Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001234.1 Hibiscus syriacus cultivar Beakdansim tig00002429_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: 108598
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1491 original size:40 final size:41
Alignment explanation
Indices: 1435--1523 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
1425 GAAAGTAAAT
1435 TTTGCAAATCCGAATTTTT-TTTTCAAACTCTTCTAGTTTGA
1 TTTGC-AATCCGAATTTTTCTTTTCAAACTCTTCTAGTTTGA
1476 TTTGCAATCCGAATTTTTCTTTTCAAACTCTTCTAGTTTGA
1 TTTGCAATCCGAATTTTTCTTTTCAAACTCTTCTAGTTTGA
1517 TTTGCAA
1 TTTGCAA
1524 ATTTTTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (41 bp):
TTTGCAATCCGAATTTTTCTTTTCAAACTCTTCTAGTTTGA
Found at i:8929 original size:90 final size:91
Alignment explanation
Indices: 8823--8995 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 91
8813 GGTGCACTAA
8823 GAGTACATCGATGCATAAAATGCATTCGATGTTTCAAAATA-GCCA-GAGTGCATCGATGCATAG
1 GAGTACATCGATGCATAAAATGCATTCGATG-TTCAAAATATGCCATG-GTGCATCGATGCATAG
*
8886 -TTTGTGCATCGATGCATCAAATGCATT
64 ATTGGTGCATCGATGCATCAAATGCATT
* * ** * *
8913 GAGTGCATCGATGCATAAAATGGATTCGATGTTCAATTTATTCCATGGTGCATCGATGCATGGAT
1 GAGTACATCGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCATAGAT
*
8978 TGGTGCATCGGTGCATCA
66 TGGTGCATCGATGCATCA
8996 CTTTGAAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 7 0.10
90 47 0.65
91 18 0.25
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (91 bp):
GAGTACATCGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCATAGAT
TGGTGCATCGATGCATCAAATGCATT
Found at i:9595 original size:25 final size:24
Alignment explanation
Indices: 9567--9698 Score: 108
Period size: 26 Copynumber: 5.1 Consensus size: 24
9557 CTTGATTCAA
9567 TTTCTTTTTTTCTTTTCTTTTCTCT
1 TTTCTTTTTTTCTTTTCTTTT-TCT
*
9592 TTTCTCTTTTCTCTTTTCTTTTT-T
1 TTTCT-TTTTTTCTTTTCTTTTTCT
*
9616 TTCTATTTCTTTTTCTTTTCTTTTT-T
1 TT-T-CTT-TTTTTCTTTTCTTTTTCT
*
9642 TCTCTTTCTTTTTCTTTTCTTTTTTTCT
1 TTTC-TT-TTTTTCTTTTC--TTTTTCT
9670 CTTTCTTTTTTTCTCTTT-TTTCTTCT
1 -TTTCTTTTTTTCT-TTTCTTT-TTCT
9696 TTT
1 TTT
9699 TTCTGATGGA
Statistics
Matches: 90, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.03
25 29 0.32
26 37 0.41
27 12 0.13
28 6 0.07
29 3 0.03
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCTTTTTTTCTTTTCTTTTTCT
Found at i:9601 original size:14 final size:14
Alignment explanation
Indices: 9582--9693 Score: 92
Period size: 14 Copynumber: 8.3 Consensus size: 14
9572 TTTTTTCTTT
9582 TCTTTTCTCTTTTC
1 TCTTTTCTCTTTTC
9596 TCTTTTCTCTTTTC
1 TCTTTTCTCTTTTC
* * *
9610 TTTTTTTTCTATT-
1 TCTTTTCTCTTTTC
9623 TCTTTT-TCTTTTC
1 TCTTTTCTCTTTTC
* *
9636 T-TTTTTTCTCTT-
1 TCTTTTCTCTTTTC
9648 TCTTTT-TCTTTTC
1 TCTTTTCTCTTTTC
*
9661 T-TTTTTTCTCTTTC
1 TCTTTTCTCT-TTTC
* *
9675 TTTTTTTCTCTTTTT
1 -TCTTTTCTCTTTTC
9690 TCTT
1 TCTT
9694 CTTTTTTCTG
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
12 19 0.24
13 19 0.24
14 31 0.39
15 4 0.05
16 7 0.09
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTCTCTTTTC
Found at i:9608 original size:21 final size:20
Alignment explanation
Indices: 9567--9683 Score: 102
Period size: 19 Copynumber: 6.0 Consensus size: 20
9557 CTTGATTCAA
*
9567 TTTCT-TTTTTTC-TTTTCT
1 TTTCTCTTTTCTCTTTTTCT
9585 TTTCTCTTTTCTCTTTTCTCT
1 TTTCTCTTTTCTCTTTT-TCT
* * *
9606 TTTCTTTTTTTTCTATTTCT
1 TTTCTCTTTTCTCTTTTTCT
*
9626 TTT-TCTTTTCTTTTTTTCT
1 TTTCTCTTTTCTCTTTTTCT
*
9645 CTTTCT-TTTTCT-TTTCTTTT
1 -TTTCTCTTTTCTCTTT-TTCT
*
9665 TTTCTC-TTTCTTTTTTTCT
1 TTTCTCTTTTCTCTTTTTCT
9684 CTTTTTTCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 15
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.06
19 34 0.42
20 24 0.30
21 18 0.22
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCTTTTCTCTTTTTCT
Found at i:9624 original size:6 final size:5
Alignment explanation
Indices: 9574--9698 Score: 95
Period size: 5 Copynumber: 24.8 Consensus size: 5
9564 CAATTTCTTT
* *
9574 TTTTC TTTTC TTTTCTC TTTTC TCTT- TTCTC TTTTC TTTT- TTTTC TATTTC
1 TTTTC TTTTC -TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC
9625 TTTTTC TTTTC -TTT- TTTTC TCTTTC TTTTTC TTTTC -TTT- TTTTC
1 -TTTTC TTTTC TTTTC TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTTC
9669 TCTTTC TTTT- TTTCTC TTTT- TTCTTC TTTT
1 T-TTTC TTTTC TTT-TC TTTTC TT-TTC TTTT
9699 TTCTGATGGA
Statistics
Matches: 99, Mismatches: 4, Indels: 34
0.72 0.03 0.25
Matches are distributed among these distances:
4 23 0.23
5 40 0.40
6 32 0.32
7 4 0.04
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:9675 original size:65 final size:64
Alignment explanation
Indices: 9567--9698 Score: 189
Period size: 65 Copynumber: 2.0 Consensus size: 64
9557 CTTGATTCAA
*
9567 TTTCTTTTTTTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTCTTTTTTT-TCTATTTCTTTTTC
1 TTTCTTTTTTTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTCTTTTTTTCTCT-TTT-TTCTTC
9631 T
64 T
*
9632 TTTCTTTTTTTCTCTTTCTTTT-TCTTTTCT-TTTTTTCTCTTTCTTTTTTTCTCTTTTTTCTTC
1 TTTCTTTTTTTCT-TTTCTTTTCTCTTTTCTCTTTTCTCT-TTTCTTTTTTTCTCTTTTTTCTTC
9695 T
64 T
9696 TTT
1 TTT
9699 TTCTGATGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
64 16 0.26
65 35 0.56
66 11 0.18
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.80
Consensus pattern (64 bp):
TTTCTTTTTTTCTTTTCTTTTCTCTTTTCTCTTTTCTCTTTTCTTTTTTTCTCTTTTTTCTTCT
Found at i:9701 original size:46 final size:46
Alignment explanation
Indices: 9575--9702 Score: 143
Period size: 48 Copynumber: 2.7 Consensus size: 46
9565 AATTTCTTTT
* *
9575 TTTCTTTTCTTTTCTCTTTTC-TCTTTTCTCTTTTCTTTTTTTTCTA
1 TTTCTTTT-TTTTCTTTTTTCTTCTTTTTTCTTTTCTTTTTTTTCTA
* *
9621 TTTCTTTTTCTTTTCTTTTTTTCTCTTTCTTTTTCTTTTC-TTTTTTTCTC
1 TTTC-TTTT-TTTTC-TTTTTTCT-TCT-TTTTTCTTTTCTTTTTTTTCTA
9671 TTTCTTTTTTTCTCTTTTTTCTTCTTTTTTCT
1 TTTCTTTTTTT-TCTTTTTTCTTCTTTTTTCT
9703 GATGGATGAG
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
46 11 0.15
47 12 0.17
48 17 0.24
49 6 0.08
50 15 0.21
51 10 0.14
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (46 bp):
TTTCTTTTTTTTCTTTTTTCTTCTTTTTTCTTTTCTTTTTTTTCTA
Found at i:12243 original size:8 final size:8
Alignment explanation
Indices: 12232--12264 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12222 AATGTACTGC
*
12232 AAATGCAA
1 AAATGCAG
12240 AAATGCAG
1 AAATGCAG
12248 AAATGCAG
1 AAATGCAG
12256 AAATG-AG
1 AAATGCAG
12263 AA
1 AA
12265 TGAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.58, C:0.09, G:0.21, T:0.12
Consensus pattern (8 bp):
AAATGCAG
Found at i:15271 original size:22 final size:22
Alignment explanation
Indices: 15225--15272 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
15215 ACCACTCGGT
*
15225 CACCGTCGGGCACTATTCCGGC
1 CACCGTCGGGCACTATTCCGAC
** *
15247 CACCGTCGGTTACTATTCTGAC
1 CACCGTCGGGCACTATTCCGAC
15269 CACC
1 CACC
15273 AGAAAATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.23
Consensus pattern (22 bp):
CACCGTCGGGCACTATTCCGAC
Found at i:16001 original size:3 final size:3
Alignment explanation
Indices: 15995--16035 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
15985 GTATTATTTG
15995 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
16036 CTATAAACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:18846 original size:30 final size:31
Alignment explanation
Indices: 18807--18873 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
18797 GGAGGACCTA
* *
18807 TCCAGAGGTCATAAAGAACCTCGGT-AACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
* *
18837 TCCATAGGTCCTGAAGAACCTAGGTAAACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
18868 TCCATA
1 TCCATA
18874 TGTTCCTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (31 bp):
TCCATAGGTCATAAAGAACCTAGGTAAACTG
Found at i:18870 original size:31 final size:31
Alignment explanation
Indices: 18820--18906 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
18810 AGAGGTCATA
*
18820 AAGAACCTCGGT-AACTGTCCATA-GGTCCT
1 AAGAACCTAGGTAAACTGTCCATATGGTCCT
*
18849 GAAGAACCTAGGTAAACTGTCCATATGTTCCT
1 -AAGAACCTAGGTAAACTGTCCATATGGTCCT
* * * *
18881 TAGAACATAGGTATATTGTCCATATG
1 AAGAACCTAGGTAAACTGTCCATATG
18907 TCACGAAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
30 11 0.22
31 33 0.67
32 5 0.10
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATATGGTCCT
Found at i:18907 original size:31 final size:29
Alignment explanation
Indices: 18829--18957 Score: 93
Period size: 31 Copynumber: 4.2 Consensus size: 29
18819 AAAGAACCTC
* * *
18829 GGTAACTGTCCATA-GGTCCTGAAGAACCTA
1 GGTAATTGTCCATATGTTCCT--AGAACATA
*
18859 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGT-AATTGTCCATATGTTCC-TAGAACATA
*
18890 GGTATATTGTCCATATG-TCACGA-AAGGCATA
1 GGTA-ATTGTCCATATGTTC-CTAGAA--CATA
18921 GGTAATTATGTCCATATGTTCCATAGAACATA
1 GGTAA-T-TGTCCATATGTTCC-TAGAACATA
18953 GGTAA
1 GGTAA
18958 ACCCTCGACT
Statistics
Matches: 82, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
29 2 0.02
30 8 0.10
31 42 0.51
32 24 0.29
33 4 0.05
34 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (29 bp):
GGTAATTGTCCATATGTTCCTAGAACATA
Found at i:18953 original size:32 final size:32
Alignment explanation
Indices: 18851--18957 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 32
18841 TAGGTCCTGA
* * *
18851 AGAACCTAGGTAA-ACTGTCCATATGTTCCTT
1 AGAACATAGGTAATATTGTCCATATGTTCCAT
*
18882 AGAACATAGGT-ATATTGTCCATATG-TCACGAA
1 AGAACATAGGTAATATTGTCCATATGTTC-C-AT
*
18914 AG-GCATAGGTAAT-TATGTCCATATGTTCCAT
1 AGAACATAGGTAATAT-TGTCCATATGTTCCAT
18945 AGAACATAGGTAA
1 AGAACATAGGTAA
18958 ACCCTCGACT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
30 3 0.05
31 33 0.53
32 24 0.39
33 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (32 bp):
AGAACATAGGTAATATTGTCCATATGTTCCAT
Found at i:19259 original size:2 final size:2
Alignment explanation
Indices: 19252--19312 Score: 113
Period size: 2 Copynumber: 30.0 Consensus size: 2
19242 TCACATGAAC
19252 AT AT AT AT AT 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 AT AT AT AT AT
19294 AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT -AT AT
19313 CTTGTTCACA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21221 original size:7 final size:7
Alignment explanation
Indices: 21209--21237 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21199 TATGTGCTTC
21209 GGATAGT
1 GGATAGT
21216 GGATAGT
1 GGATAGT
21223 GGATAGT
1 GGATAGT
21230 GGATAGT
1 GGATAGT
21237 G
1 G
21238 ATTATAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GGATAGT
Found at i:23179 original size:2 final size:2
Alignment explanation
Indices: 23172--23202 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23162 ATGAGAAGGA
23172 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 A
23203 GGAAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30910 original size:2 final size:2
Alignment explanation
Indices: 30894--31268 Score: 170
Period size: 2 Copynumber: 201.5 Consensus size: 2
30884 TCATTTATGT
30894 TA TA GTA TA -A TA TA TA T- TA TA GTA GTA TA TA GTA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA -TA TA TA -TA TA TA TA TA
* *
30935 TA T- TG TA TA -A TA TA TG T- TA TA TA TA GTA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
30974 TGG TA TA T- TA T- TA TT TA CTA TA GTA TA -A TA T- TA TA TA T-
1 T-A TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA
*
31012 TA TA TA T- TA TA T- TA T- TG T- TA TA GTA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
31049 GTA TA TA T- TA T- TA TA T- TA TA TA TA T- TA TA -A TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
31086 TG T- TA TA TA T- TA TA GTA GA TA TT TA T- TA TA T- TA TA T- TG
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
31124 TA TA TA T- TG TA GTA -A TA TT TA TA TT TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31164 CTA TA -A TA T- TA T- TA TA TA GTA TA TA TT TA TA TA T- TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
31204 TA TA CA TA TA T- TA T- TA TA T- TA TA TA TA TA GCA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
31243 T- TA TA TA TA TA TA T- TT TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31269 TATTTTTTAT
Statistics
Matches: 292, Mismatches: 24, Indels: 114
0.68 0.06 0.27
Matches are distributed among these distances:
1 43 0.15
2 220 0.75
3 29 0.10
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31194 original size:74 final size:70
Alignment explanation
Indices: 30904--31271 Score: 232
Period size: 74 Copynumber: 5.1 Consensus size: 70
30894 TATAGTATAA
* * * * *
30904 TATATATTATAGTA-GTATATAGTATATTATATATTGTATAATATATGTTATATATAGTATATAT
1 TATATATTATAATATTTATAT-TTATATTATATATTATATAATAT-T-AT-TATATAGTATATAT
*
30968 ATTATATGG
62 ATTATATTG
* * * *
30977 TATATTATTAT-TTA-CTATAGTATAATATTATATATTATATATTATATTATTGTTATAGTAT-T
1 TATA-TATTATAATATTTATA-T-TTATATTATATATTATATA--ATATTATT-ATATAGTATAT
*
31039 ATATTATATAG
60 ATATTATATTG
* **
31050 TATATATTATTATA-TTATA--TATATTATAATATTATATGTTATATATTATAGTAGATATTTAT
1 TATATATTATAATATTTATATTTATATTAT-ATATTATATAATAT-TATTATA-TAG-TA--TA-
31112 TATATTATATTG
59 TATATTATATTG
31124 TATATATTGTAGTAATATTTATATTTATATATATATATTACTATAATATTATTATATAGTATATA
1 TATATA-T-TA-TAATATTTATATTTATAT-TATATATTA-TATAATATTATTATATAGTATATA
31189 T-TTATATAT-
61 TATTATAT-TG
* *
31198 TATATA-TATACATATAT-TA-TTATATTATATA-TATAGCATATATTATTATATA-TATATAT-
1 TATATATTATA-ATATTTATATTTATATTATATATTATA-TA-ATATTATTATATAGTATATATA
31257 TT-TA-T-
63 TTATATTG
31262 TATATATTAT
1 TATATATTAT
31272 TTTTTATATT
Statistics
Matches: 248, Mismatches: 20, Indels: 62
0.75 0.06 0.19
Matches are distributed among these distances:
64 7 0.03
65 3 0.01
66 4 0.02
67 12 0.05
68 24 0.10
69 20 0.08
70 15 0.06
71 7 0.03
72 7 0.03
73 32 0.13
74 62 0.25
75 6 0.02
76 8 0.03
77 4 0.02
78 7 0.03
79 3 0.01
80 18 0.07
81 9 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (70 bp):
TATATATTATAATATTTATATTTATATTATATATTATATAATATTATTATATAGTATATATATTA
TATTG
Found at i:31244 original size:21 final size:18
Alignment explanation
Indices: 30893--31268 Score: 193
Period size: 19 Copynumber: 20.4 Consensus size: 18
30883 CTCATTTATG
30893 TTATAGTATA-ATATA-TA
1 TTATA-TATATATATATTA
30910 TTATAGTAGTATATAGTA-TA
1 TTATA-TA-TATATA-TATTA
* *
30930 TTATATATTGTATAATATATG
1 TTATATA-TATAT-ATAT-TA
30951 TTATATATAGTATATA-TA
1 TTATATATA-TATATATTA
*
30969 TTATATGGTATAT-TATTA
1 TTATAT-ATATATATATTA
30987 TT-TACTATAGTATAATATTA
1 TTATA-TATA-TAT-ATATTA
31007 -TATATTATATATTATATTA
1 TTATA-TATATA-TATATTA
*
31026 TTGT-TATAGTAT-TA-TA
1 TTATATATA-TATATATTA
*
31042 TTATATA-GTATATATTA
1 TTATATATATATATATTA
31059 TTATAT-TATATATATTA
1 TTATATATATATATATTA
*
31076 -TA-ATAT-TATATGTTA
1 TTATATATATATATATTA
*
31091 -TATATTATAGTAGATATTTA
1 TTATA-TATA-TATATA-TTA
*
31111 TTATAT-TATATTGTATATA
1 TTATATATATA-TATAT-TA
* *
31130 TTGTAGTA-ATATTTA-TA
1 TTATA-TATATATATATTA
31147 TT-TATATATATATATTA
1 TTATATATATATATATTA
*
31164 CTATA-ATAT-TATTATATA
1 TTATATATATATA-TAT-TA
* *
31182 GTATATATTTATATATTA
1 TTATATATATATATATTA
*
31200 TATATATACATATATTATTATA
1 T-TATATATATATA-TA-T-TA
31222 TTATATATATAGCATATATTA
1 TTATATATAT---ATATATTA
*
31243 TTATATATATATATTTTA
1 TTATATATATATATATTA
31261 TTATATAT
1 TTATATAT
31269 TATTTTTTAT
Statistics
Matches: 285, Mismatches: 28, Indels: 91
0.71 0.07 0.23
Matches are distributed among these distances:
15 17 0.06
16 21 0.07
17 52 0.18
18 53 0.19
19 57 0.20
20 40 0.14
21 36 0.13
22 4 0.01
23 2 0.01
24 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATATATATATATATTA
Found at i:31251 original size:25 final size:24
Alignment explanation
Indices: 31148--31256 Score: 122
Period size: 25 Copynumber: 4.6 Consensus size: 24
31138 ATATTTATAT
*
31148 TTATATATATATATTAC-TATAATA
1 TTATATATATATA-TACATATATTA
31172 TTAT-TATATAGTAT--ATAT-TTA
1 TTATATATATA-TATACATATATTA
31193 -TATATTATATATATACATATATTA
1 TTATA-TATATATATACATATATTA
31217 TTATATTATATATATAGCATATATTA
1 TTATA-TATATATATA-CATATATTA
31243 TTATATATATATAT
1 TTATATATATATAT
31257 TTTATTATAT
Statistics
Matches: 75, Mismatches: 1, Indels: 17
0.81 0.01 0.18
Matches are distributed among these distances:
20 3 0.04
21 5 0.07
22 9 0.12
23 11 0.15
24 9 0.12
25 24 0.32
26 14 0.19
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATATATATATATACATATATTA
Found at i:31278 original size:14 final size:14
Alignment explanation
Indices: 31235--31287 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
31225 TATATATAGC
* *
31235 ATATATTATTATAT
1 ATATATTATTTTTT
31249 ATATA-TATTTTATT
1 ATATATTATTTT-TT
31263 ATATATTATTTTTT
1 ATATATTATTTTTT
31277 ATATTATTATT
1 ATA-TATTATT
31288 AAAACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 5 0.15
14 16 0.47
15 13 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATATTATTTTTT
Found at i:31287 original size:18 final size:21
Alignment explanation
Indices: 30997--31288 Score: 76
Period size: 21 Copynumber: 14.1 Consensus size: 21
30987 TTTACTATAG
30997 TATA-ATATTATATATTATATAT
1 TATATATATT-TATATTAT-TAT
*
31019 TATAT-TATTGT-TA-TAGTAT
1 TATATATATT-TATATTATTAT
*
31038 TATAT-TATATAGTATATATTAT
1 TATATATATTTA-TAT-TATTAT
* *
31060 TATAT-TATATATATTA-TAA
1 TATATATATTTATATTATTAT
31079 TAT-TATATGTTATA-TATTAT
1 TATATATAT-TTATATTATTAT
* *
31099 AGTAGATATTTATTATATTA-TAT
1 --TATATATAT-TTATATTATTAT
* *
31122 TGTATATATTGTAGTAATATTTAT
1 TATATATATT-TA-TATTA-TTAT
* * *
31146 ATTTATATATATATATTACTAT
1 -TATATATATTTATATTATTAT
* *
31168 AATAT-TATTATATAGTATATAT
1 TATATATATT-TATATTAT-TAT
31190 T-TATATA-TTATA-TA-TA-
1 TATATATATTTATATTATTAT
*
31206 TACATATATTATTATATTA-TAT
1 TATATATA-T-TTATATTATTAT
* *
31228 ATATAGCATATAT-TATTA-TAT
1 -TATA-TATATTTATATTATTAT
31249 ATATATAT-TTTATTA-TA-TAT
1 -TATATATATTTA-TATTATTAT
31269 TAT-T-T-TTTATATTATTAT
1 TATATATATTTATATTATTAT
31287 TA
1 TA
31289 AAACATTTTT
Statistics
Matches: 208, Mismatches: 30, Indels: 68
0.68 0.10 0.22
Matches are distributed among these distances:
16 3 0.01
17 14 0.07
18 8 0.04
19 28 0.13
20 32 0.15
21 45 0.22
22 40 0.19
23 20 0.10
24 10 0.05
25 8 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATTTATATTATTAT
Found at i:32508 original size:17 final size:17
Alignment explanation
Indices: 32486--32541 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
32476 CTGAACCGGT
*
32486 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCG
32503 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
32520 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
32537 -TGACC
1 TTGACC
32542 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 5 0.13
17 33 0.87
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:32545 original size:23 final size:22
Alignment explanation
Indices: 32505--32548 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
32495 CCCGACTGTT
32505 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
32527 GACCCGACCGTGACCGTTGACC
1 GACCCGACC-CGACCGTTGACC
32549 GTGACCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:32549 original size:7 final size:7
Alignment explanation
Indices: 32532--32567 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
32522 GACCCGACCC
32532 GACCG-T
1 GACCGTT
32538 GACCGTT
1 GACCGTT
32545 GACCG-T
1 GACCGTT
32551 GACCGTT
1 GACCGTT
32558 GACCGTT
1 GACCGTT
32565 GAC
1 GAC
32568 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:32550 original size:13 final size:13
Alignment explanation
Indices: 32532--32563 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
32522 GACCCGACCC
32532 GACCGTGACCGTT
1 GACCGTGACCGTT
32545 GACCGTGACCGTT
1 GACCGTGACCGTT
32558 GACCGT
1 GACCGT
32564 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:33505 original size:63 final size:63
Alignment explanation
Indices: 33437--33560 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
33427 CTAATGTGAC
* * *
33437 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
33499 T
63 T
* *
33500 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
33561 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:33520 original size:32 final size:32
Alignment explanation
Indices: 33437--33560 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
33427 CTAATGTGAC
* * *
33437 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
33467 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
33500 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
33531 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
33561 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:39796 original size:10 final size:10
Alignment explanation
Indices: 39767--39835 Score: 81
Period size: 10 Copynumber: 7.1 Consensus size: 10
39757 GCTGCTGGAA
39767 AACCGGTTTG
1 AACCGGTTTG
*
39777 -ACCAGTTTTG
1 AACC-GGTTTG
39787 AACCGGTTTG
1 AACCGGTTTG
*
39797 -ACCGGTCTG
1 AACCGGTTTG
39806 AACCGGTTTG
1 AACCGGTTTG
*
39816 -ACCGGTCTG
1 AACCGGTTTG
39825 AACCGGTTTG
1 AACCGGTTTG
39835 A
1 A
39836 CCCGACCCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 19 0.39
10 27 0.55
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:39809 original size:19 final size:19
Alignment explanation
Indices: 39767--39837 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
39757 GCTGCTGGAA
* *
39767 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
39787 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
39806 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
39825 AACCGGTTTGACC
1 AACCGGTTTGACC
39838 CGACCCGACT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 36 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:39854 original size:17 final size:17
Alignment explanation
Indices: 39832--39887 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
39822 CTGAACCGGT
*
39832 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCG
39849 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
39866 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
39883 -TGACC
1 TTGACC
39888 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 5 0.13
17 33 0.87
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:39891 original size:23 final size:22
Alignment explanation
Indices: 39851--39894 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
39841 CCCGACTGTT
39851 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
39873 GACCCGACCGTGACCGTTGACC
1 GACCCGACC-CGACCGTTGACC
39895 GTGACCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:39895 original size:7 final size:7
Alignment explanation
Indices: 39878--39913 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
39868 GACCCGACCC
39878 GACCG-T
1 GACCGTT
39884 GACCGTT
1 GACCGTT
39891 GACCG-T
1 GACCGTT
39897 GACCGTT
1 GACCGTT
39904 GACCGTT
1 GACCGTT
39911 GAC
1 GAC
39914 TTTCTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (7 bp):
GACCGTT
Found at i:39896 original size:13 final size:13
Alignment explanation
Indices: 39878--39909 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
39868 GACCCGACCC
39878 GACCGTGACCGTT
1 GACCGTGACCGTT
39891 GACCGTGACCGTT
1 GACCGTGACCGTT
39904 GACCGT
1 GACCGT
39910 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:40851 original size:63 final size:63
Alignment explanation
Indices: 40783--40906 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
40773 CTAATGTGAC
* * *
40783 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
40845 T
63 T
* *
40846 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
40907 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:40866 original size:32 final size:32
Alignment explanation
Indices: 40783--40906 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
40773 CTAATGTGAC
* * *
40783 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
40813 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
40846 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
40877 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
40907 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:45619 original size:21 final size:21
Alignment explanation
Indices: 45575--45619 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
45565 GTCTCTTAAA
*
45575 TAATATATAAAAATTAAAATT
1 TAATATATAAAAATAAAAATT
*
45596 TAATAT-TATAAATAAAAATAT
1 TAATATATAAAAATAAAAAT-T
45617 TAA
1 TAA
45620 AACTATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATATAAAAATAAAAATT
Found at i:47337 original size:32 final size:32
Alignment explanation
Indices: 47301--47399 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
47291 GGGTCAACCT
* *
47301 AAGGGATTATCTTGGGGCCTAAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
* *
47333 AAGGGAATACCTTTGGGCCTTAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
* * * * *
47365 AAAGAAATACCTTGGGGCCTCATAGTCTACCC
1 AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
47397 AAG
1 AAG
47400 TGTCACCTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (32 bp):
AAGGGAATACCTTGGGGCCTAAGAGCCTACCC
Found at i:49125 original size:32 final size:31
Alignment explanation
Indices: 49088--49171 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
49078 GGGCCAACCT
*
49088 AAGGGATTATCTTGGGGCCTAAGAACCTACCC
1 AAGGGAATA-CTTGGGGCCTAAGAACCTACCC
* * *
49120 AAGGGAATACTTTTGGGCCTTAGAGCCTACCC
1 AAGGGAATAC-TTGGGGCCTAAGAACCTACCC
*
49152 AAGGAAATACCTTGGGGCCT
1 AAGGGAATA-CTTGGGGCCT
49172 CATAGTCTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 1 0.02
32 42 0.95
33 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (31 bp):
AAGGGAATACTTGGGGCCTAAGAACCTACCC
Found at i:49182 original size:32 final size:32
Alignment explanation
Indices: 49098--49186 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
49088 AAGGGATTAT
* * *
49098 CTTGGGGCCTAAGAACCTACCCAAGGGAATAC
1 CTTGGGGCCTCAGAGCCTACCCAAGGAAATAC
* * *
49130 TTTTGGGCCTTAGAGCCTACCCAAGGAAATAC
1 CTTGGGGCCTCAGAGCCTACCCAAGGAAATAC
* *
49162 CTTGGGGCCTCATAGTCTACCCAAG
1 CTTGGGGCCTCAGAGCCTACCCAAG
49187 TGTCACCTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (32 bp):
CTTGGGGCCTCAGAGCCTACCCAAGGAAATAC
Found at i:57511 original size:37 final size:37
Alignment explanation
Indices: 57459--57894 Score: 206
Period size: 36 Copynumber: 12.3 Consensus size: 37
57449 TATACATGTG
*
57459 TATATATATTATATAGTTTTTAAAATAATTTTGAAAA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* ** *
57496 CT-TATATAATATATAGTTTTTTAAATCGTTTTGAATA
1 -TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* * * * *
57533 TATATAT-ATATATA-TATAT-ATAT-A-TAT--ATA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* * * * *
57563 TATATAT-ATATATA-TATAT-ATAT-A-TAT-ATATA
1 TATATATAATATATAGTTTTTAAAATAATTTTGA-AAA
* *
57595 TATATAT-ATATATAGTTTCTAAAAC-ATTTTGAAAA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* *
57630 AATATATAATATATAGTTTTT-AAATCATTTTGAATATA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAA-A-A
* *
57668 TATATATATATATATAGTTTTTAAAA-CATTTTGAATA
1 TATATATA-ATATATAGTTTTTAAAATAATTTTGAAAA
* ** * *
57705 TATATATAATATATAATTTAAAAAACCATTTTTG-AAA
1 TATATATAATATATAGTTTTTAAAA-TAATTTTGAAAA
* * *
57742 -ACATAT-A-ATATAG-TTTTAAAACATTTTTGAAAA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* * * * * *
57775 -CTATATAACATATAG-TTTGAAAACATTTTTTAAAA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* *** * *
57810 -GTATATAATATGCGGTTTTGAAAATATTTTTG-AAA
1 TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
* * * *
57845 TATATATTATATATAGTTTTAAAACAAAATTTTTAAAA
1 TATATATAATATATAGTTTTTAAA-ATAATTTTGAAAA
*
57883 TATATATTATAT
1 TATATATAATAT
57895 TATATAGTAT
Statistics
Matches: 325, Mismatches: 51, Indels: 44
0.77 0.12 0.10
Matches are distributed among these distances:
30 30 0.09
32 27 0.08
33 16 0.05
34 12 0.04
35 54 0.17
36 79 0.24
37 53 0.16
38 29 0.09
39 22 0.07
40 3 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATAATATATAGTTTTTAAAATAATTTTGAAAA
Found at i:57535 original size:2 final size:2
Alignment explanation
Indices: 57530--57608 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
57520 ATCGTTTTGA
57530 AT AT AT AT AT 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 AT AT AT AT AT
57572 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
57609 GTTTCTAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57886 original size:36 final size:34
Alignment explanation
Indices: 57594--57894 Score: 245
Period size: 36 Copynumber: 8.4 Consensus size: 34
57584 ATATATATAT
57594 ATATATATATATATAGTTTCTAAAACA-TTTTGAAAAA
1 ATATATA-ATATATAGTTT-TAAAACATTTTTG--AAA
*
57631 ATATATAATATATAGTTTTTAAATCA-TTTTGAATATA
1 ATATATAATATATAG-TTTTAAAACATTTTTG-A-A-A
57668 TATATATATATATATAGTTTTTAAAACA-TTTTGAATA
1 -ATATATA-ATATATAG-TTTTAAAACATTTTTGAA-A
* *
57705 TATATATAATATATAATTTAAAAAACCATTTTTGAAA
1 -ATATATAATATATAGTTT-TAAAA-CATTTTTGAAA
*
57742 ACATAT-A-ATATAGTTTTAAAACATTTTTGAAA
1 ATATATAATATATAGTTTTAAAACATTTTTGAAA
* * *
57774 ACTATATAACATATAGTTTGAAAACATTTTTTAAA
1 A-TATATAATATATAGTTTTAAAACATTTTTGAAA
*** *
57809 AGTATATAATATGCGGTTTTGAAAATATTTTTGAAA
1 A-TATATAATATATAGTTTT-AAAACATTTTTGAAA
*
57845 TATATATTATATATAGTTTTAAAACAAAATTTTT-AAA
1 -ATATATAATATATAGTTTTAAAAC---ATTTTTGAAA
*
57882 ATATATATTATAT
1 ATATATAATATAT
57895 TATATAGTAT
Statistics
Matches: 223, Mismatches: 25, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
32 12 0.05
33 8 0.04
34 9 0.04
35 47 0.21
36 74 0.33
37 29 0.13
38 21 0.09
39 23 0.10
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
ATATATAATATATAGTTTTAAAACATTTTTGAAA
Found at i:57933 original size:11 final size:11
Alignment explanation
Indices: 57919--57964 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
57909 TATTATTTTA
*
57919 TTTTTATTCTT
1 TTTTTATTATT
57930 TTTTTACTTATT
1 TTTTTA-TTATT
*
57942 CTTTTATTATT
1 TTTTTATTATT
*
57953 TATTTATTATT
1 TTTTTATTATT
57964 T
1 T
57965 ACTCGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:57940 original size:15 final size:15
Alignment explanation
Indices: 57909--57956 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57899 TAGTATAGTA
* *
57909 TATTATTTTATT-TT
1 TATTCTTTTATTACT
*
57923 TATTCTTTTTTTACT
1 TATTCTTTTATTACT
*
57938 TATTCTTTTATTATT
1 TATTCTTTTATTACT
57953 TATT
1 TATT
57957 TATTATTTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTCTTTTATTACT
Found at i:59327 original size:12 final size:12
Alignment explanation
Indices: 59285--59425 Score: 80
Period size: 12 Copynumber: 11.8 Consensus size: 12
59275 TCTTTGTATC
59285 TTTTTTATTTTA
1 TTTTTTATTTTA
*
59297 TTCTTT-TTTTA
1 TTTTTTATTTTA
** *
59308 TTCATTATATTA
1 TTTTTTATTTTA
59320 TTTTTTATTTTA
1 TTTTTTATTTTA
*
59332 -TTCTTACTTTTA
1 TTTTTTA-TTTTA
59344 -TTTTT-TTTTA
1 TTTTTTATTTTA
* **
59354 TTTTTCA---GC
1 TTTTTTATTTTA
59363 TTTTTTATTTTA
1 TTTTTTATTTTA
*
59375 TTTTTCTCTTTTGA
1 TTTTT-TATTTT-A
*
59389 TTTATTATTTTA
1 TTTTTTATTTTA
59401 TTTATTTATTTGTGA
1 TTT-TTTATTT-T-A
59416 TTTATTTATT
1 TTT-TTTATT
59426 ATCATTATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
9 6 0.06
10 5 0.05
11 19 0.19
12 36 0.36
13 16 0.16
14 6 0.06
15 11 0.11
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:59378 original size:5 final size:5
Alignment explanation
Indices: 59287--59357 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
59277 TTTGTATCTT
* * *
59287 TTTTA TTTTA TTCTTT TTTTA -TTCA TTATA TTATT- TTTTA TTTTA TTCTTA
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TT-TTA
*
59338 CTTTTA TTTTT TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTT
59358 TCAGCTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 5 0.10
5 34 0.65
6 11 0.21
7 2 0.04
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:63362 original size:9 final size:8
Alignment explanation
Indices: 63348--63440 Score: 53
Period size: 9 Copynumber: 10.9 Consensus size: 8
63338 ATAAAAAATG
63348 AAAATAAA
1 AAAATAAA
63356 TAAAATAAA
1 -AAAATAAA
*
63365 GAAAGTAAA
1 -AAAATAAA
*
63374 AAAAAACAA
1 AAAATA-AA
63383 ATGAAATAAA
1 A--AAATAAA
* *
63393 GAAA-AAG
1 AAAATAAA
*
63400 GAAATAAA
1 AAAATAAA
*
63408 AAGATAAA
1 AAAATAAA
*
63416 AAAGTAAA
1 AAAATAAA
63424 CAAAATAAA
1 -AAAATAAA
63433 TAAAATAA
1 -AAAATAA
63441 TATAGGACAA
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.09
8 21 0.32
9 32 0.49
10 2 0.03
11 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:63437 original size:20 final size:20
Alignment explanation
Indices: 63343--63437 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 20
63333 GTTAGATAAA
63343 AAATGAAAATAAAT-AAAA-T
1 AAAT-AAAATAAATAAAAAGT
* * **
63362 AAAGAAAGTAAA-AAAAAAC
1 AAATAAAATAAATAAAAAGT
* * *
63381 AAATGAAATAAAGAAAAAGG
1 AAATAAAATAAATAAAAAGT
*
63401 AAATAAAA-AGATAAAAAAGT
1 AAATAAAATAAAT-AAAAAGT
*
63421 AAACAAAATAAATAAAA
1 AAATAAAATAAATAAAA
63438 TAATATAGGA
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
18 11 0.19
19 14 0.25
20 29 0.51
21 3 0.05
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (20 bp):
AAATAAAATAAATAAAAAGT
Found at i:63633 original size:24 final size:22
Alignment explanation
Indices: 63602--63649 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
63592 AATGTTAGGA
*
63602 AAAATATATAGAATATATAATAAT
1 AAAA-ATATACAATA-ATAATAAT
63626 -AAAATATACAATAATAATAAT
1 AAAAATATACAATAATAATAAT
63647 AAA
1 AAA
63650 GACAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATATACAATAATAATAAT
Found at i:63698 original size:2 final size:2
Alignment explanation
Indices: 63693--63729 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
63683 ATAAAAAATA
63693 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
63730 ACAATAATAA
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:63907 original size:15 final size:14
Alignment explanation
Indices: 63878--63945 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
63868 AAGATATTAG
63878 ATAAAAATAATAAAA
1 ATAAAAATAA-AAAA
* *
63893 GTAAAAGTAAAAAA
1 ATAAAAATAAAAAA
* * *
63907 ATAAACA-ACAAAT
1 ATAAAAATAAAAAA
63920 A-AAAAATAAAAAA
1 ATAAAAATAAAAAA
* *
63933 AGATAAATAAAAA
1 ATAAAAATAAAAA
63946 TAAGAAAAGG
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
12 4 0.10
13 10 0.25
14 18 0.45
15 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:63938 original size:10 final size:9
Alignment explanation
Indices: 63878--63953 Score: 50
Period size: 9 Copynumber: 7.9 Consensus size: 9
63868 AAGATATTAG
*
63878 ATAAAAATA
1 ATAAAAAAA
63887 ATAAAAGTAAA
1 ATAAAA--AAA
63898 AGT-AAAAAA
1 A-TAAAAAAA
63907 ATAAACAACAA
1 ATAAA-AA-AA
63918 AT--AAAAA
1 ATAAAAAAA
63925 ATAAAAAAA
1 ATAAAAAAA
63934 GATAAATAAAA
1 -ATAAA-AAAA
63945 ATAAGAAAA
1 ATAA-AAAA
63954 GGACTAAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 21
0.71 0.01 0.27
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 18 0.33
10 14 0.25
11 15 0.27
12 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:63944 original size:20 final size:20
Alignment explanation
Indices: 63878--63954 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 20
63868 AAGATATTAG
*
63878 ATAAAAATAATAAAAG-TAAA
1 ATAAAAATAAAAAAAGAT-AA
* *
63898 AGTAAAAA-AATAAACA-ACAA
1 A-TAAAAATAA-AAAAAGATAA
63918 ATAAAAAATAAAAAAAGATAA
1 AT-AAAAATAAAAAAAGATAA
*
63939 ATAAAAATAAGAAAAG
1 ATAAAAATAAAAAAAG
63955 GACTAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 1 0.02
20 28 0.62
21 16 0.36
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (20 bp):
ATAAAAATAAAAAAAGATAA
Found at i:64451 original size:49 final size:49
Alignment explanation
Indices: 64391--64499 Score: 209
Period size: 49 Copynumber: 2.2 Consensus size: 49
64381 CTTTTCGAAT
*
64391 CTTCTATTGTTTTTTCTTTCGGTATGTTCGTGTTGCCTTCGAAAAACTC
1 CTTCTATTGTTTTTTCTTTCGGTATGTTCGTATTGCCTTCGAAAAACTC
64440 CTTCTATTGTTTTTTCTTTCGGTATGTTCGTATTGCCTTCGAAAAACTC
1 CTTCTATTGTTTTTTCTTTCGGTATGTTCGTATTGCCTTCGAAAAACTC
64489 CTTCTATTGTT
1 CTTCTATTGTT
64500 CTTCATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (49 bp):
CTTCTATTGTTTTTTCTTTCGGTATGTTCGTATTGCCTTCGAAAAACTC
Found at i:65420 original size:27 final size:29
Alignment explanation
Indices: 65394--65470 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 29
65384 TTGTGTTTCA
65394 AGAAAC-ATTTTCAAAGGTTTTTTTTCAAG
1 AGAAACGA-TTTCAAAGGTTTTTTTTCAAG
65423 AGAAACGATTTCAAAGGTTTTTTGTGTTTCAAG
1 AGAAACGATTTCAAAGG--TTTT-T-TTTCAAG
65456 AGAAACGATTTCAAA
1 AGAAACGATTTCAAA
65471 TATATTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
29 15 0.35
30 1 0.02
31 4 0.09
32 1 0.02
33 22 0.51
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (29 bp):
AGAAACGATTTCAAAGGTTTTTTTTCAAG
Found at i:65458 original size:33 final size:33
Alignment explanation
Indices: 65383--65497 Score: 127
Period size: 36 Copynumber: 3.6 Consensus size: 33
65373 CTCGAAGGTC
65383 TTTGTGTTTC-A-AGAAAC-ATTTTCAAAGG--T
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTT
65412 TTT-T-TTTCAAGAGAAACGATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
**
65443 TTTGTGTTTCAAGAGAAACGATTTCAAATATATTTT
1 TTTGTGTTTCAAGAGAAACGATTTC-AA-A-GGTTT
65479 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
65498 TGTCTCAAGA
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
27 4 0.05
28 2 0.03
29 18 0.24
30 1 0.01
31 4 0.05
32 1 0.01
33 19 0.26
34 2 0.03
35 1 0.01
36 22 0.30
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTT
Found at i:65534 original size:73 final size:73
Alignment explanation
Indices: 65483--65807 Score: 384
Period size: 73 Copynumber: 4.6 Consensus size: 73
65473 TATTTTTTTG
*
65483 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
65548 ACAAAATT
66 ACAAAATT
* * * * * *
65556 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
65621 ACGAAATT
66 ACAAAATT
* * * *
65629 TGTTTCAA-AGAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAAAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
65684 AGACAAAATT
64 AGACAAAATT
* * * *
65694 TGTTTCAAGGGAAACTGTCTCAAGAGATACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
65758 ACAAAATT
66 ACAAAATT
* * *
65766 TGTTTCAAGAGAAATTGTCTTAAGAGAGACAAAAATTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
65808 TGAGTAAATT
Statistics
Matches: 211, Mismatches: 28, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
64 2 0.01
65 45 0.21
66 2 0.01
67 1 0.00
68 1 0.00
70 2 0.01
71 1 0.00
72 69 0.33
73 86 0.41
74 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:65575 original size:36 final size:36
Alignment explanation
Indices: 65483--65807 Score: 380
Period size: 36 Copynumber: 9.1 Consensus size: 36
65473 TATTTTTTTG
65483 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
65520 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
65556 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
65593 AGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
65629 TGTTTCAA-AGAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
65658 TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
65694 TGTTTCAAGGGAAACTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
65730 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
65766 TGTTTCAAGAGAAATTGTCTTAAGAGAGACAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
65803 TGTTT
1 TGTTT
65808 TGAGTAAATT
Statistics
Matches: 250, Mismatches: 25, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
28 2 0.01
29 17 0.07
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 3 0.01
36 144 0.58
37 77 0.31
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:65686 original size:138 final size:138
Alignment explanation
Indices: 65518--65779 Score: 400
Period size: 138 Copynumber: 1.9 Consensus size: 138
65508 GAGACAAAAC
* *
65518 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * *
65583 GACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAA-AGAAAACATA
66 GACAAAA-TTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATA
65647 TTCAAAGAT
130 TTCAAAGAT
*
65656 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * **
65721 TACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
66 GACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
65780 TTGTCTTAAG
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
137 38 0.34
138 73 0.66
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATAT
TCAAAGAT
Found at i:65832 original size:37 final size:35
Alignment explanation
Indices: 65656--65832 Score: 176
Period size: 36 Copynumber: 4.9 Consensus size: 35
65646 ATTCAAAGAT
* * *
65656 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
* * *
65692 TTTGTTTCAAGGGAAACTGTCTCAAGAGATACAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
* * *
65728 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
*
65764 TTTGTTTCAAGAGAAATTGTCTTAAGAGAGACAAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGAC-AAAA
* *
65801 TTTGTTT-TGAGTAAATTAGTCTCAAGTGAGAC
1 TTTGTTTAAGAG-AAATT-GTCTCAAGAGAGAC
65833 GACCCCTTGT
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
35 3 0.02
36 101 0.80
37 23 0.18
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (35 bp):
TTTGTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
Found at i:67322 original size:95 final size:94
Alignment explanation
Indices: 67122--67384 Score: 350
Period size: 95 Copynumber: 2.7 Consensus size: 94
67112 GGCTAACTGA
* * *
67122 ATCCATAAAGCTGATGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTATAG-AT
1 ATCCATAAAGCGGA-GCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-ATC-TT-TATTGTAT
*
67186 ATTATAATCACCTTTATTAGGCTAGCTGAATATT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
67220 ATCCATAAAGTCGGAGCGTTTAACCAATTGCTCTAGAGGGACAACCCAATCTTTATTGTACATTA
1 ATCCATAAAG-CGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATCTTTATTGTATATTA
*
67285 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
67315 ATCCATAAAGCCAGG-GCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATA
1 ATCCATAAAG-C-GGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATCTTTATTGTATAT-
67379 TATAAT
63 TATAAT
67385 ATTATAATAT
Statistics
Matches: 149, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
94 4 0.03
95 90 0.60
96 11 0.07
97 1 0.01
98 40 0.27
99 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (94 bp):
ATCCATAAAGCGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATCTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:71207 original size:9 final size:9
Alignment explanation
Indices: 71193--71287 Score: 66
Period size: 9 Copynumber: 9.8 Consensus size: 9
71183 ATAAAAAATG
71193 AAAATAAAA
1 AAAATAAAA
71202 AAAATAAAA
1 AAAATAAAA
71211 AAAA-AGTAAA
1 AAAATA--AAA
* *
71221 AAAACAAAT
1 AAAATAAAA
71230 AAAATAAAGA
1 AAAATAAA-A
71240 AAAATGAAATAA
1 AAAAT--AA-AA
71252 AAAGATAAAA
1 AAA-ATAAAA
*
71262 AAAAGTAAAC
1 AAAA-TAAAA
* *
71272 AAAGTAAAT
1 AAAATAAAA
71281 AAAATAA
1 AAAATAA
71288 TATATGACAA
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
8 1 0.01
9 33 0.47
10 24 0.34
11 3 0.04
12 6 0.09
13 3 0.04
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (9 bp):
AAAATAAAA
Found at i:71213 original size:10 final size:10
Alignment explanation
Indices: 71193--71284 Score: 57
Period size: 10 Copynumber: 8.9 Consensus size: 10
71183 ATAAAAAATG
71193 AAAAT-AAAA
1 AAAATAAAAA
71202 AAAATAAAAA
1 AAAATAAAAA
71212 AAAAGT--AAA
1 AAAA-TAAAAA
* *
71221 AAAA-CAAAT
1 AAAATAAAAA
*
71230 AAAATAAAGA
1 AAAATAAAAA
71240 AAAATGAAATAA
1 AAAAT-AAA-AA
71252 AAAGATAAAAA
1 AAA-ATAAAAA
*
71263 AAAGTAAACAA
1 AAAATAAA-AA
71274 AGTAAATAAAA
1 A--AAATAAAA
71285 TAATATATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
9 18 0.28
10 19 0.29
11 12 0.18
12 8 0.12
13 8 0.12
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:71234 original size:28 final size:26
Alignment explanation
Indices: 71185--71265 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 26
71175 CGTGCTAGAT
* *
71185 AAAAAATGAAAATAAAA-AAAATAAA
1 AAAAAATAAAAAAAAAATAAAATAAA
71210 AAAAAAGTAAAAAAACAAATAAAATAAA
1 AAAAAA-TAAAAAAA-AAATAAAATAAA
* *
71238 GAAAAATGAAATAAAAAGATAAAA-AAA
1 AAAAAAT-AAA-AAAAAAATAAAATAAA
71265 A
1 A
71266 GTAAACAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.13
26 6 0.13
27 7 0.15
28 23 0.50
29 4 0.09
ACGTcount: A:0.81, C:0.01, G:0.06, T:0.11
Consensus pattern (26 bp):
AAAAAATAAAAAAAAAATAAAATAAA
Found at i:71260 original size:51 final size:53
Alignment explanation
Indices: 71186--71287 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 53
71176 GTGCTAGATA
71186 AAAAATGAAAATAAAAAAAATAAAAAAAAAGTAAA-AAAACAAATAAAATAAAG
1 AAAAATGAAAATAAAAAAAAT-AAAAAAAAGTAAACAAAACAAATAAAATAAAG
* **
71239 AAAAATG-AAAT-AAAAAGATAAAAAAAAGTAAACAAAGTAAATAAAATAA
1 AAAAATGAAAATAAAAAAAATAAAAAAAAGTAAACAAAACAAATAAAATAA
71288 TATATGACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 13 0.29
51 21 0.47
52 4 0.09
53 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (53 bp):
AAAAATGAAAATAAAAAAAATAAAAAAAAGTAAACAAAACAAATAAAATAAAG
Found at i:71475 original size:24 final size:22
Alignment explanation
Indices: 71443--71680 Score: 70
Period size: 23 Copynumber: 10.7 Consensus size: 22
71433 AAATGTTAGG
71443 AAAAATATATAGAATATATAATA
1 AAAAATATATA-AATATATAATA
*
71466 ATAAAATATA-CAATA-ATAATA
1 A-AAAATATATAAATATATAATA
* * *
71487 AAAAATACA-AAAAACATAATGA
1 AAAAATATATAAATATATAAT-A
71509 AGAAAATA-ATAAAATATATAAT-
1 A-AAAATATAT-AAATATATAATA
* *
71531 ATATATATAATAACA-ATAATAATA
1 AAAAATAT-ATAA-ATAT-ATAATA
* * *
71555 ATAAAGACA-AAA-A-ATAATA
1 AAAAATATATAAATATATAATA
*
71574 AAAAATAGTAT-AATATAATAGTA
1 AAAAATA-TATAAATAT-ATAATA
* * * *
71597 AGAAATAAAAAAATCA-AAAAT-
1 AAAAATATATAAAT-ATATAATA
* *
71618 AAAGATATATAGAAAATA-AATA
1 AAAAATATATA-AATATATAATA
*
71640 GAAAAATATAATTAAAAATATAATA
1 -AAAAATAT-A-TAAATATATAATA
* *
71665 TATAAATGTATAAATA
1 -AAAAATATATAAATA
71681 AGATATTAGA
Statistics
Matches: 160, Mismatches: 30, Indels: 50
0.67 0.12 0.21
Matches are distributed among these distances:
19 11 0.07
20 13 0.08
21 30 0.19
22 21 0.13
23 42 0.26
24 31 0.19
25 12 0.08
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAATATATAAATATATAATA
Found at i:71483 original size:18 final size:18
Alignment explanation
Indices: 71460--71555 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 18
71450 TATAGAATAT
71460 ATAATAATAAAATATACA
1 ATAATAATAAAATATACA
*
71478 ATAATAATAAAAAATACA
1 ATAATAATAAAATATACA
* * *
71496 A-AA-AACATAATGA-AGA
1 ATAATAATAAAAT-ATACA
*
71512 A-AATAATAAAATATATA
1 ATAATAATAAAATATACA
*
71529 AT-ATATATATAATA-ACA
1 ATAATA-ATAAAATATACA
71546 ATAATAATAA
1 ATAATAATAA
71556 TAAAGACAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.18
17 22 0.36
18 28 0.46
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
ATAATAATAAAATATACA
Found at i:71558 original size:18 final size:19
Alignment explanation
Indices: 71460--71574 Score: 69
Period size: 18 Copynumber: 6.7 Consensus size: 19
71450 TATAGAATAT
71460 ATAATAATAA-AATATACA
1 ATAATAATAATAATATACA
*
71478 ATAATAATAA-AAAATACA
1 ATAATAATAATAATATACA
* *
71496 A-AA-AA-CATAATGA-AGA
1 ATAATAATAATAAT-ATACA
*
71512 A-AATAATAA-AATATATA
1 ATAATAATAATAATATACA
71529 AT-AT-ATATATAATA-ACA
1 ATAATAATA-ATAATATACA
*
71546 ATAATAATAATAA-AGACA
1 ATAATAATAATAATATACA
71564 A-AA-AATAATAA
1 ATAATAATAATAA
71575 AAAATAGTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
15 1 0.01
16 21 0.27
17 21 0.27
18 33 0.42
19 3 0.04
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAATAATAATAATATACA
Found at i:71574 original size:3 final size:3
Alignment explanation
Indices: 71455--71558 Score: 56
Period size: 3 Copynumber: 33.7 Consensus size: 3
71445 AAATATATAG
* * *
71455 AAT ATAT AAT AAT AA- AAT ATAC AAT AAT AAT AA- AA- AAT ACAA AAA
1 AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT AAT
* *
71500 ACAT AAT GAAG AA- AAT AAT AA- AAT ATAT AAT ATAT ATAT AAT AAC
1 A-AT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT A-AT A-AT AAT AAT
71545 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
71559 AGACAAAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
2 10 0.12
3 52 0.63
4 21 0.25
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:71710 original size:15 final size:14
Alignment explanation
Indices: 71690--71746 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
71680 AAGATATTAG
71690 ATAAAAATAATAAAA
1 ATAAAAATAA-AAAA
*
71705 ATAAAAGTAAAAAA
1 ATAAAAATAAAAAA
* *
71719 ATAAACAA-CAAATA
1 ATAAA-AATAAAAAA
71733 A-AAAAATAAAAAA
1 ATAAAAATAAAAAA
71746 A
1 A
71747 ATAAGAAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.06
13 8 0.24
14 14 0.41
15 10 0.29
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.14
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:71721 original size:20 final size:18
Alignment explanation
Indices: 71690--71747 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 18
71680 AAGATATTAG
71690 ATAAAAATAATAAAAATAAA
1 ATAAAAA-AATAAAAA-AAA
*
71710 AGTAAAAAAATAAACAACAA
1 A-TAAAAAAATAAA-AAAAA
71730 ATAAAAAAATAAAAAAAA
1 ATAAAAAAATAAAAAAAA
71748 TAAGAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 10 0.29
21 8 0.24
ACGTcount: A:0.81, C:0.03, G:0.02, T:0.14
Consensus pattern (18 bp):
ATAAAAAAATAAAAAAAA
Found at i:71747 original size:9 final size:9
Alignment explanation
Indices: 71690--71755 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 9
71680 AAGATATTAG
*
71690 ATAAAAATA
1 ATAAAAAAA
71699 ATAAAAATAA
1 ATAAAAA-AA
71709 A-AGTAAAAAA
1 ATA--AAAAAA
71719 ATAAACAACAA
1 ATAAA-AA-AA
71730 AT-AAAAAA
1 ATAAAAAAA
71738 ATAAAAAAA
1 ATAAAAAAA
71747 ATAAGAAAA
1 ATAA-AAAA
71756 GGACTAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
8 4 0.08
9 22 0.46
10 13 0.27
11 9 0.19
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:71755 original size:8 final size:8
Alignment explanation
Indices: 71692--71746 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
71682 GATATTAGAT
71692 AAAAATAA
1 AAAAATAA
71700 TAAAAAT--
1 -AAAAATAA
*
71707 AAAAGTAA
1 AAAAATAA
71715 AAAAATAAA
1 AAAAAT-AA
71724 CAACAAATAA
1 -AA-AAATAA
71734 AAAAATAA
1 AAAAATAA
71742 AAAAA
1 AAAAA
71747 ATAAGAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
6 5 0.13
8 16 0.41
9 10 0.26
10 4 0.10
11 4 0.10
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:78287 original size:32 final size:33
Alignment explanation
Indices: 78251--78328 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
78241 AAAAAATCCG
* *
78251 GGGTCGGGTTTTT-AAAGTTTGATATTTGGGTC
1 GGGTCGGGTTTTTGAAAGTGTGATATTCGGGTC
* *
78283 GGGTCGGGTTTTTGTAAGTGTGATATTCGTGTC
1 GGGTCGGGTTTTTGAAAGTGTGATATTCGGGTC
* *
78316 GGGTTGTGTTTTT
1 GGGTCGGGTTTTT
78329 TTCAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 13 0.33
33 26 0.67
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.46
Consensus pattern (33 bp):
GGGTCGGGTTTTTGAAAGTGTGATATTCGGGTC
Found at i:78447 original size:28 final size:28
Alignment explanation
Indices: 78379--78470 Score: 79
Period size: 28 Copynumber: 3.3 Consensus size: 28
78369 CGGGTTCGGG
78379 TCGGGTCGGG--TTTTTAAGTTTGC--TAT
1 TCGGGTCGGGTTTTTTTAAG--TGCAGTAT
* *
78405 TCTGGTCGGATTTTTTTTAAGTGCAGTAT
1 TCGGGTCGG-GTTTTTTTAAGTGCAGTAT
78434 TCGGGTCGGGTTTTTTTAAGT--ATGATAT
1 TCGGGTCGGGTTTTTTTAAGTGCA-G-TAT
78462 TCGGGTCGG
1 TCGGGTCGG
78471 TCGGGGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 9 0.16
27 4 0.07
28 23 0.42
29 19 0.35
ACGTcount: A:0.14, C:0.11, G:0.30, T:0.45
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGCAGTAT
Found at i:78480 original size:33 final size:32
Alignment explanation
Indices: 78437--78513 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 32
78427 GCAGTATTCG
78437 GGTCGGGTTTTTTTAAGTATGATATTCG-GGTC
1 GGTCGGG-TTTTTTAAGTATGATATTCGAGGTC
*
78469 GGTCGGGGTTTTTTAAGTGTGATATTCGAGGTC
1 GGTC-GGGTTTTTTAAGTATGATATTCGAGGTC
78502 GGATTCGGGTTT
1 GG--TCGGGTTT
78514 AGGGTGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 23 0.57
33 9 0.22
34 6 0.15
35 2 0.05
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (32 bp):
GGTCGGGTTTTTTAAGTATGATATTCGAGGTC
Found at i:78481 original size:32 final size:33
Alignment explanation
Indices: 78437--78503 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
78427 GCAGTATTCG
*
78437 GGTCGGGTTTTTTTAAGTATGATATTCG-GGTC
1 GGTCGGGGTTTTTTAAGTATGATATTCGAGGTC
*
78469 GGTCGGGGTTTTTTAAGTGTGATATTCGAGGTC
1 GGTCGGGGTTTTTTAAGTATGATATTCGAGGTC
78502 GG
1 GG
78504 ATTCGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.15, C:0.09, G:0.36, T:0.40
Consensus pattern (33 bp):
GGTCGGGGTTTTTTAAGTATGATATTCGAGGTC
Found at i:80775 original size:22 final size:22
Alignment explanation
Indices: 80725--80775 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
80715 CATTATAATC
*
80725 CTAAAT-TTTAAAATCTAAAAT
1 CTAAATCTTAAAAATCTAAAAT
* *
80746 -TATTATCTTAAAAATCTAAATT
1 CTA-AATCTTAAAAATCTAAAAT
80768 CTAAATCT
1 CTAAATCT
80776 AATCCTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
20 2 0.09
21 2 0.09
22 17 0.74
23 2 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (22 bp):
CTAAATCTTAAAAATCTAAAAT
Found at i:82325 original size:2 final size:2
Alignment explanation
Indices: 82318--82345 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82308 CTTAATCAAC
82318 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
82346 TCAATTATAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82738 original size:2 final size:2
Alignment explanation
Indices: 82692--82724 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
82682 TTGTTGAATT
82692 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 T
82725 GATCCAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83259 original size:59 final size:60
Alignment explanation
Indices: 83131--83297 Score: 158
Period size: 59 Copynumber: 2.8 Consensus size: 60
83121 TTCACCGTAT
* * * * * * ** * * * *
83131 ATCCCTAATCTATGATCCTCATTTTAAATTAGGCCATAAACTTTTGAACATTCTAATTTT
1 ATCCCCAAACTATAATCATCATTTTATATTAGTCCCCAAACTTTTGAACATGCCAAATTC
* * *
83191 ATCCTCAAACTATACT-TTCATTTTATATTAGTCCCCAAACTTTTGAACATGCCAAATTC
1 ATCCCCAAACTATAATCATCATTTTATATTAGTCCCCAAACTTTTGAACATGCCAAATTC
* *
83250 ATCCCCAAACTATAATCATCCTTCTATATT-GATCCCCAAACTTTTGAA
1 ATCCCCAAACTATAATCATCATTTTATATTAG-TCCCCAAACTTTTGAA
83298 TATTCTAATT
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
59 49 0.57
60 37 0.43
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
ATCCCCAAACTATAATCATCATTTTATATTAGTCCCCAAACTTTTGAACATGCCAAATTC
Found at i:83449 original size:60 final size:60
Alignment explanation
Indices: 83345--83463 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
83335 TGGGGTATTA
* * *
83345 TTGGGATGTTCAAAAGTTTGGGGACTAAGTTATAATAGGGGTCATAGTTTGAGGATGAAT
1 TTGGGATGTTCAAAAGTTTGGGGACTAAGTTAGAATAGGAGTCATAGTTTAAGGATGAAT
* *
83405 TTGGGATGTTCAAAAGTTTTGGGA-TCAATTTAGAAT-GAGAGTCATAGTTTAAGGATGAA
1 TTGGGATGTTCAAAAGTTTGGGGACT-AAGTTAGAATAG-GAGTCATAGTTTAAGGATGAA
83464 ATTAAAATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 2 0.04
60 50 0.96
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (60 bp):
TTGGGATGTTCAAAAGTTTGGGGACTAAGTTAGAATAGGAGTCATAGTTTAAGGATGAAT
Found at i:83474 original size:60 final size:60
Alignment explanation
Indices: 83350--83481 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
83340 TATTATTGGG
* * * * ***
83350 ATGTTCAAAAGTTTGGGGACTAAGTTATAATAGGGGTCATAGTTTGAGGATGAATTTGGG
1 ATGTTCAAAAGTTTGGGGACTAAGTTAGAATAGGAGTCATAGTTTAAGGATGAAATTAAA
* *
83410 ATGTTCAAAAGTTTTGGGA-TCAATTTAGAAT-GAGAGTCATAGTTTAAGGATGAAATTAAA
1 ATGTTCAAAAGTTTGGGGACT-AAGTTAGAATAG-GAGTCATAGTTTAAGGATGAAATTAAA
*
83470 ATGTTTAAAAGT
1 ATGTTCAAAAGT
83482 ATATGGGTCG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (60 bp):
ATGTTCAAAAGTTTGGGGACTAAGTTAGAATAGGAGTCATAGTTTAAGGATGAAATTAAA
Found at i:83496 original size:60 final size:59
Alignment explanation
Indices: 83385--83513 Score: 134
Period size: 60 Copynumber: 2.2 Consensus size: 59
83375 TATAATAGGG
* * *** * * *
83385 GTCATAGTTTGAGGATGAATTTGGGATGTTCAAAAGTTTTGGGATCAATTTAGAATGAGA
1 GTCATAGTTTAAGGATGAAATTAAAATGTTCAAAAGTTATGGGATCAATTTAAAAT-AAA
* *
83445 GTCATAGTTTAAGGATGAAATTAAAATGTTTAAAAGTATATGGG-TCGATTTAAAATAAA
1 GTCATAGTTTAAGGATGAAATTAAAATGTTCAAAAGT-TATGGGATCAATTTAAAATAAA
*
83504 TTCATAGTTT
1 GTCATAGTTT
83514 GGGATGTATG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
59 11 0.19
60 41 0.72
61 5 0.09
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (59 bp):
GTCATAGTTTAAGGATGAAATTAAAATGTTCAAAAGTTATGGGATCAATTTAAAATAAA
Found at i:87896 original size:58 final size:58
Alignment explanation
Indices: 87827--88015 Score: 211
Period size: 58 Copynumber: 3.3 Consensus size: 58
87817 AATTTTGTAT
** * *
87827 ATAAAGACCAAACTTTATAAAGTGATCAATTAAAGATTAAGGGTTTTAAAATAATCGA
1 ATAAAGACCAAACTTTATAAAGTGATCAATTAAAGATTAAACGCTTCAAAATAATCGA
* * ** *
87885 ATAAAGACCAAATTTTATAAAGTGATCAATTAATGA-TAAACGCTTCAAAATGGTTGA
1 ATAAAGACCAAACTTTATAAAGTGATCAATTAAAGATTAAACGCTTCAAAATAATCGA
* * * * * *
87942 ATAAAAATCAAACTTTATAAAGTGATTAACTAAGGATTAAACGCTTCAAAATGATC-A
1 ATAAAGACCAAACTTTATAAAGTGATCAATTAAAGATTAAACGCTTCAAAATAATCGA
*
87999 ATTAAAGATCAAACTTT
1 A-TAAAGACCAAACTTT
88016 TTCGAACCTC
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
57 46 0.41
58 65 0.59
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (58 bp):
ATAAAGACCAAACTTTATAAAGTGATCAATTAAAGATTAAACGCTTCAAAATAATCGA
Found at i:90358 original size:2 final size:2
Alignment explanation
Indices: 90351--90379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
90341 TAACCCTATT
90351 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
90380 TTTAGAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:91760 original size:123 final size:124
Alignment explanation
Indices: 91575--91837 Score: 332
Period size: 123 Copynumber: 2.1 Consensus size: 124
91565 CATATAAGTA
* * * * * *
91575 CTTTAGTTGCGTTTTTAGATAAACGCCGCAATAGGGTACATATATTGTGGCGTTTTTAGACAAGC
1 CTTTAGTGGCGTTTTCAAACAAACGCCGCAATAGGGTACATATATTGTGGCATTTTTAGACAAAC
* * * * *
91640 GCCGCTAGAA-CTTAGTACTTTAGTGG-TGTTTCTAAATAAACGCTACAAAAGAATCATT
66 GCCGCTACAACCTTA-TACTTTAGTGGACGTTTCTAAACAAACGCCACAAAAGAATCACT
* *
91698 CTTTAGTGGCGTTTTCAAACAAATGCCGCAATATGGTACATATATTGTGGCATTTTTAGACAAAC
1 CTTTAGTGGCGTTTTCAAACAAACGCCGCAATAGGGTACATATATTGTGGCATTTTTAGACAAAC
** *
91763 GTTGCTACAACCTTATACTTTAGTGGCACGTTTCTAAACAAATGCCACAAAAGAATCACT
66 GCCGCTACAACCTTATACTTTAGTGG-ACGTTTCTAAACAAACGCCACAAAAGAATCACT
* *
91823 CCTTAGTGGTGTTTT
1 CTTTAGTGGCGTTTT
91838 TGAAATAAAC
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
123 75 0.63
124 4 0.03
125 40 0.34
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (124 bp):
CTTTAGTGGCGTTTTCAAACAAACGCCGCAATAGGGTACATATATTGTGGCATTTTTAGACAAAC
GCCGCTACAACCTTATACTTTAGTGGACGTTTCTAAACAAACGCCACAAAAGAATCACT
Found at i:98840 original size:20 final size:20
Alignment explanation
Indices: 98815--98879 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
98805 TTCATCCAAT
**
98815 TTTTTAAACCTTAGACCGGA
1 TTTTTAAACCCCAGACCGGA
*
98835 TTTTTAAACCCCAAACCGGA
1 TTTTTAAACCCCAGACCGGA
*
98855 TTTTTAAACCCCAGACCAGA
1 TTTTTAAACCCCAGACCGGA
98875 TTTTT
1 TTTTT
98880 TCCGGATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:99525 original size:132 final size:132
Alignment explanation
Indices: 99288--99549 Score: 470
Period size: 132 Copynumber: 2.0 Consensus size: 132
99278 GTACGATTAT
* * *
99288 TAATGATGTTGAGGATCCGGTCCGCCCGGACTTGTTCGTTTTGACTCGAATAGCATCCCGCCGTT
1 TAATGATGCTGAGGATCCGGTCCGCCCGGACTTGTTCGTTTCGACTCAAATAGCATCCCGCCGTT
99353 TCTTTGAATGCTTGCTTTAATGGCTTCCCTGCCTTCTTCAACCAATGCACGCTTAGATTCAGCAA
66 TCTTTGAATGCTTGCTTTAATGGCTTCCCTGCCTTCTTCAACCAATGCACGCTTAGATTCAGCAA
99418 AG
131 AG
* *
99420 TAATGATGCTGAGGATCCGGTCCGCCTGGACTTGTTCGTTTCGACTCAAATGGCATCCCGCCGTT
1 TAATGATGCTGAGGATCCGGTCCGCCCGGACTTGTTCGTTTCGACTCAAATAGCATCCCGCCGTT
*
99485 TCTTTGAATGCTTGTTTTAATGGCTTCCCTGCCTTCTTCAACCAATGCACGCTTAGATTCAGCAA
66 TCTTTGAATGCTTGCTTTAATGGCTTCCCTGCCTTCTTCAACCAATGCACGCTTAGATTCAGCAA
99550 CGGCTGCTTC
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (132 bp):
TAATGATGCTGAGGATCCGGTCCGCCCGGACTTGTTCGTTTCGACTCAAATAGCATCCCGCCGTT
TCTTTGAATGCTTGCTTTAATGGCTTCCCTGCCTTCTTCAACCAATGCACGCTTAGATTCAGCAA
AG
Found at i:100601 original size:2 final size:2
Alignment explanation
Indices: 100594--100634 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
100584 CTCATTTCAA
100594 AT AT 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 AT AT A
100635 ATTGTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:100761 original size:22 final size:21
Alignment explanation
Indices: 100652--100759 Score: 71
Period size: 23 Copynumber: 5.0 Consensus size: 21
100642 ATACTTAGAG
*
100652 TAATTATAATAATTTCATTT-
1 TAATTATAATAATTTTATTTA
100672 TAATTA-AATAATATTT-TTGTA
1 TAATTATAATAAT-TTTATT-TA
* *
100693 TCAAATATATATTAATTTTAATTA
1 T--AAT-TATAATAATTTTATTTA
* *
100717 AATATTACT-ATATATATTATTTA
1 TA-ATTA-TAATA-ATTTTATTTA
100740 TAATTATAATAATTTTATTT
1 TAATTATAATAATTTTATTT
100760 TAGTGAAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 23
0.68 0.09 0.23
Matches are distributed among these distances:
19 8 0.12
20 9 0.13
21 10 0.15
22 12 0.18
23 15 0.22
24 7 0.10
25 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.54
Consensus pattern (21 bp):
TAATTATAATAATTTTATTTA
Found at i:102255 original size:21 final size:21
Alignment explanation
Indices: 102230--102270 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
102220 CTTTGATTTA
*
102230 TTGTTATGGATTTCAAGTTTG
1 TTGTTATGGATGTCAAGTTTG
102251 TTGTTATGGATGTCAAGTTT
1 TTGTTATGGATGTCAAGTTT
102271 ATTGAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.24, T:0.51
Consensus pattern (21 bp):
TTGTTATGGATGTCAAGTTTG
Found at i:104711 original size:44 final size:44
Alignment explanation
Indices: 104663--104759 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
104653 TTTATACAAA
* * * *
104663 AAACACCACTATATGTCAGAATATTTA-ACGACGTCTTCGGGAAC
1 AAACACCACTAAATATCAGAACATTTAGA-GACGTCTTCAGGAAC
* * *
104707 AAACACCCCTAAATATCAGAACATTTAGAGACGTTTTTAGGAAC
1 AAACACCACTAAATATCAGAACATTTAGAGACGTCTTCAGGAAC
*
104751 AAACGCCAC
1 AAACACCAC
104760 AAAAGAAAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (44 bp):
AAACACCACTAAATATCAGAACATTTAGAGACGTCTTCAGGAAC
Done.