Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002500.1 Hibiscus syriacus cultivar Beakdansim tig00005095_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: 72784
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:105 original size:31 final size:31
Alignment explanation
Indices: 67--128 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
57 GATCCGTAAC
67 TTTGAACCATTCACAGACTTTTAAAATGATA
1 TTTGAACCATTCACAGACTTTTAAAATGATA
98 TTTGAACCATTCACAGACTTTTAAAATGATA
1 TTTGAACCATTCACAGACTTTTAAAATGATA
129 AGTTTACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (31 bp):
TTTGAACCATTCACAGACTTTTAAAATGATA
Found at i:3608 original size:23 final size:24
Alignment explanation
Indices: 3559--3608 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
3549 CAAAAATATT
** *
3559 AAATAAAATAAAAAAATAATGTCA
1 AAATAAAATAAAAAAATAAAATAA
*
3583 AAAT-AAATAAAGAAATAAAATAA
1 AAATAAAATAAAAAAATAAAATAA
3606 AAA
1 AAA
3609 GTGATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (24 bp):
AAATAAAATAAAAAAATAAAATAA
Found at i:4969 original size:5 final size:5
Alignment explanation
Indices: 4959--5037 Score: 63
Period size: 5 Copynumber: 15.2 Consensus size: 5
4949 CTTGGAAAGA
* * * *
4959 AAAAT AAAAT AAAAAT GAAAT -TAAT AAAAT AAAAT AAAAA AGAAAT -ACAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
5009 AATAAT AATAAT AAAGAT AAAAT AAAAT A
1 AA-AAT AA-AAT AAA-AT AAAAT AAAAT A
5038 TTTTCCAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 6 0.10
5 32 0.52
6 23 0.38
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:4987 original size:25 final size:25
Alignment explanation
Indices: 4959--5023 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 25
4949 CTTGGAAAGA
*
4959 AAAATAAAATAAAAATGAAATTA-AT
1 AAAATAAAATAAAAAAGAAA-TACAT
4984 AAAATAAAATAAAAAAGAAATACAT
1 AAAATAAAATAAAAAAGAAATACAT
5009 AATAATAATAATAAA
1 AA-AATAA-AATAAA
5024 GATAAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 2 0.06
25 23 0.64
26 5 0.14
27 6 0.17
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (25 bp):
AAAATAAAATAAAAAAGAAATACAT
Found at i:5100 original size:37 final size:40
Alignment explanation
Indices: 5027--5104 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 40
5017 TAATAAAGAT
5027 AAAATAAAATATTTTCCAAAAGCTTATATAATATATATTTTC
1 AAAATAAAATATTTT-CAAAA-CTTATATAATATATATTTTC
5069 AAAA-AAAATATTTT-AAAA-TTATAT-ATCATATATTTT
1 AAAATAAAATATTTTCAAAACTTATATAAT-ATATATTTT
5105 GTGAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
36 2 0.06
37 15 0.43
39 4 0.11
41 10 0.29
42 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.42
Consensus pattern (40 bp):
AAAATAAAATATTTTCAAAACTTATATAATATATATTTTC
Found at i:5185 original size:36 final size:34
Alignment explanation
Indices: 5130--5403 Score: 177
Period size: 36 Copynumber: 7.7 Consensus size: 34
5120 AAAACTACAT
5130 AGTTTTCAAAAATGTTTTTAAAACTATATACTATATA
1 AGTTTTC-AAAATG-TTTTAAAACTATATA-TATATA
*
5167 AGTTTTCAAAATGATTTTAAAGCTATATA-ATATA
1 AGTTTTCAAAATG-TTTTAAAACTATATATATATA
* * *
5201 TGTTTTCAAAATGTTTTAAAA--AAACTATAT-TT
1 AGTTTTCAAAATGTTTTAAAACTATA-TATATATA
* *
5233 A-TTTTCATAATGTTTTAAAA-TATACATAATATA
1 AGTTTTCAAAATGTTTTAAAACTATATAT-ATATA
* * *
5266 CA-TTTTCAAAAACGTTTTAAAAATTATATATTATATTT
1 -AGTTTTC-AAAATGTTTT-AAAACTATATA-TATA-TA
*
5304 A-TTTTCAAAATGTTTTAAAAATTATATAATATATAA
1 AGTTTTCAAAATGTTTT-AAAACTATAT-ATATAT-A
* *
5340 ACGTTTTCAAACGTATTTTCAAAACTATATATTATATA
1 A-GTTTTCAAA-ATGTTTT-AAAACTATATA-TATATA
* * *
5378 TATTTTTAAAAAATGTTTTCAAACTA
1 -AGTTTT-CAAAATGTTTTAAAACTA
5404 CAAAAAAATG
Statistics
Matches: 192, Mismatches: 26, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
31 22 0.11
32 7 0.04
33 10 0.05
34 23 0.12
35 9 0.05
36 49 0.26
37 28 0.15
38 21 0.11
39 23 0.12
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (34 bp):
AGTTTTCAAAATGTTTTAAAACTATATATATATA
Found at i:5228 original size:65 final size:67
Alignment explanation
Indices: 5131--5336 Score: 190
Period size: 71 Copynumber: 3.0 Consensus size: 67
5121 AAACTACATA
*
5131 GTTTTCAAAAATGTTTTTAAAACTATATACTATA-TAAGTTTTCAAAATGATTTTAAAGCTAT-A
1 GTTTTCAAAAATG-TTTTAAAA--ATATACTATATTAA-TTTTCAAAATG-TTTTAAA-ATATAA
*
5194 TAATATAT
60 TAATATAC
* *
5202 GTTTTC-AAAATGTTTTAAAAA-A-ACTATATTTATTTTCATAATGTTTTAAAATATACATAATA
1 GTTTTCAAAAATGTTTTAAAAATATACTATATTAATTTTCAAAATGTTTTAAAATATA-ATAATA
5264 TAC
65 TAC
* * * *
5267 ATTTTCAAAAACGTTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAA-ATTATAT
1 GTTTTCAAAAATGTTTT-AAAA--ATATACTATATTAATTTTCAAAATGTTTTAAAATA-TA-AT
5331 AATATA
61 AATATA
5337 TAAACGTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
63 3 0.03
64 7 0.06
65 29 0.25
66 12 0.10
67 5 0.04
69 9 0.08
70 8 0.07
71 43 0.37
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (67 bp):
GTTTTCAAAAATGTTTTAAAAATATACTATATTAATTTTCAAAATGTTTTAAAATATAATAATAT
AC
Found at i:5372 original size:75 final size:70
Alignment explanation
Indices: 5132--5388 Score: 190
Period size: 75 Copynumber: 3.6 Consensus size: 70
5122 AACTACATAG
* * * * *
5132 TTTTCAAAAATGTTTTTAAAACTATATACTATA-TAAGTTTTCAAAATGATTTTAAAGCTAT--A
1 TTTTC-AAAACGTTTTAAAAACTATATATTATATTTA-TTTTCAAAATG-TTTTAAA-ATATAAA
* **
5194 TAATATATG
62 TAATAAACA
* * * *
5203 TTTTCAAAATGTTTT-AAAA--A-A-ACTATATTTATTTTCATAATGTTTTAAAATATACATAAT
1 TTTTCAAAACGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAATATAAATAAT
*
5263 ATACA
66 AAACA
*
5268 TTTTCAAAAACGTTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAATTATATAA
1 TTTTC-AAAACGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTT-AAAA-TATA-AA
*
5333 TATATAAACG
62 TA-ATAAACA
* * *
5343 TTTTC-AAACGTATTTTCAAAACTATATATTATATATATTTTTAAAA
1 TTTTCAAAACG--TTTTAAAAACTATATATTATATTTATTTTCAAAA
5389 AATGTTTTCA
Statistics
Matches: 156, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
63 3 0.02
64 7 0.04
65 29 0.19
66 12 0.08
67 5 0.03
69 5 0.03
70 11 0.07
71 28 0.18
72 4 0.03
73 9 0.06
74 3 0.02
75 40 0.26
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (70 bp):
TTTTCAAAACGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAATATAAATAAT
AAACA
Found at i:9322 original size:19 final size:19
Alignment explanation
Indices: 9298--9335 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
9288 CCACTTGTTT
9298 TCTTTT-GTTAAATTGCCGG
1 TCTTTTCGTTAAA-TGCCGG
9317 TCTTTTCGGTTAAATGCCG
1 TCTTTTC-GTTAAATGCCG
9336 AGAACTCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (19 bp):
TCTTTTCGTTAAATGCCGG
Found at i:11137 original size:13 final size:13
Alignment explanation
Indices: 11119--11143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11109 AATCTTAGAA
11119 ACAACTTTGAGAG
1 ACAACTTTGAGAG
11132 ACAACTTTGAGA
1 ACAACTTTGAGA
11144 CACACTTCAC
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
ACAACTTTGAGAG
Found at i:14962 original size:36 final size:36
Alignment explanation
Indices: 14915--14986 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
14905 AGATTGCCTA
14915 CTCATATGTTATTAGGATTCTAATTGTTTACCTATG
1 CTCATATGTTATTAGGATTCTAATTGTTTACCTATG
*
14951 CTCATATGTTATTAGGATTCTAATTGTTTATCTATG
1 CTCATATGTTATTAGGATTCTAATTGTTTACCTATG
14987 TTTTTCACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (36 bp):
CTCATATGTTATTAGGATTCTAATTGTTTACCTATG
Found at i:27958 original size:32 final size:31
Alignment explanation
Indices: 27907--28013 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 31
27897 TAAGGCGACC
* *
27907 CTTGGGTAGTCTTTATGGCCCCGAGATCTTTT
1 CTTGGGTAGGC-TCATGGCCCCGAGATCTTTT
* *
27939 TTTGGGTAGGC-CATGTGGCCCCGATAT-TTTT
1 CTTGGGTAGGCTCA--TGGCCCCGAGATCTTTT
* *
27970 CTTGGGTACGCTCATGGCCTCGAGAATC-TTT
1 CTTGGGTAGGCTCATGGCCCCGAG-ATCTTTT
28001 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
28014 TCAGGCCCCA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
30 9 0.15
31 30 0.49
32 22 0.36
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.36
Consensus pattern (31 bp):
CTTGGGTAGGCTCATGGCCCCGAGATCTTTT
Found at i:30713 original size:29 final size:29
Alignment explanation
Indices: 30664--30735 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
30654 ATTTGGATAT
** *
30664 GAAATTACCAAAAGCATCACTATGGGGTA
1 GAAATTACCAAAAATAGCACTATGGGGTA
30693 GAAATTACCAAAAATAGCACTATGGGGTA
1 GAAATTACCAAAAATAGCACTATGGGGTA
*
30722 AAAATTA-CAAAAAT
1 GAAATTACCAAAAAT
30736 TCCCTTGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.21
Consensus pattern (29 bp):
GAAATTACCAAAAATAGCACTATGGGGTA
Found at i:31957 original size:31 final size:31
Alignment explanation
Indices: 31919--31989 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
31909 TAATGCAACC
** *
31919 CTTGGGTAGACTTTGCGGCCTCGAGATATTT
1 CTTGGGTAGACCCTGCGGCCCCGAGATATTT
* * *
31950 CTTGGGTAGGCCCTGTGGCCCCGAGATCTTT
1 CTTGGGTAGACCCTGCGGCCCCGAGATATTT
31981 CTTGGGTAG
1 CTTGGGTAG
31990 GCCCCGTGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.32, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGACCCTGCGGCCCCGAGATATTT
Found at i:31990 original size:31 final size:31
Alignment explanation
Indices: 31935--31999 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
31925 TAGACTTTGC
* *
31935 GGCCTCGAGATATTTCTTGGGTAGGCCCTGT
1 GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
*
31966 GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
1 GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
31997 GGC
1 GGC
32000 TTTTCTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.11, C:0.28, G:0.34, T:0.28
Consensus pattern (31 bp):
GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
Found at i:41270 original size:162 final size:164
Alignment explanation
Indices: 41003--41754 Score: 820
Period size: 182 Copynumber: 4.4 Consensus size: 164
40993 TGGCGGTTTA
* * * *
41003 TGTCGATACTTTATAA-AACTGTATTGATCCACATCAATATAACATGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACC
* * *
41067 ---GGTA-AAGCGGTACCAGATATATTGAAAGTTTCGATACTTTAATACAAGTATCGACACTTTG
65 AATAGTATAAGC-G-ACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTG
*
41128 TGAATTTAAAAGAGAAGCAGTTTTAGCG-CTCATAATG
128 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCT-ATAAAG
41165 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCA
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCA
* * *
41230 ATA-TA-GAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATTGACACTTTGTGA
66 ATAGTATAAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGA
41293 ATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 ATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
*
41327 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGATAAAAATATGACAAAACCT
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAA---
* * *
41392 GTCTCTAAAGGACAAAACCGGTATAGAGCGACC-GAATATATTTAAAGTGTTGATACTTTAATAT
63 ----C-------CAATA---GTATA-AGCGACCAG-ATATATTGAAAGTGTCGATACTTTAATAT
* * * *
41456 AAGTATCGACTCTTTGTGAAATTAAAAGAGAAGCAGTTTTAGTGCCCATAAAG
112 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * *
41509 TGTCGATACTTTATAATAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAA---
* * *
41574 GTCTCTAAAGGAAAAAACCAGTATAGAGCGACCATATATATTTAAAGTGTCGATACTTTAATATA
63 --C-C----------AA-TAGTATA-AGCGACCAGATATATTGAAAGTGTCGATACTTTAATATA
*
41639 AGTATCGACAATTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
113 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* *
41691 TGTCGATACTTTATAACAATGTATCGGTCCACAATGATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACC
41755 GGTCTTGAAA
Statistics
Matches: 510, Mismatches: 42, Indels: 62
0.83 0.07 0.10
Matches are distributed among these distances:
162 197 0.39
163 5 0.01
164 5 0.01
169 1 0.00
174 1 0.00
176 5 0.01
177 1 0.00
180 5 0.01
181 1 0.00
182 286 0.56
184 2 0.00
185 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (164 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCA
ATAGTATAAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGA
ATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:41532 original size:182 final size:182
Alignment explanation
Indices: 41223--41818 Score: 901
Period size: 182 Copynumber: 3.3 Consensus size: 182
41213 AAAATATGAC
* * *
41223 AAAACCAATATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATTGACACTT
1 AAAACCAGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
41288 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCG
66 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCG
* * *
41353 ATCCACAACGATATAACAGATAAAAATATGACAAAACCTGTCTCTAAAGGAC
131 ATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGAA
* * * *
41405 AAAACCGGTATAGAGCGACCGAATATATTTAAAGTGTTGATACTTTAATATAAGTATCGACTCTT
1 AAAACCAGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* * * *
41470 TGTGAAATTAAAAGAGAAGCAGTTTTAGTGCCCATAAAGTGTCGATACTTTATAATAATGTATCG
66 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCG
* * *
41535 ATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGGTCTCTAAAGGAA
131 ATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGAA
* *
41587 AAAACCAGTATAGAGCGACC-ATATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACAAT
1 AAAACCAGTATAGAGCGACCGA-ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
41651 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATC
65 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATC
* * *
41716 GGTCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTCT-TGAAATGAA
130 GATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCT-AAAGGAA
* * * * *
41769 AAAA-TATGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
1 AAAACCA-GTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATA
41819 AGTACGCATA
Statistics
Matches: 373, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
181 3 0.01
182 370 0.99
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (182 bp):
AAAACCAGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTATCG
ATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTAAAGGAA
Found at i:44248 original size:21 final size:21
Alignment explanation
Indices: 44224--44264 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44214 GACAATCAAG
*
44224 AGTCCAAGAGAGACTTGAGAA
1 AGTCCAAGAGACACTTGAGAA
* *
44245 AGTCGAAGATACACTTGAGA
1 AGTCCAAGAGACACTTGAGA
44265 GGCATAAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.27, T:0.17
Consensus pattern (21 bp):
AGTCCAAGAGACACTTGAGAA
Found at i:44338 original size:33 final size:33
Alignment explanation
Indices: 44301--44395 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
44291 ATAGATGGAG
* *
44301 TGGTGAAAGAAGTTAAGGTGTTGAGGGGTGAAT
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAA
44334 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAA
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAA
* *
44367 TGGTTAAAGAAGTGGAGGTGTTGAGGGGT
1 TGGTGAAAGAAGTTGAGGTGTTGAGGGGT
44396 AAACTTAAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.26
Consensus pattern (33 bp):
TGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAAA
Found at i:44604 original size:18 final size:18
Alignment explanation
Indices: 44581--44619 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
44571 AAAAAAATAT
44581 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
44599 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
44617 GAA
1 GAA
44620 ATAAAGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:46193 original size:19 final size:19
Alignment explanation
Indices: 46169--46213 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
46159 AATGTAGGGT
46169 TAATTTTGCATAAGATTTA
1 TAATTTTGCATAAGATTTA
* *
46188 TAATTTTGTATATGATTTA
1 TAATTTTGCATAAGATTTA
46207 TAATTTT
1 TAATTTT
46214 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (19 bp):
TAATTTTGCATAAGATTTA
Found at i:46833 original size:199 final size:198
Alignment explanation
Indices: 46479--48038 Score: 1876
Period size: 199 Copynumber: 7.8 Consensus size: 198
46469 GTAAGCAGAT
** *
46479 GTGTCGATACATTTATAAAAAGTATCGATCAAAAAAACATCAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
46544 GGTAATTTTGTAATATAATCGGTATAAATATACCAGTTTTATGTA-AGAATATGTCTACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATG-AGAGAATAGGTCTACATAATG
** * *
46608 TATATACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGAACGC
130 TATCGACACTTTT-AAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGC
46673 ATAAA
194 ATAAA
* * *
46678 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
46743 GGTAATTTT-TCAACGTAACCGGTA-AAACTGTATCTGTTTTATGAGAGAATATGTCTACATAAT
66 GGTAATTTTGT-AATGTAACCGGTATAAA-TATACCGGTTTTATGAGAGAATAGGTCTACATAAT
* *
46806 GTATCGACACTTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGGGTGCAC
129 GTATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTGCAC
**
46871 AAATAAA
192 GCATAAA
* * * * * *
46878 GAGTCGATACATTTTTTAAAAGTGTCAATCCCAAAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
46943 GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACCTAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * * * *
47008 ATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGTCCAAAAAATGGTGCAT
131 ATCGACACTTTTAAATT-TGTGTCGATACTTTTTGTCCAGAATGAA--TCC-CAAAATGGTGCAC
*
47073 ACATAAA
192 GCATAAA
* * * * * *
47080 GTGTCAATACATTTATAAAAATTAGCGATCACATAAACATCGAAACCCATTATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
47145 GGTAATTTT-TCAATGTAACCGGTATAAATATACTGGTTTTCTGCGAGAATAGGTCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
** * * * *
47209 TATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCC
130 TATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGC
*
47274 ATTAA
194 ATAAA
* * *
47279 GTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
47344 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAAGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * *
47409 ATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACGC
131 ATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTGCACGC
47474 ATAAA
194 ATAAA
* * * * * *
47479 GTGTCGATACATTTTTAAAAAAGTGTCGATCCGAGAGACAT-TAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* *
47543 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTAT-ATGATAATAGGTCTATATAAT
65 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACATAAT
* * * * *
47607 GTATCGACACTTTTTAATTATGTGTCGATACATTTTGTCCAGAGTAAATGCCCAAAAAATAGTGC
129 GTATCGACACTTTTAAATT-TGTGTCGATACTTTTTGTCCAGAATGAAT-CCC--AAAATGGTGC
47672 ACGCATAAA
190 ACGCATAAA
* * *
47681 GTGTCGATACATTTATAAAAAGTATCGATCTCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
47746 GGTAATTTT-TCAATGTAACCGGTATAAATATATCGGTTTTATGCGAGAATAGGCCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* * * * * *
47810 TATCGACACTTATGAAATTTGTGTCGATACTTTTTGTTCAGAAGGAATGCCAAAAGGGTGCACCC
130 TATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGC
* *
47875 GTTAA
194 ATAAA
* *
47880 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
47945 GGTCATTTTGTAATGTAACTGATATAAATATACCAGTTTTATGAGAAAATAGGTC-AGCATAAAG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
*
48009 TATCGACAATTGTTAAATTTGTGTCGATAC
130 TATCGACACTT-TTAAATTTGTGTCGATAC
48039 CATTTTAAAA
Statistics
Matches: 1164, Mismatches: 170, Indels: 54
0.84 0.12 0.04
Matches are distributed among these distances:
198 6 0.01
199 482 0.41
200 316 0.27
201 49 0.04
202 301 0.26
203 10 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGCAT
AAA
Found at i:47231 original size:402 final size:398
Alignment explanation
Indices: 46479--48038 Score: 1960
Period size: 402 Copynumber: 3.9 Consensus size: 398
46469 GTAAGCAGAT
** *
46479 GTGTCGATACATTTATAAAAAGTATCGATCAAAAAAACATCAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
46544 GGTAATTTTGTAATATAATCGGTATAAATATACC-AGTTTTATGTAAGAATATGTCTACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGA-TTTTATGTGAGAATATGTCTACATAATG
** *
46608 TATATACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTGAACG
130 TATCGACAC-TTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACG
* * *
46672 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACTCATAATTATAAT
194 CATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAAT
* * * * *
46737 GTAATAGGTAATTTT-TCAACGTAACCGGTA-AAACTGTATCTGTTTTATGAGAGAATATGTCTA
259 GTAATAGGTAATTTTGT-AATGTAACCGGTATAAA-TATACCGGTTTTATGAGAGAATAGGTCTA
* *
46800 CATAATGTATCGACACTTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGG
322 GAAAATGTATCGACACTTATTAAATTTGTGTCGATACT-TTTGTCCAGAATGAATGCCCAAAAGG
*
46865 GTGCACAAATAAA
386 GTGCACACATAAA
* * * * * * *
46878 GAGTCGATACATTTTTTAAAAGTGTCAATCCCAAAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
*
46943 GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACCTAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACATAATGT
** * * * * * * * *
47008 ATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGTCCAAAAAATGGTGCAT
131 ATCGACACTTTGAAATT-GGTGTCGATACTTTTTGTCCAGAATGAATG-CC-AAAAATGGTGAAC
* * * * * *
47073 ACATAAAGTGTCAATACATTTATAAAAATTAG-CGATCACATAAACATCGAAACCCATTATTATA
193 GCATAAAGTGTCGATACATTTATAAAAAGT-GTCGATCCCAGAAACATCGAAACCCATAATTATA
* * *
47137 ATGTAATAGGTAATTTT-TCAATGTAACCGGTATAAATATACTGGTTTTCTGCGAGAATAGGTCT
257 ATGTAATAGGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
** *
47201 AGAAAATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATG-CCAAAAG
321 AGAAAATGTATCGACACTTATTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAAAG
* *
47265 GGTGCACCCATTAA
385 GGTGCACACATAAA
* *
47279 GTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
47344 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAAGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACATAATGT
47409 ATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACGC
131 ATCGACAC-TTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACGC
* * * *
47474 ATAAAGTGTCGATACATTTTTAAAAAAGTGTCGATCCGAGAGACAT-TAAACCCATAATTATAAT
195 ATAAAGTGTCGATACATTTAT-AAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAAT
* *
47538 GTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTAT-ATGATAATAGGTCTAT
259 GTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTAG
* * * *
47602 ATAATGTATCGACACTT-TTTAATTATGTGTCGATACATTTTGTCCAGAGTAAATGCCCAAAAAA
323 AAAATGTATCGACACTTATTAAATT-TGTGTCGATAC-TTTTGTCCAGAATGAATGCCC--AAAA
** *
47666 TAGTGCACGCATAAA
384 GGGTGCACACATAAA
* *
47681 GTGTCGATACATTTATAAAAAGTATCGATCTCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
47746 GGTAATTTT-TCAATGTAACCGGTATAAATATATCGGTTTTATGCGAGAATAGGCCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACATAATG
* * * * * *
47810 TATCGACACTTATGAAATTTGTGTCGATACTTTTTGTTCAGAAGGAATGCC-AAAAGGGTGCACC
130 TATCGACACTT-TGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACG
* * * *
47874 CGTTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
194 CATAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAAT
* * * * *
47939 GTAATAGGTCATTTTGTAATGTAACTGATATAAATATACCAGTTTTATGAGAAAATAGGTC-AGC
259 GTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAG-
* *
48003 ATAAA-GTATCGACAATTGTTAAATTTGTGTCGATAC
323 A-AAATGTATCGACACTTATTAAATTTGTGTCGATAC
48039 CATTTTAAAA
Statistics
Matches: 1011, Mismatches: 126, Indels: 46
0.85 0.11 0.04
Matches are distributed among these distances:
398 12 0.01
399 290 0.29
400 45 0.04
401 300 0.30
402 360 0.36
403 4 0.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (398 bp):
GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATATGTCTACATAATGT
ATCGACACTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTGAACGCA
TAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGT
AATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAGAAA
ATGTATCGACACTTATTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAAAGGGTGCA
CACATAAA
Found at i:47627 original size:601 final size:602
Alignment explanation
Indices: 46479--48038 Score: 2292
Period size: 601 Copynumber: 2.6 Consensus size: 602
46469 GTAAGCAGAT
* * *
46479 GTGTCGATACATTTATAAAAAGTATCGATCAAAAAAACATCAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATAATTATAATGTAATA
* * ** ** * * *
46544 GGTAATTTTGT-AATATAATCGGTATAAATATACCAGTTTTATGTAAGAATATGTCTACATAATG
66 GGTAATTTT-TCAATGTAACCGGTATAAATATACTGGTTTTATGCGAGAATAGGTCTAGAAAATG
** * * * * * * *
46608 TATATACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGAACGC
130 TATCGACACTTATGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCC
* * * * * *
46673 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACTCATAATTATAATG
195 ATTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * *
46738 TAATAGGTAATTTT-TCAACGTAACCGGTA-AAACTGTATCTGTTTTATGAGAGAATATGTCTAC
260 TAATAGGTAATTTTGT-AATGTAACCGGTATAAA-TATATCAGTTTTATGAGAGAATAAGTCTAC
*
46801 ATAATGTATCGACAC-TTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGG
323 ATAATGTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCAAAAAGG
* *
46865 GTGCACAAATAAAGAGTCGATACATTTTTTAAAAGTGTCAATCCCAAAGACATCGAAACCCATAA
388 GTGAACAAATAAAGAGTCGATACATTTTTAAAAAGTGTCAATCCCAAAGACATCGAAACCCATAA
* *
46930 TTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAT
453 TTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATATGAGAATAG
* *
46995 GTCTACCTAATGTATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGTCCA
518 GTCTACATAATGTATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGCCCA
* *
47060 AAAAATGGTGCATACATAAA
583 AAAAATAGTGCACACATAAA
* * * *
47080 GTGTCAATACATTTATAAAAATTAGCGATCACATAAACATCGAAACCCATTATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATAATTATAATGTAATA
*
47145 GGTAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTCTGCGAGAATAGGTCTAGAAAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGCGAGAATAGGTCTAGAAAATGT
*
47210 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
131 ATCGACACTTATGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
*
47275 TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCCATAATTATAATGT
196 TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* *
47340 AATAGGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAAGTCTACATA
261 AATAGGTAATTTTGTAATGTAACCGGTATAAATATATCAGTTTTATGAGAGAATAAGTCTACATA
* * * *
47405 ATGTATCGACACATT-TGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAATGGTG
326 ATGTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCAAAAAGGGTG
** * * * * *
47469 AACGCATAAAGTGTCGATACATTTTTAAAAAAGTGTCGATCCGAGAGACAT-TAAACCCATAATT
391 AACAAATAAAGAGTCGATACATTTTT-AAAAAGTGTCAATCCCAAAGACATCGAAACCCATAATT
* *
47533 ATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATATGATAATAGGT
455 ATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATATGAGAATAGGT
* * *
47598 CTATATAATGTATCGACACTTTTTAATTATGTGTCGATACATTTTGTCCAGAGTAAATGCCCAAA
520 CTACATAATGTATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGCCCAAA
*
47663 AAATAGTGCACGCATAAA
585 AAATAGTGCACACATAAA
* *
47681 GTGTCGATACATTTATAAAAAGTATCGATCTCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATAATTATAATGTAATA
*
47746 GGTAATTTTTCAATGTAACCGGTATAAATATA-TCGGTTTTATGCGAGAATAGGCCTAGAAAATG
66 GGTAATTTTTCAATGTAACCGGTATAAATATACT-GGTTTTATGCGAGAATAGGTCTAGAAAATG
*
47810 TATCGACACTTATGAAATTTGTGTCGATACTTTTTGTTCAGAAGGAATGCCAAAAGGGTGCACCC
130 TATCGACACTTATGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCC
*
47875 GTTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATG
195 ATTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * * * *
47940 TAATAGGTCATTTTGTAATGTAACTGATATAAATATACCAGTTTTATGAGAAAATAGGTC-AGCA
260 TAATAGGTAATTTTGTAATGTAACCGGTATAAATATATCAGTTTTATGAGAGAATAAGTCTA-CA
* *
48004 TAAAGTATCGACA-ATTGTTAAATTTGTGTCGATAC
324 TAATGTATCGACACATTATTAAATTTGTGTCGATAC
48039 CATTTTAAAA
Statistics
Matches: 864, Mismatches: 87, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
600 6 0.01
601 832 0.96
602 26 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (602 bp):
GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGCGAGAATAGGTCTAGAAAATGT
ATCGACACTTATGAAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
AATAGGTAATTTTGTAATGTAACCGGTATAAATATATCAGTTTTATGAGAGAATAAGTCTACATA
ATGTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCAAAAAGGGTG
AACAAATAAAGAGTCGATACATTTTTAAAAAGTGTCAATCCCAAAGACATCGAAACCCATAATTA
TAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGATTTTATATGAGAATAGGTC
TACATAATGTATCGACACTTTTTAATTATGCGTCAATACATTTTGTCCAGAGTAAATGCCCAAAA
AATAGTGCACACATAAA
Found at i:50869 original size:24 final size:24
Alignment explanation
Indices: 50818--50870 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
50808 TTTCATATGT
* * *
50818 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
50842 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
50866 AATTT
1 AATTT
50871 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:52164 original size:199 final size:198
Alignment explanation
Indices: 51181--52346 Score: 1322
Period size: 200 Copynumber: 5.8 Consensus size: 198
51171 AGTTTCCCAC
* * *
51181 AAAGTGTCGATACATGTTTAAAAAGTATCGATCCTAAAAACATCGAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * * *
51246 ATAGGTAAATTTACAATGTAACTGGTATAAATATACCCGTTTTTTTTTGAGAAAATAGAT-ATAC
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATA-CCG--ATTTTATGAGAGAATAGGTCA-AC
* * * *
51310 ATAATGTATCGACACATGTGGAA-TTGTGTCGATACTTTTCGTCCAAAATGAATGCCAAACGTGG
127 ATAATGTATCGACACTTTTGGAATTTGTGTCGATACTTTT-TTCCAAAATGAATGCCAAAAG-GG
*
51374 TGCACCCAT
190 TGCACGCAT
* * * *
51383 ACATTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* ** * * *
51448 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATAA
* * * * * * * *
51513 TATGTCGACACTTTT-GAATTTTGTGTCGATACTTTTTTTCCAGACTGAATCCCAAAATGCTGAA
131 TGTATCGACACTTTTGGAA-TTTGTGTCGATAC-TTTTTTCCAAAATGAATGCCAAAAGGGTGCA
**
51577 ATCAT
194 CGCAT
* * * * * *
51582 AAAATGTCGATACATTTATAAAAAAGTATCGATCTCAGAAACATTGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTT-TTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGT
* * * * * *
51647 AATAGGTAAATTTACAATGTAATCAGTATAACTATACCGGTTTTATTAGAGAATAGGTCTACATA
65 AATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATA
* * *
51712 ATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAAAAGGATTGC
130 ATGTATCGACACTTTTGGAATTTGTGTCGATACTTTTT-TCCAAAATGAATGCCAAAAGG-GTGC
51777 ACGCAT
193 ACGCAT
* *
51783 AAAGTGTCAATACATTTTTAAAAAGTATCGAT-CCATAAAACATCGAAACTGATAATTATAATGT
1 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCA-AAAACATCGAAACCGATAATTATAATGT
* * * * * *
51847 ACTAGGTAAATTTACAATGTAACCTGTATAACTATACCGGTTTTATTAGAGAATAGGTCTACATA
65 AATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATA
* *
51912 ATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAAAAGGGTTGC
130 ATGTATCGACACTTTTGGAATTTGTGTCGATACTTTTT-TCCAAAATGAATGCCAAAAGGG-TGC
51977 ACGCAT
193 ACGCAT
* *
51983 AAAGTGTCGATAGATTTTTAAAAAGTATCGATCCCAAAAA-ATCGAAACTGATAATTATAATGTA
1 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * * * *
52047 ATAAGTAAATTTACAATATAACCAGTATAAATTTACCGATTTTATGAGAAAATAGGTGAACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATAA
* * * *
52112 TATATCGACACGTTTTAG-ATTTATGTCGATACATTTTTTCCAAAATGAATGCCAAACGAGGTGC
131 TGTATCGACAC-TTTTGGAATTTGTGTCGATAC-TTTTTTCCAAAATGAATGCCAAAAG-GGTGC
* *
52176 AAGCAA
193 ACGCAT
* * *** ** * *
52182 AAAGTATCGATACA-TTTGAAATTTTATTAATCCCAAAAACATCAAAACCGATAATTATAACGTA
1 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * * * * *
52246 ATAGGTAATTTTATAATGTAACCGGTATAAAAATACCAATTTTATAAGAGAATAGGTTAACTTAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATAA
*
52311 TGTATCGACACTTTT-AAATTTGTGTCGATACTTTTT
131 TGTATCGACACTTTTGGAATTTGTGTCGATACTTTTT
52347 AAATAACACG
Statistics
Matches: 828, Mismatches: 120, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
197 5 0.01
198 39 0.05
199 282 0.34
200 380 0.46
201 34 0.04
202 88 0.11
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (198 bp):
AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCAACATAA
TGTATCGACACTTTTGGAATTTGTGTCGATACTTTTTTCCAAAATGAATGCCAAAAGGGTGCACG
CAT
Found at i:53981 original size:19 final size:19
Alignment explanation
Indices: 53957--54005 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
53947 AATGTAGGGT
53957 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
** *
53976 TAATTTTACATACGATTTA
1 TAATTTTGTATAAGATTTA
53995 TAATTTTGTAT
1 TAATTTTGTAT
54006 GTGAATACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:56712 original size:177 final size:178
Alignment explanation
Indices: 56482--56818 Score: 462
Period size: 177 Copynumber: 1.9 Consensus size: 178
56472 GCTAAATAGG
56482 TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
1 TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
* * ** * * * *
56547 GTAAATTAACAATGTAACCGGTATAAATATATTGG-TTAATTAGAAAACAGGTCAATATAATGTA
66 ATAAATTAACAATATAACCGGTATAAATATACCGGTTTAATAAGAAAACAGATCAACATAAAGTA
* *
56611 TCGACACTTTTTTAATTTGTGTCGATACTTATTATCCAGAATATAAAT
131 TCGACACTATTTAAATTTGTGTCGATACTTATTATCCAGAATATAAAT
* * *
56659 TGTCGATACATTTAT-TAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATGTAATA
1 TGTCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * * **
56723 GATAAATTTACAATATGACTGGTATAAATATACCGGTTTTATAAGAAAATAGATCTGCATAAAGT
65 GATAAATTAACAATATAACCGGTATAAATATACCGGTTTAATAAGAAAACAGATCAACATAAAGT
*
56788 ATCGACTCTATTTAAATTTGTGTCGATACTT
130 ATCGACACTATTTAAATTTGTGTCGATACTT
56819 TTTGTCCATA
Statistics
Matches: 137, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
177 88 0.64
178 49 0.36
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (178 bp):
TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
ATAAATTAACAATATAACCGGTATAAATATACCGGTTTAATAAGAAAACAGATCAACATAAAGTA
TCGACACTATTTAAATTTGTGTCGATACTTATTATCCAGAATATAAAT
Found at i:57010 original size:200 final size:198
Alignment explanation
Indices: 56653--57136 Score: 632
Period size: 200 Copynumber: 2.4 Consensus size: 198
56643 TATCCAGAAT
* *
56653 ATAAATTGTCGATACATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATATATTTATTAAAAGTATCGATCCCAA-AACATCGAAACCGATAATTATAATG
* * * * **
56718 TAATAGATAAATTTACAATATGACTGGTATAAATATACCGGTTTTATAAGAAAATAGATCTGCAT
65 TAATAGGTAAATTTACAATATGACCGATAGAAATATACCGGTTTTATAAGAAAATAGATCTAAAT
* * *
56783 AAAGTATCGACTCTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGGGGTG
130 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAAACGAGGTG
56848 CACAC
194 CACAC
** *
56853 ATAAAGTGTCGATATATTTATTAAAAGTATCGATCCCACAAACATCGAAAGTGATAATTACAATG
1 ATAAAGTGTCGATATATTTATTAAAAGTATCGATCCCA-AAACATCGAAACCGATAATTATAATG
* * *
56918 TGATAGGTAAATTTACAATGT-ACCCGATAGAAATATACCGGTTTTATGAGAAAATAGATCTAAA
65 TAATAGGTAAATTTACAATATGA-CCGATAGAAATATACCGGTTTTATAAGAAAATAGATCTAAA
* * * *
56982 TAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTG
129 TAAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTG
**
57047 CATGC
194 CACAC
* * * *
57052 ATAAAGTGTCGATATATTTA--AAATTGTATCGATCCAAAAAAATATTGAAACCGATAATTATAA
1 ATAAAGTGTCGATATATTTATTAAA-AGTATCGATCC--CAAAACATCGAAACCGATAATTATAA
*
57115 TGTAATAGGTAAATTTGCAATA
63 TGTAATAGGTAAATTTACAATA
57137 CCGGTTTACT
Statistics
Matches: 246, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
197 3 0.01
198 10 0.04
199 84 0.34
200 148 0.60
201 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (198 bp):
ATAAAGTGTCGATATATTTATTAAAAGTATCGATCCCAAAACATCGAAACCGATAATTATAATGT
AATAGGTAAATTTACAATATGACCGATAGAAATATACCGGTTTTATAAGAAAATAGATCTAAATA
AAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGCA
CAC
Found at i:57272 original size:23 final size:23
Alignment explanation
Indices: 57222--57266 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
57212 TGCCTATTTT
*
57222 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
57245 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
57267 TGTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:60530 original size:3 final size:3
Alignment explanation
Indices: 60522--60625 Score: 181
Period size: 3 Copynumber: 34.7 Consensus size: 3
60512 AGAACCAACA
* * *
60522 AAG AAG AAG GAG GAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
60570 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
60618 AAG AAG AA
1 AAG AAG AA
60626 ACATCCTACC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Done.