Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004100.1 Hibiscus syriacus cultivar Beakdansim tig00008965_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: 138271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:347 original size:19 final size:19
Alignment explanation
Indices: 315--362 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
305 AATTATACAC
315 ATACAAAA-TATAAATCGT
1 ATACAAAATTATAAATCGT
*
333 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
352 ATACAAAATTA
1 ATACAAAATTA
363 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2084 original size:33 final size:33
Alignment explanation
Indices: 2047--2112 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2037 CATCTTAATA
*
2047 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
2080 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2113 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2171 original size:21 final size:21
Alignment explanation
Indices: 2146--2189 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2136 CCCCTTATGC
2146 CTCTCAAGTATATCTTCGACT
1 CTCTCAAGTATATCTTCGACT
* *
2167 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTATATCTTCGACT
2188 CT
1 CT
2190 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTATATCTTCGACT
Found at i:4422 original size:17 final size:18
Alignment explanation
Indices: 4400--4442 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
4390 ATATATCCGG
4400 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
4417 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
4437 TATCAT
1 TATCAT
4443 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:4628 original size:158 final size:157
Alignment explanation
Indices: 4428--4761 Score: 456
Period size: 156 Copynumber: 2.1 Consensus size: 157
4418 ATCATTTTGA
* * *
4428 TACCGGTTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATC--ATTTTTACATGGTATATCGTTGTGGATCGATACA--TTTTAAAAGTATCG
*
4493 ACACATTATAGGCGGTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
62 ACACATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCAC-AAGTGTCGATCCTTATATTAAAG
* * * **
4557 TATCGACACTTTCAATATAT-CGGTAACGTTT
126 TACCGACACTTTAAATACATCCGGTAACACTT
* *
4588 TACCGGCTTTATCATTTTTACATGGTATATCGTTTTGGATCGATACATTTTAAAAGTATCGACAC
1 TACCGGTTTTATCATTTTTACATGGTATATCGTTGTGGATCGATACATTTTAAAAGTATCGACAC
* ** *
4653 TTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAGTGTCGATCCTTATATTAAAGTACCG
66 ATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCACAAGTGTCGATCCTTATATTAAAGTACCG
* *
4718 ACACTTTAAATGCATCCGGTAGCACTT
131 ACACTTTAAATACATCCGGTAACACTT
4745 TACCGGTTTTATCATTT
1 TACCGGTTTTATCATTT
4762 CTATACCGGT
Statistics
Matches: 154, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
155 16 0.10
156 71 0.46
157 24 0.16
158 31 0.20
160 12 0.08
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (157 bp):
TACCGGTTTTATCATTTTTACATGGTATATCGTTGTGGATCGATACATTTTAAAAGTATCGACAC
ATTATAGGAGGTAAAACTGCTTCTCTTTTAAATTCACAAGTGTCGATCCTTATATTAAAGTACCG
ACACTTTAAATACATCCGGTAACACTT
Found at i:5283 original size:228 final size:224
Alignment explanation
Indices: 4888--5371 Score: 832
Period size: 229 Copynumber: 2.2 Consensus size: 224
4878 ACTTTTATAC
*
4888 GTATGGACACTTTTATAAAAATG--ATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAATT
4951 TTTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAATAATTTCATTTACACAAAAATTAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAATAATTTCATTTACACAAAAATTAT
*
5016 TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAAC-A-ATTAACCAAATATA
131 TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATA
*
5079 ATAATAAATATGTTTTCCACAGTGAAATAA
196 ATAATAAATATATTTT-CACAGTGAAATAA
*
5109 GTATAGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAAAT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTC-AAAT
5174 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACACAAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTAC-ATA-TAATTTAATAATTTCATTTACACA-AAAA
*
5239 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
127 TTATTTGATT-ATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
5304 AGATAATAATAAATATATTTTCACAGTGAAATAA
191 AGATAATAATAAATATATTTTCACAGTGAAATAA
*
5338 GTATGGACACTTTTATAAAAAGGATATATACTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTT
5372 ACAATATAAC
Statistics
Matches: 247, Mismatches: 7, Indels: 10
0.94 0.03 0.04
Matches are distributed among these distances:
221 22 0.09
223 35 0.14
224 34 0.14
225 3 0.01
226 24 0.10
227 14 0.06
228 41 0.17
229 46 0.19
230 28 0.11
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (224 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAATT
TTTTAATAGTGTTTCATGTTTTCCACCTACATATAATTTAATAATTTCATTTACACAAAAATTAT
TTGATTATTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATA
ATAATAAATATATTTTCACAGTGAAATAA
Found at i:5633 original size:11 final size:11
Alignment explanation
Indices: 5617--5641 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5607 ATCCGGTACT
5617 ACCGTATATTA
1 ACCGTATATTA
5628 ACCGTATATTA
1 ACCGTATATTA
5639 ACC
1 ACC
5642 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:7765 original size:20 final size:20
Alignment explanation
Indices: 7737--7778 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
7727 CTAAATTAGG
*
7737 TATTATTATTTATTTACATT
1 TATTATTATATATTTACATT
* *
7757 TATTCTTATATATTTATATT
1 TATTATTATATATTTACATT
7777 TA
1 TA
7779 AATTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATATATTTACATT
Found at i:11562 original size:22 final size:22
Alignment explanation
Indices: 11537--11580 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11527 TATATTACAA
11537 TTATAATAT-ATTAAAATTATTT
1 TTAT-ATATCATTAAAATTATTT
* *
11559 TTATTTTTCATTAAAATTATTT
1 TTATATATCATTAAAATTATTT
11581 AAAATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATCATTAAAATTATTT
Found at i:12264 original size:22 final size:22
Alignment explanation
Indices: 12200--12282 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
12190 TTTTATAAAT
* *
12200 ATTATAT-TTTAATTAAATTACA
1 ATTATATGTTTAA-TAATTTATA
* * *
12222 TTTATATTTTTAAATAGTTTATA
1 ATTATATGTTT-AATAATTTATA
12245 ATTATATGTTTAATAATTTATA
1 ATTATATGTTTAATAATTTATA
*
12267 ATT-TAATGTTTTATAA
1 ATTAT-ATGTTTAATAA
12283 ATTAATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 29 0.58
23 18 0.36
24 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATATGTTTAATAATTTATA
Found at i:23350 original size:4 final size:4
Alignment explanation
Indices: 23341--23369 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
23331 TTGACGATGT
23341 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
23370 GTGTGTGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:25280 original size:45 final size:45
Alignment explanation
Indices: 25220--25309 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
25210 AGTTAACCAC
25220 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
1 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
*
25265 CTTACAGATAGGTCTAACTATATACAGCATGAAATGCCAAATTAA
1 CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
25310 GAGAACGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (45 bp):
CTTACAGATAGGTCTAACTATATAAAGCATGAAATGCCAAATTAA
Found at i:27477 original size:224 final size:218
Alignment explanation
Indices: 27077--27515 Score: 639
Period size: 224 Copynumber: 2.0 Consensus size: 218
27067 TTGGAAACTG
* *
27077 CATTATGTTTCTCCAACAAGATAAAACGTAATTGCAGCCTTCTATGATCTATCAAGACAGATGGT
1 CATTATGTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTATCAAGACAGATGGT
27142 TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
66 TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
* ** * * * *
27207 AGCTTCATTCATGGGTTGTAAACTTCAAATTGACCCCAGATTAACTACCTTATTTAGGGGGCAGC
131 AACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTA--TTATTGA-GGGGCAGA
*
27272 ATTTTTACCTAAAGTAGCATTAGCTA
193 ATTTCTACCTAAAGTAGCATTAGCTA
*
27298 CATTATCG-TTCTGCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTACTATCAAAGACAG
1 CATTAT-GTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGA--T-CTATC-AAGACAG
* * * * *
27362 ATGGTTCCAGGAATTTTGCCGAATAGGTCAAAAGGGTA-GATGTATGTTAACATGTAGGTAGTAA
61 ATGGTTCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAA
*
27426 CCAAAAACTTCATTCGTGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCA
126 CCAAAAACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCA
27491 GAATTTCTACCTAAAGTAGCATTAG
191 GAATTTCTACCTAAAGTAGCATTAG
27516 TTATATTCAA
Statistics
Matches: 196, Mismatches: 17, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
221 71 0.36
222 7 0.04
223 1 0.01
224 74 0.38
225 43 0.22
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (218 bp):
CATTATGTTTCTCCAACAAGATAAAACATAATTGCAGCCTTCTACGATCTATCAAGACAGATGGT
TCCAGGAAATTTGCCGAATAGGTCAAAAAGGTATCATGTATATTAACATGTAGGTAATAACCAAA
AACTTCATTCATGGGCCGTAAACTTCAAATGGACCCAAGATTAACTATTATTGAGGGGCAGAATT
TCTACCTAAAGTAGCATTAGCTA
Found at i:31653 original size:30 final size:30
Alignment explanation
Indices: 31619--31689 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
31609 CAGAGCGATC
* *
31619 AAAATATGAATAATTCAAAAGTTA-TGTGAA-
1 AAAATATGAAAAATT-AAAAG-TACAGTGAAT
31649 AAAAT-TAGAAAAATTAAAAGTACAGTGAAT
1 AAAATAT-GAAAAATTAAAAGTACAGTGAAT
31679 AAAATATGAAA
1 AAAATATGAAA
31690 GAGAGTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.06
29 11 0.31
30 21 0.60
31 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.25
Consensus pattern (30 bp):
AAAATATGAAAAATTAAAAGTACAGTGAAT
Found at i:40102 original size:20 final size:20
Alignment explanation
Indices: 40077--40169 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
40067 TTTTCCCAAT
40077 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
40097 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
40117 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
40138 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
40159 TCGCAATGCGA
1 TCGCAATGCGA
40170 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:40119 original size:41 final size:41
Alignment explanation
Indices: 40074--40169 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
40064 CGATTTTCCC
40074 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
40115 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
40156 AAATCGCAATGCGA
1 AATTCGCAATGCGA
40170 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:40123 original size:21 final size:20
Alignment explanation
Indices: 40077--40169 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
40067 TTTTCCCAAT
*
40077 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
40097 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
40117 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
40138 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
40159 TCGCAATGCGA
1 TCGCAATGCGA
40170 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:40182 original size:41 final size:41
Alignment explanation
Indices: 40096--40230 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
40086 GAATAAGTAA
* * *
40096 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
40137 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
40178 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
40219 TTCGCAACGCGA
1 ATCGCAACGCGA
40231 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:40183 original size:20 final size:20
Alignment explanation
Indices: 40158--40251 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40148 AATTGGGAAA
*
40158 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
40178 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
40199 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
40219 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
40239 TTCGCAACGCGAT
1 ATCGCAACGCGAT
40252 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:40798 original size:19 final size:19
Alignment explanation
Indices: 40774--40818 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40764 CGAGAATGAG
*
40774 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
40793 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
40812 AATCGCA
1 AATCGCA
40819 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:40836 original size:19 final size:19
Alignment explanation
Indices: 40814--41017 Score: 194
Period size: 19 Copynumber: 11.1 Consensus size: 19
40804 GAAACCAAAA
*
40814 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
40833 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40852 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
40871 TCGCGTTGTGATTTTAATT
1 TCGCGTTGCGATTTTCATT
40890 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
40910 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
40926 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
40943 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
40957 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
40976 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
40996 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
41016 TC
1 TC
41018 AACCAAAAGA
Statistics
Matches: 155, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 20 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 78 0.50
20 48 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:40912 original size:58 final size:57
Alignment explanation
Indices: 40814--40922 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
40804 GAAACCAAAA
*
40814 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
40871 TCGCGTTGTGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATT
1 TCGCATTGCGATTTTAATTTCGC-ATTGCGATTTTCATTTCGCGTTGCGATT
40923 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 20 0.43
58 27 0.57
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (57 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:40933 original size:39 final size:38
Alignment explanation
Indices: 40819--41017 Score: 161
Period size: 33 Copynumber: 5.4 Consensus size: 38
40809 CAAAATCGCA
*
40819 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTTC-TTTCGCGG
* *
40857 TTGCGATTTTCATTTCGCGTTGTGATTTTAATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTT-CTTTCGCGG
*
40896 TTGCGATTTTCATTTCGCGTTGCGATTGTC--T---GG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
* ** *
40929 TCGCGATAGTCATTTCGCGTTGCGA--TTC--TCTC-G
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
** * *
40962 TTGCGATAGTCATTTCCGCGTTGCGATTCTCATTATCTC-G
1 TTGCGATTTTCATTT-CGCGTTGCGATTTTC-TT-TCGCGG
41002 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
41018 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 14, Indels: 23
0.78 0.08 0.13
Matches are distributed among these distances:
31 3 0.02
33 39 0.29
34 10 0.07
36 3 0.02
38 33 0.24
39 29 0.21
40 18 0.13
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCTTTCGCGG
Found at i:40994 original size:20 final size:20
Alignment explanation
Indices: 40960--41017 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
40950 GCGATTCTCT
**
40960 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
40980 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
41000 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
41018 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:43698 original size:14 final size:14
Alignment explanation
Indices: 43679--43715 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
43669 CATCAATTAA
43679 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
43693 ACAAATCATCTTTT
1 ACAAATCAACATTT
43707 ACAAATCAA
1 ACAAATCAA
43716 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:44420 original size:588 final size:588
Alignment explanation
Indices: 43304--46280 Score: 5546
Period size: 588 Copynumber: 5.1 Consensus size: 588
43294 TTTAACAATT
*
43304 ATTATTGAATTCTAGGTACTTAACCAAATATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
43369 CTTTCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
43434 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
43499 AATGCGAAAATGGTTATCACAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
43564 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTG-AAA
261 TCGTTGCGATAG-CATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
43628 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
325 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
43693 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
390 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
43758 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
455 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
43823 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
520 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
*
43888 GCAA
585 ACAA
43892 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
43957 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
44022 GAGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
44087 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
44152 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAG-CATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
* *
44217 TCAATAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAAACAACATTT
325 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
44282 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
390 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
44347 ATTATTGAATCAAGAATCAACAACTTTGTGA-CCCGTACATCCATTTCACGCAGCTCACTTAAGG
455 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
44411 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
520 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
44476 ACAA
585 ACAA
44480 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
44545 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
44610 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
44675 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT---A-----
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
44732 ------CGAT----TTTCTCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
261 TCGTTGCGATAGCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
*
44787 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAAACAACATTTA
326 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
44852 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAA
391 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAA
44917 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
44982 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAA
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAA
45047 CAA
586 CAA
45050 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
45115 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
45180 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
45245 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT---A-----
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
*
45302 ------CGAT----TTTCTCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
261 TCGTTGCGATAGCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
45357 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
326 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
45422 CAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAA
391 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAA
45486 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
456 TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
*
45551 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
521 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAA
45616 CAA
586 CAA
45619 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
45684 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
45749 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
45814 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
45879 TCGTTGCGATAGCTATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAGC-ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
45944 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
325 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
46009 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
390 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
46074 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
455 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
46139 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
520 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
46204 ACAA
585 ACAA
46208 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
46273 CTGGCATT
66 CTTGCATT
46281 TGACTTACCA
Statistics
Matches: 2352, Mismatches: 15, Indels: 43
0.98 0.01 0.02
Matches are distributed among these distances:
569 624 0.27
570 505 0.21
572 1 0.00
574 4 0.00
583 4 0.00
585 1 0.00
588 815 0.35
589 398 0.17
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (588 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAGCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTA
CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAA
TTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGA
TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAA
CAA
Found at i:45426 original size:14 final size:14
Alignment explanation
Indices: 45407--45443 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45397 CATCAATTAA
45407 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
45421 ACAAATCATCTTTT
1 ACAAATCAACATTT
45435 ACAAATCAA
1 ACAAATCAA
45444 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:45499 original size:569 final size:573
Alignment explanation
Indices: 43578--46280 Score: 4974
Period size: 569 Copynumber: 4.7 Consensus size: 573
43568 TGCGATAGCC
43578 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTG-AAATCAACAAATCAACT
1 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
43642 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
66 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
43707 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
131 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
43772 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
196 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
*
43837 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAATTATTGAAT
261 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
43902 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
326 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
43967 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
391 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
*
44032 ATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
456 ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
44097 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGAT
521 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT--GA---------T-CGAT
*
44162 AGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAATAAATC
1 ----ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATC
*
44227 AACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAAACAACATTTACAAATCATC
62 AACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATC
44292 TTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAAT
127 TTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAAT
44357 CAAGAATCAACAACTTTGTGA-CCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGC
192 CAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGC
44421 AGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATT
257 AGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATT
44486 GAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCA
322 GAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCA
44551 TTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTT
387 TTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTT
44616 GAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCG
452 GAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCG
44681 AAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT-A-CGAT
517 AAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGATCGAT
*
44736 -TTTCTCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
1 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
*
44800 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAAACAACATTTACAAATCATCTTTT
66 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
44865 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
131 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
44930 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
196 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
44995 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
261 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
45060 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
326 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
45125 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
391 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
45190 ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
456 ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
45255 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT-A-CGAT
521 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGATCGAT
*
45306 -TTTCTCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
1 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
45370 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
66 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
45435 ACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
131 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
45499 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
196 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
*
45564 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGCAAATTATTGAAT
261 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
45629 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
326 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
45694 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
391 GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
45759 ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
456 ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
45824 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGAT
521 TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATT--GA---------T-CG--
45889 AGCT
572 A--T
45893 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
1 ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
45958 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
66 ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
46023 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
131 ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
46088 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
196 AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
46153 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
261 ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
*
46218 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTGGCATT
326 TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATT
46281 TGACTTACCA
Statistics
Matches: 2082, Mismatches: 11, Indels: 43
0.97 0.01 0.02
Matches are distributed among these distances:
569 624 0.30
570 505 0.24
572 1 0.00
574 4 0.00
583 2 0.00
585 2 0.00
587 1 0.00
588 545 0.26
589 398 0.19
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (573 bp):
ATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAATCAACAAATCAACT
ATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTTACAAATCATCTTTT
ACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAATTATTGAATCAAG
AATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGGATTAACCTGCAGAA
ACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAACAAATTATTGAAT
TCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAACTTGCATTAT
GTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAAC
ATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGCAATGCGAAAA
TGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGATCGAT
Found at i:46014 original size:14 final size:14
Alignment explanation
Indices: 45995--46031 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45985 CATCAATTAA
45995 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
46009 ACAAATCATCTTTT
1 ACAAATCAACATTT
46023 ACAAATCAA
1 ACAAATCAA
46032 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:47936 original size:20 final size:19
Alignment explanation
Indices: 47901--47967 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
47891 GAAACTTAAA
47901 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
47920 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
47940 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
47959 ATCGCAACG
1 ATCGCAACG
47968 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:47975 original size:14 final size:14
Alignment explanation
Indices: 47956--48043 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
47946 ATGCGAAATG
47956 AAAATCGCAACGAC
1 AAAATCGCAACGAC
47970 AAAATCGCAACG-C
1 AAAATCGCAACGAC
47983 GAAATGAATCGCAACGAC
1 --AA--AATCGCAACGAC
48001 AAAATCGCAACG-C
1 AAAATCGCAACGAC
48014 GAAATGAATCGCAACGAC
1 --AA--AATCGCAACGAC
48032 AAAATCGCAACG
1 AAAATCGCAACG
48044 CGAAACACAA
Statistics
Matches: 64, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.03
14 32 0.50
15 4 0.06
16 4 0.06
17 20 0.31
18 2 0.03
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:47996 original size:31 final size:31
Alignment explanation
Indices: 47940--48048 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
47930 GGAAATGGCT
*
47940 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG--AATCGCAACGACAAA
47973 ATCGCAACGCGAAATGAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAATCGCAACGACAAA
48004 ATCGCAACGCGAAATGAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAATCGCAACGACAAA
48035 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
48049 CACAAATCGC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 60 0.80
33 15 0.20
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (31 bp):
ATCGCAACGCGAAATGAATCGCAACGACAAA
Found at i:48077 original size:19 final size:17
Alignment explanation
Indices: 48055--48150 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
48045 GAAACACAAA
48055 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
48074 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
48090 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
48106 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
48122 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
48139 TCGCATTGCGAT
1 TCGC-TTGCGAT
48151 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:48096 original size:14 final size:14
Alignment explanation
Indices: 48077--48134 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
48067 TTTCATTTCG
48077 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
48091 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
48107 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
48123 CGTTGCGATTTT
1 CGTTGCGATTTT
48135 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48141 original size:33 final size:33
Alignment explanation
Indices: 48060--48150 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
48050 ACAAATCGCA
48060 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
48093 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
48125 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
48151 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:48186 original size:20 final size:20
Alignment explanation
Indices: 48135--48178 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
48125 TTGCGATTTT
* *
48135 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
48154 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
48174 CATTT
1 CATTT
48179 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:48688 original size:18 final size:18
Alignment explanation
Indices: 48662--48706 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
48652 GTCGATCAGA
*
48662 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
48680 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
48698 TGATGGCTC
1 TGATGGCTC
48707 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:50050 original size:20 final size:20
Alignment explanation
Indices: 50025--50062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50015 AATAGTTTCT
50025 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
50045 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
50063 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:50350 original size:21 final size:21
Alignment explanation
Indices: 50326--50368 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
50316 GATTTAGATA
50326 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
50347 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
50368 G
1 G
50369 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:50581 original size:20 final size:20
Alignment explanation
Indices: 50556--50649 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
50546 GATTATGTAT
50556 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
50576 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
50596 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
50617 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
50637 TATCGCATTGCGA
1 TATCGCGTTGCGA
50650 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:50621 original size:41 final size:42
Alignment explanation
Indices: 50576--50711 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
50566 CGAAAGTCAG
* * * *
50576 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
50617 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
50659 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
50700 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
50712 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:50650 original size:20 final size:20
Alignment explanation
Indices: 50536--50650 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
50526 CGCTTTGAAA
*
50536 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
50557 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
50577 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
50597 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
50618 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
50638 ATCGCATTGCGAT
1 ATCGCATTGCGAT
50651 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:50683 original size:20 final size:20
Alignment explanation
Indices: 50639--50731 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
50629 ATAGTCAGTA
*
50639 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
50660 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
50680 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
50701 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
50721 TCGCATTGCGA
1 TCGCATTGCGA
50732 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:50712 original size:41 final size:41
Alignment explanation
Indices: 50639--50734 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
50629 ATAGTCAGTA
* *
50639 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
50680 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
50721 TCGCATTGCGAATT
1 TCGCATTGCGAATT
50735 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:53155 original size:18 final size:18
Alignment explanation
Indices: 53132--53172 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
53122 ATTAGTCTAT
53132 GTTGAATATAAACCGTTA
1 GTTGAATATAAACCGTTA
*
53150 GTTGAATATAAATCGTTA
1 GTTGAATATAAACCGTTA
53168 GTTGA
1 GTTGA
53173 CTAACAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (18 bp):
GTTGAATATAAACCGTTA
Found at i:53301 original size:32 final size:31
Alignment explanation
Indices: 53244--53400 Score: 92
Period size: 32 Copynumber: 4.9 Consensus size: 31
53234 ATGTATCATG
* * *
53244 TCATCACTTTGAAGACATGACACATGATATA
1 TCATCACTTTGATGACATGACACATGACACA
*
53275 TTATCACTTTGGATGACAT-ACAACATGACACA
1 TCATCACTTT-GATGACATGAC-ACATGACACA
**
53307 TCATCACTTTAGATGA-ATTGACATGTG-CA-A
1 TCATCACTTT-GATGACA-TGACACATGACACA
* * *
53337 TGTCATCATTTTAGGTGACATAACGA-ATGAC-CTA
1 --TCATCACTTT-GATGACATGAC-ACATGACAC-A
*
53371 TCATCACTTTGAGTGACATGACAAATGACA
1 TCATCACTTTGA-TGACATGACACATGACA
53401 AAAAATAAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
30 1 0.01
31 16 0.16
32 74 0.76
33 5 0.05
34 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (31 bp):
TCATCACTTTGATGACATGACACATGACACA
Found at i:54567 original size:48 final size:48
Alignment explanation
Indices: 54511--54607 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
54501 GTCGAGTCTA
* *
54511 ATTTTAAACTTTTCAAGTTC-GAGTCGAGCTTAGCAATAATTGAGCTCG
1 ATTTTAAACTTTTCAAGTTCAGA-TCGAGCTCAGCAATAATCGAGCTCG
* *
54559 ATTTTAAACTTTTCGAGTTCAGATCGAGCTCAGCAATACTCGAGCTCG
1 ATTTTAAACTTTTCAAGTTCAGATCGAGCTCAGCAATAATCGAGCTCG
54607 A
1 A
54608 CTCGGGCAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 42 0.95
49 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
ATTTTAAACTTTTCAAGTTCAGATCGAGCTCAGCAATAATCGAGCTCG
Found at i:55569 original size:13 final size:13
Alignment explanation
Indices: 55551--55576 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55541 TAATATTTTG
55551 AATAATTTCAGAC
1 AATAATTTCAGAC
55564 AATAATTTCAGAC
1 AATAATTTCAGAC
55577 CAAATTCGAA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AATAATTTCAGAC
Found at i:69397 original size:2 final size:2
Alignment explanation
Indices: 69360--69386 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69350 CAAATAAAAT
69360 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
69387 CCTATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69972 original size:5 final size:5
Alignment explanation
Indices: 69962--70012 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
69952 ATTTAATCAT
* *
69962 TTTAA TTTAA TTTAA TTTAA TTTAC TTTAA -TTAA -TTAA -TTAA TTTAT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
70009 TTTA
1 TTTA
70013 TAATATCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
4 12 0.29
5 30 0.71
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:70989 original size:15 final size:14
Alignment explanation
Indices: 70953--70981 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70943 TGAAACAATC
70953 AAACGATGGTAGGA
1 AAACGATGGTAGGA
70967 AAACGATGGTAGGA
1 AAACGATGGTAGGA
70981 A
1 A
70982 TGACGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.34, T:0.14
Consensus pattern (14 bp):
AAACGATGGTAGGA
Found at i:82805 original size:16 final size:16
Alignment explanation
Indices: 82764--82809 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
82754 AGATCACAAG
82764 TAATATTTATTTAATTT
1 TAATATTT-TTTAATTT
82781 TAATATTTTTTATATTT
1 TAATATTTTTTA-ATTT
82798 T-AT-TTTTTTAAT
1 TAATATTTTTTAAT
82810 AATATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 6 0.21
17 13 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TAATATTTTTTAATTT
Found at i:84470 original size:12 final size:13
Alignment explanation
Indices: 84438--84484 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
84428 ATTTGATTTA
*
84438 AATT-TATTAACT
1 AATTATATTAAAT
*
84450 AATTATATATTAAT
1 AATTATAT-TAAAT
84464 AATTATATTAAAT
1 AATTATATTAAAT
*
84477 AATAATAT
1 AATTATAT
84485 GTTTATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 11 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTATATTAAAT
Found at i:88069 original size:3 final size:3
Alignment explanation
Indices: 88061--88133 Score: 87
Period size: 3 Copynumber: 24.0 Consensus size: 3
88051 AATATGTAAT
*
88061 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA
*
88107 TAA TAA TAA -ACT TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA
88134 AATTAAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:88533 original size:40 final size:39
Alignment explanation
Indices: 88474--88551 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
88464 TGGTTATCTA
88474 GGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCG
1 GGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCG
* *
88513 GGGGATGACACTGCTCATACGTGATGAAGAGTTCTGGTC
1 GGGG-TGACACGGCTCATACGTGATGAAGAGATCTGGTC
88552 ATCTAAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (39 bp):
GGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCG
Found at i:88553 original size:134 final size:132
Alignment explanation
Indices: 88335--88762 Score: 557
Period size: 134 Copynumber: 3.2 Consensus size: 132
88325 AGTTCGGGTC
* *
88335 ATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGTATGACACGACTCATACG
1 ATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACACG-CTCATACG
88400 TGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTTC-GTTCCTACGTGATGAGGACGGC
64 TGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAAC-TCGGTTCCTACGTGATGAGGACGGC
88464 TGGTT
128 TGGTT
88469 ATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACACTGCTCATACG
1 ATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACAC-GCTCATACG
*
88534 TGATGAAGAGTTCTGGTCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCT
64 TGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCT
*
88594 GATT
129 GGTT
* * * * * * *
88598 ATCTAGGTTGACACAGCTCCTACGTGATGAAAAGATCAGGTCAGGGGGATGACACGGTTCCTACG
1 ATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGGATGACAC-GCTCATACG
* * * *
88663 TGATGAGGACG-GCTGGCCATCTTTAGG-AGTGGTGATAACTCGGTTCCTACATGATGAGGACGG
64 TGATGAAGA-GTTCTGGTCATCTTTAGGAAG-GGTGATAACTCGGTTCCTACGTGATGAGGACGG
88726 CTGGTT
127 CTGGTT
* *
88732 ATCTATGGTTGACACGGCTCCTACGTGATGA
1 ATCTA-GGGTGACACGGCTCATACGTGATGA
88763 GGACGGCTGG
Statistics
Matches: 263, Mismatches: 19, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
128 33 0.13
129 75 0.29
130 3 0.01
131 2 0.01
132 3 0.01
133 1 0.00
134 121 0.46
135 25 0.10
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (132 bp):
ATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACACGCTCATACGTG
ATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGG
TT
Found at i:89042 original size:31 final size:31
Alignment explanation
Indices: 88961--89034 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
88951 TCAAAATTCG
* *
88961 TTTCAAGGGAAAC-GACTCAAAGATGGTTTA
1 TTTCAAGAGAAACAAACTCAAAGATGGTTTA
*
88991 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAACAAACTCAAAGATGGTT-TA
*
89022 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
89035 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 14 0.37
31 24 0.63
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATGGTTTA
Found at i:89302 original size:64 final size:66
Alignment explanation
Indices: 89225--89349 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 66
89215 AGAAACTATA
** * *
89225 TCAAGAGAGACAAAA-TTTGTTTTTAAAGAAATATACTCAAAGA-TGATTTTCAAAAGAAATTGT
1 TCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTGATTTTCAAAAGAAATTGT
89288 C
66 C
**
89289 TCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAA
1 TCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTGATTTTCAAAAGAAA
89350 CAACTCAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 15 0.28
65 24 0.45
66 14 0.26
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (66 bp):
TCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTGATTTTCAAAAGAAATTGT
C
Found at i:89357 original size:65 final size:62
Alignment explanation
Indices: 89165--89357 Score: 165
Period size: 66 Copynumber: 3.0 Consensus size: 62
89155 CGTCTTAAGT
* * * **
89165 GAGACGAAATTTGTTTCAAAGGAAACAATCCCAAAGGTTATTTTTTCATTAGAAACTATA-TCAA
1 GAGACAAAATTTGTTTCAAA-GAAACAA-CTCAAAGATT-TTTTTTCAAAAGAAAC-A-ACTCAA
89229 GA
61 GA
* * ** ***
89231 GAGACAAAATTTGTTTTTAAAGAAATATACTCAAAGA-TGATTTTCAAAAGAAATTGTCTCAAGA
1 GAGACAAAATTTG-TTTCAAAGAAACA-ACTCAAAGATTTTTTTTCAAAAGAAA-CAACTCAAGA
89295 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACAACTCAA
1 GAGACAAAA-TTTGTTT-CAAAGAAACA-ACTCAAAGATTTTTTTTCAAAAGAAACAACTCAA
89358 AGATTTTTTC
Statistics
Matches: 100, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
64 29 0.29
65 27 0.27
66 37 0.37
67 7 0.07
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (62 bp):
GAGACAAAATTTGTTTCAAAGAAACAACTCAAAGATTTTTTTTCAAAAGAAACAACTCAAGA
Found at i:89365 original size:29 final size:29
Alignment explanation
Indices: 89299--89544 Score: 110
Period size: 29 Copynumber: 8.3 Consensus size: 29
89289 TCAAGAGAGA
* *
89299 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
89327 CAAAGATTTTTTTTCAAAAGAAACA-ACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
** * * * **
89355 CAAAGATTTTTTCACGAAATTGTCTCAAGAGAGA
1 CAAAGATTTTTTTTC-AAA-AG---AAACAGACT
* * * *
89389 C-AA-ACTTTGTTTCAAAATAAATAGACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
* * * * **
89416 CAAAGATTTTTTTATGAAATTGTCTCAAGAGAGA
1 CAAAGATTTTTTT-TCAAA-AG---AAACAGACT
* * *
89450 CAAA-ACTTTGTTTT-AACAGAAATAGACT
1 CAAAGA-TTTTTTTTCAAAAGAAACAGACT
*
89478 CAAAGATATTTGTTTCAAAAGAAACA-ACT
1 CAAAGAT-TTTTTTTCAAAAGAAACAGACT
* *
89507 CAAAGATTTTTATTCAAAAGGAACAGACT
1 CAAAGATTTTTTTTCAAAAGAAACAGACT
89536 CAAAGATTT
1 CAAAGATTT
89545 ATCTCAAGAG
Statistics
Matches: 157, Mismatches: 42, Indels: 37
0.67 0.18 0.16
Matches are distributed among these distances:
27 6 0.04
28 47 0.30
29 55 0.35
30 13 0.08
31 4 0.03
32 8 0.05
33 7 0.04
34 17 0.11
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (29 bp):
CAAAGATTTTTTTTCAAAAGAAACAGACT
Found at i:89420 original size:61 final size:62
Alignment explanation
Indices: 89338--89484 Score: 226
Period size: 61 Copynumber: 2.4 Consensus size: 62
89328 AAAGATTTTT
*
89338 TTTCAAAAGAAACA-ACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGAC-AAACTTTG
1 TTTCAAAAGAAATAGACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTG
* * *
89398 TTTCAAAATAAATAGACTCAAAGATTTTTTTATGAAATTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAATAGACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTG
* *
89460 TTTTAACAGAAATAGACTCAAAGAT
1 TTTCAAAAGAAATAGACTCAAAGAT
89485 ATTTGTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 12 0.15
61 36 0.46
62 30 0.38
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (62 bp):
TTTCAAAAGAAATAGACTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTG
Found at i:89517 original size:151 final size:153
Alignment explanation
Indices: 89225--89517 Score: 430
Period size: 151 Copynumber: 1.9 Consensus size: 153
89215 AGAAACTATA
** *
89225 TCAAGAGAGACAAAATTTGTTTTTAAAGAAATATACTCAAAGATGATTTTCAAAAGAAATTGTCT
1 TCAAGAGAGACAAAATTTGTTTCAAAAGAAATAGACTCAAAGAT-ATTTTCAAAAGAAATTGTCT
* *
89290 CAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACAACT
65 CAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTGTTTCAAAAGAAACAACT
89355 CAAAGATTTTTTCACGAAATTGTC
130 CAAAGATTTTTTCACGAAATTGTC
* * ** *
89379 TCAAGAGAGACAAACTTTGTTTCAAAATAAATAGACTCAAAGAT-TTTT-TTATGAAATTGTCTC
1 TCAAGAGAGACAAAATTTGTTTCAAAAGAAATAGACTCAAAGATATTTTCAAAAGAAATTGTCTC
* *
89442 AAGAGAGACAAAACTTTGTTT-TAACAGAAATAGACTCAAAGATATTTGTTTCAAAAGAAACAAC
66 AAGAGAGACAAAACTTTGTTTCCAA-AGAAACAGACTCAAAGAT-TTTGTTTCAAAAGAAACAAC
89506 TCAAAGATTTTT
129 TCAAAGATTTTT
89518 ATTCAAAAGG
Statistics
Matches: 125, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
150 2 0.02
151 49 0.39
152 35 0.28
154 39 0.31
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (153 bp):
TCAAGAGAGACAAAATTTGTTTCAAAAGAAATAGACTCAAAGATATTTTCAAAAGAAATTGTCTC
AAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTGTTTCAAAAGAAACAACTC
AAAGATTTTTTCACGAAATTGTC
Found at i:89551 original size:28 final size:27
Alignment explanation
Indices: 89467--89558 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 27
89457 TTGTTTTAAC
* *
89467 AGAAATAGACTCAAAGATATTTGTTTCAAA
1 AGAAACAGACTCAAAG--ATTT-ATTCAAA
89497 AGAAACA-ACTCAAAGATTTTTATTCAAA
1 AGAAACAGACTCAAAGA--TTTATTCAAA
* *
89525 AGGAACAGACTCAAAGATTTATCTCAAG
1 AGAAACAGACTCAAAGATTTAT-TCAAA
89553 AGAAAC
1 AGAAAC
89559 TGTCTCAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.11
28 21 0.40
29 20 0.38
30 6 0.11
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (27 bp):
AGAAACAGACTCAAAGATTTATTCAAA
Found at i:89918 original size:105 final size:104
Alignment explanation
Indices: 89695--90001 Score: 384
Period size: 105 Copynumber: 2.9 Consensus size: 104
89685 TTTTGAAAAA
* * *
89695 CTCAAGTGATATTAATTTTGTTTCAAGT-ACAACAAATTTAAATTTGTATCTCAGAGAAAAAAAT
1 CTCAAGTGATATTAATTTTGTTTCATGTGA-AACAAATTTAAATTTGTATCTCAAAG-GAAAAAT
* ** *
89759 GTCTCAAGCGAAACGAAATTTG-TTTCGAATAAACAACAAT
64 GTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAAT
* * *
89799 CTCAAGTGAGATTAATTTTGTTTCATGTGAAGCAAATTTGAAATTTGTATCTCAAAGGAAAAATA
1 CTCAAGTGATATTAATTTTGTTTCATGTGAAACAAATTT-AAATTTGTATCTCAAAGGAAAAATG
*
89864 TCTCAAGCGAGACGAAGTTTGTTTTAAAAGAAACAACAAT
65 TCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAAT
* * * * * * * *
89904 CTCAAGTGATATTAACTTTGCTTAATGTGAAACAAATTCAAAATTTGTATATCCAAGGGAAAAGG
1 CTCAAGTGATATTAATTTTGTTTCATGTGAAACAAATT-TAAATTTGTATCTCAAAGGAAAAATG
*
89969 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAA
65 TCTCAAGCGAGACGAAATTTGTTTTAAAAGAAA
90002 TTATCTCAAG
Statistics
Matches: 175, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
104 59 0.34
105 116 0.66
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (104 bp):
CTCAAGTGATATTAATTTTGTTTCATGTGAAACAAATTTAAATTTGTATCTCAAAGGAAAAATGT
CTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAAT
Found at i:90051 original size:35 final size:36
Alignment explanation
Indices: 89968--90064 Score: 142
Period size: 35 Copynumber: 2.7 Consensus size: 36
89958 AAGGGAAAAG
* *
89968 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACT
* * *
90004 ATCTCAAGCGAGACAAAATTTGTTTTTAGA-AAACT
1 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACT
90039 GTCTCAAGCGAGACAAAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
90065 ACAAAAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
35 29 0.53
36 26 0.47
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACT
Found at i:94149 original size:32 final size:32
Alignment explanation
Indices: 94113--94174 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
94103 TGAAAAAAAG
* *
94113 ACACAAACAACAGAAAATAAATAAGTTAGTGC
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
* *
94145 ACACAAAGAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
94175 ACAGGTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
Found at i:97447 original size:3 final size:3
Alignment explanation
Indices: 97439--97505 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
97429 AATATGTAAT
*
97439 TAA TAA TAA TAA TAA TAA TAA TTAA TAA -ACA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA
*
97485 TAA -ACT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
97506 AATTAAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
2 2 0.04
3 49 0.88
4 5 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:97487 original size:21 final size:21
Alignment explanation
Indices: 97449--97505 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
97439 TAATAATAAT
97449 AATAATAATAATTAATAAACAA
1 AATAATAATAA-TAATAAACAA
**
97471 AATAATAATAATAATAAACTT
1 AATAATAATAATAATAAACAA
97492 AATAATAATAATAA
1 AATAATAATAATAA
97506 AATTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 22 0.67
22 11 0.33
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAATAATAATAATAAACAA
Found at i:100367 original size:23 final size:23
Alignment explanation
Indices: 100341--100385 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
100331 TTTGGGCTTT
100341 ATTTTGTAAAAGGG-CTCGATTTC
1 ATTTTGT-AAAGGGACTCGATTTC
*
100364 ATTTTGTGAAGGGACTCGATTT
1 ATTTTGTAAAGGGACTCGATTT
100386 TTTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (23 bp):
ATTTTGTAAAGGGACTCGATTTC
Found at i:100434 original size:3 final size:3
Alignment explanation
Indices: 100426--100476 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
100416 TGGTTTATTA
* * *
100426 AAT AAT AAT ATT TAT AAT -AT AA- ATAT TAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
100470 AAT AAT A
1 AAT AAT A
100477 TAAGGTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:100906 original size:24 final size:24
Alignment explanation
Indices: 100879--100930 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
100869 CGTTCTTTTA
*
100879 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
100903 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
100927 CGTT
1 CGTT
100931 TATGTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:100917 original size:14 final size:14
Alignment explanation
Indices: 100889--100930 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
100879 CGTTCGTGAA
100889 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
100903 CG-T---TTATGTT
1 CGTTCGGTTATGTT
100913 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
100927 CGTT
1 CGTT
100931 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:100931 original size:24 final size:24
Alignment explanation
Indices: 100889--100937 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
100879 CGTTCGTGAA
100889 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
100913 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
100937 C
1 C
100938 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:100947 original size:24 final size:24
Alignment explanation
Indices: 100895--100950 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
100885 TGAACGTTCG
* *
100895 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
100919 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
100943 TTTATGTT
1 GTTATGTT
100951 TAACCCAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:101997 original size:16 final size:16
Alignment explanation
Indices: 101972--102068 Score: 167
Period size: 16 Copynumber: 6.1 Consensus size: 16
101962 CCAAGGTTTA
101972 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
101988 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
102004 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
102020 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
102036 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
102052 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102068 T
1 T
102069 TTATTTATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 75 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:102159 original size:16 final size:16
Alignment explanation
Indices: 102138--102170 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
102128 AAAAGATTTT
102138 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102154 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102170 T
1 T
102171 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:103087 original size:20 final size:21
Alignment explanation
Indices: 103039--103098 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
103029 AACTCAGTTT
*
103039 TCAA-ATTCGCAACGCGAATA
1 TCAAGATTCGCAACGCGATTA
* *
103059 TCCAGATTCGCAACGCGATTG
1 TCAAGATTCGCAACGCGATTA
103080 T-AAGATTCGCAACGCGATT
1 TCAAGATTCGCAACGCGATT
103099 TTGAAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGATTCGCAACGCGATTA
Found at i:103123 original size:22 final size:22
Alignment explanation
Indices: 103098--103160 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
103088 GCAACGCGAT
103098 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
103120 TTTGAAAAACGTGTTGTTGCGATAG
1 TTTGAAAAA--TG-TGTTGCGAGAG
103145 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
103161 TAGTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 9 0.24
23 7 0.19
24 2 0.05
25 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:103158 original size:19 final size:19
Alignment explanation
Indices: 103134--103170 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
103124 AAAAACGTGT
103134 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
103153 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
103171 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:103521 original size:21 final size:21
Alignment explanation
Indices: 103497--103543 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
103487 CGTTGCGATT
103497 TTGGAAAATCACAACGCGAAC
1 TTGGAAAATCACAACGCGAAC
** *
103518 TTGGATTATCGCAACGCGAAC
1 TTGGAAAATCACAACGCGAAC
103539 TTGGA
1 TTGGA
103544 CTATCGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (21 bp):
TTGGAAAATCACAACGCGAAC
Found at i:103548 original size:21 final size:21
Alignment explanation
Indices: 103508--103554 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
103498 TGGAAAATCA
*
103508 CAACGCGAACTTGGATTATCG
1 CAACGCGAACTTGGACTATCG
103529 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
*
103550 TAACG
1 CAACG
103555 AATTTGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:103593 original size:20 final size:21
Alignment explanation
Indices: 103553--103593 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
103543 ACTATCGTAA
103553 CGAATTTGGAAAATCGAGTTG
1 CGAATTTGGAAAATCGAGTTG
*
103574 CGAATTTGGAAACT-GAGTTG
1 CGAATTTGGAAAATCGAGTTG
103594 AAAAATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
CGAATTTGGAAAATCGAGTTG
Found at i:111459 original size:16 final size:17
Alignment explanation
Indices: 111438--111469 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
111428 CATTCTATGC
111438 TCTTCA-TTTTAACTTA
1 TCTTCATTTTTAACTTA
111454 TCTTCATTTTTAACTT
1 TCTTCATTTTTAACTT
111470 CTATTAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (17 bp):
TCTTCATTTTTAACTTA
Found at i:114500 original size:2 final size:2
Alignment explanation
Indices: 114493--114519 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
114483 TTTCATAATT
114493 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
114520 TTATTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115193 original size:17 final size:17
Alignment explanation
Indices: 115171--115205 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
115161 AGAACGTATA
115171 AACACCTTTAAAAAAAT
1 AACACCTTTAAAAAAAT
115188 AACACCTTTAAAAAAAT
1 AACACCTTTAAAAAAAT
115205 A
1 A
115206 GCAGAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (17 bp):
AACACCTTTAAAAAAAT
Found at i:117251 original size:27 final size:27
Alignment explanation
Indices: 117221--117273 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
117211 ACGTGACATA
117221 AAGACAACATTATTAAACAATAAAAAT
1 AAGACAACATTATTAAACAATAAAAAT
117248 AAGACAACATTATTAAACAATAAAAA
1 AAGACAACATTATTAAACAATAAAAA
117274 AATAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (27 bp):
AAGACAACATTATTAAACAATAAAAAT
Found at i:118555 original size:2 final size:2
Alignment explanation
Indices: 118548--118577 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
118538 GTAAAATAAG
118548 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
118578 TAATGTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118763 original size:2 final size:2
Alignment explanation
Indices: 118756--118803 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
118746 GACATAAATT
118756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118798 TA TA TA
1 TA TA TA
118804 GGTTTATCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:133435 original size:2 final size:2
Alignment explanation
Indices: 133428--133468 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
133418 CATACAACTT
133428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
133469 TTAACATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:133612 original size:60 final size:60
Alignment explanation
Indices: 133501--133622 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
133491 GCACAAATAG
* * *
133501 TCCACCGACTATAGGTTGATGTTTTATTGAGTCTCCTAACTATTAAGAGTTACAAAATGA
1 TCCACCGACTATAGGATGATGTTTTATTGAGCCTCCTAACTATTAAAAGTTACAAAATGA
* * * * * * *
133561 TCCACCGATTATAGGATGTTGTTTTGTTGAGCCATCC-GACTTTTAAAAGTTATAGAATGA
1 TCCACCGACTATAGGATGATGTTTTATTGAGCC-TCCTAACTATTAAAAGTTACAAAATGA
133621 TC
1 TC
133623 ATATGACTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 48 0.94
61 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (60 bp):
TCCACCGACTATAGGATGATGTTTTATTGAGCCTCCTAACTATTAAAAGTTACAAAATGA
Found at i:137088 original size:3 final size:3
Alignment explanation
Indices: 137080--137107 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
137070 ACACTATGTT
137080 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
137108 CAACCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.