Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009127.1 Hibiscus syriacus cultivar Beakdansim tig00112623_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: 64136
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3677 original size:6 final size:6
Alignment explanation
Indices: 3652--3691 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3642 CAAAAGCAAC
*
3652 AAAAAG AGAAAAG AAGAAG AAAAAG AAAAAG -AAAAG AAAA
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
3692 GACTCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:8606 original size:19 final size:20
Alignment explanation
Indices: 8584--8626 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
8574 AGCATGTGAC
8584 TTCATT-AAAATCATGTATT
1 TTCATTAAAAATCATGTATT
8603 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
8623 TTCA
1 TTCA
8627 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:13053 original size:17 final size:19
Alignment explanation
Indices: 13031--13077 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
13021 GTAGGAGTCT
13031 TTTTCTTTTCTCTT-TTG-
1 TTTTCTTTTCTCTTGTTGC
13048 TTTTCTTCTT-TCTTGTTGC
1 TTTTCTT-TTCTCTTGTTGC
*
13067 TTTTTTTTTCT
1 TTTTCTTTTCT
13078 AACACTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.44
18 7 0.28
19 7 0.28
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCTCTTGTTGC
Found at i:13476 original size:33 final size:34
Alignment explanation
Indices: 13410--13514 Score: 92
Period size: 33 Copynumber: 3.1 Consensus size: 34
13400 GCCTTGTTGA
* * *
13410 TGAATG-AAGGATGAT-TTAATGGTGATGAAATGG
1 TGAATGAAAGGATGATGTTATTGGCG-TGATATGG
13443 T-AATGAAAGGATGATGTTATTGGCGTGATATGG
1 TGAATGAAAGGATGATGTTATTGGCGTGATATGG
* * *
13476 TGAAGGAATATGG-TGATGATATAGGCGTGATAATGG
1 TGAATGAA-A-GGATGATGTTATTGGCGTGAT-ATGG
13512 TGA
1 TGA
13515 TGGACTATGG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
32 4 0.07
33 18 0.30
34 12 0.20
35 17 0.28
36 9 0.15
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.30
Consensus pattern (34 bp):
TGAATGAAAGGATGATGTTATTGGCGTGATATGG
Found at i:13524 original size:36 final size:36
Alignment explanation
Indices: 13454--13566 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
13444 AATGAAAGGA
* * *
13454 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
13489 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
13525 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
13561 TGATGA
1 TGATGA
13567 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:19240 original size:33 final size:33
Alignment explanation
Indices: 19198--19266 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19188 GTTGATGAAT
*
19198 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
19231 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
19264 GAA
1 GAA
19267 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:19271 original size:13 final size:12
Alignment explanation
Indices: 19252--19348 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
19242 TTATTGGCGT
19252 GATATGGTGATG
1 GATATGGTGATG
19264 GAATATGGTGAT-
1 G-ATATGGTGATG
*
19276 GATATAG-GA-G
1 GATATGGTGATG
19286 TGATAATGGTGATG
1 -GAT-ATGGTGATG
19300 GACTATGGTGAT-
1 GA-TATGGTGATG
*
19312 GATATAGGCG-T-
1 GATAT-GGTGATG
*
19323 GATAATGGAGATG
1 GAT-ATGGTGATG
19336 GATTATGGTGATG
1 GA-TATGGTGATG
19349 AAAATAGTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
10 2 0.03
11 18 0.26
12 13 0.19
13 32 0.47
14 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:19301 original size:36 final size:36
Alignment explanation
Indices: 19250--19349 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
19240 TGTTATTGGC
19250 GTGAT-ATGGTGATGGAATATGGTGATGATATAGGA
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGA
* *
19285 GTGATAATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGA
* *
19321 GTGATAATGGAGATGGATTATGGTGATGA
1 GTGATAATGGTGATGGAATATGGTGATGA
19350 AAATAGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 5 0.08
36 55 0.92
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (36 bp):
GTGATAATGGTGATGGAATATGGTGATGATATAGGA
Found at i:22835 original size:19 final size:21
Alignment explanation
Indices: 22806--22847 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
22796 TGTAGGAGTC
*
22806 TTTTTCTTTTCTT-TTTCTTT
1 TTTTTCTTTTCTTGTTGCTTT
22826 TTTTTC-TTTCTTGTTGCTTT
1 TTTTTCTTTTCTTGTTGCTTT
22846 TT
1 TT
22848 GTTGTAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTCTTGTTGCTTT
Found at i:23232 original size:33 final size:33
Alignment explanation
Indices: 23190--23258 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
23180 GTTGATGAAT
*
23190 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
23223 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
23256 GAA
1 GAA
23259 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:23263 original size:13 final size:12
Alignment explanation
Indices: 23244--23340 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
23234 TTATTGGCGT
23244 GATATGGTGATG
1 GATATGGTGATG
23256 GAATATGGTGAT-
1 G-ATATGGTGATG
*
23268 GATATAGGCG-T-
1 GATAT-GGTGATG
23279 GATAATGGTGATG
1 GAT-ATGGTGATG
23292 GACTATGGTGAT-
1 GA-TATGGTGATG
*
23304 GATATAGGCG-T-
1 GATAT-GGTGATG
*
23315 GATAATGGAGATG
1 GAT-ATGGTGATG
23328 GATTATGGTGATG
1 GA-TATGGTGATG
23341 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:23299 original size:36 final size:36
Alignment explanation
Indices: 23229--23341 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
23219 AATGGAAGGA
* *
23229 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
23264 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
23300 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
23336 TGATGA
1 TGATGA
23342 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:24937 original size:36 final size:35
Alignment explanation
Indices: 24885--24997 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 35
24875 GATACTATTT
*
24885 TCATCACCATAATTCATCTCCATTATCACGCCTATA
1 TCATCACCAT-ATTCATCACCATTATCACGCCTATA
24921 TCATCACCATAGTTCATCACCATTATCACGCCTATA
1 TCATCACCATA-TTCATCACCATTATCACGCCTATA
* *
24957 TCATCACCATATTCCTTCACCA-TATCACGCCAATA
1 TCATCACCATATT-CATCACCATTATCACGCCTATA
*
24992 ACATCA
1 TCATCA
24998 TCCTTTCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 20 0.28
36 51 0.72
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.30
Consensus pattern (35 bp):
TCATCACCATATTCATCACCATTATCACGCCTATA
Found at i:30518 original size:33 final size:32
Alignment explanation
Indices: 30481--30545 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
30471 ATATTCCTTC
*
30481 ACCATATCA-CGCCAATAACATCATCCTTTCATT
1 ACCATATCATCACCAATAA-ATCATCC-TTCATT
* *
30514 ACCATTTCATCACCATTAAATCATCCTTCATT
1 ACCATATCATCACCAATAAATCATCCTTCATT
30546 CATCAACAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.21
33 15 0.54
34 7 0.25
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (32 bp):
ACCATATCATCACCAATAAATCATCCTTCATT
Found at i:33599 original size:25 final size:25
Alignment explanation
Indices: 33567--33622 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
33557 AAAAATGAGA
* *
33567 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTCAAGCACTCAAAAAG
* *
33591 AAAGAAAATTCCAGTACTCAAAAAG
1 AAAGAAAATTCAAGCACTCAAAAAG
33616 -AAGAAAA
1 AAAGAAAA
33623 AAACAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.12
Consensus pattern (25 bp):
AAAGAAAATTCAAGCACTCAAAAAG
Found at i:36546 original size:19 final size:20
Alignment explanation
Indices: 36522--36572 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
36512 CGTCCAAGAG
* *
36522 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
36541 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
36561 CATGTATTTTCA
1 CATGTATTTTCA
36573 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:37028 original size:19 final size:19
Alignment explanation
Indices: 36986--37025 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
36976 TATCCCATCC
*
36986 TTATTTCATTTCATTTTTA
1 TTATTTCATTTCATTCTTA
*
37005 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
37025 T
1 T
37026 ATTATCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:40974 original size:13 final size:12
Alignment explanation
Indices: 40955--41051 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
40945 TTATTGGCAT
40955 GATATGGTGATG
1 GATATGGTGATG
40967 GAATATGGTGAT-
1 G-ATATGGTGATG
*
40979 GATATAGGCG-T-
1 GATAT-GGTGATG
40990 GATAATGGTGATG
1 GAT-ATGGTGATG
41003 GACTATGGTGAT-
1 GA-TATGGTGATG
*
41015 GATATAGGCG-T-
1 GATAT-GGTGATG
*
41026 GATAATGGAGATG
1 GAT-ATGGTGATG
41039 GATTATGGTGATG
1 GA-TATGGTGATG
41052 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:41003 original size:36 final size:36
Alignment explanation
Indices: 40940--41052 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
40930 AATGGAAGGA
* * *
40940 TGATGTTATTGGCATGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
40975 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
41011 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
41047 TGATGA
1 TGATGA
41053 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 15 0.21
36 56 0.79
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:42122 original size:22 final size:22
Alignment explanation
Indices: 42082--42123 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42072 TAATATGTGG
* *
42082 TTCATAACATTAACTTCATACA
1 TTCATAACATCAACATCATACA
*
42104 TTCATAATATCAACATCATA
1 TTCATAACATCAACATCATA
42124 ACTATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (22 bp):
TTCATAACATCAACATCATACA
Found at i:50556 original size:17 final size:16
Alignment explanation
Indices: 50534--50598 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 16
50524 TGTAGGAGTC
50534 TTTCTTTTCTCTTTTGT
1 TTTCTTTT-TCTTTTGT
*
50551 TTTCTTCTTTCTTTTTT
1 TTTCTT-TTTCTTTTGT
*
50568 TTTCTTTTT-TTTTCT
1 TTTCTTTTTCTTTTGT
* *
50583 TTT-TGTTGCTTTTGT
1 TTTCTTTTTCTTTTGT
50598 T
1 T
50599 GCAGCACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
14 3 0.07
15 14 0.34
16 3 0.07
17 19 0.46
18 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTCTTTTGT
Found at i:50559 original size:24 final size:21
Alignment explanation
Indices: 50532--50595 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
50522 GTTGTAGGAG
*
50532 TCTTTCTTTTCTCTTTTGTTTTCT
1 TCTTTCTTTT-T-TTTTCTTTT-T
50556 TCTTTCTTTTTTTTTCTTTTT
1 TCTTTCTTTTTTTTTCTTTTT
* *
50577 T-TTTCTTTTTGTTGCTTTT
1 TCTTTCTTTTTTTTTCTTTT
50596 GTTGCAGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 16 0.43
21 2 0.05
22 8 0.22
23 1 0.03
24 10 0.27
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (21 bp):
TCTTTCTTTTTTTTTCTTTTT
Found at i:50571 original size:10 final size:10
Alignment explanation
Indices: 50534--50586 Score: 61
Period size: 10 Copynumber: 4.9 Consensus size: 10
50524 TGTAGGAGTC
50534 TTTCTTTTCTCT
1 TTTCTTTT-T-T
*
50546 TTTGTTTTCTT
1 TTTCTTTT-TT
50557 CTTTCTTTTTT
1 -TTTCTTTTTT
50568 TTTCTTTTTT
1 TTTCTTTTTT
50578 TTTCTTTTT
1 TTTCTTTTT
50587 GTTGCTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 19 0.50
11 3 0.08
12 16 0.42
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:50978 original size:33 final size:33
Alignment explanation
Indices: 50936--51004 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
50926 GTTGATGAAT
*
50936 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
50969 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
51002 GAA
1 GAA
51005 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:51009 original size:13 final size:12
Alignment explanation
Indices: 50990--51086 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
50980 TTATTGGCGT
50990 GATATGGTGATG
1 GATATGGTGATG
51002 GAATATGGTGAT-
1 G-ATATGGTGATG
*
51014 GATATAGGCG-T-
1 GATAT-GGTGATG
51025 GATAATGGTGATG
1 GAT-ATGGTGATG
51038 GACTATGGTGAT-
1 GA-TATGGTGATG
*
51050 GATATAGGCG-T-
1 GATAT-GGTGATG
*
51061 GATAATGGAGATG
1 GAT-ATGGTGATG
51074 GATTATGGTGATG
1 GA-TATGGTGATG
51087 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:51045 original size:36 final size:36
Alignment explanation
Indices: 50975--51087 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
50965 AATGGAAGGA
* *
50975 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
51010 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
51046 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
51082 TGATGA
1 TGATGA
51088 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:52577 original size:18 final size:20
Alignment explanation
Indices: 52554--52599 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52544 CGTCCAAAGG
52554 CATGTA-TCTCATT-AAAAT
1 CATGTATTCTCATTAAAAAT
*
52572 CATGTATTTTCATTAAAAAT
1 CATGTATTCTCATTAAAAAT
*
52592 CATATATT
1 CATGTATT
52600 TTCAAAGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 12 0.50
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (20 bp):
CATGTATTCTCATTAAAAAT
Found at i:52586 original size:19 final size:20
Alignment explanation
Indices: 52562--52603 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52552 GGCATGTATC
*
52562 TCATT-AAAATCATGTATTT
1 TCATTAAAAATCATATATTT
52581 TCATTAAAAATCATATATTT
1 TCATTAAAAATCATATATTT
52601 TCA
1 TCA
52604 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (20 bp):
TCATTAAAAATCATATATTT
Found at i:56258 original size:20 final size:21
Alignment explanation
Indices: 56209--56261 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
56199 CGGCAAAGAG
*
56209 CATGTATCTTCATTAAAAAAT
1 CATGTATTTTCATTAAAAAAT
* *
56230 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTAAAAAAT
56251 CATG-ATTTTCA
1 CATGTATTTTCA
56262 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (21 bp):
CATGTATTTTCATTAAAAAAT
Found at i:60288 original size:19 final size:20
Alignment explanation
Indices: 60264--60311 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
60254 CGGCCAAGAG
60264 CATGTATCTTCA-TTAAAA-T
1 CATGTAT-TTCATTTAAAAGT
60283 CATGTATTTCATTTAAAAGT
1 CATGTATTTCATTTAAAAGT
60303 CATGTATTT
1 CATGTATTT
60312 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAGT
Found at i:63092 original size:20 final size:23
Alignment explanation
Indices: 63067--63116 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
63057 AATTAGAAGT
63067 TGGTGAT-A-ATAGGCGTGAT-A
1 TGGTGATCATATAGGCGTGATAA
63087 TGGTGATCATATAGGCGTGATAA
1 TGGTGATCATATAGGCGTGATAA
63110 TGGTGAT
1 TGGTGAT
63117 GGACAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.26
21 1 0.04
22 11 0.41
23 8 0.30
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (23 bp):
TGGTGATCATATAGGCGTGATAA
Done.