Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004658.1 Hibiscus syriacus cultivar Beakdansim tig00010442_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: 100047
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6633 original size:34 final size:34
Alignment explanation
Indices: 6595--6752 Score: 110
Period size: 40 Copynumber: 4.5 Consensus size: 34
6585 TATATATAAG
* **
6595 ATATATATATAGTTTTTTTTTAA-ATTTGGAAACC
1 ATATATATATA-TATTTTTGAAATATTTGGAAACC
* *
6629 ATATATATATATATTTTTGAAATATTTTGAAAGC
1 ATATATATATATATTTTTGAAATATTTGGAAACC
* **
6663 ATATATAATATATAGTTTTTGAAAATATTTTTGAAAAAAT
1 ATATAT-ATATATA-TTTTTG-AAATA--TTTG-GAAACC
*
6703 ATATATAATATATAGTTTTTGTAAATATTTTG--A--
1 ATATAT-ATATATA-TTTTTG-AAATATTTGGAAACC
6736 ATATATATATATATTTT
1 ATATATATATATATTTT
6753 ATTTTATATA
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
31 4 0.04
32 7 0.07
33 14 0.13
34 26 0.25
35 8 0.08
36 6 0.06
37 5 0.05
38 3 0.03
39 3 0.03
40 29 0.28
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (34 bp):
ATATATATATATATTTTTGAAATATTTGGAAACC
Found at i:6635 original size:36 final size:37
Alignment explanation
Indices: 6595--6749 Score: 103
Period size: 36 Copynumber: 4.3 Consensus size: 37
6585 TATATATAAG
**
6595 ATATATATATAGTTTTTTTTTAA-ATTTGGAAACCAT
1 ATATATATATAGTTTTTTTGAAATATTTGGAAACCAT
* *
6631 ATATATATATA---TTTTTGAAATATTTTGAAAGCAT
1 ATATATATATAGTTTTTTTGAAATATTTGGAAACCAT
* **
6665 ATATAATATATAG--TTTTTGAAAATATTTTTGAAAAAAT
1 ATAT-ATATATAGTTTTTTTG-AAATA-TTTGGAAACCAT
* * *
6703 ATATATAATATA-TAGTTTTTGTAAATATTTTG-AA-TAT
1 ATATAT-ATATAGT-TTTTTTG-AAATATTTGGAAACCAT
6740 ATATATATAT
1 ATATATATAT
6750 TTTATTTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
33 7 0.07
34 15 0.15
35 7 0.07
36 21 0.21
37 15 0.15
38 21 0.21
39 5 0.05
40 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (37 bp):
ATATATATATAGTTTTTTTGAAATATTTGGAAACCAT
Found at i:6718 original size:40 final size:38
Alignment explanation
Indices: 6629--6748 Score: 149
Period size: 40 Copynumber: 3.2 Consensus size: 38
6619 TTTGGAAACC
**
6629 ATATAT-ATATATA-TTTTTGAAATATTTTG--AAAGC
1 ATATATAATATATAGTTTTTGAAATATTTTGAAAAAAT
6663 ATATATAATATATAGTTTTTGAAAATATTTTTGAAAAAAT
1 ATATATAATATATAGTTTTTG-AAATA-TTTTGAAAAAAT
* *
6703 ATATATAATATATAGTTTTTGTAAATATTTTGAATATAT
1 ATATATAATATATAGTTTTTG-AAATATTTTGAAAAAAT
6742 ATATATA
1 ATATATA
6749 TTTTATTTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 6 0.08
35 7 0.09
36 6 0.08
37 5 0.07
38 5 0.07
39 17 0.23
40 29 0.39
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTGAAATATTTTGAAAAAAT
Found at i:6776 original size:22 final size:22
Alignment explanation
Indices: 6736--6777 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6726 AATATTTTGA
*
6736 ATATATATATATATTTTATTTT
1 ATATATATATATATGTTATTTT
6758 ATATATATA-ATATAGTTATT
1 ATATATATATATAT-GTTATT
6778 GAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATATATATATGTTATTTT
Found at i:6807 original size:36 final size:36
Alignment explanation
Indices: 6757--6840 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
6747 TATTTTATTT
* *
6757 TATATATATAATATAGTTATTG-AAATATTTTGAAAA
1 TATATATATAATATAATT-TTGAAAACATTTTGAAAA
6793 TATATATA-ATATATAATTTTGAAAACATTTTGAAAA
1 TATATATATA-ATATAATTTTGAAAACATTTTGAAAA
6829 TATATTATATAA
1 TATA-TATATAA
6841 AATATTTATG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 4 0.10
36 32 0.76
37 5 0.12
38 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATATATAATATAATTTTGAAAACATTTTGAAAA
Found at i:6812 original size:55 final size:57
Alignment explanation
Indices: 6701--6812 Score: 158
Period size: 55 Copynumber: 2.0 Consensus size: 57
6691 TTTTGAAAAA
* * * *
6701 ATATATATAATATATAGTTTTTGTAAATATTTTGAATATATATATATATTTTATTTT
1 ATATATATAATATATAGTTATTGTAAATATTTTGAAAATATATATATATATAATTTT
6758 ATATATAT-A-ATATAGTTATTG-AAATATTTTGAAAATATATATAATATATAATTTT
1 ATATATATAATATATAGTTATTGTAAATATTTTGAAAATATATAT-ATATATAATTTT
6813 GAAAACATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 20 0.40
55 21 0.42
56 1 0.02
57 8 0.16
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (57 bp):
ATATATATAATATATAGTTATTGTAAATATTTTGAAAATATATATATATATAATTTT
Found at i:6890 original size:14 final size:14
Alignment explanation
Indices: 6868--6930 Score: 83
Period size: 14 Copynumber: 4.4 Consensus size: 14
6858 TTATATTATA
6868 TATTATTATTTATTT
1 TATT-TTATTTATTT
*
6883 TCTTTTATTTATTT
1 TATTTTATTTATTT
6897 TATTTTATTTTATTT
1 TATTTTA-TTTATTT
*
6912 TATTTTCTTT-TTT
1 TATTTTATTTATTT
6925 TATTTT
1 TATTTT
6931 GGTCCAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
13 9 0.20
14 19 0.43
15 16 0.36
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:6898 original size:5 final size:5
Alignment explanation
Indices: 6876--6930 Score: 71
Period size: 5 Copynumber: 11.6 Consensus size: 5
6866 TATATTATTA
* *
6876 TTTAT TTTCT TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT-C TTT-T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
6923 TTTAT TTT
1 TTTAT TTT
6931 GGTCCAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
4 10 0.23
5 34 0.77
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:6912 original size:24 final size:24
Alignment explanation
Indices: 6853--6930 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
6843 TATTTATGTA
* * *
6853 TTATATTATATTATATATTATTA-T
1 TTATTTTATTTTATTTATT-TTATT
*
6877 TTATTTTCTTTTATTTATTTTATT
1 TTATTTTATTTTATTTATTTTATT
6901 TTATTTTATTTTATTT-TCTTT-TT
1 TTATTTTATTTTATTTAT-TTTATT
6924 TTATTTT
1 TTATTTT
6931 GGTCCAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.28
24 34 0.72
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (24 bp):
TTATTTTATTTTATTTATTTTATT
Found at i:8100 original size:15 final size:16
Alignment explanation
Indices: 8082--8115 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
8072 TTTATTTTCC
8082 TTTATTTTTTT-ATTT
1 TTTATTTTTTTCATTT
8097 TTTATTTTTTTCATTT
1 TTTATTTTTTTCATTT
8113 TTT
1 TTT
8116 TTCTTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTATTTTTTTCATTT
Found at i:8114 original size:9 final size:8
Alignment explanation
Indices: 8066--8116 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 8
8056 CATTTTATTG
8066 ATTTATTTT
1 ATTT-TTTT
8075 ATTTTCCTTT
1 ATTTT--TTT
8085 ATTTTTTT
1 ATTTTTTT
8093 A-TTTTTT
1 ATTTTTTT
8100 ATTTTTTT
1 ATTTTTTT
8108 CATTTTTTT
1 -ATTTTTTT
8117 TCTTTGTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.18
8 11 0.29
9 12 0.32
10 8 0.21
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (8 bp):
ATTTTTTT
Found at i:8206 original size:15 final size:16
Alignment explanation
Indices: 8186--8223 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
8176 TGTTTTATTT
8186 TTTTATTTA-ATTA-A
1 TTTTATTTACATTATA
8200 CTTTTATTTACATTATA
1 -TTTTATTTACATTATA
8217 TTTTATT
1 TTTTATT
8224 ACTTTGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 11 0.52
17 1 0.05
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATTTACATTATA
Found at i:17086 original size:34 final size:35
Alignment explanation
Indices: 17018--17087 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
17008 TCTTTTTTCA
17018 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
1 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
* * *
17053 TTTCTTTTGAATTCAATTTT-TTTCATTCTATACT
1 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
17087 T
1 T
17088 CGTTTTATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
Found at i:22248 original size:39 final size:39
Alignment explanation
Indices: 22118--22355 Score: 246
Period size: 39 Copynumber: 5.9 Consensus size: 39
22108 TATATATAAG
* *
22118 ATATAATATATAGTTTTTTTATAAA-ATTTTGAAAACATAT
1 ATATAATATATAG-TTTTTGA-AAATATTTTGAAAAAATAT
* ** *
22158 ATATAATATATAGTTTTTTTTCAAAACGTTTTGAAAACATAT
1 ATATAATATATAG---TTTTTGAAAATATTTTGAAAAAATAT
22200 ATATAATATATAGTTTTT-AAAATATTTTGAAAAAATATAT
1 ATATAATATATAGTTTTTGAAAATATTTTG-AAAAA-ATAT
22240 ATATATATAATATATTGTTTTTGAAAATATTTTGAAAAAATAT
1 ATATA-AT-ATATA--GTTTTTGAAAATATTTTGAAAAAATAT
* * * *
22283 ATATAATATATGGTTTTTGAAAACATTTTGGAAATATAT
1 ATATAATATATAGTTTTTGAAAATATTTTGAAAAAATAT
* * *
22322 ATATAATATATAATCTTTGAAAATATTTTTAAAA
1 ATATAATATATAGTTTTTGAAAATATTTTGAAAA
22356 CATTTTGAAA
Statistics
Matches: 173, Mismatches: 15, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
38 9 0.05
39 61 0.35
40 22 0.13
41 9 0.05
42 41 0.24
43 9 0.05
44 11 0.06
45 11 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
ATATAATATATAGTTTTTGAAAATATTTTGAAAAAATAT
Found at i:22430 original size:12 final size:12
Alignment explanation
Indices: 22396--22454 Score: 73
Period size: 12 Copynumber: 4.5 Consensus size: 12
22386 TTATGTAATA
22396 TATTTTATTATT
1 TATTTTATTATT
22408 TACTATATTATTATT
1 TA-T-T-TTATTATT
22423 TATTTTATTATT
1 TATTTTATTATT
22435 TATTTTATTTTATT
1 TATTTTA--TTATT
22449 TATTTT
1 TATTTT
22455 TCTTTTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
12 17 0.40
13 2 0.05
14 13 0.31
15 10 0.24
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:22455 original size:27 final size:27
Alignment explanation
Indices: 22396--22454 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
22386 TTATGTAATA
22396 TATTTTATTATTTACTATATTATTATT
1 TATTTTATTATTTACTATATTATTATT
* *
22423 TATTTTATTATTTATTTTATT-TTATT
1 TATTTTATTATTTACTATATTATTATT
22449 TATTTT
1 TATTTT
22455 TCTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (27 bp):
TATTTTATTATTTACTATATTATTATT
Found at i:22470 original size:15 final size:15
Alignment explanation
Indices: 22413--22471 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
22403 TTATTTACTA
22413 TATTATTATTTA-TTT
1 TATT-TTATTTATTTT
22428 TA--TTATTTA-TTT
1 TATTTTATTTATTTT
22440 TATTTTATTTATTTT
1 TATTTTATTTATTTT
* * *
22455 TCTTTTCTTTTTTTT
1 TATTTTATTTATTTT
22470 TA
1 TA
22472 ATTTGGTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 12 0.32
14 7 0.19
15 18 0.49
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTATTTATTTT
Found at i:34039 original size:24 final size:24
Alignment explanation
Indices: 34012--34059 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34002 GAGTTTCGCA
*
34012 TTTTCT-GTTATATTTTTAAGATGC
1 TTTTCTGGTTAT-TTTGTAAGATGC
*
34036 TTTTTTGGTTATTTTGTAAGATGC
1 TTTTCTGGTTATTTTGTAAGATGC
34060 ATGCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (24 bp):
TTTTCTGGTTATTTTGTAAGATGC
Found at i:34901 original size:26 final size:26
Alignment explanation
Indices: 34865--34918 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
34855 AATGAATTCC
*
34865 TGGGGGGGGGGGAGTTCTAACTAAAA
1 TGGGGGGGGGGGAATTCTAACTAAAA
34891 TGGGGGGGGGGGAATTCTAACTAAAA
1 TGGGGGGGGGGGAATTCTAACTAAAA
34917 TG
1 TG
34919 AACCTACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.44, T:0.20
Consensus pattern (26 bp):
TGGGGGGGGGGGAATTCTAACTAAAA
Found at i:38953 original size:32 final size:33
Alignment explanation
Indices: 38902--38963 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
38892 GAATGCTGTA
* * *
38902 ATATTTTTGTTGATCTTTCTTGTCTATGAATGT
1 ATATCTTTCTTGATCTTTCTTGTCCATGAATGT
38935 ATATCTTTCTTGAT-TTTCTTGTCCATGAA
1 ATATCTTTCTTGATCTTTCTTGTCCATGAA
38964 ACAACTACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (33 bp):
ATATCTTTCTTGATCTTTCTTGTCCATGAATGT
Found at i:39907 original size:10 final size:10
Alignment explanation
Indices: 39892--39920 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
39882 TGGAGCTTTC
39892 CTTTTTTTTT
1 CTTTTTTTTT
39902 CTTTTTTTTT
1 CTTTTTTTTT
39912 -TTTTTTTTT
1 CTTTTTTTTT
39921 GCATGCATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:39907 original size:11 final size:11
Alignment explanation
Indices: 39888--39920 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
39878 AAAATGGAGC
*
39888 TTTCCTTTTTT
1 TTTCTTTTTTT
39899 TTTCTTTTTTT
1 TTTCTTTTTTT
39910 TTT-TTTTTTT
1 TTTCTTTTTTT
39920 T
1 T
39921 GCATGCATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:43284 original size:33 final size:32
Alignment explanation
Indices: 43174--43321 Score: 145
Period size: 32 Copynumber: 4.6 Consensus size: 32
43164 AAAAAATTAA
* * *
43174 GTACTAAAATGGAACAAAAAGTTAATAATGGG
1 GTACTAAAATGAAATAAAAAGTTAACAATGGG
* * * ** **
43206 ATACTAAAATAAAATAAAAAGTAAACTTTTAG
1 GTACTAAAATGAAATAAAAAGTTAACAATGGG
43238 GTACTAAAATGAAATAAAAAGTTAACAATGGGG
1 GTACTAAAATGAAATAAAAAGTTAACAAT-GGG
* * * **
43271 GTAATAAAATGAAATAAAAAGTAAAC-GTCAG
1 GTACTAAAATGAAATAAAAAGTTAACAATGGG
43302 GTACTAAAATGAAATAAAAA
1 GTACTAAAATGAAATAAAAA
43322 AGTAAACTCT
Statistics
Matches: 92, Mismatches: 23, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
31 20 0.22
32 47 0.51
33 25 0.27
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (32 bp):
GTACTAAAATGAAATAAAAAGTTAACAATGGG
Found at i:43304 original size:64 final size:64
Alignment explanation
Indices: 43174--43321 Score: 208
Period size: 64 Copynumber: 2.3 Consensus size: 64
43164 AAAAAATTAA
* * * * * *
43174 GTACTAAAATGGAACAAAAAGTTAATAATGGGATACTAAAATAAAATAAAAAGTAAACTTTTAG
1 GTACTAAAATGAAATAAAAAGTTAACAATGGGATAATAAAATAAAATAAAAAGTAAACTGTCAG
* *
43238 GTACTAAAATGAAATAAAAAGTTAACAATGGGGGTAATAAAATGAAATAAAAAGTAAAC-GTCAG
1 GTACTAAAATGAAATAAAAAGTTAACAAT-GGGATAATAAAATAAAATAAAAAGTAAACTGTCAG
43302 GTACTAAAATGAAATAAAAA
1 GTACTAAAATGAAATAAAAA
43322 AGTAAACTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
64 49 0.65
65 26 0.35
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (64 bp):
GTACTAAAATGAAATAAAAAGTTAACAATGGGATAATAAAATAAAATAAAAAGTAAACTGTCAG
Found at i:57433 original size:3 final size:3
Alignment explanation
Indices: 57421--57473 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
57411 AGCTCTAAGT
57421 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
57468 TTC TTC
1 TTC TTC
57474 CTCCTCCTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:58092 original size:2 final size:2
Alignment explanation
Indices: 58085--58121 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
58075 ACATGCAAAC
58085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58122 GTTGTTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62694 original size:5 final size:5
Alignment explanation
Indices: 62686--62720 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
62676 ATTAGATTAA
62686 ATATT ATATT ATATT ATATT AT-TAT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT
62721 TGTTTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.04
5 26 0.93
6 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:63576 original size:18 final size:18
Alignment explanation
Indices: 63550--63592 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
63540 CTTTATATTA
*
63550 TTTAATTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
63568 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
63586 TTTATTT
1 TTTATTT
63593 TAAAAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:67328 original size:34 final size:34
Alignment explanation
Indices: 67285--67369 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
67275 TATGATTGAT
67285 CTCTCGGCGTCTTCAGTTGGACTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGACTCTTCATAGGAA
* *
67319 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGACTCTTCATAGGAA
*
67353 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
67370 GCTGTGCATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGACTCTTCATAGGAA
Found at i:67444 original size:22 final size:22
Alignment explanation
Indices: 67391--67444 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
67381 GACTGGACGT
*
67391 GAGAAATCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
**
67413 GAGAGTGCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
67435 GAGAAAGCAC
1 GAGAAAGCAC
67445 AGAAATCACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.35, T:0.15
Consensus pattern (22 bp):
GAGAAAGCACGGGTTCTGCAAG
Found at i:67500 original size:23 final size:23
Alignment explanation
Indices: 67474--67517 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
67464 TCCTGCAGGG
*
67474 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGACTGCATGTGGGGGTC
67497 CTGCACGACTGCATGTGGGGG
1 CTGCACGACTGCATGTGGGGG
67518 GCATGCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.25, G:0.41, T:0.23
Consensus pattern (23 bp):
CTGCACGACTGCATGTGGGGGTC
Found at i:67524 original size:23 final size:22
Alignment explanation
Indices: 67471--67524 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
67461 GGGTCCTGCA
*
67471 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGACTGCATGTGGG
*
67493 GGTCCTGCACGACTGCATGTGGG
1 GG-GCTGCACGACTGCATGTGGG
67516 GGGCATGCA
1 GGGC-TGCA
67525 ACTGTTGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.13, C:0.24, G:0.43, T:0.20
Consensus pattern (22 bp):
GGGCTGCACGACTGCATGTGGG
Found at i:70585 original size:42 final size:42
Alignment explanation
Indices: 70536--70929 Score: 279
Period size: 37 Copynumber: 9.7 Consensus size: 42
70526 ATATATTTAC
* *
70536 TATTATTATATCAGT-AAATATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAAT-TAAATCATTAAAGTCAAGTAAT
* *
70578 TATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
*
70620 TATTATTAAATTATTAAAATTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
* * *
70657 TATTATTAAATCATT-AAAGTAATTATTATTAAAGT-TA--AAT
1 TATTATTAAATCATTAAAATTAA--ATCATTAAAGTCAAGTAAT
* * *
70697 TATTATTAAAGCATTAAATCATTAAATCATTAAAAT-AATTATTAT
1 TATTATTAAATCATTAAA--ATTAAATCATTAAAGTCAAGTA--AT
* * * *
70742 TAAATCATTAAATCATT-AAAGTAATTATTATTAAA-TC-ATTAAAGT
1 T--ATTATTAAATCATTAAAATTAA--ATCATTAAAGTCAAGT-AA-T
*
70787 TAAATCATTAAATCATTAAAATTAAATCATT--A---AAGTAAT
1 T--ATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
70826 TATTATTAAATCATTAAAATTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
*
70863 TATTATTAAATCATTAAAGTTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
* *
70900 TATTATTAAATCATTAAAGTTAAATAATTA
1 TATTATTAAATCATTAAAATTAAATCATTA
70930 TTATTAAATC
Statistics
Matches: 304, Mismatches: 24, Indels: 52
0.80 0.06 0.14
Matches are distributed among these distances:
36 6 0.02
37 120 0.39
38 5 0.02
39 2 0.01
40 21 0.07
41 14 0.05
42 63 0.21
43 9 0.03
44 10 0.03
45 25 0.08
46 17 0.06
47 12 0.04
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (42 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
Found at i:70593 original size:14 final size:14
Alignment explanation
Indices: 70576--70980 Score: 109
Period size: 14 Copynumber: 28.9 Consensus size: 14
70566 AAGTCAAGTA
70576 ATTATTATTAAATC
1 ATTATTATTAAATC
**
70590 ATTAAAATTAAATC
1 ATTATTATTAAATC
** * *
70604 ATTAAAATTAAGTA
1 ATTATTATTAAATC
*
70618 ATTATTATTAAATT
1 ATTATTATTAAATC
**
70632 ATTAAAATTAAATC
1 ATTATTATTAAATC
* * *
70646 ATTA-AAGTAATTATT
1 ATTATTATTAA--ATC
* *
70661 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
*
70678 ATTATTATTAAAGTTAA
1 ATTATTATTAAA--T-C
*
70695 ATTATTATTAAAGC
1 ATTATTATTAAATC
*
70709 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
*
70725 ---ATTA--AAATA
1 ATTATTATTAAATC
70734 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
70748 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
70765 ATTATTATTAAATC
1 ATTATTATTAAATC
*
70779 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
*
70793 ATTAAATCATTAAA--
1 ATT--ATTATTAAATC
* *
70807 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
70824 ATTATTATTAAATC
1 ATTATTATTAAATC
**
70838 ATTAAAATTAAATC
1 ATTATTATTAAATC
* *
70852 ---ATTA--AAGTA
1 ATTATTATTAAATC
70861 ATTATTATTAAATC
1 ATTATTATTAAATC
*
70875 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
70889 ---ATTA--AAGTA
1 ATTATTATTAAATC
70898 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
70912 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
70926 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
70940 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
* *
70954 ATTA-AATTTAAATA
1 ATTATTA-TTAAATC
70968 ATTATTATTAAAT
1 ATTATTATTAAAT
70981 ATGTACTCGA
Statistics
Matches: 295, Mismatches: 55, Indels: 82
0.68 0.13 0.19
Matches are distributed among these distances:
9 10 0.03
11 6 0.02
12 13 0.04
13 9 0.03
14 171 0.58
15 31 0.11
16 25 0.08
17 26 0.09
18 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:70641 original size:9 final size:8
Alignment explanation
Indices: 70579--70980 Score: 98
Period size: 8 Copynumber: 52.2 Consensus size: 8
70569 TCAAGTAATT
70579 ATTATTAA
1 ATTATTAA
*
70587 ATCATTAA
1 ATTATTAA
70595 A--ATTAA
1 ATTATTAA
*
70601 ATCATTAAA
1 ATTATT-AA
*
70610 ATTAAGTAA
1 ATT-ATTAA
70619 TTATTATTAA
1 --ATTATTAA
70629 ATTATTAA
1 ATTATTAA
70637 A--ATTAA
1 ATTATTAA
*
70643 ATCATTAA
1 ATTATTAA
*
70651 AGTAATT--
1 A-TTATTAA
70658 ATTATTAA
1 ATTATTAA
*
70666 ATCATTAA
1 ATTATTAA
*
70674 AGTAATT--
1 A-TTATTAA
70681 ATTATTAA
1 ATTATTAA
70689 AGTTA--AA
1 A-TTATTAA
70696 TTATTATTAA
1 --ATTATTAA
**
70706 AGCATTAA
1 ATTATTAA
*
70714 ATCATTAA
1 ATTATTAA
*
70722 ATCATTAAA
1 ATTATT-AA
*
70731 ATAATT--
1 ATTATTAA
70737 ATTATTAA
1 ATTATTAA
*
70745 ATCATTAA
1 ATTATTAA
*
70753 ATCATTAA
1 ATTATTAA
*
70761 AGTAATT--
1 A-TTATTAA
70768 ATTATTAA
1 ATTATTAA
*
70776 ATCATTAA
1 ATTATTAA
*
70784 A--GTTAA
1 ATTATTAA
*
70790 ATCATTAA
1 ATTATTAA
*
70798 ATCATTAA
1 ATTATTAA
70806 A--ATTAA
1 ATTATTAA
*
70812 ATCATTAA
1 ATTATTAA
*
70820 AGTAATT--
1 A-TTATTAA
70827 ATTATTAA
1 ATTATTAA
*
70835 ATCATTAA
1 ATTATTAA
70843 A--ATTAA
1 ATTATTAA
*
70849 ATCATTAA
1 ATTATTAA
*
70857 AGTAATT--
1 A-TTATTAA
70864 ATTATTAA
1 ATTATTAA
*
70872 ATCATTAA
1 ATTATTAA
*
70880 A--GTTAA
1 ATTATTAA
*
70886 ATCATTAA
1 ATTATTAA
*
70894 AGTAATT--
1 A-TTATTAA
70901 ATTATTAA
1 ATTATTAA
*
70909 ATCATTAA
1 ATTATTAA
*
70917 AGTTAAATAA
1 A-TT-ATTAA
70927 TTATTATTAA
1 --ATTATTAA
*
70937 ATCATTAA
1 ATTATTAA
*
70945 A--GTTAA
1 ATTATTAA
*
70951 ATAATTAA
1 ATTATTAA
70959 A-T-TTAA
1 ATTATTAA
*
70965 ATAATT--
1 ATTATTAA
70971 ATTATTAA
1 ATTATTAA
70979 AT
1 AT
70981 ATGTACTCGA
Statistics
Matches: 302, Mismatches: 40, Indels: 104
0.68 0.09 0.23
Matches are distributed among these distances:
6 78 0.26
7 8 0.03
8 152 0.50
9 42 0.14
10 16 0.05
11 5 0.02
12 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (8 bp):
ATTATTAA
Found at i:70664 original size:23 final size:23
Alignment explanation
Indices: 70638--70980 Score: 153
Period size: 23 Copynumber: 15.3 Consensus size: 23
70628 AATTATTAAA
70638 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
70661 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
*
70684 ATTAAA--GTT--A--AATTATT
1 ATTAAATCATTAAAGTAATTATT
* * *
70701 ATTAAAGCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
* * * *
70725 ATTAAAATAATTATTATTAA--ATC
1 ATT-AAATCATTA-AAGTAATTATT
70748 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
*
70771 ATTAAATCATTAAAGTTAA--ATC
1 ATTAAATCATTAAAG-TAATTATT
* *
70793 ATTAAATCATTAAAATTAA--ATC
1 ATTAAATCATT-AAAGTAATTATT
* * * *
70815 ATTAAAGTAATTATTATTAA--ATC
1 ATTAAA-TCATTA-AAGTAATTATT
* *
70838 ATTAAA--ATTAAA-TCATTA-A
1 ATTAAATCATTAAAGTAATTATT
* * * *
70857 AGTAATTATTATTAAA-TCATTA-A
1 ATTAA--ATCATTAAAGTAATTATT
70880 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
70904 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
*
70932 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
70954 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
70974 ATTAAAT
1 ATTAAAT
70981 ATGTACTCGA
Statistics
Matches: 261, Mismatches: 27, Indels: 67
0.74 0.08 0.19
Matches are distributed among these distances:
17 13 0.05
18 5 0.02
19 8 0.03
20 19 0.07
21 8 0.03
22 54 0.21
23 106 0.41
24 15 0.06
25 7 0.03
26 1 0.00
27 2 0.01
28 23 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:70820 original size:59 final size:60
Alignment explanation
Indices: 70748--70947 Score: 235
Period size: 59 Copynumber: 3.3 Consensus size: 60
70738 TTATTAAATC
* *
70748 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAA
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTAAA
**
70807 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTAAA
* * ** *
70867 ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 ATTAAATCATTAAAG-TAATTATTATTAAA-TCATTAAAATTAAATCATTAAAG-TAATTAA--A
70930 TTATTAAATCATTAAAGT
1 --ATTAAATCATTAAAGT
70948 TAAATAATTA
Statistics
Matches: 122, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
59 58 0.48
60 40 0.33
61 8 0.07
64 1 0.01
65 15 0.12
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (60 bp):
ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTAAA
Found at i:70923 original size:74 final size:73
Alignment explanation
Indices: 70624--70980 Score: 328
Period size: 74 Copynumber: 4.9 Consensus size: 73
70614 AGTAATTATT
* * * **
70624 ATTAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAGTAATTATTATTAA
*
70689 A--GTT-AA
65 ATCATTAAA
* * * *
70695 ATT--ATTATTAAAGCATTAAATCATTAAATCATTAAAA-TAATTATTATTAAA-TCATTAAATC
1 ATTAAATCATTAAAG--TTAAATCATTAAATCATTAAAATTAA--ATCATTAAAGTAATT--ATT
* **
70756 ATTAAAGTAATTATT
60 ATTAAA-TCATTAAA
70771 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
70836 TCATTAAA
66 TCATTAAA
* *
70844 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTA
1 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTA
70908 AATCATTAAA
64 AATCATTAAA
* * * *
70918 GTTAAATAATTATTA-TTAAATCATTAAAGT--TAAATAATTAAAT--TTAAA-TAATTATTATT
1 ATTAAATCATTA-AAGTTAAATCATTAAA-TCATTAA-AATTAAATCATTAAAGTAATTATTATT
70977 AAAT
63 AAAT
70981 ATGTACTCGA
Statistics
Matches: 241, Mismatches: 25, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
69 12 0.05
70 25 0.10
71 29 0.12
72 14 0.06
73 35 0.15
74 71 0.29
75 14 0.06
76 29 0.12
77 3 0.01
78 9 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (73 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCATTAAA
Found at i:73486 original size:18 final size:18
Alignment explanation
Indices: 73463--73527 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
73453 AAATTATTAG
*
73463 TCTCACGCTTCAGATGAA
1 TCTCACGCTTCAGACGAA
73481 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
73499 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
73517 TCTCACGCTTC
1 TCTCACGCTTC
73528 GGAAGAAGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:73956 original size:110 final size:110
Alignment explanation
Indices: 73771--73990 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
73761 AGATTCCCGC
73771 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
73836 AGAGATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 AGAGATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
73881 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
*
73946 AGATATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 AGAGATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
73991 AGTGTCATAA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (110 bp):
CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
AGAGATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
Found at i:74874 original size:13 final size:12
Alignment explanation
Indices: 74850--74882 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
74840 CAAACAACAT
74850 AAAAAAAG-AAG
1 AAAAAAAGAAAG
74861 AAAAAAAGAAAAG
1 AAAAAAAG-AAAG
74874 AAAAAAAGA
1 AAAAAAAGA
74883 CGCTTTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:79964 original size:50 final size:50
Alignment explanation
Indices: 79905--79999 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
79895 TCCCCTGAAT
* * *
79905 CGCGTTATACGCTGATTTGACGTCACGTGGGTATAGCGCGCCCCCACCCC
1 CGCGATATACGCTGATTTGACGCCACATGGGTATAGCGCGCCCCCACCCC
* *
79955 CGCGATATACGGTGATTTGGCGCCACATGGGTATAGCGCGCCCCC
1 CGCGATATACGCTGATTTGACGCCACATGGGTATAGCGCGCCCCC
80000 TGATCCGCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (50 bp):
CGCGATATACGCTGATTTGACGCCACATGGGTATAGCGCGCCCCCACCCC
Found at i:80008 original size:50 final size:50
Alignment explanation
Indices: 79889--80014 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
79879 GTAGCAGTAA
* * * *
79889 AGCGCGTCCCCTGAAT-CGCGTTATACGCTGATTTGACGTCACGTGGGTAT
1 AGCGCGCCCCCTG-ATCCGCGATATACGCTGATTTGACGCCACATGGGTAT
**** * *
79939 AGCGCGCCCCCACCCCCGCGATATACGGTGATTTGGCGCCACATGGGTAT
1 AGCGCGCCCCCTGATCCGCGATATACGCTGATTTGACGCCACATGGGTAT
*
79989 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGATCCGCGATATAC
80015 CTGGGTATCT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.17, C:0.34, G:0.27, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGATCCGCGATATACGCTGATTTGACGCCACATGGGTAT
Found at i:80118 original size:20 final size:20
Alignment explanation
Indices: 80093--80135 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
80083 CCACATCCCA
80093 ATCCTCCCTATAAATACCCC
1 ATCCTCCCTATAAATACCCC
80113 ATCCTCCCTATAAATACCCC
1 ATCCTCCCTATAAATACCCC
80133 ATC
1 ATC
80136 ATCAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.44, G:0.00, T:0.26
Consensus pattern (20 bp):
ATCCTCCCTATAAATACCCC
Found at i:80261 original size:17 final size:18
Alignment explanation
Indices: 80231--80266 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
80221 ATGTATTGAA
80231 TTTATTTAATTATTTTAC
1 TTTATTTAATTATTTTAC
80249 TTTATTTAA-TATTTTAC
1 TTTATTTAATTATTTTAC
80266 T
1 T
80267 AATATAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTATTTTAC
Found at i:80522 original size:111 final size:111
Alignment explanation
Indices: 80328--80660 Score: 589
Period size: 111 Copynumber: 3.0 Consensus size: 111
80318 TGGAAATCAT
80328 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
80393 TATTTA-ATTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGA-TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
80439 ATATCT-TGACACTTTGCTGATACAGTAACATTTTAGCGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCT-ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
*
80503 ATAATTAGATGATTTATTTAATGCATAATTATTAGATTAAGAATTAA
65 ATAATTAGATGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
80550 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
80615 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGATGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
80661 TTTTTGTAAT
Statistics
Matches: 212, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
110 1 0.00
111 209 0.99
112 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGATGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:82558 original size:21 final size:21
Alignment explanation
Indices: 82520--82574 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
82510 ACCTGCTCAG
* * *
82520 GACGACGACGACGATGACGAC
1 GACGACGATGATGGTGACGAC
*
82541 GACGATGATGATGGTGACGAC
1 GACGACGATGATGGTGACGAC
82562 GACGACGATGATG
1 GACGACGATGATG
82575 ACAGCGAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.36, T:0.13
Consensus pattern (21 bp):
GACGACGATGATGGTGACGAC
Found at i:82576 original size:18 final size:18
Alignment explanation
Indices: 82520--82576 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
82510 ACCTGCTCAG
*
82520 GACGACGACGACGATGAC
1 GACGACGACGACGATGAT
* * *
82538 GACGACGATGATGATGGT
1 GACGACGACGACGATGAT
82556 GACGACGACGACGATGAT
1 GACGACGACGACGATGAT
82574 GAC
1 GAC
82577 AGCGAGGAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.35, T:0.12
Consensus pattern (18 bp):
GACGACGACGACGATGAT
Found at i:86663 original size:114 final size:114
Alignment explanation
Indices: 86516--86749 Score: 353
Period size: 114 Copynumber: 2.1 Consensus size: 114
86506 TTAACCTCTT
* * **
86516 AAAATTAATTGAGGATATAATTTAAGCACTTATTAAATAATGGTTATATATAAAGTTT-TGTAAC
1 AAAATTAATAGAAGATATAATTTAAGCACTTATTAAATAATGACTATATATAAA-TTTATGTAAC
* *
86580 AAAAATCAACTTGATTGTATTTATATTACTTTTAATTATTTTATACTTGA
65 AAAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGA
* *
86630 AAAATTAATAGAAGATATAATTTAAGCATTTATTAAATAATGACTATATATAAATTTATGTAAGA
1 AAAATTAATAGAAGATATAATTTAAGCACTTATTAAATAATGACTATATATAAATTTATGTAACA
* * *
86695 AAAATCAATTTGATTGCATTTATATTAGTTCTAATTATTTTATACTTGG
66 AAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGA
86744 AAAATT
1 AAAATT
86750 CTACAACTCT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 3 0.03
114 105 0.97
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (114 bp):
AAAATTAATAGAAGATATAATTTAAGCACTTATTAAATAATGACTATATATAAATTTATGTAACA
AAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGA
Found at i:86893 original size:21 final size:23
Alignment explanation
Indices: 86849--86896 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
86839 CATATAATTA
*
86849 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
*
86872 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
86893 TAAA
1 TAAA
86897 CTATATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTAAAAGG
Found at i:89369 original size:13 final size:13
Alignment explanation
Indices: 89351--89377 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
89341 TTACAGACAC
89351 GCATATGAAGACT
1 GCATATGAAGACT
89364 GCATATGAAGACT
1 GCATATGAAGACT
89377 G
1 G
89378 TTCAACTATA
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:92156 original size:20 final size:20
Alignment explanation
Indices: 92131--92185 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
92121 ATATTCCCTA
92131 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
92151 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
*
92171 ATAATCTTACATTCC
1 GTAATCTTACATTCC
92186 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTG
Found at i:93631 original size:21 final size:21
Alignment explanation
Indices: 93605--93660 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
93595 GTTTCCAGAT
*
93605 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATTTTCGACTA
**
93626 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGATTTTCGACTA
*
93647 TCGCATTGCGATTT
1 TCGCAATGCGATTT
93661 ACATATTCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCGACTA
Found at i:93712 original size:21 final size:21
Alignment explanation
Indices: 93621--93715 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
93611 TGCGATTTTG
* *
93621 GACTATCGCAATGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
93642 GACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATAGTC
*
93660 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCATTGCGATAGTC
*
93683 GAAGT-TCGCATTGCGATAGTC
1 G-ACTATCGCATTGCGATAGTC
93704 GACTATCGCATT
1 GACTATCGCATT
93716 AGTCCAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 14 0.23
21 39 0.64
22 1 0.02
23 1 0.02
24 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:93741 original size:21 final size:21
Alignment explanation
Indices: 93667--93750 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
93657 ATTTACATAT
* **
93667 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAA
* **
93688 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
93709 TCGCA-T----TAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
93725 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
93746 TCGCA
1 TCGCA
93751 ACGACTGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.23
17 1 0.02
20 1 0.02
21 38 0.73
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:93844 original size:6 final size:6
Alignment explanation
Indices: 93833--93876 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
93823 GACACGTATT
93833 ACCACG ACCACG ACCCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG A-CCACG ACCACG ACCACG ACCACG ACCACG ACC
93877 CGAGACGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
5 10 0.27
6 21 0.57
7 6 0.16
ACGTcount: A:0.30, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:93850 original size:13 final size:13
Alignment explanation
Indices: 93834--93872 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
93824 ACACGTATTA
93834 CCACGACCACGAC
1 CCACGACCACGAC
93847 CCACGACCACGA-
1 CCACGACCACGAC
93859 CCACGACC-CGAC
1 CCACGACCACGAC
93871 CC
1 CC
93873 GACCCGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 10 0.40
13 12 0.48
ACGTcount: A:0.28, C:0.56, G:0.15, T:0.00
Consensus pattern (13 bp):
CCACGACCACGAC
Found at i:93877 original size:10 final size:11
Alignment explanation
Indices: 93833--93879 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 11
93823 GACACGTATT
93833 ACCACGACCACG
1 ACCACGACC-CG
93845 ACCCACGACCACG
1 A-CCACGACC-CG
93858 ACCACGACCCG
1 ACCACGACCCG
93869 ACC-CGACCCG
1 ACCACGACCCG
93879 A
1 A
93880 GACGAGACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.24
11 5 0.15
12 9 0.26
13 12 0.35
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:94270 original size:39 final size:39
Alignment explanation
Indices: 94216--94311 Score: 174
Period size: 39 Copynumber: 2.5 Consensus size: 39
94206 CCTGAATAAT
*
94216 CACATTGTATTGGAAACAAATGTTGGTAATGCTCAATCC
1 CACATAGTATTGGAAACAAATGTTGGTAATGCTCAATCC
*
94255 CACATAGTATTGGAAACAAGTGTTGGTAATGCTCAATCC
1 CACATAGTATTGGAAACAAATGTTGGTAATGCTCAATCC
94294 CACATAGTATTGGAAACA
1 CACATAGTATTGGAAACA
94312 CTATTGTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (39 bp):
CACATAGTATTGGAAACAAATGTTGGTAATGCTCAATCC
Found at i:94563 original size:21 final size:21
Alignment explanation
Indices: 94536--94589 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
94526 CGATTTACAT
94536 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
*
94557 GTTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
*
94578 AATCGCATTGCG
1 ATTCGCATTGCG
94590 TTTCTGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
ATTCGCATTGCGATAGTCCAA
Found at i:95977 original size:13 final size:13
Alignment explanation
Indices: 95959--95996 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
95949 ACGGTTCACA
95959 CGCCCCTACGCGC
1 CGCCCCTACGCGC
*
95972 CGCCCCTACGCAC
1 CGCCCCTACGCGC
95985 CGCCCCTACGCG
1 CGCCCCTACGCG
95997 TGGGGAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.61, G:0.21, T:0.08
Consensus pattern (13 bp):
CGCCCCTACGCGC
Found at i:96094 original size:41 final size:41
Alignment explanation
Indices: 96032--96109 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
96022 AGTTTTGACC
* *
96032 CTTTTGACCGACCCGACCCGGTTCGACCTGACTGCCCAACA
1 CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCCAACA
*
96073 CTTTTGACCGACCCGATCCGGTCCGACCCGACTGCCC
1 CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCC
96110 GACCCGACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.19
Consensus pattern (41 bp):
CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCCAACA
Done.