0.04
83 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (80 bp):
TTTGACAAAAAGGTGTCAATCATGCCAGTTAGATAAAAAGTTAAATACCTTTGAGTAAAAGACTA
ATGACTAACAATGCA
Found at i:853999 original size:45 final size:45
Alignment explanation
Indices: 853949--854311 Score: 476
Period size: 45 Copynumber: 8.0 Consensus size: 45
853939 ATAATAGTGT
* * *
853949 ATTATCGTCATGAAAGGATGCCATAATTAAAATTCATATGAGTGC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* * * *
853994 ATTATCGGCATAAAAGGATTCCATAATTGAAATGCATATGTGTGC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* *
854039 ATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGGGTAC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* * *
854084 ATTATCGGCATGAAAGAATGTCATAATTAAAATGCATATGGGTAC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* * * * * *
854129 ATTATCGGTATAAAATGATGACATAATTGAAATGCATATGGGTTC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
*
854174 ATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* * *
854219 ATTATCGACATGAAAGGATGCCATGATTAAAATGCATATGGGTAC
1 ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
* * *
854264 ATTATTGGCATGAAAGAATGCCATAAATGAAAATGCATAAT-GGTGC
1 ATTATCGGCATGAAAGGATGCCAT-AATTAAAATGCAT-ATGGGTGC
854310 AT
1 AT
854312 AATAAGTATG
Statistics
Matches: 281, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
45 262 0.93
46 17 0.06
47 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (45 bp):
ATTATCGGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGC
Found at i:854111 original size:135 final size:134
Alignment explanation
Indices: 853949--854311 Score: 528
Period size: 135 Copynumber: 2.7 Consensus size: 134
853939 ATAATAGTGT
* * * * *
853949 ATTATCGTCATGAAAGGATGCCATAATTAAAATTCATATGAGTGCATTATCGGCATAAAAGGATT
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTACATTATCGGCATAAAAGGATG
854014 CCATAATTGAAATGCATATGTGTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATG
66 CCATAATTGAAATGCATATG-GTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATG
854079 GGTAC
130 GGTAC
* * * * *
854084 ATTATCGGCATGAAAGAATGTCATAATTAAAATGCATATGGGTACATTATCGGTATAAAATGATG
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTACATTATCGGCATAAAAGGATG
* *
854149 ACATAATTGAAATGCATATGGGTTCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATG
66 CCATAATTGAAATGCATAT-GGTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATG
*
854214 GGTGC
130 GGTAC
* * * *
854219 ATTATCGACATGAAAGGATGCCATGATTAAAATGCATATGGGTACATTATTGGCATGAAAGAATG
1 ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTACATTATCGGCATAAAAGGATG
*
854284 CCATAAATGAAAATGCATAATGGTGCAT
66 CCATAATTG-AAATGCAT-ATGGTGCAT
854312 AATAAGTATG
Statistics
Matches: 201, Mismatches: 24, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
135 184 0.92
136 15 0.07
137 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (134 bp):
ATTATCGACATGAAAGGATGCCATAATTAAAATGCATATGGGTACATTATCGGCATAAAAGGATG
CCATAATTGAAATGCATATGGTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGG
GTAC
Found at i:857087 original size:22 final size:19
Alignment explanation
Indices: 857059--857108 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
857049 CCTATCACGA
857059 TATCGATACTACTACACTATGG
1 TATCGATACT-CT--ACTATGG
*
857081 TATCGATACTCTATTATGG
1 TATCGATACTCTACTATGG
857100 TATCGATAC
1 TATCGATAC
857109 CATTTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.56
21 2 0.07
22 10 0.37
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (19 bp):
TATCGATACTCTACTATGG
Found at i:859832 original size:13 final size:13
Alignment explanation
Indices: 859814--859838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
859804 CCTCGATAGG
859814 GTATCGATACCAA
1 GTATCGATACCAA
859827 GTATCGATACCA
1 GTATCGATACCA
859839 TTCAATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACCAA
Found at i:859890 original size:20 final size:20
Alignment explanation
Indices: 859861--859909 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
859851 TTTCAAGCAT
859861 CGATACTCCCCTAGGAGTAC
1 CGATACTCCCCTAGGAGTAC
*
859881 CGATATTCCCCTAGGAGTAC
1 CGATACTCCCCTAGGAGTAC
*
859901 TGATACTCC
1 CGATACTCC
859910 TGGTAGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
CGATACTCCCCTAGGAGTAC
Found at i:866038 original size:13 final size:13
Alignment explanation
Indices: 866015--866074 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
866005 GTCATAACCC
*
866015 GACCAGACCCGTT
1 GACCCGACCCGTT
*
866028 TACCCGACCCGTT
1 GACCCGACCCGTT
866041 GACCCGACCTGACCCGTT
1 GA--C--CC-GACCCGTT
866059 GACCCGACCCGTT
1 GACCCGACCCGTT
866072 GAC
1 GAC
866075 TCGTTGACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 23 0.59
14 2 0.05
15 1 0.03
16 1 0.03
17 2 0.05
18 10 0.26
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:866044 original size:8 final size:8
Alignment explanation
Indices: 866033--866104 Score: 71
Period size: 8 Copynumber: 9.2 Consensus size: 8
866023 CCGTTTACCC
866033 GACCCGTT
1 GACCCGTT
*
866041 GACCCGACCT
1 GACCCG--TT
866051 GACCCGTT
1 GACCCGTT
866059 GACCC---
1 GACCCGTT
866064 GACCCGTT
1 GACCCGTT
*
866072 GACTCGTT
1 GACCCGTT
*
866080 GACTCGTT
1 GACCCGTT
866088 GA-CCGTT
1 GACCCGTT
866095 GACCCGTT
1 GACCCGTT
866103 GA
1 GA
866105 TCGTTTACCG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.09
7 6 0.11
8 36 0.67
10 7 0.13
ACGTcount: A:0.15, C:0.36, G:0.25, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:866049 original size:31 final size:31
Alignment explanation
Indices: 866011--866074 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
866001 ATCGGTCATA
*
866011 ACCCGACCAGACCCGTTTACCCGACCCGTTG
1 ACCCGACCAGACCCGTTGACCCGACCCGTTG
*
866042 ACCCGACCTGACCCGTTGACCCGACCCGTTG
1 ACCCGACCAGACCCGTTGACCCGACCCGTTG
866073 AC
1 AC
866075 TCGTTGACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.45, G:0.20, T:0.16
Consensus pattern (31 bp):
ACCCGACCAGACCCGTTGACCCGACCCGTTG
Found at i:866054 original size:18 final size:18
Alignment explanation
Indices: 866033--866067 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
866023 CCGTTTACCC
866033 GACCCGTTGACCCGACCT
1 GACCCGTTGACCCGACCT
866051 GACCCGTTGACCCGACC
1 GACCCGTTGACCCGACC
866068 CGTTGACTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCCGTTGACCCGACCT
Found at i:866096 original size:15 final size:15
Alignment explanation
Indices: 866050--866123 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
866040 TGACCCGACC
866050 TGACCCGTTGACC--
1 TGACCCGTTGACCGT
*
866063 CGACCCGTTGACTCGT
1 TGACCCGTTGAC-CGT
*
866079 TGACTCGTTGACCGT
1 TGACCCGTTGACCGT
*
866094 TGACCCGTTGATCGT
1 TGACCCGTTGACCGT
*
866109 TTACCGGCGTTGACC
1 TGACC--CGTTGACC
866124 ACTGTTGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
13 11 0.22
14 1 0.02
15 20 0.41
16 10 0.20
17 7 0.14
ACGTcount: A:0.14, C:0.32, G:0.26, T:0.28
Consensus pattern (15 bp):
TGACCCGTTGACCGT
Found at i:866096 original size:23 final size:22
Alignment explanation
Indices: 866067--866114 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
866057 TTGACCCGAC
*
866067 CCGTTGACTCGTTGACTCGTTGA
1 CCGTTGACCCGTTGA-TCGTTGA
*
866090 CCGTTGACCCGTTGATCGTTTA
1 CCGTTGACCCGTTGATCGTTGA
866112 CCG
1 CCG
866115 GCGTTGACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.12, C:0.29, G:0.25, T:0.33
Consensus pattern (22 bp):
CCGTTGACCCGTTGATCGTTGA
Found at i:868648 original size:47 final size:48
Alignment explanation
Indices: 868590--868681 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 48
868580 AATTCTGTTA
* * *
868590 TGATACCTGACCTGGATTCTGATTTGATA-TTGACATGGATTATGATC
1 TGATACATGACCTGGATTCTGATATGATACTTGACATGAATTATGATC
*
868637 TGATACATGACCTGGATTCTGATATGATACTTGACTTGAATTATG
1 TGATACATGACCTGGATTCTGATATGATACTTGACATGAATTATG
868682 TTTTGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 27 0.68
48 13 0.32
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (48 bp):
TGATACATGACCTGGATTCTGATATGATACTTGACATGAATTATGATC
Found at i:868688 original size:24 final size:24
Alignment explanation
Indices: 868581--868671 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
868571 TCAAATTTGA
* *
868581 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
868605 ATTCTGATTTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
868628 ATTATGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
868652 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
868672 TTGAATTATG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 19 0.35
24 36 0.65
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:872246 original size:8 final size:8
Alignment explanation
Indices: 872233--872257 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
872223 CATCATTAAA
872233 AAAAATTC
1 AAAAATTC
872241 AAAAATTC
1 AAAAATTC
872249 AAAAATTC
1 AAAAATTC
872257 A
1 A
872258 TTAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:874538 original size:24 final size:22
Alignment explanation
Indices: 874511--874563 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
874501 TGATACTACT
* *
874511 TAGTACCGATACTACTCTTCATTG
1 TAGTACCGA-A-TACTCTTAATGG
*
874535 TAGTATC-AATACTCTTAATGG
1 TAGTACCGAATACTCTTAATGG
874556 TAGTACCG
1 TAGTACCG
874564 GTTTAGCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 16 0.67
22 1 0.04
23 1 0.04
24 6 0.25
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (22 bp):
TAGTACCGAATACTCTTAATGG
Found at i:874741 original size:225 final size:225
Alignment explanation
Indices: 874339--874788 Score: 884
Period size: 225 Copynumber: 2.0 Consensus size: 225
874329 TGATTTTTAA
874339 GTTTAGCAGTATCGATACTACAAGAACAATATCGATATTGTTCATGAAGTATCAATACCACTACC
1 GTTTAGCAGTATCGATACTACAAGAACAATATCGATATTGTTCATGAAGTATCAATACCACTACC
874404 GATGTTGAAGCCCAAAATTATACAGTAGTACCGATACTGCTAAGGCAGTACCGATATTTCATGTA
66 GATGTTGAAGCCCAAAATTATACAGTAGTACCGATACTGCTAAGGCAGTACCGATATTTCATGTA
874469 AGTTTGAGGAAAACAGAATGCTCAATTGGTACTGATACTACTTAGTACCGATACTACTCTTCATT
131 AGTTTGAGGAAAACAGAATGCTCAATTGGTACTGATACTACTTAGTACCGATACTACTCTTCATT
874534 GTAGTATCAATACTCTTAATGGTAGTACCG
196 GTAGTATCAATACTCTTAATGGTAGTACCG
874564 GTTTAGCAGTATCGATACTACAAGAACAATATCGATATTGTTCATGAAGTATCAATACCACTACC
1 GTTTAGCAGTATCGATACTACAAGAACAATATCGATATTGTTCATGAAGTATCAATACCACTACC
874629 GATGTTGAAGCCCAAAATTATACAGTAGTACCGATACTGCTAAGGCAGTACCGATATTTCATGTA
66 GATGTTGAAGCCCAAAATTATACAGTAGTACCGATACTGCTAAGGCAGTACCGATATTTCATGTA
874694 AGTTTGA-GAAAACAGAATGCTCAATTGGTACTGATACTACTTTAGTACCGATACTACTCTTCAT
131 AGTTTGAGGAAAACAGAATGCTCAATTGGTACTGATACTAC-TTAGTACCGATACTACTCTTCAT
874758 TGTAGTATCAATACTCTTAATGGTAGTACCG
195 TGTAGTATCAATACTCTTAATGGTAGTACCG
874789 ATACTACCCT
Statistics
Matches: 224, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
224 33 0.15
225 191 0.85
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (225 bp):
GTTTAGCAGTATCGATACTACAAGAACAATATCGATATTGTTCATGAAGTATCAATACCACTACC
GATGTTGAAGCCCAAAATTATACAGTAGTACCGATACTGCTAAGGCAGTACCGATATTTCATGTA
AGTTTGAGGAAAACAGAATGCTCAATTGGTACTGATACTACTTAGTACCGATACTACTCTTCATT
GTAGTATCAATACTCTTAATGGTAGTACCG
Found at i:874763 original size:24 final size:24
Alignment explanation
Indices: 874736--874795 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
874726 GATACTACTT
* *
874736 TAGTACCGATACTACTCTTCATTG
1 TAGTACCGATACTACTCTTAATGG
*
874760 TAGTATC-A-A-TACTCTTAATGG
1 TAGTACCGATACTACTCTTAATGG
874781 TAGTACCGATACTAC
1 TAGTACCGATACTAC
874796 CCTTTGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 16 0.55
22 2 0.07
23 2 0.07
24 9 0.31
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (24 bp):
TAGTACCGATACTACTCTTAATGG
Found at i:880893 original size:21 final size:20
Alignment explanation
Indices: 880864--880918 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
880854 ATAAATCATA
880864 AAATATTATAATAATGATTCG
1 AAAT-TTATAATAATGATTCG
880885 AAATGTTATAATAATGATTCG
1 AAAT-TTATAATAATGATTCG
* *
880906 TAATTTAAAATAA
1 AAATTTATAATAA
880919 CACTAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (20 bp):
AAATTTATAATAATGATTCG
Found at i:881605 original size:22 final size:22
Alignment explanation
Indices: 881580--881622 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
881570 GCTCCCACCC
*
881580 ACCTCTGCCGCTCGAATCAAAG
1 ACCTCTGCCACTCGAATCAAAG
881602 ACCTCTGCCACTCGAATCAAA
1 ACCTCTGCCACTCGAATCAAA
881623 AGACATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.37, G:0.14, T:0.19
Consensus pattern (22 bp):
ACCTCTGCCACTCGAATCAAAG
Found at i:883448 original size:17 final size:17
Alignment explanation
Indices: 883426--883475 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
883416 AAATTCTTCT
883426 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
883443 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
883457 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
883474 AA
1 AA
883476 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:883557 original size:13 final size:13
Alignment explanation
Indices: 883539--883565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
883529 TTATATAGTC
883539 TTGTGCACTATGT
1 TTGTGCACTATGT
883552 TTGTGCACTATGT
1 TTGTGCACTATGT
883565 T
1 T
883566 AATATCGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (13 bp):
TTGTGCACTATGT
Found at i:884457 original size:2 final size:2
Alignment explanation
Indices: 884445--884511 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
884435 CAAGGGATGG
884445 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
884486 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
884512 TAATGGGTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:884546 original size:12 final size:12
Alignment explanation
Indices: 884531--884557 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
884521 GATGGATGCT
884531 TCAGGTGATGGG
1 TCAGGTGATGGG
884543 TCAGGTGATGGG
1 TCAGGTGATGGG
884555 TCA
1 TCA
884558 AAAAAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.11, G:0.44, T:0.26
Consensus pattern (12 bp):
TCAGGTGATGGG
Found at i:895195 original size:15 final size:15
Alignment explanation
Indices: 895177--895206 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
895167 CCACGGTGCT
895177 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
895192 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
895207 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:899990 original size:27 final size:27
Alignment explanation
Indices: 899933--899993 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
899923 TGTATCATGT
* **
899933 CATATTATATAGCTCATTAGATTGTTA
1 CATATTACATAGCTCATTAGATCATTA
* * *
899960 CATATTACATAGTTCATTAGGTCATTG
1 CATATTACATAGCTCATTAGATCATTA
899987 CATATTA
1 CATATTA
899994 AATGTTATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (27 bp):
CATATTACATAGCTCATTAGATCATTA
Found at i:900664 original size:34 final size:34
Alignment explanation
Indices: 900621--900694 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
900611 AGGATTACCA
900621 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
900655 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
900689 AAAATA
1 AAAATA
900695 TTTTAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (34 bp):
AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
Found at i:912091 original size:31 final size:31
Alignment explanation
Indices: 912029--912098 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
912019 GTTTCAAAAC
* * * *
912029 TAATGAATTAGTCATTAATGTTATTAGTTTA
1 TAATAAATTAATCACTAATGTTATGAGTTTA
912060 TAATAAATTAATCACTAATGTTATCGA-TTTA
1 TAATAAATTAATCACTAATGTTAT-GAGTTTA
*
912091 TAAGAAAT
1 TAATAAAT
912099 CCATCCATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (31 bp):
TAATAAATTAATCACTAATGTTATGAGTTTA
Found at i:914196 original size:53 final size:53
Alignment explanation
Indices: 914112--914328 Score: 316
Period size: 53 Copynumber: 4.2 Consensus size: 53
914102 TTTCTAGGTA
* *
914112 CTAAGATATTGAGAGATGTACATACTTACACCAGTATAAATATGTGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
*
914165 CTACGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
* * * * * *
914218 CTAAGGTATTGTGAAATGTACATACTTACACCGGTGCAAGTATATGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
*
914271 CTAAGATATTGAGAGATGTAC--A--TACACCAGTGTAAGTATGTGATAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
914320 CTAAGATAT
1 CTAAGATAT
914329 GATAGTTGTT
Statistics
Matches: 147, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 32 0.22
51 1 0.01
53 114 0.78
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (53 bp):
CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
Found at i:916487 original size:12 final size:12
Alignment explanation
Indices: 916472--916526 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
916462 GTTATTTAAA
916472 CGGGTATTGGGC
1 CGGGTATTGGGC
*
916484 CGGGTATTGGGT
1 CGGGTATTGGGC
*
916496 TGGGTATTGGGC
1 CGGGTATTGGGC
* *
916508 CGGGAATCGGGC
1 CGGGTATTGGGC
916520 CGGGTAT
1 CGGGTAT
916527 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.11, C:0.15, G:0.49, T:0.25
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:916531 original size:2 final size:2
Alignment explanation
Indices: 916524--916621 Score: 87
Period size: 2 Copynumber: 51.0 Consensus size: 2
916514 TCGGGCCGGG
* * * * * *
916524 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
916565 TA T- TA AA T- TA AA TT TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
916604 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
916622 ATTATTTTAA
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
1 4 0.05
2 72 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:916666 original size:13 final size:12
Alignment explanation
Indices: 916635--916671 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
916625 ATTTTAATAT
*
916635 TATCGGGTCGGG
1 TATCGGGGCGGG
916647 TATCGGGGCGGG
1 TATCGGGGCGGG
916659 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
916672 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:919092 original size:32 final size:32
Alignment explanation
Indices: 919046--919113 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
919036 TATGTGAGTG
919046 AAGACTCTGCTTAACCTATGAACAAAAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
* *
919078 AAGACTCTGGTTAACCTATGAACAACAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
919110 AAGA
1 AAGA
919114 GACCATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (32 bp):
AAGACTCTGCTTAACCTATGAACAAAAATTTA
Found at i:919879 original size:13 final size:13
Alignment explanation
Indices: 919861--919885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
919851 AAATACACAT
919861 TAATAATTAAAAC
1 TAATAATTAAAAC
919874 TAATAATTAAAA
1 TAATAATTAAAA
919886 GTATCTGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAATTAAAAC
Done.