Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004371.1 Hibiscus syriacus cultivar Beakdansim tig00009575_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: 49045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1146 original size:13 final size:13
Alignment explanation
Indices: 1128--1154 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1118 TCTTCGGGGA
1128 CTTTTTTCTTCTT
1 CTTTTTTCTTCTT
1141 CTTTTTTCTTCTT
1 CTTTTTTCTTCTT
1154 C
1 C
1155 AGGATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTTTCTTCTT
Found at i:1364 original size:24 final size:23
Alignment explanation
Indices: 1326--1379 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1316 CTGAAACATC
*
1326 ATCAAATCCGAGTATTGACCAAT
1 ATCAAATCCGAGTATTGACCAAG
*
1349 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
1373 ATCAAAT
1 ATCAAAT
1380 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:2286 original size:20 final size:20
Alignment explanation
Indices: 2239--2288 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2229 GAGATAATAC
2239 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
2259 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
2279 AAAATCGCAA
1 AAAATCGCAA
2289 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:2527 original size:20 final size:20
Alignment explanation
Indices: 2502--2575 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
2492 CAACGGGGAA
*
2502 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
** **
2522 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-ACT
* *
2542 ATTGCAACGCGAAAATGTCT
1 ATCGCAACGCGAAAATGACT
*
2562 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
2576 TGAAAATCGC
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
19 5 0.13
20 29 0.74
21 5 0.13
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2564 original size:40 final size:40
Alignment explanation
Indices: 2500--2586 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
2490 CGCAACGGGG
*
2500 AAATCGCAACGCGAAAATGGCTATCGCAATTCGAAATGAA
1 AAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAA
* *
2540 AAATTGCAACGCGAAAATGTCTATCGCAATGCGAAATG-A
1 AAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAA
2579 AAATCGCA
1 AAATCGCA
2587 TTTCGATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 8 0.19
40 35 0.81
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAA
Found at i:2623 original size:19 final size:19
Alignment explanation
Indices: 2601--2649 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
2591 GATTTTCTCG
2601 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2620 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2639 TTGCGATTTTC
1 TTGCGATTTTC
2650 TAGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2805 original size:14 final size:14
Alignment explanation
Indices: 2786--2822 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2776 CATCAATTAA
2786 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2800 ACAAATCATCTTTT
1 ACAAATCAACATTT
2814 ACAAATCAA
1 ACAAATCAA
2823 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:4703 original size:20 final size:19
Alignment explanation
Indices: 4680--4747 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
4670 GAAACTTAAA
4680 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
4700 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4720 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4739 ATCGCAACG
1 ATCGCAACG
4748 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4755 original size:14 final size:14
Alignment explanation
Indices: 4736--4793 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4726 ATGCGAAATG
4736 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4750 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
4766 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4782 AAAATCGCAACG
1 AAAATCGCAACG
4794 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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4778 original size:32 final size:33
Alignment explanation
Indices: 4720--4798 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
4710 GGAAATGGCT
4720 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
4753 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
4785 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
4799 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:4845 original size:14 final size:14
Alignment explanation
Indices: 4826--4883 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4816 TTTCATTTCG
4826 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4840 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4856 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4872 CGTTGCGATTTT
1 CGTTGCGATTTT
4884 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4890 original size:33 final size:32
Alignment explanation
Indices: 4810--4899 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
4800 ACAAATCGCA
*
4810 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
4842 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
4874 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCATTGCGAT
4900 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 37 0.66
33 19 0.34
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:4918 original size:20 final size:19
Alignment explanation
Indices: 4884--4938 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4874 TTGCGATTTT
*
4884 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4903 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4923 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
4939 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:5446 original size:18 final size:18
Alignment explanation
Indices: 5420--5464 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5410 GTCGATCAGA
*
5420 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5438 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5456 TGATGGCTC
1 TGATGGCTC
5465 CCGAAGTGAA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6808 original size:20 final size:20
Alignment explanation
Indices: 6783--6836 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
6773 AATAGTTTCT
6783 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
6803 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
6823 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
6837 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:7097 original size:22 final size:22
Alignment explanation
Indices: 7070--7113 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7060 GATGGAGATA
7070 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
7092 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
7114 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:7387 original size:20 final size:20
Alignment explanation
Indices: 7281--7415 Score: 114
Period size: 20 Copynumber: 6.7 Consensus size: 20
7271 CGCTTTGAAA
*
7281 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
7302 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
7322 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
7342 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
7363 ATCGCATTGCGATAGT-ACGT
1 ATCGCATTGCGATAGTCA-GT
7383 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
7403 ATCGCATTGCGAT
1 ATCGCATTGCGAT
7416 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.06
20 64 0.67
21 24 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:7387 original size:61 final size:61
Alignment explanation
Indices: 7281--7418 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 61
7271 CGCTTTGAAA
* * *
7281 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
* * * * *
7342 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGT-ACGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCA-GAATCGCATTGCGAAAGTCAGT
7403 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
7419 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
60 1 0.02
61 65 0.98
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:7429 original size:61 final size:60
Alignment explanation
Indices: 7322--7456 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 60
7312 GAAAGTCAGA
* * * ** *
7322 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTACGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGAT-GTACGT
* * *
7383 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCATTGCGATTTACTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGATGTACGT
7443 ATTCGCATTGCGAA
1 A-TCGCATTGCGAA
7457 TTGGGAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 5 0.08
61 55 0.89
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (60 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATGTACGT
Found at i:7448 original size:20 final size:21
Alignment explanation
Indices: 7404--7455 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
7394 ATAGTCAGTA
*
7404 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
7425 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
7445 TCGCATTGCGA
1 TCGCATTGCGA
7456 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:13571 original size:27 final size:27
Alignment explanation
Indices: 13541--13627 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
13531 ATGACTCTGT
*
13541 ATCATTCATAATTTAATTCTGTGTTGA
1 ATCATTCATAATTTAATTCTGTGCTGA
*
13568 ATCATTCATAATTTACTTC--TGCTGA
1 ATCATTCATAATTTAATTCTGTGCTGA
* * *
13593 ATCATTCAGAATGTATTTCTGTGCTGA
1 ATCATTCATAATTTAATTCTGTGCTGA
13620 ATCATTCA
1 ATCATTCA
13628 GCACTGTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
25 21 0.40
27 32 0.60
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (27 bp):
ATCATTCATAATTTAATTCTGTGCTGA
Found at i:13640 original size:23 final size:23
Alignment explanation
Indices: 13616--13699 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
13606 TATTTCTGTG
* *
13616 CTGAATCATTCAGCACTGTTTTG
1 CTGAATCAGTCAGCACTGTTTTA
* *
13639 CTGAATCATTCAGCATTGTTTTA
1 CTGAATCAGTCAGCACTGTTTTA
*
13662 CTGAATCAGTCAGCACTATTTTA
1 CTGAATCAGTCAGCACTGTTTTA
13685 CTGAATCAGTCAGCA
1 CTGAATCAGTCAGCA
13700 TTGAATCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (23 bp):
CTGAATCAGTCAGCACTGTTTTA
Found at i:14079 original size:55 final size:56
Alignment explanation
Indices: 14012--14121 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
14002 CGAATCAAAC
14012 GATTTCAGTGGTAAA-TTTTTTTGTTATTCTTTATTATCCTGGGTTCGAGTATCAT
1 GATTTCAGTGGTAAATTTTTTTTGTTATTCTTTATTATCCTGGGTTCGAGTATCAT
*
14067 GATTTCGGTGGTAAATTTTTTTTGTTATTCTTTATTATCCTGGGTTCGAGTATCA
1 GATTTCAGTGGTAAATTTTTTTTGTTATTCTTTATTATCCTGGGTTCGAGTATCA
14122 CGAATGCTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 14 0.26
56 39 0.74
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (56 bp):
GATTTCAGTGGTAAATTTTTTTTGTTATTCTTTATTATCCTGGGTTCGAGTATCAT
Found at i:15847 original size:28 final size:28
Alignment explanation
Indices: 15811--15867 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
15801 TTTAAAAAAT
*
15811 TTGAGTTATTAAAGTTT-TATTTTATAAC
1 TTGAATTATTAAA-TTTATATTTTATAAC
**
15839 TTGAATTATTCGATTTATATTTTATAAC
1 TTGAATTATTAAATTTATATTTTATAAC
15867 T
1 T
15868 CGACTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (28 bp):
TTGAATTATTAAATTTATATTTTATAAC
Found at i:17951 original size:19 final size:19
Alignment explanation
Indices: 17927--17970 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
17917 TTGGGACAAC
*
17927 ATAAAAACGTATGATTTTA
1 ATAAAAACATATGATTTTA
* *
17946 AT-AAAACATATTATTTTT
1 ATAAAAACATATGATTTTA
17964 ATAAAAA
1 ATAAAAA
17971 ATAACGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
ATAAAAACATATGATTTTA
Found at i:21817 original size:23 final size:22
Alignment explanation
Indices: 21786--21847 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
21776 ATTCCCCTAT
*
21786 AGGGAGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTC-A
*
21809 AGGGGGAATCAGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
* *
21831 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
21848 TCTGCACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:21846 original size:22 final size:22
Alignment explanation
Indices: 21765--21847 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
21755 CAGAACCCCC
* *
21765 AGGGGGTATTGATTCCCC-T-A
1 AGGGGGAATCGATTCCCCTTCA
* *
21785 TAGGGAGAATCGGTTCCCCTTCAA
1 -AGGGGGAATCGATTCCCCTTC-A
21809 AGGGGGAATC-AGTTCCCCTTCA
1 AGGGGGAATCGA-TTCCCCTTCA
*
21831 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
21848 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
21 14 0.28
22 16 0.32
23 19 0.38
24 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:31268 original size:22 final size:21
Alignment explanation
Indices: 31226--31265 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31216 GAGTTTATTT
*
31226 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
31247 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
31266 ACAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35172 original size:2 final size:2
Alignment explanation
Indices: 35167--35193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35157 TGTGTGTGTG
35167 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35194 TATGGAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36208 original size:23 final size:22
Alignment explanation
Indices: 36173--36222 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
36163 TGCATGAAAC
36173 GTTTTCATCTGTCTCTATGGCAT
1 GTTTTCATCTGTCT-TATGGCAT
* * *
36196 GTTTTCTTTTGTCTTTTGGCAT
1 GTTTTCATCTGTCTTATGGCAT
36218 GTTTT
1 GTTTT
36223 TCAGTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.08, C:0.16, G:0.18, T:0.58
Consensus pattern (22 bp):
GTTTTCATCTGTCTTATGGCAT
Found at i:36499 original size:14 final size:16
Alignment explanation
Indices: 36470--36503 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
36460 TGATCAGATC
36470 TGTTTGTATATTTCTT
1 TGTTTGTATATTTCTT
36486 TGTTTG-AT-TTTCTT
1 TGTTTGTATATTTCTT
36500 TGTT
1 TGTT
36504 AGGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 2 0.11
16 6 0.33
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.71
Consensus pattern (16 bp):
TGTTTGTATATTTCTT
Done.