Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007553.1 Hibiscus syriacus cultivar Beakdansim tig00021203_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: 74108
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:9454 original size:23 final size:24
Alignment explanation
Indices: 9426--9475 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
9416 ATTGTGATTA
9426 TATAGGGATCAATTATAACAT-AT
1 TATAGGGATCAATTATAACATCAT
* **
9449 TATAGGGGTCGGTTATAACATCAT
1 TATAGGGATCAATTATAACATCAT
9473 TAT
1 TAT
9476 CATCATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (24 bp):
TATAGGGATCAATTATAACATCAT
Found at i:27396 original size:10 final size:10
Alignment explanation
Indices: 27355--27396 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
27345 CTTAATTTAG
27355 AAATAATAAAT
1 AAATAAT-AAT
*
27366 AAATAATACT
1 AAATAATAAT
27376 AAATAAT-AT
1 AAATAATAAT
*
27385 AAATATTAAT
1 AAATAATAAT
27395 AA
1 AA
27397 TCCTATTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.26
10 13 0.48
11 7 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATAATAAT
Found at i:29075 original size:36 final size:36
Alignment explanation
Indices: 29028--29124 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
29018 TTTATTTTTG
**
29028 CTTCACTACTCTTTTGTGAAGGCTTAATTTGCACTA
1 CTTCACTACTCTTTTGTGAAGGCTTAACATGCACTA
* ** *
29064 CTTCAGTACTCTTTTGTGAAGGCTGGACATGCACTG
1 CTTCACTACTCTTTTGTGAAGGCTTAACATGCACTA
29100 CTTCACTACTCTTTTGTGAAGGCTT
1 CTTCACTACTCTTTTGTGAAGGCTT
29125 GACTCAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (36 bp):
CTTCACTACTCTTTTGTGAAGGCTTAACATGCACTA
Found at i:44110 original size:21 final size:21
Alignment explanation
Indices: 44084--44212 Score: 84
Period size: 20 Copynumber: 6.3 Consensus size: 21
44074 TTGCATTTCA
*
44084 CGTTGCGATAGTTGGAAATCG
1 CGTTGCGATAGTTGAAAATCG
* ** **
44105 CGTTGCGAT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
44125 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* ** **
44146 CGTTGCGAT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
* ** **
44166 CGTTGCGAT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
*
44186 AGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
44207 CGTTGC
1 CGTTGC
44213 AATTTTCCAT
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 49 0.58
21 35 0.42
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:44122 original size:41 final size:41
Alignment explanation
Indices: 44077--44174 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
44067 ATTCGCATTG
* *
44077 CATTTCACGTTGCGATAGTTGGAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
44118 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
44159 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
44175 TTTCCATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:44127 original size:20 final size:20
Alignment explanation
Indices: 44102--44235 Score: 133
Period size: 20 Copynumber: 6.6 Consensus size: 20
44092 TAGTTGGAAA
44102 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
44122 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
44143 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
44163 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
44183 TCGAGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
44204 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
44224 TCGCATTGCGAT
1 TCGCGTTGCGAT
44236 AGTCTACAAT
Statistics
Matches: 87, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
20 59 0.68
21 28 0.32
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:44167 original size:61 final size:61
Alignment explanation
Indices: 44102--44235 Score: 241
Period size: 61 Copynumber: 2.2 Consensus size: 61
44092 TAGTTGGAAA
* *
44102 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
44163 TCGCGTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
*
44224 TCGCATTGCGAT
1 TCGCGTTGCGAT
44236 AGTCTACAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
Found at i:44222 original size:102 final size:102
Alignment explanation
Indices: 44077--44262 Score: 288
Period size: 102 Copynumber: 1.8 Consensus size: 102
44067 ATTCGCATTG
* * *
44077 CATTTCACGTTGCGATAGTTGGAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
1 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCATTGCGATAGTCT-AA
44141 AATCG-CGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
65 AAT-GTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
*
44179 CATTTCGA-GTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCATTGCGATAGTCTAC
1 CATTTC-ACGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCATTGCGATAGTCTAA
44243 AATGTCGTTGCGATTTTCCA
65 AATGTCGTTGCGATTTTCCA
44263 AATTCGTTGC
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
101 1 0.01
102 74 0.96
103 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (102 bp):
CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCATTGCGATAGTCTAAA
ATGTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:44290 original size:41 final size:40
Alignment explanation
Indices: 44166--44296 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 40
44156 TTCCATTTCG
* *
44166 CGTTGCGATTTTCCATTTCGAGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCAATTCGA-TTGCGATAGTCT-ACAAT-GT
* *
44207 CGTTGCAATTTTCCATTTCGCATTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAATTCG-ATTGCGATAGTCTACAATGT
*
44248 CGTTGCGATTTTCCAAATTCG-TTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCGATTGCGATAGTCTACA-ATGT
44289 CGTTGCGA
1 CGTTGCGA
44297 AAGTATACAG
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
40 16 0.20
41 57 0.71
42 7 0.09
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCGATTGCGATAGTCTACAATGT
Found at i:44294 original size:22 final size:22
Alignment explanation
Indices: 44229--44319 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
44219 CCATTTCGCA
44229 TTGCGATAGTCTACA-ATGTCG
1 TTGCGATAGTCTACAGATGTCG
* * *
44250 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAGATGTCG
*
44269 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGATGTCG
* * *
44291 TTGCGAAAGTATACAGTTGTCG
1 TTGCGATAGTCTACAGATGTCG
44313 TTGCGAT
1 TTGCGAT
44320 TTTCCAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 12 0.21
22 29 0.51
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (22 bp):
TTGCGATAGTCTACAGATGTCG
Found at i:44430 original size:6 final size:6
Alignment explanation
Indices: 44419--44450 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
44409 GACACGTATT
44419 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
44451 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:44978 original size:6 final size:6
Alignment explanation
Indices: 44967--45005 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
44957 GGTCAGTTCG
44967 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
45006 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:45115 original size:19 final size:19
Alignment explanation
Indices: 45091--45159 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
45081 TAACGAATTT
*
45091 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTAGAAAA
* **
45110 TCGCAACGATAACTGTAGACTA
1 TCGCAACG--AA-TTTAGAAAA
45132 TCGCAACGAATTTAGAAAA
1 TCGCAACGAATTTAGAAAA
45151 TCGCAACGA
1 TCGCAACGA
45160 CAACTGTAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 23 0.57
20 2 0.05
21 2 0.05
22 13 0.32
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTAGAAAA
Found at i:45137 original size:22 final size:21
Alignment explanation
Indices: 45109--45180 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
45099 AATTTGGAAA
45109 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* **
45131 ATCGCAACG-AA-TTTAGAAA
1 ATCGCAACGAAACTGTAGACT
45150 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
45172 ATCGCAACG
1 ATCGCAACG
45181 CGATTTTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 14 0.34
20 2 0.05
21 2 0.05
22 23 0.56
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:45137 original size:41 final size:41
Alignment explanation
Indices: 45091--45180 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
45081 TAACGAATTT
* *
45091 TCGCAACGAATTTGGAAAATCGCAACGATAACTGTAGACTA
1 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
45132 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
45173 TCGCAACG
1 TCGCAACG
45181 CGATTTTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
Found at i:45197 original size:21 final size:21
Alignment explanation
Indices: 45171--45311 Score: 144
Period size: 21 Copynumber: 6.9 Consensus size: 21
45161 AACTGTAGAC
45171 TATCGCAACGCGATTTTCAAA
1 TATCGCAACGCGATTTTCAAA
45192 TATCGCAACGCGATTTTCAAA
1 TATCGCAACGCGATTTTCAAA
** **
45213 TATCGCAACGCGAACTGGAAA
1 TATCGCAACGCGATTTTCAAA
*
45234 -ATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAA
* * **
45254 TATCGCAACGTGAATTGGAAA
1 TATCGCAACGCGATTTTCAAA
** **
45275 -ATCGCAACGCGAAATGGAAA
1 TATCGCAACGCGATTTTCAAA
45295 -ATCGCAACGCGATTTTC
1 TATCGCAACGCGATTTTC
45312 GCAACGAATT
Statistics
Matches: 99, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
20 46 0.46
21 53 0.54
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
TATCGCAACGCGATTTTCAAA
Found at i:45200 original size:62 final size:59
Alignment explanation
Indices: 45130--45503 Score: 246
Period size: 61 Copynumber: 6.2 Consensus size: 59
45120 AACTGTAGAC
* **
45130 TATCGCAACGAATTTAGAAAATCGCAACGAC-AACTGTAGACTATCGCAACGCGATTTTCAAA
1 TATCGCAACGAATTTGGAAAATCGCAACG-CGAACTG--GAAAATCGCAACGCGATTTTC-AA
* **
45192 TATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
1 TATCGCAACG-AATTTGGAAA-ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
*
45253 CTATCGCAACGTGAA-TTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGA--TT---
1 -TATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
** * * *
45309 T-TCGCAACGAATTTGGAAAATCGCAACGAC-AACTGTAGACTATCGCAACGACAACTGT-AGA
1 TATCGCAACGAATTTGGAAAATCGCAACG-CGAACTG--GAAAATCGCAACG-CGATTTTCA-A
* * ** * ** **
45370 CTATCGCAACGACAACTGTAGACTATCGCAATGCGAACTGGAAAATCGCAACGCGAAATGGAA
1 -TATCGCAACG--AA-TTTGGAAAATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
* * ** * *
45433 AATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGAAAAATCGCAACGCGATTTTCAA
1 TATCGCAACG-AATTTGGAA-AATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
45494 CTATCGCAAC
1 -TATCGCAAC
45504 ACGATTTTCA
Statistics
Matches: 248, Mismatches: 39, Indels: 50
0.74 0.12 0.15
Matches are distributed among these distances:
52 3 0.01
53 20 0.08
54 8 0.03
55 12 0.05
56 2 0.01
58 1 0.00
59 2 0.01
60 3 0.01
61 69 0.28
62 61 0.25
63 20 0.08
64 27 0.11
65 3 0.01
66 17 0.07
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (59 bp):
TATCGCAACGAATTTGGAAAATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAA
Found at i:45239 original size:20 final size:20
Alignment explanation
Indices: 45214--45486 Score: 136
Period size: 20 Copynumber: 13.6 Consensus size: 20
45204 ATTTTCAAAT
45214 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
45234 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
* *
45255 ATCGCAACGTGAATTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
45275 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
*
45295 ATCGCAACGCG-A-T----T
1 ATCGCAACGCGAACTGGAAA
* *
45309 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
45328 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
**
45350 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
**
45372 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
45394 ATCGCAATGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
45414 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
45434 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
*
45455 ATCGCAACGCGAACTGAAAA
1 ATCGCAACGCGAACTGGAAA
45475 ATCGCAACGCGA
1 ATCGCAACGCGA
45487 TTTTCAACTA
Statistics
Matches: 204, Mismatches: 34, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
14 6 0.03
15 1 0.00
18 1 0.00
19 7 0.03
20 93 0.46
21 33 0.16
22 60 0.29
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:45246 original size:41 final size:41
Alignment explanation
Indices: 45193--45503 Score: 198
Period size: 41 Copynumber: 7.7 Consensus size: 41
45183 ATTTTCAAAT
45193 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
* * *
45234 ATCGCAACGCGATTTTCAACTATCGCAACGTGAATTGGAAA
1 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
** ** *
45275 ATCGCAACGCGAAATGGAAA-ATCGCAACGCG-A-T----T
1 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
* * ** **
45309 TTCGCAACG-AATTTGGAAA-ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACGCGATTTTCAAATATCGCAACG-CGAACTG--GAAA
* * * * **
45350 ATCGCAACGACAACTGT-AGACTATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGATTTTCA-AATATCGCAACG-CGAACTG--GAAA
* ** ** *
45394 ATCGCAATGCGAACTGGAAA-ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
* *
45434 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGAAAA
1 ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
*
45475 ATCGCAACGCGATTTTCAACTATCGCAAC
1 ATCGCAACGCGATTTTCAAATATCGCAAC
45504 ACGATTTTCA
Statistics
Matches: 217, Mismatches: 37, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
33 16 0.07
34 10 0.05
35 1 0.00
38 1 0.00
39 1 0.00
40 26 0.12
41 110 0.51
42 14 0.06
43 7 0.03
44 31 0.14
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAAATATCGCAACGCGAACTGGAAA
Found at i:45409 original size:22 final size:22
Alignment explanation
Indices: 45328--45400 Score: 146
Period size: 22 Copynumber: 3.3 Consensus size: 22
45318 AATTTGGAAA
45328 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
45350 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
45372 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
45394 ATCGCAA
1 ATCGCAA
45401 TGCGAACTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:45460 original size:21 final size:21
Alignment explanation
Indices: 45434--45528 Score: 120
Period size: 21 Copynumber: 4.6 Consensus size: 21
45424 GAAATGGAAA
45434 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
45455 ATCGCAACGCGA-ACTGAAAA
1 ATCGCAACGCGATTTTCAACT
45475 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
45496 ATCGCAACACGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
45517 ATCGCAACGCGA
1 ATCGCAACGCGA
45529 AATGCAACGC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:46010 original size:30 final size:30
Alignment explanation
Indices: 45954--46012 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
45944 GATATATTTA
* *
45954 GTGACCAAATTATAAAATTGGTAAAGTTTG
1 GTGACCAAAGTATAAAATTGGAAAAGTTTG
* *
45984 GTGACCAAAGTATAAACTTTGAAAAGTTT
1 GTGACCAAAGTATAAAATTGGAAAAGTTT
46013 AGTCACGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
GTGACCAAAGTATAAAATTGGAAAAGTTTG
Found at i:53434 original size:31 final size:31
Alignment explanation
Indices: 53398--53464 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
53388 TATTTAGTAA
* *
53398 CAAAATTATAAATTTGGTAAAGTTT-GGTGAC
1 CAAAATTATAAACTTGGAAAAGTTTAGG-GAC
53429 CAAAA-TATAAACTTGGAAAAGTTTAGGGAC
1 CAAAATTATAAACTTGGAAAAGTTTAGGGAC
53459 CAAAAT
1 CAAAAT
53465 GAAATTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (31 bp):
CAAAATTATAAACTTGGAAAAGTTTAGGGAC
Found at i:61076 original size:12 final size:12
Alignment explanation
Indices: 61059--61083 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61049 AAATAATAAA
61059 GAATGAAAGAAT
1 GAATGAAAGAAT
61071 GAATGAAAGAAT
1 GAATGAAAGAAT
61083 G
1 G
61084 TTTGCCAAAT
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:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (12 bp):
GAATGAAAGAAT
Found at i:63162 original size:17 final size:18
Alignment explanation
Indices: 63124--63162 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
63114 AATGTTATTG
*
63124 TTATTAGAATTTTGGTTA
1 TTATTAGAAGTTTGGTTA
*
63142 TTATTATAAGTTTGG-TA
1 TTATTAGAAGTTTGGTTA
63159 TTAT
1 TTAT
63163 GTAGTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (18 bp):
TTATTAGAAGTTTGGTTA
Found at i:66492 original size:16 final size:16
Alignment explanation
Indices: 66466--66503 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
66456 CCTACTAAAG
66466 CATGATTGGGTACATAC
1 CATG-TTGGGTACATAC
*
66483 CATGTTGGGTAGATAC
1 CATGTTGGGTACATAC
66499 CATGT
1 CATGT
66504 GAATAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (16 bp):
CATGTTGGGTACATAC
Found at i:66548 original size:15 final size:15
Alignment explanation
Indices: 66523--66555 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
66513 TTAGGATGTA
66523 TATATTTGTCTATCTT
1 TATATTTGTCTAT-TT
66539 TATA-TTGTCTATTT
1 TATATTTGTCTATTT
66553 TAT
1 TAT
66556 TCTTCGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (15 bp):
TATATTTGTCTATTT
Done.