Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002575.1 Hibiscus syriacus cultivar Beakdansim tig00005219_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: 56315
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1211 original size:22 final size:22
Alignment explanation
Indices: 1186--1227 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1176 GTAAAATAAT
1186 AATAAAGATATAAATAATAGGA
1 AATAAAGATATAAATAATAGGA
* * *
1208 AATATATATATATATAATAG
1 AATAAAGATATAAATAATAG
1228 TAAAAAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (22 bp):
AATAAAGATATAAATAATAGGA
Found at i:1323 original size:31 final size:30
Alignment explanation
Indices: 1263--1321 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1253 CATATGAAAT
1263 AAATAAAAAGAATATAACTAAATACATATA
1 AAATAAAAAGAATATAACTAAATACATATA
1293 AAATATAAAAGAA-ATAA-TGAAATA-ATATA
1 AAATA-AAAAGAATATAACT-AAATACATATA
1322 TATAATAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 6 0.22
30 14 0.52
31 7 0.26
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATAAAAAGAATATAACTAAATACATATA
Found at i:2343 original size:50 final size:51
Alignment explanation
Indices: 2283--2384 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
2273 GAACCTGAAA
*
2283 TCCTACTTTTAAGTGTTTTAATCCGAAAATAATACT-ATATATTTGTTATG
1 TCCTAATTTTAAGTGTTTTAATCCGAAAATAATACTAATATATTTGTTATG
2333 TCCTAATTTTAAGTGTTTTAATCCGAAAATAATACTAATATATTTGTTATG
1 TCCTAATTTTAAGTGTTTTAATCCGAAAATAATACTAATATATTTGTTATG
2384 T
1 T
2385 TTGTTGTGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 35 0.70
51 15 0.30
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (51 bp):
TCCTAATTTTAAGTGTTTTAATCCGAAAATAATACTAATATATTTGTTATG
Found at i:3555 original size:106 final size:106
Alignment explanation
Indices: 3065--3937 Score: 1399
Period size: 106 Copynumber: 8.3 Consensus size: 106
3055 AGCCAAGATA
*
3065 CTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
* *
3130 TCGTCGTGAA--TGAACTTGCGTTGTCTTGAGCCCAATATC
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
*
3169 CTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGT-TTGACAACCAGCGGTCCC
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTT-TATTGACAACCAGCGGTCCC
* *
3233 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCC-A-GTC
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
3273 CTTTG-TGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTT-TTGACAACCAGCGGTCCCT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
*
3336 TCGTCGTGAAGTTGAACTTGCGTTGTCT-GAGTCCGATAT-
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* *
3375 CTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCC
1 CTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
*
3439 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCGATATC
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
*
3481 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
3546 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* * * *
3587 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAATCAGCGGTCCTT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
3652 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* *
3693 CTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGTGGTCCCT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
*
3758 TCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATC
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
3799 CTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCT
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
*
3863 TCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATC
66 TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
** *
3904 CTTCACTGTGAAGTTGAAATTGGCTCCGAAATTG
1 CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
3938 TTTGTTGACA
Statistics
Matches: 724, Mismatches: 34, Indels: 21
0.93 0.04 0.03
Matches are distributed among these distances:
101 6 0.01
102 53 0.07
103 43 0.06
104 155 0.21
105 135 0.19
106 332 0.46
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
Found at i:3920 original size:423 final size:416
Alignment explanation
Indices: 3071--3937 Score: 1398
Period size: 423 Copynumber: 2.1 Consensus size: 416
3061 GATACTTCGT
* *
3071 TGTGAAGCTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCG
* *
3136 TGAATGAACTTGCGTTGTCTTGAGCCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAAT
66 TGAATGAACTTGCGTTGTCTGGAGCCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
* * *
3201 TGGGAAGTTGTTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAG
131 TGGAAAATTGTTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
3266 TCCAGTCCTTTGTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTTTGACAACCAGCGG
196 TCCAATCCTTCGTGTGAAGTTAAAATTGGCTATGAAATTGGGAAATTGTTTTTGACAACCAGCGG
* * *
3331 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAGTCCGATATCTTCGTTTGTGAAGTTGAAAT
261 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAGTCCAATATCTTCGTCTGTGAAGTTAAAAT
3396 TGGCTCTGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
326 TGGCTCTGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * **
3461 GTTGTCTGGAGTCCGATATCCTTCGT
391 ATTGTCTGGAGTCCAATATCCTTCAC
3487 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCG
*
3552 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
66 TGAA--TGAACTTGCGTTGTCTGGAGCCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
* *
3617 ATTGGAAAATTGTT-TATTGACAATCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
129 ATTGGAAAATTGTTGT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3681 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
193 GAGTCC-A-ATCCTTCG-TGTGAAGTTAAAATTGGCTATGAAATTGGGAAATTGTTT-TTGACAA
*
3746 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCG-CTGTGA
254 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGAGTCCAATAT-CTTCGTCTGTGA
*
3810 AGTTAAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
317 AGTTAAAATTGGCTCTGAAATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
3874 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCAC
381 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCAC
*
3910 TGTGAAGTTGAAATTGGCTCCGAAATTG
1 TGTGAAGTTGAAATTGGCTCTGAAATTG
3938 TTTGTTGACA
Statistics
Matches: 416, Mismatches: 25, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
416 67 0.16
417 1 0.00
418 119 0.29
419 1 0.00
420 6 0.01
421 36 0.09
422 45 0.11
423 133 0.32
424 8 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (416 bp):
TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCG
TGAATGAACTTGCGTTGTCTGGAGCCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAAT
TGGAAAATTGTTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
TCCAATCCTTCGTGTGAAGTTAAAATTGGCTATGAAATTGGGAAATTGTTTTTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAGTCCAATATCTTCGTCTGTGAAGTTAAAAT
TGGCTCTGAAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
ATTGTCTGGAGTCCAATATCCTTCAC
Found at i:15291 original size:13 final size:13
Alignment explanation
Indices: 15271--15317 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
15261 TGAAATGAGG
*
15271 AAAATAAAGATAT
1 AAAATAAAAATAT
*
15284 AGAATAAAAATAT
1 AAAATAAAAATAT
*
15297 AAAATAAACATAT
1 AAAATAAAAATAT
*
15310 GAAATAAA
1 AAAATAAA
15318 TAAAAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (13 bp):
AAAATAAAAATAT
Found at i:15492 original size:18 final size:18
Alignment explanation
Indices: 15469--15516 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
15459 GTATTGAAAA
*
15469 AATAAATAAATAAATAGC
1 AATAAATAAATAAATAAC
* * *
15487 AATAAATATATATATAAT
1 AATAAATAAATAAATAAC
15505 AAT-AATAAATAA
1 AATAAATAAATAA
15517 TAATGAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAATAAATAAATAAC
Found at i:17016 original size:23 final size:23
Alignment explanation
Indices: 16990--17067 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
16980 CACCACAACT
16990 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
17013 CATATAATTGCACCGGAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
17036 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
17059 TATAATAAT
1 CAT-ATAAT
17068 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:17248 original size:104 final size:103
Alignment explanation
Indices: 17074--17292 Score: 384
Period size: 104 Copynumber: 2.1 Consensus size: 103
17064 TAATGTCCAT
* *
17074 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
17139 GACTTCACACATGTTCCAAAAAAATACATATATGTCCCG
66 AACTTCACACATGTTCC-AAAAAATACATATATGTCCCG
*
17178 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
17243 AACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACTTCACACATGTTCCAAAAAATACATATATGTCCCG
17281 AAGGACCACATA
1 AAGGACCACATA
17293 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 32 0.29
104 78 0.71
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
AACTTCACACATGTTCCAAAAAATACATATATGTCCCG
Found at i:18230 original size:64 final size:63
Alignment explanation
Indices: 18078--18239 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 63
18068 TTCCCTATCG
* ** * ** *
18078 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCAATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCAATGTTTGTTGATTAAAGA
* * * * *
18141 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTT-TTAGATTAAAA
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACCAAATACATTCAATGTTTGTT-GATT-AAA
18204 GA
62 GA
*
18206 GTGCATCGATGCACTACCTGTGCATCGATACACC
1 GTGCATCGATGCACTACCTGTGCATCGATGCACC
18240 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
63 6 0.08
64 67 0.85
65 6 0.08
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACCAAATACATTCAATGTTTGTTGATTAAAGA
Found at i:22670 original size:23 final size:23
Alignment explanation
Indices: 22644--22721 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
22634 CGCCACAGCT
22644 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
22667 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
** * *
22690 TGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
22713 TATAATAAT
1 CAT-ATAAT
22722 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:22899 original size:103 final size:103
Alignment explanation
Indices: 22728--22945 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
22718 TAATGTCCAT
* * *
22728 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
22793 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCA
* * *
22831 AATGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
22896 GACTTCACACATGTTCCAAAGAATACATATATATCCCA
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCA
22934 AAGGACCACATA
1 AAGGACCACATA
22946 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCA
Found at i:23884 original size:19 final size:19
Alignment explanation
Indices: 23860--23906 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
23850 ATTAAAAGAG
23860 TGCATCGATGCACTACCTA
1 TGCATCGATGCACTACCTA
23879 TGCATCGATGCACTACCTA
1 TGCATCGATGCACTACCTA
23898 TGCATCGAT
1 TGCATCGAT
23907 ACACCTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACTACCTA
Found at i:27046 original size:36 final size:38
Alignment explanation
Indices: 26976--27047 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
26966 AATATTTATA
*
26976 TATATATATTTTTTTAAAAAAATTAAATTCATAAAATT
1 TATATATATTTTTTTAAAAAAATTAAAATCATAAAATT
*
27014 TATATA-ATTTTTTT-ACAAAATTAAAAAT-ATAAAA
1 TATATATATTTTTTTAAAAAAATT-AAAATCATAAAA
27048 ATATTTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.42
37 12 0.39
38 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (38 bp):
TATATATATTTTTTTAAAAAAATTAAAATCATAAAATT
Found at i:31379 original size:21 final size:21
Alignment explanation
Indices: 31355--31415 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31345 AACTTTGAAA
31355 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
31376 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
31390 ATATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
31411 AAATG
1 AAATG
31416 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 4 0.14
19 4 0.14
20 4 0.14
21 9 0.31
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:31396 original size:35 final size:36
Alignment explanation
Indices: 31347--31465 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
31337 TGGTAACCAA
31347 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
31384 CTTTG-AATATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
31419 CTTTGAAAAATAGTTTTTCAAAG-TTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
31455 -GTTGAAAAATG
1 CTTTGAAAAATG
31466 ATAATGGGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 1 0.01
35 43 0.57
36 16 0.21
37 15 0.20
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:35019 original size:36 final size:36
Alignment explanation
Indices: 34906--35021 Score: 182
Period size: 35 Copynumber: 3.2 Consensus size: 36
34896 TGGTAACCAA
34906 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
34942 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
34977 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
35014 -GTTGAAAA
1 CTTTGAAAA
35022 TGATAATGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 35 0.47
36 17 0.23
37 23 0.31
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:36706 original size:4 final size:4
Alignment explanation
Indices: 36697--36727 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
36687 ATCATAACCC
36697 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
36728 AATCCGGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:40194 original size:23 final size:23
Alignment explanation
Indices: 40168--40225 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
40158 TGAATTTATT
*
40168 TTAATTAATAATGAGAGTTTTTG
1 TTAATTAATAATGAAAGTTTTTG
* *
40191 TTAAATACTAATGAAAGTTTTTG
1 TTAATTAATAATGAAAGTTTTTG
40214 TTAATTAGATAA
1 TTAATTA-ATAA
40226 ATTTATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.45
Consensus pattern (23 bp):
TTAATTAATAATGAAAGTTTTTG
Found at i:43736 original size:21 final size:17
Alignment explanation
Indices: 43694--43727 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43684 CGGTGTGTCC
43694 CAACAGTGCATAAATAA
1 CAACAGTGCATAAATAA
43711 CAACAGTGCATAAATAA
1 CAACAGTGCATAAATAA
43728 ATACAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
CAACAGTGCATAAATAA
Found at i:47643 original size:21 final size:21
Alignment explanation
Indices: 47617--47670 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
47607 ATGTAAATTA
47617 AACTTGTTATCGACCGGCACT
1 AACTTGTTATCGACCGGCACT
47638 AACTTGTTATCGACCGGCACT
1 AACTTGTTATCGACCGGCACT
47659 AACTTGTTATCG
1 AACTTGTTATCG
47671 GATTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (21 bp):
AACTTGTTATCGACCGGCACT
Found at i:50836 original size:16 final size:16
Alignment explanation
Indices: 50815--50859 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
50805 GAAAATATTT
50815 TATATAATATATAAAA
1 TATATAATATATAAAA
* * *
50831 TATATAAAATATTATA
1 TATATAATATATAAAA
50847 TATAT-ATATATAA
1 TATATAATATATAA
50860 TCTGGGCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAATATATAAAA
Done.