Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008589.1 Hibiscus syriacus cultivar Beakdansim tig00111538_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: 60538
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6353 original size:2 final size:2
Alignment explanation
Indices: 6348--6393 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6338 TTTTTAAATA
6348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6390 AT AT
1 AT AT
6394 TGAAGATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16193 original size:23 final size:23
Alignment explanation
Indices: 16162--16223 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
16152 ATAGGTAAAA
* *
16162 ATATGATGTAATATGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
16185 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
**
16208 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
16224 TAATTACTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:16277 original size:23 final size:23
Alignment explanation
Indices: 16260--16424 Score: 287
Period size: 23 Copynumber: 7.2 Consensus size: 23
16250 AATAACATAT
*
16260 TAGGTAGTGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
16283 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
16306 TAGGTAGCG-TTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
16328 TAAGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
16351 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
16374 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
**
16397 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATGTAA
16420 TAGGT
1 TAGGT
16425 TAATTACTTT
Statistics
Matches: 136, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
22 21 0.15
23 115 0.85
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:16477 original size:23 final size:23
Alignment explanation
Indices: 16451--16510 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
16441 ATCAAGCACA
*
16451 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** * *
16474 ATAATGTAATATGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
* *
16497 ATAATAAAATAGGT
1 ATAACATAATAGGT
16511 TAATTACTAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:16564 original size:23 final size:23
Alignment explanation
Indices: 16538--16597 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
16528 ATCAAACACA
*
16538 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
16561 ATAACGTAATAGGTAGCTCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
16584 ATAATAAAATAGGT
1 ATAACATAATAGGT
16598 TAATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:16570 original size:87 final size:86
Alignment explanation
Indices: 16374--16603 Score: 388
Period size: 87 Copynumber: 2.7 Consensus size: 86
16364 TATAATGTAA
**
16374 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTTTAACA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAACA
*
16439 TTATCAAGCACAATAACATAT
66 TTATCAAACACAATAACATAT
* *
16460 TAGGTACCGCTTATATAATGTAATATGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT-GAAAC
16525 ATTATCAAACACAATAACATAT
65 ATTATCAAACACAATAACATAT
* *
16547 TAGGTAGCGCTTATATAACGTAATAGGTAGCTCTTATATAATAAAATAGGTTAATTA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
16604 TTTAATTTGT
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 57 0.43
87 77 0.57
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (86 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAACA
TTATCAAACACAATAACATAT
Found at i:16869 original size:24 final size:24
Alignment explanation
Indices: 16842--16893 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16832 AACATCAAAT
16842 ACAATAA-AACAATATTATTTATTA
1 ACAATAATAACAATATTATTT-TTA
*
16866 ACAA-AATAATAATATTATTTTTA
1 ACAATAATAACAATATTATTTTTA
16889 A-AATA
1 ACAATA
16894 TTAGAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
ACAATAATAACAATATTATTTTTA
Found at i:16921 original size:14 final size:14
Alignment explanation
Indices: 16902--16946 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
16892 TATTAGAATA
*
16902 ATTTATTTAATATT
1 ATTTATTAAATATT
16916 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
16931 A-TTATTAAAATATT
1 ATTTATT-AAATATT
16945 AT
1 AT
16947 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:16960 original size:28 final size:28
Alignment explanation
Indices: 16874--17014 Score: 81
Period size: 28 Copynumber: 5.4 Consensus size: 28
16864 TAACAAAATA
*
16874 ATAATATTATTTTTAAAATATTA-GA--
1 ATAATATTATTATTAAAATATTATGATT
*
16899 ATAAT-TTA-T-TT--AATATTATTTATGT
1 ATAATATTATTATTAAAATATTA-TGAT-T
16924 A-AATATTATTATTAAAATATTAT-ATCT
1 ATAATATTATTATTAAAATATTATGAT-T
* * * *
16951 ATAATTTTATAAATAAAAAATTATGATT
1 ATAATATTATTATTAAAATATTATGATT
* ** *
16979 ATTATATT-TTATTAAAATAAAATTATT
1 ATAATATTATTATTAAAATATTATGATT
17006 ATAA-ATTAT
1 ATAATATTAT
17015 ATTTTTTATT
Statistics
Matches: 88, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
20 7 0.08
22 3 0.03
23 1 0.01
24 6 0.07
25 9 0.10
26 4 0.05
27 23 0.26
28 26 0.30
29 9 0.10
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
ATAATATTATTATTAAAATATTATGATT
Found at i:16988 original size:30 final size:31
Alignment explanation
Indices: 16954--17019 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
16944 TATATCTATA
*
16954 ATTTTA-TAAATAAAAAATTATGAT-TATTAT
1 ATTTTATTAAA-AAAAAATTATGATAAATTAT
* *
16984 ATTTTATTAAAATAAAATTATTATAAATTAT
1 ATTTTATTAAAAAAAAATTATGATAAATTAT
17015 ATTTT
1 ATTTT
17020 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTTTATTAAAAAAAAATTATGATAAATTAT
Found at i:17737 original size:28 final size:28
Alignment explanation
Indices: 17702--17791 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
17692 TATTTATGTC
17702 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
17730 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
17758 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
17785 AA-ATTAT
1 AATATTAT
17792 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:17794 original size:31 final size:31
Alignment explanation
Indices: 17731--17799 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
17721 TATATCTATA
*
17731 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
17761 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
17792 A-TTTATTA
1 ATTTTATTA
17800 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:18369 original size:198 final size:198
Alignment explanation
Indices: 17900--18578 Score: 992
Period size: 198 Copynumber: 3.4 Consensus size: 198
17890 CACATATGTT
* * * *
17900 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACC-G
1 ACATTGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGG
* * *** *
17964 TTTTATGAGAGAATATGTCTACATAATGTATCGACACAAATTTAA-AAAGTGTCGATACATTTTG
66 TTTTATGAGAAAATATGTCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTTT
* *
18028 TCCAGAATGAATGCCAAATGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATC
129 TCCAGAATGAATGCC-AACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATC
18093 CCAAAA
193 CCAAAA
* * * * *
18099 ACATAGAAACCGATAATTACAATGTAATAGGTAGATTTACAATGTACTCGGTAGAAATATATCGG
1 ACATTGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGG
18164 TTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
66 TTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
*
18229 CAGAATGAATGTCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATTCC
131 CAGAATGAATG-CCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
18294 AAAA
195 AAAA
* *
18298 A-ATTCAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATACCGG
1 ACATTGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGG
* *
18362 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
66 TTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* *
18427 CAGAATGAATGCCCAACGAGGTGCACACATAAAATGTCGATACATTTA--AAATTGTATCGATCC
131 CAGAATGAATG-CCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
18490 CAAAA
194 CAAAA
* * *
18495 ACATTGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTTA-CCAGTATAAATATACCG
1 ACATTGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCCAGTAGAAATATACCG
* *
18559 GTTTTATGATAGAATATGTC
65 GTTTTATGAGAAAATATGTC
18579 AATATAAGCG
Statistics
Matches: 438, Mismatches: 36, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
196 3 0.01
197 15 0.03
198 238 0.54
199 133 0.30
200 49 0.11
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
ACATTGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCAGTAGAAATATACCGG
TTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
CAGAATGAATGCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
AAA
Found at i:18627 original size:23 final size:23
Alignment explanation
Indices: 18571--18627 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
18561 TTTATGATAG
* *
18571 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAACGCTACCT
* **
18595 ATTACATTATATAAACGCTACCT
1 AATATGTTATATAAACGCTACCT
18618 AATATGTTAT
1 AATATGTTAT
18628 TGTGATTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAACGCTACCT
Found at i:18684 original size:23 final size:23
Alignment explanation
Indices: 18658--18714 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
18648 GTAATTAACT
18658 TATTTTATTATATAAGCGCTACC
1 TATTTTATTATATAAGCGCTACC
** *
18681 TATTACATTACATAAGCGCTACC
1 TATTTTATTATATAAGCGCTACC
* *
18704 TAATTTGTTAT
1 TATTTTATTAT
18715 TTTACTTAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.42
Consensus pattern (23 bp):
TATTTTATTATATAAGCGCTACC
Found at i:20035 original size:29 final size:29
Alignment explanation
Indices: 19992--20074 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
19982 CTCACCTAAC
19992 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
20022 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
20051 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
20075 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:24802 original size:29 final size:29
Alignment explanation
Indices: 24759--24841 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
24749 CTCACCTAAC
24759 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
24789 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
24818 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
24842 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:30443 original size:2 final size:2
Alignment explanation
Indices: 30436--30468 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30426 ATAGTAAGTA
30436 AT AT 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 AT AT A
30469 AGAAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30847 original size:2 final size:2
Alignment explanation
Indices: 30796--30828 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30786 CTTGTATAGA
30796 AT AT 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 AT AT A
30829 ATAGTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31253 original size:12 final size:11
Alignment explanation
Indices: 31225--31271 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
31215 TAACAAAATA
* *
31225 AATAATATAAA
1 AATAATACAAG
31236 AATAATACAAG
1 AATAATACAAG
31247 TAATAATACAAG
1 -AATAATACAAG
*
31259 AATAATAAAAG
1 AATAATACAAG
31270 AA
1 AA
31272 AGAGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATACAAG
Found at i:31364 original size:12 final size:12
Alignment explanation
Indices: 31342--31386 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
31332 GAATAAAAGG
31342 AAAATATAATAGT
1 AAAA-ATAATAGT
*
31355 AAAAATAATAAT
1 AAAAATAATAGT
*
31367 AAATATAATAGT
1 AAAAATAATAGT
*
31379 AATAATAA
1 AAAAATAA
31387 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:31978 original size:37 final size:37
Alignment explanation
Indices: 31937--32044 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
31927 GTGCTTGTTG
* *
31937 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
31974 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
32011 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAAC
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAAC
32045 GAAAATGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:32971 original size:106 final size:105
Alignment explanation
Indices: 32773--33829 Score: 1396
Period size: 106 Copynumber: 10.0 Consensus size: 105
32763 GCATTGTTCT
* * *
32773 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTAGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAATTGGAAATTGTTTGTTGACA
* * * * *
32837 ACCAGTC-GTCCCTTCTTTGTGAAGTTGTACTTGTGTTGTCTC
64 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
32879 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-T-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
* * ** *
32939 CAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTATTGCCTTG
66 CAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
32980 G-GTTCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* * * *
33044 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGAGTTATCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
33085 GAGTCCAATATCCTACGTTGTGAAGTTGATATTGGCTCTAAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
*
33150 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTAGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
33191 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
33256 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
33297 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
*
33362 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
33403 GAGTTCAATATCCTTCGATGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
*
33468 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
33509 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
* *
33574 CCAACGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
33615 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
33680 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
33721 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAA
* * * * *
33785 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
33826 GAGT
1 GAGT
33830 GGCACGATAT
Statistics
Matches: 850, Mismatches: 85, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
99 3 0.00
100 71 0.08
101 5 0.01
102 5 0.01
104 4 0.00
105 55 0.06
106 703 0.83
107 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:33381 original size:318 final size:317
Alignment explanation
Indices: 32772--33829 Score: 1549
Period size: 318 Copynumber: 3.4 Consensus size: 317
32762 AGCATTGTTC
* * * * *
32772 TGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTAGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * * * *
32837 ACCAGTC-GTCCCTTCTTTGTGAAGTTGTACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTG
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
* * * *
32901 AAGTTGAAATTGACTCTGAA-TGA-AA--T-TTTGTTGACAATCAGCCG-CCTCTTCGTCGTGAA
130 AAGTTGAAATTGGCTCTAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC-CTTCGTCGTGAA
* ** * * * *
32960 GTTGAGCTTGTATTGCCTTGG-GTTCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATT
194 GTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATT
* * *
33024 GGGAAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGAGTTATCT
258 GGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
33084 TGAGTCCAATATCCTACGTTGTGAAGTTGATATTGGCTCTAAAATTGGGAAATTATTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
*
33149 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTAGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
33214 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
131 AGTTGAAATTGGCTCT-AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
33279 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGG
33344 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
260 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
33402 TGAGTTCAATATCCTTCGATGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
*
33467 ACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* *
33532 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAACGGTCCCTTCATCGTGAAG
131 AGTTGAAATTGGCTCT-AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
33597 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGA
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGG
33662 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
260 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * * * *
33720 GGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATT-GTTGTTGAAA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * * *
33784 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
33830 GGCACGATAT
Statistics
Matches: 676, Mismatches: 61, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
311 1 0.00
312 127 0.19
313 2 0.00
314 3 0.00
315 2 0.00
317 52 0.08
318 487 0.72
319 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (317 bp):
TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTCTAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGG
AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:34679 original size:22 final size:22
Alignment explanation
Indices: 34654--34705 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
34644 TTGTGTTTGG
*
34654 TCAAAGGTGTAGTATTTGATGC
1 TCAAAGGTGTAGCATTTGATGC
* *
34676 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTGTAGCATTTGATGC
34698 TCAAAGGT
1 TCAAAGGT
34706 TTGATGGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTGTAGCATTTGATGC
Found at i:34706 original size:22 final size:22
Alignment explanation
Indices: 34667--34708 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
34657 AAGGTGTAGT
34667 ATTTGATGCTCAAAGGTTTGGC
1 ATTTGATGCTCAAAGGTTTGGC
34689 ATTTGATGCTCAAAGGTTTG
1 ATTTGATGCTCAAAGGTTTG
34709 ATGGGGTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGTTTGGC
Found at i:39929 original size:2 final size:2
Alignment explanation
Indices: 39922--39958 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39912 AGTAAGTAAA
39922 AT AT AT AT 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 AT AT AT AT A
39959 AAAGAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40285 original size:2 final size:2
Alignment explanation
Indices: 40278--40302 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40268 CTTGTGTAGA
40278 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 A
40303 ATAATAGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40629 original size:12 final size:12
Alignment explanation
Indices: 40607--40651 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
40597 GAATAAAAGG
40607 AAAATATAATAGT
1 AAAA-ATAATAGT
*
40620 AAAAATAATAAT
1 AAAAATAATAGT
*
40632 AAATATAATAGT
1 AAAAATAATAGT
*
40644 AATAATAA
1 AAAAATAA
40652 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:41252 original size:37 final size:38
Alignment explanation
Indices: 41211--41307 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 38
41201 GGATCCAATC
41211 TTTAGGAGTTTAAATCATAGTAGAAA-TCTATCATATT
1 TTTAGGAGTTTAAATCATAGTAGAAATTCTATCATATT
* * *
41248 TTTAGGAGTTTAAATCCTAGCA-AAATTCTATCTTATT
1 TTTAGGAGTTTAAATCATAGTAGAAATTCTATCATATT
* * *
41285 TTTAAGAGTTTGAATCGTAGTAG
1 TTTAGGAGTTTAAATCATAGTAG
41308 GACGAAAAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.06
37 48 0.94
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (38 bp):
TTTAGGAGTTTAAATCATAGTAGAAATTCTATCATATT
Found at i:41527 original size:109 final size:110
Alignment explanation
Indices: 41328--41527 Score: 294
Period size: 109 Copynumber: 1.8 Consensus size: 110
41318 TGTATTGACA
* * * *
41328 CTTATCATGTGGCAAAGAAAGAACAGACCACGTGTTATTTAATTCTAGAGTCTGAATTTACTCCT
1 CTTACCATGTGGCAAAGAAACAACAGACCACATG-T-TTTAATTCTAGAGCCTGAATTTACTCCT
*
41393 TCATAGCATTAATCCAACGTGGAACCCCATTTACAACCAATAGGACC
64 TCATAGCATTAATCCAACATGGAACCCCATTTACAACCAATAGGACC
* * *
41440 CTTACCATGTGGCAAAGCAACAACAGGCCACATG-TTTAATTCTAGAGCCTGAATTTCCTCCTTC
1 CTTACCATGTGGCAAAGAAACAACAGACCACATGTTTTAATTCTAGAGCCTGAATTTACTCCTTC
*
41504 ATAGCATTAATCCAATATGGAACC
66 ATAGCATTAATCCAACATGGAACC
41528 TTACAAGAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
109 50 0.63
112 29 0.37
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (110 bp):
CTTACCATGTGGCAAAGAAACAACAGACCACATGTTTTAATTCTAGAGCCTGAATTTACTCCTTC
ATAGCATTAATCCAACATGGAACCCCATTTACAACCAATAGGACC
Found at i:44115 original size:8 final size:8
Alignment explanation
Indices: 44098--44173 Score: 53
Period size: 8 Copynumber: 8.6 Consensus size: 8
44088 CCTCCTTTTC
*
44098 TTTTCTTT
1 TTTTCATT
44106 TTTTCATTT
1 TTTTCA-TT
*
44115 TTTTCTTCTT
1 TTTTC--ATT
44125 TTTTTCATTT
1 -TTTTCA-TT
44135 TTTTCATTTT
1 TTTTCA--TT
44145 TTTTCATT
1 TTTTCATT
44153 TTTTCATT
1 TTTTCATT
**
44161 CATTCATT
1 TTTTCATT
44169 TTTTC
1 TTTTC
44174 TCTTCAAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
8 24 0.44
9 13 0.24
10 13 0.24
11 5 0.09
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:44117 original size:9 final size:9
Alignment explanation
Indices: 44098--44160 Score: 76
Period size: 9 Copynumber: 6.9 Consensus size: 9
44088 CCTCCTTTTC
44098 TTTTC-TTT
1 TTTTCATTT
44106 TTTTCATTT
1 TTTTCATTT
*
44115 TTTTCTTCTTT
1 TTTTC--ATTT
44126 TTTTCATTT
1 TTTTCATTT
44135 TTTTCATTTT
1 TTTTCA-TTT
44145 TTTTCA-TT
1 TTTTCATTT
44153 TTTTCATT
1 TTTTCATT
44161 CATTCATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
8 13 0.27
9 18 0.38
10 9 0.19
11 8 0.17
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:44123 original size:20 final size:20
Alignment explanation
Indices: 44100--44156 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
44090 TCCTTTTCTT
44100 TTCTTTTTTTCATTTTTTTC
1 TTCTTTTTTTCATTTTTTTC
44120 TTCTTTTTTTCATTTTTTTC
1 TTCTTTTTTTCATTTTTTTC
*
44140 AT-TTTTTTTCATTTTTT
1 TTCTTTTTTTCATTTTTT
44157 CATTCATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 15 0.42
20 21 0.58
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (20 bp):
TTCTTTTTTTCATTTTTTTC
Found at i:60244 original size:6 final size:6
Alignment explanation
Indices: 60233--60308 Score: 80
Period size: 6 Copynumber: 12.3 Consensus size: 6
60223 TTTGGTACTG
* * * *
60233 TGCCAT TGCCATT TGCTAT TGCCGT TCCCAT TGCCAT TGCCATT TGCTAT
1 TGCCAT TGCCA-T TGCCAT TGCCAT TGCCAT TGCCAT TGCCA-T TGCCAT
* *
60283 TGCCGT TCCCAT TGCCAT TGCCAT TG
1 TGCCAT TGCCAT TGCCAT TGCCAT TG
60309 GACTAATGAG
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
6 46 0.82
7 10 0.18
ACGTcount: A:0.13, C:0.32, G:0.17, T:0.38
Consensus pattern (6 bp):
TGCCAT
Found at i:60269 original size:31 final size:31
Alignment explanation
Indices: 60233--60307 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
60223 TTTGGTACTG
60233 TGCCATTGCCATTTGCTATTGCCGTTCCCAT
1 TGCCATTGCCATTTGCTATTGCCGTTCCCAT
60264 TGCCATTGCCATTTGCTATTGCCGTTCCCAT
1 TGCCATTGCCATTTGCTATTGCCGTTCCCAT
60295 TGCCATTGCCATT
1 TGCCATTGCCATT
60308 GGACTAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.13, C:0.32, G:0.16, T:0.39
Consensus pattern (31 bp):
TGCCATTGCCATTTGCTATTGCCGTTCCCAT
Done.