Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004101.1 Hibiscus syriacus cultivar Beakdansim tig00008969_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: 191148
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5851 original size:44 final size:46
Alignment explanation
Indices: 5788--5874 Score: 142
Period size: 44 Copynumber: 1.9 Consensus size: 46
5778 TTTTGCTAAA
* *
5788 ATATATATAGTTTTGAAAACA-TTTTGAATATATATA-TATATAAT
1 ATATATATAATTTTGAAAACATTTTTGAAAATATATATTATATAAT
5832 ATATATATAATTTTGAAAACATTTTTGAAAATATATATTATAT
1 ATATATATAATTTTGAAAACATTTTTGAAAATATATATTATAT
5875 GATTTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 20 0.51
45 14 0.36
46 5 0.13
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (46 bp):
ATATATATAATTTTGAAAACATTTTTGAAAATATATATTATATAAT
Found at i:5886 original size:35 final size:34
Alignment explanation
Indices: 5830--6010 Score: 174
Period size: 33 Copynumber: 5.2 Consensus size: 34
5820 TATATATATA
5830 ATATA-TATATAATTTTGAAAACATTTTTGAAAAT
1 ATATATTATATAATTTTGAAAACA-TTTTGAAAAT
* *
5864 ATATATTATATGATTTTCAAAACATTTTG-AAAT
1 ATATATTATATAATTTTGAAAACATTTTGAAAAT
**
5897 ATATATTATATTGTTTTGAAAACATTTTGAAAAAATAT
1 ATATATTATATAATTTTGAAAACATTTTG---AAA-AT
* *
5935 ATATATTATATAGTTTTGAAAATGATTTTTGAAAAAT
1 ATATATTATATAATTTTGAAAA-CA-TTTTG-AAAAT
*
5972 ATATATAATATATAATTTT--AAA-ATATTGAAAAT
1 ATATAT--TATATAATTTTGAAAACATTTTGAAAAT
6005 ATATAT
1 ATATAT
6011 AGTTTTGGAA
Statistics
Matches: 128, Mismatches: 9, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
33 41 0.32
34 14 0.11
35 17 0.13
37 13 0.10
38 27 0.21
39 11 0.09
40 5 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (34 bp):
ATATATTATATAATTTTGAAAACATTTTGAAAAT
Found at i:5902 original size:33 final size:33
Alignment explanation
Indices: 5830--6041 Score: 140
Period size: 33 Copynumber: 6.3 Consensus size: 33
5820 TATATATATA
*
5830 ATATA-TATATAATTTTGAAAACATTTTTGAAAAT
1 ATATATTATATGATTTTGAAAACA-TTTTG-AAAT
*
5864 ATATATTATATGATTTTCAAAACATTTTGAAAT
1 ATATATTATATGATTTTGAAAACATTTTGAAAT
5897 ATATATTATATTG-TTTTGAAAACATTTTGAAAAAATAT
1 ATATATTATA-TGATTTTGAAAACATTTTG----AA-AT
*
5935 ATATATTATAT-AGTTTTGAAAATGATTTTTGAAAAAT
1 ATATATTATATGA-TTTTGAAAA-CA-TTTTG--AAAT
* *
5972 ATATATAATATATAATTTT--AAA-ATATTGAAA-
1 ATATAT--TATATGATTTTGAAAACATTTTGAAAT
* *
6003 ATATA-TATA-G-TTTTGGAAATATTTTTGAAA-
1 ATATATTATATGATTTTGAAAACA-TTTTGAAAT
6033 ATATATTAT
1 ATATATTAT
6042 TATTATTTAA
Statistics
Matches: 152, Mismatches: 7, Indels: 41
0.76 0.04 0.20
Matches are distributed among these distances:
26 4 0.03
28 7 0.05
29 1 0.01
30 12 0.08
31 8 0.05
32 3 0.02
33 29 0.19
34 16 0.11
35 17 0.11
37 14 0.09
38 25 0.16
39 10 0.07
40 6 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (33 bp):
ATATATTATATGATTTTGAAAACATTTTGAAAT
Found at i:5920 original size:112 final size:106
Alignment explanation
Indices: 5720--6047 Score: 321
Period size: 104 Copynumber: 3.1 Consensus size: 106
5710 GGTCTTAAAA
** * *
5720 ATATATATATTATATAGCTTTGAAAATGATTTTTG-AAAATATATATATAATATAGTTTT----T
1 ATATATATATTATATAATTTTGAAAATCATTTTTGAAAAATATATATAT-ATATAATTTTAAAAT
5780 -TTGCTAAAATATATATA-GTTTTGAAAACATTTTGAATATATAT
65 ATTG--AAAATATATATATGTTTTGAAAACATTTTGAA-ATATAT
*
5823 ATATATAATATATATATAATTTTGAAAA-CATTTTTG-AAAATATATAT-TATATGATTTTCAAA
1 ATATAT-ATAT-TATATAATTTTGAAAATCATTTTTGAAAAATATATATATATATAATTTT--AA
*
5885 ACATTTTGAAATATATATTATATTGTTTTGAAAACATTTTGAAA-A-A-
62 A-ATATTGAAA-ATATA-TATA-TGTTTTGAAAACATTTTGAAATATAT
* *
5931 ATATATATATTATATAGTTTTGAAAATGATTTTTGAAAAATATATATAATATATAATTTTAAAAT
1 ATATATATATTATATAATTTTGAAAATCATTTTTGAAAAATATATAT-ATATATAATTTTAAAAT
* *
5996 ATTGAAAATATATATA-GTTTTGGAAATATTTTTGAAA-ATAT
65 ATTGAAAATATATATATGTTTTGAAAACA-TTTTGAAATATAT
6037 AT-TAT-TATTAT
1 ATATATATATTAT
6048 TTAAAAACAA
Statistics
Matches: 193, Mismatches: 11, Indels: 41
0.79 0.04 0.17
Matches are distributed among these distances:
102 8 0.04
103 17 0.09
104 37 0.19
105 22 0.11
106 22 0.11
107 19 0.10
108 23 0.12
109 7 0.04
110 18 0.09
111 1 0.01
112 19 0.10
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (106 bp):
ATATATATATTATATAATTTTGAAAATCATTTTTGAAAAATATATATATATATAATTTTAAAATA
TTGAAAATATATATATGTTTTGAAAACATTTTGAAATATAT
Found at i:5968 original size:211 final size:213
Alignment explanation
Indices: 5598--5983 Score: 527
Period size: 211 Copynumber: 1.8 Consensus size: 213
5588 TATTATATAT
* * *
5598 ATATATATATATATATTAATATAGTATAACTTTTGCAAATATTTTTGAAAAATATAATATATAAT
1 ATATATATATATATAATAATATAGTATAACTTTTGAAAACATTTTTGAAAAATATAATATATAAT
* *
5663 TTTTAGAAAATGGTTTTTGAAAACATATAATATACTGTTTTAAAATCGGTCTTAAAAATATATAT
66 TTTCAGAAAA--G-TTTTGAAAACATATAATATACTGTTTTAAAATCGATCTTAAAAATATATAT
5728 ATTATATAGCTTTGAAAATGATTTTTGAAAATATATATATAATATAGTTTTTTTGCTAAAATATA
128 ATTATATAGCTTTGAAAATGATTTTTGAAAA-ATATATATAATATAGTTTTTTTGCTAAAATATA
5793 TATAGTTTTGAAAACATTTTGA
192 TATAGTTTTGAAAACATTTTGA
* *
5815 ATATATATATATATAAT-ATATA-TATAA-TTTTGAAAACATTTTTGAAAATATATATTATATGA
1 ATATATATATATATAATAATATAGTATAACTTTTGAAAACATTTTTGAAAA-ATATAATATATAA
* * * *
5877 TTTTCA-AAACA-TTTTG-AAATATATATTATATTGTTTTGAAAA-C-ATTTTGAAAAAATATAT
65 TTTTCAGAAA-AGTTTTGAAAACATATAATATACTGTTTT-AAAATCGATCTT--AAAAATATAT
*
5937 ATATTATATAGTTTTGAAAATGATTTTTGAAAAATATATATAATATA
126 ATATTATATAGCTTTGAAAATGATTTTTGAAAAATATATATAATATA
5984 TAATTTTAAA
Statistics
Matches: 152, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
209 3 0.02
210 33 0.22
211 51 0.34
214 22 0.14
215 22 0.14
216 5 0.03
217 16 0.11
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (213 bp):
ATATATATATATATAATAATATAGTATAACTTTTGAAAACATTTTTGAAAAATATAATATATAAT
TTTCAGAAAAGTTTTGAAAACATATAATATACTGTTTTAAAATCGATCTTAAAAATATATATATT
ATATAGCTTTGAAAATGATTTTTGAAAAATATATATAATATAGTTTTTTTGCTAAAATATATATA
GTTTTGAAAACATTTTGA
Found at i:6922 original size:13 final size:12
Alignment explanation
Indices: 6905--6958 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
6895 TTTCCTTTGA
6905 TTTTTTAATATAT
1 TTTTTTAATAT-T
*
6918 ATTTTTAA-A-T
1 TTTTTTAATATT
6928 TTTTTTAATATT
1 TTTTTTAATATT
*
6940 TTTTTTAATAAT
1 TTTTTTAATATT
6952 TTTTTTA
1 TTTTTTA
6959 TCTTATTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
12 20 0.56
13 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTAATATT
Found at i:6931 original size:23 final size:24
Alignment explanation
Indices: 6905--6966 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
6895 TTTCCTTTGA
6905 TTTTTTAATATATATTTTT-A-AAT
1 TTTTTTAATAT-TATTTTTAATAAT
*
6928 TTTTTTAATATTTTTTTTAATAAT
1 TTTTTTAATATTATTTTTAATAAT
*
6952 TTTTTT-ATCTTATTT
1 TTTTTTAATATTATTT
6967 CATTTTTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.18
23 19 0.56
24 9 0.26
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTTAATATTATTTTTAATAAT
Found at i:7053 original size:10 final size:10
Alignment explanation
Indices: 7010--7062 Score: 74
Period size: 10 Copynumber: 5.4 Consensus size: 10
7000 TTTTTATGTT
7010 TTTTCTTTAA
1 TTTTCTTTAA
7020 -TTTCTTTAA
1 TTTTCTTTAA
*
7029 TATTT-TTTGA
1 T-TTTCTTTAA
7039 TTTTCTTTAA
1 TTTTCTTTAA
7049 TTTTCTTTAA
1 TTTTCTTTAA
7059 TTTT
1 TTTT
7063 ATTTTTTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 12 0.32
10 23 0.61
11 3 0.08
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTCTTTAA
Found at i:7105 original size:30 final size:29
Alignment explanation
Indices: 7002--7129 Score: 113
Period size: 30 Copynumber: 4.4 Consensus size: 29
6992 CTCTCTTATT
* *
7002 TTTATGTTTTTT-CTTTAATTTCTTTAATA
1 TTTAT-TTTTTTCCTTTGATTTATTTAATA
* *
7031 TTT-TTTGATTTT-CTTTAATTTTCTTTAAT-
1 TTTATTT--TTTTCCTTTGA-TTTATTTAATA
* *
7060 TTTA-TTTTTTCCTTTGATTTATTTATTT
1 TTTATTTTTTTCCTTTGATTTATTTAATA
*
7088 TTTATGTTTTTTTCTTTGATTTATTTAATA
1 TTTAT-TTTTTTCCTTTGATTTATTTAATA
7118 TTTATTTTTTTC
1 TTTATTTTTTTC
7130 TAACATATTT
Statistics
Matches: 84, Mismatches: 7, Indels: 16
0.79 0.07 0.15
Matches are distributed among these distances:
27 14 0.17
28 10 0.12
29 24 0.29
30 36 0.43
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (29 bp):
TTTATTTTTTTCCTTTGATTTATTTAATA
Found at i:14969 original size:31 final size:30
Alignment explanation
Indices: 14931--14994 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
14921 TCAAAAAACA
* *
14931 TAAGATATAATCACTTTTATTTTTATTTAAT
1 TAAGATATAACCACTTTCA-TTTTATTTAAT
* *
14962 TAAGATATGACCAGTTTCATTTTATTTAAT
1 TAAGATATAACCACTTTCATTTTATTTAAT
14992 TAA
1 TAA
14995 AACGTGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (30 bp):
TAAGATATAACCACTTTCATTTTATTTAAT
Found at i:16153 original size:2 final size:2
Alignment explanation
Indices: 16148--16173 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16138 TATACTCTAG
16148 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
16174 TTGAAAGAGA
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:16345 original size:21 final size:21
Alignment explanation
Indices: 16321--16375 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
16311 TAATTTTATA
16321 TATATTAACTTGAAATATTTT
1 TATATTAACTTGAAATATTTT
* *
16342 TATATCAACTATTAAATATTTT
1 TATATTAACT-TGAAATATTTT
16364 TATTATTAACTT
1 TA-TATTAACTT
16376 AATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.31
22 13 0.45
23 7 0.24
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATTAACTTGAAATATTTT
Found at i:16345 original size:23 final size:23
Alignment explanation
Indices: 16313--16375 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
16303 ATATAATATA
16313 ATTTTATATATATTAACTTGAAAT
1 ATTTT-TATATATTAACTTGAAAT
* *
16337 A-TTTT-TATATCAACTATTAAAT
1 ATTTTTATATATTAACT-TGAAAT
16359 ATTTTTAT-TATTAACTT
1 ATTTTTATATATTAACTT
16376 AATTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 9 0.27
22 8 0.24
23 14 0.42
24 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTTTATATATTAACTTGAAAT
Found at i:16369 original size:25 final size:26
Alignment explanation
Indices: 16333--16390 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 26
16323 TATTAACTTG
*
16333 AAATATTTTTA-TATCAAC-T-ATT-
1 AAATATTTTTATTATTAACTTAATTA
16355 AAATATTTTTATTATTAACTTAATTA
1 AAATATTTTTATTATTAACTTAATTA
16381 AAATATTTTT
1 AAATATTTTT
16391 TTTTTTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 6 0.19
24 1 0.03
25 3 0.10
26 10 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATATTTTTATTATTAACTTAATTA
Found at i:16377 original size:21 final size:21
Alignment explanation
Indices: 16313--16377 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 21
16303 ATATAATATA
16313 ATTTTATATATATTAACTTGAAAT
1 ATTTT-TAT-TATTAACTT-AAAT
*
16337 ATTTTTA-TATCAACTATTAAAT
1 ATTTTTATTATTAAC--TTAAAT
16359 ATTTTTATTATTAACTTAA
1 ATTTTTATTATTAACTTAA
16378 TTAAAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 10 0.28
22 11 0.31
23 10 0.28
24 5 0.14
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTATTATTAACTTAAAT
Found at i:27301 original size:21 final size:21
Alignment explanation
Indices: 27239--27306 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
27229 ATCTTAAATT
*
27239 ATAAACCTTGAACCCTAAATC
1 ATAAACCTTGAACCCTAAACC
* *
27260 AT-AACCATATTACCCCTAAACC
1 ATAAACC-T-TGAACCCTAAACC
* *
27282 ATAAACCTTGAACCTTAAACT
1 ATAAACCTTGAACCCTAAACC
27303 ATAA
1 ATAA
27307 TTTAGGGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.11
21 16 0.43
22 13 0.35
23 4 0.11
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.25
Consensus pattern (21 bp):
ATAAACCTTGAACCCTAAACC
Found at i:27553 original size:60 final size:60
Alignment explanation
Indices: 27444--27556 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
27434 CCTTAAGCCT
* * * * * *
27444 ATTTTAAATTAGTCCTCAAACTTTTGATTATTTCAGTTTCATCCCCAAACTATGACCTTC
1 ATTTTAAATTAGTCCCCAAACTTTTGAATATTCCAATTCCATCACCAAACTATGACCTTC
* *
27504 ATTTTAAATTGGTCCCCAAACTTTTAGAATATTCCAATTCCAT-AGCAAACTAT
1 ATTTTAAATTAGTCCCCAAACTTTT-GAATATTCCAATTCCATCACCAAACTAT
27557 TCGTATACAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 31 0.70
61 13 0.30
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (60 bp):
ATTTTAAATTAGTCCCCAAACTTTTGAATATTCCAATTCCATCACCAAACTATGACCTTC
Found at i:30740 original size:17 final size:17
Alignment explanation
Indices: 30718--30756 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
30708 ATGGTTTTCA
30718 GAACCGGACCGGTTAGC
1 GAACCGGACCGGTTAGC
*
30735 GAACCGGACCGGTTAGT
1 GAACCGGACCGGTTAGC
30752 GAACC
1 GAACC
30757 AGTCATGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.13
Consensus pattern (17 bp):
GAACCGGACCGGTTAGC
Found at i:31017 original size:16 final size:16
Alignment explanation
Indices: 30996--31037 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
30986 AGGTAAACAT
30996 ATTAAATAATAATATA
1 ATTAAATAATAATATA
31012 ATTAAATAAT--TATA
1 ATTAAATAATAATATA
*
31026 ATTAAAAAATAA
1 ATTAAATAATAA
31038 ATTTGGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATAATAATATA
Found at i:32220 original size:32 final size:34
Alignment explanation
Indices: 32138--32237 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 34
32128 GTTCGGGTCG
*
32138 GGTTTTTTAAGTGTGCTATTCGGGTCGAGTCGTGTCA
1 GGTTTTTTAAGTGTGATATTCGGGTCG-G--GTGTCA
*
32175 GGTTTTTTAAAGTGAGATATTCGGGTCGGGT-T-A
1 GGTTTTTT-AAGTGTGATATTCGGGTCGGGTGTCA
32208 GGTTTTTTAAGTGTGATATTCGGGTCGGGT
1 GGTTTTTTAAGTGTGATATTCGGGTCGGGT
32238 CGAGTTTAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
32 21 0.36
33 9 0.15
34 1 0.02
35 2 0.03
37 9 0.15
38 17 0.29
ACGTcount: A:0.16, C:0.09, G:0.34, T:0.41
Consensus pattern (34 bp):
GGTTTTTTAAGTGTGATATTCGGGTCGGGTGTCA
Found at i:32858 original size:17 final size:18
Alignment explanation
Indices: 32836--32882 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
32826 TATGGAATTG
*
32836 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
32853 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
32871 TATTCCAATTCC
1 GATTCCAATTCC
32883 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.32, G:0.06, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:37751 original size:161 final size:160
Alignment explanation
Indices: 37584--37983 Score: 483
Period size: 159 Copynumber: 2.5 Consensus size: 160
37574 AGTTACATAA
* * * * * * *
37584 GTATTCTATTGTGGTATATGAGAATGTAGTTTAAATTTGGCAAAAAAAAAGTG-GCTTAAAATAA
1 GTATTCTACTATGGTTTAGGAGCATGTAGTTCAAATTTGG-AAAAAAAAA-TGAACTTAAAATAA
*
37648 ATCACAAATTGAAGAAATAAAG-AGATTATAAAAAAATAAAGGACTAAATTGAA-AAATTAAAAA
64 ATCACAAATTGAAGAAAT-AAGTAGATTATAAAAAAATAAAGGACTAAATT-AAGAAATGAAAAA
* *
37711 TTTGCTATCAAAAAGAGGAATTAAAAGTACACAT
127 ATTGCTATCAAAAAGAAGAATTAAAAGTACACAT
* *
37745 GTATTCTACTATGGTTTAGGAGCATGT-GACTCAAATTTGG-TAAAAAAATGAACTTAAAATAAA
1 GTATTCTACTATGGTTTAGGAGCATGTAG-TTCAAATTTGGAAAAAAAAATGAACTTAAAATAAA
* * * *
37808 TGACAAATTGAAGAAATAAGTAGATTATGAAAAATTGAAGGACTAAATTAAGAAATGAAAAAATT
65 TCACAAATTGAAGAAATAAGTAGATTATAAAAAAATAAAGGACTAAATTAAGAAATGAAAAAATT
* * *
37873 GTTATCGAAAAGAAGAATTGAAAGTACACAT
130 GCTATCAAAAAGAAGAATTAAAAGTACACAT
* * *
37904 GTATTCTACTATGGTTTAGGAGCATTTAGTTCAAATTTGG---TAAAAATGAACTTAAAATGAAT
1 GTATTCTACTATGGTTTAGGAGCATGTAGTTCAAATTTGGAAAAAAAAATGAACTTAAAATAAAT
* *
37966 GATAAATTGAAGAAATAA
66 CACAAATTGAAGAAATAA
37984 TGAAATAATA
Statistics
Matches: 210, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
157 37 0.18
158 7 0.03
159 133 0.63
160 2 0.01
161 31 0.15
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (160 bp):
GTATTCTACTATGGTTTAGGAGCATGTAGTTCAAATTTGGAAAAAAAAATGAACTTAAAATAAAT
CACAAATTGAAGAAATAAGTAGATTATAAAAAAATAAAGGACTAAATTAAGAAATGAAAAAATTG
CTATCAAAAAGAAGAATTAAAAGTACACAT
Found at i:37818 original size:159 final size:158
Alignment explanation
Indices: 37638--37983 Score: 502
Period size: 159 Copynumber: 2.2 Consensus size: 158
37628 AAAAAAGTGG
*
37638 CTTAAAATAAATCACAAATTGAAGAAATAAAG-AGATTATAAAAAAATAAAGGACTAAATTGAA-
1 CTTAAAATAAATGACAAATTGAAGAAATAAAGTAGATTATAAAAAAATAAAGGACTAAATT-AAG
* * *
37701 AAATTAAAAATTTGCTATCAAAAAGAGGAATTAAAAGTACACATGTATTCTACTATGGTTTAGGA
65 AAATGAAAAAATTGCTATCAAAAAGAAGAATTAAAAGTACACATGTATTCTACTATGGTTTAGGA
37766 GCATGTGA-CTCAAATTTGGTAAAAAAATGAA
130 GCAT-TGAGCTCAAATTTGGT--AAAAATGAA
* * *
37797 CTTAAAATAAATGACAAATTGAAGAAAT-AAGTAGATTATGAAAAATTGAAGGACTAAATTAAGA
1 CTTAAAATAAATGACAAATTGAAGAAATAAAGTAGATTATAAAAAAATAAAGGACTAAATTAAGA
* * *
37861 AATGAAAAAATTGTTATCGAAAAGAAGAATTGAAAGTACACATGTATTCTACTATGGTTTAGGAG
66 AATGAAAAAATTGCTATCAAAAAGAAGAATTAAAAGTACACATGTATTCTACTATGGTTTAGGAG
* *
37926 CATTTAGTTCAAATTTGGTAAAAATGAA
131 CATTGAGCTCAAATTTGGTAAAAATGAA
* *
37954 CTTAAAATGAATGATAAATTGAAGAAATAA
1 CTTAAAATAAATGACAAATTGAAGAAATAA
37984 TGAAATAATA
Statistics
Matches: 169, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
157 35 0.21
158 8 0.05
159 126 0.75
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (158 bp):
CTTAAAATAAATGACAAATTGAAGAAATAAAGTAGATTATAAAAAAATAAAGGACTAAATTAAGA
AATGAAAAAATTGCTATCAAAAAGAAGAATTAAAAGTACACATGTATTCTACTATGGTTTAGGAG
CATTGAGCTCAAATTTGGTAAAAATGAA
Found at i:39074 original size:21 final size:19
Alignment explanation
Indices: 39050--39088 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
39040 CATCTTCATT
39050 TTTTTAGTCATTTATTTTTAG
1 TTTTTAGT-ATTT-TTTTTAG
39071 TTTTTAGTATTTTTTTTA
1 TTTTTAGTATTTTTTTTA
39089 TATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTTAGTATTTTTTTTAG
Found at i:46675 original size:10 final size:10
Alignment explanation
Indices: 46656--46686 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
46646 CATTTAATAA
46656 ATAAACGAAC
1 ATAAACGAAC
*
46666 ATAAATGAAC
1 ATAAACGAAC
46676 ATAAACGAAC
1 ATAAACGAAC
46686 A
1 A
46687 ATTTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:46787 original size:27 final size:26
Alignment explanation
Indices: 46751--46823 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
46741 TATTTAAATG
*
46751 ATAAACGAACACAAACGAACGAACATA
1 ATAAACGAACACAAACAAAC-AACATA
* * *
46778 ATAAATGAACATAAACAAACAACACA
1 ATAAACGAACACAAACAAACAACATA
* *
46804 A-ACACAAACACAAA-AAACAA
1 ATAAACGAACACAAACAAACAA
46824 ACTTATTAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 6 0.16
27 17 0.45
ACGTcount: A:0.66, C:0.22, G:0.05, T:0.07
Consensus pattern (26 bp):
ATAAACGAACACAAACAAACAACATA
Found at i:51377 original size:61 final size:61
Alignment explanation
Indices: 51296--51427 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 61
51286 TCCTAGAGGG
* * *
51296 GTATTGATATTGAGACATTTTTCAAACATC-AATGCAAAATTTGGTACCGATACTCAGATTA
1 GTATTGATACTGAGACATTTTTCAAACATCGAA-GCAAAATTTGGTACCGATAATCAGAATA
* * * *
51357 GTCTTGATACTGAGATATTTTTCAAACATCGAAGCAAATTTTGGTACCGATAATTAGAATA
1 GTATTGATACTGAGACATTTTTCAAACATCGAAGCAAAATTTGGTACCGATAATCAGAATA
51418 GTATTGATAC
1 GTATTGATAC
51428 CCTAGTACAG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (61 bp):
GTATTGATACTGAGACATTTTTCAAACATCGAAGCAAAATTTGGTACCGATAATCAGAATA
Found at i:58452 original size:2 final size:2
Alignment explanation
Indices: 58445--58473 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58435 TTCGTCTTTT
58445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58474 TGTATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58627 original size:37 final size:37
Alignment explanation
Indices: 58464--58659 Score: 220
Period size: 35 Copynumber: 5.3 Consensus size: 37
58454 ATATATATAT
* * * *
58464 ATATATATATTGTATAG-TTTGAAAACATTTTTTTTAAA
1 ATATATATAATATATAGTTTTTAAAACA--TTTTTGAAA
* * *
58502 CTATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTG-AAA
* * *
58540 CATTTATATATTATATAGTTTTTAAAACA-TTTTAAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
* *
58577 ATAAATATAATATATAGTTTTTAAAGCATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
58614 ATATATAT--TATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
58649 ATATATATAAT
1 ATATATATAAT
58660 TTTTAAAGCA
Statistics
Matches: 134, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
35 34 0.25
36 24 0.18
37 22 0.16
38 20 0.15
39 34 0.25
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:58706 original size:65 final size:65
Alignment explanation
Indices: 58544--58700 Score: 165
Period size: 71 Copynumber: 2.3 Consensus size: 65
58534 TGAAAACATT
**
58544 TATATATTATATAGTTTTTAAAACATT-TTAAAAATAAATATAATATATAGTTTTTAAAGCATTT
1 TATATATTATATAGTTTTT-AAACATTATT--TGA-AAATAT-ATATA-A-TTTTTAAAGCATTT
*
58608 TTGAAAA
59 TTAAAAA
58615 TATATATTATATAGTTTTTAAAACATT-TTTGAAAATATATATAATTTTTAAAGCATTTTTAAAA
1 TATATATTATATAGTTTTT-AAACATTATTTGAAAATATATATAATTTTTAAAGCATTTTT-AAA
58679 CACA
64 -A-A
*
58683 TATGTATTATATAGTTTT
1 TATATATTATATAGTTTT
58701 GACATTATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
65 16 0.20
66 3 0.04
67 6 0.08
68 24 0.30
69 1 0.01
71 29 0.37
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (65 bp):
TATATATTATATAGTTTTTAAACATTATTTGAAAATATATATAATTTTTAAAGCATTTTTAAAAA
Found at i:58736 original size:37 final size:36
Alignment explanation
Indices: 58551--58760 Score: 108
Period size: 37 Copynumber: 5.9 Consensus size: 36
58541 ATTTATATAT
* *
58551 TATATAGTTTTTAA-AACA-TTTTAAAAA-TAAATATAA
1 TATATAG-TTTTAACAATATTTTTAAAAACT--ATATGA
** *
58587 TATATAGTTTTTAA-AGCATTTTTGAAAA-TATAT-A
1 TATATAG-TTTTAACAATATTTTTAAAAACTATATGA
* *
58621 TTATATAGTTTTTAA-AACATTTTTGAAAA-TATAT-A
1 -TATATAG-TTTTAACAATATTTTTAAAAACTATATGA
**
58656 TA-AT--TTTTAA-AGCATTTTTAAAACAC-ATATGTA
1 TATATAGTTTTAACAATATTTTTAAAA-ACTATATG-A
* *
58689 TTATATAGTTTTGACATTA-TTTTAAAAACCTATATGA
1 -TATATAGTTTTAACAATATTTTTAAAAA-CTATATGA
*
58726 TATATAAGTTTTAAGAATATTTTTAAAAACTATAT
1 TATAT-AGTTTTAACAATATTTTTAAAAACTATAT
58761 AATTTTGAAA
Statistics
Matches: 148, Mismatches: 11, Indels: 29
0.79 0.06 0.15
Matches are distributed among these distances:
30 17 0.11
31 5 0.03
33 3 0.02
34 5 0.03
35 39 0.26
36 23 0.16
37 40 0.27
38 16 0.11
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAGTTTTAACAATATTTTTAAAAACTATATGA
Found at i:60017 original size:20 final size:20
Alignment explanation
Indices: 59972--60018 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
59962 TATTTTACTT
59972 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
59993 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
60012 TATTTTT
1 TATTTTT
60019 ACCTCATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 5 0.22
20 17 0.74
21 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:61278 original size:17 final size:18
Alignment explanation
Indices: 61246--61279 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
61236 CTCACTAACC
*
61246 CTTTTATTTTTTTGTTCT
1 CTTTTATTTTTGTGTTCT
61264 CTTTTA-TTTTGTGTTC
1 CTTTTATTTTTGTGTTC
61280 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.74
Consensus pattern (18 bp):
CTTTTATTTTTGTGTTCT
Found at i:61934 original size:19 final size:19
Alignment explanation
Indices: 61900--61944 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
61890 ATTTAGACAT
61900 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
61918 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
61937 TTTGCATT
1 TTTGCATT
61945 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:65571 original size:85 final size:84
Alignment explanation
Indices: 65275--65787 Score: 621
Period size: 85 Copynumber: 6.2 Consensus size: 84
65265 GCTCAAGGCC
* * ** * * * *
65275 AGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* *
65338 TGCAGAATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* *** * * *
65357 AGAAGGGCTATCTG---CCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATT
1 AGAAGGGTTATCTGCCACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
* * * *
65419 TACAGCATAACTCAAGGCT
66 TGCAGCATAACTTAAGTCG
* *
65438 AGAAAGGTTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACGTCATT
1 AGAAGGGTTATCTGCCACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
65500 TGCAGCATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
*
65519 AGAAGGGTTATCTGCCAACCAAAGACCCCCGAGTTCGATTACAGTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCC-ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
65584 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
*
65604 ATAAGGGTTATCTGCCAACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCC-ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
65669 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* ** * * * * *
65689 AGAAGGGTTATCTGCCAACCAAAGAGCTTCGAGTTCAATTACATTCAGC-TCAACGGCACAACAT
1 AGAAGGGTTATCTGCC-ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
*
65753 TTGCAGCATAGCTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
*
65773 AGAAGGGCTATCTGC
1 AGAAGGGTTATCTGC
65788 TAAAGACCTT
Statistics
Matches: 380, Mismatches: 45, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
79 2 0.01
80 23 0.06
81 106 0.28
82 13 0.03
84 45 0.12
85 191 0.50
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
TGCAGCATAACTTAAGTCG
Found at i:66579 original size:37 final size:37
Alignment explanation
Indices: 66416--66609 Score: 216
Period size: 35 Copynumber: 5.2 Consensus size: 37
66406 CTTTATATAT
* * * *
66416 ATATATATATTGTATAG-TTTGAAAACATTTTTTTTAAA
1 ATATATATAATATATAGTTTTTAAAACA--TTTTTGAAA
* * *
66454 CTATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTG-AAA
* * *
66492 CATTTATATATTATATAGTTTTTAAAACA-TTTTAAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
* *
66529 ATAAATATAATATATAGTTTTTAAAGCATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
66566 ATATATAT--TATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
66601 ATATATATA
1 ATATATATA
66610 GTTTTTAAAG
Statistics
Matches: 133, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
35 34 0.26
36 24 0.18
37 21 0.16
38 20 0.15
39 34 0.26
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:66658 original size:65 final size:66
Alignment explanation
Indices: 66463--66668 Score: 172
Period size: 65 Copynumber: 3.0 Consensus size: 66
66453 ACTATATATA
* * *
66463 ATATATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATATAGTTTTTAAAACATT-TTAA
1 ATATATAGTTTTTAAAGCAT-TTTTAAAA-A--TATATATTATATAGTTTTT-AAACATTATT--
*
66527 AAAT-AAATAT
59 --TTGAAA-AT
*
66537 AATATATAGTTTTTAAAGCATTTTTGAAAATATATATTATATAGTTTTTAAAACA-T-TTTTGAA
1 -ATATATAGTTTTTAAAGCATTTTTAAAAATATATATTATATAGTTTTT-AAACATTATTTTGAA
66600 AAT
64 AAT
* *
66603 ATATATAGTTTTTAAAGCATTTTTAAAACACATATGTATTATATAG-TTTT-GACATTATTTTGA
1 ATATATAGTTTTTAAAGCATTTTT-AAA-A-ATATATATTATATAGTTTTTAAACATTATTTTGA
66666 AAA
63 AAA
66669 CCTATATGAT
Statistics
Matches: 117, Mismatches: 8, Indels: 20
0.81 0.06 0.14
Matches are distributed among these distances:
65 27 0.23
66 6 0.05
67 17 0.15
68 14 0.12
70 3 0.03
71 25 0.21
73 1 0.01
74 6 0.05
75 18 0.15
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (66 bp):
ATATATAGTTTTTAAAGCATTTTTAAAAATATATATTATATAGTTTTTAAACATTATTTTGAAAA
T
Found at i:67968 original size:21 final size:21
Alignment explanation
Indices: 67922--67969 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
67912 TATTTTACTT
*
67922 TATTTATTTATTATTATCATG
1 TATTTTTTTATTATTATCATG
*
67943 T-TTTTTTTAATTATTATTA-G
1 TATTTTTTT-ATTATTATCATG
67963 TATTTTT
1 TATTTTT
67970 ACCTCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
TATTTTTTTATTATTATCATG
Found at i:71801 original size:28 final size:29
Alignment explanation
Indices: 71768--71831 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
71758 ATTTAAAAAA
71768 TAAGATATGATCA-TTT-TTTTTATTTAAT
1 TAAGATATG-TCACTTTGTTTTTATTTAAT
71796 TAAGATATGTCACTTTTGTTTTTATTTAAT
1 TAAGATATGTCAC-TTTGTTTTTATTTAAT
71826 TAAGAT
1 TAAGAT
71832 GTGGTCACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 3 0.09
28 9 0.27
29 3 0.09
30 18 0.55
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (29 bp):
TAAGATATGTCACTTTGTTTTTATTTAAT
Found at i:72792 original size:33 final size:34
Alignment explanation
Indices: 72750--72819 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
72740 AAATGTGTGA
*
72750 TTATATAAAAA-AATTAACTGCTATTAATGACGG
1 TTATATAAAAATAATTAACTGCTATTAACGACGG
*
72783 TTATATAAAAATATTTAACTGCTATTAACGACGG
1 TTATATAAAAATAATTAACTGCTATTAACGACGG
72817 TTA
1 TTA
72820 ACTCGGGACG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (34 bp):
TTATATAAAAATAATTAACTGCTATTAACGACGG
Found at i:72896 original size:31 final size:28
Alignment explanation
Indices: 72835--72897 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
72825 GGACGACTAC
*
72835 ATCTTAATTAAATAACGAAAGTAACTAT
1 ATCTTAATTAAATAACGAAAGTAACAAT
*
72863 ATCTTAATTAAATAAAAACGAAATTAACAAT
1 ATCTTAATTAAAT---AACGAAAGTAACAAT
72894 ATCT
1 ATCT
72898 AATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 13 0.43
31 17 0.57
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (28 bp):
ATCTTAATTAAATAACGAAAGTAACAAT
Found at i:78148 original size:22 final size:24
Alignment explanation
Indices: 78123--78168 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
78113 TTATTAAAAT
*
78123 AAAAATATT-AT-ATTATATTTTA
1 AAAAATATTAATAAATATATTTTA
*
78145 AAAATTATTAATAAATATATTTTA
1 AAAAATATTAATAAATATATTTTA
78169 TATACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAAATATTAATAAATATATTTTA
Found at i:78177 original size:22 final size:23
Alignment explanation
Indices: 78151--78205 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
78141 TTTAAAAATT
78151 ATTAATAAATA-TATTTTAT-ATA
1 ATTAATAAATATTATTTTATGA-A
*
78173 CTTAAT-AATATTATTTTATGAA
1 ATTAATAAATATTATTTTATGAA
78195 ATTAATAAATA
1 ATTAATAAATA
78206 AAAATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 19 0.68
23 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAATAAATATTATTTTATGAA
Found at i:78271 original size:33 final size:31
Alignment explanation
Indices: 78230--78308 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 31
78220 AGTAATTTAT
* *
78230 TATATATTATTAAAATAAAATATAGTATCATA
1 TATATATTATTAAAATAAAAAATA-TATAATA
** *
78262 TATATTATTATGGAACTAAAAAATATATAATA
1 TATA-TATTATTAAAATAAAAAATATATAATA
78294 T-TATATTATTAAAAT
1 TATATATTATTAAAAT
78309 TATTAGTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 9 0.24
31 2 0.05
32 11 0.29
33 16 0.42
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (31 bp):
TATATATTATTAAAATAAAAAATATATAATA
Found at i:78307 original size:23 final size:23
Alignment explanation
Indices: 78281--78350 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
78271 ATGGAACTAA
78281 AAAATATATAATATTATATTATT
1 AAAATATATAATATTATATTATT
* *
78304 AAAAT-TATTAGTAATATATT-TT
1 AAAATATA-TAATATTATATTATT
*
78326 AATA-AT-TAATATT-T-TTATT
1 AAAATATATAATATTATATTATT
78345 AAAATA
1 AAAATA
78351 ATACTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 2 0.05
19 6 0.16
20 6 0.16
22 8 0.22
23 15 0.41
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
AAAATATATAATATTATATTATT
Found at i:80113 original size:4 final size:4
Alignment explanation
Indices: 80104--80160 Score: 69
Period size: 4 Copynumber: 14.2 Consensus size: 4
80094 TGTTATCGTT
* * * *
80104 TGTA TGTA TGTA TGCA TGTA TGTA TATA TGTA TGTA TGTA CGTA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
80152 CGTA TGTA T
1 TGTA TGTA T
80161 AACTGAGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (4 bp):
TGTA
Found at i:93316 original size:5 final size:6
Alignment explanation
Indices: 93301--93330 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
93291 TAATAAATAT
93301 TTTTTA TTTTTA -TTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
93331 ACGTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:93318 original size:11 final size:11
Alignment explanation
Indices: 93302--93327 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
93292 AATAAATATT
93302 TTTTATTTTTA
1 TTTTATTTTTA
93313 TTTTATTTTTA
1 TTTTATTTTTA
93324 TTTT
1 TTTT
93328 TATACGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:101511 original size:15 final size:15
Alignment explanation
Indices: 101491--101521 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
101481 CAACAAATAG
101491 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
101506 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
101521 A
1 A
101522 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:104591 original size:25 final size:24
Alignment explanation
Indices: 104537--104591 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
104527 TACTCGAGCT
*
104537 CGAGCTTTGACCACTATTTTTGAC
1 CGAGCTTTGACAACTATTTTTGAC
* *
104561 CAAGCTTTGACAACTTTTTTTGGAC
1 CGAGCTTTGACAACTATTTTT-GAC
104586 CGAGCT
1 CGAGCT
104592 CGAGTATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (24 bp):
CGAGCTTTGACAACTATTTTTGAC
Found at i:108221 original size:2 final size:2
Alignment explanation
Indices: 108214--108280 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
108204 TCGTGCAAGG
108214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108256 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 T
108281 CACTCTCACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:109739 original size:12 final size:13
Alignment explanation
Indices: 109708--109740 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
109698 TTGACGACCA
109708 ACAAAAAAATGAT
1 ACAAAAAAATGAT
109721 ACAAAAAAACT-AT
1 ACAAAAAAA-TGAT
109734 ACAAAAA
1 ACAAAAA
109741 TCGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.73, C:0.12, G:0.03, T:0.12
Consensus pattern (13 bp):
ACAAAAAAATGAT
Found at i:114078 original size:11 final size:11
Alignment explanation
Indices: 114057--114085 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
114047 TAACTTGGTC
114057 TTTTC-ATTCA
1 TTTTCGATTCA
114067 TTTTCGATTCA
1 TTTTCGATTCA
114078 TTTTCGAT
1 TTTTCGAT
114086 ACAGGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTTCGATTCA
Found at i:114176 original size:13 final size:13
Alignment explanation
Indices: 114158--114186 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
114148 CTGGATTCAT
114158 GGCCGGATTAGTA
1 GGCCGGATTAGTA
114171 GGCCGGATTAGTA
1 GGCCGGATTAGTA
114184 GGC
1 GGC
114187 ACGACTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.21
Consensus pattern (13 bp):
GGCCGGATTAGTA
Found at i:114267 original size:23 final size:23
Alignment explanation
Indices: 114234--114280 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
114224 TAAGCGGCTT
* *
114234 ATGTGGCAGCTGACGTGGCGATG
1 ATGTGGCAGCTGACATGACGATG
*
114257 ATGTGGTAGCTGACATGACGATG
1 ATGTGGCAGCTGACATGACGATG
114280 A
1 A
114281 CATGATAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (23 bp):
ATGTGGCAGCTGACATGACGATG
Found at i:115237 original size:19 final size:19
Alignment explanation
Indices: 115201--115237 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
115191 TTACCAATTA
* *
115201 AATTAATTTTTTTTATTTT
1 AATTAATTTTATTAATTTT
115220 AATTAATTTTATTAATTT
1 AATTAATTTTATTAATTT
115238 GCTTTAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTAATTTTATTAATTTT
Found at i:115903 original size:19 final size:17
Alignment explanation
Indices: 115881--115946 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 17
115871 TGAAACAAAT
115881 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
115900 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
* * *
115918 AGAAAAAACATATAT-A
1 ATAAAAAAAATAAATGA
*
115934 A-AAAAAGAATAAA
1 ATAAAAAAAATAAA
115947 AAAGGTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 9 0.22
16 2 0.05
17 7 0.17
18 8 0.20
19 9 0.22
20 5 0.12
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:116047 original size:17 final size:18
Alignment explanation
Indices: 116013--116054 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
116003 AACATAATGA
*
116013 AAAT-AAATAAATAGTAT
1 AAATAAAATAAATAATAT
116030 AAATAAAATAAA-AATAT
1 AAATAAAATAAATAATAT
*
116047 ATATAAAA
1 AAATAAAA
116055 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAATAAATAATAT
Found at i:116082 original size:22 final size:22
Alignment explanation
Indices: 116014--116084 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
116004 ACATAATGAA
*
116014 AATAAATAA-ATA-GTATAAATAA
1 AATAAA-AATATATGTAT-AATAT
* *
116036 AATAAAAATATATATA-AAAAT
1 AATAAAAATATATGTATAATAT
*
116057 -ATAAAAATGTATGTATAATAT
1 AATAAAAATATATGTATAATAT
116078 AATAAAA
1 AATAAAA
116085 TACTAAATAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 13 0.33
21 9 0.23
22 15 0.38
23 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAATATATGTATAATAT
Found at i:116268 original size:30 final size:30
Alignment explanation
Indices: 116206--116265 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
116196 TATATAACGT
* *
116206 TAAGAAAATATAGTAAAAAAACATAGTAAA
1 TAAGAAAATATAGTAAAAAAAAATAATAAA
*
116236 TAAGTAAATATAGATAAAAAAAAATAATAA
1 TAAGAAAATATAG-TAAAAAAAAATAATAA
116266 TAAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (30 bp):
TAAGAAAATATAGTAAAAAAAAATAATAAA
Found at i:116278 original size:31 final size:31
Alignment explanation
Indices: 116211--116348 Score: 82
Period size: 31 Copynumber: 4.2 Consensus size: 31
116201 AACGTTAAGA
* * *
116211 AAATATAG-TAAAAAAACATAGTAAATAAGT
1 AAATATAGATAAAAAAAAATAATAAATAAAT
116241 AAATATAGATAAAAAAAAATAAT-AATAAAAT
1 AAATATAGATAAAAAAAAATAATAAAT-AAAT
* *
116272 ATATATATATAATAATAGGAAAATAATATAATATAAT
1 AAATATAGATAA-AA-A--AAAATAATA-AATA-AAT
* * * *
116309 GCAAAGAAAAATGAAAAAAATTATAATAAATAAAT
1 --AAATATAGAT-AAAAAAA-AATAATAAATAAAT
116344 AAATA
1 AAATA
116349 AAATATAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
30 11 0.13
31 25 0.30
32 2 0.02
33 5 0.06
35 11 0.13
36 7 0.08
37 12 0.14
38 1 0.01
39 8 0.10
40 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (31 bp):
AAATATAGATAAAAAAAAATAATAAATAAAT
Found at i:116285 original size:24 final size:24
Alignment explanation
Indices: 116258--116308 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
116248 GATAAAAAAA
*
116258 AATAATAATAAAAT-ATATATATAT
1 AATAATAAGAAAATAATATA-ATAT
*
116282 AATAATAGGAAAATAATATAATAT
1 AATAATAAGAAAATAATATAATAT
116306 AAT
1 AAT
116309 GCAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAATAAGAAAATAATATAATAT
Found at i:116351 original size:23 final size:23
Alignment explanation
Indices: 116317--116363 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
116307 ATGCAAAGAA
116317 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
116340 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
116363 A
1 A
116364 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:117826 original size:106 final size:106
Alignment explanation
Indices: 117634--118803 Score: 1806
Period size: 106 Copynumber: 11.0 Consensus size: 106
117624 ACATTGTTTC
* * * * * *
117634 GAGTCCAATATCCTCCGTCGTAAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
117699 CCAGCCGTCCC-TCTGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTC-GTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
117740 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGTTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
117805 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
117846 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
117911 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
117952 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
118017 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
118058 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
118123 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
118164 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
118229 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
118270 GAGTCTAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATT-AGAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
* *
118334 ACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
118376 GTGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
118441 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
118482 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
118547 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
118588 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
118653 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
118694 GAGTCCAATATCCTTCCCTGTGAAGTTGAAATTGGCTCTG-AATTTGGAAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
* * * *
118758 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
118800 GAGT
1 GAGT
118804 GGCACGATAT
Statistics
Matches: 989, Mismatches: 71, Indels: 8
0.93 0.07 0.01
Matches are distributed among these distances:
105 11 0.01
106 972 0.98
107 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:120412 original size:14 final size:14
Alignment explanation
Indices: 120393--120440 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
120383 TTCTTTTTGA
120393 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
*
120407 TTTTTGTTTTCTTCT
1 TTTTTGTTCT-TTCT
120422 TTTTTGCTTCTTT-T
1 TTTTTG-TTCTTTCT
120436 TTTTT
1 TTTTT
120441 ATTTTTGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 15 0.50
15 12 0.40
16 3 0.10
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:125174 original size:13 final size:13
Alignment explanation
Indices: 125158--125210 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 13
125148 CATAATGAAA
*
125158 ATAAATAAATAGT
1 ATAAATAAATAAT
125171 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
125185 A-AAATAAA-AAT
1 ATAAATAAATAAT
125196 AT--ATAAA-AAT
1 ATAAATAAATAAT
125206 ATAAA
1 ATAAA
125211 AATGTATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 10 0.29
11 4 0.11
12 4 0.11
13 10 0.29
14 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:125232 original size:57 final size:59
Alignment explanation
Indices: 125171--125327 Score: 137
Period size: 60 Copynumber: 2.6 Consensus size: 59
125161 AATAAATAGT
* **
125171 ATAAATAAAATAATAA-AATAAAAATATATAAA-AATATAA-AAATGTATGTATAATA-TA
1 ATAAATAAAATAGTAACAATAAAAATATATAAAGAA-A-AATAAATGTACATATAATATTA
* *
125228 ATAAAATACTAAATAGTAACAATAATAATAAATAAATGAAAAATAAATGTACATATAATATTA
1 AT-AAATA--AAATAGTAACAATAAAAATATATAAA-GAAAAATAAATGTACATATAATATTA
* * *
125291 ACTAAA-AAAATAGTAATAATAGAAATATA-AAATAAAA
1 A-TAAATAAAATAGTAACAATAAAAATATATAAAGAAAA
125328 TGAAGTAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
57 2 0.02
58 9 0.11
59 3 0.04
60 26 0.32
61 16 0.20
62 16 0.20
63 8 0.10
64 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (59 bp):
ATAAATAAAATAGTAACAATAAAAATATATAAAGAAAAATAAATGTACATATAATATTA
Found at i:125968 original size:37 final size:37
Alignment explanation
Indices: 125927--126011 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
125917 GGATCATATC
* * *
125927 TTTAGGAGTTTAAATAATAGTAGAACTCTATCTTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
* ** *
125964 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
*
126001 TTTAGAAGTTT
1 TTTAGGAGTTT
126012 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:129364 original size:20 final size:18
Alignment explanation
Indices: 129318--129372 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
129308 AGTAGTCCAA
*
129318 AAAGTTTTGATACTTTTC
1 AAAGTTTCGATACTTTTC
*
129336 AAGAGTTTCGAAACTTTTCC
1 AA-AGTTTCGATACTTTT-C
129356 TAAAGTTTCGATACTTT
1 -AAAGTTTCGATACTTT
129373 GGCTCCAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 14 0.45
21 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (18 bp):
AAAGTTTCGATACTTTTC
Found at i:135366 original size:21 final size:21
Alignment explanation
Indices: 135284--135367 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
135274 CAGAACCCCA
*
135284 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
135303 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
135328 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
135349 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
135368 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:139217 original size:22 final size:21
Alignment explanation
Indices: 139175--139214 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
139165 GAGTTTGTTT
*
139175 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
139196 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
139215 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:142094 original size:24 final size:24
Alignment explanation
Indices: 142041--142114 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 24
142031 TCATAACATA
*
142041 ACATATATTCACATCAACCATATAAT
1 ACATATATTCACAT-AA-CATATAAC
*
142067 ACATATATTCA-ATAACATGTCAAC
1 ACATATATTCACATAACATAT-AAC
*
142091 ACATATAATTCATATACACATATA
1 ACATAT-ATTCACATA-ACATATA
142115 CTTCTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.10
24 10 0.24
25 7 0.17
26 15 0.37
27 5 0.12
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.31
Consensus pattern (24 bp):
ACATATATTCACATAACATATAAC
Found at i:144836 original size:20 final size:20
Alignment explanation
Indices: 144811--144865 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
144801 TGGATACTTT
144811 TCAAGAGTTTCGAAACTATC
1 TCAAGAGTTTCGAAACTATC
144831 TCAAGAGTTTCGAAACTATC
1 TCAAGAGTTTCGAAACTATC
*
144851 TCAAGAGTTTTGAAA
1 TCAAGAGTTTCGAAA
144866 ATTTCCCTAA
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:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TCAAGAGTTTCGAAACTATC
Found at i:155779 original size:22 final size:22
Alignment explanation
Indices: 155738--155782 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
155728 AAAGTTAAAC
155738 TTTTTAAATTTTAACTATAATTA
1 TTTTTAAATTTTAAC-ATAATTA
155761 TTTTTAATATTTTAA-ATAATTA
1 TTTTTAA-ATTTTAACATAATTA
155783 AATTGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAAATTTTAACATAATTA
Found at i:158289 original size:14 final size:14
Alignment explanation
Indices: 158270--158299 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
158260 TTTAGATTTT
*
158270 TTAAAATTACATTA
1 TTAAAAATACATTA
158284 TTAAAAATACATTA
1 TTAAAAATACATTA
158298 TT
1 TT
158300 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:159519 original size:9 final size:9
Alignment explanation
Indices: 159505--159536 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
159495 ATCAATTTTA
159505 TTTTTATTT
1 TTTTTATTT
159514 TTTTTA-TT
1 TTTTTATTT
159522 TTTTTATTT
1 TTTTTATTT
159531 TTTTTA
1 TTTTTA
159537 AAAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:159523 original size:8 final size:8
Alignment explanation
Indices: 159500--159534 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
159490 AAAAAATCAA
159500 TTTTATTT
1 TTTTATTT
*
159508 TTAT-TTT
1 TTTTATTT
159515 TTTTATTT
1 TTTTATTT
159523 TTTTATTT
1 TTTTATTT
159531 TTTT
1 TTTT
159535 TAAAAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTATTT
Found at i:161326 original size:6 final size:6
Alignment explanation
Indices: 161315--161340 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
161305 ATCGAAAGCA
161315 CAGGCT CAGGCT CAGGCT CAGGCT CA
1 CAGGCT CAGGCT CAGGCT CAGGCT CA
161341 ACTCCAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (6 bp):
CAGGCT
Found at i:168158 original size:28 final size:28
Alignment explanation
Indices: 168123--168204 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 28
168113 AAGATTGACT
*
168123 CAGAGATTTAGGAACCAAATTAAAGAAC
1 CAGAGATTTAGGAACCAAATTAAAGAAA
* * * * ** *
168151 CATAGATTTGGGGATCTTA-TGAAGAAA
1 CAGAGATTTAGGAACCAAATTAAAGAAA
*
168178 GAGAGATTTAGGAACCAAATTAAAGAA
1 CAGAGATTTAGGAACCAAATTAAAGAA
168205 GCTTTTTTGT
Statistics
Matches: 37, Mismatches: 16, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (28 bp):
CAGAGATTTAGGAACCAAATTAAAGAAA
Found at i:168270 original size:24 final size:24
Alignment explanation
Indices: 168243--168289 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
168233 TTTTTCGCTT
*
168243 GTTTAAATTTTAAGTTTTAATTTA
1 GTTTAAATTTTAAGTTTCAATTTA
*
168267 GTTTAAATTTTAGGTTTCAATTT
1 GTTTAAATTTTAAGTTTCAATTT
168290 TAGTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (24 bp):
GTTTAAATTTTAAGTTTCAATTTA
Found at i:168292 original size:13 final size:13
Alignment explanation
Indices: 168243--168292 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
168233 TTTTTCGCTT
*
168243 GTTTAAATTTTAA
1 GTTTAAATTTTAG
*
168256 GTTTTAA-TTTA-
1 GTTTAAATTTTAG
168267 GTTTAAATTTTAG
1 GTTTAAATTTTAG
*
168280 GTTTCAATTTTAG
1 GTTTAAATTTTAG
168293 TATATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 6 0.19
12 8 0.25
13 18 0.56
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (13 bp):
GTTTAAATTTTAG
Found at i:168985 original size:12 final size:12
Alignment explanation
Indices: 168954--168992 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
168944 ATAAAATTCT
*
168954 ATTTGAATTTAA
1 ATTTGATTTTAA
*
168966 ATTT-ATTTTGA
1 ATTTGATTTTAA
168977 ATTTGATTTTAA
1 ATTTGATTTTAA
168989 ATTT
1 ATTT
168993 TTAATTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (12 bp):
ATTTGATTTTAA
Found at i:177631 original size:41 final size:41
Alignment explanation
Indices: 177523--177907 Score: 443
Period size: 41 Copynumber: 9.4 Consensus size: 41
177513 CAAAATGGTA
* * * * *
177523 ACTTTAGTGGCGTTTTTATATAAAACGCCACGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACTCGT
**
177565 ACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTCG-
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * *
177605 ACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATAC-AAACGCCGCTATAGACTCGT
* *
177647 ACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTAGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
177688 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * ** * *
177729 AATTTTGTGGTGTTTATGTTTACAAACATCGCTATAGGCTTGT
1 ACTTTAGTGGCGTTT-T-TATACAAACGCCGCTATAGACTCGT
*
177772 ACTTTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* **
177813 ACATTAGTGGTATTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
177854 ACATTAGTGGCGTTTTTATACAAACGCCGC--TAGACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
177893 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
177908 GTTTTTTAAA
Statistics
Matches: 296, Mismatches: 43, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
39 22 0.07
40 19 0.06
41 186 0.63
42 38 0.13
43 31 0.10
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
Found at i:177800 original size:166 final size:164
Alignment explanation
Indices: 177523--177885 Score: 451
Period size: 166 Copynumber: 2.2 Consensus size: 164
177513 CAAAATGGTA
* * * *
177523 ACTTTAGTGGCGTTTTTATATAAAACGCCACGATAGAGTAGTACTTTAGCAGCGTTTTTATACAA
1 ACTTTAGTGGCGTTTTTATA-AAAACGCCGCTATAGACTAGTAATTTAGCAGCGTTTTTATACAA
* * *
177588 ACGCCGCTATAGACTCGACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGAGTAGTACTTTA
65 ACACCGCTATAGACTCGACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGACTAGTACATTA
* *
177653 GTGGCGTTTTTATATAAACGCCGCTATAGACTAGT
130 GTGGCATTTTTATACAAACGCCGCTATAGACTAGT
* ** * *
177688 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCA-TAATTTTGTGGTGTTTATGTTTAC
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACT-AGTAATTTAGCAGCGTTT-T-TATAC
* * * * * *
177752 AAACATCGCTATAGGCTTGTACTTTAGTGGTGTTTTTATAC-AAACGCCGCTATAGACTCGTACA
63 AAACACCGCTATAGACTCG-ACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGACTAGTACA
* *
177816 TTAGTGGTATTTTTATACAAACGCCGCTATAGACTCGT
127 TTAGTGGCATTTTTATACAAACGCCGCTATAGACTAGT
* *
177854 ACATTAGTGGCGTTTTTATACAAACGCCGCTA
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTA
177886 GACTTGTACT
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
164 26 0.15
165 22 0.13
166 102 0.60
167 20 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (164 bp):
ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTAGTAATTTAGCAGCGTTTTTATACAAA
CACCGCTATAGACTCGACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGACTAGTACATTAG
TGGCATTTTTATACAAACGCCGCTATAGACTAGT
Found at i:177820 original size:125 final size:123
Alignment explanation
Indices: 177523--177907 Score: 422
Period size: 125 Copynumber: 3.1 Consensus size: 123
177513 CAAAATGGTA
* * * **
177523 ACTTTAGTGGCGTTTTTATATAAAACGCCACGATAGAGTAGTACTTTAGCAGCGTTTTTATACAA
1 ACTTTAGTGGCGTTTTTATA-AAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAA
* *
177588 ACGCCGCTATAGACTCGACTTTAGCGGTGTTTTTATACAAAACGCCGCGATAGAGTAGT
65 ACGCCGCTATAGACTCGAATTTAGCGGTGTTTTTATACAAAACACCGCGATAGAGTAGT
* *
177647 ACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAAAAA
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAA
* * * * * * *
177712 CGCCGCTATAGACTCATAATTTTGTGGTGTTTATGTTTAC-AAACATCGCTATAG-GCTTGT
66 CGCCGCTATAGACTC-GAATTTAGCGGTGTTT-T-TATACAAAACACCGCGATAGAG-TAGT
* * * * **
177772 ACTTTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGTACATTAGTGGTATTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAA
* * * * *
177837 CGCCGCTATAGACTCGTACA-TTAGTGGCGTTTTTATAC-AAACGCCGC--TAGACTTGT
66 CGCCGCTATAGACTCG-A-ATTTAGCGGTGTTTTTATACAAAACACCGCGATAGAGTAGT
177893 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
177908 GTTTTTTAAA
Statistics
Matches: 223, Mismatches: 31, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
121 21 0.09
123 64 0.29
124 34 0.15
125 99 0.44
126 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (123 bp):
ACTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAA
CGCCGCTATAGACTCGAATTTAGCGGTGTTTTTATACAAAACACCGCGATAGAGTAGT
Found at i:180219 original size:36 final size:36
Alignment explanation
Indices: 180179--180258 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
180169 TGAACGGTTG
*
180179 GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
*
180215 GGAATTTAATTAACATTCTACTGCTGATGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
180251 GGAATTTA
1 GGAATTTA
180259 GTTACATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (36 bp):
GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
Found at i:181182 original size:21 final size:20
Alignment explanation
Indices: 181125--181182 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
181115 TGATTTATTA
**
181125 TTATGGATTTCATTTTTCTTG
1 TTATGGA-TTCAAGTTTCTTG
* *
181146 TTATGGATTTAAGTTTGTTG
1 TTATGGATTCAAGTTTCTTG
181166 TTATGGATGTCAAGTTT
1 TTATGGAT-TCAAGTTT
181183 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.55
Consensus pattern (20 bp):
TTATGGATTCAAGTTTCTTG
Found at i:182142 original size:24 final size:25
Alignment explanation
Indices: 182096--182142 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
182086 CCTCCAGAGG
*
182096 TATAAAGATCTTCGGTCTATCCAAC
1 TATAAAGATCCTCGGTCTATCCAAC
*
182121 TATAAAGATCCTC-GTCTGTCCA
1 TATAAAGATCCTCGGTCTATCCA
182143 TAGGTAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (25 bp):
TATAAAGATCCTCGGTCTATCCAAC
Found at i:182190 original size:31 final size:31
Alignment explanation
Indices: 182149--182257 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
182139 TCCATAGGTA
* *
182149 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCAT
* ** * *
182180 AGAACATAGGTATACCATCCATATGTCTCGAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCAT
*
182212 AG-ACATAGGTAAAACTGTCCATATGTTCCGT
1 AGAACATAGGT-AAACTGTCCATATGTTCCAT
182243 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
182258 CCTCGACTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
31 38 0.61
32 24 0.39
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCAT
Found at i:184501 original size:43 final size:43
Alignment explanation
Indices: 184438--184588 Score: 248
Period size: 43 Copynumber: 3.5 Consensus size: 43
184428 ATGTTACAAT
184438 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
**
184481 GTTTGTGGGAAAAATTCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* *
184524 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* *
184567 GTTTGTTGGACAAACGCCGCTA
1 GTTTGTGGGAAAAACGCCGCTA
184589 TATATCGTTA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
Found at i:184594 original size:43 final size:43
Alignment explanation
Indices: 184438--184613 Score: 244
Period size: 43 Copynumber: 4.1 Consensus size: 43
184428 ATGTTACAAT
*
184438 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
** *
184481 GTTTGTGGGAAAAATTCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
*
184524 GTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
* * * *** *
184567 GTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTGCGAC
1 GTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
184610 GTTT
1 GTTT
184614 TTTGTTACCA
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCGCTAAATATCAACACCTATTGCGGC
Found at i:184834 original size:2 final size:2
Alignment explanation
Indices: 184779--184818 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
184769 TATTTTTTTA
184779 AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184819 GGATAGATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:185479 original size:193 final size:194
Alignment explanation
Indices: 185148--185528 Score: 674
Period size: 193 Copynumber: 2.0 Consensus size: 194
185138 TAATTATGAT
* *
185148 GAAATGACCATCCAGCTCAGTTGGTAGAGCACAAGGTTCTTAACCTTGAGGTCGTGGGATCGAGT
1 GAAATGACCATCCAACTCAGTTGGTAGAGCACAAGGTTATTAACCTTGAGGTCGTGGGATCGAGT
*
185213 CCAACGGAGGGCATTTCATAATTCGGAGGTCTCTTACGGAAGTTGCTCTCAACCTGGTATTGGGG
66 CCAACGGAGGGCATTTCATAATTCGGAGGTCTCCTACGGAAGTTGCTCTCAACCTGGTATTGGGG
*
185278 GTAGCCTACTATCTTACCTCCCCCTTACCCCATACATATGGG-AAAAAGGGACAACCATTTTGA
131 GCAGCCTACTATCTTACCTCCCCCTTACCCCATACATATGGGAAAAAAGGGACAACCATTTTGA
185341 GAAATGACCATCCAACTCAGTTGGTAGAGCACAAGGTTATTAACCTTGAGGTCGTGGGATCGAGT
1 GAAATGACCATCCAACTCAGTTGGTAGAGCACAAGGTTATTAACCTTGAGGTCGTGGGATCGAGT
* ** *
185406 CCCACGGAGGGCATTTCATAATTCGGAGGTCTCCTACGGAAGTTGCTCTCAATTTGGTGTTGGGG
66 CCAACGGAGGGCATTTCATAATTCGGAGGTCTCCTACGGAAGTTGCTCTCAACCTGGTATTGGGG
*
185471 GCAGCCTACTATCTTACCTCCTCCTTACCCCATACATATGGGAAAAAAGGGACAACCA
131 GCAGCCTACTATCTTACCTCCCCCTTACCCCATACATATGGGAAAAAAGGGACAACCA
185529 AATATAATTA
Statistics
Matches: 178, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
193 163 0.92
194 15 0.08
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25
Consensus pattern (194 bp):
GAAATGACCATCCAACTCAGTTGGTAGAGCACAAGGTTATTAACCTTGAGGTCGTGGGATCGAGT
CCAACGGAGGGCATTTCATAATTCGGAGGTCTCCTACGGAAGTTGCTCTCAACCTGGTATTGGGG
GCAGCCTACTATCTTACCTCCCCCTTACCCCATACATATGGGAAAAAAGGGACAACCATTTTGA
Found at i:186256 original size:31 final size:31
Alignment explanation
Indices: 186218--186391 Score: 312
Period size: 31 Copynumber: 5.6 Consensus size: 31
186208 TTCATAGATT
* *
186218 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
186249 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
186280 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
186311 CCGAAGAACATAGATAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
186342 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
186373 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
186392 CCTCGACCCT
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 137 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:189716 original size:5 final size:6
Alignment explanation
Indices: 189701--189736 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
189691 TCAAATGCAT
189701 AAATAA AAAT-A AAATAA AAAT-A AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
189737 CAAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:189717 original size:11 final size:11
Alignment explanation
Indices: 189701--189736 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
189691 TCAAATGCAT
189701 AAATAAAAATA
1 AAATAAAAATA
189712 AAATAAAAATA
1 AAATAAAAATA
189723 AAATAAAAATA
1 AAATAAAAATA
189734 AAA
1 AAA
189737 CAAATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:190326 original size:29 final size:30
Alignment explanation
Indices: 190294--190351 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
190284 GAACTTAATG
190294 AGCACGAGTCGAGA-AAC-AATTTTTTAACA
1 AGCACGAGTCGA-ACAACAAATTTTTTAACA
*
190323 AGCACGATTCGAACAACAAATTTTTTAAC
1 AGCACGAGTCGAACAACAAATTTTTTAAC
190352 GAACGCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 14 0.54
30 11 0.42
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (30 bp):
AGCACGAGTCGAACAACAAATTTTTTAACA
Done.