Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000207.1 Hibiscus syriacus cultivar Beakdansim tig00000368_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: 68613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:445 original size:12 final size:12
Alignment explanation
Indices: 428--465 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
418 TTGAATTTTC
*
428 TTTTAAACTTCT
1 TTTTAATCTTCT
*
440 TTTTAATTTTCT
1 TTTTAATCTTCT
452 TTTTAATCTTCT
1 TTTTAATCTTCT
464 TT
1 TT
466 GAAATCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTAATCTTCT
Found at i:448 original size:23 final size:24
Alignment explanation
Indices: 421--465 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
411 TACCATATTG
421 AATTTTC-TTTTAAACTTCTTTTT
1 AATTTTCTTTTTAAACTTCTTTTT
*
444 AATTTTCTTTTTAATCTTCTTT
1 AATTTTCTTTTTAAACTTCTTT
466 GAAATCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (24 bp):
AATTTTCTTTTTAAACTTCTTTTT
Found at i:471 original size:12 final size:12
Alignment explanation
Indices: 425--473 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
415 ATATTGAATT
425 TTCTTTTAAA-C
1 TTCTTTTAAATC
* *
436 TTCTTTTTAATT
1 TTCTTTTAAATC
*
448 TTCTTTTTAATC
1 TTCTTTTAAATC
*
460 TTCTTTGAAATC
1 TTCTTTTAAATC
472 TT
1 TT
474 TTTATTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.63
Consensus pattern (12 bp):
TTCTTTTAAATC
Found at i:813 original size:6 final size:6
Alignment explanation
Indices: 802--879 Score: 50
Period size: 6 Copynumber: 12.2 Consensus size: 6
792 AGGCAACCCA
* * *
802 TTATTT TTATTT TTCGTTT CTTAAATTT TTATTT TTATTT TCAATT TTATTT
1 TTATTT TTATTT TT-ATTT -TT--ATTT TTATTT TTATTT TTATTT TTATTT
* *
854 TTCTGAT TTATTT GTT-TTT TTATTT T
1 TTAT-TT TTATTT -TTATTT TTATTT T
880 CCTTTGATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
5 2 0.04
6 37 0.67
7 9 0.16
8 4 0.07
9 3 0.05
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (6 bp):
TTATTT
Found at i:1418 original size:34 final size:34
Alignment explanation
Indices: 1357--1470 Score: 160
Period size: 33 Copynumber: 3.4 Consensus size: 34
1347 ATAGTGCACT
*
1357 AACAGT-AAAAAATAGTAGTATAGTTTTGGTTCG
1 AACAGTGAAAAAATAGTAGTACAGTTTTGGTTCG
* *
1390 AACAGTGAAAAAATAGCAGTACAATTTT-GTTCG
1 AACAGTGAAAAAATAGTAGTACAGTTTTGGTTCG
*
1423 AACAGTAAAAAAATAGTAGTACAGTTTTGGTTCG
1 AACAGTGAAAAAATAGTAGTACAGTTTTGGTTCG
*
1457 AACAATGAGAAAAA
1 AACAGTGA-AAAAA
1471 AAAAAGAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
33 36 0.51
34 29 0.41
35 5 0.07
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (34 bp):
AACAGTGAAAAAATAGTAGTACAGTTTTGGTTCG
Found at i:2345 original size:3 final size:3
Alignment explanation
Indices: 2337--2374 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2327 GTTTATTAAT
* *
2337 TTA TTA TTA TTA TTA TTA TT- TTA CTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2375 AATAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2354 original size:20 final size:20
Alignment explanation
Indices: 2329--2375 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2319 CCATTTTTGT
* *
2329 TTATTAATTTATTATTATTA
1 TTATTAATTTACTACTATTA
*
2349 TTATTATTTTACTACTATTA
1 TTATTAATTTACTACTATTA
2369 TTATTAA
1 TTATTAA
2376 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTAATTTACTACTATTA
Found at i:3875 original size:3 final size:3
Alignment explanation
Indices: 3867--3896 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3857 TTTTCAATAT
3867 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3897 ATCATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3913 original size:2 final size:2
Alignment explanation
Indices: 3894--3944 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
3884 TTATTATTAT
*
3894 TA TA TCA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3937 TA TA TA TA
1 TA TA TA TA
3945 AATAATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4811 original size:28 final size:26
Alignment explanation
Indices: 4771--4847 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 26
4761 TAAAATTCAT
*
4771 ATTTTAATTTATAATTTTTTCCTTTCAAA
1 ATTTT-ATATATAATTTTTT--TTTCAAA
* * *
4800 ATTTTATATATACTTATTATTTTCATA
1 ATTTTATATATAATT-TTTTTTTCAAA
4827 ATATTTATATATATATTTTTT
1 AT-TTTATATATA-ATTTTTT
4848 ATTAGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
27 8 0.21
28 21 0.54
29 10 0.26
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTATATATAATTTTTTTTTCAAA
Found at i:4843 original size:26 final size:25
Alignment explanation
Indices: 4793--4847 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
4783 AATTTTTTCC
4793 TTTCAAAATTTTATATATACTTATTAT
1 TTTCAAAATTTTATATATAC-TATT-T
*
4820 TTTCATAATATTTATATATA-TATTT
1 TTTCAAAAT-TTTATATATACTATTT
4845 TTT
1 TTT
4848 ATTAGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 8 0.31
28 10 0.38
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTCAAAATTTTATATATACTATTT
Found at i:4850 original size:30 final size:27
Alignment explanation
Indices: 4780--4850 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 27
4770 TATTTTAATT
**
4780 TATA-ATTTTTTCCTTTCAAAATTTTA
1 TATATATTTTTTATTTTCAAAATTTTA
* *
4806 TATATACTTATTATTTTCATAATATTTATA
1 TATATATTTTTTATTTTCA-AA-ATTT-TA
4836 TATATATTTTTTATT
1 TATATATTTTTTATT
4851 AGTATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 4 0.11
27 10 0.29
28 2 0.06
29 4 0.11
30 15 0.43
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATATTTTTTATTTTCAAAATTTTA
Found at i:15431 original size:18 final size:18
Alignment explanation
Indices: 15410--15491 Score: 96
Period size: 18 Copynumber: 4.4 Consensus size: 18
15400 GAAAAAAGGA
15410 AAAGAAAAAAATGAAAAT
1 AAAGAAAAAAATGAAAAT
15428 AAAGAAAATAAA-GAAAAT
1 AAAGAAAA-AAATGAAAAT
15446 AAAGAAAAAAATGAAAAT
1 AAAGAAAAAAATGAAAAT
* *
15464 GAAAAATAAAAAAT-AAAAA
1 -AAAGA-AAAAAATGAAAAT
15483 AATAGAAAA
1 AA-AGAAAA
15492 TGAGGGTCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
17 3 0.05
18 33 0.59
19 13 0.23
20 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (18 bp):
AAAGAAAAAAATGAAAAT
Found at i:15442 original size:49 final size:49
Alignment explanation
Indices: 15389--15486 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 49
15379 ATTATGCTTG
15389 AAGAAGAA-AAAG-AAAAAAGGAAAA-GAAAAA-AATGAAAATAAAGAAAATA
1 AAGAA-AATAAAGAAAAAAAGGAAAATGAAAAATAA--AAAATAAA-AAAATA
*
15438 AAGAAAATAAAGAAAAAAATGAAAATGAAAAATAAAAAATAAAAAAATA
1 AAGAAAATAAAGAAAAAAAGGAAAATGAAAAATAAAAAATAAAAAAATA
15487 GAAAATGAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
48 2 0.05
49 15 0.34
50 19 0.43
51 6 0.14
52 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (49 bp):
AAGAAAATAAAGAAAAAAAGGAAAATGAAAAATAAAAAATAAAAAAATA
Found at i:15476 original size:8 final size:9
Alignment explanation
Indices: 15410--15486 Score: 78
Period size: 9 Copynumber: 9.1 Consensus size: 9
15400 GAAAAAAGGA
15410 AAAGAAAA-
1 AAAGAAAAT
15418 AAATGAAAAT
1 AAA-GAAAAT
15428 AAAGAAAAT
1 AAAGAAAAT
15437 AAAGAAAAT
1 AAAGAAAAT
15446 AAAGAAAA-
1 AAAGAAAAT
15454 AAATGAAAAT
1 AAA-GAAAAT
*
15464 -GA-AAAAT
1 AAAGAAAAT
15471 -AA-AAAAT
1 AAAGAAAAT
15478 AAA-AAAAT
1 AAAGAAAAT
15486 A
1 A
15487 GAAAATGAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
7 11 0.18
8 14 0.23
9 34 0.55
10 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAAGAAAAT
Found at i:15864 original size:18 final size:18
Alignment explanation
Indices: 15838--15875 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15828 CAAGTTTATC
* *
15838 TTTTTGAAATTCAATTTA
1 TTTTCGAAATTAAATTTA
15856 TTTTCGAAATTAAATTTA
1 TTTTCGAAATTAAATTTA
15874 TT
1 TT
15876 CTTTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTCGAAATTAAATTTA
Found at i:16121 original size:126 final size:126
Alignment explanation
Indices: 15896--16149 Score: 499
Period size: 126 Copynumber: 2.0 Consensus size: 126
15886 AACATCTTGT
15896 AAATGGATTAACATAATCTTGAAACAAACAAAATATTTTTGGCTATCACTTTATGTTAATACTTT
1 AAATGGATTAACATAATCTTGAAACAAACAAAATATTTTTGGCTATCACTTTATGTTAATACTTT
*
15961 TAAGTTCATGGAATCCAAAGTAAGTCTTATCAACATTTGCAATCATTGTTGAAAAGCAAAC
66 TAAGTGCATGGAATCCAAAGTAAGTCTTATCAACATTTGCAATCATTGTTGAAAAGCAAAC
16022 AAATGGATTAACATAATCTTGAAACAAACAAAATATTTTTGGCTATCACTTTATGTTAATACTTT
1 AAATGGATTAACATAATCTTGAAACAAACAAAATATTTTTGGCTATCACTTTATGTTAATACTTT
16087 TAAGTGCATGGAATCCAAAGTAAGTCTTATCAACATTTGCAATCATTGTTGAAAAGCAAAC
66 TAAGTGCATGGAATCCAAAGTAAGTCTTATCAACATTTGCAATCATTGTTGAAAAGCAAAC
16148 AA
1 AA
16150 GTTATTACCA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (126 bp):
AAATGGATTAACATAATCTTGAAACAAACAAAATATTTTTGGCTATCACTTTATGTTAATACTTT
TAAGTGCATGGAATCCAAAGTAAGTCTTATCAACATTTGCAATCATTGTTGAAAAGCAAAC
Found at i:16278 original size:20 final size:20
Alignment explanation
Indices: 16253--16317 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
16243 AAATGTTTTA
16253 CGAACCAGTAATTATGGTGT
1 CGAACCAGTAATTATGGTGT
16273 CGAACCAGTAATTATGGTG-
1 CGAACCAGTAATTATGGTGT
16292 CTGAACCAGTAATTATGGTGT
1 C-GAACCAGTAATTATGGTGT
*
16313 TGAAC
1 CGAAC
16318 TAATGTTGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
CGAACCAGTAATTATGGTGT
Found at i:21152 original size:22 final size:22
Alignment explanation
Indices: 21125--21166 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21115 AAACCATTCA
21125 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
21147 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
21167 GAGCAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:21533 original size:22 final size:22
Alignment explanation
Indices: 21507--21582 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
21497 TTCTTTAAAT
21507 ATGATAGATTCTCTTTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
*
21529 ATGATAGATTCTCTCTTCAAAG
1 ATGATAGATTCTCTTTTCAAAG
*
21551 ATGAT-GCATTCTCTTTTAAAAG
1 ATGATAG-ATTCTCTTTTCAAAG
* *
21573 AAGAAAGATT
1 ATGATAGATT
21583 TATTGGATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 45 0.96
23 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTCAAAG
Found at i:22132 original size:17 final size:17
Alignment explanation
Indices: 22078--22132 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
22068 TTTCCAGATA
22078 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
*
22095 AACTT-AGCTGAA-GAGGAAG
1 AAGTTCA--T-AATGA-GAAG
22114 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
22131 AA
1 AA
22133 CTTGTTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 6 0.20
19 10 0.33
20 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.20
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:22146 original size:109 final size:107
Alignment explanation
Indices: 21936--22269 Score: 346
Period size: 120 Copynumber: 2.9 Consensus size: 107
21926 GATTTGAATC
* * * *
21936 CATCACTCGATGGATCAACATTTCCAGAGAAGTTCATAATCAAAAGAACTTATCTGAAGAAGGAA
1 CATCACTCGATGGATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTAGCTGAAG-A-G--
*
22001 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATT
62 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTC-AACT
22048 CATCACTCGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTAGCTGAAGAGGAA
1 CATCACTCGATGGATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTTAGCTGAAGAGGAA
* *
22113 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACT
65 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAACT
* * * *
22156 CTATCGCAGAAGAAGATAGATCAGCATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTT-
1 C-AT--C------A-CTCGAT--GGATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTTA
*
22220 GTCTAAAGAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
53 G-CTGAAGAGGAAG---AAGTTCATAATGAGAAGAACTTGTTCAACCTTT
22270 TGCTTGACTC
Statistics
Matches: 192, Mismatches: 13, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
108 3 0.02
109 43 0.22
111 2 0.01
112 29 0.15
113 27 0.14
117 1 0.01
118 4 0.02
119 1 0.01
120 49 0.26
123 33 0.17
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (107 bp):
CATCACTCGATGGATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTTAGCTGAAGAGGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAACT
Found at i:22255 original size:20 final size:21
Alignment explanation
Indices: 22198--22257 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
22188 TTTCCATAGA
22198 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
* *
22219 -TG-TC-TAAAGAGGAAGAA-T
1 AAGTTCATAATGA-GAAGAACT
22237 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
22258 TGTTCAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 9 0.30
21 6 0.20
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.23
Consensus pattern (21 bp):
AAGTTCATAATGAGAAGAACT
Found at i:22262 original size:20 final size:20
Alignment explanation
Indices: 22200--22263 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
22190 TCCATAGAAA
22200 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* *
22220 G-TC-TAAAGAGGAAGAA-TAA
1 GTTCATAATGA-GAAGAACT-T
22239 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
22259 GTTCA
1 GTTCA
22264 ACCTTTTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 6 0.17
19 9 0.26
20 14 0.40
21 6 0.17
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:22284 original size:123 final size:123
Alignment explanation
Indices: 22061--22464 Score: 529
Period size: 123 Copynumber: 3.3 Consensus size: 123
22051 CACTCGATGG
*
22061 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTAG-CTGAAGAGGAAG--AAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTT-GTCTGAAGAGGAAGAAAAGTTCATA
*
22123 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAA-GAAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCGCAGAAGGAAGATAGATCAGC
* *
22181 ATCAACATTTCCATAGAAAGTTCATAATGAGAAGAACTTGTCTAAAGAGGAAGAATAAGTTCATA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTGTCTGAAGAGGAAGAA-AAGTTCATA
*
22246 ATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCGTAGAAGGAA-ATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCGCAGAAGGAAGATAGATCAGC
* * ** * *
22304 ATCAACATTTCCAGAGAGAGTTCATAATGAGAATAACTAAATCTGAAGATGAAAAAAGAAGTTCA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT-TGTCTGAAGA-GGAAGAA-AAGTTCA
* ** * * *
22369 TAATGAGAAGAACTTGTTCAACC-TTTGCATGACTCTATTACAGAATG-AGATAGATAAAC
63 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCGCAGAAGGAAGATAGATCAGC
*
22428 ATCAACATTTCCA-A-AAGTGTTCATAATGAGAAGAACT
1 ATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACT
22465 AATCCCAAAA
Statistics
Matches: 251, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
119 1 0.00
120 48 0.19
122 1 0.00
123 116 0.46
124 50 0.20
125 35 0.14
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTGTCTGAAGAGGAAGAAAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTTGACTCTATCGCAGAAGGAAGATAGATCAGC
Found at i:22860 original size:3 final size:3
Alignment explanation
Indices: 22852--22889 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
22842 GTTTATTAAT
* *
22852 TTA TTA TTA TTA TTA TT- TTA CTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22890 AATAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:22884 original size:17 final size:17
Alignment explanation
Indices: 22844--22885 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
22834 CCATTTTTGT
* *
22844 TTATTAATTTATTATTA
1 TTATTATTTTACTATTA
22861 TTATTATTTTACTATTA
1 TTATTATTTTACTATTA
*
22878 TTGTTATT
1 TTATTATT
22886 ATTAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATTATTTTACTATTA
Found at i:26278 original size:13 final size:13
Alignment explanation
Indices: 26260--26284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26250 AAATATTTTA
26260 AGAATTATCTTTC
1 AGAATTATCTTTC
26273 AGAATTATCTTT
1 AGAATTATCTTT
26285 TCTTTGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
AGAATTATCTTTC
Found at i:26963 original size:12 final size:12
Alignment explanation
Indices: 26932--26973 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
26922 ATATTGAATA
* *
26932 TTCTTTTAAACT
1 TTCTTTTTAATT
26944 TTCTTTTTAATT
1 TTCTTTTTAATT
*
26956 TTCTTTTTAATC
1 TTCTTTTTAATT
26968 TTCTTT
1 TTCTTT
26974 GAAATCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTTAATT
Found at i:30010 original size:21 final size:21
Alignment explanation
Indices: 29986--30026 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29976 CTTTGAATGA
29986 TGAGTGCTTTATTTGGTTAAG
1 TGAGTGCTTTATTTGGTTAAG
30007 TGAGTGCTTTATTTGGTTAA
1 TGAGTGCTTTATTTGGTTAA
30027 TATTTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.27, T:0.49
Consensus pattern (21 bp):
TGAGTGCTTTATTTGGTTAAG
Found at i:30548 original size:46 final size:46
Alignment explanation
Indices: 30481--30577 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
30471 CTAGGGGTGA
30481 AGCTTGAGAGATGTACAAGTTTAGAATTCAGTATAGAACCGGTTCT
1 AGCTTGAGAGATGTACAAGTTTAGAATTCAGTATAGAACCGGTTCT
30527 AGCTTGAGAGATGTACAAGTTTAGAATTCAGTATAGAACCGGTTCT
1 AGCTTGAGAGATGTACAAGTTTAGAATTCAGTATAGAACCGGTTCT
30573 AGCTT
1 AGCTT
30578 TTTATTTGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (46 bp):
AGCTTGAGAGATGTACAAGTTTAGAATTCAGTATAGAACCGGTTCT
Found at i:32919 original size:17 final size:17
Alignment explanation
Indices: 32897--32934 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
32887 ATTCCGATAA
32897 AACTTCCTTAACGTATC
1 AACTTCCTTAACGTATC
* *
32914 AACTTCTTTAATGTATC
1 AACTTCCTTAACGTATC
32931 AACT
1 AACT
32935 ACGGTAGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (17 bp):
AACTTCCTTAACGTATC
Found at i:40009 original size:2 final size:2
Alignment explanation
Indices: 40004--40032 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39994 AAAAAAAATA
40004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40033 CAATAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41490 original size:69 final size:63
Alignment explanation
Indices: 41369--41791 Score: 385
Period size: 60 Copynumber: 6.8 Consensus size: 63
41359 ACGCAACTTA
* *
41369 CACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTCAT
1 CACAA-ATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAG-CAT
* *
41434 ACAACCCAAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTTAAAGTCAATTCGGTGAAG
1 -C-A--C-AAATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAG
41499 CAGT
61 CA-T
* * * * *
41503 -AC---TTGGATTTTAACTTAACAACGAAGTATATCCAATTCAAAGTCGATTTGGTGAAGCA-
1 CACAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAT
* *
41561 CA-AGATTGGATTTCAACTTTACAATGAAGGATATCCAACTCAAAG-CTAATTTGGTGAA--A-
1 CACAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTC-AATTTGGTGAAGCAT
* * * * * * *
41620 CA-ATACTTGGATTTCAACTTCACAACGAAAGATATCTAACTCAAAGCCGATTTGGTAAAGCA-
1 CACA-AATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAT
* * * * * *
41682 CA-AGATTGGATTTCAACTTCACATCGAAGGATATCCAACTCGAAGCCAATTTCGTGAA--A-
1 CACAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAT
* *
41741 CA-ATACTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTCAA
1 CACA-AATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAG-TCAA
41792 CTTCACGACG
Statistics
Matches: 302, Mismatches: 39, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
59 9 0.03
60 133 0.44
61 95 0.31
62 4 0.01
64 1 0.00
66 2 0.01
67 1 0.00
68 2 0.01
69 53 0.18
70 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (63 bp):
CACAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAT
Found at i:41518 original size:60 final size:60
Alignment explanation
Indices: 41445--41791 Score: 403
Period size: 60 Copynumber: 5.7 Consensus size: 60
41435 CAACCCAAAA
* * * *
41445 TTGGATTTCAACTTTACAACGAAGGATATCCAACTTAAAGTCAATTCGGTGAAGCAGTAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAATAC
* * * * * *
41505 TTGGATTTTAACTTAACAACGAAGTATATCCAATTCAAAGTCGATTTGGTGAAGCACA-AGA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCA-ATA-C
* * *
41566 TTGGATTTCAACTTTACAATGAAGGATATCCAACTCAAAG-CTAATTTGGTGAAACAATAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTC-AATTTGGTGAAGCAATAC
* * * * * *
41626 TTGGATTTCAACTTCACAACGAAAGATATCTAACTCAAAGCCGATTTGGTAAAGCACA-AGA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCA-ATA-C
* * * * *
41687 TTGGATTTCAACTTCACATCGAAGGATATCCAACTCGAAGCCAATTTCGTGAAACAATAC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAATAC
41747 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTCAA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAG-TCAA
41792 CTTCACGACG
Statistics
Matches: 241, Mismatches: 37, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
60 139 0.58
61 102 0.42
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (60 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTCAATTTGGTGAAGCAATAC
Found at i:41628 original size:121 final size:121
Alignment explanation
Indices: 41376--41787 Score: 549
Period size: 121 Copynumber: 3.3 Consensus size: 121
41366 TTACACAAGA
*
41376 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGTCATACAACCC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAG-----C-A--C
* * * * * *
41441 AAAATTGGATTTCAACTTTACAACGAAGGATATCCAACTTAAAG-TCAATTCGGTGAAGCAGTAC
58 AAGATTGGATTTCAACTTTACAATGAAGGATATCCAACTCAAAGCT-AATTTGGTGAAACAATAC
* * * * *
41505 TTGGATTTTAACTTAACAACGAAGTATATCCAATTCAAAGTCGATTTGGTGAAGCACAAGATTGG
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCACAAGATTGG
41570 ATTTCAACTTTACAATGAAGGATATCCAACTCAAAGCTAATTTGGTGAAACAATAC
66 ATTTCAACTTTACAATGAAGGATATCCAACTCAAAGCTAATTTGGTGAAACAATAC
* * *
41626 TTGGATTTCAACTTCACAACGAAAGATATCTAACTCAAAGCCGATTTGGTAAAGCACAAGATTGG
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCACAAGATTGG
* * * *
41691 ATTTCAACTTCAC-ATCGAAGGATATCCAACTCGAAGCCAATTTCGTGAAACAATAC
66 ATTTCAACTTTACAAT-GAAGGATATCCAACTCAAAGCTAATTTGGTGAAACAATAC
41747 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
1 TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
41788 TCAACTTCAC
Statistics
Matches: 255, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
120 2 0.01
121 202 0.79
122 1 0.00
123 1 0.00
124 1 0.00
129 48 0.19
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (121 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCACAAGATTGG
ATTTCAACTTTACAATGAAGGATATCCAACTCAAAGCTAATTTGGTGAAACAATAC
Found at i:42308 original size:3 final size:3
Alignment explanation
Indices: 42295--42337 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
42285 GCTTAAAAAA
*
42295 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42338 ACTATATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:42571 original size:47 final size:47
Alignment explanation
Indices: 42503--42675 Score: 258
Period size: 47 Copynumber: 3.7 Consensus size: 47
42493 ATCAACATGC
* * * * *
42503 TCCC-ACGTCAGCATCATACCCGATAACAACTCACATACCCTGTTAT
1 TCCCTACGCCAGCACCATACCCGATAACAGCTCTCATACCCTGTTGT
* *
42549 TCCCTACGCCAACACCATACCCGATAACAGCTCTCATACCCTATTGT
1 TCCCTACGCCAGCACCATACCCGATAACAGCTCTCATACCCTGTTGT
*
42596 TCCCTACGCCAGCACCATACCCGATAACAGCTCTCATACCATGTTGT
1 TCCCTACGCCAGCACCATACCCGATAACAGCTCTCATACCCTGTTGT
*
42643 TCCCTACGCCAGCACCATACCTGATAACAGCTC
1 TCCCTACGCCAGCACCATACCCGATAACAGCTC
42676 CCATCCTCTT
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
46 4 0.03
47 111 0.97
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (47 bp):
TCCCTACGCCAGCACCATACCCGATAACAGCTCTCATACCCTGTTGT
Found at i:43568 original size:30 final size:30
Alignment explanation
Indices: 43534--43590 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
43524 TCTGTTAATA
* *
43534 CTATTTTAATCCTTTAATTTTCTATTTGTG
1 CTATTTTAATACTTTAAATTTCTATTTGTG
**
43564 CTATTTTGGTACTTTAAATTTCTATTT
1 CTATTTTAATACTTTAAATTTCTATTT
43591 TTTTTGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (30 bp):
CTATTTTAATACTTTAAATTTCTATTTGTG
Found at i:49480 original size:23 final size:23
Alignment explanation
Indices: 49454--49510 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
49444 TCAGAATAAA
*
49454 AAAACCTTGTTTACTAGAACCGG
1 AAAACCTTGTTTACCAGAACCGG
*
49477 AAAACTCTT-TTTACCAGAGCCGG
1 AAAAC-CTTGTTTACCAGAACCGG
*
49500 -AAACTTTGTTT
1 AAAACCTTGTTT
49511 CTACACATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 17 0.59
24 3 0.10
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (23 bp):
AAAACCTTGTTTACCAGAACCGG
Found at i:55141 original size:29 final size:29
Alignment explanation
Indices: 55099--55161 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
55089 TCAGGTGATT
55099 GTAAATTTTAATAGTCGGGACTCAACAAA
1 GTAAATTTTAATAGTCGGGACTCAACAAA
*
55128 GTAAATTTTAATAGTTGGGACTCAACAAA
1 GTAAATTTTAATAGTCGGGACTCAACAAA
55157 GTAAA
1 GTAAA
55162 GTCATATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (29 bp):
GTAAATTTTAATAGTCGGGACTCAACAAA
Found at i:61838 original size:37 final size:36
Alignment explanation
Indices: 61785--61904 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
61775 ATCCCATTAT
*
61785 CATTTTTC-AAGAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
61820 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
61857 CA-TTTTCAAAAAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
61892 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
61905 TTGGTTGCCA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 34 0.45
36 8 0.11
37 34 0.45
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:61860 original size:21 final size:20
Alignment explanation
Indices: 61833--61896 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
61823 TTTTTCAAAG
61833 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
61853 AAACCATTT-TCAAA-----A
1 AAA-CATTTACCAAACTTTGA
61868 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
61888 AAATCATTT
1 AAA-CATTT
61897 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:67444 original size:36 final size:35
Alignment explanation
Indices: 67331--67447 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 35
67321 GTCATTATCA
* *
67331 TTTTCAACAAACATCTACCAAACTTTGAAAACTAT
1 TTTTCAAAAAACATTTACCAAACTTTGAAAACTAT
*
67366 TTTTCAAAGAAAACATTTACCAAAAACTTTGAAAACCA-
1 TTTTC-AA-AAAACATTTACC--AAACTTTGAAAACTAT
*
67404 TTTTCAAAAAACATTTACCAAACTTTGAAAAATTAT
1 TTTTCAAAAAACATTTACCAAACTTTG-AAAACTAT
67440 TTTTCAAA
1 TTTTCAAA
67448 GTTGGTTGCC
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
34 8 0.11
35 10 0.14
36 22 0.31
37 12 0.17
38 5 0.07
39 14 0.20
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.32
Consensus pattern (35 bp):
TTTTCAAAAAACATTTACCAAACTTTGAAAACTAT
Done.