Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:803116 original size:54 final size:54
Alignment explanation
Indices: 803039--803141 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
803029 AATTGGCACA
* * * *
803039 ATGTGTGCAACCTAAGAAATTCATAATGATTTTATGAATTTCCGTATTGACAAT
1 ATGTGTGCAACCCAAGAAATTCATAATGAGTTTATAAATTACCGTATTGACAAT
* *
803093 ATGTGTGCAACCCACGTAATTCATAATGAGTTTATAAATTACCGTATTG
1 ATGTGTGCAACCCAAGAAATTCATAATGAGTTTATAAATTACCGTATTG
803142 GCACAAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (54 bp):
ATGTGTGCAACCCAAGAAATTCATAATGAGTTTATAAATTACCGTATTGACAAT
Found at i:803233 original size:54 final size:53
Alignment explanation
Indices: 803150--803520 Score: 447
Period size: 54 Copynumber: 6.9 Consensus size: 53
803140 TGGCACAAGA
* **
803150 AATTCAAAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCACAT
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCA-AT
* *
803204 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCTAAGA
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCAA-T
* * ** *
803258 AATTAATAACGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCATGT
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCA-AT
* * * * * *
803312 AATTCATAACGAGTTTATGAATTACCGTATTGGCACTATGTATGCATCCTAAGA
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCAA-T
* * *
803366 AATTCATAATGAATTTATGAATT-TTCGTATTGGCACTATGTTTGCAACCCACAT
1 AATTCATAATGAGTTTATGAATTACT-GTATTGGCACTATGTGTGCAACCCA-AT
* *
803420 ACTTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCTAAGT
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCAA-T
* * * *
803474 AATTCATAATGATTTTATGAATTACCGTATTGACACTATGTATGCAA
1 AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAA
803521 AGCCACCGAA
Statistics
Matches: 271, Mismatches: 39, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
53 2 0.01
54 267 0.99
55 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (53 bp):
AATTCATAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCCAAT
Found at i:803335 original size:108 final size:108
Alignment explanation
Indices: 803146--803543 Score: 555
Period size: 108 Copynumber: 3.7 Consensus size: 108
803136 GTATTGGCAC
*
803146 AAGAAATTCAA-AATGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCACATAATTCA
1 AAGAAATT-AATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCACATAATTCA
803210 TAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
65 TAATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
* * **
803254 AAGAAATTAATAACGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCATGTAATTCAT
1 AAGAAATTAATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCACATAATTCAT
* * * *
803319 AACGAGTTTATGAATTACCGTATTGGCACTATGTATGCATCCT
66 AATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
* * * *
803362 AAGAAATTCATAATGAATTTATGAATTTTCGTATTGGCACTATGTTTGCAACCCACATACTTCAT
1 AAGAAATTAATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCACATAATTCAT
803427 AATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
66 AATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
* * * ** * * * ** *
803470 AAGTAATTCATAATGATTTTATGAATTACCGTATTGACACTATGTATGCAAAGCCACCGAATTTA
1 AAGAAATTAATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGC-AACCCACATAATTCA
803535 TAATGAGTT
65 TAATGAGTT
803544 GTAATATTCA
Statistics
Matches: 258, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
107 2 0.01
108 237 0.92
109 19 0.07
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (108 bp):
AAGAAATTAATAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCCACATAATTCAT
AATGAGTTTATGAATTACTGTATTGGCACTATGTGTGCAACCT
Found at i:804241 original size:21 final size:22
Alignment explanation
Indices: 804207--804248 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
804197 TTTAAATATT
804207 ATAAAGGAAGTATCGATACTCA
1 ATAAAGGAAGTATCGATACTCA
804229 ATAAAGG-AGTATCGATACTC
1 ATAAAGGAAGTATCGATACTC
804249 CCTCTCCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (22 bp):
ATAAAGGAAGTATCGATACTCA
Found at i:805032 original size:75 final size:75
Alignment explanation
Indices: 804903--805102 Score: 319
Period size: 75 Copynumber: 2.7 Consensus size: 75
804893 CCAAAAATTC
* *
804903 CAGATTGCTCAGAGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCTGAATAGTTTGGCT
1 CAGAATGCTCAGAGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCACTGAATAGTTTGGCT
804968 CTGAGAAAAA
66 CTGAGAAAAA
* *
804978 CAGAATGCTCAGAGGGAATCGATTCCCCCCCAAGGGGGTACCGATTCCCACTGAATGGTTTGGCT
1 CAGAATGCTCAGAGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCACTGAATAGTTTGGCT
805043 CTGAGAAAAA
66 CTGAGAAAAA
* * * *
805053 TAGAATGCTCGGAGGGAACCGATTTCCCCCCCAAGAGGGTATCGATTCCC
1 CAGAATGCTCAGAGGGAACCGA-TTCCCCCCCAAGGGGGTACCGATTCCC
805103 CCTGTTTAAC
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 90 0.78
76 25 0.22
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.20
Consensus pattern (75 bp):
CAGAATGCTCAGAGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCACTGAATAGTTTGGCT
CTGAGAAAAA
Found at i:807265 original size:298 final size:291
Alignment explanation
Indices: 806589--807174 Score: 883
Period size: 298 Copynumber: 2.0 Consensus size: 291
806579 AGTTGCTCTC
* * * * *
806589 AAATCCACAAAAGATGAGAGTGATTCGAATGAAGATGACGATGACGAGGAAATGGCATTGTTTAC
1 AAAT-CACAAAAGATGAGAGTGATTCGAAGGAAGATGAAGATAACCACGAAAT-GCATTGTTTA-
*
806654 TAAACGGTTCAG-AAAA--ATGAGACCTTACCGAGGAAGAAAATTCAAACGAAATTAAGGCCTCA
63 TAAACGATTCAGAAAAATGATGAGACCTTACCGAGGAAGAAAATTCAAACGAAATTAAGGCCTCA
806716 AAAATGAACTAAAGAGAAGGACCCGACATTTGCTATGAATGCAAAAAGCGGGGCATGTCAAATAT
128 AAAATGAACTAAAGAGAAGGACCCGACATTTGCTATGAATGCAAAAAGCGGGGCATGTCAAATAT
806781 GATTACCACAATTGAAGAGAAAGGGTCAATCAAAGAATAAGCACAAGGCTCATGTGGCTACATGG
193 GATTACCACAATTGAAGAGAAAGGGTCAATCAAAGAATAAGCACAAGGCTCATGTGGCTACATGG
* ** ** *
806846 AGTGATGAAGAAGGTTCCGATTGGAGTTGCTCTC
258 AGTGATGAAGAAGGTTCCGATTGAAGAGGAACTA
* * * * *
806880 AAATCCACAAAAGATGAGAGTGATTCGAATGAAGATGACGATGACGAGGAAATGGCATTGTTTAC
1 AAAT-CACAAAAGATGAGAGTGATTCGAAGGAAGATGAAGATAACCACGAAAT-GCATTGTTTA-
* *
806945 TAAACGGTTCAGAAAAATGATGAGACCTTACCGAGGAAGAAAATTCAAATGAAATTAAGGCCTCA
63 TAAACGATTCAGAAAAATGATGAGACCTTACCGAGGAAGAAAATTCAAACGAAATTAAGGCCTCA
807010 AAAATGAACTAAAAGAGAAGGACCCGATCATTTGCTATGAATGCAAAAAGCCGGGGCATGTCAAA
128 AAAATGAACT-AAAGAGAAGGACCCGA-CATTTGCTATGAATGCAAAAAG-CGGGGCATGTCAAA
807075 TATGATTACCCACAATTGAAGAGAAAGGGTCAATCAAAGAATAAGCACAAGGCTCATGTGGCTAC
190 TATGATTA-CCACAATTGAAGAGAAAGGGTCAATCAAAGAATAAGCACAAGGCTCATGTGGCTAC
807140 ATGGAGTGATGAAGAAGGTTCCGA-TGAAGAGGAAC
254 ATGGAGTGATGAAGAAGGTTCCGATTGAAGAGGAAC
807175 AAGAAGTAGC
Statistics
Matches: 282, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
291 77 0.27
292 4 0.01
294 55 0.20
295 16 0.06
296 22 0.08
297 28 0.10
298 80 0.28
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (291 bp):
AAATCACAAAAGATGAGAGTGATTCGAAGGAAGATGAAGATAACCACGAAATGCATTGTTTATAA
ACGATTCAGAAAAATGATGAGACCTTACCGAGGAAGAAAATTCAAACGAAATTAAGGCCTCAAAA
ATGAACTAAAGAGAAGGACCCGACATTTGCTATGAATGCAAAAAGCGGGGCATGTCAAATATGAT
TACCACAATTGAAGAGAAAGGGTCAATCAAAGAATAAGCACAAGGCTCATGTGGCTACATGGAGT
GATGAAGAAGGTTCCGATTGAAGAGGAACTA
Found at i:811040 original size:18 final size:18
Alignment explanation
Indices: 811015--811069 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
811005 CGATGAACCA
811015 GAAC-AGCACGAGCAGAG
1 GAACAAGCACGAGCAGAG
811032 GAACAAGCACGAGCAGAG
1 GAACAAGCACGAGCAGAG
* *
811050 GAACAAGCACAACCAGAG
1 GAACAAGCACGAGCAGAG
811068 GA
1 GA
811070 TCAAATGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 4 0.11
18 31 0.89
ACGTcount: A:0.45, C:0.24, G:0.31, T:0.00
Consensus pattern (18 bp):
GAACAAGCACGAGCAGAG
Found at i:813033 original size:4 final size:4
Alignment explanation
Indices: 813024--813048 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
813014 TTTTTCAAAC
813024 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
813049 TTCTCTCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:814086 original size:24 final size:25
Alignment explanation
Indices: 814020--814086 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
814010 CATATATATG
*
814020 TTTATTTAATTTATATTATGTTGTTTT
1 TTTATTT--TTTATATTATGTTGTTAT
814047 TTTACTTTTTT-TATTAT-TTGTTAT
1 TTTA-TTTTTTATATTATGTTGTTAT
*
814071 TTTATTTTTTAAATTA
1 TTTATTTTTTATATTA
814087 GATTGTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 6 0.17
24 14 0.39
25 6 0.17
26 3 0.08
27 4 0.11
28 3 0.08
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTATTTTTTATATTATGTTGTTAT
Found at i:815859 original size:24 final size:22
Alignment explanation
Indices: 815832--815878 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
815822 GTATGGGTAG
815832 TGCATCGACGCACATGTTAAGGGA
1 TGCATCGA--CACATGTTAAGGGA
*
815856 TGCATCGATACATGTTAAGGGA
1 TGCATCGACACATGTTAAGGGA
815878 T
1 T
815879 AGATTAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (22 bp):
TGCATCGACACATGTTAAGGGA
Found at i:817282 original size:23 final size:23
Alignment explanation
Indices: 817251--817322 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
817241 AGGGACATTT
* *
817251 TATAGGGCACTTCAGTGCAATTC
1 TATACGGCACTTCGGTGCAATTC
*
817274 TATACGGCACTTTGGTGCAATTC
1 TATACGGCACTTCGGTGCAATTC
**
817297 TATGTGGCACTTCGGTGC-ATT-
1 TATACGGCACTTCGGTGCAATTC
817318 TATAC
1 TATAC
817323 AAGCTGTGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 3 0.07
22 3 0.07
23 35 0.85
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (23 bp):
TATACGGCACTTCGGTGCAATTC
Found at i:821770 original size:2 final size:2
Alignment explanation
Indices: 821728--821758 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
821718 AGGTAAAATG
821728 AT 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 AT A
821759 ACCTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:822295 original size:23 final size:23
Alignment explanation
Indices: 822260--822327 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
822250 CATTTTATAT
*
822260 GGCACTTTGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
822283 GGCACTTCAGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
*
822306 GGCACTTCGGTGCATTTCTACG
1 GGCACTTCGGTGCAATTCTACG
822328 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:824221 original size:18 final size:18
Alignment explanation
Indices: 824194--824241 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
824184 CAGCTTGGAG
*
824194 TGATGAAGATGACTCCAA
1 TGATGCAGATGACTCCAA
824212 TGATGCAGATGACTCCAA
1 TGATGCAGATGACTCCAA
*
824230 TGATGCATATGA
1 TGATGCAGATGA
824242 AATAGCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (18 bp):
TGATGCAGATGACTCCAA
Found at i:830172 original size:24 final size:24
Alignment explanation
Indices: 830145--830193 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
830135 TCGTACTCTA
830145 TAAACCTCAAGGGTGCTGCAGTAT
1 TAAACCTCAAGGGTGCTGCAGTAT
830169 TAAACCTCAAGGGTGCTGCAGTAT
1 TAAACCTCAAGGGTGCTGCAGTAT
830193 T
1 T
830194 TAAAACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (24 bp):
TAAACCTCAAGGGTGCTGCAGTAT
Found at i:830389 original size:28 final size:28
Alignment explanation
Indices: 830331--830394 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
830321 TCCAGGGCTT
*
830331 GGGGTATTTTAGGTTATTTTACACTTCA
1 GGGGTATTTTAGGTTATTTTACAATTCA
*
830359 GGGGTATTTT-GGTTATTTTATAATTCA
1 GGGGTATTTTAGGTTATTTTACAATTCA
*
830386 AGGGTATTT
1 GGGGTATTT
830395 CAAACCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
GGGGTATTTTAGGTTATTTTACAATTCA
Found at i:834748 original size:21 final size:21
Alignment explanation
Indices: 834655--834744 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
834645 AATAATTTTC
* * *
834655 TTCATGAAAAGATTAAATCCT
1 TTCATTAAAAGGTTAAGTCCT
* *
834676 TTCATAAAAAGGTTAAGCCCT
1 TTCATTAAAAGGTTAAGTCCT
* *
834697 TTCATCAAAAGGATAAGTCCT
1 TTCATTAAAAGGTTAAGTCCT
* *
834718 TTAATTGAAAGGTTAAGTCCT
1 TTCATTAAAAGGTTAAGTCCT
834739 TTCATT
1 TTCATT
834745 GAAATGTCTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (21 bp):
TTCATTAAAAGGTTAAGTCCT
Found at i:835993 original size:30 final size:31
Alignment explanation
Indices: 835959--836038 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 31
835949 TATCATATCT
* *
835959 TTAATATTTATAAATATTA-AAAAAA-TATAA
1 TTAATA-TTATAAACATAACAAAAAATTATAA
835989 TTAATATTATAAACATAACAAAAAATTATAACA
1 TTAATATTATAAACATAACAAAAAATTAT-A-A
836022 TAATAATATTATAAACA
1 T--TAATATTATAAACA
836039 AAAAATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 10 0.24
30 12 0.29
31 3 0.07
32 1 0.02
33 2 0.05
35 14 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (31 bp):
TTAATATTATAAACATAACAAAAAATTATAA
Found at i:836139 original size:17 final size:17
Alignment explanation
Indices: 836113--836150 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
836103 CTAATTATAT
*
836113 ATTTTTATTATGATTTA
1 ATTTTGATTATGATTTA
836130 ATTTTGATTATGATTTA
1 ATTTTGATTATGATTTA
836147 ATTT
1 ATTT
836151 AAAATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (17 bp):
ATTTTGATTATGATTTA
Found at i:836681 original size:60 final size:60
Alignment explanation
Indices: 836603--836758 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 60
836593 AGAATATTAT
836603 TTTGTTGAGTCCT-AACTATTAAACGTTACAAAATGGTCCCCCAATTATATAGAGTTG-C
1 TTTGTTGAGTCCTCAACTATTAAACGTTACAAAATGGTCCCCCAATTATATAGAGTTGCC
* * * *
836661 TTTGTTGAGTCCCTCAACTATTAAACGTTGCAAAATGTTCCCCCGATTATATGGAGTTGCC
1 TTTGTTGAGT-CCTCAACTATTAAACGTTACAAAATGGTCCCCCAATTATATAGAGTTGCC
* * * *
836722 ATT-TTGAGTTCCTCGACTATTAAAAGTTCCAAAATGG
1 TTTGTTGAG-TCCTCAACTATTAAACGTTACAAAATGG
836759 CCACCCGACT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 10 0.12
59 3 0.04
60 68 0.80
61 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
TTTGTTGAGTCCTCAACTATTAAACGTTACAAAATGGTCCCCCAATTATATAGAGTTGCC
Found at i:836785 original size:31 final size:31
Alignment explanation
Indices: 836747--836819 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
836737 ACTATTAAAA
*
836747 GTTCCAAAATGGCCACCCGACTATTCATTAT
1 GTTCCAAAATCGCCACCCGACTATTCATTAT
836778 GTTCCAAAATCGCCACCCGACTATTCATTAT
1 GTTCCAAAATCGCCACCCGACTATTCATTAT
836809 GTTCCAAAATC
1 GTTCCAAAATC
836820 ATCCTTTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (31 bp):
GTTCCAAAATCGCCACCCGACTATTCATTAT
Found at i:837063 original size:31 final size:30
Alignment explanation
Indices: 837038--837098 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
837028 ATAGTCGAAT
*
837038 GACTCAACAAAGTAATTTCCTATAGTCATGG
1 GACTCAACAAAGTAATATCCTATAGTCAT-G
* *
837069 GACTTAACAAAGTAGTATCCTATAGT-ATG
1 GACTCAACAAAGTAATATCCTATAGTCATG
837098 G
1 G
837099 GAACCATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 2 0.07
31 23 0.85
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (30 bp):
GACTCAACAAAGTAATATCCTATAGTCATG
Found at i:845427 original size:22 final size:18
Alignment explanation
Indices: 845370--845415 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
845360 TAGAAGAAGG
845370 AAGAAAGAAATGAAGAAA
1 AAGAAAGAAATGAAGAAA
845388 AAGAAAGAAATGAAGAAA
1 AAGAAAGAAATGAAGAAA
845406 AAGAAAGAAA
1 AAGAAAGAAA
845416 ATAAGGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAATGAAGAAA
Found at i:845433 original size:30 final size:30
Alignment explanation
Indices: 845352--845445 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
845342 GAGATGAAAT
*
845352 AAGAAAAATA-GAAG-AAGGAAG--AAAGA
1 AAGAAAAAAAGGAAGAAAGGAAGAAAAAGA
* *
845378 AATGAAGAAAAAGAAAGAAATGAAGAAAAAGA
1 AA-GAA-AAAAAGGAAGAAAGGAAGAAAAAGA
* *
845410 AAGAAAATAAGGAAGAAAGGAAGAACAAGA
1 AAGAAAAAAAGGAAGAAAGGAAGAAAAAGA
*
845440 GAGAAA
1 AAGAAA
845446 GGAATAAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 4 0.07
29 3 0.06
30 32 0.59
31 3 0.06
32 7 0.13
ACGTcount: A:0.69, C:0.01, G:0.26, T:0.04
Consensus pattern (30 bp):
AAGAAAAAAAGGAAGAAAGGAAGAAAAAGA
Found at i:846699 original size:10 final size:9
Alignment explanation
Indices: 846686--846741 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 9
846676 AATATAATAA
846686 TAATTCTATT
1 TAATT-TATT
846696 TAATTTAATT
1 TAATTT-ATT
846706 TAATTTATT
1 TAATTTATT
*
846715 TAAATTCATT
1 T-AATTTATT
846725 T-A-TTATT
1 TAATTTATT
846732 T-ATTTATT
1 TAATTTATT
846740 TA
1 TA
846742 TTATGATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.15
8 7 0.17
9 5 0.12
10 22 0.55
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTTATT
Found at i:848149 original size:106 final size:108
Alignment explanation
Indices: 848005--848304 Score: 368
Period size: 106 Copynumber: 2.8 Consensus size: 108
847995 GATTTGAATA
* * * *
848005 ATAAATTAATTTTTATTTATTAACATTATGACTAAATTGATAGAATATATAAGTAAAAGT-ATTC
1 ATAAATTAATTTTAATTTATTAAAATTTTGACTAAATTGATAGAATATATAAGTAAAAGTGA-CC
* * *
848069 AAATGTCTAATTATATTAATTTTAAAAGTTAAAGAT-A-A-AACAT
65 AAATGTGTAATTATATCAATTTT-AAAGTT-AAGATGAGATAAAAT
*
848112 ATAAATTAATTTTAATTT-TTAAAATTTTGACTAAATTGATAGAATATAAAAGTAAAAGTGACCA
1 ATAAATTAATTTTAATTTATTAAAATTTTGACTAAATTGATAGAATATATAAGTAAAAGTGACCA
*
848176 AATGTGTAATTATATCAATTTT-ATGTTAAGATGAGATAAAAT
66 AATGTGTAATTATATCAATTTTAAAGTTAAGATGAGATAAAAT
* * *
848218 ATATAA--AA-TTTAATTTTATTAAAA-TTAGTACTAAATTGATAGAATATATAAGTCAAACTGA
1 ATA-AATTAATTTTAA-TTTATTAAAATTTTG-ACTAAATTGATAGAATATATAAGTAAAAGTGA
848279 CCAAATGTGTAATTATATCAATTTTA
63 CCAAATGTGTAATTATATCAATTTTA
848305 TTAAATTTTA
Statistics
Matches: 171, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
103 5 0.03
104 10 0.06
105 9 0.05
106 127 0.74
107 20 0.12
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (108 bp):
ATAAATTAATTTTAATTTATTAAAATTTTGACTAAATTGATAGAATATATAAGTAAAAGTGACCA
AATGTGTAATTATATCAATTTTAAAGTTAAGATGAGATAAAAT
Found at i:848388 original size:27 final size:26
Alignment explanation
Indices: 848353--848456 Score: 93
Period size: 27 Copynumber: 3.8 Consensus size: 26
848343 TTTATGTAAT
848353 ATAAGAATAAAAAATATATTTTAATAA
1 ATAAG-ATAAAAAATATATTTTAATAA
** *
848380 ATAAGAATAAAATGTATATTTTAATTTA
1 ATAAG-ATAAAAAATATATTTTAA-TAA
**
848408 ATTTGATAATAAAATATA-TTTAATAA
1 ATAAGATAA-AAAATATATTTTAATAA
*
848434 GATAAGATAAAATAAAATATTTT
1 -ATAAGATAAAA-AATATATTTT
848457 TAAAGTTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
26 4 0.07
27 43 0.70
28 14 0.23
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (26 bp):
ATAAGATAAAAAATATATTTTAATAA
Found at i:850531 original size:17 final size:18
Alignment explanation
Indices: 850511--850544 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
850501 TTTTTGTGAT
850511 TTTTTTGG-CTTTTTTTA
1 TTTTTTGGCCTTTTTTTA
850528 TTTTTTGGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
850545 TAAAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.03, C:0.09, G:0.12, T:0.76
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTA
Found at i:850925 original size:58 final size:59
Alignment explanation
Indices: 850845--850961 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 59
850835 AGATGGATAG
*
850845 GTGTCCAATCGAACCCTCCTAGTCGTAATGAAAA-GACAAACACG-TAATATGGATCTAA
1 GTGTCCAATCGAACCCTCCTAGTCGCAATGAAAAGGA-AAACACGATAATATGGATCTAA
* * * *
850903 GTGTCCTATTGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTCTAA
1 GTGTCCAATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACACGATAATATGGATCTAA
850962 CCAACCCTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (59 bp):
GTGTCCAATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACACGATAATATGGATCTAA
Found at i:853311 original size:31 final size:31
Alignment explanation
Indices: 853276--853365 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
853266 AACTTTTATC
* * * *
853276 ATTTGAATGTCAGCTATCGACTACCACCAGT
1 ATTTGAATGCCAACTACCAACTACCACCAGT
853307 ATTTGAATGCCAACTACCAACTACCACCTA-T
1 ATTTGAATGCCAACTACCAACTACCACC-AGT
* * *
853338 ATTCGAATGCCAACTACCAGCTATCACC
1 ATTTGAATGCCAACTACCAACTACCACC
853366 TACGTGATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 50 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.11, T:0.26
Consensus pattern (31 bp):
ATTTGAATGCCAACTACCAACTACCACCAGT
Found at i:853366 original size:31 final size:31
Alignment explanation
Indices: 853295--853367 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
853285 TCAGCTATCG
*
853295 ACTACCACC-AGTATTTGAATGCCAACTACCA
1 ACTACCACCTA-TATTCGAATGCCAACTACCA
853326 ACTACCACCTATATTCGAATGCCAACTACCA
1 ACTACCACCTATATTCGAATGCCAACTACCA
* *
853357 GCTATCACCTA
1 ACTACCACCTA
853368 CGTGATTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.23
Consensus pattern (31 bp):
ACTACCACCTATATTCGAATGCCAACTACCA
Found at i:856646 original size:21 final size:21
Alignment explanation
Indices: 856604--856646 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
856594 CAGTTTGAGT
* *
856604 TCGGGTCAAGTTAATTTTAGG
1 TCGGGTCAAATTAATTTCAGG
856625 TCGGGTCAATATTAA-TTCAGG
1 TCGGGTCAA-ATTAATTTCAGG
856646 T
1 T
856647 TAAAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (21 bp):
TCGGGTCAAATTAATTTCAGG
Found at i:857640 original size:26 final size:27
Alignment explanation
Indices: 857611--857678 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
857601 TGAACAAAAG
*
857611 TTTAAAGGGATT-AGATTATGATATAA
1 TTTATAGGGATTGAGATTATGATATAA
* *
857637 TTTATAGGGTTTGGAGTTTATGATATAA
1 TTTATAGGGATT-GAGATTATGATATAA
*
857665 TTTATAGGGTTTGA
1 TTTATAGGGATTGA
857679 ACTAAATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.27
27 2 0.05
28 25 0.68
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (27 bp):
TTTATAGGGATTGAGATTATGATATAA
Found at i:859643 original size:54 final size:54
Alignment explanation
Indices: 859585--859698 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
859575 AGTGAAATTT
*
859585 TAAAATGAAAACA-TTTCATCTTCTCTC-TTCACTCCCTACTTTTTAAGATTTTAG
1 TAAAATGAAAACATTTTC-TCTTCTCTCTTTC-CTCCATACTTTTTAAGATTTTAG
859639 TAAAATGAAAACATTTTCTCTTCTCTCTTTCCTCCATACTTTTTAAGATTTTAG
1 TAAAATGAAAACATTTTCTCTTCTCTCTTTCCTCCATACTTTTTAAGATTTTAG
859693 TAAAAT
1 TAAAAT
859699 TTAAAATAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
54 50 0.88
55 7 0.12
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (54 bp):
TAAAATGAAAACATTTTCTCTTCTCTCTTTCCTCCATACTTTTTAAGATTTTAG
Found at i:859720 original size:54 final size:54
Alignment explanation
Indices: 859605--859721 Score: 121
Period size: 54 Copynumber: 2.1 Consensus size: 54
859595 ACATTTCATC
* ****
859605 TTCTCTCTTCACTCCCTACTTTTTAAGATTTTAGTAAAATGAAAACATTTTCTCT
1 TTCTCT-TTCACTCCATACTTTTTAAGATTTTAGTAAAATGAAAACAGAAACTCT
* *
859660 TCTCTCTTTC-CTCCATACTTTTTAAGATTTTAGTAAAATTTAAAATAGAAACGT-T
1 T-TCTCTTTCACTCCATACTTTTTAAGATTTTAGTAAAA-TGAAAACAGAAAC-TCT
859715 TTCTCTT
1 TTCTCTT
859722 CTTTCTTCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
54 33 0.63
55 13 0.25
56 6 0.12
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (54 bp):
TTCTCTTTCACTCCATACTTTTTAAGATTTTAGTAAAATGAAAACAGAAACTCT
Found at i:859839 original size:13 final size:15
Alignment explanation
Indices: 859821--859857 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
859811 TAAATGAATC
859821 ATTTAATAA-AAAA-
1 ATTTAATAATAAAAG
859834 ATTTAA-AATAAAAG
1 ATTTAATAATAAAAG
859848 ATTTAATAAT
1 ATTTAATAAT
859858 TTAAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 10 0.48
14 6 0.29
15 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
ATTTAATAATAAAAG
Found at i:861801 original size:28 final size:28
Alignment explanation
Indices: 861716--861801 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
861706 TATGGCAATT
* *
861716 TTTATTAACATTTTAGTGCTACATCAAA
1 TTTATTAATATTTTAGTGTTACATCAAA
*
861744 TATATTAATATTTTAGTGTTACATCAAA
1 TTTATTAATATTTTAGTGTTACATCAAA
861772 TTTATTAATATTTTAGTGTTACATCAAA
1 TTTATTAATATTTTAGTGTTACATCAAA
861800 TT
1 TT
861802 ACATTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTATTAATATTTTAGTGTTACATCAAA
Found at i:863453 original size:12 final size:12
Alignment explanation
Indices: 863436--863460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
863426 GTGACTTTCG
863436 AAATATTTAATA
1 AAATATTTAATA
863448 AAATATTTAATA
1 AAATATTTAATA
863460 A
1 A
863461 TAAAAAATTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATTTAATA
Found at i:863463 original size:15 final size:15
Alignment explanation
Indices: 863443--863472 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
863433 TCGAAATATT
*
863443 TAATAAAATATTTAA
1 TAATAAAAAATTTAA
863458 TAATAAAAAATTTAA
1 TAATAAAAAATTTAA
863473 AACTCAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAAAAAATTTAA
Found at i:867189 original size:15 final size:15
Alignment explanation
Indices: 867169--867201 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
867159 AATAAAGTAG
867169 AACATTATATAAAAA
1 AACATTATATAAAAA
*
867184 AACATTATTTAAAAA
1 AACATTATATAAAAA
867199 AAC
1 AAC
867202 TCGTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (15 bp):
AACATTATATAAAAA
Found at i:868810 original size:21 final size:21
Alignment explanation
Indices: 868762--868842 Score: 126
Period size: 21 Copynumber: 3.8 Consensus size: 21
868752 ACATAGAATT
* *
868762 TGTCCCAAAGGACCACGTAGAAA
1 TGTCCCGAAGGACCACATAG--A
868785 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
868806 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
868827 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
868843 TCCTTGAGGA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 38 0.68
23 18 0.32
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:885780 original size:18 final size:18
Alignment explanation
Indices: 885757--885802 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
885747 GAAAGTCACC
* *
885757 AGCCCATTGAAGTAGAAG
1 AGCCCACTGAAGTAGAAA
885775 AGCCCACTGAAGTAGAAA
1 AGCCCACTGAAGTAGAAA
*
885793 AGCCCGCTGA
1 AGCCCACTGA
885803 CCCTGATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (18 bp):
AGCCCACTGAAGTAGAAA
Found at i:893360 original size:9 final size:9
Alignment explanation
Indices: 893346--893399 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
893336 GAACCCTCCT
893346 TTTTTTTTC
1 TTTTTTTTC
893355 TTTTTTTTC
1 TTTTTTTTC
*
893364 TCTTCTTTTC
1 T-TTTTTTTC
893374 ---TTTTTC
1 TTTTTTTTC
*
893380 ATTTTTTTC
1 TTTTTTTTC
*
893389 ATTTTTTTC
1 TTTTTTTTC
893398 TT
1 TT
893400 CTTCAAGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.13
9 26 0.68
10 7 0.18
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:893396 original size:24 final size:25
Alignment explanation
Indices: 893344--893404 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
893334 TTGAACCCTC
*
893344 CTTTT-TTTTTCTTTTTTTTCTCTT
1 CTTTTCTTTTTCATTTTTTTCTCTT
893368 CTTTTCTTTTTCATTTTTTTCAT-TT
1 CTTTTCTTTTTCATTTTTTTC-TCTT
*
893393 -TTTTCTTCTTCA
1 CTTTTCTTTTTCA
893405 AGTGTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 16 0.48
25 16 0.48
26 1 0.03
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (25 bp):
CTTTTCTTTTTCATTTTTTTCTCTT
Found at i:905494 original size:15 final size:16
Alignment explanation
Indices: 905474--905507 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
905464 AATAAAGTAG
905474 AACATTA-TATAAAAA
1 AACATTATTATAAAAA
*
905489 AACATTATTTTAAAAA
1 AACATTATTATAAAAA
905505 AAC
1 AAC
905508 TTGTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AACATTATTATAAAAA
Found at i:905782 original size:2 final size:2
Alignment explanation
Indices: 905775--905806 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
905765 ACATACATAC
*
905775 AT AT AT AT GT 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
905807 TCCTATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:905998 original size:3 final size:3
Alignment explanation
Indices: 905990--906050 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
905980 GTTGTAATCC
* * *
905990 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAG TGA TAA TAA TTAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
906035 TAA TAA TAA TTAA TAA
1 TAA TAA TAA -TAA TAA
906051 CGAACGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:907939 original size:30 final size:31
Alignment explanation
Indices: 907884--908018 Score: 166
Period size: 31 Copynumber: 4.4 Consensus size: 31
907874 AAAAATAGTT
* * *
907884 AAATTTTATTTTAACTCTGAAATTTTAGATA
1 AAATATTAATTTAACTCTTAAATTTTAGATA
*
907915 AAATATTAATTTAACTC-TAAATTTTATATA
1 AAATATTAATTTAACTCTTAAATTTTAGATA
*
907945 AAATATTAATTTAA-TACTTAAACTTTAGATA
1 AAATATTAATTTAACT-CTTAAATTTTAGATA
* * *
907976 AATTATCAATTTAACACTTAAATTTTAGATA
1 AAATATTAATTTAACTCTTAAATTTTAGATA
*
908007 AAATATCAATTT
1 AAATATTAATTT
908019 GACCTCCACA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.01
30 26 0.29
31 63 0.70
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (31 bp):
AAATATTAATTTAACTCTTAAATTTTAGATA
Found at i:908628 original size:25 final size:26
Alignment explanation
Indices: 908586--908634 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
908576 GGAAGTTATA
908586 TTAAAAATTTAAAGGGTGC-AAATTT
1 TTAAAAATTTAAAGGGTGCGAAATTT
908611 TTAAAAATTTAATA-GGTGCGAAAT
1 TTAAAAATTTAA-AGGGTGCGAAAT
908635 ATAATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (26 bp):
TTAAAAATTTAAAGGGTGCGAAATTT
Found at i:911741 original size:22 final size:22
Alignment explanation
Indices: 911710--911800 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
911700 AATTATATAT
*
911710 TATAATTTTATCA-AAATTAAAA
1 TATAAATTTAT-ATAAATTAAAA
911732 TATAAATTTATATAAATTAAAA
1 TATAAATTTATATAAATTAAAA
*** *
911754 TATAAAAAAATATAATATAAAAA
1 TATAAATTTATATAA-ATTAAAA
*
911777 CTATCAAAATCTATATAAATTAAA
1 -TAT--AAATTTATATAAATTAAA
911801 TTATTATCAT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.02
22 31 0.56
23 6 0.11
24 3 0.05
25 5 0.09
26 9 0.16
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
TATAAATTTATATAAATTAAAA
Found at i:911756 original size:12 final size:12
Alignment explanation
Indices: 911723--911768 Score: 55
Period size: 10 Copynumber: 4.2 Consensus size: 12
911713 AATTTTATCA
911723 AAATTAAAATAT
1 AAATTAAAATAT
*
911735 AAATT--TATAT
1 AAATTAAAATAT
911745 AAATTAAAATAT
1 AAATTAAAATAT
911757 AAA--AAAATAT
1 AAATTAAAATAT
911767 AA
1 AA
911769 TATAAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 18 0.60
12 12 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTAAAATAT
Found at i:911843 original size:22 final size:21
Alignment explanation
Indices: 911789--911843 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
911779 ATCAAAATCT
* *
911789 ATATAAA-TTAAATTATTATC
1 ATATAAATTTAAAGTATTATA
*
911809 AT-TATAATATAAACGTATTATA
1 ATATA-AATTTAAA-GTATTATA
911831 ATATAAATTTAAA
1 ATATAAATTTAAA
911844 TTTTTGGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.07
20 4 0.15
21 4 0.15
22 15 0.56
23 2 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATAAATTTAAAGTATTATA
Found at i:921009 original size:100 final size:100
Alignment explanation
Indices: 920883--921079 Score: 358
Period size: 100 Copynumber: 2.0 Consensus size: 100
920873 CCAGCATACC
920883 GTTTCATGGATCAGATAGCTATTATCCAGCAAAATTTAAATGAATTGGACACTTTTATTTAAGGC
1 GTTTCATGGATCAGATAGCTATTATCCAGCAAAATTTAAATGAATTGGACACTTTTATTTAAGGC
*
920948 TTAATATAAAAATAAATGTCCTATGATTCGAACTA
66 TTAATACAAAAATAAATGTCCTATGATTCGAACTA
* * *
920983 GTTTCATGGATCTGCTAGCTTTTATCCAGCAAAATTTAAATGAATTGGACACTTTTATTTAAGGC
1 GTTTCATGGATCAGATAGCTATTATCCAGCAAAATTTAAATGAATTGGACACTTTTATTTAAGGC
921048 TTAATACAAAAATAAATGTCCTATGATTCGAA
66 TTAATACAAAAATAAATGTCCTATGATTCGAA
921080 AAATATTTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (100 bp):
GTTTCATGGATCAGATAGCTATTATCCAGCAAAATTTAAATGAATTGGACACTTTTATTTAAGGC
TTAATACAAAAATAAATGTCCTATGATTCGAACTA
Found at i:922554 original size:61 final size:60
Alignment explanation
Indices: 922423--922587 Score: 177
Period size: 61 Copynumber: 2.7 Consensus size: 60
922413 TATAGTTTGT
* * * * * *
922423 GATGAAATTGAAATGTTCAAAAAGTTTTGGGACCAATTTAGAATGAAGGTCATACTTGGAG
1 GATGAAATTGAAATGTT-TAAAAGTTTAGGGACTAATTTAGAATGAAAGTCATAATTGAAG
* * * * *
922484 GTTGTAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAAAATTCATAATTTAAG
1 GATGAAATTGAAATGTTTAAAAGTTTAGGGACTAATTTAGAATG-AAAGTCATAATTGAAG
* * * *
922545 GATGAAATTGTAATTTTTAAAAGCTTAGGGACTAACTTAGAAT
1 GATGAAATTGAAATGTTTAAAAGTTTAGGGACTAATTTAGAAT
922588 ATGGATCATA
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 23 0.27
61 62 0.73
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (60 bp):
GATGAAATTGAAATGTTTAAAAGTTTAGGGACTAATTTAGAATGAAAGTCATAATTGAAG
Found at i:923047 original size:16 final size:16
Alignment explanation
Indices: 922998--923050 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
922988 AAAATAAATA
922998 AATTTGAAAGTTAAAGT
1 AATTTGAAAGTT-AAGT
*
923015 GATTT-AAA-TTAGGAGT
1 AATTTGAAAGTTA--AGT
923031 AATTTGAAAGTTAAGT
1 AATTTGAAAGTTAAGT
923047 AATT
1 AATT
923051 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 1 0.03
15 2 0.07
16 17 0.57
17 7 0.23
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (16 bp):
AATTTGAAAGTTAAGT
Found at i:924799 original size:39 final size:39
Alignment explanation
Indices: 924756--924861 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
924746 CCAAGAAAAT
* *
924756 ACCCAACAATTTATTTTCTTTTACAAAACA-GGAAATTAA
1 ACCCAACGATTTATTTTCTTTTACAAAA-ATGGAAAATAA
* *
924795 ACCCAATGATTTATTTCCTTTTACAAAAATTGGAAAATAA
1 ACCCAACGATTTATTTTCTTTTACAAAAA-TGGAAAATAA
*
924835 ATCCAACGATTTA-TTTCTTTTTACAAA
1 ACCCAACGATTTATTTTC-TTTTACAAA
924862 CCATAATCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.02
39 28 0.49
40 28 0.49
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (39 bp):
ACCCAACGATTTATTTTCTTTTACAAAAATGGAAAATAA
Found at i:924846 original size:40 final size:39
Alignment explanation
Indices: 924756--924861 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 39
924746 CCAAGAAAAT
* * *
924756 ACCCAACAATTTATTTTCTTTTACAAAACAGGAAATTAA
1 ACCCAACGATTTATTTCCTTTTACAAAACAGGAAAATAA
*
924795 ACCCAATGATTTATTTCCTTTTACAAAA-ATTGGAAAATAA
1 ACCCAACGATTTATTTCCTTTTACAAAACA--GGAAAATAA
* *
924835 ATCCAACGATTTATTTCTTTTTACAAA
1 ACCCAACGATTTATTTCCTTTTACAAA
924862 CCATAATCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 1 0.02
39 25 0.43
40 32 0.55
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (39 bp):
ACCCAACGATTTATTTCCTTTTACAAAACAGGAAAATAA
Found at i:924932 original size:39 final size:39
Alignment explanation
Indices: 924882--924986 Score: 183
Period size: 39 Copynumber: 2.7 Consensus size: 39
924872 ATAAGATTCT
924882 TAGGAAAATAAATTCAACGATTTATTTTCTTTTACAAGA
1 TAGGAAAATAAATTCAACGATTTATTTTCTTTTACAAGA
*
924921 TAGGAAAATAAATTCAACAATTTATTTTCTTTTACAAGA
1 TAGGAAAATAAATTCAACGATTTATTTTCTTTTACAAGA
* *
924960 TAGGAAAATAAATCCAATGATTTATTT
1 TAGGAAAATAAATTCAACGATTTATTT
924987 CATTTTTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (39 bp):
TAGGAAAATAAATTCAACGATTTATTTTCTTTTACAAGA
Found at i:924944 original size:137 final size:134
Alignment explanation
Indices: 924758--925054 Score: 355
Period size: 137 Copynumber: 2.2 Consensus size: 134
924748 AAGAAAATAC
* **
924758 CCAACAATTTATTTTCTTTTACAAAACAGGAAATTAAACCCAATGATTTATTTCCTTTTACAAAA
1 CCAACAATTTATTTTCTTTTACAAAACAGGAAAATAAACCCAACAATTTATTTCCTTTTAC-AAA
* * * *
924823 ATTGGAAAATAAATCCAACGATTTATTTC-TTTTTACAAACCATAATCATAT-AAGATTCTTAGG
65 ATAGGAAAATAAATCCAACGATTTATTTCATTTTT--AAA-CAGAATCAT-TCAAGATTCATAAG
924886 AAAATAAAT
126 AAAATAAAT
* * * * ** * *
924895 TCAACGATTTATTTTCTTTTACAAGATAGGAAAATAAATTCAACAATTTATTTTCTTTTACAAGA
1 CCAACAATTTATTTTCTTTTACAAAACAGGAAAATAAACCCAACAATTTATTTCCTTTTACAAAA
* * * *
924960 TAGGAAAATAAATCCAATGATTTATTTCATTTTTTAATAGAATCCTTCAAGATTCATAAGAAAAT
66 TAGGAAAATAAATCCAACGATTTATTTCATTTTTAAACAGAATCATTCAAGATTCATAAGAAAAT
925025 AAAT
131 AAAT
*
925029 CCAACAATTTATTTACTTTTACAAAA
1 CCAACAATTTATTTTCTTTTACAAAA
925055 TATAATCATT
Statistics
Matches: 135, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
133 1 0.01
134 47 0.35
135 2 0.01
136 29 0.21
137 56 0.41
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (134 bp):
CCAACAATTTATTTTCTTTTACAAAACAGGAAAATAAACCCAACAATTTATTTCCTTTTACAAAA
TAGGAAAATAAATCCAACGATTTATTTCATTTTTAAACAGAATCATTCAAGATTCATAAGAAAAT
AAAT
Found at i:925095 original size:58 final size:57
Alignment explanation
Indices: 924997--925619 Score: 641
Period size: 58 Copynumber: 10.8 Consensus size: 57
924987 CATTTTTTAA
* * * * * *
924997 TAGAATCCTTCAAGATTCAT-AAGAAAATAAATCCAACAATTTATTTACTTTTACAAA-A
1 TAGAATCATTTAAGATTC-TCAAGGAAATAAATTCAACAATTTATTT-C-CTTACAAAGT
* * *
925055 TATAATCATTTAAGATTCTCAAGGAAATAAATTCAGCAATTTATTTTCCTAACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTA-TTTCCTTACAAAGT
* * **
925113 TAGAATCATTTAAGATTATCAAGAAAATAAATTCAACAATTTATTTGATTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTT-CCTTACAAAGT
* *
925171 TGGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTTCTCTTACAAATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTTC-CTTACAAAGT
* *
925229 TAGAATCATTTAAGATTCTCAAGAAAATAAATTTAACAATTTATTTTCCTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTA-TTTCCTTACAAAGT
* * * * * *
925287 TAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTCTTTTTCCAAA-A
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTTC--CTTACAAAGT
* * * ** * ***
925345 AAGAATCATATAAGATTCT-TAGGAAAATAAATTCAATGATTTATTTTCTTTTTTTTAA--
1 TAGAATCATTTAAGATTCTCAAGG-AAATAAATTCAACAATTTA-TTTC--CTTACAAAGT
* * ** *
925403 TAGAATCCTTCAAGATTCAT-AAAAAAATAAATTCAACAATTTATTTCTTTACAAAGT
1 TAGAATCATTTAAGATTC-TCAAGGAAATAAATTCAACAATTTATTTCCTTACAAAGT
* *
925460 TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACAATTTATTTCTCTTACAAATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTTC-CTTACAAAGT
* * *
925518 TAGAATCATTTAAGATTATCAAGGAAATAAATTTAA-AATTTAGTTTCCTTACAAATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTA-TTTCCTTACAAAGT
* **
925575 TAGAATCATTCAAGATTCTCAAGGAAATAAATTCAATGATTTATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATT
925620 CTCCCCCTTC
Statistics
Matches: 482, Mismatches: 66, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
55 5 0.01
56 1 0.00
57 111 0.23
58 339 0.70
59 26 0.05
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (57 bp):
TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACAATTTATTTCCTTACAAAGT
Found at i:925833 original size:45 final size:45
Alignment explanation
Indices: 925745--925953 Score: 206
Period size: 45 Copynumber: 4.6 Consensus size: 45
925735 GAATTAATCC
* * * ** * * *
925745 TTTAATATTAGCAATCCAATAATCAAAATAAATTGATCATTTGAT
1 TTTAATTTTCGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
*
925790 TTTAATTTTCGCAACCCAATAATCAAAAGGAACTAATCTTTTGAT
1 TTTAATTTTCGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* * * *
925835 TGTAGTTTTCGCAACTCAATAATCAAAAGGAACTAATCCCTTGAT
1 TTTAATTTTCGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* ** *
925880 TTT-ATTTTCCACAACCCGGTAAT-AGAAATGAACTAATCCTTTGAT
1 TTTAATTTT-CGCAACCCAATAATCA-AAAGGAACTAATCCTTTGAT
* *
925925 TTTAATTTTTGGCAACCCAATAATAAAAA
1 TTTAA-TTTTCGCAACCCAATAATCAAAA
925954 ACATTGTATT
Statistics
Matches: 134, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
44 5 0.04
45 110 0.82
46 14 0.10
47 5 0.04
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (45 bp):
TTTAATTTTCGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:929898 original size:20 final size:20
Alignment explanation
Indices: 929859--929939 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
929849 AAAACCAGAA
929859 CCCCA-GGGGGTATCGA-TC
1 CCCCAGGGGGGTATCGATTC
929877 CCCCAGGGGGGTATCGATTC
1 CCCCAGGGGGGTATCGATTC
** * *
929897 CCCTGTGGGGGGAATCGGTTC
1 CCC-CAGGGGGGTATCGATTC
* *
929918 CCTCATGGGGGTATCGATTC
1 CCCCAGGGGGGTATCGATTC
929938 CC
1 CC
929940 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 19 0.38
21 15 0.30
ACGTcount: A:0.14, C:0.30, G:0.35, T:0.22
Consensus pattern (20 bp):
CCCCAGGGGGGTATCGATTC
Found at i:933792 original size:22 final size:21
Alignment explanation
Indices: 933750--933789 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
933740 GAGTTTATTT
*
933750 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
933771 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
933790 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:936237 original size:5 final size:6
Alignment explanation
Indices: 936220--936246 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
936210 ATCTGAGATG
936220 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
936247 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:937838 original size:17 final size:16
Alignment explanation
Indices: 937816--937851 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
937806 TTATGAGGTG
*
937816 AAAATGTTATTATTGTA
1 AAAATGTAATTATT-TA
937833 AAAATGTAATTATTTA
1 AAAATGTAATTATTTA
937849 AAA
1 AAA
937852 CAATATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (16 bp):
AAAATGTAATTATTTA
Found at i:938856 original size:28 final size:28
Alignment explanation
Indices: 938819--938872 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
938809 CCATTTTAGT
* *
938819 TTCTTCTGAAATTTTACCTGTAATATTA
1 TTCTTCTGAAAATTTACCTCTAATATTA
*
938847 TTCTTCTGAAAATTTATCTCTAATAT
1 TTCTTCTGAAAATTTACCTCTAATAT
938873 CTTCTCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.50
Consensus pattern (28 bp):
TTCTTCTGAAAATTTACCTCTAATATTA
Found at i:939607 original size:17 final size:17
Alignment explanation
Indices: 939585--939647 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
939575 TTCAGCAATT
*
939585 GCTTATATATGTCTTCA
1 GCTTATACATGTCTTCA
939602 GCTTATACATG-CTTCA
1 GCTTATACATGTCTTCA
* * *
939618 --TAAAATC-TGTCTTGA
1 GCTTATA-CATGTCTTCA
939633 GCTTATACATGTCTT
1 GCTTATACATGTCTT
939648 GAGGTTATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 5 0.14
15 5 0.14
16 6 0.17
17 19 0.54
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (17 bp):
GCTTATACATGTCTTCA
Found at i:947564 original size:2 final size:2
Alignment explanation
Indices: 947552--947591 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
947542 ATCCTTTCAA
*
947552 AT AT AT GT 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
947592 CCTTTGTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:947862 original size:11 final size:10
Alignment explanation
Indices: 947846--947939 Score: 62
Period size: 10 Copynumber: 8.9 Consensus size: 10
947836 GAAAAAACAC
947846 AAAAAAAGAA
1 AAAAAAAGAA
*
947856 AACAAAAACAA
1 AA-AAAAAGAA
*
947867 AAAGAAAGAA
1 AAAAAAAGAA
* *
947877 AGAAATAGAA
1 AAAAAAAGAA
*
947887 ATAGAAATAGAA
1 A-A-AAAAAGAA
* *
947899 AAAAAGATAA
1 AAAAAAAGAA
*
947909 AAAAATAGAA
1 AAAAAAAGAA
*
947919 GAAAAACAAGAG
1 -AAAAA-AAGAA
947931 AAAAAAAGA
1 AAAAAAAGA
947940 GAGAGAAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
10 34 0.52
11 20 0.30
12 12 0.18
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:947864 original size:21 final size:21
Alignment explanation
Indices: 947838--947877 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
947828 GAGATATAGA
947838 AAAAACACAAAA-AAAGAAAAC
1 AAAAACA-AAAAGAAAGAAAAC
947859 AAAAACAAAAAGAAAGAAA
1 AAAAACAAAAAGAAAGAAA
947878 GAAATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAGAAAGAAAAC
Found at i:947929 original size:24 final size:24
Alignment explanation
Indices: 947895--947948 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
947885 AAATAGAAAT
* *
947895 AGAAAAAAAGATAAAAAAATAGA-
1 AGAAAAAAAGAGAAAAAAAGAGAG
947918 AGAAAAACAAGAGAAAAAAAGAGAG
1 AGAAAAA-AAGAGAAAAAAAGAGAG
947943 AGAAAA
1 AGAAAA
947949 GGAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (24 bp):
AGAAAAAAAGAGAAAAAAAGAGAG
Found at i:947934 original size:10 final size:10
Alignment explanation
Indices: 947846--947957 Score: 61
Period size: 10 Copynumber: 10.7 Consensus size: 10
947836 GAAAAAACAC
947846 AAAAAAAGA-
1 AAAAAAAGAG
*
947855 AAACAAAA-AC
1 AAA-AAAAGAG
947865 AAAAAGAA-AG
1 AAAAA-AAGAG
* *
947875 AAAGAAATAG
1 AAAAAAAGAG
*
947885 AAATAGAAATAG
1 AAA-A-AAAGAG
*
947897 AAAAAAAGATA
1 AAAAAAAGA-G
947908 AAAAAATAGAAG
1 AAAAAA-AG-AG
947920 AAAAACAAGAG
1 AAAAA-AAGAG
947931 AAAAAAAGAG
1 AAAAAAAGAG
*
947941 AGAGAAAAG-G
1 A-AAAAAAGAG
947951 AAAAAAA
1 AAAAAAA
947958 TAAAGAAGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
9 13 0.15
10 31 0.37
11 20 0.24
12 18 0.21
13 2 0.02
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:947971 original size:12 final size:11
Alignment explanation
Indices: 947895--947969 Score: 64
Period size: 12 Copynumber: 6.5 Consensus size: 11
947885 AAATAGAAAT
947895 AGAAAAAAAGA
1 AGAAAAAAAGA
947906 TA-AAAAAATAGA
1 -AGAAAAAA-AGA
947918 AGAAAAACAAG-
1 AGAAAAA-AAGA
947929 AGAAAAAAAGA
1 AGAAAAAAAGA
* *
947940 GAGAGAAAAGGA
1 -AGAAAAAAAGA
*
947952 AAAAAATAAAGA
1 AGAAAA-AAAGA
947964 AGAAAA
1 AGAAAA
947970 TAGACAGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 3 0.06
11 18 0.35
12 29 0.57
13 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:950130 original size:54 final size:53
Alignment explanation
Indices: 950046--950161 Score: 133
Period size: 54 Copynumber: 2.2 Consensus size: 53
950036 TTTGGAAGTT
*
950046 TCTTGATTATTTTTAAATGAACTTTCAAAGAAGCTAAGCCTGATTTTCAGGGGG
1 TCTTGA-TATTTTTAAATGAACTTTCAAAGAAGCTAAGCCTGATTTTAAGGGGG
* * * * * * **
950100 TCTTGATGTTTTTAAATGAATTTTTTAAAGAGGTTAAGGCTGATTTTAAGGGTT
1 TCTTGATATTTTTAAATGAA-CTTTCAAAGAAGCTAAGCCTGATTTTAAGGGGG
950154 TCTTGATA
1 TCTTGATA
950162 ACTGTAAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 13 0.25
54 38 0.75
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (53 bp):
TCTTGATATTTTTAAATGAACTTTCAAAGAAGCTAAGCCTGATTTTAAGGGGG
Found at i:951269 original size:139 final size:139
Alignment explanation
Indices: 950856--951801 Score: 1333
Period size: 139 Copynumber: 6.8 Consensus size: 139
950846 AATATGAACC
* * * * * *
950856 GATCAATATTTCAAATGGAGAGTTCATAATCAGAAGAACTCATCCGATAGAA-A-G-ATAAGTTC
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAT-GAAGAGGAAGAAGTTC
* *
950918 ATAATGAGAAGAACTTGTTTAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
950983 TCACTCGAGG
130 TCACTCGAGG
*
950993 GATCAACATTTCCAGTGGAGAGTTCATAATTG-GAAGAACTCATCTGACAGAA-AGAGAAGAAGT
1 GATCAACATTTCCAGTGGAGAGTTCATAA-TGAGAAGAACTCATCTGA-TGAAGAG-GAAGAAGT
* * *
951056 TCATAATGAGAAGAACTTGTTTAACCCTAGCTCGATTCATCATATATGGAGTTGAATCAGCAACA
63 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACA
951121 CCTCACTCGAGG
128 CCTCACTCGAGG
* *
951133 GATCAACATTTCCAGTGGAGAGTTCATAGTGAGAAGAACTCATCTAATGAAGAGGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGAGGAAGAAGTTCA
*
951198 TAATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
951263 CACTCGAGG
131 CACTCGAGG
* * *
951272 GATCAACATTTCCAGGGGAGAGTTTATAATGAGAAGAACTCATCTGATG-AGGGAGAAGAAGTTC
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGAG-GAAGAAGTTC
* * *
951336 ATAATGAGAAGAACTTGTTCAATCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
*
951401 TCATTCGAGG
130 TCACTCGAGG
* * *
951411 GATCAACATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCATCTAAT-AA-A-GAAGAAGTTTA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGAGGAAGAAGTTCA
* * * * *
951473 TAATGAGAAGAATTTGTTCAACCTTAGTTCGATTCATCACATATGGAGTTGAATCAACAAAACTT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
951538 CACTCGAGG
131 CACTCGAGG
* *
951547 GATAAACATTTCCAGTGGAGGGTTCATAATGAGAAGAACTCATCTGATG-AG-GGATAAGAAGTT
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGAGG--AAGAAGTT
* *
951610 CATAATGAGAAGAACTTGTTCAACCTTATCTCGATTCAACACATATGGAGTTGAATCAGCAACAC
64 CATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACAC
*
951675 CTCACTCAAGG
129 CTCACTCGAGG
* * * *
951686 GATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCAT-TCGATGAGGA-AAAAAAGTTC
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCT-GATGAAGAGGAAGAAGTTC
* * * *
951749 ATAATGAGAAGAACTTGTTCAACCTTATCTCGTTTCCATCGCATAAGGAGTTG
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTG
951802 GAACAATACC
Statistics
Matches: 730, Mismatches: 61, Indels: 34
0.88 0.07 0.04
Matches are distributed among these distances:
136 122 0.17
137 45 0.06
138 47 0.06
139 390 0.53
140 126 0.17
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (139 bp):
GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGAGGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCT
CACTCGAGG
Found at i:951609 original size:275 final size:276
Alignment explanation
Indices: 950873--951801 Score: 1366
Period size: 275 Copynumber: 3.4 Consensus size: 276
950863 ATTTCAAATG
* ** *
950873 GAGAGTTCATAATCAGAAGAACTCATCCGAT-AGAAAGATAAGTTCATAATGAGAAGAACTTGTT
1 GAGAGTTCATAATGAGAAGAACTCATCTAATGAGAAA-AGAAGTTCATAATGAGAAGAACTTGTT
* *
950937 TAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACAT
65 CAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACAT
* **
951002 TTCCAGTGGAGAGTTCATAATTG-GAAGAACTCATCTGACAGAAAGAGAAGAAGTTCATAATGAG
130 TTCCAGTGGAGAGTTCATAA-TGAGAAGAACTCATCTGA-TGAGGGAGAAGAAGTTCATAATGAG
* * *
951066 AAGAACTTGTTTAACCCTAGCTCGATTCATCATATATGGAGTTGAATCAGCAACACCTCACTCGA
193 AAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGA
*
951131 GGGATCAACATTTCCAGTG
258 GGGATCAACATTTCCAGTT
* * *
951150 GAGAGTTCATAGTGAGAAGAACTCATCTAATGAAGAGGAAGAAGTTCATAATGAGAATAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCTAATG-AGA-AAAGAAGTTCATAATGAGAAGAACTTGT
951215 TCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACA
64 TCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACA
* *
951280 TTTCCAGGGGAGAGTTTATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGA
129 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGA
* * * *
951345 AGAACTTGTTCAATCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACCTCATTCGAG
194 AGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAG
951410 GGATCAACATTTCCAGTT
259 GGATCAACATTTCCAGTT
* *
951428 GAGAGTTCATAATGAGAAGAACTCATCTAAT-A-AAGAAGAAGTTTATAATGAGAAGAATTTGTT
1 GAGAGTTCATAATGAGAAGAACTCATCTAATGAGAA-AAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
951491 CAACCTTAGTTCGATTCATCACATATGGAGTTGAATCAACAAAACTTCACTCGAGGGATAAACAT
65 CAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACAT
* *
951556 TTCCAGTGGAGGGTTCATAATGAGAAGAACTCATCTGATGAGGGATAAGAAGTTCATAATGAGAA
130 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAA
* * *
951621 GAACTTGTTCAACCTTATCTCGATTCAACACATATGGAGTTGAATCAGCAACACCTCACTCAAGG
195 GAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGG
951686 GATCAACATTTCCAG-T
260 GATCAACATTTCCAGTT
* *
951702 GAAGAGTTCATAATGAGAAGAACTCAT-TCGATGAGGAAAAAAAGTTCATAATGAGAAGAACTTG
1 G-AGAGTTCATAATGAGAAGAACTCATCT-AATGA-GAAAAGAAGTTCATAATGAGAAGAACTTG
* * * *
951766 TTCAACCTTATCTCGTTTCCATCGCATAAGGAGTTG
63 TTCAACCTTAGCTCGATT-CATCACATATGGAGTTG
951802 GAACAATACC
Statistics
Matches: 589, Mismatches: 52, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
274 3 0.01
275 247 0.42
276 2 0.00
277 65 0.11
278 147 0.25
279 124 0.21
280 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (276 bp):
GAGAGTTCATAATGAGAAGAACTCATCTAATGAGAAAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATT
TCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAG
AACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGG
ATCAACATTTCCAGTT
Found at i:951689 original size:414 final size:418
Alignment explanation
Indices: 950872--951801 Score: 1387
Period size: 414 Copynumber: 2.2 Consensus size: 418
950862 TATTTCAAAT
* * ** *
950872 GGAGAGTTCATAATCAGAAGAACTCATCCGAT-AGAAAG-ATAAGTTCATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTG
* * * *
950935 TTTAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAAC
66 TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACCTCACTCGAGGGATCAAC
951000 ATTTCCAGTGGAGAGTTCATAATTGGAAGAACTCATCTGACAGAAAGAGAAGAAGTTCATAATGA
131 ATTTCCAGTGGAGAGTTCATAATTGGAAGAACTCATCTGACAGAAAGAGAAGAAGTTCATAATGA
* * * *
951065 GAAGAACTTGTTTAACCCTAGCTCGATTCATCATATATGGAGTTGAATCAGCAACACCTCACTCG
196 GAAGAACTTGTTCAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAACAAAACCTCACTCG
* *
951130 AGGGATCAACATTTCCAGTGGAGAGTTCATAGTGAGAAGAACTCATCTAATGAAGAGGAAGAAGT
261 AGGGATAAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTAATGAAGAGGAAGAAGT
* *
951195 TCATAATGAGAATAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACA
326 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCAACACATATGGAGTTGAATCAGCAACA
*
951260 CCTCACTCGAGGGATCAACATTTCCAGG
391 CCTCACTCAAGGGATCAACATTTCCAGG
* *
951288 GGAGAGTTTATAATGAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTG
* *
951353 TTCAATCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACCTCATTCGAGGGATCAAC
66 TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACCTCACTCGAGGGATCAAC
* * *
951418 ATTTCCAGTTGAGAGTTCATAA-TGAGAAGAACTCATCT-A-A-TAA-AGAAGAAGTTTATAATG
131 ATTTCCAGTGGAGAGTTCATAATTG-GAAGAACTCATCTGACAGAAAGAGAAGAAGTTCATAATG
* * * *
951478 AGAAGAATTTGTTCAACCTTAGTTCGATTCATCACATATGGAGTTGAATCAACAAAACTTCACTC
195 AGAAGAACTTGTTCAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAACAAAACCTCACTC
* *
951543 GAGGGATAAACATTTCCAGTGGAGGGTTCATAATGAGAAGAACTCATCTGATG-AG-GGATAAGA
260 GAGGGATAAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTAATGAAGAGG--AAGA
*
951606 AGTTCATAATGAGAAGAACTTGTTCAACCTTATCTCGATTCAACACATATGGAGTTGAATCAGCA
323 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCAACACATATGGAGTTGAATCAGCA
*
951671 ACACCTCACTCAAGGGATCAACATTTCCAGT
388 ACACCTCACTCAAGGGATCAACATTTCCAGG
* *
951702 GAAGAGTTCATAATGAGAAGAACTCAT-TCGATGA-GGAAAAAAAGTTCATAATGAGAAGAACTT
1 GGAGAGTTCATAATGAGAAGAACTCATCT-GATGAGGGAGAAAAAGTTCATAATGAGAAGAACTT
* * * *
951765 GTTCAACCTTATCTCGTTTCCATCGCATAAGGAGTTG
65 GTTCAACCTTAGCTCGATT-CATCACATATGGAGTTG
951802 GAACAATACC
Statistics
Matches: 466, Mismatches: 41, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
412 2 0.00
413 46 0.10
414 262 0.56
415 2 0.00
416 30 0.06
417 7 0.02
418 117 0.25
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (418 bp):
GGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTG
TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATAAACAACACCTCACTCGAGGGATCAAC
ATTTCCAGTGGAGAGTTCATAATTGGAAGAACTCATCTGACAGAAAGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAACAAAACCTCACTCG
AGGGATAAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTAATGAAGAGGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCAACACATATGGAGTTGAATCAGCAACA
CCTCACTCAAGGGATCAACATTTCCAGG
Found at i:956238 original size:16 final size:17
Alignment explanation
Indices: 956213--956246 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
956203 CCGAGATGTC
956213 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
956229 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
956246 A
1 A
956247 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:956972 original size:21 final size:20
Alignment explanation
Indices: 956948--957017 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
956938 GCACATAGAA
*
956948 ATGTCTCGAAAGACCATATAT
1 ATGTCCCGAAA-ACCATATAT
*
956969 ATGTCCCGAAAAACCAAACATAT
1 ATGTCCCG-AAAACC--ATATAT
* *
956992 ATGCCCCGATAAACCATATAG
1 ATGTCCCGA-AAACCATATAT
957013 ATGTC
1 ATGTC
957018 TCGATGGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 18 0.46
22 4 0.10
23 17 0.44
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (20 bp):
ATGTCCCGAAAACCATATAT
Found at i:957089 original size:21 final size:22
Alignment explanation
Indices: 957065--957123 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
957055 AAAGGACTAA
* *
957065 ATATGTTTCCCAAAGAACCGTAT
1 ATATGTATCCCAAAGAACCG-AC
*
957088 ATATGTATCCCGAAGAACCG-C
1 ATATGTATCCCAAAGAACCGAC
* *
957109 ATATATATTCCAAAG
1 ATATGTATCCCAAAG
957124 GATTAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 12 0.40
23 18 0.60
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (22 bp):
ATATGTATCCCAAAGAACCGAC
Found at i:957098 original size:23 final size:23
Alignment explanation
Indices: 957065--957114 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
957055 AAAGGACTAA
* *
957065 ATATGTTTCCCAAAGAACCGTAT
1 ATATGTATCCCAAAGAACCGCAT
*
957088 ATATGTATCCCGAAGAACCGCAT
1 ATATGTATCCCAAAGAACCGCAT
957111 ATAT
1 ATAT
957115 ATTCCAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (23 bp):
ATATGTATCCCAAAGAACCGCAT
Found at i:961369 original size:21 final size:21
Alignment explanation
Indices: 961343--961398 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
961333 CATACATATG
961343 TCCCGAAGGACCACATAAATT
1 TCCCGAAGGACCACATAAATT
*** *
961364 TCCCGAAGGACTGTATAGATT
1 TCCCGAAGGACCACATAAATT
*
961385 CCCCGAAGGACCAC
1 TCCCGAAGGACCAC
961399 TCCTTAATGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (21 bp):
TCCCGAAGGACCACATAAATT
Found at i:961498 original size:21 final size:21
Alignment explanation
Indices: 961410--961499 Score: 54
Period size: 21 Copynumber: 4.3 Consensus size: 21
961400 CCTTAATGAT
* *
961410 CACAAATATATTCCAAAGGAC
1 CACATATATATCCCAAAGGAC
* * * * *
961431 CAAATATGTGTCCCGAAGAAC
1 CACATATATATCCCAAAGGAC
** * * *
961452 CGTATATATGTTCCAAAGGAT
1 CACATATATATCCCAAAGGAC
* *
961473 TACATATATATCCCGAAGGAC
1 CACATATATATCCCAAAGGAC
961494 CACATA
1 CACATA
961500 GAACTCTCGA
Statistics
Matches: 47, Mismatches: 22, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (21 bp):
CACATATATATCCCAAAGGAC
Found at i:967935 original size:18 final size:19
Alignment explanation
Indices: 967912--967948 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
967902 TTTTGGTGCA
967912 GAGGGAAC-GATCCCCCCT
1 GAGGGAACTGATCCCCCCT
*
967930 GAGGGAACTGATTCCCCCT
1 GAGGGAACTGATCCCCCCT
967949 TTGAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (19 bp):
GAGGGAACTGATCCCCCCT
Found at i:972730 original size:19 final size:20
Alignment explanation
Indices: 972706--972745 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
972696 AATTTAATCG
*
972706 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
972725 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
972745 A
1 A
972746 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:973854 original size:21 final size:23
Alignment explanation
Indices: 973825--973868 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
973815 AGCTTAACTC
*
973825 CTAACTCA-TAATTTT-ATTTTT
1 CTAAATCATTAATTTTGATTTTT
*
973846 CTAAATCATTTATTTTGATTTTT
1 CTAAATCATTAATTTTGATTTTT
973869 GAAAGCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.59
Consensus pattern (23 bp):
CTAAATCATTAATTTTGATTTTT
Found at i:975778 original size:20 final size:20
Alignment explanation
Indices: 975753--975810 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
975743 GACCGTTACA
*
975753 TAGGGGGAATTGGTACCCCC
1 TAGGGGGAATCGGTACCCCC
975773 TAGGGGGAATCGGTACCCCC
1 TAGGGGGAATCGGTACCCCC
* *
975793 TGGGGGGAATCGATACCC
1 TAGGGGGAATCGGTACCC
975811 TCTGGACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.17
Consensus pattern (20 bp):
TAGGGGGAATCGGTACCCCC
Found at i:975867 original size:20 final size:20
Alignment explanation
Indices: 975842--975909 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
975832 GAGCCAAAAA
*
975842 CCTGGGGGGAATCGGTACCC
1 CCTGGGGGGAATCAGTACCC
* *
975862 CCTGGGGGGAATCTGT--TC
1 CCTGGGGGGAATCAGTACCC
975880 CC---GGGGAATCAGTACCC
1 CCTGGGGGGAATCAGTACCC
975897 CCTGGGGGGAATC
1 CCTGGGGGGAATC
975910 TGTTCCCTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
15 10 0.26
17 3 0.08
18 3 0.08
20 23 0.59
ACGTcount: A:0.16, C:0.28, G:0.38, T:0.18
Consensus pattern (20 bp):
CCTGGGGGGAATCAGTACCC
Found at i:975895 original size:35 final size:35
Alignment explanation
Indices: 975847--975916 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
975837 AAAAACCTGG
*
975847 GGGGAATCGGTACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
975882 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
975917 TCTTGGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (35 bp):
GGGGAATCAGTACCCCCTGGGGGGAATCTGTTCCC
Found at i:976133 original size:19 final size:20
Alignment explanation
Indices: 976106--976150 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
976096 CGAATAATTT
* *
976106 AATTGAATATATAAT-TTAA
1 AATTCAATATAAAATCTTAA
976125 AATTCAATATAAAATCTTAA
1 AATTCAATATAAAATCTTAA
976145 AATTCA
1 AATTCA
976151 TTAACACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTCAATATAAAATCTTAA
Found at i:979297 original size:20 final size:21
Alignment explanation
Indices: 979272--979313 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
979262 CCGTTACACA
979272 GGGGG-AATCGATACCCCCTG
1 GGGGGAAATCGATACCCCCTG
* *
979292 GGGGGAAATCGGTACCCTCTG
1 GGGGGAAATCGATACCCCCTG
979313 G
1 G
979314 ACATTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.26, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAAATCGATACCCCCTG
Found at i:980705 original size:21 final size:23
Alignment explanation
Indices: 980676--980719 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
980666 AGCTTAACTC
*
980676 CTAACTCA-TAATTTT-ATTTTT
1 CTAAATCATTAATTTTGATTTTT
*
980697 CTAAATCATTTATTTTGATTTTT
1 CTAAATCATTAATTTTGATTTTT
980720 GAAAGCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.59
Consensus pattern (23 bp):
CTAAATCATTAATTTTGATTTTT
Found at i:982686 original size:19 final size:19
Alignment explanation
Indices: 982662--982701 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
982652 CCATTACATA
982662 GGGGGAATCGGTACCCCCT
1 GGGGGAATCGGTACCCCCT
*
982681 GGGGGAATCGGTACCCTCT
1 GGGGGAATCGGTACCCCCT
982700 GG
1 GG
982702 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (19 bp):
GGGGGAATCGGTACCCCCT
Found at i:982981 original size:19 final size:20
Alignment explanation
Indices: 982957--982996 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
982947 AATTTAATCG
*
982957 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
982976 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
982996 A
1 A
982997 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:984748 original size:14 final size:15
Alignment explanation
Indices: 984729--984757 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
984719 TCTTATTTTT
984729 CTTTCTTC-TCTTCC
1 CTTTCTTCATCTTCC
984743 CTTTCTTCATCTTCC
1 CTTTCTTCATCTTCC
984758 TTCACCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCTTCATCTTCC
Found at i:986135 original size:20 final size:20
Alignment explanation
Indices: 986110--986151 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
986100 CCATTACATA
986110 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
*
986130 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCCCT
986150 GG
1 GG
986152 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:986437 original size:19 final size:20
Alignment explanation
Indices: 986413--986452 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
986403 AATTTAATCG
*
986413 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
986432 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
986452 A
1 A
986453 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:989596 original size:20 final size:20
Alignment explanation
Indices: 989571--989612 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
989561 CCATTACATA
989571 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
*
989591 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCCCT
989611 GG
1 GG
989613 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:989894 original size:19 final size:20
Alignment explanation
Indices: 989870--989909 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
989860 AATTTAATCG
*
989870 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
989889 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
989909 A
1 A
989910 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:993357 original size:19 final size:19
Alignment explanation
Indices: 993330--993371 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
993320 CGAATAATTT
*
993330 AATTGAATATATAAT-TTAA
1 AATTCAATATA-AATCTTAA
993349 AATTCAATATAAATCTTAA
1 AATTCAATATAAATCTTAA
993368 AATT
1 AATT
993372 TATTAACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTCAATATAAATCTTAA
Found at i:995560 original size:24 final size:23
Alignment explanation
Indices: 995533--995580 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
995523 ATCTTTTAAA
*
995533 TTTTATAAAAAATTATATATAATT
1 TTTTATAAAAAAGTATATA-AATT
*
995557 TTTTATTAAAAAGTATATAAATT
1 TTTTATAAAAAAGTATATAAATT
995580 T
1 T
995581 AAAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTATAAAAAAGTATATAAATT
Found at i:998853 original size:16 final size:16
Alignment explanation
Indices: 998834--998867 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
998824 CAATATACGA
998834 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
998850 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
998866 AT
1 AT
998868 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:998937 original size:16 final size:18
Alignment explanation
Indices: 998905--998938 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
998895 TATTAATGTA
998905 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
998923 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
998939 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:999076 original size:27 final size:26
Alignment explanation
Indices: 999015--999076 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
999005 TATAAATATG
*
999015 AAAAATATAATTATTAAATTTAGTTT
1 AAAAATATAATTATTAAATTTACTTT
*
999041 AAAATATATAA-TCTTAAATTTATTCTTT
1 AAAA-ATATAATTATTAAATTTA--CTTT
*
999069 TAAAATAT
1 AAAAATAT
999077 TGTATCAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 14 0.47
27 10 0.33
28 6 0.20
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAAATATAATTATTAAATTTACTTT
Found at i:999606 original size:130 final size:130
Alignment explanation
Indices: 999402--999649 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
999392 AATTTTCTTC
* *
999402 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
999467 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
999532 TAATTAGGTGGTTACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
999597 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGGCCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
999650 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1000107 original size:35 final size:35
Alignment explanation
Indices: 1000046--1000121 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1000036 AATTGAATTT
* *
1000046 AATTGAATTATTTTAGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
* *
1000081 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
1000116 AATTGA
1 AATTGA
1000122 GGACTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
Found at i:1010632 original size:24 final size:26
Alignment explanation
Indices: 1010605--1010653 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1010595 AGATATAATT
*
1010605 TTAAAAT-AAATGAAAGTT-TAGTTG
1 TTAAAATGAAATAAAAGTTATAGTTG
*
1010629 TTAAAATGGAATAAAAGTTATAGTT
1 TTAAAATGAAATAAAAGTTATAGTT
1010654 TAGGTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (26 bp):
TTAAAATGAAATAAAAGTTATAGTTG
Found at i:1014069 original size:21 final size:22
Alignment explanation
Indices: 1014045--1014094 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1014035 ACCGAAGTGT
* *
1014045 CACATA-TTTGTCCTGAAGGAC
1 CACATATTTTGTCCCGAAAGAC
1014066 CACATAATTTTGTCCCGAAAGAC
1 CACAT-ATTTTGTCCCGAAAGAC
1014089 CACATA
1 CACATA
1014095 GAACCCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 2 0.08
23 18 0.72
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (22 bp):
CACATATTTTGTCCCGAAAGAC
Found at i:1014089 original size:23 final size:23
Alignment explanation
Indices: 1014051--1014094 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1014041 GTGTCACATA
* *
1014051 TTTGTCCTGAAGGACCACATAAT
1 TTTGTCCCGAAAGACCACATAAT
1014074 TTTGTCCCGAAAGACCACATA
1 TTTGTCCCGAAAGACCACATA
1014095 GAACCCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (23 bp):
TTTGTCCCGAAAGACCACATAAT
Found at i:1017501 original size:14 final size:14
Alignment explanation
Indices: 1017479--1017514 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1017469 AAGTCAACGA
1017479 TCAAC-GGTCAAAG
1 TCAACGGGTCAAAG
*
1017492 TCAATGGGTCAAAG
1 TCAACGGGTCAAAG
1017506 TCAACGGGT
1 TCAACGGGT
1017515 TGACTCGGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (14 bp):
TCAACGGGTCAAAG
Found at i:1017530 original size:14 final size:14
Alignment explanation
Indices: 1017513--1017550 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1017503 AAGTCAACGG
*
1017513 GTTGACTCGGACGA
1 GTTGACTCAGACGA
1017527 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
1017541 GTTAACTCAG
1 GTTGACTCAG
1017551 TCAGGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1022507 original size:13 final size:13
Alignment explanation
Indices: 1022489--1022515 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1022479 GACTTTTTGG
1022489 GTCAAAGTCAACA
1 GTCAAAGTCAACA
1022502 GTCAAAGTCAACA
1 GTCAAAGTCAACA
1022515 G
1 G
1022516 GTTGATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:1034396 original size:6 final size:6
Alignment explanation
Indices: 1034385--1034474 Score: 85
Period size: 6 Copynumber: 14.3 Consensus size: 6
1034375 TATTACGCCT
*
1034385 AAGAAA AAGAAA AAG-AA AAGAAGA AA-AATA AGAGAAA AAGAAA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAA-A AAGAA-A A-AGAAA AAGAAA AAGAAA
* *
1034434 ATGAAA AAGAAAA GAAGAAA AAGAAA TAAGAAC AAGAAA AA
1 AAGAAA AAG-AAA -AAGAAA AAGAAA -AAGAAA AAGAAA AA
1034475 AAAGGGTTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
5 5 0.07
6 45 0.62
7 17 0.24
8 5 0.07
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:1034410 original size:14 final size:14
Alignment explanation
Indices: 1034391--1034473 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 14
1034381 GCCTAAGAAA
1034391 AAGAAAAAGAAAAG
1 AAGAAAAAGAAAAG
*
1034405 AAG-AAAA-ATAAG
1 AAGAAAAAGAAAAG
1034417 -AGAAAAAGAAAATG
1 AAGAAAAAGAAAA-G
1034431 AAAATGAAAAAGAAAAG
1 --AA-GAAAAAGAAAAG
*
1034448 AAGAAAAAG-AAAT
1 AAGAAAAAGAAAAG
*
1034461 AAGAACAAGAAAA
1 AAGAAAAAGAAAA
1034474 AAAAGGGTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.04
12 8 0.14
13 18 0.32
14 14 0.25
15 2 0.04
17 2 0.04
18 11 0.19
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:1034422 original size:31 final size:30
Alignment explanation
Indices: 1034385--1034477 Score: 116
Period size: 31 Copynumber: 2.9 Consensus size: 30
1034375 TATTACGCCT
1034385 AAGAAAAAGAAAAAGAAAAGAAGAAAAATAAG
1 AAGAAAAAGAAAAAGAAAAGAA-AAAAA-AAG
*
1034417 -AGAAAAAGAAAATGAAAATGAAAAAGAAAAG
1 AAGAAAAAGAAAAAGAAAA-GAAAAA-AAAAG
1034448 AAGAAAAAGAAATAAGAACAAGAAAAAAAA
1 AAGAAAAAGAAA-AAGAA-AAGAAAAAAAA
1034478 GGGTTCAAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
31 23 0.43
32 19 0.35
33 10 0.19
34 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (30 bp):
AAGAAAAAGAAAAAGAAAAGAAAAAAAAAG
Found at i:1035739 original size:139 final size:140
Alignment explanation
Indices: 1035476--1036192 Score: 770
Period size: 140 Copynumber: 5.2 Consensus size: 140
1035466 AACCAATCAT
* * * * *
1035476 ATTTCCAATAGAGAGTTTATACTGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCGTAATGA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
* *
1035541 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGTGACGCCTCACTTG
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGATGCCTCACTTG
1035606 AGGGATTAAC
131 AGGGATTAAC
** * * * *
1035616 ATTTTGAATAGAGAGTTCATAACGAGGAGAACTCAT-TGATAGAGGGAGAAGAAGTTCATAATGA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
* * * *
1035680 TAAGAACTTGTTCAACCTTTGCTTGATTCATCGCATTTGGAGTTAAATCAGCGATGCCTCACTTG
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGATGCCTCACTTG
1035745 AGGGATTAAC
131 AGGGATTAAC
* * * * *
1035755 ATTTCCAATGGAGAGATCATAATGAGAAGAATTCATCCAATAGATGGAGAAGAAGTTCATAATAA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
* * * *
1035820 GAAGAACTTGTTCAATCTTTGCTCGATTTATCGTA-TT----TTGAAT-AGTGACT-CCTCAGTT
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGA-TGCCTCACTT
1035878 GAGGGATTAAC
130 GAGGGATTAAC
* * * * * *
1035889 ATTTCCAATGGAAAGTTAATAATGAGAAGAACTCATCAGATAGAGGGATAAGAAATTC---AT--
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
* * ** * * *
1035949 ----AA-TTGTTCTATCTTTATTCGATTCATCGTATATGGAGTTGAATTAGTGATGCCTCACTTG
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGATGCCTCACTTG
* *
1036009 AGGGATCAAT
131 AGGGATTAAC
* * * *
1036019 ATTTCTAATAGAGAGTTCACAATGAGAAAAACTCATCCGATAGAGGGATAAGAAGTTCATAATAA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
* * * * * *
1036084 GAAGAACTTGTTAAACATTTGGTCGATTCATCGCATTTGGAGTTGAATCAGCGACGCCTCAC-TC
66 GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGATGCCTCACTTG
**
1036148 AGGGGACCAAC
131 A-GGGATTAAC
* * * *
1036159 ATTTCCAGTAGAGAGCTCGTAATGAGAAAAACTC
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTC
1036193 GCAACTTGAA
Statistics
Matches: 481, Mismatches: 76, Indels: 40
0.81 0.13 0.07
Matches are distributed among these distances:
124 24 0.05
125 3 0.01
129 7 0.01
130 71 0.15
131 2 0.00
133 2 0.00
134 71 0.15
135 6 0.01
139 131 0.27
140 164 0.34
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (140 bp):
ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATAA
GAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATTTGGAGTTGAATCAGTGATGCCTCACTTG
AGGGATTAAC
Found at i:1036082 original size:264 final size:268
Alignment explanation
Indices: 1035474--1036121 Score: 743
Period size: 264 Copynumber: 2.4 Consensus size: 268
1035464 TAAACCAATC
* * * *
1035474 ATATTTCCAATAGAGAGTTTATACTGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCGTAAT
1 ATATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
* * *
1035539 GAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGTGACGCCTCACT
66 AAGAAGAACTTGTTCAAACTTTGCTCGATTCATCG--TAT---TTTGAATCAGTGACGCCTCACT
** * * * *
1035604 TGAGGGATTAACATTTTGAATAGAGAGTTCATAACGAGGAGAACTCATTGATAGAGGGAGAAGAA
126 TGAGGGATTAACATTTCCAATAGAAAGTTAATAACGAGAAGAACTCATAGATAGAGGGAGAAGAA
* * *
1035669 GTTCATAATGATAAGAACTTGTTCAACCTTTGCTTGATTCATCGCATTTGGAGTTAAATCAGCGA
191 --T-AT-ATCAT-A-AACTTGTTCAACCTTTGATTGATTCATCGCATATGGAGTTAAATCAGCGA
*
1035734 TGCCTCACTTGAGGGATTA
250 TGCCTCACTTGAGGGATCA
* * * * * *
1035753 ACATTTCCAATGGAGAGATCATAATGAGAAGAATTCATCCAATAGATGGAGAAGAAGTTCATAAT
1 ATATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
* * * *
1035818 AAGAAGAACTTGTTCAATCTTTGCTCGATTTATCGTATTTTGAAT-AGTGACTCCTCAGTTGAGG
66 AAGAAGAACTTGTTCAAACTTTGCTCGATTCATCGTATTTTGAATCAGTGACGCCTCACTTGAGG
* * *
1035882 GATTAACATTTCCAATGGAAAGTTAATAATGAGAAGAACTCATCAGATAGAGGGATAAGAA-AT-
131 GATTAACATTTCCAATAGAAAGTTAATAACGAGAAGAACTCAT-AGATAGAGGGAGAAGAATATA
* * * * * *
1035945 TCAT-AA-TTGTTCTATCTTT-ATTCGATTCATCGTATATGGAGTTGAATTAGTGATGCCTCACT
195 TCATAAACTTGTTCAACCTTTGATT-GATTCATCGCATATGGAGTTAAATCAGCGATGCCTCACT
1036007 TGAGGGATCA
259 TGAGGGATCA
* * * *
1036017 ATATTTCTAATAGAGAGTTCACAATGAGAAAAACTCATCCGATAGAGGGATAAGAAGTTCATAAT
1 ATATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
* *
1036082 AAGAAGAACTTGTT-AAACATTTGGTCGATTCATCGCATTT
66 AAGAAGAACTTGTTCAAAC-TTTGCTCGATTCATCGTATTT
1036122 GGAGTTGAAT
Statistics
Matches: 317, Mismatches: 49, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
263 5 0.02
264 141 0.44
265 2 0.01
268 3 0.01
270 2 0.01
273 53 0.17
274 21 0.07
277 3 0.01
279 87 0.27
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (268 bp):
ATATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
AAGAAGAACTTGTTCAAACTTTGCTCGATTCATCGTATTTTGAATCAGTGACGCCTCACTTGAGG
GATTAACATTTCCAATAGAAAGTTAATAACGAGAAGAACTCATAGATAGAGGGAGAAGAATATAT
CATAAACTTGTTCAACCTTTGATTGATTCATCGCATATGGAGTTAAATCAGCGATGCCTCACTTG
AGGGATCA
Found at i:1036312 original size:3 final size:3
Alignment explanation
Indices: 1036304--1036346 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1036294 CATTTTTTAA
* * *
1036304 TAT TAT TAT TAA TAT TAT TA- TAT TAT AAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1036347 AACTAATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1036329 original size:17 final size:18
Alignment explanation
Indices: 1036304--1036346 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
1036294 CATTTTTTAA
*
1036304 TATTATTATTAATATTAT
1 TATTATTATAAATATTAT
1036322 TA-TATTATAAATATTAT
1 TATTATTATAAATATTAT
1036339 TATTATTA
1 TATTATTA
1036347 AACTAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATAAATATTAT
Found at i:1036354 original size:20 final size:18
Alignment explanation
Indices: 1036313--1036354 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1036303 ATATTATTAT
*
1036313 TAATATTATTATATTATA
1 TAATATTATTATATTAAA
1036331 -AATATTATTATTATTAAA
1 TAATATTATTA-TATTAAA
1036349 CTAATA
1 -TAATA
1036355 ACCCATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 10 0.50
18 6 0.30
20 4 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTATTATATTAAA
Done.