Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 443907
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1193 original size:12 final size:11
Alignment explanation
Indices: 1167--1220 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
1157 TTGTAGATTC
* *
1167 AAAAAAAAAAC
1 AAAAAAAATAG
1178 AAAAAAAATCAG
1 AAAAAAAAT-AG
*
1190 AAAAAAAATTG
1 AAAAAAAATAG
*
1201 AAAAAAAAATTG
1 -AAAAAAAATAG
1213 AAAAAAAA
1 AAAAAAAA
1221 AATTGCATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 17 0.45
12 21 0.55
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (11 bp):
AAAAAAAATAG
Found at i:1203 original size:11 final size:11
Alignment explanation
Indices: 1178--1220 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
1168 AAAAAAAAAC
*
1178 AAAAAAAATCAG
1 AAAAAAAAT-TG
1190 AAAAAAAATTG
1 AAAAAAAATTG
1201 AAAAAAAAATTG
1 -AAAAAAAATTG
1213 AAAAAAAA
1 AAAAAAAA
1221 AATTGCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:1225 original size:13 final size:12
Alignment explanation
Indices: 1190--1221 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1180 AAAAAATCAG
1190 AAAAAAAATTGA
1 AAAAAAAATTGA
1202 AAAAAAAATTGA
1 AAAAAAAATTGA
1214 AAAAAAAA
1 AAAAAAAA
1222 ATTGCATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:3486 original size:17 final size:18
Alignment explanation
Indices: 3447--3488 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3437 AAGAAGAAAA
3447 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
3464 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
3481 TCAAAAGA
1 ACAAAAGA
3489 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:5821 original size:20 final size:20
Alignment explanation
Indices: 5775--5821 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5765 AGCTCGTTTC
*
5775 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
5795 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
5815 CAGCTCA
1 CAGCTCA
5822 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:10270 original size:21 final size:20
Alignment explanation
Indices: 10223--10270 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
10213 AGCTCGTTTC
*
10223 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10243 CAACTCACTTCAAGCTCAATT
1 CAGCTCAC-TCAAGCTCAAGT
10264 CAGCTCA
1 CAGCTCA
10271 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:11788 original size:1 final size:1
Alignment explanation
Indices: 11784--11836 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
11774 AAAAAAATTG
* *** * *
11784 AAAAAAAAAAAAAAAAAAAGAAAAAAAAGTGAGAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11837 GTGAAAAGTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (1 bp):
A
Found at i:11798 original size:33 final size:33
Alignment explanation
Indices: 11750--11837 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 33
11740 TACTATTGTA
* ***
11750 AGAAAAAAAAGAAAAAAATTCGAAAAAAAAAT-
1 AGAAAAAAAAAAAAAAAAAAAGAAAAAAAAATG
* *
11782 TGAAAAAAAAAAAAAAAAAAAGAAAAAAAAGTG
1 AGAAAAAAAAAAAAAAAAAAAGAAAAAAAAATG
11815 AGAAAAAAAAAAGAAAAAAAAAG
1 AGAAAAAAAAAA-AAAAAAAAAG
11838 TGAAAAGTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 26 0.55
33 11 0.23
34 10 0.21
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.06
Consensus pattern (33 bp):
AGAAAAAAAAAAAAAAAAAAAGAAAAAAAAATG
Found at i:11829 original size:11 final size:11
Alignment explanation
Indices: 11752--11836 Score: 84
Period size: 11 Copynumber: 7.6 Consensus size: 11
11742 CTATTGTAAG
11752 AAAAAAAAGAA
1 AAAAAAAAGAA
***
11763 AAAAATTCGAA
1 AAAAAAAAGAA
*
11774 AAAAAAATTG-A
1 AAAAAAA-AGAA
11785 AAAAAAAA-AA
1 AAAAAAAAGAA
11795 AAAAAAAAGAA
1 AAAAAAAAGAA
*
11806 AAAAAAGTGAGAA
1 AAAAAA--AAGAA
11819 AAAAAAAAGAA
1 AAAAAAAAGAA
11830 AAAAAAA
1 AAAAAAA
11837 GTGAAAAGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
10 9 0.15
11 40 0.67
12 1 0.02
13 10 0.17
ACGTcount: A:0.84, C:0.01, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:11837 original size:25 final size:24
Alignment explanation
Indices: 11752--11840 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 24
11742 CTATTGTAAG
*
11752 AAAAAAAAG-AAAAAAATTCGA-AA
1 AAAAAAAAGAAAAAAAAGT-GAGAA
**
11775 AAAAAATTGAAAAAAAA---A-AA
1 AAAAAAAAGAAAAAAAAGTGAGAA
11795 AAAAAAAAGAAAAAAAAGTGAGAA
1 AAAAAAAAGAAAAAAAAGTGAGAA
11819 AAAAAAAAGAAAAAAAAAGTGA
1 AAAAAAAAG-AAAAAAAAGTGA
11841 AAAGTCTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
20 18 0.32
23 8 0.14
24 18 0.32
25 12 0.21
ACGTcount: A:0.81, C:0.01, G:0.11, T:0.07
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAGTGAGAA
Found at i:11843 original size:10 final size:10
Alignment explanation
Indices: 11752--11837 Score: 82
Period size: 10 Copynumber: 7.9 Consensus size: 10
11742 CTATTGTAAG
11752 AAAAAAAAGA
1 AAAAAAAAGA
**
11762 AAAAAATTCGA
1 AAAAAA-AAGA
11773 AAAAAAAATTGA
1 AAAAAAAA--GA
*
11785 AAAAAAAAAA
1 AAAAAAAAGA
11795 AAAAAAAAGA
1 AAAAAAAAGA
11805 AAAAAAAGTGAGAA
1 AAAAAAA---AG-A
11819 AAAAAAAAGA
1 AAAAAAAAGA
11829 AAAAAAAAG
1 AAAAAAAAG
11838 TGAAAAGTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
10 33 0.52
11 10 0.16
12 10 0.16
13 2 0.03
14 8 0.13
ACGTcount: A:0.83, C:0.01, G:0.10, T:0.06
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:11843 original size:11 final size:11
Alignment explanation
Indices: 11752--11843 Score: 75
Period size: 12 Copynumber: 8.3 Consensus size: 11
11742 CTATTGTAAG
11752 AAAAAAAA-G-
1 AAAAAAAATGA
*
11761 AAAAAAATTCGA
1 AAAAAAAAT-GA
11773 AAAAAAAATTGA
1 AAAAAAAA-TGA
11785 AAAAAAAA--A
1 AAAAAAAATGA
*
11794 AAAAAAAAAGA
1 AAAAAAAATGA
*
11805 AAAAAAAGTGAGA
1 AAAAAAAAT--GA
*
11818 AAAAAAAAAGA
1 AAAAAAAATGA
11829 AAAAAAAAGTGA
1 AAAAAAAA-TGA
11841 AAA
1 AAA
11844 GTCTTGTGAG
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
9 16 0.24
11 19 0.28
12 22 0.33
13 10 0.15
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:14625 original size:20 final size:20
Alignment explanation
Indices: 14579--14625 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14569 AGCTCGTTTC
*
14579 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
14599 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14619 CAGCTCA
1 CAGCTCA
14626 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25104 original size:12 final size:12
Alignment explanation
Indices: 25081--25127 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
25071 AGAGAAGAGG
25081 AAATTCGAAAAAA
1 AAATT-GAAAAAA
25094 AAATTG-AAAAA
1 AAATTGAAAAAA
*
25105 AAA-TCAAAAAA
1 AAATTGAAAAAA
25116 AAATT-AAAAAA
1 AAATTGAAAAAA
25127 A
1 A
25128 TCGAAGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 1 0.03
11 23 0.74
12 2 0.06
13 5 0.16
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (12 bp):
AAATTGAAAAAA
Found at i:25105 original size:11 final size:11
Alignment explanation
Indices: 25049--25127 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
25039 AGCATATTGT
25049 AATTGAAAAAA
1 AATTGAAAAAA
*
25060 AA-TCAAAAAA
1 AATTGAAAAAA
** **
25070 AAGAGAAGAGGA
1 AATTGAA-AAAA
25082 AATTCGAAAAAAA
1 AATT-G-AAAAAA
25095 AATTGAAAAAA
1 AATTGAAAAAA
**
25106 AATCAAAAAAA
1 AATTGAAAAAA
25117 AATT-AAAAAA
1 AATTGAAAAAA
25127 A
1 A
25128 TCGAAGTATA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
10 16 0.31
11 22 0.42
12 5 0.10
13 7 0.13
14 2 0.04
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.13
Consensus pattern (11 bp):
AATTGAAAAAA
Found at i:30800 original size:21 final size:23
Alignment explanation
Indices: 30755--30801 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
30745 TCACCTGCAA
* *
30755 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
30778 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
30799 TAA
1 TAA
30802 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:33344 original size:9 final size:10
Alignment explanation
Indices: 33326--33365 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
33316 TAGTAGTTTC
33326 TTCAAAAAAA
1 TTCAAAAAAA
33336 TTCAAAAAAA
1 TTCAAAAAAA
*
33346 ATCAAAAAAA
1 TTCAAAAAAA
33356 TTCAAAAAAA
1 TTCAAAAAAA
33366 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:33345 original size:11 final size:11
Alignment explanation
Indices: 33329--33366 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
33319 TAGTTTCTTC
33329 AAAAAAATTCA
1 AAAAAAATTCA
33340 AAAAAAA-TC-
1 AAAAAAATTCA
33349 AAAAAAATTCA
1 AAAAAAATTCA
33360 AAAAAAA
1 AAAAAAA
33367 AAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.28
10 4 0.16
11 14 0.56
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:33352 original size:20 final size:20
Alignment explanation
Indices: 33327--33376 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
33317 AGTAGTTTCT
33327 TCAAAAAAATTCAAAAAAAA
1 TCAAAAAAATTCAAAAAAAA
33347 TCAAAAAAATTCAAAAAAAA
1 TCAAAAAAATTCAAAAAAAA
*
33367 -AAAAAAAATT
1 TCAAAAAAATT
33377 TGGTTTCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (20 bp):
TCAAAAAAATTCAAAAAAAA
Found at i:33434 original size:15 final size:16
Alignment explanation
Indices: 33414--33453 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
33404 GATATCAAGT
33414 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
33429 TGAAAAAAAAATTTCG
1 TGAAAAAAAAATTTCG
33445 TGAAAAAAA
1 TGAAAAAAA
33454 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:39843 original size:11 final size:11
Alignment explanation
Indices: 39827--39871 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
39817 TAGTAGTTTC
39827 TTCAAAAAAAA
1 TTCAAAAAAAA
39838 TTCAAAAAAAAA
1 TTC-AAAAAAAA
39850 TTCAAAAAAAA
1 TTCAAAAAAAA
39861 TTCAAAAAAAA
1 TTCAAAAAAAA
39872 AAACTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:39847 original size:12 final size:12
Alignment explanation
Indices: 39830--39872 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
39820 TAGTTTCTTC
39830 AAAAAAAATTCA
1 AAAAAAAATTCA
39842 AAAAAAAATTC-
1 AAAAAAAATTCA
39853 AAAAAAAATTCA
1 AAAAAAAATTCA
39865 AAAAAAAA
1 AAAAAAAA
39873 AACTGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:39857 original size:23 final size:23
Alignment explanation
Indices: 39827--39872 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39817 TAGTAGTTTC
39827 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
39850 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
39873 AACTGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (23 bp):
TTCAAAAAAAATTCAAAAAAAAA
Found at i:39935 original size:17 final size:17
Alignment explanation
Indices: 39913--39971 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
39903 GATGTCAAGT
39913 TGAAAAAAAAAATTTCG
1 TGAAAAAAAAAATTTCG
39930 TGAAAAAAAAAA-TTCG
1 TGAAAAAAAAAATTTCG
**
39946 TGAAAAAAAATTTTTCG
1 TGAAAAAAAAAATTTCG
39963 TGAAAAAAA
1 TGAAAAAAA
39972 GAAGAAGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.36
17 25 0.64
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (17 bp):
TGAAAAAAAAAATTTCG
Found at i:39937 original size:16 final size:16
Alignment explanation
Indices: 39916--39971 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
39906 GTCAAGTTGA
39916 AAAAAAAAATTTCGTG
1 AAAAAAAAATTTCGTG
*
39932 AAAAAAAAAATTCGTG
1 AAAAAAAAATTTCGTG
*
39948 AAAAAAAATTTTTCGTG
1 AAAAAAAA-ATTTCGTG
39965 AAAAAAA
1 AAAAAAA
39972 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 23 0.64
17 13 0.36
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.23
Consensus pattern (16 bp):
AAAAAAAAATTTCGTG
Found at i:41864 original size:27 final size:27
Alignment explanation
Indices: 41834--42011 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41824 ATATTGAGTC
* * * *
41834 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41861 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41888 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41916 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41943 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41970 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41997 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42012 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41973 original size:82 final size:81
Alignment explanation
Indices: 41855--42010 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41845 TGCTATATAA
* *
41855 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41920 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41937 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42001 CACTTAGTGC
65 CACTTAGTGC
42011 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:48644 original size:17 final size:15
Alignment explanation
Indices: 48607--48645 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
48597 TATCTCCCAC
48607 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
48623 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
48640 TCATTT
1 TCATTT
48646 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:49661 original size:11 final size:12
Alignment explanation
Indices: 49642--49675 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
49632 AATGAATACA
49642 AATTTTTTTTTG
1 AATTTTTTTTTG
49654 AATTTTTTTTTG
1 AATTTTTTTTTG
49666 AATTTTTTTT
1 AATTTTTTTT
49676 CCTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:50834 original size:56 final size:55
Alignment explanation
Indices: 50718--50835 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
50708 TACATGCTTT
* * * *
50718 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
50772 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
50828 CATTAAAT
1 CATTAAAT
50836 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:51484 original size:20 final size:20
Alignment explanation
Indices: 51459--51513 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
51449 ACGAGTTAAA
* *
51459 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
51479 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
51499 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
51514 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:62539 original size:14 final size:15
Alignment explanation
Indices: 62520--62551 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
62510 TATTGATGCA
62520 TAAATTATG-TTCTT
1 TAAATTATGCTTCTT
62534 TAAATTATGCTTCTT
1 TAAATTATGCTTCTT
62549 TAA
1 TAA
62552 TTAAACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
TAAATTATGCTTCTT
Found at i:66854 original size:13 final size:13
Alignment explanation
Indices: 66838--66872 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
66828 TTTAAACAAA
*
66838 TTAATTAACTTAT
1 TTAATTAACTAAT
66851 TTAATTAACTAAT
1 TTAATTAACTAAT
*
66864 TTAACTAAC
1 TTAATTAAC
66873 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:71083 original size:20 final size:20
Alignment explanation
Indices: 71058--71112 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
71048 ACGAGTTAAA
* *
71058 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
71078 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
71098 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
71113 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:73161 original size:26 final size:26
Alignment explanation
Indices: 73125--73192 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
73115 GACATCATTT
73125 AAGACATCATTAAATTCGGTTGTAGC
1 AAGACATCATTAAATTCGGTTGTAGC
*
73151 AAGACATCATTAAATTTGGTTGTAGC
1 AAGACATCATTAAATTCGGTTGTAGC
*
73177 AAGAC-TAATTAAATTC
1 AAGACATCATTAAATTC
73193 ATCCAGACAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 9 0.23
26 30 0.77
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (26 bp):
AAGACATCATTAAATTCGGTTGTAGC
Found at i:73342 original size:13 final size:13
Alignment explanation
Indices: 73326--73360 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
73316 TTTAAACAAA
*
73326 TTAATTAACTTAT
1 TTAATTAACTAAT
73339 TTAATTAACTAAT
1 TTAATTAACTAAT
*
73352 TTAACTAAC
1 TTAATTAAC
73361 AGTAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:76222 original size:10 final size:10
Alignment explanation
Indices: 76207--76268 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
76197 TTTGAACCAT
*
76207 TACCAATTCG
1 TACCAATTCA
*
76217 TACCAAATACCA
1 TACC-AAT-TCA
*
76229 TACCATTTCA
1 TACCAATTCA
76239 TACCAATTCCA
1 TACCAATT-CA
* *
76250 TACCATTTCG
1 TACCAATTCA
76260 TACCAATTC
1 TACCAATTC
76269 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:76252 original size:21 final size:21
Alignment explanation
Indices: 76207--76269 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
76197 TTTGAACCAT
* *
76207 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
76229 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
76250 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
76270 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:78746 original size:20 final size:20
Alignment explanation
Indices: 78723--78776 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
78713 AGTTTTTCCC
*
78723 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
78743 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
78763 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
78777 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:78758 original size:30 final size:30
Alignment explanation
Indices: 78723--78796 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
78713 AGTTTTTCCC
78723 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
78753 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
78783 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
78797 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:78786 original size:20 final size:20
Alignment explanation
Indices: 78723--78787 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
78713 AGTTTTTCCC
* * * *
78723 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
78743 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
78762 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
78783 AGCTC
1 AGCTC
78788 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:80037 original size:257 final size:257
Alignment explanation
Indices: 79581--80098 Score: 1018
Period size: 257 Copynumber: 2.0 Consensus size: 257
79571 ACATGATTAT
79581 TCAACCATGCATGAACTTACACTATCCATGAACAGAGATTTAATGCTTGAAGTGTGAACATTTTT
1 TCAACCATGCATGAACTTACACTATCCATGAACAGAGATTTAATGCTTGAAGTGTGAACATTTTT
*
79646 AATTGTTGTGTGAACACATTAGTAGCTGAATTTTAATAGGCATTAGAGAGCCTATAAATAGTTTA
66 AATTGTTGTGTGAACACATTAGTAGCTAAATTTTAATAGGCATTAGAGAGCCTATAAATAGTTTA
79711 TTTTGTTTATTGTAAAAGGTTACAGAATTTGATCAATTAAACTTAATAGAACTTTTGTTCTTGTG
131 TTTTGTTTATTGTAAAAGGTTACAGAATTTGATCAATTAAACTTAATAGAACTTTTGTTCTTGTG
79776 AGGTTACCTCCTCTCTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTG
196 AGGTTACCTCCTCTCTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTG
79838 TCAACCATGCATGAACTTACACTATCCATGAACAGAGATTTAATGCTTGAAGTGTGAACATTTTT
1 TCAACCATGCATGAACTTACACTATCCATGAACAGAGATTTAATGCTTGAAGTGTGAACATTTTT
79903 AATTGTTGTGTGAACACATTAGTAGCTAAATTTTAATAGGCATTAGAGAGCCTATAAATAGTTTA
66 AATTGTTGTGTGAACACATTAGTAGCTAAATTTTAATAGGCATTAGAGAGCCTATAAATAGTTTA
79968 TTTTGTTTATTGTAAAAGGTTACAGAATTTGATCAATTAAACTTAATAGAACTTTTGTTCTTGTG
131 TTTTGTTTATTGTAAAAGGTTACAGAATTTGATCAATTAAACTTAATAGAACTTTTGTTCTTGTG
*
80033 AGGTTGCCTCCTCTCTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTG
196 AGGTTACCTCCTCTCTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTG
80095 TCAA
1 TCAA
80099 TCCGAACTCC
Statistics
Matches: 259, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
257 259 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (257 bp):
TCAACCATGCATGAACTTACACTATCCATGAACAGAGATTTAATGCTTGAAGTGTGAACATTTTT
AATTGTTGTGTGAACACATTAGTAGCTAAATTTTAATAGGCATTAGAGAGCCTATAAATAGTTTA
TTTTGTTTATTGTAAAAGGTTACAGAATTTGATCAATTAAACTTAATAGAACTTTTGTTCTTGTG
AGGTTACCTCCTCTCTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTG
Found at i:85453 original size:18 final size:18
Alignment explanation
Indices: 85432--85466 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
85422 AGAAAAGAAA
85432 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
85450 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
85467 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:88933 original size:20 final size:20
Alignment explanation
Indices: 88887--88933 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
88877 AGCTCGTTTC
*
88887 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
88907 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
88927 CAGCTCA
1 CAGCTCA
88934 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:96953 original size:10 final size:10
Alignment explanation
Indices: 96938--96964 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
96928 ATTTATTAAC
96938 AAACACATTT
1 AAACACATTT
96948 AAACACATTT
1 AAACACATTT
96958 AAACACA
1 AAACACA
96965 CTAAACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (10 bp):
AAACACATTT
Found at i:102282 original size:12 final size:12
Alignment explanation
Indices: 102258--102299 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
102248 TAGTTTCTCG
*
102258 AAAAAACTCAAA
1 AAAAAATTCAAA
*
102270 AAAGAATTCAAA
1 AAAAAATTCAAA
102282 AAAAAATTCAAA
1 AAAAAATTCAAA
102294 AAAAAA
1 AAAAAA
102300 CTAGTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:102356 original size:11 final size:12
Alignment explanation
Indices: 102340--102384 Score: 74
Period size: 13 Copynumber: 3.8 Consensus size: 12
102330 TATCAAGTTG
102340 TGAAAAAAAA-T
1 TGAAAAAAAATT
102351 TGAAAAAAAATT
1 TGAAAAAAAATT
102363 GTGAAAAAAAATT
1 -TGAAAAAAAATT
102376 TGAAAAAAA
1 TGAAAAAAA
102385 GAGCTAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.31
12 10 0.31
13 12 0.38
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:102360 original size:13 final size:12
Alignment explanation
Indices: 102342--102384 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
102332 TCAAGTTGTG
102342 AAAAAAAATTGA
1 AAAAAAAATTGA
*
102354 AAAAAAATTGTGA
1 AAAAAAAAT-TGA
*
102367 AAAAAAATTTGA
1 AAAAAAAATTGA
102379 AAAAAA
1 AAAAAA
102385 GAGCTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:102364 original size:24 final size:25
Alignment explanation
Indices: 102337--102384 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
102327 GGATATCAAG
102337 TTGTGAAAAAAAA-TTGAAAAAAAA
1 TTGTGAAAAAAAATTTGAAAAAAAA
102361 TTGTGAAAAAAAATTTGAAAAAAA
1 TTGTGAAAAAAAATTTGAAAAAAA
102385 GAGCTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (25 bp):
TTGTGAAAAAAAATTTGAAAAAAAA
Found at i:111501 original size:23 final size:23
Alignment explanation
Indices: 111443--111503 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
111433 TGTGTTATGA
111443 TTAAT-AAGTG-TTTTAATGTGT
1 TTAATAAAGTGATTTTAATGTGT
* *
111464 TTAATAAACTCATTTTAATGTGT
1 TTAATAAAGTGATTTTAATGTGT
* **
111487 TTATTGCAGTGATTTTA
1 TTAATAAAGTGATTTTA
111504 GCTTATAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 5 0.16
22 3 0.10
23 23 0.74
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.51
Consensus pattern (23 bp):
TTAATAAAGTGATTTTAATGTGT
Found at i:112475 original size:12 final size:12
Alignment explanation
Indices: 112458--112503 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
112448 TAGTAGTTTC
112458 TTCAAAAAAAAA
1 TTCAAAAAAAAA
112470 TTCAAAAAAAAA
1 TTCAAAAAAAAA
112482 -TCAAAAAAAAA
1 TTCAAAAAAAAA
112493 TTCAAAAAAAA
1 TTCAAAAAAAA
112504 TTTGGTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.33
12 22 0.67
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:112478 original size:11 final size:11
Alignment explanation
Indices: 112462--112505 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
112452 AGTTTCTTCA
112462 AAAAAAAATTC
1 AAAAAAAATTC
*
112473 AAAAAAAAATC
1 AAAAAAAATTC
112484 AAAAAAAAATTC
1 -AAAAAAAATTC
112496 AAAAAAAATT
1 AAAAAAAATT
112506 TGGTTTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:112489 original size:23 final size:23
Alignment explanation
Indices: 112459--112503 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
112449 AGTAGTTTCT
112459 TCAAAAAAAAATTCAAAAAAAAA
1 TCAAAAAAAAATTCAAAAAAAAA
112482 TCAAAAAAAAATTCAAAAAAAA
1 TCAAAAAAAAATTCAAAAAAAA
112504 TTTGGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (23 bp):
TCAAAAAAAAATTCAAAAAAAAA
Found at i:112564 original size:15 final size:15
Alignment explanation
Indices: 112544--112595 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
112534 TATCAAGTTG
112544 AAAAAAATTTCGTGAA
1 AAAAAAATTTCGTG-A
**
112560 AAAAAAAAAT-GTGA
1 AAAAAAATTTCGTGA
112574 AAAAAAATTTTCGTGA
1 AAAAAAA-TTTCGTGA
112590 AAAAAA
1 AAAAAA
112596 GAAGAAGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
16 18 0.60
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.21
Consensus pattern (15 bp):
AAAAAAATTTCGTGA
Found at i:126284 original size:13 final size:14
Alignment explanation
Indices: 126237--126287 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
126227 TCGAAAAAAG
126237 GAAAAAAAAGAAGT
1 GAAAAAAAAGAAGT
126251 GACAAAAAAATCG-AGT
1 GA-AAAAAAA--GAAGT
*
126267 TAAAAAAAAGAAG-
1 GAAAAAAAAGAAGT
126280 GAAAAAAA
1 GAAAAAAA
126288 GTGAAAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.26
14 4 0.13
15 14 0.45
16 4 0.13
17 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAGAAGT
Found at i:127183 original size:18 final size:18
Alignment explanation
Indices: 127162--127196 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
127152 AGAAAAGAAA
127162 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
127180 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
127197 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:138526 original size:21 final size:20
Alignment explanation
Indices: 138469--138530 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
138459 TTTGAACCAT
* *
138469 TACCAATTCGTATCAAATACCA
1 TACC-ATTCGTA-CCAATTCCA
*
138491 TACCATTCATACCAATTCCA
1 TACCATTCGTACCAATTCCA
138511 TACCATTTCGTACCAATTCC
1 TACCA-TTCGTACCAATTCC
138531 CAAATACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.34
21 19 0.54
22 4 0.11
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (20 bp):
TACCATTCGTACCAATTCCA
Found at i:138865 original size:18 final size:18
Alignment explanation
Indices: 138844--138885 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
138834 AAGGAGTTCG
*
138844 AAAAAAAATCAAAATAAA
1 AAAAAAAATCAAAAGAAA
*
138862 AAAAAAAATGAAAAGAAA
1 AAAAAAAATCAAAAGAAA
138880 AAAAAA
1 AAAAAA
138886 TTGCATACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.86, C:0.02, G:0.05, T:0.07
Consensus pattern (18 bp):
AAAAAAAATCAAAAGAAA
Found at i:139964 original size:21 final size:21
Alignment explanation
Indices: 139938--140000 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
139928 TTGGTATTTG
139938 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
139959 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
139980 GGTATTTGATACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
140001 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:139969 original size:11 final size:11
Alignment explanation
Indices: 139949--139981 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
139939 GAATTGGTAC
139949 GAAATGGTATG
1 GAAATGGTATG
*
139960 GAATTGGTAT-
1 GAAATGGTATG
139970 GAAATGGTATG
1 GAAATGGTATG
139981 G
1 G
139982 TATTTGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:141692 original size:15 final size:15
Alignment explanation
Indices: 141674--141708 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
141664 TTCTTTTCAA
141674 TTTTTT-TTTTGATT
1 TTTTTTATTTTGATT
141688 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
141703 TTTTTT
1 TTTTTT
141709 CGAACTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.86
Consensus pattern (15 bp):
TTTTTTATTTTGATT
Found at i:142048 original size:21 final size:21
Alignment explanation
Indices: 142022--142084 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
142012 TTGGTATTTA
142022 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
142043 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
142064 GGTATTTGATACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
142085 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:142053 original size:11 final size:11
Alignment explanation
Indices: 142033--142065 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
142023 GAATTGGTAC
142033 GAAATGGTATG
1 GAAATGGTATG
*
142044 GAATTGGTAT-
1 GAAATGGTATG
142054 GAAATGGTATG
1 GAAATGGTATG
142065 G
1 G
142066 TATTTGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:143179 original size:10 final size:10
Alignment explanation
Indices: 143164--143205 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
143154 TTTGCAAGTT
143164 TTGAGCTAAA
1 TTGAGCTAAA
* *
143174 TTGAGCTGAT
1 TTGAGCTAAA
*
143184 TTGAGCT-CA
1 TTGAGCTAAA
143193 TTGAGCTAAA
1 TTGAGCTAAA
143203 TTG
1 TTG
143206 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:145123 original size:23 final size:22
Alignment explanation
Indices: 145088--145150 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
145078 ACTCTCTCAC
*
145088 TTTTTCCTTTCTTTTT-ATCATT
1 TTTTTCTTTTCTTTTTAATC-TT
145110 TTTTTCTTTCTCTTTTTCAATCTT
1 TTTTTCTTT-TCTTTTT-AATCTT
*
145134 TTTTTCTTGTACTTTTT
1 TTTTTCTT-TTCTTTTT
145151 CTTTCTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.23
23 7 0.20
24 16 0.46
25 4 0.11
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTCTTTTCTTTTTAATCTT
Found at i:145135 original size:21 final size:21
Alignment explanation
Indices: 145089--145141 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
145079 CTCTCTCACT
* *
145089 TTTTCCTTTCTTTTTATCATTT
1 TTTT-CTTTCTTTTTATCAATC
145111 TTTTCTTTCTCTTTT-TCAATC
1 TTTTCTTTCT-TTTTATCAATC
145132 TTTT-TTTCTT
1 TTTTCTTTCTT
145142 GTACTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 5 0.18
21 14 0.50
22 8 0.29
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTTTCTTTTTATCAATC
Found at i:147351 original size:20 final size:20
Alignment explanation
Indices: 147318--147376 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
147308 TGCTCCACTC
* *
147318 AGCTCAAATCAGCTCACTTG
1 AGCTCAATTTAGCTCACTTG
* * **
147338 AGCTTATTTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACTTG
*
147358 AGCTCAATTTAGCTTACTT
1 AGCTCAATTTAGCTCACTT
147377 TCAGCCCGTC
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:149567 original size:22 final size:22
Alignment explanation
Indices: 149536--149600 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
149526 ACCTTTTTGA
*
149536 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
149559 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
149581 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
149601 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:150688 original size:27 final size:27
Alignment explanation
Indices: 150650--150701 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
150640 TGTTTGTAGG
*
150650 TACATGCATGGACAACATTGAAGATAA
1 TACATGCATGGACAACAATGAAGATAA
150677 TACATGCATGGACAACAATGAAGAT
1 TACATGCATGGACAACAATGAAGAT
150702 GCTTCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAACAATGAAGATAA
Found at i:154265 original size:23 final size:22
Alignment explanation
Indices: 154228--154282 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
154218 GCTGAATTCA
*
154228 TGAACCATCTTTAATGTTTTAGTG
1 TGAACCATCTTTAAT-TGTT-GTG
*
154252 TGAACCCT-TTTAATTGTTGTG
1 TGAACCATCTTTAATTGTTGTG
154273 TGAACACATC
1 TGAAC-CATC
154283 AGTAGCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (22 bp):
TGAACCATCTTTAATTGTTGTG
Found at i:155030 original size:22 final size:22
Alignment explanation
Indices: 155005--155046 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
154995 GTGGAAAAGT
*
155005 AAAAAAAAATCGAAAAAAATAA
1 AAAAAAAAATCAAAAAAAATAA
* *
155027 AAAAAAGATTCAAAAAAAAT
1 AAAAAAAAATCAAAAAAAAT
155047 CAAAGTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAAAAAATCAAAAAAAATAA
Found at i:155041 original size:21 final size:20
Alignment explanation
Indices: 154999--155046 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
154989 AAAAAAGTGG
*
154999 AAAAGTAAAAAAAAATCGAA
1 AAAAATAAAAAAAAATCGAA
*
155019 AAAAATAAAAAAAAGATTCAAA
1 AAAAATAAAAAAAA-A-TCGAA
155041 AAAAAT
1 AAAAAT
155047 CAAAGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 1 0.04
22 10 0.42
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (20 bp):
AAAAATAAAAAAAAATCGAA
Found at i:155049 original size:10 final size:10
Alignment explanation
Indices: 155006--155050 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
154996 TGGAAAAGTA
155006 AAAAAAAATC
1 AAAAAAAATC
* *
155016 GAAAAAAATA
1 AAAAAAAATC
155026 AAAAAAAGATTC
1 AAAAAAA-A-TC
155038 AAAAAAAATC
1 AAAAAAAATC
155048 AAA
1 AAA
155051 GTATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:155961 original size:12 final size:12
Alignment explanation
Indices: 155944--156034 Score: 62
Period size: 12 Copynumber: 7.4 Consensus size: 12
155934 AGTGCGAGCG
155944 AGAAAATGAAAA
1 AGAAAATGAAAA
* *
155956 AGAAAAAGAAAT
1 AGAAAATGAAAA
* *
155968 TGCAAA-GAAAA
1 AGAAAATGAAAA
155979 AG-AAATCGAAAA
1 AGAAAAT-GAAAA
* *
155991 AGTGAGA-GAAAA
1 AG-AAAATGAAAA
156003 AGAAAATGAAGAAA
1 AGAAAATG-A-AAA
156017 AGAAAATTGAAAA
1 AGAAAA-TGAAAA
156030 AGAAA
1 AGAAA
156035 TTGAGATTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
10 3 0.05
11 7 0.11
12 29 0.47
13 9 0.15
14 12 0.19
15 2 0.03
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (12 bp):
AGAAAATGAAAA
Found at i:156043 original size:18 final size:18
Alignment explanation
Indices: 156022--156056 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
156012 AGAAAAGAAA
156022 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
156040 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
156057 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:156065 original size:16 final size:18
Alignment explanation
Indices: 156044--156082 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
156034 ATTGAGATTG
156044 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
156060 AGAAAAAGATGTTGAAAA
1 AGAAAAAGATATTGAAAA
156078 AGAAA
1 AGAAA
156083 CGAGAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:157922 original size:217 final size:217
Alignment explanation
Indices: 157547--157980 Score: 859
Period size: 217 Copynumber: 2.0 Consensus size: 217
157537 AGCAACTATG
157547 CACATTCCATCGACCAAAGGGCTGGTGACGATGTAAAATTTCTTTTCGAGCAAGTGGCCTGATTT
1 CACATTCCATCGACCAAAGGGCTGGTGACGATGTAAAATTTCTTTTCGAGCAAGTGGCCTGATTT
157612 GGGGACATATCGCTCCAAAGAGGGAGGGAATGATACGATCCCGCTTGAGAACACCCTTGGATCAG
66 GGGGACATATCGCTCCAAAGAGGGAGGGAATGATACGATCCCGCTTGAGAACACCCTTGGATCAG
157677 CTTCCCAAGCGAGGCTTATCATCTTTTGCAAGCTTACCTAGCTCAAATTTAGCTCGTTGAGCTTA
131 CTTCCCAAGCGAGGCTTATCATCTTTTGCAAGCTTACCTAGCTCAAATTTAGCTCGTTGAGCTTA
157742 AATAAGCTCGATTCTAGCTCAA
196 AATAAGCTCGATTCTAGCTCAA
*
157764 CACATTCCATTGACCAAAGGGCTGGTGACGATGTAAAATTTCTTTTCGAGCAAGTGGCCTGATTT
1 CACATTCCATCGACCAAAGGGCTGGTGACGATGTAAAATTTCTTTTCGAGCAAGTGGCCTGATTT
157829 GGGGACATATCGCTCCAAAGAGGGAGGGAATGATACGATCCCGCTTGAGAACACCCTTGGATCAG
66 GGGGACATATCGCTCCAAAGAGGGAGGGAATGATACGATCCCGCTTGAGAACACCCTTGGATCAG
157894 CTTCCCAAGCGAGGCTTATCATCTTTTGCAAGCTTACCTAGCTCAAATTTAGCTCGTTGAGCTTA
131 CTTCCCAAGCGAGGCTTATCATCTTTTGCAAGCTTACCTAGCTCAAATTTAGCTCGTTGAGCTTA
157959 AATAAGCTCGATTCTAGCTCAA
196 AATAAGCTCGATTCTAGCTCAA
157981 TGAACTCGTT
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 216 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (217 bp):
CACATTCCATCGACCAAAGGGCTGGTGACGATGTAAAATTTCTTTTCGAGCAAGTGGCCTGATTT
GGGGACATATCGCTCCAAAGAGGGAGGGAATGATACGATCCCGCTTGAGAACACCCTTGGATCAG
CTTCCCAAGCGAGGCTTATCATCTTTTGCAAGCTTACCTAGCTCAAATTTAGCTCGTTGAGCTTA
AATAAGCTCGATTCTAGCTCAA
Found at i:158374 original size:27 final size:27
Alignment explanation
Indices: 158336--158387 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
158326 TGTTTGTAGG
* *
158336 TACATGCATGGACAGCATTGAAGATAA
1 TACATGCATGGACAACAATGAAGATAA
158363 TACATGCATGGACAACAATGAAGAT
1 TACATGCATGGACAACAATGAAGAT
158388 GCTTCAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (27 bp):
TACATGCATGGACAACAATGAAGATAA
Found at i:160191 original size:20 final size:20
Alignment explanation
Indices: 160166--160209 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
160156 TCGTTTCCAG
*
160166 CTCACTCGAGCTCAAGTCAA
1 CTCACTCAAGCTCAAGTCAA
*
160186 CTCACTCAAGCTCAATTCAA
1 CTCACTCAAGCTCAAGTCAA
160206 CTCA
1 CTCA
160210 ATCTTAACCC
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:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (20 bp):
CTCACTCAAGCTCAAGTCAA
Found at i:164013 original size:20 final size:20
Alignment explanation
Indices: 163970--164014 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
163960 AAGGAAAACG
* *
163970 AAAAAGAAAAGAAAAATGAT
1 AAAAAGAAAAGAAAAATCAC
163990 AAAAAG-AAAGAAAAAATCAC
1 AAAAAGAAAAG-AAAAATCAC
164010 AAAAA
1 AAAAA
164015 AAATGTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAATCAC
Found at i:172524 original size:18 final size:19
Alignment explanation
Indices: 172501--172549 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
172491 AAGTTTTATT
*
172501 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
172519 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
172538 TTTAATTTTTAT
1 TTT-ATTTTTAT
172550 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:172529 original size:22 final size:22
Alignment explanation
Indices: 172492--172549 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
172482 CAAGTTGTAA
* *
172492 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
172514 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
172536 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
172550 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:174358 original size:40 final size:39
Alignment explanation
Indices: 174274--174497 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 39
174264 TTGAATGATG
* * * *
174274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
174314 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
174354 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
174393 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
174432 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
174473 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
174498 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 72 0.44
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:174466 original size:79 final size:79
Alignment explanation
Indices: 174274--174497 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
174264 TTGAATGATG
* * * * *
174274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
*
174338 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
* *
174354 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
*
174418 TGCGAGTTACTAAA
66 TGCGAGATACTAAA
* *
174432 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
174496 TG
64 TG
174498 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.28
79 59 0.46
80 32 0.25
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:174519 original size:79 final size:79
Alignment explanation
Indices: 174274--174530 Score: 238
Period size: 79 Copynumber: 3.3 Consensus size: 79
174264 TTGAATGATG
* * * * * * *
174274 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
** *
174338 TGTGCGAGAT-ACTAAT
64 TGAACGAG-TGACTAAA
* *
174354 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
** *
174418 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
174432 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
*
174496 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
174512 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
174531 TACGTGATTT
Statistics
Matches: 153, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 35 0.23
79 74 0.48
80 43 0.28
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:182256 original size:40 final size:40
Alignment explanation
Indices: 182172--182393 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
182162 TTGAATGATG
* * * *
182172 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
182212 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
182252 TCCGGGCTAAG-CCCGAAGGC-GTTGTGCGA-TTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
182289 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
182329 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC-ATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
182369 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
182394 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
37 16 0.10
38 17 0.11
39 40 0.25
40 79 0.49
41 8 0.05
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:182310 original size:77 final size:78
Alignment explanation
Indices: 182172--182393 Score: 272
Period size: 77 Copynumber: 2.8 Consensus size: 78
182162 TTGAATGATG
* * * *
182172 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-GAGTTA-CAAATCCGGGCTAAG-TCCCGAAGGCATT
*
182236 TGTGCGAGATACTAAT
63 TGTGCGAGATACTAAA
* *
182252 TCCGGGCTAAG-CCCGAAGGCGTTGTGCGA-TTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTAC-AAATCCGGGCTAAGTCCCGAAGGCATTTG
*
182315 TGCGAGTTACTAAA
65 TGCGAGATACTAAA
* *
182329 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACATAA-CCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTACA-AATCCGGGCTAAGTCCCGAAGGCATTT
182393 G
64 G
182394 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
76 2 0.02
77 48 0.39
78 10 0.08
79 47 0.38
80 17 0.14
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTACAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATACTAAA
Found at i:182384 original size:117 final size:116
Alignment explanation
Indices: 182172--182388 Score: 287
Period size: 117 Copynumber: 1.9 Consensus size: 116
182162 TTGAATGATG
*
182172 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
182237 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCGTTGTGCGATTACTAAA
66 GTGCGAGATACTAA-TCCGGGCTAAGCCCGAAGGCGTTGTGCGATTACTAAA
* * * * **
182289 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
182352 TTGTGCGAGTTACATAA-CCGGGCTATGTCCCGAAGGC
64 TTGTGCGAGATAC-TAATCCGGGCTAAG-CCCGAAGGC
182389 ATTTGAACGA
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
116 10 0.11
117 67 0.77
118 10 0.11
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (116 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATCCGGGCTAAGCCCGAAGGCGTTGTGCGATTACTAAA
Found at i:182411 original size:79 final size:76
Alignment explanation
Indices: 182172--182412 Score: 238
Period size: 79 Copynumber: 3.1 Consensus size: 76
182162 TTGAATGATG
* * * *
182172 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-GAGTTA-CATAACCGGGCTAAG-TCCCGAAGGCATT
*
182236 TGTGCGAGATACTAA
63 TGTGCGAG-GACTAA
* *
182251 TTCCGGGCTAAG-CCCGAAGGCGTTGTGCGA-TTAC-TAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTACAT-AA-CCGGGCTAAGTCCCGAAGGCATT
*
182313 TGTGCGAGTTACTAAA
63 TGTGCGAG-GACT-AA
* *
182329 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACATAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTACATAACCGGGCTAAGTCCCGAAGGCATTTG
**
182394 AACGAGGAGCTATA
65 TGCGAGGA-CTA-A
182408 TCCGG
1 TCCGG
182413 TTAAATTCCG
Statistics
Matches: 137, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
75 1 0.01
76 3 0.02
77 43 0.31
78 14 0.10
79 58 0.42
80 17 0.12
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (76 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTACATAACCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGGACTAA
Found at i:186867 original size:21 final size:21
Alignment explanation
Indices: 186841--186893 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
186831 TTGGTATTTG
*
186841 GGAATTGGTTCGAAATAGTAT
1 GGAATTGGTACGAAATAGTAT
*
186862 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATAGTAT
*
186883 GGTATTTGGTA
1 GG-AATTGGTA
186894 TGACTTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATAGTAT
Found at i:195466 original size:20 final size:20
Alignment explanation
Indices: 195419--195467 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
195409 GACAAGCTGA
* * *
195419 AAGTAAGCTAAATTGAGCTC
1 AAGTGAGCTAAAATAAGCTC
**
195439 AAACGAGCTAAAATAAGCTC
1 AAGTGAGCTAAAATAAGCTC
195459 AAGTGAGCT
1 AAGTGAGCT
195468 GATTTGAGCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGTGAGCTAAAATAAGCTC
Found at i:197686 original size:23 final size:22
Alignment explanation
Indices: 197658--197709 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
197648 AAAAGTACAA
*
197658 GAAAAAAAGATTGAAAAAGAGAAG
1 GAAAAAACGA-TGAAAAAGA-AAG
197682 GAAAAAAACGAT-AAAAAGAAAG
1 G-AAAAAACGATGAAAAAGAAAG
197704 GAAAAA
1 GAAAAA
197710 GTGAGGGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 7 0.27
24 2 0.08
25 8 0.31
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (22 bp):
GAAAAAACGATGAAAAAGAAAG
Found at i:202401 original size:22 final size:23
Alignment explanation
Indices: 202346--202388 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
202336 AATATGTTTA
202346 TTTACAGTTTATTAAATTAAGTG
1 TTTACAGTTTATTAAATTAAGTG
202369 TTTACAGTTTATT-AATTAAG
1 TTTACAGTTTATTAAATTAAG
202389 CTTATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (23 bp):
TTTACAGTTTATTAAATTAAGTG
Found at i:206473 original size:30 final size:31
Alignment explanation
Indices: 206417--206474 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
206407 GATAAAAGAG
* *
206417 ACGAGCTGAAAGTAAGCTAAATTGAGCTCAA
1 ACGAGCTGAAAATAAGCTAAAGTGAGCTCAA
*
206448 ACGAGCT-AAAATAAGCTTAAGTGAGCT
1 ACGAGCTGAAAATAAGCTAAAGTGAGCT
206475 GATTTGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (31 bp):
ACGAGCTGAAAATAAGCTAAAGTGAGCTCAA
Found at i:206650 original size:21 final size:21
Alignment explanation
Indices: 206602--206650 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
206592 ATTAAGCTGG
*
206602 CACGAGGGCCAATAACTCGAT
1 CACGAGTGCCAATAACTCGAT
206623 CACGAGTGCCAATAACTCGAT
1 CACGAGTGCCAATAACTCGAT
206644 CACGAGT
1 CACGAGT
206651 TAAGAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CACGAGTGCCAATAACTCGAT
Found at i:207641 original size:40 final size:40
Alignment explanation
Indices: 207586--207669 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
207576 TATGAAATCT
207586 TTGAATTGTGAGTTATCCAATTCTCTTTGTTCTTACGGAA
1 TTGAATTGTGAGTTATCCAATTCTCTTTGTTCTTACGGAA
207626 TTGAATTGTGAGTTATCCAATTCTCTTTGTTCTTACGGAA
1 TTGAATTGTGAGTTATCCAATTCTCTTTGTTCTTACGGAA
207666 TTGA
1 TTGA
207670 TTTGACTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (40 bp):
TTGAATTGTGAGTTATCCAATTCTCTTTGTTCTTACGGAA
Found at i:210111 original size:3 final size:3
Alignment explanation
Indices: 210105--210166 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
210095 AACAGTAGCT
210105 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
210153 TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TA
210167 TTAACAAACT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:210919 original size:8 final size:7
Alignment explanation
Indices: 210879--210916 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
210869 AAAATACCGT
210879 AAAATAA
1 AAAATAA
210886 AAAATAA
1 AAAATAA
210893 AAAATAA
1 AAAATAA
*
210900 AGAATAA
1 AAAATAA
210907 AATAATAA
1 AA-AATAA
210915 AA
1 AA
210917 TAAAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:211609 original size:44 final size:44
Alignment explanation
Indices: 211559--211669 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
211549 GATCTACTCT
*
211559 ACTGCAACTTCAGAGAGATAAGATCCATCATT-TT-AATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGAT-CA-CATTCTTCAATCCGCTCC
* * * *
211603 ACTGCAACTTCAGGGAGAT-AGAATTAGATTCTTCTATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAG-ATCACATTCTTCAATCCGCTCC
211647 ACTGCAACTTCAGGGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
211670 CTATATGCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
42 3 0.05
43 5 0.09
44 48 0.83
45 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATCACATTCTTCAATCCGCTCC
Found at i:211818 original size:85 final size:84
Alignment explanation
Indices: 211642--211841 Score: 274
Period size: 85 Copynumber: 2.4 Consensus size: 84
211632 TCTTCTATCT
* * * * *
211642 GCTCCACTGCAACTTCAGGGAGATAAGACTATATGCGATCTGCTCTTTGCAACTTCAGAGAGAAA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGATGCGATCTGCTCTCTACAACTTCAGAGAGAAA
* ** *
211707 ATATTTGTGGTTTTAATCC
66 AGAACTGTGGTTTTAACCC
* * *
211726 GCTCCACTGCAACTTCAGGGAGATAGGATTGGATGTGATCTGCTCTACTACAACTTCAGAGAGAT
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGATGCGATCTGCTCT-CTACAACTTCAGAGAGAA
211791 AAGAACTGTGGTTTTAACCC
65 AAGAACTGTGGTTTTAACCC
*
211811 GCTCCACTACAACTTCAGGGAGATAGGATTA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTA
211842 TTGGCCTCAA
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 41 0.41
85 60 0.59
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTAGATGCGATCTGCTCTCTACAACTTCAGAGAGAAA
AGAACTGTGGTTTTAACCC
Found at i:211825 original size:44 final size:43
Alignment explanation
Indices: 211691--211835 Score: 141
Period size: 44 Copynumber: 3.4 Consensus size: 43
211681 CTGCTCTTTG
* * * *
211691 CAACTTCAGAGAGAAAATATTTGTGGTTTTAATCCGCTCCACTG
1 CAACTTCAGAGAGATAAGA-ATGTGGTTTTAATCCGCTCCACTA
* * * * * * *
211735 CAACTTCAGGGAGAT-AGGAT-TGGATGTGATCTGCTCTACTA
1 CAACTTCAGAGAGATAAGAATGTGGTTTTAATCCGCTCCACTA
*
211776 CAACTTCAGAGAGATAAGAACTGTGGTTTTAACCCGCTCCACTA
1 CAACTTCAGAGAGATAAGAA-TGTGGTTTTAATCCGCTCCACTA
*
211820 CAACTTCAGGGAGATA
1 CAACTTCAGAGAGATA
211836 GGATTATTGG
Statistics
Matches: 78, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
41 29 0.37
42 4 0.05
43 2 0.03
44 43 0.55
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (43 bp):
CAACTTCAGAGAGATAAGAATGTGGTTTTAATCCGCTCCACTA
Found at i:212021 original size:100 final size:100
Alignment explanation
Indices: 211891--212301 Score: 540
Period size: 100 Copynumber: 4.1 Consensus size: 100
211881 GATTTGCCAT
* * * * *
211891 CTTCAATCT-GTTAACTGCAATGTCGTGGAAACAAGATTCGCCGTCGTAGCTTCAATTTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTGTTCCA
* * * *
211955 TTACATAGCTAAGGAAGTAAGATTCGTCGTTGTAG
66 CTACACAGCCAAGGAAGTAAGATTCGCCGTTGTAG
*
211990 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTATTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTGTTCCA
* * *
212055 CTACACCA-CCAAGGAAGTAAGATTCACTGTTGTGG
66 CTACA-CAGCCAAGGAAGTAAGATTCGCCGTTGTAG
* * * * *
212090 CTTCAGTCTATTTAACTACAATATCGGGGAAACAAGATTCACCGT-AGTAGCTTCAATATGGTCC
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCA-TAGCTTCAATCTGTTCC
* * *
212154 ACTACACCGCCAGGGAAGTAAGATTCGCCGCTGTAG
65 ACTACACAGCCAAGGAAGTAAGATTCGCCGTTGTAG
*
212190 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTGTTCCA
* * * * *
212255 CTACACCGCTAGGGGAGTAAGATTTGCCGTTGTAG
66 CTACACAGCCAAGGAAGTAAGATTCGCCGTTGTAG
212290 CTTCAATCTATT
1 CTTCAATCTATT
212302 CCACTGAAAT
Statistics
Matches: 272, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
99 11 0.04
100 259 0.95
101 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAGCTTCAATCTGTTCCA
CTACACAGCCAAGGAAGTAAGATTCGCCGTTGTAG
Found at i:212027 original size:50 final size:50
Alignment explanation
Indices: 211891--212301 Score: 236
Period size: 50 Copynumber: 8.2 Consensus size: 50
211881 GATTTGCCAT
* * * *
211891 CTTCAATCT-GTTAACTGCAATGTCGTGGAAACAAGATTCGCCGTCGTAG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
* * ** * ** ** *
211940 CTTCAATTTGTTCCATTAC-ATAG-CTAAGGAAGTAAGATTCGTCGTTGTAG
1 CTTCAATCTATTTAACTACAAT-GTC-GGGGAAACAAGATTCGCCGTTGTAG
* * **
211990 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACCGTCATAG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
** **** ** ** * * *
212040 CTTCAATCTATTCCACTACACCACCAAGGAAGTAAGATTCACTGTTGTGG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
* * * *
212090 CTTCAGTCTATTTAACTACAATATCGGGGAAACAAGATTCACCGTAGTAG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
* ** ** ** * * ** *
212140 CTTCAATATGGTCCACTACACCGCCAGGGAAGTAAGATTCGCCGCTGTAG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
* **
212190 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAG
1 CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
* ** ** * ** *
212240 CTTCAATCTGTTCCACTACACCGCTAGGGG-AGTAAGATTTGCCGTTGTAG
1 CTTCAATCTATTTAACTACAATG-TCGGGGAAACAAGATTCGCCGTTGTAG
212290 CTTCAATCTATT
1 CTTCAATCTATT
212302 CCACTGAAAT
Statistics
Matches: 258, Mismatches: 98, Indels: 11
0.70 0.27 0.03
Matches are distributed among these distances:
49 11 0.04
50 239 0.93
51 8 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTTGTAG
Found at i:217997 original size:12 final size:12
Alignment explanation
Indices: 217980--218004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
217970 AAGTATATCA
217980 GCTTTAGTTTTT
1 GCTTTAGTTTTT
217992 GCTTTAGTTTTT
1 GCTTTAGTTTTT
218004 G
1 G
218005 AGGTATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (12 bp):
GCTTTAGTTTTT
Found at i:219032 original size:44 final size:44
Alignment explanation
Indices: 218969--219062 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
218959 GTCTCGACTT
218969 TCATTTTCATATGCTTATCAAATATAAGTACTATATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTACTATATTAACCAAA
* * *
219013 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAATCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTACTATATTAACCAAA
219057 TCATTT
1 TCATTT
219063 ATTGAATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTACTATATTAACCAAA
Found at i:219118 original size:66 final size:67
Alignment explanation
Indices: 219005--219130 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 67
218995 AGTACTATAT
* *
219005 TAACCAAATCATTTTCATATGCTTATCAAATATAAGTATTGTATTAATCAAATCA-TTTATTGAA
1 TAACCAAATCATTTTCATAAGCTTATCAAATATAAGCATTGTATTAATCAAATCACTTTATTGAA
219069 TA
66 TA
*
219071 TAACCAAATCATTTTCATAAGCTTATCAAATAT-AGCATCTAGT-TTAATCAATTCACTTTA
1 TAACCAAATCATTTTCATAAGCTTATCAAATATAAGCAT-T-GTATTAATCAAATCACTTTA
219131 AATTGTAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
65 4 0.07
66 44 0.81
67 6 0.11
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (67 bp):
TAACCAAATCATTTTCATAAGCTTATCAAATATAAGCATTGTATTAATCAAATCACTTTATTGAA
TA
Found at i:219690 original size:13 final size:13
Alignment explanation
Indices: 219672--219696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219662 ACACTCAAAT
219672 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
219685 TTCTCAAAAGCA
1 TTCTCAAAAGCA
219697 ATGAAGAACT
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:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:224446 original size:15 final size:15
Alignment explanation
Indices: 224426--224480 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
224416 ACTCTCCTCA
*
224426 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
224441 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
224456 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
224470 TTCTTTT-TCTC
1 TTCTTTTCTCTC
224481 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:230460 original size:23 final size:23
Alignment explanation
Indices: 230417--230461 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
230407 AACCATAACC
* **
230417 ATTTCGTACCAAATCGTATTACA
1 ATTTCGAACCAAATCACATTACA
230440 ATTTCGAACCAAATCACATTAC
1 ATTTCGAACCAAATCACATTAC
230462 CGTTTTGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (23 bp):
ATTTCGAACCAAATCACATTACA
Found at i:232576 original size:12 final size:12
Alignment explanation
Indices: 232559--232583 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
232549 AAAATCTGAT
232559 TTCAATGTGTAA
1 TTCAATGTGTAA
232571 TTCAATGTGTAA
1 TTCAATGTGTAA
232583 T
1 T
232584 GTTTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:238906 original size:16 final size:16
Alignment explanation
Indices: 238885--238916 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
238875 ATTTTGTTGC
*
238885 TAATTCTACTTTTTCA
1 TAATTCCACTTTTTCA
238901 TAATTCCACTTTTTCA
1 TAATTCCACTTTTTCA
238917 CTATCTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTCCACTTTTTCA
Found at i:239274 original size:51 final size:50
Alignment explanation
Indices: 239182--239367 Score: 194
Period size: 51 Copynumber: 3.7 Consensus size: 50
239172 CCAGTTCACA
* * * * *
239182 TAGTAGCCTACTCATAGTACTTCACATGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA--AGCTATCTGGTACACG
* * * * *
239233 TAGTAGCATGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCAAGCTATCTGGTACACG
* * * * * *
239284 TAGTAGCCTGCACATAGTACTATACATGCGACCTATCTTTCTGGCACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAAGCTATCTGGTACACG
239334 TAGTAGCCTGCACATAGTACTACACATGTGACCA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA
239368 TCACTTTCAC
Statistics
Matches: 109, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 44 0.40
51 63 0.58
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCAAGCTATCTGGTACACG
Found at i:239768 original size:46 final size:46
Alignment explanation
Indices: 239715--239808 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 46
239705 CAAAGAAAAT
239715 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
239761 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
239807 AC
1 AC
239809 GCCACACTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 46 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:242493 original size:19 final size:18
Alignment explanation
Indices: 242457--242496 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
242447 TTTCCACTCG
*
242457 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
242475 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
242494 TTT
1 TTT
242497 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:243577 original size:15 final size:15
Alignment explanation
Indices: 243557--243597 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
243547 TAGCTTCGTC
243557 TTTTTTTTTCACGAA-
1 TTTTTTTTTCAC-AAG
*
243572 TTTTTTTTGCACAAG
1 TTTTTTTTTCACAAG
243587 TTTTTTTTTCA
1 TTTTTTTTTCA
243598 ACTTGATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTTTTTTTCACAAG
Found at i:243650 original size:11 final size:11
Alignment explanation
Indices: 243634--243672 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
243624 AATAAAAACT
243634 TTTTTTTTGAA
1 TTTTTTTTGAA
*
243645 -TTTTTTT-AT
1 TTTTTTTTGAA
243654 TTTTTTTTGAA
1 TTTTTTTTGAA
243665 TTTTTTTT
1 TTTTTTTT
243673 TTGAAAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.04
10 14 0.58
11 9 0.38
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:243658 original size:20 final size:20
Alignment explanation
Indices: 243633--243671 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
243623 GAATAAAAAC
243633 TTTTTTTTTGAATTTTTTTA
1 TTTTTTTTTGAATTTTTTTA
243653 TTTTTTTTTGAATTTTTTT
1 TTTTTTTTTGAATTTTTTT
243672 TTTGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTGAATTTTTTTA
Found at i:244033 original size:13 final size:13
Alignment explanation
Indices: 244015--244059 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
244005 GGAAACTAAA
244015 TTTTTTTT-AAAT
1 TTTTTTTTAAAAT
**
244027 TTTTTTTTCGAAT
1 TTTTTTTTAAAAT
244040 TTTTTTTTGAAAAT
1 TTTTTTTT-AAAAT
244054 TTTTTT
1 TTTTTT
244060 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTAAAAT
Found at i:244040 original size:24 final size:23
Alignment explanation
Indices: 244013--244070 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
244003 ATGGAAACTA
*
244013 AATTTTTTTT-AAATTTTTTTTTCG
1 AATTTTTTTTGAAA-ATTTTTTT-G
244037 AATTTTTTTTTGAAAATTTTTTTG
1 AA-TTTTTTTTGAAAATTTTTTTG
244061 AATTTTTTTT
1 AATTTTTTTT
244071 CGAAGATGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 8 0.26
24 5 0.16
25 15 0.48
26 3 0.10
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (23 bp):
AATTTTTTTTGAAAATTTTTTTG
Found at i:244069 original size:13 final size:12
Alignment explanation
Indices: 244015--244070 Score: 76
Period size: 12 Copynumber: 4.6 Consensus size: 12
244005 GGAAACTAAA
*
244015 TTTTTTTTAAAT
1 TTTTTTTTGAAT
244027 TTTTTTTTCGAAT
1 TTTTTTTT-GAAT
*
244040 TTTTTTTTGAAA
1 TTTTTTTTGAAT
*
244052 ATTTTTTTGAAT
1 TTTTTTTTGAAT
244064 TTTTTTT
1 TTTTTTT
244071 CGAAGATGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
12 27 0.71
13 11 0.29
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGAAT
Done.