Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003575.1 Hibiscus syriacus cultivar Beakdansim tig00007545_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: 56540
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:176 original size:8 final size:8
Alignment explanation
Indices: 163--261 Score: 90
Period size: 8 Copynumber: 12.1 Consensus size: 8
153 TAATTGCTCG
163 ACTCTCAA
1 ACTCTCAA
171 ACTCTCTTAA
1 ACTCTC--AA
* *
181 ATTCTTAA
1 ACTCTCAA
*
189 ACTCTCTA
1 ACTCTCAA
*
197 ACTCTGAA
1 ACTCTCAA
*
205 ACTATCAA
1 ACTCTCAA
213 ACTCTCAA
1 ACTCTCAA
* **
221 ACTTTTGA
1 ACTCTCAA
*
229 ACTTTCAA
1 ACTCTCAA
237 ACTCTCAA
1 ACTCTCAA
245 ACTCTCAA
1 ACTCTCAA
*
253 ATTCTCAA
1 ACTCTCAA
261 A
1 A
262 ATGACTTCTA
Statistics
Matches: 72, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
8 66 0.92
10 6 0.08
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (8 bp):
ACTCTCAA
Found at i:838 original size:59 final size:60
Alignment explanation
Indices: 743--893 Score: 214
Period size: 59 Copynumber: 2.5 Consensus size: 60
733 ATAGGGATGT
* ** * * * *
743 ATTCATCTGCCAACTTCTTTGACGTCAATATGGATATGCCTTTTAGTTCC-AGGGGAGAC
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
*
802 ATTCATCTGCTAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
*
862 ATTCATCTTCCAGCTTCTTCAACCTCAATATA
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATA
894 CAGATGTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 43 0.53
60 38 0.47
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (60 bp):
ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
Found at i:2878 original size:15 final size:15
Alignment explanation
Indices: 2858--2886 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2848 ATTCGTCGTT
2858 GTCATCGTCTTGATA
1 GTCATCGTCTTGATA
2873 GTCATCGTCTTGAT
1 GTCATCGTCTTGAT
2887 CATTATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (15 bp):
GTCATCGTCTTGATA
Found at i:4810 original size:14 final size:14
Alignment explanation
Indices: 4791--4818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4781 ATAAATTATT
4791 TAAATAAATTCTAA
1 TAAATAAATTCTAA
4805 TAAATAAATTCTAA
1 TAAATAAATTCTAA
4819 CAATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAAATTCTAA
Found at i:6854 original size:29 final size:30
Alignment explanation
Indices: 6760--6854 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
6750 TACTTTTTCT
*
6760 TCTTAATTTATTAAATACATTTTATTCTTA
1 TCTTAATTTATTAAATATATTTTATTCTTA
* *
6790 ACTTAATTTATTAAATAT-TTTATATTATTA
1 TCTTAATTTATTAAATATATTT-TATTCTTA
* *
6820 -CTTTAAATT-TTAAATATATTTTATTCCTA
1 TC-TTAATTTATTAAATATATTTTATTCTTA
6849 TCTTAA
1 TCTTAA
6855 CTTAAAAGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
29 22 0.40
30 33 0.60
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (30 bp):
TCTTAATTTATTAAATATATTTTATTCTTA
Found at i:6915 original size:29 final size:29
Alignment explanation
Indices: 6883--6972 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
6873 TAAAAGTTAC
*
6883 TTATTCATATCTTAACTTATATATATATA
1 TTATTCTTATCTTAACTTATATATATATA
* * * * *
6912 TTATTCTTATTTTAACTTAAAAACACATA
1 TTATTCTTATCTTAACTTATATATATATA
*
6941 TTTATTCTTAACTTAACTTAATATATATATA
1 -TTATTCTTATCTTAACTT-ATATATATATA
6972 T
1 T
6973 AATCTTAATT
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
29 23 0.49
30 17 0.36
31 7 0.15
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (29 bp):
TTATTCTTATCTTAACTTATATATATATA
Found at i:6980 original size:29 final size:29
Alignment explanation
Indices: 6884--6985 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 29
6874 AAAAGTTACT
* *
6884 TATTCATATCTTAACTT-ATATATATATA
1 TATTCTTAACTTAACTTAATATATATATA
** * * * *
6912 TTATTCTTATTTTAACTTAAAAACACATATT
1 -TATTCTTAACTTAACTT-AATATATATATA
6943 TATTCTTAACTTAACTTAATATATATATA
1 TATTCTTAACTTAACTTAATATATATATA
* *
6972 TAATCTTAATTTAA
1 TATTCTTAACTTAA
6986 ACATATTTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 35 0.61
30 15 0.26
31 7 0.12
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTCTTAACTTAACTTAATATATATATA
Found at i:11228 original size:30 final size:30
Alignment explanation
Indices: 11188--11260 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
11178 TCCGAATAAC
11188 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
11218 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
11248 CTGTCCATAGGTC
1 CTATCCAGAGGTC
11261 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:11277 original size:30 final size:30
Alignment explanation
Indices: 11234--11314 Score: 72
Period size: 31 Copynumber: 2.6 Consensus size: 30
11224 AGAGGTCATA
* *
11234 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATAGGTCCCG
* * * *
11264 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATAGGTCCCG
* *
11295 TAGAACATAGGTATACTGTC
1 AAGAACCTAGGTA-ACTGTC
11315 TATATGTCTC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 11 0.28
31 29 0.73
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATAGGTCCCG
Found at i:12487 original size:64 final size:63
Alignment explanation
Indices: 12416--12556 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 63
12406 CTTTAGCATG
* * *
12416 TGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCAC-TCCTTA
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGG-TGCATCGATGCACTTCC-TA
* ** * *
12480 TGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAGGTGCATCGATGCACTTCCTG
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCACTTCCTA
*
12543 TGCATCGATACACA
1 TGCATCGATGCACA
12557 CTGAAGAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
63 26 0.39
64 40 0.61
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCACTTCCTA
Found at i:15990 original size:30 final size:30
Alignment explanation
Indices: 15954--16086 Score: 221
Period size: 30 Copynumber: 4.4 Consensus size: 30
15944 TCCGAAGGAC
* *
15954 CTATCCAGAGGTCATAAAGATTCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
15984 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
16014 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
16044 CTATCCAGGGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
16074 CTGTCCATAGGTC
1 CTATCCAGAGGTC
16087 CCGAAGAACC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:16103 original size:30 final size:30
Alignment explanation
Indices: 16060--16153 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
16050 AGGGGTCATA
* * *
16060 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
16090 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
16121 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
16152 AA
1 AA
16154 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:16103 original size:60 final size:60
Alignment explanation
Indices: 15954--16111 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 60
15944 TCCGAAGGAC
* ** *
15954 CTATCCAGAGGTCATAAAGATTCTTGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
16014 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGGGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * *
16074 CTGTCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGAACCTAGGT-AACTATCCA
16112 TATGTTCCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 78 0.90
61 9 0.10
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGAACCTAGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:16160 original size:31 final size:30
Alignment explanation
Indices: 16069--16164 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
16059 AAAGATCCTC
* * *
16069 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
16099 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
16130 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
16161 GGTA
1 GGTA
16165 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:17255 original size:24 final size:20
Alignment explanation
Indices: 17202--17278 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
17192 TTTCTCTTAA
17202 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
*
17222 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC---AAC
* *
17245 ATGTGCATCGATGCAGT-ACC
1 A-GTGCATCGATGCATTCAAC
*
17265 CGTGCATCGATGCA
1 AGTGCATCGATGCA
17279 CAAATCACCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.27
20 19 0.39
23 3 0.06
24 14 0.29
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:17335 original size:64 final size:63
Alignment explanation
Indices: 17247--17407 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
17237 TCTTTAGCAT
* * ** * * *
17247 GTGCATCGATGCAGTACCCGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTTCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
* ** *
17310 GATGCATCGATGCAC-TCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAG
1 G-TGCATCGATGCACTTCC-TATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
* *
17374 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATGCACA
17408 CTGAATAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 29 0.36
64 52 0.64
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTTCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
Found at i:22649 original size:46 final size:46
Alignment explanation
Indices: 22593--22728 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 46
22583 TTTTGAATAA
*
22593 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAGC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAAC
* * *
22639 ATGTATGCGAAGTAGAAATCATGCGGCTAGGTTTATTTTTCTCGAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TTGAAC
* * * * * *
22686 AAGCATGCGAATTAGATATCATGCAGTTAGGATTTTTTTTTTT
1 ATGTATGCGAACTAGAAATCATGCGGTTAGG-TTTATTTTTTT
22729 TTGTGAATGA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
46 38 0.50
47 30 0.39
48 8 0.11
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (46 bp):
ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAAC
Found at i:27422 original size:125 final size:125
Alignment explanation
Indices: 27169--27396 Score: 280
Period size: 125 Copynumber: 1.8 Consensus size: 125
27159 GAATACCCAC
* ** * * *
27169 ATTGGGGCATAACTGAACCCCCATCATTTTGAGATGACATGATTCGGACGAAGAAGGCATTGAGA
1 ATTGGGGCATAACTGAACCCACATCATGATGAAATGACAAGATTCAGACGAAGAAGGCATTGAGA
* ** * *
27234 ATAAGCCTTACAATTTGAGGTTTTGGGGTATTTTGAAGACCTGTACCAGTAAAAGATAAT
66 ATAAGCCTTACAACTTGAAATATTGGGGCATTTTGAAGACCTGTACCAGTAAAAGATAAT
* *
27294 ATTGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGATC-AAG-AGGACGTTGA
1 ATTGGGGCATAACTGAACCCACATCATGATGAAATGACAAGATTCAGA-CGAAGAAGG-CATTGA
* * *
27357 GAGTGAGTCTTACAACTTGAAATATTGGGGCATTTTGAAG
64 GAATAAGCCTTACAACTTGAAATATTGGGGCATTTTGAAG
27397 GCTTGTTCCA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
124 3 0.04
125 81 0.95
126 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (125 bp):
ATTGGGGCATAACTGAACCCACATCATGATGAAATGACAAGATTCAGACGAAGAAGGCATTGAGA
ATAAGCCTTACAACTTGAAATATTGGGGCATTTTGAAGACCTGTACCAGTAAAAGATAAT
Found at i:29726 original size:54 final size:54
Alignment explanation
Indices: 29087--29710 Score: 1050
Period size: 54 Copynumber: 11.6 Consensus size: 54
29077 GTAGTAAAGC
* * *
29087 AGAAGAAGATATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
29141 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
29195 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* *
29249 AGAAGAATATGTTTGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACTTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
**
29303 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGTAAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
29357 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
29411 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAAAAAGAGGGAGCGAACCTGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* *
29465 AGAAGAATATGTTTGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCAGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
29519 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
29573 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
29627 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * *
29681 AGAAGAAGATGTTCGAGTTCTATACTCCCT
1 AGAAGAATATGTTTGAGTTCCATACTCCCT
29711 GAACGAATAG
Statistics
Matches: 550, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 550 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (54 bp):
AGAAGAATATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
Found at i:29798 original size:55 final size:55
Alignment explanation
Indices: 29685--29808 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
29675 CCCGTAAGAA
* * * *
29685 GAAGA-TGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCATTTGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCAGACCCATTTGTC
* *
29739 GAAGATTGTTCGAG-TCTTATACTCCTTAAAAGAATAGGGAGCAGACCCGTTAT-TC
1 GAAGATTGTTCGAGTTC-TATACTCCCTAAAAGAATAGGGAGCAGACCCATT-TGTC
*
29794 GAAGATT-TTCAAGTT
1 GAAGATTGTTCGAGTT
29809 TCGCTTATCC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
54 12 0.20
55 46 0.78
56 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCAGACCCATTTGTC
Found at i:30396 original size:43 final size:43
Alignment explanation
Indices: 30335--30417 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
30325 TCATTTTTCA
* *
30335 ACAATATCACCATTGCAATTCAAGAGCAATACTGGCACAAAGC
1 ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
*
30378 ACAATATCACC-TACGCAATTTAAGAGCAATACTAGCACAA
1 ACAATATCACCAT-CGCAATTCAAGAGCAATACTAGCACAA
30418 GCAGTGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.19
Consensus pattern (43 bp):
ACAATATCACCATCGCAATTCAAGAGCAATACTAGCACAAAGC
Found at i:33761 original size:2 final size:2
Alignment explanation
Indices: 33756--33786 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
33746 ATCAAAAATG
*
33756 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33787 AATGTAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34234 original size:60 final size:59
Alignment explanation
Indices: 34097--34234 Score: 129
Period size: 60 Copynumber: 2.3 Consensus size: 59
34087 TAAAGTACAC
* *
34097 AAATAATCTCCTGACTATAAAATATTATTTTATTAAGTTCATCGACTATTAAAAATTATA
1 AAATAATCT-CTGACTATAAAACATTATTTTATTAAGTTCATCAACTATTAAAAATTATA
* * * * * *
34157 AAATGATC-CTTCAACTATAAAGCGTTATTTTATTGA-TTCCATCAACTATTAAAAGTTACT-
1 AAATAATCTC-T-GACTATAAAACATTATTTTATTAAGTT-CATCAACTATTAAAAATTA-TA
34217 AAATAATCATCTGACTAT
1 AAATAATC-TCTGACTAT
34235 TTATTATGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 55 0.89
61 2 0.03
62 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (59 bp):
AAATAATCTCTGACTATAAAACATTATTTTATTAAGTTCATCAACTATTAAAAATTATA
Done.