Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004227.1 Hibiscus syriacus cultivar Beakdansim tig00009256_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: 74930
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:4064 original size:24 final size:24
Alignment explanation
Indices: 4003--4057 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3993 TATTATGTTA
4003 AACATAAACGAACGCACATAAACG
1 AACATAAACGAACGCACATAAACG
* ** *
4027 AATATAATTGAACGCATATAAACG
1 AACATAAACGAACGCACATAAACG
4051 AACATAA
1 AACATAA
4058 CCAAACGTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (24 bp):
AACATAAACGAACGCACATAAACG
Found at i:5186 original size:22 final size:20
Alignment explanation
Indices: 5156--5198 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
5146 CATATTCATC
5156 AATCATTTTTATGAAAATATTA
1 AATCA-TTTTATGAAAAT-TTA
*
5178 AATCCTTTTATGAAAATTTA
1 AATCATTTTATGAAAATTTA
5198 A
1 A
5199 TCTCTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
AATCATTTTATGAAAATTTA
Found at i:10726 original size:10 final size:10
Alignment explanation
Indices: 10711--10735 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10701 GCCATTGATC
10711 AACAACAAGA
1 AACAACAAGA
10721 AACAACAAGA
1 AACAACAAGA
10731 AACAA
1 AACAA
10736 GAATCAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:16295 original size:21 final size:23
Alignment explanation
Indices: 16241--16322 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 23
16231 TCGATACACC
* * *
16241 GAATAGTGCATCGATGCATCCCTTT
1 GAAT-GTGCATCGATACA-CTCATT
16266 GAATGTGCATCGATACA-TCA-T
1 GAATGTGCATCGATACACTCATT
* *
16287 GAA-GATGCACCGATGCACTCATT
1 GAATG-TGCATCGATACACTCATT
16310 GAATGTGCATCGA
1 GAATGTGCATCGA
16323 GGCACACTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 4 0.09
23 11 0.23
24 13 0.28
25 4 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
GAATGTGCATCGATACACTCATT
Found at i:16318 original size:23 final size:23
Alignment explanation
Indices: 16241--16327 Score: 81
Period size: 23 Copynumber: 3.8 Consensus size: 23
16231 TCGATACACC
* *
16241 GAATAGTGCATCGATGCATCCCTTT
1 GAAT-GTGCATCGATGCA-CTCATT
*
16266 GAATGTGCATCGATACA-TCA-T
1 GAATGTGCATCGATGCACTCATT
*
16287 GAA-GATGCACCGATGCACTCATT
1 GAATG-TGCATCGATGCACTCATT
*
16310 GAATGTGCATCGAGGCAC
1 GAATGTGCATCGATGCAC
16328 ACTGCCATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.27
22 4 0.08
23 15 0.29
24 13 0.25
25 4 0.08
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
GAATGTGCATCGATGCACTCATT
Found at i:16524 original size:19 final size:20
Alignment explanation
Indices: 16502--16539 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
16492 TTACATCTTC
*
16502 AAATCCTGC-TAACATCATT
1 AAATCCTGCAAAACATCATT
*
16521 AAATCGTGCAAAACATCAT
1 AAATCCTGCAAAACATCAT
16540 CACATTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATCCTGCAAAACATCATT
Found at i:19220 original size:64 final size:65
Alignment explanation
Indices: 19065--19224 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
19055 GAATAAATTG
* * *
19065 AACATCAAATGCATTTTATGCATCAATGCACATACCATGCATCAATGCCCTCAGGTTTTTATGAA
1 AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATCAATGCACTCAGGTATTTATGAA
* * * * *
19130 AACATCGAATGCATTTTATGCGTCGATGCACA-AGCCATGTATCGATGCACTTAGGCTATTT-T-
1 AACATCAAATGCATTTTATGCATCGATGCACATA-CCATGCATCAATGCACTCAGG-TATTTATG
19192 AA
64 AA
19194 AACATCAAATGCATTTTATGCATCGATGCAC
1 AACATCAAATGCATTTTATGCATCGATGCAC
19225 CCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.39
65 47 0.57
66 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (65 bp):
AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATCAATGCACTCAGGTATTTATGAA
Found at i:19459 original size:10 final size:10
Alignment explanation
Indices: 19444--19468 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19434 GCCATTGATC
19444 AACAACAAGA
1 AACAACAAGA
19454 AACAACAAGA
1 AACAACAAGA
19464 AACAA
1 AACAA
19469 GAATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:21633 original size:2 final size:2
Alignment explanation
Indices: 21617--21649 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
21607 CTCATATCAC
*
21617 AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21650 TTACTGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:22880 original size:13 final size:13
Alignment explanation
Indices: 22862--22898 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
22852 CACATAGATA
22862 TATTTTTTTACTT
1 TATTTTTTTACTT
22875 TA-TTTTTTACTT
1 TATTTTTTTACTT
22887 TATTTATTTTAC
1 TATTT-TTTTAC
22899 CAAGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 4 0.18
14 6 0.27
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTTTTTACTT
Found at i:23028 original size:14 final size:14
Alignment explanation
Indices: 22981--23039 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
22971 TATATATATA
**
22981 TTATTTGTTTGTACC
1 TTATTTGTTT-TATT
22996 TTATTTGTTTTATTT
1 TTATTTGTTTTA-TT
23011 TTATTT-TTGTTATT
1 TTATTTGTT-TTATT
23025 TTATTTGTTTTATT
1 TTATTTGTTTTATT
23039 T
1 T
23040 AATTCCATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (14 bp):
TTATTTGTTTTATT
Found at i:24153 original size:28 final size:28
Alignment explanation
Indices: 24118--24174 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
24108 TCACACAATT
24118 TTTTTCATTTATGCTATTTTT-TCATTTA
1 TTTTTCATTT-TGCTATTTTTGTCATTTA
**
24146 TTTTTCATTTTTTTATTTTTGTCATTTA
1 TTTTTCATTTTGCTATTTTTGTCATTTA
24174 T
1 T
24175 ATATCTTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.72
Consensus pattern (28 bp):
TTTTTCATTTTGCTATTTTTGTCATTTA
Found at i:36570 original size:124 final size:124
Alignment explanation
Indices: 36403--37074 Score: 958
Period size: 124 Copynumber: 5.5 Consensus size: 124
36393 TTTACTCAAA
* * * *
36403 ATTGGATTTTAACTTTACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
*
36468 TCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAT
66 TCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
* * *
36527 ATTGGATTTCAA-TTCCACGACGAAGGATATCTAATTCGAGGCTCAACTTCACAACGAAGGGGCC
1 ATTGGATTTCAACTT-CACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCC
* *
36591 ATCCATGATTTCAACTTCACGATTAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
65 ATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
* * *
36651 ATTGGATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAACTTCACAACGAAAGAGCCA
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * *
36716 TCCACGATTTCAACTTCACGATGAAGGACATCGAGCCCACCAACAACATTCATCTTTAG
66 TCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
* * *
36775 ATTAGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGTGCCA
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* *
36840 TCCAAGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
66 TCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
* ** *
36899 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAAATTCACAAAAAAAAGGGGT
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCAC--AACGAAGGGGC
*
36964 CATCCACGATTTCAACTTCACGACGAAGGATATCGT--------GC--C---CATCTTTAG
64 CATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
* * *
37012 ATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGC
1 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGC
37075 TTTCCAGTTT
Statistics
Matches: 503, Mismatches: 41, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
111 8 0.02
113 57 0.11
116 1 0.00
118 2 0.00
123 2 0.00
124 390 0.78
125 2 0.00
126 41 0.08
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (124 bp):
ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAG
Found at i:37688 original size:2 final size:2
Alignment explanation
Indices: 37683--37707 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37673 TATATACATA
37683 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
37708 ATTTACTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38854 original size:3 final size:3
Alignment explanation
Indices: 38846--38910 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
38836 AATTATTTCC
* * *
38846 TAT TAT TAT TAT T-T T-T TAT TGTT TAT TA- TAT TCT TAT T-T AATT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T
38889 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
38911 TTCATTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 7 0.14
3 40 0.78
4 4 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:39026 original size:20 final size:21
Alignment explanation
Indices: 39001--39040 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38991 ATATATATAT
39001 ATATTTATTA-TTCTTTTATC
1 ATATTTATTACTTCTTTTATC
* *
39021 ATATTTTTTACTTGTTTTAT
1 ATATTTATTACTTCTTTTAT
39041 TAACCATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (21 bp):
ATATTTATTACTTCTTTTATC
Found at i:39163 original size:45 final size:43
Alignment explanation
Indices: 39092--39183 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
39082 ACCTTATTTG
*
39092 TTTTATTTTTGTTGTTTTTTATTTGTTTTATTTAT-TTTCATA
1 TTTTATTTTTATTGTTTTTTATTTGTTTTATTTATATTTCATA
* * *
39134 TTTTCTTTTTATTGTTATTTTACTGTTGTTTTGTTTATATTTCTTA
1 TTTTATTTTTATTGTT-TTTTA-T-TTGTTTTATTTATATTTCATA
39180 TTTT
1 TTTT
39184 TCTTATTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 14 0.33
43 5 0.12
44 1 0.02
45 12 0.29
46 10 0.24
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (43 bp):
TTTTATTTTTATTGTTTTTTATTTGTTTTATTTATATTTCATA
Found at i:40227 original size:17 final size:17
Alignment explanation
Indices: 40202--40236 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40192 CTTGTTAATT
*
40202 TTAAGTAATTATATAAA
1 TTAAGTAATTAAATAAA
*
40219 TTAATTAATTAAATAAA
1 TTAAGTAATTAAATAAA
40236 T
1 T
40237 GAAATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAGTAATTAAATAAA
Found at i:40472 original size:14 final size:14
Alignment explanation
Indices: 40424--40498 Score: 75
Period size: 14 Copynumber: 5.4 Consensus size: 14
40414 AAAAACTATT
40424 AAATAAA-TA-TAA
1 AAATAAATTATTAA
* *
40436 AAATTCAATAATTATA
1 AAA-TAAATTATTA-A
40452 AAA-AAATTATTAA
1 AAATAAATTATTAA
40465 AAATAAATTATTAA
1 AAATAAATTATTAA
* *
40479 AATTAAATAATTAA
1 AAATAAATTATTAA
40493 AAATAA
1 AAATAA
40499 TCATATTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
12 3 0.06
13 7 0.14
14 35 0.69
15 2 0.04
16 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATAAATTATTAA
Found at i:40727 original size:22 final size:22
Alignment explanation
Indices: 40699--40751 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
40689 TTTGGTTGTC
40699 AAATTGAAAAAATGATTTCTGG
1 AAATTGAAAAAATGATTTCTGG
40721 AAATTG-AAAAATGATTTCTGG
1 AAATTGAAAAAATGATTTCTGG
*
40742 AAAATGAAAA
1 AAATTGAAAA
40752 CAAAAATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (22 bp):
AAATTGAAAAAATGATTTCTGG
Found at i:42160 original size:3 final size:3
Alignment explanation
Indices: 42152--42211 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
42142 TATAAAAATA
42152 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
42199 AAT AAT AAC AAT A
1 AAT AAT AAT AAT A
42212 GCTTAAGTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43236 original size:74 final size:72
Alignment explanation
Indices: 43117--43256 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 72
43107 TAATTGTTCA
* * * * * * *
43117 TAATAACAAGTGTTGAAGAAAATAAATTTTAAGGGTAACTCCATAATAATAAGTATTGAAAAAAA
1 TAATAACAAATATTAAAGAAAATAAATTTTAAGAGTAACTCCATAATAACAAATATTAAAAAAAA
43182 TAGTCTC
66 TAGTCTC
43189 TAATAACAAATATTAAAGAAAAAGTAAATTTTAAGAGTATACT-CATAATAACAAATATTAAAAA
1 TAATAACAAATATTAAAG-AAAA-TAAATTTTAAGAGTA-ACTCCATAATAACAAATATTAAAAA
43253 AAAT
63 AAAT
43257 TAGAATTCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 15 0.26
73 4 0.07
74 36 0.62
75 3 0.05
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (72 bp):
TAATAACAAATATTAAAGAAAATAAATTTTAAGAGTAACTCCATAATAACAAATATTAAAAAAAA
TAGTCTC
Found at i:43278 original size:74 final size:72
Alignment explanation
Indices: 43117--43287 Score: 179
Period size: 74 Copynumber: 2.3 Consensus size: 72
43107 TAATTGTTCA
* * * * * * * *
43117 TAATAACAAGTGTTGAAGAAAATAAATTTTAAGGGTAACTCCATAATAATAAGTATTGAAAAAAA
1 TAATAACAAATATTAAAAAAAATAAATTTTAAGAGTAACTCCATAATAACAAATATTAAAAAAAA
43182 TAGTCTC
66 TAGTCTC
43189 TAATAACAAATATTAAAGAAAAAGTAAATTTTAAGAGTATACT-CATAATAACAAATATTAAAAA
1 TAATAACAAATATTAAA-AAAAA-TAAATTTTAAGAGTA-ACTCCATAATAACAAATATTAAAAA
43253 AAATTAGAAT-TC
63 AAA-TAG--TCTC
*
43265 TGATAA-AAA-ATTAAAAAAAATAA
1 TAATAACAAATATTAAAAAAAATAA
43288 CAAATAAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
72 17 0.20
73 9 0.11
74 41 0.49
75 9 0.11
76 7 0.08
77 1 0.01
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (72 bp):
TAATAACAAATATTAAAAAAAATAAATTTTAAGAGTAACTCCATAATAACAAATATTAAAAAAAA
TAGTCTC
Found at i:43530 original size:21 final size:21
Alignment explanation
Indices: 43482--43523 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43472 TGAACTCTTA
43482 ATAACTAGTATAAAATATAAT
1 ATAACTAGTATAAAATATAAT
43503 ATAACTAGTATAAAATATAAT
1 ATAACTAGTATAAAATATAAT
43524 TGGACTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
ATAACTAGTATAAAATATAAT
Found at i:58480 original size:18 final size:18
Alignment explanation
Indices: 58457--58525 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
58447 TTCCAACCCA
58457 ACCCAACCCGACCCGTTT
1 ACCCAACCCGACCCGTTT
* *
58475 ACCCAACCCAACCCATTT
1 ACCCAACCCGACCCGTTT
*
58493 ACCCAACCCGACCCGTTA
1 ACCCAACCCGACCCGTTT
* *
58511 ACCCGACCTGACCCG
1 ACCCAACCCGACCCG
58526 GCCCGTTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.26, C:0.51, G:0.10, T:0.13
Consensus pattern (18 bp):
ACCCAACCCGACCCGTTT
Found at i:61057 original size:24 final size:24
Alignment explanation
Indices: 61022--61123 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
61012 GAATATTTTA
* *
61022 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
61046 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * * * *
61070 TCTGATTTCTAACCTGGATTCTAT
1 TCTGATATCTGATCTGAATTCTGT
* *
61094 TCTGATATCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
*
61118 TTTGAT
1 TCTGAT
61124 TTTTGATATC
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:64676 original size:17 final size:17
Alignment explanation
Indices: 64653--64698 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
64643 GACAAAACAT
*
64653 AATACTATTTTGGTACC
1 AATACTATTTTAGTACC
* *
64670 GATACTATTTCAGTACC
1 AATACTATTTTAGTACC
64687 AATACTACTTTT
1 AATACTA-TTTT
64699 CATATCAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (17 bp):
AATACTATTTTAGTACC
Found at i:66256 original size:20 final size:21
Alignment explanation
Indices: 66220--66258 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
66210 TGATGGTTAA
66220 GGAAGAAGAAAAGAAAGAAAT
1 GGAAGAAGAAAAGAAAGAAAT
66241 GGAA-AAGAAGAA-AAAGAA
1 GGAAGAAGAA-AAGAAAGAA
66259 TGGTGTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (21 bp):
GGAAGAAGAAAAGAAAGAAAT
Found at i:69397 original size:18 final size:18
Alignment explanation
Indices: 69371--69405 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69361 TCGAAATGAA
*
69371 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
69389 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
69406 CCGGATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:70570 original size:24 final size:24
Alignment explanation
Indices: 70543--70629 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
70533 TTATATTATA
* *
70543 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCCG
* *
70567 ATACTTGACCTGGATTCTTATCCA
1 ATACTTGACCTGGATTCTGATCCG
**
70591 ATACTTGACCTGGATT-TGATTTG
1 ATACTTGACCTGGATTCTGATCCG
70614 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
70630 ATATTTTGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 19 0.35
24 36 0.65
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCCG
Done.