Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000803.1 Hibiscus syriacus cultivar Beakdansim tig00001558_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: 54460
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:5891 original size:9 final size:9
Alignment explanation
Indices: 5877--5910 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5867 TAATTATTAT
5877 TTAATAATA
1 TTAATAATA
5886 TTAATAATA
1 TTAATAATA
* *
5895 ATAATAACA
1 TTAATAATA
5904 TTAATAA
1 TTAATAA
5911 AATTGTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
TTAATAATA
Found at i:6666 original size:123 final size:123
Alignment explanation
Indices: 6308--6825 Score: 725
Period size: 123 Copynumber: 4.2 Consensus size: 123
6298 TTCTTCGTAC
* * * * * *
6308 GAGTTCTTCTTATTATGAACTCTTTCTGGAAATACTGATGTTGTTATATTTCTTTCTGCAATAGA
1 GAGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCTTTCTGCAATAGA
6373 GTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
66 GTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
* * * *
6431 GAGTTCTTCTTATTACAAACTCCTTCTTGAAATGTT-ATGTTGCTCTATCTCTTTCTGCGATAGA
1 GAGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCTTTCTGCAATAGA
** * *
6495 GTCAAGCAAAAGGTTGTTTAAATTATTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
66 GTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
* *
6553 GAGTTCTTCTTATTACGAACTCCTTCTGAAAATATTGGTGCTT-CTCTATCTCTTTCTGCAATAG
1 GAGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATG-TTGCTCTATCTCTTTCTGCAATAG
* *
6617 AGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGAT
65 AGTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
* * * ** *
6676 GAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCATTCTGTGACAGA
1 GAGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCTTTCTGCAATAGA
* * * * * * *
6741 ATCGAGAAAAAGGTTGAATACGTTCTTCAGATTATAAACTTCTTCTACCTCTTTAGAT
66 GTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
*
6799 GAGTTCTTCTTATTACAAACTCCTTCT
1 GAGTTCTTCTTATTACGAACTCCTTCT
6826 AGATTATGAA
Statistics
Matches: 350, Mismatches: 42, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
122 111 0.32
123 237 0.68
124 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
GAGTTCTTCTTATTACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCTTTCTGCAATAGA
GTCAAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGAT
Found at i:6865 original size:56 final size:57
Alignment explanation
Indices: 6765--6881 Score: 157
Period size: 56 Copynumber: 2.1 Consensus size: 57
6755 TGAATACGTT
*
6765 CTTC-AGATTATAAACTTCTTCTACCTCTTTAGATGAGTTCTTCTTATTACAAACTC
1 CTTCTAGATTATAAACTTCTTCTACCTCTTCAGATGAGTTCTTCTTATTACAAACTC
* ** * *
6821 CTTCTAGATTATGAACTTCTT-TTTCTCTTCAGATTAGTTCTTCTTATTACGAACTC
1 CTTCTAGATTATAAACTTCTTCTACCTCTTCAGATGAGTTCTTCTTATTACAAACTC
*
6877 TTTCT
1 CTTCT
6882 TGAAATATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
56 38 0.72
57 15 0.28
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.47
Consensus pattern (57 bp):
CTTCTAGATTATAAACTTCTTCTACCTCTTCAGATGAGTTCTTCTTATTACAAACTC
Found at i:7098 original size:297 final size:302
Alignment explanation
Indices: 6523--7111 Score: 836
Period size: 297 Copynumber: 2.0 Consensus size: 302
6513 TAAATTATTC
6523 AGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGAAAATAT
1 AGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGAAAATAT
* *
6588 TGGTGCTTCTCTATCTCTTTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTAT
66 TGATGCTTCTCTATCTCTTTCTGCAATA-AGTCGAGCAAAAGATTGAATAAGTTCTTCAGATTAT
* *
6653 GAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGCT
130 GAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTCCTTCTGGAAATGTTGATGCT
* * * *
6718 GCTCTATCTCATTCTGTGACAGAATCGAGAAAAAGGTTGAATACGTTCTTCAGATTATAAACTTC
195 GCTCTATATCATTCTGCGACAGAATCGAGAAAAAGGTTGAATAAGTTCTTCAAATTATAAACTTC
**
6783 TTCTACCTCTTTAGATGAGTTCTTCTTATTACAAACTCCTTCT
260 TTCTACCTCTCCAGATGAGTTCTTCTTATTACAAACTCCTTCT
* * *
6826 AGATTATGAACTTCTT-TTTCTCTTCAGATTAGTTCTTCTTATTACGAACTCTTTCTTG-AAATA
1 AGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC-TGAAAATA
* * *
6889 TTGATG-TTGCTCTATCTCATTT-TGCGAT-AGTCTAGCAAAAGATTGAATAAGTTCTTTAGATT
65 TTGATGCTT-CTCTATCTC-TTTCTGCAATAAGTCGAGCAAAAGATTGAATAAGTTCTTCAGATT
* *
6951 ATGAACTT-TT-TT-CTCTTCAGATGAGTTCTTCTCATTACGAACTCTTTCTGGAAATGTTGATT
128 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTCCTTCTGGAAATGTTGATG
* * * * *
7013 CTGCTCTATATCCTTCTGCGATA-AAGTCTAGCAAAAGGTTGAATAAGTTCTTCAAATTATTAAC
193 CTGCTCTATATCATTCTGCGACAGAA-TCGAGAAAAAGGTTGAATAAGTTCTTCAAATTATAAAC
* **
7077 TTTTTCTTTCTCTCCAGATGAGTTCTTCTTATTAC
257 TTCTTCTACCTCTCCAGATGAGTTCTTCTTATTAC
7112 GAACGTCTTC
Statistics
Matches: 256, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
296 2 0.01
297 129 0.50
298 2 0.01
299 2 0.01
300 38 0.15
301 2 0.01
302 60 0.23
303 21 0.08
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (302 bp):
AGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGAAAATAT
TGATGCTTCTCTATCTCTTTCTGCAATAAGTCGAGCAAAAGATTGAATAAGTTCTTCAGATTATG
AACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTACGAACTCCTTCTGGAAATGTTGATGCTG
CTCTATATCATTCTGCGACAGAATCGAGAAAAAGGTTGAATAAGTTCTTCAAATTATAAACTTCT
TCTACCTCTCCAGATGAGTTCTTCTTATTACAAACTCCTTCT
Found at i:7127 original size:123 final size:121
Alignment explanation
Indices: 6825--7257 Score: 529
Period size: 123 Copynumber: 3.6 Consensus size: 121
6815 AAACTCCTTC
* * *
6825 TAGATTATGAACTTCTTTTTCTCTTCAGATTAGTTCTTCTTATTACGAACTCTTTCTTGAAATAT
1 TAGATTATGAACTTCTTTTTCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGGAAATGT
* * *
6890 TGATGTTGCTCTATCTCATTTTGCGAT--AGTCTAGCAAAAGATTGAATAAGTTCTT
66 TGAT-TTGCTCTATCTCCTTCTGCGATAAAGTCTAGCAAAAGGTTGAATAAGTTCTT
*
6945 TAGATTATGAAC-T-TTTTTCTCTTCAGATGAGTTCTTCTCATTACGAACTCTTTCTGGAAATGT
1 TAGATTATGAACTTCTTTTTCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGGAAATGT
*
7008 TGATTCTGCTCTATATCCTTCTGCGATAAAGTCTAGCAAAAGGTTGAATAAGTTCTT
66 TGATT-TGCTCTATCTCCTTCTGCGATAAAGTCTAGCAAAAGGTTGAATAAGTTCTT
* * * * *
7065 CAAATTATTAACTTTTTCTTTCTCTCCAGATGAGTTCTTCTTATTACGAACGTC-TTCTGGAAAT
1 TAGATTATGAACTTCTT-TTTCTCTTCAGATGAGTTCTTCTTATTACGAAC-TCTTTCTGGAAAT
* * * ** * *
7129 GTTGGTGATGGTCTATCTCCTTCTATGATAGAA-TCAAACAAAAGGTTGAATAAGTTCTT
64 GTTGAT-TTGCTCTATCTCCTTCTGCGATA-AAGTCTAGCAAAAGGTTGAATAAGTTCTT
* * * *
7188 TAGATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTTTTTATTACGAACT-TCTTCTGGAAAT
1 TAGATTATGAACTTCTT-TTTCTCTTCAGATGAGTTCTTCTTATTACGAACTCT-TTCTGGAAAT
7252 GTTGAT
64 GTTGAT
7258 CCATCGAGTG
Statistics
Matches: 271, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
117 1 0.00
118 68 0.25
119 1 0.00
120 48 0.18
121 1 0.00
122 3 0.01
123 145 0.54
124 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (121 bp):
TAGATTATGAACTTCTTTTTCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTTCTGGAAATGT
TGATTTGCTCTATCTCCTTCTGCGATAAAGTCTAGCAAAAGGTTGAATAAGTTCTT
Found at i:8705 original size:50 final size:51
Alignment explanation
Indices: 8620--8763 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 51
8610 ATATCCCAAC
* *
8620 CTTTTTATGCTGGTGT-AGCCTTCAAGATGCTCCACATGGATTACTTCTAT
1 CTTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTAT
*
8670 CTTTTCATGCTGGTGTGAGCCTTCAAGAT-CCCCACATGGATTACTTCTGT
1 CTTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTAT
** **
8720 CTTTTCATAATGAAGTGAGCCTTCAAGATGCCCCACATGGATTA
1 CTTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTA
8764 TATGGACCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
50 59 0.69
51 26 0.31
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (51 bp):
CTTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTACTTCTAT
Found at i:10062 original size:90 final size:90
Alignment explanation
Indices: 9908--10077 Score: 234
Period size: 90 Copynumber: 1.9 Consensus size: 90
9898 CACATTTATC
* * * *
9908 AAGCTAGGTGAAACTTATCCATAAATCCGGAGCTATTAACCAATTACTCTATAGGGACATCTCAA
1 AAGCTAGCTGAAACTTATCCATAAAGCCGGAGCTATTAACCAATTACTCTAGAGGGACAACTCAA
*
9973 TCTTTATTACATATAATAGTATAAT
66 GCTTTATTACATATAATAGTATAAT
* * **
9998 AAGCTAGCTGAATA-TTATCCATAAAGCCGGGGTTATTAACCAATTGTTCTAGAGGGACAACTCA
1 AAGCTAGCTGAA-ACTTATCCATAAAGCCGGAGCTATTAACCAATTACTCTAGAGGGACAACTCA
*
10062 AGCTTTATTGCATATA
65 AGCTTTATTACATATA
10078 TAATAATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 68 0.99
91 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (90 bp):
AAGCTAGCTGAAACTTATCCATAAAGCCGGAGCTATTAACCAATTACTCTAGAGGGACAACTCAA
GCTTTATTACATATAATAGTATAAT
Found at i:15460 original size:19 final size:17
Alignment explanation
Indices: 15413--15460 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
15403 AAAATAAAAT
15413 AATAAATAAAGAATTGA
1 AATAAATAAAGAATTGA
*
15430 AAGAAATCTAAAGAATTGTA
1 AATAAA--TAAAGAATTG-A
15450 AATTAAATAAA
1 AA-TAAATAAA
15461 TCTAAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 5 0.20
19 14 0.56
20 3 0.12
21 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.25
Consensus pattern (17 bp):
AATAAATAAAGAATTGA
Found at i:17427 original size:3 final size:3
Alignment explanation
Indices: 17421--17450 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17411 AATTATTATT
17421 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17451 CATTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17909 original size:18 final size:18
Alignment explanation
Indices: 17886--17927 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
17876 TACATGTTCA
17886 AGTTTATATATCACCATT
1 AGTTTATATATCACCATT
17904 AGTTTATATATCACCATT
1 AGTTTATATATCACCATT
*
17922 AATTTA
1 AGTTTA
17928 CTATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (18 bp):
AGTTTATATATCACCATT
Found at i:19341 original size:21 final size:22
Alignment explanation
Indices: 19315--19365 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
19305 CCATGATGAA
19315 AATTAGGGATTGGGGGTCA-AG
1 AATTAGGGATTGGGGGTCAGAG
*
19336 AATTAGGGATTGTGGGTCAGAG
1 AATTAGGGATTGGGGGTCAGAG
19358 AATT-GGGA
1 AATTAGGGA
19366 AATTAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.29, C:0.04, G:0.41, T:0.25
Consensus pattern (22 bp):
AATTAGGGATTGGGGGTCAGAG
Found at i:19493 original size:14 final size:14
Alignment explanation
Indices: 19474--19502 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19464 CAATCGGGGC
19474 CTGAAAAAGGGTAA
1 CTGAAAAAGGGTAA
19488 CTGAAAAAGGGTAA
1 CTGAAAAAGGGTAA
19502 C
1 C
19503 AAATAAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.28, T:0.14
Consensus pattern (14 bp):
CTGAAAAAGGGTAA
Found at i:20653 original size:16 final size:17
Alignment explanation
Indices: 20632--20664 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20622 GCCCATTTTA
20632 CTTAA-TTGAATTTCTT
1 CTTAATTTGAATTTCTT
*
20648 CTTAATTTTAATTTCTT
1 CTTAATTTGAATTTCTT
20665 TAAATTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (17 bp):
CTTAATTTGAATTTCTT
Found at i:22363 original size:85 final size:86
Alignment explanation
Indices: 22269--22463 Score: 271
Period size: 85 Copynumber: 2.3 Consensus size: 86
22259 AAAAACAAAC
* * *
22269 TAAAGATAAT-TCCTAAAATAATATCTTAAATCCTAATTAAAACACTTAAAACTATTTTAACTAA
1 TAAAGATAATAT-CTAAAATAATATCCTAAATCCTAATTAAAACACTTAAAACCATTTAAACTAA
*
22333 AATACCTAAAACAAAGATAAAA
65 AATACCGAAAACAAAGATAAAA
*
22355 TAAA-ATAATATTTAAAATAATATCCTAAATCCTAATTAAAACACTTAAAACCATTTAAACTAAA
1 TAAAGATAATATCTAAAATAATATCCTAAATCCTAATTAAAACACTTAAAACCATTTAAACTAAA
*
22419 ATTCCGAAAACAAAGATAAAA
66 ATACCGAAAACAAAGATAAAA
22440 T--A-AT-AT-T-TAAAATAATATCCTAAA
1 TAAAGATAATATCTAAAATAATATCCTAAA
22464 CCATTTTTTT
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
80 17 0.17
81 1 0.01
82 2 0.02
83 3 0.03
85 74 0.73
86 5 0.05
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.29
Consensus pattern (86 bp):
TAAAGATAATATCTAAAATAATATCCTAAATCCTAATTAAAACACTTAAAACCATTTAAACTAAA
ATACCGAAAACAAAGATAAAA
Found at i:27045 original size:12 final size:12
Alignment explanation
Indices: 27028--27057 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27018 TAGGGCCATT
27028 AGTTTTACATCA
1 AGTTTTACATCA
*
27040 AGTTTTACATTA
1 AGTTTTACATCA
27052 AGTTTT
1 AGTTTT
27058 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:29530 original size:10 final size:10
Alignment explanation
Indices: 29515--29554 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
29505 CATTTAAATG
29515 ATAAACGAAC
1 ATAAACGAAC
29525 ATAAACGAAC
1 ATAAACGAAC
*
29535 GTAAACGAAC
1 ATAAACGAAC
*
29545 ACAAACGAAC
1 ATAAACGAAC
29555 GAACATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:29541 original size:20 final size:20
Alignment explanation
Indices: 29516--29555 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29506 ATTTAAATGA
*
29516 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
29536 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
29556 AACATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:29598 original size:27 final size:27
Alignment explanation
Indices: 29542--29599 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
29532 AACGTAAACG
* *
29542 AACACAAACGAACGAACATAATAAATA
1 AACACAAACGAACGAACATAACAAAAA
*
29569 AACATAAACGAAC-AACATAGACAAAAA
1 AACACAAACGAACGAACATA-ACAAAAA
29596 AACA
1 AACA
29600 AACTTGTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.66, C:0.19, G:0.07, T:0.09
Consensus pattern (27 bp):
AACACAAACGAACGAACATAACAAAAA
Found at i:29889 original size:24 final size:24
Alignment explanation
Indices: 29847--29924 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
29837 CCCTCTGTTC
*
29847 GAACATAAATGAACAAACATAAAT
1 GAACATAAATGAACGAACATAAAT
* * *
29871 GAGCATAAATTAACGAACACAAAT
1 GAACATAAATGAACGAACATAAAT
29895 GAACATAAATGAACGAACATATAAT
1 GAACATAAATGAACGAACATA-AAT
29920 CGAAC
1 -GAAC
29925 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 38 0.84
25 3 0.07
26 4 0.09
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.17
Consensus pattern (24 bp):
GAACATAAATGAACGAACATAAAT
Found at i:29924 original size:16 final size:14
Alignment explanation
Indices: 29846--29925 Score: 59
Period size: 14 Copynumber: 6.1 Consensus size: 14
29836 ACCCTCTGTT
29846 CGAACATAAATGAA
1 CGAACATAAATGAA
*
29860 CAAACATAAATG-A
1 CGAACATAAATGAA
*
29873 -G--CATAAATTAA
1 CGAACATAAATGAA
*
29884 CGAACACAAAT---
1 CGAACATAAATGAA
29895 -GAACATAAATGAA
1 CGAACATAAATGAA
29908 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
29924 CG
1 CG
29926 TTCACGAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
10 16 0.31
11 1 0.02
12 1 0.02
13 1 0.02
14 24 0.47
15 3 0.06
16 5 0.10
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:32417 original size:14 final size:14
Alignment explanation
Indices: 32378--32418 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
32368 TACGGGTATC
*
32378 ATAATAAAAGA-A-
1 ATAATATAAGATAT
*
32390 ATAATATAAAATAT
1 ATAATATAAGATAT
32404 ATAATATAAGATAT
1 ATAATATAAGATAT
32418 A
1 A
32419 CACAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 14 0.58
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (14 bp):
ATAATATAAGATAT
Found at i:33911 original size:10 final size:10
Alignment explanation
Indices: 33898--33924 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
33888 AAATAGTAAT
33898 AAATAAAAAC
1 AAATAAAAAC
33908 AAATAAAAAC
1 AAATAAAAAC
33918 AAATAAA
1 AAATAAA
33925 GATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAAAC
Found at i:34147 original size:18 final size:18
Alignment explanation
Indices: 34106--34146 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
34096 ATACACTAAT
* *
34106 TAAAAGAATAAAAAATCT
1 TAAAATAATAAAAAATCC
34124 TAAAATAATAAAAAGATCC
1 TAAAATAATAAAAA-ATCC
34143 TAAA
1 TAAA
34147 TTACCCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (18 bp):
TAAAATAATAAAAAATCC
Found at i:42901 original size:43 final size:43
Alignment explanation
Indices: 42809--42901 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 43
42799 TAAATATTTC
* *
42809 GCGGCGTTTGTAGTAAAAAATGCCACAATATATTTGATATATA
1 GCGGCGTTTGTAGTAAAAAACGCCACAATAGATTTGATATATA
* *
42852 GAGGCGTTTGTAGTAAAAAAACGCCACAATAGATTTGATATGT-
1 GCGGCGTTTGTAGT-AAAAAACGCCACAATAGATTTGATATATA
42895 GCGGCGT
1 GCGGCGT
42902 GTCTGACAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 19 0.43
44 25 0.57
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTAGTAAAAAACGCCACAATAGATTTGATATATA
Found at i:53934 original size:21 final size:21
Alignment explanation
Indices: 53908--53947 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53898 GTCCCCTTTA
*
53908 AAGGGGGAATCGGTTCCCTTC
1 AAGGGGGAATCGATTCCCTTC
*
53929 AAGGGGGTATCGATTCCCT
1 AAGGGGGAATCGATTCCCT
53948 CTGCACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (21 bp):
AAGGGGGAATCGATTCCCTTC
Done.