Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003098.1 Hibiscus syriacus cultivar Beakdansim tig00006467_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: 85880
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:951 original size:14 final size:14
Alignment explanation
Indices: 934--973 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
924 AAAAGCAACA
934 AAGAAAAAAAAAAG
1 AAGAAAAAAAAAAG
948 AAGAAAAACAAAAAG
1 AAGAAAAA-AAAAAG
963 -AGAAAGAAAAA
1 AAGAAA-AAAAA
974 GACTCCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAG
Found at i:954 original size:27 final size:27
Alignment explanation
Indices: 924--975 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
914 GTACTACAAC
*
924 AAAAGCAACAAAGA-AAAAAAAAAGAAG
1 AAAAACAA-AAAGAGAAAAAAAAAGAAG
*
951 AAAAACAAAAAGAGAAAGAAAAAGA
1 AAAAACAAAAAGAGAAAAAAAAAGA
976 CTCCTACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (27 bp):
AAAAACAAAAAGAGAAAAAAAAAGAAG
Found at i:960 original size:17 final size:18
Alignment explanation
Indices: 940--973 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
930 AACAAAGAAA
940 AAAAAAAG-AAGAAAAAC
1 AAAAAAAGAAAGAAAAAC
*
957 AAAAAGAGAAAGAAAAA
1 AAAAAAAGAAAGAAAAA
974 GACTCCTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAGAAAAAC
Found at i:1009 original size:5 final size:5
Alignment explanation
Indices: 999--1045 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
989 TTTGGAGTGC
*
999 AAAAG AAAAG AAAAG --AAG AAACG AAAACG AAAAG AAAACG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAAA-G AAAAG AA
1046 GCAATTTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
5 23 0.64
6 10 0.28
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1035 original size:11 final size:10
Alignment explanation
Indices: 999--1045 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
989 TTTGGAGTGC
999 AAAAGAAAAG
1 AAAAGAAAAG
1009 AAAAG--AAG
1 AAAAGAAAAG
*
1017 AAACGAAAACG
1 AAAAGAAAA-G
1028 AAAAGAAAACG
1 AAAAGAAAA-G
1039 AAAAGAA
1 AAAAGAA
1046 GCAATTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 7 0.22
10 7 0.22
11 18 0.56
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:6149 original size:19 final size:20
Alignment explanation
Indices: 6111--6153 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6101 GAAACCCCTT
*
6111 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
6131 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
6150 TGAA
1 TGAA
6154 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:8567 original size:35 final size:36
Alignment explanation
Indices: 8528--8608 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
8518 ATACGCTTGA
8528 AATGGTGATAGAAAT-TGATGATAATATAGGCGTG-C
1 AATGGTGAT-GAAATATGATGATAATATAGGCGTGAC
* * **
8563 AATGGTGATGGAATATGGTGATGTTATAGGCGTGAC
1 AATGGTGATGAAATATGATGATAATATAGGCGTGAC
8599 AATGGTGATG
1 AATGGTGATG
8609 GAAGATGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.10
35 25 0.62
36 11 0.28
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (36 bp):
AATGGTGATGAAATATGATGATAATATAGGCGTGAC
Found at i:8607 original size:36 final size:35
Alignment explanation
Indices: 8552--8628 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
8542 TTGATGATAA
*
8552 TATAGGCGTGCAATGGTGATGGAATATGGTGATGT
1 TATAGGCGTGCAATGGTGATGGAAGATGGTGATGT
8587 TATAGGCGTGACAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-CAATGGTGATGGAAGATGGTGATGT
8623 TATAGG
1 TATAGG
8629 TAGTATCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 10 0.25
36 30 0.75
ACGTcount: A:0.27, C:0.05, G:0.38, T:0.30
Consensus pattern (35 bp):
TATAGGCGTGCAATGGTGATGGAAGATGGTGATGT
Found at i:8958 original size:19 final size:20
Alignment explanation
Indices: 8916--8958 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
8906 GAAACCCCTT
8916 TGAAAATACAAGATTTTAAA
1 TGAAAATACAAGATTTTAAA
8936 TGAAAATACATA-ATTTT-AA
1 TGAAAATACA-AGATTTTAAA
8955 TGAA
1 TGAA
8959 TATAAATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAATACAAGATTTTAAA
Found at i:9697 original size:20 final size:21
Alignment explanation
Indices: 9659--9697 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9649 GATCATCTAG
* *
9659 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
9680 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
9698 TGGATGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:17823 original size:17 final size:17
Alignment explanation
Indices: 17801--17837 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
17791 GCAAGGTGGA
17801 ACATGTTTTTAGTTGCC
1 ACATGTTTTTAGTTGCC
17818 ACATGTTTTTAGTTGCC
1 ACATGTTTTTAGTTGCC
17835 ACA
1 ACA
17838 ACTATTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (17 bp):
ACATGTTTTTAGTTGCC
Found at i:26288 original size:17 final size:17
Alignment explanation
Indices: 26266--26299 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
26256 GACTTAAAAC
26266 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
26283 AAATGGTTATGGTATAG
1 AAATGGTTAGGGTATAG
26300 GGGTAGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:26609 original size:14 final size:14
Alignment explanation
Indices: 26565--26611 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
26555 TGTAGGAGTC
*
26565 TTTTCTTTC-TCTT
1 TTTTTTTTCTTCTT
*
26578 TTTGTATTTCTTCTT
1 TTT-TTTTTCTTCTT
26593 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
26607 TTTTT
1 TTTTT
26612 GTTGCTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 3 0.10
14 20 0.67
15 7 0.23
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:26836 original size:15 final size:16
Alignment explanation
Indices: 26816--26848 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
26806 AATATGAAAG
26816 AAGAAAGGAAAT-GAT
1 AAGAAAGGAAATGGAT
26831 AAGAAAGGAAATGGAT
1 AAGAAAGGAAATGGAT
26847 AA
1 AA
26849 AAATGTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (16 bp):
AAGAAAGGAAATGGAT
Found at i:33096 original size:13 final size:12
Alignment explanation
Indices: 33077--33173 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
33067 TTATTGGCGT
33077 GATATGGTGATG
1 GATATGGTGATG
33089 GAATATGGTGAT-
1 G-ATATGGTGATG
*
33101 GATATAGGCG-T-
1 GATAT-GGTGATG
33112 GATAATGGTGATG
1 GAT-ATGGTGATG
33125 GACTATGGTGAT-
1 GA-TATGGTGATG
*
33137 GATATAGGCG-T-
1 GATAT-GGTGATG
*
33148 GATAATGGAGATG
1 GAT-ATGGTGATG
33161 GATTATGGTGATG
1 GA-TATGGTGATG
33174 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:33132 original size:36 final size:36
Alignment explanation
Indices: 33062--33174 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
33052 AATGGTAGGA
* *
33062 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
33097 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
33133 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
33169 TGATGA
1 TGATGA
33175 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:33561 original size:19 final size:20
Alignment explanation
Indices: 33514--33564 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
33504 GAAACCCCTT
**
33514 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
33534 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
33553 TGAAGATACATG
1 TGAAAATACATG
33565 CTCTTGGCCG
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:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:36678 original size:14 final size:15
Alignment explanation
Indices: 36650--36693 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
36640 TTGCTTCACT
*
36650 TTTTCTTTGCTTTTTT
1 TTTTCTTT-CTTTTTC
36666 TTATTC-TTCTTTTTC
1 TT-TTCTTTCTTTTTC
36681 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
36694 GCACTCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
16 4 0.16
17 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:37162 original size:33 final size:33
Alignment explanation
Indices: 37103--37167 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
37093 TGATGAATGA
*
37103 AGGATGATTTAATGGTGATGAAATGGTAATGGT
1 AGGATGATTTAATGGTCATGAAATGGTAATGGT
* * *
37136 AGGATGATGTTATTGG-CATGATATGGTGATGG
1 AGGATGAT-TTAATGGTCATGAAATGGTAATGG
37168 AATATGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.34
Consensus pattern (33 bp):
AGGATGATTTAATGGTCATGAAATGGTAATGGT
Found at i:37210 original size:36 final size:36
Alignment explanation
Indices: 37140--37252 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
37130 AATGGTAGGA
* * *
37140 TGATGTTATTGGCATGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
37175 TGATGATATAGGCGTGATAATGGTGATCGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
37211 TGATGATATAGGTGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
37247 TGATGA
1 TGATGA
37253 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 15 0.22
36 53 0.78
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:37251 original size:13 final size:12
Alignment explanation
Indices: 37153--37252 Score: 66
Period size: 13 Copynumber: 8.3 Consensus size: 12
37143 TGTTATTGGC
37153 ATGA-TATGGTG
1 ATGATTATGGTG
*
37164 ATGGAATATGGTG
1 AT-GATTATGGTG
*
37177 ATGA-TATAGGCG
1 ATGATTAT-GGTG
*
37189 -TGATAATGGTG
1 ATGATTATGGTG
*
37200 ATCGACTATGGTG
1 AT-GATTATGGTG
37213 ATGA-TATAGGTG
1 ATGATTAT-GGTG
* *
37225 -TGATAATGGAG
1 ATGATTATGGTG
37236 ATGGATTATGGTG
1 AT-GATTATGGTG
37249 ATGA
1 ATGA
37253 AAATAGTATC
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
11 20 0.29
12 21 0.30
13 29 0.41
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
ATGATTATGGTG
Found at i:37639 original size:19 final size:20
Alignment explanation
Indices: 37592--37642 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
37582 GAAACCCCTT
**
37592 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
37612 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
37631 TGAAGATACATG
1 TGAAAATACATG
37643 CTCTTGGCCG
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:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:40752 original size:14 final size:13
Alignment explanation
Indices: 40722--40766 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
40712 TTTGCTTCAC
*
40722 TTTTTCTTTGCTT
1 TTTTTCTTTTCTT
40735 TTTTT-TTATTCTT
1 TTTTTCTT-TTCTT
40748 CTTTTTCTTTTCTT
1 -TTTTTCTTTTCTT
40762 TTTTT
1 TTTTT
40767 GCACTCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:41244 original size:35 final size:36
Alignment explanation
Indices: 41205--41316 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 36
41195 AATGGCATGA
* *
41205 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
41240 TGATGATATAGGCGTGATAATGGTGATGGACT-TGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
41275 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
41311 TGATGA
1 TGATGA
41317 AAATAGTATC
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 49 0.70
36 21 0.30
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:41703 original size:19 final size:20
Alignment explanation
Indices: 41656--41706 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
41646 GAAACCCCTT
**
41656 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
41676 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
41695 TGAAGATACATG
1 TGAAAATACATG
41707 CTCTTGGCCG
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:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:45389 original size:13 final size:12
Alignment explanation
Indices: 45370--45466 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
45360 TTATTGGCGT
45370 GATATGGTGATG
1 GATATGGTGATG
45382 GAATATGGTGAT-
1 G-ATATGGTGATG
*
45394 GATATAGGCG-T-
1 GATAT-GGTGATG
45405 GATAATGGTGATG
1 GAT-ATGGTGATG
45418 GACTATGGTGAT-
1 GA-TATGGTGATG
*
45430 GATATAGGCG-T-
1 GATAT-GGTGATG
*
45441 GATAATGGAGATG
1 GAT-ATGGTGATG
45454 GATTATGGTGATG
1 GA-TATGGTGATG
45467 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:45425 original size:36 final size:36
Alignment explanation
Indices: 45355--45467 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
45345 AATGGTAGGA
* *
45355 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
45390 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
45426 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
45462 TGATGA
1 TGATGA
45468 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:45854 original size:19 final size:20
Alignment explanation
Indices: 45807--45857 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
45797 GAAACCCCTT
**
45807 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
45827 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
45846 TGAAGATACATG
1 TGAAAATACATG
45858 CTCTTGGCCG
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:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:55804 original size:36 final size:36
Alignment explanation
Indices: 55751--55845 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
55741 GATACTATTT
* *
55751 TCATCGCCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
55787 TTATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
55823 TCATCACCATATTCCATCACCAT
1 TCATCACCATAATCCATCACCAT
55846 ATTCCATCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:55807 original size:13 final size:12
Alignment explanation
Indices: 55789--55858 Score: 65
Period size: 13 Copynumber: 5.7 Consensus size: 12
55779 CGCCTATATT
55789 ATCACCATAGTCC
1 ATCACCATA-TCC
55802 ATCACCATTAT-C
1 ATCACCA-TATCC
*
55814 A-CGCCTATAT-C
1 ATCACC-ATATCC
55825 ATCACCATATTCC
1 ATCACCATA-TCC
55838 ATCACCATATTCC
1 ATCACCATA-TCC
55851 ATCACCAT
1 ATCACCAT
55859 TATCACAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
11 11 0.22
12 7 0.14
13 30 0.60
14 2 0.04
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (12 bp):
ATCACCATATCC
Found at i:56060 original size:14 final size:15
Alignment explanation
Indices: 56026--56072 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
56016 AATTTGGAGT
56026 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
56041 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
56055 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
56072 G
1 G
56073 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:69847 original size:20 final size:21
Alignment explanation
Indices: 69809--69847 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
69799 ATTCCCCTGT
*
69809 GGGGGGAATCGGTTCCCTCAA
1 GGGGGGAATCGATTCCCTCAA
*
69830 GGGGGG-ATCGATTTCCTC
1 GGGGGGAATCGATTCCCTC
69848 TGCAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAA
Found at i:72191 original size:17 final size:17
Alignment explanation
Indices: 72169--72203 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
72159 AATTGGCCTA
72169 ATCATTACTCGATTTAC
1 ATCATTACTCGATTTAC
72186 ATCATTACTCGATTTAC
1 ATCATTACTCGATTTAC
72203 A
1 A
72204 ACATAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (17 bp):
ATCATTACTCGATTTAC
Found at i:79874 original size:90 final size:88
Alignment explanation
Indices: 79728--79897 Score: 261
Period size: 90 Copynumber: 1.9 Consensus size: 88
79718 CCTATGTGCC
*
79728 TTGCATATGACCAGCCCCCATGTCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCTC
1 TTGCATATGAACAGCCCCCATGTCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAG--CTC
79793 TCCCTATTCGGCCAAGCCATGTGTT
64 TCCCTATTCGGCCAAGCCATGTGTT
* * * *
79818 TTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATGT-CCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCT
79882 CCCTATTCGGCCAAGC
65 CCCTATTCGGCCAAGC
79898 ATCATTTCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 20 0.27
89 8 0.11
90 46 0.62
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (88 bp):
TTGCATATGAACAGCCCCCATGTCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTC
CCTATTCGGCCAAGCCATGTGTT
Found at i:80691 original size:25 final size:23
Alignment explanation
Indices: 80645--80691 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
80635 CAGAAAGAAG
**
80645 CACTCAAAAAGAAAAATTGAAAA
1 CACTCAAAAAGAAAAAAAGAAAA
80668 CACTCAAAAGAAGAAAAAAAGAAA
1 CACTC-AAA-AAGAAAAAAAGAAA
80692 GAAAAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.09
Consensus pattern (23 bp):
CACTCAAAAAGAAAAAAAGAAAA
Found at i:82464 original size:90 final size:87
Alignment explanation
Indices: 82334--82497 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 87
82324 TATGACCAGC
* * *
82334 CCCCATGTTCCTTTCATGTAGATCATTTAGGCGCCAAGATGAAGAGTTCTCTCCCTATTCGGCCA
1 CCCCATGTGCCTTGCATGTAGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGG-CA
82399 AGCCATGTATTTTGCATGTGAACAG
65 AG-CAT-TATTTTGCATGTGAACAG
* * *
82424 CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGGCAA
1 CCCCATGTGCCTTGCATGTAGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGGCAA
82489 GCATTATTT
66 GCATTATTT
82498 CCCATTCAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
87 5 0.07
88 3 0.04
89 4 0.06
90 56 0.82
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (87 bp):
CCCCATGTGCCTTGCATGTAGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGGCAA
GCATTATTTTGCATGTGAACAG
Found at i:84847 original size:20 final size:19
Alignment explanation
Indices: 84817--84859 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
84807 TTTCTTTTTC
84817 TCTTTTTTTTTGAGTGCTT
1 TCTTTTTTTTTGAGTGCTT
84836 TCTTTCTTTTTTGAGTGCTT
1 TCTTT-TTTTTTGAGTGCTT
84856 TCTT
1 TCTT
84860 CTGATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.05, C:0.14, G:0.14, T:0.67
Consensus pattern (19 bp):
TCTTTTTTTTTGAGTGCTT
Done.