Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004382.1 Hibiscus syriacus cultivar Beakdansim tig00009608_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: 71503
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:128 original size:20 final size:20
Alignment explanation
Indices: 103--175 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
93 CGATGTTTTA
*
103 AGGTATCGATACCATCCTTC
1 AGGTATCGATACCACCCTTC
* *
123 AGGTATTGATACTACCCTT-
1 AGGTATCGATACCACCCTTC
* *
142 ATAGTATCGATACTACCCTTAC
1 A-GGTATCGATACCACCCTT-C
164 A-GTATCGATACC
1 AGGTATCGATACC
176 TATCAACATG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
22 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (20 bp):
AGGTATCGATACCACCCTTC
Found at i:6155 original size:21 final size:21
Alignment explanation
Indices: 6129--6178 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6119 CACCAAAGTG
* **
6129 CCACATATTTATCCTGAAGAA
1 CCACATAATTATCCCAAAGAA
*
6150 CCACATAATTATCCCAAAGGA
1 CCACATAATTATCCCAAAGAA
6171 CCACATAA
1 CCACATAA
6179 AACCCTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCAAAGAA
Found at i:6825 original size:54 final size:54
Alignment explanation
Indices: 6736--6855 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 54
6726 GATACTTCCC
* * *
6736 TTCAAGGGTATCGATACCTCCTCATAGTACAGATACCGATA-TAGCATTCGATGT
1 TTCAAGGGTATTGATACCTCCTCATAGTACAGATACC-AAACTAGCATTCGATAT
* *
6790 TTCAAGGGTATTGATACCTCCTCA-AGGTACTGATACCAAACTGGCATTCGATAT
1 TTCAAGGGTATTGATACCTCCTCATA-GTACAGATACCAAACTAGCATTCGATAT
*
6844 TTTAAGGGTATT
1 TTCAAGGGTATT
6856 AATATCATCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 3 0.05
54 55 0.95
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (54 bp):
TTCAAGGGTATTGATACCTCCTCATAGTACAGATACCAAACTAGCATTCGATAT
Found at i:6893 original size:21 final size:21
Alignment explanation
Indices: 6868--6922 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
6858 TATCATCCTT
6868 CAGGTATCGATACCTATTCAA
1 CAGGTATCGATACCTATTCAA
6889 CAGGTATCGATACCTATTCAA
1 CAGGTATCGATACCTATTCAA
6910 CAGGTATCGATAC
1 CAGGTATCGATAC
6923 TATCCTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (21 bp):
CAGGTATCGATACCTATTCAA
Found at i:8179 original size:20 final size:20
Alignment explanation
Indices: 8137--8181 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8127 ATTTTTACAG
* *
8137 AGAAAACATCCCAAATGGTT
1 AGAAAACATCCCAAACGGCT
* *
8157 AGAAATCATCCCTAACGGCT
1 AGAAAACATCCCAAACGGCT
8177 AGAAA
1 AGAAA
8182 CAACCACAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (20 bp):
AGAAAACATCCCAAACGGCT
Found at i:9299 original size:21 final size:20
Alignment explanation
Indices: 9266--9305 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
9256 CATAATAGGA
*
9266 CTATAACGGTGTTTTTAAGTC
1 CTATAACGATG-TTTTAAGTC
*
9287 CTATAGCGATGTTTTAAGT
1 CTATAACGATGTTTTAAGT
9306 ACCACAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (20 bp):
CTATAACGATGTTTTAAGTC
Found at i:13196 original size:77 final size:76
Alignment explanation
Indices: 12971--13408 Score: 398
Period size: 77 Copynumber: 5.8 Consensus size: 76
12961 CTAAAATTGA
* * * * *
12971 CATGGTTCACTAAGAAATAGATTATGATGTAGAATGTTAATATTTTTATTAATAAAATGGGTCAT
1 CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATAGAT--T
*
13036 GC-CCAATAATGT
64 GCGCCAAGAATGT
* * ** *
13048 CATGG----CTAAGAAATAGGTTGCGATCTATAATGTTAATAATTTTTATTAATAAAA-AGGGTT
1 CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAAT-ATTTTTATTAATAAAATA-GATT
*
13108 GCACCCAAGAATGT
64 GC-GCCAAGAATGT
* * * *
13122 CATGGTTCACTAATAAATAGGTTGTTATTTGGAATGTTAATATTTTTATTAATAAAATAGATTGC
1 CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATAGATTGC
*
13187 GCTCGAGAATGT
66 GC-CAAGAATGT
* * * *
13199 CATGGTTCACTAAGAAATAGACTGCGATCTGCAATGTTAATATTTTTATTAATAAAAT-GAGTTT
1 CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATAGA-TTG
13263 CGCCCAAGAATGT
65 CG-CCAAGAATGT
* ** * * *
13276 CATAGTTCACTAAGAAATAGATTGAAATCTGGAATGTTAATATTTTTATTAATAAAATGGTTTGA
1 CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATAGATTGC
13341 G-C-A-AATGT
66 GCCAAGAATGT
* * * *
13349 TATGGTTCACTAAGAAATCA-ATTTGTTATATGG-ATAGTTAATTTTTTCTATT-ATAAAATA
1 CATGGTTCACTAAGAAAT-AGA-TTGTGATCTGGAAT-GTTAATATTTT-TATTAATAAAATA
13409 TTTAAAAGTA
Statistics
Matches: 304, Mismatches: 40, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
72 3 0.01
73 51 0.17
74 60 0.20
75 5 0.02
76 3 0.01
77 153 0.50
78 29 0.10
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (76 bp):
CATGGTTCACTAAGAAATAGATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATAGATTGC
GCCAAGAATGT
Found at i:13294 original size:154 final size:152
Alignment explanation
Indices: 12975--13366 Score: 465
Period size: 154 Copynumber: 2.6 Consensus size: 152
12965 AATTGACATG
* * * * *
12975 GTTCACTAAGAAATAGATTATGATGTAGAATGTTAATATTTTTATTAATAAAATGGGTCATGC-C
1 GTTCACTAAGAAATAGATTGTAATCTGGAATGTTAATATTTTTATTAATAAAATGGAT--TGCGC
** *
13039 CAATAATGTCATGG----CTAAGAAATAGGTTGCGATCTATAATGTTAATAATTTTTATTAATAA
64 C-A-AATGTCATGGTTCACTAAGAAATAGACTGCGATCTACAATGTTAATAATTTTTATTAATAA
* *
13100 AAAGGGTTGCACCCAAGAATGTCATG
127 AAAGAGTTGCACCCAAGAATGTCATA
* * * * *
13126 GTTCACTAATAAATAGGTTGTTATTTGGAATGTTAATATTTTTATTAATAAAATAGATTGCGCTC
1 GTTCACTAAGAAATAGATTGTAATCTGGAATGTTAATATTTTTATTAATAAAATGGATTGCGC-C
*
13191 GAGAATGTCATGGTTCACTAAGAAATAGACTGCGATCTGCAATGTTAAT-ATTTTTATTAATAAA
65 -A-AATGTCATGGTTCACTAAGAAATAGACTGCGATCTACAATGTTAATAATTTTTATTAATAAA
* * *
13255 ATGAGTTTCGCCCAAGAATGTCATA
128 AAGAGTTGCACCCAAGAATGTCATA
* * *
13280 GTTCACTAAGAAATAGATTGAAATCTGGAATGTTAATATTTTTATTAATAAAATGGTTTGAG-CA
1 GTTCACTAAGAAATAGATTGTAATCTGGAATGTTAATATTTTTATTAATAAAATGGATTGCGCCA
*
13344 AATGTTATGGTTCACTAAGAAAT
66 AATGTCATGGTTCACTAAGAAAT
13367 CAATTTGTTA
Statistics
Matches: 207, Mismatches: 28, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
149 3 0.01
150 23 0.11
151 63 0.30
152 1 0.00
154 89 0.43
155 28 0.14
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (152 bp):
GTTCACTAAGAAATAGATTGTAATCTGGAATGTTAATATTTTTATTAATAAAATGGATTGCGCCA
AATGTCATGGTTCACTAAGAAATAGACTGCGATCTACAATGTTAATAATTTTTATTAATAAAAAG
AGTTGCACCCAAGAATGTCATA
Found at i:13377 original size:228 final size:228
Alignment explanation
Indices: 12971--13408 Score: 534
Period size: 228 Copynumber: 1.9 Consensus size: 228
12961 CTAAAATTGA
* * * *
12971 CATGGTTCACTAAGAAATAGATTATGATGTAGAATGTTAATATTTTTATTAATAAAATGGGTCAT
1 CATGGTTCACTAAGAAATAGACTACGATCTAGAATGTTAATATTTTTATTAATAAAATGAGTCAT
* * * ** *
13036 GCCCAATAATGTCATGGCTAAGAAATAGGTTGCGATCTATAATGTTAATAATTTTTATTAATAAA
66 GCCCAAGAATGTCATGACTAAGAAATAGATTGAAATCTAGAATGTTAATAATTTTTATTAATAAA
* * *
13101 AAGGGTTGCACCCAAGAATGTCATGGTTCACTAATAAATAGGTTGTTATTTGGA-ATGTTAATAT
131 AAGGGTTGCACCCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTTATATGGATA-GTTAATAT
13165 TTT-TATTAATAAAATAGATTGCGCTCGAGAATGT
195 TTTCTATT-ATAAAATAGATTGCGCTCGAGAATGT
* *
13199 CATGGTTCACTAAGAAATAGACTGCGATCT-GCAATGTTAATATTTTTATTAATAAAATGAGT-T
1 CATGGTTCACTAAGAAATAGACTACGATCTAG-AATGTTAATATTTTTATTAATAAAATGAGTCA
*
13262 TCGCCCAAGAATGTCATAGTTCACTAAGAAATAGATTGAAATCTGGAATGTTAAT-ATTTTTATT
65 T-GCCCAAGAATGTCAT-G---ACTAAGAAATAGATTGAAATCTAGAATGTTAATAATTTTTATT
* * * * *
13326 AATAAAATGGTTTG-A-GC-A-AATGTTATGGTTCACTAAGAAATCAATTTGTTATATGGATAGT
125 AATAAAAAGGGTTGCACCCAAGAATGTCATGGTTCACTAAGAAAT-AAGTTGTTATATGGATAGT
*
13387 TAATTTTTTCTATTATAAAATA
189 TAATATTTTCTATTATAAAATA
13409 TTTAAAAGTA
Statistics
Matches: 179, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
227 23 0.13
228 100 0.56
229 7 0.04
230 1 0.01
231 21 0.12
232 27 0.15
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (228 bp):
CATGGTTCACTAAGAAATAGACTACGATCTAGAATGTTAATATTTTTATTAATAAAATGAGTCAT
GCCCAAGAATGTCATGACTAAGAAATAGATTGAAATCTAGAATGTTAATAATTTTTATTAATAAA
AAGGGTTGCACCCAAGAATGTCATGGTTCACTAAGAAATAAGTTGTTATATGGATAGTTAATATT
TTCTATTATAAAATAGATTGCGCTCGAGAATGT
Found at i:15458 original size:82 final size:83
Alignment explanation
Indices: 15280--15462 Score: 212
Period size: 82 Copynumber: 2.2 Consensus size: 83
15270 ATCAGATACT
15280 TTTCCGAAAA-TATTGATATTTTTTAAATTCAAAAATTAAAATATCATTTTTCACGATTATTTTA
1 TTTCC-AAAAGTATTGATATTTTTTAAATTCAAAAATTAAAATATCATTTTTCACGATTATTTTA
*
15344 ATTCGAAAGCATCAATATT
65 ATTCGAAAGCATCAATATC
* * * * * *
15363 TTTTCAAAAGTATTGATA-TTTTTAAATTCGAAAGTTAAAATATCA-TTTTCTATGTTTTTTTTT
1 TTTCCAAAAGTATTGATATTTTTTAAATTCAAAAATTAAAATATCATTTTTC-ACG-ATTATTTT
* **
15426 AATTCGAAAGTATGGATA-C
64 AATTCGAAAGCATCAATATC
*
15445 TTTCCAAATGTATTGATA
1 TTTCCAAAAGTATTGATA
15463 CTTTCCAAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
81 5 0.06
82 47 0.55
83 33 0.39
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (83 bp):
TTTCCAAAAGTATTGATATTTTTTAAATTCAAAAATTAAAATATCATTTTTCACGATTATTTTAA
TTCGAAAGCATCAATATC
Found at i:15462 original size:19 final size:19
Alignment explanation
Indices: 15435--15486 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
15425 TAATTCGAAA
*
15435 GTATGGATACTTTCCAAAT
1 GTATCGATACTTTCCAAAT
*
15454 GTATTGATACTTTCCAAAT
1 GTATCGATACTTTCCAAAT
15473 GTATCGATACTTTC
1 GTATCGATACTTTC
15487 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (19 bp):
GTATCGATACTTTCCAAAT
Found at i:16043 original size:101 final size:101
Alignment explanation
Indices: 15647--16043 Score: 419
Period size: 101 Copynumber: 4.0 Consensus size: 101
15637 TGCCCTTTTG
* * * * ** *
15647 TGTCAACCGTTTAAGTTATAAGTATGAAATCATTTATATGATGCTGAAGTAAGACAAAACATCTT
1 TGTCAATCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
* * * ** *
15712 TCTCATGATAACGTAGTAGGT-A-GTGCCCTTTT--G
66 GCTCATGATAACGTACTAGGTAACAT-CTTTTTTAAA
* *
15745 TGCCAACCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
1 TGTCAATCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
* * * *
15810 GCTGATGATAACGTACTAGGTAGCGT-TTGTTTTTAA
66 GCTCATGATAACGTACTAGGTAACATCTT-TTTTAAA
* * * * *
15846 TGTCAATCATTTAAATTTTAGGTATGAAACTGTTTATATTATGCAAAAGTAAGACAAAACATGTT
1 TGTCAATCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
* * *
15911 GCTCATGATAATGTACTAGGTAACACCTTTTTCAAA
66 GCTCATGATAACGTACTAGGTAACATCTTTTTTAAA
* * * *
15947 TGTTAATCGTTTAAGTTATATGTATGAAACCGTTTACATTATGTAAAAGTAAGACAAAACATGTT
1 TGTCAATCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
* * * *
16012 -TTCATGATAACATAATAGGCAACATCTTTTTT
66 GCTCATGATAACGTACTAGGTAACATCTTTTTT
16044 TATGTAAAAA
Statistics
Matches: 250, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
98 76 0.30
99 4 0.02
100 27 0.11
101 141 0.56
102 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (101 bp):
TGTCAATCGTTTAAGTTATAAGTATGAAACCGTTTATATTATGCAAAAGTAAGACAAAACATGTT
GCTCATGATAACGTACTAGGTAACATCTTTTTTAAA
Found at i:16478 original size:62 final size:62
Alignment explanation
Indices: 16346--16478 Score: 164
Period size: 62 Copynumber: 2.1 Consensus size: 62
16336 ATTGATTATC
* * *
16346 ATTGCATAAGTATGAATGTTTTAAATTTCGATCTTTTTATCAATTTTTTCAATTTTTAAAAGT
1 ATTG-ATAAGTATCAATATTTTAAATTTCGATCTTTTTATCAATTTTTTCAATATTTAAAAGT
* *
16409 GTCGATAAGTATCAATATTTTAAATTTCGATCTTATATT-T-AAGTTTTTT-AATATTTAAAAGT
1 ATTGATAAGTATCAATATTTTAAATTTCGATCTT-T-TTATCAA-TTTTTTCAATATTTAAAAGT
16471 ATTGATAA
1 ATTGATAA
16479 TAATATATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
62 48 0.80
63 10 0.17
64 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.49
Consensus pattern (62 bp):
ATTGATAAGTATCAATATTTTAAATTTCGATCTTTTTATCAATTTTTTCAATATTTAAAAGT
Found at i:19673 original size:19 final size:21
Alignment explanation
Indices: 19649--19704 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
19639 ACACCGGAAG
19649 GGGGTATCGATACCATAG-AA
1 GGGGTATCGATACCATAGTAA
* *
19669 TGGTAGTATCGATA-CATGGTAA
1 -GG-GGTATCGATACCATAGTAA
19691 -GGGTATCGATACCA
1 GGGGTATCGATACCA
19705 GAAAACATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 6 0.21
22 11 0.38
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (21 bp):
GGGGTATCGATACCATAGTAA
Found at i:19712 original size:94 final size:93
Alignment explanation
Indices: 19559--19760 Score: 264
Period size: 94 Copynumber: 2.2 Consensus size: 93
19549 GATTCAATTA
* *
19559 GTATCGATACCA-ATGAGGTAGTATCGATACCATGGTAAGAGTATTGATACCAGATAACATCGAA
1 GTATCGATACCATA-GAGGTAGTATCGATACCATGGTAAGAGTATCGATACCAGAAAACATCGAA
** *
19623 TTTAAAATTGGTATCGACACCGGAAGGGG
65 GCTAAAATTGGTATCGACACCAGAAGGGG
* *
19652 GTATCGATACCATAGAATGGTAGTATCGATA-CATGGTAAGGGTATCGATACCAGAAAACATTGA
1 GTATCGATACCATAG-A-GGTAGTATCGATACCATGGTAAGAGTATCGATACCAGAAAACATCGA
* * *
19716 AGCTAAAATTGGTATCGATACTAGAATGGG
64 AGCTAAAATTGGTATCGACACCAGAAGGGG
*
19746 GTATCAATACCATAG
1 GTATCGATACCATAG
19761 TATAGAAGTG
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
93 13 0.14
94 69 0.73
95 13 0.14
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (93 bp):
GTATCGATACCATAGAGGTAGTATCGATACCATGGTAAGAGTATCGATACCAGAAAACATCGAAG
CTAAAATTGGTATCGACACCAGAAGGGG
Found at i:26253 original size:45 final size:45
Alignment explanation
Indices: 26202--26346 Score: 195
Period size: 45 Copynumber: 3.5 Consensus size: 45
26192 CATAAAAGAA
26202 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
*
26247 TAATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A----
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
26281 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
1 TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
*
26326 AAATGCATATGGGTGCATTAT
1 TAATGCATATGGGTGCATTAT
26347 CGACATAAAA
Statistics
Matches: 86, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
34 26 0.30
35 3 0.03
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
44 3 0.03
45 46 0.53
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (45 bp):
TAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG
Found at i:26300 original size:79 final size:79
Alignment explanation
Indices: 26169--26558 Score: 478
Period size: 79 Copynumber: 4.9 Consensus size: 79
26159 TCATAATTAA
* *
26169 AATGCATATGGGTACATTATCGACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
26234 GATGCCATAGCTGT
66 GATGCCATAGCTGT
26248 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
*
26313 GATGCCATAGCTGA
66 GATGCCATAGCTGT
* *
26327 AATGCATATGGGTGCATTATCGACATAAAAGAGTAATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
* *
26392 GATGACATAGCTGG
66 GATGCCATAGCTGT
* *
26406 AATGTATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T--AATGCATATGGGTGCATTAT
*
26471 CGGCAT-AAA--A-G--A-A----T
55 TGGCATGAAAGGATGCCATAGCTGT
* * *
26485 AATACATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTTCATTATTGGCATTAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
*
26550 GATGTCATA
66 GATGCCATA
26559 ACTAAAATGC
Statistics
Matches: 275, Mismatches: 18, Indels: 40
0.83 0.05 0.12
Matches are distributed among these distances:
68 24 0.09
69 3 0.01
70 1 0.00
71 1 0.00
72 2 0.01
73 1 0.00
74 1 0.00
75 2 0.01
76 1 0.00
78 3 0.01
79 197 0.72
80 3 0.01
82 1 0.00
83 2 0.01
84 1 0.00
85 1 0.00
86 1 0.00
87 1 0.00
88 1 0.00
89 3 0.01
90 25 0.09
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
GATGCCATAGCTGT
Found at i:26416 original size:45 final size:45
Alignment explanation
Indices: 26361--26481 Score: 197
Period size: 45 Copynumber: 2.7 Consensus size: 45
26351 ATAAAAGAGT
*
26361 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGG
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGA
* *
26406 AATGTATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGA
* *
26451 AATGCATATGGGTGCATTATCGGCATAAAAG
1 AATGCATATGGGTGCATTATTGGCATGAAAG
26482 AATAATACAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGA
Found at i:26436 original size:124 final size:124
Alignment explanation
Indices: 26282--26515 Score: 414
Period size: 124 Copynumber: 1.9 Consensus size: 124
26272 ATAAAAGAAT
26282 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
* * * *
26347 CGACATAAAAGAGTAATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGG
66 CGACATAAAAGAATAATACATATGGGTGCATTATCGGCATAAAAGGATGACATAGCTGG
*
26406 AATGTATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
26471 CGGCATAAAAGAATAATACATATGGGTGCATTATCGGCATAAAAG
66 CGACATAAAAGAATAATACATATGGGTGCATTATCGGCATAAAAG
26516 AATAATGCAT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (124 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CGACATAAAAGAATAATACATATGGGTGCATTATCGGCATAAAAGGATGACATAGCTGG
Found at i:26544 original size:34 final size:34
Alignment explanation
Indices: 26451--26549 Score: 162
Period size: 34 Copynumber: 2.9 Consensus size: 34
26441 CCATAGCTGA
26451 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
26485 AATACATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
26519 AATGCATATGGGTTCATTATTGGCATTAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
26550 GATGTCATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:26592 original size:20 final size:21
Alignment explanation
Indices: 26567--26605 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
26557 TAACTAAAAT
26567 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGCCATTAAG
*
26587 GCATGAAATGATGCCATTA
1 GCATGAAAGGATGCCATTA
26606 CTAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (21 bp):
GCATGAAAGGATGCCATTAAG
Found at i:29391 original size:95 final size:95
Alignment explanation
Indices: 29253--29438 Score: 275
Period size: 95 Copynumber: 2.0 Consensus size: 95
29243 ATACTAACGA
* * * **
29253 GGTAGTATCGATACCATGGTAAGAGTATCGATATCAGACAACATCGAATTTAAAATTGGTATAGA
1 GGTAGTATCAATACCATGGTAAGAGTATCGATACCAGAAAACATCGAAGCTAAAATTGGTATAGA
**
29318 TACCGGAA-GGGGATATTGGTACCATATAAT
66 TACCGGAATGGGG-TATCAGTACCATATAAT
* *
29348 GGTAGTATCAATACCATGGTAAGGGTATCGATACCAGAAAACATCGAAGCTAAAATTGGTATCGA
1 GGTAGTATCAATACCATGGTAAGAGTATCGATACCAGAAAACATCGAAGCTAAAATTGGTATAGA
29413 TACCGGAATGGGGTATCAGTACCATA
66 TACCGGAATGGGGTATCAGTACCATA
29439 GTGTAGAAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 77 0.95
96 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (95 bp):
GGTAGTATCAATACCATGGTAAGAGTATCGATACCAGAAAACATCGAAGCTAAAATTGGTATAGA
TACCGGAATGGGGTATCAGTACCATATAAT
Found at i:29984 original size:79 final size:79
Alignment explanation
Indices: 29860--30181 Score: 495
Period size: 79 Copynumber: 4.1 Consensus size: 79
29850 AACTCATAAT
*
29860 TAAAATGCATATGGGTGCATTATCAACATAAAACAATAATGCATAT-GGTCGCATTATTGGCATG
1 TAAAATGCATATGGGTGCATTATCAGCATAAAACAATAATGCATATGGGT-GCATTATTGGCATG
*
29924 AAAGGATGTCATAGT
65 AAAGGATGTCATAGC
*
29939 TAAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGA
1 TAAAATGCATATGGGTGCATTATCAGCATAAAACAATAATGCATATGGGTGCATTATTGGCATGA
*
30004 AAGGATGCCATAGC
66 AAGGATGTCATAGC
* *
30018 TGAAATGCATATGGGTGCATTATC-GACATAAAAGAATAATGCATATGGGTGCATTATTGGCATG
1 TAAAATGCATATGGGTGCATTATCAG-CATAAAACAATAATGCATATGGGTGCATTATTGGCATG
*
30082 AAATGATGTCATAGC
65 AAAGGATGTCATAGC
* * * * *
30097 TGAAATGCATATGAGTGCATTATCGGTATAAAACAATAATGCATATGGGTGCATTATTGGCAGGA
1 TAAAATGCATATGGGTGCATTATCAGCATAAAACAATAATGCATATGGGTGCATTATTGGCATGA
*
30162 AAGGATGTCATAAC
66 AAGGATGTCATAGC
30176 TAAAAT
1 TAAAAT
30182 TAACGAATAA
Statistics
Matches: 226, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.00
79 221 0.98
80 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (79 bp):
TAAAATGCATATGGGTGCATTATCAGCATAAAACAATAATGCATATGGGTGCATTATTGGCATGA
AAGGATGTCATAGC
Found at i:29985 original size:34 final size:34
Alignment explanation
Indices: 29942--30158 Score: 164
Period size: 34 Copynumber: 5.7 Consensus size: 34
29932 TCATAGTTAA
*
29942 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
29976 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
*
30019 GAAATGCATATGGGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
30055 AATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
* * *
30098 GAAATGCATATGAGTGCATTATCGGTATAAAACAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
30134 AATGCATATGGGTGCATTATTGGCA
1 AATGCATATGGGTGCATTATCGGCA
30159 GGAAAGGATG
Statistics
Matches: 148, Mismatches: 13, Indels: 44
0.72 0.06 0.21
Matches are distributed among these distances:
34 70 0.47
35 6 0.04
36 2 0.01
37 2 0.01
38 4 0.03
39 2 0.01
40 2 0.01
41 3 0.02
42 2 0.01
43 2 0.01
44 6 0.04
45 47 0.32
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:30027 original size:45 final size:43
Alignment explanation
Indices: 29976--30173 Score: 162
Period size: 45 Copynumber: 4.9 Consensus size: 43
29966 ATAAAAGAAT
29976 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCTGA
* *
30021 AATGCATATGGGTGCATTATCGACAT-AAA-A-G-A-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTGA
30055 AATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAGCTGA
* * *
30100 AATGCATATGAGTGCATTATCGGTAT-AAA-A--CA-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTGA
*
30134 AATGCATATGGGTGCATTATTGGCAGGAAAGGATGTCATA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATA
30174 ACTAAAATTA
Statistics
Matches: 124, Mismatches: 11, Indels: 40
0.71 0.06 0.23
Matches are distributed among these distances:
34 46 0.37
35 6 0.05
36 2 0.02
37 2 0.02
38 3 0.02
39 3 0.02
40 3 0.02
41 3 0.02
42 2 0.02
43 1 0.01
44 6 0.05
45 47 0.38
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGCTGA
Found at i:30618 original size:21 final size:22
Alignment explanation
Indices: 30579--30620 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
30569 TCAATTTTTT
*
30579 TAATATTTAAAAGTATCGATAA
1 TAATATATAAAAGTATCGATAA
*
30601 TAATATAT-AAAGTTTCGATA
1 TAATATATAAAAGTATCGATA
30621 TTTAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (22 bp):
TAATATATAAAAGTATCGATAA
Found at i:34137 original size:20 final size:20
Alignment explanation
Indices: 34114--34163 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
34104 CTAACGAGGT
34114 AGTATCGATACCATGGTAAG
1 AGTATCGATACCATGGTAAG
34134 AGTATCGATACCATGGTAAG
1 AGTATCGATACCATGGTAAG
34154 AGTATCGATA
1 AGTATCGATA
34164 TCAGACAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (20 bp):
AGTATCGATACCATGGTAAG
Found at i:34312 original size:95 final size:95
Alignment explanation
Indices: 34134--34316 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 95
34124 CCATGGTAAG
* * **
34134 AGTATCGATACCATGGTAAGAGTATCGATATCAGACAACATCGAATTTAAAATTGGTATAGATAC
1 AGTATCAATACCATGGTAAGAGTATCGATACCAGACAACATCGAAGCTAAAATTGGTATAGATAC
*
34199 CGGAAGGGGATATTGGTACCATATAATGGT
66 CGGAAGGGGATATCGGTACCATATAATGGT
* *
34229 AGTATCAATACCATGGTAAGGGTATCGATACCAGGA-AACATCGAAGCTAAAATTGGTATCGATA
1 AGTATCAATACCATGGTAAGAGTATCGATACCA-GACAACATCGAAGCTAAAATTGGTATAGATA
*
34293 CTGGAATGGGG-TATCGGTACCATA
65 CCGGAA-GGGGATATCGGTACCATA
34317 GTATAGAAGT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 72 0.92
96 6 0.08
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (95 bp):
AGTATCAATACCATGGTAAGAGTATCGATACCAGACAACATCGAAGCTAAAATTGGTATAGATAC
CGGAAGGGGATATCGGTACCATATAATGGT
Found at i:34328 original size:95 final size:93
Alignment explanation
Indices: 34115--34329 Score: 256
Period size: 95 Copynumber: 2.3 Consensus size: 93
34105 TAACGAGGTA
* * * *
34115 GTATCGATACCATGGTA-AGAGTATCGATACCATGGTAAGAGTATCGATATCAGACAACATCGAA
1 GTATCGGTACCATAGTATAGAGTATCAATACCATGGTAAGAGTATCGATACCAGACAACATCGAA
**
34179 TTTAAAATTGGTATAGATACCGGAAGGG
66 GCTAAAATTGGTATAGATACCGGAAGGG
* * *
34207 GATATTGGTACCATA-TAATGGTAGTATCAATACCATGGTAAGGGTATCGATACCAGGA-AACAT
1 G-TATCGGTACCATAGT-ATAG-AGTATCAATACCATGGTAAGAGTATCGATACCA-GACAACAT
* *
34270 CGAAGCTAAAATTGGTATCGATACTGGAATGGG
62 CGAAGCTAAAATTGGTATAGATACCGGAA-GGG
34303 GTATCGGTACCATAGTATAGAAGTATC
1 GTATCGGTACCATAGTATAG-AGTATC
34330 GGTAGTATCA
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
92 2 0.02
93 11 0.11
94 1 0.01
95 81 0.79
96 7 0.07
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (93 bp):
GTATCGGTACCATAGTATAGAGTATCAATACCATGGTAAGAGTATCGATACCAGACAACATCGAA
GCTAAAATTGGTATAGATACCGGAAGGG
Found at i:46949 original size:34 final size:34
Alignment explanation
Indices: 46906--47083 Score: 194
Period size: 34 Copynumber: 4.9 Consensus size: 34
46896 AAGCGATCAA
*
46906 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
46940 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATTGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A---AT
46983 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
47019 AATGCATATGGGTGAATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
47053 AATGCATATGAGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
47084 GATGCCATAA
Statistics
Matches: 123, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
34 84 0.68
35 3 0.02
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 3 0.02
45 25 0.20
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:51245 original size:14 final size:14
Alignment explanation
Indices: 51226--51255 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51216 GCAAGGGTAT
51226 CAGTACTGATACAA
1 CAGTACTGATACAA
*
51240 CAGTACTGGTACAA
1 CAGTACTGATACAA
51254 CA
1 CA
51256 TCGAATTTAA
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:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (14 bp):
CAGTACTGATACAA
Found at i:51685 original size:35 final size:35
Alignment explanation
Indices: 51646--51760 Score: 132
Period size: 35 Copynumber: 3.4 Consensus size: 35
51636 CACTTTATTA
51646 ATGGAAAGAATATTGATTATGTTATTTTTATATGT
1 ATGGAAAGAATATTGATTATGTTATTTTTATATGT
* * *
51681 ATGGAAAGAATATT-ATGAATG-AATTTATATATGT
1 ATGGAAAGAATATTGAT-TATGTTATTTTTATATGT
** *
51715 -T--TTATAATATTGATTATGTTATTTTTATATGT
1 ATGGAAAGAATATTGATTATGTTATTTTTATATGT
51747 ATGGAAAGAATATT
1 ATGGAAAGAATATT
51761 ATAAATGAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
31 10 0.16
32 13 0.21
33 2 0.03
34 13 0.21
35 24 0.39
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (35 bp):
ATGGAAAGAATATTGATTATGTTATTTTTATATGT
Found at i:51853 original size:34 final size:34
Alignment explanation
Indices: 51810--52234 Score: 175
Period size: 34 Copynumber: 10.9 Consensus size: 34
51800 TCATATTTAA
* *
51810 AATGCATATGGGTGCACTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
51844 AATGTATATGGGAGCATTATTGGCATGAAAGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA-A-G--A-A--T
51886 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
51922 AATGCATATGGGTGCATTATTGGAATGAAAAGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT--AAA-A-G--A-A--T
*
51965 GAAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCT
1 --AATGCATATGGGTGCATTATCGGCAT--AA-AA-G--A-A--T
* * *
52010 GAAATGCATATGGTTGCATTATTGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
52046 AATGCATATGAGTGCATTTTTGGCATGAAAGGATGCCATAGTT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
*
52089 GAAATGCATATGGGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
52125 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G----AA-T
* *
52168 GAAATACATATGGGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
52204 AATGCATATGAGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
52235 GATGCATTAA
Statistics
Matches: 316, Mismatches: 31, Indels: 88
0.73 0.07 0.20
Matches are distributed among these distances:
34 117 0.37
35 9 0.03
36 8 0.03
37 6 0.02
38 6 0.02
39 4 0.01
40 3 0.01
41 6 0.02
42 8 0.03
43 8 0.03
44 29 0.09
45 111 0.35
46 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:51939 original size:78 final size:79
Alignment explanation
Indices: 51809--52000 Score: 314
Period size: 78 Copynumber: 2.4 Consensus size: 79
51799 TTCATATTTA
* * * *
51809 AAATGCATATGGGTGCACTATCGACATAAAAGAATAATGTATATGGGAGCATTATTGGCATG-AA
1 AAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGAGCATTATTGGAATGAAA
51873 AGATGCCATAGCTG
66 AGATGCCATAGCTG
*
51887 AAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGAATGAAA
1 AAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGAGCATTATTGGAATGAAA
51952 AGATGCCATAGCTG
66 AGATGCCATAGCTG
* *
51966 AAATGCATATGGGTGCATTATTGGCATGAAAGAAT
1 AAATGCATATGGGTGCATTATCGGCATAAAAGAAT
52001 GCCATAGCTG
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 57 0.54
79 49 0.46
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (79 bp):
AAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGAGCATTATTGGAATGAAA
AGATGCCATAGCTG
Found at i:51973 original size:45 final size:44
Alignment explanation
Indices: 51922--52189 Score: 238
Period size: 45 Copynumber: 6.5 Consensus size: 44
51912 ATAAAAGAAT
51922 AATGCATATGGGTGCATTATTGGAATGAAAAGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGAATG-AAAGATGCCATAGCTGA
*
51967 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGAATGAAAG-ATGCCATAGCTGA
*
52012 AATGCATATGGTTGCATTATT-GACAT-AAA-A-G--A-A--T--
1 AATGCATATGGGTGCATTATTGGA-ATGAAAGATGCCATAGCTGA
* * * *
52046 AATGCATATGAGTGCATTTTTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGAATGAAA-GATGCCATAGCTGA
*
52091 AATGCATATGGGTGCATTA-TCGACAT-AAA-A-G--A-A--T--
1 AATGCATATGGGTGCATTATTGGA-ATGAAAGATGCCATAGCTGA
* *
52125 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGA
1 AATGCATATGGGTGCATTATTGGAATGAAA-GATGCCATAGCTGA
*
52170 AATACATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
52190 CGACATAAAA
Statistics
Matches: 182, Mismatches: 14, Indels: 54
0.73 0.06 0.22
Matches are distributed among these distances:
34 41 0.23
35 9 0.05
36 2 0.01
37 2 0.01
38 4 0.02
39 2 0.01
40 2 0.01
41 4 0.02
42 2 0.01
43 2 0.01
44 13 0.07
45 99 0.54
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGAATGAAAGATGCCATAGCTGA
Found at i:52050 original size:79 final size:79
Alignment explanation
Indices: 51967--52239 Score: 465
Period size: 79 Copynumber: 3.5 Consensus size: 79
51957 CCATAGCTGA
* * *
51967 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGTTGCATTAT
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
52032 TGACATAAAAGAAT
66 CGACATAAAAGAAT
* *
52046 AATGCATATGAGTGCATTTTTGGCATGAAAGGATGCCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
52111 CGACATAAAAGAAT
66 CGACATAAAAGAAT
* * *
52125 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATACATATGGGTGCATTAT
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
52190 CGACATAAAAGAAT
66 CGACATAAAAGAAT
52204 AATGCATATGAGTGCATTATTGGCATGAAAGGATGC
1 AATGCATATGAGTGCATTATTGGCATGAAAGGATGC
52240 ATTAAGGCAT
Statistics
Matches: 182, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 182 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
AATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CGACATAAAAGAAT
Found at i:52074 original size:124 final size:124
Alignment explanation
Indices: 51844--52124 Score: 438
Period size: 124 Copynumber: 2.3 Consensus size: 124
51834 ATAAAAGAAT
* *
51844 AATGTATATGGGAGCATTATTGGCATGAAAG-ATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
* *
51908 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGAATGAAAAGATGCCATAGCTGA
66 CGACATAAAAGAATAATGCATATGAGTGCATTATTGGAATGAAAAGATGCCATAGCTGA
*
51967 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGTTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
* * * * *
52032 TGACATAAAAGAATAATGCATATGAGTGCATTTTTGGCATGAAAGGATGCCATAGTTGA
66 CGACATAAAAGAATAATGCATATGAGTGCATTATTGGAATGAAAAGATGCCATAGCTGA
* * *
52091 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGAAT
52125 AATGCATATG
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
123 29 0.20
124 115 0.80
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (124 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTGAAATGCATATGGGTGCATTAT
CGACATAAAAGAATAATGCATATGAGTGCATTATTGGAATGAAAAGATGCCATAGCTGA
Found at i:52162 original size:203 final size:202
Alignment explanation
Indices: 51809--52203 Score: 637
Period size: 203 Copynumber: 2.0 Consensus size: 202
51799 TTCATATTTA
* *
51809 AAATGCATATGGGTGCACTATCGACATAAAAGAATAATGTATATGGGAGCATTATTGGCATGAAA
1 AAATGCATATGGGTGCACTATCGACATAAAAGAATAATGCATATGAGAGCATTATTGGCATGAAA
*
51874 GATGCCATAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAGAATAATGCATATGGGTGCAT
66 GATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGGTGCAT
* * * * *
51939 TATTGGAATGAAAAGATGCCATAGCTGAAATGCATATGGGTGCATTATTGGCATGAAAGAATGCC
131 TATTGGAATGAAAAGATGCCATAACTGAAATACATATGGGTGCATTATCGACATAAAAGAATGCC
52004 ATAGCTG
196 ATAGCTG
* * * * *
52011 AAATGCATATGGTTGCATTATTGACATAAAAGAATAATGCATATGAGTGCATTTTTGGCATGAAA
1 AAATGCATATGGGTGCACTATCGACATAAAAGAATAATGCATATGAGAGCATTATTGGCATGAAA
*
52076 GGATGCCATAGTTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGGTGCA
66 -GATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGGTGCA
* *
52141 TTATTGGCATGAAAGGATGCCATAACTGAAATACATATGGGTGCATTATCGACATAAAAGAAT
130 TTATTGGAATGAAAAGATGCCATAACTGAAATACATATGGGTGCATTATCGACATAAAAGAAT
52204 AATGCATATG
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
202 58 0.33
203 118 0.67
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (202 bp):
AAATGCATATGGGTGCACTATCGACATAAAAGAATAATGCATATGAGAGCATTATTGGCATGAAA
GATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATATGGGTGCAT
TATTGGAATGAAAAGATGCCATAACTGAAATACATATGGGTGCATTATCGACATAAAAGAATGCC
ATAGCTG
Found at i:55322 original size:10 final size:11
Alignment explanation
Indices: 55299--55324 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55289 GGATTTAATT
55299 AAATTTATCAA
1 AAATTTATCAA
55310 AAATTTATCAA
1 AAATTTATCAA
55321 AAAT
1 AAAT
55325 AATTCAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTTATCAA
Found at i:56550 original size:25 final size:25
Alignment explanation
Indices: 56516--56570 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
56506 GGGTTCGAGA
*
56516 GAAGCTAGTTATAGACATTTCATTT
1 GAAGCTAGTTACAGACATTTCATTT
56541 GAAGCTAGTTACAGACATTTCATTT
1 GAAGCTAGTTACAGACATTTCATTT
56566 GAAGC
1 GAAGC
56571 AGCAATTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (25 bp):
GAAGCTAGTTACAGACATTTCATTT
Found at i:62426 original size:44 final size:46
Alignment explanation
Indices: 62324--62428 Score: 169
Period size: 46 Copynumber: 2.3 Consensus size: 46
62314 TTTACCTAAT
62324 CTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAG
* *
62370 CTCGTAAGCTTATTTTACCAATATACTTGCCA-TT-ATTCCATAAG
1 CTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAG
*
62414 CTCGTAAACTTATTT
1 CTCGTAAGCTTATTT
62429 GCATGGTTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 23 0.41
45 2 0.04
46 31 0.55
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (46 bp):
CTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAG
Found at i:62593 original size:40 final size:40
Alignment explanation
Indices: 62533--62654 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
62523 ACCGTAGTGC
*
62533 TACACATAAGGTTGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
* *
62573 TACAAATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
62613 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
62653 TA
1 TA
62655 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:67901 original size:26 final size:26
Alignment explanation
Indices: 67872--68073 Score: 156
Period size: 26 Copynumber: 8.5 Consensus size: 26
67862 CGCATTAACA
67872 CATCCATTT-ATGCATTTTAATTATGG
1 CATCC-TTTCATGCATTTTAATTATGG
*
67898 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
*
67918 CATCCTTTCATGCCTTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
*
67944 CATCCTTTCATGCATTTTAATTATGT
1 CATCCTTTCATGCATTTTAATTATGG
*
67970 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
** *
67990 CATCC-TTCATTTATTTTCATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
* *
68015 AATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
* *
68035 CATCCTTTAATACATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
68061 CATCCTTTCATGC
1 CATCCTTTCATGC
68074 CTTAATGCAT
Statistics
Matches: 137, Mismatches: 19, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.04
20 30 0.22
21 8 0.06
22 5 0.04
23 5 0.04
24 8 0.06
25 12 0.09
26 64 0.47
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAATTATGG
Found at i:67993 original size:46 final size:46
Alignment explanation
Indices: 67943--68191 Score: 311
Period size: 46 Copynumber: 5.6 Consensus size: 46
67933 TTTAATTATG
**
67943 GCATCCTTTCATGCATTTTAATTATGTCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
** *
67989 GCATCC-TTCATTTATTTTCATTATGGAATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
* * *
68034 GCATCCTTTAATACATTTTAATTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
* *
68080 GCAT-CATTCTATGCATTTTCATTATGGAATCCTTTCATGCCTTAAT
1 GCATCCTTTC-ATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
*
68126 GCATCATTTCATGCA---T--TT-T--AATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
*
68164 GCATCCTTTCATGCATTTTAATCATGGA
1 GCATCCTTTCATGCATTTTAATTATGGA
68192 TTCGATTTAG
Statistics
Matches: 173, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
38 33 0.19
40 1 0.01
41 3 0.02
43 2 0.01
44 1 0.01
45 43 0.25
46 87 0.50
47 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAATTATGGAATCCTTTCATGCCTTAAT
Found at i:67999 original size:91 final size:88
Alignment explanation
Indices: 67943--68147 Score: 248
Period size: 91 Copynumber: 2.2 Consensus size: 88
67933 TTTAATTATG
* * * ***
67943 GCATCCTTTCATGCATTTTAATTATGTCATCCTTTCATGCCTTAATGCATCCTTCATTTATTTTC
1 GCATCCTTTAATACATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTCA--TGCCTTC
68008 ATTATGGAATCCTTTCATGCCTTAAT
64 A-TATGGAATCCTTTCATGCCTTAAT
* *
68034 GCATCCTTTAATACATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTCTATGCATTTT
1 GCATCCTTTAATACATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTC-ATGC--CTT
68099 CATTATGGAATCCTTTCATGCCTTAAT
63 CA-TATGGAATCCTTTCATGCCTTAAT
* * *
68126 GCATCATTTCATGCATTTTAAT
1 GCATCCTTTAATACATTTTAAT
68148 CCTTTCATGC
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
90 1 0.01
91 51 0.50
92 50 0.49
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (88 bp):
GCATCCTTTAATACATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTCATGCCTTCAT
ATGGAATCCTTTCATGCCTTAAT
Found at i:68150 original size:38 final size:38
Alignment explanation
Indices: 68107--68186 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
68097 TTCATTATGG
68107 AATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
1 AATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
*
68145 AATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 AATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
68183 AATC
1 AATC
68187 ATGGATTCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (38 bp):
AATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
Done.