Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001255.1 Hibiscus syriacus cultivar Beakdansim tig00002466_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: 64493
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1059 original size:20 final size:19
Alignment explanation
Indices: 1030--1067 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1020 TTCGACGTGT
1030 GAATTCACGGGTGAGCAGG
1 GAATTCACGGGTGAGCAGG
1049 GAATATCACGGGTGAGCAG
1 GAAT-TCACGGGTGAGCAG
1068 AGAGCTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16
Consensus pattern (19 bp):
GAATTCACGGGTGAGCAGG
Found at i:1201 original size:35 final size:32
Alignment explanation
Indices: 1121--1202 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
1111 ATTAGAGGAA
*
1121 TACTCGGCGTCTTCTTCACATTTGGGGTGGAG
1 TACTCGGCGTCTTCTTCACATTTCGGGTGGAG
*
1153 TACTCGGCGTCTTCTTCACATTTCGGGTTGAG
1 TACTCGGCGTCTTCTTCACATTTCGGGTGGAG
* *
1185 TACTAGTCGTCTTCTTCA
1 TACTCGGCGTCTTCTTCA
1203 TGGAAGGGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.38
Consensus pattern (32 bp):
TACTCGGCGTCTTCTTCACATTTCGGGTGGAG
Found at i:3942 original size:9 final size:8
Alignment explanation
Indices: 3922--4188 Score: 79
Period size: 8 Copynumber: 34.1 Consensus size: 8
3912 TATCTTTACT
3922 ATTATTAA
1 ATTATTAA
3930 ATTATTAA
1 ATTATTAA
3938 A--ATTAA
1 ATTATTAA
*
3944 ATCATTAA
1 ATTATTAA
*
3952 AGTTAAATAA
1 A-TT-ATTAA
3962 TTATTATTAA
1 --ATTATTAA
*
3972 ATCATTAA
1 ATTATTAA
*
3980 A--GTTAA
1 ATTATTAA
3986 ATTATTAA
1 ATTATTAA
3994 A--ATTAA
1 ATTATTAA
*
4000 ATCATTAA
1 ATTATTAA
4008 A--ATTAA
1 ATTATTAA
*
4014 ATAATT--
1 ATTATTAA
4020 ATTATTAA
1 ATTATTAA
4028 ATTATTAA
1 ATTATTAA
*
4036 A--GTTAA
1 ATTATTAA
4042 ATTATTAA
1 ATTATTAA
*
4050 A--GTTAA
1 ATTATTAA
*
4056 ATCATTAA
1 ATTATTAA
*
4064 AGTTAAGTAA
1 A-TT-ATTAA
4074 TTATTATTAA
1 --ATTATTAA
*
4084 ATCATTAA
1 ATTATTAA
*
4092 A--GTTAA
1 ATTATTAA
*
4098 ATCATTAA
1 ATTATTAA
* *
4106 AGTAAGTAA
1 A-TTATTAA
4115 TTATTATTAA
1 --ATTATTAA
*
4125 ATCATTAA
1 ATTATTAA
*
4133 A--GTTAA
1 ATTATTAA
*
4139 ATCATTAA
1 ATTATTAA
*
4147 AGTTAGTAA
1 A-TTATTAA
4156 TGATTATTAA
1 --ATTATTAA
*
4166 ATTATTTA
1 ATTATTAA
4174 A-T-TTAA
1 ATTATTAA
*
4180 ATCATTAA
1 ATTATTAA
4188 A
1 A
4189 GTTAAATAAT
Statistics
Matches: 195, Mismatches: 30, Indels: 68
0.67 0.10 0.23
Matches are distributed among these distances:
6 52 0.27
7 1 0.01
8 95 0.49
9 12 0.06
10 27 0.14
11 6 0.03
12 2 0.01
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (8 bp):
ATTATTAA
Found at i:3944 original size:14 final size:14
Alignment explanation
Indices: 3925--4270 Score: 234
Period size: 14 Copynumber: 24.9 Consensus size: 14
3915 CTTTACTATT
*
3925 ATTAAATTATTAAA
1 ATTAAATCATTAAA
3939 ATTAAATCATTAAA
1 ATTAAATCATTAAA
* * **
3953 GTTAAATAATTATT
1 ATTAAATCATTAAA
3967 ATTAAATCATTAAA
1 ATTAAATCATTAAA
* *
3981 GTTAAATTATTAAA
1 ATTAAATCATTAAA
3995 ATTAAATCATTAAA
1 ATTAAATCATTAAA
* **
4009 ATTAAATAATTATT
1 ATTAAATCATTAAA
*
4023 ATTAAATTATTAAA
1 ATTAAATCATTAAA
* *
4037 GTTAAATTATTAAA
1 ATTAAATCATTAAA
*
4051 GTTAAATCATTAAA
1 ATTAAATCATTAAA
* * * **
4065 GTTAAGTAATTATT
1 ATTAAATCATTAAA
4079 ATTAAATCATTAAA
1 ATTAAATCATTAAA
*
4093 GTTAAATCATT-AA
1 ATTAAATCATTAAA
* * * **
4106 AGTAAGTAATTATT
1 ATTAAATCATTAAA
4120 ATTAAATCATTAAA
1 ATTAAATCATTAAA
*
4134 GTTAAATCATTAAA
1 ATTAAATCATTAAA
* *
4148 GTTAGTAATGATT---
1 ATTA--AATCATTAAA
* *
4161 ATTAAATTATTTAA
1 ATTAAATCATTAAA
*
4175 TTTAAATCATTAAA
1 ATTAAATCATTAAA
* * *
4189 GTTAAAT-AATAATC
1 ATTAAATCATTAA-A
4203 ATTAAATCATTAAA
1 ATTAAATCATTAAA
* * **
4217 GTTAAATAATTATT
1 ATTAAATCATTAAA
* **
4231 ATTAATTTTTTAAA
1 ATTAAATCATTAAA
*
4245 TTTAAATCATTAAA
1 ATTAAATCATTAAA
* *
4259 TTTAAATAATTA
1 ATTAAATCATTA
4271 TTATTTAATA
Statistics
Matches: 254, Mismatches: 70, Indels: 16
0.75 0.21 0.05
Matches are distributed among these distances:
11 6 0.02
13 16 0.06
14 222 0.87
15 4 0.02
16 6 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (14 bp):
ATTAAATCATTAAA
Found at i:3958 original size:28 final size:28
Alignment explanation
Indices: 3926--4270 Score: 261
Period size: 28 Copynumber: 12.4 Consensus size: 28
3916 TTTACTATTA
*
3926 TTAAATTATTAAAATTAAATCATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
**
3954 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
* *
3982 TTAAATTATTAAAATTAAATCATTAAAA
1 TTAAATAATTAAAATTAAATCATTAAAG
** *
4010 TTAAATAATTATTATTAAATTATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
* *
4038 TTAAATTATTAAAGTTAAATCATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
* **
4066 TTAAGTAATTATTATTAAATCATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
* * * * *
4094 TTAAATCATT-AAAGTAAGTAATTATTA-
1 TTAAATAATTAAAATTAAATCATTA-AAG
* *
4121 TTAAATCATTAAAGTTAAATCATTAAAG
1 TTAAATAATTAAAATTAAATCATTAAAG
* * ** * * *
4149 TT-AGTAATGATTATTAAATTATTTAAT
1 TTAAATAATTAAAATTAAATCATTAAAG
* * *
4176 TTAAATCATTAAAGTTAAAT-AATAATCA-
1 TTAAATAATTAAAATTAAATCATTAA--AG
* * * *
4204 TTAAATCATTAAAGTTAAATAATTATTA-
1 TTAAATAATTAAAATTAAATCATTA-AAG
* ** * *
4232 TTAATTTTTTAAATTTAAATCATTAAAT
1 TTAAATAATTAAAATTAAATCATTAAAG
4260 TTAAATAATTA
1 TTAAATAATTA
4271 TTATTTAATA
Statistics
Matches: 245, Mismatches: 63, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
27 42 0.17
28 199 0.81
29 4 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (28 bp):
TTAAATAATTAAAATTAAATCATTAAAG
Found at i:4049 original size:42 final size:40
Alignment explanation
Indices: 3926--4270 Score: 266
Period size: 42 Copynumber: 8.3 Consensus size: 40
3916 TTTACTATTA
* * * *
3926 TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTA-
1 TTAAATCATT-AAATTAAATTATTAAA-TTAAATCATTA-AAG
*
3968 TTAAATCATTAAAGTTAAATTATTAAAATTAAATCATTAAAA
1 TTAAATCATTAAA-TTAAATTATT-AAATTAAATCATTAAAG
* * *
4010 TTAAATAATTATTATTAAATTATTAAAGTTAAATTATTAAAG
1 TTAAATCATTA-AATTAAATTATTAAA-TTAAATCATTAAAG
* * *
4052 TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAA-TTAAATTATTA-AATTAAATCATTAAAG
* * * *
4094 TTAAATCATTAAAGTAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAATTAAATTATTA-AATTAAATCATTAAAG
* * * *
4135 TTAAATCATTAAAGTTAGTAATGATT--ATTAAATTATTTAAT
1 TTAAATCATTAAA-TTA--AATTATTAAATTAAATCATTAAAG
*
4176 TTAAATCATTAAAGTTAAA-TAATAATCATTAAATCATTAAAG
1 TTAAATCATTAAA-TTAAATTATTAA--ATTAAATCATTAAAG
* * * * *
4218 TTAAATAATTATTATTAATTTTTTAAATTTAAATCATTAAAT
1 TTAAATCATTA-AATTAAATTATTAAA-TTAAATCATTAAAG
*
4260 TTAAATAATTA
1 TTAAATCATTA
4271 TTATTTAATA
Statistics
Matches: 254, Mismatches: 32, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
41 78 0.31
42 157 0.62
43 10 0.04
44 5 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (40 bp):
TTAAATCATTAAATTAAATTATTAAATTAAATCATTAAAG
Found at i:4108 original size:56 final size:56
Alignment explanation
Indices: 3926--4106 Score: 317
Period size: 56 Copynumber: 3.2 Consensus size: 56
3916 TTTACTATTA
3926 TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
1 TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
* *
3982 TTAAATTATTAAAATTAAATCATTAAAATTAAATAATTATTATTAAATTATTAAAG
1 TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
* *
4038 TTAAATTATTAAAGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAG
1 TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
*
4094 TTAAATCATTAAA
1 TTAAATTATTAAA
4107 GTAAGTAATT
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (56 bp):
TTAAATTATTAAAATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
Found at i:4207 original size:83 final size:83
Alignment explanation
Indices: 3968--4228 Score: 294
Period size: 83 Copynumber: 3.1 Consensus size: 83
3958 ATAATTATTA
* * * ** * * * * *
3968 TTAAATCATTAAAGTTAAATTATTAAAATTAAATCATTAAAATTAAATAATTATTATTAAATTAT
1 TTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAGTTAAATCATTA-AAGTAAA-TAA
*
4033 TAA--AGTTAAATTATTAAAG
64 TAATCA-TTAAATCATTAAAG
* * *
4052 TTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAAGTAATT
1 TTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAGTTAAATCATTAAAGTAAATAATA
*
4117 ATTATTAAATCATTAAAG
66 ATCATTAAATCATTAAAG
* * *
4135 TTAAATCATTAAAGTT-AGTAATGATTATTAAATTATTTAATTTAAATCATTAAAGTTAAATAAT
1 TTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAGTTAAATCATTAAAG-TAAATAAT
4199 AATCATTAAATCATTAAAG
65 AATCATTAAATCATTAAAG
*
4218 TTAAATAATTA
1 TTAAATCATTA
4229 TTATTAATTT
Statistics
Matches: 154, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
82 39 0.25
83 67 0.44
84 48 0.31
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (83 bp):
TTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAGTTAAATCATTAAAGTAAATAATA
ATCATTAAATCATTAAAG
Found at i:7706 original size:20 final size:20
Alignment explanation
Indices: 7681--7719 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7671 TCTTTATCAG
*
7681 CTCACCCCGTCAATTCCCTC
1 CTCACCACGTCAATTCCCTC
*
7701 CTCACCACGTGAATTCCCT
1 CTCACCACGTCAATTCCCT
7720 GCTCCAGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.49, G:0.08, T:0.26
Consensus pattern (20 bp):
CTCACCACGTCAATTCCCTC
Found at i:10579 original size:2 final size:2
Alignment explanation
Indices: 10572--10610 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10562 CCTTTAAAAT
10572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10611 TTAAGCAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18505 original size:296 final size:296
Alignment explanation
Indices: 17877--19060 Score: 1919
Period size: 296 Copynumber: 4.0 Consensus size: 296
17867 TCGTAATTCC
* * *
17877 AAGCCACATGATCTTTCCCGAATGCTAGAAATGTATTCATATCAACAAACAATCCTCCTTCTGAC
1 AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
* * *
17942 CTCTGCAAAAAATTCGACCTCATTTGAGAGTTCTTGAAACAAATTTTG-ACAAACAGAACCTAAA
66 CTCTGC-GAAAATTCAACCTCATTTGAGAGCTCTTGAAACAAATTTTGAACAAACAGAACCTAAA
18006 AATAATACTAATAACAAAAAGAAATGGAAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACTT
130 AATAATACTAATAACAAAAAGAAATGGAAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACTT
*
18071 CCTCGGAAGCCAAACAATAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTATC
195 CCTCGGAAGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTATC
*
18136 GTATCAAAAGAGTGTTCTTAGTTAAAATTAGTTACAA
260 GTATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
* *
18173 AAGCCACGTCATCTTTTCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
1 AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
*
18238 CTCTGCGAAAATTCAACCTCATTTGAGAGCGCTTGAAACAAATTTTGAACAAACAGAACCTAAAA
66 CTCTGCGAAAATTCAACCTCATTTGAGAGCTCTTGAAACAAATTTTGAACAAACAGAACCTAAAA
* * *
18303 ATAATACTAATAACAAAAAGAAATGGAAAAAATCTTGAGTCGAGAATCCGAGCTTTAACTAACTA
131 ATAATACTAATAACAAAAAGAAATGG-AAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACTT
* * *
18368 CCTTGGATGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACATATC
195 CCTCGGAAGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTATC
18433 GTATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
260 GTATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
*
18470 AAGCCACGTGATCTTTCCCAAATGCTAG-AACGTATTCATATCAACAAACAATACTCCTTCTGAC
1 AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
* * *
18534 CTCTGCGAATATTCATCCTCATTTGAGAGCTCTTGAAACAAATTTTGAATAAACAGAACCT-AAA
66 CTCTGCGAAAATTCAACCTCATTTGAGAGCTCTTGAAACAAATTTTGAACAAACAGAACCTAAAA
* *
18598 ATAATACTAATGACAAAAAGAAATGGAAAAAAATCTTGAGTCGAGAATCTGAGCTTTAACTAACT
131 ATAATACTAATAACAAAAAGAAATGG--AAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACT
* * *
18663 TCCTCGGAAACCAAACAATAAATAAGCAAAACAAAGTCGAAACAATCATAAGTCAAAACACGTAT
194 TCCTCGGAAGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTAT
*
18728 AC-TATCAACAGAGTGTTCTTAGTTAAAACTAGTTACAA
259 -CGTATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
* *
18766 AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAGCAAACAATCCACCTTC-GAC
1 AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
* * * *
18830 CTATGCGAAAATTCAACCTCATTTGAGAGTTCTTGGAACGAATTTTGAACAAACAGAACCTAAAA
66 CTCTGCGAAAATTCAACCTCATTTGAGAGCTCTTGAAACAAATTTTGAACAAACAGAACCTAAAA
** *
18895 ATAATACTAATAACAAAACTAAATGGAAAAATCTTGAGTCAATAATCTGAGCTTTAACTAACTTC
131 ATAATACTAATAACAAAAAGAAATGGAAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACTTC
* * * *
18960 GTCGGAAGCCAAACAACAAATAAGCAAAACAAAGCCGAAACAAACAAAACTCAAAACACGTATCG
196 CTCGGAAGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTATCG
*
19025 TATCAACAGAGTGTTCTTAGTTAAAACTAGTTACAA
261 TATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
19061 CAAATCCAGT
Statistics
Matches: 825, Mismatches: 56, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
294 1 0.00
295 194 0.24
296 416 0.50
297 214 0.26
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (296 bp):
AAGCCACGTGATCTTTCCCAAATGCTAGAAACGTATTCATATCAACAAACAATCCTCCTTCTGAC
CTCTGCGAAAATTCAACCTCATTTGAGAGCTCTTGAAACAAATTTTGAACAAACAGAACCTAAAA
ATAATACTAATAACAAAAAGAAATGGAAAAATCTTGAGTCAAGAATCTGAGCTTTAACTAACTTC
CTCGGAAGCCAAACAACAAATAAGCAAAACAAAGTCGAAACAATCAAAAGTCAAAACACGTATCG
TATCAAAAGAGTGTTCTTAGTTAAAACTAGTTACAA
Found at i:25941 original size:11 final size:11
Alignment explanation
Indices: 25920--25957 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25910 GGGCTAGCCA
25920 TTTCATTTTTTC
1 TTTC-TTTTTTC
*
25932 TTTCTTTTTTT
1 TTTCTTTTTTC
25943 TTTC-TTTTTC
1 TTTCTTTTTTC
25953 TTTCT
1 TTTCT
25958 CTCAAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 10 0.43
12 4 0.17
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:26852 original size:3 final size:3
Alignment explanation
Indices: 26844--26911 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
26834 TAATATAAAT
*
26844 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
26892 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
26912 TGGATAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:27384 original size:114 final size:114
Alignment explanation
Indices: 27157--27790 Score: 1198
Period size: 114 Copynumber: 5.5 Consensus size: 114
27147 GCTCTTGATG
27157 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
27222 TCCTCTGG-AAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
62 T-CTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
27275 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
27340 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
27389 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
27454 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
27503 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
27568 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
27617 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
27682 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
27731 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
27791 CTACCTTGCA
Statistics
Matches: 512, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
113 6 0.01
114 446 0.87
115 21 0.04
118 39 0.08
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:28549 original size:50 final size:50
Alignment explanation
Indices: 28476--28616 Score: 273
Period size: 50 Copynumber: 2.8 Consensus size: 50
28466 CTTACCAAAA
28476 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
28526 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
28576 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
28617 GGCAAATTCA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:28753 original size:133 final size:133
Alignment explanation
Indices: 28526--29029 Score: 990
Period size: 133 Copynumber: 3.8 Consensus size: 133
28516 TCTGTCTAAT
*
28526 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
28591 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
28656 AAC
131 AAC
28659 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
28724 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
28789 AAC
131 AAC
28792 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
28857 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
28922 AAC
131 AAC
28925 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
28990 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
29030 TCATTTAATG
Statistics
Matches: 369, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 369 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (133 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
AAC
Found at i:30170 original size:1 final size:1
Alignment explanation
Indices: 30166--30199 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
30156 TCATTTTCTA
*
30166 TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30200 CTTCAAGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:30172 original size:28 final size:28
Alignment explanation
Indices: 30139--30203 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
30129 ACCCCCTTTC
30139 TTTTTCTTCTCTTTTTTTCATTTTCTAT
1 TTTTTCTTCTCTTTTTTTCATTTTCTAT
* * ** * *
30167 TTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTCTTCTCTTTTTTTCATTTTCTAT
30195 TTTTTCTTC
1 TTTTTCTTC
30204 AAGCATAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (28 bp):
TTTTTCTTCTCTTTTTTTCATTTTCTAT
Found at i:30176 original size:7 final size:7
Alignment explanation
Indices: 30151--30202 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
30141 TTTCTTCTCT
30151 TTTTTTC
1 TTTTTTC
* *
30158 ATTTTCTA
1 -TTTTTTC
30166 TTTTTTC
1 TTTTTTC
*
30173 TTTTTTT
1 TTTTTTC
*
30180 TTTTTTT
1 TTTTTTC
*
30187 TTTTTTT
1 TTTTTTC
30194 TTTTTTC
1 TTTTTTC
30201 TT
1 TT
30203 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:42040 original size:11 final size:11
Alignment explanation
Indices: 42019--42056 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42009 GGGCCAGCCA
42019 TTTCATTTTTTC
1 TTTC-TTTTTTC
*
42031 TTTCTTTTTTT
1 TTTCTTTTTTC
42042 TTTC-TTTTTC
1 TTTCTTTTTTC
42052 TTTCT
1 TTTCT
42057 CTCAAACAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 10 0.43
12 4 0.17
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:42951 original size:3 final size:3
Alignment explanation
Indices: 42943--43019 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
42933 TAATATAAAT
*
42943 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
42991 TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
43020 TGGATAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45040 original size:15 final size:15
Alignment explanation
Indices: 44987--45034 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
44977 AAACGAATTA
44987 ATTTTAATATT-T-T
1 ATTTTAATATTATAT
*
45000 -TTTTAA-AATAT-T
1 ATTTTAATATTATAT
45012 ATTTTAATATTATAT
1 ATTTTAATATTATAT
45027 ATTTTAAT
1 ATTTTAAT
45035 TCTATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 2 0.07
12 8 0.28
13 6 0.21
14 4 0.14
15 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTAATATTATAT
Found at i:45094 original size:21 final size:20
Alignment explanation
Indices: 45053--45095 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
45043 ATAAGATTTT
* * *
45053 AAATTTATTTAAAAGATTAA
1 AAATGTATTTAAAACAATAA
45073 AAATGTATTTAAAAACAATAA
1 AAATGTATTT-AAAACAATAA
45094 AA
1 AA
45096 TTATAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATGTATTTAAAACAATAA
Found at i:49013 original size:2 final size:2
Alignment explanation
Indices: 49006--49033 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48996 CCGACAAAGC
49006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49034 AAAAAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49645 original size:2 final size:2
Alignment explanation
Indices: 49638--49690 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
49628 ATTTGTAGAG
49638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49680 TA TA TA TA TA T
1 TA TA TA TA TA T
49691 TGTAAGTGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59151 original size:11 final size:11
Alignment explanation
Indices: 59135--59159 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59125 TTGCGTTAGC
59135 TTTTAGGGGCG
1 TTTTAGGGGCG
59146 TTTTAGGGGCG
1 TTTTAGGGGCG
59157 TTT
1 TTT
59160 GGATGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.40, T:0.44
Consensus pattern (11 bp):
TTTTAGGGGCG
Found at i:59789 original size:20 final size:20
Alignment explanation
Indices: 59753--59790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59743 ATCCTATTCC
**
59753 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
59773 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
59791 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:60030 original size:15 final size:16
Alignment explanation
Indices: 59997--60033 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59987 ATTTTACGAG
59997 TAAAATAAATTATCAT
1 TAAAATAAATTATCAT
60013 TAAAA-AAATATATC-T
1 TAAAATAAAT-TATCAT
60028 TAAAAT
1 TAAAAT
60034 CTCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATAAATTATCAT
Found at i:60413 original size:2 final size:2
Alignment explanation
Indices: 60406--60501 Score: 149
Period size: 2 Copynumber: 47.5 Consensus size: 2
60396 TTCAATCAAC
60406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
60448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA T- TCA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
60490 TA TA TCA TA TA T
1 TA TA T-A TA TA T
60502 TTTTTAAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
1 1 0.01
2 84 0.97
3 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60816 original size:36 final size:36
Alignment explanation
Indices: 60775--60854 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
60765 TTGAAAAAAT
* * * *
60775 TATTTAGTTTACAATGATAATTGTAAACTTTTATTG
1 TATTTAATTTACAATAATAATTATAAACTCTTATTG
* *
60811 TATTTAATTTACGATAATAATTATAAACTCTTATTT
1 TATTTAATTTACAATAATAATTATAAACTCTTATTG
60847 TAATTTAA
1 T-ATTTAA
60855 ATATTCAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (36 bp):
TATTTAATTTACAATAATAATTATAAACTCTTATTG
Found at i:61135 original size:2 final size:2
Alignment explanation
Indices: 61128--61159 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
61118 TGCTTGATTA
61128 AT AT AT AT 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
61160 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.