Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007017.1 Hibiscus syriacus cultivar Beakdansim tig00018127_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: 94528
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:59 original size:21 final size:22
Alignment explanation
Indices: 33--86 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
23 AAGCATATTA
33 TTTATTATATTTTTTAATTT-T
1 TTTATTATATTTTTTAATTTAT
* **
54 TTTATTTTATTTTTTGTTTTAT
1 TTTATTATATTTTTTAATTTAT
76 TTTATTTATAT
1 TTTA-TTATAT
87 ATGTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.63
22 5 0.19
23 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTATATTTTTTAATTTAT
Found at i:229 original size:20 final size:21
Alignment explanation
Indices: 189--239 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
179 TTTCATTTTT
*
189 TATTATAC-T-AT-ATTATTA
1 TATTATACTTCATCATTATCA
207 TA-TATACTTCATCATTATCA
1 TATTATACTTCATCATTATCA
*
227 TATTATATTTCAT
1 TATTATACTTCAT
240 ATGTTTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 3 0.11
19 2 0.07
20 8 0.30
21 9 0.33
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTATACTTCATCATTATCA
Found at i:268 original size:12 final size:12
Alignment explanation
Indices: 248--278 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
238 ATATGTTTCA
*
248 TTTTGTTTTATC
1 TTTTATTTTATC
260 TTTTATTTTATC
1 TTTTATTTTATC
272 TTTTATT
1 TTTTATT
279 ATTTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATC
Found at i:5683 original size:36 final size:36
Alignment explanation
Indices: 5634--6097 Score: 318
Period size: 36 Copynumber: 13.2 Consensus size: 36
5624 CTTTGAGATG
* * *
5634 GTTTATCTCAAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* *
5670 GTTTCTCTTAAAACAAATTTTGTCTGTATTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * **** *
5706 TTTTTTCTTAAAAGTTTTTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
*
5742 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * * *
5778 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* ** *
5806 TGTATTC-CTTTAAACAAATTTCATCTCTCTCGAGACA
1 -GT-TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* ** * *
5843 GTTTCTTTTGGAACTAAATTTTGTCACTTTTGAGACA
1 GTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACA
* *
5880 GTTTCTCTTGAAACAAA-TTTGTCTCGCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * *
5915 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATCTA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA-C-A
* * * *
5945 TTTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * * **
5980 ATTTCTTTTAAAACTGAGCTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACA
* * *
6017 TTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * *
6053 ATTTCCCTTAAAACAAAGTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
*
6089 GTTCCTCTT
1 GTTTCTCTT
6098 GAAGCACCAA
Statistics
Matches: 332, Mismatches: 72, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.01
29 31 0.09
30 13 0.04
35 45 0.14
36 180 0.54
37 60 0.18
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
Found at i:5924 original size:137 final size:138
Alignment explanation
Indices: 5724--6069 Score: 505
Period size: 137 Copynumber: 2.5 Consensus size: 138
5714 TAAAAGTTTT
* * *
5724 TTTGTCTCCCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
1 TTTGTCACTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * **
5789 AACAAAATCTTTGAATATGTATTCCTTTAAACAAATTTCATCTCTCTCGAGACAGTTTCTTTTGG
66 AACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTAA
*
5854 AACTAAAT
131 AACTAAAC
* * *
5862 TTTGTCACTTTTGAGACAGTTTCTCTTGAAACAAA-TTTGTCTCGCTTGAGACAGTTTCCCTTGA
1 TTTGTCACTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * *
5926 AACAAAATCTTTGAATCTATTTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAA
66 AACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTAA
* *
5991 AACTGAGC
131 AACTAAAC
* * * *
5999 TTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAATTTCCCTTAA
1 TTTGTCACTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
6064 AACAAA
66 AACAAA
6070 GTTTGTCTCT
Statistics
Matches: 184, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
137 123 0.67
138 61 0.33
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (138 bp):
TTTGTCACTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTAA
AACTAAAC
Found at i:6042 original size:73 final size:72
Alignment explanation
Indices: 5944--6100 Score: 208
Period size: 73 Copynumber: 2.2 Consensus size: 72
5934 CTTTGAATCT
* * ** **
5944 ATTTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTGAGCTTTGTCTCT
1 ATTTTCTCTTGAAACAAATTTCGTCTCTCTCGAAACAATTTCCCTTAAAACAAAG-TTTGTCTCT
6008 CTTGAGAC
65 CTTGAGAC
* *
6016 ATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAATTTCCCTTAAAACAAAGTTTGTCTCTC
1 ATTTTCTCTTGAAACAAATTTCGTCTCTCTCGAAACAATTTCCCTTAAAACAAAGTTTGTCTCTC
6081 TTGAGAC
66 TTGAGAC
* *
6088 AGTTCCTCTTGAA
1 ATTTTCTCTTGAA
6101 GCACCAATCT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 34 0.46
73 40 0.54
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (72 bp):
ATTTTCTCTTGAAACAAATTTCGTCTCTCTCGAAACAATTTCCCTTAAAACAAAGTTTGTCTCTC
TTGAGAC
Found at i:6045 original size:21 final size:20
Alignment explanation
Indices: 6020--6084 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
6010 TGAGACATTT
6020 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAA-TTTGTC
6041 TCTCTTGAAAC-AA-TT-TC
1 TCTCTTGAAACAAATTTGTC
*
6058 -C-CTTAAAACAAAGTTTGTC
1 TCTCTTGAAACAAA-TTTGTC
6077 TCTCTTGA
1 TCTCTTGA
6085 GACAGTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.06
18 4 0.11
19 2 0.06
20 3 0.08
21 15 0.42
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTGTC
Found at i:6190 original size:32 final size:33
Alignment explanation
Indices: 6154--6250 Score: 103
Period size: 32 Copynumber: 3.0 Consensus size: 33
6144 TTTTTCTTGG
*
6154 AAAAAACC-TTGAGACAGTTTCTCTTGAAACAC
1 AAAAAACCTTTGAAACAGTTTCTCTTGAAACAC
**
6186 AAAAAACCTTTGAAATTGTTTCTCTTGAAA-A-
1 AAAAAACCTTTGAAACAGTTTCTCTTGAAACAC
* *
6217 AAGGAAACCTTTGAAA-ATGTATCTCTTGAAACAC
1 AA-AAAACCTTTGAAACA-GTTTCTCTTGAAACAC
6251 CAAACCTTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.04
32 33 0.61
33 19 0.35
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (33 bp):
AAAAAACCTTTGAAACAGTTTCTCTTGAAACAC
Found at i:6207 original size:33 final size:34
Alignment explanation
Indices: 6170--6250 Score: 114
Period size: 32 Copynumber: 2.5 Consensus size: 34
6160 CCTTGAGACA
*
6170 GTTTCTCTTGAAACACAA-AAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
*
6203 GTTTCTCTTGAAA-A-AAGGAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
*
6235 GTATCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
6251 CAAACCTTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 2 0.05
32 26 0.62
33 14 0.33
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
Found at i:7928 original size:2 final size:2
Alignment explanation
Indices: 7921--7948 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7911 TTCGGTCCTC
7921 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
7949 TTTTTTTTTG
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):
AT
Found at i:8273 original size:13 final size:13
Alignment explanation
Indices: 8255--8281 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8245 TTTCGTTTTG
8255 TTTTATCTTTTAT
1 TTTTATCTTTTAT
8268 TTTTATCTTTTAT
1 TTTTATCTTTTAT
8281 T
1 T
8282 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATCTTTTAT
Found at i:11036 original size:21 final size:21
Alignment explanation
Indices: 11012--11052 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11002 TGTGGCGGAG
* *
11012 GACTAGCAGCTGGGGGTGGAA
1 GACTAGAAGCTGAGGGTGGAA
*
11033 GACTAGAAGGTGAGGGTGGA
1 GACTAGAAGCTGAGGGTGGA
11053 GGAGACAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.49, T:0.15
Consensus pattern (21 bp):
GACTAGAAGCTGAGGGTGGAA
Found at i:11867 original size:15 final size:15
Alignment explanation
Indices: 11847--11875 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11837 GAAACTTACA
11847 GTCTTTAATTCATCG
1 GTCTTTAATTCATCG
11862 GTCTTTAATTCATC
1 GTCTTTAATTCATC
11876 CTTCTTATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (15 bp):
GTCTTTAATTCATCG
Found at i:11881 original size:15 final size:15
Alignment explanation
Indices: 11847--11881 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11837 GAAACTTACA
*
11847 GTCTTTAATTCATCG
1 GTCTTTAATTCATCC
11862 GTCTTTAATTCATCC
1 GTCTTTAATTCATCC
*
11877 TTCTT
1 GTCTT
11882 ATGGTTAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.09, T:0.51
Consensus pattern (15 bp):
GTCTTTAATTCATCC
Found at i:24005 original size:23 final size:23
Alignment explanation
Indices: 23975--24050 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
23965 AGAAAATGTC
*
23975 TTTTAATATATATTAAATAAATT
1 TTTTAATATATATTAAAGAAATT
* *
23998 TTTTAATATATTTTAAAGAATTT
1 TTTTAATATATATTAAAGAAATT
* *
24021 TTTTGGAT-TGAATATTAAAGAATTT
1 TTTT-AATAT--ATATTAAAGAAATT
24046 TTTTA
1 TTTTA
24051 TTATTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 25 0.57
24 2 0.05
25 17 0.39
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTTAATATATATTAAAGAAATT
Found at i:25459 original size:20 final size:20
Alignment explanation
Indices: 25434--25473 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25424 GTCGAGGAGG
25434 AAGAGAAA-AGAAGAAGAAGA
1 AAGAGAAAGAGAA-AAGAAGA
25454 AAGAGAAAGAGAAAAGAAGA
1 AAGAGAAAGAGAAAAGAAGA
25474 GAGTTAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
AAGAGAAAGAGAAAAGAAGA
Found at i:28796 original size:18 final size:18
Alignment explanation
Indices: 28773--28810 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28763 ACAGAGAAAT
*
28773 CCCCTGTCCGTGAATAGG
1 CCCCTGTCCATGAATAGG
28791 CCCCTGTCCATGAATAGG
1 CCCCTGTCCATGAATAGG
28809 CC
1 CC
28811 TCTTTCTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.21
Consensus pattern (18 bp):
CCCCTGTCCATGAATAGG
Found at i:29364 original size:35 final size:36
Alignment explanation
Indices: 29318--29387 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
29308 AGTCAAACTA
*
29318 AATGGAAACTTC-AAGTCTTTCATTCATCGGTCTTG
1 AATGGAAACTTCAAAGTATTTCATTCATCGGTCTTG
*
29353 AATGGATACTTCAAAGTATTTCATTCATCGGTCTT
1 AATGGAAACTTCAAAGTATTTCATTCATCGGTCTT
29388 CCCTGCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (36 bp):
AATGGAAACTTCAAAGTATTTCATTCATCGGTCTTG
Found at i:35764 original size:36 final size:36
Alignment explanation
Indices: 35715--35939 Score: 346
Period size: 36 Copynumber: 6.3 Consensus size: 36
35705 AAAAATGAAC
* *
35715 ACTTGAATCGGAAGTACCGATGCTTCTTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
35751 ATTTGAATCGGAAGTGCCGATGCTTCCCTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
35787 ACTTGAATCGGAAGTGCCGATGTTTCCTTCCGTTC-
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
35822 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
35858 ATTTGAATCGGAAGTTCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
35894 ACTTGAATCGGAAGTGCTGATGCTTCAC-TCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTC-CTTCCGTTCG
35930 ACTTGAATCG
1 ACTTGAATCG
35940 ATGCAAACTT
Statistics
Matches: 172, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 33 0.19
36 138 0.80
37 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:35900 original size:107 final size:107
Alignment explanation
Indices: 35714--35939 Score: 364
Period size: 107 Copynumber: 2.1 Consensus size: 107
35704 AAAAAATGAA
*
35714 CACTTGAATCGGAAGTACCGATGCTTCTTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCC
1 CACTTGAATCGGAAGTACCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCC
*
35779 TCCGTTCGACTTGAATCGGAAGTGCCGATGTTTC-CTTCCGTT
66 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCAC-TCCGTT
** * *
35821 CACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTTCCGATGCTTCCT
1 CACTTGAATCGGAAGTACCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCC
*
35886 TCCGTTCGACTTGAATCGGAAGTGCTGATGCTTCACTCCGTT
66 TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCACTCCGTT
35928 CGACTTGAATCG
1 C-ACTTGAATCG
35940 ATGCAAACTT
Statistics
Matches: 110, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
107 99 0.90
108 11 0.10
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (107 bp):
CACTTGAATCGGAAGTACCGATGCTTCCTTCCGTTCGATTTGAATCGGAAGTGCCGATGCTTCCC
TCCGTTCGACTTGAATCGGAAGTGCCGATGCTTCACTCCGTT
Found at i:37006 original size:176 final size:176
Alignment explanation
Indices: 36779--37131 Score: 670
Period size: 176 Copynumber: 2.0 Consensus size: 176
36769 AGAAATTACA
* *
36779 CAGGAAAATATGTGTTTTTTTATTCATCTCAACAAGGACATTACATTTATAAGAAAGGTTAAGCT
1 CAGGAAAATATGTGTTTATTTATTCATCTCAACAAGGACAGTACATTTATAAGAAAGGTTAAGCT
36844 CATCAGCTCCCCAGTAACCAACTAACAAACTAACAGACCTAGTTAACCAAACTAACAAAATAACT
66 CATCAGCTCCCCAGTAACCAACTAACAAACTAACAGACCTAGTTAACCAAACTAACAAAATAACT
36909 ACCTCCTCATACACGTGTAACACTTCTTTGATAGCCATCTAACATT
131 ACCTCCTCATACACGTGTAACACTTCTTTGATAGCCATCTAACATT
* *
36955 CAGGAAAGTATGTGTTTATTTATTCATCTCAGCAAGGACAGTACATTTATAAGAAAGGTTAAGCT
1 CAGGAAAATATGTGTTTATTTATTCATCTCAACAAGGACAGTACATTTATAAGAAAGGTTAAGCT
37020 CATCAGCTCCCCAGTAACCAACTAACAAACTAACAGACCTAGTTAACCAAACTAACAAAATAACT
66 CATCAGCTCCCCAGTAACCAACTAACAAACTAACAGACCTAGTTAACCAAACTAACAAAATAACT
37085 ACCTCCTCATACACGTGTAACACTTCTTTGATAGCCATCTAACATT
131 ACCTCCTCATACACGTGTAACACTTCTTTGATAGCCATCTAACATT
37131 C
1 C
37132 CCCCTACTCT
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 173 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (176 bp):
CAGGAAAATATGTGTTTATTTATTCATCTCAACAAGGACAGTACATTTATAAGAAAGGTTAAGCT
CATCAGCTCCCCAGTAACCAACTAACAAACTAACAGACCTAGTTAACCAAACTAACAAAATAACT
ACCTCCTCATACACGTGTAACACTTCTTTGATAGCCATCTAACATT
Found at i:37822 original size:12 final size:12
Alignment explanation
Indices: 37805--37849 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
37795 GTCGGGGAGG
37805 AAGAAGAGAGAA
1 AAGAAGAGAGAA
*
37817 AAGAAGATGA-AG
1 AAGAAGA-GAGAA
37829 AAGAA-AGAGAA
1 AAGAAGAGAGAA
37840 AAGAAGAGAG
1 AAGAAGAGAG
37850 TTAATGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 7 0.25
12 17 0.61
13 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (12 bp):
AAGAAGAGAGAA
Found at i:37830 original size:21 final size:22
Alignment explanation
Indices: 37804--37846 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
37794 TGTCGGGGAG
37804 GAAGAAG-AGAGAAAAGAAGAT
1 GAAGAAGAAGAGAAAAGAAGAT
37825 GAAGAAGAAAGAGAAAAGAAGA
1 GAAGAAG-AAGAGAAAAGAAGA
37847 GAGTTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (22 bp):
GAAGAAGAAGAGAAAAGAAGAT
Found at i:40760 original size:21 final size:21
Alignment explanation
Indices: 40736--40783 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
40726 TGACTGTGGC
* *
40736 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAGAAGCTGAGGGT
* *
40757 GGAGAACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGCTGAGGGT
40778 GGAGGA
1 GGAGGA
40784 GACAAAGACG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.08, G:0.52, T:0.12
Consensus pattern (21 bp):
GGAGGACTAGAAGCTGAGGGT
Found at i:45464 original size:36 final size:35
Alignment explanation
Indices: 45407--45478 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
45397 GAAGCCAAAC
*
45407 TGAATGGAAACTTCAAGTCTTTCATTCATCGGTCT
1 TGAATGGAAACTTAAAGTCTTTCATTCATCGGTCT
*
45442 TGAATGGATACTTAAAAGTCTTTCATTCATCGGTCT
1 TGAATGGAAACTT-AAAGTCTTTCATTCATCGGTCT
45478 T
1 T
45479 ACCTGCGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (35 bp):
TGAATGGAAACTTAAAGTCTTTCATTCATCGGTCT
Found at i:46325 original size:19 final size:19
Alignment explanation
Indices: 46303--46339 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46293 TTAGTTTACG
*
46303 TTTATGATTATAAATATTC
1 TTTATAATTATAAATATTC
*
46322 TTTATAATTATGAATATT
1 TTTATAATTATAAATATT
46340 TATTCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTATAATTATAAATATTC
Found at i:46579 original size:30 final size:31
Alignment explanation
Indices: 46525--46595 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
46515 ACAAAATAAA
*
46525 TATTAAATTTATCTAATAGTTATAAAATGGT
1 TATTAAATTTATCGAATAGTTATAAAATGGT
* * *
46556 TATTATATTT-TCGAATTGTTATAAAATGAT
1 TATTAAATTTATCGAATAGTTATAAAATGGT
*
46586 CATTAAATTT
1 TATTAAATTT
46596 TATCAAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.48
Consensus pattern (31 bp):
TATTAAATTTATCGAATAGTTATAAAATGGT
Found at i:48641 original size:16 final size:16
Alignment explanation
Indices: 48620--48651 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48610 ACTATTCACA
*
48620 TGAATAGTAAATTTTG
1 TGAATAGTAAAATTTG
48636 TGAATAGTAAAATTTG
1 TGAATAGTAAAATTTG
48652 GTCGGCGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
TGAATAGTAAAATTTG
Found at i:58003 original size:21 final size:21
Alignment explanation
Indices: 57979--58025 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
57969 GACTGTGGCA
* *
57979 GAGGACTAGCAGCTGGGGGTG
1 GAGGACTAGAAGCTGAGGGTG
*
58000 GAGGACTAGAAGGTGAGGGTG
1 GAGGACTAGAAGCTGAGGGTG
58021 GAGGA
1 GAGGA
58026 GACAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.53, T:0.13
Consensus pattern (21 bp):
GAGGACTAGAAGCTGAGGGTG
Found at i:62681 original size:21 final size:20
Alignment explanation
Indices: 62641--62682 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
62631 CCAACTTACA
*
62641 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
62661 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
62682 A
1 A
62683 GTTGCATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:67339 original size:21 final size:20
Alignment explanation
Indices: 67299--67340 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
67289 CCAACTTACA
*
67299 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
67319 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
67340 A
1 A
67341 GTTGCATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:67370 original size:20 final size:20
Alignment explanation
Indices: 67342--67379 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
67332 CTATTATTAG
67342 TTGCATGACAACTAATAATT
1 TTGCATGACAACTAATAATT
*
67362 TTGCTTGACAACTAATAA
1 TTGCATGACAACTAATAA
67380 ACATGAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
TTGCATGACAACTAATAATT
Found at i:71751 original size:27 final size:27
Alignment explanation
Indices: 71721--71812 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
71711 TTAACAAAGC
71721 ATATTTATTTATGTATATATAT-TTTTA
1 ATATTTATTTAT-TATATATATATTTTA
* * * *
71748 ATA-TTATTTTATTTTATTTTTGTTTTA
1 ATATTTA-TTTATTATATATATATTTTA
* *
71775 TTATTTATTTATATATATGTATATTTT-
1 ATATTTATTTAT-TATATATATATTTTA
*
71802 ATATTTCTTTA
1 ATATTTATTTA
71813 CACGTTCTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
26 9 0.18
27 29 0.57
28 13 0.25
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (27 bp):
ATATTTATTTATTATATATATATTTTA
Found at i:71991 original size:13 final size:13
Alignment explanation
Indices: 71973--71999 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
71963 TTTCATTTTG
71973 TTTTATCTTTTAT
1 TTTTATCTTTTAT
71986 TTTTATCTTTTAT
1 TTTTATCTTTTAT
71999 T
1 T
72000 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATCTTTTAT
Found at i:77481 original size:36 final size:36
Alignment explanation
Indices: 77432--77897 Score: 356
Period size: 36 Copynumber: 13.2 Consensus size: 36
77422 CTTTGAGATG
* * *
77432 GTTTATCTCAAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
*
77468 GTTTCTCTTAAAACAAATTTTGTCTGTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * **** *
77504 TTTTTTCTTAAAAGTTTTTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
*
77540 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * * *
77576 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* ** *
77604 TGTATTC-CTTTAAACAAATTTCATCTCTCTCGAGACA
1 -GT-TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* ** *
77641 GTTTCTTTTGGAACTAAATTTTGTCTCTTTTGAGACA
1 GTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACA
* *
77678 GTTTCTCTTGAAACAAATTTTGTCTCACTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * *
77714 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATCTA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA-C-A
* * * *
77744 TTTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * * *
77779 ATTTCTTTTAAAACTGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACA
* * *
77816 TTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACA
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
* *
77852 ATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTTGTCTCTCTTGAGACA
*
77889 GTTCCTCTT
1 GTTTCTCTT
77898 GAAGCACCAA
Statistics
Matches: 340, Mismatches: 65, Indels: 49
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.01
29 31 0.09
30 13 0.04
35 14 0.04
36 193 0.57
37 86 0.25
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
Found at i:77676 original size:37 final size:36
Alignment explanation
Indices: 77615--77900 Score: 203
Period size: 37 Copynumber: 8.1 Consensus size: 36
77605 GTATTCCTTT
** * * *
77615 AAACAAATTTCATCTCTCTCGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTG
* **
77651 GAACTAAATTTTGTCTCTTTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCACTTGAGACAGTTTCTCTTG
*
77688 AAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTG
* * *
77724 AAACAAA----ATCT---TTGA-ATCTATTTTC-CTTT
1 AAACAAATTTTGTCTCACTTGAGA-C-AGTTTCTCTTG
* * * * * *
77753 AAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTA
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTG
* * * *
77789 AAACTGAGTTTTGTCTCTCTTGAGACATTTTCTCTTG
1 AAAC-AAATTTTGTCTCACTTGAGACAGTTTCTCTTG
* * * * *
77826 AAACAAATTTTGTCTCTCTTGAAACAATTTCCCTTA
1 AAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTG
* *
77862 AAACAAAGTTTTGTCTCTCTTGAGACAGTTCCTCTTG
1 AAACAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTG
77899 AA
1 AA
77901 GCACCAATCT
Statistics
Matches: 200, Mismatches: 36, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.00
29 15 0.08
30 5 0.03
32 3 0.01
33 3 0.01
35 5 0.03
36 82 0.41
37 86 0.43
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCACTTGAGACAGTTTCTCTTG
Found at i:77686 original size:138 final size:138
Alignment explanation
Indices: 77521--77868 Score: 543
Period size: 138 Copynumber: 2.5 Consensus size: 138
77511 TTAAAAGTTT
* *
77521 TTTTGTCTCCCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
77586 AAACAAAATCTTTGAATATGTATTCCTTTAAACAAATTTCATCTCTCTCGAGACAGTTTCTTTTG
66 AAACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTA
*
77651 GAACTAAA
131 AAACTAAA
* * *
77659 TTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
77724 AAACAAAATCTTTGAATCTATTTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTA
66 AAACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTA
* *
77789 AAACTGAG
131 AAACTAAA
* * *
77797 TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAATTTCCCTTA
1 TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
77862 AAACAAA
66 AAACAAA
77869 GTTTTGTCTC
Statistics
Matches: 190, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 190 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (138 bp):
TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAATCTTTGAATATATATTCCTTTAAACAAATTTCATCTCTCTCGAGACAATTTCTTTTA
AAACTAAA
Found at i:77696 original size:73 final size:72
Alignment explanation
Indices: 77615--77900 Score: 248
Period size: 73 Copynumber: 4.0 Consensus size: 72
77605 GTATTCCTTT
* * ** ** *
77615 AAACAAATTTCATCTCTCTCGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTTTTGAGACAGT
1 AAACAAATTTCGTCTCTCTCGAGACAATTTCCCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGT
77680 TTCTCTTG
65 TTCTCTTG
* * * * * * *
77688 AAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACAAA------ATCT-TTGA-ATCTAT
1 AAACAAATTTCGTCTCTCTCGAGACAATTTCCCTTAAAACAAATTTTGTCTCTCTTGAGA-C-AG
*
77745 TTTC-CTTT
64 TTTCTCTTG
** * * *
77753 AAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTGAGTTTTGTCTCTCTTGAGACATT
1 AAACAAATTTCGTCTCTCTCGAGACAATTTCCCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGT
77818 TTCTCTTG
65 TTCTCTTG
* * *
77826 AAACAAATTTTGTCTCTCTTGAAACAATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTCGTCTCTCTCGAGACAATTTCCCTTAAAACAAA-TTTTGTCTCTCTTGAGACAGT
*
77891 TCCTCTTG
65 TTCTCTTG
77899 AA
1 AA
77901 GCACCAATCT
Statistics
Matches: 170, Mismatches: 30, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
64 1 0.01
65 41 0.24
66 9 0.05
72 13 0.08
73 105 0.62
74 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (72 bp):
AAACAAATTTCGTCTCTCTCGAGACAATTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTT
TCTCTTG
Found at i:77844 original size:21 final size:21
Alignment explanation
Indices: 77819--77884 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
77809 TGAGACATTT
77819 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
77840 TCTCTTGAAAC-AA--TT-TC
1 TCTCTTGAAACAAATTTTGTC
*
77857 -C-CTTAAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
77877 TCTCTTGA
1 TCTCTTGA
77885 GACAGTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.06
18 2 0.06
19 2 0.06
20 4 0.11
21 12 0.33
22 4 0.11
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:77990 original size:32 final size:32
Alignment explanation
Indices: 77954--78050 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 32
77944 TTTTTCTTGG
*
77954 AAAAAACC-TTGAGACAGTTTCTCTTGAAACAC
1 AAAAAACCTTTGA-AAAGTTTCTCTTGAAACAC
*
77986 AAAAAACCTTTGAAATTGTTTCTCTTGAAA-A-
1 AAAAAACCTTTGAAA-AGTTTCTCTTGAAACAC
*
78017 AAGGAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 AA-AAAACCTTTGAAAA-GTTTCTCTTGAAACAC
78051 CAAACCTTCG
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 2 0.04
32 35 0.64
33 18 0.33
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (32 bp):
AAAAAACCTTTGAAAAGTTTCTCTTGAAACAC
Found at i:78007 original size:33 final size:34
Alignment explanation
Indices: 77970--78050 Score: 123
Period size: 32 Copynumber: 2.5 Consensus size: 34
77960 CCTTGAGACA
*
77970 GTTTCTCTTGAAACACAA-AAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
*
78003 GTTTCTCTTGAAA-A-AAGGAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
78035 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
78051 CAAACCTTCG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 2 0.05
32 27 0.63
33 14 0.33
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAGAAAACCTTTGAAAAT
Found at i:79884 original size:23 final size:23
Alignment explanation
Indices: 79811--79892 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 23
79801 CAAAGCATAT
*
79811 TTATTTATGTATATATATTTTTAATA
1 TTATTTAT-T-TATATATTTGT-ATA
* *
79837 TTATTTATTT-TATTTTTGTTTTA
1 TTATTTATTTATATATTTG-TATA
*
79860 TTATTTATTTATATATATGTATA
1 TTATTTATTTATATATTTGTATA
79883 TT-TTATATTT
1 TTATT-TATTT
79893 CTTTACACGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 2 0.04
23 28 0.60
24 8 0.17
25 1 0.02
26 8 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTATTTATTTATATATTTGTATA
Found at i:80074 original size:13 final size:13
Alignment explanation
Indices: 80056--80082 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
80046 TTTCATTTTG
80056 TTTTATCTTTTAT
1 TTTTATCTTTTAT
80069 TTTTATCTTTTAT
1 TTTTATCTTTTAT
80082 T
1 T
80083 ATTTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATCTTTTAT
Found at i:85866 original size:31 final size:31
Alignment explanation
Indices: 85770--85867 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
85760 TAAAACTTAC
* *
85770 AAAATAATTATTAAA-TTTATCTAA-TAGTT-
1 AAAATGATTATTAAATTTTATCAAATTA-TTA
* * *
85799 AAAATGGTTATTATATTTTATCAAATTGTTA
1 AAAATGATTATTAAATTTTATCAAATTATTA
* *
85830 TAAATGATCATTAAATTTTATCAAATTATTA
1 AAAATGATTATTAAATTTTATCAAATTATTA
85861 AAAATGA
1 AAAATGA
85868 AAATTGAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
29 12 0.22
30 10 0.18
31 33 0.60
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (31 bp):
AAAATGATTATTAAATTTTATCAAATTATTA
Found at i:91960 original size:19 final size:19
Alignment explanation
Indices: 91922--91960 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
91912 CTTGCTCTCG
* *
91922 TTTCTGTTTTTCTTCCTTT
1 TTTCTCTTTTTCTTCATTT
*
91941 TTTCTCTTTTTTTTCATTT
1 TTTCTCTTTTTCTTCATTT
91960 T
1 T
91961 GCAGGATTCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTCTTTTTCTTCATTT
Found at i:92401 original size:13 final size:14
Alignment explanation
Indices: 92378--92428 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
92368 ATTATTTATT
92378 TAATAATAATAATA
1 TAATAATAATAATA
92392 TAAT-ATAATAATA
1 TAATAATAATAATA
*
92405 TAA-AACAA-AATA
1 TAATAATAATAATA
92417 TTAATAA-AATAA
1 -TAATAATAATAA
92429 AACAAAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 4 0.12
13 20 0.62
14 8 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:92446 original size:21 final size:20
Alignment explanation
Indices: 92393--92445 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
92383 ATAATAATAT
*
92393 AATATAATAATATAAAACAA
1 AATATAATAAAATAAAACAA
92413 AATATTAATAAAATAAAACAA
1 AATA-TAATAAAATAAAACAA
92434 AATGA-AATAAAA
1 AAT-ATAATAAAA
92446 AAACTAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
21 18 0.60
22 1 0.03
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
AATATAATAAAATAAAACAA
Found at i:93059 original size:110 final size:112
Alignment explanation
Indices: 92671--93381 Score: 936
Period size: 109 Copynumber: 6.4 Consensus size: 112
92661 TTGCGCAAGT
* *
92671 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-CTCTGGAAAAGTTGATCCATC-AAG
1 TCTTCCTTCTTCAGA-GAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGCTGATCCATCGAA-
* * **
92734 TGATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTAT
63 TGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
* * * * *
92784 TCTTCCTTCTTCAGATGAGTTCTTCTCCTT-TGGGATTCTACCTGGTAATGATGATCCATCGAAT
1 TCTTCCTTCTTCAGA-GAGTTCTTCTCATTAT-GAACTCTACCTGGAAATGCTGATCCATCGAAT
* *
92848 GATGAATTCAAACAAAAAGTTGAACAAGTTATTCTCATTATGAACTTCT
64 GATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
*
92897 TCTTCATTC-TC--AGAGTTCTTCTCATTATGAACTCTACCTGGAAATG-TGATCCATC-AAGTG
1 TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAA-TG
* * * * *
92957 ATGAATTTAAACAAAAGGTTAAACAAG-TCTTCTTATTATGAAGTTCC
65 ATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
*
93004 TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCT-TCTGGAAATGCTGATCCATCGAATGA
1 TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGA
* *
93068 TGAATTCAAGC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
66 TGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
* *
93114 TC-TCCTTCTTCAGATGAGTTCTTATCATTATGAACTCTACCTGGAAATGTTGATCCATC-AAGT
1 TCTTCCTTCTTCAGA-GAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAA-T
* ** * * *
93177 GATGGATTTGAACAAAAGGTTAAACAAGTTC-TCTCATTATGAACTTTC
64 GATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
93225 TCTTCCTTCTTC--AGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGA
1 TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGA
*
93288 TGAATTCAAGCAAAAAGTTGAAC-AGTTCTTCTCATTATGAACTTCC
66 TGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
*
93334 TCTTCCTTCTTCA-TGAGTTCTTCTCATTATGAACTCTACCTGGAAATG
1 TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCTACCTGGAAATG
93382 TTTTAAGAAA
Statistics
Matches: 527, Mismatches: 52, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
107 26 0.05
108 42 0.08
109 151 0.29
110 127 0.24
111 47 0.09
112 27 0.05
113 104 0.20
114 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (112 bp):
TCTTCCTTCTTCAGAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGA
TGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCC
Found at i:93144 original size:220 final size:222
Alignment explanation
Indices: 92670--93383 Score: 1056
Period size: 220 Copynumber: 3.2 Consensus size: 222
92660 ATTGCGCAAG
*
92670 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-CTCTGGAAAAGTTGATCCATCAAG
1 TTCTTCCTTCTTC--ATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCCATCAAG
* * * * *
92734 TGATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGA
63 TGATGAATTTGAACAAAAGGTTAAACAAG-TCTTCTCATTATGAACTTACTCTTCCTTCTTCAGA
* * * * * *
92799 TGAGTTCTTCTCCTT-TGGGATTCTACCTGGTAATGATGATCCATCGAATGATGAATTCAAACAA
127 -GAGTTCTTCTCATTAT-GAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAA
*
92863 AAAGTTGAACAAGTTATTCTCATTATGAACTTC
190 AAAGTTGAACAAGTTCTTCTCATTATGAACTTC
*
92896 TTCTTCATTC-TCA-GAGTTCTTCTCATTATGAACTCTACCTGGAAATG-TGATCCATCAAGTGA
1 TTCTTCCTTCTTCATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGA
* * * *
92958 TGAATTTAAACAAAAGGTTAAACAAGTCTTCTTATTATGAAGTTCCTCTTCCTTCTTCAGAGAGT
66 TGAATTTGAACAAAAGGTTAAACAAGTCTTCTCATTATGAACTTACTCTTCCTTCTTCAGAGAGT
*
93023 TCTTCTCATTATGAACTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTT
131 TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTT
93086 GAACAAGTTCTTCTCATTATGAACTTC
196 GAACAAGTTCTTCTCATTATGAACTTC
*
93113 TTC-TCCTTCTTCAGATGAGTTCTTATCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGT
1 TTCTTCCTTCTTC--ATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGT
* *
93177 GATGGATTTGAACAAAAGGTTAAACAAGT-TCTCTCATTATGAACTTTCTCTTCCTTCTTC--AG
64 GATGAATTTGAACAAAAGGTTAAACAAGTCT-TCTCATTATGAACTTACTCTTCCTTCTTCAGAG
93239 AGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAA
128 AGTTCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAA
93304 GTTGAAC-AGTTCTTCTCATTATGAACTTC
193 GTTGAACAAGTTCTTCTCATTATGAACTTC
*
93333 CTCTTCCTTCTTCATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTT
1 TTCTTCCTTCTTCATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTT
93384 TTAAGAAAAG
Statistics
Matches: 448, Mismatches: 29, Indels: 29
0.89 0.06 0.06
Matches are distributed among these distances:
216 5 0.01
217 38 0.08
218 33 0.07
219 80 0.18
220 126 0.28
221 122 0.27
222 31 0.07
223 2 0.00
225 2 0.00
226 9 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (222 bp):
TTCTTCCTTCTTCATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGA
TGAATTTGAACAAAAGGTTAAACAAGTCTTCTCATTATGAACTTACTCTTCCTTCTTCAGAGAGT
TCTTCTCATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTT
GAACAAGTTCTTCTCATTATGAACTTC
Found at i:93637 original size:75 final size:76
Alignment explanation
Indices: 93399--93655 Score: 403
Period size: 76 Copynumber: 3.4 Consensus size: 76
93389 AAAAGAAAAA
* * *
93399 AAACATTC-TGCACTGTAGGGCTTACA-ACTGACTCGAAGGTTTTGAAAACATCAAAAAGCTCCC
1 AAACA-TCATGCACTGTAGGACTTACAGA-TGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCC
*
93462 GAAGGCTTTTTCG
64 GAAGGCTTTTTGG
* * *
93475 ACACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
93540 AGGCTTTTTGG
66 AGGCTTTTTGG
*
93551 AACCATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
93615 AGGCTTTTTGG
66 AGGCTTTTTGG
93626 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
93656 TGGGAAATAG
Statistics
Matches: 167, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
75 62 0.37
76 104 0.62
77 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Done.