Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006624.1 Hibiscus syriacus cultivar Beakdansim tig00016279_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: 47062
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6275 original size:8 final size:8
Alignment explanation
Indices: 6262--6319 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
6252 TTTAAAAAGA
6262 AAAATAAT
1 AAAATAAT
6270 AAAATAAT
1 AAAATAAT
6278 AATAATAAAT
1 AA-AAT-AAT
**
6288 AAAA-AGGG
1 AAAATA-AT
6296 AAAATAAT
1 AAAATAAT
6304 AAAATAAT
1 AAAATAAT
6312 -AAATAAT
1 AAAATAAT
6319 A
1 A
6320 GTAGTAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 8 0.20
8 22 0.54
9 6 0.15
10 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (8 bp):
AAAATAAT
Found at i:6317 original size:35 final size:36
Alignment explanation
Indices: 6220--6319 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 36
6210 AGATGAAGTT
6220 GAAAATATATAAAATAAAATAAATAATTATAATTTAAAAAG
1 GAAAATA-ATAAAAT--AATAAATAA-TATAA-TTAAAAAG
*
6261 AAAAATAATAAAATAAT-AATAATA-AA-TAAAAAGG
1 GAAAATAATAAAATAATAAATAATATAATTAAAAA-G
6295 GAAAATAATAAAATAATAAATAATA
1 GAAAATAATAAAATAATAAATAATA
6320 GTAGTAAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
33 6 0.11
34 17 0.31
35 9 0.16
36 2 0.04
37 5 0.09
38 3 0.05
40 7 0.13
41 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (36 bp):
GAAAATAATAAAATAATAAATAATATAATTAAAAAG
Found at i:6379 original size:17 final size:17
Alignment explanation
Indices: 6359--6399 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
6349 GTTGTTTTTA
6359 AAATAAAGATAAA-AATT
1 AAATAAAGA-AAATAATT
6376 AAATAAAGAAAATAATT
1 AAATAAAGAAAATAATT
6393 AAATAAA
1 AAATAAA
6400 TAATCTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AAATAAAGAAAATAATT
Found at i:7847 original size:18 final size:15
Alignment explanation
Indices: 7812--7851 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 15
7802 ATCTCTTTAA
7812 TTTATTTATTTTTCT
1 TTTATTTATTTTTCT
7827 TTTATTTAATTCTTATCT
1 TTTATTT-ATT-TT-TCT
7845 TTTATTT
1 TTTATTT
7852 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 2 0.09
18 10 0.45
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTATTTTTCT
Found at i:8384 original size:72 final size:73
Alignment explanation
Indices: 8272--8466 Score: 215
Period size: 72 Copynumber: 2.7 Consensus size: 73
8262 TAAAAAAGCT
* * *
8272 AAATATCTTAAATCCTAATTAAAACACTTAAAA-TTATTTAAACTAAAATACCT-AAAAAA-ATA
1 AAATATCTTAATTCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAAAGATA
** *
8334 ATGTTTAAA
65 AAATATAAA
8343 ATAATAT-TTAATTCCTAATTAAAATACTAAAAACCTATTTAAACT-AAATACCTAAAAAAAGAT
1 A-AATATCTTAATTCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACCTAAAAAAAGAT
8406 AAAATATAAA
64 AAAATATAAA
* *
8416 AAATATCCTAAAATT--TAATTAAAATACTCAAACCTATTTTAAACTAAAATA
1 AAATAT-CT-TAATTCCTAATTAAAATACTAAAACCTA-TTTAAACTAAAATA
8467 AAAAGATAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
70 1 0.01
71 31 0.29
72 33 0.31
73 31 0.29
74 6 0.06
75 4 0.04
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (73 bp):
AAATATCTTAATTCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAGATAA
AATATAAA
Found at i:10150 original size:5 final size:5
Alignment explanation
Indices: 10125--10237 Score: 77
Period size: 5 Copynumber: 21.8 Consensus size: 5
10115 ATCTGGAGAA
* * * *
10125 AAAATT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGTTT
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT
* * * *
10173 CTAAA- AAAAT AAAAT AAAAT AAAAT AAAAC GAAAT AAAACG AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
*
10224 GAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
10238 AATAGAACGA
Statistics
Matches: 82, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
4 7 0.09
5 60 0.73
6 12 0.15
7 1 0.01
8 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:10217 original size:21 final size:20
Alignment explanation
Indices: 10184--10251 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 20
10174 TAAAAAAATA
*
10184 AAATAAAATAAAATAAAACG
1 AAATAAAAAAAAATAAAACG
* *
10204 AAATAAAACGAAAATAAAATG
1 AAATAAAA-AAAAATAAAACG
*
10225 AAATAAAATAAAAAATAGAACG
1 AAAT-AAA-AAAAAATAAAACG
10247 AAATA
1 AAATA
10252 GGTTGCCTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.20
21 15 0.38
22 16 0.40
23 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAAAATAAAACG
Found at i:15742 original size:35 final size:36
Alignment explanation
Indices: 15672--15761 Score: 121
Period size: 35 Copynumber: 2.5 Consensus size: 36
15662 ATATATAATA
* *
15672 AATAAAATAAATAATTATAATTTAAAAAGAAAAAAT
1 AATAAAATAAATAATAATAATATAAAAAGAAAAAAT
**
15708 AATAAAATAAATAATAATAA-ATAAAAAGGGAAAAT
1 AATAAAATAAATAATAATAATATAAAAAGAAAAAAT
15743 AATAAAAT-AATAAATAATA
1 AATAAAATAAAT-AATAATA
15762 TTAGTAAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 3 0.06
35 27 0.55
36 19 0.39
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (36 bp):
AATAAAATAAATAATAATAATATAAAAAGAAAAAAT
Found at i:15761 original size:15 final size:14
Alignment explanation
Indices: 15666--15759 Score: 59
Period size: 13 Copynumber: 6.8 Consensus size: 14
15656 TTGAAAATAT
*
15666 ATAATAAATAAAAT
1 ATAATAAATAAAAA
* * *
15680 A-AATAATTATAAT
1 ATAATAAATAAAAA
* *
15693 TTAA-AAAGAAAAA
1 ATAATAAATAAAAA
*
15706 ATAATAAAATAAATA
1 ATAAT-AAATAAAAA
15721 ATAATAAATAAAAA
1 ATAATAAATAAAAA
***
15735 GGGA-AAATAATAAA
1 ATAATAAATAA-AAA
15749 ATAATAAATAA
1 ATAATAAATAA
15760 TATTAGTAAA
Statistics
Matches: 58, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
13 24 0.41
14 16 0.28
15 18 0.31
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (14 bp):
ATAATAAATAAAAA
Found at i:15826 original size:18 final size:18
Alignment explanation
Indices: 15805--15847 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15795 GTTGTTTTTA
15805 AAATAAAAGATAAA-AATT
1 AAATAAAA-ATAAATAATT
*
15823 AAATAAAATTAAATAATT
1 AAATAAAAATAAATAATT
15841 AAATAAA
1 AAATAAA
15848 TAATCTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAAATAAATAATT
Found at i:16499 original size:14 final size:15
Alignment explanation
Indices: 16464--16505 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
16454 TACTTAAAAC
16464 TATTTAAAATAA-AA
1 TATTTAAAATAATAA
**
16478 TACCTAAAA-AATAA
1 TATTTAAAATAATAA
16492 TATTTAAAATAATA
1 TATTTAAAATAATA
16506 TTCTAAATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTTAAAATAATAA
Found at i:16519 original size:71 final size:75
Alignment explanation
Indices: 16438--16627 Score: 250
Period size: 76 Copynumber: 2.6 Consensus size: 75
16428 TAAAACATCT
* *
16438 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAAATAAAATACCT-AAA-AAA-T--AATATTT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGTCAAATA-TA
*
16497 AAAATAATATTC
64 AAAATAATATCC
*
16509 TAAATCCTAATTAAAATACTAAAACCTACTTAAACTAAAATACCTAAAACAAAGTTCAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAG-TCAAATATAA
16574 AAATAATATCC
65 AAATAATATCC
*
16585 TAAAAT-TTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 T-AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
16628 AAAGATAAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
70 5 0.05
71 37 0.35
72 3 0.03
73 3 0.03
75 1 0.01
76 48 0.46
77 8 0.08
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.31
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGTCAAATATAAA
AATAATATCC
Found at i:16623 original size:24 final size:24
Alignment explanation
Indices: 16520--16627 Score: 69
Period size: 24 Copynumber: 4.3 Consensus size: 24
16510 AAATCCTAAT
*
16520 TAAAATACTAAAACCTACTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** *
16544 TAAAATACCTAAAACAAAGTTCAAA-
1 TAAAATA-CTAAAACCTA-TTTAAAC
* * *
16569 TATAAA-AATAATATCCTAAAATTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
16596 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
16620 TAAAATAC
1 TAAAATAC
16628 AAAGATAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
23 4 0.06
24 20 0.32
25 13 0.21
26 16 0.26
27 8 0.13
28 1 0.02
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:16651 original size:76 final size:75
Alignment explanation
Indices: 16439--16663 Score: 241
Period size: 76 Copynumber: 3.0 Consensus size: 75
16429 AAAACATCTT
* * *
16439 AAATCCTAATTAAAATACTTAAAA-CTATTTAAAATAAAATAC---CTAAAAAATAATATTTAAA
1 AAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
*
16500 ATAATATTCT-
65 ATAATATCCTA
* * * *
16510 AAATCCTAATTAAAATACTAAAACCTACTTAAACTAAAATACCTAAAACAAAGT-TCAA-ATATA
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAAATAT-AATAT-TT
16573 AAAATAATATCCTA
62 AAAATAATATCCTA
* *
16587 AAAT-TTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAA
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAAA
*
16651 ATATTATCCTA
65 ATAATATCCTA
16662 AA
1 AA
16664 CTTGAGTTTA
Statistics
Matches: 127, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
70 5 0.04
71 33 0.26
72 1 0.01
74 3 0.02
75 27 0.21
76 54 0.43
77 4 0.03
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (75 bp):
AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAAA
TAATATCCTA
Found at i:17348 original size:25 final size:23
Alignment explanation
Indices: 17318--17388 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
17308 TTAAATTCAT
17318 AATATTTTATATATATTAACTTAA
1 AATATTTT-TATATATTAACTTAA
17342 AAGTA-TTTT-TATATTAACTTATTA
1 AA-TATTTTTATATATTAACTTA--A
17366 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
17389 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
22 12 0.29
23 4 0.10
24 8 0.20
25 16 0.39
26 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
AATATTTTTATATATTAACTTAA
Found at i:17357 original size:22 final size:22
Alignment explanation
Indices: 17329--17388 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
17319 ATATTTTATA
17329 TATATTAACTTAAAAGTAT-TTT
1 TATATTAACTTAAAA-TATATTT
17351 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
17375 TATTATTAACTTAA
1 TA-TATTAACTTAA
17389 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 12 0.35
23 4 0.12
24 8 0.24
25 10 0.29
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:17393 original size:27 final size:24
Alignment explanation
Indices: 17338--17399 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 24
17328 ATATATTAAC
*
17338 TTAAAAGTATTTTTATATTAACTTA
1 TTAAAAATA-TTTTATATTAACTTA
*
17363 TTAAATATATTTTATTATTAACTTAA
1 TTAAAAATATTTTA-TATTAACTT-A
17389 TTTAAAAATAT
1 -TTAAAAATAT
17400 ATATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 16 0.52
26 1 0.03
27 9 0.29
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAAAATATTTTATATTAACTTA
Found at i:17581 original size:31 final size:32
Alignment explanation
Indices: 17533--17611 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
17523 TAACCCGTGA
* * *
17533 TGACTACATATTA-ATTAAATAAAAATAAAAG
1 TGACCACATCTTATATTAAATAAAAACAAAAG
* *
17564 TGACCATATCTT-TATTAAATAAAAACGAAAG
1 TGACCACATCTTATATTAAATAAAAACAAAAG
*
17595 TGATCACATCTTATATT
1 TGACCACATCTTATATT
17612 TTTCGAAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (32 bp):
TGACCACATCTTATATTAAATAAAAACAAAAG
Found at i:17965 original size:21 final size:21
Alignment explanation
Indices: 17921--17965 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17911 ATCACATCTG
*
17921 AATTTATTTTGTAATTTATGA
1 AATTTATTTTGTAATTCATGA
*
17942 AATTTATTTT-TAAATTCATTA
1 AATTTATTTTGT-AATTCATGA
17963 AAT
1 AAT
17966 ATTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
AATTTATTTTGTAATTCATGA
Found at i:23236 original size:39 final size:39
Alignment explanation
Indices: 23176--23263 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
23166 ATGCATCTTG
* *
23176 TAATATACGATTTCTGAAAATGATCACCTGCGACAGTCT
1 TAATATACGACTTCCGAAAATGATCACCTGCGACAGTCT
*
23215 TAATATACGACTTCCGGAAATGATCACCTGCGACAGTCT
1 TAATATACGACTTCCGAAAATGATCACCTGCGACAGTCT
23254 TAATATACGA
1 TAATATACGA
23264 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (39 bp):
TAATATACGACTTCCGAAAATGATCACCTGCGACAGTCT
Found at i:27268 original size:7 final size:7
Alignment explanation
Indices: 27256--27293 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
27246 GTCAAAGAAA
27256 GTCAACG
1 GTCAACG
27263 GTCAACG
1 GTCAACG
27270 GTCAACG
1 GTCAACG
27277 GTCAACG
1 GTCAACG
27284 GTCAACG
1 GTCAACG
27291 GTC
1 GTC
27294 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:27300 original size:5 final size:5
Alignment explanation
Indices: 27290--27347 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
27280 AACGGTCAAC
* *
27290 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
27339 GGTCG GGTC
1 GGTCG GGTC
27348 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:27311 original size:22 final size:22
Alignment explanation
Indices: 27283--27347 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
27273 AACGGTCAAC
27283 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27305 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27327 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
27348 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:27367 original size:19 final size:18
Alignment explanation
Indices: 27344--27421 Score: 86
Period size: 19 Copynumber: 4.2 Consensus size: 18
27334 GGTCGGGTCG
27344 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
27362 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
* *
27381 GTTC-GAACCGGTTGAAACC
1 GGTCAG-ACCGG-TCAAACC
*
27400 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
27419 GGT
1 GGT
27422 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 10 0.20
19 39 0.78
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:27381 original size:28 final size:28
Alignment explanation
Indices: 27344--27441 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
27334 GGTCGGGTCG
* *
27344 GGTCAGACCGGTCAAACCGAG-TCAGACC
1 GGTCAAACCGGTCAAACCG-GTTCAAACC
* * *
27372 GGTCAAACCGTTCGAACCGGTTGAAACC
1 GGTCAAACCGGTCAAACCGGTTCAAACC
*
27400 GGTCAAACCGGTCAGAACCGGTTGAAAACC
1 GGTCAAACCGGTCA-AACCGGTT-CAAACC
*
27430 GGTTAAACCGGT
1 GGTCAAACCGGT
27442 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
27 1 0.02
28 33 0.57
29 8 0.14
30 16 0.28
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (28 bp):
GGTCAAACCGGTCAAACCGGTTCAAACC
Found at i:27442 original size:9 final size:9
Alignment explanation
Indices: 27344--27441 Score: 88
Period size: 9 Copynumber: 10.3 Consensus size: 9
27334 GGTCGGGTCG
*
27344 GGTCAGACC
1 GGTCAAACC
27353 GGTCAAACC
1 GGTCAAACC
*
27362 GAGTCAGACC
1 G-GTCAAACC
27372 GGTCAAACC
1 GGTCAAACC
* *
27381 GTTCGAACC
1 GGTCAAACC
*
27390 GGTTGAAACC
1 GG-TCAAACC
27400 GGTCAAACC
1 GGTCAAACC
27409 GGTCAGAACC
1 GGTCA-AACC
*
27419 GGTTGAAAACC
1 GG-T-CAAACC
*
27430 GGTTAAACC
1 GGTCAAACC
27439 GGT
1 GGT
27442 TTCCAGCAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 43 0.59
10 22 0.30
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:34558 original size:7 final size:7
Alignment explanation
Indices: 34546--34576 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
34536 GTCAAAGAAA
34546 GTCAACG
1 GTCAACG
34553 GTCAACG
1 GTCAACG
34560 GTCAACG
1 GTCAACG
34567 GTCAACG
1 GTCAACG
34574 GTC
1 GTC
34577 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:34583 original size:5 final size:5
Alignment explanation
Indices: 34573--34635 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
34563 AACGGTCAAC
* *
34573 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G
34622 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
34636 AGACCGGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.06, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:34603 original size:22 final size:22
Alignment explanation
Indices: 34578--34661 Score: 132
Period size: 22 Copynumber: 3.6 Consensus size: 22
34568 TCAACGGTCG
34578 GGTCGGGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCGGGTCAAC
34600 GGTCGGGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCGGGTCAAC
34622 GGTCGGGTCGGGTCAGACCGGTCAAC
1 GGTCGGGTCGGGTC-G---GGTCAAC
34648 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
34662 AGACCGGTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
22 36 0.62
23 1 0.02
26 21 0.36
ACGTcount: A:0.10, C:0.24, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCGGGTCGGGTCGGGTCAAC
Found at i:34649 original size:26 final size:26
Alignment explanation
Indices: 34565--34672 Score: 152
Period size: 26 Copynumber: 4.3 Consensus size: 26
34555 CAACGGTCAA
* *
34565 CGGTCAACGGTCGGGTCGGGTCGGGTC
1 CGGTCAACGGTCGGGTCGGGTC-AGAC
*
34592 GGGTCAACGGTCGGGTCGGGTC-G--
1 CGGTCAACGGTCGGGTCGGGTCAGAC
34615 -GGTCAACGGTCGGGTCGGGTCAGAC
1 CGGTCAACGGTCGGGTCGGGTCAGAC
34640 CGGTCAACGGTCGGGTCGGGTCAGAC
1 CGGTCAACGGTCGGGTCGGGTCAGAC
34666 CGGTCAA
1 CGGTCAA
34673 ACCGAGTCAG
Statistics
Matches: 76, Mismatches: 1, Indels: 9
0.88 0.01 0.10
Matches are distributed among these distances:
22 21 0.28
23 1 0.01
25 1 0.01
26 32 0.42
27 21 0.28
ACGTcount: A:0.13, C:0.25, G:0.45, T:0.17
Consensus pattern (26 bp):
CGGTCAACGGTCGGGTCGGGTCAGAC
Found at i:34681 original size:19 final size:18
Alignment explanation
Indices: 34658--34736 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
34648 GGTCGGGTCG
34658 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
34676 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
34695 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
34715 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
34734 GGT
1 GGT
34737 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:34715 original size:29 final size:31
Alignment explanation
Indices: 34683--34757 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
34673 ACCGAGTCAG
34683 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
34712 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
34742 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
34758 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:34757 original size:9 final size:9
Alignment explanation
Indices: 34658--34756 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
34648 GGTCGGGTCG
*
34658 GGTCAGACC
1 GGTCAAACC
34667 GGTCAAACC
1 GGTCAAACC
*
34676 GAGTCAGACC
1 G-GTCAAACC
34686 GGTCAAACC
1 GGTCAAACC
*
34695 GGTTCGAACC
1 GG-TCAAACC
*
34705 GGTTGAAACC
1 GG-TCAAACC
34715 GGTCAAACC
1 GGTCAAACC
34724 GGTCAGAACC
1 GGTCA-AACC
*
34734 GGTTGAAAACC
1 GG-T-CAAACC
*
34745 GGTTAAACC
1 GGTCAAACC
34754 GGT
1 GGT
34757 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:43713 original size:33 final size:33
Alignment explanation
Indices: 43671--43738 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
43661 CACATTGCTA
*
43671 AAAAGGTGAAGCTCATTCTATAATGTAACTAAC
1 AAAAGGTGAAGCTCATTCCATAATGTAACTAAC
43704 AAAAGGTGAAGCTCATTCCATAATGTAACTAAC
1 AAAAGGTGAAGCTCATTCCATAATGTAACTAAC
43737 AA
1 AA
43739 TCTACCTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AAAAGGTGAAGCTCATTCCATAATGTAACTAAC
Done.