Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2503943 original size:32 final size:33
Alignment explanation
Indices: 2503855--2503954 Score: 93
Period size: 38 Copynumber: 3.0 Consensus size: 33
2503845 TCGGGCCGAG
* * *
2503855 TATATATATAT-TTAAATTAAATATATAAATAT
1 TATATATATATAATAAATTAAATTTATTAATAT
2503887 TATATATATATTTTAATTTAAATTAAATTTATTAATAT
1 TATATATATA---TAA--TAAATTAAATTTATTAATAT
2503925 TATATATATATAAT-AATT--ATTT-TTAATAT
1 TATATATATATAATAAATTAAATTTATTAATAT
2503954 T
1 T
2503955 TATCGGGCCG
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
29 8 0.14
30 4 0.07
32 14 0.24
33 1 0.02
35 4 0.07
38 28 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TATATATATATAATAAATTAAATTTATTAATAT
Found at i:2504720 original size:4 final size:4
Alignment explanation
Indices: 2504711--2504742 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
2504701 TCTATCTCTC
2504711 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
2504743 ATTATCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:2505545 original size:2 final size:2
Alignment explanation
Indices: 2505540--2505578 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2505530 CCTTTTCTAC
2505540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2505579 TATTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2507088 original size:20 final size:21
Alignment explanation
Indices: 2507063--2507114 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2507053 TTTTCCCAAT
*
2507063 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2507083 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2507104 TCGCAATGCGA
1 TCGCAATGCGA
2507115 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2507128 original size:20 final size:20
Alignment explanation
Indices: 2507103--2507196 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2507093 AATTGGGAAA
*
2507103 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2507123 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2507144 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
2507164 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2507184 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2507197 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2507177 original size:41 final size:41
Alignment explanation
Indices: 2507100--2507177 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2507090 GCGAATTGGG
* * **
2507100 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
2507141 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
2507178 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:2507776 original size:19 final size:19
Alignment explanation
Indices: 2507752--2507796 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2507742 GCAACGAGAT
*
2507752 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
2507771 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
2507790 AATCGCA
1 AATCGCA
2507797 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:2507814 original size:19 final size:19
Alignment explanation
Indices: 2507792--2507976 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
2507782 GAAACCAAAA
*
2507792 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2507811 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2507830 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
2507849 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
2507869 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
2507885 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2507902 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2507916 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
2507935 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2507955 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2507975 TC
1 TC
2507977 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2507869 original size:39 final size:38
Alignment explanation
Indices: 2507792--2507881 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2507782 GAAACCAAAA
* *
2507792 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
2507830 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
2507869 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2507882 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:2507901 original size:33 final size:33
Alignment explanation
Indices: 2507864--2507951 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
2507854 GTTGCGATTT
* *
2507864 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2507897 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
2507930 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
2507952 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:2507953 original size:20 final size:20
Alignment explanation
Indices: 2507919--2507976 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2507909 GCGATTCTCT
**
2507919 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
2507939 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
2507959 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
2507977 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:2510023 original size:42 final size:42
Alignment explanation
Indices: 2509963--2510085 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2509953 GCCCGACTCG
* * *
2509963 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2510005 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2510047 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2510086 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2510043 original size:21 final size:21
Alignment explanation
Indices: 2510019--2510085 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2510009 TCATTCCTCG
2510019 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2510040 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2510061 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2510082 AGAG
1 AGAG
2510086 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:2511461 original size:14 final size:14
Alignment explanation
Indices: 2511442--2511477 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2511432 ATTGTTTAAT
2511442 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2511456 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2511470 TGATTTGT
1 TGATTTGT
2511478 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:2511678 original size:19 final size:19
Alignment explanation
Indices: 2511656--2511773 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
2511646 CGAAATTAAA
2511656 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2511675 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2511690 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2511708 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2511723 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2511741 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2511760 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2511774 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2511702 original size:33 final size:33
Alignment explanation
Indices: 2511660--2511753 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
2511650 ATTAAATTCG
2511660 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2511693 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
2511726 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2511754 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:2514061 original size:12 final size:12
Alignment explanation
Indices: 2514046--2514070 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2514036 TTTTCGGGGA
2514046 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2514058 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2514070 C
1 C
2514071 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2515317 original size:14 final size:14
Alignment explanation
Indices: 2515298--2515334 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2515288 CATCAATTAA
2515298 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2515312 ACAAATCATCTTTT
1 ACAAATCAACATTT
2515326 ACAAATCAA
1 ACAAATCAA
2515335 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:2517271 original size:14 final size:14
Alignment explanation
Indices: 2517252--2517309 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2517242 ATGCGAAATG
2517252 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2517266 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2517282 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2517298 AAAATCGCAACG
1 AAAATCGCAACG
2517310 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2517294 original size:32 final size:33
Alignment explanation
Indices: 2517236--2517326 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2517226 GGAAATGGCT
*
2517236 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2517269 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2517301 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2517327 TGCGATTTGT
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:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2517320 original size:19 final size:19
Alignment explanation
Indices: 2517178--2517331 Score: 114
Period size: 19 Copynumber: 8.6 Consensus size: 19
2517168 TAGTTTACTT
* *
2517178 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2517198 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
2517217 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2517237 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2517256 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2517270 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2517288 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2517302 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2517321 TCGCAATGCGA
1 TCGCAACGCGA
2517332 TTTGTGTTTC
Statistics
Matches: 108, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.19
15 1 0.01
16 6 0.06
17 2 0.02
18 11 0.10
19 39 0.36
20 29 0.27
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2517362 original size:14 final size:14
Alignment explanation
Indices: 2517343--2517400 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2517333 TTGTGTTTCG
2517343 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2517357 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2517373 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2517389 CGTTGCGATTTT
1 CGTTGCGATTTT
2517401 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:2517377 original size:32 final size:33
Alignment explanation
Indices: 2517338--2517416 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2517328 GCGATTTGTG
2517338 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2517370 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2517403 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2517417 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2517415 original size:19 final size:17
Alignment explanation
Indices: 2517338--2517416 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
2517328 GCGATTTGTG
2517338 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
2517354 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
2517370 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
2517386 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
2517403 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
2517417 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:2517435 original size:20 final size:19
Alignment explanation
Indices: 2517401--2517455 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2517391 TTGCGATTTT
*
2517401 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2517420 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2517440 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2517456 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:2517976 original size:18 final size:18
Alignment explanation
Indices: 2517932--2517976 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2517922 GTCGATCAGA
*
2517932 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
** *
2517950 TGACAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
2517968 TGATGGCTC
1 TGATGGCTC
2517977 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.42, T:0.24
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:2519315 original size:20 final size:20
Alignment explanation
Indices: 2519290--2519327 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2519280 AATAGTTTCT
2519290 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2519310 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2519328 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:2519615 original size:22 final size:22
Alignment explanation
Indices: 2519590--2519633 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2519580 GATTTAGATA
2519590 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2519612 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2519634 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2519913 original size:20 final size:20
Alignment explanation
Indices: 2519819--2519913 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
2519809 GATTATGTAT
*
2519819 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2519839 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
2519859 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
2519880 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2519900 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2519914 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2519932 original size:41 final size:41
Alignment explanation
Indices: 2519841--2519975 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2519831 AAAGTCAGTA
* * * ** *
2519841 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2519881 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
2519923 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2519964 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2519976 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:2519946 original size:20 final size:20
Alignment explanation
Indices: 2519902--2519994 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2519892 ATAGTCAGTA
* **
2519902 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2519923 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2519943 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2519964 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2519984 TCGCATTGCGA
1 TCGCATTGCGA
2519995 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:2519976 original size:41 final size:41
Alignment explanation
Indices: 2519902--2519997 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2519892 ATAGTCAGTA
*
2519902 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2519943 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2519984 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2519998 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:2523571 original size:2 final size:2
Alignment explanation
Indices: 2523564--2523605 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2523554 TACTGACCTA
2523564 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
2523606 TTGAAAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2526465 original size:73 final size:73
Alignment explanation
Indices: 2526379--2526523 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 73
2526369 AGAGATCAAT
* *
2526379 TGATGGAAAATATGTGAAAATGTTCAACTCCCCCTTTTTCATTAAGAGATTGAATTTTTCAAACC
1 TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
2526444 ATACTTCA
66 ATACTTCA
* * *
2526452 TGATGAAAAATATGTGAAAATGTTTAGCTCCCCATTTTTCATTAAGAGATTGATTTTTTCAAACC
1 TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
2526517 ATACTTC
66 ATACTTC
2526524 TCCCCCTCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (73 bp):
TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
ATACTTCA
Found at i:2527520 original size:21 final size:21
Alignment explanation
Indices: 2527496--2527574 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 21
2527486 TTTAAATTAA
2527496 AATTTCTTTTTCAAAACTTTC
1 AATTTCTTTTTCAAAACTTTC
* * *
2527517 AATTTTCATTTTTGAAAGCTCT-
1 AA-TTTC-TTTTTCAAAACTTTC
* *
2527539 AAATCCTTTTTCAAAA-TTTC
1 AATTTCTTTTTCAAAACTTTC
* **
2527559 ATTTTGGTTTTCAAAA
1 AATTTCTTTTTCAAAA
2527575 TCTATTTTAG
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
19 2 0.05
20 19 0.45
21 4 0.10
22 6 0.14
23 11 0.26
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
AATTTCTTTTTCAAAACTTTC
Found at i:2527589 original size:19 final size:20
Alignment explanation
Indices: 2527547--2527592 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2527537 CTAAATCCTT
* * *
2527547 TTTCAAAATTTCATTTTGGT
1 TTTCAAAATCTCATTTTAGC
2527567 TTTCAAAATCT-ATTTTAGC
1 TTTCAAAATCTCATTTTAGC
2527586 TTTCAAA
1 TTTCAAA
2527593 GGAAAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCAAAATCTCATTTTAGC
Found at i:2528883 original size:24 final size:24
Alignment explanation
Indices: 2528836--2528900 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
2528826 AACCGGCCCA
**
2528836 ACCCGACCTGAAC-CCTTGACCTG
1 ACCCGACCTGAACTGTTTGACCTG
2528859 ACCCGACCTGAACTGTTTGACCTG
1 ACCCGACCTGAACTGTTTGACCTG
* *
2528883 ACCCAACCAGAACTGTTT
1 ACCCGACCTGAACTGTTT
2528901 TACCCGACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.22
Consensus pattern (24 bp):
ACCCGACCTGAACTGTTTGACCTG
Done.