Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001937.1 Hibiscus syriacus cultivar Beakdansim tig00003922_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: 74701
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:198 original size:28 final size:28
Alignment explanation
Indices: 158--214 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
148 ATCAATCCAA
*
158 ACCAAAGAAATACAAAGCAAACTAAGAC
1 ACCAAAGAAATACAAAGCAAACGAAGAC
186 ACCAAAGAAATACAAAGCAAACGAAGAC
1 ACCAAAGAAATACAAAGCAAACGAAGAC
214 A
1 A
215 TTGGATCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.05
Consensus pattern (28 bp):
ACCAAAGAAATACAAAGCAAACGAAGAC
Found at i:1219 original size:19 final size:18
Alignment explanation
Indices: 1182--1223 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1172 TGGGCTAGAG
*
1182 AAAATTTTGGGGGGCGGA
1 AAAATTTTGGGGAGCGGA
1200 AGAAATTTTGGTGGAG-GGA
1 A-AAATTTTGG-GGAGCGGA
1219 AAAAT
1 AAAAT
1224 GAAGCTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 13 0.62
20 3 0.14
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.24
Consensus pattern (18 bp):
AAAATTTTGGGGAGCGGA
Found at i:1598 original size:22 final size:22
Alignment explanation
Indices: 1558--1599 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1548 TAAATATTAA
* **
1558 TTAGTTTTTAAGTTTTTTAGCC
1 TTAGATTTTAAGTGCTTTAGCC
1580 TTAGATTTTAAGTGCTTTAG
1 TTAGATTTTAAGTGCTTTAG
1600 TTATTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (22 bp):
TTAGATTTTAAGTGCTTTAGCC
Found at i:4106 original size:18 final size:18
Alignment explanation
Indices: 4083--4127 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
4073 TGTATTTTTA
4083 TCATTTCATTG-TTAATAT
1 TCATTTCATTGCTT-ATAT
4101 TCATTT-A-TGCTTATAT
1 TCATTTCATTGCTTATAT
4117 TCATATTCATT
1 TCAT-TTCATT
4128 CATTAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 7 0.30
19 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (18 bp):
TCATTTCATTGCTTATAT
Found at i:8872 original size:23 final size:23
Alignment explanation
Indices: 8827--8896 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
8817 TGCCATATAG
* *
8827 AATGTCCTGAAGGA-CATCATAGA
1 AATGTCCCGAAGGACCA-CGTAGA
8850 AATGTCCCGAAGGACCACGTAGA
1 AATGTCCCGAAGGACCACGTAGA
* * * *
8873 ATTATCTCGAAGGACCGCGTAGA
1 AATGTCCCGAAGGACCACGTAGA
8896 A
1 A
8897 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (23 bp):
AATGTCCCGAAGGACCACGTAGA
Found at i:14257 original size:46 final size:46
Alignment explanation
Indices: 13962--14256 Score: 419
Period size: 46 Copynumber: 6.4 Consensus size: 46
13952 ATTTATTTGA
* * **
13962 ATAAATGAAAATGCATAACTGTACATTATTAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
14008 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
14054 ATAAATGAAAATGCATAATGGTGCATTATCGGCATAAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
14100 ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
14146 ATAAATGAAATTGGATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * * * *
14192 ATAAATGAACATGAATAACAGTGCATAATTGACATGAAAGAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
14238 ACAAATGAAAATACATAAC
1 ATAAATGAAAATGCATAAC
14257 AATGTATTAA
Statistics
Matches: 223, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 223 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:14919 original size:20 final size:18
Alignment explanation
Indices: 14894--14949 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
14884 GTTATGCTTT
14894 AAGAAGAAAAAGAAAAGAA
1 AAGAAGAAAAAG-AAAGAA
14913 AATGAAGAAAAAG--AGAA
1 AA-GAAGAAAAAGAAAGAA
14930 AA-AAGAAAAAGAGAAGAA
1 AAGAAGAAAAAGA-AAGAA
14948 AA
1 AA
14950 ATAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.27
17 6 0.18
18 6 0.18
19 2 0.06
20 10 0.30
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAGAA
Found at i:14926 original size:15 final size:15
Alignment explanation
Indices: 14900--14949 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
14890 CTTTAAGAAG
14900 AAAAAG-AAAAGA-A
1 AAAAAGAAAAAGAGA
*
14913 AATGAAGAAAAAGAGA
1 AA-AAAGAAAAAGAGA
14929 AAAAAGAAAAAGAGA
1 AAAAAGAAAAAGAGA
14944 AGAAAA
1 A-AAAA
14950 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 2 0.06
14 3 0.10
15 19 0.61
16 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAGAGA
Found at i:14955 original size:24 final size:24
Alignment explanation
Indices: 14894--14964 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
14884 GTTATGCTTT
*
14894 AAGAAGAAAAAG--AAAAGAAAATG
1 AAGAA-AAAAAGAAAAAAGAAAAAG
*
14917 AAGAAAAAGAGAAAAAAGAAAAAG
1 AAGAAAAAAAGAAAAAAGAAAAAG
*
14941 -AGAAGAAAAATAAAAATA-AAAAAG
1 AAGAA-AAAAAGAAAAA-AGAAAAAG
14965 GGGTTGAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.12
23 9 0.22
24 25 0.62
25 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (24 bp):
AAGAAAAAAAGAAAAAAGAAAAAG
Found at i:15657 original size:18 final size:18
Alignment explanation
Indices: 15630--15691 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
15620 GCCAACGAAG
*
15630 AAGAAAAGAAAGAAAAAT
1 AAGAAGAGAAAGAAAAAT
*
15648 AAGAAGAGAAAATAAAAAAT
1 AAGAAGAG-AAA-GAAAAAT
*
15668 GAA-AAGAGAAGGAAAAAT
1 -AAGAAGAGAAAGAAAAAT
15686 -AGAAGA
1 AAGAAGA
15692 AAAACCAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 13 0.36
19 5 0.14
20 11 0.31
21 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (18 bp):
AAGAAGAGAAAGAAAAAT
Found at i:15748 original size:41 final size:41
Alignment explanation
Indices: 15702--15805 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 41
15692 AAAACCAAAG
*
15702 TGAAAA-CTCAAAAGGGCGCTTTGACAAAAATGAATCTGAAGA
1 TGAAAACCT-AAAAGGGCGCTTTGACAAAAATGAATCT-AAAA
* * * *
15744 -GAAAACCTGAAAGGGCGCTTTGAGAATAGTGAATCTAAAA
1 TGAAAACCTAAAAGGGCGCTTTGACAAAAATGAATCTAAAA
*
15784 TGAAAACCTAAAAGGGCACTTT
1 TGAAAACCTAAAAGGGCGCTTT
15806 AGAGAGGATA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
40 3 0.06
41 48 0.91
42 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (41 bp):
TGAAAACCTAAAAGGGCGCTTTGACAAAAATGAATCTAAAA
Found at i:16499 original size:133 final size:131
Alignment explanation
Indices: 16247--16541 Score: 301
Period size: 133 Copynumber: 2.2 Consensus size: 131
16237 AGTATCAATC
* * * *
16247 TTTTGCTCTATTCTTCACATAAGGAGTTGAATTAGCGTAACCTTATTTTGCTCGATTCTATCACA
1 TTTTGCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTATTTTGCTCGATTCTATCACA
* * * *
16312 GAAGTATGTAGATCAACATCGGTATTTTGTTTGATCCTTCACAGAAGAAGTTGGATCAACAGTGT
66 GAAG-AGGTAGATCAACATCGGAATTATGTTTGATCCTCCACAGAAGAAGTTGGATCAACAGTGT
16377 TA
130 TA
* * *
16379 TTTTGCTCGATTCTTCATAGAAGGAGTTAAATTAGCATAATCTTATTTTTGTTCGATTCTATCAC
1 TTTTGCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTA-TTTTGCTCGATTCTATCAC
* * * * *
16444 ATGATA-AGGTAGATCAGCATTGGCAATTAT-TTTGATTCTCCACATAATG-AGTTGGATTAACA
65 A-GA-AGAGGTAGATCAACATCGG-AATTATGTTTGATCCTCCACAGAA-GAAGTTGGATCAACA
* *
16506 -TTTTT
126 GTGTTA
* * *
16511 TGTGTTACTCGATCCTTCACATAAGGAGTTA
1 T-T-TTGCTCGATTCTTCACAGAAGGAGTTA
16542 GATCAATGAC
Statistics
Matches: 134, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
132 43 0.32
133 60 0.45
134 30 0.22
135 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (131 bp):
TTTTGCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTATTTTGCTCGATTCTATCACA
GAAGAGGTAGATCAACATCGGAATTATGTTTGATCCTCCACAGAAGAAGTTGGATCAACAGTGTT
A
Found at i:17273 original size:35 final size:34
Alignment explanation
Indices: 17220--17302 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
17210 AGGTTGTTGT
*
17220 ATATTAAATAATAATTGCATGTG-A--T-A-ATA
1 ATATTAAATAATAATTGCATTTGCATGTCATATA
17249 CATATTAAAT-ATAATTGCATTTGCATGTCATATA
1 -ATATTAAATAATAATTGCATTTGCATGTCATATA
*
17283 GTATTAAATAATAATTGCAT
1 ATATTAAATAATAATTGCAT
17303 ATTTTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 12 0.27
30 10 0.22
32 1 0.02
33 9 0.20
34 13 0.29
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (34 bp):
ATATTAAATAATAATTGCATTTGCATGTCATATA
Found at i:17301 original size:34 final size:30
Alignment explanation
Indices: 17220--17302 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
17210 AGGTTGTTGT
17220 ATATTAAATAATAATTGCATGTGATAATAC
1 ATATTAAATAATAATTGCATGTGATAATAC
* * *
17250 ATATTAAAT-ATAATTGCATTTGCATGTCATAT
1 ATATTAAATAATAATTGCATGTG-A--TAATAC
17282 AGTATTAAATAATAATTGCAT
1 A-TATTAAATAATAATTGCAT
17303 ATTTTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.27
30 10 0.22
32 5 0.11
33 8 0.18
34 10 0.22
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (30 bp):
ATATTAAATAATAATTGCATGTGATAATAC
Found at i:19774 original size:2 final size:2
Alignment explanation
Indices: 19767--19807 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19757 TGTTGTACCT
19767 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
19808 CATCCCTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20104 original size:81 final size:81
Alignment explanation
Indices: 19969--20445 Score: 778
Period size: 81 Copynumber: 5.9 Consensus size: 81
19959 TAACCTTTTT
* *
19969 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
* *
20034 AATTAGGCCATTAATC
66 AGTTAGGCCATTATTC
*
20050 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTATCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
20115 AGTTAGGCCA-TATTC
66 AGTTAGGCCATTATTC
* * *
20130 TTTTACTCAACGATATTAAATCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
* *
20195 AGTTAGACCATTATTA
66 AGTTAGGCCATTATTC
20211 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
*
20276 AGTTAGACCATTATTC
66 AGTTAGGCCATTATTC
* * *
20292 TTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACCTTTCTACCAATT-GAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
* *
20356 AGTTAGGTCACTATTC
66 AGTTAGGCCATTATTC
* *
20372 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGATACCATTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
20437 AGTTAGGCC
66 AGTTAGGCC
20446 TCAAAGGCAC
Statistics
Matches: 367, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
80 146 0.40
81 221 0.60
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
AGTTAGGCCATTATTC
Found at i:20234 original size:161 final size:162
Alignment explanation
Indices: 19969--20445 Score: 798
Period size: 161 Copynumber: 3.0 Consensus size: 162
19959 TAACCTTTTT
* *
19969 TTTTACTCAAC-AGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACA
1 TTTTACTCAACGA-TATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCA
* * *
20033 CAATTAGGCCATTAATCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTAT
65 CAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTAC
20098 CTTTCTACCAATTACACAGTTAGGCCA-TATTC
130 CTTTCTACCAATTACACAGTTAGGCCATTATTC
*
20130 TTTTACTCAACGATATTAAATCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGATATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
20195 AGTTAGACCATTATTATTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
*
20260 TTTCTACCAATTACACAGTTAGACCATTATTC
131 TTTCTACCAATTACACAGTTAGGCCATTATTC
*
20292 TTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG-AC
1 TTTTACTCAACGATATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* * *
20356 AGTTAGGTCACTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGATACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
*
20421 ATTCTACCAATTACACAGTTAGGCC
131 TTTCTACCAATTACACAGTTAGGCC
20446 TCAAAGGCAC
Statistics
Matches: 296, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
161 230 0.78
162 66 0.22
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (162 bp):
TTTTACTCAACGATATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
TTTCTACCAATTACACAGTTAGGCCATTATTC
Found at i:20399 original size:242 final size:242
Alignment explanation
Indices: 19969--20442 Score: 797
Period size: 242 Copynumber: 2.0 Consensus size: 242
19959 TAACCTTTTT
19969 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACAC
* * * *
20034 AATTAGGCCATTAATCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTATC
66 AATTAGACCATTAATCTTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACC
*
20099 TTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACGATATTAAATCGTTCATCTAACT
131 TTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACGATATTAAACCGTTCATCTAACT
* * *
20164 GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGACCATTATTA
196 GGCATAATTGATACCATTCTACCAATTACACAGTTAGACCATTATTA
* *
20211 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACAC
* *
20276 AGTTAGACCATTATTCTTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACC
66 AATTAGACCATTAATCTTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACC
* * *
20341 TTTCTACCAATT-GACAGTTAGGTCACTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAAC
131 TTTCTACCAATTACACAGTTAGGCCA-TATTCTTTTACTCAACGATATTAAACCGTTCATCTAAC
20405 TGGCATAATTGATACCATTCTACCAATTACACAGTTAG
195 TGGCATAATTGATACCATTCTACCAATTACACAGTTAG
20443 GCCTCAAAGG
Statistics
Matches: 216, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
241 11 0.05
242 205 0.95
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (242 bp):
TTTTACTCAACAGTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTACAC
AATTAGACCATTAATCTTTTACTCAACGATATTAAACCGATCATCTAACTGGCATAATTGGTACC
TTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACGATATTAAACCGTTCATCTAACT
GGCATAATTGATACCATTCTACCAATTACACAGTTAGACCATTATTA
Found at i:22863 original size:47 final size:47
Alignment explanation
Indices: 22806--23020 Score: 385
Period size: 47 Copynumber: 4.6 Consensus size: 47
22796 TTATGGTTTA
*
22806 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTACGTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
22853 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
22900 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
22947 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
22994 TTGGTAAAATAAGCTTGCGAGCTTATG
1 TTGATAAAATAAGCTTACGAGCTTATG
23021 AGATAAATGA
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 162 1.00
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (47 bp):
TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
Found at i:23509 original size:13 final size:13
Alignment explanation
Indices: 23491--23527 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
23481 CCGATTCCCC
23491 CACTGTTCA-TCGT
1 CACTGTTCACT-GT
23504 CACTGTTCACTGT
1 CACTGTTCACTGT
23517 CACTGTTCACT
1 CACTGTTCACT
23528 ATTCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 22 0.96
14 1 0.04
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (13 bp):
CACTGTTCACTGT
Found at i:24094 original size:56 final size:57
Alignment explanation
Indices: 23969--24127 Score: 184
Period size: 56 Copynumber: 2.8 Consensus size: 57
23959 ATATTTTCCT
* * * *
23969 ATAC-GAACATTCATACACTTGGTATGAATTTC-TTA-GTTCGCACA-CATTGAGCCC
1 ATACAGAA-ATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
* *
24023 ATACAAAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCA-AGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
* *
24079 ATACAGAAATTCATACACTTAGTATGAATATCTTACAATTTTTGCACAC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTT--TATTTTTGCACAC
24128 TTAGTGTCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
54 27 0.30
55 5 0.06
56 44 0.49
57 2 0.02
58 12 0.13
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (57 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
Found at i:24670 original size:21 final size:20
Alignment explanation
Indices: 24644--24696 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
24634 CGATGTTGCT
24644 TGGTATCGATAC-CCTTTATC
1 TGGTATCGATACACCTTT-TC
24664 ATGGTATCGATACTACCTTTTC
1 -TGGTATCGATAC-ACCTTTTC
24686 -GGTATCGATAC
1 TGGTATCGATAC
24697 TGATTGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.37
21 12 0.40
22 2 0.07
23 5 0.17
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACACCTTTTC
Found at i:24691 original size:20 final size:21
Alignment explanation
Indices: 24645--24697 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
24635 GATGTTGCTT
24645 GGTATCGATAC-CCTTTATCA
1 GGTATCGATACTCCTTTATCA
24665 TGGTATCGATACTACCTTT-TC-
1 -GGTATCGATACT-CCTTTATCA
24686 GGTATCGATACT
1 GGTATCGATACT
24698 GATTGAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.40
21 11 0.37
22 2 0.07
23 5 0.17
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
GGTATCGATACTCCTTTATCA
Found at i:24778 original size:15 final size:15
Alignment explanation
Indices: 24755--24789 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24745 CTATAGTATT
*
24755 GGTATTGTTCTTAGC
1 GGTACTGTTCTTAGC
24770 GGTACTGTTCTTAGC
1 GGTACTGTTCTTAGC
*
24785 AGTAC
1 GGTAC
24790 CGATACCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (15 bp):
GGTACTGTTCTTAGC
Found at i:34226 original size:12 final size:12
Alignment explanation
Indices: 34209--34275 Score: 59
Period size: 11 Copynumber: 5.6 Consensus size: 12
34199 AAATTTTGGC
34209 TTTTTTTGGCTTT
1 TTTTTTTGGC-TT
*
34222 TTTTTTTTG-TT
1 TTTTTTTGGCTT
*
34233 TTTTTTT--TTT
1 TTTTTTTGGCTT
34243 GTTTTTTTGGCTT
1 -TTTTTTTGGCTT
*
34256 TTTTTTTGCCTT
1 TTTTTTTGGCTT
34268 TTCTTTTT
1 TT-TTTTT
34276 TTGGAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 2 0.04
11 16 0.35
12 13 0.28
13 15 0.33
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (12 bp):
TTTTTTTGGCTT
Found at i:34227 original size:13 final size:13
Alignment explanation
Indices: 34209--34276 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 13
34199 AAATTTTGGC
34209 TTTTTTTGGCTTT
1 TTTTTTTGGCTTT
*
34222 TTTTTTTTG-TTT
1 TTTTTTTGGCTTT
*
34234 TTTTTTT---TTG
1 TTTTTTTGGCTTT
34244 TTTTTTTGGC-TT
1 TTTTTTTGGCTTT
*
34256 TTTTTTTGCCTTT
1 TTTTTTTGGCTTT
34269 TCTTTTTT
1 T-TTTTTT
34277 TGGAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.20
12 20 0.43
13 11 0.24
14 6 0.13
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (13 bp):
TTTTTTTGGCTTT
Found at i:34248 original size:14 final size:13
Alignment explanation
Indices: 34209--34250 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
34199 AAATTTTGGC
* *
34209 TTTTTTTGGCTTT
1 TTTTTTTTGTTTT
34222 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
34235 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
34248 TTT
1 TTT
34251 GGCTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:34275 original size:35 final size:35
Alignment explanation
Indices: 34209--34278 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
34199 AAATTTTGGC
*** *
34209 TTTTTTTGGCTTTTTTTTTTTGTTTTTTTTTTTTG
1 TTTTTTTGGCTTTTTTTTTGCCTTTTCTTTTTTTG
34244 TTTTTTTGGCTTTTTTTTTGCCTTTTCTTTTTTTG
1 TTTTTTTGGCTTTTTTTTTGCCTTTTCTTTTTTTG
34279 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (35 bp):
TTTTTTTGGCTTTTTTTTTGCCTTTTCTTTTTTTG
Found at i:34651 original size:15 final size:16
Alignment explanation
Indices: 34631--34667 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
34621 GATTAGAATA
34631 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
34646 AAATAAACGAAAGATG
1 AAATAAACAAAAGATG
34662 AAATAA
1 AAATAA
34668 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:35924 original size:3 final size:3
Alignment explanation
Indices: 35918--35943 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35908 AAAACCACTG
35918 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
35944 TAAATAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40827 original size:17 final size:17
Alignment explanation
Indices: 40805--40837 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40795 TTGGTTCAGG
40805 AAACAG-TAATACAATTA
1 AAACAGATAA-ACAATTA
40822 AAACAGATAAACAATT
1 AAACAGATAAACAATT
40838 GGTTCATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AAACAGATAAACAATTA
Found at i:42156 original size:2 final size:2
Alignment explanation
Indices: 42009--42136 Score: 52
Period size: 2 Copynumber: 63.5 Consensus size: 2
41999 AAAATTGAAG
* * * *
42009 TA TA TA TA TA TA TA AA GTT TA TA TA T- TA CA TA TA TA AA T- TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
42050 TA TA GTT TA TA TT TA TA T- TA T- TA TG TA CTA TA TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
42091 TA TA TA TA TA T- TA TG TA TA AA CTA TA -A TA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
42132 TA TA T
1 TA TA T
42137 GAACTATTGA
Statistics
Matches: 91, Mismatches: 22, Indels: 26
0.65 0.16 0.19
Matches are distributed among these distances:
1 6 0.07
2 77 0.85
3 8 0.09
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42178 original size:22 final size:22
Alignment explanation
Indices: 42152--42193 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42142 ATTGAACTAT
42152 ATATAAACTACATAGTTTATTA
1 ATATAAACTACATAGTTTATTA
* *
42174 ATATAAATTATATAGTTTAT
1 ATATAAACTACATAGTTTAT
42194 AGATAGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAACTACATAGTTTATTA
Found at i:42605 original size:65 final size:63
Alignment explanation
Indices: 42486--42695 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
42476 TTTTTCAGAG
* * *
42486 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
42548 ATT
61 ATT
* *
42551 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
42615 T
63 T
* * * * *
42616 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
42680 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
42696 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:42695 original size:17 final size:19
Alignment explanation
Indices: 42667--42715 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42657 TATTTTGAAA
42667 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
42685 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
42704 CACCGATGCACT
1 CATCGATGCACT
42716 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:43455 original size:29 final size:29
Alignment explanation
Indices: 43421--43485 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
43411 TCAACATTAT
43421 ACTATATATACTATATAATTTACATATGA
1 ACTATATATACTATATAATTTACATATGA
* *
43450 ATTATATATACTATATAGTTTACATATGA
1 ACTATATATACTATATAATTTACATATGA
43479 ACTATAT
1 ACTATAT
43486 GTATAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (29 bp):
ACTATATATACTATATAATTTACATATGA
Found at i:43496 original size:13 final size:13
Alignment explanation
Indices: 43478--43522 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
43468 TTTACATATG
43478 AACTATATGTATA
1 AACTATATGTATA
43491 AACTATATGTATA
1 AACTATATGTATA
* *
43504 AACAATATATATA
1 AACTATATGTATA
43517 AACTAT
1 AACTAT
43523 GTAAACTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (13 bp):
AACTATATGTATA
Found at i:43573 original size:26 final size:26
Alignment explanation
Indices: 43529--43580 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
43519 CTATGTAAAC
*
43529 TATATAGTTTACATATGAATTATATA
1 TATATAGTTTACATATGAAATATATA
*
43555 TATATAGTTTA-TTAGTGAAATATATA
1 TATATAGTTTACATA-TGAAATATATA
43581 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (26 bp):
TATATAGTTTACATATGAAATATATA
Found at i:43618 original size:18 final size:18
Alignment explanation
Indices: 43576--43689 Score: 61
Period size: 18 Copynumber: 5.9 Consensus size: 18
43566 TTAGTGAAAT
* *
43576 ATATAAACTATTTATATA
1 ATATATACTATATATATA
43594 ATATATACTATATATATA
1 ATATATACTATATATATA
* * *
43612 A-ACTATAGTTTATAT-TT
1 ATA-TATACTATATATATA
43629 ATATACTACATACTATAGTTGATA
1 ATATA-TAC-TA-TATA--T-ATA
*
43653 TTTATATACTATATATTATA
1 -ATATATACTATATA-TATA
*
43673 TATATAAACTATATATA
1 -ATATATACTATATATA
43690 CTATATAGTA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
17 5 0.07
18 30 0.40
19 3 0.04
20 20 0.27
21 2 0.03
22 5 0.07
23 2 0.03
24 4 0.05
25 4 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATATACTATATATATA
Found at i:43625 original size:27 final size:27
Alignment explanation
Indices: 43595--43672 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
43585 ATTTATATAA
*
43595 TATATACTATATA-TATAAACTATAGTT
1 TATAT-CTATATACTATATACTATAGTT
* *
43622 TATATTTATATACTACATACTATAGTT
1 TATATCTATATACTATATACTATAGTT
* * *
43649 GATATTTATATACTATATATTATA
1 TATATCTATATACTATATACTATA
43673 TATATAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.14
27 38 0.86
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATCTATATACTATATACTATAGTT
Found at i:43694 original size:20 final size:20
Alignment explanation
Indices: 43595--43702 Score: 74
Period size: 20 Copynumber: 4.9 Consensus size: 20
43585 ATTTATATAA
*
43595 TATATACTATATATATAAAC
1 TATATATTATATATATAAAC
*
43615 TATAGT-TTATATTTATATACTAC
1 TATA-TATTATA--TATATA-AAC
* *
43638 ATACTATAGTTGATATTTATATAC
1 -TA-TATA-TT-ATATATATAAAC
43662 TATATATTATATATATAAAC
1 TATATATTATATATATAAAC
43682 TATATATACTATATAGTATAA
1 TATATAT--TATATA-TATAA
43703 TTTACGTACG
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
20 25 0.35
21 3 0.04
22 16 0.23
23 9 0.13
24 6 0.08
25 7 0.10
26 2 0.03
27 3 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATATTATATATATAAAC
Found at i:43778 original size:20 final size:19
Alignment explanation
Indices: 43755--43807 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
43745 TATAGTTGAT
43755 GTTTATATATAAACTATATA
1 GTTTATATATAAACT-TATA
* *
43775 GTTTTTATATGAAC-TATA
1 GTTTATATATAAACTTATA
*
43793 GTTTACATATAAACT
1 GTTTATATATAAACT
43808 GTAGTTGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.56
20 12 0.44
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (19 bp):
GTTTATATATAAACTTATA
Found at i:43792 original size:18 final size:18
Alignment explanation
Indices: 43771--43936 Score: 118
Period size: 18 Copynumber: 9.2 Consensus size: 18
43761 ATATAAACTA
**
43771 TATAGTTTTTATATGAAC
1 TATAGTTTACATATGAAC
*
43789 TATAGTTTACATATAAAC
1 TATAGTTTACATATGAAC
*
43807 TGTAGTTGATATTTACATATGAAC
1 --TA--T-A-GTTTACATATGAAC
43831 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
*
43849 TATA---T--ATATAAAC
1 TATAGTTTACATATGAAC
43862 TTTATAGTTTACATATGAAC
1 --TATAGTTTACATATGAAC
43882 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
*
43900 TATA---T--ATATAAAC
1 TATAGTTTACATATGAAC
43913 TTTATAGTTTACATATGAAC
1 --TATAGTTTACATATGAAC
43933 TATA
1 TATA
43937 TAAACTATTT
Statistics
Matches: 118, Mismatches: 10, Indels: 40
0.70 0.06 0.24
Matches are distributed among these distances:
13 14 0.12
15 10 0.08
18 60 0.51
19 1 0.01
20 17 0.14
22 3 0.03
23 1 0.01
24 12 0.10
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (18 bp):
TATAGTTTACATATGAAC
Found at i:43792 original size:60 final size:59
Alignment explanation
Indices: 43726--43905 Score: 155
Period size: 51 Copynumber: 3.2 Consensus size: 59
43716 TATATATAAA
* * * * **
43726 AACTATATAAAC-TATACATTATAGTTGATGTTTATATATAAACTATATAGTTTTTATATG
1 AACTATATAAACATATAAACTATAGTTGATATTTACATATAAAC--TATAGTTTACATATG
** * *
43786 AACTATAGTTTACATATAAACTGTAGTTGATATTTACATATGAACTATAGTTTACATATG
1 AACTATA-TAAACATATAAACTATAGTTGATATTTACATATAAACTATAGTTTACATATG
*
43846 AACTATAT----ATATAAAC--T--TT-ATAGTTTACATATGAACTATAGTTTACATATG
1 AACTATATAAACATATAAACTATAGTTGATA-TTTACATATAAACTATAGTTTACATATG
43897 AACTATATA
1 AACTATATA
43906 TATAAACTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
50 3 0.03
51 38 0.36
53 1 0.01
55 8 0.08
59 1 0.01
60 27 0.25
61 3 0.03
62 25 0.24
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (59 bp):
AACTATATAAACATATAAACTATAGTTGATATTTACATATAAACTATAGTTTACATATG
Found at i:43875 original size:51 final size:51
Alignment explanation
Indices: 43818--43936 Score: 238
Period size: 51 Copynumber: 2.3 Consensus size: 51
43808 GTAGTTGATA
43818 TTTACATATGAACTATAGTTTACATATGAACTATATATATAAACTTTATAG
1 TTTACATATGAACTATAGTTTACATATGAACTATATATATAAACTTTATAG
43869 TTTACATATGAACTATAGTTTACATATGAACTATATATATAAACTTTATAG
1 TTTACATATGAACTATAGTTTACATATGAACTATATATATAAACTTTATAG
43920 TTTACATATGAACTATA
1 TTTACATATGAACTATA
43937 TAAACTATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (51 bp):
TTTACATATGAACTATAGTTTACATATGAACTATATATATAAACTTTATAG
Found at i:43982 original size:24 final size:24
Alignment explanation
Indices: 43933--44152 Score: 86
Period size: 24 Copynumber: 9.0 Consensus size: 24
43923 ACATATGAAC
* *
43933 TATATAAACTATTTATA-TAGTATA
1 TATATAAACTATATAAACTA-TATA
*
43957 TATATAAACTATATAAACTATTTA
1 TATATAAACTATATAAACTATATA
* *
43981 TATAGTATA-TATATAAACTATAGTC
1 TATA-TAAACTATATAAACTATA-TA
**
44006 TATATTTA-TATACTACACACTATAGTTGA
1 TATATAAACTATA-TA-A-ACTATA--T-A
**
44035 TATTTATATGCTATAT--A-T-TATA
1 TA--TATAAACTATATAAACTATATA
*
44057 TATATAAACTATATATACTATATA
1 TATATAAACTATATAAACTATATA
** *
44081 GTATAATTTAC-ATATGAACTATATA
1 -TAT-ATAAACTATATAAACTATATA
*
44106 TA-A-AAACTATATTAACTATAGTTTA
1 TATATAAACTATATAAACTATA---TA
44131 TATATAAACTATAT--ACTATATA
1 TATATAAACTATATAAACTATATA
44153 ATACAATTTA
Statistics
Matches: 153, Mismatches: 20, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
20 10 0.07
21 2 0.01
22 18 0.12
23 2 0.01
24 47 0.31
25 39 0.25
26 7 0.05
27 16 0.10
28 1 0.01
29 2 0.01
31 5 0.03
32 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (24 bp):
TATATAAACTATATAAACTATATA
Found at i:44002 original size:20 final size:19
Alignment explanation
Indices: 43946--44572 Score: 110
Period size: 20 Copynumber: 33.7 Consensus size: 19
43936 ATAAACTATT
43946 TATATAGTATATATATAAAC
1 TATATA-TATATATATAAAC
* * * *
43966 TATATAAACTATTTATATAG
1 TATATATA-TATATATAAAC
* **
43986 TATATATATAAACTATAGTC
1 TATATATATATA-TATAAAC
* * *
44006 TATATTTATATACTACACAC
1 TATATATATATA-TATAAAC
* **
44026 TATAGT-TGATATTTATATGC
1 TATA-TAT-ATATATATAAAC
44046 TATATATTATATATATAAAC
1 TATATA-TATATATATAAAC
* *
44066 TATATATA-CTATAT--AG
1 TATATATATATATATAAAC
* * *
44082 TATA-ATTTACATATGAAC
1 TATATATATATATATAAAC
* *
44100 TATATATAAAAACTATATTAAC
1 TATATAT--ATA-TATATAAAC
44122 TATAGT-T-TATATATAAAC
1 TATA-TATATATATATAAAC
44140 TATATACTATATA-ATACAA-
1 TATATA-TATATATATA-AAC
**
44159 T-T-TATACT-TATATAATT
1 TATATATA-TATATATAAAC
* *
44176 TATACTATATAAAT-TCAAAG
1 TATA-TATATATATAT-AAAC
* *
44196 TATATATTATATGTATGAA-
1 TATATA-TATATATATAAAC
44215 TAT-TATATA-AT-TGAATAC
1 TATATATATATATAT-AA-AC
44233 -AT-TA-AT-TA-ATAAAC
1 TATATATATATATATAAAC
* *
44247 TATTTATATAGTATATACTAC
1 TATATATATA-TATATA-AAC
* * *
44268 -ATAAATAGTTTATATATAC
1 TATATATA-TATATATAAAC
* * *
44287 TATATAGTTTACATATGAAC
1 TATATA-TATATATATAAAC
* ***
44307 TATATATATAAAGTATATGG
1 TATATATATATA-TATAAAC
* *
44327 TATATATAAACTATATATTA-
1 TATATATATA-TATATA-AAC
44347 TATAGTTCATTAGTATATATAAAC
1 TATA--T-A-TA-TATATATAAAC
*
44371 TATATA-GTATATATAAAC
1 TATATATATATATATAAAC
**
44389 TATAT-GGTATATATAAAC
1 TATATATATATATATAAAC
* *
44407 TATACAT-TATATAGT--TC
1 TATATATATATATA-TAAAC
*
44424 -AT-TA-GTATATATAAAC
1 TATATATATATATATAAAC
*
44440 TATATA-GTATATATAAAC
1 TATATATATATATATAAAC
**
44458 TATAT-GGTATATATAAAC
1 TATATATATATATATAAAC
* *
44476 TATACAT-TATATAGT--TC
1 TATATATATATATA-TAAAC
*
44493 -AT-TA-GTATATATAAAC
1 TATATATATATATATAAAC
44509 TATATAT-TATATAGT----
1 TATATATATATATA-TAAAC
44524 T-TAT-TAGTATATATAAAC
1 TATATATA-TATATATAAAC
*
44542 TATATA-ATATATATAAAT
1 TATATATATATATATAAAC
*
44560 TATACAT-TATATA
1 TATATATATATATA
44573 GTTCATTAGT
Statistics
Matches: 451, Mismatches: 77, Indels: 160
0.66 0.11 0.23
Matches are distributed among these distances:
13 1 0.00
14 8 0.02
15 28 0.06
16 28 0.06
17 25 0.06
18 135 0.30
19 37 0.08
20 144 0.32
21 15 0.03
22 14 0.03
23 3 0.01
24 12 0.03
25 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (19 bp):
TATATATATATATATAAAC
Found at i:44017 original size:33 final size:33
Alignment explanation
Indices: 43915--44002 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
43905 ATATAAACTT
* * *
43915 TATAGTTTACATATGAACTATATAAACTATTTA
1 TATAGTATATATATAAACTATATAAACTATTTA
43948 TATAGTATATATATAAACTATATAAACTATTTA
1 TATAGTATATATATAAACTATATAAACTATTTA
43981 TATAGTATATATATAAACTATA
1 TATAGTATATATATAAACTATA
44003 GTCTATATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (33 bp):
TATAGTATATATATAAACTATATAAACTATTTA
Found at i:44190 original size:15 final size:15
Alignment explanation
Indices: 44157--44187 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44147 TATATAATAC
44157 AATTTATACTTATAT
1 AATTTATACTTATAT
44172 AATTTATAC-TATAT
1 AATTTATACTTATAT
44186 AA
1 AA
44188 ATTCAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTATACTTATAT
Found at i:44293 original size:18 final size:18
Alignment explanation
Indices: 44251--44563 Score: 218
Period size: 18 Copynumber: 18.2 Consensus size: 18
44241 ATAAACTATT
*
44251 TATATAGTATATACTACA-
1 TATATAGTATATA-TAAAC
* * *
44269 TAAATAGTTTATATATAC
1 TATATAGTATATATAAAC
* *
44287 TATATAGTTTACATATGAAC
1 TATATAG--TATATATAAAC
*
44307 --TATA-TA--TATAAAG
1 TATATAGTATATATAAAC
*
44320 TATATGGTATATATAAAC
1 TATATAGTATATATAAAC
**
44338 TATATA-T-TATAT-AGT
1 TATATAGTATATATAAAC
44353 TCAT-TAGTATATATAAAC
1 T-ATATAGTATATATAAAC
44371 TATATAGTATATATAAAC
1 TATATAGTATATATAAAC
*
44389 TATATGGTATATATAAAC
1 TATATAGTATATATAAAC
* **
44407 TATACA-T-TATAT-AGT
1 TATATAGTATATATAAAC
44422 TCAT-TAGTATATATAAAC
1 T-ATATAGTATATATAAAC
44440 TATATAGTATATATAAAC
1 TATATAGTATATATAAAC
*
44458 TATATGGTATATATAAAC
1 TATATAGTATATATAAAC
* **
44476 TATACA-T-TATAT-AGT
1 TATATAGTATATATAAAC
44491 TCAT-TAGTATATATAAAC
1 T-ATATAGTATATATAAAC
***
44509 TATATA-T-TATATAGTT
1 TATATAGTATATATAAAC
44525 TAT-TAGTATATATAAAC
1 TATATAGTATATATAAAC
* *
44542 TATATAATATATATAAAT
1 TATATAGTATATATAAAC
44560 TATA
1 TATA
44564 CATTATATAG
Statistics
Matches: 228, Mismatches: 41, Indels: 52
0.71 0.13 0.16
Matches are distributed among these distances:
13 5 0.02
15 17 0.07
16 36 0.16
17 37 0.16
18 126 0.55
20 7 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (18 bp):
TATATAGTATATATAAAC
Found at i:44340 original size:51 final size:50
Alignment explanation
Indices: 44272--44598 Score: 217
Period size: 51 Copynumber: 6.4 Consensus size: 50
44262 TACTACATAA
* * * *
44272 ATAGTTTATATATACTATATAGTTTACATATGAACTATATATATAAAGTAT
1 ATAGTATATATAAACTATATAG-TTATATATAAACTATATATATAAAGTAT
* ** * *
44323 ATGGTATATATAAACTATATA-TTATATAGTTCATTAGTATATATAAACTAT
1 ATAGTATATATAAACTATATAGTTATATA-TAAACTA-TATATATAAAGTAT
* * *
44374 ATAGTATATATAAACTATAT-GGTATATATAAACTATACATTATATAGT-T
1 ATAGTATATATAAACTATATAGTTATATATAAACTATATA-TATAAAGTAT
*
44423 CATTAGTATATATAAACTATATAG-TATATATAAACTATATGGTATATATAAACTAT
1 -A-TAGTATATATAAACTATATAGTTATATATAAAC--TA---TATATATAAAGTAT
* ** * *
44479 ACA-T-TATAT-AGTTCAT-TAG-TATATATAAACTATATATTATATAGTTT
1 ATAGTATATATAAACT-ATATAGTTATATATAAACTATATA-TATAAAGTAT
* * * *
44526 ATTAGTATATATAAACTATATA-ATATATATAAATTATACATTATATAGT-T
1 A-TAGTATATATAAACTATATAGTTATATATAAACTATATA-TATAAAGTAT
*
44576 CATTAGTATATATAACCTATATA
1 -A-TAGTATATATAAACTATATA
44599 TTAATTTATT
Statistics
Matches: 223, Mismatches: 31, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
46 4 0.02
47 8 0.04
48 1 0.00
49 13 0.06
50 23 0.10
51 151 0.68
52 8 0.04
53 3 0.01
54 1 0.00
55 7 0.03
56 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (50 bp):
ATAGTATATATAAACTATATAGTTATATATAAACTATATATATAAAGTAT
Found at i:44572 original size:69 final size:69
Alignment explanation
Indices: 44309--44554 Score: 399
Period size: 69 Copynumber: 3.6 Consensus size: 69
44299 ATATGAACTA
* *
44309 TATATATAAAGTATATGGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
44374 ATAG
66 ATAG
44378 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
44443 ATAG
66 ATAG
44447 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
1 TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
44512 ATA-
66 ATAG
*** * * *
44515 T-TATATAGTTTAT-TAGTATATATAAACTATATAATATATA
1 TATATATAAACTATATGGTATATATAAACTATACATTATATA
44555 TAAATTATAC
Statistics
Matches: 169, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
66 24 0.14
67 9 0.05
68 1 0.01
69 135 0.80
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (69 bp):
TATATATAAACTATATGGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTAT
ATAG
Found at i:44622 original size:84 final size:84
Alignment explanation
Indices: 44326--44622 Score: 250
Period size: 84 Copynumber: 3.5 Consensus size: 84
44316 AAAGTATATG
* * * *
44326 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATAAACTA
1 GTATATATAAACTATATATTATATAGTTAATTAGAACATATAAACTATATAATATATATAAACTA
* * *
44391 TATGGTATATATAAACTATACATTA
66 TA---CAT-TATATAGT-T-CATTA
* * ** * * **
44416 -TATAGT-T-CATTAGTATA-TATA-AACT-ATATAGTATATATAAACTATATGGTATATATAAA
1 GTATA-TATAAACTA-TATATTATATAGTTAAT-TAGAACATATAAACTATATAATATATATAAA
44475 CTATACATTATATAGTTCATTA
63 CTATACATTATATAGTTCATTA
* * * *
44497 GTATATATAAACTATATATTATATAGTTTATTAGTATATATAAACTATATAATATATATAAATTA
1 GTATATATAAACTATATATTATATAGTTAATTAGAACATATAAACTATATAATATATATAAACTA
44562 TACATTATATAGTTCATTA
66 TACATTATATAGTTCATTA
* *
44581 GTATATATAACCTATATATTAATTTA-TTAATATA-AACATATA
1 GTATATATAAACTATATATT-ATATAGTTAAT-TAGAACATATA
44623 TATTAAATGA
Statistics
Matches: 176, Mismatches: 20, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
81 6 0.03
82 10 0.06
83 13 0.07
84 83 0.47
85 8 0.05
86 2 0.01
87 37 0.21
88 7 0.04
89 9 0.05
90 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (84 bp):
GTATATATAAACTATATATTATATAGTTAATTAGAACATATAAACTATATAATATATATAAACTA
TACATTATATAGTTCATTA
Found at i:44698 original size:21 final size:20
Alignment explanation
Indices: 44673--44756 Score: 52
Period size: 21 Copynumber: 4.1 Consensus size: 20
44663 AAACAAATTT
44673 TAAATATGAAGCTTAAATTAA
1 TAAAT-TGAAGCTTAAATTAA
*
44694 TAAATTGTAA-CATTAAATTTGGAC
1 TAAATTG-AAGC-TTAAA-TT--AA
*
44718 TAAATTGAAG---AAATT-T
1 TAAATTGAAGCTTAAATTAA
44734 TAAATATGAAGCTTAAATTAA
1 TAAAT-TGAAGCTTAAATTAA
44755 TA
1 TA
44757 TATTACATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 22
0.66 0.04 0.30
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
19 2 0.04
20 11 0.22
21 14 0.29
22 2 0.04
23 2 0.04
24 8 0.16
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.36
Consensus pattern (20 bp):
TAAATTGAAGCTTAAATTAA
Found at i:44733 original size:61 final size:61
Alignment explanation
Indices: 44658--44804 Score: 213
Period size: 61 Copynumber: 2.4 Consensus size: 61
44648 TATAAGGATC
* ** *
44658 AAATTAAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTACAACATTAAATTTAGACT
* * *
44719 AAATTGAAGAAATTTTAAATATGAAGCTTAAATTAATATATTACATCATTAAATTTAGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTACAACATTAAATTTAGACT
*
44780 AAATTGAACAAATTTAAAACTATGA
1 AAATTGAACAAATTTTAAA-TATGA
44805 GACAACGCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
61 71 0.93
62 5 0.07
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTACAACATTAAATTTAGACT
Found at i:45180 original size:92 final size:92
Alignment explanation
Indices: 45025--45195 Score: 238
Period size: 92 Copynumber: 1.8 Consensus size: 92
45015 TTCATCCGTG
* *
45025 TTCATTCCAAAAACCCTCATTTGATTTTCAAAAACACCAAACCCAAACCATTTCATGT-TTTTTT
1 TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACCAAACCCAAACCATTT-ATGTCTTTTTT
*
45089 TATCAAACACCCATAATTTCAACCTTTT
65 CATCAAACACCCATAATTTCAACCTTTT
* * *
45117 TTCATCCCAAAAATCCTCCTTTGATCTTCAGAAACACCAAAACCCAAACCATTT-TGTGCTTTTT
1 TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACC-AAACCCAAACCATTTATGT-CTTTTT
45181 TCGATCAAACACCCA
64 TC-ATCAAACACCCA
45196 AAAATTCATC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
91 3 0.04
92 33 0.48
93 21 0.30
94 12 0.17
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (92 bp):
TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACCAAACCCAAACCATTTATGTCTTTTTTC
ATCAAACACCCATAATTTCAACCTTTT
Found at i:45545 original size:24 final size:24
Alignment explanation
Indices: 45510--45596 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
45500 GTCCTTAACT
* *
45510 TGAACCCTAACCAAAACCCAAACT
1 TGAACCCAAACCAAAACCCAAACC
* *
45534 TGAGCCCAAACCCAAACCCAAACC
1 TGAACCCAAACCAAAACCCAAACC
* *
45558 TGAAACCAAACCCAAACCCAAACC
1 TGAACCCAAACCAAAACCCAAACC
*
45582 TGAACCCAATCCAAA
1 TGAACCCAAACCAAA
45597 CCTGAATCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.46, C:0.40, G:0.06, T:0.08
Consensus pattern (24 bp):
TGAACCCAAACCAAAACCCAAACC
Found at i:45547 original size:6 final size:6
Alignment explanation
Indices: 45538--45581 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
45528 CAAACTTGAG
*
45538 CCCAAA CCCAAA CCCAAA CCTGAAA -CCAAA CCCAAA CCCAAA CC
1 CCCAAA CCCAAA CCCAAA CC-CAAA CCCAAA CCCAAA CCCAAA CC
45582 TGAACCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 3 0.09
6 28 0.82
7 3 0.09
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (6 bp):
CCCAAA
Found at i:45604 original size:12 final size:12
Alignment explanation
Indices: 45510--45590 Score: 72
Period size: 12 Copynumber: 6.8 Consensus size: 12
45500 GTCCTTAACT
*
45510 TGAACCCTAACC
1 TGAACCCAAACC
** *
45522 AAAACCCAAACT
1 TGAACCCAAACC
*
45534 TGAGCCCAAACC
1 TGAACCCAAACC
**
45546 CAAACCCAAACC
1 TGAACCCAAACC
*
45558 TGAAACCAAACC
1 TGAACCCAAACC
**
45570 CAAACCCAAACC
1 TGAACCCAAACC
45582 TGAACCCAA
1 TGAACCCAA
45591 TCCAAACCTG
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.46, C:0.41, G:0.06, T:0.07
Consensus pattern (12 bp):
TGAACCCAAACC
Found at i:45612 original size:18 final size:17
Alignment explanation
Indices: 45575--45633 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
45565 AAACCCAAAC
*
45575 CCAAACCTGAACCCAAT
1 CCAAACCTGAACCGAAT
*
45592 CCAAACCTGAATCTGAAT
1 CCAAACCTGAA-CCGAAT
*
45610 CCAAACCCGAACCCGAAT
1 CCAAACCTGAA-CCGAAT
45628 CCAAAC
1 CCAAAC
45634 TATTCGAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 11 0.31
18 25 0.69
ACGTcount: A:0.41, C:0.39, G:0.08, T:0.12
Consensus pattern (17 bp):
CCAAACCTGAACCGAAT
Found at i:45628 original size:24 final size:23
Alignment explanation
Indices: 45518--45623 Score: 104
Period size: 24 Copynumber: 4.5 Consensus size: 23
45508 CTTGAACCCT
* * *
45518 AACCAAAACCCAAACTTGAGCCCA
1 AACCCAAACCCAAACCTGA-ACCA
45542 AACCCAAACCCAAACCTGAAACCA
1 AACCCAAACCCAAACCTG-AACCA
*
45566 AACCCAAACCCAAACCTGAACCC
1 AACCCAAACCCAAACCTGAACCA
* ** *
45589 AATCCAAACCTGAATCTGAATCCA
1 AACCCAAACCCAAACCTGAA-CCA
*
45613 AACCCGAACCC
1 AACCCAAACCC
45624 GAATCCAAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 20 0.29
24 47 0.69
25 1 0.01
ACGTcount: A:0.44, C:0.41, G:0.07, T:0.08
Consensus pattern (23 bp):
AACCCAAACCCAAACCTGAACCA
Found at i:48518 original size:2 final size:2
Alignment explanation
Indices: 48511--48557 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48501 TAAGGGAGTT
48511 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
48553 TA TA T
1 TA TA T
48558 CTAATAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50422 original size:23 final size:23
Alignment explanation
Indices: 50396--50473 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
50386 CTTAAAGTAG
50396 GATGCTTGTTGAATTGATGCAAC
1 GATGCTTGTTGAATTGATGCAAC
50419 GATGCTTGTTGAATTGATGCAAC
1 GATGCTTGTTGAATTGATGCAAC
* * *
50442 GATGCTTGCTGAATTGATACAAT
1 GATGCTTGTTGAATTGATGCAAC
50465 GATGCTTGT
1 GATGCTTGT
50474 CGTTTGATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (23 bp):
GATGCTTGTTGAATTGATGCAAC
Found at i:51125 original size:18 final size:18
Alignment explanation
Indices: 51066--51125 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
51056 AAAGAATTGG
51066 AATTAATATAAAAATCAA
1 AATTAATATAAAAATCAA
* * * *
51084 ATTTATAATATACAAATTAT
1 A-AT-TAATATAAAAATCAA
*
51104 AATTAATATAAAAACCAA
1 AATTAATATAAAAATCAA
51122 AATT
1 AATT
51126 TAAAAAGTAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
18 16 0.52
19 2 0.06
20 13 0.42
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAATATAAAAATCAA
Found at i:51269 original size:16 final size:16
Alignment explanation
Indices: 51235--51269 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
51225 TGAATCAATT
*
51235 ACAAGTCAGGTTCATA
1 ACAAGTCAGGTTCAAA
*
51251 ACAAGTCAGGTTGAAA
1 ACAAGTCAGGTTCAAA
51267 ACA
1 ACA
51270 TGTAGGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (16 bp):
ACAAGTCAGGTTCAAA
Found at i:51501 original size:2 final size:2
Alignment explanation
Indices: 51494--51569 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
51484 CCTACTATTC
51494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51570 CTGTGTGTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54173 original size:17 final size:17
Alignment explanation
Indices: 54148--54186 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
54138 CGATTTAAAA
*
54148 AAAAAATATTTTTTAAT
1 AAAATATATTTTTTAAT
*
54165 AAAATATATTTTTTATT
1 AAAATATATTTTTTAAT
54182 AAAAT
1 AAAAT
54187 TTACGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATATATTTTTTAAT
Found at i:54667 original size:35 final size:35
Alignment explanation
Indices: 54608--54719 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
54598 AAAACATTCC
* *
54608 TCAATTTCATTATAAATCCC-AAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCTAAATTTCAAAATAAT
*
54643 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
* *
54678 TCAATTACATTCTAAACCCTAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAACCCTAAATTTC-AAAATAAT
54713 TCAATTT
1 TCAATTT
54720 AAGGAGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.07
35 63 0.93
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:55784 original size:35 final size:34
Alignment explanation
Indices: 55735--55847 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
55725 TAAAAAGACA
* *
55735 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
55770 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
55805 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
55840 GAAATTGA
1 GAAATTGA
55848 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:64049 original size:20 final size:20
Alignment explanation
Indices: 64024--64062 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
64014 CCGGAGATCG
64024 TTATTAT-TATTATTTTATTA
1 TTATTATAT-TTATTTTATTA
64044 TTATTATATTTATTTTATT
1 TTATTATATTTATTTTATT
64063 TTTTGTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTATATTTATTTTATTA
Found at i:70591 original size:25 final size:25
Alignment explanation
Indices: 70563--70618 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
70553 AACTACGTGC
70563 CTATGTGAATAAATGTGATAATGAA
1 CTATGTGAATAAATGTGATAATGAA
70588 CTATGTGAATAAATGTGATAATGAA
1 CTATGTGAATAAATGTGATAATGAA
70613 CTATGT
1 CTATGT
70619 AATCCTTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (25 bp):
CTATGTGAATAAATGTGATAATGAA
Found at i:70595 original size:15 final size:15
Alignment explanation
Indices: 70575--70618 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
70565 ATGTGAATAA
70575 ATGTGATAATGAACT
1 ATGTGATAATGAACT
70590 ATGTG--AAT-AA--
1 ATGTGATAATGAACT
70600 ATGTGATAATGAACT
1 ATGTGATAATGAACT
70615 ATGT
1 ATGT
70619 AATCCTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 5 0.21
12 5 0.21
13 5 0.21
15 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (15 bp):
ATGTGATAATGAACT
Found at i:70792 original size:18 final size:18
Alignment explanation
Indices: 70769--70803 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
70759 GTTCTTAAGG
70769 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
70787 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
70804 AATTCTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:74422 original size:3 final size:3
Alignment explanation
Indices: 74416--74483 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
74406 TTTATTATCG
*
74416 TTA TTA TTA TT- TTA TTTA TTA CTA TTA -TA TT- TT- TTA TTA -TA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
74457 TTA TTA TTA TTT TTA TTA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TT
74484 TATTTACATT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 10 0.18
3 39 0.71
4 6 0.11
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:74430 original size:20 final size:19
Alignment explanation
Indices: 74405--74488 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 19
74395 TCATCCATTT
*
74405 TTTTATTATCGTTATTATTA
1 TTTTATTAT-ATTATTATTA
* *
74425 TTTTATTTATTACTATTATATT
1 TTTTA-TTA-TATTATTAT-TA
74447 TTTTATTATATTATTATTA
1 TTTTATTATATTATTATTA
74466 TTTTTATTATA-TATTATTTA
1 -TTTTATTATATTATTA-TTA
74486 TTT
1 TTT
74489 ACATTACAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 9 0.17
20 26 0.48
21 12 0.22
22 7 0.13
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTATTATATTATTATTA
Found at i:74442 original size:30 final size:29
Alignment explanation
Indices: 74408--74465 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
74398 TCCATTTTTT
* *
74408 TATTATCGTTATTATTATTTTATTTATTAC
1 TATTATAGTTATTATTATATTA-TTATTAC
* *
74438 TATTATATTTTTTATTATATTATTATTA
1 TATTATAGTTATTATTATATTATTATTA
74466 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (29 bp):
TATTATAGTTATTATTATATTATTATTAC
Found at i:74446 original size:23 final size:23
Alignment explanation
Indices: 74420--74481 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
74410 TTATCGTTAT
74420 TATTATTTTATT-TATTACTATTA
1 TATT-TTTTATTATATTACTATTA
*
74443 TATTTTTTATTATATTATTATTA
1 TATTTTTTATTATATTACTATTA
74466 T-TTTTATTA-TATATTA
1 TATTTT-TTATTATATTA
74482 TTTATTTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTTTTTATTATATTACTATTA
Found at i:74494 original size:20 final size:19
Alignment explanation
Indices: 74427--74494 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 19
74417 TATTATTATT
74427 TTATTTATTACTATTATAT-
1 TTATTTATTAC-ATTATATA
*
74446 TT-TTTATTATATTAT-TA
1 TTATTTATTACATTATATA
74463 TTATTT-TT--ATTATATA
1 TTATTTATTACATTATATA
74479 TTATTTATTTACATTA
1 TTATTTA-TTACATTA
74495 CAGACCAGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
15 5 0.12
16 9 0.22
17 9 0.22
18 12 0.29
19 2 0.05
20 4 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATTACATTATATA
Done.