Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005191.1 Hibiscus syriacus cultivar Beakdansim tig00011726_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: 81344
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:881 original size:21 final size:20
Alignment explanation
Indices: 857--917 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
847 TGGAATCGGG
857 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGG-C
* * **
878 CTCTTCAATGATGACAGTGGC
1 CTCTTGAATGGTGGGAG-GGC
*
899 CTCTTGAACGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
918 GACTCTCGAG
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.25
Consensus pattern (20 bp):
CTCTTGAATGGTGGGAGGGC
Found at i:1387 original size:20 final size:19
Alignment explanation
Indices: 1362--1425 Score: 78
Period size: 18 Copynumber: 3.4 Consensus size: 19
1352 TAGTTTACTT
*
1362 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
1382 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
1400 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACTAAAA
1418 TCGCAACG
1 TCGCAACG
1426 ACATAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 27 0.68
20 13 0.32
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:1435 original size:14 final size:14
Alignment explanation
Indices: 1416--1471 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1406 CGCGAAATGA
*
1416 AATCGCAACGACAT
1 AATCGCAACGAAAT
1430 AATCGCAATGCGAAAT
1 AATCGCAA--CGAAAT
*
1446 GAAATCGCAACGAAAG
1 --AATCGCAACGAAAT
1462 AATCGCAACG
1 AATCGCAACG
1472 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
16 10 0.28
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAT
Found at i:1443 original size:32 final size:32
Alignment explanation
Indices: 1398--1488 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
1388 CGCGAAACCA
* *
1398 AATCGCAACGCGAAATGAAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAATCGCAACGAAAG
*
1430 AATCGCAATGCGAAATGAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAATCGCAACGAAAG
1462 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATG-AAATCGCAA
1489 TGCGATTTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 45 0.83
33 9 0.17
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGAAAG
Found at i:1453 original size:18 final size:18
Alignment explanation
Indices: 1379--1493 Score: 120
Period size: 18 Copynumber: 6.8 Consensus size: 18
1369 ACGAAACTTA
**
1379 AAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAATG
1397 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
1415 AAATCGCAA--CGACAT-
1 AAATCGCAACGCGAAATG
*
1430 -AATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
1447 AAATCGCAA--CGAAA-G
1 AAATCGCAACGCGAAATG
1462 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
1479 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1494 TTTGGTTTCG
Statistics
Matches: 83, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
14 16 0.19
15 1 0.01
16 20 0.24
17 1 0.01
18 33 0.40
19 12 0.14
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:1455 original size:50 final size:46
Alignment explanation
Indices: 1380--1471 Score: 121
Period size: 50 Copynumber: 1.9 Consensus size: 46
1370 CGAAACTTAA
1380 AATCGCAACGCGAAACCAAATCGCAACGCGAAATGAAATCGCAACGACAT
1 AATCGCAACGCGAAACCAAATCGCAA--CGAAA-G-AATCGCAACGACAT
* **
1430 AATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAACG
1 AATCGCAACGCGAAACCAAATCGCAACGAAAGAATCGCAACG
1472 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 10 0.26
47 1 0.03
48 5 0.13
50 23 0.59
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.11
Consensus pattern (46 bp):
AATCGCAACGCGAAACCAAATCGCAACGAAAGAATCGCAACGACAT
Found at i:1535 original size:33 final size:32
Alignment explanation
Indices: 1489--1579 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
1479 AAAATCGCAA
1489 TGCGATTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTGGTTTCGCGTTGCGATTC-TGTCGT
1521 TGCGATTATGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATT-TGGTTTCGCGTTGCGATTCTGTCGT
**
1554 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGA-TTTGGTTTCGCGTTGCGATT
1580 TTAAGTTCGT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 7 0.13
33 43 0.80
34 4 0.07
ACGTcount: A:0.09, C:0.19, G:0.29, T:0.44
Consensus pattern (32 bp):
TGCGATTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1575 original size:19 final size:19
Alignment explanation
Indices: 1551--1596 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1541 GCGATTCTGT
* *
1551 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAAGTTCG
1570 CGTTGCGATTTTAAGTTCG
1 CGTTGCGATTTTAAGTTCG
*
1589 TGTTGCGA
1 CGTTGCGA
1597 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTAAGTTCG
Found at i:1960 original size:186 final size:187
Alignment explanation
Indices: 1639--2021 Score: 684
Period size: 186 Copynumber: 2.0 Consensus size: 187
1629 TTGAATGGAT
1639 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1704 AGTTAGCAGAATTGGCAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
66 AGTTAGCAGAATTGG-AGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACA
*
1769 AATACTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGC-AA-CGAAC
130 AATACTATTTCACAGTG-TAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAC
1826 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTTAAAGAATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TTAAAGAATACA
1891 CAGTTTAGCAGAATT-G-GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC
65 CAG-TTAGCAGAATTGGAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC
*
1954 AAATACTATTTCACAGTGTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAT
129 AAATACTATTTCACAGTGTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAC
2013 AAATTTACT
1 AAATTTACT
2022 AAGCAATCTA
Statistics
Matches: 190, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
185 31 0.16
186 67 0.35
187 65 0.34
188 16 0.08
189 11 0.06
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (187 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTAGCAGAATTGGAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
ATACTATTTCACAGTGTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAC
Found at i:2049 original size:18 final size:18
Alignment explanation
Indices: 2026--2075 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2016 TTTACTAAGC
2026 AATCTAAGTGAAATGGCT
1 AATCTAAGTGAAATGGCT
2044 AATCTAAGTGAAATGGCT
1 AATCTAAGTGAAATGGCT
2062 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
2076 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (18 bp):
AATCTAAGTGAAATGGCT
Found at i:3734 original size:14 final size:14
Alignment explanation
Indices: 3715--3804 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3705 TTGAAATGAA
3715 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3729 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3746 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3762 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3781 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3795 AATCGCAACG
1 AATCGCAACG
3805 CGAAATAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3752 original size:33 final size:33
Alignment explanation
Indices: 3707--3820 Score: 201
Period size: 33 Copynumber: 3.5 Consensus size: 33
3697 TCTTTTGGTT
3707 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3740 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3773 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3806 GAAATAAAAATCGCA
1 GAAATGAAAATCGCA
3821 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3819 original size:19 final size:19
Alignment explanation
Indices: 3729--3820 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
3719 GCAACGAGAG
* *
3729 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
3748 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3762 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3781 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
3795 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
3814 AATCGCA
1 AATCGCA
3821 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.45
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3869 original size:33 final size:36
Alignment explanation
Indices: 3821--3905 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 36
3811 AAAAATCGCA
**
3821 TGCGATTTTGGTTTCGCGTTGCG-A-T-TCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGAAGTATCTCTCGT
3854 TGCGATTTTCATTTCGCGTTGCGACAGTCATCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGA-AGT-ATCTCTCGT
3892 TGCGATTTTCATTT
1 TGCGATTTTCATTT
3906 ATCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
33 21 0.47
35 1 0.02
36 1 0.02
38 22 0.49
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (36 bp):
TGCGATTTTCATTTCGCGTTGCGAAGTATCTCTCGT
Found at i:3875 original size:19 final size:19
Alignment explanation
Indices: 3851--3905 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
3841 GCGATTCTCT
3851 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** * *
3870 CGTTGCGACAGTCATCTCT
1 CGTTGCGATTTTCATTTCG
3889 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
3906 ATCTCGTTGC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4039 original size:33 final size:33
Alignment explanation
Indices: 3997--4067 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3987 AATACTAACT
3997 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
4030 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
4063 TGAAA
1 TGAAA
4068 TCTAGTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:4292 original size:21 final size:22
Alignment explanation
Indices: 4241--4294 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4231 TGGTTGTGAG
**
4241 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4263 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
4284 GGATTTCTTCG
1 GGATTTCTTCG
4295 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:4464 original size:20 final size:20
Alignment explanation
Indices: 4439--4632 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4429 CTTTAAATAT
4439 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4459 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4481 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4500 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4520 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4540 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4560 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4580 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4600 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4620 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4633 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4626 original size:60 final size:60
Alignment explanation
Indices: 4439--4632 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4429 CTTTAAATAT
**
4439 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
4500 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
4560 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
4620 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4633 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:4649 original size:21 final size:21
Alignment explanation
Indices: 4619--4701 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4609 ATTTTCATAT
*
4619 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4640 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4661 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4682 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4702 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4692 original size:42 final size:43
Alignment explanation
Indices: 4599--4697 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
4589 ATTTATGTGT
* *
4599 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
4640 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
4682 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
4698 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:5255 original size:19 final size:20
Alignment explanation
Indices: 5231--5280 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
5221 AATGACCAAT
5231 AAATCGCAACGCGATAT-CA
1 AAATCGCAACGCGATATACA
* *
5250 AAATCGCAACGCGATTTAGA
1 AAATCGCAACGCGATATACA
5270 AAATCGCAACG
1 AAATCGCAACG
5281 TTAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGATATACA
Found at i:5312 original size:18 final size:19
Alignment explanation
Indices: 5267--5317 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
5257 AACGCGATTT
*
5267 AGAAAATCGCAACGTTAAA
1 AGAAAATCGCAACGGTAAA
*
5286 AGAAAATCGCAACGGTCAA
1 AGAAAATCGCAACGGTAAA
5305 AG-AAATCGCAACG
1 AGAAAATCGCAACG
5318 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
AGAAAATCGCAACGGTAAA
Found at i:5377 original size:20 final size:20
Alignment explanation
Indices: 5352--5559 Score: 389
Period size: 20 Copynumber: 10.4 Consensus size: 20
5342 TTTAGAAGAA
5352 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5372 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5392 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5412 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5432 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5452 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5472 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
5492 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
5512 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
* *
5532 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAG
5552 AATCGCAA
1 AATCGCAA
5560 CGTTGAAAAT
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 184 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:5674 original size:6 final size:6
Alignment explanation
Indices: 5663--5694 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5653 GACACGTATT
5663 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5695 CGAGACGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:6413 original size:6 final size:6
Alignment explanation
Indices: 6402--6454 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
6392 GGTGGGTCGG
6402 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
6450 GTGGT
1 GTGGT
6455 AATACGTGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.34
Consensus pattern (6 bp):
GTGGTC
Found at i:6556 original size:20 final size:20
Alignment explanation
Indices: 6531--6574 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6521 TTTTTAACTA
*
6531 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
6551 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
6571 TTCT
1 TTCT
6575 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:6584 original size:20 final size:20
Alignment explanation
Indices: 6561--6856 Score: 177
Period size: 20 Copynumber: 14.6 Consensus size: 20
6551 TTCTTTTTAA
6561 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
6581 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
6601 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
6621 CATTGCGATTTTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
6641 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
6661 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
6684 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
6704 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
6724 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
6744 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* **
6767 CGTTGCGATTTCTTTTGA-C-
1 CGTTGCGATTT-TCTAAATCG
*** **
6786 CGTTGCGATTTTCTTTTTTAA
1 CGTTGCGATTTTC-TAAATCG
*
6807 CGTTGCGA-TTTCTAAACCG
1 CGTTGCGATTTTCTAAATCG
* *
6826 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
6845 CGTTGCGATTTT
1 CGTTGCGATTTT
6857 ATTGGTCATT
Statistics
Matches: 221, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.00
19 38 0.17
20 136 0.62
21 14 0.06
22 4 0.02
23 28 0.13
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:6607 original size:40 final size:40
Alignment explanation
Indices: 6563--6776 Score: 230
Period size: 40 Copynumber: 5.2 Consensus size: 40
6553 CTTTTTAACG
* * * *
6563 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* * * * *
6603 TTGCGATTCTATAAATCGCATTGCGATTTTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
6643 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
* * *
6686 TTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
* *
6726 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCGCA
6769 TTGCGATT
1 TTGCGATT
6777 TCTTTTGACC
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
40 91 0.62
41 2 0.01
42 4 0.03
43 49 0.34
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCA
Found at i:6725 original size:83 final size:83
Alignment explanation
Indices: 6563--6774 Score: 277
Period size: 83 Copynumber: 2.6 Consensus size: 83
6553 CTTTTTAACG
* * * * * *
6563 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
* * * *
6625 GCGATTTTCTCAGTCGCA
66 GCGATTATATAAATCGCA
* * *
6643 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
6708 GCGATTATATAAATCGCA
66 GCGATTATATAAATCGCA
*
6726 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
6775 TTTCTTTTGA
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 89 0.78
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
GCGATTATATAAATCGCA
Found at i:6789 original size:19 final size:19
Alignment explanation
Indices: 6767--6819 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
6757 TTCTAAATCG
*
6767 CGTTGCGATTTCTTTTGAC
1 CGTTGCGATTTCTTTTGAA
*
6786 CGTTGCGATTTTCTTTTTTAA
1 CGTTGCGA-TTTC-TTTTGAA
6807 CGTTGCGATTTCT
1 CGTTGCGATTTCT
6820 AAACCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.30
20 8 0.27
21 13 0.43
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (19 bp):
CGTTGCGATTTCTTTTGAA
Found at i:6813 original size:83 final size:83
Alignment explanation
Indices: 6543--6837 Score: 235
Period size: 83 Copynumber: 3.6 Consensus size: 83
6533 CTTTTGACCG
* * * * * * * *
6543 TTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATT
1 TTGCGATTTTCTTATTAACATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
* *
6605 GCGATTCTATAAATCGCA
66 GCGATTCTTTTAATCGCA
* * ** * *
6623 TTGCGATTTTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTTTCTTATTAACATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
* * *
6688 GCGACTCTCTCAATCGCA
66 GCGATTCTTTTAATCGCA
* * * * **
6706 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTTTCTTATTAACATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
* *
6771 GCGATTTCTTTTGA-C-CG
66 GCGA-TTCTTTTAATCGCA
* * * *
6788 TTGCGATTTTCTTTTTTAACGTTGCGATTTCTA--AACCGCGTTGCGATTTT
1 TTGCGATTTTC-TTATTAACATTGCGA-TTCTATCAATCGCATTGCGATTTT
6838 GATATCGCGT
Statistics
Matches: 173, Mismatches: 36, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
80 36 0.21
82 28 0.16
83 99 0.57
84 10 0.06
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.41
Consensus pattern (83 bp):
TTGCGATTTTCTTATTAACATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
GCGATTCTTTTAATCGCA
Found at i:6831 original size:19 final size:19
Alignment explanation
Indices: 6807--6856 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6797 TCTTTTTTAA
6807 CGTTGCGATTTCT-AAACCG
1 CGTTGCGATTT-TGAAACCG
* *
6826 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAACCG
6845 CGTTGCGATTTT
1 CGTTGCGATTTT
6857 ATTGGTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTGAAACCG
Found at i:9252 original size:2 final size:2
Alignment explanation
Indices: 9245--9319 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
9235 CCAGCCATTC
9245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9320 GTAACTGAAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24631 original size:23 final size:23
Alignment explanation
Indices: 24564--24650 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
24554 TCATATAAAT
*
24564 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
24587 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
24612 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
24635 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
24651 TATAATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.60
24 2 0.04
25 17 0.33
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:37059 original size:44 final size:41
Alignment explanation
Indices: 36982--37074 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 41
36972 GCAACGCGGT
* *
36982 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGATAG
37023 TTTGAAAAATGTGTTATTGCGATAGTGAAAAAGTGTTGCGATAG
1 TTTGAAAAATGTG---TTGCGATAGTGAAAAAGTGTTGCGATAG
37067 --TGAAAAAT
1 TTTGAAAAAT
37075 CCAAAATAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 13 0.28
42 8 0.17
44 26 0.55
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGATAG
Found at i:37073 original size:19 final size:20
Alignment explanation
Indices: 36984--37074 Score: 114
Period size: 19 Copynumber: 4.4 Consensus size: 20
36974 AACGCGGTTT
36984 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
*
37004 T-TAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
37023 TTTGAAAAATGTGTTATTGCGATAG
1 --TGAAAAATGTG---TTGCGATAG
37048 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
37067 TGAAAAAT
1 TGAAAAAT
37075 CCAAAATAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
19 33 0.53
20 1 0.02
21 1 0.02
22 11 0.18
23 7 0.11
25 9 0.15
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.33
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:39244 original size:19 final size:19
Alignment explanation
Indices: 39208--39246 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39198 GATTTCGTGG
* *
39208 ATATATAAAAATATTTAAA
1 ATATATAAAAAAACTTAAA
*
39227 ATATTTAAAAAAACTTAAA
1 ATATATAAAAAAACTTAAA
39246 A
1 A
39247 AATGGAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATATAAAAAAACTTAAA
Found at i:47901 original size:150 final size:149
Alignment explanation
Indices: 47562--47903 Score: 354
Period size: 150 Copynumber: 2.3 Consensus size: 149
47552 TTATTCTTGG
*
47562 AATCTTTCCCA-CTGATTCGGATTCCGCCTTACTCGAATCATAATAATGTACACCATGCACAGTT
1 AATCTTTCCCATCTGATTCGGATTCCG-CTTACTAGAATCATAATAATGTACACCATGCACAGTT
* * * *
47626 GTTTCATAATCCGATGAAGCAATGGAACTAGATCTCTTAGGATCATCAATGGGATGTTTGAAGGA
65 GTTTCATAATCCAATGAAGCAATGGAACTAGAACTCTTACGATCATCAACGGGATGTTTGAAGGA
* * ** *
47691 AGCTTCACCTGTCATTGTCA
130 AGATTCACCTGCCACCGCCA
* ** * *
47711 AATTTTTTAC-TACTGATTTC-GAGTTCCGCCTACTCA-AATCATGATAATGTACACCATGCACA
1 AATCTTTCCCAT-CTGA-TTCGGA-TTCCGCTTACT-AGAATCATAATAATGTACACCATGCACA
* * * *
47773 GTTGTTTCATATTCCAATGGATCAATGGAACTGGAACTCTTACGATCATCAACGGGATGTTTGAA
62 GTTGTTTCATAATCCAATGAAGCAATGGAACTAGAACTCTTACGATCATCAACGGGATGTTTGAA
***
47838 GGAAGATT-TGTTAGCCACCGCCGA
127 GGAAGATTCACCT-GCCACCGCC-A
* *
47862 AATCTTTCCCATC-GATTCGGATTTCGTCTTGCTAGAATCATA
1 AATCTTTCCCATCTGATTCGGATTCCG-CTTACTAGAATCATA
47904 GTAGAGTTCT
Statistics
Matches: 153, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
149 16 0.10
150 119 0.78
151 17 0.11
152 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (149 bp):
AATCTTTCCCATCTGATTCGGATTCCGCTTACTAGAATCATAATAATGTACACCATGCACAGTTG
TTTCATAATCCAATGAAGCAATGGAACTAGAACTCTTACGATCATCAACGGGATGTTTGAAGGAA
GATTCACCTGCCACCGCCA
Found at i:56505 original size:4 final size:4
Alignment explanation
Indices: 56496--56520 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56486 TTCACATGAA
56496 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
56521 TCTGGCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:62847 original size:49 final size:48
Alignment explanation
Indices: 62775--62869 Score: 172
Period size: 49 Copynumber: 2.0 Consensus size: 48
62765 CCACTAGACT
*
62775 GCAAAATGGTTGAAATAGACAAACGTTAAACCTAACTTAACATGGGACA
1 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTT-ACATGGGACA
62824 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGA
1 GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGA
62870 TACTATCACG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 8 0.18
49 37 0.82
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (48 bp):
GCAAAAAGGTTGAAATAGACAAACGTTAAACCTAACTTACATGGGACA
Found at i:65311 original size:20 final size:20
Alignment explanation
Indices: 65283--65418 Score: 108
Period size: 20 Copynumber: 7.2 Consensus size: 20
65273 ATTAGCAACA
* *
65283 TAATAAAAACTGATTCTATC
1 TAATTAAAACTGATCCTATC
* *
65303 TAATTAAAAATGATCCTATA
1 TAATTAAAACTGATCCTATC
* * *
65323 GAATAAAAACTGATTCTATC
1 TAATTAAAACTGATCCTATC
*
65343 TAATTAAAAATGATCCTATC
1 TAATTAAAACTGATCCTATC
*
65363 TAA-T--AACT-A----ATA
1 TAATTAAAACTGATCCTATC
* * *
65375 GAATAAAAACTGATTCTATC
1 TAATTAAAACTGATCCTATC
65395 TAATTAAAACTGATCCTATC
1 TAATTAAAACTGATCCTATC
65415 TAAT
1 TAAT
65419 ATTTAATTTA
Statistics
Matches: 87, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
12 4 0.05
15 4 0.05
16 2 0.02
17 3 0.03
19 1 0.01
20 73 0.84
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (20 bp):
TAATTAAAACTGATCCTATC
Found at i:65368 original size:40 final size:40
Alignment explanation
Indices: 65282--65368 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
65272 AATTAGCAAC
65282 ATAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
65322 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
65362 CTAATAA
1 ATAATAA
65369 CTAATAGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (40 bp):
ATAATAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
Found at i:65381 original size:52 final size:52
Alignment explanation
Indices: 65320--65419 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
65310 AAATGATCCT
65320 ATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
1 ATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
*
65372 ATAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 ATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
65420 TTTAATTTAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (52 bp):
ATAGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
Found at i:69996 original size:20 final size:20
Alignment explanation
Indices: 69968--70104 Score: 101
Period size: 20 Copynumber: 7.2 Consensus size: 20
69958 ATTAGCAACA
*
69968 TAATAAAAACTGATTCTATC
1 TAATTAAAACTGATTCTATC
* * *
69988 TAATTAAAAATGATCCTATA
1 TAATTAAAACTGATTCTATC
* *
70008 GAATAAAAAACTGATTCTATC
1 TAAT-TAAAACTGATTCTATC
* *
70029 TAATTAAAAATGATTTTATC
1 TAATTAAAACTGATTCTATC
*
70049 TAA-T--AACT-A----ATA
1 TAATTAAAACTGATTCTATC
* *
70061 GAATAAAAACTGATTCTATC
1 TAATTAAAACTGATTCTATC
*
70081 TAATTAAAACTGATCCTATC
1 TAATTAAAACTGATTCTATC
70101 TAAT
1 TAAT
70105 ATTTAATTTA
Statistics
Matches: 87, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
12 4 0.05
15 4 0.05
16 2 0.02
17 3 0.03
19 1 0.01
20 58 0.67
21 15 0.17
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (20 bp):
TAATTAAAACTGATTCTATC
Found at i:70054 original size:41 final size:41
Alignment explanation
Indices: 69967--70105 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 41
69957 AATTAGCAAC
69967 ATAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
* *
70007 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATTTTATCTAAT
1 ATAATAAAAAACTGATTCTATCTAATTAAAAATGA---T-CCT-AT
*
70053 AACTAATAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTAT
1 -A-TAAT---A-AAAAACTGATTCTATCTAATTAAAAATGATCCTAT
*
70100 CTAATA
1 ATAATA
70106 TTTAATTTAG
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
40 4 0.05
41 29 0.36
42 1 0.01
44 1 0.01
45 6 0.07
46 2 0.02
47 3 0.04
48 5 0.06
49 1 0.01
51 1 0.01
52 28 0.35
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (41 bp):
ATAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTAT
Found at i:70084 original size:52 final size:53
Alignment explanation
Indices: 70005--70105 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
69995 AAATGATCCT
**
70005 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATTTTATCTAATAACTA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
*
70058 ATAGAAT-AAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
70106 TTTAATTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (53 bp):
ATAGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTA
Found at i:75250 original size:21 final size:21
Alignment explanation
Indices: 75211--75251 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
75201 TATTATTCCA
*
75211 CTCGACTCGTTGTTCATTAAG
1 CTCGACTCGTTCTTCATTAAG
75232 CTCGACTCGTTACTT-ATTAA
1 CTCGACTCGTT-CTTCATTAA
75252 TCTCACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (21 bp):
CTCGACTCGTTCTTCATTAAG
Found at i:75407 original size:42 final size:39
Alignment explanation
Indices: 75331--75413 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 39
75321 GAGTTTTTTG
*
75331 TATTAAAATAATATTATTAATTAATAATATTTTATTATT
1 TATTAAAATAATATTATTAACTAATAATATTTTATTATT
* * *
75370 TATTAAAATAATAAATTACTTAACTCATTATGTTTTATTATT
1 TATTAAAATAAT--ATTA-TTAACTAATAATATTTTATTATT
75412 TA
1 TA
75414 ATTATTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.32
41 4 0.11
42 21 0.57
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (39 bp):
TATTAAAATAATATTATTAACTAATAATATTTTATTATT
Found at i:75408 original size:39 final size:39
Alignment explanation
Indices: 75323--75408 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 39
75313 TTAGGGTTGA
*
75323 GTTTT-TTGTATTAAAATAATATTATTAATTAATAATAT
1 GTTTTATTGTATTAAAATAATATAATTAATTAATAATAT
* * *
75361 TTTATTATT-TATTAAAATAATA-AATTACTTAACTCATTAT
1 GTT-TTATTGTATTAAAATAATATAATTAATTAA-T-AATAT
75401 GTTTTATT
1 GTTTTATT
75409 ATTTAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
38 10 0.26
39 21 0.54
40 8 0.21
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (39 bp):
GTTTTATTGTATTAAAATAATATAATTAATTAATAATAT
Found at i:78843 original size:23 final size:22
Alignment explanation
Indices: 78820--78862 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
78810 CTAAACAAGC
78820 CCAAAAATCGTATCTGCTAAAG
1 CCAAAAATCGTATCTGCTAAAG
* * *
78842 CCTAGAATCGTATCTTCTAAA
1 CCAAAAATCGTATCTGCTAAA
78863 CTCGCGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (22 bp):
CCAAAAATCGTATCTGCTAAAG
Done.