Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:1988037 original size:93 final size:93
Alignment explanation
Indices: 1987723--1988658 Score: 1840
Period size: 93 Copynumber: 10.1 Consensus size: 93
1987713 TAGATTGCTT
*
1987723 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1987788 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1987816 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1987880 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1987908 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1987973 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988001 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988066 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988094 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988158 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988186 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988251 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988279 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988344 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1988372 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988437 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988465 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988530 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988558 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988623 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1988651 AGTAAATT
1 AGTAAATT
1988659 ATCCATTCAA
Statistics
Matches: 838, Mismatches: 3, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.22
93 654 0.78
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1988220 original size:278 final size:278
Alignment explanation
Indices: 1987723--1988658 Score: 1845
Period size: 278 Copynumber: 3.4 Consensus size: 278
1987713 TAGATTGCTT
*
1987723 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1987788 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1987853 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
1987918 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
1987983 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
1988001 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988066 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1988131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
1988196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
1988261 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
1988279 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1988344 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1988409 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1988474 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
195 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
1988539 GTTTTGTCTTTTGGTTGAA
260 GTTTTGTCTTTTGGTTGAA
1988558 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1988623 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATT
1988659 ATCCATTCAA
Statistics
Matches: 655, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
278 431 0.66
279 224 0.34
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:1988426 original size:17 final size:17
Alignment explanation
Indices: 1988396--1988428 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1988386 GTTGCTGCCA
1988396 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
1988413 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
1988429 AAATAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:1988742 original size:19 final size:19
Alignment explanation
Indices: 1988702--1988830 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1988692 TAGTTTACTT
* *
1988702 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1988722 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1988741 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1988760 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1988774 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1988793 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1988807 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1988826 TCGCA
1 TCGCA
1988831 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:1988781 original size:33 final size:32
Alignment explanation
Indices: 1988738--1988830 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1988728 CGCGAAACCA
**
1988738 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1988770 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1988803 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1988831 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:1988828 original size:52 final size:52
Alignment explanation
Indices: 1988702--1988830 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1988692 TAGTTTACTT
**
1988702 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1988754 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1988807 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1988831 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:1988848 original size:19 final size:19
Alignment explanation
Indices: 1988826--1988960 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1988816 GAAACCAAAA
*
1988826 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1988845 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1988861 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1988878 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1988894 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1988911 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1988930 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1988950 TCGTGTTGCGA
1 TCGCGTTGCGA
1988961 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:1988867 original size:14 final size:14
Alignment explanation
Indices: 1988848--1988904 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1988838 TTTCATTTCG
1988848 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1988862 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1988879 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1988895 CGTTGCGATT
1 CGTTGCGATT
1988905 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:1988873 original size:33 final size:33
Alignment explanation
Indices: 1988831--1988923 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1988821 CAAAATCGCA
*
1988831 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1988864 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1988897 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1988924 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:1990903 original size:14 final size:14
Alignment explanation
Indices: 1990884--1990919 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1990874 ATTGTTTAAT
1990884 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1990898 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1990912 TGATTTGT
1 TGATTTGT
1990920 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1991042 original size:19 final size:19
Alignment explanation
Indices: 1991026--1991127 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1991016 AAAAATGACT
1991026 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1991045 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1991064 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1991078 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1991097 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1991117 ATCGCAATGCG
1 ATCGCAATGCG
1991128 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1991183 original size:19 final size:19
Alignment explanation
Indices: 1991156--1991604 Score: 554
Period size: 19 Copynumber: 25.4 Consensus size: 19
1991146 GATTATCTCG
1991156 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991175 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991194 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1991208 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991246 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991265 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991284 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1991298 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991317 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991336 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1991350 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991369 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991388 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991407 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991426 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
1991440 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991459 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991478 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1991492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1991511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1991530 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1991544 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1991564 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1991578 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1991597 TTGCGATT
1 TTGCGATT
1991605 GTATTTTCCG
Statistics
Matches: 376, Mismatches: 18, Indels: 72
0.81 0.04 0.15
Matches are distributed among these distances:
14 47 0.12
16 45 0.12
17 40 0.11
18 3 0.01
19 229 0.61
20 12 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1991196 original size:52 final size:51
Alignment explanation
Indices: 1991134--1991604 Score: 345
Period size: 52 Copynumber: 8.9 Consensus size: 51
1991124 TGCGTTTATA
*
1991134 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTACGATTTTC
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1991186 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1991238 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA-TTTC---TCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
1991297 GTTGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
1991349 GTTGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
** * * *
1991399 ATTTCGCATTGCGATTT-TAATTTCGCA-TTGCGA-TTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCTCGTTGCG-ATTTTC-ATTTC-G-CATTGCGATTTTC
* * * * *
1991451 ATTTCGCATTGCGATTT-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* * * * *
1991503 ATTTCGCATTGCGATTT-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
1991555 ATTTCCGCATTGCGATTT-TCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTCTC--GTTGCGATTTTCATTTCGCATTGCGATT
1991605 GTATTTTCCG
Statistics
Matches: 371, Mismatches: 27, Indels: 41
0.85 0.06 0.09
Matches are distributed among these distances:
50 20 0.05
51 9 0.02
52 254 0.68
53 30 0.08
54 7 0.02
55 9 0.02
57 30 0.08
58 3 0.01
59 9 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (51 bp):
ATTTCGCATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1991301 original size:142 final size:142
Alignment explanation
Indices: 1991118--1991604 Score: 801
Period size: 142 Copynumber: 3.5 Consensus size: 142
1991108 GAAATGAAAA
* * * *
1991118 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTACGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGAT
*
1991182 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
65 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1991247 TGCGATTTTCATT
130 TGCGATTTTCATT
1991260 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1991325 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
66 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
1991390 GCGATTTTCATT
131 GCGATTTTCATT
1991402 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1991467 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
66 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
*
1991532 GCGA--TTC-TC
131 GCGATTTTCATT
* * *
1991541 TCG--TTGCGATTTTCATTTCCGCATTGCGATT-T-TCATGTTGGGATTTTCATTTCGCGTTGCG
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTCTGTC--GTTGCGATTTTCATTTCGCATTGCG
1991602 ATT
63 ATT
1991605 GTATTTTCCG
Statistics
Matches: 332, Mismatches: 9, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
136 2 0.01
137 15 0.05
138 38 0.11
139 4 0.01
140 3 0.01
142 267 0.80
143 3 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (142 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
GCGATTTTCATT
Found at i:1993902 original size:12 final size:12
Alignment explanation
Indices: 1993885--1993909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1993875 TCTTCGGGGA
1993885 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1993897 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1993909 C
1 C
1993910 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:1994118 original size:24 final size:24
Alignment explanation
Indices: 1994084--1994130 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1994074 CTGAAACATC
1994084 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1994108 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1994131 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1994841 original size:20 final size:20
Alignment explanation
Indices: 1994813--1995181 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
1994803 AAATTTCAGT
* * * *
1994813 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1994833 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1994853 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1994873 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1994893 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1994913 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1994933 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1994953 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1994973 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1994993 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1995013 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1995033 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
*
1995053 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1995073 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1995093 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1995113 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1995133 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1995153 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1995173 GTTGCGATT
1 GTTGCGATT
1995182 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1996792 original size:62 final size:62
Alignment explanation
Indices: 1996713--1996838 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
1996703 GCTATGTTTG
* * *
1996713 TAAATGAATTGGGTTTGAACAAATAAATTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
1 TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
*
1996775 TAAATGAATCGAGTTTGAGCAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
1 TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
1996837 TA
1 TA
1996839 CTCGTCCCAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (62 bp):
TAAATGAATCGAGTTTGAACAAATAAACTTGTGTTTGTATTTCTTTGTTTACTTTTGAAGCA
Found at i:1998656 original size:36 final size:36
Alignment explanation
Indices: 1998616--1998756 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
1998606 GAATAAGAAA
* *
1998616 AACGAAAGAAAGCGTCGACACTTCCGATTCAAGTAG
1 AACGAAAGGAAGCATCGACACTTCCGATTCAAGTAG
*
1998652 AACGAAAGGAAGCATCGGCACTTCCGATTCAAGTCA-
1 AACGAAAGGAAGCATCGACACTTCCGATTCAAGT-AG
* * *
1998688 AACGGAAGGAAGCATTGACACTTCCGATTCAAGTCG
1 AACGAAAGGAAGCATCGACACTTCCGATTCAAGTAG
* * * *
1998724 AAC-AGAAGGATGTATCG-CACTTTCGTTTCAAGT
1 AACGA-AAGGAAGCATCGACACTTCCGATTCAAGT
1998757 GTTCATCTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
35 14 0.16
36 74 0.83
37 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.21
Consensus pattern (36 bp):
AACGAAAGGAAGCATCGACACTTCCGATTCAAGTAG
Found at i:2003505 original size:44 final size:44
Alignment explanation
Indices: 2003437--2003562 Score: 198
Period size: 44 Copynumber: 2.9 Consensus size: 44
2003427 TCTGACATGT
* * *
2003437 CTGCGAACCAAACATAATATGGAATTAGATTTCAATTCTATTTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
*
2003481 CTGCCAACCAAACATAATATGGAATTGGATTCCAATTCTATTTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
* *
2003525 CTGCCAACCAAACAAAATATTGAATTGGATTACAATTC
1 CTGCCAACCAAACATAATATGGAATTGGATTACAATTC
2003563 CTGACAGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (44 bp):
CTGCCAACCAAACATAATATGGAATTGGATTACAATTCTATTTC
Found at i:2012644 original size:23 final size:22
Alignment explanation
Indices: 2012575--2012653 Score: 115
Period size: 23 Copynumber: 3.6 Consensus size: 22
2012565 ACACCTAACA
2012575 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
2012597 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
2012618 GTGCATCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
2012641 GTGCATCGATGCA
1 GTGCATCGATGCA
2012654 CAAGGCCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
21 18 0.37
22 12 0.24
23 19 0.39
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:2012673 original size:43 final size:42
Alignment explanation
Indices: 2012574--2012658 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 42
2012564 TACACCTAAC
* *
2012574 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
*
2012616 AGGTGCATCGATGCATGCCTTGAATGTGCATCGATGCACAAGG
1 A-GTGCATCGATGCAT-CCTTGAATGTGCATCGATACACAAGG
2012659 CCATGCATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 14 0.37
44 23 0.61
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (42 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
Found at i:2014232 original size:32 final size:30
Alignment explanation
Indices: 2014188--2014251 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
2014178 TGTTTCTGGA
* *
2014188 TTGTTTGTTTTGGATTATTAAATGTTTGAAT
1 TTGTTTGGTTTGGATGATTAAAT-TTTGAAT
**
2014219 TTGTTATGGTTTGGATGATTGGATTTTGAAT
1 TTGTT-TGGTTTGGATGATTAAATTTTGAAT
2014250 TT
1 TT
2014252 AATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.56
Consensus pattern (30 bp):
TTGTTTGGTTTGGATGATTAAATTTTGAAT
Found at i:2014954 original size:45 final size:45
Alignment explanation
Indices: 2014905--2014992 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
2014895 GAACATCGAA
* *
2014905 TGCATTTTATGCATCGATGAACATACCATGCATCAATGCACTCAG
1 TGCATTTGATGCATCGATGAACAAACCATGCATCAATGCACTCAG
* **
2014950 TGCATTTGATGCATCGATGCACAAACCATGCATTGATGCACTC
1 TGCATTTGATGCATCGATGAACAAACCATGCATCAATGCACTC
2014993 TGGCTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGAACAAACCATGCATCAATGCACTCAG
Found at i:2016371 original size:30 final size:30
Alignment explanation
Indices: 2016337--2016397 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2016327 TTGTCATATG
2016337 ACTTATATCT-TATGATCATATAATCACATA
1 ACTTATAT-TATATGATCATATAATCACATA
** *
2016367 ACTTATATTATATTCTCATATTATCACATA
1 ACTTATATTATATGATCATATAATCACATA
2016397 A
1 A
2016398 TCATGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (30 bp):
ACTTATATTATATGATCATATAATCACATA
Found at i:2019336 original size:21 final size:21
Alignment explanation
Indices: 2019310--2019349 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2019300 CCGTGTAAAA
2019310 ATGTCCCGAAGGACCACATTT
1 ATGTCCCGAAGGACCACATTT
2019331 ATGTCCCGAAGGACCACAT
1 ATGTCCCGAAGGACCACAT
2019350 AGATATCCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATTT
Found at i:2019358 original size:21 final size:21
Alignment explanation
Indices: 2019313--2019361 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2019303 TGTAAAAATG
** *
2019313 TCCCGAAGGACCACATTTATG
1 TCCCGAAGGACCACATAGATA
2019334 TCCCGAAGGACCACATAGATA
1 TCCCGAAGGACCACATAGATA
2019355 TCCCGAA
1 TCCCGAA
2019362 TGACGACTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (21 bp):
TCCCGAAGGACCACATAGATA
Found at i:2019765 original size:38 final size:38
Alignment explanation
Indices: 2019722--2019800 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
2019712 ATATATCTTG
*
2019722 TCACATGACTTATATCT-TATGATCATATAATCACATAA
1 TCACATAACTTATAT-TATATGATCATATAATCACATAA
** *
2019760 TCACATAACTTATATTATATTCTCATATTATCACATAA
1 TCACATAACTTATATTATATGATCATATAATCACATAA
2019798 TCA
1 TCA
2019801 TGTATTTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (38 bp):
TCACATAACTTATATTATATGATCATATAATCACATAA
Found at i:2033286 original size:30 final size:29
Alignment explanation
Indices: 2033205--2033286 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
2033195 TATAGGGCCC
* * *
2033205 AATTATTTTAATACTTATTATTAAGGTTT
1 AATTTTTTTAATATTTATTATTAAGGGTT
*
2033234 AATTTTTTTCAATATTTA-TATTATGGGTT
1 AATTTTTTT-AATATTTATTATTAAGGGTT
2033263 AATTTTTTCTAATATTTATTATTA
1 AATTTTTT-TAATATTTATTATTA
2033287 GGGGATTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 33 0.72
30 13 0.28
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.59
Consensus pattern (29 bp):
AATTTTTTTAATATTTATTATTAAGGGTT
Found at i:2033658 original size:192 final size:187
Alignment explanation
Indices: 2033319--2033697 Score: 681
Period size: 192 Copynumber: 2.0 Consensus size: 187
2033309 TTTTTTAATA
2033319 TTTGTATAAGTGTCCAATTTTTTTGTCATATTTTTTATAACATTTGTTATTAAGTTCAATTTTAT
1 TTTGTATAAGTGTCCAATTTTTTTGTCATATTTTTTATAACATTTGTTATTAAGTTCAATTTTAT
2033384 CAATACTTCTTATTAGGGGTGTGTTAAAATTTAATTACTTTTCTAATAATTTTTGTTATACGAGT
66 CAATACTTCTTATTAGGGGTGTGTTAAAATTTAATTACTTTTCTAATAATTTTTGTTATACGAGT
2033449 CCAATTTTTCAGTACTTTTATTAGAGGTCCAAATTTTTAATATTTTTTATTATAAGC
131 CCAATTTTTCAGTACTTTTATTAGAGGTCCAAATTTTTAATATTTTTTATTATAAGC
2033506 TTTGTATAAGTGTCCAATTTTTTTGTCAATATTTTTTATAACATTTGTTATTAAGAGTTCAATTT
1 TTTGTATAAGTGTCCAATTTTTTTGTC-ATATTTTTTATAACATTTGTTATT-A-AGTTCAATTT
2033571 TATCAATACTTCTTATTAGGGGTGTATGTTAAAA-TTAATTACTTTTCTAAT-ATTATTTGTTAT
63 TATCAATACTTCTTATTAGGGGTG--TGTTAAAATTTAATTACTTTTCTAATAATT-TTTGTTA-
2033634 TACGAGTCCAATTTTTCAGTACTTTTATTAGAGGTCCAAATTTTTAATATTTTTTATTATAAGC
124 TACGAGTCCAATTTTTCAGTACTTTTATTAGAGGTCCAAATTTTTAATATTTTTTATTATAAGC
2033698 ATACTCTTAA
Statistics
Matches: 185, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
187 27 0.15
188 24 0.13
189 1 0.01
190 37 0.20
191 24 0.13
192 72 0.39
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (187 bp):
TTTGTATAAGTGTCCAATTTTTTTGTCATATTTTTTATAACATTTGTTATTAAGTTCAATTTTAT
CAATACTTCTTATTAGGGGTGTGTTAAAATTTAATTACTTTTCTAATAATTTTTGTTATACGAGT
CCAATTTTTCAGTACTTTTATTAGAGGTCCAAATTTTTAATATTTTTTATTATAAGC
Found at i:2033687 original size:28 final size:28
Alignment explanation
Indices: 2033624--2033692 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2033614 TTTCTAATAT
*
2033624 TATTTGTTATTACGAGTCCAATTTTTCAG
1 TATTT-TTATTACGAGTCCAATTTTTCAA
*
2033653 TACTTTTATTA-GAGGTCCAAATTTTT-AA
1 TATTTTTATTACGA-GTCC-AATTTTTCAA
2033681 TATTTTTTATTA
1 TA-TTTTTATTA
2033693 TAAGCATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 13 0.38
29 19 0.56
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TATTTTTATTACGAGTCCAATTTTTCAA
Found at i:2041254 original size:60 final size:60
Alignment explanation
Indices: 2041188--2041356 Score: 150
Period size: 60 Copynumber: 2.8 Consensus size: 60
2041178 TAAATCCACT
2041188 TTTTAAATTAATCCCTAAA-TTTATAA-ATATTTCAATTCCAT-CCCTAAACTATGA-CTATCA
1 TTTTAAATTAATCCCTAAACTTTATAACAT-TTT-AATTCCATACCC-AAACTATGACCT-TCA
* * * *
2041248 TTTTAAATTTATCCTTAAACTTTTTAACATTTTAATTTCATACCCAAACTATGACCTTCA
1 TTTTAAATTAATCCCTAAACTTTATAACATTTTAATTCCATACCCAAACTATGACCTTCA
* ** * * * *
2041308 TTCTAAATTGGTCCCCCAAACTTTTTCAACATTTCAATTTCA-ACCCAAA
1 TTTTAAATTAAT-CCCTAAACTTTAT-AACATTTTAATTCCATACCCAAA
2041357 TTATATGTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
60 45 0.48
61 32 0.34
62 16 0.17
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.40
Consensus pattern (60 bp):
TTTTAAATTAATCCCTAAACTTTATAACATTTTAATTCCATACCCAAACTATGACCTTCA
Found at i:2042201 original size:22 final size:22
Alignment explanation
Indices: 2042172--2042213 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2042162 ACGTGTTCGC
2042172 TTAAAATTTAATTT-TTTTATA
1 TTAAAATTTAATTTATTTTATA
*
2042193 TTAATAATTTATTTTATTTTA
1 TTAA-AATTTAATTTATTTTA
2042214 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTAAAATTTAATTTATTTTATA
Found at i:2042221 original size:18 final size:18
Alignment explanation
Indices: 2042180--2042219 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2042170 GCTTAAAATT
2042180 TAATTT-TTTTATATTAA
1 TAATTTATTTTATATTAA
*
2042197 TAATTTATTTTATTTTAA
1 TAATTTATTTTATATTAA
2042215 -AATTT
1 TAATTT
2042220 TAATTGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTATTTTATATTAA
Found at i:2045165 original size:15 final size:16
Alignment explanation
Indices: 2045134--2045167 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2045124 CCACCATTTT
*
2045134 TCATAACCCTTAAATC
1 TCATAACCCTCAAATC
2045150 TCATAA-CCTCAAATC
1 TCATAACCCTCAAATC
2045165 TCA
1 TCA
2045168 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
TCATAACCCTCAAATC
Found at i:2054786 original size:14 final size:14
Alignment explanation
Indices: 2054767--2054793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2054757 TACATTTTCA
2054767 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
2054781 TTCTTCATTCTTT
1 TTCTTCATTCTTT
2054794 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:2058348 original size:8 final size:8
Alignment explanation
Indices: 2058335--2058437 Score: 99
Period size: 8 Copynumber: 13.0 Consensus size: 8
2058325 AAAAAGAATG
2058335 AATGAAAA
1 AATGAAAA
2058343 AATGAAAA
1 AATGAAAA
*
2058351 AGTG-AAA
1 AATGAAAA
2058358 AA-GAAAA
1 AATGAAAA
*
2058365 AATAAAAAA
1 AAT-GAAAA
2058374 AATGAAAA
1 AATGAAAA
2058382 AA-G-AAA
1 AATGAAAA
2058388 AA-GAAAAA
1 AATG-AAAA
*
2058396 AATAAAAAA
1 AAT-GAAAA
*
2058405 AATAAAAAA
1 AAT-GAAAA
2058414 AATGAAAA
1 AATGAAAA
2058422 AATGAAAA
1 AATGAAAA
2058430 AATGAAAA
1 AATGAAAA
2058438 GAAAAAAGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
6 7 0.09
7 10 0.12
8 42 0.51
9 23 0.28
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
AATGAAAA
Found at i:2058361 original size:30 final size:30
Alignment explanation
Indices: 2058339--2058450 Score: 128
Period size: 31 Copynumber: 3.9 Consensus size: 30
2058329 AGAATGAATG
*
2058339 AAAAAATGAAAAAGTGAAAAAGAAAAAATAA
1 AAAAAATGAAAAA-AGAAAAAGAAAAAATAA
2058370 AAAAAATGAAAAAAGAAAAAGAAAAAAATAA
1 AAAAAATGAAAAAAGAAAAAG-AAAAAATAA
* *
2058401 AAAAAAT---AAAA-AAAATGAAAAAAT-G
1 AAAAAATGAAAAAAGAAAAAGAAAAAATAA
*
2058426 AAAAAATGAAAAGA-AAAAAGAAAAA
1 AAAAAATGAAAAAAGAAAAAGAAAAA
2058451 GGAGGGTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.10
26 7 0.10
27 5 0.07
28 17 0.24
30 7 0.10
31 29 0.40
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (30 bp):
AAAAAATGAAAAAAGAAAAAGAAAAAATAA
Found at i:2058431 original size:1 final size:1
Alignment explanation
Indices: 2058355--2058415 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
2058345 TGAAAAAGTG
* * ** * * * *
2058355 AAAAAGAAAAAATAAAAAAAATGAAAAAAGAAAAAGAAAAAAATAAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2058416 TGAAAAAATG
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (1 bp):
A
Found at i:2058449 original size:5 final size:6
Alignment explanation
Indices: 2058340--2058451 Score: 50
Period size: 7 Copynumber: 17.0 Consensus size: 6
2058330 GAATGAATGA
*
2058340 AAAAATG AAAAAGTG AAAAAG AAAAA- ATAAAA- AAAATG AAAAAAG AAAAAG
1 AAAAA-G AAAAA--G AAAAAG AAAAAG A-AAAAG AAAAAG -AAAAAG AAAAAG
* * *
2058391 AAAAAA ATAAAAA AAATAAA AAAAATG AAAAAATG AAAAA- ATGAAAAG
1 AAAAAG A-AAAAG AAA-AAG AAAAA-G -AAAAA-G AAAAAG A--AAAAG
2058439 AAAAAAG AAAAAG
1 -AAAAAG AAAAAG
2058452 GAGGGTTCGA
Statistics
Matches: 89, Mismatches: 4, Indels: 25
0.75 0.03 0.21
Matches are distributed among these distances:
5 5 0.06
6 33 0.37
7 36 0.40
8 14 0.16
9 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (6 bp):
AAAAAG
Found at i:2058450 original size:8 final size:8
Alignment explanation
Indices: 2058355--2058451 Score: 60
Period size: 8 Copynumber: 11.8 Consensus size: 8
2058345 TGAAAAAGTG
2058355 AAAAAGAA
1 AAAAAGAA
2058363 AAAATA-AA
1 AAAA-AGAA
2058371 AAAAATG-A
1 AAAAA-GAA
2058379 AAAAAGAA
1 AAAAAGAA
2058387 AAAGAA-AA
1 AAA-AAGAA
2058395 AAATAA-AA
1 AAA-AAGAA
2058403 AAAATA-AA
1 AAAA-AGAA
2058411 AAAAATGAA
1 AAAAA-GAA
*
2058420 AAAATGAA
1 AAAAAGAA
*
2058428 AAAATGAA
1 AAAAAGAA
*
2058436 AAGAAAAAA
1 AA-AAAGAA
2058445 GAAAAAG
1 -AAAAAG
2058452 GAGGGTTCGA
Statistics
Matches: 74, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
7 4 0.05
8 52 0.70
9 16 0.22
10 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.07
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2060068 original size:105 final size:105
Alignment explanation
Indices: 2059361--2060053 Score: 1134
Period size: 105 Copynumber: 6.6 Consensus size: 105
2059351 TCAACAACAA
* * *
2059361 TCAAATCCACCACAGAAGGAGGTGACCCAATATTTCCAGAACAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
2059426 CCTAAAGGTGAAGGTTTGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
*
2059466 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
2059531 CCTAAAGGAGAAGGTTCATAATGAGAAGAACTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
*
2059571 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
2059636 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * *
2059676 TCAAATCCACCGCAGAATGAGGTAAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
2059741 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* *
2059781 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* **
2059846 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* *
2059886 TCAAATCCACCGCAGAACGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
2059951 CTTAAAGGAGAAGTTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * * *
2059991 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
2060054 ATCCGACAAA
Statistics
Matches: 559, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 559 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (105 bp):
TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
Found at i:2061827 original size:21 final size:22
Alignment explanation
Indices: 2061789--2061855 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 22
2061779 TACCATTAAA
* * *
2061789 GTATGTTTTATGTTTTATATAT
1 GTATATTTTTTGTATTATATAT
2061811 GTAT-TTTTTTGTATTAT-TAT
1 GTATATTTTTTGTATTATATAT
*
2061831 -TATATTACTTTGTA-TATATAT
1 GTATATT-TTTTGTATTATATAT
2061852 -TATA
1 GTATA
2061856 GCATGATAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 3 0.08
20 8 0.21
21 24 0.62
22 4 0.10
ACGTcount: A:0.27, C:0.01, G:0.09, T:0.63
Consensus pattern (22 bp):
GTATATTTTTTGTATTATATAT
Found at i:2062203 original size:21 final size:21
Alignment explanation
Indices: 2062160--2062232 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
2062150 TTTTCCCAAT
** *
2062160 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
2062180 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
2062201 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
2062222 TCGCAATGCGA
1 TCGCAATGCGA
2062233 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:2062276 original size:21 final size:21
Alignment explanation
Indices: 2062242--2062290 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2062232 ATACTGACTA
2062242 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCAATTTTCCTAAT
* *
2062263 TCGCATTGCGATTTTCCTAAT
1 TCGCAATGCAATTTTCCTAAT
2062284 TCGCAAT
1 TCGCAAT
2062291 AAATCGCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (21 bp):
TCGCAATGCAATTTTCCTAAT
Found at i:2062288 original size:62 final size:61
Alignment explanation
Indices: 2062089--2062290 Score: 167
Period size: 62 Copynumber: 3.3 Consensus size: 61
2062079 CGCAAATTAG
* * * * *
2062089 TTTCCAGATTCGCAACGC-AATTATGACTATCGCAATGCGATTTTCCAATTTCGCGTTACGAT
1 TTTCCAAATTCGCAATGCGAA-TATGACTATCGCAATGCAATTTTCCAA-TTCGCATTGCGAT
* * * *** * * *
2062151 TTTCCCAATTCGCAATGCGAATAAGTA-AATCGCAATGCGAATTTGGAAAATCGCAATGCGAA
1 TTTCCAAATTCGCAATGCGAATATG-ACTATCGCAATGC-AATTTTCCAATTCGCATTGCGAT
** *
2062213 TTTGGAAAATCGCAATGCG-ATACTGACTATCGCAATGCAATTTTCCTAATTCGCATTGCGAT
1 TTTCCAAATTCGCAATGCGAATA-TGACTATCGCAATGCAATTTTCC-AATTCGCATTGCGAT
*
2062275 TTTCCTAATTCGCAAT
1 TTTCCAAATTCGCAAT
2062291 AAATCGCAAT
Statistics
Matches: 104, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
61 9 0.09
62 86 0.83
63 9 0.09
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (61 bp):
TTTCCAAATTCGCAATGCGAATATGACTATCGCAATGCAATTTTCCAATTCGCATTGCGAT
Found at i:2062902 original size:18 final size:19
Alignment explanation
Indices: 2062879--2062922 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
2062869 GCAACGAGAG
*
2062879 AATCGCAACGCGAAA-TAA
1 AATCGCAACGCGAAACCAA
2062897 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
2062916 AATCGCA
1 AATCGCA
2062923 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:2062969 original size:33 final size:33
Alignment explanation
Indices: 2062923--2063019 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
2062913 CAAAATCGCA
**
2062923 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
2062956 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
2062989 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
2063020 ATTATCTCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.75
34 15 0.25
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:2062978 original size:19 final size:17
Alignment explanation
Indices: 2062931--2063017 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 17
2062921 CATTGCGATT
2062931 TTCATTTCGCGTTGCGA
1 TTCATTTCGCGTTGCGA
*
2062948 TTC---TCTCGTTGCGA
1 TTCATTTCGCGTTGCGA
2062962 TAGTCATTTCGCGTTGCGA
1 T--TCATTTCGCGTTGCGA
*
2062981 TTC---TCTCGTTGCGA
1 TTCATTTCGCGTTGCGA
2062995 TAGTCATTTCCGCGTTGCGA
1 T--TCATTT-CGCGTTGCGA
2063015 TTC
1 TTC
2063018 TCATTATCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
14 22 0.40
16 4 0.07
17 5 0.09
18 2 0.04
19 12 0.22
20 10 0.18
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (17 bp):
TTCATTTCGCGTTGCGA
Found at i:2063021 original size:20 final size:19
Alignment explanation
Indices: 2062918--2063044 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
2062908 GAAACCAAAA
* *
2062918 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
2062937 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2062953 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
2062970 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2062986 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
2063003 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* * *
2063023 ATCTCGTTGCAATTTTCATT
1 -TCGCGTTGCGATTCTCATT
2063043 TC
1 TC
2063045 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
14 22 0.27
16 2 0.02
17 2 0.02
19 27 0.33
20 29 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:2065190 original size:42 final size:42
Alignment explanation
Indices: 2065114--2065202 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
2065104 GACTCGCCTG
* * *
2065114 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
2065156 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
2065198 TCATC
1 TCATC
2065203 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:2066594 original size:14 final size:14
Alignment explanation
Indices: 2066559--2066594 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2066549 GATTGTTTAA
2066559 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
2066573 GTGA-TTGTAAAAG
1 TTGATTTGTAAAAG
2066586 TTGATTTGT
1 TTGATTTGT
2066595 TTAATTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2066724 original size:19 final size:19
Alignment explanation
Indices: 2066700--2066758 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2066690 AAACTGTACT
2066700 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2066719 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2066733 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2066752 ATCGCAA
1 ATCGCAA
2066759 CGAGAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2066745 original size:33 final size:33
Alignment explanation
Indices: 2066700--2066763 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2066690 AAACTGTACT
* *
2066700 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2066733 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGA
2066764 AATTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2066775 original size:19 final size:19
Alignment explanation
Indices: 2066700--2066766 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
2066690 AAACTGTACT
* *
2066700 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
*
2066719 ATCGCAATGAG--A-G--A
1 ATCGCAACGAGAAATGAAA
*
2066733 ATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
2066752 ATCGCAACGAGAAAT
1 ATCGCAACGAGAAAT
2066767 TAAATTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:2066829 original size:32 final size:32
Alignment explanation
Indices: 2066775--2066864 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 32
2066765 ATTAAATTCG
2066775 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
* *
2066808 CGTTGCGATTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTCATTTCGCATTGCGATTCCCT
2066840 CGTTGCGATTTCA-TTCGCA-TGCGAT
1 CGTTGCGATTTCATTTCGCATTGCGAT
2066865 AGTAATTTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 6 0.11
31 5 0.09
32 35 0.65
33 8 0.15
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTCCCT
Found at i:2070231 original size:39 final size:40
Alignment explanation
Indices: 2070148--2070236 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 40
2070138 TGCGAATTTG
* * *
2070148 GAAAATCACAATGCGATACTGACTATCGCAACGAGATAAC
1 GAAAATCGCAACGAGATACTGACTATCGCAACGAGATAAC
* *
2070188 -AAAATCGCAACGAGATTCTGACT-TCGCAACGAGAT-TC
1 GAAAATCGCAACGAGATACTGACTATCGCAACGAGATAAC
2070225 TGAAAATCGCAA
1 -GAAAATCGCAA
2070237 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
37 1 0.02
38 12 0.29
39 29 0.69
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (40 bp):
GAAAATCGCAACGAGATACTGACTATCGCAACGAGATAAC
Found at i:2070507 original size:20 final size:20
Alignment explanation
Indices: 2070453--2070511 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
2070443 AATCACAAAA
**
2070453 CGAAAATGGCTATCGCAATT
1 CGAAAATGGCTATCGCAACG
***
2070473 CG-AAATGAAAAATCGCAACG
1 CGAAAATG-GCTATCGCAACG
2070493 CGAAAATGGCTATCGCAAC
1 CGAAAATGGCTATCGCAAC
2070512 TAGAAAATCG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
19 5 0.17
20 19 0.66
21 5 0.17
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
CGAAAATGGCTATCGCAACG
Found at i:2070574 original size:19 final size:19
Alignment explanation
Indices: 2070538--2070624 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
2070528 GAAATGAAAA
2070538 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2070554 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2070571 TCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2070590 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2070609 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
2070625 TCGTTGCGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 2 0.03
19 47 0.75
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2070784 original size:14 final size:14
Alignment explanation
Indices: 2070767--2070793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2070757 ACAATCAACA
2070767 TTTACAAATCATTT
1 TTTACAAATCATTT
2070781 TTTACAAATCATT
1 TTTACAAATCATT
2070794 AAACAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTACAAATCATTT
Found at i:2072698 original size:33 final size:33
Alignment explanation
Indices: 2072651--2072730 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
2072641 GGAAATGGCT
* * *
2072651 ATCGCAATGTGAAATGCAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2072684 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2072717 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2072731 CACCAAATCG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2072705 original size:19 final size:19
Alignment explanation
Indices: 2072608--2072709 Score: 79
Period size: 20 Copynumber: 5.5 Consensus size: 19
2072598 CACGAAACTT
*
2072608 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCG-AAATG
*
2072628 ACAATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATG
*** *
2072648 GCTATCGCAATGTGAAATG
1 AAAATCGCAATGCGAAATG
* *
2072667 CAAATCGCAAT--G--A-C
1 AAAATCGCAATGCGAAATG
2072681 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
2072700 AAAATCGCAA
1 AAAATCGCAA
2072710 CGACAAAATC
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 24 0.37
20 26 0.40
21 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:2072719 original size:14 final size:14
Alignment explanation
Indices: 2072668--2072725 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
2072658 TGTGAAATGC
*
2072668 AAATCGCAATGACA
1 AAATCGCAACGACA
*
2072682 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
2072701 AAATCGCAACGACA
1 AAATCGCAACGACA
2072715 AAATCGCAACG
1 AAATCGCAACG
2072726 CGAAACACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:2072762 original size:19 final size:18
Alignment explanation
Indices: 2072738--2072833 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
2072728 AAACACCAAA
2072738 TCGCATTGCGACTTTCATT
1 TCGCATTGCGA-TTTCATT
*
2072757 TCGCATTGCGA-TT--TG
1 TCGCATTGCGATTTCATT
2072772 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
2072789 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
2072805 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
2072822 TCGCATTGCGAT
1 TCGCATTGCGAT
2072834 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
13 6 0.10
14 6 0.10
15 9 0.15
16 4 0.06
17 10 0.16
18 4 0.06
19 23 0.37
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:2072810 original size:33 final size:33
Alignment explanation
Indices: 2072743--2072833 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2072733 CCAAATCGCA
*
2072743 TTGCGACTTTCATTTCGCATTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2072775 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2072808 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2072834 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 24 0.42
33 33 0.58
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2072840 original size:19 final size:20
Alignment explanation
Indices: 2072818--2072861 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2072808 TTGCGATTTT
2072818 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
** *
2072837 CATTTCCGTGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
2072857 CATTT
1 CATTT
2072862 TCATGTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:2072868 original size:20 final size:20
Alignment explanation
Indices: 2072827--2072869 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2072817 TCATTTCGCA
*
2072827 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCATG
* *
2072847 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCATG
2072867 TTG
1 TTG
2072870 TGAAAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCATG
Found at i:2073370 original size:18 final size:17
Alignment explanation
Indices: 2073344--2073387 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2073334 GTCGATCAGA
*
2073344 TGATGGCTCTGGGTGAGG
1 TGAT-GCTCTGGGCGAGG
2073362 TGATAGCTCTGGGCGAGG
1 TGAT-GCTCTGGGCGAGG
2073380 TGATGCTC
1 TGATGCTC
2073388 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (17 bp):
TGATGCTCTGGGCGAGG
Found at i:2073602 original size:18 final size:19
Alignment explanation
Indices: 2073564--2073609 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
2073554 GTCGATCAGA
*
2073564 TGATGGCTCTGGGGTGAGG
1 TGATGGCTCTGGGGCGAGG
*
2073583 TGATAGCTCT-GGGCGAGG
1 TGATGGCTCTGGGGCGAGG
2073601 TGATGGCTC
1 TGATGGCTC
2073610 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.13, C:0.15, G:0.46, T:0.26
Consensus pattern (19 bp):
TGATGGCTCTGGGGCGAGG
Found at i:2073663 original size:222 final size:218
Alignment explanation
Indices: 2073234--2073674 Score: 846
Period size: 222 Copynumber: 2.0 Consensus size: 218
2073224 GATAAACATC
2073234 GTGGCATCTTTGCCGTCGCCTATCTTGCGGTGATGGTGGAGAAGAGGCTCGATGATGTGACAGAA
1 GTGGCATCTTTGCCGTCGCCTATCTTGCGGTGATGGTGGAGAAGAGGCTCGATGATGTGACAGAA
2073299 TAGGAGAGGCTGTCGTTGTGGAGGTGTATAGTCGGGTCGATCAGATGATGGCTCTGGGTGAGGTG
66 TAGGAGAGGCTGTCGTTGTGGAGGTGTATAGTCGGGTCGATCAGATGATGGCTCTGGGTGAGGTG
2073364 ATAGCTCTGGGCGAGGTGATGCTCCCGAAGTGGAGCTGCTCATCACCGTTCCATCAAAAAAATGC
131 ATAGCTCTGGGCGAGGTGATGCTCCCGAAGTGGAGCTGCTCATCACCGTTCCATCAAAAAAATGC
2073429 TTACTAGCTTGCCACCAATCAGT
196 TTACTAGCTTGCCACCAATCAGT
2073452 GTGGCATCTTTGCCGGTCGCCTATCTTGCGGTGATGGTGGAGAAGAGGCTCGATGATGTGACAGA
1 GTGGCATCTTTGCC-GTCGCCTATCTTGCGGTGATGGTGGAGAAGAGGCTCGATGATGTGACAGA
2073517 ATAGGAGATGGCTGTCGTTGTGGAGGTGTATAGTCGGGTCGATCAGATGATGGCTCTGGGGTGAG
65 ATAGGAGA-GGCTGTCGTTGTGGAGGTGTATAGTCGGGTCGATCAGATGATGGCTCT-GGGTGAG
2073582 GTGATAGCTCTGGGCGAGGTGATGGCTCCCGAAGTGGAGCTGCTCATCACCGTTCCATCAAAAAA
128 GTGATAGCTCTGGGCGAGGTGAT-GCTCCCGAAGTGGAGCTGCTCATCACCGTTCCATCAAAAAA
2073647 ATGCTTACTAGCTTGCCACCAATCAGT
192 ATGCTTACTAGCTTGCCACCAATCAGT
2073674 G
1 G
2073675 GCAAGCTCAG
Statistics
Matches: 219, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
218 14 0.06
219 58 0.26
220 48 0.22
221 30 0.14
222 69 0.32
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.26
Consensus pattern (218 bp):
GTGGCATCTTTGCCGTCGCCTATCTTGCGGTGATGGTGGAGAAGAGGCTCGATGATGTGACAGAA
TAGGAGAGGCTGTCGTTGTGGAGGTGTATAGTCGGGTCGATCAGATGATGGCTCTGGGTGAGGTG
ATAGCTCTGGGCGAGGTGATGCTCCCGAAGTGGAGCTGCTCATCACCGTTCCATCAAAAAAATGC
TTACTAGCTTGCCACCAATCAGT
Found at i:2074957 original size:20 final size:20
Alignment explanation
Indices: 2074909--2074967 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2074899 AATAGTTTCT
** *
2074909 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
2074929 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
2074949 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
2074968 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:2075254 original size:22 final size:22
Alignment explanation
Indices: 2075227--2075270 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2075217 GATGGAGATA
2075227 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2075249 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2075271 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2075543 original size:61 final size:61
Alignment explanation
Indices: 2075437--2075574 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
2075427 CGCTTTGAAA
* * * * *
2075437 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGAGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2075498 ATCTCGTTGCGATTTTGTATTATCGCATTGAGATAGTAAGCATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGAGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2075559 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2075575 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGAGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2075568 original size:20 final size:20
Alignment explanation
Indices: 2075437--2075571 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
2075427 CGCTTTGAAA
*
2075437 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2075458 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
2075478 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2075498 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* * *
2075519 ATCGCATTGAGATAGTAAGC
1 ATCGCATTGCGATAGTCAGT
2075539 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2075559 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2075572 TTTCCCAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 22 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2077464 original size:3 final size:3
Alignment explanation
Indices: 2077456--2077548 Score: 95
Period size: 3 Copynumber: 31.7 Consensus size: 3
2077446 GGCCCGTTTG
* * *
2077456 TAA TAA TAA TTAA TAA T-A TAT TAG TAA -AA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* *
2077500 TTA TAA TAA TAA TAA TAA TAA TTA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2077547 TA
1 TA
2077549 TTTAAATGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
2 8 0.11
3 64 0.84
4 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2077937 original size:112 final size:112
Alignment explanation
Indices: 2077785--2079068 Score: 1232
Period size: 113 Copynumber: 11.3 Consensus size: 112
2077775 GAATAGCTCT
* *
2077785 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGC
1 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGC
*
2077849 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCCTTCCT-TTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTT-CTTCCTCTTCA
* * * **
2077897 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
*
2077962 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* *
2078009 GATGAG-TCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078073 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCA
* * * *
2078121 GATGAGTTCTTCTCATTAT-AACTTT-TCTGGAAGTGTTAATCCATCAAGTGATGAATTCGAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
* * *
2078184 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* *** * * * * * *
2078231 GA--AGTTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATTCATCAAGT-AAGAATTCAGGGA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078293 AAAGGTTG-ACAAATTCTTCTCATTATG-ATTTCTTCTTCCTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* ** * * * *** *
2078338 GATGAGTTCTTCTCATTATGAACTCTAACT-GACACTGCTGATCCACCGGGTGATGAATTTAAGC
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGA-AATGTTGATCCATCAAATGATGAATTCAAGC
* * ***
2078402 AAAAAGTTGAACAAGTTCTTCTTC-TTCA--AATGAGTTCTT-CTCATT-A
65 AAAAGGTTGAACAAATTCTTC-TCATT-ATGAATTTCTTCTTCCTC-TTCA
*** * * * * * * * *
2078448 TGAATTTCTTTTTCCTC-TTCA-GATAAGTTCTTCTCATTATGAACT-TT--TTC-TGGAAAGGC
1 -G-ATGAGTTCTT-CTCATT-ATG--AA-CT-TTCTC--T-GGAAATGTTGATCCAT-CAAATGA
* * * * ** * * **
2078507 TG-A-TCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCAT-TATGAACTTCT
54 TGAATTCAAGCAAA--A-G--GTTGAAC--AAA-TT---C---TTCTCATTATGAAT-TTCTTCT
2078569 TCTTCCTTCTTCA
104 T---CC-TCTTCA
* * * **
2078582 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078647 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* * * * **
2078694 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078759 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGG-TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCA
* * * * * *
2078808 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078873 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCA
* * * * * *
2078921 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
2078986 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCA
2079034 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
2079069 AGCTAACTCA
Statistics
Matches: 982, Mismatches: 128, Indels: 123
0.80 0.10 0.10
Matches are distributed among these distances:
107 19 0.02
108 35 0.04
109 52 0.05
110 47 0.05
111 191 0.19
112 204 0.21
113 243 0.25
114 73 0.07
115 2 0.00
116 21 0.02
117 2 0.00
118 2 0.00
119 9 0.01
120 2 0.00
121 2 0.00
122 4 0.00
123 3 0.00
125 9 0.01
126 3 0.00
127 3 0.00
128 19 0.02
129 9 0.01
130 8 0.01
131 4 0.00
132 9 0.01
133 4 0.00
134 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
Found at i:2078220 original size:17 final size:17
Alignment explanation
Indices: 2078198--2078254 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2078188 GTTAAACAAG
2078198 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
2078215 TTCTTCTTCCTCT-TCAGAAG
1 TTCTTC-TCAT-TAT--GAAC
2078235 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
2078252 TTC
1 TTC
2078255 CTCTGGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
17 12 0.39
18 5 0.16
19 5 0.16
20 9 0.29
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.47
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2078466 original size:131 final size:130
Alignment explanation
Indices: 2078306--2078554 Score: 365
Period size: 131 Copynumber: 1.9 Consensus size: 130
2078296 GGTTGACAAA
*
2078306 TTCTTCTCATTATGATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-GA
1 TTCTTCTCATTATGATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTAACTGGA
** *** *
2078370 CACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTTCTTCAAATGA
66 -AAGGCTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTTCTTCAAATGA
2078435 G
130 G
* * **
2078436 TTCTTCTCATTATGAATTTCTTTTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTTCTGG
1 TTCTTCTCATTATG-ATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTAACTGG
*
2078501 AAAGGCTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
65 AAAGGCTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
2078555 CATTATGAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
130 14 0.13
131 89 0.85
132 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (130 bp):
TTCTTCTCATTATGATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTAACTGGA
AAGGCTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTTCTTCAAATGAG
Found at i:2078877 original size:226 final size:225
Alignment explanation
Indices: 2077785--2079068 Score: 1612
Period size: 226 Copynumber: 5.7 Consensus size: 225
2077775 GAATAGCTCT
* * *
2077785 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGC
1 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGC
*
2077849 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCCTTCC-T-TTCAGATGAGTTCTTCTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTT-CTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
2077912 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGGATTTGAGCAAAAGGTTGAACAAA
129 TTATGAACCTTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTTGAGCAAAAGGTTGAACAAA
*
2077976 TTCTTCTCATTATGAATTTCTTCTTCTTCTTCA
193 TTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* * *
2078009 GATGAG-TCTTCTCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
2078073 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
2078138 AT-AA-CTTTTCTGGAAGTGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTC
131 ATGAACCTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAATTC
*
2078201 TTCTCATTATGAACTTCTTCTTCCTCTTCA
196 TTCTCATTATGAATTTCTTCTTCCTCTTCA
* ** * * * * * *
2078231 GA--AGTTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATTCATCAAGT-AAGAATTCAGGGA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
2078293 AAAGGTTG-ACAAATTCTTCTCATTATG-ATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * ** * *
2078355 ATGAA-C-TCTAACT-GACACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAG
131 ATGAACCTTCT--CTGGA-AATGTTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTG---AA-
*
2078417 TTCTTCTTCTTCAAATGAGTTCTTCTCATTATGAATTTCTTTTTCCTCTTCA
189 -----------C-AA--A-TTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* * * * * *
2078469 GATAAGTTCTTCTCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAAATGATGAATTTAAACA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
* * *
2078534 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
2078599 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAA-TGATGGATTTGAGCAAAAGGTTGAACAAATT
131 ATGAACCTTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTTGAGCAAAAGGTTGAACAAATT
2078663 CTTCTCATTATGAATTTCTTCTTCCTCTTCA
195 CTTCTCATTATGAATTTCTTCTTCCTCTTCA
* * * * **
2078694 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
2078759 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
66 AAAGG-TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * ** *
2078824 TATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATT
130 TATGAACCTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAATT
2078889 CTTCTCATTATGAATTTCTTCTTCCTTCTTCA
195 CTTCTCATTATGAATTTCTTCTTCC-TCTTCA
* * * * *
2078921 GATGAGTTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
2078986 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2079051 ATGAACTTTCTCTGGAAA
131 ATGAACCTTCTCTGGAAA
2079069 AGCTAACTCA
Statistics
Matches: 920, Mismatches: 99, Indels: 80
0.84 0.09 0.07
Matches are distributed among these distances:
217 27 0.03
218 17 0.02
219 51 0.06
220 20 0.02
221 37 0.04
222 86 0.09
223 91 0.10
224 29 0.03
225 96 0.10
226 212 0.23
227 65 0.07
228 2 0.00
229 1 0.00
234 1 0.00
235 2 0.00
238 33 0.04
240 39 0.04
241 17 0.02
242 18 0.02
243 11 0.01
244 60 0.07
245 2 0.00
246 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (225 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACCTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAGCAAAAGGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCCTCTTCA
Found at i:2079518 original size:22 final size:22
Alignment explanation
Indices: 2079493--2079547 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2079483 CCATAAAGTT
*
2079493 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
2079515 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2079537 TCATCTTTGAA
1 TCATCTTTGAA
2079548 GAGTGTGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2082309 original size:79 final size:80
Alignment explanation
Indices: 2082124--2082459 Score: 438
Period size: 79 Copynumber: 4.2 Consensus size: 80
2082114 CTTATTTCTA
* * *
2082124 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAACAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
2082188 AGAACACTTCCAGAAGATG
65 A-AACACTTCC--AAGATG
*
2082207 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAG-TCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
2082271 GAACACTTCC-AGATG
66 -AACACTTCCAAGATG
*
2082286 CTATGAACAAATTCATCTTCTAAATTC-ATGATTGGTTTTGCCAAACCAGATCA-ATAACTCAAA
1 CTATGAACAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
2082349 AACAC-TCCAGAAGATG
66 AACACTTCC--AAGATG
* * *
2082365 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTTTGCCAAACCAGATCAGAT--CTCAAA
1 CTATGAACAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
2082428 AA-ACTTCCAGAAGATG
66 AACACTTCC--AAGATG
* *
2082444 CTATGAGCACATTCAT
1 CTATGAACAAATTCAT
2082460 TTGTTCCATT
Statistics
Matches: 237, Mismatches: 8, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
76 3 0.01
77 5 0.02
78 34 0.14
79 99 0.42
80 25 0.11
81 2 0.01
82 25 0.11
83 44 0.19
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (80 bp):
CTATGAACAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
AACACTTCCAAGATG
Found at i:2084125 original size:197 final size:196
Alignment explanation
Indices: 2083792--2084185 Score: 715
Period size: 197 Copynumber: 2.0 Consensus size: 196
2083782 ATTGAAAATG
2083792 AAAAGATTTTTGCAAAAGTATTACCCTTTCAGGTTCACAATATCGAATCATAAACAAGGAGTTTA
1 AAAAGATTTTTGCAAAAGTATTACCCTTTCAGGTTCACAATATCGAATCATAAACAAGGAGTTTA
2083857 ATGAATATCAAATAAATCAACTACACCTTTTAAATCATTCAAAAATCATAGTCCTATGGCAAGTG
66 ATGAATATCAAATAAATCAACTACACCTTTTAAATCATTCAAAAATCATAGTCCTATGGCAAGTG
2083922 TCAAAATTATTGACTGATTTGAGGTGTAGGTTGATTTTGGTAAAGTAGGTTCTTTC-AGTTGGTT
131 TCAAAATTATTGACTGATTTGAGGTGTAGGTTGATTTTGGTAAAGTAGGTTCTTTCAAGTTGGTT
2083986 C
196 C
2083987 AAAAGATTTTTGC-AAAGTATTACCCCTTTCAGGTTTCACAATATAATCGAATCAT-AACAAGGA
1 AAAAGATTTTTGCAAAAGTATTA-CCCTTTCAGG-TTCAC-A-AT-ATCGAATCATAAACAAGGA
2084050 GTTTAATGAATATCAAATAAATCAACTACA-CTTTTAAATCATTCAAAAATCATAGTCCTATGGC
61 GTTTAATGAATATCAAATAAATCAACTACACCTTTTAAATCATTCAAAAATCATAGTCCTATGGC
2084114 AAGTGTCAAAATTATTGACTGATTTGAGGTGTAGGTTGATTTTGGTAAAGTAGGTTCTTTCAAGT
126 AAGTGTCAAAATTATTGACTGATTTGAGGTGTAGGTTGATTTTGGTAAAGTAGGTTCTTTCAAGT
2084179 TGGTTC
191 TGGTTC
2084185 A
1 A
2084186 GTATGTCGCT
Statistics
Matches: 193, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
194 9 0.05
195 23 0.12
196 5 0.03
197 96 0.50
198 50 0.26
199 10 0.05
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (196 bp):
AAAAGATTTTTGCAAAAGTATTACCCTTTCAGGTTCACAATATCGAATCATAAACAAGGAGTTTA
ATGAATATCAAATAAATCAACTACACCTTTTAAATCATTCAAAAATCATAGTCCTATGGCAAGTG
TCAAAATTATTGACTGATTTGAGGTGTAGGTTGATTTTGGTAAAGTAGGTTCTTTCAAGTTGGTT
C
Found at i:2084812 original size:6 final size:6
Alignment explanation
Indices: 2084798--2084850 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
2084788 CTTTATTCGA
* * * *
2084798 TTTTCC TTTTTC TTTTTTT TTTTTC TTCTTC TTTTTC TTCTTC TTCTTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC
2084848 TTT
1 TTT
2084851 GCTGGATGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:2086801 original size:26 final size:25
Alignment explanation
Indices: 2086763--2086824 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
2086753 AAATGTAATT
*
2086763 GTAAAAATGAAATGTAAATACAAAC
1 GTAAAAATGAAATGCAAATACAAAC
* *
2086788 GTAAAAATGCAAATGCAAATTCAAAT
1 GTAAAAATG-AAATGCAAATACAAAC
*
2086814 GTAAATATGAA
1 GTAAAAATGAA
2086825 TGTAACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (25 bp):
GTAAAAATGAAATGCAAATACAAAC
Found at i:2086909 original size:7 final size:7
Alignment explanation
Indices: 2086875--2086916 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2086865 ATAAAAGTAT
2086875 AAATGCA
1 AAATGCA
* *
2086882 CAATGAA
1 AAATGCA
2086889 AAATGCA
1 AAATGCA
2086896 AAGATGCA
1 AA-ATGCA
2086904 AAATGC-
1 AAATGCA
2086910 AAATGCA
1 AAATGCA
2086917 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:2088416 original size:18 final size:18
Alignment explanation
Indices: 2088395--2088444 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 18
2088385 ATAATAAATA
2088395 AATAAAATAAAAAATAAT
1 AATAAAATAAAAAATAAT
*
2088413 AAT-ATAT-AAAAA-AAT
1 AATAAAATAAAAAATAAT
2088428 AATAAGTAATAAAAAAT
1 AATAA--AATAAAAAAT
2088445 TTGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 6 0.24
16 6 0.24
17 3 0.12
18 5 0.20
19 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAAAAAATAAT
Found at i:2088441 original size:15 final size:15
Alignment explanation
Indices: 2088382--2088431 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2088372 TTAATTCTTG
*
2088382 AATATAATAAATAAAT
1 AATAT-ATAAAAAAAT
*
2088398 AAAATA-AAAAATAAT
1 AATATATAAAAA-AAT
2088413 AATATATAAAAAAAT
1 AATATATAAAAAAAT
2088428 AATA
1 AATA
2088432 AGTAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.14
15 16 0.55
16 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATATAAAAAAAT
Found at i:2089145 original size:13 final size:13
Alignment explanation
Indices: 2089129--2089157 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2089119 ATTATATATT
2089129 ATAAAAATATTTA
1 ATAAAAATATTTA
2089142 AT-AAAATATTTA
1 ATAAAAATATTTA
2089154 ATAA
1 ATAA
2089158 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAAAATATTTA
Found at i:2089149 original size:12 final size:12
Alignment explanation
Indices: 2089132--2089157 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2089122 ATATATTATA
2089132 AAAATATTTAAT
1 AAAATATTTAAT
2089144 AAAATATTTAAT
1 AAAATATTTAAT
2089156 AA
1 AA
2089158 TATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATATTTAAT
Found at i:2090432 original size:3 final size:3
Alignment explanation
Indices: 2090424--2090519 Score: 97
Period size: 3 Copynumber: 31.7 Consensus size: 3
2090414 GGCCCGTTTG
* * *
2090424 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAA -ATA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA
* * *
2090470 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2090518 TA
1 TA
2090520 TTTAAATGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 3 0.04
3 69 0.90
4 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2093917 original size:21 final size:21
Alignment explanation
Indices: 2093887--2093926 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2093877 AAAAAATACT
* * *
2093887 TAAAATATTATTATTTTTATA
1 TAAAACATTAATAATTTTATA
2093908 TAAAACATTAATAATTTTA
1 TAAAACATTAATAATTTTA
2093927 AAAAATCCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAACATTAATAATTTTATA
Found at i:2097494 original size:5 final size:5
Alignment explanation
Indices: 2097479--2097517 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
2097469 AAAAAAGTTA
*
2097479 ATTAGT ATTAT ATTAT ATTAT ATTAT ATTAT ATGAT ATT
1 ATTA-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
2097518 GGTGAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:2098777 original size:12 final size:12
Alignment explanation
Indices: 2098760--2098784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2098750 CGTGCTGCGT
2098760 TGGTGATGAGCG
1 TGGTGATGAGCG
2098772 TGGTGATGAGCG
1 TGGTGATGAGCG
2098784 T
1 T
2098785 CGTCGAATCA
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:0.16, C:0.08, G:0.48, T:0.28
Consensus pattern (12 bp):
TGGTGATGAGCG
Found at i:2103502 original size:30 final size:30
Alignment explanation
Indices: 2103466--2103537 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2103456 CCCGAAGGAC
*
2103466 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
2103496 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
2103526 CTGTCCATAGGT
1 CTATCCAGAGGT
2103538 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:2103584 original size:31 final size:31
Alignment explanation
Indices: 2103524--2103648 Score: 119
Period size: 31 Copynumber: 4.0 Consensus size: 31
2103514 GATCCTCGGC
* *
2103524 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
** *
2103555 AACTGTCCATATGTTCCTTAGAAAATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
2103586 TATTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* * *
2103617 ATTCTGTCAATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
2103649 TACCCTCGAC
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
30 3 0.04
31 47 0.64
32 21 0.28
33 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:2105000 original size:64 final size:64
Alignment explanation
Indices: 2104803--2105023 Score: 171
Period size: 64 Copynumber: 3.5 Consensus size: 64
2104793 CAATAAAAGT
** * ** * * **** *
2104803 ATGCATCGATGCACTACCGATGCATCGGTGCATAAAATGCATTCGATGTTGT-ATTATCGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTT-TCATTATTAAAGAG
* * * ** * * *
2104867 ATGCATCAATGCA-TGCCTTATGCATCGATGCACTAATTGCATTTGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACGAATTGCATTCAATGTTTCATTATTAAAGAG
*
2104931 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGT-TTCATTATTAAAGAG
**
2104994 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
2105024 ACACCTTCAA
Statistics
Matches: 128, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
63 4 0.03
64 119 0.93
65 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTTTCATTATTAAAGAG
Found at i:2108130 original size:30 final size:30
Alignment explanation
Indices: 2108090--2108161 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2108080 CCCGAAGGAC
* *
2108090 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
2108120 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
2108150 CTGTCCATAGGT
1 CTATCCAGAGGT
2108162 TCCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:2108207 original size:30 final size:31
Alignment explanation
Indices: 2108148--2108271 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
2108138 GATCCTCGGC
* *
2108148 AACTGTCCATAGGTTCCGA-AGAACCTAGGTA
1 AACTGTCCATATGTTCC-ATAGAACATAGGTA
2108179 AACTGTCCATATGTTCC-TAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * *
2108209 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCATAGAACATAGGTA
* *
2108240 ATTCTGTCAATATGTTCCATAGAACATAGGTA
1 A-ACTGTCCATATGTTCCATAGAACATAGGTA
2108272 TACCCTCGAC
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
30 24 0.31
31 32 0.41
32 22 0.28
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:2109500 original size:64 final size:64
Alignment explanation
Indices: 2109413--2109589 Score: 182
Period size: 64 Copynumber: 2.8 Consensus size: 64
2109403 CAATAAAAGT
* * *
2109413 ATGCATCGATGCACTACC-GATGCATCGGTGCA-TAAAATGCATTCGATGTTGT-ATTATCACTG
1 ATGCATCGATGCACT-CCTTATGCATCGATGCACT-AAATGCATTCGATGTT-TCATTATCAATG
2109475 GG
63 GG
* * * *
2109477 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTTGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-CCTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATCAATGGG
* * * * *
2109541 ATGAATCGATGCACTACTTATGCATCGATACACGAATTGCATTCGATGT
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTAAATGCATTCGATGT
2109590 ATTTATTTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
63 4 0.04
64 90 0.94
65 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTAAATGCATTCGATGTTTCATTATCAATGGG
Found at i:2109613 original size:64 final size:64
Alignment explanation
Indices: 2109413--2109637 Score: 179
Period size: 64 Copynumber: 3.5 Consensus size: 64
2109403 CAATAAAAGT
** * * ** * * ** *
2109413 ATGCATCGATGCACTACCGATGCATCGGTGCATAAAATGCATTCGATGTTGT-ATTATCACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATACACGAATTGCATTCGATGTT-TCATTATTAAAGAG
* * * * * * *
2109477 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTTGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATACACGAATTGCATTCGATGTTTCATTATTAAAGAG
* *
2109541 ATGAATCGATGCACTACTTATGCATCGATACACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATACACGAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
2109604 AGTGCATCGATGCACTACCAATACATCGATACAC
1 A-TGCATCGATGCACTACTTATGCATCGATACAC
2109638 CTTCAAACAA
Statistics
Matches: 132, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
63 4 0.03
64 123 0.93
65 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATACACGAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:2114214 original size:22 final size:21
Alignment explanation
Indices: 2114159--2114218 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2114149 TTGGGATTTA
* * *
2114159 ATTTTAATTTTAAAATTTAAG
1 ATTTAAATCTTAAATTTTAAG
2114180 ATTTAAATCTTAAGATTTTAAG
1 ATTTAAATCTTAA-ATTTTAAG
*
2114202 A-TTAAATATTTAAATTT
1 ATTTAAAT-CTTAAATTT
2114219 GAAACTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTTAAATCTTAAATTTTAAG
Found at i:2116428 original size:183 final size:181
Alignment explanation
Indices: 2116119--2116482 Score: 694
Period size: 183 Copynumber: 2.0 Consensus size: 181
2116109 ATTGTTCAGA
2116119 TGGATCAATAAACGCAAACATATTCTACGAAATAGGGGTTAGTATTGTCATAATCAACCATTAAA
1 TGGATCAATAAACGCAAACATATTCTACGAAATAGGGGTTAGTATTGTCATAATCAACCATTAAA
2116184 TTAAGGAGAAGAGAAACCATTCTTAAGGCAATAATAATTGAGTTTTATGTTTCATGTGGAGCTCC
66 TTAAGGAGAAGAGAAACCATTCTTAAGGCAATAATAATTGAGTTTTATGTTTCATGTGGAGCTCC
2116249 ATCATAAAATATACGCAGACGCGAAGGACAAGATAACGCCACGTAACCCCG
131 ATCATAAAATATACGCAGACGCGAAGGACAAGATAACGCCACGTAACCCCG
2116300 TGGATCAATAAACGCAAACATATTCTTACGAAATAGTGGGTTAGTATTGTCATAATCAACCATTA
1 TGGATCAATAAACGCAAACATATTC-TACGAAATAG-GGGTTAGTATTGTCATAATCAACCATTA
2116365 AATTAAGGAGAAGAGAAACCATTCTTAAGGCAATAATAATTGAGTTTTATG-TTCATCGTGGAGC
64 AATTAAGGAGAAGAGAAACCATTCTTAAGGCAATAATAATTGAGTTTTATGTTTCAT-GTGGAGC
2116429 TCCATCATAAAATATACGCAGACGCGAAGGACAAGATAACGCCACGTAACCCCG
128 TCCATCATAAAATATACGCAGACGCGAAGGACAAGATAACGCCACGTAACCCCG
2116483 ACGCAGACAA
Statistics
Matches: 180, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
181 25 0.14
182 15 0.08
183 140 0.78
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (181 bp):
TGGATCAATAAACGCAAACATATTCTACGAAATAGGGGTTAGTATTGTCATAATCAACCATTAAA
TTAAGGAGAAGAGAAACCATTCTTAAGGCAATAATAATTGAGTTTTATGTTTCATGTGGAGCTCC
ATCATAAAATATACGCAGACGCGAAGGACAAGATAACGCCACGTAACCCCG
Found at i:2117529 original size:37 final size:38
Alignment explanation
Indices: 2117479--2117554 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
2117469 AAGCAGCTGC
2117479 TGGCTGGGCTCATTTTGTGTC-GTAACAGGTATTTTCT
1 TGGCTGGGCTCATTTTGTGTCAGTAACAGGTATTTTCT
2117516 TGGCTGGGCTCATTTTGTGTCAGTAACAGGTATTTTCT
1 TGGCTGGGCTCATTTTGTGTCAGTAACAGGTATTTTCT
2117554 T
1 T
2117555 TATTTCCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 21 0.55
38 17 0.45
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.43
Consensus pattern (38 bp):
TGGCTGGGCTCATTTTGTGTCAGTAACAGGTATTTTCT
Found at i:2121930 original size:20 final size:20
Alignment explanation
Indices: 2121905--2121944 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2121895 ATACATGGTA
2121905 TTATTTCTGTTTAATAGTTT
1 TTATTTCTGTTTAATAGTTT
2121925 TTATTTCTGTTTAATAGTTT
1 TTATTTCTGTTTAATAGTTT
2121945 GAAGTGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.65
Consensus pattern (20 bp):
TTATTTCTGTTTAATAGTTT
Found at i:2123828 original size:57 final size:55
Alignment explanation
Indices: 2123767--2123877 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 55
2123757 GACGCTCATT
*
2123767 TATGACGGT-CATTGAGCGTCATTGAAACCCCCGTCATAAATTAA-TATGACACACATG
1 TATGAC-GTACATTGAGCGTCATTG-AA-CCCCGTCATAAATGAAGT-TGACACACATG
* * * *
2123824 TATGACTTACATTGCGTGTCATTGAAGCCCGTCATAAATGAAGTTGACACACAT
1 TATGACGTACATTGAGCGTCATTGAACCCCGTCATAAATGAAGTTGACACACAT
2123878 TTGTGTGTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
55 24 0.51
56 4 0.09
57 19 0.40
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (55 bp):
TATGACGTACATTGAGCGTCATTGAACCCCGTCATAAATGAAGTTGACACACATG
Found at i:2129845 original size:15 final size:15
Alignment explanation
Indices: 2129820--2129875 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2129810 GATGCTTTCT
*
2129820 TTTTCCTTCTTTGATG
1 TTTT-CTTCTTTGACG
2129836 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
2129851 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
2129866 TTGTCTTCTT
1 TTTTCTTCTT
2129876 ACCCATGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.07, C:0.20, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:2133006 original size:16 final size:16
Alignment explanation
Indices: 2132985--2133015 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2132975 GAATTGATGC
2132985 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
2133001 AAAGAGAAAAAGGGA
1 AAAGAGAAAAAGGGA
2133016 GGAAGCATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAAAGGGAA
Found at i:2134669 original size:19 final size:20
Alignment explanation
Indices: 2134645--2134684 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2134635 AATTTAATCG
* *
2134645 AATATATAAT-TTAAATTTC
1 AATATAAAATCTTAAAATTC
2134664 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
2134684 A
1 A
2134685 TTAACACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:2137227 original size:23 final size:23
Alignment explanation
Indices: 2137167--2137228 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
2137157 GTACCCTCAG
* *
2137167 GGGGGTATCAATACCCATTCAAA
1 GGGGGTATCGATACTCATTCAAA
* *
2137190 GAGGGTATCGATACTTATTCAAA
1 GGGGGTATCGATACTCATTCAAA
2137213 GGGGGTATCGATACTC
1 GGGGGTATCGATACTC
2137229 TATGCACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (23 bp):
GGGGGTATCGATACTCATTCAAA
Found at i:2142919 original size:21 final size:22
Alignment explanation
Indices: 2142894--2142950 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
2142884 ATATGCCTGA
2142894 GGGTATCGATACC-TCCTG-AT-G
1 GGGTATCGATACCAT--TGCATGG
*
2142915 GGGTATCGGTACCATTGCATGG
1 GGGTATCGATACCATTGCATGG
2142937 GGGTATCGATACCA
1 GGGTATCGATACCA
2142951 CTAGGGGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 15 0.48
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGTATCGATACCATTGCATGG
Found at i:2143231 original size:19 final size:20
Alignment explanation
Indices: 2143207--2143246 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2143197 AATTTAATCG
* *
2143207 AATATATAAT-TTAAATTTC
1 AATATAAAATCTTAAAATTC
2143226 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
2143246 A
1 A
2143247 TTAACACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:2145373 original size:112 final size:113
Alignment explanation
Indices: 2145257--2145492 Score: 395
Period size: 113 Copynumber: 2.1 Consensus size: 113
2145247 TATTCATTTC
2145257 AATAAAAAATATCAATTTAATTTATGACGGGACAATGATTC-GTC-GAAAATTTTATTCAACTTT
1 AATAAAAAATATCAATTTAATTTATGACGGGACAATGATTCTGTCAG-AAATTTTATTCAACTTT
* *
2145320 AATTATAATATACCAATTTAATTTGTGATGGAATAATCATTCCGTCGGA
65 AATTAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGTCGGA
* *
2145369 AATAAAAAATATCAATTTAATTTATGACGGGATAATGATTCTGTCAGAAATTTTGTTCAACTTTA
1 AATAAAAAATATCAATTTAATTTATGACGGGACAATGATTCTGTCAGAAATTTTATTCAACTTTA
* *
2145434 ATTAAAATATATCAATTTAATTTGTGATAGAATAATCATTCTGTCGGA
66 ATTAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGTCGGA
2145482 AATAAAAAATA
1 AATAAAAAATA
2145493 ACTGCATTTA
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
112 40 0.34
113 75 0.65
114 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (113 bp):
AATAAAAAATATCAATTTAATTTATGACGGGACAATGATTCTGTCAGAAATTTTATTCAACTTTA
ATTAAAATATACCAATTTAATTTGTGATAGAATAATCATTCCGTCGGA
Found at i:2151740 original size:31 final size:31
Alignment explanation
Indices: 2151702--2151774 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
2151692 AAAAGTTTTT
* *
2151702 AAATTTGTGATGGAATATGTGGACTCATCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
2151733 AAATTTGTGACGGAATATGTGGACCCATCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
*
2151764 AAATTTCTGAC
1 AAATTTGTGAC
2151775 AAATTCACCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (31 bp):
AAATTTGTGACGGAATATGTGGACCCATCAC
Found at i:2153163 original size:13 final size:13
Alignment explanation
Indices: 2153145--2153202 Score: 71
Period size: 13 Copynumber: 4.1 Consensus size: 13
2153135 CACAACACGA
2153145 CCGACCCGTTGAC
1 CCGACCCGTTGAC
2153158 CCGACCCGTTGAC
1 CCGACCCGTTGAC
2153171 CCGACCCGATCCGTTGAC
1 CCGA--C---CCGTTGAC
2153189 CCGACCCGTTGAC
1 CCGACCCGTTGAC
2153202 C
1 C
2153203 GTTAATCGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 26 0.65
15 1 0.03
16 1 0.03
18 12 0.30
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.16
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:2153178 original size:18 final size:18
Alignment explanation
Indices: 2153155--2153196 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2153145 CCGACCCGTT
2153155 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
2153173 GACCCGATCCGTTGACCC
1 GACCCGACCCGTTGACCC
2153191 GACCCG
1 GACCCG
2153197 TTGACCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:2155977 original size:32 final size:31
Alignment explanation
Indices: 2155903--2156025 Score: 88
Period size: 32 Copynumber: 3.9 Consensus size: 31
2155893 CTAATGTGAC
* *
2155903 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
2155934 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
* * *
2155966 TCTTAGGTAGGCCCCACGGCCTTCAAAATC-T
1 TCTTAGGTAGGCCCTACGGCCCT-AAGATCAT
* *
2155997 ATCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 -TCTTAGGTAGGCCCTAC-GGCCCTAAGAT
2156026 GTTCCCTTAG
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
31 29 0.42
32 36 0.52
33 4 0.06
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:2172842 original size:32 final size:31
Alignment explanation
Indices: 2172784--2172843 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2172774 CTATATTCTA
*
2172784 TCAAAAAAAAAAGAACTGAAGAATGCAAACC
1 TCAAAAAAAAAAGAACTCAAGAATGCAAACC
*
2172815 TCAAAAAAAATA-AACATCAAGACATGCAA
1 TCAAAAAAAAAAGAAC-TCAAGA-ATGCAA
2172844 GTCCAAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 16 0.64
32 6 0.24
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.12
Consensus pattern (31 bp):
TCAAAAAAAAAAGAACTCAAGAATGCAAACC
Found at i:2174149 original size:21 final size:20
Alignment explanation
Indices: 2174063--2174220 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
2174053 AAATGACCAA
**
2174063 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2174082 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2174102 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2174122 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2174143 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2174164 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
2174184 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2174205 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2174221 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2174213 original size:20 final size:20
Alignment explanation
Indices: 2174188--2174380 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
2174178 GATTTTCCAG
* ** *
2174188 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2174208 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2174228 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2174248 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2174268 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
** *
2174288 AATCGCAATACGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2174308 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2174328 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
2174349 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2174369 AATCGCAACGCG
1 AATCGCAACGCG
2174381 ATTTTTAAAG
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 127 0.86
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2174789 original size:32 final size:32
Alignment explanation
Indices: 2174751--2174819 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
2174741 ATTTCACTTA
2174751 GATTTCATTTCGCGTTACGATTCTCTCGTTAC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTAC
* * *
2174783 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTAC
2174815 GATTT
1 GATTT
2174820 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTAC
Done.