Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001606.1 Hibiscus syriacus cultivar Beakdansim tig00003190_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: 65533
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3089 original size:114 final size:114
Alignment explanation
Indices: 2687--3271 Score: 637
Period size: 114 Copynumber: 5.1 Consensus size: 114
2677 CAATTCTTTA
* * * *
2687 TGTGATGGAAATGAGCTAAGGTTGAACAAGTTATTCTCATTATGAATTTC-TC-CCTCAT-AGGA
1 TGTGATGG-AATCAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCATCA-GA
* * * ** * *
2749 TGAGTTATTCTTATTATGAACCCTGTACTGGAAATGTTGAT-CATCTCCTTC
64 TGAGTTCTTCTCATTATGAACTCT-CCCTTGAAATGTTGATCCACCTCCTTC
** * * * * *
2800 TGTGATGGAATCAAACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCCCTCGTCGGAT
1 TGTGATGGAATCAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTCATCAGAT
* * * *
2865 GAGTTCTTCTCATTATGAACTC-CTACTAGAAATGTTGA-CCACCTCATTT
65 GAGTTCTTCTCATTATGAACTCTC-CCTTGAAATGTTGATCCACCTCCTTC
* * * *
2914 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTATTCTCTTTATGAACTTCTTCTCCTTCATCAGA
1 TGTGATGGAATC-AGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC-TCATCAGA
2979 TGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTC
64 TGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTC
* * *
3030 TGTGATTGAAT-ATCCAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCACTCATCAGAT
1 TGTGATGGAATCAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-CTCATCAGAT
* *
3094 GAGTTCTTCTCATTATGAACTCTCCCCTGAAATGTTGATCCACCTACTTC
65 GAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTC
** * * * * *
3144 CATGATGTAATCGAGCTAAGGTTGAAAAAGTTCTTCTCATTATGAACTTATTATCCTTCATC-GA
1 TGTGATGGAATC-AGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC-TCATCAG-
* * * *
3208 AAGAGTTCTTTTCATTATTAACTCTCCCCTGAAATGTTGATCCACCTCCTTC
63 ATGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTC
3260 TGTGATGGAATC
1 TGTGATGGAATC
3272 GTCAAGTCTT
Statistics
Matches: 399, Mismatches: 58, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
112 32 0.08
113 10 0.03
114 134 0.34
115 105 0.26
116 118 0.30
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (114 bp):
TGTGATGGAATCAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCATCAGATG
AGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTC
Found at i:3225 original size:230 final size:229
Alignment explanation
Indices: 2689--3271 Score: 709
Period size: 230 Copynumber: 2.5 Consensus size: 229
2679 ATTCTTTATG
* * * *
2689 TGATGGAAAT-GAGCTAAGGTTGAACAAGTTATTCTCATTATGAA--TTTCTCCCTCATAGGATG
1 TGATGG-AATCGAGCTAAGGTTGAAAAAGTTATTCTCATTATGAACTTTTCTCCTTCATCGAATG
* * ** * *
2751 AGTTATTCTT-ATTATGAACCCTGTACTGGAAATGTTGAT-CATCTCCTTCTGTGATGGAATCAA
65 AGTTCTT-TTCATTATGAACTCT-CCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAA
* * *
2814 ACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATT
128 ACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATT
* ***
2879 ATGAACTCCTACTAGAAATGTTGACCACCTCATTTTG
193 ATGAACTCCCACTAGAAATGTTGACCACCTCATTCCA
*
2916 TGATGGAATCGAGCTAAGGTT-AAACAAGTTATTCTCTTTATGAACTTCTTCTCCTTCATC-AGA
1 TGATGGAATCGAGCTAAGGTTGAAA-AAGTTATTCTCATTATGAACTT-TTCTCCTTCATCGA-A
* * *
2979 TGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATTGAAT-AT
63 TGAGTTCTTTTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAA
* * * * *
3043 CCAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATT
128 ACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATT
*
3108 ATGAACTCTCCCCT-GAAATGTTGATCCACCT-ACTTCCA
193 ATGAACTC-CCACTAGAAATGTTGA-CCACCTCA-TTCCA
* * * *
3146 TGATGTAATCGAGCTAAGGTTGAAAAAGTTCTTCTCATTATGAACTTATTATCCTTCATCGAAAG
1 TGATGGAATCGAGCTAAGGTTGAAAAAGTTATTCTCATTATGAACTT-TTCTCCTTCATCGAATG
* *
3211 AGTTCTTTTCATTATTAACTCTCCCCTGAAATGTTGATCCACCTCCTTCTGTGATGGAATC
65 AGTTCTTTTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATC
3272 GTCAAGTCTT
Statistics
Matches: 305, Mismatches: 37, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
226 5 0.02
227 35 0.11
229 92 0.30
230 169 0.55
231 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (229 bp):
TGATGGAATCGAGCTAAGGTTGAAAAAGTTATTCTCATTATGAACTTTTCTCCTTCATCGAATGA
GTTCTTTTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAACA
AGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATTATG
AACTCCCACTAGAAATGTTGACCACCTCATTCCA
Found at i:4228 original size:239 final size:236
Alignment explanation
Indices: 3673--4463 Score: 1022
Period size: 239 Copynumber: 3.3 Consensus size: 236
3663 CTCGAAGAAA
* * * *
3673 TTATCATCTTGCTCGAAAGGCTTATAGATGACTTGAAGGATTTAAGCATCATACTCGAAAGACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
* * *
3738 ACTGATGGCTCGAAGGACTTACTAAGTAAAAAACTTTGGAAATCGTTTTCTTACTTTTTAAAAAA
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTAC---TT-AAAAA
* * *
3803 AATTAATTTT-AAAAAATTATTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTGTTTTGAAA
127 AATCAATTTTCAAAAAA-TATTTAAATGAGAAACTTTGGAAATC-TTTTCTCATTT-TTTTGAAA
* * *
3867 ATCATGTGAAAAATCC-AGCCTAACGATCTTATGGATGGTCC-AAAGAAC
189 ATCATGTGAAAAATCCTACCCTAA-GGTCTTATGGATGGCCCGAAAG-AC
* * * * *
3915 TTATCATCTTGCTCAAAAGGCTTTTAGATGACC-GAAGGATTTAGGCATAATGTTTGAAAGGCTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
3979 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
* *
4044 AATTTTCATAAAATATTTAAATGAGAAACTTTGGAAACCATTTTCCTCATTTTTTTCGAAAATCA
131 AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATC-TTTT-CTCATTTTTTT-GAAAATCA
4109 TGTGAAAACATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
193 TGTGAAAA-ATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
* * *
4154 TTATCATCTTGCTCAAAAGTCTTATAGAT-ACCTGAAAGATTTAGGCATCATGCTCGAAATACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
* *
4218 ATTGATGGCCCAAAAGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
* *
4283 AATTTTCAGAAAAGATTTAAATGAGAAACTTTGG-AATCTTTTTCTCATTTTTTTTGAAAATCAT
131 AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATC-TTTTCTCA-TTTTTTTGAAAATCAT
* * * * * *
4347 GTGAAAATATCATGCCCGAAGGTCTTATGGATGTCCGGATA-AC
194 GTGAAAA-ATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
** * * * *
4390 TTATCATCTTGCTGGAAAGGCTTATAGATGACCCGAAGGATTCA-GCATCATTCTCAAAAGACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
*
4454 ACTCATGGCC
66 ACTGATGGCC
4464 TGAGGGACTT
Statistics
Matches: 487, Mismatches: 53, Indels: 24
0.86 0.09 0.04
Matches are distributed among these distances:
236 53 0.11
237 103 0.21
238 47 0.10
239 168 0.34
240 10 0.02
241 76 0.16
242 30 0.06
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (236 bp):
TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATCTTTTCTCATTTTTTTGAAAATCATGT
GAAAAATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
Found at i:4674 original size:54 final size:54
Alignment explanation
Indices: 4477--4976 Score: 498
Period size: 53 Copynumber: 9.4 Consensus size: 54
4467 GGGACTTACT
* * * ** * * * *
4477 CATCAAGAAACCCTTGAAAATCAAACTTAGTTTC-TTAAAAAATCATTGGAAGA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * * * *
4530 CATAAAGAAACCCTTGAAAATAAGGCTTAGCTCCTTT-AAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* *
4583 CATCAA-AAACCCCTAAAAATCAGGCTCAGCTTCTTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* *
4636 CATCAAGAAACCCCTAAAAATTAGGCTTATCTTATTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * * *
4690 CATCAACAAACCCCTAAAAATCATGCTTAGCTTCTTTCAAAAATCA-TTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * * *
4743 CATCAA-AAA-CCCTGAAAATCAAGCTTAGCTTCTTTCAAAAATCATTTGAATA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* *
4795 CATCAAGAAACCCTTAAAAATTATGCTTAGCTT-TTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* ** *
4848 CATCAAGAAACCCCTAAAAATTATGCTTAAATTCTTTCAAAAATCATTTGAAGAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAG--A
* * * * * * * *
4904 TCATCAAGAAACTTCC-GAAAA-TCGGACTCAGATTTTTTAAAAATT-ATTTGAAAA
1 -CATCAAGAAAC-CCCTAAAAATTAGG-CTTAGCTTCTTTCAAAATTCATTTGAAGA
4958 CATCAAGAAACCCCTAAAA
1 CATCAAGAAACCCCTAAAA
4977 TCAAACTTAG
Statistics
Matches: 382, Mismatches: 52, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
51 33 0.09
52 42 0.11
53 144 0.38
54 122 0.32
56 10 0.03
57 29 0.08
58 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (54 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
Found at i:5783 original size:15 final size:17
Alignment explanation
Indices: 5761--5809 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
5751 CCATGCATGC
5761 AGGGGTATCGGTACCC-
1 AGGGGTATCGGTACCCA
* *
5777 A-GGGTATTGATACCCA
1 AGGGGTATCGGTACCCA
5793 TAGGGGTATCGGTACCC
1 -AGGGGTATCGGTACCC
5810 TTTTTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.46
16 1 0.04
17 1 0.04
18 12 0.46
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (17 bp):
AGGGGTATCGGTACCCA
Found at i:5948 original size:22 final size:23
Alignment explanation
Indices: 5887--5948 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
5877 TCGGAACCTA
5887 GGGTATCGATACCCATTCATAGG
1 GGGTATCGATACCCATTCATAGG
* *
5910 GGGTATTGATACTCATTCATA-G
1 GGGTATCGATACCCATTCATAGG
5932 GGGTATC-AGTACCCATT
1 GGGTATCGA-TACCCATT
5949 TGCATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 19 0.56
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (23 bp):
GGGTATCGATACCCATTCATAGG
Found at i:7379 original size:28 final size:28
Alignment explanation
Indices: 7312--7385 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
7302 TTAGGCTGAC
*
7312 TTGGGAAAGTAGA-GTGTTTCAGATTAAT
1 TTGGGGAAGTA-ATGTGTTTCAGATTAAT
*
7340 TTGGGGAAGTAATGTGTTTCAGGTTAAT
1 TTGGGGAAGTAATGTGTTTCAGATTAAT
* * *
7368 TTTGGGAGGTAATATGTT
1 TTGGGGAAGTAATGTGTT
7386 ACATGTTGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.39
Consensus pattern (28 bp):
TTGGGGAAGTAATGTGTTTCAGATTAAT
Found at i:8190 original size:25 final size:24
Alignment explanation
Indices: 8157--8245 Score: 85
Period size: 24 Copynumber: 3.7 Consensus size: 24
8147 TGATTTTTTT
8157 TTTTTTTTTTCTCTTTTTCTTAT-
1 TTTTTTTTTTCTCTTTTTCTTATA
* * *
8180 TTATTTATTTTCTCTATTT-TTATG
1 TT-TTTTTTTTCTCTTTTTCTTATA
*
8204 TTTTTTTTCTTCT-TTTTACTATATA
1 TTTTTTTT-TTCTCTTTTTCT-TATA
8229 TTCTTTTTTTTCTCTTT
1 TT-TTTTTTTTCTCTTT
8246 ATGTTGTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
23 14 0.26
24 21 0.40
25 9 0.17
26 9 0.17
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTTCTCTTTTTCTTATA
Found at i:9581 original size:20 final size:20
Alignment explanation
Indices: 9556--9609 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
9546 TATAGATGCT
9556 AATGCAAAGATGCACATGTA
1 AATGCAAAGATGCACATGTA
9576 AATGCAAAGATGCACATGTA
1 AATGCAAAGATGCACATGTA
*
9596 AATGCAAATATGCA
1 AATGCAAAGATGCA
9610 AAAAATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
AATGCAAAGATGCACATGTA
Found at i:10868 original size:17 final size:17
Alignment explanation
Indices: 10846--10878 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10836 ACACCGTTTC
10846 ATTTTAATGTGTGATCG
1 ATTTTAATGTGTGATCG
10863 ATTTTAATGTGTGATC
1 ATTTTAATGTGTGATC
10879 TAGACACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (17 bp):
ATTTTAATGTGTGATCG
Found at i:19674 original size:74 final size:74
Alignment explanation
Indices: 19589--19810 Score: 435
Period size: 74 Copynumber: 3.0 Consensus size: 74
19579 GTGTGTATGC
*
19589 ATGTATGTATGTTATTTACTGAATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
1 ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
19654 TTTGAGTTG
66 TTTGAGTTG
19663 ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
1 ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
19728 TTTGAGTTG
66 TTTGAGTTG
19737 ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
1 ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
19802 TTTGAGTTG
66 TTTGAGTTG
19811 TGACTTTATC
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 147 1.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (74 bp):
ATGTATGTATGTTATTTACTGTATATTTTAAGAAAATGAGAGTAGATCATTAATTGATGGTAATA
TTTGAGTTG
Found at i:21270 original size:10 final size:10
Alignment explanation
Indices: 21255--21300 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
21245 TCATTTTTTA
21255 AAAAATAAAT
1 AAAAATAAAT
21265 AAAAATACAAT
1 AAAAATA-AAT
*
21276 AAAAATGAATT
1 AAAAAT-AAAT
*
21287 AAAAATGAAT
1 AAAAATAAAT
21297 AAAA
1 AAAA
21301 TTCATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 13 0.42
11 17 0.55
12 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:21280 original size:21 final size:21
Alignment explanation
Indices: 21255--21300 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21245 TCATTTTTTA
21255 AAAAAT-AAATAAAAATACAAT
1 AAAAATGAAATAAAAAT-CAAT
* *
21276 AAAAATGAATTAAAAATGAAT
1 AAAAATGAAATAAAAATCAAT
21297 AAAA
1 AAAA
21301 TTCATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAATGAAATAAAAATCAAT
Found at i:21878 original size:19 final size:19
Alignment explanation
Indices: 21851--21898 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
21841 AACTTTATAT
21851 TTTATTTTTATTG-AATTTTA
1 TTTA-TTTT-TTGCAATTTTA
*
21871 TTTATTTTTTGCACTTTTA
1 TTTATTTTTTGCAATTTTA
21890 TTTATTTTT
1 TTTATTTTT
21899 AAAAAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTATTTTTTGCAATTTTA
Found at i:26297 original size:20 final size:19
Alignment explanation
Indices: 26233--26306 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
26223 ATATAGAGTA
*
26233 GTATCGATACCGATTCAAGTG
1 GTATCGATACC-A-TGAAGTG
* * *
26254 GTATCGATACCAAGAGGGG
1 GTATCGATACCATGAAGTG
26273 AGTATCGATACCATGAAGATG
1 -GTATCGATACCATGAAG-TG
26294 GTATCGATACCAT
1 GTATCGATACCAT
26307 TTGATCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (19 bp):
GTATCGATACCATGAAGTG
Found at i:27255 original size:81 final size:81
Alignment explanation
Indices: 27084--28273 Score: 1605
Period size: 81 Copynumber: 14.8 Consensus size: 81
27074 ACTATTCTAA
* * ** * * *
27084 AGTAAAAGATAAATAGCCTAGCTGTGCATTTGACAGAAATATATCAATTATG-C-TTTAGAGGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27147 CGATTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
*
27163 AGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27228 CGGTTAAAGATCGTTG
66 CGGTTAAAGACCGTTG
* * * * * *
27244 AGTAAAAGATAAATGGCTTAGTTGTGCATTTGACAGAAAGGTATCAATTATG-TATGTTAAATGA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCA-GTTAGATGA
* ** *
27308 ATGGTTAAAGAATGATG
65 ACGGTTAAAGACCGTTG
* *
27325 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAATGTATCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27390 CGGTTAAAGACAGTTG
66 CGGTTAAAGACCGTTG
* * * *
27406 CGTAAAAGATAAATGGCCTAGCTGTGTATTTGGTAGAAAGAG-GTCAATTATGCCAATTAGATGA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAG-GTGTCAATTATGCCAGTTAGATGA
*
27470 ACGGTTAAAGACCGCTG
65 ACGGTTAAAGACCGTTG
*
27487 AGTAAACGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27552 CGGTTAATGACCGTTG
66 CGGTTAAAGACCGTTG
* * *
27568 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAATTAGATAAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
27633 CGGTTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
* * * **
27649 AGTGAAAGATAAATGGCTTAGTTGTGCATTTGGCAGAAATATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27714 CGATTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
* * * *
27730 AGTAAAAGATAAATTGCCTAGCTATGCATTTTGCAGAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
27795 CGGTTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
* * *
27811 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTTGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
27876 CAGTTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
* *
27892 AGT---A-A-ACAT--CCTAG-TAGTGCATTTGGCAGAAAGGTGTTAATTATGCCAGTTAGATGA
1 AGTAAAAGATAAATGGCCTAGCT-GTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGA
*
27949 ACGGTTCAAGACCGTTG
65 ACGGTTAAAGACCGTTG
* * ** *
27966 AGTAAAAGATAAATGGCCTACCTGTGCATCTGGCAGAAATATGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
**
28031 CGGTTAAAGATTGTTG
66 CGGTTAAAGACCGTTG
* * * * *
28047 AGTAAAAGATAAATGGCCTAGTTTTGCATTTGGCAGAAAAGTGTCAATTACGGCAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
28112 CGGTTAAAGAACGTTG
66 CGGTTAAAGACCGTTG
* * *
28128 AGTAAAAGATAAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
28193 CGGTTAAAGACCGTTG
66 CGGTTAAAGACCGTTG
* * * * * *
28209 AGTAAAAGATAAATGACTTAACTGTGCATTTGACAGATAA-GTGTCAATCATGCAAGTTAGATGA
1 AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGA-AAGGTGTCAATTATGCCAGTTAGATGA
28273 A
65 A
28274 AAGTTAAATG
Statistics
Matches: 979, Mismatches: 116, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
73 1 0.00
74 60 0.06
76 3 0.00
77 2 0.00
78 2 0.00
79 49 0.05
80 3 0.00
81 854 0.87
82 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
AGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
CGGTTAAAGACCGTTG
Found at i:28442 original size:47 final size:49
Alignment explanation
Indices: 28333--28449 Score: 150
Period size: 49 Copynumber: 2.4 Consensus size: 49
28323 ATATAAACGG
* *
28333 TACATAAGTGGTATGAAAGGATGTCATATAGATATAAAATGTATAACAA
1 TACATAAGTGGTATGAAAGGACGTCATAAAGATATAAAATGTATAACAA
* * *
28382 TGCATAATTGGTATGAATGGACGTCATAAAG-TA-AAAATGTA-AACAA
1 TACATAAGTGGTATGAAAGGACGTCATAAAGATATAAAATGTATAACAA
*
28428 TACATAAAGGGGTATGAAAGGA
1 TACAT-AAGTGGTATGAAAGGA
28450 TGCTCAAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
46 9 0.16
47 21 0.36
48 2 0.03
49 26 0.45
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (49 bp):
TACATAAGTGGTATGAAAGGACGTCATAAAGATATAAAATGTATAACAA
Found at i:33156 original size:33 final size:32
Alignment explanation
Indices: 33111--33187 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
33101 TTAAACTTTG
*
33111 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTATTTAAGTA
*
33143 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTATTTAAGTA
33176 TTTCAATTATCG
1 TTTCAATTATCG
33188 TAAACTTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTATTTAAGTA
Found at i:35414 original size:19 final size:18
Alignment explanation
Indices: 35390--35461 Score: 117
Period size: 19 Copynumber: 3.8 Consensus size: 18
35380 ATAAGACCTA
35390 GTGCATCGGTACACTTCGG
1 GTGCATCGGTACACTT-GG
35409 GTGCATCGGTACACTTGG
1 GTGCATCGGTACACTTGG
35427 AGTGCATCGGTACACTTGGG
1 -GTGCATCGGTACACTT-GG
35447 GTGCATCGGTACACT
1 GTGCATCGGTACACT
35462 AATTACATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
18 2 0.04
19 47 0.92
20 2 0.04
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (18 bp):
GTGCATCGGTACACTTGG
Found at i:35440 original size:38 final size:38
Alignment explanation
Indices: 35389--35461 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
35379 TATAAGACCT
35389 AGTGCATCGGTACACTTCGGGTGCATCGGTACACTTGG
1 AGTGCATCGGTACACTTCGGGTGCATCGGTACACTTGG
*
35427 AGTGCATCGGTACACTTGGGGTGCATCGGTACACT
1 AGTGCATCGGTACACTTCGGGTGCATCGGTACACT
35462 AATTACATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (38 bp):
AGTGCATCGGTACACTTCGGGTGCATCGGTACACTTGG
Found at i:35536 original size:65 final size:64
Alignment explanation
Indices: 35447--35603 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 64
35437 TACACTTGGG
* * *
35447 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-
35510 AT
63 AT
* * *
35512 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGTATCGATGCATGGCT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGAT
35576 GTGCATCGGTATACA-AAAATGCATTCGA
1 GTGCATCGG--TACATAAAATGCATTCGA
35604 ATTAGGGTGT
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
64 11 0.13
65 65 0.79
66 6 0.07
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGAT
Found at i:37749 original size:13 final size:13
Alignment explanation
Indices: 37731--37765 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
37721 AATGGGCAAT
*
37731 TTTGAAAATTATG
1 TTTGAAAATAATG
*
37744 TTTGAAAACAATG
1 TTTGAAAATAATG
37757 TTTGAAAAT
1 TTTGAAAAT
37766 CAATATGGAG
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:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:38255 original size:20 final size:20
Alignment explanation
Indices: 38230--38280 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
38220 CCGATGAGTG
38230 TATCGATGCACTGCATAATC
1 TATCGATGCACTGCATAATC
38250 TATCGATGCACTGCATAATC
1 TATCGATGCACTGCATAATC
38270 TATCGATGCAC
1 TATCGATGCAC
38281 ATTCAAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCGATGCACTGCATAATC
Found at i:38320 original size:44 final size:44
Alignment explanation
Indices: 38270--38367 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
38260 CTGCATAATC
* *
38270 TATCGATGCACATTCAAGGAA-TGCATCGGTGCACCT-TCATAGTG
1 TATCGATGCACATTCAA-AAATTGCATCGGTACA-CTGTCATAGTG
* * *
38314 TATCGATACATATTCAAAAATTGCATGGGTACACTGTCATAGTG
1 TATCGATGCACATTCAAAAATTGCATCGGTACACTGTCATAGTG
38358 TATCGATGCA
1 TATCGATGCA
38368 TTGCACATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.09
44 42 0.91
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
TATCGATGCACATTCAAAAATTGCATCGGTACACTGTCATAGTG
Found at i:42425 original size:116 final size:116
Alignment explanation
Indices: 42243--42532 Score: 490
Period size: 116 Copynumber: 2.5 Consensus size: 116
42233 TTTTCCATAC
* *
42243 TTTCAAATTTCATTTTTGAAAGCTCTAAATACTTCTTCAATATTTCATTTGATTTTCAAAATCCA
1 TTTCAGATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTTCATTTGATTTTCAAAATCCA
* *
42308 TTTTAGTTTCTAGAAGAAGTTTGTTTAATTTGAAATTTTCCTTTTCAAAGT
66 TTTTAGTTTCTAGAAGAAGTTTGTTTAATTTGAAAATTTACTTTTCAAAGT
*
42359 TTTCAGATTTCATTTTTGAAAGTTCTAAATCCTTCTTCAATATTTCATTTGATTTTCAAAATCCA
1 TTTCAGATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTTCATTTGATTTTCAAAATCCA
* *
42424 TTTTATTTTCTAGAAGAAGTTTGTTTAATTTGAAAATTTATTTTTCAAAGT
66 TTTTAGTTTCTAGAAGAAGTTTGTTTAATTTGAAAATTTACTTTTCAAAGT
* *
42475 TTTCAGATTTCATTTTTGAAAGCTCTAACTCCTTTTTCAATATTTCATTTTGATTTTC
1 TTTCAGATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTTCA-TTTGATTTTC
42533 CAAGTCTGTT
Statistics
Matches: 163, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
116 153 0.94
117 10 0.06
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (116 bp):
TTTCAGATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTTCATTTGATTTTCAAAATCCA
TTTTAGTTTCTAGAAGAAGTTTGTTTAATTTGAAAATTTACTTTTCAAAGT
Found at i:43969 original size:65 final size:64
Alignment explanation
Indices: 43875--44028 Score: 188
Period size: 65 Copynumber: 2.4 Consensus size: 64
43865 TACACTTGGG
* * *
43875 GTGCATCGGTACACT-AATTACATTCGATGTTT-AA-AAAGAGCCAGGAGTGCATCGATGCATGG
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAAA-A-CCAGGAGTGCATCAATGCATGG
*
43937 TTT
63 -AT
* *
43940 GTGCATCGGTACATAAAATGCATTTGATGTTTCAATAAAATCAGGAGTGCATCAATGCATGGAT
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCAATGCATGGAT
*
44004 GTGCATCAGTACATAAAATGCATTC
1 GTGCATCGGTACATAAAATGCATTC
44029 AAATTAGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
64 25 0.32
65 47 0.60
66 3 0.04
67 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCAATGCATGGAT
Found at i:48768 original size:6 final size:6
Alignment explanation
Indices: 48757--48783 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
48747 AGATACAGAG
48757 GAGGAT GAGGAT GAGGAT GAGGAT GAG
1 GAGGAT GAGGAT GAGGAT GAGGAT GAG
48784 AAATTCGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGGAT
Found at i:53861 original size:15 final size:15
Alignment explanation
Indices: 53813--53864 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 15
53803 CACATTCTAG
**
53813 TAATTTTAAAAAATA
1 TAATTTTAAATTATA
*
53828 T-ATTTAAAATTA-A
1 TAATTTTAAATTATA
53841 -AATTTTAAATTATA
1 TAATTTTAAATTATA
53855 TAATTTTAAA
1 TAATTTTAAA
53865 AAGAACACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 11 0.37
14 9 0.30
15 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTTTAAATTATA
Found at i:53887 original size:76 final size:77
Alignment explanation
Indices: 53795--53949 Score: 269
Period size: 76 Copynumber: 2.0 Consensus size: 77
53785 TGATTAATTG
*
53795 ACACGTGCCACATTCTAGTAATTTTAAAAAATAT-ATTTAAAA-TTAAAATTTTAAATTATATAA
1 ACACGTGCCACATTCTAGTAATTTTAAAAAA-ATCATTTAAAATTTAAAAATTTAAATTATATAA
53858 TTTTAAAAAGAAC
65 TTTTAAAAAGAAC
*
53871 ACACGTGTCACATTCTAGTAATTTTAAAAAAATCATTTAAAATTTAAAAATTTAAATTATATAAT
1 ACACGTGCCACATTCTAGTAATTTTAAAAAAATCATTTAAAATTTAAAAATTTAAATTATATAAT
53936 TTTAAAAAGAAC
66 TTTAAAAAGAAC
53948 AC
1 AC
53950 GCACAAAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
75 2 0.03
76 38 0.51
77 35 0.47
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (77 bp):
ACACGTGCCACATTCTAGTAATTTTAAAAAAATCATTTAAAATTTAAAAATTTAAATTATATAAT
TTTAAAAAGAAC
Found at i:56187 original size:15 final size:15
Alignment explanation
Indices: 56167--56218 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
56157 GACCCCTAAA
56167 AATAAAAATAAAATT
1 AATAAAAATAAAATT
*
56182 AATAAAAATATAATAT
1 AATAAAAATAAAAT-T
* *
56198 AATATAATATAAAAAT
1 AATA-AAAATAAAATT
56214 AATAA
1 AATAA
56219 TAAGCTTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 14 0.45
16 10 0.32
17 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAAATAAAATT
Found at i:56189 original size:21 final size:22
Alignment explanation
Indices: 56163--56221 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
56153 CTTGGACCCC
*
56163 TAAAAATAAAAATAAAATTA-A
1 TAAAAATAAAAATAAAATAATA
* *
56184 TAAAAATATAATATAATATAATA
1 TAAAAATA-AAAATAAAATAATA
*
56207 TAAAAATAATAATAA
1 TAAAAATAAAAATAA
56222 GCTTACTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.26
22 14 0.45
23 9 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAATAAAAATAAAATAATA
Found at i:56452 original size:36 final size:35
Alignment explanation
Indices: 56325--56502 Score: 159
Period size: 38 Copynumber: 4.9 Consensus size: 35
56315 TCCAAGAATA
* *
56325 TTTAAAAAC-TATA-TATACATTTTCAAAAGTATGTT
1 TTTAAAATCATATATTATACGTTTTCAAAA--ATGTT
* *
56360 TTCAAAA-CTATATTATATATATGTTTTTCAAAAATGTT
1 TTTAAAATC-ATA-TAT-TATACG-TTTTCAAAAATGTT
* *
56398 CTT-AAACCATATATTATACGTTTTCAAAAATGTTT
1 TTTAAAATCATATATTATACGTTTTCAAAAATG-TT
*
56433 TTTAAAATCATATATTATACGTTTTCAAAACTATTTT
1 TTTAAAATCATATATTATACGTTTTCAAAA--ATGTT
56470 TTTAAAAAGT-ATATATTATACGTTTTCAAAAAT
1 TTT-AAAA-TCATATATTATACGTTTTCAAAAAT
56503 AAGTTTCCAA
Statistics
Matches: 121, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
34 13 0.11
35 15 0.12
36 32 0.26
37 13 0.11
38 34 0.28
39 5 0.04
40 9 0.07
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (35 bp):
TTTAAAATCATATATTATACGTTTTCAAAAATGTT
Found at i:56484 original size:38 final size:36
Alignment explanation
Indices: 56325--56527 Score: 148
Period size: 38 Copynumber: 5.5 Consensus size: 36
56315 TCCAAGAATA
* * *
56325 TTTAAAAA-CTATA-TATACATTTTCAAAAGTATGTT
1 TTTAAAAATATATATTATACGTTTTCAAAA-TATTTT
* * * *
56360 TTCAAAACTATATTATATATATGTTTTTCAAAA-ATGTT
1 TTTAAAAATATA-TAT-TATACG-TTTTCAAAATATTTT
* **
56398 CTT-AAACCATATATTATACGTTTTCAAAA-ATGTTT
1 TTTAAAAATATATATTATACGTTTTCAAAATAT-TTT
56433 TTT-AAAATCATATATTATACGTTTTCAAAACTATTTT
1 TTTAAAAAT-ATATATTATACGTTTTCAAAA-TATTTT
**
56470 TTTAAAAAGTATATATTATACGTTTTCAAAAATAAGTT
1 TTTAAAAA-TATATATTATACGTTTTC-AAAATATTTT
**
56508 TCCAAAAACTATATATTATA
1 TTTAAAAA-TATATATTATA
56528 TATTTTTAAA
Statistics
Matches: 138, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
34 11 0.08
35 18 0.13
36 26 0.19
37 15 0.11
38 50 0.36
39 9 0.07
40 9 0.07
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (36 bp):
TTTAAAAATATATATTATACGTTTTCAAAATATTTT
Done.