Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007756.1 Hibiscus syriacus cultivar Beakdansim tig00110022_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: 227904
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:9815 original size:21 final size:20
Alignment explanation
Indices: 9791--9830 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9781 AAATTTTGGC
9791 TTTTTTGGCTCTTTTTTTTTG
1 TTTTTTGGC-CTTTTTTTTTG
*
9812 TTTTTTTGCCTTTTTTTTT
1 TTTTTTGGCCTTTTTTTTT
9831 TTTGCCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTTTGGCCTTTTTTTTTG
Found at i:9817 original size:8 final size:8
Alignment explanation
Indices: 9804--9867 Score: 78
Period size: 8 Copynumber: 8.0 Consensus size: 8
9794 TTTGGCTCTT
9804 TTTTTTTG
1 TTTTTTTG
9812 TTTTTTTG
1 TTTTTTTG
**
9820 CCTTTTT-
1 TTTTTTTG
9827 TTTTTTTG
1 TTTTTTTG
9835 CCTTTTTTTG
1 --TTTTTTTG
9845 -TTTTTTG
1 TTTTTTTG
9852 TTTTTTTG
1 TTTTTTTG
9860 TTTTTTTG
1 TTTTTTTG
9868 AAAAAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
7 12 0.25
8 28 0.58
10 8 0.17
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:9817 original size:23 final size:22
Alignment explanation
Indices: 9791--9867 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 22
9781 AAATTTTGGC
* *
9791 TTTTTTGGCTCTTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTTTGT
9813 TTTTTTGCCTTTTTTTTTTTTGCCT
1 TTTTTTGCC-TTTTTTTTTTTG--T
**
9838 TTTTTTGTTTTTTGTTTTTTTGT
1 TTTTTTGCCTTTT-TTTTTTTGT
9861 TTTTTTG
1 TTTTTTG
9868 AAAAAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 8 0.17
23 19 0.40
24 4 0.09
25 16 0.34
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.81
Consensus pattern (22 bp):
TTTTTTGCCTTTTTTTTTTTGT
Found at i:9841 original size:33 final size:33
Alignment explanation
Indices: 9804--9867 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
9794 TTTGGCTCTT
9804 TTTTTTTGTTTTTTTGCCTTTTT-TTTTTTTGCC
1 TTTTTTTG-TTTTTTGCCTTTTTGTTTTTTTGCC
**
9837 TTTTTTTGTTTTTTGTTTTTTTGTTTTTTTG
1 TTTTTTTGTTTTTTGCCTTTTTGTTTTTTTG
9868 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (33 bp):
TTTTTTTGTTTTTTGCCTTTTTGTTTTTTTGCC
Found at i:9855 original size:15 final size:16
Alignment explanation
Indices: 9804--9865 Score: 83
Period size: 15 Copynumber: 3.9 Consensus size: 16
9794 TTTGGCTCTT
9804 TTTTTTTGTTTTTTTGC
1 TTTTTTTG-TTTTTTGC
*
9821 CTTTTTT-TTTTTTGCC
1 TTTTTTTGTTTTTTG-C
9837 TTTTTTTGTTTTTTG-
1 TTTTTTTGTTTTTTGC
9852 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
9866 TGAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 21 0.51
16 7 0.17
17 13 0.32
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (16 bp):
TTTTTTTGTTTTTTGC
Found at i:13253 original size:13 final size:13
Alignment explanation
Indices: 13231--13260 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13221 TCTAAACACC
13231 TTTC-ACATACCT
1 TTTCAACATACCT
13243 TTTCAACATACCT
1 TTTCAACATACCT
13256 TTTCA
1 TTTCA
13261 TATTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:26638 original size:19 final size:21
Alignment explanation
Indices: 26595--26646 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
26585 GAAACCCCTT
26595 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
26616 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
26635 TGAAGATACATG
1 TGAAAATACATG
26647 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:29826 original size:34 final size:32
Alignment explanation
Indices: 29769--29840 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
29759 CTTTGGTTGC
*
29769 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
29800 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
29834 TTTCTTT
1 TTTCTTT
29841 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:30599 original size:19 final size:21
Alignment explanation
Indices: 30556--30607 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
30546 GAAACCCCTT
30556 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
30577 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
30596 TGAAGATACATG
1 TGAAAATACATG
30608 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:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:32656 original size:19 final size:20
Alignment explanation
Indices: 32632--32674 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
32622 AGCATTTATC
*
32632 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
32651 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
32671 TTCA
1 TTCA
32675 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:37181 original size:16 final size:16
Alignment explanation
Indices: 37147--37193 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
37137 AAAACATCTC
*
37147 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
37163 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
37178 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
37191 TAT
1 TAT
37194 TTCCAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:37195 original size:12 final size:13
Alignment explanation
Indices: 37168--37196 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37158 TTTCTTATCC
37168 TTTCATTTCTTTA
1 TTTCATTTCTTTA
37181 TTTCATTTC-TTA
1 TTTCATTTCTTTA
37193 TTTC
1 TTTC
37197 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:39162 original size:9 final size:9
Alignment explanation
Indices: 39148--39174 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39138 TCTTTCTGAA
39148 TTTCTTTTT
1 TTTCTTTTT
39157 TTTCTTTTT
1 TTTCTTTTT
39166 TTTCTTTTT
1 TTTCTTTTT
39175 GCCTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:46450 original size:14 final size:14
Alignment explanation
Indices: 46431--46460 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
46421 TGAGCTAATA
46431 TGAGCTAATTACCT
1 TGAGCTAATTACCT
46445 TGAGCTAATTACCT
1 TGAGCTAATTACCT
46459 TG
1 TG
46461 CTGCCATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (14 bp):
TGAGCTAATTACCT
Found at i:50520 original size:15 final size:14
Alignment explanation
Indices: 50487--50536 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
50477 AATAAGAAAT
*
50487 AAGAAATGGAA-GA
1 AAGAAATGAAATGA
50500 AAGAAATGAAATGA
1 AAGAAATGAAATGA
*
50514 TAAGAAAGGAAATGGA
1 -AAGAAATGAAAT-GA
50530 AAGAAAT
1 AAGAAAT
50537 ATTATCAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 17 0.55
16 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:53251 original size:11 final size:12
Alignment explanation
Indices: 53213--53255 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
53203 CAAGTGCTAT
53213 AATAAAAAGCAAA
1 AATAAAAAG-AAA
53226 AA-AAAGAAGAAA
1 AATAAA-AAGAAA
53238 AATAAAAAG-AA
1 AATAAAAAGAAA
53249 AATAAAA
1 AATAAAA
53256 GACTCTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.32
12 11 0.39
13 8 0.29
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (12 bp):
AATAAAAAGAAA
Found at i:53257 original size:10 final size:11
Alignment explanation
Indices: 53213--53255 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 11
53203 CAAGTGCTAT
53213 AATAAAAAGCAA
1 AATAAAAAG-AA
*
53225 AAAAAAGAAGAAA
1 AATAAA-AAG-AA
53238 AATAAAAAGAA
1 AATAAAAAGAA
53249 AATAAAA
1 AATAAAA
53256 GACTCTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 9 0.33
12 8 0.30
13 10 0.37
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (11 bp):
AATAAAAAGAA
Found at i:53333 original size:21 final size:21
Alignment explanation
Indices: 53295--53334 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53285 GAAAGAAAAG
*
53295 AAAAAAAGAAATTCAAAAGCA
1 AAAAAAAGAAATTAAAAAGCA
53316 AAAAAAAGAGAA-TAAAAAG
1 AAAAAAAGA-AATTAAAAAG
53335 TTACAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAATTAAAAAGCA
Found at i:55338 original size:33 final size:33
Alignment explanation
Indices: 55296--55364 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
55286 GTTGATGAAT
*
55296 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
55329 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
55362 GAA
1 GAA
55365 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:59197 original size:33 final size:33
Alignment explanation
Indices: 59118--59221 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
59108 ATACAATCTG
* *
59118 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
59154 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
59187 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
59220 TC
1 TC
59222 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:59642 original size:14 final size:14
Alignment explanation
Indices: 59619--59664 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
59609 TTTGGAGTGC
59619 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
*
59634 AAAAGAAGAATA-A
1 AAAAGAAGAAAAGA
*
59647 AAAA-AAGCAAAGA
1 AAAAGAAGAAAAGA
59660 AAAAG
1 AAAAG
59665 TGAAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:59674 original size:26 final size:27
Alignment explanation
Indices: 59617--59674 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
59607 AATTTGGAGT
*
59617 GCAAAAGAAAGAAAAGAAAAAGAAGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
* * *
59644 -TAAAAAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
59669 GCAAAA
1 GCAAAA
59675 CTGCAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.03
Consensus pattern (27 bp):
GCAAAAAAAAGAAAAGAAAAAGAAGAA
Found at i:63204 original size:33 final size:33
Alignment explanation
Indices: 63125--63228 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
63115 ATACAATCTG
* *
63125 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
63161 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
63194 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
63227 TC
1 TC
63229 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:70792 original size:36 final size:36
Alignment explanation
Indices: 70752--70928 Score: 255
Period size: 36 Copynumber: 4.9 Consensus size: 36
70742 AACACCATCT
*
70752 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
70788 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
70824 TCTATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
70860 TCCATCTCCATTATCACGCCTATATCATCAACATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
70896 TCCACCACCATTATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
70929 ACTTATAAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 127 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:76531 original size:33 final size:33
Alignment explanation
Indices: 76452--76555 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
76442 ATACAATCTG
* *
76452 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
76488 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
76521 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
76554 TC
1 TC
76556 ATTCATCAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:86285 original size:33 final size:33
Alignment explanation
Indices: 86243--86311 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
86233 GTTGATGAAT
*
86243 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
86276 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
86309 GAA
1 GAA
86312 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:88858 original size:33 final size:33
Alignment explanation
Indices: 88779--88882 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
88769 ATACAATCTG
* *
88779 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
88815 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
88848 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
88881 TC
1 TC
88883 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:91062 original size:33 final size:33
Alignment explanation
Indices: 90983--91086 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
90973 ATACAATCTG
* *
90983 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
91019 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
91052 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
91085 TC
1 TC
91087 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:93266 original size:33 final size:33
Alignment explanation
Indices: 93187--93290 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
93177 ATACAATCTG
* *
93187 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
93223 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
93256 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
93289 TC
1 TC
93291 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:95730 original size:20 final size:20
Alignment explanation
Indices: 95689--95736 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
95679 TTTCTATCAC
* *
95689 TTTCATTTCTTTCATTTCCA
1 TTTCCTTTCTTTAATTTCCA
95709 TTTCCTTTCTTATAATTT-CA
1 TTTCCTTTCTT-TAATTTCCA
*
95729 TTCCCTTT
1 TTTCCTTT
95737 TTGATGTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCCTTTCTTTAATTTCCA
Found at i:96411 original size:19 final size:21
Alignment explanation
Indices: 96361--96412 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
96351 GAAACCCCTT
96361 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
96382 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
96401 TGAAGATACATG
1 TGAAAATACATG
96413 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:98863 original size:19 final size:20
Alignment explanation
Indices: 98822--98872 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
98812 GAAACCCCTT
*
98822 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
98842 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
98861 TGAAGATACATG
1 TGAAAATACATG
98873 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:102236 original size:6 final size:6
Alignment explanation
Indices: 102225--102287 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 6
102215 TTTTTTTGAA
*
102225 TTTCTT TTTC-T TTTCTT TTT-TT TTTCTT TTTCTGAAT TTTCTT CTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT---T TTTCTT TTTCTT
*
102274 TTTGTCT TTTCTT T
1 TTTCT-T TTTCTT T
102288 CTTTTTGTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
5 10 0.21
6 26 0.55
7 5 0.11
9 6 0.13
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:102239 original size:11 final size:11
Alignment explanation
Indices: 102225--102257 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
102215 TTTTTTTGAA
102225 TTTCTTTTTCT
1 TTTCTTTTTCT
*
102236 TTTCTTTTTTT
1 TTTCTTTTTCT
102247 TTTCTTTTTCT
1 TTTCTTTTTCT
102258 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:102266 original size:37 final size:37
Alignment explanation
Indices: 102209--102293 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
102199 CCTTGGCTTG
* *
102209 CTTTCTTTTTTTTGAATTTCTTTTTCTTTTCT-T-TTTT
1 CTTTC-TTTTTCTGAATTTCTTCTTCTTTT-TGTCTTTT
*
102246 TTTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCTTTT
1 CTTTCTTTTTCTGAA-TTTCTTCTTCTTTTTGTCTTTT
102284 CTTTCTTTTT
1 CTTTCTTTTT
102294 GTACTCCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.24
37 18 0.44
38 13 0.32
ACGTcount: A:0.05, C:0.15, G:0.04, T:0.76
Consensus pattern (37 bp):
CTTTCTTTTTCTGAATTTCTTCTTCTTTTTGTCTTTT
Found at i:103061 original size:19 final size:20
Alignment explanation
Indices: 103015--103064 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
103005 AAACCCCTTT
* *
103015 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTTAAA
103035 GAAAATACATGA-TTTTAAA
1 GAAAATACATGATTTTTAAA
*
103054 GAAGATACATG
1 GAAAATACATG
103065 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAA
Found at i:106416 original size:18 final size:18
Alignment explanation
Indices: 106395--106476 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
106385 CCTTGGCTTG
106395 CTTTCTTTTTTTGAATTT
1 CTTTCTTTTTTTGAATTT
* ***
106413 CTTT-TTCTTTTCTTTTT
1 CTTTCTTTTTTTGAATTT
* *
106430 TTTTCTTTTTCTGAATTT
1 CTTTCTTTTTTTGAATTT
**
106448 -TCTTCTTTTTTTGTCTTTT
1 CT-TTCTTTTTTTG-AATTT
106467 CTTTCTTTTT
1 CTTTCTTTTT
106477 GTACTCCAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
17 13 0.28
18 22 0.47
19 11 0.23
20 1 0.02
ACGTcount: A:0.05, C:0.15, G:0.04, T:0.77
Consensus pattern (18 bp):
CTTTCTTTTTTTGAATTT
Found at i:106433 original size:10 final size:11
Alignment explanation
Indices: 106410--106441 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
106400 TTTTTTTGAA
106410 TTTCTTTTTCT
1 TTTCTTTTTCT
106421 TTTCTTTTT-T
1 TTTCTTTTTCT
106431 TTTCTTTTTCT
1 TTTCTTTTTCT
106442 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:107237 original size:19 final size:20
Alignment explanation
Indices: 107196--107246 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
107186 GAAACCCCTT
*
107196 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
107216 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
107235 TGAAGATACATG
1 TGAAAATACATG
107247 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:110604 original size:21 final size:21
Alignment explanation
Indices: 110580--110626 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
110570 CTTGGCTTGC
110580 TTTCTTTT-TTTTGAATTTCTT
1 TTTCTTTTCTTTT-AATTTCTT
**
110601 TTTCTTTTCTTTTTTTTTCTT
1 TTTCTTTTCTTTTAATTTCTT
110622 TTTCT
1 TTTCT
110627 GAATTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTCTTTTCTTTTAATTTCTT
Found at i:110618 original size:10 final size:11
Alignment explanation
Indices: 110595--110626 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
110585 TTTTTTTGAA
110595 TTTCTTTTTCT
1 TTTCTTTTTCT
110606 TTTCTTTTT-T
1 TTTCTTTTTCT
110616 TTTCTTTTTCT
1 TTTCTTTTTCT
110627 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:110661 original size:28 final size:25
Alignment explanation
Indices: 110601--110661 Score: 59
Period size: 28 Copynumber: 2.3 Consensus size: 25
110591 TGAATTTCTT
110601 TTTCTTTTCTTTTTTTTTCTTTTTC
1 TTTCTTTTCTTTTTTTTTCTTTTTC
*** *
110626 TGAATTTTCTTCTTATTTTTGTCTTTTC
1 TTTCTTTTCTT-TT-TTTTTCT-TTTTC
110654 TTTCTTTT
1 TTTCTTTT
110662 TGTACTCTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
25 8 0.31
26 2 0.08
27 6 0.23
28 10 0.38
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTCTTTTCTTTTTTTTTCTTTTTC
Found at i:111424 original size:19 final size:20
Alignment explanation
Indices: 111383--111433 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
111373 GAAACCCCTT
*
111383 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
111403 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
111422 TGAAGATACATG
1 TGAAAATACATG
111434 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:114795 original size:21 final size:21
Alignment explanation
Indices: 114771--114817 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
114761 CTTGGCTTGC
114771 TTTCTTTT-TTTTGAATTTCTT
1 TTTCTTTTCTTTT-AATTTCTT
**
114792 TTTCTTTTCTTTTTTTTTCTT
1 TTTCTTTTCTTTTAATTTCTT
114813 TTTCT
1 TTTCT
114818 GAATTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTCTTTTCTTTTAATTTCTT
Found at i:114809 original size:10 final size:11
Alignment explanation
Indices: 114786--114817 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
114776 TTTTTTTGAA
114786 TTTCTTTTTCT
1 TTTCTTTTTCT
114797 TTTCTTTTT-T
1 TTTCTTTTTCT
114807 TTTCTTTTTCT
1 TTTCTTTTTCT
114818 GAATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:115615 original size:19 final size:20
Alignment explanation
Indices: 115574--115624 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
115564 GAAACCCCTT
*
115574 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
115594 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
115613 TGAAGATACATG
1 TGAAAATACATG
115625 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:118984 original size:6 final size:6
Alignment explanation
Indices: 118973--119030 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
118963 TTTTTTTGAA
* *
118973 TTTCTT TTTCTT TTT-TT TTTCTT TTTCTGAAT TTTCTT CTTCTT TTTGTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT---T TTTCTT TTTCTT TTTCT-T
119024 TTTCTT T
1 TTTCTT T
119031 CTTTTTGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 5 0.12
6 27 0.63
7 5 0.12
9 6 0.14
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:118994 original size:32 final size:35
Alignment explanation
Indices: 118958--119037 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 35
118948 CTTGGCTTGC
*
118958 TTTCTTTTTTTTGAA-TTTCTTTTTCTTTTT-T-T
1 TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
*
118990 TTTC-TTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
119024 TTTCTTTCTTTTTG
1 TTTCTTT-TTTTTG
119038 TACTCCAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 9 0.22
32 18 0.45
33 1 0.03
34 5 0.12
35 2 0.05
36 5 0.12
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (35 bp):
TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
Found at i:123150 original size:6 final size:6
Alignment explanation
Indices: 123139--123196 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
123129 TTTTTTTGAA
* *
123139 TTTCTT TTTCTT TTT-TT TTTCTT TTTCTGAAT TTTCTT CTTCTT TTTGTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT---T TTTCTT TTTCTT TTTCT-T
123190 TTTCTT T
1 TTTCTT T
123197 CTTTTTTGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 5 0.12
6 27 0.63
7 5 0.12
9 6 0.14
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:123160 original size:32 final size:35
Alignment explanation
Indices: 123124--123202 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 35
123114 CTTGGCTTGC
*
123124 TTTCTTTTTTTTGAA-TTTCTTTTTCTTTTT-T-T
1 TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
*
123156 TTTC-TTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
123190 TTTCTTTCTTTTT
1 TTTCTTT-TTTTT
123203 TGTACTCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 9 0.23
32 18 0.46
33 1 0.03
34 5 0.13
35 2 0.05
36 4 0.10
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (35 bp):
TTTCTTTTTTTTGAATTTTCTTCTTCTTTTTGTCT
Found at i:127329 original size:28 final size:28
Alignment explanation
Indices: 127287--127351 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
127277 CTTGGCTTGC
* * * *
127287 TTTCTTTTTTTTGAATTTTTTTTTTTTTT
1 TTTC-TTTTTCTGAATTTTCTTCTTCTTT
127316 TTTCTTTTTCTGAATTTTCTTCTTCTTT
1 TTTCTTTTTCTGAATTTTCTTCTTCTTT
*
127344 TGTCTTTT
1 TTTCTTTT
127352 CTTTCTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.06, C:0.11, G:0.05, T:0.78
Consensus pattern (28 bp):
TTTCTTTTTCTGAATTTTCTTCTTCTTT
Found at i:132114 original size:1 final size:1
Alignment explanation
Indices: 132110--132171 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
132100 TTTTTGGCTC
* ** ** * * *
132110 TTTTTTTGTTTTTTTGCTTTTTTTTTTTTTCCTTTTTTGTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
132172 AAAAAAAATA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (1 bp):
T
Found at i:132121 original size:8 final size:8
Alignment explanation
Indices: 132110--132170 Score: 81
Period size: 8 Copynumber: 7.9 Consensus size: 8
132100 TTTTTGGCTC
132110 TTTTTTTG
1 TTTTTTTG
132118 TTTTTTTG
1 TTTTTTTG
*
132126 CTTTTTT-
1 TTTTTTTG
*
132133 TTTTTTTC
1 TTTTTTTG
*
132141 CTTTTTTG
1 TTTTTTTG
132149 -TTTTTTG
1 TTTTTTTG
132156 TTTTTTTG
1 TTTTTTTG
132164 TTTTTTT
1 TTTTTTT
132171 TAAAAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
7 13 0.28
8 34 0.72
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:132121 original size:19 final size:17
Alignment explanation
Indices: 132099--132139 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
132089 AAATTTTGGC
132099 TTTTTTGGCTCTTTTTTT
1 TTTTTTGGCT-TTTTTTT
*
132117 GTTTTTTTGCTTTTTTTT
1 -TTTTTTGGCTTTTTTTT
132135 TTTTT
1 TTTTT
132140 CCTTTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (17 bp):
TTTTTTGGCTTTTTTTT
Found at i:132134 original size:31 final size:29
Alignment explanation
Indices: 132099--132162 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
132089 AAATTTTGGC
*
132099 TTTTTTGGCTCTTTTTTTGTTTTTTTGCTTT
1 TTTTTTGGCTCCTTTTTTG-TTTTTTG-TTT
***
132130 TTTTTTTTTTCCTTTTTTGTTTTTTGTTT
1 TTTTTTGGCTCCTTTTTTGTTTTTTGTTT
132159 TTTT
1 TTTT
132163 GTTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.24
30 7 0.24
31 15 0.52
ACGTcount: A:0.00, C:0.08, G:0.09, T:0.83
Consensus pattern (29 bp):
TTTTTTGGCTCCTTTTTTGTTTTTTGTTT
Found at i:132136 original size:15 final size:15
Alignment explanation
Indices: 132111--132169 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
132101 TTTTGGCTCT
132111 TTTTTTGTTTTTTTGC
1 TTTTTT-TTTTTTTGC
*
132127 TTTTTTTTTTTTTCC
1 TTTTTTTTTTTTTGC
*
132142 TTTTTTGTTTTTTG-
1 TTTTTTTTTTTTTGC
132156 TTTTTTTGTTTTTT
1 TTTTTTT-TTTTTT
132170 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 6 0.16
15 26 0.68
16 6 0.16
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTTGC
Found at i:132145 original size:23 final size:23
Alignment explanation
Indices: 132110--132162 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
132100 TTTTTGGCTC
**
132110 TTTTTTTGTTTTTTTGCTTTTTT-
1 TTTTTTTCCTTTTTTG-TTTTTTG
132133 TTTTTTTCCTTTTTTGTTTTTTG
1 TTTTTTTCCTTTTTTGTTTTTTG
132156 TTTTTTT
1 TTTTTTT
132163 GTTTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.87
Consensus pattern (23 bp):
TTTTTTTCCTTTTTTGTTTTTTG
Found at i:132766 original size:16 final size:16
Alignment explanation
Indices: 132745--132777 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
132735 TTGGAGTGTG
132745 AAGATTAATCTCCCTC
1 AAGATTAATCTCCCTC
132761 AAGATTAATCTCCCTC
1 AAGATTAATCTCCCTC
132777 A
1 A
132778 CAAGAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (16 bp):
AAGATTAATCTCCCTC
Found at i:133865 original size:19 final size:20
Alignment explanation
Indices: 133824--133874 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
133814 GAAACCCCTT
*
133824 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
133844 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
133863 TGAAGATACATG
1 TGAAAATACATG
133875 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:137239 original size:19 final size:21
Alignment explanation
Indices: 137196--137247 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
137186 GAAACCCCTT
137196 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
*
137217 TGAAAATACATTA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
137236 TGAAGATACATG
1 TGAAAATACATG
137248 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:140477 original size:35 final size:37
Alignment explanation
Indices: 140405--140484 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
140395 ATACTATTTC
* *
140405 CATCACCATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTACCATGCCTATAT
*
140442 CATCACCATAGTCCATC-ACCA-TACCATGCCTATAT
1 CATCACCATAATCCATCTACCATTACCATGCCTATAT
140477 CATCACCA
1 CATCACCA
140485 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTACCATGCCTATAT
Found at i:144376 original size:13 final size:13
Alignment explanation
Indices: 144358--144382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
144348 AGATACTATT
144358 TCCATCACCATAG
1 TCCATCACCATAG
144371 TCCATCACCATA
1 TCCATCACCATA
144383 TCACGCCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.40, G:0.04, T:0.24
Consensus pattern (13 bp):
TCCATCACCATAG
Found at i:167315 original size:24 final size:22
Alignment explanation
Indices: 167283--167340 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
167273 CTTGGCTTGA
167283 TTTC-TCTTTTGAATTTCTTTTCT
1 TTTCTTCTTTTG-ATTT-TTTTCT
167306 TTTCTTCTTTTCTGATTTTTTTCT
1 TTTCTTC-TTT-TGATTTTTTTCT
167330 TTT-TATCTTTT
1 TTTCT-TCTTTT
167341 TCTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
22 1 0.03
23 8 0.26
24 13 0.42
25 7 0.23
26 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTCTTCTTTTGATTTTTTTCT
Found at i:167324 original size:16 final size:14
Alignment explanation
Indices: 167296--167352 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
167286 CTCTTTTGAA
167296 TTTCTTTTCT-TTT
1 TTTCTTTTCTATTT
*
167309 CTTCTTTTCTGATTTT
1 TTTCTTTTCT-A-TTT
167325 TTTCTTTT-TATCTT
1 TTTCTTTTCTAT-TT
167339 TTTCTTTTCT-TTT
1 TTTCTTTTCTATTT
167352 T
1 T
167353 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 13 0.35
14 12 0.32
15 2 0.05
16 10 0.27
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTCTTTTCTATTT
Found at i:167346 original size:19 final size:19
Alignment explanation
Indices: 167300--167352 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
167290 TTTGAATTTC
167300 TTTTCTTTTCTTCTTTTCTG
1 TTTTCTTTTCTT-TTTTCTG
*
167320 ATTT-TTTTCTTTTTATCT-
1 TTTTCTTTTCTTTTT-TCTG
167338 TTTTCTTTTCTTTTT
1 TTTTCTTTTCTTTTT
167353 GCACTCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 20 0.69
20 3 0.10
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTTCTG
Found at i:168470 original size:23 final size:23
Alignment explanation
Indices: 168444--168488 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
168434 AAATCCAGCA
168444 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
168467 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
168489 AGAAAAGAAA
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:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:171741 original size:19 final size:21
Alignment explanation
Indices: 171700--171751 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
171690 GAAACCCCTT
171700 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
171721 TGAAAATACATG-TTTTT-AA
1 TGAAAATACATGATTTTTAAA
*
171740 TGAATATACATG
1 TGAAAATACATG
171752 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 5 0.17
21 12 0.40
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:175748 original size:35 final size:36
Alignment explanation
Indices: 175702--175806 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
175692 AAATAGAATT
*
175702 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
*
175737 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
* *
175773 TGGTGATGATATAAGCGTGATAATGATGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
175807 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACGA
Found at i:176172 original size:31 final size:31
Alignment explanation
Indices: 176134--176198 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
176124 GGCAAAGTAC
176134 ATGTCTTAAAATGAAAATAAATGATGCTTGG
1 ATGTCTTAAAATGAAAATAAATGATGCTTGG
176165 ATGTCTTAAAATGAAAATAAATGATGCTTGG
1 ATGTCTTAAAATGAAAATAAATGATGCTTGG
176196 ATG
1 ATG
176199 AGGGAAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (31 bp):
ATGTCTTAAAATGAAAATAAATGATGCTTGG
Found at i:177669 original size:33 final size:33
Alignment explanation
Indices: 177627--177695 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
177617 GTTGATGAAT
*
177627 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
177660 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
177693 GAA
1 GAA
177696 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:182137 original size:33 final size:33
Alignment explanation
Indices: 182095--182163 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
182085 GTTGATGAAT
*
182095 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
182128 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
182161 GAA
1 GAA
182164 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:184481 original size:248 final size:248
Alignment explanation
Indices: 184043--184551 Score: 1002
Period size: 248 Copynumber: 2.1 Consensus size: 248
184033 TATTCTATCA
184043 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
1 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
184108 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
66 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
184173 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
131 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
184238 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
196 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
184291 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
1 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
184356 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
66 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
184421 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
131 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
184486 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
196 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
*
184539 TAAGCATG-ATTCA
1 TAACCATGCATTCA
184552 ATTCATTCGT
Statistics
Matches: 260, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
247 5 0.02
248 255 0.98
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (248 bp):
TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
Found at i:186117 original size:19 final size:19
Alignment explanation
Indices: 186093--186139 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
186083 AACAAAAATA
186093 AAAGTGCAAAAAGAAGTGC
1 AAAGTGCAAAAAGAAGTGC
* **
186112 AAAGTGGAAAGTGAAGTGC
1 AAAGTGCAAAAAGAAGTGC
186131 AAAGT-CAAA
1 AAAGTGCAAA
186140 GAAAGCAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.51, C:0.09, G:0.28, T:0.13
Consensus pattern (19 bp):
AAAGTGCAAAAAGAAGTGC
Found at i:186202 original size:18 final size:19
Alignment explanation
Indices: 186164--186202 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
186154 ATCAGAAAAG
*
186164 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
186183 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
186201 AA
1 AA
186203 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:188488 original size:248 final size:248
Alignment explanation
Indices: 188050--188558 Score: 1002
Period size: 248 Copynumber: 2.1 Consensus size: 248
188040 TATTCTATCA
188050 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
1 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
188115 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
66 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
188180 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
131 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
188245 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
196 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
188298 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
1 TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
188363 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
66 CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
188428 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
131 CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
188493 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
196 CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
*
188546 TAAGCATG-ATTCA
1 TAACCATGCATTCA
188559 ATTCATTCGT
Statistics
Matches: 260, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
247 5 0.02
248 255 0.98
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (248 bp):
TAACCATGCATTCACATGTTAGTATAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGAT
CATGTCATTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGATATTATTATTA
CATGTTTCCATTTATCATTTATTATGAATACCATGTTAAATGATATTCATGCATACAACATATAT
CCACAATATTATTTCAAGTATGTTAAGTATGTTATATTAGTCTTGCATTCATT
Found at i:190936 original size:16 final size:16
Alignment explanation
Indices: 190915--190946 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
190905 TAGTTAGCTC
190915 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
190931 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
190947 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:192380 original size:18 final size:19
Alignment explanation
Indices: 192355--192439 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 19
192345 GTGCAAAAAT
192355 AAAG-AAAAGACAAAAAG-
1 AAAGAAAAAGACAAAAAGA
* *
192372 AAAGAAAAATCAGAAAGAAGA
1 AAAGAAAAA-GACAAA-AAGA
* *
192393 AAAGAAGAAGAAAAGAAAAGA
1 AAAGAAAAAG-ACA-AAAAGA
*
192414 AAAGAAGAAGA-AAAAAGA
1 AAAGAAAAAGACAAAAAGA
192432 AAAGAAAA
1 AAAGAAAA
192440 GAAAAGAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
17 4 0.07
18 17 0.30
19 5 0.09
20 4 0.07
21 24 0.43
22 2 0.04
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAGACAAAAAGA
Found at i:192388 original size:17 final size:17
Alignment explanation
Indices: 192348--192446 Score: 70
Period size: 17 Copynumber: 6.0 Consensus size: 17
192338 AATTGGAGTG
*
192348 CAAAAATAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
192365 CAAAAAGAAAGAAAA-A
1 CAAAAAGAAAGAAAAGA
*
192381 TCAGAAAG-AAGAAAAG-
1 -CAAAAAGAAAGAAAAGA
*
192397 -AAGAAGAAAAGAAAAGA
1 CAAAAAG-AAAGAAAAGA
192414 -AAAGAAG-AAGAAAA-A
1 CAAA-AAGAAAGAAAAGA
192429 -AGAAAAGAAAAGAAAAGA
1 CA-AAAAG-AAAGAAAAGA
192447 GAAGTTCAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.06
15 5 0.07
16 25 0.37
17 29 0.43
18 4 0.06
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:192408 original size:5 final size:5
Alignment explanation
Indices: 192389--192446 Score: 80
Period size: 5 Copynumber: 10.8 Consensus size: 5
192379 AATCAGAAAG
192389 AAGAA AAGAA GAAGAA AAGAA AAGAA AAGAA GAAGAAAA AAGAA AAGAA
1 AAGAA AAGAA -AAGAA AAGAA AAGAA AAGAA -AAG--AA AAGAA AAGAA
192438 AAGAA AAGA
1 AAGAA AAGA
192447 GAAGTTCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 36 0.73
6 8 0.16
7 3 0.06
8 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:192412 original size:49 final size:43
Alignment explanation
Indices: 192355--192446 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 43
192345 GTGCAAAAAT
192355 AAAGAAAAGACAAA-AAGAAAGAAAAATCAGAAAGAAGAAAAGAAGAAGA
1 AAAGAAAAGA-AAAGAAG-AAGAAAAA--AG-AA-AAGAAAAGAA-AAGA
192404 AAAGAAAAGAAAAGAAGAAGAAAAAAGAAAAGAAAAGAAAAGA
1 AAAGAAAAGAAAAGAAGAAGAAAAAAGAAAAGAAAAGAAAAGA
192447 GAAGTTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
43 4 0.10
44 10 0.24
45 2 0.05
46 2 0.05
48 11 0.26
49 13 0.31
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (43 bp):
AAAGAAAAGAAAAGAAGAAGAAAAAAGAAAAGAAAAGAAAAGA
Found at i:192414 original size:28 final size:27
Alignment explanation
Indices: 192350--192443 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 27
192340 TTGGAGTGCA
* *
192350 AAAATAAAGAA-AAGACAAAAAGAAAGAA
1 AAAAGAAAGAAGAAGA-AAAAAGAAA-AG
192378 AAATCAGAAAGAAGAA-AAGAAGAAGAAAAG
1 AAA--AGAAAGAAGAAGAA-AA-AAGAAAAG
192408 AAAAGAAAAGAAGAAGAAAAAAGAAAAG
1 AAAAG-AAAGAAGAAGAAAAAAGAAAAG
192436 AAAAGAAA
1 AAAAGAAA
192444 AGAGAAGTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
27 3 0.05
28 18 0.32
29 12 0.21
30 16 0.28
31 8 0.14
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAAGAAAGAAGAAGAAAAAAGAAAAG
Found at i:194550 original size:16 final size:16
Alignment explanation
Indices: 194529--194560 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
194519 TAGTTAGCTC
194529 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
194545 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
194561 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:195986 original size:18 final size:18
Alignment explanation
Indices: 195965--195999 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
195955 TTACACACTT
195965 TGCCACAACAACACCATC
1 TGCCACAACAACACCATC
*
195983 TGCCACGACAACACCAT
1 TGCCACAACAACACCAT
196000 TCATACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11
Consensus pattern (18 bp):
TGCCACAACAACACCATC
Found at i:205208 original size:21 final size:21
Alignment explanation
Indices: 205169--205212 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
205159 GCCATCTCTA
205169 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
205191 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
205212 T
1 T
205213 AATTTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:209877 original size:13 final size:13
Alignment explanation
Indices: 209861--209886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
209851 AAAGAGAGGC
209861 AAAAAACAAAAAA
1 AAAAAACAAAAAA
209874 AAAAAACAAAAAA
1 AAAAAACAAAAAA
209887 GCTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAA
Done.