Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002563.1 Hibiscus syriacus cultivar Beakdansim tig00005202_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: 52439
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9541 original size:22 final size:22
Alignment explanation
Indices: 9513--9561 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
9503 AACGGTAGAA
9513 GAATTTCACTATGAGAAAATAG
1 GAATTTCACTATGAGAAAATAG
9535 GAATTTCACTATGAGAAAATAG
1 GAATTTCACTATGAGAAAATAG
9557 GAATT
1 GAATT
9562 ACAATTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (22 bp):
GAATTTCACTATGAGAAAATAG
Found at i:11337 original size:3 final size:3
Alignment explanation
Indices: 11329--11373 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
11319 CTCGGGTTAA
*
11329 AAT AAT AAT AAT ATAT AA- ATT AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11373 A
1 A
11374 TATATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 31 0.84
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12316 original size:23 final size:20
Alignment explanation
Indices: 12275--12320 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 20
12265 AAAAAATATT
12275 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCGTTTACG
12295 TTCATTTATTGTGCTCGTTTACG
1 TTCATTTA-TGT--TCGTTTACG
12318 TTC
1 TTC
12321 GTTCATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
23 12 0.52
ACGTcount: A:0.13, C:0.17, G:0.15, T:0.54
Consensus pattern (20 bp):
TTCATTTATGTTCGTTTACG
Found at i:12377 original size:37 final size:36
Alignment explanation
Indices: 12279--12377 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
12269 AATATTTTCA
12279 TTTATGTTCGTTT-A--CGTTCATTTATTGTGCTCG
1 TTTATGTTCGTTTCATTCGTTCATTTATTGTGCTCG
* * * *
12312 TTTACGTTCG-TTCATTTGTATTCATTTATTGTGTTTG
1 TTTATGTTCGTTTCATTCG--TTCATTTATTGTGCTCG
*
12349 TTTATGTTCGTTTACATTCGTTCGTTTAT
1 TTTATGTTCGTTT-CATTCGTTCATTTAT
12378 GTCCGTTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
32 2 0.04
33 10 0.19
35 1 0.02
37 32 0.62
38 2 0.04
39 5 0.10
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (36 bp):
TTTATGTTCGTTTCATTCGTTCATTTATTGTGCTCG
Found at i:12384 original size:14 final size:14
Alignment explanation
Indices: 12365--12412 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
12355 TTCGTTTACA
*
12365 TTCGTTCGTTTATG
1 TTCGTTCATTTATG
* *
12379 TCCGTTCATTTGTG
1 TTCGTTCATTTATG
12393 TTCGTTCATTTATG
1 TTCGTTCATTTATG
12407 TTCGTT
1 TTCGTT
12413 TATCATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.08, C:0.17, G:0.19, T:0.56
Consensus pattern (14 bp):
TTCGTTCATTTATG
Found at i:12385 original size:28 final size:28
Alignment explanation
Indices: 12354--12412 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
12344 GTTTGTTTAT
* *
12354 GTTCGTTTACATTCGTTCGTTTATGTCC
1 GTTCATTTACATTCGTTCATTTATGTCC
*** *
12382 GTTCATTTGTGTTCGTTCATTTATGTTC
1 GTTCATTTACATTCGTTCATTTATGTCC
12410 GTT
1 GTT
12413 TATCATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.10, C:0.17, G:0.19, T:0.54
Consensus pattern (28 bp):
GTTCATTTACATTCGTTCATTTATGTCC
Found at i:12991 original size:14 final size:14
Alignment explanation
Indices: 12972--13014 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12962 ATCAGAAATA
12972 TAACTATATATATT
1 TAACTATATATATT
* *
12986 TAACTATTTATATA
1 TAACTATATATATT
*
13000 TAAATAATATATATT
1 TAACT-ATATATATT
13015 ATATATTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
TAACTATATATATT
Found at i:14399 original size:2 final size:2
Alignment explanation
Indices: 14394--14426 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
14384 TATTTGTGTG
*
14394 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14427 GACTGTGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16667 original size:39 final size:38
Alignment explanation
Indices: 16624--16700 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 38
16614 ATGATATTTT
16624 AATTTGTTAGATTTTATAACTTTGTATACCTTAATCCCG
1 AATTTGTTAGATTTTATAACTTTGTATACCTT-ATCCCG
*
16663 AATTTGTTTGATTTTATAACTTTGTATACCTTATCCCG
1 AATTTGTTAGATTTTATAACTTTGTATACCTTATCCCG
16701 TCCCGAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 6 0.16
39 31 0.84
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (38 bp):
AATTTGTTAGATTTTATAACTTTGTATACCTTATCCCG
Found at i:17176 original size:20 final size:21
Alignment explanation
Indices: 17138--17179 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17128 CACAATTAGA
**
17138 TTAAATGTTATTTTCTTTAAT
1 TTAAATGTTATTTAATTTAAT
17159 TTAAAT-TTATTTAATTTAAT
1 TTAAATGTTATTTAATTTAAT
17179 T
1 T
17180 ATTTAACCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTAAATGTTATTTAATTTAAT
Found at i:17838 original size:34 final size:33
Alignment explanation
Indices: 17769--17840 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
17759 TATAAGTATA
17769 ATAAA-TAAAATATTAATTTTTTTTAAAAATAT
1 ATAAATTAAAATATTAATTTTTTTTAAAAATAT
* *
17801 ATAAATTATAAAT-TTAATTTTCTTTTAATAATGT
1 ATAAATTA-AAATATTAATTTT-TTTTAAAAATAT
17835 ATAAAT
1 ATAAAT
17841 CAATGTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 5 0.14
33 10 0.29
34 20 0.57
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
ATAAATTAAAATATTAATTTTTTTTAAAAATAT
Found at i:17992 original size:2 final size:2
Alignment explanation
Indices: 17985--18011 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17975 TTACCTACTT
17985 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
18012 TATGTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26188 original size:40 final size:41
Alignment explanation
Indices: 26052--26229 Score: 270
Period size: 41 Copynumber: 4.4 Consensus size: 41
26042 TATCCTAATT
26052 CTTAATAAC-AATAAACTAAAGATAATTTTTTTTAACTCTAC
1 CTTAATAACTAATAAACTAAAGATAA-TTTTTTTAACTCTAC
**
26093 CTTAATTCCTAATAAACTAAAGATAATTTTTTTAACTCTAC
1 CTTAATAACTAATAAACTAAAGATAATTTTTTTAACTCTAC
** *
26134 CTTAATTCCTAATAAACTAAAGATAATTTTTTTATCTCTAC
1 CTTAATAACTAATAAACTAAAGATAATTTTTTTAACTCTAC
26175 CTTAATAAC-AATAAACTAAAGATAATTTTTTTAACTCTAC
1 CTTAATAACTAATAAACTAAAGATAATTTTTTTAACTCTAC
**
26215 CTTAATTCCTAATAA
1 CTTAATAACTAATAA
26230 GATAATAAAT
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 37 0.29
41 74 0.58
42 16 0.13
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.40
Consensus pattern (41 bp):
CTTAATAACTAATAAACTAAAGATAATTTTTTTAACTCTAC
Found at i:26203 original size:81 final size:83
Alignment explanation
Indices: 26061--26229 Score: 297
Period size: 81 Copynumber: 2.1 Consensus size: 83
26051 TCTTAATAAC
**
26061 AATAAACTAAAGATAATTTTTTTTAACTCTACCTTAATTCCTAATAAACTAAAGATAATTTTTTT
1 AATAAACTAAAGATAATTTTTTTTAACTCTACCTTAATAACTAATAAACTAAAGATAATTTTTTT
26126 AACTCTACCTTAATTCCT
66 AACTCTACCTTAATTCCT
*
26144 AATAAACTAAAGATAA-TTTTTTTATCTCTACCTTAATAAC-AATAAACTAAAGATAATTTTTTT
1 AATAAACTAAAGATAATTTTTTTTAACTCTACCTTAATAACTAATAAACTAAAGATAATTTTTTT
26207 AACTCTACCTTAATTCCT
66 AACTCTACCTTAATTCCT
26225 AATAA
1 AATAA
26230 GATAATAAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
81 46 0.55
82 21 0.25
83 16 0.19
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (83 bp):
AATAAACTAAAGATAATTTTTTTTAACTCTACCTTAATAACTAATAAACTAAAGATAATTTTTTT
AACTCTACCTTAATTCCT
Found at i:34425 original size:16 final size:16
Alignment explanation
Indices: 34390--34424 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
34380 GAATCAAACC
*
34390 AAAATAAAATTGGAAT
1 AAAATAAAATTGAAAT
34406 AAAATAAAA-TGAAAT
1 AAAATAAAATTGAAAT
34421 AAAA
1 AAAA
34425 AAATTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (16 bp):
AAAATAAAATTGAAAT
Found at i:34562 original size:22 final size:22
Alignment explanation
Indices: 34475--34563 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 22
34465 AATAACAAAT
* *
34475 AAATATATATATATAAATTAATA
1 AAATATATATATGTAAACTAA-A
* * * *
34498 AAA-AGATA-ATGAAAATTAAC
1 AAATATATATATGTAAACTAAA
* *
34518 ATATATATATATGTAATCTAAA
1 AAATATATATATGTAAACTAAA
*
34540 AAATATATATAT-TAAAGTAAA
1 AAATATATATATGTAAACTAAA
34561 AAA
1 AAA
34564 GAAAATGCAT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
20 2 0.04
21 23 0.45
22 23 0.45
23 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATATATATATGTAAACTAAA
Found at i:35748 original size:38 final size:39
Alignment explanation
Indices: 35668--35760 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
35658 CGAGGGTTTG
*
35668 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
* * * *
35707 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTT-TTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
35745 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
35761 TATCTCAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 19 0.39
39 30 0.61
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.42
Consensus pattern (39 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTGT
Found at i:35795 original size:36 final size:36
Alignment explanation
Indices: 35746--35862 Score: 132
Period size: 36 Copynumber: 3.2 Consensus size: 36
35736 TTTTTTTTTG
*
35746 TGTTTCAAGAGAAACTATCTCAAGAGGAACAAAATT
1 TGTTTCAAAAGAAACTATCTCAAGAGGAACAAAATT
*
35782 TGTTTCAAAAGAAACTCTCTCAAGA-GAGACAAAACTT
1 TGTTTCAAAAGAAACTATCTCAAGAGGA-ACAAAA-TT
* * *
35819 AG-TTCTAAAAGAAACTGTCTCAAG-GGAAACGAAATT
1 TGTTTC-AAAAGAAACTATCTCAAGAGG-AACAAAATT
35855 TGTTTCAA
1 TGTTTCAA
35863 GGAAAAGATA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
35 2 0.03
36 37 0.54
37 29 0.42
38 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTATCTCAAGAGGAACAAAATT
Found at i:35959 original size:102 final size:103
Alignment explanation
Indices: 35780--35970 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 103
35770 AGGAACAAAA
*
35780 TTTGTTTCAAAAGAAACTCTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTCTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
35845 AAACGAAATTTGTTTCAAG-GAAAAGATATTCAAAGAT
66 AAACGAAATTTGTTTCAAGAGAAAAGATATTCAAAGAT
** * * * *
35882 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAGGAAAATTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTCTCTCAAGAGAGACAAAACTTAGTTCTAAAAG-AAACTGTCTCAAGA
*
35945 GAGAC-AAGATTTTGTTTCAAGAGAAA
65 GAAACGAA-A-TTTGTTTCAAGAGAAA
35971 CTATCTCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
100 7 0.09
101 22 0.29
102 44 0.57
103 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (103 bp):
TTTGTTTCAAAAGAAACTCTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AAACGAAATTTGTTTCAAGAGAAAAGATATTCAAAGAT
Found at i:35978 original size:37 final size:36
Alignment explanation
Indices: 35877--35979 Score: 136
Period size: 36 Copynumber: 2.8 Consensus size: 36
35867 AAGATATTCA
35877 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAA-GGAAACTGTCTCAAGAGAGAC
* * *
35914 AA-AATTTGTTTAAAGGAAAATTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGG-AAACTGTCTCAAGAGAGAC
*
35950 AAGATTTTGTTTCAAGAGAAACTATCTCAA
1 AAGATTTTGTTTCAAG-GAAACTGTCTCAA
35980 AACTCGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 2 0.04
36 30 0.54
37 23 0.41
38 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (36 bp):
AAGATTTTGTTTCAAGGAAACTGTCTCAAGAGAGAC
Found at i:36095 original size:37 final size:37
Alignment explanation
Indices: 36044--36116 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
36034 TCAAGGTTTA
*
36044 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
36081 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
36117 AATTTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:36130 original size:36 final size:37
Alignment explanation
Indices: 36046--36130 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
36036 AAGGTTTATG
* **
36046 TTTC-AAGAGAAACTATCTCAAGGGAGACAAAATTTTG
1 TTTCAAAG-GAAACTATCTCAAGAGAGACAAAATTTAA
*
36083 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
36119 TTTCAAAGGAAA
1 TTTCAAAGGAAA
36131 TGTTTATGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.31
37 27 0.64
38 2 0.05
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
Found at i:36158 original size:93 final size:93
Alignment explanation
Indices: 36039--36406 Score: 363
Period size: 93 Copynumber: 3.9 Consensus size: 93
36029 CGTTTTCAAG
*
36039 GTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
* * *
36104 GAGAGACAAAATTAATTTCAAAGGAAAT
66 GCGAGATAAAATTAATTTCAAGGGAAAT
* * *
36132 GTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
*
36197 GCGAGATAAAATTTATTTCAAGGGAAAT
66 GCGAGATAAAATTAATTTCAAGGGAAAT
*** * *
36225 G----T-TTTCAATG-TTTA-TGTTTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCA
1 GTTTATGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCA
* * *
36283 ATCGAGATAAAATTCATTTTAAGGGAAATATTTTCAAT
65 AGCGAGATAAAATTAATTTCAAGGG----A-----AAT
* * * ** * *
36321 GTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTCTCAA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
* * *
36386 GGGAGATGAAATTAGTTTCAA
66 GCGAGATAAAATTAATTTCAA
36407 TGAAAACAGA
Statistics
Matches: 223, Mismatches: 35, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
87 61 0.27
88 7 0.03
89 2 0.01
91 1 0.00
93 86 0.39
96 4 0.02
100 2 0.01
101 7 0.03
102 53 0.24
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (93 bp):
GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
GCGAGATAAAATTAATTTCAAGGGAAAT
Found at i:36307 original size:87 final size:87
Alignment explanation
Indices: 36063--36334 Score: 321
Period size: 87 Copynumber: 3.1 Consensus size: 87
36053 AGAAACTATC
* * *
36063 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGG
*** *
36128 AAATGTTTATGTTTCAA-GAGAAACTGTC
66 AAATG----T-TTTCAATG-TTTA-TGTT
* * * *
36156 TCAAAGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGG
36221 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * * *
36243 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTTAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGG
* *
36308 AAATATTTTCAATGTTTATATT
66 AAATGTTTTCAATGTTTATGTT
36330 TCAAG
1 TCAAG
36335 AGAAACTGTC
Statistics
Matches: 158, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
87 86 0.54
88 7 0.04
89 2 0.01
93 63 0.40
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:36850 original size:106 final size:106
Alignment explanation
Indices: 36665--36869 Score: 317
Period size: 106 Copynumber: 1.9 Consensus size: 106
36655 GCCAGCCGCC
*
36665 CCTTCGCTGTGAAGTTGAAATTGGTTCCGAAATTGGGAAATTATTTGTTAACAACCAGCTGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTAACAACCAGCTGTCCC
*
36730 TTCGTTGGGAAGTTGAACTTGTGTTGTCTCGAGTCCAATAT
66 TTCATTGGGAAGTTGAACTTGTGTTGTCTCGAGTCCAATAT
* * *
36771 CCTTCGTTGTGAAGTTGAAATTGGCTCTC-AAATTGGGAAATTGTTTGTTGACAACCAG-TCGTC
1 CCTTCGCTGTGAAGTTGAAATTGGCTC-CGAAATTGGGAAATTATTTGTTAACAACCAGCT-GTC
36834 CCTTCATTGTGG-AGTTGAACTTGTGTTGTCTCGAGT
64 CCTTCATTG-GGAAGTTGAACTTGTGTTGTCTCGAGT
36870 GGCACGATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
105 1 0.01
106 87 0.96
107 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
CCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTAACAACCAGCTGTCCC
TTCATTGGGAAGTTGAACTTGTGTTGTCTCGAGTCCAATAT
Found at i:37523 original size:32 final size:32
Alignment explanation
Indices: 37447--37560 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
37437 TTTGCATTAG
* * * * *
37447 GATGTTGAATTTTCCAAAGATGCCCCAATATTC
1 GATGTTGAA-TCTCAAAAAATGCCCCAACATTT
37480 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
* * *
37512 GTTGTTAAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
37544 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
37561 GATGTCCTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
32 56 0.81
33 13 0.19
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:41938 original size:3 final size:3
Alignment explanation
Indices: 41930--41995 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
41920 ATATGAGGTA
* * *
41930 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAA AAC AA- AGAG AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT
41975 AAAT AAT AAT AAT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AA
41996 GATGAATCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.05
3 47 0.84
4 5 0.09
5 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:41951 original size:14 final size:14
Alignment explanation
Indices: 41934--41960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41924 GAGGTAAATA
41934 ATAATAATAATAAT
1 ATAATAATAATAAT
41948 ATAATAATAATAA
1 ATAATAATAATAA
41961 AAACAAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Done.