Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2487
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: 76845
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4220 original size:76 final size:78
Alignment explanation
Indices: 4119--4322 Score: 218
Period size: 76 Copynumber: 2.6 Consensus size: 78
4109 GAGATAATAA
* * * * *
4119 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
4183 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* * **
4195 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
4260 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * *
4274 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
4323 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 3 0.03
79 45 0.43
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:4314 original size:28 final size:28
Alignment explanation
Indices: 4274--4345 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
4264 GGAATAAAGC
** *
4274 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4302 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4330 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4346 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:4403 original size:52 final size:52
Alignment explanation
Indices: 4334--4503 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 52
4324 AAATAACGAG
* * * *
4334 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCAGGA
** * *
4386 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCAGGA
* * *
4439 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCA-GA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGAGTTTTGAA-AATAAAACCAGGA
4490 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
4504 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
51 4 0.04
52 83 0.84
53 12 0.12
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCAGGA
Found at i:4522 original size:28 final size:28
Alignment explanation
Indices: 4490--4558 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
4480 TAAAACCAGA
4490 GTTGGAGTATCCCCTCGA-AAATAACGGG
1 GTTGGAGTATCCCC-CGATAAATAACGGG
* *
4518 GTTGGAGTAT-CCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCGATAAATAACGGG
4545 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
4559 GATTGTGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 21 0.57
28 13 0.35
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (28 bp):
GTTGGAGTATCCCCCGATAAATAACGGG
Found at i:6991 original size:13 final size:13
Alignment explanation
Indices: 6973--6998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6963 ACAAAGATCC
6973 ATGTATCGATACA
1 ATGTATCGATACA
6986 ATGTATCGATACA
1 ATGTATCGATACA
6999 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:6994 original size:33 final size:33
Alignment explanation
Indices: 6952--7018 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6942 AAAATTTCCA
***
6952 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
6985 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
7018 A
1 A
7019 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:7062 original size:19 final size:18
Alignment explanation
Indices: 7038--7105 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
7028 CAGTAGCTAA
7038 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
7057 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
7072 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
7089 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
7106 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:7078 original size:13 final size:13
Alignment explanation
Indices: 7060--7084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7050 ACAATACTTA
7060 TGTATCGATACAT
1 TGTATCGATACAT
7073 TGTATCGATACA
1 TGTATCGATACA
7085 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7082 original size:32 final size:32
Alignment explanation
Indices: 7041--7103 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7031 TAGCTAATTA
*
7041 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
7073 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
7104 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:7185 original size:21 final size:21
Alignment explanation
Indices: 7161--7217 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
7151 CATTTGTAGG
7161 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
7182 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
7203 ATGTATCGATACATT
1 ATGTATCGATACATT
7218 TAAATTTTTT
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:10697 original size:14 final size:14
Alignment explanation
Indices: 10658--10697 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
10648 ATCTCTTAAA
*
10658 ATAAAATAAAAATT
1 ATAAAATAAAAAAT
*
10672 A-AAAATTAAAAAT
1 ATAAAATAAAAAAT
10685 ATAAAATAAAAAA
1 ATAAAATAAAAAA
10698 AACTAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAATAAAAAAT
Found at i:10705 original size:7 final size:6
Alignment explanation
Indices: 10655--10696 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 6
10645 TACATCTCTT
10655 AAAAT- AAAATA AAAATTA AAAATTA AAAATA TAAAATA AAAA
1 AAAATA AAAATA AAAA-TA AAAA-TA AAAATA -AAAATA AAAA
10697 AAACTAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.15
6 10 0.29
7 19 0.56
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:11183 original size:23 final size:25
Alignment explanation
Indices: 11147--11192 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
11137 CAAATATAAT
* *
11147 ATAATTATACAATATGATATGAAAA
1 ATAATTATACAATACGACATGAAAA
11172 ATAA-TATA-AATACGACATGAA
1 ATAATTATACAATACGACATGAA
11193 TAGATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 4 0.21
25 4 0.21
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.28
Consensus pattern (25 bp):
ATAATTATACAATACGACATGAAAA
Found at i:15605 original size:52 final size:52
Alignment explanation
Indices: 15527--15654 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
15517 CGAAATATGA
*
15527 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
15579 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
15631 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
15655 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:15681 original size:13 final size:13
Alignment explanation
Indices: 15663--15687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15653 CAAAGATCAG
15663 TGTATCGATACAA
1 TGTATCGATACAA
15676 TGTATCGATACA
1 TGTATCGATACA
15688 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:15765 original size:33 final size:33
Alignment explanation
Indices: 15728--15794 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
15718 AGTAGCTTAA
15728 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
15761 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
15794 A
1 A
15795 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:15768 original size:13 final size:13
Alignment explanation
Indices: 15750--15774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15740 CAAAAAAATA
15750 TGTATCGATACAT
1 TGTATCGATACAT
15763 TGTATCGATACA
1 TGTATCGATACA
15775 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16793 original size:171 final size:171
Alignment explanation
Indices: 16593--16987 Score: 682
Period size: 171 Copynumber: 2.3 Consensus size: 171
16583 TTTTAGAGAT
* *
16593 GATGAAGGTGCCAATATGCCGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
16658 GTGATAAAGATGCCAATATGTTGATTCATGGCCAATGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
16723 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
16764 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
16829 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
16894 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
16935 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
16988 GTGCCAATGT
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
171 167 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:17202 original size:49 final size:49
Alignment explanation
Indices: 16901--17994 Score: 1275
Period size: 49 Copynumber: 22.7 Consensus size: 49
16891 GGATGTCAAC
* *
16901 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* *
16953 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
*
16996 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* *
17048 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * * **
17091 GTGCTGATTTAAGGCCAGCTACATTGGACTTAATGGT-GGGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
17139 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * *
17188 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * * *
17237 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
*
17286 GTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* * *
17337 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* *
17386 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* *
17438 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* *
17481 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGAAAAGGTGCCGAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* *
17533 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * **
17576 GTGCTGATTCAAGGCCAGCTACATTGGACTTAATGGT-GGGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
17624 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * *
17673 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * * *
17722 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
*
17771 GTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
* * * *
17822 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * * *
17871 ATGCTGATTCAGGGCCAGCTATATTGGGC-T-----TAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* *
17914 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
* * * *
17963 ATACTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTA
17995 GAAGGGTTGC
Statistics
Matches: 903, Mismatches: 90, Indels: 101
0.83 0.08 0.09
Matches are distributed among these distances:
43 188 0.21
44 5 0.01
46 4 0.00
48 98 0.11
49 377 0.42
51 82 0.09
52 149 0.17
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAAT
Found at i:17473 original size:22 final size:22
Alignment explanation
Indices: 17448--17515 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
17438 ATGCTGATTC
17448 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
17470 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
17491 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
17513 AAG
1 AAG
17516 ATGGAAAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 11 0.33
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:17810 original size:485 final size:485
Alignment explanation
Indices: 16834--17994 Score: 1953
Period size: 485 Copynumber: 2.4 Consensus size: 485
16824 GAAAAGTGAT
* * * * * * *
16834 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCA
* *
16899 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
60 ATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
*
16964 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
125 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAA
17029 AGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTG
190 AGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTG
*
17094 CTGATTTAAGGCCAGCTACATTGGACTTAATGGTGGGGTGCCAATGTGCTGATTCAAGGCCAGCT
255 CTGATTCAAGGCCAGCTACATTGGACTTAATGGTGGGGTGCCAATGTGCTGATTCAAGGCCAGCT
17159 ACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
320 ACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
17224 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
385 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
17289 CTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGA
450 CTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGA
17325 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
17390 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
17455 GCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
131 GCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
17520 AAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATT
196 AAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATT
17585 CAAGGCCAGCTACATTGGACTTAATGGTGGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
261 CAAGGCCAGCTACATTGGACTTAATGGTGGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
17650 GACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
326 GACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
17715 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
391 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
17780 CAAGGCCAGCTACATTGGACTTAAGATGGA
456 CAAGGCCAGCTACATTGGACTTAAGATGGA
* *
17810 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * * *
17875 TGATTCAGGGCCAGCTATATTGGGCTT-AA-A--G-----GTGCCAATGTGCTGATTCAAGGCCA
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
* * * *
17931 GCTACATTGGACTTAAAGATGAAGATGCCAATATACTGATTCAAGGCCAGCTATATTGGGCTTA
131 GCTATATTGGACTT-AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
17995 GAAGGGTTGC
Statistics
Matches: 641, Mismatches: 23, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
476 37 0.06
477 2 0.00
478 1 0.00
479 1 0.00
481 2 0.00
482 36 0.06
483 1 0.00
484 2 0.00
485 511 0.80
486 4 0.01
489 1 0.00
491 43 0.07
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (485 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
GCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
AAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATT
CAAGGCCAGCTACATTGGACTTAATGGTGGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
GACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
CAAGGCCAGCTACATTGGACTTAAGATGGA
Found at i:17970 original size:92 final size:92
Alignment explanation
Indices: 17810--17999 Score: 335
Period size: 92 Copynumber: 2.1 Consensus size: 92
17800 TTAAGATGGA
* *
17810 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATAC
*
17875 TGATTCAGGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGGCTT
*
17902 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATAC
17967 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGGCTT
17994 AGAAGG
1 A-AAGG
18000 GTTGCCACCG
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 89 0.96
93 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATAC
TGATTCAAGGCCAGCTATATTGGGCTT
Found at i:18038 original size:33 final size:35
Alignment explanation
Indices: 17994--18063 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
17984 TATTGGGCTT
17994 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
18028 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
18062 AG
1 AG
18064 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:18106 original size:34 final size:33
Alignment explanation
Indices: 18068--18664 Score: 572
Period size: 34 Copynumber: 17.6 Consensus size: 33
18058 AGGAAGGGAG
* *
18068 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
18102 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAG---GAA
* * *
18140 AAAGGTGCCACGGAGTTATGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
18174 AAAAGTGCCACGGAGTTATGGGCTTAAAAGG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
18205 --A--TGCCACGGAGTTGTGGGCTTAGAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
18235 AGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 A-AAGGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
*
18272 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
18307 AAAGTGTGCCACAGAGTTGTGGGCTTCAAAA-GAA
1 AAAG-GTGCCACGGAGTTGTGGGCTT-AAAAGGAA
18341 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
*
18377 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
18412 AAAGTGTGCCACAGAGTTGTGGGCTTTAAACA-GAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
18447 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
18481 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
18515 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
18549 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * **
18581 AAAGGTGCCACGAAGCTGTGGGCTTTGAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * * *
18613 AAA-ATGCCACTGAGTCGTGGACTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
18644 AAAGATGCCACTGAGTCGTGG
1 AAAGGTGCCACGGAGTTGTGG
18665 ACTTTGAGCA
Statistics
Matches: 491, Mismatches: 40, Indels: 66
0.82 0.07 0.11
Matches are distributed among these distances:
27 24 0.05
29 1 0.00
31 23 0.05
32 51 0.10
33 30 0.06
34 145 0.30
35 106 0.22
36 35 0.07
37 68 0.14
38 8 0.02
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:18210 original size:27 final size:27
Alignment explanation
Indices: 18179--18232 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
18169 ATGAAAAAAG
18179 TGCCACGGAGTTATGGGCTTAAAAGGA
1 TGCCACGGAGTTATGGGCTTAAAAGGA
* *
18206 TGCCACGGAGTTGTGGGCTTAGAAGGA
1 TGCCACGGAGTTATGGGCTTAAAAGGA
18233 AAAGAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (27 bp):
TGCCACGGAGTTATGGGCTTAAAAGGA
Found at i:18376 original size:105 final size:101
Alignment explanation
Indices: 18206--18606 Score: 549
Period size: 105 Copynumber: 3.9 Consensus size: 101
18196 CTTAAAAGGA
* *
18206 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 TGCCACAGAGTTGTGGGCTTA-AAAG-AAA-AAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGA
18271 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTG
61 AAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTG
18313 TGCCACAGAGTTGTGGGCTTCAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
1 TGCCACAGAGTTGTGGGCTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAA
18378 AAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTG
63 AAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTG
*
18418 TGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACAGAGTTGTGGGC-TTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAA
* * *
18483 AGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAA-AG
64 AGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGTG
* *
18520 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGG-AAA
1 TGCCACAGAGTTGTGGGC-TT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAA
* *
18583 AGGTGCCACGAAGCTGTGGGCTTT
64 AGGTGCCACGGAGTTGTGGGCTTT
18607 GAAGAAAAAA
Statistics
Matches: 275, Mismatches: 13, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
100 21 0.08
101 6 0.02
102 55 0.20
103 28 0.10
104 7 0.03
105 100 0.36
106 35 0.13
107 22 0.08
108 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (101 bp):
TGCCACAGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAG
GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTG
Found at i:18687 original size:31 final size:31
Alignment explanation
Indices: 18617--18762 Score: 231
Period size: 31 Copynumber: 4.7 Consensus size: 31
18607 GAAGAAAAAA
* *
18617 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGA-
1 TGCCACTGAGTCGTGGACTTT-GA-GAAGAGAT
*
18649 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
18680 TGCCACTGGGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
18711 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
18742 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
18763 AAAAAGGTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.05
31 81 0.76
32 21 0.20
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:18734 original size:62 final size:63
Alignment explanation
Indices: 18486--18765 Score: 257
Period size: 63 Copynumber: 4.4 Consensus size: 63
18476 AAGAAAAAGG
* * * * * * *
18486 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
1 TGCCACTGAGTCGTGGACTTTAAAG--GAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAAG-AG
*
18550 AAGG
62 -A-T
* * * * * *
18554 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCAC-GAAG-CTGTGGGCTTTGAAGAA-AAA
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTG-AGTC-GTGGACTTTG-AGAAGAGA
*
18616 A
63 T
*
18617 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGAT
* * *
18680 TGCCACTGGGTCGTGGACTTT-GA-GAAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
18742 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
18766 AAGGTATTTG
Statistics
Matches: 182, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
61 6 0.03
62 54 0.30
63 68 0.37
64 3 0.02
65 2 0.01
66 18 0.10
67 8 0.04
68 17 0.09
69 6 0.03
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.23
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:27023 original size:52 final size:52
Alignment explanation
Indices: 26945--27072 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
26935 CGAAATATGA
*
26945 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
26997 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
27049 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
27073 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:27099 original size:13 final size:13
Alignment explanation
Indices: 27081--27105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27071 CAAAGATCAG
27081 TGTATCGATACAA
1 TGTATCGATACAA
27094 TGTATCGATACA
1 TGTATCGATACA
27106 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27183 original size:33 final size:33
Alignment explanation
Indices: 27146--27212 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
27136 AGTAGCTTAA
27146 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
27179 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
27212 A
1 A
27213 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:27186 original size:13 final size:13
Alignment explanation
Indices: 27168--27192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27158 CAAAAAAATA
27168 TGTATCGATACAT
1 TGTATCGATACAT
27181 TGTATCGATACA
1 TGTATCGATACA
27193 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:32427 original size:51 final size:51
Alignment explanation
Indices: 32312--32427 Score: 119
Period size: 51 Copynumber: 2.3 Consensus size: 51
32302 AAACATATTT
* * * *** *
32312 TATAAAAAATAAAATAATTGAGAAAGAAAATCTTGAAAAATAGAAAATCAAA
1 TATAAAGAA-AAAATAATTGAAAAACAAAAAAATGAAAAATAGAAAATAAAA
*
32364 T-TAAAAGGAAAAATAATTGAAAAACAAAAAAATGAAAAATA-AAATATAAAA
1 TAT-AAAGAAAAAATAATTGAAAAACAAAAAAATGAAAAATAGAAA-ATAAAA
32415 TATAAAGAAAAAA
1 TATAAAGAAAAAA
32428 ATTTACATAC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
50 3 0.06
51 43 0.83
52 6 0.12
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.19
Consensus pattern (51 bp):
TATAAAGAAAAAATAATTGAAAAACAAAAAAATGAAAAATAGAAAATAAAA
Found at i:35204 original size:13 final size:13
Alignment explanation
Indices: 35186--35210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35176 TTCAACGATT
35186 TGTATCGATACAA
1 TGTATCGATACAA
35199 TGTATCGATACA
1 TGTATCGATACA
35211 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:40257 original size:21 final size:21
Alignment explanation
Indices: 40233--40286 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
40223 TTCTACAATT
40233 TGTATCAATACAACAAGTGAA
1 TGTATCAATACAACAAGTGAA
*
40254 TGTATCAATAC-ATAAGTGAA
1 TGTATCAATACAACAAGTGAA
*
40274 TGTATCGATACAA
1 TGTATCAATACAA
40287 GACTCTGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCAATACAACAAGTGAA
Found at i:40469 original size:102 final size:101
Alignment explanation
Indices: 40322--40507 Score: 284
Period size: 102 Copynumber: 1.8 Consensus size: 101
40312 TCTAAAAAGA
* * ** *
40322 AAATGTATCGATACATTTTTATTCTATTGATATATTCTAGGTTTGATCCAAATGTATCGATACAT
1 AAATATATCGATACATTTTTATTATATCAATATATTCTAGGTTTGACCCAAATGTATCGATACAT
*
40387 TCTTCATTGTATCAATACATTATGGGTTTTTTACCT
66 TCTTCAATGTATCAATACATTATGGGTTTTTTACCT
*
40423 AAATATATCGATACATTATTTATTATATCAATATATT-TGGGTTTTGACCCAAATGTATCGATAC
1 AAATATATCGATACATT-TTTATTATATCAATATATTCTAGG-TTTGACCCAAATGTATCGATAC
40487 ATTCTTCAATGTATCAATACA
64 ATTCTTCAATGTATCAATACA
40508 GTTAGTTAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
101 19 0.25
102 57 0.75
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (101 bp):
AAATATATCGATACATTTTTATTATATCAATATATTCTAGGTTTGACCCAAATGTATCGATACAT
TCTTCAATGTATCAATACATTATGGGTTTTTTACCT
Found at i:40502 original size:50 final size:51
Alignment explanation
Indices: 40322--40505 Score: 203
Period size: 50 Copynumber: 3.6 Consensus size: 51
40312 TCTAAAAAGA
* * ** * * *
40322 AAATGTATCGATACATT-TTTATTCTATTGATATATTCTAGG-TTTGATCC
1 AAATGTATCGATACATTCTTCATTGTATCAATATATTATGGGTTTTGACCC
* * *
40371 AAATGTATCGATACATTCTTCATTGTATCAATACATTATGGGTTTTTTACCT
1 AAATGTATCGATACATTCTTCATTGTATCAATATATTATGGG-TTTTGACCC
* * * *
40423 AAATATATCGATACATTATTTATTATATCAATATATT-TGGGTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCAATATATTATGGGTTTTGACCC
*
40473 AAATGTATCGATACATTCTTCAATGTATCAATA
1 AAATGTATCGATACATTCTTCATTGTATCAATA
40506 CAGTTAGTTA
Statistics
Matches: 110, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
49 17 0.15
50 52 0.47
51 4 0.04
52 37 0.34
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTCTTCATTGTATCAATATATTATGGGTTTTGACCC
Found at i:52050 original size:11 final size:11
Alignment explanation
Indices: 52018--52056 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52008 TACCTTAATT
52018 TTTCTTTTTTCC
1 TTTCTTTTTT-C
*
52030 TCTCTTTTTTC
1 TTTCTTTTTTC
*
52041 TTTCTTTTTTT
1 TTTCTTTTTTC
52052 TTTCT
1 TTTCT
52057 CTGTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:52075 original size:27 final size:28
Alignment explanation
Indices: 52017--52076 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
52007 TTACCTTAAT
* *
52017 TTTTCTTTTTTCCTCTCTTTTTTCTTTC
1 TTTTCTTTTTTCCTCTCTTTTTTCTGTA
*
52045 TTTT-TTTTTT-CTCTGTTTTTTTCTGTA
1 TTTTCTTTTTTCCTCT-CTTTTTTCTGTA
52072 TTTTC
1 TTTTC
52077 CCCAAAGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (28 bp):
TTTTCTTTTTTCCTCTCTTTTTTCTGTA
Found at i:52741 original size:166 final size:164
Alignment explanation
Indices: 52541--53077 Score: 623
Period size: 166 Copynumber: 3.2 Consensus size: 164
52531 AACATATACA
** * * *
52541 AAAAAAATTCAAAATTCATG-AAATAAATTGAATTTTTTAAAACTAATTTA-ATGAGAGTTTAAT
1 AAAAAAATGAAAAACTCATGAAAATAAA-TGAATTTTTCAAAACTAATTTACATGA-A-TTAAAT
** * * * * *
52604 GACAATATTAGATGAATTTTAAAAATTTTAAACCGAAGAAAATCCCCCCAAAAACATTTATGGAA
63 GATGATATTTGATGAATATTAAAAATTTTGAACC-AAGAAAATCCCCCCGAAAACCTTTATGGAA
* * * * *
52669 TAAAAAATTCAATTTTTTGGAAACAGGGGCATTTCAAG
127 TAGAAAACTCAATTTTTCGGAAACAAGGGAATTTCAAG
* *
52707 AAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTTATTCACTATGAATTAAATGA
1 AAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTAC-ATGAATTAAATGA
* *
52772 TGATATTTGATGAATATTAAAAATTTTGAATCAAGAAAAATCCCCCCGAAAACCTTTGTGGAATA
65 TGATATTTGATGAATATTAAAAATTTTGAACCAAG-AAAATCCCCCCGAAAACCTTTATGGAATA
* ** * *
52837 GAAAACTCAATTTTCCAAAAATAAGGAAATTTCAAG
129 GAAAACTCAATTTTTCGGAAACAAGGGAATTTCAAG
* * * *
52873 GAAAAAATGAAAAACTCATGAAAATAAATAAATTTTTCAAAACTGATTTACTATGAATTAAATAA
1 AAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTAC-ATGAATTAAATGA
* * ** *
52938 TGATATTTGATGAATATTAAAAATTTTGAACTC-AGAAAAACCTCTTGAAAACCTTTATGAAATA
65 TGATATTTGATGAATATTAAAAATTTTGAAC-CAAGAAAATCCCCCCGAAAACCTTTATGGAATA
* * * *
53002 GAAAACTCAGTTTTTCGGAAACATGAGAATTTGAAG
129 GAAAACTCAATTTTTCGGAAACAAGGGAATTTCAAG
53038 -AAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAA
1 AAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAA
53078 GTGATCTAAT
Statistics
Matches: 318, Mismatches: 48, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
164 39 0.12
165 53 0.17
166 213 0.67
167 9 0.03
168 4 0.01
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.30
Consensus pattern (164 bp):
AAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTACATGAATTAAATGAT
GATATTTGATGAATATTAAAAATTTTGAACCAAGAAAATCCCCCCGAAAACCTTTATGGAATAGA
AAACTCAATTTTTCGGAAACAAGGGAATTTCAAG
Found at i:54109 original size:41 final size:39
Alignment explanation
Indices: 53990--54698 Score: 166
Period size: 41 Copynumber: 17.3 Consensus size: 39
53980 GGTGTCTACA
* *
53990 CTCTAACTTGTTGGTTTTATCGAGTTTGCCCTAG-CTAACCC
1 CTCTAACTTGTTGGCTTTATCGA-TTT-CCCTTGTC-AACCC
* * *
54031 CTCTAA-TTAGTTGACTTTATTGATTTTTCCCTTGTCAATCC
1 CTCTAACTT-GTTGGCTTTATCGA--TTTCCCTTGTCAACCC
* *
54072 CTCTAACTTGTTGGCTTTATTGATTTCACCTTGGTCAA-TC
1 CTCTAACTTGTTGGCTTTATCGATTTC-CCTT-GTCAACCC
* * * * **
54112 CTTTAAATCTGTTGGTTTTATCGGTTTCACCTTACCCAACCC
1 CTCTAACT-TGTTGGCTTTATCGATTTC-CCTT-GTCAACCC
* * *
54154 CTCTAA-TTGGTTGACTTTATCAATTTCGCCCTTGTCAAGCC
1 CTCTAACTT-GTTGGCTTTATCGATTT--CCCTTGTCAACCC
* ** * ** * *
54195 CTCTAACCTGTTGGCTTCGTCGGTTTTGGCTTGGCCAACCT
1 CTCTAACTTGTTGGCTTTATC-GATTTCCCTT-GTCAACCC
* * * * *
54236 CTCTAA-TTGGTTGACTTTATTAGTTTTTCCTTGGTCTACCC
1 CTCTAACTT-GTTGGCTTTA-TCGATTTCCCTT-GTCAACCC
* * * * * *
54277 CTCTAACCTATTGGCTTTAGCGGTTTTACCTTGGCCAACCC
1 CTCTAACTTGTTGGCTTTATC-GATTTCCCTT-GTCAACCC
* * * * * *
54318 CTATAACTGGTTGACTTTAT-TAGTTTCGATCTAGTCAA-CC
1 CTCTAACTTGTTGGCTTTATCGA-TTTC--CCTTGTCAACCC
* * * * *
54358 CTTTAAACCTATTGGCTTTATC-AGTTTCGCCCTGGCCAACCC
1 CTCT-AACTTGTTGGCTTTATCGA-TTT--CCCTTGTCAACCC
* * *
54400 CACTAA-TTGGTTGACTTTATC-AGTTTCACCCTAGTC-ACTCC
1 CTCTAACTT-GTTGGCTTTATCGA-TTT--CCCTTGTCAAC-CC
* * * * * * * *
54441 TTCTAACCTATTAGCTTTGTCAGTTTTGCCCTAGCCAACCC
1 CTCTAACTTGTTGGCTTTATC-GATTT-CCCTTGTCAACCC
* * * *
54482 CTCTAACTTGTTGACTTTATCGATTTTGCCTTAGCCAACCT
1 CTCTAACTTGTTGGCTTTATCGA-TTTCCCTT-GTCAACCC
* ** ** *
54523 CTCTAACTTATTAACTTTATTAATTTTACCCTAGTCAA-CC
1 CTCTAACTTGTTGGCTTTATCGA-TTT-CCCTTGTCAACCC
** * * * *
54563 CTCTTTGCTTGTTGGTTTTATCGGTTTCACTTTAGCCAACCC
1 CTC-TAACTTGTTGGCTTTATCGATTTC-CCTT-GTCAACCC
** *
54605 CTCTAACTTGTTAACTTTATCGATTTTGCCCTAGTCAACCC
1 CTCTAACTTGTTGGCTTTATCGA-TTT-CCCTTGTCAACCC
* * * * *
54646 TTTTTACTTGTTGGCTTTATTGATTTCACCCTAG-CTAACCC
1 CTCTAACTTGTTGGCTTTATCGATTT--CCCTTGTC-AACCC
*
54687 CTTTAACTTGTT
1 CTCTAACTTGTT
54699 AACTCTATAG
Statistics
Matches: 485, Mismatches: 140, Indels: 86
0.68 0.20 0.12
Matches are distributed among these distances:
39 5 0.01
40 46 0.09
41 384 0.79
42 47 0.10
43 3 0.01
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (39 bp):
CTCTAACTTGTTGGCTTTATCGATTTCCCTTGTCAACCC
Found at i:54191 original size:82 final size:81
Alignment explanation
Indices: 54070--54501 Score: 338
Period size: 82 Copynumber: 5.3 Consensus size: 81
54060 CCTTGTCAAT
* * * * *
54070 CCCTCTAACTT-GTTGGCTTTATT-GATTTC-ACCTTGGTCAATCCTTTAAATCTGTTGGTTTTA
1 CCCTCTAA-TTGGTTGACTTTATTAG-TTTCGACCTT-GTCAACCCTTT-AACCTATTGGCTTTA
**
54132 TCGGTTTCACCTTACCCAAC
62 TCGGTTTCACCTTGGCCAAC
* * * * * **
54152 CCCTCTAATTGGTTGACTTTATCAATTTCGCCCTTGTCAAGCCCTCTAACCTGTTGGCTTCGTCG
1 CCCTCTAATTGGTTGACTTTATTAGTTTCGACCTTGTCAA-CCCTTTAACCTATTGGCTTTATCG
***
54217 GTTTTGGCTTGGCCAAC
65 GTTTCACCTTGGCCAAC
* ** * * *
54234 CTCTCTAATTGGTTGACTTTATTAGTTT-TTCCTTGGTCTACCCCTCTAACCTATTGGCTTTAGC
1 CCCTCTAATTGGTTGACTTTATTAGTTTCGACCTT-GTC-AACCCTTTAACCTATTGGCTTTATC
*
54298 GGTTTTACCTTGGCCAAC
64 GGTTTCACCTTGGCCAAC
* * * * *
54316 CCCTATAACTGGTTGACTTTATTAGTTTCGATCTAGTCAACCCTTTAAACCTATTGGCTTTATCA
1 CCCTCTAATTGGTTGACTTTATTAGTTTCGACCTTGTCAACCCTTT-AACCTATTGGCTTTATCG
* *
54381 GTTTCGCCCTGGCCAAC
65 GTTTCACCTTGGCCAAC
* * * * *
54398 CCCACTAATTGGTTGACTTTATCAGTTTC-ACCCTAGTC-ACTCCTTCTAACCTATTAGCTTTGT
1 CCCTCTAATTGGTTGACTTTATTAGTTTCGA-CCTTGTCAAC-CCTT-TAACCTATTGGCTTTAT
* ** * *
54461 CAGTTTTGCCCTAGCCAAC
63 CGGTTTCACCTTGGCCAAC
54480 CCCTCTAACTT-GTTGACTTTAT
1 CCCTCTAA-TTGGTTGACTTTAT
54502 CGATTTTGCC
Statistics
Matches: 287, Mismatches: 51, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
81 15 0.05
82 258 0.90
83 14 0.05
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.39
Consensus pattern (81 bp):
CCCTCTAATTGGTTGACTTTATTAGTTTCGACCTTGTCAACCCTTTAACCTATTGGCTTTATCGG
TTTCACCTTGGCCAAC
Found at i:54331 original size:164 final size:164
Alignment explanation
Indices: 54123--54507 Score: 416
Period size: 164 Copynumber: 2.3 Consensus size: 164
54113 TTTAAATCTG
* * * * * * *
54123 TTGGTTTTATCGGTTTCACCTTACCCAACCCCTCTAATTGGTTGACTTTATCAATTTCGCCCTTG
1 TTGGCTTTAGCGGTTTTACCTTAGCCAACCCCTCTAACTGGTTGACTTTATCAATTTCGACCTAG
* * * * * * * *
54188 TCAAGCCCTCT-AACCTGTTGGCTTCGTCGGTTTTGGCTTGGCCAACCTCTCTAATTGGTTGACT
66 TCAA-CCCTCTAAACCTATTGGCTTCATCAGTTTCGCCCTGGCCAACCCCACTAATTGGTTGACT
* ** * *
54252 TTATTAGTTTTTCCTTGGTCTAC-CCCTCTAACCTA
130 TTATCAGTTTCACCCTAGTC-ACTCCCTCTAACCTA
* * * * *
54287 TTGGCTTTAGCGGTTTTACCTTGGCCAACCCCTATAACTGGTTGACTTTATTAGTTTCGATCTAG
1 TTGGCTTTAGCGGTTTTACCTTAGCCAACCCCTCTAACTGGTTGACTTTATCAATTTCGACCTAG
* *
54352 TCAACCCTTTAAACCTATTGGCTTTATCAGTTTCGCCCTGGCCAACCCCACTAATTGGTTGACTT
66 TCAACCCTCTAAACCTATTGGCTTCATCAGTTTCGCCCTGGCCAACCCCACTAATTGGTTGACTT
*
54417 TATCAGTTTCACCCTAGTCACTCCTTCTAACCTA
131 TATCAGTTTCACCCTAGTCACTCCCTCTAACCTA
* * * * * *
54451 TTAGCTTT-GTCAGTTTTGCCCTAGCCAACCCCTCTAACTTGTTGACTTTATCGATTT
1 TTGGCTTTAG-CGGTTTTACCTTAGCCAACCCCTCTAACTGGTTGACTTTATCAATTT
54508 TGCCTTAGCC
Statistics
Matches: 180, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
163 8 0.04
164 172 0.96
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.39
Consensus pattern (164 bp):
TTGGCTTTAGCGGTTTTACCTTAGCCAACCCCTCTAACTGGTTGACTTTATCAATTTCGACCTAG
TCAACCCTCTAAACCTATTGGCTTCATCAGTTTCGCCCTGGCCAACCCCACTAATTGGTTGACTT
TATCAGTTTCACCCTAGTCACTCCCTCTAACCTA
Found at i:54502 original size:82 final size:82
Alignment explanation
Indices: 54147--54502 Score: 362
Period size: 82 Copynumber: 4.3 Consensus size: 82
54137 TTCACCTTAC
* * * * *
54147 CCAACCCCTCTAATTGGTTGACTTTATCAATTTCGCCCTTGTCAAGCCCTCTAACCTGTTGGCTT
1 CCAACCCCTCTAATTGGTTGACTTTATCAGTTTCACCCTAGTCAACCCCTCTAACCTATTGGCTT
* * * *
54212 CGTCGGTTTTGGCTTGG
66 TGTCAGTTTTGCCCTGG
* * ** * * *
54229 CCAACCTCTCTAATTGGTTGACTTTATTAGTTTTTCCTTGGTCTACCCCTCTAACCTATTGGCTT
1 CCAACCCCTCTAATTGGTTGACTTTATCAGTTTCACCCTAGTCAACCCCTCTAACCTATTGGCTT
* * *
54294 TAG-CGGTTTTACCTTGG
66 T-GTCAGTTTTGCCCTGG
* * * * *
54311 CCAACCCCTATAACTGGTTGACTTTATTAGTTTCGA-TCTAGTCAA-CCCTTTAAACCTATTGGC
1 CCAACCCCTCTAATTGGTTGACTTTATCAGTTTC-ACCCTAGTCAACCCCTCT-AACCTATTGGC
* *
54374 TTTATCAGTTTCGCCCTGG
64 TTTGTCAGTTTTGCCCTGG
* * *
54393 CCAACCCCACTAATTGGTTGACTTTATCAGTTTCACCCTAGTC-ACTCCTTCTAACCTATTAGCT
1 CCAACCCCTCTAATTGGTTGACTTTATCAGTTTCACCCTAGTCAAC-CCCTCTAACCTATTGGCT
*
54457 TTGTCAGTTTTGCCCTAG
65 TTGTCAGTTTTGCCCTGG
54475 CCAACCCCTCTAACTT-GTTGACTTTATC
1 CCAACCCCTCTAA-TTGGTTGACTTTATC
54503 GATTTTGCCT
Statistics
Matches: 226, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
81 7 0.03
82 212 0.94
83 7 0.03
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.38
Consensus pattern (82 bp):
CCAACCCCTCTAATTGGTTGACTTTATCAGTTTCACCCTAGTCAACCCCTCTAACCTATTGGCTT
TGTCAGTTTTGCCCTGG
Found at i:54528 original size:82 final size:81
Alignment explanation
Indices: 54070--54675 Score: 325
Period size: 82 Copynumber: 7.4 Consensus size: 81
54060 CCTTGTCAAT
* * * * * * * * * *
54070 CCCTCTAACTTGTTGGCTTTATTGATTTCACCTTGGTCAATCCTTTAAATCTGTTGGTTTTATCG
1 CCCTCTAACTTGTTGACTTTATCGATTTCACCTTAGTCAACCCTCT-AACCTATTAGCTTTATCA
** * *
54135 GTTTCACCTTACCCAAC
65 GTTTTGCCCTAGCCAAC
* * * * **
54152 CCCTCTAA-TTGGTTGACTTTATCAATTTCGCCCTT-GTCAAGCCCTCTAACCTGTTGGCTTCGT
1 CCCTCTAACTT-GTTGACTTTATCGATTTC-ACCTTAGTCAA-CCCTCTAACCTATTAGCTTTAT
* * * *
54215 CGGTTTTGGCTTGGCCAAC
63 CAGTTTTGCCCTAGCCAAC
* * ** * * * *
54234 CTCTCTAA-TTGGTTGACTTTAT-TAGTTTTTCCTTGGTCTACCCCTCTAACCTATTGGCTTTAG
1 CCCTCTAACTT-GTTGACTTTATCGA-TTTCACCTTAGTC-AACCCTCTAACCTATTAGCTTTAT
* * * *
54297 CGGTTTTACCTTGGCCAAC
63 CAGTTTTGCCCTAGCCAAC
* * * * * *
54316 CCCTATAACTGGTTGACTTTAT-TAGTTTCGATC-TAGTCAACCCTTTAAACCTATTGGCTTTAT
1 CCCTCTAACTTGTTGACTTTATCGA-TTTC-ACCTTAGTCAACCCTCT-AACCTATTAGCTTTAT
* *
54379 CAGTTTCGCCCTGGCCAAC
63 CAGTTTTGCCCTAGCCAAC
* * *
54398 CCCACTAA-TTGGTTGACTTTATC-AGTTTCACCCTAGTC-ACTCCTTCTAACCTATTAGCTTTG
1 CCCTCTAACTT-GTTGACTTTATCGA-TTTCACCTTAGTCAAC-CC-TCTAACCTATTAGCTTTA
54460 TCAGTTTTGCCCTAGCCAAC
62 TCAGTTTTGCCCTAGCCAAC
** * * * *
54480 CCCTCTAACTTGTTGACTTTATCGATTTTGCCTTAGCCAACCTCTCTAACTTATTAACTTTATTA
1 CCCTCTAACTTGTTGACTTTATCGATTTCACCTTAGTCAACC-CTCTAACCTATTAGCTTTATCA
* * *
54545 ATTTTACCCTAGTCAA-
65 GTTTTGCCCTAGCCAAC
** ** * * * * * *
54561 CCCTCTTTGCTTGTTGGTTTTATCGGTTTCACTTTAGCCAACCCCTCTAACTTGTTAACTTTATC
1 CCCTC-TAACTTGTTGACTTTATCGATTTCACCTTAGTCAA-CCCTCTAACCTATTAGCTTTATC
*
54626 -GATTTTGCCCTAGTCAAC
64 AG-TTTTGCCCTAGCCAAC
* * * * *
54644 CCTTTTTACTTGTTGGCTTTATTGATTTCACC
1 CCCTCTAACTTGTTGACTTTATCGATTTCACC
54676 CTAGCTAACC
Statistics
Matches: 422, Mismatches: 80, Indels: 44
0.77 0.15 0.08
Matches are distributed among these distances:
81 23 0.05
82 375 0.89
83 24 0.06
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (81 bp):
CCCTCTAACTTGTTGACTTTATCGATTTCACCTTAGTCAACCCTCTAACCTATTAGCTTTATCAG
TTTTGCCCTAGCCAAC
Found at i:54686 original size:82 final size:82
Alignment explanation
Indices: 54455--54702 Score: 289
Period size: 82 Copynumber: 3.0 Consensus size: 82
54445 AACCTATTAG
* * * * * * * **
54455 CTTTGTCAGTTTTGCCCTAGCCAACCCCTCTAACTTGTTGACTTTATCGATTTTGCCTTAGCCAA
1 CTTTATCAATTTTGCCCTAGTCAACCCTTTTTACTTGTTGGCTTTATCGATTTCACCTTAGCCAA
* *
54520 CCTCTCTAACTTATTAA
66 CCCCTCTAACTTGTTAA
* * * * * * *
54537 CTTTATTAATTTTACCCTAGTCAACCCTCTTTGCTTGTTGGTTTTATCGGTTTCACTTTAGCCAA
1 CTTTATCAATTTTGCCCTAGTCAACCCTTTTTACTTGTTGGCTTTATCGATTTCACCTTAGCCAA
54602 CCCCTCTAACTTGTTAA
66 CCCCTCTAACTTGTTAA
* * * *
54619 CTTTATCGATTTTGCCCTAGTCAACCCTTTTTACTTGTTGGCTTTATTGATTTCACCCTAGCTAA
1 CTTTATCAATTTTGCCCTAGTCAACCCTTTTTACTTGTTGGCTTTATCGATTTCACCTTAGCCAA
*
54684 CCCCTTTAACTTGTTAA
66 CCCCTCTAACTTGTTAA
54701 CT
1 CT
54703 CTATAGGTTC
Statistics
Matches: 136, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 136 1.00
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (82 bp):
CTTTATCAATTTTGCCCTAGTCAACCCTTTTTACTTGTTGGCTTTATCGATTTCACCTTAGCCAA
CCCCTCTAACTTGTTAA
Found at i:54697 original size:123 final size:123
Alignment explanation
Indices: 54472--54698 Score: 307
Period size: 123 Copynumber: 1.8 Consensus size: 123
54462 AGTTTTGCCC
* *
54472 TAGCCAACCCCTCTAACTTGTTGACTTTATCGATTTTGCCTTAGCCAACCTCTCTAACTTATTAA
1 TAGCCAACCCCTCTAACTTGTTAACTTTATCGATTTTGCCCTAGCCAACCTCTCTAACTTATTAA
* *
54537 CTTTATTAATTTTACCCTAGTCAACCCTCTTTGCTTGTTGGTTTTATCGGTTTCACTT
66 CTTTATTAATTTCACCCTAGTCAACCCTCTTTACTTGTTGGTTTTATCGGTTTCACTT
* * * * *
54595 TAGCCAACCCCTCTAACTTGTTAACTTTATCGATTTTGCCCTAGTCAACC-CTTTTTACTTGTTG
1 TAGCCAACCCCTCTAACTTGTTAACTTTATCGATTTTGCCCTAGCCAACCTC-TCTAACTTATTA
* *
54659 GCTTTATTGATTTCACCCTAG-CTAACCC-CTTTAACTTGTT
65 ACTTTATTAATTTCACCCTAGTC-AACCCTCTTT-ACTTGTT
54699 AACTCTATAG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
122 6 0.07
123 84 0.93
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (123 bp):
TAGCCAACCCCTCTAACTTGTTAACTTTATCGATTTTGCCCTAGCCAACCTCTCTAACTTATTAA
CTTTATTAATTTCACCCTAGTCAACCCTCTTTACTTGTTGGTTTTATCGGTTTCACTT
Found at i:55892 original size:13 final size:13
Alignment explanation
Indices: 55851--55903 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
55841 CCGTTACAAG
55851 CAATGTATCGATA
1 CAATGTATCGATA
55864 CAA--T-TC-AT-
1 CAATGTATCGATA
55872 C-ATGTATCGATA
1 CAATGTATCGATA
*
55884 CATTGTATCGATA
1 CAATGTATCGATA
55897 CAATGTA
1 CAATGTA
55904 CCATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:55896 original size:33 final size:33
Alignment explanation
Indices: 55854--55918 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
55844 TTACAAGCAA
*
55854 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
55887 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
55919 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:56631 original size:27 final size:27
Alignment explanation
Indices: 56587--56640 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
56577 TCGGTTAAAG
* * *
56587 AGATTTTGTTCCCTTAGATAAAAATTT
1 AGATTTTCTCCCCCTAGATAAAAATTT
56614 AGATTTTCTCCCCCTAGATAAAAATTT
1 AGATTTTCTCCCCCTAGATAAAAATTT
56641 TCTCCCCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (27 bp):
AGATTTTCTCCCCCTAGATAAAAATTT
Found at i:56653 original size:20 final size:21
Alignment explanation
Indices: 56616--56660 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
56606 AAAAATTTAG
56616 ATTTTCTCCCCCTAGATAAAA
1 ATTTTCTCCCCCTAGATAAAA
*
56637 ATTTTCT-CCCCTTGATAAAA
1 ATTTTCTCCCCCTAGATAAAA
56657 ATTT
1 ATTT
56661 ATTTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTTTCTCCCCCTAGATAAAA
Found at i:63361 original size:20 final size:20
Alignment explanation
Indices: 63336--63412 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
63326 GTAAAAAGAC
*
63336 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTGA
63356 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
63376 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
63396 AGAATGTATTGATACAT
1 AGAATGTATCGATACAT
63413 CTGGGTAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Done.