Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2154
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: 53857
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Found at i:1033 original size:40 final size:39
Alignment explanation
Indices: 989--1120 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 39
979 CGGGTATGTC
989 CCCGAAGGCATTGTATGCTAGTGATTATTCCGGGCTAAGA
1 CCCGAAGGCATT-TATGCTAGTGATTATTCCGGGCTAAGA
* * * * *
1029 CCCGAAGGCATTT-TGTCGAGTTGCTATAAT-CGGGCTTATGT
1 CCCGAAGGCATTTATG-CTAG-TGAT-TATTCCGGGC-TAAGA
1070 CGCCGAAGGCA-TTATGCTAGTGATT-TATCCGGGCTAAGAA
1 C-CCGAAGGCATTTATGCTAGTGATTAT-TCCGGGCTAAG-A
1110 CCCG-AGGCATT
1 CCCGAAGGCATT
1121 GGTGGCGAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
38 7 0.10
39 13 0.18
40 29 0.40
41 12 0.17
42 11 0.15
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CCCGAAGGCATTTATGCTAGTGATTATTCCGGGCTAAGA
Found at i:1094 original size:80 final size:80
Alignment explanation
Indices: 937--1136 Score: 241
Period size: 81 Copynumber: 2.5 Consensus size: 80
927 GCGATGATAA
* *
937 CCGGACTAAGATCCGAAGGCA-TTTGTGCGATGTTGCTATATCCGGGTATGTCCCCGAAGGCATT
1 CCGGGCTAAGACCCGAAGGCATTTTGT-CGA-GTTGCTATATCCGGGTATGTCCCCGAAGGCATT
1001 GTATGCTAGTGA-TTATT
64 GTATGCTAGTGATTTA-T
*
1018 CCGGGCTAAGACCCGAAGGCATTTTGTCGAGTTGCTATAAT-CGGGCTTATGTCGCCGAAGGCA-
1 CCGGGCTAAGACCCGAAGGCATTTTGTCGAGTTGCTAT-ATCCGGG--TATGTCCCCGAAGGCAT
1081 T-TATGCTAGTGATTTAT
63 TGTATGCTAGTGATTTAT
* *
1098 CCGGGCTAAGAACCCG-AGGCATTGGTGGCGAGTTGCTAT
1 CCGGGCTAAG-ACCCGAAGGCATT-TTGTCGAGTTGCTAT
1137 TATGCTGGCT
Statistics
Matches: 107, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
80 41 0.38
81 46 0.43
82 20 0.19
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTTGTCGAGTTGCTATATCCGGGTATGTCCCCGAAGGCATTGT
ATGCTAGTGATTTAT
Found at i:10077 original size:47 final size:47
Alignment explanation
Indices: 9920--10360 Score: 584
Period size: 49 Copynumber: 9.3 Consensus size: 47
9910 GTGAACATGA
* *
9920 ATATATGAGATAAGGGCCTAATGGGCGATGTGATGAAATGTGAAAAGTGGTGT
1 ATATATGTGATAA-GGCCTAATGGCCGATGTGATG-AATGTG-AAA---GTGT
9973 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
10022 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
10069 ATATATGTGATAAGGCCCTAAT-GCCGATGTGATG-ATGTGAAAGTGT
1 ATATATGTGATAAGG-CCTAATGGCCGATGTGATGAATGTGAAAGTGT
10115 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
10164 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
10210 -TATATGTGATAA-G-CTAATAGG-CGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAAT-GGCCGATGTGATGAATGTGAAAGTGT
10254 ATATAATGTG-TAAGG-CTAAAT-GCCGATGTGATG-ATGTGAAAGTGT
1 ATAT-ATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGT
* **
10299 AATATATGTGATAAGGCCTAAT-GCC-AAGTGAATGTGTGTGGAAAGTGT
1 -ATATATGTGATAAGGCCTAATGGCCGATGTG-ATGAATGT-GAAAGTGT
*
10347 ATAAATGTGATAAG
1 ATATATGTGATAAG
10361 TCCGAAGGGC
Statistics
Matches: 363, Mismatches: 5, Indels: 46
0.88 0.01 0.11
Matches are distributed among these distances:
43 27 0.07
44 3 0.01
45 46 0.13
46 75 0.21
47 63 0.17
48 14 0.04
49 94 0.26
50 3 0.01
51 6 0.02
52 20 0.06
53 12 0.03
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (47 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
Found at i:10143 original size:142 final size:143
Alignment explanation
Indices: 9920--10360 Score: 629
Period size: 142 Copynumber: 3.1 Consensus size: 143
9910 GTGAACATGA
* *
9920 ATATATGAGATAAGGGCCTAATGGGCGATGTGATGAAATGTGAAAAGTGGTGTATATATGTGATA
1 ATATATGTGATAA-GGCCTAATAGGCGATGTGATG-AATGTG-AAA---GTGTATATATGTGATA
9985 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
60 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
10050 GTGATGAATGTGAAAGTGT
125 GTGATGAATGTGAAAGTGT
*
10069 ATATATGTGATAAGGCCCTAAT-GCCGATGTGATG-ATGTGAAAGTGTATATATGTGATAAGGCC
1 ATATATGTGATAAGG-CCTAATAGGCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
10132 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
65 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
10197 GAATGTGAAAGTG-
130 GAATGTGAAAGTGT
10210 -TATATGTGATAA-G-CTAATAGGCGATGTGATGAATGTGAAAGTGTATATAATGTG-TAAGG-C
1 ATATATGTGATAAGGCCTAATAGGCGATGTGATGAATGTGAAAGTGTATAT-ATGTGATAAGGCC
*
10270 TAAAT-GCCGATGTGATG-ATGTGAAAGTGTA-ATATATGTGATAAGGCCTAAT-GCC-AAGTGA
65 T-AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG-
**
10330 ATGTGTGTGGAAAGTGT
128 ATGAATGT-GAAAGTGT
*
10347 ATAAATGTGATAAG
1 ATATATGTGATAAG
10361 TCCGAAGGGC
Statistics
Matches: 275, Mismatches: 7, Indels: 30
0.88 0.02 0.10
Matches are distributed among these distances:
134 4 0.01
135 9 0.03
136 28 0.10
137 18 0.07
138 36 0.13
139 25 0.09
140 17 0.06
142 99 0.36
145 3 0.01
146 5 0.02
148 13 0.05
149 18 0.07
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (143 bp):
ATATATGTGATAAGGCCTAATAGGCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTGT
Found at i:10345 original size:185 final size:188
Alignment explanation
Indices: 9907--10360 Score: 626
Period size: 185 Copynumber: 2.4 Consensus size: 188
9897 ACTGTGACTG
* * * * *
9907 GATGTGAACA-TGAATATATGAGATAAGGGCCTAATGGGCGATGTGATGAAATGTGAAAAGTGGT
1 GATGTGAA-AGTGTATATATGTGATAA-GGCCTAATGGCCGAAGTGATG-AATGTGGAAAGT-GT
*
9971 GTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
62 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG---ATATATGTGATAAG
10036 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCCTAATGCCGATGTGA
124 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CCTAATGCCGATGTGA
10101 T
188 T
*
10102 GATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT-GAAAGTGTATAT
1 GATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGGAAAGTGTATAT
10166 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATGTGATAA-G-CTAAT
66 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTAAT
10228 AGG-CGATGTGATGAATGTGAAAGTGTATATAATGTG-TAAGG-CTAAATGCCGATGTGAT
131 -GGCCGATGTGATGAATGTGAAAGTGTATAT-ATGTGATAAGGCCT-AATGCCGATGTGAT
**
10286 GATGTGAAAGTGTAATATATGTGATAAGGCCTAAT-GCC-AAGTGAATGTGTGTGGAAAGTGTAT
1 GATGTGAAAGTGT-ATATATGTGATAAGGCCTAATGGCCGAAGTG-ATGAATGTGGAAAGTGTAT
10349 A-A-ATGTGATAAG
64 ATATATGTGATAAG
10361 TCCGAAGGGC
Statistics
Matches: 244, Mismatches: 8, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
183 16 0.07
184 37 0.15
185 69 0.28
186 8 0.03
187 12 0.05
191 49 0.20
192 5 0.02
193 5 0.02
194 21 0.09
195 22 0.09
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (188 bp):
GATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAAGTGATGAATGTGGAAAGTGTATAT
ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATGTGATAAGGCCTAAT
GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGCCGATGTGAT
Found at i:10530 original size:36 final size:35
Alignment explanation
Indices: 10475--10551 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 35
10465 TCGAGCTCTA
* * *
10475 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGG
1 AAGA-CCGATAACTACGTGTGGAGATTATGTCCGGG
*
10511 TAAGACCGATAACTTCGTGTGGAGATTATGTCCGGG
1 -AAGACCGATAACTACGTGTGGAGATTATGTCCGGG
10547 AAGAC
1 AAGAC
10552 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 5 0.14
36 27 0.75
37 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (35 bp):
AAGACCGATAACTACGTGTGGAGATTATGTCCGGG
Found at i:11807 original size:39 final size:39
Alignment explanation
Indices: 11754--12021 Score: 405
Period size: 39 Copynumber: 6.8 Consensus size: 39
11744 GAGAATTGAG
*
11754 AGTGA-ATATCCGGGCTAAGTCCGAAGAGCATTCCTGCT
1 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCT
11792 AGTGATATATCCGGGCTAAGTCCCGAAGAGCCATTCGTGCT
1 AGTGATATATCCGGGCTAAGT-CCGAAGAG-CATTCGTGCT
11833 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCT
11872 AGTGATATATCCGGGCTAAGTCCCG-AGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
*
11911 AGTGATATATCCGGGCTAAGTCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCT
* **
11950 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCT-AAGTCCGAAGAGCATTCGTGCT
* * *
11990 GGTGTTATATCCGGGCTAGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTC-CGAAGAGCA
12022 ATCATGCTGG
Statistics
Matches: 211, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
38 8 0.04
39 112 0.53
40 61 0.29
41 30 0.14
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
AGTGATATATCCGGGCTAAGTCCGAAGAGCATTCGTGCT
Found at i:15981 original size:25 final size:25
Alignment explanation
Indices: 15953--16031 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
15943 CTAATGGCCG
15953 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
15978 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
16000 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
16025 ATGTGAT
1 ATGTGAT
16032 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:16092 original size:49 final size:47
Alignment explanation
Indices: 15906--16368 Score: 795
Period size: 47 Copynumber: 9.7 Consensus size: 47
15896 TTAGGATTCT
* * * *
15906 ATGTGATGGATGTGAACA-TGAAAATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
15953 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16000 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16047 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
16096 ATGTGATGAATGTCAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
16145 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16192 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
16241 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTATTGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16288 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG-CG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16334 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
16369 TCCCGAAGGG
Statistics
Matches: 403, Mismatches: 8, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
46 38 0.09
47 224 0.56
49 141 0.35
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:16119 original size:96 final size:95
Alignment explanation
Indices: 15906--16368 Score: 801
Period size: 96 Copynumber: 4.9 Consensus size: 95
15896 TTAGGATTCT
* * *
15906 ATGTGATGGATGTGAACA-TGA-AAATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAA-AGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
15969 AGTGTATATATGTGATAAGGCCTAATGGCCG
65 AGTGTATATATGTGATAAGGCCTAATGGCCG
16000 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
16064 GTGTATATATATGTGATAAGGCCTAATGGCCG
66 GTG--TATATATGTGATAAGGCCTAATGGCCG
*
16096 ATGTGATGAATGTCAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
16161 AGTGTATATATGTGATAAGGCCTAATGGCCG
65 AGTGTATATATGTGATAAGGCCTAATGGCCG
16192 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
16257 AGTGTATATATGTGATAAGGCCTATTGGCCG
65 AGTGTATATATGTGATAAGGCCTAATGGCCG
16288 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGG-CGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
16351 GTGTATATATGTGATAAG
66 GTGTATATATGTGATAAG
16369 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 6, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
93 38 0.11
94 85 0.24
96 187 0.52
98 47 0.13
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (95 bp):
ATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:24298 original size:42 final size:42
Alignment explanation
Indices: 24232--24335 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
24222 CCTAACAAAC
* * * ** *
24232 GCCTGACACACTGGTGTGTAAGGCCATTTTGAGAGTTACACG
1 GCCTGACACATTGGCGTGTGAGGCCATTTCAAGAGTTACAAG
* *
24274 GCCTGCCACATTGGCGTGTGAGGCCATTTCAAGAGTTGCAAG
1 GCCTGACACATTGGCGTGTGAGGCCATTTCAAGAGTTACAAG
* *
24316 GCCTGGCACATGGGCGTGTG
1 GCCTGACACATTGGCGTGTG
24336 GGTTGGCCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (42 bp):
GCCTGACACATTGGCGTGTGAGGCCATTTCAAGAGTTACAAG
Found at i:26274 original size:42 final size:42
Alignment explanation
Indices: 26213--26294 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
26203 GGTGTAGGGG
* * *
26213 ACACATGGCCAGATCACACGCCTATGGGGCTGCCCGTGTGTC
1 ACACACGGCCAGATCACACGCCCATGGGGCTACCCGTGTGTC
* *
26255 ACACACGGCCTAGA-CACACGCCCATGTGTCTACCCGTGTG
1 ACACACGGCC-AGATCACACGCCCATGGGGCTACCCGTGTG
26295 GACAAAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (42 bp):
ACACACGGCCAGATCACACGCCCATGGGGCTACCCGTGTGTC
Found at i:27625 original size:56 final size:56
Alignment explanation
Indices: 27539--27714 Score: 325
Period size: 56 Copynumber: 3.1 Consensus size: 56
27529 ACAAGGGATG
27539 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
27595 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAAAAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
27651 ATGGGCAAACCATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
27707 ATGGGCAA
1 ATGGGCAA
27715 TAAACTAATA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 116 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:27755 original size:112 final size:112
Alignment explanation
Indices: 27539--27757 Score: 248
Period size: 112 Copynumber: 2.0 Consensus size: 112
27529 ACAAGGGATG
27539 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
* * ** ** *** *
27604 ACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAAAAAGAAGC
66 ACATATCAAGAAACATGAAGTGAGAAAACAAAAAGAAAAAAAGAAGC
* *
27651 ATGGGCAAACCATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAAT
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-
* *
27716 AA-ACTAAT-AAGAAA-TTGAAG-GAAGAAAACAAAGAGAAAAAAA
65 AACA-T-ATCAAGAAACATGAAGTG-AGAAAACAAAAAGAAAAAAA
27758 TGTGTTCATC
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
111 1 0.01
112 79 0.89
113 8 0.09
114 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (112 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
ACATATCAAGAAACATGAAGTGAGAAAACAAAAAGAAAAAAAGAAGC
Found at i:29275 original size:79 final size:82
Alignment explanation
Indices: 29139--29323 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
29129 TCGAATGATG
* *
29139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
29203 TGTGCGAGATACTA-AT
66 TGTGCGAGATACTATAA
* * * **
29219 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
29281 TTGTGCGAGTTACTATAA
65 TTGTGCGAGATACTATAA
*
29299 T-CGGGCTATGACCCGAAGGCATTTG
1 TCCGGGCTAAGACCCGAAGGCATTTG
29324 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.62
80 34 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (82 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATAA
Found at i:29330 original size:40 final size:39
Alignment explanation
Indices: 29139--29323 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
29129 TCGAATGATG
* * * *
29139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
29179 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
29219 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29258 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29299 T-CGGGCTATGACCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
29324 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29345 original size:79 final size:79
Alignment explanation
Indices: 29192--29356 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
29182 GGACTAAGAT
* **
29192 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
29257 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
29271 CCGAAGGCATTTGTGCGAGTTACTATAAT-CGGGCTATGACCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTA-AATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29334 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29350 CCGAAGG
1 CCGAAGG
29357 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
79 48 0.64
80 27 0.36
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:33909 original size:48 final size:48
Alignment explanation
Indices: 33853--34118 Score: 381
Period size: 48 Copynumber: 5.5 Consensus size: 48
33843 ATGAGATCCT
33853 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
*
33901 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
* * ** * *
33949 GTGTAAGACCATGTCTGGGACATGGCATCAACGTTGATATAAGAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
* * * *
33997 GTGTAAGACCATGTCTGGGACATGGCATCAACGTTGATATGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
* *
34045 ATGTAAGACCATGTCTGGGACATGGCATC-GACATTGATGTGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAG-CATTGATATGTGTGCCA
* *
34093 GTGTAAGACCATATCTGGGATATGGC
1 GTGTAAGACCATGTCTGGGACATGGC
34119 GTTGATATGA
Statistics
Matches: 198, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
48 198 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCA
Found at i:34118 original size:144 final size:144
Alignment explanation
Indices: 33853--34118 Score: 451
Period size: 144 Copynumber: 1.8 Consensus size: 144
33843 ATGAGATCCT
* * * *
33853 GTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGTGCCAGTGTAAGACCATGTCTG
1 GTGTAAGACCATGTCTGGGACATGGCATCAACATTGATATGAGAGCCAATGTAAGACCATGTCTG
* *
33918 GGACATGGCATCGGCATTGATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACGT
66 GGACATGGCATCGACATTGATATGTGTGCCAGTGTAAGACCATATCTGGGACATGGCATCAACGT
33983 TGATATAAGAGCTA
131 TGATATAAGAGCTA
*
33997 GTGTAAGACCATGTCTGGGACATGGCATCAACGTTGATATGAGAGCCAATGTAAGACCATGTCTG
1 GTGTAAGACCATGTCTGGGACATGGCATCAACATTGATATGAGAGCCAATGTAAGACCATGTCTG
* *
34062 GGACATGGCATCGACATTGATGTGTGTGCCAGTGTAAGACCATATCTGGGATATGGC
66 GGACATGGCATCGACATTGATATGTGTGCCAGTGTAAGACCATATCTGGGACATGGC
34119 GTTGATATGA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 113 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (144 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAACATTGATATGAGAGCCAATGTAAGACCATGTCTG
GGACATGGCATCGACATTGATATGTGTGCCAGTGTAAGACCATATCTGGGACATGGCATCAACGT
TGATATAAGAGCTA
Found at i:35976 original size:16 final size:16
Alignment explanation
Indices: 35955--35996 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35945 TGAATAGATG
* *
35955 AAAGCCGAAAAGTCGA
1 AAAGCCAAAAAGTCAA
35971 AAAGCCAAAAAGTCAA
1 AAAGCCAAAAAGTCAA
*
35987 AAAGCTAAAA
1 AAAGCCAAAA
35997 CTTCAGCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.60, C:0.17, G:0.17, T:0.07
Consensus pattern (16 bp):
AAAGCCAAAAAGTCAA
Found at i:38545 original size:49 final size:49
Alignment explanation
Indices: 38379--38603 Score: 306
Period size: 49 Copynumber: 4.5 Consensus size: 49
38369 TGAGGTCGGA
* * * * *
38379 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* **
38430 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
*
38480 TGTGCAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
38529 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
38578 TGTGTAGTGCTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
38604 TGCATACCAG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 78 0.50
50 45 0.29
51 33 0.21
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:38554 original size:99 final size:100
Alignment explanation
Indices: 38378--38614 Score: 316
Period size: 99 Copynumber: 2.4 Consensus size: 100
38368 GTGAGGTCGG
* *
38378 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACGTGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAGTACTAA
* **
38443 GTGCAGGCTACTACGTGTATCAGATGGTTAGGTCAC
66 GTGCAGGCTACTACGTGTACCAGATAATT-GGTCAC
* * * * *
38479 GTGTGCAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACGTGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAGTACTAA
*
38542 GTGCAGGCTACTACGTGTACCGGATAATTGGTCAC
66 GTGCAGGCTACTACGTGTACCAGATAATTGGTCAC
* * * *
38577 ATGTGTAGTGCTATGTGCAGGCTACTATGCATACCAGA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
38615 TAGCTTTGGC
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 37 0.31
99 45 0.38
100 1 0.01
101 35 0.30
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (100 bp):
ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAGTACTAA
GTGCAGGCTACTACGTGTACCAGATAATTGGTCAC
Found at i:45477 original size:40 final size:40
Alignment explanation
Indices: 45383--45527 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
45373 TACTCGAATG
*
45383 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
45424 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
45464 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
45504 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
45528 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:53277 original size:39 final size:38
Alignment explanation
Indices: 53233--53387 Score: 154
Period size: 39 Copynumber: 3.9 Consensus size: 38
53223 CAGATATAAC
* *
53233 CACTAGCAC-AAGGCCTTCGAGTCTTAGCCCGGATATGGT
1 CACTAGCACAAATGCCTTCG-GACTTAGCCCGGATAT-GT
*
53272 CACTAGCATAAATGCCTTCGGACTTAGCCCGGATTATG-
1 CACTAGCACAAATGCCTTCGGACTTAGCCCGGA-TATGT
* *
53310 C-CTAGCACAAATGCCTTCGGATCTTAGTCCGGATGTAGT
1 CACTAGCACAAATGCCTTCGGA-CTTAGCCCGGATAT-GT
* *
53349 CGCTTAGCACAAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CAC-TAGCAC-AAATGCCTTC-GGACTTAGCCCGGATAT
53388 CATTCGAGTA
Statistics
Matches: 98, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
37 21 0.21
38 12 0.12
39 22 0.22
40 13 0.13
41 6 0.06
42 21 0.21
43 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (38 bp):
CACTAGCACAAATGCCTTCGGACTTAGCCCGGATATGT
Found at i:53326 original size:77 final size:79
Alignment explanation
Indices: 53235--53385 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 79
53225 GATATAACCA
* * *
53235 CTAGCACAAGGCCTTC-GAGTCTTAGCCCGGATATGGTCAC-TAGCA-TAAATGCCTTC-GGACT
1 CTAGCACAAGGCCTTCGGA-TCTTAGCCCGGATATAGTCACTTAGCACAAAAAGCCTTCGGGACT
53296 TAGCCCGGATTATGC
65 TAGCCCGGATTATGC
* * * *
53311 CTAGCACAAATGCCTTCGGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAAGCCTTCGGGACT
1 CTAGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGTCACTTAGCACAAAAAGCCTTCGGGACT
53376 TAGCCCGGAT
65 TAGCCCGGAT
53386 ATCATTCGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
76 7 0.11
77 25 0.40
78 7 0.11
79 9 0.14
80 15 0.24
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (79 bp):
CTAGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTCACTTAGCACAAAAAGCCTTCGGGACTT
AGCCCGGATTATGC
Done.