Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008582.1 Hibiscus syriacus cultivar Beakdansim tig00111516_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: 105326
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3836 original size:54 final size:54
Alignment explanation
Indices: 3778--4020 Score: 348
Period size: 54 Copynumber: 4.6 Consensus size: 54
3768 TAAACAAATT
*** * * * *
3778 ATGAATTCCGTGCCTTGCACACCTAGTGTCGAAACAGATATTCATCCTCATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGG
* * * *
3832 ATGAATTCCATGAAAAGCACACTTAGTGCCGAAACGGTTATTCCTCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGG
*
3886 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAATGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGG
*
3940 ATGAATTCCGTGAAATG--CACTTA-TGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGG
3991 ATGAATTCCGTGAAATGCACACTTAGTGTC
1 ATGAATTCCGTGAAATGCACACTTAGTGTC
4021 TATTGGGTAA
Statistics
Matches: 167, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
51 43 0.26
52 6 0.04
53 6 0.04
54 112 0.67
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGG
Found at i:4426 original size:41 final size:42
Alignment explanation
Indices: 4338--4430 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
4328 TGGCCCTTCA
4338 GTATCGATACCTATGCCATGATATTGATACTACCCTACTATG
1 GTATCGATACCTATGCCATGATATTGATACTACCCTACTATG
4380 GTATCGATACCTATGCCATGATATTGATAC-ACCCTACTATG
1 GTATCGATACCTATGCCATGATATTGATACTACCCTACTATG
4421 GTATCGATAC
1 GTATCGATAC
4431 ACCCTTCCGG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 21 0.41
42 30 0.59
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
GTATCGATACCTATGCCATGATATTGATACTACCCTACTATG
Found at i:4429 original size:21 final size:21
Alignment explanation
Indices: 4363--4435 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
4353 CCATGATATT
4363 GATACTACCCTACTATGGTATC
1 GATAC-ACCCTACTATGGTATC
** * * * *
4385 GATAC-CTATGCCATGATATT
1 GATACACCCTACTATGGTATC
4405 GATACACCCTACTATGGTATC
1 GATACACCCTACTATGGTATC
4426 GATACACCCT
1 GATACACCCT
4436 TCCGGTATCG
Statistics
Matches: 38, Mismatches: 12, Indels: 3
0.72 0.23 0.06
Matches are distributed among these distances:
20 14 0.37
21 19 0.50
22 5 0.13
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (21 bp):
GATACACCCTACTATGGTATC
Found at i:4531 original size:95 final size:94
Alignment explanation
Indices: 4420--4598 Score: 288
Period size: 95 Copynumber: 1.9 Consensus size: 94
4410 ACCCTACTAT
*
4420 GGTATCGATACACCCTTCCGGTATCGATACCAAAATTAGCTTCGAAG-TGCCTTGGTATCGATAT
1 GGTATCGATACACCCTTCCGGTATCGATACCAAAATTAGCTTCGAAGTTACC-TGGTATCGATA-
4484 CCCTCACCATGGTATCAATACTACTATGCTA
64 CCCTCACCATGGTATCAATACTACTATGCTA
* * * *
4515 GGTATTGATACCCCCTTCCGGTATCGATACCAAAATTAGGTTCGATGTTACCTGGTATCGATACC
1 GGTATCGATACACCCTTCCGGTATCGATACCAAAATTAGCTTCGAAGTTACCTGGTATCGATACC
4580 CTCACCATGGTATCAATAC
66 CTCACCATGGTATCAATAC
4599 CACCTCATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
94 21 0.27
95 54 0.69
96 3 0.04
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (94 bp):
GGTATCGATACACCCTTCCGGTATCGATACCAAAATTAGCTTCGAAGTTACCTGGTATCGATACC
CTCACCATGGTATCAATACTACTATGCTA
Found at i:6175 original size:15 final size:16
Alignment explanation
Indices: 6157--6186 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6147 TTGTCGGTTT
6157 TATTTTTT-GTTTTTC
1 TATTTTTTAGTTTTTC
6172 TATTTTTTAGTTTTT
1 TATTTTTTAGTTTTT
6187 TAATAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (16 bp):
TATTTTTTAGTTTTTC
Found at i:8156 original size:24 final size:21
Alignment explanation
Indices: 8129--8175 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
8119 CTCAAATCTG
8129 ACCCTAAATTTAATTAGAAGTTTA
1 ACCCT-AATTTAATTA-AA-TTTA
*
8153 ACCCTAATTTTATTAAATTTA
1 ACCCTAATTTAATTAAATTTA
8174 AC
1 AC
8176 ATAATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 9 0.41
24 5 0.23
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (21 bp):
ACCCTAATTTAATTAAATTTA
Found at i:10005 original size:24 final size:26
Alignment explanation
Indices: 9981--10029 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
9971 CATTTTGTAT
9981 TTAG-TTACAT-ACT-ATTGAAATTA
1 TTAGATTACATAACTAATTGAAATTA
*
10004 TTAGATTACATAATTAATTGAAATTA
1 TTAGATTACATAACTAATTGAAATTA
10030 ATATCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 2 0.09
26 10 0.45
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (26 bp):
TTAGATTACATAACTAATTGAAATTA
Found at i:10206 original size:3 final size:3
Alignment explanation
Indices: 10198--10237 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
10188 AAATTATATG
* * *
10198 ATA ATA ATA ATA ATA ATA ATA ACA ACA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10238 AAGGCTGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:12952 original size:18 final size:18
Alignment explanation
Indices: 12929--12964 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12919 AAACAGTAAT
12929 TAGGTATTGTTATGCATA
1 TAGGTATTGTTATGCATA
12947 TAGGTATTGTTATGCATA
1 TAGGTATTGTTATGCATA
12965 CATTCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (18 bp):
TAGGTATTGTTATGCATA
Found at i:14283 original size:31 final size:31
Alignment explanation
Indices: 14245--14311 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
14235 TTTTAAACAC
**
14245 TTTGATCCAAGAAGCCAAGTTCAGGTGGCAA
1 TTTGATCCAAGAAGCCAAGTTCAGGTACCAA
*
14276 TTTGATCCAAGAAGCCAAGTTTAGGTACCAA
1 TTTGATCCAAGAAGCCAAGTTCAGGTACCAA
14307 TTTGA
1 TTTGA
14312 ATCTTAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (31 bp):
TTTGATCCAAGAAGCCAAGTTCAGGTACCAA
Found at i:24285 original size:89 final size:89
Alignment explanation
Indices: 24133--24311 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
24123 ACCCTTCTCC
*
24133 TCCATGACAGGCTCCAGCCTTTCAAACCAGAAAGACAATGCCTCCCACTTGTCCTCCATCGCTGC
1 TCCATGACAGGCTCCAGCCTTTCAAACCAGAAAGACAATGCCTCCCACTTGTCCTCCACCGCTGC
24198 AACTTTCTCCTCCACGGACTTAAA
66 AACTTTCTCCTCCACGGACTTAAA
24222 TCCATGACAGGCTCCAGCCTTTCAAACCAGAAAGACAATGCCTCCCACTTGTCCTCCACCGCTGC
1 TCCATGACAGGCTCCAGCCTTTCAAACCAGAAAGACAATGCCTCCCACTTGTCCTCCACCGCTGC
24287 AACTTTCTCCTCCACGGACTTAAA
66 AACTTTCTCCTCCACGGACTTAAA
24311 T
1 T
24312 ACAATCAGAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.23
Consensus pattern (89 bp):
TCCATGACAGGCTCCAGCCTTTCAAACCAGAAAGACAATGCCTCCCACTTGTCCTCCACCGCTGC
AACTTTCTCCTCCACGGACTTAAA
Found at i:30046 original size:55 final size:55
Alignment explanation
Indices: 29980--30089 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
29970 ATCGTCAACC
29980 CAAAGCTTCTCACTGATTTTTTCTATTCACCCAATCCTTTAGCTCTCTCTGTTAT
1 CAAAGCTTCTCACTGATTTTTTCTATTCACCCAATCCTTTAGCTCTCTCTGTTAT
30035 CAAAGCTTCTCACTGATTTTTTCTATTCACCCAATCCTTTAGCTCTCTCTGTTAT
1 CAAAGCTTCTCACTGATTTTTTCTATTCACCCAATCCTTTAGCTCTCTCTGTTAT
30090 TTTTATGTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.20, C:0.29, G:0.07, T:0.44
Consensus pattern (55 bp):
CAAAGCTTCTCACTGATTTTTTCTATTCACCCAATCCTTTAGCTCTCTCTGTTAT
Found at i:33865 original size:21 final size:21
Alignment explanation
Indices: 33831--33870 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33821 TGTTGTATAT
*
33831 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
33851 AGCCGTTTGGAGATGATTTT
1 AGCCG-TTGGAGATGATTTT
33871 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:34004 original size:20 final size:21
Alignment explanation
Indices: 33979--34046 Score: 86
Period size: 20 Copynumber: 3.3 Consensus size: 21
33969 TTCGTGTATG
33979 GATGCACA-ACAGGATGCATC
1 GATGCACAGACAGGATGCATC
* **
33999 GATGCACAGCCTTGATGCATC
1 GATGCACAGACAGGATGCATC
*
34020 GATGCACAGA-AGGATGTATC
1 GATGCACAGACAGGATGCATC
34040 GATGCAC
1 GATGCAC
34047 TAATTGCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 22 0.55
21 18 0.45
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
GATGCACAGACAGGATGCATC
Found at i:34136 original size:21 final size:21
Alignment explanation
Indices: 34068--34165 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
34058 GGTGTTTGAG
*
34068 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
* * *
34088 TGTATAGATGCACT--AGTGCA
1 TGCATGGATGCACTGCAG-GGA
34108 TGTGCATGGATGCACTGCAGGGA
1 --TGCATGGATGCACTGCAGGGA
*
34131 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
34152 TGCATGGATGCACT
1 TGCATGGATGCACT
34166 TTGACACCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 12 0.19
21 34 0.53
22 12 0.19
23 2 0.03
24 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:34266 original size:29 final size:29
Alignment explanation
Indices: 34245--34302 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
34235 AAACTTTGAA
34245 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
34274 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
34303 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:34292 original size:30 final size:30
Alignment explanation
Indices: 34245--34304 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
34235 AAACTTTGAA
34245 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
34274 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
34305 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:36937 original size:41 final size:41
Alignment explanation
Indices: 36892--36974 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
36882 CTAGTCGTTG
* * *
36892 CAGCCTTCG-TGCATGGATGCACAGCATGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGAAAGATGCATCGATGCA
* *
36933 CAGCCTTGATTCATCGATGTACAGAAAGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAAGATGCATCGATGCA
36974 C
1 C
36975 TAATTGCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAAGATGCATCGATGCA
Found at i:36947 original size:21 final size:20
Alignment explanation
Indices: 36901--36974 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
36891 GCAGCCTTCG
*
36901 TGCATGGATGCACAGCATGA
1 TGCATCGATGCACAGCATGA
*
36921 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CATGA
* * * *
36942 TTCATCGATGTACAGAAAGA
1 TGCATCGATGCACAGCATGA
36962 TGCATCGATGCAC
1 TGCATCGATGCAC
36975 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACAGCATGA
Found at i:37173 original size:29 final size:29
Alignment explanation
Indices: 37152--37209 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
37142 AAACTTTGAA
37152 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
37181 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
37210 TGCCTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:37199 original size:30 final size:30
Alignment explanation
Indices: 37152--37211 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
37142 AAACTTTGAA
37152 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
37181 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
37212 CCTTAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:38301 original size:75 final size:76
Alignment explanation
Indices: 38201--38407 Score: 274
Period size: 75 Copynumber: 2.7 Consensus size: 76
38191 CGTTGAACAT
* ** *
38201 GGGGGAATCGGTACC-CCTGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACA
** *
38265 AAAATGTTTAG
66 AAAACATTCAG
* * *
38276 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACA
*
38340 AAACCATTCAG
66 AAAACATTCAG
* *
38351 GGGGGAATCGGTTCCTCCTATGGGGGGAAATCGGTTCCCTCTGAGTATTCTGGAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGG-AATCGGTTCCCTCCGAGCATTCTGGAATT
38408 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 81 0.70
76 8 0.07
77 26 0.23
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACA
AAAACATTCAG
Found at i:41023 original size:20 final size:20
Alignment explanation
Indices: 40994--41031 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40984 AGAACCCCAG
*
40994 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
41014 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
41032 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:41066 original size:20 final size:21
Alignment explanation
Indices: 41013--41074 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
41003 GATTCCCCTG
41013 TGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGAATCGGTT-CCC-TCAA
*
41036 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGAATCGGTTCCCTCAA
* *
41056 TGGGGGGATCGATTCCCTC
1 TGGGGGAATCGGTTCCCTC
41075 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCTCAA
Found at i:46931 original size:75 final size:75
Alignment explanation
Indices: 46827--47032 Score: 270
Period size: 75 Copynumber: 2.7 Consensus size: 75
46817 CGTTGAACAT
* ** *
46827 GGGGGAATCGGTACC-CCTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
** *
46891 AAATGTTTAG
66 AAACATTCAG
* * *
46901 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
*
46966 AACCATTCAG
66 AAACATTCAG
* *
46976 GGGGGAATCGGTTCCTCCTATGGGGGGAAATCGGTTCCCTCTGAGTATTCTGGAATT
1 GGGGGAATCGGTTCCTCCTAT-GGGGG-AATCGGTTCCCTCCGAGCATTCTGGAATT
47033 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 14 0.12
75 70 0.61
76 5 0.04
77 26 0.23
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAACAA
AAACATTCAG
Found at i:47703 original size:107 final size:109
Alignment explanation
Indices: 47583--47873 Score: 426
Period size: 107 Copynumber: 2.7 Consensus size: 109
47573 CTCTTATTAC
* **
47583 TCGACCTTATGGTGACCTGATCCGGGGTAAGATCCACATTATTATGGTTCTCACTTTGCTAACCA
1 TCGACCTTGTGGTGACCTGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
47648 CT-A-TTTTATTTTATTTTTATATATTTGTTTGCATTATTCGAT
66 CTAACTTTTATTTTATTTTTATATATTTGTTTGCATTATTCGAT
*
47690 TCGACCTTGTGGTGACCCGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
1 TCGACCTTGTGGTGACCTGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
47755 CTAACGTTTTTATTTTATTTTTATATATTTGTTTGCATTATTCGAT
66 CTAAC--TTTTATTTTATTTTTATATATTTGTTTGCATTATTCGAT
* ** * * * * * *
47801 TCGACCTTGTGGTTACCTGAT-TTGGGTAAGATCCACATTATTAAGGTCCAAACTCTACTAACAA
1 TCGACCTTGTGGTGACCTGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
47865 CTAACTTTT
66 CTAACTTTT
47874 CTAACATACT
Statistics
Matches: 166, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
107 63 0.38
108 5 0.03
110 40 0.24
111 58 0.35
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (109 bp):
TCGACCTTGTGGTGACCTGATCCGGGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCA
CTAACTTTTATTTTATTTTTATATATTTGTTTGCATTATTCGAT
Found at i:48178 original size:15 final size:16
Alignment explanation
Indices: 48160--48197 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
48150 ATTCTATTAT
48160 TTTATTTTTCT-GCAC
1 TTTATTTTTCTCGCAC
* *
48175 TTTAATTTTCTCGCAT
1 TTTATTTTTCTCGCAC
48191 TTTATTT
1 TTTATTT
48198 CAATCCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTATTTTTCTCGCAC
Found at i:48193 original size:31 final size:31
Alignment explanation
Indices: 48130--48197 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
48120 TTTTTATTTA
**
48130 TTATTTTTCTCGCACTTTAAATTCTATTATT
1 TTATTTTTCTCGCACTTTAAATTCTAGCATT
* *
48161 TTATTTTTCT-GCACTTTAATTTTCTCGCATT
1 TTATTTTTCTCGCACTTTAA-ATTCTAGCATT
48192 TTATTT
1 TTATTT
48198 CAATCCCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.19, C:0.16, G:0.04, T:0.60
Consensus pattern (31 bp):
TTATTTTTCTCGCACTTTAAATTCTAGCATT
Found at i:48194 original size:16 final size:15
Alignment explanation
Indices: 48158--48242 Score: 50
Period size: 15 Copynumber: 5.7 Consensus size: 15
48148 AAATTCTATT
*
48158 ATTTTATTTTTCTGC
1 ATTTTAATTTTCTGC
*
48173 ACTTTAATTTTCTCGC
1 ATTTTAATTTTCT-GC
*
48189 ATTTT-A-TTTCAATCC
1 ATTTTAATTTTC--TGC
* * *
48204 CTTTTAATTTCCAGC
1 ATTTTAATTTTCTGC
*
48219 A-TTTAATTTTCTGT
1 ATTTTAATTTTCTGC
*
48233 ATTTTCATTT
1 ATTTTAATTT
48243 AAACATCTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
14 15 0.29
15 25 0.49
16 8 0.16
17 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.58
Consensus pattern (15 bp):
ATTTTAATTTTCTGC
Found at i:49629 original size:32 final size:32
Alignment explanation
Indices: 49593--49663 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
49583 CTAAACCTGA
49593 ACCCGAATATCACACTTAAAAAAACC-GACCCG
1 ACCCGAATATCACACTT-AAAAAACCTGACCCG
*
49625 ACCCGAATATCACACTTAAAAAACCTGACCTG
1 ACCCGAATATCACACTTAAAAAACCTGACCCG
49657 ACCCGAA
1 ACCCGAA
49664 CCGAACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.42, C:0.34, G:0.10, T:0.14
Consensus pattern (32 bp):
ACCCGAATATCACACTTAAAAAACCTGACCCG
Found at i:56616 original size:139 final size:139
Alignment explanation
Indices: 56464--56736 Score: 361
Period size: 139 Copynumber: 2.0 Consensus size: 139
56454 TAAATCATCC
56464 CTAAAGACAGCTAGACATCCTCAACA-AAAAGGAACAATGTCGTCCACCGACCATATCTCCTCAA
1 CTAAAGACAGCTAGACATCCTCAACACAAAA-GAACAATGTCGTCCACCGACCATATCTCCTCAA
* * ** * * *
56528 TATGAAGGAGCATTGTCATCATCAGAAAACCAGACTTCCTCAATGCGAAGAAATCGTGTTGTCTC
65 CACGAAGGAGCAGCGTCATCATCAGAAAA-CAAACTTCCTCAATGCAAAGAAATCGTATTGTCTC
56593 CAAATTTTCTT
129 CAAATTTTCTT
* * * * *
56604 CTAAA-ACGGCTAGACTTGCTCAACACGAAAGAACAATGTCGTCCACTGACCATATCTCCTCAAC
1 CTAAAGACAGCTAGACATCCTCAACACAAAAGAACAATGTCGTCCACCGACCATATCTCCTCAAC
* * * * *
56668 GCGAAGGAGCAGCGTCATCCTCAGATAACAAACTTCCTCAATGCAAAGGAATCGTATTGTCTCTA
66 ACGAAGGAGCAGCGTCATCATCAGAAAACAAACTTCCTCAATGCAAAGAAATCGTATTGTCTCCA
56733 AATT
131 AATT
56737 ATCCAAATTG
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 36 0.31
139 71 0.62
140 8 0.07
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (139 bp):
CTAAAGACAGCTAGACATCCTCAACACAAAAGAACAATGTCGTCCACCGACCATATCTCCTCAAC
ACGAAGGAGCAGCGTCATCATCAGAAAACAAACTTCCTCAATGCAAAGAAATCGTATTGTCTCCA
AATTTTCTT
Found at i:57056 original size:122 final size:122
Alignment explanation
Indices: 56798--57092 Score: 398
Period size: 122 Copynumber: 2.4 Consensus size: 122
56788 CGACCAGAAC
* * *
56798 TCTTCAACATGGATGAGCACTGTCGTCTTTAGCACCAAATTATCTCTAGATTGACCTAACTTCCT
1 TCTTCAACATGGATGAGCACTGTCGTCTTCAACACCAAATTATCTCCAGATTGACCTAACTTCCT
* * *
56863 CAACGAGAAAAACATCGTCATCTTTAACAAACAATTTATTTGAAAGCGATCAGATCT
66 CAACGAGAAAAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
* * * * *
56920 T-TTCAACACGGATGAGTA-TAGTTGTCTTCAACACCAAATTATCTCCAGATTGACCTGATTTCC
1 TCTTCAACATGGATGAGCACT-GTCGTCTTCAACACCAAATTATCTCCAGATTGACCTAACTTCC
* * *
56983 TCAATGAGAAGGAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATTAGAT-T
65 TCAACGAGAA-AAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
* * *
57041 TCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAAGTTATATCCAGATT
1 TCTTCAACATGGATGAGCACTGTCGTCTTCAACACCAAATTATCTCCAGATT
57093 AACTTGAAGT
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
120 1 0.01
121 63 0.42
122 85 0.57
123 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (122 bp):
TCTTCAACATGGATGAGCACTGTCGTCTTCAACACCAAATTATCTCCAGATTGACCTAACTTCCT
CAACGAGAAAAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
Found at i:57127 original size:122 final size:121
Alignment explanation
Indices: 56798--57129 Score: 395
Period size: 122 Copynumber: 2.7 Consensus size: 121
56788 CGACCAGAAC
* * *
56798 TCTTCAACATGGATGAGCACTGTCGTCTTTAGCACCAAATTATCTCTAGATTGACCT-AACTTCC
1 TCTTCAACATGGATGAGCA-TGTCGTCTTCAACACCAAATTATCTCCAGATTGACCTGAA-TTCC
* * *
56862 TCAACGAGAA-AAACATCGTCATCTTTAACAAACAATTTATTTGAAAGCGATCAGATCT
64 TCAAC-AGAAGAAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
* * * *
56920 T-TTCAACACGGATGAGTATAGTTGTCTTCAACACCAAATTATCTCCAGATTGACCTGATTTCCT
1 TCTTCAACATGGATGAGCAT-GTCGTCTTCAACACCAAATTATCTCCAGATTGACCTGAATTCCT
* * *
56984 CAATGAGAAGGAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATTAGAT-T
65 CAA-CAGAAGAAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
* * * * *
57041 TCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAAGTTATATCCAGATTAACTTGAAGTCCT
1 TCTTCAACATGGATGAGCA-TGTCGTCTTCAACACCAAATTATCTCCAGATTGACCTGAATTCCT
57106 CAACATGAAGAAACAAT-GTCATCT
65 CAACA-GAAGAAAC-ATCGTCATCT
57130 CTGAATCCTC
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
120 1 0.01
121 62 0.35
122 112 0.63
123 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (121 bp):
TCTTCAACATGGATGAGCATGTCGTCTTCAACACCAAATTATCTCCAGATTGACCTGAATTCCTC
AACAGAAGAAACATCGTCATCTTCAACAAACAATTTATCTGAAAGCAATCAGATCT
Found at i:58094 original size:29 final size:29
Alignment explanation
Indices: 58062--58123 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
58052 TTATGATGTG
**
58062 TTATCTAATTGCATATTAATTACTAACTT
1 TTATCTAATTGCATATTAACCACTAACTT
* * * *
58091 TTATTTTATTGCGTATTAGCCACTAACTT
1 TTATCTAATTGCATATTAACCACTAACTT
58120 TTAT
1 TTAT
58124 TTTCTTGCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (29 bp):
TTATCTAATTGCATATTAACCACTAACTT
Found at i:58151 original size:4 final size:4
Alignment explanation
Indices: 58142--58170 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
58132 TTTCTAACCA
58142 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
58171 GTTTCTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:58273 original size:122 final size:122
Alignment explanation
Indices: 58145--58402 Score: 292
Period size: 122 Copynumber: 2.1 Consensus size: 122
58135 CTAACCATTA
* * * * *
58145 TTTATTTATTTATTTATTTATTTATTGTTT-CTCTTATT-ACTCGACCTTATGGTGACCCGGTCC
1 TTTATTTATTT-TTTATATATAT-TTGTTTGC-ATTATTCACTCAACCTTATGGTGACCCGATCC
* *
58208 GAGGTAAGATCCACATTATTATGGTTCGGACTTTGCTAACTACTAAATTTTTTA-TTTA-T
63 GAGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCACT-AATTTTTTATTTTATT
* * * * *
58267 TTTATTT-TATTTTTATATATATTTGTTTGCATTATTCGATTCAATCTTGTGGTGACTCGATCTG
1 TTTATTTAT-TTTTTATATATATTTGTTTGCATTATTC-ACTCAACCTTATGGTGACCCGATCCG
* *
58331 GGGTCAGATCCACATTATTATGGTTCGAACTTTGCTAACCACTAATTTTTTATTTTATT
64 AGGTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCACTAATTTTTTATTTTATT
*
58390 TTTATATATTTTT
1 TTTATTTATTTTT
58403 GCATTATTAG
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
120 11 0.10
121 20 0.18
122 71 0.62
123 11 0.10
124 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (122 bp):
TTTATTTATTTTTTATATATATTTGTTTGCATTATTCACTCAACCTTATGGTGACCCGATCCGAG
GTAAGATCCACATTATTATGGTTCGAACTTTGCTAACCACTAATTTTTTATTTTATT
Found at i:58459 original size:108 final size:112
Alignment explanation
Indices: 58266--58479 Score: 305
Period size: 108 Copynumber: 1.9 Consensus size: 112
58256 TTTTTATTTA
*
58266 TTTTATTTTATTTTTATATATATTTGTTTGCATTATTCGATTCAATCTTGTGGTGACTCGATCTG
1 TTTTATTTTATTTTTATATATATTTGTTTGCATTATTAGATTCAATCTTGTGGTGACTCGATCTG
* * * * *
58331 GGGTCAGATCCACATTATTATGGTTC-GAACTTTGCTAACCACTAATT
66 GGATAAAATCCACATTATTATGATTCAG-ACTCTGCTAACCACTAATT
*
58378 TTTTATTTTA-TTTT-TATATA-TT-TTTGCATTATTAGATTCGA-CATTGTGGTGACTCGATCT
1 TTTTATTTTATTTTTATATATATTTGTTTGCATTATTAGATTCAATC-TTGTGGTGACTCGATCT
58438 GGGATAAAATCCACATTATTATGATTCAGACTCTGCTAACCA
65 GGGATAAAATCCACATTATTATGATTCAGACTCTGCTAACCA
58480 TTAACATCTA
Statistics
Matches: 93, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
107 1 0.01
108 69 0.74
109 3 0.03
110 6 0.06
111 4 0.04
112 10 0.11
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.45
Consensus pattern (112 bp):
TTTTATTTTATTTTTATATATATTTGTTTGCATTATTAGATTCAATCTTGTGGTGACTCGATCTG
GGATAAAATCCACATTATTATGATTCAGACTCTGCTAACCACTAATT
Found at i:58551 original size:32 final size:32
Alignment explanation
Indices: 58500--58596 Score: 104
Period size: 35 Copynumber: 2.9 Consensus size: 32
58490 ACTTTTCTAA
* *
58500 CATACTAATATTCTAACTTTTATTTTATTGTT
1 CATACTAACATACTAACTTTTATTTTATTGTT
*
58532 CATACTAACATACTGACTTTTTTATTTTTATTGTT
1 CATACTAACATACTAAC--TTTTA-TTTTATTGTT
* * * *
58567 CTTATTAACTTACTAACATTTATTTTATTG
1 CATACTAACATACTAACTTTTATTTTATTG
58597 CACAAACTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
32 22 0.41
33 4 0.07
34 5 0.09
35 23 0.43
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (32 bp):
CATACTAACATACTAACTTTTATTTTATTGTT
Found at i:58799 original size:15 final size:16
Alignment explanation
Indices: 58781--58818 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
58771 ATTCCAGTAT
58781 TTTATTTTTCT-GCAC
1 TTTATTTTTCTCGCAC
* *
58796 TTTAATTTTCTCGCAT
1 TTTATTTTTCTCGCAC
58812 TTTATTT
1 TTTATTT
58819 CAGTCCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTATTTTTCTCGCAC
Found at i:59683 original size:21 final size:21
Alignment explanation
Indices: 59657--59702 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
59647 GATTTCTGGG
* *
59657 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
59678 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
59699 CAAG
1 CAAG
59703 CGAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:59773 original size:23 final size:22
Alignment explanation
Indices: 59729--59773 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59719 AATGTCATGG
*
59729 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
59751 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
59774 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:61204 original size:31 final size:31
Alignment explanation
Indices: 61078--61205 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
61068 AGAGTCGAGG
*
61078 GTTTACCTATGTTCTACGGAATATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
61109 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
61141 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
61172 GTTTACCTAGGTTCTTCGGGACCTATGAACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
61203 GTT
1 GTT
61206 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:61225 original size:30 final size:30
Alignment explanation
Indices: 61191--61255 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
61181 GGTTCTTCGG
61191 GACCTATGAACAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
* * *
61221 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
61251 GACCT
1 GACCT
61256 CTGGATAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (30 bp):
GACCTATGAACAGTTACCGAGGATCTTTAT
Found at i:61256 original size:30 final size:30
Alignment explanation
Indices: 61202--61263 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
61192 ACCTATGAAC
61202 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
61232 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
61262 AG
1 AG
61264 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:70980 original size:20 final size:20
Alignment explanation
Indices: 70952--70994 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
70942 CTTATTCCAT
70952 AATAATTATTTAATAAAATA
1 AATAATTATTTAATAAAATA
* * *
70972 AATATTTATTTTATTAAATA
1 AATAATTATTTAATAAAATA
70992 AAT
1 AAT
70995 CTAATTACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTATTTAATAAAATA
Found at i:72515 original size:64 final size:65
Alignment explanation
Indices: 72389--72517 Score: 179
Period size: 64 Copynumber: 2.0 Consensus size: 65
72379 TAGTCTCAAT
* * * *
72389 TCAACACAAGATGTTCATATTAAAAATATCACACAAGAGTATCAAATCTCAATAATACAATAAAA
1 TCAACACAAGATGTTCAAAATAAAAATATCACACAAGAGTATCAAATCTCAACAACACAATAAAA
* * * *
72454 TCAACATAAGATGTTCAAAAT-AAAATATCACACAAGAGTATCAAGTCTTAACAACATAATAAAA
1 TCAACACAAGATGTTCAAAATAAAAATATCACACAAGAGTATCAAATCTCAACAACACAATAAAA
72518 GAGGTAGTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 38 0.68
65 18 0.32
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (65 bp):
TCAACACAAGATGTTCAAAATAAAAATATCACACAAGAGTATCAAATCTCAACAACACAATAAAA
Found at i:73873 original size:21 final size:21
Alignment explanation
Indices: 73847--73888 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
73837 TCACAAGAGT
73847 TCGAACTTTCATAATGGAAAA
1 TCGAACTTTCATAATGGAAAA
73868 TCGAACTTTCATAATGGAAAA
1 TCGAACTTTCATAATGGAAAA
73889 ATCAAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
TCGAACTTTCATAATGGAAAA
Found at i:76964 original size:22 final size:22
Alignment explanation
Indices: 76937--76989 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
76927 TTTCGATTCT
*
76937 AATGGAGTTTGATTACTTCTAA
1 AATGGAATTTGATTACTTCTAA
76959 AATGGAATTTGATTACTTCTAA
1 AATGGAATTTGATTACTTCTAA
76981 AATGGAATT
1 AATGGAATT
76990 ATGCAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (22 bp):
AATGGAATTTGATTACTTCTAA
Found at i:80030 original size:51 final size:52
Alignment explanation
Indices: 79952--80086 Score: 175
Period size: 53 Copynumber: 2.6 Consensus size: 52
79942 TATTTTATTG
* * * *
79952 TGTGATA-TTTTATTTTGAACATGTTGTGTTG-TTGAGATTTAGTACTCTTT
1 TGTGATATTTTTATTTTGAACATCTTGTGTTGATTGAGACTTAATACTCTTA
* *
80002 TGTGATATTTTTAATATGAACATCTTGTGTTGATTTGAGACTTAATACTCTTA
1 TGTGATATTTTTATTTTGAACATCTTGTGTTGA-TTGAGACTTAATACTCTTA
* *
80055 TGTAATATTTTTATTTTGCACATCTTGTGTTG
1 TGTGATATTTTTATTTTGAACATCTTGTGTTG
80087 GTTTATTGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
50 7 0.10
51 21 0.29
53 44 0.61
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (52 bp):
TGTGATATTTTTATTTTGAACATCTTGTGTTGATTGAGACTTAATACTCTTA
Found at i:84359 original size:15 final size:14
Alignment explanation
Indices: 84341--84376 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
84331 TCAAAATTAT
84341 TATATATCATATGCA
1 TATATATCATAT-CA
*
84356 TATATATCTTATCA
1 TATATATCATATCA
84370 TATATAT
1 TATATAT
84377 TATGTTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (14 bp):
TATATATCATATCA
Found at i:85404 original size:29 final size:29
Alignment explanation
Indices: 85319--85420 Score: 134
Period size: 29 Copynumber: 3.5 Consensus size: 29
85309 TTTCATTTAA
* *
85319 GTATCTAAAGTA-TTTTTAGTCAAAATAA
1 GTATCTAAAATATTTTTTAGTCAAAATAG
* *
85347 GTACCTAAAATTATCTTTTTGGTCAAAATAG
1 GTATCTAAAA-TAT-TTTTTAGTCAAAATAG
85378 GTATCTAAAATATTTTTTAGTCAAAATAG
1 GTATCTAAAATATTTTTTAGTCAAAATAG
*
85407 GTATCTAAAGTATT
1 GTATCTAAAATATT
85421 CAATTTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 8 0.12
29 30 0.47
30 3 0.05
31 23 0.36
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (29 bp):
GTATCTAAAATATTTTTTAGTCAAAATAG
Found at i:85734 original size:17 final size:18
Alignment explanation
Indices: 85714--85755 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
85704 ATTTTTAAAA
85714 TATTA-AAATAAT-TTATT
1 TATTATAAA-AATATTATT
85731 TATTATAAAAATATTATT
1 TATTATAAAAATATTATT
85749 T-TTATAA
1 TATTATAA
85756 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTATAAAAATATTATT
Found at i:85837 original size:34 final size:35
Alignment explanation
Indices: 85799--85864 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
85789 TTATTTACTA
*
85799 AATTAATAT-TTTTATATTATATTT-TTAAAATGTT
1 AATTAATATATTTTA-AATATATTTATTAAAATGTT
* *
85833 AATTAGTATATTTTAAATATCTTTATTAAAAT
1 AATTAATATATTTTAAATATATTTATTAAAAT
85865 ATTATTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (35 bp):
AATTAATATATTTTAAATATATTTATTAAAATGTT
Found at i:85860 original size:23 final size:24
Alignment explanation
Indices: 85803--85860 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
85793 TTACTAAATT
* *
85803 AATATTTTTA-TATTATATTTTTA
1 AATATCTTTATTAGTATATTTTTA
* *
85826 AA-ATGTTAATTAGTATA-TTTTA
1 AATATCTTTATTAGTATATTTTTA
85848 AATATCTTTATTA
1 AATATCTTTATTA
85861 AAATATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (24 bp):
AATATCTTTATTAGTATATTTTTA
Found at i:85887 original size:28 final size:29
Alignment explanation
Indices: 85856--85931 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
85846 TAAATATCTT
*
85856 TATTAAAATATTATTAGATT-GTTATTAA
1 TATTAAAATATTATTAGATTCATTATTAA
* * *
85884 TATTAAATATATAAATAATATTCATTATTAA
1 TATTAAA-ATAT-TATTAGATTCATTATTAA
85915 TAATTAATAATATTATT
1 T-ATTAA-AATATTATT
85932 TCTATGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.19
29 4 0.11
30 6 0.16
31 10 0.27
32 9 0.24
33 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (29 bp):
TATTAAAATATTATTAGATTCATTATTAA
Found at i:86037 original size:23 final size:23
Alignment explanation
Indices: 85990--86059 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
85980 ATTATTAAAA
85990 TAAAAATATT-AT-ATTATATTAT
1 TAAAAATATTAATAATTATATT-T
*
86012 TAAAAATATTAATAAATATATTT
1 TAAAAATATTAATAATTATATTT
* *
86035 TAAATATTTTAATAATTAATATTT
1 TAAAAATATTAATAATT-ATATTT
86059 T
1 T
86060 GATTAAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.24
23 17 0.41
24 14 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAAATATTAATAATTATATTT
Found at i:86091 original size:11 final size:11
Alignment explanation
Indices: 86077--86115 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
86067 ATGAAATTAA
86077 AATATTTTATT
1 AATATTTTATT
86088 AATATTTTATT
1 AATATTTTATT
86099 AATATTTTATT
1 AATATTTTATT
86110 AATATT
1 AATATT
86116 AAATTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATATTTTATT
Found at i:86436 original size:32 final size:28
Alignment explanation
Indices: 86367--86451 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 28
86357 AATAGTTTAG
*
86367 GTATTTATTTTGACATAAAATACTTAAT
1 GTATTTATTTTGACAAAAAATACTTAAT
** *
86395 GTACCTATTTTGACTTAAAAAAATAACTTCAT
1 GTATTTATTTTGAC---AAAAAAT-ACTTAAT
*
86427 GTATTTATTTTTGCCCAAAAAATAC
1 GTATTTA-TTTTG-ACAAAAAATAC
86452 GTTAGGTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
28 12 0.27
30 2 0.05
31 13 0.30
32 11 0.25
33 5 0.11
34 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (28 bp):
GTATTTATTTTGACAAAAAATACTTAAT
Found at i:89770 original size:22 final size:22
Alignment explanation
Indices: 89753--89819 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
89743 CTCGTATAAA
89753 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
89775 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
89797 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
89819 T
1 T
89820 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:90154 original size:29 final size:29
Alignment explanation
Indices: 90112--90183 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
90102 TTTTCCGCAT
**
90112 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* * *
90141 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
90170 ATTCATGTCATGTA
1 ATTCATGTCATGTA
90184 TCATAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:90601 original size:67 final size:66
Alignment explanation
Indices: 90485--90634 Score: 203
Period size: 67 Copynumber: 2.3 Consensus size: 66
90475 CTTTTCTCAT
* * * *
90485 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
90550 A
66 A
* * *
90551 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGA
90615 TAA
64 TAA
*
90618 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
90635 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 20 0.27
67 53 0.72
68 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
A
Found at i:90645 original size:67 final size:66
Alignment explanation
Indices: 90486--90656 Score: 186
Period size: 67 Copynumber: 2.6 Consensus size: 66
90476 TTTTCTCATG
* * * *
90486 GGGGAATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
*
90550 AG
65 AA
* * *
90552 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
90616 AAA
64 AAA
* *
90619 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
90657 AACCCAGAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
66 19 0.21
67 65 0.71
68 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATAA
A
Found at i:96723 original size:21 final size:22
Alignment explanation
Indices: 96684--96749 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
96674 CTCGTATAAA
96684 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
96706 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
96727 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
96749 T
1 T
96750 TTGTCCATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.49
22 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:97081 original size:29 final size:29
Alignment explanation
Indices: 97039--97110 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
97029 TTTTCCGCAT
**
97039 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* * *
97068 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
97097 ATTCATGTCATGTA
1 ATTCATGTCATGTA
97111 TCATAATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:97525 original size:66 final size:65
Alignment explanation
Indices: 97410--97558 Score: 192
Period size: 66 Copynumber: 2.3 Consensus size: 65
97400 TTTTTCTCAT
* * * *
97410 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTT-CCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
97475 A
65 A
* * *
97476 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
97540 AA
64 AA
*
97542 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
97559 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
65 7 0.10
66 65 0.89
67 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (65 bp):
GGGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATAA
Found at i:102289 original size:53 final size:54
Alignment explanation
Indices: 102208--102314 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 54
102198 TTATTCCATA
* * *
102208 TGGTTATCTTAAAGGTCGTGATTTAAATATGTTTAAGCAAATGATAGCCTTCAT
1 TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
102262 TGGTT-TCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
1 TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
102315 GTATTATTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
53 45 0.90
54 5 0.10
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (54 bp):
TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
Found at i:104749 original size:20 final size:21
Alignment explanation
Indices: 104724--104775 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
104714 TTTTCCCAAT
*
104724 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
104744 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
104765 TCGCAATGCGA
1 TCGCAATGCGA
104776 TACTGATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:104806 original size:16 final size:17
Alignment explanation
Indices: 104768--104812 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
104758 GGGAAAATCG
*
104768 CAATGCGATACTGATATCG
1 CAATGCGATAC--ATATCA
104787 CAATGCGATAC-TATCA
1 CAATGCGATACATATCA
104803 CAATGCGATA
1 CAATGCGATA
104813 ATACAAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 14 0.56
19 11 0.44
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (17 bp):
CAATGCGATACATATCA
Done.