Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 182 of 313
Found at i:56287617 original size:102 final size:102
Alignment explanation
Indices: 56287452--56289094 Score: 1375
Period size: 102 Copynumber: 15.7 Consensus size: 102
56287442 TCTTTTCTTT
** * *
56287452 TTCTT-TTCTTCTTTTTCTTCTTTTCGGTTTCATC-CTCAGCCCCTGCATCAATTGCACCGTCAA
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACT----CCCTACATCAATTGCACCATCAA
* * * *
56287515 CAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTC
62 CAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
* * *
56287556 TTCTTCTTCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCACTATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-
* * * *
56287621 AGCAACAGCAATAGCCTCTATAGCCTCCTCATTCTCTTTGTTCTTC
61 A-CAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTG--C-TC
*
56287667 TTCTTCTTCTTCTTCTTCTTCTTTTTCTGCTTTTCAATTTCATCACCCCCTACATCAATTGCACC
1 TTCTTCTTCTTC-T-TT-TTC----T-T-CTTTTCAATTTCATCACTCCCTACATCAATTGCACC
56287732 ATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
57 ATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
*
56287778 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCATTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
*
56287843 AGCAATAGACTCAATAGCATCCTCATTTTC---G---
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
*
56287874 ----T-TGC-TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAA-
* ** ** *** ** *
56287933 CTGCCTCTCTCGCTGCAGCCGC-TACCTCCCTCTC--TGCTGC
65 CAG-CAATAGC-CT-CAATAGCAT-CCTCATTTTCATTGCT-C
* ** ** * ** * ** * * ** *
56287973 CTCCGC-TCTAAGTTGTTGCTGGAGTTCTTC-ATCTTCTTCTTTTTCTTATTTTCAATTTCATCA
1 TTCTTCTTCT-TCTT-TTTCT--TCTT-TTCAAT-TTCATC-ACTCCCTA-CATCAA-TT--GCA
* * * * ** * * *
56288036 CTCCCTGCATCAATTGCACCATCAACAACAGCAATAGCCTCCTCATTCTCTTTGTTCTTCTTC
55 ----C--CATCAA---CAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTG-----C-TC
56288099 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
56288164 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
56288201 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
* *
56288266 AGCAATAGACTCAATAGCATCCTCATTTTCGTTG--C
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
* *
56288301 -TC-T-TT-TTC---TTC--C-TTTCAATTTCATCACTCCCCATATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
56288356 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
* * *
56288393 TTCTTCTTTTTCTTTTTATTCTTTTCAATTTCATTC-CTCCCTACATCAATTGCCCCATCCACAA
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCA-TCACTCCCTACATCAATTGCACCAT---C-A
* * *
56288457 CAGCAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTC
61 -A-CAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTG--C-TC
*
56288504 TTCCTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCATTATCAAC
1 -T--TCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGC---A-C--C
* * *
56288569 AACAGCAACAGCAATATCCTCAATAGCATCCTCATTTTCATTGCTC
57 ATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
* * *
56288615 TTCTTCTTTTTCTTTTTATTCTTTTCAATTTCATTACTCCCTACATCAATTGCACCATCCACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCAT---C-A-
56288680 AGCAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTG---
61 A-CAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
* *
56288720 --C-TCTTCTTCTTTTTCTTATTTTCATTTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
*
56288782 AGCAATAGCCTCAATAGCATTCTCATTTTCATTG---
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
56288816 --C-TCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
56288878 AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTC
66 AGCAATAGCCTCAATAGCATCCTCATTTTCATTG--C-TC
* *
56288918 TTCTTCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACTATCAACAAC
1 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-
* *
56288983 AGCAACAGCAATAGCCTCAATGGCAT-CTACATTCTCATTGCTC
61 A-CAACAGCAATAGCCTCAATAGCATCCT-CATTTTCATTGCTC
* **
56289026 TTCTTCTTCTTATTTTTCTT-TGTTTCAATTTCATCAGC-CCCTATGTC-ATTAGCACCATCAAC
1 TTCTTCTTCTTCTTTTTCTTCT-TTTCAATTTCATCA-CTCCCTACATCAATT-GCACCATCAAC
*
56289088 AGCAGCA
63 AACAGCA
56289095 GCAACAGCCT
Statistics
Matches: 1279, Mismatches: 136, Indels: 250
0.77 0.08 0.15
Matches are distributed among these distances:
90 126 0.10
91 5 0.00
92 4 0.00
93 8 0.01
94 12 0.01
95 3 0.00
96 136 0.11
97 3 0.00
98 2 0.00
99 6 0.00
100 1 0.00
101 1 0.00
102 276 0.22
103 7 0.01
104 9 0.01
105 86 0.07
106 9 0.01
107 6 0.00
108 241 0.19
109 13 0.01
110 10 0.01
111 75 0.06
112 6 0.00
113 4 0.00
114 119 0.09
115 1 0.00
116 2 0.00
117 6 0.00
118 3 0.00
119 15 0.01
120 46 0.04
121 8 0.01
122 9 0.01
123 6 0.00
125 4 0.00
126 7 0.01
127 4 0.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.40
Consensus pattern (102 bp):
TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
AGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTC
Found at i:56287667 original size:3 final size:3
Alignment explanation
Indices: 56287661--56287694 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
56287651 ATTCTCTTTG
*
56287661 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
56287695 GCTTTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:56287730 original size:222 final size:215
Alignment explanation
Indices: 56287442--56289094 Score: 1190
Period size: 222 Copynumber: 7.8 Consensus size: 215
56287432 CTCTGCTGCA
* ** * *
56287442 TCTT-TTCTTTTTCTTTTCTTCTTTTTCTTCTTTTCGGTTTCATCCTCAGCCCCTGCATCAATTG
1 TCTTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCA---TCACCCCCTACATCAATTG
* * * * * *
56287506 CACCGTCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTCTTCTTCTTCTTC
63 CACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTT
* *
56287571 TTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCACTATCAACAACAGCAACAGCAATAGC
128 TTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-A-CAACAGCAATAGC
* *
56287636 CTCTATAGCCTCCTCATTCTCTTTGTTCT
187 CTCAATAGCATCCTCATTCTCTTTGTTCT
*
56287665 TCTTCTTCTTCTTCTTCTTCTTCTTTTTCTGCTTTTCAATTTCATCACCCCCTACATCAATTGCA
1 TCTTCTTCTTCTTCTT-TTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCA
56287730 CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTT
65 CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTT
* *
56287795 CTTCTTTTCAATTTCATCATTCCCTACATCAATTGCACCATCAACAACAGCAATAGACTCAATAG
130 CTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAG
* * *
56287860 CATCCTCATTTTCGTTGCTCT
195 CATCCTCATTCTCTTTGTTCT
* * * ** ** * * * ** * * **
56287881 TTTTCTTCTT-TTCAATTTCATCACTCCCTAC--ATCAATTGCACCATCAACAACCTGCCTCTCT
1 TCTTCTTCTTCTTC-TTTTCTTCTTTTTCTTCTTTTCAATT---TCATC-ACCCCCTACATCAAT
* ** * ** * * ** * * * *
56287943 CGCTGCAGCCGCTAC--C--T-CCCTCTCTGCTGCCTCCGCTCTAAGTTGTTGC-TGGAGTTCTT
61 TGCACCATCAACAACAGCAATAGCCTCAAT--AGCAT-C-CTC--A-TT-TT-CAT--TGCTCTT
* * *
56288002 CATCTTCTTCTTTTTCTTATTTTCAATTTCATCACTCCCTGCATCAATTGCACCATCAACAACAG
115 CTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAG
56288067 CAATAG---C-----C-TCCTCATTCTCTTTG---T
180 CAATAGCCTCAATAGCATCCTCATTCTCTTTGTTCT
*
56288091 TCTTCTTCTTCTTC--TTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC
1 TCTTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCAC
56288154 CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTTC
66 CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTTC
*
56288219 TTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGACTCAATAGC
131 TTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGC
* * *
56288284 ATCCTCATTTTCGTTGCTCT
196 ATCCTCATTCTCTTTGTTCT
* * * * ** ** * * * * * ** * * *
56288304 TTTTCTTCCT-TTCAATTTCATC--ACTCCCCATATCAATTGCACCATCAACAACAGCAATAG--
1 TCTTCTTCTTCTTC-TTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCA
* * * *
56288364 CC-T---CAATAGC-AT--CCTC-AT----T-TTCA-TTGC--T-CTTCTTCTTTTTC-T-TT-T
65 CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGC-TCTTCTTCTTCTTCTTTT
* *
56288409 TATTCTTTTCAATTTCATTC-CTCCCTACATCAATTGCCCCATCCACAACAGCAACAGCAATAGC
129 TCTTCTTTTCAATTTCA-TCACTCCCTACATCAATTGCACCAT---C-A-A-CAACAGCAATAGC
*
56288473 CTCAATAGCCTCCTCATTCTCTTTGTTCT
187 CTCAATAGCATCCTCATTCTCTTTGTTCT
* *
56288502 TCTTC--C-TCTTC--TTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCAT
1 TCTTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGC--
* * * *
56288562 TATCAACAACAGCAACAGCAATATCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTTTTC
64 -A-C--CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTC
* * * *
56288627 TTTTTATTCTTTTCAATTTCATTACTCCCTACATCAATTGCACCATCCACAACAGCAACAG---C
125 TTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTC
* ** * *
56288689 AATAG---CCTCAATAGC----ATCC
190 AATAGCATCCTCATTCTCTTTGTTCT
* * * * * *
56288708 TCATT-TTCAT-TGCTCTTCTTCTTTTTCTTATTTTCATTTTCATCACTCCCTACATCAATTGCA
1 TC-TTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCA
*
56288771 CCATCAACAACAGCAATAGCCTCAATAGCATTCTCATTTTCATTG-----C-TCTTCTTCTTTTT
65 CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTT
56288830 CTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAG
130 CTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAG
* *
56288895 CATCCTCATTTTCATTG----
195 CATCCTCATTCTCTTTGTTCT
* *
56288912 -C-TCTTCTTCTTC--TTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCAC
1 TCTTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCAC
* * *
56288973 TATCAACAACAGCAACAGCAATAGCCTCAATGGCAT-CTACATTCTCATTGCTCTTCTTCTTCTT
66 ---CATC-A-A-CAACAGCAATAGCCTCAATAGCATCCT-CATTTTCATTGCTCTTCTTCTTCTT
* ** *
56289037 ATTTTTCTT-TGTTTCAATTTCATCAGC-CCCTATGTC-ATTAGCACCATCAACAGCAGCA
124 CTTTTTCTTCT-TTTCAATTTCATCA-CTCCCTACATCAATT-GCACCATCAACAACAGCA
56289095 GCAACAGCCT
Statistics
Matches: 1133, Mismatches: 181, Indels: 242
0.73 0.12 0.16
Matches are distributed among these distances:
192 38 0.03
193 9 0.01
194 2 0.00
195 35 0.03
196 5 0.00
197 4 0.00
198 108 0.10
199 2 0.00
201 127 0.11
202 5 0.00
203 9 0.01
204 57 0.05
205 2 0.00
206 27 0.02
207 55 0.05
208 16 0.01
209 5 0.00
210 86 0.08
211 12 0.01
212 13 0.01
213 111 0.10
214 5 0.00
215 20 0.02
216 67 0.06
217 22 0.02
218 2 0.00
219 17 0.02
220 5 0.00
221 4 0.00
222 225 0.20
223 4 0.00
224 10 0.01
225 24 0.02
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.40
Consensus pattern (215 bp):
TCTTCTTCTTCTTCTTTTCTTCTTTTTCTTCTTTTCAATTTCATCACCCCCTACATCAATTGCAC
CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTTC
TTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGC
ATCCTCATTCTCTTTGTTCT
Found at i:56288096 original size:3 final size:3
Alignment explanation
Indices: 56288090--56288121 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
56288080 ATTCTCTTTG
*
56288090 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
56288122 TTCAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:56288274 original size:423 final size:408
Alignment explanation
Indices: 56287461--56289094 Score: 1597
Period size: 423 Copynumber: 3.9 Consensus size: 408
56287451 TTTCTTTTCT
** * *
56287461 TCTTTTTCTTCTTTTCGGTTTCATC-CTCAGCCCCTGCATCAATTGCACCGTCAACAA-CAGCAA
1 TCTTTTTCTTCTTTTCAATTTCATCACT----CCCTACATCAATTGCACCATCAACAACCAGCAA
* * * * * * * * * *
56287524 TAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTCTTCTTCTTCTTCTTCTTCTTTTCAATTTCA
62 TAGCCTCAACAGCATCCTCACTCTCATTGCTCTCCCTCTTTTTCTTTTTATTCTTTTCAATTTCA
* * * * * * * * ** *
56287589 -TCACTCCCTGCATCAATTGCACTATCAACAACAGCAACAGCAATAGCCTCTATAGCCTCCTCAT
127 TTC-CTCACTACATCAACT-CCCCATCCACAACAGCAACAGCAACAACAGCAATAGCCTCCTCAT
* *
56287653 TCTCTTTGTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTTTCTGCTTTTCAATTTCATCACCCCCT
190 TCTCTTTG------TTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCT
56287718 ACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTT
249 ACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTT
*
56287783 CTTCTTCTTTTTCTTCTTTTCAATTTCATCATTCCCTACATCAATTGCACCATCAACAACAGCAA
314 CTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAA
56287848 TAGACTCAATAGCATCCTCATTTTCGTTGC
379 TAGACTCAATAGCATCCTCATTTTCGTTGC
* ** **
56287878 TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACCTGCCTCTCT
1 TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACCAG-CAATAG
* * *
56287943 CGCTGCAGCCGC-TACCTCCCTCTC--TGCTGCCTCCGCTCTAAGTTGTTGCTGGAGTTCTTCA-
65 C-CT-CAACAGCAT-CCTCACTCTCATTGCT--CTCC-CTCT---TT-TT-CT----TT-TT-AT
** * * * * ** * *
56288004 TCTTCTTCTTTTTCTTATT-TTCAATTTCATC-ACT-CCC-TGCATCAATTGCACCATCAACAAC
113 TCTT-TTCAATTTC--ATTCCTC-ACTACATCAACTCCCCATCCA-CAACAGCAACAGCAACAAC
56288065 AGCAATAGCCTCCTCATTCTCTTTGTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTT
173 AGCAATAGCCTCCTCATTCTCTTTGTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTT
56288130 CATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCA
238 CATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCA
56288195 TTGCTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATC
303 TTGCTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATC
56288260 AACAACAGCAATAGACTCAATAGCATCCTCATTTTCGTTGC
368 AACAACAGCAATAGACTCAATAGCATCCTCATTTTCGTTGC
* * *
56288301 TCTTTTTCTTCCTTTCAATTTCATCACTCCCCATATCAATTGCACCATCAACAA-CAGCAATAGC
1 TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACCAGCAATAGC
* * * * *
56288365 CTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTTTTCTTTTTATTCTTTTCAATTTCATTCC
66 CTCAACAGCATCCTCACTCTCATTGCTCTCCCTCTTTTTCTTTTTATTCTTTTCAATTTCATTCC
* * * * **
56288430 TCCCTACATCAATTGCCCCATCCACAACAGCAACAGCAATAGCCTCAATAGCCTCCTCATTCTCT
131 TCACTACATCAACT-CCCCATCCACAACAGCAACAGCAACAACAGCAATAGCCTCCTCATTCTCT
* *
56288495 TTGTTCTTCTTCCTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGC
195 TTGTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGC
* * * *
56288560 ATTATCAACAACAGCAACAGCAATATCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTTT
260 ---A-C--CATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCT
* *
56288625 TCTTTTTATTCTTTTCAATTTCATTACTCCCTACATCAATTGCACCATCCACAACAGCAACAGCA
319 TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCAT---C-A-A-CAACAGCA
* *
56288690 ATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTC
378 ATAGACTCAATAGCATCCTCATTTTC---G-T-TGC
* *
56288726 TTCTTTTTCTTATTTTCATTTTCATCACTCCCTACATCAATTGCACCATCAACAA-CAGCAATAG
1 -TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACCAGCAATAG
* * * * *
56288790 CCTCAATAGCATTCTCATTTTCATTGCTCT---TC---TTCTTTTTCTTCTTTTCAATTTCA-TC
65 CCTCAACAGCATCCTCACTCTCATTGCTCTCCCTCTTTTTCTTTTTATTCTTTTCAATTTCATTC
* * * * * * * *
56288848 ACTCCCTACATCAATTGCACCATCAACAACAGCAATAG---C--C-TCAATAGCATCCTCATTTT
130 -CTCACTACATCAACT-CCCCATCCACAACAGCAACAGCAACAACAGCAATAGCCTCCTCATTCT
* *
56288907 CATTG--C-TCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATT
193 CTTTGTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATT
* * *
56288969 GCACTATCAACAACAGCAACAGCAATAGCCTCAATGGCAT-CTACATTCTCATTGCTCTTCTTCT
258 GCAC---CATC-A-A-CAACAGCAATAGCCTCAATAGCATCCT-CATTTTCATTGCTCTTCTTCT
* ** *
56289033 TCTTATTTTTCTT-TGTTTCAATTTCATCAGC-CCCTATGTC-ATTAGCACCATCAACAGCAGCA
316 TCTTCTTTTTCTTCT-TTTCAATTTCATCA-CTCCCTACATCAATT-GCACCATCAACAACAGCA
56289095 GCAACAGCCT
Statistics
Matches: 1041, Mismatches: 114, Indels: 136
0.81 0.09 0.11
Matches are distributed among these distances:
405 15 0.01
406 5 0.00
407 10 0.01
408 112 0.11
409 6 0.01
410 6 0.01
411 135 0.13
412 3 0.00
413 2 0.00
414 146 0.14
415 5 0.00
416 6 0.01
417 27 0.03
418 21 0.02
419 20 0.02
420 93 0.09
421 7 0.01
422 3 0.00
423 264 0.25
424 3 0.00
425 2 0.00
426 87 0.08
428 3 0.00
429 42 0.04
430 7 0.01
431 4 0.00
432 6 0.01
433 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.40
Consensus pattern (408 bp):
TCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACCAGCAATAGC
CTCAACAGCATCCTCACTCTCATTGCTCTCCCTCTTTTTCTTTTTATTCTTTTCAATTTCATTCC
TCACTACATCAACTCCCCATCCACAACAGCAACAGCAACAACAGCAATAGCCTCCTCATTCTCTT
TGTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCA
CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTTTT
CTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAATAGACTCAATAG
CATCCTCATTTTCGTTGC
Found at i:56289001 original size:111 final size:105
Alignment explanation
Indices: 56288817--56289036 Score: 334
Period size: 105 Copynumber: 2.0 Consensus size: 105
56288807 TTTTCATTGC
* *
56288817 TCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGCA
1 TCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCAACAACAACAGCA
*
56288882 ATAGCCTCAATAGCATCCT-CATTTTCATTGCTCTTCTTCT
66 ATAGCCTCAATAGCAT-CTACATTCTCATTGCTCTTCTTCT
56288922 TCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACTATCAACAACAGCA
1 TCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCAC---CAAC-A-A-CA
*
56288987 ACAGCAATAGCCTCAATGGCATCTACATTCTCATTGCTCTTCTTCT
60 ACAGCAATAGCCTCAATAGCATCTACATTCTCATTGCTCTTCTTCT
56289033 TCTT
1 TCTT
56289037 ATTTTTCTTT
Statistics
Matches: 104, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
105 50 0.48
108 3 0.03
109 1 0.01
110 3 0.03
111 47 0.45
ACGTcount: A:0.24, C:0.31, G:0.05, T:0.40
Consensus pattern (105 bp):
TCTTCTTCTTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCAACAACAACAGCA
ATAGCCTCAATAGCATCTACATTCTCATTGCTCTTCTTCT
Found at i:56289102 original size:111 final size:110
Alignment explanation
Indices: 56288303--56289094 Score: 801
Period size: 108 Copynumber: 7.5 Consensus size: 110
56288293 TTCGTTGCTC
* * * *
56288303 TTTTTCTTCCTTTCAATTTCATCACTCCCCATATCAATTGCACCAT---C-A-A-CAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
* * *
56288362 AGCCTCAATAGCATCCTCATTTTCATTG-C-TCTTCTTCTTTTTC
66 AGCCTCAATAGCATCCTCATTCTCATTGCCTTCTTCTTCTTCTTA
* * * *
56288405 TTTTTATTCTTTTCAATTTCATTC-CTCCCTACATCAATTGCCCCATCCACAACAGCAACAGCAA
1 TTTTTCTTCTTTTCAAATTCA-TCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAA
* * * *
56288469 TAGCCTCAATAGCCTCCTCATTCTCTTTGTTCTTCTTCCTCTTCTTCTTC
65 TAGCCTCAATAGCATCCTCATTCTCATTG--C--CTTCTTCTTCTTCTTA
* * **
56288519 TTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCATTATCAACAACAGCAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
* * * *
56288584 ATCCTCAATAGCATCCTCATTTTCATTG-C-TCTTCTTCTTTTTC
66 AGCCTCAATAGCATCCTCATTCTCATTGCCTTCTTCTTCTTCTTA
* * * *
56288627 TTTTTATTCTTTTCAATTTCATTACTCCCTACATCAATTGCACCATCCACAACAGCAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
*
56288692 AGCCTCAATAGCATCCTCATTTTCATTG----C-TCTTCTTC---
66 AGCCTCAATAGCATCCTCATTCTCATTGCCTTCTTCTTCTTCTTA
* **
56288729 TTTTTCTTATTTTCATTTTCATCACTCCCTACATCAATTGCACCAT---C-A-A-CAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
* *
56288788 AGCCTCAATAGCATTCTCATTTTCATTG----C-TCTTCTTC---
66 AGCCTCAATAGCATCCTCATTCTCATTGCCTTCTTCTTCTTCTTA
*
56288825 TTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCAT---C-A-A-CAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
* *
56288884 AGCCTCAATAGCATCCTCATTTTCATTGCTCTTCTTCTTCTTCTTC
66 AGCCTCAATAGCATCCTCATTCTCATTGC-CTTCTTCTTCTTCTTA
*
56288930 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACTATCAACAACAGCAACAGCAAT
1 TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
*
56288995 AGCCTCAATGGCAT-CTACATTCTCATTG-C-TCTTCTTCTTCTTA
66 AGCCTCAATAGCATCCT-CATTCTCATTGCCTTCTTCTTCTTCTTA
* ** *
56289038 TTTTTCTT-TGTTTCAATTTCATCAGC-CCCTATGTC-ATTAGCACCATCAACAGCAGCA
1 TTTTTCTTCT-TTTCAAATTCATCA-CTCCCTACATCAATT-GCACCATCAACAACAGCA
56289095 GCAACAGCCT
Statistics
Matches: 609, Mismatches: 48, Indels: 60
0.85 0.07 0.08
Matches are distributed among these distances:
96 130 0.21
97 1 0.00
98 1 0.00
99 1 0.00
101 1 0.00
102 88 0.14
103 2 0.00
105 52 0.09
106 2 0.00
107 5 0.01
108 191 0.31
109 4 0.01
110 3 0.00
111 33 0.05
113 3 0.00
114 92 0.15
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.40
Consensus pattern (110 bp):
TTTTTCTTCTTTTCAAATTCATCACTCCCTACATCAATTGCACCATCAACAACAGCAACAGCAAT
AGCCTCAATAGCATCCTCATTCTCATTGCCTTCTTCTTCTTCTTA
Found at i:56290145 original size:17 final size:18
Alignment explanation
Indices: 56290123--56290157 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
56290113 AGTGGCGGCA
*
56290123 CTATTATAA-TTTTTTTT
1 CTATTAAAACTTTTTTTT
56290140 CTATTAAAACTTTTTTTT
1 CTATTAAAACTTTTTTTT
56290158 TTCTTTTCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
CTATTAAAACTTTTTTTT
Found at i:56293455 original size:235 final size:239
Alignment explanation
Indices: 56293047--56293628 Score: 762
Period size: 235 Copynumber: 2.4 Consensus size: 239
56293037 ACCTAACTTC
* * * * *
56293047 ATTCATATTTTAATTTTACATCAATCAACAAATTCAATTCAATTCACTTTCAGCAACTTTTCATT
1 ATTCATATTTTAATCTTA-ATCAATCAATAAATTC-A---AATTCAATTTCCGCAACTTTTCCTT
* * * * *
56293112 CACTTTCTCACCAACCAAAAAACAGATCAAACCAAAAAAGAAAAACAGATGAAATTTTGACTTTG
61 CACTTTTTCACCAACCAAACAACAGATCAAACCAAAAAAGAAAAACAAATGAAATTTAGACTTTA
* * *
56293177 CAAAAACATGATCATGCAAGCTTAAGGATCTTTAAGATCAAATTCCCGTTTGTTGACCGAGAAAA
126 CAAAAACATAATCATGCAAGCTTAAAGACCTTTAAGATCAAATTCCCGTTTGTTGACCGAGAAAA
* * * * * *
56293242 CGGATGACAAGAAGTATTTACTATTCATACATGTAAGCCTAACATCGTA
191 CGGATGAAAAGAAGTATTTACCACTCAGACATGTAAACCTAACATCATA
* *
56293291 ATTCATATTTTAATCTT-A-C-ATCAATAAATTCAAATTCAAATTCCGCAACTTTCCCTTCACTT
1 ATTCATATTTTAATCTTAATCAATCAATAAATTCAAATTCAATTTCCGCAACTTTTCCTTCACTT
* *
56293353 TTTCACCAACCAAACAACAGATCAAACC-AAAAATAAAAACAAATGAAATTTAGACTTTACAAAT
66 TTTCACCAACCAAACAACAGATCAAACCAAAAAAGAAAAACAAATGAAATTTAGACTTTACAAAA
* * * *
56293417 ACATAATCATGTAAGCTTAAAGACCTTTAAGATCAAATTCCCGTTTGTTTATCGAGAAAACTGAT
131 ACATAATCATGCAAGCTTAAAGACCTTTAAGATCAAATTCCCGTTTGTTGACCGAGAAAACGGAT
*
56293482 GAAAAGAAGTTTTTACCACTCAGACATGTAAACCTAACATCATA
196 GAAAAGAAGTATTTACCACTCAGACATGTAAACCTAACATCATA
* * * *
56293526 ATTTATATTTTAATTTTACATCAATCAATAAATTCAAATTCATTTTCCGCAACTTTTCCTCCACT
1 ATTCATATTTTAATCTTA-ATCAATCAATAAATTCAAATTCAATTTCCGCAACTTTTCCTTCACT
* *
56293591 TTTTCACCAACC-AACAACAGA-AAAAGCAAAAAAGAAAA
65 TTTTCACCAACCAAACAACAGATCAAACCAAAAAAGAAAA
56293629 GAAAAAGAAA
Statistics
Matches: 296, Mismatches: 37, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
235 141 0.48
236 51 0.17
237 5 0.02
238 19 0.06
239 51 0.17
240 11 0.04
241 1 0.00
242 1 0.00
244 16 0.05
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (239 bp):
ATTCATATTTTAATCTTAATCAATCAATAAATTCAAATTCAATTTCCGCAACTTTTCCTTCACTT
TTTCACCAACCAAACAACAGATCAAACCAAAAAAGAAAAACAAATGAAATTTAGACTTTACAAAA
ACATAATCATGCAAGCTTAAAGACCTTTAAGATCAAATTCCCGTTTGTTGACCGAGAAAACGGAT
GAAAAGAAGTATTTACCACTCAGACATGTAAACCTAACATCATA
Found at i:56293633 original size:19 final size:17
Alignment explanation
Indices: 56293609--56293651 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
56293599 AACCAACAAC
56293609 AGAAAAAGCAAAAAAGAAA
1 AGAAAAAG-AAAAAA-AAA
56293628 AGAAAAAGAAAAAAAAA
1 AGAAAAAGAAAAAAAAA
*
56293645 AGGAAAA
1 AGAAAAA
56293652 CAGATGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAAAAAAAA
Found at i:56293635 original size:11 final size:11
Alignment explanation
Indices: 56293618--56293651 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
56293608 CAGAAAAAGC
56293618 AAAAAAGAAAA
1 AAAAAAGAAAA
*
56293629 GAAAAAGAAAA
1 AAAAAAGAAAA
56293640 AAAAAAGGAAAA
1 AAAAAA-GAAAA
56293652 CAGATGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:56298793 original size:65 final size:62
Alignment explanation
Indices: 56298692--56298819 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 62
56298682 ATCCTTGGTT
* * *
56298692 TATTCGAAAGATAAAAAAGAAGAGGGAAAGGAGGTTAATGGGCTAAAACCACAAATAGGAAA
1 TATTCGAAAGATAAAAAAAAAGAGCGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAA
*
56298754 TATTCGAAAGATTAAAAAAAAAAAGAGCGAAA-GATGGTTAATGGGCTAAAAACACTAATAGGAA
1 TATTCGAAAGA-T--AAAAAAAAAGAGCGAAAGGA-GGTTAATGGGCTAAAAACACAAATAGGAA
56298818 A
62 A
56298819 T
1 T
56298820 GGGCTAAAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 11 0.19
63 1 0.02
64 2 0.03
65 44 0.76
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (62 bp):
TATTCGAAAGATAAAAAAAAAGAGCGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAA
Found at i:56304315 original size:25 final size:25
Alignment explanation
Indices: 56304287--56304339 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
56304277 AATTTAAACC
56304287 CAAAACATAATAATTCTTATTAATT
1 CAAAACATAATAATTCTTATTAATT
56304312 CAAAACATAATAATTCTTATTAATT
1 CAAAACATAATAATTCTTATTAATT
56304337 CAA
1 CAA
56304340 CTTTGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (25 bp):
CAAAACATAATAATTCTTATTAATT
Found at i:56307659 original size:3 final size:3
Alignment explanation
Indices: 56307651--56307706 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
56307641 AAGGGTCTCT
56307651 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
56307699 TTC TTC TT
1 TTC TTC TT
56307707 TTTCCTCGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:56314619 original size:25 final size:25
Alignment explanation
Indices: 56314572--56314619 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
56314562 TATTGTAGTA
* *
56314572 TTATGTATTATGATTGATTTAATTC
1 TTATGTATTATAATTGATATAATTC
56314597 TTATGTATTATAAATT-ATATAAT
1 TTATGTATTAT-AATTGATATAAT
56314620 ATAAAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (25 bp):
TTATGTATTATAATTGATATAATTC
Found at i:56320775 original size:22 final size:22
Alignment explanation
Indices: 56320730--56320776 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
56320720 AGCTTTAATA
* *
56320730 TTCAATTTGGTACTTGACCGTT
1 TTCAATTTGATACATGACCGTT
56320752 TTCAATTTGATACATGAGCC-TT
1 TTCAATTTGATACATGA-CCGTT
56320774 TTC
1 TTC
56320777 TTTTTGTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (22 bp):
TTCAATTTGATACATGACCGTT
Found at i:56321225 original size:9 final size:9
Alignment explanation
Indices: 56321211--56321320 Score: 67
Period size: 9 Copynumber: 12.8 Consensus size: 9
56321201 ATATTTCTCA
56321211 TAAAAATAT
1 TAAAAATAT
56321220 TAAAAATGAT
1 TAAAAAT-AT
56321230 ATAAAAATA-
1 -TAAAAATAT
*
56321239 TAAAAAAAT
1 TAAAAATAT
56321248 TATTAAAATA-
1 TA--AAAATAT
56321258 -AAAAATAT
1 TAAAAATAT
56321266 T--AAATAT
1 TAAAAATAT
56321273 T--AAATAT
1 TAAAAATAT
56321280 T-AAAATA-
1 TAAAAATAT
**
56321287 TAAACTTAT
1 TAAAAATAT
*
56321296 TAAAATTAT
1 TAAAAATAT
*
56321305 AAAAAATAT
1 TAAAAATAT
*
56321314 AAAAAAT
1 TAAAAAT
56321321 CTAATAAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
7 21 0.25
8 16 0.19
9 32 0.38
10 3 0.04
11 12 0.14
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (9 bp):
TAAAAATAT
Found at i:56321254 original size:20 final size:21
Alignment explanation
Indices: 56321210--56321267 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
56321200 AATATTTCTC
* *
56321210 ATAAAAATAT-TAAAAATGAT
1 ATAAAAATATAAAAAAATTAT
56321230 ATAAAAATATAAAAAAATTAT
1 ATAAAAATATAAAAAAATTAT
*
56321251 -T-AAAATA-AAAAATATTA
1 ATAAAAATATAAAAAAATTA
56321268 AATATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.26
19 6 0.18
20 11 0.32
21 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAAAAATATAAAAAAATTAT
Found at i:56321262 original size:16 final size:15
Alignment explanation
Indices: 56321241--56321301 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 15
56321231 TAAAAATATA
56321241 AAAAAATTATTAAAAT
1 AAAAAA-TATTAAAAT
56321257 AAAAAATATT-AAAT
1 AAAAAATATTAAAAT
**
56321271 ATTAAATATTAAAAT
1 AAAAAATATTAAAAT
**
56321286 ATAAACTTATTAAAAT
1 A-AAAAATATTAAAAT
56321302 TATAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 12 0.32
15 9 0.24
16 16 0.43
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAATATTAAAAT
Found at i:56321270 original size:14 final size:14
Alignment explanation
Indices: 56321241--56321283 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
56321231 TAAAAATATA
56321241 AAAAAATTATTAAAAT
1 AAAAAA-TATT-AAAT
56321257 AAAAAATATTAAAT
1 AAAAAATATTAAAT
**
56321271 ATTAAATATTAAA
1 AAAAAATATTAAA
56321284 ATATAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 15 0.60
15 4 0.16
16 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAATATTAAAT
Found at i:56321276 original size:22 final size:23
Alignment explanation
Indices: 56321248--56321316 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
56321238 ATAAAAAAAT
56321248 TATTAAAATA-AAAAATATTAAA-
1 TATTAAAATATAAAAATA-TAAAC
*
56321270 TATT-AAATATTAAAATATAAAC
1 TATTAAAATATAAAAATATAAAC
56321292 TTATTAAAATTATAAAAAATATAAA
1 -TATTAAAA-TAT-AAAAATATAAA
56321317 AAATCTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 9 0.23
22 10 0.26
23 4 0.10
24 3 0.08
25 3 0.08
26 10 0.26
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (23 bp):
TATTAAAATATAAAAATATAAAC
Found at i:56321338 original size:9 final size:9
Alignment explanation
Indices: 56321210--56321368 Score: 60
Period size: 9 Copynumber: 16.9 Consensus size: 9
56321200 AATATTTCTC
56321210 ATAAAAA-T
1 ATAAAAATT
56321218 ATTAAAAATGAT
1 A-TAAAAAT--T
56321230 ATAAAAATAT
1 ATAAAAAT-T
*
56321240 AAAAAAATT
1 ATAAAAATT
*
56321249 ATTAAAA-T
1 ATAAAAATT
56321257 A-AAAAA-T
1 ATAAAAATT
*
56321264 ATTAAATATT
1 A-TAAAAATT
56321274 AAATATTAAAA-T
1 --ATA--AAAATT
*
56321286 AT-AAACTT
1 ATAAAAATT
*
56321294 ATTAAAATT
1 ATAAAAATT
*
56321303 ATAAAAAAT
1 ATAAAAATT
*
56321312 ATAAAAAAT
1 ATAAAAATT
*
56321321 CTAATAAATT
1 ATAA-AAATT
*
56321331 ATAAAAATA
1 ATAAAAATT
*
56321340 ATTATAAATT
1 A-TAAAAATT
*
56321350 AATAAAACTT
1 -ATAAAAATT
56321360 ATATAAAAT
1 ATA-AAAAT
56321369 ATTTAAAATT
Statistics
Matches: 115, Mismatches: 19, Indels: 32
0.69 0.11 0.19
Matches are distributed among these distances:
7 9 0.08
8 6 0.05
9 48 0.42
10 35 0.30
11 10 0.09
12 4 0.03
13 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:56321395 original size:57 final size:56
Alignment explanation
Indices: 56321285--56321407 Score: 131
Period size: 57 Copynumber: 2.2 Consensus size: 56
56321275 AATATTAAAA
* * *
56321285 TATAAACTTATTAAAATTATAAAAAATATAAAAAATCTAATAAATTATAAAAATAAT
1 TATAAA-TTAATAAAATTATAAAAAATATAAAAAATCTAAAAAAGTATAAAAATAAT
* ** * **
56321342 TATAAATTAATAAAACTTATATAAAATATTTAAAAT-TAAAAAACGTATTAAAATTCT
1 TATAAATTAATAAAA-TTATAAAAAATATAAAAAATCTAAAAAA-GTATAAAAATAAT
56321399 TATAAATTA
1 TATAAATTA
56321408 CAAAATATAG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
56 14 0.25
57 41 0.75
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (56 bp):
TATAAATTAATAAAATTATAAAAAATATAAAAAATCTAAAAAAGTATAAAAATAAT
Found at i:56325058 original size:130 final size:130
Alignment explanation
Indices: 56324825--56325079 Score: 465
Period size: 130 Copynumber: 2.0 Consensus size: 130
56324815 CATCTCTAGA
*
56324825 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTATCCTTTGAAATTGTT
1 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTATCCTTTGAAATTGCT
56324890 AACATTTACGTTTATCGAAACTAGTTATCACCGACACATAAAATGCGTATCAGTGATATTGTTAG
66 AACATTTACGTTTATCGAAACTAGTTATCACCGACACATAAAATGCGTATCAGTGATATTGTTAG
*
56324955 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTGTCCTTTGAAATTGCT
1 TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTATCCTTTGAAATTGCT
* * *
56325020 AACATTTATGTTTATCGAAACTAGTTATCACCTACACATGAAATGCGTATCAGTGATATT
66 AACATTTACGTTTATCGAAACTAGTTATCACCGACACATAAAATGCGTATCAGTGATATT
56325080 ACATCTGAAA
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 120 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (130 bp):
TTGTAAAGGGGAGACAACCAAGCAAATCTAAGTTCAGATTATTGTTAGTATCCTTTGAAATTGCT
AACATTTACGTTTATCGAAACTAGTTATCACCGACACATAAAATGCGTATCAGTGATATTGTTAG
Found at i:56325185 original size:11 final size:11
Alignment explanation
Indices: 56325165--56325244 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
56325155 TTTAATGGTA
56325165 GAATAGAAGTT
1 GAATAGAAGTT
*
56325176 GAATACAAGTT
1 GAATAGAAGTT
* *
56325187 AAATAGAATGGTA
1 GAATAGAA--GTT
56325200 GAATAGAAGTT
1 GAATAGAAGTT
*
56325211 GAATACAAGTT
1 GAATAGAAGTT
* *
56325222 AAATAGAATGGTA
1 GAATAGAA--GTT
56325235 GAATAGAAGT
1 GAATAGAAGT
56325245 ACAACAAAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
11 36 0.67
13 18 0.33
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.25
Consensus pattern (11 bp):
GAATAGAAGTT
Found at i:56325197 original size:35 final size:35
Alignment explanation
Indices: 56325158--56325244 Score: 174
Period size: 35 Copynumber: 2.5 Consensus size: 35
56325148 TACAAAGTTT
56325158 AATGGTAGAATAGAAGTTGAATACAAGTTAAATAG
1 AATGGTAGAATAGAAGTTGAATACAAGTTAAATAG
56325193 AATGGTAGAATAGAAGTTGAATACAAGTTAAATAG
1 AATGGTAGAATAGAAGTTGAATACAAGTTAAATAG
56325228 AATGGTAGAATAGAAGT
1 AATGGTAGAATAGAAGT
56325245 ACAACAAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.25
Consensus pattern (35 bp):
AATGGTAGAATAGAAGTTGAATACAAGTTAAATAG
Found at i:56327562 original size:2 final size:2
Alignment explanation
Indices: 56327557--56327581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56327547 TTTAAATAGC
56327557 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
56327582 TACCGGCGAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56332198 original size:4 final size:4
Alignment explanation
Indices: 56332191--56332215 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56332181 ATTAATTGAA
56332191 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
56332216 CCTTGCCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:56332580 original size:3 final size:3
Alignment explanation
Indices: 56332572--56332621 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
56332562 AGGAGACTCA
* * *
56332572 GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT GAT GGT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
56332620 GA
1 GA
56332622 AAGTGAGGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:56334657 original size:6 final size:6
Alignment explanation
Indices: 56334646--56334678 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
56334636 ATTTTTAAGT
56334646 TAAAAA TAAAAA TAAAAA TAAAAA T-AAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
56334679 TTAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:56345242 original size:22 final size:22
Alignment explanation
Indices: 56345217--56345261 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56345207 GAAGGTTTTG
56345217 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
56345239 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
56345261 T
1 T
56345262 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:56348937 original size:22 final size:22
Alignment explanation
Indices: 56348909--56348953 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56348899 AGGGGGAGTG
56348909 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
56348931 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
56348953 T
1 T
56348954 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:56359923 original size:45 final size:45
Alignment explanation
Indices: 56359859--56359945 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
56359849 GGTTCTCAAT
56359859 CTATATTTATTTTGATATATGCCCCAATCGCATATGAACTTTGAA
1 CTATATTTATTTTGATATATGCCCCAATCGCATATGAACTTTGAA
56359904 CTATATTTATTTTGATATATGCCCCAATCGCATATGAACTTT
1 CTATATTTATTTTGATATATGCCCCAATCGCATATGAACTTT
56359946 TTATAGATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (45 bp):
CTATATTTATTTTGATATATGCCCCAATCGCATATGAACTTTGAA
Found at i:56363824 original size:22 final size:21
Alignment explanation
Indices: 56363768--56363868 Score: 80
Period size: 22 Copynumber: 4.7 Consensus size: 21
56363758 ATATACGAAA
56363768 ATAATACTATATATAA-AAAAT
1 ATAATACTA-ATATAATAAAAT
**
56363789 ATATATACGCATATAATAAAAT
1 ATA-ATACTAATATAATAAAAT
56363811 ATAAGTACTAATATTAATAAAAAT
1 ATAA-TACTAATA-TAAT-AAAAT
** *
56363835 ATAATAGGAATAAAAT-AAAT
1 ATAATACTAATATAATAAAAT
* *
56363855 GTAATAATAATATA
1 ATAATACTAATATA
56363869 CACAATATGA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 14 0.22
21 10 0.16
22 21 0.33
23 10 0.16
24 9 0.14
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (21 bp):
ATAATACTAATATAATAAAAT
Found at i:56364158 original size:23 final size:22
Alignment explanation
Indices: 56364122--56364164 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
56364112 TATATATAAA
*
56364122 TAATAATGATATTAGAAATACC
1 TAATAATAATATTAGAAATACC
56364144 TAATATATAATATTAGAAATA
1 TAATA-ATAATATTAGAAATA
56364165 TATACATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
TAATAATAATATTAGAAATACC
Found at i:56364175 original size:11 final size:11
Alignment explanation
Indices: 56364161--56364227 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
56364151 TAATATTAGA
56364161 AATATATACAT
1 AATATATACAT
56364172 AATATATA-A-
1 AATATATACAT
* *
56364181 AAAATATATAT
1 AATATATACAT
* * *
56364192 AATGTAGTATTAA
1 AATATA-TA-CAT
56364205 AATATATACAT
1 AATATATACAT
56364216 AATATATACAT
1 AATATATACAT
56364227 A
1 A
56364228 TTAAAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 7 0.16
10 2 0.04
11 25 0.56
12 4 0.09
13 7 0.16
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (11 bp):
AATATATACAT
Found at i:56364175 original size:20 final size:20
Alignment explanation
Indices: 56364130--56364220 Score: 67
Period size: 22 Copynumber: 4.2 Consensus size: 20
56364120 AATAATAATG
*
56364130 ATATTAGAAATACCTAATATATA
1 ATATTAGAAATA--T-ATACATA
56364153 ATATTAGAAATATATACATA
1 ATATTAGAAATATATACATA
* *
56364173 ATATATAAAAAATATATATAATGTA
1 ATAT-T-AGAAATATATA-CA--TA
*
56364198 GTATTA-AAATATATACATA
1 ATATTAGAAATATATACATA
56364217 ATAT
1 ATAT
56364221 ATACATATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.09
20 10 0.18
21 3 0.05
22 19 0.33
23 14 0.25
24 1 0.02
25 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (20 bp):
ATATTAGAAATATATACATA
Found at i:56364238 original size:44 final size:45
Alignment explanation
Indices: 56364154--56364238 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
56364144 TAATATATAA
* *
56364154 TATTAGAAATATATACATAATATATAAAAAATATATATAATGTAG
1 TATTAGAAATATATACATAATATATAAAAAATAAAAATAATGTAG
* * *
56364199 TATTA-AAATATATACATAATATATACATATTAAAAATAAT
1 TATTAGAAATATATACATAATATATAAAAAATAAAAATAAT
56364239 AATAATGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 30 0.86
45 5 0.14
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (45 bp):
TATTAGAAATATATACATAATATATAAAAAATAAAAATAATGTAG
Found at i:56364251 original size:18 final size:20
Alignment explanation
Indices: 56364214--56364252 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
56364204 AAATATATAC
56364214 ATAATATATACATATTAAAA
1 ATAATATATACATATTAAAA
*
56364234 ATAATA-ATA-ATGTTAAAA
1 ATAATATATACATATTAAAA
56364252 A
1 A
56364253 CAACTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
ATAATATATACATATTAAAA
Found at i:56375564 original size:47 final size:47
Alignment explanation
Indices: 56375455--56375565 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
56375445 CCGGGATAAG
* *
56375455 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
56375502 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
56375549 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
56375566 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:56388142 original size:44 final size:40
Alignment explanation
Indices: 56388060--56388147 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 40
56388050 GAATATATCA
* *
56388060 CACCATTGAAGACTTTAAACCAATCTAAAGTTTTGAATAT
1 CACCATTGAAGACTTTAAACCAATCTAAAATTTCGAATAT
56388100 CACCATTGAAGACTTTAAACCAATCTATTGAACATTTCGAATAT
1 CACCATTGAAGACTTTAAACCAATCTA---AA-ATTTCGAATAT
56388144 CACC
1 CACC
56388148 TCCGATCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 27 0.64
43 2 0.05
44 13 0.31
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.31
Consensus pattern (40 bp):
CACCATTGAAGACTTTAAACCAATCTAAAATTTCGAATAT
Found at i:56395379 original size:18 final size:18
Alignment explanation
Indices: 56395356--56395448 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
56395346 CCCAACTACT
*
56395356 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
56395374 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
56395392 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
56395410 GTATATGTGAATAGTTCT
1 GTATACGTGAATAGTACC
56395428 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
56395446 GTA
1 GTA
56395449 ACGGTCGTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:56396085 original size:40 final size:40
Alignment explanation
Indices: 56396029--56396148 Score: 204
Period size: 40 Copynumber: 3.0 Consensus size: 40
56396019 TCCAATACTA
* *
56396029 TAAATATCTATCTTCTCTGTAACTCTTCTCATTCATCAAT
1 TAAATATCCATTTTCTCTGTAACTCTTCTCATTCATCAAT
56396069 TAAATATCCATTTTCTCTGTAACTCTTCTCATTCATCAAT
1 TAAATATCCATTTTCTCTGTAACTCTTCTCATTCATCAAT
* *
56396109 TAAATATCCAATTTCTCTGTAACTCTTCTTATTCATCAAT
1 TAAATATCCATTTTCTCTGTAACTCTTCTCATTCATCAAT
56396149 CACCTTCTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.28, C:0.24, G:0.03, T:0.45
Consensus pattern (40 bp):
TAAATATCCATTTTCTCTGTAACTCTTCTCATTCATCAAT
Found at i:56402640 original size:25 final size:26
Alignment explanation
Indices: 56402602--56402664 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
56402592 AACAATATGG
56402602 ACCATA-TATAGATTAATATCTGTGC
1 ACCATATTATAGATTAATATCTGTGC
56402627 ACCATATTAT-GATTAATATCTGTGC
1 ACCATATTATAGATTAATATCTGTGC
*
56402652 AGCATA-TATAGAT
1 ACCATATTATAGAT
56402665 ACACACATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 3 0.09
25 29 0.83
26 3 0.09
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (26 bp):
ACCATATTATAGATTAATATCTGTGC
Found at i:56406862 original size:25 final size:25
Alignment explanation
Indices: 56406828--56406878 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
56406818 TCAACACGTC
*
56406828 GGATATTATCTCCGGTTAGAGTTTT
1 GGATATTATCTCCGGTTAGAATTTT
56406853 GGATATTATCTCCGGTTAGAATTTT
1 GGATATTATCTCCGGTTAGAATTTT
56406878 G
1 G
56406879 TCTCATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.43
Consensus pattern (25 bp):
GGATATTATCTCCGGTTAGAATTTT
Found at i:56407674 original size:20 final size:20
Alignment explanation
Indices: 56407632--56407674 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
56407622 AACTTTGCTT
*
56407632 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGCA
*
56407652 AAATTTATGAATAAAAAAG-A
1 AAATTTAAG-ATAAAAAAGCA
56407672 AAA
1 AAA
56407675 GAGTCCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGCA
Found at i:56425728 original size:3 final size:3
Alignment explanation
Indices: 56425720--56425744 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56425710 TTTCCAACCA
56425720 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
56425745 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56425749 original size:3 final size:3
Alignment explanation
Indices: 56425743--56425777 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
56425733 ATAATAATAA
56425743 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56425778 ATACCAATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56434793 original size:6 final size:7
Alignment explanation
Indices: 56434776--56434800 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56434766 CCAGTTTGTT
56434776 TTTTTTA
1 TTTTTTA
56434783 TTTTTTA
1 TTTTTTA
56434790 TTTTTTA
1 TTTTTTA
56434797 TTTT
1 TTTT
56434801 AGTACTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:56442141 original size:22 final size:23
Alignment explanation
Indices: 56442099--56442146 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
56442089 TATATATATC
*
56442099 ATATTTTATATTTTTATATAA-A
1 ATATTTTATATATTTATATAAGA
56442121 ATATTTTATAATATTT-TATAAGA
1 ATATTTTAT-ATATTTATATAAGA
56442144 ATA
1 ATA
56442147 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATTTTATATATTTATATAAGA
Found at i:56442833 original size:13 final size:13
Alignment explanation
Indices: 56442815--56442846 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
56442805 ATTGTCGCAT
56442815 TCTCTCTCGAAGG
1 TCTCTCTCGAAGG
56442828 TCTCTCTCGAAGG
1 TCTCTCTCGAAGG
56442841 TCTCTC
1 TCTCTC
56442847 CAGAACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.34, G:0.19, T:0.34
Consensus pattern (13 bp):
TCTCTCTCGAAGG
Found at i:56452255 original size:14 final size:14
Alignment explanation
Indices: 56452236--56452265 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56452226 AAATCAAAGG
56452236 GATGGAGATTTAGA
1 GATGGAGATTTAGA
56452250 GATGGAGATTTAGA
1 GATGGAGATTTAGA
56452264 GA
1 GA
56452266 AGCAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GATGGAGATTTAGA
Found at i:56452352 original size:14 final size:14
Alignment explanation
Indices: 56452333--56452362 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56452323 AATGGTGGAA
*
56452333 GGATTTTGATTTGG
1 GGATTTCGATTTGG
56452347 GGATTTCGATTTGG
1 GGATTTCGATTTGG
56452361 GG
1 GG
56452363 GAAAAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.40, T:0.43
Consensus pattern (14 bp):
GGATTTCGATTTGG
Found at i:56452410 original size:13 final size:13
Alignment explanation
Indices: 56452392--56452424 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
56452382 GGGGATACCC
*
56452392 ATTTTAGGGGGAA
1 ATTTTAGGGAGAA
56452405 ATTTTAGGGAGAA
1 ATTTTAGGGAGAA
56452418 ATTTTAG
1 ATTTTAG
56452425 ACATTCCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (13 bp):
ATTTTAGGGAGAA
Found at i:56453499 original size:17 final size:17
Alignment explanation
Indices: 56453473--56453507 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56453463 GGGGTTATAG
* *
56453473 TTTAGTATTTAGGTGTT
1 TTTAGGATTTAGGGGTT
56453490 TTTAGGATTTAGGGGTT
1 TTTAGGATTTAGGGGTT
56453507 T
1 T
56453508 AGTGTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (17 bp):
TTTAGGATTTAGGGGTT
Found at i:56453560 original size:54 final size:54
Alignment explanation
Indices: 56453450--56453566 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 54
56453440 GTTTTTTGGA
* * *
56453450 GTTTAGGGTTTTAGGGGTTATAGTTTAGTATTTAGGTGTTTTTAGGATTTAGGG
1 GTTTAGGGTTTTAGGGGTTATAGATTAGTATTCAGATGTTTTTAGGATTTAGGG
* * * * * *
56453504 GTTTAGTGTTTTAGGGGTTATAGATTAGTGTTCATTATTTTTTTGGGGTTTAGGG
1 GTTTAGGGTTTTAGGGGTTATAGATTAGTATTCA-GATGTTTTTAGGATTTAGGG
*
56453559 TTTTAGGG
1 GTTTAGGG
56453567 ATTATATGAC
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
54 30 0.59
55 21 0.41
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.50
Consensus pattern (54 bp):
GTTTAGGGTTTTAGGGGTTATAGATTAGTATTCAGATGTTTTTAGGATTTAGGG
Found at i:56453622 original size:41 final size:41
Alignment explanation
Indices: 56453577--56453754 Score: 243
Period size: 41 Copynumber: 4.4 Consensus size: 41
56453567 ATTATATGAC
* * **
56453577 TTTTAGCGGCATTTTGCCAAAAGCGTTGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
56453618 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGTTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
56453659 TTTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
** *
56453699 TTTTAGCGGCGTTTTACCAAAAAATGCCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTACC-AAAAGCGCCGCTAATGCTCTGGT
*
56453740 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
56453755 TGGTGTTTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 19 0.15
41 105 0.85
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:56459080 original size:30 final size:30
Alignment explanation
Indices: 56459013--56459080 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
56459003 CACCCTTAAA
* * *
56459013 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
56459043 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
56459072 AGTATTTAC
1 A-TATTTAC
56459081 TATTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:56469879 original size:115 final size:115
Alignment explanation
Indices: 56469750--56469979 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 115
56469740 ACATCACTTT
*
56469750 TATTTTCACTCAATATTCATATCAATTTCACATACTTACCTCAAGTTTTATTTACCATACATAAC
1 TATTTTCACTCAATATTCATATCAATTTCACATACTTACCTCAAGTCTTATTTACCATACATAAC
56469815 AATTAAAATTTCAGCAATCAATAATAATTAAAATTCGAATTATAGTAATA
66 AATTAAAATTTCAGCAATCAATAATAATTAAAATTCGAATTATAGTAATA
*
56469865 TATTTTCACTCAATATTCATATCAATTTCACATACTTACCTCAAGTCTTATTTACCATACTTAAC
1 TATTTTCACTCAATATTCATATCAATTTCACATACTTACCTCAAGTCTTATTTACCATACATAAC
56469930 AATTAAAATTTCAGCAATCAATAATAATTAAAATTCGAATTATAGTAATA
66 AATTAAAATTTCAGCAATCAATAATAATTAAAATTCGAATTATAGTAATA
56469980 CACACCGTAA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (115 bp):
TATTTTCACTCAATATTCATATCAATTTCACATACTTACCTCAAGTCTTATTTACCATACATAAC
AATTAAAATTTCAGCAATCAATAATAATTAAAATTCGAATTATAGTAATA
Found at i:56478059 original size:25 final size:24
Alignment explanation
Indices: 56478038--56478102 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 24
56478028 ACAAAATTCT
56478038 TAACATGAAATTTATCATAAATTAG
1 TAAC-TGAAATTTATCATAAATTAG
56478063 TAACTGGAAATTTATCATAAATTAG
1 TAACT-GAAATTTATCATAAATTAG
56478088 TAACTGAAAATTTAT
1 TAACTG-AAATTTAT
56478103 GTATAATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (24 bp):
TAACTGAAATTTATCATAAATTAG
Found at i:56484498 original size:28 final size:28
Alignment explanation
Indices: 56484464--56484523 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
56484454 CAAAAAATAA
* *
56484464 ATAATTTATTTTCGTTAAATACATGTGT
1 ATAATTTACTTTCGGTAAATACATGTGT
56484492 ATAATTTACTTTCGGTAAATACATGTGT
1 ATAATTTACTTTCGGTAAATACATGTGT
56484520 ATAA
1 ATAA
56484524 ATAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (28 bp):
ATAATTTACTTTCGGTAAATACATGTGT
Found at i:56499454 original size:3 final size:3
Alignment explanation
Indices: 56499448--56499475 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56499438 AATGCAGCAG
56499448 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
56499476 AGCAATAGTA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:56500393 original size:39 final size:39
Alignment explanation
Indices: 56500339--56500419 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
56500329 TAATTATGGC
56500339 TCAACTCTATCCATTGGCCCACGGGAATGCAACACTCTT
1 TCAACTCTATCCATTGGCCCACGGGAATGCAACACTCTT
56500378 TCAACTCTATCCATTGGCCCACGGGAATGCAACACTCTT
1 TCAACTCTATCCATTGGCCCACGGGAATGCAACACTCTT
56500417 TCA
1 TCA
56500420 CCATTTTGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (39 bp):
TCAACTCTATCCATTGGCCCACGGGAATGCAACACTCTT
Found at i:56506671 original size:13 final size:13
Alignment explanation
Indices: 56506653--56506680 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56506643 AAAAAATTTC
56506653 CACGACCAAAACA
1 CACGACCAAAACA
56506666 CACGACCAAAACA
1 CACGACCAAAACA
56506679 CA
1 CA
56506681 GGGTTACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.39, G:0.07, T:0.00
Consensus pattern (13 bp):
CACGACCAAAACA
Found at i:56508330 original size:25 final size:26
Alignment explanation
Indices: 56508302--56508384 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
56508292 GGTAGATCCT
56508302 AAGAGCCATTAATTGGGAAGCTC-CA
1 AAGAGCCATTAATTGGGAAGCTCACA
* *
56508327 AAGAGCCATTAATTAGGAAGTTCACA
1 AAGAGCCATTAATTGGGAAGCTCACA
* * * * *
56508353 AAAATCCTTTAATCGGGAAGCTCACG
1 AAGAGCCATTAATTGGGAAGCTCACA
56508379 AAGAGC
1 AAGAGC
56508385 AATATATGGA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 21 0.46
26 25 0.54
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (26 bp):
AAGAGCCATTAATTGGGAAGCTCACA
Found at i:56508917 original size:5 final size:5
Alignment explanation
Indices: 56508909--56508933 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56508899 TTCATATTTT
56508909 ATTCA ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA
56508934 CATCTTAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:56512644 original size:27 final size:26
Alignment explanation
Indices: 56512618--56512669 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
56512608 AACGAAAAGC
56512618 CCTC-TCTCGAGCCATATAACGGGAAG
1 CCTCGTCT-GAGCCATATAACGGGAAG
*
56512644 -CTCGTGTGAGCCATATAACGGGAAG
1 CCTCGTCTGAGCCATATAACGGGAAG
56512669 C
1 C
56512670 TTATCCGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (26 bp):
CCTCGTCTGAGCCATATAACGGGAAG
Found at i:56512679 original size:25 final size:25
Alignment explanation
Indices: 56512625--56512743 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 25
56512615 AGCCCTCTCT
*
56512625 CGAGCCATATAACGGGAAGCTCGTG
1 CGAGCCATATAACGGGAAGCTCATG
* * *
56512650 TGAGCCATATAACGGGAAGCTTATC
1 CGAGCCATATAACGGGAAGCTCATG
** * * *
56512675 CGAGCTGTATAACAGGAAGCTAATA
1 CGAGCCATATAACGGGAAGCTCATG
** *
56512700 AAAGCCATA-ATCGGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATG
* *
56512724 TGAGCCA-ATAACGGGTAGCT
1 CGAGCCATATAACGGGAAGCT
56512744 TCAAAGAGCC
Statistics
Matches: 71, Mismatches: 22, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
23 1 0.01
24 25 0.35
25 45 0.63
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTCATG
Found at i:56512765 original size:73 final size:73
Alignment explanation
Indices: 56512627--56512902 Score: 195
Period size: 73 Copynumber: 3.7 Consensus size: 73
56512617 CCCTCTCTCG
* * ** **
56512627 AGCCATATAACGGGAAGCTCGTGTGAGCCATATAACGGGAAGCTT-ATCCGAGCTGTATAA-CAG
1 AGCCATATATCGGGAAGCTCATGTGAGCCA-ATAACGGGAAGCTTCA-AAGAGCCAT-TAATCAG
56512690 GAAGCTAATAAA
63 GAAGCT-ATAAA
*
56512702 AGCCATA-ATCGGGAAGCTCATGTGAGCCAATAACGGGTAGCTTCAAAGAGCCATTAATCAGGAA
1 AGCCATATATCGGGAAGCTCATGTGAGCCAATAACGGGAAGCTTCAAAGAGCCATTAATCAGGAA
* *
56512766 GCTCTGAAT
66 GCTAT-AAA
* * * ** * ** *
56512775 AGTCATATATCGGGAAGTTCAAGCAAGCC-ATATCGGGAAGCTTCGGAGAGCCATTAATTAGGAA
1 AGCCATATATCGGGAAGCTCATGTGAGCCAATAACGGGAAGCTTCAAAGAGCCATTAATCAGGAA
*
56512839 GCTCACAAA
66 GCT-ATAAA
* * * * *
56512848 GAGCC-TTTAATCGAGAAGCTCACGAAGAGCCAAATAACGGGATGC-TCATAAGAGC
1 -AGCCATAT-ATCGGGAAGCTCATG-TGAGCC-AATAACGGGAAGCTTCA-AAGAGC
56512903 TATGGTGTGT
Statistics
Matches: 157, Mismatches: 33, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
72 4 0.03
73 72 0.46
74 53 0.34
75 11 0.07
76 2 0.01
77 15 0.10
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (73 bp):
AGCCATATATCGGGAAGCTCATGTGAGCCAATAACGGGAAGCTTCAAAGAGCCATTAATCAGGAA
GCTATAAA
Found at i:56512857 original size:26 final size:26
Alignment explanation
Indices: 56512821--56512879 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
56512811 GAAGCTTCGG
56512821 AGAGCCATTAATTAG-GAAGCTCACAA
1 AGAGCCATTAA-TAGAGAAGCTCACAA
* * *
56512847 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCATTAATAGAGAAGCTCACAA
56512873 AGAGCCA
1 AGAGCCA
56512880 AATAACGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (26 bp):
AGAGCCATTAATAGAGAAGCTCACAA
Found at i:56521085 original size:12 final size:12
Alignment explanation
Indices: 56521068--56521092 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56521058 GAATTTCGAT
56521068 TGCCAGGCCGTG
1 TGCCAGGCCGTG
56521080 TGCCAGGCCGTG
1 TGCCAGGCCGTG
56521092 T
1 T
56521093 AGGTGGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.40, T:0.20
Consensus pattern (12 bp):
TGCCAGGCCGTG
Found at i:56521425 original size:42 final size:43
Alignment explanation
Indices: 56521358--56521439 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
56521348 CCATGTGAGA
* *
56521358 CACATGAGCAGAGGACACGGACATGTGTCCAAGTCGTGTGAAC
1 CACACGAGCAGAGGACACGGACATGTGTCCAAGCCGTGTGAAC
* *
56521401 CACACGAGCA-AGGGCACGGGCATGTGTCCAAGCCGTGTG
1 CACACGAGCAGAGGACACGGACATGTGTCCAAGCCGTGTG
56521440 GCTTGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 26 0.74
43 9 0.26
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.15
Consensus pattern (43 bp):
CACACGAGCAGAGGACACGGACATGTGTCCAAGCCGTGTGAAC
Found at i:56523139 original size:26 final size:29
Alignment explanation
Indices: 56523093--56523154 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
56523083 TAAGATAGCC
56523093 ATATAAAAACTTTCAATAAATA-AAAAAT-
1 ATATAAAAACTTT-AATAAATATAAAAATA
*
56523121 ATATAAAAA-TTT-ATGAAATATTAAAATA
1 ATATAAAAACTTTAAT-AAATATAAAAATA
56523149 ATATAA
1 ATATAA
56523155 TATAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 5 0.17
27 8 0.27
28 15 0.50
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (29 bp):
ATATAAAAACTTTAATAAATATAAAAATA
Found at i:56526366 original size:20 final size:20
Alignment explanation
Indices: 56526343--56526384 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
56526333 CATTATACAA
*
56526343 TTAAATTAATTA-TTAAAATT
1 TTAAA-TAATTAGATAAAATT
56526363 TT-AATAATTAGATAAAATT
1 TTAAATAATTAGATAAAATT
56526382 TTA
1 TTA
56526385 CCCAATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
18 6 0.32
19 11 0.58
20 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATAATTAGATAAAATT
Found at i:56530572 original size:36 final size:36
Alignment explanation
Indices: 56530526--56530597 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
56530516 GGGGGGGGGG
* *
56530526 GGAATAAGTTGGGTAATTGGAGGGGGGAGAGGAAGC
1 GGAATAAGTTGGGTAATTGGAGAGCGGAGAGGAAGC
* *
56530562 GGAATCAGTTGGGTAATTGGAGAGCGTAGAGGAAGC
1 GGAATAAGTTGGGTAATTGGAGAGCGGAGAGGAAGC
56530598 ATTTGACAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.46, T:0.18
Consensus pattern (36 bp):
GGAATAAGTTGGGTAATTGGAGAGCGGAGAGGAAGC
Found at i:56539166 original size:63 final size:63
Alignment explanation
Indices: 56539067--56539325 Score: 509
Period size: 63 Copynumber: 4.1 Consensus size: 63
56539057 AGGAGAAAAC
56539067 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
1 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
56539130 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
1 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
56539193 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
1 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
*
56539256 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCGTGCTTGAGGGCATAGATATTT
1 TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
56539319 TACAAAA
1 TACAAAA
56539326 CAATACCTGA
Statistics
Matches: 195, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 195 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (63 bp):
TACAAAATAATTCCTCTGTTAACTTTTGAATGATTGGAAGCTTGCTTGAGGGCATAGATATTT
Found at i:56550558 original size:16 final size:17
Alignment explanation
Indices: 56550524--56550564 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
56550514 ATTATTTTAA
56550524 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA-CATAT
56550541 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAACATAT
56550557 A-TTTAATT
1 ATTTTAATT
56550565 TTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATTAAACATAT
Found at i:56550635 original size:66 final size:65
Alignment explanation
Indices: 56550565--56550759 Score: 173
Period size: 66 Copynumber: 3.1 Consensus size: 65
56550555 ATATTTAATT
56550565 TTAATTATTTAAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1 TTAATTATTTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
56550630 A
65 A
* * * * **
56550631 TTAATTA-TTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TTAAT
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
56550684 A
65 A
* * *
56550685 ATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAA
1 TTAATTAT-TTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAA
56550749 TA
64 TA
*
56550751 TTGATTATT
1 TTAATTATT
56550760 AAGAATTTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
54 13 0.13
55 6 0.06
56 7 0.07
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 10 0.10
66 21 0.21
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
Found at i:56550647 original size:120 final size:120
Alignment explanation
Indices: 56550523--56550790 Score: 448
Period size: 120 Copynumber: 2.2 Consensus size: 120
56550513 AATTATTTTA
* ** *
56550523 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATTTTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
56550587 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
56550643 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
56550708 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
56550763 AATTTTATTAAATTATATATTTTAATTA
1 AATTTTATTAAATTATATATTTTAATTA
56550791 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
120 137 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:56550683 original size:15 final size:15
Alignment explanation
Indices: 56550648--56550699 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56550638 TTAAGAATTT
*
56550648 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56550662 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56550676 TATTTAATAATAAT-
1 TATTTAATTATAATA
56550690 TATGTTAATT
1 TAT-TTAATT
56550700 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:56550781 original size:61 final size:61
Alignment explanation
Indices: 56550596--56550783 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
56550586 TTATAGTATA
*
56550596 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
56550657 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
56550716 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
56550777 ATATATT
1 ATATATT
56550784 TTAATTANNN
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 25 0.26
61 36 0.38
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:56556211 original size:23 final size:23
Alignment explanation
Indices: 56556181--56556227 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
56556171 GAGAATGGGT
56556181 GGGGGAGAATGTCACGGGCCGCA
1 GGGGGAGAATGTCACGGGCCGCA
56556204 GGGGGAGAATGTCACGGGCCGCA
1 GGGGGAGAATGTCACGGGCCGCA
56556227 G
1 G
56556228 TTCAAAGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.49, T:0.09
Consensus pattern (23 bp):
GGGGGAGAATGTCACGGGCCGCA
Found at i:56570196 original size:6 final size:7
Alignment explanation
Indices: 56570179--56570203 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56570169 AGTGTCCCTT
56570179 CCCCCCA
1 CCCCCCA
56570186 CCCCCCA
1 CCCCCCA
56570193 CCCCCCA
1 CCCCCCA
56570200 CCCC
1 CCCC
56570204 TCACATCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (7 bp):
CCCCCCA
Found at i:56572255 original size:5 final size:5
Alignment explanation
Indices: 56572245--56572277 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
56572235 ATACATAGAT
56572245 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
56572278 TATAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:56576555 original size:12 final size:12
Alignment explanation
Indices: 56576538--56576562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56576528 TTCTAGTTCT
56576538 TTTATATATATA
1 TTTATATATATA
56576550 TTTATATATATA
1 TTTATATATATA
56576562 T
1 T
56576563 AATTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATATATA
Found at i:56576589 original size:19 final size:21
Alignment explanation
Indices: 56576549--56576603 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
56576539 TTATATATAT
*
56576549 ATTTATATATATATAATTTTA
1 ATTTATATATATATAATATTA
56576570 ATTTATATAT-TA-AATATTAAAA
1 ATTTATATATATATAATATT---A
56576592 ATTTATATATAT
1 ATTTATATATAT
56576604 TTCAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 5 0.17
20 2 0.07
21 10 0.34
22 11 0.38
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATATATATATAATATTA
Found at i:56576995 original size:23 final size:23
Alignment explanation
Indices: 56576969--56577022 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
56576959 TGATTTTTAA
*
56576969 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
56576992 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
56577015 ACTTAGAA
1 ATTTAGAA
56577023 AAAATCTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:56576996 original size:13 final size:13
Alignment explanation
Indices: 56576978--56577020 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
56576968 AATTTTGAAT
56576978 TATTTAGTGATAA
1 TATTTAGTGATAA
56576991 TATTTAG-GAT--
1 TATTTAGTGATAA
56577001 TATTTAGTGATAA
1 TATTTAGTGATAA
*
56577014 TACTTAG
1 TATTTAG
56577021 AAAAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:56577920 original size:25 final size:23
Alignment explanation
Indices: 56577875--56577939 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
56577865 TTATTTATCC
* *
56577875 ATTTATTTTATTTTCTATTTTTGA
1 ATTT-TTTTATTTTATTTTTTTGA
*
56577899 ATTTGTTTTTATTTTATTTTTTTGT
1 A-TT-TTTTTATTTTATTTTTTTGA
*
56577924 ATTTTCTTATTTTATT
1 ATTTTTTTATTTTATT
56577940 ATCTTAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 12 0.34
24 3 0.09
25 19 0.54
26 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (23 bp):
ATTTTTTTATTTTATTTTTTTGA
Found at i:56581558 original size:44 final size:44
Alignment explanation
Indices: 56581394--56581597 Score: 172
Period size: 43 Copynumber: 4.7 Consensus size: 44
56581384 ATACAATGTC
* * **
56581394 ATATCTCAGATATGGTCTTACATGTTATCACATAT-C-AGTGCCA
1 ATATCCCAGATATGGTCTTACACGAAATCACATATACGA-TGCCA
*
56581437 ATAGCCCA-ACTATGGTCTTACACGAAATCACATA-ACGATGCCA
1 ATATCCCAGA-TATGGTCTTACACGAAATCACATATACGATGCCA
* * * *
56581480 ATGTCCCAGACATGGTCTTACACGTAATCACATATATCGATGTC-
1 ATATCCCAGATATGGTCTTACACGAAATCACATATA-CGATGCCA
* *
56581524 ATATCCCAGATATGGTCTTACAC-AAAGTCTCATATAAAGATGCC-
1 ATATCCCAGATATGGTCTTACACGAAA-TCACATAT-ACGATGCCA
* * *
56581568 ATAGCCCA-ACTATGATCTTATACGAAATCA
1 ATATCCCAGA-TATGGTCTTACACGAAATCA
56581598 TGTAATGCCA
Statistics
Matches: 131, Mismatches: 20, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.01
43 64 0.49
44 56 0.43
45 10 0.08
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (44 bp):
ATATCCCAGATATGGTCTTACACGAAATCACATATACGATGCCA
Found at i:56595119 original size:23 final size:22
Alignment explanation
Indices: 56595058--56595124 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
56595048 ACCTGATCAG
56595058 TATACGACACATAAGTGCCTGA
1 TATACGACACATAAGTGCCTGA
* *
56595080 -A-ACGACACACGAGGTGCCTGA
1 TATACGACACA-TAAGTGCCTGA
56595101 TATACGACACATAAAGTGCCTGA
1 TATACGACACAT-AAGTGCCTGA
56595124 T
1 T
56595125 CGGCAAAGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 8 0.22
21 10 0.27
22 1 0.03
23 18 0.49
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (22 bp):
TATACGACACATAAGTGCCTGA
Found at i:56596074 original size:14 final size:14
Alignment explanation
Indices: 56596057--56596102 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
56596047 TATTTATATT
56596057 ATAATAATAATTTA
1 ATAATAATAATTTA
*
56596071 ATAATACTAATTTA
1 ATAATAATAATTTA
56596085 ATAATAATAATTTA
1 ATAATAATAATTTA
56596099 ATAA
1 ATAA
56596103 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:56601130 original size:15 final size:16
Alignment explanation
Indices: 56601110--56601143 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56601100 TCTTATGAAT
56601110 TTTATA-ATTTTAAAA
1 TTTATATATTTTAAAA
*
56601125 TTTATATATTTTAATA
1 TTTATATATTTTAAAA
56601141 TTT
1 TTT
56601144 CAGATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATATATTTTAAAA
Found at i:56601875 original size:31 final size:29
Alignment explanation
Indices: 56601807--56601875 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
56601797 ATGACATTTA
*
56601807 TATTTAATGTAATATTAATATAATTTTTT
1 TATTTAATATAATATTAATATAATTTTTT
* * *
56601836 AATATTAATATAAATATTATTATTAGTTTTTT
1 TAT-TTAATAT-AATATTAATA-TAATTTTTT
56601868 TATTTAAT
1 TATTTAAT
56601876 TAGATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.06
30 6 0.19
31 14 0.44
32 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
TATTTAATATAATATTAATATAATTTTTT
Found at i:56608020 original size:29 final size:29
Alignment explanation
Indices: 56607959--56608020 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
56607949 TAACAAGGGT
* **
56607959 TCAAAAGGACACTCTCACTATCAGTTCTA
1 TCAAAAAGACACTCTCACTATCAGTTAAA
56607988 -CAAAAAGACACTCTCACTATCAGTTAAA
1 TCAAAAAGACACTCTCACTATCAGTTAAA
56608016 TCAAA
1 TCAAA
56608021 TAATACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (29 bp):
TCAAAAAGACACTCTCACTATCAGTTAAA
Found at i:56608804 original size:7 final size:7
Alignment explanation
Indices: 56608792--56608839 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
56608782 CAGATGCACG
56608792 GGGAAAT
1 GGGAAAT
56608799 GGGAAAT
1 GGGAAAT
*
56608806 GGGGAAT
1 GGGAAAT
*
56608813 GGGGAA-
1 GGGAAAT
56608819 GGGAAAT
1 GGGAAAT
56608826 -GGAAAT
1 GGGAAAT
56608832 GGGAAAT
1 GGGAAAT
56608839 G
1 G
56608840 TATTTTAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 11 0.30
7 26 0.70
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (7 bp):
GGGAAAT
Found at i:56609968 original size:108 final size:105
Alignment explanation
Indices: 56609767--56610146 Score: 430
Period size: 101 Copynumber: 3.7 Consensus size: 105
56609757 GGAAAAAGAA
* *
56609767 GAAAAAGGAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGTAC----AAAAAA
1 GAAAAATGAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTAAAAAA
*
56609828 AAATTCTTTTTTTTCGTGTCAGAATCAAATATCAATATAC
66 AAATTCTTTTTTTTCGTGTCAGAATCAGATATCAATATAC
* *
56609868 GAAAAATGAAAAAAAAATTTTAGGTTCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAA
1 GAAAAATGAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC-AA-TTAAAA
*
56609933 AAAAATTTCTTTTTTTTCGTGTCAGAATCAGATATCAGTATAC
64 AAAAA-TTCTTTTTTTTCGTGTCAGAATCAGATATCAATATAC
* * * * *
56609976 GAAAAAAATAAAAAAAAAATTTTGGGTGCTGGCCTTTAAATGGCCGACACCCAATACAATTTAAA
1 G--AAAAATGAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTAAA
*
56610041 AAAAAA--------TTT-GTGTCAAAATCAGATATCAATATAC
63 AAAAAATTCTTTTTTTTCGTGTCAGAATCAGATATCAATATAC
* ** *
56610075 GAAAAA--AATTTAAAATTTCTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTAAA
1 GAAAAATGAA--AAAAAAAT-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTAAA
56610138 AAAAAATTC
63 AAAAAATTC
56610147 GTGTCAAAAT
Statistics
Matches: 241, Mismatches: 23, Indels: 31
0.82 0.08 0.11
Matches are distributed among these distances:
95 2 0.01
97 21 0.09
98 34 0.14
99 24 0.10
100 3 0.01
101 51 0.21
107 9 0.04
108 36 0.15
109 14 0.06
110 47 0.20
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (105 bp):
GAAAAATGAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTAAAAAA
AAATTCTTTTTTTTCGTGTCAGAATCAGATATCAATATAC
Found at i:56610165 original size:97 final size:99
Alignment explanation
Indices: 56609948--56610187 Score: 340
Period size: 97 Copynumber: 2.4 Consensus size: 99
56609938 TTTCTTTTTT
* * *
56609948 TTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAAATTTTGGGTGCTGGCCTTT
1 TTCGTGTCAAAATCAGATATCAGTATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
56610013 AAATGGCCGACACCCAATACAATTTAAAAAAAAA
66 AAATGGCCGACACCCAATACAATTTAAAAAAAAA
* * * ****
56610047 TTTGTGTCAAAATCAGATATCAATATACGAAAAAAATTTAAAATTTCTTTT-GGTGCTGGCCTGT
1 TTCGTGTCAAAATCAGATATCAGTATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
* * *
56610111 CAATGGCCGGCACCCAGTACAA-TTAAAAAAAAA
66 AAATGGCCGACACCCAATACAATTTAAAAAAAAA
*
56610144 TTCGTGTCAAAATCAGATATCAGTATACGAATAAAATTAAAAAA
1 TTCGTGTCAAAATCAGATATCAGTATACGAAAAAAATTAAAAAA
56610188 TATATATTTT
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
97 50 0.41
98 31 0.25
99 42 0.34
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (99 bp):
TTCGTGTCAAAATCAGATATCAGTATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGCCTGT
AAATGGCCGACACCCAATACAATTTAAAAAAAAA
Found at i:56610288 original size:86 final size:85
Alignment explanation
Indices: 56610115--56610279 Score: 206
Period size: 92 Copynumber: 1.9 Consensus size: 85
56610105 GCCTGTCAAT
*
56610115 GGCCGGCACCCAGTACAATTAAAAAAAAATTCGTGTCAAAATCAGATATCAGTATACGAATAAAA
1 GGCCGGCACCCAGTACAATTAAAAAAAAATTCGTGTCAAAATCAGATACCAGTATACGAATAAAA
56610180 TTAAAAAATATATATTTTTTG
66 TTAAAAAATATATA-TTTTTG
* * *
56610201 GGCCGGCACCCAGTACAAATTAAAAAAAATTCTTTTTCGTGTCAGAATCGGATACCAGTATACGA
1 GGCCGGCACCCAGTAC-AATTAAAAAAAA-----ATTCGTGTCAAAATCAGATACCAGTATACGA
*
56610266 A-AAATATAAAAAAA
60 ATAAA-ATTAAAAAA
56610280 AATTTTGGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
86 16 0.24
87 12 0.18
91 3 0.04
92 36 0.54
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (85 bp):
GGCCGGCACCCAGTACAATTAAAAAAAAATTCGTGTCAAAATCAGATACCAGTATACGAATAAAA
TTAAAAAATATATATTTTTG
Found at i:56610435 original size:116 final size:115
Alignment explanation
Indices: 56610233--56610445 Score: 320
Period size: 116 Copynumber: 1.8 Consensus size: 115
56610223 AAAAAAATTC
* * *
56610233 TTTTTCGTGTCAGAATCGGATACCAGTATACGAAAAATATAAAAAAAAATTTTGGGTGCTGACCT
1 TTTTTCGTGTCAAAATCAGATACCAATATACGAAAAATATAAAAAAAAATTTTGGGTGCTGACCT
56610298 GTCAACGGCCGGCACCCAGTACAAT-TTTAAAACAATTTTTTTTTTCATT
66 GTCAACGGCCGGCACCCAGTACAATCTTTAAAACAATTTTTTTTTTCATT
* * * *
56610347 TTTTTCGTGTCAAAATCAGATATCAATATACGAAAAAAATTTAAAAAAAATTTTTGGGTGCTGGC
1 TTTTTCGTGTCAAAATCAGATACCAATATACG--AAAAATATAAAAAAAAATTTTGGGTGCTGAC
* *
56610412 CTGTTAATGGCCGGCACCCAGTACAATCTTTAAA
64 CTGTCAACGGCCGGCACCCAGTACAATCTTTAAA
56610446 TTTTTTTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
114 28 0.32
116 53 0.61
117 6 0.07
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (115 bp):
TTTTTCGTGTCAAAATCAGATACCAATATACGAAAAATATAAAAAAAAATTTTGGGTGCTGACCT
GTCAACGGCCGGCACCCAGTACAATCTTTAAAACAATTTTTTTTTTCATT
Found at i:56610697 original size:111 final size:107
Alignment explanation
Indices: 56610487--56611190 Score: 869
Period size: 111 Copynumber: 6.4 Consensus size: 107
56610477 TATCCAAATT
** * *
56610487 TTTTTTTTGATTTTTTTCGTATACTGATATCTGATTTTGACATGAAAAAAAAG-ATTTTTTTTTA
1 TTTTTTTAAATTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGAATTTTTTTTAA
* *
56610551 ATTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCCAAAAA
66 ATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAA
*
56610593 TTTTTTTAAATTTTTTTCGTATACTGATATCTGATTTTGACTCGAAAAAAAAAAGAAAGTTTTTT
1 TTTTTTTAAATTTTTTTCGTATACTGATATCTGATTTTGACACG--AAAAAAAAG-AA-TTTTTT
*
56610658 TTAAATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAT
62 TTAAATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAA
56610704 TTTTTTTAAAATTTTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGAA-TTTTTT
1 TTTTTTT-AAA--TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGAATTTTTTT
** * **
56610768 TAAATTGTACTGGGTGCCGGCCATTGGTAGGCCAGCACCCAAATT
63 TAAATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAA
** * * * * *
56610813 TTTTTTTTTACTTTTTTCCTATACTGATATCTGATTCTGACATGAAAAAAAAGAAAATTTTTTTA
1 TTTTTTTAAATTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAG-AATTTTTTTTA
*
56610878 AATTGTACTGGGTGCCGGCCATTGACAAACCAGCACCCAAAAAAA
65 AATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCC--AAAAA
56610923 TTTTTTTACAATTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAACAAAGAATTTTTTT
1 TTTTTTTA-AATTTTTTTCGTATACTGATATCTGATTTTGACACG-AAAAA-AAAGAA--TTTTT
*
56610988 TTTAAATTTGTACTGGGTGCCAGCCATTGACA-AGCCAGCACCCAAAAA
61 TTTAAA-TTGTACTGGGTGCCGGCCATTGACAGA-CCAGCACCCAAAAA
* * *
56611036 TATTTTTTAAAATTTTTTTTCGTATATTAATATCTGATTTTGACACGAAAAAAATGAATTTTTTT
1 T-TTTTTT-AAA-TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGAATTTTTTT
* * * * **
56611101 TAAAATTATATTGGGTGCCGGCCATTGACAGGCCAACA-CCAAATT
63 T-AAATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAA
** *
56611146 TTTTATTTTTA-TTTTTTCGTATACTGATATCTGATTCTGACACGA
1 TTTT-TTTAAATTTTTTTCGTATACTGATATCTGATTTTGACACGA
56611191 TTTTTTTTTT
Statistics
Matches: 525, Mismatches: 48, Indels: 49
0.84 0.08 0.08
Matches are distributed among these distances:
106 79 0.15
107 33 0.06
108 52 0.10
109 58 0.11
110 20 0.04
111 123 0.23
112 22 0.04
113 15 0.03
114 57 0.11
115 66 0.13
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (107 bp):
TTTTTTTAAATTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGAATTTTTTTTAA
ATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAAA
Found at i:56610735 original size:220 final size:217
Alignment explanation
Indices: 56610497--56611239 Score: 919
Period size: 220 Copynumber: 3.4 Consensus size: 217
56610487 TTTTTTTTGA
*
56610497 TTTTTTTCGTATACTGATATCTGATTTTGACATGAAAAAAAAGATTTTTTTTTAA-TTGTACTGG
1 TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGATTTTTTTTTAATTTGTACTGG
*
56610561 GTGTCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTAAATTTTTTTCGTATACTGATATCTG
66 GTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTAAATTTTTTTCGTATACTGATATCTG
56610626 ATTTTGACTCGAAAAAAAAAAGAAAGTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGAC
131 ATTTTGACTCG--AAAAAAAAGAAA-TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGAC
56610691 CAGCACCCAAAATTTTTTTTAAAATT
193 CAGCACCCAAAATTTTTTTT-AAATT
* *
56610717 TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGA-ATTTTTTTAAATTGTACTGG
1 TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGATTTTTTTTTAATTTGTACTGG
** ** ** * *
56610781 GTGCCGGCCATTGGTAGGCCAGCACCCAAATTTTTTTTTTTACTTTTTTCCTATACTGATATCTG
66 GTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTAAATTTTTTTCGTATACTGATATCTG
* * *
56610846 ATTCTGACAT-GAAAAAAAAGAAAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAAACCA
131 ATTTTGAC-TCGAAAAAAAAGAAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGACCA
*
56610910 GCACCCAAAAAAATTTTTTTACAA--
195 GCACCC--AAAATTTTTTTTA-AATT
56610934 TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAACAAAGAATTTTTTTTTTAAATTTGT
1 TTTTTTTCGTATACTGATATCTGATTTTGACACG-AAAAA-AAAG-A-TTTTTTTTT-AATTTGT
* * *
56610999 ACTGGGTGCCAGCCATTGACAAGCCAGCACCCAAAAATATTTTTTAAAATTTTTTTTCGTATATT
61 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAT-TTTTTT-AAA-TTTTTTTCGTATACT
* * * * *
56611064 AATATCTGATTTTGACACGAAAAAAATG-AATTTTTTTTAAAATTATATTGGGTGCCGGCCATTG
123 GATATCTGATTTTGACTCGAAAAAAAAGAAATTTTTTTT-AAATTGTACTGGGTGCCGGCCATTG
* *
56611128 ACAGGCCAACA-CC-AAATTTTTTATT---TT
187 ACAGACCAGCACCCAAAATTTTTT-TTAAATT
* **
56611155 TATTTTTTCGTATACTGATATCTGATTCTGACACG-------ATTTTTTTTTTTAATTTGTACTG
1 T-TTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGATTTTTTTTTAATTTGTACTG
*
56611213 GGTGCCGGCCATTGATAGGCCAGCACC
65 GGTGCCGGCCATTGACAGGCCAGCACC
56611240 AATTTTTTTT
Statistics
Matches: 458, Mismatches: 45, Indels: 50
0.83 0.08 0.09
Matches are distributed among these distances:
210 35 0.08
211 9 0.02
213 1 0.00
217 79 0.17
218 18 0.04
219 26 0.06
220 117 0.26
221 2 0.00
222 47 0.10
223 40 0.09
224 6 0.01
225 12 0.03
226 66 0.14
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (217 bp):
TTTTTTTCGTATACTGATATCTGATTTTGACACGAAAAAAAAGATTTTTTTTTAATTTGTACTGG
GTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTAAATTTTTTTCGTATACTGATATCTG
ATTTTGACTCGAAAAAAAAGAAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGACCAG
CACCCAAAATTTTTTTTAAATT
Found at i:56614002 original size:22 final size:22
Alignment explanation
Indices: 56613967--56614009 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56613957 TATTAGTTAC
*
56613967 ATTTTAATTTTTAAT-AATTAT
1 ATTTTAAGTTTTAATGAATTAT
56613988 ATTTTACAGTTTTAATGAATTA
1 ATTTTA-AGTTTTAATGAATTA
56614010 ATTGAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTTAAGTTTTAATGAATTAT
Found at i:56616778 original size:69 final size:70
Alignment explanation
Indices: 56616702--56616831 Score: 192
Period size: 70 Copynumber: 1.9 Consensus size: 70
56616692 TATTAAAAAA
* * * * *
56616702 TATATTAAAATTTTTAAATTTGGTTATACTTAA-ATTTT-TTTAATATGTTTAAAATTTTAATAT
1 TATATTAAAA-ATTTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAATAT
56616765 ATTAAG
65 ATTAAG
56616771 TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAA
1 TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAA
56616832 AATTTTTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
68 19 0.35
69 15 0.28
70 20 0.37
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (70 bp):
TATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTAATATA
TTAAG
Found at i:56616858 original size:17 final size:16
Alignment explanation
Indices: 56616810--56616860 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
56616800 CAACATTTTC
56616810 TTTAACATATTTAAAAT
1 TTTAA-ATATTTAAAAT
*
56616827 TTTAAAATTTTTTAAAAT
1 TTT-AAA-TATTTAAAAT
56616845 TTTAAATATATTAAAA
1 TTTAAATAT-TTAAAA
56616861 AAAATTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 14 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAATATTTAAAAT
Found at i:56616861 original size:18 final size:17
Alignment explanation
Indices: 56616810--56616860 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
56616800 CAACATTTTC
*
56616810 TTTAACATATTTAAAAT
1 TTTAAAATATTTAAAAT
*
56616827 TTTAAAATTTTTTAAAAT
1 TTTAAAA-TATTTAAAAT
56616845 TTT-AAATATATTAAAA
1 TTTAAAATAT-TTAAAA
56616861 AAAATTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 2 0.07
17 15 0.52
18 12 0.41
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATATTTAAAAT
Found at i:56616898 original size:9 final size:9
Alignment explanation
Indices: 56616884--56616945 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 9
56616874 CATATTAAAA
56616884 AAATATATT
1 AAATATATT
56616893 AAATATATT
1 AAATATATT
*
56616902 AAA-ATTTT
1 AAATATATT
56616910 AAA-ATA-T
1 AAATATATT
* *
56616917 ATATATTTT
1 AAATATATT
*
56616926 AAAAAT-TT
1 AAATATATT
*
56616934 TAATATATT
1 AAATATATT
56616943 AAA
1 AAA
56616946 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.07
8 17 0.41
9 21 0.51
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATATATT
Found at i:56616913 original size:8 final size:8
Alignment explanation
Indices: 56616900--56616956 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
56616890 ATTAAATATA
56616900 TTAAAATT
1 TTAAAATT
56616908 TTAAAA-T
1 TTAAAATT
* *
56616915 ATATATATT
1 TTA-AAATT
56616924 TTAAAAATT
1 TT-AAAATT
* *
56616933 TTAATATA
1 TTAAAATT
56616941 TTAAAATT
1 TTAAAATT
56616949 TTAAAATT
1 TTAAAATT
56616957 GATTATACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
7 3 0.08
8 26 0.68
9 8 0.21
10 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TTAAAATT
Found at i:56616930 original size:25 final size:25
Alignment explanation
Indices: 56616888--56616954 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
56616878 TTAAAAAAAT
*
56616888 ATATTAAATATATT-AAAATTTTAAA
1 ATATTAAA-ATTTTAAAAATTTTAAA
* *
56616913 ATA-TATATATTTTAAAAATTTTAAT
1 ATATTA-AAATTTTAAAAATTTTAAA
56616938 ATATTAAAATTTTAAAA
1 ATATTAAAATTTTAAAA
56616955 TTGATTATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 6 0.17
25 27 0.77
26 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTAAAATTTTAAAAATTTTAAA
Found at i:56616939 original size:17 final size:16
Alignment explanation
Indices: 56616885--56616952 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
56616875 ATATTAAAAA
*
56616885 AATATATTAAATATATT
1 AATATATTAAA-ATTTT
* * *
56616902 AAAATTTTAAAA-TAT
1 AATATATTAAAATTTT
*
56616917 ATATATTTTAAAAATTTT
1 A-ATATATT-AAAATTTT
56616935 AATATATTAAAATTTT
1 AATATATTAAAATTTT
56616951 AA
1 AA
56616953 AATTGATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 2 0.05
16 17 0.41
17 19 0.46
18 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTAAAATTTT
Found at i:56617088 original size:165 final size:165
Alignment explanation
Indices: 56616766--56617087 Score: 434
Period size: 165 Copynumber: 1.9 Consensus size: 165
56616756 TTTTAATATA
*
56616766 TTAAGTATATTAAAAATTTAAAATTGGTTATACTCAACATTTTCTTTAACATATTTAAAATTTTA
1 TTAAGTATATTAAAAATTTAAAATTGATTATACTCAACATTTTCTTTAACATATTTAAAATTTTA
56616831 AAATTTTTTAAAATTTTAAATATATTAAAAAAAATTCTCTTTACATATTAAAAAAATATATTAAA
66 AAATTTTTTAAAATTTTAAATATATTAAAAAAAATTCTCTTTACATATTAAAAAAATATATTAAA
56616896 TATATTAAAATTTTAAAATATATATATTTTAAAAATT
131 TATATTAAAATTTT--AATATATATATTTTAAAAATT
* * * ** *
56616933 TTAA-TATATTAAAATTTTAAAATTGATTATACTTAACATTTT-TTTAATATATTTAATTTTTTT
1 TTAAGTATATTAAAAATTTAAAATTGATTATACTCAACATTTTCTTTAACATATTTAAAATTTTA
* ** * * *
56616996 AAGTTTTTTAAAATTTTAAATATATTAAGAAAAGCTTTTTTGACTTTACCTATTAAAAATATATA
66 AAATTTTTTAAAATTTTAAATATATTAA-AAAA--AATTCT--CTTTACATATTAAAAAAATATA
*
56617061 TTAAGTATATTAAAATTTTAA-ATATAT
126 TTAAATATATTAAAATTTTAATATATAT
56617088 TAAAATTTTA
Statistics
Matches: 136, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
165 44 0.32
166 39 0.29
167 10 0.07
168 5 0.04
170 38 0.28
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (165 bp):
TTAAGTATATTAAAAATTTAAAATTGATTATACTCAACATTTTCTTTAACATATTTAAAATTTTA
AAATTTTTTAAAATTTTAAATATATTAAAAAAAATTCTCTTTACATATTAAAAAAATATATTAAA
TATATTAAAATTTTAATATATATATTTTAAAAATT
Found at i:56617107 original size:18 final size:17
Alignment explanation
Indices: 56617061--56617099 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
56617051 AAAATATATA
*
56617061 TTAAGTATATTAAAATT
1 TTAAATATATTAAAATT
56617078 TTAAATATATTAAAATT
1 TTAAATATATTAAAATT
56617095 TTAAA
1 TTAAA
56617100 ATTAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAAATT
Found at i:56617134 original size:20 final size:21
Alignment explanation
Indices: 56617101--56617140 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56617091 AATTTTAAAA
*
56617101 TTAATTATACTTAATATTTTT
1 TTAATTATACTTAAAATTTTT
*
56617122 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
56617141 AGAAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATTATACTTAAAATTTTT
Found at i:56617955 original size:26 final size:28
Alignment explanation
Indices: 56617919--56617979 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
56617909 AAAAATAACT
56617919 AAAATATTAT-AA-TTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTTATTTACC
56617945 AAAATATTATAAATTTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTTATTTACC
56617973 AAAATAT
1 AAAATAT
56617980 ATCAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 10 0.30
27 2 0.06
28 21 0.64
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAATATTATAAATTTTTTTTATTTACC
Found at i:56618051 original size:27 final size:27
Alignment explanation
Indices: 56618021--56618072 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
56618011 GGCCAATCAC
56618021 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
56618048 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
56618073 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:56618382 original size:19 final size:19
Alignment explanation
Indices: 56618358--56618453 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
56618348 TCTAATTAAG
*
56618358 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
56618377 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
*
56618395 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
56618414 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
56618432 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
56618451 TAA
1 TAA
56618454 AATATAAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:56618399 original size:37 final size:37
Alignment explanation
Indices: 56618358--56618453 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
56618348 TCTAATTAAG
56618358 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
56618395 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
*
56618432 TAATAACTCTATTTTCATTTAA
1 TAATAACTCTATTTTAATTTAA
56618454 AATATAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:56618680 original size:28 final size:27
Alignment explanation
Indices: 56618618--56618682 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
56618608 TAAGGGAATA
*
56618618 TATTAAATTTATAAAATTAAAATAGTT
1 TATTAAATTTATAAAATTAAAATAGGT
* *
56618645 TAATTTAATTTTTTAAAATTAAAATAGAGT
1 T-A-TTAAATTTATAAAATTAAAATAG-GT
56618675 TATTAAAT
1 TATTAAAT
56618683 GAGAATAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 6 0.19
29 22 0.71
30 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (27 bp):
TATTAAATTTATAAAATTAAAATAGGT
Found at i:56618682 original size:19 final size:19
Alignment explanation
Indices: 56618660--56618723 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
56618650 TAATTTTTTA
56618660 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * *
56618679 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
*
56618697 ATATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
56618716 AAATTAAA
1 AAATTAAA
56618724 CTATTTTAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
AAATTAAAATAGAGTTATT
Found at i:56619060 original size:27 final size:27
Alignment explanation
Indices: 56619001--56619060 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
56618991 CATTTTAGTC
* *
56619001 CATTGGCACCATTGGTGCCGCCAATCT
1 CATTGGCACCATTGATGCCGCCAATAT
* *
56619028 CTTTGGCACCTTTGATGCCGCCAATAT
1 CATTGGCACCATTGATGCCGCCAATAT
*
56619055 GATTGG
1 CATTGG
56619061 ACTGATCATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.30
Consensus pattern (27 bp):
CATTGGCACCATTGATGCCGCCAATAT
Done.