Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold344
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: 1758742
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 7 of 11
Found at i:1056492 original size:20 final size:20
Alignment explanation
Indices: 1056465--1056519 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1056455 TAAAATTTCC
*
1056465 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1056485 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1056505 AAATGTATCGATACA
1 AAATGTATCGATACA
1056520 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1056667 original size:21 final size:21
Alignment explanation
Indices: 1056643--1056699 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1056633 CATTTGTAGG
1056643 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1056664 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1056685 ATGTATCGATACATT
1 ATGTATCGATACATT
1056700 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1057530 original size:55 final size:55
Alignment explanation
Indices: 1057455--1058571 Score: 1119
Period size: 55 Copynumber: 19.5 Consensus size: 55
1057445 TGAGGAGTAA
* *
1057455 AAAG-TGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
*
1057509 AAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT-G
*
1057565 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* * ** * *
1057619 AAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCATTCTGCTTTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTG
* * * *
1057680 AAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTACTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-G
*
1057736 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTTCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* * **
1057790 AAAGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACT-
1 AAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTG
* * * *
1057850 AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTG
* * *
1057910 -AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTG
* *
1057969 -AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTCTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT-G
* * *
1058024 AAA-ATGCCACCAGCTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGATTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* **
1058078 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTG
* * * *
1058139 AAAAATGCCACCAACCTATGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-G
*
1058195 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* * * **
1058249 AAAGGTGCCACCAACCTGCGTGGGCTTTGCAAAGAAAAAGCATCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTG
* * * *
1058310 AAAAATGCCACCAACCTGTGTGGACTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-G
* *
1058366 AAA-ATGTCACCAACTTATGTGGGCTTTAAGAGAAAAGGTGTCCTGCTCTTTGAGGACTG
1 AAAGATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTG
* * *
1058425 -AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGCGTCCTGCTCTTTGAGGACTAG
1 AAAGATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACT-G
*
1058485 AAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGG
1 AAAGATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACT-G
*
1058545 AAA-ATGCCACCAACTTGTGGGGGCTTT
1 AAAGATGCCACCAACTTGTGTGGGCTTT
1058572 TAAAAGGAAA
Statistics
Matches: 923, Mismatches: 88, Indels: 98
0.83 0.08 0.09
Matches are distributed among these distances:
53 2 0.00
54 42 0.05
55 389 0.42
56 38 0.04
58 2 0.00
59 153 0.17
60 143 0.15
61 148 0.16
64 6 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
AAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1057737 original size:171 final size:166
Alignment explanation
Indices: 1057455--1058578 Score: 1174
Period size: 171 Copynumber: 6.5 Consensus size: 166
1057445 TGAGGAGTAA
* **
1057455 AAAG-TGCCACCAA-CTCGTGTGGGCTTTGAAAG-GCGTCCTGCTCTTTGAGGACTGAAAGGTGC
1 AAAGATGCCACCAACCT-GTGTGGGCTTTAAAAGAGCGTCCTGCTCTTTGAGGACTGAAAAATGC
* *
1057517 CACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTG
65 CACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTG
* *
1057582 TGTGGGCTTTG-AAAGGTGTCCTGCTCTTTGGGGACTG
129 TGTGGGCTTTGAAAAGGCGTCCTGCTCTTTGAGGACTG
* * * *
1057619 AAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCATTCTGCTTTTTGAGGACTGAAAA
1 AAAGATGCCACCAACCTGTGTGGGCTTT-AAAAG----AGCGTCCTGCTCTTTGAGGACTGAAAA
* * *
1057684 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTACTCTTTGAGGACTGGAAAATGCCACCAA
61 ATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAA
* *
1057749 CTTGTGTGGGCTTTG-AAAGGTGTTCTGCTCTTTGAGGACTG
125 CTTGTGTGGGCTTTGAAAAGGCGTCCTGCTCTTTGAGGACTG
* * * * *
1057790 AAAGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACT-AAAG
1 AAAGATGCCACCAACCTGTGTGGGCTTT-AAAAG----AGCGTCCTGCTCTTTGAGGACTGAAAA
* * * * *
1057854 GTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCA
61 ATGCCACCAACTTGTGTGGGCTTT-----AAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCA
* * *
1057919 CCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCGCTCTTTGAGGACTG
121 CCAACTTGTGTGGGCTTT----GAAAAGGCGTCCTGCTCTTTGAGGACTG
* * * * *
1057969 -AAGGTGCCACCAACTTGTGTGGGCTTTAAGAG-GTGTCCTGCTCTCTGAGGACT-AGAAAATGC
1 AAAGATGCCACCAACCTGTGTGGGCTTTAAAAGAGCGTCCTGCTCTTTGAGGACTGA-AAAATGC
* * * *
1058031 CACCAGCTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGATTGAAAGGTGCCACCAACTTG
65 CACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTG
*
1058096 TGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTG
129 TGTGGGCTTTGAAAAG-----GCGTCCTGCTCTTTGAGGACTG
* * * *
1058139 AAAAATGCCACCAACCTATGTGGGCTTTAAAAG-GTGTCCTGCTCTTTGAGGACTGGAAAATGCC
1 AAAGATGCCACCAACCTGTGTGGGCTTTAAAAGAGCGTCCTGCTCTTTGAGGACTGAAAAATGCC
* * * *
1058203 ACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTGC
66 ACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGT
* *
1058268 GTGGGCTTTGCAAAGAAAAAGCATCCTGCTCTTTGAGGACTG
130 GTGGGCTTT-----GAAAAGGCGTCCTGCTCTTTGAGGACTG
* * * * *
1058310 AAAAATGCCACCAACCTGTGTGGACTTTAAAAG-GTGTCCTGCTCTTTGAGGACTGGAAAATGTC
1 AAAGATGCCACCAACCTGTGTGGGCTTTAAAAGAGCGTCCTGCTCTTTGAGGACTGAAAAATGCC
* *
1058374 ACCAACTTATGTGGGCTTTAAGAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAAC
66 ACCAACTTGTGTGGGCTTT-----AAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAAC
*
1058439 TTGTGTGGGCTTTAAGAGAAAAAGCGTCCTGCTCTTTGAGGACTAG
126 TTGTGTGGGCTTT----GAAAAGGCGTCCTGCTCTTTGAGGACT-G
* *
1058485 AAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAA
1 AAAGATGCCACCAACCTGTGTGGGCTTTAAAAG---A-GCGTCCTGCTCTTTGAGGACTGAAAAA
*
1058549 TGCCACCAACTTGTGGGGGCTTTTAAAAGG
62 TGCCACCAACTTGTGTGGGC-TTTAAAAGG
1058579 AAAAGGCATC
Statistics
Matches: 840, Mismatches: 76, Indels: 77
0.85 0.08 0.08
Matches are distributed among these distances:
164 4 0.00
165 25 0.03
166 6 0.01
168 24 0.03
169 24 0.03
170 43 0.05
171 404 0.48
172 19 0.02
173 23 0.03
174 81 0.10
175 55 0.07
176 32 0.04
177 4 0.00
178 27 0.03
179 66 0.08
180 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (166 bp):
AAAGATGCCACCAACCTGTGTGGGCTTTAAAAGAGCGTCCTGCTCTTTGAGGACTGAAAAATGCC
ACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTG
TGGGCTTTGAAAAGGCGTCCTGCTCTTTGAGGACTG
Found at i:1058109 original size:29 final size:29
Alignment explanation
Indices: 1058028--1058109 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 29
1058018 GACTAGAAAA
*
1058028 TGCCACCAGCTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** * *
1058057 TGTCCTGC-TCTT-TG-GGG-ATTGAAAGG
1 TG-CCACCAACTTGTGTGGGCTTTGAAAGG
1058083 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
1058110 AGAAAAAGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
25 3 0.08
26 13 0.32
27 5 0.12
28 5 0.12
29 11 0.28
30 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:1059618 original size:29 final size:28
Alignment explanation
Indices: 1059569--1059640 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 28
1059559 GCTTAAGTAG
*
1059569 GTTTTTTCTTTTCTCTCTTTTTCTTTGTTTT
1 GTTTTTT-TTTT-TCTCTTTTT-TTTCTTTT
1059600 GTTTTTTTTTTTC-CGTTTTTTTTCTTTT
1 GTTTTTTTTTTTCTC-TTTTTTTTCTTTT
1059628 GCTTTTTTTTTTT
1 G-TTTTTTTTTTT
1059641 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 9 0.24
29 18 0.47
30 4 0.11
31 7 0.18
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (28 bp):
GTTTTTTTTTTTCTCTTTTTTTTCTTTT
Found at i:1059635 original size:15 final size:15
Alignment explanation
Indices: 1059570--1059637 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
1059560 CTTAAGTAGG
1059570 TTTTTTCTTTT-CTCT
1 TTTTTTCTTTTGCT-T
* *
1059585 CTTTTTC-TTTGTTTT
1 TTTTTTCTTTTG-CTT
* *
1059600 GTTTTTTTTTTTCCGTT
1 -TTTTTTCTTTTGC-TT
1059617 TTTTTTCTTTTGCTT
1 TTTTTTCTTTTGCTT
1059632 TTTTTT
1 TTTTTT
1059638 TTTGAAGAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
14 3 0.08
15 15 0.38
16 17 0.43
17 5 0.12
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTTGCTT
Found at i:1072133 original size:28 final size:28
Alignment explanation
Indices: 1072084--1072153 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1072074 AATCGGGATT
*** * *
1072084 GGAGTATCCCCTCGGAAGTAACGGGGTG
1 GGAGTATCCCCGATGAAATAACGAGGTG
*
1072112 GGAGTATCCCCGATGAAATAACGAGGTT
1 GGAGTATCCCCGATGAAATAACGAGGTG
*
1072140 GGAGTATCCTCGAT
1 GGAGTATCCCCGAT
1072154 TGTGAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (28 bp):
GGAGTATCCCCGATGAAATAACGAGGTG
Found at i:1072199 original size:52 final size:50
Alignment explanation
Indices: 1072136--1072306 Score: 164
Period size: 52 Copynumber: 3.3 Consensus size: 50
1072126 GAAATAACGA
* * * *
1072136 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCG
** * *
1072187 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCG
* * **
1072239 GGATTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTT-AGCGATAAAACCGG
1 GG-TTGGAGTATCCCCGATTGTG-AAAAATTGGAGTTTTGA-AAATAAAACC-G
1072292 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1072307 TCAGAAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
51 4 0.04
52 83 0.84
53 12 0.12
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCG
Found at i:1072352 original size:27 final size:28
Alignment explanation
Indices: 1072289--1072364 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
1072279 GCGATAAAAC
*
1072289 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1072317 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1072344 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1072365 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.58
28 19 0.42
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1072466 original size:212 final size:212
Alignment explanation
Indices: 1072072--1072473 Score: 603
Period size: 212 Copynumber: 1.9 Consensus size: 212
1072062 AGAGAAAAAA
* * *
1072072 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTGGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTGGGAGTATCCCCGATGAAATAACGAG
* * *
1072137 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGCATTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
* *
1072202 CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGATTGGAGTATCCCCGATTGTGAAAAA
131 CGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGGATTGGAATATCCCCGATTGTGAAAAA
1072267 ATTAGTGTTTTAGCGAT
196 ATTAGTGTTTTAGCGAT
* * * *
1072284 AAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTGGGAGTATCCCCGATGAAATAACGAG
*
1072348 GTTGGAGTATCCCCGATTGTGAAGAAATTGGCATTTTTTGGAAATAAAATCGGAGTTAGAGTATT
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGCA-TTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * * *
1072413 CCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATC-GGAGTTTGAATATCCCCGATTGTG
129 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGGA-TTGGAATATCCCCGATTGTG
1072474 GAGAATTGAG
Statistics
Matches: 170, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 32 0.19
212 100 0.59
213 38 0.22
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTGGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGCATTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
CGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGGATTGGAATATCCCCGATTGTGAAAAA
ATTAGTGTTTTAGCGAT
Found at i:1074852 original size:13 final size:13
Alignment explanation
Indices: 1074834--1074859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1074824 ACAAAGATCC
1074834 ATGTATCGATACA
1 ATGTATCGATACA
1074847 ATGTATCGATACA
1 ATGTATCGATACA
1074860 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1074923 original size:19 final size:18
Alignment explanation
Indices: 1074899--1074998 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
1074889 CAGTAGCTAA
1074899 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1074918 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1074933 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1074950 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1074965 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1074982 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1074999 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1074939 original size:13 final size:13
Alignment explanation
Indices: 1074921--1074977 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1074911 ACAATACTTA
1074921 TGTATCGATACAT
1 TGTATCGATACAT
1074934 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
1074952 ATGTATCGATACAT
1 -TGTATCGATACAT
1074966 TGTATCGATACA
1 TGTATCGATACA
1074978 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1074943 original size:32 final size:32
Alignment explanation
Indices: 1074902--1074996 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
1074892 TAGCTAATTA
*
1074902 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1074934 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1074966 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1074997 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1075078 original size:21 final size:21
Alignment explanation
Indices: 1075054--1075110 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1075044 CATTTGTAGG
1075054 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1075075 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1075096 ATGTATCGATACATT
1 ATGTATCGATACATT
1075111 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1077471 original size:52 final size:52
Alignment explanation
Indices: 1077386--1077510 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1077376 ATATGAAAAG
* *
1077386 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
* *
1077438 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
1077490 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1077511 AAGATCAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
Found at i:1077521 original size:52 final size:52
Alignment explanation
Indices: 1077386--1077530 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 52
1077376 ATATGAAAAG
* * *
1077386 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAATGTATCGATACATCTAGGCAAAT
*** *
1077438 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTAGGCAAAT
1077490 TTGCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
1077531 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 4 0.05
52 80 0.95
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTAGGCAAAT
Found at i:1077534 original size:13 final size:13
Alignment explanation
Indices: 1077516--1077543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1077506 ATACAAAGAT
1077516 CAATGTATCGATA
1 CAATGTATCGATA
1077529 CAATGTATCGATA
1 CAATGTATCGATA
1077542 CA
1 CA
1077544 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1077641 original size:33 final size:33
Alignment explanation
Indices: 1077584--1077650 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1077574 AGTAGCTTAA
*
1077584 ATTGTATCGATACAAAAAAATATGTATTGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1077617 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1077650 A
1 A
1077651 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1083063 original size:23 final size:23
Alignment explanation
Indices: 1083037--1083082 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1083027 GCTCAGAGAT
1083037 GTTTTCCTAAAGACTGATACTTG
1 GTTTTCCTAAAGACTGATACTTG
*
1083060 GTTTTCCTAAAGGCTGATACTTG
1 GTTTTCCTAAAGACTGATACTTG
1083083 TCCCGATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
GTTTTCCTAAAGACTGATACTTG
Found at i:1085966 original size:51 final size:51
Alignment explanation
Indices: 1085898--1086003 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
1085888 GAAATAACGA
* * * *
1085898 GGTTAGAGTATCTCCGATGGTGAAAAATCGATATTTTAGAAATAAAATCGG
1 GGTTAGAATATCCCCGATGATGAAAAATCAATATTTTAGAAATAAAATCGG
* *
1085949 GGTTAGAATATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAATCGG
1 GGTTAGAATATCCCCGATGATGAAAAATCAATATTTTAGAAATAAAATCGG
1086000 GGTT
1 GGTT
1086004 TGAGTACCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (51 bp):
GGTTAGAATATCCCCGATGATGAAAAATCAATATTTTAGAAATAAAATCGG
Found at i:1086030 original size:79 final size:79
Alignment explanation
Indices: 1085947--1086231 Score: 319
Period size: 79 Copynumber: 3.6 Consensus size: 79
1085937 AAATAAAATC
* *
1085947 GGGGTTAGAATATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTTGAGTACC
1 GGGGTTAGAGTATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTACC
1086012 CCTTCAAAAATAAT
66 CCTTCAAAAATAAT
* * * *
1086026 GGGGTTTGAGTATCCCCGATGATGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAATATC
1 GGGGTTAGAGTATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTA-C
1086091 CCCTT-AAAAATAAT
65 CCCTTCAAAAATAAT
* * * * *
1086105 -GGGTTAGAGTATCCTCAAT--TGTGAGAAATCAGTGTTTTAAAAATAAAACCGGGGTTGGAGT-
1 GGGGTTAGAGTATCCCCGATGATG-GA-AAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTA
** *
1086166 GTCCTCTCAAAAATAAC
64 CCCCT-TCAAAAATAAT
* * ** * *
1086183 GGGGTTGGAGTATCCCCGATGATGAAAAATCGGTATTTTGGAAATAAAA
1 GGGGTTAGAGTATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAA
1086232 ACATCAATAA
Statistics
Matches: 172, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
76 5 0.03
77 3 0.02
78 54 0.31
79 101 0.59
80 7 0.04
81 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GGGGTTAGAGTATCCCCGATGATGGAAAATCAATGTTTTAGAAATAAAATCGGGGTTGGAGTACC
CCTTCAAAAATAAT
Found at i:1086093 original size:130 final size:130
Alignment explanation
Indices: 1085860--1086093 Score: 335
Period size: 130 Copynumber: 1.8 Consensus size: 130
1085850 TATTTTCGAG
* * *
1085860 ATAAAAACGGGATTAGAGTATCCCCTCAGAAATAACGAGGTTAGAGTATCTCCGATGGTGAAAAA
1 ATAAAAACGGGATTAGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAAAAA
*
1085925 TCGATATTTTAGAAATAAAATCGGGGTTAGAATATCCCCGATGATGGAAAATCAATGTTTTAGAA
66 TCGATATTTTAGAAATAAAATCAGGGTTAGAATATCCCCGATGATGGAAAATCAATGTTTTAGAA
* * * * * * *
1085990 ATAAAATCGGGGTTTGAGTA-CCCCTTCAAAAATAATGGGGTTTGAGTATCCCCGATGATGGAAA
1 ATAAAAACGGGATTAGAGTATCCCC-TCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAAAA
* *
1086054 ATCGATGTTTTAGAAATAAAATCAGGGTTGGAATATCCCC
65 ATCGATATTTTAGAAATAAAATCAGGGTTAGAATATCCCC
1086094 TTAAAAATAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 4 0.04
130 86 0.96
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (130 bp):
ATAAAAACGGGATTAGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAAAAA
TCGATATTTTAGAAATAAAATCAGGGTTAGAATATCCCCGATGATGGAAAATCAATGTTTTAGAA
Found at i:1088952 original size:20 final size:21
Alignment explanation
Indices: 1088903--1088959 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1088893 TAATGGAACA
*
1088903 AAGGGAACCAACCTCTTCAAT
1 AAGGAAACCAACCTCTTCAAT
* *
1088924 AAGGAAACCAACCTCTTTACT
1 AAGGAAACCAACCTCTTCAAT
1088945 AA-GAAACCAACCTCT
1 AAGGAAACCAACCTCT
1088960 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (21 bp):
AAGGAAACCAACCTCTTCAAT
Found at i:1089381 original size:21 final size:20
Alignment explanation
Indices: 1089333--1089381 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1089323 TCCTTTAAAA
*
1089333 AAAGAACCAACTTTTTCAAT
1 AAAGAACCAACATTTTCAAT
*
1089353 AAAGGAACCAACATTTTCATT
1 AAA-GAACCAACATTTTCAAT
1089374 AAGAGAAC
1 AA-AGAAC
1089382 TAATTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (20 bp):
AAAGAACCAACATTTTCAAT
Found at i:1089794 original size:59 final size:59
Alignment explanation
Indices: 1089700--1089813 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
1089690 ATATGCCTAC
*
1089700 TTATAGGAACATAAAAGTATAACAAAATGTAAATAAAG-TATATATTTTAGAAGCCAAT
1 TTATAGGAACATAAAAGTATAACAAAATATAAATAAAGATATATATTTTAGAAGCCAAT
* * * * *
1089758 TTATATGAACATATAAGATATAACAATATATTAATAAAGATATATATTTTGGAAGC
1 TTATAGGAACATAAAAG-TATAACAAAATATAAATAAAGATATATATTTTAGAAGC
1089814 ATAATTTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 15 0.31
59 18 0.38
60 15 0.31
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.32
Consensus pattern (59 bp):
TTATAGGAACATAAAAGTATAACAAAATATAAATAAAGATATATATTTTAGAAGCCAAT
Found at i:1089879 original size:22 final size:23
Alignment explanation
Indices: 1089854--1089908 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
1089844 CATATATGAT
1089854 TATAACTGAATATACATAT-AAA
1 TATAACTGAATATACATATGAAA
* * * *
1089876 TATAACTAAATGTATATATGACA
1 TATAACTGAATATACATATGAAA
1089899 -ATAACTGAAT
1 TATAACTGAAT
1089909 TCCATGCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
TATAACTGAATATACATATGAAA
Found at i:1098363 original size:6 final size:6
Alignment explanation
Indices: 1098321--1098345 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1098311 TAATTTGGCC
1098321 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
1098346 CAATAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1098374 original size:21 final size:20
Alignment explanation
Indices: 1098334--1098375 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1098324 TTTTATTTTT
* *
1098334 ATTTTTATTTTTCAATAAAC
1 ATTTCTATTTTTCAACAAAC
1098354 ATTTCTATTTTTCAACCAAAC
1 ATTTCTATTTTTCAA-CAAAC
1098375 A
1 A
1098376 AATTTTCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTCTATTTTTCAACAAAC
Found at i:1098733 original size:16 final size:16
Alignment explanation
Indices: 1098712--1098765 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1098702 TCGAAACTTG
1098712 AAATGATCCGAATCCA
1 AAATGATCCGAATCCA
** * *
1098728 AAATGAT-TTAAACTCG
1 AAATGATCCGAATC-CA
1098744 AAATGATCCGAATCCA
1 AAATGATCCGAATCCA
1098760 AAATGA
1 AAATGA
1098766 CCCGCACCCA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (16 bp):
AAATGATCCGAATCCA
Found at i:1098747 original size:32 final size:32
Alignment explanation
Indices: 1098705--1098765 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1098695 GATTGACTCG
*
1098705 AAACTTGAAATGATCCGAATCCAAAATGATTT
1 AAACTCGAAATGATCCGAATCCAAAATGATTT
1098737 AAACTCGAAATGATCCGAATCCAAAATGA
1 AAACTCGAAATGATCCGAATCCAAAATGA
1098766 CCCGCACCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (32 bp):
AAACTCGAAATGATCCGAATCCAAAATGATTT
Found at i:1100703 original size:15 final size:15
Alignment explanation
Indices: 1100683--1100713 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1100673 CTTGCGCTCA
1100683 CAAGCTACATAGGTT
1 CAAGCTACATAGGTT
1100698 CAAGCTACATAGGTT
1 CAAGCTACATAGGTT
1100713 C
1 C
1100714 GACTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (15 bp):
CAAGCTACATAGGTT
Found at i:1104510 original size:50 final size:51
Alignment explanation
Indices: 1104451--1104565 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
1104441 TGAACAGTAC
* *
1104451 ATGTATCGATACATTCTG-TTTTTTACCCATATGTATCGATACATTG-TTCA
1 ATGTATCGATACATTCTGTTTTTTTACCCAGATGTATCGATACATTGAAT-A
*
1104501 ATGTATCGATACATTCTGTTTTTTTACCTAGATGTATCGATACATTGAATA
1 ATGTATCGATACATTCTGTTTTTTTACCCAGATGTATCGATACATTGAATA
1104552 ATGTATCGATACAT
1 ATGTATCGATACAT
1104566 CTAGTTAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
50 18 0.30
51 41 0.68
52 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTCTGTTTTTTTACCCAGATGTATCGATACATTGAATA
Found at i:1110698 original size:3 final size:3
Alignment explanation
Indices: 1110690--1110744 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
1110680 GTCATATCAT
*
1110690 ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1110738 ATA ATA A
1 ATA ATA A
1110745 AACTAAGCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1111922 original size:20 final size:20
Alignment explanation
Indices: 1111881--1111929 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1111871 ACATTTCTAG
*
1111881 TATGTATCGATACACTCACC
1 TATGTATCGATACACTAACC
1111901 TATGTATCGATACA-TAACCC
1 TATGTATCGATACACTAA-CC
1111921 TATTGTATC
1 TA-TGTATC
1111930 AATATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (20 bp):
TATGTATCGATACACTAACC
Found at i:1132067 original size:51 final size:51
Alignment explanation
Indices: 1132011--1132148 Score: 204
Period size: 51 Copynumber: 2.7 Consensus size: 51
1132001 ATTTGCCTGC
* *
1132011 ATGTATCGATACATTGAAGAATGTATCGATACATTTAGGTCAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAACACAGA
* * * *
1132062 ATGTATCAATACAATGAAGAATATATCGATACATGTAGGTCAAAACATAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAACACAGA
* *
1132113 ATGTATCGATACAATGAAAAATGTAACGATACATTT
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT
1132149 TCATTCCATA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTAGGTCAAAACACAGA
Found at i:1132884 original size:29 final size:29
Alignment explanation
Indices: 1132761--1132999 Score: 212
Period size: 29 Copynumber: 8.1 Consensus size: 29
1132751 AAATTTTTCC
* *
1132761 CAAAGTCCACGACTCAGT-GCACCCTTTT
1 CAAAGTTCACGACTCAGTGGCACCCTTCT
*
1132789 CAAAGTCCACGACTCAGTGGACATACCCTTCT
1 CAAAGTTCACGACTCAGTGG-C--ACCCTTCT
* * * *
1132821 CAAAGTTTATGGCTTAGTAGGCACCCTTCT
1 CAAAGTTCACGACTCAGT-GGCACCCTTCT
* * * * *
1132851 TAAAGTTCATGACTCAATGTCACCCTCCT
1 CAAAGTTCACGACTCAGTGGCACCCTTCT
1132880 CAAAGTAT-ACGACTCAGTGGCACCCTTCT
1 CAAAGT-TCACGACTCAGTGGCACCCTTCT
* * *
1132909 CAAAGTCCATGACTCAGTGGCACCTTTCT
1 CAAAGTTCACGACTCAGTGGCACCCTTCT
* *
1132938 CAAAGTTCACGACTTAGTGGTACCCTTCT
1 CAAAGTTCACGACTCAGTGGCACCCTTCT
* * * * * *
1132967 CAAAGTCCACAAATTAGTGGCATCCTCCT
1 CAAAGTTCACGACTCAGTGGCACCCTTCT
1132996 CAAA
1 CAAA
1133000 AACCCACACA
Statistics
Matches: 172, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
28 18 0.10
29 108 0.63
30 23 0.13
32 21 0.12
33 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CAAAGTTCACGACTCAGTGGCACCCTTCT
Found at i:1132986 original size:87 final size:87
Alignment explanation
Indices: 1132756--1132999 Score: 247
Period size: 87 Copynumber: 2.8 Consensus size: 87
1132746 CAACCAAATT
* * * *
1132756 TTTCCCAAAGTCCACGACTCAGTGCACCCTTTTCAAAGTCCACGACTCAGTGGACATACCCTTCT
1 TTTCTCAAAGTTCACGACTCAGTGTACCCTTCTCAAAGTCCACGACTCAGTGG-C--ACCCTTCT
** * *
1132821 CAAAGTTTATGGCTTAGTAGGCACC
63 CAAAGTCCATGACTCAGTAGGCACC
* * * * * **
1132846 CTTCTTAAAGTTCATGACTCAATGTCACCCTCCTCAAAGTATACGACTCAGTGGCACCCTTCTCA
1 TTTCTCAAAGTTCACGACTCAGTGT-ACCCTTCTCAAAGTCCACGACTCAGTGGCACCCTTCTCA
1132911 AAGTCCATGACTCAGT-GGCACC
65 AAGTCCATGACTCAGTAGGCACC
* * * * * *
1132933 TTTCTCAAAGTTCACGACTTAGTGGTACCCTTCTCAAAGTCCACAAATTAGTGGCATCCTCCTCA
1 TTTCTCAAAGTTCACGACTCAGT-GTACCCTTCTCAAAGTCCACGACTCAGTGGCACCCTTCTCA
1132998 AA
65 AA
1133000 AACCCACACA
Statistics
Matches: 124, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
87 57 0.46
88 24 0.19
90 19 0.15
91 24 0.19
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (87 bp):
TTTCTCAAAGTTCACGACTCAGTGTACCCTTCTCAAAGTCCACGACTCAGTGGCACCCTTCTCAA
AGTCCATGACTCAGTAGGCACC
Found at i:1133039 original size:32 final size:32
Alignment explanation
Indices: 1132963--1133071 Score: 109
Period size: 32 Copynumber: 3.5 Consensus size: 32
1132953 AGTGGTACCC
*
1132963 TTCTCAAAGT-C-CACAAATTAGTGGCATCC-
1 TTCTCAAAGTCCACACAAATTGGTGGCATCCT
* **
1132992 TCCTCAAAAACCCACACAAATTGGTGGCATCCT
1 TTCTC-AAAGTCCACACAAATTGGTGGCATCCT
* *
1133025 TTCTCAAAGTCCACA-AAAGCTGGTGGCATCTT
1 TTCTCAAAGTCCACACAAA-TTGGTGGCATCCT
*
1133057 TTTTCAAAGTCCACA
1 TTCTCAAAGTCCACA
1133072 TCAGTTAGCG
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 4 0.06
30 3 0.05
31 4 0.06
32 50 0.77
33 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (32 bp):
TTCTCAAAGTCCACACAAATTGGTGGCATCCT
Found at i:1133289 original size:94 final size:92
Alignment explanation
Indices: 1133004--1133312 Score: 357
Period size: 92 Copynumber: 3.3 Consensus size: 92
1132994 CTCAAAAACC
* * ** * *
1133004 CACACAAATTGGTGGCATCCTTTCTCAAAGTCCACAAAAGCTGGTGGCATCTTTTTTCAAAGTCC
1 CACACAAGTTAGTGGCATCCTTTCTCAAAGTCCACATGAGCTAGTGGCATCTTTTTTCAAAGTTC
* * * * *
1133069 ACATCAGTTAGCGGCACCCCAAAAGCC
66 GCATAAGCTAGCGACACCCCAAAAGCT
* *
1133096 CATACAAGTTAGTGGCATCCTTTCTCAAAGTCCACATGAGCTAGTAGCATCTTTTTTCAAAGTTC
1 CACACAAGTTAGTGGCATCCTTTCTCAAAGTCCACATGAGCTAGTGGCATCTTTTTTCAAAGTTC
* * *
1133161 GCACAAGCTGGCAACACCCCAAAAGCT
66 GCATAAGCTAGCGACACCCCAAAAGCT
** *
1133188 CACACAAGTTAGTGGCATCCTTTCTCAAAGTCCATGGTGAGCTAGTGGCATTTTTTTTTCAAAGT
1 CACACAAGTTAGTGGCATCCTTTCTCAAAGTCCA-CATGAGCTAGTGGCA-TCTTTTTTCAAAGT
* * * * *
1133253 TCGCATGAGCAAGTGACACCCAAAAAGTT
64 TCGCATAAGCTAGCGACACCCCAAAAGCT
* * *
1133282 CACACAAGTTGGTGGCTTCTTTTCTCAAAGT
1 CACACAAGTTAGTGGCATCCTTTCTCAAAGT
1133313 TTGCACAAGC
Statistics
Matches: 183, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
92 109 0.60
93 12 0.07
94 62 0.34
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (92 bp):
CACACAAGTTAGTGGCATCCTTTCTCAAAGTCCACATGAGCTAGTGGCATCTTTTTTCAAAGTTC
GCATAAGCTAGCGACACCCCAAAAGCT
Found at i:1133564 original size:58 final size:57
Alignment explanation
Indices: 1133421--1133575 Score: 159
Period size: 58 Copynumber: 2.7 Consensus size: 57
1133411 AATGGCATCT
* * * * *
1133421 CTTTC-TAAGCCTAATGTCGTTAGCCTTGAATTAACACATTGGCACTTGTCAAACCTT
1 CTTTCTTAAGCCCAATGTCGTT-GCCTTGAATTAGCATATTGGCACTAGTCAAACCTA
* * * * * *
1133478 TTTTCTCAAGCCCAATGTTGTTGGCCTTGATTTAGCATATTGGCACTAGTTAGACCTA
1 CTTTCTTAAGCCCAATGTCGTT-GCCTTGAATTAGCATATTGGCACTAGTCAAACCTA
* *
1133536 CTTTCTTAAGCCCAATGTCGCTGCCCTTGAATCAGCATAT
1 CTTTCTTAAGCCCAATGTCGTTG-CCTTGAATTAGCATAT
1133576 CGGTACTCTC
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
57 5 0.06
58 73 0.94
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (57 bp):
CTTTCTTAAGCCCAATGTCGTTGCCTTGAATTAGCATATTGGCACTAGTCAAACCTA
Found at i:1133664 original size:52 final size:52
Alignment explanation
Indices: 1133549--1133928 Score: 305
Period size: 52 Copynumber: 7.4 Consensus size: 52
1133539 TCTTAAGCCC
* * ** *
1133549 AATGTCGCTGCCCTTGAATCAGCATATCGGTA-C--TCTCATCTTTAAGTCT
1 AATGTCGCTGGCCTTGAATCAGCATATTGACACCTTTATCATCTTTAAGTCT
* *
1133598 AATGTCGCTAGCCTTGAATCAGTATATTGACACCCTTT-TCATCTTTAAGTCT
1 AATGTCGCTGGCCTTGAATCAGCATATTGACA-CCTTTATCATCTTTAAGTCT
* * *
1133650 AATGTTGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCT
1 AATGTCGCTGGCCTTGAATCAGCATATTGACACCTTTATCATCTTTAAGTCT
* * * * * *
1133702 AATGTCACTAGCCTTAAATTAGCACATT-AGCACTTTTATCATCTTTAAGT-T
1 AATGTCGCTGGCCTTGAATCAGCATATTGA-CACCTTTATCATCTTTAAGTCT
* * * * *
1133753 CGATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTATCATCTTTAAGTCC
1 -AATGTCGCTGGCCTTGAATCAGCATATTGACACCTTTATCATCTTTAAGTCT
* * * * * *
1133806 AATATCGTTGGCCTTGAATTAACATATT-AGCA--TTCTAATCATCTTTAACTTT
1 AATGTCGCTGGCCTTGAATCAGCATATTGA-CACCTT-T-ATCATCTTTAAGTCT
* * * * * *
1133858 AATGTCGTTGGCCTTAAATCAGCACATTGGCA-CTCTTATCATCTTTAATTCC
1 AATGTCGCTGGCCTTGAATCAGCATATTGACACCT-TTATCATCTTTAAGTCT
* *
1133910 AATGTTGC-GGGCTTGAATC
1 AATGTCGCTGGCCTTGAATC
1133929 TACACATTGG
Statistics
Matches: 265, Mismatches: 51, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
49 26 0.10
50 2 0.01
51 16 0.06
52 217 0.82
53 3 0.01
54 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (52 bp):
AATGTCGCTGGCCTTGAATCAGCATATTGACACCTTTATCATCTTTAAGTCT
Found at i:1133714 original size:104 final size:102
Alignment explanation
Indices: 1133549--1133914 Score: 371
Period size: 104 Copynumber: 3.6 Consensus size: 102
1133539 TCTTAAGCCC
* * * * *
1133549 AATGTCGCTGCCCTTGAATCAGCATATCGGTAC---TCTCATCTTTAAGTCTAATGTCGCTAGCC
1 AATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCCAATGTCGCTAGCC
* *
1133611 TTGAATCAGTATATT-GACACCCTTTTCATCTTTAAGTCT
66 TTGAATTAGCATATTAG-CA-CCTTTTCATCTTTAAGT-T
* * *
1133650 AATGTTGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCTAATGTCACTAGCC
1 AATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCCAATGTCGCTAGCC
* * *
1133715 TTAAATTAGCACATTAGCACTTTTATCATCTTTAAGTT
66 TTGAATTAGCATATTAGCACCTTT-TCATCTTTAAGTT
* * * * * * *
1133753 CGATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTATCATCTTTAAGTCCAATATCGTTGGC
1 -AATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCCAATGTCGCTAGC
* * ** *
1133818 CTTGAATTAACATATTAGCATTCTAATCATCTTTAACTTT
65 CTTGAATTAGCATATTAGCA-CCTTTTCATCTTTAA-GTT
* * * * *
1133858 AATGTCGTTGGCCTTAAATCAGCACATTGGCACTCTTATCATCTTTAATTCCAATGT
1 AATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCCAATGT
1133915 TGCGGGCTTG
Statistics
Matches: 218, Mismatches: 39, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
101 29 0.13
103 5 0.02
104 180 0.83
105 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (102 bp):
AATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTATCATCTTTAAGTCCAATGTCGCTAGCC
TTGAATTAGCATATTAGCACCTTTTCATCTTTAAGTT
Found at i:1133771 original size:156 final size:156
Alignment explanation
Indices: 1133584--1133905 Score: 416
Period size: 156 Copynumber: 2.1 Consensus size: 156
1133574 ATCGGTACTC
*
1133584 TCATCTTTAAGTCTAATGTCGCTAGCCTTGAATCAGTATATTGACACCCTTT-TCATCTTTAAGT
1 TCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGTATATTGACA-CCTTTATCATCTTTAAGT
* * * * * * *
1133648 CTAATGTTGCTGGCCTTGAATCAGCATATTGGCACTT-TTATCATCTTTAAGTCTAATGTCACTA
65 CCAATATCGCTGGCCTTGAATCAACATATTAGCA-TTCTAATCATCTTTAACTCTAATGTCACTA
* *
1133712 GCCTTAAATTAGCACATTAGCACTTTTA
129 GCCTTAAATCAGCACATTAGCACTCTTA
* * *
1133740 TCATCTTTAAGT-TCGATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTATCATCTTTAAGT
1 TCATCTTTAAGTCT-AATATCGCTAGCCTTGAATCAGTATATTGACACCTTTATCATCTTTAAGT
* * * ** *
1133804 CCAATATCGTTGGCCTTGAATTAACATATTAGCATTCTAATCATCTTTAACTTTAATGTCGTTGG
65 CCAATATCGCTGGCCTTGAATCAACATATTAGCATTCTAATCATCTTTAACTCTAATGTCACTAG
*
1133869 CCTTAAATCAGCACATTGGCACTCTTA
130 CCTTAAATCAGCACATTAGCACTCTTA
1133896 TCATCTTTAA
1 TCATCTTTAA
1133906 TTCCAATGTT
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
155 8 0.06
156 135 0.94
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (156 bp):
TCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGTATATTGACACCTTTATCATCTTTAAGTC
CAATATCGCTGGCCTTGAATCAACATATTAGCATTCTAATCATCTTTAACTCTAATGTCACTAGC
CTTAAATCAGCACATTAGCACTCTTA
Found at i:1135068 original size:30 final size:30
Alignment explanation
Indices: 1135034--1135093 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1135024 GACATGATGA
1135034 AACACATTGTCATCATGGGCCGCTGAGCAT
1 AACACATTGTCATCATGGGCCGCTGAGCAT
*
1135064 AACACATTGTCATCATGGGCTGCTGAGCAT
1 AACACATTGTCATCATGGGCCGCTGAGCAT
1135094 TTACTGTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (30 bp):
AACACATTGTCATCATGGGCCGCTGAGCAT
Found at i:1137389 original size:96 final size:97
Alignment explanation
Indices: 1137186--1137404 Score: 259
Period size: 96 Copynumber: 2.3 Consensus size: 97
1137176 CCCCATATTT
* * * *
1137186 CGAAGAGATATTCCAACTCTATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCTTAAATTT
1 CGAAGAGATACTCCAACCCTATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCTAAATTA
* * *
1137251 TCATTAATCAGTATACTTCAACCTCATTCTTC
66 TCATCAATCAGTACACTTCAACCTCATTCCTC
*
1137283 TGAAGAGATACTCCAACCCTATTTTT-AACTTGTCAAGATTTAAATCTTATTTTTGCCTAAATTA
1 CGAAGAGATACTCCAACCCTATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCTAAATTA
* *
1137347 TCATCATTGGAG-ACACTGT-AACC-CTATTCCTC
66 TCATCAAT-CAGTACACT-TCAACCTC-ATTCCTC
* *
1137379 CGAGGGGATACTCCAATCCC-ATTTTT
1 CGAAGAGATACTCCAA-CCCTATTTTT
1137405 CAACCAAAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 75 0.71
97 29 0.28
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (97 bp):
CGAAGAGATACTCCAACCCTATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTGCCTAAATTA
TCATCAATCAGTACACTTCAACCTCATTCCTC
Found at i:1139041 original size:16 final size:16
Alignment explanation
Indices: 1139020--1139059 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1139010 ATTTTTATAT
*
1139020 TTAAATAAAATTTTAA
1 TTAAATAAAATTCTAA
*
1139036 TTAAATATAATTCTAA
1 TTAAATAAAATTCTAA
*
1139052 CTAAATAA
1 TTAAATAA
1139060 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATAAAATTCTAA
Found at i:1139100 original size:14 final size:14
Alignment explanation
Indices: 1139078--1139168 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 14
1139068 AAATTAATCT
*
1139078 AATTTATAATTTAA
1 AATTAATAATTTAA
*
1139092 AATTAATAAATTAA
1 AATTAATAATTTAA
* *
1139106 ATTTAA-ATTATTAA
1 AATTAATAAT-TTAA
*
1139120 ACTTAAATAA-TTAA
1 AATT-AATAATTTAA
*
1139134 ATTTAA-AATTTAA
1 AATTAATAATTTAA
* *
1139147 AATAAATCAAATTAA
1 AATTAAT-AATTTAA
*
1139162 AAATAAT
1 AATTAAT
1139169 TCAAAAATTT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.03
13 11 0.19
14 31 0.53
15 13 0.22
16 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTAATAATTTAA
Found at i:1139125 original size:28 final size:27
Alignment explanation
Indices: 1139078--1139162 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
1139068 AAATTAATCT
*
1139078 AATTTATAATTTAAAATTAATAAATTA
1 AATTTAAAATTTAAAATTAATAAATTA
* *
1139105 AATTTAAATTATTAAACTTAA-ATAATTA
1 AATTTAAAAT-TTAAAATTAATA-AATTA
*
1139133 AATTTAAAATTTAAAATAAATCAAATTA
1 AATTTAAAATTTAAAATTAAT-AAATTA
1139161 AA
1 AA
1139163 AATAATTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 17 0.35
28 30 0.62
29 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
AATTTAAAATTTAAAATTAATAAATTA
Found at i:1139164 original size:16 final size:16
Alignment explanation
Indices: 1139139--1139173 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1139129 ATTAAATTTA
*
1139139 AAATTTAAAATAAATC
1 AAATTAAAAATAAATC
*
1139155 AAATTAAAAATAATTC
1 AAATTAAAAATAAATC
1139171 AAA
1 AAA
1139174 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAAAAATAAATC
Found at i:1140263 original size:17 final size:18
Alignment explanation
Indices: 1140243--1140276 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1140233 TACTATTTTT
1140243 AATTATATTA-TATTTAA
1 AATTATATTATTATTTAA
1140260 AATTATATTATTATTTA
1 AATTATATTATTATTTA
1140277 TTAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATATTATTATTTAA
Found at i:1140517 original size:19 final size:19
Alignment explanation
Indices: 1140481--1140523 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1140471 ATTTTATTTG
1140481 TTTTATTTTCAAACTAAT-
1 TTTTATTTTCAAACTAATA
* *
1140499 TTTTATTTTTAATCTTAATA
1 TTTTATTTTCAAAC-TAATA
1140519 TTTTA
1 TTTTA
1140524 ATAATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 4 0.19
20 5 0.24
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATTTTCAAACTAATA
Found at i:1140618 original size:22 final size:22
Alignment explanation
Indices: 1140584--1140643 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
1140574 TTAAATTTAA
*
1140584 TTAATAATAATTTA-TAATATTT
1 TTAATATTAATTTACTAAT-TTT
*
1140606 TTAATATTGATTTACCTAATTTT
1 TTAATATTAATTTA-CTAATTTT
*
1140629 TTTATATTACATTTA
1 TTAATATTA-ATTTA
1140644 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 12 0.39
23 10 0.32
24 9 0.29
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATATTAATTTACTAATTTT
Found at i:1140642 original size:24 final size:24
Alignment explanation
Indices: 1140598--1140643 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1140588 TAATAATTTA
*
1140598 TAATATTTTTAATATTGATTTACC
1 TAATATTTTTAATATTCATTTACC
*
1140622 TAAT-TTTTTTATATTACATTTA
1 TAATATTTTTAATATT-CATTTA
1140644 TGTAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (24 bp):
TAATATTTTTAATATTCATTTACC
Found at i:1140986 original size:11 final size:10
Alignment explanation
Indices: 1140960--1141026 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
1140950 TATATTTTAT
1140960 TAAAA-ATT-
1 TAAAATATTA
1140968 TAAAATATTA
1 TAAAATATTA
1140978 T-AAATATATA
1 TAAAATAT-TA
1140988 TAAAATATTA
1 TAAAATATTA
* *
1140998 AAAAATATCA
1 TAAAATATTA
*
1141008 -ATAA-ATT-
1 TAAAATATTA
1141015 TAAAATATTA
1 TAAAATATTA
1141025 TA
1 TA
1141027 TTAAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 10 0.21
9 15 0.32
10 16 0.34
11 6 0.13
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAATATTA
Found at i:1140993 original size:20 final size:19
Alignment explanation
Indices: 1140957--1141035 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
1140947 ATATATATTT
1140957 TATTAAAA-AT-T-TAAAA
1 TATTAAAATATATATAAAA
1140973 TATTATAAATATATATAAAA
1 TATTA-AAATATATATAAAA
*
1140993 TATTAAAAAATATCA-ATAAA
1 TATTAAAATATAT-ATA-AAA
1141013 T-TTAAAATATTATATTAAAA
1 TATTAAAATA-TATA-TAAAA
1141033 TAT
1 TAT
1141036 ATTGATATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 2 0.04
19 17 0.33
20 22 0.43
21 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAAATATATATAAAA
Found at i:1141010 original size:27 final size:28
Alignment explanation
Indices: 1140962--1141024 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1140952 TATTTTATTA
* *
1140962 AAAAT-TTAAAATATTATAAATATATAT
1 AAAATATTAAAATAATATAAATAAATAT
* *
1140989 AAAATATTAAAA-AATATCAATAAATTT
1 AAAATATTAAAATAATATAAATAAATAT
1141016 AAAATATTA
1 AAAATATTA
1141025 TATTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATATTAAAATAATATAAATAAATAT
Found at i:1141031 original size:19 final size:19
Alignment explanation
Indices: 1140970--1141031 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1140960 TAAAAATTTA
*
1140970 AAATATTATAAATATATATA
1 AAATATTA-AAATATATATT
* *
1140990 AAATATTAAAAAATATCAAT
1 AAATATTAAAATATAT-ATT
1141010 AAAT-TTAAAATATTATATT
1 AAATATTAAAATA-TATATT
1141029 AAA
1 AAA
1141032 ATATATTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATTAAAATATATATT
Found at i:1141063 original size:16 final size:15
Alignment explanation
Indices: 1141019--1141063 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
1141009 TAAATTTAAA
*
1141019 ATATTATATTAAAAT
1 ATATTATATTAATAT
1141034 ATATTGATATTAATAT
1 ATATT-ATATTAATAT
1141050 ATATTAATATTAAT
1 ATATT-ATATTAAT
1141064 TAATTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATTATATTAATAT
Found at i:1142050 original size:2 final size:2
Alignment explanation
Indices: 1142043--1142082 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1142033 CACGCAACAG
1142043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1142083 TTAGCAGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1145160 original size:11 final size:11
Alignment explanation
Indices: 1145141--1145185 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1145131 CGGTAATTTA
*
1145141 TATATTTATAT
1 TATAATTATAT
1145152 TATAATTATGAT
1 TATAATTAT-AT
*
1145164 T-TTATTATAT
1 TATAATTATAT
1145174 TATAATTATAT
1 TATAATTATAT
1145185 T
1 T
1145186 TAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATAATTATAT
Found at i:1145174 original size:22 final size:21
Alignment explanation
Indices: 1145146--1145186 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1145136 ATTTATATAT
1145146 TTATATTATAATTATGATTTTA
1 TTATATTATAATTAT-ATTTTA
1145168 TTATATTATAATTATATTT
1 TTATATTATAATTATATTT
1145187 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATATTATAATTATATTTTA
Found at i:1145817 original size:2 final size:2
Alignment explanation
Indices: 1145812--1145872 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
1145802 TTTTTATGTT
* * *
1145812 TA TA TA TA TA TA TA TA TA TA -A TA TGC TGA T- TG TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA
1145854 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1145873 GCTGATCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.91
3 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1153720 original size:28 final size:27
Alignment explanation
Indices: 1153628--1154134 Score: 523
Period size: 27 Copynumber: 18.4 Consensus size: 27
1153618 CAACCTTTTT
*
1153628 CTTTTAAAGTCCACAACTCCGTGGCAAC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1153656 CTTTTAAGTCCACAGCTCC-TGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* ** *
1153682 CTTTAAAGTCCACAACTCTATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1153709 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1153737 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1153764 CTTTTACGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1153791 CTTTTAAGTCCACAGCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1153818 CTTTTAAGTCTACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1153845 CTTTTAAGTCCATAACTCCGTGGCAGCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1153873 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
* * **
1153901 TTTTTCAAGTCCATAACTTTGTGGCAGCC
1 CTTTT-AAGTCCACAACTCCGTGGCA-CC
*
1153930 CTTTTTAAGTCCATAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
* *
1153958 CTTTTAAAGTCCACAACTCCATGACAACC
1 CTTTT-AAGTCCACAACTCCGTGGC-ACC
* ***
1153987 CTTTTAAGTCTACAACTCTACGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1154014 CTTTTAAGTCCACAACTCTGTGATACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** * * *
1154041 CTTTTAAGTGTACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * * * *
1154068 ATTTCAAAG-CCTACAAGTCAGTGGCATC
1 CTTT-TAAGTCC-ACAACTCCGTGGCACC
* **
1154096 ATTTTAAGTCCACAACTCTATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1154123 CTTTTAAGTCCA
1 CTTTTAAGTCCA
1154135 TAAGTCAGTG
Statistics
Matches: 406, Mismatches: 61, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
26 22 0.05
27 218 0.54
28 111 0.27
29 51 0.13
30 4 0.01
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1154108 original size:82 final size:81
Alignment explanation
Indices: 1154015--1154180 Score: 260
Period size: 82 Copynumber: 2.0 Consensus size: 81
1154005 TACGGCACCC
* * ** *
1154015 TTTTAAGTCCACAACTCTGTGATACCCTTTTAAGTGTACAAGTCAGTGGCATCATTTCAAAGCCT
1 TTTTAAGTCCACAACTCTATGACACCCTTTTAAGTCCACAAGTCAGTGGCATCATTTCAAA-CCC
1154080 ACAAGTCAGTGGCATCA
65 ACAAGTCAGTGGCATCA
* *
1154097 TTTTAAGTCCACAACTCTATGGCACCCTTTTAAGTCCATAAGTCAGTGGCATCATTTCAAACCCA
1 TTTTAAGTCCACAACTCTATGACACCCTTTTAAGTCCACAAGTCAGTGGCATCATTTCAAACCCA
1154162 CAAGTCAGTGGCATCA
66 CAAGTCAGTGGCATCA
1154178 TTT
1 TTT
1154181 CAAAGCCTAC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 22 0.29
82 55 0.71
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (81 bp):
TTTTAAGTCCACAACTCTATGACACCCTTTTAAGTCCACAAGTCAGTGGCATCATTTCAAACCCA
CAAGTCAGTGGCATCA
Found at i:1154111 original size:109 final size:109
Alignment explanation
Indices: 1153988--1154209 Score: 309
Period size: 109 Copynumber: 2.0 Consensus size: 109
1153978 ATGACAACCC
* * * * * ****
1153988 TTTTAAGTCTACAACTCTACGGCACCCTTTTAAGTCCACAACTCTGTGATACCCTTTTAAGTGTA
1 TTTTAAGTCCACAACTCTACGGCACCCTTTTAAGTCCACAACTCAGTGACACCATTTCAAACCCA
1154053 CAAGTCAGTGGCATCATTTCAAAGCCTACAAGTCAGTGGCATCA
66 CAAGTCAGTGGCATCATTTCAAAGCCTACAAGTCAGTGGCATCA
* * * * *
1154097 TTTTAAGTCCACAACTCTATGGCACCCTTTTAAGTCCATAAGTCAGTGGCATCATTTCAAACCCA
1 TTTTAAGTCCACAACTCTACGGCACCCTTTTAAGTCCACAACTCAGTGACACCATTTCAAACCCA
*
1154162 CAAGTCAGTGGCATCATTTCAAAGCCTACAAGTCAGTGGCATCC
66 CAAGTCAGTGGCATCATTTCAAAGCCTACAAGTCAGTGGCATCA
1154206 TTTT
1 TTTT
1154210 CAAATCCCAC
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (109 bp):
TTTTAAGTCCACAACTCTACGGCACCCTTTTAAGTCCACAACTCAGTGACACCATTTCAAACCCA
CAAGTCAGTGGCATCATTTCAAAGCCTACAAGTCAGTGGCATCA
Found at i:1154146 original size:27 final size:27
Alignment explanation
Indices: 1153628--1154209 Score: 467
Period size: 27 Copynumber: 21.2 Consensus size: 27
1153618 CAACCTTTTT
* *
1153628 CTTTTAAAGTCCACAACTCCGTGGCAAC
1 CTTTT-AAGTCCACAACTCAGTGGCACC
* *
1153656 CTTTTAAGTCCACAGCTC-CTGGCACC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* *
1153682 CTTTAAAGTCCACAACTCTA-TGGCATC
1 CTTTTAAGTCCACAACTC-AGTGGCACC
*
1153709 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCAGTGGCACC
* *
1153737 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* * **
1153764 CTTTTACGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* *
1153791 CTTTTAAGTCCACAGCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* * *
1153818 CTTTTAAGTCTACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* *
1153845 CTTTTAAGTCCATAACTCCGTGGCAGCC
1 CTTTTAAGTCCACAACTCAGTGGCA-CC
*
1153873 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCAGTGGCACC
* * **
1153901 TTTTTCAAGTCCATAACTTTGTGGCAGCC
1 CTTTT-AAGTCCACAACTCAGTGGCA-CC
* *
1153930 CTTTTTAAGTCCATAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCAGTGGCACC
*
1153958 CTTTTAAAGTCCACAACTCCA-TGACAACC
1 CTTTT-AAGTCCACAACT-CAGTGGC-ACC
* *
1153987 CTTTTAAGTCTACAACTCTA-CGGCACC
1 CTTTTAAGTCCACAACTC-AGTGGCACC
* **
1154014 CTTTTAAGTCCACAACTCTGTGATACC
1 CTTTTAAGTCCACAACTCAGTGGCACC
** * *
1154041 CTTTTAAGTGTACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* * * *
1154068 ATTTCAAAG-CCTACAAGTCAGTGGCATC
1 CTTT-TAAGTCC-ACAACTCAGTGGCACC
*
1154096 ATTTTAAGTCCACAACTCTA-TGGCACC
1 CTTTTAAGTCCACAACTC-AGTGGCACC
* * *
1154123 CTTTTAAGTCCATAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* * ** * *
1154150 ATTTCAAACCCACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCAGTGGCACC
* * * *
1154177 ATTTCAAAG-CCTACAAGTCAGTGGCATC
1 CTTT-TAAGTCC-ACAACTCAGTGGCACC
1154205 CTTTT
1 CTTTT
1154210 CAAATCCCAC
Statistics
Matches: 463, Mismatches: 70, Indels: 43
0.80 0.12 0.07
Matches are distributed among these distances:
26 23 0.05
27 255 0.55
28 129 0.28
29 52 0.11
30 4 0.01
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCAGTGGCACC
Found at i:1154201 original size:28 final size:28
Alignment explanation
Indices: 1154052--1154599 Score: 506
Period size: 28 Copynumber: 19.5 Consensus size: 28
1154042 TTTTAAGTGT
* *
1154052 ACAAGTCAGTGGCATCATTTCAAAGCCT
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * *
1154080 ACAAGTCAGTGGCATCATTT-TAAGTCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * * *
1154107 ACAACTCTA-TGGCACCCTTT-TAAGTCC
1 ACAAGTC-AGTGGCATCCTTTCAAAGCCC
* *
1154134 ATAAGTCAGTGGCATCATTTCAAA-CCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* *
1154161 ACAAGTCAGTGGCATCATTTCAAAGCCT
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
*
1154189 ACAAGTCAGTGGCATCCTTTTCAAATCCC
1 ACAAGTCAGTGGCATCC-TTTCAAAGCCC
* * * **
1154218 ACGAA-TTAGTGGTACCCTTTCAAAGGTC
1 AC-AAGTCAGTGGCATCCTTTCAAAGCCC
* *
1154246 ACAAGTCAATGGCATCCTTCTCAAAGCCT
1 ACAAGTCAGTGGCATCCTT-TCAAAGCCC
* *
1154275 ATGAA-TCAGTGGCA-CTCTTTCAAAACCC
1 A-CAAGTCAGTGGCATC-CTTTCAAAGCCC
* * *
1154303 ACAAGTCAGTGGCACCCTTTCAAAACAC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * *
1154331 ACAAGTCAGTGGCATCTTTTTAAAGCCT
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
1154359 ACAAGTCAGTGGCATCCTTTTCAAAGCCC
1 ACAAGTCAGTGGCATCC-TTTCAAAGCCC
*
1154388 ACGAA-TCAGTGGCA-CCTTTTCATAGCCC
1 AC-AAGTCAGTGGCATCC-TTTCAAAGCCC
*
1154416 ACAAGTCAATGGCA-CCTTTCCAAAGCCC
1 ACAAGTCAGTGGCATCCTTT-CAAAGCCC
** *
1154444 ATGAGTTAGTGGCATCCTTTCAAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
1154472 ACAAGTCAGTGGCAT-CTCTTCAAAGCCC
1 ACAAGTCAGTGGCATCCT-TTCAAAGCCC
** *
1154500 ATGAGTCAGTGGCATCCTTCCAAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * *
1154528 ACGAGTCAGTAGCATCCTTCCAAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * * *
1154556 ACGAGTTAGTGGCATCTTTTTAAAGCCCAC
1 ACAAGTCAGTGGCATCCTTTCAAAG-CC-C
1154586 ACAAGTCAGTGGCA
1 ACAAGTCAGTGGCA
1154600 ACTTTCTCTA
Statistics
Matches: 432, Mismatches: 67, Indels: 40
0.80 0.12 0.07
Matches are distributed among these distances:
26 1 0.00
27 76 0.18
28 268 0.62
29 68 0.16
30 19 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
ACAAGTCAGTGGCATCCTTTCAAAGCCC
Found at i:1155824 original size:20 final size:21
Alignment explanation
Indices: 1155801--1155853 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1155791 ACAATTCAAA
** *
1155801 GTATCGATACATGTTACA-AT
1 GTATCGATACATGAAAAAGAT
1155821 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
1155842 GTATCGATACAT
1 GTATCGATACAT
1155854 TTCTTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:1160006 original size:15 final size:15
Alignment explanation
Indices: 1159986--1160016 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1159976 TAAAAATGTC
*
1159986 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1160001 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1160016 C
1 C
1160017 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1162283 original size:20 final size:20
Alignment explanation
Indices: 1162240--1162285 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1162230 AAATCTTTTG
1162240 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1162261 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1162281 CAAAA
1 CAAAA
1162286 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1167775 original size:97 final size:97
Alignment explanation
Indices: 1167598--1167772 Score: 219
Period size: 97 Copynumber: 1.8 Consensus size: 97
1167588 AAATTTATTT
* * * * * *
1167598 ATCGGGGATACTCCAACCCTATTCCTCCGAAGGGATACTCCAACCTCGCTTTTAAACCCATCAAG
1 ATCGAGGATACTCCAACCCCACTCCTCCGAAGGGATACTCCAACCTCACTTTTAAACCCATAAAA
**
1167663 GTTTAAATCTTTTTCTTGCTTAAATTGTCATC
66 AATTAAATCTTTTTCTTGCTTAAATTGTCATC
* * * *
1167695 ATCGAGGATACTCCAACCCCACTCCTCCGAGGGGATACTCCAACCTCATTTTTCAA-TCA-AAAA
1 ATCGAGGATACTCCAACCCCACTCCTCCGAAGGGATACTCCAACCTCACTTTTAAACCCATAAAA
1167758 AATTAAATCATTTTT
66 AATTAAATC-TTTTT
1167773 TCTCTCTCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
95 9 0.14
96 7 0.11
97 49 0.75
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (97 bp):
ATCGAGGATACTCCAACCCCACTCCTCCGAAGGGATACTCCAACCTCACTTTTAAACCCATAAAA
AATTAAATCTTTTTCTTGCTTAAATTGTCATC
Found at i:1169329 original size:60 final size:60
Alignment explanation
Indices: 1169262--1169382 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
1169252 CAAAATCTCT
* * * * * * *
1169262 TACCAAATCATAATCCCATGAATCTTTCTCCAAATCCTTATTCAATTTCTCTCATCCTAA
1 TACCAAATCACAATCCCACGAATCTCTCTCCAAATACTCATTCAATTCCTCTCAACCTAA
* *
1169322 TACCAAATCACAATCCTACGAATCTCTCTCCAAATACTCATTTAATTCCTCTCAACCTAA
1 TACCAAATCACAATCCCACGAATCTCTCTCCAAATACTCATTCAATTCCTCTCAACCTAA
1169382 T
1 T
1169383 TCCTAAAAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (60 bp):
TACCAAATCACAATCCCACGAATCTCTCTCCAAATACTCATTCAATTCCTCTCAACCTAA
Found at i:1177494 original size:2 final size:2
Alignment explanation
Indices: 1177487--1177517 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1177477 TTTGAAATTT
1177487 TA TA 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 TA TA T
1177518 TGATATCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1181586 original size:21 final size:20
Alignment explanation
Indices: 1181553--1181591 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1181543 CACCAACCAC
*
1181553 AAAAAAAAAAAAAGGTCAAG
1 AAAAAAAAAAAAAAGTCAAG
*
1181573 AAAATAAAATAAAAAGTCA
1 AAAA-AAAAAAAAAAGTCA
1181592 GTAAAAGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAAAAGTCAAG
Found at i:1183765 original size:2 final size:2
Alignment explanation
Indices: 1183758--1183788 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1183748 ATTTGAATAA
1183758 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1183789 TGATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1184380 original size:25 final size:26
Alignment explanation
Indices: 1184329--1184384 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1184319 CGTATGTATT
*
1184329 ATTTATTATAATTTTAATAATTAAAA
1 ATTTAATATAATTTTAATAATTAAAA
*
1184355 ATTTAATATATTTTTGAATAA-T-AAA
1 ATTTAATATAATTTT-AATAATTAAAA
1184380 ATTTA
1 ATTTA
1184385 CTTCTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 14 0.52
27 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAATATAATTTTAATAATTAAAA
Found at i:1185528 original size:25 final size:25
Alignment explanation
Indices: 1185504--1185558 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1185494 TTAAATAACA
1185504 ATAA-AAA-ATAAAATTATCTGAAAC
1 ATAATAAAGATAAAATT-TCTGAAAC
*
1185528 ATAATAAAGCTAAAATTTCTGAAAC
1 ATAATAAAGATAAAATTTCTGAAAC
*
1185553 CTAATA
1 ATAATA
1185559 TCAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
26 7 0.26
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (25 bp):
ATAATAAAGATAAAATTTCTGAAAC
Found at i:1185663 original size:21 final size:19
Alignment explanation
Indices: 1185635--1185674 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
1185625 AATATATTTA
1185635 AAACTAATTTTTTATCAATT
1 AAACTAA-TTTTTATCAATT
1185655 AAACTTAATTTTTATCAATT
1 AAAC-TAATTTTTATCAATT
1185675 TTTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (19 bp):
AAACTAATTTTTATCAATT
Found at i:1186531 original size:23 final size:22
Alignment explanation
Indices: 1186471--1186528 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
1186461 AATTAAAAAA
* * *
1186471 ATTTAGTTTATTAATAATTTTTT
1 ATTTATTTTATT-TTAAGTTTTT
1186494 ACTTT-TTTTA-TTTAAGTTTTT
1 A-TTTATTTTATTTTAAGTTTTT
1186515 ATTTATTTTATTTT
1 ATTTATTTTATTTT
1186529 TAAATGATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.10
21 14 0.48
22 4 0.14
23 5 0.17
24 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (22 bp):
ATTTATTTTATTTTAAGTTTTT
Found at i:1194731 original size:17 final size:18
Alignment explanation
Indices: 1194709--1194757 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
1194699 TTATTTATTT
1194709 GATATTTAAAAATTT-TA
1 GATATTTAAAAATTTATA
*
1194726 GATA-TTAAACATTTATA
1 GATATTTAAAAATTTATA
1194743 -AT-TTT-AAAATTTATA
1 GATATTTAAAAATTTATA
1194758 TTTTTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 9 0.32
16 13 0.46
17 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
GATATTTAAAAATTTATA
Found at i:1194762 original size:15 final size:16
Alignment explanation
Indices: 1194730--1194763 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1194720 ATTTTAGATA
1194730 TTAAACATTTATAATT
1 TTAAACATTTATAATT
*
1194746 TTAAA-ATTTATATTT
1 TTAAACATTTATAATT
1194761 TTA
1 TTA
1194764 CATAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAACATTTATAATT
Found at i:1194787 original size:19 final size:18
Alignment explanation
Indices: 1194754--1194813 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
1194744 TTTTAAAATT
*
1194754 TATATTTTTACATAAACATA
1 TATATTTATACATAAA-A-A
1194774 TATATTTATA-ATAAAAA
1 TATATTTATACATAAAAA
* *
1194791 TATATTTATATAT-ATAA
1 TATATTTATACATAAAAA
1194808 TATATT
1 TATATT
1194814 GTATTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 20 0.54
18 3 0.08
19 5 0.14
20 9 0.24
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTTATACATAAAAA
Found at i:1195960 original size:2 final size:2
Alignment explanation
Indices: 1195953--1195986 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1195943 TGCCCAGCCA
1195953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1195987 TTAAAGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196467 original size:2 final size:2
Alignment explanation
Indices: 1196460--1196488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1196450 TAAGGTAAGA
1196460 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 A
1196489 CATTACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1208616 original size:14 final size:12
Alignment explanation
Indices: 1208599--1208644 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1208589 ATATTATTTT
1208599 AATAATATTTCAAA
1 AATAA-ATTT-AAA
1208613 AATAAATTTAAA
1 AATAAATTTAAA
1208625 AAT--ATTTAAAA
1 AATAAATTT-AAA
1208636 AATAAATTT
1 AATAAATTT
1208645 CAGAATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.14
11 6 0.21
12 6 0.21
13 8 0.28
14 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAAATTTAAA
Found at i:1208622 original size:23 final size:23
Alignment explanation
Indices: 1208596--1208658 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1208586 CAAATATTAT
* *
1208596 TTTAATAATATTTCAAAAATAAA
1 TTTAAAAATATTTAAAAAATAAA
1208619 TTTAAAAATATTTAAAAAATAAA
1 TTTAAAAATATTTAAAAAATAAA
* * *
1208642 TTTCAGAATATCTAAAA
1 TTTAAAAATATTTAAAA
1208659 GTAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTAAAAATATTTAAAAAATAAA
Found at i:1208841 original size:1 final size:1
Alignment explanation
Indices: 1208837--1208864 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1208827 TGGCTGATTG
1208837 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1208865 CTGTTTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1210053 original size:16 final size:16
Alignment explanation
Indices: 1210034--1210071 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1210024 AATGCCAGCT
1210034 TTTTAAAATTCA-TCAA
1 TTTTAAAATTCAGT-AA
*
1210050 TTTTAAATTTCAGTAA
1 TTTTAAAATTCAGTAA
1210066 TTTTAA
1 TTTTAA
1210072 TTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTAAAATTCAGTAA
Found at i:1210157 original size:17 final size:18
Alignment explanation
Indices: 1210131--1210175 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1210121 ATTTCATTAG
* *
1210131 ATAAAAAAATAATTATA-
1 ATAAATAAATAATGATAC
1210148 ATAAATAAATAATGATAC
1 ATAAATAAATAATGATAC
1210166 TATAAATAAA
1 -ATAAATAAA
1210176 ATAAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
19 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAAATAAATAATGATAC
Found at i:1210888 original size:21 final size:21
Alignment explanation
Indices: 1210849--1210888 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1210839 AATTTTTTAA
*
1210849 TTCATTAAATAATATAATTTT
1 TTCATTAAATAATAGAATTTT
1210870 TTCATATAAATAAT-GAATT
1 TTCAT-TAAATAATAGAATT
1210889 ACTTGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (21 bp):
TTCATTAAATAATAGAATTTT
Found at i:1210968 original size:40 final size:43
Alignment explanation
Indices: 1210913--1211000 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 43
1210903 TAAAAATAAT
**
1210913 TTAATTTTGAAAACCTCTG-T-A-TTTTTATAAATCTATTGAA
1 TTAATTTCAAAAACCTCTGATCATTTTTTATAAATCTATTGAA
1210953 TTAATTTCAAAAACCTCTGTAATGCATTTTTTATAAATCTATTGAA
1 TTAATTTCAAAAACCTCTG--AT-CATTTTTTATAAATCTATTGAA
1210999 TT
1 TT
1211001 TAAAATATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
40 17 0.43
43 1 0.03
45 1 0.03
46 21 0.52
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (43 bp):
TTAATTTCAAAAACCTCTGATCATTTTTTATAAATCTATTGAA
Found at i:1211516 original size:7 final size:7
Alignment explanation
Indices: 1211504--1211544 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
1211494 ATCCTAATCT
1211504 TATAATA
1 TATAATA
1211511 TATAATA
1 TATAATA
1211518 TATAATA
1 TATAATA
*
1211525 AATAATA
1 TATAATA
1211532 TAATAATAA
1 T-ATAAT-A
1211541 TATA
1 TATA
1211545 TTATTTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 20 0.67
8 8 0.27
9 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TATAATA
Found at i:1211902 original size:14 final size:15
Alignment explanation
Indices: 1211879--1211918 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1211869 ATTTATGAAA
*
1211879 TTAATAATTTT-TCC
1 TTAATTATTTTGTCC
1211893 TTAATTATTTTGTCC
1 TTAATTATTTTGTCC
1211908 TTAATTATTTT
1 TTAATTATTTT
1211919 CTTACTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (15 bp):
TTAATTATTTTGTCC
Found at i:1213602 original size:21 final size:21
Alignment explanation
Indices: 1213565--1213616 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1213555 TTATATAAAA
*
1213565 AATATATATAAATAATAAATAT-
1 AATATA-ATAAAAAAT-AATATG
1213587 AATATAATAAAAAATAATATG
1 AATATAATAAAAAATAATATG
*
1213608 ATTATAATA
1 AATATAATA
1213617 TATTACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AATATAATAAAAAATAATATG
Found at i:1213616 original size:11 final size:10
Alignment explanation
Indices: 1213565--1213678 Score: 64
Period size: 9 Copynumber: 11.7 Consensus size: 10
1213555 TTATATAAAA
1213565 AATATA-TAT
1 AATATATTAT
*
1213574 AA-ATAATA-
1 AATATATTAT
*
1213582 AATATAATAT
1 AATATATTAT
* **
1213592 AATAAAAAAT
1 AATATATTAT
1213602 AATATGATTAT
1 AATAT-ATTAT
1213613 AATATATTACAT
1 AATATATT--AT
1213625 AAATATATTA-
1 -AATATATTAT
*
1213635 AATTTA-TAT
1 AATATATTAT
1213644 AA-ATA-TAT
1 AATATATTAT
*
1213652 AATATTTTA-
1 AATATATTAT
1213661 AATATAATTAT
1 AATAT-ATTAT
1213672 AATATAT
1 AATATAT
1213679 AAAAATATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
8 14 0.17
9 24 0.29
10 22 0.26
11 14 0.17
12 2 0.02
13 8 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
AATATATTAT
Found at i:1213619 original size:59 final size:60
Alignment explanation
Indices: 1213556--1213713 Score: 136
Period size: 59 Copynumber: 2.7 Consensus size: 60
1213546 TTGGCAGAAT
*
1213556 TATATAAAAAATATATATAAATAATAAATATAATATAATAAAAAAT-AATATGATTATAA
1 TATATAAAAAATATATATAAATAATAAATATAATATAATAAAAAATAAATATAATTATAA
* * * ***
1213615 TATATTACATAAATATAT-TAAAT-TTATATA-AATAT-ATAATATTTTAAATATAATTATAA
1 TATA-TA-AAAAATATATATAAATAATAAATATAATATAATAA-AAAATAAATATAATTATAA
*
1213674 TATAT-AAAAATATA-A-AAATATATTAATATAA-ATACATAAA
1 TATATAAAAAATATATATAAATA-ATAAATATAATATA-ATAAA
1213714 TTATTAAACT
Statistics
Matches: 78, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
55 4 0.05
56 8 0.10
57 10 0.13
58 11 0.14
59 29 0.37
60 7 0.09
61 9 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (60 bp):
TATATAAAAAATATATATAAATAATAAATATAATATAATAAAAAATAAATATAATTATAA
Found at i:1213674 original size:6 final size:7
Alignment explanation
Indices: 1213565--1213680 Score: 52
Period size: 6 Copynumber: 17.3 Consensus size: 7
1213555 TTATATAAAA
1213565 AATATAT
1 AATATAT
*
1213572 -ATAAAT
1 AATATAT
*
1213578 AATAAAT
1 AATATAT
1213585 -ATAATAT
1 AAT-ATAT
* *
1213592 AATAAAA
1 AATATAT
1213599 AATAATAT
1 AAT-ATAT
*
1213607 GAT-TAT
1 AATATAT
1213613 AATATAT
1 AATATAT
* *
1213620 TACATA-
1 AATATAT
1213626 AATATATT
1 AATATA-T
1213634 AA-AT-T
1 AATATAT
*
1213639 TATATA-
1 AATATAT
1213645 AATATAT
1 AATATAT
*
1213652 AATATTTT
1 AATA-TAT
1213660 AA-ATAT
1 AATATAT
1213666 AAT-TAT
1 AATATAT
1213672 AATATAT
1 AATATAT
1213679 AA
1 AA
1213681 AAATATAAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 26
0.66 0.13 0.21
Matches are distributed among these distances:
5 2 0.03
6 33 0.41
7 33 0.41
8 12 0.15
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:1215477 original size:22 final size:22
Alignment explanation
Indices: 1215438--1215491 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1215428 TAAAAAATTT
1215438 AAAACT-AAAAGACTAAATAAA
1 AAAACTAAAAAGACTAAATAAA
1215459 AAAACTAAAAAGA-TAAAATAAA
1 AAAACTAAAAAGACT-AAATAAA
*
1215481 ATAAAATAAAA
1 A-AAACTAAAA
1215492 CCTGTCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 7 0.24
22 14 0.48
23 8 0.28
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAACTAAAAAGACTAAATAAA
Found at i:1223904 original size:32 final size:33
Alignment explanation
Indices: 1223868--1223932 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1223858 ACAATTGTGT
* *
1223868 ATGTATCGATACAACG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
*
1223900 ATGTATCGATACAAAGCATAATGTATTGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
1223933 TCTGGATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:1223905 original size:13 final size:13
Alignment explanation
Indices: 1223887--1223913 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1223877 TACAACGATC
1223887 ATGTATCGATACA
1 ATGTATCGATACA
1223900 ATGTATCGATACA
1 ATGTATCGATACA
1223913 A
1 A
1223914 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1224496 original size:28 final size:28
Alignment explanation
Indices: 1224458--1224514 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 28
1224448 TTATGAATGC
1224458 AATAAACCAATCAAAG-TTTTA-CATGT
1 AATAAACCAATCAAAGATTTTATCATGT
* *
1224484 AATAAACTTCAATTAAGGATTTTATCATGT
1 AATAAAC--CAATCAAAGATTTTATCATGT
1224514 A
1 A
1224515 CAACTCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.28
28 7 0.28
29 5 0.20
30 6 0.24
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (28 bp):
AATAAACCAATCAAAGATTTTATCATGT
Found at i:1224896 original size:30 final size:30
Alignment explanation
Indices: 1224860--1224916 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1224850 GATGAATTTT
**
1224860 AAAAATTTTA-AACTTAGAAAAATCTCACCA
1 AAAAATTTTATAAAGTAG-AAAATCTCACCA
1224890 AAAAATTTTATAAAGTAGAAAATCTCA
1 AAAAATTTTATAAAGTAGAAAATCTCA
1224917 TATATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAAATTTTATAAAGTAGAAAATCTCACCA
Found at i:1225875 original size:41 final size:40
Alignment explanation
Indices: 1225841--1226536 Score: 128
Period size: 41 Copynumber: 17.0 Consensus size: 40
1225831 AACAAGCTAC
*
1225841 AAAGGTTGATCGAGATAAAACCATACGAGTCAACAAATAA
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAATAA
* * * *
1225881 AAGAGGTTGA-CTAGGATGAAACCATATGAGTGAACAATTGAGA
1 AA-AGGTTGATCGA-GATGAAACCATACGAGTCAACAAAT-A-A
* * *
1225924 AAA-GTTGATCGAGATGAAACTATACGATTCAACGAATAA
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAATAA
* * * ** * * * *
1225963 GAAGGGTTG-GCTAGGACAAAACTATACAAGCCAATAAA-AGA
1 -AAAGGTTGATCGA-GATGAAACCATACGAGTCAACAAATA-A
* * * * * ** *
1226004 GAAAAGTTGATGGAAATGAGACTATATAAGTCAACGAATAA
1 -AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAATAA
* * * *
1226045 GAAAGGTT-AACCAGGATGAAACCATACAAGTCAAC---GAA
1 -AAAGGTTGATCGA-GATGAAACCATACGAGTCAACAAATAA
* * * ** * * * *
1226083 AGAGGTTGATTGGGACAAAACCATACAAGTTAGCAAACGAGA
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAA-TA-A
* * * * *
1226125 AAAGATT-AACTGGGATGAAACCATATGAGTCAACAAATGAG
1 AAAGGTTGATC-GAGATGAAACCATACGAGTCAACAAAT-AA
* * * * * ***
1226166 AAGGGTTGA-CGAGAATAAAACCATATGAGTTAATGAAAGGG
1 AAAGGTTGATCGAG-ATGAAACCATACGAGTCAA-CAAATAA
* * * *
1226207 AAATGTTGAT-TAGACTGAAACCATATGAGTCAACAAACTAG
1 AAAGGTTGATCGAGA-TGAAACCATACGAGTCAACAAA-TAA
* ** * * * * *
1226248 AAAGATTGATTAAGACGAAACTATATGAGTCAATAAATGAG
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAAT-AA
** * ** * * *
1226289 AAAGACTAATCGAGATGAAACCATATAAGTTAACGAAAGAG
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAAC-AAATAA
* * * * *
1226330 AAAGGTTGAGT-GGGATGGAACAATACAAG-CTAACAAGTTAGA
1 AAAGGTTGA-TCGAGATGAAACCATACGAGTC-AACAA-ATA-A
* * * * * * *
1226372 AATGGGTTGATTGGGACGAAACCATACAAGT-AAAAAAAAA
1 AA-AGGTTGATCGAGATGAAACCATACGAGTCAACAAATAA
* * *
1226412 AAAGAAAAGTTAATCGGGATGAAACTATACGAGTCAACAAATATA
1 AAAG----GTTGATCGAGATGAAACCATACGAGTCAACAAATA-A
* * * * *
1226457 AAAGGTTGATCGAGATAAAACTATACAAGACAA-AGAATGAG
1 AAAGGTTGATCGAGATGAAACCATACGAGTCAACA-AAT-AA
* * * *
1226498 AAAGGTTGA-CTAGGATGAAACTATACAAGTCAACGAATA
1 AAAGGTTGATCGA-GATGAAACCATACGAGTCAACAAATA
1226537 GGAAATGATG
Statistics
Matches: 477, Mismatches: 133, Indels: 92
0.68 0.19 0.13
Matches are distributed among these distances:
37 23 0.05
38 3 0.01
39 2 0.00
40 28 0.06
41 313 0.66
42 52 0.11
43 45 0.09
44 6 0.01
45 5 0.01
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAGGTTGATCGAGATGAAACCATACGAGTCAACAAATAA
Found at i:1225949 original size:82 final size:83
Alignment explanation
Indices: 1225845--1226086 Score: 247
Period size: 82 Copynumber: 3.0 Consensus size: 83
1225835 AGCTACAAAG
* * * **
1225845 GTTGATCGAGATAAAACCATACGAGTCAACAAATAA-AAGAGGTTGACTAGGATGAAACCATATG
1 GTTGATCGAGATGAAACTATACGAGTCAACGAATAAGAAGAGGTTGACTAGGATGAAACCATACA
** **
1225909 AGTGAACAATTGAGAAAA
66 AGCCAACAAAAGAGAAAA
* * ** *
1225927 GTTGATCGAGATGAAACTATACGATTCAACGAATAAGAAG-GGTTGGCTAGGACAAAACTATACA
1 GTTGATCGAGATGAAACTATACGAGTCAACGAATAAGAAGAGGTTGACTAGGATGAAACCATACA
*
1225991 AGCCAATAAAAGAGAAAA
66 AGCCAACAAAAGAGAAAA
* * * ** * *
1226009 GTTGATGGAAATGAGACTATATAAGTCAACGAATAAGAA-AGGTTAACCAGGATGAAACCATACA
1 GTTGATCGAGATGAAACTATACGAGTCAACGAATAAGAAGAGGTTGACTAGGATGAAACCATACA
* *
1226073 AGTCAACGAAAGAG
66 AGCCAACAAAAGAG
1226087 GTTGATTGGG
Statistics
Matches: 128, Mismatches: 30, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
82 125 0.98
83 3 0.02
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (83 bp):
GTTGATCGAGATGAAACTATACGAGTCAACGAATAAGAAGAGGTTGACTAGGATGAAACCATACA
AGCCAACAAAAGAGAAAA
Found at i:1226556 original size:41 final size:40
Alignment explanation
Indices: 1226428--1226557 Score: 127
Period size: 41 Copynumber: 3.2 Consensus size: 40
1226418 AAGTTAATCG
* * **
1226428 GGATGAAACTATACGAGTCAACAAATATAAAAGGTTGATC
1 GGATGAAACTATACAAGTCAACGAATAGGAAAGGTTGATC
* * * *
1226468 GAGATAAAACTATACAAGACAAAGAAT-GAGAAAGGTTGACTA
1 G-GATGAAACTATACAAGTCAACGAATAG-GAAAGGTTGA-TC
* *
1226510 GGATGAAACTATACAAGTCAACGAATAGGAAATGATGATC
1 GGATGAAACTATACAAGTCAACGAATAGGAAAGGTTGATC
1226550 GTGATGAA
1 G-GATGAA
1226558 TCTTACTTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
40 3 0.04
41 65 0.92
42 3 0.04
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (40 bp):
GGATGAAACTATACAAGTCAACGAATAGGAAAGGTTGATC
Found at i:1227187 original size:19 final size:20
Alignment explanation
Indices: 1227165--1227203 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1227155 AACATATACA
*
1227165 TGTAAA-ATCAACATCATAT
1 TGTAAAGATCAACATAATAT
1227184 TGTAAAGATCAACATAATAT
1 TGTAAAGATCAACATAATAT
1227204 CAACACAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (20 bp):
TGTAAAGATCAACATAATAT
Found at i:1227270 original size:2 final size:2
Alignment explanation
Indices: 1227263--1227299 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1227253 ATCAAGAAAG
1227263 AT 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 AT A
1227300 AACAAGCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1231546 original size:21 final size:21
Alignment explanation
Indices: 1231509--1231549 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1231499 AAATTATAGT
*
1231509 TTTATTAATAAATAATTAAAA
1 TTTAATAATAAATAATTAAAA
1231530 TTTAATAA-AAATAAATTAAA
1 TTTAATAATAAAT-AATTAAA
1231550 TAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAATAATAAATAATTAAAA
Found at i:1232977 original size:15 final size:16
Alignment explanation
Indices: 1232947--1232984 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1232937 AAAAATATAA
*
1232947 AAAATAACATAAAAAT
1 AAAATAACAAAAAAAT
1232963 AAAAT-ACAAAAAAAT
1 AAAATAACAAAAAAAT
*
1232978 AACATAA
1 AAAATAA
1232985 AATAACTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAACAAAAAAAT
Found at i:1234941 original size:20 final size:20
Alignment explanation
Indices: 1234909--1234949 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1234899 AATTTTATTC
1234909 AAATTTAATTATAAAATAAT
1 AAATTTAATTATAAAATAAT
1234929 AAATATTAA-TATAAAATAAT
1 AAAT-TTAATTATAAAATAAT
1234949 A
1 A
1234950 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTAATTATAAAATAAT
Found at i:1237223 original size:20 final size:20
Alignment explanation
Indices: 1237198--1237259 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1237188 TTTGTAATAG
1237198 CAAATTACATAAATCATTAT
1 CAAATTACATAAATCATTAT
*
1237218 CAAATTACATACAAACATTAT
1 CAAATTACATA-AATCATTAT
* *
1237239 AAAATTACATAAATTATTAT
1 CAAATTACATAAATCATTAT
1237259 C
1 C
1237260 GAAACTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.34
Consensus pattern (20 bp):
CAAATTACATAAATCATTAT
Found at i:1237238 original size:21 final size:20
Alignment explanation
Indices: 1237198--1237251 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
1237188 TTTGTAATAG
*
1237198 CAAATTACATAAATCATTAT
1 CAAATTACATAAAACATTAT
1237218 CAAATTACATACAAACATTAT
1 CAAATTACATA-AAACATTAT
*
1237239 AAAATTACATAAA
1 CAAATTACATAAA
1237252 TTATTATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (20 bp):
CAAATTACATAAAACATTAT
Found at i:1237447 original size:2 final size:2
Alignment explanation
Indices: 1237440--1237473 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1237430 AATTAGGTTA
1237440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1237474 CTTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1238504 original size:13 final size:13
Alignment explanation
Indices: 1238480--1238512 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1238470 TATCACAAAA
1238480 ATATTT-TTTATT
1 ATATTTATTTATT
1238492 ATATTTATTTATT
1 ATATTTATTTATT
*
1238505 ATAATTAT
1 ATATTTAT
1238513 AAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATATTTATTTATT
Found at i:1238559 original size:23 final size:23
Alignment explanation
Indices: 1238506--1238570 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
1238496 TTATTTATTA
*
1238506 TAATTATAAATT-TAATAAATAT
1 TAATTATCAATTATAATAAATAT
*
1238528 TATTGTATCAATTATAATAAATAT
1 TAAT-TATCAATTATAATAAATAT
1238552 TAATTATCAA-TATTAATAA
1 TAATTATCAATTA-TAATAA
1238571 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.14
23 19 0.51
24 13 0.35
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTATCAATTATAATAAATAT
Found at i:1238834 original size:3 final size:3
Alignment explanation
Indices: 1238828--1238869 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1238818 TATTCGCCAA
1238828 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1238870 TAAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1244517 original size:40 final size:41
Alignment explanation
Indices: 1244473--1244555 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 41
1244463 TATTTGTCAA
1244473 ATTAAATAAATAA-TT-ATGAATAAAAT-T-TTTATGTTTATTT
1 ATTAAATAAATAAGTTCA--AATAAAATGTGTTTA-GTTTATTT
1244513 ATTAAATAAATAAGTTCAAATAAAATGTGTTTAGTTTATTT
1 ATTAAATAAATAAGTTCAAATAAAATGTGTTTAGTTTATTT
1244554 AT
1 AT
1244556 ATTCATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
40 21 0.54
41 13 0.33
42 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (41 bp):
ATTAAATAAATAAGTTCAAATAAAATGTGTTTAGTTTATTT
Found at i:1254435 original size:20 final size:20
Alignment explanation
Indices: 1254389--1254440 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1254379 GTTGGGCTTA
* *
1254389 ATATATCGATACATTTTACC
1 ATATATCGATACAATTAACC
* *
1254409 ATGTATCGATACAATTAATC
1 ATATATCGATACAATTAACC
*
1254429 ATATATCAATAC
1 ATATATCGATAC
1254441 TATGTATCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (20 bp):
ATATATCGATACAATTAACC
Done.