Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007509.1 Hibiscus syriacus cultivar Beakdansim tig00020859_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: 104939
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1047 original size:32 final size:32
Alignment explanation
Indices: 988--1054 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
978 GTTGATGAAT
*
988 GAAGGATGATTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTAATGGCGATGAAATGGTAATG
* * *
1020 GAAGGATGATGTATTGGCG-TGATATGGTGATG
1 GAAGGATGAT-TAATGGCGATGAAATGGTAATG
1052 GAA
1 GAA
1055 TATAGTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.33, C:0.01, G:0.37, T:0.28
Consensus pattern (32 bp):
GAAGGATGATTAATGGCGATGAAATGGTAATG
Found at i:5443 original size:31 final size:31
Alignment explanation
Indices: 5385--5443 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5375 TTGATGAATG
*
5385 AAGGATGATTTAATGGTGATGAAATGGTAAT
1 AAGGATGATTTAATGGCGATGAAATGGTAAT
* *
5416 AAGGATGATGTTATTGGCG-TGATATGGT
1 AAGGATGAT-TTAATGGCGATGAAATGGT
5444 GATGGAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (31 bp):
AAGGATGATTTAATGGCGATGAAATGGTAAT
Found at i:22594 original size:36 final size:36
Alignment explanation
Indices: 22554--22622 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
22544 TAAGATACTA
22554 CCTATAACATCACCACCTTCCATCACCATTTTCACG
1 CCTATAACATCACCACCTTCCATCACCATTTTCACG
*
22590 CCTATAACATCACCATCTTCCATCACCATTTTC
1 CCTATAACATCACCACCTTCCATCACCATTTTC
22623 CATCACCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.41, G:0.01, T:0.30
Consensus pattern (36 bp):
CCTATAACATCACCACCTTCCATCACCATTTTCACG
Found at i:22632 original size:13 final size:13
Alignment explanation
Indices: 22597--22632 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
22587 ACGCCTATAA
*
22597 CATCACCATCTTC
1 CATCACCATTTTC
22610 CATCACCATTTTC
1 CATCACCATTTTC
22623 CATCACCATT
1 CATCACCATT
22633 GCACGCCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:22663 original size:48 final size:49
Alignment explanation
Indices: 22561--22668 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 49
22551 CTACCTATAA
** * *
22561 CATCACCACCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTC
1 CATCACCATTTTCCATCACCATTTGCACGCCTATAACATCACCAACTTC
** *
22610 CATCACCATTTTCCATCACCA-TTGCACGCCTATATTATCATCAACTTC
1 CATCACCATTTTCCATCACCATTTGCACGCCTATAACATCACCAACTTC
*
22658 TATCACCATTT
1 CATCACCATTT
22669 CACGCTTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 32 0.63
49 19 0.37
ACGTcount: A:0.27, C:0.38, G:0.03, T:0.32
Consensus pattern (49 bp):
CATCACCATTTTCCATCACCATTTGCACGCCTATAACATCACCAACTTC
Found at i:23086 original size:7 final size:6
Alignment explanation
Indices: 23067--23107 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
23057 CAAAAGCTAC
* *
23067 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
23108 GACTCCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:23095 original size:19 final size:18
Alignment explanation
Indices: 23067--23107 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
23057 CAAAAGCTAC
*
23067 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAA-AAG
*
23086 AAAAACAAAAAGAGAAAG
1 AAAAACAAAAAGAAAAAG
23104 AAAA
1 AAAA
23108 GACTCCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:23405 original size:17 final size:17
Alignment explanation
Indices: 23383--23416 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
23373 TATCCTACCC
23383 CTATACCATAACCATTT
1 CTATACCATAACCATTT
23400 CTATACCATAACCATTT
1 CTATACCATAACCATTT
23417 TTTTAAGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:27256 original size:19 final size:19
Alignment explanation
Indices: 27232--27279 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
27222 TCTTTTCTTT
27232 TCTTCTTTTCTG-ATTTTTC
1 TCTTCTTTT-TGTATTTTTC
*
27251 TCTTCTTTTTGTCTTTTTC
1 TCTTCTTTTTGTATTTTTC
27270 T-TTCTTTTTG
1 TCTTCTTTTTG
27280 CACTCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (19 bp):
TCTTCTTTTTGTATTTTTC
Found at i:27569 original size:16 final size:17
Alignment explanation
Indices: 27543--27579 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
27533 GAATAATAAT
27543 ATAAGTAATGAAAAGAA
1 ATAAGTAATGAAAAGAA
*
27560 ATAA-TAATGAAATGAA
1 ATAAGTAATGAAAAGAA
27576 ATAA
1 ATAA
27580 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.22
Consensus pattern (17 bp):
ATAAGTAATGAAAAGAA
Found at i:29389 original size:27 final size:28
Alignment explanation
Indices: 29337--29401 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
29327 AAAGAAAATC
*
29337 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
29365 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
29392 AGAAAAGAAA
1 AGAAAAGAAA
29402 AGAAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:29421 original size:4 final size:5
Alignment explanation
Indices: 29391--29420 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
29381 ATTCAAAAAG
29391 AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
29421 GTTGAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:31861 original size:13 final size:13
Alignment explanation
Indices: 31843--31868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31833 TGGACAAATA
31843 TGAAAAGGTATGT
1 TGAAAAGGTATGT
31856 TGAAAAGGTATGT
1 TGAAAAGGTATGT
31869 GATAGTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:37956 original size:33 final size:33
Alignment explanation
Indices: 37912--37980 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
37902 CATCACCATA
*
37912 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
37945 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
37978 TTC
1 TTC
37981 ATTCATCAAC
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:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:41838 original size:33 final size:33
Alignment explanation
Indices: 41794--41862 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
41784 CATCACCATA
*
41794 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
41827 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
41860 TTC
1 TTC
41863 ATTCATCAAC
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:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:42206 original size:36 final size:36
Alignment explanation
Indices: 42154--42270 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
42144 GTTAGCCTTA
42154 CATCAACCATAGTCCATCACCATTATCACGCCTATAT
1 CATC-ACCATAGTCCATCACCATTATCACGCCTATAT
*
42191 CATCACCATATTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
42227 CATCACCATAGTCCATCACCATTATCACGCCTAAAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
42263 TATCACCA
1 CATCACCA
42271 ACTTATAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 72 0.95
37 4 0.05
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
CATCACCATAGTCCATCACCATTATCACGCCTATAT
Found at i:42680 original size:12 final size:11
Alignment explanation
Indices: 42649--42696 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 11
42639 AAAGTGCTAC
42649 AAAA-AAAAAG
1 AAAAGAAAAAG
42659 CAATAAGAAAGAAG
1 -AA-AAGAAA-AAG
42673 AAAAGAAAAGAG
1 AAAAGAAAA-AG
42685 AAAAGAAAAAG
1 AAAAGAAAAAG
42696 A
1 A
42697 CTCCTACATC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 19 0.58
13 5 0.15
14 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:48036 original size:11 final size:11
Alignment explanation
Indices: 48003--48091 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
47993 ACAATCTGTC
48003 CATCACCATTAT
1 CATCACCA-TAT
*
48015 CA-CGCCTATAT
1 CATCACC-ATAT
48026 CATCACCATATT
1 CATCACCATA-T
48038 CCATCACCATAT
1 -CATCACCATAT
*
48050 CA-CACCAATAA
1 CATCACC-ATAT
48061 CATCATCC-T-T
1 CATCA-CCATAT
* *
48071 CCATTACCATTT
1 -CATCACCATAT
48083 CATCACCAT
1 CATCACCAT
48092 TAAATCATCC
Statistics
Matches: 61, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
10 6 0.10
11 32 0.52
12 11 0.18
13 12 0.20
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:48080 original size:33 final size:33
Alignment explanation
Indices: 48036--48104 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
48026 CATCACCATA
48036 TTCCATCACCATATCA-CACCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
48069 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
48102 TTC
1 TTC
48105 ATTCATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:52459 original size:33 final size:33
Alignment explanation
Indices: 52380--52483 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
52370 ATACAATCTG
* *
52380 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
52416 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
52449 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
52482 TC
1 TC
52484 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:57246 original size:21 final size:19
Alignment explanation
Indices: 57213--57254 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
57203 GTTCTTTCTT
57213 ATTTATCTTATATTATATC
1 ATTTATCTTATATTATATC
*
57232 ATTTATACATTATATTCTATC
1 ATTTAT-C-TTATATTATATC
57253 AT
1 AT
57255 AATCATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 13 0.65
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTATCTTATATTATATC
Found at i:58542 original size:35 final size:34
Alignment explanation
Indices: 58467--58570 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 34
58457 ATTAGTGGTT
* * *
58467 ATATAGGCGTGAAATGGTGATAGAAGGTGGT-ACGG
1 ATATAGGCGTG-AATGGTGATGGAAGATGGTGA-TG
*
58502 ATATAGGCGTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTG-AATGGTGATGGAAGATGGTGATG
* *
58537 TTATAGGCGTGAATTAGTGATGGAAGATGGTGAT
1 ATATAGGCGTGAA-TGGTGATGGAAGATGGTGAT
58571 TTTAGGTAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.03
35 56 0.95
36 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.27
Consensus pattern (34 bp):
ATATAGGCGTGAATGGTGATGGAAGATGGTGATG
Found at i:61468 original size:6 final size:6
Alignment explanation
Indices: 61457--61500 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
61447 GATGTAGGAG
61457 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
61501 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 20 0.57
7 10 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:61480 original size:12 final size:12
Alignment explanation
Indices: 61457--61500 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
61447 GATGTAGGAG
61457 TCTTTTTC-TTT
1 TCTTTTTCTTTT
61468 TCTTTTTCTTTT
1 TCTTTTTCTTTT
61480 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
61493 TCTCTTTT
1 TCT-TTTT
61501 TGTTGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.27
12 7 0.23
13 14 0.47
14 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:61490 original size:19 final size:17
Alignment explanation
Indices: 61457--61500 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
61447 GATGTAGGAG
61457 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
61474 TCTTTTTCTTCTTTCTTTT
1 TCTTTTTC-T-TTTCTTTT
61493 TCTCTTTT
1 TCT-TTTT
61501 TGTTGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 11 0.46
20 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:61721 original size:16 final size:16
Alignment explanation
Indices: 61702--61740 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
61692 TTTGATAATT
*
61702 AAGAAATGAAAATGGA
1 AAGAAATGAAAATAGA
*
61718 AAG-AATTAAAATAGA
1 AAGAAATGAAAATAGA
61733 AAGAAATG
1 AAGAAATG
61741 TTATCAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AAGAAATGAAAATAGA
Found at i:65654 original size:15 final size:15
Alignment explanation
Indices: 65624--65665 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
65614 GATATAGGAG
65624 TCTTTTTCTT-TTCTT
1 TCTTTTT-TTCTTCTT
65639 T-TTGTTTTTCTTCTT
1 TCTT-TTTTTCTTCTT
65654 TCTTTTTTTCTT
1 TCTTTTTTTCTT
65666 TTTGTTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.17
15 18 0.75
16 2 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TCTTTTTTTCTTCTT
Found at i:65879 original size:16 final size:16
Alignment explanation
Indices: 65860--65897 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
65850 TTTGATCATT
65860 AAGAAATTAAAATGGA
1 AAGAAATTAAAATGGA
*
65876 AAG-AATTGAAATGGA
1 AAGAAATTAAAATGGA
65891 AAGAAAT
1 AAGAAAT
65898 GTTATCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
AAGAAATTAAAATGGA
Found at i:66133 original size:35 final size:34
Alignment explanation
Indices: 66033--66142 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 34
66023 TTGGTGGTTA
* * * *
66033 TATAGGCGTGAAATGGTGATAGAAGGTGGTAAGGA
1 TATAGGCGTGAAATGGTGATA-AAGATGGTGATGT
* * *
66068 TATAGGTGTGCAATGGTAATAAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGAT-AAAGATGGTGATGT
66103 TATAGGCGTGAAATGGTGATGAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGAT-AAAGATGGTGATGT
66138 T-TAGG
1 TATAGG
66143 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 4 0.06
35 58 0.92
36 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (34 bp):
TATAGGCGTGAAATGGTGATAAAGATGGTGATGT
Found at i:68341 original size:24 final size:24
Alignment explanation
Indices: 68306--68365 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
68296 GACAATGTAC
68306 TTGGAA-TGTCAACGAACACAACTT
1 TTGGAACT-TCAACGAACACAACTT
* ** **
68330 TTGGAACTTCAAGGAATGCTTCTT
1 TTGGAACTTCAACGAACACAACTT
68354 TTGGAACTTCAA
1 TTGGAACTTCAA
68366 ATGGTATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (24 bp):
TTGGAACTTCAACGAACACAACTT
Found at i:69794 original size:12 final size:12
Alignment explanation
Indices: 69777--69831 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
69767 GATATAGGAG
69777 TCTTTTTTCTTT
1 TCTTTTTTCTTT
69789 TCTTTTTGT-TTT
1 TCTTTTT-TCTTT
*
69801 TCTTATTTCTTT
1 TCTTTTTTCTTT
*
69813 T-TTTCTTTTTGTT
1 TCTTT-TTTCT-TT
69826 TCTTTT
1 TCTTTT
69832 GTTGCAGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 3 0.09
12 24 0.69
13 5 0.14
14 3 0.09
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.82
Consensus pattern (12 bp):
TCTTTTTTCTTT
Found at i:69813 original size:18 final size:19
Alignment explanation
Indices: 69787--69834 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
69777 TCTTTTTTCT
69787 TTTCTTTTTGTTT-TTCTTA
1 TTTC-TTTTGTTTCTTCTTA
* *
69806 TTTCTTTT-TTTCTTTTTG
1 TTTCTTTTGTTTCTTCTTA
69824 TTTCTTTTGTT
1 TTTCTTTTGTT
69835 GCAGCACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTCTTTTGTTTCTTCTTA
Found at i:70042 original size:16 final size:15
Alignment explanation
Indices: 70023--70061 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
70013 TTTGATCATT
70023 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
70039 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
70054 AAGAAATG
1 AAGAAATG
70062 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:70281 original size:35 final size:35
Alignment explanation
Indices: 70195--70306 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
70185 ATTGGTGGTT
* * * *
70195 TTATAGGTGTGAAATGGTGATAGAAGGTGGTAAGG
1 TTATAGGTGTGAAATGGTGATGGAAGATGGTGATG
* * * *
70230 ATATACGTGTGCAATGGTAATGGAAGATGGTGATG
1 TTATAGGTGTGAAATGGTGATGGAAGATGGTGATG
*
70265 TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
1 TTATAGGTGTGAAATGGTGATGGAAGATGGTGATG
70300 TT-TAGGT
1 TTATAGGT
70307 AGTATCTTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 4 0.06
35 59 0.94
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.30
Consensus pattern (35 bp):
TTATAGGTGTGAAATGGTGATGGAAGATGGTGATG
Found at i:73971 original size:15 final size:15
Alignment explanation
Indices: 73941--73982 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
73931 GATATAGGAG
73941 TCTTTTTCTT-TTCTT
1 TCTTTTT-TTCTTCTT
73956 T-TTGTTTTTCTTCTT
1 TCTT-TTTTTCTTCTT
73971 TCTTTTTTTCTT
1 TCTTTTTTTCTT
73983 TTTGTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.17
15 18 0.75
16 2 0.08
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TCTTTTTTTCTTCTT
Found at i:74205 original size:16 final size:15
Alignment explanation
Indices: 74186--74224 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
74176 TTTGATCATT
74186 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
74202 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
74217 AAGAAATG
1 AAGAAATG
74225 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:74781 original size:19 final size:20
Alignment explanation
Indices: 74734--74784 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
74724 GAAACCCCTT
**
74734 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
74754 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
74773 TGAAGATACATG
1 TGAAAATACATG
74785 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:76573 original size:35 final size:35
Alignment explanation
Indices: 76485--76656 Score: 209
Period size: 35 Copynumber: 4.9 Consensus size: 35
76475 GTCCTTTCAT
*
76485 ACCATCTTCCATCACCATTTTCACGCCTATAACATC
1 ACCATCTTCCATCACCA-TTGCACGCCTATAACATC
* * * *
76521 ACCATCTTCCATTACCATTGCACGCCTATATCCTT
1 ACCATCTTCCATCACCATTGCACGCCTATAACATC
* * * *
76556 ACCACCTTCTATCACCATTTTCACACCTATAACATC
1 ACCATCTTCCATCACCA-TTGCACGCCTATAACATC
* * *
76592 ACCATCTTTCATTATCATTGCACGCCTATAACATC
1 ACCATCTTCCATCACCATTGCACGCCTATAACATC
*
76627 ACCATCTTCCATTACCATTGCACGCCTATA
1 ACCATCTTCCATCACCATTGCACGCCTATA
76657 TCCTTACCAC
Statistics
Matches: 113, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
35 72 0.64
36 41 0.36
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.32
Consensus pattern (35 bp):
ACCATCTTCCATCACCATTGCACGCCTATAACATC
Found at i:76574 original size:71 final size:71
Alignment explanation
Indices: 76484--76656 Score: 249
Period size: 71 Copynumber: 2.5 Consensus size: 71
76474 AGTCCTTTCA
76484 TACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCCATTACCATTGCACGCCTA
1 TACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCCATTACCATTGCACGCCTA
* *
76549 TATCCT
66 TAACAT
* * * * *
76555 TACCACCTTCTATCACCATTTTCACACCTATAACATCACCATCTTTCATTATCATTGCACGCCTA
1 TACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCCATTACCATTGCACGCCTA
76620 TAACAT
66 TAACAT
* * *
76626 CACCATCTTCCATTACCA-TTGCACGCCTATA
1 TACCATCTTCCATCACCATTTTCACGCCTATA
76657 TCCTTACCAC
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
70 11 0.12
71 78 0.88
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.32
Consensus pattern (71 bp):
TACCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCCATTACCATTGCACGCCTA
TAACAT
Found at i:78551 original size:15 final size:15
Alignment explanation
Indices: 78518--78551 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
78508 TATTAGCTTT
*
78518 ATAATATATTCTATT
1 ATAATATATTCTATG
*
78533 ATAATATATTTTATG
1 ATAATATATTCTATG
78548 ATAA
1 ATAA
78552 GAATATTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
ATAATATATTCTATG
Found at i:80127 original size:14 final size:14
Alignment explanation
Indices: 80108--80140 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
80098 AAAGCACTCA
80108 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
80122 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
80136 AAAAG
1 AAAAG
80141 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:84335 original size:14 final size:14
Alignment explanation
Indices: 84316--84348 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
84306 AAAGCACTCA
84316 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
84330 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
84344 AAAAG
1 AAAAG
84349 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:92747 original size:14 final size:14
Alignment explanation
Indices: 92728--92760 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
92718 AAAGCACTCA
92728 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
92742 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
92756 AAAAG
1 AAAAG
92761 TTGGAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Done.