Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005116.1 Hibiscus syriacus cultivar Beakdansim tig00011503_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: 178380
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:68 original size:34 final size:33
Alignment explanation
Indices: 20--100 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 33
10 AAAAATGACT
* * *
20 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
53 ATCGCAATTGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAA-TGCGAAATGAAAATCGCAACGACAAA
*
87 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
101 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 13 0.30
34 30 0.70
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:77 original size:20 final size:19
Alignment explanation
Indices: 20--79 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 19
10 AAAAATGACT
20 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
53 ATCGCAATTGCGAAATGAAA
1 ATCGCAA-TGCGAAATGAAA
73 ATCGCAA
1 ATCGCAA
80 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.30
15 2 0.06
17 2 0.06
19 9 0.27
20 10 0.30
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:128 original size:19 final size:19
Alignment explanation
Indices: 106--305 Score: 122
Period size: 19 Copynumber: 11.7 Consensus size: 19
96 CGAAACTAAA
106 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
125 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
140 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
158 TTCGCATTGTGA-TTTC--
1 TTCGCGTTGCGATTTTCAT
*
174 -T--CGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
190 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
209 TTCGCGTTGCGATTTT-AGT
1 TTCGCGTTGCGATTTTCA-T
228 TTCGCGTTGCGA-TTT--T
1 TTCGCGTTGCGATTTTCAT
*
244 GT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
261 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
276 -TCTCGTTGCGA-TTTCAT
1 TTCGCGTTGCGATTTTCAT
293 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
306 AGACATTAAG
Statistics
Matches: 137, Mismatches: 22, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
13 7 0.05
14 29 0.21
15 7 0.05
16 5 0.04
17 9 0.07
18 18 0.13
19 62 0.45
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:152 original size:33 final size:33
Alignment explanation
Indices: 110--305 Score: 236
Period size: 33 Copynumber: 5.8 Consensus size: 33
100 ACTAAATTCG
* *
110 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
143 CGTTGCGATTTTCATTTCGCATTGTGATT-TCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
175 CGTTGTGATTTTCATTTCGCATTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---TCT
* * *
213 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
246 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
279 CGTTGCGA-TTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
306 AGACATTAAG
Statistics
Matches: 140, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
32 46 0.33
33 64 0.46
34 2 0.01
36 1 0.01
37 1 0.01
38 26 0.19
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:267 original size:103 final size:103
Alignment explanation
Indices: 106--312 Score: 310
Period size: 103 Copynumber: 2.0 Consensus size: 103
96 CGAAACTAAA
* *
106 TTCGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGTGAT
1 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAT
* *
171 T-TCTCGTTGTGATTTTCATTTCGCATTGCGATAGTCAT
66 TCTCTCGTTGCGA-TTTCATTTCGCATTGCGATAGACAT
***
209 TTCGCGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGA
1 TTCGCGTTGCGATTTTCA-TTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
*
273 TTCTCTCGTTGCGATTTCATTTCGCGTTGCGATAGACAT
65 TTCTCTCGTTGCGATTTCATTTCGCATTGCGATAGACAT
312 T
1 T
313 AAGATGATTG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
102 1 0.01
103 83 0.88
104 10 0.11
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (103 bp):
TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAT
TCTCTCGTTGCGATTTCATTTCGCATTGCGATAGACAT
Found at i:2618 original size:12 final size:12
Alignment explanation
Indices: 2601--2633 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2591 TTCTTTGGGA
2601 TTCTTCTTCTTT
1 TTCTTCTTCTTT
2613 TTCTTCTTCTTT
1 TTCTTCTTCTTT
2625 TTCTTCTTC
1 TTCTTCTTC
2634 AGTGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:2842 original size:24 final size:24
Alignment explanation
Indices: 2808--2861 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2798 CTGAAAAATC
2808 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2832 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2856 ATCAAA
1 ATCAAA
2862 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3727 original size:20 final size:20
Alignment explanation
Indices: 3704--3974 Score: 317
Period size: 20 Copynumber: 13.4 Consensus size: 20
3694 GTCAGAATCT
3704 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
3724 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
3744 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
3764 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
3784 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
* * **
3804 CATTGCGATTTTCCAAATTCG
1 CGTTGCGA-TTTACGTATTCG
*
3825 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
* * **
3845 CATTGCGATTTTCCAAATTCG
1 CGTTGCGA-TTTACGTATTCG
*
3866 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
* * *
3886 CATTGCGATTTTCCTATTCG
1 CGTTGCGATTTACGTATTCG
** *
3906 TATTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
* * **
3926 CATTGCGATTTTCCAAATTCG
1 CGTTGCGA-TTTACGTATTCG
3947 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
3967 CATTGCGA
1 CGTTGCGA
3975 ATTAGGAAAA
Statistics
Matches: 209, Mismatches: 39, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
20 164 0.78
21 45 0.22
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:3836 original size:41 final size:41
Alignment explanation
Indices: 3704--3974 Score: 395
Period size: 41 Copynumber: 6.7 Consensus size: 41
3694 GTCAGAATCT
* * * **
3704 CGTTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
* * * **
3744 CGTTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
3784 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
3825 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
*
3866 CGTTGCGATTTACGTAATCGCATTGCGATTTTCC-TATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
**
3906 TATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
*
3947 CGTTGCGATTTACGTATTCGCATTGCGA
1 CGTTGCGATTTACGTAATCGCATTGCGA
3975 ATTAGGAAAA
Statistics
Matches: 217, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
40 103 0.47
41 114 0.53
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
Found at i:3904 original size:122 final size:121
Alignment explanation
Indices: 3704--3974 Score: 434
Period size: 122 Copynumber: 2.2 Consensus size: 121
3694 GTCAGAATCT
* ** * *
3704 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCGCGTTG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAAATTCGCGTTGCGATTTACGTAATCGCATTG
* *
3769 CGATTTACGTATTCGCGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
66 CGATTTACCTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
* *
3825 CGTTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAATCGCATT
1 CGTTGCGATTTACGTATTCGCATTGCGA-TTTACAAATTCGCGTTGCGATTTACGTAATCGCATT
* *
3890 GCGATTTTCCTATTCGTATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
65 GCGATTTACCTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
3947 CGTTGCGATTTACGTATTCGCATTGCGA
1 CGTTGCGATTTACGTATTCGCATTGCGA
3975 ATTAGGAAAA
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 26 0.19
122 111 0.81
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAAATTCGCGTTGCGATTTACGTAATCGCATTG
CGATTTACCTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
Found at i:3995 original size:21 final size:21
Alignment explanation
Indices: 3971--4016 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3961 TATTCGCATT
3971 GCGAA-TTAGGAAAATCGCAAC
1 GCGAATTTAGG-AAATCGCAAC
* *
3992 GCGAATTTTGGAAATCGCAAT
1 GCGAATTTAGGAAATCGCAAC
4013 GCGA
1 GCGA
4017 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTTAGGAAATCGCAAC
Found at i:7893 original size:18 final size:18
Alignment explanation
Indices: 7870--7905 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7860 TAATGTAAAA
7870 CTGCTTTCTTTAAAGAAT
1 CTGCTTTCTTTAAAGAAT
7888 CTGCTTTCTTTAAAGAAT
1 CTGCTTTCTTTAAAGAAT
7906 AGAATCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
CTGCTTTCTTTAAAGAAT
Found at i:10293 original size:21 final size:22
Alignment explanation
Indices: 10267--10316 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
10257 TTCACTTTTT
10267 TAAAAAATCAA-TAAAATACAA
1 TAAAAAATCAATTAAAATACAA
* *
10288 TAAAAAA-GAATTAAAATTCAA
1 TAAAAAATCAATTAAAATACAA
10309 TAAAAAAT
1 TAAAAAAT
10317 GTAAACATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAAAAATCAATTAAAATACAA
Found at i:11793 original size:6 final size:6
Alignment explanation
Indices: 11784--11808 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11774 GTCGTGGTCG
11784 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
11809 ACGTGTAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:11919 original size:21 final size:21
Alignment explanation
Indices: 11871--11963 Score: 102
Period size: 21 Copynumber: 4.6 Consensus size: 21
11861 GAAATAGAAA
*
11871 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
11892 A--GCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
11911 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
11931 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
11952 ATCGCAACGCGA
1 ATCGCAACGCGA
11964 ACTGGAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 18 0.32
20 14 0.25
21 24 0.43
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:11919 original size:60 final size:61
Alignment explanation
Indices: 11848--11963 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 61
11838 ACAACTGTAG
**
11848 ACTATCGCAACGCGAAATAGAAAATCGTAACGCGATTTTCAACTA-GCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATAGAAAATCACAACGCGATTTTCAACTACGCAACGCGATTTTCA
*
11908 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGA
1 ACTATCGCAACGCGAAATAGAAAATCACAACGCGATTTTCAACTA-CGCAACGCGA
11964 ACTGGAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 42 0.82
62 9 0.18
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (61 bp):
ACTATCGCAACGCGAAATAGAAAATCACAACGCGATTTTCAACTACGCAACGCGATTTTCA
Found at i:11940 original size:20 final size:20
Alignment explanation
Indices: 11911--11984 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
11901 ATTTTCAACT
11911 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
11931 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
11952 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
11972 ATCGCAACGCGAA
1 ATCGCAACGCGAA
11985 TTTGCGATAG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:11941 original size:41 final size:41
Alignment explanation
Indices: 11894--11983 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
11884 TTTCAACTAG
11894 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCA
1 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCA
* *
11935 CAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCG
1 CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCA
11976 CAACGCGA
1 CAACGCGA
11984 ATTTGCGATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (41 bp):
CAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCA
Found at i:18448 original size:25 final size:25
Alignment explanation
Indices: 18420--18471 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18410 TATTTTACTT
18420 TTTATTATGTGATGTTTAAGAATGG
1 TTTATTATGTGATGTTTAAGAATGG
18445 TTTATTATGTGATGTTTAAGAATGG
1 TTTATTATGTGATGTTTAAGAATGG
18470 TT
1 TT
18472 ATGGGTCGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (25 bp):
TTTATTATGTGATGTTTAAGAATGG
Found at i:35686 original size:3 final size:3
Alignment explanation
Indices: 35678--35724 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
35668 TTTTGTTATG
35678 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35725 TCAGATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:51435 original size:2 final size:2
Alignment explanation
Indices: 51430--51461 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51420 ACACACACAC
51430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51462 GCATCTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55511 original size:21 final size:23
Alignment explanation
Indices: 55487--55537 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
55477 GAAAAATATG
55487 ATAAAAAT-TA-GATTT-TAGATT
1 ATAAAAATATATGATTTGTA-ATT
*
55508 ATAAAAATATATTATTTGTAATT
1 ATAAAAATATATGATTTGTAATT
55531 ATAAAAA
1 ATAAAAA
55538 AGTTTCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 14 0.54
24 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
ATAAAAATATATGATTTGTAATT
Found at i:56804 original size:6 final size:7
Alignment explanation
Indices: 56776--56808 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
56766 CGGCGACTAT
56776 GGAAAGG
1 GGAAAGG
56783 GGAAAGG
1 GGAAAGG
56790 GGAAAGG
1 GGAAAGG
*
56797 GGAAGGG
1 GGAAAGG
56804 GGAAA
1 GGAAA
56809 AAGAATTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
GGAAAGG
Found at i:77894 original size:31 final size:31
Alignment explanation
Indices: 77856--77923 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
77846 TTACATTAGA
77856 GACCATATTGCAAACGGACTAAATGTTGAGG-
1 GACCATATTGCAAACGGACTAAATGTTG-GGT
77887 GACCATATTGCAAACGGACTAAATGTTGGGT
1 GACCATATTGCAAACGGACTAAATGTTGGGT
77918 GACCAT
1 GACCAT
77924 TACTATACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATGTTGGGT
Found at i:82936 original size:45 final size:45
Alignment explanation
Indices: 82837--82940 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
82827 AAGCACAGGA
* *
82837 AGTGCATCGATGCACCCATTAAAAAGGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAAGGAAAACATCGAAGGCAATT
* * **
82882 AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATT
1 AGTGCATCGATGCA-CCCATTAAAAAGGAAAACATCGAAGGCAATT
* *
82927 TGTGTATCGATGCA
1 AGTGCATCGATGCA
82941 TGGGTAGTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 45 0.90
46 5 0.10
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAAGGAAAACATCGAAGGCAATT
Found at i:90090 original size:145 final size:147
Alignment explanation
Indices: 89880--90171 Score: 554
Period size: 146 Copynumber: 2.0 Consensus size: 147
89870 ATCAGCCAAG
89880 GTGACGAAGGAATTTATATATAGTGGCACCCACATTGAAACGACAAGTAATACGCGTAAAACGCG
1 GTGACGAAGGAATTTATATATAGTGGCACCCACATTGAAACGACAAGTAATACGCGTAAAACGCG
89945 TTAAAGGACGGCCAGATCA-TTTTTTTTAAACAACCCTACAC-TTTAACTGTTTGCAGTAAAACA
66 TTAAAGGACGGCCAGATCATTTTTTTTTAAACAACCCTACACTTTTAACTGTTTGCAGTAAAACA
90008 ACAAATGATAACTAAAA
131 ACAAATGATAACTAAAA
90025 GTGACGAAGGAATTTATATATAGTGGTCACCCACATTGAAACGACAAGTAATACGCGT-AAACGC
1 GTGACGAAGGAATTTATATATAGTGG-CACCCACATTGAAACGACAAGTAATACGCGTAAAACGC
90089 GTTAAAGGACGGCCAGATCATTTTTTTTTAAACAACCCTACACTTTTAACTGTTTGCAGTAAAAC
65 GTTAAAGGACGGCCAGATCATTTTTTTTTAAACAACCCTACACTTTTAACTGTTTGCAGTAAAAC
90154 AACAAATGATAACTAAAA
130 AACAAATGATAACTAAAA
90172 TACAATTTAA
Statistics
Matches: 144, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
145 52 0.36
146 53 0.37
147 39 0.27
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (147 bp):
GTGACGAAGGAATTTATATATAGTGGCACCCACATTGAAACGACAAGTAATACGCGTAAAACGCG
TTAAAGGACGGCCAGATCATTTTTTTTTAAACAACCCTACACTTTTAACTGTTTGCAGTAAAACA
ACAAATGATAACTAAAA
Found at i:91754 original size:29 final size:28
Alignment explanation
Indices: 91719--91786 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
91709 GAGGGAGTCT
*
91719 ATGGCGACCTACAAGATCGTCAGGAGTGC
1 ATGGCGACCTACAAGATCG-CAGGAGGGC
* *
91748 ATGGCGACCTACAAGGTCGCCGGAGGGC
1 ATGGCGACCTACAAGATCGCAGGAGGGC
*
91776 ATGACGACCTA
1 ATGGCGACCTA
91787 TGCTTGGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (28 bp):
ATGGCGACCTACAAGATCGCAGGAGGGC
Found at i:91783 original size:28 final size:29
Alignment explanation
Indices: 91723--91786 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
91713 GAGTCTATGG
* *
91723 CGACCTACAAGATCGTCAGGAGTGCATGG
1 CGACCTACAAGATCGTCAGGAGGGCATGA
* *
91752 CGACCTACAAGGTCG-CCGGAGGGCATGA
1 CGACCTACAAGATCGTCAGGAGGGCATGA
91780 CGACCTA
1 CGACCTA
91787 TGCTTGGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.27, C:0.28, G:0.31, T:0.14
Consensus pattern (29 bp):
CGACCTACAAGATCGTCAGGAGGGCATGA
Found at i:100640 original size:2 final size:2
Alignment explanation
Indices: 100633--100669 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
100623 TCCCGACTCG
100633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100670 ATAAAGACTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105740 original size:13 final size:14
Alignment explanation
Indices: 105722--105750 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
105712 AATAACTAAG
105722 AAATATTATA-AAT
1 AAATATTATATAAT
105735 AAATATTATATAAT
1 AAATATTATATAAT
105749 AA
1 AA
105751 TCACATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTATATAAT
Found at i:114836 original size:2 final size:2
Alignment explanation
Indices: 114829--114855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
114819 TGCAAAGCAT
114829 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 T
114856 GAATTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115215 original size:2 final size:2
Alignment explanation
Indices: 115208--115235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
115198 TCTGATGTAA
115208 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
115236 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:115240 original size:2 final size:2
Alignment explanation
Indices: 115235--115260 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
115225 TCTCTCTCTC
115235 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
115261 AGTTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115755 original size:41 final size:38
Alignment explanation
Indices: 115710--115789 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 38
115700 TTTCCACCCT
*
115710 AAACCCGACCCGACCCAAACAGTGCATTTTTTTTAAAAAAA
1 AAACCCGACCCGACCCAAAC-CT--ATTTTTTTTAAAAAAA
**
115751 AAACCCGACCCGACCTGAACCTATTTTTTTTAAAAAAA
1 AAACCCGACCCGACCCAAACCTATTTTTTTTAAAAAAA
115789 A
1 A
115790 TCCGACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 17 0.47
40 1 0.03
41 18 0.50
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (38 bp):
AAACCCGACCCGACCCAAACCTATTTTTTTTAAAAAAA
Found at i:128217 original size:19 final size:19
Alignment explanation
Indices: 128179--128274 Score: 75
Period size: 19 Copynumber: 4.7 Consensus size: 19
128169 GATTCACAAC
* *
128179 GCGATTGTGAAAAATATGTT
1 GCGATAGTG-AAAATGTGTT
*
128199 GCGATAGTTAAAATGTGTT
1 GCGATAGTGAAAATGTGTT
*
128218 GCGAGAGTTTGAAAAACGTGTTGTT
1 GCGATAG--TG-AAAA--TG-TGTT
*
128243 GCGATAGTGAAAAAGTGTT
1 GCGATAGTGAAAATGTGTT
*
128262 GCAATAGTGAAAA
1 GCGATAGTGAAAA
128275 ATCTAAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
19 31 0.50
20 8 0.13
21 1 0.02
22 8 0.13
23 2 0.03
24 2 0.03
25 10 0.16
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.30
Consensus pattern (19 bp):
GCGATAGTGAAAATGTGTT
Found at i:128785 original size:61 final size:63
Alignment explanation
Indices: 128681--128818 Score: 226
Period size: 61 Copynumber: 2.2 Consensus size: 63
128671 TTTTGGATTG
128681 GACTATCGCAACGCGAACTTTGACGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTTGA-GACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTC
* * *
128745 GACTATCGCAACGTGAAC-TTG-GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTG
1 GACTATCGCAACGCGAACTTTGAGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTC
128806 GACTATCGCAACG
1 GACTATCGCAACG
128819 AATTTGGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
61 51 0.72
63 3 0.04
64 17 0.24
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.20
Consensus pattern (63 bp):
GACTATCGCAACGCGAACTTTGAGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTC
Found at i:128793 original size:40 final size:40
Alignment explanation
Indices: 128749--128896 Score: 269
Period size: 40 Copynumber: 3.7 Consensus size: 40
128739 AACTTCGACT
*
128749 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
128789 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
* *
128829 ATCGCAACGCGAACTTTGACTATCGCAACAAATTTGGAAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
128869 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
128897 AATCGCGTTG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:128857 original size:61 final size:60
Alignment explanation
Indices: 128681--128837 Score: 199
Period size: 61 Copynumber: 2.5 Consensus size: 60
128671 TTTTGGATTG
** *
128681 GACTATCGCAACGCGAACTTTGACGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACG-GAAC-TTG--GAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
** *
128745 GACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTG
1 GACTATCGCAACG-GAACTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
*
128806 GACTATCGCAAC-GAATTTGGAAAATCGCAACG
1 GACTATCGCAACGGAACTTGGAAAATCGCAACG
128838 CGAACTTTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
59 17 0.20
61 50 0.57
63 3 0.03
64 17 0.20
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (60 bp):
GACTATCGCAACGGAACTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
Found at i:128962 original size:20 final size:20
Alignment explanation
Indices: 128939--129011 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
128929 AAATTAGAGT
128939 TCGCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATAGTCAGAA
** *
128959 TCGCAATGCGAT--TCTGTATTA
1 TCGCGTTGCGATAGTCAG-A--A
128980 TCGCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATAGTCAGAA
129000 TCGCGTTGCGAT
1 TCGCGTTGCGAT
129012 TTTGTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 23 0.55
21 11 0.26
22 1 0.02
23 3 0.07
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCAGAA
Found at i:128989 original size:21 final size:21
Alignment explanation
Indices: 128965--129033 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
128955 AGAATCGCAA
128965 TGCGATTCTGTATTATCGCGT
1 TGCGATTCTGTATTATCGCGT
*
128986 TGCGATAGTCAG-A--ATCGCGT
1 TGCGAT--TCTGTATTATCGCGT
*
129006 TGCGATTTTGTATTATCGCGT
1 TGCGATTCTGTATTATCGCGT
*
129027 TGAGATT
1 TGCGATT
129034 TACATATTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 13 0.33
21 19 0.49
22 1 0.03
23 3 0.08
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (21 bp):
TGCGATTCTGTATTATCGCGT
Found at i:128996 original size:41 final size:41
Alignment explanation
Indices: 128939--129028 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
128929 AAATTAGAGT
128939 TCGCGTTGCGATAGTCAGAATCGCAATGCGATTCTGTATTA
1 TCGCGTTGCGATAGTCAGAATCGCAATGCGATTCTGTATTA
** *
128980 TCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTA
1 TCGCGTTGCGATAGTCAGAATCGCAATGCGATTCTGTATTA
129021 TCGCGTTG
1 TCGCGTTG
129029 AGATTTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCAGAATCGCAATGCGATTCTGTATTA
Found at i:129121 original size:19 final size:19
Alignment explanation
Indices: 129097--129133 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
129087 TGCAATACTG
*
129097 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
129116 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
129134 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:130065 original size:22 final size:19
Alignment explanation
Indices: 130038--130085 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
130028 GGAGAATTAA
*
130038 TATTATTTTTAATAGTAATAT
1 TATTATTTTGAATA-T-ATAT
130059 TAGTTATTTTGAATATATAT
1 TA-TTATTTTGAATATATAT
130079 TATTATT
1 TATTATT
130086 AAGTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 3 0.12
22 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATTATTTTGAATATATAT
Found at i:132038 original size:29 final size:30
Alignment explanation
Indices: 132006--132065 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
131996 CGTAAACAGT
*
132006 CACAACAATCCTCTCAACCCG-AAAAATCA
1 CACAACAAACCTCTCAACCCGTAAAAATCA
* * *
132035 CACAACAAACTTTTCAACCCGTAAATATCA
1 CACAACAAACCTCTCAACCCGTAAAAATCA
132065 C
1 C
132066 CCGGCAATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.43, C:0.35, G:0.03, T:0.18
Consensus pattern (30 bp):
CACAACAAACCTCTCAACCCGTAAAAATCA
Found at i:134985 original size:29 final size:29
Alignment explanation
Indices: 134952--135007 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
134942 GCCTTTCTGC
*
134952 AAAGGGTGT-TAGATCGGGAAATATATATG
1 AAAGGGTGTAT-GATAGGGAAATATATATG
*
134981 AAAGGGTGTATGATAGGTAAATATATA
1 AAAGGGTGTATGATAGGGAAATATATA
135008 ACGAAAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.29, T:0.29
Consensus pattern (29 bp):
AAAGGGTGTATGATAGGGAAATATATATG
Found at i:136329 original size:28 final size:28
Alignment explanation
Indices: 136298--136351 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
136288 CGTAGGACCA
136298 ATATGTCCCGTAGGACCACGTAGAACAC
1 ATATGTCCCGTAGGACCACGTAGAACAC
*
136326 ATATGTCCCGTAGGACCGCGTAGAAC
1 ATATGTCCCGTAGGACCACGTAGAAC
136352 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.19
Consensus pattern (28 bp):
ATATGTCCCGTAGGACCACGTAGAACAC
Found at i:139144 original size:15 final size:15
Alignment explanation
Indices: 139124--139153 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
139114 TATCACAATC
139124 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
139139 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
139154 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:149991 original size:11 final size:11
Alignment explanation
Indices: 149975--150001 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
149965 AATTGATCTT
149975 ATTAAACCTTA
1 ATTAAACCTTA
149986 ATTAAACCTTA
1 ATTAAACCTTA
149997 ATTAA
1 ATTAA
150002 GAAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTAAACCTTA
Found at i:150758 original size:21 final size:22
Alignment explanation
Indices: 150728--150768 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
150718 TATGTTTTAA
*
150728 AAAATTAAAATATAATATATAC
1 AAAATTAAAAGATAATATATAC
*
150750 AAAA-TAAAAGATACTATAT
1 AAAATTAAAAGATAATATAT
150769 GATTATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATTAAAAGATAATATATAC
Found at i:158786 original size:6 final size:6
Alignment explanation
Indices: 158775--158805 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
158765 CAATAAGACA
158775 CCATGT CCATGT CCATGT CCATGT CCATGT C
1 CCATGT CCATGT CCATGT CCATGT CCATGT C
158806 GAACGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
CCATGT
Found at i:163928 original size:57 final size:57
Alignment explanation
Indices: 163840--164068 Score: 377
Period size: 57 Copynumber: 4.0 Consensus size: 57
163830 GTTGGAGGAA
* *
163840 GAATACTTACAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGTGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
*
163897 GAATACTTGCAGGTTTCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
*
163954 GAATACTTGCAGGTTCCTCAGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * * *
164011 GATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGAGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
164068 G
1 G
164069 TATGGTTATG
Statistics
Matches: 161, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 161 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.35
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:169196 original size:28 final size:28
Alignment explanation
Indices: 169164--169220 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 28
169154 ATTAGAAATG
169164 AACTACCTAGTAGTTATCCTTATCTA-TT
1 AACTA-CTAGTAGTTATCCTTATCTATTT
169192 -A--ACTAGTAGTTATCCTTATCTATTT
1 AACTACTAGTAGTTATCCTTATCTATTT
169217 AACT
1 AACT
169221 TTCTAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
24 20 0.80
25 3 0.12
26 1 0.04
27 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (28 bp):
AACTACTAGTAGTTATCCTTATCTATTT
Found at i:169197 original size:24 final size:25
Alignment explanation
Indices: 169170--169220 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
169160 AATGAACTAC
169170 CTAGTAGTTATCCTTATCTA-TTAA
1 CTAGTAGTTATCCTTATCTATTTAA
169194 CTAGTAGTTATCCTTATCTATTTAA
1 CTAGTAGTTATCCTTATCTATTTAA
169219 CT
1 CT
169221 TTCTAAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (25 bp):
CTAGTAGTTATCCTTATCTATTTAA
Found at i:173657 original size:25 final size:25
Alignment explanation
Indices: 173629--173679 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
173619 ATAAAATAGT
*
173629 TTAGTTTAATCATCTAAACCACAAG
1 TTAGTTTAATCATCAAAACCACAAG
173654 TTAGTTTAATCATCAAAACCACAAG
1 TTAGTTTAATCATCAAAACCACAAG
173679 T
1 T
173680 AAAGTGTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAGTTTAATCATCAAAACCACAAG
Found at i:177886 original size:23 final size:22
Alignment explanation
Indices: 177836--177894 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
177826 CTCGTATAAA
*
177836 TGCACCTAAGTGCCACGTAGAT
1 TGCACCGAAGTGCCACGTAGAT
*
177858 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAG-AT
177881 TGCACCG-AGTGCCA
1 TGCACCGAAGTGCCA
177895 TATAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 24 0.73
23 9 0.27
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCACGTAGAT
Done.