Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008952.1 Hibiscus syriacus cultivar Beakdansim tig00112280_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: 63771
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8272 original size:20 final size:21
Alignment explanation
Indices: 8247--8314 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
8237 TTTTCCCAAT
*
8247 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
8267 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
8288 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
8309 TCGCAA
1 TCGCAA
8315 CGAGATACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 11 0.29
21 25 0.66
22 2 0.05
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:8357 original size:20 final size:20
Alignment explanation
Indices: 8309--8360 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
8299 TAATAAAAAA
*
8309 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTTACTT
8329 TCGCAACGCGATA-TTGACTT
1 TCGCAACGCGATACTT-ACTT
*
8349 TTGCAACGCGAT
1 TCGCAACGCGAT
8361 TTACATAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATACTTACTT
Found at i:8938 original size:19 final size:19
Alignment explanation
Indices: 8914--8958 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
8904 GGAACGAGAG
* **
8914 AATCGCTACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
8933 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
8952 AATCGCA
1 AATCGCA
8959 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:8976 original size:19 final size:19
Alignment explanation
Indices: 8954--9066 Score: 92
Period size: 20 Copynumber: 6.1 Consensus size: 19
8944 GAAACCAAAA
*
8954 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
8973 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
8987 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
9006 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
9026 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
9045 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
9065 TC
1 TC
9067 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 29 0.38
20 34 0.44
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:11149 original size:21 final size:21
Alignment explanation
Indices: 11125--11191 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11115 TCATTCCTCG
11125 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
11146 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
11167 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
11188 AGAG
1 AGAG
11192 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:11149 original size:42 final size:42
Alignment explanation
Indices: 11069--11191 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
11059 GCCCGACTCG
* * * * * * *
11069 CCTATCATCCCTCAAGATTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
11111 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
11153 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
11192 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:12566 original size:14 final size:14
Alignment explanation
Indices: 12547--12582 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12537 ATTGTTTAAT
12547 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
12561 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
12575 TGATTTGT
1 TGATTTGT
12583 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:12807 original size:33 final size:33
Alignment explanation
Indices: 12765--12957 Score: 334
Period size: 33 Copynumber: 5.8 Consensus size: 33
12755 ATTAAATTCG
*
12765 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* **
12798 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
12831 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
12864 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
12897 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
12930 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
12958 AGTAATTTCC
Statistics
Matches: 151, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
32 2 0.01
33 147 0.97
34 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:12871 original size:14 final size:14
Alignment explanation
Indices: 12852--12939 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
12842 TCATTTCGCA
12852 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
12866 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
12883 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
12899 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
12916 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
12932 TTGCGATT
1 TTGCGATT
12940 TTCATTTCGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:16587 original size:20 final size:20
Alignment explanation
Indices: 16562--16619 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
16552 ATTCATTTGA
*
16562 CTATCGCAACGCGAAAATTG
1 CTATCGCAACGCGAAAATGG
16582 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
16602 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
16620 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:16662 original size:14 final size:16
Alignment explanation
Indices: 16642--16715 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
16632 TGAAAATCGC
16642 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
16657 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
16674 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
16693 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
16709 -TTGCGAT
1 ATTGCGAT
16716 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:16679 original size:19 final size:19
Alignment explanation
Indices: 16638--16705 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
16628 GAAATGAAAA
16638 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
16654 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
16671 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
16690 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
16706 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:16681 original size:52 final size:52
Alignment explanation
Indices: 16619--16733 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
16609 AACGAGAAAA
* ***
16619 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
16671 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
16723 TCGCGTTGCGA
1 TCGCATTGCGA
16734 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:18756 original size:20 final size:19
Alignment explanation
Indices: 18721--18787 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
18711 GAAACTTAAA
18721 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
18740 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
18760 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
18779 ATCGCAACG
1 ATCGCAACG
18788 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:18795 original size:14 final size:14
Alignment explanation
Indices: 18776--18833 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
18766 ATGCGAAATG
18776 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
18790 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
18806 ATGAAATCGCAAAGAC
1 A--AAATCGCAACGAC
*
18822 AAATTCGCAACG
1 AAAATCGCAACG
18834 CGAAACACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 7 0.20
18 9 0.26
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:18823 original size:32 final size:33
Alignment explanation
Indices: 18760--18838 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
18750 GGAAATGGCT
* *
18760 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
18793 ATCGCAACGCGAAATG-AAATCGCAAAGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
*
18825 TTCGCAACGCGAAA
1 ATCGCAACGCGAAA
18839 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAAAGACAAA
Found at i:18825 original size:18 final size:18
Alignment explanation
Indices: 18719--18819 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
18709 ACGAAACTTA
*
18719 AAATCGCAACGCGAAATG
1 AAATCGCAAAGCGAAATG
* *
18737 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAAAGC-GAAAT-G
** *
18758 CTATCGCAATGCGAAATG
1 AAATCGCAAAGCGAAATG
*
18776 AAAATCGC-AA-CGACA--
1 -AAATCGCAAAGCGAAATG
*
18791 AAATCGCAACGCGAAATG
1 AAATCGCAAAGCGAAATG
18809 AAATCGCAAAG
1 AAATCGCAAAG
18820 ACAAATTCGC
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
14 7 0.11
15 1 0.02
16 4 0.06
17 4 0.06
18 13 0.20
19 20 0.31
20 15 0.23
21 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (18 bp):
AAATCGCAAAGCGAAATG
Found at i:18867 original size:19 final size:17
Alignment explanation
Indices: 18845--18940 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
18835 GAAACACAAA
18845 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
18864 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
18880 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
18896 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
18912 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
18929 TCGCATTGCGAT
1 TCGC-TTGCGAT
18941 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:18886 original size:14 final size:14
Alignment explanation
Indices: 18867--18924 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
18857 TTTCATTTCG
18867 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
18881 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
18897 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
18913 CGTTGCGATTTT
1 CGTTGCGATTTT
18925 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:18931 original size:33 final size:33
Alignment explanation
Indices: 18850--18940 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
18840 ACAAATCGCA
18850 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
18883 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
18915 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
18941 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:18959 original size:20 final size:19
Alignment explanation
Indices: 18925--18979 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
18915 TTGCGATTTT
*
18925 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
18944 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
18964 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
18980 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:19478 original size:18 final size:18
Alignment explanation
Indices: 19452--19496 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19442 GTCGATCAGA
*
19452 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
19470 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
19488 TGATGGCTC
1 TGATGGCTC
19497 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:20838 original size:20 final size:20
Alignment explanation
Indices: 20813--20850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20803 AATAGTTTCT
20813 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
20833 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
20851 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:21139 original size:22 final size:22
Alignment explanation
Indices: 21114--21157 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21104 GATTTAGATA
*
21114 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
21136 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
21158 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:21355 original size:21 final size:22
Alignment explanation
Indices: 21325--21420 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 22
21315 CGCTTTGAAA
*
21325 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* *
21346 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGTAAGT
* * * * *
21366 ATCTCGTTGCGATT-TTTTATT
1 ATCGCATTGCGATTATGTAAGT
*
21387 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGTAAGT
21407 ATCGCATTGCGATT
1 ATCGCATTGCGATT
21421 TTCCCAATTC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.05
20 29 0.51
21 25 0.44
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:21388 original size:41 final size:41
Alignment explanation
Indices: 21325--21422 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
21315 CGCTTTGAAA
* *
21325 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * * * *
21366 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
21407 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
21423 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:21438 original size:41 final size:41
Alignment explanation
Indices: 21347--21481 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
21337 TTATGTATTA
* * * ** *
21347 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
21387 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
21429 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
21470 TCGCGTTGCGAT
1 TCGCGTTGCGAT
21482 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:21452 original size:20 final size:20
Alignment explanation
Indices: 21408--21500 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
21398 ATAGTCAGTA
* **
21408 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
21429 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
21449 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
21470 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
21490 TCGCATTGCGA
1 TCGCATTGCGA
21501 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:21482 original size:41 final size:41
Alignment explanation
Indices: 21408--21503 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
21398 ATAGTCAGTA
*
21408 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
21449 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
21490 TCGCATTGCGAATT
1 TCGCATTGCGAATT
21504 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:27191 original size:33 final size:33
Alignment explanation
Indices: 27144--27214 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
27134 ACAAAGTTTA
* *
27144 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
27176 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
27209 CGATAA
1 CGATAA
27215 TTAAAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:27250 original size:21 final size:21
Alignment explanation
Indices: 27209--27250 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27199 CTTCCAAGTT
*
27209 CGATAATTAAAACAAAGTTTA
1 CGATAATTAAAACAAAATTTA
* *
27230 CGATAATTGAAATAAAATTTA
1 CGATAATTAAAACAAAATTTA
27251 AAAATAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAATTTA
Found at i:37284 original size:24 final size:22
Alignment explanation
Indices: 37257--37316 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
37247 ATCCACTCCC
37257 CTTATATTCTCACCA-AATGTTCTT
1 CTTAT-TTCT-ACCATAAT-TTCTT
*
37281 CTTATTTCTTCCATAATTTCTT
1 CTTATTTCTACCATAATTTCTT
* *
37303 CTTCTTTCTGCCAT
1 CTTATTTCTACCAT
37317 TCTAAGTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 20 0.62
23 7 0.22
24 5 0.16
ACGTcount: A:0.18, C:0.27, G:0.03, T:0.52
Consensus pattern (22 bp):
CTTATTTCTACCATAATTTCTT
Found at i:46688 original size:29 final size:29
Alignment explanation
Indices: 46612--46688 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
46602 CTTCCCAGCA
* *
46612 TAGGTCTCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
46641 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
46670 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
46689 CCTGCTCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.14, C:0.35, G:0.26, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:46765 original size:14 final size:14
Alignment explanation
Indices: 46735--46781 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
46725 CCTCGCATAG
* *
46735 CTCGCTCGAATGGC
1 CTCGGTCGAATGCC
*
46749 CTCGGTCGGATGCC
1 CTCGGTCGAATGCC
46763 CTCGGTCGAATGCC
1 CTCGGTCGAATGCC
*
46777 TTCGG
1 CTCGG
46782 ATGCCCAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.11, C:0.34, G:0.32, T:0.23
Consensus pattern (14 bp):
CTCGGTCGAATGCC
Found at i:50925 original size:14 final size:14
Alignment explanation
Indices: 50906--50932 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50896 AAATAACATA
50906 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
50920 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
50933 ACTAAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:52709 original size:2 final size:2
Alignment explanation
Indices: 52702--52737 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52692 TGTGTTTATT
52702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52738 GTAGAAGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58525 original size:2 final size:2
Alignment explanation
Indices: 58466--58509 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
58456 CTAATTTATC
*
58466 AT AT AT AT CT 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
58508 AT
1 AT
58510 GATAAATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60881 original size:2 final size:2
Alignment explanation
Indices: 60874--60910 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60864 TTTAATTGAA
60874 AT AT 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 AT AT A
60911 GAAGTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.