Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004695.1 Hibiscus syriacus cultivar Beakdansim tig00010540_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: 52839
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:180 original size:16 final size:16
Alignment explanation
Indices: 159--189 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
149 GAATGCATTT
159 TATGCATCGATGCACG
1 TATGCATCGATGCACG
175 TATGCATCGATGCAC
1 TATGCATCGATGCAC
190 TCAGGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (16 bp):
TATGCATCGATGCACG
Found at i:279 original size:64 final size:61
Alignment explanation
Indices: 146--298 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 61
136 CACTCACCAT
* *
146 ATCGAATGCATTTTATGCATCGATGCACGTATGCATCGATGCACTCAGGTTTCATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGCATGCATCGAGGCACTCAGGTTTCATGAAAAC
* * *
207 ATCTAATGCATTTTATGCATCGATGCACAGACCATGCATCGAGGCACTCAGGCTTGT-TTG-AAG
1 ATCGAATGCATTTTATGCATCGATGCAC-G--CATGCATCGAGGCACTCAGG-TT-TCATGAAAA
270 C
61 C
*
271 ATCGAATGCATTTTATGCATTGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
299 TCTTAGTGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
61 27 0.34
62 1 0.01
64 47 0.59
65 4 0.05
66 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (61 bp):
ATCGAATGCATTTTATGCATCGATGCACGCATGCATCGAGGCACTCAGGTTTCATGAAAAC
Found at i:4349 original size:15 final size:17
Alignment explanation
Indices: 4329--4363 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
4319 TAGTCCTCTT
4329 TTCTTCTTT-TTA-TTC
1 TTCTTCTTTGTTAGTTC
4344 TTCTTCTTTGTTAGTTC
1 TTCTTCTTTGTTAGTTC
4361 TTC
1 TTC
4364 ACAAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 3 0.17
17 6 0.33
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (17 bp):
TTCTTCTTTGTTAGTTC
Found at i:7652 original size:3 final size:3
Alignment explanation
Indices: 7644--7684 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
7634 ACAAAATTTG
7644 TAA TAA TAA TTAA TAA -AA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7685 AATTATATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:7909 original size:43 final size:40
Alignment explanation
Indices: 7845--7956 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 40
7835 TGTTGGGGAC
* *
7845 GACACTGCTCATACGCGATGAAGAGTTCGGGTCGTCTAAGG-G-T
1 GACACGGCTCATACGTGATGAAGAGTTC---TCGTC--AGGAGAT
* * *
7888 GACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGAGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTCGTCAGGAGAT
7928 GACACGGCTCATACGTGATGAAGAGTTCT
1 GACACGGCTCATACGTGATGAAGAGTTCT
7957 GGCCATCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.05
39 1 0.02
40 32 0.53
43 24 0.40
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (40 bp):
GACACGGCTCATACGTGATGAAGAGTTCTCGTCAGGAGAT
Found at i:8253 original size:65 final size:63
Alignment explanation
Indices: 8174--8308 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 63
8164 GATGGTAAAT
*
8174 TTTGTTTTCAAAGAAACAAACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACAAAA-
1 TTTGTTTCCAAAGAAACAAACTCAAAGATTTTTC--AAAAGAAACTATCTCAAAAGAGACAAAAC
* * * * * * *
8238 TTTGTTTCCCAAAGAAACATATTCAATGATTTTTCAAAAGAAATTGTCTCAAGATAGACAAAAC
1 TTTGTTT-CCAAAGAAACAAACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACAAAAC
8302 TTTGTTT
1 TTTGTTT
8309 TTCAGAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 24 0.39
64 14 0.23
65 23 0.38
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (63 bp):
TTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACAAAAC
Found at i:8546 original size:31 final size:31
Alignment explanation
Indices: 8486--8546 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
8476 AAGGGAAATG
*
8486 ACTCAAAGATGGTTTTATTTCAAGAGAAACAA
1 ACTCAAAGAT-GTTTGATTTCAAGAGAAACAA
*
8518 ACTCAAAGAT-TTTGATTTTCTAGAGAAAC
1 ACTCAAAGATGTTTGA-TTTCAAGAGAAAC
8547 TGCCTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 12 0.46
32 10 0.38
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATGTTTGATTTCAAGAGAAACAA
Found at i:8886 original size:38 final size:38
Alignment explanation
Indices: 8810--8888 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
8800 CGAGACAATT
*
8810 TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAAGTTTG
1 TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAACTTTG
* **
8848 TTTTTTTGAGAAAAC-GATCTCAAGTGAGATCAACTTTG
1 TTTTTTTAAGAAAACTG-TCTCAAGTGAGAGAAACTTTG
8886 TTT
1 TTT
8889 AATGTGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (38 bp):
TTTTTTTAAGAAAACTGTCTCAAGTGAGAGAAACTTTG
Found at i:9502 original size:4 final size:4
Alignment explanation
Indices: 9493--9540 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
9483 CTTTTATATA
* *
9493 ATGT ATGT ATG- -TGT ATAT ATGT TTGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
9539 AT
1 AT
9541 TGATGTTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
4 36 0.95
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATGT
Found at i:9519 original size:18 final size:19
Alignment explanation
Indices: 9487--9538 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
9477 ATACAACTTT
9487 TATATAATGTATGTATGTG
1 TATATAATGTATGTATGTG
*
9506 TATAT-ATGTTTGTA--TG
1 TATATAATGTATGTATGTG
*
9522 TATGT-ATGTATGTATGT
1 TATATAATGTATGTATGT
9539 ATTGATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 14 0.50
18 9 0.32
19 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (19 bp):
TATATAATGTATGTATGTG
Found at i:9546 original size:12 final size:13
Alignment explanation
Indices: 9493--9546 Score: 69
Period size: 12 Copynumber: 4.3 Consensus size: 13
9483 CTTTTATATA
9493 ATGTATGTATGTGT
1 ATGTATGTAT-TGT
*
9507 ATATATGT-TTGT
1 ATGTATGTATTGT
9519 ATGTATGTA-TGT
1 ATGTATGTATTGT
9531 ATGTATGTATTG-
1 ATGTATGTATTGT
9543 ATGT
1 ATGT
9547 TTGCTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 26 0.72
13 3 0.08
14 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
ATGTATGTATTGT
Found at i:10717 original size:23 final size:20
Alignment explanation
Indices: 10691--10740 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
10681 GTCAAGGGAC
*
10691 TCTTTGTCTTTGTGCTTTTGTCT
1 TCTTTGTCTTT-TGCTATT-T-T
*
10714 TCTTTTTCTTTTGCTATTTT
1 TCTTTGTCTTTTGCTATTTT
10734 TCTTTGT
1 TCTTTGT
10741 ACTCTGCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 6 0.25
23 10 0.42
ACGTcount: A:0.02, C:0.16, G:0.12, T:0.70
Consensus pattern (20 bp):
TCTTTGTCTTTTGCTATTTT
Found at i:14467 original size:21 final size:22
Alignment explanation
Indices: 14443--14483 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14433 ACATATGATG
14443 TAAAATAA-AATATTTACAACA
1 TAAAATAACAATATTTACAACA
*
14464 TAAAATAACATTATTTACAA
1 TAAAATAACAATATTTACAA
14484 TATATGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAACAATATTTACAACA
Found at i:16363 original size:3 final size:3
Alignment explanation
Indices: 16355--16389 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
16345 ACAAAATTTG
*
16355 TAA TAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16390 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16378 original size:17 final size:17
Alignment explanation
Indices: 16356--16399 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16346 CAAAATTTGT
*
16356 AATAATAATATTAATAA
1 AATAATAATAATAATAA
16373 AATAATAATAATAATAA
1 AATAATAATAATAATAA
*
16390 ATTAA-AATAA
1 AATAATAATAA
16400 AATTATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:21319 original size:133 final size:132
Alignment explanation
Indices: 21062--21416 Score: 485
Period size: 133 Copynumber: 2.6 Consensus size: 132
21052 AGTTCGGGTG
* * *
21062 ATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACAC-GCTCATACG
* * * * *
21127 TGATGAAGCGTTCTTGGCCATCTTTAGGAAGTGTGATAACTCGATTCCTACGCGATGAGGACGGC
64 TGATGAAGAGTTC-TGGCCATCTTTAAGAAGGGCGATAACACGATTCCTACGCGATGAGGACGGC
21192 TGGTT
128 TGGTT
* * * * *
21197 ATCTAGGGGTGACAAGGCTCCTACGCGATGAGGAGATCTAGTCAGGGATGAAACGACTCATATGT
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACG-CTCATACGT
* * *
21262 GATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGTCTG
65 GATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAACACGATTCCTACGCGATGAGGACGGCTG
21327 GTT
130 GTT
* * *
21330 ATCTAGGGGTGACGCGGCTCCTACGTGATGAAGAGATATGGTCAGGAGATGACACGGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGG-GATGACAC-GCTCATACG
21395 TGATGAAGAGTTCTGGCCATCT
64 TGATGAAGAGTTCTGGCCATCT
21417 CTAGGGATAA
Statistics
Matches: 193, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
133 90 0.47
134 65 0.34
135 38 0.20
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (132 bp):
ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACGCTCATACGTG
ATGAAGAGTTCTGGCCATCTTTAAGAAGGGCGATAACACGATTCCTACGCGATGAGGACGGCTGG
TT
Found at i:21758 original size:29 final size:30
Alignment explanation
Indices: 21709--21939 Score: 125
Period size: 29 Copynumber: 7.9 Consensus size: 30
21699 ACAAAACTTT
21709 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
21739 GTTTCAAAAGAAA-TGACTCAAAGA-TTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
21766 -TTTCACGAAATTGTCTTAAGAGAAA--CAAA-ACTTTG
1 GTTTCA--AAA--G----AA-ACAAACTCAAAGATTTTG
* **
21801 G-TTCAAAAGAAACAGACTCAAAGA-AAT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
21828 -TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* * *
21856 ATTTCAAAAGAAAC-AACTCACATACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
* *
21885 ATTTCAAAAGAAAC-AACTCACAGACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
*
21914 GTTTCAAGAGAAACAAACTCAAAGAT
1 GTTTCAAAAGAAACAAACTCAAAGAT
21940 AGGTTTTGTT
Statistics
Matches: 162, Mismatches: 17, Indels: 45
0.72 0.08 0.20
Matches are distributed among these distances:
26 17 0.10
27 15 0.09
28 11 0.07
29 72 0.44
30 27 0.17
31 1 0.01
33 4 0.02
34 9 0.06
35 5 0.03
36 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:21861 original size:91 final size:91
Alignment explanation
Indices: 21644--21855 Score: 259
Period size: 91 Copynumber: 2.3 Consensus size: 91
21634 CTCAAATTTT
* * *
21644 TTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTT
1 TTTTCAAAAGAAACA-ACTCAAAGATTTTTTTCAAG-AAAACTGTCTCAAGAGAAACAAAACTTT
* **
21709 GTTTCAAAAGAAACAAACTCAAAGATTT
64 GGTTCAAAAGAAACAAACTCAAAGATAA
** * * *
21737 TGGTTTCAAAAGAAATGACTCAAAGA-TTTTTTCACG-AAATTGTCTTAAGAGAAACAAAACTTT
1 T--TTTCAAAAGAAACAACTCAAAGATTTTTTTCAAGAAAACTGTCTCAAGAGAAACAAAACTTT
*
21800 GGTTCAAAAGAAACAGACTCAAAGA-AA
64 GGTTCAAAAGAAACAAACTCAAAGATAA
21827 TTTTCAAAAGAAACAACTCAAAGATTTTT
1 TTTTCAAAAGAAACAACTCAAAGATTTTT
21856 ATTTCAAAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
88 21 0.21
89 4 0.04
90 1 0.01
91 47 0.46
93 9 0.09
94 9 0.09
95 11 0.11
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (91 bp):
TTTTCAAAAGAAACAACTCAAAGATTTTTTTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGG
TTCAAAAGAAACAAACTCAAAGATAA
Found at i:21952 original size:33 final size:31
Alignment explanation
Indices: 21828--21989 Score: 131
Period size: 29 Copynumber: 5.4 Consensus size: 31
21818 TCAAAGAAAT
* *
21828 TTTCAAAAGAAAC-AACTCAAAGAT-TTTTA
1 TTTCAAGAGAAACAAACTCAAAGATGTTTTG
* * * * *
21857 TTTCAAAAGAAAC-AACTCACATA-CTTTTA
1 TTTCAAGAGAAACAAACTCAAAGATGTTTTG
* * *
21886 TTTCAAAAGAAAC-AACTCACAGA-CTTTTG
1 TTTCAAGAGAAACAAACTCAAAGATGTTTTG
21915 TTTCAAGAGAAACAAACTCAAAGATAGGTTTTG
1 TTTCAAGAGAAACAAACTCAAAGAT--GTTTTG
* * *
21948 TTTCAAGGGAAACAATCTTAAAGATG-TTTG
1 TTTCAAGAGAAACAAACTCAAAGATGTTTTG
*
21978 TTTTAAGAGAAA
1 TTTCAAGAGAAA
21990 TTGTCTTAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
29 65 0.56
30 23 0.20
31 1 0.01
33 27 0.23
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATGTTTTG
Found at i:22081 original size:66 final size:65
Alignment explanation
Indices: 21967--22174 Score: 215
Period size: 64 Copynumber: 3.2 Consensus size: 65
21957 AAACAATCTT
* * * * ** *
21967 AAAGATGTTTGTTTTAAGAGAAATTGTCTTAAAAGAGACAAACCTTTGTTTTCATAA-AAACAGA
1 AAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCA-AAGAAACATA
* *
22031 TTT
63 CTC
* * *
22034 AAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGTGACAAAATTTTGTTTCCAAAGAAACATACT
1 AAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
22099 C
65 C
* * *
22100 AAAGA-TTCTTTCAAAAGAAAC-GTTCTCAAAAGAGACAAAATTTTGTTATCAAATAAACATACT
1 AAAGATTTTTTTCAAAAGAAACTG-TCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
22163 C
65 C
22164 AAAGATTTTTT
1 AAAGATTTTTT
22175 CATTTTGTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 53 0.45
65 10 0.08
66 48 0.41
67 6 0.05
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (65 bp):
AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTC
Found at i:22246 original size:100 final size:101
Alignment explanation
Indices: 22089--22269 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 101
22079 TGTTTCCAAA
*
22089 GAAACATACTCAAAGATTCTTTCAAAAGAAACGTTCTCAAAAGAGACAAAATTTTGTTATC-AAA
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAACGTTCTCAAAAGAGACAAAATTTTGTT-TCAAAA
* *
22153 TAAACATACTCAAAGATTTTTTCATTTTGTTTTAGGT
65 GAAACAGACTCAAAGATTTTTTCATTTTGTTTTAGGT
* * * *
22190 GAAACAGACTCAAATATT-TTTCAATAA-AATC-TGTCTCAAGAGAGACAAAGTTTTGTTTCAAA
1 GAAACAGACTCAAAGATTCTTTCAA-AAGAAACGT-TCTCAAAAGAGACAAAATTTTGTTTCAAA
*
22252 AGAAATAGACTCAAAGAT
64 AGAAACAGACTCAAAGAT
22270 CCTTTGTTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
99 3 0.04
100 48 0.70
101 18 0.26
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (101 bp):
GAAACAGACTCAAAGATTCTTTCAAAAGAAACGTTCTCAAAAGAGACAAAATTTTGTTTCAAAAG
AAACAGACTCAAAGATTTTTTCATTTTGTTTTAGGT
Found at i:22295 original size:30 final size:31
Alignment explanation
Indices: 22241--22299 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
22231 GAGACAAAGT
22241 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
22272 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
22300 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:22377 original size:36 final size:36
Alignment explanation
Indices: 22337--22474 Score: 172
Period size: 36 Copynumber: 3.8 Consensus size: 36
22327 ATAATTTGGA
*
22337 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * *
22373 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
22409 AAATTGTCTCAAGCGAGACAACGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
** *
22444 AAAACGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
22475 AATGTGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
35 7 0.08
36 78 0.88
37 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:33103 original size:17 final size:17
Alignment explanation
Indices: 33081--33119 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
33071 AAAATATATT
33081 ATTTTAATTTAATTGTA
1 ATTTTAATTTAATTGTA
33098 ATTTTAATTTAATTGTA
1 ATTTTAATTTAATTGTA
33115 ATTTT
1 ATTTT
33120 TTTAAACTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTTTAATTTAATTGTA
Found at i:36588 original size:39 final size:39
Alignment explanation
Indices: 36523--36600 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
36513 TCAGTAGTCC
* *
36523 TGTTTTAATCTATATTATCTATATTATTGCTGTTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
* * *
36562 TGTTTTAATCTATGTTATGTAGATTATTGTTGCTTTAAT
1 TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
36601 CTATGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (39 bp):
TGTTTTAATCTATATTATCTAGATTATTGCTGCTTTAAT
Found at i:48989 original size:14 final size:14
Alignment explanation
Indices: 48966--48996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48956 ATTATTTAAA
48966 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
48980 TTATTTGAATTTAT
1 TTATTAGAATTTAT
48994 TTA
1 TTA
48997 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:50257 original size:46 final size:46
Alignment explanation
Indices: 50204--50295 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
50194 ACCAAGTCCT
50204 CAATATCATCATAAGATTTGCAGCTTCCAAGTCGAATACTATTTGA
1 CAATATCATCATAAGATTTGCAGCTTCCAAGTCGAATACTATTTGA
50250 CAATATCATCATAAGATTTGCAGCTTCCAAGTCGAATACTATTTGA
1 CAATATCATCATAAGATTTGCAGCTTCCAAGTCGAATACTATTTGA
50296 TAATTTATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (46 bp):
CAATATCATCATAAGATTTGCAGCTTCCAAGTCGAATACTATTTGA
Found at i:52728 original size:49 final size:50
Alignment explanation
Indices: 52655--52777 Score: 176
Period size: 49 Copynumber: 2.5 Consensus size: 50
52645 AGATGCACGT
* * *
52655 ATGTAAGTATATATTTATTGTTAGGCTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
52704 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
*
52754 ATATAAGTATGTGTTTAATTGTTA
1 ATGTAAGTATGTGTTT-ATTGTTA
52778 CACTTTTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 44 0.68
50 15 0.23
51 6 0.09
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (50 bp):
ATGTAAGTATGTGTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Done.