Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003000.1 Hibiscus syriacus cultivar Beakdansim tig00006208_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 183846
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2885 original size:24 final size:25
Alignment explanation
Indices: 2850--2904 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2840 ACTTGGAGCC
*
2850 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
2874 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
2898 TCAAGTG
1 TCAAGTG
2905 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:4192 original size:5 final size:5
Alignment explanation
Indices: 4182--4207 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4172 CTTCAACTTC
4182 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
4208 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:8348 original size:16 final size:16
Alignment explanation
Indices: 8327--8359 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
8317 TTCTGCCACC
8327 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
8343 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
8359 T
1 T
8360 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:11696 original size:12 final size:12
Alignment explanation
Indices: 11661--11700 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
11651 TCCTTAATCT
11661 TTTCTTTATCTTA
1 TTTC-TTATCTTA
*
11674 TTT-TAATCTTA
1 TTTCTTATCTTA
11685 TTTCTTATCTTA
1 TTTCTTATCTTA
11697 TTTC
1 TTTC
11701 CAGCACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 11 0.46
13 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTATCTTA
Found at i:11696 original size:23 final size:22
Alignment explanation
Indices: 11654--11699 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
11644 TTGCAATTCC
11654 TTAATCTTTTCTTTATCTTATT
1 TTAATCTTTTCTTTATCTTATT
11676 TTAATCTTATT-TCTTATCTTATT
1 TTAATCTT-TTCT-TTATCTTATT
11699 T
1 T
11700 CCAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAATCTTTTCTTTATCTTATT
Found at i:12009 original size:13 final size:12
Alignment explanation
Indices: 11979--12008 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
11969 TTTTTAGTGC
11979 TAAAAATAAGAT
1 TAAAAATAAGAT
11991 TAAAAATAAGAT
1 TAAAAATAAGAT
12003 TAAAAA
1 TAAAAA
12009 AGATAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (12 bp):
TAAAAATAAGAT
Found at i:16655 original size:12 final size:12
Alignment explanation
Indices: 16638--16665 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16628 TTTAGTACTG
16638 AAAATAAGATTA
1 AAAATAAGATTA
16650 AAAATAAGATTA
1 AAAATAAGATTA
16662 AAAA
1 AAAA
16666 AGATAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
AAAATAAGATTA
Found at i:20672 original size:24 final size:25
Alignment explanation
Indices: 20637--20691 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
20627 ACTTGGAGCC
*
20637 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
20661 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
20685 TCAAGTG
1 TCAAGTG
20692 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:22891 original size:26 final size:26
Alignment explanation
Indices: 22855--22922 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
22845 AATGAACCAC
22855 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
*
22881 ATGCAAGGCACATTGGGGCTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
* *
22907 ATGCAAAGAACATGGG
1 ATGCAAGGCACATGGG
22923 TGTTCTAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.32, T:0.19
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGATCAT
Found at i:29169 original size:16 final size:16
Alignment explanation
Indices: 29148--29178 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29138 TCTTCCACCA
*
29148 ATGTTAGAATGCAAAT
1 ATGTTAGAAAGCAAAT
29164 ATGTTAGAAAGCAAA
1 ATGTTAGAAAGCAAA
29179 CGAGCTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
ATGTTAGAAAGCAAAT
Found at i:31283 original size:11 final size:11
Alignment explanation
Indices: 31269--31324 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
31259 TCTTTTTGAA
31269 TTCTTTTTCTT
1 TTCTTTTTCTT
31280 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
31293 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
31306 TGTCTTTTTC-T
1 T-TCTTTTTCTT
31317 TTCTTTTT
1 TTCTTTTT
31325 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:31293 original size:19 final size:18
Alignment explanation
Indices: 31269--31324 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
31259 TCTTTTTGAA
31269 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
31287 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
31306 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
31324 T
1 T
31325 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:32773 original size:16 final size:16
Alignment explanation
Indices: 32752--32782 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32742 TCTTCCACCA
*
32752 ATGTTAGAATGCAAAT
1 ATGTTAGAAAGCAAAT
32768 ATGTTAGAAAGCAAA
1 ATGTTAGAAAGCAAA
32783 CGAGCTAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
ATGTTAGAAAGCAAAT
Found at i:36420 original size:25 final size:25
Alignment explanation
Indices: 36370--36421 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
36360 CGTCATTTCT
*
36370 TTTGAAATTTACAAAAGATGTGTCA
1 TTTGAAATTTACAAAACATGTGTCA
36395 TTTGAAATTATA-AAGAACATGT-TCA
1 TTTGAAATT-TACAA-AACATGTGTCA
36420 TT
1 TT
36422 AACCTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (25 bp):
TTTGAAATTTACAAAACATGTGTCA
Found at i:39067 original size:17 final size:16
Alignment explanation
Indices: 39041--39077 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
39031 CATTCAAGAA
39041 GAAA-AAAAAGAAATT
1 GAAAGAAAAAGAAATT
39056 GCAAAGAAAAAGAAATT
1 G-AAAGAAAAAGAAATT
39073 GAAAG
1 GAAAG
39078 CACAAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 12 0.60
ACGTcount: A:0.68, C:0.03, G:0.19, T:0.11
Consensus pattern (16 bp):
GAAAGAAAAAGAAATT
Found at i:39086 original size:16 final size:17
Alignment explanation
Indices: 39045--39077 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39035 CAAGAAGAAA
39045 AAAAAGAAATTGCAAAG
1 AAAAAGAAATTGCAAAG
39062 AAAAAGAAATTG-AAAG
1 AAAAAGAAATTGCAAAG
39078 CACAAGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.12
Consensus pattern (17 bp):
AAAAAGAAATTGCAAAG
Found at i:43006 original size:24 final size:21
Alignment explanation
Indices: 42971--43013 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
42961 GGCTCATTCT
*
42971 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
42994 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
43014 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:44281 original size:23 final size:24
Alignment explanation
Indices: 44224--44281 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
44214 ACTTTTCTTT
*
44224 CTTTCTTTTTCTTCTTTTTGAGTG
1 CTTTCATTTTCTTCTTTTTGAGTG
*
44248 CTTTCAATTTCTTC-TTTTGAGTG
1 CTTTCATTTTCTTCTTTTTGAGTG
*
44271 CTTTTATTTTC
1 CTTTCATTTTC
44282 CTTGCTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.09, C:0.17, G:0.10, T:0.64
Consensus pattern (24 bp):
CTTTCATTTTCTTCTTTTTGAGTG
Found at i:49287 original size:19 final size:21
Alignment explanation
Indices: 49263--49314 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
49253 CAGCCAAGAG
*
49263 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
49282 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
49303 CATGTATTTTCA
1 CATGTATTTTCA
49315 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:53525 original size:23 final size:24
Alignment explanation
Indices: 53490--53536 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
53480 AAAATCATTG
* *
53490 AAGAAACGTACAAAAAGAAAGCAA
1 AAGAAAAGTACAAAAACAAAGCAA
*
53514 AAGAAAAG-ACAAAATCAAAGCAA
1 AAGAAAAGTACAAAAACAAAGCAA
53537 GAAATAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.68, C:0.13, G:0.15, T:0.04
Consensus pattern (24 bp):
AAGAAAAGTACAAAAACAAAGCAA
Found at i:57681 original size:2 final size:2
Alignment explanation
Indices: 57674--57747 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
57664 AGTTATTTTA
57674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57748 TCTACCTATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59405 original size:13 final size:13
Alignment explanation
Indices: 59384--59421 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
59374 GAGAAAAATT
59384 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
*
59397 AGAAGAAAAGAAA
1 AGAAAAAAAGAAA
*
59410 AGAAAAAGAGAA
1 AGAAAAAAAGAA
59422 GTTCAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:64523 original size:91 final size:91
Alignment explanation
Indices: 64366--64548 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
64356 CCTAGAACAC
64366 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
64431 AAGAGTTCTCTCCCTATTCAGCCAAG
66 AAGAGTTCTCTCCCTATTCAGCCAAG
** * * * * * *
64457 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATTTGGTTCATTTAGGTGCCAATATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
64522 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCAGCCAAG
64548 C
1 C
64549 ATCAACTACC
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCAGCCAAG
Found at i:70337 original size:30 final size:30
Alignment explanation
Indices: 70298--70378 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
70288 CACTAAGGAA
*
70298 AGCTCAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
70328 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
*
70358 AGCTGAACTTAGCTAGAGGAG
1 AGCTGAACTTAGCTGGAGGAG
70379 AGCTTTGGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.22
Consensus pattern (30 bp):
AGCTGAACTTAGCTGGAGGAGCTAGCATGT
Found at i:75468 original size:195 final size:195
Alignment explanation
Indices: 75136--75525 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 195
75126 ATACACACTG
*
75136 ATCATGAGGCATTAAAGCATATCAAAGGACAACACAAACTCAACAGGAGACATGCCAAATGGGTA
1 ATCATGAGGCATTAAAGCATATCAAAGGACAACACAAACTCAACAGGAGACATACCAAATGGGTA
75201 GAATTCCTTGAGTCTTTTCCTTATGTCATACACTACAAGAAATGAAAGGACAATATTGTGGCAGA
66 GAATTCCTTGAGTCTTTTCCTTATGTCATACACTACAAGAAATGAAAGGACAATATTGTGGCAGA
75266 TGCTCTTTCACGCAGGTATGTCTTACTTAACACTTTGGATTCCAAACTTTTTGGTTTTTTCATTC
131 TGCTCTTTCACGCAGGTATGTCTTACTTAACACTTTGGATTCCAAACTTTTTGGTTTTTTCATTC
75331 ATCATGAGGCATTAAAGCATATCAAAGGACAACACAAACTCAACAGGAGACATACCAAATGGGTA
1 ATCATGAGGCATTAAAGCATATCAAAGGACAACACAAACTCAACAGGAGACATACCAAATGGGTA
75396 GAATTCCTTGAGTCTTTTCCTTATGTCATACACTACAAGAAATGAAAGGACAATATTGTGGCAGA
66 GAATTCCTTGAGTCTTTTCCTTATGTCATACACTACAAGAAATGAAAGGACAATATTGTGGCAGA
75461 TGCTCTTTCACGCAGGTATGTCTTACTTAACACTTTGGATTCCAAACTTTTTGGTTTTTTCATTC
131 TGCTCTTTCACGCAGGTATGTCTTACTTAACACTTTGGATTCCAAACTTTTTGGTTTTTTCATTC
75526 GTTAAAGAAC
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (195 bp):
ATCATGAGGCATTAAAGCATATCAAAGGACAACACAAACTCAACAGGAGACATACCAAATGGGTA
GAATTCCTTGAGTCTTTTCCTTATGTCATACACTACAAGAAATGAAAGGACAATATTGTGGCAGA
TGCTCTTTCACGCAGGTATGTCTTACTTAACACTTTGGATTCCAAACTTTTTGGTTTTTTCATTC
Found at i:75798 original size:11 final size:13
Alignment explanation
Indices: 75766--75800 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
75756 TGGCCAAAGA
75766 TGAAAAGGTATGG
1 TGAAAAGGTATGG
75779 TGAAAAGGTAT-G
1 TGAAAAGGTATGG
75791 TG-AAAGGTAT
1 TGAAAAGGTAT
75801 TTAGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
13 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (13 bp):
TGAAAAGGTATGG
Found at i:78397 original size:21 final size:21
Alignment explanation
Indices: 78344--78398 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
78334 AAAATTGAGC
*
78344 AAAG-AAAACAAAGCACTCAA
1 AAAGAAAAAGAAAGCACTCAA
** **
78364 AAAGAAATTGAAAGCACTTGA
1 AAAGAAAAAGAAAGCACTCAA
78385 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
78399 AAAGAAAAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.64, C:0.11, G:0.16, T:0.09
Consensus pattern (21 bp):
AAAGAAAAAGAAAGCACTCAA
Found at i:79577 original size:19 final size:20
Alignment explanation
Indices: 79536--79586 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
79526 TGAAACCCTT
*
79536 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
79556 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
79575 TGAAGATACATG
1 TGAAAATACATG
79587 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:83718 original size:19 final size:19
Alignment explanation
Indices: 83694--83735 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
83684 TGAACCCCTT
*
83694 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
83713 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
83732 TGAA
1 TGAA
83736 GCATGCTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:89722 original size:14 final size:15
Alignment explanation
Indices: 89688--89730 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
89678 ATATAGGCGT
89688 GAATGGTGAT--AAA
1 GAATGGTGATGGAAA
89701 GAATGGTGATGGAAA
1 GAATGGTGATGGAAA
89716 G-ATGGTGATGGAAA
1 GAATGGTGATGGAAA
89730 G
1 G
89731 GTAGTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.36
14 14 0.50
15 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.21
Consensus pattern (15 bp):
GAATGGTGATGGAAA
Found at i:92493 original size:22 final size:22
Alignment explanation
Indices: 92453--92494 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
92443 AAATATGTGG
*
92453 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
92475 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
92495 ACTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:93697 original size:96 final size:96
Alignment explanation
Indices: 93533--93710 Score: 356
Period size: 96 Copynumber: 1.9 Consensus size: 96
93523 ATCATAATGA
93533 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
1 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
93598 CTATAAAGAGCAAAGACTCAGACTTTATATT
66 CTATAAAGAGCAAAGACTCAGACTTTATATT
93629 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
1 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
93694 CTATAAAGAGCAAAGAC
66 CTATAAAGAGCAAAGAC
93711 CCAGCCTTAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (96 bp):
GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
CTATAAAGAGCAAAGACTCAGACTTTATATT
Found at i:93764 original size:96 final size:95
Alignment explanation
Indices: 93533--93750 Score: 271
Period size: 96 Copynumber: 2.3 Consensus size: 95
93523 ATCATAATGA
* * *
93533 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
1 GCTCC-ATAAGGGATGGTAAACAAGGAATGGACACTATCTTAGAATAACCAAGGAAGAACCAGTG
* * * *
93598 CTATAAAGAGCAAAGACTCAGACTTTATATT
65 CTATAAAGAGCAAAGACCCAGACTTCAAATC
* * *
93629 GCTCCAATAAGGGATGGTAAATAAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTG
1 GCTCC-ATAAGGGATGGTAAACAAGGAATGGACACTATCTTAGAATAACCAAGGAAGAACCAGTG
*
93694 CTATAAAGAGCAAAGACCCAGCCTTACAAATC
65 CTATAAAGAGCAAAGACCCAGACTT-CAAATC
* *
93726 G-TTC-TAAGGGGTGGT-AACAAGGAAT
1 GCTCCATAAGGGATGGTAAACAAGGAAT
93751 TTGACCCACT
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
93 9 0.08
94 10 0.09
96 90 0.80
97 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (95 bp):
GCTCCATAAGGGATGGTAAACAAGGAATGGACACTATCTTAGAATAACCAAGGAAGAACCAGTGC
TATAAAGAGCAAAGACCCAGACTTCAAATC
Found at i:93873 original size:361 final size:359
Alignment explanation
Indices: 93227--93899 Score: 1231
Period size: 361 Copynumber: 1.9 Consensus size: 359
93217 AAGACTCAAA
*
93227 GAAGAACCAATGTTAAAGAACAAATACCCAGACTTTATATTGCTCCAATAAGGGATGATAAATAA
1 GAAGAACCAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTCCAATAAGGGATGATAAATAA
93292 GGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTGCTATAAAGAGCAAAGACCCAGCCT
66 GGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTGCTATAAAGAGCAAAGACCCAGCCT
93357 TACAAATCGTTCAAAGGGGTGGTAACAAGGAATTTGACCCACTATCTATATAGAGATAGGAACCA
131 TACAAATCGTTCAAAGGGGTGGTAACAAGGAATTTGACCCACTATCTATATAGAGATAGGAACCA
*
93422 GAATTATCATAATGAAAGGAATTGACACCACAAGTAACAAGTTACTTGTTTGGTCGATAAAAGTC
196 AAATTATCATAATGAAAGGAATTGACACCACAAGTAACAAGTTACTTGTTTGGTCGATAAAAGTC
93487 ACAAGGACTTAAACAAGAGATAATCTCACTTAATTCATCATAATGAGCTCCAATAAGGGATGGTA
261 ACAAGGACTTAAACAAGAGATAATCTCACTTAATTCATCATAATGAGCTCCAATAAGGGATGGTA
93552 AATAAGGAATGGATAGTATCTTAGAATAACCAAG
326 AATAAGGAATGGATAGTATCTTAGAATAACCAAG
* * * *
93586 GAAGAACCAGTGCTATAAAGAGCAAAGACTCAGACTTTATATTGCTCCAATAAGGGATGGTAAAT
1 GAAGAACCAATG-T-TAAAGAACAAAGACCCAGACTTTATATTGCTCCAATAAGGGATGATAAAT
93651 AAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTGCTATAAAGAGCAAAGACCCAGC
64 AAGGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTGCTATAAAGAGCAAAGACCCAGC
*
93716 CTTACAAATCGTTCTAAGGGGTGGTAACAAGGAATTTGACCCACTATCTATATAGAGATAGGAAC
129 CTTACAAATCGTTCAAAGGGGTGGTAACAAGGAATTTGACCCACTATCTATATAGAGATAGGAAC
*
93781 CAAAATTATCATAATGAAAGGAATTGACGCCACAAGTAACAAGTTACTTGTTTGGTCGAT-AAAG
194 CAAAATTATCATAATGAAAGGAATTGACACCACAAGTAACAAGTTACTTGTTTGGTCGATAAAAG
*
93845 TCACAAGGACTTAAACAAGAGAATAATCTCACTTAATTCATCATGATGAGCTCCA
259 TCACAAGGACTTAAACAAGAG-ATAATCTCACTTAATTCATCATAATGAGCTCCA
93900 TTATAATGCA
Statistics
Matches: 302, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
359 11 0.04
360 26 0.09
361 265 0.88
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (359 bp):
GAAGAACCAATGTTAAAGAACAAAGACCCAGACTTTATATTGCTCCAATAAGGGATGATAAATAA
GGAATGGATAGTATCTTAGAATAACCAAGGAAGAACCAGTGCTATAAAGAGCAAAGACCCAGCCT
TACAAATCGTTCAAAGGGGTGGTAACAAGGAATTTGACCCACTATCTATATAGAGATAGGAACCA
AAATTATCATAATGAAAGGAATTGACACCACAAGTAACAAGTTACTTGTTTGGTCGATAAAAGTC
ACAAGGACTTAAACAAGAGATAATCTCACTTAATTCATCATAATGAGCTCCAATAAGGGATGGTA
AATAAGGAATGGATAGTATCTTAGAATAACCAAG
Found at i:95028 original size:15 final size:15
Alignment explanation
Indices: 94993--95021 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
94983 GTGCTTCAAC
94993 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
95007 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
95022 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:95070 original size:28 final size:27
Alignment explanation
Indices: 95016--95073 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
95006 TTTCTTTGCT
* * *
95016 TTTCTTCTTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGGAGTGCTGCAATTTC
*
95043 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAGTGCTGCAATTTC
95071 TTT
1 TTT
95074 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAGTGCTGCAATTTC
Found at i:96036 original size:91 final size:91
Alignment explanation
Indices: 95854--96027 Score: 267
Period size: 91 Copynumber: 1.9 Consensus size: 91
95844 GGTAGTTGAT
* * *
95854 GCTTGGCCGGATAGGGAGATAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATA
1 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATA
*
95919 AGGGCTGATCACATGCAAACTACATG
66 AGGGCTGATCACATACAAACTACATG
* *
95945 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATA
* * *
96010 GGGGCTGGTCATATACAA
66 AGGGCTGATCACATACAA
96028 GGCACATGGG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (91 bp):
GCTTAGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATA
AGGGCTGATCACATACAAACTACATG
Found at i:99523 original size:19 final size:21
Alignment explanation
Indices: 99499--99550 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
99489 TAGCCAAGAG
*
99499 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
99518 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
99539 CATGTATTTTCA
1 CATGTATTTTCA
99551 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:103650 original size:19 final size:19
Alignment explanation
Indices: 103626--103674 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
103616 CGGCCAAGAG
103626 CATGTATCTTCATTAAAA-T
1 CATGTAT-TTCATTAAAAGT
103645 CATGTATTGTCAATTAAAAGT
1 CATGTATT-TC-ATTAAAAGT
103666 CATGTATTT
1 CATGTATTT
103675 TCAAAGGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 8 0.30
21 9 0.33
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (19 bp):
CATGTATTTCATTAAAAGT
Found at i:103662 original size:20 final size:21
Alignment explanation
Indices: 103637--103678 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
103627 ATGTATCTTC
103637 ATTAAAA-TCATGTATTGTCA
1 ATTAAAAGTCATGTATTGTCA
*
103657 ATTAAAAGTCATGTATTTTCA
1 ATTAAAAGTCATGTATTGTCA
103678 A
1 A
103679 AGGGGCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
ATTAAAAGTCATGTATTGTCA
Found at i:105298 original size:15 final size:15
Alignment explanation
Indices: 105263--105291 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
105253 GTGCTTCAAC
105263 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
105277 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
105292 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:105340 original size:28 final size:27
Alignment explanation
Indices: 105286--105343 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
105276 TTTCTTTGCT
* * *
105286 TTTCTTCTTTTTGAGTGCTGGATTTTC
1 TTTCTTCTTTTGGAGTGCTGCAATTTC
*
105313 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAGTGCTGCAATTTC
105341 TTT
1 TTT
105344 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAGTGCTGCAATTTC
Found at i:116569 original size:16 final size:16
Alignment explanation
Indices: 116535--116581 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
116525 ATAACATCTC
*
116535 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
116551 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
116566 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
116579 TAT
1 TAT
116582 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:116583 original size:12 final size:13
Alignment explanation
Indices: 116556--116584 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
116546 TTTCTTATCC
116556 TTTCATTTCTTTA
1 TTTCATTTCTTTA
116569 TTTCATTTC-TTA
1 TTTCATTTCTTTA
116581 TTTC
1 TTTC
116585 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:120016 original size:14 final size:14
Alignment explanation
Indices: 119997--120037 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
119987 AAGATACTAC
119997 CTTTCCATCACCAT
1 CTTTCCATCACCAT
120011 CTTTCCATCACCAT
1 CTTTCCATCACCAT
* *
120025 -TCTCTATCACCAT
1 CTTTCCATCACCAT
120038 TCACGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:120035 original size:13 final size:13
Alignment explanation
Indices: 120000--120039 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
119990 ATACTACCTT
*
120000 TCCATCACCATCTT
1 TCCATCACCAT-TC
120014 TCCATCACCATTC
1 TCCATCACCATTC
*
120027 TCTATCACCATTC
1 TCCATCACCATTC
120040 ACGCCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:123472 original size:19 final size:20
Alignment explanation
Indices: 123448--123498 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
123438 CGGCCAAGAG
* *
123448 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
123467 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
123487 CATGTATTTTCA
1 CATGTATTTTCA
123499 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:123950 original size:20 final size:20
Alignment explanation
Indices: 123914--123951 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
123904 TTTTTATTTA
*
123914 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
123934 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
123952 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:124245 original size:5 final size:5
Alignment explanation
Indices: 124244--124270 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
124234 ATCAGAAAAG
124244 AAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AA
124271 AGAGAAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:127657 original size:19 final size:20
Alignment explanation
Indices: 127633--127683 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
127623 CGGCCAAGAG
* *
127633 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
127652 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
127672 CATGTATTTTCA
1 CATGTATTTTCA
127684 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:128135 original size:20 final size:20
Alignment explanation
Indices: 128099--128136 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
128089 TTTTTATTTA
*
128099 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
128119 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
128137 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:130971 original size:26 final size:26
Alignment explanation
Indices: 130941--131005 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
130931 GAACCACATA
* *
130941 CAAGGCTCATGGGGGCTGGTCATATG
1 CAAGGCACATGGGGGCTGATCATATG
130967 CAAGGCACATGGGGGCTGATCATATG
1 CAAGGCACATGGGGGCTGATCATATG
* *
130993 CAAAGCATATGGG
1 CAAGGCACATGGG
131006 TGTTCTAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.20
Consensus pattern (26 bp):
CAAGGCACATGGGGGCTGATCATATG
Found at i:132755 original size:24 final size:21
Alignment explanation
Indices: 132720--132762 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
132710 GGCTCATTCT
*
132720 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
132743 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
132763 AACTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:135294 original size:19 final size:21
Alignment explanation
Indices: 135251--135302 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
135241 GAAACCCCTT
135251 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
135272 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
135291 TGAAGATACATG
1 TGAAAATACATG
135303 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:136251 original size:30 final size:31
Alignment explanation
Indices: 136211--136270 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
136201 ACATGCTGCC
**
136211 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
136242 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
136271 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:138689 original size:11 final size:10
Alignment explanation
Indices: 138650--138699 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
138640 TTTTGAATTC
138650 TTTTTCTT-T
1 TTTTTCTTCT
138659 TATTTTCTTCT
1 T-TTTTCTTCT
138670 TTTCTTCTTCT
1 TTT-TTCTTCT
138681 TTTTGTCTT-T
1 TTTT-TCTTCT
138691 TTCTTTCTT
1 TT-TTTCTT
138700 TTTGCACTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 17 0.47
11 18 0.50
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:138702 original size:11 final size:10
Alignment explanation
Indices: 138650--138702 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
138640 TTTTGAATTC
138650 TTTTTCTTTT
1 TTTTTCTTTT
*
138660 ATTTTCTTCTT
1 TTTTTCTT-TT
*
138671 TTCTTCTTCTT
1 TTTTTCTT-TT
*
138682 TTTGTCTTTT
1 TTTTTCTTTT
*
138692 TCTTTCTTTT
1 TTTTTCTTTT
138702 T
1 T
138703 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:139465 original size:19 final size:20
Alignment explanation
Indices: 139423--139473 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
139413 GAAACCCCTT
139423 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
139443 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
139462 TGAAGATACATG
1 TGAAAATACATG
139474 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:140422 original size:30 final size:31
Alignment explanation
Indices: 140382--140441 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
140372 ACATGCTGCC
**
140382 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
140413 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
140442 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:144849 original size:35 final size:37
Alignment explanation
Indices: 144780--144849 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
144770 ATAAGATACA
* *
144780 ATATGTCCATCACCATTATCACGCCTATATCATCACC
1 ATATGTCCATCACCATTATCACGCCAATAACATCACC
144817 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGCCAATAACATCA
144850 TCCTTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
36 10 0.32
37 4 0.13
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.27
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCAATAACATCACC
Found at i:144864 original size:33 final size:33
Alignment explanation
Indices: 144785--144893 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 33
144775 ATACAATATG
* *
144785 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
144821 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
144854 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
*
144887 TCAATCA
1 TCCATCA
144894 TCAACAAGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 27 0.43
34 7 0.11
35 17 0.27
36 12 0.19
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:148757 original size:33 final size:33
Alignment explanation
Indices: 148678--148786 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 33
148668 ATACAATCTG
* *
148678 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
148714 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
148747 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
*
148780 TCAATCA
1 TCCATCA
148787 TCAACAAGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 27 0.43
34 7 0.11
35 17 0.27
36 12 0.19
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:152739 original size:27 final size:28
Alignment explanation
Indices: 152709--152761 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
152699 TTTGCTTATC
* *
152709 TTCTTTTTGAATGC-TGAATTTCTTTCT
1 TTCTTTTGGAATGCTTCAATTTCTTTCT
*
152736 TTCTTTTGGAGTGCTTCAATTTCTTT
1 TTCTTTTGGAATGCTTCAATTTCTTT
152762 TCTGATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.58
Consensus pattern (28 bp):
TTCTTTTGGAATGCTTCAATTTCTTTCT
Found at i:153613 original size:26 final size:26
Alignment explanation
Indices: 153583--153647 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
153573 GAACCACATA
153583 CAAGGCACATGGGGGCTGATCATATG
1 CAAGGCACATGGGGGCTGATCATATG
153609 CAAGGCACATGGGGGCTGATCATATG
1 CAAGGCACATGGGGGCTGATCATATG
*
153635 CAAAGCACATGGG
1 CAAGGCACATGGG
153648 TGTTCTAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.17
Consensus pattern (26 bp):
CAAGGCACATGGGGGCTGATCATATG
Found at i:154923 original size:21 final size:21
Alignment explanation
Indices: 154897--154946 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
154887 TTTGGAGTAC
*
154897 AAAAAAGATAAAAAAAGACGAA
1 AAAAAAGA-AAAAAAAGAAGAA
154919 AAAAAAGAAAAAAAAGAAGAA
1 AAAAAAGAAAAAAAAGAAGAA
154940 AAGAAAA
1 AA-AAAA
154947 AGAATAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAGAAGAA
Found at i:154928 original size:9 final size:9
Alignment explanation
Indices: 154906--154947 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
154896 CAAAAAAGAT
154906 AAAAAAAGACG
1 AAAAAAA-A-G
154917 AAAAAAAAG
1 AAAAAAAAG
154926 AAAAAAAAG
1 AAAAAAAAG
*
154935 -AAGAAAAG
1 AAAAAAAAG
154943 AAAAA
1 AAAAA
154948 GAATAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 1 0.04
11 7 0.25
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:157441 original size:25 final size:24
Alignment explanation
Indices: 157408--157455 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
157398 CAACGCATAC
157408 ATTTATGGAAGGACAAAGGGACATG
1 ATTTATGGAAGGACAAA-GGACATG
* * *
157433 ATTTTTGGAATGATAAAGGACAT
1 ATTTATGGAAGGACAAAGGACAT
157456 AAACGTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (24 bp):
ATTTATGGAAGGACAAAGGACATG
Found at i:158767 original size:19 final size:21
Alignment explanation
Indices: 158743--158794 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
158733 CGGCCAAGAG
*
158743 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
158762 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
158783 CATGTATTTTCA
1 CATGTATTTTCA
158795 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:159686 original size:2 final size:2
Alignment explanation
Indices: 159679--159784 Score: 212
Period size: 2 Copynumber: 53.0 Consensus size: 2
159669 AGTTATTTTC
159679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159763 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
159785 GTGATCATGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160073 original size:30 final size:31
Alignment explanation
Indices: 160021--160080 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
160011 CTTAGCTTTA
**
160021 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
160051 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
160081 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:161013 original size:19 final size:21
Alignment explanation
Indices: 160989--161040 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
160979 CGGCCAAGAG
*
160989 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
161008 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
161029 CATGTATTTTCA
1 CATGTATTTTCA
161041 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:161494 original size:20 final size:20
Alignment explanation
Indices: 161466--161509 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
161456 GCCATCTCTC
*
161466 TTTCATTTATT-TCTATTTCA
1 TTTCATTTATTATATA-TTCA
*
161486 TTTCCTTTATTATATATTCA
1 TTTCATTTATTATATATTCA
161506 TTTC
1 TTTC
161510 TTAAGACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTTATTATATATTCA
Found at i:161789 original size:14 final size:13
Alignment explanation
Indices: 161772--161821 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
161762 GTGCAAAAAG
161772 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
161786 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
161799 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
161810 AAAGAAAAAGAA
1 AAAGAAAAAGAA
161822 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:161818 original size:19 final size:18
Alignment explanation
Indices: 161766--161821 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
161756 ATTGGAGTGC
161766 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
161783 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
161802 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
161821 A
1 A
161822 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:161819 original size:11 final size:11
Alignment explanation
Indices: 161766--161821 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
161756 ATTGGAGTGC
161766 AAAAAG-AAAG
1 AAAAAGAAAAG
161776 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
161790 AAGAAGAAAAG
1 AAAAAGAAAAG
161801 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
161814 AAAAAGAA
1 AAAAAGAA
161822 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:164250 original size:30 final size:31
Alignment explanation
Indices: 164198--164257 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
164188 CTTAGCTTTA
**
164198 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
164228 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
164258 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:165189 original size:19 final size:21
Alignment explanation
Indices: 165165--165216 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
165155 CGGCCAAGAG
*
165165 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
165184 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
165205 CATGTATTTTCA
1 CATGTATTTTCA
165217 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:165843 original size:2 final size:2
Alignment explanation
Indices: 165836--165911 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
165826 CCTTACATCA
165836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
165878 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
165912 GTTATTATGA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175498 original size:91 final size:90
Alignment explanation
Indices: 175318--175498 Score: 213
Period size: 91 Copynumber: 2.0 Consensus size: 90
175308 CCTAGAACAC
* *
175318 CCATGTGCCTTGCATATGACCAGCCCCCTTGTGCCCTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCCTGCATATGGATCATTTAGGCGCCAAGATG
* * *
175383 AAGAGTTCTCTCCGTATTCGGCCAAG
66 AAGAGATCTATCCG-ATTCAGCCAAG
** * * * *
175409 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCCTGCATATGGATCATTTAGGCGCCAAGATG
175474 AATG-GCCATCTATCC-ATTCAGCCAA
66 AA-GAG--ATCTATCCGATTCAGCCAA
175499 TCACCATTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
91 69 0.91
92 1 0.01
93 6 0.08
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (90 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCCTGCATATGGATCATTTAGGCGCCAAGATG
AAGAGATCTATCCGATTCAGCCAAG
Found at i:179108 original size:13 final size:12
Alignment explanation
Indices: 179089--179153 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
179079 ATATAGGCGT
179089 GATATGGTGATG
1 GATATGGTGATG
179101 GAATATGGTGAT-
1 G-ATATGGTGATG
*
179113 GATATAGGCG-T-
1 GATAT-GGTGATG
179124 GATAATGGTGATG
1 GAT-ATGGTGATG
179137 GACTATGGTGAT-
1 GA-TATGGTGATG
179149 GATAT
1 GATAT
179154 AGGCGTGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:179144 original size:36 final size:35
Alignment explanation
Indices: 179071--179162 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 35
179061 ATTTATAAGT
*
179071 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
*
179106 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAATA
179142 TGGTGATGATATAGGCGTGAT
1 TGGTGATGATATAGGCGTGAT
179163 GGTTAGAAGC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
35 20 0.37
36 34 0.63
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:180908 original size:20 final size:19
Alignment explanation
Indices: 180869--180918 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
180859 CGGCCAAGAG
* *
180869 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
180888 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
180908 CATG-ATTTTCA
1 CATGTATTTTCA
180919 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Done.