Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003931.1 Hibiscus syriacus cultivar Beakdansim tig00008496_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: 118028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13909 original size:26 final size:24
Alignment explanation
Indices: 13850--13908 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
13840 AAAAGGGAAG
13850 TTTTATTTTCTCTTCCTCTCTATT
1 TTTTATTTTCTCTTCCTCTCTATT
* * * *
13874 TGTCACTTTTCTTTTTCTACTCTATT
1 TTTTA-TTTTCTCTTCCT-CTCTATT
13900 TTTTATTTT
1 TTTTATTTT
13909 TGCTGGATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 3 0.11
25 14 0.52
26 10 0.37
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTATTTTCTCTTCCTCTCTATT
Found at i:15921 original size:26 final size:26
Alignment explanation
Indices: 15887--15999 Score: 119
Period size: 26 Copynumber: 4.4 Consensus size: 26
15877 AATGAATAAG
*
15887 TTTTG-AAAAATGCTTGAT-AAAGAA
1 TTTTGAAAAAATGTTTGATGAAAGAA
*
15911 GTTTTGAAAAAAT-TTTGATGAAAAAA
1 -TTTTGAAAAAATGTTTGATGAAAGAA
15937 TTTTTG-AAAAATGTTTGATGAAA-ATA
1 -TTTTGAAAAAATGTTTGATGAAAGA-A
*
15963 TTTTGAAAAAATTGTTTGATAAAAGAA
1 TTTTGAAAAAA-TGTTTGATGAAAGAA
*
15990 TTTTTAAAAA
1 TTTTGAAAAA
16000 TATTTCCCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
25 22 0.29
26 32 0.42
27 21 0.28
28 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.14, T:0.38
Consensus pattern (26 bp):
TTTTGAAAAAATGTTTGATGAAAGAA
Found at i:15928 original size:51 final size:51
Alignment explanation
Indices: 15884--16000 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 51
15874 TTGAATGAAT
15884 AAGTTTTGAAAAATGCTTGAT-AAAGA-AGTTTTGAAAAAATTTTGATGAAAA
1 AAGTTTTGAAAAATGCTTGATGAAA-ATA-TTTTGAAAAAATTTTGATGAAAA
* *
15935 AATTTTTGAAAAATGTTTGATGAAAATATTTTGAAAAAATTGTTTGAT-AAAA
1 AAGTTTTGAAAAATGCTTGATGAAAATATTTTGAAAAAA-T-TTTGATGAAAA
*
15987 GAA-TTTTTAAAAAT
1 -AAGTTTTGAAAAAT
16001 ATTTCCCCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
51 31 0.53
52 19 0.33
53 8 0.14
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.38
Consensus pattern (51 bp):
AAGTTTTGAAAAATGCTTGATGAAAATATTTTGAAAAAATTTTGATGAAAA
Found at i:15932 original size:14 final size:14
Alignment explanation
Indices: 15915--15993 Score: 71
Period size: 14 Copynumber: 5.9 Consensus size: 14
15905 AAAGAAGTTT
15915 TGAAAAAATTTTGA
1 TGAAAAAATTTTGA
15929 TGAAAAAATTTT--
1 TGAAAAAATTTTGA
15941 TG-AAAAATGTTTGA
1 TGAAAAAAT-TTTGA
*
15955 TGAAAATATTTTGA
1 TGAAAAAATTTTGA
*
15969 --AAAAATTGTTTGA
1 TGAAAAAAT-TTTGA
15982 T-AAAAGAATTTT
1 TGAAAA-AATTTT
15994 TAAAAATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.11
12 10 0.19
13 5 0.09
14 26 0.48
15 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (14 bp):
TGAAAAAATTTTGA
Found at i:15947 original size:13 final size:13
Alignment explanation
Indices: 15912--16004 Score: 54
Period size: 13 Copynumber: 7.2 Consensus size: 13
15902 GATAAAGAAG
15912 TTTTG-AAAAAA-
1 TTTTGAAAAAAAT
15923 TTTTGATGAAAAAAT
1 TTTTGA--AAAAAAT
15938 TTTTG--AAAAAT
1 TTTTGAAAAAAAT
* **
15949 GTTTGATGAAAAT
1 TTTTGAAAAAAAT
15962 ATTTTG-AAAAAAT
1 -TTTTGAAAAAAAT
15975 TGTTTGATAAAAGAAT
1 T-TTTGA-AAAA-AAT
*
15991 TTTT-AAAAATAT
1 TTTTGAAAAAAAT
16003 TT
1 TT
16005 CCCCTTATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
11 15 0.23
12 5 0.08
13 18 0.28
14 11 0.17
15 12 0.18
16 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAAAAT
Found at i:16000 original size:26 final size:25
Alignment explanation
Indices: 15873--16000 Score: 118
Period size: 26 Copynumber: 5.0 Consensus size: 25
15863 ATTTTCAAAA
* *
15873 TTTGAATGAATAAGTTTTGAAAAATG
1 TTTG-ATGAAAAAATTTTGAAAAATG
* *
15899 CTTGAT-AAAGAAGTTTTGAAAAAAT-
1 TTTGATGAAA-AAATTTTG-AAAAATG
15924 TTTGATGAAAAAATTTTTGAAAAATG
1 TTTGATGAAAAAA-TTTTGAAAAATG
*
15950 TTTGATGAAAATATTTTGAAAAAATTG
1 TTTGATGAAAAAATTTTG-AAAAA-TG
*
15977 TTTGAT-AAAAGAATTTTTAAAAAT
1 TTTGATGAAAA-AATTTTGAAAAAT
16001 ATTTCCCCTT
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
24 2 0.02
25 29 0.33
26 43 0.49
27 13 0.15
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.38
Consensus pattern (25 bp):
TTTGATGAAAAAATTTTGAAAAATG
Found at i:19061 original size:19 final size:19
Alignment explanation
Indices: 19037--19079 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19027 ACATCTGTAG
*
19037 CATGGGCAGCATGTTCCAA
1 CATGGGCAGCATGGTCCAA
* *
19056 CATGGGCGGCATGGTGCAA
1 CATGGGCAGCATGGTCCAA
19075 CATGG
1 CATGG
19080 CCTGTGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (19 bp):
CATGGGCAGCATGGTCCAA
Found at i:24612 original size:18 final size:18
Alignment explanation
Indices: 24589--24626 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
24579 AGTGAGGATT
24589 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
*
24607 GGGCAGTGGTCCATCATG
1 GGGCAGTGGTCCAGCATG
24625 GG
1 GG
24627 CCTCTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:24719 original size:19 final size:19
Alignment explanation
Indices: 24673--24720 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
24663 ACCTGACATC
24673 TGCAGCATGGGCAGCATGG
1 TGCAGCATGGGCAGCATGG
*
24692 TCCAGCATGGGC-GACATGG
1 TGCAGCATGGGCAG-CATGG
*
24711 TGCAACATGG
1 TGCAGCATGG
24721 CCTGTGCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.17
Consensus pattern (19 bp):
TGCAGCATGGGCAGCATGG
Found at i:26718 original size:19 final size:19
Alignment explanation
Indices: 26675--26718 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
26665 TAGTTTTTAT
26675 TAAAAACAACATAATTAAA
1 TAAAAACAACATAATTAAA
*
26694 TCAAAAACAACA-ATTTAAAA
1 T-AAAAACAACATAATT-AAA
26714 TAAAA
1 TAAAA
26719 TAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (19 bp):
TAAAAACAACATAATTAAA
Found at i:27178 original size:23 final size:21
Alignment explanation
Indices: 27124--27178 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 21
27114 ACCCGACGGG
*
27124 TGTATCAGTAC-ACCTAGGAG
1 TGTATCAGTACAACCTAGGAA
*
27144 TGTATC-GATACAGATCTAAGGAA
1 TGTATCAG-TACA-ACCT-AGGAA
27167 TGTATCAGTACA
1 TGTATCAGTACA
27179 CATTCATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
22 3 0.11
23 14 0.50
24 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
TGTATCAGTACAACCTAGGAA
Found at i:34218 original size:22 final size:23
Alignment explanation
Indices: 34193--34238 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
34183 TTAGTATTAT
*
34193 AATTAAAATAATCTA-ATTTAAA
1 AATTAAAATAATCAACATTTAAA
*
34215 AATTAAACTAATCAACATTTAAA
1 AATTAAAATAATCAACATTTAAA
34238 A
1 A
34239 TATTGTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTAAAATAATCAACATTTAAA
Found at i:42003 original size:24 final size:25
Alignment explanation
Indices: 41939--42007 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 25
41929 ATTTCTCGTT
*
41939 TTTCTTTTTCTGTTCTATTTTTTATT
1 TTTCTTTTTCTGTTCT-TTTTTTATC
**
41965 TTTGCTCGATT-TGTTCTTTTTTT-TC
1 TTT-CT-TTTTCTGTTCTTTTTTTATC
41990 TTTCTTTTTCTGTTCTTT
1 TTTCTTTTTCTGTTCTTT
42008 GATTGATGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.06
24 10 0.29
25 4 0.11
26 9 0.26
27 8 0.23
28 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.07, T:0.74
Consensus pattern (25 bp):
TTTCTTTTTCTGTTCTTTTTTTATC
Found at i:42697 original size:21 final size:21
Alignment explanation
Indices: 42672--42713 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42662 TTTATGTTGG
* *
42672 AAATTATCTCGAGTGAAATAA
1 AAATTATCTCAAGAGAAATAA
*
42693 AAATTATTTCAAGAGAAATAA
1 AAATTATCTCAAGAGAAATAA
42714 TCTCAAGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
AAATTATCTCAAGAGAAATAA
Found at i:43611 original size:20 final size:20
Alignment explanation
Indices: 43586--43623 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43576 TTTGGTTCAC
43586 GGAATGTAAAATTACCAGTG
1 GGAATGTAAAATTACCAGTG
*
43606 GGAATGTAAGATTACCAG
1 GGAATGTAAAATTACCAG
43624 GTAATAGGAT
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:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATGTAAAATTACCAGTG
Found at i:45413 original size:35 final size:37
Alignment explanation
Indices: 45342--45414 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
45332 GTTAGAAAAT
* *
45342 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
45379 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
45414 A
1 A
45415 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:45753 original size:3 final size:3
Alignment explanation
Indices: 45745--45772 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
45735 TTTGTCCCAT
45745 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45773 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45837 original size:21 final size:21
Alignment explanation
Indices: 45807--45881 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
45797 ATTTTATAGA
* *
45807 CCCAGTTCTAGAACCCAAAGG
1 CCCAGATCTAGAACCCAGAGG
45828 CCCAGATCTAGAACCCAGAGG
1 CCCAGATCTAGAACCCAGAGG
* *
45849 CCCAGATCCAGAACCCGGAGG
1 CCCAGATCTAGAACCCAGAGG
45870 -CCATGATCTAGA
1 CCCA-GATCTAGA
45882 CCCGACCCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (21 bp):
CCCAGATCTAGAACCCAGAGG
Found at i:45948 original size:23 final size:23
Alignment explanation
Indices: 45918--45971 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
45908 TTAGCATCTT
45918 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
45941 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
45964 CTCCGCCG
1 CTCCGCCG
45972 TCATGTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.11, C:0.54, G:0.15, T:0.20
Consensus pattern (23 bp):
CTCCGCCGCCTCTACTCCAACTG
Found at i:47155 original size:27 final size:29
Alignment explanation
Indices: 47103--47160 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
47093 TATTTATTTT
* *
47103 ATTTTATTTTATTAAAATTCTATTTATAA
1 ATTTAATTTTATTAAAATTCTATTTAAAA
47132 ATTTAATTTTA-T-AAATTACT-TTTAAAA
1 ATTTAATTTTATTAAAATT-CTATTTAAAA
47159 AT
1 AT
47161 AATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 13 0.50
28 3 0.12
29 10 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTAATTTTATTAAAATTCTATTTAAAA
Found at i:47921 original size:26 final size:26
Alignment explanation
Indices: 47869--47955 Score: 68
Period size: 28 Copynumber: 3.2 Consensus size: 26
47859 TAATTCTTTC
* *
47869 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATA--TATTA
*
47897 TTTTCATAATATTTATATGTATATT-
1 TTTTCATAATATTTATATATATATTA
* * * *
47922 TTTTTATTAATATTTTTATTTTATTTTA
1 TTTTCA-TAATATTTATA-TATATATTA
47950 TTTTCA
1 TTTTCA
47956 AGTATTAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 5 0.10
26 14 0.29
27 6 0.12
28 23 0.48
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTCATAATATTTATATATATATTA
Found at i:48507 original size:46 final size:49
Alignment explanation
Indices: 48417--48508 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 49
48407 AATTTATTTC
* * *
48417 ATTTTTCCTAAATAAATGCATGTCAATTAGAAATCATGCAGTTAGGTTA
1 ATTTTTCCTAAACAAATGCATGTCAACTAGAAAGCATGCAGTTAGGTTA
*
48466 ATTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATG-AGGTTAGG
1 ATTTTTCCTAAACAAATGCATGTCAACTAGAAAGCATGCA-GTTAGG
48509 AGTTATACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
45 1 0.03
46 18 0.47
47 5 0.13
48 6 0.16
49 8 0.21
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (49 bp):
ATTTTTCCTAAACAAATGCATGTCAACTAGAAAGCATGCAGTTAGGTTA
Found at i:52854 original size:32 final size:32
Alignment explanation
Indices: 52814--52880 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
52804 AGAGTCTGGA
* *
52814 AACAAGAAGTATCTCTACGAGATGAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
52846 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
52878 AAC
1 AAC
52881 CATTTCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (32 bp):
AACAAGAAGTATCTCTACCAGATAAGCATAAC
Found at i:56722 original size:22 final size:22
Alignment explanation
Indices: 56697--56781 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
56687 ATATCTACAT
*
56697 TCTTCAAAGATAATAGATTTTC
1 TCTTCAAAGATAATAGATTCTC
*
56719 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
56741 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
* * *
56763 TTTTCAAAGAAAAAAGATT
1 TCTTCAAAGATAATAGATT
56782 TATTGGATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATAATAGATTCTC
Found at i:57391 original size:121 final size:121
Alignment explanation
Indices: 57085--57416 Score: 495
Period size: 123 Copynumber: 2.7 Consensus size: 121
57075 CAATCGATGG
* * *
57085 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
57150 ATGAGAAGAACTTGTTCAACCTTTTGCACGACTCTATCAAAAAAGGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACC-TTTGCACGACTCTATCAAAAAAGGAGATAGATCAGC
* * *
57208 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
* * * * * *
57272 AATGAGAATAGCTTGTTCAACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
64 AATGAGAAGAACTTGTTCAACCTTTGCACGACTCTATCAAAAAAGGAGATAGATCAGC
*
57330 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*
57395 TGAGAAGAATTTGTTCAACCTT
66 TGAGAAGAACTTGTTCAACCTT
57417 GCCTTAATTC
Statistics
Matches: 187, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
121 62 0.33
122 52 0.28
123 73 0.39
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (121 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTGCACGACTCTATCAAAAAAGGAGATAGATCAGC
Found at i:57497 original size:137 final size:137
Alignment explanation
Indices: 57331--57689 Score: 551
Period size: 137 Copynumber: 2.6 Consensus size: 137
57321 TAGATCAGCA
* *
57331 TCAACATTTCCAGAA-GTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATA
* * * *
57394 ATGAGAAGAATTTGTTCAACCTTGCCTTAATTCATTACATATGAAGCCAAATTAACAACCCCTCT
65 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCT
57459 TTTGAGGG
130 TTTGAGGG
*
57467 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAATAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
* * *** **
57532 TGAGAAGAACTTGTTCAACCTTGCTTTAATTCATCATATATGAAGTTGAATCAATGACACCTCTT
66 TGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
57597 TTGAGGG
131 TTGAGGG
* *
57604 TCATCATTTCCAGAAGGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
57669 TGAGAAGAACTTGTTCAACCT
66 TGAGAAGAACTTGTTCAACCT
57690 ATTGCTAGAT
Statistics
Matches: 204, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
136 18 0.09
137 186 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (137 bp):
TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
TGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
TTGAGGG
Found at i:57940 original size:3 final size:3
Alignment explanation
Indices: 57932--57959 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
57922 TTTGTCCCAT
57932 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
57960 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58023 original size:21 final size:21
Alignment explanation
Indices: 57991--58068 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
57981 TTAATTTTAT
*
57991 AGGCCCAAATCTAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
*
58012 AGGCTCAGATCTAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
*
58033 AGGCCCAGATCCAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
58054 AGGCCCAGATCTAGA
1 AGGCCCAGATCTAGA
58069 CCGACCCAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.31, C:0.32, G:0.27, T:0.10
Consensus pattern (21 bp):
AGGCCCAGATCTAGAACCCGG
Found at i:60627 original size:3 final size:3
Alignment explanation
Indices: 60619--60732 Score: 165
Period size: 3 Copynumber: 38.0 Consensus size: 3
60609 CCATATTGAT
* * * *
60619 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
60667 TTA TTA TTA TAA TTA TTA TTA TCA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60715 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
60733 AATATATTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:61269 original size:15 final size:15
Alignment explanation
Indices: 61249--61290 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
61239 ACAACACAGC
61249 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
61264 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
61279 AAAGAAGAGAAA
1 AAAGAAAAGAAA
61291 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:61274 original size:20 final size:20
Alignment explanation
Indices: 61249--61290 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
61239 ACAACACAGC
*
61249 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
61269 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
61289 AA
1 AA
61291 CTTACTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:62125 original size:15 final size:15
Alignment explanation
Indices: 62100--62137 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
62090 GTTCTAGTTG
*
62100 TATTTTTATTGTTT-
1 TATTTTAATTGTTTA
62114 TAATTTTAATTGTTTA
1 T-ATTTTAATTGTTTA
62130 TATTTTAA
1 TATTTTAA
62138 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TATTTTAATTGTTTA
Found at i:66125 original size:15 final size:15
Alignment explanation
Indices: 66105--66136 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66095 ATCAATACCT
66105 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
66120 TTTTGCATACATTCA
1 TTTTGCATACATGCA
66135 TT
1 TT
66137 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:73501 original size:18 final size:17
Alignment explanation
Indices: 73463--73546 Score: 89
Period size: 19 Copynumber: 4.6 Consensus size: 17
73453 ATTATGATTG
73463 AAGAAAAATGAAAA-AAAGA
1 AAGAAAAA--AAAAGAAA-A
73482 AAGAAAAAAAAAGAAGGAA
1 AAGAAAAAAAAAGAA--AA
73501 AAGAAAAAAAAGAGAAAA
1 AAGAAAAAAAA-AGAAAA
*
73519 AAGAAAAAAAGAGAAAA
1 AAGAAAAAAAAAGAAAA
73536 AAGAAGAAAAA
1 AAGAA-AAAAA
73547 GGGGGGGTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
17 15 0.25
18 19 0.32
19 20 0.34
20 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AAGAAAAAAAAAGAAAA
Found at i:73531 original size:17 final size:17
Alignment explanation
Indices: 73464--73547 Score: 95
Period size: 17 Copynumber: 5.0 Consensus size: 17
73454 TTATGATTGA
*
73464 AGAAAAATGAAAAAAAG
1 AGAAAAAAGAAAAAAAG
73481 A-AAGAAAA-AAAAAGAAG
1 AGAA-AAAAGAAAAA-AAG
*
73498 -GAAAAGA-AAAAAAAG
1 AGAAAAAAGAAAAAAAG
73513 AGAAAAAAGAAAAAAAG
1 AGAAAAAAGAAAAAAAG
73530 AGAAAAAAGAAGAAAAAG
1 AGAAAAAAGAA-AAAAAG
73548 GGGGGGTCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.05
16 21 0.36
17 28 0.48
18 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (17 bp):
AGAAAAAAGAAAAAAAG
Found at i:73546 original size:9 final size:9
Alignment explanation
Indices: 73472--73547 Score: 65
Period size: 9 Copynumber: 8.8 Consensus size: 9
73462 GAAGAAAAAT
73472 GAAAAA-AA
1 GAAAAAGAA
73480 GAAAGAA-AA
1 GAAA-AAGAA
73489 -AAAAAGAA
1 GAAAAAGAA
*
73497 GGAAAAGAA
1 GAAAAAGAA
*
73506 AAAAAAG-A
1 GAAAAAGAA
73514 GAAAAAAGAA
1 G-AAAAAGAA
73524 -AAAAAG-A
1 GAAAAAGAA
73531 GAAAAAAGAA
1 G-AAAAAGAA
73541 GAAAAAG
1 GAAAAAG
73548 GGGGGGTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.05
8 16 0.29
9 34 0.61
10 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:74901 original size:85 final size:84
Alignment explanation
Indices: 74698--75166 Score: 732
Period size: 83 Copynumber: 5.6 Consensus size: 84
74688 AAATGCCAGG
*
74698 TGCTCATAGCATCTTCTGGAAGT-TTCTTTGAGTTATCTAATCTGGTTTGGCAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
74762 GAATTTGG-AAGA-GTAATA
66 GAATTTGGAAAGATG-AATA
* * * * * *
74780 TTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAGTTATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
*
74845 GAATTTGGAAAGATGAATG
66 GAATTTGGAAAGATGAATA
*
74864 TGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
74929 TGAATTTGGAAA-ATGAATA
65 TGAATTTGGAAAGATGAATA
* * * * *
74948 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAGTTATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
*
75013 GAATTTGGAAAGATGAATG
66 GAATTTGGAAAGATGAATA
*
75032 TGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
75097 TGAATTTGGAAA-ATGAATA
65 TGAATTTGGAAAGATGAATA
75116 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
75167 TATGAACCCC
Statistics
Matches: 350, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
82 22 0.06
83 155 0.44
84 40 0.11
85 133 0.38
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (84 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATT
GAATTTGGAAAGATGAATA
Found at i:74980 original size:168 final size:168
Alignment explanation
Indices: 74703--75168 Score: 882
Period size: 168 Copynumber: 2.8 Consensus size: 168
74693 CCAGGTGCTC
*
74703 ATAGCATCTTCTGGAAGT-TTCTTTGAGTTATCTAATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
74767 TGGAAGA-GTAATATTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
66 TGGAAAATG-AATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
74831 TAAAACTAGTTATTGAATTTGGAAAGATGAATGTGCCCA
130 TAAAACTAGTTATTGAATTTGGAAAGATGAATGTGCCCA
74870 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
74935 TGGAAAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
66 TGGAAAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
75000 AAAACTAGTTATTGAATTTGGAAAGATGAATGTGCCCA
131 AAAACTAGTTATTGAATTTGGAAAGATGAATGTGCCCA
75038 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
75103 TGGAAAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
66 TGGAAAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
75168 A
131 A
75169 TGAACCCCAA
Statistics
Matches: 294, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
167 18 0.06
168 275 0.94
169 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (168 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TGGAAAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
AAAACTAGTTATTGAATTTGGAAAGATGAATGTGCCCA
Found at i:76404 original size:230 final size:228
Alignment explanation
Indices: 76033--76510 Score: 764
Period size: 230 Copynumber: 2.1 Consensus size: 228
76023 TTTCCAGTTC
*
76033 GAGTTCATAATGAGAAGAA-CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 GAGTTCATAATGAGAAGAACCTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGT
*
76097 TCAAACCTTTCGCTCAAATCCATCATTTGATGGATTAGCTTTACCAGAGAAAGTTCATAATGAGA
66 TCAAACCTTTCGCTCAAATCCATCATTTGATGGATCAGCTTTACCAGAGAAAGTTCATAATGAGA
* *
76162 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCCTTTTGCTTG
131 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CCTTTTGCTTA
*
76227 AATTCATCATTTGATGGATCAGCAGCGCCAAGG-A
195 AATTCATCATTTGATGGATCAACAGCGCC-AGGTA
76261 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAAC-C-TCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTT
* * *
76326 GTTC-AATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGA
64 GTTCAAACCTTTCGCTCAAATCCATCATTTGATGGATCAGCTTTACCAGAGAAAGTTCATAATGA
* * * *
76390 GAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
129 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTT
* **
76455 AAATTCATCATTTGATGGATTAACATTGCCAGGTA
194 AAATTCATCATTTGATGGATCAACAGCGCCAGGTA
76490 GAGTTCATAATGAGAAGAACC
1 GAGTTCATAATGAGAAGAACC
76511 CTAGGGCCAC
Statistics
Matches: 231, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
228 23 0.10
229 55 0.24
230 108 0.47
231 45 0.19
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (228 bp):
GAGTTCATAATGAGAAGAACCTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGT
TCAAACCTTTCGCTCAAATCCATCATTTGATGGATCAGCTTTACCAGAGAAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTAA
ATTCATCATTTGATGGATCAACAGCGCCAGGTA
Found at i:76464 original size:113 final size:113
Alignment explanation
Indices: 76034--76509 Score: 641
Period size: 114 Copynumber: 4.2 Consensus size: 113
76024 TTCCAGTTCG
76034 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
76099 AAACCTTTCGCTCAAATCCATCATTTGATGGATTAGCTTTACCAGAGAA
66 -AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCATTGCCAGAGAA
* * * *
76148 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
** * ** *
76213 AACCCTTTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCA-AGGAG
66 AA-CCTTTTGCTCAAATCCATCATTTGATGGATCAGCATTGCCAGA-GAA
*
76262 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * *
76327 TTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAA
63 TTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCATTGCCAGAGAA
* *
76378 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * *
76443 AACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAG
66 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCATTGCCAGAG-AA
76491 AGTTCATAATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
76510 CCTAGGGCCA
Statistics
Matches: 315, Mismatches: 40, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
112 1 0.00
113 102 0.32
114 114 0.36
116 54 0.17
117 44 0.14
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCATTGCCAGAGAA
Found at i:76843 original size:11 final size:10
Alignment explanation
Indices: 76829--76869 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
76819 ACAACACAGC
76829 AAAGAAACAGA
1 AAAGAAA-AGA
76840 AAAG-AAAGA
1 AAAGAAAAGA
76849 AAAGAAAAG-
1 AAAGAAAAGA
*
76858 AAAGAAGAGA
1 AAAGAAAAGA
76868 AA
1 AA
76870 CTTACTCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 15 0.56
10 8 0.30
11 4 0.15
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:76852 original size:5 final size:5
Alignment explanation
Indices: 76829--76869 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
76819 ACAACACAGC
*
76829 AAAGA AACAGA AAAG- AAAGA AAAGA AAAG- AAAGA AGAGA AA
1 AAAGA AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
76870 CTTACTCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 8 0.26
5 18 0.58
6 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:76856 original size:14 final size:14
Alignment explanation
Indices: 76829--76869 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
76819 ACAACACAGC
76829 AAAGAAACAGAAAAG
1 AAAGAAA-AGAAAAG
76844 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
*
76858 AAAGAAGAGAAA
1 AAAGAAAAGAAA
76870 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:77704 original size:15 final size:16
Alignment explanation
Indices: 77680--77717 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
77670 TTCTAGTTGT
*
77680 ATTTTTATTGTTT-TA
1 ATTTTAATTGTTTATA
77695 ATTTTAATTGTTTATA
1 ATTTTAATTGTTTATA
*
77711 TTTTTAA
1 ATTTTAA
77718 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
ATTTTAATTGTTTATA
Found at i:82428 original size:3 final size:3
Alignment explanation
Indices: 82412--82453 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
82402 ATTGCAAATA
82412 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
82454 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:82905 original size:134 final size:134
Alignment explanation
Indices: 82652--83136 Score: 726
Period size: 134 Copynumber: 3.6 Consensus size: 134
82642 GTTTGGGTCG
* * * * *
82652 TCTAAGGGTGACACAGCTCCTACGTGATGA-G-GATCTAGTCAGGGG-ATAACACTGCTCATACG
1 TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTC-GGGGAATGACACGGCTCATACG
* * * *
82714 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAGG-TGATAACTCAGTTCCTACGCGATGAGGACTG
65 TGATGAAGAGTTC-TGGCCATTTTTA-GAAAGGATGATAACTCGGTTCCTACGTGATGAGGACGG
82778 ATGGTTA
128 ATGGTTA
* * * *
82785 TCTATGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGGGAATGACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGGCTCATACGT
* * *
82850 GATGAAAAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTATGTGATGAGGACGGTTG
66 GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACGGATG
82915 GTTA
131 GTTA
* * *
82919 TCTAAGTGTGACACGACTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGGCTCATACGT
*
82984 GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACGGCTG
66 GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACGGATG
83049 GTTA
131 GTTA
*
83053 TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGGCTCATACGT
83118 GATGAAGAGTTCTGGCCAT
66 GATGAAGAGTTCTGGCCAT
83137 CTATAGGGAT
Statistics
Matches: 320, Mismatches: 28, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
133 34 0.11
134 253 0.79
135 33 0.10
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
TCTAAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGGCTCATACGT
GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACGGATG
GTTA
Found at i:83188 original size:29 final size:29
Alignment explanation
Indices: 83152--83233 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
83142 GGGATAATGA
*
83152 TTTCAAAAGAAACCGACTCAAAGATGATG
1 TTTCAAAAGAAACAGACTCAAAGATGATG
83181 TTTCAAAAGAAACAGACTCAAAGATGATG
1 TTTCAAAAGAAACAGACTCAAAGATGATG
* *
83210 TTTCAAAAGGAACATACTCAAAGA
1 TTTCAAAAGAAACAGACTCAAAGA
83234 ATTTTTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (29 bp):
TTTCAAAAGAAACAGACTCAAAGATGATG
Found at i:83424 original size:15 final size:15
Alignment explanation
Indices: 83388--83425 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
83378 CAAAGATTTT
*
83388 TCTCAAAAAAAAATG
1 TCTCAAGAAAAAATG
*
83403 TCTCAAGAAAAACTG
1 TCTCAAGAAAAAATG
83418 TCTCAAGA
1 TCTCAAGA
83426 GAGACAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (15 bp):
TCTCAAGAAAAAATG
Found at i:83543 original size:58 final size:57
Alignment explanation
Indices: 83440--83580 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 57
83430 CAAAACTTTG
*
83440 TTTCAAAAGAAACAGACTCAAAGA-ATTTTTTCAAAAGAAATAACTCGA-AGA-TTATTA
1 TTTCAAAAGAAACA-ACTCAAAGATATTTTTTCAAAAGAAACAACTC-ACAGACTT-TTA
* * *
83497 TTTCAAAAGAAACAACTCACAGATTTTTATTTCAAAAGAAACAACTCACAGACTTTTG
1 TTTCAAAAGAAACAACTCAAAGATATTT-TTTCAAAAGAAACAACTCACAGACTTTTA
*
83555 TTTCAAGAGAAACAAACTCAAAGATA
1 TTTCAAAAGAAAC-AACTCAAAGATA
83581 GGTTTTGTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 8 0.11
57 18 0.25
58 34 0.47
59 12 0.17
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (57 bp):
TTTCAAAAGAAACAACTCAAAGATATTTTTTCAAAAGAAACAACTCACAGACTTTTA
Found at i:83590 original size:33 final size:31
Alignment explanation
Indices: 83436--83629 Score: 147
Period size: 29 Copynumber: 6.5 Consensus size: 31
83426 GAGACAAAAC
* * *
83436 TTTGTTTCAAAAGAAACAGACTCAAAGA--A
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGT
* * *
83465 TTT-TTTCAAAAGAAA-TAACTCGAAGAT-T
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGT
* * * *
83493 ATTATTTCAAAAGAAAC-AACTCACAGAT-T
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGT
* * * *
83522 TTTATTTCAAAAGAAAC-AACTCACAGA-CT
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGT
83551 TTTGTTTCAAGAGAAACAAACTCAAAGATAGGT
1 TTTGTTTCAAGAGAAACAAACTCAAAGAT--GT
* *
83584 TTTGTTTCAAGGGAAACAATCTCAAAGATG-
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGT
*
83614 TTTGTTTTAAGAGAAA
1 TTTGTTTCAAGAGAAA
83630 TTGTCTTAAA
Statistics
Matches: 141, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.06
28 14 0.10
29 67 0.48
30 23 0.16
31 1 0.01
33 28 0.20
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (31 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATGT
Found at i:83780 original size:64 final size:65
Alignment explanation
Indices: 83637--83816 Score: 199
Period size: 64 Copynumber: 2.8 Consensus size: 65
83627 AAATTGTCTT
** * * * * *
83637 AAAAGAGACAAACCTTTGTTTTCATAA-AAACATATTTAAAGATTTTTCTTCAAAAGGAACTGTC
1 AAAAG-GACAAAATTTTGTTATCA-AAGAAACATACTCAAAGATTTCT-TTCAAAAGAAACTGTC
83701 TCA
63 TCA
*
83704 AAAAGGACAAAATTTTGTT-TCCAAAGAAACATACTCAAAG-TTTCTTTCAAAAGAAACTTTCTC
1 AAAAGGACAAAATTTTGTTAT-CAAAGAAACATACTCAAAGATTTCTTTCAAAAGAAACTGTCTC
83767 -
65 A
*
83767 AAAAGAGATAAAATTTTGTTATCAAAGAAACATACTCAAAGATTT-TTTCA
1 AAAAG-GACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTCTTTCA
83817 TTTTGTTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
63 5 0.05
64 53 0.53
65 11 0.11
66 26 0.26
67 5 0.05
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (65 bp):
AAAAGGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTCTTTCAAAAGAAACTGTCTCA
Found at i:83820 original size:37 final size:37
Alignment explanation
Indices: 83779--83850 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
83769 AAGAGATAAA
*
83779 ATTTTGTTATCA-AAGAAACATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAGAAGAAACAGACTCAAAGATTTTTTC
* **
83816 ATTTTGTTTTAGGTGAAACAGACTCAAAGATTTTT
1 ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTT
83851 CAATAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (37 bp):
ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTTTC
Found at i:83907 original size:101 final size:101
Alignment explanation
Indices: 83729--83910 Score: 224
Period size: 101 Copynumber: 1.8 Consensus size: 101
83719 TGTTTCCAAA
* * * *
83729 GAAACATACTCAAAGTTTCTTTCAAAAGAAACTTTCTCAAAAGAGATAAAATTTTGTTATCAAAG
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAG
*
83794 AAACATACTCAAAGATTTTTTCATTTTGTTTTAGGT
66 AAACAGACTCAAAGATTTTTTCATTTTGTTTTAGGT
* * * * *
83830 GAAACAGACTCAAAGATT-TTTCAATA-AAACATGTCTCAATAGAGACAAAGTTTTTTTTTCAAA
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAAC-TGTCTCAAAAGAGACAAAATTTTGTTATC-AA
* *
83893 AGAAATAGATTCAAAGAT
64 AGAAACAGACTCAAAGAT
83911 CCTTTATTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
99 4 0.06
100 30 0.45
101 33 0.49
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (101 bp):
GAAACAGACTCAAAGATTCTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAG
AAACAGACTCAAAGATTTTTTCATTTTGTTTTAGGT
Found at i:84018 original size:36 final size:35
Alignment explanation
Indices: 83978--84067 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 35
83968 ATAATTTGGA
83978 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAACATTTGTTTTT-GAG
* *
84014 AAATTGTCTCAAATGAGACAACGTTTGTTTTTGAG
1 AAATTGTCTCAAGTGAGACAACATTTGTTTTTGAG
**
84049 AAAACGATCTCAAGTGAGA
1 AAATTG-TCTCAAGTGAGA
84068 TCTTCTTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 7 0.15
36 41 0.85
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (35 bp):
AAATTGTCTCAAGTGAGACAACATTTGTTTTTGAG
Found at i:84206 original size:108 final size:105
Alignment explanation
Indices: 84049--84363 Score: 332
Period size: 108 Copynumber: 3.0 Consensus size: 105
84039 TGTTTTTGAG
* * **
84049 AAAACGATCTCAAGTGAGATCTTCTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTCAA
1 AAAACAATCTCAACTGAGATCAACTTTGTTTAATGTG-AAACAAATTCGAAATTTGTA-TCTCAA
84114 AGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
64 AGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
** * * * *
84156 AATAACAATCTCATGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATATCA
1 AA-AACAATCTCAACTGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCGAAATTTGTATCTCA
* * * * ** *
84220 AAGAAAAAAATGTCTCAACCAAGACGAAGTTTGTTTT--ATGAG
63 AAG-GAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
* * *
84262 AAAGCGATCTCAACTGAGATCAACTTTGTTTAATGTGAAACAAATTC-AAATTTTGTATCTTAAA
1 AAAACAATCTCAACTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAA-TTTGTATCTCAAA
* **
84326 GGAAAATTGTCTCAAGTGAGACGAAATTTGTTTTGAAA
65 GGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
84364 GAAATTGTCT
Statistics
Matches: 169, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
103 32 0.19
104 31 0.18
105 17 0.10
106 4 0.02
107 9 0.05
108 64 0.38
109 10 0.06
110 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (105 bp):
AAAACAATCTCAACTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAG
GAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAAAAA
Found at i:84782 original size:12 final size:12
Alignment explanation
Indices: 84767--84815 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
84757 TATATATATA
*
84767 TGTATGTCTGTT
1 TGTATGTATGTT
*
84779 TGTATGTATGTA
1 TGTATGTATGTT
84791 TGTATGTATGTGT
1 TGTATGTATGT-T
84804 TG-ATGTATGTT
1 TGTATGTATGTT
84815 T
1 T
84816 TTCTCAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (12 bp):
TGTATGTATGTT
Found at i:84813 original size:4 final size:4
Alignment explanation
Indices: 84765--84801 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
84755 TATATATATA
* *
84765 TATG TATG TCTG TTTG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
84802 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.19, C:0.03, G:0.24, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:90474 original size:16 final size:15
Alignment explanation
Indices: 90453--90482 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
90443 ATACTACATG
90453 AAAATATATAATATTC
1 AAAATATAT-ATATTC
90469 AAAATATATATATT
1 AAAATATATATATT
90483 TGCTTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATATATATTC
Found at i:90649 original size:26 final size:25
Alignment explanation
Indices: 90601--90649 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
90591 GAAGAGCTAA
*
90601 ATAATAAATACAAATAAACATATCC
1 ATAATAAATACAAATAAAAATATCC
90626 ATAATATAATAC-AATAAATAATAT
1 ATAATA-AATACAAATAAA-AATAT
90650 AGGTACCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
ATAATAAATACAAATAAAAATATCC
Found at i:92065 original size:9 final size:9
Alignment explanation
Indices: 92051--92092 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
92041 TTGAAAATTG
92051 AAAATAAAT
1 AAAATAAAT
92060 AAAATATAAT
1 AAAATA-AAT
92070 AATAAT-AAT
1 AA-AATAAAT
92079 AATAATAAAT
1 AA-AATAAAT
92089 AAAA
1 AAAA
92093 AAAGAAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 17 0.57
10 10 0.33
11 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATAAAT
Found at i:94075 original size:32 final size:32
Alignment explanation
Indices: 94035--94102 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
94025 TATATATATA
94035 ATAT-TAATAAATT-TA-ATTTAATTTAAAAAAT
1 ATATATAAT-AATTATATATTTAATTT-AAAAAT
* *
94066 ATATATAATATTTATATATTTAATTTAAATAT
1 ATATATAATAATTATATATTTAATTTAAAAAT
94098 ATATA
1 ATATA
94103 CCCTGCCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 7 0.22
32 16 0.50
33 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATATATAATAATTATATATTTAATTTAAAAAT
Found at i:94153 original size:22 final size:23
Alignment explanation
Indices: 94128--94178 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
94118 GTTTAAATAA
94128 TCGTTTATACTAAAC-GAGATAC
1 TCGTTTATACTAAACGGAGATAC
*
94150 TCGTTTATGCTAAACGGAGATAC
1 TCGTTTATACTAAACGGAGATAC
*
94173 CCGTTT
1 TCGTTT
94179 TCCTGCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (23 bp):
TCGTTTATACTAAACGGAGATAC
Found at i:94568 original size:20 final size:20
Alignment explanation
Indices: 94532--94569 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
94522 CAAAAAACAA
94532 TAAAAAAACAATATCTTCCC
1 TAAAAAAACAATATCTTCCC
*
94552 TAAAGAAAA-AATTTCTTC
1 TAAA-AAAACAATATCTTC
94570 AGTTTCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAAAACAATATCTTCCC
Found at i:95937 original size:22 final size:22
Alignment explanation
Indices: 95912--95962 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
95902 CTACGGCGGC
95912 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
95934 ATCCGTCCCTATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
95956 ATTCGTC
1 ATCCGTC
95963 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:95967 original size:20 final size:21
Alignment explanation
Indices: 95912--95969 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
95902 CTACGGCGGC
*
95912 ATCCGTCCCCATCTCCGACGAA
1 ATCCGT-CCTATCTCCGACGAA
95934 ATCCGTCCCTATCTCCGACGAA
1 ATCCGT-CCTATCTCCGACGAA
*
95956 ATTCGT-CTATCTCC
1 ATCCGTCCTATCTCC
95970 ATCTCTCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.24
22 26 0.76
ACGTcount: A:0.21, C:0.41, G:0.12, T:0.26
Consensus pattern (21 bp):
ATCCGTCCTATCTCCGACGAA
Found at i:96371 original size:20 final size:20
Alignment explanation
Indices: 96332--96398 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
96322 AAATCGCAAC
96332 GCGATTTT-AGTTTT-GCGTT
1 GCGATTTTCA-TTTTCGCGTT
96351 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
96371 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
96391 GCAATTTT
1 GCGATTTT
96399 AAGTTTCAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:98081 original size:21 final size:21
Alignment explanation
Indices: 98054--98106 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
98044 GTTAGGGGAG
*
98054 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * **
98075 TTGCGTGAGGAGGTTGGTACT
1 TTACGTGATGAGGTCAGTACT
98096 TTACGTGATGA
1 TTACGTGATGA
98107 CAATGGTGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:98562 original size:21 final size:21
Alignment explanation
Indices: 98515--98606 Score: 107
Period size: 21 Copynumber: 4.5 Consensus size: 21
98505 CACCTGTCAT
*
98515 CGTTCAAGAGGCCCC-CT-AT
1 CGTTCAAGAGGCCCCTCTCAC
* * *
98534 CTTTCAAGAGGACCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCAC
* *
98555 CATTCAAGAGGCCCCTCTCAT
1 CGTTCAAGAGGCCCCTCTCAC
98576 CGTTCAAGAGGCCCCTCTCAC
1 CGTTCAAGAGGCCCCTCTCAC
*
98597 CGTTTAAGAG
1 CGTTCAAGAG
98607 CCTGATCCAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.22
20 1 0.02
21 46 0.77
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCTCAC
Found at i:100110 original size:20 final size:19
Alignment explanation
Indices: 100087--100167 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
100077 CTTTCGCAAC
*
100087 GCAAAGGTCAAATTCGCGTT
1 GCAAA-GTCAAATGCGCGTT
* ***
100107 GCAAAAGTCAAATTCGCAAC
1 GC-AAAGTCAAATGCGCGTT
*
100127 GCGAAAGTCAAACGCGCGTT
1 GC-AAAGTCAAATGCGCGTT
*
100147 GCGAAGTCAAATGCGCGTT
1 GCAAAGTCAAATGCGCGTT
100166 GC
1 GC
100168 GAATTTTACT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 17 0.35
20 29 0.59
21 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (19 bp):
GCAAAGTCAAATGCGCGTT
Found at i:100137 original size:40 final size:39
Alignment explanation
Indices: 100079--100158 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 39
100069 AAGGTACACT
**
100079 TTCGCAACGCAAAGGTCAAATTCGCGTTGCAAAAGTCAAA
1 TTCGCAACGCAAAGGTCAAACGCGCGTTGC-AAAGTCAAA
*
100119 TTCGCAACGCGAAA-GTCAAACGCGCGTTGCGAAGTCAAA
1 TTCGCAACGC-AAAGGTCAAACGCGCGTTGCAAAGTCAAA
100158 T
1 T
100159 GCGCGTTGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 9 0.25
40 24 0.67
41 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (39 bp):
TTCGCAACGCAAAGGTCAAACGCGCGTTGCAAAGTCAAA
Found at i:100155 original size:19 final size:19
Alignment explanation
Indices: 100131--100170 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
100121 CGCAACGCGA
100131 AAGTCAAACGCGCGTTGCG
1 AAGTCAAACGCGCGTTGCG
*
100150 AAGTCAAATGCGCGTTGCG
1 AAGTCAAACGCGCGTTGCG
100169 AA
1 AA
100171 TTTTACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (19 bp):
AAGTCAAACGCGCGTTGCG
Found at i:100240 original size:49 final size:49
Alignment explanation
Indices: 100166--100262 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
100156 AATGCGCGTT
* * * *
100166 GCGAATTTTACTTTCACATTTCGAATTTGATTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCACATTGCGAATTTAACTTTCGCAACAATCGCAAC
* *
100215 GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTCGCAACAATCGCAA
1 GCGAATTTGACTTTCACATTGCGAATTTAACTTTCGCAACAATCGCAA
100263 TAAAAAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (49 bp):
GCGAATTTGACTTTCACATTGCGAATTTAACTTTCGCAACAATCGCAAC
Found at i:102987 original size:12 final size:12
Alignment explanation
Indices: 102970--103003 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
102960 GGTTGTGGGT
102970 TTTGATATTGTG
1 TTTGATATTGTG
102982 TTTGATATTGTG
1 TTTGATATTGTG
*
102994 TTTGGTATTG
1 TTTGATATTG
103004 GAAATGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:103819 original size:20 final size:20
Alignment explanation
Indices: 103796--103862 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
103786 AAATATAACC
103796 TGCGAAATTAAAATTCGTGT
1 TGCGAAATTAAAATTCGTGT
* *
103816 TGCG-AATTCAAAAATCGAGT
1 TGCGAAATT-AAAATTCGTGT
* * *
103836 TGCGAATTTGAAATCCAGTGT
1 TGCGAAATTAAAATTC-GTGT
103857 TGCGAA
1 TGCGAA
103863 TTTGGAAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.11
20 21 0.57
21 12 0.32
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
TGCGAAATTAAAATTCGTGT
Found at i:103872 original size:41 final size:40
Alignment explanation
Indices: 103796--103986 Score: 128
Period size: 40 Copynumber: 4.8 Consensus size: 40
103786 AAATATAACC
* * ***
103796 TGCGAAATTAAAATTCGTGTTGCGAATTCAAAAATCGAGT
1 TGCGAATTTGAAATTCGTGTTGCGAATTTGGAAATCGAGT
*
103836 TGCGAATTTGAAATCCAGTGTTGCGAATTTGGAAATCGCA-T
1 TGCGAATTTGAAATTC-GTGTTGCGAATTTGGAAATCG-AGT
* * *
103877 TGTGAATTTG-ACTTCTGTGTTGCAAATTAT--AAATTCGAGT
1 TGCGAATTTGAAATTC-GTGTTGCGAATT-TGGAAA-TCGAGT
*
103917 TGCG-ATTT-ACATATTCGCGTTGCGAATTTGGAAA-CTGAGT
1 TGCGAATTTGA-A-ATTCGTGTTGCGAATTTGGAAATC-GAGT
* * *
103957 TGCGAAATTCGAGA-TCGCGTTGCGAATTTG
1 TGCG-AATTTGAAATTCGTGTTGCGAATTTG
103987 TTGGTCATTT
Statistics
Matches: 120, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
39 10 0.08
40 69 0.57
41 36 0.30
42 4 0.03
43 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (40 bp):
TGCGAATTTGAAATTCGTGTTGCGAATTTGGAAATCGAGT
Found at i:108845 original size:69 final size:69
Alignment explanation
Indices: 108734--108871 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
108724 TTGGGTTTGC
108734 GGCTAAATCTTGGGAAAGATGGGTGAACTTCATTGCTTTTAGAAATATAATCATTTTGTTAAAAA
1 GGCTAAATCTTGGGAAAGATGGGTGAACTTCATTGCTTTTAGAAATATAATCATTTTGTTAAAAA
108799 CATG
66 CATG
108803 GGCTAAATCTTGGGAAAGATGGGTGAACTTCATTGCTTTTAGAAATATAATCATTTTGTTAAAAA
1 GGCTAAATCTTGGGAAAGATGGGTGAACTTCATTGCTTTTAGAAATATAATCATTTTGTTAAAAA
108868 CATG
66 CATG
108872 ATATTGATGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (69 bp):
GGCTAAATCTTGGGAAAGATGGGTGAACTTCATTGCTTTTAGAAATATAATCATTTTGTTAAAAA
CATG
Found at i:112283 original size:18 final size:18
Alignment explanation
Indices: 112260--112302 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
112250 CTTTAATTTA
*
112260 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
112278 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
112296 TTTATTT
1 TTTATTT
112303 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:115911 original size:34 final size:34
Alignment explanation
Indices: 115868--115941 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
115858 GTGCAGTGCA
* *
115868 AAAAAATAGCAGTACAATTTTAGTTCGAACAATT
1 AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
*
115902 AAAAAATAGCAGTACAATTTTGGTTCAAACAATG
1 AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
115936 AAAAAA
1 AAAAAA
115942 GAGAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (34 bp):
AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
Done.