Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008581.1 Hibiscus syriacus cultivar Beakdansim tig00111515_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: 59527
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:916 original size:4 final size:4
Alignment explanation
Indices: 907--958 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
897 TAAACTTGTT
* * * * *
907 TTTA TTTA TTTG TTTA TTAA TGTA TTTA TTTA ATTA TGTTT TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
956 TTT
1 TTT
959 TGTTTCTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
4 34 0.92
5 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1046 original size:23 final size:23
Alignment explanation
Indices: 973--1096 Score: 83
Period size: 23 Copynumber: 5.3 Consensus size: 23
963 TCTTAATGTT
*
973 TTTATTTAAATATGAAATTTTTA
1 TTTATTTAATTATGAAATTTTTA
** * *
996 TTTATTTTGTTCT-CAATGTCTTTA
1 TTTATTTAATTATGAAAT-T-TTTA
1020 -TTATTTAATTATGAAATTTTTA
1 TTTATTTAATTATGAAATTTTTA
* * * *
1042 TTTATTTTATTTCTTAATGTTTTTA
1 TTTA-TTTAATTATGAA-ATTTTTA
**
1067 -TTATTTAATTATGTACTTTTTTA
1 TTTATTTAATTATG-AAATTTTTA
1090 TTTATTT
1 TTTATTT
1097 TGTTTCTTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
22 7 0.09
23 36 0.48
24 26 0.35
25 6 0.08
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTATTTAATTATGAAATTTTTA
Found at i:1064 original size:24 final size:24
Alignment explanation
Indices: 991--1119 Score: 67
Period size: 24 Copynumber: 5.5 Consensus size: 24
981 AATATGAAAT
* *
991 TTTTATTTATTTT-GTTCTCAATG
1 TTTTATTTATTTTATTTCTTAATG
* **
1014 TCTTTA-TTATTTAATTAT-GAAAT-
1 T-TTTATTTATTTTATT-TCTTAATG
1037 TTTTATTTATTTTATTTCTTAATG
1 TTTTATTTATTTTATTTCTTAATG
* * * *
1061 TTTT-TATTATTTAATTAT-GTACTT
1 TTTTAT-TTATTTTATT-TCTTAATG
*
1085 TTTTATTTATTTTGTTTCTT-ATG
1 TTTTATTTATTTTATTTCTTAATG
1108 TTTT-TATTATTT
1 TTTTAT-TTATTT
1120 AATTGTTTGA
Statistics
Matches: 79, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
22 6 0.08
23 33 0.42
24 37 0.47
25 3 0.04
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (24 bp):
TTTTATTTATTTTATTTCTTAATG
Found at i:1078 original size:47 final size:47
Alignment explanation
Indices: 905--1123 Score: 271
Period size: 47 Copynumber: 4.9 Consensus size: 47
895 GATAAACTTG
* * *
905 TTTTTATTTA-TTTGTTTATTAATG--TAT-TTATTTAATTATG--T
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAAA
*
946 TTTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAAATATGAAA
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAAA
* *
990 TTTTTATTTATTTTG-TTCTCAATGTCTTTATTATTTAATTATGAAA
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAAA
* **
1036 TTTTTATTTATTTTATTTCTTAATGTTTTTATTATTTAATTATGTACT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATG-AAA
1084 TTTTTATTTATTTTGTTTCTT-ATGTTTTTATTATTTAATT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATT
1124 GTTTGAATTG
Statistics
Matches: 158, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
41 10 0.06
42 27 0.17
43 8 0.05
44 15 0.09
45 3 0.02
46 29 0.18
47 45 0.28
48 21 0.13
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (47 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAAA
Found at i:3168 original size:5 final size:5
Alignment explanation
Indices: 3155--3197 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3145 GTCCGTCCTT
* * *
3155 CTCGT CTCGG CTCGG CTC-G CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
3198 TGGTCGTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.05, C:0.42, G:0.35, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:3206 original size:6 final size:6
Alignment explanation
Indices: 3195--3219 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3185 TCGGCTCGGC
3195 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
3220 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:12201 original size:20 final size:21
Alignment explanation
Indices: 12167--12206 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12157 TTTGATATTG
12167 ATAAATATTAATTTA-AATTA
1 ATAAATATTAATTTATAATTA
**
12187 ATAAATATTTTTTTATAATT
1 ATAAATATTAATTTATAATT
12207 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATATTAATTTATAATTA
Found at i:13222 original size:19 final size:17
Alignment explanation
Indices: 13187--13225 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
13177 ATTTGATTTC
13187 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
13204 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
13223 TCT
1 TCT
13226 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:13471 original size:15 final size:16
Alignment explanation
Indices: 13420--13459 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
13410 GGACGTGGCA
13420 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
13435 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
13451 GCGGCTGGA
1 GCGGCTGGA
13460 TTAGAGGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.17, C:0.17, G:0.57, T:0.07
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:13480 original size:17 final size:15
Alignment explanation
Indices: 13431--13471 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
13421 CGGTGGAGGC
**
13431 AGAGGCGGCTGGAGGC
1 AGAGGCGGCTGGA-TT
13447 AGAGGCGGCTGGATT
1 AGAGGCGGCTGGATT
13462 AGAGGCGGCT
1 AGAGGCGGCT
13472 AGGGATTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.20, C:0.17, G:0.51, T:0.12
Consensus pattern (15 bp):
AGAGGCGGCTGGATT
Found at i:13594 original size:3 final size:3
Alignment explanation
Indices: 13588--13671 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
13578 ATATATTATT
* * *
13588 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA T-A TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
13635 TTA TAA TAA TAA TTA TAA TTA T-A TTA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13672 ATTAATATGG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:13632 original size:32 final size:32
Alignment explanation
Indices: 13590--13665 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
13580 ATATTATTTA
* *
13590 ATAATAATAATAA-TATTTATAATAATAATAAT
1 ATAATTATAATAATTA-TAATAATAATAATAAT
*
13622 ATAATTATAATAATTATAATAATAATTATAAT
1 ATAATTATAATAATTATAATAATAATAATAAT
13654 -TATATTATAATA
1 ATA-ATTATAATA
13666 TAATAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 2 0.05
32 35 0.90
33 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAATTATAATAATTATAATAATAATAATAAT
Found at i:13986 original size:41 final size:40
Alignment explanation
Indices: 13919--14026 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 40
13909 GAATAAGCTC
13919 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCGCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTT--CTT
13961 TTGATGAGTTCTT-TCATTATGAACTTCTTCATCCTTCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
** *
14000 TCAATGAGTTATTCTCATTATGAACTT
1 TTGATGAGTTCTTCTCATTATGAACTT
14027 TCTCTAGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 13 0.21
40 13 0.21
41 23 0.37
42 13 0.21
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (40 bp):
TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
Found at i:14468 original size:113 final size:112
Alignment explanation
Indices: 14064--14494 Score: 669
Period size: 112 Copynumber: 3.9 Consensus size: 112
14054 TCTCCTTCTG
* *
14064 TGATAGAATTATGCAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTC--CCTTCTTCAGA
1 TGAT-GAATTATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
14126 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAATGCTGATCCATCAAT
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAT
14173 TGATGAATTCATGTAAAAGGTTG-ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATT-ATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
14237 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAA
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAT
* *
14285 TGATGGATT-TG-AGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 TGATGAATTATGTA--AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
14348 ACGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAT
64 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAT
* * * *
14397 TGATGAATTCATGTAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTCCTTCAGA
1 TGATGAATT-ATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
14462 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
65 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
14495 TGTCAATCCA
Statistics
Matches: 296, Mismatches: 15, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
108 5 0.02
109 39 0.13
110 6 0.02
111 40 0.14
112 126 0.43
113 77 0.26
114 2 0.01
115 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
TGATGAATTATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAT
Found at i:14485 original size:225 final size:221
Alignment explanation
Indices: 14076--14521 Score: 732
Period size: 225 Copynumber: 2.0 Consensus size: 221
14066 ATAGAATTAT
* * *
14076 GCAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCCCTTCTTCAGATGAGTTCTTCTCATT
1 GCAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCCCTTCTTCAGACGAGTTCTTCTCATT
* *
14141 ATGAACTTCTCTGGAAATGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGACAAGTTCTT
66 ATGAACTTCTCTGGAAAAGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGACAAATTCTT
*
14206 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
131 CTCATTATGAACTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
* *
14271 G-CTGATCCATCAAATGATGGATTTGA
196 GTC-AATCCATCAAATGATAGATTTGA
*
14297 GCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCA
1 GCAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTC--CCTTCTTCAGACGAGTTCTTCTCA
14362 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAAT
64 TTATGAAC-TTCTCTGGAAAAGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTG-ACAAAT
* *
14427 TCTTCTTATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
127 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
14492 AAATGTCAATCCATCAAATGATAGATTTGA
192 AAAAGTCAATCCATCAAATGATAGATTTGA
14522 ATCTTTGCTA
Statistics
Matches: 208, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
221 36 0.17
223 31 0.15
224 48 0.23
225 92 0.44
226 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (221 bp):
GCAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCCCTTCTTCAGACGAGTTCTTCTCATT
ATGAACTTCTCTGGAAAAGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGACAAATTCTT
CTCATTATGAACTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
GTCAATCCATCAAATGATAGATTTGA
Found at i:15924 original size:83 final size:83
Alignment explanation
Indices: 15200--15909 Score: 1262
Period size: 83 Copynumber: 8.6 Consensus size: 83
15190 GTAGTTCTTA
* * * *
15200 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTTTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
*
15264 AATTCAATGATTGGTTCAG
65 AATTCAATGATTGGTTCTG
* * *
15283 CCAAACCAGATTAGATAACTCAAAGAACACTTTCAGAATATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
15348 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
15366 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
15431 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
15449 CCAAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
15514 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
15532 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGGTGCTATTG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTA
15596 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
15615 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
15680 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
15698 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTTATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
*
15763 ATTCAATGATTAGTTCTG
66 ATTCAATGATTGGTTCTG
15781 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
15846 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
15864 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
15910 TGGCAAATTC
Statistics
Matches: 601, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.01
83 595 0.99
84 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:17086 original size:16 final size:16
Alignment explanation
Indices: 17065--17135 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
17055 CCCCCTTTTT
17065 TCTTTTTCTTTTTCTC
1 TCTTTTTCTTTTTCTC
17081 TCTTTTT-TTTTTCT-
1 TCTTTTTCTTTTTCTC
* *
17095 T-TTTCTTTTATTTTCTT
1 TCTTT-TTCT-TTTTCTC
17112 TCTTTTTTCTTTCTTCTC
1 TC-TTTTTCTTT-TTCTC
17130 T-TTTTT
1 TCTTTTT
17136 TTTCTTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 8 0.17
16 18 0.39
17 3 0.07
18 8 0.17
19 3 0.07
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTTCTTTTTCTC
Found at i:17091 original size:21 final size:21
Alignment explanation
Indices: 17061--17141 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 21
17051 TGACCCCCCT
17061 TTTTTCTTTTTCTTTTTCTCTC
1 TTTTT-TTTTTCTTTTTCTCTC
17083 TTTTTTTTTTCTTTTTCT-T-
1 TTTTTTTTTTCTTTTTCTCTC
*
17102 TTATTTTCTTTCTTTTTTCTTTCTTC
1 TT-TTTTTTTTC-TTTTTC--TC-TC
17128 TCTTTTTTTTTCTT
1 T-TTTTTTTTTCTT
17142 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.04
20 9 0.18
21 19 0.39
22 5 0.10
23 1 0.02
25 3 0.06
26 9 0.18
27 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTTTTTCTTTTTCTCTC
Found at i:17098 original size:27 final size:26
Alignment explanation
Indices: 17059--17141 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 26
17049 CTTGACCCCC
17059 CTTTTTTCTTTTTCTTTTTCTCTCTTT
1 CTTTTTTCTTTTTCTTTTT-TCTCTTT
* *
17086 TTTTTTTCTTTTTCTTTTATTTTCTTT
1 CTTTTTTCTTTTTCTTTT-TTCTCTTT
17113 CTTTTTTCTTTCTTCTCTTTTT-T-TTT
1 CTTTTTTCTTT-TTCT-TTTTTCTCTTT
17139 CTT
1 CTT
17142 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
26 6 0.12
27 34 0.68
28 7 0.14
29 3 0.06
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (26 bp):
CTTTTTTCTTTTTCTTTTTTCTCTTT
Found at i:17139 original size:15 final size:15
Alignment explanation
Indices: 17060--17142 Score: 84
Period size: 15 Copynumber: 5.5 Consensus size: 15
17050 TTGACCCCCC
17060 TTTT-TTCT-TTTTCT
1 TTTTCTTCTCTTTT-T
17074 TTTTC-TCTCTTTTTT
1 TTTTCTTCTC-TTTTT
* *
17089 TTTTCTTTTTCTTTTA
1 TTTTC-TTCTCTTTTT
17105 TTTTCTT-TCTTTTT
1 TTTTCTTCTCTTTTT
17119 TCTTTCTTCTCTTTTT
1 T-TTTCTTCTCTTTTT
17135 TTTTCTTC
1 TTTTCTTC
17143 AAGCATAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 14 0.24
15 21 0.36
16 21 0.36
17 3 0.05
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTCTCTTTTT
Found at i:29482 original size:19 final size:17
Alignment explanation
Indices: 29447--29485 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29437 ATTTGATTTC
29447 TCTGTGTTTCTCTTCTT
1 TCTGTGTTTCTCTTCTT
*
29464 TCTGTGTATTTTCTGTCTT
1 TCTGTGT-TTCTCT-TCTT
29483 TCT
1 TCT
29486 TTGTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.13, T:0.64
Consensus pattern (17 bp):
TCTGTGTTTCTCTTCTT
Found at i:29707 original size:16 final size:16
Alignment explanation
Indices: 29682--29718 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
29672 GGACGTGGCA
29682 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
29697 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
29713 GCGGCT
1 GCGGCT
29719 AGGGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.16, C:0.19, G:0.57, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:29843 original size:3 final size:3
Alignment explanation
Indices: 29835--29912 Score: 120
Period size: 3 Copynumber: 26.0 Consensus size: 3
29825 TATATTTATT
* * *
29835 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29883 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29913 ATAAATTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:29922 original size:18 final size:17
Alignment explanation
Indices: 29834--29923 Score: 89
Period size: 18 Copynumber: 5.4 Consensus size: 17
29824 ATATATTTAT
29834 TTAATAATAATAAT-AA
1 TTAATAATAATAATAAA
* *
29850 -TAATATTTATAAT-AA
1 TTAATAATAATAATAAA
*
29865 -TAATAATAATAATAAT
1 TTAATAATAATAATAAA
*
29881 TATAATAATAATAATAAT
1 T-TAATAATAATAATAAA
29899 TATAATAATAATAAATAAA
1 T-TAATAATAAT-AATAAA
29918 TTAATA
1 TTAATA
29924 TGGGTAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
15 24 0.38
16 1 0.02
18 33 0.52
19 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATAATAATAATAAA
Found at i:48477 original size:21 final size:22
Alignment explanation
Indices: 48448--48489 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
48438 TTGCTCAACT
*
48448 TTAACAATTTTCAATTTCATTA
1 TTAACAATTTTAAATTTCATTA
48470 TTAA-AATTTTAAATTTCATT
1 TTAACAATTTTAAATTTCATT
48490 CTTTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAACAATTTTAAATTTCATTA
Found at i:51269 original size:21 final size:21
Alignment explanation
Indices: 51243--51284 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51233 ATTCGAGGCT
* *
51243 AGACCATAGAACAGGGTAGCA
1 AGACCAAAAAACAGGGTAGCA
*
51264 AGACCAAAAAATAGGGTAGCA
1 AGACCAAAAAACAGGGTAGCA
51285 GATTCTGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.17, G:0.26, T:0.10
Consensus pattern (21 bp):
AGACCAAAAAACAGGGTAGCA
Found at i:57590 original size:108 final size:109
Alignment explanation
Indices: 57402--57614 Score: 358
Period size: 108 Copynumber: 2.0 Consensus size: 109
57392 TGGAAATCAT
* *
57402 ATATCTCTACACTTTGATGATACAGTAATATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
1 ATATCTCGACACTTTGATGATACAGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
*
57467 ATTTAGTTGATTTA-TTAATGCATGA-TATTAGATTAAGAATAA
66 AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATAA
* *
57509 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGATGATACAGTAACATTTTAACG-TTTAATTTAATTTAAATTATTAGTAA
57574 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGA
65 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGA
57615 TTAATTTTTG
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
107 34 0.35
108 40 0.41
109 11 0.11
110 13 0.13
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (109 bp):
ATATCTCGACACTTTGATGATACAGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAAT
AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATAA
Done.