Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_51
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: 337032
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:2200 original size:12 final size:11
Alignment explanation
Indices: 2153--2192 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
2143 AGTTGTAAAG
*
2153 TTTTATTTTTAT
1 TTTTATTTAT-T
2165 TTTTATTTATT
1 TTTTATTTATT
2176 TATTTATTTATT
1 T-TTTATTTATT
2188 TTTTA
1 TTTTA
2193 CTTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:2200 original size:16 final size:15
Alignment explanation
Indices: 2154--2209 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
2144 GTTGTAAAGT
2154 TTTA-TTTTTATT--
1 TTTATTTTTTATTAA
*
2166 TTTATTTATTTATTTA
1 TTTATTT-TTTATTAA
2182 TTTATTTTTTACTTAA
1 TTTATTTTTTA-TTAA
*
2198 TTTAATTTTTAT
1 TTTATTTTTTAT
2210 GTAAATATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
12 4 0.11
13 2 0.05
14 6 0.16
15 5 0.14
16 20 0.54
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATTAA
Found at i:12180 original size:20 final size:20
Alignment explanation
Indices: 12157--12210 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
12147 AGTTTTTCCC
*
12157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
12177 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
12197 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
12211 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:12192 original size:30 final size:30
Alignment explanation
Indices: 12157--12230 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
12147 AGTTTTTCCC
12157 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
12187 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
*
12217 AGCTTGTTTGAGCT
1 AGCTCGTTTGAGCT
12231 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:12220 original size:20 final size:20
Alignment explanation
Indices: 12157--12220 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
12147 AGTTTTTCCC
* * * *
12157 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
12177 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
12196 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
12217 AGCT
1 AGCT
12221 TGTTTGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 27 0.79
21 4 0.12
22 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:18435 original size:37 final size:37
Alignment explanation
Indices: 18385--18464 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
18375 CTTATTACGA
* *
18385 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
18422 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
18459 GGTCTT
1 AGTCTT
18465 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:18654 original size:47 final size:47
Alignment explanation
Indices: 18583--18987 Score: 553
Period size: 47 Copynumber: 8.6 Consensus size: 47
18573 CCCTTCGGGA
** * *
18583 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
18630 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
18677 CTTATCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
18724 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * * *
18771 CTTGTCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
18818 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
18865 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
18913 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
18960 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
18988 TATTCAATTA
Statistics
Matches: 325, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.00
47 262 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:23658 original size:40 final size:40
Alignment explanation
Indices: 23601--24143 Score: 887
Period size: 40 Copynumber: 13.6 Consensus size: 40
23591 CCAGCATGAT
* *
23601 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
23641 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23681 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23721 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23761 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
23801 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23841 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23881 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
23921 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
23961 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
24001 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
24041 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
24082 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
24122 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
24144 CATCATTCGA
Statistics
Matches: 473, Mismatches: 25, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
39 3 0.01
40 449 0.95
41 21 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:25870 original size:37 final size:37
Alignment explanation
Indices: 25820--25899 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
25810 CTTATTACGA
* *
25820 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
25857 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
25894 GGTCTT
1 AGTCTT
25900 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:26089 original size:47 final size:47
Alignment explanation
Indices: 26018--26422 Score: 553
Period size: 47 Copynumber: 8.6 Consensus size: 47
26008 CCCTTCGGGA
** * *
26018 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACACATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* * * *
26065 CTTATCTCACATACACATGCTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
26112 CTTATCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
26159 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * * *
26206 CTTGTCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
26253 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
26300 CCTATTCACACATACACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTA-TCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
26348 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGC
1 CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
26395 CCTATTCACACATATACACT-TTCACATT
1 CTTA-TCACACATATACA-TGTTCACATT
26423 TATTCAATTA
Statistics
Matches: 325, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.00
47 262 0.81
48 61 0.19
49 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:31721 original size:20 final size:20
Alignment explanation
Indices: 31698--31736 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31688 AAGCTCAAAC
31698 AAGCTAAAGTAAGCTAAATT
1 AAGCTAAAGTAAGCTAAATT
* * *
31718 AAGCTCATGTGAGCTAAAT
1 AAGCTAAAGTAAGCTAAAT
31737 CGAGCTGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AAGCTAAAGTAAGCTAAATT
Found at i:33556 original size:33 final size:33
Alignment explanation
Indices: 33518--33580 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
33508 GATTACTCAC
33518 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
33551 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
33581 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:33607 original size:21 final size:21
Alignment explanation
Indices: 33578--33633 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
33568 CAAGCTCTCT
*
33578 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
33599 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
33620 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
33634 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:33626 original size:14 final size:14
Alignment explanation
Indices: 33577--33633 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
33567 TCAAGCTCTC
33577 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
33590 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
33604 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
33618 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
33632 TT
1 TT
33634 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:33693 original size:18 final size:18
Alignment explanation
Indices: 33595--33698 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
33585 TCTTTTTTCG
33595 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
33614 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
33634 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
33652 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
33670 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
33688 CTTTTTGTTTT
1 CTTTTTCTTTT
33699 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:33715 original size:6 final size:6
Alignment explanation
Indices: 33595--33702 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
33585 TCTTTTTTCG
* * * **
33595 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
33646 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
33694 -GTTTT CTTT
1 CTTTTT CTTT
33703 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:34670 original size:26 final size:25
Alignment explanation
Indices: 34640--34701 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
34630 TTTAAACTTG
34640 ATTTTTTTTTGCTC-ACCTTTTTTTTC
1 ATTTTTTTTTGCTCGA--TTTTTTTTC
34666 -TTTTTTTTTGCTCGATTTTTTTTC
1 ATTTTTTTTTGCTCGATTTTTTTTC
34690 ACTTTTTTTTTG
1 A-TTTTTTTTTG
34702 AATTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.27
25 13 0.39
26 11 0.33
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (25 bp):
ATTTTTTTTTGCTCGATTTTTTTTC
Found at i:34737 original size:12 final size:11
Alignment explanation
Indices: 34722--34751 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
34712 TCAATCAAAT
34722 TTTTTTTTTCGA
1 TTTTTTTTT-GA
34734 TTTTTTTTTGA
1 TTTTTTTTTGA
34745 TTTTTTT
1 TTTTTTT
34752 GTTACTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:36259 original size:20 final size:20
Alignment explanation
Indices: 36236--36274 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36226 AAGCTCAAAC
36236 AAGCTAAAGTAAGCTAAATT
1 AAGCTAAAGTAAGCTAAATT
* * *
36256 AAGCTCATGTGAGCTAAAT
1 AAGCTAAAGTAAGCTAAAT
36275 CGAGCTGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AAGCTAAAGTAAGCTAAATT
Found at i:38962 original size:27 final size:27
Alignment explanation
Indices: 38918--38989 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
38908 TTTTTTTCTT
38918 TTTTTTTTGCTCGATTTTTTTTC-A-C--
1 TTTTTTTT--TCGATTTTTTTTCAATCAA
38943 TTTTTTTTT-GAATTTTTTTTCAATCAA
1 TTTTTTTTTCG-ATTTTTTTTCAATCAA
38970 TTTTTTTTTCGATTTTTTTT
1 TTTTTTTTTCGATTTTTTTT
38990 GTTACTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
22 1 0.02
23 11 0.27
24 1 0.02
25 9 0.22
27 18 0.44
28 1 0.02
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.72
Consensus pattern (27 bp):
TTTTTTTTTCGATTTTTTTTCAATCAA
Found at i:42090 original size:23 final size:22
Alignment explanation
Indices: 42038--42090 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42028 TCCACGTCTT
*
42038 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42060 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42083 TTTCTTTT
1 TTTCTTTT
42091 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:45962 original size:27 final size:27
Alignment explanation
Indices: 45932--45986 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
45922 ATTTGTCAAA
45932 AGTCCTTTTACAAGAAAATGAGTAACT
1 AGTCCTTTTACAAGAAAATGAGTAACT
45959 AGTCCTTTTACAAGAAAATGAGTAACT
1 AGTCCTTTTACAAGAAAATGAGTAACT
45986 A
1 A
45987 TTTATAGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (27 bp):
AGTCCTTTTACAAGAAAATGAGTAACT
Found at i:48447 original size:22 final size:22
Alignment explanation
Indices: 48396--48461 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
48386 GGTATTTGGG
** *
48396 AATTGGTTTGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
48417 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
48439 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
48462 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:51966 original size:23 final size:21
Alignment explanation
Indices: 51940--51992 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
51930 AAAAAAGTGA
*
51940 AAAAGAAATTGAAGAAAGAAGAG
1 AAAAGAAATTGAA-AAAGAA-AC
* *
51963 AAAATAAGTTTGAAAAAGAAAC
1 AAAAGAA-ATTGAAAAAGAAAC
51985 AAAAGAAA
1 AAAAGAAA
51993 AAGACAAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAAGAAATTGAAAAAGAAAC
Found at i:54583 original size:12 final size:12
Alignment explanation
Indices: 54546--54618 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
54536 AATAGTGAGA
*
54546 GAAAAAGAAAAT
1 GAAAAAGAAATT
54558 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
54573 GAAAAAGAAATT
1 GAAAAAGAAATT
* ** *
54585 GAGATTGAGATT
1 GAAAAAGAAATT
54597 GAGAAAA-AAATT
1 GA-AAAAGAAATT
54609 GAAAAAGAAA
1 GAAAAAGAAA
54619 AAGATGTTGA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.09
12 25 0.53
13 7 0.15
14 6 0.13
15 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:58773 original size:20 final size:20
Alignment explanation
Indices: 58748--58802 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
58738 TGTGGTTCAA
*
58748 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
58768 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
58788 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
58803 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:66727 original size:22 final size:22
Alignment explanation
Indices: 66697--66740 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66687 TTTGGTATTT
66697 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
66719 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
66741 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:72792 original size:23 final size:23
Alignment explanation
Indices: 72762--72806 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
72752 TAGTTTCTCG
*
72762 AAAAAAAACTCGAAAAAAAATTC
1 AAAAAAAACTCAAAAAAAAATTC
*
72785 AAAAAAAATTCAAAAAAAAATT
1 AAAAAAAACTCAAAAAAAAATT
72807 TGGTTTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAAAACTCAAAAAAAAATTC
Found at i:72806 original size:12 final size:11
Alignment explanation
Indices: 72762--72803 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
72752 TAGTTTCTCG
*
72762 AAAAAAAACTC
1 AAAAAAAATTC
72773 GAAAAAAAATTC
1 -AAAAAAAATTC
72785 AAAAAAAATTC
1 AAAAAAAATTC
72796 AAAAAAAA
1 AAAAAAAA
72804 ATTTGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:72866 original size:14 final size:14
Alignment explanation
Indices: 72844--72896 Score: 88
Period size: 15 Copynumber: 3.6 Consensus size: 14
72834 GATATCAAGT
72844 TGAAAAAAAATTTCG
1 TGAAAAAAAA-TTCG
72859 TGAAAAAAAATTCG
1 TGAAAAAAAATTCG
72873 TGAAAAAAAAATTCG
1 TG-AAAAAAAATTCG
72888 TGAAAAAAA
1 TGAAAAAAA
72897 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
14 13 0.35
15 24 0.65
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (14 bp):
TGAAAAAAAATTCG
Found at i:79472 original size:17 final size:18
Alignment explanation
Indices: 79450--79486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79440 TGGAATAAAC
79450 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
79467 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
79485 TT
1 TT
79487 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:81242 original size:12 final size:12
Alignment explanation
Indices: 81225--81295 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 12
81215 TTAAAGTAAC
81225 AAAAAAATCAAA
1 AAAAAAATCAAA
*
81237 AAAAAATTCGAAA
1 AAAAAAATC-AAA
*
81250 AAAAAATTGATTGAAA
1 AAAAAA---A-TCAAA
*
81266 AAAAAATTCAAA
1 AAAAAAATCAAA
* *
81278 AAAAAAGTGAAA
1 AAAAAAATCAAA
81290 AAAAAA
1 AAAAAA
81296 TCGAGCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 28 0.60
13 9 0.19
16 9 0.19
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATCAAA
Found at i:81306 original size:16 final size:15
Alignment explanation
Indices: 81287--81340 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
81277 AAAAAAAGTG
81287 AAAAAAAAATCGAGCA
1 AAAAAAAAAT-GAGCA
**
81303 AAAAAAAAGAAAAGCA
1 AAAAAAAA-ATGAGCA
**
81319 AAAAAAAGGTGAGCA
1 AAAAAAAAATGAGCA
81334 AAAAAAA
1 AAAAAAA
81341 TCAAGTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.35
16 19 0.61
17 1 0.03
ACGTcount: A:0.74, C:0.07, G:0.15, T:0.04
Consensus pattern (15 bp):
AAAAAAAAATGAGCA
Found at i:81307 original size:40 final size:40
Alignment explanation
Indices: 81225--81310 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 40
81215 TTAAAGTAAC
* *
81225 AAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTG-AAA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA--GCAAA
*
81266 AAAAAATTCAAAAAAAAAGT-GAAAAAAAAATCGAGCAAA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAAA
81305 AAAAAA
1 AAAAAA
81311 GAAAAGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 9 0.22
40 13 0.32
41 18 0.44
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (40 bp):
AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAAA
Found at i:84158 original size:17 final size:18
Alignment explanation
Indices: 84136--84172 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
84126 TGGAATAAAC
84136 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
84153 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
84171 TT
1 TT
84173 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:86477 original size:22 final size:22
Alignment explanation
Indices: 86449--86492 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
86439 TTTTGAACCA
86449 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
86471 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
86493 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:100990 original size:10 final size:10
Alignment explanation
Indices: 100974--101031 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
100964 CAACTCCGAC
100974 CAGCTCAATT
1 CAGCTCAATT
* *
100984 GAGCTCATTT
1 CAGCTCAATT
100994 CAGCTCAA-T
1 CAGCTCAATT
101003 CGAGCTCAATT
1 C-AGCTCAATT
*
101014 TAGCTACAATT
1 CAGCT-CAATT
101025 CAGCTCA
1 CAGCTCA
101032 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:100997 original size:20 final size:20
Alignment explanation
Indices: 100974--101034 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
100964 CAACTCCGAC
100974 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
100994 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
101015 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
101035 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:102422 original size:11 final size:11
Alignment explanation
Indices: 102370--102425 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
102360 ATTGGAGTAA
102370 CAAAAAAAA-T
1 CAAAAAAAATT
102380 CAAAAAAAATT
1 CAAAAAAAATT
102391 CGAAAAAAAATTGATT
1 C--AAAAAAA---ATT
*
102407 GAAAAAAAATT
1 CAAAAAAAATT
102418 CAAAAAAA
1 CAAAAAAA
102426 GTGAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 9 0.24
11 12 0.32
13 7 0.18
14 7 0.18
16 3 0.08
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.16
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:102450 original size:16 final size:16
Alignment explanation
Indices: 102429--102466 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
102419 AAAAAAAGTG
102429 AAAAAAAA-ATCGAGCA
1 AAAAAAAAGAT-GAGCA
*
102445 AAAAAAAAGGTGAGCA
1 AAAAAAAAGATGAGCA
102461 AAAAAA
1 AAAAAA
102467 TCAAGTTAAA
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:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGATGAGCA
Found at i:102452 original size:29 final size:27
Alignment explanation
Indices: 102419--102489 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
102409 AAAAAAATTC
*
102419 AAAAAAAGTGAAAAAAAAATCGAGCAAA
1 AAAAAAAGTGAAAAAAAAATCAAG-AAA
* * *
102447 AAAAAAGGTGAGCAAAAAAATCAAGTTAA
1 AAAAAAAGTGA-AAAAAAAATCAAG-AAA
102476 AAAAAAAGTGAAAA
1 AAAAAAAGTGAAAA
102490 GTTTTGCGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.69, C:0.06, G:0.15, T:0.10
Consensus pattern (27 bp):
AAAAAAAGTGAAAAAAAAATCAAGAAA
Found at i:103382 original size:18 final size:18
Alignment explanation
Indices: 103361--103395 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
103351 AGAAAAGAAA
103361 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
103379 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
103396 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:105477 original size:10 final size:10
Alignment explanation
Indices: 105461--105518 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
105451 CAACTCCGAC
105461 CAGCTCAATT
1 CAGCTCAATT
* *
105471 GAGCTCATTT
1 CAGCTCAATT
105481 CAGCTCAA-T
1 CAGCTCAATT
105490 CGAGCTCAATT
1 C-AGCTCAATT
*
105501 TAGCTACAATT
1 CAGCT-CAATT
105512 CAGCTCA
1 CAGCTCA
105519 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:105484 original size:20 final size:20
Alignment explanation
Indices: 105461--105521 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
105451 CAACTCCGAC
105461 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
105481 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
105502 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
105522 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:110359 original size:22 final size:22
Alignment explanation
Indices: 110331--110374 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
110321 TTTTGAACCA
110331 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
110353 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
110375 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:115735 original size:20 final size:20
Alignment explanation
Indices: 115712--115765 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
115702 AGTTTTTCCC
*
115712 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
115732 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
115752 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
115766 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:115747 original size:30 final size:30
Alignment explanation
Indices: 115712--115785 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
115702 AGTTTTTCCC
115712 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
115742 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
115772 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
115786 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:115775 original size:20 final size:20
Alignment explanation
Indices: 115712--115776 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
115702 AGTTTTTCCC
* * * *
115712 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
115732 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
115751 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
115772 AGCTC
1 AGCTC
115777 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:117439 original size:20 final size:20
Alignment explanation
Indices: 117384--117442 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
117374 TTGGATTTTA
* *
117384 AAAAAAAAAGAGAATAAATTC
1 AAAAAAAAAGA-AAAAAAATC
**
117405 AAAAAAAAATCAAAAAAATC
1 AAAAAAAAAGAAAAAAAATC
*
117425 GAAAAAAAAGAAAAAAAA
1 AAAAAAAAAGAAAAAAAA
117443 AGAAGTGACA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAAATC
Found at i:118535 original size:17 final size:18
Alignment explanation
Indices: 118503--118536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
118493 AAAAGAGAGT
*
118503 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
118521 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
118537 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:119809 original size:20 final size:20
Alignment explanation
Indices: 119786--119839 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
119776 AGTTTTTCCC
*
119786 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
119806 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
119826 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
119840 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:119821 original size:30 final size:30
Alignment explanation
Indices: 119786--119859 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
119776 AGTTTTTCCC
119786 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
119816 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
119846 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
119860 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:119849 original size:20 final size:20
Alignment explanation
Indices: 119786--119850 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
119776 AGTTTTTCCC
* * * *
119786 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
119806 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
119825 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
119846 AGCTC
1 AGCTC
119851 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:124596 original size:11 final size:10
Alignment explanation
Indices: 124571--124631 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
124561 ACCAATAAAA
124571 TAAA-TGAGC
1 TAAATTGAGC
*
124580 TGAATTGTAGC
1 TAAATTG-AGC
124591 TAAATTGAGC
1 TAAATTGAGC
**
124601 TCGATTGAGC
1 TAAATTGAGC
124611 TGAAA-TGAGC
1 T-AAATTGAGC
*
124621 TCAATTGAGC
1 TAAATTGAGC
124631 T
1 T
124632 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:124632 original size:20 final size:20
Alignment explanation
Indices: 124572--124632 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
124562 CCAATAAAAT
*
124572 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
124592 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
124613 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
124633 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:126693 original size:33 final size:33
Alignment explanation
Indices: 126655--126717 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
126645 GATTACTCAC
126655 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
126688 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
126718 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:126763 original size:14 final size:15
Alignment explanation
Indices: 126734--126774 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
126724 TTTTTTCGCT
*
126734 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTTA
126747 TTTTC-TTTTCTTTA
1 TTTTCTTTTTCTTTA
126761 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
126775 CACTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
14 6 0.25
15 8 0.33
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTCTTTA
Found at i:126852 original size:6 final size:6
Alignment explanation
Indices: 126732--126839 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
126722 TCTTTTTTCG
* * **
126732 CTTTTT CTTTTT CAATTTT CTTTTCT TTATTTT CTTTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTT-T CT-TTTT CTTTTT CTTTTT CTTTTT
* * ** *
126783 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
126831 -GTTTT CTTT
1 CTTTTT CTTT
126840 CAATTTCTTT
Statistics
Matches: 76, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
5 5 0.07
6 58 0.76
7 10 0.13
8 3 0.04
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:131414 original size:30 final size:30
Alignment explanation
Indices: 131380--131476 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
131370 AGCTCACTCC
131380 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
131410 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
131440 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
131470 TAGCTCA
1 TAGCTCA
131477 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:134183 original size:5 final size:5
Alignment explanation
Indices: 134162--134235 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
134152 ACATTCTTGT
* * *
134162 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGAA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAG-A
134210 AAAGA AAATGA AATA-A AAAGA AAAGA
1 AAAGA AAA-GA AA-AGA AAAGA AAAGA
134236 GAGGCAAGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 35 0.62
6 18 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:134183 original size:16 final size:16
Alignment explanation
Indices: 134162--134235 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
134152 ACATTCTTGT
*
134162 AAAGAAAAAACAAAG-A
1 AAAGAAAAGA-AAAGAA
134178 AAAGAAAAGAAAAAGAA
1 AAAGAAAAG-AAAAGAA
* *
134195 AAAG-CAAGAGAAGAA
1 AAAGAAAAGAAAAGAA
*
134210 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
134226 AAAGAAAAGA
1 AAAGAAAAGA
134236 GAGGCAAGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
15 11 0.23
16 29 0.62
17 7 0.15
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:134188 original size:21 final size:21
Alignment explanation
Indices: 134162--134233 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
134152 ACATTCTTGT
134162 AAAGAAAAA-ACAAAGAAAAGA
1 AAAGAAAAAGA-AAAGAAAAGA
*
134183 AAAGAAAAAGAAAA-AGCAAGA
1 AAAGAAAAAGAAAAGA-AAAGA
*
134204 GAAGAAAAAGAAAATGAAATA-A
1 AAAGAAAAAGAAAA-GAAA-AGA
134226 AAAGAAAA
1 AAAGAAAA
134234 GAGAGGCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 1 0.02
21 29 0.69
22 10 0.24
23 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGAAAAGAAAAGA
Found at i:134212 original size:27 final size:27
Alignment explanation
Indices: 134162--134235 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
134152 ACATTCTTGT
134162 AAAGAAAAAACAAAGAAAAGAAAAGAA
1 AAAGAAAAAACAAAGAAAAGAAAAGAA
* *
134189 AAAGAAAAAGC-AAGAGAAGAAAAAGAA
1 AAAGAAAAAACAAAGAAAAG-AAAAGAA
* *
134216 AATGAAATAA-AAAGAAAAGA
1 AAAGAAAAAACAAAGAAAAGA
134236 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.21
27 31 0.79
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (27 bp):
AAAGAAAAAACAAAGAAAAGAAAAGAA
Found at i:134315 original size:11 final size:12
Alignment explanation
Indices: 134283--134313 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
134273 TTGAGAGAAC
134283 TTGAAAAAGCCT
1 TTGAAAAAGCCT
134295 TTGAAAAAGCCT
1 TTGAAAAAGCCT
134307 TTGAAAA
1 TTGAAAA
134314 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:136528 original size:30 final size:30
Alignment explanation
Indices: 136494--136590 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
136484 AGCTCACTCC
136494 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
136524 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
136554 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
136584 TAGCTCA
1 TAGCTCA
136591 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:140798 original size:56 final size:55
Alignment explanation
Indices: 140682--140799 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
140672 TGCATGCTTT
* * * *
140682 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTGAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTGAATTCATGTTTTGCTGCA
* *
140736 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTGAATTCATGT-TTTGCTGCA
140792 CATTAAAT
1 CATTAAAT
140800 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 27 0.50
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTGAATTCATGTTTTGCTGCA
Found at i:141455 original size:20 final size:20
Alignment explanation
Indices: 141430--141476 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
141420 AATTCAGCTT
*
141430 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
141450 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
141470 GAATGAG
1 GAATGAG
141477 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:153075 original size:20 final size:20
Alignment explanation
Indices: 153029--153075 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
153019 AGCTCGTTTC
*
153029 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
153049 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
153069 CAGCTCA
1 CAGCTCA
153076 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:154605 original size:12 final size:13
Alignment explanation
Indices: 154588--154616 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
154578 AGGAAATTTG
154588 AAAAAAAAAA-TC
1 AAAAAAAAAATTC
154600 AAAAAAAAAATTC
1 AAAAAAAAAATTC
154613 AAAA
1 AAAA
154617 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:158467 original size:20 final size:20
Alignment explanation
Indices: 158421--158467 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
158411 AGCTCGTTTC
*
158421 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
158441 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
158461 CAGCTCA
1 CAGCTCA
158468 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:162638 original size:19 final size:18
Alignment explanation
Indices: 162602--162641 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
162592 TTTCCACTCG
*
162602 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
162620 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
162639 TTT
1 TTT
162642 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:162773 original size:18 final size:17
Alignment explanation
Indices: 162714--162774 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
162704 GCACTCTTTC
*
162714 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
162733 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
162750 TGTTTCTTTTTCGATTTCT
1 T-TTTCTTTTTCAATTT-T
162769 TTTTCT
1 TTTTCT
162775 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:163749 original size:17 final size:18
Alignment explanation
Indices: 163727--163763 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
163717 TGGAATAAAC
163727 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
163744 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
163762 TT
1 TT
163764 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:165550 original size:13 final size:13
Alignment explanation
Indices: 165532--165562 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
165522 AGGAAATTTG
165532 AAAAAAAATTCAA
1 AAAAAAAATTCAA
165545 AAAAAAAATTCAA
1 AAAAAAAATTCAA
165558 AAAAA
1 AAAAA
165563 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:166546 original size:17 final size:17
Alignment explanation
Indices: 166509--166548 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
166499 AAATCAAAAG
* **
166509 AAAAGAAAAAGAGATTG
1 AAAAGAAAAAGAAATCA
166526 AAAAGAAAAAGAAATCA
1 AAAAGAAAAAGAAATCA
166543 AAAAGA
1 AAAAGA
166549 GAGTGAGGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAATCA
Found at i:168376 original size:17 final size:18
Alignment explanation
Indices: 168354--168390 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
168344 TGGAATAAAC
168354 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
168371 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
168389 TT
1 TT
168391 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:170143 original size:13 final size:13
Alignment explanation
Indices: 170111--170150 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
170101 ACTAGCTCTC
170111 TTTTTTTTCACAA
1 TTTTTTTTCACAA
170124 TTATTTTTTCACAA
1 TT-TTTTTTCACAA
170138 TTTTTTTTCACAA
1 TTTTTTTTCACAA
170151 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:170205 original size:12 final size:12
Alignment explanation
Indices: 170188--170233 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
170178 TGGAAACTAG
170188 TTTTTTTCGAAT
1 TTTTTTTCGAAT
*
170200 TTTTTTTTGAATT
1 TTTTTTTCGAA-T
*
170213 TTTTTTTCGAGT
1 TTTTTTTCGAAT
170225 TTTTTTTCG
1 TTTTTTTCG
170234 TGAAACTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:170206 original size:13 final size:13
Alignment explanation
Indices: 170188--170231 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
170178 TGGAAACTAG
170188 TTTTTTTCGAATT
1 TTTTTTTCGAATT
170201 TTTTTTT-GAATT
1 TTTTTTTCGAATT
*
170213 TTTTTTTCGAGTT
1 TTTTTTTCGAATT
170226 TTTTTT
1 TTTTTT
170232 CGTGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:170755 original size:22 final size:22
Alignment explanation
Indices: 170712--170754 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
170702 AAGGGCATAA
*
170712 AATGCTCTTTAAAACTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
*
170734 AATGATCTTT-AAGCTCCTTTT
1 AATGATCTTTAAAACTCCTTTT
170755 TTAACAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGATCTTTAAAACTCCTTTT
Found at i:172214 original size:285 final size:284
Alignment explanation
Indices: 171773--172346 Score: 1139
Period size: 285 Copynumber: 2.0 Consensus size: 284
171763 CTTATGCCTT
171773 AAGCTTCTTTAGGAAACTTCCTAGCAATTTCCTAGATACATTCATAAACAAAATCTAAATAATAA
1 AAGCTTCTTTAGGAAACTTCCTAGCAATTTCCTAGATACATTCATAAACAAAATCTAAATAATAA
171838 CCTTCTAGAAGAGATGATTCGGCTGGCCCCTTTTATGGCTAAAATTCACATTCAACTAATGTTTT
66 CCTTCTAGAAGAGATGATTCGGCTGGCCCCTTTTATGGCTAAAATTCACATTCAACTAATGTTTT
171903 TAAAAGAGATTAATTACTGCTTTGGAGAAGAGAAATGGGCAGCTTGAAAAGTTATGCTTCTTTGG
131 TAAAAGAGATTAATTACTGCTTTGGAGAAGAGAAATGGGCAGCTTGAAAAGTTATGCTTCTTTGG
171968 CCGAATATGAGCAGCCACCAAGTGAATTGGCTGCTGGAAATTATGAAGCACTCTTTGGCCATTGA
196 CCGAATATGAGCAGCCACCAAGTGAATTGGCTGCTGGAAATTATGAAGCACTCTTTGGCCATTGA
172033 TCTCCACGAAATTGACCCTTAGAG
261 TCTCCACGAAATTGACCCTTAGAG
172057 AAGCTTCTTTAGGAAACTTCCTAGCAATTTCCTAGATACATTCATAAACAAAAATCTAAATAATA
1 AAGCTTCTTTAGGAAACTTCCTAGCAATTTCCTAGATACATTCATAAAC-AAAATCTAAATAATA
172122 ACCTTCTAGAAGAGATGATTCGGCTGGCCCCTTTTATGGCTAAAATTCACATTCAACTAATGTTT
65 ACCTTCTAGAAGAGATGATTCGGCTGGCCCCTTTTATGGCTAAAATTCACATTCAACTAATGTTT
172187 TTAAAAGAGATTAATTACTGCTTTGGAGAAGAGAAATGGGCAGCTTGAAAAGTTATGCTTCTTTG
130 TTAAAAGAGATTAATTACTGCTTTGGAGAAGAGAAATGGGCAGCTTGAAAAGTTATGCTTCTTTG
172252 GCCGAATATGAGCAGCCACCAAGTGAATTGGCTGCTGGAAATTATGAAGCACTCTTTGGCCATTG
195 GCCGAATATGAGCAGCCACCAAGTGAATTGGCTGCTGGAAATTATGAAGCACTCTTTGGCCATTG
172317 ATCTCCACGAAATTGACCCTTAGAG
260 ATCTCCACGAAATTGACCCTTAGAG
172342 AAGCT
1 AAGCT
172347 CAAAACAGCA
Statistics
Matches: 289, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
284 49 0.17
285 240 0.83
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (284 bp):
AAGCTTCTTTAGGAAACTTCCTAGCAATTTCCTAGATACATTCATAAACAAAATCTAAATAATAA
CCTTCTAGAAGAGATGATTCGGCTGGCCCCTTTTATGGCTAAAATTCACATTCAACTAATGTTTT
TAAAAGAGATTAATTACTGCTTTGGAGAAGAGAAATGGGCAGCTTGAAAAGTTATGCTTCTTTGG
CCGAATATGAGCAGCCACCAAGTGAATTGGCTGCTGGAAATTATGAAGCACTCTTTGGCCATTGA
TCTCCACGAAATTGACCCTTAGAG
Found at i:181637 original size:22 final size:24
Alignment explanation
Indices: 181606--181667 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
181596 TAAATCAGGT
*
181606 CAAGATACATTAAAATC-GG-CAG
1 CAAGACACATTAAAATCTGGACAG
181628 CAAGACACATTAAAATCTGGCAACAG
1 CAAGACACATTAAAATCTGG--ACAG
181654 CAAGACACATTAAA
1 CAAGACACATTAAA
181668 CCTTTACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 16 0.46
23 2 0.06
26 17 0.49
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.16
Consensus pattern (24 bp):
CAAGACACATTAAAATCTGGACAG
Found at i:182024 original size:99 final size:99
Alignment explanation
Indices: 181902--182181 Score: 449
Period size: 99 Copynumber: 2.8 Consensus size: 99
181892 ATAAATACGC
181902 AAACTAAA-TAAGCTGAGTTCAAGCTGGTTCGAGTTCATGGAGCTAAAATTGAGCTGAGTTCAAC
1 AAACTAAATTAAGCTGAGTTCAAGCTGGTTCGAGTTCATGGAGCTAAAATTGAGCTGAGTTCAAC
181966 TTGCAAAAGATTGCATGGAGCTAAACAAATGCAT
66 TTGCAAAAGATTGCATGGAGCTAAACAAATGCAT
182000 AAACTAAATTAAGCTGAGTTCAAGCTGGTTCGAGTTCATGGAGCTAAAATTGAGCTGAGTTCAAC
1 AAACTAAATTAAGCTGAGTTCAAGCTGGTTCGAGTTCATGGAGCTAAAATTGAGCTGAGTTCAAC
* *
182065 TTGCAAAAGATTGCATGGAGCTAAATAAATGTAT
66 TTGCAAAAGATTGCATGGAGCTAAACAAATGCAT
* * *
182099 AAACTAAATTAAGCTGAGTTTAAGCTGATTCAAAG-TCATGGAGCTAAAATTGAGCTGAGGTT-A
1 AAACTAAATTAAGCTGAGTTCAAGCTGGTTC-GAGTTCATGGAGCTAAAATTGAGCTGA-GTTCA
* * *
182162 GCTTGTAAAAAATTGCATGG
64 ACTTGCAAAAGATTGCATGG
182182 TGAAACCGTG
Statistics
Matches: 171, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
98 8 0.05
99 158 0.92
100 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (99 bp):
AAACTAAATTAAGCTGAGTTCAAGCTGGTTCGAGTTCATGGAGCTAAAATTGAGCTGAGTTCAAC
TTGCAAAAGATTGCATGGAGCTAAACAAATGCAT
Found at i:188010 original size:18 final size:18
Alignment explanation
Indices: 187989--188028 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
187979 GATTGAGAGT
* * *
187989 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
188007 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
188025 GAAA
1 GAAA
188029 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:190864 original size:22 final size:22
Alignment explanation
Indices: 190813--190878 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
190803 GGTATTTGGG
* *
190813 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
190834 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
190856 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
190879 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:193716 original size:21 final size:21
Alignment explanation
Indices: 193667--193733 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
193657 CCTCTTTGAA
* * *
193667 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
193690 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
193711 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
193732 CC
1 CC
193734 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:194088 original size:11 final size:12
Alignment explanation
Indices: 194032--194074 Score: 68
Period size: 12 Copynumber: 3.4 Consensus size: 12
194022 ATAGGTGCGT
194032 AAAAAAAAAGTTCG
1 AAAAAAAAA-TT-G
194046 AAAAAAAAATTG
1 AAAAAAAAATTG
194058 AAAAAAAAATTG
1 AAAAAAAAATTG
194070 AAAAA
1 AAAAA
194075 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.62
13 2 0.07
14 9 0.31
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:194137 original size:1 final size:1
Alignment explanation
Indices: 194131--194157 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
194121 AAAGATCCGT
194131 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
194158 GAGTCTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:196363 original size:17 final size:17
Alignment explanation
Indices: 196331--196380 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
196321 GCGAAAATAC
196331 AAAAGAAAAGAAAAATGAT
1 AAAA-AAAAG-AAAATGAT
196350 AAAAAAAAGAAAAT--T
1 AAAAAAAAGAAAATGAT
* *
196365 CAAAAAAAGAGAATGA
1 AAAAAAAAGAAAATGA
196381 AAAGAGAGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.48
17 5 0.19
18 5 0.19
19 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (17 bp):
AAAAAAAAGAAAATGAT
Found at i:200666 original size:21 final size:21
Alignment explanation
Indices: 200617--200683 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
200607 CCTCTTTGAA
* * *
200617 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
200640 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
200661 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
200682 CC
1 CC
200684 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:204530 original size:12 final size:12
Alignment explanation
Indices: 204501--204560 Score: 95
Period size: 12 Copynumber: 5.0 Consensus size: 12
204491 TAGTAGTTTC
204501 TTCAAAAAAGAAA
1 TTCAAAAAA-AAA
204514 TTCAAAAAAAAA
1 TTCAAAAAAAAA
*
204526 ATC-AAAAAAAA
1 TTCAAAAAAAAA
204537 TTCAAAAAAAAA
1 TTCAAAAAAAAA
204549 TTCAAAAAAAAA
1 TTCAAAAAAAAA
204561 ATTTGGTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
11 10 0.23
12 25 0.57
13 9 0.20
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:204537 original size:23 final size:23
Alignment explanation
Indices: 204505--204559 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
204495 AGTTTCTTCA
204505 AAAAAGAAATTCAAAAAAAAAATC
1 AAAAA-AAATTCAAAAAAAAAATC
*
204529 AAAAAAAATTCAAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAAAATC
204552 AAAAAAAA
1 AAAAAAAA
204560 AATTTGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAAAATC
Found at i:204561 original size:13 final size:13
Alignment explanation
Indices: 204501--204563 Score: 89
Period size: 13 Copynumber: 5.2 Consensus size: 13
204491 TAGTAGTTTC
*
204501 TTCAAAAAAGAAA
1 TTCAAAAAAAAAA
204514 TTCAAAAAAAAAA
1 TTCAAAAAAAAAA
204527 -TC--AAAAAAAA
1 TTCAAAAAAAAAA
204537 TTC-AAAAAAAAA
1 TTCAAAAAAAAAA
204549 TTCAAAAAAAAAA
1 TTCAAAAAAAAAA
204562 TT
1 TT
204564 TGGTTTCCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
10 8 0.17
11 2 0.04
12 13 0.28
13 23 0.50
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.17
Consensus pattern (13 bp):
TTCAAAAAAAAAA
Found at i:204621 original size:15 final size:16
Alignment explanation
Indices: 204601--204641 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
204591 GATATCAAGT
204601 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
204616 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA-TTTCG
204633 TGAAAAAAA
1 TGAAAAAAA
204642 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:207518 original size:20 final size:20
Alignment explanation
Indices: 207495--207541 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
207485 GGGTTAAGAT
*
207495 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
207515 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
207535 TGAGCTG
1 TGAGCTG
207542 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:209253 original size:48 final size:48
Alignment explanation
Indices: 209198--209303 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
209188 TTGTCTTTTC
*
209198 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
209246 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
209294 TTTCTTTTTC
1 TTTCTTTTTC
209304 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:211887 original size:20 final size:20
Alignment explanation
Indices: 211864--211910 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
211854 GGGTTAAGAT
*
211864 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* * *
211884 TGAGTTGACTTGAGGTCGAG
1 TGAGCTGAATTGAGCTCGAG
211904 TGAGCTG
1 TGAGCTG
211911 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.11, G:0.38, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:213445 original size:22 final size:22
Alignment explanation
Indices: 213394--213459 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
213384 GGTATTTGGG
* *
213394 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
213415 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
213437 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
213460 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:217046 original size:13 final size:12
Alignment explanation
Indices: 217028--217088 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 12
217018 TCGTAGCTTC
217028 AAAAAAAAAGTT-
1 AAAAAAAAA-TTG
217040 AAAAAAAAAGTTTG
1 AAAAAAAAA--TTG
217054 AAAAAAAAATCTG
1 AAAAAAAAAT-TG
217067 AAAAAAAAATTG
1 AAAAAAAAATTG
217079 CAAAAAAAAA
1 -AAAAAAAAA
217089 AAATTGCATA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
12 12 0.27
13 23 0.52
14 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:219373 original size:24 final size:25
Alignment explanation
Indices: 219346--219399 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
219336 ATGAGTGATA
*
219346 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
219370 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
219394 AAAAAA
1 AAAAAA
219400 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:227797 original size:16 final size:15
Alignment explanation
Indices: 227774--227807 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
227764 CTTTTCAAAA
227774 TTTTTTTTGATTTTT
1 TTTTTTTTGATTTTT
227789 TTTTATTTTGATTTTT
1 TTTT-TTTTGATTTTT
227805 TTT
1 TTT
227808 CGAACTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTTTTGATTTTT
Found at i:229928 original size:13 final size:13
Alignment explanation
Indices: 229910--229934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229900 ACAAAAAAAT
229910 AAAAAAATTTGAA
1 AAAAAAATTTGAA
229923 AAAAAAATTTGA
1 AAAAAAATTTGA
229935 TTGAAAAAAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:229994 original size:34 final size:33
Alignment explanation
Indices: 229951--230020 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
229941 AAAAAAATTC
*
229951 AAAAAGAAAAGTGAAAAAAAAA-TCGAGCAAAAAA
1 AAAAAGAAAAG-AAAAAAAAAAGT-GAGCAAAAAA
229985 AAAAAGAAAAGAAAAAAAAAAGGTGAGCAAAAAA
1 AAAAAGAAAAGAAAAAAAAAA-GTGAGCAAAAAA
230019 AA
1 AA
230021 TCAAGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 9 0.27
34 23 0.70
35 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (33 bp):
AAAAAGAAAAGAAAAAAAAAAGTGAGCAAAAAA
Found at i:231085 original size:18 final size:18
Alignment explanation
Indices: 231059--231162 Score: 64
Period size: 18 Copynumber: 5.6 Consensus size: 18
231049 AAATTGAAAG
*
231059 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
231077 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
* * *
231095 AAAAGATAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
** * *
231113 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
231131 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
231152 AAAAGAAAAAG
1 AAAAGAAAAAG
231163 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 5
0.72 0.23 0.06
Matches are distributed among these distances:
18 44 0.70
19 5 0.08
20 8 0.13
21 6 0.10
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:231087 original size:6 final size:6
Alignment explanation
Indices: 231055--231162 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
231045 AAAGAAATTG
* * ** * *
231055 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAT
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
231102 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
231153 AAAGAA AAAG
1 AAAGAA AAAG
231163 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
5 4 0.05
6 57 0.78
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:231142 original size:14 final size:13
Alignment explanation
Indices: 231123--231160 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
231113 AAAAGTGAGA
231123 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
231135 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
231150 GAAAAAGAAAA
1 GAAAAAGAAAA
231161 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:231157 original size:13 final size:12
Alignment explanation
Indices: 231041--231160 Score: 54
Period size: 12 Copynumber: 10.0 Consensus size: 12
231031 AGAAAGAGAT
*
231041 TGAAAAAGAAAT
1 TGAAAAAGAAAA
231053 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
231063 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
231074 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
231086 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
*
231099 -GATAAAG-AAA
1 TGAAAAAGAAAA
* * *
231109 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
231123 -GAAAAAGAAAA
1 TGAAAAAGAAAA
231134 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
231148 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
231161 AGCGAAAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 33 0.41
13 14 0.17
14 12 0.15
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:231197 original size:12 final size:12
Alignment explanation
Indices: 231166--231197 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
231156 GAAAAAGCGA
*
231166 AAAAAGAATTTG
1 AAAAAGAGTTTG
231178 AAAAAGAGTTTG
1 AAAAAGAGTTTG
231190 AAAAAGAG
1 AAAAAGAG
231198 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:234279 original size:21 final size:21
Alignment explanation
Indices: 234250--234312 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
234240 TTGGTATTTG
234250 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
234271 GGAACTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
234292 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
234313 ATGGTTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:237887 original size:14 final size:13
Alignment explanation
Indices: 237868--237918 Score: 84
Period size: 14 Copynumber: 3.8 Consensus size: 13
237858 TAGCTCTCTC
237868 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
237881 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAT
237895 TTTTTTTTCAAAAT
1 TTTTTTTTC-AAAT
237909 TTTTTTTTCA
1 TTTTTTTTCA
237919 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.31
14 24 0.67
15 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:237908 original size:28 final size:27
Alignment explanation
Indices: 237868--237921 Score: 99
Period size: 28 Copynumber: 2.0 Consensus size: 27
237858 TAGCTCTCTC
237868 TTTTTTTTCAAATTTTTTTTTCACAAT
1 TTTTTTTTCAAATTTTTTTTTCACAAT
237895 TTTTTTTTCAAAATTTTTTTTTCACAA
1 TTTTTTTTC-AAATTTTTTTTTCACAA
237922 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTTTTCAAATTTTTTTTTCACAAT
Found at i:242300 original size:21 final size:23
Alignment explanation
Indices: 242255--242301 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
242245 TCACCTGCAA
* *
242255 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
242278 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
242299 TAA
1 TAA
242302 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:244192 original size:23 final size:22
Alignment explanation
Indices: 244141--244192 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
244131 CCTCGTCTTT
*
244141 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
244163 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
244186 TTCTTTT
1 TTCTTTT
244193 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:244862 original size:10 final size:10
Alignment explanation
Indices: 244846--244903 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
244836 CAACTCCGAC
244846 CAGCTCAATT
1 CAGCTCAATT
* *
244856 GAGCTCATTT
1 CAGCTCAATT
244866 CAGCTCAA-T
1 CAGCTCAATT
244875 CGAGCTCAATT
1 C-AGCTCAATT
*
244886 TAGCTACAATT
1 CAGCT-CAATT
244897 CAGCTCA
1 CAGCTCA
244904 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:244869 original size:20 final size:20
Alignment explanation
Indices: 244846--244906 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
244836 CAACTCCGAC
244846 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
244866 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
244887 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
244907 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:247857 original size:194 final size:194
Alignment explanation
Indices: 247293--249672 Score: 4022
Period size: 194 Copynumber: 12.3 Consensus size: 194
247283 GTGCGCGGAA
247293 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
247358 CCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* * * *
247423 AAACCATGTTATATGCACAAGTATCATCACCATCAAAAAAGCTTATTTCATTTTACAAACAGTA
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
247487 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
247552 CCTAAGAAAATT-TTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
*
247616 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
247680 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTATAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* *
247745 CCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTTCAGTCTTGGAGCATT
66 CCTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGAGTCTTGGGGCATT
* * * *
247809 GAAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACTGTA
130 GAAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
247874 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
247939 CCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* *
248004 AAACCATATTATATGCACATGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
248068 ACTCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* * *
248133 CCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGATAAGTTTCAGTCTTGGAGCATT
66 CCTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGAGTCTTGGGGCATT
* * * *
248197 GAAACCATGTTATATGCACATATATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAAC-GTA
130 GAAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
248261 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* * *
248326 CCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAGGTTCGAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* * *
248391 AAACCATATTATATGCACATGTATCACCACCATCAAAGAAGTTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* * ** *
248455 ACTCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTCGGGGGCTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* *
248520 CCTAAGAAAATTACTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATGG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* * * *
248585 AAACCATGTTATGTGCACATGTATCATCAACATCAAAGAAGATTAATTAATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* * * *
248649 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACATGACTTGTTTACACCCCTAGAAGTCAG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
248714 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAATCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
*
248779 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
248843 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTTGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
248908 CTTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTT-ATGTCTTGGGGCAT
66 CCTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGA-GTCTTGGGGCAT
* * *
248971 TGAAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGGTTAATTCGTTTTACAAACAGT
129 TGAAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGT
*
249036 A
194 G
* *
249037 ACTCCACTGTAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
249102 CCTAAGAAAATT-TTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* *
249166 AAACCATATTATATGCACATGCATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* * **
249230 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGTCAA
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* *
249295 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCAAAAGACAAGTTTCAGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* *
249360 AAACCATGTTATATGCACAAGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* *
249424 ACTCCATTATAGCGAGCCCAACTTGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
249489 CCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTTCAGTCTTGGGGCATT
66 CCTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGAGTCTTGGGGCATT
249553 GAAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
130 GAAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
249618 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTA-ACCCCT
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCT
249673 GTATCAGAAT
Statistics
Matches: 2049, Mismatches: 125, Indels: 25
0.93 0.06 0.01
Matches are distributed among these distances:
193 557 0.27
194 1490 0.73
195 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (194 bp):
ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
Found at i:248395 original size:581 final size:582
Alignment explanation
Indices: 247292--249672 Score: 4078
Period size: 581 Copynumber: 4.1 Consensus size: 582
247282 TGTGCGCGGA
247292 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
1 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
247357 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
66 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
* * * * *
247422 GAAACCATGTTATATGCACAAGTATCATCACCATCAAAAAAGCTTATTTCATTTTACAAACAGTA
131 GAAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* *
247487 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
196 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACAG
*
247552 CCTAAGAAAATT-TTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
261 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTG
247616 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
326 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
*
247681 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTATAAGACTGC
391 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
* *
247746 CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTTCAGTCTTGGAGCATTGA
456 CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGGTTCAGTCTTGGGGCATTGA
* *
247811 AACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACTGT
521 AACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCATTTTACAAACAGT
*
247873 AACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACT
1 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
247938 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
66 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
*
248003 GAAACCATATTATATGCACATGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 GAAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* * *
248068 ACTCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
196 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACAG
* *
248133 CCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGATAAGTTTCAGTCTTGGAGCATT
261 CCTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTCAGTCTTGGGGCATT
* *
248197 GAAACCATGTTATATGCACATA-TATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAAC-GT
325 GAAACCATGTTATATGCACA-AGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGT
* *
248260 AACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACT
389 GACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
*
248325 GCCTAAGAAAATTTTTAGCAACTTATTATTGAA-GGTCATAAGAC-AGGTTCGAGTCTTGGGGCA
454 GCCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGGTTC-AGTCTTGGGGCA
* * * *
248388 TTGAAACCATATTATATGCACATGTATCACCACCATCAAAGAAGTTTAATTCATTTTACAAACAG
517 TTGAAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCATTTTACAAACAG
248453 T
582 T
* * * ** *
248454 GACTCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTCGGGGGCT
1 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
** *
248519 GCCTAAGAAAATTACTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATG
66 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
* * * * *
248584 GAAACCATGTTATGTGCACATGTATCATCAACATCAAAGAAGATTAATTAATTTTACAAACAGTG
131 GAAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* *
248649 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACATGACTTGTTTACACCCCTAGAAGTCAG
196 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACAG
* *
248714 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAATCTTGGGGCATTG
261 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTG
248779 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
326 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
*
248844 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTTGAAGACTGC
391 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
* *
248909 TTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAA-GTTTATGTCTTGGGGCATTG
456 CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGGTTCA-GTCTTGGGGCATTG
* *
248973 AAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGGTTAATTCGTTTTACAAACAGT
520 AAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCATTTTACAAACAGT
* *
249036 AACTCCACTGTAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACT
1 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
249101 GCCTAAGAAAA-TTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
66 GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
*
249165 GAAACCATATTATATGCACATGCATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
131 GAAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
* *
249230 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGTCAA
196 ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACAG
*
249295 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCAAAAGACAAGTTTCAGTCTTGGGGCATTG
261 CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTG
*
249360 AAACCATGTTATATGCACAAGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
326 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
* *
249425 CTCCATTATAGCGAGCCCAACTTGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
391 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
*
249490 CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTTCAGTCTTGGGGCATTGA
456 CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGGTTCAGTCTTGGGGCATTGA
*
249555 AACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGT
521 AACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCATTTTACAAACAGT
*
249617 GACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTA-ACCCCT
1 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCT
249673 GTATCAGAAT
Statistics
Matches: 1690, Mismatches: 98, Indels: 25
0.93 0.05 0.01
Matches are distributed among these distances:
580 12 0.01
581 1321 0.78
582 355 0.21
583 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (582 bp):
AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
GCCTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATT
GAAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
ACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACAG
CCTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTG
AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
CTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGGTTCAGTCTTGGGGCATTGA
AACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCATTTTACAAACAGT
Found at i:248783 original size:775 final size:774
Alignment explanation
Indices: 247293--249672 Score: 4142
Period size: 775 Copynumber: 3.1 Consensus size: 774
247283 GTGCGCGGAA
247293 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
247358 CCTAAGAAAATTTTTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGAGTCTTGGGGCATT
66 CCTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTT-AGTCTTGGGGCATT
* *
247422 GAAACCATGTTATATGCACA-AGTATCATCACCATCAAAAAAGCTTATTTCATTTTACAAACAGT
129 GAAACCATGTTATATGCACATA-TATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACAGT
*
247486 AACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACT
193 AACTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACT
247551 GCCTAAGAAAATTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
258 GCCTAAGAAAATTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTG
* *
247616 AAACCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
323 AAACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
*
247681 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTATAAGACTGC
388 CTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGC
*
247746 CTAAGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTTCAGTCTTGGAGCATTG
453 CTAAGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTCAGTCTTGGGGCATTG
* * * *
247810 AAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACTGTAA
517 AAACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGA
247875 CTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
582 CTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
*
247940 CTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGA
647 CTAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGA
* *
248005 AACCATATTATATGCACATGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
712 AACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
248068 ACTCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
* *
248133 CCTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGATAAGTTTCAGTCTTGGAGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTT-AGTCTTGGGGCATTG
248198 AAACCATGTTATATGCACATATATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAAC-GTAA
130 AAACCATGTTATATGCACATATATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACAGTAA
248262 CTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
195 CTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
* *
248327 CTAAGAAAATTTTTAGCAACTTATTATTGAAGGTCATAAGACAGGTTCGAGTCTTGGGGCATTGA
260 CTAAGAAAA-TTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGA
* *
248392 AACCATATTATATGCACATGTATCACCACCATCAAAGAAGTTTAATTCATTTTACAAACAGTGAC
324 AACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGAC
* * ** *
248457 TCCACTATAGCGAGCCCAACAAGCTCACATGTAACTTGACTTGTTTACACCCCTCGGGGGCTGCC
389 TCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGCC
* * *
248522 TAAGAAAATTACTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATGGAA
454 TAAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTGAA
* * * *
248587 ACCATGTTATGTGCACATGTATCATCAACATCAAAGAAGATTAATTAATTTTACAAACAGTGACT
519 ACCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACT
* * *
248652 CCACTATAGCGAGCCCAACTAGCTCACATGGAACATGACTTGTTTACACCCCTAGAAGTCAGCCT
584 CCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGCCT
*
248717 AAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAATCTTGGGGCATTGAAA
649 AAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAAA
*
248782 CCATGTTATATGCACAAGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
714 CCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
*
248843 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTTGAAGACTG
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
*
248908 CTTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTTATGTCTTGGGGCATTG
66 CCTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTTA-GTCTTGGGGCATTG
* *
248973 AAACCATGTTATATGCACATGTATCATCACCATCAAAAAAGGTTAATTCGTTTTACAAACAGTAA
130 AAACCATGTTATATGCACATATATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACAGTAA
*
249038 CTCCACTGTAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
195 CTCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGC
249103 CTAAGAAAATTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAA
260 CTAAGAAAATTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAA
*
249168 ACCATATTATATGCACATGCATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACT
325 ACCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACT
* * **
249233 CCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGTCAACCT
390 CCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGCCT
*
249298 AAGAAAATTATTAGCAACTTATTATTGAAGGTCAAAAGACAAGTTTCAGTCTTGGGGCATTGAAA
455 AAGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTGAAA
* *
249363 CCATGTTATATGCACAAGTATCACCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACTC
520 CCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACTC
* * *
249428 CATTATAGCGAGCCCAACTTGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGCCTA
585 CACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGCCTA
*
249493 AGAAAATTATTAGCAACTTATTATT-AAGGGTCATAAGACAAGTTTCAGTCTTGGGGCATTGAAA
650 AGAAAATTATTAGCAACTTATTATTGAA-GGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAAA
249557 CCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
714 CCATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
249618 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTA-ACCCCT
1 ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCT
249673 GTATCAGAAT
Statistics
Matches: 1518, Mismatches: 80, Indels: 15
0.94 0.05 0.01
Matches are distributed among these distances:
774 88 0.06
775 1350 0.89
776 80 0.05
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (774 bp):
ACTCCACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTG
CCTAAGAAAATTATTAGCAACTTATTATTAAGGGTCATAAGACAAGTTTAGTCTTGGGGCATTGA
AACCATGTTATATGCACATATATCATCACCATCAAAAAAGCTTAATTCGTTTTACAAACAGTAAC
TCCACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGCC
TAAGAAAATTTTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAAA
CCATATTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACTC
CACTATAGCGAGCCCAACTAGCTCACATGTAACTTGACTTGTTTACACCCCTAGAAGACTGCCTA
AGAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTCAGTCTTGGGGCATTGAAAC
CATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTGACTCC
ACTATAGCGAGCCCAACTAGCTCACATGGAACTTGACTTGTTTACACCCCTAGAAGACTGCCTAA
GAAAATTATTAGCAACTTATTATTGAAGGTCATAAGACAAGTTTGAGTCTTGGGGCATTGAAACC
ATGTTATATGCACATGTATCATCACCATCAAAGAAGCTTAATTCATTTTACAAACAGTG
Found at i:253821 original size:14 final size:14
Alignment explanation
Indices: 253802--253856 Score: 103
Period size: 14 Copynumber: 4.0 Consensus size: 14
253792 ACTAGCTCTC
253802 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
253816 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
253830 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
253844 -TTTTTTTTCACAA
1 TTTTTTTTTCACAA
253857 CTTGATATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
13 13 0.32
14 28 0.68
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:253914 original size:13 final size:12
Alignment explanation
Indices: 253896--253941 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
253886 TGGAAACTAG
253896 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
253908 TTTTTTTTTGAA
1 TTTTTTTTTCAA
*
253920 TTTTTTTTTCGA
1 TTTTTTTTTCAA
*
253932 GTTTTTTTTC
1 TTTTTTTTTC
253942 GAGAAACTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCAA
Done.