Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004818.1 Hibiscus syriacus cultivar Beakdansim tig00010860_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: 49892
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:342 original size:21 final size:21
Alignment explanation
Indices: 320--388 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
310 ATGCAAGAAC
* *
320 GGATGCATTATTGGCATGAAC
1 GGATGCATTATTAGCATGAAA
341 GGATGCATTATTAGCATGAAA
1 GGATGCATTATTAGCATGAAA
362 GGATGCATTATTAGCATGAAA
1 GGATGCATTATTAGCATGAAA
383 GGATGC
1 GGATGC
389 CATAACTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (21 bp):
GGATGCATTATTAGCATGAAA
Found at i:490 original size:95 final size:95
Alignment explanation
Indices: 253--672 Score: 507
Period size: 95 Copynumber: 4.5 Consensus size: 95
243 GAATGAATGA
* ** *
253 ATAACTAGAAATGCATGAACGGATGCATTA-AAGCATGAAAGGATGCCATAACTAAAAATGCAAG
1 ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGCCATAACTAAAAATGCATG
* *
317 AACGGATGCATTATTGGCATGAACGGATG-C
66 AACGGATGCATTA-AGGCATGAAAGGATGCC
** * *
347 AT---T-ATTA-GCATGAAAGGATGCATTATTAGCATGAAAGGATGCCATAACTAAAAATGCATG
1 ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGCCATAACTAAAAATGCATG
* *
407 AAC-TATTGCATTAAGGTATGAAAGGATGCC
66 AACGGA-TGCATTAAGGCATGAAAGGATGCC
* * * *
437 ATAACTAAAAATACATGAACGGATGCATTATTGGCATGAACGGATGCCATAACTAAAAATTCACG
1 ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGCCATAACTAAAAATGCATG
*
502 AACAGATGCATTAAGGCATGAAAGGATGCC
66 AACGGATGCATTAAGGCATGAAAGGATGCC
* * * ** *
532 ATAACTAAAAATGCATGAACGGTTACATTATTGGCATGAACGGATGCTGTAACTAAAAATGTATG
1 ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGCCATAACTAAAAATGCATG
*
597 AACGGATGCATTAAGGCATGAAAGGATGCT
66 AACGGATGCATTAAGGCATGAAAGGATGCC
* * * *
627 ATAACTGAAAATGCATGAACGGATGTATTA-AGGCATGAATGGATGC
1 ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGC
673 ATTAAGGCAT
Statistics
Matches: 281, Mismatches: 36, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
89 30 0.11
90 46 0.16
91 1 0.00
93 1 0.00
94 18 0.06
95 184 0.65
96 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.23
Consensus pattern (95 bp):
ATAACTAAAAATGCATGAACGGATGCATTATTGGCATGAAAGGATGCCATAACTAAAAATGCATG
AACGGATGCATTAAGGCATGAAAGGATGCC
Found at i:495 original size:48 final size:47
Alignment explanation
Indices: 253--672 Score: 487
Period size: 47 Copynumber: 9.0 Consensus size: 47
243 GAATGAATGA
* *
253 ATAACTAGAAATGCATGAACGGATGCATTAAAGCATGAAAGGATGCC
1 ATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCC
* * *
300 ATAACTAAAAATGCAAGAACGGATGCATTATTGGCATGAACGGATG-C
1 ATAACTAAAAATGCATGAACGGATGCATTA-AGGCATGAAAGGATGCC
** *
347 AT---T-ATTA-GCATGAAAGGATGCATTATTA-GCATGAAAGGATGCC
1 ATAACTAAAAATGCATGAACGGATGCATTA--AGGCATGAAAGGATGCC
* *
390 ATAACTAAAAATGCATGAAC-TATTGCATTAAGGTATGAAAGGATGCC
1 ATAACTAAAAATGCATGAACGGA-TGCATTAAGGCATGAAAGGATGCC
* * *
437 ATAACTAAAAATACATGAACGGATGCATTATTGGCATGAACGGATGCC
1 ATAACTAAAAATGCATGAACGGATGCATTA-AGGCATGAAAGGATGCC
* * *
485 ATAACTAAAAATTCACGAACAGATGCATTAAGGCATGAAAGGATGCC
1 ATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCC
* * * * *
532 ATAACTAAAAATGCATGAACGGTTACATTATTGGCATGAACGGATGCT
1 ATAACTAAAAATGCATGAACGGATGCATTA-AGGCATGAAAGGATGCC
* * *
580 GTAACTAAAAATGTATGAACGGATGCATTAAGGCATGAAAGGATGCT
1 ATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCC
* * *
627 ATAACTGAAAATGCATGAACGGATGTATTAAGGCATGAATGGATGC
1 ATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
673 ATTAAGGCAT
Statistics
Matches: 315, Mismatches: 45, Indels: 26
0.82 0.12 0.07
Matches are distributed among these distances:
42 28 0.09
43 6 0.02
44 1 0.00
46 2 0.01
47 170 0.54
48 108 0.34
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.23
Consensus pattern (47 bp):
ATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCC
Found at i:698 original size:20 final size:20
Alignment explanation
Indices: 594--692 Score: 90
Period size: 20 Copynumber: 4.6 Consensus size: 20
584 CTAAAAATGT
*
594 ATGAACGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
614 ATGAAAGGATGCTATAACTGAAAATGC
1 ATGAAAGGATGC-AT---T---AAGGC
* *
641 ATGAACGGATGTATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
661 ATGAATGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
681 ATGAAAGGATGC
1 ATGAAAGGATGC
693 CATAAGTGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
20 44 0.69
21 2 0.03
23 1 0.02
24 1 0.02
26 2 0.03
27 14 0.22
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:1196 original size:29 final size:29
Alignment explanation
Indices: 1164--1238 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
1154 AATGGTTAAG
1164 CACTGTTGAGTAAAAGATGAAAGGTCAAA
1 CACTGTTGAGTAAAAGATGAAAGGTCAAA
* *
1193 CACTGTTGAGTAAAAGATGAACGGTTAAA
1 CACTGTTGAGTAAAAGATGAAAGGTCAAA
* *
1222 CAATGTCGAGTAAAAGA
1 CACTGTTGAGTAAAAGA
1239 ATAATGGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (29 bp):
CACTGTTGAGTAAAAGATGAAAGGTCAAA
Found at i:4717 original size:39 final size:39
Alignment explanation
Indices: 4663--4742 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
4653 CTATCCAATC
4663 CTCCTCGATTATGCTTCTAGGGGTCTCCACGAACCCTGA
1 CTCCTCGATTATGCTTCTAGGGGTCTCCACGAACCCTGA
* * *
4702 CTCCTCGATTATGCTTTTAGGGTTCTCCATGAACCCTGA
1 CTCCTCGATTATGCTTCTAGGGGTCTCCACGAACCCTGA
4741 CT
1 CT
4743 ATCTCTGGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (39 bp):
CTCCTCGATTATGCTTCTAGGGGTCTCCACGAACCCTGA
Found at i:7953 original size:19 final size:17
Alignment explanation
Indices: 7927--7969 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
7917 TTTGGAGGAT
7927 AAAA-ATAATTTATTAATA
1 AAAATATAATTT-TT-ATA
*
7945 AAAATATAATTTTTTTA
1 AAAATATAATTTTTATA
7962 AAAATATA
1 AAAATATA
7970 TGATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 6 0.26
19 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATATAATTTTTATA
Found at i:8991 original size:347 final size:344
Alignment explanation
Indices: 8348--8997 Score: 797
Period size: 347 Copynumber: 1.9 Consensus size: 344
8338 TCACTCTTAA
* * * *
8348 TATCAGTCTTAATAGGAGGTATTTATAATGGTAATTTATTATGTGTTAGTCGTAGGCTGACCATG
1 TATCAGTCTTAATAGGAGGTATTTATAATGGT-ATTGATTATATGTTAGTCGTAGGCTAACCATA
* * * *
8413 ACTATTCATAGGTCAACAAGCTATGTACATATGATAATCAGATTTATAATTCCGTTCGATGCATC
65 ACTATTCATAGGTCAACAAGATAGGTACATATGATAATCAGATTTAGAATTCCGTTCAATGCATC
* * * * * * *
8478 ACGTAAATATGTTAGAAGTCTTGTCTCTGTGTTGAAGTCGATTAAGAACTTGTATTTAGGGAGTG
130 ACATAAACATGTCAGAAGTCTTGTCTATGTGTTGAAGTCGACTAAGAACCTATATTTAGGGAGTG
* * * *
8543 TAGACTAGTCGAAAGTTCTGGTAGATTAAGAAATCTATCCAAAGACCGTGACTAGTGGAGAACTA
195 TAGACTAATCGAAAGTTCTGATAGATGAAGAAAGCTATCCAAAGACCGTGACTAGTGGAGAACTA
* *
8608 ACAATTTCAGTGAATCTGATCTAACAAAGATTCAAAAAATTTCAATTAACATCCTTATAAATATA
260 ACAATTCCAGTGAATCTAATCTAACAAAGATTCAAAAAATTTCAATTAACATCCTTATAAATATA
8673 ATAAACTGATTTTACCTCCT
325 ATAAACTGATTTTACCTCCT
* * *
8693 TATCAGTCTTAATAGGAGGTATTTATAGTGGCT-TTGATGTATATGTTAGTTGTA-GCGTAATCA
1 TATCAGTCTTAATAGGAGGTATTTATAATGG-TATTGAT-TATATGTTAGTCGTAGGC-TAACCA
* * * * *
8756 TAACTATTCGTAGGTCAATAAGATAGGTAGATATGATAATCAGATTTAGGATTTCGTTCTAAATG
63 TAACTATTCATAGGTCAACAAGATAGGTACATATGATAATCAGATTTAGAATTCCGTTC--AATG
* * * * * *
8821 CATCATATAAGCCTGTCAGAAGTCTTGTTTATGTGTTGAAGTCGACTAGGAGCCTATATTTAGGG
126 CATCACATAAACATGTCAGAAGTCTTGTCTATGTGTTGAAGTCGACTAAGAACCTATATTTAGGG
* * *
8886 -GCTGTAGACTAATC-AGATGTTTTGATAGATGAA-AAAGCTTATCCAAAGACCTTGACTAGTGG
191 AG-TGTAGACTAATCGA-AAGTTCTGATAGATGAAGAAAGC-TATCCAAAGACCGTGACTAGTGG
* * * * *
8948 AGAACTAACAATTCCGGTGAATCTAATCTGACGAAGGTTCAAAAATTTTC
253 AGAACTAACAATTCCAGTGAATCTAATCTAACAAAGATTCAAAAAATTTC
8998 GAAGACCATC
Statistics
Matches: 254, Mismatches: 43, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
344 6 0.02
345 97 0.38
346 7 0.03
347 144 0.57
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (344 bp):
TATCAGTCTTAATAGGAGGTATTTATAATGGTATTGATTATATGTTAGTCGTAGGCTAACCATAA
CTATTCATAGGTCAACAAGATAGGTACATATGATAATCAGATTTAGAATTCCGTTCAATGCATCA
CATAAACATGTCAGAAGTCTTGTCTATGTGTTGAAGTCGACTAAGAACCTATATTTAGGGAGTGT
AGACTAATCGAAAGTTCTGATAGATGAAGAAAGCTATCCAAAGACCGTGACTAGTGGAGAACTAA
CAATTCCAGTGAATCTAATCTAACAAAGATTCAAAAAATTTCAATTAACATCCTTATAAATATAA
TAAACTGATTTTACCTCCT
Found at i:11893 original size:16 final size:17
Alignment explanation
Indices: 11872--11906 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11862 ATTCAAATGG
11872 TAATTTTTTTTAAA-AA
1 TAATTTTTTTTAAATAA
11888 TAATTTTTTTTAAATAA
1 TAATTTTTTTTAAATAA
11905 TA
1 TA
11907 TTACTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTTTTTAAATAA
Found at i:15635 original size:3 final size:3
Alignment explanation
Indices: 15629--15657 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15619 ATATATATTT
15629 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
15658 TAAATATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17096 original size:3 final size:3
Alignment explanation
Indices: 17088--17207 Score: 142
Period size: 3 Copynumber: 40.7 Consensus size: 3
17078 TGGGTTTGTA
* *
17088 AAT AAT AAT AAT AAT AAT ATT AAT AAAT AAT AAT AAT -AT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* *
17133 AA- AAT AAT AAT AAT AAT -AT AAT TAT AA- AAA AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
17176 AAAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17208 CAAATGGATG
Statistics
Matches: 103, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
2 10 0.10
3 83 0.81
4 10 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17120 original size:25 final size:25
Alignment explanation
Indices: 17086--17207 Score: 136
Period size: 25 Copynumber: 5.1 Consensus size: 25
17076 TTTGGGTTTG
17086 TAAATAATAATAATAATAATATTAA
1 TAAATAATAATAATAATAATATTAA
17111 TAAATAATAATAAT-AT-A-ATT-A
1 TAAATAATAATAATAATAATATTAA
17132 TAAAATAATAATAATAAT-ATAATT-A
1 T-AAATAATAATAATAATAAT-ATTAA
*
17157 TAAA-AA-AATAATAATAA-ATAAA
1 TAAATAATAATAATAATAATATTAA
*
17179 TAAAATAATAATAATAATAATAATAA
1 T-AAATAATAATAATAATAATATTAA
17205 TAA
1 TAA
17208 CAAATGGATG
Statistics
Matches: 84, Mismatches: 3, Indels: 20
0.79 0.03 0.19
Matches are distributed among these distances:
21 4 0.05
22 27 0.32
23 10 0.12
24 7 0.08
25 32 0.38
26 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAATAATAATAATAATAATATTAA
Found at i:17635 original size:122 final size:122
Alignment explanation
Indices: 17434--17949 Score: 659
Period size: 122 Copynumber: 4.3 Consensus size: 122
17424 TTCTTCTCAT
* * * *
17434 TCTTCAGATGAGTTCTTCTCATTATGAACATT-TCTGGAAATA-TTAATGCTGATCTATCTCCTT
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AGTTGATTCTGATCTATCTCCTT
* *
17497 TTGTGATAGAA-TCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCT
65 CTGTGATA-AAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
*
17555 TCTTCAGATACGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCTGATCTATCTCCTTC
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCTGATCTATCTCCTTC
*
17620 TGTGATAAAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCC
66 TGTGATAAAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
* * *
17677 TCTTCAGATAAGTTCTTCTCATTATAAACTTTCTCTGGAAAAGTTTATGT-TGATCTATCTACTT
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-TCTGATCTATCTCCTT
*
17741 CTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
65 CTGTGATAAAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
* ***
17799 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA-TC----C-A--TCGAAC
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCTGATCTATCTCCTTC
* * * * * *
17856 ---GATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATCAACTTCTTCTTCC
66 TGTGATAAAGTCATGC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
*
17911 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-CTGG
1 -TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGG
17950 CAATGCTAAT
Statistics
Matches: 357, Mismatches: 30, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
111 9 0.03
112 38 0.11
113 32 0.09
114 5 0.01
116 1 0.00
117 1 0.00
120 1 0.00
121 32 0.09
122 237 0.66
123 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (122 bp):
TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATTCTGATCTATCTCCTTC
TGTGATAAAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
Found at i:17973 original size:113 final size:113
Alignment explanation
Indices: 17758--18044 Score: 389
Period size: 113 Copynumber: 2.5 Consensus size: 113
17748 AGAGTCATGC
* *
17758 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
17822 ATGAACTTTCTATGGAAAAGTTGATCCATCGAACGATGAATTCAAGCA
66 ATGAACTTTCTATGGAAAAGCTAATCCATCGAACGATGAATTCAAACA
* *
17870 AAAGGTTAAACAAGTTCTTCTCATTATCAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * ** *
17935 ATGAACTCTTC-CTGGCAATGCTAATCCATCGAGTGATGAATTTAAACA
66 ATGAACT-TTCTATGGAAAAGCTAATCCATCGAACGATGAATTCAAACA
* * * *
17983 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTTTTCTGATGAGTTCTTCT
1 AAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
18045 TTTTCTGATG
Statistics
Matches: 153, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
112 38 0.25
113 62 0.41
114 53 0.35
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTATGGAAAAGCTAATCCATCGAACGATGAATTCAAACA
Found at i:18048 original size:19 final size:19
Alignment explanation
Indices: 18018--18082 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
18008 TATGAATTTC
18018 TTCTTCCTTTTTCTGATGAG
1 TTCTT-CTTTTTCTGATGAG
18038 TTCTTCTTTTTCTGATGAG
1 TTCTTCTTTTTCTGATGAG
* *
18057 TTCTCCTTTTTCTAATGAG
1 TTCTTCTTTTTCTGATGAG
18076 TTCTTCT
1 TTCTTCT
18083 CATTATGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 37 0.88
20 5 0.12
ACGTcount: A:0.11, C:0.20, G:0.12, T:0.57
Consensus pattern (19 bp):
TTCTTCTTTTTCTGATGAG
Found at i:18326 original size:22 final size:22
Alignment explanation
Indices: 18301--18385 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
18291 AAATCCAACA
* * *
18301 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
*
18323 AATCTATCATCTTTGGAGAGAG
1 AATCTATCATCTTTGAAGAGAG
18345 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
18367 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
18386 ATGTAGATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:19760 original size:17 final size:17
Alignment explanation
Indices: 19715--19770 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
19705 TTCTATATAT
19715 TTTTTCATCATTTTTT-
1 TTTTTCATCATTTTTTC
19731 TTCATTTC--C-TTTTTTC
1 TT--TTTCATCATTTTTTC
19747 TTTTTCATCATTTTTTC
1 TTTTTCATCATTTTTTC
*
19764 TTCTTCA
1 TTTTTCA
19771 AGCATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 6 0.18
17 13 0.39
18 4 0.12
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTCATCATTTTTTC
Found at i:27113 original size:15 final size:15
Alignment explanation
Indices: 27090--27121 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27080 TGCAATGAAT
27090 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
27105 AATGCATGTATGCAA
1 AATGAATGTATGCAA
27120 AA
1 AA
27122 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:30471 original size:28 final size:26
Alignment explanation
Indices: 30425--30482 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
30415 CATTAATAAT
*
30425 AAAAAATAATATATATAAATATTATG
1 AAAAAATAATATATATAAAAATTATG
*
30451 AAAATAATAAGTATATATAAAAATTTTG
1 AAAA-AATAA-TATATATAAAAATTATG
30479 AAAA
1 AAAA
30483 GCAAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 19 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAATAATATATATAAAAATTATG
Found at i:32796 original size:3 final size:3
Alignment explanation
Indices: 32788--32866 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
32778 TGGGTCTGTA
* *
32788 AAT AAT AAT AAT AAT ATT AAT AAAT AAT AAT AAT -AT AAT TAT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
*
32832 AAT AAT AAT AGT AAT AAAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
32867 CAAATGGATG
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
2 6 0.09
3 53 0.82
4 6 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32814 original size:22 final size:23
Alignment explanation
Indices: 32787--32866 Score: 107
Period size: 22 Copynumber: 3.7 Consensus size: 23
32777 TTGGGTCTGT
32787 AAATAATAATAATAATATTAAT-
1 AAATAATAATAATAATATTAATA
32809 AAATAATAATAAT-ATAATT-ATA
1 AAATAATAATAATAAT-ATTAATA
*
32831 AAATAATAATAGTAATA--AATA
1 AAATAATAATAATAATATTAATA
32852 AAATAATAATAATAA
1 AAATAATAATAATAA
32867 CAAATGGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
21 21 0.40
22 29 0.56
23 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (23 bp):
AAATAATAATAATAATATTAATA
Found at i:33363 original size:21 final size:21
Alignment explanation
Indices: 33337--33384 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
33327 GTTTCCAGAT
*
33337 TCGCAACGATAACTTCGACTA
1 TCGCAACGAGAACTTCGACTA
* * *
33358 TCGCAATGCGAACTTGGACTA
1 TCGCAACGAGAACTTCGACTA
33379 TCGCAA
1 TCGCAA
33385 TGACTGGTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAACGAGAACTTCGACTA
Found at i:33385 original size:21 final size:21
Alignment explanation
Indices: 33347--33386 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33337 TCGCAACGAT
33347 AACTTCGACTATCGCAATGCG
1 AACTTCGACTATCGCAATGCG
*
33368 AACTTGGACTATCGCAATG
1 AACTTCGACTATCGCAATG
33387 ACTGGTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
AACTTCGACTATCGCAATGCG
Found at i:34117 original size:21 final size:21
Alignment explanation
Indices: 34093--34207 Score: 176
Period size: 21 Copynumber: 5.4 Consensus size: 21
34083 GCAATACCGT
34093 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
*
34114 TCGCAACGGATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
* * *
34135 TCGTAACGCGAACTTCGAATAAA
1 TCGCAA--CGAATTTGGAATAAA
34158 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
34179 TCGCAACGAATTTGGAATAAA
1 TCGCAACGAATTTGGAATAAA
34200 TCGCAACG
1 TCGCAACG
34208 CGAACTTCGA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
21 67 0.80
23 17 0.20
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAACGAATTTGGAATAAA
Found at i:34171 original size:44 final size:42
Alignment explanation
Indices: 34093--34207 Score: 158
Period size: 44 Copynumber: 2.7 Consensus size: 42
34083 GCAATACCGT
* * *
34093 TCGCAACGAATTTGGAATAAATCGCAACGGATTTGGAATAAA
1 TCGCAACGAACTTCGAATAAATCGCAACGAATTTGGAATAAA
*
34135 TCGTAACGCGAACTTCGAATAAATCGCAACGAATTTGGAATAAA
1 TCGCAA--CGAACTTCGAATAAATCGCAACGAATTTGGAATAAA
* *
34179 TCGCAACGAATTTGGAATAAATCGCAACG
1 TCGCAACGAACTTCGAATAAATCGCAACG
34208 CGAACTTCGA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
42 26 0.41
44 38 0.59
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (42 bp):
TCGCAACGAACTTCGAATAAATCGCAACGAATTTGGAATAAA
Found at i:34197 original size:65 final size:65
Alignment explanation
Indices: 34093--34217 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 65
34083 GCAATACCGT
* *
34093 TCGCAACGAATTTGGAATAAATCGCAACGGATTTGGAATAAATCGTAACGCGAACTTCGAATAAA
1 TCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAATAAA
34158 TCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
1 TCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
34218 CTATCGCAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.22
Consensus pattern (65 bp):
TCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAATAAA
Found at i:34223 original size:21 final size:21
Alignment explanation
Indices: 34199--34253 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
34189 TTTGGAATAA
34199 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
34220 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
34241 ATCGCAATGCGAA
1 ATCGCAACGCGAA
34254 TATGTAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:34254 original size:65 final size:63
Alignment explanation
Indices: 34093--34247 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 63
34083 GCAATACCGT
* * *
34093 TCGCAACGAATTTGGAATAAATCGCAACGGATTTGGAATAAATCGTAACGCGAACTTCGAATAAA
1 TCGCAACGAACTTGGAAT-AATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAAT-AA
* *
34158 TCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT-A
1 TCGCAACGAACTTGGAAT-AATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAATAA
*
34221 TCGCAACGCGAACTTGGACT-ATCGCAA
1 TCGCAA--CGAACTTGGAATAATCGCAA
34248 TGCGAATATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
63 14 0.17
65 69 0.83
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (63 bp):
TCGCAACGAACTTGGAATAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAATAA
Found at i:38435 original size:18 final size:19
Alignment explanation
Indices: 38398--38436 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
38388 TTTGTGAGGT
*
38398 AAAAATGTTATTATTGTAA
1 AAAAATGTAATTATTGTAA
38417 AAAAATGTAATTATT-TAA
1 AAAAATGTAATTATTGTAA
38435 AA
1 AA
38437 TAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AAAAATGTAATTATTGTAA
Found at i:38534 original size:17 final size:17
Alignment explanation
Indices: 38512--38544 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38502 TGAGATCATA
*
38512 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
38529 ATATTATATTTTATAT
1 ATATTATATTTTATAT
38545 AATTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:40001 original size:24 final size:22
Alignment explanation
Indices: 39967--40013 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 22
39957 TTTTGTGATA
39967 TAAATTTAATTGATTTTTAATT
1 TAAATTTAATTGATTTTTAATT
39989 TAAATATTCAATTGATTTTTAATT
1 TAAAT-TT-AATTGATTTTTAATT
40013 T
1 T
40014 TGGAACATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 16 0.70
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TAAATTTAATTGATTTTTAATT
Found at i:46801 original size:18 final size:18
Alignment explanation
Indices: 46773--46823 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
46763 AAATAATTAA
46773 AATAA-ATATAAAATTTT
1 AATAATATATAAAATTTT
*
46790 AATAATATATAAATAATTT
1 AATAATATATAAA-ATTTT
46809 -AT-ATGATATAAAATT
1 AATAAT-ATATAAAATT
46824 AAATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATATATAAAATTTT
Found at i:46807 original size:20 final size:19
Alignment explanation
Indices: 46763--46809 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
46753 ACTTAAATCA
*
46763 AAATAATTAAAATAAATAT
1 AAATAATTTAAATAAATAT
*
46782 -AA-AATTTTAATAATATAT
1 AAATAATTTAAATAA-ATAT
46800 AAATAATTTA
1 AAATAATTTA
46810 TATGATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 2 0.09
20 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAAATAAATAT
Found at i:46872 original size:23 final size:24
Alignment explanation
Indices: 46841--46887 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
46831 TATAATATAA
*
46841 TATT-AAAAAATTAATATTTAATT
1 TATTAAAAAAATTAATATTAAATT
*
46864 TATTTAAAAAATTAATATTAAATT
1 TATTAAAAAAATTAATATTAAATT
46888 AATATCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTAAAAAAATTAATATTAAATT
Found at i:46917 original size:61 final size:63
Alignment explanation
Indices: 46814--46970 Score: 234
Period size: 61 Copynumber: 2.5 Consensus size: 63
46804 AATTTATATG
*
46814 ATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
1 ATATTAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
*
46878 ATATTAAATTAATATCTAT-A-ATAATATTAAAATATTAATATTTAATTTATTTAAAAAATTA
1 ATATTAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
*
46939 ATATTAAAATTAAAATC-A-AATATAATA-TAAAA
1 ATATT-AAATTAATATCTATAATATAATATTAAAA
46971 TTAAATAAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
61 52 0.60
62 17 0.20
63 9 0.10
64 9 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (63 bp):
ATATTAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
Found at i:46923 original size:24 final size:25
Alignment explanation
Indices: 46883--46944 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
46873 AATTAATATT
46883 AAATTAATATCTATAATA-ATATTAAA
1 AAATTAATAT-TATAATATAT-TTAAA
* *
46909 ATATTAATATT-TAATTTATTTAAA
1 AAATTAATATTATAATATATTTAAA
46933 AAATTAATATTA
1 AAATTAATATTA
46945 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 19 0.61
25 3 0.10
26 9 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATTAATATTATAATATATTTAAA
Found at i:48277 original size:15 final size:17
Alignment explanation
Indices: 48245--48277 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
48235 ACACTCGAAT
48245 TAAACAAATTTCTTTTA
1 TAAACAAATTTCTTTTA
48262 TAAA-AAATTT-TTTTA
1 TAAACAAATTTCTTTTA
48277 T
1 T
48278 TTTGTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAACAAATTTCTTTTA
Done.