Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008178.1 Hibiscus syriacus cultivar Beakdansim tig00110775_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: 287176
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:849 original size:18 final size:18
Alignment explanation
Indices: 823--857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
813 TCGAAAGGAC
*
823 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
841 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
858 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:4828 original size:20 final size:20
Alignment explanation
Indices: 4783--4856 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
4773 AGACATTCAT
4783 TTGACTATCGCAACGC-G-A
1 TTGACTATCGCAACGCGGAA
*
4801 TATGACTATCGCAAAGCGGAA
1 T-TGACTATCGCAACGCGGAA
4822 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
4842 ATGACTATCGCAACG
1 TTGACTATCGCAACG
4857 AGAGAATCAC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 14 0.28
20 33 0.66
21 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:4898 original size:20 final size:20
Alignment explanation
Indices: 4873--4913 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4863 TCACAATGCG
4873 AAATGAAAATCGCAACGCGA
1 AAATGAAAATCGCAACGCGA
4893 AAATGAAAATCGCAACGCGA
1 AAATGAAAATCGCAACGCGA
4913 A
1 A
4914 TTAGTTTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (20 bp):
AAATGAAAATCGCAACGCGA
Found at i:4960 original size:33 final size:32
Alignment explanation
Indices: 4918--5015 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 32
4908 CGCGAATTAG
*
4918 TTTCGCGTTGCGATTTCATTTTCGCATTGCGA
1 TTTCTCGTTGCGATTTCATTTTCGCATTGCGA
*
4950 TTCTCTCGTTGCGCTTTTCA-TTTCGCATTGCGA
1 TT-TCTCGTTGCG-ATTTCATTTTCGCATTGCGA
* * *
4983 -TTCTCGTTGCGATAGTCATTTCCGCGTTGCGA
1 TTTCTCGTTGCGAT-TTCATTTTCGCATTGCGA
5015 T
1 T
5016 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
30 1 0.02
31 13 0.24
32 14 0.25
33 22 0.40
34 5 0.09
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (32 bp):
TTTCTCGTTGCGATTTCATTTTCGCATTGCGA
Found at i:5137 original size:14 final size:13
Alignment explanation
Indices: 5104--5153 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
5094 AATAATTATG
5104 TACAAATCAA-TT
1 TACAAATCAACTT
*
5116 AAACAAATCAACATT
1 -TACAAATCAAC-TT
*
5131 TACAAATCATCTT
1 TACAAATCAACTT
5144 TACAAATCAA
1 TACAAATCAA
5154 TTAAACAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 20 0.65
14 9 0.29
15 2 0.06
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (13 bp):
TACAAATCAACTT
Found at i:6610 original size:42 final size:42
Alignment explanation
Indices: 6531--6623 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
6521 CCTCTTCAAC
* * *
6531 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
6573 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
6615 GATGACAGG
1 GATGACAGG
6624 TGAGTCAGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:7121 original size:20 final size:20
Alignment explanation
Indices: 7096--7164 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
7086 TGAAACTAAA
7096 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
7116 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
7136 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
7156 ATCGCAACG
1 ATCGCAACG
7165 TTTGTAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:7222 original size:33 final size:33
Alignment explanation
Indices: 7180--7329 Score: 131
Period size: 33 Copynumber: 4.4 Consensus size: 33
7170 AATAAAAAAA
* *
7180 TCGCATTGCGATTCTCTCGTTACGATAGTCAAT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
*
7213 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATT
1 TCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCATT
* * * * **
7252 TCGCGTTGCGATTTTGTTGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
*
7285 TCGCATTGC-ATTCTCTCGTTGCGATAGCCATTT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCA-TT
*
7318 TCGCGTTGCGAT
1 TCGCATTGCGAT
7330 AATCATTTTC
Statistics
Matches: 92, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
32 15 0.16
33 42 0.46
34 2 0.02
35 5 0.05
37 5 0.05
39 23 0.25
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:7237 original size:20 final size:19
Alignment explanation
Indices: 7202--7263 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
7192 TCTCTCGTTA
*
7202 CGATAGTCAATTCGCATTG
1 CGATAGTCATTTCGCATTG
7221 CGATAGTCATTTTCGCATTG
1 CGATAGTCA-TTTCGCATTG
*
7241 CGATAGTCATTTCGCGTTG
1 CGATAGTCATTTCGCATTG
7260 CGAT
1 CGAT
7264 TTTGTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 22 0.55
20 18 0.45
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (19 bp):
CGATAGTCATTTCGCATTG
Found at i:7324 original size:20 final size:20
Alignment explanation
Indices: 7301--7347 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7291 TGCATTCTCT
*
7301 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAACCATTTTCG
*
7321 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAACCATTTTCG
*
7341 CATTGCG
1 CGTTGCG
7348 TAGTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAACCATTTTCG
Found at i:8365 original size:20 final size:20
Alignment explanation
Indices: 8340--8377 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8330 GAATGCTAGA
*
8340 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
8360 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
8378 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:8397 original size:11 final size:11
Alignment explanation
Indices: 8381--8417 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
8371 TCCCCCATAA
8381 AAAAAAAGAAG
1 AAAAAAAGAAG
8392 AAAAAAGAGAAG
1 AAAAAA-AGAAG
8404 AAAAAAAGAAG
1 AAAAAAAGAAG
8415 AAA
1 AAA
8418 GACTAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:8397 original size:12 final size:12
Alignment explanation
Indices: 8380--8417 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
8370 TTCCCCCATA
8380 AAAAAAAAGAAG
1 AAAAAAAAGAAG
*
8392 AAAAAAGAGAAG
1 AAAAAAAAGAAG
8404 -AAAAAAAGAAG
1 AAAAAAAAGAAG
8415 AAA
1 AAA
8418 GACTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:15132 original size:21 final size:21
Alignment explanation
Indices: 15090--15132 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15080 TTTCTGGGCT
* *
15090 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
15111 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
15132 A
1 A
15133 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:15234 original size:16 final size:17
Alignment explanation
Indices: 15207--15238 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
15197 TATAAAAAAA
15207 AAGAAGAAAAGAAGAAG
1 AAGAAGAAAAGAAGAAG
15224 AAGAA-AAAAGAAGAA
1 AAGAAGAAAAGAAGAA
15239 AGACTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAGAAGAAG
Found at i:15241 original size:14 final size:13
Alignment explanation
Indices: 15200--15238 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
15190 TCCCCCATAT
*
15200 AAAAAAAAAGAAG
1 AAAAAAGAAGAAG
15213 AAAAGAAGAAGAAG
1 AAAA-AAGAAGAAG
15227 AAAAAAGAAGAA
1 AAAAAAGAAGAA
15239 AGACTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAG
Found at i:18156 original size:20 final size:20
Alignment explanation
Indices: 18133--18202 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
18123 TCTGAAACTT
18133 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
18153 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
18173 ACTATTGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
18192 AAAATCACAAC
1 AAAATCGCAAC
18203 GACAGAATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.51, C:0.21, G:0.14, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:18576 original size:22 final size:22
Alignment explanation
Indices: 18548--18604 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
18538 AAGATTTCGC
18548 CGGAGATGGAGACTGATATCGT
1 CGGAGATGGAGACTGATATCGT
* *
18570 CGGAGATGGGGACTGATTTCGT
1 CGGAGATGGAGACTGATATCGT
18592 CGGAGATGGAGAC
1 CGGAGATGGAGAC
18605 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.40, T:0.21
Consensus pattern (22 bp):
CGGAGATGGAGACTGATATCGT
Found at i:18824 original size:20 final size:20
Alignment explanation
Indices: 18808--18891 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
18798 CAGATTCACG
*
18808 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
18828 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
18848 TTACGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
18868 TTGCAATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
18888 TTGC
1 TTGC
18892 TAATTAGGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:22880 original size:40 final size:42
Alignment explanation
Indices: 22800--22894 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 42
22790 ACATATAGAA
* ** *
22800 AAACGCCGTAATAGGGTGGTTTATTGCGGCGTTTTTTA-C-C
1 AAACGCCGTAATAGAGTGGTAAATTGCGGCGTTTTATACCAC
*
22840 AAACGCCGCAATAGAGTGGTAAATTAGCGGCG-TTTATACCAC
1 AAACGCCGTAATAGAGTGGTAAATT-GCGGCGTTTTATACCAC
22882 AAACGCCGTAATA
1 AAACGCCGTAATA
22895 TATTAACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 26 0.57
41 7 0.15
42 13 0.28
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (42 bp):
AAACGCCGTAATAGAGTGGTAAATTGCGGCGTTTTATACCAC
Found at i:23061 original size:41 final size:41
Alignment explanation
Indices: 23006--23164 Score: 180
Period size: 41 Copynumber: 3.9 Consensus size: 41
22996 TTTATTCTTA
* *
23006 AAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
* *
23047 AAACGCCGCAATAGTGTTAATCACTAGTGGCGTTTTTAGA-
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
** * * *
23087 AAATCGTTGCAATAGTTTTAATCAACAGTGGCGTTTTTTA-AC
1 AAA-CGCCGCAATAGTGTTAATCAATAGTGGC-ATTTTTAGAC
**
23129 AAACGCCATAATAGTG-TAATCAATAGTGGCATTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTT
23165 TTTATAAACG
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
39 5 0.05
40 16 0.16
41 68 0.69
42 9 0.09
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTTAGAC
Found at i:23164 original size:40 final size:41
Alignment explanation
Indices: 22987--23180 Score: 164
Period size: 41 Copynumber: 4.7 Consensus size: 41
22977 GATTACACAT
* *
22987 ATAGTGGCATTTATTCT-TAAAACGCCGCAATAGTGATAATAA
1 ATAGTGGCATTT-TT-TAGAAAACGCCGCAATAGTGATAATCA
*
23029 ATAGTGGCA-TTTTTAGACAAACGCCGCAATAGTGTTAATCA
1 ATAGTGGCATTTTTTAGA-AAACGCCGCAATAGTGATAATCA
* * ** **
23070 CTAGTGGC-GTTTTTAGAAAATCGTTGCAATAGTTTTAATCA
1 ATAGTGGCATTTTTTAGAAAA-CGCCGCAATAGTGATAATCA
* * **
23111 ACAGTGGCGTTTTTTA-ACAAACGCCATAATAGTG-TAATCA
1 ATAGTGGCATTTTTTAGA-AAACGCCGCAATAGTGATAATCA
**
23151 ATAGTGGCATTTTTTTTATAAACGCCGCAA
1 ATAGTGGCATTTTTTAGA-AAACGCCGCAA
23181 AATGTTAAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 25 0.20
41 80 0.65
42 18 0.15
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (41 bp):
ATAGTGGCATTTTTTAGAAAACGCCGCAATAGTGATAATCA
Found at i:24805 original size:41 final size:41
Alignment explanation
Indices: 24732--24854 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 41
24722 CGCTAAAAAT
*
24732 TTGTACTTTAGTGGTGTTTTTG-ACATAAACGCCGCAATAGAG
1 TTGTACTTTAGTGG-CTTTTTGTA-ATAAACGCCGCAATAGAG
* ** *
24774 TTGTAATTTAGTGGCTTTTTGTAATAAACGCCATAATAGTG
1 TTGTACTTTAGTGGCTTTTTGTAATAAACGCCGCAATAGAG
* * *
24815 -TGTCCCTTAGTGGCATTTTTGTAATAAACGCCGCAGTAGA
1 TTGTACTTTAGTGGC-TTTTTGTAATAAACGCCGCAATAGA
24855 ATAGTTCCTT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
40 11 0.16
41 42 0.63
42 14 0.21
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (41 bp):
TTGTACTTTAGTGGCTTTTTGTAATAAACGCCGCAATAGAG
Found at i:32825 original size:43 final size:42
Alignment explanation
Indices: 32762--33143 Score: 289
Period size: 43 Copynumber: 8.9 Consensus size: 42
32752 TGTTTTTAGC
* * *
32762 AAAAACGCCGTAAAAAATCAATACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTG-G
* * *
32805 AAAAACGCCGCAAAACATCAAAACCTACTACGACGTTTGTGG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTGG
* * *
32847 AATAAACGTCGCAAAACATCAAAATCTAATGCGGCGTTTGTGG
1 AA-AAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTGG
* * * * *
32890 GAAAACGCCGCAAAACATCAACATCTACTACGGCGTTTGTGG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTGG
* * * *
32932 GAAAACGCCGCAAAACATCAACACCTACTGCGACGTTT-TAGAG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGT-G-G
** * * ** * **
32975 AAAAAAACATCGCTAAATATCATTACCTATTGCGGCGTTTATCTA
1 --AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGT-GG
* * * * * * *
33020 AAAAACGCCGCTAAATATCAACACCTATTACGGCATTTTTCTG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGT-GG
* * *
33063 ACAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGTGTG
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTG-G
* * * * * *
33106 ACAAACGCCGCTAAATATCAATACATATTGCAGCGTTT
1 AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTT
33144 TTTGTTTAAA
Statistics
Matches: 284, Mismatches: 48, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.00
42 75 0.26
43 178 0.63
45 29 0.10
46 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCAAAACATCAAAACCTATTGCGGCGTTTGTGG
Found at i:32921 original size:85 final size:85
Alignment explanation
Indices: 32762--32979 Score: 269
Period size: 85 Copynumber: 2.6 Consensus size: 85
32752 TGTTTTTAGC
* * * * *
32762 AAAAACGCCGTAAAAAATCAATACCTATTGCGGCGTTTGTGAGAAAAACGCCGCAAAACATCAAA
1 AAAAACGCCGCAAAACATCAAAATCTAATGCGGCGTTTGTGAGAAAAACGCCGCAAAACATCAAA
32827 ACCTACTACGACGTTTGTGG
66 ACCTACTACGACGTTTGTGG
* *
32847 AATAAACGTCGCAAAACATCAAAATCTAATGCGGCGTTTGTG-GGAAAACGCCGCAAAACATCAA
1 AA-AAACGCCGCAAAACATCAAAATCTAATGCGGCGTTTGTGAGAAAAACGCCGCAAAACATCAA
* * *
32911 CATCTACTACGGCGTTTGTGG
65 AACCTACTACGACGTTTGTGG
* * * * *
32932 GAAAACGCCGCAAAACATCAACACCTACTGCGACGTTT-TAGAGAAAAA
1 AAAAACGCCGCAAAACATCAAAATCTAATGCGGCGTTTGT-GAGAAAAA
32980 AACATCGCTA
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 32 0.28
85 47 0.42
86 33 0.29
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (85 bp):
AAAAACGCCGCAAAACATCAAAATCTAATGCGGCGTTTGTGAGAAAAACGCCGCAAAACATCAAA
ACCTACTACGACGTTTGTGG
Found at i:35079 original size:2 final size:2
Alignment explanation
Indices: 35072--35105 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35062 TATTATTTAT
*
35072 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35106 AATAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35121 original size:3 final size:3
Alignment explanation
Indices: 35106--35171 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
35096 TATTTATATA
* * **
35106 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
35149 AA- AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
35172 TTGCAAATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 8 0.16
3 40 0.78
4 3 0.06
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:35154 original size:45 final size:43
Alignment explanation
Indices: 35105--35208 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 43
35095 ATATTTATAT
35105 AAATAATAAAAATAATAATAATG-AAATAATAATTAAAGCAATAAA
1 AAATAATAAAAATAATAATAATGCAAATAATAATT-AA--AATAAA
* * *
35150 AAATAATAATAATAAAATAATATTGCAAATAATGATTAAAATAAA
1 AAATAATAA-AA-ATAATAATAATGCAAATAATAATTAAAATAAA
35195 AGAA-AATAAAAATA
1 A-AATAATAAAAATA
35209 TAGTATTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
43 2 0.04
44 2 0.04
45 21 0.41
46 4 0.08
47 12 0.24
48 10 0.20
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (43 bp):
AAATAATAAAAATAATAATAATGCAAATAATAATTAAAATAAA
Found at i:35201 original size:48 final size:48
Alignment explanation
Indices: 35106--35208 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
35096 TATTTATATA
*
35106 AATAATAAAAATAATAATAATGAAATAATAATTAAAGCAATAAAAAAT
1 AATAATAAAAATAATAATAATGAAATAATAATTAAAACAATAAAAAAT
* * * *
35154 AATAATAATAA-AATAATATTGCAAATAATGATTAAAATAA-AAGAAAAT
1 AATAATAAAAATAATAATAATG-AAATAATAATTAAAACAATAA-AAAAT
*
35202 AAAAATA
1 AATAATA
35209 TAGTATTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 11 0.23
48 36 0.77
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (48 bp):
AATAATAAAAATAATAATAATGAAATAATAATTAAAACAATAAAAAAT
Found at i:37465 original size:76 final size:76
Alignment explanation
Indices: 36647--37438 Score: 1413
Period size: 76 Copynumber: 10.4 Consensus size: 76
36637 ATGAAATATT
* * * ** **
36647 GAAATCATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGAAAACATCAAAAAGCTCTA
1 GAAA-CATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
36712 GAAGGCTTTTTG
65 GAAGGCTTTTTG
*
36724 AAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
36789 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
36800 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
36865 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
36876 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGATCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
36941 AAGGCTTTTTG
66 AAGGCTTTTTG
36952 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37017 AAGGCTTTTTG
66 AAGGCTTTTTG
*
37028 GAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37093 AAGGCTTTTTG
66 AAGGCTTTTTG
*
37104 GAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37169 AAGGCTTTTTG
66 AAGGCTTTTTG
*
37180 GAAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37245 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
37256 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCGCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37321 AAGGCTTTTTG
66 AAGGCTTTTTG
37332 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
37397 AAGGCTTTTTG
66 AAGGCTTTTTG
*
37408 GAAACATCATGCACTGTAGGACTTACAGATG
1 GAAACATCATGCACTGCAGGACTTACAGATG
37439 TGGGAAATAG
Statistics
Matches: 689, Mismatches: 26, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
76 686 1.00
77 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:37766 original size:167 final size:166
Alignment explanation
Indices: 37441--37766 Score: 530
Period size: 167 Copynumber: 2.0 Consensus size: 166
37431 TACAGATGTG
* * *
37441 GGAAATAGTTTATTAAGTACAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
** *
37506 TAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
66 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
37571 TTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
131 TTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
37607 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTAC-TTTCAACAATTTCA-TTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
* **
37670 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTCTGTTTTTTTTAAATAACATGT
66 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCA-T-T-ATTTTTCAAAATAACATGT
37735 TGATTGGGTAACATGCCCCAATCTCAAGATAA
128 TGATTGGGTAACATGCCCCAATCTCAAGATAA
37767 TGCTAATTTT
Statistics
Matches: 148, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
164 41 0.28
165 15 0.10
166 44 0.30
167 48 0.32
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (166 bp):
GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
TTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
Found at i:38311 original size:22 final size:22
Alignment explanation
Indices: 38286--38340 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
38276 AATAAAGCTT
38286 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
* *
38308 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
38330 TCATCTTTGAA
1 TCATCTTTGAA
38341 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:39739 original size:75 final size:74
Alignment explanation
Indices: 39645--39820 Score: 201
Period size: 74 Copynumber: 2.4 Consensus size: 74
39635 CAGGATCTTG
* * *
39645 TGGGCCTTCAGCATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGAT
1 TGGGCTTTCAGCATGCCCCAACATTTGGCTAATA-AA-TATTCAAAATACATCAACAGTTCTGAT
39709 TCTGATTGAAA
64 TCTGATTGAAA
* * * * * ** *
39720 TGGGCTTTCAGCATGCCCCAGCATTTTGTTGATAAATATTCAGAATATTTCAACATTTCTGATTC
1 TGGGCTTTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTC
39785 TGATTGAAA
66 TGATTGAAA
* * *
39794 AGGGTTTTCAGCATGCCCCAATATTTG
1 TGGGCTTTCAGCATGCCCCAACATTTG
39821 CTTCTTGTTA
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
74 54 0.64
75 23 0.27
76 7 0.08
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (74 bp):
TGGGCTTTCAGCATGCCCCAACATTTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTC
TGATTGAAA
Found at i:40974 original size:114 final size:114
Alignment explanation
Indices: 40774--40994 Score: 372
Period size: 114 Copynumber: 1.9 Consensus size: 114
40764 CATGCAGTTC
*
40774 ATCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAACA
40839 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAATTT
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAATTT
* *
40888 ATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAA-TCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACT-AGATCAGATAACTCAAAGAAC
* * *
40952 AGTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
65 ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAG
40995 AACGTGGCAC
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 99 0.99
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAATTT
Found at i:43239 original size:2 final size:2
Alignment explanation
Indices: 43232--43259 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43222 ACAACAAGGG
43232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43260 TTGAAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45532 original size:7 final size:7
Alignment explanation
Indices: 45522--45572 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
45512 TAAAAGTATG
*
45522 AATGCAA
1 AATGAAA
45529 AATGAAA
1 AATGAAA
45536 AATGAAA
1 AATGAAA
*
45543 AGATGCAA
1 A-ATGAAA
45551 AATG-AA
1 AATGAAA
45557 AATGAATA
1 AATGAA-A
*
45565 TATGAAA
1 AATGAAA
45572 A
1 A
45573 GGTGTTTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 6 0.16
7 19 0.51
8 12 0.32
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.18
Consensus pattern (7 bp):
AATGAAA
Found at i:47906 original size:16 final size:15
Alignment explanation
Indices: 47883--47925 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
47873 GAATAAAATA
47883 AATAATAAAAATAAT
1 AATAATAAAAATAAT
47898 AATATATAAAAATAAT
1 AATA-ATAAAAATAAT
47914 AAGTAATAAAAA
1 AA-TAATAAAAA
47926 ATTTGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 20 0.77
17 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
AATAATAAAAATAAT
Found at i:48710 original size:2 final size:2
Alignment explanation
Indices: 48703--48748 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
48693 AAATATTATT
* * *
48703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48745 TA TA
1 TA TA
48749 AATAATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:48780 original size:3 final size:3
Alignment explanation
Indices: 48749--48817 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
48739 TATTTATATA
* ** * *
48749 AAT AAT AAA AAT AAT GTT AAT GA- AAT AAT AATT AA- AGT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT
48794 AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
48818 TTGCAAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:48795 original size:19 final size:20
Alignment explanation
Indices: 48752--48817 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
48742 TTATATAAAT
* ** *
48752 AATAAAAATAATGTTAATGA
1 AATAATAATAATAATAATAA
*
48772 AATAATAATTAA-AGTAAT-A
1 AATAATAA-TAATAATAATAA
48791 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
48811 AATAATA
1 AATAATA
48818 TTGCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.08
19 14 0.36
20 19 0.49
21 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATAATAATAATAATAATAA
Found at i:48837 original size:12 final size:12
Alignment explanation
Indices: 48771--48839 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
48761 AATGTTAATG
48771 AAATAATAATTA
1 AAATAATAATTA
* *
48783 AAGTAATAAATA
1 AAATAATAATTA
48795 ATAATAATAATAATA
1 A-AATAATAAT--TA
*
48810 AAATAAT-ATTGC
1 AAATAATAATT-A
*
48822 AAATAATGATTA
1 AAATAATAATTA
48834 AAATAA
1 AAATAA
48840 AAGAAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 1 0.02
12 24 0.52
13 12 0.26
14 6 0.13
15 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
AAATAATAATTA
Found at i:57321 original size:105 final size:105
Alignment explanation
Indices: 57113--57335 Score: 270
Period size: 105 Copynumber: 2.1 Consensus size: 105
57103 GATTGTCCAT
* * * *
57113 AAGGACCACATA-TAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* *
57177 AAGGCCTCATACATCCTCCAAATAATACATATACGTCCCG
66 AAGGCCTCATACATCCTCCAAAGAATACATATACATCCCG
* * *
57217 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATACTAAGGACCAAATACGTGTCTC-A
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* ** * * * *
57281 AAGGACCTCATAGATGTTCCATAGGATACCTATATATCCCG
66 AAGG-CCTCATACATCCTCCAAAGAATACATATACATCCCG
*
57322 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
57336 CCCTCGACTA
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 16 0.16
105 84 0.84
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
AAGGCCTCATACATCCTCCAAAGAATACATATACATCCCG
Found at i:57532 original size:53 final size:52
Alignment explanation
Indices: 57475--57638 Score: 118
Period size: 53 Copynumber: 3.1 Consensus size: 52
57465 ACACATACAT
57475 GTAATCACGTAGTTCATATCAATTCTCATATGATTTCTTATTCATATAATCAC
1 GTAATCACGTAGTTCATATCAATTCTCATATGATTTC-TATTCATATAATCAC
* ** * * * * *** ** *
57528 GTAATTCACTTA-CACATAGCACATTTTCATGT-AATTC-AAAGATATCCCTTAGC
1 GTAA-TCACGTAGTTCATATCA-ATTCTCATATGATTTCTATTCATAT-AATCA-C
* *
57581 TTAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATATCAATTCTCATATGATTTC-TATTCATATAATCAC
57634 GTAAT
1 GTAAT
57639 TCACTTACAT
Statistics
Matches: 74, Mismatches: 29, Indels: 16
0.62 0.24 0.13
Matches are distributed among these distances:
51 5 0.07
52 16 0.22
53 32 0.43
54 16 0.22
55 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (52 bp):
GTAATCACGTAGTTCATATCAATTCTCATATGATTTCTATTCATATAATCAC
Found at i:57610 original size:106 final size:106
Alignment explanation
Indices: 57476--57689 Score: 383
Period size: 106 Copynumber: 2.0 Consensus size: 106
57466 CACATACATG
*
57476 TAATCACGTAGTTCATATCAATTCTCATATGATTTCTTATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
*
57541 ACATAGCACATTTTCATGTAATTCAAAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTCAAAGATATCCCTTACCT
*
57582 TAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
* *
57647 ATATAGCACATTTTCATGTAATTCACAGATATCCCTTACCT
66 ACATAGCACATTTTCATGTAATTCAAAGATATCCCTTACCT
57688 TA
1 TA
57690 TATCTCTTAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (106 bp):
TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATTTTCATGTAATTCAAAGATATCCCTTACCT
Found at i:58940 original size:22 final size:22
Alignment explanation
Indices: 58909--58989 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
58899 TCGGTTGAGG
* *
58909 GGGTATCGATTCCCCTTTAAAT
1 GGGTACCGATTCCCCTTTGAAT
*
58931 GGGTACCGATTCCCCCTTGAAT
1 GGGTACCGATTCCCCTTTGAAT
* *
58953 GGATACCGATT-CCCATTGAAT
1 GGGTACCGATTCCCCTTTGAAT
* *
58974 GAGTACCAATTCCCCT
1 GGGTACCGATTCCCCT
58990 AGCCCAGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.35
22 32 0.65
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (22 bp):
GGGTACCGATTCCCCTTTGAAT
Found at i:58973 original size:21 final size:21
Alignment explanation
Indices: 58928--58987 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
58918 TTCCCCTTTA
* *
58928 AATGGGTACCGATTCCCCCTTG
1 AATGGATACCGATT-CCCATTG
58950 AATGGATACCGATTCCCATTG
1 AATGGATACCGATTCCCATTG
*
58971 AAT-GAGTACCAATTCCC
1 AATGGA-TACCGATTCCC
58988 CTAGCCCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 19 0.56
22 13 0.38
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (21 bp):
AATGGATACCGATTCCCATTG
Found at i:76037 original size:23 final size:21
Alignment explanation
Indices: 75985--76046 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
75975 TTTTGGTGCA
*
75985 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
76005 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
76026 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
76047 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:86211 original size:15 final size:15
Alignment explanation
Indices: 86174--86212 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
86164 CAGAGCCTCA
86174 TAATCATTCAGCATT
1 TAATCATTCAGCATT
86189 TGAATCATTCAGC-TCT
1 T-AATCATTCAGCAT-T
86205 TAATCATT
1 TAATCATT
86213 ATGAAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (15 bp):
TAATCATTCAGCATT
Found at i:86916 original size:23 final size:23
Alignment explanation
Indices: 86890--86940 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
86880 TGCACCTAAC
86890 TGTCAAGTAGAATTGCACCGGAG
1 TGTCAAGTAGAATTGCACCGGAG
** *
86913 TGTCGCGTAGAATTGCACCGTAG
1 TGTCAAGTAGAATTGCACCGGAG
86936 TGTCA
1 TGTCA
86941 TATAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (23 bp):
TGTCAAGTAGAATTGCACCGGAG
Found at i:94088 original size:23 final size:23
Alignment explanation
Indices: 94062--94112 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
94052 CGTATAAATG
*
94062 CACCTAACTGCCACGTAGAATTA
1 CACCGAACTGCCACGTAGAATTA
* * *
94085 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAACTGCCACGTAGAATTA
94108 CACCG
1 CACCG
94113 TAGTGCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (23 bp):
CACCGAACTGCCACGTAGAATTA
Found at i:94117 original size:23 final size:23
Alignment explanation
Indices: 94070--94120 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
94060 TGCACCTAAC
94070 TGCCACGTAGAATTACACCGAAG
1 TGCCACGTAGAATTACACCGAAG
* * *
94093 TGCCGCGTAGAATTGCACCGTAG
1 TGCCACGTAGAATTACACCGAAG
94116 TGCCA
1 TGCCA
94121 TATAATAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCCACGTAGAATTACACCGAAG
Found at i:102081 original size:17 final size:15
Alignment explanation
Indices: 102043--102073 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
102033 AAATGCTATC
102043 TTATATTTTTTATAT
1 TTATATTTTTTATAT
102058 TTATATTTTTTATAT
1 TTATATTTTTTATAT
102073 T
1 T
102074 ATTTTATTAG
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATATTTTTTATAT
Found at i:110374 original size:64 final size:66
Alignment explanation
Indices: 110304--110447 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 66
110294 ATGCACTCCT
** ** *
110304 TATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGG-ATGCATCGATGCA-TTA-
1 TATGCATCGATGCATCAAAGGCATTCGATGTT-CTATTTT-AAAGGAATGCATCGATGCACTTAT
110366 G-A
64 GAA
*
110368 TATGCATCGATGCATCAAAGGCATTCGATGTTCTCTTTTAAAGGAATGCATCGATGCACTTATGA
1 TATGCATCGATGCATCAAAGGCATTCGATGTTCTATTTTAAAGGAATGCATCGATGCACTTATGA
110433 A
66 A
*
110434 TGTGCATCGATGCA
1 TATGCATCGATGCA
110448 CCTTGTCCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 5 0.07
63 18 0.26
64 31 0.45
65 1 0.01
66 14 0.20
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (66 bp):
TATGCATCGATGCATCAAAGGCATTCGATGTTCTATTTTAAAGGAATGCATCGATGCACTTATGA
A
Found at i:114575 original size:64 final size:63
Alignment explanation
Indices: 114431--114639 Score: 197
Period size: 64 Copynumber: 3.3 Consensus size: 63
114421 TCTTTCAATG
* * * *
114431 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATT-
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTCTT-TTA
* * * * ** * *
114494 AATGAGATGTATTGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTA
1 AAGGA-ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TTCTTTT-
114559 A
63 A
* ** * * *
114560 AAGG-ATGCATCGATGCATTAGATATGCATCGATGCATCAAAGGCATTTGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TTCTTTTA
114623 AAGGAATGCATCGATGC
1 AAGGAATGCATCGATGC
114640 TTATGTGCAT
Statistics
Matches: 115, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
63 8 0.07
64 101 0.88
65 3 0.03
66 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (63 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTTCTTTTA
Found at i:122589 original size:6 final size:6
Alignment explanation
Indices: 122580--122609 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
122570 CTTTTTCTTT
122580 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
122610 GTTTGTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTCA
Found at i:123242 original size:25 final size:25
Alignment explanation
Indices: 123198--123250 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
123188 GGTAAAATAA
123198 AAAGAATAAAGAAAGGAAATAAAAGT
1 AAAGAATAAAGAAAGGAAATAAAA-T
123224 AAAG-ATAAA-AAAGGTAAATAAAAT
1 AAAGAATAAAGAAAGG-AAATAAAAT
123248 AAA
1 AAA
123251 CAACATGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.35
25 13 0.50
26 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (25 bp):
AAAGAATAAAGAAAGGAAATAAAAT
Found at i:124088 original size:2 final size:2
Alignment explanation
Indices: 124045--124069 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
124035 GTAATAAATA
124045 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
124070 ATAATGTTTA
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:124263 original size:3 final size:3
Alignment explanation
Indices: 124252--124515 Score: 98
Period size: 3 Copynumber: 87.3 Consensus size: 3
124242 AATTGTGTAG
* *
124252 ATA AT- ATA ATA ATA ATA A-A ATA AT- ATA TTT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
124297 A-A GATA A-A AGA TCTA A-A A-A AGTAA ATA A-A A-A CATA ATA ATA
1 ATA -ATA ATA ATA -ATA ATA ATA A-T-A ATA ATA ATA -ATA ATA ATA
* *
124338 TATA GTA ATAA ATAA ATA A-A ATA ATGGA A-A ATA ATA AAA ATA ATA
1 -ATA ATA AT-A AT-A ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA
** * *
124383 ACG ATA ATA A-A A-A AGTG A-A ATA TATA TATA ATA ATA TATA ATA GTA
1 ATA ATA ATA ATA ATA A-TA ATA ATA -ATA -ATA ATA ATA -ATA ATA ATA
**
124429 A-A A-A ATA ATA ACG ATA ATA ATA ATTA A-A ATA A-A ATA TATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -AT-A ATA
124473 ATA TATA ATA ATA ATA A-A ATA TATA ATA ATA ATTA ATA CATA A
1 ATA -ATA ATA ATA ATA ATA ATA -ATA ATA ATA A-TA ATA -ATA A
124516 ATATAAGGTA
Statistics
Matches: 204, Mismatches: 23, Indels: 68
0.69 0.08 0.23
Matches are distributed among these distances:
2 35 0.17
3 120 0.59
4 44 0.22
5 5 0.02
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:124370 original size:10 final size:9
Alignment explanation
Indices: 124319--124505 Score: 60
Period size: 10 Copynumber: 19.8 Consensus size: 9
124309 CTAAAAAAGT
124319 AAATAA-AA
1 AAATAATAA
*
124327 ACATAATAA
1 AAATAATAA
* *
124336 TATATAGTAA
1 -AAATAATAA
124346 TAAATAA-ATA
1 -AAATAATA-A
*
124356 AAATAATGGA
1 AAATAAT-AA
124366 AAATAATAA
1 AAATAATAA
124375 AAATAATAA
1 AAATAATAA
**
124384 CGATAATAA
1 AAATAATAA
* *
124393 AAA-AGT-G
1 AAATAATAA
124400 AAATATATATA
1 AAATA-ATA-A
*
124411 TAATAATATA
1 AAATAATA-A
* *
124421 TAATAGTAAA
1 AAATAAT-AA
124431 AAATAATAA
1 AAATAATAA
**
124440 CGATAATAA
1 AAATAATAA
* *
124449 TAATTAAAATA
1 -AAATAATA-A
124460 AAATATATAA
1 AAATA-ATAA
124470 ATAATATATAA
1 A-AATA-ATAA
*
124481 TAATAAT-A
1 AAATAATAA
124489 AAATATATAA
1 AAATA-ATAA
*
124499 TAATAAT
1 AAATAAT
124506 TAATACATAA
Statistics
Matches: 133, Mismatches: 30, Indels: 31
0.69 0.15 0.16
Matches are distributed among these distances:
7 3 0.02
8 13 0.10
9 43 0.32
10 57 0.43
11 17 0.13
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AAATAATAA
Found at i:124434 original size:56 final size:57
Alignment explanation
Indices: 124367--124498 Score: 171
Period size: 56 Copynumber: 2.3 Consensus size: 57
124357 AATAATGGAA
* *
124367 AATAAT-AAAAATAATAACGATAATAAAAAAGTGAAAT-ATATATAT-AATAATATAT
1 AATAATAAAAAATAATAACGATAAT-AAAAAGTAAAATAAAATATATAAATAATATAT
* * *
124422 AATAGTAAAAAATAATAACGATAATAATAATTAAAATAAAATATATAAATAATATAT
1 AATAATAAAAAATAATAACGATAATAAAAAGTAAAATAAAATATATAAATAATATAT
124479 AATAATAATAAAATATATAA
1 AATAATAA-AAAATA-ATAA
124499 TAATAATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
55 14 0.21
56 25 0.38
57 17 0.26
58 6 0.09
59 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (57 bp):
AATAATAAAAAATAATAACGATAATAAAAAGTAAAATAAAATATATAAATAATATAT
Found at i:124451 original size:80 final size:78
Alignment explanation
Indices: 124285--124504 Score: 211
Period size: 80 Copynumber: 2.8 Consensus size: 78
124275 TATATTTATA
* * *
124285 ATAATAATAATAAAGATAAAAGATCTAAAAAAGTAAATAAAAACATAATAATATATAGTAATAAA
1 ATAATAATAATAAAAATAAAAGATATAAAAAAGTAAATAAAAACATAATAATATATAATAATAAA
*
124350 TAAATAAAATAATG
66 TAAAT-AAATAACG
* * * * *
124364 -GAA-AATAATAAAAATAATAACGATAATAAAAAAGTGAAATATATATATAATAATATATAATAG
1 ATAATAATAATAAAAATAA-AA-GAT-ATAAAAAAGT-AAATAAAAACATAATAATATATAATAA
124427 TAAA-AAAT-AATAACG
62 TAAATAAATAAATAACG
* * * *
124442 ATAATAATAATTAAAATAAAATATATAAATAA-TATATAATAATA-ATAA-AATATATAATAATA
1 ATAATAATAATAAAAATAAAAGATATAAAAAAGTAAATAA-AA-ACATAATAATATATAATAATA
124504 A
64 A
124505 TTAATACATA
Statistics
Matches: 116, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
75 18 0.16
76 6 0.05
77 21 0.18
78 12 0.10
79 7 0.06
80 26 0.22
81 26 0.22
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (78 bp):
ATAATAATAATAAAAATAAAAGATATAAAAAAGTAAATAAAAACATAATAATATATAATAATAAA
TAAATAAATAACG
Found at i:124462 original size:29 final size:29
Alignment explanation
Indices: 124252--124518 Score: 72
Period size: 28 Copynumber: 9.2 Consensus size: 29
124242 AATTGTGTAG
*
124252 ATAATATAATA-ATAATAA-AATAATATAT
1 ATAA-ATAATATATAATAATAATAAAATAT
* *
124280 TTATAATAATA-ATAATAA-AGATAAAAGAT
1 ATA-AATAATATATAATAATA-ATAAAATAT
* * *
124309 CTAAAAAAGTAAATAA-AA-ACATAATAATAT
1 ATAAATAA-TATATAATAATA-ATAA-AATAT
*
124339 ATAGTAATAAATAAATAA-AATAATGGAAAATA-
1 ATA--AAT-AATATATAATAATAAT--AAAATAT
**
124371 ATAAA-AATA-ATAACGATAATAAAA-A-
1 ATAAATAATATATAATAATAATAAAATAT
*
124396 AGTGAAATATATATATAATAAT-ATATAATAGT
1 A-T-AAATA-ATATATAATAATAATAAAATA-T
* * *
124428 AAAAAATAATAACGATAATAATAATTAAA-AT
1 -ATAAATAAT-A-TATAATAATAATAAAATAT
124459 A-AAAT-ATATA-AATAATATATAATAATA-
1 ATAAATAATATATAATAATA-ATAA-AATAT
* *
124486 AT-AA-AATATATAATAATAAT-TAATAC
1 ATAAATAATATATAATAATAATAAAATAT
124512 ATAAATA
1 ATAAATA
124519 TAAGGTACCG
Statistics
Matches: 186, Mismatches: 20, Indels: 66
0.68 0.07 0.24
Matches are distributed among these distances:
25 13 0.07
26 11 0.06
27 22 0.12
28 41 0.22
29 31 0.17
30 22 0.12
31 7 0.04
32 25 0.13
33 12 0.06
34 2 0.01
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (29 bp):
ATAAATAATATATAATAATAATAAAATAT
Found at i:124509 original size:25 final size:25
Alignment explanation
Indices: 124442--124520 Score: 99
Period size: 25 Copynumber: 3.0 Consensus size: 25
124432 AATAATAACG
124442 ATAATAATAATTAA-AATAAAATAT
1 ATAATAATAATTAATAATAAAATAT
124466 ATAAATAATATATAATAATAATAAAATAT
1 AT-AATAATA-AT--TAATAATAAAATAT
124495 ATAATAATAATTAATACAT-AAATAT
1 ATAATAATAATTAATA-ATAAAATAT
124520 A
1 A
124521 AGGTACCGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
24 2 0.04
25 19 0.39
26 4 0.08
27 2 0.04
28 10 0.20
29 12 0.24
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (25 bp):
ATAATAATAATTAATAATAAAATAT
Found at i:130693 original size:18 final size:18
Alignment explanation
Indices: 130650--130695 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
130640 CCTTAACATG
**
130650 TGCATCGATGCACTCCTA
1 TGCATCGATGCACTAATA
130668 TGCATCGATGCACTAAT-
1 TGCATCGATGCACTAATA
130685 TGCATTCGATG
1 TGCA-TCGATG
130696 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (18 bp):
TGCATCGATGCACTAATA
Found at i:131443 original size:21 final size:21
Alignment explanation
Indices: 131418--131463 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
131408 TCATTCGCAT
*
131418 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCACAAC
* *
131439 GCGAATTTGGAAAATCACAAT
1 GCGAATTAGGAAAATCACAAC
131460 GCGA
1 GCGA
131464 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:135731 original size:6 final size:6
Alignment explanation
Indices: 135716--135744 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
135706 CTTTTTCTTT
135716 TTTTCA -TTTCA TTTTCA TTTTCA TTTTCA
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
135745 GTTTGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTCA
Found at i:136367 original size:25 final size:26
Alignment explanation
Indices: 136289--136381 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 26
136279 AAGAAAATAC
136289 AAATAAAAATAAATGAATAAAATAAAGAGGGT
1 AAAT-AAAATAAA-GAAT-AAA-AAA-A-GGT
* *
136321 AAA-ATAA-AAAGAATAAAGAAAGG-
1 AAATAAAATAAAGAATAAAAAAAGGT
136344 AAATAAAAGTAAAG-ATAAAAAAAGGT
1 AAATAAAA-TAAAGAATAAAAAAAGGT
136370 AAATAAAATAAA
1 AAATAAAATAAA
136382 CAACATGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
23 3 0.06
24 5 0.09
25 15 0.28
26 14 0.26
27 3 0.06
28 4 0.08
29 3 0.06
30 3 0.06
32 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (26 bp):
AAATAAAATAAAGAATAAAAAAAGGT
Found at i:136575 original size:4 final size:4
Alignment explanation
Indices: 136408--136556 Score: 54
Period size: 4 Copynumber: 34.8 Consensus size: 4
136398 AAACATATTA
* * * *
136408 AAAT AAAT AAAT AAAGT AAACA AAACT AAAA AAAT AAAG AGAT AAAT AAAT
1 AAAT AAAT AAAT AAA-T AAA-T AAA-T AAAT AAAT AAAT AAAT AAAT AAAT
* * *
136459 AATGT AAAT AAA- ATAT AATAT AAAAT ATAA- AATT AAAT AAATT AAAT
1 AA-AT AAAT AAAT AAAT AA-AT -AAAT A-AAT AAAT AAAT AAA-T AAAT
* * *
136506 ATAT GAAAGT -AAT -AAT AAGAAT AACAT ATAC ACAAT AAAT AAAT AAAT
1 AAAT -AAA-T AAAT AAAT -A-AAT AA-AT AAAT A-AAT AAAT AAAT AAAT
136554 AAA
1 AAA
136557 GCGATGAGAA
Statistics
Matches: 109, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
3 7 0.06
4 64 0.59
5 32 0.29
6 6 0.06
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:137257 original size:2 final size:2
Alignment explanation
Indices: 137159--137237 Score: 133
Period size: 2 Copynumber: 39.5 Consensus size: 2
137149 GTAATAAATA
*
137159 AT AT AT AT AT AT AT AT CAT AT AT AT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
137202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137238 ATGTTTAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.01
2 70 0.96
3 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137418 original size:3 final size:3
Alignment explanation
Indices: 137410--137665 Score: 105
Period size: 3 Copynumber: 84.7 Consensus size: 3
137400 GTGTAGATAT
*
137410 TAA TAA TAA TAA -AA TAA -ATA TTA TAA TAA TAA TAA TAA -AGA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA
* * *
137454 -AA GATC TAA -AA -AA GTAAA TAA -AA -ACA TAA TAA T-A TAA TAG TAA
1 TAA TA-A TAA TAA TAA -T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* **
137497 TAAA TAAA TAA -AA TAA TCGAA -AA TAA TAA AAA TAA TAA CGA TAA TAA
1 T-AA T-AA TAA TAA TAA T--AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
137544 TAA -AA -AA GTGA -AA TATA TATA TAA TAA TATA TAA TAG TAA -AA AAA
1 TAA TAA TAA -TAA TAA TA-A TA-A TAA TAA TA-A TAA TAA TAA TAA TAA
** *
137589 TAA TAA CGA TAA TAA TAA TAA AAA TAA -AA TATA TAAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TA-A TAA
137636 TAA TAA TAA -AA TATA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TA
137666 CAAAATATAA
Statistics
Matches: 198, Mismatches: 24, Indels: 62
0.70 0.08 0.22
Matches are distributed among these distances:
2 30 0.15
3 128 0.65
4 35 0.18
5 5 0.03
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:137519 original size:10 final size:9
Alignment explanation
Indices: 137469--137660 Score: 65
Period size: 10 Copynumber: 19.8 Consensus size: 9
137459 CTAAAAAAGT
137469 AAATAA-AA
1 AAATAATAA
*
137477 ACATAATAA
1 AAATAATAA
*
137486 TATAATAGTAA
1 -A-AATAATAA
137497 TAAATAA-ATA
1 -AAATAATA-A
*
137507 AAATAATCGA
1 AAATAAT-AA
137517 AAATAATAA
1 AAATAATAA
137526 AAATAATAA
1 AAATAATAA
137535 CGATAATAATAA
1 --A-AATAATAA
*
137547 AAA-AGTGAA
1 AAATAAT-AA
137556 ATATATATATAA
1 A-A-ATA-ATAA
*
137568 TAATATATAA
1 AAATA-ATAA
* *
137578 TAGTAA-AA
1 AAATAATAA
137586 AAATAATAA
1 AAATAATAA
137595 CGATAATAATAA
1 --A-AATAATAA
137607 TAAA-AAT-A
1 -AAATAATAA
137615 AAATATATAA
1 AAATA-ATAA
137625 ATAATATATAA
1 A-AATA-ATAA
*
137636 TAATAAT-A
1 AAATAATAA
137644 AAATATATAA
1 AAATA-ATAA
*
137654 TAATAAT
1 AAATAAT
137661 TAATACAAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 47
0.70 0.08 0.23
Matches are distributed among these distances:
7 3 0.02
8 20 0.14
9 38 0.26
10 41 0.28
11 22 0.15
12 19 0.13
13 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (9 bp):
AAATAATAA
Found at i:137540 original size:87 final size:81
Alignment explanation
Indices: 137432--137616 Score: 194
Period size: 87 Copynumber: 2.2 Consensus size: 81
137422 AATAAATATT
* *
137432 ATAATAATAATAATAAAGATAAAAGATCTAAAAAAGT-AAATAAAAACATAATAATATAATAGTA
1 ATAATAAAAATAATAAAGATAAAA-A--TAAAAAAGTGAAATAAAAACATAATAATAT-ATAATA
137496 ATAAATAAATAAAATAATCGAAA
62 ATAAA-AAA-AAAATAA-CGAAA
* * * * * *
137519 ATAATAAAAATAATAACGATAATAATAAAAAAGTGAAATATATATATAATAATATATAATAGTAA
1 ATAATAAAAATAATAAAGATAAAAATAAAAAAGTGAAATAAAAACATAATAATATATAATAATAA
* *
137584 AAAAATAATAACGATA
66 AAAAAAAATAACGAAA
137600 ATAATAATAAA-AATAAA
1 ATAATAA-AAATAATAAA
137617 ATATATAAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
81 16 0.19
82 9 0.11
83 3 0.04
84 18 0.21
85 17 0.20
86 1 0.01
87 21 0.25
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (81 bp):
ATAATAAAAATAATAAAGATAAAAATAAAAAAGTGAAATAAAAACATAATAATATATAATAATAA
AAAAAAAATAACGAAA
Found at i:137543 original size:58 final size:59
Alignment explanation
Indices: 137469--137656 Score: 181
Period size: 60 Copynumber: 3.2 Consensus size: 59
137459 CTAAAAAAGT
* * *
137469 AAATAAAAAC-ATAATAATATAATAGT-AATAAATAAATAA-AATA-ATCGAA-AATAATAA
1 AAATAATAACGATAATAATAAAAAAGTAAATAAATAAATAATAATATAT--AATAATAA-AA
* * *
137526 AAATAATAACGATAATAATAAAAAAGTGAAATATATATATAATAATATATAATAGTAAAA
1 AAATAATAACGATAATAATAAAAAAGT-AAATAAATAAATAATAATATATAATAATAAAA
* *
137586 AAATAATAACGATAATAATAATAAAAATAAAATATATAAATAAT-ATATAATAATAATAAAA
1 AAATAATAACGATAATAATAA-AAAAGT-AAATAAATAAATAATAATAT-ATAATAATAAAA
*
137647 TATATAATAA
1 -AAATAATAA
137657 TAATTAATAC
Statistics
Matches: 111, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
57 9 0.08
58 14 0.13
60 40 0.36
61 38 0.34
62 10 0.09
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (59 bp):
AAATAATAACGATAATAATAAAAAAGTAAATAAATAAATAATAATATATAATAATAAAA
Found at i:137603 original size:60 final size:58
Alignment explanation
Indices: 137518--137653 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 58
137508 AATAATCGAA
*
137518 AATAATAAAAATAATAACGATAATAATAA-AAAAGTGAAATATATATATAATAATATATAAT
1 AATAA-AAAAATAATAACGATAATAATAATAAAAAT-AAA-ATATATA-AATAATATATAAT
*
137579 AGTAAAAAAATAATAACGATAATAATAATAAAAATAAAATATATAAATAATATATAAT
1 AATAAAAAAATAATAACGATAATAATAATAAAAATAAAATATATAAATAATATATAAT
*
137637 AATAATAAAATATATAA
1 AATAAAAAAATA-ATAA
137654 TAATAATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
58 23 0.33
59 11 0.16
60 26 0.38
61 9 0.13
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (58 bp):
AATAAAAAAATAATAACGATAATAATAATAAAAATAAAATATATAAATAATATATAAT
Found at i:137665 original size:60 final size:61
Alignment explanation
Indices: 137518--137653 Score: 192
Period size: 58 Copynumber: 2.3 Consensus size: 61
137508 AATAATCGAA
*
137518 AATAATAAAA-ATAATAACGATAATAATAAAAAAGTGAAATATATATATAATAATATATAAT
1 AATAATAAAATAT-ATAACGATAATAATAAAAAAATGAAATATATATATAATAATATATAAT
* *
137579 AGTAAAAAAATA-ATAACGATAATAATAATAAAAAT-AAA-ATATATA-AATAATATATAAT
1 AATAATAAAATATATAACGATAATAATAA-AAAAATGAAATATATATATAATAATATATAAT
137637 AATAATAAAATATATAA
1 AATAATAAAATATATAA
137654 TAATAATTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
58 23 0.34
59 11 0.16
60 19 0.28
61 13 0.19
62 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (61 bp):
AATAATAAAATATATAACGATAATAATAAAAAAATGAAATATATATATAATAATATATAAT
Found at i:145150 original size:19 final size:19
Alignment explanation
Indices: 145122--145158 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
145112 TTTGTACAAC
*
145122 AAATAAATAATGAATATAT
1 AAATAAATAATCAATATAT
*
145141 AAATATATAATCAATATA
1 AAATAAATAATCAATATA
145159 ATATATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAAATAATCAATATAT
Found at i:146864 original size:13 final size:14
Alignment explanation
Indices: 146845--146878 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
146835 TTGAACCCAC
146845 CTTTTTTTTTCTCT
1 CTTTTTTTTTCTCT
*
146859 -TTTTTTTTTTTCT
1 CTTTTTTTTTCTCT
146872 CTTTTTT
1 CTTTTTT
146879 CCTTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTTTTTCTCT
Found at i:146866 original size:15 final size:15
Alignment explanation
Indices: 146846--146878 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
146836 TGAACCCACC
146846 TTTTTTTTTCTCTTT
1 TTTTTTTTTCTCTTT
146861 TTTTTTTTTCTCTTT
1 TTTTTTTTTCTCTTT
146876 TTT
1 TTT
146879 CCTTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTCTCTTT
Found at i:146884 original size:15 final size:15
Alignment explanation
Indices: 146851--146884 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
146841 CCACCTTTTT
**
146851 TTTTCTCTTTTTTTT
1 TTTTCTCTTTTTTCC
146866 TTTTCTCTTTTTTCC
1 TTTTCTCTTTTTTCC
146881 TTTT
1 TTTT
146885 TTCAATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTCTTTTTTCC
Found at i:146944 original size:16 final size:16
Alignment explanation
Indices: 146923--146953 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
146913 CACCCTAAAC
*
146923 GTTTTTTCTCTTTTTT
1 GTTTTTTCCCTTTTTT
146939 GTTTTTTCCCTTTTT
1 GTTTTTTCCCTTTTT
146954 CTTTCTTCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (16 bp):
GTTTTTTCCCTTTTTT
Found at i:157304 original size:14 final size:14
Alignment explanation
Indices: 157287--157313 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
157277 AATGAACGAA
157287 TAAAATAAAAAGAG
1 TAAAATAAAAAGAG
157301 TAAAATAAAAAGA
1 TAAAATAAAAAGA
157314 AGAAAGAAAG
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:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (14 bp):
TAAAATAAAAAGAG
Found at i:157393 original size:4 final size:4
Alignment explanation
Indices: 157386--157526 Score: 81
Period size: 4 Copynumber: 33.0 Consensus size: 4
157376 AGAAACAGAT
* * * * *
157386 TAAA TAAA TAAA TAAA GTAAA CAAA AAAA TAAA GAGA TAAA TAAA TAATG
1 TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A
*
157436 TAAA TAAAA TATAA T-AA TAAA TTAAA TAAA TTAAA TATA TGAAA -ATAA
1 TAAA T-AAA TA-AA TAAA TAAA -TAAA TAAA -TAAA TAAA T-AAA TA-AA
* *
157484 T-AA TAAGAA TAACA TATA CACAA TAAA TAAA TAAA TAAA TAAA
1 TAAA T-A-AA TAA-A TAAA TA-AA TAAA TAAA TAAA TAAA TAAA
157527 AGCGAGGAGA
Statistics
Matches: 107, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
3 7 0.07
4 67 0.63
5 30 0.28
6 3 0.03
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:157406 original size:17 final size:17
Alignment explanation
Indices: 157339--157466 Score: 84
Period size: 17 Copynumber: 7.4 Consensus size: 17
157329 AAAAGTAAAG
157339 ATAAA-AAAGGTAAATAAA
1 ATAAATAAA-GTAAAT-AA
*
157357 ATAAACAACATGTAAATAA
1 ATAAATAA-A-GTAAATAA
* * * *
157376 AGAAACAGATTAAATAA
1 ATAAATAAAGTAAATAA
*
157393 ATAAATAAAGTAAACAA
1 ATAAATAAAGTAAATAA
* *
157410 AAAAATAAAG-AGATAA
1 ATAAATAAAGTAAATAA
*
157426 ATAAATAATGTAAATAAA
1 ATAAATAAAGTAAAT-AA
157444 ATATAAT-AA-TAAATTAA
1 ATA-AATAAAGTAAA-TAA
157461 ATAAAT
1 ATAAAT
157467 TAAATATATG
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
16 15 0.17
17 40 0.45
18 13 0.15
19 13 0.15
20 7 0.08
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (17 bp):
ATAAATAAAGTAAATAA
Found at i:158405 original size:21 final size:21
Alignment explanation
Indices: 158379--158422 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
158369 ATTTCTGGGA
* *
158379 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
158400 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
158421 AA
1 AA
158423 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:160128 original size:23 final size:23
Alignment explanation
Indices: 160101--160160 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
160091 ATTATTATAT
160101 GGCACTATGGTGCAATTCTACGC
1 GGCACTATGGTGCAATTCTACGC
* *
160124 GGCACTACGGTGCAATTCTACGT
1 GGCACTATGGTGCAATTCTACGC
160147 GGCACT-TCGGTGCA
1 GGCACTAT-GGTGCA
160161 TTTATATGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTATGGTGCAATTCTACGC
Found at i:165169 original size:23 final size:23
Alignment explanation
Indices: 165143--165202 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
165133 ATTATTATAT
*
165143 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
165166 GGCACTACGATGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
165189 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
165203 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:166415 original size:27 final size:27
Alignment explanation
Indices: 166383--166437 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
166373 GACTACCAAA
166383 AATAATAGTAATAAATAATATATATATAAT
1 AATAAT-GT-ATAAA-AATATATATATAAT
*
166413 AATAATGTTTAAAAATATATATATA
1 AATAATGTATAAAAATATATATATA
166438 CCCCATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 4 0.17
29 2 0.08
30 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AATAATGTATAAAAATATATATATAAT
Found at i:166602 original size:3 final size:3
Alignment explanation
Indices: 166596--166850 Score: 67
Period size: 3 Copynumber: 84.3 Consensus size: 3
166586 TGTAGATAGT
* *
166596 ATA ATA ATA ATA A-A ATA AT- ATA TTT ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
166641 GACTA A-A GAT- CTA A-A A-A AGTAA ATA A-A AAA CATA ATA AT- ATA
1 -A-TA ATA -ATA ATA ATA ATA A-T-A ATA ATA ATA -ATA ATA ATA ATA
* * * **
166683 ATA GTA ATAA ATAA ATA A-A ATA ACCGA A-A ATA ATA AAA ATA ATA ACG
1 ATA ATA AT-A AT-A ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA
*
166730 ATA ATA ATA A-A A-A AGTG A-A ATA TATA TATA ATA ATA A-A ATA TATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA -ATA -ATA ATA ATA ATA ATA -ATA
* * * ** * *
166775 ATA GTA AAA AAA ATA ACG ATA ATA ATA A-A AAA ATG A-A ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
166819 TATA ATA TATA ATA ATA ATA ATTA ATA CATA A
1 -ATA ATA -ATA ATA ATA ATA A-TA ATA -ATA A
166851 ATGTAAGGTA
Statistics
Matches: 192, Mismatches: 29, Indels: 62
0.68 0.10 0.22
Matches are distributed among these distances:
2 29 0.15
3 120 0.62
4 38 0.20
5 5 0.03
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:166737 original size:21 final size:20
Alignment explanation
Indices: 166687--166808 Score: 86
Period size: 21 Copynumber: 5.8 Consensus size: 20
166677 AATATAATAG
166687 TAATAAATAAATAAAATAACCGA
1 TAAT-AATAAA-AAAATAA-CGA
*
166710 AAATAATAAAAATAATAACGA
1 TAATAATAAAAA-AATAACGA
* **
166731 TAATAATAAAAAAGTGAAATATA
1 TAATAATAAAAAAAT--AA-CGA
* *
166754 TATATAATAATAAAAT-A-TA
1 TA-ATAATAAAAAAATAACGA
*
166773 TAATAGTAAAAAAAATAACGA
1 TAATAAT-AAAAAAATAACGA
166794 TAATAATAAAAAAAT
1 TAATAATAAAAAAAT
166809 GAAATATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
18 4 0.05
19 11 0.14
20 11 0.14
21 24 0.30
22 13 0.16
23 6 0.08
24 11 0.14
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (20 bp):
TAATAATAAAAAAATAACGA
Found at i:166790 original size:63 final size:64
Alignment explanation
Indices: 166711--166845 Score: 211
Period size: 63 Copynumber: 2.1 Consensus size: 64
166701 AATAACCGAA
* *
166711 AATAATAAAAATAATAACGATAATAATAAAAAAGTGAAATATATATATAATA-ATAA-AATATAT
1 AATAATAAAAAAAATAACGATAATAATAAAAAAATGAAATATATATATAATATATAATAATA-AT
*
166774 AATAGTAAAAAAAATAACGATAATAATAAAAAAATGAAATATATATATAATATATAATAATAAT
1 AATAATAAAAAAAATAACGATAATAATAAAAAAATGAAATATATATATAATATATAATAATAAT
166838 AATTAATA
1 AA-TAATA
166846 CATAAATGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
63 49 0.75
64 8 0.12
65 8 0.12
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (64 bp):
AATAATAAAAAAAATAACGATAATAATAAAAAAATGAAATATATATATAATATATAATAATAAT
Found at i:166823 original size:21 final size:21
Alignment explanation
Indices: 166736--166823 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 21
166726 AACGATAATA
*
166736 ATAAAAAAGTGAAATATATAT
1 ATAAAAAAATGAAATATATAT
* *
166757 AT--AATAATAAAATATATAAT
1 ATAAAAAAATGAAATATAT-AT
166777 AGTAAAAAAAAT-AACGATA-ATA-
1 A-T-AAAAAAATGAA--ATATATAT
166799 ATAAAAAAATGAAATATATAT
1 ATAAAAAAATGAAATATATAT
166820 ATAA
1 ATAA
166824 TATATAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
19 15 0.28
20 14 0.26
21 10 0.19
22 1 0.02
23 3 0.06
24 7 0.13
25 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (21 bp):
ATAAAAAAATGAAATATATAT
Found at i:167843 original size:19 final size:19
Alignment explanation
Indices: 167819--167857 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
167809 AATCTATACA
*
167819 ATAAATAAATAATGAATAT
1 ATAAATAAATAATCAATAT
*
167838 ATAAATATATAATCAATAT
1 ATAAATAAATAATCAATAT
167857 A
1 A
167858 ATATATGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATAAATAATCAATAT
Found at i:175023 original size:21 final size:21
Alignment explanation
Indices: 174983--175023 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
174973 TCTGGGCTGA
* *
174983 GGGAATCGGTACCCATTCAAG
1 GGGAATCGATACCCACTCAAG
*
175004 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
175024 CGAATATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAG
Found at i:175074 original size:19 final size:19
Alignment explanation
Indices: 175050--175086 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
175040 GAATGCTAGA
*
175050 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
175069 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
175087 TACAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:183805 original size:33 final size:32
Alignment explanation
Indices: 183761--183855 Score: 127
Period size: 33 Copynumber: 2.9 Consensus size: 32
183751 GAATGAGTTG
* *
183761 TGTTTGTTGGATTTGTTCAAAATGTATGGGCTA
1 TGTTTGCTGGATTT-TTCAGAATGTATGGGCTA
*
183794 TGTTTGCTGGATTTTTTCAGAATCTATGGGCTA
1 TGTTTGCTGGA-TTTTTCAGAATGTATGGGCTA
*
183827 TGTGTGCTGGATGTTTTCAGAATGTATGG
1 TGTTTGCTGGAT-TTTTCAGAATGTATGG
183856 ATGTAGGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.02
33 51 0.93
34 3 0.05
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.44
Consensus pattern (32 bp):
TGTTTGCTGGATTTTTCAGAATGTATGGGCTA
Found at i:186648 original size:37 final size:38
Alignment explanation
Indices: 186606--186694 Score: 144
Period size: 38 Copynumber: 2.3 Consensus size: 38
186596 TTTATTTTGT
*
186606 TCGGGTCGGGTTTTTT-AAGTGTGATATTCGGGTTGAG
1 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
*
186643 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
186681 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
186695 AGTGTAACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 16 0.33
38 24 0.50
39 8 0.17
ACGTcount: A:0.11, C:0.10, G:0.39, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGAG
Found at i:187588 original size:31 final size:31
Alignment explanation
Indices: 187550--187614 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
187540 GAATCTCAAC
*
187550 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
187581 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
187612 AAC
1 AAC
187615 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:189887 original size:44 final size:44
Alignment explanation
Indices: 189761--189930 Score: 297
Period size: 44 Copynumber: 3.9 Consensus size: 44
189751 TCTGACAAGT
* *
189761 CTGCGAACCAAACAGAATATGGAATTGGATTCCAATCCCATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTTC
*
189805 CTACCAACCAAACAGAA-ATGGAATTGGATTCCAATTCCATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTTC
*
189848 CTGCCAACCAAACAGAATAGGGAATTGGATTCCAATTCCATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTTC
189892 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCC
189931 TTACAGATTC
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
43 41 0.34
44 78 0.66
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (44 bp):
CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTTC
Found at i:189979 original size:18 final size:18
Alignment explanation
Indices: 189919--190000 Score: 114
Period size: 18 Copynumber: 4.7 Consensus size: 18
189909 TATGGAATTG
189919 GATTCCAATTCCTT-ACA
1 GATTCCAATTCCTTCACA
*
189936 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
* *
189953 GATTTCAATTCCTTCAGA
1 GATTCCAATTCCTTCACA
*
189971 GATTACAATTCCTTCACA
1 GATTCCAATTCCTTCACA
189989 GATTCCAATTCC
1 GATTCCAATTCC
190001 CTCATAAACA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
16 3 0.05
17 22 0.39
18 32 0.56
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:190886 original size:29 final size:29
Alignment explanation
Indices: 190819--190925 Score: 146
Period size: 29 Copynumber: 3.7 Consensus size: 29
190809 ACACAATTAT
190819 CACCCTTTTAAGAAATATTTACG-AA-TAA
1 CACCCTTTTAA-AAATATTTACGAAACTAA
190847 CACCCTTTTAAAAATATTTACGAAACTAA
1 CACCCTTTTAAAAATATTTACGAAACTAA
** *
190876 CACTATTTTAAAAATATTTACGAAACTGA
1 CACCCTTTTAAAAATATTTACGAAACTAA
* *
190905 CACCCTTTTAGAAATAATTAC
1 CACCCTTTTAAAAATATTTAC
190926 AAAATTAGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
27 11 0.16
28 13 0.19
29 46 0.66
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACGAAACTAA
Found at i:190937 original size:29 final size:29
Alignment explanation
Indices: 190819--190938 Score: 127
Period size: 29 Copynumber: 4.2 Consensus size: 29
190809 ACACAATTAT
*
190819 CACCCTTTTAAGAAATATTTAC-GAA-TAA
1 CACCCTTTTAA-AAATATTTACAAAACTAA
*
190847 CACCCTTTTAAAAATATTTACGAAACTAA
1 CACCCTTTTAAAAATATTTACAAAACTAA
** * *
190876 CACTATTTTAAAAATATTTACGAAACTGA
1 CACCCTTTTAAAAATATTTACAAAACTAA
* * * *
190905 CACCCTTTTAGAAATAATTACAAAATTAG
1 CACCCTTTTAAAAATATTTACAAAACTAA
190934 CACCC
1 CACCC
190939 GATTAACGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
27 10 0.13
28 13 0.17
29 55 0.71
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACAAAACTAA
Found at i:191019 original size:19 final size:19
Alignment explanation
Indices: 190969--191020 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
190959 GGTAGGGTCG
* *
190969 GGTCGGACCGGTTCAGACC
1 GGTCAGACCGGTTTAGACC
* * * *
190988 AGTCAAACTGGTTTGGACC
1 GGTCAGACCGGTTTAGACC
191007 GGTCAGACCGGTTT
1 GGTCAGACCGGTTT
191021 CAAGCTGGCC
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (19 bp):
GGTCAGACCGGTTTAGACC
Found at i:194296 original size:430 final size:430
Alignment explanation
Indices: 193496--194357 Score: 1697
Period size: 430 Copynumber: 2.0 Consensus size: 430
193486 GTTCAACAAT
193496 GGTAACTTTACATGTGCACCATTCTATTCATTATTTATTTTCTTTTCTTATTTTAAAGTTATAAC
1 GGTAACTTTACATGTGCACCATTCTATTCATTATTTATTTTCTTTTCTTATTTTAAAGTTATAAC
193561 TAGTTTACTAATGCCTTTGGTAACTTTACCTTTTTCCTTGGGATTTATAAAAATTTACAGGAATT
66 TAGTTTACTAATGCCTTTGGTAACTTTACCTTTTTCCTTGGGATTTATAAAAATTTACAGGAATT
*
193626 AGTCATAATGATGAAGTTGATACATCCAGTGTTTTTCCTTTTGTGCAAGTATGTCTCTGCAATTC
131 AGTCATAATGATGAAGTTGATACATCCAGTGTTTTGCCTTTTGTGCAAGTATGTCTCTGCAATTC
193691 TCCCTTTTGCCAGGGTTGGAATTTTAGGGTTTTTAGTAGCTCAATTTTTTTTCTTTTTCTCATTC
196 TCCCTTTTGCCAGGGTTGGAATTTTAGGGTTTTTAGTAGCTCAATTTTTTTTCTTTTTCTCATTC
193756 CTCCTTTTTGAATTAAATTATGTATTTTGAAAGCTTTCCAATGAGAGCTTTAATTAGATTAGGAG
261 CTCCTTTTTGAATTAAATTATGTATTTTGAAAGCTTTCCAATGAGAGCTTTAATTAGATTAGGAG
193821 AAAAATAAGTGGTTGCTTGTGTATTTTACTTTCTTTCTTTATAATGTTTTTTGTTTTGTTTTAAT
326 AAAAATAAGTGGTTGCTTGTGTATTTTACTTTCTTTCTTTATAATGTTTTTTGTTTTGTTTTAAT
193886 GATATACTTTATAATGTGTTGGTTGCAGGAAGCCCTTGAC
391 GATATACTTTATAATGTGTTGGTTGCAGGAAGCCCTTGAC
193926 GGTAACTTTACATGTGCACCATTCTATTCATTATTTATTTTCTTTTCTTATTTTAAAGTTATAAC
1 GGTAACTTTACATGTGCACCATTCTATTCATTATTTATTTTCTTTTCTTATTTTAAAGTTATAAC
193991 TAGTTTACTAATGCCTTTGGTAACTTTACCTTTTTCCTTGGGATTTATAAAAATTTACAGGAATT
66 TAGTTTACTAATGCCTTTGGTAACTTTACCTTTTTCCTTGGGATTTATAAAAATTTACAGGAATT
*
194056 AGTCATAATGATGAAGTTGATACATTCAGTGTTTTGCCTTTTGTGCAAGTATGTCTCTGCAATTC
131 AGTCATAATGATGAAGTTGATACATCCAGTGTTTTGCCTTTTGTGCAAGTATGTCTCTGCAATTC
*
194121 TCCCTTTTGCCAGGGTTGGAATTTTAGGGTTTTTAGTAGCTCAATTTTTTTTCTTTTTCTCATTG
196 TCCCTTTTGCCAGGGTTGGAATTTTAGGGTTTTTAGTAGCTCAATTTTTTTTCTTTTTCTCATTC
194186 CTCCTTTTTGAATTAAATTATGTATTTTGAAAGCTTTCCAATGAGAGCTTTAATTAGATTAGGAG
261 CTCCTTTTTGAATTAAATTATGTATTTTGAAAGCTTTCCAATGAGAGCTTTAATTAGATTAGGAG
194251 AAAAATAAGTGGTTGCTTGTGTATTTTACTTTCTTTCTTTATAATGTTTTTTGTTTTGTTTTAAT
326 AAAAATAAGTGGTTGCTTGTGTATTTTACTTTCTTTCTTTATAATGTTTTTTGTTTTGTTTTAAT
194316 GATATACTTTATAATGTGTTGGTTGCAGGAAGCCCTTGAC
391 GATATACTTTATAATGTGTTGGTTGCAGGAAGCCCTTGAC
194356 GG
1 GG
194358 CATTGAGTTT
Statistics
Matches: 429, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
430 429 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (430 bp):
GGTAACTTTACATGTGCACCATTCTATTCATTATTTATTTTCTTTTCTTATTTTAAAGTTATAAC
TAGTTTACTAATGCCTTTGGTAACTTTACCTTTTTCCTTGGGATTTATAAAAATTTACAGGAATT
AGTCATAATGATGAAGTTGATACATCCAGTGTTTTGCCTTTTGTGCAAGTATGTCTCTGCAATTC
TCCCTTTTGCCAGGGTTGGAATTTTAGGGTTTTTAGTAGCTCAATTTTTTTTCTTTTTCTCATTC
CTCCTTTTTGAATTAAATTATGTATTTTGAAAGCTTTCCAATGAGAGCTTTAATTAGATTAGGAG
AAAAATAAGTGGTTGCTTGTGTATTTTACTTTCTTTCTTTATAATGTTTTTTGTTTTGTTTTAAT
GATATACTTTATAATGTGTTGGTTGCAGGAAGCCCTTGAC
Found at i:199258 original size:169 final size:167
Alignment explanation
Indices: 199013--199327 Score: 531
Period size: 169 Copynumber: 1.9 Consensus size: 167
199003 AAATTAAATG
* *
199013 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTAGAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
*
199078 ATAAATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTATTGAATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAATT
199143 GAGTTTTAAATGGTTTATATATAATATATTTAATATT
131 GAGTTTTAAATGGTTTATATATAATATATTTAATATT
*
199180 TTTTTAATTAAAAAAAATAGTTTAGAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
1 TTTTTAATT-AAAAAAA-AGTTTAGAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
* * * *
199245 ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATATTAAATTATTAA
64 AGATAAATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAA
*
199310 TTGGGTTTTAAATGGTTT
129 TTGAGTTTTAAATGGTTT
199328 GGGCTGAGCC
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
167 9 0.07
168 6 0.04
169 122 0.89
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (167 bp):
TTTTTAATTAAAAAAAAGTTTAGAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTATTGAATATTAAATTATTAATT
GAGTTTTAAATGGTTTATATATAATATATTTAATATT
Found at i:210643 original size:29 final size:28
Alignment explanation
Indices: 210587--210640 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
210577 ATGCAGGAGG
* * **
210587 TGTCACATTCAAAATTCGGGGCAGAAGA
1 TGTCACATTCAAAAATCAGAACAGAAGA
210615 TGTCACATTCAAAAATCAGAACAGAA
1 TGTCACATTCAAAAATCAGAACAGAA
210641 AGAAGACCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (28 bp):
TGTCACATTCAAAAATCAGAACAGAAGA
Found at i:223085 original size:27 final size:27
Alignment explanation
Indices: 223033--223085 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
223023 ATATGTTATA
**
223033 TTGAATTCTAACTTTTTTTTTGATAAG
1 TTGAATTCTAACTTTTTTCCTGATAAG
223060 TTGAATTCTAACTTTTTTACCT-ATAA
1 TTGAATTCTAACTTTTTT-CCTGATAA
223086 TATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (27 bp):
TTGAATTCTAACTTTTTTCCTGATAAG
Found at i:223680 original size:22 final size:23
Alignment explanation
Indices: 223648--223690 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
223638 TGTCTAAAAT
* *
223648 AATAAGTTTTTTAATTTTAATGA
1 AATAAGTTTTTAAATTATAATGA
223671 AATAA-TTTTTAAATTATAAT
1 AATAAGTTTTTAAATTATAAT
223691 TTTTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
AATAAGTTTTTAAATTATAATGA
Found at i:230807 original size:21 final size:21
Alignment explanation
Indices: 230771--230831 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
230761 CTTCGGGACG
**
230771 TATATGTAATCATTTGGAACA
1 TATATGTGGTCATTTGGAACA
*
230792 TATATGTGGTCCTTTGAGACACA
1 TATATGTGGTCATTTG-GA-ACA
230815 TAT-T-TGGTCATTTGGAA
1 TATATGTGGTCATTTGGAA
230832 TATGTATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 22 0.65
22 3 0.09
23 6 0.18
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (21 bp):
TATATGTGGTCATTTGGAACA
Found at i:230914 original size:23 final size:23
Alignment explanation
Indices: 230887--230947 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
230877 TTTTATATGG
230887 CACTTCGGTGCATTTCTACGCGA
1 CACTTCGGTGCATTTCTACGCGA
* * *
230910 CACTTCGGTACATTTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGA
230933 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
230948 TATACGAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.34
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGA
Found at i:233988 original size:21 final size:21
Alignment explanation
Indices: 233962--234018 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
233952 CATATGAAAT
233962 TTGTCCCGAAAGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
*
233983 TTGTCCCGAATGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
*
234004 TTGTCCCGAAGGACC
1 TTGTCCCGAAAGACC
234019 TATGAAACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAAGACCACTGTA
Found at i:246231 original size:23 final size:23
Alignment explanation
Indices: 246179--246242 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
246169 ACATTTTATA
*
246179 TGGCACTTCGGTACATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*** *
246202 CAACACTTTGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
246225 TGGCACTTCGTTGCATTT
1 TGGCACTTCGGTGCATTT
246243 AATACGAGCT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:247247 original size:22 final size:22
Alignment explanation
Indices: 247219--247260 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
247209 TTGTAATAAT
247219 ATTAAAAAAAATAATTATTTTA
1 ATTAAAAAAAATAATTATTTTA
* *
247241 ATTAAAAAATATACTTATTT
1 ATTAAAAAAAATAATTATTT
247261 ATATATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAAAAAAATAATTATTTTA
Found at i:250387 original size:2 final size:2
Alignment explanation
Indices: 250380--250430 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
250370 TAATAATCAA
250380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250422 AT AT AT AT A
1 AT AT AT AT A
250431 CACACACACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:268523 original size:20 final size:21
Alignment explanation
Indices: 268478--268531 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
268468 ACATTCATGA
268478 GGTATCGATA-CATGAAGAAC
1 GGTATCGATACCATGAAGAAC
** *
268498 AATATCGATACCAT-AAGGAC
1 GGTATCGATACCATGAAGAAC
268518 GGTATCGATACCAT
1 GGTATCGATACCAT
268532 CTTTGAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (21 bp):
GGTATCGATACCATGAAGAAC
Found at i:270616 original size:13 final size:13
Alignment explanation
Indices: 270600--270635 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
270590 GCCCCGATTA
*
270600 CCCGATTATCCGC
1 CCCGATTACCCGC
270613 CCCGATTACCCGC
1 CCCGATTACCCGC
270626 CCCGA-TACCC
1 CCCGATTACCC
270636 AACCCGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.17, C:0.53, G:0.14, T:0.17
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:270713 original size:19 final size:19
Alignment explanation
Indices: 270689--270728 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
270679 AATAAATTTA
270689 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
270708 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
270727 AT
1 AT
270729 ATACCTGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:270746 original size:12 final size:12
Alignment explanation
Indices: 270729--270757 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
270719 ATATATATAT
270729 ATACCTGGCCCA
1 ATACCTGGCCCA
270741 ATACCTGGCCCA
1 ATACCTGGCCCA
270753 ATACC
1 ATACC
270758 CGTTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.41, G:0.14, T:0.17
Consensus pattern (12 bp):
ATACCTGGCCCA
Found at i:274241 original size:27 final size:27
Alignment explanation
Indices: 274211--274265 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
274201 TCATCTGTTA
274211 TCTGTTAGACAAACAGTAATGACTTGT
1 TCTGTTAGACAAACAGTAATGACTTGT
274238 TCTGTTAGACAAACAGTAATGACTTGT
1 TCTGTTAGACAAACAGTAATGACTTGT
274265 T
1 T
274266 TGCTACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (27 bp):
TCTGTTAGACAAACAGTAATGACTTGT
Found at i:275173 original size:77 final size:77
Alignment explanation
Indices: 275044--275195 Score: 180
Period size: 77 Copynumber: 2.0 Consensus size: 77
275034 GCTATGAAAT
* * * * *
275044 AGTTATCCTGAAGGAGCTTTAAGTTGATATGAAATAATTAATTTAACCATGTATATTTAGTGGAA
1 AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAATTAATTTAACCATGTATATGTAGTGGAA
275109 AAGTGTTGAAGA
66 AAGTGTTGAAGA
* * * * *
275121 AGTTAACCCGAAGGATCTTTAAATCGATGTGAAAT-ATCTAATTTTACTATGTATGTGTAGTGGA
1 AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAAT-TAATTTAACCATGTATATGTAGTGGA
**
275185 AACTTGTTGAA
65 AAAGTGTTGAA
275196 ACAGGCAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
76 2 0.03
77 60 0.97
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (77 bp):
AGTTAACCCGAAGGAGCTTTAAATCGATATGAAATAATTAATTTAACCATGTATATGTAGTGGAA
AAGTGTTGAAGA
Found at i:277275 original size:24 final size:24
Alignment explanation
Indices: 277231--277277 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
277221 ATAAAGAACC
*
277231 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
277255 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
277278 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Done.