Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:204958 original size:22 final size:21
Alignment explanation
Indices: 204885--204971 Score: 88
Period size: 22 Copynumber: 4.1 Consensus size: 21
204875 TAGTATACCC
*
204885 ATACCATGGTATCGATACTACT
1 ATACTATGGTATCGATACT-CT
* *
204907 ATACTATGGTATTGATAC-CC
1 ATACTATGGTATCGATACTCT
*
204927 ATACCATGGTATCGATACTACT
1 ATACTATGGTATCGATACT-CT
*
204949 ATATTATGGTA-CTGATACTCT
1 ATACTATGGTATC-GATACTCT
204970 AT
1 AT
204972 TATTATATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 17 0.31
21 5 0.09
22 32 0.59
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (21 bp):
ATACTATGGTATCGATACTCT
Found at i:205066 original size:22 final size:21
Alignment explanation
Indices: 205036--205094 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
205026 ATTGATACCC
*
205036 ATACCATGGTATCGATACTACT
1 ATACTATGGTATCGATACT-CT
205058 ATACTATGGTA-CTGATACTCT
1 ATACTATGGTATC-GATACTCT
*
205079 AT--TACGGTATCGATAC
1 ATACTATGGTATCGATAC
205095 CAATTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 11 0.33
20 1 0.03
21 5 0.15
22 16 0.48
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (21 bp):
ATACTATGGTATCGATACTCT
Found at i:205093 original size:19 final size:21
Alignment explanation
Indices: 205043--205094 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
205033 CCCATACCAT
*
205043 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
205065 GGTA-CTGATACT-CTAT-TAC
1 GGTATC-GATACTACTATATAC
205084 GGTATCGATAC
1 GGTATCGATAC
205095 CAATTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 5 0.19
22 10 0.37
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:208261 original size:15 final size:16
Alignment explanation
Indices: 208233--208262 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
208223 AGTGAATATT
208233 CACATATCTAGCATAC
1 CACATATCTAGCATAC
208249 CACATAT-TAGCATA
1 CACATATCTAGCATA
208263 TTCAACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (16 bp):
CACATATCTAGCATAC
Found at i:212353 original size:20 final size:20
Alignment explanation
Indices: 212339--212379 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
212329 TTTCTCTTTG
212339 AGAAAAGAGTGTTCTCAAGA
1 AGAAAAGAGTGTTCTCAAGA
212359 AGAAAAGAGTGTTCTCAAGA
1 AGAAAAGAGTGTTCTCAAGA
212379 A
1 A
212380 TTGGGGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (20 bp):
AGAAAAGAGTGTTCTCAAGA
Found at i:212876 original size:134 final size:133
Alignment explanation
Indices: 212631--212990 Score: 461
Period size: 134 Copynumber: 2.7 Consensus size: 133
212621 ACTCAACACT
* *
212631 TTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTAAATATTCC
1 TTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCC
* * * *
212696 CTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTAGAACAG
66 CTGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCT-AAAAAAAAGCAGAACAG
212761 ATCA
130 ATCA
* * * * *
212765 TTCTCTTTCAATATTTGATATTCCATGAGTAACAGTGGAACAAGTATGCCTCAATTCAATCTTCC
1 TTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCC
* * *
212830 CTG-AGTAACAGTGGAATGAATCAATGTCCCTAAATTTGATTTTCCCTAAAAAAAAGCAGAACAG
66 CTGAAG-AACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAAAAAGCAGAACAG
*
212894 ATCC
130 ATCA
* * * * * * * *
212898 CTCATTTTTCAAGATTTAATCTTCCCTGAGTAAAAGTGGAATAAGTCTACCTCGATTCCATCTTC
1 TTC-TATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTC
* *
212963 CCTGAAGAAAAGTGGAATGAGTCAACGT
65 CCTGAAGAACAGTGGAATGAATCAACGT
212991 TTCTCGATTT
Statistics
Matches: 193, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
133 21 0.11
134 170 0.88
135 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (133 bp):
TTCTATTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCC
CTGAAGAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAAAAAGCAGAACAGA
TCA
Found at i:213167 original size:3 final size:3
Alignment explanation
Indices: 213159--213207 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
213149 TTGTCCCGAC
*
213159 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
213205 ATT
1 ATT
213208 TTAGGCTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:215601 original size:131 final size:131
Alignment explanation
Indices: 215370--215861 Score: 585
Period size: 131 Copynumber: 3.8 Consensus size: 131
215360 GAGAATAATA
* * * * * * * *
215370 ATATCTTTTCATTTCGGTTGGAGTAATAAATGACCGCTCTAAGGCACGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCTC
* * * * * ** * * * *
215435 GATTGAAAATAATTTGATACTATCATTCTCTCTCGAATTAATATTGATTTTTATGATGGAATAGT
66 GATTGAAAATAATTAGATATTATCGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAGT
215500 G
131 G
* *
215501 ATATCTCTTCATTTCGATTGGAGCAATAAATGAGTGCTTTAAGGTATGAGAGATTATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCTC
* *
215566 GATTGAAAATCATTAGATATTATTGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAGT
66 GATTGAAAATAATTAGATATTATCGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAGT
215631 G
131 G
* * * * *
215632 ATATCTGTTCATTTCGATTGAAGCAATAAATGACTGCTTTAAGGTATTAGGGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCTC
* * * *
215697 GAGTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAAT
66 GATTGAAAATAATTAGATATTATCGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAGT
215762 G
131 G
* * * *
215763 ATATTTCTTCATTTTGATTGGAGTAATAAATGACTTCTTTAAGGTATGAGAGGA-CATTTATTCT
1 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGA-GATCATTTATTCT
* * *
215827 --ATGTTAGATATAATTAGATATTATTGTTTTCACTC
65 CGAT-TGA-AAATAATTAGATATTATCGTTTTCACTC
215862 TTAAAATTAT
Statistics
Matches: 309, Mismatches: 49, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 306 0.99
132 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (131 bp):
ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGATCATTTATTCTC
GATTGAAAATAATTAGATATTATCGTTTTCACTCGAATCGATGTTGAATTTTAAGACGGAATAGT
G
Found at i:216396 original size:14 final size:14
Alignment explanation
Indices: 216377--216430 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 14
216367 AAATAATAAA
216377 AATATATTATTTAT
1 AATATATTATTTAT
216391 AATATAATTATTATAAT
1 AATAT-ATTATT-T-AT
*
216408 AATATATATATTAAT
1 AATATAT-TATTTAT
216423 GAATATAT
1 -AATATAT
216431 AATAATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 10 0.29
17 11 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AATATATTATTTAT
Found at i:222068 original size:21 final size:20
Alignment explanation
Indices: 222034--222096 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
222024 GAAGAGTTAA
222034 AATA-ATAA-AATATATTATT
1 AATATATAATAATATATTA-T
*
222053 TATATATAATAATATACTTAT
1 AATATATAATAATATA-TTAT
*
222074 AATAT-TAATGAATATATAAT
1 AATATATAAT-AATATATTAT
222094 AAT
1 AAT
222097 GTTTGAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.08
20 14 0.38
21 17 0.46
22 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AATATATAATAATATATTAT
Found at i:223209 original size:26 final size:26
Alignment explanation
Indices: 223173--223234 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
223163 AGATGCCGGC
223173 TTTACAATGTTAATGCTGATACTATT
1 TTTACAATGTTAATGCTGATACTATT
223199 TTTACAATGTTAATGCTGATACTATT
1 TTTACAATGTTAATGCTGATACTATT
223225 TTTACAATGT
1 TTTACAATGT
223235 CAAAAGTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (26 bp):
TTTACAATGTTAATGCTGATACTATT
Found at i:227676 original size:32 final size:31
Alignment explanation
Indices: 227619--227679 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
227609 ATCTACAATT
*
227619 TTAAATTAAAATATTCATATTATTATATTTTA
1 TTAAAGTAAAATATT-ATATTATTATATTTTA
227651 TTAAAGTAAAATATT-TATTAAATTATATT
1 TTAAAGTAAAATATTATATT--ATTATATT
227680 AAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
32 22 0.85
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TTAAAGTAAAATATTATATTATTATATTTTA
Found at i:227973 original size:117 final size:112
Alignment explanation
Indices: 227748--227961 Score: 258
Period size: 117 Copynumber: 1.9 Consensus size: 112
227738 ATTATTAAAC
* * **
227748 TATTAAAATTTATAATATTAAAATAAGAATATTATATTATATTTAAGGAATATATTTTAAATATT
1 TATTAAAATTTATAATATTAAAATAAAAATATTATATTATATTTAAGAAATATATAATAAATA-T
*
227813 TAATAATCCAATAATATTATTTTTGTGAAAATGATAAATAATATTAGTT
65 TAAT-ATCCAATAATAATATTTTTGTGAAAATGATAAATAATATTAGTT
227862 TATTAATAATTTATTATATATTAAAATAAAAATATTATATTATATTATAA-AAAT-TATCAATAA
1 TATTAA-AATTTA-TA-ATATTAAAATAAAAATATTATATTATATT-TAAGAAATATAT-AATAA
* *
227925 ATA-TAAT-T-TAATAATGAATATTTTTGTTAAAATGATA
61 ATATTAATATCCAATAAT-AATATTTTTGTGAAAATGATA
227962 CTCAAATAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
112 6 0.07
113 20 0.23
114 6 0.07
115 10 0.11
116 5 0.06
117 37 0.43
118 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (112 bp):
TATTAAAATTTATAATATTAAAATAAAAATATTATATTATATTTAAGAAATATATAATAAATATT
AATATCCAATAATAATATTTTTGTGAAAATGATAAATAATATTAGTT
Found at i:231681 original size:2 final size:2
Alignment explanation
Indices: 231619--231667 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
231609 GTTGTGTAAG
231619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
231661 AT AT AT A
1 AT AT AT A
231668 CAAAAAGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:234133 original size:54 final size:54
Alignment explanation
Indices: 233654--234502 Score: 940
Period size: 54 Copynumber: 15.7 Consensus size: 54
233644 TATACAGTCG
* * ** * * *
233654 TTCATCAACACATGATGAATTCTGTGGGTTGCACACATAGTGCCTG-TACGGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC-GAAACGGTTA
* * * * * * * * *
233708 TTCATTAAC-TCATGATAAATTCCGTGAGTTGAACACATAGTGCTTG-TACGATTG
1 TTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGC-CGAAACGGTTA
* ** * * * *
233762 TTCATCAAC-TCATGATGAATTTCGTGGGTTGCACACATAGTGCCTG-TACGATTG
1 TTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGCC-GAAACGGTTA
* ** * * * *
233816 TTCATCAAC-TCATGATGAATTTCGTGGGTTGCACACATAGTACCTG-TACGGTTG
1 TTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGCC-GAAACGGTTA
* * * ** * * *
233870 TTCATCAAC-TCGTGATGAATTTCATGGGTTGCACACATAGTGCTGAAACAGTTA
1 TTCATCAACAT-ATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* * *
233924 TTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGTCGAAACAGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
*
233978 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAGCGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* * * *
234032 TTTATCAACATATGATGAATTCCATTAATTGCACACTTAGTGCCGAAACGATTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* *
234086 TTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGTCGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* ** * * * * *
234140 TTCATCAACATATAACAAATTCCATGAATTGTACACTTAGCGTCGAAATGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* *
234194 TTCATCAACATATGACGAATTCCGTGAATTGCACACTTAGTGTCGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* * * *
234248 TTCATCAACATATGACGAATTCAGTGAATTGTACACTTAGTGTCGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
234302 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* *
234356 TTCATCAACATATGATGAATTCCGTGAATTGTACACTTAGTGCCGAAATGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* * **
234410 TTCATCAGCATATGACGAATTCCGTGAATTGCACACTTAGTGTTGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
* *
234464 TTCATCAAAATATGATGAATTCCATGAATTGCACACTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTA
234503 ATACCTATTT
Statistics
Matches: 711, Mismatches: 79, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 709 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTA
Found at i:234212 original size:26 final size:26
Alignment explanation
Indices: 234183--234266 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
234173 CACTTAGCGT
234183 CGAAATGGTTATTCATCAACATATGA
1 CGAAATGGTTATTCATCAACATATGA
* * * * *
234209 CGAATTCCGTGAATTGCA-C-ACTTAGTGT
1 CGAAAT-GGT-TATT-CATCAACATA-TGA
*
234237 CGAAACGGTTATTCATCAACATATGA
1 CGAAATGGTTATTCATCAACATATGA
234263 CGAA
1 CGAA
234267 TTCAGTGAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
25 2 0.05
26 15 0.37
27 12 0.29
28 10 0.24
29 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (26 bp):
CGAAATGGTTATTCATCAACATATGA
Found at i:234872 original size:22 final size:21
Alignment explanation
Indices: 234842--234900 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
234832 ATTGATACCC
*
234842 ATACCATGGTATCGATACTACT
1 ATACTATGGTATCGATACT-CT
234864 ATACTATGGTA-CTGATACTCT
1 ATACTATGGTATC-GATACTCT
*
234885 AT--TACGGTATCGATAC
1 ATACTATGGTATCGATAC
234901 CAATTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 11 0.33
20 1 0.03
21 5 0.15
22 16 0.48
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (21 bp):
ATACTATGGTATCGATACTCT
Found at i:234899 original size:19 final size:21
Alignment explanation
Indices: 234849--234900 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
234839 CCCATACCAT
*
234849 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
234871 GGTA-CTGATACT-CTAT-TAC
1 GGTATC-GATACTACTATATAC
234890 GGTATCGATAC
1 GGTATCGATAC
234901 CAATTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
21 5 0.19
22 10 0.37
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:238083 original size:15 final size:16
Alignment explanation
Indices: 238055--238084 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
238045 AGTGAATATT
238055 CACATATCTAGCATAC
1 CACATATCTAGCATAC
238071 CACATAT-TAGCATA
1 CACATATCTAGCATA
238085 TTCAACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (16 bp):
CACATATCTAGCATAC
Found at i:242146 original size:19 final size:19
Alignment explanation
Indices: 242122--242170 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
242112 CATTACTCAA
*
242122 GCCACTGTCATTACGTATC
1 GCCACTGTCATAACGTATC
242141 GCCACTGTCATAACGTATC
1 GCCACTGTCATAACGTATC
242160 GCCACTTGTCA
1 GCCAC-TGTCA
242171 ATATAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (19 bp):
GCCACTGTCATAACGTATC
Found at i:244309 original size:2 final size:2
Alignment explanation
Indices: 244302--244331 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
244292 AGCAATATTA
244302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244332 CTTTTGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247932 original size:22 final size:22
Alignment explanation
Indices: 247906--247949 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
247896 ACACAATTAA
247906 TCTCAACAAAACCAATAGCACC
1 TCTCAACAAAACCAATAGCACC
*
247928 TCTCAACAAAATCAATAGCACC
1 TCTCAACAAAACCAATAGCACC
247950 GTCAGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.34, G:0.05, T:0.16
Consensus pattern (22 bp):
TCTCAACAAAACCAATAGCACC
Found at i:253452 original size:28 final size:28
Alignment explanation
Indices: 253391--253458 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
253381 AAGGAAAGGA
* *
253391 CTAAAATACCCTTAAACTATAAAATGAC
1 CTAAAATACCCCTAAACTATAAAATAAC
* * *
253419 C-AAAATACCCCTAAAGTGTGAAATAAC
1 CTAAAATACCCCTAAACTATAAAATAAC
253446 CTAAAATAACCCC
1 CTAAAAT-ACCCC
253459 AAGCCTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 22 0.67
28 6 0.18
29 5 0.15
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.21
Consensus pattern (28 bp):
CTAAAATACCCCTAAACTATAAAATAAC
Found at i:255178 original size:33 final size:38
Alignment explanation
Indices: 255139--255218 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 38
255129 ACAAAATACA
255139 ACATTCC-C-AGTAATCCT-ATT-CC-CTGGTAATCTT
1 ACATTCCACTAGTAATCCTAATTCCCACTGGTAATCTT
*
255172 ACATTCCCACTAGTAATCTTACATTCCCACTGGTAATCTT
1 ACATT-CCACTAGTAATCCTA-ATTCCCACTGGTAATCTT
255212 ACATTCC
1 ACATTCC
255219 GTGAACAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
33 5 0.13
34 2 0.05
35 1 0.03
36 8 0.21
38 3 0.08
39 4 0.10
40 16 0.41
ACGTcount: A:0.26, C:0.31, G:0.07, T:0.35
Consensus pattern (38 bp):
ACATTCCACTAGTAATCCTAATTCCCACTGGTAATCTT
Found at i:255189 original size:20 final size:20
Alignment explanation
Indices: 255164--255218 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
255154 CTATTCCCTG
255164 GTAATCTTACATTCCCACTA
1 GTAATCTTACATTCCCACTA
*
255184 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTA
255204 GTAATCTTACATTCC
1 GTAATCTTACATTCC
255219 GTGAACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTA
Found at i:255278 original size:32 final size:32
Alignment explanation
Indices: 255238--255313 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
255228 ACGCACCCTA
** * *
255238 AGGC-CCAAGGTATTCCCTTGGGTAGGCTTTT
1 AGGCTCCAAGGTACACCCTTGGGTAGGCTCTC
* *
255269 AGGCTCCAAGGTACACTCTTGGGTAGTCTCTC
1 AGGCTCCAAGGTACACCCTTGGGTAGGCTCTC
255301 AGGCTCCAAGGTA
1 AGGCTCCAAGGTA
255314 ATCATTTAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (32 bp):
AGGCTCCAAGGTACACCCTTGGGTAGGCTCTC
Found at i:256703 original size:31 final size:30
Alignment explanation
Indices: 256655--256732 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
256645 TCATTAATGA
*
256655 CGCACTTTAGCATTTCTCCCAAGGGGCGTGG
1 CGCACGTTAGCA-TTCTCCCAAGGGGCGTGG
* *
256686 CGCATGTTAGCACTTCTCTCAAGGGGCGTGG
1 CGCACGTTAGCA-TTCTCCCAAGGGGCGTGG
256717 CGCACGTTAGCATTCT
1 CGCACGTTAGCATTCT
256733 ATCCCAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27
Consensus pattern (30 bp):
CGCACGTTAGCATTCTCCCAAGGGGCGTGG
Found at i:257683 original size:29 final size:29
Alignment explanation
Indices: 257638--257694 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
257628 AGTGTTGGCC
*
257638 GTAGGTCGCCATGCACTCCAGGCGACCTT
1 GTAGGTCGCCATACACTCCAGGCGACCTT
* *
257667 GTAGGTTGCCATACACTCCGGGCGACCT
1 GTAGGTCGCCATACACTCCAGGCGACCT
257695 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATACACTCCAGGCGACCTT
Found at i:257784 original size:29 final size:29
Alignment explanation
Indices: 257751--257806 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
257741 TCCCAACACA
*
257751 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
257780 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
257807 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:257873 original size:33 final size:32
Alignment explanation
Indices: 257810--257893 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
257800 GCGACCTACC
*
257810 CTCGCTCGGCTT-CCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCTCGGATGCCCTCGCATAG
*
257842 CTCGCTCGGTTGCCCTCGGATGCCCTTGCATAG
1 CTCGCTCGGTTG-CCTCGGATGCCCTCGCATAG
* *
257875 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGG-TTGCCTCGG
257894 TCGGATGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
31 2 0.04
32 9 0.20
33 32 0.71
34 2 0.04
ACGTcount: A:0.08, C:0.37, G:0.27, T:0.27
Consensus pattern (32 bp):
CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
Found at i:257897 original size:14 final size:14
Alignment explanation
Indices: 257875--257975 Score: 76
Period size: 14 Copynumber: 6.4 Consensus size: 14
257865 CCTTGCATAG
*
257875 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
257889 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
257903 CTCGGATGCTCTCGGATGGC
1 CTC-G--G---TCGGATGGC
257923 CTCGGATGCTCTCGGATGGC
1 CTC-G--G---TCGGATGGC
*
257943 CTCGGTCGGATGAC
1 CTCGGTCGGATGGC
257957 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
257971 CTCGG
1 CTCGG
257976 ATGCCCAGCG
Statistics
Matches: 78, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
14 42 0.54
15 1 0.01
17 2 0.03
19 1 0.01
20 32 0.41
ACGTcount: A:0.09, C:0.30, G:0.38, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:257919 original size:20 final size:20
Alignment explanation
Indices: 257894--257947 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
257884 ATGGCCTCGG
257894 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
257914 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
257934 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
257948 TCGGATGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:257961 original size:10 final size:10
Alignment explanation
Indices: 257894--257947 Score: 76
Period size: 10 Copynumber: 5.4 Consensus size: 10
257884 ATGGCCTCGG
257894 TCGGATGGCC
1 TCGGATGGCC
257904 TCGGAT-GCTC
1 TCGGATGGC-C
257914 TCGGATGGCC
1 TCGGATGGCC
257924 TCGGAT-GCTC
1 TCGGATGGC-C
257934 TCGGATGGCC
1 TCGGATGGCC
257944 TCGG
1 TCGG
257948 TCGGATGACC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.10
10 32 0.80
11 4 0.10
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:263008 original size:18 final size:20
Alignment explanation
Indices: 262987--263026 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
262977 ATAAAATTTA
262987 ATTTGA-AT-TTAAAAATAT
1 ATTTGAGATATTAAAAATAT
*
263005 ATTTGAGATATTAAAACTAT
1 ATTTGAGATATTAAAAATAT
263025 AT
1 AT
263027 ATAAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (20 bp):
ATTTGAGATATTAAAAATAT
Found at i:264520 original size:18 final size:19
Alignment explanation
Indices: 264487--264522 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
264477 CTTTATTTAT
264487 GTTATAGTTATATTTAAAA
1 GTTATAGTTATATTTAAAA
*
264506 GTTATA-TTTTATTTAAA
1 GTTATAGTTATATTTAAA
264523 TTTTCATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
GTTATAGTTATATTTAAAA
Found at i:269636 original size:21 final size:21
Alignment explanation
Indices: 269606--269681 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
269596 GATTTACATA
* *
269606 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATATTCCAAG
* *
269627 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TATTCCAAG
269650 TT--CGTTGCGATATTCCAAG
1 TTCGCGTTGCGATATTCCAAG
269669 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
269682 TTATTCTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.20
21 28 0.62
23 8 0.18
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATATTCCAAG
Found at i:269667 original size:42 final size:42
Alignment explanation
Indices: 269612--269709 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
269602 CATATTCGCA
269612 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTAC-AAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATT-CTAAATTCG
* *
269654 TTGCGATATTCCAAGTTCGCGTTGCGATTTATTCTAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCG
269696 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
269710 AATCGCAACG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.02
42 51 0.98
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTCG
Found at i:269698 original size:21 final size:20
Alignment explanation
Indices: 269631--269702 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
269621 TCCAAGTTCG
269631 CGTTGCGATTTATTACAAATT
1 CGTTGCGATTTATT-CAAATT
*
269652 CGTTGCGA--TATTCCAAGTT
1 CGTTGCGATTTATT-CAAATT
269671 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTC-AAATT
*
269694 TGTTGCGAT
1 CGTTGCGAT
269703 AGTCCAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 9 0.21
21 24 0.57
22 1 0.02
23 8 0.19
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTATTCAAATT
Found at i:269816 original size:12 final size:12
Alignment explanation
Indices: 269799--269823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
269789 GACACGTATT
269799 ACCATGACCACG
1 ACCATGACCACG
269811 ACCATGACCACG
1 ACCATGACCACG
269823 A
1 A
269824 GACGAGACAC
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:0.36, C:0.40, G:0.16, T:0.08
Consensus pattern (12 bp):
ACCATGACCACG
Found at i:269848 original size:40 final size:39
Alignment explanation
Indices: 269788--269870 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
269778 GACGTGTCGA
* * *
269788 AGACACGTATTACCATGACCACGACCATGACCACGAGACG
1 AGACACATATTACCACGACCACGACCACGA-CACGAGACG
* *
269828 AGACACATATTATCACGACCACGACCACGAGACGAGACG
1 AGACACATATTACCACGACCACGACCACGACACGAGACG
269867 AGAC
1 AGAC
269871 GGCGGCGCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 12 0.32
40 26 0.68
ACGTcount: A:0.37, C:0.31, G:0.20, T:0.11
Consensus pattern (39 bp):
AGACACATATTACCACGACCACGACCACGACACGAGACG
Found at i:270629 original size:21 final size:20
Alignment explanation
Indices: 270604--270857 Score: 106
Period size: 21 Copynumber: 12.3 Consensus size: 20
270594 ATTTTGGACT
*
270604 ATCGCAACGAATTTGGTATAA
1 ATCGCAACGAACTTGG-ATAA
*
270625 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGA-TAA
270646 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGG-ATAA
* *
270667 ATCGCAACGCAAACATCGACT--
1 ATCGCAACG--AACTTGGA-TAA
270688 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGG-ATAA
*
270709 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGA-TAA
270730 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGA-TAA
* *
270751 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAACTTGG-ATAA
*
270772 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGA-TAA
270793 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAACTTGGA-TAA
*
270812 ATTGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGA-TAA
*
270833 ATCGCAACGAATTTGGA-AA
1 ATCGCAACGAACTTGGATAA
270852 ATCGCA
1 ATCGCA
270858 TTGCGATAGT
Statistics
Matches: 190, Mismatches: 18, Indels: 52
0.73 0.07 0.20
Matches are distributed among these distances:
19 55 0.29
20 3 0.02
21 98 0.52
22 4 0.02
23 30 0.16
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAACTTGGATAA
Found at i:270649 original size:42 final size:42
Alignment explanation
Indices: 270600--270748 Score: 235
Period size: 42 Copynumber: 3.5 Consensus size: 42
270590 TGCGATTTTG
* * *
270600 GACTATCGCAACGAATTTGGTATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
270642 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACATC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
270684 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
270726 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
270749 CTATCGCAAC
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
42 88 0.90
44 10 0.10
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:270713 original size:63 final size:61
Alignment explanation
Indices: 270646--270801 Score: 186
Period size: 63 Copynumber: 2.5 Consensus size: 61
270636 AACTTCGACT
* *
270646 ATCGCAACGAACTTGGAATAAATCGCAACGCAAACATCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTCGAAT--ATCGCAACGCAAACATCGACTATCGCAACAAACTTGGAATAA
* * * * *
270709 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
1 ATCGCAA--CGAACTTCGAATATCGCAACGCAAACATCGACTATCGCAACAAACTTGGAATAA
*
270772 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAA--CGAACTTCGAATATCGCAACG
270802 AACTTGGACT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
63 74 0.88
65 10 0.12
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (61 bp):
ATCGCAACGAACTTCGAATATCGCAACGCAAACATCGACTATCGCAACAAACTTGGAATAA
Found at i:270755 original size:42 final size:42
Alignment explanation
Indices: 270625--270841 Score: 216
Period size: 42 Copynumber: 5.2 Consensus size: 42
270615 TTTGGTATAA
* *
270625 ATCGCAATGCGAACTTCGACTATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
* * *
270665 AAATCGCAACGCAAACATCGACTATCGCAA--CGAACTTGGAAT
1 --ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
270707 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
* * * * *
270751 ATCGCAA--CAAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTGGACT
* *
270793 ATCGCAA--CGAACTTGGACTATTGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
270833 ATCGCAACG
1 ATCGCAACG
270842 AATTTGGAAA
Statistics
Matches: 153, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
40 34 0.22
42 108 0.71
44 11 0.07
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
Found at i:270830 original size:63 final size:62
Alignment explanation
Indices: 270684--270830 Score: 233
Period size: 63 Copynumber: 2.3 Consensus size: 62
270674 CGCAAACATC
270684 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC-CGAACTTG
* *
270747 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACCGAACTTG
*
270808 GACTATTGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
270831 CTATCGCAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
61 18 0.23
63 59 0.77
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (62 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACCGAACTTG
Found at i:270882 original size:21 final size:21
Alignment explanation
Indices: 270853--270905 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
270843 ATTTGGAAAA
*
270853 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
270874 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
270895 TCGCGTTGCGA
1 TCGCGTTGCGA
270906 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:271129 original size:19 final size:19
Alignment explanation
Indices: 271105--271152 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
271095 CGAAGTCTAC
271105 TAATCAAAGTCAACTTGTT
1 TAATCAAAGTCAACTTGTT
271124 TAATCAAAGTCAACTTGTT
1 TAATCAAAGTCAACTTGTT
271143 TAATCAAAGT
1 TAATCAAAGT
271153 TAACCCAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (19 bp):
TAATCAAAGTCAACTTGTT
Found at i:271281 original size:16 final size:16
Alignment explanation
Indices: 271260--271305 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
271250 GTTAAACGAC
* *
271260 CAAAGTCAAATTGAGT
1 CAAAGTCTAATTAAGT
*
271276 CAAAGTTTAATTAAGT
1 CAAAGTCTAATTAAGT
271292 CAAAGTCTAATTAA
1 CAAAGTCTAATTAA
271306 TATAAAGGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (16 bp):
CAAAGTCTAATTAAGT
Found at i:278582 original size:14 final size:15
Alignment explanation
Indices: 278563--278602 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
278553 TTTCTGTCTA
*
278563 TATGCAGAGATTT-T
1 TATGCAGGGATTTAT
278577 TATGCAGGGATTTAT
1 TATGCAGGGATTTAT
278592 T-TGCAGGGATT
1 TATGCAGGGATT
278603 ACTTCCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (15 bp):
TATGCAGGGATTTAT
Found at i:279937 original size:16 final size:16
Alignment explanation
Indices: 279908--279945 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
279898 TTTACTTCAG
*
279908 AATGA-TTAAGTGCTA
1 AATGATTTAAATGCTA
*
279923 AATGATTTAAATGCTG
1 AATGATTTAAATGCTA
279939 AATGATT
1 AATGATT
279946 CAGAGGCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (16 bp):
AATGATTTAAATGCTA
Found at i:280032 original size:27 final size:27
Alignment explanation
Indices: 279999--280092 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
279989 GATAATGGTT
*
279999 CTGAATCATTCAGAATGCCCTTCTGTG
1 CTGAATCATTCAGAATGACCTTCTGTG
*
280026 CTGAATCATTTAGAATGACCTTCTGTG
1 CTGAATCATTCAGAATGACCTTCTGTG
* *
280053 CTGAATCATTTAGAATGACCTTCTGTA
1 CTGAATCATTCAGAATGACCTTCTGTG
280080 CTGAATCATTCAG
1 CTGAATCATTCAG
280093 CACTGTTTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
CTGAATCATTCAGAATGACCTTCTGTG
Found at i:280187 original size:20 final size:21
Alignment explanation
Indices: 280146--280188 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
280136 CGAAATAAAC
280146 GCGCTGAAAGGTTCAGCATTCA
1 GCGCTGAAAGGTTCA-CATTCA
*
280168 GCGCTGAATGGTTC-CATTCA
1 GCGCTGAAAGGTTCACATTCA
280188 G
1 G
280189 AGTCAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
GCGCTGAAAGGTTCACATTCA
Found at i:281512 original size:15 final size:15
Alignment explanation
Indices: 281492--281543 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
281482 TAATAAGGTT
281492 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
281507 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
281522 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
281537 ATTTATT
1 ATTTATT
281544 AGTATTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:281573 original size:32 final size:32
Alignment explanation
Indices: 281522--281838 Score: 132
Period size: 32 Copynumber: 9.4 Consensus size: 32
281512 TTTTAAAATA
* *
281522 ATTTATTATAAAATAATTTATTAGTATTGATTG
1 ATTTATT-TTAAATAATTTATTAGTATGGATTG
281555 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
** **
281587 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * * * *
281616 ATTGTAGTTGTATGGATTGATTTATT--T-T-AAATA
1 ATT-TA-TT-T-T-AAATAATTTATTAGTATGGATTG
* * * *
281649 ATTTATTAGTATAGATTGATTTATTTAAATATGTATTG
1 ATTTATT--T-TA-AATAATTTA-TT-AGTATGGATTG
281687 A-TTATTTT-AATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
281717 ATTTATTTTAAAATAGGATGATTTATTATTGTAGTTGTATGG
1 ATTTATTTT-AAAT---A--ATTTATTA--GTA--TGGATTG
*
281759 ATTGATTCATTTTAAATATTTTATTAGTATGGATTG
1 A-T--TT-ATTTTAAATAATTTATTAGTATGGATTG
*
281795 ATTTATTTTAAATAATTTATTATTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
281827 ATTTATTATAAA
1 ATTTATTTTAAA
281839 ATATTGATTG
Statistics
Matches: 222, Mismatches: 29, Indels: 67
0.70 0.09 0.21
Matches are distributed among these distances:
29 3 0.01
30 17 0.08
31 15 0.07
32 102 0.46
33 19 0.09
34 7 0.03
35 2 0.01
36 8 0.04
37 6 0.03
38 14 0.06
40 10 0.05
42 7 0.03
43 1 0.00
45 6 0.03
46 5 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:281592 original size:18 final size:18
Alignment explanation
Indices: 281569--281616 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
281559 ATTTTAAATA
*
281569 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
281587 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
281609 ATTTATTA
1 ATTTATTA
281617 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:281634 original size:80 final size:81
Alignment explanation
Indices: 281540--282492 Score: 536
Period size: 80 Copynumber: 11.7 Consensus size: 81
281530 TAAAATAATT
* *
281540 TATTAGTATTGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTA-TTT-AAATATGG
281605 ATTGATT-TATT-AT-TG
64 ATTGATTATATTAATATG
*
281620 TAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAATATGTA
1 TA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAATATGGA
* *
281684 TTGATTATTTTAATAATT
65 TTGATTATATTAAT-ATG
* * **
281702 TATTAGTATGGATTGATTTATTTT--A-AA---A-TAGGAT-GATTTA-TTATTGTAGTTGTATG
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATT-TA--AATATG
* *
281758 GATTGATTCATTTTAAATATTT
63 GATTGATT-ATATT-AATA-TG
* * *
281780 TATTAGTATGGATTGATTTATTTTAAATAATTTATTATTATGGATTGATTTATTATAAAATATTG
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATT-T-AAATATGG
281845 ATTGATT-TATT-AT-TG
64 ATTGATTATATTAATATG
*
281860 TAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 TA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTA-TTT-AAATATG
* *
281924 GATTGATTTATTTTAAATAATT
63 GATTGA-TTATATT-AAT-ATG
** **
281946 TATTAGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAGTTT---TATG
1 TATTAGTATGGATTGATTTATTTTAAATA-ATTTATTAGTATAGATTGATT-TA-TTTAAATATG
* *
282004 GATTGATTCATTTTAAATATTT
63 GATTGATT-ATATT-AATA-TG
* ** * ** * * * *
282026 TATTAGTATGGATTGATTTATTTTAAAAAATGGATT-GCTTTATTTTAAATAATTTATTAGTATG
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAG-TATAGATTGATTTATTTA--AATATG
* *
282090 GATTGATTTATTTTAAAATGG
63 GATTGA-TTATATTAATAT-G
* * ** **
282111 ATTGATTTATTATTGTAGTTGTATGATTGATTTATTAAATAATTTATTAGTAT-GAATTGATTTA
1 --T-A-TTAGTA-TGGA-TTG-AT--TTATTTTAAA---TAATTTATTAGTATAG-ATTGATTTA
* * *
282175 TTTTAAA-ATAGATTGATT-TTTTAAATAATT
53 -TTTAAATATGGATTGATTATATT-AAT-ATG
* * * * * * *
282205 TATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTTTA-AATAATTTA-TT-AGTA
1 TATTAGTATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAGATTGATTTATTTAAATA
282267 TGGATTGATT-TA-T--T-T-
61 TGGATTGATTATATTAATATG
* *
282282 TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATG
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTA-TTT-AAATATG
282345 GA-TGATT-TATT-AT-TG
63 GATTGATTATATTAATATG
*
282360 T-TT-GTATGAATTGATTTATTTTAAATAATTTATTAGTAT-GTATTGATTT-TTTAAATATGGA
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTAAATATGGA
**
282421 TTGATTAT-TTTGTA-G
65 TTGATTATATTAATATG
282436 T-TT-GTATGGATTGATTTATTTTAAATAATTTATTA-T-TAGGATTGATTTATTTAAATA
1 TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATA-GATTGATTTATTTAAATA
282493 ATTTAGTATG
Statistics
Matches: 704, Mismatches: 82, Indels: 178
0.73 0.09 0.18
Matches are distributed among these distances:
71 5 0.01
72 11 0.02
73 5 0.01
74 19 0.03
75 36 0.05
76 84 0.12
77 53 0.08
78 45 0.06
79 11 0.02
80 171 0.24
81 16 0.02
82 32 0.05
83 9 0.01
84 30 0.04
85 16 0.02
86 73 0.10
87 16 0.02
88 5 0.01
89 9 0.01
90 8 0.01
91 4 0.01
92 3 0.00
93 4 0.01
94 10 0.01
95 10 0.01
96 1 0.00
97 13 0.02
98 5 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (81 bp):
TATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTAAATATGGAT
TGATTATATTAATATG
Found at i:281771 original size:128 final size:133
Alignment explanation
Indices: 281551--281808 Score: 454
Period size: 128 Copynumber: 2.0 Consensus size: 133
281541 ATTAGTATTG
281551 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
*
281616 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTA-TTTAAATA
66 ATTGTAGTTGTATGGATTGATTCATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA
281680 TGT
131 TGT
281683 ATTGA-TTATTTT-AATAATTTATTAGTATGGATTGATTTATTTTAAAATA-GGA-TGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
* *
281744 ATTGTAGTTGTATGGATTGATTCATTTTAAATATTTTATTAGTATGGATTGATTTATTTTAAATA
66 ATTGTAGTTGTATGGATTGATTCATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA
281809 ATTTATTATT
Statistics
Matches: 122, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
128 62 0.51
129 11 0.09
130 37 0.30
131 7 0.06
132 5 0.04
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (133 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
ATTGTAGTTGTATGGATTGATTCATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA
TGT
Found at i:281801 original size:18 final size:17
Alignment explanation
Indices: 281778--281836 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
281768 TTTTAAATAT
281778 TTTATTAGTATGGATTGA
1 TTTATTA-TATGGATTGA
* * *
281796 TTTATT-T-T-AAATAA
1 TTTATTATATGGATTGA
281810 TTTATTATTATGGATTGA
1 TTTATTA-TATGGATTGA
281828 TTTATTATA
1 TTTATTATA
281837 AAATATTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 3 0.10
18 16 0.52
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TTTATTATATGGATTGA
Found at i:281903 original size:32 final size:32
Alignment explanation
Indices: 281865--281972 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
281855 TATTGTAGTT
281865 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
281897 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
281920 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
281951 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
281973 ATATGGATTG
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 14 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 36 0.55
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:281923 original size:22 final size:22
Alignment explanation
Indices: 281898--281940 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
281888 AATTTATTAG
281898 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
281920 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
281941 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:281936 original size:134 final size:134
Alignment explanation
Indices: 281786--282248 Score: 773
Period size: 134 Copynumber: 3.5 Consensus size: 134
281776 ATTTTATTAG
* * *
281786 TATGGATTGATTTATTTTAAATAATTTATTATTATGGATTGATTTATTATAAAATATTGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
281851 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
281916 AAAA
131 AAAA
281920 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* * *
281985 TTATTATTGTAGTTTTATGGATTGATTCATTTTAAATATTTTATTAGTATGGATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
282050 AAAA
131 AAAA
* *
282054 AATGGATTGCTTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA-ATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
282117 TTATTATTGTAGTTGTAT-GATTGATTTA--TTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
282179 AAAA
131 AAAA
*
282183 TA--GATTGA-TT-TTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
282244 TTATT
66 TTATT
282249 TTAAATAATT
Statistics
Matches: 312, Mismatches: 15, Indels: 11
0.92 0.04 0.03
Matches are distributed among these distances:
125 35 0.11
126 5 0.02
127 20 0.06
129 37 0.12
131 9 0.03
132 27 0.09
133 3 0.01
134 176 0.56
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
AAAA
Found at i:281937 original size:54 final size:54
Alignment explanation
Indices: 281754--281989 Score: 248
Period size: 54 Copynumber: 4.3 Consensus size: 54
281744 ATTGTAGTTG
* *
281754 TATGGATTGATTCATTTTAAATATTTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* ** * * * * ***
281807 TA---ATTTA-TTATTATGGATTGATTTATTATAAAATATTGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATT-TTAAATAATTTA-T-T--AGTATGGATTGATTTA-T-TT-TA-AAA
281866 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
281920 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
281974 TATGGATTGATTTATT
1 TATGGATTGATTTATT
281990 ATTGTAGTTT
Statistics
Matches: 147, Mismatches: 22, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
49 4 0.03
50 11 0.07
51 1 0.01
52 1 0.01
53 2 0.01
54 84 0.57
55 3 0.02
56 4 0.03
57 2 0.01
58 14 0.10
59 2 0.01
60 1 0.01
61 1 0.01
62 12 0.08
63 5 0.03
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:282002 original size:54 final size:53
Alignment explanation
Indices: 281866--282358 Score: 402
Period size: 54 Copynumber: 9.4 Consensus size: 53
281856 ATTGTAGTTG
281866 TATGGATTGATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTATT--ATAATTTATTAGTATGGATTGATTTATTTTAAAA
281920 TATGGATTGATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTATT--ATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * *
281974 TATGGATTGATTTATTATTGT-A-GT-TT--TATGGATTGATTCATTTT-AAA
1 TATGGATTGATTTATTATTATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * * ** *
282021 TATTTTATTAGTATGGATTGATT-TATTTTA-AAAAATGGATTGCTTTATTTT-AAA
1 TA-TGGATT-G-ATTTATT-ATTATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * ** ** *
282075 TA---ATTTA-TTAGTATGGATTGATTTATTTTAAAATGGATTGATTTATTATTGTAG
1 TATGGATTGATTTATTAT-TA-TAATTTA--TTAGTATGGATTGATTTATT-TTAAAA
* *
282129 T-TGTATGATTGATTTATTA-AATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATG---GATTGATTTATTATTATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * *
282183 TA--GATTGATTTTTTA-AATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTATTATAATTTATTAGTATGGATTGATTTATTTTAAAA
282233 TATGGATTGATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTATT--ATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
282287 TATGGATTGATTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTATT--ATAATTTATTAGTATGGATTGATTTATTTTAAAA
282341 TATGGA-TGATTTATTATT
1 TATGGATTGATTTATTATT
282359 GTTTGTATGA
Statistics
Matches: 367, Mismatches: 40, Indels: 64
0.78 0.08 0.14
Matches are distributed among these distances:
46 2 0.01
47 7 0.02
48 22 0.06
49 6 0.02
50 59 0.16
51 4 0.01
52 30 0.08
53 12 0.03
54 190 0.52
55 19 0.05
57 6 0.02
58 1 0.00
59 4 0.01
60 5 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (53 bp):
TATGGATTGATTTATTATTATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:282036 original size:32 final size:31
Alignment explanation
Indices: 282000--282339 Score: 128
Period size: 32 Copynumber: 11.7 Consensus size: 31
281990 ATTGTAGTTT
*
282000 TATGGATTGATTCATTTTAAATATTTTATTAG
1 TATGGATTGATTTATTTTAAATA-TTTATTAG
282032 TATGGATTGATTTATTTT-AA-A---A--A-
1 TATGGATTGATTTATTTTAAATATTTATTAG
*
282055 -ATGGATTGCTTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAT-ATTTATTAG
* *
282086 TATGGATTGATTTATTTTAAAATGGATTGATTTAT
1 TATGGATTGATTTATTTT-AAAT--ATTTA-TTAG
*
282121 TATTGTAGTTGTATGATTGATTTATTAAATAATTTATTAG
1 TA-TGGA-TTG-AT--TT-ATTT--TAAAT-ATTTATTAG
*
282161 TATGAATTGATTTATTTT-AA-A---A-TAG
1 TATGGATTGATTTATTTTAAATATTTATTAG
* * ** * *
282186 -ATTGATT-TTTTA-AAT-AATTTA--TTAG
1 TATGGATTGATTTATTTTAAATATTTATTAG
*
282211 TATGTATTGATTTATTTT--A-A---A--A-
1 TATGGATTGATTTATTTTAAATATTTATTAG
282233 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAT-ATTTATTAG
282265 TATGGATTGATTTATTTT--A-A---A--A-
1 TATGGATTGATTTATTTTAAATATTTATTAG
282287 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAT-ATTTATTAG
*
282319 TATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
282340 ATATGGATGA
Statistics
Matches: 234, Mismatches: 25, Indels: 98
0.66 0.07 0.27
Matches are distributed among these distances:
22 54 0.23
23 8 0.03
24 8 0.03
25 8 0.03
26 9 0.04
27 5 0.02
28 3 0.01
29 3 0.01
30 3 0.01
31 6 0.03
32 72 0.31
33 4 0.02
34 8 0.03
35 7 0.03
36 3 0.01
37 5 0.02
38 5 0.02
39 3 0.01
40 7 0.03
41 8 0.03
42 4 0.02
43 1 0.00
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (31 bp):
TATGGATTGATTTATTTTAAATATTTATTAG
Found at i:282061 original size:22 final size:22
Alignment explanation
Indices: 282033--282074 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
282023 TTTTATTAGT
282033 ATGGATTGATTTATTTTAAAAA
1 ATGGATTGATTTATTTTAAAAA
*
282055 ATGGATTGCTTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
282075 TAATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAA
Found at i:282236 original size:22 final size:22
Alignment explanation
Indices: 282211--282253 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
282201 AATTTATTAG
*
282211 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
282233 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
282254 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:282243 original size:233 final size:234
Alignment explanation
Indices: 282000--282568 Score: 721
Period size: 233 Copynumber: 2.5 Consensus size: 234
281990 ATTGTAGTTT
* *
282000 TATGGATTGATTCATTTTAAATATTTTATTAGTATGGATTGATTTATTTTAAAAAATGGATTGCT
1 TATGGATTGATTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAAATGGATTGAT
*
282065 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA-ATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGA-TGATTTATTATTGT-
282128 GTTGTATG-ATTGATTTA-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAA-ATAGATTG
129 -TTGTATGAATTGATTTATTTAAATAATTTATTAGTATGAATTGA-TT-TTTTAAATATAGATTG
282190 ATT-TTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
191 ATTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
* *
282233 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAAATGGATTGAT
282298 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATGATTTATTATTGTTT
66 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATGATTTATTATTGTTT
* *
282363 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTTTTAAATATGGATTGATTA
131 GTATGAATTGATTTA-TTTAAATAATTTATTAGTATGAATTGATTTTTTAAATATAGATTGATTA
* * *
282428 TTTT--GT-A-GT-TT-GTATGGATTGATTTATTTTAAATAATTTA
195 TTTTAAATAATTTATTAGTATGTATTGATTTATTTT--A-AA---A
* *
282468 TTATTAGGATTGATTTA-TTTAAATAA--T-TTAGTATGGATTGATTT-TTTT--AAAATAGA-T
1 -TA-T-GGATTGATTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAAATGGATT
* * *
282525 GATTTATTTTAAATAATTTTTTTGTATGAATTTA-TTATTTTAAA
63 GATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
282569 TAATTTATTA
Statistics
Matches: 305, Mismatches: 15, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
229 28 0.09
230 34 0.11
231 8 0.03
232 10 0.03
233 120 0.39
234 46 0.15
235 36 0.12
236 2 0.01
237 10 0.03
238 11 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (234 bp):
TATGGATTGATTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAAATGGATTGAT
TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATGATTTATTATTGTTT
GTATGAATTGATTTATTTAAATAATTTATTAGTATGAATTGATTTTTTAAATATAGATTGATTAT
TTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
Found at i:282290 original size:22 final size:22
Alignment explanation
Indices: 282265--282307 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
282255 AATTTATTAG
282265 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
282287 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
282308 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:282478 original size:31 final size:29
Alignment explanation
Indices: 282415--282518 Score: 121
Period size: 28 Copynumber: 3.7 Consensus size: 29
282405 ATTTTTTAAA
* *
282415 TATGGATTGA-TTATTTT--GTAGTTT-G
1 TATGGATTGATTTATTTTAAATAATTTAG
*
282440 TATGGATTGATTTATTTTAAATAATTTAT
1 TATGGATTGATTTATTTTAAATAATTTAG
282469 TATTAGGATTGATTTA-TTTAAATAATTTAG
1 TA-T-GGATTGATTTATTTTAAATAATTTAG
282499 TATGGATTGATTT-TTTTAAA
1 TATGGATTGATTTATTTTAAA
282519 ATAGATGATT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
25 10 0.15
26 7 0.10
28 21 0.31
29 3 0.04
30 16 0.24
31 11 0.16
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (29 bp):
TATGGATTGATTTATTTTAAATAATTTAG
Found at i:282563 original size:77 final size:79
Alignment explanation
Indices: 282444--282615 Score: 215
Period size: 77 Copynumber: 2.2 Consensus size: 79
282434 AGTTTGTATG
* *
282444 GATTGATTTATTTTAAATAATTTATTATTA-GGATTGATTTATTTAAATAATTTAGTATGGATTG
1 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTTAGTATGGATTG
282508 ATTTTTTTAAAATA
66 ATTTTTTTAAAATA
* * * *
282522 GA-TGATTTATTTTAAATAATTTTTTTGTATGAATTTA-TTATTTTAAATAATTTATTAGTATTG
1 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTTAAATAA--T-TTAGTATGG
*
282585 ATTGATTTATTTAAAATA
62 ATTGATTTTTTTAAAATA
282603 TGATTGATTTATT
1 -GATTGATTTATT
282616 ATGCATTTGT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
77 27 0.34
78 16 0.20
80 1 0.01
81 25 0.31
82 2 0.03
83 9 0.11
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (79 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTTAGTATGGATTG
ATTTTTTTAAAATA
Found at i:282575 original size:17 final size:17
Alignment explanation
Indices: 282528--282578 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
282518 AATAGATGAT
282528 TTATTTTAAATAATTT-
1 TTATTTTAAATAATTTA
*
282544 TT-TTGT--ATGAATTTA
1 TTATTTTAAAT-AATTTA
282559 TTATTTTAAATAATTTA
1 TTATTTTAAATAATTTA
282576 TTA
1 TTA
282579 GTATTGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.07
14 5 0.18
15 5 0.18
16 5 0.18
17 9 0.32
18 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
TTATTTTAAATAATTTA
Found at i:282585 original size:105 final size:105
Alignment explanation
Indices: 282436--282785 Score: 298
Period size: 105 Copynumber: 3.2 Consensus size: 105
282426 TATTTTGTAG
* * * *
282436 TTTGTATGGATTGATTTATTTTAAATAATTTATTATTAGGATTGATTTATTTAAATAATTTAGTA
1 TTTGTATGAATTGATTTATTTTAAATAA--T-TTATTAGTATTGATTGATTTAAATAA---AATA
* *
282501 TGGATTGATTT-TTTTAAAATAG-ATGATTTAT-TTTAAATAATTTT
60 T-GATTGATTTATTATAAAATAGTATGATTTATATTTAAATAATTTA
* **
282545 TTTGTATGAATTTA-TTATTTTAAATAATTTATTAGTATTGATTGATTTATTTAAAATATGATTG
1 TTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTAAATAAAATATGATTG
** * * *
282609 ATTTATTATGCATTTGTATGATTTTTATTTAAATAATTTA
66 ATTTATTATAAAATAGTATGATTTATATTTAAATAATTTA
* **
282649 TTAGTAT-ATATTGATTTATTTTAAATAATTTATTAGTA-TGAATTGATTTATTTTAAAATATGG
1 TTTGTATGA-ATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTA-AATAAAATAT-G
* ** * * *
282712 ATTGCTTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTA
62 ATTGATTTATTA-TAAAATAGTAT-GATT--TATA-TTTAAATAATTTA
*
282761 TTAGTATGAATTGATTTATTTTAAA
1 TTTGTATGAATTGATTTATTTTAAA
282786 ATATGGATTG
Statistics
Matches: 208, Mismatches: 19, Indels: 25
0.83 0.08 0.10
Matches are distributed among these distances:
101 9 0.04
102 10 0.05
103 9 0.04
104 24 0.12
105 54 0.26
106 11 0.05
107 12 0.06
108 22 0.11
109 16 0.08
111 4 0.02
112 36 0.17
113 1 0.00
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (105 bp):
TTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTAAATAAAATATGATTG
ATTTATTATAAAATAGTATGATTTATATTTAAATAATTTA
Found at i:282598 original size:31 final size:32
Alignment explanation
Indices: 282524--282705 Score: 172
Period size: 32 Copynumber: 5.4 Consensus size: 32
282514 TTAAAATAGA
* *
282524 TGATTTATTTTAAATAATTTTTTTGTATGAAT
1 TGATTTATTTTAAATAATTTATTAGTATGAAT
*
282556 TTA-TTATTTTAAATAATTTATTAGTATTG-AT
1 TGATTTATTTTAAATAATTTATTAGTA-TGAAT
* * * *
282587 TGATTTATTTAAAATATGATTGATTTATTATGCATTTGT
1 TGATTTATTTTAAATA--ATTTA-TTAGTATG-A---AT
*
282626 ATGATTTTTATTTAAATAATTTATTAGTAT-ATAT
1 -TGATTTAT-TTTAAATAATTTATTAGTATGA-AT
282660 TGATTTATTTTAAATAATTTATTAGTATGAAT
1 TGATTTATTTTAAATAATTTATTAGTATGAAT
282692 TGATTTATTTTAAA
1 TGATTTATTTTAAA
282706 ATATGGATTG
Statistics
Matches: 123, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
31 25 0.20
32 51 0.41
33 8 0.07
34 8 0.07
35 5 0.04
36 1 0.01
38 6 0.05
39 5 0.04
40 7 0.06
41 7 0.06
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.56
Consensus pattern (32 bp):
TGATTTATTTTAAATAATTTATTAGTATGAAT
Found at i:282790 original size:22 final size:22
Alignment explanation
Indices: 282765--282807 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
282755 AATTTATTAG
282765 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
282787 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
282808 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:283023 original size:10 final size:10
Alignment explanation
Indices: 283008--283033 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
282998 TTTTTTGCTA
283008 CAGATGCCTG
1 CAGATGCCTG
283018 CAGATGCCTG
1 CAGATGCCTG
283028 CAGATG
1 CAGATG
283034 TGGTCCGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.31, T:0.19
Consensus pattern (10 bp):
CAGATGCCTG
Found at i:293504 original size:35 final size:36
Alignment explanation
Indices: 293434--293506 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
293424 AGAGAGAGGG
293434 TTTGGTTCTAGAAAATATTTTATATTTTCATTTTTT
1 TTTGGTTCTAGAAAATATTTTATATTTTCATTTTTT
* * * *
293470 TTTGTTTC-AGAAAGTAGTTTTTTATTTTTATTTTTT
1 TTTGGTTCTAGAAAATA-TTTTATATTTTCATTTTTT
293506 T
1 T
293507 GAAAATTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 7 0.22
36 25 0.78
ACGTcount: A:0.22, C:0.04, G:0.10, T:0.64
Consensus pattern (36 bp):
TTTGGTTCTAGAAAATATTTTATATTTTCATTTTTT
Found at i:294183 original size:25 final size:24
Alignment explanation
Indices: 294136--294183 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
294126 TAATTTTTTA
* *
294136 AAAAATAAAAAAATTGTTTAGATT
1 AAAAATAAAAAAATTATTAAGATT
*
294160 AAAAATATAAATAATTATTAAGAT
1 AAAAATA-AAAAAATTATTAAGAT
294184 ATTCAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAAATAAAAAAATTATTAAGATT
Found at i:298032 original size:33 final size:30
Alignment explanation
Indices: 297987--298049 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
297977 CTGGATATTG
297987 TTGAATTCTATTTCTAATATATAAATGATTTT
1 TTGAATTCTATTT-T-ATATATAAATGATTTT
* * *
298019 TTGAACTTGTATTTTATCTATAAATTATTTT
1 TTGAA-TTCTATTTTATATATAAATGATTTT
298050 ACAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 14 0.52
32 6 0.22
33 7 0.26
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (30 bp):
TTGAATTCTATTTTATATATAAATGATTTT
Found at i:304061 original size:19 final size:20
Alignment explanation
Indices: 303989--304061 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
303979 CGTTGGACAT
* *
303989 AAAGTATCAAAACT-TTAGGG
1 AAAGTATCGAAACTCTT-GAG
* *
304009 AAAGTTTTGAAACTCTTGAG
1 AAAGTATCGAAACTCTTGAG
* * *
304029 ATAGTTTGGAAACTCTTGA-
1 AAAGTATCGAAACTCTTGAG
304048 AAAGTATCGAAACT
1 AAAGTATCGAAACT
304062 TTTTGGGAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 11 0.26
20 30 0.70
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (20 bp):
AAAGTATCGAAACTCTTGAG
Found at i:307013 original size:2 final size:2
Alignment explanation
Indices: 307006--307045 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
306996 AACTGACGCA
307006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
307046 CAATATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308709 original size:17 final size:18
Alignment explanation
Indices: 308687--308721 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
308677 TTAAGTCCTT
*
308687 GCCTATTACAG-ACACAA
1 GCCTATAACAGCACACAA
308704 GCCTATAACAGCACACAA
1 GCCTATAACAGCACACAA
308722 AGCTAAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.31, G:0.11, T:0.14
Consensus pattern (18 bp):
GCCTATAACAGCACACAA
Found at i:311075 original size:3 final size:3
Alignment explanation
Indices: 311065--311101 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
311055 ATAAAAATAA
*
311065 TAT T-T TAT TAT T-T TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
311102 ATTTTACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:312179 original size:17 final size:18
Alignment explanation
Indices: 312159--312193 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
312149 AAGAGGAACA
312159 AAAAAAAAAGAGA-AAGG
1 AAAAAAAAAGAGAGAAGG
*
312176 AAAACAAAAGAGAGAAGG
1 AAAAAAAAAGAGAGAAGG
312194 GAGACGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAGAGAAGG
Found at i:313221 original size:56 final size:57
Alignment explanation
Indices: 313151--313337 Score: 207
Period size: 56 Copynumber: 3.2 Consensus size: 57
313141 CAAATTTCTA
* * * **
313151 TTTTTTCTTTTTTAGTCCCTAAAGATTCTATTTTTGTTATTTTAGTCCTTTAAG-TT-
1 TTTTTTCTATTTTAGTCCTTTAACTTTCTATTTTTG-TATTTTAGTCCTTTAAGTTTC
* * *
313207 TTTTTTCTATTTTAGTCCTTTAACTTTCTGTTTTAGCTATTTTATTCCTTTAAGTTTC
1 TTTTTTCTATTTTAGTCCTTTAACTTTCTATTTTTG-TATTTTAGTCCTTTAAGTTTC
* * *
313265 TTTTTTGCTATTTTGGTCCTTTAACTTTCTATTTTTGTAATTTAGTCCTTTAAGCTTC
1 TTTTTT-CTATTTTAGTCCTTTAACTTTCTATTTTTGTATTTTAGTCCTTTAAGTTTC
*
313323 TGTTATTTTTATTTT
1 T-TT-TTTCTATTTT
313338 GATCACTTAA
Statistics
Matches: 110, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
56 45 0.41
57 2 0.02
58 25 0.23
59 35 0.32
60 3 0.03
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (57 bp):
TTTTTTCTATTTTAGTCCTTTAACTTTCTATTTTTGTATTTTAGTCCTTTAAGTTTC
Found at i:313284 original size:29 final size:30
Alignment explanation
Indices: 313131--313323 Score: 191
Period size: 30 Copynumber: 6.6 Consensus size: 30
313121 GTAATTACTG
* * * * *
313131 TTTAGCCCTTCAAATTTCTATTTTTTCTTT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* * * *
313161 TTTAGTCCCTAAAGATTCTATTTTTGTTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
313191 TTTAGTCCTTTAAG-TT-T-TTTTT-CTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* * *
313217 TTTAGTCCTTTAACTTTCTGTTTTAGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
*
313247 TTTATTCCTTTAAGTTTCT-TTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* * *
313276 TTTGGTCCTTTAACTTTCTATTTTTG-TAA
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
*
313305 TTTAGTCCTTTAAGCTTCT
1 TTTAGTCCTTTAAGTTTCT
313324 GTTATTTTTA
Statistics
Matches: 135, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
26 16 0.12
27 7 0.05
28 2 0.01
29 49 0.36
30 61 0.45
ACGTcount: A:0.17, C:0.16, G:0.08, T:0.59
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
Found at i:313336 original size:29 final size:28
Alignment explanation
Indices: 313151--313337 Score: 148
Period size: 29 Copynumber: 6.5 Consensus size: 28
313141 CAAATTTCTA
* * * *
313151 TTTTTTCTTTTTTAGTCCCTAAAGATTC
1 TTTTTTCTATTTTAGTCCTTTAAGCTTC
*
313179 TATTTTTGTTATTTTAGTCCTTTAAG-TT-
1 T-TTTTT-CTATTTTAGTCCTTTAAGCTTC
313207 TTTTTTCTATTTTAGTCCTTTAA-CTTTC
1 TTTTTTCTATTTTAGTCCTTTAAGC-TTC
* * *
313235 TGTTTTAGCTATTTTATTCCTTTAAGTTTC
1 T-TTTT-TCTATTTTAGTCCTTTAAGCTTC
*
313265 TTTTTTGCTATTTTGGTCCTTTAA-CTTTC
1 TTTTTT-CTATTTTAGTCCTTTAAGC-TTC
* *
313294 TATTTTTGTAATTTAGTCCTTTAAGCTTC
1 T-TTTTTCTATTTTAGTCCTTTAAGCTTC
*
313323 TGTTATTTTTATTTT
1 T-TT-TTTCTATTTT
313338 GATCACTTAA
Statistics
Matches: 128, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
26 16 0.12
27 7 0.05
28 3 0.02
29 54 0.42
30 48 0.38
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (28 bp):
TTTTTTCTATTTTAGTCCTTTAAGCTTC
Found at i:313338 original size:59 final size:57
Alignment explanation
Indices: 313176--313338 Score: 204
Period size: 59 Copynumber: 2.8 Consensus size: 57
313166 TCCCTAAAGA
* *
313176 TTCTATTTTTGTTATTTTAGTCCTTTAAGTT-TTTTTTCTATTTTAGTCCTTTAACT
1 TTCTATTTTTGCTATTTTAGTCCTTTAAGTTCTTTTTTCTATTTTGGTCCTTTAACT
* * *
313232 TTCTGTTTTAGCTATTTTATTCCTTTAAGTTTCTTTTTTGCTATTTTGGTCCTTTAACT
1 TTCTATTTTTGCTATTTTAGTCCTTTAAG-TTCTTTTTT-CTATTTTGGTCCTTTAACT
* *
313291 TTCTATTTTTG-TAATTTAGTCCTTTAAGCTTCTGTTATTTTTATTTTG
1 TTCTATTTTTGCTATTTTAGTCCTTTAAG-TTCT-TT-TTTCTATTTTG
313339 ATCACTTAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
56 25 0.27
57 2 0.02
58 25 0.27
59 36 0.40
60 3 0.03
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63
Consensus pattern (57 bp):
TTCTATTTTTGCTATTTTAGTCCTTTAAGTTCTTTTTTCTATTTTGGTCCTTTAACT
Found at i:315377 original size:30 final size:31
Alignment explanation
Indices: 315341--315401 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
315331 TCTTTCTTGC
*
315341 ACTAACTC-GTTTCTCTCTTTTGTTTGTGTT
1 ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
* *
315371 ACTAACTCATTTTTTTCTCATTTGTTTGTGT
1 ACTAACTCA-GTTTCTCTCATTTGTTTGTGT
315402 CATTTTCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
32 18 0.69
ACGTcount: A:0.13, C:0.18, G:0.11, T:0.57
Consensus pattern (31 bp):
ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
Found at i:319215 original size:32 final size:32
Alignment explanation
Indices: 319174--319243 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
319164 TGAAGCAAGA
* *
319174 AACATCGAATGTTGGGGCATCTTTGGAGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
* *
319206 AACATCGAATATTGGAGTATCTTTGGGGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
319238 AACATC
1 AACATC
319244 CTTATGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (32 bp):
AACATCGAATATTGGAGCATCTTTGGAGATTC
Found at i:319493 original size:65 final size:65
Alignment explanation
Indices: 319373--319531 Score: 162
Period size: 67 Copynumber: 2.4 Consensus size: 65
319363 TAGAAAAATA
* * * * *
319373 TTTGAGTCTGATTCTCTGGAAACAAATTTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAA-A-A
1 TTTGAGTGTGTTTC-CTTGAAACAAAATTTTATCTCTC-TGAAACAATTTCTTTTGA-AAACACA
319436 AGTC
63 A-TC
* * * *
319440 TTTGAGTTTGTTTCCTTTGAAACAAAATTTTATCTCTC-GAGACAGTTTCTTTTGAAAACACCTA
1 TTTGAGTGTGTTTCC-TTGAAACAAAATTTTATCTCTCTGAAACAATTTCTTTTGAAAACA-CAA
319504 TC
64 TC
319506 TTTGAGTGTGTTTCCTTGAAACAAAA
1 TTTGAGTGTGTTTCCTTGAAACAAAA
319532 CACCTATCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
64 3 0.04
65 27 0.34
66 17 0.22
67 32 0.41
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (65 bp):
TTTGAGTGTGTTTCCTTGAAACAAAATTTTATCTCTCTGAAACAATTTCTTTTGAAAACACAATC
Found at i:319533 original size:34 final size:34
Alignment explanation
Indices: 319494--319559 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
319484 GTTTCTTTTG
319494 AAAACACCTATCTTTGAGT-GTGTTTCCTTGAAAC
1 AAAACACCTATCTTTGAGTCGT-TTTCCTTGAAAC
319528 AAAACACCTATCTTTGAGTCGTTTTCCTTGAA
1 AAAACACCTATCTTTGAGTCGTTTTCCTTGAA
319560 TCGAATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (34 bp):
AAAACACCTATCTTTGAGTCGTTTTCCTTGAAAC
Found at i:319870 original size:130 final size:130
Alignment explanation
Indices: 319632--320109 Score: 616
Period size: 130 Copynumber: 3.7 Consensus size: 130
319622 GAAACCATAA
* * * * *
319632 TCCCTAAAGATGGCCTACCATCCTTATCACGTAGGAACCGTGTCATCCCCCGACTAGACCTCCTT
1 TCCC-AAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTC
* *
319697 ATCACGTAGGAGCCATGTCACCCATGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCA
65 ATCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCA
319762 T
130 T
* * *
319763 TCCCAAAGATAGTC-TACCATCCTCATCACGTAGGAATCATGTCATCCCCCGACCAGATCTCCTC
1 TCCCAAAGAT-GGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTC
* * * * * * *
319827 ATCACGTAGGAGTCGGGTCACCCCTGATATCTAGGCGTCCTCATAACTTAGGAACCGTGTTATCA
65 ATCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCA
319892 T
130 T
* * ** * *
319893 TCCTAAAGATGGCTTGTCGTCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTAA
1 TCCCAAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
* * * * *
319958 TCACGTAGGAGCTGTGTTACCCCTGATAACCAGTCGTCATCATCATATAGGAATCGTGTTATCAT
66 TCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCAT
* ** * * * *
320023 TCCTAAAGATGGCATGTCGTCCTCATCACGTAGAAACCGTGTCATCCCCCGACCATACCTCCTCA
1 TCCCAAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
320088 TCACGTAGGAGCCGTGTCACCC
66 TCACGTAGGAGCCGTGTCACCC
320110 TTAGACGACC
Statistics
Matches: 302, Mismatches: 43, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
129 2 0.01
130 294 0.97
131 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (130 bp):
TCCCAAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
TCACGTAGGAGCCGTGTCACCCCTGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCAT
Found at i:320095 original size:260 final size:260
Alignment explanation
Indices: 319634--320109 Score: 693
Period size: 260 Copynumber: 1.8 Consensus size: 260
319624 AACCATAATC
* * * *
319634 CCTAAAGATGGCCTACCATCCTTATCACGTAGGAACCGTGTCATCCCCCGACTAGACCTCCTTAT
1 CCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTAAT
*
319699 CACGTAGGAGCCATGTCACCCATGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCATT
66 CACGTAGGAGCCATGTCACCCATGATAACCAGTCGTCATCATCACATAGGAACCGTGTTATCATT
* * * *
319764 CCCAAAGATAGTCTACCATCCTCATCACGTAGGAATCATGTCATCCCCCGACCAGATCTCCTCAT
131 CCCAAAGATAGGCTACCATCCTCATCACGTAGAAACCATGTCATCCCCCGACCAGACCTCCTCAT
*
319829 CACGTAGGAGTCGGGTCACCCCTGATATCTAGGCGTCCTCATAACTTAGGAACCGTGTTATCATT
196 CACGTAGGAGCCGGGTCACCCCTGATATCTAGGCGTCCTCATAACTTAGGAACCGTGTTATCATT
* ** *
319894 CCTAAAGATGGCTTGTCGTCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTAAT
1 CCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTAAT
** * * * *
319959 CACGTAGGAGCTGTGTTACCCCTGATAACCAGTCGTCATCATCATATAGGAATCGTGTTATCATT
66 CACGTAGGAGCCATGTCACCCATGATAACCAGTCGTCATCATCACATAGGAACCGTGTTATCATT
* ** * * *
320024 CCTAAAGAT-GGCATGTCGTCCTCATCACGTAGAAACCGTGTCATCCCCCGACCATACCTCCTCA
131 CCCAAAGATAGGC-TACCATCCTCATCACGTAGAAACCATGTCATCCCCCGACCAGACCTCCTCA
*
320088 TCACGTAGGAGCCGTGTCACCC
195 TCACGTAGGAGCCGGGTCACCC
320110 TTAGACGACC
Statistics
Matches: 188, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
259 2 0.01
260 186 0.99
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (260 bp):
CCTAAAGATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTAAT
CACGTAGGAGCCATGTCACCCATGATAACCAGTCGTCATCATCACATAGGAACCGTGTTATCATT
CCCAAAGATAGGCTACCATCCTCATCACGTAGAAACCATGTCATCCCCCGACCAGACCTCCTCAT
CACGTAGGAGCCGGGTCACCCCTGATATCTAGGCGTCCTCATAACTTAGGAACCGTGTTATCATT
Found at i:320315 original size:3 final size:3
Alignment explanation
Indices: 320307--320351 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
320297 TACAAAACAA
320307 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
320352 ACATATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:321012 original size:17 final size:19
Alignment explanation
Indices: 320992--321031 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
320982 AAAAACAAAT
320992 AGGAAAA-AA-AGAGAGAA
1 AGGAAAACAAGAGAGAGAA
321009 AGGAAAACAAGAGAGAGAA
1 AGGAAAACAAGAGAGAGAA
321028 AGGA
1 AGGA
321032 TAAGAATCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 2 0.10
19 12 0.57
ACGTcount: A:0.65, C:0.03, G:0.33, T:0.00
Consensus pattern (19 bp):
AGGAAAACAAGAGAGAGAA
Found at i:322063 original size:59 final size:58
Alignment explanation
Indices: 322000--322161 Score: 155
Period size: 59 Copynumber: 2.7 Consensus size: 58
321990 AGCCTTTTAA
* * *
322000 ATTTTTTTATTTTAGTCCCTTAAGATTCTATTTTTGTTATTTTAGTCCTTTAACTTTCT
1 ATTTTTCTATTTTAGTCCTTTAAG-TTCTATTTTTATTATTTTAGTCCTTTAACTTTCT
* * * * *
322059 ATTTTAGCTATTTTAGTCCTTTAAGTT-TTTGTTTTACTATTTTGGTCCTTTAACTTTTT
1 ATTTT-TCTATTTTAGTCCTTTAAGTTCTAT-TTTTATTATTTTAGTCCTTTAACTTTCT
* * * * *
322118 GTTTTTGTAATTTAGTCCTTTAAGCTTCTGTTATTTTTTATTTT
1 ATTTTTCTATTTTAGTCCTTTAAG-TTCTATT-TTTATTATTTT
322162 GATCCCTTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
58 18 0.22
59 38 0.46
60 27 0.33
ACGTcount: A:0.17, C:0.12, G:0.09, T:0.62
Consensus pattern (58 bp):
ATTTTTCTATTTTAGTCCTTTAAGTTCTATTTTTATTATTTTAGTCCTTTAACTTTCT
Found at i:322108 original size:29 final size:29
Alignment explanation
Indices: 322037--322140 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 29
322027 CTATTTTTGT
* *
322037 TATTTTAGTCCTTTAACTTTCTATTTTAGC
1 TATTTTAGTCCTTTAACTTTTTGTTTTA-C
*
322067 TATTTTAGTCCTTTAAGTTTTTGTTTTAC
1 TATTTTAGTCCTTTAACTTTTTGTTTTAC
* **
322096 TATTTTGGTCCTTTAACTTTTTGTTTTTG
1 TATTTTAGTCCTTTAACTTTTTGTTTTAC
*
322125 TAATTTAGTCCTTTAA
1 TATTTTAGTCCTTTAA
322141 GCTTCTGTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
29 40 0.62
30 25 0.38
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (29 bp):
TATTTTAGTCCTTTAACTTTTTGTTTTAC
Found at i:322149 original size:29 final size:29
Alignment explanation
Indices: 322001--322149 Score: 131
Period size: 30 Copynumber: 5.1 Consensus size: 29
321991 GCCTTTTAAA
* * * *
322001 TTTTTTTATTTTAGTCCCTTAAGATTCTA
1 TTTTTGTATTTTAGTCCTTTAAGCTTCTG
*
322030 TTTTTGTTATTTTAGTCCTTTAA-CTTTCTA
1 TTTTTG-TATTTTAGTCCTTTAAGC-TTCTG
* * *
322060 TTTTAGCTATTTTAGTCCTTTAAGTTTTTG
1 TTTTTG-TATTTTAGTCCTTTAAGCTTCTG
** * *
322090 TTTTACTATTTTGGTCCTTTAA-CTTTTTG
1 TTTTTGTATTTTAGTCCTTTAAGC-TTCTG
*
322119 TTTTTGTAATTTAGTCCTTTAAGCTTCTG
1 TTTTTGTATTTTAGTCCTTTAAGCTTCTG
322148 TT
1 TT
322150 ATTTTTTATT
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
29 49 0.49
30 50 0.51
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (29 bp):
TTTTTGTATTTTAGTCCTTTAAGCTTCTG
Found at i:323256 original size:20 final size:20
Alignment explanation
Indices: 323231--323324 Score: 118
Period size: 20 Copynumber: 4.6 Consensus size: 20
323221 TAGTTGAAAA
323231 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
323251 TCGCGTTGTGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
323271 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
323293 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
323313 TCGCGTTGCGAT
1 TCGCGTTGCGAT
323325 AGTTAACTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
20 45 0.73
21 2 0.03
22 15 0.24
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:327510 original size:19 final size:21
Alignment explanation
Indices: 327486--327535 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
327476 CATACATGTG
327486 GTATCGATACTTTCT-A-TGA
1 GTATCGATACTTTCTAATTGA
*
327505 GTATCGATAC-TTCTAATTTA
1 GTATCGATACTTTCTAATTGA
327525 GTATCGATACT
1 GTATCGATACT
327536 GATATTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 12 0.44
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (21 bp):
GTATCGATACTTTCTAATTGA
Found at i:334374 original size:14 final size:13
Alignment explanation
Indices: 334351--334381 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
334341 TTTCATTATG
334351 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
334364 TTTTTTGCTTTTTC
1 TTTTTT-CTTTTTC
334378 TTTT
1 TTTT
334382 CTTTTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:335608 original size:13 final size:13
Alignment explanation
Indices: 335590--335614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335580 CTGGTACCTG
335590 AAAAATTAAAATA
1 AAAAATTAAAATA
335603 AAAAATTAAAAT
1 AAAAATTAAAAT
335615 CAAAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:335628 original size:21 final size:21
Alignment explanation
Indices: 335602--335645 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
335592 AAATTAAAAT
335602 AAAAAATTAAAATCAAAGAAA
1 AAAAAATTAAAATCAAAGAAA
335623 AAAAAATTAAAATCAAAGAAA
1 AAAAAATTAAAATCAAAGAAA
335644 AA
1 AA
335646 TAGAAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAAATTAAAATCAAAGAAA
Found at i:336111 original size:22 final size:21
Alignment explanation
Indices: 336071--336112 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
336061 CGAAAGTAGA
*
336071 AAATAAAAACTTAAGTAAAAT
1 AAATAAAAACTTAAATAAAAT
*
336092 AAATAAAAGCATTAAATAAAA
1 AAATAAAAAC-TTAAATAAAA
336113 ATTTAAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (21 bp):
AAATAAAAACTTAAATAAAAT
Found at i:337658 original size:10 final size:10
Alignment explanation
Indices: 337645--337676 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
337635 ATTTTCATTC
337645 TTTTTTTTC-
1 TTTTTTTTCT
337654 TTTTTTTTCT
1 TTTTTTTTCT
337664 TTTTTTTTCT
1 TTTTTTTTCT
337674 TTT
1 TTT
337677 CGAATACTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:337659 original size:8 final size:9
Alignment explanation
Indices: 337642--337676 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
337632 ACCATTTTCA
337642 TTCTTTTTT
1 TTCTTTTTT
337651 TTCTTTTTT
1 TTCTTTTTT
337660 TTCTTTTTTT
1 TTC-TTTTTT
337670 TTCTTTT
1 TTCTTTT
337677 CGAATACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:339001 original size:32 final size:32
Alignment explanation
Indices: 338957--339027 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
338947 CTAGTACTTG
* * *
338957 AAAAATTAAAATTAAAGTTAAAATCAAAG-AACA
1 AAAAAATAAATTTAAAG-AAAAAT-AAAGAAACA
*
338990 AAAAAATAAATTTGAAGAAAAATAAAGAAACA
1 AAAAAATAAATTTAAAGAAAAATAAAGAAACA
339022 AAAAAA
1 AAAAAA
339028 AGGAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 4 0.12
32 15 0.45
33 14 0.42
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (32 bp):
AAAAAATAAATTTAAAGAAAAATAAAGAAACA
Found at i:339285 original size:7 final size:7
Alignment explanation
Indices: 339246--339284 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
339236 AAGTATTAAA
339246 GAAAGGG
1 GAAAGGG
339253 GAAAGGG
1 GAAAGGG
339260 GAAAGGG
1 GAAAGGG
339267 GAAAGGG
1 GAAAGGG
*
339274 GAAAAGG
1 GAAAGGG
339281 GAAA
1 GAAA
339285 ATAGGTTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (7 bp):
GAAAGGG
Found at i:339933 original size:21 final size:22
Alignment explanation
Indices: 339888--339939 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
339878 ATTCAATCAA
339888 TATCGATA-C-TGATAAGGTAG
1 TATCGATACCATGATAAGGTAG
*
339908 TATCGATACCATGATAAGG-GG
1 TATCGATACCATGATAAGGTAG
339929 TATCGATACCA
1 TATCGATACCA
339940 AGAAACATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 8 0.28
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (22 bp):
TATCGATACCATGATAAGGTAG
Found at i:340426 original size:59 final size:59
Alignment explanation
Indices: 340361--340931 Score: 734
Period size: 59 Copynumber: 9.7 Consensus size: 59
340351 ATGGCACTAA
* *
340361 GTGTGCTAAAAAGATAAGGAAATAATACTAAGTGTATGGATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * *
340420 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTTCAGATAGGGCATTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
340479 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * * *
340538 GTGTGCTAAAAATATAAGGAAGTCCTACTAAGTGTATGGATTTCCAGATAGGTCACTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* **
340597 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGGATTTCCAGATAGGGCACTAA
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * * * **
340656 GTGTGCTAAAAATATAAGAAAATCATACTAAGTGTATGAATTTCCAAATAGGGTAGTAA
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* **
340715 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGGGCACTAA
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * * * **
340774 GTGTGCTAAAATGTTAA-GAAATCATACTAAATGTATGAATTTCCATATAAGGCGTTTC
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
** * * * * *
340832 GTACGCTAAAATGTTAA-GAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTT
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*** * *
340890 GTACACTAAAATGTTAA-GAAATCATACTAAGTGTATGAATTT
1 GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTT
340932 TCGTATAGGA
Statistics
Matches: 471, Mismatches: 41, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
58 127 0.27
59 344 0.73
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
GTGTGCTAAAAAGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
Found at i:341439 original size:20 final size:22
Alignment explanation
Indices: 341401--341440 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
341391 TTTTAGTAGA
341401 AAAAGCATCCCCAAATGGCTCC
1 AAAAGCATCCCCAAATGGCTCC
341423 AAAA-CATCCCC-AATGGCT
1 AAAAGCATCCCCAAATGGCT
341441 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAAGCATCCCCAAATGGCTCC
Found at i:344564 original size:20 final size:19
Alignment explanation
Indices: 344489--344566 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 19
344479 AGGGTGTCAA
*
344489 AGTGCATCCACGCACCCTGC
1 AGTGCATCCATGCA-CCTGC
* *
344509 AGGGCATCCGTGCACCTGCCAC
1 AGTGCATCCATGCACCTG---C
**
344531 TAGTGCATTGATGCACCATGC
1 -AGTGCATCCATGCACC-TGC
344552 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
344567 TCAAACACCT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.09
20 24 0.55
21 1 0.02
22 1 0.02
23 12 0.27
24 2 0.05
ACGTcount: A:0.22, C:0.36, G:0.23, T:0.19
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:345019 original size:34 final size:33
Alignment explanation
Indices: 344976--345046 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
344966 TTTTTTAAAG
*
344976 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* * *
345010 GGGAAAGGTTCTAGTTTATCCTGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
345043 GGGA
1 GGGA
345047 GATGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:360865 original size:20 final size:20
Alignment explanation
Indices: 360840--360889 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
360830 CTGTACAAAT
* *
360840 AGTACCGATATTGTTTGAAC
1 AGTACCGATAATGTGTGAAC
360860 AGTACCGATAATGTGTGAAC
1 AGTACCGATAATGTGTGAAC
360880 AGTACCGATA
1 AGTACCGATA
360890 CTCAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (20 bp):
AGTACCGATAATGTGTGAAC
Found at i:361349 original size:34 final size:33
Alignment explanation
Indices: 361310--361380 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
361300 TTTTGTAAAG
*
361310 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* * *
361344 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
361377 GGGA
1 GGGA
361381 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:364314 original size:20 final size:20
Alignment explanation
Indices: 364289--364332 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
364279 CTATATTGTA
364289 TGAATAGTACCGATACTATG
1 TGAATAGTACCGATACTATG
** *
364309 TGAATAGTATTGATACTGTG
1 TGAATAGTACCGATACTATG
364329 TGAA
1 TGAA
364333 CAATAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (20 bp):
TGAATAGTACCGATACTATG
Found at i:368684 original size:16 final size:16
Alignment explanation
Indices: 368663--368693 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
368653 TTTGCATACC
368663 TAATGAATTTTAAATA
1 TAATGAATTTTAAATA
368679 TAATGAATTTTAAAT
1 TAATGAATTTTAAAT
368694 TAAATAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATGAATTTTAAATA
Found at i:372007 original size:16 final size:17
Alignment explanation
Indices: 371986--372025 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
371976 TAATCTATGT
371986 AAGAAAAA-GAAAAAGA
1 AAGAAAAATGAAAAAGA
*
372002 AAGAAAAATGAAAATGA
1 AAGAAAAATGAAAAAGA
372019 AAGAAAA
1 AAGAAAA
372026 TTGAGTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AAGAAAAATGAAAAAGA
Found at i:372506 original size:23 final size:22
Alignment explanation
Indices: 372479--372525 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
372469 AAAATGAATA
*
372479 AAATTTAAATTAATTTTTATTTT
1 AAATTTAAACTAA-TTTTATTTT
**
372502 AAATTTATGCTAATTTTATTTT
1 AAATTTAAACTAATTTTATTTT
372524 AA
1 AA
372526 TATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AAATTTAAACTAATTTTATTTT
Found at i:374962 original size:18 final size:18
Alignment explanation
Indices: 374938--374993 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
374928 CGAGGGTTTT
*
374938 AAGTGGTCCTTCGGGACA
1 AAGTGGTCATTCGGGACA
*
374956 TAGTGGTCATTCGGGACA
1 AAGTGGTCATTCGGGACA
*
374974 AAGTAGTCATTCGGGACA
1 AAGTGGTCATTCGGGACA
374992 AA
1 AA
374994 TTTTAAGTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (18 bp):
AAGTGGTCATTCGGGACA
Done.