Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002062.1 Hibiscus syriacus cultivar Beakdansim tig00004205_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: 357801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:203771 original size:3 final size:3
Alignment explanation
Indices: 203763--203827 Score: 96
Period size: 3 Copynumber: 21.3 Consensus size: 3
203753 TGACACATAA
*
203763 CTC CTC CTC CTC CTC CTC C-C TCTCC CTC CTC CTC CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC -CT-C CTC CTC CTC CTC CTC CTC CTC
203809 CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC C
203828 GAAAATCCAC
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 1 0.02
3 53 0.93
4 2 0.04
5 1 0.02
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:204326 original size:94 final size:92
Alignment explanation
Indices: 204145--204328 Score: 334
Period size: 94 Copynumber: 2.0 Consensus size: 92
204135 GTCTTGTGTT
204145 TTAACAAAGGGGAAAATCAAGTAAAAATTTTTAACGAAATGTTCCCTAACTTGCATATTTGTTCA
1 TTAACAAAGGGGAAAATCAAGTAAAAATTTTTAACGAAATGTTCCCTAACTTGCATATTTGTTCA
204210 ATTTAAATTCATCTTCATACATTCCCA
66 ATTTAAATTCATCTTCATACATTCCCA
204237 TTAACAAAGGGGAAAATCAAGTAAAAATTTTTAACTGAAAATGTTCCCTAACTTGGCATATTTGT
1 TTAACAAAGGGGAAAATCAAGTAAAAATTTTTAAC-G-AAATGTTCCCTAACTT-GCATATTTGT
204302 TCAATTT-AATTCATCTTCATACATTCC
63 TCAATTTAAATTCATCTTCATACATTCC
204329 AGCTGCCAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
92 35 0.39
93 1 0.01
94 36 0.40
95 17 0.19
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (92 bp):
TTAACAAAGGGGAAAATCAAGTAAAAATTTTTAACGAAATGTTCCCTAACTTGCATATTTGTTCA
ATTTAAATTCATCTTCATACATTCCCA
Found at i:225891 original size:31 final size:31
Alignment explanation
Indices: 225846--225908 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
225836 ATTGAGTTAA
* *
225846 ACTCGATTTAAAAATTTTGAAATAAAGCTCG
1 ACTCGACTTAAAAATTCTGAAATAAAGCTCG
* *
225877 ACTCGACTTGAAAATTCTGAAATAGAGCTCG
1 ACTCGACTTAAAAATTCTGAAATAAAGCTCG
225908 A
1 A
225909 ATTGATTCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
ACTCGACTTAAAAATTCTGAAATAAAGCTCG
Found at i:227868 original size:20 final size:20
Alignment explanation
Indices: 227843--227915 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
227833 ATGCTCATAC
*
227843 GGGTATCGATACTGCATGTA
1 GGGTATCGATACTGCAAGTA
227863 GGGTATCGATACTGCAAGTA
1 GGGTATCGATACTGCAAGTA
227883 GGGTATCGATACTGCAAGTA
1 GGGTATCGATACTGCAAGTA
*
227903 GGGTATCAATACT
1 GGGTATCGATACT
227916 ACTCACTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACTGCAAGTA
Found at i:230857 original size:34 final size:34
Alignment explanation
Indices: 230819--230889 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
230809 ATTGACCTGC
230819 TATGCAAAACATAAACATATAATCATATTTATAT
1 TATGCAAAACATAAACATATAATCATATTTATAT
230853 TATGCAAAACATAAACATATAATCATATTTATAT
1 TATGCAAAACATAAACATATAATCATATTTATAT
230887 TAT
1 TAT
230890 ATGGTATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (34 bp):
TATGCAAAACATAAACATATAATCATATTTATAT
Found at i:243384 original size:116 final size:117
Alignment explanation
Indices: 243142--243419 Score: 398
Period size: 116 Copynumber: 2.3 Consensus size: 117
243132 CAAGCCCAAC
* * *
243142 TCACTACACCACCAGCTTTTTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
1 TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
243207 AACTTATAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
66 -----A-AATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
* * *
243265 TCACTATACCATCAGCTGTCTTAATTGGATGATGATGCTCAGTAGAAGAATATGAACAAAGTTAG
1 TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
243330 -AATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCCT-CA
66 AAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCA-CCTGCA
*
243381 TCACTATACCACCAGCTGAATCTTAGCTGGATGATGATG
1 TCACTATACCACCAGCTG--TCTTAGTTGGATGATGATG
243420 ATCTTCCTTT
Statistics
Matches: 143, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
116 64 0.45
117 3 0.02
118 17 0.12
123 59 0.41
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (117 bp):
TCACTATACCACCAGCTGTCTTAGTTGGATGATGATGCTAAGTAGAAGAATATGAACAAAGTTAG
AAATTAAATAATAATAATAACTTAACTCACTGATTCACTCAACTCACCTGCA
Found at i:245091 original size:2 final size:2
Alignment explanation
Indices: 245084--245125 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
245074 CATGTCACAG
245084 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- 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
245124 AT
1 AT
245126 TCAGTTTGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245109 original size:13 final size:12
Alignment explanation
Indices: 245084--245125 Score: 70
Period size: 11 Copynumber: 3.7 Consensus size: 12
245074 CATGTCACAG
245084 ATATATATATAT
1 ATATATATATAT
245096 ATATATAT-TAT
1 ATATATATATAT
245107 ATATATATA-AT
1 ATATATATATAT
245118 ATATATAT
1 ATATATAT
245126 TCAGTTTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATATAT
Found at i:245963 original size:103 final size:103
Alignment explanation
Indices: 245803--246007 Score: 383
Period size: 103 Copynumber: 2.0 Consensus size: 103
245793 CCCTCGTCCA
* * *
245803 ATACCTGAATGACAATTGCGACAGTTAGATTAAAAACCTCGCGTTGTGTTTTGTACATGTGCTGC
1 ATACCCGAATGACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGC
245868 TTGAATGCCGCTGCTTTTGGTTCGGTATCTGTCATCCC
66 TTGAATGCCGCTGCTTTTGGTTCGGTATCTGTCATCCC
245906 ATACCCGAATGACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGC
1 ATACCCGAATGACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGC
245971 TTGAATGCCGCTGCTTTTGGTTCGGTATCTGTCATCC
66 TTGAATGCCGCTGCTTTTGGTTCGGTATCTGTCATCC
246008 AATCCAAGTG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (103 bp):
ATACCCGAATGACAATTGCGACAGTTAGATTAAAAACCTCGCCTTGTGTTTTGTACATGCGCTGC
TTGAATGCCGCTGCTTTTGGTTCGGTATCTGTCATCCC
Found at i:247024 original size:3 final size:3
Alignment explanation
Indices: 247006--247139 Score: 71
Period size: 3 Copynumber: 42.7 Consensus size: 3
246996 TCACATATAG
* *
247006 TAT TAT ATAC TAT TAT TAT TAT TAT TCAT GT-T TAAT TAT TAT CCA-
1 TAT TAT -TAT TAT TAT TAT TAT TAT T-AT -TAT T-AT TAT TAT -TAT
* * *
247051 TGT TAT GTAT TAT TAT TAT TAT TAT CACT TAT TAT T-T GT-T TAG TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT TAT TAT
* *
247097 TA- TATT TAT TAT TAT ATAT TAT AAT AAT TAGT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TA
247140 AGAACATTGA
Statistics
Matches: 104, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
2 5 0.05
3 78 0.75
4 20 0.19
5 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:247063 original size:16 final size:16
Alignment explanation
Indices: 247021--247063 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
247011 TATACTATTA
*
247021 TTATTATTATTCATGT
1 TTATTATTATCCATGT
247037 TTAATTATTATCCATG-
1 TT-ATTATTATCCATGT
247053 TTATGTATTAT
1 TTAT-TATTAT
247064 TATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 10 0.42
17 12 0.50
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (16 bp):
TTATTATTATCCATGT
Found at i:247072 original size:16 final size:16
Alignment explanation
Indices: 247053--247137 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 16
247043 ATTATCCATG
247053 TTATGTATTATTATTA
1 TTATGTATTATTATTA
*
247069 TTAT-TATCACTTATTA
1 TTATGTATTA-TTATTA
*
247085 TT-TGT-TTAGTATTA
1 TTATGTATTATTATTA
*
247099 -TATTTATTATTATATA
1 TTATGTATTATTAT-TA
*
247115 TTATAATAATTAGTTATTA
1 TTAT-GT-ATTA-TTATTA
247134 TTAT
1 TTAT
247138 TAAGAACATT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.02
14 7 0.13
15 13 0.24
16 15 0.28
17 3 0.06
18 1 0.02
19 10 0.19
20 4 0.07
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (16 bp):
TTATGTATTATTATTA
Found at i:254302 original size:2 final size:2
Alignment explanation
Indices: 254295--254320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
254285 ATCCATTCCC
254295 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
254321 CCTTTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256321 original size:15 final size:16
Alignment explanation
Indices: 256297--256330 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
256287 ATTTTAGCCA
*
256297 TATTATGTATTAAT-T
1 TATTAAGTATTAATAT
256312 TATTAAGTATTAATAT
1 TATTAAGTATTAATAT
256328 TAT
1 TAT
256331 GCATACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TATTAAGTATTAATAT
Found at i:258890 original size:28 final size:27
Alignment explanation
Indices: 258841--258895 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
258831 CGATATACTT
*
258841 AATATATTATATAAAAATAAGATAATAG
1 AATATATTATAGAAAAATAAGA-AATAG
258869 AATATATTATAGAAAAGA-AAGAAATAG
1 AATATATTATAGAAAA-ATAAGAAATAG
258896 GTACAAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 19 0.76
29 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (27 bp):
AATATATTATAGAAAAATAAGAAATAG
Found at i:266277 original size:27 final size:28
Alignment explanation
Indices: 266241--266299 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
266231 AACGCCTACT
*
266241 TATTGTATTTGTATTATATAAAT-AAT-TA
1 TATTGTATTTG-A-TATAAAAATAAATGTA
266269 TATT-TATTTGATATAAAAATAAATGTA
1 TATTGTATTTGATATAAAAATAAATGTA
266296 TATT
1 TATT
266300 ATATAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.29
26 4 0.14
27 12 0.43
28 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (28 bp):
TATTGTATTTGATATAAAAATAAATGTA
Found at i:266305 original size:21 final size:23
Alignment explanation
Indices: 266252--266305 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
266242 ATTGTATTTG
* *
266252 TATTATATAAATAATTATATTTA
1 TATTATATAAATAATTAAATGTA
266275 T-TTGATATAAA-AA-TAAATGTA
1 TATT-ATATAAATAATTAAATGTA
266296 TATTATATAA
1 TATTATATAA
266306 TATATATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 13 0.48
22 6 0.22
23 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTATATAAATAATTAAATGTA
Found at i:268979 original size:13 final size:13
Alignment explanation
Indices: 268961--268985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
268951 ATAGATTAAC
268961 AGTCTTCATATGT
1 AGTCTTCATATGT
268974 AGTCTTCATATG
1 AGTCTTCATATG
268986 CGCATCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:272696 original size:29 final size:31
Alignment explanation
Indices: 272639--272698 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
272629 CAATTTAAGG
*
272639 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
272670 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
272699 TTCCAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:272787 original size:19 final size:19
Alignment explanation
Indices: 272763--272812 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
272753 AATGTTTTTA
*
272763 TGAACAATAATTTACTATT
1 TGAACAATAAATTACTATT
*
272782 TGAACAGTAAATTACTATT
1 TGAACAATAAATTACTATT
*
272801 TGAACAGTAAAT
1 TGAACAATAAAT
272813 CACTGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (19 bp):
TGAACAATAAATTACTATT
Found at i:272825 original size:19 final size:19
Alignment explanation
Indices: 272776--272828 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
272766 ACAATAATTT
* *
272776 ACTATTTGAACAGTAAATT
1 ACTATTTAAACAGTAAATC
*
272795 ACTATTTGAACAGTAAATC
1 ACTATTTAAACAGTAAATC
*
272814 ACTGTTTAAACAGTA
1 ACTATTTAAACAGTA
272829 CCCCGAGGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (19 bp):
ACTATTTAAACAGTAAATC
Found at i:272961 original size:21 final size:21
Alignment explanation
Indices: 272935--272976 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
272925 ATTTGAATAT
*
272935 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
272956 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
272977 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:273038 original size:21 final size:21
Alignment explanation
Indices: 273005--273044 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
272995 TTTTTGCAGA
*
273005 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
273027 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
273045 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:273894 original size:30 final size:32
Alignment explanation
Indices: 273825--273902 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
273815 TAAGACTATG
273825 CTCATAATAACAAATAATGAAAAAACTTAGAT
1 CTCATAATAACAAATAATGAAAAAACTTAGAT
* * *
273857 TTC-TAATAAAAAATACTGAAAAAA-TTAGA-
1 CTCATAATAACAAATAATGAAAAAACTTAGAT
273886 CTCATAATAACAAATAA
1 CTCATAATAACAAATAA
273903 ATATTAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 2 0.05
30 16 0.41
31 19 0.49
32 2 0.05
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.26
Consensus pattern (32 bp):
CTCATAATAACAAATAATGAAAAAACTTAGAT
Found at i:277702 original size:59 final size:60
Alignment explanation
Indices: 277622--277734 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
277612 GTCCTCCGAA
*
277622 TATAGAGTATTGCTTTATTAAGTCAATCAACTATTAAAAGTTATAAAACGGTCATCCAAT
1 TATAGAGTATTGCTTTATTAAGTCAATCAACTATTAAAAGTTACAAAACGGTCATCCAAT
* * * * *
277682 TATAGAGT-TTGCTTTGTTAAGTCATTCTACTGTTAAAAGTTACAAAATGGTCA
1 TATAGAGTATTGCTTTATTAAGTCAATCAACTATTAAAAGTTACAAAACGGTCA
277735 CCCGACTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 39 0.83
60 8 0.17
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (60 bp):
TATAGAGTATTGCTTTATTAAGTCAATCAACTATTAAAAGTTACAAAACGGTCATCCAAT
Found at i:278032 original size:52 final size:52
Alignment explanation
Indices: 277954--278060 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
277944 TCGTCGGGTG
277954 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
1 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
*
278006 ATCATTTTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
1 ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
278058 ATC
1 ATC
278061 GAAAGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (52 bp):
ATCATTCTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATA
Found at i:278102 original size:60 final size:60
Alignment explanation
Indices: 278009--278122 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
277999 TTTTATAATC
* * * *
278009 ATTTTGTAACTTTTAATAGTCGATGTACTTAATAAAGTAACATTTTATAATCGAAAGACT
1 ATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAATAACATTTTATAATCGAAAGACT
* * *
278069 ATTTTATAATTTTTAATAGTCGAAGGACTTAATAAAATAATATTTTATATTCGA
1 ATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAATAACATTTTATAATCGA
278123 TGGACCATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAATAACATTTTATAATCGAAAGACT
Found at i:279004 original size:21 final size:20
Alignment explanation
Indices: 278975--279015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
278965 AACTATAAAT
*
278975 AAAATTTAAATTGATATATA
1 AAAATTTAAATAGATATATA
*
278995 AAAATATTAAATAGGTATATA
1 AAAAT-TTAAATAGATATATA
279016 TCTGCAGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
AAAATTTAAATAGATATATA
Found at i:280520 original size:23 final size:22
Alignment explanation
Indices: 280494--280536 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
280484 AGAAAAAACA
*
280494 TAAATTGTCATATAAATAAAAAT
1 TAAATT-TCAAATAAATAAAAAT
*
280517 TAAATTTTAAATAAATAAAA
1 TAAATTTCAAATAAATAAAA
280537 CACTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATTTCAAATAAATAAAAAT
Found at i:280827 original size:12 final size:12
Alignment explanation
Indices: 280810--280835 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
280800 AGAAATGTAA
280810 GTCAACACTGGG
1 GTCAACACTGGG
280822 GTCAACACTGGG
1 GTCAACACTGGG
280834 GT
1 GT
280836 TTCATGTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (12 bp):
GTCAACACTGGG
Found at i:286017 original size:22 final size:23
Alignment explanation
Indices: 285989--286048 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 23
285979 TTATTTTTGA
285989 TGGA-TTTAATTCCACCTTTCGG
1 TGGATTTTAATTCCACCTTTCGG
*
286011 TGGATTTGTTTAATGCCACCTTTCGG
1 TGGA--T-TTTAATTCCACCTTTCGG
286037 TGGATTTTAATT
1 TGGATTTTAATT
286049 TTCAACAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 6 0.19
24 1 0.03
26 21 0.66
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (23 bp):
TGGATTTTAATTCCACCTTTCGG
Found at i:286029 original size:26 final size:26
Alignment explanation
Indices: 285993--286043 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
285983 TTTTGATGGA
*
285993 TTTAATTCCACCTTTCGGTGGATTTG
1 TTTAATGCCACCTTTCGGTGGATTTG
286019 TTTAATGCCACCTTTCGGTGGATTT
1 TTTAATGCCACCTTTCGGTGGATTT
286044 TAATTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (26 bp):
TTTAATGCCACCTTTCGGTGGATTTG
Found at i:286846 original size:32 final size:32
Alignment explanation
Indices: 286801--286900 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
286791 TTCGGTGCAG
* * * *
286801 AAACTTTTTAGTGATATATTATTTTATTTTAA
1 AAACTTTTCAGTGATATATAACTTCATTTTAA
*
286833 AAACTTTTCAGTGATATATAACTTCATTTTAG
1 AAACTTTTCAGTGATATATAACTTCATTTTAA
* *
286865 AAATTTTTCAGTGATATATCACTTCATTTTAGA
1 AAACTTTTCAGTGATATATAACTTCATTTTA-A
286898 AAA
1 AAA
286901 AACATTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
32 56 0.95
33 3 0.05
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (32 bp):
AAACTTTTCAGTGATATATAACTTCATTTTAA
Found at i:286997 original size:140 final size:139
Alignment explanation
Indices: 286833--287369 Score: 591
Period size: 140 Copynumber: 3.8 Consensus size: 139
286823 TTTATTTTAA
*
286833 AAACTTTTCAGTGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAGA
1 AAACTTTTCAATGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAGA
* * * * * ** * *
286898 AAAAACATTTTTTTCTCATAGACCATTTAATGTACAATGACAACAACTTTTCGATGCTTAATTAA
66 AAAAAAATTATTTTCTCATACACCATTTAATGCACAATGACAAAAAAATTTC-ATGCTCAATTAC
*
286963 TTCACTTTAG
130 TTCACTTCAG
* * * * *
286973 AAACTTTTCAGTGATATATAACTTCATTTTAGAAATTTTTCAGTTATATATCGCTTTATTTAAG-
1 AAACTTTTCAATGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAGA
* * * *
287037 AAAAATATCATTTTCTCATACATCATTTAATGCAAAATGACAAAAAAATTTCAATGAC-CAATTA
66 AAAAAAATTATTTTCTCATACACCATTTAATGCACAATGACAAAAAAATTTC-ATG-CTCAATTA
287101 CTTCACTTCAG
129 CTTCACTTCAG
* * * * * *
287112 AAAC-TTTCTAATGATACATAACTTCATTTCAGAAACTTTTCATTGATATTTCACTTCATTTCAG
1 AAACTTTTC-AATGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAG
* * **
287176 AAAAAAAATTCTTTTCTCATACACCGTTTAATGCACAATGACAAAAAAAAAATCAGTGCTCAATT
65 AAAAAAAATTATTTTCTCATACACCATTTAATGCACAATGAC-AAAAAAATTTCA-TGCTCAATT
*
287241 ACTTCACTGCAG
128 ACTTCACTTCAG
* ** *
287253 AAACTTTTCAATGATGTATAACTTCATTTCATA-AAATTTTT-AGTGACGTATCACTTCATTCTA
1 AAACTTTTCAATGATATATAACTTCATTT--TAGAAATTTTTCAGTGATATATCACTTCATTTTA
** * * * *
287316 G-AAAAATGTCATTTTCTCATACATCATTTAATACACAATGACAAAAAACTTTCA
64 GAAAAAAAATTATTTTCTCATACACCATTTAATGCACAATGACAAAAAAATTTCA
287370 ATTAGATGAG
Statistics
Matches: 331, Mismatches: 57, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
138 4 0.01
139 117 0.35
140 132 0.40
141 66 0.20
142 11 0.03
143 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (139 bp):
AAACTTTTCAATGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAGA
AAAAAAATTATTTTCTCATACACCATTTAATGCACAATGACAAAAAAATTTCATGCTCAATTACT
TCACTTCAG
Found at i:287004 original size:32 final size:32
Alignment explanation
Indices: 286963--287023 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
286953 GCTTAATTAA
286963 TTCACTTTAGAAACTTTTCAGTGATATATAAC
1 TTCACTTTAGAAACTTTTCAGTGATATATAAC
* * *
286995 TTCATTTTAGAAATTTTTCAGTTATATAT
1 TTCACTTTAGAAACTTTTCAGTGATATAT
287024 CGCTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (32 bp):
TTCACTTTAGAAACTTTTCAGTGATATATAAC
Found at i:287039 original size:32 final size:32
Alignment explanation
Indices: 286963--287039 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
286953 GCTTAATTAA
286963 TTCACTTT-AGAAACTTTTCAGTGATATATAAC
1 TTCA-TTTAAGAAACTTTTCAGTGATATATAAC
* * * **
286995 TTCATTTTAGAAATTTTTCAGTTATATATCGC
1 TTCATTTAAGAAACTTTTCAGTGATATATAAC
*
287027 TTTATTTAAGAAA
1 TTCATTTAAGAAA
287040 AATATCATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 3 0.08
32 35 0.92
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (32 bp):
TTCATTTAAGAAACTTTTCAGTGATATATAAC
Found at i:287159 original size:32 final size:32
Alignment explanation
Indices: 287100--287178 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
287090 ATGACCAATT
*
287100 ACTTCACTTCAGAAACTTTCTAATGATACATA
1 ACTTCATTTCAGAAACTTTCTAATGATACATA
* ** *
287132 ACTTCATTTCAGAAACTTT-TCATTGATATTTC
1 ACTTCATTTCAGAAACTTTCT-AATGATACATA
287164 ACTTCATTTCAGAAA
1 ACTTCATTTCAGAAA
287179 AAAAATTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (32 bp):
ACTTCATTTCAGAAACTTTCTAATGATACATA
Found at i:287359 original size:280 final size:279
Alignment explanation
Indices: 286844--287371 Score: 704
Period size: 280 Copynumber: 1.9 Consensus size: 279
286834 AACTTTTCAG
* * * * * *
286844 TGATATATAACTTCATTTTAGAAATTTTTCAGTGATATATCACTTCATTTTAGAAAAAACATTTT
1 TGATACATAACTTCATTTCAGAAACTTTTCAGTGATATATCACTTCATTTCAGAAAAAAAATTCT
* * * **** * **
286909 TTTCTCATAGACCATTTAATGTACAATGACAACAACTTTTCGATGCTTAATTAATTCACTTTAGA
66 TTTCTCATACACCATTTAATGCACAATGACAAAAAAAAATCGATGCTCAATTAATTCACTGCAGA
* * * * *
286974 AACTTTTCAGTGATATATAACTTCATTTTAGAAATTTTTCAGTTATATATCGCTTTATTTAAGAA
131 AACTTTTCAATGATATATAACTTCATTTTAGAAATTTTTCAGTGACATATCACTTCATTTAAGAA
*
287039 AAATATCATTTTCTCATACATCATTTAATGCAAAATGACAAAAAAATTTCAATGACCAATTACTT
196 AAATATCATTTTCTCATACATCATTTAATACAAAATGACAAAAAAATTTCAATGACCAATTACTT
287104 CACTTCAGAAACTTTCTAA
261 CACTTCAGAAACTTTCTAA
* *
287123 TGATACATAACTTCATTTCAGAAACTTTTCATTGATATTTCACTTCATTTCAGAAAAAAAATTCT
1 TGATACATAACTTCATTTCAGAAACTTTTCAGTGATATATCACTTCATTTCAGAAAAAAAATTCT
* *
287188 TTTCTCATACACCGTTTAATGCACAATGACAAAAAAAAAATC-AGTGCTCAATTACTTCACTGCA
66 TTTCTCATACACCATTTAATGCACAATGAC-AAAAAAAAATCGA-TGCTCAATTAATTCACTGCA
* *
287252 GAAACTTTTCAATGATGTATAACTTCATTTCATA-AAATTTTT-AGTGACGTATCACTTCATTCT
129 GAAACTTTTCAATGATATATAACTTCATTT--TAGAAATTTTTCAGTGACATATCACTTCATT-T
* * *
287315 -AGAAAAATGTCATTTTCTCATACATCATTTAATACACAATGACAAAAAACTTTCAAT
191 AAGAAAAATATCATTTTCTCATACATCATTTAATACAAAATGACAAAAAAATTTCAAT
287372 TAGATGAGTT
Statistics
Matches: 213, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
279 85 0.40
280 117 0.55
281 9 0.04
282 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (279 bp):
TGATACATAACTTCATTTCAGAAACTTTTCAGTGATATATCACTTCATTTCAGAAAAAAAATTCT
TTTCTCATACACCATTTAATGCACAATGACAAAAAAAAATCGATGCTCAATTAATTCACTGCAGA
AACTTTTCAATGATATATAACTTCATTTTAGAAATTTTTCAGTGACATATCACTTCATTTAAGAA
AAATATCATTTTCTCATACATCATTTAATACAAAATGACAAAAAAATTTCAATGACCAATTACTT
CACTTCAGAAACTTTCTAA
Found at i:287862 original size:36 final size:35
Alignment explanation
Indices: 287821--287931 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 35
287811 GGTGTATGTA
* * * *
287821 AGGTTTATTATATTTATGTCCTTAACGTAATGTGTT
1 AGGTTTGTTATTTTTATCTCCTTAATGTAATGT-TT
* * *
287857 AGGTTTGTTATTTTTATCTTCTTAATATATTGTTT
1 AGGTTTGTTATTTTTATCTCCTTAATGTAATGTTT
287892 ATGGTTTGTTATTTTTATCTCCTTAATGTAATGGTTT
1 A-GGTTTGTTATTTTTATCTCCTTAATGTAAT-GTTT
287929 AGG
1 AGG
287932 GTTTAGGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 3 0.05
36 55 0.87
37 5 0.08
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.55
Consensus pattern (35 bp):
AGGTTTGTTATTTTTATCTCCTTAATGTAATGTTT
Found at i:292286 original size:35 final size:36
Alignment explanation
Indices: 292218--292291 Score: 114
Period size: 37 Copynumber: 2.1 Consensus size: 36
292208 AAAAGAAAAG
292218 AATATGGAAGTCCAAACACAGCAACTATATTCACTCC
1 AATATGGAAGTCCAAACACA-CAACTATATTCACTCC
* *
292255 AATATGGAAGTCCAAACTC-TAACTATATTCACTCC
1 AATATGGAAGTCCAAACACACAACTATATTCACTCC
292290 AA
1 AA
292292 AAGGTGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 17 0.49
37 18 0.51
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (36 bp):
AATATGGAAGTCCAAACACACAACTATATTCACTCC
Found at i:293871 original size:16 final size:16
Alignment explanation
Indices: 293850--293883 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
293840 TTACTATCCA
*
293850 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
293866 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
293882 CG
1 CG
293884 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:299559 original size:15 final size:15
Alignment explanation
Indices: 299494--299560 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
299484 AATTTATAAT
299494 AATTAAGTATTAAAA
1 AATTAAGTATTAAAA
* * * *
299509 TACTAAATACTAAAA
1 AATTAAGTATTAAAA
* * *
299524 AGTAAAGTCTTAAATAA
1 AATTAAGTATT-AA-AA
299541 AATTAAGTATTAAAA
1 AATTAAGTATTAAAA
299556 AATTA
1 AATTA
299561 CAAATCCATT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
15 22 0.61
16 4 0.11
17 10 0.28
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (15 bp):
AATTAAGTATTAAAA
Found at i:308899 original size:29 final size:29
Alignment explanation
Indices: 308848--308905 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
308838 GTGTTGGTCG
*
308848 TAGGTCGCCATGCCATCCGGGCGACCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
* * *
308877 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
308906 GAGAGAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.28, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCCCGGCGACCTAC
Found at i:309070 original size:29 final size:29
Alignment explanation
Indices: 309029--309105 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
309019 GAGGAGCAGG
309029 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
309058 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
309087 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
309106 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:310335 original size:82 final size:82
Alignment explanation
Indices: 310159--310335 Score: 230
Period size: 82 Copynumber: 2.2 Consensus size: 82
310149 ATAGTAACGT
* * * * *
310159 TAGTGGCTTTTCTTCGACAAACGCCACAACAGAGTAGTATTTTAGAGGCGTTTTTATACAAACGC
1 TAGTGGCTTTTTTTCGACAAACGACACAACAAAGTAGCACTTTAGAGGCGTTTTTATACAAACGC
*
310224 CGCAATAAGTCCATCTA
66 CACAATAAGTCCATCTA
* * * *
310241 TAGTGGAATTTTTTT-GACAAACGACGCAACAAAGTAGCACTTTGGCGGCGTTTTTATACAAACG
1 TAGTGG-CTTTTTTTCGACAAACGACACAACAAAGTAGCACTTTAGAGGCGTTTTTATACAAACG
* *
310305 CCACAATAGGTTCATCTA
65 CCACAATAAGTCCATCTA
310323 TAGTGGCTTTTTT
1 TAGTGGCTTTTTT
310336 CAATAAACAC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 6 0.07
82 69 0.85
83 6 0.07
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (82 bp):
TAGTGGCTTTTTTTCGACAAACGACACAACAAAGTAGCACTTTAGAGGCGTTTTTATACAAACGC
CACAATAAGTCCATCTA
Found at i:310371 original size:82 final size:81
Alignment explanation
Indices: 310166--310387 Score: 191
Period size: 82 Copynumber: 2.7 Consensus size: 81
310156 CGTTAGTGGC
* * * * * * *
310166 TTTTCTTCGACAAACGCCACAACAGAGTAGTATTTTAGAGGCGTTTTTATACAAACGCCGCAATA
1 TTTT-TTCAACAAACGAC-CAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCACAATA
310231 AGTCCATCTATAGTGGAA
64 AGTCCATCTATAGTGGAA
** * * *
310249 TTTTTTTGACAAACGACGCAACAAAGTAGCACTTTGGCGGCGTTTTTATACAAACGCCACAATAG
1 TTTTTTCAACAAACGAC-CAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCACAATAA
* *
310314 GTTCATCTATAGTGG-C
65 GTCCATCTATAGTGGAA
* * *
310330 TTTTTTCAATAAAC-A-CAACTATATGTTATAACATTTAGCGGCAGTTTTT-TACAAACGC
1 TTTTTTCAACAAACGACCAAC-A-AAG-TAGAAC-TTTAGCGGC-GTTTTTATACAAACGC
310388 TACGAAAGGA
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
78 4 0.03
79 1 0.01
80 3 0.03
81 15 0.13
82 82 0.71
83 10 0.09
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (81 bp):
TTTTTTCAACAAACGACCAACAAAGTAGAACTTTAGCGGCGTTTTTATACAAACGCCACAATAAG
TCCATCTATAGTGGAA
Found at i:314734 original size:22 final size:22
Alignment explanation
Indices: 314706--314762 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
314696 ACATAGGCTG
314706 TGTATCGATACCCAGTGAGGGA
1 TGTATCGATACCCAGTGAGGGA
314728 TGTATCGATACCCAGTGAGGGA
1 TGTATCGATACCCAGTGAGGGA
*
314750 TGTATAGATACCC
1 TGTATCGATACCC
314763 TATAGAGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (22 bp):
TGTATCGATACCCAGTGAGGGA
Found at i:316537 original size:12 final size:12
Alignment explanation
Indices: 316520--316544 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
316510 TTAAATGGAT
316520 TAATGATAATAA
1 TAATGATAATAA
316532 TAATGATAATAA
1 TAATGATAATAA
316544 T
1 T
316545 GTGAATAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATGATAATAA
Found at i:321938 original size:21 final size:21
Alignment explanation
Indices: 321914--321953 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
321904 GCGTAGAATT
321914 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
321935 TGTCCCGAATGACCACATA
1 TGTCCCGAAGGACCACATA
321954 TAACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:322804 original size:24 final size:20
Alignment explanation
Indices: 322755--322812 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
322745 TTCTCATTGA
*
322755 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
322775 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
322798 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
322813 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:326201 original size:6 final size:6
Alignment explanation
Indices: 326190--326217 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
326180 TTAACAAAGA
326190 TGCTAT TGCTAT TGCTAT TGCTAT TGCT
1 TGCTAT TGCTAT TGCTAT TGCTAT TGCT
326218 TGTTGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (6 bp):
TGCTAT
Found at i:335963 original size:2 final size:2
Alignment explanation
Indices: 335956--335984 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
335946 AATTGATAAG
335956 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 A
335985 AATCAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338333 original size:29 final size:29
Alignment explanation
Indices: 338299--338357 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
338289 CCTAAATTAA
338299 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
338328 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
338357 T
1 T
338358 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:343020 original size:29 final size:29
Alignment explanation
Indices: 342986--343044 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
342976 CCTAAATTAA
342986 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
343015 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
343044 T
1 T
343045 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:349067 original size:3 final size:3
Alignment explanation
Indices: 349059--349084 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
349049 GGTTAGCTTT
349059 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
349085 TTAAATCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:353838 original size:3 final size:3
Alignment explanation
Indices: 353830--354811 Score: 1181
Period size: 3 Copynumber: 337.7 Consensus size: 3
353820 GGAAATGGAA
353830 CTT CTT CTT CTT CTT CTT C-T CTT C-T CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
353876 CTT -TT CTT CTT CTT CTT CTT CTT -TT CTT CTT CTT -TT CTT -TT TTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
353920 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
353966 CTT -TT CTT -TT TTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
*
354012 CTT C-T CTT -TT CTT C-T CTT CTT CTT TTT CTT CTT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
354056 CTTT CTT CTT CTT CTT -TT CTTT CTT CTT CTT CTT -TCT CTT CTT CTT
1 C-TT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CT-T CTT CTT CTT
*
354102 CTT CTT CTT CTTT CTT CTT CTT TTT CTT CTT CTT CTT CTT -TCT CTTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T C-TT
354149 CTT CTT CTT CTT -TT CTT CTT C-T CTT CTT CTT CTT CTT -TT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
354194 CTT CTTT CTT -TT CTT CTT C-T CTT CTT CTT CTT CTT CTT CTTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT
* *
354239 CTTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
354285 -TT C-T CTT CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
354330 CTT CTT CTT CTT CTT CTT C-T CTT CTT CTT CTT -TT TTT CTT CTT -TCT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
* * * * * * * ** *
354376 CCT CCT CTC CTC CTCT CTC CTC CTC CTT CTTT CTT CTCT CTT CCC CTC
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT C-TT CTT CT-T CTT CTT CTT
*
354424 CTT CCTA CTT CTT CTTT CTT CTT CTT CTT CTT CTT CTT ACTT -TT -TT
1 CTT -CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT
354470 CTT CTT -TT C-T CTT CTT -TT C-T CTT CTT CTT CTT -TT -TT CTT -TT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
354511 CTT CTT CTT CTT CTT CTTT CTT -TT CTT CTT C-T CTT CTTT CTT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT C-TT CTT CTT
*
354556 CTT CTT CTT CTT C-T CTT CTT CTT CTT -TT CTT CTT CTT TTT CTT -TT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
354601 C-T ATT C-T CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT C-T CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
354645 CTTT CTT CTT CTT CTT CTT C-T CTT CTT CTT ATT CTT CTT -TT CTT
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
354689 CTT ATT CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
354736 CTT C-T CTT -TT CTT -TT CTT CTT -TCT CTT CTT CTT CTT CTTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT C-TT CTT
354779 CTT CTT CTTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT
354812 GGAGGAACGG
Statistics
Matches: 873, Mismatches: 31, Indels: 150
0.83 0.03 0.14
Matches are distributed among these distances:
2 103 0.12
3 713 0.82
4 56 0.06
5 1 0.00
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Done.