Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009392.1 Hibiscus syriacus cultivar Beakdansim tig00113292_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: 42692
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:207 original size:3 final size:3
Alignment explanation
Indices: 199--255 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
189 GTTAAAAATA
199 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
245 TAG TAT TAT TA
1 TAT TAT TAT TA
256 AGTGTGTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:13536 original size:16 final size:16
Alignment explanation
Indices: 13513--13596 Score: 77
Period size: 16 Copynumber: 5.2 Consensus size: 16
13503 AAAAAGGAAC
13513 AAAT-AAAAAGATGAA
1 AAATGAAAAAGATGAA
*
13528 AAATGAAAAAAATGAA
1 AAATGAAAAAGATGAA
*
13544 AAA-GAAAAAAAATGAA
1 AAATG-AAAAAGATGAA
13560 AAATGAAAAAAGAAATGAAA
1 AAATG-AAAAAG--ATG-AA
13580 AAAT-AAAAAGA-GAA
1 AAATGAAAAAGATGAA
13594 AAA
1 AAA
13597 GGAGGGTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.08
15 6 0.10
16 28 0.46
17 7 0.11
18 6 0.10
19 3 0.05
20 6 0.10
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAATGAAAAAGATGAA
Found at i:13538 original size:9 final size:9
Alignment explanation
Indices: 13526--13570 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
13516 TAAAAAGATG
13526 AAAAATGAA
1 AAAAATGAA
13535 AAAAATGAA
1 AAAAATGAA
*
13544 AAAGA--AA
1 AAAAATGAA
13551 AAAAATG--
1 AAAAATGAA
13558 AAAAATGAA
1 AAAAATGAA
13567 AAAA
1 AAAA
13571 GAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
7 13 0.43
9 17 0.57
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (9 bp):
AAAAATGAA
Found at i:15037 original size:105 final size:105
Alignment explanation
Indices: 14817--15071 Score: 341
Period size: 105 Copynumber: 2.4 Consensus size: 105
14807 CTCGCTTGAG
*
14817 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * *
14882 TGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * * *
14924 GAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* * **
14989 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
*
15029 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
15072 CACGAGAAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
104 5 0.04
105 112 0.87
106 1 0.01
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (105 bp):
GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:15252 original size:3 final size:3
Alignment explanation
Indices: 15237--15285 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
15227 AGTTAAAAAA
* *
15237 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15284 TA
1 TA
15286 AGTGTGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:27514 original size:88 final size:87
Alignment explanation
Indices: 27424--27811 Score: 506
Period size: 88 Copynumber: 4.4 Consensus size: 87
27414 ATGTAAAAAT
* * ** * *
27424 GGTAAGGTCTTACCCTTGCACATAGCAAAAAAGCCTGGGAAACGGTAAAGTCTTACCCTTGCACA
1 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAACGGTAAGGACTTACCCTTGCACA
*
27489 TAGCAAAGGAGCCTGCGGTAAAT
66 TAGCAAAGGAGCCTGCGGT-AAC
*
27512 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAACGGTAAGGACTTATCCTTGCACA
1 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAACGGTAAGGACTTACCCTTGCACA
* *
27577 TAGAAAAGGAGCCTACGGTAAC
66 TAGCAAAGGAGCCTGCGGTAAC
** * * *
27599 GGTAAGGACTTACCCTTGCACATAATAGAGGAGCATGCTGTAACGGTAAGGACTTACCCTTGCAC
1 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG-GGAAACGGTAAGGACTTACCCTTGCAC
* * *
27664 ATAACAGAGGAGCCTTCGGTAAC
65 ATAGCAAAGGAGCCTGCGGTAAC
* * * ** *
27687 GATAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGCGATAATGACAAGGACTTACCCTTGTAC
1 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGA-AACGGTAAGGACTTACCCTTGCAC
* *
27752 ATAGCAGAGGAGCTTGCGGTAAC
65 ATAGCAAAGGAGCCTGCGGTAAC
*
27775 GGTAAGGACTTACCCTTGCACATAACAGAGGAGCCTG
1 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG
27812 ATGAAAACAG
Statistics
Matches: 263, Mismatches: 35, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
87 37 0.14
88 226 0.86
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (87 bp):
GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAACGGTAAGGACTTACCCTTGCACA
TAGCAAAGGAGCCTGCGGTAAC
Found at i:27616 original size:44 final size:44
Alignment explanation
Indices: 27424--27811 Score: 457
Period size: 44 Copynumber: 8.8 Consensus size: 44
27414 ATGTAAAAAT
* ** *
27424 GGTAAGGTCTTACCCTTGCACATAGCAA-AAAAGCCTG-GGAAAC
1 GGTAAGGACTTACCCTTGCACATAG-AAGAGGAGCCTGCGGTAAC
* * *
27467 GGTAAAGTCTTACCCTTGCACATAGCAA-AGGAGCCTGCGGTAAAT
1 GGTAAGGACTTACCCTTGCACATAG-AAGAGGAGCCTGCGGT-AAC
* *
27512 GGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG-GGAAAC
1 GGTAAGGACTTACCCTTGCACATAGAAGAGGAGCCTGCGGTAAC
* * *
27555 GGTAAGGACTTATCCTTGCACATAGAAAAGGAGCCTACGGTAAC
1 GGTAAGGACTTACCCTTGCACATAGAAGAGGAGCCTGCGGTAAC
* *
27599 GGTAAGGACTTACCCTTGCACATA-ATAGAGGAGCATGCTGTAAC
1 GGTAAGGACTTACCCTTGCACATAGA-AGAGGAGCCTGCGGTAAC
*
27643 GGTAAGGACTTACCCTTGCACATA-ACAGAGGAGCCTTCGGTAAC
1 GGTAAGGACTTACCCTTGCACATAGA-AGAGGAGCCTGCGGTAAC
* * * *
27687 GATAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGCGATAAT
1 GGTAAGGACTTACCCTTGCACATAGAAGAGGAGCCTGCGGTAAC
** * * *
27731 GACAAGGACTTACCCTTGTACATAGCAGAGGAGCTTGCGGTAAC
1 GGTAAGGACTTACCCTTGCACATAGAAGAGGAGCCTGCGGTAAC
27775 GGTAAGGACTTACCCTTGCACATA-ACAGAGGAGCCTG
1 GGTAAGGACTTACCCTTGCACATAGA-AGAGGAGCCTG
27812 ATGAAAACAG
Statistics
Matches: 299, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
43 70 0.23
44 195 0.65
45 34 0.11
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (44 bp):
GGTAAGGACTTACCCTTGCACATAGAAGAGGAGCCTGCGGTAAC
Found at i:33462 original size:23 final size:23
Alignment explanation
Indices: 33428--33492 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
33418 CAACACAGCT
*
33428 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
33451 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
33474 CGTAGAAATGCATCGAAGT
1 CGTAGAAATGCACCGAAGT
33493 ACCATATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:37365 original size:23 final size:23
Alignment explanation
Indices: 37319--37365 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37309 ATAATATGTA
*
37319 ACTATTCATCGTGAATGAATATG
1 ACTATTCATCGTGAATGAACATG
*
37342 ACTATTCATGGTGAAT-AGACATG
1 ACTATTCATCGTGAATGA-ACATG
37365 A
1 A
37366 TTATGTATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (23 bp):
ACTATTCATCGTGAATGAACATG
Found at i:39853 original size:21 final size:21
Alignment explanation
Indices: 39827--39873 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
39817 ATCCAGGCGA
39827 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
39848 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
39869 CATAC
1 CATAC
39874 AAGCCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (21 bp):
CATACGGGGTGACATACGAGC
Found at i:39872 original size:9 final size:9
Alignment explanation
Indices: 39860--39899 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
39850 TACGGGGTGA
39860 CATACGAGC
1 CATACGAGC
*
39869 CATACAAGC
1 CATACGAGC
39878 CATATACGAGC
1 C--ATACGAGC
39889 CATACGAGC
1 CATACGAGC
39898 CA
1 CA
39900 ATGGAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:39886 original size:20 final size:20
Alignment explanation
Indices: 39861--39899 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39851 ACGGGGTGAC
39861 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
39881 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
39900 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:39943 original size:28 final size:28
Alignment explanation
Indices: 39902--39958 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
39892 ACGAGCCAAT
* *
39902 GGAGAGGTCGCCATGCAGTCTTATACGA
1 GGAGAGGTCACCATGCAGTCTTAGACGA
39930 GGAGAGGTCACCATGCAGTCTTAGACGA
1 GGAGAGGTCACCATGCAGTCTTAGACGA
39958 G
1 G
39959 TCATACGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.19
Consensus pattern (28 bp):
GGAGAGGTCACCATGCAGTCTTAGACGA
Found at i:40027 original size:29 final size:29
Alignment explanation
Indices: 39977--40110 Score: 216
Period size: 29 Copynumber: 4.6 Consensus size: 29
39967 GCCAATGGAG
* *
39977 AGGTCGCCATGCAG-CCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
40006 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
40035 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
**
40064 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
40093 AGGTCGCCATGTAGTCCC
1 AGGTCGCCATGTAGTCCC
40111 ATGTAGTCCT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 98 0.98
30 2 0.02
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:40470 original size:25 final size:26
Alignment explanation
Indices: 40420--40470 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
40410 CTTGGTCGCC
**
40420 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
40446 GAGATTGCAGCCG-AGAAAGAAAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
40471 AGGGAGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.08
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:40856 original size:37 final size:38
Alignment explanation
Indices: 40806--41034 Score: 117
Period size: 37 Copynumber: 5.7 Consensus size: 38
40796 GTATTTTATA
*
40806 ATTATTAGT-AATAATTATTAAATCATTAGTATTAAATC
1 ATTATTA-TAAATAATTATTAAATCATTAGTATAAAATC
* * *
40844 A-TATTATAAATAATTACTAAATAATTATTATAAAATC
1 ATTATTATAAATAATTATTAAATCATTAGTATAAAATC
* * *
40881 ATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATTATTATAA--ATAATTATTAAATCATTAGT--AT-A--AAATC
* * * *
40926 ATTAAATATTTAAA-ACATTATTAAATCATT--TTTATAATG
1 ATT--AT-TATAAATA-ATTATTAAATCATTAGTATAAAATC
* * * *
40965 ATTATTACTAAATCATTATTATAATGATTATTATCAAATC
1 ATTATTA-TAAATAATTATTA-AATCATTAGTATAAAATC
* * *
41005 ATTACTATAATGATTATTATCAAATCATTA
1 ATTATTATAA--ATAATTATTAAATCATTA
41035 CTAAATCATC
Statistics
Matches: 145, Mismatches: 26, Indels: 38
0.69 0.12 0.18
Matches are distributed among these distances:
36 2 0.01
37 44 0.30
38 15 0.10
39 9 0.06
40 33 0.23
41 9 0.06
42 3 0.02
43 1 0.01
44 1 0.01
45 8 0.06
46 14 0.10
47 2 0.01
48 4 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (38 bp):
ATTATTATAAATAATTATTAAATCATTAGTATAAAATC
Found at i:40881 original size:51 final size:51
Alignment explanation
Indices: 40814--41161 Score: 135
Period size: 51 Copynumber: 7.0 Consensus size: 51
40804 TAATTATTAG
*
40814 TAATAATTATTAAATCATTAGTATTAAATCA-TATTAT-AAATAATTACTAAA
1 TAATAATTATAAAATCATTAGTA-T-AATCATTATTATCAAATAATTACTAAA
* * * *
40865 TAATTATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTAAA
1 TAATAATTATAAAATCATTAGTATAATCATTATTATCAAATAATTACTAAA
* * * * * **
40916 TCATCAAATCATTAAAT-ATT--TA-AAACATTA-T-T-AAATCATTTTTATAA
1 TAAT--AATTATAAAATCATTAGTATAATCATTATTATCAAATAATTACTA-AA
* * * * *
40963 TGATTATTACT-AAATCATTATTATAATGATTATTATCAAATCATTACTATAA
1 TAATAATTA-TAAAATCATTAGTATAATCATTATTATCAAATAATTACTA-AA
* * * * * * *
41015 TGATTATTATCAAATCATTACTA-AATCATCAAATCATTAAAT-ATT--TAAA
1 TAATAATTATAAAATCATTAGTATAATCAT--TATTATCAAATAATTACTAAA
** * *
41064 T--T-A-T-TAAAATCATTTTTATAATGATTATTA-CTAAATCATTA-TATAA
1 TAATAATTATAAAATCATTAGTATAATCATTATTATC-AAATAATTACTA-AA
* * * * * * *
41110 TGATTATTATCAAATCATTACTGTAATGATTATTATCAAATCATTACTAAA
1 TAATAATTATAAAATCATTAGTATAATCATTATTATCAAATAATTACTAAA
41161 T
1 T
41162 CAAATCATTA
Statistics
Matches: 233, Mismatches: 36, Indels: 56
0.72 0.11 0.17
Matches are distributed among these distances:
43 7 0.03
44 14 0.06
45 15 0.06
46 18 0.08
47 7 0.03
48 4 0.02
49 20 0.09
50 13 0.06
51 77 0.33
52 42 0.18
53 16 0.07
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (51 bp):
TAATAATTATAAAATCATTAGTATAATCATTATTATCAAATAATTACTAAA
Found at i:40905 original size:26 final size:26
Alignment explanation
Indices: 40819--41155 Score: 237
Period size: 26 Copynumber: 13.6 Consensus size: 26
40809 ATTAGTAATA
* * *
40819 ATTATTAAATCATTAGTATTAAATCA-T
1 ATTATCAAATCATTATTA-T-AATGATT
* * *
40846 ATTAT-AAATAATTACTA-AATAATT
1 ATTATCAAATCATTATTATAATGATT
*
40870 ATTATAAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
* * *
40896 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATGATT
* * * * **
40921 A-AATC-ATTAAATATT-TAA--AAC
1 ATTATCAAATCATTATTATAATGATT
* *
40942 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
40968 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
*
40994 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
* * *
41020 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATGATT
* * * *
41045 A-AATC-ATTAAATATT-TAA--ATT
1 ATTATCAAATCATTATTATAATGATT
*
41066 ATTA--AAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
41090 ATTA-CTAAATCATTA-TATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
* *
41115 ATTATCAAATCATTACTGTAATGATT
1 ATTATCAAATCATTATTATAATGATT
41141 ATTATCAAATCATTA
1 ATTATCAAATCATTA
41156 CTAAATCAAA
Statistics
Matches: 247, Mismatches: 42, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
21 12 0.05
22 6 0.02
23 26 0.11
24 22 0.09
25 45 0.18
26 130 0.53
27 6 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:41014 original size:124 final size:123
Alignment explanation
Indices: 40819--41210 Score: 597
Period size: 124 Copynumber: 3.2 Consensus size: 123
40809 ATTAGTAATA
* * * *
40819 ATTATTAAATCATTAGTATTA-AATCA-TATTA-TAAATAATTACTA-AATAATTATTATAAAAT
1 ATTATTAAATCATT--T-TTATAATGATTATTACTAAATCATTA-TATAATGATTATTATCAAAT
*
40880 CATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAAC
62 CATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAAC
40942 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTA-TATAATGATTATTATCAAATCAT
41007 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTT--AA-
65 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAAC
41063 ATTATTAAAATCATTTTTATAATGATTATTACTAAATCATTATATAATGATTATTATCAAATCAT
1 ATTATT-AAATCATTTTTATAATGATTATTACTAAATCATTATATAATGATTATTATCAAATCAT
* *
41128 TACTGTAATGATTATTATCAAATCATTACT-AA--ATCAAATCATTAAATATTTAAATC
65 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAAC
41184 ATTATTAAATCATTTTTATAATGATTA
1 ATTATTAAATCATTTTTATAATGATTA
41211 ATAAATACAT
Statistics
Matches: 253, Mismatches: 8, Indels: 19
0.90 0.03 0.07
Matches are distributed among these distances:
118 19 0.08
120 27 0.11
121 69 0.27
122 42 0.17
123 25 0.10
124 71 0.28
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (123 bp):
ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATATAATGATTATTATCAAATCATT
ACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAAAC
Found at i:41067 original size:98 final size:95
Alignment explanation
Indices: 40866--41131 Score: 296
Period size: 98 Copynumber: 2.8 Consensus size: 95
40856 ATTACTAAAT
* * * *
40866 AATTATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATCAAATCATTA
1 AATTATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT--TATTATCA
* * *
40930 AAT-ATTTA-AAACATTATTAAATCATTTTTATA
63 AATCA-TTACTAACATCATCAAATCATTTTTATA
40962 ATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCA
1 A--ATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCA
41027 AATCATTACTAA-ATCATCAAATCATTAAATATT-TA
63 AATCATTACTAACATCATCAAATCATT---T-TTATA
*
41062 AATTATTA-AAATCATTTTTATAATGATTATTA-CTAAATCATTA-TATAATGATTATTATCAAA
1 AATTATTATAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAA
41124 TCATTACT
65 TCATTACT
41132 GTAATGATTA
Statistics
Matches: 151, Mismatches: 8, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
95 28 0.19
96 33 0.22
97 23 0.15
98 55 0.36
99 6 0.04
100 4 0.03
101 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (95 bp):
AATTATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAAT
CATTACTAACATCATCAAATCATTTTTATA
Done.