Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3548
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: 272223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1916 original size:18 final size:19
Alignment explanation
Indices: 1893--1934 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1883 AACAAGTGAG
1893 GAAAAAGA-AAAAGAGAAT
1 GAAAAAGACAAAAGAGAAT
*
1911 GAAAAAGAGCAAAAGAGATT
1 GAAAAAGA-CAAAAGAGAAT
1931 GAAA
1 GAAA
1935 GTGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (19 bp):
GAAAAAGACAAAAGAGAAT
Found at i:5184 original size:11 final size:10
Alignment explanation
Indices: 5170--5214 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
5160 AAAATTTTGA
5170 AAAAAAAATAG
1 AAAAAAAAT-G
*
5181 AAAAAAAATC
1 AAAAAAAATG
*
5191 AAAAAAATTG
1 AAAAAAAATG
5201 AAAAAAAA-G
1 AAAAAAAATG
5210 AAAAA
1 AAAAA
5215 TTGATACGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 6 0.20
10 15 0.50
11 9 0.30
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:5196 original size:20 final size:20
Alignment explanation
Indices: 5171--5208 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5161 AAATTTTGAA
5171 AAAAAAATAGAAAAAAAATC
1 AAAAAAATAGAAAAAAAATC
*
5191 AAAAAAATTGAAAAAAAA
1 AAAAAAATAGAAAAAAAA
5209 GAAAAATTGA
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:0.82, C:0.03, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAAAAATAGAAAAAAAATC
Found at i:5214 original size:20 final size:20
Alignment explanation
Indices: 5170--5214 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5160 AAAATTTTGA
*
5170 AAAAAAAATAGAAAAAAAAT
1 AAAAAAAATAGAAAAAAAAG
* *
5190 CAAAAAAATTGAAAAAAAAG
1 AAAAAAAATAGAAAAAAAAG
5210 AAAAA
1 AAAAA
5215 TTGATACGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.82, C:0.02, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAAAAATAGAAAAAAAAG
Found at i:5716 original size:17 final size:17
Alignment explanation
Indices: 5686--5719 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5676 AATTTACCTT
5686 GTTTATTTTATTATTAG
1 GTTTATTTTATTATTAG
5703 GTTTAATTTT-TTATTAG
1 GTTT-ATTTTATTATTAG
5720 TTTTTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (17 bp):
GTTTATTTTATTATTAG
Found at i:8310 original size:23 final size:22
Alignment explanation
Indices: 8284--8336 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8274 TGAGAGTGAA
*
8284 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
8307 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
8329 AAAAGAAA
1 AAAAGAAA
8337 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:11207 original size:17 final size:15
Alignment explanation
Indices: 11170--11208 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
11160 TCTATCTCCC
11170 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
11186 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
11203 TCATTT
1 TCATTT
11209 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:12127 original size:27 final size:28
Alignment explanation
Indices: 12084--12152 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
12074 TTTCAATCAC
* *
12084 TCTTTTTTTTTTCAATTTCGATTTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTT
12112 TCTTTTTTTTTT-AATTCCGAATTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTT
12139 TCTTCTTTTTTTTC
1 TCTT-TTTTTTTTC
12153 TTCAATACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (28 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTT
Found at i:12212 original size:11 final size:11
Alignment explanation
Indices: 12196--12237 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
12186 GAATACAAAC
12196 TTTTTTTTGAA
1 TTTTTTTTGAA
12207 TTTTTTTTTCGAA
1 -TTTTTTTT-GAA
*
12220 TTTTTTTCGAA
1 TTTTTTTTGAA
12231 TTTTTTT
1 TTTTTTT
12238 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:12214 original size:13 final size:13
Alignment explanation
Indices: 12196--12237 Score: 63
Period size: 11 Copynumber: 3.5 Consensus size: 13
12186 GAATACAAAC
12196 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
12208 TTTTTTTTCGAA-
1 TTTTTTTTCGAAT
12220 -TTTTTTTCGAAT
1 TTTTTTTTCGAAT
12232 TTTTTT
1 TTTTTT
12238 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.41
12 8 0.30
13 8 0.30
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:15357 original size:15 final size:16
Alignment explanation
Indices: 15318--15358 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
15308 AACAACACTC
15318 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
15334 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
15348 CTTTCTTTTTC
1 CTTTCTTTTTC
15359 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:15553 original size:17 final size:15
Alignment explanation
Indices: 15516--15554 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
15506 TATGTCCCAC
15516 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
15532 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
15549 TCATTT
1 TCATTT
15555 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:16492 original size:34 final size:33
Alignment explanation
Indices: 16449--16531 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
16439 TTTCAATCAC
* *
16449 TCTTTTTTTTTTCAATTTCG-ATTTTCTTTTCTTT
1 TCTTTTTTTTTTCAATTCCGAATTTT-TTTT-TCT
16483 TCTTTTTTTTTT-AATTCCGAATTTTTTTTTCT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTTTTCT
16515 TCTTTTTTTTCTTCAAT
1 TCTTTTTTTT-TTCAAT
16532 ACTAAATACA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 12 0.27
33 12 0.27
34 20 0.45
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.72
Consensus pattern (33 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTTTTTCT
Found at i:16594 original size:13 final size:13
Alignment explanation
Indices: 16569--16616 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
16559 GAATACAAAC
16569 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
16581 TTTATTTTTCGAA
1 TTTTTTTTTCGAA
16594 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
16607 TTTTTTTTTC
1 TTTTTTTTTC
16617 CTTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 8 0.24
13 25 0.76
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:16623 original size:26 final size:25
Alignment explanation
Indices: 16569--16625 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
16559 GAATACAAAC
*
16569 TTTTTTTTTGAATTTATTTTTCGAA
1 TTTTTTTTTGAATTTATTTTTCCAA
*
16594 TTTTTTTTTCGAATTTTTTTTTCC--
1 TTTTTTTTT-GAATTTATTTTTCCAA
16618 TTTTTTTT
1 TTTTTTTT
16626 ACAATACCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.28
25 9 0.31
26 12 0.41
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTTTTTTTGAATTTATTTTTCCAA
Found at i:25455 original size:12 final size:12
Alignment explanation
Indices: 25438--25462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25428 ATCTTCAAGT
25438 TTGAGGTGTGAA
1 TTGAGGTGTGAA
25450 TTGAGGTGTGAA
1 TTGAGGTGTGAA
25462 T
1 T
25463 GGCTTAGATG
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:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (12 bp):
TTGAGGTGTGAA
Found at i:25955 original size:20 final size:19
Alignment explanation
Indices: 25932--25995 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
25922 AAGCTCAAAC
25932 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25952 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25972 AAGCTCATGTAGCTAAATC
1 GAGCTAAAGTAGCTAAATT
25991 GAGCT
1 GAGCT
25996 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 13 0.36
20 18 0.50
21 3 0.08
22 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:27803 original size:33 final size:33
Alignment explanation
Indices: 27765--27827 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
27755 GATTACTCAC
27765 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
27798 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
27828 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:27854 original size:21 final size:21
Alignment explanation
Indices: 27825--27880 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
27815 CAAGCTCTCT
*
27825 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
27846 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
27867 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
27881 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:27873 original size:14 final size:14
Alignment explanation
Indices: 27824--27880 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
27814 TCAAGCTCTC
27824 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
27837 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
27851 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
27865 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
27879 TT
1 TT
27881 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:27909 original size:17 final size:16
Alignment explanation
Indices: 27889--27959 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
27879 TTCTCTCACT
27889 TTTTCGATTTCTTTTTC
1 TTTTC-ATTTCTTTTTC
27906 TTTTGCAATTTCTTTTTC
1 TTTT-C-ATTTCTTTTTC
*
27924 TTTTCATTTTCTTTTTG
1 TTTTCA-TTTCTTTTTC
**
27941 TTTTC-TTTCAATTTC
1 TTTTCATTTCTTTTTC
27956 TTTT
1 TTTT
27960 TCAATCTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
15 11 0.23
16 1 0.02
17 19 0.40
18 16 0.34
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTTCATTTCTTTTTC
Found at i:27939 original size:12 final size:12
Alignment explanation
Indices: 27844--27962 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
27834 TTTTTTCGCT
27844 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
27857 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
27871 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
27882 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
27896 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
27906 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
27919 TTTTC-TTTTCA
1 TTTTCTTTTTCA
*
27930 TTTTCTTTTT-G
1 TTTTCTTTTTCA
27941 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
27951 ATTTCTTTTTCA
1 TTTTCTTTTTCA
27963 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 18 0.22
12 34 0.41
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:27939 original size:18 final size:18
Alignment explanation
Indices: 27842--27944 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
27832 TCTTTTTTCG
27842 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
27861 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
27881 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
27899 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
27917 CTTTTTC-TTTTCATTTT
1 CTTTTTCTTTTTCATTTT
*
27934 CTTTTTGTTTT
1 CTTTTTCTTTT
27945 CTTTCAATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
17 15 0.23
18 31 0.48
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:27955 original size:21 final size:22
Alignment explanation
Indices: 27919--27960 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
27909 TGCAATTTCT
*
27919 TTTTCTTTTCATTTTCTTTTTG
1 TTTTCTTTTCAATTTCTTTTTG
27941 TTTTC-TTTCAATTTCTTTTT
1 TTTTCTTTTCAATTTCTTTTT
27961 CAATCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCAATTTCTTTTTG
Found at i:27961 original size:6 final size:6
Alignment explanation
Indices: 27842--27948 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
27832 TCTTTTTTCG
* * * **
27842 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
27893 CGATTT CTTTTT CTTTTG CAATTT CTTTTT C-TTTT CATTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
27940 -GTTTT CTTT
1 CTTTTT CTTT
27949 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
5 9 0.12
6 52 0.71
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:29040 original size:29 final size:27
Alignment explanation
Indices: 28983--29046 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
28973 TTAAACTTGA
*
28983 TTTTTTTTTGCTCACCTTTTTTTTTCTT
1 TTTTTTTTTGCTCA-CTTTTTTTTACTT
29011 TTCTTTTTTTGCTCGA-TTTTTTTTCACTT
1 TT-TTTTTTTGCTC-ACTTTTTTTT-ACTT
29040 TTTTTTT
1 TTTTTTT
29047 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 15 0.47
29 16 0.50
30 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (27 bp):
TTTTTTTTTGCTCACTTTTTTTTACTT
Found at i:29042 original size:12 final size:12
Alignment explanation
Indices: 29027--29062 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29017 TTTTGCTCGA
*
29027 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
29039 TTTTTTTTGAAT
1 TTTTTTTTCAAT
29051 TTTTTTTTCAAT
1 TTTTTTTTCAAT
29063 CAAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:30709 original size:20 final size:19
Alignment explanation
Indices: 30686--30750 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
30676 AAGCTCAAAC
30686 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
30706 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
30726 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
30746 GAGCT
1 GAGCT
30751 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:33074 original size:17 final size:18
Alignment explanation
Indices: 33047--33082 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
33037 AGGCAGCAAT
33047 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
33065 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
33082 A
1 A
33083 AATGAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:45744 original size:22 final size:23
Alignment explanation
Indices: 45714--45756 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
45704 AATCCCTCTA
45714 TCAAAAATTCTCT-TTGAGTTCT
1 TCAAAAATTCTCTCTTGAGTTCT
* *
45736 TCAAGAATTTTCTCTTGAGTT
1 TCAAAAATTCTCTCTTGAGTT
45757 TTCTTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (23 bp):
TCAAAAATTCTCTCTTGAGTTCT
Found at i:48198 original size:22 final size:23
Alignment explanation
Indices: 48173--48221 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
48163 ATCAGCTTCT
48173 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
48195 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
*
48217 CTAAT
1 TTAAT
48222 CATACCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:56016 original size:23 final size:22
Alignment explanation
Indices: 55964--56017 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
55954 TCCACGTCTT
*
55964 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55986 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
56009 TTTCTTTTC
1 TTTCTTTTC
56018 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:57272 original size:9 final size:9
Alignment explanation
Indices: 57258--57291 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57248 GAATTTCGTA
*
57258 TTTTTTGAT
1 TTTTTTGAC
57267 TTTTTTGAC
1 TTTTTTGAC
57276 TTTTTTGAC
1 TTTTTTGAC
57285 TTATTTT
1 TT-TTTT
57292 TTTGCAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:63079 original size:19 final size:22
Alignment explanation
Indices: 63038--63089 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
63028 GTAATGAAAG
*
63038 AAAGA-CAGAAAAAGAAATC-A
1 AAAGAGCAAAAAAAGAAATCAA
*
63058 AAAGAG-AAAAAAAG-AATGAA
1 AAAGAGCAAAAAAAGAAATCAA
63078 AAAGAGCAAAAA
1 AAAGAGCAAAAA
63090 GAGATTGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 19 0.70
21 5 0.19
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.04
Consensus pattern (22 bp):
AAAGAGCAAAAAAAGAAATCAA
Found at i:67386 original size:21 final size:22
Alignment explanation
Indices: 67362--67407 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
67352 TTAAAACAAG
67362 TGAGGAAAAAG-AAAAAGAGAA
1 TGAGGAAAAAGCAAAAAGAGAA
* *
67383 TGA-GAAAGAGCAAAAAGAGAT
1 TGAGGAAAAAGCAAAAAGAGAA
67404 TGAG
1 TGAG
67408 AGTGAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.59, C:0.02, G:0.30, T:0.09
Consensus pattern (22 bp):
TGAGGAAAAAGCAAAAAGAGAA
Found at i:72303 original size:22 final size:22
Alignment explanation
Indices: 72275--72318 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
72265 TTTTGAACCA
72275 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
72297 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
72319 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:81538 original size:19 final size:18
Alignment explanation
Indices: 81503--81553 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
81493 ATTGTAGTTT
81503 TTGAAAAAAAATCAAAAAAA
1 TTGAAAAAAAA--AAAAAAA
**
81523 TTGAAAAGAAAAAAAAATT
1 TTGAAAA-AAAAAAAAAAA
81542 TTGAAAAAAAAA
1 TTGAAAAAAAAA
81554 TATTGCATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 7 0.25
21 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (18 bp):
TTGAAAAAAAAAAAAAAA
Found at i:92241 original size:14 final size:14
Alignment explanation
Indices: 92213--92264 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
92203 TAGCTCTCTC
92213 TTTTTTTCA-AA-T
1 TTTTTTTCACAATT
92225 TTTTTTTCACAATT
1 TTTTTTTCACAATT
*
92239 TTTTTTTCAAAATT
1 TTTTTTTCACAATT
92253 TTTTTTTCACAA
1 TTTTTTTCACAA
92265 CTTGATATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.25
13 2 0.06
14 25 0.69
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTTCACAATT
Found at i:92347 original size:12 final size:12
Alignment explanation
Indices: 92302--92347 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
92292 TAGAAACTAG
92302 TTTTTTTCGA-T
1 TTTTTTTCGAGT
* *
92313 TTTTTTTTGAAT
1 TTTTTTTCGAGT
*
92325 TTATTTTCGAGT
1 TTTTTTTCGAGT
92337 TTTTTTTCGAG
1 TTTTTTTCGAG
92348 AAACTACTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (12 bp):
TTTTTTTCGAGT
Found at i:96258 original size:23 final size:23
Alignment explanation
Indices: 96224--96312 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
96214 ATGGTTTGGG
* *
96224 TTTGGTATGAAATGGTAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
96247 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
96270 TTTGGTACGAAATGGAAATGTAA
1 TTTGGTACGAAATGGAAATGTAA
*
96293 TTTGGTTCGAAATGGAAATG
1 TTTGGTACGAAATGGAAATG
96313 GTTCAAAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (23 bp):
TTTGGTACGAAATGGAAATGTAA
Found at i:97429 original size:29 final size:31
Alignment explanation
Indices: 97367--97431 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
97357 AGCAAAAATT
*
97367 AATTGAGCTGAATTTGTAAGTATTTGAGCTA
1 AATTGAGCTGAATTTGTAACTATTTGAGCTA
97398 AATTGAGCTG-ATTTG-AACTCA-TTGAGCTA
1 AATTGAGCTGAATTTGTAACT-ATTTGAGCTA
97427 AATTG
1 AATTG
97432 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.50
30 6 0.19
31 10 0.31
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (31 bp):
AATTGAGCTGAATTTGTAACTATTTGAGCTA
Found at i:108857 original size:10 final size:11
Alignment explanation
Indices: 108811--108851 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
108801 TTATACTTCG
*
108811 ATTTTTTTTTA
1 ATTTTTTTTCA
108822 ATTTTTTTTCA
1 ATTTTTTTTCA
108833 ATTTTTTTTCA
1 ATTTTTTTTCA
108844 ATTTTTTT
1 ATTTTTTT
108852 GAATTTCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:111845 original size:20 final size:20
Alignment explanation
Indices: 111822--111868 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
111812 GGGTTAAGAT
*
111822 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
111842 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
111862 TGAGCTG
1 TGAGCTG
111869 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:117665 original size:59 final size:63
Alignment explanation
Indices: 117602--117743 Score: 148
Period size: 70 Copynumber: 2.2 Consensus size: 63
117592 ATTTAAAGGG
*
117602 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
* * * *
117661 AAGCATAGACTTGCATTTAAGGTGATGTTCAACAGTAGCAATAAAGGAGTTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
117726 ATGTA
59 ATGTA
117731 AAGCATAGACATG
1 AAGCATAGACATG
117744 TATTTAAGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
59 11 0.17
60 5 0.08
64 1 0.02
67 1 0.02
70 48 0.73
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
Found at i:117740 original size:70 final size:70
Alignment explanation
Indices: 117627--117759 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
117617 TTAAATCAGC
*
117627 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACTTGCATTTAAGGTGATGTTCA
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
117692 ACAGT
66 ACAGT
* * *
117697 AGCAATAAAGGAGTTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTGTT
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTT
117760 GGGCATGCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (70 bp):
AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
ACAGT
Found at i:119703 original size:30 final size:30
Alignment explanation
Indices: 119647--119703 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
119637 TGGGCTCAAA
* **
119647 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
119677 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
119704 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:126161 original size:20 final size:20
Alignment explanation
Indices: 126136--126182 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
126126 GCTCGTTTTC
126136 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
* *
126156 CAGCTCATTCGTGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
126176 CAGCTCA
1 CAGCTCA
126183 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:127779 original size:23 final size:23
Alignment explanation
Indices: 127753--127798 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
127743 ACCAACCAGA
127753 AGCCCTTTGATGTTCATGAAAAT
1 AGCCCTTTGATGTTCATGAAAAT
127776 AGCCCTTTGATGTTCATGAAAAT
1 AGCCCTTTGATGTTCATGAAAAT
127799 GGCTACTTGA
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:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (23 bp):
AGCCCTTTGATGTTCATGAAAAT
Found at i:127963 original size:70 final size:70
Alignment explanation
Indices: 127873--128009 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
127863 TTGCATGCCC
127873 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
127938 TGTTG
66 TGTTG
* *
127943 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
128008 TG
66 TG
128010 ATTTAATTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:129570 original size:12 final size:12
Alignment explanation
Indices: 129553--129591 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
129543 ATCGAAATTC
129553 AAAAAAA-AAGT
1 AAAAAAAGAAGT
129564 AAAAAAAGAAG-
1 AAAAAAAGAAGT
129575 AAAAAAAGAAGT
1 AAAAAAAGAAGT
129587 GAAAA
1 -AAAA
129592 GTCTTGCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 18 0.72
12 3 0.12
13 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (12 bp):
AAAAAAAGAAGT
Found at i:132677 original size:21 final size:21
Alignment explanation
Indices: 132632--132694 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
132622 TTTGAACCAT
* *
132632 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
132654 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
132675 TACCATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
132695 CAAATACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 25 0.66
22 13 0.34
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:136169 original size:12 final size:12
Alignment explanation
Indices: 136154--136216 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
136144 TCAAGCTCTC
136154 TTTCAATTTCTT
1 TTTCAATTTCTT
*
136166 TTTCCACTCGTTCTT
1 TTT-CAAT--TTCTT
136181 TTTC---TTCTT
1 TTTCAATTTCTT
136190 TTTCAATTTCTT
1 TTTCAATTTCTT
*
136202 TTTCAATCTCTT
1 TTTCAATTTCTT
136214 TTT
1 TTT
136217 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 3 0.07
14 1 0.02
15 8 0.19
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:136275 original size:15 final size:14
Alignment explanation
Indices: 136255--136302 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
136245 CTCATTTTCA
136255 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
136270 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
136284 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
136299 TCTT
1 TCTT
136303 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:136307 original size:22 final size:21
Alignment explanation
Indices: 136255--136313 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
136245 CTCATTTTCA
* *
136255 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
136276 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
136297 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
136314 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:138860 original size:82 final size:82
Alignment explanation
Indices: 138704--138866 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 82
138694 TTTTACTTCC
* * * *
138704 CTTTAAATACCGTTCCATGCATGGGAACATCTCCTTAATGCATGTTTCCTTTGCCATTAAGTAGC
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAATGCATGTCTCCTTAGCCATTAAGTAGC
138769 CGAATTTCAATGACCTT
66 CGAATTTCAATGACCTT
* * **
138786 CTTTAAATGCCGTTCCTTGCATGTTAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTT-AATGCATGTCTCCTTAGCCATTAAGTAG
138851 CCGAA-TTCAATGACCT
65 CCGAATTTCAATGACCT
138867 GCAGACACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 41 0.57
83 31 0.43
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (82 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAATGCATGTCTCCTTAGCCATTAAGTAGC
CGAATTTCAATGACCTT
Found at i:142350 original size:18 final size:18
Alignment explanation
Indices: 142327--142361 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
142317 CTTTTTTTTT
142327 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
142345 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
142362 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:143307 original size:11 final size:11
Alignment explanation
Indices: 143293--143321 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
143283 TTTTTTTTCC
143293 TTTTTTTTG-A
1 TTTTTTTTGAA
143303 TTTTTTTTGAA
1 TTTTTTTTGAA
143314 TTTTTTTT
1 TTTTTTTT
143322 CTGAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:146740 original size:18 final size:20
Alignment explanation
Indices: 146709--146750 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
146699 AAAATCAGTC
*
146709 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
146727 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
146747 AAAA
1 AAAA
146751 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Found at i:147860 original size:18 final size:20
Alignment explanation
Indices: 147829--147870 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
147819 AAAATCAGTC
*
147829 AAAAAAGTCAAAA-T-AATA
1 AAAAAAGACAAAATTCAATA
*
147847 AAAAAAGACGAAATTCAATA
1 AAAAAAGACAAAATTCAATA
147867 AAAA
1 AAAA
147871 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAAGACAAAATTCAATA
Found at i:154730 original size:10 final size:10
Alignment explanation
Indices: 154706--154754 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
154696 GCTCGTTTTC
*
154706 CAGCTCACTT
1 CAGCTCAATT
* *
154716 GAGCTCAAGT
1 CAGCTCAATT
154726 CAGCTC-ATT
1 CAGCTCAATT
154735 CGAGCTCAATT
1 C-AGCTCAATT
154746 CAGCTCAAT
1 CAGCTCAAT
154755 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:154731 original size:20 final size:20
Alignment explanation
Indices: 154706--154752 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
154696 GCTCGTTTTC
154706 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
154726 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
154746 CAGCTCA
1 CAGCTCA
154753 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:156345 original size:10 final size:10
Alignment explanation
Indices: 156330--156368 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
156320 AGAAGTGAGC
156330 AAAAAAAAGT
1 AAAAAAAAGT
156340 -AAAAAAAGT
1 AAAAAAAAGT
*
156349 AAAAAAAAGA
1 AAAAAAAAGT
156359 AGAAAAAAAG
1 A-AAAAAAAG
156369 AAGAAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
AAAAAAAAGT
Found at i:156380 original size:14 final size:13
Alignment explanation
Indices: 156303--156380 Score: 53
Period size: 14 Copynumber: 6.3 Consensus size: 13
156293 AAAAAATTCG
156303 AAAAAAAGAA--A
1 AAAAAAAGAAGTA
156314 AAAAAAAGAAGTGA
1 AAAAAAAGAAGT-A
*
156328 GCAAAAAA-AAGT-
1 -AAAAAAAGAAGTA
156340 --AAAAA-AAGTA
1 AAAAAAAGAAGTA
*
156350 AAAAAAAGAAGAA
1 AAAAAAAGAAGTA
*
156363 AAAAAGAAGAAGTG
1 AAAAA-AAGAAGTA
156377 AAAA
1 AAAA
156381 GTCTTGCGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
9 9 0.17
11 10 0.19
12 5 0.09
13 9 0.17
14 15 0.28
15 6 0.11
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (13 bp):
AAAAAAAGAAGTA
Found at i:159140 original size:21 final size:21
Alignment explanation
Indices: 159091--159142 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
159081 GAAAAGAATA
*
159091 ATGAAAATGAAAACGAAAATG
1 ATGAAAATGAAAAAGAAAATG
*
159112 A-AAGAAATGAAAAAGAAAAAT-
1 ATGA-AAATGAAAAAG-AAAATG
159133 ATGAAAATGA
1 ATGAAAATGA
159143 GATTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.04
21 18 0.72
22 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.13
Consensus pattern (21 bp):
ATGAAAATGAAAAAGAAAATG
Found at i:159189 original size:12 final size:12
Alignment explanation
Indices: 159172--159247 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
159162 AGTGAAAAGC
159172 AAAAAGAGATTG
1 AAAAAGAGATTG
*
159184 AAAAAGAAATTG
1 AAAAAGAGATTG
*
159196 --AAAGAGA-AG
1 AAAAAGAGATTG
*
159205 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
159220 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
159232 AAAGAGAGCTTG
1 AAAAAGAGATTG
159244 AAAA
1 AAAA
159248 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:159213 original size:15 final size:15
Alignment explanation
Indices: 159195--159228 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
159185 AAAAGAAATT
159195 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
159210 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
159225 GAAA
1 GAAA
159229 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:162663 original size:10 final size:10
Alignment explanation
Indices: 162639--162687 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
162629 GCTCATTTTC
*
162639 CAGCTCACTT
1 CAGCTCAATT
* *
162649 GAGCTCAAGT
1 CAGCTCAATT
162659 CAGCTC-ATT
1 CAGCTCAATT
162668 CGAGCTCAATT
1 C-AGCTCAATT
162679 CAGCTCAAT
1 CAGCTCAAT
162688 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:162664 original size:20 final size:20
Alignment explanation
Indices: 162639--162685 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
162629 GCTCATTTTC
162639 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
162659 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
162679 CAGCTCA
1 CAGCTCA
162686 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:185097 original size:12 final size:12
Alignment explanation
Indices: 185082--185124 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
185072 TTCACTCGTT
*
185082 TCTTTTGCAAAC
1 TCTTTTGCAATC
* *
185094 TCTTTTTCAATT
1 TCTTTTGCAATC
*
185106 TCTTTTTCAATC
1 TCTTTTGCAATC
185118 TCTTTTG
1 TCTTTTG
185125 TTTTTTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (12 bp):
TCTTTTGCAATC
Found at i:185191 original size:12 final size:12
Alignment explanation
Indices: 185149--185190 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
185139 TTTTCATCTT
185149 TTTCTTTTTC-A
1 TTTCTTTTTCAA
185160 TTTC--TTTCAA
1 TTTCTTTTTCAA
185170 TTTCTTTTTCAA
1 TTTCTTTTTCAA
185182 TGTTCTTTT
1 T-TTCTTTT
185191 CTCGCTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 4 0.15
12 7 0.26
13 7 0.26
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:194198 original size:20 final size:20
Alignment explanation
Indices: 194175--194221 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
194165 GGGTTAAGAT
*
194175 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
194195 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
194215 TGAGCTG
1 TGAGCTG
194222 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:196610 original size:24 final size:24
Alignment explanation
Indices: 196582--196629 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
196572 TTTGCATGGT
196582 AATCTGAATCTGTCCATTCACATG
1 AATCTGAATCTGTCCATTCACATG
196606 AATCTGAATCTGTCCATTCACATG
1 AATCTGAATCTGTCCATTCACATG
196630 CGTTATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (24 bp):
AATCTGAATCTGTCCATTCACATG
Found at i:198180 original size:406 final size:405
Alignment explanation
Indices: 197422--198231 Score: 1467
Period size: 406 Copynumber: 2.0 Consensus size: 405
197412 AGAGCAGAAT
197422 TGATACGGGGTTGCACGCGAACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAGATC
1 TGATACGGGGTTGCACGCGAACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAGATC
* * * *
197487 TAAATGAATAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTGAAATTAAATC
66 TAAACGAACAGATCTAAAATGAAAACAAAGAACAAGATTAAACTAATCAGATCTGAAATTAAATC
* * *
197552 CCCAAATTCAATTAAATGAGCAGCAAGGAACAAAGAACGAATGAATAAATGTATTTGGAGTTCAA
131 ACCAAATTCAATTAAACGAGCAGCAAGGAACAAAGAACGAATGAATAAATGTATTCGGAGTTCAA
*
197617 GAAGATGAAATCGAACTCCAATAGTGAAATCCCACAAGCCGAATCTGCCAAGGACACCAAAACAG
196 GAAGATGAAATCGAACTCCAATAGTGAAATCCCACAAGCCGAATCTGCCAAGAACACCAAAACAG
197682 TAAGTAGATTGAAACAATCAGATTTTTAATTGGAAGATTAGGGATTTGGGCGACAAAAAGAAAAG
261 TAAGTAGATTGAAACAATCAGATTTTTAATTGGAAGATTAGGGATTTGGGCGACAAAAAGAAAAG
*
197747 AAAGAAATAGATGAAATTGAACGGTTCAAGAAGTGAATTTAAGTTGCGATTCGGTCCAATTGAAC
326 AAAGAAATAGATGAAATTGAACGGTTCAAGAAGTGAATTTAAGTTGCGATTCGGTCCAATAGAAC
197812 ACCCAAGATGAATTG
391 ACCCAAGATGAATTG
* * * * *
197827 TGATACTGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCATGGGAAACTCCTACGAAAGCTC
1 TGATACGGGGTTGCACGCGAACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAGATC
197892 TAAACGAACAGATCTAAAAATGAAAACAAAGAACAAGATTAAACTAATCAGATCTGAAATTAAAT
66 TAAACGAACAGATCT-AAAATGAAAACAAAGAACAAGATTAAACTAATCAGATCTGAAATTAAAT
197957 CACCAAATTCAATTAAACGAGCAGCAAGGAACAAAGAACGAATGAATAAATGTATTCGGAGTTCA
130 CACCAAATTCAATTAAACGAGCAGCAAGGAACAAAGAACGAATGAATAAATGTATTCGGAGTTCA
*
198022 AGAAGATGAAATCGAACTCCAATAGTGAAATCCCACAAGCCGAATCTGCCAAGAACACCAACACA
195 AGAAGATGAAATCGAACTCCAATAGTGAAATCCCACAAGCCGAATCTGCCAAGAACACCAAAACA
*
198087 GTAAGTAGATTGAAACAATCAGATTTTTAATTGGAAGATTAGGGATTTGGGCGGCAAAAAGAAAA
260 GTAAGTAGATTGAAACAATCAGATTTTTAATTGGAAGATTAGGGATTTGGGCGACAAAAAGAAAA
198152 GAAAGAAATAGATGAAATTGAACGGTTCAAGAAGTGAATTTAAGTTGCGATTCGGTCCAATAGAA
325 GAAAGAAATAGATGAAATTGAACGGTTCAAGAAGTGAATTTAAGTTGCGATTCGGTCCAATAGAA
198217 CACCCAAGATGAATT
390 CACCCAAGATGAATT
198232 TCCCAAATTT
Statistics
Matches: 388, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
405 73 0.19
406 315 0.81
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (405 bp):
TGATACGGGGTTGCACGCGAACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAGATC
TAAACGAACAGATCTAAAATGAAAACAAAGAACAAGATTAAACTAATCAGATCTGAAATTAAATC
ACCAAATTCAATTAAACGAGCAGCAAGGAACAAAGAACGAATGAATAAATGTATTCGGAGTTCAA
GAAGATGAAATCGAACTCCAATAGTGAAATCCCACAAGCCGAATCTGCCAAGAACACCAAAACAG
TAAGTAGATTGAAACAATCAGATTTTTAATTGGAAGATTAGGGATTTGGGCGACAAAAAGAAAAG
AAAGAAATAGATGAAATTGAACGGTTCAAGAAGTGAATTTAAGTTGCGATTCGGTCCAATAGAAC
ACCCAAGATGAATTG
Found at i:213207 original size:19 final size:21
Alignment explanation
Indices: 213171--213234 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
213161 AGAAAAGAAA
213171 AAAAACAAAAAGATGAGTGAT
1 AAAAACAAAAAGATGAGTGAT
*
213192 AAAAA-AAAGAGA-GAGTGATT
1 AAAAACAAAAAGATGAGTGA-T
* *
213212 CAAAAGAAAAAGAAATGAGTGAT
1 AAAAACAAAAAG--ATGAGTGAT
213235 GAGATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
21 10 0.29
23 2 0.06
24 6 0.17
ACGTcount: A:0.61, C:0.03, G:0.22, T:0.14
Consensus pattern (21 bp):
AAAAACAAAAAGATGAGTGAT
Found at i:215189 original size:20 final size:20
Alignment explanation
Indices: 215166--215219 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
215156 AGTTTTTCCC
*
215166 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
215186 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
215206 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
215220 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:215201 original size:30 final size:30
Alignment explanation
Indices: 215166--215239 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
215156 AGTTTTTCCC
215166 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
215196 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
215226 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
215240 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:215229 original size:20 final size:20
Alignment explanation
Indices: 215166--215230 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
215156 AGTTTTTCCC
* * * *
215166 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
215186 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
215205 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
215226 AGCTC
1 AGCTC
215231 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:216929 original size:20 final size:20
Alignment explanation
Indices: 216906--216952 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
216896 GGGTTAAGAT
*
216906 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
216926 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
216946 TGAGCTG
1 TGAGCTG
216953 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:218674 original size:48 final size:48
Alignment explanation
Indices: 218622--218727 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
218612 TTGTCTTTTC
*
218622 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
218670 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
218718 TTTCTTTTTC
1 TTTCTTTTTC
218728 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:219767 original size:11 final size:10
Alignment explanation
Indices: 219753--219792 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
219743 CTTTTCACTT
219753 TTTTTTTGTTC
1 TTTTTTT-TTC
219764 TTTTTTTTTAC
1 TTTTTTTTT-C
219775 TTTTTTTTTC
1 TTTTTTTTTC
219785 TCTTTTTT
1 T-TTTTTT
219793 GCTCACTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:219767 original size:12 final size:11
Alignment explanation
Indices: 219752--219792 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
219742 ACTTTTCACT
219752 TTTTTTTTGTTC
1 TTTTTTTT-TTC
*
219764 TTTTTTTTTAC
1 TTTTTTTTTTC
219775 TTTTTTTTTCTC
1 TTTTTTTTT-TC
219787 TTTTTT
1 TTTTTT
219793 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:219776 original size:24 final size:23
Alignment explanation
Indices: 219744--219808 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
219734 CTCATAAGAC
*
219744 TTTTCACTTTTTTTTTGTTCTTTT
1 TTTTCACTTTTTTTTT-CTCTTTT
*
219768 TTTTTACTTTTTTTTTCTCTTTT
1 TTTTCACTTTTTTTTTCTCTTTT
*
219791 TTGCTCACTTCTTTTTTT
1 TT-TTCACTT-TTTTTTT
219809 TTTTTGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.23
24 20 0.57
25 7 0.20
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (23 bp):
TTTTCACTTTTTTTTTCTCTTTT
Found at i:221340 original size:20 final size:20
Alignment explanation
Indices: 221317--221363 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
221307 GGGTTAAGAT
*
221317 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
221337 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
221357 TGAGCTG
1 TGAGCTG
221364 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:245512 original size:20 final size:20
Alignment explanation
Indices: 245466--245512 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
245456 AGCTTGTTTC
*
245466 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
245486 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
245506 CAGCTCA
1 CAGCTCA
245513 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:249002 original size:20 final size:20
Alignment explanation
Indices: 248979--249025 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
248969 GGGTTAAAAT
*
248979 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
248999 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
249019 TGAGCTG
1 TGAGCTG
249026 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:249649 original size:48 final size:47
Alignment explanation
Indices: 249570--249675 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
249560 GAGTGTCATG
*
249570 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
249618 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
249666 GAAAAAGAAA
1 GAAAAAGAAA
249676 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:251438 original size:10 final size:10
Alignment explanation
Indices: 251423--251484 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
251413 TTTGAACCAT
*
251423 TACCAATTCG
1 TACCAATTCA
*
251433 TACCAAATACCA
1 TACC-AAT-TCA
*
251445 TACCATTTCA
1 TACCAATTCA
251455 TACCAATTCCA
1 TACCAATT-CA
* *
251466 TACCATTTCG
1 TACCAATTCA
251476 TACCAATTC
1 TACCAATTC
251485 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:251468 original size:21 final size:21
Alignment explanation
Indices: 251423--251485 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
251413 TTTGAACCAT
* *
251423 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
251445 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
251466 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
251486 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:252619 original size:15 final size:15
Alignment explanation
Indices: 252587--252620 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
252577 GTTCAACGAA
*
252587 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
252602 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
252617 GAGG
1 GAGG
252621 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:256314 original size:10 final size:10
Alignment explanation
Indices: 256299--256360 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
256289 TTTGAACCAT
*
256299 TACCAATTCG
1 TACCAATTCA
*
256309 TACCAAATACCA
1 TACC-AAT-TCA
*
256321 TACCATTTCA
1 TACCAATTCA
256331 TACCAATTCCA
1 TACCAATT-CA
* *
256342 TACCATTTCG
1 TACCAATTCA
256352 TACCAATTC
1 TACCAATTC
256361 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:256344 original size:21 final size:21
Alignment explanation
Indices: 256299--256361 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
256289 TTTGAACCAT
* *
256299 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
256321 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
256342 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
256362 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:256691 original size:13 final size:12
Alignment explanation
Indices: 256675--256709 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
256665 AAGGAGTTCG
256675 AAAAAAATTGAA
1 AAAAAAATTGAA
256687 AAAAAAATTGAA
1 AAAAAAATTGAA
256699 AAAAACAATTG
1 AAAAA-AATTG
256710 CATACGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:257510 original size:15 final size:15
Alignment explanation
Indices: 257478--257511 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
257468 GTTCAACGAA
*
257478 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
257493 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
257508 GAGG
1 GAGG
257512 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:262060 original size:20 final size:20
Alignment explanation
Indices: 262037--262083 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
262027 GGGTTAAGAT
*
262037 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
262057 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
262077 TGAGCTG
1 TGAGCTG
262084 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:265505 original size:20 final size:19
Alignment explanation
Indices: 265482--265546 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
265472 AAGCTCAAAC
265482 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
265502 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
265522 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
265542 GAGCT
1 GAGCT
265547 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:267360 original size:33 final size:33
Alignment explanation
Indices: 267322--267384 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
267312 GATTACTCAC
267322 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
267355 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
267385 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:267459 original size:12 final size:12
Alignment explanation
Indices: 267459--267534 Score: 59
Period size: 12 Copynumber: 6.6 Consensus size: 12
267449 TCGATTTCTT
*
267459 TTTCTTTTGCAA
1 TTTCTTTTTCAA
**
267471 TTTCTTTTTCTT
1 TTTCTTTTTCAA
**
267483 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
267495 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
267505 TTT-TCTTTCAA
1 TTTCTTTTTCAA
267516 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
267528 TCTCTTT
1 TTTCTTT
267535 CTCCTTTTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 3 0.06
12 42 0.81
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:267525 original size:6 final size:6
Alignment explanation
Indices: 267399--267512 Score: 86
Period size: 6 Copynumber: 18.7 Consensus size: 6
267389 TCTTTTTTCG
* * * **
267399 CTTTTT CTTTTT CAATTTT CTTTTCT TTATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTT-T CT-TTTT CTTTTT CTTTTT CTTTTT
** * ** *
267450 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CTTTTT CGTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
267498 CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTT
267513 CAATTTCTTT
Statistics
Matches: 80, Mismatches: 24, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
5 4 0.05
6 64 0.80
7 9 0.11
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:268561 original size:15 final size:15
Alignment explanation
Indices: 268543--268592 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
268533 TTTAACTTGA
268543 TTTTTTTTGCTCACT
1 TTTTTTTTGCTCACT
**
268558 TTTTTTTT-CTTTCT
1 TTTTTTTTGCTCACT
268572 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
268587 TTTTTT
1 TTTTTT
268593 CACTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:268598 original size:29 final size:28
Alignment explanation
Indices: 268529--268603 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
268519 CTTTTCACTT
* **
268529 TTTTTTTAACTTGATTTTTTTTGCTCAC
1 TTTTTTTCACTTTTTTTTTTTTGCTCAC
**
268557 TTTTTTTTTCTTTCTTTTTTTTTGCTCGA-
1 TTTTTTTCACTTT-TTTTTTTTTGCTC-AC
268586 TTTTTTTCACTTTTTTTT
1 TTTTTTTCACTTTTTTTT
268604 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 15 0.38
29 23 0.59
30 1 0.03
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTTTTTCACTTTTTTTTTTTTGCTCAC
Found at i:270262 original size:20 final size:19
Alignment explanation
Indices: 270239--270303 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
270229 AAGCTCAAAC
270239 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
270259 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
270279 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
270299 GAGCT
1 GAGCT
270304 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.