Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:2646447 original size:21 final size:21
Alignment explanation
Indices: 2646401--2646476 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2646391 TTGCAGCCTT
* *
2646401 GATGCATGGATGCATGGC-AT
1 GATGCATCGATGCATGGCAAG
2646421 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
*
2646442 GATGCATCGATGCATGGAAAG
1 GATGCATCGATGCATGGCAAG
*
2646463 GGTGCATCGATGCA
1 GATGCATCGATGCA
2646477 CTAATTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:2646522 original size:20 final size:22
Alignment explanation
Indices: 2646497--2646594 Score: 71
Period size: 21 Copynumber: 4.6 Consensus size: 22
2646487 TCGATGAATG
2646497 GATGCATGGATGCATTA-CCT-
1 GATGCATGGATGCATTAGCCTA
* **
2646517 GATGCATCGATGCATTAGTGTA
1 GATGCATGGATGCATTAGCCTA
* ***
2646539 GATGCATGGATGCACT-GCAGG
1 GATGCATGGATGCATTAGCCTA
* *
2646560 GATGCATGGATGCACT-G-CAA
1 GATGCATGGATGCATTAGCCTA
2646580 GGATGCATGGATGCA
1 -GATGCATGGATGCA
2646595 CTGCAGGGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.25
21 33 0.52
22 14 0.22
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (22 bp):
GATGCATGGATGCATTAGCCTA
Found at i:2646565 original size:21 final size:21
Alignment explanation
Indices: 2646539--2646617 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
2646529 CATTAGTGTA
2646539 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
*
2646560 GATGCATGGATGCACTGCAAG
1 GATGCATGGATGCACTGCAGG
2646581 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
2646602 GATGCATGGATGCACT
1 GATGCATGGATGCACT
2646618 TTGACACCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:2646732 original size:30 final size:30
Alignment explanation
Indices: 2646698--2646757 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2646688 AACTTTGAAT
2646698 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
* *
2646728 AAATTCAATTCCAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
2646758 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2647868 original size:75 final size:75
Alignment explanation
Indices: 2647736--2647929 Score: 235
Period size: 75 Copynumber: 2.6 Consensus size: 75
2647726 GAAGTGGGCC
* ** * *
2647736 TTCAGCATGCCCCAGCATTTGCTGATATGAACGTTCAAAATACACCAATATTCCTGATTATGTTT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACACCAATATTACTGATTATGATT
2647801 GAAAAGGGTT
66 GAAAAGGGTT
* * * * * * *
2647811 TTTAGCATGCCCCAACATTGGCTTATACAAACGTTCAAAATGCATCAGTATTACTGATTTTGATT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACACCAATATTACTGATTATGATT
*
2647876 GAAAGGGGTT
66 GAAAAGGGTT
* * * *
2647886 TTCAGCATACCCCAACATTTGCTGATACAGATGTTAAAAATACA
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACA
2647930 TTCACATTAC
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 98 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACACCAATATTACTGATTATGATT
GAAAAGGGTT
Found at i:2651246 original size:7 final size:7
Alignment explanation
Indices: 2651221--2651312 Score: 73
Period size: 7 Copynumber: 12.9 Consensus size: 7
2651211 GATTCAAGTT
*
2651221 TTTTTTA
1 TTTTTTC
2651228 TTTTTT-
1 TTTTTTC
*
2651234 ATTTTT-
1 TTTTTTC
*
2651240 TTCTTT-
1 TTTTTTC
2651246 TTTTTTC
1 TTTTTTC
2651253 TTTTTTCCC
1 TTTTTT--C
2651262 TTTTTTCC
1 TTTTTT-C
2651270 TTTTTTCC
1 TTTTTT-C
2651278 TTTTTTCC
1 TTTTTT-C
2651286 TTTTTTC
1 TTTTTTC
*
2651293 CTTTTTC
1 TTTTTTC
*
2651300 TTTTTCC
1 TTTTTTC
2651307 TTTTTT
1 TTTTTT
2651313 TCTTCTACAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
6 14 0.19
7 29 0.39
8 24 0.32
9 7 0.09
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:2651256 original size:8 final size:8
Alignment explanation
Indices: 2651219--2651316 Score: 76
Period size: 8 Copynumber: 12.2 Consensus size: 8
2651209 TTGATTCAAG
2651219 TTTTTTT-
1 TTTTTTTC
*
2651226 TATTTTTTA
1 T-TTTTTTC
2651235 TTTTTTTC
1 TTTTTTTC
2651243 TTTTTTTTTC
1 --TTTTTTTC
*
2651253 TTTTTTCC
1 TTTTTTTC
*
2651261 CTTTTTTC
1 TTTTTTTC
*
2651269 CTTTTTTC
1 TTTTTTTC
*
2651277 CTTTTTTC
1 TTTTTTTC
*
2651285 CTTTTTTC
1 TTTTTTTC
*
2651293 -CTTTTTC
1 TTTTTTTC
*
2651300 -TTTTTCC
1 TTTTTTTC
2651307 TTTTTTTC
1 TTTTTTTC
2651315 TT
1 TT
2651317 CTACAAGGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
7 12 0.15
8 57 0.73
9 1 0.01
10 8 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2651265 original size:24 final size:22
Alignment explanation
Indices: 2651238--2651313 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 22
2651228 TTTTTTATTT
2651238 TTTTCTTTTTTTTTCTTTTTTCCC
1 TTTT-TTTTTTTTTCTTTTTT-CC
*
2651262 TTTTTTCCTTTTTTCCTTTTTTCC
1 TTTTTT--TTTTTTTCTTTTTTCC
**
2651286 TTTTTTCCTTTTTC-TTTTTCC
1 TTTTTTTTTTTTTCTTTTTTCC
2651307 TTTTTTT
1 TTTTTTT
2651314 CTTCTACAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.29
22 5 0.11
23 2 0.04
24 12 0.27
25 13 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTTTTTCTTTTTTCC
Found at i:2651313 original size:16 final size:17
Alignment explanation
Indices: 2651236--2651313 Score: 85
Period size: 17 Copynumber: 4.9 Consensus size: 17
2651226 TATTTTTTAT
*
2651236 TTTTTTCTTTTTTTTTC
1 TTTTTTCCTTTTTTTTC
* *
2651253 TTTTTTCCCTTTTTTCC
1 TTTTTTCCTTTTTTTTC
*
2651270 TTTTTTCC-TTTTTTCC
1 TTTTTTCCTTTTTTTTC
2651286 TTTTTTCC---TTTTTC
1 TTTTTTCCTTTTTTTTC
2651300 -TTTTTCCTTTTTTT
1 TTTTTTCCTTTTTTT
2651314 CTTCTACAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.13
14 5 0.09
16 20 0.37
17 22 0.41
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCCTTTTTTTTC
Found at i:2651314 original size:9 final size:8
Alignment explanation
Indices: 2651245--2651312 Score: 97
Period size: 8 Copynumber: 8.8 Consensus size: 8
2651235 TTTTTTTCTT
*
2651245 TTTTTTTC
1 TTTTTTCC
2651253 TTTTTTCCC
1 TTTTTT-CC
2651262 TTTTTTCC
1 TTTTTTCC
2651270 TTTTTTCC
1 TTTTTTCC
2651278 TTTTTTCC
1 TTTTTTCC
2651286 TTTTTTCC
1 TTTTTTCC
2651294 -TTTTT-C
1 TTTTTTCC
2651300 -TTTTTCC
1 TTTTTTCC
2651307 TTTTTT
1 TTTTTT
2651313 TCTTCTACAA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
6 6 0.11
7 6 0.11
8 37 0.66
9 7 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2656284 original size:24 final size:24
Alignment explanation
Indices: 2656242--2656303 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
2656232 TAATACATTA
*
2656242 AAAATAA-A-ATA-AAACATTAAT
1 AAAATAATATATATAAACATTAAG
* *
2656263 AAAATAATATATATAAATATTAGG
1 AAAATAATATATATAAACATTAAG
2656287 AAAATAATGAGTATATA
1 AAAATAAT-A-TATATA
2656304 TAAAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 1 0.03
23 3 0.09
24 15 0.45
25 1 0.03
26 6 0.18
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
AAAATAATATATATAAACATTAAG
Found at i:2656994 original size:20 final size:20
Alignment explanation
Indices: 2656961--2656999 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2656951 AAAAAATAGA
2656961 TAAATATATATATTATAAAAG
1 TAAATATATATATT-TAAAAG
*
2656982 TAAA-ATATTTATTTAAAA
1 TAAATATATATATTTAAAA
2657000 ATATCAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAATATATATATTTAAAAG
Found at i:2657252 original size:25 final size:25
Alignment explanation
Indices: 2657224--2657271 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2657214 GTATTAAAAA
2657224 TAAACATATAAAATTAAAA-TATAAC
1 TAAACA-ATAAAATTAAAACTATAAC
*
2657249 TAAACAATGAAATTAAAACTATA
1 TAAACAATAAAATTAAAACTATA
2657272 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAACAATAAAATTAAAACTATAAC
Found at i:2657326 original size:30 final size:30
Alignment explanation
Indices: 2657258--2657329 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
2657248 CTAAACAATG
* *
2657258 AAATTAAAACTATATATTTAAAATATATAA
1 AAATTAAAACTATATAATTAAAATAAATAA
*
2657288 AAAATAAAACT-TATAATT-AAATAAATGAA
1 AAATTAAAACTATATAATTAAAATAAAT-AA
2657317 AATATTAAAACTA
1 AA-ATTAAAACTA
2657330 GTGACTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.20
29 10 0.29
30 18 0.51
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (30 bp):
AAATTAAAACTATATAATTAAAATAAATAA
Found at i:2658702 original size:3 final size:3
Alignment explanation
Indices: 2658694--2658758 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
2658684 GGGCATGTAG
* *
2658694 TAA TAA TAA TAA TAA TAG T-A TAA -AA TAA T-A TAA TAA TAG T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2658738 -AA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
2658759 TTATTATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 10 0.19
3 42 0.81
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2658728 original size:21 final size:21
Alignment explanation
Indices: 2658695--2658752 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
2658685 GGCATGTAGT
2658695 AATAATAATAATAATAGTATAA
1 AATAAT-ATAATAATAGTATAA
2658717 AATAATATAATAATAGTATAA
1 AATAATATAATAATAGTATAA
2658738 AATAATATAATAATA
1 AATAATATAATAATA
2658753 ATAATATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 30 0.83
22 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAATATAATAATAGTATAA
Found at i:2667872 original size:2 final size:2
Alignment explanation
Indices: 2667865--2667895 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2667855 TTATTTTACA
2667865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2667896 AAGTAGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2670226 original size:10 final size:10
Alignment explanation
Indices: 2670211--2670235 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2670201 ATGTTAGATA
2670211 AAATAAAAAT
1 AAATAAAAAT
2670221 AAATAAAAAT
1 AAATAAAAAT
2670231 AAATA
1 AAATA
2670236 TGAAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:2670316 original size:9 final size:9
Alignment explanation
Indices: 2670267--2670319 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
2670257 ATGCTAGTAT
2670267 AATAATAAT-
1 AATAA-AATA
2670276 AATAAACATA
1 AATAAA-ATA
*
2670286 AAGAAAATA
1 AATAAAATA
2670295 AATAAAA-A
1 AATAAAATA
2670303 AATAAAATA
1 AATAAAATA
*
2670312 GATAAAAT
1 AATAAAAT
2670320 TTAGTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 9 0.24
9 24 0.63
10 5 0.13
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (9 bp):
AATAAAATA
Found at i:2677871 original size:169 final size:158
Alignment explanation
Indices: 2677615--2678056 Score: 493
Period size: 158 Copynumber: 2.7 Consensus size: 158
2677605 CAAAGGTAAG
*
2677615 GGACTAAATTGAAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGTAAGTATAA-ATGTATTC
1 GGACTAAATTG--AAAAT--AAAATTTGTTATCAAAAAGAGGAATTGAAAGTA-AACATGTATTC
2677679 TACTATGATTTAGGAGCATGTGACTCAAATTTGGTAAAAAACGGA-GGAC-TAAAAGAAGAATAA
61 TACTATGATTTAGGAGCATGTGACTCAAATTTGGTAAAAAAC--ATGGACTTAAAA-AA-AAT-A
2677742 ACATGTAAAAAAACAAAAACAAATTGAAGATTATGAAAAATTGAA
121 AC--G-AAAAAAA-AAAAA-AAA--GAAGATTATGAAAAATTGAA
* *
2677787 GGACTAAATTGAAAATAAAAGCTTGTTATCAAAAAGAGGAATTGAAATTAAACATGTATTCTACT
1 GGACTAAATTGAAAATAAAA-TTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTACT
* * * * * ***
2677852 A-CATATTAGGATCATGTGACTTAAATTTGGT--AAAACATGGACTTAAAATAAATGACGAATTG
65 ATGAT-TTAGGAGCATGTGACTCAAATTTGGTAAAAAACATGGACTTAAAAAAAATAACGAAAAA
*
2677914 AATAAAAAAAGAAGATTATGAAAAATTGAA
129 AAAAAAAAAAGAAGATTATGAAAAATTGAA
* *
2677944 AGACTAAATTAAAAAAATAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTAC
1 GGACTAAATT--GAAAATAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTAC
* **
2678009 TATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAA-ATGGACTTAA
64 TATGATTTAGGAGCATGTGACTCAAATTTGGTAAAAAACATGGACTTAA
2678057 GATGAAGGAG
Statistics
Matches: 238, Mismatches: 22, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
157 29 0.12
158 65 0.27
159 23 0.10
160 8 0.03
161 4 0.02
162 1 0.00
164 2 0.01
165 4 0.02
166 5 0.02
167 10 0.04
168 8 0.03
169 63 0.26
170 5 0.02
172 11 0.05
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (158 bp):
GGACTAAATTGAAAATAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTACTA
TGATTTAGGAGCATGTGACTCAAATTTGGTAAAAAACATGGACTTAAAAAAAATAACGAAAAAAA
AAAAAAAAGAAGATTATGAAAAATTGAA
Found at i:2680926 original size:30 final size:30
Alignment explanation
Indices: 2680892--2680971 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
2680882 GCCTCAAGGT
*
2680892 TACCCGCCATCCGGATATCCTCCTGCTCAG
1 TACCCGCCAACCGGATATCCTCCTGCTCAG
* * *
2680922 TACCCTCCAACTGGTTATCCTCCTGCTCAG
1 TACCCGCCAACCGGATATCCTCCTGCTCAG
* * *
2680952 TACCCTCCAACTGGTTATCC
1 TACCCGCCAACCGGATATCC
2680972 AGCACCTGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.17, C:0.41, G:0.14, T:0.28
Consensus pattern (30 bp):
TACCCGCCAACCGGATATCCTCCTGCTCAG
Found at i:2692151 original size:21 final size:21
Alignment explanation
Indices: 2692112--2692151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2692102 GTATTACACC
*
2692112 AAGAAAAGAATGGTAGAAACG
1 AAGAAAAGAATGATAGAAACG
* *
2692133 AAGAAGAGAATGATTGAAA
1 AAGAAAAGAATGATAGAAA
2692152 ATCTGGCCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.28, T:0.12
Consensus pattern (21 bp):
AAGAAAAGAATGATAGAAACG
Found at i:2692324 original size:198 final size:197
Alignment explanation
Indices: 2691972--2692368 Score: 721
Period size: 198 Copynumber: 2.0 Consensus size: 197
2691962 AGCCTTTGAC
2691972 ATATACAGGAGCTTGGATTGAAGGTGACTTAAATTTAGTAATGCCAACATTCAATTAATGATGTC
1 ATATACAGGAGCTTGGATTGAAGGTGACTTAAATTTAGTAATGCCAACATTCAATTAATGATGTC
2692037 CCAACGTCCTCTCTGAACGTACGAGTGAAGGTGACTTGAATTTGAGTAATACGCATTTTAATATT
66 CCAACGTCCTCTCTGAACGTACGAGTGAAGGTGACTTGAATTTGAGTAATACGCATTTTAATATT
2692102 GTATTACACCAAGAAAAGAATGGTAG-AAACGAAGAAGAGAATGATTGAAAATCTGGCCTAGTTT
131 GTATTACACCAAGAAAAGAATGGTAGAAAACGAAGAAGAGAATGATTGAAAATCTGGCCTAGTTT
2692166 TT
196 TT
2692168 ATATACAGGAGCTTGGATTGAAGGTGACTTAAATTTTAGTAATGCCAACATTCAATTTAATGATG
1 ATATACAGGAGCTTGGATTGAAGGTGACTTAAA-TTTAGTAATGCCAACATTCAA-TTAATGATG
2692233 TCCCAACGTCCTCTCTGAACGTACGAGTGAAGGTGACTTGAATTTGAGTAATACGCATTTCTAAT
64 TCCCAACGTCCTCTCTGAACGTACGAGTGAAGGTGACTTGAATTTGAGTAATACGCATTT-TAAT
2692298 ATTGTATTATCAACC-A-AAAA-AATGGTAGAAAACGAAGAAGAGAATGATTGAAAATCTGGCCT
128 ATTGTATTA-C-ACCAAGAAAAGAATGGTAGAAAACGAAGAAGAGAATGATTGAAAATCTGGCCT
2692360 AGTTTTT
191 AGTTTTT
2692367 AT
1 AT
2692369 TCATAAGCTC
Statistics
Matches: 195, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
196 33 0.17
197 21 0.11
198 77 0.39
199 59 0.30
200 2 0.01
201 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (197 bp):
ATATACAGGAGCTTGGATTGAAGGTGACTTAAATTTAGTAATGCCAACATTCAATTAATGATGTC
CCAACGTCCTCTCTGAACGTACGAGTGAAGGTGACTTGAATTTGAGTAATACGCATTTTAATATT
GTATTACACCAAGAAAAGAATGGTAGAAAACGAAGAAGAGAATGATTGAAAATCTGGCCTAGTTT
TT
Found at i:2697753 original size:19 final size:19
Alignment explanation
Indices: 2697731--2697769 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2697721 GTTTACCAAC
*
2697731 AATTATAAAGTTTTTATTT
1 AATTATAAACTTTTTATTT
*
2697750 AATTATGAACTTTTTATTT
1 AATTATAAACTTTTTATTT
2697769 A
1 A
2697770 CTTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTATAAACTTTTTATTT
Found at i:2697839 original size:26 final size:25
Alignment explanation
Indices: 2697781--2697829 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
2697771 TTTTCTTGTT
2697781 AATGTTTTTATTATTTAATTGTTCG
1 AATGTTTTTATTATTTAATTGTTCG
*
2697806 AATTGTTTTTATTATTTAGTTGTT
1 AA-TGTTTTTATTATTTAATTGTT
2697830 TTTCATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (25 bp):
AATGTTTTTATTATTTAATTGTTCG
Found at i:2700249 original size:60 final size:59
Alignment explanation
Indices: 2700156--2700270 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
2700146 CTCCACGATG
* * * * * *
2700156 TCGACATTTAGGTCGAAGAAGCTGATAGTTGAATGCCTTCCCCTTGAACTTAAAGGTGTC
1 TCGACATTGAGGTCAAAGAAGCTCACAATTGAATG-CTTCCCCTGGAACTTAAAGGTGTC
* * *
2700216 TCGACATTGAGGTTAAAGAAGCTCACAATTGAATGCTTTCCCTGGAACTTGAAGG
1 TCGACATTGAGGTCAAAGAAGCTCACAATTGAATGCTTCCCCTGGAACTTAAAGG
2700271 CATCGTGTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 17 0.37
60 29 0.63
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (59 bp):
TCGACATTGAGGTCAAAGAAGCTCACAATTGAATGCTTCCCCTGGAACTTAAAGGTGTC
Found at i:2701074 original size:12 final size:13
Alignment explanation
Indices: 2701057--2701107 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
2701047 TTTTACAACC
2701057 ACAAAAAATTA-T
1 ACAAAAAATTAGT
2701069 ACAAAATAATTAGT
1 ACAAAA-AATTAGT
*
2701083 ACAATAAAATTTGT
1 ACAA-AAAATTAGT
* *
2701097 TCAAATAATTA
1 ACAAAAAATTA
2701108 AATATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 6 0.19
13 10 0.31
14 14 0.44
15 2 0.06
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (13 bp):
ACAAAAAATTAGT
Found at i:2701841 original size:29 final size:29
Alignment explanation
Indices: 2701808--2701886 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
2701798 CGACGACCGA
*
2701808 TATATTTACCGATCTAACACCGGTCAGAC
1 TATATTTACCGATCTAACACCAGTCAGAC
* *
2701837 TATATTTCCCTATCTAACACCAGTCAGAC
1 TATATTTACCGATCTAACACCAGTCAGAC
**
2701866 TATATTTATTGATCTAACACC
1 TATATTTACCGATCTAACACC
2701887 CTTTGCAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.33
Consensus pattern (29 bp):
TATATTTACCGATCTAACACCAGTCAGAC
Found at i:2707997 original size:29 final size:30
Alignment explanation
Indices: 2707943--2708011 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
2707933 CATTTTACAG
*
2707943 AAATAGCACCCCTTTTCGAATTAATTACCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
* *
2707973 AAATAGCACTCATTTT-GAATTAATTCCCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
2708002 TAATAGCACC
1 AAATAGCACC
2708012 AAAATTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (30 bp):
AAATAGCACCCATTTTCGAATTAATTACCA
Found at i:2708019 original size:29 final size:28
Alignment explanation
Indices: 2707960--2708040 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
2707950 ACCCCTTTTC
* **
2707960 GAATTAATTACCAAAATAGCACTCATTTT
1 GAATTAATTCCCAAAATAGCAC-CAAATT
*
2707989 GAATTAATTCCCATAATAGCACCAAAATT
1 GAATTAATTCCCAAAATAGCACC-AAATT
* * *
2708018 GAATAAATTCTCAGAATAGCACC
1 GAATTAATTCCCAAAATAGCACC
2708041 GGTCAACGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 1 0.02
29 43 0.98
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (28 bp):
GAATTAATTCCCAAAATAGCACCAAATT
Found at i:2708071 original size:18 final size:18
Alignment explanation
Indices: 2708041--2708093 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
2708031 GAATAGCACC
2708041 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
2708058 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
*
2708076 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
2708094 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 7 0.22
18 25 0.78
ACGTcount: A:0.11, C:0.19, G:0.49, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2708109 original size:10 final size:10
Alignment explanation
Indices: 2708096--2708121 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2708086 TTGGGTCGTG
2708096 ACCGGTCAAA
1 ACCGGTCAAA
2708106 ACCGGTCAAA
1 ACCGGTCAAA
2708116 ACCGGT
1 ACCGGT
2708122 TTCCAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.31, G:0.23, T:0.12
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2715280 original size:29 final size:30
Alignment explanation
Indices: 2715217--2715285 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
2715207 CATTTTACAG
*
2715217 AAATAGCACCCCTTTTCGAATTAATTACCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
2715247 AAATAGCACCCATTTT-GAATTAATTCCCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
2715276 TAATAGCACC
1 AAATAGCACC
2715286 AAAATCGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATAGCACCCATTTTCGAATTAATTACCA
Found at i:2715295 original size:29 final size:29
Alignment explanation
Indices: 2715232--2715309 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
2715222 GCACCCCTTT
* * **
2715232 TCGAATTAATTACCAAAATAGCACCCATT
1 TCGAATTAATTCCCAAAATAGCACCAAAA
* *
2715261 TTGAATTAATTCCCATAATAGCACCAAAA
1 TCGAATTAATTCCCAAAATAGCACCAAAA
* *
2715290 TCGAATAAATTCCCAGAATA
1 TCGAATTAATTCCCAAAATA
2715310 TTCAACGGTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.27
Consensus pattern (29 bp):
TCGAATTAATTCCCAAAATAGCACCAAAA
Found at i:2721009 original size:20 final size:20
Alignment explanation
Indices: 2720984--2721042 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
2720974 TTTTCCGAAT
* *
2720984 TCGCAATGCAAATATGTAAA
1 TCGCAATGCGAATCTGTAAA
*
2721004 TCGCAACGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
2721024 TCGCAATGCGAATCTGTAA
1 TCGCAATGCGAATCTGTAA
2721043 TTCGTAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:2721066 original size:20 final size:20
Alignment explanation
Indices: 2721041--2721088 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2721031 GCGAATCTGT
* *
2721041 AATTCGTAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
2721061 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
2721081 AATTCGCA
1 AATTCGCA
2721089 GTGCGATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:2721125 original size:21 final size:20
Alignment explanation
Indices: 2721058--2721131 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
2721048 AACACATAAG
*
2721058 TCAAATTCGCAACACAGAA-G
1 TCAAATTCGCAACAC-GAATT
***
2721078 TCAAATTCGCAGTGCG-ATT
1 TCAAATTCGCAACACGAATT
2721097 TCCAAATTCGCAACACTGAATT
1 T-CAAATTCGCAACAC-GAATT
2721119 TCAAATTCGCAAC
1 TCAAATTCGCAAC
2721132 TCGATTTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 23 0.53
21 13 0.30
22 4 0.09
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:2721146 original size:41 final size:40
Alignment explanation
Indices: 2721059--2721138 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
2721049 ACACATAAGT
*
2721059 CAAATTCGCAACACAGAAGTCAAATTCGCAGTGCGATTTC
1 CAAATTCGCAACACAGAAGTCAAATTCGCACTGCGATTTC
* *
2721099 CAAATTCGCAACACTGAATTTCAAATTCGCAACT-CGATTT
1 CAAATTCGCAACACAGAA-GTCAAATTCGC-ACTGCGATTT
2721139 TTGAATTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 17 0.49
41 16 0.46
42 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACACAGAAGTCAAATTCGCACTGCGATTTC
Found at i:2722449 original size:19 final size:19
Alignment explanation
Indices: 2722421--2722467 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2722411 CGTGGCGCAT
2722421 GATTGCAAAGAGGATAAAA
1 GATTGCAAAGAGGATAAAA
*
2722440 GATTGTAAAGAGGATAAAA
1 GATTGCAAAGAGGATAAAA
2722459 GATTGCAAA
1 GATTGCAAA
2722468 ATGTTTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.26, T:0.19
Consensus pattern (19 bp):
GATTGCAAAGAGGATAAAA
Found at i:2723456 original size:46 final size:46
Alignment explanation
Indices: 2723389--2723485 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
2723379 CAAACACTAG
* *
2723389 AAGATGTCGGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
1 AAGATGCCGGGTTTGAAAGATGGTCAAGAGTACATCAACCTGGAGC
2723435 AAGATGCCGGGTTTGAAAGATGGTCAAGAGTACATCAACCTGGAGC
1 AAGATGCCGGGTTTGAAAGATGGTCAAGAGTACATCAACCTGGAGC
2723481 AAGAT
1 AAGAT
2723486 ATGGTTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (46 bp):
AAGATGCCGGGTTTGAAAGATGGTCAAGAGTACATCAACCTGGAGC
Found at i:2724570 original size:22 final size:22
Alignment explanation
Indices: 2724545--2724588 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2724535 CGATTATTGC
*
2724545 GAAAATCAAATTCAAAACGCGA
1 GAAAATAAAATTCAAAACGCGA
* **
2724567 GAAAGTAAAATTCGCAACGCGA
1 GAAAATAAAATTCAAAACGCGA
2724589 ATTTGACTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
GAAAATAAAATTCAAAACGCGA
Found at i:2726045 original size:21 final size:21
Alignment explanation
Indices: 2726021--2726112 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 21
2726011 GTGAATCGGG
*
2726021 CTCTTGAACGGCGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
2726042 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
2726063 CTATTGAACGGTGGGAAGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * *
2726084 CTTTTGAAAGAT-AG-GGGGC
1 CTCTTGAACGGTGGGAGGGGC
2726103 CTCTTGAACG
1 CTCTTGAACG
2726113 ATGACAGGTG
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.21
20 1 0.02
21 44 0.77
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:2726084 original size:42 final size:40
Alignment explanation
Indices: 2726024--2726112 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 40
2726014 AATCGGGCTC
* *
2726024 TTGAACGGCGGGAGGGGCCTCTTGAACGATGAGAGGGGCCTA
1 TTGAACGGCGGGAAGGGCCTCTTGAAAGAT-AG-GGGGCCTA
* * *
2726066 TTGAACGGTGGGAAGGGCCTTTTGAAAGATAGGGGGCCTC
1 TTGAACGGCGGGAAGGGCCTCTTGAAAGATAGGGGGCCTA
2726106 TTGAACG
1 TTGAACG
2726113 ATGACAGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 14 0.33
41 2 0.05
42 26 0.62
ACGTcount: A:0.22, C:0.17, G:0.40, T:0.20
Consensus pattern (40 bp):
TTGAACGGCGGGAAGGGCCTCTTGAAAGATAGGGGGCCTA
Found at i:2726762 original size:42 final size:42
Alignment explanation
Indices: 2726687--2726785 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
2726677 GTGATAGAAT
* ** * *
2726687 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGACTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
* *
2726729 AGGTGATGGCTCTGGGTGTCAAGCTGTAGAATCGACTTGATC
1 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
*
2726771 AGGTGATGACTCTCG
1 AGGTGATGGCTCTCG
2726786 AAGTGGGGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
Found at i:2728280 original size:20 final size:20
Alignment explanation
Indices: 2728270--2728313 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2728260 ATCGCAATGT
2728270 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
2728290 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
2728310 GAAA
1 GAAA
2728314 CTAAATTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2728361 original size:20 final size:20
Alignment explanation
Indices: 2728319--2728361 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2728309 CGAAACTAAA
* * *
2728319 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
2728339 TTCGCGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
2728359 TTC
1 TTC
2728362 AAAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:2728723 original size:22 final size:22
Alignment explanation
Indices: 2728696--2728754 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
2728686 GAGATAGACG
2728696 GATTTCGCCGGAGATGGGGACA
1 GATTTCGCCGGAGATGGGGACA
*
2728718 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACA
* *
2728740 GATGTCGCCGTAGAT
1 GATTTCGCCGGAGAT
2728755 ATTGAAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.41, T:0.20
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACA
Found at i:2728875 original size:19 final size:20
Alignment explanation
Indices: 2728853--2728890 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2728843 AATATTGTGT
2728853 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
2728872 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
2728891 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:2728922 original size:20 final size:20
Alignment explanation
Indices: 2728897--2728945 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2728887 TAAACGCGCT
2728897 TTGCGAATTTAACTTATGTG
1 TTGCGAATTTAACTTATGTG
*
2728917 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTAACTTATGTG
2728937 TTGCGAATT
1 TTGCGAATT
2728946 ACAAATTCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTAACTTATGTG
Found at i:2728999 original size:20 final size:20
Alignment explanation
Indices: 2728936--2729002 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2728926 TGACTTATGT
*
2728936 GTTGCGAATTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
2728956 GTTACGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
*
2728976 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
2728996 GTTGCGA
1 GTTGCGA
2729003 ATTTGGAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:2729929 original size:75 final size:74
Alignment explanation
Indices: 2729840--2730065 Score: 244
Period size: 76 Copynumber: 3.1 Consensus size: 74
2729830 TAAACTCAAG
* * ** *
2729840 TTTAGGATAATATTTTAAACATTATATTTTTTCTTTGTATTTTAGTTTAAATTGGTTTTAGTATT
1 TTTAGGATATTATTTTAAATATTATATTTTTTCAGT-TATTTTAGTTTAAATAGGTTTTAGTATT
*
2729905 TTAATTAAGT
65 TTAATTAAGA
* * * *
2729915 TTTAGGATATTATTTTTATATTTTATCTTTGTTTCAGTTATTTTAGTTTAAATAGGTTTTATTAT
1 TTTAGGATATTA-TTTTAAATATTATATTT-TTTCAGTTATTTTAGTTTAAATAGGTTTTAGTAT
*
2729980 TTTAATTAGGA
64 TTTAATTAAGA
* * **
2729991 TTTAGAATATTATTTTAAATATTA-ATTTTTT-AGGTA-TTTAGTTTAAATA-GTTTTAAGCGTT
1 TTTAGGATATTATTTTAAATATTATATTTTTTCAGTTATTTTAGTTTAAATAGGTTTT-AGTATT
*
2730052 TTAATTAGGA
65 TTAATTAAGA
2730062 TTTA
1 TTTA
2730066 AGATGTTTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
70 5 0.04
71 30 0.23
72 4 0.03
73 3 0.02
74 3 0.02
75 21 0.16
76 58 0.45
77 5 0.04
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (74 bp):
TTTAGGATATTATTTTAAATATTATATTTTTTCAGTTATTTTAGTTTAAATAGGTTTTAGTATTT
TAATTAAGA
Found at i:2730681 original size:17 final size:18
Alignment explanation
Indices: 2730659--2730700 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2730649 CTTTAGATTA
2730659 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
* *
2730676 TTTATTTAATTCTTATTT
1 TTTATTTAATTATTATCT
2730694 TTTATTT
1 TTTATTT
2730701 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2732908 original size:12 final size:12
Alignment explanation
Indices: 2732893--2732923 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2732883 GAAAATCATT
2732893 TTGAAATCAAAA
1 TTGAAATCAAAA
2732905 TTGAAATCAAAA
1 TTGAAATCAAAA
2732917 TTGAAAT
1 TTGAAAT
2732924 TACTCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
TTGAAATCAAAA
Found at i:2739283 original size:117 final size:118
Alignment explanation
Indices: 2739063--2739284 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 118
2739053 CTTTCAAGTC
* *
2739063 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAGTCCTTCTTCAAGATTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAACTCCTTCTTCAACATTT
* *
2739128 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * *
2739181 AAAA-TTTCTTTTTCAA-AGTTTTCAGATTTCGTTTTTGAAAGCTCTAACTCCTTTCTT-AACAT
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAACTCC-TTCTTCAACAT
** *
2739243 TTCATTTTGATTTTTTAAATCTATTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
2739285 ATCATTTTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 1 0.01
117 77 0.85
118 13 0.14
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAACTCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:2745420 original size:5 final size:5
Alignment explanation
Indices: 2745410--2745506 Score: 88
Period size: 5 Copynumber: 18.8 Consensus size: 5
2745400 TCGTTCCATT
* * ** *
2745410 TTTTA TTTTA TTTCA TTTTA TTTTTA TTTTCTA TTTTA GTAAA CTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA -TTT-TA TTTTA TTTTA TTTTA
* *
2745458 TTTTCA TTCTA -TTTA TTTTA TTTTA ATTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2745507 TCTCTAAACA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
4 3 0.04
5 54 0.72
6 16 0.21
7 2 0.03
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:2747197 original size:74 final size:73
Alignment explanation
Indices: 2747121--2747349 Score: 248
Period size: 76 Copynumber: 3.1 Consensus size: 73
2747111 TAAACTCAAG
* *
2747121 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAAATATTATATTTT-T-TTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
2747186 TTAATTAAGT
64 TTAATTAAGA
* * *
2747196 TTTAGGATATTATTTT-TATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAATA
1 TTTAGGATATTATTTTAAATATTATAT-TTT-TTTT--GTATTTTAGTTTAAATAGGTTTTAGTA
*
2747260 TTTTAATTAGGA
62 TTTTAATTAAGA
* * * *
2747272 TTTAGAATATTATTTTAAATATTAT-TATTTTTAGTTATTTTTAGTTTAAATA-GTTTTAAGTGT
1 TTTAGGATATTATTTTAAATATTATATTTTTTTTG-TA-TTTTAGTTTAAATAGGTTTT-AGTAT
*
2747335 TTTAATTAGGA
63 TTTAATTAAGA
2747346 TTTA
1 TTTA
2747350 AGATGTTTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
72 1 0.01
73 7 0.05
74 45 0.34
75 21 0.16
76 52 0.39
77 6 0.05
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (73 bp):
TTTAGGATATTATTTTAAATATTATATTTTTTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTT
AATTAAGA
Found at i:2747961 original size:16 final size:18
Alignment explanation
Indices: 2747940--2747980 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
2747930 TTGTAGATTA
2747940 TTTATTTAATTATT-T-T
1 TTTATTTAATTATTATCT
*
2747956 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2747974 TTTATTT
1 TTTATTT
2747981 TAAAAGGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.59
17 1 0.05
18 8 0.36
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2748072 original size:19 final size:19
Alignment explanation
Indices: 2748027--2748078 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2748017 TACTATTATT
2748027 TATTAT-TTTATTATTTTC
1 TATTATATTTATTATTTTC
** *
2748045 CCTTTTATTTATTATTTTC
1 TATTATATTTATTATTTTC
2748064 TATTATATTTTATTA
1 TATTATA-TTTATTA
2748079 AATCTTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 3 0.12
19 16 0.62
20 7 0.27
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATATTTATTATTTTC
Found at i:2750892 original size:19 final size:20
Alignment explanation
Indices: 2750870--2750909 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2750860 GTGGAGATTT
*
2750870 ATAGAAG-AAGAGAAATAAA
1 ATAGAAGAAAGAAAAATAAA
2750889 ATAGAAGAAAGAAAAATAAA
1 ATAGAAGAAAGAAAAATAAA
2750909 A
1 A
2750910 AGATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (20 bp):
ATAGAAGAAAGAAAAATAAA
Found at i:2754993 original size:16 final size:16
Alignment explanation
Indices: 2754972--2755003 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2754962 CAGTTTGAAC
*
2754972 GAAAATTAAAGAAAAT
1 GAAAATAAAAGAAAAT
2754988 GAAAATAAAAGAAAAT
1 GAAAATAAAAGAAAAT
2755004 AATTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (16 bp):
GAAAATAAAAGAAAAT
Found at i:2756866 original size:139 final size:139
Alignment explanation
Indices: 2756701--2757183 Score: 489
Period size: 139 Copynumber: 3.5 Consensus size: 139
2756691 CCTAAGACCT
* * **
2756701 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTC-ATGCATAAAAGGGAGGACCAAA
1 ATTTTAGCAATTTATTGAATCAAATAATTAAAATAGAACCTCGA-GCATAAAAACGAGGACCAAA
* *
2756765 TTAAAAAATCTCCTAAAGTAAAGGACTAAAGTGAAATTAAACCTAAGACAAAGGCTCTAATATTA
65 TTAAAAAATCTCCTAAAGTAAAGAACTAAAGTGAAATTAAACCTAAAACAAAGGCTCTAATATTA
2756830 ATCCTAACCA
130 ATCCTAACCA
* *
2756840 ATTTTAGCAATCTATTGAATCAAATAATTAAAATAGAACCTCGAGTATAAAAACGAGGACCAAAT
1 ATTTTAGCAATTTATTGAATCAAATAATTAAAATAGAACCTCGAGCATAAAAACGAGGACCAAAT
* * * *
2756905 TAAAAATTCTCCTAAATTAAAGAACTAAAGTGAAATTCAACCTAAAATAAAGGCTCTAATATTAA
66 TAAAAAATCTCCTAAAGTAAAGAACTAAAGTGAAATTAAACCTAAAACAAAGGCTCTAATATTAA
* *
2756970 TCTTGACCA
131 TCCTAACCA
* * * * ** * * * * *
2756979 ATTTTAACAATTTATTGGATCGAACAATTATTATGGAACATTGAGCATAAAAACGACGATCAAAT
1 ATTTTAGCAATTTATTGAATCAAATAATTAAAATAGAACCTCGAGCATAAAAACGAGGACCAAAT
* * * * * * ** *
2757044 TAAAAATTCAT-CTAAA-TTAAGTAAGTAAAGTAAAATT-AATCTGAAATGAAGGCTCTAATGTT
66 TAAAAAATC-TCCTAAAGTAAAG-AACTAAAGTGAAATTAAACCTAAAACAAAGGCTCTAATATT
2757106 AATCCTAACC-
129 AATCCTAACCA
** * * * * * *
2757116 ---TTAGTTATTTATTGGATCGAATAGTTAAAAT-GAAACCTCGGGCATAAAAGCGATGACCAAA
1 ATTTTAGCAATTTATTGAATCAAATAATTAAAATAG-AACCTCGAGCATAAAAACGAGGACCAAA
2757177 TTAAAAA
65 TTAAAAA
2757184 TTCACCTATA
Statistics
Matches: 291, Mismatches: 49, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
133 1 0.00
134 53 0.18
138 33 0.11
139 202 0.69
140 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (139 bp):
ATTTTAGCAATTTATTGAATCAAATAATTAAAATAGAACCTCGAGCATAAAAACGAGGACCAAAT
TAAAAAATCTCCTAAAGTAAAGAACTAAAGTGAAATTAAACCTAAAACAAAGGCTCTAATATTAA
TCCTAACCA
Found at i:2757846 original size:21 final size:22
Alignment explanation
Indices: 2757820--2757878 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
2757810 ATTATCCAAT
*
2757820 AAGCTTGACATCCATAACAA-C
1 AAGCTTGAAATCCATAACAACC
2757841 AAGCTTGAAATCCATAACAACC
1 AAGCTTGAAATCCATAACAACC
2757863 AA-CTTGAAATCCATAA
1 AAGCTTGAAATCCATAA
2757879 TAATAAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.46, C:0.25, G:0.08, T:0.20
Consensus pattern (22 bp):
AAGCTTGAAATCCATAACAACC
Found at i:2759642 original size:110 final size:110
Alignment explanation
Indices: 2759453--2759661 Score: 373
Period size: 110 Copynumber: 1.9 Consensus size: 110
2759443 GAAACTTCCG
*
2759453 TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
1 TAGATCCAACACCACTCGATTCCTAATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
* * *
2759518 CGCAAATCACTTAATTTTCTCGTGGGCATAATATAGGAACTTTCA
66 CGCAAATCAATTAATTTTCTCCTAGGCATAATATAGGAACTTTCA
2759563 TAGATCCAACACCACTCGATTCCTAATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
1 TAGATCCAACACCACTCGATTCCTAATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
*
2759628 CGTAAATCAATTAATTTTCTCCTAGGCATAATAT
66 CGCAAATCAATTAATTTTCTCCTAGGCATAATAT
2759662 TTGTAATAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 94 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (110 bp):
TAGATCCAACACCACTCGATTCCTAATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
CGCAAATCAATTAATTTTCTCCTAGGCATAATATAGGAACTTTCA
Found at i:2761273 original size:22 final size:22
Alignment explanation
Indices: 2761245--2761301 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2761235 GGGTTACAGT
2761245 GGTCCTTCGGGATATATCCAGG
1 GGTCCTTCGGGATATATCCAGG
** * *
2761267 GGTCCTTCGGGACGTATCTAGT
1 GGTCCTTCGGGATATATCCAGG
2761289 GGTCCTTCGGGAT
1 GGTCCTTCGGGAT
2761302 GTAATGGTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.14, C:0.23, G:0.33, T:0.30
Consensus pattern (22 bp):
GGTCCTTCGGGATATATCCAGG
Found at i:2768430 original size:64 final size:64
Alignment explanation
Indices: 2768232--2768431 Score: 219
Period size: 65 Copynumber: 3.1 Consensus size: 64
2768222 TTTTCAGAGT
** * * *
2768232 GATGCACCAAGCCATGCATCGATGCAC-CATGAATAAATTG-AACATCGAATGAATTTCATGCAC
1 GATGCACC-AGCCATGCATCGATGCACTC-TGAATATTTTGAAACATCGAATGCATTTGATGCAT
2768295 C
64 C
* * *
2768296 GATGCA-CATACTATGCATCGATGCACTCAGAAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 GATGCACCA-GCCATGCATCGATGCACTCTGAATATTT-TG-AAACATCGAATGCATTTGATGCA
2768359 TC
63 TC
** **
2768361 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACCTGATGCATC
1 GATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATTTGATGCATC
2768425 GATGCAC
1 GATGCAC
2768432 TCTTAGTGCA
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.02
63 22 0.19
64 37 0.32
65 48 0.42
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (64 bp):
GATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATTTGATGCATC
Found at i:2769662 original size:24 final size:20
Alignment explanation
Indices: 2769628--2769685 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2769618 ATGCACAGGT
2769628 AGTGCATCGATGCACCCGTTAAG
1 AGTGCATCGATGCA-CCGTT--G
* *
2769651 AGATGCATCGATACACTGTTG
1 AG-TGCATCGATGCACCGTTG
2769672 AGTGCATCGATGCA
1 AGTGCATCGATGCA
2769686 TACCTTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
23 6 0.19
24 11 0.35
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (20 bp):
AGTGCATCGATGCACCGTTG
Found at i:2771707 original size:41 final size:41
Alignment explanation
Indices: 2771647--2771757 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
2771637 TATTGCATCA
* **
2771647 TTTGTTTCAAAAACGCCACTAAAGAACTATTCTTTTGCGGTG
1 TTTGTTT-AAAAACGCCACTAAAGAACTATTCTTTTGCAGCC
*
2771689 TTTGTTTAAAAATGCCACTAAAGAA-TGATTCTTTTGCAGCC
1 TTTGTTTAAAAACGCCACTAAAGAACT-ATTCTTTTGCAGCC
* *
2771730 TTTGTTTAGAAACGCCACTAAAGTACTA
1 TTTGTTTAAAAACGCCACTAAAGAACTA
2771758 GGTTTTAGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 51 0.85
42 8 0.13
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (41 bp):
TTTGTTTAAAAACGCCACTAAAGAACTATTCTTTTGCAGCC
Found at i:2774815 original size:18 final size:18
Alignment explanation
Indices: 2774788--2774833 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2774778 TGCAAAAATG
2774788 GTACCGATACCCAAAGGA
1 GTACCGATACCCAAAGGA
* *
2774806 GTATCGATACCCAAAGGG
1 GTACCGATACCCAAAGGA
2774824 GTACCGATAC
1 GTACCGATAC
2774834 TACTTTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (18 bp):
GTACCGATACCCAAAGGA
Found at i:2789198 original size:30 final size:30
Alignment explanation
Indices: 2789164--2789232 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
2789154 ACAAGCTTTA
*
2789164 GAAAATTTGGGGACC-ATTCTATAAATTTTT-
1 GAAAAGTTGGGGACCAATTCT-T-AATTTTTG
2789194 GAAAAGTTGGGGACCAATTCTTAATTTTTG
1 GAAAAGTTGGGGACCAATTCTTAATTTTTG
2789224 GAAAAGTTG
1 GAAAAGTTG
2789233 TAAATGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 7 0.19
30 24 0.67
31 5 0.14
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (30 bp):
GAAAAGTTGGGGACCAATTCTTAATTTTTG
Found at i:2791033 original size:23 final size:23
Alignment explanation
Indices: 2791007--2791067 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
2790997 TCTTATATGA
*
2791007 CACTACGGTGCATTTCTATGCGG
1 CACTTCGGTGCATTTCTATGCGG
* * *
2791030 CACTTCGGTGTAATTCTATGTGG
1 CACTTCGGTGCATTTCTATGCGG
2791053 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
2791068 ATACGAGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTATGCGG
Found at i:2791845 original size:22 final size:22
Alignment explanation
Indices: 2791822--2791901 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
2791812 GGTATTGTTT
*
2791822 ACGGTACTGTTCATTACTATTT
1 ACGGTACTGTTCATTACTATTC
2791844 ACGGTACTGTTCATTACTATTC
1 ACGGTACTGTTCATTACTATTC
*
2791866 ACGGTACTGTTCATTACTGTTC
1 ACGGTACTGTTCATTACTATTC
* *
2791888 ATGGTATTGTTCAT
1 ACGGTACTGTTCAT
2791902 ATCGTATAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (22 bp):
ACGGTACTGTTCATTACTATTC
Found at i:2795462 original size:15 final size:16
Alignment explanation
Indices: 2795423--2795464 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2795413 AAATTACTAT
*
2795423 TTTATTTTATTTATTA
1 TTTATATTATTTATTA
2795439 TTT-TATTATTTA-TA
1 TTTATATTATTTATTA
*
2795453 TTTATCTTATTT
1 TTTATATTATTT
2795465 TCAAACAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 15 0.65
16 3 0.13
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATATTATTTATTA
Found at i:2797296 original size:2 final size:2
Alignment explanation
Indices: 2797289--2797314 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2797279 ATTGGACCAC
2797289 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2797315 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2798109 original size:2 final size:2
Alignment explanation
Indices: 2798102--2798143 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2798092 ATTCTAAATA
2798102 AT AT AT 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
2798144 GCTTATGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2802883 original size:17 final size:17
Alignment explanation
Indices: 2802861--2802902 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2802851 TTGTTTGGTG
2802861 ATAGAATCAAAATTTTA
1 ATAGAATCAAAATTTTA
2802878 ATAGAATCAAAATTTTA
1 ATAGAATCAAAATTTTA
*
2802895 ATGGAATC
1 ATAGAATC
2802903 TCTGGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAGAATCAAAATTTTA
Found at i:2819013 original size:23 final size:23
Alignment explanation
Indices: 2818987--2819034 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2818977 TATAAGTACA
*
2818987 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2819010 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2819033 AT
1 AT
2819035 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2819801 original size:421 final size:414
Alignment explanation
Indices: 2819143--2819989 Score: 1526
Period size: 421 Copynumber: 2.0 Consensus size: 414
2819133 GGATCGATAC
2819143 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATATTTCATTTGCACAAAAATTAT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATATTTCATTTGCACAAAAATTAT
2819208 TTGATTGTTTTGATATTTTAAAATTATTTAGAATTTTAATTTAATAATAATATACCGTAACGTAA
66 TTGATTGTTTTGATATTTTAAAATTATTTAGAATTTTAATTT-ATAATAATATACCGTAACGTAA
2819273 AAATAAATCATTAGCGCCTATAATTACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTA
130 AAATAAATCATTAGCGCCTATAATTACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTA
2819338 ATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATA
195 ATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATA
2819403 TAACCATTACCTATTACATTATATAAACGATACCTA-TACA-T-TATAAGGGCTACCTATTACAT
260 TAACCATTACCTATTACATTATATAAACGATACCTATTA-ATTATATAAGGGCTACCTATTACAT
2819465 C-TATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTA
324 CATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTT-TAAAAAGGATCGATAC-TTTTTTA
2819529 AAACTTATGTAATTTATGTTTCAATTTT
387 AAACTTATGTAATTTATGTTTCAATTTT
2819557 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACCAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAAT-ATTTCATTTGCA-CAAAAATT
2819622 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT-TAATAATAT-CCGTA
64 ATTTGATTGTTTTGATA-TTT-T-AAA-ATTATTTAGAA-TTTTAATTTATAATAATATACCGTA
2819685 ACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGA
124 ACGTAAAAATAAATCATTAG-CGCCTATAATTACT-AATTAATATCTTAAAACTCACTCAAAAGA
2819750 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
187 TAACCTT-AATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
2819815 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTAATTATATAAGGGCTACC
251 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTAATTATATAAGGGCTACC
2819880 TATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTTAAAAAGGATCGATACT
316 TATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTTAAAAAGGATCGATACT
2819945 TTTTTAAAACTTATGTAATTTATGTTTCAATTTT
381 TTTTTAAAACTTATGTAATTTATGTTTCAATTTT
2819979 TTTAACAGTGT
1 TTTAACAGTGT
2819990 ACTGCGAATT
Statistics
Matches: 419, Mismatches: 0, Indels: 20
0.95 0.00 0.05
Matches are distributed among these distances:
414 43 0.10
415 12 0.03
416 25 0.06
417 3 0.01
418 26 0.06
419 26 0.06
420 47 0.11
421 112 0.27
422 49 0.12
423 38 0.09
424 38 0.09
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (414 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATATTTCATTTGCACAAAAATTAT
TTGATTGTTTTGATATTTTAAAATTATTTAGAATTTTAATTTATAATAATATACCGTAACGTAAA
AATAAATCATTAGCGCCTATAATTACTAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAA
TTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATAT
AACCATTACCTATTACATTATATAAACGATACCTATTAATTATATAAGGGCTACCTATTACATCA
TATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTTAAAAAGGATCGATACTTTTTTAAAAC
TTATGTAATTTATGTTTCAATTTT
Found at i:2819879 original size:22 final size:23
Alignment explanation
Indices: 2819831--2819892 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
2819821 ATATAACCAT
2819831 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2819854 TACCTATTA-ATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2819876 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2819893 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2822243 original size:11 final size:11
Alignment explanation
Indices: 2822227--2822251 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2822217 CTTCAAGTTA
2822227 TTTTTCTTCTT
1 TTTTTCTTCTT
2822238 TTTTTCTTCTT
1 TTTTTCTTCTT
2822249 TTT
1 TTT
2822252 ATTTTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:2822416 original size:11 final size:11
Alignment explanation
Indices: 2822400--2822444 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
2822390 AAACCTAGAT
*
2822400 TTTTTGTTTTA
1 TTTTTGTTTCA
2822411 TTTTTGTTTCA
1 TTTTTGTTTCA
2822422 TTTTTGTTTCA
1 TTTTTGTTTCA
2822433 TTTTTGTTTCA
1 TTTTTGTTTCA
2822444 T
1 T
2822445 ACTCTTTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.76
Consensus pattern (11 bp):
TTTTTGTTTCA
Found at i:2823411 original size:26 final size:28
Alignment explanation
Indices: 2823344--2823419 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 28
2823334 TTCTAAATAA
*
2823344 ATTAAATTACTTAAATTAATTATTATTTTT
1 ATTAAATTA--TAATTTAATTATTATTTTT
* *
2823374 AATAAAAATATAATTTAATTA-TATTTTT
1 -ATTAAATTATAATTTAATTATTATTTTT
*
2823402 -TTAAATTATAATTAAATT
1 ATTAAATTATAATTTAATT
2823420 TTAATAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 15 0.38
28 7 0.18
29 10 0.26
31 7 0.18
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTAAATTATAATTTAATTATTATTTTT
Found at i:2823427 original size:21 final size:20
Alignment explanation
Indices: 2823380--2823428 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2823370 TTTTAATAAA
*
2823380 AATATAATTTAATTATATTTT
1 AATA-AATTTAATTAAATTTT
**
2823401 TTTAAATTATAATTAAATTTT
1 AATAAATT-TAATTAAATTTT
2823422 AATAAAT
1 AATAAAT
2823429 GATTAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAAATTTAATTAAATTTT
Found at i:2826664 original size:39 final size:39
Alignment explanation
Indices: 2826578--2826665 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
2826568 ACGCAGCAGA
**
2826578 ATGCTCATCATCCGGACTTACAACTCTCGATGTAACAGG
1 ATGCTCATCATCCGGACTTACAACTCTCGATGTAACAAC
* * *
2826617 ATGCTCATCATCCGGACTTGCAACTTTCGATGCT-CCAAC
1 ATGCTCATCATCCGGACTTACAACTCTCGATG-TAACAAC
*
2826656 ATGTTCATCA
1 ATGCTCATCA
2826666 ACTGCGCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 41 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (39 bp):
ATGCTCATCATCCGGACTTACAACTCTCGATGTAACAAC
Found at i:2834534 original size:12 final size:12
Alignment explanation
Indices: 2834508--2834554 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
2834498 TCCCCGAATA
*
2834508 ATAAA-ATAAAA
1 ATAAAGATAAAG
2834519 ATAAAGATAAAG
1 ATAAAGATAAAG
2834531 ATAAAGATAAAG
1 ATAAAGATAAAG
2834543 ATAAAAGATAAA
1 AT-AAAGATAAA
2834555 AGGAAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
11 5 0.15
12 19 0.58
13 9 0.27
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (12 bp):
ATAAAGATAAAG
Found at i:2834540 original size:18 final size:18
Alignment explanation
Indices: 2834508--2834555 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2834498 TCCCCGAATA
2834508 ATAAA-ATAAAAATAAAG
1 ATAAAGATAAAAATAAAG
*
2834525 ATAAAGATAAAGATAAAG
1 ATAAAGATAAAAATAAAG
2834543 ATAAAAGATAAAA
1 AT-AAAGATAAAA
2834556 GGAAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 5 0.19
18 13 0.48
19 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
ATAAAGATAAAAATAAAG
Found at i:2839049 original size:21 final size:19
Alignment explanation
Indices: 2839024--2839079 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
2839014 TTTTTTCAAT
2839024 TAAATCATTATTTTATTAAA
1 TAAAT-ATTATTTTATTAAA
2839044 TAAA-ATTATTTTATTAAA
1 TAAATATTATTTTATTAAA
*
2839062 TAAAATAATATTTTATTA
1 T-AAATATTATTTTATTA
2839080 TTATTTCGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 15 0.45
19 3 0.09
20 15 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATATTATTTTATTAAA
Found at i:2839051 original size:18 final size:18
Alignment explanation
Indices: 2839030--2839079 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
2839020 CAATTAAATC
2839030 ATTATTTTATTAAATAAA
1 ATTATTTTATTAAATAAA
2839048 ATTATTTTATTAAATAAA
1 ATTATTTTATTAAATAAA
2839066 ATAATATTTTATTA
1 AT--TATTTTATTA
2839080 TTATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 20 0.67
20 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATTTTATTAAATAAA
Found at i:2839468 original size:14 final size:14
Alignment explanation
Indices: 2839430--2839460 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2839420 TGGTCATTTG
*
2839430 TTTCGGAAAATAGA
1 TTTCAGAAAATAGA
2839444 TTTCAGAAAATAGA
1 TTTCAGAAAATAGA
2839458 TTT
1 TTT
2839461 TGTAAAATGA
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:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (14 bp):
TTTCAGAAAATAGA
Found at i:2839797 original size:42 final size:43
Alignment explanation
Indices: 2839732--2839814 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
2839722 ATATTTTATT
* *
2839732 AGAATAAAATTATTATAAATTATATTAATTATTTATTAAAATA
1 AGAATAAAATTATTATAAATTATAATAATTACTTATTAAAATA
* *
2839775 AGAATAATA-TATTATTAATTATAATAATTACTTATTAAAA
1 AGAATAAAATTATTATAAATTATAATAATTACTTATTAAAA
2839815 CAATAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (43 bp):
AGAATAAAATTATTATAAATTATAATAATTACTTATTAAAATA
Found at i:2840839 original size:2 final size:2
Alignment explanation
Indices: 2840832--2840869 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2840822 TCATACCCTC
*
2840832 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2840870 CCCTCTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2843942 original size:35 final size:35
Alignment explanation
Indices: 2843896--2843997 Score: 136
Period size: 34 Copynumber: 2.9 Consensus size: 35
2843886 CTTAGGTCCG
* *
2843896 TAAGGAATTACCAGCTAATCAGTGTTGAACCTATA
1 TAAGGAATTACCAGCTGATCAGAGTTGAACCTATA
* *
2843931 TAAGGAATTACCAG-TCGATC-GGGCTGAACCTATA
1 TAAGGAATTACCAGCT-GATCAGAGTTGAACCTATA
2843965 TAAGGAATTACCAGCTTGATCAGAGTTGAACCT
1 TAAGGAATTACCAGC-TGATCAGAGTTGAACCT
2843998 CCATACTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 27 0.47
35 21 0.36
36 10 0.17
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (35 bp):
TAAGGAATTACCAGCTGATCAGAGTTGAACCTATA
Found at i:2845927 original size:29 final size:29
Alignment explanation
Indices: 2845895--2845954 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2845885 GCTTACAGGG
2845895 TTTATCCTCATTCATTTATTCTAAGTCGT
1 TTTATCCTCATTCATTTATTCTAAGTCGT
2845924 TTTATCCTCATTCATTTATTCTAAGTCGT
1 TTTATCCTCATTCATTTATTCTAAGTCGT
2845953 TT
1 TT
2845955 CGACTATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (29 bp):
TTTATCCTCATTCATTTATTCTAAGTCGT
Found at i:2849185 original size:31 final size:31
Alignment explanation
Indices: 2849143--2849219 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
2849133 ATGGCCAAGT
*
2849143 ATATGTCAAAACATGTACATGAATATGACGC
1 ATATGTTAAAACATGTACATGAATATGACGC
* *
2849174 ATATGTTAAAACATGTATATGAATATGATGC
1 ATATGTTAAAACATGTACATGAATATGACGC
2849205 ATATGTTAAAACATG
1 ATATGTTAAAACATG
2849220 CATGCACATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (31 bp):
ATATGTTAAAACATGTACATGAATATGACGC
Found at i:2849222 original size:16 final size:16
Alignment explanation
Indices: 2849172--2849222 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2849162 TGAATATGAC
2849172 GCATATGTTAAAACAT
1 GCATATGTTAAAACAT
* **
2849188 GTATATG--AATATGAT
1 GCATATGTTAA-AACAT
2849203 GCATATGTTAAAACAT
1 GCATATGTTAAAACAT
2849219 GCAT
1 GCAT
2849223 GCACATGCAC
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 2 0.08
15 9 0.35
16 13 0.50
17 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (16 bp):
GCATATGTTAAAACAT
Found at i:2854494 original size:34 final size:34
Alignment explanation
Indices: 2854451--2854521 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
2854441 AATGACATGT
2854451 TGATAATCAAATTGCCACAACCAAATCACGTTTG
1 TGATAATCAAATTGCCACAACCAAATCACGTTTG
2854485 TGATAATCAAATTGCCACAACCAAATCACGTTTG
1 TGATAATCAAATTGCCACAACCAAATCACGTTTG
2854519 TGA
1 TGA
2854522 AGATCCAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (34 bp):
TGATAATCAAATTGCCACAACCAAATCACGTTTG
Found at i:2855323 original size:20 final size:20
Alignment explanation
Indices: 2855298--2855341 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2855288 ATTTTCTAAT
*
2855298 TCAACTTTTTGAATTATGTC
1 TCAACTTTGTGAATTATGTC
*
2855318 TCAACTTTGTGAATTGTGTC
1 TCAACTTTGTGAATTATGTC
2855338 TCAA
1 TCAA
2855342 AGTTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (20 bp):
TCAACTTTGTGAATTATGTC
Found at i:2855347 original size:20 final size:20
Alignment explanation
Indices: 2855307--2855347 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2855297 TTCAACTTTT
**
2855307 TGAATTATGTCTCAACTTTG
1 TGAATTATGTCTCAAAGTTG
*
2855327 TGAATTGTGTCTCAAAGTTG
1 TGAATTATGTCTCAAAGTTG
2855347 T
1 T
2855348 TTTTAAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (20 bp):
TGAATTATGTCTCAAAGTTG
Found at i:2856021 original size:17 final size:16
Alignment explanation
Indices: 2856001--2856035 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
2855991 AGATTATAAA
2856001 TAAAATTTAAAATATTT
1 TAAAATTTAAAAT-TTT
2856018 TAAAATTTAAAATTTT
1 TAAAATTTAAAATTTT
2856034 TA
1 TA
2856036 GAGAGATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAAATTTAAAATTTT
Found at i:2864149 original size:20 final size:20
Alignment explanation
Indices: 2864124--2864397 Score: 223
Period size: 20 Copynumber: 13.6 Consensus size: 20
2864114 GATTTTCCAG
** *
2864124 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
2864144 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
2864164 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
2864183 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
2864205 AATCGCAACTCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
2864225 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
2864246 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2864266 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
2864286 AATCGTAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
2864306 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
2864326 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
2864346 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATCCGT-A
*
2864367 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
2864387 AATCGCAACGC
1 AATCGCAACGC
2864398 AATTTTTAAA
Statistics
Matches: 201, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.00
20 149 0.74
21 50 0.25
22 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:2864230 original size:41 final size:41
Alignment explanation
Indices: 2864185--2864396 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
2864175 GATTCTGACT
* * *
2864185 ATCGCAACGAGTATCCGTAAAATCGCAACTCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
2864226 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2864267 ATCGCAACGAGAATACGT-AAATCGTAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
2864307 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2864347 ATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
2864388 ATCGCAACG
1 ATCGCAACG
2864397 CAATTTTTAA
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.46
41 84 0.54
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:2866504 original size:18 final size:18
Alignment explanation
Indices: 2866458--2866507 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2866448 TTTACTCGTA
*
2866458 ATTTCACTTAAATTAACC
1 ATTTCACTTAGATTAACC
2866476 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2866494 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2866508 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:2866673 original size:94 final size:94
Alignment explanation
Indices: 2866512--2866891 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
2866502 TAGATTGCTT
* * *
2866512 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2866577 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
2866606 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2866671 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
2866700 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTATACTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2866765 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
2866794 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2866859 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2866887 AGTAA
1 AGTAA
2866892 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 246 0.90
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2867021 original size:33 final size:33
Alignment explanation
Indices: 2866979--2867058 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
2866969 AAAAATGACT
*
2866979 ATCGCAACGCGAAATAAAAATCACAACTAGAGA
1 ATCGCAACGCGAAATAAAAATCACAACGAGAGA
* *
2867012 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATAAAAATCACAACGAGAGA
* *
2867045 ATCGTAACGTGAAA
1 ATCGCAACGCGAAA
2867059 CTATAATTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATAAAAATCACAACGAGAGA
Found at i:2867094 original size:19 final size:18
Alignment explanation
Indices: 2867070--2867161 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
2867060 TATAATTGCG
2867070 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
2867088 ATTGCGA--TT-ATCTCG-
1 -TTGCGATTTTCATTTCGC
2867103 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
2867121 GTTGCGATTCTC--TT-G-
1 -TTGCGATTTTCATTTCGC
*
2867136 TTGTGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
2867154 GTTGCGAT
1 -TTGCGAT
2867162 AGTGATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 15 0.26
16 10 0.18
17 10 0.18
19 22 0.39
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.48
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:2867110 original size:33 final size:33
Alignment explanation
Indices: 2867068--2867161 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2867058 ACTATAATTG
*
2867068 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
*
2867101 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
* *
2867134 TGTTGTGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
2867162 AGTGATTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
Found at i:2867663 original size:42 final size:42
Alignment explanation
Indices: 2867587--2867705 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
2867577 GACTCGCCTG
* * * * * *
2867587 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* *
2867629 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
2867671 TCA-TCCTTGAAGAGGT-CTCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCACTCCCACCGTTCAAGAG
2867706 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.08
42 57 0.89
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:2869075 original size:14 final size:14
Alignment explanation
Indices: 2869056--2869091 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2869046 ATTGTTTAAT
2869056 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2869070 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2869084 TGATTTGT
1 TGATTTGT
2869092 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2869214 original size:19 final size:19
Alignment explanation
Indices: 2869198--2869257 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
2869188 AAAAATGACT
2869198 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2869217 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2869231 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2869250 ATCGCAAT
1 ATCGCAAT
2869258 TGTTTGAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2870709 original size:24 final size:24
Alignment explanation
Indices: 2870682--2870735 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2870672 TTGAAAAAGC
2870682 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
2870706 ATCATAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2870730 ATCAAA
1 ATCAAA
2870736 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2871615 original size:20 final size:20
Alignment explanation
Indices: 2871593--2871705 Score: 91
Period size: 20 Copynumber: 5.5 Consensus size: 20
2871583 TAGTCAGAAT
* *
2871593 CTCATTGCGATTTACGTATT
1 CTCATTGCGATTTACGGATA
* * *
2871613 CTCGTTGTGATTTTCGGATA
1 CTCATTGCGATTTACGGATA
* * * *
2871633 CGCAATGCGATTTTACGTATT
1 CTCATTGCGA-TTTACGGATA
* *
2871654 GTCGTTGCGATTTACGGATA
1 CTCATTGCGATTTACGGATA
*
2871674 CGCATTGCGATTTTACGGATA
1 CTCATTGCGA-TTTACGGATA
*
2871695 CTCGTTGCGAT
1 CTCATTGCGAT
2871706 AGTCAGAATC
Statistics
Matches: 68, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 37 0.54
21 31 0.46
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CTCATTGCGATTTACGGATA
Found at i:2871659 original size:41 final size:41
Alignment explanation
Indices: 2871598--2871705 Score: 155
Period size: 41 Copynumber: 2.7 Consensus size: 41
2871588 AGAATCTCAT
* *
2871598 TGCGA-TTTACGTATTCTCGTTGTGATTTTCGGATACGCAA
1 TGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCAA
* *
2871638 TGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCAT
1 TGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCAA
* *
2871679 TGCGATTTTACGGATACTCGTTGCGAT
1 TGCGATTTTACGTATTCTCGTTGCGAT
2871706 AGTCAGAATC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
40 5 0.08
41 55 0.92
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
TGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCAA
Found at i:2871664 original size:21 final size:21
Alignment explanation
Indices: 2871638--2871705 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2871628 GGATACGCAA
* *
2871638 TGCGATTTTACGTATTGTCGT
1 TGCGATTTTACGGATAGTCGT
*
2871659 TGCGA-TTTACGGATACG-CAT
1 TGCGATTTTACGGATA-GTCGT
*
2871679 TGCGATTTTACGGATACTCGT
1 TGCGATTTTACGGATAGTCGT
2871700 TGCGAT
1 TGCGAT
2871706 AGTCAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
TGCGATTTTACGGATAGTCGT
Found at i:2871721 original size:61 final size:60
Alignment explanation
Indices: 2871576--2871728 Score: 146
Period size: 61 Copynumber: 2.5 Consensus size: 60
2871566 GAAATTCAGT
* * * * * * *
2871576 ATTGCGATAGTCAGAATCTCATTGCGATTTACGTATTCTCGTTGTGATTTTCGGATACGC
1 ATTGCGATAGTCAGAATCGCGTTGCGATTTACGGATACGCATTGCGATTTTCGGATACGC
* * * * * *
2871636 AATGCGAT-TTTACGTATTGTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACTC
1 ATTGCGATAGTCA-GAATCG-CGTTGCGATTTACGGATACGCATTGCGATTTT-CGGATACGC
*
2871698 GTTGCGATAGTCAGAATCGCGTTGCGATTTA
1 ATTGCGATAGTCAGAATCGCGTTGCGATTTA
2871729 TATGTTCACG
Statistics
Matches: 70, Mismatches: 19, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
59 2 0.03
60 10 0.14
61 38 0.54
62 18 0.26
63 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATTTACGGATACGCATTGCGATTTTCGGATACGC
Found at i:2871723 original size:41 final size:42
Alignment explanation
Indices: 2871577--2871727 Score: 143
Period size: 41 Copynumber: 3.7 Consensus size: 42
2871567 AAATTCAGTA
*
2871577 TTGCGATAGTCAGAAT-CTCATTGCGA-TTTACGTATTCTCG
1 TTGCGATAGTCAGAATACGCATTGCGATTTTACGTATTCTCG
* ** * * *
2871617 TTGTGATTTTC-GGATACGCAATGCGATTTTACGTATTGTCG
1 TTGCGATAGTCAGAATACGCATTGCGATTTTACGTATTCTCG
* * * *
2871658 TTGCGAT--TTACGGATACGCATTGCGATTTTACGGATACTCG
1 TTGCGATAGTCA-GAATACGCATTGCGATTTTACGTATTCTCG
*
2871699 TTGCGATAGTCAGAAT-CGCGTTGCGATTT
1 TTGCGATAGTCAGAATACGCATTGCGATTT
2871728 ATATGTTCAC
Statistics
Matches: 89, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
39 4 0.04
40 16 0.18
41 64 0.72
42 3 0.03
43 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCAGAATACGCATTGCGATTTTACGTATTCTCG
Found at i:2871740 original size:20 final size:20
Alignment explanation
Indices: 2871717--2871766 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2871707 GTCAGAATCG
*
2871717 CGTTGCGATTTAT-ATGTTCA
1 CGTTGCGATTT-TCATATTCA
*
2871737 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCA
2871757 CGTTGCGATT
1 CGTTGCGATT
2871767 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCA
Found at i:2871865 original size:20 final size:19
Alignment explanation
Indices: 2871816--2871869 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2871806 ATTCTTCATA
2871816 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
2871835 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2871856 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2871870 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2873990 original size:23 final size:23
Alignment explanation
Indices: 2873964--2874011 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2873954 ATAAAGTACA
*
2873964 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2873987 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2874010 AT
1 AT
2874012 TTATCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2874733 original size:3 final size:3
Alignment explanation
Indices: 2874725--2874811 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
2874715 ACTTGTTTGG
* * * **
2874725 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
2874773 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2874812 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:2874748 original size:18 final size:18
Alignment explanation
Indices: 2874725--2874826 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
2874715 ACTTGTTTGG
2874725 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
2874743 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
2874761 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
2874779 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
2874797 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
2874815 AGCTTCATCTTC
1 ATCATCATCTTC
2874827 TGCGACCGCT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:2874792 original size:42 final size:42
Alignment explanation
Indices: 2874733--2874823 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
2874723 GGATCATCAT
*
2874733 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
2874775 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
2874817 CTTCATC
1 CTTCATC
2874824 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Done.