Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001466.1 Hibiscus syriacus cultivar Beakdansim tig00002841_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: 1236886
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:2578 original size:30 final size:30
Alignment explanation
Indices: 2543--2633 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
2533 CCCGAATGAC
* *
2543 CTATCCATATGTTCCGAAGAACATATGTAA
1 CTATCCATATGTCCCGAAGAACATAGGTAA
*
2573 CTATCCATATGTCCCGAAGGACATAGGTAAA
1 CTATCCATATGTCCCGAAGAACATAGGT-AA
* * *
2604 CTGTCTATATGTCTCGAA-AGACATA-GTAA
1 CTATCCATATGTCCCGAAGA-ACATAGGTAA
2633 C
1 C
2634 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.06
30 27 0.52
31 22 0.42
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (30 bp):
CTATCCATATGTCCCGAAGAACATAGGTAA
Found at i:3339 original size:21 final size:21
Alignment explanation
Indices: 3309--3366 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
3299 AGGGTGTCAA
*
3309 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCCTGC
*
3330 AGTGCGTCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
3351 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
3367 TGCCACTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:3453 original size:20 final size:20
Alignment explanation
Indices: 3428--3482 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3418 AATGCAATTA
*
3428 GTGCATCAATGCACCCTGCT
1 GTGCATCCATGCACCCTGCT
3448 GTGCATCCATGCACCCTGCT
1 GTGCATCCATGCACCCTGCT
3468 GTGCATCCATGCACC
1 GTGCATCCATGCACC
3483 AAGGCTGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (20 bp):
GTGCATCCATGCACCCTGCT
Found at i:12039 original size:25 final size:25
Alignment explanation
Indices: 11990--12041 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
11980 AAGGATATAA
11990 TAAATGAATAAATAAATAGATAATG
1 TAAATGAATAAATAAATAGATAATG
12015 TAAATGAATAAATAAATAGATAATG
1 TAAATGAATAAATAAATAGATAATG
12040 TA
1 TA
12042 TGTACTGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (25 bp):
TAAATGAATAAATAAATAGATAATG
Found at i:17762 original size:36 final size:36
Alignment explanation
Indices: 17715--17851 Score: 211
Period size: 36 Copynumber: 3.8 Consensus size: 36
17705 TACATCATTT
* *
17715 CGTTCAACTTGAATCGGAAGTGCCGATGCTTCCTTC
1 CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTC
17751 CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTC
1 CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTC
* *
17787 AGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTTC
1 CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTC
* * *
17823 CGTTTGACTTAAATCGGAAGTGTCGATGC
1 CGTTCGACTTGAATCGGAAGTGCCGATGC
17852 TTTCTTTCGT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (36 bp):
CGTTCGACTTGAATCGGAAGTGCCGATGCCTCCTTC
Found at i:18685 original size:17 final size:17
Alignment explanation
Indices: 18663--18701 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
18653 CCATACGTCG
18663 GCGGCCTTCCATTTTAA
1 GCGGCCTTCCATTTTAA
18680 GCGGCCTTCCATTTTAA
1 GCGGCCTTCCATTTTAA
18697 GCGGC
1 GCGGC
18702 GATGGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (17 bp):
GCGGCCTTCCATTTTAA
Found at i:20571 original size:11 final size:11
Alignment explanation
Indices: 20555--20617 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
20545 AAAATTACAT
20555 TATTAAAAATA
1 TATTAAAAATA
20566 TATTAAAAATA
1 TATTAAAAATA
* * **
20577 CACTATTAATA
1 TATTAAAAATA
20588 -ATTATAAAAT-
1 TATTA-AAAATA
20598 T-TTAAAAATA
1 TATTAAAAATA
*
20608 TGTTAAAAAT
1 TATTAAAAAT
20618 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 29 0.71
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:20572 original size:25 final size:24
Alignment explanation
Indices: 20543--20598 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
20533 TTTAGATTTT
*
20543 TTAAAATTACATTATTAAAAATATA
1 TTAAAATTACACTATTAAAAAT-TA
* *
20568 TTAAAAATACACTATTAATAATTA
1 TTAAAATTACACTATTAAAAATTA
20592 -TAAAATT
1 TTAAAATT
20599 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 19 0.70
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAAATTACACTATTAAAAATTA
Found at i:23689 original size:31 final size:31
Alignment explanation
Indices: 23647--23771 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
23637 AGGGTCGAGG
*
23647 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
23678 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
23709 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
23740 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
23771 G
1 G
23772 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:24277 original size:21 final size:21
Alignment explanation
Indices: 24252--24294 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
24242 AAAGAATATA
24252 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
24273 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
24294 T
1 T
24295 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:26936 original size:18 final size:19
Alignment explanation
Indices: 26902--26957 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
26892 AAGAGGGAGG
*
26902 GAAAAAATATAATAATAATA
1 GAAAAAAAAT-ATAATAATA
26922 GAAAAAAAATA-AATAAT-
1 GAAAAAAAATATAATAATA
* *
26939 GTAAATAAATATAATAATA
1 GAAAAAAAATATAATAATA
26958 AAGAAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 12 0.39
19 1 0.03
20 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
GAAAAAAAATATAATAATA
Found at i:26979 original size:36 final size:38
Alignment explanation
Indices: 26899--26980 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
26889 TATAAGAGGG
26899 AGGG-AAAAAATATAATAATAATAGAAAAAAAATAAAT
1 AGGGTAAAAAATATAATAATAATAGAAAAAAAATAAAT
** **
26936 AATGTAAATAAATATAATAATAA-AG-AAGTAAA-AAAT
1 AGGGTAAA-AAATATAATAATAATAGAAAAAAAATAAAT
26972 AGGGTAAAA
1 AGGGTAAAA
26981 TACAAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
35 1 0.03
36 10 0.27
37 7 0.19
38 5 0.14
39 14 0.38
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (38 bp):
AGGGTAAAAAATATAATAATAATAGAAAAAAAATAAAT
Found at i:28762 original size:105 final size:105
Alignment explanation
Indices: 28512--29008 Score: 833
Period size: 105 Copynumber: 4.8 Consensus size: 105
28502 TAATTGTTTA
* *
28512 TTGACAACCAGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
28577 TTGTGAAGTTGAAATTGGCTCTGA-A-T-GAAA-TT-TTG
66 TTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
* *
28612 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTCCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
28677 TTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
66 TTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
* *
28717 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
28782 TTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG
66 TTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
*
28822 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
28887 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTA
66 TTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTG
28929 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
28994 TTGTGAAGTTGAAAT
66 TTGTGAAGTTGAAAT
29009 CCACTCTCGA
Statistics
Matches: 373, Mismatches: 17, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
100 85 0.23
101 1 0.00
102 1 0.00
103 4 0.01
104 2 0.01
105 193 0.52
106 7 0.02
107 80 0.21
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (105 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
Found at i:29727 original size:66 final size:67
Alignment explanation
Indices: 29656--29813 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
29646 GAAACGAAAT
* *
29656 TTTGTTTTAAGGGAGATA-AAT-TCAAAGA-TTTGTGTTTCAAGAGAAACTGTCTCATAGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGAC
29718 AAAA
64 AAAA
*
29722 TTTGTTTCGAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
29787 AA
66 AA
**
29789 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
29814 GAGAGACGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
64 1 0.01
65 4 0.05
66 19 0.23
67 59 0.71
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAAGGAGACAA
AA
Found at i:29738 original size:36 final size:35
Alignment explanation
Indices: 29688--29959 Score: 187
Period size: 36 Copynumber: 7.9 Consensus size: 35
29678 CAAAGATTTG
*
29688 TGTTTCAAGAGAAACTGTCTCATAGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCA-AGGAGACAAAATT
* ** **
29724 TGTTTCGAGGGAAACAATCTCAA--AG---ATTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
*
29754 GTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTC-AAGGAGACAAAATT
* * *
29791 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
** * * *
29827 CATTTCAAGGGAAA-TGTTTTCAA--TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATT
29855 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAA-GGAGACAAAA-TT
* *
29893 TGTTTCAAAGGAAACTGTCTCAAGAGAGAC-AAAGT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
29928 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
29960 TGGTGAGCAC
Statistics
Matches: 182, Mismatches: 30, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
28 5 0.03
29 13 0.07
30 5 0.03
31 17 0.09
32 3 0.02
33 3 0.02
34 2 0.01
35 35 0.19
36 68 0.37
37 27 0.15
38 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:29888 original size:101 final size:101
Alignment explanation
Indices: 29755--29941 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 101
29745 AAAGATTTTG
* *
29755 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
29819 ACGAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 AC-AAAGTT-ATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
29856 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
*
29921 ACAAAGTTGTTTCAAGGGAAA
66 ACAAAGTTATTTCAAGGGAAA
29942 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
101 47 0.60
102 31 0.40
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
ACAAAGTTATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:29907 original size:37 final size:36
Alignment explanation
Indices: 29866--29959 Score: 145
Period size: 35 Copynumber: 2.6 Consensus size: 36
29856 TGTTTCAGGA
* *
29866 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAG
1 GAAACTGTCTCAAGAGAGACAAAA-GTTGTTTCAAAG
*
29903 GAAACTGTCTCAAGAGAGAC-AAAGTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAAGTTGTTTCAAAG
29938 GAAACTGTCTCAAGAGAGACAA
1 GAAACTGTCTCAAGAGAGACAA
29960 TGGTGAGCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 30 0.57
36 4 0.08
37 19 0.36
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAAGTTGTTTCAAAG
Found at i:30428 original size:18 final size:18
Alignment explanation
Indices: 30401--30436 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30391 TGATGAATCC
* *
30401 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
30419 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
30437 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:30876 original size:22 final size:22
Alignment explanation
Indices: 30851--30899 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
30841 TTGTGTTTGG
* *
30851 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
30873 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
30895 TCAAA
1 TCAAA
30900 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:30906 original size:22 final size:22
Alignment explanation
Indices: 30863--30906 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30853 AAAGGTTTGG
* * *
30863 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
30885 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
30907 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:31557 original size:8 final size:7
Alignment explanation
Indices: 31546--31615 Score: 50
Period size: 8 Copynumber: 8.9 Consensus size: 7
31536 TTTTTGCTCT
31546 TTTTTTCC
1 TTTTTT-C
31554 TTTTGTTC
1 TTTT-TTC
*
31562 TTGTTTC
1 TTTTTTC
31569 TCTTTTTC
1 T-TTTTTC
*
31577 TTTGTTTTT
1 -TT-TTTTC
31586 TTTTTTGC
1 TTTTTT-C
31594 TTTTTTGC
1 TTTTTT-C
31602 TTCTTTTC
1 TT-TTTTC
31610 TTTTTT
1 TTTTTT
31616 GTTCTTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 12 0.23
8 29 0.56
9 11 0.21
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:31614 original size:16 final size:16
Alignment explanation
Indices: 31569--31621 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
31559 TTCTTGTTTC
* *
31569 TCTTTTTCTTTGTTTTT
1 TCTTTTGCTTT-TTTGT
*
31586 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
31603 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
31618 TCTT
1 TCTT
31622 GATTGGATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.16
16 11 0.35
17 15 0.48
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:35005 original size:18 final size:19
Alignment explanation
Indices: 34971--35026 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
34961 AAGAGGGAGG
*
34971 GAAAAAATATAATAATAATA
1 GAAAAAAAAT-ATAATAATA
34991 GAAAAAAAATA-AATAAT-
1 GAAAAAAAATATAATAATA
* *
35008 GTAAATAAATATAATAATA
1 GAAAAAAAATATAATAATA
35027 AAGAAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.29
18 12 0.39
19 1 0.03
20 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
GAAAAAAAATATAATAATA
Found at i:35048 original size:36 final size:38
Alignment explanation
Indices: 34968--35049 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
34958 TATAAGAGGG
34968 AGGG-AAAAAATATAATAATAATAGAAAAAAAATAAAT
1 AGGGTAAAAAATATAATAATAATAGAAAAAAAATAAAT
** **
35005 AATGTAAATAAATATAATAATAA-AG-AAGTAAA-AAAT
1 AGGGTAAA-AAATATAATAATAATAGAAAAAAAATAAAT
35041 AGGGTAAAA
1 AGGGTAAAA
35050 TACAAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
35 1 0.03
36 10 0.27
37 7 0.19
38 5 0.14
39 14 0.38
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (38 bp):
AGGGTAAAAAATATAATAATAATAGAAAAAAAATAAAT
Found at i:38125 original size:31 final size:31
Alignment explanation
Indices: 38087--38304 Score: 375
Period size: 31 Copynumber: 7.0 Consensus size: 31
38077 AGGGTCGAGG
*
38087 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
38118 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
38149 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
38180 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
38211 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
38242 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
38273 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
38304 G
1 G
38305 GTCTTTCGGG
Statistics
Matches: 180, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 179 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:60399 original size:16 final size:16
Alignment explanation
Indices: 60366--60399 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60356 TTACTATTCA
*
60366 CGTGAATAGCGAATTT
1 CGTGAATAGCGAAATT
*
60382 CGTGAATAGTGAAATT
1 CGTGAATAGCGAAATT
60398 CG
1 CG
60400 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (16 bp):
CGTGAATAGCGAAATT
Found at i:61170 original size:15 final size:16
Alignment explanation
Indices: 61150--61181 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
61140 TGGCAGATCC
61150 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
61165 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
61181 A
1 A
61182 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:69452 original size:3 final size:3
Alignment explanation
Indices: 69440--69489 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
69430 TATTAAAAAA
*
69440 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69488 AA
1 AA
69490 ACCCTCGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:70131 original size:31 final size:31
Alignment explanation
Indices: 70096--70155 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
70086 ATAATACCAA
* *
70096 AACATTTAGTCTATTTTCAATATGGTCCCTC
1 AACATTTAATCCATTTTCAATATGGTCCCTC
*
70127 AACATTTAATCCGTTTTCAATATGGTCCC
1 AACATTTAATCCATTTTCAATATGGTCCC
70156 CGACGTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (31 bp):
AACATTTAATCCATTTTCAATATGGTCCCTC
Found at i:70726 original size:34 final size:34
Alignment explanation
Indices: 70688--70759 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
70678 TCACTCGTCA
70688 AAACTAAATATGCTTAATTCGGATTAGTCAAGAT
1 AAACTAAATATGCTTAATTCGGATTAGTCAAGAT
70722 AAACTAAATATGCTTAATTCGGATTAGTCAAGAT
1 AAACTAAATATGCTTAATTCGGATTAGTCAAGAT
70756 AAAC
1 AAAC
70760 CTTGAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (34 bp):
AAACTAAATATGCTTAATTCGGATTAGTCAAGAT
Found at i:72336 original size:34 final size:34
Alignment explanation
Indices: 72298--72374 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
72288 TTTTTTCATG
* *
72298 CATGATGACATAATATTATTGTCTGTACATTATA
1 CATGATGACATAATATTATTGTCGGTAAATTATA
* * *
72332 CATGATGATATGATATTGTTGTCGGTAAATTATA
1 CATGATGACATAATATTATTGTCGGTAAATTATA
*
72366 CAGGATGAC
1 CATGATGAC
72375 GTGATATCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (34 bp):
CATGATGACATAATATTATTGTCGGTAAATTATA
Found at i:72550 original size:3 final size:3
Alignment explanation
Indices: 72544--72592 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
72534 TTTTCATTTG
72544 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72592 A
1 A
72593 CTAAATAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:74759 original size:2 final size:2
Alignment explanation
Indices: 74752--74777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74742 TGTTTTCATA
74752 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
74778 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77090 original size:31 final size:31
Alignment explanation
Indices: 77052--77114 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
77042 AGGGTCGAGG
*
77052 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
77083 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTAGGTTCTTCGGGATCTATGGACT
77114 G
1 G
77115 GTCCTTCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGATCTATGGACT
Found at i:77402 original size:17 final size:18
Alignment explanation
Indices: 77376--77409 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
77366 AATGATAATG
77376 ATGATATATGTT-TATGT
1 ATGATATATGTTATATGT
*
77393 ATGATTTATGTTATATG
1 ATGATATATGTTATATG
77410 AAATATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
ATGATATATGTTATATGT
Found at i:80300 original size:64 final size:62
Alignment explanation
Indices: 80232--80452 Score: 209
Period size: 64 Copynumber: 3.5 Consensus size: 62
80222 TTGAAGGTGT
*
80232 ATCGATGCA-CAGGAAGTGCATCGATGCACTCTTTTAAAATAAAAACATCGAATGCAATTCATGC
1 ATCGATGCATCAGGTAGTGCATCGATGCA-TC--TTAAAATAAAAACATCGAATGCAATTCATGC
* * **
80296 ATCGATGCAT-AAGTAGTGCATCGATGCATCCCATTAATAAT-GAAACATCGAATGCAATTGGTG
1 ATCGATGCATCAGGTAGTGCATCGATGCAT--C-TTAA-AATAAAAACATCGAATGCAATTCATG
80359 C
62 C
* * * * * *
80360 ATCGATGCATAAGG-AGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATCAGGTAGTGCATCGATGCATCTTA-AAATAA-A-AACATCGAATGCAATTCATGC
*
80424 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCATCAGGTAGTGCATCGATGCAT
80453 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
61 5 0.04
62 1 0.01
63 3 0.02
64 116 0.89
65 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (62 bp):
ATCGATGCATCAGGTAGTGCATCGATGCATCTTAAAATAAAAACATCGAATGCAATTCATGC
Found at i:87069 original size:14 final size:15
Alignment explanation
Indices: 87052--87089 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
87042 GCCATAGGCC
87052 AATTATCATA-TTTT
1 AATTATCATATTTTT
*
87066 AATTTTCATATTTTT
1 AATTATCATATTTTT
*
87081 AATGATCAT
1 AATTATCAT
87090 TAGTGCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTATCATATTTTT
Found at i:87247 original size:55 final size:55
Alignment explanation
Indices: 87163--87280 Score: 218
Period size: 55 Copynumber: 2.1 Consensus size: 55
87153 AAACTCAGTT
87163 TGTTTCATTCACAAATATCAATATTCGAAGCACAAACCTTGCTTATTGAATATAG
1 TGTTTCATTCACAAATATCAATATTCGAAGCACAAACCTTGCTTATTGAATATAG
*
87218 TGTTTCATTCACAAATATCAATATTCGAAGCACATACCTTGCTTATTGAATATAG
1 TGTTTCATTCACAAATATCAATATTCGAAGCACAAACCTTGCTTATTGAATATAG
*
87273 TGTCTCAT
1 TGTTTCAT
87281 CCCTTAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
TGTTTCATTCACAAATATCAATATTCGAAGCACAAACCTTGCTTATTGAATATAG
Found at i:90944 original size:18 final size:18
Alignment explanation
Indices: 90921--90961 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
90911 TTATTATAAA
90921 ATAATATTTATTCAAAAG
1 ATAATATTTATTCAAAAG
90939 ATAATATTTATTCAAAAG
1 ATAATATTTATTCAAAAG
90957 ATAAT
1 ATAAT
90962 CATATGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
ATAATATTTATTCAAAAG
Found at i:103986 original size:20 final size:20
Alignment explanation
Indices: 103961--104001 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
103951 TATTTTATTG
103961 TTTTTAATTAA-GTAATTAAT
1 TTTTTAA-TAATGTAATTAAT
*
103981 TTTTTAATAATTTAATTAAT
1 TTTTTAATAATGTAATTAAT
104001 T
1 T
104002 AATTTGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATGTAATTAAT
Found at i:104020 original size:28 final size:28
Alignment explanation
Indices: 103963--104021 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
103953 TTTTATTGTT
* *
103963 TTTAATTAAGTAATTAATTTTTTAATAA
1 TTTAATTAAGTAATTAAGTTTATAATAA
* *
103991 TTTAATTAATTAATTTGAGTTTATAA-AA
1 TTTAATTAAGTAA-TTAAGTTTATAATAA
104019 TTT
1 TTT
104022 TAACTTATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (28 bp):
TTTAATTAAGTAATTAAGTTTATAATAA
Found at i:104134 original size:2 final size:2
Alignment explanation
Indices: 104127--104156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
104117 ATTTCTAATA
104127 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
104157 TCATGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104812 original size:25 final size:27
Alignment explanation
Indices: 104750--104812 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 27
104740 TTTTTAATTT
*
104750 TCATTTATTTAAATTTTACATATTTAA
1 TCATTTATTTAAATTTTACAAATTTAA
**
104777 TC-TTTCCTTAAA-TTTA-AAATTTAAA
1 TCATTTATTTAAATTTTACAAATTT-AA
104802 TCATTT-TTTAA
1 TCATTTATTTAA
104813 TATAAAGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 5 0.17
25 12 0.40
26 11 0.37
27 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (27 bp):
TCATTTATTTAAATTTTACAAATTTAA
Found at i:110561 original size:37 final size:36
Alignment explanation
Indices: 110485--110555 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
110475 TGAAGACCGG
* *
110485 TCAATAATGTAAAAAAAGGTGTTGATTGATATGCTA
1 TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
110521 TCAATAATGT-AAAAAAGGTGTCGATTAATATGCTA
1 TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
110556 CATCAACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.32
Consensus pattern (36 bp):
TCAATAATGTAAAAAAAGGTGTCGATTAATATGCTA
Found at i:112520 original size:23 final size:23
Alignment explanation
Indices: 112484--112547 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
112474 CAGCTCATAT
*
112484 AAATGCACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * *
112507 AATTACACCTAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
112530 AAATGCACCGAAGTGCCA
1 AAATACACCGAAGTGCCA
112548 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:113014 original size:30 final size:30
Alignment explanation
Indices: 112955--113014 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
112945 TCAAATTTAT
* *
112955 CATTTATTCACATAAATCAATTACTCATAG
1 CATTTAATCACATAAATCAATTACGCATAG
112985 CATTTAATCACATAGAA-C-ATATACGCATAG
1 CATTTAATCACATA-AATCAAT-TACGCATAG
113015 TGCTTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.08
30 22 0.85
31 2 0.08
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (30 bp):
CATTTAATCACATAAATCAATTACGCATAG
Found at i:120604 original size:31 final size:31
Alignment explanation
Indices: 120563--120622 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
120553 TCACTTCAAC
*
120563 CTCATATCATTTCAAGTTGTTTAAGATGTAG
1 CTCATATCATTTCAAGTTATTTAAGATGTAG
* *
120594 CTCATGTCATTTTAAGTTATTTAAGATGT
1 CTCATATCATTTCAAGTTATTTAAGATGT
120623 GGGTCATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (31 bp):
CTCATATCATTTCAAGTTATTTAAGATGTAG
Found at i:122664 original size:31 final size:31
Alignment explanation
Indices: 122577--122664 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
122567 ATTTTTAAAA
* *
122577 ATTATAAAATGATTATTAAATTTATTAAATT
1 ATTATAAAATGATCATTAAATTTATCAAATT
* * *
122608 ATTATAAAACGATCATTAATTTTATCGAATT
1 ATTATAAAATGATCATTAAATTTATCAAATT
*
122639 ATTATAAAATGGTCATTAAATTTATC
1 ATTATAAAATGATCATTAAATTTATC
122665 CAACTTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATTATAAAATGATCATTAAATTTATCAAATT
Found at i:124874 original size:30 final size:30
Alignment explanation
Indices: 124838--124897 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
124828 AAGAACACTC
124838 GAATATCAAATAGTATACTAATTTAAAGAA
1 GAATATCAAATAGTATACTAATTTAAAGAA
124868 GAATATCAAATAGTATACTAATTTAAAGAA
1 GAATATCAAATAGTATACTAATTTAAAGAA
124898 AGCTGCAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (30 bp):
GAATATCAAATAGTATACTAATTTAAAGAA
Found at i:127955 original size:33 final size:33
Alignment explanation
Indices: 127915--127981 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
127905 AACTCTTATA
127915 TAAATTATGTTGGATTATATATTACAAATATGG
1 TAAATTATGTTGGATTATATATTACAAATATGG
127948 TAAATTATGTTGGATTATATATTACAAATATGG
1 TAAATTATGTTGGATTATATATTACAAATATGG
127981 T
1 T
127982 GTTAGCTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (33 bp):
TAAATTATGTTGGATTATATATTACAAATATGG
Found at i:135986 original size:24 final size:24
Alignment explanation
Indices: 135950--135999 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
135940 CTCAAAGTCA
135950 TTGTACTCCTTTTAAAATTGAAAT
1 TTGTACTCCTTTTAAAATTGAAAT
* *
135974 TTGTAGTCTTTTTAAAATTGAAAT
1 TTGTACTCCTTTTAAAATTGAAAT
135998 TT
1 TT
136000 AGTCATCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (24 bp):
TTGTACTCCTTTTAAAATTGAAAT
Found at i:145296 original size:2 final size:2
Alignment explanation
Indices: 145289--145316 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
145279 GCTAGGGAAA
145289 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
145317 TACCTAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147997 original size:6 final size:6
Alignment explanation
Indices: 147982--148019 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
147972 GGTTAAATTT
*
147982 ATTA-A ATTAGA ATTAGA ATTAGA ATTATA ATTA-A ATTA
1 ATTAGA ATTAGA ATTAGA ATTAGA ATTAGA ATTAGA ATTA
148020 ATAAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (6 bp):
ATTAGA
Found at i:148032 original size:21 final size:21
Alignment explanation
Indices: 148007--148064 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
147997 GAATTAGAAT
148007 TATAATTAAATTAATAAAATA
1 TATAATTAAATTAATAAAATA
* ** *
148028 TATAAATAATAAGAATCAAATA
1 TATAATTAA-ATTAATAAAATA
* *
148050 TGTAATTATATTAAT
1 TATAATTAAATTAAT
148065 TTACTTAACT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
TATAATTAAATTAATAAAATA
Found at i:156942 original size:3 final size:3
Alignment explanation
Indices: 156934--156997 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
156924 CAGTTTACTT
* * *
156934 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTG
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
156980 TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
156998 AATAAATATT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:158364 original size:12 final size:12
Alignment explanation
Indices: 158334--158371 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
158324 ATTACTTTTA
158334 TATTTTAATTAT
1 TATTTTAATTAT
**
158346 TGCTTTAATTAT
1 TATTTTAATTAT
158358 TATTTT-ATTAT
1 TATTTTAATTAT
158369 TAT
1 TAT
158372 CTTAGTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:158392 original size:2 final size:2
Alignment explanation
Indices: 158379--158411 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
158369 TATCTTAGTC
*
158379 AT AT AA AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158412 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:164000 original size:18 final size:19
Alignment explanation
Indices: 163977--164012 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
163967 AAGAAAGAAG
163977 AAAAAAAAAC-ACAAAAAT
1 AAAAAAAAACAACAAAAAT
163995 AAAAAAAAACAACAAAAA
1 AAAAAAAAACAACAAAAA
164013 AGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (19 bp):
AAAAAAAAACAACAAAAAT
Found at i:166302 original size:115 final size:115
Alignment explanation
Indices: 166093--166321 Score: 341
Period size: 115 Copynumber: 2.0 Consensus size: 115
166083 AAGTGCCATG
* * *
166093 TGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* * * * * * *
166158 TGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATAAATTT
*
166208 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
* *
166273 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTAAAAGATAAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATAAATT
166322 GCATGATCAT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATAAATTT
Found at i:168331 original size:54 final size:54
Alignment explanation
Indices: 168249--168408 Score: 203
Period size: 59 Copynumber: 2.9 Consensus size: 54
168239 GAAATCTTGG
*
168249 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCCGAA
* * *
168303 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGCTTCCTTGACCAATAATCCGAG
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATG-TT--TT-ACGAA-CATCCGAA
* * * *
168362 CAGAAACTACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
168409 CAGTGATTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
54 37 0.41
55 6 0.07
56 2 0.02
57 2 0.02
58 6 0.07
59 38 0.42
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCCGAA
Found at i:169540 original size:76 final size:76
Alignment explanation
Indices: 169449--170195 Score: 1345
Period size: 76 Copynumber: 9.8 Consensus size: 76
169439 CTATTTCTCA
169449 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169514 AGCCTTCGGGT
66 AGCCTTCGGGT
*
169525 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169590 AGCCTTCGGGT
66 AGCCTTCGGGT
*
169601 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169666 AGCCTTCGGGT
66 AGCCTTCGGGT
*
169677 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169742 AGCC-TCAGGGT
66 AGCCTTC-GGGT
169753 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
169818 AGCCTTAGGGT
66 AGCCTTCGGGT
*
169829 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
169894 AAGCCTTAGGGT
65 AAGCCTTCGGGT
*
169906 TATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169971 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
169982 CATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
170047 AGCCTTCGGGT
66 AGCCTTCGGGT
*
170058 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
170123 A-CCCTCAGGGT
66 AGCCTTC-GGGT
*
170134 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
170196 TAAGACCTCT
Statistics
Matches: 649, Mismatches: 18, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
75 6 0.01
76 568 0.88
77 75 0.12
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:170184 original size:381 final size:380
Alignment explanation
Indices: 169449--170195 Score: 1422
Period size: 381 Copynumber: 2.0 Consensus size: 380
169439 CTATTTCTCA
169449 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
169514 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
169579 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTTC
169644 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
* *
169709 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTTCAGTGC
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAATCCTTCAGTGC
169774 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
326 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
*
169829 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
169894 AAGCCTTAGGGTTATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
169959 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTT
130 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTT
170024 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
195 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
170089 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAATCCTTCAGTG
260 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAATCCTTCAGTG
170154 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
325 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
170196 TAAGACCTCT
Statistics
Matches: 359, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
380 32 0.09
381 327 0.91
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (380 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCACGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAATCCTTCAGTGC
ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:170357 original size:3 final size:3
Alignment explanation
Indices: 170349--170409 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
170339 CAGTTTACTT
* * *
170349 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTG TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
170395 TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
170410 AATAAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:171189 original size:13 final size:13
Alignment explanation
Indices: 171171--171195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171161 ACCGTTTACG
171171 GTGGCCGGCGGCA
1 GTGGCCGGCGGCA
171184 GTGGCCGGCGGC
1 GTGGCCGGCGGC
171196 GGAGTACGGT
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:0.04, C:0.32, G:0.56, T:0.08
Consensus pattern (13 bp):
GTGGCCGGCGGCA
Found at i:184839 original size:13 final size:13
Alignment explanation
Indices: 184797--184828 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
184787 ACTCCAAAAG
184797 AAATTTCATTCAA
1 AAATTTCATTCAA
184810 AAATTTCATTCAA
1 AAATTTCATTCAA
184823 AAATTT
1 AAATTT
184829 TATCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTCATTCAA
Found at i:192001 original size:20 final size:22
Alignment explanation
Indices: 191970--192046 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 22
191960 GAATCTTTAA
191970 TATATATTTATTTTTAGT-TATT
1 TATAT-TTTATTTTTAGTATATT
*
191992 TA-ATTTTATTTTTAGTATTTT
1 TATATTTTATTTTTAGTATATT
* * *
192013 TATATTTAATTTTTTGAATATTTT
1 TATATTTTA-TTTTT-AGTATATT
192037 TATATTTTAT
1 TATATTTTAT
192047 AATTAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 12 0.26
21 7 0.15
22 7 0.15
23 6 0.13
24 15 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TATATTTTATTTTTAGTATATT
Found at i:197510 original size:2 final size:2
Alignment explanation
Indices: 197503--197529 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
197493 ATATGATTAT
197503 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 T
197530 TTCTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:200851 original size:23 final size:23
Alignment explanation
Indices: 200821--200944 Score: 142
Period size: 23 Copynumber: 5.4 Consensus size: 23
200811 CATACGAATT
* *
200821 GAAGAATAAGAAATGTGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
*
200844 GAAGAATAAGAAATGAGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
* *
200867 GAAGAAGAAAAAATGGGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
* * *
200890 GAAAAAGAAGAAA-CATGTATATG
1 GAAGAAGAAGAAATGA-GTTTATG
**
200913 GAAGAAGAATCAATGAGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
200936 GAAGAAGAA
1 GAAGAAGAA
200945 AAAAAAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
23 84 0.99
24 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.27, T:0.23
Consensus pattern (23 bp):
GAAGAAGAAGAAATGAGTTTATG
Found at i:202993 original size:229 final size:227
Alignment explanation
Indices: 202588--203036 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
202578 GTAAATTATC
* * *
202588 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* **
202653 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAAACAAATAAAATTT
202718 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
202783 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
202816 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
202881 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAAACAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAAACAAATAAAATT
* *
202946 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
203011 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
203037 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 40 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAAACAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:203132 original size:19 final size:19
Alignment explanation
Indices: 203087--203144 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
203077 TATATTGATC
* *
203087 CAAAACGATATACCAGGTAA
1 CAAAATGATAAACC-GGTAA
*
203107 -AATATGATAAACCGGTAA
1 CAAAATGATAAACCGGTAA
203125 CAAAATGATAAAACCGGTAA
1 CAAAATGAT-AAACCGGTAA
203145 ATTTAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.16
19 17 0.53
20 10 0.31
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.17
Consensus pattern (19 bp):
CAAAATGATAAACCGGTAA
Found at i:203290 original size:20 final size:19
Alignment explanation
Indices: 203267--203313 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
203257 CGATATAACA
*
203267 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATCATAAAACC
203287 GGTAACAAAATCATAAAACC
1 GGTAA-AAAATCATAAAACC
203307 GGTAAAA
1 GGTAAAA
203314 TGATACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATCATAAAACC
Found at i:205593 original size:21 final size:21
Alignment explanation
Indices: 205546--205610 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
205536 AAGACAATCA
* *
205546 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
205568 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
205588 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
205609 AG
1 AG
205611 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:205700 original size:33 final size:33
Alignment explanation
Indices: 205644--205709 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
205634 AAATAGATGG
* * *
205644 AGTGGTGAAAGAAGTAGATGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
* *
205677 AGTGGTGAAAGAAGTTGGGGTGTTAAGAGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
205710 TATTAAGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
Found at i:207525 original size:19 final size:19
Alignment explanation
Indices: 207501--207549 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
207491 AATGTCGAGT
207501 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
207520 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
207539 TATTTTTGTAT
1 TAATTTTGTAT
207550 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:208622 original size:199 final size:199
Alignment explanation
Indices: 207668--209235 Score: 2892
Period size: 199 Copynumber: 7.9 Consensus size: 199
207658 CAATATGGCC
* * *
207668 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* *
207733 ACCAAAAGTATAATGTAATATGGAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
207798 ATAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
207863 ATGGAA
194 ATGGAA
* *
207869 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
207934 CCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
207999 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
208064 TGGAA
195 TGGAA
*
208069 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
208133 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
208198 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
208262 TAAA
196 GGAA
208266 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
208331 C-AAAGTATAATGTAATATGTAATTTTTCAATTTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
208395 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
208460 TAAA
196 GGAA
208464 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
208529 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
208594 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
208659 GGAA
196 GGAA
208663 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
208728 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
208793 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
208858 GGAA
196 GGAA
208862 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
208927 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
208992 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
209057 GGAA
196 GGAA
**
209061 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
209125 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
209190 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTCTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
209236 CTAATTTAAA
Statistics
Matches: 1346, Mismatches: 18, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
197 162 0.12
198 368 0.27
199 586 0.44
200 195 0.14
201 35 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:210713 original size:12 final size:12
Alignment explanation
Indices: 210696--210784 Score: 61
Period size: 12 Copynumber: 7.4 Consensus size: 12
210686 GGTCGCAGAA
*
210696 GATGAAGCTGAC
1 GATGAAGATGAC
210708 GATGAAGATGAC
1 GATGAAGATGAC
* *
210720 GATGATGATGAT
1 GATGAAGATGAC
* *
210732 GATGATGATGAA
1 GATGAAGATGAC
* ** *
210744 GCTGGCGATGAA
1 GATGAAGATGAC
* *
210756 GATGATGACGAC
1 GATGAAGATGAC
* *
210768 GATGATGATGAT
1 GATGAAGATGAC
210780 GATGA
1 GATGA
210785 TGAAGATGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:210728 original size:3 final size:3
Alignment explanation
Indices: 210708--210797 Score: 90
Period size: 3 Copynumber: 30.0 Consensus size: 3
210698 TGAAGCTGAC
* * * * ** *
210708 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAT GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
210756 GAT GAT GAC GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
210798 CCAAACAAGT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:212560 original size:184 final size:184
Alignment explanation
Indices: 212251--212961 Score: 1289
Period size: 184 Copynumber: 3.9 Consensus size: 184
212241 CTTTCAACAT
** * * * * * *
212251 ATTATAATAAAATAGGTAAATTTGCAATATAACTGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
*
212316 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
212381 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
212435 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
212500 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
212565 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCAGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
212619 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
212684 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
212749 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
212803 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
* *
212868 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
212933 AATGTGTCGATACCA-TTGAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
212962 GTAATTTGAA
Statistics
Matches: 512, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
183 13 0.03
184 499 0.97
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:213655 original size:25 final size:25
Alignment explanation
Indices: 213621--213685 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
213611 TTATCATTAA
213621 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
213646 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
213671 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
213686 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:214004 original size:23 final size:23
Alignment explanation
Indices: 213973--214036 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
213963 ATAGGTAAAC
*
213973 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
213996 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
214019 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
214037 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:214043 original size:23 final size:23
Alignment explanation
Indices: 213973--214045 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
213963 ATAGGTAAAC
* **
213973 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
213996 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
214019 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
214042 ATAT
1 ATAT
214046 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:214348 original size:25 final size:25
Alignment explanation
Indices: 214314--214364 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
214304 ACAACAAATC
*
214314 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
214339 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
214364 A
1 A
214365 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:214680 original size:18 final size:18
Alignment explanation
Indices: 214659--214695 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
214649 GTAATTGGAG
214659 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
214677 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
214695 T
1 T
214696 ATTTATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:214703 original size:24 final size:23
Alignment explanation
Indices: 214650--214700 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
214640 ATTTCATATG
*
214650 TAATTGGAGTTTGAATTTAAATT
1 TAATTTGAGTTTGAATTTAAATT
214673 TCAATTTGAGTTTGAATTTCAATATT
1 T-AATTTGAGTTTGAATTT-AA-ATT
214699 TA
1 TA
214701 TTTCGGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 16 0.67
25 3 0.12
26 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (23 bp):
TAATTTGAGTTTGAATTTAAATT
Found at i:215409 original size:23 final size:23
Alignment explanation
Indices: 215378--215441 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
215368 ATAGGTAAAC
*
215378 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
215401 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
215424 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
215442 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:215448 original size:23 final size:23
Alignment explanation
Indices: 215378--215450 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
215368 ATAGGTAAAC
* **
215378 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
215401 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
215424 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
215447 ATAT
1 ATAT
215451 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:225230 original size:30 final size:30
Alignment explanation
Indices: 225196--225268 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
225186 CCCGAAGGAC
225196 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
225226 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
225256 CTGTCCATAGGTC
1 CTATCCAGAGGTC
225269 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:225364 original size:63 final size:61
Alignment explanation
Indices: 225251--225379 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
225241 AAAGATCCTC
* *
225251 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
225312 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
225375 GGTAA
1 GGTAA
225380 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:225374 original size:32 final size:31
Alignment explanation
Indices: 225254--225381 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
225244 GATCCTCGGT
* * * *
225254 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
225285 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
225316 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
225348 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
225379 AAC
1 AAC
225382 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:225950 original size:22 final size:22
Alignment explanation
Indices: 225906--225947 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
225896 TAAATCAATT
*
225906 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
225928 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
225948 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:226428 original size:21 final size:21
Alignment explanation
Indices: 226398--226442 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
226388 GTTGTTCGTT
*
226398 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
226419 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
226440 TTG
1 TTG
226443 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:229530 original size:29 final size:30
Alignment explanation
Indices: 229488--229559 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
229478 CCCGAAGGAC
229488 CTATCCAGAGGTCAT-AAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
229517 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
229547 CTGTCCATAGGTC
1 CTATCCAGAGGTC
229560 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:229617 original size:62 final size:62
Alignment explanation
Indices: 229542--229670 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 62
229532 AAAGATCCTC
* * *
229542 GGTAACTGTCCATAGGTCCCG-AAGAACCTAGGT-AAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAAG-ACATAGGTAAAACTGCCCATATGTTCCGTAGAACATA
* *
229603 GGTATACTGTCCATATGTCTCGAAAGACATAGGTAAAACTGCCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAAGACATAGGTAAAACTGCCCATATGTTCCGTAGAACATA
229666 GGTAA
1 GGTAA
229671 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 4 0.07
62 23 0.38
63 33 0.55
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (62 bp):
GGTAACTGTCCATAGGTCCCGAAAGACATAGGTAAAACTGCCCATATGTTCCGTAGAACATA
Found at i:229665 original size:32 final size:31
Alignment explanation
Indices: 229545--229672 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
229535 GATCCTCGGT
* * * *
229545 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
229576 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
229607 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
*
229639 AACTGCCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
229670 AAC
1 AAC
229673 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.63
32 22 0.27
33 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:230702 original size:21 final size:21
Alignment explanation
Indices: 230678--230722 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
230668 TGTTGTTCGT
* *
230678 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
230699 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
230720 TTG
1 TTG
230723 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:234449 original size:60 final size:61
Alignment explanation
Indices: 234321--234451 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 61
234311 TTAACGGTGT
** * *
234321 AGTGGTATAACAAAAACGTAAATCAAAGTTTAATGCTATAATTGATAAAATTGAAAGTTCA
1 AGTGGTATAACAAAAACAAAAATCAAAATTTAATGCTATAATTGACAAAATTGAAAGTTCA
* * * * * * *
234382 A-TTGTATAACTAAAACAAAAATTAAAATTTAGTGTTATAATTGACAAGATTGAGAGTT-A
1 AGTGGTATAACAAAAACAAAAATCAAAATTTAATGCTATAATTGACAAAATTGAAAGTTCA
234441 AGTGGTATAAC
1 AGTGGTATAAC
234452 GAGACAACAC
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 2 0.04
60 54 0.95
61 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (61 bp):
AGTGGTATAACAAAAACAAAAATCAAAATTTAATGCTATAATTGACAAAATTGAAAGTTCA
Found at i:237542 original size:38 final size:38
Alignment explanation
Indices: 237491--237563 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
237481 CGATCCATGT
237491 AGGATCGAGATTATGTTTTAGCTTGTTGAATTGAATAC
1 AGGATCGAGATTATGTTTTAGCTTGTTGAATTGAATAC
237529 AGGATCGAGATTATGTTTTAGCTTGTTGAATTGAA
1 AGGATCGAGATTATGTTTTAGCTTGTTGAATTGAA
237564 AGAGATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.40
Consensus pattern (38 bp):
AGGATCGAGATTATGTTTTAGCTTGTTGAATTGAATAC
Found at i:240503 original size:23 final size:23
Alignment explanation
Indices: 240469--240512 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
240459 ATATTAAAAT
*
240469 AATAATAATTTTAAATTTTTAAA
1 AATAATAATTTTAAAATTTTAAA
240492 AATAA-AAGTTTTAAAATTTTA
1 AATAATAA-TTTTAAAATTTTA
240513 TCAACCCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAATAATTTTAAAATTTTAAA
Found at i:242135 original size:7 final size:7
Alignment explanation
Indices: 242123--242152 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
242113 TAAGATGAAG
242123 ATGGAGA
1 ATGGAGA
242130 ATGGAGA
1 ATGGAGA
242137 ATGGAGA
1 ATGGAGA
*
242144 AGGGAGA
1 ATGGAGA
242151 AT
1 AT
242153 CAATAGGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (7 bp):
ATGGAGA
Found at i:248798 original size:35 final size:35
Alignment explanation
Indices: 248759--248872 Score: 142
Period size: 35 Copynumber: 3.2 Consensus size: 35
248749 CAACTTTGAA
248759 AAAATGATTTTTAAAGTTTGGTAAATGTTTTTTTG
1 AAAATGATTTTTAAAGTTTGGTAAATGTTTTTTTG
* * *
248794 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGATTTTTAAAGTTTGGTAAATGTTTTTTTG
* *
248829 AAAAAT-AGTTTTTCAAAGTTTGGTAGATG-TTTGTTG
1 -AAAATGA-TTTTT-AAAGTTTGGTAAATGTTTTTTTG
248865 AAAATGAT
1 AAAATGAT
248873 AATGAGATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
35 38 0.57
36 15 0.22
37 14 0.21
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (35 bp):
AAAATGATTTTTAAAGTTTGGTAAATGTTTTTTTG
Found at i:248851 original size:37 final size:37
Alignment explanation
Indices: 248752--248868 Score: 145
Period size: 37 Copynumber: 3.2 Consensus size: 37
248742 TGGCAACCAA
248752 CTTTGAAAAA-ATGATTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-G-TTTTTCAAAGTTTGGTAAATGTTT
* *
248789 TTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
248824 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
248861 -GTTGAAAA
1 CTTTGAAAA
248869 TGATAATGAG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
34 4 0.06
35 23 0.33
36 16 0.23
37 27 0.39
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:253403 original size:35 final size:36
Alignment explanation
Indices: 253357--253465 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
253347 TGGCAACCAA
*
253357 CTTTGAAAAAATGTTTTTCAAAGTTTGGTTAATGTTT
1 CTTTG-AAAAATGTTTTTCAAAGTTTGGTAAATGTTT
* *
253394 TTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
253429 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
253466 GATGAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 32 0.49
36 5 0.08
37 28 0.43
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:255652 original size:8 final size:8
Alignment explanation
Indices: 255641--255674 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
255631 ATATTTTAAA
*
255641 TTATTTAT
1 TTATATAT
255649 TTATATAT
1 TTATATAT
255657 TTATATAT
1 TTATATAT
255665 TTATATAT
1 TTATATAT
255673 TT
1 TT
255675 TAAATACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTATATAT
Found at i:256370 original size:10 final size:10
Alignment explanation
Indices: 256344--256378 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
256334 TCAACATCTA
*
256344 CTTTCGGTGG
1 CTTTAGGTGG
256354 CCTTTAGGTGG
1 -CTTTAGGTGG
256365 CTTTAGGTGG
1 CTTTAGGTGG
256375 CTTT
1 CTTT
256379 GGGGGCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.06, C:0.17, G:0.34, T:0.43
Consensus pattern (10 bp):
CTTTAGGTGG
Found at i:260172 original size:23 final size:23
Alignment explanation
Indices: 260140--260205 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
260130 TTTGTTAGCG
*
260140 TTCACGAACATATTCGTTTAACA
1 TTCACAAACATATTCGTTTAACA
* ** *
260163 TTCGCAAACATGCTCGTTTAACG
1 TTCACAAACATATTCGTTTAACA
*
260186 TTCACGAACATATTCGTTTA
1 TTCACAAACATATTCGTTTA
260206 TATGTTTGCC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (23 bp):
TTCACAAACATATTCGTTTAACA
Found at i:265225 original size:20 final size:21
Alignment explanation
Indices: 265186--265230 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
265176 AATAGAACAT
* *
265186 AATAAGATAATATAACATAAA
1 AATAAAATAATATAAAATAAA
265207 AATAAAATAA-ATAAAATAAA
1 AATAAAATAATATAAAATAAA
265227 AATA
1 AATA
265231 TTACTATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AATAAAATAATATAAAATAAA
Found at i:267054 original size:3 final size:3
Alignment explanation
Indices: 267046--267125 Score: 74
Period size: 3 Copynumber: 26.7 Consensus size: 3
267036 GTAACTTGAA
* * * * *
267046 AAT AAT AAT AAA AAT AAT ATT AAT AAT AAT AAT AGT AAT AAT GAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
267094 AATT AA- AATT AA- AAT AAT AAT AGT AAT AAT AA
1 AA-T AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
267126 CATCGGGCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 4 0.07
3 53 0.87
4 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:274292 original size:22 final size:24
Alignment explanation
Indices: 274261--274307 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
274251 TTCTCCCTAG
*
274261 AATTTTTAAAGTTTACCTC-CTAA
1 AATTTTAAAAGTTTACCTCTCTAA
*
274284 AATTTTAAAAGTTTGCCTCTCTAA
1 AATTTTAAAAGTTTACCTCTCTAA
274308 CATAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (24 bp):
AATTTTAAAAGTTTACCTCTCTAA
Found at i:276365 original size:20 final size:21
Alignment explanation
Indices: 276340--276381 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
276330 TTTATTTACT
276340 GTTGAATG-GAACCATTCAGC
1 GTTGAATGCGAACCATTCAGC
*
276360 GTTGAATGCTTAACCATTCAGC
1 GTTGAATGC-GAACCATTCAGC
276382 ATTCAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (21 bp):
GTTGAATGCGAACCATTCAGC
Found at i:276453 original size:23 final size:26
Alignment explanation
Indices: 276423--276483 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 26
276413 AAGACTGTGT
276423 TGAATGATTCAGCA-AAA-TAC-TAC
1 TGAATGATTCAGCATAAAGTACATAC
*
276446 TGAATGATTCAGCATTAAAGTACATTC
1 TGAATGATTCAGCA-TAAAGTACATAC
276473 TGAATGATTCA
1 TGAATGATTCA
276484 TAACCATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 14 0.42
25 3 0.09
26 3 0.09
27 13 0.39
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (26 bp):
TGAATGATTCAGCATAAAGTACATAC
Found at i:277845 original size:19 final size:20
Alignment explanation
Indices: 277821--277882 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
277811 ATTTTGACCA
277821 TTTAGCCGCCCATGCATTG-
1 TTTAGCCGCCCATGCATTGT
277840 TTTAGCCGCCC---CACTTGT
1 TTTAGCCGCCCATGCA-TTGT
277858 TTTCAGCCGCCCATGCATTGAT
1 TTT-AGCCGCCCATGCATTG-T
277880 TTT
1 TTT
277883 CAATAATCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.06
17 3 0.08
18 3 0.08
19 19 0.53
21 3 0.08
22 6 0.17
ACGTcount: A:0.15, C:0.32, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTAGCCGCCCATGCATTGT
Found at i:284679 original size:7 final size:7
Alignment explanation
Indices: 284667--284715 Score: 98
Period size: 7 Copynumber: 7.0 Consensus size: 7
284657 TGTATATAAA
284667 CTCATCC
1 CTCATCC
284674 CTCATCC
1 CTCATCC
284681 CTCATCC
1 CTCATCC
284688 CTCATCC
1 CTCATCC
284695 CTCATCC
1 CTCATCC
284702 CTCATCC
1 CTCATCC
284709 CTCATCC
1 CTCATCC
284716 AATCAAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCATCC
Found at i:289721 original size:20 final size:21
Alignment explanation
Indices: 289677--289725 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
289667 TGGTTTCAAA
*
289677 TTAAATTTAAATTACATTTTT
1 TTAAATTTAAATTACATTCTT
*
289698 TTAAATTTAAA-TATATTCTT
1 TTAAATTTAAATTACATTCTT
289718 TTAAATTT
1 TTAAATTT
289726 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAATTTAAATTACATTCTT
Found at i:292351 original size:92 final size:91
Alignment explanation
Indices: 292218--292390 Score: 267
Period size: 92 Copynumber: 1.9 Consensus size: 91
292208 CCCGAAGTCT
* *
292218 AGTTCAATTCATTCATGCAATTGAGATTGCATATGTATTCACTTTAGCAACAAACAAA-AACAAC
1 AGTTCAATTCATTCATACAATTGAGATTGCATATATATTCACTTTAGCAA-AAA-AAACAACAAC
292282 CCCTAAAACCTAAATATGTTACCCCCAA
64 CCCTAAAACCTAAATATGTTACCCCCAA
* * *
292310 AGTTCAGTTCATTCATACAATTGAGATTGCGTATATTTTCACTTTAGCAAAAAAAACAACAACCC
1 AGTTCAATTCATTCATACAATTGAGATTGCATATATATTCACTTTAGCAAAAAAAACAACAACCC
*
292375 CTAAACCCTAAATATG
66 CTAAAACCTAAATATG
292391 AAACCCCTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
90 3 0.04
91 26 0.35
92 45 0.61
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (91 bp):
AGTTCAATTCATTCATACAATTGAGATTGCATATATATTCACTTTAGCAAAAAAAACAACAACCC
CTAAAACCTAAATATGTTACCCCCAA
Found at i:293490 original size:14 final size:14
Alignment explanation
Indices: 293467--293505 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
293457 TTGAGGACCA
*
293467 TGGAAAGGGGAAAG
1 TGGAAGGGGGAAAG
293481 TGGAAGGGGGAAAG
1 TGGAAGGGGGAAAG
* *
293495 AGAAAGGGGGA
1 TGGAAGGGGGA
293506 GGGGGACGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.54, T:0.05
Consensus pattern (14 bp):
TGGAAGGGGGAAAG
Found at i:296506 original size:42 final size:43
Alignment explanation
Indices: 296447--296528 Score: 139
Period size: 42 Copynumber: 1.9 Consensus size: 43
296437 ATAGGGTCAT
296447 AGTGGTAGATATTGGGATTCAATTTTCGAAG-TTTTGGTTCAC
1 AGTGGTAGATATTGGGATTCAATTTTCGAAGTTTTTGGTTCAC
* *
296489 AGTGGTAGATCTTGGGATTCAATTTTTGAAGTTTTTGGTT
1 AGTGGTAGATATTGGGATTCAATTTTCGAAGTTTTTGGTT
296529 TACTGTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 29 0.78
43 8 0.22
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (43 bp):
AGTGGTAGATATTGGGATTCAATTTTCGAAGTTTTTGGTTCAC
Found at i:297519 original size:15 final size:15
Alignment explanation
Indices: 297501--297539 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
297491 TTTTTATATA
*
297501 TTTATAATTTATTAT
1 TTTATAATTTATGAT
297516 TTTATAATTTATGAT
1 TTTATAATTTATGAT
*
297531 TTTTTAATT
1 TTTATAATT
297540 ATCCTTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTATAATTTATGAT
Found at i:297600 original size:10 final size:10
Alignment explanation
Indices: 297566--297608 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
297556 AATGTTTTCT
297566 ATTTTTAATA
1 ATTTTTAATA
*
297576 AATTTTAAT-
1 ATTTTTAATA
297585 ATTTTTAATA
1 ATTTTTAATA
297595 ATTTTT--TA
1 ATTTTTAATA
297603 ATTTTT
1 ATTTTT
297609 CTCTTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.27
9 8 0.27
10 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:297600 original size:19 final size:18
Alignment explanation
Indices: 297491--297600 Score: 70
Period size: 18 Copynumber: 6.3 Consensus size: 18
297481 GGTCACGATT
*
297491 TTTTTATATATTT-ATAA
1 TTTTTATATTTTTAATAA
*
297508 TTTAT-TA-TTTT-ATAA
1 TTTTTATATTTTTAATAA
* *
297523 TTTATGAT-TTTTTAATTA
1 TTT-TTATATTTTTAATAA
** *
297541 TCCTTAGATTTTT-ATAA
1 TTTTTATATTTTTAATAA
*
297558 TGTTTTCTATTTTTAATAAA
1 T-TTTTATATTTTTAAT-AA
*
297578 TTTTAATATTTTTAATAA
1 TTTTTATATTTTTAATAA
297596 TTTTT
1 TTTTT
297601 TAATTTTTCT
Statistics
Matches: 68, Mismatches: 17, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
15 10 0.15
16 2 0.03
17 15 0.22
18 23 0.34
19 15 0.22
20 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTTATATTTTTAATAA
Found at i:297606 original size:18 final size:18
Alignment explanation
Indices: 297548--297608 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
297538 TTATCCTTAG
297548 ATTTTT-ATAATGTTTTCT-
1 ATTTTTAATAAT-TTTT-TA
* *
297566 ATTTTTAATAAATTTTAA
1 ATTTTTAATAATTTTTTA
297584 TATTTTTAATAATTTTTTA
1 -ATTTTTAATAATTTTTTA
297603 ATTTTT
1 ATTTTT
297609 CTCTTAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 16 0.44
19 20 0.56
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTTAATAATTTTTTA
Done.