Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006155.1 Hibiscus syriacus cultivar Beakdansim tig00014626_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: 94901
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11096 original size:23 final size:23
Alignment explanation
Indices: 11063--11117 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
11053 CCACCTCATG
*
11063 CATATCATGCATATTGTATACGT
1 CATATCGTGCATATTGTATACGT
11086 CATATCGTGCATATTGTATACGT
1 CATATCGTGCATATTGTATACGT
*
11109 TATATCGTG
1 CATATCGTG
11118 TCGAATGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (23 bp):
CATATCGTGCATATTGTATACGT
Found at i:12359 original size:17 final size:18
Alignment explanation
Indices: 12337--12370 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12327 CAGAATGCAA
12337 AAATGG-TACCGATACCC
1 AAATGGCTACCGATACCC
12354 AAATGGCTACCGATACC
1 AAATGGCTACCGATACC
12371 AAAGGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (18 bp):
AAATGGCTACCGATACCC
Found at i:13465 original size:10 final size:10
Alignment explanation
Indices: 13452--13481 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
13442 AAATAAGAGA
13452 AAAGAAGAAG
1 AAAGAAGAAG
13462 AAAGAAGAAG
1 AAAGAAGAAG
13472 AGAAGAAGAA
1 A-AAGAAGAA
13482 AGTTAAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAG
Found at i:16883 original size:19 final size:18
Alignment explanation
Indices: 16859--16899 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
16849 ACTGAAACGG
16859 GGTTTTTT-GATTCGGTTC
1 GGTTTTTTAG-TTCGGTTC
16877 AGGTTTTTTAGTTCGGTTC
1 -GGTTTTTTAGTTCGGTTC
16896 GGTT
1 GGTT
16900 CGATTTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.07, C:0.10, G:0.29, T:0.54
Consensus pattern (18 bp):
GGTTTTTTAGTTCGGTTC
Found at i:35132 original size:22 final size:21
Alignment explanation
Indices: 35104--35145 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35094 TTTAAAAATT
35104 TTAAAGGTAATACCGATACTCA
1 TTAAAGG-AATACCGATACTCA
* *
35126 TTAAAGGAGTATCGATACTC
1 TTAAAGGAATACCGATACTC
35146 CCTGTCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (21 bp):
TTAAAGGAATACCGATACTCA
Found at i:36009 original size:17 final size:18
Alignment explanation
Indices: 35968--36012 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
35958 GTGATGGTGT
*
35968 TATTATTATTTAATAAAA
1 TATTATTATTTAAGAAAA
*
35986 TATTATTATTTGAGAAAA
1 TATTATTATTTAAGAAAA
36004 -ATTATTATT
1 TATTATTATT
36013 ATTAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTATTATTTAAGAAAA
Found at i:39843 original size:18 final size:18
Alignment explanation
Indices: 39820--39892 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
39810 GTTCAGTATT
39820 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
39838 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
39857 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
39876 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
39893 GTATATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 32 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:39866 original size:38 final size:38
Alignment explanation
Indices: 39819--39893 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
39809 CGTTCAGTAT
*
39819 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
*
39857 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTG
39894 TATATCCCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.20
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:40043 original size:21 final size:20
Alignment explanation
Indices: 39996--40050 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
39986 CTATCACTTC
39996 TCATATAGCACATAATTTATT
1 TCATATA-CACATAATTTATT
*
40017 TCATATACACATGATTCT-TT
1 TCATATACACATAATT-TATT
*
40037 TCAATATTCACATA
1 TC-ATATACACATA
40051 CATGTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (20 bp):
TCATATACACATAATTTATT
Found at i:40524 original size:63 final size:64
Alignment explanation
Indices: 40457--40598 Score: 196
Period size: 63 Copynumber: 2.2 Consensus size: 64
40447 ATTCCTTAAC
* *
40457 GGGTGCATCGATGCACTACTTATGCATCGGTGCACGAATCACATTCGATGTTTTTATTCAAT-A
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACGAATCACATTCGATGTTTTAATTCAATCA
* * ** **
40520 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTTAATTTTATCA
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACGAATCACATTCGATGTTTTAATTCAATCA
*
40584 GAGTGCATCGATGCA
1 GGGTGCATCGATGCA
40599 TATTGAATGT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
63 54 0.78
64 15 0.22
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATGCACGAATCACATTCGATGTTTTAATTCAATCA
Found at i:51137 original size:35 final size:34
Alignment explanation
Indices: 51056--51142 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
51046 ATTTGGTATT
*
51056 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
51090 TAAATGATAACAAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
51128 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
51143 ACTGAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.11
35 26 0.55
36 1 0.02
37 5 0.11
38 10 0.21
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:51382 original size:21 final size:21
Alignment explanation
Indices: 51356--51397 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
51346 ACTCCTTATT
51356 GTCATCATCGTCGTCATCGTC
1 GTCATCATCGTCGTCATCGTC
*
51377 GTCATCATTGTCGTCATCGTC
1 GTCATCATCGTCGTCATCGTC
51398 ATTGTCGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (21 bp):
GTCATCATCGTCGTCATCGTC
Found at i:53483 original size:18 final size:17
Alignment explanation
Indices: 53451--53496 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
53441 GAATTATATT
53451 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
53468 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
53486 ATTAAATATAT
1 AGTAAA-ATAT
53497 AATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:59246 original size:33 final size:34
Alignment explanation
Indices: 59196--59275 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
59186 CATATGTTTC
59196 GTTCGTTCATTTACGTTC-GTGAACGTTCGGTTAT
1 GTTCGTTCATTTACGTTCGGT-AACGTTCGGTTAT
* * *
59230 GTTCGTT-ATGTT-CGTTCGGTTATGTTCGTTTAT
1 GTTCGTTCAT-TTACGTTCGGTAACGTTCGGTTAT
59263 GTTCGTTCATTTA
1 GTTCGTTCATTTA
59276 TGTTTAACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.50
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCGGTAACGTTCGGTTAT
Found at i:59248 original size:23 final size:24
Alignment explanation
Indices: 59219--59279 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
59209 CGTTCGTGAA
59219 CGTTCGGTTATGTTCG-TTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
59242 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
**
59266 CGTTCATTTATGTT
1 CGTTCGGTTATGTT
59280 TAACCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.54
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:59251 original size:14 final size:13
Alignment explanation
Indices: 59230--59270 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
59220 GTTCGGTTAT
59230 GTTCGTTATGTTC
1 GTTCGTTATGTTC
59243 GTTCGGTTATGTTC
1 GTTC-GTTATGTTC
59257 G-T--TTATGTTC
1 GTTCGTTATGTTC
59267 GTTC
1 GTTC
59271 ATTTATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
13 5 0.20
14 10 0.40
ACGTcount: A:0.07, C:0.15, G:0.24, T:0.54
Consensus pattern (13 bp):
GTTCGTTATGTTC
Found at i:60332 original size:16 final size:16
Alignment explanation
Indices: 60311--60371 Score: 122
Period size: 16 Copynumber: 3.8 Consensus size: 16
60301 GGGTCTCCAA
60311 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
60327 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
60343 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
60359 CGTTTATGTTCGT
1 CGTTTATGTTCGT
60372 TTATTTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.07, C:0.13, G:0.25, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:60338 original size:10 final size:10
Alignment explanation
Indices: 60323--60375 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
60313 TTTATGTTCG
60323 TGTTCGTTTA
1 TGTTCGTTTA
60333 TGTTCG----
1 TGTTCGTTTA
60339 TGTTCGTTTA
1 TGTTCGTTTA
60349 TGTTCG----
1 TGTTCGTTTA
60355 TGTTCGTTTA
1 TGTTCGTTTA
60365 TGTTCGTTTA
1 TGTTCGTTTA
60375 T
1 T
60376 TTATTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:65352 original size:30 final size:30
Alignment explanation
Indices: 65318--65417 Score: 200
Period size: 30 Copynumber: 3.3 Consensus size: 30
65308 CTGGTATGAC
65318 TAAGAATTTGGAGATATGAACTTTAGGTAT
1 TAAGAATTTGGAGATATGAACTTTAGGTAT
65348 TAAGAATTTGGAGATATGAACTTTAGGTAT
1 TAAGAATTTGGAGATATGAACTTTAGGTAT
65378 TAAGAATTTGGAGATATGAACTTTAGGTAT
1 TAAGAATTTGGAGATATGAACTTTAGGTAT
65408 TAAGAATTTG
1 TAAGAATTTG
65418 AGACTTAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TAAGAATTTGGAGATATGAACTTTAGGTAT
Found at i:68934 original size:32 final size:32
Alignment explanation
Indices: 68893--68956 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
68883 TACCGAAATG
68893 TGATCGAATATACGAGGACATATAAGATCCTA
1 TGATCGAATATACGAGGACATATAAGATCCTA
68925 TGATCGAATATACGAGGACATATAAGATCCTA
1 TGATCGAATATACGAGGACATATAAGATCCTA
68957 GTTAATTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (32 bp):
TGATCGAATATACGAGGACATATAAGATCCTA
Found at i:73865 original size:33 final size:32
Alignment explanation
Indices: 73804--73877 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
73794 AATAGAAATC
73804 AATCAGAACCGAAATTAACTCGAACCGAAAG-A
1 AATC-GAACCGAAATTAACTCGAACCGAAAGTA
* * *
73836 AATCTGAACCGAATTTTAACTTGATCCGAAAGTA
1 AATC-GAACCGAA-ATTAACTCGAACCGAAAGTA
73870 AATCGAAC
1 AATCGAAC
73878 AAAATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 12 0.33
33 19 0.53
34 5 0.14
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (32 bp):
AATCGAACCGAAATTAACTCGAACCGAAAGTA
Found at i:73884 original size:33 final size:33
Alignment explanation
Indices: 73818--73910 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 33
73808 AGAACCGAAA
**
73818 TTAACTCGAACCGAAAGAAATCTGAACCGAATT
1 TTAACTCGAACCGAAAGAAATCTGAACAAAATT
* *
73851 TTAACTTGATCCGAAAGTAAATC-GAACAAAA-T
1 TTAACTCGAACCGAAAG-AAATCTGAACAAAATT
* * * * *
73883 TTAACCCGATCTGAAAGCAACCTGAACA
1 TTAACTCGAACCGAAAGAAATCTGAACA
73911 TATTGAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 3 0.06
32 20 0.41
33 21 0.43
34 5 0.10
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (33 bp):
TTAACTCGAACCGAAAGAAATCTGAACAAAATT
Found at i:74657 original size:20 final size:20
Alignment explanation
Indices: 74632--74701 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
74622 AGTGACGCAC
74632 CGATGCACCAATCCATGCAT
1 CGATGCACCAATCCATGCAT
74652 CGATGCACCAATCCATGCAT
1 CGATGCACCAATCCATGCAT
74672 CGATGCACCAATCCATGCAT
1 CGATGCACCAATCCATGCAT
74692 CGATGCACCA
1 CGATGCACCA
74702 TGAATTAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.19
Consensus pattern (20 bp):
CGATGCACCAATCCATGCAT
Found at i:74789 original size:17 final size:19
Alignment explanation
Indices: 74761--74809 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
74751 TATTTTGAAA
74761 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
74779 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
74798 CACCGATGCACT
1 CATCGATGCACT
74810 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:77742 original size:19 final size:19
Alignment explanation
Indices: 77718--77761 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
77708 CACTGACACT
77718 TAATTACGATTAATTTATA
1 TAATTACGATTAATTTATA
** *
77737 TAATTACTTTTAATTTATT
1 TAATTACGATTAATTTATA
77756 TAATTA
1 TAATTA
77762 TTTTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATTACGATTAATTTATA
Found at i:77766 original size:19 final size:19
Alignment explanation
Indices: 77727--77765 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
77717 TTAATTACGA
77727 TTAATTTATATAATTACTT
1 TTAATTTATATAATTACTT
*
77746 TTAATTTATTTAATTA-TT
1 TTAATTTATATAATTACTT
77764 TT
1 TT
77766 TTAAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAATTTATATAATTACTT
Found at i:77868 original size:79 final size:80
Alignment explanation
Indices: 77731--77887 Score: 244
Period size: 79 Copynumber: 2.0 Consensus size: 80
77721 TTACGATTAA
* * * * * *
77731 TTTATATAATTACTTTTAATTTATTTAATTATTTTTTAAGGTTTTGTCTTGATTAATCTTAATTT
1 TTTATATAATTACTATCAATTTATTTAATTATCTTCTAAGGCTTTATCTTGATTAATCTTAATTT
77796 ATGTTGCACATCTAG
66 ATGTTGCACATCTAG
*
77811 TTTAT-TAATTACTATCAATTTATTTAATTGTCTTCTAAGGCTTTATCTTGATTAATCTTAATTT
1 TTTATATAATTACTATCAATTTATTTAATTATCTTCTAAGGCTTTATCTTGATTAATCTTAATTT
77875 ATGTTGCACATCT
66 ATGTTGCACATCT
77888 GATTTCTGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 65 0.93
80 5 0.07
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (80 bp):
TTTATATAATTACTATCAATTTATTTAATTATCTTCTAAGGCTTTATCTTGATTAATCTTAATTT
ATGTTGCACATCTAG
Found at i:78232 original size:28 final size:28
Alignment explanation
Indices: 78200--78253 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
78190 TTCGAATAAC
*
78200 AACCTTTGTAAGGTGTGTGTTGTAAAAA
1 AACCTTTGTAAGGCGTGTGTTGTAAAAA
78228 AACCTTTGTAAGGCGTGTGTTGTAAA
1 AACCTTTGTAAGGCGTGTGTTGTAAA
78254 TAAATTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (28 bp):
AACCTTTGTAAGGCGTGTGTTGTAAAAA
Found at i:87038 original size:15 final size:15
Alignment explanation
Indices: 87005--87035 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
86995 CATAGTTACC
87005 AATAAAACTAAACTA
1 AATAAAACTAAACTA
87020 AATAAAA-TAAACTA
1 AATAAAACTAAACTA
87034 AA
1 AA
87036 ATAGTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAAACTAAACTA
Found at i:91681 original size:135 final size:134
Alignment explanation
Indices: 91473--92292 Score: 1088
Period size: 134 Copynumber: 6.1 Consensus size: 134
91463 AGAGTGGTGG
* *
91473 AGTGAATCAAAATTTTCTCGAGTCTGACCTTCCCTAAAGAGTAGTGGAGCATATTCTTTTTTCTT
1 AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTC-TTTTTCTT
** * *
91538 TCAGATTTGGTCTTTTTGAAGAGCAGTGAAGCAAATCACATTCGATTTAATCTTCCCTGAAGAGT
65 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGC
91603 AGTGA
130 AGTGA
* * * ** *
91608 GGTGAATCAAAGTTTTCATTGAGTCTGACCTCCTTTAAAGAGTAGCGGAGCAGATTCTTTTTCTT
1 AGTGAATCAAAATTTTC-TCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTTTTTCTT
* *
91673 TCAAATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGC
65 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGC
*
91738 A-TTA
130 AGTGA
* * * *
91742 AGGTGCATCAACATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCATACTCTTTTTCTT
1 A-GTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTTTTTCTT
* ** *
91807 TTAGATTTGGTCTTCCTGAAGAATAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAAC
65 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGC
91872 AGTGA
130 AGTGA
* *
91877 GGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTCTTTTTTTCT
1 AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTC--TTTTTCT
** *
91942 TTCAGATTTGGTCTTCCTGAAGAATAGTGAAGAAAATCACATTCGATTCAATCTTCCCTGAAGAG
64 TTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAG
*
92007 AAGTGA
129 CAGTGA
* * * * *
92013 AGTGGATCAAAGTTTTTCTCAAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTATTTTTCTT
1 AGTGAATCAAA-ATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTTTTTCTT
* * * *
92078 TCAAATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTTCTTGAAAAGC
65 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGC
*
92143 AGCGA
130 AGTGA
* * * * * * *
92148 AGTGAATCAAAATTTTCTCGAGTATGGCCTCTCATAAAGAATAACGGAGCATATTCTTCTTCTTT
1 AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTTTTTCTTT
* * * **
92213 CAGAGTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCA-AGTGT-AATTCTGTCTTCCCTGAAGAG
66 CAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACA-T-TCGATTCAATCTTCCCTGAAGAG
92276 CAGTGA
129 CAGTGA
92282 AGTGAATCAAA
1 AGTGAATCAAA
92293 TTCTTACGAG
Statistics
Matches: 599, Mismatches: 78, Indels: 17
0.86 0.11 0.02
Matches are distributed among these distances:
133 1 0.00
134 262 0.44
135 178 0.30
136 116 0.19
137 42 0.07
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (134 bp):
AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATATTCTTTTTCTTT
CAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGAAGAGCA
GTGA
Found at i:92224 original size:405 final size:404
Alignment explanation
Indices: 91473--92292 Score: 1171
Period size: 405 Copynumber: 2.0 Consensus size: 404
91463 AGAGTGGTGG
*
91473 AGTGAATCAAAATTTTCTCGAGTCTGACCTTCCCTAAAGAGTAGTGGAGCATATTCTTTTTTCTT
1 AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTCTTTTTTCTT
** * * * *
91538 TCAGATTTGGTCTTTTTGAAGAGCAGTGAAGCAAATCACATTCGATTTAATCTTCCCTGAAGAGT
66 TCAGATTTGGTCTTCCTGAAGAACAGTGAAGAAAATCACATTCGATTCAATCTTCCCTGAAGAGA
* ** ** *
91603 AGTGAGGTGAATCAAAGTTTTCATTGAGTCTGACCTCCTTTAAAGAGTAGCGGAGCAGATTCTTT
131 AGTGAAGTGAATCAAAGTTTTCATCAAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTATTT
91668 TTCTTTCAAATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGA
196 TTCTTTCAAATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGA
* ** * * * * * *
91733 AGAGCATTAAGGTGCATCAACATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCATACT
261 AAAGCACGAAGGTGAATCAAAATTTTCTCGAGTATGACCTCCCATAAAGAATAACAGAGCATACT
* * * * *
91798 CTTTTTCTTTTAGATTTGGTCTTCCTGAAGAATAGTGAAGCAAATCACA-T-TCGATTCAATCTT
326 CTTCTTCTTTCAGAGTTGGTCTTCCTGAAGAACAGTGAAGCAAATCA-AGTGT-AATTCAATCTT
91861 CCCTGAAGAACAGTGA
389 CCCTGAAGAACAGTGA
*
91877 GGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTCTTTTTTTCT
1 AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTC-TTTTTTCT
*
91942 TTCAGATTTGGTCTTCCTGAAGAATAGTGAAGAAAATCACATTCGATTCAATCTTCCCTGAAGAG
65 TTCAGATTTGGTCTTCCTGAAGAACAGTGAAGAAAATCACATTCGATTCAATCTTCCCTGAAGAG
* * *
92007 AAGTGAAGTGGATCAAAGTTTTTC-TCAAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTAT
130 AAGTGAAGTGAATCAAAG-TTTTCATCAAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTAT
* * *
92071 TTTTCTTTCAAATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTTCTT
194 TTTTCTTTCAAATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCT
* * *
92136 GAAAAGCAGCGAA-GTGAATCAAAATTTTCTCGAGTATGGCCTCTCATAAAGAATAACGGAGCAT
259 GAAAAGCA-CGAAGGTGAATCAAAATTTTCTCGAGTATGACCTCCCATAAAGAATAACAGAGCAT
* * * **
92200 ATTCTTCTTCTTTCAGAGTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCAAGTGTAATTCTGTCT
323 ACTCTTCTTCTTTCAGAGTTGGTCTTCCTGAAGAACAGTGAAGCAAATCAAGTGTAATTCAATCT
*
92265 TCCCTGAAGAGCAGTGA
388 TCCCTGAAGAACAGTGA
92282 AGTGAATCAAA
1 AGTGAATCAAA
92293 TTCTTACGAG
Statistics
Matches: 366, Mismatches: 45, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
404 55 0.15
405 303 0.83
406 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (404 bp):
AGTGAATCAAAATTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGTGGAGCATATTCTTTTTTCTT
TCAGATTTGGTCTTCCTGAAGAACAGTGAAGAAAATCACATTCGATTCAATCTTCCCTGAAGAGA
AGTGAAGTGAATCAAAGTTTTCATCAAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTATTT
TTCTTTCAAATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCACATTCGATTCAATCTTCCCTGA
AAAGCACGAAGGTGAATCAAAATTTTCTCGAGTATGACCTCCCATAAAGAATAACAGAGCATACT
CTTCTTCTTTCAGAGTTGGTCTTCCTGAAGAACAGTGAAGCAAATCAAGTGTAATTCAATCTTCC
CTGAAGAACAGTGA
Done.