Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008077.1 Hibiscus syriacus cultivar Beakdansim tig00110579_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: 593651
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:420259 original size:18 final size:18
Alignment explanation
Indices: 420219--420264 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
420209 ATTTAAAATT
* *
420219 ATTTAT-ATATTTATATT
1 ATTTATAATATATATATG
420236 ATTTTATAATATATATATG
1 A-TTTATAATATATATATG
420255 ATTTATAATA
1 ATTTATAATA
420265 AAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
19 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTATAATATATATATG
Found at i:421105 original size:18 final size:18
Alignment explanation
Indices: 421067--421105 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
421057 AATGGAAATG
*
421067 GCAATAGAAGCAGAAGTA
1 GCAATAGAAGCAGAAGCA
* *
421085 GCAATAGCAGCAGCAGCA
1 GCAATAGAAGCAGAAGCA
421103 GCA
1 GCA
421106 GCTTGTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.08
Consensus pattern (18 bp):
GCAATAGAAGCAGAAGCA
Found at i:421304 original size:17 final size:17
Alignment explanation
Indices: 421282--421315 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
421272 CCGCATCTCT
421282 CAGCCACCCACTTCCTC
1 CAGCCACCCACTTCCTC
421299 CAGCCACCCACTTCCTC
1 CAGCCACCCACTTCCTC
421316 TTCCACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.59, G:0.06, T:0.18
Consensus pattern (17 bp):
CAGCCACCCACTTCCTC
Found at i:426831 original size:20 final size:20
Alignment explanation
Indices: 426806--426856 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
426796 CACGAAATGT
426806 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
*
426826 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGAGAATAA
426846 AAGATTACCAG
1 AAGATTACCAG
426857 GGAATATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:426861 original size:18 final size:18
Alignment explanation
Indices: 426806--426862 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 18
426796 CACGAAATGT
426806 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-G-GAATAA
426826 AAGATTACCAGTGGGAATAA
1 AAGATTACCA--GGGAATAA
426846 AAGATTACCAGGGAATA
1 AAGATTACCAGGGAATA
426863 TGATTACTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.20
20 26 0.74
21 1 0.03
22 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (18 bp):
AAGATTACCAGGGAATAA
Found at i:428254 original size:30 final size:30
Alignment explanation
Indices: 428218--428278 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
428208 TCAGCAGATG
*
428218 TGCATGGAAGCTTGGAGCTCTTGGCGTCTT
1 TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
* *
428248 TGCATGGAAGGTTGGATCTCTCGGCGTCTT
1 TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
428278 T
1 T
428279 AACACAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.34
Consensus pattern (30 bp):
TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
Found at i:429264 original size:174 final size:173
Alignment explanation
Indices: 428975--429335 Score: 659
Period size: 174 Copynumber: 2.1 Consensus size: 173
428965 TTTTAAAGTT
* * *
428975 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGGTAT
1 TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAATAAGAGTAAATTATAAAAAGTTGGTAT
*
429040 ACTATGTTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
66 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
*
429105 GATTAAATTACAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
131 GATTAAATTACAAAGTTTAAAAATGTTGAGAACCAAATAGTAA
*
429148 TTAGGGATCATTTTGTAAAATTTGATGAATTCAAGGAATAAAGAGTAAATTATAAAAAGTTGGTA
1 TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAAT-AAGAGTAAATTATAAAAAGTTGGTA
429213 TACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAG
65 TACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAG
429278 GGATTAAATTACAAAGTTTAAAAATGTTGAGAACCAAATAGTAA
130 GGATTAAATTACAAAGTTTAAAAATGTTGAGAACCAAATAGTAA
429322 TTAGGGATCATTTT
1 TTAGGGATCATTTT
429336 ATATTTGATG
Statistics
Matches: 181, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
173 36 0.20
174 145 0.80
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (173 bp):
TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAATAAGAGTAAATTATAAAAAGTTGGTAT
ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
GATTAAATTACAAAGTTTAAAAATGTTGAGAACCAAATAGTAA
Found at i:430422 original size:14 final size:14
Alignment explanation
Indices: 430016--430412 Score: 257
Period size: 14 Copynumber: 28.8 Consensus size: 14
430006 TTTATTATTA
*
430016 TTAAATTATTAAAG
1 TTAAATCATTAAAG
430030 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
430044 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
430058 TTAAATCATTAAAG
1 TTAAATCATTAAAG
** * * *
430072 CCAAGTAATTATTA-
1 TTAAATCATTA-AAG
430086 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
430100 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* * *
430114 TTAAATTATTTAAT
1 TTAAATCATTAAAG
430128 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
430142 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
*
430156 TTAAATCATTAAAT
1 TTAAATCATTAAAG
430170 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
430184 TTAAATAATT--A-
1 TTAAATCATTAAAG
*
430195 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
430209 TTAAATCATTATAG
1 TTAAATCATTAAAG
* * *
430223 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
430237 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
430251 TTAAGTCATTATTA-
1 TTAAATCATTA-AAG
*
430265 TTAAATTATTAAAG
1 TTAAATCATTAAAG
*
430279 TAAAATCATTAAAG
1 TTAAATCATTAAAG
* *
430293 TTAAGTCATTATTA-
1 TTAAATCATTA-AAG
* **
430307 TTAAATCATTTACT
1 TTAAATCATTAAAG
*
430321 TTAAATTATTAAAG
1 TTAAATCATTAAAG
*
430335 TTAAATAATT--A-
1 TTAAATCATTAAAG
430346 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
430360 TTAAAT-AATAATTA-
1 TTAAATCATTAA--AG
* *
430374 TTAAATTATTAAAT
1 TTAAATCATTAAAG
*
430388 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
430402 TTAAATAATTA
1 TTAAATCATTA
430413 TTATTAAATA
Statistics
Matches: 296, Mismatches: 63, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
11 18 0.06
12 2 0.01
13 13 0.04
14 250 0.84
15 13 0.04
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:433704 original size:17 final size:17
Alignment explanation
Indices: 433676--433720 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
433666 AAAATAGAAA
433676 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
433694 CATCGATGCAATTAGTG
1 CATCGATGCAATTAGTG
433711 CATCGATGCA
1 CATCGATGCA
433721 TCCCAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (17 bp):
CATCGATGCAATTAGTG
Found at i:434962 original size:31 final size:31
Alignment explanation
Indices: 434876--434999 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 31
434866 GAGTCGAGGG
434876 TATACCTATGTTCTACGGAACATATGGACAGA
1 TATACCTATGTTCTACGGAACATATGGACA-A
*
434908 -ATTACCTATG-TCTTTC-GAGACATATGGACAA
1 TA-TACCTATGTTC-TACGGA-ACATATGGACAA
*
434939 TATACCTATGTTCTAAGGAACATATGGA-AA
1 TATACCTATGTTCTACGGAACATATGGACAA
* * * *
434969 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 -TATACCTATGTTCTACGGAACATATGGACA
435000 GTTGCCAAGG
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
30 2 0.03
31 47 0.62
32 27 0.36
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TATACCTATGTTCTACGGAACATATGGACAA
Found at i:435043 original size:30 final size:30
Alignment explanation
Indices: 434989--435060 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
434979 GTTCTTCGGA
* * *
434989 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
435019 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
435049 ACCTCTGGATAG
1 ACCTCTGGATAG
435061 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:443184 original size:106 final size:106
Alignment explanation
Indices: 443062--444313 Score: 2035
Period size: 106 Copynumber: 11.9 Consensus size: 106
443052 TGTGCACGAT
* ** * * *
443062 TCCCTTCGTCGGGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAG
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * ** *
443127 TCGGCCCTGAGATTGAGAAACTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
443168 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * * ** *
443233 TCGGCCCTGAGATTGGGAAACTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
443274 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
443339 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
443380 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
443445 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
443486 TCCCTTCGTCGTGAAGTTGAACTTACATTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
443551 TTGGCTCTGAATTTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
443592 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
443657 TTGGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
443698 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
443763 TTGGCTCTGAATTTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
443804 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
443869 TTGGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
443910 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
443975 TTGGCTCTGAATTTGAGAAGTTGGTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
444016 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTCTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
444081 TTGG----GAAATT-----G-T--TTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
**
444110 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * *
444175 TTGGCTCTGAAATTGAGAAGTTGTTTGTCGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
444216 TCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
**
444281 TTGGCTCTGAAATTG-GAAAGTTATTTATTGACA
66 TTGGCTCTGAAATTGAG-AAGTTGGTTATTGACA
444314 GACAACTTTT
Statistics
Matches: 1090, Mismatches: 43, Indels: 26
0.94 0.04 0.02
Matches are distributed among these distances:
94 83 0.08
96 1 0.00
97 1 0.00
98 6 0.01
102 5 0.00
103 1 0.00
104 1 0.00
105 1 0.00
106 991 0.91
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
Found at i:444160 original size:94 final size:96
Alignment explanation
Indices: 443999--444285 Score: 416
Period size: 94 Copynumber: 2.9 Consensus size: 96
443989 GAGAAGTTGG
443999 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
1 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
*
444064 TCGTTCTGAAGTTGAAATTGG-GAAATT-GT
66 TCGTTGTGAAGTTGAAATTGGCGAAATTAGT
**
444093 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCT
1 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
444158 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
66 TCGTTGTGAAGTTGAAATTGG--C-GAAATT----AGT
* *
444196 TGTTTGTCGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATAT
1 T-TAT-T-GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
*
444261 CCTTCGCTGTGAAGTTGAAATTGGC
63 CCTTCGTTGTGAAGTTGAAATTGGC
444286 TCTGAAATTG
Statistics
Matches: 173, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
94 83 0.48
98 6 0.03
103 3 0.02
104 3 0.02
105 1 0.01
106 77 0.45
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (96 bp):
TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
TCGTTGTGAAGTTGAAATTGGCGAAATTAGT
Found at i:444218 original size:200 final size:200
Alignment explanation
Indices: 443875--444284 Score: 712
Period size: 200 Copynumber: 2.0 Consensus size: 200
443865 GAAATTGGCT
* *
443875 TTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
1 TTGAAATTGGGAAATTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
* *
443940 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGGTTATTG
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATCG
* *
444005 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTC
131 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTC
444070 TGAAG
196 TGAAG
* **
444075 TTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTG
1 TTGAAATTGGGAAATTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
* *
444140 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTCG
66 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATCG
*
444205 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTG
131 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTC
444270 TGAAG
196 TGAAG
444275 TTGAAATTGG
1 TTGAAATTGG
444285 CTCTGAAATT
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
200 198 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (200 bp):
TTGAAATTGGGAAATTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTG
TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATCG
ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGCTC
TGAAG
Found at i:451832 original size:33 final size:33
Alignment explanation
Indices: 451788--451859 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
451778 TTGCAAGGTG
*
451788 GCCTCAACCCTCAGTGCACCCTGATGTGTGCTA
1 GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
* *
451821 GCCTCAGCCCTCAGTGCACCCCGATGTGTGCTG
1 GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
451854 GCCTCA
1 GCCTCA
451860 CCACTAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (33 bp):
GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
Found at i:452021 original size:10 final size:10
Alignment explanation
Indices: 451991--452015 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
451981 CAGCGGTATC
451991 GACCCTAGGT
1 GACCCTAGGT
452001 GACCCTAGGT
1 GACCCTAGGT
452011 GACCC
1 GACCC
452016 CTGGTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (10 bp):
GACCCTAGGT
Found at i:454418 original size:35 final size:35
Alignment explanation
Indices: 454361--454436 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
454351 ACAAAATAAT
* *
454361 AATAACAAAGTACGAATAATATATA-TATATAAAATA
1 AATAAAAAAGTAC-AATAATATAAATTA-ATAAAATA
*
454397 AATAAAAAAGTA-AATATATATAAATTAATAAATTA
1 AATAAAAAAGTACAATA-ATATAAATTAATAAAATA
454432 AATAA
1 AATAA
454437 CGAAAAGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.11
35 18 0.51
36 13 0.37
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (35 bp):
AATAAAAAAGTACAATAATATAAATTAATAAAATA
Found at i:454707 original size:2 final size:2
Alignment explanation
Indices: 454660--454688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
454650 CTTGTGTAGA
454660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
454689 ATAGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454890 original size:2 final size:2
Alignment explanation
Indices: 454883--454938 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
454873 GAACATACGC
454883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
454924 AT A- AT AA AT A- AT AT A
1 AT AT AT AT AT AT AT AT A
454939 AAAATAATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:454956 original size:12 final size:11
Alignment explanation
Indices: 454930--454970 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
454920 ATATATAATA
* *
454930 AATAATATAAA
1 AATAATACAAG
454941 AATAATACAAG
1 AATAATACAAG
454952 TAATAATACAAG
1 -AATAATACAAG
454964 AATAATA
1 AATAATA
454971 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:455083 original size:25 final size:25
Alignment explanation
Indices: 454984--455098 Score: 67
Period size: 25 Copynumber: 4.4 Consensus size: 25
454974 AGAAAGAGAA
*
454984 AGTAAAAAATATAAT-AATAATAAAAT
1 AGTAAAAAA-ATAATAAAT-ATATAAT
*
455010 A-TAAAAAATATACATATATATATAAAT
1 AGTAAAAAA-ATA-ATAAATATAT-AAT
* **
455037 AAGTAGAATAAA-AGGAAA-ATATAAT
1 -AGTA-AAAAAATAATAAATATATAAT
*
455062 AGTAAAAAAATAATAAATATATAGT
1 AGTAAAAAAATAATAAATATATAAT
*
455087 AATAATAAAAAT
1 AGTAA-AAAAAT
455099 GCAAAGAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
23 5 0.07
24 8 0.12
25 24 0.35
26 16 0.23
27 7 0.10
28 2 0.03
29 3 0.04
30 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (25 bp):
AGTAAAAAAATAATAAATATATAAT
Found at i:455686 original size:37 final size:37
Alignment explanation
Indices: 455645--455749 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
455635 GTGCTTGTAG
* * *
455645 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* *
455682 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
455719 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
455750 GACGAAAAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:456791 original size:106 final size:106
Alignment explanation
Indices: 456479--457415 Score: 1348
Period size: 106 Copynumber: 8.9 Consensus size: 106
456469 AGCATTGTTC
* * * ** *
456479 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
456544 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
456585 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA---GGAAA-T-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * * *
456644 ATCAACCG-CCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
456684 TGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
456749 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
456790 TGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* *
456855 ACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
456896 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
456961 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
457002 TGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTTTGAAATTGGGAAAATATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
457067 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
457108 GGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* *
457173 ATCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
457214 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
*
457279 ACCACCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
457320 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAACTGTTTATTGATA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
457385 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
457416 CCACTCTCGA
Statistics
Matches: 751, Mismatches: 73, Indels: 14
0.90 0.09 0.02
Matches are distributed among these distances:
99 64 0.09
100 17 0.02
101 1 0.00
102 5 0.01
103 4 0.01
104 1 0.00
105 16 0.02
106 643 0.86
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:458154 original size:22 final size:22
Alignment explanation
Indices: 458128--458204 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
458118 TTGTGTTTGG
458128 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
458150 TCAAAGGTTTGACATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
458172 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
458194 TCAACGGTTTG
1 TCAAAGGTTTG
458205 ATAGGGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:462107 original size:22 final size:22
Alignment explanation
Indices: 462067--462132 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
462057 CTCGTATAAA
462067 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
462088 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
462110 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
462132 T
1 T
462133 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 12 0.27
22 32 0.73
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:462451 original size:29 final size:29
Alignment explanation
Indices: 462418--462489 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
462408 TTTTCTGCAT
**
462418 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
462447 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
462476 ATTCATGTCATGTA
1 ATTCATGTCATGTA
462490 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:462821 original size:19 final size:20
Alignment explanation
Indices: 462784--462821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
462774 CTTTTTCTCA
*
462784 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
462804 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
462822 TCAAGCAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:462900 original size:66 final size:64
Alignment explanation
Indices: 462785--462954 Score: 216
Period size: 66 Copynumber: 2.6 Consensus size: 64
462775 TTTTTCTCAT
* * *
462785 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG-T
462850 GA
63 GA
* * *
462852 GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTGA
1 GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGTGA
*
462916 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG---GGGTACCGATTCCCCT
462955 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
63 6 0.06
64 16 0.17
65 3 0.03
66 49 0.53
67 19 0.20
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (64 bp):
GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGTGA
Found at i:468986 original size:22 final size:22
Alignment explanation
Indices: 468945--469012 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
468935 CTCGTATAAA
468945 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
468968 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
468990 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
469012 T
1 T
469013 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:469273 original size:30 final size:31
Alignment explanation
Indices: 469232--469291 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
469222 TAGACATAGT
*
469232 ATTTCCATACCTTTAACACATAG-TCATATC
1 ATTTACATACCTTTAACACATAGTTCATATC
*
469262 ATTTACATACCTTTATCACATAGTTCATAT
1 ATTTACATACCTTTAACACATAGTTCATAT
469292 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTTCATATC
Found at i:469339 original size:29 final size:29
Alignment explanation
Indices: 469306--469377 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
469296 TTTTCTGCAT
**
469306 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
469335 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
469364 ATTCATGTCATGTA
1 ATTCATGTCATGTA
469378 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:469798 original size:67 final size:66
Alignment explanation
Indices: 469680--469832 Score: 207
Period size: 67 Copynumber: 2.3 Consensus size: 66
469670 TTTTTCTCAT
* * *
469680 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG
469745 ATGA
63 ATGA
* * * *
469749 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
469814 A
66 A
*
469815 GGGGGTATCGGTTTCCCC
1 GGGGGTATCGGTTCCCCC
469833 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
66 23 0.30
67 41 0.54
69 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:469836 original size:22 final size:21
Alignment explanation
Indices: 469811--469854 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
469801 ATTCATTTCG
* *
469811 TTGAGGGGGTATCGGTTTCCCC
1 TTGAAGGGGTATC-GATTCCCC
*
469833 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
469854 T
1 T
469855 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:472408 original size:14 final size:14
Alignment explanation
Indices: 472375--472459 Score: 65
Period size: 14 Copynumber: 6.3 Consensus size: 14
472365 GAAAGCAAAG
*
472375 ATAAAATAATAAGTA
1 ATAAAA-AATAAATA
472390 A-AAAAAATAAATA
1 ATAAAAAATAAATA
* *
472403 ATAAAATATATAT-
1 ATAAAAAATAAATA
*
472416 ATAAAAGA-AAATA
1 ATAAAAAATAAATA
472429 A-AAGAAAATAAATA
1 ATAA-AAAATAAATA
472443 A-AACAAAAT-AATA
1 ATAA-AAAATAAATA
472456 ATAA
1 ATAA
472460 CAAAGTACGA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
12 5 0.09
13 24 0.41
14 28 0.48
15 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (14 bp):
ATAAAAAATAAATA
Found at i:472429 original size:30 final size:28
Alignment explanation
Indices: 472375--472430 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 28
472365 GAAAGCAAAG
472375 ATAAAATAATAAGTAAAAAAAATAAATA
1 ATAAAATAATAAGTAAAAAAAATAAATA
472403 ATAAAATATATATA-TAAAAGAAAATAAA
1 ATAAAATA-ATA-AGTAAAA-AAAATAAA
472431 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.32
29 8 0.32
30 9 0.36
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (28 bp):
ATAAAATAATAAGTAAAAAAAATAAATA
Found at i:472453 original size:10 final size:10
Alignment explanation
Indices: 472416--472440 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
472406 AAATATATAT
472416 ATAAAAGAAA
1 ATAAAAGAAA
472426 ATAAAAGAAA
1 ATAAAAGAAA
472436 ATAAA
1 ATAAA
472441 TAAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (10 bp):
ATAAAAGAAA
Found at i:472453 original size:67 final size:66
Alignment explanation
Indices: 472377--472510 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
472367 AAGCAAAGAT
* * *
472377 AAAATAATAAGTAAAAAAAATAAATAATAAAATATATATATAAAAGAAAATAAAAGAAAATAAAT
1 AAAATAATAA-T-AACAAAAT-AAGAATAAAATATATATATAAAA-AAAATAAAAAAAAATAAAT
472442 AAAAC
62 AAAAC
* * * * * *
472447 AAAATAATAATAACAAAGTACGAATAATATATATATATATAATAAATAAAAAAAAATATATAAA
1 AAAATAATAATAACAAAATAAGAATAAAATATATATATAAAAAAAATAAAAAAAAATAAATAAA
472511 TTAATAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
66 19 0.35
67 19 0.35
68 6 0.11
69 1 0.02
70 10 0.18
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (66 bp):
AAAATAATAATAACAAAATAAGAATAAAATATATATATAAAAAAAATAAAAAAAAATAAATAAAA
C
Found at i:472804 original size:2 final size:2
Alignment explanation
Indices: 472746--472788 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
472736 CTTGTGTAGA
472746 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
472788 A
1 A
472789 GTAAAATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:473026 original size:12 final size:11
Alignment explanation
Indices: 472998--473038 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
472988 ATACAAAATA
* *
472998 AATAATATAAA
1 AATAATACAAG
473009 AATAATACAAG
1 AATAATACAAG
473020 TAATAATACAAG
1 -AATAATACAAG
473032 AATAATA
1 AATAATA
473039 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:473083 original size:26 final size:27
Alignment explanation
Indices: 473057--473106 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
473047 GAGAAAGTAA
473057 AAAAATATA-ATA-ATAATA-AAATAT
1 AAAAATATACATATATAATATAAATAT
473081 AAAAATATACATATATAATATAAATA
1 AAAAATATACATATATAATATAAATA
473107 AGTAGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 6 0.26
27 5 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATATACATATATAATATAAATAT
Found at i:473091 original size:62 final size:61
Alignment explanation
Indices: 473025--473166 Score: 143
Period size: 62 Copynumber: 2.3 Consensus size: 61
473015 ACAAGTAATA
473025 ATACA-AGAATAATAAAAAGAAAG-AGAAAGTAAA-AAAATATAATAATAATAAAATATAA-AAA
1 ATACATAGAATAATAAAAA-AAAGTAG-AA-TAAAGAAAATATAATAATAA-AAAA-ATAATAAA
473086 T
61 T
* * * *
473087 ATACATA-TATAATATAAATAAGTAGAATAAAGGAAAATATAATAGTAAAAAAATAATAAAT
1 ATACATAGAATAATAAAAAAAAGTAGAATAAA-GAAAATATAATAATAAAAAAATAATAAAT
473148 ATA-ATAGTAATAATAAAAA
1 ATACATAG-AATAATAAAAA
473167 TGCAAAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
60 11 0.16
61 16 0.24
62 39 0.58
63 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.23
Consensus pattern (61 bp):
ATACATAGAATAATAAAAAAAAGTAGAATAAAGAAAATATAATAATAAAAAAATAATAAAT
Found at i:473757 original size:37 final size:37
Alignment explanation
Indices: 473716--473820 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
473706 GTGCTTGTGG
* * *
473716 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
473753 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
473790 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
473821 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:477834 original size:20 final size:20
Alignment explanation
Indices: 477811--477881 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
477801 TGCGATTTTC
*
477811 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
477831 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
477851 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
477870 CAAATTCGCAAC
1 CAAATTCGCAAC
477882 TGAATTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:477874 original size:19 final size:19
Alignment explanation
Indices: 477850--477897 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
477840 AACGCGAAAG
477850 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
477869 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
477888 TCAAATTCGC
1 TCAAATTCGC
477898 GACAGGTTTA
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:0.35, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:478278 original size:15 final size:15
Alignment explanation
Indices: 478224--478282 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
478214 TTGATTTTCC
478224 GGAAAATGAATTACT
1 GGAAAATGAATTACT
* **
478239 AGAATTTGAATTACT
1 GGAAAATGAATTACT
*
478254 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
478269 GGAAAATGAATTAC
1 GGAAAATGAATTAC
478283 ATTTCTGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 3 0.08
15 30 0.81
16 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:478292 original size:20 final size:20
Alignment explanation
Indices: 478267--478314 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
478257 ATTTGAATTA
478267 CTGGAAAATGAATTACATTT
1 CTGGAAAATGAATTACATTT
478287 CTGGAAAATGAATTACATTT
1 CTGGAAAATGAATTACATTT
478307 CTGGAAAA
1 CTGGAAAA
478315 CATCTGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
CTGGAAAATGAATTACATTT
Found at i:478614 original size:90 final size:86
Alignment explanation
Indices: 478458--478627 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
478448 ATTATTATTT
* * * * *
478458 TAAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATT
1 TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
*
478523 AATATTGGTATATTTTAGTGAAA
66 -A-ATTAGTATATTTTAGTGAAA
* *
478546 TAAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-TTAAAAA
1 TAAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTATATTAATAAAAA
478609 TATTAATTAGTATATTTTA
62 TATTAATTAGTATATTTTA
478628 AATATCTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 23 0.33
89 7 0.10
90 16 0.23
91 15 0.21
92 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
AATTAGTATATTTTAGTGAAA
Found at i:478678 original size:29 final size:30
Alignment explanation
Indices: 478643--478714 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 30
478633 CTTTACTAAA
*
478643 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTTAAATATATAAAAAATTATTAT
478672 -TCATTA-TTAAATATATAAAAAATTATTAT
1 AT-ATTATTTAAATATATAAAAAATTATTAT
*
478701 ATATTATTAAAATA
1 ATATTATTTAAATA
478715 AAAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 16 0.43
29 14 0.38
30 7 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATTATTTAAATATATAAAAAATTATTAT
Found at i:478683 original size:28 final size:27
Alignment explanation
Indices: 478643--478732 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 27
478633 CTTTACTAAA
478643 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAA-AATATTAT
478672 -TCATTATTAAATATATAAAAAATTATTAT
1 AT-ATTATTAAATATAT-AAAAA-TATTAT
*
478701 ATATTATTAAA-ATA-AAAAATATAAT
1 ATATTATTAAATATATAAAAATATTAT
*
478726 ATCTTAT
1 ATATTAT
478733 ATTATTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
25 11 0.20
26 5 0.09
28 16 0.29
29 22 0.40
30 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAATATTAT
Found at i:478696 original size:26 final size:27
Alignment explanation
Indices: 478644--478722 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
478634 TTTACTAAAA
478644 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
478672 TCATTATTAAATATATAAAAAATTATTAT
1 T-ATTATTAAATATATAAATAA-TATTAT
478701 ATATTATTAAA-ATA-AAA-AATAT
1 -TATTATTAAATATATAAATAATAT
478723 AATATCTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 3 0.06
28 19 0.40
29 19 0.40
30 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:478814 original size:50 final size:53
Alignment explanation
Indices: 478699--478814 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 53
478689 AAAAATTATT
*
478699 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTAA
* * *
478752 TTATATTATTAAACT-AAAAATAT-A-ATGTTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTAT-AATA-TAATTAA
478803 ATATATT-TTAAA
1 ATATATTATTAAA
478815 TATTTTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
50 19 0.34
51 13 0.23
52 11 0.20
53 13 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (53 bp):
ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTAA
Found at i:479381 original size:39 final size:39
Alignment explanation
Indices: 479338--479424 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
479328 TCCGATGCTC
* *
479338 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGATCATATGGTGCCAAGCAAAAGAAA
* *
479377 ATCAAAATCCAAATATCATATGGTTCCAAGCAAAAGAAA
1 ATCAAAATCCAAAGATCATATGGTGCCAAGCAAAAGAAA
479416 ATCAAAATC
1 ATCAAAATC
479425 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGATCATATGGTGCCAAGCAAAAGAAA
Found at i:479854 original size:61 final size:63
Alignment explanation
Indices: 479723--479863 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
479713 TTTTAAAAAC
*
479723 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
479788 A
63 A
* * ** *
479789 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
479850 AACAAATCAACTTT
1 AACAAATCAACTTT
479864 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:481251 original size:21 final size:21
Alignment explanation
Indices: 481227--481322 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
481217 GGCGGGACCA
* *
481227 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGAGAGGGGCCT
* * * *
481248 CTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGAGAGGGGCCT
*
481269 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAATGATGAGAGGGGCCT
481290 CTTGAATGAT-ATGAGGGGCCT
1 CTTGAATGATGA-GAGGGGCCT
481311 CTTGAATGATGA
1 CTTGAATGATGA
481323 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (21 bp):
CTTGAATGATGAGAGGGGCCT
Found at i:481306 original size:42 final size:42
Alignment explanation
Indices: 481227--481326 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
481217 GGCGGGACCA
* * * * *
481227 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
* *
481269 CTTCG-ATGATGATAGGGGCCTCTTGAATGATATGAGGGGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
481311 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
481327 TGCATCGGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 47 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
Found at i:481773 original size:21 final size:21
Alignment explanation
Indices: 481724--481773 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
481714 ACCATTATCT
481724 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
* *
481745 TGATGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
481766 TCACGTAA
1 TCACGTAA
481774 TTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:481896 original size:12 final size:12
Alignment explanation
Indices: 481879--481911 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
481869 AGGCTCGATG
481879 ATGTGATGGAAT
1 ATGTGATGGAAT
481891 ATGTGATGGAAT
1 ATGTGATGGAAT
*
481903 AGGTGATGG
1 ATGTGATGG
481912 TGGAGGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.30
Consensus pattern (12 bp):
ATGTGATGGAAT
Found at i:483501 original size:20 final size:20
Alignment explanation
Indices: 483485--483539 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
483475 TCTGAAACTT
483485 AAATTCGCAACGCGAAAATGA
1 AAATTCGCAACGCGAAAAT-A
*
483506 AAA-TCGCAACGCAAAAATGA
1 AAATTCGCAACGCGAAAAT-A
483526 AAATT-GCAACGCGA
1 AAATTCGCAACGCGA
483540 TTTTAGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:483596 original size:20 final size:20
Alignment explanation
Indices: 483536--483598 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
483526 AAATTGCAAC
*
483536 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
483555 GAGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
483575 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
483595 GCGA
1 GCGA
483599 ATTTGGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 7 0.18
20 32 0.82
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:483908 original size:22 final size:22
Alignment explanation
Indices: 483851--483908 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
483841 TCTGAGAGAT
483851 GGAGAT-A-GACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGTC
* * * *
483871 AGAAATGGGGATGGATTTCGTC
1 GGAGATGAGGACGGATTTCGTC
483893 GGAGATGAGGACGGAT
1 GGAGATGAGGACGGAT
483909 ATCGCCGTAG
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 4 0.14
22 24 0.86
ACGTcount: A:0.28, C:0.10, G:0.40, T:0.22
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGTC
Found at i:484639 original size:18 final size:19
Alignment explanation
Indices: 484604--484641 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
484594 CACGGAATGT
484604 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
484624 AAGATTATCA-GGGAATAA
1 AAGATTATCAGGGGAATAA
484642 GATTACAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:484862 original size:37 final size:36
Alignment explanation
Indices: 484790--484863 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
484780 GTTTGAAAAT
*
484790 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
484826 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
484863 A
1 A
484864 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 21 0.64
38 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:487766 original size:32 final size:32
Alignment explanation
Indices: 487730--487792 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
487720 AACATTTGAT
*
487730 TTTCATTTCTTTCGCCAAATTATTTCAAAGAA
1 TTTCATTTCTTTCACCAAATTATTTCAAAGAA
* *
487762 TTTCATTTCTTTCACTAAATTATTTGAAAGA
1 TTTCATTTCTTTCACCAAATTATTTCAAAGA
487793 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (32 bp):
TTTCATTTCTTTCACCAAATTATTTCAAAGAA
Found at i:491447 original size:58 final size:57
Alignment explanation
Indices: 491293--491468 Score: 185
Period size: 58 Copynumber: 3.0 Consensus size: 57
491283 GAATTTGGGA
* * * *
491293 ATGAAATTGGAATATTCAAAAGTTTACGGACCAATTTAGAAA-AAGGGTCATAGTTTAGGG
1 ATGAAATTGAAATATTCAAAAG-TTAAGGACCAATTTA-AAATAAGAGTTATAGTTT--GG
* * * *
491353 ATGAAATT-AGAATGTTCAAAAGTTCAAAGACTAATTTAAAATGAGAGTTATAGTTTGG
1 ATGAAATTGA-AATATTCAAAAGTT-AAGGACCAATTTAAAATAAGAGTTATAGTTTGG
* *
491411 ATGAAATTGAAATATTCAAAAGTCTAAGGGCCAATTTAAAATAAGAGTTATACTTTGG
1 ATGAAATTGAAATATTCAAAAGT-TAAGGACCAATTTAAAATAAGAGTTATAGTTTGG
491469 GGGACATATG
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
58 50 0.52
59 7 0.07
60 40 0.41
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (57 bp):
ATGAAATTGAAATATTCAAAAGTTAAGGACCAATTTAAAATAAGAGTTATAGTTTGG
Found at i:495095 original size:14 final size:14
Alignment explanation
Indices: 495059--495116 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
495049 GTCAGAGGGA
* *
495059 AAAAATGAATAAAT
1 AAAAATAAAAAAAT
* *
495073 GAAAA-AAAAGAAT
1 AAAAATAAAAAAAT
495086 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
*
495100 AAAAATAAATAAAT
1 AAAAATAAAAAAAT
495114 AAA
1 AAA
495117 TAAAATATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 9 0.25
14 27 0.75
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:495209 original size:18 final size:18
Alignment explanation
Indices: 495160--495213 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
495150 AAAATAGAAA
*
495160 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
495181 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
495200 AATA-TAATATAAAA
1 AATAGTAATATAAAA
495214 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:495214 original size:18 final size:19
Alignment explanation
Indices: 495164--495214 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
495154 TAGAAAAATA
*
495164 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
495184 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
495203 ATAATATAAAAA
1 ATAATATAAAAA
495215 AACCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:495435 original size:20 final size:19
Alignment explanation
Indices: 495412--495460 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
495402 ATATTTTTAA
*
495412 AAAAAAGTATATATA-TATAT
1 AAAAAA-TAAATATAGTAT-T
495432 AAAATAATAAATATAGTATT
1 AAAA-AATAAATATAGTATT
495452 AAAAAATAA
1 AAAAAATAA
495461 CCAAATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 16 0.62
21 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAAATAAATATAGTATT
Found at i:495445 original size:22 final size:22
Alignment explanation
Indices: 495420--495513 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
495410 AAAAAAAAGT
495420 ATATATATATATAAAATAATAA
1 ATATATATATATAAAATAATAA
* *
495442 ATATAGTAT-TAAAAAATAACCAA
1 ATATA-TATATATAAAATAA-TAA
* *
495465 ATGA-ATATAAAT-AAATAAAAA
1 AT-ATATATATATAAAATAATAA
* * *
495486 ATATATGTATAGATAATAAT-A
1 ATATATATATATAAAATAATAA
495507 ATATATA
1 ATATATA
495514 GTGTAAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
22 28 0.51
23 9 0.16
24 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
ATATATATATATAAAATAATAA
Found at i:495501 original size:23 final size:24
Alignment explanation
Indices: 495470--495518 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
495460 ACCAAATGAA
495470 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
495493 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
495517 TA
1 TA
495519 AAAAATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:496013 original size:37 final size:37
Alignment explanation
Indices: 495972--496076 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
495962 GTGCTTGTGG
* * * *
495972 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
* * *
496009 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
*
496046 ATTCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
496077 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTAT
Found at i:497115 original size:106 final size:106
Alignment explanation
Indices: 496807--497953 Score: 1725
Period size: 106 Copynumber: 10.9 Consensus size: 106
496797 GCATTATTCC
* * * * *
496807 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * *
496872 TCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
496913 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T--G-AACT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * * *
496972 TCAACCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
497014 G-GTCCAAGATCCTTCATTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
497078 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
497119 GAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
497184 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
497225 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
497290 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
497331 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
497396 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
497437 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
497502 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
497543 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
497608 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
497649 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
497714 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
497755 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
497820 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
497861 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
497926 CCAGCGGTCCCTTCATTGTGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
497954 TGTTGTCTTG
Statistics
Matches: 955, Mismatches: 77, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
99 1 0.00
100 77 0.08
101 7 0.01
102 2 0.00
104 2 0.00
105 7 0.01
106 859 0.90
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:498797 original size:22 final size:22
Alignment explanation
Indices: 498771--498869 Score: 173
Period size: 22 Copynumber: 4.5 Consensus size: 22
498761 TTATGTTTGG
498771 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
498793 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
498815 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
498837 TCATAA-GTTTGGCATTTGATGC
1 TCA-AAGGTTTGGCATTTGATGC
*
498859 TCAATGGTTTG
1 TCAAAGGTTTG
498870 ATGGGGTAGC
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
21 1 0.01
22 71 0.96
23 2 0.03
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:499555 original size:172 final size:173
Alignment explanation
Indices: 499264--499610 Score: 592
Period size: 172 Copynumber: 2.0 Consensus size: 173
499254 TAAATAGGCC
*
499264 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
*
499329 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTAGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTAGGAAATG
499394 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* *
499439 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTTATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
*
499501 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTAGGAAATG
499566 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
499611 TTTTAGGGAA
Statistics
Matches: 165, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 14 0.08
172 100 0.61
174 1 0.01
175 50 0.30
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTAGGAAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:499678 original size:31 final size:30
Alignment explanation
Indices: 499643--499710 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
499633 TTTTTTGTCC
* *
499643 CTTTTTCTTTTTGATTTTTGTT-CTTGTTTCT
1 CTTTTT-TCTTTGATTTTTGTTGCTTCTTT-T
* *
499674 CTTTTTTCTTTGTTTTTTTTTGCTTCTTTT
1 CTTTTTTCTTTGATTTTTGTTGCTTCTTTT
499704 CTTTTTT
1 CTTTTTT
499711 GTTCTTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.78
Consensus pattern (30 bp):
CTTTTTTCTTTGATTTTTGTTGCTTCTTTT
Found at i:499685 original size:23 final size:26
Alignment explanation
Indices: 499659--499717 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 26
499649 CTTTTTGATT
499659 TTTGTTCTTGTTT-C-TCTTTT-TTC
1 TTTGTTCTTGTTTGCTTCTTTTCTTC
* * *
499682 TTTGTTTTTTTTTGCTTCTTTTCTTT
1 TTTGTTCTTGTTTGCTTCTTTTCTTC
499708 TTTGTTCTTG
1 TTTGTTCTTG
499718 ATTGGATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 11 0.39
24 1 0.04
25 6 0.21
26 10 0.36
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (26 bp):
TTTGTTCTTGTTTGCTTCTTTTCTTC
Found at i:499693 original size:32 final size:30
Alignment explanation
Indices: 499644--499720 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 30
499634 TTTTTGTCCC
* *
499644 TTTTTCTTTTTGATTTTTGTTCTTGTTTCTCT
1 TTTTTCTTTTTGATTTTT-TGCTTCTTT-TCT
*
499676 TTTTTCTTTGTT-TTTTTTTGCTTCTTTTCT
1 TTTTTCTTT-TTGATTTTTTGCTTCTTTTCT
* *
499706 TTTTTGTTCTTGATT
1 TTTTTCTTTTTGATT
499721 GGATCTTCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.05
30 12 0.32
31 7 0.19
32 14 0.38
33 2 0.05
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.77
Consensus pattern (30 bp):
TTTTTCTTTTTGATTTTTTGCTTCTTTTCT
Found at i:504294 original size:24 final size:25
Alignment explanation
Indices: 504245--504310 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 25
504235 GGAAAAAATG
* *
504245 AATAAATGAAAAAATAAAGAATAAA
1 AATAAATAAAAAAATAAAGAAGAAA
* * *
504270 AATCAGTAAAAAAATAAA-AGGAAA
1 AATAAATAAAAAAATAAAGAAGAAA
*
504294 AATAAATAAATAAATAA
1 AATAAATAAAAAAATAA
504311 TAATATAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (25 bp):
AATAAATAAAAAAATAAAGAAGAAA
Found at i:504318 original size:8 final size:8
Alignment explanation
Indices: 504298--504410 Score: 71
Period size: 10 Copynumber: 13.9 Consensus size: 8
504288 AGGAAAAATA
504298 AATA-AAT
1 AATATAAT
504305 AA-ATAAT
1 AATATAAT
504312 AATATAAT
1 AATATAAT
504320 ATATATATAT
1 A-ATATA-AT
504330 ATATATATAT
1 A-ATATA-AT
504340 ATATATATAT
1 A-ATATA-AT
504350 AATAT-AT
1 AATATAAT
504357 AAATGAGTAA-
1 -AAT-A-TAAT
504367 AATATAAT
1 AATATAAT
504375 AATCATAA-
1 AAT-ATAAT
*
504383 CA-ATAAT
1 AATATAAT
504390 AATATAAT
1 AATATAAT
504398 -ATA-AAT
1 AATATAAT
504404 AATATAA
1 AATATAA
504411 AAAAAAAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 27
0.76 0.02 0.23
Matches are distributed among these distances:
6 8 0.09
7 19 0.21
8 21 0.23
9 17 0.19
10 24 0.27
11 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (8 bp):
AATATAAT
Found at i:504325 original size:2 final size:2
Alignment explanation
Indices: 504313--504357 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
504303 ATAAATAATA
504313 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504353 AT AT A
1 AT AT A
504358 AATGAGTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:504647 original size:19 final size:19
Alignment explanation
Indices: 504589--504650 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
504579 TAATAAGCTT
*
504589 ATAAGTA-AAATATTTAAAA
1 ATAAGTATATATA-TTAAAA
504608 A-AAGTATATATATATATAAA
1 ATAAGTATATATAT-TA-AAA
504628 ATAA-TATATAGTATTAAAA
1 ATAAGTATATA-TATTAAAA
504647 ATAA
1 ATAA
504651 CCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 6 0.16
19 14 0.38
20 12 0.32
21 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAGTATATATATTAAAA
Found at i:504691 original size:23 final size:24
Alignment explanation
Indices: 504660--504708 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
504650 ACCAAATGAA
504660 TATAAATAAATAA-AAAATATA-TG
1 TATAAAT-AATAATAAAATATAGTG
* *
504683 TATAGATAATAATAATATATAGTG
1 TATAAATAATAATAAAATATAGTG
504707 TA
1 TA
504709 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAGTG
Found at i:505214 original size:37 final size:36
Alignment explanation
Indices: 505168--505268 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
505158 CTTGTGGATC
* * *
505168 CTATCTTTAGGAGTTTAAATCATAGTAGAATTCTA-T
1 CTAT-TTTAGGAGTTTGAATCCTAGTAGAATTATATT
* *
505204 CATATTTTTAGGAGTTTGAATCCTAGCAAAATTATATT
1 C-TA-TTTTAGGAGTTTGAATCCTAGTAGAATTATATT
505242 CTATTTTAGGAGTTTGAATCCTAGTAG
1 CTATTTTAGGAGTTTGAATCCTAGTAG
505269 GACAAAAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 23 0.42
37 29 0.53
38 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
CTATTTTAGGAGTTTGAATCCTAGTAGAATTATATT
Found at i:509341 original size:30 final size:31
Alignment explanation
Indices: 509287--509361 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
509277 TTGATGAATT
* * *
509287 AAATTTTAATTTAATCATTAAATTTTGGATA
1 AAATATTAATTTAATCACTAAATTTTAGATA
509318 AAATATTAATTTAATC-CTAAATTTTAGATA
1 AAATATTAATTTAATCACTAAATTTTAGATA
509348 AAATATTAATTTAA
1 AAATATTAATTTAA
509362 CTCGTATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 26 0.63
31 15 0.37
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATATTAATTTAATCACTAAATTTTAGATA
Found at i:514922 original size:15 final size:16
Alignment explanation
Indices: 514902--514940 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
514892 GTTTACTTCA
514902 GAATGATT-AAACGCT
1 GAATGATTCAAACGCT
*
514917 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
514933 GAATGATT
1 GAATGATT
514941 TAGAGGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:515041 original size:23 final size:23
Alignment explanation
Indices: 515015--515059 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
515005 AATGTACTTC
* *
515015 TTTGCTGAATCATTCAACACTGT
1 TTTGCTAAATCAGTCAACACTGT
* *
515038 TTTGTTAAATCAGTCAGCACTG
1 TTTGCTAAATCAGTCAACACTG
515060 AATCATTCAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (23 bp):
TTTGCTAAATCAGTCAACACTGT
Found at i:515441 original size:122 final size:125
Alignment explanation
Indices: 515294--515552 Score: 393
Period size: 124 Copynumber: 2.1 Consensus size: 125
515284 AGACGGTACC
* *
515294 GATTTTGTTATTGTTGTACATAAC-AAACCGGTAAAAA-TACCGAAAACATCATTAATTCTA-CT
1 GATTTTGTTATTGTTGTACATAACAAAACCGATAAAAATTACCAAAAACATCATTAATTCTACCT
*
515356 GGTTTTGTTATTATTTTGGCATTTTACCT-GGTTTCTTAACAAAATCGGTAAAA-CGCTACT
66 -GTTTTGTTATTATTTTGGCATTTTA-CTGGGTTTCTTAACAAAACCGGTAAAAGCGCTACT
* * *
515416 GGTTTTGTTATTGTTGTGCATAACAAAACCGATAAAAATTACCAAAAACATCATTATTTCTACCT
1 GATTTTGTTATTGTTGTACATAACAAAACCGATAAAAATTACCAAAAACATCATTAATTCTACCT
*
515481 GTTTTGTTATTATTTTGGTATTTTACTGGGTTTCTTAACAAAACCGGTAAAAGCGCTACT
66 GTTTTGTTATTATTTTGGCATTTTACTGGGTTTCTTAACAAAACCGGTAAAAGCGCTACT
*
515541 TATTTTGTTATT
1 GATTTTGTTATT
515553 TTTTACCGAT
Statistics
Matches: 123, Mismatches: 9, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
122 22 0.18
123 14 0.11
124 68 0.55
125 19 0.15
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (125 bp):
GATTTTGTTATTGTTGTACATAACAAAACCGATAAAAATTACCAAAAACATCATTAATTCTACCT
GTTTTGTTATTATTTTGGCATTTTACTGGGTTTCTTAACAAAACCGGTAAAAGCGCTACT
Found at i:516255 original size:3 final size:3
Alignment explanation
Indices: 516249--516296 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
516239 TTTTTAATAA
** * *
516249 TAT TAT TAT TAT CGT TGT TAT TAT TAT TAT TAT TAT TAT AAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
516296 T
1 T
516297 TACATTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:517641 original size:72 final size:72
Alignment explanation
Indices: 517524--517676 Score: 288
Period size: 72 Copynumber: 2.1 Consensus size: 72
517514 TTTTGGCCAC
517524 TGTTTTATGGGTTAATAATGATTTAGATACCTATATCTTTACCAGGTTTTACATTATAGTCATCA
1 TGTTTTATGGGTTAATAATGATTTAGATACCTATATCTTTACCAGGTTTTACATTATAGTCATCA
*
517589 GGAGGCT
66 AGAGGCT
517596 TGTTTTATGGGTTAATAATGATTTAGATACCTATATCTTTACCAGGTTTTACATTATAGTCATCA
1 TGTTTTATGGGTTAATAATGATTTAGATACCTATATCTTTACCAGGTTTTACATTATAGTCATCA
517661 AGAGGCT
66 AGAGGCT
*
517668 TATTTTATG
1 TGTTTTATG
517677 CGTTTGTTCT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 79 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (72 bp):
TGTTTTATGGGTTAATAATGATTTAGATACCTATATCTTTACCAGGTTTTACATTATAGTCATCA
AGAGGCT
Found at i:518080 original size:2 final size:2
Alignment explanation
Indices: 518073--518106 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
518063 TTGAATGTTC
518073 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
518107 TACCAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519832 original size:30 final size:32
Alignment explanation
Indices: 519796--519855 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
519786 TCTTACCAAT
519796 ACTAACTAATTT-TT-TCTTTTGTTTGTGTAC
1 ACTAACTAATTTCTTCTCTTTTGTTTGTGTAC
**
519826 ACTAACTTGTTTCTTCTCTTTTGTTTGTGT
1 ACTAACTAATTTCTTCTCTTTTGTTTGTGT
519856 TATTTTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
32 14 0.54
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (32 bp):
ACTAACTAATTTCTTCTCTTTTGTTTGTGTAC
Found at i:524065 original size:36 final size:37
Alignment explanation
Indices: 524014--524086 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
524004 TGAGAATTTT
* * *
524014 AAAATAAATTTTTGTCTCGCTTGAGACAATTTCTCTC
1 AAAACAAATTTTTGTCTCACATGAGACAATTTCTCTC
* *
524051 AAAACAAA-TTTTGTCTCACATGAGACATTTTTTCTC
1 AAAACAAATTTTTGTCTCACATGAGACAATTTCTCTC
524087 TCTGAGATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (37 bp):
AAAACAAATTTTTGTCTCACATGAGACAATTTCTCTC
Found at i:524365 original size:25 final size:25
Alignment explanation
Indices: 524315--524379 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
524305 GAGATAGTTT
*
524315 CTCTTAAATAAATCTTTGAGTCTGTTC
1 CTCTTAAA-AAA-ATTTGAGTCTGTTC
* * *
524342 CTTTTAAAAAAATTTGAGTTTGTTT
1 CTCTTAAAAAAATTTGAGTCTGTTC
*
524367 CTCTTAACAAAAT
1 CTCTTAAAAAAAT
524380 CATCTTTGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 22 0.69
26 3 0.09
27 7 0.22
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (25 bp):
CTCTTAAAAAAATTTGAGTCTGTTC
Found at i:524858 original size:28 final size:28
Alignment explanation
Indices: 524827--524908 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 28
524817 GAAACACATT
524827 ATCTTTGAGTTGGCTTT-TCTTGAAACAA
1 ATCTTTGAGTTGG-TTTCTCTTGAAACAA
*
524855 ATCTTTGAGTCT-GTTTCTTTTGAAACAA
1 ATCTTTGAGT-TGGTTTCTCTTGAAACAA
*
524883 ATCTTTGAGTCGGTTTCTCTTGAAAC
1 ATCTTTGAGTTGGTTTCTCTTGAAAC
524909 CATAATCCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.06
28 44 0.92
29 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTTCTCTTGAAACAA
Found at i:525045 original size:53 final size:53
Alignment explanation
Indices: 524913--525063 Score: 198
Period size: 53 Copynumber: 2.8 Consensus size: 53
524903 TGAAACCATA
* *
524913 ATCCCTAAATAT-GTCCAGCCATCCTCATCACGTAAAAACTGTATTATCTACATT
1 ATCCCTAAATATGGT-CAGCCATCCTCATCACGT-AGAACTGTGTTATCTACATT
* *
524967 ATCCCTAAATATGG-CTAGCCGTCCTCATCACGTAGAACTGTGTTATCTACCTT
1 ATCCCTAAATATGGTC-AGCCATCCTCATCACGTAGAACTGTGTTATCTACATT
* *
525020 ATCCCTAAAGATGGTCAGCCATCCTCATCACGTAGGAACCGTGT
1 ATCCCTAAATATGGTCAGCCATCCTCATCACGTA-GAACTGTGT
525064 CATCCCCCGA
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
53 48 0.56
54 37 0.43
55 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (53 bp):
ATCCCTAAATATGGTCAGCCATCCTCATCACGTAGAACTGTGTTATCTACATT
Found at i:525420 original size:16 final size:16
Alignment explanation
Indices: 525380--525429 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
525370 GGTATTACCC
525380 GACCTGTTTTCAA-CT
1 GACCTGTTTTCAACCT
*
525395 GACTTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
525411 GACCTATTTTTAACCT
1 GACCTGTTTTCAACCT
525427 GAC
1 GAC
525430 TGTAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:526175 original size:20 final size:19
Alignment explanation
Indices: 526152--526242 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 19
526142 GGTTACATAT
*
526152 ATAGTTTATATAACATATAA
1 ATAGTTTATAT-ACATATAC
526172 ATAGATTGTATATATACATATAC
1 ATAG--T-T-TATATACATATAC
*
526195 TATAGGTTATAT--ATATAC
1 -ATAGTTTATATACATATAC
526213 ATAGTTTATATACATTATAC
1 ATAGTTTATATACA-TATAC
526233 ATAGTTTATA
1 ATAGTTTATA
526243 CATACATGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
17 10 0.17
18 6 0.10
19 1 0.02
20 24 0.40
21 1 0.02
22 1 0.02
23 8 0.13
24 9 0.15
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (19 bp):
ATAGTTTATATACATATAC
Found at i:526187 original size:24 final size:24
Alignment explanation
Indices: 526158--526215 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
526148 ATATATAGTT
*
526158 TATATA-ACATATA-AATAGATTG
1 TATATATACATATACAATAGATTA
* *
526180 TATATATACATATACTATAGGTTA
1 TATATATACATATACAATAGATTA
526204 TATATATACATA
1 TATATATACATA
526216 GTTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
TATATATACATATACAATAGATTA
Found at i:526462 original size:2 final size:2
Alignment explanation
Indices: 526455--526483 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
526445 TTATATGATT
526455 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
526484 CATAGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:526535 original size:18 final size:18
Alignment explanation
Indices: 526512--526582 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
526502 GTACTATAAG
526512 TTACATATATAGTTTACA
1 TTACATATATAGTTTACA
* * *
526530 TTACATGTATACATATACTATAA
1 TTACATATATA-GT-T--TA-CA
526553 GTTACATATATAGTTTACA
1 -TTACATATATAGTTTACA
*
526572 TTACATGTATA
1 TTACATATATA
526583 CACATACTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 20 0.50
19 2 0.05
20 3 0.08
22 3 0.08
23 2 0.05
24 10 0.25
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.42
Consensus pattern (18 bp):
TTACATATATAGTTTACA
Found at i:526543 original size:42 final size:42
Alignment explanation
Indices: 526496--526605 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
526486 TAGTTTATAC
*
526496 ATACATGTACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
526538 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
526580 ATACACATACTATAAGTTACATATAT
1 ATACATATACTATAAGTTACATATAT
526606 TAACTATTGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
Found at i:526557 original size:24 final size:24
Alignment explanation
Indices: 526530--526601 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
526520 ATAGTTTACA
526530 TTACATGTATACATATACTATAAG
1 TTACATGTATACATATACTATAAG
* * *
526554 TTACATATATA-GT-T--TA-CA-
1 TTACATGTATACATATACTATAAG
*
526572 TTACATGTATACACATACTATAAG
1 TTACATGTATACATATACTATAAG
526596 TTACAT
1 TTACAT
526602 ATATTAACTA
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
18 10 0.29
19 1 0.03
20 3 0.09
22 3 0.09
23 2 0.06
24 16 0.46
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (24 bp):
TTACATGTATACATATACTATAAG
Found at i:526730 original size:7 final size:7
Alignment explanation
Indices: 526720--526768 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
526710 AGTTTATAAA
526720 GTTTAGG
1 GTTTAGG
526727 GTTTAGG
1 GTTTAGG
*
526734 ATTTAGG
1 GTTTAGG
*
526741 GTTTAAG
1 GTTTAGG
526748 GTTTAGG
1 GTTTAGG
* *
526755 ATATAGG
1 GTTTAGG
526762 GTTTAGG
1 GTTTAGG
526769 ATTTTTATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:526744 original size:21 final size:21
Alignment explanation
Indices: 526720--526768 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
526710 AGTTTATAAA
*
526720 GTTTAGGGTTTAGGATTTAGG
1 GTTTAGGGTTTAGGATATAGG
*
526741 GTTTAAGGTTTAGGATATAGG
1 GTTTAGGGTTTAGGATATAGG
526762 GTTTAGG
1 GTTTAGG
526769 ATTTTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
GTTTAGGGTTTAGGATATAGG
Found at i:526988 original size:2 final size:2
Alignment explanation
Indices: 526826--526980 Score: 171
Period size: 2 Copynumber: 79.0 Consensus size: 2
526816 TGTTTCTTTA
526826 AT AT AT AT AT AT AT AT AT -T 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
526867 AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
526908 AT A- AT -T AT AC AT AT AA ACT AT AT AT TT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
526949 AGT -T TT AT AT AT AT AC ACT AT AT AT AT A- AT AT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
526981 TTTATATACT
Statistics
Matches: 131, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
1 7 0.05
2 119 0.91
3 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:526994 original size:39 final size:37
Alignment explanation
Indices: 526828--527010 Score: 158
Period size: 35 Copynumber: 4.9 Consensus size: 37
526818 TTTCTTTAAT
* *
526828 ATATATATATATATATTATATATATATATATATATAT-
1 ATAT-TATATATATTTTATATATATACATATATATATA
* *
526865 ATATTATATATA-TATATATATATATATATATATATA
1 ATATTATATATATTTTATATATATACATATATATATA
* * * * * *
526901 CTATAATATA-ATTATACATATAAAC-TATATATTTA
1 ATATTATATATATTTTATATATATACATATATATATA
*
526936 TATATACATATATAGTTTTATATATATACACTATATATATA
1 -ATAT-TATATATA-TTTTATATATATACA-TATATATATA
* *
526977 ATATTTTATATACTTTTATAGTTTATACATATAT
1 ATATTATATATA-TTTTATA-TATATACATATAT
527011 TTACATGGTT
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
35 31 0.26
36 29 0.24
37 9 0.08
38 1 0.01
39 29 0.24
40 11 0.09
41 9 0.08
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (37 bp):
ATATTATATATATTTTATATATATACATATATATATA
Found at i:527077 original size:90 final size:90
Alignment explanation
Indices: 526981--527166 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 90
526971 TATATAATAT
* * * * *
526981 TTTATATACTTTTATAGTTTATACA-TATATTTACATGGTTTATATATA-TTCACATAAACATAA
1 TTTATATAATTATATAGTTT-TA-ATTATATATACATAGTTTATATATAGTGCACAT-AA-ATAA
527044 TTTATATAT-AACT-TAATAATTATATAG
62 TTTATATATGAACTATAATAATTATATAG
*
527071 TTTATATAATTATATAGTTTTAATTTTATATACATAGTTTATATATAGTGCACATAAATAATTTA
1 TTTATATAATTATATAGTTTTAATTATATATACATAGTTTATATATAGTGCACATAAATAATTTA
***
527136 TATATGGTTTATAATAATTATATAG
66 TATATGAACTATAATAATTATATAG
527161 TTTATA
1 TTTATA
527167 ATATAAATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 14 0.17
89 25 0.30
90 44 0.53
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (90 bp):
TTTATATAATTATATAGTTTTAATTATATATACATAGTTTATATATAGTGCACATAAATAATTTA
TATATGAACTATAATAATTATATAG
Found at i:527196 original size:20 final size:19
Alignment explanation
Indices: 527128--527197 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 19
527118 GTGCACATAA
*
527128 ATAA-TTTATATATGGTTT
1 ATAATTTTATATATAGTTT
**
527146 ATAATAAT-TATATAGTTT
1 ATAATTTTATATATAGTTT
* *
527164 ATAA-TATAAATATAGTTT
1 ATAATTTTATATATAGTTT
527182 ATATATTTTATATATA
1 ATA-ATTTTATATATA
527198 TATATATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 2 0.05
18 29 0.71
19 2 0.05
20 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
ATAATTTTATATATAGTTT
Found at i:527218 original size:28 final size:27
Alignment explanation
Indices: 527153--527205 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
527143 TTTATAATAA
*
527153 TTATATAGTTTATAATATAAATATAGT
1 TTATATATTTTATAATATAAATATAGT
*
527180 TTATATATTTTATATATATATATATA
1 TTATATATTTTATA-ATATAAATATA
527206 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
TTATATATTTTATAATATAAATATAGT
Found at i:528366 original size:3 final size:3
Alignment explanation
Indices: 528360--528410 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
528350 TTTTTAATAA
** *
528360 TAT TAT TAT TAT CGT TAT T-T TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
528407 TAT T
1 TAT T
528411 TTAATTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:530077 original size:2 final size:2
Alignment explanation
Indices: 530070--530095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
530060 TTGAATGTTC
530070 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
530096 TACCAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:531160 original size:64 final size:64
Alignment explanation
Indices: 531087--531220 Score: 216
Period size: 64 Copynumber: 2.1 Consensus size: 64
531077 AAATATGTCA
*
531087 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCC-GATTAAATGCCTATTTTATT
1 ATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCCAG-TTAAATGCCTATTTTATT
* * *
531151 ATATAAGCGCTACCTAATATATTATTTTATTTGATAATATTTTCAGTTAAATGCCTATTTTATT
1 ATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCCAGTTAAATGCCTATTTTATT
531215 ATATAA
1 ATATAA
531221 ACCTTACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
64 64 0.98
65 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.46
Consensus pattern (64 bp):
ATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCCAGTTAAATGCCTATTTTATT
Found at i:531229 original size:64 final size:64
Alignment explanation
Indices: 531087--531239 Score: 202
Period size: 64 Copynumber: 2.4 Consensus size: 64
531077 AAATATGTCA
* * *
531087 ATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGATTAAATGCCTATTTTATT
1 ATATAAACGCTACCTAATATATTATTGTACTTGATAATATTTCAGATTAAATGCCTATTTTATT
* * *
531151 ATATAAGCGCTACCTAATATATTATTTTATTTGATAATATTTTCAG-TTAAATGCCTATTTTATT
1 ATATAAACGCTACCTAATATATTATTGTACTTGATAATA-TTTCAGATTAAATGCCTATTTTATT
* *
531215 ATATAAAC-CTTACCTATTACATTAT
1 ATATAAACGC-TACCTAATATATTAT
531240 ATAAGTGATA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 1 0.01
64 74 0.93
65 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (64 bp):
ATATAAACGCTACCTAATATATTATTGTACTTGATAATATTTCAGATTAAATGCCTATTTTATT
Found at i:532627 original size:21 final size:21
Alignment explanation
Indices: 532601--532641 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
532591 TTCCAGATTC
532601 GCAACGCGAACTTCGACTATT
1 GCAACGCGAACTTCGACTATT
*
532622 GCAACGCGAACTTGGACTAT
1 GCAACGCGAACTTCGACTAT
532642 CACAATGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
GCAACGCGAACTTCGACTATT
Found at i:532822 original size:6 final size:6
Alignment explanation
Indices: 532811--532835 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
532801 GACACGTATT
532811 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
532836 GACAACCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:532845 original size:17 final size:18
Alignment explanation
Indices: 532823--532857 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
532813 CACGACCACG
532823 ACCACGAC-CACGAGACA
1 ACCACGACACACGAGACA
*
532840 ACCACGACAGACGAGACA
1 ACCACGACACACGAGACA
532858 GACGGCGGCG
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:0.43, C:0.37, G:0.20, T:0.00
Consensus pattern (18 bp):
ACCACGACACACGAGACA
Found at i:533388 original size:19 final size:19
Alignment explanation
Indices: 533364--533420 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
533354 TCGTTGCGAT
533364 TTTGGACTATCGCAATGAA
1 TTTGGACTATCGCAATGAA
** *
533383 TTTGGAAAATCGCAACGCGAA
1 TTTGGACTATCGCAA--TGAA
*
533404 CTTGGACTATCGCAATG
1 TTTGGACTATCGCAATG
533421 CGAATATGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TTTGGACTATCGCAATGAA
Found at i:547297 original size:11 final size:11
Alignment explanation
Indices: 547283--547312 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
547273 TCATCTTCTT
547283 TTTTCTCTAGA
1 TTTTCTCTAGA
547294 TTTTCTCTAGA
1 TTTTCTCTAGA
547305 TTTTCTCT
1 TTTTCTCT
547313 TTTCTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (11 bp):
TTTTCTCTAGA
Found at i:547746 original size:24 final size:24
Alignment explanation
Indices: 547719--547785 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
547709 AATAATTCAA
547719 GAGTTCGACTGAAGCTCGAGACTC
1 GAGTTCGACTGAAGCTCGAGACTC
547743 GAGTTCGACT-AGAGCTCGAGACTC
1 GAGTTCGACTGA-AGCTCGAGACTC
*
547767 GAGCTCGACTGAAGCTCGA
1 GAGTTCGACTGAAGCTCGA
547786 TTTTGAGCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.19
Consensus pattern (24 bp):
GAGTTCGACTGAAGCTCGAGACTC
Found at i:547750 original size:13 final size:13
Alignment explanation
Indices: 547731--547774 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
547721 GTTCGACTGA
547731 AGCTCGAGACTCG
1 AGCTCGAGACTCG
* *
547744 AGTTC--GACTAG
1 AGCTCGAGACTCG
547755 AGCTCGAGACTCG
1 AGCTCGAGACTCG
547768 AGCTCGA
1 AGCTCGA
547775 CTGAAGCTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (13 bp):
AGCTCGAGACTCG
Done.