Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004387.1 Hibiscus syriacus cultivar Beakdansim tig00009618_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: 51800
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9577 original size:120 final size:121
Alignment explanation
Indices: 9410--9638 Score: 302
Period size: 120 Copynumber: 1.9 Consensus size: 121
9400 TACTTATTGA
*
9410 GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGGGAGAAATAGATAAGATAATTGGGTAGAC
1 GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATAATTGGGTAGAC
** * *
9475 ATTGATGAATTGCAGAG-GGTTATTTTTT-TTACAAAAAGTTTAGGTTAGGAGTGT
66 ACAGATAAATTGAAGAGAGGTTATTTTTTGTTACAAAAAGTTTAGGTTAGGAGTGT
* * * * * *
9529 GGGTCCTGAGTAGAAGAAAAAAAATTTTGAGGT-GTAGAGAGAAGTAGATAAGATTATTGGGTCG
1 GGGTCCTGAGCAAAAG-AAAAAAATGTTGAGGTCG-AGAGAGAAATAGATAAGATAATTGGGTAG
* *
9593 ACACAGATAAATTGAAGAGAGTTTTTTTTTTGTTACAAAAAGTTTA
64 ACACAGATAAATTGAAGAGAGGTTATTTTTTGTTACAAAAAGTTTA
9639 TGTCAAGAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
119 15 0.16
120 55 0.59
121 9 0.10
122 14 0.15
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.30
Consensus pattern (121 bp):
GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATAATTGGGTAGAC
ACAGATAAATTGAAGAGAGGTTATTTTTTGTTACAAAAAGTTTAGGTTAGGAGTGT
Found at i:11460 original size:69 final size:69
Alignment explanation
Indices: 11347--11568 Score: 214
Period size: 69 Copynumber: 3.2 Consensus size: 69
11337 CCTGTTTGTG
* ** * * * * **
11347 AGTCACTTTAATCCTTC-GGAGTTCCTGTGCGAGTCAACCGAAATAATTACGATTAGGTGCTTTC
1 AGTCACTCTAATCCTTCAGGACATCC-GTCCAAGTCACCCAAAATAATTACGATTAGGTGCTCCC
11411 GTGCA
65 GTGCA
*
11416 AGTCACTCTAATCCTTCAGGA-ATCCGATCCAAGTCACCCAAAATAATTATGATTAGGTGCTCCC
1 AGTCACTCTAATCCTTCAGGACATCCG-TCCAAGTCACCCAAAATAATTACGATTAGGTGCTCCC
*
11480 GTGTA
65 GTGCA
* * * *** * * * *
11485 AGTCACTCTAATCCTTCGGGACTTTCGTGTGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCT
1 AGTCACTCTAATCCTTCAGGACATCCGTCCAAGTCACCCAAAATAATTACGATTAGGTGCTCCCG
11550 TGCA
66 TGCA
*
11554 AGACACTCTAATCCT
1 AGTCACTCTAATCCT
11569 ACGAGCCTCC
Statistics
Matches: 127, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
68 1 0.01
69 120 0.94
70 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (69 bp):
AGTCACTCTAATCCTTCAGGACATCCGTCCAAGTCACCCAAAATAATTACGATTAGGTGCTCCCG
TGCA
Found at i:11588 original size:69 final size:69
Alignment explanation
Indices: 11373--11590 Score: 172
Period size: 69 Copynumber: 3.2 Consensus size: 69
11363 CGGAGTTCCT
* * * * * ** * *
11373 GTGCGAGTCAACCGAAATAATTACGATTAGGTGCTTTCGTGCAAGTCACTCTAATCCTTC-AGGA
1 GTGCGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCGTGCAAGACACTCTAATCCTACGA-GA
*
11437 ATC-C
65 CTCTC
* * * * * * * * * *
11441 GATCCAAGTCACCCAAAATAATTATGATTAGGTGCTCCCGTGTAAGTCACTCTAATCCTTCGGGA
1 G-TGCGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCGTGCAAGACACTCTAATCCTACGAGA
*
11506 CTTTC
65 CTCTC
* * *
11511 GTGTGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCTTGCAAGACACTCTAATCCTACGAGCC
1 GTGCGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCGTGCAAGACACTCTAATCCTACGAGAC
11576 TC-C
66 TCTC
11579 TGTGCGAGTCAC
1 -GTGCGAGTCAC
11591 TCGGAATACT
Statistics
Matches: 120, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
68 2 0.02
69 116 0.97
70 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (69 bp):
GTGCGAGTCACCCAAAAAAATCACGATTAGGTCCTCCCGTGCAAGACACTCTAATCCTACGAGAC
TCTC
Found at i:11890 original size:76 final size:76
Alignment explanation
Indices: 11779--12359 Score: 580
Period size: 76 Copynumber: 7.8 Consensus size: 76
11769 AGAATTCTAG
* * * * *
11779 CAGTGAAACATAACATTAACTTACACTAGTGAAATGAATACATAATTCTAGCACTAAACTTATAA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
*
11844 CATGATTTCAA
66 CATAATTTCAA
* * * * * * *
11855 CAGTCAAACTTAAAATTTACTTACACTAGTTAAATGAATATGTGATTCTAGCACTAAACTTAAT-
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTT-ATC
* *
11919 ACATGATTTCAG
65 ACATAATTTCAA
* * * * * *
11931 CAGTGAAACTTAACATTGATTTACTCCATTGAAATGAATATGTAATTCTAGCACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
*
11996 CATAATTTAAA
66 CATAATTTCAA
* * **
12007 CAGTGAAACTTAACATTGACTTATACGAGTGAAATGAATACGTAATTCCAGCTTTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
*
12072 CATAATTCCAA
66 CATAATTTCAA
* * * ** *
12083 TAGTGAAACTTAACATTAACTTACACCAAAGAAATGAATACGTAATTCCAACACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
*
12148 CATAATTCCAA
66 CATAATTTCAA
* * *
12159 CAATGAAATTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAACACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
* *
12224 CCTAA-TTCTAG
66 CATAATTTC-AA
* * * *
12235 CAATGAAATTTAAC-----C--A-A-TA---AAATGAATATGTAATTCCAACACTAAACTTATCA
1 CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
* *
12288 CATAATTCCAG
66 CATAATTTCAA
* * * * *
12299 TAGCGAAACTTAACATTGACTTACA-TCAGTGAAATGAATAAGTAACTCCAACACTAAACTT
1 CAGTGAAACTTAACATTGACTTACACT-AGTGAAATGAATACGTAATTCCAGCACTAAACTT
12360 TGAAGCTTAA
Statistics
Matches: 429, Mismatches: 60, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
64 49 0.11
65 2 0.00
67 2 0.00
68 1 0.00
69 2 0.00
71 2 0.00
72 2 0.00
73 1 0.00
75 4 0.01
76 362 0.84
77 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (76 bp):
CAGTGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCA
CATAATTTCAA
Found at i:12312 original size:64 final size:64
Alignment explanation
Indices: 12190--12312 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
12180 TACACTAGTG
* * * *
12190 AAATGAATACGTAATTCCAACACTAAACTTATCACCTAATTCTAGCAATGAAATTTAACCAATA
1 AAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAACGAAACTTAACCAATA
* * *
12254 AAATGAATATGTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCGAAACTTAAC
1 AAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAACGAAACTTAAC
12313 ATTGACTTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (64 bp):
AAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAACGAAACTTAACCAATA
Found at i:12359 original size:140 final size:138
Alignment explanation
Indices: 12101--12505 Score: 482
Period size: 140 Copynumber: 2.9 Consensus size: 138
12091 CTTAACATTA
* *
12101 ACTTACACCAA-AGAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAACAATGA
1 ACTTACACCAATA-AAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGA
* *
12165 AATTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACCTAAT
65 AATTTAACATTGACTTACACAAGTGAAATGAATAAGTAATTCCAACACTAAACTTATCA-CTAAT
*
12230 TCTAGCAATG
129 TCTAACAATG
* * * *
12240 AAATTTA-ACCAATAAAATGAATATGTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCG
1 --ACTTACACCAATAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTG
* * * *
12304 AAACTTAACATTGACTTACATC-AGTGAAATGAATAAGTAACTCCAACACTAAACTT-TGA--AG
64 AAATTTAACATTGACTTACA-CAAGTGAAATGAATAAGTAATTCCAACACTAAACTTATCACTAA
* *
12365 CT-TAACATTG
128 TTCTAACAATG
* * * * * *
12375 ACTTACATCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATCCCTGCAGTGAA
1 ACTTACACCAATAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAA
* * * *
12440 ATTTAACATTGACATACACAAGTGAAATGAATAGGTAATTCCAGCACTAAATTTATCACATAATT
66 ATTTAACATTGACTTACACAAGTGAAATGAATAAGTAATTCCAACACTAAACTTATCAC-TAATT
12505 C
130 C
12506 ATGCAGTAAA
Statistics
Matches: 222, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
133 5 0.02
134 96 0.43
135 8 0.04
136 2 0.01
138 2 0.01
139 2 0.01
140 101 0.45
141 6 0.03
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (138 bp):
ACTTACACCAATAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAA
ATTTAACATTGACTTACACAAGTGAAATGAATAAGTAATTCCAACACTAAACTTATCACTAATTC
TAACAATG
Found at i:12412 original size:58 final size:58
Alignment explanation
Indices: 12307--12417 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
12297 AGTAGCGAAA
12307 CTTAACATTGACTTACATCAGTGAAATGAATAAGTAACTCCAACACTAAACTTTGAAG
1 CTTAACATTGACTTACATCAGTGAAATGAATAAGTAACTCCAACACTAAACTTTGAAG
* * *
12365 CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTCCAGCACTAAACTT
1 CTTAACATTGACTTACATCAGTGAAATGAATAAGTAACTCCAACACTAAACTT
12418 ATCACATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (58 bp):
CTTAACATTGACTTACATCAGTGAAATGAATAAGTAACTCCAACACTAAACTTTGAAG
Found at i:12496 original size:76 final size:75
Alignment explanation
Indices: 12365--12548 Score: 269
Period size: 76 Copynumber: 2.4 Consensus size: 75
12355 AACTTTGAAG
12365 CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATCC
1 CTTAACATTGACTTACA-CAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATCC
* *
12430 CTGCAGTGAAA
65 ATGCAGTAAAA
* * * * *
12441 TTTAACATTGACATACACAAGTGAAATGAATAGGTAATTCCAGCACTAAATTTATCACATAATTC
1 CTTAACATTGACTTACAC-AGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATCC
12506 ATGCAGTAAAA
65 ATGCAGTAAAA
*
12517 CTTAATATTGACTTACACCAGTGAAATGAATA
1 CTTAACATTGACTTACA-CAGTGAAATGAATA
12549 TGCAACGATG
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
75 1 0.01
76 94 0.98
77 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (75 bp):
CTTAACATTGACTTACACAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATCCA
TGCAGTAAAA
Found at i:12921 original size:2 final size:2
Alignment explanation
Indices: 12914--12938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12904 TATAAGAATT
12914 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12939 GTTACATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19139 original size:16 final size:17
Alignment explanation
Indices: 19118--19155 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
19108 TAAGAAAAAA
*
19118 ATATGAAATAT-ATATC
1 ATATGAAATATGAAATC
19134 ATATG-AATATGAAATC
1 ATATGAAATATGAAATC
19150 ATATGA
1 ATATGA
19156 GAGGTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (17 bp):
ATATGAAATATGAAATC
Found at i:19583 original size:32 final size:32
Alignment explanation
Indices: 19542--19629 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
19532 AGTCGAGGGT
19542 TTACCTATGTTCTACGAAACATATGGACAGAA
1 TTACCTATGTTCTACGAAACATATGGACAGAA
* * * *
19574 TTACCTATG-TCTTTCGAGATATATGGACAGTA
1 TTACCTATGTTC-TACGAAACATATGGACAGAA
* * *
19606 -GACCTATGTTCTAAGGAACATATG
1 TTACCTATGTTCTACGAAACATATG
19630 TATAGTTTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
31 17 0.39
32 27 0.61
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTACGAAACATATGGACAGAA
Found at i:23038 original size:18 final size:20
Alignment explanation
Indices: 23015--23057 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
23005 AATAATTAAA
*
23015 CATCGAATGCA-ATGA-GTG
1 CATCGAATGCACAGGACGTG
23033 CATCG-ATGCACAGGACGTG
1 CATCGAATGCACAGGACGTG
23052 CATCGA
1 CATCGA
23058 TACACCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (20 bp):
CATCGAATGCACAGGACGTG
Found at i:23781 original size:65 final size:64
Alignment explanation
Indices: 23651--23801 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 64
23641 AATTAAATTG
* * * * *
23651 AACATCGAATGCATTTCATGCATTGATGCACATACCATGCACCGATGCACTGAGGATGTTATGAA
1 AACATCGAATGCATTTGATGCATCGATACACATACCATGCACCGATGCACTCAGGATATTATG-A
* * * * * *
23716 AACATTGAATGCATTTGATGCATCGATACACCA-GCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATACA-CATACCATGCACCGATGCACTCAGGATATTATGA
*
23780 AACATCGAATGCACTTGATGCA
1 AACATCGAATGCATTTGATGCA
23802 CTCTTAGTGC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 21 0.29
65 49 0.68
66 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATACACATACCATGCACCGATGCACTCAGGATATTATGA
Found at i:23911 original size:13 final size:13
Alignment explanation
Indices: 23893--23922 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
23883 GCATCGGTGC
23893 ACTGACGCTCTCA
1 ACTGACGCTCTCA
23906 ACTGACGCTCTCA
1 ACTGACGCTCTCA
23919 ACTG
1 ACTG
23923 CTTTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (13 bp):
ACTGACGCTCTCA
Found at i:24056 original size:17 final size:16
Alignment explanation
Indices: 24029--24060 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
24019 GAAGCCACTG
24029 ATCAACAACAAGAAAC
1 ATCAACAACAAGAAAC
24045 ATCAAGCAACAAGAAA
1 ATCAA-CAACAAGAAA
24061 TCATAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.22, G:0.09, T:0.06
Consensus pattern (16 bp):
ATCAACAACAAGAAAC
Found at i:29328 original size:23 final size:22
Alignment explanation
Indices: 29256--29336 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
29246 ACACTTAACA
*
29256 GTGCATCAATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* *
29280 GTGCATCGATTCAT-CTTG-TT
1 GTGCATCGATGCATCCTTGAAT
*
29300 GATGCACCGATGCATGCCTTGAAT
1 G-TGCATCGATGCAT-CCTTGAAT
29324 GTGCATCGATGCA
1 GTGCATCGATGCA
29337 CAGGGTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 1 0.02
23 15 0.33
24 14 0.30
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:32392 original size:18 final size:17
Alignment explanation
Indices: 32349--32396 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
32339 GAAGCCACTG
32349 ATCAAG-AACAAGAAAC
1 ATCAAGAAACAAGAAAC
32365 ATCAAGAAACAAGAAATC
1 ATCAAGAAACAAGAAA-C
32383 AT-AGAGAAACAAGA
1 ATCA-AGAAACAAGA
32397 GAGAAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
18 13 0.45
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (17 bp):
ATCAAGAAACAAGAAAC
Found at i:38680 original size:27 final size:27
Alignment explanation
Indices: 38622--38692 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
38612 AGCAACAAGT
* *
38622 TTTTTTAGCGAGCACAAGTCGAGTAAA
1 TTTTTTAACGAGCACAAGTCAAGTAAA
* **
38649 -ATTTTAACGAGCAACAAGTCAAGTCTA
1 TTTTTTAACGAGC-ACAAGTCAAGTAAA
*
38676 TTTTTTAACGACCACAA
1 TTTTTTAACGAGCACAA
38693 ATTGAACACT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 10 0.29
27 15 0.43
28 10 0.29
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (27 bp):
TTTTTTAACGAGCACAAGTCAAGTAAA
Found at i:39660 original size:29 final size:29
Alignment explanation
Indices: 39618--39675 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
39608 TATTTTAACA
39618 TAGTTTAATGACCATTTGTGTGCTTGACC
1 TAGTTTAATGACCATTTGTGTGCTTGACC
*
39647 TAGTTTAATGACCATTTGTGTGTTTGACC
1 TAGTTTAATGACCATTTGTGTGCTTGACC
39676 CGTAGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (29 bp):
TAGTTTAATGACCATTTGTGTGCTTGACC
Found at i:49888 original size:119 final size:121
Alignment explanation
Indices: 49748--49983 Score: 314
Period size: 119 Copynumber: 2.0 Consensus size: 121
49738 TACTGATTGA
* *
49748 GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGGGAGAAATAGATAAGTTTATTGGGTCGAC
1 GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGAC
** * * * *
49813 ATTGATGAATTGCAGAG-GGTTATTTTTT-TTACAAAAAGTTTAGGTCAGGAATGT
66 ACAGATAAATTGAAGAGAGCTTATTTTTTGTTACAAAAAATTTAGGTCAGGAATGT
* * * ** *
49867 GGGTCCTGAGTAGAAGAAAAAATTGTTGAGGTTTAGAGAGAAGTAGATAAGATTATTGGGTCGAC
1 GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGAC
* *
49932 ACAGATAAATTGAAGAGAGCTTTTTTTTTGTTACAAAAAATTTATGTCAGGA
66 ACAGATAAATTGAAGAGAGCTTATTTTTTGTTACAAAAAATTTAGGTCAGGA
49984 GTGACTCTCC
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
119 70 0.71
120 9 0.09
121 20 0.20
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (121 bp):
GGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGAC
ACAGATAAATTGAAGAGAGCTTATTTTTTGTTACAAAAAATTTAGGTCAGGAATGT
Done.