Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004126.1 Hibiscus syriacus cultivar Beakdansim tig00009027_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: 60436
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2081 original size:22 final size:21
Alignment explanation
Indices: 2039--2078 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2029 GAGTTTGTTT
*
2039 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2060 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2079 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4048 original size:63 final size:63
Alignment explanation
Indices: 3979--4158 Score: 209
Period size: 63 Copynumber: 2.8 Consensus size: 63
3969 TTGGAACACT
* **
3979 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
* * **
4042 TGATGCATCGATGCATGTA-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGAAGT-GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * * *
4106 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATACATTCGATGTT
1 TGA-TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
4159 CAATTAATTC
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
62 1 0.01
63 43 0.43
64 15 0.15
65 40 0.40
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:4130 original size:19 final size:19
Alignment explanation
Indices: 4106--4144 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4096 GAAAATATTC
4106 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
4125 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
4144 A
1 A
4145 ATACATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:4141 original size:65 final size:64
Alignment explanation
Indices: 4000--4158 Score: 221
Period size: 65 Copynumber: 2.5 Consensus size: 64
3990 TGCACCAAGT
* * *
4000 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGATGCATCGATGCATGTATA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGATGCATCGATGCATGGAGA
* **
4063 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGA-TGCATCGATGCATGGAGA
* * *
4128 GTGCATCGGTGCATGGAATACATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
4159 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 28 0.33
64 13 0.15
65 43 0.51
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:4198 original size:65 final size:64
Alignment explanation
Indices: 4000--4206 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 64
3990 TGCACCAAGT
* * * * ** *
4000 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGATGCATCGATGCATGTAT-A
1 GTGCATCGGTGCATCAAATACATTCGATGTTTCAAAATATTCAGATGCATCGATGCATGTATGA
* * * *
4063 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-G
1 GTGCATCGGTGCATCAAATACATTCGATG-TTTCAAAATATTCAGA-TGCATCGATGCATGTATG
4127 A
64 A
** *
4128 GTGCATCGGTGCATGGAATACATTCGATG-TTC-AATTAATTCATCGATGCATCGATGCATGTAC
1 GTGCATCGGTGCATCAAATACATTCGATGTTTCAAAAT-ATTCA--GATGCATCGATGCATGTA-
4191 TGA
62 TGA
4194 -TGCATCGGTGCAT
1 GTGCATCGGTGCAT
4207 ACCTTTGAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
62 3 0.02
63 35 0.28
64 28 0.23
65 56 0.45
66 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTGCATCAAATACATTCGATGTTTCAAAATATTCAGATGCATCGATGCATGTATGA
Found at i:9524 original size:19 final size:19
Alignment explanation
Indices: 9500--9537 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9490 TATAACACGG
9500 GTAAA-TAAAAATTGAGTGA
1 GTAAATTAAAAATT-AGTGA
*
9519 GTAAATTAAACATTAGTGA
1 GTAAATTAAAAATTAGTGA
9538 CCAAATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (19 bp):
GTAAATTAAAAATTAGTGA
Found at i:14311 original size:14 final size:14
Alignment explanation
Indices: 14294--14333 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
14284 AGTTCGTTTG
14294 TTTATGTTCATTCA
1 TTTATGTTCATTCA
* *
14308 TTTATGTTTATTCG
1 TTTATGTTCATTCA
14322 TTTATGTTCATT
1 TTTATGTTCATT
14334 TATGTTCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:23678 original size:21 final size:20
Alignment explanation
Indices: 23651--23749 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 20
23641 AATCAGTTTC
23651 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
23672 GAAAATCACAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
23693 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
23713 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
23734 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
23750 ACACATAAAT
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:23778 original size:20 final size:20
Alignment explanation
Indices: 23717--23949 Score: 281
Period size: 20 Copynumber: 11.6 Consensus size: 20
23707 GATTTTCCAG
* ** *
23717 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
23737 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
23757 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
23777 AACCGCAACGTGTATTCGTA
1 AATCGCAACGCGTATCCGTA
* *
23797 AATCGTAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23817 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23837 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23857 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23877 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
23897 AGTCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
23918 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23938 AATCGCAACGCG
1 AATCGCAACGCG
23950 ATTTTTAAAG
Statistics
Matches: 183, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 164 0.90
21 18 0.10
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:24347 original size:14 final size:14
Alignment explanation
Indices: 24328--24384 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
24318 TTTCATTTCG
24328 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
24342 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
24361 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
24375 CGTTGCGATT
1 CGTTGCGATT
24385 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.25, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:24357 original size:33 final size:33
Alignment explanation
Indices: 24318--24388 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
24308 TTCACTTAGA
24318 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
24351 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
24384 TTTCA
1 TTTCA
24389 AGTTAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:24366 original size:19 final size:18
Alignment explanation
Indices: 24316--24366 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
24306 ATTTCACTTA
24316 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
*
24334 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
24348 GATTTTCATTTCGCGTTGC
1 GA-TTTCATTTCGCGTTGC
24367 TATTCTCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 10 0.38
16 3 0.12
17 3 0.12
18 2 0.08
19 8 0.31
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.45
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:24494 original size:21 final size:21
Alignment explanation
Indices: 24468--24538 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
24458 TGCAGAAGAG
24468 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
24489 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
24509 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
24531 TCGCAACG
1 TCGCAACG
24539 GCTTTTTAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 9 0.21
21 24 0.57
22 9 0.21
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:25028 original size:14 final size:14
Alignment explanation
Indices: 25009--25044 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
24999 ATTGTTTAAT
25009 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25023 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25037 TGATTTGT
1 TGATTTGT
25045 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25168 original size:20 final size:19
Alignment explanation
Indices: 25151--25249 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
25141 AAAAATGACT
25151 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25171 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25190 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
25204 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25223 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25243 ATCGCAA
1 ATCGCAA
25250 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 28 0.41
20 26 0.38
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:25243 original size:53 final size:52
Alignment explanation
Indices: 25151--25268 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 52
25141 AAAAATGACT
25151 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
25204 ATCGTAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
25257 ATCACAATGCGA
1 ATCGCAATGCGA
25269 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 19 0.31
53 42 0.69
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:25327 original size:53 final size:52
Alignment explanation
Indices: 25264--25481 Score: 302
Period size: 53 Copynumber: 4.1 Consensus size: 52
25254 AGAATCACAA
25264 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
25317 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
25370 TACGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTGTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-T-TC-TCT-CG--T
*
25428 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
25475 TGCGATT
1 TGCGATT
25482 GTAATTTCTG
Statistics
Matches: 154, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
47 8 0.05
49 2 0.01
50 2 0.01
51 2 0.01
52 11 0.07
53 110 0.71
54 2 0.01
55 3 0.02
56 3 0.02
58 11 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:25392 original size:72 final size:72
Alignment explanation
Indices: 25264--25467 Score: 254
Period size: 72 Copynumber: 2.8 Consensus size: 72
25254 AGAATCACAA
* * * * * *
25264 TGCGATTTTCATTT-CGCATTGCGATTTTCAT-TTCCGCA-TTGCGATTCTCTCGTTGCGATTTT
1 TGCGATTGTCATTTCCGCATTGCGATTCTCATGTTACG-ATTTTC-ATT-TCGCATTGCGATTTT
25326 CATTTCGCAT
63 CATTTCGCAT
*
25336 TGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTACGATTTTCATTTCGCATTGCGATTTTCA
1 TGCGATTGTCATTTCCGCATTGCGATTCTCAT-GTTACGATTTTCATTTCGCATTGCGATTTTCA
25400 TTTCGCAT
65 TTTCGCAT
* **
25408 TGCGATTGTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTGTCATTTCCGCATTGCGATTCTCATGTTACGATTTTCATTTCGCATTGCGATT
25468 CTCTCGTTGC
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
72 92 0.78
73 19 0.16
74 7 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
TGCGATTGTCATTTCCGCATTGCGATTCTCATGTTACGATTTTCATTTCGCATTGCGATTTTCAT
TTCGCAT
Found at i:25489 original size:33 final size:33
Alignment explanation
Indices: 25335--25481 Score: 170
Period size: 33 Copynumber: 4.2 Consensus size: 33
25325 TCATTTCGCA
25335 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
25369 TTACGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
25405 CATTGCGATTGTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
25441 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
25474 TTGCGATT
1 TTGCGATT
25482 GTAATTTCTG
Statistics
Matches: 95, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.01
33 32 0.34
34 27 0.28
35 3 0.03
36 6 0.06
37 3 0.03
38 13 0.14
39 10 0.11
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:27780 original size:12 final size:12
Alignment explanation
Indices: 27763--27787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27753 TCTTCGGGGA
27763 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27775 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27787 C
1 C
27788 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27996 original size:24 final size:24
Alignment explanation
Indices: 27962--28008 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27952 CTGAAACATC
27962 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
27986 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
28009 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:28729 original size:20 final size:20
Alignment explanation
Indices: 28701--28929 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
28691 AAATTTCAGT
* * *
28701 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28721 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28741 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
28761 GTTGCAATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
28781 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28801 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28821 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
28841 GTTGCGATTTACAGATACAC
1 GTTGCGATTTACGGATTCGC
* *
28861 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
28881 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
28901 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
28921 GTTGCGATT
1 GTTGCGATT
28930 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:29960 original size:31 final size:30
Alignment explanation
Indices: 29915--30005 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 30
29905 TTCGAAGATA
* *
29915 TTTTTGAAAAACATATAGTTTTTAGAATGCGG
1 TTTTTG-AAAACATATAGTTTTTAAAATG-AG
* *
29947 TTTTTGAAAACATATATAGCTTTTAAAATGAT
1 TTTTTGAAAAC--ATATAGTTTTTAAAATGAG
*
29979 TTTTTGGAAAACATATAGTTTTAAAAA
1 TTTTT-GAAAACATATAGTTTTTAAAA
30006 CATATTTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 18 0.36
32 11 0.22
33 21 0.42
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (30 bp):
TTTTTGAAAACATATAGTTTTTAAAATGAG
Found at i:30014 original size:31 final size:32
Alignment explanation
Indices: 29912--30014 Score: 79
Period size: 33 Copynumber: 3.2 Consensus size: 32
29902 GTTTTCGAAG
* * **
29912 ATATTTTTGAAAAACATATAGTTTTTAGAATGC
1 ATATTTTTGGAAAACATATAGCTTTTA-AAAAC
** **
29945 -GGTTTTT-GAAAACATATATAGCTTTTAAAATG
1 ATATTTTTGGAAAAC--ATATAGCTTTTAAAAAC
29977 AT-TTTTTGGAAAACATATAG-TTTTAAAAAC
1 ATATTTTTGGAAAACATATAGCTTTTAAAAAC
30007 ATATTTTT
1 ATATTTTT
30015 CAAAAATATA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
30 10 0.18
31 16 0.29
32 12 0.22
33 17 0.31
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.44
Consensus pattern (32 bp):
ATATTTTTGGAAAACATATAGCTTTTAAAAAC
Found at i:30026 original size:31 final size:31
Alignment explanation
Indices: 29915--30026 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 31
29905 TTCGAAGATA
* * ** **
29915 TTTTTGAAAAACATATAGTTTTTAGAATGCGG
1 TTTTTGAAAAATATATAGCTTTTA-AAAACAT
**
29947 TTTTTGAAAACATATATAGCTTTTAAAATGAT
1 TTTTTGAAAA-ATATATAGCTTTTAAAAACAT
* *
29979 TTTTTGGAAAACATATAG-TTTTAAAAACAT
1 TTTTTGAAAAATATATAGCTTTTAAAAACAT
*
30009 ATTTTTCAAAAATATATA
1 -TTTTTGAAAAATATATA
30027 CATATTTATT
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
30 10 0.16
31 21 0.33
32 21 0.33
33 12 0.19
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTTTGAAAAATATATAGCTTTTAAAAACAT
Found at i:32532 original size:17 final size:17
Alignment explanation
Indices: 32506--32540 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
32496 CACCGTTCCC
32506 ATACCAGATCAT-GAGG
1 ATACCAGATCATGGAGG
32522 ATACTCAGATCATGGAGG
1 ATAC-CAGATCATGGAGG
32540 A
1 A
32541 GCATCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (17 bp):
ATACCAGATCATGGAGG
Found at i:33845 original size:24 final size:24
Alignment explanation
Indices: 33813--33881 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
33803 TCAAGATGAC
* * *
33813 TCATATGCTGCAAAAGCACACGCT
1 TCATCTGCTGCAAAAGCACAAGAT
*
33837 TCATCTGCTACAAAAGCACAAGAT
1 TCATCTGCTGCAAAAGCACAAGAT
*
33861 TCATCGGCTGCAAAAGCACAA
1 TCATCTGCTGCAAAAGCACAA
33882 ACTTCTGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.19
Consensus pattern (24 bp):
TCATCTGCTGCAAAAGCACAAGAT
Found at i:38589 original size:201 final size:200
Alignment explanation
Indices: 38278--39212 Score: 1052
Period size: 201 Copynumber: 4.7 Consensus size: 200
38268 TTTGTCAATA
* * * *
38278 AAAACTTTCGAGTTTGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGCTAGCAACGAGGAGC
1 AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
* * *
38343 TACTTTCCGGTTGAATTTTAAA-CAGAGGTCTTTAAGTCAAGAAGAAAACCTAGGTTGGCTGCGA
66 TACTTTTCGGTTGAAGTTTAAACCA-AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGA
* * * *
38407 TTTAGAAACAATGAACTATCTCCCAGCCGAATTTATAGCATAGCTCAAGGCAAGAAGGGTTATAT
130 TTTAGCAACAATGAACTATCTCCCAGCCTAATTTACAACATAGCTCAAGG-AAGAAGGGTTATAT
38472 GTCAACG
194 GTCAACG
* * ** *
38479 AAAACTTTCGAGTTTGATTTCATTCAGCTCGAGGGTATATCAACCGCATGGTAGCAGCGATGAAC
1 AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
* * * **
38544 TACTTTTTGGTTGAAGTTTAAATCAAGGTCTTTAAGTCGAGAAGAAGACCTAGGTTGGCTATGAT
66 TACTTTTCGGTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGAT
* * * * *
38609 TTAGCAATAAGGAACTATCTCACAACCTAATTTACAACATAGCTCAAGGAGAGAAGGGTTATTTG
131 TTAGCAACAATGAACTATCTCCCAGCCTAATTTACAACATAGCTCAAGGA-AGAAGGGTTATATG
38674 TCAACG
195 TCAACG
* ** ** **
38680 AAAACTTTCGAGTTCGATTCCATTTAGCTTAAACGCGTATCAATTGCATGGTAGCAGCGAGGAAC
1 AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
* * *
38745 TACTTTTCGGTTGAAGTTTAAACCGAGGTATTTAAGTCAAGAAGAAGACCTAGGTTGACTGCGAT
66 TACTTTTCGGTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGAT
* * * ** * *
38810 TTAGCAAC-ATGGAACTATCTCCC--CCTAATTTACAACGTAACTTAAGTCG-AGAAAAGATGTA
131 TTAGCAACAAT-GAACTATCTCCCAGCCTAATTTACAACATAGCTCAAG--GAAGAAGGGTTATA
38871 TGTCAACG
193 TGTCAACG
* * *
38879 AAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCAATGAAC
1 AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
* * * *
38944 TA-TTTTCCGGTTGAAGTTTAAAACGAGGTCTTTAAGTCAAGAAGAAGA-CTTGTGTTGGTTGCG
66 TACTTTT-CGGTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGACCTAG-GTTGGCTGCG
* * *
39007 ATTTAGCAACAATGAACTATCTTCCAGCCTAATTTACAGCATA-CTCGA-GAA-AA--GTTATCA
129 ATTTAGCAACAATGAACTATCTCCCAGCCTAATTTACAACATAGCTCAAGGAAGAAGGGTTAT-A
*
39067 -GTCAACA
193 TGTCAACG
* * * * * * *
39074 AAAACTTTTGAGTTCAATTTCATTCAGCTCGAGGGCGTATAAACCACATGGTAGTAGCGAGAAAC
1 AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
* * * * * * ** *
39139 TACTTTTCAGTTGAATTTTAAACCAAAGTCTTTAAG-CTAGAAGAAAACCAAGGTTAACTACGAT
66 TACTTTTCGGTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGAT
*
39203 TTGGCAACAA
131 TTAGCAACAA
39213 AAAGTCACTT
Statistics
Matches: 619, Mismatches: 101, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
194 26 0.04
195 92 0.15
196 5 0.01
197 3 0.00
198 8 0.01
199 160 0.26
200 7 0.01
201 316 0.51
202 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (200 bp):
AAAACTTTCGAGTTCGATTCCATTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAAC
TACTTTTCGGTTGAAGTTTAAACCAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGAT
TTAGCAACAATGAACTATCTCCCAGCCTAATTTACAACATAGCTCAAGGAAGAAGGGTTATATGT
CAACG
Found at i:39043 original size:400 final size:399
Alignment explanation
Indices: 38240--39211 Score: 1163
Period size: 400 Copynumber: 2.4 Consensus size: 399
38230 AAAACCGTTC
* ** * *
38240 ACAACATAGCTCAAGGTGAGAAAAAATATTTGTCAATAAAAACTTTCGAGTTTGATTCCATTCAG
1 ACAACATAGCTCAAGGAGAG-AAAGTTATTTGTCAACAAAAACTTTCGAGTTCGATTCCATTCAG
* * * * *
38305 CTCGAGGGCGTATCAACCGCATGCTAGCAACGAGGAGCTACTTTCCGGTTGAATTTTAAACAGAG
65 CTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACCGAG
* *
38370 GTCTTTAAGTCAAGAAGAAAACCTAGGTTGGCTGCGATTTAGAAACAATGAACTATCTCCCAGCC
130 GTCTTTAAGTCAAGAAGAAAACCTAGGTTGACTGCGATTTAGCAAC-ATGAACTATCTCCCA-CC
* * * ** * * * *
38435 GAATTTATAGCATAGCTCAAGGCAAGAAGGGTTATATGTCAACGAAAACTTTCGAGTTTGATTTC
193 GAATTTACAACATAACTCAAGGCAAGAAAAGATATATGTCAACGAAAACTTTCAAGTTCGATTCC
* * *
38500 ATTCAGCTCGAGGGTATATCAACCGCATGGTAGCAGCGATGAACTACTTTTTGGTTGAAGTTTAA
258 ATTCAGCTCGAGGGCATATCAACCGCATGGTAGCAGCAATGAACTACTTTTCGGTTGAAGTTTAA
* * * *
38565 ATCAAGGTCTTTAAGTCGAGAAGAAGACCTAGGTTGGCTATGATTTAGCAATAAGGAACTATCTC
323 AACAAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATCTC
38630 ACAACCTAATTT
388 ACAACCTAATTT
* * *
38642 ACAACATAGCTCAAGGAGAGAAGGGTTATTTGTCAACGAAAACTTTCGAGTTCGATTCCATTTAG
1 ACAACATAGCTCAAGGAGAGAA-AGTTATTTGTCAACAAAAACTTTCGAGTTCGATTCCATTCAG
** ** ** *
38707 CTTAAACGCGTATCAATTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAAGTTTAAACCGAG
65 CTCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACCGAG
* * *
38772 GTATTTAAGTCAAGAAGAAGACCTAGGTTGACTGCGATTTAGCAACATGGAACTATCTCCC-CCT
130 GTCTTTAAGTCAAGAAGAAAACCTAGGTTGACTGCGATTTAGCAACAT-GAACTATCTCCCACCG
* * * * *
38836 AATTTACAACGTAACTTAAGTCGAGAAAAGATGTATGTCAACGAAAACTTTCAAGTTCGATTCCA
194 AATTTACAACATAACTCAAGGCAAGAAAAGATATATGTCAACGAAAACTTTCAAGTTCGATTCCA
*
38901 TTCAGCTCGAGGGCGTATCAACCGCATGGTAGCAGCAATGAACTA-TTTTCCGGTTGAAGTTTAA
259 TTCAGCTCGAGGGCATATCAACCGCATGGTAGCAGCAATGAACTACTTTT-CGGTTGAAGTTTAA
* * * * *
38965 AACGAGGTCTTTAAGTCAAGAAGAAGA-CTTGTGTTGGTTGCGATTTAGCAACAATGAACTATCT
323 AACAAGGTCTTTAAGTCAAGAAGAAGACCTAG-GTTGGCTACGATTTAGCAACAAGGAACTATC-
*
39029 TC-CAGCCTAATTT
386 TCACAACCTAATTT
* ** * * *
39042 ACAGCATA-CTC---GAGA-AAAGTTATCAGTCAACAAAAACTTTTGAGTTCAATTTCATTCAGC
1 ACAACATAGCTCAAGGAGAGAAAGTTATTTGTCAACAAAAACTTTCGAGTTCGATTCCATTCAGC
* * * * * * *
39102 TCGAGGGCGTATAAACCACATGGTAGTAGCGAGAAACTACTTTTCAGTTGAATTTTAAACCAAAG
66 TCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACCGAGG
* * * * *
39167 TCTTTAAG-CTAGAAGAAAACCAAGGTTAACTACGATTTGGCAACA
131 TCTTTAAGTCAAGAAGAAAACCTAGGTTGACTGCGATTTAGCAACA
39212 AAAAGTCACT
Statistics
Matches: 482, Mismatches: 83, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
393 31 0.06
394 93 0.19
395 2 0.00
396 4 0.01
399 10 0.02
400 175 0.36
401 6 0.01
402 161 0.33
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (399 bp):
ACAACATAGCTCAAGGAGAGAAAGTTATTTGTCAACAAAAACTTTCGAGTTCGATTCCATTCAGC
TCGAGGGCGTATCAACCGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACCGAGG
TCTTTAAGTCAAGAAGAAAACCTAGGTTGACTGCGATTTAGCAACATGAACTATCTCCCACCGAA
TTTACAACATAACTCAAGGCAAGAAAAGATATATGTCAACGAAAACTTTCAAGTTCGATTCCATT
CAGCTCGAGGGCATATCAACCGCATGGTAGCAGCAATGAACTACTTTTCGGTTGAAGTTTAAAAC
AAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTACGATTTAGCAACAAGGAACTATCTCACA
ACCTAATTT
Found at i:40002 original size:18 final size:17
Alignment explanation
Indices: 39969--40022 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
39959 TAGTTTTTGA
39969 ATATATTTTTGAAAAAC
1 ATATATTTTTGAAAAAC
39986 ATATAGTTTTT-AGAAAAC
1 ATATA-TTTTTGA-AAAAC
40004 --A-ATTTTTG-AAAAC
1 ATATATTTTTGAAAAAC
40017 ATATAT
1 ATATAT
40023 AGTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 2 0.06
16 3 0.10
17 6 0.19
18 10 0.32
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (17 bp):
ATATATTTTTGAAAAAC
Found at i:40014 original size:32 final size:31
Alignment explanation
Indices: 39957--40053 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
39947 AATAATAAAG
* *
39957 TATAGTTTTT-GAATATATTTTTGAAAAACA
1 TATAGTTTTTAGAAAAAATTTTTGAAAAACA
*
39987 TATAGTTTTTAGAAAACAATTTTTGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAA-ACA
* *
40020 TATAGTTTTTA-AAAATGATTTTTGGAAAACA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAAACA
40051 TAT
1 TAT
40054 TTTTCGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.18
31 9 0.16
32 25 0.44
33 13 0.23
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (31 bp):
TATAGTTTTTAGAAAAAATTTTTGAAAAACA
Found at i:40028 original size:33 final size:32
Alignment explanation
Indices: 39957--40053 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 32
39947 AATAATAAAG
* * *
39957 TATAGTTTTT-GAATATATTTTTGAAAA-ACA
1 TATAGTTTTTAGAAAAAATTTTTGAAAACATA
39987 TATAGTTTTTAGAAAACAATTTTTGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTTGAAAACATA
*
40020 TATAGTTTTTA-AAAATGATTTTTGGAAAACATA
1 TATAGTTTTTAGAAAA-AATTTTT-GAAAACATA
40053 T
1 T
40054 TTTTCGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
30 10 0.17
31 4 0.07
32 21 0.36
33 23 0.40
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (32 bp):
TATAGTTTTTAGAAAAAATTTTTGAAAACATA
Found at i:47782 original size:15 final size:15
Alignment explanation
Indices: 47762--47793 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47752 ACTAGTACTA
47762 CTCTACAATTCACGT
1 CTCTACAATTCACGT
47777 CTCTACAATTCACGT
1 CTCTACAATTCACGT
47792 CT
1 CT
47794 TAAGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.34, G:0.06, T:0.34
Consensus pattern (15 bp):
CTCTACAATTCACGT
Found at i:53245 original size:22 final size:22
Alignment explanation
Indices: 53217--53261 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53207 ACTACGCAAA
53217 GAACACATCATTTTTATTGTCG
1 GAACACATCATTTTTATTGTCG
*
53239 GAACACATTATTTTTATTGTCG
1 GAACACATCATTTTTATTGTCG
53261 G
1 G
53262 TTCGCCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (22 bp):
GAACACATCATTTTTATTGTCG
Done.