Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008040.1 Hibiscus syriacus cultivar Beakdansim tig00110527_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: 437554
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:240 original size:14 final size:14
Alignment explanation
Indices: 221--253 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
211 AAAGCACTCA
221 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
235 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
249 AAAAG
1 AAAAG
254 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:2953 original size:11 final size:13
Alignment explanation
Indices: 2921--2950 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2911 TGGCCAAAGA
2921 TGAAAAGGTATGT
1 TGAAAAGGTATGT
2934 TGAAAAGGTATG-
1 TGAAAAGGTATGT
2946 TGAAA
1 TGAAA
2951 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:8561 original size:19 final size:21
Alignment explanation
Indices: 8518--8569 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
8508 GAAACCCCTT
8518 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
8539 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
8558 TGAAGATACATG
1 TGAAAATACATG
8570 CTCTTGGCTG
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:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:10059 original size:24 final size:23
Alignment explanation
Indices: 10019--10066 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10009 ATAAAGTTGT
* *
10019 TAATTTTTATGATCCAATGAACA
1 TAATTTTTAGGATCCAAGGAACA
*
10042 TAATTTTTGGGATGCCAAGGAACA
1 TAATTTTTAGGAT-CCAAGGAACA
10066 T
1 T
10067 GATCATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (23 bp):
TAATTTTTAGGATCCAAGGAACA
Found at i:12322 original size:23 final size:24
Alignment explanation
Indices: 12295--12350 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
12285 TTAGATAATG
**
12295 CAAAAGAACAAT-AAAAGGAAATT
1 CAAAAGAACAATAAAAAGGAAAAA
12318 CAAAAGAACAATAAAAAGGAAAAA
1 CAAAAGAACAATAAAAAGGAAAAA
12342 CAAAAGAAC
1 CAAAAGAAC
12351 CTAAAGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.70, C:0.11, G:0.12, T:0.07
Consensus pattern (24 bp):
CAAAAGAACAATAAAAAGGAAAAA
Found at i:14853 original size:12 final size:12
Alignment explanation
Indices: 14833--14866 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14823 CACGCCTACA
14833 CCATCACCATTT
1 CCATCACCATTT
*
14845 CCATTACCATTT
1 CCATCACCATTT
14857 -CATCACCATT
1 CCATCACCATT
14867 GAAGCATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.35
Consensus pattern (12 bp):
CCATCACCATTT
Found at i:17006 original size:20 final size:20
Alignment explanation
Indices: 16981--17030 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
16971 TCATATCACA
16981 TGTCCATTCATGAACCAACT
1 TGTCCATTCATGAACCAACT
*
17001 TGTCCATTCATTAACCAACT
1 TGTCCATTCATGAACCAACT
*
17021 TGTCCCTTCA
1 TGTCCATTCA
17031 CCCTCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (20 bp):
TGTCCATTCATGAACCAACT
Found at i:24467 original size:25 final size:25
Alignment explanation
Indices: 24424--24473 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
24414 CTTTCTTTAT
*
24424 CATCTTCCATTATCATTCTTTCAAC
1 CATCTTCCATTATCATTCTTACAAC
**
24449 CATCTTCCATTATTTTTCTTACAAC
1 CATCTTCCATTATCATTCTTACAAC
24474 AACAACATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (25 bp):
CATCTTCCATTATCATTCTTACAAC
Found at i:24872 original size:9 final size:8
Alignment explanation
Indices: 24859--24896 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
24849 AGGAGTTCAA
24859 AAAAAAGC
1 AAAAAAGC
*
24867 ACAAAAAGA
1 A-AAAAAGC
24876 AAAAAAGC
1 AAAAAAGC
24884 AAAAAAG-
1 AAAAAAGC
24891 AAAAAA
1 AAAAAA
24897 TTTACAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 6 0.22
8 14 0.52
9 7 0.26
ACGTcount: A:0.82, C:0.08, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGC
Found at i:24880 original size:17 final size:16
Alignment explanation
Indices: 24858--24896 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
24848 AAGGAGTTCA
24858 AAAAAAAGCACAAAAAG
1 AAAAAAAGCA-AAAAAG
24875 AAAAAAAGCAAAAAAG
1 AAAAAAAGCAAAAAAG
24891 AAAAAA
1 AAAAAA
24897 TTTACAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAGCAAAAAAG
Found at i:29542 original size:21 final size:23
Alignment explanation
Indices: 29503--29545 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
29493 CTCTATCCCT
*
29503 TCTTTATTTCATTTGATTTATTA
1 TCTTTATTTCATTTCATTTATTA
29526 TCTTTA-TT-ATTTCATTTATT
1 TCTTTATTTCATTTCATTTATT
29546 CTTCCTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (23 bp):
TCTTTATTTCATTTCATTTATTA
Found at i:29810 original size:21 final size:22
Alignment explanation
Indices: 29783--29841 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
29773 TGGAGTGCAA
*
29783 AAAGAAAGAAAAAGACAAAAAG
1 AAAGAAAGAAAAAGAAAAAAAG
*
29805 -AAGAAA-AAATTAGAAAAAAAG
1 AAAGAAAGAAA-AAGAAAAAAAG
29826 AAAAGAAAAGAAAAAG
1 -AAAG-AAAGAAAAAG
29842 TAATTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
23 3 0.10
24 5 0.17
25 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (22 bp):
AAAGAAAGAAAAAGAAAAAAAG
Found at i:29837 original size:18 final size:18
Alignment explanation
Indices: 29781--29840 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
29771 ATTGGAGTGC
*
29781 AAAAAG-AAAGAAAAAGAC
1 AAAAAGAAAAG-AAAAGAA
*
29799 AAAAAGAAGAAAAAATTAGAA
1 AAAAAGAA-AAGAAA--AGAA
29820 AAAAAGAAAAGAAAAGAA
1 AAAAAGAAAAGAAAAGAA
29838 AAA
1 AAA
29841 GTAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 7 0.20
21 11 0.31
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAGAA
Found at i:32998 original size:25 final size:25
Alignment explanation
Indices: 32934--33005 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
32924 TAGGCGTGCA
* *
32934 ATGGTGATGGAGTATGGTGAT-G-TT
1 ATGGTGAT-GAGAATGGTGATGGATG
* * *
32958 ATTGTCATGACAATGGTGATGGATG
1 ATGGTGATGAGAATGGTGATGGATG
32983 ATGGTGATGAGAATGGTGATGGA
1 ATGGTGATGAGAATGGTGATGGA
33006 ATATGATGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
25 21 0.55
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (25 bp):
ATGGTGATGAGAATGGTGATGGATG
Found at i:33015 original size:25 final size:25
Alignment explanation
Indices: 32964--33016 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
32954 TGTTATTGTC
*
32964 ATGACAATGGTGATGGATGATGGTG
1 ATGACAATGGTGATGGATGATGATG
*
32989 ATGAGAATGGTGATGGAAT-ATGATG
1 ATGACAATGGTGATGG-ATGATGATG
33014 ATG
1 ATG
33017 TTATAGGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.38, T:0.28
Consensus pattern (25 bp):
ATGACAATGGTGATGGATGATGATG
Found at i:44602 original size:37 final size:36
Alignment explanation
Indices: 44557--44670 Score: 144
Period size: 37 Copynumber: 3.2 Consensus size: 36
44547 TTGGTGGTTA
*
44557 TATAGGCGTGAAATGGTGATAGAAGTTGGTGATGAT
1 TATAGGCGTGAAATGGTGATGGAAGTTGGTGATGAT
*
44593 ATATAGGCGTGCAATGGTGATGGAA-TATGGTGATG-T
1 -TATAGGCGTGAAATGGTGATGGAAGT-TGGTGATGAT
* *
44629 TATAGGCGTGACAATGGTAATGGAAGATGGTGAT-AT
1 TATAGGCGTGA-AATGGTGATGGAAGTTGGTGATGAT
44665 TATAGG
1 TATAGG
44671 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
35 10 0.15
36 28 0.41
37 30 0.44
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TATAGGCGTGAAATGGTGATGGAAGTTGGTGATGAT
Found at i:44652 original size:36 final size:36
Alignment explanation
Indices: 44557--44670 Score: 144
Period size: 36 Copynumber: 3.2 Consensus size: 36
44547 TTGGTGGTTA
*
44557 TATAGGCGTGA-AATGGTGATAGAAGT-TGGTGATGAT
1 TATAGGCGTGACAATGGTGATGGAA-TATGGTGATG-T
44593 ATATAGGCGTG-CAATGGTGATGGAATATGGTGATGT
1 -TATAGGCGTGACAATGGTGATGGAATATGGTGATGT
* * *
44629 TATAGGCGTGACAATGGTAATGGAAGATGGTGATAT
1 TATAGGCGTGACAATGGTGATGGAATATGGTGATGT
44665 TATAGG
1 TATAGG
44671 TAGTATCTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
35 10 0.14
36 30 0.43
37 30 0.43
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TATAGGCGTGACAATGGTGATGGAATATGGTGATGT
Found at i:48124 original size:65 final size:65
Alignment explanation
Indices: 48044--48174 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
48034 GGGTGGTCTT
48044 ATAAAAGGAAGAAAATAAAGAAAGGTTCACTTACTATGCAAAGATACTCACCACCTTCCTAGAAG
1 ATAAAAGGAAGAAAATAAAGAAAGGTTCACTTACTATGCAAAGATACTCACCACCTTCCTAGAAG
48109 ATAAAAGGAAGAAAATAAAGAAAGGTTCACTTACTATGCAAAGATACTCACCACCTTCCTAGAAG
1 ATAAAAGGAAGAAAATAAAGAAAGGTTCACTTACTATGCAAAGATACTCACCACCTTCCTAGAAG
48174 A
1 A
48175 AACAATCAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (65 bp):
ATAAAAGGAAGAAAATAAAGAAAGGTTCACTTACTATGCAAAGATACTCACCACCTTCCTAGAAG
Found at i:59076 original size:19 final size:20
Alignment explanation
Indices: 59042--59090 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
59032 AACCCCTTTG
*
59042 AAAATACATGATTTTTGATA
1 AAAATACATGATTTTTAATA
*
59062 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATA
*
59081 AAGATACATG
1 AAAATACATG
59091 CTCTTCGACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTTAATA
Found at i:63273 original size:19 final size:20
Alignment explanation
Indices: 63233--63282 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
63223 AAACCCCTTA
*
63233 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTTAAT
63253 GAAAATACATGA-TTTTAAT
1 GAAAATACATGATTTTTAAT
*
63272 GAAGATACATG
1 GAAAATACATG
63283 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAT
Found at i:73246 original size:24 final size:26
Alignment explanation
Indices: 73203--73261 Score: 95
Period size: 24 Copynumber: 2.3 Consensus size: 26
73193 ATTTTCTTTT
*
73203 CTTTTTCTTCTTTTTTGAGTGCTTGA
1 CTTTTTCTTCTTTTTGGAGTGCTTGA
73229 CTTTTT-TTC-TTTTGGAGTGCTTGA
1 CTTTTTCTTCTTTTTGGAGTGCTTGA
73253 CTTTTTCTT
1 CTTTTTCTT
73262 TGTTGATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 20 0.65
25 5 0.16
26 6 0.19
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.63
Consensus pattern (26 bp):
CTTTTTCTTCTTTTTGGAGTGCTTGA
Found at i:78044 original size:45 final size:45
Alignment explanation
Indices: 77981--78161 Score: 272
Period size: 45 Copynumber: 4.0 Consensus size: 45
77971 ATAAAATTTC
* * *
77981 TTACCAATATATTTACCATTTATCCCATAAACTCGTAAGCTAATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
* * *
78026 TTATCATTATACTTACCATTTATCCCATAAGTTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
*
78071 TTACCAATATACTTACCATTTATCCCATAAGCTTGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
* * *
78116 TTACCAATATACATAACATATATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
78161 T
1 T
78162 ATATGTTTAT
Statistics
Matches: 122, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
Found at i:78315 original size:40 final size:40
Alignment explanation
Indices: 78236--78331 Score: 92
Period size: 40 Copynumber: 2.5 Consensus size: 40
78226 ATAGGAGTCA
* * * * *
78236 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGTAGTGTTGAGGTCGAGCTTTACCCACCT
*
78276 AATAATGCACCGTAGTGTTGAGGTCG-GGTTCTACCCACCT
1 AATAATGCACCGTAGTGTTGAGGTCGAGCTT-TACCCACCT
*
78316 CAT-A--CACCGTAGTGTT
1 AATAATGCACCGTAGTGTT
78332 TTGTATTGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 12 0.25
39 4 0.08
40 32 0.67
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGTAGTGTTGAGGTCGAGCTTTACCCACCT
Found at i:83592 original size:21 final size:21
Alignment explanation
Indices: 83568--83608 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
83558 GTAGAAGATA
* *
83568 AGGAAGGATTACCTTGGTAAG
1 AGGAAGAAGTACCTTGGTAAG
*
83589 AGGATGAAGTACCTTGGTAA
1 AGGAAGAAGTACCTTGGTAA
83609 TGTTCTCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Consensus pattern (21 bp):
AGGAAGAAGTACCTTGGTAAG
Found at i:84276 original size:23 final size:25
Alignment explanation
Indices: 84250--84304 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
84240 AAATCCAGCA
84250 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
84273 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
84298 AAGAAAA
1 AAGAAAA
84305 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:84312 original size:5 final size:5
Alignment explanation
Indices: 84302--84333 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
84292 AAGAGGAAGA
84302 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
84334 GTTGAAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:88981 original size:24 final size:21
Alignment explanation
Indices: 88942--88995 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 21
88932 ATTTTTGAGA
88942 CTTTTTTTGG-CTTTTTGATTTTT
1 CTTTTTTTGGCCTTTTT-A--TTT
88965 CTTTTTTTCGGCCTTTTTATTT
1 CTTTTTTT-GGCCTTTTTATTT
88987 CTTTTTTTG
1 CTTTTTTTG
88996 TTGTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.03
22 11 0.38
23 8 0.28
24 3 0.10
25 6 0.21
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (21 bp):
CTTTTTTTGGCCTTTTTATTT
Found at i:98809 original size:20 final size:20
Alignment explanation
Indices: 98780--98817 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
98770 TTTCAGAGGA
98780 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
98800 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
98818 GAATATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:98985 original size:64 final size:65
Alignment explanation
Indices: 98828--99006 Score: 188
Period size: 64 Copynumber: 2.8 Consensus size: 65
98818 GAATATATTG
* * *
98828 AACATC-AACTGCAGTTTATACATCGATGCAC-TCTTCATGAATCGATGCACTCAGGTTTTAATG
1 AACATCGAA-TGCATTTTATACATCGATGCACATC-TCATGAATCGATGCACTCAGGTCTTAATA
98891 AA
64 AA
* * * * *
98893 AACATCGATTGCATTTTATGCATCGATGCACATAC-CATGCATCGATGCACTTAGG-CTTATTAA
1 AACATCGAATGCATTTTATACATCGATGCACAT-CTCATGAATCGATGCACTCAGGTCTTAATAA
98956 A
65 A
* * *
98957 AACATCGAATGCATTTTATACATTGATGCACA-CTTAGTGCATCGATGCAC
1 AACATCGAATGCATTTTATACATCGATGCACATCTCA-TGAATCGATGCAC
99007 ACTTAGTGCA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 48 0.49
65 44 0.45
66 2 0.02
67 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (65 bp):
AACATCGAATGCATTTTATACATCGATGCACATCTCATGAATCGATGCACTCAGGTCTTAATAAA
Found at i:99005 original size:19 final size:19
Alignment explanation
Indices: 98980--99025 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
98970 TTTTATACAT
98980 TGATGCACACTTAGTGCA-
1 TGATGCACACTTAGTGCAC
98998 TCGATGCACACTTAGTGCAC
1 T-GATGCACACTTAGTGCAC
99018 TGATGCAC
1 TGATGCAC
99026 TAAGTGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (19 bp):
TGATGCACACTTAGTGCAC
Found at i:105021 original size:14 final size:14
Alignment explanation
Indices: 104989--105034 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
104979 TTATTTTTTT
*
104989 ATTTAATTT-TAGC
1 ATTTAATTTCTAAC
*
105002 ATTTAATTTCTAAT
1 ATTTAATTTCTAAC
*
105016 ATTTAAATTCTAAC
1 ATTTAATTTCTAAC
105030 ATTTA
1 ATTTA
105035 GATTCTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (14 bp):
ATTTAATTTCTAAC
Found at i:105048 original size:14 final size:14
Alignment explanation
Indices: 105001--105041 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
104991 TTAATTTTAG
*
105001 CATTTAATTTCTAA
1 CATTTAAATTCTAA
*
105015 TATTTAAATTCTAA
1 CATTTAAATTCTAA
*
105029 CATTTAGATTCTA
1 CATTTAAATTCTA
105042 TAATTTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (14 bp):
CATTTAAATTCTAA
Found at i:105104 original size:24 final size:24
Alignment explanation
Indices: 105073--105129 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
105063 TTCTTTATAA
105073 ATTCAACTTTAAATTTTGCTTTTT
1 ATTCAACTTTAAATTTTGCTTTTT
*
105097 ATTCAACTTTAAATTTTTCTTTTT
1 ATTCAACTTTAAATTTTGCTTTTT
105121 ATTCAACTT
1 ATTCAACTT
105130 AGTCCTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTCAACTTTAAATTTTGCTTTTT
Found at i:105271 original size:29 final size:31
Alignment explanation
Indices: 105206--105271 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
105196 ATTTTCTTTA
*
105206 TTAA-TTCAAGCATTAAAGTTTGTATTTGTT
1 TTAATTTCAAGCATTAAAGTTTGCATTTGTT
* *
105236 TTAATTTC-AGCATTGAATTTTGCATTT-TT
1 TTAATTTCAAGCATTAAAGTTTGCATTTGTT
105265 TTAATTT
1 TTAATTT
105272 AATCTCTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.28
30 20 0.62
31 3 0.09
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.55
Consensus pattern (31 bp):
TTAATTTCAAGCATTAAAGTTTGCATTTGTT
Found at i:105764 original size:21 final size:20
Alignment explanation
Indices: 105740--106122 Score: 287
Period size: 21 Copynumber: 18.4 Consensus size: 20
105730 CATATTCGTA
*
105740 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
* *
105761 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
105782 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
105803 TTGCGATTTATTCCAAATTTG
1 TTGCGA-TTATTCCAAGTTCG
*
105824 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
105845 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
105866 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
105887 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
105908 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
105929 TTGCGATTTATTCCAAATTAG
1 TTGCGA-TTATTCCAAGTTCG
*
105950 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
105971 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
105992 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
106013 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
106034 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
106055 TTGCGA-TAGTCCAAGTTCG
1 TTGCGATTATTCCAAGTTCG
* *
106074 TTGCGA-TAGTCGAAGTTCG
1 TTGCGATTATTCCAAGTTCG
* *
106093 CATTGTGATTTATTCCAAATTCG
1 --TTGCGA-TTATTCCAAGTTCG
106116 TTGCGAT
1 TTGCGAT
106123 AGTCCAAAAT
Statistics
Matches: 308, Mismatches: 32, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
19 65 0.21
20 1 0.00
21 188 0.61
23 54 0.18
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTATTCCAAGTTCG
Found at i:105855 original size:105 final size:103
Alignment explanation
Indices: 105740--106092 Score: 500
Period size: 105 Copynumber: 3.4 Consensus size: 103
105730 CATATTCGTA
* *
105740 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCCG
*
105803 TTGCGATTTATTCCAAATTTGTTGCGATTTATTCCAAATTCG
62 TTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
* * *
105845 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCCAAATTC-CGTT
*
105910 GCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTAG
64 GCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
* * *
105950 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCCAAATTC-CGTT
106015 GCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
64 GCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
*
106055 TTGCGATAGTCCAAGTT--CGTTGCGA-TAGTCGAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAGTTCG
106093 CATTGTGATT
Statistics
Matches: 234, Mismatches: 10, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
101 11 0.05
103 16 0.07
105 198 0.85
107 9 0.04
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (103 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCCAAATTCCGTTGC
GATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
Found at i:106766 original size:18 final size:16
Alignment explanation
Indices: 106733--106769 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
106723 TCTCGTCTCG
106733 GGTCGGGTCGGGTCAT
1 GGTCGGGTCGGGTCAT
106749 GGTCGTGGTCGTGGTCAT
1 GGTCG-GGTCG-GGTCAT
106767 GGT
1 GGT
106770 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (16 bp):
GGTCGGGTCGGGTCAT
Found at i:106895 original size:21 final size:19
Alignment explanation
Indices: 106858--106977 Score: 96
Period size: 19 Copynumber: 5.9 Consensus size: 19
106848 TCGTTGCGAT
106858 TTTGGAATATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
106877 TTTGGAATAAATCGGAACGCAAA
1 TTTGGAAT--ATCGCAACG--AA
* * *
106900 CTTCGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
106919 TTTGGAATAAATCGCAACACGAA
1 TTTGGAAT--ATCGC-A-ACGAA
* * *
106942 CTTCGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
106961 TTTGGAAAATCGCAACG
1 TTTGGAATATCGCAACG
106978 CGAACTTCGA
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
19 33 0.42
20 1 0.01
21 26 0.33
22 1 0.01
23 17 0.22
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:106924 original size:42 final size:42
Alignment explanation
Indices: 106865--106996 Score: 223
Period size: 42 Copynumber: 3.2 Consensus size: 42
106855 GATTTTGGAA
* *
106865 TATCGCAACGAATTTGGAATAAATCGGAACGCAAACTTCGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
*
106907 TATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
106949 TATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGAC
1 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
106989 TATCGCAA
1 TATCGCAA
106997 TGCGAACTTG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
40 29 0.34
41 1 0.01
42 56 0.65
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGAC
Found at i:107018 original size:21 final size:21
Alignment explanation
Indices: 106898--107148 Score: 129
Period size: 21 Copynumber: 11.8 Consensus size: 21
106888 TCGGAACGCA
*
106898 AACTTCGACTATCGCAA--CG
1 AACTTGGACTATCGCAATGCG
* * **
106917 AATTTGGAATAAATCGCAACACG
1 AACTTGGACT--ATCGCAATGCG
*
106940 AACTTCGACTATCGCAA--CG
1 AACTTGGACTATCGCAATGCG
* ** *
106959 AATTTGGAAAATCGCAACGCG
1 AACTTGGACTATCGCAATGCG
*
106980 AACTTCGACTATCGCAATGCG
1 AACTTGGACTATCGCAATGCG
107001 AACTTGGACTATCGCAATGC-
1 AACTTGGACTATCGCAATGCG
* * *
107021 AAATATGTA-AATCGCAATGCG
1 AACT-TGGACTATCGCAATGCG
* * * * *
107042 ATAGTCGAAGT-TCGCGTTGCGATAGTCG
1 A-ACTTGGACTAT--C---GCAAT-G-CG
* ** *
107070 AATTTGGAAAATCGCAACGCG
1 AACTTGGACTATCGCAATGCG
*
107091 AACTTCGACTATCGCAATGCG
1 AACTTGGACTATCGCAATGCG
107112 AACTTGGACTATCGCAATGCG
1 AACTTGGACTATCGCAATGCG
*
107133 AACTTCGACTATCGCA
1 AACTTGGACTATCGCA
107149 TTACGATTTA
Statistics
Matches: 176, Mismatches: 38, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
19 22 0.12
20 13 0.07
21 111 0.63
22 3 0.02
23 13 0.07
26 5 0.03
27 5 0.03
28 4 0.02
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (21 bp):
AACTTGGACTATCGCAATGCG
Found at i:107198 original size:21 final size:21
Alignment explanation
Indices: 107167--107258 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
107157 TACATATTCG
* *
107167 CATTGCAATAGTCCAAGTTCT
1 CATTGCGATAGTCCAAGTTCA
* *
107188 TATTGTGATAGTCCAAGTTCA
1 CATTGCGATAGTCCAAGTTCA
* *
107209 CATTGCGATAGTCCATGTTCG
1 CATTGCGATAGTCCAAGTTCA
* *
107230 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCA
*
107251 CGTTGCGA
1 CATTGCGA
107259 ATCTGGAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCA
Found at i:107257 original size:42 final size:42
Alignment explanation
Indices: 107163--107258 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
107153 GATTTACATA
* ** *
107163 TTCGCATTGCAATAGTCCAAGTTCTTATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
* * *
107205 TTCACATTGCGATAGTCCATGTTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
*
107247 TTCGCGTTGCGA
1 TTCGCATTGCGA
107259 ATCTGGAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
Found at i:109203 original size:15 final size:15
Alignment explanation
Indices: 109183--109213 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
109173 TCATAATAAG
109183 TTTATGAATTTCTGT
1 TTTATGAATTTCTGT
*
109198 TTTATGAATTTTTGT
1 TTTATGAATTTCTGT
109213 T
1 T
109214 GGACACTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.13, T:0.65
Consensus pattern (15 bp):
TTTATGAATTTCTGT
Found at i:109513 original size:81 final size:81
Alignment explanation
Indices: 109423--110284 Score: 1186
Period size: 81 Copynumber: 10.7 Consensus size: 81
109413 AAAATAAAGG
*
109423 ATTAATGGCCTAGTTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
109488 TACCTTTGAGTAAAAT
66 TACCTTTGAGTAAAAT
* *
109504 ATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTCAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* *
109569 TATCTTTGAGTAAAAG
66 TACCTTTGAGTAAAAT
* *
109585 ATTAATGGCCTAGTTGTGCATTTGATAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* *
109650 TGCCTTTGAGTAAAAG
66 TACCTTTGAGTAAAAT
* * * * *
109666 ATTAATGGTCTAGCTGTGCAATTGACAGAAATGTGTCAATTATTCTAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
109731 TACCTTTGAGTAAAAT
66 TACCTTTGAGTAAAAT
* * * *
109747 ATTACTGGCCTAGTTGTGCATTTGACAGAAAAGTGTTAATTATGCCAATTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* *
109812 TACCTTTCAGTAAAAG
66 TACCTTTGAGTAAAAT
* * * *
109828 ATTAA-----TAATTGTGCATTTGATAGAAAGGTGT-ATATTATGCCAGTTATATGAAAGGTTAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCA-ATTATGCCAGTTAGATGAAAGGTTAA
109887 ATACCTTTGAGTAAAAT
65 ATACCTTTGAGTAAAAT
* * *
109904 ATTAATGGCCTAGATGTGCATTTGACATAAAGGTGTCAATTATGCCA-TTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
**
109968 TATATTTGAGTAAAAT
66 TACCTTTGAGTAAAAT
* *
109984 ATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATACCAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
110049 TACCTTTGAGTAAAAT
66 TACCTTTGAGTAAAAT
* * * ** * *
110065 ATTAATGG-CTTGCCTATGCAACTGACAGAAA-GATGTCAATTATGCAAGTTAGATGAAACGTTA
1 ATTAATGGCCTAG-TTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGGTTA
*
110128 AATACCTTTGAGTAAAAG
64 AATACCTTTGAGTAAAAT
* * **
110146 ATTAATGGCCTAGTTATGCATTTGACAGAAATGTATCAATTATGTTAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
*
110211 TACCTTTGAGTCAAAT
66 TACCTTTGAGTAAAAT
* * * *
110227 ATTAATGGCCTAGCTGTGCATTTGACAGGAA-GTTGTCAATCATGCAAGTTAGATGAAA
1 ATTAATGGCCTAGTTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
110285 AGCTATATGC
Statistics
Matches: 691, Mismatches: 77, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
75 1 0.00
76 67 0.10
80 78 0.11
81 540 0.78
82 5 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
ATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
TACCTTTGAGTAAAAT
Found at i:114939 original size:13 final size:13
Alignment explanation
Indices: 114921--114946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
114911 TTTTGAGGTG
114921 TCACATTAGGGCC
1 TCACATTAGGGCC
114934 TCACATTAGGGCC
1 TCACATTAGGGCC
114947 ACTGGAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
TCACATTAGGGCC
Found at i:117982 original size:20 final size:20
Alignment explanation
Indices: 117946--117985 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
117936 TCAGGTTTAG
*
117946 GTTAACTCAATTCGGTTCAA
1 GTTAACTCAACTCGGTTCAA
117966 GTTAACTCAAACT-GGTTCAA
1 GTTAACTC-AACTCGGTTCAA
117986 ATAGATTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (20 bp):
GTTAACTCAACTCGGTTCAA
Found at i:118807 original size:20 final size:21
Alignment explanation
Indices: 118779--118829 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
118769 GCCTAAAAGT
* * *
118779 TTCAGAAATTC-ATTGTTTAG
1 TTCATAAATTCAATTATTTAA
118799 TTCATAAA-TCAATTATTTAA
1 TTCATAAATTCAATTATTTAA
118819 TTCTATAAATT
1 TTC-ATAAATT
118830 TTAAACTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 5 0.20
22 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (21 bp):
TTCATAAATTCAATTATTTAA
Found at i:119772 original size:15 final size:15
Alignment explanation
Indices: 119749--119787 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
119739 AAGCCAATGT
*
119749 TCGAGGCAATCATAA
1 TCGAAGCAATCATAA
*
119764 TCGAAGCAATCGTAA
1 TCGAAGCAATCATAA
119779 TCGAAGCAA
1 TCGAAGCAA
119788 AATCAAGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (15 bp):
TCGAAGCAATCATAA
Found at i:123982 original size:24 final size:24
Alignment explanation
Indices: 123955--124009 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
123945 AAGATTTTGA
123955 TGTTGTCTGGGACATCTTCATACG
1 TGTTGTCTGGGACATCTTCATACG
123979 TGTTGTCTGGGACATCTTCATACG
1 TGTTGTCTGGGACATCTTCATACG
124003 TGTTGTC
1 TGTTGTC
124010 AATGCGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (24 bp):
TGTTGTCTGGGACATCTTCATACG
Found at i:125563 original size:35 final size:34
Alignment explanation
Indices: 125498--125566 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
125488 CACTCTAAAA
*
125498 ATGGTACCGATACTACCTATCGGTATCGATACCC
1 ATGGTACCAATACTACCTATCGGTATCGATACCC
125532 ATGGTACCAATACTACC-ACTTCGGTATCGATACCC
1 ATGGTACCAATACTACCTA--TCGGTATCGATACCC
125567 TGTGAAGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 1 0.03
34 16 0.50
35 15 0.47
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (34 bp):
ATGGTACCAATACTACCTATCGGTATCGATACCC
Found at i:125909 original size:34 final size:34
Alignment explanation
Indices: 125866--125935 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
125856 TGAGAATCTT
125866 ACTAAATTTCCAACATGATCTAATTTCATTTCTA
1 ACTAAATTTCCAACATGATCTAATTTCATTTCTA
125900 ACTAAATTTCCAACATGATCTAATTTCATTTCTA
1 ACTAAATTTCCAACATGATCTAATTTCATTTCTA
125934 AC
1 AC
125936 ACTTTATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (34 bp):
ACTAAATTTCCAACATGATCTAATTTCATTTCTA
Found at i:130458 original size:125 final size:123
Alignment explanation
Indices: 130304--130551 Score: 399
Period size: 125 Copynumber: 2.0 Consensus size: 123
130294 CTTCACGCCA
130304 TTATCATACATATCATGAGGAATTTTTCATCTTCATCTTACTTCATTTTTATTTATGATCATTTT
1 TTATCATACATATCATGAGGAATTTTTCATCTTCATCTTACTTCATTTTTA-TT-T-ATCATTTT
*
130369 GTTCATTTTTTA-TATTATTCATCTATATGATATAATTAGAAAATTTGGTTTTGGTTTTAT
63 GTTCATTTTTTAGTATTATTCATCTATATGATATAATTAGAAAAATTGGTTTTGGTTTTAT
* * *
130429 TTATCATATATGTCATGAGGAATTTTTCATCTTCATCTTTCTTCATTTTTATTTATCATTTTGTT
1 TTATCATACATATCATGAGGAATTTTTCATCTTCATCTTACTTCATTTTTATTTATCATTTTGTT
* *
130494 CATTTTTTATGTATTATTTATCTATATGATATAGTTAGAAAAATTGGTTTTGGTTTTA
66 CATTTTTTA-GTATTATTCATCTATATGATATAATTAGAAAAATTGGTTTTGGTTTTA
130552 CGTGATTAAA
Statistics
Matches: 115, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
122 20 0.17
123 1 0.01
124 46 0.40
125 48 0.42
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (123 bp):
TTATCATACATATCATGAGGAATTTTTCATCTTCATCTTACTTCATTTTTATTTATCATTTTGTT
CATTTTTTAGTATTATTCATCTATATGATATAATTAGAAAAATTGGTTTTGGTTTTAT
Found at i:130476 original size:23 final size:22
Alignment explanation
Indices: 130450--130500 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
130440 GTCATGAGGA
130450 ATTTTTCATCT-TCATCTTTCTTC
1 ATTTTT-ATCTATCAT-TTTCTTC
* *
130473 ATTTTTATTTATCATTTTGTTC
1 ATTTTTATCTATCATTTTCTTC
130495 ATTTTT
1 ATTTTT
130501 TATGTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTTTATCTATCATTTTCTTC
Found at i:130501 original size:23 final size:22
Alignment explanation
Indices: 130461--130512 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
130451 TTTTTCATCT
*
130461 TCATCTTTCTTCATTTTTATTTA
1 TCAT-TTTCTTCATTTTTATGTA
*
130484 TCATTTTGTTCATTTTTTATGTA
1 TCATTTTCTTCA-TTTTTATGTA
*
130507 TTATTT
1 TCATTT
130513 ATCTATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (22 bp):
TCATTTTCTTCATTTTTATGTA
Found at i:137316 original size:24 final size:25
Alignment explanation
Indices: 137270--137317 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
137260 CACCATGATC
* * *
137270 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
137295 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTCTTCAGGTTCCTCATC
137318 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:151219 original size:22 final size:22
Alignment explanation
Indices: 151171--151219 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
151161 TGAACAGTGT
* *
151171 ATTTTTTTTTTTTCTTCGAACT
1 ATTTTTTTTTTTTCTGCGAACA
*
151193 CTTTTTTTTTTTTC-GCGGAACA
1 ATTTTTTTTTTTTCTGC-GAACA
151215 ATTTT
1 ATTTT
151220 ACCTTTGTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.63
Consensus pattern (22 bp):
ATTTTTTTTTTTTCTGCGAACA
Found at i:163548 original size:18 final size:19
Alignment explanation
Indices: 163513--163561 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
163503 AATTTATATT
*
163513 TAATTTAATTATTTATAAA
1 TAATTTAATTATTAATAAA
163532 TAATTTAA-TATTAATAAA
1 TAATTTAATTATTAATAAA
* *
163550 TACTTAAATTAT
1 TAATTTAATTAT
163562 ATTAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTTAATTATTAATAAA
Found at i:163779 original size:15 final size:15
Alignment explanation
Indices: 163756--163786 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
163746 TATTACAGAT
163756 AATACTAAAATATAA
1 AATACTAAAATATAA
*
163771 AATATTAAAATATAA
1 AATACTAAAATATAA
163786 A
1 A
163787 GGACTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AATACTAAAATATAA
Found at i:164946 original size:7 final size:7
Alignment explanation
Indices: 164931--164964 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
164921 TTCAGGTTAT
*
164931 ATAAATA
1 ATAATTA
164938 ATAATTA
1 ATAATTA
164945 AT-ATTA
1 ATAATTA
164951 ATAATTA
1 ATAATTA
164958 ATAATTA
1 ATAATTA
164965 TATATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAATTA
Found at i:164954 original size:13 final size:13
Alignment explanation
Indices: 164936--164960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
164926 GTTATATAAA
164936 TAATAATTAATAT
1 TAATAATTAATAT
164949 TAATAATTAATA
1 TAATAATTAATA
164961 ATTATATATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATTAATAT
Found at i:164959 original size:20 final size:20
Alignment explanation
Indices: 164931--164975 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
164921 TTCAGGTTAT
*
164931 ATAAATAATAATTA-ATATTA
1 ATAATTAATAATTATATA-TA
164951 ATAATTAATAATTATATATA
1 ATAATTAATAATTATATATA
164971 ATAAT
1 ATAAT
164976 GTACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATTAATAATTATATATA
Found at i:164962 original size:16 final size:16
Alignment explanation
Indices: 164929--164975 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
164919 CTTTCAGGTT
164929 ATATAAATAATAATTA
1 ATATAAATAATAATTA
*
164945 ATATTAATAATTAA-TA
1 ATATAAATAA-TAATTA
*
164961 ATTATATATAATAAT
1 A-TATAAATAATAAT
164976 GTACATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAATAATAATTA
Found at i:165512 original size:18 final size:18
Alignment explanation
Indices: 165491--165534 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
165481 TATACACATT
*
165491 ATATATTACATATTTATA
1 ATATATTACATAGTTATA
**
165509 ATATATTTTATAGTTATA
1 ATATATTACATAGTTATA
165527 ATATATTA
1 ATATATTA
165535 TATTTATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
ATATATTACATAGTTATA
Found at i:165547 original size:22 final size:19
Alignment explanation
Indices: 165503--165552 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
165493 ATATTACATA
165503 TTTATAATATATTTTATAG
1 TTTATAATATATTTTATAG
*
165522 -TTATAATATATTATATTTATG
1 TTTATAATATATT-T-TATA-G
165543 TTTATAATAT
1 TTTATAATAT
165553 TGAACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 3 0.12
21 1 0.04
22 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTATAATATATTTTATAG
Found at i:166695 original size:11 final size:10
Alignment explanation
Indices: 166676--166739 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 10
166666 TATATATATA
166676 TATTATTTTTT
1 TATT-TTTTTT
166687 TATTCTTTTTT
1 TATT-TTTTTT
166698 TATTTTTTATT
1 TATTTTTT-TT
166709 T-TTTATTTTT
1 TATTT-TTTTT
166719 TATTTTTTATT
1 TATTTTTT-TT
166730 TATTTCTTTT
1 TATTT-TTTT
166740 GGTTTTTGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
10 13 0.28
11 31 0.66
12 3 0.06
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:166705 original size:7 final size:7
Alignment explanation
Indices: 166693--166730 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
166683 TTTTTATTCT
166693 TTTTTTA
1 TTTTTTA
166700 TTTTTTA
1 TTTTTTA
166707 TTTTTTA
1 TTTTTTA
166714 TTTTTTA
1 TTTTTTA
166721 TTTTTTA
1 TTTTTTA
166728 TTT
1 TTT
166731 ATTTCTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:166717 original size:21 final size:22
Alignment explanation
Indices: 166676--166739 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
166666 TATATATATA
166676 TATTATTTT-TTTATTCT-TTTTT
1 TATT-TTTTATTTATT-TATTTTT
166698 TATTTTTTATTT-TTTATTTTT
1 TATTTTTTATTTATTTATTTTT
*
166719 TATTTTTTATTTATTTCTTTT
1 TATTTTTTATTTATTTATTTT
166740 GGTTTTTGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 1 0.03
21 23 0.61
22 14 0.37
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (22 bp):
TATTTTTTATTTATTTATTTTT
Found at i:170349 original size:20 final size:19
Alignment explanation
Indices: 170322--170359 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
170312 ATATTTTGAA
170322 TTTTTATTTTCCATGTTTG
1 TTTTTATTTTCCATGTTTG
170341 TTTTCTATTTTCCATGTTT
1 TTTT-TATTTTCCATGTTT
170360 TTACATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.11, C:0.13, G:0.08, T:0.68
Consensus pattern (19 bp):
TTTTTATTTTCCATGTTTG
Found at i:177682 original size:55 final size:56
Alignment explanation
Indices: 177613--177720 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 56
177603 AATACTTCAC
* * * * *
177613 TTAGGATGAAAACCCGAGAGGGCATCCTAAGTCGAAAAAGA-AAAAAGAAAAACAT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGAAAAAGAAAAACAT
* *
177668 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTAAAAAAAAGAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGAAAAAGAAAAA
177721 AAATAAGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 34 0.76
56 11 0.24
ACGTcount: A:0.54, C:0.14, G:0.20, T:0.12
Consensus pattern (56 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATCAAAAAAAAGAAAAAGAAAAACAT
Found at i:179020 original size:20 final size:19
Alignment explanation
Indices: 178988--179026 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
178978 GCACATGTTA
178988 ATGGATGCATCGATACACT
1 ATGGATGCATCGATACACT
* *
179007 ATGGAATGCGTCGATGCACT
1 ATGG-ATGCATCGATACACT
179027 TCTAGGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (19 bp):
ATGGATGCATCGATACACT
Found at i:180894 original size:25 final size:25
Alignment explanation
Indices: 180866--180917 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
180856 TAATATTATA
* *
180866 TAGTTAAATTAGATGTACTTAAGTT
1 TAGTTAAATTAGATATACCTAAGTT
180891 TAGTTAAATTAGATATACCTAAGTT
1 TAGTTAAATTAGATATACCTAAGTT
180916 TA
1 TA
180918 CTTATCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (25 bp):
TAGTTAAATTAGATATACCTAAGTT
Found at i:186210 original size:31 final size:31
Alignment explanation
Indices: 186175--186237 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
186165 ATCATTTTTA
*
186175 TTAATAATCTAAATTATTTTACCAATGAAGG
1 TTAATAATCTAAATTATTTTAACAATGAAGG
*
186206 TTAATACTCTAAATTATTTTAACAATGAAGG
1 TTAATAATCTAAATTATTTTAACAATGAAGG
186237 T
1 T
186238 AACAAATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
TTAATAATCTAAATTATTTTAACAATGAAGG
Found at i:196589 original size:20 final size:19
Alignment explanation
Indices: 196561--196608 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
196551 TACTATTCAT
*
196561 TACTGTTCACACAGTATCAA
1 TACTATTCACACAGTA-CAA
*
196581 TACTATTCATACAGTACAA
1 TACTATTCACACAGTACAA
196600 TACTATTCA
1 TACTATTCA
196609 TAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (19 bp):
TACTATTCACACAGTACAA
Found at i:196602 original size:19 final size:20
Alignment explanation
Indices: 196561--196610 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
196551 TACTATTCAT
* *
196561 TACTGTTCACACAGTATCAA
1 TACTATTCATACAGTATCAA
196581 TACTATTCATACAGTA-CAA
1 TACTATTCATACAGTATCAA
196600 TACTATTCATA
1 TACTATTCATA
196611 AAAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:196869 original size:18 final size:19
Alignment explanation
Indices: 196822--196870 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
196812 ATGTTTAATG
196822 AAAAAGATACTAATTGTTT
1 AAAAAGATACTAATTGTTT
196841 ACAAAAGGATA-TCAATTG-TT
1 A-AAAA-GATACT-AATTGTTT
196861 AAAAAGATAC
1 AAAAAGATAC
196871 ACCAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.15
19 5 0.19
20 8 0.31
21 9 0.35
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAAAGATACTAATTGTTT
Found at i:199274 original size:44 final size:45
Alignment explanation
Indices: 199154--199279 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
199144 TATAAAATCT
* *
199154 CTTACCATTTATCCCATAAGCTCGTAAGCTTAATTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
199199 CTTACCATTTACATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
199246 CTTACCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
199280 GCAAGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:199431 original size:40 final size:40
Alignment explanation
Indices: 199387--199505 Score: 220
Period size: 40 Copynumber: 3.0 Consensus size: 40
199377 GTAGTGCTAT
199387 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
* *
199427 ACATAAGGTCGTTCCCACCATATACACTGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
199467 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
199506 TAAACCTGCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
Found at i:203322 original size:6 final size:5
Alignment explanation
Indices: 203287--203384 Score: 58
Period size: 6 Copynumber: 18.4 Consensus size: 5
203277 TCTCTCATTT
* *
203287 TTTTC TGTT- TTTTC TTTTC TTTCTC GTTTTC ATTT- TTTTC TTCTTC
1 TTTTC TTTTC TTTTC TTTTC TTT-TC -TTTTC TTTTC TTTTC TT-TTC
* *
203333 TTTTTC ATTTTC ATTTTC TATTTT TTTTC TTCTTC TATT- TTTTC TTCTTC
1 -TTTTC -TTTTC -TTTTC T-TTTC TTTTC TT-TTC TTTTC TTTTC TT-TTC
203383 TT
1 TT
203385 ATAATATATT
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
4 9 0.12
5 26 0.35
6 34 0.46
7 5 0.07
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:203324 original size:27 final size:26
Alignment explanation
Indices: 203294--203349 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
203284 TTTTTTTCTG
*
203294 TTTTTTCTTTTCTTTCTCGTTTTCAT
1 TTTTTTCTTTTCTTTCTCATTTTCAT
*
203320 TTTTTTCTTCTTCTTTTTCATTTTCAT
1 TTTTTTCTT-TTCTTTCTCATTTTCAT
203347 TTT
1 TTT
203350 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTTCTTTTCTTTCTCATTTTCAT
Found at i:203330 original size:20 final size:22
Alignment explanation
Indices: 203301--203343 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
203291 CTGTTTTTTC
203301 TTTTCTTTC-TCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
*
203322 TTTTC-TTCTTCTTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
203343 T
1 T
203344 CATTTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTCTTCGTTTTCATTT
Found at i:203351 original size:21 final size:21
Alignment explanation
Indices: 203296--203351 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
203286 TTTTTCTGTT
203296 TTTTCTTTTCTTTCTCGTTTTCA
1 TTTTCTTTTC-TTCTC-TTTTCA
*
203319 TTTTTTTCTTCTTCT-TTTTCA
1 TTTTCTT-TTCTTCTCTTTTCA
203340 TTTTCATTTTCT
1 TTTTC-TTTTCT
203352 ATTTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 14 0.48
22 2 0.07
23 10 0.34
24 3 0.10
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTCTTTTCTTCTCTTTTCA
Found at i:203373 original size:15 final size:15
Alignment explanation
Indices: 203355--203383 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
203345 ATTTTCTATT
203355 TTTTTTCTTCTTCTA
1 TTTTTTCTTCTTCTA
203370 TTTTTTCTTCTTCT
1 TTTTTTCTTCTTCT
203384 TATAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCTTCTTCTA
Found at i:204489 original size:6 final size:6
Alignment explanation
Indices: 204472--204502 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
204462 ACCCTTGTAT
*
204472 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
204503 TATGGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:206354 original size:44 final size:45
Alignment explanation
Indices: 206234--206359 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
206224 TATAAAATCT
*
206234 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
206279 CTTACCATTTACATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
206326 CTTACCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
206360 GCAAGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:206519 original size:40 final size:40
Alignment explanation
Indices: 206464--206585 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
206454 ACCGTAGTGC
*
206464 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
206504 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
206544 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
206584 TA
1 TA
206586 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:209799 original size:34 final size:34
Alignment explanation
Indices: 209746--209812 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
209736 CCTTTACAAC
*
209746 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTTA
1 TCCCTAGTTTTTCAAGGGCTAAACTAGAACCTTA
* *
209780 TCCCTAGCTTTTT-AAGGGCTCAGCTAGAACCTT
1 TCCCTAG-TTTTTCAAGGGCTAAACTAGAACCTT
209813 TCCTTTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGTTTTTCAAGGGCTAAACTAGAACCTTA
Found at i:210058 original size:20 final size:20
Alignment explanation
Indices: 210033--210075 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
210023 GTCGTATATG
210033 GCCGTTGGGGATGTTTTGGA
1 GCCGTTGGGGATGTTTTGGA
210053 GCCGTTGGGGATGTTTTGGA
1 GCCGTTGGGGATGTTTTGGA
210073 GCC
1 GCC
210076 ATTGAGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.14, G:0.44, T:0.33
Consensus pattern (20 bp):
GCCGTTGGGGATGTTTTGGA
Found at i:210084 original size:20 final size:20
Alignment explanation
Indices: 210041--210084 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
210031 TGGCCGTTGG
* *
210041 GGATGTTTTGGAGCCGTTGG
1 GGATGTTTTGGAGCCATTGA
210061 GGATGTTTTGGAGCCATTGA
1 GGATGTTTTGGAGCCATTGA
210081 GGAT
1 GGAT
210085 TCATTTTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.41, T:0.34
Consensus pattern (20 bp):
GGATGTTTTGGAGCCATTGA
Found at i:210201 original size:20 final size:20
Alignment explanation
Indices: 210176--210223 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
210166 CTTGAAATTA
*
210176 CTGTAGCAGTATCGGTACCC
1 CTGTAGCAGTATCGATACCC
210196 CTGTAGCAGTATCGATACCC
1 CTGTAGCAGTATCGATACCC
210216 CTGTAGCA
1 CTGTAGCA
210224 TTCTAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (20 bp):
CTGTAGCAGTATCGATACCC
Found at i:223260 original size:93 final size:93
Alignment explanation
Indices: 223140--223326 Score: 342
Period size: 93 Copynumber: 2.0 Consensus size: 93
223130 AACCTCACAA
223140 GTCACTCCAAGAAAGTAACACAACGAGAGGCAAGTAAGCCGATCTTGTACTCTTTAAAACTCACT
1 GTCACTCCAAGAAAGTAACACAACGAGAGGCAAGTAAGCCGATCTTGTACTCTTTAAAACTCAC-
223205 TTACCAAGTAGTCTTTCACAGTTCGTATCG
65 TTACCAAGTAGTCTTT-ACAGTTCGTATCG
223235 GTCACTCC-AG-AAGTAACACAACGAGAGGCAAGTAAGCCGATCTTGTACTCTTTAAAACTCACT
1 GTCACTCCAAGAAAGTAACACAACGAGAGGCAAGTAAGCCGATCTTGTACTCTTTAAAACTCACT
223298 TACCAAGTAGTCTTTACAGTTCGTATCG
66 TACCAAGTAGTCTTTACAGTTCGTATCG
223326 G
1 G
223327 AGTTGATTAC
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
91 14 0.15
92 16 0.17
93 52 0.57
94 2 0.02
95 8 0.09
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (93 bp):
GTCACTCCAAGAAAGTAACACAACGAGAGGCAAGTAAGCCGATCTTGTACTCTTTAAAACTCACT
TACCAAGTAGTCTTTACAGTTCGTATCG
Found at i:228731 original size:10 final size:11
Alignment explanation
Indices: 228705--228731 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
228695 AAATTTTGGC
228705 TTTTTTTGTTT
1 TTTTTTTGTTT
228716 TTTTTTTGTTT
1 TTTTTTTGTTT
228727 TTTTT
1 TTTTT
228732 AAAACAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:234643 original size:14 final size:14
Alignment explanation
Indices: 234605--234647 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
234595 TGATCCCTGA
*
234605 TTTCTAATCTATGG
1 TTTCTAATCTCTGG
*
234619 ATTCTAATCTCTGG
1 TTTCTAATCTCTGG
*
234633 TTTTTAATCTCTGG
1 TTTCTAATCTCTGG
234647 T
1 T
234648 ATTTGATACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTCTAATCTCTGG
Found at i:248684 original size:18 final size:18
Alignment explanation
Indices: 248664--248697 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
248654 AATTTTGGCT
248664 TTTTTTTTG-CTTTTTTG
1 TTTTTTTTGCCTTTTTTG
248681 TTTTTTTTGCCTTTTTT
1 TTTTTTTTGCCTTTTTT
248698 TTTGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (18 bp):
TTTTTTTTGCCTTTTTTG
Found at i:252585 original size:14 final size:14
Alignment explanation
Indices: 252566--252600 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
252556 AAACTTGAGG
252566 GATGCATTGTCCTC
1 GATGCATTGTCCTC
252580 GATGCATTGTCCTC
1 GATGCATTGTCCTC
*
252594 AATGCAT
1 GATGCAT
252601 GAGAACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (14 bp):
GATGCATTGTCCTC
Found at i:259043 original size:20 final size:21
Alignment explanation
Indices: 259005--259043 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
258995 CATCAAGGTC
* *
259005 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATAAAATCT
259026 TTTGTCGAAGCCA-AAAAT
1 TTTGTCGAAGCCATAAAAT
259044 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (21 bp):
TTTGTCGAAGCCATAAAATCT
Found at i:273142 original size:17 final size:16
Alignment explanation
Indices: 273101--273142 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
273091 AGATATCCTT
273101 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
273117 -AAAATAATTTTGAAAGA
1 TAAAATAATTTT--AAGA
273134 TAAAA-AATT
1 TAAAATAATT
273143 GACATGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:273841 original size:261 final size:257
Alignment explanation
Indices: 273282--273814 Score: 877
Period size: 261 Copynumber: 2.0 Consensus size: 257
273272 TTGAAAATTT
273282 GAATATACATTTAAATCATGATCCTATTAAAAAAAAATTCGAAGAGGGAAATTATTTCATATGGA
1 GAATATACA-TTAAAT-AT-ATCC-ATT-AAAAAAAATTCGAAGAGGGAAATTATTTCATATGGA
273347 AAATCTTAAAAAATACACTCCTTGTCAGTTAAGACACGTTTTTATGGGTTCTCCATACAAAAGGT
61 AAATCTTAAAAAATACACTCCTTGTCAGTTAAGACACGTTTTTATGGGTTCTCCATACAAAAGGT
273412 CATTACCATGTTTTTTCTTAAATTATGTATTAATATAAAAAGGTAATAAAATAAATAAAGAAATC
126 CATTACCATGTTTTTTCTTAAATTATGTATTAATATAAAAAGGTAATAAAATAAATAAAGAAATC
*
273477 CTTGAGTATATATAAAAAATATTATTGAATGAATAATTCTTGAAAACATATTCATTGTAGTCAAT
191 CTTGAGTATATATAAAAAATATTATTGAATGAATAATTCTTGAAAACATATTCATTGTAGTCAAG
**
273542 TT
256 GA
273544 GAATATACATTTAAATCATGATCCTATTAAAAAAAATTCGAAGAGGGAAATTATTTCATATGGAA
1 GAATATACA-TTAAAT-AT-ATCC-ATTAAAAAAAATTCGAAGAGGGAAATTATTTCATATGGAA
273609 AATCTTAAAAAATACACTCCTTGTCAGTTAAGACACGTTTTTATGGGTTCTCCATACAAAAGGTC
62 AATCTTAAAAAATACACTCCTTGTCAGTTAAGACACGTTTTTATGGGTTCTCCATACAAAAGGTC
273674 ATTACCATGTTTTTTCTTAAATTATGTATTTAATATAAAAAAGGTAAATAAAATAAAATAAAGAA
127 ATTACCATGTTTTTTCTTAAATTATGTA-TTAATAT-AAAAAGGT-AATAAAAT-AAATAAAGAA
273739 ATCCCTTGAGTATATATAAAAAAATATTATTTTGAATGAATAATTCTTGAAAACATATTCATTGT
188 AT-CCTTGAGTATATAT-AAAAAATATTA--TTGAATGAATAATTCTTGAAAACATATTCATTG-
273804 TAGTCAAGGA
248 TAGTCAAGGA
273814 G
1 G
273815 CGTTTACATA
Statistics
Matches: 259, Mismatches: 3, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
261 130 0.50
262 35 0.14
263 8 0.03
264 8 0.03
265 12 0.05
266 14 0.05
267 11 0.04
269 33 0.13
270 8 0.03
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (257 bp):
GAATATACATTAAATATATCCATTAAAAAAAATTCGAAGAGGGAAATTATTTCATATGGAAAATC
TTAAAAAATACACTCCTTGTCAGTTAAGACACGTTTTTATGGGTTCTCCATACAAAAGGTCATTA
CCATGTTTTTTCTTAAATTATGTATTAATATAAAAAGGTAATAAAATAAATAAAGAAATCCTTGA
GTATATATAAAAAATATTATTGAATGAATAATTCTTGAAAACATATTCATTGTAGTCAAGGA
Found at i:274123 original size:4 final size:4
Alignment explanation
Indices: 274116--274155 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
274106 TATCCTATAT
* *
274116 ATAC ATAC ATAC ATAC ATAC ATAC ATAT A-AC ATAC GTAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
274156 ATATGAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 2 0.06
4 29 0.94
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:276430 original size:23 final size:23
Alignment explanation
Indices: 276383--276430 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
276373 AATAACATAT
* **
276383 TAGGTAGCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
276406 TAGGTAGTGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
276429 TA
1 TA
276431 TGTTAATTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:276496 original size:23 final size:23
Alignment explanation
Indices: 276470--276520 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
276460 AATAACATAT
* **
276470 TAGGTAGCATTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
*
276493 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
276516 TAGGT
1 TAGGT
276521 TAATTACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:276507 original size:87 final size:87
Alignment explanation
Indices: 276361--276528 Score: 300
Period size: 87 Copynumber: 1.9 Consensus size: 87
276351 TAATCGGAAT
* * *
276361 ATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCATTTATATAATGTAATAGGTAGCGCTTATATAATA
*
276426 AAATATGTTAATTACTGGAAAC
66 AAATAGGTTAATTACTGGAAAC
276448 ATTATCAAGCACAATAACATATTAGGTAGCATTTATATAATGTAATAGGTAGCGCTTATATAATA
1 ATTATCAAGCACAATAACATATTAGGTAGCATTTATATAATGTAATAGGTAGCGCTTATATAATA
276513 AAATAGGTTAATTACT
66 AAATAGGTTAATTACT
276529 TAATTTGTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (87 bp):
ATTATCAAGCACAATAACATATTAGGTAGCATTTATATAATGTAATAGGTAGCGCTTATATAATA
AAATAGGTTAATTACTGGAAAC
Found at i:279364 original size:199 final size:199
Alignment explanation
Indices: 279023--279975 Score: 1448
Period size: 199 Copynumber: 4.8 Consensus size: 199
279013 AAATATTGAT
* * * * * * * * * *
279023 ACAAATTTTAAAAGTGTCCATACATTAAT-TTGACCTATTTTCTAATTATACTGGTATATTTATG
1 ACAAATTTAAAAAGTGTCGATACATT-ATGTAGACCTATTTTCTCATAAAACCGATATATTTCTA
* * *
279087 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGTGATCGATA
65 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATA
*
279152 CAATTTTAAATGTATCGACACTTTATGGGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTA
130 CAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTA
279217 TCGAC
195 TCGAC
* *
279222 CCAAATTTAAAAATTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATATATTTCTAC
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATATATTTCTAC
* * *
279287 CGATTATATTGTAAATTTACCTATTACATTATAATTATAGGTTTCAATGTTTTTGGGATCGATAC
66 CGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATAC
*
279352 AATTTTAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTAT
131 AATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTAT
279417 CGAC
196 CGAC
* *
279421 ACAAATTTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA-CAAGTATATTTCTA
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGA-TATATTTCTA
* *
279485 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTTGATGATTTTGGGATCGATA
65 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATA
*
279550 CAATTTTAAATGTATCGACACTTTATGCGTGCATCTCGTTGGGCATTCATTCTGGACAAAAAGTA
130 CAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTA
279615 TCGAC
195 TCGAC
* * * *
279620 ACAAATTTATAAAGTGTCAATACATTTTGTAGACCTATTTTTCTCATAAAACCGGTATATTTCTA
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTA-TTTTCTCATAAAACCGATATATTTCTA
** * *
279685 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGATGTTTTTGTGATTGATA
65 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATA
* * *
279750 TAATTTTAAATGTATCGACACTTTATGCGTGCATCTCGTTGGGCATTCATTATGGACAAAAAGTA
130 CAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTA
279815 TCGAC
195 TCGAC
* * *
279820 ACAAATTTAGAAAGTGTCGATACA-TAAGTAGATCTATTTTCTCATAAAACC-AGTATATTTCTA
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGA-TATATTTCTA
*
279883 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
65 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATA
*
279948 CAATTTTAAAAAT-TATCGATACTTTATG
130 CAATTTT--AAATGTATCGACACTTTATG
279976 TTTACCTATT
Statistics
Matches: 692, Mismatches: 55, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
198 96 0.14
199 419 0.61
200 176 0.25
201 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGATATATTTCTAC
CGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGATCGATAC
AATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTAT
CGAC
Found at i:281442 original size:24 final size:24
Alignment explanation
Indices: 281423--281471 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
281413 CGAAATTTAT
281423 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
281447 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
281470 AT
1 AT
281472 AGGAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:281446 original size:18 final size:18
Alignment explanation
Indices: 281423--281459 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
281413 CGAAATTTAT
281423 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
281441 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
281459 A
1 A
281460 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:281478 original size:24 final size:24
Alignment explanation
Indices: 281426--281478 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
281416 AATTTATATT
*
281426 GAAATTCAAACTCAAATTGAAATT
1 GAAATTCAAACTCAAATTGAAATG
* *
281450 TAAATTCAAACTCCAATT-AAATAG
1 GAAATTCAAACTCAAATTGAAAT-G
281474 GAAAT
1 GAAAT
281479 GAACATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (24 bp):
GAAATTCAAACTCAAATTGAAATG
Found at i:284053 original size:15 final size:15
Alignment explanation
Indices: 284012--284057 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
284002 GAAGAAGTGA
*
284012 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
284028 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
284045 TTGGTTGAGAAGA
1 TTGGTTGAGAAGA
284058 ATTTTGAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 6 0.22
18 8 0.30
ACGTcount: A:0.26, C:0.04, G:0.41, T:0.28
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:284733 original size:199 final size:199
Alignment explanation
Indices: 284383--284848 Score: 736
Period size: 199 Copynumber: 2.3 Consensus size: 199
284373 AATTTAGAAA
* * * ** *
284383 GTGTCAATACATTATGTAGACCTATTTTCTCAT-AAACCGGTATATTTATACTAGTTAAATTGTA
1 GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTACATTGTA
*
284447 AATTTACCTATTACATTGTAATTATCGATTTCGAAGTTCTTGGGATCGATACAATTTTAAATGTA
66 AATTTACCTATTACATTGTAATTATCGATTTCGAAGTTCTTGGGAACGATACAATTTTAAATGTA
284512 TCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTCTGGACAAAACGTATCGACACTTTTAAA
131 TCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTCTGGACAAAACGTATCGACACTTTTAAA
284577 ATTT
196 ATTT
284581 GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTACATTGTA
1 GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTACATTGTA
* * * * *
284646 AATTTACCTATTGCATTGTAATTATCGGTTTTGATGTTTTTGGGAACGATACAATTTTAAATGTA
66 AATTTACCTATTACATTGTAATTATCGATTTCGAAGTTCTTGGGAACGATACAATTTTAAATGTA
* * *
284711 TCGACACTTTATGTGTGCACCTAGTTTGGCATTCATTCTGGACAAAACGTATCGACACTTTTTAA
131 TCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTCTGGACAAAACGTATCGACACTTTTAAA
284776 ATTT
196 ATTT
* * * * * *
284780 GTGCCGATACTTTATGTATACCTATTTTCTCATAAAATCGATATATTTCTATCGGGTACATTGTA
1 GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTACATTGTA
284845 AATT
66 AATT
284849 ACCCTCATAA
Statistics
Matches: 246, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
198 31 0.13
199 215 0.87
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (199 bp):
GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGTTACATTGTA
AATTTACCTATTACATTGTAATTATCGATTTCGAAGTTCTTGGGAACGATACAATTTTAAATGTA
TCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTCTGGACAAAACGTATCGACACTTTTAAA
ATTT
Found at i:284871 original size:44 final size:44
Alignment explanation
Indices: 284808--284892 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
284798 TACCTATTTT
* *
284808 CTCATAAAATCGATATATTTCTATCGGGTACATTGTAAATTACC
1 CTCATAAAATCGATATATTTATATCGGGTACACTGTAAATTACC
* *
284852 CTCATAAAATCGGTATATTTATATCGGTTACACTGTAAATT
1 CTCATAAAATCGATATATTTATATCGGGTACACTGTAAATT
284893 TACCTATTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (44 bp):
CTCATAAAATCGATATATTTATATCGGGTACACTGTAAATTACC
Found at i:285085 original size:243 final size:243
Alignment explanation
Indices: 284609--285091 Score: 684
Period size: 243 Copynumber: 2.0 Consensus size: 243
284599 GACCTATTTT
* * * * * *
284609 CTCATAAAACCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTGCATTGTAATTATCGG
1 CTCATAAAACCGGTATATTTATACCGGTTACACTGTAAATTTACCTATTACATTATAATTACCGA
*
284674 TTTTGATGTTTTTGGGAACGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTAGTTTG
66 TTTTGATGTTTTTAGGAACGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTAGTTTG
* * ** ** * *
284739 GCATTCATTCTGGACAAAACGTATCGACACTTTTTAAATTTGTGCCGATACTTTATGTATACCTA
131 GCATTCATTCTGAACAAAAAGTATCGACACAATTTAAATAAGTGCCGATACATTATGTAGACCTA
* * *
284804 TTTTCTCATAAAATCGATATATTTCTATCGGGTACATTGTAAATTACC
196 TTTTCTCATAAAACCGATATATTTATAACGGGTACATTGTAAATTACC
* *
284852 CTCATAAAATCGGTATATTTATATCGGTTACACTGTAAATTTACCTATTACATTATAATTACCGA
1 CTCATAAAACCGGTATATTTATACCGGTTACACTGTAAATTTACCTATTACATTATAATTACCGA
* *
284917 TTTTGATGTTTTTAGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGTGTGCACCTAGTT
66 TTTTGATGTTTTTAGGAACGATACAATTT--TAAATGTATCGACACTTTATGTGTGCACCTAGTT
* * *
284981 TGTCATTCATTCTGAACAAAAAGTATTGACACAAATTTAAA-AAGTGTCGATACATTATGTAGAC
129 TGGCATTCATTCTGAACAAAAAGTATCGACAC-AATTTAAATAAGTGCCGATACATTATGTAGAC
*
285045 CTATTTTCTCAT-AAACCGATATATTTATAACGGTTACATTGTAAATT
193 CTATTTTCTCATAAAACCGATATATTTATAACGGGTACATTGTAAATT
285092 TACCTATTAC
Statistics
Matches: 211, Mismatches: 26, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
242 3 0.01
243 110 0.52
244 92 0.44
245 6 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (243 bp):
CTCATAAAACCGGTATATTTATACCGGTTACACTGTAAATTTACCTATTACATTATAATTACCGA
TTTTGATGTTTTTAGGAACGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTAGTTTG
GCATTCATTCTGAACAAAAAGTATCGACACAATTTAAATAAGTGCCGATACATTATGTAGACCTA
TTTTCTCATAAAACCGATATATTTATAACGGGTACATTGTAAATTACC
Found at i:285263 original size:128 final size:127
Alignment explanation
Indices: 285035--285267 Score: 342
Period size: 128 Copynumber: 1.8 Consensus size: 127
285025 TGTCGATACA
* * *
285035 TTATGTAGACCTATTTTCTCATAAACCGATATATTTATAACGGTTACATTGTAAATTTACCTATT
1 TTATGTAGACCTATTTTCTAATAAACAGATATATTTATAACGGTTACATTATAAATTTACCTATT
* * *
285100 ACATTGTAATTATCGGTTTCGATGTTTTTGTGATCGATACTTTTAATAAATGTATCAACACT
66 ACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAATGTATCAACACT
* * *
285162 TTATGTTGACCTATTTTCTAATTAAATCAG-TATATTTCTACCGGTTACATTATAAATTTACCTA
1 TTATGTAGACCTATTTTCTAA-TAAA-CAGATATATTTATAACGGTTACATTATAAATTTACCTA
**
285226 TTACATTATAATTATCGGTTTTTATGTTGTTGGGATCGATAC
64 TTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATAC
285268 AATTTTAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
127 19 0.20
128 72 0.77
129 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (127 bp):
TTATGTAGACCTATTTTCTAATAAACAGATATATTTATAACGGTTACATTATAAATTTACCTATT
ACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAATGTATCAACACT
Found at i:285306 original size:128 final size:127
Alignment explanation
Indices: 285032--285296 Score: 340
Period size: 128 Copynumber: 2.1 Consensus size: 127
285022 AAGTGTCGAT
* * * *
285032 ACATTATGTAGACCTATTTTCTCA-TAAA-CCGATATATTTATAACGGTTACATTGTAAATTTAC
1 ACATTATGTTGACCTATTTTCTAATTAAATCAG-TATATTTATAACGGTTACATTATAAATTTAC
* * *
285095 CTATTACATTGTAATTATCGGTTTCGATGTTTTTGTGATCGATACTTTTAATAAATGTATCAAC
65 CTATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAA-GTATCAAC
* * *
285159 ACTTTATGTTGACCTATTTTCTAATTAAATCAGTATATTTCTACCGGTTACATTATAAATTTACC
1 ACATTATGTTGACCTATTTTCTAATTAAATCAGTATATTTATAACGGTTACATTATAAATTTACC
** *
285224 TATTACATTATAATTATCGGTTTTTATGTTGTTGGGATCGATACAATTTTAA-AACA-TATCAAT
66 TATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATAC--TTTTAATAA-AGTATCAAC
285287 ACATTATGTT
1 ACATTATGTT
285297 TACTAATTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
127 21 0.18
128 87 0.73
129 4 0.03
130 7 0.06
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (127 bp):
ACATTATGTTGACCTATTTTCTAATTAAATCAGTATATTTATAACGGTTACATTATAAATTTACC
TATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAAGTATCAAC
Found at i:285326 original size:128 final size:126
Alignment explanation
Indices: 285032--285353 Score: 339
Period size: 128 Copynumber: 2.5 Consensus size: 126
285022 AAGTGTCGAT
* * * *
285032 ACATTATGTAGACCTATTTTCTCA-TAAACCGATATATTTATAACGGTTACATTGTAAATTTACC
1 ACATTATGTTGACCTATTTTCTAATTAAACAG-TATATTTATACCGGTTACATTGTAAATTTACC
* * *
285096 TATTACATTGTAATTATCGGTTTCGATGTTTTTGTGATCGATACTTTTAATAAATGTATCAAC
65 TATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAA-GTATCAAC
* * *
285159 ACTTTATGTTGACCTATTTTCTAATTAAATCAGTATATTTCTACCGGTTACATTATAAATTTACC
1 ACATTATGTTGACCTATTTTCTAATTAAA-CAGTATATTTATACCGGTTACATTGTAAATTTACC
** *
285224 TATTACATTATAATTATCGGTTTTTATGTTGTTGGGATCGATACAATTTTAA-AACA-TATCAAT
65 TATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATAC--TTTTAATAA-AGTATCAAC
* * * * * * **
285287 ACATTATGTTTA-CTAATTTTTTCATTTTAAA-AGTGTATTTTTTCCACTTACATTGTAAATTTA
1 ACATTATGTTGACCT-ATTTTCT-A-ATTAAACAGTATATTTATACCGGTTACATTGTAAATTTA
285350 CCTA
63 CCTA
285354 ATACTTTAAA
Statistics
Matches: 164, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
127 23 0.14
128 124 0.76
129 5 0.03
130 12 0.07
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (126 bp):
ACATTATGTTGACCTATTTTCTAATTAAACAGTATATTTATACCGGTTACATTGTAAATTTACCT
ATTACATTATAATTATCGGTTTCGATGTTGTTGGGATCGATACTTTTAATAAAGTATCAAC
Found at i:288127 original size:118 final size:117
Alignment explanation
Indices: 287905--288114 Score: 273
Period size: 118 Copynumber: 1.8 Consensus size: 117
287895 AAGTATCAAC
* * * *
287905 ATGTATAAGAAACATGTACAACAACCTATTTCTAACTTTTTTCATCTCATACATAATTACATTCA
1 ATGTATAAGAAACATGTACAACAACATAGTGCTAACTTTTCTCATCTCATACATAATTACATTCA
* * * * ** *
287970 GATACAACAACCTATTACTGACTTTTCTCATCTCATACATAATTACTCTTACT
66 GATACAACAACCTATAAATGAC-ATACAAATCCCATACATAATTACTCTTACT
288023 ATGTATAAGAAACATGTACAACAACATAGTGCTAACTTTTCTCATCTCATACATAATTACATTCA
1 ATGTATAAGAAACATGTACAACAACATAGTGCTAACTTTTCTCATCTCATACATAATTACATTCA
*
288088 GATACAA-AA-TTATAAATCGA-ATACAAA
66 GATACAACAACCTATAAAT-GACATACAAA
288115 ATTTCCCTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
115 3 0.04
116 5 0.06
117 4 0.05
118 68 0.85
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (117 bp):
ATGTATAAGAAACATGTACAACAACATAGTGCTAACTTTTCTCATCTCATACATAATTACATTCA
GATACAACAACCTATAAATGACATACAAATCCCATACATAATTACTCTTACT
Found at i:292719 original size:182 final size:182
Alignment explanation
Indices: 292407--293432 Score: 1560
Period size: 182 Copynumber: 5.6 Consensus size: 182
292397 TACGTGTACT
*
292407 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTA-CGAGTTTTGTCATTTCGAGACT
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCG-GTTTTGTCATTTCGAGACC
* *
292471 GGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATTGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
* *
292536 TTTATAGGCGCTATTACTGCTTCACTTTTAAATTCCAAAAGCGTCGATACTTA
130 TTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
292589 TGTTAAAGTATCGACACTTTCAACATATCTGGTTGCGCTTTACCGGTTTTATCATTTCGAGACTG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
*
292654 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
292719 TTATAGGCGCTATTACTACTTCTCTTTTAAATTCTAAAAGTGCCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
292771 TATTAAAGTATCGACACTTTCAACATATCCGGTAACGCTTTACTGATTTTGACATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
*
292836 GTTTTGTCATATTTTTATCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
292901 TTATAGGTGCTATTACTGCTTTTCTTTTAAATTCTAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
292953 TATTAAAGTATCGACACTTTCAACATATCCGGTAACGCTTTACTGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* * *
293018 ATTTTGTCATATTTTTATCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGTCACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
293083 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
293135 TATTAAAGCATCTACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
* *
293200 GTTTT-TCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATGGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
293264 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCAATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * ** ** * * *
293316 T-TTCAATGGAATCGTTACTTT-ATACATATTAGGTAGTGCTTTACCGGTTTTGTCATAAT-GAA
1 TATT-AA-AGTATCGACACTTTCA-ACATATCCGGTAGCGCTTTACCGGTTTTGTCAT-TTCGAG
* * *
293378 ACCGG-TTTGATCATATTTTTACCTGTTATACTATTATGGATCGATATATTTTTAT
62 ACCGGTTTTG-TCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
293433 TTGTATCGAT
Statistics
Matches: 781, Mismatches: 56, Indels: 13
0.92 0.07 0.02
Matches are distributed among these distances:
180 2 0.00
181 113 0.14
182 620 0.79
183 46 0.06
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:293681 original size:2 final size:2
Alignment explanation
Indices: 293669--293697 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
293659 GACCTTGTAG
293669 AT AT A- 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
293698 TCACATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:294759 original size:23 final size:24
Alignment explanation
Indices: 294733--294778 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
294723 ATTAATCAAA
294733 ATTAAATATGAAATATAT-TATAC
1 ATTAAATATGAAATATATATATAC
* * *
294756 ATTACATATTATATATATATATA
1 ATTAAATATGAAATATATATATA
294779 TATAGGTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTAAATATGAAATATATATATAC
Found at i:295611 original size:2 final size:2
Alignment explanation
Indices: 295604--295644 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
295594 TTGCATAAAT
295604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
295645 CATTCTCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:297818 original size:23 final size:22
Alignment explanation
Indices: 297792--297835 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
297782 TACATAAATG
297792 GTATAGGGAGTATCGATACCATA
1 GTATA-GGAGTATCGATACCATA
*
297815 GTATAGTAGTATCGATACCAT
1 GTATAGGAGTATCGATACCAT
297836 GGTAGGGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
GTATAGGAGTATCGATACCATA
Found at i:298266 original size:49 final size:49
Alignment explanation
Indices: 298213--298577 Score: 427
Period size: 49 Copynumber: 7.5 Consensus size: 49
298203 CTATAATGCA
* * * *
298213 AGTTAAATGCATAATGGTGCATTTTTGCCAGAAAGGTTCCACTACTG-C
1 AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* * *
298261 AAGTTAAATGCATAATGGTGCATTTTCGGCAGAAAGGTGTCACTAATG-C
1 -AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* *
298310 AAGTTAAATGCATAATGGTGCATTTTTGGCATAAAGGTGCCACTAATG-C
1 -AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* *
298359 AAATTAAATGCATAATGGTGCATTTTT-GCAAGAAAGGTGCCACTAATGAC
1 -AGTTAAATGCATAACGGTGCATTTTTGGC-AGAAAGGTGCCACTAATGAC
* * * * *
298409 AGGTAAATGTATAACGATGCA-TTTTGGCATAAAGGTACCACTAATGAC
1 AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* * * *
298457 AGTTAAATGTATAACAGTGCATTTTTTGTAGAAAGGTGCCACTAATGAC
1 AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* * *
298506 AGTTAAATGCATAGCGGTGCA-TTTTGGCATAAAGGTGCCACTAATGAT
1 AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
* *
298554 AGTTAAATGTATAACGGTGTATTT
1 AGTTAAATGCATAACGGTGCATTT
298578 CGGCATAAAA
Statistics
Matches: 277, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
48 83 0.30
49 193 0.70
50 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (49 bp):
AGTTAAATGCATAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGAC
Found at i:298482 original size:97 final size:97
Alignment explanation
Indices: 298213--298577 Score: 452
Period size: 97 Copynumber: 3.8 Consensus size: 97
298203 CTATAATGCA
* * * * * *
298213 AGTTAAATGCATAATGGTGCATTTTTGCCAGAAAGGTTCCACTACTGCAAGTTAAATGCATAATG
1 AGTTAAATGCATAACGGTGCATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAAATGCATAACG
* *
298278 GTGCATTTTCGGCAGAAAGGTGTCACTAATG-C
66 GTGCATTTT-TGCAGAAAGGTGCCACTAATGAC
* * *
298310 AAGTTAAATGCATAATGGTGCATTTTTGGCATAAAGGTGCCACTAATGCAAATTAAATGCATAAT
1 -AGTTAAATGCATAACGGTGCATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAAATGCATAAC
298375 GGTGCATTTTTGCAAGAAAGGTGCCACTAATGAC
65 GGTGCATTTTTGC-AGAAAGGTGCCACTAATGAC
* * * * *
298409 AGGTAAATGTATAACGATGCA-TTTTGGCATAAAGGTACCACTAATG-ACAGTTAAATGTATAAC
1 AGTTAAATGCATAACGGTGCATTTTTGGCATAAAGGTGCCACTAATGCA-AGTTAAATGCATAAC
* *
298472 AGTGCATTTTTTGTAGAAAGGTGCCACTAATGAC
65 GGTGCA-TTTTTGCAGAAAGGTGCCACTAATGAC
* *
298506 AGTTAAATGCATAGCGGTGCA-TTTTGGCATAAAGGTGCCACTAATG-ATAGTTAAATGTATAAC
1 AGTTAAATGCATAACGGTGCATTTTTGGCATAAAGGTGCCACTAATGCA-AGTTAAATGCATAAC
*
298569 GGTGTATTT
65 GGTGCATTT
298578 CGGCATAAAA
Statistics
Matches: 238, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
96 4 0.02
97 124 0.52
98 109 0.46
99 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (97 bp):
AGTTAAATGCATAACGGTGCATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAAATGCATAACG
GTGCATTTTTGCAGAAAGGTGCCACTAATGAC
Done.