Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008415.1 Hibiscus syriacus cultivar Beakdansim tig00111193_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: 525802
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:188281 original size:2 final size:2
Alignment explanation
Indices: 188274--188302 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
188264 TAGATAAGAG
188274 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188303 TGGGAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:188294 original size:13 final size:13
Alignment explanation
Indices: 188276--188301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
188266 GATAAGAGAT
188276 ATATATATATATA
1 ATATATATATATA
188289 ATATATATATATA
1 ATATATATATATA
188302 TTGGGAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:188294 original size:15 final size:15
Alignment explanation
Indices: 188274--188302 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
188264 TAGATAAGAG
188274 ATATATATATATATA
1 ATATATATATATATA
188289 ATATATATATATAT
1 ATATATATATATAT
188303 TGGGAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:190303 original size:21 final size:21
Alignment explanation
Indices: 190204--190303 Score: 53
Period size: 21 Copynumber: 4.8 Consensus size: 21
190194 AACGCGATCC
** *
190204 CCAGAATCGCAAATC-AGTTT
1 CCAGAATCGCAACGCGATTTT
*
190224 CCAAAATCGCAACGCGATTCTT
1 CCAGAATCGCAACGCGATT-TT
* * * **
190246 -GACAATCGCAATGCGATAGT
1 CCAGAATCGCAACGCGATTTT
* **
190266 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAACGCGATTTT
190287 CCAGAATCGCAACGCGA
1 CCAGAATCGCAACGCGA
190304 ATATGAAAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
20 15 0.25
21 40 0.68
22 4 0.07
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
CCAGAATCGCAACGCGATTTT
Found at i:190316 original size:20 final size:20
Alignment explanation
Indices: 190291--190503 Score: 277
Period size: 20 Copynumber: 10.6 Consensus size: 20
190281 GATTTTCCAG
* ** *
190291 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
190311 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
190331 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
190351 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
190371 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
190391 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
190411 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
190431 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
190451 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
190472 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
190492 AATCGCAACGCG
1 AATCGCAACGCG
190504 ATTTTTAAAG
Statistics
Matches: 169, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 149 0.88
21 19 0.11
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:190912 original size:33 final size:33
Alignment explanation
Indices: 190873--190943 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
190863 TTCACTTAGA
190873 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
190906 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
190939 TTTCA
1 TTTCA
190944 AGTAGTATTT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:191048 original size:21 final size:20
Alignment explanation
Indices: 191022--191128 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
191012 TGCAGAAGAG
191022 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
191043 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
*
191063 TCTGCAACAAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
191085 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
191099 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
191118 TCGCAACGAGA
1 TCGCAACGAGA
191129 GAATCGCAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 23 0.34
22 10 0.15
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:191102 original size:14 final size:14
Alignment explanation
Indices: 191083--191139 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
191073 GAAAAATGAA
191083 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
191097 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
191116 AATCGCAACGAGAG
1 AATCGCAACGAGAG
191130 AATCGCAACG
1 AATCGCAACG
191140 CGAAACCAAA
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:191113 original size:33 final size:33
Alignment explanation
Indices: 191076--191155 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
191066 GCAACAAGAA
191076 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
191109 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
191142 AAACCAAAATCGCA
1 AAATGAAAATCGCA
191156 TTTCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:191209 original size:20 final size:20
Alignment explanation
Indices: 191159--191210 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
191149 AATCGCATTT
191159 CGATTTTCATTTCTCTCGTTG
1 CGATTTTCA-TTCTCTCGTTG
***
191180 CGACAGTCATTCTCTCGTTG
1 CGATTTTCATTCTCTCGTTG
191200 CGATTTTCATT
1 CGATTTTCATT
191211 TCAACCAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.46
Consensus pattern (20 bp):
CGATTTTCATTCTCTCGTTG
Found at i:193028 original size:92 final size:92
Alignment explanation
Indices: 192872--193091 Score: 397
Period size: 92 Copynumber: 2.4 Consensus size: 92
192862 TAGATTGCTT
* * *
192872 AGTAAATTATTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACGCTGTGAAATAGTAT
1 AGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
192936 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
192963 AGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
193028 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
193055 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
193092 AATACCCTGA
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 29 0.23
92 62 0.50
93 33 0.27
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (92 bp):
AGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:193225 original size:14 final size:14
Alignment explanation
Indices: 193206--193262 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
193196 CGAAACTTAA
193206 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
193220 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
193239 AATCGCAACGACAG
1 AATCGCAACGAGAG
193253 AATCGCAACG
1 AATCGCAACG
193263 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:193244 original size:19 final size:18
Alignment explanation
Indices: 193220--193310 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 18
193210 GCAACGAGAG
193220 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
193239 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
193253 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
193272 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
**
193286 AATCGCAACGCGAACCAA
1 AATCGCAACGCGAAAGAA
193304 AATCGCA
1 AATCGCA
193311 TTGCAATTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 10 0.17
19 16 0.27
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:193246 original size:33 final size:33
Alignment explanation
Indices: 193188--193310 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
193178 TAGTTTACTT
* * *
193188 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
193222 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
* *
193255 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
193288 TCGCAACGCG-AACCAAAATCGCA
1 TCGCAACGCGAAATCAAAATCGCA
193311 TTGCAATTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 13 0.16
33 58 0.70
34 12 0.14
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:193288 original size:14 final size:14
Alignment explanation
Indices: 193237--193295 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
193227 ACGCGAAATG
193237 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
193251 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
193270 AAAATCGCAACGAC
1 AAAATCGCAACGAC
193284 AAAATCGCAACG
1 AAAATCGCAACG
193296 CGAACCAAAA
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:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:193341 original size:19 final size:19
Alignment explanation
Indices: 193317--193463 Score: 160
Period size: 19 Copynumber: 7.9 Consensus size: 19
193307 CGCATTGCAA
193317 TTTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
*
193336 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCGTTGCGAT
*
193354 -TTC-TGT--CGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
193369 TTTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
**
193388 TTTGGTTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
** *
193407 TTTGGTTTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
*
193426 TCTCATTTCGCGTTGCGAT
1 TTTCATTTCGCGTTGCGAT
* *
193445 TTTAAGTTTCGTGTTGCGA
1 TTTCA-TTTCGCGTTGCGA
193464 AAGTAACTAT
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
14 7 0.06
16 5 0.05
17 5 0.05
19 79 0.73
20 12 0.11
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TTTCATTTCGCGTTGCGAT
Found at i:193378 original size:52 final size:54
Alignment explanation
Indices: 193317--193447 Score: 176
Period size: 52 Copynumber: 2.4 Consensus size: 54
193307 CGCATTGCAA
193317 TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCGTTGCGAT
** * *
193369 TTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGG--T-TCGTTGCGAT
*
193426 TCTCATTTCGCGTTGCGATTTT
1 TTTCATTTCGCGTTGCGATTTT
193448 AAGTTTCGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
52 37 0.54
53 1 0.01
57 31 0.45
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (54 bp):
TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCGTTGCGAT
Found at i:195565 original size:20 final size:19
Alignment explanation
Indices: 195531--195606 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 19
195521 ATCGCAATGC
195531 TTTTCATTTCGCATTGCGA
1 TTTTCATTTCGCATTGCGA
195550 TTTTCATTTCCGCATTGCGA
1 TTTTCATTT-CGCATTGCGA
*
195570 --TTC-TCTCG--TTGCGA
1 TTTTCATTTCGCATTGCGA
*
195584 TTTTCATTTTGCATTGCGA
1 TTTTCATTTCGCATTGCGA
195603 TTTT
1 TTTT
195607 TTGTGTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
14 6 0.12
16 5 0.10
17 5 0.10
18 3 0.06
19 19 0.40
20 10 0.21
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (19 bp):
TTTTCATTTCGCATTGCGA
Found at i:195862 original size:52 final size:53
Alignment explanation
Indices: 195754--195985 Score: 279
Period size: 52 Copynumber: 4.5 Consensus size: 53
195744 ATCGCAATGC
195754 ATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG-TTGCG
1 ATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGATTGCG
*
195807 ATTTTCATTTTGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCG
1 ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGATTGCG
* *
195859 ATTTTCATTTCGCATTGCGATTTTCATTGCG-ATTTTC-ATT-TC-CGCATTGCG
1 ATTTTCATTTCGCATTGCGATTTTCATTTCGCA-TTGCGATTCTCTCG-ATTGCG
* *
195910 A--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-ATTGCG
195961 ATTTTCATTTCCGCATTGCGATTTT
1 ATTTTCATTT-CGCATTGCGATTTT
195986 TCTGTTGGGA
Statistics
Matches: 155, Mismatches: 9, Indels: 26
0.82 0.05 0.14
Matches are distributed among these distances:
46 19 0.12
47 2 0.01
48 6 0.04
49 5 0.03
50 3 0.02
51 20 0.13
52 55 0.35
53 31 0.20
54 2 0.01
55 2 0.01
57 10 0.06
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.47
Consensus pattern (53 bp):
ATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGATTGCG
Found at i:195888 original size:12 final size:12
Alignment explanation
Indices: 195871--195898 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
195861 TTTCATTTCG
195871 CATTGCGATTTT
1 CATTGCGATTTT
195883 CATTGCGATTTT
1 CATTGCGATTTT
195895 CATT
1 CATT
195899 TCCGCATTGC
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:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (12 bp):
CATTGCGATTTT
Found at i:195999 original size:71 final size:70
Alignment explanation
Indices: 195802--196016 Score: 327
Period size: 71 Copynumber: 3.1 Consensus size: 70
195792 GATTCTCTCG
195802 TTGCGATTTTCATTTTGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTGCGA-TTTCA-TTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA
195866 TTTCGCA
64 TTTCGCA
195873 TTGCGA--T--TTT-CATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TTGCGATTTCATTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
195933 TCGCA
66 TCGCA
* *
195938 TTGCGATTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-TTTCTGTTGGGATTTTCA
1 TTGCGATTTCATTT-GCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCGATTTTCA
196002 TTTCGCA
64 TTTCGCA
196009 TTGCGATT
1 TTGCGATT
196017 CTCTCGTTGC
Statistics
Matches: 134, Mismatches: 2, Indels: 16
0.88 0.01 0.11
Matches are distributed among these distances:
64 17 0.13
65 46 0.34
67 1 0.01
68 1 0.01
69 3 0.02
70 3 0.02
71 63 0.47
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (70 bp):
TTGCGATTTCATTTGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
TCGCA
Found at i:196038 original size:33 final size:33
Alignment explanation
Indices: 195821--196030 Score: 300
Period size: 33 Copynumber: 6.2 Consensus size: 33
195811 TCATTTTGCA
195821 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
195854 TTGCGATTTTCATTTCGCATTGCGATT-T-TCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
195885 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
195919 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG
*
195954 CATTGCGATTTTCATTTCCGCATTGCGATT-TTTCTG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTC-G
*
195990 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
196023 TTGCGATT
1 TTGCGATT
196031 GTAATTTCCG
Statistics
Matches: 161, Mismatches: 6, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
31 17 0.11
32 13 0.08
33 58 0.36
34 37 0.23
35 8 0.05
36 1 0.01
37 17 0.11
38 10 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:196045 original size:53 final size:52
Alignment explanation
Indices: 195885--196049 Score: 167
Period size: 53 Copynumber: 3.1 Consensus size: 52
195875 GCGATTTTCA
* * **
195885 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTGTAATTTCGTG
* * * *
195938 TTGCGA-TTTCATTTCGCATTGCGATT-T-TCATTTCCGCATTGCGATTTTTC-TG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTG-TA-ATTTCGTG
*
195990 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTT-CGTG
196043 TTGCGAT
1 TTGCGAT
196050 AGTCAAATGC
Statistics
Matches: 89, Mismatches: 14, Indels: 18
0.74 0.12 0.15
Matches are distributed among these distances:
49 2 0.02
50 5 0.06
51 18 0.20
52 15 0.17
53 42 0.47
54 5 0.06
55 2 0.02
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCGTG
Found at i:197150 original size:80 final size:79
Alignment explanation
Indices: 197018--197176 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 79
197008 AATCCACTTC
197018 CGATAAGCTTTTACAGCCTTCCATATGTCCATTTGTGCTTTTTTATACCAGCAGACCTTGATTTT
1 CGATAAGCTTTTACAGCCTTCCATATGTCCATTTGTGCTTTTTTATACCAGCAGACCTTGATTTT
197083 AGATTTCTATACAA
66 AGATTTCTATACAA
197097 CGATAAGCTTTTACAGCCTTCCAGTATGTCCATTTGTGCTTTTTTATACCAGCAGACCTTGATTT
1 CGATAAGCTTTTACAGCCTTCCA-TATGTCCATTTGTGCTTTTTTATACCAGCAGACCTTGATTT
197162 TAGATTTCTATACAA
65 TAGATTTCTATACAA
197177 ATGAACACCA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 23 0.29
80 56 0.71
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (79 bp):
CGATAAGCTTTTACAGCCTTCCATATGTCCATTTGTGCTTTTTTATACCAGCAGACCTTGATTTT
AGATTTCTATACAA
Found at i:199136 original size:20 final size:20
Alignment explanation
Indices: 199108--199335 Score: 228
Period size: 20 Copynumber: 11.4 Consensus size: 20
199098 AAATTTCAGT
* * *
199108 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
199128 GTTGCGATTTACGGATAT--C
1 GTTGCGATTTACGGAT-TCGC
* *
199147 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
199167 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
199187 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
199207 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
199227 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
199247 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
199267 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
199287 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
199307 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
199327 GTTGCGATT
1 GTTGCGATT
199336 CTTGAAAATC
Statistics
Matches: 179, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
18 1 0.01
19 16 0.09
20 160 0.89
21 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:199330 original size:60 final size:60
Alignment explanation
Indices: 199108--199335 Score: 253
Period size: 60 Copynumber: 3.8 Consensus size: 60
199098 AAATTTCAGT
* * * * * * *
199108 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
** *
199167 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * * * *
199227 ATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * ** *
199287 GTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTTACGGATACGCGTTGCGATT
199336 CTTGAAAATC
Statistics
Matches: 141, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 34 0.24
60 106 0.75
61 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:199388 original size:21 final size:20
Alignment explanation
Indices: 199303--199400 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
199293 ATTTATGTGT
* *
199303 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
199323 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
199344 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
199365 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
199386 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
199401 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:199396 original size:42 final size:43
Alignment explanation
Indices: 199303--199401 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
199293 ATTTATGTGT
* *
199303 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
199344 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
199386 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
199402 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:200278 original size:30 final size:30
Alignment explanation
Indices: 200242--200351 Score: 103
Period size: 30 Copynumber: 4.0 Consensus size: 30
200232 CAGTGACCAT
* *
200242 CATAGGTCTCCAGGAGCACATGGCGACCTC
1 CATAGGTCTCCAGGAACACACGGCGACCTC
*
200272 CATAGGTCTCCAGGAACACACGGTGACCT-
1 CATAGGTCTCCAGGAACACACGGCGACCTC
* *
200301 -AT--G-----AGGAGCACATGGCGACCTC
1 CATAGGTCTCCAGGAACACACGGCGACCTC
*
200323 CATAGGTCTCCAGGAACACACGGTGACCT
1 CATAGGTCTCCAGGAACACACGGCGACCT
200352 ATGGAGTGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
21 15 0.24
23 2 0.03
25 1 0.02
26 1 0.02
28 2 0.03
30 41 0.66
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.16
Consensus pattern (30 bp):
CATAGGTCTCCAGGAACACACGGCGACCTC
Found at i:200313 original size:51 final size:51
Alignment explanation
Indices: 200253--200354 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
200243 ATAGGTCTCC
200253 AGGAGCACATGGCGACCTCCATAGGTCTCCAGGAACACACGGTGACCTATG
1 AGGAGCACATGGCGACCTCCATAGGTCTCCAGGAACACACGGTGACCTATG
200304 AGGAGCACATGGCGACCTCCATAGGTCTCCAGGAACACACGGTGACCTATG
1 AGGAGCACATGGCGACCTCCATAGGTCTCCAGGAACACACGGTGACCTATG
200355 GAGTGTTGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (51 bp):
AGGAGCACATGGCGACCTCCATAGGTCTCCAGGAACACACGGTGACCTATG
Found at i:203199 original size:2 final size:2
Alignment explanation
Indices: 203192--203278 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
203182 CCGCCCCGAT
* * *
203192 TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA T- TT TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
203230 TA -A T- TA TA TA TA TA -A TA TA -A TA TA TA -A TT TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
203266 TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA
203279 ATCTTCGGGT
Statistics
Matches: 70, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
1 11 0.16
2 59 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:203239 original size:36 final size:35
Alignment explanation
Indices: 203191--203280 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 35
203181 CCCGCCCCGA
* *
203191 TTATA-TATATATATATATAATAT--TTTATATTTT
1 TTATATTA-ATATATATATAATATAATATATAATTT
203224 TTATATTAATTATATATATAATATAATATATAATTT
1 TTATATTAA-TATATATATAATATAATATATAATTT
203260 TTATATTAATATATATATAAT
1 TTATATTAATATATATATAAT
203281 CTTCGGGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
33 6 0.12
34 16 0.31
35 12 0.24
36 17 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATATTAATATATATATAATATAATATATAATTT
Found at i:203253 original size:25 final size:25
Alignment explanation
Indices: 203197--203278 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 25
203187 CCGATTATAT
*
203197 ATATATATATATAATATTTTATATT-
1 ATATATATATATAAT-TTATATATTA
*
203222 -T-TTTATAT-TAA-TTATATATATA
1 ATATATATATATAATTTATATAT-TA
*
203244 ATATA-ATATATAATTTTTATATTA
1 ATATATATATATAATTTATATATTA
203268 ATATATATATA
1 ATATATATATA
203279 ATCTTCGGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
20 7 0.15
21 1 0.02
22 3 0.07
23 11 0.24
24 12 0.26
25 12 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATATATATAATTTATATATTA
Found at i:204989 original size:31 final size:31
Alignment explanation
Indices: 204951--205044 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
204941 TCCCGAAGAC
* * *
204951 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAAAACATAGGTAAA
*
204982 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAAAACATAGGTAAA
*
205013 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAAAACATAGGTAAA
205044 C
1 C
205045 CATATGTCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAAAACATAGGTAAA
Found at i:205995 original size:22 final size:21
Alignment explanation
Indices: 205970--206029 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
205960 TTCGCTTGAG
*
205970 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
205992 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
206012 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
206030 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:206656 original size:8 final size:8
Alignment explanation
Indices: 206644--206680 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
206634 AAATCATTGA
*
206644 ACTTTTCA
1 ACTTTTCC
206652 ACTTTTCC
1 ACTTTTCC
206660 ACTTTTCC
1 ACTTTTCC
206668 ACTTTTCC
1 ACTTTTCC
206676 ACTTT
1 ACTTT
206681 AATCACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.51
Consensus pattern (8 bp):
ACTTTTCC
Found at i:221948 original size:111 final size:111
Alignment explanation
Indices: 221747--222074 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
221737 TGGAAATCAT
*
221747 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAA-TTAA-TT-AA--ATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
221807 TATTTAGTTGATTTATTTAATGCATTATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
** *
221853 ATATCTCGACTTTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
221918 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
221964 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
222029 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
222075 TTTTTTGTAA
Statistics
Matches: 207, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
106 40 0.19
107 4 0.02
108 2 0.01
109 2 0.01
111 159 0.77
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
Found at i:223605 original size:18 final size:18
Alignment explanation
Indices: 223582--223616 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
223572 GCAGCCACCT
223582 CAGCCATATATGATGCCG
1 CAGCCATATATGATGCCG
223600 CAGCCATATATGATGCC
1 CAGCCATATATGATGCC
223617 ATCATAGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (18 bp):
CAGCCATATATGATGCCG
Found at i:223679 original size:27 final size:27
Alignment explanation
Indices: 223623--223679 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
223613 TGCCATCATA
* * *
223623 GCCTTTCCATTACCATATGCCGCCATC
1 GCCTTTCAATTACCAGATGCCGCCACC
* *
223650 GCCTTTCAATTACCAGATGCTGCCGCC
1 GCCTTTCAATTACCAGATGCCGCCACC
223677 GCC
1 GCC
223680 GTCTTCACCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.40, G:0.16, T:0.26
Consensus pattern (27 bp):
GCCTTTCAATTACCAGATGCCGCCACC
Found at i:223992 original size:3 final size:3
Alignment explanation
Indices: 223984--224057 Score: 58
Period size: 3 Copynumber: 24.7 Consensus size: 3
223974 ACCTGCTCAG
* * * * **
223984 GAC GAC GAC GAT GAC GAT GAC GAC GAT GAC GAT GGT GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
* ** *
224032 GAC GAT GGT GAC GAC GAC AAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
224058 TGATGATGAC
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.23, G:0.35, T:0.09
Consensus pattern (3 bp):
GAC
Found at i:224008 original size:9 final size:9
Alignment explanation
Indices: 223984--224038 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
223974 ACCTGCTCAG
*
223984 GACGACGAC
1 GACGACGAT
*
223993 GATGACGAT
1 GACGACGAT
224002 GACGACGAT
1 GACGACGAT
* *
224011 GACGATGGT
1 GACGACGAT
*
224020 GACGACGAC
1 GACGACGAT
224029 GACGACGAT
1 GACGACGAT
224038 G
1 G
224039 GTGACGACGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:224014 original size:21 final size:21
Alignment explanation
Indices: 223984--224063 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
223974 ACCTGCTCAG
* *
223984 GACGACGACGATGACGATGAC
1 GACGACGACGATGATGACGAC
* *
224005 GACGATGACGATGGTGACGAC
1 GACGACGACGATGATGACGAC
*
224026 GACGACGACGATGGTGACGAC
1 GACGACGACGATGATGACGAC
*
224047 GACAACGACGATGATGA
1 GACGACGACGATGATGA
224064 TGACAGCGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.35, T:0.11
Consensus pattern (21 bp):
GACGACGACGATGATGACGAC
Found at i:225981 original size:18 final size:18
Alignment explanation
Indices: 225958--225994 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
225948 ACCAACCTGG
225958 AAGTTCGTTGTAAGATGC
1 AAGTTCGTTGTAAGATGC
225976 AAGTTCGTTGTAAGATGC
1 AAGTTCGTTGTAAGATGC
225994 A
1 A
225995 TCTCATTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
AAGTTCGTTGTAAGATGC
Found at i:228035 original size:50 final size:51
Alignment explanation
Indices: 227962--228072 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 51
227952 TAGCGCAGAG
* * *
227962 CAGGGGGCGCGCTATACCCCACGT-GTAACCCAGTCAGCATATAGCGCGGTA
1 CAGGGGGCGCGCTATACCCCACGTGGT-ACCAAATCAGCATATAACGCGGTA
* * *
228013 CAGGGGG-GCGCTATACTCCACGTGGTGCCAAATCAGCATATAACGCGGTT
1 CAGGGGGCGCGCTATACCCCACGTGGTACCAAATCAGCATATAACGCGGTA
228063 CAGGGGGCGC
1 CAGGGGGCGC
228073 ACTTTACTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 41 0.79
51 11 0.21
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACCCCACGTGGTACCAAATCAGCATATAACGCGGTA
Found at i:228410 original size:19 final size:19
Alignment explanation
Indices: 228386--228422 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
228376 ATAACCAACA
* *
228386 AAATCGCAATGCGATCTCT
1 AAATCGAAACGCGATCTCT
228405 AAATCGAAACGCGATCTC
1 AAATCGAAACGCGATCTC
228423 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGAAACGCGATCTCT
Found at i:228499 original size:21 final size:21
Alignment explanation
Indices: 228459--228499 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
228449 CGCAATGCGA
* *
228459 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTACAAAATCGCG
*
228480 TTGCGATTTTATAAAATCGC
1 TTGCGATTTTACAAAATCGC
228500 AATGCGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTACAAAATCGCG
Found at i:228505 original size:21 final size:20
Alignment explanation
Indices: 228481--228528 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
228471 AAATTCGCGT
*
228481 TGCGATTTTATAAAATCGCAA
1 TGCGATTATAT-AAATCGCAA
* *
228502 TGCGAATATGTAAATCGCAA
1 TGCGATTATATAAATCGCAA
*
228522 CGCGATT
1 TGCGATT
228529 CTGACTATCG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
TGCGATTATATAAATCGCAA
Found at i:228538 original size:20 final size:20
Alignment explanation
Indices: 228515--228587 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
228505 GAATATGTAA
228515 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
228535 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
228555 ATTGCAACGCGATTCTGTCT
1 ATCGCAACGCGATTCTGACT
228575 ATCGCAACGCGAT
1 ATCGCAACGCGAT
228588 AATACATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:228540 original size:40 final size:40
Alignment explanation
Indices: 228495--228586 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
228485 ATTTTATAAA
*
228495 ATCGCAATGCGAATATGTA-AATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATG-ACAATCGCAACGCGATTCTGACT
* * * *
228535 ATCGCAACGCGATTATGACTATTGCAACGCGATTCTGTCT
1 ATCGCAACGCGAATATGACAATCGCAACGCGATTCTGACT
228575 ATCGCAACGCGA
1 ATCGCAACGCGA
228587 TAATACATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGATTCTGACT
Found at i:228778 original size:22 final size:22
Alignment explanation
Indices: 228753--228803 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
228743 CTACGGCATC
*
228753 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACAAA
*
228775 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
228797 ATCCGTC
1 ATCCGTC
228804 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:229269 original size:20 final size:20
Alignment explanation
Indices: 229244--229314 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
229234 CATTTCGCGC
229244 TGCGATAGTCAAATTCACGT
1 TGCGATAGTCAAATTCACGT
229264 TGCGATAGTCAAATTCACGT
1 TGCGATAGTCAAATTCACGT
*
229284 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCAAATTCACGT
229304 TGCGATAGTCA
1 TGCGATAGTCA
229315 TTTTTGTGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
TGCGATAGTCAAATTCACGT
Found at i:229325 original size:20 final size:20
Alignment explanation
Indices: 229262--229349 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
229252 TCAAATTCAC
** **
229262 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
** *
229282 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
*
229302 GTTGCGATAGTCATTTTTGT
1 GTTGCGATAGTCATTTTCGT
**
229322 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
229342 GTTACGAT
1 GTTGCGAT
229350 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:229359 original size:20 final size:20
Alignment explanation
Indices: 229320--229359 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
229310 AGTCATTTTT
* * *
229320 GTGTTGCGATTTTCATTTTC
1 GTGTTACGATTTTAAGTTTC
229340 GTGTTACGATTTTAAGTTTC
1 GTGTTACGATTTTAAGTTTC
229360 AGAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (20 bp):
GTGTTACGATTTTAAGTTTC
Found at i:231212 original size:20 final size:20
Alignment explanation
Indices: 231189--231257 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
231179 GAAACTTAAA
231189 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
231209 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
231229 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
231249 ATCGCAACG
1 ATCGCAACG
231258 AGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:231299 original size:33 final size:34
Alignment explanation
Indices: 231249--231324 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
231239 GAATTTGACT
*
231249 ATCGCAACGAGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
* * *
231282 ATCGCAACGTGAAAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
231316 ATCGCAACG
1 ATCGCAACG
231325 CGGATTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:231356 original size:19 final size:20
Alignment explanation
Indices: 231329--231367 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
231319 GCAACGCGGA
*
231329 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
231349 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
231368 ATCTTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:231398 original size:20 final size:20
Alignment explanation
Indices: 231373--231440 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
231363 CGATTATCTT
231373 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
231393 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAAATT-CGC
231413 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
231433 GTTGCGAT
1 GTTGCGAT
231441 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:231398 original size:34 final size:37
Alignment explanation
Indices: 231354--231441 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 37
231344 CGATTTTTAT
*
231354 TTCGCATTGCGATTA-TC-TT-GTTGCGATAGTCAAA
1 TTCGCGTTGCGATTAGTCATTCGTTGCGATAGTCAAA
231388 TTCGCGTTGCGA-TAGTCATTTCCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTAGTCA-TT---CGTTGCGATAGTCAAA
231428 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
231442 TTAAGTTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
33 2 0.04
34 13 0.29
36 2 0.04
40 27 0.60
41 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (37 bp):
TTCGCGTTGCGATTAGTCATTCGTTGCGATAGTCAAA
Found at i:231451 original size:20 final size:20
Alignment explanation
Indices: 231428--231469 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
231418 GATAGTCAAA
231428 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
231448 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
231468 TT
1 TT
231470 TAGAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:231457 original size:40 final size:40
Alignment explanation
Indices: 231372--231460 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
231362 GCGATTATCT
*
231372 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
* **
231412 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTAAGTTT-CG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAA-TTTCCG
231452 TGTTGCGAT
1 TGTTGCGAT
231461 TTTAAGTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 40 0.93
41 3 0.07
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
Found at i:231977 original size:21 final size:21
Alignment explanation
Indices: 231951--232026 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
231941 CTCACCTGTA
*
231951 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
231972 ATCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
** * *
231992 CATCCCTCAAGAGTCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
232014 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
232027 TCACTGTCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:232046 original size:42 final size:42
Alignment explanation
Indices: 231946--232067 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
231936 CTCGACTCAC
* * * *
231946 CTGTAATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCA
* ** * *
231988 CTATCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGTCA
1 CTGTCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCA
* ** * *
232030 CTGTCATCGTTGAAGAGGTTCCTCCCACCATTCAAGAG
1 CTGTCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAG
232068 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCA
Found at i:233618 original size:20 final size:20
Alignment explanation
Indices: 233593--233670 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
233583 AGGTACACTT
*
233593 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
233613 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
233633 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
* * *
233653 TCACAACGTGAAAGTCAA
1 TCGCAACGCGAAACTCAA
233671 TTCGCGTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:233637 original size:40 final size:40
Alignment explanation
Indices: 233593--233670 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
233583 AGGTACACTT
* * *
233593 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCACAACGCGAAAGTCAAAA
* *
233633 TCGCAATGCGAAAGCCAAAATCACAACGTGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCACAACGCGAAAGTCAA
233671 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCACAACGCGAAAGTCAAAA
Found at i:233736 original size:20 final size:20
Alignment explanation
Indices: 233709--233845 Score: 211
Period size: 20 Copynumber: 6.8 Consensus size: 20
233699 GCAATTTTCT
* *
233709 CGTTGCGATAGTCAACTTCC
1 CGTTGCGATAGTCAAATTCG
* * *
233729 CATTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
233749 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
233769 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
233789 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
233809 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
233829 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
233846 GAATGTGTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 109 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:234068 original size:140 final size:140
Alignment explanation
Indices: 233816--234098 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
233806 TCGCGTTGCG
*
233816 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
*
233881 TAGCAATGTTCAAAATCAAGTTACTAATGCATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
233946 AATACACATA
131 AATACACATA
233956 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
*
234021 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
234086 AATACACATA
131 AATACACATA
234096 ATA
1 ATA
234099 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:235414 original size:17 final size:16
Alignment explanation
Indices: 235380--235409 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
235370 CCAGATATTT
235380 GGATATCCGAATTTTC
1 GGATATCCGAATTTTC
235396 GGATATCCG-ATTTT
1 GGATATCCGAATTTT
235410 TTCGGTTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (16 bp):
GGATATCCGAATTTTC
Found at i:237644 original size:24 final size:24
Alignment explanation
Indices: 237610--237663 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
237600 CTGAAACATC
*
237610 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
237634 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
237658 ATCAAA
1 ATCAAA
237664 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:237677 original size:24 final size:24
Alignment explanation
Indices: 237610--237677 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
237600 CTGAAACATC
* * *
237610 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
237634 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
237658 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
237678 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:238553 original size:21 final size:21
Alignment explanation
Indices: 238523--238573 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
238513 GTCAGAATCA
238523 AGTTGCGATTATGTATTATCG
1 AGTTGCGATTATGTATTATCG
*
238544 AGTTGTGATTATGTATTATCG
1 AGTTGCGATTATGTATTATCG
*
238565 CGTTGCGAT
1 AGTTGCGAT
238574 AGTCAGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (21 bp):
AGTTGCGATTATGTATTATCG
Found at i:238586 original size:20 final size:20
Alignment explanation
Indices: 238482--238632 Score: 110
Period size: 20 Copynumber: 7.5 Consensus size: 20
238472 TTGAAATTCA
*
238482 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
238502 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
** **
238522 AAGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
* * **
238543 GAGTTGTGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
238564 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* * *
238584 GCGTTGCGAT-TTACATATTC
1 GCGTTGCGATAGT-CAGAATC
* *
238604 GCATTGCGATAGTCAAAATC
1 GCGTTGCGATAGTCAGAATC
238624 GCGTTGCGA
1 GCGTTGCGA
238633 ATCTGGAAAC
Statistics
Matches: 107, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.03
20 69 0.64
21 33 0.31
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:249938 original size:2 final size:2
Alignment explanation
Indices: 249931--249968 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
249921 TTTAAAGTGA
249931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249969 TAGTAAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254005 original size:31 final size:31
Alignment explanation
Indices: 253968--254047 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
253958 TTCGATAATA
*
253968 TAATAATTATTTTATAGTATTTAAATAAATT
1 TAATAATTATTTTATAATATTTAAATAAATT
* * *
253999 TAATAATAATTTTATAATCTTTTAATAAATT
1 TAATAATTATTTTATAATATTTAAATAAATT
*
254030 TAATAAGTATTTTATAAT
1 TAATAATTATTTTATAAT
254048 TTTTTAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (31 bp):
TAATAATTATTTTATAATATTTAAATAAATT
Found at i:254041 original size:11 final size:10
Alignment explanation
Indices: 253968--254047 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
253958 TTCGATAATA
253968 TAATAATTATT
1 TAATAA-TATT
* *
253979 TTATAGTATT
1 TAATAATATT
253989 TAAATAA-ATT
1 T-AATAATATT
253999 TAATAATAATT
1 TAATAAT-ATT
* *
254010 TTATAATCTTT
1 TAATAAT-ATT
254021 TAATAA-ATT
1 TAATAATATT
254030 TAATAAGTATT
1 TAATAA-TATT
*
254041 TTATAAT
1 TAATAAT
254048 TTTTTAAACT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
9 13 0.24
10 10 0.19
11 31 0.57
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (10 bp):
TAATAATATT
Found at i:257054 original size:201 final size:203
Alignment explanation
Indices: 256706--257116 Score: 783
Period size: 201 Copynumber: 2.0 Consensus size: 203
256696 TTACTCTTTA
256706 GACTTTTGGGATGCTCTTCTATGTTTCTTAGCTATGTGGGATTGTTTTTTTAAAAAAAAAATTAA
1 GACTTTTGGGATGCTCTTCTATGTTTCTTAGCTATGTGGGATTGTTTTTTT-AAAAAAAAATTAA
256771 ACCAAACAATATCATTTTGTTATGATTTTTTTAGCCCCAAATTTATTTTTTAATTATAGTTATAT
65 ACCAAACAATATCATTTTGTTATGATTTTTTTAGCCCCAAATTTATTTTTTAATTATAGTTATAT
256836 AATTATATTTATTATTTAATATGTTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTT
130 AATTATATTTATTATTTAATATGTTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTT
256901 GTTTCACTT
195 GTTTCACTT
256910 GACTTTTGGGATGCTCTTCTATGTTTCTTAGCTATGTGGGATTGTTTTTTT-AAAAAAAATTAAA
1 GACTTTTGGGATGCTCTTCTATGTTTCTTAGCTATGTGGGATTGTTTTTTTAAAAAAAAATTAAA
*
256974 CCAAATAATATCATTTTGTTATGA-TTTTTTAGCCCCAAATTTATTTTTTAATTATAGTTATATA
66 CCAAACAATATCATTTTGTTATGATTTTTTTAGCCCCAAATTTATTTTTTAATTATAGTTATATA
257038 ATTATATTTATTATTTAATATGTTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTTG
131 ATTATATTTATTATTTAATATGTTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTTG
257103 TTTCACTT
196 TTTCACTT
257111 GA-TTTT
1 GACTTTT
257117 ATGGTTTTTA
Statistics
Matches: 206, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
200 4 0.02
201 115 0.56
202 36 0.17
204 51 0.25
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (203 bp):
GACTTTTGGGATGCTCTTCTATGTTTCTTAGCTATGTGGGATTGTTTTTTTAAAAAAAAATTAAA
CCAAACAATATCATTTTGTTATGATTTTTTTAGCCCCAAATTTATTTTTTAATTATAGTTATATA
ATTATATTTATTATTTAATATGTTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTTG
TTTCACTT
Found at i:258068 original size:41 final size:41
Alignment explanation
Indices: 257923--258303 Score: 355
Period size: 41 Copynumber: 9.3 Consensus size: 41
257913 ATACTTGTGT
* * ** *
257923 TTTAGTGGCGTTTGTATATAAACGCCGCTACCTACT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
** * **
257963 TTTAGTGGCGTTTTCGTATAAACGCCGCTAAATAAT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
** * *
258003 AATAGTGGCGTTTTAAGCACAAACGCCGCTAAATGCTCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATGCTCGTAC
* * **
258045 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATAAT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
* * * *
258085 TATAGTGACGTTTTAAGCACAAACGCCGCTAAATGCTCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATGCTCGTAC
* *
258127 TTTAGTGGCGTTTTTGTACAAACGCCGCCAAA-GACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
* * *
258168 TTTAGCGACGTTTTTATACAAACGCCGCCAAA-GAC-CTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTC-GTAC
* *
258209 TTTAGTGGCGTTTTTATACAAACGCCGCCAAA-GACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
* * *
258250 TTTAGTGGCGTTTTTATGCAAACGCCGCCAAA-GACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
258291 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
258304 CTGCGGCTAA
Statistics
Matches: 292, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
40 64 0.22
41 195 0.67
42 33 0.11
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
Found at i:258180 original size:123 final size:122
Alignment explanation
Indices: 257923--258305 Score: 441
Period size: 123 Copynumber: 3.1 Consensus size: 122
257913 ATACTTGTGT
* ** * *
257923 TTTAGTGGCGTTTGTATATAAACGCCGCTACCTACTGTACTTTAGTGGCGTTTTCGTATAAACGC
1 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTAGTACAAACGC
** ** * * *
257988 CGCTAAATAAT-GTACAATAGTGGCGTTTTAAGCACAAACGCCGCTAAATG-CTCGTAC
66 CGCTAAATGCTCGTACTTTAGTGGCGTTTT-TGTACAAACGCCGCCAAA-GACTCGTAC
* * * *
258045 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATAATGTACTATAGTGACGTTTTAAGCACAAACG
1 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTT-AGTACAAACG
258110 CCGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTAC
65 CCGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTAC
* * * * * *
258168 TTTAGCGACGTTTTTATACAAACGCCGCCAAAGACCTGTACTTTAGTGGCGTTTTTA-TACAAAC
1 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATA-CTGTACTTTAGTGGCG-TTTTAGTACAAAC
* * * * *
258232 GCCGCCAAA-GACCCGTACTTTAGTGGCGTTTTTATGCAAACGCCGCCAAAGACCCGTAC
64 GCCGCTAAATG-CTCGTACTTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTAC
258291 TTTAGTGGCGTTTCT
1 TTTAGTGGCGTTTCT
258306 GCGGCTAAAC
Statistics
Matches: 221, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
122 50 0.23
123 137 0.62
124 30 0.14
125 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (122 bp):
TTTAGTGGCGTTTCTATATAAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTAGTACAAACGC
CGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTAC
Found at i:258331 original size:41 final size:41
Alignment explanation
Indices: 258122--258331 Score: 194
Period size: 41 Copynumber: 5.1 Consensus size: 41
258112 GCTAAATGCT
* *
258122 CGTACTTTAGTGGCGTTTTTGTA--CAAACGCCGCCAAAGACT
1 CGTACTTTAGTGGCG-TTTTG-AGGCAAACGCCCCCAAAGACC
* * * ** *
258163 CGTACTTTAGCGACGTTTTTATACAAACGCCGCCAAAGACC
1 CGTACTTTAGTGGCGTTTTGAGGCAAACGCCCCCAAAGACC
* * ** *
258204 TGTACTTTAGTGGCGTTTTTATACAAACGCCGCCAAAGACC
1 CGTACTTTAGTGGCGTTTTGAGGCAAACGCCCCCAAAGACC
* * *
258245 CGTACTTTAGTGGCGTTTTTATGCAAACGCCGCCAAAGACC
1 CGTACTTTAGTGGCGTTTTGAGGCAAACGCCCCCAAAGACC
* *
258286 CGTACTTTAGTGGCGTTTCTGCGGCTAAAC-CCCCCAAA-ACA
1 CGTACTTTAGTGGCGTTT-TGAGGC-AAACGCCCCCAAAGACC
258327 CGTAC
1 CGTAC
258332 GCACTTGAAT
Statistics
Matches: 151, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 4 0.03
41 132 0.87
42 10 0.07
43 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (41 bp):
CGTACTTTAGTGGCGTTTTGAGGCAAACGCCCCCAAAGACC
Found at i:259321 original size:2 final size:2
Alignment explanation
Indices: 259314--259352 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
259304 CTTCCTGTTG
* *
259314 TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC CC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
259353 TTTTAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:262364 original size:26 final size:26
Alignment explanation
Indices: 262328--262381 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
262318 TGTATCTTGT
262328 TTCCCTGCATTTTGTGATTTTAATCA
1 TTCCCTGCATTTTGTGATTTTAATCA
262354 TTCCCTGCATTTTGTGATTTTAATCA
1 TTCCCTGCATTTTGTGATTTTAATCA
262380 TT
1 TT
262382 AATTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (26 bp):
TTCCCTGCATTTTGTGATTTTAATCA
Found at i:263276 original size:43 final size:42
Alignment explanation
Indices: 263228--263751 Score: 647
Period size: 43 Copynumber: 12.2 Consensus size: 42
263218 GAATGGTAAT
* *
263228 TATAGATCTGACTTTTTGCGGCGTTTGTGTCCAAAAACGTCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
263271 TATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
263314 TATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * **
263357 TATAGATCCGTA-CTTTTGCAGCGTTTGTATATAAAAACGCCGC
1 TATAGATCTG-ACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * *
263400 TAAATATCTAACCTTTTGCGGCGTTTGTGTCCAAAAACGCCAC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * *
263443 TATAGATCTGTCCTTTTGCAGCATTTGTATCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
263486 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
263528 TATAGATCTTGACCTTTTGCGGCATTTGTATCCAAAAACGCCGC
1 TATAGATC-TGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
263572 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
263614 TATAGATCTCGACCTTTTGCGGCATTTGTTCCATAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
263657 TAGAGATCTTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
1 TATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
263700 TGTATATATC-GACCTTTTGCGACGTTTGTTCCAAAAACGCCGC
1 --TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
263743 TATAGATCT
1 TATAGATCT
263752 TGAACTATAG
Statistics
Matches: 412, Mismatches: 60, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
41 7 0.02
42 40 0.10
43 338 0.82
44 21 0.05
45 6 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
Found at i:265786 original size:15 final size:15
Alignment explanation
Indices: 265766--265851 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
265756 ATTTTATTGG
*
265766 TATGTGAAAATGTTA
1 TATGTGAAAATGTTC
* *
265781 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
*
265796 TATATGAAAATGTTC
1 TATGTGAAAATGTTC
* *
265811 TATTTGAAAATGTGC
1 TATGTGAAAATGTTC
* *
265826 TAAGTGAAAACGTTC
1 TATGTGAAAATGTTC
*
265841 TACGTGAAAAT
1 TATGTGAAAAT
265852 ACCTTATGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 58 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:266040 original size:24 final size:24
Alignment explanation
Indices: 265982--266050 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
265972 GAGTCGAGGG
* *
265982 TTCTATGCGGTCCTTTGGGAC-AA
1 TTCTAAGCGGTCCTTCGGGACAAA
* * *
266005 CTCTACGTGGTCCTTCGGGACAAA
1 TTCTAAGCGGTCCTTCGGGACAAA
266029 TTCTAAGCGGTCCTTCGGGACA
1 TTCTAAGCGGTCCTTCGGGACA
266051 TATATATGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (24 bp):
TTCTAAGCGGTCCTTCGGGACAAA
Found at i:268749 original size:31 final size:31
Alignment explanation
Indices: 268677--268768 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
268667 TATGTCTTTT
* * *
268677 GGGACATATGGACAGTATACCTATGTTCTAA
1 GGGACATATGGACAGTTTACCTAGGTTCTTA
* * *
268708 TGAACATATGGACAGTTTACCTAGGTTCTTC
1 GGGACATATGGACAGTTTACCTAGGTTCTTA
* *
268739 GGGACCTATGGACAGATTACCTAGGTTCTT
1 GGGACATATGGACAGTTTACCTAGGTTCTT
268769 TATGAAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (31 bp):
GGGACATATGGACAGTTTACCTAGGTTCTTA
Found at i:269948 original size:13 final size:13
Alignment explanation
Indices: 269932--269966 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
269922 CTTAATTTTT
269932 TTATATTTTTAAA
1 TTATATTTTTAAA
269945 TTATATTTTTAAA
1 TTATATTTTTAAA
*
269958 ATATATTTT
1 TTATATTTT
269967 ATGAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTTTTAAA
Found at i:274425 original size:30 final size:31
Alignment explanation
Indices: 274389--274461 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
274379 ACATTCATAG
274389 CACATGTTCATATAAGCTCATA-A-CTTC-TTT
1 CACATGTTCATATAA--TCATATAGCTTCTTTT
* *
274419 CACATGTACATGTAATCATATAGCTTCTTTT
1 CACATGTTCATATAATCATATAGCTTCTTTT
274450 CACATAGTTCAT
1 CACAT-GTTCAT
274462 GTCACTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 1 0.03
30 17 0.47
31 8 0.22
32 5 0.14
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (31 bp):
CACATGTTCATATAATCATATAGCTTCTTTT
Found at i:275972 original size:2 final size:2
Alignment explanation
Indices: 275965--275990 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
275955 GTTTAATGCA
275965 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
275991 CTAAGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277089 original size:15 final size:15
Alignment explanation
Indices: 277069--277098 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
277059 ATTGGATGGT
277069 AGTGATAATTAGTTA
1 AGTGATAATTAGTTA
277084 AGTGATAATTAGTTA
1 AGTGATAATTAGTTA
277099 GGTGTGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
AGTGATAATTAGTTA
Found at i:284766 original size:13 final size:13
Alignment explanation
Indices: 284748--284773 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284738 GTTTGAGTTG
284748 CCCTGAATGAGAA
1 CCCTGAATGAGAA
284761 CCCTGAATGAGAA
1 CCCTGAATGAGAA
284774 AGTACTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
CCCTGAATGAGAA
Found at i:295279 original size:20 final size:20
Alignment explanation
Indices: 295233--295273 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
295223 TATAGTATGA
*
295233 AATAAAATAAAAAATTATTT
1 AATAAAATAAAAAATAATTT
*
295253 AATAAAATAACAAATAATTT
1 AATAAAATAAAAAATAATTT
295273 A
1 A
295274 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAATAAAAAATAATTT
Found at i:312566 original size:20 final size:19
Alignment explanation
Indices: 312529--312601 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
312519 AAGAGGTAAC
**
312529 TAATATGACAAATTTGGTTGG
1 TAAT-TGACAAAACTGGTT-G
312550 TAATTGACAAAACTGGTTG
1 TAATTGACAAAACTGGTTG
* *
312569 AAATTTGACAAAACTTGTT-
1 TAA-TTGACAAAACTGGTTG
312588 TCAATTTGACAAAA
1 T-AA-TTGACAAAA
312602 TCGATAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 38 0.84
21 4 0.09
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (19 bp):
TAATTGACAAAACTGGTTG
Found at i:313905 original size:21 final size:18
Alignment explanation
Indices: 313883--313927 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
313873 ACCAGAACCT
313883 TCTTCTCAACCAAGGTCA
1 TCTTCTCAACCAAGGTCA
*
313901 TCTTCTCAACCAAGGTCT
1 TCTTCTCAACCAAGGTCA
*
313919 TATTCTCAA
1 TCTTCTCAA
313928 GTAAGGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (18 bp):
TCTTCTCAACCAAGGTCA
Found at i:317538 original size:190 final size:190
Alignment explanation
Indices: 317204--317585 Score: 617
Period size: 190 Copynumber: 2.0 Consensus size: 190
317194 CACTACTTGT
*
317204 TATTTACGACTATTTTCAATATACCGAAACACTTTTATTCGTTTACATTGTTAATTTACCTATTA
1 TATTTACGACTATTTTCAATATACCGAAACACTTTTATCCGTTTACATTGTTAATTTACCTATTA
* * *
317269 CTTTAAAATAATAGGTTTCTAAATTCCATGTATCGATATTTGTTATTTACATGTATAAAGTATTG
66 CTTTAAAATAATAGGTTTCGAAATTCCATGTATCGATACTTGTTATTTACATGTATAAAGTATCG
* * * *
317334 ATATTTAGCTAAATTAATAATGTAAACGGTAAAAGTCTACCAG-TGTAATGAAAATAGGCG
131 ATACTTAACTAAATTAACAATGTAAACGATAAAAGTCTACC-GCTGTAATGAAAATAGGCG
* *
317394 TATTTACGGCTATTTTCATTATACC-ATAACACTTTTATCCGTTTACATTGTTAATTTACCTATT
1 TATTTACGACTATTTTCAATATACCGA-AACACTTTTATCCGTTTACATTGTTAATTTACCTATT
*
317458 ACTTTAAAGTAATAGGTTTCGAAATTCCAAT-TATCGATACTTGTTATTTACATGTATAAAGTAT
65 ACTTTAAAATAATAGGTTTCGAAATTCC-ATGTATCGATACTTGTTATTTACATGTATAAAGTAT
317522 CGATACTTAACTAAATTAACAATGTAAACGATAAAAGTCTACCGCTGTAATGAAAATAGGCG
129 CGATACTTAACTAAATTAACAATGTAAACGATAAAAGTCTACCGCTGTAATGAAAATAGGCG
317584 TA
1 TA
317586 AATAACAAGT
Statistics
Matches: 178, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
189 2 0.01
190 174 0.98
191 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (190 bp):
TATTTACGACTATTTTCAATATACCGAAACACTTTTATCCGTTTACATTGTTAATTTACCTATTA
CTTTAAAATAATAGGTTTCGAAATTCCATGTATCGATACTTGTTATTTACATGTATAAAGTATCG
ATACTTAACTAAATTAACAATGTAAACGATAAAAGTCTACCGCTGTAATGAAAATAGGCG
Found at i:317959 original size:74 final size:77
Alignment explanation
Indices: 317875--318040 Score: 212
Period size: 77 Copynumber: 2.2 Consensus size: 77
317865 CTTAACCGGT
* * *
317875 TAAAATAAAATAGGCCCTACATATTACGTTA-ATTACCTACAAGTTTGT-T-TAAAGGTTACTAA
1 TAAAATAAAATAGGCCCTACATATTACGTTATAATACCTACAAGTTTCTATAAAAAGGTTACTAA
317937 TAATGTAAAAGA
66 TAATGTAAAAGA
* * * ** *
317949 TAAAATAAAATAGGCGCTACCTATTATGTTATAATACCTACTTGTTTCTATAAAAATGTTACTAA
1 TAAAATAAAATAGGCCCTACATATTACGTTATAATACCTACAAGTTTCTATAAAAAGGTTACTAA
* *
318014 TAATGTAAACGG
66 TAATGTAAAAGA
318026 TAAAATAAAATAGGC
1 TAAAATAAAATAGGC
318041 GTAATTGTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 28 0.36
75 13 0.17
76 1 0.01
77 36 0.46
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (77 bp):
TAAAATAAAATAGGCCCTACATATTACGTTATAATACCTACAAGTTTCTATAAAAAGGTTACTAA
TAATGTAAAAGA
Found at i:318705 original size:200 final size:200
Alignment explanation
Indices: 318077--318855 Score: 859
Period size: 199 Copynumber: 3.9 Consensus size: 200
318067 ATGCCCATAC
* * * *
318077 CGATACTTTTATTCCAGTATGGTTCTCAAACAA-TT-TACCCTCAACAAAGAATCGATACCCATA
1 CGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGTA-CGT-AACAAAGTATCGATACACATA
* * *
318140 TATAAAGTATCGATACTGGAAATTTCGAAACCTATTAC--T--AGTAATAGGTAAATTTACAATG
64 TATAAAGTATCAATACTGGTAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATG
** *
318201 AAAATGATAAAAGTATACCGATATAATGATAATAGGCGTAAACATAAAGTATCTATACTTTTTAT
129 AAAACAATAAAAGTATACCGATATAATGATAATAGGCGTAAACATAAAGTATCGATA-TTTTTAT
*
318266 CTCGGTAT
193 ATCGGTAT
* * *
318274 CGATACTTTTATTCTAGTATGCTTATCAAACAATTTG-A-AT-ACAAAAGTATCGATACACATAT
1 CGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGTACGTAAC-AAAGTATCGATACACATAT
* *
318336 ATAAAGTACCAATACTTGG-AATTTCAAAACCTATTACTTTAAAGTAATATGTAAATTTACAATG
65 ATAAAGTATCAATAC-TGGTAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATG
* * * * * * * *
318400 TAAACAATAAAA-TATACTGGTATAATGATAATATGAGTAAACATAAAATATCTATATAATTTAT
129 AAAACAATAAAAGTATACCGATATAATGATAATAGGCGTAAACATAAAGTATCGATAT-TTTTAT
318464 ATCGGTAT
193 ATCGGTAT
* * * *
318472 CGATACTTTTATTCCAATATCCTTCTTAAACAATTTGTACGTAACAAAGTATCAATAC-CTATAT
1 CGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGTACGTAACAAAGTATCGATACAC-ATAT
* * * *
318536 TTAAAGTATCAATACTGGTAATTTCGAAACCTATTACTTTAAAATAATAGGTAAATTTACAATGT
65 ATAAAGTATCAATACTGGTAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGA
*** * *** * *
318601 AAATGGTAAAAGTCTACCGGGGTAACGATAATAGGCGTAAA-TTATAAGTATCGATATGTTTTAT
130 AAACAATAAAAGTATACCGATATAATGATAATAGGCGTAAACATA-AAGTATCGATAT-TTTTAT
*
318665 ATCGATAT
193 ATCGGTAT
* * * * *
318673 CGATATTTTTATT-CAGTATGCTTCTCAAACAATTTGCACGCAA-AACGTATCGATACACATATG
1 CGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGTACGTAACAAAGTATCGATACACATATA
* * ** *
318736 TAAAGTATCGACACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGAA
66 TAAAGTATCAATACTGGTAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAA
* * * * *
318801 AACAATAAAAGTCTACCGATATAATGATAATACGCGTAAATATCAAGTATTGATA
131 AACAATAAAAGTATACCGATATAATGATAATAGGCGTAAACATAAAGTATCGATA
318856 CACATGTATA
Statistics
Matches: 488, Mismatches: 76, Indels: 34
0.82 0.13 0.06
Matches are distributed among these distances:
194 2 0.00
195 47 0.10
196 4 0.01
197 32 0.07
198 86 0.18
199 149 0.31
200 110 0.23
201 58 0.12
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (200 bp):
CGATACTTTTATTCCAGTATGCTTCTCAAACAATTTGTACGTAACAAAGTATCGATACACATATA
TAAAGTATCAATACTGGTAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGAA
AACAATAAAAGTATACCGATATAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTATATC
GGTAT
Found at i:319446 original size:85 final size:85
Alignment explanation
Indices: 319289--319453 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
319279 TAATATTGAT
* * * * *
319289 AACAAATTAAGTAATTAACCTATTTTGTTATCGTCATATTTCTAAGGCCTCGACAGCTTTAAACA
1 AACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGACCTCCACAGCTTTAAAAA
*
319354 GGAGCTACCTATTACATTAA
66 AGAGCTACCTATTACATTAA
* *
319374 AACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGACC-CCATC-GGTTTAAAA
1 AACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGACCTCCA-CAGCTTTAAAA
*
319437 AAGACGCTACTTATTAC
65 AAGA-GCTACCTATTAC
319454 GTTACATAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 12 0.17
85 57 0.83
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (85 bp):
AACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGACCTCCACAGCTTTAAAAA
AGAGCTACCTATTACATTAA
Found at i:322454 original size:17 final size:17
Alignment explanation
Indices: 322432--322465 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
322422 ATCCTGAAAT
322432 GAACTCCTCACTAAGCC
1 GAACTCCTCACTAAGCC
322449 GAACTCCTCACTAAGCC
1 GAACTCCTCACTAAGCC
322466 ACACTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.41, G:0.12, T:0.18
Consensus pattern (17 bp):
GAACTCCTCACTAAGCC
Found at i:330555 original size:3 final size:3
Alignment explanation
Indices: 330542--330660 Score: 202
Period size: 3 Copynumber: 39.7 Consensus size: 3
330532 TTTTTACCCA
* *
330542 TAT TAT AAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
330590 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
330638 TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
330661 AAAATATTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:331109 original size:19 final size:20
Alignment explanation
Indices: 331085--331140 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
331075 CCTGAAAAAA
331085 AAAAGAAAAAACAGAGACC-
1 AAAAGAAAAAACAGAGACCG
*
331104 AAAAGAAGAACACAGAG-CCGG
1 AAAAGAA-AAAACAGAGACC-G
331125 AAAA-AAAAAACAGAGA
1 AAAAGAAAAAACAGAGA
331141 AATAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 17 0.55
20 10 0.32
21 4 0.13
ACGTcount: A:0.66, C:0.14, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAACAGAGACCG
Found at i:332782 original size:15 final size:13
Alignment explanation
Indices: 332762--332799 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
332752 ATGTTTTATT
332762 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
332777 TTATTTTATTTCA
1 TTATTTTATTTCA
332790 TTA-TTTATTT
1 TTATTTTATTT
332800 TACTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:343405 original size:1 final size:1
Alignment explanation
Indices: 343399--343471 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
343389 ATGCTTGAAG
* * * * * * * * * *
343399 AAAAAAAAAGAAGAAGAAAAAAAAAGAAAAAAGAAAAAGAAAGAAAGAAAAAAGAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
343464 AAAAAAAA
1 AAAAAAAA
343472 TGGAGGTCAA
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (1 bp):
A
Found at i:343413 original size:13 final size:13
Alignment explanation
Indices: 343395--343471 Score: 81
Period size: 13 Copynumber: 5.9 Consensus size: 13
343385 TATTATGCTT
343395 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
343408 GAAGAAGAAAAAAA
1 GAAGAA-AAAAAAA
343422 -AAGAAAAAAGAAA
1 GAAGAAAAAA-AAA
343435 -AAGAAAGAAAGAAA
1 GAAGAAA-AAA-AAA
*
343449 AAAG-AAAAAAAA
1 GAAGAAAAAAAAA
343461 GAA-AAAAAAAA
1 GAAGAAAAAAAA
343472 TGGAGGTCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
12 16 0.28
13 23 0.40
14 16 0.28
15 3 0.05
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:343416 original size:16 final size:16
Alignment explanation
Indices: 343396--343470 Score: 93
Period size: 16 Copynumber: 4.8 Consensus size: 16
343386 ATTATGCTTG
*
343396 AAGAAAAAAAAAGAAG
1 AAGAAAAAAAAAGAAA
343412 AAGAAAAAAAAAGAAAA
1 AAGAAAAAAAAAG-AAA
*
343429 AAGAAAAAGAAAG--A
1 AAGAAAAAAAAAGAAA
343443 AAGAAAAAAGAAA-AAA
1 AAGAAAAAA-AAAGAAA
343459 AAGAAAAAAAAA
1 AAGAAAAAAAAA
343471 ATGGAGGTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.17
15 6 0.12
16 23 0.44
17 14 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAGAAA
Found at i:343425 original size:10 final size:10
Alignment explanation
Indices: 343396--343470 Score: 89
Period size: 10 Copynumber: 7.2 Consensus size: 10
343386 ATTATGCTTG
343396 AAGAAAAAAA
1 AAGAAAAAAA
343406 AAGAAGAAGAAA
1 AAGAA-AA-AAA
*
343418 AAAAAAGAAAA
1 AAGAAA-AAAA
*
343429 AAGAAAAAGA
1 AAGAAAAAAA
343439 AAGAAAGAAAA
1 AAGAAA-AAAA
343450 AAG-AAAAAA
1 AAGAAAAAAA
343459 AAGAAAAAAA
1 AAGAAAAAAA
343469 AA
1 AA
343471 ATGGAGGTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.12
10 24 0.43
11 17 0.30
12 8 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:343436 original size:30 final size:31
Alignment explanation
Indices: 343396--343467 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
343386 ATTATGCTTG
343396 AAGAAAAAA-AAAGAAGAAGAAAAAAAAAGAAAA
1 AAGAAAAAAGAAAG-A-AAGAAAAAAAAA-AAAA
*
343429 AAG-AAAAAGAAAGAAAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAGAAAGAAAAAAAAAAAAA
343459 AAGAAAAAA
1 AAGAAAAAA
343468 AAAATGGAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 7 0.19
31 16 0.44
32 6 0.17
33 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (31 bp):
AAGAAAAAAGAAAGAAAGAAAAAAAAAAAAA
Found at i:343471 original size:20 final size:20
Alignment explanation
Indices: 343400--343471 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 20
343390 TGCTTGAAGA
343400 AAAAAAAAGAAGAAGAAAAAA-
1 AAAAAAAA-AAGAA-AAAAAAG
*
343421 AAAGAAAAAAGAAAAAGAAAG
1 AAAAAAAAAAGAAAAA-AAAG
*
343442 AAAGAAAAAAGAAAAAAAAG
1 AAAAAAAAAAGAAAAAAAAG
343462 AAAAAAAAAA
1 AAAAAAAAAA
343472 TGGAGGTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.06
20 21 0.45
21 23 0.49
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAAAAAAAAG
Found at i:344747 original size:83 final size:83
Alignment explanation
Indices: 344607--346036 Score: 2298
Period size: 83 Copynumber: 17.2 Consensus size: 83
344597 CATTAACTGA
344607 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
344672 ATCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* * *
344690 GAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
344755 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
344773 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
344838 ACCAACCATTGAATTTAA
66 ACCAATCATTGAATTTAG
* *
344856 AAGATAAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
344920 AACCAACCATTGAATTT-G
65 AACCAATCATTGAATTTAG
* * *
344938 AAAGATAAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 -AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
345003 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
*
345022 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
345087 ACCAACCATTGAATTTAA
66 ACCAATCATTGAATTTAG
* *
345105 AAGATAAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
345169 AACCAACCATTGAATTT-G
65 AACCAATCATTGAATTTAG
* *
345187 AAAGATAAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 -AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
*
345251 GAATCAATCATTGAATTTAG
64 GAACCAATCATTGAATTTAG
*
345271 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
345335 AATCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
*
345354 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
345419 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
345437 GAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
345502 ACCAACCATTGAATTTGG
66 ACCAATCATTGAATTTAG
*
345520 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
345585 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* * *
345603 GAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
345668 ATCAATCATTAAATTTAG
66 ACCAATCATTGAATTTAG
* *
345686 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
* *
345751 ACCAACCATTGAATTTGG
66 ACCAATCATTGAATTTAG
*
345769 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
345834 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
345852 GAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
* *
345916 AATCAATCATTAAATTTAG
65 AACCAATCATTGAATTTAG
* * *
345935 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
346000 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTAG
*
346018 AAGATGAATTTGCTCATAG
1 AAGATGAATTTGTTCATAG
346037 TAGAAATAAG
Statistics
Matches: 1265, Mismatches: 72, Indels: 20
0.93 0.05 0.01
Matches are distributed among these distances:
82 12 0.01
83 1241 0.98
84 12 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTAG
Found at i:347060 original size:113 final size:112
Alignment explanation
Indices: 346765--347317 Score: 852
Period size: 110 Copynumber: 5.0 Consensus size: 112
346755 CAAAGATTCA
* * * *
346765 AATCTATCATTTGATGGATTTACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATAT-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
346830 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-C-TTTACCTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
346876 AATTCATCACTGGATGGATAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
346940 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
346988 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAAAACTCATATGAAGA
1 AATCCATCATTTGATGGAT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
347053 AGCAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
347101 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAAACTCATCTGAAG
1 AATCCATCATTTGATGGAT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAG-AACTCATCTGAAG
347166 AA--AAGAAGAAG-TCATAA-GAGAAGAATTTGTTCAACCTTTTACCTG
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
347211 AATTCATCAATTGATGGATTATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGA-TATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
347275 AGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
347318 GCATAATTCT
Statistics
Matches: 412, Mismatches: 19, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
108 15 0.04
109 21 0.05
110 140 0.34
111 30 0.07
112 54 0.13
113 134 0.33
114 18 0.04
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AATCCATCATTTGATGGATATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:347189 original size:223 final size:223
Alignment explanation
Indices: 346765--347317 Score: 850
Period size: 223 Copynumber: 2.5 Consensus size: 223
346755 CAAAGATTCA
* * * *
346765 AATCTATCATTTGATGGATTTACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATAT-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
346830 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-C-TTTACCTGAATTCATCACTGGATGG
65 AGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTGGATGG
*
346893 ATATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
130 ATATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATA
346958 ATGAGAAGAATTTGTTCAACCTTTTACCTG
194 ATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
346988 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAAAACTCATATGAAGA
1 AATCCATCATTTGATGGAT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
347053 AGCAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGG
65 AGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTGGATGG
347118 ATCATCTTTT-CCAGAGAAAGTTCATAATGAGAAGAAACTCATCTGAAGAA-AAGAAGAAG-TCA
130 AT-AT-TTTTGCCAGAGAAAGTTCATAATGAGAAG-AACTCATCTGAAGAAGAAGAAGAAGTTCA
347180 TAA-GAGAAGAATTTGTTCAACCTTTTACCTG
192 TAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
347211 AATTCATCAATTGATGGATTATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGA-TATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
347275 AGAAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTT
65 AGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
347318 GCATAATTCT
Statistics
Matches: 305, Mismatches: 18, Indels: 15
0.90 0.05 0.04
Matches are distributed among these distances:
222 70 0.23
223 149 0.49
224 9 0.03
225 33 0.11
226 25 0.08
227 19 0.06
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (223 bp):
AATCCATCATTTGATGGATATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCACTGGATGGA
TATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
GAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:347641 original size:3 final size:3
Alignment explanation
Indices: 347628--347745 Score: 127
Period size: 3 Copynumber: 39.3 Consensus size: 3
347618 TTTTTACCCA
* *
347628 TAT TA- TAT TAT TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
347674 TA- TAT TAT TAT TATT TAT TAT TAT TAT ATAT TAT TA- TCT TAT CAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
*
347719 TAT TAT CAT TAT TAAT TAT TAAT TAT T
1 TAT TAT TAT TAT T-AT TAT T-AT TAT T
347746 TAAATACATA
Statistics
Matches: 97, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
2 7 0.07
3 78 0.80
4 12 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:347704 original size:43 final size:44
Alignment explanation
Indices: 347629--347745 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 44
347619 TTTTACCCAT
*
347629 ATTATATTATTATTATTATTATCATTATTATATTATTA-TTATC
1 ATTATATTATTATTATTATTATTATTATTATATTATTACTTATC
347672 ATTATATTATTATTATTTATTATTATTA-TATATTATTATCTTATC
1 ATTATATTATTATTA-TTATTATTATTATTATATTATTA-CTTATC
*
347717 ATTATTATCATTATTAATTATTAATTATT
1 ATTA-TATTATTATT-ATTATT-ATTATT
347746 TAAATACATA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
43 25 0.38
44 11 0.17
45 9 0.14
46 14 0.21
47 7 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (44 bp):
ATTATATTATTATTATTATTATTATTATTATATTATTACTTATC
Found at i:348588 original size:204 final size:200
Alignment explanation
Indices: 348186--348589 Score: 756
Period size: 204 Copynumber: 2.0 Consensus size: 200
348176 AAAGAAGAAC
348186 ACAGAGCCGGAAAAAAAAACAGAGAAAATATAAAAGAAAATACTACCAACGATCTCAGTCAACAT
1 ACAGAGCCGGAAAAAAAAACAGAGAAAATATAAAAGAAAATACTACCAACGATCTCAGTCAACAT
348251 CCCACAACCAGCAACCAAAAATAGAAGGAAAAAAAGGAGAGAAGCTTACGAGAAAGCCACGACCA
66 CCCACAACCAGCAACCAAAAATAGAAGGAAAAAAAGGAGAGAAGCTTACGAGAAAGCCACGACCA
348316 CCGGAACCCTCCAAACGTCACGACAACCTTCGAAAAACCGAATGTATTTTCCTAGATTTGCTCCG
131 CCGGAACCCTCCAAACGTCACGACAACCTTCGAAAAACCGAATGTATTTTCCTAGATTTGCTCCG
348381 GTTGG
196 GTTGG
348386 ACAGAGCCGGAAAAAAAAACAGAGAAATAATATAAAAGAAAACTACTACCAACGATCTCAGTCAA
1 ACAGAGCCGGAAAAAAAAACAGAG-AA-AATATAAAAGAAAA-TACTACCAACGATCTCAGTCAA
348451 CATCCCACAACCAGCAACCAAAAATAGAAGGAAAAAAAGGAGAGAAGCTTACCGAGAAAGCCACG
63 CATCCCACAACCAGCAACCAAAAATAGAAGGAAAAAAAGGAGAGAAGCTTA-CGAGAAAGCCACG
348516 ACCACCGGAACCCTCCAAACGTCACCGACAACCTTCG-AAAACCGAATGTATTTTCCTAGATTTG
127 ACCACCGGAACCCTCCAAACGTCA-CGACAACCTTCGAAAAACCGAATGTATTTTCCTAGATTTG
348580 CTCCGGTTGG
191 CTCCGGTTGG
348590 GAGCTTTTTA
Statistics
Matches: 199, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
200 24 0.12
201 2 0.01
202 14 0.07
203 73 0.37
204 74 0.37
205 12 0.06
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (200 bp):
ACAGAGCCGGAAAAAAAAACAGAGAAAATATAAAAGAAAATACTACCAACGATCTCAGTCAACAT
CCCACAACCAGCAACCAAAAATAGAAGGAAAAAAAGGAGAGAAGCTTACGAGAAAGCCACGACCA
CCGGAACCCTCCAAACGTCACGACAACCTTCGAAAAACCGAATGTATTTTCCTAGATTTGCTCCG
GTTGG
Found at i:350873 original size:19 final size:20
Alignment explanation
Indices: 350832--350873 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
350822 TCAAACTAAG
*
350832 TTATTAAGGTTTCGTTGCCTTA
1 TTATTAAGGTTTCGAT--CTTA
350854 TTATTAAGGTTTCGAT-TTA
1 TTATTAAGGTTTCGATCTTA
350873 T
1 T
350874 GTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (20 bp):
TTATTAAGGTTTCGATCTTA
Found at i:353720 original size:21 final size:21
Alignment explanation
Indices: 353656--353746 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
353646 GGGTGCTCAA
* * *
353656 TATCGATACAAGATAAACTGG
1 TATCCATACAGGATGAACTGG
*
353677 TATCCATATC-GGA-GGACTGG
1 TATCCATA-CAGGATGAACTGG
**
353697 TATCCATACAGGATGAGTTGG
1 TATCCATACAGGATGAACTGG
* * *
353718 TATTCGTACTGGATGAACTGG
1 TATCCATACAGGATGAACTGG
353739 TATCCATA
1 TATCCATA
353747 TCCAAGATTG
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.02
20 16 0.30
21 35 0.66
22 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
TATCCATACAGGATGAACTGG
Found at i:356802 original size:199 final size:199
Alignment explanation
Indices: 356461--356821 Score: 503
Period size: 199 Copynumber: 1.8 Consensus size: 199
356451 TATTTGCTTG
* *
356461 CATAAATACCAAATATAGATACTTTTATATATGTATGAATAATTTTACTCCAGTATGCTTCTCAA
1 CATAAATACCAAATATAGATACTTTTATATAGGTATGAATAATTTTACTCCAGTATGATTCTCAA
* * * **
356526 ATAATTTGCACACAAAATGTGTCGATACACATATATAAAGTATCGATACTTAGAATTTTGAAACC
66 ACAATTTGCACACAAAATGTATCCATACACATATATAAAGTATCGATACTTAGAATTTCAAAACC
** * *
356591 TATCAATTTAAAGTTATAGGTTAATTAACAATATAAACGGTAAAAGTCTATCGGTATATTGATAA
131 TATCAATTTAAAGAAATAAGTAAATTAACAATATAAACGGTAAAAGTCTATCGGTATATTGATAA
356656 TATA
196 TATA
* * *
356660 CATAAATATCAAGTATCA-ATACTTTTATATAGGTATTG-ATACA-TTTATTCCAGTATGATTCT
1 CATAAATACCAAATAT-AGATACTTTTATATAGGTA-TGAATA-ATTTTACTCCAGTATGATTCT
* *
356722 CAAACAATTTGCACGCAAAATGTATCCATACACATATATAAAGTATCGATACTTATAATTTCAAA
63 CAAACAATTTGCACACAAAATGTATCCATACACATATATAAAGTATCGATACTTAGAATTTCAAA
* * *
356787 ACTTATTACTTTAAAGAAATAAGTAAATTAACAAT
128 ACCTATCAATTTAAAGAAATAAGTAAATTAACAAT
356822 GTACACAGTA
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
199 136 0.97
200 4 0.03
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (199 bp):
CATAAATACCAAATATAGATACTTTTATATAGGTATGAATAATTTTACTCCAGTATGATTCTCAA
ACAATTTGCACACAAAATGTATCCATACACATATATAAAGTATCGATACTTAGAATTTCAAAACC
TATCAATTTAAAGAAATAAGTAAATTAACAATATAAACGGTAAAAGTCTATCGGTATATTGATAA
TATA
Found at i:356977 original size:131 final size:131
Alignment explanation
Indices: 356743--357225 Score: 630
Period size: 131 Copynumber: 3.7 Consensus size: 131
356733 CACGCAAAAT
* * * * *
356743 GTATCCATACACATATATAAAGTATCGATACTTATAATTTCAAAACTTATTACTTTAAAGAAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATA
*
356808 AGTAAATTAACAATGTACACAGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
66 AGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
356873 A
131 A
* * * * * *
356874 GTATCGATACCCATATACAAAGTATTGATACTTATATTTTCGAAACCTATTAATTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATA
* **
356939 AGTAAATTAATAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCACAAATGTCCA
66 AGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
357004 A
131 A
* * *
357005 GTATTGATACTCATATATAAATTATCGATACTTATAATTTTGAAACATATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATA
* * ** * * * *
357070 TGTAAATTAACAATGTATACTATAAACGTTTCTACCGATATAATAAAAATAGGTGTAAATGTACA
66 AGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
357135 A
131 A
** * *
357136 GTAT-GAATA-TTGTCATAT-AAGTATCGATATTTTATAATTTCGAAACATATTACTTTAAAATA
1 GTATCG-ATACTCAT-ATATAAAGTATCGATA-CTTATAATTTCGAAACATATTACTTTAAAGTA
* *
357198 ATATGTAAATTAACAATATACACGGTAA
63 ATAAGTAAATTAACAATGTACACGGTAA
357226 TATGTTGATA
Statistics
Matches: 306, Mismatches: 43, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
130 13 0.04
131 293 0.96
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (131 bp):
GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCGAAACATATTACTTTAAAGTAATA
AGTAAATTAACAATGTACACGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTCCA
A
Found at i:359540 original size:26 final size:26
Alignment explanation
Indices: 359504--359554 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
359494 CTTTTGAAAA
*
359504 TTTAAATTTGGGTATGTTCCTGTGTT
1 TTTAAATTTGGGTATGTTCATGTGTT
*
359530 TTTAGATTTGGGTATGTTCATGTGT
1 TTTAAATTTGGGTATGTTCATGTGT
359555 AATCTCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.06, G:0.25, T:0.53
Consensus pattern (26 bp):
TTTAAATTTGGGTATGTTCATGTGTT
Found at i:365529 original size:18 final size:17
Alignment explanation
Indices: 365508--365546 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
365498 AGGGAATTAA
*
365508 AATCTGTGAATGAATTGG
1 AATCTGT-AAGGAATTGG
*
365526 AATCTGTCAGGAATTGG
1 AATCTGTAAGGAATTGG
365543 AATC
1 AATC
365547 CAATTACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (17 bp):
AATCTGTAAGGAATTGG
Found at i:366349 original size:254 final size:251
Alignment explanation
Indices: 365912--366573 Score: 825
Period size: 256 Copynumber: 2.5 Consensus size: 251
365902 AAAAACAGTG
365912 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
1 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* *
365977 TTTTTCGAGTCGGGTCTAGTCGGGTATTTTTCACCCTAAACCCGAATTCGACCCGACCCTAATAT
66 TTTTTCGGGTC-GG----GTCGGGTATTTTTCACCCTAAA-CC-----CGACCCGACCCGAATAT
*
366042 CACACTTAAAAAAACCAACCCGGCCAAAATAAAGTTTCACCCAACCCGA-C-CCGAATATATGAA
120 CACACTTAAAAAAACCAACCCGACCAAAATAAAGTTT---CCAACCCGACCACCGAATATATGAA
*
366105 TTAGAAACCCAACCTGACTCAACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAA-AATG
182 TTAGAAACCCAACCCGA---AA--CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATG
366168 ACTTAATTGA
242 ACTTAATTGA
* * *
366178 AAAAAATTTTATATAGAGAGGTATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATAT
1 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* *
366243 TTGTT-GGGTCGGGTCGGGTATTTTTCACCCTAAACCCGACCCGACCCGAATACCACACTTAAAA
66 TTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGACCCGACCCGAATATCACACTTAAAA
366307 AAACCGACCCGACCCGACCAAAATAAAGTTT-C-ACCCGACCCGATCCGAATATATGAATTAGAA
131 AAACC-A----ACCCGACCAAAATAAAGTTTCCAACCCGA-CC-A-CCGAATATATGAATTAGAA
*
366370 ACCCGACCCGAAACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGA
188 ACCCAACCCGAAACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGA
* * *
366434 AAAAAATTATATATAGAGGGGTATTATTGTAGTTATTTCTAAATATATAAGATAAAATTATATAT
1 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* * *
366499 ATTTTTCGGGTCGGGTTGAGTATTTTTCATCCTAAACCCGAACCCGACTCGACCCGAATATCACA
66 -TTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCG-A--C--C-CGACCCGAATATCACA
366564 CTTAAAAAAA
124 CTTAAAAAAA
366574 AACCTGACCC
Statistics
Matches: 355, Mismatches: 21, Indels: 42
0.85 0.05 0.10
Matches are distributed among these distances:
254 53 0.15
255 21 0.06
256 76 0.21
257 4 0.01
258 30 0.08
259 50 0.14
260 22 0.06
261 1 0.00
263 1 0.00
264 27 0.08
265 4 0.01
266 66 0.19
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (251 bp):
AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
TTTTTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGACCCGACCCGAATATCACACTTAAAA
AAACCAACCCGACCAAAATAAAGTTTCCAACCCGACCACCGAATATATGAATTAGAAACCCAACC
CGAAACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGA
Found at i:371958 original size:25 final size:24
Alignment explanation
Indices: 371918--371964 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
371908 TTTTTTTTTT
*
371918 AAAATATCTTAGTCTTTATATTATA
1 AAAATATCTTAATC-TTATATTATA
*
371943 AAAATATTTTAATCTTATATTA
1 AAAATATCTTAATCTTATATTA
371965 CAACTAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
AAAATATCTTAATCTTATATTATA
Done.