Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009276.1 Hibiscus syriacus cultivar Beakdansim tig00112959_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: 285815
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
File 2 of 2
Found at i:135179 original size:19 final size:19
Alignment explanation
Indices: 135139--135267 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
135129 TAGTTTACTT
* *
135139 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
135159 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
135178 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
135197 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
135211 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
135230 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
135244 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
135263 TCGCA
1 TCGCA
135268 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:135218 original size:33 final size:32
Alignment explanation
Indices: 135175--135267 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
135165 CGCGAAACCA
**
135175 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
135207 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
135240 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
135268 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:135265 original size:52 final size:52
Alignment explanation
Indices: 135139--135267 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
135129 TAGTTTACTT
** *
135139 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
135191 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
135244 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
135268 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:135285 original size:19 final size:19
Alignment explanation
Indices: 135263--135435 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
135253 GAAACCAAAA
*
135263 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
135282 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
135298 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
135315 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
135331 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
135348 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
135367 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
135386 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
135405 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
135425 TCGTGTTGCGA
1 TCGCGTTGCGA
135436 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 79 0.62
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:135304 original size:14 final size:14
Alignment explanation
Indices: 135285--135341 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
135275 TTTCATTTCG
135285 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
135299 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
135316 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
135332 CGTTGCGATT
1 CGTTGCGATT
135342 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:135393 original size:38 final size:38
Alignment explanation
Indices: 135263--135435 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
135253 GAAACCAAAA
*
135263 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
135298 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
135331 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
135367 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
135405 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
135436 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:137369 original size:14 final size:14
Alignment explanation
Indices: 137350--137385 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
137340 ATTGTTTAAT
137350 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
137364 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
137378 TGATTTGT
1 TGATTTGT
137386 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:137506 original size:19 final size:19
Alignment explanation
Indices: 137490--137587 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
137480 AAAAATGACT
137490 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
137509 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
137528 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
137542 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
137561 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
137581 ATCGCAA
1 ATCGCAA
137588 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:137619 original size:53 final size:53
Alignment explanation
Indices: 137490--137606 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
137480 AAAAATGACT
137490 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
137542 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
137595 ATCGCAATGCGA
1 ATCGCAATGCGA
137607 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:137624 original size:19 final size:19
Alignment explanation
Indices: 137596--137817 Score: 250
Period size: 19 Copynumber: 12.7 Consensus size: 19
137586 AACGAGAGAA
* *
137596 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
137615 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
137631 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137648 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
137667 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
137683 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137700 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137719 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137738 TCGCATTGCGATTTT-A--
1 TCGCATTGCGATTTTCATT
137754 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
137771 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
137789 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
137805 TCGCATTGCGATT
1 TCGCATTGCGATT
137818 CTCTCGTTGC
Statistics
Matches: 174, Mismatches: 8, Indels: 42
0.78 0.04 0.19
Matches are distributed among these distances:
14 33 0.19
15 1 0.01
16 19 0.11
17 15 0.09
18 4 0.02
19 90 0.52
20 12 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:137659 original size:52 final size:52
Alignment explanation
Indices: 137596--137817 Score: 294
Period size: 52 Copynumber: 4.2 Consensus size: 52
137586 AACGAGAGAA
* *
137596 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
137648 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
137700 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTT-A--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATT
* *
137754 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
137805 TCGCATTGCGATT
1 TCGCATTGCGATT
137818 CTCTCGTTGC
Statistics
Matches: 152, Mismatches: 6, Indels: 23
0.84 0.03 0.13
Matches are distributed among these distances:
48 9 0.06
49 1 0.01
50 2 0.01
51 6 0.04
52 95 0.62
53 18 0.12
54 6 0.04
55 4 0.03
56 1 0.01
57 10 0.07
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:137677 original size:71 final size:69
Alignment explanation
Indices: 137602--137789 Score: 156
Period size: 71 Copynumber: 2.7 Consensus size: 69
137592 AGAATCGCAA
** *
137602 TGCGATTTTAATTTCGCATTGCGAT--TC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTT
1 TGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTT
*
137662 TCAT
66 TAAT
* * *
137666 TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1 TGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
*
137730 TTTTCAT
63 TTTTAAT
* ** *
137737 TTCGCA-TTGCGATTTTATCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCG-ATTTGC-A-TTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCAT
137790 GTTGGGATTT
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
64 5 0.05
65 4 0.04
66 10 0.09
68 2 0.02
69 4 0.04
71 63 0.59
72 19 0.18
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (69 bp):
TGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTT
TAAT
Found at i:137825 original size:67 final size:70
Alignment explanation
Indices: 137634--137850 Score: 307
Period size: 71 Copynumber: 3.1 Consensus size: 70
137624 GATTCTCTCG
137634 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCA-TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
137699 TT-CGCA
64 TTCCGCA
* *
137705 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTATCGTTGCGATTTTCAT
1 TTGCGATTTTCA-TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
137770 TTCCGCA
64 TTCCGCA
* * *
137777 TTGCGATTTTCA-T-G-TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT
1 TTGCGATTTTCATTCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
**
137839 CCGTG
66 CCGCA
137844 TTGCGAT
1 TTGCGAT
137851 AGTCAAATGC
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
67 53 0.39
69 1 0.01
70 1 0.01
71 65 0.48
72 16 0.12
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (70 bp):
TTGCGATTTTCATTCGATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
CCGCA
Found at i:137839 original size:33 final size:33
Alignment explanation
Indices: 137653--137831 Score: 243
Period size: 33 Copynumber: 5.2 Consensus size: 33
137643 TCATTTCGCA
137653 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
137686 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
137722 CATTGCGATTTTCATTTCGCATTGCGATTTTATCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
137757 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
137791 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
137824 TTGCGATT
1 TTGCGATT
137832 GTAATTTCCG
Statistics
Matches: 131, Mismatches: 7, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.01
33 62 0.47
34 29 0.22
35 8 0.06
36 6 0.05
38 25 0.19
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:140129 original size:12 final size:12
Alignment explanation
Indices: 140112--140148 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
140102 TCTTCGGGGA
140112 CTTTTTCTTCTT
1 CTTTTTCTTCTT
140124 CTTTTTCTTCTT
1 CTTTTTCTTCTT
140136 CTTTTTCTTCTT
1 CTTTTTCTTCTT
140148 C
1 C
140149 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:140357 original size:24 final size:24
Alignment explanation
Indices: 140323--140369 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
140313 CTGAAACATC
140323 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
140347 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
140370 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:141080 original size:20 final size:20
Alignment explanation
Indices: 141052--141281 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
141042 AAATTTCAGT
* * *
141052 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
141072 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
141092 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
141112 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
141132 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
141152 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
141172 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
141192 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
141212 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
141232 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
141252 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
141272 GTTGCGATTT
1 GTTGCGATTT
141282 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:141298 original size:21 final size:21
Alignment explanation
Indices: 141268--141350 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
141258 ATTTTCATAT
*
141268 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
141289 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
141310 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
141331 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
141351 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:141341 original size:42 final size:43
Alignment explanation
Indices: 141248--141346 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
141238 ATTTATGTGT
*
141248 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
141289 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
141331 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
141347 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:143369 original size:27 final size:27
Alignment explanation
Indices: 143319--143370 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
143309 CTAGTAATTT
* *
143319 TTAAAATTTTATTTAAAATTAGAAAAA
1 TTAAAATTATATTTAAAATAAGAAAAA
143346 TTAAAATTATATTTTAAAA-AAGAAA
1 TTAAAATTATA-TTTAAAATAAGAAA
143371 TTTTGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAAAATTATATTTAAAATAAGAAAAA
Found at i:152707 original size:74 final size:74
Alignment explanation
Indices: 152581--152720 Score: 217
Period size: 74 Copynumber: 1.9 Consensus size: 74
152571 GAATCGTCTC
*
152581 ATTTGACTTAGACCCGCAAAGGAGAGTCACCCAAAAAACCTAGACTGACTTAAACCACGAAGGGG
1 ATTTGACTTAGACCCGCAAAGGAGAGTCACCCAAAAAACCAAGACTGACTTAAACCACGAAGGGG
152646 ATTCGACTT
66 ATTCGACTT
* * * * **
152655 ATTTGACTTAGACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGCCTTAAACCGTGAAGGGG
1 ATTTGACTTAGACCCGCAAAGGAGAGTCACCCAAAAAACCAAGACTGACTTAAACCACGAAGGGG
152720 A
66 A
152721 GTCGTCTCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (74 bp):
ATTTGACTTAGACCCGCAAAGGAGAGTCACCCAAAAAACCAAGACTGACTTAAACCACGAAGGGG
ATTCGACTT
Found at i:152736 original size:74 final size:72
Alignment explanation
Indices: 152574--152874 Score: 237
Period size: 72 Copynumber: 4.1 Consensus size: 72
152564 CAAGTTCGAA
* * * * * **
152574 TCGTCTCATTTGACTTAGACCCGCAAAGGAGAGTCACCCAAAAAACCTAGACTGACTTAAACCAC
1 TCGTCTCACTTGACTT--ACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGACTTAAACCGT
*
152639 GAAGGGGAT
64 GAAGGGGAG
* * * *
152648 TCGACTTATTTGACTTAGACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGCCTTAAACCGT
1 TCGTCTCACTTGACTT--ACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGACTTAAACCGT
152713 GAAGGGGAG
64 GAAGGGGAG
* * * * * * * * * *
152722 TCGTCTCACATGACTTTCCTGTGAAGGGGATTCATCCGAAGAATCATGA-TCGACTTAAACTGTG
1 TCGTCTCACTTGACTTACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACT-GACTTAAACCGTG
*
152786 AAGGGGAA
65 AAGGGGAG
* * * ** * * * *
152794 TCATCTAACTTGGAATT-CCCATGAAGGGGAGTTACCCAAAGAATCAAGTCCGACTTAAACCGTG
1 TCGTCTCACTT-GACTTACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGACTTAAACCGTG
152858 AAGGGGAG
65 AAGGGGAG
*
152866 TCGTTTCAC
1 TCGTCTCAC
152875 ATGGCTTTCT
Statistics
Matches: 181, Mismatches: 43, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
71 1 0.01
72 100 0.55
73 4 0.02
74 76 0.42
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (72 bp):
TCGTCTCACTTGACTTACCCGCGAAGGGGAGTCACCCAAAGAACCAAGACTGACTTAAACCGTGA
AGGGGAG
Found at i:152787 original size:72 final size:72
Alignment explanation
Indices: 152672--152898 Score: 226
Period size: 72 Copynumber: 3.2 Consensus size: 72
152662 TTAGACCCGC
* * * * *
152672 GAAGGGGAGTCACCCAAAGAACCAAGACTGCCTTAAACCGTGAAGGGGAGTCGTCTCACATGACT
1 GAAGGGGATTCACCCAAAGAATCAAGTCCGACTTAAACCGTGAAGGGGAGTCGTCTCACATGACT
152737 TTCCTGT
66 TTCCTGT
* * * * * * * *
152744 GAAGGGGATTCATCCGAAGAATCATGAT-CGACTTAAACTGTGAAGGGGAATCATCTAACTTGGA
1 GAAGGGGATTCACCCAAAGAATCAAG-TCCGACTTAAACCGTGAAGGGGAGTCGTCTCACAT-GA
* **
152808 -ATTCCCAT
64 CTTTCCTGT
* *
152816 GAAGGGGAGTT-ACCCAAAGAATCAAGTCCGACTTAAACCGTGAAGGGGAGTCGTTTCACATGGC
1 GAAGGGGA-TTCACCCAAAGAATCAAGTCCGACTTAAACCGTGAAGGGGAGTCGTCTCACATGAC
* *
152880 TTTCTTGC
65 TTTCCTGT
152888 GAAGGGGATTC
1 GAAGGGGATTC
152899 GTCTTGCTTG
Statistics
Matches: 118, Mismatches: 31, Indels: 12
0.73 0.19 0.07
Matches are distributed among these distances:
71 4 0.03
72 110 0.93
73 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (72 bp):
GAAGGGGATTCACCCAAAGAATCAAGTCCGACTTAAACCGTGAAGGGGAGTCGTCTCACATGACT
TTCCTGT
Found at i:153467 original size:21 final size:22
Alignment explanation
Indices: 153422--153503 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
153412 TATAGTTTTG
153422 TTTG-AAA-ATAATATATAGTT
1 TTTGAAAACATAATATATAGTT
*
153442 TTTGAAAACATATTATATAG-T
1 TTTGAAAACATAATATATAGTT
153463 TTTGAAAACATAATATATAGTT
1 TTTGAAAACATAATATATAGTT
*
153485 TTTGAAAATATAATATATA
1 TTTGAAAACATAATATATA
153504 TTATATAGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
20 4 0.07
21 23 0.41
22 29 0.52
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTGAAAACATAATATATAGTT
Found at i:153487 original size:43 final size:41
Alignment explanation
Indices: 153422--153503 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 41
153412 TATAGTTTTG
*
153422 TTTGAAAATAATATATAGTTTTTGAAAACATATTATATAGT
1 TTTGAAAATAATATATAGTTTTTGAAAACATAATATATAGT
*
153463 TTTGAAAACATAATATATAGTTTTTGAAAATATAATATATA
1 TTTG-AAA-ATAATATATAGTTTTTGAAAACATAATATATA
153504 TTATATAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 4 0.11
42 3 0.08
43 30 0.81
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (41 bp):
TTTGAAAATAATATATAGTTTTTGAAAACATAATATATAGT
Found at i:153529 original size:27 final size:29
Alignment explanation
Indices: 153476--153535 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
153466 GAAAACATAA
*
153476 TATATAGTTTTTGAAAATATAATATATAT
1 TATATAGTTTTTGAAAATATAATATATAG
153505 TATATAGTTTTT-AAAATATAA-ATATAG
1 TATATAGTTTTTGAAAATATAATATATAG
153532 TATA
1 TATA
153536 CATATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.30
28 9 0.30
29 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (29 bp):
TATATAGTTTTTGAAAATATAATATATAG
Found at i:153583 original size:19 final size:18
Alignment explanation
Indices: 153552--153593 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
153542 ATTATTAGTA
*
153552 TTTTTTCTTTTTCTTTTT
1 TTTTTTCTATTTCTTTTT
153570 TTTTTATCTATTTCTTTTT
1 TTTTT-TCTATTTCTTTTT
153589 TTTTT
1 TTTTT
153594 GGTCCAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTCTATTTCTTTTT
Found at i:161444 original size:18 final size:18
Alignment explanation
Indices: 161415--161467 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
161405 GTTCTTAAGG
161415 AGTGGTCCTTCGCGACAT
1 AGTGGTCCTTCGCGACAT
* * *
161433 ATTGGTCATTCGTGACAT
1 AGTGGTCCTTCGCGACAT
*
161451 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGCGACA
161468 AAATATATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGCGACAT
Found at i:161886 original size:21 final size:21
Alignment explanation
Indices: 161862--161901 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
161852 TAATTGAGGA
161862 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
161883 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
161902 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:166763 original size:18 final size:18
Alignment explanation
Indices: 166740--166829 Score: 108
Period size: 18 Copynumber: 4.8 Consensus size: 18
166730 GTTCTTAAGG
166740 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
166758 AGTGGTCCTTTGGGATAAAT
1 AGTGGTCCTTCGGG--ACAT
*
166778 CAGTGGTCCTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
166797 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
166815 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
166830 TAAATATACA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
18 42 0.68
19 3 0.05
20 3 0.05
21 14 0.23
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:167264 original size:21 final size:22
Alignment explanation
Indices: 167224--167264 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
167214 TTAATTGAGG
*
167224 AAAAGGGTATATAAATAAGTAT
1 AAAAGGATATATAAATAAGTAT
*
167246 AAAAGGATAT-TAGATAAGT
1 AAAAGGATATATAAATAAGT
167265 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (22 bp):
AAAAGGATATATAAATAAGTAT
Found at i:172142 original size:21 final size:21
Alignment explanation
Indices: 172098--172156 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
172088 GTTCTTAAGG
*
172098 AGTGATCCTTCGGGAC--AT-
1 AGTGGTCCTTCGGGACAAATC
*
172116 AGTGGTCCTTTGGGACAAATC
1 AGTGGTCCTTCGGGACAAATC
172137 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGACAAAT
172157 ATACAGTGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.40
20 2 0.06
21 19 0.54
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACAAATC
Found at i:172574 original size:21 final size:21
Alignment explanation
Indices: 172548--172587 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
172538 TAATTGAGGA
172548 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
172569 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
172588 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:174208 original size:74 final size:74
Alignment explanation
Indices: 174072--174210 Score: 181
Period size: 74 Copynumber: 1.9 Consensus size: 74
174062 AAATTGTCAC
* ** * * * *
174072 ATTTGACTTAGACCCGCGAAGGGGAGTCATCTAAAGAACCAAAATTAACTTAAATCGAGAATGAG
1 ATTTGACTTAGACCCACGAAGAAGAGTCACCCAAAGAACCAAAACTAACTTAAATCCAGAATGAG
174137 GGTCGTCTT
66 GGTCGTCTT
* *
174146 ATTTGACTTAGACCCACGAAGAAGAGTCGCCCAAAGAACCAAAACTGACTTAAA-CCATGAATGA
1 ATTTGACTTAGACCCACGAAGAAGAGTCACCCAAAGAACCAAAACTAACTTAAATCCA-GAATGA
174210 G
65 G
174211 AGTCATCTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 2 0.04
74 53 0.96
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (74 bp):
ATTTGACTTAGACCCACGAAGAAGAGTCACCCAAAGAACCAAAACTAACTTAAATCCAGAATGAG
GGTCGTCTT
Found at i:174375 original size:72 final size:71
Alignment explanation
Indices: 174164--174416 Score: 179
Period size: 72 Copynumber: 3.5 Consensus size: 71
174154 TAGACCCACG
* * * * * * * *
174164 AAGAAGAGTCGCCCAAAGAACCAAAACTGACTTAAACCAT-GAATGAGAGTCATCTCATATGGCT
1 AAGAAGAGTC-ACCAAAGAATCAAGACCGACTTAAACCATGGAA-GGGAGTCGTCTCACATGGAT
*
174228 TTCCCGCG
64 TTCCCGCA
** ** * * * * * * * * *
174236 AAGGGGAGTCATCTGAAGAATCAAGACCGACTTAAATCATGAAATGGAGTTGTTTAACTTAGTTT
1 AAGAAGAGTCA-CCAAAGAATCAAGACCGACTTAAACCATGGAAGGGAGTCGTCTCACATGGATT
174301 TCCCGCA
65 TCCCGCA
*
174308 AAGAAGAGTCACACAAAGAATCAAGACCGACTTAAACCATGGAAGGGAGTCGTCTCACCTGGATT
1 AAGAAGAGTCAC-CAAAGAATCAAGACCGACTTAAACCATGGAAGGGAGTCGTCTCACATGGATT
*
174373 TCCCGTGA
65 TCCCG-CA
* * * *
174381 AAGGA-AGTCATCCAAGGAAT-AAGAACAACTTAAACC
1 AAGAAGAGTCA-CCAAAGAATCAAGACCGACTTAAACC
174417 GCGAAGGGGA
Statistics
Matches: 137, Mismatches: 39, Indels: 11
0.73 0.21 0.06
Matches are distributed among these distances:
71 15 0.11
72 114 0.83
73 8 0.06
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (71 bp):
AAGAAGAGTCACCAAAGAATCAAGACCGACTTAAACCATGGAAGGGAGTCGTCTCACATGGATTT
CCCGCA
Found at i:176888 original size:13 final size:13
Alignment explanation
Indices: 176849--176887 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
176839 ACATAAATAA
176849 AAAAATCATAAAAT
1 AAAAAT-ATAAAAT
*
176863 TAAAATATAAAAT
1 AAAAATATAAAAT
176876 AAAAAGTATAAA
1 AAAAA-TATAAA
176888 TTTATAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAAATATAAAAT
Found at i:178806 original size:18 final size:18
Alignment explanation
Indices: 178785--178832 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
178775 AGGCTTGGCT
178785 GATCCTTTAGGTTCAGCC
1 GATCCTTTAGGTTCAGCC
* * ** *
178803 GATCCTTGAGATTTGGTC
1 GATCCTTTAGGTTCAGCC
178821 GATCCTTTAGGT
1 GATCCTTTAGGT
178833 GTCTTCTGCT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (18 bp):
GATCCTTTAGGTTCAGCC
Found at i:181361 original size:18 final size:18
Alignment explanation
Indices: 181338--181374 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
181328 CCGATCTGTG
181338 ACAGGGAAGAAGAATTTA
1 ACAGGGAAGAAGAATTTA
* *
181356 ACAGGGATGAGGAATTTA
1 ACAGGGAAGAAGAATTTA
181374 A
1 A
181375 ATGACTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (18 bp):
ACAGGGAAGAAGAATTTA
Found at i:187951 original size:18 final size:18
Alignment explanation
Indices: 187925--187970 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
187915 AATATTTTAT
187925 ACATCTTAACTTAAATTC
1 ACATCTTAACTTAAATTC
* * * *
187943 ACATATTAAATTAATTTT
1 ACATCTTAACTTAAATTC
187961 ACATCTTAAC
1 ACATCTTAAC
187971 ATCAAAAACT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (18 bp):
ACATCTTAACTTAAATTC
Found at i:188062 original size:30 final size:30
Alignment explanation
Indices: 187986--188068 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
187976 AAACTATTTT
*
187986 TTATTTTAACTTATTAAATATAT-TTTTATTC
1 TTATTTTAA-TT-TTAAAAATATATTTTATTC
* **
188017 TT-TTCGTAA-CCTAAAAATATATTTTATTC
1 TTATT-TTAATTTTAAAAATATATTTTATTC
188046 TTATTTTAATTTTAAAAATATAT
1 TTATTTTAATTTTAAAAATATAT
188069 ATTTTAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 8 0.20
29 13 0.32
30 15 0.37
31 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.55
Consensus pattern (30 bp):
TTATTTTAATTTTAAAAATATATTTTATTC
Found at i:188117 original size:31 final size:32
Alignment explanation
Indices: 188029--188117 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
188019 TTCGTAACCT
* * *
188029 AAAAATATATTTTATTCTTATTTTAATTTTAA
1 AAAAATATATTTTATTCTTATCTTAAATTAAA
* * * *
188061 AAATATATATTTTAATATTAACTTAAATTAAA
1 AAAAATATATTTTATTCTTATCTTAAATTAAA
*
188093 AAAAAT-TAATTTATTCTTATCTTAA
1 AAAAATATATTTTATTCTTATCTTAA
188118 CTTGAATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
31 15 0.33
32 30 0.67
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (32 bp):
AAAAATATATTTTATTCTTATCTTAAATTAAA
Found at i:188137 original size:31 final size:30
Alignment explanation
Indices: 187986--188138 Score: 112
Period size: 31 Copynumber: 5.0 Consensus size: 30
187976 AAACTATTTT
* *
187986 TTATTTTAACTTATTAAAT-ATATTTTTATTC
1 TTATCTTAACTTA-AAAATAATA-TTTTATTC
* * *
188017 TTTTCGTAACCTAAAAAT-ATATTTTATTC
1 TTATCTTAACTTAAAAATAATATTTTATTC
* * * *
188046 TTATTTTAATTTTAAAAATATATATTTTAATA
1 TTATCTTAA-CTTAAAAATA-ATATTTTATTC
* * * *
188078 TTAACTTAAATTAAAAAAAATTAATTTATTC
1 TTATCTTAACTTAAAAATAA-TATTTTATTC
*
188109 TTATCTTAACTTGAATAATAATATTTTATT
1 TTATCTTAACTT-AAAAATAATATTTTATT
188139 ATGATGATAT
Statistics
Matches: 93, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
29 14 0.15
30 15 0.16
31 42 0.45
32 22 0.24
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (30 bp):
TTATCTTAACTTAAAAATAATATTTTATTC
Found at i:188201 original size:31 final size:30
Alignment explanation
Indices: 188163--188235 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
188153 AATTTAAGAT
188163 GATAAAAATATAATATATTTTTTGTAGTTAA
1 GATAAAAATATAATATA-TTTTTGTAGTTAA
*
188194 GATAAAAATAAAATATATTTTTGTAGTTAA
1 GATAAAAATATAATATATTTTTGTAGTTAA
*
188224 AATAAAAATATA
1 GATAAAAATATA
188236 TTTTTAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 23 0.59
31 16 0.41
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (30 bp):
GATAAAAATATAATATATTTTTGTAGTTAA
Found at i:188217 original size:30 final size:30
Alignment explanation
Indices: 188163--188265 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 30
188153 AATTTAAGAT
*
188163 GATAAAAATATAATATATTTTTTGTAGTTAA
1 GATAAAAATAAAATATA-TTTTTGTAGTTAA
188194 GATAAAAATAAAATATATTTTTGTAGTT--
1 GATAAAAATAAAATATATTTTTGTAGTTAA
* *
188222 -A-AAATA-AAAATATATTTTT-AAGTTAA
1 GATAAAAATAAAATATATTTTTGTAGTTAA
*
188248 GATAAGAATAAAATATAT
1 GATAAAAATAAAATATAT
188266 GTTTAAAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
24 4 0.06
25 13 0.21
26 4 0.06
27 2 0.03
28 3 0.05
29 9 0.15
30 11 0.18
31 16 0.26
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (30 bp):
GATAAAAATAAAATATATTTTTGTAGTTAA
Found at i:188225 original size:24 final size:23
Alignment explanation
Indices: 188198--188257 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
188188 AGTTAAGATA
*
188198 AAAATAAAATATATTTTTGTAGTT
1 AAAATAAAATATATTTTT-AAGTT
188222 AAAATAAAAATATATTTTTAAGTT
1 AAAAT-AAAATATATTTTTAAGTT
*
188246 AAGATAAGAATA
1 AAAATAA-AATA
188258 AAATATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.06
24 17 0.53
25 13 0.41
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.38
Consensus pattern (23 bp):
AAAATAAAATATATTTTTAAGTT
Found at i:188278 original size:54 final size:56
Alignment explanation
Indices: 188174--188282 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 56
188164 ATAAAAATAT
* * ** *
188174 AATATATTTTTTGTAGTTAAGATAAAAATAAAATATATTTTTGTAGTTAAAATAAA
1 AATATATTTTTTGAAGTTAAGATAAAAATAAAATATATGTTTAAAATTAAAATAAA
*
188230 AATATA-TTTTT-AAGTTAAGATAAGAATAAAATATATGTTTAAAATTAAAATAA
1 AATATATTTTTTGAAGTTAAGATAAAAATAAAATATATGTTTAAAATTAAAATAA
188283 GAATTAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 36 0.77
55 5 0.11
56 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.40
Consensus pattern (56 bp):
AATATATTTTTTGAAGTTAAGATAAAAATAAAATATATGTTTAAAATTAAAATAAA
Found at i:188281 original size:24 final size:24
Alignment explanation
Indices: 188198--188282 Score: 71
Period size: 29 Copynumber: 3.3 Consensus size: 24
188188 AGTTAAGATA
** *
188198 AAAATAAAATATATTTTTGTAGTT
1 AAAATAAAATATATTTTTAAAATT
*
188222 AAAATAAAAATATATTTTTAAGTTAAGAT
1 AAAAT-AAAATATATTTTTAA---AA-TT
*
188251 AAGAATAAAATATATGTTTAAAATT
1 AA-AATAAAATATATTTTTAAAATT
188276 AAAATAA
1 AAAATAA
188283 GAATTAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
24 10 0.20
25 16 0.33
26 2 0.04
28 1 0.02
29 17 0.35
30 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (24 bp):
AAAATAAAATATATTTTTAAAATT
Found at i:188283 original size:30 final size:29
Alignment explanation
Indices: 188228--188439 Score: 103
Period size: 30 Copynumber: 7.2 Consensus size: 29
188218 AGTTAAAATA
* *
188228 AAAATATATTTTTAAGTTAAGATAAGAAT
1 AAAATATATTTTAAAATTAAGATAAGAAT
*
188257 AAAATATATGTTTAAAATTAAAATAAGAAT
1 AAAATATAT-TTTAAAATTAAGATAAGAAT
* * *
188287 TAATTATA-TTTAATAATTTAAGGTAAGAAT
1 AAAATATATTTTAA-AA-TTAAGATAAGAAT
* *
188317 AGAATATA-TTTAATAATTTAA-TTAAAGAAT
1 AAAATATATTTTAA-AA-TTAAGAT-AAGAAT
* * ** *
188347 ATAATTTA-TGCAATAAGTTAAGATAATAAT
1 AAAATATATTTTAA-AA-TTAAGATAAGAAT
* * * * *
188377 ACAATAT-TTTTTAAGTTAAGAGAAAGACT
1 AAAATATATTTTAAAATTAAGA-TAAGAAT
* * *
188406 GAAATATATTTCT-AAGTTAAAATAAGAAT
1 AAAATATATTT-TAAAATTAAGATAAGAAT
188435 AAAAT
1 AAAAT
188440 CTGTTTTTTT
Statistics
Matches: 141, Mismatches: 33, Indels: 18
0.73 0.17 0.09
Matches are distributed among these distances:
28 11 0.08
29 31 0.22
30 97 0.69
31 2 0.01
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (29 bp):
AAAATATATTTTAAAATTAAGATAAGAAT
Found at i:188345 original size:60 final size:59
Alignment explanation
Indices: 188240--188383 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 59
188230 AATATATTTT
**
188240 TAAGTTAAGATAAGAATAAAATATATGTTTAAAATTAAAATAAGAAT-TAATTATATTTAA
1 TAAGTTAAGATAAGAATAAAATATA-GTTTAAAATTAAAATAAGAATATAATT-TATGCAA
* * * * *
188300 TAATTTAAGGTAAGAATAGAATATA-TTTAATAATTTAATTAAAGAATATAATTTATGCAA
1 TAAGTTAAGATAAGAATAAAATATAGTTTAA-AATTAAAAT-AAGAATATAATTTATGCAA
* *
188360 TAAGTTAAGATAATAATACAATAT
1 TAAGTTAAGATAAGAATAAAATAT
188384 TTTTTAAGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
58 5 0.07
59 7 0.10
60 53 0.76
61 5 0.07
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (59 bp):
TAAGTTAAGATAAGAATAAAATATAGTTTAAAATTAAAATAAGAATATAATTTATGCAA
Found at i:189621 original size:20 final size:20
Alignment explanation
Indices: 189571--189622 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
189561 TAATAAAAAA
* *
189571 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
189591 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
189611 TCGCAATGCGAT
1 TCGCAACGCGAT
189623 TTACATAGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:190195 original size:19 final size:19
Alignment explanation
Indices: 190171--190215 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
190161 GCAATGAGAT
*
190171 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
190190 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
190209 AATCGCA
1 AATCGCA
190216 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:190233 original size:19 final size:19
Alignment explanation
Indices: 190211--190395 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
190201 GAAACCAAAA
*
190211 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
190230 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
190249 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
190268 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
190288 TCGTGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
190304 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
190321 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
190335 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
190354 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
190374 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
190394 TC
1 TC
190396 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:190288 original size:39 final size:38
Alignment explanation
Indices: 190211--190395 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
190201 GAAACCAAAA
*
190211 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
190249 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
190288 TCGTGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
190321 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
190354 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
190394 TC
1 TC
190396 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 37 0.30
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:190372 original size:20 final size:20
Alignment explanation
Indices: 190338--190395 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
190328 GCGATTCTCT
**
190338 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
190358 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
190378 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
190396 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:192457 original size:42 final size:41
Alignment explanation
Indices: 192397--192518 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 41
192387 GCCCGACTCG
* * *
192397 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCC-CTCCCACCGTTCAAGAGGCC
* *
192439 CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCC
* * ** * *
192480 ACTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCCTCCCACCGTTCAAGAG
192519 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
41 27 0.41
42 39 0.59
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (41 bp):
CCTATCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCC
Found at i:192517 original size:21 final size:21
Alignment explanation
Indices: 192456--192518 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
192446 TTCCTCGAGA
192456 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
** * *
192477 G-CCACTGTCATCGTTGAAGAG
1 GTCC-CTCCCACCGTTCAAGAG
*
192498 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
192519 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCGTTCAAGAG
Found at i:193358 original size:14 final size:14
Alignment explanation
Indices: 193339--193396 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
193329 ATGCGAAATG
193339 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
193353 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
193369 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
193385 AAAATCGCAACG
1 AAAATCGCAACG
193397 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:193381 original size:32 final size:33
Alignment explanation
Indices: 193323--193401 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
193313 GGAAATGGCT
*
193323 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
193356 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
193388 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
193402 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:193430 original size:19 final size:19
Alignment explanation
Indices: 193408--193489 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
193398 GAAACACAAA
193408 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
193427 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
193445 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
193461 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
193478 TCGCATTGCGAT
1 TCGCATTGCGAT
193490 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 4 0.07
17 4 0.07
18 21 0.38
19 17 0.31
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:193505 original size:39 final size:35
Alignment explanation
Indices: 193408--193519 Score: 97
Period size: 33 Copynumber: 3.1 Consensus size: 35
193398 GAAACACAAA
193408 TCGCATTGCGATTTTCATTTCGCGTTGCGA-TTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTTCATT
*
193445 TCGCGTTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGATTTTCATT
**
193478 TCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCATT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGATTTTCATT
193517 TCG
1 TCG
193520 TGTTGCGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
31 1 0.02
32 11 0.18
33 18 0.29
34 1 0.02
37 10 0.16
38 3 0.05
39 17 0.27
40 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (35 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTTCATT
Found at i:193508 original size:20 final size:19
Alignment explanation
Indices: 193474--193527 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
193464 TTGCGATTTT
*
193474 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
193493 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
193513 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
193528 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:193526 original size:19 final size:19
Alignment explanation
Indices: 193408--193527 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
193398 GAAACACAAA
* **
193408 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
*
193427 TCGCGTTGCGAT-TTCATT
1 TCGCGTTGCGATAGTCATT
193445 TCGCGTTGCG--A-T--TT
1 TCGCGTTGCGATAGTCATT
**
193459 T-GTCGTTGCGATTTTCATT
1 TCG-CGTTGCGATAGTCATT
* *
193478 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
193497 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAGTCATT
*
193517 TCGTGTTGCGA
1 TCGCGTTGCGA
193528 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
13 1 0.01
14 10 0.12
16 1 0.01
17 1 0.01
18 16 0.19
19 36 0.43
20 18 0.22
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:194027 original size:17 final size:17
Alignment explanation
Indices: 194000--194039 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
193990 GTCGATCAGA
*
194000 TGATGGCTCTGGGTGAGG
1 TGAT-GCTCTGGGCGAGG
194018 TGATGCTCTGGGCGAGG
1 TGATGCTCTGGGCGAGG
194035 TGATG
1 TGATG
194040 GCTCCCGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.12, C:0.12, G:0.47, T:0.28
Consensus pattern (17 bp):
TGATGCTCTGGGCGAGG
Found at i:195379 original size:20 final size:20
Alignment explanation
Indices: 195354--195391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
195344 AATAGTTTCT
195354 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
195374 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
195392 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:195680 original size:22 final size:22
Alignment explanation
Indices: 195655--195697 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
195645 ATTTAGATAA
195655 ACGGATTTCGCCGGAGATGGGG
1 ACGGATTTCGCCGGAGATGGGG
*
195677 ACGGATTTCGTCGGAGATGGG
1 ACGGATTTCGCCGGAGATGGG
195698 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (22 bp):
ACGGATTTCGCCGGAGATGGGG
Found at i:195956 original size:41 final size:41
Alignment explanation
Indices: 195904--195981 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
195894 CGAAAGTCAG
* * *
195904 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
*
195945 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
195982 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:195978 original size:20 final size:20
Alignment explanation
Indices: 195865--195978 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
195855 CGCTTTGAAA
195865 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
195885 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
195905 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
195925 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
195946 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
195966 ATCGCATTGCGAT
1 ATCGCATTGCGAT
195979 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 58 0.77
21 13 0.17
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:195996 original size:21 final size:21
Alignment explanation
Indices: 195967--196040 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
195957 ATAGTAAGTA
195967 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
195988 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
196008 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
196029 TCGCGTTGCGAT
1 TCGCATTGCGAT
196041 GTACTTATTC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:195997 original size:41 final size:41
Alignment explanation
Indices: 195947--196059 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
195937 TTTTTTATTA
*
195947 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAAT
* **
195988 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
**
196029 TCGCGTTGCGATGTACTTATTCGCATTGCGA
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGA
196060 ATTGGGAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 4 0.06
41 62 0.94
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
Found at i:196011 original size:20 final size:20
Alignment explanation
Indices: 195967--196059 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
195957 ATAGTAAGTA
* **
195967 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
195988 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
196008 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
196029 TCGCGTTGCGATGTACTTAT
1 TCGCATTGCGATTTACTTAT
196049 TCGCATTGCGA
1 TCGCATTGCGA
196060 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.54
21 26 0.46
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:196694 original size:18 final size:20
Alignment explanation
Indices: 196645--196694 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
196635 ATAGCATAGC
*
196645 AAAGGAGATAAAATTATAAA
1 AAAGGATATAAAATTATAAA
196665 AAAGGAT-T-AAATTA-AAA
1 AAAGGATATAAAATTATAAA
*
196682 TAA-GATATAAAAT
1 AAAGGATATAAAAT
196695 GGAAGACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.12
17 6 0.23
18 10 0.38
19 1 0.04
20 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAGGATATAAAATTATAAA
Found at i:205131 original size:153 final size:152
Alignment explanation
Indices: 204882--205188 Score: 557
Period size: 153 Copynumber: 2.0 Consensus size: 152
204872 AAAAACGACC
204882 AAAATAAAATAAAATTGAAACTGAAATAGCATAGTTAATGAGATAAATATATAAAGGACTAAATT
1 AAAATAAAATAAAATTGAAACTGAAATAGCATAGTTAATGAGATAAATATATAAAGGACTAAATT
204947 AAATAAGATATAAAAATAGAGGATAAAGAGCATGATTTT-CCAAATCCTTTT-AAAAACACAAAT
66 AAATAAGATATAAAAATAGAGGATAAAGAGCATGATTTTCCCAAATCCTTTTAAAAAACACAAAT
205010 CTGGTATAAAATCTAAAAAAAA
131 CTGGTATAAAATCTAAAAAAAA
205032 AAAATAAAATAAAA-TGAAACTGAAATAGCATAGTTAATGAGATAAAATTATAATAAAGGACTAA
1 AAAATAAAATAAAATTGAAACTGAAATAGCATAGTTAATGAGAT-AAA-TAT-ATAAAGGACTAA
205096 ATTAAAATAAGATATAAAAATAGAGGATAAAGAGCATGATTTTCCCAAATCCTTTTAAAAAACAC
63 ATT-AAATAAGATATAAAAATAGAGGATAAAGAGCATGATTTTCCCAAATCCTTTTAAAAAACAC
205161 AAATCTGGTATAAAATCTAAAAAAAA
127 AAATCTGGTATAAAATCTAAAAAAAA
205187 AA
1 AA
205189 GAAAGCTTGT
Statistics
Matches: 151, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
149 29 0.19
150 17 0.11
151 3 0.02
152 15 0.10
153 39 0.26
154 12 0.08
155 36 0.24
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (152 bp):
AAAATAAAATAAAATTGAAACTGAAATAGCATAGTTAATGAGATAAATATATAAAGGACTAAATT
AAATAAGATATAAAAATAGAGGATAAAGAGCATGATTTTCCCAAATCCTTTTAAAAAACACAAAT
CTGGTATAAAATCTAAAAAAAA
Found at i:206156 original size:36 final size:36
Alignment explanation
Indices: 206103--206208 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
206093 GTGCGCTACA
*
206103 TCCTTCCGTTTGACTTGAATCGGAAGTGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* ** *
206139 TCCTTTCGTTCTTCTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* *
206175 TCCTTCCGTTCGACTTGAATCGGACGTGTAGATG
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATG
206209 AAATCATAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.36
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
Found at i:209962 original size:17 final size:18
Alignment explanation
Indices: 209940--210013 Score: 71
Period size: 17 Copynumber: 4.0 Consensus size: 18
209930 TCGGTTTGCA
209940 AAAAAACCGG-TTTTTTT
1 AAAAAACCGGATTTTTTT
*
209957 AAAAAACCGGAATTTTTCGGAT
1 AAAAAACCGG-ATTTTT---TT
* *
209979 AAAAATCCAG-TTTTTTT
1 AAAAAACCGGATTTTTTT
209996 AAAAAACCGGATTTTTTT
1 AAAAAACCGGATTTTTTT
210014 CCGGATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
17 19 0.42
18 7 0.16
19 5 0.11
20 5 0.11
22 9 0.20
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AAAAAACCGGATTTTTTT
Found at i:209983 original size:39 final size:41
Alignment explanation
Indices: 209940--210035 Score: 151
Period size: 39 Copynumber: 2.4 Consensus size: 41
209930 TCGGTTTGCA
*
209940 AAAAAACCGGTTTTTTTAAAAAACCGGA-ATTTTT-CGGAT
1 AAAAAACCAGTTTTTTTAAAAAACCGGATATTTTTCCGGAT
* *
209979 AAAAATCCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
1 AAAAAACCAGTTTTTTTAAAAAACCGGATATTTTTCCGGAT
210020 AAAAAACCAGTTTTTT
1 AAAAAACCAGTTTTTT
210036 ATCCGGTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 26 0.51
40 5 0.10
41 20 0.39
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (41 bp):
AAAAAACCAGTTTTTTTAAAAAACCGGATATTTTTCCGGAT
Found at i:210022 original size:24 final size:23
Alignment explanation
Indices: 209996--210081 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 23
209986 CAGTTTTTTT
209996 AAAAAACCGGATTTTTTTCCGG-A
1 AAAAAACCGG-TTTTTTTCCGGTA
*
210019 TAAAAAACCAGTTTTTTATCCGGTTTGA
1 -AAAAAACCGGTTTTTT-TCCGG--T-A
*
210047 AAAAAACCGGTTTTTAATCCGGTA
1 AAAAAACCGGTTTTT-TTCCGGTA
210071 AAAAAACCGGT
1 AAAAAACCGGT
210082 CGTTCAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
23 6 0.11
24 26 0.49
25 1 0.02
27 19 0.36
28 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (23 bp):
AAAAAACCGGTTTTTTTCCGGTA
Found at i:210625 original size:86 final size:82
Alignment explanation
Indices: 210530--210814 Score: 207
Period size: 82 Copynumber: 3.4 Consensus size: 82
210520 TTTATCAATT
* *
210530 AAAAATAATATATGATTTAAACTTG-TTTAAAA-AGTTGTTTTACAATTATTT-TTAAATGATAA
1 AAAAATAATATAT-ATTTAAACTTGTTTTAAAATAATTATTTTACAA--ATTTCTT-AATGATAA
*
210592 ATGAATAACAAATATTGTAA-AA
62 ATG--TAACAAACATTGTAAGAA
* * *
210614 AAGAATATAATATA-ATATAAATTTGTTTTAAAATAATTATTTTATAAATTTCTTAATGATAAAT
1 AA-AA-ATAATATATATTTAAACTTGTTTTAAAATAATTATTTTACAAATTTCTTAATGATAAAT
*
210678 GTAACAAACGTTGTAAGAA
64 GTAACAAACATTGTAAGAA
* * *
210697 AAAAATAATATATAATTT-AA-TTTTTTTAAAAATAATTATTCTA-AAA--T-TAAATGATAAAT
1 AAAAATAATATAT-ATTTAAACTTGTTTT-AAAATAATTATTTTACAAATTTCTTAATGATAAAT
* *
210756 CAATAA-AAATATTGTAAGAA
64 --GTAACAAACATTGTAAGAA
* * * *
210776 AGAAAAAACATGTCTAATTTAAACTTGTTTAAAAATAAT
1 A-AAAATA-ATATAT-ATTTAAACTTGTTTTAAAATAAT
210815 CATATAAAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 32
0.77 0.09 0.15
Matches are distributed among these distances:
78 11 0.07
79 14 0.08
80 8 0.05
81 26 0.16
82 41 0.25
83 12 0.07
84 26 0.16
85 11 0.07
86 18 0.11
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (82 bp):
AAAAATAATATATATTTAAACTTGTTTTAAAATAATTATTTTACAAATTTCTTAATGATAAATGT
AACAAACATTGTAAGAA
Found at i:210808 original size:82 final size:82
Alignment explanation
Indices: 210580--210814 Score: 241
Period size: 82 Copynumber: 2.9 Consensus size: 82
210570 TACAATTATT
* * * *
210580 TTTAAATGATAAATGAATAACAAATATTGTAAAAAAGAATATAA-TATAATATAAATTTGTTTTA
1 TTTAAATGATAAAT-AATAACAAATATTGTAAGAAAGAAAATAATTATAATTTAAATTTGTTTAA
*
210644 AAATAATTATTTTATAAA
65 AAATAATTATTCTATAAA
* * ** *
210662 TTTCTTAATGATAAAT-GTAACAAACGTTGTAAGAAA-AAAATAATATATAATTT-AATTTTTTT
1 -TT-TAAATGATAAATAATAACAAATATTGTAAGAAAGAAAATAAT-TATAATTTAAATTTGTTT
210724 AAAAATAATTATTCTA-AAA
63 AAAAATAATTATTCTATAAA
* * *
210743 -TTAAATGATAAATCAATAA-AAATATTGTAAGAAAGAAAAAACATGTCTAATTTAAACTTGTTT
1 TTTAAATGATAAAT-AATAACAAATATTGTAAGAAAGAAAATA-AT-TATAATTTAAATTTGTTT
210806 AAAAATAAT
63 AAAAATAAT
210815 CATATAAAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
78 11 0.09
79 14 0.11
80 8 0.06
81 18 0.14
82 54 0.43
83 9 0.07
84 11 0.09
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (82 bp):
TTTAAATGATAAATAATAACAAATATTGTAAGAAAGAAAATAATTATAATTTAAATTTGTTTAAA
AATAATTATTCTATAAA
Found at i:211572 original size:2 final size:2
Alignment explanation
Indices: 211567--211606 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
211557 ATTTTGTGTG
211567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
211607 GAACATAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:218079 original size:12 final size:12
Alignment explanation
Indices: 218062--218089 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
218052 AAGGGTGCGT
218062 AGGATAAGGATG
1 AGGATAAGGATG
218074 AGGATAAGGATG
1 AGGATAAGGATG
218086 AGGA
1 AGGA
218090 GGTGTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
AGGATAAGGATG
Found at i:219674 original size:40 final size:39
Alignment explanation
Indices: 219586--219674 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
219576 TTTATGAATT
*
219586 TAATATTAATAAAATATTTTAATATCATTTTAATCAAAA
1 TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
* * *
219625 TATTAATTATTAAAATATATTTATTAAT-ATTTCTAAT-AATA
1 TAAT-ATTATTAAAATAT-TTTAAT-ATCATTT-TAATCAAAA
219666 TAATATTAT
1 TAATATTAT
219675 ATTTTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
39 3 0.07
40 17 0.41
41 15 0.37
42 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (39 bp):
TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
Found at i:219676 original size:22 final size:23
Alignment explanation
Indices: 219646--219692 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
219636 AAAATATATT
219646 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
219669 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
219691 TA
1 TA
219693 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:219833 original size:19 final size:18
Alignment explanation
Indices: 219809--219877 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
219799 ATATTATTAA
219809 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
219828 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
219846 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
219868 ATT-TTAATAA
1 ATTATTAATAA
219878 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:219836 original size:54 final size:54
Alignment explanation
Indices: 219741--219878 Score: 140
Period size: 54 Copynumber: 2.5 Consensus size: 54
219731 TTTTTATTTT
* *
219741 AATAATATATAATAAATTATTAATAAAATTTATATTTTTTAT-TAATTTAATAGA
1 AATAATATATAATAAATTATTAATAAAATTAATATTATTTATAT-ATTTAATAGA
* *
219795 AATAATAT-TATTAAATTATTAATAATGAA-TAATATTATTTATATATTTAATATTA
1 AATAATATATAATAAATTATTAATAA--AATTAATATTATTTATATATTTAATA-GA
*
219850 ATATAATAATCTAATAATATT-TTAATAAA
1 A-ATAAT-ATATAATAA-ATTATTAATAAA
219879 GATATTTAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
53 16 0.23
54 27 0.38
55 5 0.07
56 6 0.08
57 2 0.03
58 12 0.17
59 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (54 bp):
AATAATATATAATAAATTATTAATAAAATTAATATTATTTATATATTTAATAGA
Found at i:219852 original size:27 final size:27
Alignment explanation
Indices: 219772--219857 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
219762 AATAAAATTT
* *
219772 ATATTTTTTAT-TAATTTAATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
219799 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
219826 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
219855 ATA
1 ATA
219858 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 8 0.17
27 18 0.39
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:219868 original size:103 final size:101
Alignment explanation
Indices: 219656--219868 Score: 219
Period size: 103 Copynumber: 2.1 Consensus size: 101
219646 TATTAATATT
* *
219656 TCTAATAATATAATATTATATTTTTAATATTATAATAAAATAATCAATTATATTATAATAATATA
1 TCTAATAATAAAATATTATATTTTTAATATTATAATAAAATAATCAATTAAATTATAATAATATA
*
219721 AGATATTATATTTTTATTTTAATAATATATAATAAA
66 AGATATTATATTTATATTTTAATAATATATAATAAA
* *
219757 T-TATTAATAAAAT-TTATATTTTTTATTAATT-TAATAGAAATAAT-ATTATTAAATTATTAAT
1 TCTAATAATAAAATATTATA-TTTTTAAT-ATTATAATA-AAATAATCA--ATTAAATTA-TAAT
*
219818 AATGA-ATA-ATA-T-TATTTATATATTTAATATTAATATAAT-AA
60 AAT-ATA-AGATATTATATTTATAT-TTTAATAAT-ATATAATAAA
219859 TCTAATAATA
1 TCTAATAATA
219869 TTTTAATAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 20
0.78 0.06 0.17
Matches are distributed among these distances:
99 5 0.05
100 23 0.24
101 19 0.20
102 20 0.21
103 25 0.27
104 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (101 bp):
TCTAATAATAAAATATTATATTTTTAATATTATAATAAAATAATCAATTAAATTATAATAATATA
AGATATTATATTTATATTTTAATAATATATAATAAA
Found at i:220029 original size:35 final size:35
Alignment explanation
Indices: 219955--220022 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
219945 TATAATTTAT
* **
219955 ATATTTTTATTTCAATAAAATATATATCAATATTA
1 ATATTTTTATTTCAATAAAATATAAAAAAATATTA
219990 ATATTTTTA-TT-AATAAAATTATAAAAAAATATT
1 ATATTTTTATTTCAATAAAA-TATAAAAAAATATT
220023 TCATATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 7 0.24
34 13 0.45
35 9 0.31
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (35 bp):
ATATTTTTATTTCAATAAAATATAAAAAAATATTA
Found at i:220287 original size:14 final size:14
Alignment explanation
Indices: 220268--220297 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
220258 CCAGAAATAT
*
220268 AATTCATTTTCCAG
1 AATTCAATTTCCAG
220282 AATTCAATTTCCAG
1 AATTCAATTTCCAG
220296 AA
1 AA
220298 AACTAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:224771 original size:2 final size:2
Alignment explanation
Indices: 224764--224832 Score: 62
Period size: 2 Copynumber: 38.0 Consensus size: 2
224754 CCGTCCCGAT
*
224764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
224804 T- TT TA TA T- TT TA TA T- TA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224833 ATGTTTTATA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
1 7 0.12
2 50 0.88
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:224783 original size:14 final size:13
Alignment explanation
Indices: 224762--224855 Score: 78
Period size: 12 Copynumber: 7.8 Consensus size: 13
224752 CCCCGTCCCG
224762 ATTATATATATAT
1 ATTATATATATAT
224775 A-TATATATATAT
1 ATTATATATATAT
224787 A-TATATA-ATAT
1 ATTATATATATAT
* *
224798 TTTATAT-TTTAT
1 ATTATATATATAT
*
224810 ATTTTATAT-TA-
1 ATTATATATATAT
224821 ATTATATATATAAT
1 ATTATATATAT-AT
* *
224835 GTTTTATAT-TA-
1 ATTATATATATAT
224846 ATTATATATA
1 ATTATATATA
224856 AAATATTTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
11 19 0.29
12 35 0.54
13 4 0.06
14 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:224804 original size:7 final size:7
Alignment explanation
Indices: 224794--224819 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
224784 TATATATATA
224794 ATATTTT
1 ATATTTT
224801 ATATTTT
1 ATATTTT
224808 ATATTTT
1 ATATTTT
224815 ATATT
1 ATATT
224820 AATTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATATTTT
Found at i:224828 original size:25 final size:25
Alignment explanation
Indices: 224772--224864 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
224762 ATTATATATA
* *
224772 TATATATAT-ATATATATATATAATAT
1 TATATATATAATAT-TTTATATTA-AT
* * *
224798 TTTATATTTTATATTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
*
224823 TATATATATAATGTTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
*
224848 TATATATAAAATATTTT
1 TATATATATAATATTTT
224865 CGGGTTCGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
25 38 0.68
26 14 0.25
27 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TATATATATAATATTTTATATTAAT
Found at i:226998 original size:37 final size:36
Alignment explanation
Indices: 226913--227048 Score: 170
Period size: 37 Copynumber: 3.8 Consensus size: 36
226903 TTTCGTCCTA
226913 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
226948 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-ATTTT
* * *
226983 GCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-TT
* * *
227021 CTATGATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
227049 CCATAAGCAC
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.32
35 3 0.03
37 55 0.61
38 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:227601 original size:16 final size:18
Alignment explanation
Indices: 227580--227614 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
227570 TTTACTCATT
227580 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
227596 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
227614 T
1 T
227615 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:230893 original size:22 final size:22
Alignment explanation
Indices: 230833--230904 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
230823 AAAAGCAAAA
* *
230833 AAAAAAAATAAAGAAAAAGAG-
1 AAAAACAACAAAGAAAAAGAGC
* *
230854 AAACAAGAACAAAAAAAAAGAGC
1 AAA-AACAACAAAGAAAAAGAGC
*
230877 AAAAATCAA-AAAGAAAAAGGGAC
1 AAAAA-CAACAAAGAAAAAGAG-C
230900 AAAAA
1 AAAAA
230905 GCACATGCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 3 0.07
22 27 0.66
23 11 0.27
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAAACAACAAAGAAAAAGAGC
Found at i:231520 original size:22 final size:22
Alignment explanation
Indices: 231492--231535 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
231482 AGCTACCCCA
231492 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
231514 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
231536 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:232528 original size:36 final size:36
Alignment explanation
Indices: 232485--232728 Score: 218
Period size: 36 Copynumber: 6.9 Consensus size: 36
232475 ACTAGAAGAG
* *
232485 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
*
232521 TTTTGTCTATCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
*
232557 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
* * * *
232593 ------ATAT-TTG-GATATGTTTTCTTTGAAACAAA
1 TTTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAA
* ** ** * *
232622 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAC
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAAC-AAA
* * *
232659 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAATC-AA
1 TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
* *
232694 TTTTCGTCTATCTTGAGACAGTTACTCTTGAAACA
1 TTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACA
232729 CAAAATCTTC
Statistics
Matches: 170, Mismatches: 26, Indels: 23
0.78 0.12 0.11
Matches are distributed among these distances:
28 3 0.02
29 18 0.11
30 3 0.02
35 6 0.04
36 107 0.63
37 33 0.19
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:233633 original size:105 final size:105
Alignment explanation
Indices: 233401--234061 Score: 918
Period size: 105 Copynumber: 6.3 Consensus size: 105
233391 GCCATCCGCG
* * * * * *
233401 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
233466 GGGACGGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
233510 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
233575 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
233615 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTTAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
233680 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
233720 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
233785 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
233825 ATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCAAGACGAAGAG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
233890 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
233925 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
233990 ACGGTTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
234031 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
234062 TGGAACAATG
Statistics
Matches: 503, Mismatches: 43, Indels: 15
0.90 0.08 0.03
Matches are distributed among these distances:
100 80 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 302 0.60
106 83 0.17
107 3 0.01
109 22 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:234694 original size:37 final size:36
Alignment explanation
Indices: 234609--234744 Score: 170
Period size: 37 Copynumber: 3.8 Consensus size: 36
234599 TTTCGTCCTA
234609 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
234644 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-ATTTT
* * *
234679 GCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTCTA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-TT
* * *
234717 CTATGATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
234745 CCATAAGCAC
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.32
35 3 0.03
37 55 0.61
38 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:235264 original size:20 final size:20
Alignment explanation
Indices: 235239--235276 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
235229 ATTATTATTA
235239 TTTTACTTATATATATATAC
1 TTTTACTTATATATATATAC
* *
235259 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
235277 TTTACTCATT
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:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATAC
Found at i:235298 original size:21 final size:19
Alignment explanation
Indices: 235268--235308 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
235258 CTTTTACTTT
235268 TTTATATATTTTACTCATTTA
1 TTTATATATTTTA-T-ATTTA
*
235289 TTTATCTATTTTATATTTA
1 TTTATATATTTTATATTTA
235308 T
1 T
235309 CCTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATATTTTATATTTA
Found at i:238834 original size:31 final size:31
Alignment explanation
Indices: 238792--238868 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
238782 AGTAAAATTA
*
238792 AAAGTTTAGTAGTATAAACGATATAATACCT
1 AAAGTTCAGTAGTATAAACGATATAATACCT
238823 AAAGTTCAGTAGTATAAACGATATAATACCT
1 AAAGTTCAGTAGTATAAACGATATAATACCT
238854 AAAGTTCAGTAGTAT
1 AAAGTTCAGTAGTAT
238869 CTGACGCAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (31 bp):
AAAGTTCAGTAGTATAAACGATATAATACCT
Found at i:246629 original size:13 final size:13
Alignment explanation
Indices: 246611--246647 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
246601 TTAATAAATA
246611 AAATTGAGTGAAT
1 AAATTGAGTGAAT
246624 AAATTGAGTGAAT
1 AAATTGAGTGAAT
246637 AAATTGAGTGA
1 AAATTGAGTGA
246648 CAAAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (13 bp):
AAATTGAGTGAAT
Found at i:247968 original size:30 final size:29
Alignment explanation
Indices: 247934--248016 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
247924 TGATATATAT
* * *
247934 AACTTTTCAAAATTATATTTTTGGTCCTTA
1 AACTTTTCAAAATTATATTTTAGCTAC-TA
* *
247964 AACTTTTCAAAGTTTATACTTTAGCTACTA
1 AACTTTTCAAA-ATTATATTTTAGCTACTA
247994 AAC-TTTCAAAACTTATATTTTAG
1 AACTTTTCAAAA-TTATATTTTAG
248017 TCACTAGCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 17 0.39
30 16 0.36
31 11 0.25
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (29 bp):
AACTTTTCAAAATTATATTTTAGCTACTA
Found at i:255977 original size:16 final size:16
Alignment explanation
Indices: 255956--255986 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
255946 ATGATTTATC
255956 TATTTATATAATGTAT
1 TATTTATATAATGTAT
*
255972 TATTTATTTAATGTA
1 TATTTATATAATGTA
255987 CTTTAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TATTTATATAATGTAT
Found at i:263862 original size:83 final size:82
Alignment explanation
Indices: 263556--263903 Score: 297
Period size: 83 Copynumber: 4.0 Consensus size: 82
263546 CTCGAACTTG
* *
263556 TTTTAC-TCTACTACTCTTCCGTGAAGTTCTCATACTTTGCTGAAAAATCTATTCCACTACTCTT
1 TTTTACTTC-ACTACTCTTCCGTGAAGTT-TGATAATTTGCTGAAAAATCTATTCCACTACTCTT
*
263620 TCGTGGAGTTCAGATTTGC
64 TCGTGGAGTTCAAATTTGC
* * * * * * *
263639 TTTTACTTCATTACTTTTTCATGAAGTTTGAAAATGATTAACTTGACAAGAATCTAATTTCACTA
1 TTTTACTTCACTACTCTTCCGTGAAGTTTGATAAT--TT-GC-TGA-AA-AATCT-ATTCCACTA
* * *
263704 CTC-TTCTGTGAATATTAGATTCAAAATTGA
59 CTCTTTC-GTG-----GAG-TTCAAATTTGC
* * * * *
263734 ATTTGCTTCCATTACTCTTCCGTGGAA-TTTGATACTTTGCTGAAAAATCTGTTCCACTACTCTT
1 TTTTACTT-CACTACTCTTCCGT-GAAGTTTGATAATTTGCTGAAAAATCTATTCCACTACTCTT
*
263798 TTGTGGAGTTCAAATTTGC
64 TCGTGGAGTTCAAATTTGC
* * *
263817 TTTTACTTCACTACTCTTCCGTGAAGATTTTATAATTTGCTGAAAAATATGTTCCACTACTCTTT
1 TTTTACTTCACTACTCTTCCGTGAAG-TTTGATAATTTGCTGAAAAATCTATTCCACTACTCTTT
*
263882 CGTGGAGTTCAGATTTGC
65 CGTGGAGTTCAAATTTGC
263900 TTTT
1 TTTT
263904 GTGTTTGCTT
Statistics
Matches: 210, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
81 3 0.01
82 17 0.08
83 91 0.43
84 6 0.03
85 1 0.00
86 3 0.01
87 2 0.01
88 8 0.04
89 27 0.13
90 7 0.03
91 2 0.01
92 3 0.01
93 1 0.00
94 4 0.02
95 14 0.07
96 18 0.09
97 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (82 bp):
TTTTACTTCACTACTCTTCCGTGAAGTTTGATAATTTGCTGAAAAATCTATTCCACTACTCTTTC
GTGGAGTTCAAATTTGC
Found at i:264467 original size:22 final size:22
Alignment explanation
Indices: 264442--264490 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
264432 GATAAAGCTT
* *
264442 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCCA
*
264464 TCATCTTTAAAAATAGAATCCA
1 TCATCTTTAAAAAGAGAATCCA
264486 TCATC
1 TCATC
264491 CTTGCAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCCA
Found at i:266064 original size:17 final size:17
Alignment explanation
Indices: 266042--266077 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
266032 CTCCATTTCA
266042 ATTCTCTAAAATCTTTG
1 ATTCTCTAAAATCTTTG
266059 ATTCTCTAAAATCTTTG
1 ATTCTCTAAAATCTTTG
266076 AT
1 AT
266078 CCTATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTCTCTAAAATCTTTG
Found at i:268980 original size:24 final size:24
Alignment explanation
Indices: 268953--269003 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
268943 TGGTGGTTGA
*
268953 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
268977 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
269001 TTT
1 TTT
269004 GTTCTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:269507 original size:22 final size:22
Alignment explanation
Indices: 269480--269533 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
269470 GTGAGGATTA
*
269480 TTTTATTTTCATTCTATTTTCT
1 TTTTATTTACATTCTATTTTCT
269502 TTTTATTTACATTCTATTTTCT
1 TTTTATTTACATTCTATTTTCT
269524 TTTTATTTAC
1 TTTTATTTAC
269534 TGTTTTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTACATTCTATTTTCT
Found at i:269530 original size:11 final size:11
Alignment explanation
Indices: 269479--269531 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
269469 CGTGAGGATT
269479 ATTTTATTTTC
1 ATTTTATTTTC
*
269490 ATTCTATTTTC
1 ATTTTATTTTC
* *
269501 TTTTTATTTAC
1 ATTTTATTTTC
*
269512 ATTCTATTTTC
1 ATTTTATTTTC
*
269523 TTTTTATTT
1 ATTTTATTT
269532 ACTGTTTTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTATTTTC
Found at i:270008 original size:16 final size:16
Alignment explanation
Indices: 269989--270019 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
269979 AAAAACAGTA
269989 AATAAAAATAAAATAG
1 AATAAAAATAAAATAG
270005 AATAAAAATAAAATA
1 AATAAAAATAAAATA
270020 ATCCTTACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAATAG
Found at i:270540 original size:24 final size:24
Alignment explanation
Indices: 270496--270545 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
270486 ATAAAGAACC
*
270496 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
270520 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
270544 AA
1 AA
270546 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:273843 original size:26 final size:25
Alignment explanation
Indices: 273808--273882 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 25
273798 AGAAGATGAG
273808 TAAAAGAAAGAGAAAAAGTAAAAGT
1 TAAAAGAAAGAGAAAAAGTAAAAGT
*
273833 TAAAATGAAAGAGAAAAA-T-TAA--
1 TAAAA-GAAAGAGAAAAAGTAAAAGT
*
273855 -AAAAGAAAGAG-AAAAGAAAAAGT
1 TAAAAGAAAGAGAAAAAGTAAAAGT
273878 TAAAA
1 TAAAA
273883 ATTTAAGAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
19 4 0.10
20 7 0.17
21 6 0.15
24 6 0.15
25 6 0.15
26 12 0.29
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (25 bp):
TAAAAGAAAGAGAAAAAGTAAAAGT
Found at i:273890 original size:26 final size:27
Alignment explanation
Indices: 273812--273891 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 27
273802 GATGAGTAAA
* *
273812 AGAAAGAGAAAAAG-T-AAAAGTTAAA
1 AGAAAGAGAAAAAGTTAAAAAATTAAG
**
273837 ATGAAAGAGAAAAA-TTAAAAAAGAAAG
1 A-GAAAGAGAAAAAGTTAAAAAATTAAG
*
273864 AGAAA-AGAAAAAGTTAAAAATTTAAG
1 AGAAAGAGAAAAAGTTAAAAAATTAAG
273890 AG
1 AG
273892 GGAAAAGGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.18
26 29 0.66
27 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.14
Consensus pattern (27 bp):
AGAAAGAGAAAAAGTTAAAAAATTAAG
Found at i:274152 original size:18 final size:18
Alignment explanation
Indices: 274129--274164 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
274119 CGGTATGGTC
274129 CCTACAAATCATATCAAA
1 CCTACAAATCATATCAAA
274147 CCTACAAATCATATCAAA
1 CCTACAAATCATATCAAA
274165 AATTAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (18 bp):
CCTACAAATCATATCAAA
Found at i:278824 original size:20 final size:21
Alignment explanation
Indices: 278787--278826 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
278777 AAATTAAGTT
278787 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
278808 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
278827 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:279081 original size:19 final size:19
Alignment explanation
Indices: 279057--279095 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
279047 TCGAATGAAT
*
279057 TCCATGTACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
279076 TCCATGCATCGATGTACTC
1 TCCATGCACCGATGCACTC
279095 T
1 T
279096 GAATATTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:279146 original size:65 final size:63
Alignment explanation
Indices: 279043--279202 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 63
279033 GAATTAATTG
* * * *** * *
279043 AACATCGAATGAATTCCATGTACCGATGCACTCTCCATGCATCGATGTACTCTGAATA-TTTTCA
1 AACATCGAATGCATTTCATGTATCGATGCACAAGCCATG-ATCGATGCA-TCAGAATATTTTTC-
279107 A
63 A
* **
279108 AACATCGAATGCATTTGATGTATCGATGCACAAGCCATGATCGATGCATCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGTATCGATGCACAAGCCATGATCGATGCATCAGAATATTTTTCA
*
279171 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGTATCGATGCACA
279203 CTTGGTGCAC
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 36 0.44
64 13 0.16
65 32 0.40
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGTATCGATGCACAAGCCATGATCGATGCATCAGAATATTTTTCA
Found at i:285001 original size:20 final size:21
Alignment explanation
Indices: 284972--285027 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
284962 TTTGTGCTTC
*
284972 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
284992 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
285014 ATGCATCGATGCAT
1 ATGCATCGATGCAT
285028 AGACCATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Done.