Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:818619 original size:2 final size:2
Alignment explanation
Indices: 818612--818646 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
818602 TCAAAGAGTG
818612 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
818647 TTTGATTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:821068 original size:36 final size:36
Alignment explanation
Indices: 821020--821344 Score: 200
Period size: 36 Copynumber: 9.4 Consensus size: 36
821010 GAAGATTTTG
*
821020 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* * *
821056 TGTTTTAGGAGAAA-TAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACT--ATCTCAAGAGAGACAAAATT
* *
821085 TGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
821121 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
821157 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * * * * * *
821194 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* * * *
821230 TTTTTCCAA-AAAAACATAT-TC-----A-A-ATATTT
1 TGTTT-CAAGAGAAAC-TATCTCAAGAGAGACAAAATT
* * * *
821259 TGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* * * *
821295 TGTTTCAAGGGAAATTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
821331 TATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
821345 TGTTTTCAAT
Statistics
Matches: 229, Mismatches: 37, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
28 7 0.03
29 28 0.12
30 3 0.01
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 3 0.01
36 145 0.63
37 36 0.16
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
Found at i:821120 original size:65 final size:67
Alignment explanation
Indices: 820969--821134 Score: 221
Period size: 65 Copynumber: 2.5 Consensus size: 67
820959 TGAAAAACGG
* **
820969 TCTCAAGGGAAACAAAATTTTGTTTTAAGG-GAAATAAATTTGAAGATTTTGTGTTTCAAGAGAA
1 TCTCAAGGGAGACAAAA-TTTGTTTT-AGGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAA
821033 ACTA
64 ACTA
*
821037 TCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAAC
1 TCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
821100 TA
66 TA
* * * *
821102 TCTCAAGAGAGACGAAATTTGTTTCAAGAGAAA
1 TCTCAAGGGAGACAAAATTTGTTTTAGGAGAAA
821135 CTGTCTCAAG
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 45 0.51
66 6 0.07
67 22 0.25
68 16 0.18
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (67 bp):
TCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
TA
Found at i:821128 original size:21 final size:21
Alignment explanation
Indices: 821104--821168 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
821094 GGAAACTATC
821104 TCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
* *
821125 TC---A-AGA-GAAA-CTGTC
1 TCAAGAGAGACGAAATTTGTT
821140 TCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
*
821161 TTAAGAGA
1 TCAAGAGA
821169 AACTGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 3 0.09
18 2 0.06
19 3 0.09
20 4 0.12
21 12 0.36
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACGAAATTTGTT
Found at i:821216 original size:37 final size:36
Alignment explanation
Indices: 821083--821344 Score: 236
Period size: 36 Copynumber: 7.4 Consensus size: 36
821073 ATTCAAAGAT
* *
821083 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
821119 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
821155 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
821191 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAT
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
821228 TTTTTTTCCAA-AAAAACATAT-TC---A-A-A--TAT
1 TTTGTTT-CAAGAGAAAC-TGTCTCAAGAGAGACGAAA
* * * *
821257 TTTGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
821293 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
821329 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
821345 TGTTTTCAAT
Statistics
Matches: 185, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.03
29 12 0.06
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
36 129 0.70
37 34 0.18
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:821330 original size:20 final size:20
Alignment explanation
Indices: 821269--821330 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
821259 TGTTTCAAGG
*
821269 GAAATTGTCTTAAGAGAGAC
1 GAAATTGTCTCAAGAGAGAC
* *
821289 AAAATTTGTTTC-A-AG-G--
1 GAAA-TTGTCTCAAGAGAGAC
821305 GAAATTGTCTCAAGAGAGAC
1 GAAATTGTCTCAAGAGAGAC
821325 GAAATT
1 GAAATT
821331 TATTTCAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
15 6 0.19
16 4 0.13
17 2 0.06
18 2 0.06
19 2 0.06
20 10 0.32
21 5 0.16
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (20 bp):
GAAATTGTCTCAAGAGAGAC
Found at i:821432 original size:102 final size:102
Alignment explanation
Indices: 821259--821600 Score: 528
Period size: 102 Copynumber: 3.4 Consensus size: 102
821249 TCAAATATTT
* * * * *
821259 TGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAA-TTTGTTTCAAGGGAAATTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
821323 ACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
821360 TGTTTCAAGAGAAACTGTCTTAAGGGAGGA-AAAATTTTGTTTTAAGGGAAACTATCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTTAAGGGA-GACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
821424 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
65 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
821462 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAG
1 TGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
821527 ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
821564 TGTTTCAAGAGAAACTATCTCT-AGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCT-TAAGGGAGACAAAATTT
821601 AGTTCCAAAA
Statistics
Matches: 222, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
101 30 0.14
102 192 0.86
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:821513 original size:37 final size:36
Alignment explanation
Indices: 821462--821548 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
821452 TCAATGTTTA
* * *
821462 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAA-TT
* *
821499 TGTTTCAAGGGAAACTATCTCAATCGAGATAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATT
**
821535 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
821549 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 14 0.33
37 29 0.67
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATT
Found at i:822015 original size:106 final size:106
Alignment explanation
Indices: 821830--822152 Score: 484
Period size: 106 Copynumber: 3.0 Consensus size: 106
821820 TGTATTGTTC
* * * * * * *
821830 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAATTAAGAAATTGGTTGTTTACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
* * * * *
821895 GCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
821936 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
822001 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
822042 CGAGTCCAATATCATTCACTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
*
822107 ACCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
822148 CGAGT
1 CGAGT
822153 GGCACGATAT
Statistics
Matches: 196, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 196 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:822788 original size:32 final size:33
Alignment explanation
Indices: 822752--822843 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
822742 CCAAAGATGT
* *
822752 CCCAATATTCGATGTTAAATCTCAAAAAAA-GC
1 CCCAACATTTGATGTTAAATCTCAAAAAAATGC
822784 CCCAACATTTGATGTTAAATCT-AAAAAAATTGC
1 CCCAACATTTGATGTTAAATCTCAAAAAAA-TGC
*
822817 CCCAACATTTGATGTTGAATCTTCAAA
1 CCCAACATTTGATGTTAAATC-TCAAA
822844 GATGCCCTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
31 7 0.13
32 20 0.38
33 22 0.42
34 1 0.02
35 3 0.06
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (33 bp):
CCCAACATTTGATGTTAAATCTCAAAAAAATGC
Found at i:823862 original size:69 final size:69
Alignment explanation
Indices: 823746--823883 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
823736 TGTCTCTCTC
*
823746 TTGATGTTCCATGATCTTCAAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCAAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
823811 TCAT
66 TCAT
* * * * *
823815 TTGATGCTCTATGATCTTCGAGT-GAAGTGGTTCAGTGATTC-GAAAATGATTGTGCTTGATCAA
1 TTGATGCTCCATGATCTTCAAGTAG-AGTGATGCAGTAATTCAG-AAATGATTGTGCTTGATCAA
823878 TCTCAT
64 TCTCAT
823884 AGTTTAAATC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 2 0.03
69 59 0.97
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCAAGTAGAGTGATGCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:823990 original size:16 final size:16
Alignment explanation
Indices: 823964--824006 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
823954 AATTTTTCTT
823964 TTTTATTTTCTCTTTGC
1 TTTT-TTTTCTCTTTGC
* *
823981 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTCTTTGC
*
823997 TTTTTGTTCT
1 TTTTTTTTCT
824007 GATTGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTTTTTCTCTTTGC
Found at i:827199 original size:16 final size:17
Alignment explanation
Indices: 827167--827205 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
827157 TATTAAGAAA
827167 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
827184 AAAATAA-AGGAAAAAT
1 AAAATAATAGAAAAAAT
*
827200 ATAATA
1 AAAATA
827206 TATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:830204 original size:22 final size:22
Alignment explanation
Indices: 830176--830240 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
830166 AAAAGACCAC
830176 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
830198 TATGTCCCGAAGGACCAC----
1 TATGTCCCGAAGGACCACTGTA
* *
830216 TATGTCTCGAATGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
830238 TAT
1 TAT
830241 CCCTTGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 16 0.43
22 21 0.57
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:830215 original size:40 final size:40
Alignment explanation
Indices: 830160--830240 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
830150 ATTGAATATT
830160 TGTCCCAAAAGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCAAAAGACCACTATGTCCCGAAGGACCACTGTATA
* * * *
830200 TGTCCCGAAGGACCACTATGTCTCGAATGACCACTGTATA
1 TGTCCCAAAAGACCACTATGTCCCGAAGGACCACTGTATA
830240 T
1 T
830241 CCCTTGAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
TGTCCCAAAAGACCACTATGTCCCGAAGGACCACTGTATA
Found at i:830221 original size:18 final size:18
Alignment explanation
Indices: 830160--830234 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
830150 ATTGAATATT
* *
830160 TGTCCCAAAAGACCACTA
1 TGTCCCGAAGGACCACTA
830178 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
830200 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
830218 TGTCTCGAATGACCACT
1 TGTCCCGAAGGACCACT
830235 GTATATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 31 0.63
22 18 0.37
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:831068 original size:21 final size:21
Alignment explanation
Indices: 831039--831079 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
831029 TTTTTTCTTT
831039 AGGGCGGAATC-GATACCCCCC
1 AGGGCGGAATCTG-TACCCCCC
*
831060 AGGGGGGAATCTGTACCCCC
1 AGGGCGGAATCTGTACCCCC
831080 TGCACAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.22, C:0.34, G:0.32, T:0.12
Consensus pattern (21 bp):
AGGGCGGAATCTGTACCCCCC
Found at i:831957 original size:19 final size:20
Alignment explanation
Indices: 831918--831962 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
831908 TCCAGAATCC
*
831918 TCTCATATCTTCTTCCTTCT
1 TCTCTTATCTTCTTCCTTCT
831938 T-TCTTATCTTCTTCAC-TCT
1 TCTCTTATCTTCTTC-CTTCT
831957 TCTCTT
1 TCTCTT
831963 CTTCCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (20 bp):
TCTCTTATCTTCTTCCTTCT
Found at i:832464 original size:21 final size:21
Alignment explanation
Indices: 832423--832464 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
832413 TTATGGGCTG
* *
832423 GGGGAATCGGTACCCATTCAA
1 GGGGAATCGATACCCACTCAA
*
832444 GGGGAATCGATACCCCCTCAA
1 GGGGAATCGATACCCACTCAA
832465 CGAATATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGGAATCGATACCCACTCAA
Found at i:833194 original size:23 final size:23
Alignment explanation
Indices: 833150--833194 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
833140 ATTATTATAT
* *
833150 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGATGCAATTATACGC
* *
833173 GGCACTTCGATGCATTTATACG
1 GGCACTACGATGCAATTATACG
833195 AGCTGTGGTG
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:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGC
Found at i:839266 original size:21 final size:21
Alignment explanation
Indices: 839225--839266 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
839215 TTCTGGGCTG
* *
839225 GGGGAATCGGTACCCATTCAA
1 GGGGAATCGATACCCACTCAA
*
839246 GGGGAATCGATACCCCCTCAA
1 GGGGAATCGATACCCACTCAA
839267 TGAATATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGGAATCGATACCCACTCAA
Found at i:839997 original size:23 final size:23
Alignment explanation
Indices: 839953--839997 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
839943 ATTATTATAT
*
839953 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
839976 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
839998 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:842153 original size:22 final size:22
Alignment explanation
Indices: 842121--842166 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
842111 TTATCTCTTA
842121 TTTAAAATTTAGAATCTAAGAT
1 TTTAAAATTTAGAATCTAAGAT
* * *
842143 TTTAAATTTTAGAATTTATGAT
1 TTTAAAATTTAGAATCTAAGAT
842165 TT
1 TT
842167 AATGGGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTAAAATTTAGAATCTAAGAT
Found at i:842688 original size:2 final size:2
Alignment explanation
Indices: 842681--842711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
842671 CCCTAAGCGC
842681 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
842712 GAGAGAGAGA
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:842716 original size:2 final size:2
Alignment explanation
Indices: 842711--842738 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
842701 ATATATATAT
842711 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
842739 GACTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:850711 original size:20 final size:21
Alignment explanation
Indices: 850688--850730 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
850678 GAGTATTAAT
850688 ACTGAGG-G-TTCGGTATCGAG
1 ACTGAGGAGCTTC-GTATCGAG
850708 ACTGAGGAGCTTCGTATCGAG
1 ACTGAGGAGCTTCGTATCGAG
850729 AC
1 AC
850731 CGAGTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 11 0.52
22 3 0.14
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
ACTGAGGAGCTTCGTATCGAG
Found at i:870204 original size:59 final size:59
Alignment explanation
Indices: 870122--870249 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
870112 CAGCAGGCTG
* * * *
870122 CATATTCGGGATTACACTAAAGTATAATTAGTGTATATAGTGGGCACAATCTTATGTGT
1 CATATTCGGGACTACACTAAAGTATAACTAGTGTATATAGTGGACACAACCTTATGTGT
** * * * *
870181 CATATTCGGGACTGTACTTAAGTATACCTAGTGTATATGGTGGACACGACCTTATGTGT
1 CATATTCGGGACTACACTAAAGTATAACTAGTGTATATAGTGGACACAACCTTATGTGT
*
870240 CATACTCGGG
1 CATATTCGGG
870250 TTAGCACTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (59 bp):
CATATTCGGGACTACACTAAAGTATAACTAGTGTATATAGTGGACACAACCTTATGTGT
Found at i:877561 original size:14 final size:14
Alignment explanation
Indices: 877538--877575 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
877528 TCTGCCTATA
*
877538 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
877551 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
877566 TGCAGGGATT
1 TGCAGGGATT
877576 ACTGCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:879928 original size:25 final size:25
Alignment explanation
Indices: 879895--879948 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
879885 TCTTTCATTT
879895 TTTTCACCTAAATCAACAAGAAGTA
1 TTTTCACCTAAATCAACAAGAAGTA
*
879920 TTTTCACCTAAATCAACAAGCAGTA
1 TTTTCACCTAAATCAACAAGAAGTA
879945 TTTT
1 TTTT
879949 GTGTCTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.33
Consensus pattern (25 bp):
TTTTCACCTAAATCAACAAGAAGTA
Found at i:883883 original size:81 final size:83
Alignment explanation
Indices: 883785--883948 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 83
883775 TATACCTGCA
*
883785 TTTGCATTCATATGACAGCATA-C-ATTCGTGTAACACATTGCATTCATATTTGCACTTAAGATT
1 TTTGCATTCACATGACAGCATATCAATT-GTGTAACACATTGCATTCATATTTGCACTTAAGATT
*
883848 TTT-ACGTATTGTTTATGT
65 TTTCACGTATTGTTAATGT
*** * *
883866 TTTGCATTCACATGACAGCATATCAATTGTGTAGTTCATTGCTTTCATCTTTGCACTTAAGATTT
1 TTTGCATTCACATGACAGCATATCAATTGTGTAACACATTGCATTCATATTTGCACTTAAGATTT
*
883931 TTCACGTGTTGTTAATGT
66 TTCACGTATTGTTAATGT
883949 CATTTGAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
81 21 0.29
82 35 0.49
83 16 0.22
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (83 bp):
TTTGCATTCACATGACAGCATATCAATTGTGTAACACATTGCATTCATATTTGCACTTAAGATTT
TTCACGTATTGTTAATGT
Found at i:888013 original size:11 final size:13
Alignment explanation
Indices: 887982--888015 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
887972 TGCCAAAGAT
887982 GAAAAGGTATGTC
1 GAAAAGGTATGTC
887995 GAAAAGGTATG-C
1 GAAAAGGTATGTC
888007 G-AAAGGTAT
1 GAAAAGGTAT
888016 CTAGTGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 11 0.52
ACGTcount: A:0.41, C:0.06, G:0.32, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTC
Found at i:891849 original size:18 final size:18
Alignment explanation
Indices: 891824--891862 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
891814 TTCAAAAACA
891824 TAAAAAAAGA-GAATGAGAT
1 TAAAAAAA-ATGAATGA-AT
891843 TAAAAAAAATGAATGAAT
1 TAAAAAAAATGAATGAAT
891861 TA
1 TA
891863 TTCTCACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (18 bp):
TAAAAAAAATGAATGAAT
Found at i:896926 original size:35 final size:35
Alignment explanation
Indices: 896887--896972 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
896877 AAAACAATCA
* *
896887 TCAATTTCATTCTAAACCCCAATTTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
896922 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
896957 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
896973 ATACTTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:896966 original size:21 final size:21
Alignment explanation
Indices: 896941--896983 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
896931 TTCTAAACCC
896941 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
896962 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
896983 T
1 T
896984 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:897138 original size:16 final size:18
Alignment explanation
Indices: 897106--897139 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
897096 TATTAATGTA
897106 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
897124 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
897140 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:897811 original size:130 final size:130
Alignment explanation
Indices: 897608--897855 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
897598 AATTTTCTTC
* * *
897608 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
897673 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
897738 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
897803 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
897856 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:899324 original size:60 final size:60
Alignment explanation
Indices: 899132--899315 Score: 271
Period size: 60 Copynumber: 3.1 Consensus size: 60
899122 TTGGGTGATA
* * * * * *
899132 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGTAACACTATATAGTC-AGAGGATC
1 ATTTTATAACTTTTAATATTCGAGGGACTTAATAAAGTAATACTCTATAGTCGAG-GGATC
* * *
899192 ATTTTATAACTTTTAATATTTGAGGGACTTAATAAAGTAATACTCTATAATCGATGGATC
1 ATTTTATAACTTTTAATATTCGAGGGACTTAATAAAGTAATACTCTATAGTCGAGGGATC
899252 ATTTTATAACTTTTAATATTCGAGGGACTTAATAAAGTAATACTCTATAGTCGAGGGATC
1 ATTTTATAACTTTTAATATTCGAGGGACTTAATAAAGTAATACTCTATAGTCGAGGGATC
899312 ATTT
1 ATTT
899316 GTGTACTTTA
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
60 110 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAATATTCGAGGGACTTAATAAAGTAATACTCTATAGTCGAGGGATC
Found at i:900196 original size:16 final size:17
Alignment explanation
Indices: 900175--900206 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
900165 TTTGGAATTA
900175 AAATTTTAAG-GATTTG
1 AAATTTTAAGAGATTTG
900191 AAATTTTAAGAGATTT
1 AAATTTTAAGAGATTT
900207 TAGAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (17 bp):
AAATTTTAAGAGATTTG
Found at i:900643 original size:120 final size:114
Alignment explanation
Indices: 900478--900689 Score: 280
Period size: 114 Copynumber: 1.8 Consensus size: 114
900468 ACACAGATGA
* ** * *
900478 TATCTTATATTTTTAGTCCGTCTGATTTTGATCTCTGATTTAAAAAAAAATAATGGTTTTGGTCT
1 TATCTTATATTTTCAGTCCGTCCAATTTTGATCACCGA-TT----AAAAA-AATGGTTTTGGTCT
*
900543 CTTATGTTATCAATACGTTTGGTTTTAGTCCCTCGGTCGTTGACTACACGAGTGT
60 CTTATATTATCAATACGTTTGGTTTTAGTCCCTCGGTCGTTGACTACACGAGTGT
* * *
900598 TATCTTATGTTTTCGGTCCGTCCAATTTTGATCACCGGTTAAAAAAATGGTTTTGGTCTCTTATA
1 TATCTTATATTTTCAGTCCGTCCAATTTTGATCACCGATTAAAAAAATGGTTTTGGTCTCTTATA
*
900663 TTATCAATACGTTTTGTTTTAGTCCCT
66 TTATCAATACGTTTGGTTTTAGTCCCT
900690 TGGGCGTTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
114 45 0.55
115 5 0.06
119 2 0.02
120 30 0.37
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.45
Consensus pattern (114 bp):
TATCTTATATTTTCAGTCCGTCCAATTTTGATCACCGATTAAAAAAATGGTTTTGGTCTCTTATA
TTATCAATACGTTTGGTTTTAGTCCCTCGGTCGTTGACTACACGAGTGT
Found at i:902824 original size:2 final size:2
Alignment explanation
Indices: 902817--902842 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
902807 ACATACATTA
902817 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
902843 TATCGTAAAA
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:910484 original size:20 final size:20
Alignment explanation
Indices: 910461--910511 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
910451 TGACCCTTCA
*
910461 ATATCGATACTAATCCT-TTG
1 ATATCGATACCAA-CCTATTG
*
910481 ATATCTATACCAACCTATTG
1 ATATCGATACCAACCTATTG
*
910501 GTATCGATACC
1 ATATCGATACC
910512 CCAGACTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (20 bp):
ATATCGATACCAACCTATTG
Found at i:910594 original size:22 final size:20
Alignment explanation
Indices: 910542--910595 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
910532 TGGGTAAAGT
*
910542 AGTATTGATACTCTAGGATG
1 AGTATCGATACTCTAGGATG
* *
910562 AGTATCAATACTCTAGTACTG
1 AGTATCGATACTCTAGGA-TG
910583 AGGTATCGATACT
1 A-GTATCGATACT
910596 TGTCTCAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCTAGGATG
Found at i:914322 original size:15 final size:16
Alignment explanation
Indices: 914297--914326 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
914287 GAGATAATTA
914297 AAATCATATATATATC
1 AAATCATATATATATC
914313 AAAT-ATATATATAT
1 AAATCATATATATAT
914327 TAACTCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATCATATATATATC
Found at i:915503 original size:13 final size:13
Alignment explanation
Indices: 915485--915519 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
915475 ATATTACCCT
915485 TAATTAAATTAAA
1 TAATTAAATTAAA
915498 TAATTAAATTAAA
1 TAATTAAATTAAA
915511 TAATTAAAT
1 TAATTAAAT
915520 CAAGTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATTAAATTAAA
Found at i:917082 original size:3 final size:3
Alignment explanation
Indices: 917067--917145 Score: 90
Period size: 3 Copynumber: 26.3 Consensus size: 3
917057 TATGTAACAT
* * *
917067 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TGTA TTA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA
*
917114 TTA TAA TAA T-A TAA TAA TAA TAA TAA -AA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
917146 TTTAATATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.06
3 58 0.88
4 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:917111 original size:17 final size:16
Alignment explanation
Indices: 917076--917157 Score: 80
Period size: 17 Copynumber: 5.1 Consensus size: 16
917066 TTAATAATAG
*
917076 TAATAATAATAAT-AA
1 TAATAATTATAATAAA
*
917091 TAATAATGTATTATAAA
1 TAATAAT-TATAATAAA
917108 TAATAATTATAATAATA
1 TAATAATTATAATAA-A
*
917125 TAATAATAATAAT-AA
1 TAATAATTATAATAAA
*
917140 -AATAATTTTAATATAA
1 TAATAATTATAATA-AA
917156 TA
1 TA
917158 TTTATAACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
14 10 0.18
15 8 0.15
16 14 0.25
17 23 0.42
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
TAATAATTATAATAAA
Found at i:917112 original size:26 final size:24
Alignment explanation
Indices: 917067--917157 Score: 100
Period size: 26 Copynumber: 3.8 Consensus size: 24
917057 TATGTAACAT
917067 TAATAA-TAGTAATAATAATAATAA
1 TAATAATTA-TAATAATAATAATAA
* *
917091 TAATAATGTATTATAAATAATAATTA
1 TAATAAT-TATAAT-AATAATAATAA
917117 TAATAA-TATAATAATAATAATAA
1 TAATAATTATAATAATAATAATAA
*
917140 -AATAATTTTAAT-ATAATA
1 TAATAATTATAATAATAATA
917158 TTTATAACCC
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 11 0.19
23 15 0.26
24 11 0.19
25 3 0.05
26 18 0.31
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATAATTATAATAATAATAATAA
Found at i:917151 original size:14 final size:14
Alignment explanation
Indices: 917069--917157 Score: 76
Period size: 14 Copynumber: 6.4 Consensus size: 14
917059 TGTAACATTA
*
917069 ATAATAGTAATAAT
1 ATAATAATAATAAT
917083 AATAATAATAATAAT
1 -ATAATAATAATAAT
* *
917098 GT-ATTAT-A-AAT
1 ATAATAATAATAAT
*
917109 AATAATTATAATAAT
1 -ATAATAATAATAAT
917124 ATAATAATAATAAT
1 ATAATAATAATAAT
* **
917138 AAAATAATTTTAAT
1 ATAATAATAATAAT
917152 ATAATA
1 ATAATA
917158 TTTATAACCC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
11 3 0.05
12 2 0.03
13 9 0.15
14 31 0.51
15 16 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:917507 original size:55 final size:55
Alignment explanation
Indices: 917348--917752 Score: 479
Period size: 55 Copynumber: 7.5 Consensus size: 55
917338 CTCTCTCTTT
* * * * * *
917348 CTTCAGGGAGTGTAAAACTCAAACAATCTTCATA-AAACGAGTCTGTTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTCTGCTCCCTATTC
* * * *
917403 TTTCAGAGAGTATAGGGCTCG----ATCTTTAACAAACGTGT-TCGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCT-GCTCCCTATTC
* * * * *
917454 CTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCTGCTCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
*
917509 CTTCAGAGAGTATAAGACT----CAATCTTCAACAAACGTGTCTCCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
* ** *
917560 CTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATTGTGTCTGCTCCTTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
*
917615 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
* * ** * *
917670 CTTCAGAGAGTATAAGACTCGAACCATTTTCAACAATTGTGTATGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
917725 CTTCAGAGAGTATAAGACTCGAACAATC
1 CTTCAGAGAGTATAAGACTCGAACAATC
917753 GTGTCTACTC
Statistics
Matches: 303, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.01
51 88 0.29
55 212 0.70
56 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTC
Found at i:917507 original size:106 final size:106
Alignment explanation
Indices: 917334--917808 Score: 477
Period size: 106 Copynumber: 4.5 Consensus size: 106
917324 GACCATCGGT
* * * * * * * * *
917334 TTCGCTCTCTCTTTCTTCAGGGAGTGTAAAACTCAAACAATCTTCATA-AAACGAGTCTGTTCCC
1 TTCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTCTGCTCCC
* * *
917398 TA-TTCTTTCAGAGAGTATAGGGCTCGATCTTTAACAAACGTG
65 TATTTC-TTCAGAGAGTATAAGACTCGATCTTCAACAAACGTG
* * * *
917440 TTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCTGCTCTCT
1 TTCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCT
*
917505 ATTTCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTG
66 ATTTCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTG
* ** *
917546 TCTC-CTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATTGTGTCTGCTCCT
1 T-TCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCC
* *
917610 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTG
65 TATTTCTTCAGAGAGTATAAGACTCG----ATCTTCAACAAACGTG
* * ** *
917656 -TCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACCATTTTCAACAATTGTGTATGCTCCC
1 TTC-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCC
*
917720 TATTTCTTCAGAGAGTATAAGACTCG------AACAATCGTG
65 TATTTCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTG
* * * * * *
917756 -TCTACTCCCTATTTCTTTAGAGAGTATAAAACTTGAACAATCTTCCACAAACG
1 TTC-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
917809 GGTTCGCTCC
Statistics
Matches: 316, Mismatches: 44, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
100 53 0.17
105 1 0.00
106 160 0.51
107 5 0.02
108 2 0.01
110 95 0.30
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (106 bp):
TTCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCT
ATTTCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTG
Found at i:917621 original size:161 final size:163
Alignment explanation
Indices: 917443--917752 Score: 462
Period size: 161 Copynumber: 1.9 Consensus size: 163
917433 AAACGTGTTC
* * *
917443 GCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCTGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAAACGTGTCTGCTCCCTATT
* *
917508 TCTTCAGAGAGTATAAGACTC-A-ATCTTCAACAAACGTGTCTCCTCCCTATTCCTTCAGAGAGT
66 CCTTCAGAGAGTATAAGACTCAACATCTTCAACAAACGTGTATCCTCCCTATTCCTTCAGAGAGT
917571 ATAAGACTCAAACAATCTTCAACAATTGTGTCT
131 ATAAGACTCAAACAATCTTCAACAATTGTGTCT
* * *
917604 GCTCCTTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAAACGTGTCTGCTCCCTATT
* ** * *
917669 CCTTCAGAGAGTATAAGACTCGAACCATTTTCAACAATTGTGTATGCTCCCTATTTCTTCAGAGA
66 CCTTCAGAGAGTATAAGACTC-AA-CATCTTCAACAAACGTGTATCCTCCCTATTCCTTCAGAGA
*
917734 GTATAAGACTCGAACAATC
129 GTATAAGACTCAAACAATC
917753 GTGTCTACTC
Statistics
Matches: 131, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 79 0.60
163 1 0.01
165 51 0.39
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (163 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAACCTTCAACAAACGTGTCTGCTCCCTATT
CCTTCAGAGAGTATAAGACTCAACATCTTCAACAAACGTGTATCCTCCCTATTCCTTCAGAGAGT
ATAAGACTCAAACAATCTTCAACAATTGTGTCT
Found at i:917765 original size:45 final size:45
Alignment explanation
Indices: 917701--917797 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
917691 AACCATTTTC
* * *
917701 AACAATTGTGTATGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
1 AACAATCGTGTATACTCCCTATTTCTTCAGAGAGTATAAAACTCG
* * *
917746 AACAATCGTGTCTACTCCCTATTTCTTTAGAGAGTATAAAACTTG
1 AACAATCGTGTATACTCCCTATTTCTTCAGAGAGTATAAAACTCG
917791 AACAATC
1 AACAATC
917798 TTCCACAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (45 bp):
AACAATCGTGTATACTCCCTATTTCTTCAGAGAGTATAAAACTCG
Found at i:917826 original size:100 final size:100
Alignment explanation
Indices: 917646--917827 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 100
917636 AACAATCTTC
* * * * ** *
917646 AACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACCATTTTCAACAATTGTG
1 AACAATCGTGTCTACTCCCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACGGG
*
917711 TATGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
66 TATGCTCCATATTTCTTCAGAGAGTATAAGACTCG
* * * *
917746 AACAATCGTGTCTACTCCCTATTTCTTTAGAGAGTATAAAACTTGAACAATCTTCCACAAACGGG
1 AACAATCGTGTCTACTCCCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACGGG
*
917811 T-TCGCTCCATCTTTCTT
66 TAT-GCTCCATATTTCTT
917828 TCAGGAAGTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 1 0.01
100 67 0.99
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (100 bp):
AACAATCGTGTCTACTCCCTATTCCTTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACGGG
TATGCTCCATATTTCTTCAGAGAGTATAAGACTCG
Found at i:917863 original size:56 final size:56
Alignment explanation
Indices: 917760--918342 Score: 582
Period size: 56 Copynumber: 10.5 Consensus size: 56
917750 ATCGTGTCTA
* * * * **
917760 CTCCCTATTTCTTT-A-GAGAGTATAAAACTTGAACAATCTTCCACAAACGGGTTCG
1 CTCCCTCTTTCTTTCAGGA-AGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
* * * *
917815 CTCCATCTTTCTTTCAGGAAGTATAGAACTCGGATAATGTTCTGCAAACGAGTTCG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
917871 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
* * *
917927 CTCCCTCTTTTTTTTCAGGAAGTATAGAACT-GAAATAATCTTCTGCAAACGGTTTTG
1 CTCCCTC-TTTCTTTCAGGAAGTATAGAACTCG-AATAATCTTCTGCAAACGGGTTCG
* ** *
917984 CTCCCTCTTTCTTTCAGGAAGTATAGAGCTCGAATAATCTTCTGCAAACAAGTTTG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
* * * *
918040 CTCCATCTTTCTTTCAGGAAGTATAGAACTCAAATAATCTTCTGCAAATGGGTTTG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
* * *
918096 CTCCTTCTTTATTTCAGGAAGTATAGAACTCGAATAATCTTCTACAAACGGG-TCTG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTC-G
* * * * * * **
918152 CTCCCTCTTTCTCT-AGGGAGTATGGAACTTGAA-CATCTTCTTCTTACGGGTTCG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
* * * * *
918206 CTCCCTCTTTCTCT-AGGGAA-TATGGAACTAGAA-CATATTCTG-AAGACGGGTTCG
1 CTCCCTCTTTCTTTCA-GGAAGTATAGAACTCGAATAATCTTCTGCAA-ACGGGTTCG
* * * * * * *
918260 CTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAA-CATCTTAT-TATTACGGGTTCG
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCA-AACGGGTTCG
* * *
918314 CTCCCTCTTTCTCT-AGGGAGTATGGAACT
1 CTCCCTCTTTCTTTCAGGAAGTATAGAACT
918343 TGAACATCTT
Statistics
Matches: 461, Mismatches: 55, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
53 3 0.01
54 129 0.28
55 34 0.07
56 241 0.52
57 54 0.12
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (56 bp):
CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACGGGTTCG
Found at i:918078 original size:169 final size:168
Alignment explanation
Indices: 917778--918292 Score: 571
Period size: 169 Copynumber: 3.1 Consensus size: 168
917768 TTCTTTAGAG
* * * * * *
917778 AGTATAAAACTTGAACAATCTTCCACAAACGGGTTCGCTCCATCTTTCTTTCAGGAAGTATAGAA
1 AGTATAGAACTCGAATAATCTTCTACAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGAA
* * * * *
917843 CTCGGATAATGTTCTGCAAACGAGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAA
66 CTCGAATAATCTTCTGCAAACAAGTTCGCTCCATCTTTCTTTCAGGAAGTATAGAACTCAAATAA
*
917908 TCTTCTGCAAACGGGTTCGCTCCCTCTTTTTTTTCAGGA
131 TCTTCTGCAAACGGGTTCGCTCCCTC-TTTATTTCAGGA
* *
917947 AGTATAGAACT-GAAATAATCTTCTGCAAACGGTTTTGCTCCCTCTTTCTTTCAGGAAGTATAGA
1 AGTATAGAACTCG-AATAATCTTCTACAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGA
* *
918011 GCTCGAATAATCTTCTGCAAACAAGTTTGCTCCATCTTTCTTTCAGGAAGTATAGAACTCAAATA
65 ACTCGAATAATCTTCTGCAAACAAGTTCGCTCCATCTTTCTTTCAGGAAGTATAGAACTCAAATA
* * *
918076 ATCTTCTGCAAATGGGTTTGCTCCTTCTTTATTTCAGGA
130 ATCTTCTGCAAACGGGTTCGCTCCCTCTTTATTTCAGGA
* * * *
918115 AGTATAGAACTCGAATAATCTTCTACAAACGGGTCTGCTCCCTCTTTCTCT-AGGGAGTATGGAA
1 AGTATAGAACTCGAATAATCTTCTACAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGAA
* * * ** ** * * *
918179 CTTGAA-CATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT-AGGGAA-TATGGAACT-AGAA-
66 CTCGAATAATCTTCTGCAAACAAGTTCGCTCCATCTTTCTTTCA-GGAAGTATAGAACTCA-AAT
* * * * *
918239 CATATTCTG-AAGACGGGTTCGCTCCCTCTTTCTCT-AGGG
129 AATCTTCTGCAA-ACGGGTTCGCTCCCTCTTTATTTCAGGA
*
918278 AGTATGGAACTCGAA
1 AGTATAGAACTCGAA
918293 CATCTTATTA
Statistics
Matches: 296, Mismatches: 45, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
163 19 0.06
164 26 0.09
165 11 0.04
166 30 0.10
167 15 0.05
168 57 0.19
169 138 0.47
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (168 bp):
AGTATAGAACTCGAATAATCTTCTACAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGAA
CTCGAATAATCTTCTGCAAACAAGTTCGCTCCATCTTTCTTTCAGGAAGTATAGAACTCAAATAA
TCTTCTGCAAACGGGTTCGCTCCCTCTTTATTTCAGGA
Found at i:918201 original size:54 final size:54
Alignment explanation
Indices: 918143--918354 Score: 327
Period size: 54 Copynumber: 3.9 Consensus size: 54
918133 TCTTCTACAA
*
918143 ACGGG-TCTGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCTTCTT
1 ACGGGTTC-GCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCTTATT
* * * * **
918197 ACGGGTTCGCTCCCTCTTTCTCTAGGGAATATGGAACTAGAACATATTCTGAAG
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCTTATT
* *
918251 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTATTATT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCTTATT
918305 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCT
918355 CTTGCTTCAC
Statistics
Matches: 141, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 139 0.99
55 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAACATCTTCTTATT
Found at i:918416 original size:37 final size:37
Alignment explanation
Indices: 918356--918437 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
918346 ACATCTTCTC
918356 TTGCTTCACTACTTCTTTATGAAGGCTTATAG-ATGAT
1 TTGCTTCACTACTTCTTTATGAAGGCTTA-AGTATGAT
* *
918393 TTGCTTCACTAC-TCTTTCGTGAAGGCTTAAGTTTGAT
1 TTGCTTCACTACTTCTTT-ATGAAGGCTTAAGTATGAT
918430 TTGCTTCA
1 TTGCTTCA
918438 AAGGTCGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 7 0.17
37 34 0.83
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.44
Consensus pattern (37 bp):
TTGCTTCACTACTTCTTTATGAAGGCTTAAGTATGAT
Found at i:918792 original size:37 final size:36
Alignment explanation
Indices: 918735--918883 Score: 185
Period size: 37 Copynumber: 4.1 Consensus size: 36
918725 CTGATAATCT
918735 GATGGTTTGCTTCAAC-ACTCTTCTAG-GAAGGCTTAA
1 GATGGTTTGCTTC-ACTACTCTTC-AGTGAAGGCTTAA
* * *
918771 AATGGATTTGCTTCACTACTCTTCGGTGAAGACTTAA
1 GATGG-TTTGCTTCACTACTCTTCAGTGAAGGCTTAA
* ** *
918808 GATGGTTTTCTTCACTACTCTTTGGTGAAGGATTAA
1 GATGGTTTGCTTCACTACTCTTCAGTGAAGGCTTAA
918844 GATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
1 GATGG-TTTGCTTCACTACTCTTCAGTGAAGGCTTAA
918881 GAT
1 GAT
918884 TGACTTTGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
36 39 0.40
37 58 0.60
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (36 bp):
GATGGTTTGCTTCACTACTCTTCAGTGAAGGCTTAA
Found at i:918854 original size:73 final size:73
Alignment explanation
Indices: 918735--918883 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 73
918725 CTGATAATCT
* *
918735 GATGGTTTGCTTCAACACTCTTCTAGGAAGGCTTAAAATGGATTTGCTTCACTACTCTTCGGTGA
1 GATGGTTTGCTTCAACACTCTTCTAGGAAGGATTAAAATGGATTTGCTTCACTACTCTTCAGTGA
918800 AGACTTAA
66 AGACTTAA
* * *
918808 GATGGTTTTCTTC-ACTACTCTT-TGGTGAAGGATTAAGATGGATTTGCTTCACTACTCTTCAGT
1 GATGGTTTGCTTCAAC-ACTCTTCTAG-GAAGGATTAAAATGGATTTGCTTCACTACTCTTCAGT
*
918871 GAAGGCTTAA
64 GAAGACTTAA
918881 GAT
1 GAT
918884 TGACTTTGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 4 0.06
73 64 0.94
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (73 bp):
GATGGTTTGCTTCAACACTCTTCTAGGAAGGATTAAAATGGATTTGCTTCACTACTCTTCAGTGA
AGACTTAA
Found at i:920346 original size:125 final size:125
Alignment explanation
Indices: 920115--920626 Score: 706
Period size: 125 Copynumber: 4.1 Consensus size: 125
920105 ACTAGTCCCA
* * * * * *
920115 CAACATCAACTTATACTGGTACGGGCCTTCAAAATGCCACAACACCTCAAATTGTATGGCTCATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATT
* * * **
920180 C-TCAAGGCTTTCTTGGTCT-ATATCTTGTCATCTCAACATGATGTGGGTTCAGTCACGCCC
66 CTTC-ATGCCTCCTTGGTCTGA-ATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* * * *
920240 CAATATTACCTTATACTGGTACGTGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCGTT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATT
* *
920305 CTTCATGCTTCCTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
66 CTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* *
920365 CAACATTATCTTATACTGGTACGGACCTTCAAAATGCCCCATCACCTC-AATTATAGGGCTCATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATT
* * * *
920429 CTTTACGCCTCCTTGGTCTGAATCTTGTCATCTCAATATGATGTAGGTTCAGTCGTGCCC
66 CTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* * * * * *
920489 CAACATTAACTTATACCGATACGGGCCTTCAAAATGTCCCATCACTTCAAATTATAAGGCTCACT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATT
* *
920554 CTGCATGCCTCCTTGGTCTGAATCTTGTCATCTCAATATGATGTGGGTTCAGTCGTGCCC
66 CTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
920614 CAACATTATCTTA
1 CAACATTATCTTA
920627 ACTTGAATGT
Statistics
Matches: 345, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
124 110 0.32
125 232 0.67
126 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (125 bp):
CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATT
CTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
Found at i:920569 original size:249 final size:250
Alignment explanation
Indices: 920115--920626 Score: 740
Period size: 249 Copynumber: 2.1 Consensus size: 250
920105 ACTAGTCCCA
* * * * *
920115 CAACATCAACTTATACTGGTACGGGCCTTCAAAATGCCACAACACCTCAAATTGTATGGCTCATT
1 CAACATTATCTTATACTGGTACGGACCTTCAAAATGCCACAACACCTCAAATTATAGGGCTCATT
* * * * *
920180 CTCAAGGCTTTCTTGGTCTATATCTTGTCATCTCAACATGATGTGGGTTCAGTCACGCCCCAATA
66 CTCAACGCCTCCTTGGTCTATATCTTGTCATCTCAACATGATGTAGGTTCAGTCACGCCCCAACA
* * * * ** *
920245 TTACCTTATACTGGTACGTGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCGTTCTTCA
131 TTAACTTATACCGATACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCACTCTGCA
* *
920310 TGCTTCCTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
196 TGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
* *
920365 CAACATTATCTTATACTGGTACGGACCTTCAAAATGCCCCATCACCTC-AATTATAGGGCTCATT
1 CAACATTATCTTATACTGGTACGGACCTTCAAAATGCCACAACACCTCAAATTATAGGGCTCATT
** * **
920429 CTTTACGCCTCCTTGGTCTGA-ATCTTGTCATCTCAATATGATGTAGGTTCAGTCGTGCCCCAAC
66 CTCAACGCCTCCTTGGTCT-ATATCTTGTCATCTCAACATGATGTAGGTTCAGTCACGCCCCAAC
* *
920493 ATTAACTTATACCGATACGGGCCTTCAAAATGTCCCATCACTTCAAATTATAAGGCTCACTCTGC
130 ATTAACTTATACCGATACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCACTCTGC
*
920558 ATGCCTCCTTGGTCTGAATCTTGTCATCTCAATATGATGTGGGTTCAGTCGTGCCC
195 ATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
920614 CAACATTATCTTA
1 CAACATTATCTTA
920627 ACTTGAATGT
Statistics
Matches: 232, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
249 188 0.81
250 44 0.19
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (250 bp):
CAACATTATCTTATACTGGTACGGACCTTCAAAATGCCACAACACCTCAAATTATAGGGCTCATT
CTCAACGCCTCCTTGGTCTATATCTTGTCATCTCAACATGATGTAGGTTCAGTCACGCCCCAACA
TTAACTTATACCGATACGGGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCACTCTGCA
TGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCC
Found at i:921774 original size:2 final size:2
Alignment explanation
Indices: 921763--921809 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
921753 TTGAATACAC
921763 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
921804 AT AT AT
1 AT AT AT
921810 GTTGGGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:924530 original size:21 final size:21
Alignment explanation
Indices: 924499--924553 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
924489 CCTCCAATGC
924499 GAAGTGGTCTTCATGTCTTTAT
1 GAAG-GGTCTTCATGTCTTTAT
924521 GAAGGGTCTTCATGTCTTTAT
1 GAAGGGTCTTCATGTCTTTAT
* *
924542 CAATGGTCTTCA
1 GAAGGGTCTTCA
924554 GATCTCCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (21 bp):
GAAGGGTCTTCATGTCTTTAT
Found at i:927243 original size:2 final size:2
Alignment explanation
Indices: 927234--927290 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
927224 AAACAAATAG
927234 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
927275 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
927291 CAAGAGATCG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:927946 original size:3 final size:3
Alignment explanation
Indices: 927932--927989 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
927922 TATGTAACAT
* * *
927932 TAA TAG TAA TAA TAA TAA TAA TAA TGTA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
927978 TAA TAA T-A TAA T
1 TAA TAA TAA TAA T
927990 TTTAATATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:931804 original size:13 final size:13
Alignment explanation
Indices: 931786--931812 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
931776 TATGTAGTAG
931786 ATCTACAATACAT
1 ATCTACAATACAT
931799 ATCTACAATACAT
1 ATCTACAATACAT
931812 A
1 A
931813 AAAGCAATGG
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ATCTACAATACAT
Found at i:942631 original size:22 final size:22
Alignment explanation
Indices: 942606--942648 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
942596 CTGACCATTG
942606 AATTTGACCAAAGTTGACTTTA
1 AATTTGACCAAAGTTGACTTTA
* *
942628 AATTTGTCCAAGGTTGACTTT
1 AATTTGACCAAAGTTGACTTT
942649 GACTTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
AATTTGACCAAAGTTGACTTTA
Found at i:949269 original size:66 final size:67
Alignment explanation
Indices: 949120--949344 Score: 226
Period size: 69 Copynumber: 3.3 Consensus size: 67
949110 TTGTGATGAA
** *
949120 AGCTCACATGGGGTCCAAGAAACTTATGAAGGTACGACTAA-TATAAATAATGGAAGTGGTTGTA
1 AGCTCACATGGGGTCCAAGAAA-TTATGAAGGTGTGACAAATTATAAATAATGG-AGTGG-TGTA
949184 TTGGC
63 TTGGC
* * * * * *
949189 AACTCACATAGGGTCTAAGGAAATTGTGATGGTGTGAC-AATTATATATAATGAGAGTGGTG-A-
1 AGCTCACATGGGGTCCAA-GAAATTATGAAGGTGTGACAAATTATAAATAATG-GAGTGGTGTAT
949251 TGGC
64 TGGC
*
949255 AGCTCACATGGGGTCCAAAGAAATTATGAAGGTGTGACAAATT-TAAATAATGGGAGTGGTTGTG
1 AGCTCACATGGGGTCC-AAGAAATTATGAAGGTGTGACAAATTATAAATAAT-GGAGTGG-TGTA
*
949319 TTGGT
63 TTGGC
* *
949324 AACTCACATGGAGTCCAAGAA
1 AGCTCACATGGGGTCCAAGAA
949345 GAAAGTCATG
Statistics
Matches: 129, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
66 47 0.36
67 10 0.08
68 9 0.07
69 58 0.45
70 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.27
Consensus pattern (67 bp):
AGCTCACATGGGGTCCAAGAAATTATGAAGGTGTGACAAATTATAAATAATGGAGTGGTGTATTG
GC
Found at i:949445 original size:33 final size:33
Alignment explanation
Indices: 949403--949468 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
949393 TATGGGATCC
*
949403 AAGAAGGGAATCACGATGTTGACAATAATAATG
1 AAGAAGGGAATCACGATGCTGACAATAATAATG
949436 AAGAAGGGAATCACGATGCTGACAATAATAATG
1 AAGAAGGGAATCACGATGCTGACAATAATAATG
949469 GTAGTAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (33 bp):
AAGAAGGGAATCACGATGCTGACAATAATAATG
Found at i:958673 original size:18 final size:18
Alignment explanation
Indices: 958647--958681 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
958637 AACAATCATA
*
958647 ATTTGAATAGAAAAATTC
1 ATTTAAATAGAAAAATTC
958665 ATTTAAATAGAAAAATT
1 ATTTAAATAGAAAAATT
958682 AATAAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (18 bp):
ATTTAAATAGAAAAATTC
Found at i:961091 original size:29 final size:29
Alignment explanation
Indices: 961056--961133 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
961046 GTTAGGGGCG
*
961056 AACTTAAACTTATAAAATTTCAAGGGACA
1 AACTTAAACTTATAAAATTTCAAGAGACA
*
961085 AACTTAAACTTATAAAATTTCAAGAGACG
1 AACTTAAACTTATAAAATTTCAAGAGACA
961114 AACTTAAACTTATAAAATTT
1 AACTTAAACTTATAAAATTT
961134 TAGAGGATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (29 bp):
AACTTAAACTTATAAAATTTCAAGAGACA
Found at i:961736 original size:41 final size:42
Alignment explanation
Indices: 961653--961740 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 42
961643 TTGGAACCGG
* *
961653 AACCTGTTGCATCGGTTCCTAAAAAATGGGAACTGGAATCGA
1 AACCTGTTGCATCAGTTCCTAAAAAATGGGAACCGGAATCGA
* *
961695 AACCTGTT-CAATCAGTTCCT-AAAATTGGGATCCGGAATCGA
1 AACCTGTTGC-ATCAGTTCCTAAAAAATGGGAACCGGAATCGA
961736 AACCT
1 AACCT
961741 ATAGGTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
41 24 0.59
42 17 0.41
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
AACCTGTTGCATCAGTTCCTAAAAAATGGGAACCGGAATCGA
Found at i:964914 original size:2 final size:2
Alignment explanation
Indices: 964907--964940 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
964897 AATAATTAAT
964907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
964941 TAATAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:964961 original size:24 final size:26
Alignment explanation
Indices: 964910--964996 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 26
964900 AATTAATTAT
* * * *
964910 ATATATATATATATATATATATATATA
1 ATATAAATATATATTTA-ATTTAAATA
*
964937 ATATTAATA-A-ATTTAATTTAAATA
1 ATATAAATATATATTTAATTTAAATA
964961 A-A-AAATATATATTTAATTTAAAT-
1 ATATAAATATATATTTAATTTAAATA
*
964984 ATATATATATATA
1 ATATAAATATATA
964997 CCCGGCTCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
22 4 0.08
23 3 0.06
24 22 0.45
25 12 0.24
26 1 0.02
27 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATAAATATATATTTAATTTAAATA
Found at i:964976 original size:19 final size:19
Alignment explanation
Indices: 964952--964991 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
964942 AATAAATTTA
964952 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
964971 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
964990 AT
1 AT
964992 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:965038 original size:12 final size:12
Alignment explanation
Indices: 965009--965059 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
964999 CGGCTCGATT
*
965009 CCCGGCCCAATA
1 CCCGACCCAATA
965021 -CCGACCCAATA
1 CCCGACCCAATA
965032 CCCGACCCAATA
1 CCCGACCCAATA
*
965044 CCCGGCCCAATA
1 CCCGACCCAATA
965056 CCCG
1 CCCG
965060 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.27, C:0.51, G:0.14, T:0.08
Consensus pattern (12 bp):
CCCGACCCAATA
Found at i:965057 original size:24 final size:24
Alignment explanation
Indices: 964994--965059 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
964984 ATATATATAT
* * * *
964994 ATACCCGGCTCGATTCCCGGCCCA
1 ATACCCGGCCCAATACCCGACCCA
*
965018 ATA-CCGACCCAATACCCGACCCA
1 ATACCCGGCCCAATACCCGACCCA
965041 ATACCCGGCCCAATACCCG
1 ATACCCGGCCCAATACCCG
965060 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.26, C:0.47, G:0.15, T:0.12
Consensus pattern (24 bp):
ATACCCGGCCCAATACCCGACCCA
Found at i:965523 original size:10 final size:10
Alignment explanation
Indices: 965484--965533 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
965474 TTCATCACAC
965484 CAAATTCTCT
1 CAAATTCTCT
*
965494 CAATTTCTCT
1 CAAATTCTCT
*
965504 CAACTTCTCT
1 CAAATTCTCT
*
965514 CAAATACTCT
1 CAAATTCTCT
* *
965524 TATATTCTCT
1 CAAATTCTCT
965534 GTTTAATGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:965599 original size:18 final size:17
Alignment explanation
Indices: 965572--965624 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 17
965562 ATATTTTGTA
965572 TTTAACTTATTTAAGTAT
1 TTTAACTTATTTAA-TAT
*
965590 TTTAATTTATTTAATAT
1 TTTAACTTATTTAATAT
*
965607 TTT-ACTTATATAAT-T
1 TTTAACTTATTTAATAT
965622 TTT
1 TTT
965625 TTTGCAGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.12
16 9 0.28
17 6 0.19
18 13 0.41
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTAACTTATTTAATAT
Found at i:967978 original size:35 final size:33
Alignment explanation
Indices: 967939--968023 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
967929 GTATTTCAGT
967939 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
967974 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
968009 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
968024 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:980093 original size:17 final size:17
Alignment explanation
Indices: 980052--980096 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
980042 TTATTGGACT
*
980052 ATTCACAGCCTCTAGCA
1 ATTCACATCCTCTAGCA
980069 ATTCACATCCTCTAGCA
1 ATTCACATCCTCTAGCA
980086 ATTCACATCCT
1 ATTCACATCCT
980097 AAGCTTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (17 bp):
ATTCACATCCTCTAGCA
Found at i:984354 original size:46 final size:45
Alignment explanation
Indices: 984285--984377 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 45
984275 TTGTTAATGT
* * *
984285 TTCATCTCTTTTGAATGAAATGAAATGAAGTGGTTTTTTTCTTAATA
1 TTCATCTCTTTTCAATGAAATGAAAT-AACT-GTTTTTTTCCTAATA
984332 TTCATCTC-TTTCAATGAAATGAAATAACTGTTTTTTTCCTAATA
1 TTCATCTCTTTTCAATGAAATGAAATAACTGTTTTTTTCCTAATA
984376 TT
1 TT
984378 TTGTAGTGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 16 0.37
45 3 0.07
46 16 0.37
47 8 0.19
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (45 bp):
TTCATCTCTTTTCAATGAAATGAAATAACTGTTTTTTTCCTAATA
Found at i:988768 original size:24 final size:24
Alignment explanation
Indices: 988741--988823 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
988731 AACACAAATG
* *
988741 AACGAACATAAACGAACGGATGTA
1 AACGAACACAAACGAACGAATGTA
* *
988765 AACGAATACAAACGAACGAATGCA
1 AACGAACACAAACGAACGAATGTA
* *
988789 AACGAACACAAACGAACAAACGTA
1 AACGAACACAAACGAACGAATGTA
988813 AACGAACACAA
1 AACGAACACAA
988824 TAAATGAACA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.55, C:0.22, G:0.16, T:0.07
Consensus pattern (24 bp):
AACGAACACAAACGAACGAATGTA
Found at i:988782 original size:14 final size:14
Alignment explanation
Indices: 988765--988795 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
988755 AACGGATGTA
988765 AACGAATACAAACG
1 AACGAATACAAACG
*
988779 AACGAATGCAAACG
1 AACGAATACAAACG
988793 AAC
1 AAC
988796 ACAAACGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAATACAAACG
Found at i:989066 original size:24 final size:24
Alignment explanation
Indices: 989029--989103 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
989019 CTAAACATAA
* *
989029 ATAAACACACATAAACGAACGAAC
1 ATAAACAAACATAAATGAACGAAC
* * *
989053 ATAAACAAATATAAATGAGCAAAC
1 ATAAACAAACATAAATGAACGAAC
*
989077 ATAAACGAACATAAATGAACGAAC
1 ATAAACAAACATAAATGAACGAAC
989101 ATA
1 ATA
989104 TTACTAAATG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
ATAAACAAACATAAATGAACGAAC
Found at i:990060 original size:2 final size:2
Alignment explanation
Indices: 990053--990085 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
990043 CAATAATACC
990053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
990086 TCAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:990514 original size:27 final size:27
Alignment explanation
Indices: 990476--990530 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
990466 AAAAGCGGTA
*
990476 TAATTTATTCACTTATTACTCT-AGCCT
1 TAATTTAGTCACTTATTACT-TGAGCCT
990503 TAATTTAGTCACTTATTACTTGAGCCT
1 TAATTTAGTCACTTATTACTTGAGCCT
990530 T
1 T
990531 TCTATAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (27 bp):
TAATTTAGTCACTTATTACTTGAGCCT
Found at i:997929 original size:23 final size:23
Alignment explanation
Indices: 997903--997950 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
997893 TGTGACACAC
*
997903 TTTTCTCTGCTCATGTGGCACGT
1 TTTTCTCTACTCATGTGGCACGT
* *
997926 TTTTCTTTACTCTTGTGGCACGT
1 TTTTCTCTACTCATGTGGCACGT
997949 TT
1 TT
997951 CTGTTAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.50
Consensus pattern (23 bp):
TTTTCTCTACTCATGTGGCACGT
Found at i:998789 original size:24 final size:24
Alignment explanation
Indices: 998762--998811 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
998752 TGGTGGTTGA
*
998762 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
998786 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
998810 TT
1 TT
998812 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1001127 original size:17 final size:17
Alignment explanation
Indices: 1001105--1001137 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1001095 ATGAGCTTTA
*
1001105 CTTCATTGTCAAGGCGC
1 CTTCATAGTCAAGGCGC
1001122 CTTCATAGTCAAGGCG
1 CTTCATAGTCAAGGCG
1001138 TCTTACTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (17 bp):
CTTCATAGTCAAGGCGC
Found at i:1005724 original size:20 final size:20
Alignment explanation
Indices: 1005682--1005732 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1005672 TAACTTTTTC
* *
1005682 TTTTCTCTTTCTTTATTAAT
1 TTTTCTTTTTCATTATTAAT
1005702 TTTTCTTTTTCATT-TTAACT
1 TTTTCTTTTTCATTATTAA-T
*
1005722 TTTACTTTTTC
1 TTTTCTTTTTC
1005733 TCTTTCCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTTTTCATTATTAAT
Found at i:1009042 original size:24 final size:23
Alignment explanation
Indices: 1009010--1009059 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1009000 TGGTGGTTGA
*
1009010 TTTTATGGT-TGTTTGAACTTTAT
1 TTTTATGGTATATTT-AACTTTAT
*
1009033 TTTTAATGGTATATTTAAGTTTAT
1 TTTT-ATGGTATATTTAACTTTAT
1009057 TTT
1 TTT
1009060 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (23 bp):
TTTTATGGTATATTTAACTTTAT
Found at i:1010182 original size:28 final size:28
Alignment explanation
Indices: 1010137--1010262 Score: 209
Period size: 28 Copynumber: 4.5 Consensus size: 28
1010127 CATAAGTAGT
1010137 TTTATGAAGGTTAT-TGAATTGTTCTGATG
1 TTTA-GAAGGTT-TCTGAATTGTTCTGATG
1010166 TTTAGAAGGTTTCTGAATTGTTCTGATG
1 TTTAGAAGGTTTCTGAATTGTTCTGATG
*
1010194 TTGAGAAGGTTTCTGAATTGTTCTGATG
1 TTTAGAAGGTTTCTGAATTGTTCTGATG
1010222 TTTAGAAGGTTTCTGAATTGTTCTGATG
1 TTTAGAAGGTTTCTGAATTGTTCTGATG
*
1010250 TTTATAAGGTTTC
1 TTTAGAAGGTTTC
1010263 ATTCTCTTCG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
27 1 0.01
28 88 0.95
29 4 0.04
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (28 bp):
TTTAGAAGGTTTCTGAATTGTTCTGATG
Found at i:1017671 original size:3 final size:3
Alignment explanation
Indices: 1017663--1017728 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
1017653 AATTTTTTCA
* * * *
1017663 TAT TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAG CAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
1017712 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1017729 AAAATATAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
3 52 0.96
4 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1019529 original size:11 final size:11
Alignment explanation
Indices: 1019505--1019551 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1019495 ATATACTAAT
1019505 TTATTTTAATTA
1 TTATTTT-ATTA
1019517 TTATTTTATTA
1 TTATTTTATTA
1019528 TTA-TTTATTTA
1 TTATTTTA-TTA
*
1019539 TT-TTTTAATA
1 TTATTTTATTA
1019549 TTA
1 TTA
1019552 AGAAATGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 8 0.26
11 16 0.52
12 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:1025404 original size:8 final size:8
Alignment explanation
Indices: 1025391--1025427 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
1025381 GAAGAAGAAA
1025391 AAAAAAGG
1 AAAAAAGG
*
1025399 AAAAAAGA
1 AAAAAAGG
1025407 AAAAAAGG
1 AAAAAAGG
1025415 AAAAAAGG
1 AAAAAAGG
1025423 AAAAA
1 AAAAA
1025428 TTGAACCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1029587 original size:20 final size:22
Alignment explanation
Indices: 1029541--1029598 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1029531 TACATCTACA
1029541 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
1029563 CTCTTCGAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
1029585 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
1029599 ACGCTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:1030384 original size:45 final size:45
Alignment explanation
Indices: 1030330--1030437 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
1030320 TTTTTGATAT
* ** * * **
1030330 TTTCGAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAAAATGC
*
1030375 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAAAATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAAAATGC
1030420 TTTCAAAAAGCCTTCGGG
1 TTTC-AAAA-CCTTCGGG
1030438 AGCTTTTTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 41 0.77
46 4 0.08
47 8 0.15
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAAAATGC
Found at i:1030455 original size:76 final size:76
Alignment explanation
Indices: 1030375--1030613 Score: 379
Period size: 76 Copynumber: 3.1 Consensus size: 76
1030365 TGCATGATGC
** * *
1030375 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAAAATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAG
1030440 CTTTTTGATAT
66 CTTTTTGATAT
* * * * *
1030451 TTTCAAAACATTCGGGTTATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGAGAG
1 TTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAG
*
1030516 TTTTTTGATAT
66 CTTTTTGATAT
*
1030527 TTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAG
1030592 CTTTTTGATAT
66 CTTTTTGATAT
1030603 TTTCAAAACCT
1 TTTCAAAACCT
1030614 CAGGGCCATT
Statistics
Matches: 147, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 147 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (76 bp):
TTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAG
CTTTTTGATAT
Found at i:1030488 original size:121 final size:121
Alignment explanation
Indices: 1030271--1030503 Score: 387
Period size: 121 Copynumber: 1.9 Consensus size: 121
1030261 CTATTTCTCA
** *
1030271 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCGA
1 CATCCATAAGACCTGCAGTGCAAAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
1030336 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
66 AACATTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
1030392 CATCCATAAGACCTGCAGTGCAAAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAAAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
1030457 AACATTCGGGTTATCTGTAAGACCTAT-AGTGCATGATGTTTTCAAAA
66 AACATTCGGGTCATCTGTAAGACCT-TCAGTGCATGATGCTTTCAAAA
1030504 AGCCTTCGAG
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
121 103 0.99
122 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (121 bp):
CATCCATAAGACCTGCAGTGCAAAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AACATTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:1030795 original size:3 final size:3
Alignment explanation
Indices: 1030776--1030850 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
1030766 TTTTTCATAA
* * * *
1030776 TAT TTT TAT TTT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1030824 ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TAT TAT TAT TAT TA
1030851 AAAATATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1031927 original size:2 final size:2
Alignment explanation
Indices: 1031920--1031960 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1031910 CTTTCTTGTT
1031920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1031961 TAGGATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1032560 original size:135 final size:135
Alignment explanation
Indices: 1032421--1032674 Score: 345
Period size: 136 Copynumber: 1.9 Consensus size: 135
1032411 CCTATTAATA
* *
1032421 AATTTAATTTTATATAAATTA-TT-TTAATATTTGTTTA-TTTTTTAATATTAAGAAATTGGCTG
1 AATTT-ATTTTA-AT-AATTATTTATTAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTG
** * *
1032483 TCTTAAAGTACCTAGAAGTCCTTTTATGATA-TTCTTAAATAAATAAATATCCTATTTTTATAAA
63 TCTTAAAACACATAGAAGTCATTTTATGATATTTC-TAAATAAATAAATATCCTATTTTTATAAA
1032547 TTATATACT
127 TTATATACT
*
1032556 AATTTATTTTAATTATTATTTTATTAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTGTC
1 AATTTATTTTAATAATTA-TTTATTAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTGTC
* * *
1032621 TTAAAACACATAGAAGTCATTTTCTGATATTTCTAAGTAAATAAATATCTTATT
65 TTAAAACACATAGAAGTCATTTTATGATATTTCTAAATAAATAAATATCCTATT
1032675 AATATATTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
132 4 0.04
133 2 0.02
134 8 0.08
135 18 0.17
136 69 0.66
137 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (135 bp):
AATTTATTTTAATAATTATTTATTAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTGTCT
TAAAACACATAGAAGTCATTTTATGATATTTCTAAATAAATAAATATCCTATTTTTATAAATTAT
ATACT
Found at i:1035138 original size:26 final size:28
Alignment explanation
Indices: 1035078--1035139 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
1035068 GAGTATTGCT
*
1035078 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
1035109 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
1035135 GAGCT
1 GAGCT
1035140 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:1035760 original size:16 final size:17
Alignment explanation
Indices: 1035730--1035772 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1035720 ATATTTTTTT
1035730 AAAAAATTCTAAGAAAA-A
1 AAAAAATT-T-AGAAAATA
*
1035748 AATAAATTTAGAAAATA
1 AAAAAATTTAGAAAATA
1035765 AAAAAATT
1 AAAAAATT
1035773 CGAAGGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAAAATTTAGAAAATA
Found at i:1040162 original size:109 final size:110
Alignment explanation
Indices: 1039948--1040150 Score: 277
Period size: 109 Copynumber: 1.9 Consensus size: 110
1039938 CCAAATCATT
*
1039948 ATCTTCTTCTTTATCTCATATTCTCATTCCTCAATCTTAAAGCATAAAATCTCCATGTTTTGCTC
1 ATCTTCTTCTTTATCTCATATTCTCATTCCTCAATCTTAAAGCATAAAATCTCCATGTTTTGCTA
* *
1040013 TACTCTTTCTTTAATCCATCATTTTAATCTAAATTGAAAATAACC
66 TACTCTTTCTTTAATCCACCATTATAATCTAAATTGAAAATAACC
* * *
1040058 ATCTTCTTCTTTATC-CAATACTTTTC-TTTCTCAATCTT-AAGCATAAAATCTCCATGTTTTGT
1 ATCTTCTTCTTTATCTC-ATA-TTCTCATTCCTCAATCTTAAAGCATAAAATCTCCATGTTTTGC
* ** *
1040120 TATGCTCTTTCTTTGGTTCACCATTATAATC
64 TATACTCTTTCTTTAATCCACCATTATAATC
1040151 AAGATTTAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
109 48 0.59
110 29 0.36
111 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (110 bp):
ATCTTCTTCTTTATCTCATATTCTCATTCCTCAATCTTAAAGCATAAAATCTCCATGTTTTGCTA
TACTCTTTCTTTAATCCACCATTATAATCTAAATTGAAAATAACC
Found at i:1043030 original size:36 final size:35
Alignment explanation
Indices: 1042913--1043086 Score: 255
Period size: 35 Copynumber: 5.0 Consensus size: 35
1042903 TGAATAAAAA
*
1042913 GAACGAAAGG-AGCATCGACACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
* *
1042947 GAACGAAAGGAAGCATCGACACTTTCGATTTAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
* *
1042982 GAACGGACGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
1043017 CGAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
1 -GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
* *
1043053 --ACGGAAGAAAGCATCGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
1043086 G
1 G
1043087 TTCATCTTTT
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
33 31 0.24
34 10 0.08
35 54 0.42
36 33 0.26
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:1043041 original size:71 final size:68
Alignment explanation
Indices: 1042923--1043086 Score: 256
Period size: 71 Copynumber: 2.4 Consensus size: 68
1042913 GAACGAAAGG
* *
1042923 AGCATCGACACTTTCGATTCAAGTGAACGAAAGGAAGCATCGACACTTTCGATTTAAGTGAACGG
1 AGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCGACACTTTCGATTCAAGT--ACGG
* *
1042988 ACGGA
64 AAGAA
*
1042993 AGCATCGGCACTTTCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTTCGATTCAAGTACGGA
1 AGCATCGGCACTTTCGATTCAAGT-GAACGAAAGGAAGCATCGACACTTTCGATTCAAGTACGGA
1043058 AGAA
65 AGAA
1043062 AGCATCGGCACTTTCGATTCAAGTG
1 AGCATCGGCACTTTCGATTCAAGTG
1043087 TTCATCTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
68 1 0.01
69 31 0.35
70 23 0.26
71 33 0.38
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.22
Consensus pattern (68 bp):
AGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTACGGAA
GAA
Found at i:1044050 original size:81 final size:81
Alignment explanation
Indices: 1043915--1044063 Score: 237
Period size: 81 Copynumber: 1.8 Consensus size: 81
1043905 TTTAATTCTC
* * *
1043915 AAATAATACTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACTAGAATAT
1 AAATAAGACTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACCAAAATAT
1043980 TTATTTTACTTTGTTA
66 TTATTTTACTTTGTTA
* *
1043996 AAATAAGATTAAATTGAGAGAATATGTAATCAATAATG-ACCAAATGTGTAATTATACCAAAATA
1 AAATAAGACTAAATTGAGAGAATATGTAAGCAATAA-GAACCAAATGTGTAATTATACCAAAATA
1044060 TTTA
65 TTTA
1044064 ACTATCACTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 61 0.98
82 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (81 bp):
AAATAAGACTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACCAAAATAT
TTATTTTACTTTGTTA
Found at i:1044090 original size:81 final size:80
Alignment explanation
Indices: 1043915--1044080 Score: 199
Period size: 81 Copynumber: 2.0 Consensus size: 80
1043905 TTTAATTCTC
* * * *
1043915 AAATAATACTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACTAGAATAT
1 AAATAAGATTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACCAAAATAT
* * **
1043980 TTATTTTACTTTGTT
66 TTATATCACTTTCCT
*
1043995 AAAATAAGATTAAATTGAGAGAATATGTAATCAATAATG-ACCAAATGTGTAATTATACCAAAAT
1 -AAATAAGATTAAATTGAGAGAATATGTAAGCAATAA-GAACCAAATGTGTAATTATACCAAAAT
1044059 ATTTAACTATCACTTTACCT
64 ATTT-A-TATCACTTT-CCT
1044079 AA
1 AA
1044081 TTTGTTAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
81 60 0.83
82 2 0.03
83 9 0.12
84 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (80 bp):
AAATAAGATTAAATTGAGAGAATATGTAAGCAATAAGAACCAAATGTGTAATTATACCAAAATAT
TTATATCACTTTCCT
Found at i:1044574 original size:16 final size:19
Alignment explanation
Indices: 1044553--1044594 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1044543 GTGGCAGCAG
1044553 CTTCTTCT-TCTTC-T-TT
1 CTTCTTCTCTCTTCATATT
1044569 CTTCTTCTCTCTTCATATT
1 CTTCTTCTCTCTTCATATT
1044588 CTTCTTC
1 CTTCTTC
1044595 CATCTTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 5 0.22
18 1 0.04
19 9 0.39
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (19 bp):
CTTCTTCTCTCTTCATATT
Found at i:1050602 original size:103 final size:103
Alignment explanation
Indices: 1050423--1050635 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
1050413 GGGTCTACGC
1050423 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
* *
1050488 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
1050526 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
*
1050591 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
1050629 AGTCCTT
1 GGTCCTT
1050636 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1050685 original size:23 final size:23
Alignment explanation
Indices: 1050652--1050742 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
1050642 ATTATTATAT
*
1050652 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
1050675 AGCACTCCGGTGCAATTCTACAC
1 GGCACTTCGGTGCAATTCTACGC
*
1050698 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
1050721 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
1050743 AGCTGTGGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1054622 original size:33 final size:34
Alignment explanation
Indices: 1054571--1054674 Score: 113
Period size: 32 Copynumber: 3.0 Consensus size: 34
1054561 TCTCATGTGC
1054571 AAAGTTGACCACCTACCAAAGATGAATTTTCCAAT
1 AAAGTTG-CCACCTACCAAAGATGAATTTTCCAAT
* * * *
1054606 -AAGTTGCCACCAACC-AAGATGAAATTCCCATGT
1 AAAGTTGCCACCTACCAAAGATGAATTTTCCA-AT
1054639 GCAAAGTTGGCCACCTACCAAAGATGAATTTTCCAA
1 --AAAGTT-GCCACCTACCAAAGATGAATTTTCCAA
1054675 CTTGCCAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.24
33 9 0.16
34 6 0.11
36 5 0.09
37 9 0.16
38 13 0.24
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (34 bp):
AAAGTTGCCACCTACCAAAGATGAATTTTCCAAT
Found at i:1054653 original size:37 final size:38
Alignment explanation
Indices: 1054547--1054666 Score: 144
Period size: 38 Copynumber: 3.3 Consensus size: 38
1054537 TATTTTATGG
* *
1054547 ACCAAAGATGAAATTCTCATGTGCAAAGTTGACCACCT
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
* * * *
1054585 ACCAAAGATGAATTTTCCA-AT---AAGTT-GCCACCA
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
1054618 ACC-AAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
1 ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
1054655 ACCAAAGATGAA
1 ACCAAAGATGAA
1054667 TTTTCCAACT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.20
33 9 0.14
34 5 0.08
36 5 0.08
37 10 0.15
38 24 0.36
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (38 bp):
ACCAAAGATGAAATTCCCATGTGCAAAGTTGGCCACCT
Found at i:1055363 original size:19 final size:19
Alignment explanation
Indices: 1055323--1055362 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
1055313 TAAAGTGAAC
1055323 AAAATTAAATAATTAATAA
1 AAAATTAAATAATTAATAA
1055342 AAAATATAAA-AA-T-ATAA
1 AAAAT-TAAATAATTAATAA
1055359 AAAA
1 AAAA
1055363 ATAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 7 0.35
20 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATTAAATAATTAATAA
Found at i:1055367 original size:28 final size:27
Alignment explanation
Indices: 1055323--1055378 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1055313 TAAAGTGAAC
* *
1055323 AAAATTAAATAATTAATAAAAAATATA
1 AAAATTAAAAAAATAATAAAAAATATA
* *
1055350 AAAATATAAAAAAATAATATATAATATA
1 AAAAT-TAAAAAAATAATAAAAAATATA
1055378 A
1 A
1055379 GTGAATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATTAAAAAAATAATAAAAAATATA
Found at i:1055519 original size:15 final size:15
Alignment explanation
Indices: 1055499--1055544 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1055489 AATACTAATA
*
1055499 TATTATATTATATTG
1 TATTATTTTATATTG
* *
1055514 TATTATTTTATTTTA
1 TATTATTTTATATTG
*
1055529 TTTTATTTTATATTG
1 TATTATTTTATATTG
1055544 T
1 T
1055545 TAATTAGCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTG
Found at i:1055719 original size:16 final size:16
Alignment explanation
Indices: 1055700--1055734 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1055690 TTTAAACTTA
*
1055700 TTTTAATATAATAATT
1 TTTTAAAATAATAATT
1055716 TTTTAAAATAATAATT
1 TTTTAAAATAATAATT
1055732 TTT
1 TTT
1055735 ATCACTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATAATAATT
Found at i:1066865 original size:19 final size:19
Alignment explanation
Indices: 1066821--1066875 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1066811 ATCCGGGTTA
1066821 TAAT-TTATTATTATATTAT
1 TAATATTATTATTAT-TTAT
* * *
1066840 CATTATTATTCTTATTTAT
1 TAATATTATTATTATTTAT
*
1066859 TAATATTATTTTTATTT
1 TAATATTATTATTATTT
1066876 TCAGATTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATATTATTATTATTTAT
Done.