Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007807.1 Hibiscus syriacus cultivar Beakdansim tig00110126_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: 2195110
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 9 of 9
Found at i:2091933 original size:24 final size:24
Alignment explanation
Indices: 2091898--2091944 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2091888 CACCATGATA
* *
2091898 TGTATTTCTTCAGTTTCTTCGTCT
1 TGTATTTCTTCAGGTTCCTCGTCT
2091922 TGTATTGT-TTCAGGTTCCTCGTC
1 TGTATT-TCTTCAGGTTCCTCGTC
2091945 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.09, C:0.21, G:0.17, T:0.53
Consensus pattern (24 bp):
TGTATTTCTTCAGGTTCCTCGTCT
Found at i:2096773 original size:35 final size:35
Alignment explanation
Indices: 2096727--2096834 Score: 198
Period size: 35 Copynumber: 3.1 Consensus size: 35
2096717 TGTCTATAGG
*
2096727 CTTGGTGTTGGTTTGGCTAAGCCTTCATAAAGGGA
1 CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGGGA
2096762 CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGGGA
1 CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGGGA
*
2096797 CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGAGA
1 CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGGGA
2096832 CTT
1 CTT
2096835 CATAAAGGTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (35 bp):
CTTGGTGTTGGTTCGGCTAAGCCTTCATAAAGGGA
Found at i:2103994 original size:22 final size:23
Alignment explanation
Indices: 2103946--2103998 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2103936 TGCTTTTATT
2103946 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTT-TTTTTGAGTGCTTTCAA
*
2103970 TTTCTTTTTTTGAGTGCTTT-GA
1 TTTCTTTTTTTGAGTGCTTTCAA
2103992 TTTCTTT
1 TTTCTTT
2103999 GCTGGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.09, C:0.13, G:0.13, T:0.64
Consensus pattern (23 bp):
TTTCTTTTTTTGAGTGCTTTCAA
Found at i:2105491 original size:19 final size:21
Alignment explanation
Indices: 2105467--2105518 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2105457 CGACCAAGAG
*
2105467 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2105486 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2105507 CATGTATTTTCA
1 CATGTATTTTCA
2105519 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2106249 original size:11 final size:11
Alignment explanation
Indices: 2106235--2106289 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
2106225 AGAAAAGACA
2106235 AAAAGAAGAAG
1 AAAAGAAGAAG
2106246 AAAAGAAG-A-
1 AAAAGAAGAAG
2106255 AAAAGAA-AAG
1 AAAAGAAGAAG
*
2106265 AAAAAAAGAAG
1 AAAAGAAGAAG
*
2106276 AAAAGAAAAAG
1 AAAAGAAGAAG
2106287 AAA
1 AAA
2106290 TTCAAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.21
10 7 0.18
11 23 0.61
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:2106251 original size:8 final size:8
Alignment explanation
Indices: 2106240--2106282 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
2106230 AGACAAAAAG
2106240 AAGAAGAA
1 AAGAAGAA
2106248 AAGAAG-A
1 AAGAAGAA
2106255 AA-AAGAA
1 AAGAAGAA
*
2106262 AAGAAAAA
1 AAGAAGAA
2106270 AAGAAGAA
1 AAGAAGAA
2106278 AAGAA
1 AAGAA
2106283 AAAGAAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 3 0.10
7 6 0.19
8 22 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:2106285 original size:22 final size:21
Alignment explanation
Indices: 2106217--2106289 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 21
2106207 ATTGGAGTAC
2106217 AAAAAGAAAGAAAAGACAAAAAG
1 AAAAAGAAA-AAAAGA-AAAAAG
* *
2106240 AAGAAGAAAAGAAG-AAAAAG
1 AAAAAGAAAAAAAGAAAAAAG
2106260 -AAAAGAAAAAAAGAAGAAAAG
1 AAAAAGAAAAAAAGAA-AAAAG
2106281 AAAAAGAAA
1 AAAAAGAAA
2106290 TTCAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.26
20 7 0.16
21 5 0.12
22 12 0.28
23 8 0.19
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAAGAAAAAAG
Found at i:2106288 original size:33 final size:33
Alignment explanation
Indices: 2106223--2106289 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
2106213 GTACAAAAAG
* *
2106223 AAAGAAAAGACAAAAAGAAGAAGAAAAGAAGAA
1 AAAGAAAAGAAAAAAAGAAGAAGAAAAAAAGAA
2106256 AAAGAAAAGAAAAAAAGAAGAA-AAGAAAAAGAA
1 AAAGAAAAGAAAAAAAGAAGAAGAA-AAAAAGAA
2106289 A
1 A
2106290 TTCAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (33 bp):
AAAGAAAAGAAAAAAAGAAGAAGAAAAAAAGAA
Found at i:2106296 original size:27 final size:27
Alignment explanation
Indices: 2106218--2106289 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 27
2106208 TTGGAGTACA
*
2106218 AAAAGAA-AGAAAAGACAAA-AAGAAGAAG
1 AAAAGAAGA-AAAAGA-AAAGAA-AAAAAG
2106246 AAAAGAAGAAAAAGAAAAGAAAAAAAG
1 AAAAGAAGAAAAAGAAAAGAAAAAAAG
2106273 AAGAA-AAGAAAAAGAAA
1 AA-AAGAAGAAAAAGAAA
2106290 TTCAAAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 22 0.55
28 17 0.43
29 1 0.03
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (27 bp):
AAAAGAAGAAAAAGAAAAGAAAAAAAG
Found at i:2109412 original size:19 final size:21
Alignment explanation
Indices: 2109388--2109439 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2109378 CGGCCAAGAG
*
2109388 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2109407 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2109428 CATGTATTTTCA
1 CATGTATTTTCA
2109440 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2115800 original size:17 final size:17
Alignment explanation
Indices: 2115778--2115835 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2115768 TCAAAAAATA
*
2115778 AACTAGTTTGATGAATG
1 AACTAGTTTAATGAATG
*
2115795 AACTAGTTTAATTAATG
1 AACTAGTTTAATGAATG
* * *
2115812 AACTAACTTTATTCAATG
1 AACT-AGTTTAATGAATG
2115830 AACTAG
1 AACTAG
2115836 ATGCATGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (17 bp):
AACTAGTTTAATGAATG
Found at i:2115829 original size:18 final size:18
Alignment explanation
Indices: 2115791--2115834 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2115781 TAGTTTGATG
*
2115791 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
2115808 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
2115825 CAATGAACTA
1 -AATGAACTA
2115835 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:2118799 original size:17 final size:17
Alignment explanation
Indices: 2118777--2118930 Score: 146
Period size: 17 Copynumber: 8.9 Consensus size: 17
2118767 AATTAAGGGT
*
2118777 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
2118794 TAGTTTCATGAATGAAC
1 TAGTTTAATGAATGAAC
*
2118811 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
* * *
2118828 TAACTTTATTAAATGAAC
1 T-AGTTTAATGAATGAAC
* * ** *
2118846 TTGTAATCTTGAATAAAC
1 TAGT-TTAATGAATGAAC
* *
2118864 TAGTTTGATGAATGAAT
1 TAGTTTAATGAATGAAC
* *
2118881 TAGTTTGATGAATGAAT
1 TAGTTTAATGAATGAAC
2118898 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
2118915 TAGTTTAATCAATGAA
1 TAGTTTAATGAATGAA
2118931 ATACTTAGTT
Statistics
Matches: 113, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
17 87 0.77
18 26 0.23
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:2118865 original size:53 final size:52
Alignment explanation
Indices: 2118780--2118930 Score: 151
Period size: 52 Copynumber: 2.9 Consensus size: 52
2118770 TAAGGGTTAG
* *
2118780 TTTAATAAATGAACTAGTTTCATGAATGAACTAGTTTAATCAATGAACTAAC
1 TTTAATAAATGAACTAGTATCATGAATAAACTAGTTTAATCAATGAACTAAC
* * * * * * *
2118832 TTTATTAAATGAACTTGTAATCTTGAATAAACTAGTTTGATGAATGAA-TTAG
1 TTTAATAAATGAACTAGT-ATCATGAATAAACTAGTTTAATCAATGAACTAAC
* * * * * *
2118884 TTTGATGAATGAATTAGTTTAATGAATGAACTAGTTTAATCAATGAA
1 TTTAATAAATGAACTAGTATCATGAATAAACTAGTTTAATCAATGAA
2118931 ATACTTAGTT
Statistics
Matches: 78, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
51 23 0.29
52 31 0.40
53 24 0.31
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (52 bp):
TTTAATAAATGAACTAGTATCATGAATAAACTAGTTTAATCAATGAACTAAC
Found at i:2122521 original size:20 final size:22
Alignment explanation
Indices: 2122483--2122534 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
2122473 CATTAGAAAC
*
2122483 TAAAATGATATA-AACAT-AAG
1 TAAAATGAAATAGAACATAAAG
2122503 TAAAATGAAATAGAA-ATAAAG
1 TAAAATGAAATAGAACATAAAG
2122524 T--AATGAAATAG
1 TAAAATGAAATAG
2122535 TTGGTAGCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 13 0.45
21 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
TAAAATGAAATAGAACATAAAG
Found at i:2130227 original size:13 final size:12
Alignment explanation
Indices: 2130204--2130273 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 12
2130194 CTTTTTGAAC
2130204 TTCTTTTTTCTT
1 TTCTTTTTTCTT
2130216 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
2130229 TTCTTCTTTTCTGAT
1 TTCTT-TTTTCT--T
*
2130244 TT-TTTTTTCTC
1 TTCTTTTTTCTT
2130255 TTCTTTTTGTCTT
1 TTCTTTTT-TCTT
2130268 TTCTTT
1 TTCTTT
2130274 CTTTTTGCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
11 2 0.04
12 12 0.24
13 29 0.58
14 4 0.08
15 3 0.06
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:2130229 original size:8 final size:8
Alignment explanation
Indices: 2130216--2130278 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
2130206 CTTTTTTCTT
2130216 TTCTTTTC
1 TTCTTTTC
2130224 TTCTTTTC
1 TTCTTTTC
2130232 TTCTTTTC
1 TTCTTTTC
**
2130240 TGATTTT-
1 TTCTTTTC
2130247 TT-TTTCTC
1 TTCTTT-TC
2130255 TTCTTTT-
1 TTCTTTTC
2130262 TGTCTTTTC
1 T-TCTTTTC
2130271 TTTCTTTT
1 -TTCTTTT
2130279 TGCACTCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 30 0.65
9 9 0.20
10 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2130260 original size:31 final size:30
Alignment explanation
Indices: 2130214--2130271 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2130204 TTCTTTTTTC
2130214 TTTTCTTTTCTTCTTTTCT-TCTTTTCTGAT
1 TTTTCTTTTCTTCTTTT-TGTCTTTTCTGAT
*
2130244 TTTTTTTTCTCTTCTTTTTGTCTTTTCT
1 TTTTCTTT-TCTTCTTTTTGTCTTTTCT
2130272 TTCTTTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTTCTTTTCTTCTTTTTGTCTTTTCTGAT
Found at i:2130279 original size:31 final size:30
Alignment explanation
Indices: 2130203--2130279 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
2130193 TCTTTTTGAA
*
2130203 CTTC-TTT-TTTCTTTTCTTTTCTTCTTTT
1 CTTCTTTTCTTTCTTTTTTTTTCTTCTTTT
*
2130231 CTTCTTTTCTGATT-TTTTTTTCTCTTCTTTT
1 CTTCTTTTCT--TTCTTTTTTTTTCTTCTTTT
2130262 -TGTCTTTTCTTTCTTTTT
1 CT-TCTTTTCTTTCTTTTT
2130280 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 4 0.10
29 5 0.12
30 7 0.17
31 23 0.56
32 2 0.05
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (30 bp):
CTTCTTTTCTTTCTTTTTTTTTCTTCTTTT
Found at i:2134811 original size:13 final size:13
Alignment explanation
Indices: 2134789--2134818 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2134779 ACTAAACACC
2134789 TTTC-ACATACCT
1 TTTCAACATACCT
2134801 TTTCAACATACCT
1 TTTCAACATACCT
2134814 TTTCA
1 TTTCA
2134819 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:2140909 original size:7 final size:7
Alignment explanation
Indices: 2140892--2140943 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
2140882 TTCTTGCTGA
2140892 TTTTC-T
1 TTTTCTT
2140898 TTTTCTT
1 TTTTCTT
2140905 TTTTCTT
1 TTTTCTT
2140912 TTTTCTT
1 TTTTCTT
2140919 TTTTCTCT
1 TTTTCT-T
2140927 TTGTAT-TT
1 TT-T-TCTT
2140935 TTTTCTT
1 TTTTCTT
2140942 TT
1 TT
2140944 GAATGAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.15
7 26 0.63
8 6 0.15
9 2 0.05
10 1 0.02
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:2141620 original size:3 final size:3
Alignment explanation
Indices: 2141612--2141640 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2141602 ATCTATAGTT
2141612 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2141641 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2145181 original size:31 final size:31
Alignment explanation
Indices: 2145146--2145208 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2145136 TCGCCAAAGG
2145146 TCATGTCCTTTGTTTGAAGAGTCACATCCTT
1 TCATGTCCTTTGTTTGAAGAGTCACATCCTT
2145177 TCATGTCCTTTGTTTGAAGAGTCACATCCTT
1 TCATGTCCTTTGTTTGAAGAGTCACATCCTT
2145208 T
1 T
2145209 GGCAACTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (31 bp):
TCATGTCCTTTGTTTGAAGAGTCACATCCTT
Found at i:2147734 original size:19 final size:20
Alignment explanation
Indices: 2147691--2147742 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2147681 GAAACCCCTT
*
2147691 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTAAA
2147712 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2147731 TGAAGATACATG
1 TGAAAATACATG
2147743 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2150642 original size:15 final size:15
Alignment explanation
Indices: 2150622--2150672 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2150612 TGATATGGTA
2150622 ATGAAATAGGAAAAG
1 ATGAAATAGGAAAAG
2150637 ATG-AA-A-GAAAAGG
1 ATGAAATAGGAAAA-G
2150650 AAATGAAATAGGAAAAG
1 --ATGAAATAGGAAAAG
2150667 ATGAAA
1 ATGAAA
2150673 GAAAGGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 5 0.17
13 2 0.07
14 2 0.07
15 12 0.40
16 2 0.07
17 2 0.07
18 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (15 bp):
ATGAAATAGGAAAAG
Found at i:2150655 original size:30 final size:30
Alignment explanation
Indices: 2150621--2150690 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
2150611 ATGATATGGT
2150621 AATGAAATAGGAAAAGATGAAAGAAAAGGA
1 AATGAAATAGGAAAAGATGAAAGAAAAGGA
*
2150651 AATGAAATAGGAAAAGATGAAAGAAAGGGA
1 AATGAAATAGGAAAAGATGAAAGAAAAGGA
2150681 AATGAAATAG
1 AATGAAATAG
2150691 TAAGAAAGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.11
Consensus pattern (30 bp):
AATGAAATAGGAAAAGATGAAAGAAAAGGA
Found at i:2150850 original size:28 final size:26
Alignment explanation
Indices: 2150819--2150876 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
2150809 TTTGAATGTA
2150819 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTC-TTTT
* *
2150847 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
2150873 CTTT
1 CTTT
2150877 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 12 0.44
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (26 bp):
CTTTGAATCTTTCTTCCTTTTCTTTT
Found at i:2150933 original size:21 final size:21
Alignment explanation
Indices: 2150909--2150950 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2150899 TATAGGAGTA
* * *
2150909 TTCTTTTTTCTTTTTGTTTTT
1 TTCTTCTTTCTTGTTGCTTTT
2150930 TTCTTCTTTCTTGTTGCTTTT
1 TTCTTCTTTCTTGTTGCTTTT
2150951 GTTGCAGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (21 bp):
TTCTTCTTTCTTGTTGCTTTT
Found at i:2153582 original size:30 final size:30
Alignment explanation
Indices: 2153548--2153621 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
2153538 ATGCATGTCA
**
2153548 TGAGCTAAGTATATTATCATATAATAAATG
1 TGAGCTAAGTATACCATCATATAATAAATG
2153578 TGAGCTAAGTATACCATCATATAATAAATG
1 TGAGCTAAGTATACCATCATATAATAAATG
2153608 TGAGCTAATGTATA
1 TGAGCTAA-GTATA
2153622 AGGTCTAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 36 0.88
31 5 0.12
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (30 bp):
TGAGCTAAGTATACCATCATATAATAAATG
Found at i:2162613 original size:27 final size:29
Alignment explanation
Indices: 2162569--2162633 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 29
2162559 CTTTTTTTTC
*
2162569 TTTTCTTTTCTTTCTTTTTGAGTGCTTGAA
1 TTTT-TTTTCTTTCTTTTTGAGTGCTTCAA
2162599 TTTTTTTTC-TT-TTTTTGAGTGCTTCAA
1 TTTTTTTTCTTTCTTTTTGAGTGCTTCAA
*
2162626 TTTCTTTT
1 TTTTTTTT
2162634 GTTGAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 22 0.67
28 2 0.06
29 5 0.15
30 4 0.12
ACGTcount: A:0.09, C:0.12, G:0.11, T:0.68
Consensus pattern (29 bp):
TTTTTTTTCTTTCTTTTTGAGTGCTTCAA
Found at i:2172608 original size:14 final size:13
Alignment explanation
Indices: 2172591--2172640 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
2172581 GTGCAAAAAG
2172591 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
2172605 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
2172618 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
2172629 AAAGAAAAAGAA
1 AAAGAAAAAGAA
2172641 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:2172637 original size:19 final size:18
Alignment explanation
Indices: 2172585--2172640 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
2172575 ATTGGAGTGC
2172585 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
2172602 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
2172621 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
2172640 A
1 A
2172641 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:2172638 original size:11 final size:11
Alignment explanation
Indices: 2172585--2172640 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
2172575 ATTGGAGTGC
2172585 AAAAAG-AAAG
1 AAAAAGAAAAG
2172595 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
2172609 AAGAAGAAAAG
1 AAAAAGAAAAG
2172620 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
2172633 AAAAAGAA
1 AAAAAGAA
2172641 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Done.