Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 24
Found at i:2963625 original size:14 final size:14
Alignment explanation
Indices: 2963606--2963695 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2963596 TTTCATTTCG
2963606 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2963620 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
2963639 CGTTGCGCTTCTCT
1 CGTTGCGATTCTCT
2963653 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2963670 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2963686 CGTTGCGATT
1 CGTTGCGATT
2963696 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.08, C:0.27, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2963631 original size:33 final size:33
Alignment explanation
Indices: 2963589--2963703 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
2963579 CAAAATCGCA
2963589 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2963622 TTGCGATTTTCATTTCGCGTTGCGCTTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2963655 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2963688 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2963704 AAAAAAAGAC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2965656 original size:232 final size:234
Alignment explanation
Indices: 2965250--2965715 Score: 909
Period size: 232 Copynumber: 2.0 Consensus size: 234
2965240 CTGATAGTAT
2965250 CGTTGCAGAATGAGGTTCATACTCTACGCAACGAGGTAAGTTTAAGATTTTCCATATTTAACTTA
1 CGTTGCAGAATGAGGTTCATACTCTACGCAACGAGGTAAGTTTAAGATTTTCCATATTTAACTTA
2965315 ATGATAAATTTACTCGTAATTTCACTAGATTAGCCATTTCACTTAGATTGCTTAGTAAATTTATT
66 ATGATAAATTTACTCGTAATTTCACTAGATTAGCCATTTCACTTAGATTGCTTAGTAAATTTATT
*
2965380 CGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA-TTGTGTTTG-T
131 CGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTT
2965443 TTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC
196 TTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC
2965482 CGTTGCAGAATGAGGTTCATACTCTACGCAACGAGGTAAGTTTAAGATTTTCCATATTTAACTTA
1 CGTTGCAGAATGAGGTTCATACTCTACGCAACGAGGTAAGTTTAAGATTTTCCATATTTAACTTA
2965547 ATGATAAATTTACTCGTAATTTCACTAGATTAGCCATTTCACTTAGATTGCTTAGTAAATTTATT
66 ATGATAAATTTACTCGTAATTTCACTAGATTAGCCATTTCACTTAGATTGCTTAGTAAATTTATT
2965612 CGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTT
131 CGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTT
2965677 TTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC
196 TTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC
2965716 AATTCTGCTA
Statistics
Matches: 231, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
232 183 0.79
233 8 0.03
234 40 0.17
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (234 bp):
CGTTGCAGAATGAGGTTCATACTCTACGCAACGAGGTAAGTTTAAGATTTTCCATATTTAACTTA
ATGATAAATTTACTCGTAATTTCACTAGATTAGCCATTTCACTTAGATTGCTTAGTAAATTTATT
CGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTT
TTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC
Found at i:2965894 original size:92 final size:93
Alignment explanation
Indices: 2965600--2966067 Score: 858
Period size: 92 Copynumber: 5.1 Consensus size: 93
2965590 TAGATTGCTT
*
2965600 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2965665 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2965693 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTC-TTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2965754 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
2965782 AGTAAATTTGTTCGATTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2965847 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2965874 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2965938 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2965966 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2966031 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2966059 AGTAAATTT
1 AGTAAATTT
2966068 ATCCATTCAA
Statistics
Matches: 362, Mismatches: 7, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
89 72 0.20
90 12 0.03
91 23 0.06
92 154 0.43
93 101 0.28
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2966151 original size:19 final size:19
Alignment explanation
Indices: 2966111--2966239 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2966101 TAGTTTACTT
* *
2966111 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2966131 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2966150 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2966169 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2966183 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2966202 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2966216 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2966235 TCGCA
1 TCGCA
2966240 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2966190 original size:33 final size:32
Alignment explanation
Indices: 2966147--2966239 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2966137 CGCGAAACCA
**
2966147 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2966179 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2966212 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2966240 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2966237 original size:52 final size:52
Alignment explanation
Indices: 2966111--2966239 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2966101 TAGTTTACTT
**
2966111 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2966163 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2966216 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2966240 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2966257 original size:19 final size:19
Alignment explanation
Indices: 2966235--2966369 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2966225 GAAACCAAAA
*
2966235 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2966254 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2966270 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2966287 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2966303 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2966320 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2966339 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2966359 TCGTGTTGCGA
1 TCGCGTTGCGA
2966370 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2966276 original size:14 final size:14
Alignment explanation
Indices: 2966257--2966313 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2966247 TTTCATTTCG
2966257 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2966271 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2966288 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2966304 CGTTGCGATT
1 CGTTGCGATT
2966314 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2966282 original size:33 final size:33
Alignment explanation
Indices: 2966240--2966332 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2966230 CAAAATCGCA
*
2966240 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2966273 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2966306 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2966333 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2968202 original size:14 final size:14
Alignment explanation
Indices: 2968183--2968214 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2968173 GTTTAATTGA
2968183 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
*
2968197 TTGTAAAAGTTGAT
1 TTGTAAAAGATGAT
2968211 TTGT
1 TTGT
2968215 GTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:2968336 original size:19 final size:19
Alignment explanation
Indices: 2968320--2968420 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2968310 AAAAATGACT
2968320 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2968339 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2968358 ATCGCAA--CG-AA-G--A
1 ATCGCAATGCGAAATGAAA
2968371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2968390 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2968410 ATCGCAATGCG
1 ATCGCAATGCG
2968421 TTTATAATTT
Statistics
Matches: 75, Mismatches: 0, Indels: 14
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.11
15 3 0.04
16 4 0.05
17 3 0.04
19 38 0.51
20 19 0.25
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2968469 original size:33 final size:34
Alignment explanation
Indices: 2968427--2968580 Score: 197
Period size: 33 Copynumber: 4.5 Consensus size: 34
2968417 TGCGTTTATA
* *
2968427 ATTTCGCATTGCGATTATC-TCGTTGCTATTTTC
1 ATTTCGCATTGCGATTTTCATCGTTGCGATTTTC
2968460 ATTTCGCATTGCGATTTTCATTCGCATTGGCGATTTTC
1 ATTTCGCATTGCGATTTTCA-TCG--TT-GCGATTTTC
*
2968498 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATCGTTGCGATTTTC
*
2968531 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTTTCATCGTTGCGATTTTC
*
2968565 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2968581 GTATTTTCCG
Statistics
Matches: 108, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
33 42 0.39
34 31 0.29
35 4 0.04
36 3 0.03
37 2 0.02
38 26 0.24
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (34 bp):
ATTTCGCATTGCGATTTTCATCGTTGCGATTTTC
Found at i:2968505 original size:20 final size:19
Alignment explanation
Indices: 2968449--2968580 Score: 133
Period size: 19 Copynumber: 7.4 Consensus size: 19
2968439 GATTATCTCG
*
2968449 TTGCTATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2968468 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
2968486 TTGGCGATTTTCATTTCGCA
1 TT-GCGATTTTCATTTCGCA
*
2968506 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2968520 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2968540 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2968554 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2968573 TTGCGATT
1 TTGCGATT
2968581 GTATTTTCCG
Statistics
Matches: 95, Mismatches: 5, Indels: 26
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.18
16 9 0.09
17 6 0.06
18 11 0.12
19 32 0.34
20 20 0.21
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2970310 original size:68 final size:67
Alignment explanation
Indices: 2970198--2970335 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 67
2970188 AACAGCAACT
2970198 CAAAGCGTCCATCTCTATCTGTTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATTGT
1 CAAAGCGTCCATCTCTATCTGTTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATTGT
2970263 GA
66 GA
2970265 CAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATTG
1 CAAAGCGTCCATCTCTATCTG-TTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATTG
2970330 TGA
65 TGA
2970333 CAA
1 CAA
2970336 TAAGCAGTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 21 0.30
68 49 0.70
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (67 bp):
CAAAGCGTCCATCTCTATCTGTTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATTGT
GA
Found at i:2970863 original size:12 final size:12
Alignment explanation
Indices: 2970846--2970870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2970836 TCTTCGGGGA
2970846 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2970858 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2970870 C
1 C
2970871 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2971797 original size:20 final size:20
Alignment explanation
Indices: 2971769--2972137 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
2971759 AAATTTAAGT
* * * *
2971769 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2971789 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2971809 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2971829 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2971849 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2971869 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2971889 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2971909 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2971929 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2971949 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2971969 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
2971989 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2972009 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2972029 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2972049 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2972069 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2972089 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2972109 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2972129 GTTGCGATT
1 GTTGCGATT
2972138 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2972717 original size:17 final size:17
Alignment explanation
Indices: 2972695--2972741 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2972685 TAATTATTTT
* *
2972695 TAAAAAATTCAAATATA
1 TAAAAAATTAAAATAAA
*
2972712 TAAAAATTTAAAATAAA
1 TAAAAAATTAAAATAAA
*
2972729 TAAAATATTAAAA
1 TAAAAAATTAAAA
2972742 CTAATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAAATTAAAATAAA
Found at i:2975743 original size:29 final size:29
Alignment explanation
Indices: 2975709--2975767 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2975699 TGTTTATTGT
* *
2975709 TAATAGATTTGTTATCATTAATTGTTATA
1 TAATAGATTGGTTATCATTAATTATTATA
2975738 TAATAGATTGGTTATCATTAATTATTATA
1 TAATAGATTGGTTATCATTAATTATTATA
2975767 T
1 T
2975768 TGTAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (29 bp):
TAATAGATTGGTTATCATTAATTATTATA
Found at i:2977397 original size:29 final size:29
Alignment explanation
Indices: 2977342--2977397 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
2977332 AATTCAGAAT
* * *
2977342 TTTCATATTTCATTTTCATCTTTTTTTAC
1 TTTCATATTTCATATTCATATTATTTTAC
2977371 TTTCATA-TTCATATTCATATTCATTTT
1 TTTCATATTTCATATTCATATT-ATTTT
2977398 CAAATTGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.21, C:0.16, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTCATATTTCATATTCATATTATTTTAC
Found at i:2977432 original size:19 final size:19
Alignment explanation
Indices: 2977383--2977435 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
2977373 TCATATTCAT
* *
2977383 ATTCAT-ATTCATTTTCAA
1 ATTCATAATTTATTTCCAA
* *
2977401 ATTGAGAACTTTATTTCCAA
1 ATTCATAA-TTTATTTCCAA
2977421 ATTCATAATTTATTT
1 ATTCATAATTTATTT
2977436 TCATATTCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 4 0.15
19 8 0.30
20 15 0.56
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (19 bp):
ATTCATAATTTATTTCCAA
Found at i:2977443 original size:19 final size:19
Alignment explanation
Indices: 2977378--2977464 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 19
2977368 TACTTTCATA
*
2977378 TTCATATTCAT-ATTCATT
1 TTCATATTCATAATTTATT
* * *
2977396 TTCAAATTGAGAACTTTATT
1 TTCATATTCATAA-TTTATT
* *
2977416 TCCAAATTCATAATTTATT
1 TTCATATTCATAATTTATT
* ** *
2977435 TTCATATTCACAGCTTAAT
1 TTCATATTCATAATTTATT
2977454 TTCATATTCAT
1 TTCATATTCAT
2977465 TGCCCAATGT
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.15
19 30 0.57
20 15 0.28
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (19 bp):
TTCATATTCATAATTTATT
Found at i:2977463 original size:38 final size:37
Alignment explanation
Indices: 2977378--2977464 Score: 93
Period size: 39 Copynumber: 2.3 Consensus size: 37
2977368 TACTTTCATA
* * *
2977378 TTCATATTCATATTCATTTTCAAATTGAGAACTTTAT
1 TTCATATTCATATTCATTTTCAAATTCACAACTTAAT
* * * *
2977415 TTCCAAATTCATAATTTATTTTCATATTCACAGCTTAAT
1 TT-CATATTCAT-ATTCATTTTCAAATTCACAACTTAAT
2977454 TTCATATTCAT
1 TTCATATTCAT
2977465 TGCCCAATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
37 2 0.05
38 16 0.40
39 22 0.55
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (37 bp):
TTCATATTCATATTCATTTTCAAATTCACAACTTAAT
Found at i:2979056 original size:23 final size:24
Alignment explanation
Indices: 2979016--2979070 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
2979006 GTTTGCATAA
* * *
2979016 AATTTTTAGTTTTCTATTATTTAG
1 AATTTTTAATATTCTATTAATTAG
2979040 AATTTTTAATATT-TATTAATTAG
1 AATTTTTAATATTCTATTAATTAG
*
2979063 GATTTTTA
1 AATTTTTA
2979071 GTTTGTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (24 bp):
AATTTTTAATATTCTATTAATTAG
Found at i:2986632 original size:3 final size:3
Alignment explanation
Indices: 2986624--2986659 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2986614 TTAAGCACAC
*
2986624 AAG AAG AAG AA- ATG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2986660 GTTCCAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:2995463 original size:14 final size:15
Alignment explanation
Indices: 2995437--2995466 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2995427 TTCTATTTTA
2995437 TTTTTATTCTGAATT
1 TTTTTATTCTGAATT
2995452 TTTTTATT-TGAATT
1 TTTTTATTCTGAATT
2995466 T
1 T
2995467 CATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTTATTCTGAATT
Found at i:2995628 original size:2 final size:2
Alignment explanation
Indices: 2995623--2995653 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2995613 TATATATATA
2995623 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2995654 ATGTAATACC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2998113 original size:46 final size:47
Alignment explanation
Indices: 2998060--2998172 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 47
2998050 GTAACCATGC
2998060 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTG-AAAA
* * * * **
2998106 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA-TTAAATGGCAAGTATATTGAAAA
*
2998154 AAATAAGCTTATTAGCTTA
1 AAATAAGCTTATGAGCTTA
2998173 TGGGATAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 22 0.39
48 20 0.36
49 14 0.25
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGAAAA
Found at i:2998171 original size:48 final size:46
Alignment explanation
Indices: 2998060--2998180 Score: 136
Period size: 48 Copynumber: 2.6 Consensus size: 46
2998050 GTAACCATGC
*
2998060 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
* * * **
2998106 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAAA
* *
2998154 AAATAAGCTTATTAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
2998181 AAGGTACGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.03
46 23 0.37
48 24 0.38
49 14 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:2998979 original size:16 final size:15
Alignment explanation
Indices: 2998958--2998997 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
2998948 GCCTCTTGTT
2998958 TTTATTTTATTTATTA
1 TTTATTTTA-TTATTA
2998974 TTTATTTCTATTATTA
1 TTTATTT-TATTATTA
2998990 -TTATTTTA
1 TTTATTTTA
2998998 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 6 0.26
16 13 0.57
17 2 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:2999060 original size:3 final size:3
Alignment explanation
Indices: 2999052--2999100 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2999042 TTCAATTAAT
2999052 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2999100 T
1 T
2999101 AATACAACCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2999189 original size:6 final size:6
Alignment explanation
Indices: 2999180--2999250 Score: 133
Period size: 6 Copynumber: 11.8 Consensus size: 6
2999170 ACTACTACTA
2999180 CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG
1 CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG CTATTG
*
2999228 CTATTG CTATTG CTATTA CTATT
1 CTATTG CTATTG CTATTG CTATT
2999251 TTACTCATTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.51
Consensus pattern (6 bp):
CTATTG
Found at i:3002568 original size:24 final size:23
Alignment explanation
Indices: 3002541--3002602 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3002531 TGAGTTTTCA
*
3002541 TAGAATTTTTAGTTTTATATTATT
1 TAGAATTTTTAGTTTT-TATTAAT
* *
3002565 TAGAATTTTTAATATTTATTAAT
1 TAGAATTTTTAGTTTTTATTAAT
*
3002588 TAGGATTTTTAGTTT
1 TAGAATTTTTAGTTT
3002603 GTTAGGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (23 bp):
TAGAATTTTTAGTTTTTATTAAT
Found at i:3004049 original size:20 final size:20
Alignment explanation
Indices: 3004026--3004064 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3004016 ATCCAATTTC
3004026 ACATTATAACATCAAATTCA
1 ACATTATAACATCAAATTCA
* *
3004046 ACATTCTAACATTAAATTC
1 ACATTATAACATCAAATTC
3004065 CAGTTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ACATTATAACATCAAATTCA
Found at i:3006240 original size:31 final size:30
Alignment explanation
Indices: 3006133--3006396 Score: 190
Period size: 30 Copynumber: 8.4 Consensus size: 30
3006123 ATTAAAAATA
* * **
3006133 TATTTTTATATTAACTTATTAAATATATTT
1 TATTCTTATCTTAACTTAAAAAATATATTT
* * * * *
3006163 TATTCTTGTCATGACCT-AAAAGTATATTT
1 TATTCTTATCTTAACTTAAAAAATATATTT
*
3006192 TATTCTTATTTTAACTTAAAAAATATATTT
1 TATTCTTATCTTAACTTAAAAAATATATTT
*
3006222 TAGTCTTTATCTTAACTTAAAAAATATATTT
1 TATTC-TTATCTTAACTTAAAAAATATATTT
3006253 TATTCTTATCTTAACTTATTACATAAATTATTAAATATAT
1 TATTCTTATCTTAACTTA--A-A-AAA-TA-T--AT-T-T
* * ** *
3006293 TCTATTCTTATCTTAAATTATTAAATATAATT
1 TA--TTCTTATCTTAACTTAAAAAATATATTT
* * * *
3006325 AATTCTTATTTTAACTTAAAACATATCTTT
1 TATTCTTATCTTAACTTAAAAAATATATTT
* *
3006355 TATTTTTATCTTAACTT-AGAAATATATTT
1 TATTCTTATCTTAACTTAAAAAATATATTT
*
3006384 TATTTTTATCTTA
1 TATTCTTATCTTA
3006397 TCTACAAAAA
Statistics
Matches: 182, Mismatches: 38, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
29 43 0.24
30 74 0.41
31 28 0.15
32 2 0.01
33 2 0.01
34 4 0.02
35 2 0.01
36 2 0.01
37 2 0.01
38 5 0.03
39 1 0.01
40 2 0.01
42 15 0.08
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (30 bp):
TATTCTTATCTTAACTTAAAAAATATATTT
Found at i:3006291 original size:132 final size:130
Alignment explanation
Indices: 3006148--3006396 Score: 338
Period size: 132 Copynumber: 1.9 Consensus size: 130
3006138 TTATATTAAC
* * * * * *
3006148 TTATTAAATATATTTTATTCTTGTCATGACCTA-AAAGTATATTTTATTCTTATTTTAACTTAAA
1 TTATTAAATATATTCTATTCTTATCATAAACTATAAA-TATAATTAATTCTTATTTTAACTTAAA
3006212 AAATATATTTTAGTCTTTATCTTAACTTAAAAAATATATTTTATTCTTATCTTAACTTATTACAT
65 AAATATATTTTA-TCTTTATCTTAACTT-AAAAATATATTTTATTCTTATCTTAACTTATTACAT
3006277 AAA
128 AAA
* *
3006280 TTATTAAATATATTCTATTCTTATCTTAAATTATTAAATATAATTAATTCTTATTTTAACTTAAA
1 TTATTAAATATATTCTATTCTTATCATAAACTA-TAAATATAATTAATTCTTATTTTAACTTAAA
* * * * *
3006345 ACATATCTTTTATTTTTATCTTAACTTAGAAATATATTTTATTTTTATCTTA
65 AAATATATTTTATCTTTATCTTAACTTAAAAATATATTTTATTCTTATCTTA
3006397 TCTACAAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
131 23 0.23
132 41 0.40
133 35 0.34
134 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (130 bp):
TTATTAAATATATTCTATTCTTATCATAAACTATAAATATAATTAATTCTTATTTTAACTTAAAA
AATATATTTTATCTTTATCTTAACTTAAAAATATATTTTATTCTTATCTTAACTTATTACATAAA
Found at i:3006300 original size:42 final size:43
Alignment explanation
Indices: 3006243--3006325 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
3006233 TTAACTTAAA
* * *
3006243 AAATATATTTTATTCTTATCTTAACTTATTACATA-AATTATT
1 AAATATATTCTATTCTTATCTTAAATTATTAAATATAATTATT
3006285 AAATATATTCTATTCTTATCTTAAATTATTAAATATAATTA
1 AAATATATTCTATTCTTATCTTAAATTATTAAATATAATTA
3006326 ATTCTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (43 bp):
AAATATATTCTATTCTTATCTTAAATTATTAAATATAATTATT
Found at i:3006349 original size:72 final size:73
Alignment explanation
Indices: 3006212--3006349 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 73
3006202 TTAACTTAAA
* * * * **
3006212 AAATATATTTTAGTCTTTATCTTAACTTAAAAAATATATTTTATTCTTATCTTAACTTATTACAT
1 AAATATATTCTAGTCTTTATCTTAAATTAAAAAATATAATTAATTCTTATCTTAACTTAAAACAT
3006277 AAATTATT
66 AAATTATT
* ** *
3006285 AAATATATTCTATTC-TTATCTTAAATTATTAAATATAATTAATTCTTATTTTAACTTAAAACAT
1 AAATATATTCTAGTCTTTATCTTAAATTAAAAAATATAATTAATTCTTATCTTAACTTAAAACAT
3006349 A
66 A
3006350 TCTTTTATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
72 42 0.76
73 13 0.24
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (73 bp):
AAATATATTCTAGTCTTTATCTTAAATTAAAAAATATAATTAATTCTTATCTTAACTTAAAACAT
AAATTATT
Found at i:3006364 original size:102 final size:103
Alignment explanation
Indices: 3006185--3006372 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 103
3006175 GACCTAAAAG
* * * * *
3006185 TATATTTTATTCTTATTTTAACTTAAAAAATATATTTTAGTCTTTATCTTAACTTAAAAAATATA
1 TATATTCTATTCTTATCTTAAATTAAAAAATATAATTAAGTCTTTATCTTAACTTAAAAAATATA
3006250 TTTTATTCTTATCTTAACTTATTACATAAATTATTAAA
66 TTTTATTCTTATCTTAACTTATTACATAAATTATTAAA
** * * * *
3006288 TATATTCTATTCTTATCTTAAATTATTAAATATAATTAATTC-TTATTTTAACTTAAAACATATC
1 TATATTCTATTCTTATCTTAAATTAAAAAATATAATTAAGTCTTTATCTTAACTTAAAAAATATA
*
3006352 TTTTATTTTTATCTTAACTTA
66 TTTTATTCTTATCTTAACTTA
3006373 GAAATATATT
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
102 39 0.53
103 34 0.47
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.53
Consensus pattern (103 bp):
TATATTCTATTCTTATCTTAAATTAAAAAATATAATTAAGTCTTTATCTTAACTTAAAAAATATA
TTTTATTCTTATCTTAACTTATTACATAAATTATTAAA
Found at i:3006535 original size:25 final size:25
Alignment explanation
Indices: 3006484--3006532 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3006474 AAGAATATCT
* *
3006484 TATATTTTTTAAATTTAAGATTAAA
1 TATATTTTTTAAATTTAAAATAAAA
3006509 TATATTTTTTAAA-TTAAAATAAAA
1 TATATTTTTTAAATTTAAAATAAAA
3006533 ATAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TATATTTTTTAAATTTAAAATAAAA
Found at i:3006544 original size:27 final size:27
Alignment explanation
Indices: 3006505--3006574 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
3006495 AATTTAAGAT
3006505 TAAATATATTTTTTAAATTA-AAATAAAAA
1 TAAA-ATA-TTTTTAAATTACAAA-AAAAA
** *
3006534 TAAAATATTTTTAGGTTACGAAAAAAA
1 TAAAATATTTTTAAATTACAAAAAAAA
*
3006561 TAAAATATATTTAA
1 TAAAATATTTTTAA
3006575 TAAGTTAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 26 0.74
28 5 0.14
29 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (27 bp):
TAAAATATTTTTAAATTACAAAAAAAA
Found at i:3006735 original size:11 final size:11
Alignment explanation
Indices: 3006719--3006748 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3006709 AAAAATATAT
3006719 TAAATTTAAAA
1 TAAATTTAAAA
3006730 TAAA-TTAAAA
1 TAAATTTAAAA
3006740 TAAATTTAA
1 TAAATTTAA
3006749 TCATCCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:3007875 original size:34 final size:32
Alignment explanation
Indices: 3007836--3007905 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3007826 TTTTGTAAAG
* *
3007836 GGGAAAGGTTCTAGCTTAGCTCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3007870 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3007902 GGGA
1 GGGA
3007906 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3010791 original size:20 final size:20
Alignment explanation
Indices: 3010766--3010824 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
3010756 ATCATATTGT
3010766 CCAGGGGGTATAGATTCCCC
1 CCAGGGGGTATAGATTCCCC
* *
3010786 CCA-GGGGAACAGATTCCCC
1 CCAGGGGGTATAGATTCCCC
*
3010805 CCAGGGGGTATCGATTCCCC
1 CCAGGGGGTATAGATTCCCC
3010825 GGGAACAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTATAGATTCCCC
Found at i:3010824 original size:18 final size:17
Alignment explanation
Indices: 3010803--3010857 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
3010793 AACAGATTCC
3010803 CCCCAGGGGGTATCGATT
1 CCCCA-GGGGTATCGATT
*
3010821 CCCC--GGG-AACAGATT
1 CCCCAGGGGTATC-GATT
3010836 CCCCCAGGGGTATCGATT
1 -CCCCAGGGGTATCGATT
3010854 CCCC
1 CCCC
3010858 GGGTACAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
16 4 0.13
17 4 0.13
18 11 0.37
19 2 0.07
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.18
Consensus pattern (17 bp):
CCCCAGGGGTATCGATT
Found at i:3010824 original size:19 final size:18
Alignment explanation
Indices: 3010770--3010857 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
3010760 TATTGTCCAG
*
3010770 GGGGTATAGATTCCCCCCA
1 GGGGTATCGATT-CCCCCA
*
3010789 GGGG-AACAGATTCCCCCCA
1 GGGGTATC-GATT-CCCCCA
3010808 GGGGGTATCGATT-CCCC-
1 -GGGGTATCGATTCCCCCA
*
3010825 -GGG-AACAGATTCCCCCA
1 GGGGTATC-GATTCCCCCA
3010842 GGGGTATCGATTCCCC
1 GGGGTATCGATTCCCC
3010858 GGGTACAGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
14 2 0.04
15 7 0.12
16 4 0.07
18 16 0.29
19 17 0.30
20 8 0.14
21 2 0.04
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.18
Consensus pattern (18 bp):
GGGGTATCGATTCCCCCA
Found at i:3010837 original size:15 final size:15
Alignment explanation
Indices: 3010817--3010872 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3010807 AGGGGGTATC
3010817 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
3010832 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
3010850 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
3010865 GATTCCCC
1 GATTCCCC
3010873 CCTACATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:3010851 original size:33 final size:34
Alignment explanation
Indices: 3010766--3010873 Score: 146
Period size: 33 Copynumber: 3.1 Consensus size: 34
3010756 ATCATATTGT
*
3010766 CCAGGGGGTATAGATTCCCCCCAGGGGAACAGATTCCCC
1 CCAGGGGGTATCGATT--CCCC--GGGAACAGATT-CCC
3010805 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCC
1 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCC
*
3010839 CCA-GGGGTATCGATTCCCCGGGTACAGATTCCC
1 CCAGGGGGTATCGATTCCCCGGGAACAGATTCCC
3010872 CC
1 CC
3010874 CTACATGGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
33 31 0.46
34 6 0.09
35 11 0.16
37 4 0.06
39 15 0.22
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (34 bp):
CCAGGGGGTATCGATTCCCCGGGAACAGATTCCC
Found at i:3011090 original size:21 final size:21
Alignment explanation
Indices: 3011057--3011096 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3011047 TTTTTGCAGA
*
3011057 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3011079 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3011097 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3012103 original size:13 final size:13
Alignment explanation
Indices: 3012081--3012113 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3012071 AAGTTTTAAA
3012081 AAAAATATATTTTT
1 AAAAA-ATATTTTT
3012095 AAAAAATATTTTT
1 AAAAAATATTTTT
3012108 AAAAAA
1 AAAAAA
3012114 ATCTGAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAAATATTTTT
Found at i:3012794 original size:18 final size:19
Alignment explanation
Indices: 3012759--3012805 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3012749 TGATTTTATT
* *
3012759 TATCTATTTATTACTTTTTA
1 TATCT-TTTTTTACTTTTGA
3012779 TATCTTTTTTTA-TTTTGA
1 TATCTTTTTTTACTTTTGA
*
3012797 TATATTTTT
1 TATCTTTTT
3012806 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.54
19 6 0.25
20 5 0.21
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (19 bp):
TATCTTTTTTTACTTTTGA
Found at i:3016678 original size:95 final size:91
Alignment explanation
Indices: 3016568--3016814 Score: 346
Period size: 95 Copynumber: 2.7 Consensus size: 91
3016558 AATATAATTA
* *
3016568 TATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATG
1 TATA-ATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
3016633 GATAAGATTCAGCTAGCCTGATAAAGTTG
65 GATAAGATTCAGCTAGCCTGATAAAG--G
*
3016662 ATTATAATATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 --TATAATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
*
3016727 GGATAATATTCAGCTAGCCTGATAAAGG
64 GGATAAGATTCAGCTAGCCTGATAAAGG
* *
3016755 -AT-AT-TATAAT--A-C-TGAGCGGTCCCTCTAGAGCAATTGGTTAAACGTCCCGGCTTTATGG
1 TATAATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
3016813 AT
66 AT
3016815 CTAGTTAGCC
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
84 45 0.31
85 1 0.01
86 1 0.01
88 6 0.04
89 2 0.01
90 2 0.01
93 1 0.01
95 82 0.57
96 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (91 bp):
TATAATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGG
Found at i:3018106 original size:84 final size:84
Alignment explanation
Indices: 3017965--3018875 Score: 959
Period size: 84 Copynumber: 11.0 Consensus size: 84
3017955 TTTTTTATTT
* * * *
3017965 ATTTGCACCATAACTCAAGGCTAAAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
*
3018030 CTCAACTCAAAGGCACATC
66 CTCAGCTCAAAGGCACATC
* ** * *
3018049 ATTTGCAGCAGAACTCAAGGCTAAAAGGGTTATCAACCAATACAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
* **
3018114 ATCAGCTCAAAGGTGCATC
66 CTCAGCTCAAAGGCACATC
* * * * *
3018133 ATTTGCAGTATAGCTTAAGGC-AAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
3018197 ACTCAGCTCAAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
*
3018217 ATTTGCAGCATAACTCAAGGC-AAGAATGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
3018281 ACTCAGCTCAAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
* * * * * * * *
3018301 ATTTGTAACATAGCTCAAGGCGAGAAGGGATA-CTTGCTAACAAAAGACATTCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATC-TGCCAACAAAAGACCTTCGAGTTCGATTAC
* * *
3018365 ACTTAGCTCAAATG--CATT
65 ACTCAGCTCAAAGGCACATC
* * *
3018383 ATTTGCAGCATAGCTTAAGGC-AAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
**
3018443 ACTCATTTCAAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
* * * * *
3018463 ATTTGCAACATAGC-CAAAGG-TGAGAA-GGTCTATTTGCCAACAAAAGACCTTCAAGTTCGATT
1 ATTTGCAGCATAACTC-AAGGCT-AAAAGGGT-TATCTGCCAACAAAAGACCTTCGAGTTCGATT
*
3018525 ACACTCAGCTCAAAGGCACATT
63 ACACTCAGCTCAAAGGCACATC
* * *
3018547 ATTTGCAGCATAACTCAAGGATAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTATA
1 ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
* **
3018612 TTCAGCTCAAAGGTGCATC
66 CTCAGCTCAAAGGCACATC
* * * * * *
3018631 ATTTACAGCATAGCTCAAGG-GAAGAAGGGCTATCT----ACCAAAGACTTTCGAGTTCGATTAC
1 ATTTGCAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
*
3018691 ATTCAGCTCAAAGGCACATC
65 ACTCAGCTCAAAGGCACATC
** * * ***
3018711 ATTTATAGCATAACTCAAGGCTAGAAGGGTTATTTATTAACAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
*
3018776 CTCAGCTCAAAGGCACATA
66 CTCAGCTCAAAGGCACATC
* * *
3018795 ATTTACAGCATGACTCAAGGC-AAGAAGGGTTATCTG-C--C-AAAGACCTTCGAGTTCAATTAC
1 ATTTGCAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC
* * * *
3018855 ATTCAACTCAGAGGCAAATC
65 ACTCAGCTCAAAGGCACATC
3018875 A
1 A
3018876 AATTTACATC
Statistics
Matches: 697, Mismatches: 105, Indels: 54
0.81 0.12 0.06
Matches are distributed among these distances:
78 31 0.04
79 3 0.00
80 131 0.19
81 5 0.01
82 30 0.04
83 7 0.01
84 484 0.69
85 6 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCACATC
Found at i:3018905 original size:330 final size:331
Alignment explanation
Indices: 3017973--3018959 Score: 1042
Period size: 330 Copynumber: 3.0 Consensus size: 331
3017963 TTATTTGCAC
* * * * * * ** *
3017973 CATAACTCAAGGCTAAAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTCGACTACGCTCAACTC
1 CATAGCTCAAGGCGAGAAGGGATA-CTGCTAACAAAAGACATTCGAGTTCGATTACATTCAGCTC
* * * * * *
3018038 AAAGGCACATCATTTGCAGCAGAACTCAAGGCTAAAAGGGTTATCAACCAATACAAGACCTTCGA
65 AAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTAT-TACTAACAAAAGACCTTCGA
* ** * * *
3018103 GTTCGATTACAATCAGCTCAAAGGTGCATCATTTGCAGTATAGCTTAAGGCAAGAAGGGCTATCT
129 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCT
3018168 GCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTC
194 G-C--CCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTC
* * *
3018233 AAGGCAAGAATGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
256 AAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGGCAC
**
3018298 ATCATTTGTAA
321 ATCATTTACAA
3018309 CATAGCTCAAGGCGAGAAGGGATACTTGCTAACAAAAGACATTCGAGTTCGATTACACTT-AGCT
1 CATAGCTCAAGGCGAGAAGGGATAC-TGCTAACAAAAGACATTCGAGTTCGATTACA-TTCAGCT
* * * * * * * *
3018373 CAAATG--CATTATTTGCAGCATAGCTTAAGGCAAGAAGGGCTA-T-CT-GCCAAAGACCTTCGA
64 CAAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTACTAACAAAAGACCTTCGA
** * **
3018433 GTTCGATTACACTCATTTCAAAGGCACATCATTTGCAACATAGC-CAAAGGTGAGAA-GGTCTAT
129 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTC-AAGGCAAGAAGGGT-TAT
* * *
3018496 TTGCCAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGCAGCATAAC
192 CTGCC--C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAAC
3018561 TCAAGG-ATAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGG
254 TCAAGGCA-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGG
** *
3018625 TGCATCATTTACAG
318 CACATCATTTACAA
* * *
3018639 CATAGCTCAAGG-GAAGAAGGGCTA-T-CT-ACCAAAGACTTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCG-AGAAGGGATACTGCTAACAAAAGACATTCGAGTTCGATTACATTCAGCTC
** *
3018700 AAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATTTATTAACAAAAGACCTTCGA
65 AAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTA-TTACTAACAAAAGACCTTCGA
* *
3018765 GTTCGATTACACTCAGCTCAAAGGCACATAATTTACAGCAT-GACTCAAGGCAAGAAGGGTTATC
129 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAG-CTCAAGGCAAGAAGGGTTATC
* * * * * * * *
3018829 TG-CCAAAGACCTTCGAGTTCAATTACATTCAACTCAGAGGCAAATCAAATTTACATCATAGCT-
193 TGCCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAACTC
* * * * * *
3018892 AATGGCGAGAAGGGCTATCTGTCAAC-AAA-A-TTGTCGAGTTCGATT-TCATTCAGCTCAATGA
256 AA-GGCAAGAAGGGTTATCTGCCAACAAAAGACCT-TCGAGTTCGATTAT-ATTCAGCTCAAAGG
3018953 CACATCA
318 CACATCA
3018960 ACCACACTAC
Statistics
Matches: 541, Mismatches: 85, Indels: 58
0.79 0.12 0.08
Matches are distributed among these distances:
325 2 0.00
326 33 0.06
327 5 0.01
328 95 0.18
329 12 0.02
330 236 0.44
331 4 0.01
332 63 0.12
333 4 0.01
334 29 0.05
335 1 0.00
336 56 0.10
337 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (331 bp):
CATAGCTCAAGGCGAGAAGGGATACTGCTAACAAAAGACATTCGAGTTCGATTACATTCAGCTCA
AAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATTACTAACAAAAGACCTTCGAGT
TCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGC
CCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGC
AAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTATATTCAGCTCAAAGGCACATCAT
TTACAA
Found at i:3019605 original size:36 final size:37
Alignment explanation
Indices: 3019528--3019840 Score: 356
Period size: 36 Copynumber: 8.5 Consensus size: 37
3019518 TGAAATATAT
3019528 ATATATAATATATAG-TTTTAGAAAGCATTTT-GAAAAC
1 ATATATAATATATAGTTTTTA-AAA-CATTTTGGAAAAC
3019565 ATATATAATATATAGTTTTTAAAACATTTTGGAAAA-
1 ATATATAATATATAGTTTTTAAAACATTTTGGAAAAC
*
3019601 ATATATAATATATAGTTTTTAAAACATTTTGG-AAAT
1 ATATATAATATATAGTTTTTAAAACATTTTGGAAAAC
*
3019637 ATATATAATATATAGTTTTTAAAACATTTT-GAAAAT
1 ATATATAATATATAGTTTTTAAAACATTTTGGAAAAC
* *
3019673 TTATATAATATATAGTTTTTAAAA-ATATTTTGAAAAC
1 ATATATAATATATAGTTTTTAAAACAT-TTTGGAAAAC
* *
3019710 TTATATAATATATAAGTTTTTAAAACATTTTGGAAAAT
1 ATATATAATATAT-AGTTTTTAAAACATTTTGGAAAAC
* * *
3019748 ATATAT-A-ATATAG-TTTTAAAATATTTTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAACA-TTTTGGAAAAC
* * * **
3019783 ATATTATATTATATGGTTTTGAAAAACATTTTTTAAAATC
1 ATA-TATAATATATAGTTTT-TAAAACATTTTGGAAAA-C
*
3019823 ATATATAAAATATAGTTT
1 ATATATAATATATAGTTT
3019841 AAAAAAATAT
Statistics
Matches: 245, Mismatches: 16, Indels: 28
0.85 0.06 0.10
Matches are distributed among these distances:
34 9 0.04
35 21 0.09
36 105 0.43
37 42 0.17
38 34 0.14
39 26 0.11
40 8 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAACATTTTGGAAAAC
Found at i:3019656 original size:72 final size:73
Alignment explanation
Indices: 3019486--3019840 Score: 393
Period size: 73 Copynumber: 4.8 Consensus size: 73
3019476 TTATAAATAT
* ** *
3019486 ATATATATATTATATAGTTTGCAAATA-ATTTTTGAAATATATATATATAATATATAG-TTTTAG
1 ATATATATAATATATAGTTTTTAAA-ACA-TTTTGGAA-A-ATATATATAATATATAGTTTTTA-
3019549 AAAGCATTTTGAAA
61 AAA-CATTTTGAAA
*
3019563 ACATATATAATATATAGTTTTTAAAACATTTTGGAAAA-ATATATAATATATAGTTTTTAAAACA
1 ATATATATAATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATAGTTTTTAAAACA
*
3019627 TTTTGGAA
66 TTTTGAAA
* *
3019635 ATATATATAATATATAGTTTTTAAAACATTTT-GAAAATTTATATAATATATAGTTTTTAAAAAT
1 ATATATATAATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATAGTTTTT-AAAAC
3019699 ATTTTGAAA
65 ATTTTGAAA
3019708 ACT-TATATAATATATAAGTTTTTAAAACATTTTGGAAAATATATAT-A-ATATAG-TTTTAAAA
1 A-TATATATAATATAT-AGTTTTTAAAACATTTTGGAAAATATATATAATATATAGTTTTTAAAA
*
3019769 TATTTTTTGAAA
64 CA--TTTTGAAA
* * * ** *
3019781 ATATATTATATTATATGGTTTTGAAAAACATTTTTTAAAATCATATATAAAATATAGTTT
1 ATATA-TATAATATATAGTTTT-TAAAACATTTTGGAAAAT-ATATATAATATATAGTTT
3019841 AAAAAAATAT
Statistics
Matches: 246, Mismatches: 16, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
71 11 0.04
72 64 0.26
73 65 0.26
74 49 0.20
75 18 0.07
76 9 0.04
77 28 0.11
78 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (73 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGGAAAATATATATAATATATAGTTTTTAAAACA
TTTTGAAA
Found at i:3019860 original size:4 final size:4
Alignment explanation
Indices: 3019851--3019885 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3019841 AAAAAAATAT
*
3019851 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTCA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3019886 TTTCTTTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3021214 original size:19 final size:18
Alignment explanation
Indices: 3021183--3021246 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
3021173 AATTTTCTTA
*
3021183 TTATTTCTTTTATTCTAT
1 TTATTTATTTTATTCTAT
3021201 TTATTTGATTTTATTCTAT
1 TTATTT-ATTTTATTCTAT
*
3021220 TTATCTA-TTTATTTCTAT
1 TTATTTATTTTA-TTCTAT
3021238 TTA-TTATTT
1 TTATTTATTT
3021247 ATTTTGATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.15
18 18 0.45
19 16 0.40
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (18 bp):
TTATTTATTTTATTCTAT
Found at i:3021242 original size:4 final size:4
Alignment explanation
Indices: 3021191--3021281 Score: 55
Period size: 4 Copynumber: 21.8 Consensus size: 4
3021181 TATTATTTCT
*
3021191 TTTA TTCTA TTTA TTTGA TTTTA TTCTA TTTA TCTA TTTA TTTCTA TTTA
1 TTTA TT-TA TTTA TTT-A -TTTA TT-TA TTTA TTTA TTTA -TT-TA TTTA
* *
3021241 -TTA TTTA TTT- TGATA TATT- TTTA TTTA TTTA TCT- TTTA TTT
1 TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTT
3021282 GTTATGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
3 8 0.12
4 40 0.58
5 16 0.23
6 5 0.07
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:3021259 original size:17 final size:17
Alignment explanation
Indices: 3021210--3021266 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
3021200 TTTATTTGAT
*
3021210 TTTA-TTCTATTTATCTA
1 TTTATTTCTATATAT-TA
*
3021227 TTTATTTCTATTTATTA
1 TTTATTTCTATATATTA
3021244 TTTATTT-TGATATATT-
1 TTTATTTCT-ATATATTA
3021260 TTTATTT
1 TTTATTT
3021267 ATTTATCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 8 0.22
17 19 0.51
18 10 0.27
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTCTATATATTA
Found at i:3021269 original size:10 final size:10
Alignment explanation
Indices: 3021200--3021270 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
3021190 TTTTATTCTA
3021200 TTTATTTGA-T
1 TTTATTT-ATT
3021210 TTTATTCTATT
1 TTTATT-TATT
3021221 TATCTATTTATT
1 T-T-TATTTATT
*
3021233 TCTATTTA--
1 TTTATTTATT
3021241 -TTATTTATT
1 TTTATTTATT
* *
3021250 TTGATATATT
1 TTTATTTATT
3021260 TTTATTTATT
1 TTTATTTATT
3021270 T
1 T
3021271 ATCTTTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
7 6 0.12
10 29 0.60
11 3 0.06
12 6 0.12
13 4 0.08
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTATTTATT
Found at i:3021414 original size:12 final size:13
Alignment explanation
Indices: 3021392--3021420 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3021382 AGAATCAGGT
3021392 TTTTGAATTTTAA
1 TTTTGAATTTTAA
3021405 TTTT-AATTTTAA
1 TTTTGAATTTTAA
3021417 TTTT
1 TTTT
3021421 TACAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:3022433 original size:16 final size:17
Alignment explanation
Indices: 3022404--3022450 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
3022394 AATTTGAATT
3022404 TAAAAATATTTAAAAATAC
1 TAAAAATA--TAAAAATAC
*
3022423 T-CAAATATAAAAATAC
1 TAAAAATATAAAAATAC
3022439 TAAAAATATAAA
1 TAAAAATATAAA
3022451 TTAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.40
17 9 0.36
18 5 0.20
19 1 0.04
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAATATAAAAATAC
Found at i:3022463 original size:21 final size:21
Alignment explanation
Indices: 3022439--3022505 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
3022429 ATAAAAATAC
*
3022439 TAAAAATATAAATTAAATTAT
1 TAAAAATATAAATTATATTAT
3022460 TAAAAAT-TAAA-TATA-TAT
1 TAAAAATATAAATTATATTAT
*
3022478 TACAAATACTAAATT-TATTAT
1 TAAAAATA-TAAATTATATTAT
3022499 TAAAAAT
1 TAAAAAT
3022506 GAATACATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.23
19 3 0.08
20 10 0.26
21 17 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATATAAATTATATTAT
Found at i:3022464 original size:20 final size:21
Alignment explanation
Indices: 3022441--3022503 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
3022431 AAAAATACTA
*
3022441 AAAATA-TAAATTAAATTATT
1 AAAATACTAAATTATATTATT
*
3022461 AAAA-ATTAAA-TATA-TATT
1 AAAATACTAAATTATATTATT
3022479 ACAAATACTAAATT-TATTATT
1 A-AAATACTAAATTATATTATT
3022500 AAAA
1 AAAA
3022504 ATGAATACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 5 0.14
19 7 0.19
20 18 0.50
21 6 0.17
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATACTAAATTATATTATT
Found at i:3023219 original size:26 final size:26
Alignment explanation
Indices: 3023190--3023246 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
3023180 ATTTTAAAAA
3023190 ATATTGATAAAAAAATCACATCAAAT
1 ATATTGATAAAAAAATCACATCAAAT
3023216 ATATTGATAAAAAAATCACATCAAAT
1 ATATTGATAAAAAAATCACATCAAAT
3023242 ATATT
1 ATATT
3023247 TTTTAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.30
Consensus pattern (26 bp):
ATATTGATAAAAAAATCACATCAAAT
Found at i:3023513 original size:6 final size:6
Alignment explanation
Indices: 3023497--3023573 Score: 136
Period size: 6 Copynumber: 12.5 Consensus size: 6
3023487 AGAGATTCTA
3023497 TTTTCGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTTGC
1 TTTT-GC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC -TTTTGC
3023547 TTTTGC TTTTGC TTTTGC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTT
3023574 GCAAGTTCAG
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
6 59 0.86
7 10 0.14
ACGTcount: A:0.00, C:0.17, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGC
Found at i:3028040 original size:14 final size:15
Alignment explanation
Indices: 3028021--3028053 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3028011 AGAAATTGTC
*
3028021 ATCTTAATTC-AATT
1 ATCTTAATCCTAATT
3028035 ATCTTAATCCTAATT
1 ATCTTAATCCTAATT
3028050 ATCT
1 ATCT
3028054 GAGTAGGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCTTAATCCTAATT
Found at i:3035310 original size:20 final size:20
Alignment explanation
Indices: 3035285--3035337 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3035275 GACCAACAAA
3035285 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
3035305 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
3035325 TTCGCAACGCGAA
1 TTCGCAACGCGAA
3035338 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:3035349 original size:20 final size:20
Alignment explanation
Indices: 3035326--3035372 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3035316 GTTTCCAATT
3035326 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
3035346 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
3035366 TCGCAAC
1 TCGCAAC
3035373 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:3035389 original size:20 final size:21
Alignment explanation
Indices: 3035366--3035492 Score: 160
Period size: 20 Copynumber: 6.3 Consensus size: 21
3035356 AATTTGTAAA
3035366 TCGCAACACAGA-AGTCAAAT
1 TCGCAACACAGATAGTCAAAT
*
3035386 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
3035406 TCGCAA-AGCA-ATAGTCAAAT
1 TCGCAACA-CAGATAGTCAAAT
*
3035426 TCGCAACACA-AAAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
*
3035446 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
*
3035466 TCGCAACACA-AAAGTCAAAT
1 TCGCAACACAGATAGTCAAAT
3035486 TCGCAAC
1 TCGCAAC
3035493 TGAATTTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.02
20 91 0.97
21 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (21 bp):
TCGCAACACAGATAGTCAAAT
Found at i:3035389 original size:60 final size:60
Alignment explanation
Indices: 3035325--3035492 Score: 227
Period size: 60 Copynumber: 2.8 Consensus size: 60
3035315 AGTTTCCAAT
* *
3035325 TTCGCAACGCGAATATGT-AAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-ATA-GTCAAATTCGCAACGC-AA-TAGTCAAATTCGCAACACAAAAGTCAAA
*
3035385 TTCGCAACGCGATAGTCAAATTCGCAAAGCAATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACGCAATAGTCAAATTCGCAACACAAAAGTCAAA
* *
3035445 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAAC
1 TTCGCAACGCGATAGTCAAATTCGCAACGCAATAGTCAAATTCGCAAC
3035493 TGAATTTCAA
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
58 5 0.05
59 11 0.11
60 82 0.84
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (60 bp):
TTCGCAACGCGATAGTCAAATTCGCAACGCAATAGTCAAATTCGCAACACAAAAGTCAAA
Found at i:3035410 original size:40 final size:41
Alignment explanation
Indices: 3035366--3035492 Score: 181
Period size: 40 Copynumber: 3.2 Consensus size: 41
3035356 AATTTGTAAA
* * *
3035366 TCGCAACACAGA-AGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAGATAGTCAAATTCGCAACACAAAAGTCAAAT
3035406 TCGCAA-AGCA-ATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACA-CAGATAGTCAAATTCGCAACACAAAAGTCAAAT
*
3035446 TCGCAACGC-GATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGATAGTCAAATTCGCAACACAAAAGTCAAAT
3035486 TCGCAAC
1 TCGCAAC
3035493 TGAATTTCAA
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
39 2 0.03
40 77 0.97
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (41 bp):
TCGCAACACAGATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:3035525 original size:20 final size:19
Alignment explanation
Indices: 3035480--3035550 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
3035470 AACACAAAAG
3035480 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
3035499 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
3035519 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
3035539 T-AATTTCGCAAC
1 TCAAATTCGCAAC
3035551 AGGTTTTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 23 0.52
20 21 0.48
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:3035551 original size:19 final size:19
Alignment explanation
Indices: 3035524--3035570 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3035514 GATTTTCGAA
3035524 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
3035543 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
3035561 TTCGCAACAC
1 TTCGCAACAC
3035571 AAGTGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:3035734 original size:16 final size:16
Alignment explanation
Indices: 3035713--3035743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3035703 TCTCTAATTT
3035713 TTTTTACATAATTTTG
1 TTTTTACATAATTTTG
*
3035729 TTTTTATATAATTTT
1 TTTTTACATAATTTT
3035744 TCAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTG
Found at i:3036548 original size:24 final size:24
Alignment explanation
Indices: 3036495--3036549 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3036485 CAGTATTCGA
* *
3036495 AATTTGATCTTGGTCAATACCCGG
1 AATTTGACCTTGGTCAATACCCAG
*
3036519 AATTTGACCTTGGTCAATACTCAG
1 AATTTGACCTTGGTCAATACCCAG
*
3036543 ATTTTGA
1 AATTTGA
3036550 TGATGTGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (24 bp):
AATTTGACCTTGGTCAATACCCAG
Found at i:3038804 original size:18 final size:18
Alignment explanation
Indices: 3038781--3038816 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3038771 AAGCAAAAGG
*
3038781 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3038799 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3038817 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3039191 original size:14 final size:14
Alignment explanation
Indices: 3039153--3039191 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3039143 ATAGTCAAAT
3039153 TCGCAACGCG-AAA
1 TCGCAACGCGAAAA
3039166 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
3039180 TCGCAACGCGAA
1 TCGCAACGCGAA
3039192 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:3039351 original size:66 final size:65
Alignment explanation
Indices: 3039269--3039444 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 65
3039259 AATTTAAAAC
3039269 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
3039334 A
65 A
* * *
3039335 AACAAATCAACTTTTACAAATCAATTAAACAAAC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
3039399 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
3039445 GTGTACCCCA
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 33 0.33
68 4 0.04
69 15 0.15
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:3040873 original size:42 final size:42
Alignment explanation
Indices: 3040792--3040890 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
3040782 GCGGGCGGGA
* * *
3040792 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGGG
* * *
3040834 CTTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGTG
1 CCTCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGGG
3040876 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
3040891 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGGG
Found at i:3040897 original size:21 final size:21
Alignment explanation
Indices: 3040792--3040890 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
3040782 GCGGGCGGGA
*
3040792 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
3040813 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
3040834 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
3040855 CCTCTTGAACGAT-AGGAGGTG
1 CCTCTTGAACGATGA-GAGGGG
*
3040876 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
3040891 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:3043095 original size:14 final size:14
Alignment explanation
Indices: 3043076--3043114 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
3043066 CTAAAATCGC
*
3043076 GTTGCGATTTTGGT
1 GTTGCGATTTTAGT
3043090 GTTGCGATTTTAGT
1 GTTGCGATTTTAGT
3043104 GTTGCGATTTT
1 GTTGCGATTTT
3043115 CATTTTCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTAGT
Found at i:3043141 original size:20 final size:20
Alignment explanation
Indices: 3043096--3043134 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3043086 TGGTGTTGCG
* *
3043096 ATTTTAGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGAATTTC
3043116 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
3043135 ATATTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:3043508 original size:22 final size:22
Alignment explanation
Indices: 3043481--3043529 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3043471 AGATAGACGG
3043481 ATTTCGCCGGAGATGGGAACGA
1 ATTTCGCCGGAGATGGGAACGA
* * *
3043503 ATTTCGCCGGGGATGGGGACGG
1 ATTTCGCCGGAGATGGGAACGA
3043525 ATTTC
1 ATTTC
3043530 ACCGTAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.22
Consensus pattern (22 bp):
ATTTCGCCGGAGATGGGAACGA
Found at i:3043666 original size:20 final size:20
Alignment explanation
Indices: 3043643--3043736 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
3043633 ATGTTTCGCA
*
3043643 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATTGCG
* *
3043663 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
* *
3043683 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
*
3043703 TTGCGAATTTGGCTATTGCG
1 TTGCGAATTTGACTATTGCG
3043723 TTGCGAATTTGACT
1 TTGCGAATTTGACT
3043737 TCTGTGTTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTATTGCG
Found at i:3043765 original size:40 final size:40
Alignment explanation
Indices: 3043643--3043771 Score: 104
Period size: 40 Copynumber: 3.2 Consensus size: 40
3043633 ATGTTTCGCA
* * ** **
3043643 TTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACT-TCTGTGTTACGAATTTGACAATTACG
* * * * *
3043683 TTGCGAATTTGACTTTTGTGTTGCGAATTTGGCTATTGCG
1 TTGCGAATTTGACTTCTGTGTTACGAATTTGACAATTACG
3043723 TTGCGAATTTGACTTCTGTGTTACG-ATTT-ACAAATTCACG
1 TTGCGAATTTGACTTCTGTGTTACGAATTTGAC-AATT-ACG
3043763 TTGC-AATTT
1 TTGCGAATTT
3043772 ACAGATTCGC
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 13 0.17
40 62 0.82
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTTCTGTGTTACGAATTTGACAATTACG
Found at i:3043766 original size:60 final size:60
Alignment explanation
Indices: 3043643--3043789 Score: 149
Period size: 60 Copynumber: 2.5 Consensus size: 60
3043633 ATGTTTCGCA
* * * ***
3043643 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACGAATTTGACATTCACG
* *
3043703 TTGCGAATTTGGCTATTGCGTTGCGAATTTGACTTCTGTGTTACG-ATTT-ACAAATTCACG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACGAATTTGAC--ATTCACG
*
3043763 TTGC-AATTT-ACAGATTCGCGTTGCGAA
1 TTGCGAATTTGAC-TA-TCGCGTTGCGAA
3043790 ATTGGAAACT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
58 3 0.04
59 10 0.14
60 59 0.82
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (60 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACGAATTTGACATTCACG
Found at i:3043773 original size:20 final size:20
Alignment explanation
Indices: 3043748--3043786 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3043738 CTGTGTTACG
3043748 ATTTACAAATTCACGTTGCA
1 ATTTACAAATTCACGTTGCA
* *
3043768 ATTTACAGATTCGCGTTGC
1 ATTTACAAATTCACGTTGC
3043787 GAAATTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
ATTTACAAATTCACGTTGCA
Found at i:3056355 original size:65 final size:64
Alignment explanation
Indices: 3056286--3056461 Score: 189
Period size: 65 Copynumber: 2.7 Consensus size: 64
3056276 TGGAACACTT
* * * * *
3056286 AGTGCATCGGTGCATTAAGGGTGCATTGATGCATAAATTGCATTCGATGTTTCAA-ACAAGCCTG
1 AGTGCATCGATGCATT-AGGGTGCATCGATGCATAAAATGCATTCGATATTTCAATAAAAGCCT-
3056350 G
64 G
* * * *
3056351 AGTGCATCGATGCATGGTA-TGTGCATCGATGCATAAAATGTATTCGATATTTTAATAAAATCCT
1 AGTGCATCGATGCAT--TAGGGTGCATCGATGCATAAAATGCATTCGATATTTCAATAAAAGCCT
3056415 G
64 G
3056416 AGTGCATCGATGCA-T-GGTTGTGCATCGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCATTAGG--GTGCATCGATGCATAAAATGCATTCGA
3056462 AATGGTGTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
64 26 0.28
65 59 0.63
66 7 0.07
67 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATTAGGGTGCATCGATGCATAAAATGCATTCGATATTTCAATAAAAGCCTG
Found at i:3056391 original size:19 final size:19
Alignment explanation
Indices: 3056352--3056391 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3056342 CAAGCCTGGA
***
3056352 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAAT
3056371 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
3056390 GT
1 GT
3056392 ATTCGATATT
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:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATAAAAT
Found at i:3056460 original size:64 final size:65
Alignment explanation
Indices: 3056306--3056461 Score: 226
Period size: 65 Copynumber: 2.4 Consensus size: 65
3056296 TGCATTAAGG
* * * *
3056306 GTGCATTGATGCATAAATTGCATTCGATGTTTCAAACAAGCCTGGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATATTTCAAAAAAGCCTGGAGTGCATCGATGCATGGTAT
* * *
3056371 GTGCATCGATGCATAAAATGTATTCGATATTTTAATAAAATCCT-GAGTGCATCGATGCATGGT-
1 GTGCATCGATGCATAAAATGCATTCGATATTTCAA-AAAAGCCTGGAGTGCATCGATGCATGGTA
3056434 T
65 T
3056435 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
3056462 AATGGTGTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 27 0.33
65 49 0.60
66 6 0.07
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATATTTCAAAAAAGCCTGGAGTGCATCGATGCATGGTAT
Found at i:3063922 original size:3 final size:3
Alignment explanation
Indices: 3063875--3063910 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3063865 CAAAATTAAG
*
3063875 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3063911 GGTGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:3067253 original size:36 final size:38
Alignment explanation
Indices: 3067186--3067262 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
3067176 TTTTTATATT
3067186 TTTAATTTTGTAAAAAAAATTATATAAATATTATG-AA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATGCAA
* * *
3067223 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTGCAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATGCAA
3067260 TTT
1 TTT
3067263 GTAATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 14 0.39
37 22 0.61
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATGCAA
Found at i:3073518 original size:26 final size:28
Alignment explanation
Indices: 3073486--3073538 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
3073476 ACCTTTGATG
3073486 TTTTATTTGG-TATTTGG-TACTTATGT
1 TTTTATTTGGTTATTTGGATACTTATGT
*
3073512 TTTTATTTGGTTATTTGGATATTTATG
1 TTTTATTTGGTTATTTGGATACTTATG
3073539 ACTTGTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.42
27 7 0.29
28 7 0.29
ACGTcount: A:0.17, C:0.02, G:0.19, T:0.62
Consensus pattern (28 bp):
TTTTATTTGGTTATTTGGATACTTATGT
Found at i:3074165 original size:21 final size:21
Alignment explanation
Indices: 3074123--3074215 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 21
3074113 TGTAAGTTTT
* *
3074123 GGATCAATCCCTTTCAC-TAAA
1 GGATCAATCCC-TTGACGAAAA
*
3074144 GGATCAATCCCTTGAGGAAAA
1 GGATCAATCCCTTGACGAAAA
* * *
3074165 GG-TAAATCCCTTCACCAAAA
1 GGATCAATCCCTTGACGAAAA
* * * *
3074185 TGATCGATCCCTCGATGAAAA
1 GGATCAATCCCTTGACGAAAA
*
3074206 GGATCGATCC
1 GGATCAATCC
3074216 ATTCCTCTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
20 18 0.33
21 37 0.67
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
GGATCAATCCCTTGACGAAAA
Found at i:3074195 original size:41 final size:41
Alignment explanation
Indices: 3074128--3074207 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
3074118 GTTTTGGATC
* *
3074128 AATCCCTTTCACTAAAGGATCAATCCCTTGAGGAAAAGGTA
1 AATCCCTTTCACAAAAGGATCAATCCCTCGAGGAAAAGGTA
* * *
3074169 AATCCC-TTCACCAAAATGATCGATCCCTCGATGAAAAGG
1 AATCCCTTTCA-CAAAAGGATCAATCCCTCGAGGAAAAGG
3074208 ATCGATCCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 4 0.12
41 29 0.88
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AATCCCTTTCACAAAAGGATCAATCCCTCGAGGAAAAGGTA
Found at i:3083740 original size:43 final size:43
Alignment explanation
Indices: 3083715--3084115 Score: 518
Period size: 43 Copynumber: 9.3 Consensus size: 43
3083705 TTCTCTTACC
*
3083715 TTTAGTGGCGTTTTTCACCACAAACG-CGCTAATGCTATTGGT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
* * * *
3083757 TTTAGTGGCATTTTTTACAACAAATGCCGCTAATGCTATTGAT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
3083800 TTTAGTGGCGTTTTTTTACCACAAACGCCGCTAATGCTATTGGT
1 TTTAGTGGCG-TTTTTTACCACAAACGCCGCTAATGCTATTGGT
* * * *
3083844 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGTTATTGAT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
* ** * *
3083887 TTAAGTGGCGTTTTTTTGTCACAAATGCCACTAATGCTATTGGT
1 TTTAGTGGCG-TTTTTTACCACAAACGCCGCTAATGCTATTGGT
**
3083931 TTTAGTGGCGTTTTTTTGCACAAACGCCGCTAATGCTATTGGT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
* * *
3083974 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGAT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
* * * *
3084017 TTAAGTGGCGTTTTTTTGCCACAAATGCCACTAATGCTATTGGT
1 TTTAGTGGCG-TTTTTTACCACAAACGCCGCTAATGCTATTGGT
* ***
3084061 TTTAGTGGCGTTTTTT-GCACAAACATTGCTAATGCTATTGGT
1 TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
3084103 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
3084116 GTAATACAAA
Statistics
Matches: 314, Mismatches: 41, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
42 55 0.18
43 144 0.46
44 115 0.37
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (43 bp):
TTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTATTGGT
Found at i:3083850 original size:87 final size:87
Alignment explanation
Indices: 3083688--3084112 Score: 529
Period size: 87 Copynumber: 4.9 Consensus size: 87
3083678 GGCGTTTGTG
* * * * *
3083688 GCCAAAAACGCCGCTAATTCTCTT-ACCTTTAGTGGCGTTTTTCACCACAAACG-CGCTAATGCT
1 GCCACAAACGCCGCTAATGCTATTGA-TTTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCT
3083751 ATTGGTTTTAGTGGC-ATTTTTT
65 ATTGGTTTTAGTGGCGATTTTTT
* * *
3083773 ACAACAAATGCCGCTAATGCTATTGATTTTAGTGGCGTTTTTTTACCACAAACGCCGCTAATGCT
1 GCCACAAACGCCGCTAATGCTATTGATTTTAGTGGCG-TTTTTTACCACAAACGCCGCTAATGCT
3083838 ATTGGTTTTAGTGGC-ATTTTTT
65 ATTGGTTTTAGTGGCGATTTTTT
* * ** * *
3083860 GCCACAAACGCCGCTAATGTTATTGATTTAAGTGGCGTTTTTTTGTCACAAATGCCACTAATGCT
1 GCCACAAACGCCGCTAATGCTATTGATTTTAGTGGCG-TTTTTTACCACAAACGCCGCTAATGCT
*
3083925 ATTGGTTTTAGTGGCGTTTTTTT
65 ATTGGTTTTAGTGGCGATTTTTT
* * *
3083948 G-CACAAACGCCGCTAATGCTATTGGTTTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTA
1 GCCACAAACGCCGCTAATGCTATTGATTTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTA
* * *
3084012 TTGATTTAAGTGGCGTTTTTTT
66 TTGGTTTTAGTGGCGATTTTTT
* * * * ***
3084034 GCCACAAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTT-GCACAAACATTGCTAATGCTA
1 GCCACAAACGCCGCTAATGCTATTGATTTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTA
3084098 TTGGTTTTAGTGGCG
66 TTGGTTTTAGTGGCG
3084113 TTTGTAATAC
Statistics
Matches: 299, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
85 28 0.09
86 92 0.31
87 172 0.58
88 7 0.02
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (87 bp):
GCCACAAACGCCGCTAATGCTATTGATTTTAGTGGCGTTTTTTACCACAAACGCCGCTAATGCTA
TTGGTTTTAGTGGCGATTTTTT
Found at i:3083959 original size:130 final size:130
Alignment explanation
Indices: 3083715--3084111 Score: 613
Period size: 130 Copynumber: 3.1 Consensus size: 130
3083705 TTCTCTTACC
* ** * * *
3083715 TTTAGTGGCGTTTTTCACCACAAACG-CGCTAATGCTATTGGTTTTAGTGGC-ATTTTTT-ACAA
1 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGATTTAAGTGGCGTTTTTTTGAC-A
* * *
3083777 CAAATGCCGCTAATGCTATTGATTTTAGTGGCGTTTTTTTACCACAAACGCCGCTAATGCTATTG
65 CAAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTTT-GCACAAACGCCGCTAATGCTATTG
3083842 GT
129 GT
* *
3083844 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGTTATTGATTTAAGTGGCGTTTTTTTGTCAC
1 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGATTTAAGTGGCGTTTTTTTGACAC
3083909 AAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTTTGCACAAACGCCGCTAATGCTATTGGT
66 AAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTTTGCACAAACGCCGCTAATGCTATTGGT
*
3083974 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGATTTAAGTGGCGTTTTTTTGCCAC
1 TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGATTTAAGTGGCGTTTTTTTGACAC
***
3084039 AAATGCCACTAATGCTATTGGTTTTAGTGGCG-TTTTTTGCACAAACATTGCTAATGCTATTGGT
66 AAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTTTGCACAAACGCCGCTAATGCTATTGGT
3084103 TTTAGTGGC
1 TTTAGTGGC
3084112 GTTTGTAATA
Statistics
Matches: 249, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
129 61 0.24
130 142 0.57
131 45 0.18
132 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (130 bp):
TTTAGTGGCATTTTTTGCCACAAACGCCGCTAATGCTATTGATTTAAGTGGCGTTTTTTTGACAC
AAATGCCACTAATGCTATTGGTTTTAGTGGCGTTTTTTTGCACAAACGCCGCTAATGCTATTGGT
Found at i:3086713 original size:101 final size:102
Alignment explanation
Indices: 3086548--3086749 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 102
3086538 AGAACTCGCT
3086548 GTATCTCCTCAACAATCAAGTCTCCAACAAACGCCCCCAAAATCGAACACATTTTTGGAGGTTTC
1 GTATCTCCTCAACAATCAAGTCTCCAACAAACGCCCCCAAAATCGAACACATTTTTGGAGGTTTC
3086613 ATTTGGGTGATTCTG-AAAGATTGATAAAGATAGAAG
66 ATTTGGGTGATTCTGAAAAGATTGATAAAGATAGAAG
3086649 GTATCTTCCTCAACAATCAAGTCTCCAACAAACG-CCCCAAAATCGAACACATTTTTGGAGGTTT
1 GTATC-TCCTCAACAATCAAGTCTCCAACAAACGCCCCCAAAATCGAACACATTTTTGGAGGTTT
3086713 CATTTGGGTGATTCTGAAAAGATTGATAAAGATAGAA
65 CATTTGGGTGATTCTGAAAAGATTGATAAAGATAGAA
3086750 TTGTAATATT
Statistics
Matches: 99, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
101 51 0.52
102 48 0.48
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (102 bp):
GTATCTCCTCAACAATCAAGTCTCCAACAAACGCCCCCAAAATCGAACACATTTTTGGAGGTTTC
ATTTGGGTGATTCTGAAAAGATTGATAAAGATAGAAG
Found at i:3088659 original size:3 final size:3
Alignment explanation
Indices: 3088653--3088710 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
3088643 TAACCACCAC
* *
3088653 CAT CAT CA- CGT CAT CAT CAT CAT CAT CAT CGT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3088700 CAT CAT CAT CA
1 CAT CAT CAT CA
3088711 CATAAACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:3088954 original size:12 final size:13
Alignment explanation
Indices: 3088921--3088966 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
3088911 ATATATTCCT
*
3088921 TTTATTTTATTTA
1 TTTATATTATTTA
*
3088934 -TAATATTATTTA
1 TTTATATTATTTA
3088946 TTTAT-TTA-TTA
1 TTTATATTATTTA
3088957 TTTATATTAT
1 TTTATATTAT
3088967 AAATTAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.30
12 16 0.59
13 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTATTTA
Found at i:3089177 original size:16 final size:17
Alignment explanation
Indices: 3089150--3089185 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3089140 ATATATAAGA
3089150 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
3089167 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
3089183 AAA
1 AAA
3089186 ATAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:3093691 original size:3 final size:3
Alignment explanation
Indices: 3093683--3093709 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3093673 AGAACTCTCC
3093683 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
3093710 TCTCTTCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3094715 original size:15 final size:15
Alignment explanation
Indices: 3094685--3094723 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3094675 TATGTTTTTG
3094685 TATGTATTATAAGATA
1 TATGT-TTATAAGATA
*
3094701 TATGTTTATATGATA
1 TATGTTTATAAGATA
*
3094716 CATGTTTA
1 TATGTTTA
3094724 AGTGTCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (15 bp):
TATGTTTATAAGATA
Found at i:3095116 original size:17 final size:18
Alignment explanation
Indices: 3095073--3095141 Score: 115
Period size: 17 Copynumber: 3.9 Consensus size: 18
3095063 AGGGTTCTAC
3095073 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
3095091 GTGGTCCTTCTGGACATA
1 GTGGTCCTTCGGGACATA
3095109 GT-GTCCTTCGGGACAT-
1 GTGGTCCTTCGGGACATA
3095125 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
3095142 TCATACCCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
16 2 0.04
17 27 0.56
18 19 0.40
ACGTcount: A:0.14, C:0.23, G:0.32, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3095407 original size:73 final size:74
Alignment explanation
Indices: 3095329--3095476 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 74
3095319 GACAGGTTGG
3095329 TTTTTTGGTATAGTTATATAATTGTTACATGATGTGTATATATGGTAAGA-G-AA-AGTAATATG
1 TTTTTTGGTATAGTTATATAATTGTTACATGATGTG--TATATGGTAAGAGGAAAGAGTAATATG
3095391 ATAAAGGGATT
64 ATAAAGGGATT
3095402 TTTTTTGGTATAGTTATATAATTGTTACATGATGTGTATATGGTAAGAGGAAAGAGTAATATGAT
1 TTTTTTGGTATAGTTATATAATTGTTACATGATGTGTATATGGTAAGAGGAAAGAGTAATATGAT
3095467 AAAGGGATT
66 AAAGGGATT
3095476 T
1 T
3095477 AAATGATGAT
Statistics
Matches: 72, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
71 12 0.17
72 1 0.01
73 38 0.53
74 21 0.29
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (74 bp):
TTTTTTGGTATAGTTATATAATTGTTACATGATGTGTATATGGTAAGAGGAAAGAGTAATATGAT
AAAGGGATT
Found at i:3097117 original size:14 final size:15
Alignment explanation
Indices: 3097092--3097124 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3097082 TTTGAGAATT
*
3097092 ATAAATAAAAATTTA
1 ATAAATAAAAATATA
3097107 ATAAA-AAAAATATA
1 ATAAATAAAAATATA
3097121 ATAA
1 ATAA
3097125 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATAAAAATATA
Found at i:3097129 original size:2 final size:2
Alignment explanation
Indices: 3097116--3097152 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3097106 AATAAAAAAA
*
3097116 AT AT A- AT A- AT AT AT AT AT AG 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 AT AT AT AT A
3097153 ATAAACCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3098715 original size:20 final size:20
Alignment explanation
Indices: 3098690--3098729 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3098680 CTAGTAAATG
3098690 CAATAGTGAGCATACTCATA
1 CAATAGTGAGCATACTCATA
*
3098710 CAATAGTGAGTATACTCATA
1 CAATAGTGAGCATACTCATA
3098730 TACTGCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (20 bp):
CAATAGTGAGCATACTCATA
Found at i:3099387 original size:20 final size:22
Alignment explanation
Indices: 3099362--3099401 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3099352 TGTTGTATAT
3099362 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3099382 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3099402 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3099546 original size:21 final size:20
Alignment explanation
Indices: 3099502--3099596 Score: 127
Period size: 21 Copynumber: 4.7 Consensus size: 20
3099492 GCAGCCTTCG
* * *
3099502 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGCAAGA
3099522 TGCATCGATGCACAGCCAAGA
1 TGCATCGATGCACAG-CAAGA
*
3099543 TGCATCGATGCACAACCAAGA
1 TGCATCGATGCAC-AGCAAGA
*
3099564 TGCATCGATGCACAGAAAGA
1 TGCATCGATGCACAGCAAGA
3099584 TGCATCGATGCAC
1 TGCATCGATGCAC
3099597 TAATTGCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 32 0.48
21 34 0.51
22 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAAGA
Found at i:3099664 original size:22 final size:23
Alignment explanation
Indices: 3099631--3099673 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3099621 ATGGATGCAC
3099631 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
3099654 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
3099674 GCAGGGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:3099688 original size:21 final size:20
Alignment explanation
Indices: 3099617--3099715 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
3099607 CGGTGTTTGA
*
3099617 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
3099637 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
3099659 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
3099679 GATACATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
3099701 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3099716 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.42
22 17 0.25
23 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:3099862 original size:34 final size:29
Alignment explanation
Indices: 3099794--3099853 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
3099784 AAAATTTGAA
*
3099794 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
3099823 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
3099854 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:3101376 original size:28 final size:30
Alignment explanation
Indices: 3101345--3101401 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 30
3101335 AAAAATTTAA
3101345 TAAATTCAATT-AAGTCCAAAAA-CATTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTG
3101373 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAACCATTT
3101402 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 11 0.41
29 11 0.41
30 5 0.19
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTG
Found at i:3105240 original size:13 final size:13
Alignment explanation
Indices: 3105222--3105246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3105212 TTGATATTAC
3105222 TTTTGAAAAGTGA
1 TTTTGAAAAGTGA
3105235 TTTTGAAAAGTG
1 TTTTGAAAAGTG
3105247 TTGTAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:3106516 original size:28 final size:28
Alignment explanation
Indices: 3106477--3106536 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
3106467 TTGAGTATTT
3106477 TATTATAATATTAAAAATATT-ATATATA
1 TATTATAATATTAAAAATATTAATA-ATA
* *
3106505 TATTATATTATTAGAAATATTAATAATA
1 TATTATAATATTAAAAATATTAATAATA
3106533 TATT
1 TATT
3106537 TTAAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TATTATAATATTAAAAATATTAATAATA
Found at i:3106988 original size:33 final size:33
Alignment explanation
Indices: 3106942--3107006 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3106932 GTACAACAGG
*
3106942 CATCATATTATATCATG-CACACAAGAGAAGAGT
1 CATCATATCATATCATGACA-ACAAGAGAAGAGT
3106975 CATCATATCATATCATGACAACAAGAGAAGAG
1 CATCATATCATATCATGACAACAAGAGAAGAG
3107007 AGGTTAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (33 bp):
CATCATATCATATCATGACAACAAGAGAAGAGT
Done.