Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008359.1 Hibiscus syriacus cultivar Beakdansim tig00111098_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: 1252926
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:273 original size:32 final size:32
Alignment explanation
Indices: 232--296 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
222 AAGATTAAAA
232 GACACAAATTTCGTCCATATCGAATATCCTCT
1 GACACAAATTTCGTCCATATCGAATATCCTCT
264 GACACAAATTTCGTCCATATCGAATATCCTCT
1 GACACAAATTTCGTCCATATCGAATATCCTCT
296 G
1 G
297 TCATAGAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (32 bp):
GACACAAATTTCGTCCATATCGAATATCCTCT
Found at i:899 original size:43 final size:43
Alignment explanation
Indices: 838--993 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
828 ACCAGCGGTC
838 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
* * ** * * ** ***
881 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT---ACGTTG--TCTGGA-GTCCA-ATAT
*
931 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
*
975 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
994 ATTGTCTCTG
Statistics
Matches: 81, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
43 38 0.47
44 1 0.01
45 3 0.04
46 8 0.10
48 7 0.09
49 3 0.04
50 1 0.01
51 20 0.25
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
Found at i:1047 original size:98 final size:98
Alignment explanation
Indices: 815--1500 Score: 1175
Period size: 98 Copynumber: 7.0 Consensus size: 98
805 AATCGGGAAG
*
815 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
880 TCCTTCGTTGTGAAGTTGAAATTGG----GAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
909 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
974 TCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
*
1007 TTGTTTATTGACAACCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
1072 TCCTTCGTTGTGAAGTTAAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
1105 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1170 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
*
1203 TTGTTTATTGACAACCAGCGGTCCCTTGGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1268 TCCTTCGTTGTGAAGTTGAAATTGGC-CTTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAA
1301 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1366 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
* * *
1399 TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTTGCCGTGAAGTTGAACTTGCGTTGTCTGGAG
1 -T------TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
1464 TCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
59 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1501 GGTAAAACCT
Statistics
Matches: 564, Mismatches: 15, Indels: 15
0.95 0.03 0.03
Matches are distributed among these distances:
94 88 0.16
97 1 0.00
98 383 0.68
99 2 0.00
105 90 0.16
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
Found at i:1187 original size:196 final size:196
Alignment explanation
Indices: 716--1494 Score: 1262
Period size: 196 Copynumber: 3.9 Consensus size: 196
706 AAATTACTTG
* * * * *
716 TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGCCCAATCTCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
781 TTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTC
66 TTGTGAAGTTGAAATTGGCTCTG--A-----AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTC
*
846 GTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG---GAA
124 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAA
908 ATTGTTTA
189 ATTGTTTA
916 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
981 TTGTGAAGTTGAAATTGTCTCTGAAA-TTGTTTATTGACAACCAGCGGTCTCTTCGTCGTGAAGT
66 TTGTGAAGTTGAAATTGGCTCTGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
1045 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCCCTGAAATTGTT
131 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG-CCTGAAATTGTT
1110 TA
195 TA
1112 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
1177 TTGTGAAGTTGAAATTGGCTCTGAAA-TTGTTTATTGACAACCAGCGGTCCCTTGGTCGTGAAGT
66 TTGTGAAGTTGAAATTGGCTCTGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1241 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTTGAAATTGTT
131 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCC-TGAAATTGTT
1306 TA
195 TA
1308 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
1373 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTTGCCG
66 TTGTGAAGTTGAAATTGGCTCTG-AA---AG--TTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1438 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
125 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1495 ACTCTGGGTA
Statistics
Matches: 550, Mismatches: 17, Indels: 21
0.94 0.03 0.04
Matches are distributed among these distances:
192 87 0.16
193 2 0.00
195 2 0.00
196 288 0.52
197 2 0.00
198 1 0.00
200 83 0.15
203 85 0.15
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (196 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCTGAAATTGTTT
A
Found at i:1189 original size:43 final size:43
Alignment explanation
Indices: 1128--1385 Score: 122
Period size: 43 Copynumber: 5.4 Consensus size: 43
1118 ACCAGCGGTC
1128 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
1171 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT
*
1225 CCCTTGGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * * *
1269 CCTTCGTTGTGAAGTTGAAATTGGCCTTGAAAT-TGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-GCGTTG---TCTG--GAGT-CCAA-TA----T
1323 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1367 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1386 ATTGGCTCTG
Statistics
Matches: 154, Mismatches: 35, Indels: 52
0.64 0.15 0.22
Matches are distributed among these distances:
43 57 0.37
44 8 0.05
45 3 0.02
46 7 0.05
47 2 0.01
48 6 0.04
49 6 0.04
50 6 0.04
51 2 0.01
52 7 0.05
53 3 0.02
54 8 0.05
55 39 0.25
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1288 original size:294 final size:295
Alignment explanation
Indices: 648--1500 Score: 1259
Period size: 294 Copynumber: 2.8 Consensus size: 295
638 AATGCAAGAA
* * * * **
648 GCGTTGTTTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGAGAAATTAC
1 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G-TCT----CT--GAAATTGT
* * * * * *
713 TTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGCCCAATCTCCT
58 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
778 TCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTC
123 TCGTTGTGAAGTTGAAATTGGCTCTG--A-----AAGTTGTTTATTGACAACCAGCGGTCCCTTC
*
843 GTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG---
181 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
905 -GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
246 TGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
954 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGTTTATTGAC
1 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGTTTATTGAC
*
1019 AACCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
66 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
* *
1084 AAGTTAAAATTGGCCCTGAAA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAGTTGAAATTGGCTCTGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
1148 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTG
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTG
*
1213 ACAACCAGCGGTCCCTTGGTCGTGAAGTTGAACTT
261 ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
1248 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-CTTGAAATTGTTTATTGA
1 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTC-TGAAATTGTTTATTGA
1312 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
65 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
* * * *
1377 GAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTTGCCGTGAA
130 GAAGTTGAAATTGGCTCTG-AA---AG--TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
1442 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
189 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1501 GGTAAAACCT
Statistics
Matches: 509, Mismatches: 26, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
290 89 0.17
291 2 0.00
293 1 0.00
294 190 0.37
295 2 0.00
296 1 0.00
298 89 0.17
300 2 0.00
301 90 0.18
304 3 0.01
305 1 0.00
306 39 0.08
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (295 bp):
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTCTCTGAAATTGTTTATTGAC
AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
AAGTTGAAATTGGCTCTGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTTATTG
ACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
Found at i:1481 original size:105 final size:106
Alignment explanation
Indices: 1297--1500 Score: 365
Period size: 105 Copynumber: 1.9 Consensus size: 106
1287 AATTGGCCTT
*
1297 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
1362 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGA
* *
1403 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTTGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1467 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
66 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1501 GGTAAAACCT
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 90 0.96
106 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGA
Found at i:2349 original size:46 final size:46
Alignment explanation
Indices: 2279--2411 Score: 212
Period size: 46 Copynumber: 2.9 Consensus size: 46
2269 TGTTTTTCTA
2279 TTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCATCCTAAACGTT
1 TTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCATCCTAAACGTT
* * *
2325 TTTTTTTCAATTTAGGGTGTCCTTTCGGGTTTTCACCCTAAACGTT
1 TTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCATCCTAAACGTT
* * *
2371 TTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCATCCTAA
2412 GCGAAATATT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (46 bp):
TTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCATCCTAAACGTT
Found at i:10098 original size:20 final size:21
Alignment explanation
Indices: 10045--10106 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
10035 TTCCCCTGTG
10045 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
10069 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
10089 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
10107 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:22313 original size:6 final size:6
Alignment explanation
Indices: 22304--22373 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 6
22294 TAAAAAGAAA
* * *
22304 AAAAAT AAAAAT AATAAGT AAGAAAT AAAAAT AAGAAAT AAAGAAA AAGAAAA
1 AAAAAT AAAAAT AA-AAAT AA-AAAT AAAAAT AA-AAAT AAA-AAT AA-AAAT
*
22357 AGAAAAT ATAAAT AAAA
1 A-AAAAT AAAAAT AAAA
22374 CAAATGATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
6 22 0.42
7 28 0.54
8 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:22349 original size:8 final size:7
Alignment explanation
Indices: 22298--22361 Score: 59
Period size: 6 Copynumber: 9.9 Consensus size: 7
22288 ATTTAGTAAA
22298 AAGAAA-
1 AAGAAAT
22304 AA-AAAT
1 AAGAAAT
22310 AA-AAAT
1 AAGAAAT
* *
22316 AATAAGT
1 AAGAAAT
22323 AAGAAAT
1 AAGAAAT
22330 AA-AAAT
1 AAGAAAT
22336 AAGAAAT
1 AAGAAAT
22343 AAAGAAA-
1 -AAGAAAT
22350 AAGAAA-
1 AAGAAAT
22356 AAGAAA
1 AAGAAA
22362 ATATAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 3 0.06
6 28 0.55
7 14 0.27
8 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (7 bp):
AAGAAAT
Found at i:22353 original size:27 final size:24
Alignment explanation
Indices: 22295--22373 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 24
22285 TAAATTTAGT
22295 AAAAAGAAAAAAAATAAAAATAATA
1 AAAAAGAAAAAAAATAAAAATAA-A
**
22320 AGTAAGAAATAAAAATAAGAAATAAA
1 AAAAAGAAA-AAAAATAA-AAATAAA
*
22346 GAAAAAGAAAAAGAAAATATAAATAAA
1 -AAAAAG-AAAA-AAAATAAAAATAAA
22373 A
1 A
22374 CAAATGATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
25 7 0.16
26 10 0.23
27 18 0.41
28 9 0.20
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAAGAAAAAAAATAAAAATAAA
Found at i:22364 original size:21 final size:21
Alignment explanation
Indices: 22306--22361 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
22296 AAAAGAAAAA
* *
22306 AAATAAAAATAATAAGT-AAG
1 AAATAAAAATAAGAAATAAAG
22326 AAATAAAAATAAGAAATAAAG
1 AAATAAAAATAAGAAATAAAG
22347 AAA-AAGAAA-AAGAAA
1 AAATAA-AAATAAGAAA
22362 ATATAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 23 0.72
21 9 0.28
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (21 bp):
AAATAAAAATAAGAAATAAAG
Found at i:43788 original size:14 final size:14
Alignment explanation
Indices: 43769--43797 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43759 ACTGCAATTT
43769 TATTTTAATAAAAA
1 TATTTTAATAAAAA
43783 TATTTTAATAAAAA
1 TATTTTAATAAAAA
43797 T
1 T
43798 GAATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATTTTAATAAAAA
Found at i:56220 original size:18 final size:18
Alignment explanation
Indices: 56189--56230 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
56179 TCCATCAAAT
*
56189 ATTTTTTTTATTTTCTAA
1 ATTTTTTTTATTTTATAA
56207 ATTTTATTTT-TTTTATAA
1 ATTTT-TTTTATTTTATAA
56225 ATTTTT
1 ATTTTT
56231 AAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTTTATTTTATAA
Found at i:57054 original size:61 final size:62
Alignment explanation
Indices: 56980--57216 Score: 214
Period size: 61 Copynumber: 3.8 Consensus size: 62
56970 ATTTGGGTCC
* * * *
56980 TTTAAAAAGTAATTATATCAGAATAAAAATA-TTAATTTTGGCTTGGGGCCCACCCAGGCTG
1 TTTAAAAATTAATTATATTAGAATAAAAATAGTTAATTTTGGTTTGGGGCCCACCCAGACTG
* ** * **
57041 TTTAAAAATTAATTATATTACAATAAAAATTAGTT--TTTTCATTTTGGGCCCA-CTTGAACTG
1 TTTAAAAATTAATTATATTAGAATAAAAA-TAGTTAATTTTGGTTTGGGGCCCACCCAG-ACTG
* * ** * ** * *
57102 TTTAAAAATTAAATATATTAGAATAAAAATATTTTTTTTTGGTTTGTGGTTCACACAAACTG
1 TTTAAAAATTAATTATATTAGAATAAAAATAGTTAATTTTGGTTTGGGGCCCACCCAGACTG
* *
57164 TTTAAAAATTAATTATATTATAATAAAAATA-CTAATTTTTTGGTTTGGGGCCC
1 TTTAAAAATTAATTATATTAGAATAAAAATAGTTAA--TTTTGGTTTGGGGCCC
57217 TGGGCAGGTG
Statistics
Matches: 137, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
60 6 0.04
61 70 0.51
62 46 0.34
63 15 0.11
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (62 bp):
TTTAAAAATTAATTATATTAGAATAAAAATAGTTAATTTTGGTTTGGGGCCCACCCAGACTG
Found at i:59299 original size:2 final size:2
Alignment explanation
Indices: 59292--59318 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59282 TTGTTTAAGT
59292 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59319 CAATAAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62581 original size:16 final size:16
Alignment explanation
Indices: 62560--62598 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
62550 AATGATAATG
62560 TGACATTATCTTATGA
1 TGACATTATCTTATGA
*
62576 TGACATTATTTTATGA
1 TGACATTATCTTATGA
*
62592 TAACATT
1 TGACATT
62599 TTCACATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (16 bp):
TGACATTATCTTATGA
Found at i:76875 original size:21 final size:22
Alignment explanation
Indices: 76850--76895 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
76840 TAATTATACA
76850 TTTAGCACCTAAACTATC-ATT
1 TTTAGCACCTAAACTATCAATT
* *
76871 TTTAGTACCTAAACTTTCAATT
1 TTTAGCACCTAAACTATCAATT
76893 TTT
1 TTT
76896 TCAAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTAGCACCTAAACTATCAATT
Found at i:77982 original size:60 final size:60
Alignment explanation
Indices: 77907--78026 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
77897 TGTCTACATA
* *
77907 TGGTTGGATGAAAAAACAATTAGAAAAGCCCAAGCAATGTTGACAGGAGCTAAGAGAATC
1 TGGTTGGATGAAAAAACAATTAGAAAAGCCCAAGCAATGTTAACAGAAGCTAAGAGAATC
* * *
77967 TGGTTGGATGGAAAAACAATTAGAAAAGCCCAAGCAATGTTAACAGAAGTTAAGGGAATC
1 TGGTTGGATGAAAAAACAATTAGAAAAGCCCAAGCAATGTTAACAGAAGCTAAGAGAATC
78027 AAACCCAGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.19
Consensus pattern (60 bp):
TGGTTGGATGAAAAAACAATTAGAAAAGCCCAAGCAATGTTAACAGAAGCTAAGAGAATC
Found at i:78497 original size:106 final size:110
Alignment explanation
Indices: 78373--78599 Score: 248
Period size: 109 Copynumber: 2.1 Consensus size: 110
78363 AAATTAAAAT
* * * *
78373 CAAAATATTACAAAAGTTTAAGCTGA-CGGGACATTAGAAAT-CC-CGATAATAAAATAAGTTAA
1 CAAAATGTTACAAAAGTTTAAACTGATCGGGACATTAGAAATCCCACGACAACAAAATAAGTTAA
* * * *
78435 TTACTTATTTTGTTATTAAT-ATTATCAACATATTAGGTAGCG-C
66 TTACTCATTTTGTTATAAATAAATATCAACATACTAGGTAGCGTC
* * * * * *
78478 CTAAAATGTTACCAAAGTTTAAATTGATGGGGGCATTCGAAATCCCACGACAACAAAATATGTTA
1 C-AAAATGTTACAAAAGTTTAAACTGATCGGGACATTAGAAATCCCACGACAACAAAATAAGTTA
* * *
78543 ATTTCTCATTTTGTTATAAATAAATATTAACATACTAGGTTGCGTC
65 ATTACTCATTTTGTTATAAATAAATATCAACATACTAGGTAGCGTC
78589 CAATAATGTTA
1 CAA-AATGTTA
78600 TTTTGAATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
105 1 0.01
106 21 0.21
107 12 0.12
108 2 0.02
109 33 0.34
110 20 0.20
111 9 0.09
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (110 bp):
CAAAATGTTACAAAAGTTTAAACTGATCGGGACATTAGAAATCCCACGACAACAAAATAAGTTAA
TTACTCATTTTGTTATAAATAAATATCAACATACTAGGTAGCGTC
Found at i:79905 original size:3 final size:3
Alignment explanation
Indices: 79858--79892 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
79848 TTCATTTAAA
79858 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
79893 ATAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:82072 original size:26 final size:27
Alignment explanation
Indices: 82020--82076 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
82010 TAATTCTTTC
*
82020 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
82048 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
82074 TTT
1 TTT
82077 ATTTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 8 0.31
28 18 0.69
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:82081 original size:19 final size:19
Alignment explanation
Indices: 82057--82099 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
82047 ATTTTCATAA
*
82057 TATTTATATGTATAT-TATT
1 TATTTATATATATATAT-TT
82076 TATTTATATATATATATTT
1 TATTTATATATATATATTT
82095 TATTT
1 TATTT
82100 TATTTTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTATATATATATATTT
Found at i:82085 original size:15 final size:14
Alignment explanation
Indices: 82045--82104 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
82035 TATATACTTA
*
82045 TTATTTTCATAATAT
1 TTATTTT-ATATTAT
*
82060 TTATATGTATATTAT
1 TTAT-TTTATATTAT
82075 TTA-TTTATATATAT
1 TTATTTTATAT-TAT
* *
82089 ATATTTTATTTTAT
1 TTATTTTATATTAT
82103 TT
1 TT
82105 TCATGTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 6 0.17
14 9 0.25
15 19 0.53
16 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TTATTTTATATTAT
Found at i:82113 original size:15 final size:14
Alignment explanation
Indices: 82094--82132 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
82084 TATATATATT
82094 TTATTTTATTTTCA
1 TTATTTTATTTTCA
82108 TGTATTTTA-TTTCA
1 T-TATTTTATTTTCA
82122 TTA-TTTATTTT
1 TTATTTTATTTT
82133 TCTGTCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 7 0.30
15 7 0.30
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (14 bp):
TTATTTTATTTTCA
Found at i:92749 original size:16 final size:17
Alignment explanation
Indices: 92727--92791 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 17
92717 TATTACGTTT
*
92727 GAAGAAAAAAAAATGAA
1 GAAGAAAAAAAAAAGAA
92744 -AAGAAAAAAAAGAAGAA
1 GAAGAAAAAAAA-AAGAA
92761 GAAGAAGAAGAAAAAAGAA
1 GAAGAA-AA-AAAAAAGAA
92780 GAAGAAAAAAAA
1 GAAGAAAAAAAA
92792 GGGGGGTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
16 11 0.26
17 8 0.19
18 7 0.16
19 13 0.30
20 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAGAAAAAAAAAAGAA
Found at i:92752 original size:13 final size:13
Alignment explanation
Indices: 92727--92789 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
92717 TATTACGTTT
*
92727 GAAGAAAAAAAAA
1 GAAGAAGAAAAAA
92740 TGAA-AAGAAAAAA
1 -GAAGAAGAAAAAA
*
92753 -AAGAAG-AAGAA
1 GAAGAAGAAAAAA
92764 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
92777 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
92790 AAGGGGGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.14
12 9 0.21
13 25 0.58
14 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:92752 original size:15 final size:15
Alignment explanation
Indices: 92742--92792 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
92732 AAAAAAAATG
92742 AAAAGAA-AA-AAAA
1 AAAAGAAGAAGAAAA
92755 GAAGAAGAAGAAGAAGAA
1 -AA-AAGAAGAAGAA-AA
92773 AAAAGAAGAAGAAAA
1 AAAAGAAGAAGAAAA
92788 AAAAG
1 AAAAG
92793 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 2 0.06
15 12 0.36
16 13 0.39
17 4 0.12
18 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAGAAAA
Found at i:92759 original size:3 final size:3
Alignment explanation
Indices: 92753--92785 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
92743 AAAGAAAAAA
92753 AAG AAG AAG AAG AAG AAG AA- AA- AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
92786 AAAAAAGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:94240 original size:24 final size:23
Alignment explanation
Indices: 94197--94241 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
94187 GTTCATAATG
*
94197 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
94220 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
94242 AACTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:94250 original size:113 final size:113
Alignment explanation
Indices: 94051--94717 Score: 706
Period size: 113 Copynumber: 5.8 Consensus size: 113
94041 CCATCATTCA
* * *
94051 ATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * **
94116 TCGTAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCCTCACCCG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
* * * *
94164 GTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
94229 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
* * * * *
94277 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * * * *
94342 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATTATTTG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
* * *
94390 ATGGATCAACATTGCCAGGTGGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-A
1 ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGA
* * *
94452 A-TTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTG
63 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
* ** * *
94502 ATGGATCAGCTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGT
1 ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * * *
94563 TCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTC-ATCAC---------TTG
* * * * *
94620 ATTAGCATCAACCATT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 A-T-GGATC-AGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
94684 AGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
63 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
94718 AATGACTCTA
Statistics
Matches: 469, Mismatches: 62, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
106 7 0.01
107 1 0.00
108 6 0.01
109 40 0.09
110 1 0.00
112 74 0.16
113 236 0.50
114 1 0.00
115 5 0.01
116 12 0.03
118 3 0.01
119 1 0.00
120 36 0.08
121 4 0.01
123 3 0.01
124 39 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
ATGGATCAGCATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTTG
Found at i:94733 original size:124 final size:120
Alignment explanation
Indices: 94517--94796 Score: 395
Period size: 124 Copynumber: 2.3 Consensus size: 120
94507 TCAGCTTTTT
94517 CAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGAAGAAGAAGTTCACAATGAGAAGAGC
1 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCACAATGAGAAGAGC
* * * * * *
94579 TTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAACCATTC
66 TTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC---C
*
94637 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAG
1 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCACAATGAGAAGAG
* * *
94702 CTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCC
65 CTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACCC
*
94758 CAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
94797 AGAGAAAAAT
Statistics
Matches: 144, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
120 32 0.22
121 4 0.03
122 34 0.24
123 4 0.03
124 70 0.49
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (120 bp):
CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCACAATGAGAAGAGC
TTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACCC
Found at i:95016 original size:18 final size:17
Alignment explanation
Indices: 94928--95019 Score: 68
Period size: 18 Copynumber: 5.5 Consensus size: 17
94918 GAAGATACTC
94928 ATATT-TTTTATT-TAA
1 ATATTATTTTATTATAA
*
94943 ATATTATTTATATTATCA
1 ATATTATTT-TATTATAA
* *
94961 TTATTATTATAATTAT--
1 ATATTATT-TTATTATAA
*
94977 -TATTATTATTATTATTA
1 ATATTATT-TTATTATAA
*
94994 TTATTATTTTATTAATAA
1 ATATTATTTTATT-ATAA
95012 ATATTATT
1 ATATTATT
95020 ACAGGCCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
15 19 0.30
16 3 0.05
17 9 0.14
18 31 0.49
19 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTTTATTATAA
Found at i:95020 original size:3 final size:3
Alignment explanation
Indices: 94944--95007 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
94934 TTTATTTAAA
* *
94944 TAT TAT T-T ATAT TAT CAT TAT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
94989 TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TA
95008 ATAAATATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 3 0.06
3 50 0.93
4 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:95209 original size:16 final size:15
Alignment explanation
Indices: 95183--95212 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
95173 ACTCATCCAG
95183 AATGAACCCTAGGGT
1 AATGAACCCTAGGGT
95198 AATGATACCCTAGGG
1 AATGA-ACCCTAGGG
95213 ACCACGCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (15 bp):
AATGAACCCTAGGGT
Found at i:99511 original size:23 final size:23
Alignment explanation
Indices: 99485--99569 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
99475 CACAAAAGTG
*
99485 CCACGTAGAAATGTCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* * * *
99508 CCACATAGTATTGTCCCGAAGAA
1 CCACATAGAAATGTCCCAAAGGA
*** *
99531 CCGTGTAGAAATGTCCCAAATGA
1 CCACATAGAAATGTCCCAAAGGA
*
99554 CCACATAGAATTGTCC
1 CCACATAGAAATGTCC
99570 TGAATGACCG
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (23 bp):
CCACATAGAAATGTCCCAAAGGA
Found at i:99586 original size:46 final size:46
Alignment explanation
Indices: 99490--99586 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
99480 AAGTGCCACG
* **
99490 TAGAAATGTCCCAAAGGACCACATAGTATTGTCCCGAAGAACCGTG
1 TAGAAATGTCCCAAAGGACCACATAGAATTGTCCCGAAGAACCGCA
* *
99536 TAGAAATGTCCCAAATGACCACATAGAATTGTCCTGAATG-ACCGCA
1 TAGAAATGTCCCAAAGGACCACATAGAATTGTCCCGAA-GAACCGCA
99582 TAGAA
1 TAGAA
99587 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (46 bp):
TAGAAATGTCCCAAAGGACCACATAGAATTGTCCCGAAGAACCGCA
Found at i:99716 original size:45 final size:45
Alignment explanation
Indices: 99662--99774 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 45
99652 TTATAACAGT
* * *
99662 TCACATAACTTATATCACATAGGCATGTAATCACATAGTTTATTA
1 TCACATAACTTATATCACATAGGCATATAATCACATAGATCATTA
* * *** * *
99707 TCACATAACTCATGTCACATTTTCATATAGTCACATAGATCATTG
1 TCACATAACTTATATCACATAGGCATATAATCACATAGATCATTA
*
99752 TCATATAACTTATATCACATAGG
1 TCACATAACTTATATCACATAGG
99775 TTCATATCAC
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (45 bp):
TCACATAACTTATATCACATAGGCATATAATCACATAGATCATTA
Found at i:101155 original size:24 final size:23
Alignment explanation
Indices: 101111--101160 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
101101 AAAGAAAAGT
*
101111 AAAAGAAAAGCCAACTCAAAAGAC
1 AAAAGAAAAGCCAACT-AAAAAAC
101135 AAAAGAAAAGCCAAAC-AAAAAAC
1 AAAAGAAAAGCC-AACTAAAAAAC
101158 AAA
1 AAA
101161 CAAGAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 12 0.50
25 3 0.12
ACGTcount: A:0.70, C:0.18, G:0.10, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAGCCAACTAAAAAAC
Found at i:107880 original size:15 final size:15
Alignment explanation
Indices: 107860--107896 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
107850 AGCAATGTTA
107860 GCTGCTGGTTCTAGT
1 GCTGCTGGTTCTAGT
107875 GCTGCTGGTTCTAGT
1 GCTGCTGGTTCTAGT
*
107890 GTTGCTG
1 GCTGCTG
107897 TTGCTGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.35, T:0.41
Consensus pattern (15 bp):
GCTGCTGGTTCTAGT
Found at i:107895 original size:18 final size:17
Alignment explanation
Indices: 107854--107896 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 17
107844 TGCTTCAGCA
107854 ATGTTAGCTGCTGGTTCT
1 ATGTT-GCTGCTGGTTCT
107872 A-G-TGCTGCTGGTTCT
1 ATGTTGCTGCTGGTTCT
107887 AGTGTTGCTG
1 A-TGTTGCTG
107897 TTGCTGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 2 0.09
18 6 0.27
ACGTcount: A:0.09, C:0.16, G:0.33, T:0.42
Consensus pattern (17 bp):
ATGTTGCTGCTGGTTCT
Found at i:109799 original size:20 final size:21
Alignment explanation
Indices: 109765--109803 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
109755 TGCTACTGCA
*
109765 GAAACAGCAGGGTATGGGCTG
1 GAAACAGCAGAGTATGGGCTG
109786 GAAA-AGCAGAGTATGGGC
1 GAAACAGCAGAGTATGGGC
109804 AGCGTGGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.13, G:0.41, T:0.13
Consensus pattern (21 bp):
GAAACAGCAGAGTATGGGCTG
Found at i:113611 original size:21 final size:22
Alignment explanation
Indices: 113577--113618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
113567 CTATCCCTAA
*
113577 CTTAAAACTATAAATTATAATC
1 CTTAAAACTATAAATCATAATC
*
113599 CTTAAACCT-TAAATCATAAT
1 CTTAAAACTATAAATCATAAT
113619 ATCATTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (22 bp):
CTTAAAACTATAAATCATAATC
Found at i:113942 original size:21 final size:21
Alignment explanation
Indices: 113918--113983 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
113908 GCAAATTCGC
113918 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** *
113939 GTTGAAAATAGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
113959 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
113980 GTTG
1 GTTG
113984 AAAATCGCCC
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:113969 original size:41 final size:41
Alignment explanation
Indices: 113922--114036 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 41
113912 ATTCGCGTTG
*
113922 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
** *
113963 CATTTCGCGTTGCGATAGTTGAAAATCGC-CCGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
114003 CATTTCGC---GCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
114037 AGTCTACAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
37 18 0.27
38 5 0.07
40 16 0.24
41 28 0.42
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:114056 original size:22 final size:22
Alignment explanation
Indices: 114028--114102 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
114018 TTGAAAATCG
114028 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
114050 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
114069 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
114091 TGTTGCGATAGT
1 CGTTGCGATAGT
114103 TTAAAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 10 0.24
20 5 0.12
21 5 0.12
22 21 0.51
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:114092 original size:19 final size:20
Alignment explanation
Indices: 114028--114092 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
114018 TTGAAAATCG
114028 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAG-T-T
** * *
114050 CGTTGCGATTTTCCA-AATT
1 CGTTGCGATAGTCTACAGTT
114069 CGTTGCGATAGTCTACAGTT
1 CGTTGCGATAGTCTACAGTT
114089 -GTTG
1 CGTTG
114093 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.50
20 4 0.12
21 1 0.03
22 12 0.35
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCTACAGTT
Found at i:114215 original size:22 final size:22
Alignment explanation
Indices: 114191--114272 Score: 118
Period size: 22 Copynumber: 3.8 Consensus size: 22
114181 CCACGACCAC
114191 GAGACGAGACGAGACGGACG-G-C
1 GAGACGAGACG-GACGG-CGAGAC
114213 GAGACGAGACGGACGGCGAGAC
1 GAGACGAGACGGACGGCGAGAC
114235 GAGACGAGACGGACGGCGAGAC
1 GAGACGAGACGGACGGCGAGAC
114257 GAGACG-GACGG-CGGCG
1 GAGACGAGACGGACGGCG
114273 GCGGCACGCG
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.12
21 11 0.19
22 40 0.69
ACGTcount: A:0.29, C:0.23, G:0.48, T:0.00
Consensus pattern (22 bp):
GAGACGAGACGGACGGCGAGAC
Found at i:114217 original size:17 final size:17
Alignment explanation
Indices: 114195--114269 Score: 105
Period size: 17 Copynumber: 4.1 Consensus size: 17
114185 GACCACGAGA
114195 CGAGACGAGACGGACGG
1 CGAGACGAGACGGACGG
114212 CGAGACGAGACGGACGGCGAG
1 CGAGACGAGACGGA---CG-G
114233 ACGAGACGAGACGGACGG
1 -CGAGACGAGACGGACGG
114251 CGAGACGAGACGGACGG
1 CGAGACGAGACGGACGG
114268 CG
1 CG
114270 GCGGCGGCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
17 33 0.62
18 1 0.02
19 2 0.04
20 2 0.04
21 1 0.02
22 14 0.26
ACGTcount: A:0.29, C:0.24, G:0.47, T:0.00
Consensus pattern (17 bp):
CGAGACGAGACGGACGG
Found at i:114244 original size:39 final size:39
Alignment explanation
Indices: 114190--114269 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
114180 ACCACGACCA
114190 CGAGACGAGACGAGACGGACGGCGAGACGAGACGGACGG
1 CGAGACGAGACGAGACGGACGGCGAGACGAGACGGACGG
114229 CGAGACGAGACGAGACGGACGGCGAGACGAGACGGACGG
1 CGAGACGAGACGAGACGGACGGCGAGACGAGACGGACGG
114268 CG
1 CG
114270 GCGGCGGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.24, G:0.46, T:0.00
Consensus pattern (39 bp):
CGAGACGAGACGAGACGGACGGCGAGACGAGACGGACGG
Found at i:116086 original size:26 final size:25
Alignment explanation
Indices: 116057--116117 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
116047 TCTTAATTTA
116057 TTATGAGAAAACAAATAATCTCTAAC
1 TTATGA-AAAACAAATAATCTCTAAC
* *
116083 TTATGAAAAA-TAATAATCTTTAAC
1 TTATGAAAAACAAATAATCTCTAAC
116107 TTA-GAAAAACA
1 TTATGAAAAACA
116118 CTTTCATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 6 0.19
24 15 0.48
25 4 0.13
26 6 0.19
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (25 bp):
TTATGAAAAACAAATAATCTCTAAC
Found at i:116506 original size:20 final size:20
Alignment explanation
Indices: 116483--116522 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
116473 ATTAAAAAGG
* *
116483 TAAAATTTAAAAATGATTAA
1 TAAAAATTAAAAATAATTAA
116503 TAAAAATTAAAAATAATTAA
1 TAAAAATTAAAAATAATTAA
116523 CCTCTATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAAATTAAAAATAATTAA
Found at i:116556 original size:37 final size:39
Alignment explanation
Indices: 116504--116595 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 39
116494 AATGATTAAT
* *
116504 AAAAATTAAAAATAATTAACCTCTATTGGATTT-TTCAA-
1 AAAAATT-ATAATAATTAACCTCTATTGCATTTATTCAAG
* * *
116542 AAATATTATAATAATTAACGTTTATTGCATTTAATTCAAG
1 AAAAATTATAATAATTAACCTCTATTGCATTT-ATTCAAG
116582 AAAAATTATAATAA
1 AAAAATTATAATAA
116596 ATTTGTGGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 21 0.47
38 6 0.13
39 5 0.11
40 13 0.29
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (39 bp):
AAAAATTATAATAATTAACCTCTATTGCATTTATTCAAG
Found at i:118047 original size:11 final size:12
Alignment explanation
Indices: 118000--118051 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
117990 ATGCTTAAAA
118000 TAAT-TTTATTT
1 TAATATTTATTT
*
118011 TATATATTTAATAT
1 TA-ATATTT-ATTT
118025 TAATATTATATTT
1 TAATATT-TATTT
118038 TAATA-TTATTT
1 TAATATTTATTT
118049 TAA
1 TAA
118052 ATAAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 10 0.29
12 3 0.09
13 16 0.46
14 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TAATATTTATTT
Found at i:118076 original size:29 final size:30
Alignment explanation
Indices: 117995--118108 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 30
117985 AATAAATGCT
* *
117995 TAAAATAATTTTATTTT-AT-ATATTTAATA
1 TAAAAT-ATTATATTTTAATAATATTTAAAA
* * *
118024 T-TAATATTATATTTTAATATTATTTTAAA
1 TAAAATATTATATTTTAATAATATTTAAAA
118053 TAAAATATTA-ATTATTAA-AATATTTAAAA
1 TAAAATATTATATT-TTAATAATATTTAAAA
**
118082 TATATTTATTAATATTTCTAATAATAT
1 TA-AAATATT-ATATTT-TAATAATAT
118109 AATATTATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
27 9 0.14
28 5 0.08
29 23 0.35
30 16 0.24
31 2 0.03
32 6 0.09
33 5 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAAATATTATATTTTAATAATATTTAAAA
Found at i:118136 original size:26 final size:25
Alignment explanation
Indices: 118095--118196 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 25
118085 ATTTATTAAT
* *
118095 ATTTCTAATAATATAAT-AT-TATA
1 ATTTTTAATATTATAATAATATATA
118118 ATTTTTAATATTATAATAATATACTCA
1 ATTTTTAATATTATAATAATATA-T-A
* *
118145 ATTATATTATTATTAT-ATAAGATATTA
1 ATT-T-TTAATATTATAATAATATA-TA
118172 TATTTTT-AT-TT-TAATAATATATA
1 -ATTTTTAATATTATAATAATATATA
118195 AT
1 AT
118197 AAATTATTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
22 2 0.03
23 18 0.28
24 11 0.17
25 3 0.05
26 3 0.05
27 6 0.09
28 12 0.19
29 9 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTTTTAATATTATAATAATATATA
Found at i:118171 original size:23 final size:23
Alignment explanation
Indices: 118145--118227 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
118135 AATATACTCA
*
118145 ATTATATTATTATTATATAAGAT
1 ATTATATTATTATTATATAAAAT
* * *
118168 ATTATATTTTTATTTTAATAATAT
1 ATTATATTATTATTAT-ATAAAAT
* *
118192 ATAATA-AATTATTA-ATAAAAT
1 ATTATATTATTATTATATAAAAT
118213 -TTATATTACTTATTA
1 ATTATATTA-TTATTA
118228 ATTTCATAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.09
21 7 0.15
22 6 0.13
23 19 0.40
24 11 0.23
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
ATTATATTATTATTATATAAAAT
Found at i:118781 original size:26 final size:26
Alignment explanation
Indices: 118745--118795 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
118735 TCGTGCTTGT
118745 AAAAATAATTTGAATCTAATATTTGG
1 AAAAATAATTTGAATCTAATATTTGG
118771 AAAAATAATTTGAATCTAATATTTG
1 AAAAATAATTTGAATCTAATATTTG
118796 TTTATAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (26 bp):
AAAAATAATTTGAATCTAATATTTGG
Found at i:130268 original size:21 final size:22
Alignment explanation
Indices: 130244--130326 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 22
130234 TTGGTGCAGA
*
130244 GGGAATCGATCCCCCCCATGA-
1 GGGAACCGATCCCCCCCATGAG
* ** *
130265 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATCCCCCCCATG-AG
*
130288 GGGAACCGATTCCCCCCCA-CAG
1 GGGAACCGA-TCCCCCCCATGAG
* *
130310 GGGAATCGATACCCCCC
1 GGGAACCGATCCCCCCC
130327 TGTGGTTCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 23 0.48
22 10 0.21
23 9 0.19
24 6 0.12
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATCCCCCCCATGAG
Found at i:138701 original size:21 final size:21
Alignment explanation
Indices: 138675--138727 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
138665 GTTTCCAGAT
*
138675 TCGCAACGTGAACATCAACTA
1 TCGCAACGCGAACATCAACTA
* *
138696 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCAACTA
*
138717 TCGCAATGCGA
1 TCGCAACGCGA
138728 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:138780 original size:42 final size:42
Alignment explanation
Indices: 138723--138892 Score: 285
Period size: 42 Copynumber: 4.1 Consensus size: 42
138713 ACTATCGCAA
138723 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
138763 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* *
138805 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
138845 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
138887 TGCGAT
1 TGCGAT
138893 AGTCGAAGTT
Statistics
Matches: 120, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
40 42 0.35
41 2 0.02
42 76 0.63
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:138832 original size:82 final size:82
Alignment explanation
Indices: 138731--138934 Score: 322
Period size: 82 Copynumber: 2.5 Consensus size: 82
138721 AATGCGATTT
*
138731 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
*
138796 AGTTCGTGTTGCGATAG
66 AGTTCGCGTTGCGATAG
138813 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
138878 AGTTCGCGTTGCGATAG
66 AGTTCGCGTTGCGATAG
* *
138895 TCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGAT
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGAT
138935 AGTCGAAGTT
Statistics
Matches: 114, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
82 87 0.76
84 17 0.15
86 10 0.09
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (82 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCGCGTTGCGATAG
Found at i:138909 original size:42 final size:41
Alignment explanation
Indices: 138781--139190 Score: 528
Period size: 42 Copynumber: 9.8 Consensus size: 41
138771 ATTCCAAATT
* *
138781 CGTTGCGA-TAGTCCAAGTTCGTGTTGCGATAGTCCAAGTT--
1 CGTTGCGATTATTCCAAGTTC--GTTGCGATAGTCGAAGTTCG
* * * *
138821 CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--
1 CGTTGCGATTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCG
*
138863 CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCG
138905 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
* *
138947 CGTTACGATTTATTCCAAGTTCATTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
138989 TGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
139031 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
139073 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAATTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
139115 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
139157 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTC
139191 TAAAATCGCA
Statistics
Matches: 347, Mismatches: 15, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
40 34 0.10
42 303 0.87
44 10 0.03
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
CGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
Found at i:139309 original size:5 final size:5
Alignment explanation
Indices: 139287--139327 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
139277 CGTATTACCA
139287 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGAC
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGAC
139328 TCGAGACGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:140102 original size:19 final size:19
Alignment explanation
Indices: 140078--140142 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 19
140068 TCGTTGCGAT
140078 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
140097 TTTGGAATAAATCGCAACGTGAA
1 TTTGGACT--ATCGCAAC--GAA
*
140120 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
140139 TTTG
1 TTTG
140143 TAATAAATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.34
21 16 0.42
23 9 0.24
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:140112 original size:21 final size:21
Alignment explanation
Indices: 140086--140157 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
140076 ATTTTGGACT
140086 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
140107 ATCGCAACGTGAACTTGGACT--
1 ATCGCAAC--GAATTTGGAATAA
*
140128 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
*
140149 ATCGTAACG
1 ATCGCAACG
140158 CGAACTGCGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 8 0.20
21 24 0.59
23 9 0.22
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:140138 original size:42 final size:42
Alignment explanation
Indices: 140079--140163 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
140069 CGTTGCGATT
*
140079 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
140121 TTGGACTATCGCAACGAATTTGTAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
140163 T
1 T
140164 GCGAACTTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:140484 original size:3 final size:3
Alignment explanation
Indices: 140476--140559 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
140466 ATTTCATGAA
140476 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
140524 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
140560 TTTAAAGAGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:147328 original size:15 final size:15
Alignment explanation
Indices: 147304--147350 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
147294 AGGGATTGCT
*
147304 GATGAGGATGAAGAA
1 GATGATGATGAAGAA
*
147319 GATGATGATGACAG-T
1 GATGATGATGA-AGAA
*
147334 GATGCTGATGAAGAA
1 GATGATGATGAAGAA
147349 GA
1 GA
147351 GACTGAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.36, T:0.19
Consensus pattern (15 bp):
GATGATGATGAAGAA
Found at i:147604 original size:27 final size:27
Alignment explanation
Indices: 147549--147607 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
147539 TTGGGGGTAG
* *
147549 TGATGACGAGGAAGATGGGGTTGAGGA
1 TGATGACGAGGAAGATGGGGATAAGGA
*
147576 TGATGACGAGGAAGA-GGTGGATAATGA
1 TGATGACGAGGAAGATGG-GGATAAGGA
147603 TGATG
1 TGATG
147608 TAGATTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.32, C:0.03, G:0.44, T:0.20
Consensus pattern (27 bp):
TGATGACGAGGAAGATGGGGATAAGGA
Found at i:149123 original size:21 final size:21
Alignment explanation
Indices: 149098--149143 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
149088 GATGAATGAA
*
149098 GAAGAAGATGCAGAAGAGGAG
1 GAAGAAGATGAAGAAGAGGAG
* * *
149119 GAAGAAGTTGAAGATGATGAG
1 GAAGAAGATGAAGAAGAGGAG
149140 GAAG
1 GAAG
149144 TGTTGCCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.41, T:0.11
Consensus pattern (21 bp):
GAAGAAGATGAAGAAGAGGAG
Found at i:150348 original size:21 final size:20
Alignment explanation
Indices: 150301--150351 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
150291 TAATGTTATT
150301 TAATA-TATAAAATAAAATA
1 TAATATTATAAAATAAAATA
* **
150320 TAAAATTATAAAATATATTTA
1 TAATATTATAAAATA-AAATA
150341 TAATATTATAA
1 TAATATTATAA
150352 TTTCCTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 13 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATATTATAAAATAAAATA
Found at i:155983 original size:2 final size:2
Alignment explanation
Indices: 155976--156024 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
155966 ACAAACCCTT
155976 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
156017 TA TA TA TA
1 TA TA TA TA
156025 CTAACATTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:160061 original size:31 final size:30
Alignment explanation
Indices: 160026--160106 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
160016 CCCAAAATAT
160026 AACTTTTAAAATTTTATATTTTTAGTCCCTA
1 AACTTTTAAAATTTTATATTTTTAGTCCC-A
* * * *
160057 AACTTTTATAACTTTATA-CTTTAGTTCCA
1 AACTTTTAAAATTTTATATTTTTAGTCCCA
* * *
160086 AACTTTCAAATTTTTACATTT
1 AACTTTTAAAATTTTATATTT
160107 CAATCACTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 14 0.36
30 9 0.23
31 16 0.41
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (30 bp):
AACTTTTAAAATTTTATATTTTTAGTCCCA
Found at i:162505 original size:32 final size:32
Alignment explanation
Indices: 162461--162560 Score: 98
Period size: 32 Copynumber: 3.1 Consensus size: 32
162451 GAGATCAGAT
162461 CACATACTAGTAAGTG-TGACATTAAGATAATG
1 CACATACTAGTAAGTGTTG-CATTAAGATAATG
*
162493 CACA-ACTGAGTAAGTGTTGCATTCAGATAATG
1 CACATACT-AGTAAGTGTTGCATTAAGATAATG
* * * * *
162525 CACAT-CAATGTTAGTGTCGCATTTAGAGAATG
1 CACATACTA-GTAAGTGTTGCATTAAGATAATG
162557 CACA
1 CACA
162561 ATAGTTACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.07
32 52 0.90
33 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (32 bp):
CACATACTAGTAAGTGTTGCATTAAGATAATG
Found at i:172217 original size:12 final size:11
Alignment explanation
Indices: 172149--172217 Score: 53
Period size: 9 Copynumber: 6.7 Consensus size: 11
172139 TTCATACCCG
172149 AAATAATATAT
1 AAATAATATAT
*
172160 ATATATATATAT
1 AAATA-ATATAT
172172 ATAATAATA-AT
1 A-AATAATATAT
172183 -AATAATA-AT
1 AAATAATATAT
172192 -AATAATA-AT
1 AAATAATATAT
*
172201 AAAT-AT-CAT
1 AAATAATATAT
172210 AAATAATA
1 AAATAATA
172218 ACCAGTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 26 0.52
10 5 0.10
11 6 0.12
12 10 0.20
13 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATAATATAT
Found at i:172218 original size:3 final size:3
Alignment explanation
Indices: 172150--172202 Score: 63
Period size: 3 Copynumber: 16.7 Consensus size: 3
172140 TCATACCCGA
172150 AAT AAT -AT ATAT ATAT ATAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
172198 AAT AA
1 AAT AA
172203 ATATCATAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 31 0.65
4 15 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:172988 original size:21 final size:21
Alignment explanation
Indices: 172962--173003 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
172952 AGTACCATGA
*
172962 ACATTGCTACAGTGCATCGAT
1 ACATTGCTACAGTGCACCGAT
172983 ACATTGCTACAGTGCACCGAT
1 ACATTGCTACAGTGCACCGAT
173004 GCACTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
ACATTGCTACAGTGCACCGAT
Found at i:173438 original size:200 final size:203
Alignment explanation
Indices: 173095--173497 Score: 753
Period size: 200 Copynumber: 2.0 Consensus size: 203
173085 AAACATTACA
173095 AAACTCTATCATATGATTTTACAAACCGATTAGAACATATAGGATTTAAACCTTTATTTACATGC
1 AAACTCTATCATATGATTTTACAAACCGATTAGAACATATAGGATTTAAACCTTTATTTACATGC
173160 TAACCTTTATCTTTATTACAAAAATACTATAATACATTTTTTTTCCTGATCTGATCTTTGGAAAG
66 TAACCTTTATCTTTATTACAAAAATACTATAATACATTTTTTTTCCTGATCTGATCTTTGGAAAG
173225 GAGGAATTGACCTGTCTTGCATAACTCTTATCAATC-TCCTCTTCTCAGAACC-ACGCGTG-AAC
131 GAGGAATTGACCTGTCTTGCATAACTCTTATCAATCTTCCTCTTCTCAGAACCTACGCGTGAAAC
173287 AATCACAC
196 AATCACAC
173295 AAACTCTATCATATGATTTTACAAACCGATTAGAACATATAGGATTTAAACCTTTATTTACATGC
1 AAACTCTATCATATGATTTTACAAACCGATTAGAACATATAGGATTTAAACCTTTATTTACATGC
173360 TAACCTTTATCTTTATTAC-AAAATAC-ATACTATACATTTTTTTTCCTGATCTGATCTTTGGAA
66 TAACCTTTATCTTTATTACAAAAATACTATA--ATACATTTTTTTTCCTGATCTGATCTTTGGAA
173423 AGGAGGAATTGACCTGTCTTGCATAACTCTTATCAATCTTCCTCTTCTCAGAACCTACGCGTGAA
129 AGGAGGAATTGACCTGTCTTGCATAACTCTTATCAATCTTCCTCTTCTCAGAACCTACGCGTGAA
173488 ACAATCACAC
194 ACAATCACAC
173498 GCTAAGTCGT
Statistics
Matches: 198, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
198 3 0.02
199 7 0.04
200 154 0.78
201 16 0.08
202 7 0.04
203 11 0.06
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (203 bp):
AAACTCTATCATATGATTTTACAAACCGATTAGAACATATAGGATTTAAACCTTTATTTACATGC
TAACCTTTATCTTTATTACAAAAATACTATAATACATTTTTTTTCCTGATCTGATCTTTGGAAAG
GAGGAATTGACCTGTCTTGCATAACTCTTATCAATCTTCCTCTTCTCAGAACCTACGCGTGAAAC
AATCACAC
Found at i:173936 original size:31 final size:31
Alignment explanation
Indices: 173900--173993 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
173890 CACGAAGGAC
* *
173900 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
173931 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
173962 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
173993 C
1 C
173994 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:174778 original size:20 final size:20
Alignment explanation
Indices: 174753--174816 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
174743 TCCATGCATT
174753 GATGCACCCTTTAATGAATC
1 GATGCACCCTTTAATGAATC
*
174773 GATGCACCCTTTAATGTATC
1 GATGCACCCTTTAATGAATC
*
174793 GATGCACCCTTTAATGCATC
1 GATGCACCCTTTAATGAATC
174813 GATG
1 GATG
174817 TACCTTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (20 bp):
GATGCACCCTTTAATGAATC
Found at i:179879 original size:25 final size:21
Alignment explanation
Indices: 179831--179872 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
179821 GTGAATCATA
*
179831 TGAAAATGTTCTATGTGTAAG
1 TGAAAATGTTCTATATGTAAG
179852 TGAACAATGTGTCTATATGTA
1 TGAA-AATGT-TCTATATGTA
179873 TATGTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (21 bp):
TGAAAATGTTCTATATGTAAG
Found at i:179885 original size:62 final size:60
Alignment explanation
Indices: 179815--179943 Score: 143
Period size: 62 Copynumber: 2.1 Consensus size: 60
179805 ATAAGCTTTC
** * * *
179815 TGATATGTGAATCATATGAAAATGTTCTATGTGTAAGTGAACAATGTGTCTATATGTATATG
1 TGATATGTGAATCATATGAAAATGAGCTATGTG-AA-AGAACAATGAGACTATATGTATATG
* * * * *
179877 TGATATGTGATTTATATGACAATGAGCTATGTGAAAGAACTATGAGACTATGTGTATATG
1 TGATATGTGAATCATATGAAAATGAGCTATGTGAAAGAACAATGAGACTATATGTATATG
179937 TGA-ATGT
1 TGATATGT
179944 ATGATAACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 4 0.07
60 23 0.40
61 2 0.04
62 28 0.49
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.37
Consensus pattern (60 bp):
TGATATGTGAATCATATGAAAATGAGCTATGTGAAAGAACAATGAGACTATATGTATATG
Found at i:187063 original size:31 final size:31
Alignment explanation
Indices: 187028--187183 Score: 144
Period size: 31 Copynumber: 5.0 Consensus size: 31
187018 CCCGAATGAC
* *
187028 CAGTCCATAGATTTCGAAGAACCTAGGTAAT
1 CAGTCCATAGATTTCGAAGAACATAGGTAAA
187059 CAGTCCAT--ATGTTCTGAAGAACATAGGTAAA
1 CAGTCCATAGAT-TTC-GAAGAACATAGGTAAA
**
187090 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTTCGAAGAACATAGGTAAA
* *
187121 CAGTCCAT-G-TGTCCCGAAGAACATAAGTAAA
1 CAGTCCATAGAT-T-TCGAAGAACATAGGTAAA
**
187152 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTTCGAAGAACATAGGTAAA
187183 C
1 C
187184 CCTCGACCCT
Statistics
Matches: 108, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
29 4 0.04
30 3 0.03
31 97 0.90
32 1 0.01
33 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGATTTCGAAGAACATAGGTAAA
Found at i:187109 original size:62 final size:62
Alignment explanation
Indices: 187042--187183 Score: 230
Period size: 62 Copynumber: 2.3 Consensus size: 62
187032 CCATAGATTT
* * * * *
187042 CGAAGAACCTAGGTAATCAGTCCATATGTTCTGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAAGTAAACAGTCCATATGTCC
*
187104 CGAAGAACATAGGTAAACAGTCCATGTGTCCCGAAGAACATAAGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAAGTAAACAGTCCATATGTCC
187166 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
187184 CCTCGACCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (62 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAAGTAAACAGTCCATATGTCC
Found at i:189869 original size:532 final size:532
Alignment explanation
Indices: 188865--189940 Score: 2037
Period size: 532 Copynumber: 2.0 Consensus size: 532
188855 GGCAGATTTC
*
188865 ACCAATTTGCATTTTTGGCTTATTCACTAATTCTATTAGCTCACCAAATGCACATGTATGCATAA
1 ACCAATTTGCATTTTTAGCTTATTCACTAATTCTATTAGCTCACCAAATGCACATGTATGCATAA
*
188930 ACCATAAATCACATAGAAATTAGGAGTCACTTCTTACCATAGTAACTCCTTCAATGGCTTACCGC
66 ACCACAAATCACATAGAAATTAGGAGTCACTTCTTACCATAGTAACTCCTTCAATGGCTTACCGC
188995 AAGCCAATGTTCATTTGATAACATAAATACAAATTAAATTTGCACTCACCAGGTATCTTTAGCTT
131 AAGCCAATGTTCATTTGATAACATAAATACAAATTAAATTTGCACTCACCAGGTATCTTTAGCTT
*
189060 GTAAACCTTCCTTAGAGATTTACATTTCATCCTTAAGCTTCTCTTTACATTTAATAATGTTTGAT
196 GTAAACCTTCCTTAGAGATTCACATTTCATCCTTAAGCTTCTCTTTACATTTAATAATGTTTGAT
*
189125 ATTGATTTCAAACACACAATATAAATGAGAATTATTACAAAACATATACAAATTCAAACCACATG
261 ATTGATTTCAAACACACAATATAAATGAGAATTATTAAAAAACATATACAAATTCAAACCACATG
189190 TTAGAATCTTACTAACATAGGCAGACATTAGAAAATAAATTCATAAAAATCTCCCGATGCTCATT
326 TTAGAATCTTACTAACATAGGCAGACATTAGAAAATAAATTCATAAAAATCTCCCGATGCTCATT
189255 TGATACTAATTTCATGTCACAATGTAAATGTTGACCTTAACACTTCTAATTGACCAATCAACTTC
391 TGATACTAATTTCATGTCACAATGTAAATGTTGACCTTAACACTTCTAATTGACCAATCAACTTC
189320 CTTTTTATCCAAATTTCACATAACATTTCACTTAAGTTCCCAACTTTTTCATATTTATGATTTGA
456 CTTTTTATCCAAATTTCACATAACATTTCACTTAAGTTCCCAACTTTTTCATATTTATGATTTGA
*
189385 ACCTCAGCTTTT
521 ACCTCAACTTTT
189397 ACCAATTTGCATTTTTAGCTTATTCACTAATTCTATTAGCTCACCAAATGCACATGTATGCATAA
1 ACCAATTTGCATTTTTAGCTTATTCACTAATTCTATTAGCTCACCAAATGCACATGTATGCATAA
189462 ACCACAAATCACATAGAAATTAGGAGTCACTTCTTACCATAGTAACTCCTTCAATGGCTTACCGC
66 ACCACAAATCACATAGAAATTAGGAGTCACTTCTTACCATAGTAACTCCTTCAATGGCTTACCGC
189527 AAGCCAATGTTCATTTGATAACATAAATACAAATTAAATTTGCACTCACCAGGTATCTTTAGCTT
131 AAGCCAATGTTCATTTGATAACATAAATACAAATTAAATTTGCACTCACCAGGTATCTTTAGCTT
189592 GTAAACCTTCCTTAGAGATTCACATTTCATCCTTAAGCTTCTCTTTACATTTAATAATGTTTGAT
196 GTAAACCTTCCTTAGAGATTCACATTTCATCCTTAAGCTTCTCTTTACATTTAATAATGTTTGAT
*
189657 ATTGATTTCAAACACACAATATAAATGAGAATTATTAAAAAACATATACAAATTTAAACCACATG
261 ATTGATTTCAAACACACAATATAAATGAGAATTATTAAAAAACATATACAAATTCAAACCACATG
* *
189722 TTAGAATCTTACTAACATAGGCAGACATTAGAAAATAAATTCCTAAAAATCTTCCGATGCTCATT
326 TTAGAATCTTACTAACATAGGCAGACATTAGAAAATAAATTCATAAAAATCTCCCGATGCTCATT
*
189787 TGATATTAATTTCATGAT-ACAATGTAAATGTTGACCTTAACACTTCTAATTGACCAATCAACTT
391 TGATACTAATTTCATG-TCACAATGTAAATGTTGACCTTAACACTTCTAATTGACCAATCAACTT
189851 CCTTTTTATCCAAATTTCACATAACATTTCACTTAAGTTCCCAACTTTTTCATATTTATGATTTG
455 CCTTTTTATCCAAATTTCACATAACATTTCACTTAAGTTCCCAACTTTTTCATATTTATGATTTG
189916 AACCTCAACTTTT
520 AACCTCAACTTTT
*
189929 ACTAACTTTGCA
1 ACCAA-TTTGCA
189941 AAATAATCCA
Statistics
Matches: 532, Mismatches: 10, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
532 525 0.99
533 7 0.01
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (532 bp):
ACCAATTTGCATTTTTAGCTTATTCACTAATTCTATTAGCTCACCAAATGCACATGTATGCATAA
ACCACAAATCACATAGAAATTAGGAGTCACTTCTTACCATAGTAACTCCTTCAATGGCTTACCGC
AAGCCAATGTTCATTTGATAACATAAATACAAATTAAATTTGCACTCACCAGGTATCTTTAGCTT
GTAAACCTTCCTTAGAGATTCACATTTCATCCTTAAGCTTCTCTTTACATTTAATAATGTTTGAT
ATTGATTTCAAACACACAATATAAATGAGAATTATTAAAAAACATATACAAATTCAAACCACATG
TTAGAATCTTACTAACATAGGCAGACATTAGAAAATAAATTCATAAAAATCTCCCGATGCTCATT
TGATACTAATTTCATGTCACAATGTAAATGTTGACCTTAACACTTCTAATTGACCAATCAACTTC
CTTTTTATCCAAATTTCACATAACATTTCACTTAAGTTCCCAACTTTTTCATATTTATGATTTGA
ACCTCAACTTTT
Found at i:191946 original size:146 final size:147
Alignment explanation
Indices: 191708--192005 Score: 562
Period size: 146 Copynumber: 2.0 Consensus size: 147
191698 ATAGATTATA
191708 CTATAATTTTAAATCAAATAAACACACATAAATATATTAAAATGATCATCCAGCTCAGTTGGTAA
1 CTATAATTTTAAATCAAATAAACACAC---AATATATTAAAATGATCATCCAGCTCAGTTGGTAA
191773 AGCACAACGTTCTTAACCTTAAGATCGTGGGATCGAATTCTACGGAGGGCATTTCATAATTTGGA
63 AGCACAACGTTCTTAACCTTAAGATCGTGGGATCGAATTCTACGGAGGGCATTTCATAATTTGGA
191838 GGTCTCTTACGAAAGCTGTT
128 GGTCTCTTACGAAAGCTGTT
191858 CTATAATTTTAAATCAAATAAACACAC-ATATATTAAAATGATCATCCAGCTCAGTTGGTAAAGC
1 CTATAATTTTAAATCAAATAAACACACAATATATTAAAATGATCATCCAGCTCAGTTGGTAAAGC
191922 ACAACGTTCTTAACCTTAAGATCGTGGGATCGAATTCTACGGAGGGCATTTCATAATTTGGAGGT
66 ACAACGTTCTTAACCTTAAGATCGTGGGATCGAATTCTACGGAGGGCATTTCATAATTTGGAGGT
191987 CTCTTACGAAAGCTGTT
131 CTCTTACGAAAGCTGTT
192004 CT
1 CT
192006 CAACCTGATG
Statistics
Matches: 148, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
146 121 0.82
150 27 0.18
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (147 bp):
CTATAATTTTAAATCAAATAAACACACAATATATTAAAATGATCATCCAGCTCAGTTGGTAAAGC
ACAACGTTCTTAACCTTAAGATCGTGGGATCGAATTCTACGGAGGGCATTTCATAATTTGGAGGT
CTCTTACGAAAGCTGTT
Found at i:199170 original size:14 final size:14
Alignment explanation
Indices: 199151--199228 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
199141 TTATATTACA
199151 TTTAAAAATGTATT
1 TTTAAAAATGTATT
*
199165 TTTAAAAATTTATAAT
1 TTTAAAAATGTAT--T
* *
199181 TATCAATAATGTATT
1 T-TTAAAAATGTATT
*
199196 TTT---AATATATT
1 TTTAAAAATGTATT
* *
199207 TTTAATAATGTAAT
1 TTTAAAAATGTATT
199221 TTTAAAAA
1 TTTAAAAA
199229 ATCTAAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
11 10 0.20
14 26 0.53
15 2 0.04
16 2 0.04
17 9 0.18
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (14 bp):
TTTAAAAATGTATT
Found at i:200266 original size:19 final size:20
Alignment explanation
Indices: 200227--200266 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
200217 TGGTTCACGG
*
200227 AATGTAAGATTATCAGTGGA
1 AATGTAAGATTACCAGTGGA
200247 AATGTAAGATTACCAG-GGA
1 AATGTAAGATTACCAGTGGA
200266 A
1 A
200267 TAGGGAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.25
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGGA
Found at i:207633 original size:16 final size:16
Alignment explanation
Indices: 207612--207651 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
207602 AGAAACCACA
207612 AAAGAATTAACAAATC
1 AAAGAATTAACAAATC
207628 AAAGAATTAACAAATC
1 AAAGAATTAACAAATC
207644 AAAGAATT
1 AAAGAATT
207652 GGATCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
AAAGAATTAACAAATC
Found at i:208613 original size:2 final size:2
Alignment explanation
Indices: 208606--208639 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
208596 CTACCGCCGT
*
208606 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
208640 CACACACGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209376 original size:2 final size:2
Alignment explanation
Indices: 209367--209396 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
209357 AAAATATAAA
209367 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
209397 ATCGGGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211934 original size:50 final size:51
Alignment explanation
Indices: 211859--211957 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 51
211849 AAACAAACCT
*
211859 CACGTGGCGCCAAATCAGCGTATAACGCGCTGCAG-GGGCGCGTCTTACCC
1 CACGTGGCGCCAAATCAGCGTATAACGCGCTACAGAGGGCGCGTCTTACCC
211909 CACGTGGCGCCAAATCAGCGTATAACGCGCTACAGAGGGCGCGTCTTAC
1 CACGTGGCGCCAAATCAGCGTATAACGCGCTACAGAGGGCGCGTCTTAC
211958 TGTAAAGGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 34 0.72
51 13 0.28
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.16
Consensus pattern (51 bp):
CACGTGGCGCCAAATCAGCGTATAACGCGCTACAGAGGGCGCGTCTTACCC
Found at i:213733 original size:15 final size:15
Alignment explanation
Indices: 213713--213746 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
213703 CATAAATTCG
213713 TAATTTAAAAAAATA
1 TAATTTAAAAAAATA
*
213728 TAATTTTAAAAAATA
1 TAATTTAAAAAAATA
213743 -AATT
1 TAATT
213747 ATACATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTTAAAAAAATA
Found at i:214493 original size:96 final size:99
Alignment explanation
Indices: 214385--214601 Score: 332
Period size: 100 Copynumber: 2.2 Consensus size: 99
214375 ATGAATGAAC
* *
214385 ACGAACATAAATGAAC-AA-AAAAA-TTCTTGTTCATGTACGTTCATTAAGAAATGTAGCTTGTT
1 ACGAACACAAATGAACGAACAAAAAGTTCTTGTTCATGTACGTTCATTAAGAAATGTAGATTGTT
214447 AGTGTTCGTTCATGTTCATTCATTTAAATGATAA
66 AGTGTTCGTTCATGTTCATTCATTTAAATGATAA
* * *
214481 ACGAACACAAATGAACGAACAAAAAGTTTCTTGTTCATGTTCGTTCGTTAAGGAATGTAGATTGT
1 ACGAACACAAATGAACGAACAAAAAG-TTCTTGTTCATGTACGTTCATTAAGAAATGTAGATTGT
* * *
214546 TCGTGTTCGTTCATGTTCGTTTATTTAAATGATAA
65 TAGTGTTCGTTCATGTTCATTCATTTAAATGATAA
214581 ACGAACACAAATGAACGAACA
1 ACGAACACAAATGAACGAACA
214602 TAAACGAACG
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
96 15 0.14
97 2 0.02
98 5 0.05
100 87 0.80
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (99 bp):
ACGAACACAAATGAACGAACAAAAAGTTCTTGTTCATGTACGTTCATTAAGAAATGTAGATTGTT
AGTGTTCGTTCATGTTCATTCATTTAAATGATAA
Found at i:214894 original size:14 final size:14
Alignment explanation
Indices: 214874--214936 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 14
214864 GTTTGGGCTA
*
214874 AACATAAATGAATG
1 AACATAAACGAATG
*
214888 CACATAAACG-A-G
1 AACATAAACGAATG
*
214900 -A-ATAAACAAATG
1 AACATAAACGAATG
*
214912 AACATAAATGAATG
1 AACATAAACGAATG
214926 AACATAAACGA
1 AACATAAACGA
214937 GTATAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 6 0.15
11 2 0.05
12 2 0.05
13 2 0.05
14 27 0.69
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.16
Consensus pattern (14 bp):
AACATAAACGAATG
Found at i:215572 original size:2 final size:2
Alignment explanation
Indices: 215565--215599 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
215555 AATACCATCA
215565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
215600 AGCCATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:220386 original size:2 final size:2
Alignment explanation
Indices: 220379--220405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
220369 ACAGTAAACG
220379 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
220406 GTCGCAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:220829 original size:29 final size:28
Alignment explanation
Indices: 220773--220829 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
220763 TAAATTGAAA
*
220773 ATAAAATAAAGAAAAAAACTAACAACAT
1 ATAAAATAAAGAAAAAAACAAACAACAT
* * *
220801 ATAAAATAAGGACAAAAAGCAAACGACAT
1 ATAAAATAAAGA-AAAAAACAAACAACAT
220830 GACCAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (28 bp):
ATAAAATAAAGAAAAAAACAAACAACAT
Found at i:221094 original size:12 final size:13
Alignment explanation
Indices: 221069--221097 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
221059 AGATATATAT
221069 AATAAATAAATAA
1 AATAAATAAATAA
221082 AATAAAT-AATAA
1 AATAAATAAATAA
221094 AATA
1 AATA
221098 CTAATAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:221154 original size:42 final size:46
Alignment explanation
Indices: 221061--221166 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 46
221051 ATGCATATAG
221061 ATATATATAATAAATAAATAAAATAAATAATAAAATACTAATAACAC
1 ATATATATAATAAATAAATAAAATAAATAAT-AAATACTAATAACAC
*
221108 ATATATGTAA-AAATAAAATAAAA-AAACTAAT-AATACT-ATAA-A-
1 ATATATATAATAAAT-AAATAAAATAAA-TAATAAATACTAATAACAC
221150 ATATATA-AATAAA-AAAT
1 ATATATATAATAAATAAAT
221167 TAGAATTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
40 4 0.07
41 2 0.04
42 9 0.17
43 1 0.02
44 4 0.07
45 6 0.11
46 7 0.13
47 21 0.39
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (46 bp):
ATATATATAATAAATAAATAAAATAAATAATAAATACTAATAACAC
Found at i:222968 original size:106 final size:106
Alignment explanation
Indices: 222783--222987 Score: 358
Period size: 106 Copynumber: 1.9 Consensus size: 106
222773 TTGTGTTGCT
222783 TCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGAC
1 TCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGAC
222848 AACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTC
66 AACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTC
* * *
222889 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAGTTGTTTGTTGA
1 TCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAG-TGTTTGTTGA
*
222953 CAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTG
65 CAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTG
222988 TGCTATCTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
105 7 0.07
106 87 0.93
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (106 bp):
TCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGAC
AACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTC
Found at i:223033 original size:65 final size:64
Alignment explanation
Indices: 222902--223054 Score: 193
Period size: 65 Copynumber: 2.4 Consensus size: 64
222892 AGTCCAATAT
* * * * * *
222902 CCTTCGCTGTGAAGTTGAAATTG-GCTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAACGGCC
* *
222965 CCTTCGTTGTGAAGTTGAACTTGTGCTATCTTAAACTGGGAAATT-TTTGTTGACAACCAACGGT
1 CCTTCGTTGTGAAGTTGAACTTGTGC--TCTGAAACTGGGAAATTGTTTGTTGACAACCAACGGC
223029 C
64 C
*
223030 CCTTCGTCGTGAAGTTGAACTTGTG
1 CCTTCGTTGTGAAGTTGAACTTGTG
223055 TTGTCTCGAG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 21 0.27
64 2 0.03
65 41 0.53
66 14 0.18
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAACTTGTGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAACGGCC
Found at i:223060 original size:171 final size:162
Alignment explanation
Indices: 222796--223152 Score: 509
Period size: 171 Copynumber: 2.1 Consensus size: 162
222786 AGGCCAATAT
* * * *
222796 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGACAACCAGCGGCCCC
1 CCTTCGTTGTGAAGTTGAACTTGACTCTGAAACTGGGAAAGTGTTTGTTGACAACCAACGGCCCC
*
222861 TTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
*
222926 CTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGCC
131 CTC-------GGGAAATTGTTTGTTGACAGCCAGCGGCC
* * * *
222965 CCTTCGTTGTGAAGTTGAACTTGTGCTATCTTAAACTGGGAAA-TTTTTGTTGACAACCAACGGT
1 CCTTCGTTGTGAAGTTGAACTTG-AC--TCTGAAACTGGGAAAGTGTTTGTTGACAACCAACGGC
*
223029 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
63 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
223094 TGGCTCGGGAAATTGTTTGTTGACAGTCAGCGGCC
128 TGGCTCGGGAAATTGTTTGTTGACAGCCAGCGGCC
223129 CCTTCGTTGTGAAGTTGAACTTGA
1 CCTTCGTTGTGAAGTTGAACTTGA
223153 GCTGTCTCGA
Statistics
Matches: 172, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
164 50 0.29
169 21 0.12
170 1 0.01
171 87 0.51
172 13 0.08
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (162 bp):
CCTTCGTTGTGAAGTTGAACTTGACTCTGAAACTGGGAAAGTGTTTGTTGACAACCAACGGCCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
CTCGGGAAATTGTTTGTTGACAGCCAGCGGCC
Found at i:223132 original size:99 final size:99
Alignment explanation
Indices: 223002--223258 Score: 390
Period size: 99 Copynumber: 2.6 Consensus size: 99
222992 ATCTTAAACT
* * * * *
223002 GGGAAATT-TTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 GGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
* *
223066 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CCAATATCATTCGCTGTGAAGTTGAAATTGGATC
* *
223100 GGGAAATTGTTTGTTGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGAGCTGTCTCGAGT
1 GGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
** *
223165 CCAATATCATTTTCTGTGAAGTTGAAATTGGATT
66 CCAATATCATTCGCTGTGAAGTTGAAATTGGATC
*
223199 GGGAAATTGTTTGTTGACAGCCAGCGGCCCATTCGTTGTGAAGTTGAACTTGTGCTGTCT
1 GGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
223259 TTAAACTGGG
Statistics
Matches: 143, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 8 0.06
99 135 0.94
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (99 bp):
GGGAAATTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
CCAATATCATTCGCTGTGAAGTTGAAATTGGATC
Found at i:223279 original size:164 final size:167
Alignment explanation
Indices: 223100--223420 Score: 420
Period size: 164 Copynumber: 1.9 Consensus size: 167
223090 AAATTGGCTC
** *
223100 GGGAAATTGTTTGTTGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGAGCTGTCTCGAGT
1 GGGAAATTGTTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGAGCTGTCTCGAGT
* * *
223165 CCAATATCATT-TTCTGTGAAGTTGAAATTGG-ATTGG-GAAATTGTTTGTTGACAGCCAGCGG-
66 CCAATATCATTCGT-TGTGAAGTTGAAATTGGAATTGGAGAAA-TGTTTGATGACAACCAGCGGT
*
223226 CCCATTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACT
129 CCC-TTCGTCGTGAAGTTGAACTTGTGCTGTCTTTAAACT
* * * *
223266 GGGAAA-T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGAGCTGTCTCGAGT
*
223329 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGC
66 CCAATATCATTCGTTGTGAAGTTGAAATTGG-----AATTGGAGAAATGTTTGATGACAACCAGC
223394 GGTCCCTTCGTCGTGAAGTTGAACTTG
126 GGTCCCTTCGTCGTGAAGTTGAACTTG
223421 CGTTGTCTGG
Statistics
Matches: 134, Mismatches: 12, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
164 76 0.57
165 2 0.01
166 6 0.04
170 43 0.32
171 7 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (167 bp):
GGGAAATTGTTTGTTGACAACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGAGCTGTCTCGAGT
CCAATATCATTCGTTGTGAAGTTGAAATTGGAATTGGAGAAATGTTTGATGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGTGCTGTCTTTAAACT
Found at i:223311 original size:263 final size:263
Alignment explanation
Indices: 222773--223525 Score: 969
Period size: 263 Copynumber: 2.8 Consensus size: 263
222763 CCAATGCAAG
* *
222773 TTGTGTTG-CTTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAG
1 TTGTGTTGTC-TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG------GGAAA-
222837 TGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATAT
58 TGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATAT
* *
222902 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGCCCC
123 CCTTCTCTGTGAAGTTGAAATT-G--C-G--ATTGGGAAATTGTTTGTTGACAGCCAGCGG-CCC
222967 TTCGTTGTGAAGTTGAACTTGTGCTATCTTAAACTGGGAAATTTTTGTTGACAACCAACGGTCCC
181 TTCGTTGTGAAGTTGAACTTGTGCTATCTTAAACTGGGAAATTTTTGTTGACAACCAACGGTCCC
223032 TTCGTCGTGAAGTTGAAC
246 TTCGTCGTGAAGTTGAAC
223050 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC-GGGAAATTGTTTGT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGGAAA-TGTTTGT
** * * * *
223114 TGACAGTCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGAGCTGTCTCGAGTCCAATATCATTTTC
65 TGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCTC
223179 TGTGAAGTTGAAATTG-GATTGGGAAATTGTTTGTTGACAGCCAGCGGCCCATTCGTTGTGAAGT
130 TGTGAAGTTGAAATTGCGATTGGGAAATTGTTTGTTGACAGCCAGCGGCCC-TTCGTTGTGAAGT
* *
223243 TGAACTTGTGCTGTCTTTAAACTGGGAAA-TTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
194 TGAACTTGTGCTATC-TTAAACTGGGAAATTTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAG
223307 TTGAAC
258 TTGAAC
* * *
223313 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATG
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC-----TGG-GAAATG
* * * *
223378 TTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
60 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCC
* * *
223443 TTCGT-TGTGAAGTTGAAATTTGCTCTAAATTGGAGAAA-TGTTTGATGACAACCAGCGGTCCCT
125 TTC-TCTGTGAAGTTGAAA-TTG--C--GATTGG-GAAATTGTTTGTTGACAGCCAGCGG-CCCT
*
223506 TCGTCGTGAAGTTGAACTTG
182 TCGTTGTGAAGTTGAACTTG
223526 CGTTATCTGG
Statistics
Matches: 427, Mismatches: 30, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
262 3 0.01
263 143 0.33
264 13 0.03
265 1 0.00
269 76 0.18
270 93 0.22
275 43 0.10
276 8 0.02
277 46 0.11
278 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (263 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGGAAATGTTTGTT
GACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCTCT
GTGAAGTTGAAATTGCGATTGGGAAATTGTTTGTTGACAGCCAGCGGCCCTTCGTTGTGAAGTTG
AACTTGTGCTATCTTAAACTGGGAAATTTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTG
AAC
Found at i:223323 original size:65 final size:67
Alignment explanation
Indices: 223198--223323 Score: 186
Period size: 65 Copynumber: 1.9 Consensus size: 67
223188 GAAATTGGAT
* * *
223198 TGGGAAATTGTTTGTTGACAGCCAGCGGCCCATTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAA
1 TGGGAAATTGTTTGTTGACAACCAGCGGCCCATTCGTCGTGAAGTTGAACTTGCGCTGTCTTTAA
223263 AC
66 AC
*
223265 TGGGAAA-T-TTTGTTGACAACCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 TGGGAAATTGTTTGTTGACAACCAGCGG-CCCATTCGTCGTGAAGTTGAACTTGCGCTGTCT
223324 GGAGTCCAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
65 43 0.80
66 4 0.07
67 7 0.13
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (67 bp):
TGGGAAATTGTTTGTTGACAACCAGCGGCCCATTCGTCGTGAAGTTGAACTTGCGCTGTCTTTAA
AC
Found at i:223415 original size:105 final size:105
Alignment explanation
Indices: 223230--223670 Score: 700
Period size: 105 Copynumber: 4.2 Consensus size: 105
223220 CAGCGGCCCA
* * *
223230 TTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGG-GAAAT-TTTGTTGACAACCAGCGGTC
1 TTCGTTGTGAAGTTGAAATTG-GC--TC--TAAATTGGAGAAATGTTTGATGACAACCAGCGGTC
223293 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
61 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
223338 TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
1 TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
223403 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
66 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
223443 TTCGTTGTGAAGTTGAAATTTGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
1 TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
* *
223508 GTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCT
66 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* *
223548 TTCG-T-T----TTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTC
1 TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
*
223607 GTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCC
66 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
223647 TTCGTTGTGAAGTTGAAATTGGCT
1 TTCGTTGTGAAGTTGAAATTGGCT
223671 ATGGGTAAAA
Statistics
Matches: 313, Mismatches: 12, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
99 91 0.29
100 1 0.00
101 1 0.00
103 8 0.03
104 6 0.02
105 184 0.59
107 2 0.01
108 20 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TTCGTTGTGAAGTTGAAATTGGCTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
Found at i:223634 original size:204 final size:208
Alignment explanation
Indices: 223230--223667 Score: 699
Period size: 204 Copynumber: 2.1 Consensus size: 208
223220 CAGCGGCCCA
* *
223230 TTCGTTGTGAAGTTGAACTTGTGCTGTCTTTAAACTGGGAAATTTTGTTGACAACCAGCGGTCCC
1 TTCGTTGTGAAGTTGAAATTGTGC-GTC-TTAAACTGGGAAATTTTGATGACAACCAGCGGTCCC
*
223295 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
64 TTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGTTGT--A-TTGAAATTGG
*
223360 CTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
126 CTCTAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTT
223425 GTCTGGAGTCCAATATCC
191 GTCTGGAGTCCAATATCC
*
223443 TTCGTTGTGAAGTTGAAATT-TGC-TC-TAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCC
1 TTCGTTGTGAAGTTGAAATTGTGCGTCTTAAACTGG-GAAAT-TTTGATGACAACCAGCGGTCCC
*
223505 TTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCTTTCG-T-T-TTGAAATTGGCTC
64 TTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGTTGTATTGAAATTGGCTC
* *
223567 TGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTC
129 TAAATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTC
223632 TGGAGTCCAATATCC
194 TGGAGTCCAATATCC
223647 TTCGTTGTGAAGTTGAAATTG
1 TTCGTTGTGAAGTTGAAATTG
223668 GCTATGGGTA
Statistics
Matches: 214, Mismatches: 8, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
204 110 0.51
208 8 0.04
209 6 0.03
210 68 0.32
212 3 0.01
213 19 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (208 bp):
TTCGTTGTGAAGTTGAAATTGTGCGTCTTAAACTGGGAAATTTTGATGACAACCAGCGGTCCCTT
CGTCGTGAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGTTGTATTGAAATTGGCTCTA
AATTGGAGAAATGTTTGATGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTG
GAGTCCAATATCC
Found at i:224514 original size:60 final size:62
Alignment explanation
Indices: 224407--224526 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 62
224397 CTCTTCTTTT
* * *
224407 GTTCTTTTTTCCTCTTTTTCTTTTCTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAAC
1 GTTCTTTTTTCCTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
* *
224469 GTTCTTTTCTTTC-CTTTTT-TTTT-TCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 GTTCTTTT-TTCCTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
224527 GTAAAGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 31 0.60
61 4 0.08
62 14 0.27
63 3 0.06
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.49
Consensus pattern (62 bp):
GTTCTTTTTTCCTCTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
Found at i:231048 original size:39 final size:39
Alignment explanation
Indices: 230994--231070 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
230984 GCAGGTGCAA
* * *
230994 CTTTCGCTTTGGTAGC-GAATGAGTCCCCGGGTAGTATTG
1 CTTTCCCTTTAGTAGCAG-ATGAGTCCCCGGGTAATATTG
*
231033 CTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATATT
1 CTTTCCCTTTAGTAGCAGATGAGTCCCCGGGTAATATT
231071 CTGGGTGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (39 bp):
CTTTCCCTTTAGTAGCAGATGAGTCCCCGGGTAATATTG
Found at i:234838 original size:2 final size:2
Alignment explanation
Indices: 234831--234872 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
234821 AGAAGATAAA
* *
234831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
234873 TAACTTGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234944 original size:12 final size:13
Alignment explanation
Indices: 234919--234947 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
234909 AGATATATAT
234919 AATAAATAAATAA
1 AATAAATAAATAA
234932 AATAAAT-AATAA
1 AATAAATAAATAA
234944 AATA
1 AATA
234948 CTAATAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:235004 original size:42 final size:46
Alignment explanation
Indices: 234911--235016 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 46
234901 ATGCATATAG
*
234911 ATATATATAATAAATAAATAAAATAAATAATAAAATACTAATAACAC
1 ATATATATAATAAATAAATAAAAAAAATAAT-AAATACTAATAACAC
*
234958 ATATATGTAA-AAATAAAATAAAAAAAATAAT-AATACT-ATAA-A-
1 ATATATATAATAAAT-AAATAAAAAAAATAATAAATACTAATAACAC
235000 ATATATA-AATAAA-AAAT
1 ATATATATAATAAATAAAT
235017 TAGAATTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
40 4 0.07
41 2 0.04
42 9 0.17
43 1 0.02
44 4 0.07
45 6 0.11
46 4 0.07
47 24 0.44
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (46 bp):
ATATATATAATAAATAAATAAAAAAAATAATAAATACTAATAACAC
Found at i:240366 original size:31 final size:31
Alignment explanation
Indices: 240328--240386 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
240318 TTACGTCAGG
**
240328 GACCATATTGCAAACGGACTAAATGTTGAGA
1 GACCATATTGCAAACAAACTAAATGTTGAGA
*
240359 GACCATATTGTAAACAAACTAAATGTTG
1 GACCATATTGCAAACAAACTAAATGTTG
240387 GAGGATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAACAAACTAAATGTTGAGA
Found at i:242312 original size:31 final size:31
Alignment explanation
Indices: 242277--242348 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
242267 AACTTTTAAA
242277 ATTTGTAATATAAT-CCTCCAACATTTAGTCC
1 ATTTGTAATATAATCCCT-CAACATTTAGTCC
** * *
242308 ATTTGTAATATGGTCCCTTAACATTTAGTTC
1 ATTTGTAATATAATCCCTCAACATTTAGTCC
242339 ATTTGTAATA
1 ATTTGTAATA
242349 AGGTCCCCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (31 bp):
ATTTGTAATATAATCCCTCAACATTTAGTCC
Found at i:242354 original size:31 final size:31
Alignment explanation
Indices: 242296--242355 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
242286 ATAATCCTCC
*
242296 AACATTTAGTCCATTTGTAATATGGTCCCTT
1 AACATTTAGTCCATTTGTAATAAGGTCCCTT
*
242327 AACATTTAGTTCATTTGTAATAAGGTCCC
1 AACATTTAGTCCATTTGTAATAAGGTCCC
242356 CGACGTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (31 bp):
AACATTTAGTCCATTTGTAATAAGGTCCCTT
Found at i:242932 original size:2 final size:2
Alignment explanation
Indices: 242925--242974 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
242915 GAATGAGTAG
242925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
242967 TA TA TA TA
1 TA TA TA TA
242975 AAGTGGATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.