Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005741.1 Hibiscus syriacus cultivar Beakdansim tig00013428_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: 64110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3254 original size:21 final size:21
Alignment explanation
Indices: 3228--3271 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3218 CACAGGCATC
3228 GCGAGGTAGTCCTATATGATT
1 GCGAGGTAGTCCTATATGATT
3249 GCGAGGTAGTCCTATATGATT
1 GCGAGGTAGTCCTATATGATT
3270 GC
1 GC
3272 TCTTTCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (21 bp):
GCGAGGTAGTCCTATATGATT
Found at i:5031 original size:15 final size:15
Alignment explanation
Indices: 5007--5042 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4997 ATATCATTAA
*
5007 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
5022 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
5037 ATTAAA
1 ATTAAA
5043 CGTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:9242 original size:14 final size:14
Alignment explanation
Indices: 9205--9242 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
9195 ACTCGTTCGA
9205 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
9219 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
9233 ATGGCTTCGG
1 ATGGCCTCGG
9243 ATGCCCAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:10093 original size:20 final size:20
Alignment explanation
Indices: 10068--10125 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
10058 GTAATTCGCG
10068 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
10088 TTGCGATAGTACTGTTTACA
1 TTGCGATAGTACTGTTTACA
*
10108 TTGCGATAGTATTGTTTA
1 TTGCGATAGTACTGTTTA
10126 TCTATATCGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTACTGTTTACA
Found at i:10131 original size:77 final size:75
Alignment explanation
Indices: 10035--10291 Score: 338
Period size: 77 Copynumber: 3.3 Consensus size: 75
10025 TTCGCGTTGT
* * * **
10035 GATAGT-TGTGTTTACCTATATCGGTAATTCGCGTTGCGATAGTACTG-TTTACATTGCGATAGT
1 GATAGTAT-TGTTTACCTATATCGGTAATTAGCGTTGCGA-A-T-TTGAATCGCATTGCGATAGT
10098 ACTGTTTACATTGC
62 ACTGTTTACATTGC
*
10112 GATAGTATTGTTTATCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTAC
1 GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG--AATCGCATTGCGATAGTAC
10177 TGTTTACATTGC
64 TGTTTACATTGC
* * *
10189 GATAGTGTTGTTTACCTATATCGGTAATTAACGTTGCGAATTTGAAAATCGCATTGCGATAATAC
1 GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG--AATCGCATTGCGATAGTAC
10254 TGTTTACATTGC
64 TGTTTACATTGC
*
10266 GATAGTACTGTTTACCTATATCGGTA
1 GATAGTATTGTTTACCTATATCGGTA
10292 TAAAGAAAAT
Statistics
Matches: 164, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
74 2 0.01
75 1 0.01
76 1 0.01
77 159 0.97
78 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (75 bp):
GATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAATCGCATTGCGATAGTACTG
TTTACATTGC
Found at i:10263 original size:20 final size:20
Alignment explanation
Indices: 10240--10280 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
10230 TTGAAAATCG
10240 CATTGCGATAATACTGTTTA
1 CATTGCGATAATACTGTTTA
*
10260 CATTGCGATAGTACTGTTTA
1 CATTGCGATAATACTGTTTA
10280 C
1 C
10281 CTATATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
CATTGCGATAATACTGTTTA
Found at i:16464 original size:17 final size:16
Alignment explanation
Indices: 16437--16470 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16427 TTAAAATTTT
16437 TAAAAATTTTTATATA
1 TAAAAATTTTTATATA
*
16453 TAAAATATTTTTTTATA
1 TAAAA-ATTTTTATATA
16470 T
1 T
16471 TTTATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAAATTTTTATATA
Found at i:18092 original size:13 final size:14
Alignment explanation
Indices: 18074--18111 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
18064 TTCATGTTCT
18074 TTTTCTTGTTAA-G
1 TTTTCTTGTTAAGG
*
18087 TTTTCTAGTTAAGG
1 TTTTCTTGTTAAGG
18101 TTTATCTTGTT
1 TTT-TCTTGTT
18112 GCATGGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.61
Consensus pattern (14 bp):
TTTTCTTGTTAAGG
Found at i:24857 original size:2 final size:2
Alignment explanation
Indices: 24850--24880 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24840 TTGTTTGAGC
24850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24881 GATGACGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27434 original size:6 final size:6
Alignment explanation
Indices: 27423--27450 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
27413 AGACACGTAT
27423 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
27451 CGAGACAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:27963 original size:6 final size:6
Alignment explanation
Indices: 27938--27974 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
27928 GTCCGTCTCG
*
27938 GGTCG- GGTCG- GGTAGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
27975 ATTGGTATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.03, C:0.14, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:27980 original size:6 final size:6
Alignment explanation
Indices: 27971--28031 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
27961 GTCGTGGTCG
* * * *
27971 TGGTAT TGGTAT TGGTAT TGGTAT TGGTAA TGGTAA TGGTAA TGGTAA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
28019 TGGTAA TGGTAA T
1 TGGTAA TGGTAA T
28032 ACGTGTCTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (6 bp):
TGGTAA
Found at i:27980 original size:12 final size:12
Alignment explanation
Indices: 27943--27980 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
27933 TCTCGGGTCG
27943 GGTCG-GGTAGT
1 GGTCGTGGTAGT
*
27954 GGTCGTGGTCGT
1 GGTCGTGGTAGT
*
27966 GGTCGTGGTATT
1 GGTCGTGGTAGT
27978 GGT
1 GGT
27981 ATTGGTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.05, C:0.11, G:0.50, T:0.34
Consensus pattern (12 bp):
GGTCGTGGTAGT
Found at i:29554 original size:26 final size:28
Alignment explanation
Indices: 29493--29554 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
29483 ACACCTCGTA
29493 GATACTTAAAATCTCTAAGAAAAACAAC
1 GATACTTAAAATCTCTAAGAAAAACAAC
* *
29521 -ATTTCTTAAAATCTTTAA-AAAAA-AAC
1 GA-TACTTAAAATCTCTAAGAAAAACAAC
29547 GATACTTA
1 GATACTTA
29555 CTTTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 8 0.28
27 7 0.24
28 14 0.48
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (28 bp):
GATACTTAAAATCTCTAAGAAAAACAAC
Found at i:31917 original size:15 final size:15
Alignment explanation
Indices: 31893--31965 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
31883 TTGGTTTTCC
31893 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
31908 GGAATTTGAATTACT
1 GGAAAATGAATTACT
31923 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
31938 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
31952 GGAAAATGAATTAC
1 GGAAAATGAATTAC
31966 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:31963 original size:29 final size:30
Alignment explanation
Indices: 31893--31965 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
31883 TTGGTTTTCC
31893 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
31923 GGAAAATGAATTACTGGAATTTGAATT-CT
1 GGAAAATGAATTACTGGAATTTGAATTACT
31952 GGAAAATGAATTAC
1 GGAAAATGAATTAC
31966 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:31971 original size:20 final size:20
Alignment explanation
Indices: 31948--31997 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
31938 GGAATTTGAA
31948 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
31968 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
31988 TTCTGGAAAA
1 TTCTGGAAAA
31998 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:32229 original size:29 final size:28
Alignment explanation
Indices: 32166--32266 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 28
32156 CTTTACTAAA
*
32166 ATATTATTGAAATATATAAATAATATTATT
1 ATATTATT-AAATATATAAAAAAT-TTATT
*
32196 -CATTATTAAATATATAAAAAATTTATAT
1 ATATTATTAAATATATAAAAAATTTAT-T
* * *
32224 ATATTATTAAA-ATAAAATAAAATATCTT
1 ATATTATTAAATATATAA-AAAATTTATT
*
32252 ATATTATTATATATA
1 ATATTATTAAATATA
32267 ATTGATATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.07
28 31 0.52
29 25 0.42
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATTTATT
Found at i:32296 original size:14 final size:14
Alignment explanation
Indices: 32277--32325 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
32267 ATTGATATTT
*
32277 ATATAATATTAAAA
1 ATATAATATTAATA
32291 ATATAATATTATATTA
1 ATATAATATTA-A-TA
*
32307 TTATAATATTAATA
1 ATATAATATTAATA
32321 ATATA
1 ATATA
32326 TTTTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.57
15 2 0.07
16 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAATATTAATA
Found at i:32305 original size:30 final size:29
Alignment explanation
Indices: 32262--32325 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
32252 ATATTATTAT
32262 ATATAATTGATATT-TATATAATATTAAAA
1 ATATAATTGATATTAT-TATAATATTAAAA
* *
32291 ATATAATATTATATTATTATAATATTAATA
1 ATATAAT-TGATATTATTATAATATTAAAA
32321 ATATA
1 ATATA
32326 TTTTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 7 0.23
30 23 0.74
31 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATATAATTGATATTATTATAATATTAAAA
Found at i:32308 original size:8 final size:8
Alignment explanation
Indices: 32278--32324 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
32268 TTGATATTTA
32278 TATAATAT
1 TATAATAT
*
32286 TA-AA-AA
1 TATAATAT
32292 TATAATAT
1 TATAATAT
*
32300 TATATTAT
1 TATAATAT
32308 TATAATAT
1 TATAATAT
32316 TAATAATAT
1 T-ATAATAT
32325 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
6 3 0.09
7 4 0.12
8 18 0.56
9 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TATAATAT
Found at i:32344 original size:22 final size:21
Alignment explanation
Indices: 32290--32336 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
32280 TAATATTAAA
*
32290 AATA-TAATATTATATTATTAT
1 AATATTAATAATATATT-TTAT
32311 AATATTAATAATATATTTTA-
1 AATATTAATAATATATTTTAT
32331 AATATT
1 AATATT
32337 TTAATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTAATAATATATTTTAT
Found at i:32597 original size:42 final size:41
Alignment explanation
Indices: 32507--32625 Score: 211
Period size: 42 Copynumber: 2.9 Consensus size: 41
32497 AATTCTGACA
*
32507 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACATT
32548 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACAC-GGAAAACATT
*
32590 TTCCGGAAAACGAATTACGTGAAACAAACACTGAAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAA
32626 TTCGGGGAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
41 35 0.47
42 40 0.53
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.17
Consensus pattern (41 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACATT
Found at i:49533 original size:35 final size:35
Alignment explanation
Indices: 49472--49546 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
49462 TTCATGTTCA
* *
49472 AAATTTCAAAACACCTTAATTTCATTCTAAACCCT
1 AAATTTCAAAACACATTAATTACATTCTAAACCCT
* *
49507 AAATTTCAAAATA-ATTCAATTACATTCTAAACCTT
1 AAATTTCAAAACACATT-AATTACATTCTAAACCCT
49542 AAATT
1 AAATT
49547 GAAGTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATTTCAAAACACATTAATTACATTCTAAACCCT
Found at i:49590 original size:35 final size:35
Alignment explanation
Indices: 49542--49654 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
49532 TCTAAACCTT
* ** *
49542 AAATTGAAGTATTTTATAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
49577 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
49612 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
49647 AAATTGAA
1 AAATTGAA
49655 GACTACTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:60822 original size:22 final size:22
Alignment explanation
Indices: 60776--60848 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
60766 ATACAATAAA
* *
60776 TAATATTATTTATCATAAAA-CT
1 TAATATTATTT-TTATAAAATAT
60798 TAATATTATTTTTATAAAATAT
1 TAATATTATTTTTATAAAATAT
60820 TAAAATAATTTATTTTTATTAAAATAT
1 T--AAT-A-TTATTTTTA-TAAAATAT
60847 TA
1 TA
60849 TTTTTTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
21 7 0.16
22 13 0.30
24 3 0.07
25 2 0.05
26 9 0.21
27 9 0.21
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTATTTTTATAAAATAT
Found at i:60855 original size:18 final size:19
Alignment explanation
Indices: 60817--60853 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
60807 TTTTATAAAA
60817 TATTAAAATAATTTATTTT
1 TATTAAAATAATTTATTTT
60836 TATTAAAAT-A-TTATTTT
1 TATTAAAATAATTTATTTT
60853 T
1 T
60854 TAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTAAAATAATTTATTTT
Found at i:61089 original size:22 final size:24
Alignment explanation
Indices: 61064--61115 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
61054 TTTATTGCAA
*
61064 TATTAAAAATA-TAAT-ATTATAT
1 TATTAAAAATATTAATAAATATAT
*
61086 TATTAGAAATATTAATAAATATAT
1 TATTAAAAATATTAATAAATATAT
61110 T-TTAAA
1 TATTAAA
61116 TGTTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.40
23 8 0.32
24 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATTAAAAATATTAATAAATATAT
Found at i:61089 original size:30 final size:32
Alignment explanation
Indices: 61049--61108 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
61039 ATATATATTG
* *
61049 ATTATTTTATT-GCAATATTAA-AAATATAAT
1 ATTATATTATTAGAAATATTAATAAATATAAT
61079 ATTATATTATTAGAAATATTAATAAATATA
1 ATTATATTATTAGAAATATTAATAAATATA
61109 TTTTAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 9 0.35
32 7 0.27
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTATATTATTAGAAATATTAATAAATATAAT
Found at i:62817 original size:23 final size:23
Alignment explanation
Indices: 62789--62839 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
62779 AAATATTGTA
*
62789 TTTTAATTAAATTACATTTATAT
1 TTTTAATTAAATTACAATTATAT
*
62812 TTTTAATTAAATTATAATTATAT
1 TTTTAATTAAATTACAATTATAT
*
62835 ATTTA
1 TTTTA
62840 GTACTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAATTAAATTACAATTATAT
Found at i:62862 original size:15 final size:15
Alignment explanation
Indices: 62829--62871 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
62819 TAAATTATAA
*
62829 TTATATATTTAGTACT
1 TTATA-ATTTAATACT
*
62845 TTATAATTTAATATT
1 TTATAATTTAATACT
*
62860 TTATAAATTAAT
1 TTATAATTTAAT
62872 TCAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATAATTTAATACT
Done.