Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008725.1 Hibiscus syriacus cultivar Beakdansim tig00111787_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: 33097
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:45 original size:18 final size:18
Alignment explanation
Indices: 1--63 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
*
1 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAAT-AA
*
21 TAT-GCAACGCGAAATAA
1 AATCGCAACGCGAAATAA
*
38 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-TAA
57 AATCGCA
1 AATCGCA
64 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.08
18 16 0.43
19 16 0.43
20 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:81 original size:19 final size:19
Alignment explanation
Indices: 59--228 Score: 181
Period size: 19 Copynumber: 9.1 Consensus size: 19
49 GAAACCAAAA
*
59 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
78 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
97 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
116 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
136 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
152 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
169 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
188 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
208 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
227 TC
1 TC
229 AACCAAAAGA
Statistics
Matches: 132, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 3 0.02
19 72 0.55
20 43 0.33
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:226 original size:39 final size:37
Alignment explanation
Indices: 59--228 Score: 170
Period size: 39 Copynumber: 4.5 Consensus size: 37
49 GAAACCAAAA
*
59 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCATT
*
97 TCGCGTTGCGATTTTAATTTCGCAGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGC-GTTGCGATTTTCATT
* **
136 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATT-TCATTTCGCGTTGCGATTTTCATT
* *
169 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGAT-TTCATTT-CGCGTTGCGATTTTCATT
*
208 ATCTCGTTGCGATTTCATTTC
1 -TCGCGTTGCGATTTCATTTC
229 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 12, Indels: 20
0.77 0.08 0.14
Matches are distributed among these distances:
33 26 0.24
35 1 0.01
36 2 0.02
38 25 0.23
39 45 0.41
40 11 0.10
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (37 bp):
TCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCATT
Found at i:2290 original size:21 final size:21
Alignment explanation
Indices: 2266--2332 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2256 TCATTCCTCG
2266 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2287 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2308 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2329 AGAG
1 AGAG
2333 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3698 original size:14 final size:14
Alignment explanation
Indices: 3679--3714 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3669 ATTGTTTAAT
3679 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3693 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3707 TGATTTGT
1 TGATTTGT
3715 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3915 original size:19 final size:19
Alignment explanation
Indices: 3893--4010 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
3883 CGAAATTAAA
3893 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3912 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3927 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3945 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3960 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3978 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3997 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4011 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3939 original size:33 final size:33
Alignment explanation
Indices: 3897--3990 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3887 ATTAAATTCG
3897 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
3930 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3963 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3991 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:7671 original size:14 final size:14
Alignment explanation
Indices: 7652--7688 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
7642 CATCAATTAA
7652 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
7666 ACAAATCATCTTTT
1 ACAAATCAACATTT
7680 ACAAATCAA
1 ACAAATCAA
7689 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:9574 original size:19 final size:18
Alignment explanation
Indices: 9548--9666 Score: 94
Period size: 19 Copynumber: 6.9 Consensus size: 18
9538 ACGAAACTTA
9548 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
9566 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
9587 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
9605 AAAATCGCAA--CG-AA--
1 -AAATCGCAACGCGAAATG
9619 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
9637 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
9651 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
9667 CACAAATCGC
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
13 9 0.11
14 9 0.11
15 2 0.02
16 12 0.14
17 2 0.02
18 11 0.13
19 22 0.27
20 15 0.18
21 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:9623 original size:13 final size:13
Alignment explanation
Indices: 9605--9661 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 13
9595 ATGCGAAATG
9605 AAAATCGCAACGA
1 AAAATCGCAACGA
9618 AAAATCGCAACGCGAA
1 AAAATCGCAA--CG-A
9634 ATGAAATCGCAACGA
1 A--AAATCGCAACGA
9649 CAAAATCGCAACG
1 -AAAATCGCAACG
9662 CGAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 10 0.26
14 11 0.29
15 3 0.08
16 5 0.13
18 9 0.24
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAATCGCAACGA
Found at i:9633 original size:32 final size:32
Alignment explanation
Indices: 9589--9666 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
9579 GGAAATGGCT
*
9589 ATCGCAATGCGAAATGAAAATCGCAACGA-AAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
9621 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
9653 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
9667 CACAAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 12 0.27
32 32 0.73
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:9695 original size:19 final size:17
Alignment explanation
Indices: 9673--9768 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
9663 GAAACACAAA
9673 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
9692 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
9708 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
9724 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
9740 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
9757 TCGCATTGCGAT
1 TCGC-TTGCGAT
9769 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:9714 original size:14 final size:14
Alignment explanation
Indices: 9695--9752 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
9685 TTTCATTTCG
9695 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9709 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
9725 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
9741 CGTTGCGATTTT
1 CGTTGCGATTTT
9753 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9759 original size:33 final size:33
Alignment explanation
Indices: 9678--9768 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
9668 ACAAATCGCA
9678 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
9711 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
9743 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
9769 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:9787 original size:20 final size:19
Alignment explanation
Indices: 9753--9807 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
9743 TTGCGATTTT
*
9753 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
9772 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
9792 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
9808 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:10306 original size:18 final size:18
Alignment explanation
Indices: 10280--10324 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
10270 GTCGATCAGA
*
10280 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
10298 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
10316 TGATGGCTC
1 TGATGGCTC
10325 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:11666 original size:20 final size:20
Alignment explanation
Indices: 11641--11685 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
11631 AATAGTTTCT
11641 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
11661 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
11681 GAAAA
1 GAAAA
11686 ACTAAAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11954 original size:22 final size:22
Alignment explanation
Indices: 11929--11972 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11919 GATTTAGATA
11929 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
11951 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
11973 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:12185 original size:20 final size:20
Alignment explanation
Indices: 12160--12253 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
12150 GATTATGTAT
12160 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12180 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
12200 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
12221 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12241 TATCGCATTGCGA
1 TATCGCGTTGCGA
12254 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:12254 original size:20 final size:20
Alignment explanation
Indices: 12140--12254 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
12130 CGATTTGAAA
*
12140 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
12161 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
12181 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
12201 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
12222 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12242 ATCGCATTGCGAT
1 ATCGCATTGCGAT
12255 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:12273 original size:41 final size:41
Alignment explanation
Indices: 12182--12316 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
12172 AAAGTCAGTA
* * * ** *
12182 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
12222 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
12264 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
12305 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12317 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:12287 original size:20 final size:20
Alignment explanation
Indices: 12243--12335 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
12233 ATAGTCAGTA
* **
12243 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
12264 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
12284 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
12305 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
12325 TCGCATTGCGA
1 TCGCATTGCGA
12336 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:12317 original size:41 final size:41
Alignment explanation
Indices: 12243--12338 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
12233 ATAGTCAGTA
*
12243 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12284 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12325 TCGCATTGCGAATT
1 TCGCATTGCGAATT
12339 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:16955 original size:23 final size:23
Alignment explanation
Indices: 16929--16973 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16919 TATACTCTAA
*
16929 CTCGTGTTACATTTATTAATTAG
1 CTCGTGTTAAATTTATTAATTAG
16952 CTCGTGTTAAATTTATTAATTA
1 CTCGTGTTAAATTTATTAATTA
16974 ACTCTCGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (23 bp):
CTCGTGTTAAATTTATTAATTAG
Found at i:17881 original size:20 final size:20
Alignment explanation
Indices: 17856--17948 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
17846 TTTTCCCAAT
17856 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
17876 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
17896 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
17917 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
17938 TCGCAATGCGA
1 TCGCAATGCGA
17949 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:17898 original size:41 final size:41
Alignment explanation
Indices: 17853--17948 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
17843 CGATTTTCCC
17853 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
17894 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
17935 AAATCGCAATGCGA
1 AATTCGCAATGCGA
17949 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:17902 original size:21 final size:20
Alignment explanation
Indices: 17856--17948 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
17846 TTTTCCCAAT
*
17856 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
17876 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
17896 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
17917 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
17938 TCGCAATGCGA
1 TCGCAATGCGA
17949 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:17983 original size:21 final size:20
Alignment explanation
Indices: 17934--17984 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17924 GCGAATTGGG
* *
17934 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
17954 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
17975 AAAATCGCAA
1 AAAATCGCAA
17985 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:18004 original size:20 final size:21
Alignment explanation
Indices: 17979--18030 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
17969 TAATAAAAAA
*
17979 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTAACTT
17999 TCGCAAC-ACGATACTAACTT
1 TCGCAACGACGATACTAACTT
18019 TCGCAACG-CGAT
1 TCGCAACGACGAT
18031 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTAACTT
Found at i:18011 original size:41 final size:41
Alignment explanation
Indices: 17934--18011 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
17924 GCGAATTGGG
* * **
17934 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
17975 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
18012 CTAACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:18575 original size:19 final size:19
Alignment explanation
Indices: 18532--18596 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
18522 CGAGAATGAG
* *
18532 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
18552 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
18571 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
18590 AATCGCA
1 AATCGCA
18597 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:18669 original size:39 final size:38
Alignment explanation
Indices: 18592--18762 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 38
18582 GAAACCAAAA
* *
18592 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
18630 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
* * * **
18669 TCGCGTTGCGA--TT-GTCT-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
** * *
18702 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTAATTT-CGCGTTGCGATTTTCATT
* *
18741 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTAATTTC
18763 AACCAAAAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
33 23 0.21
35 2 0.02
36 4 0.04
37 2 0.02
38 22 0.20
39 39 0.36
40 17 0.16
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:18739 original size:20 final size:19
Alignment explanation
Indices: 18592--18762 Score: 190
Period size: 19 Copynumber: 9.1 Consensus size: 19
18582 GAAACCAAAA
*
18592 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18611 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
18630 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
18649 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
18669 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
18685 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
18702 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
18721 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
18741 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
18761 TC
1 TC
18763 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 68 0.51
20 50 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:20822 original size:42 final size:42
Alignment explanation
Indices: 20762--20884 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
20752 GCCCGACTCG
* * *
20762 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
20804 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
20846 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
20885 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:20842 original size:21 final size:21
Alignment explanation
Indices: 20818--20884 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20808 TCATTCCTCG
20818 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
20839 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
20860 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
20881 AGAG
1 AGAG
20885 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:22258 original size:14 final size:14
Alignment explanation
Indices: 22239--22274 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22229 ATTGTTTAAT
22239 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
22253 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
22267 TGATTTGT
1 TGATTTGT
22275 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:22475 original size:19 final size:19
Alignment explanation
Indices: 22453--22570 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
22443 CGAAATTAAA
22453 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22472 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
22487 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22505 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
22520 -TCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
22538 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
22557 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
22571 GGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 16 0.23
16 6 0.08
17 6 0.08
19 33 0.46
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:22499 original size:33 final size:33
Alignment explanation
Indices: 22457--22550 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
22447 ATTAAATTCG
22457 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
22490 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
22523 CGTTGCAATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
22551 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:24863 original size:12 final size:12
Alignment explanation
Indices: 24846--24870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24836 TCTTCGGGGA
24846 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24858 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24870 C
1 C
24871 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:25074 original size:24 final size:24
Alignment explanation
Indices: 25044--25103 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
25034 TCTGAAACAT
*
25044 CATCAAAATTCGTGTATTGACCAA
1 CATCAAAATTCGGGTATTGACCAA
* *
25068 CATCAAAGTCCGGGTATTGACCAA
1 CATCAAAATTCGGGTATTGACCAA
* *
25092 GATCAAATTTCG
1 CATCAAAATTCG
25104 AATACTGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (24 bp):
CATCAAAATTCGGGTATTGACCAA
Found at i:26253 original size:14 final size:14
Alignment explanation
Indices: 26234--26270 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26224 CATCAATTAA
26234 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26248 ACAAATCATCTTTT
1 ACAAATCAACATTT
26262 ACAAATCAA
1 ACAAATCAA
26271 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28173 original size:20 final size:19
Alignment explanation
Indices: 28138--28204 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
28128 GAAACTTAAA
28138 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
28157 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
28177 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
28196 ATCGCAACG
1 ATCGCAACG
28205 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:28212 original size:14 final size:14
Alignment explanation
Indices: 28193--28250 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
28183 ATGCGAAATG
28193 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
28207 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
28223 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
28239 AAAATCGCAACG
1 AAAATCGCAACG
28251 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:28235 original size:32 final size:33
Alignment explanation
Indices: 28177--28255 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
28167 GGAAATGGCT
*
28177 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
28210 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
28242 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
28256 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:28289 original size:19 final size:19
Alignment explanation
Indices: 28262--28382 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
28252 GAAACACAAA
*
28262 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
28281 TCACGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
28297 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
28313 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
28332 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
28351 TCTGCGTTGCGATAGTCATTT
1 TC-GCGTTGCGATTTTCA-TT
*
28372 TCGTGTTGCGA
1 TCGCGTTGCGA
28383 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
14 11 0.13
16 4 0.05
18 11 0.13
19 33 0.39
20 21 0.25
21 4 0.05
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28881 original size:18 final size:18
Alignment explanation
Indices: 28855--28899 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28845 GTCGATCAGA
*
28855 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
28873 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
28891 TGATGGCTC
1 TGATGGCTC
28900 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:30235 original size:20 final size:20
Alignment explanation
Indices: 30210--30247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30200 AATAGTTTCT
30210 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
30230 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
30248 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:30536 original size:22 final size:22
Alignment explanation
Indices: 30511--30554 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30501 GATTTAGATA
30511 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
30533 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
30555 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:30767 original size:20 final size:20
Alignment explanation
Indices: 30742--30835 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
30732 GATTATGTAT
30742 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
30762 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
30782 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
30803 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
30823 TATCGCATTGCGA
1 TATCGCGTTGCGA
30836 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:30836 original size:20 final size:20
Alignment explanation
Indices: 30722--30836 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
30712 CGCTTTGAAA
*
30722 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
30743 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
30763 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
30783 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
30804 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
30824 ATCGCATTGCGAT
1 ATCGCATTGCGAT
30837 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:30855 original size:41 final size:41
Alignment explanation
Indices: 30764--30898 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
30754 AAAGTCAGTA
* * * ** *
30764 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
30804 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
30846 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
30887 TCGCGTTGCGAT
1 TCGCGTTGCGAT
30899 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:30869 original size:20 final size:20
Alignment explanation
Indices: 30825--30917 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
30815 ATAGTCAGTA
* **
30825 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
30846 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
30866 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
30887 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
30907 TCGCATTGCGA
1 TCGCATTGCGA
30918 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:30899 original size:41 final size:41
Alignment explanation
Indices: 30825--30920 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
30815 ATAGTCAGTA
*
30825 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
30866 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
30907 TCGCATTGCGAATT
1 TCGCATTGCGAATT
30921 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:31615 original size:20 final size:20
Alignment explanation
Indices: 31590--31682 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
31580 TTTTCCCAAT
31590 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
31610 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
31630 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
31651 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
31672 TCGCAATGCGA
1 TCGCAATGCGA
31683 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:31632 original size:41 final size:41
Alignment explanation
Indices: 31587--31682 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
31577 CGATTTTCCC
31587 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
31628 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
31669 AAATCGCAATGCGA
1 AATTCGCAATGCGA
31683 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:31636 original size:21 final size:20
Alignment explanation
Indices: 31590--31682 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
31580 TTTTCCCAAT
*
31590 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
31610 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
31630 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
31651 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
31672 TCGCAATGCGA
1 TCGCAATGCGA
31683 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:31738 original size:20 final size:20
Alignment explanation
Indices: 31713--31759 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
31703 TAATAAAAAA
*
31713 TCGCAACGAGATACTTACTT
1 TCGCAACGAGATACTAACTT
*
31733 TCGCAAC-CGATACTAACTT
1 TCGCAACGAGATACTAACTT
31752 TCGCAACG
1 TCGCAACG
31760 CGATTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTAACTT
Found at i:31746 original size:19 final size:20
Alignment explanation
Indices: 31672--31763 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
31662 ATTGGGAAAA
* * *
31672 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTAACTT
* * ***
31692 TCGCAATGCGATAATAAAAAA
1 TCGCAACGCGATACT-AACTT
* *
31713 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTAACTT
31733 TCGCAAC-CGATACTAACTT
1 TCGCAACGCGATACTAACTT
31752 TCGCAACGCGAT
1 TCGCAACGCGAT
31764 TTACTTAGCG
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
19 17 0.30
20 26 0.46
21 14 0.25
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTAACTT
Found at i:32315 original size:19 final size:19
Alignment explanation
Indices: 32272--32336 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
32262 CGAGAATGAG
* *
32272 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
32292 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
32311 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
32330 AATCGCA
1 AATCGCA
32337 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:32354 original size:19 final size:19
Alignment explanation
Indices: 32332--32501 Score: 181
Period size: 19 Copynumber: 9.1 Consensus size: 19
32322 GAAACCAAAA
*
32332 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32351 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
32370 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
32389 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
32409 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
32425 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
32442 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
32461 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
32481 ATCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
32500 TC
1 TC
32502 AACCAAAAGA
Statistics
Matches: 132, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 3 0.02
19 72 0.55
20 43 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32499 original size:39 final size:37
Alignment explanation
Indices: 32332--32501 Score: 170
Period size: 39 Copynumber: 4.5 Consensus size: 37
32322 GAAACCAAAA
*
32332 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCATT
*
32370 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGC-GTTGCGATTTTCATT
* **
32409 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATT-TCATTTCGCGTTGCGATTTTCATT
* *
32442 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGAT-TTCATTT-CGCGTTGCGATTTTCATT
*
32481 ATCTCGTTGCGATTTCATTTC
1 -TCGCGTTGCGATTTCATTTC
32502 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 12, Indels: 20
0.77 0.08 0.14
Matches are distributed among these distances:
33 26 0.24
35 1 0.01
36 2 0.02
38 25 0.23
39 45 0.41
40 11 0.10
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (37 bp):
TCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCATT
Done.