Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003809.1 Hibiscus syriacus cultivar Beakdansim tig00008164_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: 92848
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:1218 original size:18 final size:18
Alignment explanation
Indices: 1195--1238 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1185 TTTAATTTGC
1195 TTATTTAATTATT-TTCTT
1 TTATTTAATTATTATT-TT
*
1213 TTATTTAATTCTTATTTT
1 TTATTTAATTATTATTTT
1231 TTATTTAA
1 TTATTTAA
1239 AAACAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTAATTATTATTTT
Found at i:1819 original size:14 final size:15
Alignment explanation
Indices: 1795--1823 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1785 ATATACGTGT
1795 TGGTCATATAAATGG
1 TGGTCATATAAATGG
1810 TGGT-ATATAAATGG
1 TGGTCATATAAATGG
1824 GTATTCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (15 bp):
TGGTCATATAAATGG
Found at i:7254 original size:34 final size:34
Alignment explanation
Indices: 7206--7274 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
7196 GTTAAGGAAC
7206 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
1 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
*
7240 ACCTGTTATAGTCAATTTCACACGAGCACTCAAA
1 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
7274 A
1 A
7275 ATTTCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (34 bp):
ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
Found at i:9449 original size:136 final size:135
Alignment explanation
Indices: 9283--9555 Score: 377
Period size: 135 Copynumber: 2.0 Consensus size: 135
9273 AAACAAATTA
* *
9283 TTATCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATA-TTATTCTCCTTTCAGATTTGGTCTT
1 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCA-AGTTATTCTCCTTTCAGATTTGGTCTT
** * * * * * *
9347 CCCTGAAGAGGAGCAAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATC
65 -CCTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATC
9412 AAAAGTT
129 AAAAGTT
* *
9419 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTCTTCTTCTTTCAGATTTGGTCTTC
1 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTATTCTCCTTTCAGATTTGGTCTTC
* **
9484 CTGAAGAGTAGTGAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
66 CTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
*
9549 AATTT
131 AAGTT
9554 TT
1 TT
9556 GAGATCTAAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
135 62 0.52
136 58 0.48
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (135 bp):
TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTATTCTCCTTTCAGATTTGGTCTTC
CTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
AAGTT
Found at i:12558 original size:15 final size:15
Alignment explanation
Indices: 12538--12571 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
12528 CACATAAATA
12538 TCTTTAAAGAAATTG
1 TCTTTAAAGAAATTG
12553 TCTTTAAAGAAATTG
1 TCTTTAAAGAAATTG
12568 TCTT
1 TCTT
12572 GAATTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (15 bp):
TCTTTAAAGAAATTG
Found at i:22691 original size:46 final size:45
Alignment explanation
Indices: 22567--22692 Score: 121
Period size: 46 Copynumber: 2.8 Consensus size: 45
22557 GTAACCATGC
* * *
22567 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAAAGGTAAGTATATTGAAAA
* * * **
22612 AAATAA--TAATAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAAA-GGTAAGTATATTGAAAA
*
22658 AAATAAGCTTATGAGCTTATGGGATGAAAGGTAAG
1 AAATAAGCTTATGAGCTTATGGAAT-AAAGGTAAG
22693 AAATTTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 13 0.20
45 9 0.14
46 26 0.41
47 3 0.05
48 13 0.20
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAAGGTAAGTATATTGAAAA
Found at i:29756 original size:51 final size:47
Alignment explanation
Indices: 29652--29772 Score: 120
Period size: 51 Copynumber: 2.5 Consensus size: 47
29642 GTAACCATGC
*
29652 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAAATA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG---AAAATA
* * **
29702 ATAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA-A
1 A-AATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAATA
29751 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
29773 GATGAAAGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 21 0.34
49 2 0.03
50 2 0.03
51 22 0.35
53 1 0.02
54 14 0.23
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAATA
Found at i:32768 original size:46 final size:46
Alignment explanation
Indices: 32152--32761 Score: 769
Period size: 46 Copynumber: 13.3 Consensus size: 46
32142 TAAACCGAAT
** *
32152 CCATAACTAAAATGCATGAAAAGATGCATTAATGCATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * * *
32198 CCAAAATTAAAATGCATGAACGGTTGCATTAAGGTATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
32244 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* ** * *
32290 CTATAACT-AAATGCATGAACATATTCAATAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* *
32335 CCATAATTAAAATGCATGTAA-GGATGCATTAAGGCATGAAAGGATA
1 CCATAACTAAAATGCATG-AACGGATGCATTAAGGCATGAAAGGATG
* *
32381 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* *
32427 TCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * * * *
32473 TCATAACTAAAATGCATGAAAGAATGAATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * *
32519 ACATAACTAAAATGCATGATCGGATGCACTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * *
32565 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG-AAGGCACG
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGG-ATG
* * * *
32611 CCATAACTAAAATGCATGAAAGGAAGCATTAAGGCATTAAAGGATT
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
* * * *
32657 CCATAATTAAAATACATGAGA-GGATACATTAAGGAATGAAAGGATG
1 CCATAACTAAAATGCATGA-ACGGATGCATTAAGGCATGAAAGGATG
* * * ** *
32703 CCATGATTAAAATGCATGAACGGATGCATTAATGCATGAAACTATA
1 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
*
32749 CCATAACTGAAAT
1 CCATAACTAAAAT
32762 TAATGAATAA
Statistics
Matches: 486, Mismatches: 71, Indels: 14
0.85 0.12 0.02
Matches are distributed among these distances:
45 46 0.09
46 433 0.89
47 7 0.01
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
Found at i:37370 original size:46 final size:46
Alignment explanation
Indices: 37313--37727 Score: 645
Period size: 46 Copynumber: 9.0 Consensus size: 46
37303 TAAATAGAAT
* *
37313 CCATAACTAAAATGAATGAAAGGATGCATTAAGGCATGAAAGGATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
37359 CCATAATTAAAATGCATGAATGGATGCATTACGGCAAGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
37405 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATT
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
37451 CCATAACTAAAATGCATGAAATGATGCATTAAGGTATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
37497 CCATAATTAAAATGCATGAACA-GATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGGATG
37543 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
37589 CCATAACTAAAATGCATGAAAGGATG-AGTTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCA-TTAAGGCATGAAAGGATG
* * *
37635 ACGTAACTAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
37681 CCATAATTAAATTGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
37727 C
1 C
37728 ATTAAGGCAT
Statistics
Matches: 338, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.01
46 334 0.99
47 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:37765 original size:46 final size:46
Alignment explanation
Indices: 37714--37879 Score: 224
Period size: 46 Copynumber: 3.6 Consensus size: 46
37704 ATGCATTAAG
* *
37714 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * *
37760 ACATGAAAGCATGCATCAAGGCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * *
37806 GCATGAAATGATGCATTAAGGGATGAAAGGATGCCATGATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * * *
37852 GCATGAACGGATGTATTAATGAATGAAA
1 GCATGAAAGGATGCATTAAGGCATGAAA
37880 AGTGACCATA
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 104 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
Found at i:37833 original size:158 final size:158
Alignment explanation
Indices: 37556--37858 Score: 484
Period size: 158 Copynumber: 1.9 Consensus size: 158
37546 TAACTAAAAT
* * *
37556 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGAGTTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATGAGTCAA
*
37621 GGCATGAAAGGATGACGTAACTAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGACATAACTAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATGCCATA
*
37686 ATTAAATTGCATGAAATGATGCATTAAG
131 ATTAAAATGCATGAAATGATGCATTAAG
*
37714 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATACATGAAAGCATGCA-TCA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATG-AGTCA
* * *
37778 AGGCATGAAAGGATGCCATAATTAAAATGCATGAAAT-GATGCATTAAGGGATGAAAGGATGCCA
65 AGGCATGAAAGGATGACATAACTAAAATGCATG-AATGGATGCATTAAGGCATGAAAGGATGCCA
*
37842 TGATTAAAATGCATGAA
129 TAATTAAAATGCATGAA
37859 CGGATGTATT
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
158 129 0.97
159 4 0.03
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (158 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATGAGTCAA
GGCATGAAAGGATGACATAACTAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATGCCATA
ATTAAAATGCATGAAATGATGCATTAAG
Found at i:37904 original size:92 final size:92
Alignment explanation
Indices: 37716--37904 Score: 209
Period size: 92 Copynumber: 2.1 Consensus size: 92
37706 GCATTAAGGC
*
37716 ATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATACATGAAAGCATGCATCAAGG
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATGCATCAAGG
* * * *
37781 CATGAAAGGATGCCATAATTAAAATGC
66 AATGAAAAGATGCCATAACTAAAATGA
* * * * * * * * * *
37808 ATGAAATGATGCATTAAGGGATGAAAGGATGCCATGATTAAAATGCATGAACGGATGTATTAATG
1 ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATGCATCAAGG
* *
37873 AATGAAAAG-TGACCATAACTGAAATTA
66 AATGAAAAGATG-CCATAACTAAAATGA
37900 ATGAA
1 ATGAA
37905 TAACTACTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
91 2 0.03
92 77 0.97
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (92 bp):
ATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATACATGAAAGCATGCATCAAGG
AATGAAAAGATGCCATAACTAAAATGA
Found at i:44314 original size:19 final size:17
Alignment explanation
Indices: 44281--44316 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
44271 GGGGTTTTGG
44281 TAAAAATGATTAAATAA
1 TAAAAATGATTAAATAA
44298 TAAAAATCGATTTAAATAA
1 TAAAAAT-GA-TTAAATAA
44317 AAATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAAAATGATTAAATAA
Found at i:65967 original size:34 final size:33
Alignment explanation
Indices: 65882--65980 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
65872 AATTGGAAAG
65882 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
65915 TTTGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
65948 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
65981 TGTATATGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 43 0.72
34 17 0.28
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:70725 original size:34 final size:33
Alignment explanation
Indices: 70637--70732 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
70627 TGACAAGTTG
70637 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
70670 G-AAATGTCATCTTGGTTGGTGGCCAACTTA-TT
1 GAAAAT-TCATCTTGGTTGGTGGCCAACTTATTT
*
70702 GAAAAATTCATCTTTGGTAGGTGGCCAACTT
1 G-AAAATTCATC-TTGGTTGGTGGCCAACTT
70733 TGCACATGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
32 7 0.12
33 30 0.52
34 21 0.36
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
Found at i:77385 original size:25 final size:25
Alignment explanation
Indices: 77348--77399 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
77338 ATTTCCAGCT
*
77348 TTGATTTCCAGCCTCCAA-ATTTGAC
1 TTGATTTACAGCC-CCAACATTTGAC
* *
77373 TTGATTTATAGCCCCAACTTTTGAC
1 TTGATTTACAGCCCCAACATTTGAC
77398 TT
1 TT
77400 CCAACACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (25 bp):
TTGATTTACAGCCCCAACATTTGAC
Found at i:80059 original size:17 final size:18
Alignment explanation
Indices: 80035--80084 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
80025 TTAGGATATT
80035 ATTAATAAAACAATAACA
1 ATTAATAAAACAATAACA
*
80053 A-TAATAAACAACAATAATA
1 ATTAAT-AA-AACAATAACA
80072 ATTAAT-AAACAAT
1 ATTAATAAAACAAT
80085 TAATACCGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.36
18 4 0.14
19 10 0.36
20 4 0.14
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTAATAAAACAATAACA
Found at i:88416 original size:22 final size:22
Alignment explanation
Indices: 88386--88436 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
88376 CATGGGCCTA
* *
88386 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACATT
*
88408 ATGGACCTATTTGTAAGACATT
1 ATGGACCTAGTTGTAAGACATT
88430 ATGGACC
1 ATGGACC
88437 CTAAGGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACATT
Found at i:91137 original size:12 final size:13
Alignment explanation
Indices: 91118--91153 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
91108 ATGATAATTA
91118 ATATACTTTATTT
1 ATATACTTTATTT
91131 A-ATACTTATATTT
1 ATATACTT-TATTT
91144 ATATACTTTA
1 ATATACTTTA
91154 ATACTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 6 0.29
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATACTTTATTT
Found at i:91173 original size:22 final size:22
Alignment explanation
Indices: 91128--91181 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
91118 ATATACTTTA
** * *
91128 TTTAATACTTATATTTATATAC
1 TTTAATACTTATATCCAAACAC
91150 TTTAATACTTATATCCAAACAC
1 TTTAATACTTATATCCAAACAC
*
91172 TTTATTACTT
1 TTTAATACTT
91182 TACATTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATACTTATATCCAAACAC
Found at i:91207 original size:15 final size:15
Alignment explanation
Indices: 91177--91223 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
91167 AACACTTTAT
*
91177 TACTTTACAT-TATA
1 TACTTTATATATATA
91191 TACTTTATATATATA
1 TACTTTATATATATA
** *
91206 TAGATTATATATGTA
1 TACTTTATATATATA
91221 TAC
1 TAC
91224 AAATTGAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (15 bp):
TACTTTATATATATA
Found at i:91337 original size:25 final size:24
Alignment explanation
Indices: 91290--91335 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
91280 TGATGAGGGA
91290 TGAAATTGAATTAATTATAAAATT
1 TGAAATTGAATTAATTATAAAATT
*
91314 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
91336 ATGGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATT
Found at i:91695 original size:23 final size:23
Alignment explanation
Indices: 91640--91695 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
91630 AATTATAATA
* *
91640 TATATATATATATATGTATGTATG
1 TATA-ATATGTATATGAATGTATG
91664 TATAATATGTATATGAATGTTATG
1 TATAATATGTATATGAATG-TATG
91688 -ATAATATG
1 TATAATATG
91696 ATGCATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (23 bp):
TATAATATGTATATGAATGTATG
Found at i:91776 original size:6 final size:6
Alignment explanation
Indices: 91731--91765 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
91721 TACTTTATGT
*
91731 ATATAT ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
91766 TACTTATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:91781 original size:14 final size:14
Alignment explanation
Indices: 91730--91774 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
91720 ATACTTTATG
*
91730 TATATATATATACA
1 TATACATATATACA
91744 TATAC--ATATACA
1 TATACATATATACA
*
91756 TATACATATATACT
1 TATACATATATACA
91770 TATAC
1 TATAC
91775 TTTTATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TATACATATATACA
Found at i:92314 original size:24 final size:24
Alignment explanation
Indices: 92277--92355 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 24
92267 TATGATGCAT
92277 GTATATAT-AATGTAAAATAT-AA
1 GTATATATAAATGTAAAATATAAA
*
92299 GTATATATAAAGTGTAAACTATAAA
1 GTATATATAAA-TGTAAAATATAAA
* * *
92324 GTATATAT-ACTTTAAAGTATAAA
1 GTATATATAAATGTAAAATATAAA
*
92347 GTGTATATA
1 GTATATATA
92356 TATATATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
22 8 0.17
23 20 0.42
24 10 0.21
25 10 0.21
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (24 bp):
GTATATATAAATGTAAAATATAAA
Found at i:92751 original size:2 final size:2
Alignment explanation
Indices: 92218--92731 Score: 117
Period size: 2 Copynumber: 258.0 Consensus size: 2
92208 TTAAAACAAT
*
92218 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
92259 T- TA TA -A TA TA TGA TG CA TG TA TA TA TA -A TG TA -A AA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
92298 -A GTA TA TA TA AA GTG TA AA CTA TA AA GTA TA TA TA CTT TA AA GTA
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA -TA TA TA -TA
* *
92343 TA AA GTG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
92386 TA TA TA TA TA T- TA TA AA CTA TA AA GTA TA -A GTA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA
* * * * *
92426 -A GTA TA TA TA TA AA T- TA AA GTA TA TA TA CTT TT TA CTA -A AA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA
* * *
92467 CTT TA TA TA TA T- TA TA AA CT- TA TA TA TA TA AA GTA TA -A T-
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
92506 TA -A GGA -A CA AA AA TA TA TA -A GTA TA TA -A TA TA AA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * *
92545 TA -A GTA TA TA GTA TA TA TA CA TA TA AA GTA -A AA GTA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
92587 AA CTA TA AA TA TA TA TA TA TA TA TA TA TA TA GT- TC TA GTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
92629 -A T- TA TA TA CA TA TA TA TA -A TA TA AA CTA TA -A GTA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
92668 TA TA AA AA GTA TA -A T- TA TA -A GA T- TA AA GTA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
92707 TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
92732 CTCTATTCTT
Statistics
Matches: 378, Mismatches: 66, Indels: 136
0.65 0.11 0.23
Matches are distributed among these distances:
1 35 0.09
2 310 0.82
3 33 0.09
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Done.