Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004285.1 Hibiscus syriacus cultivar Beakdansim tig00009396_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: 56913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1238 original size:55 final size:55
Alignment explanation
Indices: 1165--1273 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
1155 AAAAATACTT
* *
1165 CGTTTAGGATGAAAACCCGAAAGGGA-GTCCTAAGTTGAAAAAAGAAAAAGAAAAA
1 CGTTTAGGATGAAAACCCGAAA-GGACGCCCTAAATTGAAAAAAGAAAAAGAAAAA
*
1220 CGTTTAGGGTGAAAACCCGAAAGGACGCCCTAAATTGAAAAAAGAAAAAGAAAA
1 CGTTTAGGATGAAAACCCGAAAGGACGCCCTAAATTGAAAAAAGAAAAAGAAAA
1274 GAGAAAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 3 0.06
55 47 0.94
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.14
Consensus pattern (55 bp):
CGTTTAGGATGAAAACCCGAAAGGACGCCCTAAATTGAAAAAAGAAAAAGAAAAA
Found at i:1269 original size:6 final size:6
Alignment explanation
Indices: 1258--1307 Score: 57
Period size: 6 Copynumber: 7.8 Consensus size: 6
1248 CCTAAATTGA
1258 AAAAAG AAAAAG AAAAGAG AAAAAAG AACAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAA-AG -AAAAAG -A-AAAAG AAAAAG AAAAAG AAAAA
1308 TAAGTTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
6 19 0.47
7 7 0.17
8 9 0.22
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1275 original size:11 final size:11
Alignment explanation
Indices: 1258--1307 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1248 CCTAAATTGA
1258 AAAAAGAAAAAG
1 AAAAAG-AAAAG
1270 AAAAGAGAAAA-
1 AAAA-AGAAAAG
* *
1281 AAGAACAAAAG
1 AAAAAGAAAAG
1292 AAAAAGAAAAG
1 AAAAAGAAAAG
1303 AAAAA
1 AAAAA
1308 TAAGTTGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 8 0.25
13 2 0.06
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1281 original size:8 final size:7
Alignment explanation
Indices: 1256--1301 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
1246 GCCCTAAATT
1256 GAAAAAA
1 GAAAAAA
1263 G-AAAAA
1 GAAAAAA
*
1269 GAAAAGA
1 GAAAAAA
1276 GAAAAAA
1 GAAAAAA
1283 GAACAAAA
1 GAA-AAAA
1291 G-AAAAA
1 GAAAAAA
1297 GAAAA
1 GAAAA
1302 GAAAAATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 11 0.32
7 18 0.53
8 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1283 original size:14 final size:14
Alignment explanation
Indices: 1264--1307 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1254 TTGAAAAAAG
1264 AAAAAGAAAAGAGA
1 AAAAAGAAAAGAGA
*
1278 AAAAAGAACAAAAG-
1 AAAAAGAA-AAGAGA
1292 AAAAAGAAAAGA-A
1 AAAAAGAAAAGAGA
1305 AAA
1 AAA
1308 TAAGTTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.23
14 16 0.62
15 4 0.15
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAGA
Found at i:2579 original size:106 final size:106
Alignment explanation
Indices: 2383--2844 Score: 567
Period size: 106 Copynumber: 4.5 Consensus size: 106
2373 GACGAAGGGG
* *
2383 CTTCCCAACTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGATAGCACAAGC
1 CTTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
*
2447 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAATAA
66 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
* *
2488 TTTCCCAACTTCAGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
1 CTTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
2553 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
66 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
* * * * *
2594 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCTAGACAACACAAGC
1 CTTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
* * * *
2659 TCAACTTTACGACGAAGGGACGGCTGATTGT---C--A-AA
66 TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
* * *
2694 -TT--C-A-TTCAGAGTCAATTTCAACTTCAC-GATGAAGGATATTAGACTCAAGACAGCACAAG
1 CTTCCCAACTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTCAAGACAGCACAAG
** *
2753 CTCAACTTCACAACGAAGGGGCGGCTGACTGTCAACAAATAA
65 CTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
* * * * * *
2795 TTTCCC-AGTTCATAACCAATTTCAACGTCAC-GACGGAGGATATTGGACTC
1 CTTCCCAACTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2845 GGAGCAATAC
Statistics
Matches: 311, Mismatches: 34, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
95 75 0.24
96 1 0.00
97 1 0.00
98 1 0.00
99 2 0.01
100 3 0.01
101 3 0.01
102 2 0.01
103 1 0.00
104 2 0.01
105 45 0.14
106 175 0.56
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (106 bp):
CTTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
TCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA
Found at i:2769 original size:95 final size:95
Alignment explanation
Indices: 2603--2787 Score: 271
Period size: 95 Copynumber: 1.9 Consensus size: 95
2593 ACTTCCCAAT
* * *
2603 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCTAGACAACACAAGCTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
* *
2668 CGACGAAGGGACGGCTGATTGTCAAATTCA
66 CAACGAAGGGACGGCTGACTGTCAAATTCA
* * * * *
2698 TTCAGAGTCAATTTCAACTTCACGATGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
*
2763 CAACGAAGGGGCGGCTGACTGTCAA
66 CAACGAAGGGACGGCTGACTGTCAA
2788 CAAATAATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (95 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGACGGCTGACTGTCAAATTCA
Found at i:4871 original size:14 final size:14
Alignment explanation
Indices: 4842--4893 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
4832 GGTGTATTTT
4842 TTTATTTATCTA-TA
1 TTTATTTAT-TATTA
4856 TTTATTTATTATTA
1 TTTATTTATTATTA
**
4870 TTCCTTTATTATTA
1 TTTATTTATTATTA
*
4884 TTTTTTTATT
1 TTTATTTATT
4894 TTAATCTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 31 0.94
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:7524 original size:3 final size:3
Alignment explanation
Indices: 7511--7606 Score: 183
Period size: 3 Copynumber: 31.7 Consensus size: 3
7501 TCCAACATCA
7511 AAG ACAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
7557 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
7605 AA
1 AA
7607 AATGGAGATT
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 89 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8868 original size:21 final size:23
Alignment explanation
Indices: 8826--8873 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
8816 ATACTAAAGT
*
8826 TATTATGTTCATATAATTTTTTGA
1 TATTATGTTCATAT-ATTTTTTAA
8850 TATTATGTTCAT-T-TTTTTTAA
1 TATTATGTTCATATATTTTTTAA
8871 TAT
1 TAT
8874 GGACAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
23 1 0.04
24 12 0.52
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (23 bp):
TATTATGTTCATATATTTTTTAA
Found at i:20426 original size:5 final size:5
Alignment explanation
Indices: 20416--20471 Score: 55
Period size: 5 Copynumber: 11.6 Consensus size: 5
20406 TAATAATTGT
** *
20416 TATAA TATAA T-TGT TATAA TAT-A TATAA TATAA TAGTAA TA-AT TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA-TAA TATAA TATAA
20464 TATAA TAT
1 TATAA TAT
20472 TTATAACCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 9 0.22
5 27 0.66
6 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:20427 original size:14 final size:14
Alignment explanation
Indices: 20408--20469 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
20398 AATAATACTA
*
20408 ATAATTGTTATAAT
1 ATAATTATTATAAT
*
20422 ATAATTGTTATAAT
1 ATAATTATTATAAT
*
20436 AT-ATATAATATAAT
1 ATAAT-TATTATAAT
*
20450 AGTAATAATTATAAT
1 A-TAATTATTATAAT
20465 ATAAT
1 ATAAT
20470 ATTTATAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.05
14 28 0.68
15 9 0.22
16 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
ATAATTATTATAAT
Found at i:20434 original size:23 final size:22
Alignment explanation
Indices: 20394--20470 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
20384 TAAATGATAT
* *
20394 TAATAATAATACTAATAATTGTTA
1 TAAT-ATAATAGTAATAATT-ATA
* *
20418 TAATATAATTGTTATAATATATA
1 TAATATAATAGTAATAAT-TATA
20441 TAATATAATAGTAATAA-T-TA
1 TAATATAATAGTAATAATTATA
20461 TAATATAATA
1 TAATATAATA
20471 TTTATAACCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.26
21 1 0.02
23 28 0.61
24 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (22 bp):
TAATATAATAGTAATAATTATA
Found at i:20470 original size:14 final size:14
Alignment explanation
Indices: 20415--20477 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
20405 CTAATAATTG
**
20415 TTATAATATAATTG
1 TTATAATATAATAA
20429 TTATAATATATATAA
1 TTATAATATA-ATAA
20444 -TATAATAGTAATAA
1 TTATAATA-TAATAA
*
20458 TTATAATATAATAT
1 TTATAATATAATAA
20472 TTATAA
1 TTATAA
20478 CCAAGACAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
14 32 0.74
15 11 0.26
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
TTATAATATAATAA
Found at i:20860 original size:48 final size:48
Alignment explanation
Indices: 20804--20937 Score: 241
Period size: 48 Copynumber: 2.8 Consensus size: 48
20794 AAATCGAGGC
20804 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
*
20852 AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
* *
20900 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATCT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
20938 GGGGGAGTTG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (48 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAG
Found at i:20980 original size:161 final size:161
Alignment explanation
Indices: 20715--21037 Score: 556
Period size: 161 Copynumber: 2.0 Consensus size: 161
20705 TGTCACTCAT
20715 GGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATATGGG
1 GGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATATGGG
*
20780 AAAGTTGATTCATTAAATCGAGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGG
66 AAAGTTGATTCATTAAATCGAGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG
* *
20845 AAAAGAGAGACTTGTTTCACTTACTCTGAAG
131 AAAAGAGAGACATGTTCCACTTACTCTGAAG
*
20876 GGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGG
1 GGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATATGGG
** * *
20941 GGAGTTGATTCATTGAATCGAGGCAGATTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG
66 AAAGTTGATTCATTAAATCGAGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG
**
21006 AAAAGAGAGACATGTTCCGTTTACTCTGAAG
131 AAAAGAGAGACATGTTCCACTTACTCTGAAG
21037 G
1 G
21038 TAAGATCAGA
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (161 bp):
GGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAGATATGGG
AAAGTTGATTCATTAAATCGAGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAG
AAAAGAGAGACATGTTCCACTTACTCTGAAG
Found at i:20988 original size:113 final size:113
Alignment explanation
Indices: 20852--21164 Score: 484
Period size: 113 Copynumber: 2.8 Consensus size: 113
20842 TGGAAAAGAG
*
20852 AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCTTAC
1 AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
* *
20917 TCTGAAGGGAATATCAGATCTGGGGGAG-TTGATTCATTGAATCGAGGC
66 TCTGAAGGAAAGATCAGATCTGGGGGAGCTT-ATTCATTGAATCGAGGC
* * * *
20965 AGATTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAAAAGAGAGACATGTTCCGTTTAC
1 AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
* *
21030 TCTGAAGGTAAGATCAGATCTAGGGGAGCTTATTCATTGAATCGAGGC
66 TCTGAAGGAAAGATCAGATCTGGGGGAGCTTATTCATTGAATCGAGGC
* * * *
21078 ATACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTATTTCGCTTAC
1 AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
*
21143 TCTGAAGGAAAGATCATATCTG
66 TCTGAAGGAAAGATCAGATCTG
21165 AAAGTCTCGG
Statistics
Matches: 180, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
113 178 0.99
114 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (113 bp):
AGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
TCTGAAGGAAAGATCAGATCTGGGGGAGCTTATTCATTGAATCGAGGC
Found at i:26231 original size:16 final size:16
Alignment explanation
Indices: 26212--26244 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26202 GCTGTAGAGA
26212 ATATAATATATAGATC
1 ATATAATATATAGATC
26228 ATATAATATATAGATC
1 ATATAATATATAGATC
26244 A
1 A
26245 GAAGAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
ATATAATATATAGATC
Found at i:28986 original size:3 final size:3
Alignment explanation
Indices: 28978--29068 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
28968 TAAATGATAT
* * * * *
28978 TAA TAA TAA TAC TAA TAA TTA TTA TAA T-A TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
29025 TAA -AA TAA TAA TAA TAA T-A TAA TAG TAA TAA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29069 TTTATAATCT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 8 0.11
3 66 0.89
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:29011 original size:14 final size:13
Alignment explanation
Indices: 28992--29076 Score: 80
Period size: 14 Copynumber: 6.0 Consensus size: 13
28982 AATAATACTA
28992 ATAATTATTATAAT
1 ATAA-TATTATAAT
29006 ATAATTATTATAAT
1 ATAA-TATTATAAT
**
29020 AATAATAAAATAAT
1 -ATAATATTATAAT
*
29034 AATAATAATATAAT
1 -ATAATATTATAAT
29048 AGTAATAATTATAAT
1 A-TAAT-ATTATAAT
29063 ATAATATTTATAAT
1 ATAATA-TTATAAT
29077 CTGACAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.03
14 49 0.78
15 12 0.19
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (13 bp):
ATAATATTATAAT
Found at i:29026 original size:20 final size:19
Alignment explanation
Indices: 28978--29076 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 19
28968 TAAATGATAT
28978 TAATAATAATACTAATAATTA
1 TAATAATAATA-TAAT-ATTA
28999 T--T-ATAATATAATTATTA
1 TAATAATAATATAA-TATTA
*
29016 TAATAATAATA-AA-ATAA
1 TAATAATAATATAATATTA
*
29033 TAATAATAATATAATAGTAA
1 TAATAATAATATAATA-TTA
*
29053 TAATTATAATATAATATTTA
1 TAATAATAATATAATA-TTA
29073 TAAT
1 TAAT
29077 CTGACAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
17 22 0.33
18 9 0.13
19 5 0.07
20 30 0.45
21 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
TAATAATAATATAATATTA
Found at i:29035 original size:17 final size:17
Alignment explanation
Indices: 28978--29068 Score: 76
Period size: 17 Copynumber: 5.3 Consensus size: 17
28968 TAAATGATAT
*
28978 TAATAATAATACTAATAA
1 TAATAATAATAATAA-AA
* * *
28996 TTATTATAAT-ATAATTA
1 TAATAATAATAATAA-AA
*
29013 TTATAATAATAATAAAA
1 TAATAATAATAATAAAA
*
29030 TAATAATAATAATATAA
1 TAATAATAATAATAAAA
* * *
29047 TAGTAATAATTATAATA
1 TAATAATAATAATAAAA
29064 TAATA
1 TAATA
29069 TTTATAATCT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
17 47 0.80
18 12 0.20
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAATAATAATAAAA
Found at i:29785 original size:27 final size:24
Alignment explanation
Indices: 29726--29811 Score: 97
Period size: 27 Copynumber: 3.5 Consensus size: 24
29716 AAATCGGTTT
*
29726 TAAAAAAACCGGATTTT--TCCGG
1 TAAAAAAACCGGTTTTTAATCCGG
*
29748 -ATAAAAAACCGGTTTTTTATCCGG
1 TA-AAAAAACCGGTTTTTAATCCGG
29772 TTTGAAAAAAACCGGTTTTTAATCCGG
1 --T-AAAAAAACCGGTTTTTAATCCGG
29799 TAAAAAAACCGGT
1 TAAAAAAACCGGT
29812 CGTTCAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.02
22 14 0.25
24 17 0.31
25 1 0.02
27 21 0.38
28 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (24 bp):
TAAAAAAACCGGTTTTTAATCCGG
Found at i:30925 original size:30 final size:29
Alignment explanation
Indices: 30832--30976 Score: 127
Period size: 30 Copynumber: 4.9 Consensus size: 29
30822 AACAGTAATT
*
30832 ATAGACACTTAAAGGACTAAAA-AGT-AAA
1 ATAGAAACTT-AAGGACTAAAATAGTAAAA
* *
30860 ACA-AAACTTAAAGGACTATAAAT-GAAAAA
1 ATAGAAACTT-AAGGACTA-AAATAGTAAAA
* * *
30889 ACAGAAAGTTAAGGGACCAAAATAGTAAAA
1 ATAGAAACTTAA-GGACTAAAATAGTAAAA
* *
30919 ATAGAAACCTAAAGGACTAAAATAGCCAAAA
1 ATAGAAA-CTTAAGGACTAAAATAG-TAAAA
*
30950 ATAGAAACTTAAGGACTAATATAGTAA
1 ATAGAAACTTAAGGACTAAAATAGTAA
30977 TAGCATAAAC
Statistics
Matches: 95, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
27 14 0.15
28 6 0.06
29 14 0.15
30 47 0.49
31 14 0.15
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.17
Consensus pattern (29 bp):
ATAGAAACTTAAGGACTAAAATAGTAAAA
Found at i:30934 original size:60 final size:60
Alignment explanation
Indices: 30838--30976 Score: 144
Period size: 60 Copynumber: 2.4 Consensus size: 60
30828 AATTATAGAC
* * *
30838 ACTTAAAGGACTAAAA-AGT-AAAACA-AAACTTAAAGGACTATAAAT-G-AAAAAACAGAA
1 ACTT-AAGGACCAAAATAGTAAAAATAGAAACCTAAAGGACTA-AAATAGCAAAAAACAGAA
* * *
30895 AGTTAAGGGACCAAAATAGTAAAAATAGAAACCTAAAGGACTAAAATAGCCAAAAATAGAA
1 ACTTAA-GGACCAAAATAGTAAAAATAGAAACCTAAAGGACTAAAATAGCAAAAAACAGAA
* *
30956 ACTTAAGGACTAATATAGTAA
1 ACTTAAGGACCAAAATAGTAA
30977 TAGCATAAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
56 2 0.03
57 11 0.16
58 3 0.04
59 9 0.13
60 28 0.42
61 14 0.21
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (60 bp):
ACTTAAGGACCAAAATAGTAAAAATAGAAACCTAAAGGACTAAAATAGCAAAAAACAGAA
Found at i:31546 original size:2 final size:2
Alignment explanation
Indices: 31541--31616 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
31531 TTTTCTAAAT
*
31541 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31583 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31617 ACTCCCAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32465 original size:3 final size:3
Alignment explanation
Indices: 32445--32508 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
32435 AATGTAAATG
* ** *
32445 TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA CGA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32492 GTAA T-A TAA TAA TAA TA
1 -TAA TAA TAA TAA TAA TA
32509 TATTAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39774 original size:16 final size:16
Alignment explanation
Indices: 39753--39788 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39743 AGTTTCTTAA
*
39753 GTGCCCATATTGCTTT
1 GTGCCCACATTGCTTT
39769 GTGCCCACATTGCTTT
1 GTGCCCACATTGCTTT
39785 GTGC
1 GTGC
39789 TCTAACTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.28, G:0.22, T:0.39
Consensus pattern (16 bp):
GTGCCCACATTGCTTT
Found at i:43262 original size:22 final size:26
Alignment explanation
Indices: 43234--43292 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
43224 GACGAACCAT
43234 TGAATTCATT-G-ATA-TC-GTAGCG
1 TGAATTCATTGGAATATTCTGTAGCG
*
43256 TGAATTCATTTGGAATATTCTTTAGCG
1 TGAATTCA-TTGGAATATTCTGTAGCG
43283 TGAATTCATT
1 TGAATTCATT
43293 CATTGAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 8 0.26
23 2 0.06
24 1 0.03
25 3 0.10
26 4 0.13
27 13 0.42
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (26 bp):
TGAATTCATTGGAATATTCTGTAGCG
Found at i:56155 original size:30 final size:30
Alignment explanation
Indices: 56100--56156 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56090 TATATATATA
56100 TATTTATTATTATTTTTATCTATATTTACT
1 TATTTATTATTATTTTTATCTATATTTACT
*
56130 TATTTATTATGTTTTTTTA-CTATATTT
1 TATTTATTAT-TATTTTTATCTATATTT
56157 CCAAACGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (30 bp):
TATTTATTATTATTTTTATCTATATTTACT
Found at i:56319 original size:15 final size:16
Alignment explanation
Indices: 56294--56334 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
56284 TTATACATAC
56294 ATTTTTATATTTTTA-T
1 ATTTTT-TATTTTTATT
56310 ATTTTTTA-TTTTATT
1 ATTTTTTATTTTTATT
56325 ATTTATTTAT
1 ATTT-TTTAT
56335 ACATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTATTTTTATT
Done.