Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008583.1 Hibiscus syriacus cultivar Beakdansim tig00111517_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: 73233
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:295 original size:66 final size:66
Alignment explanation
Indices: 180--328 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 66
170 TTTTTCTCAT
* * *
180 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
245 A
66 A
* * *
246 GGGGGTATCGGTTCCCCCCCTGGGGGTA-CGATTCCCCTCT-AGCATTCTGGAAATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCT-TAAGCAATCTGGAAATCATATACGA
309 TAA
64 TAA
*
312 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
329 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 67 0.91
67 7 0.09
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
A
Found at i:339 original size:66 final size:66
Alignment explanation
Indices: 181--350 Score: 177
Period size: 66 Copynumber: 2.6 Consensus size: 66
171 TTTTCTCATG
* * * *
181 GGGGAATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
*
245 AG
65 AA
* * *
247 GGGGTATCGGTTCCCCCCCTGGGGGTA-CGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
310 AAA
64 AAA
* *
313 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
351 AACCCAGAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
64 6 0.07
66 67 0.74
67 17 0.19
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATAA
A
Found at i:6384 original size:22 final size:22
Alignment explanation
Indices: 6359--6425 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
6349 GCTCGTATAA
6359 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
6381 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
6403 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
6425 T
1 T
6426 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:6760 original size:29 final size:29
Alignment explanation
Indices: 6718--6789 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
6708 TTTTCCGCAT
**
6718 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* * *
6747 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
6776 ATTCATGTCATGTA
1 ATTCATGTCATGTA
6790 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:7207 original size:66 final size:66
Alignment explanation
Indices: 7092--7240 Score: 210
Period size: 66 Copynumber: 2.3 Consensus size: 66
7082 TTTTTCTCAT
* * * *
7092 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
7157 A
66 A
* * *
7158 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
7222 AA
65 AA
*
7224 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
7241 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 73 0.99
67 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATA
A
Found at i:12064 original size:54 final size:54
Alignment explanation
Indices: 11982--12089 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
11972 TTATTCCATA
* * *
11982 TGGTTATCTTAAAGGTCGTGATTTAAATATGTTTAAGCAAATGATAGCCTTCAT
1 TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
12036 TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
1 TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
12090 GTATTATTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (54 bp):
TGGTTATCTTAAAGATCGTGATTTAAATATGGTTAAGCAAATGATAACCTTCAT
Found at i:14591 original size:20 final size:21
Alignment explanation
Indices: 14566--14617 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
14556 TTTTCCCAAT
*
14566 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
14586 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
14607 TCGCAATGCGA
1 TCGCAATGCGA
14618 TACTGACTAT
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:14631 original size:20 final size:19
Alignment explanation
Indices: 14606--14720 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
14596 AATTGGGAAA
14606 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
14626 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAC-TACT
* * *
14646 ATCACAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
14667 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
14687 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
14707 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
14721 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 45 0.59
21 24 0.32
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:14671 original size:41 final size:41
Alignment explanation
Indices: 14626--14720 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
14616 GATACTGACT
* *
14626 ATCGCAATGCGATACTTACTATCACAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCACAACGCGATAATACAAA
* * * * *
14667 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCACAACGCGATAATACAAA
14708 ATCGCAATGCGAT
1 ATCGCAATGCGAT
14721 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGATACTGACTATCACAACGCGATAATACAAA
Found at i:14916 original size:22 final size:22
Alignment explanation
Indices: 14888--14931 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14878 CACTCTCTCA
**
14888 CCCATCTCCTTCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
14910 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
14932 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:15251 original size:20 final size:20
Alignment explanation
Indices: 15194--15242 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
15184 GTGATTCTCT
**
15194 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
15214 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
15234 TGTTGCGAT
1 CGTTGCGAT
15243 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:15443 original size:25 final size:24
Alignment explanation
Indices: 15389--15443 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
15379 TGTTTATTAT
* *
15389 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
15413 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
15439 TGTTT
1 TGTTT
15444 ATTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:16593 original size:18 final size:18
Alignment explanation
Indices: 16572--16616 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
16562 TCCACTTCGG
*
16572 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
16590 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
16608 GAGCCATCA
1 GAGCCATCA
16617 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:17123 original size:20 final size:20
Alignment explanation
Indices: 17098--17143 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
17088 TAGTTTACTT
*
17098 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
17118 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
17138 TCGCAA
1 TCGCAA
17144 AGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:17152 original size:19 final size:20
Alignment explanation
Indices: 17109--17153 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
17099 CGCAACATGA
*
17109 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAAAGCGG
*
17129 AAATGGCTATCGCAAAGC-G
1 AAATGACTATCGCAAAGCGG
17148 AAATGA
1 AAATGA
17154 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAAAGCGG
Found at i:17159 original size:19 final size:19
Alignment explanation
Indices: 17137--17228 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
17127 GGAAATGGCT
17137 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
17156 ATCGC-AA-CG--A-CAAA
1 ATCGCAAAGCGAAATGAAA
* *
17170 ATCGCAATGCGAAATGATA
1 ATCGCAAAGCGAAATGAAA
*
17189 ATCGC-AA-CG--A-CAAA
1 ATCGCAAAGCGAAATGAAA
*
17203 ATCGCAACGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
17222 ATCGCAA
1 ATCGCAA
17229 TGTGATTTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
14 15 0.28
15 4 0.07
16 4 0.07
17 4 0.07
18 5 0.09
19 22 0.41
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:17172 original size:14 final size:14
Alignment explanation
Indices: 17153--17211 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
17143 AAGCGAAATG
17153 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
17167 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
17183 ATGATAATCGCAACGAC
1 A--A-AATCGCAACGAC
17200 AAAATCGCAACG
1 AAAATCGCAACG
17212 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.53
15 1 0.03
16 4 0.11
17 4 0.11
18 1 0.03
19 8 0.21
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:17182 original size:33 final size:33
Alignment explanation
Indices: 17137--17228 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
17127 GGAAATGGCT
17137 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
* *
17170 ATCGCAATGCGAAATGATAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
*
17203 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAAAGCGAAATGAAAATCGCAA
17229 TGTGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGACAAA
Found at i:17305 original size:20 final size:19
Alignment explanation
Indices: 17271--17326 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
17261 TTGCGATTTT
*
17271 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
17290 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
17310 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
17327 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:17709 original size:15 final size:15
Alignment explanation
Indices: 17689--17718 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17679 CGACTCACCT
17689 GTCATCCCTCAAGAG
1 GTCATCCCTCAAGAG
17704 GTCATCCCTCAAGAG
1 GTCATCCCTCAAGAG
17719 TCCCCTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
GTCATCCCTCAAGAG
Found at i:17778 original size:21 final size:21
Alignment explanation
Indices: 17712--17781 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
17702 AGGTCATCCC
*
17712 TCAAGAGT-CCCCTCCAATCGT
1 TCAAGAGTCCCCCTCC-ACCGT
* * * *
17733 TCAAGAGGCCCCTATCCTCC-C
1 TCAAGAGTCCCC-CTCCACCGT
17754 TCAAGAGTCCCCCTCCACCGT
1 TCAAGAGTCCCCCTCCACCGT
17775 TCAAGAG
1 TCAAGAG
17782 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 5 0.14
21 25 0.68
22 4 0.11
23 3 0.08
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCCTCCACCGT
Found at i:17802 original size:42 final size:43
Alignment explanation
Indices: 17705--17793 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 43
17695 CCTCAAGAGG
* *
17705 TCATCCCTCAAGAGT-CCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCTCCAACCGTTCAAGAGGCCACTA
* *
17747 TCCTCCCTCAAGAGTCCCCCTCC-ACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCTCCAACCGTTCAAGAGGCCACTA
17789 TCATC
1 TCATC
17794 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 34 0.83
43 7 0.17
ACGTcount: A:0.21, C:0.43, G:0.15, T:0.21
Consensus pattern (43 bp):
TCATCCCTCAAGAGTCCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:19374 original size:19 final size:19
Alignment explanation
Indices: 19352--19411 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
19342 GCAACGGGAG
*
19352 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
19371 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
19385 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
19404 AATCGCAA
1 AATCGCAA
19412 CGAGAGAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.23
16 6 0.17
17 5 0.14
19 16 0.46
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:19377 original size:33 final size:33
Alignment explanation
Indices: 19339--19442 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 33
19329 GAAACTGACT
*
19339 ATCGCAACGGGAGAATCGCAATGCAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAATGAAA
* *
19372 ATCGCAACGAAAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAATGAAA
* *
19405 ATCGCAACGAGAGAATCGCAACGCGAAACT-AAA
1 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
19438 ATCGC
1 ATCGC
19443 GTTGCGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
33 60 0.95
34 3 0.05
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCAAAATGAAA
Found at i:19388 original size:14 final size:14
Alignment explanation
Indices: 19371--19427 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19361 GCAAAATGAA
19371 AATCGCAACGAAAG
1 AATCGCAACGAAAG
19385 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
19402 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
19418 AATCGCAACG
1 AATCGCAACG
19428 CGAAACTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 6 0.16
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:19484 original size:33 final size:33
Alignment explanation
Indices: 19442--19535 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
19432 ACTAAAATCG
*
19442 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
19475 CGTTGCGATTTTGATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
19508 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
19536 GGTCAAATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:19534 original size:19 final size:18
Alignment explanation
Indices: 19439--19535 Score: 57
Period size: 19 Copynumber: 5.6 Consensus size: 18
19429 GAAACTAAAA
19439 TCGCGTTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
**
19458 TCGCTTTGCGA--TTC-CC
1 TCGC-TTGCGATTTTCATT
*
19474 TCG-TTGCGATTTTGATT
1 TCGCTTGCGATTTTCATT
**
19491 TCGCATTGCGA--TTC-CC
1 TCGC-TTGCGATTTTCATT
19507 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
19524 TCGCATTGCGAT
1 TCGC-TTGCGAT
19536 GGTCAAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
14 12 0.21
16 11 0.19
17 11 0.19
19 23 0.40
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:19782 original size:20 final size:20
Alignment explanation
Indices: 19754--19804 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
19744 TTTTGATTGC
19754 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
*
19774 CTTTAGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
19794 CTTTCGCAACG
1 CTTTCGCAACG
19805 AGATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:20583 original size:24 final size:24
Alignment explanation
Indices: 20556--20602 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20546 AAATTTAATC
20556 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACCCGGACTTTGATA
* *
20580 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACCCGGACTTTGAT
20603 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACCCGGACTTTGATA
Found at i:20794 original size:12 final size:12
Alignment explanation
Indices: 20777--20801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20767 ATATAATCCT
20777 GAAGAAGAAAAA
1 GAAGAAGAAAAA
20789 GAAGAAGAAAAA
1 GAAGAAGAAAAA
20801 G
1 G
20802 TCACCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:23046 original size:19 final size:19
Alignment explanation
Indices: 23024--23148 Score: 100
Period size: 19 Copynumber: 7.4 Consensus size: 19
23014 GGAAATTACT
23024 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
23043 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
23057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
23076 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
* *
23090 TTCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
23109 ATCGCAA--CG-AGTG--A
1 ATCGCAATGCGAAATGAAA
23123 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
23142 ATCGCAA
1 ATCGCAA
23149 CGCAAATTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 26 0.32
15 4 0.05
16 7 0.09
17 6 0.07
18 4 0.05
19 34 0.42
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:23066 original size:33 final size:33
Alignment explanation
Indices: 23024--23150 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
23014 GGAAATTACT
23024 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
23057 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
23089 TTTCGCAATGCAAAATGAAAATCGCAACGAGTGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
23123 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
23151 CAAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:23131 original size:66 final size:66
Alignment explanation
Indices: 23025--23157 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
23015 GAAATTACTA
* *
23025 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
23090 T
66 T
*
23091 TCGCAATGCAAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
23156 T
66 T
23157 T
1 T
23158 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCAAAT
T
Found at i:23203 original size:19 final size:19
Alignment explanation
Indices: 23179--23244 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
23169 GCGATTCTCT
23179 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
23198 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
23217 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
23236 CATTGCGAT
1 CATTGCGAT
23245 AGTACTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:23204 original size:33 final size:34
Alignment explanation
Indices: 23159--23244 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 34
23149 CGCAAATTTA
* *
23159 ATTTCGCGTTGCGATTC-TCTCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTCGCATTGCGATTTTC
23192 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC--TTCGCATTGCGATTTTC
23230 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
23245 AGTACTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
33 13 0.28
35 3 0.07
36 1 0.02
38 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTCGCATTGCGATTTTC
Found at i:23376 original size:13 final size:15
Alignment explanation
Indices: 23352--23385 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
23342 CATCAATTAA
23352 ACAAATCAAC-TTTT
1 ACAAATCAACTTTTT
23366 ACAAATC-ACTTTTT
1 ACAAATCAACTTTTT
23380 ACAAAT
1 ACAAAT
23386 AAATTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (15 bp):
ACAAATCAACTTTTT
Found at i:24829 original size:42 final size:42
Alignment explanation
Indices: 24744--24832 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
24734 GTGAATCGGG
* *
24744 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* * *
24786 CTCTTGAACGGTGGGATGGGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAACG-ATGACAGGGGC
24828 CTCTT
1 CTCTT
24833 CAATAATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 32 0.80
43 4 0.10
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:25193 original size:94 final size:94
Alignment explanation
Indices: 25081--25271 Score: 346
Period size: 94 Copynumber: 2.0 Consensus size: 94
25071 TATATTTCAA
*
25081 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTT
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
*
25146 AGCAGAATTGGCAGCAACCGAACAAATTT
66 AACAGAATTGGCAGCAACCGAACAAATTT
*
25175 ACTTTCAACCAAAAGACAAATCAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
*
25240 AACAGAATTGGCAGCAACCGAATAAATTT
66 AACAGAATTGGCAGCAACCGAACAAATTT
25269 ACT
1 ACT
25272 AAGCAATCTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (94 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
AACAGAATTGGCAGCAACCGAACAAATTT
Found at i:27009 original size:20 final size:19
Alignment explanation
Indices: 26964--27095 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
26954 TCTTTTGGTT
*
26964 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
26983 GATAATGAGAATTGCAACGC
1 GA-AATGAAAATCGCAACGC
**
27003 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
27023 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
27042 GAAATGAACATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
27059 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
*
27075 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
27094 GA
1 GA
27096 TTTTGGTTTC
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.51
20 28 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:27124 original size:19 final size:19
Alignment explanation
Indices: 27091--27157 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
27081 AAAATCGCAA
**
27091 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
27110 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
* **
27129 TGCAATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
27149 TGCGATTTT
1 TGCGATTTT
27158 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:27702 original size:20 final size:20
Alignment explanation
Indices: 27677--27768 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
27667 GCTATGTAAA
*
27677 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
* *
27697 TCGCATTGCGATTTCCCTAAT
1 TCGCATTGCGATTTACAT-AT
* *
27718 TCGCATTGCGATTTACTTAG
1 TCGCATTGCGATTTACATAT
27738 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
27758 TCGCATTGCGA
1 TCGCATTGCGA
27769 ATTATGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:27742 original size:41 final size:40
Alignment explanation
Indices: 27677--27768 Score: 139
Period size: 41 Copynumber: 2.3 Consensus size: 40
27667 GCTATGTAAA
* * *
27677 TCGCATTGCGATTTACGTATTCGCATTGCGATTTCCCTAAT
1 TCGCATTGCGATTTACGTAGTCGCATTGCGATTTACAT-AT
*
27718 TCGCATTGCGATTTACTTAGTCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACGTAGTCGCATTGCGATTTACATAT
27758 TCGCATTGCGA
1 TCGCATTGCGA
27769 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAGTCGCATTGCGATTTACATAT
Found at i:27789 original size:21 final size:21
Alignment explanation
Indices: 27765--27823 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
27755 TATTCGCATT
*
27765 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
*
27786 GCGAA-TACGTAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
*
27806 GCGAA-TACGTAAATCGCA
1 GCGAATTACGAAAATCGCA
27824 TTGTGATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 31 0.86
21 5 0.14
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:27801 original size:20 final size:20
Alignment explanation
Indices: 27776--27823 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
27766 CGAATTATGA
27776 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
27796 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
27816 AAATCGCA
1 AAATCGCA
27824 TTGTGATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
AAATCGCAACGCGAATACGT
Found at i:27803 original size:61 final size:62
Alignment explanation
Indices: 27672--27803 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 62
27662 ATGGCGCTAT
* * * * * ** *
27672 GTAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTCCCTAATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTACATATTCGCATTGCGAATTACCAAAATCGCAACGCGATATAC
* * **
27734 -TTAGTCGCATTGCGATTTACATATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATAC
1 GTAAATCGCATTGCGATTTACATATTCGCATTGCGAATTACCAAAATCGCAACGCGATATAC
27794 GTAAATCGCA
1 GTAAATCGCA
27804 ACGCGAATAC
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
60 3 0.05
61 52 0.95
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (62 bp):
GTAAATCGCATTGCGATTTACATATTCGCATTGCGAATTACCAAAATCGCAACGCGATATAC
Found at i:27841 original size:20 final size:20
Alignment explanation
Indices: 27818--27869 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
27808 GAATACGTAA
* *
27818 ATCGCATTGTGATAGTAAGT
1 ATCGCATTGCGATAATAAGT
*
27838 ATCGCATTGCGATAATCAGT
1 ATCGCATTGCGATAATAAGT
27858 ATCGCATTGCGA
1 ATCGCATTGCGA
27870 ATTTCCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAATAAGT
Found at i:27888 original size:21 final size:21
Alignment explanation
Indices: 27859--27913 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
27849 ATAATCAGTA
*
27859 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
27880 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
27900 TCGCATTGCGAATT
1 TCGCATTGCGAATT
27914 GGGAAAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGAATTTACCAAT
Found at i:27981 original size:21 final size:21
Alignment explanation
Indices: 27941--27981 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27931 ACTGTAGACA
** *
27941 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
27962 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
27982 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:28524 original size:23 final size:24
Alignment explanation
Indices: 28493--28537 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
28483 ATTTAAATCA
28493 GTAATAAATT-TTGATTTAATTTTT
1 GTAATAAATTGTTGA-TTAATTTTT
28517 GTAA-AAATTGTTGATTAATTT
1 GTAATAAATTGTTGATTAATTT
28538 ATTTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (24 bp):
GTAATAAATTGTTGATTAATTTTT
Found at i:29579 original size:69 final size:69
Alignment explanation
Indices: 29502--29675 Score: 296
Period size: 69 Copynumber: 2.5 Consensus size: 69
29492 AAAATAGAAG
* *
29502 CAACACTAAAACGACTTGATTTGAATAAATTAATTTATTCGAATCAAGTTGAGGCAGCTC-AGAT
1 CAACACTAAAACGACATGATTCGAATAAATTAATTTATTCGAATCAAGTTGAGGCAGCTCGA-AT
29566 ATAAA
65 ATAAA
29571 CAACACTAAAACGACATGATTCGAATAAATTAATTTATTCGAATCAAGTTGAGGCAGCTCGAATA
1 CAACACTAAAACGACATGATTCGAATAAATTAATTTATTCGAATCAAGTTGAGGCAGCTCGAATA
29636 TAAA
66 TAAA
* *
29640 CAACTCTAAAACGACATGATTCAAATAAATTAATTT
1 CAACACTAAAACGACATGATTCGAATAAATTAATTT
29676 TTTAAAATAT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 99 0.99
70 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.28
Consensus pattern (69 bp):
CAACACTAAAACGACATGATTCGAATAAATTAATTTATTCGAATCAAGTTGAGGCAGCTCGAATA
TAAA
Found at i:29787 original size:40 final size:40
Alignment explanation
Indices: 29729--29822 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
29719 AATTTATTTG
* * *
29729 AATTAATTTATTCAAATCAAGTTGAGGCGGGTCGAATATA
1 AATTAATTTATTTAAATCAAGTCGAGACGGGTCGAATATA
*
29769 AATTAATTTATTTGAATCAAGTCGAGACGGGTCGAATATA
1 AATTAATTTATTTAAATCAAGTCGAGACGGGTCGAATATA
29809 AATTAATTTATTTA
1 AATTAATTTATTTA
29823 TTTGGGCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (40 bp):
AATTAATTTATTTAAATCAAGTCGAGACGGGTCGAATATA
Found at i:38419 original size:18 final size:18
Alignment explanation
Indices: 38396--38436 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
38386 AACGTTAAAG
38396 CTTGTGTAATGGAGACAA
1 CTTGTGTAATGGAGACAA
*
38414 CTTGTGTAATGGAGACAG
1 CTTGTGTAATGGAGACAA
38432 CTTGT
1 CTTGT
38437 ATGAGGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (18 bp):
CTTGTGTAATGGAGACAA
Found at i:43761 original size:380 final size:380
Alignment explanation
Indices: 43060--44583 Score: 2985
Period size: 380 Copynumber: 4.0 Consensus size: 380
43050 TAAATCATAG
43060 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
1 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
43125 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
66 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
43190 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
131 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
*
43255 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGCGAAGG
196 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
*
43320 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAAAATTGTCGCGCAATGA
261 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
*
43385 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCAGCTCCATCAACATTCAAAC
326 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
43440 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
1 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
43505 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
66 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
*
43570 AAAGGCAGCATTAGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
131 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
43635 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
196 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
43700 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
261 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
43765 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
326 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
43820 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
1 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
43885 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
66 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
*
43950 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTACACAATTGAATTGGACAAGGAGGA
131 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
**
44015 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCAAGAAGG
196 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
44080 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
261 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
44145 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
326 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
44200 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
1 ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
44265 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
66 AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
44330 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
131 AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
44395 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
196 CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
44460 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
261 CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
44525 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
326 ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
44580 ATGT
1 ATGT
44584 CCGGTCTGGT
Statistics
Matches: 1133, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
380 1133 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (380 bp):
ATGTTCAAGAATGGACAAAGAGAATCAACTAATTTAACGCGAGTGTTCCTTCCCGAGGTGTCCAA
AGAAAGCTAGTTGTCCATGCATTTTGTCAGAGACTATGTATTGCTCTCACCAATGGACAGGAACT
AAAGGCAGCATTGGGGTCTTGTCTTATCTTGATTACTTGTGCACAATTGAATTGGACAAGGAGGA
CTTCAAAGTCATGCAACCAGGCAACTTGGAATCCGTGATATGCAACCCAAAGCTCAGCGTGAAGG
CTATCTATGATTCCAATTATTTTGTTGAAGTGGATGAGACAATTACCAATATTGTCGCGCAATGA
ACACCTACAGAGCCGAATCCCGAGCTTGCTGAGGCTGCTCCATCAACATTCAAAC
Found at i:45016 original size:32 final size:32
Alignment explanation
Indices: 44957--45042 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
44947 TTTTCACCTT
44957 AAACCCGAACCCGACCCAAATACCACACTTAAA
1 AAACCCG-ACCCGACCCAAATACCACACTTAAA
* *
44990 AAACCCGACTCGACCCGAAA-ATCACACTTAAA
1 AAACCCGACCCGACCC-AAATACCACACTTAAA
* *
45022 AAACCCTACCCGACCAAAATA
1 AAACCCGACCCGACCCAAATA
45043 AAGTTTTCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 3 0.07
32 33 0.72
33 10 0.22
ACGTcount: A:0.45, C:0.37, G:0.07, T:0.10
Consensus pattern (32 bp):
AAACCCGACCCGACCCAAATACCACACTTAAA
Found at i:49329 original size:25 final size:26
Alignment explanation
Indices: 49279--49332 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
49269 ATGACCAAAA
* *
49279 AAATTTAAAATATATTTAAGAATATT
1 AAATGTAAAATATATATAAGAATATT
49305 AAATGTAAAA-ATATATAA-AATTATT
1 AAATGTAAAATATATATAAGAA-TATT
49330 AAA
1 AAA
49333 AACGAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 14 0.56
26 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
AAATGTAAAATATATATAAGAATATT
Found at i:56682 original size:22 final size:22
Alignment explanation
Indices: 56628--56684 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
56618 GCAACGCGAT
* *
56628 TTTGAAAAATGCGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
56650 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
56669 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
56685 TTGCGATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 15 0.52
20 2 0.07
21 2 0.07
22 10 0.34
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:56699 original size:22 final size:21
Alignment explanation
Indices: 56640--56718 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 21
56630 TGAAAAATGC
*
56640 GTTGCGATAGTTAAAA-TG-T
1 GTTGCGATAGTGAAAAGTGTT
*
56659 GTTGCGAGAGTTTGAAAAACGTGTT
1 GTTGCGATAG--TG-AAAA-GTGTT
*
56684 GTTGCGATAGTGAAAA-AG-T
1 GTTGCGATAGTGAAAAGTGTT
*
56703 GTTACGATAGTGAAAA
1 GTTGCGATAGTGAAAA
56719 ATCCAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 25 0.51
20 1 0.02
21 1 0.02
22 8 0.16
23 2 0.04
24 2 0.04
25 10 0.20
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.30
Consensus pattern (21 bp):
GTTGCGATAGTGAAAAGTGTT
Found at i:56710 original size:19 final size:19
Alignment explanation
Indices: 56683--56719 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56673 AAAAACGTGT
*
56683 TGTTGCGATAGTGAAAAAG
1 TGTTACGATAGTGAAAAAG
56702 TGTTACGATAGTGAAAAA
1 TGTTACGATAGTGAAAAA
56720 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
TGTTACGATAGTGAAAAAG
Found at i:57176 original size:21 final size:21
Alignment explanation
Indices: 57120--57216 Score: 85
Period size: 19 Copynumber: 4.8 Consensus size: 21
57110 ACCAGTCGTT
* *
57120 GCGAACTTGGACTATTGCAA-
1 GCGAACTTGGAATATCGCAAC
* *
57140 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGAATATCGCAAC
* *
57160 GCGAACTTCGACTATCGCAA-
1 GCGAACTTGGAATATCGCAAC
* *
57180 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGAATATCGCAAC
*
57200 GCGAACTTGGATTATCG
1 GCGAACTTGGAATATCG
57217 AAAAATCGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
19 30 0.52
21 28 0.48
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (21 bp):
GCGAACTTGGAATATCGCAAC
Found at i:57180 original size:40 final size:40
Alignment explanation
Indices: 57120--57216 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 40
57110 ACCAGTCGTT
*
57120 GCGAACTTGGACTATTGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
*
57160 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
*
57200 GCGAACTTGGATTATCG
1 GCGAACTTGGACTATCG
57217 AAAAATCGCG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (40 bp):
GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
Found at i:57528 original size:18 final size:18
Alignment explanation
Indices: 57505--57545 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
57495 GAGTATATTT
57505 TATTTTTAAGTTAAAATA
1 TATTTTTAAGTTAAAATA
*
57523 TATTTTTAAGTTAAGATA
1 TATTTTTAAGTTAAAATA
57541 T-TTTT
1 TATTTT
57546 AAAAGTTACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTTTTAAGTTAAAATA
Found at i:57543 original size:16 final size:17
Alignment explanation
Indices: 57505--57547 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
57495 GAGTATATTT
*
57505 TATTTTTAAGTTAAAATA
1 TATTTTTAAGTT-AAAGA
57523 TATTTTTAAGTT-AAGA
1 TATTTTTAAGTTAAAGA
57539 TATTTTTAA
1 TATTTTTAA
57548 AAGTTACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.50
18 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TATTTTTAAGTTAAAGA
Found at i:57551 original size:18 final size:18
Alignment explanation
Indices: 57505--57558 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
57495 GAGTATATTT
* *
57505 TATTTTTAAGTTAAAATA
1 TATTTTAAAGTTAAGATA
*
57523 TATTTTTAAGTTAAGATA
1 TATTTTAAAGTTAAGATA
*
57541 T-TTTTAAAAGTTACGATA
1 TATTTT-AAAGTTAAGATA
57559 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (18 bp):
TATTTTAAAGTTAAGATA
Found at i:57929 original size:21 final size:21
Alignment explanation
Indices: 57876--57923 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
57866 AATTATTCAA
57876 AAAAATTAAA-TA-TCAAAAAT
1 AAAAATTAAATTACT-AAAAAT
57896 AAAAATTAAATTACTAAAAATT
1 AAAAATTAAATTACTAAAAA-T
57918 AAAAAT
1 AAAAAT
57924 ATATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.40
21 7 0.28
22 8 0.32
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATTAAATTACTAAAAAT
Found at i:58122 original size:14 final size:14
Alignment explanation
Indices: 58103--58132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58093 TTATAAATTC
58103 TTATAAAAATAAAA
1 TTATAAAAATAAAA
*
58117 TTATAAAATTAAAA
1 TTATAAAAATAAAA
58131 TT
1 TT
58133 TATGTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTATAAAAATAAAA
Found at i:58655 original size:12 final size:12
Alignment explanation
Indices: 58634--58668 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58624 CCAAATTAAT
*
58634 TCATCTGTCATA
1 TCATCAGTCATA
58646 TCATCAGTCATA
1 TCATCAGTCATA
*
58658 TCATCAATCAT
1 TCATCAGTCAT
58669 GTAACCATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (12 bp):
TCATCAGTCATA
Done.