Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2158558 original size:14 final size:14
Alignment explanation
Indices: 2158539--2158595 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2158529 TTTCATTTCG
2158539 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2158553 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
2158570 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
2158586 CGTTGCGATT
1 CGTTGCGATT
2158596 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2158646 original size:37 final size:38
Alignment explanation
Indices: 2158517--2158688 Score: 177
Period size: 33 Copynumber: 4.8 Consensus size: 38
2158507 GAAACCAAAA
2158517 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
2158552 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
**
2158585 T--CGTTGCGATTTTCATTTCGCGTTGCGATT-TGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
2158620 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
2158658 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
2158689 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 53 0.46
34 2 0.02
35 3 0.03
37 26 0.22
38 18 0.16
39 11 0.09
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:2160623 original size:14 final size:14
Alignment explanation
Indices: 2160604--2160639 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2160594 ATTGTTTAAT
2160604 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2160618 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2160632 TGATTTGT
1 TGATTTGT
2160640 GTAATTGATG
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:2160763 original size:20 final size:18
Alignment explanation
Indices: 2160746--2160862 Score: 115
Period size: 19 Copynumber: 6.7 Consensus size: 18
2160736 AAAAATGACT
2160746 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
2160766 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
2160785 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
2160799 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
2160817 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
*
2160837 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
2160851 ATCGCAATGCGA
1 ATCGCAATGCGA
2160863 TTTTCATTTC
Statistics
Matches: 86, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
14 16 0.19
16 9 0.10
17 8 0.09
18 12 0.14
19 22 0.26
20 19 0.22
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:2160832 original size:52 final size:52
Alignment explanation
Indices: 2160746--2160862 Score: 209
Period size: 52 Copynumber: 2.2 Consensus size: 52
2160736 AAAAATGACT
2160746 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2160799 ATCGCAATGCGAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
2160851 ATCGCAATGCGA
1 ATCGCAATGCGA
2160863 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 12 0.19
52 41 0.65
53 10 0.16
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2160880 original size:19 final size:19
Alignment explanation
Indices: 2160852--2161112 Score: 269
Period size: 19 Copynumber: 14.7 Consensus size: 19
2160842 AACGAGAGAA
*
2160852 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2160871 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2160890 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2160907 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
2160923 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2160942 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
*
2160959 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
2160976 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2160995 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
*
2161012 TCG--TTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
2161029 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2161048 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2161067 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
2161084 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2161100 TCGCATTGCGATT
1 TCGCATTGCGATT
2161113 CTCTCGTTGC
Statistics
Matches: 204, Mismatches: 13, Indels: 50
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.02
14 22 0.11
15 4 0.02
16 16 0.08
17 16 0.08
18 15 0.07
19 86 0.42
20 40 0.20
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2160994 original size:105 final size:103
Alignment explanation
Indices: 2160858--2161126 Score: 380
Period size: 105 Copynumber: 2.6 Consensus size: 103
2160848 AGAATCGCAA
*
2160858 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTCATT
1 TGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTCATT
2160923 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GT
66 TCGCATTGCGATTTTCATTT-CGCATTGCGATT-T-TCAGT
*
2160963 TGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTACGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGA-TTTCAT
*
2161028 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
65 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
* *** *** *
2161067 TCCGCATTGCGATTTCATGTTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCG-ATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
2161127 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
103 4 0.03
104 28 0.19
105 90 0.60
106 27 0.18
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (103 bp):
TGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTCATT
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
Found at i:2161000 original size:53 final size:53
Alignment explanation
Indices: 2160858--2161126 Score: 388
Period size: 52 Copynumber: 5.1 Consensus size: 53
2160848 AGAATCGCAA
2160858 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
2160911 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
2160963 TGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
2161016 TACGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATT-T-TCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GT
* * *** *
2161067 TCCGCA-TTGCGATTTCATGTTGGGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
2161120 TGCGATT
1 TGCGATT
2161127 GTAATTTCCG
Statistics
Matches: 197, Mismatches: 12, Indels: 14
0.88 0.05 0.06
Matches are distributed among these distances:
50 2 0.01
51 8 0.04
52 97 0.49
53 88 0.45
54 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:2161038 original size:72 final size:71
Alignment explanation
Indices: 2160879--2161112 Score: 254
Period size: 72 Copynumber: 3.3 Consensus size: 71
2160869 TTTCGCATTG
* *
2160879 CGATTTTCATTTCCGCATTGCGA--TT-CTCTCG--TTGCGA-TTTCATTT-CGCATTGCGATTT
1 CGATTTTCATTT-CGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TT
*
2160937 TCAT-TTC
64 TCATGTTA
* * *
2160944 CGCA-TTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 CG-ATTTTC-ATT-TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
2161008 TCTC-TCGTTA
63 T-TCAT-GTTA
*
2161018 CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTC
1 CGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTC
*
2161083 ATGTTG
66 ATGTTA
*
2161089 GGATTTTCATTTCGCATTGCGATT
1 CGATTTTCATTTCGCATTGCGATT
2161113 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 12, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
65 5 0.04
66 12 0.08
67 1 0.01
68 2 0.01
69 4 0.03
71 34 0.24
72 61 0.43
73 16 0.11
74 7 0.05
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (71 bp):
CGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTC
ATGTTA
Found at i:2163404 original size:12 final size:12
Alignment explanation
Indices: 2163387--2163411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2163377 TCTTCGGGGA
2163387 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2163399 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2163411 C
1 C
2163412 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2163617 original size:24 final size:24
Alignment explanation
Indices: 2163583--2163629 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2163573 CTGAAACATC
2163583 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2163607 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2163630 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2164347 original size:20 final size:20
Alignment explanation
Indices: 2164319--2164547 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
2164309 AAATTTCAGT
* * *
2164319 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2164339 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2164359 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2164379 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2164399 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2164419 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2164439 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2164459 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
2164479 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2164499 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2164519 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2164539 GTTGCGATT
1 GTTGCGATT
2164548 CTGGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2171125 original size:29 final size:29
Alignment explanation
Indices: 2171092--2171171 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
2171082 AAATTAAGTT
*
2171092 GATGTCATTGCTTACATCGATTAGGAGAA
1 GATGTCATTGCTTACATCAATTAGGAGAA
2171121 GATGTCATTGCTTACATCAATTAGGAGAA
1 GATGTCATTGCTTACATCAATTAGGAGAA
*
2171150 GATATCATTGCTTACATCAATT
1 GATGTCATTGCTTACATCAATT
2171172 TAGTTAGGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGGAGAA
Found at i:2174436 original size:18 final size:18
Alignment explanation
Indices: 2174413--2174540 Score: 157
Period size: 18 Copynumber: 6.9 Consensus size: 18
2174403 AGGGATTATC
2174413 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2174431 AGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACAT
2174449 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2174467 AGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACAT
* * *
2174485 AGTGGTCATTTGGGATATATT
1 AGTGGTCCTTCGGG--ACA-T
2174506 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2174524 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGGGACA
2174541 AATATTCAGT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
18 76 0.81
19 2 0.02
20 3 0.03
21 13 0.14
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2174460 original size:36 final size:36
Alignment explanation
Indices: 2174413--2174540 Score: 175
Period size: 36 Copynumber: 3.5 Consensus size: 36
2174403 AGGGATTATC
2174413 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
2174449 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
* * * * *
2174485 AGTGGTCATTTGGGATATATTAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGG--ACA-TAGTGGTCCTTCAGGATAT
*
2174524 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGGGACA
2174541 AATATTCAGT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
36 48 0.60
37 2 0.03
38 2 0.03
39 28 0.35
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (36 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
Found at i:2174531 original size:57 final size:54
Alignment explanation
Indices: 2174413--2174534 Score: 172
Period size: 57 Copynumber: 2.2 Consensus size: 54
2174403 AGGGATTATC
* *
2174413 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATATAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCATTCAGGATATAGTGGTCCTTCGGGACAT
* **
2174467 AGTGGTCCTTCAGGATATAGTGGTCATTTGGGATATATTAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCATTCAGG--ATA-TAGTGGTCCTTCGGGACAT
2174524 AGTGGTCCTTC
1 AGTGGTCCTTC
2174535 GAGACAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
54 27 0.45
56 3 0.05
57 30 0.50
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (54 bp):
AGTGGTCCTTCAGGACATAGTGGTCATTCAGGATATAGTGGTCCTTCGGGACAT
Found at i:2181964 original size:15 final size:15
Alignment explanation
Indices: 2181944--2181974 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2181934 TGAATTAAGT
2181944 GAATAACTTAGATAA
1 GAATAACTTAGATAA
*
2181959 GAATAACTTGGATAA
1 GAATAACTTAGATAA
2181974 G
1 G
2181975 TCTGGAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (15 bp):
GAATAACTTAGATAA
Found at i:2182152 original size:21 final size:20
Alignment explanation
Indices: 2182085--2182223 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
2182075 AAATGACCAA
***
2182085 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2182105 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2182125 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2182146 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2182167 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2182187 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2182208 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2182224 ACACATAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 43 0.48
21 46 0.51
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2182252 original size:20 final size:20
Alignment explanation
Indices: 2182191--2182419 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
2182181 GATTTTCAAG
* ** *
2182191 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2182211 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2182231 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
2182251 AACCGCAACGTGTATCCATA
1 AATCGCAACGCGTATCCGTA
*
2182271 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2182291 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2182311 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2182331 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2182351 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2182371 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2182391 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2182411 AATCACAAC
1 AATCGCAAC
2182420 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 169 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2183151 original size:24 final size:24
Alignment explanation
Indices: 2183112--2183158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2183102 AAATTTGGTC
2183112 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2183136 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2183159 CATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2183350 original size:12 final size:12
Alignment explanation
Indices: 2183333--2183357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2183323 ATATAATCCT
2183333 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2183345 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2183357 G
1 G
2183358 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:2185707 original size:19 final size:19
Alignment explanation
Indices: 2185686--2185915 Score: 292
Period size: 19 Copynumber: 12.7 Consensus size: 19
2185676 TCCCAACAAG
2185686 AAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2185706 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2185725 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2185744 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
2185758 GAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2185778 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2185797 AAATCGCAA--CG--AT-A
1 AAATCGCAATGCGAAATGA
*
2185811 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2185830 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
2185849 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
2185863 GAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
2185883 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
*
2185902 AAATCGCATTGCGA
1 AAATCGCAATGCGA
2185916 TTCTCTCGTT
Statistics
Matches: 186, Mismatches: 7, Indels: 35
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.16
15 4 0.02
16 4 0.02
17 8 0.04
18 2 0.01
19 101 0.54
20 38 0.20
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:2185741 original size:52 final size:51
Alignment explanation
Indices: 2185641--2185909 Score: 371
Period size: 52 Copynumber: 5.1 Consensus size: 51
2185631 CGGAAATTAC
* *** *
2185641 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAATCG-C
1 AATCGCAAC-AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAA
* *
2185693 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2185745 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAC-AGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
2185798 AATCGCAACGATAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAC-AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2185850 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAC-AGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2185903 AATCGCA
1 AATCGCA
2185910 TTGCGATTCT
Statistics
Matches: 199, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
51 6 0.03
52 103 0.52
53 90 0.45
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (51 bp):
AATCGCAACAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2185929 original size:105 final size:104
Alignment explanation
Indices: 2185641--2185909 Score: 418
Period size: 105 Copynumber: 2.6 Consensus size: 104
2185631 CGGAAATTAC
* *** * * *
2185641 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAACAAGAAATCG-CAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAAT-GAAAAT-C-GCAAC
2185704 GA-AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 GATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2185745 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAT
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAT
2185810 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 A-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2185850 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
2185910 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
103 5 0.03
104 28 0.18
105 121 0.79
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (104 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAT
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2185949 original size:53 final size:52
Alignment explanation
Indices: 2185886--2186001 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
2185876 GAAATGAAAA
*
2185886 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
2185938 TCCGCATTGCGATTTTTATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2185991 TCGCATTGCGA
1 TCGCATTGCGA
2186002 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2185964 original size:19 final size:19
Alignment explanation
Indices: 2185924--2186011 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
2185914 GATTCTCTCG
2185924 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
2185944 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2185963 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2185977 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2185996 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2186012 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 6 0.10
19 26 0.44
20 14 0.24
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2188008 original size:19 final size:19
Alignment explanation
Indices: 2187966--2188086 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
2187956 TAGTTTACTT
* *
2187966 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
2187986 TCGCAATGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
2188005 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2188024 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
2188043 TTGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
2188057 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2188076 TCGCAATGCGA
1 TCGCAACGCGA
2188087 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
14 7 0.09
16 5 0.06
17 5 0.06
19 51 0.65
20 11 0.14
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2188035 original size:38 final size:33
Alignment explanation
Indices: 2187982--2188081 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 33
2187972 CACGAAACTT
* *
2187982 AAAATCGCAATGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G--A-C
*
2188020 AAAATCGCAACGCGAAATGAAAATTGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
*
2188053 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
2188082 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
33 28 0.49
34 1 0.02
36 1 0.02
38 27 0.47
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:2188117 original size:14 final size:14
Alignment explanation
Indices: 2188098--2188156 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2188088 TTTGGTTTCG
2188098 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2188112 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2188129 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2188145 CGTTGCGATTTT
1 CGTTGCGATTTT
2188157 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2188124 original size:33 final size:33
Alignment explanation
Indices: 2188082--2188205 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2188072 AAAATCGCAA
*
2188082 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2188115 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2188148 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2188181 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2188206 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2188136 original size:19 final size:18
Alignment explanation
Indices: 2188082--2188173 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
2188072 AAAATCGCAA
2188082 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2188101 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
2188115 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2188134 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2188148 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2188167 TGCGATT
1 TGCGATT
2188174 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:2188183 original size:14 final size:14
Alignment explanation
Indices: 2188131--2188187 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2188121 TTTGGTTTCG
*
2188131 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2188145 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2188164 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2188178 CGTTGCGATT
1 CGTTGCGATT
2188188 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2188579 original size:185 final size:185
Alignment explanation
Indices: 2188253--2188626 Score: 707
Period size: 185 Copynumber: 2.0 Consensus size: 185
2188243 ATGGATTGCA
*
2188253 TTAC-TTCAACCAATAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTT
2188317 AGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA
66 AGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA
2188382 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
2188437 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
2188502 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACT
65 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
2188566 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
2188622 TTACT
1 TTACT
2188627 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
184 4 0.02
185 96 0.52
186 86 0.46
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA
TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2188622 original size:92 final size:93
Alignment explanation
Indices: 2188253--2188626 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
2188243 ATGGATTGCA
*
2188253 TTAC-TTCAACCAATAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2188316 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2188344 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2188409 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2188437 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2188502 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2188530 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2188594 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2188622 TTACT
1 TTACT
2188627 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
91 4 0.01
92 96 0.34
93 179 0.64
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2190297 original size:20 final size:20
Alignment explanation
Indices: 2190266--2190362 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
2190256 TTTTGGTTGA
2190266 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2190286 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2190306 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
2190325 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
2190340 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2190360 AAT
1 AAT
2190363 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2190318 original size:21 final size:21
Alignment explanation
Indices: 2190264--2190328 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2190254 TCTTTTGGTT
2190264 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2190285 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2190305 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2190326 GAA
1 GAA
2190329 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2190332 original size:14 final size:14
Alignment explanation
Indices: 2190313--2190369 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2190303 GAGAAATGAA
2190313 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2190327 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2190346 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2190360 AATCGCAACG
1 AATCGCAACG
2190370 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2190345 original size:33 final size:33
Alignment explanation
Indices: 2190264--2190386 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2190254 TCTTTTGGTT
*
2190264 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
2190305 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2190338 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2190371 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2190387 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2190460 original size:21 final size:20
Alignment explanation
Indices: 2190414--2190506 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
2190404 GTTGCGATTC
2190414 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
2190433 TCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCA-TTT
**
2190454 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
2190475 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
2190495 ATCTCGTTGCGA
1 -TCTCGTTGCGA
2190507 CTCTTCTGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 16 0.26
20 9 0.15
21 31 0.50
22 6 0.10
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:2190482 original size:42 final size:40
Alignment explanation
Indices: 2190414--2190506 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 40
2190404 GTTGCGATTC
** * *
2190414 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
2190454 TCTCGTTGCAGATAGTCATTTTCACGTTGCGATTTTCATTTA
1 TCTCGTTGC-GATAGTCA-TTTCACGTTGCGATTTTCATTTA
2190496 TCTCGTTGCGA
1 TCTCGTTGCGA
2190507 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 9 0.19
41 8 0.17
42 30 0.64
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
Found at i:2190628 original size:33 final size:33
Alignment explanation
Indices: 2190586--2190656 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2190576 AATACTAACT
2190586 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
2190619 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
2190652 TGAAA
1 TGAAA
2190657 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:2191061 original size:20 final size:20
Alignment explanation
Indices: 2191035--2191107 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
2191025 ACTTTAAAAA
2191035 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* *
2191055 ACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACG-GAT
* **
2191075 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGAT
2191095 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2191108 CTGGAAAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGGAT
Found at i:2199961 original size:2 final size:2
Alignment explanation
Indices: 2199954--2199978 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2199944 ATCAGGCATC
2199954 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2199979 TCTACCTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2211462 original size:32 final size:31
Alignment explanation
Indices: 2211381--2211462 Score: 83
Period size: 37 Copynumber: 2.4 Consensus size: 31
2211371 ATAATATTAC
2211381 AAATTATAAAATATTTATATATTTTCTTTAAA
1 AAATTA-AAAATATTTATATATTTTCTTTAAA
* *
2211413 AAATTAAATTCATAATATTTATATAATTTTTTTTATA
1 AAATT-AA---A-AATATTTATAT-ATTTTCTTTAAA
2211450 AAATTAAAAATAT
1 AAATTAAAAATAT
2211463 AAAAAAGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
35 1 0.02
36 13 0.31
37 15 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATTAAAAATATTTATATATTTTCTTTAAA
Found at i:2216396 original size:36 final size:36
Alignment explanation
Indices: 2216325--2216396 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
2216315 TTATATTTTA
*
2216325 AATTTTGTAAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAATTATATAAATATTATCAATTT
*
2216361 AATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
2216397 GTAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (36 bp):
AATTTTGTAAAAAAATTATATAAATATTATCAATTT
Found at i:2216578 original size:20 final size:20
Alignment explanation
Indices: 2216542--2216579 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2216532 ATCCTATTCC
**
2216542 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2216562 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2216580 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2219933 original size:68 final size:68
Alignment explanation
Indices: 2219858--2219995 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 68
2219848 AACTCTCAAT
* *
2219858 CACCTAATATTGAACACTTATATCTTGACATTCATAATACTCGAACTCGAAATTTTAAGAAATAA
1 CACCTAATATTAAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGAAATAA
2219923 CAA
66 CAA
* * * *
2219926 CACCTAATATTAAACATTTATATCTTAACATTCATGATACTCGAACTCGAAATTTTAAGGAATGA
1 CACCTAATATTAAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGAAATAA
2219991 CAA
66 CAA
2219994 CA
1 CA
2219996 ACCCCTCTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (68 bp):
CACCTAATATTAAACACTTATATCTTAACATTCATAATACTCGAACTCGAAATTTTAAGAAATAA
CAA
Found at i:2220957 original size:25 final size:24
Alignment explanation
Indices: 2220929--2220986 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
2220919 TTATTTTTTC
*
2220929 AAAAAAATTAAAAATATTACTAAAT
1 AAAAAAAATAAAAAT-TTACTAAAT
*
2220954 AAAATAAAATCAAAATTTACTAAAT
1 AAAA-AAAATAAAAATTTACTAAAT
2220979 AAAAAAAA
1 AAAAAAAA
2220987 CTCTAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 4 0.13
25 17 0.57
26 9 0.30
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAAAAAATAAAAATTTACTAAAT
Found at i:2220994 original size:26 final size:26
Alignment explanation
Indices: 2220939--2220995 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
2220929 AAAAAAATTA
2220939 AAAATATTACTAAATAAAATAAAATC
1 AAAATATTACTAAATAAAATAAAATC
2220965 AAAAT-TTACTAAATAAAA-AAAACTC
1 AAAATATTACTAAATAAAATAAAA-TC
2220990 TAAAAT
1 -AAAAT
2220996 CTTTTATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 10 0.34
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAATATTACTAAATAAAATAAAATC
Found at i:2221195 original size:17 final size:16
Alignment explanation
Indices: 2221169--2221202 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2221159 TATATTATGC
2221169 TTTTAATTTTTTGAAT
1 TTTTAATTTTTTGAAT
*
2221185 TTTTGAATTTTTTTAAT
1 TTTT-AATTTTTTGAAT
2221202 T
1 T
2221203 AAACCTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTTGAAT
Found at i:2221519 original size:29 final size:29
Alignment explanation
Indices: 2221487--2221542 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2221477 TAGGGGGACG
*
2221487 AACTTGAATTTATAAAATT-TCAGGGGGTA
1 AACTTGAACTTATAAAATTCT-AGGGGGTA
2221516 AACTTGAACTTATAAAATTCTAGGGGG
1 AACTTGAACTTATAAAATTCTAGGGGG
2221543 AGCTAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (29 bp):
AACTTGAACTTATAAAATTCTAGGGGGTA
Found at i:2223391 original size:14 final size:14
Alignment explanation
Indices: 2223372--2223398 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2223362 GGAGACCCTT
2223372 AAAATTTCAATTTG
1 AAAATTTCAATTTG
2223386 AAAATTTCAATTT
1 AAAATTTCAATTT
2223399 TAGACCCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAATTTCAATTTG
Found at i:2246269 original size:35 final size:35
Alignment explanation
Indices: 2246223--2246295 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
2246213 TGAGTTTAAT
* *
2246223 GAGCAAAGAGTCGAGCACCGAACTTAATGAGCAAC
1 GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
* * * *
2246258 GAGCAATGAGTCCAGCAGCGAGCTTAACGAGCACC
1 GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
2246293 GAG
1 GAG
2246296 TTTAACGAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.11
Consensus pattern (35 bp):
GAGCAAAGAGTCCAGCACCGAACTTAACGAGCAAC
Found at i:2246295 original size:16 final size:16
Alignment explanation
Indices: 2246271--2246306 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2246261 CAATGAGTCC
*
2246271 AGCAGCGAGCTTAACG
1 AGCACCGAGCTTAACG
*
2246287 AGCACCGAGTTTAACG
1 AGCACCGAGCTTAACG
2246303 AGCA
1 AGCA
2246307 ACAAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.14
Consensus pattern (16 bp):
AGCACCGAGCTTAACG
Found at i:2246313 original size:16 final size:17
Alignment explanation
Indices: 2246281--2246324 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2246271 AGCAGCGAGC
* *
2246281 TTAACGAGCACCGAG-T
1 TTAACGAGCAACAAGTT
2246297 TTAACGAGCAACAAGTT
1 TTAACGAGCAACAAGTT
2246314 TTAACGAGCAA
1 TTAACGAGCAA
2246325 GAATCGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
TTAACGAGCAACAAGTT
Found at i:2247522 original size:16 final size:16
Alignment explanation
Indices: 2247501--2247534 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2247491 TTACTATTCA
2247501 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2247517 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2247533 CG
1 CG
2247535 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2259625 original size:9 final size:9
Alignment explanation
Indices: 2259610--2259640 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2259600 ATTCTCCTCC
2259610 CCTCCTTCT
1 CCTCCTTCT
*
2259619 TCTCCTTCT
1 CCTCCTTCT
2259628 CCTCCTTCT
1 CCTCCTTCT
2259637 CCTC
1 CCTC
2259641 GAGTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (9 bp):
CCTCCTTCT
Found at i:2260899 original size:14 final size:14
Alignment explanation
Indices: 2260880--2260919 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2260870 AATGAACATA
*
2260880 AACGAACACGAACG
1 AACGAACACAAACG
*
2260894 AACGAACATAAACG
1 AACGAACACAAACG
2260908 AAC-AACACAAAC
1 AACGAACACAAAC
2260920 AAAAAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:2261190 original size:14 final size:14
Alignment explanation
Indices: 2261171--2261216 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
2261161 GCCCTCTGTT
2261171 CGAACATAAATGAA
1 CGAACATAAATGAA
2261185 CGAACATAAATGAA
1 CGAACATAAATGAA
*
2261199 CAAACATATAATCGAA
1 CGAACATA-AAT-GAA
2261215 CG
1 CG
2261217 TTCACGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:2261460 original size:26 final size:26
Alignment explanation
Indices: 2261426--2261480 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
2261416 ATAAAATATT
2261426 TTTTGAACAATAATCCCCTTAGTAGA
1 TTTTGAACAATAATCCCCTTAGTAGA
2261452 TTTTGAACAATAATCCCCTTAGTAGA
1 TTTTGAACAATAATCCCCTTAGTAGA
2261478 TTT
1 TTT
2261481 GTTAGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTTGAACAATAATCCCCTTAGTAGA
Found at i:2274369 original size:27 final size:28
Alignment explanation
Indices: 2274300--2274571 Score: 120
Period size: 27 Copynumber: 9.7 Consensus size: 28
2274290 CCAGAATTTA
* *
2274300 GATTGAAGCACAGAGGTGCTCAGTCATA
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
** *
2274328 G-TTGGCTGCATAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* *
2274355 GATTGAAGCACAGAGGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
2274383 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
** * *
2274409 GGCTGAAGCACAGAGGTGCTCAGTCATTTT
1 GATTGAAGCACAGAGGTGCTCAGTC--CTC
** * *
2274439 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
*
2274468 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
** *
2274496 TTTTGGCTA-CACAGAGGTG-TCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
* *
2274524 GATTGAAGCACAGAGGTGCTCAATCGTTC
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
**
2274553 -ATTCTAGCACAGAGGTGCT
1 GATTGAAGCACAGAGGTGCT
2274572 ATGGATTCAG
Statistics
Matches: 179, Mismatches: 42, Indels: 46
0.67 0.16 0.17
Matches are distributed among these distances:
26 8 0.04
27 72 0.40
28 58 0.32
29 21 0.12
30 4 0.02
31 5 0.03
32 11 0.06
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:2274524 original size:56 final size:55
Alignment explanation
Indices: 2274252--2274548 Score: 296
Period size: 56 Copynumber: 5.3 Consensus size: 55
2274242 TTTAGGTTGT
** * * * * * *
2274252 AGCACAGAGGTGCTCAATCA-TTCCA-ATGCACAGAGGTGCCAGAATTTAGATTGA
1 AGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-CTCTCGATTGA
* ** * * *
2274306 AGCACAGAGGTGCTCAGTCATAGTTGGCTGCATAGAGGTGTCAG-TCCTCGATTGA
1 AGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCT-CTCGATTGA
* * **
2274361 AGCACAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCCCGGCTGA
1 AGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCTCGATTGA
* * * *
2274415 AGCACAGAGGTGCTCAGTCATTTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGA
1 AGCACAGAGGTGCTCAATCA----TTTTTAGCTACACAGAGGTGTCAGCTCTCGATTGA
*
2274474 AGCACAGAGGTGCTCAATCACTTTTTGGCTACACAGAGGTGTCAGCTCTCGATTGA
1 AGCACAGAGGTGCTCAATCA-TTTTTAGCTACACAGAGGTGTCAGCTCTCGATTGA
2274530 AGCACAGAGGTGCTCAATC
1 AGCACAGAGGTGCTCAATC
2274549 GTTCATTCTA
Statistics
Matches: 200, Mismatches: 34, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
54 63 0.31
55 27 0.14
56 64 0.32
59 46 0.23
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (55 bp):
AGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCTCGATTGA
Found at i:2274799 original size:81 final size:81
Alignment explanation
Indices: 2274664--2274821 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
2274654 GCGAGTTACA
*
2274664 AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
2274729 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
*
2274745 AAGAATGGTTCGCACACGAAATGGCGGA-TCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCT
1 AAGAATGGTTCGCACACGAAATGGCGGAGT-AACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCT
2274809 ACCGAGCCAGTTG
65 ACCGAGCCAGTTG
2274822 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 1 0.01
81 71 0.99
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:2279034 original size:20 final size:20
Alignment explanation
Indices: 2278989--2279034 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2278979 GACCAACAAA
*
2278989 ATCGCAATGCGATCACTAAT
1 ATCGCAACGCGATCACTAAT
* *
2279009 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCACTAAT
2279028 ATCGCAA
1 ATCGCAA
2279035 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCACTAAT
Found at i:2279165 original size:20 final size:20
Alignment explanation
Indices: 2279140--2279274 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
2279130 AATTGGGAAA
*
2279140 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2279160 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
2279180 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
2279201 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2279221 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2279241 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2279261 TTCACAACGCGATA
1 ATCGCAACGCGATA
2279275 ATACATAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2279203 original size:61 final size:61
Alignment explanation
Indices: 2279137--2279253 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
2279127 GCGAATTGGG
* * * * * *
2279137 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
* *
2279198 AAAATCGCAACGAGATACTGACTTTCGCAACGCAATACTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGAT
2279254 TCTGACTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:2279295 original size:41 final size:41
Alignment explanation
Indices: 2279160--2279294 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
2279150 GATACTGACT
* * * * *
2279160 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACATA
* * *
2279201 ATCGCAACGAGATACTGACTTTCGCAACGCAATACTGAC-T-
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-ACATA
* * *
2279241 TTCGCAACGCGATTCTGACTTTCACAACGCGATAATACATA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACATA
*
2279282 ATCGCAATGCGAT
1 ATCGCAACGCGAT
2279295 TTTCTAAGCG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.41
41 40 0.53
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACATA
Found at i:2279490 original size:22 final size:22
Alignment explanation
Indices: 2279462--2279505 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2279452 CACTCTCTCA
2279462 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2279484 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2279506 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2279794 original size:20 final size:20
Alignment explanation
Indices: 2279769--2279837 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
2279759 ACGATTCTCT
2279769 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
2279789 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2279809 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
2279829 TGTTGCGAT
1 CGTTGCGAT
2279838 TTTCATTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2279843 original size:20 final size:20
Alignment explanation
Indices: 2279769--2279847 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
2279759 ACGATTCTCT
**
2279769 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
**
2279789 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2279809 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2279829 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2279848 AGAAACTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2281185 original size:18 final size:18
Alignment explanation
Indices: 2281164--2281208 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2281154 TCCACTTCGG
*
2281164 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2281182 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2281200 GAGCCATCA
1 GAGCCATCA
2281209 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2281744 original size:19 final size:20
Alignment explanation
Indices: 2281690--2281756 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2281680 TAGTTTACTT
* *
2281690 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2281710 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2281730 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2281749 TCGCAACG
1 TCGCAACG
2281757 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2281764 original size:14 final size:14
Alignment explanation
Indices: 2281745--2281803 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2281735 ATGCGAAATG
2281745 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2281759 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2281778 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2281792 AAAATCGCAACG
1 AAAATCGCAACG
2281804 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2281771 original size:33 final size:33
Alignment explanation
Indices: 2281729--2281820 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
2281719 GGAAATGGCT
2281729 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2281762 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2281795 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2281821 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2281783 original size:19 final size:19
Alignment explanation
Indices: 2281729--2281825 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
2281719 GGAAATGGCT
2281729 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2281748 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2281762 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2281781 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2281795 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2281814 ATCGCAATGCGA
1 ATCGCAATGCGA
2281826 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2281885 original size:19 final size:19
Alignment explanation
Indices: 2281863--2281906 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2281853 TTGCGATTTT
2281863 CATTTCACATTGCGATAGC
1 CATTTCACATTGCGATAGC
* * *
2281882 CATTTTCGCGTTGCGATAGT
1 CA-TTTCACATTGCGATAGC
2281902 CATTT
1 CATTT
2281907 TCGCGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTTCACATTGCGATAGC
Found at i:2281895 original size:20 final size:20
Alignment explanation
Indices: 2281872--2281918 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2281862 TCATTTCACA
2281872 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
*
2281892 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
2281912 TTGCGAT
1 TTGCGAT
2281919 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:2281928 original size:20 final size:20
Alignment explanation
Indices: 2281885--2281943 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2281875 CGATAGCCAT
* *
2281885 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
2281905 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
* *
2281925 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGATAGTAA
2281944 ACTATTCTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:2283837 original size:14 final size:14
Alignment explanation
Indices: 2283818--2283853 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2283808 ATTGTTTAAT
2283818 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2283832 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2283846 TGATTTGT
1 TGATTTGT
2283854 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2284017 original size:19 final size:19
Alignment explanation
Indices: 2283993--2284057 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
2283983 GCAACGAGAG
2283993 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2284012 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2284031 AATCACAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
2284045 AATCGCAATGCGA
1 AATCGCAATGCGA
2284058 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2284101 original size:20 final size:20
Alignment explanation
Indices: 2284076--2284153 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
2284066 TCGCATTGCG
*
2284076 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
2284096 ATTTTCGCGTTGCGATAGCT
1 ATTTTCGCGTTGCGATAGCC
2284116 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2284136 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2284154 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2284575 original size:20 final size:20
Alignment explanation
Indices: 2284489--2284583 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
2284479 GATTCTGTAT
* *
2284489 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2284509 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2284529 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
2284550 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2284570 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2284584 TTTACCAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.70
21 14 0.22
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2284597 original size:41 final size:41
Alignment explanation
Indices: 2284510--2284604 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
2284500 GAAAGTCAGA
* * ** *
2284510 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
2284551 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
2284593 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2284605 TTACTTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2286275 original size:13 final size:13
Alignment explanation
Indices: 2286228--2286264 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2286218 AACCCGACCC
2286228 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2286241 TACCCGACCAGTT
1 GACCCGACCCGTT
2286254 GACCCGACCCG
1 GACCCGACCCG
2286265 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2289178 original size:31 final size:30
Alignment explanation
Indices: 2289108--2289181 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
2289098 TAATGTGACA
* *
2289108 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGACCCTAAGATCATT
** **
2289139 CTCGGGTAGGCCTGCGACCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGACCCTAAGAT-CATT
2289170 CTTAGGTAGGCC
1 CTTAGGTAGGCC
2289182 CCACGGCCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGACCCTAAGATCATT
Found at i:2291330 original size:13 final size:13
Alignment explanation
Indices: 2291283--2291319 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2291273 GTCATAACCC
2291283 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2291296 TACCCGACCAGTT
1 GACCCGACCCGTT
2291309 GACCCGACCCG
1 GACCCGACCCG
2291320 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2294242 original size:31 final size:30
Alignment explanation
Indices: 2294172--2294245 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
2294162 TAATGTGACA
* *
2294172 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGACCCTAAGATCATT
** **
2294203 CTCGGGTAGGCCTGCGACCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGACCCTAAGAT-CATT
2294234 CTTAGGTAGGCC
1 CTTAGGTAGGCC
2294246 CCACGGCCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGACCCTAAGATCATT
Found at i:2296369 original size:13 final size:13
Alignment explanation
Indices: 2296351--2296399 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
2296341 ACCCGACCCG
2296351 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2296364 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
2296377 ACCCGACCAGTTG
1 ACCCGACCCGTTT
2296390 ACCCGACCCG
1 ACCCGACCCG
2296400 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2296400 original size:18 final size:18
Alignment explanation
Indices: 2296377--2296412 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2296367 CGACCCGTTT
2296377 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
2296395 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
2296413 TTGACCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:2296410 original size:8 final size:8
Alignment explanation
Indices: 2296399--2296441 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
2296389 GACCCGACCC
2296399 GACCCGTT
1 GACCCGTT
2296407 GACCCGTT
1 GACCCGTT
2296415 GA-CCGTT
1 GACCCGTT
2296422 GACCCGTT
1 GACCCGTT
2296430 GA-CCGTT
1 GACCCGTT
2296437 GACCC
1 GACCC
2296442 ACGTTGACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:2296422 original size:7 final size:7
Alignment explanation
Indices: 2296402--2296440 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
2296392 CCGACCCGAC
2296402 CCGTTGA
1 CCGTTGA
2296409 CCCGTTGA
1 -CCGTTGA
2296417 CCGTTGA
1 CCGTTGA
2296424 CCCGTTGA
1 -CCGTTGA
2296432 CCGTTGA
1 CCGTTGA
2296439 CC
1 CC
2296441 CACGTTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:2296422 original size:15 final size:15
Alignment explanation
Indices: 2296402--2296441 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2296392 CCGACCCGAC
2296402 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2296417 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2296432 CCGTTGACCC
1 CCGTTGACCC
2296442 ACGTTGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:2299337 original size:31 final size:30
Alignment explanation
Indices: 2299267--2299340 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
2299257 TAATGTGACA
* *
2299267 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGACCCTAAGATCATT
** **
2299298 CTCGGGTAGGCCTGCGACCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGACCCTAAGAT-CATT
2299329 CTTAGGTAGGCC
1 CTTAGGTAGGCC
2299341 CCACGGCCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGACCCTAAGATCATT
Found at i:2301466 original size:13 final size:13
Alignment explanation
Indices: 2301448--2301496 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
2301438 ACCCGACCCG
2301448 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2301461 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
2301474 ACCCGACCAGTTG
1 ACCCGACCCGTTT
2301487 ACCCGACCCG
1 ACCCGACCCG
2301497 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2301497 original size:18 final size:18
Alignment explanation
Indices: 2301474--2301509 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2301464 CGACCCGTTT
2301474 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
2301492 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
2301510 TTGACCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:2301507 original size:8 final size:8
Alignment explanation
Indices: 2301496--2301538 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
2301486 GACCCGACCC
2301496 GACCCGTT
1 GACCCGTT
2301504 GACCCGTT
1 GACCCGTT
2301512 GA-CCGTT
1 GACCCGTT
2301519 GACCCGTT
1 GACCCGTT
2301527 GA-CCGTT
1 GACCCGTT
2301534 GACCC
1 GACCC
2301539 ACGTTGACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:2301519 original size:7 final size:7
Alignment explanation
Indices: 2301499--2301537 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
2301489 CCGACCCGAC
2301499 CCGTTGA
1 CCGTTGA
2301506 CCCGTTGA
1 -CCGTTGA
2301514 CCGTTGA
1 CCGTTGA
2301521 CCCGTTGA
1 -CCGTTGA
2301529 CCGTTGA
1 CCGTTGA
2301536 CC
1 CC
2301538 CACGTTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:2301519 original size:15 final size:15
Alignment explanation
Indices: 2301499--2301538 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2301489 CCGACCCGAC
2301499 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2301514 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
2301529 CCGTTGACCC
1 CCGTTGACCC
2301539 ACGTTGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.38, G:0.25, T:0.25
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:2304434 original size:31 final size:30
Alignment explanation
Indices: 2304364--2304437 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
2304354 TAATGTGACA
*
2304364 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** **
2304395 CTCGGGTAGGCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGGCCCTAAGAT-CATT
2304426 CTTAGGTAGGCC
1 CTTAGGTAGGCC
2304438 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:2305403 original size:21 final size:21
Alignment explanation
Indices: 2305378--2305425 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2305368 CCTAATATTG
2305378 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2305399 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2305420 TAATGT
1 CAATGT
2305426 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2310000 original size:21 final size:21
Alignment explanation
Indices: 2309975--2310022 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2309965 CCTAATATTG
2309975 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2309996 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2310017 TAATGT
1 CAATGT
2310023 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2312868 original size:28 final size:28
Alignment explanation
Indices: 2312828--2312909 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
2312818 TTGTAAACGA
2312828 GCCTATCAAAAGAAACTAAATTATGTGG
1 GCCTATCAAAAGAAACTAAATTATGTGG
2312856 GCCTATCAAAAGAAACTAAATTATGTGG
1 GCCTATCAAAAGAAACTAAATTATGTGG
*
2312884 GCCTATCAAAAGAAACTAAGTTATGT
1 GCCTATCAAAAGAAACTAAATTATGT
2312910 TATTATTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (28 bp):
GCCTATCAAAAGAAACTAAATTATGTGG
Found at i:2313014 original size:17 final size:17
Alignment explanation
Indices: 2312992--2313025 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2312982 AGCTAATTTC
*
2312992 GATTAACTAAAGATTAA
1 GATTAACAAAAGATTAA
2313009 GATTAACAAAAGATTAA
1 GATTAACAAAAGATTAA
2313026 AAGTCAGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
GATTAACAAAAGATTAA
Found at i:2313503 original size:20 final size:20
Alignment explanation
Indices: 2313478--2313566 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
2313468 AAATCGTATA
*
2313478 TTGCGATTCTGGGTATCGCG
1 TTGCGATTCTGGGAATCGCG
* **
2313498 TTGCGATTTTCAAGAATCGCG
1 TTGCGATTCT-GGGAATCGCG
* * **
2313519 TTGCGATT-TTGGAAACTGAT
1 TTGCGATTCTGGGAATC-GCG
*
2313539 TTGCGATTCTGGGGATCGCG
1 TTGCGATTCTGGGAATCGCG
2313559 TTGCGATT
1 TTGCGATT
2313567 TTTATTTCGC
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
19 4 0.08
20 28 0.54
21 20 0.38
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTGGGAATCGCG
Found at i:2317569 original size:182 final size:182
Alignment explanation
Indices: 2317276--2317754 Score: 721
Period size: 182 Copynumber: 2.6 Consensus size: 182
2317266 CGATCAAAAT
* * *
2317276 AAAAAATGTATCGATCCA-TATAAATATAACAGGTAAAAATATGACAAAACCGGTCA-CGAAAA-
1 AAAAAATGTATCGATCCACAAT-GATATAACATGTAAAAATATGACAAAACCGGT-ATC-AAAAT
* * ** *
2317338 GACAATACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
63 GATAAAACCGGTAAATAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
2317403 CTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
128 CTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
* *
2317458 TAAAAATGTATCGATCCACAATGATATAATATGTAAAAATATGACAAAACCGGTATCAAAATGAT
1 AAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGACAAAACCGGTATCAAAATGAT
*
2317523 AAAACCGGTAAATTGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAATAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
** *
2317588 TGTGAATTTAAAAGAGAAGTAGTTTTAGCGTCTATAAAGTGTCGATACTTTA
131 TGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
* * * * *
2317640 AAAAAATGTATCAATCCACAACGATATAACATGTAAAATTATGACAAAACCGATATCGAAATGAT
1 AAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGACAAAACCGGTATCAAAATGAT
* *
2317705 AAAATCGGTAAATAGCTACCGGATATATTGAAAGTATCGATACTTTAATA
66 AAAACCGGTAAATAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
2317755 AGTACGTGTA
Statistics
Matches: 271, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
181 5 0.02
182 264 0.97
183 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAAAATGTATCGATCCACAATGATATAACATGTAAAAATATGACAAAACCGGTATCAAAATGAT
AAAACCGGTAAATAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
Found at i:2317835 original size:21 final size:21
Alignment explanation
Indices: 2317809--2317863 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
2317799 TATCCTATCG
2317809 AAAGTATCGACACCTGACATA
1 AAAGTATCGACACCTGACATA
2317830 AAAGTATCGACACCTGACATA
1 AAAGTATCGACACCTGACATA
2317851 AAAGTATCGACAC
1 AAAGTATCGACAC
2317864 TTTTGTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAGTATCGACACCTGACATA
Found at i:2319598 original size:22 final size:23
Alignment explanation
Indices: 2319546--2319602 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
2319536 AACTTTTTTT
* *
2319546 ATTTTTTTATATAAAATGATAGT
1 ATTTTATTATATAAAATGATAGA
* *
2319569 ATAGTTATTATATAAAATTATA-A
1 AT-TTTATTATATAAAATGATAGA
2319592 ATTTTATTATA
1 ATTTTATTATA
2319603 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATTTTATTATATAAAATGATAGA
Found at i:2319912 original size:15 final size:15
Alignment explanation
Indices: 2319892--2319922 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2319882 GTTGTATTGG
2319892 GGGATGACAGTGAGA
1 GGGATGACAGTGAGA
*
2319907 GGGATGACGGTGAGA
1 GGGATGACAGTGAGA
2319922 G
1 G
2319923 AAAACAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.52, T:0.13
Consensus pattern (15 bp):
GGGATGACAGTGAGA
Found at i:2320029 original size:21 final size:21
Alignment explanation
Indices: 2320005--2320069 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2319995 AAGACAATCA
2320005 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
*
2320026 AGAGTCTAAGAGAAACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
* *
2320047 AGAGTCGAAGAGACACTTGAG
1 AGAGTCAAAGAGAAACTTGAG
2320068 AG
1 AG
2320070 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAG
Found at i:2320154 original size:33 final size:33
Alignment explanation
Indices: 2320117--2320182 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2320107 AAATAGATGG
*
2320117 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
2320150 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2320183 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2321367 original size:4 final size:4
Alignment explanation
Indices: 2321358--2321406 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
2321348 TAAGAGATTG
2321358 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2321406 G
1 G
2321407 AAAGGACATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:2322000 original size:19 final size:19
Alignment explanation
Indices: 2321976--2322024 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2321966 AATGTAGGGT
2321976 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2321995 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2322014 TAATTTTGTAT
1 TAATTTTGTAT
2322025 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2322934 original size:200 final size:199
Alignment explanation
Indices: 2322398--2323337 Score: 1061
Period size: 200 Copynumber: 4.7 Consensus size: 199
2322388 ATAGAGAGTA
*
2322398 TCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGATA
1 TCGATCCCA-AAACATCGAAACCCATAAGTATAATGTAATAGGT-AATTTTCAATGTAACCGGTA
* * * * ** * *
2322463 TAAATATATCGATTTTATGAGAGAATAGGTCTACAACATGTATCGATACTTGTGGAGATCGTGTC
64 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAGTTTGTGTC
* * * * * * * *
2322528 GATACTTTTAGAACATATTCAAATCCCAGAAA-GGTGCACCCATATAGTGT-TGATACATTTTTA
129 GATACTTTTTGAACAGAATCAAAT-CCAAAAAGGGTGAACCAATAAAGTGTCTGATACATTTTCA
2322591 AAAAGTG
193 AAAAGTG
2322598 TCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTCAATGTAACCGGTAT
1 TCGATCCCA-AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTCAATGTAACCGGTAT
* * *
2322663 AAATATACTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGATACTTTTTAATTTTGTGTCG
65 AAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAGTTTGTGTCG
** * * * *
2322728 ATACTTTTTGTCCAGAAT-GAATGTCAAAAAGGGTAAACGAATAAAGTGTCTG-TACATTTTCAA
130 ATACTTTTTGAACAGAATCAAAT-CCAAAAAGGGTGAACCAATAAAGTGTCTGATACATTTTCAA
2322791 AAAGTG
194 AAAGTG
*
2322797 TCGATCCCAAATACATCGAAACCCATAAGTATAATGTAATAGATAATTTTTCAATGTAACCGGTA
1 TCGATCCCAAA-ACATCGAAACCCATAAGTATAATGTAATAGGTAA-TTTTCAATGTAACCGGTA
* * * * * *
2322862 TAAATATACCGGGTTTATTAGAAAATAGGCCTACAATATGTATCGACACTTTTTAATTTTGTGTC
64 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAGTTTGTGTC
** * * * *
2322927 GATACTTTTTGTCCAGAAT-GAATACCAAAAAGGGTGAACGAATAAAATGTC-GGTACATTTTCA
129 GATACTTTTTGAACAGAATCAAAT-CCAAAAAGGGTGAACCAATAAAGTGTCTGATACATTTTCA
2322990 AAAAGTG
193 AAAAGTG
* *
2322997 TCGATCCCAAATACATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTA
1 TCGATCCCAAA-ACATCGAAACCCATAAGTATAATGTAATAGGTAA-TTTTCAATGTAACCGGTA
* * * ** * *
2323062 TAAATATACCGGATTTATGAGAGAATAGGTCTACAAGATGTATCGACACTTGTGGAGATCGTGTC
64 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAGTTTGTGTC
* * * * * * *
2323127 AATACTTTTGGAACAGAATCAAATCCCAAAAGGGTGCACCCATAAAGTGTC-GATATATTTTTAA
129 GATACTTTTTGAACAGAATCAAATCCAAAAAGGGTGAACCAATAAAGTGTCTGATACATTTTCAA
2323191 AAAGTG
194 AAAGTG
* * * ** *
2323197 TCGATCCCAAAAACATCGAAATCCATAATTATAATGTAATATGTAATTTTCTAATAAAACCGATA
1 TCGATCCC-AAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTC-AATGTAACCGGTA
* ** * * * * *
2323262 TAACTATACCATTTTTATGAGAAAATAAGTC-ATCATA-AAGTATCGACAATTTTTAAATTTGTG
64 TAAATATACCGGTTTTATGAGAGAATAGGTCTA-CA-ACATGTATCGACACTTTTTAAGTTTGTG
2323325 TCGATACTATTTT
127 TCGATACT-TTTT
2323338 AAATATTGCA
Statistics
Matches: 643, Mismatches: 86, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
198 10 0.02
199 167 0.26
200 456 0.71
201 10 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
TCGATCCCAAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTCAATGTAACCGGTATA
AATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAGTTTGTGTCGA
TACTTTTTGAACAGAATCAAATCCAAAAAGGGTGAACCAATAAAGTGTCTGATACATTTTCAAAA
AGTG
Found at i:2323675 original size:18 final size:18
Alignment explanation
Indices: 2323652--2323691 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2323642 CAACCCAGGT
*
2323652 CTTCTCAACCACAATCTC
1 CTTCTCAACCACAACCTC
2323670 CTTCTCAACCACAACCTC
1 CTTCTCAACCACAACCTC
2323688 CTTC
1 CTTC
2323692 ACAAACAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.47, G:0.00, T:0.28
Consensus pattern (18 bp):
CTTCTCAACCACAACCTC
Found at i:2326379 original size:21 final size:20
Alignment explanation
Indices: 2326342--2326382 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2326332 ATATGTCTAC
2326342 AATATGTATCGACACTTTTT
1 AATATGTATCGACACTTTTT
* *
2326362 AATATTGTGTCGATACTTTTT
1 AATA-TGTATCGACACTTTTT
2326383 GACCAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (20 bp):
AATATGTATCGACACTTTTT
Found at i:2326572 original size:200 final size:200
Alignment explanation
Indices: 2326229--2327337 Score: 1632
Period size: 200 Copynumber: 5.6 Consensus size: 200
2326219 GTATCTATAC
* ** * *
2326229 ATTTTCAAAAAGTATCGATCCCAAAAACATCAAAATCGATAATTATAATGTAATAGGTAATTTTG
1 ATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTTG
* *
2326294 TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATATGTCTACAATATGTATCGACACTT
66 TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
* * *
2326359 TTTAATATTGTGTCGATACTTTTTGACCAAAATGGATGTCAAAAAGGGTTAACACACAAAGTGTC
131 TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
2326424 GATAT
196 GATAT
* * *
2326429 ATTTTCAAAAAGTATCGATTTCAAAAACATCGTAACCGATAATTATAATATAATAGGTAATTTTG
1 ATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTTG
* *
2326494 TAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
66 TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
*
2326559 TTTAATATTGTGTCGATACTTTTTGTCTAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
131 TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
2326624 GATAT
196 GATAT
* **
2326629 ATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGCCAATTTTG
1 ATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTTG
* *
2326694 TAATATAACCGATATAAATATACC-AATTTAT--GAG---A-G---A-AACATGTATCGACACTT
66 TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
* * * *
2326748 TTTAATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTGAACAAATAAAGTGTC
131 TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
*
2326813 GATAC
196 GATAT
* * ** * * * *
2326818 ATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAATCGATAATTATAAAGTAATAGTTAATTTTT
1 ATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTTG
* * * *
2326883 TAATATAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCTACAATATGTATCGACACTT
66 TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
* *
2326948 TTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACGCACAAAGTGTC
131 TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
*
2327013 GATAC
196 GATAT
2327018 ATTTTCAAAAAGTGA-CGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTT
1 ATTTTCAAAAAGT-ATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTT
* * * *
2327082 GTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAAGTCTACAACATATATTGAAACT
65 GTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACT
* * *
2327147 TTTTAATATTGTATCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACGCACAAAGTGT
130 TTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGT
2327212 CGATAT
195 CGATAT
*
2327218 ATTTTCAAAAAGTGA-CGATTCCAAAAACATCGTAATCGATAATTATAATGTAATAGATAATTTT
1 ATTTTCAAAAAGT-ATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTT
* * * *
2327282 GTAATATAACCAGTACAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGT
65 GTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGT
2327338 TGTGTCGATA
Statistics
Matches: 824, Mismatches: 73, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
189 161 0.20
190 6 0.01
192 3 0.00
193 1 0.00
194 1 0.00
195 1 0.00
196 1 0.00
197 3 0.00
199 6 0.01
200 641 0.78
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (200 bp):
ATTTTCAAAAAGTATCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAATTTTG
TAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTTAACACACAAAGTGTC
GATAT
Found at i:2326957 original size:389 final size:392
Alignment explanation
Indices: 2326225--2327337 Score: 1633
Period size: 389 Copynumber: 2.8 Consensus size: 392
2326215 AGATGTATCT
* * ** * *
2326225 ATACATTTTCAAAAAGTATCGATCCCAAAAACATCAAAATCGATAATTATAATGTAATAGGTAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
*
2326290 TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATATGTCTACAATATGTATCGAC
66 TTTGTAATATAACCGGTATAAATATACCGATTTTAT--GAG---A-G--TACAACATGTATCGAC
* * *
2326355 ACTTTTTAATATTGTGTCGATACTTTTTGACCAAAATGGATGTCAAAAAGGGTTAACACACAAAG
123 ACTTTTTAATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACACACAAAG
* * *
2326420 TGTCGATATATTTTCAAAAAGTATCGATTTCAAAAACATCGTAACCGATAATTATAATA-TAATA
188 TGTCGATATATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAATCGATAATTATAA-AGTAATA
* *
2326484 GGTAATTTTGTAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGT
252 GATAATTTTGTAATATAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGT
* *
2326549 ATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCTAGAATGGATGCCAAAAAGGGTTAACAC
317 ATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACAC
2326614 ACAAAGTGTCG
382 ACAAAGTGTCG
* **
2326625 ATATATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGCCAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
* *
2326690 TTTGTAATATAACCGATATAAATATACC-AATTTATGAGAG-A-AACATGTATCGACACTTTTTA
66 TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGTACAACATGTATCGACACTTTTTA
* * *
2326752 ATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTGAACAAATAAAGTGTCGATA
131 ATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACACACAAAGTGTCGATA
* * ** *
2326817 CATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAATCGATAATTATAAAGTAATAGTTAATTTT
196 TATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAATCGATAATTATAAAGTAATAGATAATTTT
* *
2326882 TTAATATAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCTACAATATGTATCGACACT
261 GTAATATAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACT
*
2326947 TTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACGCACAAAGTGT
326 TTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACACACAAAGTGT
2327012 CG
391 CG
*
2327014 ATACATTTTCAAAAAGTGACGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
1 ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
* * *
2327079 TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAAGTCTACAACATATATTGAA
66 TTTGTAATATAACCGGTATAAATATACCGATTTTAT--GAG----AG--TACAACATGTATCGAC
* *
2327144 ACTTTTTAATATTGTATCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACGCACAAAG
123 ACTTTTTAATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACACACAAAG
* *
2327209 TGTCGATATATTTTCAAAAAGTGACGATTCCAAAAACATCGTAATCGATAATTATAATGTAATAG
188 TGTCGATATATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAATCGATAATTATAAAGTAATAG
* * *
2327274 ATAATTTTGTAATATAACC-AGTACAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGT
253 ATAATTTTGTAATATAACCGA-TATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGT
2327338 TGTGTCGATA
Statistics
Matches: 643, Mismatches: 57, Indels: 26
0.89 0.08 0.04
Matches are distributed among these distances:
388 1 0.00
389 348 0.54
390 7 0.01
392 3 0.00
393 1 0.00
394 1 0.00
396 2 0.00
397 3 0.00
399 8 0.01
400 269 0.42
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (392 bp):
ATACATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAACCGATAATTATAATGTAATAGATAAT
TTTGTAATATAACCGGTATAAATATACCGATTTTATGAGAGTACAACATGTATCGACACTTTTTA
ATATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTTAACACACAAAGTGTCGATA
TATTTTCAAAAAGTGTCGATTCCAAAAACATCGTAATCGATAATTATAAAGTAATAGATAATTTT
GTAATATAACCGATATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACT
TTTTAATATTGTGTCGATACTTTTTGTCCAGAATAGATGCCAAAAAGGGTTAACACACAAAGTGT
CG
Found at i:2326968 original size:21 final size:20
Alignment explanation
Indices: 2326931--2326971 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2326921 ATAGGTCTAC
2326931 AATATGTATCGACACTTTTT
1 AATATGTATCGACACTTTTT
* *
2326951 AATATTGTGTCGATACTTTTT
1 AATA-TGTATCGACACTTTTT
2326972 GTCCAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (20 bp):
AATATGTATCGACACTTTTT
Found at i:2327471 original size:167 final size:167
Alignment explanation
Indices: 2327184--2327504 Score: 489
Period size: 167 Copynumber: 1.9 Consensus size: 167
2327174 CCATAATGGA
* * *
2327184 TGCCAAAAAGGGTTAACGCACAAAGTGTCGATATATTTTCAAAAAGTGACGATTCCAAAAACATC
1 TGCCAAAAAGGGTGAACGAACAAAGTGTCGATATATTTTCAAAAAGTGACGATCCCAAAAACATC
** * * * *
2327249 GTAATCGATAATTATAATGTAATAGATAATTTTGTAATATAACCAGTACAAATATACCGGTTTTA
66 AAAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCAATACAAATATACCAGTTTTA
*
2327314 TGAGAGAATATGTCTACAACATGTTGTGTCGATACTT
131 TGAGAGAATAGGTCTACAACATGTTGTGTCGATACTT
* *
2327351 TGCCAAAAAGGGTGAACGAATAAAGTGTCGATATATTTTCAAAAAGTGTCGATCCCAAAAACATC
1 TGCCAAAAAGGGTGAACGAACAAAGTGTCGATATATTTTCAAAAAGTGACGATCCCAAAAACATC
* * * *
2327416 AAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTAATATAAATATATCAGTTTTA
66 AAAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCAATACAAATATACCAGTTTTA
*
2327481 TGAGATAATAGGTCTACAACATGT
131 TGAGAGAATAGGTCTACAACATGT
2327505 ATCGATACTT
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
167 137 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (167 bp):
TGCCAAAAAGGGTGAACGAACAAAGTGTCGATATATTTTCAAAAAGTGACGATCCCAAAAACATC
AAAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCAATACAAATATACCAGTTTTA
TGAGAGAATAGGTCTACAACATGTTGTGTCGATACTT
Found at i:2329149 original size:17 final size:17
Alignment explanation
Indices: 2329123--2329156 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2329113 ATACGATTTA
* *
2329123 TAATTTTGTATGTGATG
1 TAATTATGTATGAGATG
2329140 TAATTATGTATGAGATG
1 TAATTATGTATGAGATG
2329157 AGAAAAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
TAATTATGTATGAGATG
Done.