Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008920.1 Hibiscus syriacus cultivar Beakdansim tig00112224_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1287743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:6795 original size:35 final size:37
Alignment explanation
Indices: 6726--6805 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
6716 ATACTATTTC
*
6726 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
6763 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
6798 CATCACCA
1 CATCACCA
6806 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:7210 original size:12 final size:11
Alignment explanation
Indices: 7183--7226 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
7173 CTACAACAAA
7183 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
7196 AAAGAAGAAAAG
1 AAA-AAGAAAAG
7208 AAAAGAGAAAAG
1 AAAA-AGAAAAG
7220 AAAAAGA
1 AAAAAGA
7227 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:10660 original size:35 final size:37
Alignment explanation
Indices: 10591--10670 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
10581 ATACTATTTC
*
10591 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
10628 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
10663 CATCACCA
1 CATCACCA
10671 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:11967 original size:19 final size:20
Alignment explanation
Indices: 11938--11988 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
11928 GGCCAAGAGC
*
11938 ATGTATCTTCA-TT-AAAAT
1 ATGTATTTTCATTTAAAAAT
11956 ATTGTATTTTCATTTAAAAAT
1 A-TGTATTTTCATTTAAAAAT
11977 CATGTATTTTCA
1 -ATGTATTTTCA
11989 AAGGGTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.32
20 2 0.07
21 15 0.54
22 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (20 bp):
ATGTATTTTCATTTAAAAAT
Found at i:15598 original size:19 final size:21
Alignment explanation
Indices: 15574--15625 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15564 CAGCCAAGAG
*
15574 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
15593 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
15614 CATGTATTTTCA
1 CATGTATTTTCA
15626 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:18129 original size:7 final size:6
Alignment explanation
Indices: 18114--18172 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
18104 GTGAAAAAAG
* * *
18114 AAAGAA AAAGACA AAAG-A AGAGAA AAAGAA GAA-AA GAAG-A AAAG-A
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
18159 AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AA
18173 TTTCAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 18 0.40
6 22 0.49
7 5 0.11
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:18139 original size:27 final size:28
Alignment explanation
Indices: 18108--18171 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
18098 ATTGGAGTGA
*
18108 AAAAAGAAAGAAAA-AGACAAAAGAAGAG
1 AAAAAGAAAGAAAAGA-ACAAAAGAAAAG
*
18136 AAAAAG-AAGAAAAGAAGAAAAGAAAAG
1 AAAAAGAAAGAAAAGAACAAAAGAAAAG
18163 AAAAAGAAA
1 AAAAAGAAA
18172 ATTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAGAAAAGAACAAAAGAAAAG
Found at i:19457 original size:24 final size:24
Alignment explanation
Indices: 19442--19495 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
19432 AAAATCATGG
*
19442 CTTTTGAAAAACCAAAAGATGTGA
1 CTTTTGAAAAACCAAAAGATATGA
* * **
19466 CTTTTGAAGAACCAATAGCCATGA
1 CTTTTGAAAAACCAAAAGATATGA
19490 CTTTTG
1 CTTTTG
19496 GTGATTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
CTTTTGAAAAACCAAAAGATATGA
Found at i:21758 original size:19 final size:20
Alignment explanation
Indices: 21720--21762 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
21710 GAAACCCCTT
*
21720 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
21740 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
21759 TGAA
1 TGAA
21763 GATAAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:24268 original size:11 final size:11
Alignment explanation
Indices: 24252--24291 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
24242 ACTTTCTTCA
24252 CTTTTCTTTTT
1 CTTTTCTTTTT
24263 CTTTTCTTTTT
1 CTTTTCTTTTT
24274 C--TTCTTTTT
1 CTTTTCTTTTT
24283 CTTTTCTTT
1 CTTTTCTTT
24292 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:24781 original size:35 final size:36
Alignment explanation
Indices: 24734--24801 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
24724 ATTTATAAGT
24734 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
24769 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
24802 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:25894 original size:19 final size:20
Alignment explanation
Indices: 25856--25898 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
25846 GAAACCCCTT
*
25856 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
25876 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
25895 TGAA
1 TGAA
25899 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:27946 original size:36 final size:36
Alignment explanation
Indices: 27894--28006 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
27884 GATACTATTT
* *
27894 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
27930 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
27966 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
28001 ACATCA
1 TCATCA
28007 TCTTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:27949 original size:13 final size:11
Alignment explanation
Indices: 27927--27992 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
27917 TATCGCGCCT
27927 ATATCATCACC
1 ATATCATCACC
27938 ATAGTCCATCACC
1 ATA-T-CATCACC
*
27951 ATTATCA-CGCC
1 A-TATCATCACC
27962 TATATCATCACC
1 -ATATCATCACC
27974 ATATTCCATCACC
1 ATA-T-CATCACC
27987 ATATCA
1 ATATCA
27993 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:29803 original size:13 final size:12
Alignment explanation
Indices: 29785--29830 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
29775 ATTTTTTTTT
29785 CAAAAACAAAAAA
1 CAAAAA-AAAAAA
29798 CAAAAAAAAAAA
1 CAAAAAAAAAAA
29810 GGC-AAAAAAAAAA
1 --CAAAAAAAAAAA
29823 CAAAAAAA
1 CAAAAAAA
29831 GAGCCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.03
12 12 0.40
13 16 0.53
14 1 0.03
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:29817 original size:21 final size:23
Alignment explanation
Indices: 29787--29842 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
29777 TTTTTTTTCA
* *
29787 AAAACAAAAAACAAAAAAAAAAAGGC
1 AAAA-AAAAAACAAA--AAAAGAGCC
29813 AAAAAAAAAACAAAAAAAGAGCC
1 AAAAAAAAAACAAAAAAAGAGCC
29836 AAAAAAA
1 AAAAAAA
29843 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 14 0.50
25 10 0.36
26 4 0.14
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAAAGAGCC
Found at i:29849 original size:22 final size:21
Alignment explanation
Indices: 29791--29842 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
29781 TTTTCAAAAA
29791 CAAAAAACAAAA-AAAAAAAGG
1 CAAAAAA-AAAACAAAAAAAGG
29812 CAAAAAAAAAACAAAAAAAGAG
1 CAAAAAAAAAACAAAAAAAG-G
*
29834 CCAAAAAAA
1 CAAAAAAAA
29843 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.81, C:0.12, G:0.08, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAACAAAAAAAGG
Found at i:34416 original size:17 final size:17
Alignment explanation
Indices: 34392--34437 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
34382 AAAAGCAACA
34392 AAAAGAAAAAGAAAGA-
1 AAAAGAAAAAGAAAGAG
34408 AAGAAGAAAACA-AAAGAG
1 AA-AAGAAAA-AGAAAGAG
34426 AAAAGAAAAAGA
1 AAAAGAAAAAGA
34438 CTCCTACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAAGAG
Found at i:34427 original size:23 final size:22
Alignment explanation
Indices: 34392--34437 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
34382 AAAAGCAACA
*
34392 AAAAGAAAAAG-AAAGAAAGAAG
1 AAAACAAAAAGAAAAGAAA-AAG
34414 AAAACAAAAGAGAAAAGAAAAAG
1 AAAACAAAA-AGAAAAGAAAAAG
34437 A
1 A
34438 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAACAAAAAGAAAAGAAAAAG
Found at i:34493 original size:14 final size:15
Alignment explanation
Indices: 34459--34505 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
34449 AATTTGGAGT
34459 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
34474 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
34488 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
34505 G
1 G
34506 TTAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:37890 original size:36 final size:36
Alignment explanation
Indices: 37838--37950 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
37828 GATACTATTT
* *
37838 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
37874 TCATCACAATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
37910 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
37945 ACATCA
1 TCATCA
37951 TCTTTCCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 16 0.24
36 52 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:37921 original size:11 final size:11
Alignment explanation
Indices: 37871--37937 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 11
37861 TATCGCGCCT
*
37871 ATATCATCACA
1 ATATCATCACC
37882 ATAGTCCATCACC
1 ATA-T-CATCACC
*
37895 ATTATCA-CGCC
1 A-TATCATCACC
37906 TATATCATCACC
1 -ATATCATCACC
37918 ATATTCCATCACC
1 ATA-T-CATCACC
37931 ATATCAT
1 ATATCAT
37938 GCCAATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
11 17 0.37
12 9 0.20
13 18 0.39
14 2 0.04
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:37984 original size:33 final size:33
Alignment explanation
Indices: 37921--37985 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
37911 CATCACCATA
*
37921 TTCCATCACCATATCATGCCAATAACATCATCT
1 TTCCATCACCATATCATACCAATAACATCATCT
* * *
37954 TTCCATTACCATTTCATCACCATTAA-ATCATC
1 TTCCATCACCATATCAT-ACCAATAACATCATC
37986 CTTCATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (33 bp):
TTCCATCACCATATCATACCAATAACATCATCT
Found at i:40952 original size:11 final size:11
Alignment explanation
Indices: 40936--40975 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
40926 ACTTTCTTCA
40936 CTTTTCTTTTT
1 CTTTTCTTTTT
40947 CTTTTCTTTTT
1 CTTTTCTTTTT
*
40958 C--ATCTTTTT
1 CTTTTCTTTTT
40967 CTTTTCTTT
1 CTTTTCTTT
40976 CTTTGGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:43069 original size:11 final size:11
Alignment explanation
Indices: 43053--43092 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
43043 ACTTTCTTCA
43053 CTTTTCTTTTT
1 CTTTTCTTTTT
43064 CTTTTCTTTTT
1 CTTTTCTTTTT
*
43075 C--ATCTTTTT
1 CTTTTCTTTTT
43084 CTTTTCTTT
1 CTTTTCTTT
43093 CTTTGGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:45188 original size:11 final size:11
Alignment explanation
Indices: 45172--45211 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
45162 ACTTTCTTCA
45172 CTTTTCTTTTT
1 CTTTTCTTTTT
45183 CTTTTCTTTTT
1 CTTTTCTTTTT
*
45194 C--ATCTTTTT
1 CTTTTCTTTTT
45203 CTTTTCTTT
1 CTTTTCTTT
45212 CTTTGATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:46103 original size:19 final size:20
Alignment explanation
Indices: 46065--46107 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
46055 GAAACCCCTT
*
46065 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
46085 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
46104 TGAA
1 TGAA
46108 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:47002 original size:19 final size:20
Alignment explanation
Indices: 46945--46994 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
46935 ATAATGGGTT
*
46945 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
46964 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
46984 TAAG-AATGAAA
1 TAAGTAATGAAA
46995 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:51237 original size:9 final size:9
Alignment explanation
Indices: 51225--51284 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
51215 TTTTGAAATC
51225 TTTTTCTTT
1 TTTTTCTTT
51234 TTTTTCTTCT
1 TTTTTCTT-T
51244 TCTTTTCTGAATT
1 T-TTTTCT---TT
*
51257 TTCTTC-TT
1 TTTTTCTTT
51265 TTTTTCTTT
1 TTTTTCTTT
*
51274 TCTTTCTTT
1 TTTTTCTTT
51283 TT
1 TT
51285 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 7 0.17
9 19 0.46
10 2 0.05
11 6 0.15
12 4 0.10
13 2 0.05
14 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:51249 original size:20 final size:20
Alignment explanation
Indices: 51226--51281 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
51216 TTTGAAATCT
51226 TTTTCTTTTTTTTCTTCTTC
1 TTTTCTTTTTTTTCTTCTTC
*** *
51246 TTTTCTGAATTTTCTTCTTT
1 TTTTCTTTTTTTTCTTCTTC
*
51266 TTTTCTTTTCTTTCTT
1 TTTTCTTTTTTTTCTT
51282 TTTGCACTCC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTCTTC
Found at i:51264 original size:32 final size:30
Alignment explanation
Indices: 51212--51278 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
51202 TTGCTTTTTC
51212 TCTTTTTGAAATCTTTTTCTTTTTTTTCTTCT
1 TCTTTTTGAAATCTTTTTC-TTTTTTTCTT-T
51244 TCTTTTCTG-AAT-TTTCTTCTTTTTTTCTTT
1 TCTTTT-TGAAATCTTT-TTCTTTTTTTCTTT
51274 TCTTT
1 TCTTT
51279 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 6 0.18
31 13 0.39
32 12 0.36
33 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.73
Consensus pattern (30 bp):
TCTTTTTGAAATCTTTTTCTTTTTTTCTTT
Found at i:51593 original size:19 final size:20
Alignment explanation
Indices: 51536--51585 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
51526 ATAATGGGTT
*
51536 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
51555 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
51575 TAAG-AATGAAA
1 TAAGTAATGAAA
51586 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:55828 original size:9 final size:9
Alignment explanation
Indices: 55816--55875 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
55806 TTTTGAAATC
55816 TTTTTCTTT
1 TTTTTCTTT
55825 TTTTTCTTCT
1 TTTTTCTT-T
55835 TCTTTTCTGAATT
1 T-TTTTCT---TT
*
55848 TTCTTC-TT
1 TTTTTCTTT
55856 TTTTTCTTT
1 TTTTTCTTT
*
55865 TCTTTCTTT
1 TTTTTCTTT
55874 TT
1 TT
55876 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 7 0.17
9 19 0.46
10 2 0.05
11 6 0.15
12 4 0.10
13 2 0.05
14 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:55840 original size:20 final size:20
Alignment explanation
Indices: 55817--55872 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
55807 TTTGAAATCT
55817 TTTTCTTTTTTTTCTTCTTC
1 TTTTCTTTTTTTTCTTCTTC
*** *
55837 TTTTCTGAATTTTCTTCTTT
1 TTTTCTTTTTTTTCTTCTTC
*
55857 TTTTCTTTTCTTTCTT
1 TTTTCTTTTTTTTCTT
55873 TTTGCACTCC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTCTTC
Found at i:55855 original size:32 final size:30
Alignment explanation
Indices: 55803--55869 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
55793 TTGCTTTTTC
55803 TCTTTTTGAAATCTTTTTCTTTTTTTTCTTCT
1 TCTTTTTGAAATCTTTTTC-TTTTTTTCTT-T
55835 TCTTTTCTG-AAT-TTTCTTCTTTTTTTCTTT
1 TCTTTT-TGAAATCTTT-TTCTTTTTTTCTTT
55865 TCTTT
1 TCTTT
55870 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 6 0.18
31 13 0.39
32 12 0.36
33 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.73
Consensus pattern (30 bp):
TCTTTTTGAAATCTTTTTCTTTTTTTCTTT
Found at i:56184 original size:19 final size:20
Alignment explanation
Indices: 56127--56176 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
56117 ATAATGGGTT
*
56127 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
56146 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
56166 TAAG-AATGAAA
1 TAAGTAATGAAA
56177 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:60129 original size:11 final size:11
Alignment explanation
Indices: 60113--60152 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
60103 ACTTTCTTCA
60113 CTTTTCTTTTT
1 CTTTTCTTTTT
60124 CTTTTCTTTTT
1 CTTTTCTTTTT
*
60135 C--TTATTTTT
1 CTTTTCTTTTT
60144 CTTTTCTTT
1 CTTTTCTTT
60153 CTTTGGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:60351 original size:19 final size:21
Alignment explanation
Indices: 60327--60378 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
60317 CGGCCAAGAG
*
60327 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
60346 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
60367 CATGTATTTTCA
1 CATGTATTTTCA
60379 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:65788 original size:18 final size:18
Alignment explanation
Indices: 65765--65804 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
65755 TGTAGGAGTC
65765 TTTTCTT-TTGCTTTTTGT
1 TTTTCTTCTTGC-TTTTGT
*
65783 TTTTCTTCTTTCTTTTGT
1 TTTTCTTCTTGCTTTTGT
65801 TTTT
1 TTTT
65805 TGTTGCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTGCTTTTGT
Found at i:66353 original size:26 final size:26
Alignment explanation
Indices: 66323--66383 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
66313 AATCATATAG
66323 TATGCAAGCGAATGGTAACATATGAT
1 TATGCAAGCGAATGGTAACATATGAT
66349 TATGCAAGCGAATGGTAACATATGAT
1 TATGCAAGCGAATGGTAACATATGAT
*
66375 TATTCAAGC
1 TATGCAAGC
66384 ATAGTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (26 bp):
TATGCAAGCGAATGGTAACATATGAT
Found at i:72211 original size:36 final size:36
Alignment explanation
Indices: 72159--72261 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
72149 GATACTATTT
* *
72159 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
72195 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
72231 TCATCACCATATTCCATCACCA-TATCACGCC
1 TCATCACCATAATCCATCACCATTATCACGCC
72262 AACAACATCA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 9 0.14
36 54 0.86
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:72214 original size:13 final size:11
Alignment explanation
Indices: 72192--72257 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
72182 TATCGCGCCT
72192 ATATCATCACC
1 ATATCATCACC
72203 ATAGTCCATCACC
1 ATA-T-CATCACC
*
72216 ATTATCA-CGCC
1 A-TATCATCACC
72227 TATATCATCACC
1 -ATATCATCACC
72239 ATATTCCATCACC
1 ATA-T-CATCACC
72252 ATATCA
1 ATATCA
72258 CGCCAACAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:72756 original size:14 final size:15
Alignment explanation
Indices: 72722--72768 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
72712 AATTTGGAGT
72722 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
72737 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
72751 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
72768 G
1 G
72769 TGAAACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:78169 original size:17 final size:17
Alignment explanation
Indices: 78121--78188 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
78111 TGAACTTCTC
78121 TTTTTCTTTTC-TTTT-A
1 TTTTT-TTTTCTTTTTGA
*
78137 TTATTTTCTTCATTTTTGA
1 TT-TTTTTTTC-TTTTTGA
78156 TTTTTTTTTCTTTTTG-
1 TTTTTTTTTCTTTTTGA
*
78172 TCTTTTCTTTCTTTTTG
1 T-TTTTTTTTCTTTTTG
78189 CACTCCAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 7 0.16
17 23 0.52
18 11 0.25
19 3 0.07
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTCTTTTTGA
Found at i:78178 original size:34 final size:35
Alignment explanation
Indices: 78121--78188 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
78111 TGAACTTCTC
78121 TTTTTCTTTTCTTTTATTATTTTC-TTCATTTTTGA
1 TTTTTCTTTTCTTTTATTATTTTCTTTC-TTTTTGA
*
78156 TTTTT-TTTTCTTTT-TGTCTTTTCTTTCTTTTTG
1 TTTTTCTTTTCTTTTAT-TATTTTCTTTCTTTTTG
78189 CACTCCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 1 0.03
34 21 0.70
35 8 0.27
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (35 bp):
TTTTTCTTTTCTTTTATTATTTTCTTTCTTTTTGA
Found at i:82302 original size:23 final size:24
Alignment explanation
Indices: 82272--82324 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
82262 AAAAATAGAA
*
82272 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
**
82295 AAGAAATTTCCAGCACTCAAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
82319 AAGAAA
1 AAGAAA
82325 AGCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (24 bp):
AAGAAATTTAAAGCACTCAAAAAG
Found at i:91492 original size:13 final size:11
Alignment explanation
Indices: 91473--91532 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 11
91463 TACAATCTGT
91473 TCATCACCATA
1 TCATCACCATA
*
91484 GTCCATCACCGTA
1 -T-CATCACCATA
*
91497 TCA-CGCCTATA
1 TCATCACC-ATA
91508 TCATCACCATA
1 TCATCACCATA
91519 GTCTATCACCATA
1 -TC-ATCACCATA
91532 T
1 T
91533 AACGACTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
10 3 0.08
11 10 0.26
12 8 0.21
13 18 0.46
ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28
Consensus pattern (11 bp):
TCATCACCATA
Found at i:91519 original size:35 final size:35
Alignment explanation
Indices: 91473--91551 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
91463 TACAATCTGT
* * * *
91473 TCATCACCATAGTCCATCACCGTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATATAACGACTAAA
*
91508 TCATCACCATAGTCTATCACCATATAACGACTAAA
1 TCATCACCATAGTCCATCACCATATAACGACTAAA
91543 TCATCACCA
1 TCATCACCA
91552 AATTCCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.25
Consensus pattern (35 bp):
TCATCACCATAGTCCATCACCATATAACGACTAAA
Found at i:97059 original size:13 final size:11
Alignment explanation
Indices: 97040--97102 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 11
97030 TACAATATGT
97040 TCATCACCATA
1 TCATCACCATA
97051 GTCCATCACCATA
1 -T-CATCACCATA
*
97064 TCA-CGCCTATA
1 TCATCACC-ATA
97075 TCATCACCATA
1 TCATCACCATA
97086 CTCCATCACCATA
1 -T-CATCACCATA
97099 TCAT
1 TCAT
97103 GCCTAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 14 0.32
12 7 0.16
13 20 0.45
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (11 bp):
TCATCACCATA
Found at i:97126 original size:35 final size:35
Alignment explanation
Indices: 97040--97118 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
97030 TACAATATGT
* *
97040 TCATCACCATAGTCCATCACCATATCACGCCTATA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
*
97075 TCATCACCATACTCCATCACCATATCATGCCTAAA
1 TCATCACCATACTCCATCACCATATCACGCCTAAA
97110 TCATCACCA
1 TCATCACCA
97119 AATTCCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.25
Consensus pattern (35 bp):
TCATCACCATACTCCATCACCATATCACGCCTAAA
Found at i:100309 original size:24 final size:25
Alignment explanation
Indices: 100273--100320 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
100263 CACCATGATC
* * *
100273 TGCATTTTATTCAGTTTCTTCATCT
1 TGCATTGTATTCAGGTTCCTCATCT
100298 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTATTCAGGTTCCTCATC
100321 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTATTCAGGTTCCTCATCT
Found at i:115624 original size:35 final size:36
Alignment explanation
Indices: 115557--115624 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
115547 ATACAATCTG
*
115557 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCAGCACCATAT
* *
115593 TCCATCACCA-TATCACTCCTATATTAGCACCA
1 TCCATCACCATTATCACGCCTATATCAGCACCA
115625 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCAGCACCATAT
Found at i:116256 original size:24 final size:25
Alignment explanation
Indices: 116212--116261 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
116202 TTACTATTTC
*
116212 ATTTCATTTTCTTTCATCTTTTCTT
1 ATTTCATTTACTTTCATCTTTTCTT
116237 ATTTCA-TTACTTT-ATCCTTTTCTT
1 ATTTCATTTACTTTCAT-CTTTTCTT
116261 A
1 A
116262 ACCTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATCTTTTCTT
Found at i:119589 original size:19 final size:20
Alignment explanation
Indices: 119542--119592 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
119532 GAAACCCCTT
**
119542 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
119562 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
119581 TGAAGATACATG
1 TGAAAATACATG
119593 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:122241 original size:23 final size:25
Alignment explanation
Indices: 122202--122255 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
122192 CTTTTTTCTT
122202 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
122227 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
122250 TTTCTT
1 TTTCTT
122256 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:124766 original size:23 final size:25
Alignment explanation
Indices: 124727--124780 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
124717 TCTTTTTCTT
124727 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
124752 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
124775 TTTCTT
1 TTTCTT
124781 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:127331 original size:23 final size:25
Alignment explanation
Indices: 127292--127345 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
127282 TCTTTTTCTT
127292 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
127317 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
127340 TTTCTT
1 TTTCTT
127346 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:131313 original size:24 final size:24
Alignment explanation
Indices: 131286--131340 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
131276 CCAACTTTTC
131286 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
131309 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
131333 CTTCTTTT
1 TTTCTTTT
131341 ATGATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:165301 original size:15 final size:16
Alignment explanation
Indices: 165228--165300 Score: 55
Period size: 16 Copynumber: 4.5 Consensus size: 16
165218 GGGTTAAAAA
165228 TATTATCTTTAGTT-AT
1 TATTAT-TTTAGTTCAT
*
165244 TATTATTTTAGAGTT-AA
1 TATTATTTT--AGTTCAT
*
165261 GA-TATGTTTAGTTCAT
1 TATTAT-TTTAGTTCAT
165277 TATTATTTTA-TTCAT
1 TATTATTTTAGTTCAT
165292 TAGTTATTT
1 TA-TTATTT
165301 AAGACCTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 14 0.30
16 21 0.45
17 12 0.26
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.59
Consensus pattern (16 bp):
TATTATTTTAGTTCAT
Found at i:179841 original size:24 final size:21
Alignment explanation
Indices: 179807--179849 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
179797 TCCACAAGAT
*
179807 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
179829 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
179850 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:181851 original size:19 final size:19
Alignment explanation
Indices: 181827--181863 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
181817 AGAGCATGTA
*
181827 TTTTCATTAAAGTCTTGTT
1 TTTTCATTAAAATCTTGTT
181846 TTTTCATTAAAATCTTGT
1 TTTTCATTAAAATCTTGT
181864 CATTTTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTTCATTAAAATCTTGTT
Found at i:183281 original size:23 final size:25
Alignment explanation
Indices: 183242--183295 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
183232 TCTTTTTCTT
183242 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
183267 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
183290 TTTCTT
1 TTTCTT
183296 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:204128 original size:9 final size:9
Alignment explanation
Indices: 204116--204155 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
204106 TTTTTTGAAA
204116 TTTTGGCTT
1 TTTTGGCTT
204125 TTTTGGCTT
1 TTTTGGCTT
* *
204134 TTTTTGTTT
1 TTTTGGCTT
*
204143 TTTTGCCTT
1 TTTTGGCTT
204152 TTTT
1 TTTT
204156 TTTGTTGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:204136 original size:10 final size:10
Alignment explanation
Indices: 204116--204156 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
204106 TTTTTTGAAA
204116 TTTTGGC-TT
1 TTTTGGCTTT
204125 TTTTGGCTTT
1 TTTTGGCTTT
204135 TTTT-G-TTT
1 TTTTGGCTTT
*
204143 TTTTGCCTTT
1 TTTTGGCTTT
204153 TTTT
1 TTTT
204157 TTGTTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 7 0.25
9 8 0.29
10 13 0.46
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.76
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:213664 original size:36 final size:36
Alignment explanation
Indices: 213617--213721 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
213607 GATACAATCT
*
213617 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATAATCACCATA
213653 GTCCATCACCATTATCACGCCTATATAATCACCATA
1 GTCCATCACCATTATCACGCCTATATAATCACCATA
* * *
213689 TTCAATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATAATCACCA
213722 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATAATCACCATA
Found at i:215563 original size:90 final size:91
Alignment explanation
Indices: 215409--215590 Score: 260
Period size: 90 Copynumber: 2.0 Consensus size: 91
215399 CCTAGAACAC
* *
215409 CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCACCAAGATG
215474 AAGAGT-TCTCTCCCTATTCGGCCAAG
66 AAGA-TCTCTCTCCCTATTCGGCCAAG
** * * * * *
215500 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCACCAAGATG
215564 AAGATCTCTCTCCCTATTCGGCCAAG
66 AAGATCTCTCTCCCTATTCGGCCAAG
215590 C
1 C
215591 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 1 0.01
90 61 0.75
91 19 0.23
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCACCAAGATG
AAGATCTCTCTCCCTATTCGGCCAAG
Found at i:216433 original size:24 final size:23
Alignment explanation
Indices: 216375--216434 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
216365 AAAATCAGCA
*
216375 AAGAAAATA-AAAGCACTCAAAAT
1 AAGAAAA-AGAAAGCACTCAAAAG
* **
216398 AATAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
216422 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
216435 AAAGAAAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.63, C:0.10, G:0.15, T:0.12
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:216496 original size:11 final size:11
Alignment explanation
Indices: 216480--216507 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
216470 TCAACAAGCA
216480 ATATTTCAATT
1 ATATTTCAATT
216491 ATATTTCAATT
1 ATATTTCAATT
216502 ATATTT
1 ATATTT
216508 TACTTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTTCAATT
Found at i:224033 original size:18 final size:19
Alignment explanation
Indices: 224010--224062 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
224000 ATTTGTTTTT
*
224010 CAAAAAAACAAAAACAAA-
1 CAAAAAAACAAAAAAAAAC
*
224028 CAAAAAAATAAAAAAAAAC
1 CAAAAAAACAAAAAAAAAC
*
224047 CAAAAAAGCAAAAAAA
1 CAAAAAAACAAAAAAA
224063 GCAAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAAC
Found at i:224051 original size:9 final size:9
Alignment explanation
Indices: 224011--224068 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
224001 TTTGTTTTTC
224011 AAAAAAACA
1 AAAAAAACA
224020 AAAACAAACA
1 AAAA-AAACA
224030 AAAAAATA-A
1 AAAAAA-ACA
*
224039 AAAAAAACC
1 AAAAAAACA
*
224048 AAAAAAGCA
1 AAAAAAACA
*
224057 AAAAAAGCA
1 AAAAAAACA
224066 AAA
1 AAA
224069 TTTCAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
8 1 0.02
9 32 0.74
10 10 0.23
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (9 bp):
AAAAAAACA
Found at i:233600 original size:5 final size:5
Alignment explanation
Indices: 233586--233620 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
233576 GTGCTTCAAC
*
233586 TTTC- TTTCT TTTCT TTTCT TATCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
233621 CTTTTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:233612 original size:15 final size:14
Alignment explanation
Indices: 233586--233625 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
233576 GTGCTTCAAC
233586 TTTCTTTCTTTTCT
1 TTTCTTTCTTTTCT
233600 TTTCTTATCTTTTCT
1 TTTCTT-TCTTTTCT
233615 TTTC-TTCTTTT
1 TTTCTTTCTTTT
233626 TGAATGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 7 0.28
15 12 0.48
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTCTTTTCT
Found at i:233649 original size:27 final size:28
Alignment explanation
Indices: 233610--233674 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
233600 TTTCTTATCT
*
233610 TTTCTTTTCTTCTTTTTGAATGC-TGAA
1 TTTCTTTTCTTCTTTTGGAATGCTTGAA
* *
233637 TTTC-TTTCTTTCTTTTGGAGTGCTTTAA
1 TTTCTTTTC-TTCTTTTGGAATGCTTGAA
233665 TTTCTTTTCT
1 TTTCTTTTCT
233675 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 8 0.25
29 4 0.12
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.63
Consensus pattern (28 bp):
TTTCTTTTCTTCTTTTGGAATGCTTGAA
Found at i:237484 original size:23 final size:25
Alignment explanation
Indices: 237445--237498 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
237435 TCTTTTTCTT
237445 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
237470 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
237493 TTTCTT
1 TTTCTT
237499 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:240553 original size:23 final size:25
Alignment explanation
Indices: 240513--240566 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
240503 TCTTTTTCTT
*
240513 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTAAGTGCTTTCAA
* *
240538 TTTCTT-C-TTTTAAGTGCTTTGAT
1 TTTCTTCCTTTTTAAGTGCTTTCAA
240561 TTTCTT
1 TTTCTT
240567 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
24 1 0.04
25 6 0.23
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTAAGTGCTTTCAA
Found at i:247207 original size:16 final size:16
Alignment explanation
Indices: 247180--247227 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
247170 AATTGGAGTG
247180 CAAAAAGAAAGAAAATA
1 CAAAAAG-AAGAAAATA
*
247197 CAAAAAGAAGAAAATT
1 CAAAAAGAAGAAAATA
*
247213 CGGAAAAGAAGAAAA
1 C-AAAAAGAAGAAAA
247228 AGAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.71, C:0.06, G:0.17, T:0.06
Consensus pattern (16 bp):
CAAAAAGAAGAAAATA
Found at i:248228 original size:15 final size:17
Alignment explanation
Indices: 248208--248240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
248198 CTTTTACCAA
248208 ATCAAG-TG-TTTGAAG
1 ATCAAGATGCTTTGAAG
248223 ATCAAGATGCTTTGAAG
1 ATCAAGATGCTTTGAAG
248240 A
1 A
248241 AAATCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (17 bp):
ATCAAGATGCTTTGAAG
Found at i:252164 original size:17 final size:17
Alignment explanation
Indices: 252142--252196 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
252132 AATTGTAGTG
252142 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
**
252159 CAAAAAG-AAGAAAATT
1 CAAAAAGAAAGAAAAGA
*
252175 CAGAAAAGAAAAAAAAGA
1 CA-AAAAGAAAGAAAAGA
252193 -AAAA
1 CAAAA
252197 GATTTCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 12 0.39
17 13 0.42
18 6 0.19
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:252172 original size:25 final size:23
Alignment explanation
Indices: 252144--252195 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
252134 TTGTAGTGCA
252144 AAAAGAAAGAAAAGACAAAAAGAAG
1 AAAAGAAAGAAAAGA-AAAAA-AAG
***
252169 AAAATTCAGAAAAGAAAAAAAAG
1 AAAAGAAAGAAAAGAAAAAAAAG
252192 AAAA
1 AAAA
252196 AGATTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 5 0.21
25 12 0.50
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGAAAAGAAAAAAAAG
Found at i:252207 original size:26 final size:26
Alignment explanation
Indices: 252151--252214 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
252141 GCAAAAAGAA
*
252151 AGAAAAG-ACAAAAAGAAGAAAATTC
1 AGAAAAGAAAAAAAAGAAGAAAATTC
252176 AGAAAAGAAAAAAAAGAA-AAAGATTTC
1 AGAAAAGAAAAAAAAGAAGAAA-A-TTC
*
252203 A-AAAAGAGAAAA
1 AGAAAAGAAAAAA
252215 GCAAGCCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 10 0.29
26 20 0.59
27 4 0.12
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.08
Consensus pattern (26 bp):
AGAAAAGAAAAAAAAGAAGAAAATTC
Found at i:253760 original size:15 final size:17
Alignment explanation
Indices: 253735--253768 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
253725 TAAAGGTCCT
253735 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
253751 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
253767 AA
1 AA
253769 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:253857 original size:25 final size:22
Alignment explanation
Indices: 253828--253873 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
253818 TTTTTAACCC
253828 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
253853 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
253874 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:257657 original size:10 final size:10
Alignment explanation
Indices: 257637--257701 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
257627 TTTTTTAAAA
257637 TTTTGGC-TT
1 TTTTGGCTTT
257646 TTTTGGCTTT
1 TTTTGGCTTT
*
257656 TTTTGCCTTTTT
1 TTTTGGC--TTT
*
257668 TTTTGCCTTT
1 TTTTGGCTTT
**
257678 TTTTGTTTTT
1 TTTTGGCTTT
*
257688 TTTTTG-TTT
1 TTTTGGCTTT
257697 TTTTG
1 TTTTG
257702 AAAAAAATAG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
9 14 0.30
10 23 0.49
12 10 0.21
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:257668 original size:12 final size:12
Alignment explanation
Indices: 257653--257681 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
257643 CTTTTTTGGC
257653 TTTTTTTGCCTT
1 TTTTTTTGCCTT
257665 TTTTTTTGCCTT
1 TTTTTTTGCCTT
257677 TTTTT
1 TTTTT
257682 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:257689 original size:11 final size:11
Alignment explanation
Indices: 257653--257700 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
257643 CTTTTTTGGC
*
257653 TTTTTTTGCCTT
1 TTTTTTTG-TTT
**
257665 TTTTTTTG-CC
1 TTTTTTTGTTT
257675 TTTTTTTGTTT
1 TTTTTTTGTTT
257686 TTTTTTTGTTT
1 TTTTTTTGTTT
257697 TTTT
1 TTTT
257701 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 8 0.26
11 15 0.48
12 8 0.26
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:258479 original size:15 final size:17
Alignment explanation
Indices: 258454--258487 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
258444 TAAAGGTCCT
258454 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
258470 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
258486 AA
1 AA
258488 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:258576 original size:25 final size:22
Alignment explanation
Indices: 258547--258592 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
258537 TTTTTAACCC
258547 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
258572 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
258593 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:268120 original size:19 final size:20
Alignment explanation
Indices: 268096--268146 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
268086 TGGCCAGGAG
* *
268096 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
268115 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
268135 CATGTATTTTCA
1 CATGTATTTTCA
268147 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:268923 original size:23 final size:23
Alignment explanation
Indices: 268893--268937 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
268883 TTTCTTCCTT
268893 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
* *
268916 TTTTGAGTGCTTTGATTTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
268938 TGCTGGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.13, G:0.16, T:0.60
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:273064 original size:12 final size:12
Alignment explanation
Indices: 273047--273073 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
273037 AATTAATCTG
273047 GGTATATCTTGA
1 GGTATATCTTGA
273059 GGTATATCTTGA
1 GGTATATCTTGA
273071 GGT
1 GGT
273074 CCCAATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (12 bp):
GGTATATCTTGA
Found at i:281485 original size:19 final size:21
Alignment explanation
Indices: 281442--281493 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
281432 GAAACCCCTT
281442 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
281463 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
281482 TGAAGATACATG
1 TGAAAATACATG
281494 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:284689 original size:8 final size:8
Alignment explanation
Indices: 284678--284710 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
284668 TCTTTTTCTT
*
284678 TTCTTTTA
1 TTCTTTTC
284686 TTCTTTTC
1 TTCTTTTC
284694 TTCTTTTC
1 TTCTTTTC
284702 TTCTTTTC
1 TTCTTTTC
284710 T
1 T
284711 GATTTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:284710 original size:13 final size:12
Alignment explanation
Indices: 284665--284703 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
284655 CTTTTTGAAC
284665 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
284678 TTCTTTTATTCTT
1 TTCTTTT-TTCTT
284691 TTCTTCTTTTCTT
1 TTCTT-TTTTCTT
284704 CTTTTCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 19 0.79
14 2 0.08
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:289018 original size:8 final size:8
Alignment explanation
Indices: 289007--289054 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
288997 AATTTTCTTT
289007 TTCTTTTC
1 TTCTTTTC
289015 TTCTTTTC
1 TTCTTTTC
**
289023 TGATTTTC
1 TTCTTTTC
289031 TTCTTTT-
1 TTCTTTTC
289038 TGTCTTTTC
1 T-TCTTTTC
289047 TTTCTTTT
1 -TTCTTTT
289055 TGCACTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 1 0.03
8 25 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:289043 original size:27 final size:27
Alignment explanation
Indices: 288989--289043 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
288979 GCTTGCTTTC
*
288989 TCTTTTTGAATTTTCTTTTTCTTTTCT
1 TCTTTTTGAATTTTCTTTTTCTTGTCT
289016 TCTTTTCTG-ATTTTCTTCTTT-TTGTCT
1 TCTTTT-TGAATTTTCTT-TTTCTTGTCT
289043 T
1 T
289044 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (27 bp):
TCTTTTTGAATTTTCTTTTTCTTGTCT
Found at i:289045 original size:16 final size:16
Alignment explanation
Indices: 289004--289056 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
288994 TTGAATTTTC
289004 TTTT-TCTTTTCTTCT
1 TTTTGTCTTTTCTTCT
*
289019 TTTCTG-ATTTTCTTCT
1 TTT-TGTCTTTTCTTCT
289035 TTTTGTCTTTTCTTTCT
1 TTTTGTCTTTTC-TTCT
289052 TTTTG
1 TTTTG
289057 CACTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 18 0.56
17 9 0.28
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTGTCTTTTCTTCT
Found at i:291536 original size:19 final size:21
Alignment explanation
Indices: 291493--291544 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
291483 GAAACCCCTT
291493 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
291514 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
291533 TGAAGATACATG
1 TGAAAATACATG
291545 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:292362 original size:26 final size:25
Alignment explanation
Indices: 292333--292381 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
292323 ATAATATCAG
*
292333 ATAAGTATATGAATTATTATAAAGTA
1 ATAAGAATATGAA-TATTATAAAGTA
* *
292359 ATAAGAATGTGCATATTATAAAG
1 ATAAGAATATGAATATTATAAAG
292382 GTGTGAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (25 bp):
ATAAGAATATGAATATTATAAAGTA
Found at i:295585 original size:36 final size:35
Alignment explanation
Indices: 295486--295596 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 35
295476 TTGGTGGTTA
* * * * * *
295486 TATAGGTGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
** * *
295521 TATAGGCGTGCAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
295556 TATAGGCGTAAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGT-AAAATGGTGATGGAAGATGGTGATGT
295592 T-TAGG
1 TATAGG
295597 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 40 0.63
36 23 0.37
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
Found at i:303769 original size:13 final size:12
Alignment explanation
Indices: 303741--303784 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
303731 GGCTTTTTTG
303741 TTTTTTTTTGCC
1 TTTTTTTTTGCC
*
303753 TTTTGTTTTGCC
1 TTTTTTTTTGCC
*
303765 -TTTTTTTTG-T
1 TTTTTTTTTGCC
303775 TTTTTTTTTG
1 TTTTTTTTTG
303785 AAAAAATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGCC
Found at i:307077 original size:90 final size:91
Alignment explanation
Indices: 306961--307142 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
306951 GGGAAATGAT
*
306961 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
307025 CGGGCTGTTCACATGCAAAACACATG
66 CGGGCTGGTCACATGCAAAACACATG
* * *
307051 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
* * **
307116 GGGGCTGGTCATATGCAAGGCACATG
66 CGGGCTGGTCACATGCAAAACACATG
307142 G
1 G
307143 GTGTTCTAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 60 0.73
91 22 0.27
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
CGGGCTGGTCACATGCAAAACACATG
Found at i:307927 original size:13 final size:13
Alignment explanation
Indices: 307909--307967 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
307899 ATAGGCGTGA
307909 TATGGTGATGGAT
1 TATGGTGATGGAT
307922 TATGGTGAT-GA-
1 TATGGTGATGGAT
307933 TATAGGTG-T-GAT
1 TAT-GGTGATGGAT
* *
307945 AATGGTGATGGAA
1 TATGGTGATGGAT
307958 TATGGTGATG
1 TATGGTGATG
307968 ATATAGGCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.26
12 9 0.23
13 20 0.51
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.36
Consensus pattern (13 bp):
TATGGTGATGGAT
Found at i:307951 original size:11 final size:11
Alignment explanation
Indices: 307906--307990 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
307896 AATATAGGCG
307906 TGATATGGTGA
1 TGATATGGTGA
307917 TGGATTATGGTGA
1 T-GA-TATGGTGA
307930 TGATATAGGTG-
1 TGATAT-GGTGA
307941 TGATAATGGTGA
1 TGAT-ATGGTGA
307953 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
307966 TGATATAGGCG-
1 TGATAT-GGTGA
307977 TGATAATGGTGA
1 TGAT-ATGGTGA
307989 TG
1 TG
307991 GACAGATTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 23 0.37
12 19 0.31
13 18 0.29
14 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.36, T:0.34
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:307951 original size:23 final size:24
Alignment explanation
Indices: 307906--307992 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 24
307896 AATATAGGCG
*
307906 TGATATGGTGATGGATTATGGTGA
1 TGATATGGTGATGGATAATGGTGA
307930 TGATATAGGTG-T-GATAATGGTGA
1 TGATAT-GGTGATGGATAATGGTGA
*
307953 TGGAATATGGTGAT-GAT-ATAGGCG-
1 T-G-ATATGGTGATGGATAAT-GGTGA
307977 TGATAATGGTGATGGA
1 TGAT-ATGGTGATGGA
307993 CAGATTGTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.04
23 20 0.37
24 17 0.31
25 15 0.28
ACGTcount: A:0.29, C:0.01, G:0.37, T:0.33
Consensus pattern (24 bp):
TGATATGGTGATGGATAATGGTGA
Found at i:307962 original size:36 final size:36
Alignment explanation
Indices: 307891--307992 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
307881 TAACATAGGC
* *
307891 GTGATAATATAGGCGTGAT-ATGGTGATGGATTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
*
307926 GTGATGATATAGGTGTGATAATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATG
307962 GTGATGATATAGGCGTGATAATGGTGATGGA
1 GTGATGATATAGGCGTGATAATGGTGATGGA
307993 CAGATTGTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.27
36 45 0.73
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGAATATG
Found at i:312630 original size:29 final size:30
Alignment explanation
Indices: 312584--312643 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
312574 GATGATCTTG
*
312584 ATGAAGGATGTTGATGATGTTG-ATACTGAA
1 ATGAAGGATGGTGATGATGTTGTAT-CTGAA
*
312614 ATGAA-GATGGTGGTGATGTTGTATCTGAA
1 ATGAAGGATGGTGATGATGTTGTATCTGAA
312643 A
1 A
312644 CTCTCCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (30 bp):
ATGAAGGATGGTGATGATGTTGTATCTGAA
Found at i:316014 original size:17 final size:18
Alignment explanation
Indices: 315982--316016 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
315972 GGTTAGGGTA
*
315982 GAAAGAATATAAGAAATG
1 GAAAGAATAGAAGAAATG
316000 GAAAG-ATAGAAGAAATG
1 GAAAGAATAGAAGAAATG
316017 ATTTAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (18 bp):
GAAAGAATAGAAGAAATG
Found at i:316642 original size:20 final size:21
Alignment explanation
Indices: 316605--316643 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
316595 GATGGTCTTG
*
316605 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
316626 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
316644 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:319167 original size:15 final size:15
Alignment explanation
Indices: 319147--319182 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
319137 ATGAGTAATT
319147 AAGAATGGAAATGGA
1 AAGAATGGAAATGGA
*
319162 AAGAATTGAAATGGA
1 AAGAATGGAAATGGA
*
319177 TAGAAT
1 AAGAAT
319183 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (15 bp):
AAGAATGGAAATGGA
Found at i:319371 original size:35 final size:36
Alignment explanation
Indices: 319324--319393 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
319314 ATTTAGAAGT
*
319324 TGGTGATAATATAGGCGTGAT-ATGGTGATGGACAA
1 TGGTGATAATATAGGCATGATAATGGTGATGGACAA
*
319359 TGGTGATGATATAGGCATGATAATGGTGATGGACA
1 TGGTGATAATATAGGCATGATAATGGTGATGGACA
319394 GATTGTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGGCATGATAATGGTGATGGACAA
Found at i:320595 original size:18 final size:17
Alignment explanation
Indices: 320561--320599 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
320551 TAGGAGTATT
320561 TTTTCTTTTCTTTTTGC
1 TTTTCTTTTCTTTTTGC
320578 TTTTCTTCTT-TTTGTTGC
1 TTTTCTT-TTCTTT-TTGC
320596 TTTT
1 TTTT
320600 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTGC
Found at i:324890 original size:13 final size:13
Alignment explanation
Indices: 324872--324898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
324862 AAACACCTTT
324872 AACATACCTTTTC
1 AACATACCTTTTC
324885 AACATACCTTTTC
1 AACATACCTTTTC
324898 A
1 A
324899 TCTTTGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (13 bp):
AACATACCTTTTC
Found at i:328484 original size:19 final size:20
Alignment explanation
Indices: 328429--328486 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
328419 ATAATGGGTT
*
328429 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
328448 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
328468 TAAG-AAT-AAAATGAAATAA
1 TAAGTAATGAAAAT-AAATAA
328487 ATAAAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 8 0.23
19 22 0.63
20 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:332069 original size:35 final size:37
Alignment explanation
Indices: 332023--332102 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
332013 TTTGAGAATT
*
332023 TGGTGATGATATAGGCGTGAT-ATGG-TGATGAACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
* *
332058 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
332095 TGGTGATG
1 TGGTGATG
332103 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
Found at i:337685 original size:35 final size:37
Alignment explanation
Indices: 337639--337718 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
337629 TTTGAGAATT
* * *
337639 TGGTGATGATATATGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
337674 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
337711 TGGTGATG
1 TGGTGATG
337719 GAAATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.34
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:342890 original size:2 final size:2
Alignment explanation
Indices: 342879--342950 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
342869 TAACTATAGG
342879 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
342920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
342951 GAAAATAACT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:345876 original size:11 final size:11
Alignment explanation
Indices: 345862--345917 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
345852 CTCTTTTGAA
345862 TTTCTTTTTCT
1 TTTCTTTTTCT
345873 TTTCTTTTTTTCT
1 TTTC--TTTTTCT
*
345886 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
345898 TGTCTTTTTCT
1 TTTCTTTTTCT
345909 TTTCTTTTT
1 TTTCTTTTT
345918 GCACTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.08
11 17 0.47
12 3 0.08
13 10 0.28
14 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:346287 original size:20 final size:21
Alignment explanation
Indices: 346250--346288 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
346240 GATGGTCTTG
*
346250 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
346271 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
346289 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:350092 original size:19 final size:20
Alignment explanation
Indices: 350045--350095 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
350035 GAAACCCCTT
**
350045 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
350065 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
350084 TGAAGATACATG
1 TGAAAATACATG
350096 CTCTTGGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:370772 original size:21 final size:20
Alignment explanation
Indices: 370738--370800 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
370728 TTTCAAAACC
*
370738 AAAAAA-AATAAAAAATGCA
1 AAAAAACAAAAAAAAATGCA
*
370757 AAAAAACAAAACAAAAAAGCCA
1 AAAAAACAAAA-AAAAATG-CA
***
370779 AAATTTCAAAAAAAAATGCA
1 AAAAAACAAAAAAAAATGCA
370799 AA
1 AA
370801 CGAAGGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.17
20 7 0.20
21 12 0.34
22 10 0.29
ACGTcount: A:0.75, C:0.11, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAAACAAAAAAAAATGCA
Done.