Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003591.1 Hibiscus syriacus cultivar Beakdansim tig00007576_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: 85562
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:594 original size:21 final size:21
Alignment explanation
Indices: 565--617 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
555 ATTCTGACTA
565 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
586 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
607 TCGCAATGCGA
1 TCGCATTGCGA
618 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:637 original size:41 final size:41
Alignment explanation
Indices: 592--683 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
582 AAATTCGCGT
* * *
592 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAA
* **
633 TGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAA
674 TGCGATTTAC
1 TGCGATTTAC
684 ATAGCGCCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:650 original size:21 final size:20
Alignment explanation
Indices: 607--678 Score: 117
Period size: 20 Copynumber: 3.5 Consensus size: 20
597 TTTTCCTAAT
607 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
627 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
648 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
668 TCGCAATGCGA
1 TCGCAATGCGA
679 TTTACATAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1267 original size:20 final size:20
Alignment explanation
Indices: 1196--1266 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1186 TTCTAAACTT
*
1196 AAAATCGCAACATGAAAATG
1 AAAATCGCAACAGGAAAATG
*
1216 AAAATCGCAACACGAAAATG
1 AAAATCGCAACAGGAAAATG
**
1236 ACTATCGCAAC-GGAGAAATG
1 AAAATCGCAACAGGA-AAATG
1256 AAAATCGCAAC
1 AAAATCGCAAC
1267 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACAGGAAAATG
Found at i:1291 original size:33 final size:33
Alignment explanation
Indices: 1239--1330 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
1229 GAAAATGACT
*
1239 ATCGCAACGGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAAC-GCGAAATGAAAATCGCAACGAGAGA
* *
1273 ATCGCAACGCGAAATGAAAATCACAACGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1306 ATCGCAACGCGAAACT-AAAATCGCA
1 ATCGCAACGCGAAA-TGAAAATCGCA
1331 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 44 0.83
34 9 0.17
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1382 original size:20 final size:19
Alignment explanation
Indices: 1326--1403 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 19
1316 GAAACTAAAA
*
1326 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1345 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1364 TACGCGTTGCGATTTTCA-T
1 T-CGCGTTGCGATTTTCATT
* *
1383 TCTCGTTGAGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1402 TC
1 TC
1404 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.28
19 22 0.44
20 14 0.28
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3287 original size:94 final size:94
Alignment explanation
Indices: 3080--3550 Score: 738
Period size: 94 Copynumber: 5.1 Consensus size: 94
3070 TAGATTGCTT
* * * * *
3080 AGTAAATTTATTCGGTTGTTGCCAATACTGCTAAA-T-TGT-TT-ATTAACAGTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3141 ATTTGTCTTTTGTGTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGT-TTTGTCTTTTGGTTGAA
*
3171 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3236 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
3265 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3330 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3359 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3424 ATTTGTCTTTGTTTTGTCATTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * * *
3453 AGTAAATTTGTCCGTTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTAATACTCTAAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3518 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3546 AGTAA
1 AGTAA
3551 TGCAATCCAT
Statistics
Matches: 356, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
91 33 0.09
92 1 0.00
93 24 0.07
94 273 0.77
95 25 0.07
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3671 original size:20 final size:20
Alignment explanation
Indices: 3646--3703 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
3636 GGTTGAAATT
3646 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAATG
* *
3666 AAAATCGCAACGCGA-AACG
1 AAAATCGCAACGAGAGAATG
3685 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
3704 CGCAACGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAATG
Found at i:3710 original size:33 final size:33
Alignment explanation
Indices: 3666--3763 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
3656 CGAGAGAATG
*
3666 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * *
3699 AGAATCGCAACGCGAAATGAAGATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
3732 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
3764 CGAAACTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 45 0.80
34 11 0.20
ACGTcount: A:0.47, C:0.26, G:0.20, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:3755 original size:20 final size:20
Alignment explanation
Indices: 3732--3769 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3722 TCGCAACGAC
3732 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
3752 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
3770 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:3802 original size:19 final size:18
Alignment explanation
Indices: 3779--3901 Score: 91
Period size: 19 Copynumber: 7.0 Consensus size: 18
3769 CTATAATCGC
3779 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
* *
3797 TATTGCGA--TTC-TCTC-
1 -GTTGCGATTTTCATTTCG
*
3812 GTTGTGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
*
3830 CGTTGCGA--TTC-TCTC-
1 -GTTGCGATTTTCATTTCG
*
3845 GTTGCGATTTTCGTTTCG
1 GTTGCGATTTTCATTTCG
*
3863 CGTTGCGATTTTCATTCTCTC
1 -GTTGCGATTTTCATT-TC-G
3884 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
3902 CGTGAAAATG
Statistics
Matches: 81, Mismatches: 11, Indels: 25
0.69 0.09 0.21
Matches are distributed among these distances:
14 12 0.15
16 12 0.15
17 12 0.15
19 28 0.35
20 17 0.21
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (18 bp):
GTTGCGATTTTCATTTCG
Found at i:3888 original size:20 final size:20
Alignment explanation
Indices: 3837--3898 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
3827 TCGCGTTGCG
3837 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
3857 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3876 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3896 ATT
1 ATT
3899 TCGCGTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3891 original size:39 final size:33
Alignment explanation
Indices: 3778--3904 Score: 164
Period size: 33 Copynumber: 3.7 Consensus size: 33
3768 ACTATAATCG
**
3778 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
3811 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
3844 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG------ATTCTCT
3883 CGTTGCGATTTTCATTTCGCGT
1 CGTTGCGATTTTCATTTCGCGT
3905 GAAAATGATT
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
33 54 0.66
39 28 0.34
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:3961 original size:25 final size:25
Alignment explanation
Indices: 3933--3980 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3923 GTAGGTTTTA
3933 GATGTATAGAAAGTGTTGTTTGAAG
1 GATGTATAGAAAGTGTTGTTTGAAG
*
3958 GATGTGTAGAAAGTGTTGTTTGA
1 GATGTATAGAAAGTGTTGTTTGA
3981 GCAAATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (25 bp):
GATGTATAGAAAGTGTTGTTTGAAG
Found at i:4323 original size:19 final size:19
Alignment explanation
Indices: 4301--4451 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4291 CGAAACTAAA
4301 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4320 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
4335 -CCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
4353 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4368 -TCTCTTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4386 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4401 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
4419 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
4438 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4452 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 26 0.27
16 8 0.08
17 8 0.08
19 44 0.46
20 10 0.10
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4347 original size:33 final size:33
Alignment explanation
Indices: 4305--4431 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
4295 ACTAAATTCG
* *
4305 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
4338 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
4371 CTTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
4404 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4432 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:4450 original size:20 final size:19
Alignment explanation
Indices: 4404--4458 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4394 GCGATTCTCT
**
4404 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
4423 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
4443 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
4459 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:6997 original size:24 final size:24
Alignment explanation
Indices: 6965--7018 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
6955 CTGAAAAATC
6965 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
6989 ATCAAAATCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
7013 ATCAAA
1 ATCAAA
7019 TTTTGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:7890 original size:20 final size:20
Alignment explanation
Indices: 7859--7989 Score: 88
Period size: 21 Copynumber: 6.5 Consensus size: 20
7849 GAAATTCAGT
*
7859 ATTGCGATTACGTAAATCGC
1 ATTGCGAATACGTAAATCGC
*
7879 AATGCGAATACGT-AATCGC
1 ATTGCGAATACGTAAATCGC
* * * *
7898 ATTGCGATTTTCCTAATTCGC
1 ATTGCGA-ATACGTAAATCGC
*
7919 ATTGCGATTTACGT-AATCGC
1 ATTGCGA-ATACGTAAATCGC
* *
7939 ATTGCGAATTAGGAAAATCGC
1 ATTGCGAA-TACGTAAATCGC
** *
7960 AACGCGAATTTA-GGAAATCGC
1 ATTGCGAA--TACGTAAATCGC
7981 ATTGCGAAT
1 ATTGCGAAT
7990 CTGGAAATTG
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
19 13 0.15
20 29 0.33
21 43 0.49
22 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (20 bp):
ATTGCGAATACGTAAATCGC
Found at i:7919 original size:21 final size:20
Alignment explanation
Indices: 7859--7945 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
7849 GAAATTCAGT
*
7859 ATTGCGA-TTACGTAAATCGC
1 ATTGCGATTTACCT-AATCGC
* * *
7879 AATGCGA-ATACGTAATCGC
1 ATTGCGATTTACCTAATCGC
*
7898 ATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTACCTAA-TCGC
*
7919 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACCTAATCGC
7939 ATTGCGA
1 ATTGCGA
7946 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
19 12 0.21
20 27 0.47
21 18 0.32
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (20 bp):
ATTGCGATTTACCTAATCGC
Found at i:7960 original size:41 final size:41
Alignment explanation
Indices: 7859--7989 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
7849 GAAATTCAGT
*
7859 ATTGCG-ATTACGTAAATCGCAATGCGA-ATACGTAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
* * * * *
7898 ATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
* * * * *
7939 ATTGCGAATTAGGAAAATCGCAACGCGAATTTAGGAAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCG-ATTTACGTAATCGC
7981 ATTGCGAAT
1 ATTGCGAAT
7990 CTGGAAATTG
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
39 6 0.08
40 16 0.22
41 30 0.41
42 21 0.29
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
Found at i:8843 original size:215 final size:213
Alignment explanation
Indices: 8460--8896 Score: 673
Period size: 215 Copynumber: 2.0 Consensus size: 213
8450 TTTACCCTAA
* *
8460 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGA
1 ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATCCGA
* *
8525 CCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAATATTTTTATTTA
66 CCCGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAATATTTTTATTTA
**
8590 ATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATATTTTCGGGTCGGCCCGGTTTTT
131 ATAAAAACAGTGACTTAATCCGACCCGACCCAAA-T-TATATATTTTCGGGTCGGCCCAATTTTT
8655 TTCACCCTAAACCCGAACCCG
194 TTCACCCTAAACCCG-ACCCG
* *
8676 ACCCAACCCGACCCAAATATCACACTT-AAAAAACCCGACCAGAACAAAATAAAGTTTCATCTGA
1 ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATCCGA
*
8740 -CCGACCCAAATATATGAATTAGAAATCCG-GCCAACCCGAAATAATAAAAAATATATTTTTATT
66 CCCGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAAT-AAAAA-ATATTTTTATT
* * * * *
8803 TAATAAAAACAGTGACTTAATCCGACCTGATCCGAATTATATATTTTCGGGTCGGTCTAATTTTT
129 TAATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATTTTCGGGTCGGCCCAATTTTT
8868 TTCACCCTAAACCCGACCCG
194 TTCACCCTAAACCCGACCCG
*
8888 TCCCGACCC
1 ACCCGACCC
8897 AAATATATGA
Statistics
Matches: 203, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
212 12 0.06
213 53 0.26
214 34 0.17
215 79 0.39
216 25 0.12
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (213 bp):
ACCCGACCCGACCCAAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATCCGA
CCCGACCCAAATATATGAATTAGAAATCCGACCCAACCCGAAATAATAAAAAATATTTTTATTTA
ATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATTTTCGGGTCGGCCCAATTTTTTT
CACCCTAAACCCGACCCG
Found at i:14421 original size:14 final size:15
Alignment explanation
Indices: 14386--14429 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
14376 TCATTATTTT
14386 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
14402 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
14416 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
14430 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:16736 original size:51 final size:51
Alignment explanation
Indices: 16655--16753 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
16645 TAAGGAAAAT
*
16655 ATAGACTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAATTA
1 ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAATTA
*
16706 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAA
1 ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAA
16754 CTCTCCCCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (51 bp):
ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAATTA
Found at i:18321 original size:370 final size:369
Alignment explanation
Indices: 17842--18577 Score: 1445
Period size: 370 Copynumber: 2.0 Consensus size: 369
17832 ACCAAAATCT
17842 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
1 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
17907 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
66 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
*
17972 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTTCAAGAGATCAATATTTCCTGTCATA
131 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
*
18037 TGATTTGATGCACCCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGT
196 TGATTTGATGCA-CCGAGTCTATTATCCATTGTACCGAGAAAGCATATGGATTATTTCCATCAGT
18102 AGTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTA
260 AGTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTA
18167 TCTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
325 TCTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
18212 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
1 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
18277 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
66 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
18342 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
131 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
18407 TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGAAAGCATATGGATTATTTCCATCAGTA
196 TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGAAAGCATATGGATTATTTCCATCAGTA
18472 GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTAT
261 GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTAT
18537 CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGG
326 CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGG
18578 CAATATGAGG
Statistics
Matches: 364, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
369 158 0.43
370 206 0.57
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (369 bp):
TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGAAAGCATATGGATTATTTCCATCAGTA
GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTAT
CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
Found at i:25525 original size:2 final size:2
Alignment explanation
Indices: 25518--25542 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25508 TCAATAACAA
25518 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25543 ATTCAACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30119 original size:16 final size:15
Alignment explanation
Indices: 30093--30123 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
30083 ATGTATGACC
30093 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
30108 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
30124 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:30302 original size:4 final size:4
Alignment explanation
Indices: 30271--30330 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
30261 GACCTGAAAC
* * **
30271 AAAT -AAT AAAT AAGT AAAT GAAAA AAAT AAAT AAAT AAAT AAAT GGAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
30319 AAAT TAAT AAAT
1 AAAT AAAT AAAT
30331 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 3 0.07
4 38 0.86
5 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:30313 original size:25 final size:24
Alignment explanation
Indices: 30265--30330 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
30255 ATCCTGGACC
* *
30265 TGAAACAAATAATAAATAAGTAAA
1 TGAAAAAAATAATAAATAAATAAA
30289 TGAAAAAAATAAATAAATAAATAAA
1 TGAAAAAAAT-AATAAATAAATAAA
* * *
30314 TGGATAAATTAATAAAT
1 TGAAAAAAATAATAAAT
30331 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (24 bp):
TGAAAAAAATAATAAATAAATAAA
Found at i:30416 original size:33 final size:33
Alignment explanation
Indices: 30373--30530 Score: 228
Period size: 33 Copynumber: 4.8 Consensus size: 33
30363 ATACTTTTAA
*
30373 AAAAAATAATTTTCAAAACTATATAATATTTTT
1 AAAAACTAATTTTCAAAACTATATAATATTTTT
30406 AAAAACTAATTTTCAAAACTATAT-ATATTTTT
1 AAAAACTAATTTTCAAAACTATATAATATTTTT
*
30438 TAAAACTAATTTTCAAAACTATATAATATATATTT
1 AAAAACTAATTTTCAAAACTATATAATAT-T-TTT
* * *
30473 TAAAACTAATTTTCAAAATTATATAATATTATT
1 AAAAACTAATTTTCAAAACTATATAATATTTTT
* *
30506 AGAAACTAATTTTCAAAATTATATA
1 AAAAACTAATTTTCAAAACTATATA
30531 CGTTTTTTCA
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
32 31 0.27
33 52 0.45
34 2 0.02
35 31 0.27
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAAACTAATTTTCAAAACTATATAATATTTTT
Found at i:30512 original size:100 final size:100
Alignment explanation
Indices: 30337--30605 Score: 296
Period size: 100 Copynumber: 2.7 Consensus size: 100
30327 AAATTAATTA
* *
30337 AAAACATTTTTAAAACTATACAATATATACTTTTAAAAAAAATAATTTTCAAAACTATATAATAT
1 AAAATATTTTTAAAACTATATAATATATA-TTTT--AAAAAATAATTTTCAAAACTATATAATAT
* *
30402 TTTTAAAAACTAATTTTCAAAACTATATATATTTTTT-
63 TATTAAAAACTAATTTTCAAAACTATATACATTTTTTC
* * *
30439 AAAACTAATTTTCAAAACTATATAATATATATTTT-AAAACTAATTTTCAAAATTATATAATATT
1 AAAA-T-ATTTTTAAAACTATATAATATATATTTTAAAAAATAATTTTCAAAACTATATAATATT
* * *
30503 ATTAGAAACTAATTTTCAAAATTATATACGTTTTTTC
64 ATTAAAAACTAATTTTCAAAACTATATACATTTTTTC
* * * * *
30540 AAAATGTTTTTAAAAGCTATATATTATATATACTT-AAAAA-AGTTTTCAAAAC-AAATAATATG
1 AAAATATTTTTAAAA-CTATATAATATATAT-TTTAAAAAATAATTTTCAAAACTATATAATAT-
30602 TATT
63 TATT
30606 TTCAAAATGT
Statistics
Matches: 143, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
99 16 0.11
100 87 0.61
101 10 0.07
102 4 0.03
103 4 0.03
104 22 0.15
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (100 bp):
AAAATATTTTTAAAACTATATAATATATATTTTAAAAAATAATTTTCAAAACTATATAATATTAT
TAAAAACTAATTTTCAAAACTATATACATTTTTTC
Found at i:30703 original size:36 final size:35
Alignment explanation
Indices: 30535--30694 Score: 128
Period size: 36 Copynumber: 4.5 Consensus size: 35
30525 TATATACGTT
* * *
30535 TTTTCAAAATGTTTTTAAAAGCTATATATTATATA
1 TTTTCAAAATGATTTCAAAAACTATATATTATATA
* * * * * * *
30570 TACTTAAAAAAGTTTTC-AAAAC-AAATAATATGTA
1 T-TTTCAAAATGATTTCAAAAACTATATATTATATA
* *
30604 TTTTCAAAATGTTTTCAAAAATTATATATTATATA
1 TTTTCAAAATGATTTCAAAAACTATATATTATATA
* * *
30639 TTTTCGAAAT-ATTTAAAAAAAACCATATATTATATAA
1 TTTTCAAAATGATTT--CAAAAACTATATATTATAT-A
30676 TTTTCAAAATGATTTCAAA
1 TTTTCAAAATGATTTCAAA
30695 TTATATATAA
Statistics
Matches: 96, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
33 12 0.12
34 17 0.18
35 23 0.24
36 30 0.31
37 10 0.10
38 4 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (35 bp):
TTTTCAAAATGATTTCAAAAACTATATATTATATA
Found at i:31378 original size:82 final size:81
Alignment explanation
Indices: 31314--32640 Score: 878
Period size: 85 Copynumber: 16.0 Consensus size: 81
31304 GCTTGATTTT
* *
31314 CCTCTAAGTTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
31379 GCTGCAAATGATGTGC
66 GCTGCAAATGATGTGC
* * * ** * *
31395 CCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
*
31460 ACTGCAAATGATGTG-
66 GCTGCAAATGATGTGC
* * * * * * * * *
31475 CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGC
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTT--T-AGCAGATAGCCCTTCTCGACTTAAGC
* * *
31540 TATGCTGTAAATAATATGC
63 TATGCTGCAAATGATGTGC
* * * * * *
31559 CCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
1 CCTCGAAGCTGAATATAATCGAACTCGAA-GGTCTTTA----GCAGATAGCCCTTCTCGACTTAA
* *
31623 GTTATACTGCAAATGATGTGC
61 GCTATGCTGCAAATGATGTGC
* ** * * *
31644 CTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
*
31709 TCTGCAAATGATGTG-
66 GCTGCAAATGATGTGC
* * *** * * * * * *
31724 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGT-GACAGATAACCCTTCTAGCCTTGAG
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTT---TAG-CAGATAGCCCTTCTCGACTTAAG
* * *
31788 TTATGCTGTAAATGATATGC
62 CTATGCTGCAAATGATGTGC
* * * * * *
31808 CCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
1 CCTCGAAGCTGAATATAATCGAACTCGAA-GGTCTTTA----GCAGATAGCCCTTCTCGACTTAA
* *
31872 GTTATACTGCAAATGATGTGC
61 GCTATGCTGCAAATGATGTGC
* ** * * *
31893 CTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
*
31958 TCTGCAAATGATGTG-
66 GCTGCAAATGATGTGC
* * *** * * * * * *
31973 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGT-GACAGATAACCCTTCTAGCCTTGAG
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTT---TAG-CAGATAGCCCTTCTCGACTTAAG
* * *
32037 TTATGCTGTAAATGATATGC
62 CTATGCTGCAAATGATGTGC
* * * * * *
32057 CCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
1 CCTCGAAGCTGAATATAATCGAACTCGAA-GGTCTTTA----GCAGATAGCCCTTCTCGACTTAA
* *
32121 GTTATACTGCAAATGATGTGC
61 GCTATGCTGCAAATGATGTGC
* ** * * *
32142 CTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
*
32207 TCTGCAAATGATGTG-
66 GCTGCAAATGATGTGC
* * *** * * * * * *
32222 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGT-GACAGATAACCCTTCTAGCCTTGAG
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTT---TAG-CAGATAGCCCTTCTCGACTTAAG
* * *
32286 TTATGCTGTAAATGATATGC
62 CTATGCTGCAAATGATGTGC
* * * * * *
32306 CCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
1 CCTCGAAGCTGAATATAATCGAACTCGAA-GGTCTTTA----GCAGATAGCCCTTCTCGACTTAA
* *
32370 GTTATACTGCAAATGATGTGC
61 GCTATGCTGCAAATGATGTGC
* ** * * * * * * * *
32391 CTTCGAAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTT--AG-CAGATAGCCCTTCTCGACTTAAGC
* *
32456 TATGCTGTAAATGATATGC
63 TATGCTGCAAATGATGTGC
* * * * * *
32475 CCTTGAAGCTGAGTGTAATCGAACT-TAAGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAG
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTA----GCAGATAGCCCTTCTCGACTTAAG
* *
32539 TTATACTGCAAATGATGTGC
62 CTATGCTGCAAATGATGTGC
* ** * * *
32559 CTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
* *
32624 TCTGCAAATGATATGC
66 GCTGCAAATGATGTGC
32640 C
1 C
32641 TTTGAGCGTA
Statistics
Matches: 1008, Mismatches: 184, Indels: 108
0.78 0.14 0.08
Matches are distributed among these distances:
80 116 0.12
81 230 0.23
82 5 0.00
83 159 0.16
84 227 0.23
85 263 0.26
86 8 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (81 bp):
CCTCGAAGCTGAATATAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGC
Found at i:31678 original size:249 final size:249
Alignment explanation
Indices: 31351--32642 Score: 2004
Period size: 249 Copynumber: 5.2 Consensus size: 249
31341 AAGGTCTTTA
* * * * * ** *
31351 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
* * * *
31416 AACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
* * * * * *
31481 AGCTGAGTGTAGTCGAACTCGAAGGTCTT-GGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGC
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGT-GACAGATAACCCTTCTAGCCTTGAGTTATGC
*
31545 TGTAAATAATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
195 TGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
31600 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
31665 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
31730 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
31795 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
196 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
31849 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
31914 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
31979 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
32044 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
196 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
32098 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
32163 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
32228 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
32293 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
196 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
32347 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
* * * * * * * * * *
32412 AACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCC
66 AACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CC
* * * * * * * * * *
32477 TTGAAGCTGAGTGTAATCGAACT-TAAGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTT
127 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGGGTGACAGATAACCCTTCTAGCCTTGAGTT
* * * ** * **
32541 ATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTC--T--TTG
191 ATGCTGTAAATGATATGCCCTT-GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
* * * * *
32596 GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTT
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTT
32643 TGAGCGTAGT
Statistics
Matches: 984, Mismatches: 52, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
249 847 0.86
250 4 0.00
251 2 0.00
252 44 0.04
253 87 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCAAAGGTCTTGGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
Found at i:36092 original size:18 final size:19
Alignment explanation
Indices: 36051--36095 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
36041 AGTTAATGTG
36051 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
36070 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
36088 AATGCAAA
1 AATGCAAA
36096 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:39049 original size:16 final size:15
Alignment explanation
Indices: 39023--39053 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39013 ATGTATGACC
39023 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
39038 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
39054 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:39232 original size:4 final size:4
Alignment explanation
Indices: 39201--39260 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
39191 GACCTGAAAC
* * **
39201 AAAT -AAT AAAT AAGT AAAT GAAAA AAAT AAAT AAAT AAAT AAAT GGAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
39249 AAAT TAAT AAAT
1 AAAT AAAT AAAT
39261 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 3 0.07
4 38 0.86
5 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:39243 original size:25 final size:24
Alignment explanation
Indices: 39195--39260 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
39185 ATCCTGGACC
* *
39195 TGAAACAAATAATAAATAAGTAAA
1 TGAAAAAAATAATAAATAAATAAA
39219 TGAAAAAAATAAATAAATAAATAAA
1 TGAAAAAAAT-AATAAATAAATAAA
* * *
39244 TGGATAAATTAATAAAT
1 TGAAAAAAATAATAAAT
39261 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (24 bp):
TGAAAAAAATAATAAATAAATAAA
Found at i:39303 original size:22 final size:19
Alignment explanation
Indices: 39274--39339 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
39264 TTAAAAACAT
39274 TTTTAAAACTATACAATATA
1 TTTTAAAACTATA-AATATA
39294 CTTTTAAAA--A-AAATA-A
1 -TTTTAAAACTATAAATATA
39310 TTTTCAAAACTATATAATATA
1 TTTT-AAAACTATA-AATATA
39331 TTTTTAAAA
1 -TTTTAAAA
39340 ACTAATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 4 0.11
16 5 0.13
17 4 0.11
18 2 0.05
19 2 0.05
20 4 0.11
21 13 0.34
22 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAAACTATAAATATA
Found at i:39347 original size:35 final size:35
Alignment explanation
Indices: 39264--39469 Score: 272
Period size: 35 Copynumber: 5.8 Consensus size: 35
39254 AATAAATTAA
* *
39264 TTAAAAAC--ATTTTTAAAACTATACAATATACTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATA-TTT
* *
39298 TAAAAAAAATAATTTTCAAAACTATATAATATATTT
1 T-TAAAAACTAATTTTCAAAACTATATAATATATTT
39334 TTAAAAACTAATTTTCAAAACTATATAATATATTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATA-TTT
39370 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAACTAATTTTCAAAACTATAT-A-ATATAT-TT
* *
39408 TTAAAAACTAATTTTCAAAATTATATAATATATAT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* *
39443 TTAGAAACTAATTTTCAAAATTATATA
1 TTAAAAACTAATTTTCAAAACTATATA
39470 TACGTTTTTT
Statistics
Matches: 156, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
34 1 0.01
35 61 0.39
36 39 0.25
37 23 0.15
38 32 0.21
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (35 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATTT
Found at i:39440 original size:109 final size:106
Alignment explanation
Indices: 39264--39547 Score: 319
Period size: 109 Copynumber: 2.7 Consensus size: 106
39254 AATAAATTAA
* **
39264 TTAAAAAC-ATTTTTAAAACTATACAATATACT-T-TTAAAAAAAATAATTTTCAAAACTATATA
1 TTAAAAACTATTTTTAAAACTATATAATATA-TATATT-TTAAAAATAATTTTCAAAACTATATA
*
39326 ATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATTTT
64 ATATATTTTTAAAAACTAATTTTCAAAACTATAT-ATACATTTT
* *
39370 TTAAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAATTATATA
1 TTAAAAACT-ATTTTTAAAACTATATAATATATATATTTTAAAAA-TAATTTTCAAAACTATATA
* * * *
39435 ATATATATTTAGAAACTAATTTTCAAAATTATATATACGTTTT
64 ATATATTTTTAAAAACTAATTTTCAAAACTATATATACATTTT
* * * * *
39478 TTCAAAA-TGTTTTTAAAAGCTATATATTATATATA-CTTAAAAA-AAGTTTTCAAAACAATATA
1 TTAAAAACTATTTTTAAAA-CTATATAATATATATATTTTAAAAATAA-TTTTCAAAACTATATA
*
39540 ATGTATTT
64 ATATATTT
39548 CAAAAATGTT
Statistics
Matches: 152, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
104 2 0.01
105 20 0.13
106 23 0.15
107 17 0.11
108 39 0.26
109 51 0.34
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (106 bp):
TTAAAAACTATTTTTAAAACTATATAATATATATATTTTAAAAATAATTTTCAAAACTATATAAT
ATATTTTTAAAAACTAATTTTCAAAACTATATATACATTTT
Found at i:39643 original size:36 final size:35
Alignment explanation
Indices: 39311--39634 Score: 141
Period size: 35 Copynumber: 9.2 Consensus size: 35
39301 AAAAAATAAT
* * *
39311 TTTC-AAAACTATATAATATAT-TTTTAAAAACTAA
1 TTTCAAAAACTATATATTATATATTTTCAAAA-TGA
* * * *
39345 TTTTC-AAAACTATATAATATATTTTTTAAAAACTAA
1 -TTTCAAAAACTATATATTATATATTTTCAAAA-TGA
* *
39381 TTTTC-AAAACTATATAATATATATATTTTAAAAACTAA
1 -TTTCAAAAACTATAT-AT-TATATATTTTCAAAA-TGA
* * ** * *
39419 TTTTC-AAAATTATATAATATATATTTAGAAACTAA
1 -TTTCAAAAACTATATATTATATATTTTCAAAATGA
* ** * *
39454 TTTTC-AAAATTATATA-TACGTTTTTTCAAAATGT
1 -TTTCAAAAACTATATATTATATATTTTCAAAATGA
* * ** * *
39488 TTTTAAAAGCTATATATTATATATACTTAAAAAAAGT
1 TTTCAAAAACTATATATTATATAT--TTTCAAAATGA
* * *
39525 TTTC-AAAAC-A-ATATAATGTA-TTTCAAAAATGT
1 TTTCAAAAACTATATATTATATATTTTC-AAAATGA
* *
39557 TTTCAAAAATTATATATTATATATTTTCGAAAT-A
1 TTTCAAAAACTATATATTATATATTTTCAAAATGA
* *
39591 TTTAAAAAAACCATATATTATATAATTTTCAAAATGA
1 TTT-CAAAAACTATATATTATAT-ATTTTCAAAATGA
39628 TTTCAAA
1 TTTCAAA
39635 TTATATATAA
Statistics
Matches: 233, Mismatches: 41, Indels: 29
0.77 0.14 0.10
Matches are distributed among these distances:
31 2 0.01
32 10 0.04
33 7 0.03
34 31 0.13
35 73 0.31
36 61 0.26
37 17 0.07
38 32 0.14
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (35 bp):
TTTCAAAAACTATATATTATATATTTTCAAAATGA
Found at i:40795 original size:19 final size:18
Alignment explanation
Indices: 40773--40816 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
40763 AAAATAAAAA
40773 TAATATAGTTAAATAAT-AT
1 TAATATAG-T-AATAATAAT
40792 TAATAATAGTAATAATAAT
1 TAAT-ATAGTAATAATAAT
40811 TAATAT
1 TAATAT
40817 TAAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATATAGTAATAATAAT
Found at i:43831 original size:7 final size:7
Alignment explanation
Indices: 43819--43843 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43809 TCCCAAGCCA
43819 TGCATTT
1 TGCATTT
43826 TGCATTT
1 TGCATTT
43833 TGCATTT
1 TGCATTT
43840 TGCA
1 TGCA
43844 GATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (7 bp):
TGCATTT
Found at i:46911 original size:17 final size:18
Alignment explanation
Indices: 46879--46912 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46869 GTTTGATTAA
46879 CACAAAGTCCAAACCAAT
1 CACAAAGTCCAAACCAAT
*
46897 CACAAA-TCTAAACCAA
1 CACAAAGTCCAAACCAA
46913 ATACAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.32, G:0.03, T:0.12
Consensus pattern (18 bp):
CACAAAGTCCAAACCAAT
Found at i:47932 original size:16 final size:16
Alignment explanation
Indices: 47913--47964 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
47903 ACATTGCATT
47913 TTGATCACTTGTATTA
1 TTGATCACTTGTATTA
* **
47929 TTGATTTA-TTAAATT-
1 TTGA-TCACTTGTATTA
47944 TTGATCACTTGTATTA
1 TTGATCACTTGTATTA
47960 TTGAT
1 TTGAT
47965 TTATTAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 14 0.52
17 2 0.07
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (16 bp):
TTGATCACTTGTATTA
Found at i:47948 original size:31 final size:31
Alignment explanation
Indices: 47910--47984 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
47900 AAAACATTGC
47910 ATTTTGATCACTTGTATTATTGATTTATTAA
1 ATTTTGATCACTTGTATTATTGATTTATTAA
47941 ATTTTGATCACTTGTATTATTGATTTATTAA
1 ATTTTGATCACTTGTATTATTGATTTATTAA
47972 ATTTTGATCACTT
1 ATTTTGATCACTT
47985 ACGTTATCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (31 bp):
ATTTTGATCACTTGTATTATTGATTTATTAA
Found at i:48113 original size:31 final size:30
Alignment explanation
Indices: 48073--48139 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
48063 TTAATTTTTA
* * *
48073 ATTTTACCTCTAAATTTTAGATAAAATATC
1 ATTTTACCTCTAAACTTTAAACAAAATATC
48103 ATTTTGACCTCTAAACTTTAAACAAAATATC
1 ATTTT-ACCTCTAAACTTTAAACAAAATATC
48134 ATTTTA
1 ATTTTA
48140 GGTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTTTACCTCTAAACTTTAAACAAAATATC
Found at i:48287 original size:7 final size:8
Alignment explanation
Indices: 48273--48298 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
48263 ACAAAATACG
48273 TAAAAAAA
1 TAAAAAAA
48281 TAAAAAAA
1 TAAAAAAA
48289 TAAAAAAA
1 TAAAAAAA
48297 TA
1 TA
48299 CATATGCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:55500 original size:37 final size:37
Alignment explanation
Indices: 55446--55516 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
55436 TTACCTAAAA
*
55446 TTTTTACTTTTCGTTTTTCTATAATTGTGGGGTACGT
1 TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTACGT
* *
55483 TTTTTACTTTTCTTTTTTCTATAGTTGCGGGGTA
1 TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTA
55517 TGGTTAAGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (37 bp):
TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTACGT
Found at i:63148 original size:14 final size:14
Alignment explanation
Indices: 63129--63159 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
63119 CCGAATTGCT
63129 CAAAAGTTGAATAA
1 CAAAAGTTGAATAA
63143 CAAAAGTTGAATAA
1 CAAAAGTTGAATAA
63157 CAA
1 CAA
63160 TTAGCTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (14 bp):
CAAAAGTTGAATAA
Found at i:63252 original size:27 final size:27
Alignment explanation
Indices: 63222--63278 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
63212 ACTTTGATCG
63222 AGTCAATCTCGTCTCACTTATAACCCT
1 AGTCAATCTCGTCTCACTTATAACCCT
63249 AGTCAATCTCGTCTCACTTATAACCCT
1 AGTCAATCTCGTCTCACTTATAACCCT
63276 AGT
1 AGT
63279 TACCGCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.33
Consensus pattern (27 bp):
AGTCAATCTCGTCTCACTTATAACCCT
Found at i:64034 original size:15 final size:15
Alignment explanation
Indices: 64014--64044 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
64004 GAGTCTCCTC
64014 CACTGGCTCCTCAGT
1 CACTGGCTCCTCAGT
64029 CACTGGCTCCTCAGT
1 CACTGGCTCCTCAGT
64044 C
1 C
64045 GCAACCTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.42, G:0.19, T:0.26
Consensus pattern (15 bp):
CACTGGCTCCTCAGT
Found at i:68604 original size:22 final size:23
Alignment explanation
Indices: 68556--68605 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
68546 AAAATATATT
* *
68556 TTATATTGAAATTTAGTATACAA
1 TTATATTGAAATTTAATATAAAA
*
68579 -TATATTGATA-TTAATATAAAA
1 TTATATTGAAATTTAATATAAAA
68600 TTATAT
1 TTATAT
68606 ATATTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
TTATATTGAAATTTAATATAAAA
Found at i:73138 original size:21 final size:19
Alignment explanation
Indices: 73114--73152 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
73104 GGAAACCACC
73114 CTTCTATCTTAGTTTCTCTTT
1 CTTCTATC-T-GTTTCTCTTT
*
73135 CTTCTCTCTGTTTCTCTT
1 CTTCTATCTGTTTCTCTT
73153 AAGGTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (19 bp):
CTTCTATCTGTTTCTCTTT
Found at i:76923 original size:23 final size:23
Alignment explanation
Indices: 76897--76940 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
76887 TTAATTTCTG
76897 TTTGGGTGTTA-TTTGTGTAAAAC
1 TTTGGGTGTTAGTTT-TGTAAAAC
76920 TTTGGGTGTTAGTTTTGTAAA
1 TTTGGGTGTTAGTTTTGTAAA
76941 TATTTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.50
Consensus pattern (23 bp):
TTTGGGTGTTAGTTTTGTAAAAC
Found at i:79383 original size:24 final size:24
Alignment explanation
Indices: 79356--79404 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
79346 TGGTGATGGT
79356 TTATAGACTATGACTGATATATGA
1 TTATAGACTATGACTGATATATGA
* ** *
79380 TTATTGGTTTTGACTGATATATGA
1 TTATAGACTATGACTGATATATGA
79404 T
1 T
79405 AACGATGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (24 bp):
TTATAGACTATGACTGATATATGA
Found at i:79708 original size:82 final size:82
Alignment explanation
Indices: 79568--79779 Score: 291
Period size: 82 Copynumber: 2.6 Consensus size: 82
79558 AGATGCTCCA
* * * *
79568 TTAGGTTGGCTCCCTTTGCTGTGTGCTTAGGTTAAGCCCTATTGACTTACGAATTTAAGGATACA
1 TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
*
79633 TA-CCTCAAAGCCTATCC
66 -AGACTCAAAGCCTATCC
* *
79650 TTAGGTTGGCTCCCATTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATACA
1 TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
79715 AGACTCAAAGCCTATCC
66 AGACTCAAAGCCTATCC
* * * *
79732 TTAGGTTGGCCTCCTTTTTGTCGTGTGTTTAAGGTAAGCCCTATGGAC
1 TTAGGTTGG-CTCC-CTTTGCCGTGTGCTTAGGGTAAGCCCTATGGAC
79780 GCAGTTATGG
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 82 0.71
83 4 0.03
84 28 0.24
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (82 bp):
TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
AGACTCAAAGCCTATCC
Found at i:80700 original size:9 final size:9
Alignment explanation
Indices: 80668--80740 Score: 83
Period size: 10 Copynumber: 7.7 Consensus size: 9
80658 CTGCTGGAAA
80668 ACCGGTTTG
1 ACCGGTTTG
*
80677 ACCAGTTTTG
1 ACC-GGTTTG
80687 AACCGGTTTG
1 -ACCGGTTTG
*
80697 ACCGGTTCG
1 ACCGGTTTG
80706 AACCGGTTTG
1 -ACCGGTTTG
*
80716 ACCGGTCTG
1 ACCGGTTTG
80725 AACCGGTTTG
1 -ACCGGTTTG
80735 ACCGGT
1 ACCGGT
80741 CTGAACCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 25 0.46
10 26 0.48
11 3 0.06
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:80710 original size:19 final size:19
Alignment explanation
Indices: 80667--80749 Score: 123
Period size: 19 Copynumber: 4.3 Consensus size: 19
80657 GCTGCTGGAA
* *
80667 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
80687 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
80706 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
80725 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
80744 AACCGG
1 AACCGG
80750 GTTCACCCGA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
18 1 0.02
19 45 0.75
20 14 0.23
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:80776 original size:17 final size:17
Alignment explanation
Indices: 80754--80790 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
80744 AACCGGGTTC
*
80754 ACCCGACCCGACTGTTG
1 ACCCGACCCGACCGTTG
80771 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
80788 ACC
1 ACC
80791 GTGACCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:80797 original size:6 final size:7
Alignment explanation
Indices: 80780--80822 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
80770 GACCCGACCC
80780 GACCGTT
1 GACCGTT
80787 GACCG-T
1 GACCGTT
80793 GACCGTT
1 GACCGTT
80800 GACCG-T
1 GACCGTT
80806 GACCGTT
1 GACCGTT
*
80813 GACCATT
1 GACCGTT
80820 GAC
1 GAC
80823 TTTCTTTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:80798 original size:13 final size:13
Alignment explanation
Indices: 80780--80816 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
80770 GACCCGACCC
80780 GACCGTTGACCGT
1 GACCGTTGACCGT
80793 GACCGTTGACCGT
1 GACCGTTGACCGT
80806 GACCGTTGACC
1 GACCGTTGACC
80817 ATTGACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:80805 original size:20 final size:20
Alignment explanation
Indices: 80780--80822 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
80770 GACCCGACCC
*
80780 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCATT
80800 GACCG-TGACCGTTGACCATT
1 GACCGTTGACCG-TGACCATT
80820 GAC
1 GAC
80823 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCATT
Done.