Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007940.1 Hibiscus syriacus cultivar Beakdansim tig00110356_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: 1348078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:95 original size:20 final size:21
Alignment explanation
Indices: 51--102 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
41 ATAGTCAGTA
*
51 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
72 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
92 TCGCATTGCGA
1 TCGCATTGCGA
103 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:13873 original size:23 final size:24
Alignment explanation
Indices: 13847--13894 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
13837 CGAAACTATG
13847 ACCTAAA-TATCGATACTCTTGAA
1 ACCTAAAGTATCGATACTCTTGAA
13870 ACCTAAAGTATCGATACTCTTGAA
1 ACCTAAAGTATCGATACTCTTGAA
13894 A
1 A
13895 GAGTATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (24 bp):
ACCTAAAGTATCGATACTCTTGAA
Found at i:15023 original size:40 final size:40
Alignment explanation
Indices: 14962--15041 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
14952 TTAGGTAAAG
14962 TACATAAATGGTCATTGGACTATAGGATACTATTTTATTA
1 TACATAAATGGTCATTGGACTATAGGATACTATTTTATTA
* * * *
15002 TACATAAATGGTCCTTTGACTATATGATATTATTTTATTA
1 TACATAAATGGTCATTGGACTATAGGATACTATTTTATTA
15042 AGTCCTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (40 bp):
TACATAAATGGTCATTGGACTATAGGATACTATTTTATTA
Found at i:15928 original size:76 final size:76
Alignment explanation
Indices: 15802--15942 Score: 255
Period size: 76 Copynumber: 1.9 Consensus size: 76
15792 TTATGTGAAA
*
15802 CATATTTTTTGATTTTCTCACTTTCGTTGATCAGCCCTAATCCCAACCCAACACAACCAACTGTC
1 CATATTTTTCGATTTTCTCACTTTCGTTGATCAGCCCTAATCCCAACCCAACACAACCAACTGTC
15867 TGTGATCAATG
66 TGTGATCAATG
* *
15878 CATATTTTTCGATTTTCTCACTTTCGTTGTTCAGCCCTAATCCCAACCCAACACAACCAGCTGTC
1 CATATTTTTCGATTTTCTCACTTTCGTTGATCAGCCCTAATCCCAACCCAACACAACCAACTGTC
15943 CGTGGTCTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (76 bp):
CATATTTTTCGATTTTCTCACTTTCGTTGATCAGCCCTAATCCCAACCCAACACAACCAACTGTC
TGTGATCAATG
Found at i:16551 original size:6 final size:6
Alignment explanation
Indices: 16534--16577 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
16524 ATGGCTCAAG
* * *
16534 CAGCAC CGGCAC CCGCAC CCGCAC CAGCAC CAGCAC CAGGCAC C
1 CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CA-GCAC C
16578 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.25, C:0.55, G:0.20, T:0.00
Consensus pattern (6 bp):
CAGCAC
Found at i:27157 original size:60 final size:59
Alignment explanation
Indices: 27057--27217 Score: 189
Period size: 60 Copynumber: 2.7 Consensus size: 59
27047 GATTAATTCG
* ** ** * *
27057 GGGATGAAATTAGGATATTCAAAAGTTTGGGGACCGATTTATAA-AGATGGTCATGGTTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAGAGAT--TCATAGTTTA
* *
27117 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGATTCGTAGTTTC
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAA-GAGATTCATAGTTTA
* *
27177 GTGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
27218 AAATAAAGGT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
60 84 0.95
62 4 0.05
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAGAGATTCATAGTTTA
Found at i:27158 original size:29 final size:29
Alignment explanation
Indices: 27126--27222 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
27116 AGGGATGAAA
27126 TTAGAATATTCAAAAGTTTAAGGACTAAT
1 TTAGAATATTCAAAAGTTTAAGGACTAAT
** * *
27155 TTAGAATGAGATTC-GTAGTTT-CGTGA-TGAAA
1 TTAGAAT---ATTCAAAAGTTTAAG-GACT-AAT
*
27186 TTGGAATATTCAAAAGTTTAAGGACTAAT
1 TTAGAATATTCAAAAGTTTAAGGACTAAT
*
27215 TTAAAATA
1 TTAGAATA
27223 AAGGTTATAG
Statistics
Matches: 49, Mismatches: 11, Indels: 16
0.64 0.14 0.21
Matches are distributed among these distances:
28 4 0.08
29 22 0.45
30 4 0.08
31 15 0.31
32 4 0.08
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (29 bp):
TTAGAATATTCAAAAGTTTAAGGACTAAT
Found at i:29806 original size:149 final size:149
Alignment explanation
Indices: 29568--29870 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
29558 GAAGTGCCGT
*
29568 GTAGAATTGCACCGTAGTGCCATATAATAATGTTCATAAGGACCACATATTATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATC
*
29633 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATAT
66 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATAC
29698 ATATATCCCGAAGGACCGC
131 ATATATCCCGAAGGACCGC
29717 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATC
*
29782 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACATAATATAC
66 ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATAC
29847 ATATATCCCGAAGGACCGC
131 ATATATCCCGAAGGACCGC
29866 GTAGA
1 GTAGA
29871 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (149 bp):
GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATC
ATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATAC
ATATATCCCGAAGGACCGC
Found at i:31327 original size:64 final size:63
Alignment explanation
Indices: 31229--31389 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
31219 TAATGAAGGT
* *
31229 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
31292 GG
62 GC
*
31294 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
31358 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
31390 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:35048 original size:151 final size:151
Alignment explanation
Indices: 34698--35158 Score: 790
Period size: 151 Copynumber: 3.1 Consensus size: 151
34688 CACCAAAGTG
34698 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
*
34763 TATACATATAC---TACTAGGGATCAAGTATTTATCTTTCAAGACTTCACACATGTTCCACATAA
66 -AT-CATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTCCAC---A
*
34825 TATATATATATATATATCCCGAAGGAC
126 GA-ATATATATATATATCCCGAAGGAC
34852 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
*
34917 ATCATATACATATACTAGGGACCAAGTATGTATCTTTCAAGACTTCACACATGTTCCACAGAATA
66 ATCATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTCCACAGAATA
34982 TATATATATATCCCGAAGGAC
131 TATATATATATCCCGAAGGAC
35003 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
1 CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
*
35068 ATCATATACATATACTA-GGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAG-A-A
66 ATCATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTCCACAGAATA
35130 TATATATATATCCCGAAGGAC
131 TATATATATATCCCGAAGGAC
35151 CGCGTAGA
1 CGCGTAGA
35159 CCCTCGACTC
Statistics
Matches: 299, Mismatches: 5, Indels: 12
0.95 0.02 0.04
Matches are distributed among these distances:
148 30 0.10
149 1 0.00
150 41 0.14
151 106 0.35
152 9 0.03
153 2 0.01
154 65 0.22
155 45 0.15
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (151 bp):
CGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGA
ATCATATACATATACTAGGGATCAAGTATGTATCTTTCAAGACTTCACACATGTTCCACAGAATA
TATATATATATCCCGAAGGAC
Found at i:36612 original size:63 final size:63
Alignment explanation
Indices: 36515--36674 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
36505 TAATGAAGGT
* *
36515 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-G
*
36578 G
63 C
*
36579 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
36643 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
36675 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
62 1 0.01
63 30 0.35
64 51 0.59
65 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:37736 original size:76 final size:76
Alignment explanation
Indices: 37646--38274 Score: 1060
Period size: 76 Copynumber: 8.3 Consensus size: 76
37636 TTTAGAAAAG
* * *
37646 ATCATGCACTGAAGGACTTACAGATGACCCGAAGACTTTGAAAACATCAAAAAACTCCCGAAGTC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
37711 TTTTTGGAAAC
66 TTTTTGGAAAC
*
37722 ATCATGCACTGAAGGACTT--A-ATGACCCGAAGACTTTGAAAACATCAAAAAGC-CCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
37783 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
37794 ATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTTGAAAACATCAAAAAGCTCCCGATGG
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCGAAGG
37859 CTTTTTGGAAAC
65 CTTTTTGGAAAC
37871 ATCATGCACTGAAGGACTT--AGATGACCCGAAGGCTTTGAAAACATCAAAAAGC-CCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
37933 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
37944 ATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTTGAAAACATC-AAAAGCTCCCGAAGG
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCGAAGG
38008 CTTTTTGGAAAC
65 CTTTTTGGAAAC
38020 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
38085 TTTTTGGAAAC
66 TTTTTGGAAAC
38096 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
38161 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
38172 ATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTTGAAAACATCAAAAAGCTCCCGAAGG
1 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCGAAGG
38237 CTTTTTGGAAAC
65 CTTTTTGGAAAC
38249 ATCATGCACTGCAA-GACTTACAGATG
1 ATCATGCACTG-AAGGACTTACAGATG
38275 TGGGAAATAG
Statistics
Matches: 526, Mismatches: 15, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
72 38 0.07
73 69 0.13
74 21 0.04
75 54 0.10
76 241 0.46
77 101 0.19
78 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
ATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:38973 original size:22 final size:22
Alignment explanation
Indices: 38948--39003 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
38938 CATAAAGCTT
* *
38948 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
38970 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
38993 TCATCTTTGAA
1 TCATCTTTGAA
39004 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:48653 original size:11 final size:10
Alignment explanation
Indices: 48617--48669 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
48607 ATAGTAAAAC
48617 AATAATTAAA
1 AATAATTAAA
*
48627 GTAATAATTTAA
1 --AATAATTAAA
48639 AATATATTAAA
1 AATA-ATTAAA
*
48650 AATAATAAAA
1 AATAATTAAA
48660 AATAAATTAA
1 AAT-AATTAA
48670 GTTAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.34
11 14 0.40
12 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AATAATTAAA
Found at i:49890 original size:3 final size:3
Alignment explanation
Indices: 49884--49931 Score: 60
Period size: 3 Copynumber: 15.0 Consensus size: 3
49874 AATAATTATT
*
49884 TAA TAA TAA TACA CTAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A -TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
49932 ATTTAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
3 34 0.85
4 4 0.10
5 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:49913 original size:27 final size:25
Alignment explanation
Indices: 49873--49940 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 25
49863 TTTGGGCTTG
49873 TAATAATTATTTAATAATAATACACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
49901 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
49926 TAATAA-ATTTAATAA
1 TAATAATATTTAATAA
49941 AAAAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 9 0.22
25 9 0.22
26 1 0.03
27 15 0.38
28 6 0.15
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:56112 original size:2 final size:2
Alignment explanation
Indices: 56105--56143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56095 CTCATTGCAG
56105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56144 CTGGACATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60626 original size:17 final size:18
Alignment explanation
Indices: 60592--60627 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
60582 AACACGTGTC
60592 ATATTTTAGTAATTTTAA
1 ATATTTTAGTAATTTTAA
*
60610 ATATTTTA-TATTTTTAA
1 ATATTTTAGTAATTTTAA
60627 A
1 A
60628 AAACTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTTTAGTAATTTTAA
Found at i:65112 original size:24 final size:24
Alignment explanation
Indices: 65007--65113 Score: 63
Period size: 24 Copynumber: 4.5 Consensus size: 24
64997 ATATTTTATC
* * *
65007 TGATTTCTTATTTGAATTCTGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
65031 TGACATCTGATATGAAATATGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * *
65055 TG-TTTCTTAACATGGATTCTGTTA
1 TGATTTCTGATC-TGAATTATGTTT
**
65079 TGATAGCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
65103 TGATTTCTGAT
1 TGATTTCTGAT
65114 ATCTCCGTTT
Statistics
Matches: 56, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
23 4 0.07
24 47 0.84
25 5 0.09
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:67050 original size:20 final size:19
Alignment explanation
Indices: 67027--67072 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
67017 GGAAACTGAT
* *
67027 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
67047 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
67066 TTGCGAT
1 TTGCGAT
67073 TTTGTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:67062 original size:19 final size:19
Alignment explanation
Indices: 67038--67074 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
67028 TGCGATACTG
*
67038 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
67057 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
67075 TGTTGGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:72583 original size:8 final size:8
Alignment explanation
Indices: 72570--72639 Score: 131
Period size: 8 Copynumber: 8.8 Consensus size: 8
72560 TAAATCATTG
72570 AACTTTTC
1 AACTTTTC
72578 AACTTTTC
1 AACTTTTC
72586 AACTTTTC
1 AACTTTTC
72594 AACTTTTC
1 AACTTTTC
72602 AACTTTTC
1 AACTTTTC
72610 AACTTTTC
1 AACTTTTC
72618 AACTTTTC
1 AACTTTTC
72626 AACTTTTC
1 AACTTTTC
*
72634 CACTTT
1 AACTTT
72640 AATCACCAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 61 1.00
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (8 bp):
AACTTTTC
Found at i:84254 original size:173 final size:173
Alignment explanation
Indices: 83965--84313 Score: 626
Period size: 173 Copynumber: 2.0 Consensus size: 173
83955 TCAGATTGTT
83965 AAATCTTATTCATTTATGGTCCTCAATATTGCTTGCAATGCCTTATCAGAGAACATTTCTCTTTA
1 AAATCTTATTCATTTATGGTCCTCAATATTGCTTGCAATGCCTTATCAGAGAACATTTCTCTTTA
* * * *
84030 ACTTGCTTGGAAGTAGTGCAGTTGAGCATCTTAAGATAGTTCCCAGGTGGTTTCAGCAATTGAGT
66 ACTTGCTTGGAAGTAGTGCACTTAAGCATCTTAAGATAGTTCCCAGGTGGTTTCAGCAAATAAGT
*
84095 AGTTTATGCAAACTAAAAAACAATTAACATTTGCTTGCCCATA
131 AGTTTATGCAAACCAAAAAACAATTAACATTTGCTTGCCCATA
*
84138 AAATCTTATTCATTTATGGTCCTCAATATTGCTTGCAATGCCTTATCGGAGAACATTTCTCTTTA
1 AAATCTTATTCATTTATGGTCCTCAATATTGCTTGCAATGCCTTATCAGAGAACATTTCTCTTTA
84203 ACTTGCTTGGAAGTAGTGCACTTAAGCATCTTAAGATAGTTCCCAGGTGGTTTCAGCAAATAAGT
66 ACTTGCTTGGAAGTAGTGCACTTAAGCATCTTAAGATAGTTCCCAGGTGGTTTCAGCAAATAAGT
* *
84268 AGTTTATGCAAACCATAAAACAATTAACATTTGCTTGCCCGTA
131 AGTTTATGCAAACCAAAAAACAATTAACATTTGCTTGCCCATA
84311 AAA
1 AAA
84314 CAACCCCCTT
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 168 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (173 bp):
AAATCTTATTCATTTATGGTCCTCAATATTGCTTGCAATGCCTTATCAGAGAACATTTCTCTTTA
ACTTGCTTGGAAGTAGTGCACTTAAGCATCTTAAGATAGTTCCCAGGTGGTTTCAGCAAATAAGT
AGTTTATGCAAACCAAAAAACAATTAACATTTGCTTGCCCATA
Found at i:87919 original size:22 final size:22
Alignment explanation
Indices: 87891--87939 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
87881 CATTTAAAAA
87891 TAATTTTAAAA-ATAAAATAATT
1 TAATTTTAAAATATAAAA-AATT
87913 TAATTTTAAAATATAAAAAATT
1 TAATTTTAAAATATAAAAAATT
*
87935 AAATT
1 TAATT
87940 CATTTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATTTTAAAATATAAAAAATT
Found at i:90568 original size:17 final size:17
Alignment explanation
Indices: 90532--90587 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
90522 AAAACCTACC
* *
90532 TGCTTTAATGAACT-CA
1 TGCTTAAATGAAATGCA
90548 TGCTTAAATGAAATGCA
1 TGCTTAAATGAAATGCA
*
90565 TGCTTAAAT-AAGTAGCA
1 TGCTTAAATGAAAT-GCA
90582 TGCTTA
1 TGCTTA
90588 TTAATTTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.43
17 20 0.57
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (17 bp):
TGCTTAAATGAAATGCA
Found at i:90805 original size:10 final size:10
Alignment explanation
Indices: 90792--90823 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
90782 AAGCTCTAAT
*
90792 AAGCTTCTTG
1 AAGCTTCTCG
90802 AAGCTTCTCG
1 AAGCTTCTCG
90812 AAGCTTCTCG
1 AAGCTTCTCG
90822 AA
1 AA
90824 TGTAAACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (10 bp):
AAGCTTCTCG
Found at i:96023 original size:14 final size:13
Alignment explanation
Indices: 96001--96053 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
95991 TAAGTTAGAG
*
96001 TTTAGGGTTTATAA
1 TTTATGGTTTA-AA
96015 TTTATGGTTTAAA
1 TTTATGGTTTAAA
96028 TGTTATGGGTTTAAGA
1 T-TTAT-GGTTTAA-A
*
96044 TTTAAGGTTT
1 TTTATGGTTT
96054 TAAGTTAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 3 0.09
14 19 0.56
15 10 0.29
16 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (13 bp):
TTTATGGTTTAAA
Found at i:96040 original size:15 final size:14
Alignment explanation
Indices: 96001--96047 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
95991 TAAGTTAGAG
96001 TTTA-GGGTTTATAA
1 TTTATGGGTTTA-AA
96015 TTTAT-GGTTTAAA
1 TTTATGGGTTTAAA
96028 TGTTATGGGTTTAAGA
1 T-TTATGGGTTTAA-A
96044 TTTA
1 TTTA
96048 AGGTTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 14 0.48
15 10 0.34
16 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (14 bp):
TTTATGGGTTTAAA
Found at i:97122 original size:22 final size:22
Alignment explanation
Indices: 97076--97122 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
97066 AGTATGTACA
*
97076 TATGTATTTTATTTTATTGTGT
1 TATGTATTTTATTTTATTATGT
97098 TATGT-TTATTATGTTTATTAT-T
1 TATGTATT-TTAT-TTTATTATGT
97120 TAT
1 TAT
97123 TTTTGTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 2 0.09
22 13 0.59
23 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (22 bp):
TATGTATTTTATTTTATTATGT
Found at i:100813 original size:2 final size:2
Alignment explanation
Indices: 100806--100853 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
100796 AATAGAAGTA
100806 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
100848 AT AT AT
1 AT AT AT
100854 TTATCAGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101831 original size:103 final size:102
Alignment explanation
Indices: 101607--101823 Score: 371
Period size: 103 Copynumber: 2.1 Consensus size: 102
101597 GTCGAGGGTC
101607 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAATGTGTGAAGTCTGGTGAGACACATACT
* * *
101672 TGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAAGAACGA
*
101709 TATATGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAA-ATGTGTGAAGTCTGGTGAGACACATAC
* *
101774 TTGATCCCTAGTATATGTATATGATTCTTAAGGAACGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAAGAACGA
101812 TATGTGGTCCTT
1 TATGTGGTCCTT
101824 ATGGACATTA
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 36 0.34
103 71 0.66
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAAATGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAAGAACGA
Found at i:101866 original size:23 final size:23
Alignment explanation
Indices: 101833--101907 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
101823 TATGGACATT
101833 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* * *
101854 ATTCTATGCGGCACTCCTGTGCA
1 ATTATATGCGGCACTACGGTGCA
* * *
101877 ATTATATGTGGCACTTCGGTGTA
1 ATTATATGCGGCACTACGGTGCA
101900 ATTATATG
1 ATTATATG
101908 AGTTGTGGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
23 38 0.86
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:105009 original size:21 final size:21
Alignment explanation
Indices: 104967--105009 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
104957 TTTCTGGGCT
*
104967 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
104988 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
105009 A
1 A
105010 ACGAACATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:105905 original size:2 final size:2
Alignment explanation
Indices: 105898--105926 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
105888 ATAGAAGTAC
105898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105927 GTTTATCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106805 original size:103 final size:103
Alignment explanation
Indices: 106681--106895 Score: 360
Period size: 103 Copynumber: 2.1 Consensus size: 103
106671 AGTCAGGGTC
*
106681 TATGTGGTCCTTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
106746 TTGATC-CTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTC-TAGCATATGTATATGATTCTTAAGAAATGA
* *
106784 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
106849 TTGATCTCTAGTATATGTATATGATTCTTAAGAAATGA
66 TTGATCTCTAGCATATGTATATGATTCTTAAGAAATGA
106887 TATGTGGTC
1 TATGTGGTC
106896 CTTATGAACA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 104 0.99
104 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCTCTAGCATATGTATATGATTCTTAAGAAATGA
Found at i:106941 original size:23 final size:23
Alignment explanation
Indices: 106908--106982 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
106898 TATGAACATT
106908 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
106929 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
106952 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
106975 ATTATATG
1 ATTATATG
106983 AGCTGTGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.13
23 41 0.87
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:107179 original size:24 final size:24
Alignment explanation
Indices: 107127--107179 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
107117 TTTTATGATA
* * *
107127 GTATATATATGGTATATGTTATAT
1 GTATATACATGGTACATGTTATAG
107151 G-ATATACATGAGTACATGTTA-AG
1 GTATATACATG-GTACATGTTATAG
107174 GTATAT
1 GTATAT
107180 GTGAATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.42
Consensus pattern (24 bp):
GTATATACATGGTACATGTTATAG
Found at i:109179 original size:38 final size:37
Alignment explanation
Indices: 109108--109213 Score: 180
Period size: 38 Copynumber: 2.9 Consensus size: 37
109098 CAAATTGTAA
109108 AATATTTATAT-ATTTTCTTT-AAAAAATTAAATTCAT
1 AATATTTATATAATTTT-TTTAAAAAAATTAAATTCAT
109144 AATATTTATATAATTTTTTTAAAAAAAATTAAATTCAT
1 AATATTTATATAATTTTTTT-AAAAAAATTAAATTCAT
109182 AATATTTATATAATTTTTTTAAAAAAATTAAA
1 AATATTTATATAATTTTTTTAAAAAAATTAAA
109214 AATATAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
36 14 0.21
37 17 0.25
38 36 0.54
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (37 bp):
AATATTTATATAATTTTTTTAAAAAAATTAAATTCAT
Found at i:109985 original size:16 final size:16
Alignment explanation
Indices: 109964--109998 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
109954 GTCACTGAAT
*
109964 TTTACTCTCCCCTCTA
1 TTTACTCTCCCCTATA
*
109980 TTTACTCTCTCCTATA
1 TTTACTCTCCCCTATA
109996 TTT
1 TTT
109999 TTTAGTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTACTCTCCCCTATA
Found at i:115396 original size:7 final size:7
Alignment explanation
Indices: 115384--115418 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
115374 AAAGGACTAA
115384 AGCCATC
1 AGCCATC
115391 AGCCATC
1 AGCCATC
115398 AGCCATC
1 AGCCATC
115405 AGCCATC
1 AGCCATC
115412 AGCCATC
1 AGCCATC
115419 TTTCCATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
AGCCATC
Found at i:117162 original size:13 final size:13
Alignment explanation
Indices: 117144--117170 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
117134 TTTGATTAAT
117144 AAAATTAATAAAA
1 AAAATTAATAAAA
117157 AAAATTAATAAAA
1 AAAATTAATAAAA
117170 A
1 A
117171 TCTAAGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATTAATAAAA
Found at i:125505 original size:29 final size:28
Alignment explanation
Indices: 125469--125535 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
125459 CATTTTACAC
*
125469 AAATAGCACCCTTTTAAAAAAAATTACCA
1 AAATAGCACCCATTTAAAAAAAATT-CCA
** **
125498 AAATAGCACCCATTTCGAATTAATTCCA
1 AAATAGCACCCATTTAAAAAAAATTCCA
125526 AAATAGCACC
1 AAATAGCACC
125536 AAAACTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
AAATAGCACCCATTTAAAAAAAATTCCA
Found at i:125604 original size:18 final size:18
Alignment explanation
Indices: 125562--125606 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
125552 CCATAATAGC
125562 ACCGGTCAACGGGTCGGG
1 ACCGGTCAACGGGTCGGG
* * *
125580 TCGGGTCAACGGGTCGTG
1 ACCGGTCAACGGGTCGGG
125598 ACCGGTCAA
1 ACCGGTCAA
125607 AACCGGTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.40, T:0.16
Consensus pattern (18 bp):
ACCGGTCAACGGGTCGGG
Found at i:126159 original size:2 final size:2
Alignment explanation
Indices: 126147--126178 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
126137 CAATTCACGC
126147 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
126179 AACCAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:127851 original size:7 final size:8
Alignment explanation
Indices: 127817--127852 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
127807 AGAAGCTGCA
127817 GAAAAGGG
1 GAAAAGGG
127825 GAAAAGGG
1 GAAAAGGG
127833 GAAAAGGG
1 GAAAAGGG
127841 GAAAA-GG
1 GAAAAGGG
127848 GAAAA
1 GAAAA
127853 TTGTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (8 bp):
GAAAAGGG
Found at i:133079 original size:2 final size:2
Alignment explanation
Indices: 133072--133127 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
133062 CCTCCAGCAT
133072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
133114 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
133128 AAAGTTGAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:136646 original size:22 final size:23
Alignment explanation
Indices: 136596--136646 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
136586 TAATAACATA
* *
136596 TATTTATGACACATGTTTTTCTG
1 TATTTATAACACATGTTTTTATG
* *
136619 TTTTTATAACATAT-TTTTTATG
1 TATTTATAACACATGTTTTTATG
136641 TATTTA
1 TATTTA
136647 GGTATGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (23 bp):
TATTTATAACACATGTTTTTATG
Found at i:138531 original size:5 final size:5
Alignment explanation
Indices: 138521--138549 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
138511 TATCTCGGGT
138521 ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATAT
138550 CAATTGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:143462 original size:157 final size:157
Alignment explanation
Indices: 143176--143492 Score: 634
Period size: 157 Copynumber: 2.0 Consensus size: 157
143166 AGATATATAT
143176 AAAAGAAGTCACATTGCTATATTTTTATTCTGGAATCCTAAAATGTATTAAGTAATAATGATTGC
1 AAAAGAAGTCACATTGCTATATTTTTATTCTGGAATCCTAAAATGTATTAAGTAATAATGATTGC
143241 AATTGGAATAATTTGAGTACATTGTTCTCAGTAATGATGTATGGTGATGTGGAGACGTACCTCTG
66 AATTGGAATAATTTGAGTACATTGTTCTCAGTAATGATGTATGGTGATGTGGAGACGTACCTCTG
143306 CAGTGGATTTGCTGCAATTTTTCACAG
131 CAGTGGATTTGCTGCAATTTTTCACAG
143333 AAAAGAAGTCACATTGCTATATTTTTATTCTGGAATCCTAAAATGTATTAAGTAATAATGATTGC
1 AAAAGAAGTCACATTGCTATATTTTTATTCTGGAATCCTAAAATGTATTAAGTAATAATGATTGC
143398 AATTGGAATAATTTGAGTACATTGTTCTCAGTAATGATGTATGGTGATGTGGAGACGTACCTCTG
66 AATTGGAATAATTTGAGTACATTGTTCTCAGTAATGATGTATGGTGATGTGGAGACGTACCTCTG
143463 CAGTGGATTTGCTGCAATTTTTCACAG
131 CAGTGGATTTGCTGCAATTTTTCACAG
143490 AAA
1 AAA
143493 CTGCTATTCT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (157 bp):
AAAAGAAGTCACATTGCTATATTTTTATTCTGGAATCCTAAAATGTATTAAGTAATAATGATTGC
AATTGGAATAATTTGAGTACATTGTTCTCAGTAATGATGTATGGTGATGTGGAGACGTACCTCTG
CAGTGGATTTGCTGCAATTTTTCACAG
Found at i:161093 original size:11 final size:11
Alignment explanation
Indices: 161077--161105 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
161067 CTAATGATTA
161077 TTAATAAAAAT
1 TTAATAAAAAT
161088 TTAAT-AAAAT
1 TTAATAAAAAT
161098 TTAATAAA
1 TTAATAAA
161106 TTATTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTAATAAAAAT
Found at i:164264 original size:228 final size:229
Alignment explanation
Indices: 163850--164315 Score: 916
Period size: 228 Copynumber: 2.0 Consensus size: 229
163840 AATTAGGCAT
163850 CTTTGTTTGAACTGAATGTAGTTGTGAATATTGAGATGGCAATGGCCTGATGTGTTGATTTTTGT
1 CTTT-TTTGAACTGAATGTAGTTGTGAATATTGAGATGGCAATGGCCTGATGTGTTGATTTTTGT
163915 CTTCATCTTGTATGCTGGAATTGAAATGTTCAACCGACTTTCCTTGACATGCTTTTCATCAACCC
65 CTTCATCTTGTATGCTGGAATTGAAATGTTCAACCGACTTTCCTTGACATGCTTTTCATCAACCC
163980 TTTTCTTGAGAATGGGGTGCAGTGTATAAACCGGAAGTTATCAAGCTAAGGTCGTATTCCTGTGA
130 TTTTCTTGAGAATGGGGTGCAGTGTATAAACCGGAAGTTATCAAGCTAAGGTCGTATTCCTGTGA
164045 AATTTCTATGATGAAGCATATAAAGATGTCAAGAA
195 AATTTCTATGATGAAGCATATAAAGATGTCAAGAA
164080 CTTTTTTGAACTGAA-GTAGTTGTGAATATTGAGATGGCAATGGCCTGATGTGTTGATTTTTGTC
1 CTTTTTTGAACTGAATGTAGTTGTGAATATTGAGATGGCAATGGCCTGATGTGTTGATTTTTGTC
164144 TTCATCTTGTATGCTGGAATTGAAATGTTCAACCGACTTTCCTTGACATGCTTTTCATCAACCCT
66 TTCATCTTGTATGCTGGAATTGAAATGTTCAACCGACTTTCCTTGACATGCTTTTCATCAACCCT
164209 TTTCTTGAGAATGGGGTGCAGTGTATAAACCGGAAGTTATCAAGCTAAGGTCGTATTCCTGTGAA
131 TTTCTTGAGAATGGGGTGCAGTGTATAAACCGGAAGTTATCAAGCTAAGGTCGTATTCCTGTGAA
164274 ATTTCTATGATGAAGCATATAAAGATGTCAAGAA
196 ATTTCTATGATGAAGCATATAAAGATGTCAAGAA
164308 CTTTTTTG
1 CTTTTTTG
164316 TTGCTTATGC
Statistics
Matches: 236, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
228 221 0.94
229 11 0.05
230 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (229 bp):
CTTTTTTGAACTGAATGTAGTTGTGAATATTGAGATGGCAATGGCCTGATGTGTTGATTTTTGTC
TTCATCTTGTATGCTGGAATTGAAATGTTCAACCGACTTTCCTTGACATGCTTTTCATCAACCCT
TTTCTTGAGAATGGGGTGCAGTGTATAAACCGGAAGTTATCAAGCTAAGGTCGTATTCCTGTGAA
ATTTCTATGATGAAGCATATAAAGATGTCAAGAA
Found at i:167669 original size:27 final size:27
Alignment explanation
Indices: 167629--167686 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
167619 AAATATATAA
167629 AAAAAAATACATACTACAAGAACATAC
1 AAAAAAATACATACTACAAGAACATAC
* *
167656 AAAAAAATATATACTACAAGAACATAT
1 AAAAAAATACATACTACAAGAACATAC
167683 AAAA
1 AAAA
167687 TCATCCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (27 bp):
AAAAAAATACATACTACAAGAACATAC
Found at i:169410 original size:2 final size:2
Alignment explanation
Indices: 169403--169444 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
169393 AAATTTAAGA
169403 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
169445 GCGCGAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:171714 original size:6 final size:6
Alignment explanation
Indices: 171705--171756 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
171695 AATGTTAAAT
* * *
171705 AAATAA AAATAA AAATAA TAA-AA ACATAA ATAATAA TAATAA TAAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA -AAATAA
171754 AAA
1 AAA
171757 AATGAAATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 3 0.08
6 25 0.68
7 9 0.24
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:171715 original size:25 final size:25
Alignment explanation
Indices: 171670--171717 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
171660 AAAAATCAAA
*
171670 AATGTTAGACAAAAAATAATAAATT
1 AATGTTAAACAAAAAATAATAAATT
*
171695 AATGTTAAATAAATAAA-AATAAA
1 AATGTTAAACAAA-AAATAATAAA
171718 AATAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (25 bp):
AATGTTAAACAAAAAATAATAAATT
Found at i:171724 original size:15 final size:15
Alignment explanation
Indices: 171701--171759 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
171691 AATTAATGTT
171701 AAATAAATAAAAATAA
1 AAAT-AATAAAAATAA
* *
171717 AAATAATAAAAACAT
1 AAATAATAAAAATAA
*
171732 AAATAATAATAATAA
1 AAATAATAAAAATAA
171747 TAAATAA-AAAAAT
1 -AAATAATAAAAAT
171760 GAAATCACAG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 26 0.72
16 10 0.28
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:173728 original size:106 final size:106
Alignment explanation
Indices: 173595--174117 Score: 763
Period size: 106 Copynumber: 5.0 Consensus size: 106
173585 TGTTTCAAGG
* * * *
173595 CCAATATCCTCCGTCGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
173660 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
173701 CCATTATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
173766 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
173807 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA--G-TTCTT---AGCCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
* ** * * *
173865 CGGCCCCTTCGTTTTGAAGTTGAACTTGTGCTGTCTCGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* ** * *
173906 CCAATATCCTTAGCCGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
173971 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
174012 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
*
174077 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
174118 GGAACGATAT
Statistics
Matches: 370, Mismatches: 40, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
99 79 0.21
100 2 0.01
102 5 0.01
103 5 0.01
105 1 0.00
106 278 0.75
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:173966 original size:205 final size:205
Alignment explanation
Indices: 173656--174117 Score: 663
Period size: 205 Copynumber: 2.2 Consensus size: 205
173646 TTATTGACAA
* * * * * **
173656 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCATTATCCTTCGTTGTGAA
1 CCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTAGCCGTGAA
* * * *
173721 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 GTTGAAATTGGATCCGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
173786 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG
131 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAG
173851 AAGTTCTTAG
196 AAGTTCTTAG
** *
173861 CCAGCGGCCCCTTCGTTTTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTAGCCGTGAA
1 CCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTAGCCGTGAA
*
173926 GTTGAAATTGGATCCGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
66 GTTGAAATTGGATCCGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
173991 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGG
131 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAG
*
174056 AAGTTGTTTATTG
196 AAGTT-CTTA--G
* * *
174069 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGT
1 ----CCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGT
174118 GGAACGATAT
Statistics
Matches: 225, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
205 182 0.81
206 3 0.01
208 1 0.00
212 39 0.17
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (205 bp):
CCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTAGCCGTGAA
GTTGAAATTGGATCCGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAG
AAGTTCTTAG
Found at i:175520 original size:23 final size:23
Alignment explanation
Indices: 175494--175575 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 23
175484 TCCCTTTTTC
*
175494 TTTTGATTTTTGGTTCTTTTCTT
1 TTTTGATTTTTGATTCTTTTCTT
*
175517 TTTTG-TTCTTGATTCTTTT-TT
1 TTTTGATTTTTGATTCTTTTCTT
* * *
175538 TTATTTATTTTTGCTTCTTTGCTT
1 TT-TTGATTTTTGATTCTTTTCTT
*
175562 TTTTG-TTCTTGATT
1 TTTTGATTTTTGATT
175576 GGATCTTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.09
22 21 0.45
23 18 0.38
24 4 0.09
ACGTcount: A:0.06, C:0.10, G:0.11, T:0.73
Consensus pattern (23 bp):
TTTTGATTTTTGATTCTTTTCTT
Found at i:175532 original size:17 final size:15
Alignment explanation
Indices: 175500--175571 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
175490 TTTCTTTTGA
*
175500 TTTTTGGTTCTTTTC
1 TTTTTTGTTCTTTTC
175515 TTTTTTGTTCTTGATTC
1 TTTTTTGTTCTT--TTC
*
175532 TTTTTT-TT-ATTT-
1 TTTTTTGTTCTTTTC
* *
175544 ATTTTTGCTTCTTTGC
1 TTTTTTG-TTCTTTTC
175560 TTTTTTGTTCTT
1 TTTTTTGTTCTT
175572 GATTGGATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.11
13 2 0.04
14 2 0.04
15 19 0.42
16 8 0.18
17 9 0.20
ACGTcount: A:0.04, C:0.11, G:0.10, T:0.75
Consensus pattern (15 bp):
TTTTTTGTTCTTTTC
Found at i:176665 original size:7 final size:7
Alignment explanation
Indices: 176655--176680 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
176645 TGAAAAGTAG
176655 ATGCAAA
1 ATGCAAA
176662 ATGCAAA
1 ATGCAAA
176669 ATGCAAA
1 ATGCAAA
176676 ATGCA
1 ATGCA
176681 TGAAATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:178442 original size:3 final size:3
Alignment explanation
Indices: 178436--178485 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
178426 ATTAATGTTA
*
178436 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- CAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
178481 AAT AA
1 AAT AA
178486 AAAAAAATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.93
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:179912 original size:25 final size:23
Alignment explanation
Indices: 179864--179912 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
179854 ATGTAACAAA
179864 AACAATAAATAAATAAATAATAT
1 AACAATAAATAAATAAATAATAT
* *
179887 AACACATAATATATATATATAATAT
1 AACA-ATAA-ATAAATAAATAATAT
179912 A
1 A
179913 TTTTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 14 0.64
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AACAATAAATAAATAAATAATAT
Found at i:185646 original size:21 final size:21
Alignment explanation
Indices: 185616--185689 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
185606 GATTTACATA
*
185616 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
185637 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCGAAG
185660 TT--CGTTGCG--AGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
185677 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
185690 TTATTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
17 7 0.17
19 7 0.17
21 18 0.45
23 8 0.20
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:185678 original size:40 final size:40
Alignment explanation
Indices: 185629--185709 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
185619 GCATTGCGAT
185629 AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCG
1 AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCG
185669 AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCG
1 AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCG
185709 A
1 A
185710 TAGTCCAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (40 bp):
AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCG
Found at i:185707 original size:21 final size:21
Alignment explanation
Indices: 185641--185710 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
185631 TCGAAGTTCG
185641 CGTTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCTAAATT
* * *
185662 CGTTGCG----AGTCGAAGTT
1 CGTTGCGATTTATTCTAAATT
185679 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTCTAAATT
185702 CGTTGCGAT
1 CGTTGCGAT
185711 AGTCCAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 7 0.19
19 7 0.19
21 16 0.43
23 7 0.19
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCTAAATT
Found at i:186440 original size:21 final size:21
Alignment explanation
Indices: 186414--186460 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
186404 TGGACTATCA
186414 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
186435 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
186456 CAACG
1 CAACG
186461 CGAACTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACGAATTTGGAATAAATCG
Found at i:186476 original size:21 final size:21
Alignment explanation
Indices: 186452--186506 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
186442 TTTGGAATAA
*
186452 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
186473 ATCGCAATGCGAACTTGGATT
1 ATCGCAATGCGAACTTCGACT
186494 ATCGCAATGCGAA
1 ATCGCAATGCGAA
186507 TATGTAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:188223 original size:14 final size:14
Alignment explanation
Indices: 188204--188239 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
188194 TTGGTTTTGG
*
188204 TCTCCAGTACCGAA
1 TCTCCAGCACCGAA
*
188218 TCTCCAGCACTGAA
1 TCTCCAGCACCGAA
188232 TCTCCAGC
1 TCTCCAGC
188240 TATGAGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.22
Consensus pattern (14 bp):
TCTCCAGCACCGAA
Found at i:196772 original size:4 final size:4
Alignment explanation
Indices: 196763--196798 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
196753 TTTCTTTACC
196763 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
196799 CTATTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:207262 original size:105 final size:105
Alignment explanation
Indices: 207076--207845 Score: 1174
Period size: 105 Copynumber: 7.4 Consensus size: 105
207066 AGGTTTTACC
*
207076 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207141 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATA
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
207181 CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207246 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
207286 CAGGGCCAATTTCAACTTCACAACGAATGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
207351 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* ** *
207391 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207456 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
207496 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
207561 ACGAAGGGACCGCTGGTTGTCAATAAAAAGGTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTTCTCAAATT
* *
207602 CAGAGACAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
207667 ACGAAGGGACCGCTGGTTGTCAACAAA-A-TT-TC--ATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * ** * * *
207702 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTATACTCGAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** **
207767 ACGAAGGGATGGCTGGTTGTCAACAAACAATTTC-CCGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* *
207807 CCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGAC
1 -CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
207846 CCGGAACAAT
Statistics
Matches: 615, Mismatches: 42, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
100 86 0.14
102 3 0.00
103 5 0.01
105 393 0.64
106 128 0.21
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:208341 original size:26 final size:26
Alignment explanation
Indices: 208303--208352 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
208293 TAGTATATAG
*
208303 TATATATACATTACATAATATATACA
1 TATATATACATTACATAACATATACA
*
208329 TATATTATA-ATTATATAACATATA
1 TATA-TATACATTACATAACATATA
208353 TCACATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (26 bp):
TATATATACATTACATAACATATACA
Found at i:217106 original size:7 final size:7
Alignment explanation
Indices: 217094--217124 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
217084 TTATCATGTG
217094 CACTGTC
1 CACTGTC
217101 CACTGTC
1 CACTGTC
217108 CACTGTC
1 CACTGTC
217115 CACTGTC
1 CACTGTC
217122 CAC
1 CAC
217125 ATTTCTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.45, G:0.13, T:0.26
Consensus pattern (7 bp):
CACTGTC
Found at i:220523 original size:6 final size:6
Alignment explanation
Indices: 220508--220540 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
220498 GTTGGCTAAA
*
220508 TCATTC TCATTG TCATTG TCATTG TCATTG TCA
1 TCATTG TCATTG TCATTG TCATTG TCATTG TCA
220541 ACTACTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.48
Consensus pattern (6 bp):
TCATTG
Found at i:220975 original size:14 final size:14
Alignment explanation
Indices: 220941--220973 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
220931 GGGTTAGAGC
220941 TTAGGGTTTATAAT
1 TTAGGGTTTATAAT
220955 TTAGGGTTT-TAAT
1 TTAGGGTTTATAAT
220968 TTAGGG
1 TTAGGG
220974 GTATAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTATAAT
Found at i:227071 original size:83 final size:83
Alignment explanation
Indices: 226968--227188 Score: 390
Period size: 83 Copynumber: 2.7 Consensus size: 83
226958 CTCAACTAGA
* * *
226968 TCCAAATATCGATCA-AAGGATGCTCCAAGAAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGAC
1 TCCAAATTTCGAT-AGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGAC
227032 AGAGAAACAGCTCGGTCGG
65 AGAGAAACAGCTCGGTCGG
227051 TCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGACA
1 TCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGACA
227116 GAGAAACAGCTCGGTCGG
66 GAGAAACAGCTCGGTCGG
*
227134 TCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGGAAGAGCT
1 TCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCT
227189 TGCCTCAATC
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 1 0.01
83 132 0.99
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.15
Consensus pattern (83 bp):
TCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGACA
GAGAAACAGCTCGGTCGG
Found at i:227543 original size:83 final size:83
Alignment explanation
Indices: 227410--227562 Score: 218
Period size: 83 Copynumber: 1.8 Consensus size: 83
227400 AACAGTTCGA
*
227410 AGCAAAGGAAGAAGAGCTCCACTCAAAAGAGAAAAAACTCAGCATGGTCCAAATATCGATTGAAG
1 AGCAAAGGAAGAAGAGCTCCACTCAAAAGAGAAAAAACTCAGCATGGTCCAAATATCCATTGAAG
227475 AATGCACGAGCAGCTTGG
66 AATGCACGAGCAGCTTGG
* * * * * *
227493 AGCAAAGGATGAAGAGCTCCATTCAAAAGAGAAACAACTCCG-ATCTGTCCAACTATCCATTGAA
1 AGCAAAGGAAGAAGAGCTCCACTCAAAAGAGAAAAAACTCAGCAT-GGTCCAAATATCCATTGAA
*
227557 GGATGC
65 GAATGC
227563 CCCAAGCAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 2 0.03
83 59 0.97
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (83 bp):
AGCAAAGGAAGAAGAGCTCCACTCAAAAGAGAAAAAACTCAGCATGGTCCAAATATCCATTGAAG
AATGCACGAGCAGCTTGG
Found at i:227650 original size:406 final size:405
Alignment explanation
Indices: 226868--227684 Score: 943
Period size: 406 Copynumber: 2.0 Consensus size: 405
226858 AGGATATTCC
* * *
226868 GAGGACATCGAATTGAAAAACCAGGTGTTCAATGCTATACAAATGTCCATTGAAGAACAAAGCCA
1 GAGGACATCGAATTGAAAAACCAGGAGTTCAATGCTATACAAATGACCATTGAAGAACAAAGCAA
* * *
226933 GAAACTCCATTCAAAAGAGAGCCAACTCAACTAGATCCAAATATCGATCAAAGGATGCTCCAAGA
66 GAAACTCCATTCAAAAGAGAG-CAACTCAACTAGATCCAAATATCAATCAAAAGATGCACCAAGA
* ** * * * * *
226998 AGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGACAGAGAAACAGCTCGGTCGGTCCAAATTTCGA
130 AGCTCGAAGAAAAGGAGAAAGAGCTCCACTCAAAAGAGAAAAAACTCGATCGGTCCAAATATCGA
* ** * *
227063 TAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTTGACAGAGAAACAGCTC
195 TAGAAGAATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTCAAAAGAGAAACAACTC
* * * * *
227128 GGTCGGTCCAAATTTCGATAGAAGGATGCACCAAGCAGCTCGAAGAAAAGGAGGAAGAGCTTGCC
260 GATCGGTCCAAATATCCATAGAAGGATGCACCAAGCAGCTCCAAGAAAAGGAGGAAGAGCTTACC
* * *
227193 TCAATCAAAAACTCAATCTTGGAGTGCACTAAGTAGCTTAAATCAAAACAACAGCAG-CTTGAAG
325 TCAATCAAAAACTCAATCTTGGAGAGCACCAAGGAGCTTAAATCAAAACAACAGCAGAC-TGAAG
*
227257 CAATACGAAAATCACAG
389 CAATACAAAAATCACAG
* * ***
227274 GAGGATATCGAATTGAAAAAACCAGGAGTTCAGTGCTATACAAATGACCATTGAAGAATGTAGTC
1 GAGGACATCGAATTG-AAAAACCAGGAGTTCAATGCTATACAAATGACCATTGAAGAACAAAG-C
* * * * *
227339 AAG-AACTTCATTCGAAAGAGAG-AACTCAGCTCGGTCCAAATATCAAT-AGAAAGATGCACCAA
64 AAGAAACTCCATTCAAAAGAGAGCAACTCAACTAGATCCAAATATCAATCA-AAAGATGCACCAA
* *
227401 -ACAGTTCGAAGCAAAGGA-AGAAGAGCTCCACTCAAAAGAGAAAAAACTCAGCAT-GGTCCAAA
128 GA-AGCTCGAAGAAAAGGAGA-AAGAGCTCCACTCAAAAGAGAAAAAACTC-G-ATCGGTCCAAA
* * * * *
227463 TATCGATTGAAGAATGCA-CGAGCAGCTTGGAGCAAAGGATG-AAGAGCTCCATTCAAAAGAGAA
189 TATCGATAGAAGAATGCACCAAGCAGCTCGAAGAAAAGGA-GAAAGAGCTCCATTCAAAAGAGAA
* * * * * *
227526 ACAACTCCGATCTGTCCAACTATCCATTGAAGGATGCCCCAAGCAGTTCCAAG-CAAGAGAGGAA
253 ACAACT-CGATCGGTCCAAATATCCATAGAAGGATGCACCAAGCAGCTCCAAGAAAAG-GAGGAA
* * * *
227590 GAGCTTATCTCAATCAAAAACTCAATTTTGGAGAGCACCAAGGAGCTTGAATCGAAACAACAGCA
316 GAGCTTACCTCAATCAAAAACTCAATCTTGGAGAGCACCAAGGAGCTTAAATCAAAACAACAGCA
* *
227655 GACTGATGCAATACAAAAATCTCAG
381 GACTGAAGCAATACAAAAATCACAG
227680 GAGGA
1 GAGGA
227685 AATCTCTGGC
Statistics
Matches: 343, Mismatches: 57, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
404 3 0.01
405 113 0.33
406 164 0.48
407 60 0.17
408 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (405 bp):
GAGGACATCGAATTGAAAAACCAGGAGTTCAATGCTATACAAATGACCATTGAAGAACAAAGCAA
GAAACTCCATTCAAAAGAGAGCAACTCAACTAGATCCAAATATCAATCAAAAGATGCACCAAGAA
GCTCGAAGAAAAGGAGAAAGAGCTCCACTCAAAAGAGAAAAAACTCGATCGGTCCAAATATCGAT
AGAAGAATGCACCAAGCAGCTCGAAGAAAAGGAGAAAGAGCTCCATTCAAAAGAGAAACAACTCG
ATCGGTCCAAATATCCATAGAAGGATGCACCAAGCAGCTCCAAGAAAAGGAGGAAGAGCTTACCT
CAATCAAAAACTCAATCTTGGAGAGCACCAAGGAGCTTAAATCAAAACAACAGCAGACTGAAGCA
ATACAAAAATCACAG
Found at i:234909 original size:42 final size:42
Alignment explanation
Indices: 234845--234936 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
234835 AATCGACCAA
*
234845 ATTCTCATTCATCGTCACATTTTTCCACAACATGATCTCATC
1 ATTCTCATTCATCATCACATTTTTCCACAACATGATCTCATC
* *
234887 ATTCTCATTCATCATCAGATTTTTCCACAACATGATCTCCTC
1 ATTCTCATTCATCATCACATTTTTCCACAACATGATCTCATC
234929 ATTCTCAT
1 ATTCTCAT
234937 CGGGGAAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (42 bp):
ATTCTCATTCATCATCACATTTTTCCACAACATGATCTCATC
Found at i:245870 original size:81 final size:81
Alignment explanation
Indices: 245767--245928 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
245757 CCAATGCCCA
*
245767 AGCATCAACAGAAAAAACGTAAGACTTATATTAGATATGTAACATATGAAAAACTATTGTAATGA
1 AGCATCAACAGAAAAAACGTAAGACTTATATTAGATATGTAACATATGAAAAACTACTGTAATGA
245832 AAGTTTTCCCATTCAG
66 AAGTTTTCCCATTCAG
*
245848 AGCATCGACAGAAAAAACGTAAGACTTATATTAGATATGTAACATATGAAAAACTACTGTAATGA
1 AGCATCAACAGAAAAAACGTAAGACTTATATTAGATATGTAACATATGAAAAACTACTGTAATGA
245913 AAGTTTTCCCATTCAG
66 AAGTTTTCCCATTCAG
245929 TTCCTAACTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (81 bp):
AGCATCAACAGAAAAAACGTAAGACTTATATTAGATATGTAACATATGAAAAACTACTGTAATGA
AAGTTTTCCCATTCAG
Found at i:248197 original size:23 final size:23
Alignment explanation
Indices: 248177--248226 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
248167 CTTTGTGATT
*
248177 CGTTTTTCTCTGTTCTTGTGACA
1 CGTTTTTCTCTGCTCTTGTGACA
*
248200 CGTTTTTCTCTGCTCTTGTGGCA
1 CGTTTTTCTCTGCTCTTGTGACA
248223 CGTT
1 CGTT
248227 CTTTATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.06, C:0.24, G:0.20, T:0.50
Consensus pattern (23 bp):
CGTTTTTCTCTGCTCTTGTGACA
Found at i:255699 original size:17 final size:19
Alignment explanation
Indices: 255671--255710 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
255661 GACCCGAAAT
255671 AATATATTTATT-AAAAAA
1 AATATATTTATTCAAAAAA
*
255689 AATAT-TTTATTCAATAAA
1 AATATATTTATTCAAAAAA
255707 AATA
1 AATA
255711 GGAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATATTTATTCAAAAAA
Found at i:256768 original size:23 final size:23
Alignment explanation
Indices: 256742--256791 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
256732 CTAATTTATA
* *
256742 ATATTTTTTACAAAATA-TATTTT
1 ATATATTTTA-AAAATATTATTTG
*
256765 ATATATTTTAAAATTATTATTTG
1 ATATATTTTAAAAATATTATTTG
256788 ATAT
1 ATAT
256792 GACACATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATTTTAAAAATATTATTTG
Found at i:258074 original size:14 final size:14
Alignment explanation
Indices: 258052--258105 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
258042 TTCGTGAACA
258052 TTCGATTATGTTCG
1 TTCGATTATGTTCG
*
258066 TTCGGTTATG-T--
1 TTCGATTATGTTCG
*
258077 TT-GTTTATGTTCG
1 TTCGATTATGTTCG
258090 TTCGATTATGTTCG
1 TTCGATTATGTTCG
258104 TT
1 TT
258106 TATGTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 3 0.09
14 21 0.64
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (14 bp):
TTCGATTATGTTCG
Found at i:258084 original size:24 final size:24
Alignment explanation
Indices: 258057--258126 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
258047 GAACATTCGA
*
258057 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
258081 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
258105 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
258127 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:258865 original size:10 final size:10
Alignment explanation
Indices: 258850--258924 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
258840 GGGTCTCCAA
258850 CGTTTATGTT
1 CGTTTATGTT
258860 CGTTTATGTT
1 CGTTTATGTT
258870 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
258881 ATGTTCGTGTT
1 -CGTTTATGTT
258892 CGTTTATGTT
1 CGTTTATGTT
258902 CG----TGTT
1 CGTTTATGTT
258908 CGTTTATGTT
1 CGTTTATGTT
258918 CGTTTAT
1 CGTTTAT
258925 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:258881 original size:16 final size:16
Alignment explanation
Indices: 258856--258920 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
258846 CCAACGTTTA
258856 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
258872 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
258888 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
258904 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
258920 T
1 T
258921 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:259011 original size:16 final size:16
Alignment explanation
Indices: 258990--259022 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
258980 AAAAAAATTT
258990 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
259006 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
259022 T
1 T
259023 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:262819 original size:16 final size:16
Alignment explanation
Indices: 262798--262838 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
262788 TTTACTTCAA
*
262798 AATGATTCAAGCGTTG
1 AATGATTCAAACGTTG
*
262814 AATGATTCAAATGTTG
1 AATGATTCAAACGTTG
*
262830 AATCATTCA
1 AATGATTCA
262839 GAGGCTCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (16 bp):
AATGATTCAAACGTTG
Found at i:273379 original size:23 final size:22
Alignment explanation
Indices: 273331--273385 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
273321 ATTTTTTTAA
**
273331 ATAAAATATTTAAATTCAAAAT
1 ATAAAATATTTAAAAACAAAAT
*
273353 ATAAAATATTTAAAAACTTAAAT
1 ATAAAATATTTAAAAAC-AAAAT
273376 ATAATAATAT
1 ATAA-AATAT
273386 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 15 0.54
23 8 0.29
24 5 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAATATTTAAAAACAAAAT
Found at i:273390 original size:23 final size:23
Alignment explanation
Indices: 273349--273402 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
273339 TTTAAATTCA
*
273349 AAATATAA-AATATTTAAAAACTT
1 AAATATAATAATA-TTAAAAAATT
273372 AAATATAATAATA-TAAAAAATT
1 AAATATAATAATATTAAAAAATT
273394 -AAT-TAATAA
1 AAATATAATAA
273403 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.21
21 3 0.10
22 8 0.28
23 8 0.28
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAATAATATTAAAAAATT
Found at i:276769 original size:21 final size:21
Alignment explanation
Indices: 276734--276816 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
276724 AGAACCCATG
*
276734 GGGGGTATCGATTCCCTT-AA
1 GGGGGAATCGATTCCCTTCAA
*
276754 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCC-TTC-AA
*
276778 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTCAA
*
276800 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
276817 CTGCACTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.04
21 16 0.30
22 15 0.28
23 14 0.26
24 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:276804 original size:22 final size:22
Alignment explanation
Indices: 276734--276815 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
276724 AGAACCCATG
*
276734 GGGGGTATCGATT-CCCTT-AA
1 GGGGGAATCGATTCCCCTTCAA
* *
276754 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
*
276778 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
276800 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
276816 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.04
21 9 0.17
22 20 0.38
23 17 0.33
24 4 0.08
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:282948 original size:23 final size:23
Alignment explanation
Indices: 282882--282939 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
282872 TGAATATCTT
282882 TATATTTTTTAATTTAAAATATA
1 TATATTTTTTAATTTAAAATATA
282905 TATATTTTTTAATTTAAAATATA
1 TATATTTTTTAATTTAAAATATA
282928 TATATTTTTTAA
1 TATATTTTTTAA
282940 AATCAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTTTTTAATTTAAAATATA
Found at i:288187 original size:10 final size:10
Alignment explanation
Indices: 288169--288318 Score: 93
Period size: 10 Copynumber: 13.6 Consensus size: 10
288159 TGTTTTTTAT
*
288169 GTTTGTGTTC
1 GTTTATGTTC
288179 GTTTATGTTC
1 GTTTATGTTC
*
288189 ATTTATTGTGTTC
1 GTTTA---TGTTC
288202 GTTTATGTTC
1 GTTTATGTTC
*
288212 ATTTATTGTGTTC
1 GTTTA---TGTTC
288225 GTTTATGTTC
1 GTTTATGTTC
*
288235 ATTATTATGTTC
1 -GT-TTATGTTC
288247 GTTTATGTTC
1 GTTTATGTTC
*
288257 ATTTATTGTGTTC
1 GTTTA---TGTTC
*
288270 GTTTATGTTTAT
1 GTTTATG-TT-C
* *
288282 TTATTATATTC
1 GT-TTATGTTC
288293 GTTTATGTTC
1 GTTTATGTTC
*
288303 ATTTATGTTC
1 GTTTATGTTC
288313 GTTTAT
1 GTTTAT
288319 CATTTAAATG
Statistics
Matches: 109, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
10 62 0.57
11 5 0.05
12 11 0.10
13 31 0.28
ACGTcount: A:0.15, C:0.08, G:0.16, T:0.61
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:288197 original size:23 final size:23
Alignment explanation
Indices: 288171--288308 Score: 233
Period size: 23 Copynumber: 6.0 Consensus size: 23
288161 TTTTTTATGT
288171 TTGTGTTCGTTTATGTTCATTTA
1 TTGTGTTCGTTTATGTTCATTTA
288194 TTGTGTTCGTTTATGTTCATTTA
1 TTGTGTTCGTTTATGTTCATTTA
288217 TTGTGTTCGTTTATGTTCA-TTA
1 TTGTGTTCGTTTATGTTCATTTA
*
288239 TTATGTTCGTTTATGTTCATTTA
1 TTGTGTTCGTTTATGTTCATTTA
*
288262 TTGTGTTCGTTTATGTTTATTTA
1 TTGTGTTCGTTTATGTTCATTTA
* *
288285 TTATATTCGTTTATGTTCATTTA
1 TTGTGTTCGTTTATGTTCATTTA
288308 T
1 T
288309 GTTCGTTTAT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
22 21 0.19
23 87 0.81
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (23 bp):
TTGTGTTCGTTTATGTTCATTTA
Found at i:288284 original size:68 final size:66
Alignment explanation
Indices: 288174--288318 Score: 245
Period size: 68 Copynumber: 2.2 Consensus size: 66
288164 TTTATGTTTG
* *
288174 TGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTA
1 TGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTTATTATATTCGTTTATGTTCA-T-
288239 TTA
64 TTA
*
288242 TGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTTATTTATTATATTCGTTTATGTTCATTT
1 TGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTTATTATATTCGTTTATGTTCATTT
288307 A
66 A
288308 TGTTCGTTTAT
1 TGTTCGTTTAT
288319 CATTTAAATG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 14 0.19
67 1 0.01
68 59 0.80
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.61
Consensus pattern (66 bp):
TGTTCGTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTTATTATATTCGTTTATGTTCATTT
A
Found at i:289683 original size:2 final size:2
Alignment explanation
Indices: 289676--289720 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
289666 CTCACTTTCC
289676 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
289718 AT A
1 AT A
289721 ATGCCTATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:299222 original size:19 final size:20
Alignment explanation
Indices: 299195--299233 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
299185 CCTTTCCTTG
299195 GTATAGATAC-CCATAAACA
1 GTATAGATACTCCATAAACA
* *
299214 GTATCGATACTCTATAAACA
1 GTATAGATACTCCATAAACA
299234 TATTATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (20 bp):
GTATAGATACTCCATAAACA
Found at i:300668 original size:50 final size:50
Alignment explanation
Indices: 300588--300684 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
300578 GTGGAATCAA
* *
300588 GAGATATACAACTCGCTTTCTCCTTAACCTTCCCAGTGTTGGGATTTCGT
1 GAGATATACAACTCGCTTTCTCCTCAACCTTCCCAATGTTGGGATTTCGT
* *
300638 GAGATATACAACTCGCTTTCTCCTCGACCTTTCCAATGTTGGGATTT
1 GAGATATACAACTCGCTTTCTCCTCAACCTTCCCAATGTTGGGATTT
300685 GAAAGAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (50 bp):
GAGATATACAACTCGCTTTCTCCTCAACCTTCCCAATGTTGGGATTTCGT
Found at i:301498 original size:26 final size:26
Alignment explanation
Indices: 301448--301507 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
301438 TTAATTTAAA
301448 ATAATATTATTTAAATAATTAAAATAT
1 ATAA-ATTATTTAAATAATTAAAATAT
301475 ATAAATTATTTTACAAT-ATT-AAATAT
1 ATAAATTA-TTTA-AATAATTAAAATAT
*
301501 AAAAATT
1 ATAAATT
301508 TCAAATTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 16 0.53
27 11 0.37
28 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATTATTTAAATAATTAAAATAT
Found at i:301513 original size:7 final size:7
Alignment explanation
Indices: 301503--301529 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
301493 TTAAATATAA
301503 AAATTTC
1 AAATTTC
301510 AAATTTC
1 AAATTTC
301517 AAATTTC
1 AAATTTC
301524 AAATTT
1 AAATTT
301530 TGTATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTC
Found at i:314161 original size:24 final size:22
Alignment explanation
Indices: 314134--314183 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
314124 TACTATTTAA
314134 ATTATAATAAATAATTATAAATGT
1 ATTATAATAAATAATT-TAAA-GT
**
314158 ATTATTTTAAATAATTTAAAGT
1 ATTATAATAAATAATTTAAAGT
314180 ATTA
1 ATTA
314184 ATATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTATAATAAATAATTTAAAGT
Found at i:320098 original size:24 final size:24
Alignment explanation
Indices: 320066--320113 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
320056 ATATCGAATA
*
320066 AACAATGATCTATTTACTCGGTTT
1 AACAATGATCTAATTACTCGGTTT
320090 AACAATGATCTAATTACTCGGTTT
1 AACAATGATCTAATTACTCGGTTT
320114 TACGACACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (24 bp):
AACAATGATCTAATTACTCGGTTT
Found at i:320470 original size:28 final size:28
Alignment explanation
Indices: 320430--320493 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
320420 GAAATGAAAC
320430 AAAAGAAATCAGCAAGTGAGAATTGTTG
1 AAAAGAAATCAGCAAGTGAGAATTGTTG
320458 AAAAGAAATCAGCAAGTGAGAATTGTTG
1 AAAAGAAATCAGCAAGTGAGAATTGTTG
320486 AAAAGAAA
1 AAAAGAAA
320494 ATTACTTCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (28 bp):
AAAAGAAATCAGCAAGTGAGAATTGTTG
Found at i:326265 original size:36 final size:36
Alignment explanation
Indices: 326214--326285 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
326204 CTGAAAGACA
* *
326214 GAGCTATAATTTTCAGAAGTGTCCAAATGGTTTTTT
1 GAGCTATAATGTTCAGAAGCGTCCAAATGGTTTTTT
* *
326250 GAGCTATAATGTTCAGTAGCGTCTAAATGGTTTTTT
1 GAGCTATAATGTTCAGAAGCGTCCAAATGGTTTTTT
326286 TGTTCTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (36 bp):
GAGCTATAATGTTCAGAAGCGTCCAAATGGTTTTTT
Found at i:337876 original size:17 final size:17
Alignment explanation
Indices: 337854--337889 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
337844 ATCGGTATAG
337854 ATACCAAAA-CTCAATAT
1 ATACCAAAATC-CAATAT
337871 ATACCAAAATCCAATAT
1 ATACCAAAATCCAATAT
337888 AT
1 AT
337890 CACATAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (17 bp):
ATACCAAAATCCAATAT
Found at i:340089 original size:16 final size:17
Alignment explanation
Indices: 340061--340098 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
340051 CCACCTTTTC
340061 TTCT-TCTTCTTCTTCA
1 TTCTCTCTTCTTCTTCA
340077 TTCTCTCTT-TTCTTCA
1 TTCTCTCTTCTTCTTCA
*
340093 TCCTCT
1 TTCTCT
340099 ACTAAGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCTCTCTTCTTCTTCA
Found at i:341921 original size:17 final size:18
Alignment explanation
Indices: 341881--341922 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
341871 TCATGTATCT
*
341881 CAAAACCCGATATATCTAC
1 CAAAACCCGATATAGC-AC
*
341900 TAAAACCCGATATAGC-C
1 CAAAACCCGATATAGCAC
341917 CAAAAC
1 CAAAAC
341923 ACTCTTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.45, C:0.31, G:0.07, T:0.17
Consensus pattern (18 bp):
CAAAACCCGATATAGCAC
Found at i:342293 original size:29 final size:29
Alignment explanation
Indices: 342237--342293 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
342227 ACTAATATAA
* * * *
342237 GATAAAATTATATTTTAATTTTTTAAATT
1 GATAAAATTATAATCTAATTCTTCAAATT
*
342266 GATAAAATTTTAATCTAATTCTTCAAAT
1 GATAAAATTATAATCTAATTCTTCAAAT
342294 AATTATAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (29 bp):
GATAAAATTATAATCTAATTCTTCAAATT
Found at i:344564 original size:13 final size:13
Alignment explanation
Indices: 344546--344570 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
344536 TTTTATTGTT
344546 TTTAGAATTATTG
1 TTTAGAATTATTG
344559 TTTAGAATTATT
1 TTTAGAATTATT
344571 ATAAAAGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTTAGAATTATTG
Found at i:346188 original size:22 final size:22
Alignment explanation
Indices: 346163--346225 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
346153 AAACGATAAA
*
346163 AAAACATGTTATAAAAGTAGAG
1 AAAATATGTTATAAAAGTAGAG
*
346185 AAAATATATTATAAAAGTAGAG
1 AAAATATGTTATAAAAGTAGAG
* *
346207 AAAATGTGTCATAAAAGTA
1 AAAATATGTTATAAAAGTA
346226 TAATTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (22 bp):
AAAATATGTTATAAAAGTAGAG
Found at i:355292 original size:100 final size:100
Alignment explanation
Indices: 355021--355355 Score: 327
Period size: 100 Copynumber: 3.4 Consensus size: 100
355011 AAAAAAATAA
* * * * *
355021 TTTCATACTT-TAACTTAAACGATTGATATTAAAAAAGGGTGTCACCTAATACATTATTATGAGC
1 TTTCATACTTATAACTTAAACGATTGAAATTAAAAAA-TGTGTCACCTAATACGTTATCATGAAC
* **
355085 AACTTGTTTTGTCTTACTTTTGCATAATATAAATGG
65 AACATGTTTTGTCTTACTTTTGCATAATATAAACAG
* * * ** * * * * * *
355121 TTTCATATTTATTACATAATA-TTTTGACA-TAAAAAATGTGTTACCTACTACGATATCATAAAA
1 TTTCATACTTATAACTTAA-ACGATTGAAATTAAAAAATGTGTCACCTAATACGTTATCATGAAC
* *
355184 AACATGTTTTATCTTACTTTTGCACAATATAAACAG
65 AACATGTTTTGTCTTACTTTTGCATAATATAAACAG
* * * * * * *
355220 TTTTATACTTATAACTTAAACGATTAAAATTAAAAAATATGTGACCTAGTACGTTATCACGATCA
1 TTTCATACTTATAACTTAAACGATTGAAATTAAAAAATGTGTCACCTAATACGTTATCATGAACA
* *
355285 ACATGTTTTGTCTTACTTTCGTATAATATAAACAG
66 ACATGTTTTGTCTTACTTTTGCATAATATAAACAG
** *
355320 TGGCATACTTATAACTTAAACGATTGATA-TAAAAAA
1 TTTCATACTTATAACTTAAACGATTGAAATTAAAAAA
355356 GGCGATACAT
Statistics
Matches: 186, Mismatches: 45, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
98 1 0.01
99 75 0.40
100 98 0.53
101 11 0.06
102 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (100 bp):
TTTCATACTTATAACTTAAACGATTGAAATTAAAAAATGTGTCACCTAATACGTTATCATGAACA
ACATGTTTTGTCTTACTTTTGCATAATATAAACAG
Found at i:355603 original size:69 final size:70
Alignment explanation
Indices: 355523--355694 Score: 185
Period size: 68 Copynumber: 2.5 Consensus size: 70
355513 AAAAATTTGG
** * * * ***
355523 AAGTATCGATATTTGTGAAAAAGTATTGATGTC-TTGCAGCCTTCTCATTTTTTAT-TTTTTTAA
1 AAGTATCGATATTTGTGAAAAAGTATTGATAACTTTACAACATTCTCATTTACCATGTTTTTT-A
355586 ATACGAA
65 ATAC-AA
*
355593 AA-TATCGATATTTGTGGAAAA-TATTGA-AACTTTACAACATTCTCATTTACCATGTTTTTTAA
1 AAGTATCGATATTTGTGAAAAAGTATTGATAACTTTACAACATTCTCATTTACCATGTTTTTTAA
*
355655 TTCAA
66 TACAA
*
355660 AAGTATCGATATTTGTGTAAAAGTATTGAT-ACTTT
1 AAGTATCGATATTTGTGAAAAAGTATTGATAACTTT
355695 TGAATTAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
67 5 0.06
68 44 0.51
69 35 0.41
70 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (70 bp):
AAGTATCGATATTTGTGAAAAAGTATTGATAACTTTACAACATTCTCATTTACCATGTTTTTTAA
TACAA
Found at i:359642 original size:13 final size:13
Alignment explanation
Indices: 359605--359645 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
359595 TTCCTTATAT
359605 TATTAAATATTTA
1 TATTAAATATTTA
* *
359618 TGTTAAACATTTA
1 TATTAAATATTTA
*
359631 TATTAGATATTTA
1 TATTAAATATTTA
359644 TA
1 TA
359646 ACTGTAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (13 bp):
TATTAAATATTTA
Found at i:359765 original size:17 final size:18
Alignment explanation
Indices: 359743--359777 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
359733 GGATTTTTAT
359743 CTAAATAAAC-TTAATAA
1 CTAAATAAACTTTAATAA
*
359760 CTAAATAATCTTTAATAA
1 CTAAATAAACTTTAATAA
359778 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
CTAAATAAACTTTAATAA
Found at i:360764 original size:21 final size:23
Alignment explanation
Indices: 360723--360775 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
360713 CATATTTAAC
360723 ATGTTA-AAAGCGAAACAC-AAA
1 ATGTTATAAAGCGAAACACAAAA
* *
360744 ATGTTATAACGCGGAAC-CAAAA
1 ATGTTATAAAGCGAAACACAAAA
*
360766 AAGTTATAAA
1 ATGTTATAAA
360776 TGTAGTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.19
Consensus pattern (23 bp):
ATGTTATAAAGCGAAACACAAAA
Found at i:361072 original size:77 final size:76
Alignment explanation
Indices: 360982--361280 Score: 305
Period size: 77 Copynumber: 3.9 Consensus size: 76
360972 GCAGGTTGTG
**
360982 CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTTTGATCTAGAATGTTAATA-TTTTATTAATA
1 CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTACGATCTAGAATGTTAATATTTTTATTAATA
361046 AAATGGGTTGCCA
66 AAATGGGTTG--A
* **
361059 CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTGCGATCTTTAATGTTAATATTTTTATTAATA
1 CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTACGATCTAGAATGTTAATATTTTTATTAATA
* * *
361124 ACATGAGTTTGG
66 AAATG-GGTTGA
* * * * * * *
361136 CCTAATAATATAATGGTTCAATAAGAAATATGTTACGATATAGAATGTTAATATTTTTATTAATA
1 CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTACGATCTAGAATGTTAATATTTTTATTAATA
*
361201 AAATGGGTTGTG
66 AAATGGGTTG-A
* * * * * * * * * *
361213 CACAAGAGTATTATGGTCCACTAAGAAAGCAAGTTGCAATATATAATGTTAATATTTTTATT-AT
1 CCCAAGAATGTCATGGTTCACTAAGAAA-TAAGTTACGATCTAGAATGTTAATATTTTTATTAAT
361277 AAAA
65 AAAA
361281 AATTGAAAGT
Statistics
Matches: 187, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
76 4 0.02
77 136 0.73
78 43 0.23
79 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (76 bp):
CCCAAGAATGTCATGGTTCACTAAGAAATAAGTTACGATCTAGAATGTTAATATTTTTATTAATA
AAATGGGTTGA
Found at i:362109 original size:102 final size:100
Alignment explanation
Indices: 361723--362147 Score: 408
Period size: 100 Copynumber: 4.2 Consensus size: 100
361713 TATTTTGTTA
* *
361723 TGCTCGTGATAACATAGTAGGT-TGCATTTTTTTTAATGTCAATCGTTTAAGTTATAAGTATGAA
1 TGCTCATGATAACATAGTAGGTATGC-TTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAA
** * * *
361787 ACTGTTTAAATGATGCAAAAGCAAAACAAAACATGT
65 ACCATTTATATTATGCAAAAGCAAGACAAAACATGT
** * * *
361823 TTATCATGGTAACATAGTAGGTA-GCGTCTTTTTTT-ATTTCAACCGTTTAAGTTATAAGTATAA
1 TGCTCATGATAACATAGTAGGTATGC-T-TTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGA
*** *
361886 AATTGTTTAATATTGTGCAAAAGCAAGACAAAACATGT
64 AACCATTT-ATATTATGCAAAAGCAAGACAAAACATGT
* * * * * * ** *
361924 TGCTCACGATAACATACTTGATA-GCGTGTTTTTAATGTCAACCGTTTAAACTATGAGTATGAAA
1 TGCTCATGATAACATAGTAGGTATGCTTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAA
* *
361988 TCATTTATATTATGCAAAAGTAAGACAAAACATGT
66 CCATTTATATTATGCAAAAGCAAGACAAAACATGT
* * **
362023 TGCTCATGATAACATATTAGGTAGTGTCTTTTTTTTAATGTTAATTGTTTAAGTTATAAGTATGA
1 TGCTCATGATAACATAGTAGGTA-TG-CTTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGA
** * * *
362088 AACCATTTATATTATATAAAAGTAAGACAAAATAGGT
64 AACCATTTATATTATGCAAAAGCAAGACAAAACATGT
** * *
362125 TTTTCATGAAAACATAATAGGTA
1 TGCTCATGATAACATAGTAGGTA
362148 ACACCTTTTT
Statistics
Matches: 266, Mismatches: 52, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
99 52 0.20
100 82 0.31
101 51 0.19
102 81 0.30
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (100 bp):
TGCTCATGATAACATAGTAGGTATGCTTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAA
CCATTTATATTATGCAAAAGCAAGACAAAACATGT
Found at i:362156 original size:102 final size:102
Alignment explanation
Indices: 361749--362159 Score: 265
Period size: 102 Copynumber: 4.1 Consensus size: 102
361739 GTAGGTTGCA
* ** ** * * * * *
361749 TTTTTTTTAATGTCAATCGTTTAAGTTATAAGTATGAAACTGTTTAAATGATGCAAAAGCAAAAC
1 TTTTTTTTAATGTCAACCGTTTAAACTATAAGTATGAAACCATTTATATTATACAAAAGTAAGAC
* ** ** * * **
361814 AAAACATGTTTATCATGGTAACATAGTAGGTAGCGTC
66 AAAACAGGTTGCTCATGAAAACATAATAGGTAACACC
* ** * *** * * *
361851 -TTTTTTT-ATTTCAACCGTTTAAGTTATAAGTATAAAATTGTTTAATATTGTGCAAAAGCAAGA
1 TTTTTTTTAATGTCAACCGTTTAAACTATAAGTATGAAACCATTT-ATATTATACAAAAGTAAGA
* * * * * * *
361914 CAAAACATGTTGCTCACGATAACATACT---TGATAGC
65 CAAAACAGGTTGCTCATGAAAACATAATAGGTAACACC
* * * * *
361949 GTGTTTTTAATGTCAACCGTTTAAACTATGAGTATGAAATCATTTATATTATGCAAAAGTAAGAC
1 TTTTTTTTAATGTCAACCGTTTAAACTATAAGTATGAAACCATTTATATTATACAAAAGTAAGAC
* * * ****
362014 AAAACATGTTGCTCATGATAACATATTAGGTAGTGTC
66 AAAACAGGTTGCTCATGAAAACATAATAGGTAACACC
* ** ** *
362051 TTTTTTTTAATGTTAATTGTTTAAGTTATAAGTATGAAACCATTTATATTATATAAAAGTAAGAC
1 TTTTTTTTAATGTCAACCGTTTAAACTATAAGTATGAAACCATTTATATTATACAAAAGTAAGAC
* **
362116 AAAATAGGTTTTTCATGAAAACATAATAGGTAACACC
66 AAAACAGGTTGCTCATGAAAACATAATAGGTAACACC
362153 TTTTTTT
1 TTTTTTT
362160 ATGCAAAAGT
Statistics
Matches: 248, Mismatches: 55, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
98 2 0.01
99 49 0.20
100 61 0.25
101 45 0.18
102 91 0.37
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (102 bp):
TTTTTTTTAATGTCAACCGTTTAAACTATAAGTATGAAACCATTTATATTATACAAAAGTAAGAC
AAAACAGGTTGCTCATGAAAACATAATAGGTAACACC
Done.