Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009294.1 Hibiscus syriacus cultivar Beakdansim tig00113003_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: 46348
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:34 original size:20 final size:20
Alignment explanation
Indices: 4--176 Score: 215
Period size: 20 Copynumber: 8.7 Consensus size: 20
1 AAA
4 ATCGC-ATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
23 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
43 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
63 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
83 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
104 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
124 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
144 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
164 TTCGCAACGCGAT
1 ATCGCAATGCGAT
177 TTACATAGCG
Statistics
Matches: 141, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
19 7 0.05
20 119 0.84
21 13 0.09
22 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:162 original size:81 final size:81
Alignment explanation
Indices: 23--176 Score: 227
Period size: 81 Copynumber: 1.9 Consensus size: 81
13 GATACTGACT
* * * *
23 ATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGC
1 ATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTATCGC
*
88 AATGCGATAATACAAA
66 AACGCGATAATACAAA
* * * *
104 ATCGCAACGAGATACTGACTTTCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACTTTCGC
1 ATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTATCGC
169 AACGCGAT
66 AACGCGAT
177 TTACATAGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (81 bp):
ATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTATCGC
AACGCGATAATACAAA
Found at i:2570 original size:17 final size:17
Alignment explanation
Indices: 2548--2580 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2538 GTTGCTGCCA
2548 ATTCTTCTAA-ACTGTGT
1 ATTCTT-TAACACTGTGT
2565 ATTCTTTAACACTGTG
1 ATTCTTTAACACTGTG
2581 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
ATTCTTTAACACTGTGT
Found at i:2913 original size:21 final size:21
Alignment explanation
Indices: 2889--3039 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
2879 TCATTCCTCG
2889 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
2910 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
2931 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
2952 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
2973 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2994 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3015 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3036 AGAG
1 AGAG
3040 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2913 original size:42 final size:42
Alignment explanation
Indices: 2837--3039 Score: 203
Period size: 42 Copynumber: 4.8 Consensus size: 42
2827 GACTCGCCTG
* * * * * * *
2837 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2879 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
2921 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2963 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
3005 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
3040 CCCGATTCAC
Statistics
Matches: 132, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 4 0.03
42 126 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3018 original size:84 final size:84
Alignment explanation
Indices: 2834--3009 Score: 352
Period size: 84 Copynumber: 2.1 Consensus size: 84
2824 CTCGACTCGC
2834 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2899 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
2918 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2983 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
3002 CTGTCATC
1 CTGTCATC
3010 GTTGAAGAGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:3039 original size:84 final size:84
Alignment explanation
Indices: 2834--3039 Score: 297
Period size: 84 Copynumber: 2.5 Consensus size: 84
2824 CTCGACTCGC
* * * *
2834 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2899 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
2918 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2983 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
3002 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
3040 CCCGATTCAC
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
84 110 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:4415 original size:14 final size:14
Alignment explanation
Indices: 4396--4431 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4386 ATTGTTTAAT
4396 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4410 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4424 TGATTTGT
1 TGATTTGT
4432 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:4562 original size:19 final size:19
Alignment explanation
Indices: 4538--4584 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
4528 AAAAAGTACT
*
4538 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
4557 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
4576 ATCGCAACG
1 ATCGCAACG
4585 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:4631 original size:19 final size:19
Alignment explanation
Indices: 4609--4759 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
4599 CGAAATTAAA
4609 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4628 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4643 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
4661 TTCGCATGGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
4675 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4694 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4709 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** ** *
4727 TTCGTATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4746 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4760 AGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 27 0.30
16 6 0.07
17 6 0.07
19 43 0.47
20 9 0.10
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4655 original size:33 final size:32
Alignment explanation
Indices: 4613--4739 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
4603 ATTAAATTCG
4613 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
4646 CGTTGCGATTTTCATTTCGCATGGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
4679 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
4712 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4740 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4691 original size:66 final size:66
Alignment explanation
Indices: 4606--4730 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
4596 ACGCGAAATT
*
4606 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATGGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATGGC
4671 G
66 G
*
4672 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCG
4731 TATTGCGATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATGGC
G
Found at i:7047 original size:12 final size:12
Alignment explanation
Indices: 7030--7054 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7020 CCTTCGGGGA
7030 CTTTTTCTTCTT
1 CTTTTTCTTCTT
7042 CTTTTTCTTCTT
1 CTTTTTCTTCTT
7054 C
1 C
7055 AGAATTATAT
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:8095 original size:20 final size:21
Alignment explanation
Indices: 8070--8118 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
8060 TCCTAATTCA
*
8070 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
8090 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
8111 CAATGCGA
1 CAATGCGA
8119 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:8192 original size:20 final size:20
Alignment explanation
Indices: 8145--8194 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8135 GAGATAATAC
8145 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
8165 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
8185 AAAATCGCAA
1 AAAATCGCAA
8195 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:8502 original size:20 final size:20
Alignment explanation
Indices: 8408--8494 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
8398 CAACGGGGAA
*
8408 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
* *
8428 ATCACAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
** * **
8448 ATCGCAATTCG-AAATAAAA
1 ATCGCAACGCGAAAATGACT
8467 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
8487 ATCGCAAC
1 ATCGCAAC
8495 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.25
20 40 0.75
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:8562 original size:19 final size:19
Alignment explanation
Indices: 8540--8607 Score: 136
Period size: 19 Copynumber: 3.6 Consensus size: 19
8530 GCTTTTCACG
8540 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
8559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
8578 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
8597 TTGCGATTTTC
1 TTGCGATTTTC
8608 TCGTTGCGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:8563 original size:33 final size:33
Alignment explanation
Indices: 8521--8617 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 33
8511 GAAATGAAAA
*
8521 TCGCATTGCGCTTTTCACGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCACGTTGCGATTTTCATT
8554 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCA---CG--TTGCGATTTTCATT
*
8592 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCACGTTGCGAT
8618 AGTCAGTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 23 0.40
35 2 0.04
36 2 0.04
38 30 0.53
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCACGTTGCGATTTTCATT
Found at i:8763 original size:14 final size:14
Alignment explanation
Indices: 8744--8780 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8734 CATCAATTAA
8744 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
8758 ACAAATCATCTTTT
1 ACAAATCAACATTT
8772 ACAAATCAA
1 ACAAATCAA
8781 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:10670 original size:20 final size:20
Alignment explanation
Indices: 10647--10700 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
10637 GAAACTTAAA
10647 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
10667 ATCGCAACGCGAAAATGGCT
1 ATCGCAATGCGAAAATGACT
10687 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
10701 TGAAAATCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:10753 original size:32 final size:33
Alignment explanation
Indices: 10687--10765 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
10677 GAAAATGGCT
10687 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
* * *
10720 ATTGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
10752 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
10766 CATAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:10795 original size:18 final size:18
Alignment explanation
Indices: 10772--10834 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
10762 GAAACATAAA
10772 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
10790 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
10806 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
10823 TCGCATTGCGAT
1 TCGCATTGCGAT
10835 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 15 0.39
19 6 0.16
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:10853 original size:20 final size:19
Alignment explanation
Indices: 10819--10873 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
10809 TTGCGATTTT
*
10819 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
10838 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
10858 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
10874 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:11382 original size:18 final size:18
Alignment explanation
Indices: 11356--11400 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
11346 GTCGATCAGA
* *
11356 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
11374 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
11392 TGATGGCTC
1 TGATGGCTC
11401 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:12820 original size:20 final size:20
Alignment explanation
Indices: 12722--12820 Score: 117
Period size: 20 Copynumber: 5.0 Consensus size: 20
12712 AATAGTTTCT
** *
12722 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
* *
12742 GAAAATGATTATCGCAACAC
1 GAAAATGACTATCGCAACGC
12762 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
12782 GAATTTGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
12802 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
12821 AGAGAATCGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:13113 original size:22 final size:22
Alignment explanation
Indices: 13083--13126 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13073 GATGGAGATA
13083 GACGAATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
* *
13105 GACGGATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
13127 TAAGAGAGTG
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:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:13357 original size:41 final size:41
Alignment explanation
Indices: 13294--13388 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
13284 CGCTTTGAAA
*
13294 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
* * * *
13335 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
13376 ATCGCATTGCGAT
1 ATCGCATTGCGAT
13389 AGTCAGTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
Found at i:13380 original size:20 final size:19
Alignment explanation
Indices: 13294--13408 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 19
13284 CGCTTTGAAA
*
13294 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
*
13315 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
13335 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
13356 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
13376 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
*
13396 ATCGTATTGCGAT
1 ATCGCATTGCGAT
13409 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 46 0.60
21 24 0.31
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:13393 original size:61 final size:62
Alignment explanation
Indices: 13294--13411 Score: 170
Period size: 61 Copynumber: 1.9 Consensus size: 62
13284 CGCTTTGAAA
* *
13294 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGTATC-TCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGT-ATTGCGATTTTGTATT
*
13356 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGTATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGTATTGCGATTTT
13412 CCCAATTCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
60 2 0.04
61 36 0.71
62 13 0.25
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGTATTGCGATTTTGTATT
Found at i:13427 original size:61 final size:61
Alignment explanation
Indices: 13294--13429 Score: 152
Period size: 61 Copynumber: 2.2 Consensus size: 61
13284 CGCTTTGAAA
* * ** *
13294 ATCGCATTGCGATTATGT-ATTATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAAT
*
13356 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGT-ATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATC-TCATTGCGATTTT-CCAAT
*
13418 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
13430 TTACTTATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
60 2 0.03
61 47 0.73
62 15 0.23
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAAT
Found at i:30939 original size:30 final size:31
Alignment explanation
Indices: 30864--30942 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 31
30854 AAATGATGTT
* *
30864 ATTTTAGGCACTAAACTCTAGAAATATATCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
30895 ATTTT-GTCACTAAACTTTAAAAATAT-TCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
30924 ATTTTAGGCATTAAACTTT
1 ATTTTAGGCACTAAACTTT
30943 TTCGACCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.19
30 29 0.69
31 5 0.12
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (31 bp):
ATTTTAGGCACTAAACTTTAAAAATATATCA
Found at i:43212 original size:161 final size:157
Alignment explanation
Indices: 42952--43267 Score: 544
Period size: 161 Copynumber: 2.0 Consensus size: 157
42942 TATTCGGGTC
* *
42952 GGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACTTTATAT
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAATATATATAATTTTACCTTATAT
* *
43017 ATTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTTTCAATTAAGTCACTG-TTTTA
66 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTA
43081 TTGAATAAAAATAATTTTTTTTATTTT
131 TTGAATAAAAATAATTTTTTTTATTTT
43108 GGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGGACCCGACCCGGAAAATATATATAATTTTACCT
1 GGGTCGGGTTCGGGTTTAGGGTG-AAAAA---GACCCGACCC-GAAAATATATATAATTTTACCT
43173 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGT
61 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGT
43238 TTTTATTGAATAAAAATAATTTTTTTTATT
126 TTTTATTGAATAAAAATAATTTTTTTTATT
43268 ATTTCGTGTC
Statistics
Matches: 150, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
156 23 0.15
157 5 0.03
160 9 0.06
161 83 0.55
162 30 0.20
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (157 bp):
GGGTCGGGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAATATATATAATTTTACCTTATAT
ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTA
TTGAATAAAAATAATTTTTTTTATTTT
Found at i:43702 original size:18 final size:17
Alignment explanation
Indices: 43656--43703 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
43646 ATATGGAATT
* *
43656 AGATTTCAATTCCTGAC
1 AGATTACAATTCCTCAC
*
43673 ATATTACAATTCCTTCAC
1 AGATTACAATTCC-TCAC
*
43691 AGATTCCAATTCC
1 AGATTACAATTCC
43704 CTCATAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (17 bp):
AGATTACAATTCCTCAC
Done.