Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002590.1 Hibiscus syriacus cultivar Beakdansim tig00005243_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: 52718
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:3191 original size:14 final size:11
Alignment explanation
Indices: 3160--3189 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3150 ATTAAGTCTC
3160 AATTTTTAATA
1 AATTTTTAATA
3171 AATTTTTAATA
1 AATTTTTAATA
3182 ATATTTTT
1 A-ATTTTT
3190 TTTCTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTTAATA
Found at i:3530 original size:34 final size:35
Alignment explanation
Indices: 3487--3558 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 35
3477 ACCATAATAT
* *
3487 CATTAAGTCTCAATAAGTCTAAAAT-AAATAACAC
1 CATTAAGTCTCAATAAATCTAAAATAAAAAAACAC
3521 CATTAAGTCTCAATAAATCTAAAATAAAAAAACAC
1 CATTAAGTCTCAATAAATCTAAAATAAAAAAACAC
3556 CAT
1 CAT
3559 AACACTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 24 0.69
35 11 0.31
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (35 bp):
CATTAAGTCTCAATAAATCTAAAATAAAAAAACAC
Found at i:9179 original size:20 final size:20
Alignment explanation
Indices: 9151--9189 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9141 TTCATGAATG
*
9151 GGTCAACGCAAGCGTAATCT
1 GGTCAACGCAAGCGCAATCT
*
9171 GGTCGACGCAAGCGCAATC
1 GGTCAACGCAAGCGCAATC
9190 CGGGCTGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (20 bp):
GGTCAACGCAAGCGCAATCT
Found at i:12310 original size:16 final size:17
Alignment explanation
Indices: 12289--12321 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12279 GTTTATAAGT
12289 GAAATT-TATTTTATAC
1 GAAATTATATTTTATAC
12305 GAAATTGATATTTTATA
1 GAAATT-ATATTTTATA
12322 AAAGTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
GAAATTATATTTTATAC
Found at i:13142 original size:31 final size:30
Alignment explanation
Indices: 13107--13181 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
13097 AATTGGTTTT
* *
13107 CTGGAAAATGAATTACT-AAAATTTTAAATTA
1 CTGGAAATTGAATTACTGAAAA--ATAAATTA
* *
13138 CTGGAATTTGAATTACTGAAAAATGAATTA
1 CTGGAAATTGAATTACTGAAAAATAAATTA
13168 CTGGAAATTGAATT
1 CTGGAAATTGAATT
13182 CAGGAAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 19 0.50
31 15 0.39
32 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (30 bp):
CTGGAAATTGAATTACTGAAAAATAAATTA
Found at i:13153 original size:15 final size:15
Alignment explanation
Indices: 13133--13197 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
13123 TAAAATTTTA
*
13133 AATTACTGGAATTTG
1 AATTACTGGAAATTG
* *
13148 AATTACTGAAAAATG
1 AATTACTGGAAATTG
13163 AATTACTGGAAATTG
1 AATTACTGGAAATTG
* *
13178 AATT-CAGGAAAATG
1 AATTACTGGAAATTG
13192 AATTAC
1 AATTAC
13198 ATTTCTGGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 12 0.29
15 30 0.71
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.31
Consensus pattern (15 bp):
AATTACTGGAAATTG
Found at i:13169 original size:30 final size:29
Alignment explanation
Indices: 13133--13197 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
13123 TAAAATTTTA
* *
13133 AATTACTGGAATTTGAATTACTGAAAAATG
1 AATTACTGGAAATTGAATT-CAGAAAAATG
*
13163 AATTACTGGAAATTGAATTCAGGAAAATG
1 AATTACTGGAAATTGAATTCAGAAAAATG
13192 AATTAC
1 AATTAC
13198 ATTTCTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.31
Consensus pattern (29 bp):
AATTACTGGAAATTGAATTCAGAAAAATG
Found at i:13600 original size:34 final size:31
Alignment explanation
Indices: 13525--13601 Score: 77
Period size: 34 Copynumber: 2.4 Consensus size: 31
13515 GTAATAGTGT
13525 TATATT-ATATTTTAAAAATATTAATTAGTA
1 TATATTAATATTTTAAAAATATTAATTAGTA
* *
13555 TATTTTAAATATCTTTATTAAATATT-ATTAGATTA
1 TATATT-AATAT-TTTA-AAAATATTAATTAG--TA
13590 TATATTAATATT
1 TATATTAATATT
13602 AAATATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
30 5 0.13
32 4 0.11
33 10 0.26
34 12 0.32
35 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (31 bp):
TATATTAATATTTTAAAAATATTAATTAGTA
Found at i:13757 original size:52 final size:52
Alignment explanation
Indices: 13646--13759 Score: 121
Period size: 52 Copynumber: 2.2 Consensus size: 52
13636 CAAAATTTAT
**
13646 TATATATTTATTAAAATAAAAATATAATATCTTATATTATTATAATATAATTGA
1 TATAT-TTTATTAAAATAAAAATATAATA-CTTATATTATTATAATATAATAAA
13700 T-TATTTTATTATAATATTAAAAATAT-ATA-TTATATTA-TA-AATATTAATAAA
1 TATATTTTATTA-AA-A-TAAAAATATAATACTTATATTATTATAATA-TAATAAA
13751 TATATTTTA
1 TATATTTTA
13760 AATATTTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
50 4 0.08
51 8 0.15
52 22 0.42
53 5 0.09
54 5 0.09
55 9 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TATATTTTATTAAAATAAAAATATAATACTTATATTATTATAATATAATAAA
Found at i:13777 original size:30 final size:28
Alignment explanation
Indices: 13660--13778 Score: 84
Period size: 30 Copynumber: 4.1 Consensus size: 28
13650 TATTTATTAA
* * * *
13660 AATAAAAATATAATATCTTATATTATTAT
1 AATAAATATATATTATATTATAATATT-T
*
13689 AATATAAT-TGATTATTTTATTATAATA-TT
1 AATA-AATAT-A-TATTATATTATAATATTT
13718 AA-AAATATATATTATATTATAA-ATATT
1 AATAAATATATATTATATTATAATAT-TT
* *
13745 AATAAATATATTTTAAATATTTTAATATTT
1 AATAAATATATATT--ATATTATAATATTT
13775 AATA
1 AATA
13779 TTTTGATGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
25 1 0.01
26 12 0.17
27 8 0.11
28 12 0.17
29 8 0.11
30 18 0.25
31 13 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
AATAAATATATATTATATTATAATATTT
Found at i:14246 original size:15 final size:15
Alignment explanation
Indices: 14226--14291 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
14216 TTCTGGAAAA
14226 TGAATTACTAGAATT
1 TGAATTACTAGAATT
*
14241 TGAATTACTGGAATT
1 TGAATTACTAGAATT
* **
14256 TTAATTACT-GAAAAA
1 TGAATTACTAG-AATT
14271 TGAATTACTAGAATT
1 TGAATTACTAGAATT
14286 TGAATT
1 TGAATT
14292 CAGGAAAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 1 0.02
15 40 0.95
16 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (15 bp):
TGAATTACTAGAATT
Found at i:14262 original size:30 final size:30
Alignment explanation
Indices: 14241--14307 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
14231 TACTAGAATT
* *
14241 TGAATTACTGGAATTTTAATTACTGAAAAA
1 TGAATTACTAGAATTTGAATTACTGAAAAA
* *
14271 TGAATTACTAGAATTTGAATT-CAGGAAAA
1 TGAATTACTAGAATTTGAATTACTGAAAAA
14300 TGAATTAC
1 TGAATTAC
14308 ATTTTTGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (30 bp):
TGAATTACTAGAATTTGAATTACTGAAAAA
Found at i:14573 original size:20 final size:20
Alignment explanation
Indices: 14536--14578 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
14526 AATTTATTTA
**
14536 TTATTAAATATTTTTATAATT
1 TTATTAAATATTGGTAT-ATT
14557 TTATT-AATATTGGTATATT
1 TTATTAAATATTGGTATATT
14576 TTA
1 TTA
14579 GTGAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTAAATATTGGTATATT
Found at i:14697 original size:19 final size:19
Alignment explanation
Indices: 14673--14743 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
14663 TTAAATATCT
*
14673 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
14692 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
14711 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
14731 TTATTAAATATAT
1 TTATTAAA-ATAT
14744 ACAAAATTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:14834 original size:31 final size:31
Alignment explanation
Indices: 14798--14867 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
14788 ATATTATTAT
* *
14798 AATATATTGATTATTTTATTGT-AATATTAAA
1 AATATATT-ATTATATTATTATAAATATTAAA
* *
14829 AATATAATATTATATTATTATAAATATTATA
1 AATATATTATTATATTATTATAAATATTAAA
14860 AATATATT
1 AATATATT
14868 TTAAATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
AATATATTATTATATTATTATAAATATTAAA
Found at i:14839 original size:22 final size:22
Alignment explanation
Indices: 14814--14855 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
14804 TTGATTATTT
*
14814 TATTGTAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
14836 TATTATATTATTATAAATAT
1 TATTATAATATTAAAAATAT
14856 TATAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:14859 original size:25 final size:25
Alignment explanation
Indices: 14752--14884 Score: 70
Period size: 25 Copynumber: 5.5 Consensus size: 25
14742 ATACAAAATT
**
14752 TATTAT-ATATT-TATTAAAATAAA
1 TATTATAATATTATATTATTATAAA
*
14775 -AATATAATATCTTATATTATTATAATA
1 TATTATAATA--TTATATTATTATAA-A
* * *
14802 TATTGATTATTTTAT-TGTAATATTAAA
1 TATT-ATAATATTATAT-TATTA-TAAA
*
14829 -AATATAATATTATATTATTATAAA
1 TATTATAATATTATATTATTATAAA
14853 TATTATAA-A-TATA-T-TT-TAAA
1 TATTATAATATTATATTATTATAAA
*
14873 TATTTTAATATT
1 TATTATAATATT
14885 TAATATTTTG
Statistics
Matches: 84, Mismatches: 13, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.13
21 3 0.04
22 6 0.07
23 7 0.08
24 5 0.06
25 20 0.24
26 13 0.15
27 10 0.12
28 5 0.06
29 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTATAATATTATATTATTATAAA
Found at i:15146 original size:42 final size:42
Alignment explanation
Indices: 15090--15181 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
15080 TTCCTACAAC
* * * *
15090 CAAACACTGGAAAACATTTTTCGGAAAACGTATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
*
15132 CAAACACGGGAAAACATTTTCCGAAAAATGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
15174 CAAACACG
1 CAAACACG
15182 AGATTTCGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.20
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
Found at i:22572 original size:111 final size:111
Alignment explanation
Indices: 22430--22768 Score: 561
Period size: 111 Copynumber: 3.1 Consensus size: 111
22420 ATTACAAAAA
* *
22430 TTAATTCTTACTCTAATAATCATGCTTTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
22495 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTATCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
*
22541 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATAATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * **
22606 AATTAAAACGATAAAATATTATTGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
*
22652 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
** *
22717 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
*
22763 ATAATT
1 TTAATT
22769 TCCATCCGAA
Statistics
Matches: 210, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 210 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
Found at i:24470 original size:5 final size:5
Alignment explanation
Indices: 24454--24490 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
24444 CGTATTACCA
24454 CGACC ACGACC CGACC CGACC CGACC CGACC CGACC C
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGACC C
24491 AAGACGGACG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.22, C:0.59, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:25169 original size:21 final size:21
Alignment explanation
Indices: 25139--25275 Score: 120
Period size: 21 Copynumber: 6.6 Consensus size: 21
25129 GATTTACATA
*
25139 TTCGTATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
25160 TTCGCGTTGCGATAGTTC-AAG
1 TTCGCATTGCGATAG-TCGAAG
* *
25181 TTCGCGTTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
* **
25201 TATCGCATTGCGAT-TTATATA-
1 T-TCGCATTGCGATAGTCGA-AG
* *
25222 TTCGCATTGCGATAGTCCAAC
1 TTCGCATTGCGATAGTCGAAG
*
25243 TACGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
25264 TTCGCGTTGCGA
1 TTCGCATTGCGA
25276 ATCTAAAAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
20 18 0.19
21 73 0.78
22 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:25253 original size:83 final size:83
Alignment explanation
Indices: 25115--25275 Score: 252
Period size: 83 Copynumber: 1.9 Consensus size: 83
25105 TGCGATTTTG
* * * * *
25115 GACTATCGCATTGCGATTTACATATTCGTATTGCGATAGTCGAAGTTCGCGTTGCGATAGTTC-A
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTACGCATTGCGATAG-TCGA
25179 AGTTCGCGTTGCGATAGTC
65 AGTTCGCGTTGCGATAGTC
*
25198 GACTATCGCATTGCGATTTATATATTCGCATTGCGATAGTCCAACTACGCATTGCGATAGTCGAA
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTACGCATTGCGATAGTCGAA
25263 GTTCGCGTTGCGA
66 GTTCGCGTTGCGA
25276 ATCTAAAAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 2 0.03
83 69 0.97
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (83 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAACTACGCATTGCGATAGTCGAA
GTTCGCGTTGCGATAGTC
Found at i:30940 original size:8 final size:8
Alignment explanation
Indices: 30927--30967 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
30917 CTCATTTTCA
30927 GAGAATTT
1 GAGAATTT
30935 GAGAATTT
1 GAGAATTT
*
30943 -AGAGTTT
1 GAGAATTT
*
30950 GGGAATTT
1 GAGAATTT
30958 GAGAATTT
1 GAGAATTT
30966 GA
1 GA
30968 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:31272 original size:128 final size:128
Alignment explanation
Indices: 31038--31485 Score: 817
Period size: 128 Copynumber: 3.5 Consensus size: 128
31028 TAATCGGAGT
31038 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
31102 AATTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
31165 ACTATTTACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
31230 CATTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACTTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
31293 ACTATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
31358 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATAACAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
31421 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
31486 AATTACATTA
Statistics
Matches: 307, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
127 50 0.16
128 257 0.84
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:32056 original size:21 final size:21
Alignment explanation
Indices: 32030--32102 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
32020 TATGGTATAA
* * *
32030 AACCCTGCGAGCTAGGCATGT
1 AACCCTGCGGGCTCGGAATGT
32051 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
32072 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
32093 AACCCTGCGG
1 AACCCTGCGG
32103 AGATGGCATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTCGGAATGT
Found at i:43032 original size:10 final size:10
Alignment explanation
Indices: 43017--43091 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
43007 CATTTAATAA
43017 ATAAACGAAC
1 ATAAACGAAC
43027 ATAAACG-AC
1 ATAAACGAAC
*
43036 ---CACGAAC
1 ATAAACGAAC
43043 ATAAACGAAC
1 ATAAACGAAC
** *
43053 ACGAAC-ATAA
1 ATAAACGA-AC
43063 ATGAACACGAAC
1 AT-AA-ACGAAC
43075 ATAAACGAAC
1 ATAAACGAAC
43085 ATAAACG
1 ATAAACG
43092 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 3 0.06
7 2 0.04
9 3 0.06
10 32 0.65
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.23, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:43042 original size:16 final size:16
Alignment explanation
Indices: 43021--43085 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
43011 TAATAAATAA
*
43021 ACGAACATAAACGACC
1 ACGAACATAAACGAAC
43037 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
43053 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
43069 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
43085 A
1 A
43086 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:44206 original size:14 final size:14
Alignment explanation
Indices: 44189--44241 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
44179 GAACATAAAT
44189 GAACATAACCGAAC
1 GAACATAACCGAAC
44203 GAACAT-A---AAC
1 GAACATAACCGAAC
44213 GAACATAACCGAAC
1 GAACATAACCGAAC
44227 GAACATAACCGAAC
1 GAACATAACCGAAC
44241 G
1 G
44242 TTCACGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.08
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:44251 original size:24 final size:24
Alignment explanation
Indices: 44179--44240 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
44169 ATAAATGAAT
*
44179 GAACATAAATGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
44203 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
44227 GAACATAACCGAAC
1 GAACATAAACGAAC
44241 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.13, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:47471 original size:16 final size:16
Alignment explanation
Indices: 47447--47485 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
47437 TATCGCCGAC
*
47447 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
47463 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
47479 CGTAAAT
1 CG-AAAT
47486 AGTAACCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Done.