Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002739.1 Hibiscus syriacus cultivar Beakdansim tig00005648_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: 90991
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1665 original size:23 final size:23
Alignment explanation
Indices: 1639--1686 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1629 ATTTTTATCT
1639 CTTAAGACGTAACACTTTTGTCC
1 CTTAAGACGTAACACTTTTGTCC
*
1662 CTTAAGACGTAACATTTTTGTCC
1 CTTAAGACGTAACACTTTTGTCC
1685 CT
1 CT
1687 AATAAGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (23 bp):
CTTAAGACGTAACACTTTTGTCC
Found at i:5414 original size:86 final size:86
Alignment explanation
Indices: 5174--5955 Score: 901
Period size: 85 Copynumber: 9.2 Consensus size: 86
5164 CACCTGAGAA
* * * * * *
5174 AAGGCGATAAGGGTTATCT-ACAACAAAAGACCTTTGAGTTTGATTACATTCAGCTCAAAGACAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
*
5238 ATCAAATTTGCAGCATAGCTC
66 ATCAAATTTGCAGCATAACTC
* * * * * * *
5259 AAGGCGAGAAGGGCTATCTGTCAAC-CAAGACCTTCGAGTTTGATTACATTAAACTTAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* * *
5323 ATCAAATTTACAACATAACTT
66 ATCAAATTTGCAGCATAACTC
* * * *
5344 AAGGCGAGAAGGGTTATATGTCAACAAAAGACATTCGATTTCGATTACATTCAGTTCAAAGGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* *
5409 ATCAAATTCGTAGCATAACTC
66 ATCAAATTTGCAGCATAACTC
* * * * * *
5430 AAGGCTAGAAGGGTTATATGCCAACAAAGGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
** *
5495 ATCAAATTTATAGAATAACTC
66 ATCAAATTTGCAGCATAACTC
* *
5516 AAGGCGAGAA-GGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
5580 ATCAAATTTGCAGCATAACTC
66 ATCAAATTTGCAGCATAACTC
* * * * *
5601 AAGGAGATAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCACCTCAAAGG-AT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCA-
* * *
5664 TATCATA-TTACAACATAACTC
65 TATCAAATTTGCAGCATAACTC
* * * *
5685 AAGGCGAGAAGGG-TA---GTCAAC-CAAGACCTTTGAGTTCGATTACACTCAGCTCAAAAGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
5745 ATC-AATTTGCAGCATAACTC
66 ATCAAATTTGCAGCATAACTC
* * * * *
5765 -AGGTGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTAGATTAAGCTCAAAGACAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* *
5829 ATCCAATTCGCAG-AGTATAGCTC
66 ATCAAATTTGCAGCA-TA-A-CTC
* * *
5852 AAGGCGAGAAGGGTTATCTGTCAAC-ACAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
*
5916 ATCGAATTTGCAGCATAACTC
66 ATCAAATTTGCAGCATAACTC
*
5937 AAGGCAAGAAGGGTTATCT
1 AAGGCGAGAAGGGTTATCT
5956 TTCACCAATT
Statistics
Matches: 595, Mismatches: 85, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
79 12 0.02
80 57 0.10
81 1 0.00
83 8 0.01
84 60 0.10
85 235 0.39
86 150 0.25
87 49 0.08
88 23 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (86 bp):
AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
ATCAAATTTGCAGCATAACTC
Found at i:5539 original size:171 final size:171
Alignment explanation
Indices: 5174--6370 Score: 1323
Period size: 171 Copynumber: 7.2 Consensus size: 171
5164 CACCTGAGAA
* * * * *
5174 AAGGCGATAAGGGTTATCT-ACAACAAAAGACCTTTGAGTTTGATTACATTCAGCTCAAAGACAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * *
5238 ATCAAATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTTGAT
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
* * * *
5303 TACATTAAACTTAAAGGCACATCAAATTTACAACATAACTT
131 TACATTCAGCTCAAAGGCACATCAAATTTACAACATAACTC
* * * * * * *
5344 AAGGCGAGAAGGGTTATATGTCAACAAAAGACATTCGATTTCGATTACATTCAGTTCAAAGGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * * * * * *
5409 ATCAAATTCGTAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAGGACCTTTGAGTTCGA
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAA-GACCTTCGAGTTCGA
*
5474 TTACATTCAGCTCAAAGGCACATCAAATTTATAGA-ATAACTC
130 TTACATTCAGCTCAAAGGCACATCAAATTTACA-ACATAACTC
*
5516 AAGGCGAGAA-GGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* *
5580 ATCAAATTTGCAGCATAACTCAAGGAGATAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
* * * *
5645 TACACTCACCTCAAAGG-ATTATCATA-TTACAACATAACTC
131 TACATTCAGCTCAAAGGCA-CATCAAATTTACAACATAACTC
* * *
5685 AAGGCGAGAAGGG-TA---GTCAAC-CAAGACCTTTGAGTTCGATTACACTCAGCTCAAAAGCAT
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * *
5745 ATC-AATTTGCAGCATAACTC-AGGTGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGA
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGA
* * * * * ** * *
5808 TTAGATTAAGCTCAAAGACATATCCAATTCGCAGAGTATAGCTC
130 TTACATTCAGCTCAAAGGCACATCAAATTTACA-A-CATAACTC
* *
5852 AAGGCGAGAAGGGTTATCTGTCAAC-ACAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * *
5916 ATCGAATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTTTC-ACC-A-A--TT--A---C---
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
*
5968 -AC--TCAGCTCAAAGGAACATCAAATTTACAACATAACTC
131 TACATTCAGCTCAAAGGCACATCAAATTTACAACATAACTC
*
6006 AAGGCGAGAAGGGTTATCTGTTAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * * *
6071 ATCGAATTT--AGTATAACTGAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
* * *
6134 TACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC
131 TACATTCAGCTCAAAGGCACATCAAATTTACAACATAACTC
* * * * * *
6175 -AGGCGAGAA-AGTTATCTGTTAACAAAAGACCTTCGAGTTCGATTATATTCAGCTTAAAGGCAC
1 AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
* * * * *
6238 GTCAAATTTACAGTATAACTCAAGGCGAG-AGGGTTATCTGTCAA-TAAGACCTTCGAGTTTGAT
66 ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
* * ** * *
6301 T-CTATTCAGATCAAGGGCATGTCAAATTTACAACATAGCTT
131 TAC-ATTCAGCTCAAAGGCACATCAAATTTACAACATAACTC
* ** *
6342 AAGTCGAGAAAAGTTATTTGTCAACAAAA
1 AAGGCGAGAAGGGTTATCTGTCAACAAAA
6371 ATCGTCGAGT
Statistics
Matches: 876, Mismatches: 112, Indels: 79
0.82 0.10 0.07
Matches are distributed among these distances:
153 29 0.03
154 33 0.04
155 48 0.05
156 21 0.02
158 3 0.00
160 1 0.00
162 1 0.00
163 22 0.03
164 52 0.06
165 45 0.05
166 8 0.01
167 128 0.15
168 35 0.04
169 90 0.10
170 55 0.06
171 210 0.24
172 77 0.09
173 18 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (171 bp):
AAGGCGAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCAC
ATCAAATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGAT
TACATTCAGCTCAAAGGCACATCAAATTTACAACATAACTC
Found at i:6005 original size:69 final size:69
Alignment explanation
Indices: 5894--6024 Score: 217
Period size: 69 Copynumber: 1.9 Consensus size: 69
5884 TTCGAGTTCG
* * * *
5894 ATTACACTCAGCTCAAAGGCACATCGAATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTTTC
1 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCAAGAAGGGTTATCTTTC
5959 ACCA
66 ACCA
*
5963 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCT
1 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCAAGAAGGGTTATCT
6025 GTTAACAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (69 bp):
ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCAAGAAGGGTTATCTTTC
ACCA
Found at i:6145 original size:238 final size:238
Alignment explanation
Indices: 5473--6191 Score: 830
Period size: 238 Copynumber: 3.0 Consensus size: 238
5463 TTTGAGTTCG
* *
5473 ATTACATTCAGCTCAAAGGCACATCAAATTTATAGA-ATAACTCAAGGCGAGAA-GGTTATCTGT
1 ATTACACTCAGCTCAAAGGCACATCAAATTTACA-ACATAACTCAAGGCGAGAAGGGTTATCTGT
*
5536 CAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTGCAGCATAACTC
65 CAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTT--AGTATAACTC
* *
5601 AAGG-AGATAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCACCTCAAAGG-AT
128 AAGGCA-AGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA-
* * * * * *
5664 TATC-ATATTACAACATAACTCAAGGCGAGAAGGGTAGTCAACCAAGACCTTTGAGTTCG
191 CATCAAT-TTACAGCATAACTCAAGGCGAGAAGGGT--T--------ATCTTTCAG-CCA
* * * * * *
5723 ATTACACTCAGCTCAAAAGCATATC-AATTTGCAGCATAACTC-AGGTGAGAAGGGCTATCTGTC
1 ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTC
* * * * * * * *
5786 AACAAAAGACCTTCGAGTTCGATTAGATTAAGCTCAAAGACATATCCAATTCGCAGAGTATAGCT
66 AACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATT----TAGTATAACT
*
5851 CAAGGCGAGAAGGGTTATCTGTCAA-CACAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
127 CAAGGCAAGAAGGGTTATCTGTCAACCA-AGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* *
5915 CATCGAATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTTTCA-CCA
191 CATC-AATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTTTCAGCCA
* *
5963 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTT
1 ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTC
* * *
6028 AACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCGAATTTAGTATAACTGAAG
66 AACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTAGTATAACTCAAG
6093 GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
131 GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-
* *
6158 AATTTACAGCATAGCTC-AGGCGAGAA-AGTTATCT
195 AATTTACAGCATAACTCAAGGCGAGAAGGGTTATCT
6192 GTTAACAAAA
Statistics
Matches: 403, Mismatches: 52, Indels: 42
0.81 0.10 0.08
Matches are distributed among these distances:
236 7 0.02
237 8 0.02
238 86 0.21
239 2 0.00
240 23 0.06
241 15 0.04
242 68 0.17
248 8 0.02
249 68 0.17
250 25 0.06
251 65 0.16
252 26 0.06
253 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (238 bp):
ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTC
AACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTAGTATAACTCAAG
GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA
ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTTTCAGCCA
Found at i:6146 original size:83 final size:85
Alignment explanation
Indices: 5963--6386 Score: 443
Period size: 83 Copynumber: 5.0 Consensus size: 85
5953 TCTTTCACCA
* * *
5963 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTT
1 ATTACACTCAGCTCAAAGGCACATCAAATTTA-AGCATAACTCAAGGCGAGAAGGGTTATCTGTC
*
6028 AACAAAAGACCTTTGAGTTCG
65 AACAAAAGACCTTCGAGTTCG
* * * *
6049 ATTACACTCAGCTCAAAGGCACATCGAATTT-AGTATAACTGAAGGCAAGAAGGGTTATCTGTCA
1 ATTACACTCAGCTCAAAGGCACATCAAATTTAAGCATAACTCAAGGCGAGAAGGGTTATCTGTCA
*
6113 AC-CAAGACCTTCGAGTTCG
66 ACAAAAGACCTTCGAGTTCG
* * *
6132 ATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC-AGGCGAGAA-AGTTATCTGTT
1 ATTACACTCAGCTCAAAGGCACATCAAATTTA-AGCATAACTCAAGGCGAGAAGGGTTATCTGTC
6195 AACAAAAGACCTTCGAGTTCG
65 AACAAAAGACCTTCGAGTTCG
* * * * *
6216 ATTATATTCAGCTTAAAGGCACGTCAAATTTACAGTATAACTCAAGGCGAG-AGGGTTATCTGTC
1 ATTACACTCAGCTCAAAGGCACATCAAATTTA-AGCATAACTCAAGGCGAGAAGGGTTATCTGTC
* *
6280 -A-ATAAGACCTTCGAGTTTG
65 AACAAAAGACCTTCGAGTTCG
* * * ** * * * * ** *
6299 ATT-CTATTCAGATCAAGGGCATGTCAAATTTACAACATAGCTTAAGTCGAGAAAAGTTATTTGT
1 ATTAC-ACTCAGCTCAAAGGCACATCAAATTTA-AGCATAACTCAAGGCGAGAAGGGTTATCTGT
* *
6363 CAACAAAA-ATCGTCGAGTTCG
64 CAACAAAAGACCTTCGAGTTCG
6384 ATT
1 ATT
6387 CCATTCACTC
Statistics
Matches: 285, Mismatches: 44, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
83 113 0.40
84 103 0.36
85 37 0.13
86 32 0.11
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (85 bp):
ATTACACTCAGCTCAAAGGCACATCAAATTTAAGCATAACTCAAGGCGAGAAGGGTTATCTGTCA
ACAAAAGACCTTCGAGTTCG
Found at i:6289 original size:167 final size:167
Alignment explanation
Indices: 5963--6386 Score: 532
Period size: 167 Copynumber: 2.5 Consensus size: 167
5953 TCTTTCACCA
* * *
5963 ATTACACTCAGCTCAAAGGAACATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTT
1 ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTC-AGGCGAGAA-AGTTATCTGTT
* * *
6028 AACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCGAATTTAGTATAACTGAAG
64 AACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTAGTATAACTCAAG
6093 GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCG
129 GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCG
*
6132 ATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAGGCGAGAAAGTTATCTGTTAA
1 ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAGGCGAGAAAGTTATCTGTTAA
* * * *
6197 CAAAAGACCTTCGAGTTCGATTATATTCAGCTTAAAGGCACGTCAAATTTACAGTATAACTCAAG
66 CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTT--AGTATAACTCAAG
* * *
6262 GCGAG-AGGGTTATCTGTCAA-TAAGACCTTCGAGTTTG
129 GCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCG
* * * ** * * *
6299 ATT-CTATTCAGATCAAGGGCATGTCAAATTTACAACATAGCTTAAGTCGAGAAAAGTTATTTGT
1 ATTAC-ACTCAGCTCAAAGGCACATCAAATTTACAACATAGC-TCAGGCGAG-AAAGTTATCTGT
* * *
6363 CAACAAAA-ATCGTCGAGTTCGATT
63 TAACAAAAGACCTTCGAGTTCGATT
6387 CCATTCACTC
Statistics
Matches: 224, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
166 1 0.00
167 104 0.46
168 45 0.20
169 74 0.33
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (167 bp):
ATTACACTCAGCTCAAAGGCACATCAAATTTACAACATAGCTCAGGCGAGAAAGTTATCTGTTAA
CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTAGTATAACTCAAGGC
AAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCG
Found at i:7144 original size:12 final size:11
Alignment explanation
Indices: 7130--7175 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
7120 TATTATGTTG
7130 TATATTATATA
1 TATATTATATA
*
7141 GTATA-AATATA
1 -TATATTATATA
7152 TATATTATATCA
1 TATATTATAT-A
7164 TATATTATATA
1 TATATTATATA
7175 T
1 T
7176 CATTGTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 4 0.13
11 11 0.37
12 15 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
TATATTATATA
Found at i:8610 original size:24 final size:23
Alignment explanation
Indices: 8581--8632 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
8571 ATTTTTATTT
* * *
8581 ATTTATTTATTATTTCTTTCTTCG
1 ATTTATTTAATATTTATTT-TTCA
8605 ATTTATTTAATATTTATTTTTCA
1 ATTTATTTAATATTTATTTTTCA
8628 ATTTA
1 ATTTA
8633 ACTTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTATTTAATATTTATTTTTCA
Found at i:12528 original size:20 final size:21
Alignment explanation
Indices: 12503--12547 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12493 TCAGAAATGT
* *
12503 TAAAAA-ATTAATGTTTTAGG
1 TAAAAATAATAATGATTTAGG
*
12523 TAAAAATAATAATGATTTATG
1 TAAAAATAATAATGATTTAGG
12544 TAAA
1 TAAA
12548 TTTTTTTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (21 bp):
TAAAAATAATAATGATTTAGG
Found at i:23168 original size:9 final size:9
Alignment explanation
Indices: 23154--23183 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
23144 TATTTTCTTC
23154 TTATTTTAT
1 TTATTTTAT
23163 TTATTTTAT
1 TTATTTTAT
*
23172 TTATTTTTT
1 TTATTTTAT
23181 TTA
1 TTA
23184 CTGTCTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTAT
Found at i:26457 original size:15 final size:15
Alignment explanation
Indices: 26437--26465 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26427 CACATACAAA
26437 ACAACAAAAAAATAG
1 ACAACAAAAAAATAG
26452 ACAACAAAAAAATA
1 ACAACAAAAAAATA
26466 ATAAATTACC
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:0.76, C:0.14, G:0.03, T:0.07
Consensus pattern (15 bp):
ACAACAAAAAAATAG
Found at i:27397 original size:20 final size:20
Alignment explanation
Indices: 27361--27399 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27351 GACACTGAGA
*
27361 GTGCATGACGACTTTCAACC
1 GTGCATGACGACCTTCAACC
27381 GTGCATGGA-GACCTTCAAC
1 GTGCAT-GACGACCTTCAAC
27400 AGCTCACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (20 bp):
GTGCATGACGACCTTCAACC
Found at i:28213 original size:20 final size:20
Alignment explanation
Indices: 28169--28421 Score: 107
Period size: 20 Copynumber: 12.5 Consensus size: 20
28159 AATGACCAAT
* * *
28169 AAAATCGTAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
28188 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
28208 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
28228 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
28248 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
28269 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
28292 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
28312 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
28332 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
28352 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
28372 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
28392 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
28412 ATAATCGCAA
1 AAAATCGCAA
28422 GAATAGTTAA
Statistics
Matches: 189, Mismatches: 36, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.08
20 145 0.77
21 14 0.07
23 14 0.07
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:28356 original size:40 final size:40
Alignment explanation
Indices: 28294--28421 Score: 193
Period size: 40 Copynumber: 3.2 Consensus size: 40
28284 TTTAGAAGAA
* *
28294 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* * *
28334 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
* *
28374 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAT
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
28414 AATCGCAA
1 AATCGCAA
28422 GAATAGTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
Found at i:28365 original size:60 final size:60
Alignment explanation
Indices: 28294--28421 Score: 220
Period size: 60 Copynumber: 2.1 Consensus size: 60
28284 TTTAGAAGAA
* *
28294 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGACTGAGAG
* *
28354 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAT
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGACTGAGAG
28414 AATCGCAA
1 AATCGCAA
28422 GAATAGTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (60 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGACTGAGAG
Found at i:28499 original size:6 final size:6
Alignment explanation
Indices: 28488--28548 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
28478 GCGGACGTGT
28488 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACC- CGACC-
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA
28534 CGACC- CGACC- CGACC
1 CGACCA CGACCA CGACC
28549 CGAGACGAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.36
6 35 0.64
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:29254 original size:6 final size:6
Alignment explanation
Indices: 29238--29275 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
29228 TCTCGTCTCG
29238 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
29276 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:29378 original size:20 final size:20
Alignment explanation
Indices: 29353--29396 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29343 TTTTTAACTA
*
29353 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
29373 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
29393 TTCT
1 TTCT
29397 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:29406 original size:20 final size:20
Alignment explanation
Indices: 29383--29700 Score: 183
Period size: 20 Copynumber: 15.6 Consensus size: 20
29373 TTCTTTTTAA
29383 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
29403 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
29423 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
29443 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
29463 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
29483 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
29506 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
29526 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
29546 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
29566 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
29589 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
29610 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
29628 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
29650 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
29670 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
29689 CGTTGCGATTTT
1 CGTTGCGATTTT
29701 ATTGGTCATT
Statistics
Matches: 243, Mismatches: 44, Indels: 23
0.78 0.14 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 176 0.72
21 14 0.06
22 6 0.02
23 28 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:29429 original size:40 final size:40
Alignment explanation
Indices: 29385--29596 Score: 244
Period size: 40 Copynumber: 5.2 Consensus size: 40
29375 CTTTTTAACG
* * * *
29385 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* * * *
29425 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
29465 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
* *
29508 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
29548 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
29591 TTGCGA
1 TTGCGA
29597 ACTTGGAAGC
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
40 92 0.62
41 3 0.02
42 6 0.04
43 47 0.32
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
Found at i:29532 original size:83 final size:83
Alignment explanation
Indices: 29385--29596 Score: 286
Period size: 83 Copynumber: 2.6 Consensus size: 83
29375 CTTTTTAACG
* * * * * *
29385 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
* * *
29447 GCGATTCTCTCAGTCGCA
66 GCGATTCTATAAATCGCA
* * *
29465 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
29530 GCGATTCTATAAATCGCA
66 GCGATTCTATAAATCGCA
*
29548 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
29597 ACTTGGAAGC
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 90 0.78
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
GCGATTCTATAAATCGCA
Found at i:29690 original size:19 final size:20
Alignment explanation
Indices: 29650--29700 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
29640 TTCTTTTTAA
*
29650 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
29670 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
29689 CGTTGCGATTTT
1 CGTTGCGATTTT
29701 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:35007 original size:20 final size:20
Alignment explanation
Indices: 34982--35019 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34972 TTTGGTTCAC
34982 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
*
35002 GGAATGTAAGATTACCAG
1 GGAATGGAAGATTACCAG
35020 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:35243 original size:37 final size:36
Alignment explanation
Indices: 35171--35244 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
35161 GTTGAAAAAT
* *
35171 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
*
35207 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
35244 A
1 A
35245 AAATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:50005 original size:39 final size:39
Alignment explanation
Indices: 49949--50105 Score: 151
Period size: 39 Copynumber: 4.1 Consensus size: 39
49939 ATATACATAC
* * *
49949 ATATATATTATACAG-TTTGAAATCATTTTTAAAATATAT
1 ATATATAATATATAGTTTTGAAAACATTTTTAAAA-ATAT
* *
49988 ATATATAATATATAGTTTTGAAAACATGTTTAAAAACAT
1 ATATATAATATATAGTTTTGAAAACATTTTTAAAAATAT
* * * * * *
50027 TTATTTATTATATAGTTTTTAGAACA-TTTTGAAAATA-
1 ATATATAATATATAGTTTTGAAAACATTTTTAAAAATAT
* * *
50064 A-ATATAATATATAGTTTTTAAAACATTTTTGAAAATGT
1 ATATATAATATATAGTTTTGAAAACATTTTTAAAAATAT
50102 ATAT
1 ATAT
50106 TATATAGTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
36 21 0.22
37 10 0.10
38 9 0.09
39 39 0.41
40 17 0.18
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (39 bp):
ATATATAATATATAGTTTTGAAAACATTTTTAAAAATAT
Found at i:50081 original size:75 final size:71
Alignment explanation
Indices: 49990--50140 Score: 203
Period size: 71 Copynumber: 2.1 Consensus size: 71
49980 AAATATATAT
* *
49990 ATATAATATATAGTTTTGAAAACATGTTTAAAAACATTTATTTATTATATAGTTTTTAGAACATT
1 ATATAATATATAGTTTTGAAAACAT-TTTAAAAA-ATGTA--TATTATATAGTTTTTAAAACATT
50055 TTGAAAATAA
62 TTGAAAATAA
* ** **
50065 ATATAATATATAGTTTTTAAAACATTTTTGAAAATGTATATTATATAGTTTTTAAAATGTTTTGA
1 ATATAATATATAGTTTTGAAAACATTTTAAAAAATGTATATTATATAGTTTTTAAAACATTTTGA
50130 AAATAA
66 AAATAA
50136 ATATA
1 ATATA
50141 GTTTTTAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
71 35 0.51
73 4 0.06
74 6 0.09
75 24 0.35
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (71 bp):
ATATAATATATAGTTTTGAAAACATTTTAAAAAATGTATATTATATAGTTTTTAAAACATTTTGA
AAATAA
Found at i:50082 original size:36 final size:36
Alignment explanation
Indices: 49990--50140 Score: 153
Period size: 36 Copynumber: 4.1 Consensus size: 36
49980 AAATATATAT
* * **
49990 ATATAATATATAGTTTTGAAAACATGTTTAAAAACATTT
1 ATATAATATATAGTTTTTAAAACAT-TTT-GAAA-ATAA
* * *
50029 ATTTATTATATAGTTTTTAGAACATTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
50065 ATATAATATATAGTTTTTAAAACATTTTTGAAAAT--
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAATAA
* * **
50100 GTATATTATATAGTTTTTAAAATGTTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
50136 ATATA
1 ATATA
50141 GTTTTTAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
34 10 0.11
35 20 0.21
36 27 0.29
37 13 0.14
38 3 0.03
39 21 0.22
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:50150 original size:18 final size:18
Alignment explanation
Indices: 50123--50157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50113 TTTTTAAAAT
*
50123 GTTTTGAAAATAAATATA
1 GTTTTGAAAAAAAATATA
*
50141 GTTTTTAAAAAAAATAT
1 GTTTTGAAAAAAAATAT
50158 TTTGAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
GTTTTGAAAAAAAATATA
Found at i:50163 original size:104 final size:99
Alignment explanation
Indices: 50036--50324 Score: 287
Period size: 104 Copynumber: 2.8 Consensus size: 99
50026 TTTATTTATT
* * *
50036 ATATAGTTTTTAGAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTTTTGAAAATG
1 ATATAGTTTTAAAAACATTTTGAAAAAAAATATAATATATAGTTTTTAAAACATTTTTGAAAAT-
50101 TATATTATATAGTTTTTAAAAT-GTTTTGAAAATAA
65 TATATTATATAGTTTTTAAAATAGTTTTGAAAA-AA
* * * * * *
50136 ATATAGTTTTTAAAAAAAATATTTTGAAAACATATATATTATATAGTTTTGAAATCA-TTTTGAA
1 ATATAG-TTTT---AAAAACATTTTGAAAAAAAATATAATATATAGTTTTTAAAACATTTTTGAA
* * **
50200 AACTTATATGGTATATAGTTTTAAAAATATTTTTGAAAACC
62 AA-TTATAT--TATATAGTTTTTAAAATAGTTTTGAAAAAA
* * * *
50241 ATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATA-ATTTTAAAATATTTTTTGAAAA
1 ATATAGTTTTAAAAACATTTTGAAAAAAA-ATATAATATATAGTTTTTAAAACA-TTTTTGAAAA
50305 TATATATTATATAGGTTTTT
64 T-TATATTATATA-GTTTTT
50325 GGAAAATATT
Statistics
Matches: 153, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
100 6 0.04
101 31 0.20
102 17 0.11
103 28 0.18
104 40 0.26
105 22 0.14
106 9 0.06
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (99 bp):
ATATAGTTTTAAAAACATTTTGAAAAAAAATATAATATATAGTTTTTAAAACATTTTTGAAAATT
ATATTATATAGTTTTTAAAATAGTTTTGAAAAAA
Found at i:50197 original size:69 final size:65
Alignment explanation
Indices: 50067--50238 Score: 170
Period size: 69 Copynumber: 2.5 Consensus size: 65
50057 GAAAATAAAT
* * *
50067 ATAATATATAGTTTTTAAAACATTTTTGAAAATGTATATTATATAGTTTTTAAAATGTTTTGAAA
1 ATAATATATAGTTTTTAAAAAATTTTTGAAAATATATATTATATAGTTTTTAAAATATTTTGAAA
*
50132 ATAA-ATATAGTTTTTAAAAAAAATATTTTGAAAACATATATATTATATAG-TTTTGAAATCATT
1 ATAATATATAGTTTTT--AAAAAAT-TTTTG-AAA-ATATATATTATATAGTTTTTAAAAT-ATT
50195 TTGAAA
60 TTGAAA
50201 ACTTATATGGTATATAG-TTTTAAAAATATTTTTGAAAA
1 A--TA-A---TATATAGTTTTTAAAAA-ATTTTTGAAAA
50239 CCATATAGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 22
0.77 0.03 0.19
Matches are distributed among these distances:
64 11 0.12
65 4 0.04
66 6 0.07
67 5 0.06
68 11 0.12
69 23 0.26
71 3 0.03
72 4 0.04
73 10 0.11
74 2 0.02
75 4 0.04
76 6 0.07
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (65 bp):
ATAATATATAGTTTTTAAAAAATTTTTGAAAATATATATTATATAGTTTTTAAAATATTTTGAAA
Found at i:50201 original size:36 final size:36
Alignment explanation
Indices: 50150--50245 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
50140 AGTTTTTAAA
*
50150 AAAAATATTTTGAAAACATATATATTATATAGTTTT
1 AAAAATATTTTGAAAACATATATAGTATATAGTTTT
* * *
50186 -GAAATCATTTTGAAAACTTATATGGTATATAGTTTT
1 AAAAAT-ATTTTGAAAACATATATAGTATATAGTTTT
50222 AAAAATATTTTTGAAAACCATATA
1 AAAAATA-TTTTGAAAA-CATATA
50246 GTTTTGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
35 4 0.08
36 28 0.56
37 13 0.26
38 5 0.10
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (36 bp):
AAAAATATTTTGAAAACATATATAGTATATAGTTTT
Found at i:50254 original size:65 final size:66
Alignment explanation
Indices: 50176--50304 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
50166 CATATATATT
* * ** ** *
50176 ATATAGTTTTGAAATCATTTT-GAAAACTTATATGGTATATAGTTTTAAAA-ATATTTTTGAAAA
1 ATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATAATTTTAAAATAT-TTTTTGAAAA
50239 CC
65 CC
50241 ATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATAATTTTAAAATATTTTTTGAAAA
1 ATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATAATTTTAAAATATTTTTTGAAAA
50305 TATATATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
65 20 0.36
66 33 0.60
67 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (66 bp):
ATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATAATTTTAAAATATTTTTTGAAAAC
C
Found at i:50267 original size:29 final size:29
Alignment explanation
Indices: 50212--50267 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
50202 CTTATATGGT
* **
50212 ATATAGTTTTAAAAATATTTTTGAAAACC
1 ATATAGTTTTAAAAACATTTTCAAAAACC
*
50241 ATATAGTTTTGAAAACATTTTCAAAAA
1 ATATAGTTTTAAAAACATTTTCAAAAA
50268 AATATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAGTTTTAAAAACATTTTCAAAAACC
Found at i:50282 original size:37 final size:35
Alignment explanation
Indices: 50241--50323 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
50231 TTTGAAAACC
50241 ATATAGTTTTGAAAACATTTTCAAAAAAATATATAAT
1 ATATAGTTTT-AAAACATTTT-AAAAAAATATATAAT
* * *** *
50278 ATATAATTTTAAAATATTTTTTGAAAATATATATT
1 ATATAGTTTTAAAACATTTTAAAAAAATATATAAT
50313 ATATAGGTTTT
1 ATATA-GTTTT
50324 TGGAAAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 16 0.42
36 13 0.34
37 9 0.24
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATAGTTTTAAAACATTTTAAAAAAATATATAAT
Found at i:50310 original size:65 final size:65
Alignment explanation
Indices: 50175--50310 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 65
50165 ACATATATAT
* * ** ** *
50175 TATATAGTTTTGAAATCATTTTGAAAACTTATATGGTATATAGTTTTAAAAATATTTTTGAAAAC
1 TATATAGTTTTGAAAACATTTTAAAAAAATATATAATATATAATTTTAAAAATATTTTTGAAAAC
*
50240 CATATAGTTTTGAAAACATTTTCAAAAAAATATATAATATATAATTTT-AAAATATTTTTTGAAA
1 TATATAGTTTTGAAAACATTTT-AAAAAAATATATAATATATAATTTTAAAAATA-TTTTTGAAA
50304 A-
64 AC
50305 TATATA
1 TATATA
50311 TTATATAGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 31 0.52
66 29 0.48
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (65 bp):
TATATAGTTTTGAAAACATTTTAAAAAAATATATAATATATAATTTTAAAAATATTTTTGAAAAC
Found at i:50357 original size:22 final size:22
Alignment explanation
Indices: 50334--50375 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
50324 TGGAAAATAT
50334 TTTATTT-TATCTTTATTATTA
1 TTTATTTATATCTTTATTATTA
* *
50355 TTTATTTATTTCTTTTTTATT
1 TTTATTTATATCTTTATTATT
50376 TTGTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTATATCTTTATTATTA
Found at i:50373 original size:25 final size:26
Alignment explanation
Indices: 50345--50402 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
50335 TTATTTTATC
*
50345 TTTATTATT-ATTTATTTATTTC-TTT
1 TTTATT-TTGATTTATTAATTTCATTT
*
50370 TTTATTTTGTTTTATTAATTTCATTT
1 TTTATTTTGATTTATTAATTTCATTT
50396 TTTATTT
1 TTTATTT
50403 CATTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 17 0.59
26 10 0.34
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTATTTTGATTTATTAATTTCATTT
Found at i:50404 original size:12 final size:12
Alignment explanation
Indices: 50333--50409 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 12
50323 TTGGAAAATA
*
50333 TTTTATTTTATCT
1 TTTTATTTCAT-T
50346 TTATTA-TT-ATT
1 TT-TTATTTCATT
50357 TATTTATTTC-TT
1 T-TTTATTTCATT
**
50369 TTTTATTTTGTT
1 TTTTATTTCATT
50381 TTATTAATTTCATT
1 TT-TT-ATTTCATT
50395 TTTTATTTCATT
1 TTTTATTTCATT
50407 TTT
1 TTT
50410 CTTTCCAGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
11 12 0.22
12 23 0.43
13 8 0.15
14 11 0.20
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTTATTTCATT
Found at i:51658 original size:16 final size:14
Alignment explanation
Indices: 51633--51730 Score: 60
Period size: 13 Copynumber: 7.1 Consensus size: 14
51623 TAAAATCCAA
51633 TTTT-TATTTATCATT
1 TTTTCTATTTAT--TT
51648 TTTTCTATTTATTT
1 TTTTCTATTTATTT
51662 TTTTCTATTT-TTT
1 TTTTCTATTTATTT
*** *
51675 TAAACTTATTTAATT
1 TTTTC-TATTTATTT
*
51690 TTTT-TATTTAATT
1 TTTTCTATTTATTT
* * *
51703 TTTCCTCTTT-TTC
1 TTTTCTATTTATTT
*
51716 TTTTGTATTTATTT
1 TTTTCTATTTATTT
51730 T
1 T
51731 GATTTGTTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
13 25 0.40
14 24 0.38
15 7 0.11
16 7 0.11
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTTCTATTTATTT
Found at i:53874 original size:24 final size:24
Alignment explanation
Indices: 53844--53899 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
53834 CAAAGAAGAT
53844 GGAGGAAAAAATCAAGCAGTTGGA
1 GGAGGAAAAAATCAAGCAGTTGGA
*
53868 GGAGGAAAAAATCAAGTAGTTGGA
1 GGAGGAAAAAATCAAGCAGTTGGA
53892 GGA-GAAAA
1 GGAGGAAAA
53900 TGAAGGTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.48, C:0.05, G:0.34, T:0.12
Consensus pattern (24 bp):
GGAGGAAAAAATCAAGCAGTTGGA
Found at i:53908 original size:22 final size:21
Alignment explanation
Indices: 53843--53910 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 21
53833 GCAAAGAAGA
*
53843 TGGAGGAAAAAATCAAGCAGT
1 TGGAGGAAAAAATCAAGTAGT
53864 TGGAGGAGGAAAAAATCAAGTAGT
1 T---GGAGGAAAAAATCAAGTAGT
* *
53888 TGGAGGAGAAAATGAAGGTAGT
1 TGGAGGAAAAAATCAA-GTAGT
53910 T
1 T
53911 AAAGGAGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 14 0.35
22 6 0.15
24 20 0.50
ACGTcount: A:0.44, C:0.04, G:0.34, T:0.18
Consensus pattern (21 bp):
TGGAGGAAAAAATCAAGTAGT
Found at i:55597 original size:95 final size:95
Alignment explanation
Indices: 55433--55621 Score: 272
Period size: 95 Copynumber: 2.0 Consensus size: 95
55423 ATATTATTTA
* ** ** *
55433 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTTCAGCTTTATGGATAAT
1 TATACAATAAAACTTGAGCGGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
*
55498 ATTCAGCTAGCCTGATAAAGGTGATTATAC
66 ATTCAGCTAACCTGATAAAGGTGATTATAC
* *
55528 TATACAATAAAACTTGAGCGGTCCCTCTA-AGGCAATTGGTTAAACTCCCCGGCTTTATGGATAA
1 TATACAATAAAACTTGAGCGGTCCCTCTAGA-GCAATTGGTTAAACGCCCCAGCTTTATGGATAA
*
55592 GATTCAGCTAACCTGATAAAGGTGTTTATA
65 GATTCAGCTAACCTGATAAAGGTGATTATA
55622 TATTAAGCTG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 82 0.99
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCGGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:56993 original size:85 final size:84
Alignment explanation
Indices: 56764--57412 Score: 590
Period size: 85 Copynumber: 7.8 Consensus size: 84
56754 AAAACAAACT
* * * * * * * ** *
56764 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCACC-AAGACCTTCGAGTTCGACCACGC
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
* * ** *
56828 CCAGC-TCCAATGCACATT
66 TCAGCTTCGAGGGCACATC
* * * * *
56846 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCCTCAAGTTCGATTACAC
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
*
56908 TCAGCTTCGAGGGCATATC
66 TCAGCTTCGAGGGCACATC
* * *
56927 ATTTACATCATAACTCAAGGT-TAGAAGGGTTATCTGTCACCAAAAGACCCGCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAA-GTCTAGAAGGGTTATCTGTCACC-AAAGACCCTCGAGTTCGATTAC
56991 ACTCAGCTTCGAGGGCACATC
64 ACTCAGCTTCGAGGGCACATC
* * * * *
57012 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTC-ACCAAAGACCCTCGAGTTCGATTACA
* * *
57077 CTTAGC-TCCAAGGCACATC
65 CTCAGCTTCGAGGGCACATC
* * * * * * * *
57096 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CTAAAGAACCTCGAGTTTGATTTCAC
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
57158 TCAGCTTCGAGGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * *
57177 ATTTACAGCATAATTCAA-TGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGATTTCGACTAC
1 ATTTGCAGCATAACTCAAGT-CTAGAAGGGTTATCTGTCACC-AAAGACCCTCGAGTTCGATTAC
* * *
57241 GCTCAGC-TCCAAGGCACATC
64 ACTCAGCTTCGAGGGCACATC
* * * * * * *
57261 ATTTGTAGCATAGCTTAAGTCAAGAAGGGATAT-T-T-GCCAAAGACCCGCGAGTTCGATTACAC
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
*
57323 TCAGCTTTGAGGGCACATC
66 TCAGCTTCGAGGGCACATC
* * * * * *
57342 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTTGTCAACAAAGACCTTTGAGTCCGATTACAC
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
57407 TCAGCT
66 TCAGCT
57413 CAACAACACA
Statistics
Matches: 454, Mismatches: 93, Indels: 38
0.78 0.16 0.06
Matches are distributed among these distances:
79 1 0.00
80 70 0.15
81 114 0.25
82 35 0.08
83 2 0.00
84 111 0.24
85 118 0.26
86 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCCTCGAGTTCGATTACAC
TCAGCTTCGAGGGCACATC
Found at i:57188 original size:165 final size:164
Alignment explanation
Indices: 56839--57439 Score: 660
Period size: 165 Copynumber: 3.6 Consensus size: 164
56829 CAGCTCCAAT
* * * * *
56839 GCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCCTCAAGTTCG
1 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCG
* * * * * * * * * *
56901 ATTACACTCAGCTTCGAGGGCATATCATTTACATCATAACTCAAGGT-TAGAAGGGTTATCTGTC
66 ACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAA-GTCAAGAAGGGATATCTG--
56965 ACCAAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGG
127 --CAAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGG
57005 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTC
1 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTC
* * * * *
57070 GACTACGCTTAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTA
65 GACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGATATCTGCAA
* * * *
57135 AAGAACCTCGAGTTTGATTTCACTCAGCTTCGAGG
130 AAGACCCGCGAGTTCGATTACACTCAGCTTCGAGG
* * *
57170 GCACATCATTTACAGCATAA-TTCAA-TGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGATT
1 GCACATCATTTGCAGCATAACTT-AAGT-CGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGT
* * *
57233 TCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCAAGAAGGGATATTTGC
63 TCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGATATCTGC
* *
57298 CAAAGACCCGCGAGTTCGATTACACTCAGCTTTGAGG
128 AAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGG
* * * * * * *
57335 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTTGTCAACAAAGACCTTTGAGTCCG
1 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCG
* * *
57400 ATTACACTCAGCTCAACAA--CACATCATTTGCGGTATAGCT
66 ACTACACTCAGCTC--CAAGGCACATCATTTGCAGCATAGCT
57440 CAGGGCTAGA
Statistics
Matches: 374, Mismatches: 49, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
164 50 0.13
165 215 0.57
166 45 0.12
168 2 0.01
169 37 0.10
170 25 0.07
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (164 bp):
GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCG
ACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGATATCTGCAAA
AGACCCGCGAGTTCGATTACACTCAGCTTCGAGG
Found at i:57248 original size:250 final size:248
Alignment explanation
Indices: 56786--57370 Score: 764
Period size: 250 Copynumber: 2.4 Consensus size: 248
56776 GCTCAAGGCC
* * * * * *
56786 AGAAGGGCTATCTGCCACC-AAGACCTTCGAGTTCGACCACGCCCAGCTCCAATGCACATTATTT
1 AGAAGGGATATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
56850 GCAGCATAACTTAAGTCGAGAAGGGCTATCTGCTAAAGACCCTCAAGTTCGATTACACTCAGCTT
66 GCAGCATAACTTAAGTCGAGAAGGGCTATCTGCTAAAGAACCTCAAGTTCGATTACACTCAGCTT
* * *
56915 CGAGGGCATATCATTTACATCATAACTCAAGGTTAGAAGGGTTATCTGTCACCAAAAGACCCGCG
131 CGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCCGCG
* * * *
56980 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
196 AGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* *
57034 AGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCACATCATT
1 AGAAGGGATATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
57099 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGAACCTCGAGTTTGATTTCACTCAGCT
65 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCTAAAGAACCTCAAGTTCGATTACACTCAGCT
* * **
57164 TCGAGGGCACATCATTTACAGCATAATTCAATGCTAGAAGGGTTATCTGTCACCAAAAGACCTTC
130 TCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCCGC
* * * *
57229 GATTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCA
195 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* ** * * ** *
57283 AGAAGGGATAT-T-T-GCCAAAGACCCGCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATT
1 AGAAGGGATATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* * *
57345 TGCAGCATAACTCAAGGCTAGAAGGG
65 TGCAGCATAACTTAAGTCGAGAAGGG
57371 TTATTTGTCA
Statistics
Matches: 293, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
245 26 0.09
246 35 0.12
247 1 0.00
248 15 0.05
249 43 0.15
250 173 0.59
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (248 bp):
AGAAGGGATATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCGAGAAGGGCTATCTGCTAAAGAACCTCAAGTTCGATTACACTCAGCTT
CGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCCGCG
AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
Found at i:57929 original size:39 final size:38
Alignment explanation
Indices: 57857--58047 Score: 158
Period size: 37 Copynumber: 5.1 Consensus size: 38
57847 ATATACATAC
* * * *
57857 ATATATATTATACAG-TTTGAAATCATTTAAAAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAAAAT
*
57894 ATATATAATATATAGTTTTGAAAACATGTTTAAAAACAT
1 ATATATAATATATAGTTTTGAAAACAT-TTTAAAAAAAT
* * * * *
57933 TTATATATTATATAGTTTTTAGAACATTTT-GAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAAAAT
* * * **
57970 AAATATAATATATAGTTTTTAAAACGTTTT-TGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTAAAAAAAT
* * *
58007 GTATAT--TATATAGTTTTTAAAACGTTTTGAAAATAAAT
1 ATATATAATATATAGTTTTGAAAACATTTT-AAAA-AAAT
58045 ATA
1 ATA
58048 GTTAAAAAAA
Statistics
Matches: 126, Mismatches: 23, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
35 22 0.17
37 53 0.42
38 19 0.15
39 32 0.25
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTAAAAAAAT
Found at i:57989 original size:37 final size:36
Alignment explanation
Indices: 57888--58141 Score: 215
Period size: 36 Copynumber: 7.1 Consensus size: 36
57878 ATCATTTAAA
* *
57888 AAAAATATATATAATATATAGTTTTGAAAACATGTTTA
1 AAAAAT-TATATAATATATAGTTTTTAAAACAT-TTTG
* *
57926 AAAACATTTATATATTATATAGTTTTTAGAACATTTTG
1 AAAA-A-TTATATAATATATAGTTTTTAAAACATTTTG
* *
57964 AAAAATAAATATAATATATAGTTTTTAAAACGTTTTTG
1 AAAAAT-TATATAATATATAGTTTTTAAAAC-ATTTTG
*
58002 -AAAATGTATAT--TATATAGTTTTTAAAACGTTTTG
1 AAAAAT-TATATAATATATAGTTTTTAAAACATTTTG
***
58036 ---AA--A-ATAA-ATATAGTTAAAAAAACATTTTG
1 AAAAATTATATAATATATAGTTTTTAAAACATTTTG
* * *
58065 AAAACA-TATATATTATATAGTTTTGAAATCATTTTG
1 AAAA-ATTATATAATATATAGTTTTTAAAACATTTTG
* *
58101 AAAACTTATATAATATATAGTTTTTAAAATATTTTTG
1 AAAAATTATATAATATATAGTTTTTAAAACA-TTTTG
58138 AAAA
1 AAAA
58142 CTATATAGTT
Statistics
Matches: 176, Mismatches: 25, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.01
29 19 0.11
32 3 0.02
33 1 0.01
34 6 0.03
35 20 0.11
36 44 0.25
37 40 0.23
38 16 0.09
39 24 0.14
40 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAAATTATATAATATATAGTTTTTAAAACATTTTG
Found at i:58062 original size:101 final size:99
Alignment explanation
Indices: 57955--58228 Score: 263
Period size: 101 Copynumber: 2.7 Consensus size: 99
57945 TAGTTTTTAG
57955 AACATTTTGAAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAAAATGTATATTATATAG
1 AACATTTTGAAAAATAAATATAATATATAGTTTTTAAAAC-TTTTTGAAAAT-TATATTATATAG
*
58020 TTTTTAAAA-CGTTTTGAAAA-TAAATATAGTTAAAAA
64 TTTTTAAAATAGTTTTGAAAACT--ATATAGTTAAAAA
* * * *
58056 AACATTTTGAAAACAT--ATATATTATATAGTTTTGAAATCATTTTGAAAACTTATATAATATAT
1 AACATTTTGAAAA-ATAAATATAATATATAGTTTTTAAAACTTTTTGAAAA-TTATAT--TATAT
* ***
58119 AGTTTTTAAAATATTTTTGAAAACTATATAGTTTTGAA
62 AGTTTTTAAAATAGTTTTGAAAACTATATAGTTAAAAA
* * * *
58157 AACATTTTTCAAAAA-AATATTTAATATATA-ATTTTAAATATTTTTTTGAAAATATATATTATA
1 AACA-TTTTGAAAAATAA-ATATAATATATAGTTTTTAAA-A-CTTTTTGAAAAT-TATATTATA
58220 TAGGTTTTT
61 TA-GTTTTT
58229 GGAAAATATT
Statistics
Matches: 142, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
99 14 0.10
100 21 0.15
101 44 0.31
102 31 0.22
103 18 0.13
104 14 0.10
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (99 bp):
AACATTTTGAAAAATAAATATAATATATAGTTTTTAAAACTTTTTGAAAATTATATTATATAGTT
TTTAAAATAGTTTTGAAAACTATATAGTTAAAAA
Found at i:58146 original size:29 final size:29
Alignment explanation
Indices: 58114--58170 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
58104 ACTTATATAA
* * *
58114 TATATAGTTTTTAAAATATTTTTGAAAAC
1 TATATAGTTTTGAAAACATTTTTCAAAAC
58143 TATATAGTTTTGAAAACATTTTTCAAAA
1 TATATAGTTTTGAAAACATTTTTCAAAA
58171 AAATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (29 bp):
TATATAGTTTTGAAAACATTTTTCAAAAC
Found at i:58147 original size:65 final size:66
Alignment explanation
Indices: 58078--58214 Score: 172
Period size: 67 Copynumber: 2.1 Consensus size: 66
58068 ACATATATAT
* * ** *
58078 TATATAGTTTTGAAATCA-TTTT-GAAAACTTATATAATATATAGTTTTTAAA-ATATTTTTGAA
1 TATATAGTTTTGAAAACATTTTTCAAAAAAATATATAATATATA-ATTTTAAATATATTTTTGAA
58140 AA
65 AA
* *
58142 CTATATAGTTTTGAAAACATTTTTCAAAAAAATATTTAATATATAATTTTAAATATTTTTTTGAA
1 -TATATAGTTTTGAAAACATTTTTCAAAAAAATATATAATATATAATTTTAAATATATTTTTGAA
58207 AA
65 AA
58209 TATATA
1 TATATA
58215 TTATATAGGT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
65 17 0.27
66 17 0.27
67 28 0.45
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (66 bp):
TATATAGTTTTGAAAACATTTTTCAAAAAAATATATAATATATAATTTTAAATATATTTTTGAAA
A
Found at i:58273 original size:21 final size:22
Alignment explanation
Indices: 58249--58298 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
58239 TTATTTTATC
*
58249 TTTATTATT-ATTTATTTC-TTT
1 TTTATT-TTAATTAATTTCATTT
58270 TTTATTTTAATTAATTTCATTT
1 TTTATTTTAATTAATTTCATTT
58292 TTTATTT
1 TTTATTT
58299 CATTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 10 0.38
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTAATTAATTTCATTT
Found at i:58295 original size:22 final size:20
Alignment explanation
Indices: 58249--58310 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
58239 TTATTTTATC
*
58249 TTTATTATTATTTATTTCTTT
1 TTTATT-TTATTAATTTCTTT
58270 TTTATTTTAATTAATTTCATTT
1 TTTATTTT-ATTAATTTC-TTT
*
58292 TTTATTTCATT--TTTCTTT
1 TTTATTTTATTAATTTCTTT
58310 T
1 T
58311 CAAGTCCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 2 0.05
21 17 0.46
22 10 0.27
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTAATTTCTTT
Found at i:60654 original size:2 final size:2
Alignment explanation
Indices: 60647--60671 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60637 CGATAGTTGG
60647 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
60672 AAATTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65349 original size:2 final size:2
Alignment explanation
Indices: 65338--65382 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
65328 ACCTAATGAA
65338 AT AT -T 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 AT AT
65379 AT AT
1 AT AT
65383 TTGATTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:65408 original size:10 final size:10
Alignment explanation
Indices: 65338--65414 Score: 73
Period size: 10 Copynumber: 7.3 Consensus size: 10
65328 ACCTAATGAA
65338 ATATTATATAT
1 ATATT-TATAT
*
65349 ATATATATAT
1 ATATTTATAT
*
65359 ATATATATAT
1 ATATTTATAT
*
65369 ATATATATAT
1 ATATTTATAT
*
65379 ATATTTGATTT
1 ATATTT-ATAT
65390 AATTATTTATAT
1 -A-TATTTATAT
*
65402 ATATTTATTT
1 ATATTTATAT
65412 ATA
1 ATA
65415 CATTATAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
10 41 0.71
11 8 0.14
12 4 0.07
13 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
ATATTTATAT
Found at i:65932 original size:42 final size:41
Alignment explanation
Indices: 65832--65938 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
65822 ACCCGAAGGT
* * * * *
65832 CTTATAGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGG
1 CTTACAGATGACCCGAAGGACTTATCATCATGCTCGAAAGC
* * *
65873 CTTACAAATGACTCGAAGGATTTAATCATCATGCTCGAAAGC
1 CTTACAGATGACCCGAAGGACTT-ATCATCATGCTCGAAAGC
* *
65915 CTTACTGATGTCCCGAAGGACTTA
1 CTTACAGATGACCCGAAGGACTTA
65939 CTAAGTAAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (41 bp):
CTTACAGATGACCCGAAGGACTTATCATCATGCTCGAAAGC
Found at i:66292 original size:176 final size:176
Alignment explanation
Indices: 65998--66372 Score: 588
Period size: 176 Copynumber: 2.1 Consensus size: 176
65988 ACATTAAATG
* *
65998 AGAAACTTTGAAAATCGCTTTCTTATTTTTCAAATTCATGTGAAAACATCCTGCCCGAAGGTCTT
1 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
* * * *
66063 ATAGATGACATGAAGGACTTATCATATTGTTCGAAAGGCTTACAAATGACCCGAAGGATTTAATC
66 ATAGATGACACGAAGGACTTATCATATTGCTCAAAAGACTTACAAATGACCCGAAGGATTTAATC
66128 ATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTACTAAGTA
131 ATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTACTAAGTA
* * *
66174 AGAAACTTTGAAAATCGTTTTCTCATTTTTTAAATTCATGTGAAAACATCCTACCTGAAGGTCTT
1 AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
* * * *
66239 ATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTTAATC
66 ATAGATGACACGAAGGACTTATCATATTGCTCAAAAGACTTACAAATGACCCGAAGGATTTAATC
* *
66304 ATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACTAAGTA
131 ATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTACTAAGTA
* * *
66350 CGAAACTTTGGAAATCTCTTTCT
1 AGAAACTTTGAAAATCGCTTTCT
66373 TACTTTTAAA
Statistics
Matches: 180, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
176 180 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (176 bp):
AGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
ATAGATGACACGAAGGACTTATCATATTGCTCAAAAGACTTACAAATGACCCGAAGGATTTAATC
ATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTACTAAGTA
Found at i:66318 original size:42 final size:41
Alignment explanation
Indices: 66236--66342 Score: 142
Period size: 42 Copynumber: 2.6 Consensus size: 41
66226 ACCTGAAGGT
* *
66236 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
* * *
66277 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGA
* *
66319 CTTACTGATGGCCCGAATGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
66343 CTAAGTACGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:66782 original size:236 final size:237
Alignment explanation
Indices: 66174--66815 Score: 944
Period size: 237 Copynumber: 2.7 Consensus size: 237
66164 TTACTAAGTA
** * *
66174 AGAAACTTTGAAAATCGTTTTCTCATTTTTTAAATTCATGTGAAAACATCCTACCTGAAGGTCTT
1 AGAAACTTTGAAAATCACTTTCT-AATTTTTAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
* *
66239 ATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTTAATC
65 ATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAATGATTTAATC
* * *
66304 ATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACTAAGTACGAAACTTTGGAAATCTCT
130 ATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACTAAGTAAGAAACTTTAGAAATCGCT
***
66369 TTCTTACTTTTAAAAAATTTCATCTTATGGAAATGTTTAAATG
195 TTCTTACTTTTAAAAAATTTCATCTTATGGAAAACATTAAATG
* * *
66412 AGAAACTTTGAAAATCTCTTTCTAGTTTTTAAATTCATGTGAAAACATCCTACTCGAAGGTCTTA
1 AGAAACTTTGAAAATCACTTTCTAATTTTTAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA
* * * * * *
66477 TGGATGGCCCAAAGGACTTATCATCTTACTCAAAAGACTTATAGATGAACCGGATTATTTAATCA
66 TGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAATGATTTAATCA
* *
66542 TCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAATAAACTTTAGAAATCGCTT
131 TCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACTAAGTAAGAAACTTTAGAAATCGCTT
* * *
66607 TCTTACTTTTCAAAGATTTCATTTTAT-GAAAACATTAAATG
196 TCTTACTTTTAAAAAATTTCATCTTATGGAAAACATTAAATG
* ** * *
66648 AGAAACTTTGAAAATCACTTTCTAATTTTCAAATTCATGTGAAAACATAATGCCCAAAGGTCTTA
1 AGAAACTTTGAAAATCACTTTCTAATTTTTAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA
* * * *
66713 TGGATGGCCTGAAGGACTTATCATCCTGCTCGAAAGACTTACAGATGACCCGAATGATTTAACCA
66 TGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAATGATTTAATCA
*
66778 TCATGCTCAAAAGACTTACTGATGGCCCGAATGACTTA
131 TCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTA
66816 TCATCTTTAG
Statistics
Matches: 360, Mismatches: 44, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
236 159 0.44
237 180 0.50
238 21 0.06
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (237 bp):
AGAAACTTTGAAAATCACTTTCTAATTTTTAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA
TGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAATGATTTAATCA
TCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACTAAGTAAGAAACTTTAGAAATCGCTT
TCTTACTTTTAAAAAATTTCATCTTATGGAAAACATTAAATG
Done.