Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000928.1 Hibiscus syriacus cultivar Beakdansim tig00001852_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: 81577
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:4183 original size:102 final size:103
Alignment explanation
Indices: 3926--4245 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
3916 TAATGTCCAT
*
3926 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATTAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
3991 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
4029 AAGAACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATAAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
*
4094 GACCTCACACATGTTCCAAAGAATACATATATGT-CCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
4131 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
*
4196 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
4234 AAGGACCACATA
1 AAGGACCACATA
4246 GACCCTCTAC
Statistics
Matches: 207, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
102 97 0.47
103 110 0.53
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATAAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:4810 original size:21 final size:21
Alignment explanation
Indices: 4792--4849 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
4782 TCGTTTGAGG
4792 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
4813 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
4834 GCGTATCGATTCCCCT
1 GGGTATCGATTCCCCT
4850 AGCCCAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:10899 original size:22 final size:23
Alignment explanation
Indices: 10853--10902 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
10843 CAGCTCATAT
*
10853 AATTGCACCTAAGTACCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* *
10876 AATTGCACCGGAGTA-CGCGTAG
1 AATTGCACCGAAGTACCACGTAG
10898 AATTG
1 AATTG
10903 TACTGTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:11115 original size:103 final size:103
Alignment explanation
Indices: 10931--11246 Score: 545
Period size: 103 Copynumber: 3.1 Consensus size: 103
10921 TAATGTCCAT
*
10931 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
10996 GACTTCA-ATCACGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACA-CATGTTCCAAAGAATACATATATGTCCCG
*
11034 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
11099 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11137 AAGGACCAC--ATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
11200 GACTTCACACATG-TCCAAAGAATAC--ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
11235 AAGGACCACATA
1 AAGGACCACATA
11247 GACCCTCTAC
Statistics
Matches: 204, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
98 19 0.09
100 13 0.06
101 65 0.32
103 106 0.52
104 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12743 original size:17 final size:16
Alignment explanation
Indices: 12721--12800 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 16
12711 AAAAAAGAAG
12721 AAGAAAAAAGAGAAAAA
1 AAGAAAAAAGA-AAAAA
12738 AAG-AAAAAGCAAAAGAA
1 AAGAAAAAAG-AAAA-AA
* * *
12755 AATAAAAAACAAAAGA
1 AAGAAAAAAGAAAAAA
*
12771 AATAAAAAAGCAAAAATA
1 AAGAAAAAAG-AAAAA-A
12789 AAGAAAAAAGAA
1 AAGAAAAAAGAA
12801 CAAGACGCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 19 0.37
17 18 0.35
18 15 0.29
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:12745 original size:29 final size:27
Alignment explanation
Indices: 12712--12805 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 27
12702 ATCAAGAACA
12712 AAAAAGAAGAAGAAAAAAGAGAAAAAAAG
1 AAAAAGAA-AAGAAAAAA-AGAAAAAAAG
12741 AAAAAGCAAAAGAAAATAAA-AAACAAAAG
1 AAAAAG-AAAAGAAAA-AAAGAAA-AAAAG
12770 AAATAA-AAAAGCAAAAATAA-AGAAAAAAG
1 AAA-AAGAAAAG-AAAAA-AAGA-AAAAAAG
*
12799 AACAAGA
1 AAAAAGA
12806 CGCTTATACA
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
28 11 0.20
29 37 0.66
30 8 0.14
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (27 bp):
AAAAAGAAAAGAAAAAAAGAAAAAAAG
Found at i:12761 original size:16 final size:18
Alignment explanation
Indices: 12741--12785 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
12731 AGAAAAAAAG
12741 AAAAAGCAAAAGAAA-ATA
1 AAAAAGCAAAAGAAATA-A
12759 AAAAA-CAAAAGAAAT-A
1 AAAAAGCAAAAGAAATAA
12775 AAAAAGCAAAA
1 AAAAAGCAAAA
12786 ATAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (18 bp):
AAAAAGCAAAAGAAATAA
Found at i:12761 original size:23 final size:23
Alignment explanation
Indices: 12705--12800 Score: 74
Period size: 23 Copynumber: 4.2 Consensus size: 23
12695 AGATCCAATC
* *
12705 AAGAACAAAAAAGAAGAAGAAAA
1 AAGAAAAAAAAAGAAAAAGAAAA
* *
12728 AAGAGAAAAAAAGAAAAAG-CAA
1 AAGAAAAAAAAAGAAAAAGAAAA
12750 AAGAAAATAAAAA-ACAAAAGAAATA
1 AAGAAAA-AAAAAGA-AAAAGAAA-A
** *
12775 AA-AAAGCAAAA-ATAAAGAAAA
1 AAGAAAAAAAAAGAAAAAGAAAA
12796 AAGAA
1 AAGAA
12801 CAAGACGCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.05
22 18 0.31
23 31 0.53
24 4 0.07
25 3 0.05
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAAAGAAAA
Found at i:12763 original size:12 final size:11
Alignment explanation
Indices: 12705--12797 Score: 62
Period size: 11 Copynumber: 7.8 Consensus size: 11
12695 AGATCCAATC
12705 AAGAACAAAAAA
1 AAGAA-AAAAAA
12717 GAAGAAGAAAAAA
1 -AAGAA-AAAAAA
*
12730 GAGAAAAAAAGA
1 AAGAAAAAAA-A
12742 AA-AAGCAAAAGAA
1 AAGAA--AAAA-AA
*
12755 AATAAAAAACAA
1 AAGAAAAAA-AA
*
12767 AAGAAATAAAA
1 AAGAAAAAAAA
* *
12778 AAGCAAAAATA
1 AAGAAAAAAAA
12789 AAGAAAAAA
1 AAGAAAAAA
12798 GAACAAGACG
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
11 25 0.38
12 19 0.29
13 18 0.28
14 3 0.05
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:12779 original size:11 final size:10
Alignment explanation
Indices: 12711--12797 Score: 63
Period size: 10 Copynumber: 8.6 Consensus size: 10
12701 AATCAAGAAC
*
12711 AAAAAAGAAG
1 AAAAAAAAAG
*
12721 AAGAAAAAAG
1 AAAAAAAAAG
*
12731 AGAAAAAAAG
1 AAAAAAAAAG
12741 AAAAAGCAAAAG
1 AAAAA--AAAAG
*
12753 --AAAATAA-
1 AAAAAAAAAG
*
12760 AAAACAAAAG
1 AAAAAAAAAG
12770 AAATAAAAAAG
1 AAA-AAAAAAG
*
12781 CAAAAATAAAG
1 -AAAAAAAAAG
12792 AAAAAA
1 AAAAAA
12798 GAACAAGACG
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 31 0.53
11 12 0.20
12 8 0.14
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:14407 original size:43 final size:43
Alignment explanation
Indices: 14333--14415 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
14323 CGAAGGGGCC
* *
14333 ATCCACGATTTCAACTCCACGAATGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTCCACGAACGAGGATATCATGCCCACAA
* * *
14376 ATCCACGATTTCAACTTCACG-GCGAATGATATCATGCCCA
1 ATCCACGATTTCAACTCCACGAACG-AGGATATCATGCCCA
14416 TCTACACAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGAACGAGGATATCATGCCCACAA
Found at i:14857 original size:37 final size:36
Alignment explanation
Indices: 14810--14898 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
14800 AACAAGGGTC
*
14810 GTCTCGCTTGAGACTA-ATT-TACTCAAAATAAAGTTTT
1 GTCTCTCTTGAGAC-AGATTCTACTCAAAA-AAA-TTTT
* * *
14847 GTCTCTCTTGAGACAGTTTCTATTGAAAAAAATTTT
1 GTCTCTCTTGAGACAGATTCTACTCAAAAAAATTTT
14883 GTCTCTCTTGAGACAG
1 GTCTCTCTTGAGACAG
14899 TTTCCCTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 21 0.46
37 18 0.39
38 7 0.15
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (36 bp):
GTCTCTCTTGAGACAGATTCTACTCAAAAAAATTTT
Found at i:14888 original size:36 final size:36
Alignment explanation
Indices: 14834--15085 Score: 202
Period size: 36 Copynumber: 7.1 Consensus size: 36
14824 TAATTTACTC
*
14834 AAAATAAAGTTTTGTCTCTCTTGAGACAGTTTCTATTG
1 AAAA-AAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
14872 AAAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
14908 AAACAAAA-------TCT-TTGA-ATATGTTT-TCTTTG
1 AAA-AAAATTTTGTCTCTCTTGAGACA-GTTTCTC-TTG
* * * * *
14937 AAACAAATTTCGTCTC-CATTAAGACAATTTCTTTTGG
1 AAAAAAATTTTGTCTCTC-TTGAGACAGTTTCTCTT-G
** ** *
14974 AACTAAGCTTTGTCTCTATTGAGACAGTTTCTCTTG
1 AAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
15010 AAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
15046 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAA-AAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
15083 AAA
1 AAA
15086 CACCAACCTT
Statistics
Matches: 168, Mismatches: 29, Indels: 35
0.72 0.12 0.15
Matches are distributed among these distances:
28 6 0.04
29 14 0.08
30 3 0.02
35 2 0.01
36 71 0.42
37 68 0.40
38 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (36 bp):
AAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:14999 original size:37 final size:36
Alignment explanation
Indices: 14929--15087 Score: 178
Period size: 37 Copynumber: 4.4 Consensus size: 36
14919 TTGAATATGT
* * * * *
14929 TTTCT-TTGAAACAAATTTCGTCTCCATTAAGACAA
1 TTTCTCTTGAAACAAGTTTTGTCTCTATTGAGACAG
* * *
14964 TTTCTTTTGGAACTAAGCTTTGTCTCTATTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTATTGAGACAG
*
15001 TTTCTCTTGAAACATA-TTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACA-AGTTTTGTCTCTATTGAGACAG
* *
15037 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTATTGAGACAG
15074 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
15088 CCAACCTTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
35 5 0.05
36 39 0.37
37 62 0.58
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTATTGAGACAG
Found at i:15059 original size:73 final size:73
Alignment explanation
Indices: 14929--15087 Score: 205
Period size: 73 Copynumber: 2.2 Consensus size: 73
14919 TTGAATATGT
** * *
14929 TTTCT-TTGAAACAAATTTCGTCTCCATTAAGACAATTTCTTTTGGAACTAAGCTTTGTCTCTAT
1 TTTCTCTTGAAACAAATTTCGTCTCCATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTAT
14993 TGAGACAG
66 TGAGACAG
* * * * * *
15001 TTTCTCTTGAAACATATTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTCGTCTC-CATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTA
15065 TTGAGACAG
65 TTGAGACAG
15074 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
15088 CCAACCTTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
72 5 0.07
73 69 0.92
74 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCATTAAGACAATTTCCCTTGAAACAAAGCTTTGTCTCTAT
TGAGACAG
Found at i:15144 original size:67 final size:69
Alignment explanation
Indices: 15035--15188 Score: 183
Period size: 67 Copynumber: 2.3 Consensus size: 69
15025 CTCTTGAGAC
* * * * **
15035 AGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCT-TGAA-AC-ACCAACCTTT
1 AGTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTGT-AACACAAAAAACCTTT
15097 G-AAT
65 GTAAT
*
15101 ATGTTTCTCTTTAAACAAAATTTTGCCTCCCTGTG-GACAGTTTCTCTGTAACACAAAAAACCTT
1 A-GTTTCTCTTGAAACAAAATTTTGCCTCCCT-TGAGACAGTTTCTCTGTAACACAAAAAACCTT
15165 TGTAAT
64 TGTAAT
15171 AGTTTCTCTTGAAACAAA
1 AGTTTCTCTTGAAACAAA
15189 CAAAAACCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
66 1 0.01
67 39 0.53
68 5 0.07
69 25 0.34
70 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (69 bp):
AGTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTGTAACACAAAAAACCTTTG
TAAT
Found at i:15198 original size:34 final size:32
Alignment explanation
Indices: 15139--15218 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 32
15129 CCCTGTGGAC
* * *
15139 AGTTTCTC-TGTAACACAAAAAACCTTTGTAAT
1 AGTTTCTCTTGAAACAAAAAAAACCTTTG-AAA
15171 AGTTTCTCTTGAAACAAACAAAAACCTTTGAAA
1 AGTTTCTCTTGAAACAAA-AAAAACCTTTGAAA
15204 ATGTTTCTCTTGAAA
1 A-GTTTCTCTTGAAA
15219 TACAAAAGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 8 0.19
33 10 0.24
34 24 0.57
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (32 bp):
AGTTTCTCTTGAAACAAAAAAAACCTTTGAAA
Found at i:17122 original size:7 final size:6
Alignment explanation
Indices: 17097--17130 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
17087 AAAGGTAAGC
17097 AATTTA AA-TTA AATTTA AATTTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AA-TTTA AATTTA AATT
17131 ATAATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:17123 original size:13 final size:13
Alignment explanation
Indices: 17097--17130 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
17087 AAAGGTAAGC
17097 AATTTAAA--TTA
1 AATTTAAATTTTA
17108 AATTTAAATTTTA
1 AATTTAAATTTTA
17121 AATTTAAATT
1 AATTTAAATT
17131 ATAATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
13 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:23731 original size:23 final size:23
Alignment explanation
Indices: 23705--23758 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
23695 AAATGCACTA
23705 AAGTGCCACGTAGAATTACACCG
1 AAGTGCCACGTAGAATTACACCG
* * *
23728 AAGTACCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTACACCG
*
23751 GAGTGCCA
1 AAGTGCCA
23759 TATAAAATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTACACCG
Found at i:25353 original size:20 final size:20
Alignment explanation
Indices: 25316--25353 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25306 TTCCCCTTGA
*
25316 AGTGCATCGATACTTTCTAC
1 AGTGCATCGATACATTCTAC
*
25336 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
25354 TTAACATGTA
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:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:25452 original size:64 final size:62
Alignment explanation
Indices: 25364--25522 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 62
25354 TTAACATGTA
* *
25364 CATCGATGCACTACCCATGCATCGATACACAAAT-CACCTTCGATGTTTTCA-TTTTAAGGGGGT
1 CATCGATGCACT-CCTATGCATCGATACACAAATGCA--TTCGATGTTTCCATTTTTAA-GGGGT
25427 G
62 G
* * * *
25428 CATCGATGCACTCCTTATGTATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGGGTG
1 CATCGATGCACTCC-TATGCATCGATACAC-AAATGCATTCGATGTTTCCATTTTTAAGGGGTG
*
25492 CATCGATGCACTTCCTGTGCATCGATACACA
1 CATCGATGCAC-TCCTATGCATCGATACACA
25523 CTGAACAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
63 3 0.04
64 64 0.79
65 12 0.15
66 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (62 bp):
CATCGATGCACTCCTATGCATCGATACACAAATGCATTCGATGTTTCCATTTTTAAGGGGTG
Found at i:28514 original size:23 final size:23
Alignment explanation
Indices: 28498--28579 Score: 155
Period size: 23 Copynumber: 3.6 Consensus size: 23
28488 CGTATAAATA
28498 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
28521 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
28544 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
28567 CACCGAAGTGCCA
1 CACCGAAGTGCCA
28580 TATAAAATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:30080 original size:20 final size:20
Alignment explanation
Indices: 30055--30092 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30045 TTCCCCTTGA
30055 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
30075 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
30093 GTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:32858 original size:60 final size:61
Alignment explanation
Indices: 32791--32911 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 61
32781 TCAATCCCAT
* * * *
32791 CTCAAATTAT-AATTATCATTTTAAATT-ATTCATTATAA-TTTTCAATATTCTAATTTCATC
1 CTCAAATTATGAATT-TCATTTTAAATTAATT-ATTAAAATTTTTAAATAATATAATTTCATC
*
32851 CTCAAATTATGAATTTCTTTTTAAATTAATTATTAAAATTTTTAAATAATATAATTTCATC
1 CTCAAATTATGAATTTCATTTTAAATTAATTATTAAAATTTTTAAATAATATAATTTCATC
32912 TCAGACTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 27 0.51
61 26 0.49
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (61 bp):
CTCAAATTATGAATTTCATTTTAAATTAATTATTAAAATTTTTAAATAATATAATTTCATC
Found at i:36973 original size:12 final size:12
Alignment explanation
Indices: 36951--36989 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
36941 AAATTATAAC
*
36951 TAATAATATTAAT
1 TAAT-ATATTAAA
*
36964 TATTATATTAAA
1 TAATATATTAAA
36976 TAATATATTAAA
1 TAATATATTAAA
36988 TA
1 TA
36990 TATTTATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATATTAAA
Found at i:40001 original size:8 final size:8
Alignment explanation
Indices: 39988--40028 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
39978 CTCATTTTCA
39988 GAGAATTT
1 GAGAATTT
39996 GAGAATTT
1 GAGAATTT
*
40004 -AGAGTTT
1 GAGAATTT
*
40011 GGGAATTT
1 GAGAATTT
40019 GAGAATTT
1 GAGAATTT
40027 GA
1 GA
40029 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:40043 original size:23 final size:23
Alignment explanation
Indices: 39990--40041 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
39980 CATTTTCAGA
* *
39990 GAATTTGAGAATTTAGAGTTTGG
1 GAATTTGAGAATTTAAAGATTGG
*
40013 GAATTTGAGAATTTGAAAGATTGT
1 GAATTTGAGAATTT-AAAGATTGG
40037 GAATT
1 GAATT
40042 GAAGTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (23 bp):
GAATTTGAGAATTTAAAGATTGG
Found at i:40327 original size:128 final size:128
Alignment explanation
Indices: 40099--40979 Score: 1547
Period size: 128 Copynumber: 6.9 Consensus size: 128
40089 TAATCAGAGT
*
40099 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
40164 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
40227 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
40292 CATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
40355 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTA
40419 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
40483 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGGCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
40548 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACT--ATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
40609 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
40673 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATTAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
40736 ACTATTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
40801 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
40864 ACTATTCATATGAAGGCGCGTTCCCGGGGG-GCGTCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* *
40928 CATTGCCCTATTATGTCACTCATGTCCCTCAGGAACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
40980 AATCAGGTAA
Statistics
Matches: 719, Mismatches: 29, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
125 76 0.11
126 46 0.06
127 130 0.18
128 466 0.65
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:40805 original size:381 final size:383
Alignment explanation
Indices: 40099--40979 Score: 1545
Period size: 381 Copynumber: 2.3 Consensus size: 383
40089 TAATCAGAGT
40099 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
40164 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA-ATATATCAGTACCTATTATTTCAC
* * *
40229 TATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTATCA
130 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
40294 TTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAG
195 TTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAG
* * *
40359 GGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTTCAGAGAATATGTTATCATT
260 GGCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
40424 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
325 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
40483 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGGCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
40548 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACT-ATATATCAGTACCTATTATTTCACT
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAATATATCAGTACCTATTATTTCACT
40612 ATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
131 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
* *
40676 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATTAGTACCTATTATTTCACTA-
196 TGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AG
**
40740 TTCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
260 GGCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
40805 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
325 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
40864 ACTATTCATATGAAGGCGCGTTCCCGGGGG-GCGTCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
40928 CATTGCCCTATTATGTCACTCATGTCCCTCAGGAACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA-ATATATCAGTA
40980 AATCAGGTAA
Statistics
Matches: 475, Mismatches: 19, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
380 69 0.15
381 246 0.52
382 58 0.12
384 102 0.21
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (383 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAATATATCAGTACCTATTATTTCACT
ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
TGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGG
GCACATGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:41439 original size:33 final size:33
Alignment explanation
Indices: 41378--41475 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
41368 AAATTTAATG
*
41378 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATAT-ATTTATATTTTAAAT
* * *
41412 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATA-TATTTATATTTTAAAT
*
41445 TTAAATTTCGAATAATA-ATTTGTATTTTAAA
1 TTAAATTTCGAATAATATATTTATATTTTAAA
41476 AACATTTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 11 0.20
33 27 0.49
34 17 0.31
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTAAATTTCGAATAATATATTTATATTTTAAAT
Found at i:42192 original size:33 final size:32
Alignment explanation
Indices: 42150--42237 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
42140 AAAATAATTC
*
42150 TAAATAAATAATAATTATATAAATATTATT-TTAA
1 TAAA-AAATAATAATTATATAAATA-TATTAAT-A
* *
42184 TAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
42216 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
42238 AAATACTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 23 0.50
33 19 0.41
34 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:42214 original size:30 final size:34
Alignment explanation
Indices: 42150--42228 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
42140 AAAATAATTC
* *
42150 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
42184 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
42216 TAAAAAATAATAA
1 TAAAAAATAATAA
42229 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:45338 original size:78 final size:78
Alignment explanation
Indices: 45194--45365 Score: 265
Period size: 78 Copynumber: 2.2 Consensus size: 78
45184 TCATCGGATG
* * * * *
45194 AGTTC-TCTCATTATGAACTCTTCACTGGCAATGTTGATCCACCTCTTTCTGTGATGGAATTAGG
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAGG
45258 CAAAGATTGAAAA
66 CAAAGATTGAAAA
* *
45271 AGTTCTTCTCATTATGAATTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCGGG
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAGG
*
45336 CAAAGATTGAACA
66 CAAAGATTGAAAA
45349 AGTTCTTCTCATTATGA
1 AGTTCTTCTCATTATGA
45366 GTTTCTTCTC
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 5 0.06
78 81 0.94
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (78 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAGG
CAAAGATTGAAAA
Found at i:48688 original size:20 final size:20
Alignment explanation
Indices: 48646--48689 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
48636 TTATCGTTCG
* *
48646 ATGTTATATTAAATGAATGA
1 ATGTTATATTAAATCAATAA
**
48666 ATGTTATATTACTTCAATAA
1 ATGTTATATTAAATCAATAA
48686 ATGT
1 ATGT
48690 AAGTACATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTTATATTAAATCAATAA
Found at i:49275 original size:34 final size:34
Alignment explanation
Indices: 49237--49302 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
49227 AGAAATAAGT
49237 TAGTGCATGTAAGATAATCGAAAAAGATAAAATG
1 TAGTGCATGTAAGATAATCGAAAAAGATAAAATG
49271 TAGTGCATGTAAGATAATCGAAAAAGATAAAA
1 TAGTGCATGTAAGATAATCGAAAAAGATAAAA
49303 GGACTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.23
Consensus pattern (34 bp):
TAGTGCATGTAAGATAATCGAAAAAGATAAAATG
Found at i:52076 original size:3 final size:3
Alignment explanation
Indices: 52068--52127 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
52058 GGGTTTGTAA
* * * * *
52068 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT GAT AAT GAT -AT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52115 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
52128 TAGGGCGAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53313 original size:30 final size:30
Alignment explanation
Indices: 53277--53336 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
53267 AATCTCTCTC
*
53277 CTTGGACACTTTTTTTCTTTGCTATTGTGG
1 CTTGGACACTTTTTTTCTCTGCTATTGTGG
53307 CTTGGACACTTTTTTTCTCTGCTATTGTGG
1 CTTGGACACTTTTTTTCTCTGCTATTGTGG
53337 TGCGATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.20, T:0.52
Consensus pattern (30 bp):
CTTGGACACTTTTTTTCTCTGCTATTGTGG
Found at i:53753 original size:11 final size:11
Alignment explanation
Indices: 53737--53769 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
53727 AGTTGTCATT
53737 GTTAAAAA-ACA
1 GTTAAAAAGA-A
53748 GTTAAAAAGAA
1 GTTAAAAAGAA
53759 GTTAAAAAGAA
1 GTTAAAAAGAA
53770 TCAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.64, C:0.03, G:0.15, T:0.18
Consensus pattern (11 bp):
GTTAAAAAGAA
Found at i:56549 original size:36 final size:36
Alignment explanation
Indices: 56502--56689 Score: 277
Period size: 36 Copynumber: 5.2 Consensus size: 36
56492 GAAAACGAAC
* *
56502 ACTTGGATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* *
56538 ACTTGAATCGGAAGTGTCGATACTTTCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
56574 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* * *
56610 ATTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
* * *
56646 ATTTGAATCGGAAGTGACGATACTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
*
56682 ATTTGAAT
1 ACTTGAAT
56690 TGTCGGTGCA
Statistics
Matches: 139, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 139 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
Found at i:58218 original size:19 final size:19
Alignment explanation
Indices: 58190--58226 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58180 ACATTAGCAG
*
58190 TGCATGTTCTAGAATGCAA
1 TGCATATTCTAGAATGCAA
58209 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
58227 TATTCCAATA
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:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAA
Found at i:59696 original size:2 final size:2
Alignment explanation
Indices: 59689--59713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59679 AAACTCTCAC
59689 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
59714 AATTCATTTT
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:61203 original size:14 final size:14
Alignment explanation
Indices: 61184--61214 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
61174 TTACTTCTCT
61184 TAATTGTTAAGTAA
1 TAATTGTTAAGTAA
61198 TAATTGTTAAGTAA
1 TAATTGTTAAGTAA
61212 TAA
1 TAA
61215 AGCATTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
TAATTGTTAAGTAA
Found at i:70163 original size:24 final size:24
Alignment explanation
Indices: 70136--70192 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
70126 ACTTTGGGAT
70136 GCAAATGGATAGGATTCAAACATG
1 GCAAATGGATAGGATTCAAACATG
70160 GCAAATGGATAGGATTCAAACATG
1 GCAAATGGATAGGATTCAAACATG
*
70184 GAAAATGGA
1 GCAAATGGA
70193 CAACAAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (24 bp):
GCAAATGGATAGGATTCAAACATG
Found at i:74980 original size:36 final size:36
Alignment explanation
Indices: 74898--75039 Score: 223
Period size: 36 Copynumber: 4.0 Consensus size: 36
74888 TGAACAAGAA
*
74898 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT-
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
74933 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* *
74969 GAACGGAAGGAAGCATCGACACTTTCGATTCAAATC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* * *
75005 GAACGGAAAGAGGCATCGGCACTTTTGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
75040 GTTCATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 34 0.35
36 64 0.65
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
Found at i:77109 original size:17 final size:17
Alignment explanation
Indices: 77087--77129 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
77077 TGTGGGTGCC
77087 GTCACGTTTTCGGTCAT
1 GTCACGTTTTCGGTCAT
77104 GTCACGTTTTCGGTCAT
1 GTCACGTTTTCGGTCAT
77121 GTCACGTTT
1 GTCACGTTT
77130 ACCGCAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (17 bp):
GTCACGTTTTCGGTCAT
Done.