Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000217.1 Hibiscus syriacus cultivar Beakdansim tig00000385_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: 69160
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:233 original size:2 final size:2
Alignment explanation
Indices: 226--377 Score: 117
Period size: 2 Copynumber: 78.5 Consensus size: 2
216 TCCTTAGTTC
226 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
* * * *
268 AT GT AT GT AT GT AT AT A- AT AT AT -T AT AT AT AT GT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * *
309 A- AT AT AT A- AGT TT AT AT AT AA ACT AT AT -T TT AT AT -T AT AA
1 AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
349 ACT AT AT AT -T AT -T AT A- AGT -T AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A
378 ATTATGTTAT
Statistics
Matches: 120, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
1 10 0.08
2 106 0.88
3 4 0.03
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:335 original size:19 final size:20
Alignment explanation
Indices: 313--354 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
303 TGATATAATA
313 TATAAGTTTATA-TATAAAC
1 TATAAGTTTATATTATAAAC
*
332 TAT-ATTTTATATTATAAAC
1 TATAAGTTTATATTATAAAC
351 TATA
1 TATA
355 TATTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TATAAGTTTATATTATAAAC
Found at i:355 original size:19 final size:18
Alignment explanation
Indices: 319--365 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
309 AATATATAAG
319 TTTATATATAAACTATAT
1 TTTATATATAAACTATAT
337 TTTATATTATAAACTATAT
1 TTTATA-TATAAACTATAT
*
356 ATTAT-TATAA
1 TTTATATATAA
366 GTTATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 16 0.59
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATAAACTATAT
Found at i:386 original size:17 final size:18
Alignment explanation
Indices: 351--389 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
341 TATTATAAAC
*
351 TATATATTATTATAAGTTA
1 TATATATAATTAT-AGTTA
370 TATATATAATTAT-GTTA
1 TATATATAATTATAGTTA
387 TAT
1 TAT
390 GAACTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TATATATAATTATAGTTA
Found at i:407 original size:13 final size:14
Alignment explanation
Indices: 391--424 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
381 ATGTTATATG
*
391 AACTATATATGTA-
1 AACTATACATGTAT
404 AACTATACATGTAT
1 AACTATACATGTAT
418 AACTATA
1 AACTATA
425 AAAGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (14 bp):
AACTATACATGTAT
Found at i:431 original size:14 final size:14
Alignment explanation
Indices: 391--432 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
381 ATGTTATATG
*
391 AACTATATATGTA-
1 AACTATAAATGTAT
*
404 AACTATACATGTAT
1 AACTATAAATGTAT
*
418 AACTATAAAAGTAT
1 AACTATAAATGTAT
432 A
1 A
433 TTTTATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (14 bp):
AACTATAAATGTAT
Found at i:2200 original size:15 final size:16
Alignment explanation
Indices: 2180--2209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2170 TTTAATAGAA
2180 GAAA-TTCTCATTGTG
1 GAAATTTCTCATTGTG
2195 GAAATTTCTCATTGT
1 GAAATTTCTCATTGT
2210 AATGTCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (16 bp):
GAAATTTCTCATTGTG
Found at i:3094 original size:18 final size:18
Alignment explanation
Indices: 3071--3113 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3061 CTTCCTTTAT
3071 GTGAGCATTGAATAACAA
1 GTGAGCATTGAATAACAA
*
3089 GTGAGCATTGCATAACAA
1 GTGAGCATTGAATAACAA
*
3107 GTAAGCA
1 GTGAGCA
3114 GTACCGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (18 bp):
GTGAGCATTGAATAACAA
Found at i:10505 original size:12 final size:12
Alignment explanation
Indices: 10488--10515 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10478 ATGATTGAAT
10488 ATTTAAATTTTA
1 ATTTAAATTTTA
10500 ATTTAAATTTTA
1 ATTTAAATTTTA
10512 ATTT
1 ATTT
10516 TTGCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTAAATTTTA
Found at i:15877 original size:43 final size:43
Alignment explanation
Indices: 15808--15926 Score: 175
Period size: 43 Copynumber: 2.8 Consensus size: 43
15798 TTCAAGCCAG
15808 ATTTCAACTCCACGACGGAGGATATCATGCCCACAAATCCACA
1 ATTTCAACTCCACGACGGAGGATATCATGCCCACAAATCCACA
* * *
15851 ATTTTAACTCCACGACGGAGGGTATCATGCCCACAAATCCACG
1 ATTTCAACTCCACGACGGAGGATATCATGCCCACAAATCCACA
* * * *
15894 ATTTCAACTTCACGATGAAGGATATCGTGCCCA
1 ATTTCAACTCCACGACGGAGGATATCATGCCCA
15927 TGTACACAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCATGCCCACAAATCCACA
Found at i:16333 original size:83 final size:80
Alignment explanation
Indices: 16177--16470 Score: 257
Period size: 83 Copynumber: 3.6 Consensus size: 80
16167 TCGTGCCCAA
* * * * * * *
16177 TGCAACATAACTCAATGTTAGAAGGGTTAGCTGTCATCGAAGACCTTCATGTTCGACTACGCTCA
1 TGCAACATAACTCAAGGCTAGAAGGGTTATCTG-CA-CAAAGACCTTCAAGTTCGATTACACTCA
16242 GCTCCAAGGCACATCATT
64 GCT-CAAGGCACATCATT
* * *
16260 TGCAACAGAACTCAAGGCTAGAAGGGTTATTTGCCAACAAATGACCTTCAAGTTTGATTACACTC
1 TGCAACATAACTCAAGGCTAGAAGGGTTATCTG-C-ACAAA-GACCTTCAAGTTCGATTACACTC
16325 AGCTCAAGGCACATCATT
63 AGCTCAAGGCACATCATT
* * * * * * * *
16343 TGCAGCATAGCTTAAGGCAAGAAAGGCTATCTGC-TAAAGACCTTCGAGTTCGATTACACTCAGC
1 TGCAACATAACTCAAGGCTAGAAGGGTTATCTGCACAAAGACCTTCAAGTTCGATTACACTCAGC
*
16407 TCAAAGGCATATCATT
66 TC-AAGGCACATCATT
* * * * * * *
16423 TTCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTT
1 TGCAACATAACTCAAGGCTAGAAGGGTTATCTG-C-A-CAAAGACCTT
16471 TCGAGGTATA
Statistics
Matches: 176, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
79 26 0.15
80 44 0.25
81 1 0.01
82 1 0.01
83 71 0.40
84 33 0.19
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (80 bp):
TGCAACATAACTCAAGGCTAGAAGGGTTATCTGCACAAAGACCTTCAAGTTCGATTACACTCAGC
TCAAGGCACATCATT
Found at i:16435 original size:80 final size:79
Alignment explanation
Indices: 16216--16456 Score: 257
Period size: 80 Copynumber: 3.0 Consensus size: 79
16206 GCTGTCATCG
* * * * * * * *
16216 AAGACCTTCATGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACAGAACTCAAGGCTAG
1 AAGACCTTCAAGTTCGATTACACTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
* * * *
16281 AAGGGTTATTTGCCAACA
65 AAAGGCTATCTG-C--TA
*
16299 AATGACCTTCAAGTTTGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
1 AA-GACCTTCAAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
16364 AAAGGCTATCTGCTA
65 AAAGGCTATCTGCTA
* * * * *
16379 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTTTCAGCATAGCTTAAGTCGAG
1 AAGACCTTCAAGTTCGATTACACTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGGCAAG
*
16444 AAGGGCTATCTGC
65 AAAGGCTATCTGC
16457 CAACCAAAGA
Statistics
Matches: 136, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
79 26 0.19
80 45 0.33
82 1 0.01
83 41 0.30
84 23 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (79 bp):
AAGACCTTCAAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAGA
AAGGCTATCTGCTA
Found at i:16654 original size:83 final size:83
Alignment explanation
Indices: 16480--16929 Score: 536
Period size: 83 Copynumber: 5.5 Consensus size: 83
16470 TTCGAGGTAT
* * * *
16480 ATCATTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGT--AA-ACCTTCAAGTTCGAT
1 ATCA-TTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTC-GTCAAAGACCTTCGAGTTCGAT
* *
16542 TACACTTAGCTCAAAGACAC
64 TACACTCAGCTCAAAGGCAC
* * *
16562 ATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGTTTA
1 ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTCGTCAAAGACCTTCGAGTTCGATTA
* *
16627 TACTCAGCTCAAAGGCAT
66 CACTCAGCTCAAAGGCAC
* * * *
16645 ATCATTTGCAGCGTAAGTCAAGGCAAGAAGGGTTATTTGTCGTCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTCGTCAAAGACCTTCGAGTTCGATTA
16710 CACTCAGCTCAAAGGCAC
66 CACTCAGCTCAAAGGCAC
* * * * * * * *
16728 ATCATTTGCAACATAACTCAAGGCTAGAAGGGTTTTTTGCCAATAAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTC-GTCAAAGACCTTCGAGTTCGATT
* *
16793 ACACTCAACT-TAAGGCAC
65 ACACTCAGCTCAAAGGCAC
* * *
16811 ATCATTTGTAGCATAACTTAAGGCAAGAAAGGCTATCTG-C--CAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTCGTCAAAGACCTTCGAGTTCGATTA
16873 CACTCAGCTCAAAGGCAC
66 CACTCAGCTCAAAGGCAC
* * * *
16891 ATCATTTGCAGCATAGCTTAAGTCTAGAAGGGCTATCTG
1 ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTG
16930 CCAACAAAAG
Statistics
Matches: 321, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
79 29 0.09
80 43 0.13
81 34 0.11
82 7 0.02
83 178 0.55
84 30 0.09
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATCTGTCGTCAAAGACCTTCGAGTTCGATTA
CACTCAGCTCAAAGGCAC
Found at i:17007 original size:391 final size:395
Alignment explanation
Indices: 16571--17304 Score: 1048
Period size: 391 Copynumber: 1.9 Consensus size: 395
16561 CATCATTTGC
* * *
16571 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGTTTATACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTCGT-AAAGACCTTCGAGTTCGATTACACTCAGCT
* * * *
16636 CAAAGGCATATCATTTGCAGCGTAAGTCAAGGCAAGAAGGGTTATTTGTCGTCAAAGACCTTCGA
65 CAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGA
* * *
16701 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTTTTT
130 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGTTATCT
* * *
16766 GCCAATAAAAGACCTTCGAGTTCGATTACACTCAACT-TAAGGCACATCATTTGTAGCATAACTT
195 GCC-ATAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTC
* *
16830 AAGGCAAGAAAGGCTATCTG-C-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
259 AAGGCAAGAAAGGCTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCAAAT
*
16893 C-ATTTGCAGCATAGCTTAAGTCTAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATC
324 CAATTTACAGCATAGCTTAAGTCTAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATC
16957 ATTTTAT
389 ATTTTAT
*
16964 AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGT-AA-ACCTTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTC-GTAAAGACCTTCGAGTTCGATTACACTCAGCT
* * *
17027 CAATGGTACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGA
65 CAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGA
* * * *
17092 GTTTGATTACACTTAGCTCAAAGGCATATCATTTGCAACGTAACTCAAGGCGAGAAGGGTTATCT
130 GTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGTTATCT
* * * * *
17157 GTCGTCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCGTAACTCA
195 GCCATAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTCA
* * * * * * * *
17222 AGGCGAGAAGGGGTATTTGTCATCAAAGACCTTCGAGTTTGATTGCATTCAACTCAGAGGCAAAT
260 AGGCAAGAAAGGCTATCTGTCA-CAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCAAAT
17287 CAAATTTACAGCATAGCT
324 C-AATTTACAGCATAGCT
17305 CAAGCCGAGG
Statistics
Matches: 297, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
390 30 0.10
391 181 0.61
392 3 0.01
393 30 0.10
394 39 0.13
396 14 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (395 bp):
AGCATAACTCAAGGCGAGAAGGGCTATCTGTCGTAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGAG
TTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCGAGAAGGGTTATCTG
CCATAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAACTCAA
GGCAAGAAAGGCTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCAAATCA
ATTTACAGCATAGCTTAAGTCTAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATCAT
TTTAT
Found at i:17083 original size:474 final size:474
Alignment explanation
Indices: 16177--17288 Score: 1742
Period size: 474 Copynumber: 2.3 Consensus size: 474
16167 TCGTGCCCAA
* * ** * * * * *
16177 TGCAACATAACTCAATGTTAGAAGGGTTAGCTGTCATCGAAGACCTTC-ATGTTCGACTACGCTC
1 TGCAACGTAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGA-GTTCGATTACACTC
* * * *
16241 AGCTCCAAGGCACATCATTTGCAACAGAACTCAAGGCTAGAAGGGTTATTTGCCAACAAATGACC
65 AGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAATAAAAGACC
* * *
16306 TTCAAGTTTGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGGCAAGAAAGGCT
130 TTCGAGTTTGATTACACTCAACTCAAGGCACATCATTTGCAGCATAACTTAAGGCAAGAAAGGCT
* * *
16371 ATCTGCTAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCATTTTCAGCATAGCTT
195 ATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTT
* * *
16436 AAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTTCGAGGTATATCATTTTACAGCATAGCTCA
260 AAGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATCATTTTACAGCATAGCTCA
*
16501 AGGCGAGAAGGGCTATCTGTCAGTAAACCTTCAAGTTCGATTACACTTAGCTCAAAGACACATCA
325 AGGCGAGAAGGGCTATCTGTCAGTAAACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCA
* *
16566 TTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGTTTATACT
390 TTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACT
16631 CAGCTCAAAGGCATATCATT
455 CAGCTCAAAGGCATATCATT
* * *
16651 TGCAGCGTAAGTCAAGGCAAGAAGGGTTATTTGTCGTCAAAGACCTTCGAGTTCGATTACACTCA
1 TGCAACGTAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTCA
*
16716 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTTTTTGCCAATAAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAATAAAAGACCT
* * *
16781 TCGAGTTCGATTACACTCAACTTAAGGCACATCATTTGTAGCATAACTTAAGGCAAGAAAGGCTA
131 TCGAGTTTGATTACACTCAACTCAAGGCACATCATTTGCAGCATAACTTAAGGCAAGAAAGGCTA
16846 TCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTA
196 TCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTA
* *
16911 AGTCTAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATCATTTTATAGCATAGCTCAA
261 AGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATCATTTTACAGCATAGCTCAA
* * **
16976 GGCGAGAAGGGCTATCTGTCAGTAAACCTTCGAGTTCGATTACACTCAGCTCAATGGTACATCAT
326 GGCGAGAAGGGCTATCTGTCAGTAAACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCAT
* *
17041 TTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTTGATTACACTT
391 TTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTC
17106 AGCTCAAAGGCATATCATT
456 AGCTCAAAGGCATATCATT
*
17125 TGCAACGTAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTCA
1 TGCAACGTAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
17190 GCTCAAAGGCACATCATTTGCAGCGTAACTCAAGGCGAGAAGGGGTATTTGTC-ATCAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAATAAAAGACCT
* * *
17254 TCGAGTTTGATTGCATTCAACTCAGAGGCAAATCA
131 TCGAGTTTGATTACACTCAACTCA-AGGCACATCA
17289 AATTTACAGC
Statistics
Matches: 580, Mismatches: 56, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
473 30 0.05
474 549 0.95
475 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (474 bp):
TGCAACGTAACTCAAGGCAAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATTTGCCAATAAAAGACCT
TCGAGTTTGATTACACTCAACTCAAGGCACATCATTTGCAGCATAACTTAAGGCAAGAAAGGCTA
TCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTA
AGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTTCGAGGCACATCATTTTACAGCATAGCTCAA
GGCGAGAAGGGCTATCTGTCAGTAAACCTTCAAGTTCGATTACACTCAGCTCAAAGACACATCAT
TTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTTCGATTACACTC
AGCTCAAAGGCATATCATT
Found at i:17123 original size:83 final size:83
Alignment explanation
Indices: 16948--17313 Score: 459
Period size: 83 Copynumber: 4.4 Consensus size: 83
16938 AGACCTTTCG
** * *
16948 AGGCACATCATTTTATAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGT--AA-ACCTTCGAG
1 AGGCACATCA-TTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-GTCAAAGACCTTCGAG
17010 TTCGATTACACTCAGCTCAA
64 TTCGATTACACTCAGCTCAA
* *
17030 TGGTACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
1 AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
* *
17095 TGATTACACTTAGCTCAA
66 CGATTACACTCAGCTCAA
* * *
17113 AGGCATATCATTTGCAACGTAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
1 AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
17178 CGATTACACTCAGCTCAA
66 CGATTACACTCAGCTCAA
* * * *
17196 AGGCACATCATTTGCAGCGTAACTCAAGGCGAGAAGGGGTATTTGTCATCAAAGACCTTCGAGTT
1 AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
* * * * *
17261 TGATTGCATTCAACTCAG
66 CGATTACACTCAGCTCAA
* * * *
17279 AGGCAAATCAAATTTACAGCATAGCTCAAGCCGAG
1 AGGCACATC--ATTTGCAGCATAACTCAAGGCGAG
17314 GTTTTCAACT
Statistics
Matches: 249, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
80 2 0.01
81 33 0.13
82 10 0.04
83 184 0.74
85 20 0.08
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (83 bp):
AGGCACATCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCGTCAAAGACCTTCGAGTT
CGATTACACTCAGCTCAA
Found at i:20953 original size:14 final size:14
Alignment explanation
Indices: 20930--20960 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20920 ATTCGGTTAT
*
20930 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
20944 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
20958 GTT
1 GTT
20961 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:20953 original size:24 final size:24
Alignment explanation
Indices: 20921--20967 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
20911 TTCGTGAACA
20921 TTCGGTTATGTTCGTTTATGTTCG
1 TTCGGTTATGTTCGTTTATGTTCG
20945 TTCGGTTATGTTCGTTTATGTTC
1 TTCGGTTATGTTCGTTTATGTTC
20968 ATTCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.23, T:0.55
Consensus pattern (24 bp):
TTCGGTTATGTTCGTTTATGTTCG
Found at i:20977 original size:24 final size:24
Alignment explanation
Indices: 20919--20980 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
20909 TGTTCGTGAA
*
20919 CATTCGGTTATGTTCGTTTATGTT
1 CATTCAGTTATGTTCGTTTATGTT
* *
20943 CGTTCGGTTATGTTCGTTTATGTT
1 CATTCAGTTATGTTCGTTTATGTT
*
20967 CATTCATTTATGTT
1 CATTCAGTTATGTT
20981 TAACCCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CATTCAGTTATGTTCGTTTATGTT
Found at i:22081 original size:24 final size:25
Alignment explanation
Indices: 22049--22105 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
22039 TGGTCTCCAA
22049 CGTTTATGTTCGTGTT-TTCGTGTT
1 CGTTTATGTTCGTGTTCTTCGTGTT
*
22073 CGTTTATGTTCGTGTTCGTTTGTGTT
1 CGTTTATGTTCGTGTTC-TTCGTGTT
22099 CGTTTAT
1 CGTTTAT
22106 TTATTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 16 0.53
26 14 0.47
ACGTcount: A:0.05, C:0.12, G:0.25, T:0.58
Consensus pattern (25 bp):
CGTTTATGTTCGTGTTCTTCGTGTT
Found at i:22086 original size:16 final size:16
Alignment explanation
Indices: 22065--22101 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
22055 TGTTCGTGTT
22065 TTCGTGTTCGTTTATG
1 TTCGTGTTCGTTTATG
*
22081 TTCGTGTTCGTTTGTG
1 TTCGTGTTCGTTTATG
22097 TTCGT
1 TTCGT
22102 TTATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.14, G:0.27, T:0.57
Consensus pattern (16 bp):
TTCGTGTTCGTTTATG
Found at i:22150 original size:31 final size:31
Alignment explanation
Indices: 22112--22192 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
22102 TTATTTATTA
22112 AATGAACGAACATGAACAAGTTAGATTCCTT
1 AATGAACGAACATGAACAAGTTAGATTCCTT
22143 AATGAACGAACATGAACAAGTTAGATTCCTT
1 AATGAACGAACATGAACAAGTTAGATTCCTT
*
22174 AATAAACGAACATGAACAA
1 AATGAACGAACATGAACAA
22193 AAAAAAATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGTTAGATTCCTT
Found at i:32454 original size:15 final size:15
Alignment explanation
Indices: 32435--32492 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
32425 TTTCTCATCT
*
32435 CTGAATGATTCAGTT
1 CTGAATGATTCAGTG
32450 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
32465 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
**
32480 CTGCCTGATTCAG
1 CTGAATGATTCAG
32493 CAAAATAGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:32705 original size:16 final size:16
Alignment explanation
Indices: 32686--32716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32676 GTTTAATTCA
32686 ATTAAATATTAAATAT
1 ATTAAATATTAAATAT
*
32702 ATTATATATTAAATA
1 ATTAAATATTAAATA
32717 GAAAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATATTAAATAT
Found at i:38920 original size:23 final size:23
Alignment explanation
Indices: 38878--38922 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38868 GATATAACAG
*
38878 TTCAGTTTCTTTCCCTTTTCATT
1 TTCAGTTTCTTTCCCCTTTCATT
38901 TTCAGTTTAC-TTCCCCTTTCAT
1 TTCAGTTT-CTTTCCCCTTTCAT
38923 CTTTTAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.11, C:0.29, G:0.04, T:0.56
Consensus pattern (23 bp):
TTCAGTTTCTTTCCCCTTTCATT
Found at i:61075 original size:21 final size:20
Alignment explanation
Indices: 61035--61078 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
61025 AAAAAGAAGA
*
61035 AAAAAAGAATTTGGAGTTTT
1 AAAAAAGAACTTGGAGTTTT
*
61055 AAAAAAGAAACTTGTGATTTTT
1 AAAAAAG-AACTTG-GAGTTTT
61077 AA
1 AA
61079 TGAGGGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (20 bp):
AAAAAAGAACTTGGAGTTTT
Found at i:68550 original size:13 final size:13
Alignment explanation
Indices: 68516--68550 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
68506 ACGCTCAATA
68516 CGCGTCATAAATG
1 CGCGTCATAAATG
*
68529 CGTGTCATAAATG
1 CGCGTCATAAATG
*
68542 CGCGCCATA
1 CGCGTCATA
68551 GATTTATGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (13 bp):
CGCGTCATAAATG
Done.