Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001032.1 Hibiscus syriacus cultivar Beakdansim tig00002054_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: 50485
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:4967 original size:27 final size:28
Alignment explanation
Indices: 4927--4980 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
4917 TCAAAAATTA
*
4927 AAAAAAATATATAATT-ATTATAAATAT
1 AAAAAAATAGATAATTAATTATAAATAT
*
4954 AAAAAATTAGATAATTCAATTATAAAT
1 AAAAAAATAGATAATT-AATTATAAAT
4981 GTGTGCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAAAAATAGATAATTAATTATAAATAT
Found at i:6107 original size:48 final size:50
Alignment explanation
Indices: 5941--6120 Score: 210
Period size: 51 Copynumber: 3.6 Consensus size: 50
5931 TCATACTACA
* * * *
5941 AAAAAAATGTAGCACTTAGCACATACTTACATCAGTGTAAATGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCAGTGTAAA-GAATAAAAC
* *
5992 AAACAAGTGTAGCACTTAACACATACTTACACCAGTGTAAGTGAA-AAAAC
1 AAAAAAGTGTAGCACTTAACACATACTTACACCAGTGTAA-AGAATAAAAC
* *
6042 CAAAAAGTGTAGGACTTAACACATAC-TACTA-C-G-GTACAAGAATAAAAC
1 AAAAAAGTGTAGCACTTAACACATACTTAC-ACCAGTGTA-AAGAATAAAAC
6090 AAAAAAGTGTAGCACTTAACACATAC-TACAC
1 AAAAAAGTGTAGCACTTAACACATACTTACAC
6121 ACGTATAAGT
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
47 7 0.06
48 34 0.30
49 4 0.04
50 28 0.25
51 39 0.35
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (50 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCAGTGTAAAGAATAAAAC
Found at i:6652 original size:49 final size:48
Alignment explanation
Indices: 6566--6659 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
6556 CCCCTAGGGT
* *
6566 GTAAGTGAATAAAATAAAAAGTCTAGTACTTAACACATACTTACAACA
1 GTAAGTAAATAAAATAAAAAGTCTAGCACTTAACACATACTTACAACA
* *
6614 GTAAGTAAATAAACTAAAAAAGTGTAGCACTTAACACATACTTACA
1 GTAAGTAAATAAAAT-AAAAAGTCTAGCACTTAACACATACTTACA
6660 TCGATGTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 13 0.32
49 28 0.68
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (48 bp):
GTAAGTAAATAAAATAAAAAGTCTAGCACTTAACACATACTTACAACA
Found at i:10971 original size:11 final size:11
Alignment explanation
Indices: 10955--10984 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
10945 TCAATTGAGG
10955 TGAGTTTTTCA
1 TGAGTTTTTCA
10966 TGAGTTTTTCA
1 TGAGTTTTTCA
10977 TGAGTTTT
1 TGAGTTTT
10985 AGATTATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.57
Consensus pattern (11 bp):
TGAGTTTTTCA
Found at i:11061 original size:26 final size:26
Alignment explanation
Indices: 11028--11085 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
11018 CCTTCCCCCA
11028 TTTTTTATTA-TTTTA-TTAA-TAAT
1 TTTTTTATTATTTTTATTTAATTAAT
11051 TTTTTTATTATTTTTATTTAATTAAT
1 TTTTTTATTATTTTTATTTAATTAAT
*
11077 TTTTGTATT
1 TTTTTTATT
11086 TAATAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 10 0.32
24 5 0.16
25 4 0.13
26 12 0.39
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTTATTATTTTTATTTAATTAAT
Found at i:11092 original size:16 final size:16
Alignment explanation
Indices: 11061--11106 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
11051 TTTTTTATTA
11061 TTTTTATTTAATTAAT
1 TTTTTATTTAATTAAT
11077 TTTTGTATTTAA-TAAT
1 TTTT-TATTTAATTAAT
*
11093 TTTTTATTTTATTA
1 TTTTTATTTAATTA
11107 TAAATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTTATTTAATTAAT
Found at i:11390 original size:13 final size:13
Alignment explanation
Indices: 11367--11412 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
11357 AACAAAAAAA
11367 AAAAAATATTAAAT
1 AAAAAA-ATTAAAT
*
11381 AAAAAAATTAATT
1 AAAAAAATTAAAT
*
11394 AATAAAA-T-AAT
1 AAAAAAATTAAAT
11405 AAAAAAAT
1 AAAAAAAT
11413 AGGGTAAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 8 0.30
12 1 0.04
13 12 0.44
14 6 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:12184 original size:23 final size:26
Alignment explanation
Indices: 12138--12184 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
12128 ATTTCCATTA
*
12138 TTATTATTATTTATTTCATTTATACT
1 TTATTATTATTTATTTCATATATACT
12164 TTATT-TT-TTTATTT-ATATATA
1 TTATTATTATTTATTTCATATATA
12185 TATATATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 2 0.10
26 5 0.25
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (26 bp):
TTATTATTATTTATTTCATATATACT
Found at i:12253 original size:26 final size:27
Alignment explanation
Indices: 12232--12281 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12222 TTTATTTCTG
*
12232 TTTTTTA-TTTATTAC-TATTATTATT
1 TTTTTTATTTTAATACTTATTATTATT
12257 TTTTTTATTTTAATACTTATTATTA
1 TTTTTTATTTTAATACTTATTATTA
12282 CTATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTATTTTAATACTTATTATTATT
Found at i:12276 original size:24 final size:24
Alignment explanation
Indices: 12232--12280 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12222 TTTATTTCTG
*
12232 TTTTTTATTTATTACTATTATTATT
1 TTTTTTATTTAATAC-ATTATTATT
12257 TTTTTTATTTTAATAC-TTATTATT
1 TTTTTTA-TTTAATACATTATTATT
12281 ACTATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTTATTTAATACATTATTATT
Found at i:19022 original size:23 final size:23
Alignment explanation
Indices: 18992--19038 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18982 TATATGGAAT
18992 TACGGTGCAATTCTACGTGGCAC
1 TACGGTGCAATTCTACGTGGCAC
*
19015 TACGGTGCAATTCTACTTGGCAC
1 TACGGTGCAATTCTACGTGGCAC
19038 T
1 T
19039 TCAGTGCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
TACGGTGCAATTCTACGTGGCAC
Found at i:19045 original size:23 final size:23
Alignment explanation
Indices: 18996--19054 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
18986 TGGAATTACG
*
18996 GTGCAATTCTACGTGGCACTACG
1 GTGCAATTCTACGTGGCACTACA
* *
19019 GTGCAATTCTACTTGGCACTTCA
1 GTGCAATTCTACGTGGCACTACA
19042 GTGC-ATCTCTACG
1 GTGCAAT-TCTACG
19055 CGGTCCTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 2 0.06
23 29 0.94
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTACA
Found at i:20284 original size:17 final size:16
Alignment explanation
Indices: 20253--20286 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20243 CACGTGAGGA
20253 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
20269 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
20286 T
1 T
20287 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:25414 original size:19 final size:21
Alignment explanation
Indices: 25377--25419 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
25367 TTACTTTTTC
25377 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
25397 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
25417 TTT
1 TTT
25420 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:25425 original size:19 final size:20
Alignment explanation
Indices: 25376--25425 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
25366 TTTACTTTTT
*
25376 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
25396 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
25415 CTTTTACCTTT
1 CTTTTACCTTT
25426 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:26731 original size:27 final size:27
Alignment explanation
Indices: 26701--26755 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
26691 TATCCGCCCA
26701 CTGTCCCTGTCGAAGAAACACCCAGCC
1 CTGTCCCTGTCGAAGAAACACCCAGCC
26728 CTGTCCCTGTCGAAGAAACACCCAGCC
1 CTGTCCCTGTCGAAGAAACACCCAGCC
26755 C
1 C
26756 CATCCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.42, G:0.18, T:0.15
Consensus pattern (27 bp):
CTGTCCCTGTCGAAGAAACACCCAGCC
Found at i:26761 original size:27 final size:27
Alignment explanation
Indices: 26704--26761 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
26694 CCGCCCACTG
**
26704 TCCCTGTCGAAGAAACACCCAGCCCTG
1 TCCCTGTCGAAGAAACACCCAGCCCCA
26731 TCCCTGTCGAAGAAACACCCAGCCCCA
1 TCCCTGTCGAAGAAACACCCAGCCCCA
26758 TCCC
1 TCCC
26762 AGCACCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.45, G:0.16, T:0.14
Consensus pattern (27 bp):
TCCCTGTCGAAGAAACACCCAGCCCCA
Found at i:29299 original size:17 final size:16
Alignment explanation
Indices: 29268--29301 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29258 CACGTGAGGA
29268 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
29284 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
29301 T
1 T
29302 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:30263 original size:21 final size:22
Alignment explanation
Indices: 30223--30264 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
30213 GTGGCAGTAC
*
30223 TGTAGCAGGGGAATCGATTCCT
1 TGTAGCAGGGGAACCGATTCCT
*
30245 TGTAGCA-GGGTACCGATTCC
1 TGTAGCAGGGGAACCGATTCC
30265 CTATTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (22 bp):
TGTAGCAGGGGAACCGATTCCT
Found at i:36742 original size:14 final size:14
Alignment explanation
Indices: 36723--36749 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36713 GATCAGAATT
36723 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
36737 TCAAGATTCCAGA
1 TCAAGATTCCAGA
36750 CATGCAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:37371 original size:99 final size:99
Alignment explanation
Indices: 37198--37385 Score: 286
Period size: 99 Copynumber: 1.9 Consensus size: 99
37188 GATATCGTGC
* * * * *
37198 CAATTTCAACTTCACAGTGAATGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
* *
37263 GGACGGCTGATTGTCAACAAACAACTTTCAGAGT
66 GGACAGCTGACTGTCAACAAACAACTTTCAGAGT
* *
37297 CAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACGGTGAAG
1 CAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
*
37362 GGGCAGCTGACTGTCAACAAACAA
66 GGACAGCTGACTGTCAACAAACAA
37386 TTTGTCAGTT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (99 bp):
CAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGCGAAG
GGACAGCTGACTGTCAACAAACAACTTTCAGAGT
Found at i:37626 original size:280 final size:273
Alignment explanation
Indices: 37228--37780 Score: 858
Period size: 280 Copynumber: 2.0 Consensus size: 273
37218 ATGATATTGG
* *
37228 ACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGATTGTCAACAAACAACTTTCA
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTTCA
* * *
37293 GAGTCAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACGGT
66 GAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGC
* *
37358 GAAGGGGCAGCTGACTGTCAACAAACAATTT-GTCAGTTTCAGAGCCAATTTCAACTTCACGACG
131 GAAGGGGCAGCTGACTGTCAACAAACAATTTCCT-AGTTCCAGAGCCAATTTCAACTTCACGACG
*
37422 GAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAA-TGATATCCA
195 GAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACAAAGT-ATATCCA
*
37486 ATTACCAGGCTCAAC
259 ATTACCAAGCTCAAC
* *
37501 ACTCAAGACAGCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAA-----C
* * * * *
37566 AATTTCATAGTCAATTTTAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACT
61 --TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACT
*
37631 TCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCTAGTTCCAGAGCCAATTTCAACTTC
124 TCACAGCGAAGGGGCAGCTGACTGTCAACAAACAATTTCCTAGTTCCAGAGCCAATTTCAACTTC
37696 ACGACGGAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACAAAGTAT
189 ACGACGGAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACAAAGTAT
37761 ATCCAATTACCAAGCTCAAC
254 ATCCAATTACCAAGCTCAAC
37781 TTCACGACGG
Statistics
Matches: 254, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
273 55 0.22
278 1 0.00
280 196 0.77
281 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (273 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAACTTTCA
GAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGC
GAAGGGGCAGCTGACTGTCAACAAACAATTTCCTAGTTCCAGAGCCAATTTCAACTTCACGACGG
AGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACAAAGTATATCCAAT
TACCAAGCTCAAC
Found at i:37630 original size:106 final size:106
Alignment explanation
Indices: 37501--37717 Score: 283
Period size: 106 Copynumber: 2.0 Consensus size: 106
37491 CAGGCTCAAC
* * **
37501 ACTCAAGACAGCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* * * *
37566 AATTTCATAGTCAATTTTAACTTCAC-AGCGAAGGATATTAG
66 AATTCCAGAGCCAATTTCAACTTCACGA-CGAAGGATATTAG
* * * *
37607 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCT
1 ACTCGAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* * *
37672 AGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACGACGAAGGATATTAG
37713 ACTCG
1 ACTCG
37718 GAGCAATACA
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 94 0.99
107 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAGCACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
AATTCCAGAGCCAATTTCAACTTCACGACGAAGGATATTAG
Found at i:38914 original size:25 final size:25
Alignment explanation
Indices: 38874--38932 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
38864 ATTTCCATTA
*
38874 TTATTATTTTTTATTTCATTTA-TACT
1 TTATT-TTTTTTATTT-ATATATTACT
38900 TTATTTTTTTTATTTATATATTACT
1 TTATTTTTTTTATTTATATATTACT
38925 TTGATTTT
1 TT-ATTTT
38933 CATATTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 16 0.53
26 10 0.33
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (25 bp):
TTATTTTTTTTATTTATATATTACT
Found at i:38993 original size:28 final size:28
Alignment explanation
Indices: 38953--39024 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
38943 TTAATTTCTT
* * * *
38953 TTATTTCTGTTTTTTCTATTTATTAC-TA
1 TTATTACTATTTTTTAT-TTTAATACTTA
*
38981 TTATTATTATTTTTTATTTTAATACTTA
1 TTATTACTATTTTTTATTTTAATACTTA
39009 TTATTACTATTATTTT
1 TTATTACTATT-TTTT
39025 TATACCTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 7 0.19
28 25 0.69
29 4 0.11
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (28 bp):
TTATTACTATTTTTTATTTTAATACTTA
Found at i:39053 original size:2 final size:2
Alignment explanation
Indices: 39046--39082 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
39036 TATAAGTTAT
39046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
39083 ACTTGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40632 original size:10 final size:10
Alignment explanation
Indices: 40617--40648 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
40607 AACACTAGCA
40617 TACATATATT
1 TACATATATT
40627 TACATATATT
1 TACATATATT
40637 TACATATATT
1 TACATATATT
40647 TA
1 TA
40649 TATTGTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (10 bp):
TACATATATT
Found at i:49572 original size:19 final size:19
Alignment explanation
Indices: 49548--49623 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
49538 TGTACAAGTG
49548 AAATTATATTAT-TAAATAA
1 AAATTAT-TTATATAAATAA
49567 AAATTATTTATATAAA-AA
1 AAATTATTTATATAAATAA
** *
49585 TCCATCTATAATATATTAAATAA
1 -AAAT-TAT-TTATA-TAAATAA
49608 AAATTATTTATATAAA
1 AAATTATTTATATAAA
49624 ATTCATCGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 6 0.13
19 17 0.38
20 7 0.16
21 7 0.16
22 6 0.13
23 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTATTTATATAAATAA
Found at i:49636 original size:40 final size:41
Alignment explanation
Indices: 49557--49642 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
49547 GAAATTATAT
*
49557 TATTAAATAAAAATTATTTATATAAAAATCCATCTATAATA
1 TATTAAATAAAAATTATTTATATAAAAATCCATCGATAATA
*
49598 TATTAAATAAAAATTATTTATAT-AAAATTCATCGATAATA
1 TATTAAATAAAAATTATTTATATAAAAATCCATCGATAATA
49638 TATTA
1 TATTA
49643 TTTTATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 20 0.47
41 23 0.53
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (41 bp):
TATTAAATAAAAATTATTTATATAAAAATCCATCGATAATA
Done.