Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007010.1 Hibiscus syriacus cultivar Beakdansim tig00018093_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: 523506
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:11145 original size:7 final size:7
Alignment explanation
Indices: 10963--11141 Score: 304
Period size: 7 Copynumber: 25.6 Consensus size: 7
10953 GTACCCTCCT
10963 CCCTGAA
1 CCCTGAA
10970 CCCTGAA
1 CCCTGAA
10977 CCCTGAA
1 CCCTGAA
10984 CCCTGAA
1 CCCTGAA
10991 CCCTGAA
1 CCCTGAA
10998 CCCTGAA
1 CCCTGAA
11005 CCCTGAA
1 CCCTGAA
11012 CCCTGAA
1 CCCTGAA
11019 CCCTGAA
1 CCCTGAA
11026 CCCTGAA
1 CCCTGAA
11033 CCCTGAA
1 CCCTGAA
11040 CCCTGAA
1 CCCTGAA
11047 CCCTGAA
1 CCCTGAA
11054 CCCTGAA
1 CCCTGAA
11061 CCCTGAA
1 CCCTGAA
11068 CCCTGAA
1 CCCTGAA
11075 CCCTGAA
1 CCCTGAA
11082 CCCTGAA
1 CCCTGAA
*
11089 CCCTGAC
1 CCCTGAA
*
11096 CCCTGAC
1 CCCTGAA
*
11103 CCCTGAC
1 CCCTGAA
*
11110 CCCTGAC
1 CCCTGAA
*
11117 CCCTGAC
1 CCCTGAA
11124 CCCTGAA
1 CCCTGAA
*
11131 CCCTAAA
1 CCCTGAA
11138 CCCT
1 CCCT
11142 AAACTTCCGA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 169 1.00
ACGTcount: A:0.26, C:0.46, G:0.13, T:0.15
Consensus pattern (7 bp):
CCCTGAA
Found at i:16091 original size:7 final size:7
Alignment explanation
Indices: 16081--16273 Score: 305
Period size: 7 Copynumber: 27.6 Consensus size: 7
16071 GTACCCTCCT
16081 CCCTGAA
1 CCCTGAA
16088 CCCTGAA
1 CCCTGAA
16095 CCCTGAA
1 CCCTGAA
16102 CCCTGAA
1 CCCTGAA
*
16109 CCCTAAA
1 CCCTGAA
16116 CCCTGAA
1 CCCTGAA
16123 CCCTGAA
1 CCCTGAA
16130 CCCTGAA
1 CCCTGAA
16137 CCCTGAA
1 CCCTGAA
16144 CCCTGAA
1 CCCTGAA
16151 CCCTGAA
1 CCCTGAA
16158 CCCTGAA
1 CCCTGAA
16165 CCCTGAA
1 CCCTGAA
16172 CCCTGAA
1 CCCTGAA
16179 CCCTGAA
1 CCCTGAA
*
16186 CCCTAAA
1 CCCTGAA
16193 CCCTGAA
1 CCCTGAA
16200 CCCTGAA
1 CCCTGAA
16207 CCCTGAA
1 CCCTGAA
*
16214 CCCTGAC
1 CCCTGAA
*
16221 CCCTGAC
1 CCCTGAA
*
16228 CCCTGAC
1 CCCTGAA
*
16235 CCCTGAC
1 CCCTGAA
*
16242 CCCTGAC
1 CCCTGAA
*
16249 CCCTGAC
1 CCCTGAA
16256 CCCTGAA
1 CCCTGAA
*
16263 CCCTAAA
1 CCCTGAA
16270 CCCT
1 CCCT
16274 AAACTTCCGA
Statistics
Matches: 179, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 179 1.00
ACGTcount: A:0.26, C:0.47, G:0.12, T:0.15
Consensus pattern (7 bp):
CCCTGAA
Found at i:31733 original size:30 final size:30
Alignment explanation
Indices: 31697--31764 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
31687 ACTGCAAGTC
31697 CCATCAACGTGCGTTCCACCA-GTGCCTGCT
1 CCATCAACGTGCGTTCCACCATGTG-CTGCT
* *
31727 CCATCAACGTGTGTTCCACCATGTGCTTCT
1 CCATCAACGTGCGTTCCACCATGTGCTGCT
31757 CCATCAAC
1 CCATCAAC
31765 ACATGACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.26
Consensus pattern (30 bp):
CCATCAACGTGCGTTCCACCATGTGCTGCT
Found at i:35290 original size:21 final size:21
Alignment explanation
Indices: 35260--35303 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35250 TACACACTCG
* *
35260 TATTATAATTATTTATAATAT
1 TATTAAAATTATCTATAATAT
35281 TATTAAAATTATCTATAATAT
1 TATTAAAATTATCTATAATAT
35302 TA
1 TA
35304 ATTATTAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAAAATTATCTATAATAT
Found at i:39004 original size:113 final size:113
Alignment explanation
Indices: 38866--39096 Score: 408
Period size: 113 Copynumber: 2.0 Consensus size: 113
38856 AGTTTTGTCA
* *
38866 TTTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTCAATATAT
1 TTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCAATACTTTCAATATAT
* *
38931 CAGGTAAAGCGCTACTGGTTTTGTTATTTTTTTACCGATTTTGTTATT
66 CAGGTAAAGCGCTACCGATTTTGTTATTTTTTTACCGATTTTGTTATT
38979 TTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCAATACTTTCAATATAT
1 TTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCAATACTTTCAATATAT
* *
39044 TAGGTAAAGCGCTACCGATTTTGTTATTTTTTTACCGGTTTTGTTATT
66 CAGGTAAAGCGCTACCGATTTTGTTATTTTTTTACCGATTTTGTTATT
39092 TTTTT
1 TTTTT
39097 ACCGGTTTTA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (113 bp):
TTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCAATACTTTCAATATAT
CAGGTAAAGCGCTACCGATTTTGTTATTTTTTTACCGATTTTGTTATT
Found at i:39085 original size:20 final size:20
Alignment explanation
Indices: 39056--39105 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
39046 GGTAAAGCGC
*
39056 TACCGATTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
39076 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
39096 TACCGGTTTT
1 TACCGGTTTT
39106 ACCAGAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (20 bp):
TACCGGTTTTGTTATTTTTT
Found at i:39613 original size:20 final size:19
Alignment explanation
Indices: 39571--39610 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39561 AGGTAAAGCG
*
39571 TTACCGGTTTTGTTATTTT
1 TTACCGGTTTTATTATTTT
39590 TTACCGGTTTTATTATTTT
1 TTACCGGTTTTATTATTTT
39609 TT
1 TT
39611 TACATGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (19 bp):
TTACCGGTTTTATTATTTT
Found at i:39727 original size:20 final size:21
Alignment explanation
Indices: 39683--39724 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39673 GGTAAAGCGC
39683 TACCGGTTTTGTTATTTTTTT
1 TACCGGTTTTGTTATTTTTTT
39704 TACCGGTTTTGTTATTTTTTT
1 TACCGGTTTTGTTATTTTTTT
39725 ACCTAATATA
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:0.10, C:0.10, G:0.14, T:0.67
Consensus pattern (21 bp):
TACCGGTTTTGTTATTTTTTT
Found at i:39769 original size:113 final size:112
Alignment explanation
Indices: 39484--39826 Score: 501
Period size: 113 Copynumber: 3.1 Consensus size: 112
39474 TAATAAAACT
* * * * *
39484 GGTTTTGTCATATATTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATAT
1 GGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGAT-CTTTTTATAAAAGGATCGATAC
*** *
39549 TTTCAATATGCCAGGTAAAGCGTTACCGGTTTTGTTA--TTTTTTACC
65 TTTCAATATATTAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
* *
39595 GGTTTTATTATTTTTTTACATGTTATATTGTAAAGTATCGATACTTTTTATAAAAGGATCGATAC
1 GGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGAT-CTTTTTATAAAAGGATCGATAC
39660 TTTCAATATATTAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
65 TTTCAATATATTAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
** *
39708 GGTTTTGTTATTTTTTTACCTAATATATTGTAAAGTATCGATCTTTTTTATAAAAAGATCGATAC
1 GGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATC-TTTTTATAAAAGGATCGATAC
* *
39773 TTTCAATATATTAGGTAAATCGCTACCGGTTTTGTTATTTTTTTTACT
65 TTTCAATATATTAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
39821 GGTTTT
1 GGTTTT
39827 ACCGAAAATG
Statistics
Matches: 210, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
111 90 0.43
112 1 0.00
113 119 0.57
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (112 bp):
GGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCTTTTTATAAAAGGATCGATACT
TTCAATATATTAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTTACC
Found at i:40197 original size:24 final size:25
Alignment explanation
Indices: 40170--40238 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
40160 AGCATCAAAT
40170 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
40194 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
40217 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
40239 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:40488 original size:23 final size:23
Alignment explanation
Indices: 40453--40556 Score: 100
Period size: 23 Copynumber: 4.2 Consensus size: 23
40443 CCAGTAATTA
**
40453 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
40476 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAGCGCT
**
40499 ACCTAATATGTTATTGTTTATATAAGCGCT
1 ACC---TA--TTA--CATTATATAAGCGCT
40529 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
40552 ACCTA
1 ACCTA
40557 ATTTGTTATT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
23 41 0.62
25 3 0.05
26 2 0.03
27 2 0.03
28 3 0.05
30 15 0.23
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:40536 original size:53 final size:53
Alignment explanation
Indices: 40463--40566 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
40453 ACCTATTTTA
40463 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGT
1 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGT
* *
40516 TTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATT
1 TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATT
40567 TTACTTGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (53 bp):
TTATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGT
Found at i:41323 original size:20 final size:20
Alignment explanation
Indices: 41298--41337 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41288 ACTTAATACT
*
41298 CGACTCGAAAAGATCGTGAG
1 CGACTCAAAAAGATCGTGAG
*
41318 CGACTCAAAAAGCTCGTGAG
1 CGACTCAAAAAGATCGTGAG
41338 TAGCTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.28, T:0.15
Consensus pattern (20 bp):
CGACTCAAAAAGATCGTGAG
Found at i:47118 original size:2 final size:2
Alignment explanation
Indices: 47111--47175 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
47101 AGACCATCTT
47111 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47153 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
47176 ATACAAACAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:47972 original size:21 final size:23
Alignment explanation
Indices: 47948--47996 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
47938 GCTGTAACAA
*
47948 TCTCCT-CTTCATTTTCCT-TCT
1 TCTCCTCCTCCATTTTCCTCTCT
* *
47969 TCTCTTCCTCCCTTTTCCTCTCT
1 TCTCCTCCTCCATTTTCCTCTCT
47992 TCTCC
1 TCTCC
47997 CTCCAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (23 bp):
TCTCCTCCTCCATTTTCCTCTCT
Found at i:50806 original size:16 final size:15
Alignment explanation
Indices: 50785--50826 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
50775 TTTAAGTTTA
50785 TTTTATTTTTACTGTT-
1 TTTTATTTTT--TGTTG
*
50801 TTTTATTATTTGTTG
1 TTTTATTTTTTGTTG
50816 TTTTATTTTTT
1 TTTTATTTTTT
50827 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 9 0.39
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTGTTG
Found at i:57812 original size:16 final size:16
Alignment explanation
Indices: 57791--57824 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
57781 GGACCCTAGG
57791 TTGTTTTGTGATGAAT
1 TTGTTTTGTGATGAAT
*
57807 TTGTTTTGTGATTAAT
1 TTGTTTTGTGATGAAT
57823 TT
1 TT
57825 CTTTCGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (16 bp):
TTGTTTTGTGATGAAT
Found at i:64366 original size:20 final size:21
Alignment explanation
Indices: 64341--64381 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
64331 ATTTAAAGTA
*
64341 GGTATCGGTAC-CCCCTATAG
1 GGTATCGATACTCCCCTATAG
64361 GGTATCGATACTTCCCCTATA
1 GGTATCGATAC-TCCCCTATA
64382 TAAGGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
GGTATCGATACTCCCCTATAG
Found at i:66316 original size:218 final size:218
Alignment explanation
Indices: 65938--66374 Score: 874
Period size: 218 Copynumber: 2.0 Consensus size: 218
65928 AAGTGCTTCG
65938 TAGGGGGCCATTTTGATGTTTGATTAGTAACTATTGTTGTAAGAGAACTCAACAAGTGGTAAATA
1 TAGGGGGCCATTTTGATGTTTGATTAGTAACTATTGTTGTAAGAGAACTCAACAAGTGGTAAATA
66003 TCTTTCCCACGATCCTTTGAACTCAATAACACAAGCTCTCAGCATATCTTCCAGAATTTGGATAG
66 TCTTTCCCACGATCCTTTGAACTCAATAACACAAGCTCTCAGCATATCTTCCAGAATTTGGATAG
66068 TCCGCTCAGACTGTCCATCTGTCTGATGATGAAACGTTGTGCTAAATTTCAGTCGAGTGCCTAAC
131 TCCGCTCAGACTGTCCATCTGTCTGATGATGAAACGTTGTGCTAAATTTCAGTCGAGTGCCTAAC
66133 TCTCTATGCAAGGTCTTCCAGAA
196 TCTCTATGCAAGGTCTTCCAGAA
66156 TAGGGGGCCATTTTGATGTTTGATTAGTAACTATTGTTGTAAGAGAACTCAACAAGTGGTAAATA
1 TAGGGGGCCATTTTGATGTTTGATTAGTAACTATTGTTGTAAGAGAACTCAACAAGTGGTAAATA
66221 TCTTTCCCACGATCCTTTGAACTCAATAACACAAGCTCTCAGCATATCTTCCAGAATTTGGATAG
66 TCTTTCCCACGATCCTTTGAACTCAATAACACAAGCTCTCAGCATATCTTCCAGAATTTGGATAG
66286 TCCGCTCAGACTGTCCATCTGTCTGATGATGAAACGTTGTGCTAAATTTCAGTCGAGTGCCTAAC
131 TCCGCTCAGACTGTCCATCTGTCTGATGATGAAACGTTGTGCTAAATTTCAGTCGAGTGCCTAAC
66351 TCTCTATGCAAGGTCTTCCAGAA
196 TCTCTATGCAAGGTCTTCCAGAA
66374 T
1 T
66375 CTCGAAGTAA
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 219 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (218 bp):
TAGGGGGCCATTTTGATGTTTGATTAGTAACTATTGTTGTAAGAGAACTCAACAAGTGGTAAATA
TCTTTCCCACGATCCTTTGAACTCAATAACACAAGCTCTCAGCATATCTTCCAGAATTTGGATAG
TCCGCTCAGACTGTCCATCTGTCTGATGATGAAACGTTGTGCTAAATTTCAGTCGAGTGCCTAAC
TCTCTATGCAAGGTCTTCCAGAA
Found at i:74220 original size:21 final size:21
Alignment explanation
Indices: 74194--74233 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
74184 TATAGGTTCA
74194 TTTTTTCAT-TTATTTTATTAC
1 TTTTTT-ATGTTATTTTATTAC
74215 TTTTTTATGTTATTTTATT
1 TTTTTTATGTTATTTTATT
74234 TTTTTCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTATGTTATTTTATTAC
Found at i:88357 original size:20 final size:21
Alignment explanation
Indices: 88324--88363 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
88314 CCTTCAAATA
88324 AATAAATAAATTCAAAATAAT
1 AATAAATAAATTCAAAATAAT
88345 AATAAAT-AATTCAAAATAA
1 AATAAATAAATTCAAAATAA
88364 ATTATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAATAAATTCAAAATAAT
Found at i:88424 original size:18 final size:18
Alignment explanation
Indices: 88319--88424 Score: 112
Period size: 18 Copynumber: 5.8 Consensus size: 18
88309 TATATCCTTC
88319 AAATAAATAAATAAATTCA
1 AAATAAATAAAT-AATTCA
88338 AAATAATAATAAATAATTCA
1 AAAT-A-AATAAATAATTCA
*
88358 AAATAAAT---T-ATTAA
1 AAATAAATAAATAATTCA
*
88372 AGGAATAAATAAATTATTCA
1 A--AATAAATAAATAATTCA
*
88392 AAATAAATAAATAATTTA
1 AAATAAATAAATAATTCA
88410 AAATAAATAAATAAT
1 AAATAAATAAATAAT
88425 ACCTCCGGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.07
15 1 0.01
16 7 0.09
18 33 0.44
19 6 0.08
20 16 0.21
21 7 0.09
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATAAATAAATAATTCA
Found at i:101105 original size:9 final size:9
Alignment explanation
Indices: 101091--101116 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
101081 GATTTGAATT
101091 TTTTCAAAG
1 TTTTCAAAG
101100 TTTTCAAAG
1 TTTTCAAAG
101109 TTTTCAAA
1 TTTTCAAA
101117 AATAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (9 bp):
TTTTCAAAG
Found at i:102683 original size:19 final size:20
Alignment explanation
Indices: 102659--102706 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
102649 AATGATTTTC
* * *
102659 TTTTGAAAGTTAAAATG-GA
1 TTTTGAAAATCAAAATGAAA
102678 TTTTGAAAATCAAAATGAAA
1 TTTTGAAAATCAAAATGAAA
102698 TTTTGAAAA
1 TTTTGAAAA
102707 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (20 bp):
TTTTGAAAATCAAAATGAAA
Found at i:110149 original size:29 final size:29
Alignment explanation
Indices: 110098--110155 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
110088 GTGTTGACCG
* *
110098 TAGGTCGCCATGCCTTTCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
110127 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
110156 AAGAGATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:110234 original size:23 final size:23
Alignment explanation
Indices: 110199--110250 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
110189 GCTGGGCATC
* *
110199 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
*
110222 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
110245 CGAGGG
1 CGAGGG
110251 AATCCGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.38, T:0.10
Consensus pattern (23 bp):
CGAGGGCAACCGAACGAGCTATG
Found at i:110257 original size:23 final size:24
Alignment explanation
Indices: 110206--110258 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
110196 ATCCGAGGCC
*
110206 ATCCGAACGAGCTATGCGAGGGCA
1 ATCCGAGCGAGCTATGCGAGGGCA
110230 A-CCGAGCGAGCTATGCGAGGG-A
1 ATCCGAGCGAGCTATGCGAGGGCA
110252 ATCCGAG
1 ATCCGAG
110259 GGAAGCTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 24 0.89
24 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.36, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCGAGGGCA
Found at i:110326 original size:28 final size:28
Alignment explanation
Indices: 110276--110357 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
110266 GAGCGAGGGT
* *
110276 AGGTCGCCCTGAGTGCATGGCGACCAACA
1 AGGTCGCCC-GGGGGCATGGCGACCAACA
**
110305 AGGTCGCCCGGGGGCATGGCGACTTACA
1 AGGTCGCCCGGGGGCATGGCGACCAACA
*
110333 AGGTCGCCCGGAGGGCATGTCGACC
1 AGGTCGCCCGG-GGGCATGGCGACC
110358 TATGTGTTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 26 0.57
29 20 0.43
ACGTcount: A:0.20, C:0.30, G:0.37, T:0.13
Consensus pattern (28 bp):
AGGTCGCCCGGGGGCATGGCGACCAACA
Found at i:113316 original size:287 final size:287
Alignment explanation
Indices: 112800--113659 Score: 1623
Period size: 287 Copynumber: 3.0 Consensus size: 287
112790 TTAATACAAT
112800 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
1 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
112865 AAATAGTATATCCATTAATGTGACTTAAACCAATCGGTTTGTGACCGAATTACCCATCACATAAT
66 AAATAGTATATCCATTAATGTGACTTAAACCAATCGGTTTGTGACCGAATTACCCATCACATAAT
*
112930 CGACTGCCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
131 CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
*
112995 GTGCTCGCCCTTAAGTACAAACTCAAGATTGTCGAATGCAGCACAAAAGAAAAAGTAAAGACGAA
196 GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCACAAAAGAAAAAGTAAAGACGAA
113060 AAGTAGTTATTTTTTTTATAGGAATTG
261 AAGTAGTTATTTTTTTTATAGGAATTG
113087 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
1 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
*
113152 AAATAGTATATCCATTAATGTGACTTAAACTAATCGGTTTGTGACCGAATTACCCATCACATAAT
66 AAATAGTATATCCATTAATGTGACTTAAACCAATCGGTTTGTGACCGAATTACCCATCACATAAT
*
113217 CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATAAAGTTGGTTTATAACAATGT
131 CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
*
113282 GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCAC-AAAGGAAAAGTAAAGACGAA
196 GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCACAAAAGAAAAAGTAAAGACGAA
113346 AAGTAGTTATTTTTTTTTATAGGAATTG
261 AAGTAGTTA-TTTTTTTTATAGGAATTG
113374 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
1 TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
* * *
113439 AAATAGTATATCTATTAATGTGACTTAAACCAATCGGTTCGTGACCTAATTACCCATCACATAAT
66 AAATAGTATATCCATTAATGTGACTTAAACCAATCGGTTTGTGACCGAATTACCCATCACATAAT
113504 CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
131 CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
*
113569 GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCACAAAGGAAAAAGTAAAGACGAA
196 GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCACAAAAGAAAAAGTAAAGACGAA
113634 AAGTAGTTATTTTTTTTATAGGAATT
261 AAGTAGTTATTTTTTTTATAGGAATT
113660 ATAGGCCTCA
Statistics
Matches: 559, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
286 28 0.05
287 504 0.90
288 27 0.05
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (287 bp):
TAAATGAGTTCAAGTATACAAGTTATGCAATTAAAATGACCCCTTGAATCTTAAAATCTTAAAAT
AAATAGTATATCCATTAATGTGACTTAAACCAATCGGTTTGTGACCGAATTACCCATCACATAAT
CGACTGTCGTACTAACTGAAATCAACAAAATCGAAGATGTTGATTAAGTTGGTTTATAACAATGT
GTGCTCGCCCTTAAGTACAGACTCAAGATTGTCGAATGCAGCACAAAAGAAAAAGTAAAGACGAA
AAGTAGTTATTTTTTTTATAGGAATTG
Found at i:114060 original size:68 final size:68
Alignment explanation
Indices: 113974--114106 Score: 212
Period size: 68 Copynumber: 2.0 Consensus size: 68
113964 GCTGACTCAA
* * * * *
113974 TCCATAAAAGATAAAATCAAAAACAAAATCCTGAACTTCCGCACGAACAGATAACCAGAAACAGC
1 TCCATAAAAGACAAAATCAAAAACAAAATCATGAACTTCCACACGAACAGAGAACAAGAAACAGC
114039 ATC
66 ATC
*
114042 TCCATAAAAGACAAAATCAAAAACAAAATCATGAACTTCCACACGAACAGAGAACAAGAATCAGC
1 TCCATAAAAGACAAAATCAAAAACAAAATCATGAACTTCCACACGAACAGAGAACAAGAAACAGC
114107 TTCCGCCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.52, C:0.24, G:0.11, T:0.14
Consensus pattern (68 bp):
TCCATAAAAGACAAAATCAAAAACAAAATCATGAACTTCCACACGAACAGAGAACAAGAAACAGC
ATC
Found at i:120533 original size:29 final size:29
Alignment explanation
Indices: 120491--120548 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
120481 AATCGCAGAC
120491 CCGCTCTCCCTCTTCGTATATATTTATTT
1 CCGCTCTCCCTCTTCGTATATATTTATTT
120520 CCGCTCTCCCTCTTCGTATATATTTATTT
1 CCGCTCTCCCTCTTCGTATATATTTATTT
120549 GCAGATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (29 bp):
CCGCTCTCCCTCTTCGTATATATTTATTT
Found at i:122596 original size:23 final size:23
Alignment explanation
Indices: 122566--122619 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
122556 CTCAACAATG
122566 GCCATCATGGATGGTCCCTTGGA
1 GCCATCATGGATGGTCCCTTGGA
122589 GCCATCATGGATGGTCCCTTGGA
1 GCCATCATGGATGGTCCCTTGGA
122612 GCCATCAT
1 GCCATCAT
122620 CGTCAACTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
GCCATCATGGATGGTCCCTTGGA
Found at i:125276 original size:192 final size:194
Alignment explanation
Indices: 124947--125332 Score: 758
Period size: 192 Copynumber: 2.0 Consensus size: 194
124937 TATGGGCTTC
124947 AAATCGAGATGAATTATAGAGGCAAGTGAGGTTTCCCAAAAGCTCTTAATTTCTTCCAAATAAGA
1 AAATCGAGATGAATTATAGAGGCAAGTGAGGTTTCCCAAAAGCTCTTAATTTCTTCCAAATAAGA
125012 CTACAAGTGAGCAGTAATAATGCTTATTTCAAACGTAGAAACGAGATAAAGTAGGGTGAAATAAG
66 CTACAAGTGAGCAGTAATAATGCTTATTTCAAACGTAGAAACGAGATAAAGTAGGGTGAAATAAG
125077 ACTAACCTCTTTTGAATGCTCGGGAAACGATCAAGACATCCTAGTTCCTTTAGAAAAGCTAGTA
131 ACTAACCTCTTTTGAATGCTCGGGAAACGATCAAGACATCCTAGTTCCTTTAGAAAAGCTAGTA
125141 AAATCGAGATGAATTATAGAGGCAAGTGAGGTTTCCCAAAAGCTCTTAATTTCTTCCAAAT-A-A
1 AAATCGAGATGAATTATAGAGGCAAGTGAGGTTTCCCAAAAGCTCTTAATTTCTTCCAAATAAGA
125204 CTACAAGTGAGCAGTAATAATGCTTATTTCAAACGTAGAAACGAGATAAAGTAGGGTGAAATAAG
66 CTACAAGTGAGCAGTAATAATGCTTATTTCAAACGTAGAAACGAGATAAAGTAGGGTGAAATAAG
125269 ACTAACCTCTTTTGAATGCTCGGGAAACGATCAAGACATCCTAGTTCCTTTAGAAAAGCTAGTA
131 ACTAACCTCTTTTGAATGCTCGGGAAACGATCAAGACATCCTAGTTCCTTTAGAAAAGCTAGTA
125333 GTCTCGAATG
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 130 0.68
193 1 0.01
194 61 0.32
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (194 bp):
AAATCGAGATGAATTATAGAGGCAAGTGAGGTTTCCCAAAAGCTCTTAATTTCTTCCAAATAAGA
CTACAAGTGAGCAGTAATAATGCTTATTTCAAACGTAGAAACGAGATAAAGTAGGGTGAAATAAG
ACTAACCTCTTTTGAATGCTCGGGAAACGATCAAGACATCCTAGTTCCTTTAGAAAAGCTAGTA
Found at i:128011 original size:19 final size:18
Alignment explanation
Indices: 127958--128003 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
127948 AATATAACGA
*
127958 TTATTTTAATTTATTTAT
1 TTATTTTAATTTATTTAG
*
127976 TTATTTTGGATTTATTTAG
1 TTATTTT-AATTTATTTAG
127995 TTATTTTAA
1 TTATTTTAA
128004 ATTAATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
TTATTTTAATTTATTTAG
Found at i:128027 original size:31 final size:31
Alignment explanation
Indices: 127986--128050 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
127976 TTATTTTGGA
* *
127986 TTTATTTAGTTATTTTAAATTAATTTGTTTG
1 TTTAATTAGTTATTTCAAATTAATTTGTTTG
* *
128017 TTTAATTAGTTATTTCGAATTTATTTGTTTG
1 TTTAATTAGTTATTTCAAATTAATTTGTTTG
128048 TTT
1 TTT
128051 CTAAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.65
Consensus pattern (31 bp):
TTTAATTAGTTATTTCAAATTAATTTGTTTG
Found at i:130604 original size:19 final size:21
Alignment explanation
Indices: 130571--130609 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
130561 TGGAAATTAA
*
130571 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
130591 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
130610 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:132993 original size:3 final size:3
Alignment explanation
Indices: 132985--133018 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
132975 TATACCCACA
* *
132985 CTC CTC CTC CTT CTC CTT CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
133019 CTTCAAACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
CTC
Found at i:135288 original size:114 final size:112
Alignment explanation
Indices: 135079--135305 Score: 436
Period size: 114 Copynumber: 2.0 Consensus size: 112
135069 CTTCCATTCT
135079 GGAGACTTAAGTGCCTCATGTACACTGATGGAACATCATCAACAACAGTTCCTAGGTAAGTTTGG
1 GGAGACTTAAGTGCCTCATGTACACTGATGGAACATCATCAACAACAGTTCCTAGGTAAGTTTGG
135144 GTTTATACACACCGCATTTACTTCGAGTCATTATTGGGTGGTTATTG
66 GTTTATACACACCGCATTTACTTCGAGTCATTATTGGGTGGTTATTG
135191 GGAGACTTAAGTGCCTCATGTACACTGCATGGAACATCATCAACAACAGTTCCTAGGTAAGTTTT
1 GGAGACTTAAGTGCCTCATGTACACTG-ATGGAACATCATCAACAACAGTTCCTAGGTAAG-TTT
135256 GGGTTTATACACACCGCATTTACTTCGAGTCATTATTGGGTGGTTATTG
64 GGGTTTATACACACCGCATTTACTTCGAGTCATTATTGGGTGGTTATTG
135305 G
1 G
135306 CCCGAGCAAC
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 27 0.24
113 33 0.29
114 53 0.47
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (112 bp):
GGAGACTTAAGTGCCTCATGTACACTGATGGAACATCATCAACAACAGTTCCTAGGTAAGTTTGG
GTTTATACACACCGCATTTACTTCGAGTCATTATTGGGTGGTTATTG
Found at i:139418 original size:23 final size:23
Alignment explanation
Indices: 139372--139419 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
139362 AAATAGATCA
* *
139372 ATATAAGCGTTATCTATTACATT
1 ATATAAGCGTTACCTAATACATT
*
139395 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGTTACCTAATACATT
139418 AT
1 AT
139420 TGTACTTGAT
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:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (23 bp):
ATATAAGCGTTACCTAATACATT
Found at i:140101 original size:61 final size:62
Alignment explanation
Indices: 140022--140141 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 62
140012 TCAGCAAGGC
* *
140022 TTAAAGTAAAAATAAGTACTTTAATTATGTT-TTTTT-TGCTTTAGGTATTTGAACTATAGT
1 TTAAAGTAAAAATAAGTACCTAAATTATGTTCTTTTTATGCTTTAGGTATTTGAACTATAGT
*
140082 TTAAAGTAAAAAATAAGTACCTAAATTTTGTTCTTTTTATGCTTTAGGTATTTGAACTAT
1 TTAAAGT-AAAAATAAGTACCTAAATTATGTTCTTTTTATGCTTTAGGTATTTGAACTAT
140142 TGCTTAGTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
60 7 0.13
61 21 0.39
62 5 0.09
63 21 0.39
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (62 bp):
TTAAAGTAAAAATAAGTACCTAAATTATGTTCTTTTTATGCTTTAGGTATTTGAACTATAGT
Found at i:141859 original size:156 final size:158
Alignment explanation
Indices: 141575--141890 Score: 609
Period size: 156 Copynumber: 2.0 Consensus size: 158
141565 TTATGAAGAA
141575 CAACCCACCAGTCTCGATTCACAGGGGGAGAAGACCAGATCTAAACGTTCAGCTGCGATACCTGC
1 CAACCCACCAGTCTCGATTCACAGGGGGAGAAGACCAGATCTAAACGTTCAGCTGCGATACCTGC
141640 AACTTAACTCCCGAGCTAGCATCTTTCATAAATCTCGAGGCATATCATGTGGTGAAAATTGGC-T
66 AACTTAACTCCCGAGCTAGCATCTTTCATAAATCTCGAGGCATATCATGTGGTGAAAATTGGCTT
141704 TT-TCTGACAAATTACAGATTTGGGATG
131 TTATCTGACAAATTACAGATTTGGGATG
141731 CAACCCACCAGTCTCGATTCACAGGGGGAGAAGACCAGATCTAAACGTTCAGCTGCGATACCTGC
1 CAACCCACCAGTCTCGATTCACAGGGGGAGAAGACCAGATCTAAACGTTCAGCTGCGATACCTGC
141796 AACTTAACTCCCGAGCTAGCATCTTTCATAAATCTCGAGGCATATCATGTGGTGAAAATTGGCTT
66 AACTTAACTCCCGAGCTAGCATCTTTCATAAATCTCGAGGCATATCATGTGGTGAAAATTGGCTT
141861 TTAATCTGACAAATTACAGATTTGGGATG
131 TT-ATCTGACAAATTACAGATTTGGGATG
141890 C
1 C
141891 CTGTATATAC
Statistics
Matches: 157, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
156 128 0.82
157 3 0.02
159 26 0.17
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (158 bp):
CAACCCACCAGTCTCGATTCACAGGGGGAGAAGACCAGATCTAAACGTTCAGCTGCGATACCTGC
AACTTAACTCCCGAGCTAGCATCTTTCATAAATCTCGAGGCATATCATGTGGTGAAAATTGGCTT
TTATCTGACAAATTACAGATTTGGGATG
Found at i:151025 original size:26 final size:26
Alignment explanation
Indices: 150996--151063 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
150986 AGCAGGGATA
150996 AGCTGAGATAATATACGAAGCTGGCT
1 AGCTGAGATAATATACGAAGCTGGCT
*
151022 AGCTGAGATAATATACGAAGCTGTCT
1 AGCTGAGATAATATACGAAGCTGGCT
* *
151048 AGTTGAAATATATATA
1 AGCTGAGATA-ATATA
151064 TATGATCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 33 0.87
27 5 0.13
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (26 bp):
AGCTGAGATAATATACGAAGCTGGCT
Found at i:152890 original size:28 final size:27
Alignment explanation
Indices: 152839--152892 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
152829 ACTATATATG
152839 ATATATGTGTATTACATATAAATAAAT
1 ATATATGTGTATTACATATAAATAAAT
* *
152866 ATATATGTATTATTACATATGAATAAA
1 ATATATGT-GTATTACATATAAATAAA
152893 ACTATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATATGTGTATTACATATAAATAAAT
Found at i:153902 original size:2 final size:2
Alignment explanation
Indices: 153895--153926 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
153885 ATCAATTTTA
153895 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
153927 GATGAATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154064 original size:16 final size:16
Alignment explanation
Indices: 154040--154081 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
154030 TAATATAAGT
154040 ATATATATACTTATAC
1 ATATATATACTTATAC
* *
154056 ATATGTATAATTATAC
1 ATATATATACTTATAC
*
154072 CTATATATAC
1 ATATATATAC
154082 AATTACACAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATATACTTATAC
Found at i:154113 original size:4 final size:4
Alignment explanation
Indices: 154106--154300 Score: 134
Period size: 4 Copynumber: 48.5 Consensus size: 4
154096 ACACACACAC
154106 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA-
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* ** * * *
154153 AGTAT TTAT ATAT AGGT ATGT ATAT AAAT ATAT AAAT ATAT ATA- AGTAT
1 A-TAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A-TAT
* * * *
154202 ATGT ATAT ATA- AGTAT ATAC ATA- AGTAT ATAT A-AGT ATAT ATGT TTGAT
1 ATAT ATAT ATAT A-TAT ATAT ATAT A-TAT ATAT ATA-T ATAT ATAT AT-AT
* * ** *
154251 GTAT ACA- AGTAT ATGC ATA- AGTAT GTAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT A-TAT ATAT ATAT A-TAT ATAT ATAT ATAT ATAT ATAT ATAT
154299 AT
1 AT
154301 CTTTAAACAT
Statistics
Matches: 151, Mismatches: 25, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
3 7 0.05
4 137 0.91
5 7 0.05
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:154119 original size:10 final size:10
Alignment explanation
Indices: 154106--154300 Score: 134
Period size: 10 Copynumber: 19.4 Consensus size: 10
154096 ACACACACAC
154106 ATATATATAT
1 ATATATATAT
154116 ATATATATAT
1 ATATATATAT
154126 ATATATATAT
1 ATATATATAT
154136 ATATATATAT
1 ATATATATAT
154146 ATATATA-AGT
1 ATATATATA-T
*
154156 ATTTATATAT
1 ATATATATAT
** *
154166 AGGTATGTAT
1 ATATATATAT
*
154176 ATAAATATAT
1 ATATATATAT
*
154186 AAATATATAT
1 ATATATATAT
*
154196 A-AGTATATGT
1 ATA-TATATAT
154206 ATATATA-AGT
1 ATATATATA-T
*
154216 ATATACATA-
1 ATATATATAT
154225 AGTATATATA-
1 A-TATATATAT
*
154235 AGTATATATGT
1 A-TATATATAT
* * *
154246 TTGATGTATAC
1 AT-ATATATAT
**
154257 A-AGTATATGC
1 ATA-TATATAT
*
154267 ATA-AGTATGT
1 ATATA-TATAT
154277 ATATATATAT
1 ATATATATAT
154287 ATATATATAT
1 ATATATATAT
154297 ATAT
1 ATAT
154301 CTTTAAACAT
Statistics
Matches: 148, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
9 5 0.03
10 133 0.90
11 10 0.07
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:154728 original size:2 final size:2
Alignment explanation
Indices: 154723--154751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
154713 ACTCATATGA
154723 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 A
154752 AAAAAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:155000 original size:14 final size:13
Alignment explanation
Indices: 154974--155012 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
154964 TTAATTTATT
154974 GATTATAATTAA-
1 GATTATAATTAAG
154986 GATTTATAATATAAG
1 GA-TTATAAT-TAAG
155001 GATTATAATTAA
1 GATTATAATTAA
155013 TATAGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 10 0.42
15 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (13 bp):
GATTATAATTAAG
Found at i:157476 original size:30 final size:30
Alignment explanation
Indices: 157442--157499 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
157432 TTTCTTCCCC
* *
157442 TAAAATTTTATAAGTTTAAGTTCACCCCAT
1 TAAAATTTTACAAGTTTAACTTCACCCCAT
*
157472 TAAAATTTTACAAGTTTTACTTCACCCC
1 TAAAATTTTACAAGTTTAACTTCACCCC
157500 TAACTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAAATTTTACAAGTTTAACTTCACCCCAT
Found at i:160281 original size:19 final size:19
Alignment explanation
Indices: 160257--160303 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
160247 CATGAAAGTT
160257 ATTGATCCAGAATGTATTA
1 ATTGATCCAGAATGTATTA
160276 ATTGATCCAGAATGTATTA
1 ATTGATCCAGAATGTATTA
*
160295 GTTGATCCA
1 ATTGATCCA
160304 TGAGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (19 bp):
ATTGATCCAGAATGTATTA
Found at i:174367 original size:19 final size:20
Alignment explanation
Indices: 174325--174375 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
174315 AATTTTACGA
174325 ATTTA-AAATTTAATATATT
1 ATTTATAAATTTAATATATT
* *
174344 TTTTATAAATTTAATTTA-T
1 ATTTATAAATTTAATATATT
*
174363 ATTTATAGATTTA
1 ATTTATAAATTTA
174376 GTTAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTATAAATTTAATATATT
Found at i:174383 original size:19 final size:19
Alignment explanation
Indices: 174325--174383 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
174315 AATTTTACGA
*
174325 ATTTA-AAATTTAATATATT
1 ATTTATAAATTTAAT-TAAT
* *
174344 TTTTATAAATTTAATTTAT
1 ATTTATAAATTTAATTAAT
* *
174363 ATTTATAGATTTAGTTAAT
1 ATTTATAAATTTAATTAAT
174382 AT
1 AT
174384 AAAAAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTTATAAATTTAATTAAT
Found at i:190603 original size:14 final size:14
Alignment explanation
Indices: 190584--190618 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
190574 CACAACGCAG
190584 CGTAACGCCTGCAT
1 CGTAACGCCTGCAT
190598 CGTAACGCCTGCAT
1 CGTAACGCCTGCAT
190612 CGTAACG
1 CGTAACG
190619 TTTTTTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (14 bp):
CGTAACGCCTGCAT
Found at i:191324 original size:22 final size:23
Alignment explanation
Indices: 191292--191334 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
191282 AAGATATAAA
*
191292 ATTTTTATATTTGT-AGTTATGT
1 ATTTTTATATTTCTAAGTTATGT
*
191314 ATTTTTTTATTTCTAAGTTAT
1 ATTTTTATATTTCTAAGTTAT
191335 ATAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (23 bp):
ATTTTTATATTTCTAAGTTATGT
Found at i:191522 original size:19 final size:20
Alignment explanation
Indices: 191478--191522 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
191468 ATTTGTTTTT
191478 AATAAATTTTTATTTATGAA
1 AATAAATTTTTATTTATGAA
* *
191498 ATTAAATTTTTATTT-TTAA
1 AATAAATTTTTATTTATGAA
191517 AATAAA
1 AATAAA
191523 ATATTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAAATTTTTATTTATGAA
Found at i:201236 original size:139 final size:142
Alignment explanation
Indices: 200985--201274 Score: 550
Period size: 139 Copynumber: 2.1 Consensus size: 142
200975 AAAAATGGTC
200985 TAATGAAAGCATAATGAAGTTGCCAAGCTTGATCGACAGTAAGGAGAGGTTAATTTCGAACCAAG
1 TAATGAAAGCATAATGAAGTTGCCAAGCTTGATCGACAGTAAGGAGAGGTTAATTTCGAACCAAG
201050 AAGCTCTAATTCAACAGAGTAATCCGTTAGTCTCAATGGGGGATATTGCAAAAG-AAAATCAGAA
66 AAGCTCTAATTCAACAGAGTAATCCGTTAGTCTCAATGGGGGATATTGCAAAAGAAAAATCAGAA
201114 -TATGGTCTTTA
131 CTATGGTCTTTA
201125 -AATGAAAGCATAATGAAGTTGCCAAGCTTGATCGACAGTAAGGAGAGGTTAATTTCGAACCAAG
1 TAATGAAAGCATAATGAAGTTGCCAAGCTTGATCGACAGTAAGGAGAGGTTAATTTCGAACCAAG
201189 AAGCTCTAATTCAACAGAGTAATCCGTTAGTCTCAATGGGGGATATTGCAAAAGAAAAATCAGAA
66 AAGCTCTAATTCAACAGAGTAATCCGTTAGTCTCAATGGGGGATATTGCAAAAGAAAAATCAGAA
201254 CTATGGTCTTTA
131 CTATGGTCTTTA
*
201266 TAAGGAAAG
1 TAATGAAAG
201275 GAAGAGTTAT
Statistics
Matches: 146, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
139 118 0.81
140 10 0.07
141 11 0.08
142 7 0.05
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (142 bp):
TAATGAAAGCATAATGAAGTTGCCAAGCTTGATCGACAGTAAGGAGAGGTTAATTTCGAACCAAG
AAGCTCTAATTCAACAGAGTAATCCGTTAGTCTCAATGGGGGATATTGCAAAAGAAAAATCAGAA
CTATGGTCTTTA
Found at i:212726 original size:22 final size:22
Alignment explanation
Indices: 212694--212766 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
212684 CCTTCTTTTT
212694 TCGCCGGCAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
*
212716 TCGCCGACAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
* *
212738 TCGTCGGCAGTCACAGCTTCCA
1 TCGCCGGCAGTCACAGCCTCCA
212760 TCGCCGG
1 TCGCCGG
212767 GCGCTAACAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.18, C:0.42, G:0.23, T:0.16
Consensus pattern (22 bp):
TCGCCGGCAGTCACAGCCTCCA
Found at i:218491 original size:19 final size:20
Alignment explanation
Indices: 218460--218504 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
218450 GGGGTACATA
218460 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGATCCG
* *
218480 ATGCGG-CTGATGCGGTCTG
1 ATGCGGTCTGATGCGATCCG
218499 ATGCGG
1 ATGCGG
218505 GCCGATGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (20 bp):
ATGCGGTCTGATGCGATCCG
Found at i:218499 original size:10 final size:10
Alignment explanation
Indices: 218460--218504 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
218450 GGGGTACATA
218460 ATGCGGTCTG
1 ATGCGGTCTG
* *
218470 ATGCGATCCG
1 ATGCGGTCTG
218480 ATGCGG-CTG
1 ATGCGGTCTG
218489 ATGCGGTCTG
1 ATGCGGTCTG
218499 ATGCGG
1 ATGCGG
218505 GCCGATGCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (10 bp):
ATGCGGTCTG
Found at i:218926 original size:16 final size:16
Alignment explanation
Indices: 218902--218938 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
218892 GATAAGTTCT
*
218902 TTTTA-TTGCAATAGC
1 TTTTAGTTGCAAAAGC
218917 TTTTAGTTGCAAAAGC
1 TTTTAGTTGCAAAAGC
218933 TTTTAG
1 TTTTAG
218939 CTTTTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (16 bp):
TTTTAGTTGCAAAAGC
Found at i:219037 original size:16 final size:16
Alignment explanation
Indices: 219012--219066 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
219002 TAGATAAGTT
*
219012 CTTTTTGTTGCAATAG
1 CTTTTAGTTGCAATAG
219028 CTTTTAGTTGCAATAG
1 CTTTTAGTTGCAATAG
*
219044 CTTTTAGTTGCAAAAG
1 CTTTTAGTTGCAATAG
219060 CTTTTAG
1 CTTTTAG
219067 CTTTTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (16 bp):
CTTTTAGTTGCAATAG
Found at i:219037 original size:112 final size:112
Alignment explanation
Indices: 218840--219050 Score: 395
Period size: 112 Copynumber: 1.9 Consensus size: 112
218830 ATGTGTACTA
*
218840 AAACAATTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
218905 TATTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
66 TATTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
218952 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
1 AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
* *
219017 TGTTGCAATAGCTTTTAGTTGCAATAGCTTTTAG
66 TATTGCAATAGCTTTTAGTTGCAAAAGCTTTTAG
219051 TTGCAAAAGC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 96 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (112 bp):
AAACAAGTTGTTTTTTGTTGCTTAAATGAATGAACTGTTTTTACGTCCTATAGATAAGTTCTTTT
TATTGCAATAGCTTTTAGTTGCAAAAGCTTTTAGCTTTTAGAAACAT
Found at i:225167 original size:25 final size:25
Alignment explanation
Indices: 225134--225209 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
225124 CAAATCAAAG
*
225134 AGAACGGACATGATCAATTCTAGCA
1 AGAATGGACATGATCAATTCTAGCA
225159 AGAATGGACATGATCAATTCTAGCA
1 AGAATGGACATGATCAATTCTAGCA
225184 AGAATGGACATGATCAATTCTAGCA
1 AGAATGGACATGATCAATTCTAGCA
225209 A
1 A
225210 TCTATTTCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
AGAATGGACATGATCAATTCTAGCA
Found at i:227685 original size:58 final size:59
Alignment explanation
Indices: 227622--227735 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
227612 TAGGGGTTAG
* * * *
227622 TTTAGAAT-GGTTCATAATTTTGGG-ATCGATGTAGAATATTTTAAAGATTATGGATCAA
1 TTTAGAATGGGGTCATAA-CTTGGGAATCGATATAGAATATTTTAAAGATTAGGGATCAA
* * *
227680 TTTAGAATGGGGTCATAACTTGGGAATTGATATATAATGTTTTAAAGATTAGGGAT
1 TTTAGAATGGGGTCATAACTTGGGAATCGATATAGAATATTTTAAAGATTAGGGAT
227736 TAGTATAGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 13 0.28
59 34 0.72
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (59 bp):
TTTAGAATGGGGTCATAACTTGGGAATCGATATAGAATATTTTAAAGATTAGGGATCAA
Found at i:254396 original size:23 final size:23
Alignment explanation
Indices: 254368--254488 Score: 89
Period size: 23 Copynumber: 5.2 Consensus size: 23
254358 ATATTAAACA
254368 ATGTTTGTGAACATTAAATGAAT
1 ATGTTTGTGAACATTAAATGAAT
* * * * *
254391 ATGTTTATTAATAAATAAGTGAAT
1 ATGTTTGTGAA-CATTAAATGAAT
***** *
254415 ATGTCCACAAACATTAAACGAAT
1 ATGTTTGTGAACATTAAATGAAT
** *
254438 ATGTTTGTGAATGTTAAATGAAG
1 ATGTTTGTGAACATTAAATGAAT
* *
254461 ATTTTTGTGAACATTAAATGAAC
1 ATGTTTGTGAACATTAAATGAAT
254484 ATGTT
1 ATGTT
254489 CCCGAATATA
Statistics
Matches: 70, Mismatches: 27, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
23 54 0.77
24 16 0.23
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (23 bp):
ATGTTTGTGAACATTAAATGAAT
Found at i:258166 original size:20 final size:20
Alignment explanation
Indices: 258138--258188 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
258128 TGATAAAATA
258138 AAAAT-TATACGTAAT-TGAT
1 AAAATATATAC-TAATATGAT
*
258157 AAAATATATAACTAGTGATGAT
1 AAAATATAT-ACTAAT-ATGAT
258179 AAAATATATA
1 AAAATATATA
258189 AATATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.19
20 6 0.22
21 3 0.11
22 13 0.48
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAATATATACTAATATGAT
Found at i:259029 original size:18 final size:19
Alignment explanation
Indices: 258994--259030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
258984 CACGGAATGT
258994 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
259014 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
259031 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:261421 original size:30 final size:30
Alignment explanation
Indices: 261385--261444 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
261375 GGAAGTGACA
*
261385 TGTTTTACGATTGGAGTGATGAACTGCGAG
1 TGTTTTACGATTGGAGTGATGAACCGCGAG
*
261415 TGTTTTATGATTGGAGTGATGAACCGCGAG
1 TGTTTTACGATTGGAGTGATGAACCGCGAG
261445 GAAATAACGA
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:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (30 bp):
TGTTTTACGATTGGAGTGATGAACCGCGAG
Found at i:271959 original size:42 final size:42
Alignment explanation
Indices: 271900--271995 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
271890 GGGATTGGGT
* * * *
271900 GCCAAAGCAGGGGCCATTGTCACTG-AACTAGGGGGTGCAGCC
1 GCCAAAACAGGGACCATTGCCACTGAAAC-AGGGGGAGCAGCC
* *
271942 GCCAAAACAGGGACCATTGCCACTGAAACCGGGGGAGCTGCC
1 GCCAAAACAGGGACCATTGCCACTGAAACAGGGGGAGCAGCC
271984 GCCAAAACAGGG
1 GCCAAAACAGGG
271996 GGCGATGCCG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.28, C:0.28, G:0.33, T:0.10
Consensus pattern (42 bp):
GCCAAAACAGGGACCATTGCCACTGAAACAGGGGGAGCAGCC
Found at i:272004 original size:21 final size:21
Alignment explanation
Indices: 271972--272115 Score: 89
Period size: 21 Copynumber: 6.9 Consensus size: 21
271962 CACTGAAACC
* *
271972 GGGGGAGCTGCCGCCAAAACA
1 GGGGGAGATGCCGCCAAAGCA
* * *
271993 GGGGGCGATGCCGACACTA-CA
1 GGGGGAGATGCCGCCA-AAGCA
* * *
272014 GGAGGCA-ATGCCGACACAGCA
1 GG-GGGAGATGCCGCCAAAGCA
* * * * * *
272035 GGGGGTGTTGTCGACAAGGCG
1 GGGGGAGATGCCGCCAAAGCA
272056 GGGGGAG-TGGCCGCCAAAGCA
1 GGGGGAGAT-GCCGCCAAAGCA
272077 GGGGGAG-TGGCCGCCAAAGCA
1 GGGGGAGAT-GCCGCCAAAGCA
*
272098 GGGGGAGTTGCCGCCAAA
1 GGGGGAGATGCCGCCAAA
272116 TCGGAGGGTG
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.04
21 90 0.92
22 4 0.04
ACGTcount: A:0.24, C:0.24, G:0.43, T:0.08
Consensus pattern (21 bp):
GGGGGAGATGCCGCCAAAGCA
Found at i:272077 original size:42 final size:41
Alignment explanation
Indices: 272031--272171 Score: 131
Period size: 42 Copynumber: 3.4 Consensus size: 41
272021 ATGCCGACAC
* *
272031 AGCAGGGGGTGTTGTCGACAAGGCGGGGGGAGTGGCCGCCAA
1 AGCAGGGGGTGTTG-CGACAAAGCAGGGGGAGTGGCCGCCAA
* * * *
272073 AGCAGGGGGAGTGGCCGCCAAAGCAGGGGGAGTTGCCGCCAA
1 AGCAGGGGGTGTTG-CGACAAAGCAGGGGGAGTGGCCGCCAA
* * * * *
272115 ATC-GGAGGGTGTTGCTGATAAAGCCGGGGGAGTGGCCTCCAT
1 AGCAGG-GGGTGTTGC-GACAAAGCAGGGGGAGTGGCCGCCAA
*
272157 AGCAGGGGGCGTTGC
1 AGCAGGGGGTGTTGC
272172 CGCCAAATCG
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
41 3 0.04
42 73 0.94
43 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.46, T:0.13
Consensus pattern (41 bp):
AGCAGGGGGTGTTGCGACAAAGCAGGGGGAGTGGCCGCCAA
Found at i:272099 original size:63 final size:63
Alignment explanation
Indices: 272031--272208 Score: 167
Period size: 63 Copynumber: 2.8 Consensus size: 63
272021 ATGCCGACAC
* * * * *
272031 AGCAGGGGGTGTTGTCGACAAGGCGGGGGGAGTGGCCGCCAAAGCAGGGGGAGTGGCCGCCAA
1 AGCAGGGGGAGTTGCCGACAAAGCGGAGGGAGTGGCCGACAAAGCAGGGGGAGTGGCCGCCAA
* * * * * * * * *
272094 AGCAGGGGGAGTTGCCGCCAAATCGGAGGGTGTTGCTGATAAAGCCGGGGGAGTGGCCTCCAT
1 AGCAGGGGGAGTTGCCGACAAAGCGGAGGGAGTGGCCGACAAAGCAGGGGGAGTGGCCGCCAA
* * * * * * *
272157 AGCAGGGGGCGTTGCCGCCAAATCGGAGGGTGTTGCCGATAAAGCCGGGGGA
1 AGCAGGGGGAGTTGCCGACAAAGCGGAGGGAGTGGCCGACAAAGCAGGGGGA
272209 ACTGCCGGAG
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 99 1.00
ACGTcount: A:0.21, C:0.21, G:0.45, T:0.13
Consensus pattern (63 bp):
AGCAGGGGGAGTTGCCGACAAAGCGGAGGGAGTGGCCGACAAAGCAGGGGGAGTGGCCGCCAA
Found at i:272128 original size:21 final size:20
Alignment explanation
Indices: 272056--272208 Score: 108
Period size: 21 Copynumber: 7.3 Consensus size: 20
272046 CGACAAGGCG
*
272056 GGGGGAGTGGCCGCCAAAGC
1 GGGGGAGTTGCCGCCAAAGC
*
272076 AGGGGGAGTGGCCGCCAAAGC
1 -GGGGGAGTTGCCGCCAAAGC
*
272097 AGGGGGAGTTGCCGCCAAATC
1 -GGGGGAGTTGCCGCCAAAGC
* * **
272118 GGAGGGTGTTGCTGATAAAGCC
1 GG-GGGAGTTGCCGCCAAAG-C
* * *
272140 GGGGGAGTGGCCTCCATAGC
1 GGGGGAGTTGCCGCCAAAGC
* *
272160 AGGGGGCGTTGCCGCCAAATC
1 -GGGGGAGTTGCCGCCAAAGC
* **
272181 GGAGGGTGTTGCCGATAAAGCC
1 GG-GGGAGTTGCCGCCAAAG-C
272203 GGGGGA
1 GGGGGA
272209 ACTGCCGGAG
Statistics
Matches: 103, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
20 5 0.05
21 92 0.89
22 6 0.06
ACGTcount: A:0.21, C:0.22, G:0.44, T:0.13
Consensus pattern (20 bp):
GGGGGAGTTGCCGCCAAAGC
Found at i:274264 original size:39 final size:38
Alignment explanation
Indices: 274184--274259 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
274174 CATTAAACCT
*
274184 TTTTATATTTTAAATTTTGTAAAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAAATTATATAAA
* *
274222 TTTTATGAATTTAAATTTT-TTAAAGAAAA-TATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAAATTATATAAA
274259 T
1 T
274260 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 9 0.26
38 14 0.41
39 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (38 bp):
TTTTATAATTTAAATTTTGTAAAAAAAAATTATATAAA
Found at i:275340 original size:2 final size:2
Alignment explanation
Indices: 275333--275366 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
275323 ACAAATATGC
275333 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
275367 GAGTTAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:280758 original size:130 final size:130
Alignment explanation
Indices: 280594--280844 Score: 376
Period size: 130 Copynumber: 1.9 Consensus size: 130
280584 TTTAGTCCTT
* * *
280594 ATTATTTATATATGCTATCAATATGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAT
1 ATTATTTATATATACAATCAATATAGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAT
* * * * * * * *
280659 CAGGATCTGACATTTGTCAGCACATGGTCCTGACACGTGTCATTAGTGATACATGTTGCAACCTA
66 CAAGATATAACATATGTCAACACATGATCATGACACGTGTCATTAGTGACACATGTTGCAACCTA
*
280724 ATTATTTATATATACAATCAATTTAGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAT
1 ATTATTTATATATACAATCAATATAGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAT
* *
280789 CAAGATATAACATATGTCAACACATGATCATGACATGTGTCATTGGTGACACATGT
66 CAAGATATAACATATGTCAACACATGATCATGACACGTGTCATTAGTGACACATGT
280845 CACCACCTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (130 bp):
ATTATTTATATATACAATCAATATAGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAT
CAAGATATAACATATGTCAACACATGATCATGACACGTGTCATTAGTGACACATGTTGCAACCTA
Found at i:281122 original size:26 final size:26
Alignment explanation
Indices: 281092--281181 Score: 148
Period size: 26 Copynumber: 3.5 Consensus size: 26
281082 AAATAATGAG
281092 AAAATATTATATTTTTTTACAATAAA
1 AAAATATTATATTTTTTTACAATAAA
* *
281118 AAAATATTATA--TTTTTACAGTAAG
1 AAAATATTATATTTTTTTACAATAAA
281142 AAAATATTATATTTTTTTACAATAAA
1 AAAATATTATATTTTTTTACAATAAA
281168 AAAATATTATATTT
1 AAAATATTATATTT
281182 GATAAATTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
24 22 0.38
26 36 0.62
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATATTATATTTTTTTACAATAAA
Found at i:281398 original size:17 final size:19
Alignment explanation
Indices: 281376--281412 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
281366 ATTTCTTATT
281376 AAAAATA-AAAT-ATTCAA
1 AAAAATATAAATGATTCAA
281393 AAAAATATAAATGATTCAA
1 AAAAATATAAATGATTCAA
281412 A
1 A
281413 CATTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAATATAAATGATTCAA
Found at i:284987 original size:43 final size:43
Alignment explanation
Indices: 284926--285012 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
284916 GCCAACCAAA
284926 CGAAGGAATGTGGATTTCATTCCCATGAGAATATCACATTCCC
1 CGAAGGAATGTGGATTTCATTCCCATGAGAATATCACATTCCC
* *
284969 CGAAGGAGTGTGGATTTCATTCTCATGAGAATATCACATTCCC
1 CGAAGGAATGTGGATTTCATTCCCATGAGAATATCACATTCCC
285012 C
1 C
285013 CAACCAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CGAAGGAATGTGGATTTCATTCCCATGAGAATATCACATTCCC
Found at i:285556 original size:19 final size:19
Alignment explanation
Indices: 285514--285558 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
285504 ATGAGATATC
*
285514 TACATCAACAATCATCAGA
1 TACATCAACAATCACCAGA
285533 TACATCAACAATCACCA-A
1 TACATCAACAATCACCAGA
285551 TCACATCA
1 T-ACATCA
285559 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (19 bp):
TACATCAACAATCACCAGA
Found at i:288888 original size:6 final size:6
Alignment explanation
Indices: 288859--288904 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
288849 CTTCCGTTAA
*
288859 TCCTCT T-CTTT TCCCTCTT TCCTCT TCCTCT TCCTCT TCCTCT TCC
1 TCCTCT TCCTCT T-CCTC-T TCCTCT TCCTCT TCCTCT TCCTCT TCC
288905 GTTAACGTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 23 0.66
7 6 0.17
8 2 0.06
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCTCT
Found at i:297935 original size:13 final size:13
Alignment explanation
Indices: 297917--297943 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
297907 CATAGTTGAA
297917 CAGTCTTCATATG
1 CAGTCTTCATATG
297930 CAGTCTTCATATG
1 CAGTCTTCATATG
297943 C
1 C
297944 GCGTCTGTAA
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:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:300811 original size:24 final size:24
Alignment explanation
Indices: 300779--300831 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
300769 CCATAATAGC
*
300779 ATAGAAAAAGTGTGTCAC-AAGAGT
1 ATAGAAAAAATGTGTCACAAAGA-T
300803 ATAGAAAAAATGTGTCACAAAGAT
1 ATAGAAAAAATGTGTCACAAAGAT
300827 ATAGA
1 ATAGA
300832 TTCTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (24 bp):
ATAGAAAAAATGTGTCACAAAGAT
Found at i:300885 original size:23 final size:23
Alignment explanation
Indices: 300859--300903 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
300849 AAAAACTCAA
* *
300859 GAAAAAAAACAAAGACATAATAT
1 GAAAAAAAACAAAAAAATAATAT
*
300882 GAAAAAGAACAAAAAAATAATA
1 GAAAAAAAACAAAAAAATAATA
300904 ATCACCGACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (23 bp):
GAAAAAAAACAAAAAAATAATAT
Found at i:303896 original size:22 final size:21
Alignment explanation
Indices: 303871--303911 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
303861 TATAAAAAAT
303871 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
303893 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
303912 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:303982 original size:26 final size:26
Alignment explanation
Indices: 303938--303990 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
303928 GTCCGATTTT
* *
303938 TTCGACCGATTGAACCAGTGGATCGA
1 TTCGACCGATTAAACCAGTGAATCGA
* *
303964 TTCGACCGGTTAAATCAGTGAATCGA
1 TTCGACCGATTAAACCAGTGAATCGA
303990 T
1 T
303991 AACATGATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (26 bp):
TTCGACCGATTAAACCAGTGAATCGA
Found at i:305303 original size:22 final size:21
Alignment explanation
Indices: 305273--305314 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
305263 ATTATGATCT
* *
305273 AAATTAAATTTATTACTTTTAA
1 AAATAAAATATATTA-TTTTAA
305295 AAATAAAATATATTATTTTA
1 AAATAAAATATATTATTTTA
305315 CAATGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATAAAATATATTATTTTAA
Found at i:305402 original size:21 final size:20
Alignment explanation
Indices: 305376--305415 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
305366 TAGCTGGTAT
305376 GTCTTCTGATTTCTCTTCTTC
1 GTCTTCTGATTT-TCTTCTTC
305397 GTCTTCTGATTTTCTTCTT
1 GTCTTCTGATTTTCTTCTT
305416 GTTTGATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.05, C:0.25, G:0.10, T:0.60
Consensus pattern (20 bp):
GTCTTCTGATTTTCTTCTTC
Found at i:311271 original size:24 final size:26
Alignment explanation
Indices: 311224--311271 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
311214 GATACGTTCA
* *
311224 TTTCCATGCTATTTATTTGTTTATTT
1 TTTCCATGCTATTTAATTGATTATTT
311250 TTTCC-TGCT-TTTAATTGATTAT
1 TTTCCATGCTATTTAATTGATTAT
311272 GTTCATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 4 0.20
26 5 0.25
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTCCATGCTATTTAATTGATTATTT
Found at i:318245 original size:60 final size:61
Alignment explanation
Indices: 318119--318252 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 61
318109 AACATAATAA
* * * * * ** *
318119 ATAGTCGAGTGACCATTTTGTAACTTTTTAATAGTCGAGGGACTCAACAAAGTAACTCCAT
1 ATAGTCGAGAGACCATTCTATAACTTTTTAATAGTCAAGAGACTCAACAAAACAAATCCAT
*
318180 TTAGTCGAGAGACCATTCTATAAC-TTTTAATAGTCAAGAGACTCAACAAAACAATATCC-T
1 ATAGTCGAGAGACCATTCTATAACTTTTTAATAGTCAAGAGACTCAACAAAACAA-ATCCAT
318240 ATAGTCGAGAGAC
1 ATAGTCGAGAGAC
318253 TATCTGTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 39 0.63
61 23 0.37
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (61 bp):
ATAGTCGAGAGACCATTCTATAACTTTTTAATAGTCAAGAGACTCAACAAAACAAATCCAT
Found at i:326709 original size:22 final size:22
Alignment explanation
Indices: 326684--326726 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
326674 ACACTGCAAG
326684 CACGAATTAATTTATCTTAGTA
1 CACGAATTAATTTATCTTAGTA
326706 CACGAATTAATTTATCTTAGT
1 CACGAATTAATTTATCTTAGT
326727 GGTTAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
CACGAATTAATTTATCTTAGTA
Found at i:328772 original size:14 final size:14
Alignment explanation
Indices: 328755--328807 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
328745 ACCTAAACTA
*
328755 TAAATCTTAAATCC
1 TAAAACTTAAATCC
*
328769 TAAACCTTAAA-CAC
1 TAAAACTTAAATC-C
328783 TAAAACTTAAATCC
1 TAAAACTTAAATCC
*
328797 TAAAACCTAAA
1 TAAAACTTAAA
328808 ATCTAACCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 32 0.94
15 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAACTTAAATCC
Found at i:328791 original size:28 final size:27
Alignment explanation
Indices: 328743--328807 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
328733 CCCAAATTCA
*
328743 AAACCTAAACTATAAATCTTAAATCCT
1 AAACCTAAACTATAAAACTTAAATCCT
328770 AAACCTTAAAC-ACTAAAACTTAAATCCT
1 AAACC-TAAACTA-TAAAACTTAAATCCT
328798 AAAACCTAAA
1 -AAACCTAAA
328808 ATCTAACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.18
28 23 0.68
29 5 0.15
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (27 bp):
AAACCTAAACTATAAAACTTAAATCCT
Found at i:336932 original size:2 final size:2
Alignment explanation
Indices: 336925--336953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
336915 AGATAAATTT
336925 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 T
336954 TGAAATATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338517 original size:20 final size:20
Alignment explanation
Indices: 338494--338545 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
338484 AACGCGATCC
338494 CCAGAATCGCAAATCAATTT
1 CCAGAATCGCAAATCAATTT
*
338514 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAATTT
*
338534 CCAAAATCGCAA
1 CCAGAATCGCAA
338546 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAATTT
Found at i:338562 original size:21 final size:20
Alignment explanation
Indices: 338536--338633 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
338526 ATCAGTTTCC
338536 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
338557 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
338576 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
338597 ACATAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
338619 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
338634 ACACATAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 40 0.66
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:338695 original size:20 final size:20
Alignment explanation
Indices: 338601--338969 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
338591 GATTTTACAT
* ** *
338601 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
338621 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
338641 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
338661 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
338681 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
338701 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
338721 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
338741 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
338761 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
338781 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
338801 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
338821 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
338841 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
338861 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
338881 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
338901 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
338921 AATTGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
338941 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
338961 AATCACAAC
1 AATCGCAAC
338970 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:339695 original size:24 final size:24
Alignment explanation
Indices: 339651--339697 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
339641 AAATTTGGTC
*
339651 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
339675 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
339698 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:339889 original size:12 final size:12
Alignment explanation
Indices: 339872--339896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
339862 ATATAATCCT
339872 GAAGAAGAAAAA
1 GAAGAAGAAAAA
339884 GAAGAAGAAAAA
1 GAAGAAGAAAAA
339896 G
1 G
339897 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:342202 original size:19 final size:19
Alignment explanation
Indices: 342180--342486 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
342170 CGGAAAATAC
*
342180 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
342199 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
342213 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
342233 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
342247 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342266 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
342285 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
342299 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
342318 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342337 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
342356 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
342370 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
342389 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342408 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342427 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
342441 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342460 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
342479 AATCGCAA
1 AATCGCAA
342487 CGAGATAATC
Statistics
Matches: 251, Mismatches: 11, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 15 0.06
18 3 0.01
19 154 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:342232 original size:34 final size:33
Alignment explanation
Indices: 342180--342508 Score: 135
Period size: 33 Copynumber: 9.5 Consensus size: 33
342170 CGGAAAATAC
*
342180 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* *
342213 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
*
342247 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * * **
342285 AATCGCAACGAGAGAATCG-CAATGCGAAATA-AA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGAGAA
*
342318 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * *
342356 AATCGCAA--CGACAT---AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
342389 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
342427 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* *
342460 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
342493 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
342509 TATAAACGCA
Statistics
Matches: 245, Mismatches: 25, Indels: 52
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.00
32 8 0.03
33 110 0.45
34 30 0.12
35 15 0.06
36 14 0.06
37 1 0.00
38 57 0.23
39 8 0.03
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:342295 original size:52 final size:52
Alignment explanation
Indices: 342208--342486 Score: 299
Period size: 52 Copynumber: 5.2 Consensus size: 52
342198 AAATCCCAAC
*
342208 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
342261 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
* *
342313 ATAAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAC
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
*
342368 AT---AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
342422 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
342474 ATGAAAATCGCAA
1 ATGAAAATCGCAA
342487 CGAGATAATC
Statistics
Matches: 210, Mismatches: 6, Indels: 21
0.89 0.03 0.09
Matches are distributed among these distances:
52 158 0.75
53 16 0.08
54 7 0.03
55 10 0.05
56 1 0.00
57 18 0.09
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:342331 original size:71 final size:71
Alignment explanation
Indices: 342247--342486 Score: 435
Period size: 71 Copynumber: 3.4 Consensus size: 71
342237 GCAACGAGAG
*
342247 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
342312 AATAAA
66 AATAAA
* *
342318 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
*
342383 AATTAA
66 AATAAA
342389 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
*
342454 AATGAA
66 AATAAA
342460 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
342487 CGAGATAATC
Statistics
Matches: 163, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 163 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATAAA
Found at i:342524 original size:71 final size:69
Alignment explanation
Indices: 342180--342506 Score: 295
Period size: 71 Copynumber: 4.7 Consensus size: 69
342170 CGGAAAATAC
* *
342180 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAA-ATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAAT-C-GAAGA-G-AAA-CGCAATG
*
342241 CG--A-GAG
61 CGAAATGAA
*
342247 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-AGAGAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAAATCGCAATCGAAGAGAAACGCAATGC
*
342310 GAAATAAA
62 GAAATGAA
* * *
342318 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-ACATAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAAATCGCAATCGAAGAGAAACGCAATGC
*
342381 GAAATTAA
62 GAAATGAA
*
342389 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAA-AGAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAAATCGCAATCGAAGAGAAACGCAATGC
342452 GAAATGAA
62 GAAATGAA
*
342460 AATCGCAATGCGAAATGAAAATCGCAACGA-GATAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAAT-CGAA
342507 ATTATAAACG
Statistics
Matches: 235, Mismatches: 11, Indels: 27
0.86 0.04 0.10
Matches are distributed among these distances:
66 15 0.06
67 28 0.12
68 8 0.03
69 5 0.02
70 2 0.01
71 163 0.69
72 14 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATCGAAGAGAAACGCAATGCGAAA
TGAA
Found at i:342605 original size:19 final size:19
Alignment explanation
Indices: 342515--342597 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
342505 AAATTATAAA
342515 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
342534 CCGCATTGCGA--TTC-TCT
1 -CGCATTGCGATTTTCATTT
342551 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
342568 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
342587 CGCATTGCGAT
1 CGCATTGCGAT
342598 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 5 0.09
17 6 0.11
18 3 0.05
19 26 0.46
20 10 0.18
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:342723 original size:14 final size:14
Alignment explanation
Indices: 342704--342740 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
342694 CATCAATTAC
342704 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
342718 ACAAATCATCTTTT
1 ACAAATCAACTTTT
342732 ACAAATCAA
1 ACAAATCAA
342741 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:344703 original size:19 final size:19
Alignment explanation
Indices: 344663--344797 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
344653 TACTTTACTT
* *
344663 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
344683 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
344702 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
344721 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
344735 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
344754 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
344768 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
344787 TCGCAATGCGA
1 TCGCAACGCGA
344798 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:344738 original size:14 final size:14
Alignment explanation
Indices: 344719--344775 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
344709 GCGAAATGAA
344719 AATCGCAACGACAG
1 AATCGCAACGACAG
*
344733 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
344752 AATCGCAACGAAAG
1 AATCGCAACGACAG
344766 AATCGCAACG
1 AATCGCAACG
344776 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:344742 original size:33 final size:33
Alignment explanation
Indices: 344700--344792 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
344690 GCGAAACCAA
*
344700 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
344733 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
344766 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
344793 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:344789 original size:52 final size:54
Alignment explanation
Indices: 344663--344797 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 54
344653 TACTTTACTT
*
344663 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
*
344721 TCGCAA-CGACA-G--AATCGCAACGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
344768 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
344798 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 39 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:344815 original size:19 final size:19
Alignment explanation
Indices: 344793--344901 Score: 112
Period size: 19 Copynumber: 6.3 Consensus size: 19
344783 AAAATCGCAA
344793 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
344812 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
344826 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
344845 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
344859 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
344878 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
344897 TGCGA
1 TGCGA
344902 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
14 22 0.30
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 44 0.60
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:344835 original size:33 final size:33
Alignment explanation
Indices: 344793--344884 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
344783 AAAATCGCAA
344793 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
344826 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
344859 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
344885 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:345247 original size:93 final size:93
Alignment explanation
Indices: 344945--345692 Score: 1452
Period size: 93 Copynumber: 8.1 Consensus size: 93
344935 TTGAATGGAT
344945 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345010 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345038 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA--G-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345100 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345128 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345193 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345221 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345285 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345313 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345378 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345406 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345471 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345499 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345563 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345591 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
345656 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
345684 AAATTTACT
1 AAATTTACT
345693 AAGCAATCTA
Statistics
Matches: 649, Mismatches: 1, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
90 89 0.14
91 1 0.00
92 185 0.29
93 374 0.58
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:345400 original size:185 final size:186
Alignment explanation
Indices: 344945--345692 Score: 1452
Period size: 185 Copynumber: 4.0 Consensus size: 186
344935 TTGAATGGAT
344945 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345010 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
345075 TACTATTTCACA--G-TAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
345128 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345193 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
345258 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
345313 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345378 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
345443 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
345499 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
345563 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
345628 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
345684 AAATTTACT
1 AAATTTACT
345693 AAGCAATCTA
Statistics
Matches: 560, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
182 9 0.02
183 132 0.24
184 1 0.00
185 326 0.58
186 92 0.16
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:345469 original size:278 final size:278
Alignment explanation
Indices: 344945--345692 Score: 1457
Period size: 278 Copynumber: 2.7 Consensus size: 278
344935 TTGAATGGAT
344945 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
345010 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
345075 TACTATTTCACA--G-TAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
345137 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
195 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
345202 GAATTGGCAGCAACCGAAC
260 GAATTGGCAGCAACCGAAC
345221 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
345286 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
345351 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
345416 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
345481 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
345499 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
345564 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
345629 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
345693 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
275 102 0.22
276 39 0.08
277 1 0.00
278 326 0.70
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:347418 original size:14 final size:14
Alignment explanation
Indices: 347399--347469 Score: 88
Period size: 14 Copynumber: 4.7 Consensus size: 14
347389 TTGAAATGAA
347399 AATCGCAACGAGAG
1 AATCGCAACGAGAG
347413 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
347427 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
347446 AATCGCAACGAGAG
1 AATCGCAACGAGAG
347460 AATCGCAACG
1 AATCGCAACG
347470 CGAAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 34 0.68
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:347455 original size:33 final size:33
Alignment explanation
Indices: 347413--347485 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
347403 GCAACGAGAG
**
347413 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
347446 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
347479 AATCGCA
1 AATCGCA
347486 GCGATTCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.22, T:0.08
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAACCAA
Found at i:347666 original size:33 final size:33
Alignment explanation
Indices: 347624--347694 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
347614 AATACTAACT
*
347624 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
347657 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
347690 TGAAA
1 TGAAA
347695 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:347928 original size:22 final size:22
Alignment explanation
Indices: 347876--347930 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
347866 TGGTTGTGAG
**
347876 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
347898 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
347920 GGATTTCTTCG
1 GGATTTCTTCG
347931 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Done.