Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001503.1 Hibiscus syriacus cultivar Beakdansim tig00002947_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: 66280
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:180 original size:21 final size:21
Alignment explanation
Indices: 113--239 Score: 86
Period size: 19 Copynumber: 6.1 Consensus size: 21
103 TGGACTATCA
113 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
* * *
134 CAATGCGAACTTGGACT--ATCA
1 CAA--CGAATTTGGAATAAATCG
*
155 CAACGAGTTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
* * *
176 CAACGCGAACTTCGACT--ATCG
1 CAA--CGAATTTGGAATAAATCG
* * *
197 CAACAAACTTGGACT--ATCG
1 CAACGAATTTGGAATAAATCG
216 CAACGAATTTGGAATAAATCG
1 CAACGAATTTGGAATAAATCG
237 CAA
1 CAA
240 TGCGAACTTC
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
19 35 0.43
21 29 0.35
23 18 0.22
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
CAACGAATTTGGAATAAATCG
Found at i:207 original size:61 final size:61
Alignment explanation
Indices: 130--360 Score: 299
Period size: 61 Copynumber: 3.8 Consensus size: 61
120 TTTGGAATAA
*
130 ATCGCAATGCGAACTTGGACTATCACAACGAGTTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
193 ATCGCAACAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
254 ATCGCAACGAACTTGGACTATCGCAACACGAACTTGGACT--ATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGACTATCAC-A-ACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
315 ATCGCAACGCGAACTTGGATTATCACAACGAATTTGG-A-AAATCGCA
1 ATCGCAA--CGAACTTGGACTATCACAACGAATTTGGAATAAATCGCA
361 TTGTGATAGT
Statistics
Matches: 149, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
61 114 0.77
62 2 0.01
63 33 0.22
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (61 bp):
ATCGCAACGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:257 original size:21 final size:21
Alignment explanation
Indices: 130--344 Score: 212
Period size: 21 Copynumber: 10.4 Consensus size: 21
120 TTTGGAATAA
*
130 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* ** *
151 ATCACAA--CGAGTTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
170 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
193 ATCGCAA--CAAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
212 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
231 AAATCGCAATGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
254 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
273 ATCGCAACACGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
294 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
315 ATCGCAACGCGAACTTGGATT
1 ATCGCAACGCGAACTTGGACT
*
336 ATCACAACG
1 ATCGCAACG
345 AATTTGGAAA
Statistics
Matches: 163, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
19 53 0.33
21 93 0.57
23 17 0.10
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:309 original size:103 final size:102
Alignment explanation
Indices: 102--323 Score: 329
Period size: 103 Copynumber: 2.2 Consensus size: 102
92 CGTTGCGATT
* * **
102 TTGGACTATCACAACGAATTTGGAATAAATCGCAATGCGAACTTGGACTATCACAACGAGTTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCACAACGAACTTGG
*
167 AATAAATCGCAACGCGAACTTCGACTATCGCAACAAAC
66 AAT-AATCGCAACACGAACTTCGACTATCGCAACAAAC
*
205 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCACAACGAACTTGG
* * *
270 ACT-ATCGCAACACGAACTTGGACTATCGCAACGCGAAC
66 AATAATCGCAACACGAACTTCGACTATCGCAA--CAAAC
308 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
324 CGAACTTGGA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
101 26 0.24
103 82 0.76
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (102 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCACAACGAACTTGG
AATAATCGCAACACGAACTTCGACTATCGCAACAAAC
Found at i:328 original size:42 final size:40
Alignment explanation
Indices: 102--344 Score: 215
Period size: 42 Copynumber: 5.9 Consensus size: 40
92 CGTTGCGATT
* * * *
102 TTGGACTATCACAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAAC
* ** *
144 TTGGACTATCACAACGAGTTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAAC
* * *
186 TTCGACTATCGCAACAAACTTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAAC
* *
224 TTGGAATAAATCGCAATGCGAACTTCGACTATCGCAA--CGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGACTATCGCAACGCGAAC
266 TTGGACTATCGCAACACGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGC-A-ACGAACTTGGACTATCGCAACGCGAAC
* *
308 TTGGACTATCGCAACGCGAACTTGGATTATCACAACG
1 TTGGACTATCGCAA--CGAACTTGGACTATCGCAACG
345 AATTTGGAAA
Statistics
Matches: 173, Mismatches: 18, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.05
40 38 0.22
41 2 0.01
42 124 0.72
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAAC
Found at i:389 original size:21 final size:21
Alignment explanation
Indices: 356--408 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
346 ATTTGGAAAA
* *
356 TCGCATTGTGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
377 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
398 TCTCGTTGCGA
1 TCGCGTTGCGA
409 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:673 original size:26 final size:26
Alignment explanation
Indices: 637--696 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
627 ATATGATCTG
* *
637 TAAAAGTGACTGAAACTGACTAGAGT
1 TAAAACTGACTGAAACCGACTAGAGT
*
663 TAAAACTGACTGAAACCGACTCGAGT
1 TAAAACTGACTGAAACCGACTAGAGT
689 TAAAACTG
1 TAAAACTG
697 TTTTTAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.22
Consensus pattern (26 bp):
TAAAACTGACTGAAACCGACTAGAGT
Found at i:963 original size:16 final size:16
Alignment explanation
Indices: 916--978 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
906 TGGTATTACC
*
916 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
* * *
932 GACCT-ATATGAACCT
1 GACCTGTTTTTAACCT
947 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
963 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
979 TACTTGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.30
16 28 0.70
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:1307 original size:22 final size:24
Alignment explanation
Indices: 1269--1321 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1259 CAATGATTAA
1269 ATGTAAATTAATATAGTTTAA-TT
1 ATGTAAATTAATATAGTTTAATTT
1292 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
1315 ATGTAAA
1 ATGTAAA
1322 AAAATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:3833 original size:24 final size:25
Alignment explanation
Indices: 3806--3858 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
3796 GTTCGAGTGT
* *
3806 GGTTCGGGTTCGAGTTTGGGTTTG-
1 GGTTCGGGTTCAAGTTTGGGGTTGA
*
3830 GGTTTGGGTTCAAGTTTGGGGTTGA
1 GGTTCGGGTTCAAGTTTGGGGTTGA
3855 GGTT
1 GGTT
3859 AAGGTTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.08, C:0.06, G:0.45, T:0.42
Consensus pattern (25 bp):
GGTTCGGGTTCAAGTTTGGGGTTGA
Found at i:3846 original size:12 final size:12
Alignment explanation
Indices: 3811--3849 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3801 AGTGTGGTTC
3811 GGGTTCGAGTTT
1 GGGTTCGAGTTT
* *
3823 GGGTTTGGGTTT
1 GGGTTCGAGTTT
*
3835 GGGTTCAAGTTT
1 GGGTTCGAGTTT
3847 GGG
1 GGG
3850 GTTGAGGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.05, G:0.46, T:0.41
Consensus pattern (12 bp):
GGGTTCGAGTTT
Found at i:4322 original size:20 final size:19
Alignment explanation
Indices: 4277--4324 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
4267 AATGAACTTC
4277 TAGAGAGAATGGAGAGAATT
1 TAGAGAGAATGGAGAG-ATT
*
4297 TTGAGAGAATCGGAGAG-TT
1 TAGAGAGAAT-GGAGAGATT
4316 TGAGAGAGA
1 T-AGAGAGA
4325 GAGCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.21
Consensus pattern (19 bp):
TAGAGAGAATGGAGAGATT
Found at i:4584 original size:29 final size:28
Alignment explanation
Indices: 4552--4625 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 28
4542 TCCCTATATA
*
4552 ATTAATTTAATAA-ACTATTTATAATTAAT
1 ATTAATATAATAATA-TA-TTATAATTAAT
*
4581 ATTAATATACATTATATATTATAATTAAT
1 ATTAATATA-ATAATATATTATAATTAAT
4610 ATTAATATAATTAATA
1 ATTAATATAA-TAATA
4626 ATAATATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 1 0.03
29 32 0.82
30 5 0.13
31 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATATAATAATATATTATAATTAAT
Found at i:4597 original size:15 final size:15
Alignment explanation
Indices: 4571--4632 Score: 83
Period size: 15 Copynumber: 4.2 Consensus size: 15
4561 ATAAACTATT
4571 TATAATTAATATTAA
1 TATAATTAATATTAA
*
4586 TATACATT-ATA-TAT
1 TATA-ATTAATATTAA
4600 TATAATTAATATTAA
1 TATAATTAATATTAA
*
4615 TATAATTAATAATAA
1 TATAATTAATATTAA
4630 TAT
1 TAT
4633 TGACTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.07
14 9 0.22
15 26 0.63
16 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATTAATATTAA
Found at i:4601 original size:23 final size:24
Alignment explanation
Indices: 4546--4632 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 24
4536 ATTTCATCCC
*
4546 TATATAATTAAT-TTAATAAACTAT
1 TATATAATTAATATTAATATAC-AT
4570 T-TATAATTAATATTAATATACAT
1 TATATAATTAATATTAATATACAT
4593 TATAT-ATT-ATAATTAATAT---T
1 TATATAATTAAT-ATTAATATACAT
* *
4613 AATATAATTAATAATAATAT
1 TATATAATTAATATTAATAT
4633 TGACTTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
20 5 0.09
21 10 0.18
22 4 0.07
23 24 0.44
24 12 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATAATTAATATTAATATACAT
Found at i:4721 original size:25 final size:25
Alignment explanation
Indices: 4675--4722 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
4665 TGTAATTAAT
* **
4675 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAAGATAAACTATAAA
*
4700 ATTAATATCAAAGATAAACTATA
1 ATTAATATAAAAGATAAACTATA
4723 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (25 bp):
ATTAATATAAAAGATAAACTATAAA
Found at i:4730 original size:32 final size:31
Alignment explanation
Indices: 4668--4738 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
4658 TATAATTTGT
* *
4668 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATAAAGATAAAATATAGTCTATAA
* * *
4699 AATTAATATCAAAGATAAACTATATTTTAT-A
1 AATTAATAT-AAAGATAAAATATAGTCTATAA
4730 AATT-ATATA
1 AATTAATATA
4739 GTATAGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.03
30 4 0.12
31 14 0.41
32 15 0.44
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (31 bp):
AATTAATATAAAGATAAAATATAGTCTATAA
Found at i:4914 original size:36 final size:35
Alignment explanation
Indices: 4869--4943 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
4859 TAATGTAAAC
* *
4869 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAATTTATAAACTATATACT-CATTAATACAAAT
* * *
4905 TATAATTTATAAACTATATACTTATTAATATAAGT
1 TATAATTTATAAACTATATACTCATTAATACAAAT
4940 TATA
1 TATA
4944 GTTAAGATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 14 0.41
36 20 0.59
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (35 bp):
TATAATTTATAAACTATATACTCATTAATACAAAT
Found at i:4998 original size:20 final size:21
Alignment explanation
Indices: 4957--4998 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
4947 AAGATAATTA
4957 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
4979 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
4999 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:5015 original size:21 final size:21
Alignment explanation
Indices: 4986--5033 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4976 AGTACATTAA
* * *
4986 TATAAACTATAGTTTATAAAT
1 TATATACTATAGGTTATAAAC
5007 TATATACTATAGGTTATAAAC
1 TATATACTATAGGTTATAAAC
5028 TATATA
1 TATATA
5034 GTACAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (21 bp):
TATATACTATAGGTTATAAAC
Found at i:5131 original size:20 final size:20
Alignment explanation
Indices: 5076--5137 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5066 TAGGTTACAT
*
5076 ATATAGTTTATATACATATA
1 ATATAGGTTATATACATATA
* *
5096 ATAGATTGTATATATACATATA
1 ATATA-GGT-TATATACATATA
*
5118 CTATAGGTTATATACATATA
1 ATATAGGTTATATACATATA
5138 GTTTATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 16 0.47
21 3 0.09
22 15 0.44
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATAGGTTATATACATATA
Found at i:5137 original size:15 final size:14
Alignment explanation
Indices: 5113--5146 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5103 GTATATATAC
5113 ATATACTATAGGTT
1 ATATACTATAGGTT
*
5127 ATATACATATAGTTT
1 ATATAC-TATAGGTT
5142 ATATA
1 ATATA
5147 TACTATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (14 bp):
ATATACTATAGGTT
Found at i:5160 original size:20 final size:19
Alignment explanation
Indices: 5078--5162 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
5068 GGTTACATAT
*
5078 ATAGTTTATATACA-TATA
1 ATAGTTTATATATACTATA
5096 ATAGATTGTATATATACATATA
1 ATAG-TT-TATATATAC-TATA
*
5118 CTATAG-GT-TATATAC-AT-
1 --ATAGTTTATATATACTATA
5135 ATAGTTTATATATACTATA
1 ATAGTTTATATATACTATA
5154 CATAGTTTA
1 -ATAGTTTA
5163 GACATACATG
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
15 4 0.08
16 1 0.02
17 7 0.13
18 8 0.15
19 2 0.04
20 22 0.42
21 1 0.02
22 4 0.08
24 4 0.08
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (19 bp):
ATAGTTTATATATACTATA
Found at i:5206 original size:57 final size:57
Alignment explanation
Indices: 5062--5217 Score: 169
Period size: 57 Copynumber: 2.7 Consensus size: 57
5052 TTGTTTATAA
* *
5062 ACTATAGGTTACATATATAGTTTA-TATACATATA-ATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATTATACATATACATAGATTGTAGACATACATAT
* *
5117 ACTATAGGTTATATACATATAGTTTATATATAC-TATACATAG-TT-TAGACATACATGT
1 ACTATAGGTTACAT--ATATAGTTTAT-TATACATATACATAGATTGTAGACATACATAT
*
5174 ACTATAAGTTACATATATAGTTTACATGTATACATATACTATAG
1 ACTATAGGTTACATATATAGTTT--AT-TATACATATAC-ATAG
5218 GTTACTTATA
Statistics
Matches: 85, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
55 22 0.26
57 39 0.46
58 11 0.13
59 13 0.15
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (57 bp):
ACTATAGGTTACATATATAGTTTATTATACATATACATAGATTGTAGACATACATAT
Found at i:5372 original size:14 final size:14
Alignment explanation
Indices: 5334--5384 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
5324 ACATATATCA
*
5334 TTTAGGGTTTAGGG
1 TTTAGGGTTTAAGG
* **
5348 TATAGTATTTAAGG
1 TTTAGGGTTTAAGG
*
5362 TTTAGGGTTTAATG
1 TTTAGGGTTTAAGG
5376 -TTAGGGTTT
1 TTTAGGGTTT
5385 CTATAAACTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:5442 original size:23 final size:24
Alignment explanation
Indices: 5409--5453 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5399 TAATTTACTT
5409 TATATAATTTATATATA-TATATA
1 TATATAATTTATATATACTATATA
*
5432 TATATAGTTTATATATACTATA
1 TATATAATTTATATATACTATA
5454 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATAATTTATATATACTATATA
Found at i:5458 original size:20 final size:20
Alignment explanation
Indices: 5422--5469 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5412 ATAATTTATA
*
5422 TATATATA-TATATATAGTT
1 TATATATACTATACATAGTT
5441 TATATATACTATACATAGTT
1 TATATATACTATACATAGTT
*
5461 TATACATAC
1 TATATATAC
5470 ATGTACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATATACTATACATAGTT
Found at i:5495 original size:35 final size:36
Alignment explanation
Indices: 5455--5528 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
5445 TATACTATAC
*
5455 ATAGTTTATA-CATACATGTACTATAAGTTACATAT
1 ATAGTTTATAGCATACATATACTATAAGTTACATAT
* *
5490 ATAGTTTATATGTATACATATACTATAGGTTACATAT
1 ATAGTTTATA-GCATACATATACTATAAGTTACATAT
5527 AT
1 AT
5529 TAACTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (36 bp):
ATAGTTTATAGCATACATATACTATAAGTTACATAT
Found at i:5699 original size:2 final size:2
Alignment explanation
Indices: 5694--5754 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
5684 TTATATAGTT
* *
5694 TA TA TA TA TG TA TA TG T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5735 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
5755 CATAGTTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5762 original size:301 final size:299
Alignment explanation
Indices: 5126--5931 Score: 1191
Period size: 301 Copynumber: 2.7 Consensus size: 299
5116 TACTATAGGT
* *
5126 TATATACATATAGTTTATATATACTATACATAGTTTAGACATACATGTACTATAAGTTACATATA
1 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
* *
5191 TAGTTTACATGTATACATATACTATAGGTTACTTATATTAACTATTGTTTATAGACTATAGGTTA
66 TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTGTTTATAGACTATAGGTTA
* *
5256 ATGTTACTATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATGAATTGTGAC
131 ATGTTACTATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAATTGTGTC
* ** * * * * *
5321 TATACATATATCATTTAGGGTTTAGGGTATAGTATTTAAGGTTTAGGGTTTAATGTTAGGGTTTC
196 TATACATATATCATTGAGGGTTTAGGGTATAGTATTTAAACTATAGGATGTAATGTTA-GCTTTA
*
5386 TATAAACTATAAGTAATTTACTTTATATAATTTATATATA
260 TATAAACTATAAGTAATTTACTTTATATAATATATATATA
5426 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
1 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
*
5491 TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTATTTATAGACTATAGGTTA
66 TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTGTTTATAGACTATAGGTTA
*
5556 ATGTTACATATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATTAATTGTGT
131 ATGTTAC-TATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAATTGTGT
* * * *
5621 CTATATATATATCGTTGAGGGTTTAGGGT-TGAGGGTTTCTATAAACTATA-TATGTAAT-TTA-
195 CTATACATATATCATTGAGGGTTTAGGGTAT-A--GTAT-T-TAAACTATAGGATGTAATGTTAG
***
5682 CTTTATATAGTTTAT-A-TATATGTATA-TGTTATATATATATATATATA
255 CTTTATATAAACTATAAGTA-AT-T-TACT-TTATATA-ATATATATATA
*
5729 TATATATATATA-TATATATATA-TATACATAGTTTATACATACATGTACTATAAGTTACATATA
1 TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
5792 TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTGTTTATAGACTATAGGTTA
66 TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTGTTTATAGACTATAGGTTA
* *
5857 ATGTTAC-ATATAATTTATATGAACTATTGTTTATATAAACTATATATGAATTATCAACTGTGTC
131 ATGTTACTATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAATTGTGTC
5921 TATACATATAT
196 TATACATATAT
5932 AGTTTATAAA
Statistics
Matches: 466, Mismatches: 29, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
299 66 0.14
300 136 0.29
301 206 0.44
302 18 0.04
303 28 0.06
304 6 0.01
305 6 0.01
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (299 bp):
TATATATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACATATA
TAGTTTATATGTATACATATACTATAGGTTACATATATTAACTATTGTTTATAGACTATAGGTTA
ATGTTACTATATAATTTATATAAACTATTGTTTATATAAACTATATATGAATTATCAATTGTGTC
TATACATATATCATTGAGGGTTTAGGGTATAGTATTTAAACTATAGGATGTAATGTTAGCTTTAT
ATAAACTATAAGTAATTTACTTTATATAATATATATATA
Found at i:6072 original size:2 final size:2
Alignment explanation
Indices: 6065--6139 Score: 70
Period size: 2 Copynumber: 39.0 Consensus size: 2
6055 TTCTATAAAC
* *
6065 TA TA TA TA TA TA TA T- TA TT TA TA GA T- TA CT- TA TA T- TA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
*
6104 TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6140 ATGTTAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
1 5 0.08
2 54 0.89
3 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6224 original size:15 final size:15
Alignment explanation
Indices: 6200--6234 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
6190 CATATAACAT
*
6200 ACACATAACACACAC
1 ACACACAACACACAC
6215 ACACACAACACACAC
1 ACACACAACACACAC
6230 ACACA
1 ACACA
6235 TAGTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.43, G:0.00, T:0.03
Consensus pattern (15 bp):
ACACACAACACACAC
Found at i:6233 original size:13 final size:13
Alignment explanation
Indices: 6209--6234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6199 TACACATAAC
6209 ACACACACACACA
1 ACACACACACACA
6222 ACACACACACACA
1 ACACACACACACA
6235 TAGTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (13 bp):
ACACACACACACA
Found at i:6308 original size:13 final size:13
Alignment explanation
Indices: 6234--6319 Score: 64
Period size: 13 Copynumber: 6.1 Consensus size: 13
6224 ACACACACAC
6234 ATAGTTTATATAT
1 ATAGTTTATATAT
* * *
6247 ATGGTTCATATAAAC
1 ATAGTT--TATATAT
* *
6262 ATAATTTATATGT
1 ATAGTTTATATAT
6275 ATAGCTTATATTAATTAT
1 ATAG-TT-TA-T-A-TAT
6293 ATAGTTTATATAT
1 ATAGTTTATATAT
6306 ATAGTTTATATAT
1 ATAGTTTATATAT
6319 A
1 A
6320 AACTTATATT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
13 29 0.52
14 3 0.05
15 12 0.21
16 3 0.05
17 3 0.05
18 6 0.11
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:6345 original size:19 final size:20
Alignment explanation
Indices: 6303--6356 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
6293 ATAGTTTATA
*
6303 TATATAGTTTATATATAAACT
1 TATATAATTTA-ATATAAACT
*
6324 TATATTATTTAATATAAA-T
1 TATATAATTTAATATAAACT
6343 TATATAATTTAATA
1 TATATAATTTAATA
6357 CTTTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 7 0.23
21 9 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATAATTTAATATAAACT
Found at i:6349 original size:9 final size:9
Alignment explanation
Indices: 6323--6374 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
6313 ATATATAAAC
*
6323 TTATATTAT
1 TTATATAAT
*
6332 TTAATATAAA
1 TT-ATATAAT
6342 TTATATAAT
1 TTATATAAT
*
6351 TTA-ATACT
1 TTATATAAT
6359 TTATATAAT
1 TTATATAAT
6368 TTATATA
1 TTATATA
6375 TTGTTTACAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.19
9 22 0.61
10 7 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATATAAT
Found at i:6523 original size:21 final size:21
Alignment explanation
Indices: 6494--6546 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
6484 ACATAAATCT
* *
6494 TATATATTATATA-TTTATATA
1 TATAAATTACATAGTTTAT-TA
6515 TATAAATTACATAGTTTATTA
1 TATAAATTACATAGTTTATTA
*
6536 -ATAAACTACAT
1 TATAAATTACAT
6547 GTAAATTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAAATTACATAGTTTATTA
Found at i:6571 original size:2 final size:2
Alignment explanation
Indices: 6564--6611 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
6554 ACATATAAAC
* * * *
6564 TA TA TA TA T- TA TA TA TT TG TC TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6605 TA TA TA T
1 TA TA TA T
6612 TCAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (2 bp):
TA
Found at i:7598 original size:14 final size:14
Alignment explanation
Indices: 7581--7610 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7571 TAATTTATAA
7581 TTTTTATCATAATT
1 TTTTTATCATAATT
*
7595 TTTTTATTATAATT
1 TTTTTATCATAATT
7609 TT
1 TT
7611 AAATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTATCATAATT
Found at i:10174 original size:30 final size:32
Alignment explanation
Indices: 10140--10206 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 32
10130 TCTGGTCATG
* *
10140 TGTACATAAATGATTATGTGACACAT-G-ACA
1 TGTACATAAATGATGATATGACACATGGTACA
*
10170 TGTACATAAATGATGATATGACTCATGGTACA
1 TGTACATAAATGATGATATGACACATGGTACA
10202 TGTAC
1 TGTAC
10207 GTAAGTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 23 0.72
31 1 0.03
32 8 0.25
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTACATAAATGATGATATGACACATGGTACA
Found at i:15533 original size:3 final size:3
Alignment explanation
Indices: 15489--15514 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15479 ACCTCAACTA
15489 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
15515 TTCCACTTTA
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:15550 original size:18 final size:17
Alignment explanation
Indices: 15527--15570 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
15517 CCACTTTAAC
* *
15527 TCTTCTTTTTTTCTTCTT
1 TCTTCTTTGTATCTT-TT
15545 TCTTCTTCTGTATCTTTT
1 TCTTCTT-TGTATCTTTT
15563 TCTTCTTT
1 TCTTCTTT
15571 CATTCTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (17 bp):
TCTTCTTTGTATCTTTT
Found at i:16651 original size:3 final size:3
Alignment explanation
Indices: 16645--16746 Score: 204
Period size: 3 Copynumber: 34.0 Consensus size: 3
16635 TATGGAGGAG
16645 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
16693 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
16741 GAA GAA
1 GAA GAA
16747 ACACATGAGT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19303 original size:22 final size:19
Alignment explanation
Indices: 19264--19312 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
19254 GTCAATTATC
*
19264 TCATTTTTTAATACTAAAT
1 TCATTTTTTAATAATAAAT
*
19283 GTTATTTTTTAATAGTATAAAT
1 -TCATTTTTTAATA--ATAAAT
19305 TCATTTTT
1 TCATTTTT
19313 AAAATTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 7 0.29
22 5 0.21
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (19 bp):
TCATTTTTTAATAATAAAT
Found at i:26137 original size:3 final size:3
Alignment explanation
Indices: 26129--26182 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
26119 AAATTTAGTA
* *
26129 AAT AAT AAT GAT AAT AAT AAT -AT ATT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
26174 AAT AAT AAT
1 AAT AAT AAT
26183 CTATATTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:26291 original size:22 final size:22
Alignment explanation
Indices: 26263--26331 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
26253 AATTTTGCGG
26263 CTAGCACAGTTTGAAACCGTAA
1 CTAGCACAGTTTGAAACCGTAA
26285 CTAGCACAGTTTGAAACCGTAA
1 CTAGCACAGTTTGAAACCGTAA
26307 CTAGCACAGTTTGAAACCGTAA
1 CTAGCACAGTTTGAAACCGTAA
26329 CTA
1 CTA
26332 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (22 bp):
CTAGCACAGTTTGAAACCGTAA
Found at i:27365 original size:20 final size:20
Alignment explanation
Indices: 27341--27395 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
27331 AAATAAAAGC
27341 GAAAAGTAAAAACTTAAAAA
1 GAAAAGTAAAAACTTAAAAA
*
27361 TAAAAGTAAAAACTTAAAAA
1 GAAAAGTAAAAACTTAAAAA
*
27381 GAAAAGCAAAAACTT
1 GAAAAGTAAAAACTT
27396 TATTGAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.16
Consensus pattern (20 bp):
GAAAAGTAAAAACTTAAAAA
Found at i:27379 original size:27 final size:27
Alignment explanation
Indices: 27328--27380 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
27318 CATTTTAAAA
* *
27328 TAAAAATAAAAGCGAAAAGTAAAAACT
1 TAAAAATAAAAGCAAAAACTAAAAACT
*
27355 TAAAAATAAAAGTAAAAACTTAAAAA
1 TAAAAATAAAAGCAAAAAC-TAAAAA
27381 GAAAAGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.17
Consensus pattern (27 bp):
TAAAAATAAAAGCAAAAACTAAAAACT
Found at i:27537 original size:23 final size:24
Alignment explanation
Indices: 27511--27589 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 24
27501 AAATCCTAAG
* *
27511 AGATAATTCCTAAAAAATT-GAGA
1 AGATAATTCCTAAAAAATTACAAA
*
27534 AGATAATTTCT-AAAAATTACAAA
1 AGATAATTCCTAAAAAATTACAAA
* *
27557 AGATAATCCCTAATAAATTACAAA
1 AGATAATTCCTAAAAAATTACAAA
27581 AGATAATTC
1 AGATAATTC
27590 ATATAATTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 7 0.15
23 21 0.45
24 19 0.40
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (24 bp):
AGATAATTCCTAAAAAATTACAAA
Found at i:28526 original size:14 final size:15
Alignment explanation
Indices: 28495--28530 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28485 ACCAAACTAT
*
28495 TTTTTCTGCTCTGTA
1 TTTTTCTGCTCTGAA
28510 TTTTTCTGCTCT-AA
1 TTTTTCTGCTCTGAA
28524 TTTTTCT
1 TTTTTCT
28531 ACACTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.08, C:0.19, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTTCTGCTCTGAA
Found at i:30263 original size:10 final size:10
Alignment explanation
Indices: 30241--30271 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
30231 CTTTAGTACC
30241 TAAAAATATAA
1 TAAAAATA-AA
30252 TAAAAATAAA
1 TAAAAATAAA
30262 TAAAAATAAA
1 TAAAAATAAA
30272 AAATAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:32902 original size:32 final size:34
Alignment explanation
Indices: 32866--32935 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
32856 CCTTACAAAC
* *
32866 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
32898 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
32932 TCCC
1 TCCC
32936 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:33318 original size:20 final size:20
Alignment explanation
Indices: 33282--33342 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
33272 CTTTTAGACA
*
33282 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
* * *
33302 GGGGGGATCTGTTCCCCCTA
1 GGGGGAATCTGTACCCCCTG
33322 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
33342 G
1 G
33343 ACAATATGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.13, C:0.30, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:33952 original size:26 final size:26
Alignment explanation
Indices: 33923--33994 Score: 135
Period size: 26 Copynumber: 2.8 Consensus size: 26
33913 ATACTTTATG
33923 CAATACCAATTGTTGAAATTTGATAT
1 CAATACCAATTGTTGAAATTTGATAT
33949 CAATACCAATTGTTGAAATTTGATAT
1 CAATACCAATTGTTGAAATTTGATAT
*
33975 CAATACCAATTGTTAAAATT
1 CAATACCAATTGTTGAAATT
33995 AAGTGCATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (26 bp):
CAATACCAATTGTTGAAATTTGATAT
Found at i:36133 original size:19 final size:19
Alignment explanation
Indices: 36096--36168 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
36086 CGTTAGACAG
* *
36096 GGGGGGAATCGGTGCCCCT
1 GGGGGGAATCTGTACCCCT
* *
36115 AGGGGGGAATCTGTTCCCTT
1 -GGGGGGAATCTGTACCCCT
*
36135 TGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTA-CCCCT
36155 GGGGGGAATCTGTA
1 GGGGGGAATCTGTA
36169 TCACCTGGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (19 bp):
GGGGGGAATCTGTACCCCT
Found at i:37139 original size:24 final size:25
Alignment explanation
Indices: 37098--37145 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
37088 AAGGAAAATA
37098 AAATTAATTCTAAAGAAA-TTAAAG
1 AAATTAATTCTAAAGAAACTTAAAG
*
37122 AAATTAATT-TAGATGAAACTTAAA
1 AAATTAATTCTA-AAGAAACTTAAA
37146 CGGTAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.67
25 5 0.24
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (25 bp):
AAATTAATTCTAAAGAAACTTAAAG
Found at i:45447 original size:55 final size:55
Alignment explanation
Indices: 45366--45525 Score: 232
Period size: 55 Copynumber: 2.9 Consensus size: 55
45356 CATAGTGTCC
45366 GTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTACAT
1 GTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTACAT
* * * * *
45421 GTACGATGATTCATTAACTCAAGATGAATTCCGTGAATATGCACACA-AAGTGCTT
1 GTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACA-AGAAGTACAT
* * *
45476 GCACGGTGATTCATCAACTCATGATAAATTCCGTGAATATGCACATGAAG
1 GTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAG
45526 CATTCAAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
55 91 0.99
56 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
GTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTACAT
Found at i:45896 original size:94 final size:94
Alignment explanation
Indices: 45769--45953 Score: 246
Period size: 94 Copynumber: 2.0 Consensus size: 94
45759 TACTTCTATA
* *** * * * *
45769 CTATGGTACCGATATCCCTTTGGGTATCGATACCAAAAATAGGTTCGATGTTGCTTGGTATCGAT
1 CTATGGTACCGATACCCCTACCGGTATCAATACCAAAAATAGATTCGAAGTTGATTGGTATCGAT
*
45834 A-CCTTTACCATGGTATCGATACTACTCT
66 ACCCCTTACCATGGTATCGATACTACTCT
* *
45862 CTATGGTACCGATACCCCCTACCGGTATCAATACCAAAATTAGATTCGAAGTTGATTTGTATCGA
1 CTATGGTACCGATA-CCCCTACCGGTATCAATACCAAAAATAGATTCGAAGTTGATTGGTATCGA
*
45927 TACCCCTTATCATGGTATCGATACTAC
65 TACCCCTTACCATGGTATCGATACTAC
45954 CTCATCAATA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
93 14 0.18
94 42 0.54
95 22 0.28
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (94 bp):
CTATGGTACCGATACCCCTACCGGTATCAATACCAAAAATAGATTCGAAGTTGATTGGTATCGAT
ACCCCTTACCATGGTATCGATACTACTCT
Found at i:52204 original size:55 final size:55
Alignment explanation
Indices: 52125--52337 Score: 363
Period size: 55 Copynumber: 3.9 Consensus size: 55
52115 ACACATAGTA
*
52125 CCTGTATGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTG
1 CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTG
* *
52180 CCTCTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTG
1 CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTG
*
52235 CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACATGAAGTG
1 CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTG
* * *
52290 CATGTATGGTGATTCATCAACTCATGATGAATTCTGTGAATATGCACA
1 CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACA
52338 CAAAGTGTCT
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 150 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (55 bp):
CCTGTACGGTGATTCATCAACTCATGATGAATTCCGTGAATATGCACAAGAAGTG
Found at i:52344 original size:55 final size:55
Alignment explanation
Indices: 52086--52344 Score: 360
Period size: 55 Copynumber: 4.7 Consensus size: 55
52076 ACGAGAATTT
* *** * * * *
52086 ATCAACTCATGATGAATTTCGTG-GGCTGTACACATAGTACCTGTATGGTGATTC
1 ATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTGATTC
*
52140 ATCAACTCATGATGAATTCCGTGAATATGCACA-AGAAGTGCCTCTACGGTGATTC
1 ATCAACTCATGATGAATTCCGTGAATATGCACACA-AAGTGCCTGTACGGTGATTC
*
52195 ATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTC
1 ATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTGATTC
** * *
52250 ATCAACTCATGATGAATTCCGTGAATATGCACATGAAGTGCATGTATGGTGATTC
1 ATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTGATTC
*
52305 ATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTG
1 ATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTG
52345 TCTATAGTAC
Statistics
Matches: 185, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
54 23 0.12
55 162 0.88
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (55 bp):
ATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGGTGATTC
Found at i:52794 original size:20 final size:20
Alignment explanation
Indices: 52769--52841 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 20
52759 GATGTTGCCC
*
52769 GGTATCGATACCCTTACCAT
1 GGTATCGATACCCCTACCAT
* *
52789 GGTATCAATACTACCCTACTAT
1 GGTATCGATAC--CCCTACCAT
* *
52811 GGTACCGATACCCCCTATCA-
1 GGTATCGATA-CCCCTACCAT
52831 -GTATCGATACC
1 GGTATCGATACC
52842 AAAATTAGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
20 10 0.24
21 6 0.14
22 15 0.36
23 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCCCTACCAT
Found at i:52895 original size:95 final size:95
Alignment explanation
Indices: 52694--52895 Score: 219
Period size: 95 Copynumber: 2.1 Consensus size: 95
52684 TATTACCCTG
* * * * ** *
52694 GTATCGATACTTCTATACTATGGTACTGATACCCCCCTTTGGGTATCGATACCAAAAATAGGTTC
1 GTATCGATACTACCATACTATGGTACCGATACCCCCCTATCAGTATCGATACCAAAAATAGATTC
* *
52759 GATGTTGCCCGGTATCGATACCCTTACCAT
66 GAAGTTGCCCGGTATCGATACCCTCACCAT
* * *
52789 GGTATCAATACTACCCTACTATGGTACCGATA-CCCCCTATCAGTATCGATACCAAAATTAGATT
1 -GTATCGATACTACCATACTATGGTACCGATACCCCCCTATCAGTATCGATACCAAAAATAGATT
*** *
52853 CGAAGTTGTTTGGTATCGATACTACCTCATCAT
65 CGAAGTTGCCCGGTATCGATAC--CCTCACCAT
52886 -TATCGATACT
1 GTATCGATACT
52896 GATTGAACCA
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
95 54 0.62
96 26 0.30
97 7 0.08
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (95 bp):
GTATCGATACTACCATACTATGGTACCGATACCCCCCTATCAGTATCGATACCAAAAATAGATTC
GAAGTTGCCCGGTATCGATACCCTCACCAT
Found at i:55140 original size:32 final size:31
Alignment explanation
Indices: 55072--55193 Score: 104
Period size: 32 Copynumber: 3.9 Consensus size: 31
55062 CTAAAGTGAC
* * * *
55072 CCTTAGGTAGGCTCTTAA-GCCCCGAGATATT
1 CCTTGGGTAGGCTC-TAAGGCCCCAAGGTAAT
* **
55103 CCCTTGGGTAGGCTCTGTA-GCCCCAAGGTTCTT
1 -CCTTGGGTAGGCTCT-AAGGCCCCAAGG-TAAT
*
55136 CCTTGAGTAGGCTCTAAGGCCCCAAGGTAAT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTAAT
* *
55167 CCTTGGGTAAGCTCTAAGGCCTCAAGG
1 CCTTGGGTAGGCTCTAAGGCCCCAAGG
55194 CATTACCTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 28 0.37
32 44 0.59
33 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.26
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTAAT
Found at i:55181 original size:31 final size:32
Alignment explanation
Indices: 55104--55193 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
55094 CGAGATATTC
* **
55104 CCTTGGGTAGGCTCTGTA-GCCCCAAGGTTCTT
1 CCTTGGGTAGGCTCT-AAGGCCCCAAGGTTAAT
*
55136 CCTTGAGTAGGCTCTAAGGCCCCAAGG-TAAT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTTAAT
* *
55167 CCTTGGGTAAGCTCTAAGGCCTCAAGG
1 CCTTGGGTAGGCTCTAAGGCCCCAAGG
55194 CATTACCTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 27 0.54
32 23 0.46
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.26
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTTAAT
Found at i:57724 original size:6 final size:6
Alignment explanation
Indices: 57713--57740 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
57703 AGATCAACGG
57713 TTTCAA TTTCAA TTTCAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTC
57741 CCCCCTTCAC
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:0.29, C:0.18, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTCAA
Found at i:61797 original size:31 final size:30
Alignment explanation
Indices: 61762--61857 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
61752 TCAAACTAGT
61762 TACTTAAACTATTATATGTAATTACTTTAAG
1 TACTTAAACTATTATATGTAA-TACTTTAAG
* * * *
61793 TACTTCAATTATTTTTTGGTCAA-AC--T-AG
1 TACTTAAACTATTATAT-GT-AATACTTTAAG
61821 TTACTTAAACTATTATATGTAATCACTTTAAG
1 -TACTTAAACTATTATATGTAAT-ACTTTAAG
61853 TACTT
1 TACTT
61858 CAATTATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
27 2 0.04
28 4 0.08
29 16 0.33
31 21 0.43
32 4 0.08
33 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (30 bp):
TACTTAAACTATTATATGTAATACTTTAAG
Found at i:61819 original size:60 final size:60
Alignment explanation
Indices: 61741--61876 Score: 247
Period size: 60 Copynumber: 2.3 Consensus size: 60
61731 TAACTAAATT
*
61741 ATTA-TTTTTGGTCAAACTAGTTACTTAAACTATTATATGTAATTACTTTAAGTACTTCA
1 ATTATTTTTTGGTCAAACTAGTTACTTAAACTATTATATGTAATCACTTTAAGTACTTCA
61800 ATTATTTTTTGGTCAAACTAGTTACTTAAACTATTATATGTAATCACTTTAAGTACTTCA
1 ATTATTTTTTGGTCAAACTAGTTACTTAAACTATTATATGTAATCACTTTAAGTACTTCA
*
61860 ATTATTTTTTTGTCAAA
1 ATTATTTTTTGGTCAAA
61877 AAAAAATCTC
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 4 0.05
60 70 0.95
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (60 bp):
ATTATTTTTTGGTCAAACTAGTTACTTAAACTATTATATGTAATCACTTTAAGTACTTCA
Found at i:62839 original size:28 final size:30
Alignment explanation
Indices: 62785--62841 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
62775 AATATTTTCA
*
62785 AAAAAAAGTTTGGTTTGATTAACGGTTAAAG
1 AAAAAAAGTTTGGTTTAATT-ACGGTTAAAG
62816 AAAAAAAGTTTGG-TTAATT-CGGTTAA
1 AAAAAAAGTTTGGTTTAATTACGGTTAA
62842 TGATAATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
30 5 0.20
31 13 0.52
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (30 bp):
AAAAAAAGTTTGGTTTAATTACGGTTAAAG
Found at i:64381 original size:24 final size:23
Alignment explanation
Indices: 64354--64406 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
64344 CCACTAGGGG
*
64354 CACATAGGATTTGTCCCGAAGGAC
1 CACATA-GATTTGTCCCAAAGGAC
64378 CACAT--ATTTGTCCCAAAGGAC
1 CACATAGATTTGTCCCAAAGGAC
64399 CACATAGA
1 CACATAGA
64407 ACCCTCGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 20 0.77
23 1 0.04
24 5 0.19
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
CACATAGATTTGTCCCAAAGGAC
Found at i:64388 original size:21 final size:21
Alignment explanation
Indices: 64362--64404 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
64352 GGCACATAGG
*
64362 ATTTGTCCCGAAGGACCACAT
1 ATTTGTCCCAAAGGACCACAT
64383 ATTTGTCCCAAAGGACCACAT
1 ATTTGTCCCAAAGGACCACAT
64404 A
1 A
64405 GAACCCTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (21 bp):
ATTTGTCCCAAAGGACCACAT
Found at i:64634 original size:15 final size:15
Alignment explanation
Indices: 64614--64656 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
64604 TCTTATAACA
64614 CATATCACATAACTT
1 CATATCACATAACTT
64629 CATATCACATAACTT
1 CATATCACATAACTT
64644 CATATCACATAAC
1 CATATCACATAAC
64657 ATATAATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (15 bp):
CATATCACATAACTT
Found at i:65805 original size:23 final size:20
Alignment explanation
Indices: 65779--65829 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
65769 ACATACTATA
65779 GTATCGATAACTACCCTCTTATG
1 GTATCGATAACT-CCC-CTTA-G
65802 GTATCGAT-ACTCCCCTTAG
1 GTATCGATAACTCCCCTTAG
*
65821 GTACCGATA
1 GTATCGATA
65830 CCATTTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.31
20 4 0.15
21 3 0.12
22 3 0.12
23 8 0.31
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATAACTCCCCTTAG
Done.