Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004086.1 Hibiscus syriacus cultivar Beakdansim tig00008940_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: 81225
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1876 original size:44 final size:44
Alignment explanation
Indices: 1828--1926 Score: 180
Period size: 44 Copynumber: 2.2 Consensus size: 44
1818 AATAAGTGTA
* *
1828 TGATTACATGAGTACAAGATATAAAGCATGTGAAAAGAGATATG
1 TGATTACATGAGTACAAGATATAAAGCATGTGAAAAAAGAAATG
1872 TGATTACATGAGTACAAGATATAAAGCATGTGAAAAAAGAAATG
1 TGATTACATGAGTACAAGATATAAAGCATGTGAAAAAAGAAATG
1916 TGATTACATGA
1 TGATTACATGA
1927 AAGTATGATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (44 bp):
TGATTACATGAGTACAAGATATAAAGCATGTGAAAAAAGAAATG
Found at i:3425 original size:38 final size:39
Alignment explanation
Indices: 3381--3470 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 39
3371 GTTGAACAAG
*
3381 TTCTCATTATGAACTT-T-TTCT-TTTTCTTGGATGAGTTC
1 TTCTCATTATGAACTTCTATTCTCTTTTC--AGATGAGTTC
*
3419 TTCTCATTATAAACTTCTATTCTCTTTTCAGATGAGTTC
1 TTCTCATTATGAACTTCTATTCTCTTTTCAGATGAGTTC
3458 TTCTCATTATGAA
1 TTCTCATTATGAA
3471 TCTCCACTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 15 0.33
39 22 0.48
40 4 0.09
41 5 0.11
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (39 bp):
TTCTCATTATGAACTTCTATTCTCTTTTCAGATGAGTTC
Found at i:3879 original size:259 final size:257
Alignment explanation
Indices: 3414--3885 Score: 677
Period size: 259 Copynumber: 1.8 Consensus size: 257
3404 TTCTTGGATG
** * *
3414 AGTTCTTCTCATTATAAACTTCTATTCTCTTTTCAGATGAGTTCTTCTCATTATGAATCTCCACT
1 AGTTCTTCTCATTATAAACTTCTATTCTCTCATCAGATGAGTTCTTCTCATTATGAACCTCCACC
* *
3479 GGAAATGTTGAATCCTGAGTGAGGGTTGCTTATTCAACTCCATATGCGATGAATTGAGCTAAGGT
66 GGAAATGTTGAATCCTGAGTGAGGGTTGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGT
3544 TGAAAAAGTTATTCTATTATGAACTTCTTCTCCCTCATCAGATAAGTTCTTCCCATTATGAACTC
131 TGAAAAAGTTATTCTATTATGAACTTCTTCTCCCTCATCAGATAAGTTCTTCCCATTATGAACTC
*
3609 TCAATTGGAAATGTTGATGTTAATTTATCTCCTTCTGTGATATATTCAGAAAAAGGTTGAAC
196 TCAATTGGAAATATTGATGTTAATTTATCTCCTTCTGTGATATATTCAGAAAAAGGTTGAAC
*
3671 AGTTCTTCTCATTATGAAA-TTC--TTCTCCTCATCAGATGAGTTTTTCTCATTATGAACCCTCC
1 AGTTCTTCTCATTAT-AAACTTCTATTCT-CTCATCAGATGAGTTCTTCTCATTATGAA-CCTCC
3733 ACCGGAAATGTTG-ATCCCTCGAGTGAAGGGTTGCTGATTCAACTCCATATGCGATGAATCGAGC
63 ACCGGAAATGTTGAAT-CCT-GAGTG-AGGGTTGCTGATTCAACTCCATATGCGATGAATCGAGC
* * * * * * * *
3797 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGATTTGTTCTCATTA
125 TAAGGTTGAAAAAGTTATTCT-ATTATGAACTTCTTCTCCCTCATCAGATAAGTTCTTCCCATTA
*
3862 TGAACT-TC-TTCTGGAAATATTGAT
189 TGAACTCTCAAT-TGGAAATATTGAT
3886 CCCCCAAGTG
Statistics
Matches: 190, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
255 4 0.02
256 28 0.15
257 37 0.19
258 9 0.05
259 69 0.36
260 43 0.23
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (257 bp):
AGTTCTTCTCATTATAAACTTCTATTCTCTCATCAGATGAGTTCTTCTCATTATGAACCTCCACC
GGAAATGTTGAATCCTGAGTGAGGGTTGCTGATTCAACTCCATATGCGATGAATCGAGCTAAGGT
TGAAAAAGTTATTCTATTATGAACTTCTTCTCCCTCATCAGATAAGTTCTTCCCATTATGAACTC
TCAATTGGAAATATTGATGTTAATTTATCTCCTTCTGTGATATATTCAGAAAAAGGTTGAAC
Found at i:3919 original size:138 final size:136
Alignment explanation
Indices: 3661--4069 Score: 515
Period size: 138 Copynumber: 3.0 Consensus size: 136
3651 TATTCAGAAA
*
3661 AAGGTTGAAC-AGTTCTTCTCATTATGAAATTCTTC-TCCTCATCAGATGAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATCAGATGA-TTTTTCTCATTAT
* * * * * *
3724 GAACCCTCCACCGGAAATGTTGATCCCTCGAGTGAAGGGTTGCTGATTCAACTCCATATGCGATG
65 GAA-CTTCCACCGGAAAT-TTGATCCCCCAAGTGAGGGGTCGATGATTCAACTCCATATGCGATG
3789 AATCGAGCT
128 AATCGAGCT
*
3798 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGATTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATCAGATGATTT-TTCTCATTAT
** * * * *
3863 GAACTTCTTCTGGAAATATTGATCCCCCAAGTGAGGGGTCGATTATTCAGCTCCATATGTGATGA
65 GAACTTCCACCGGAAAT-TTGATCCCCCAAGTGAGGGGTCGATGATTCAACTCCATATGCGATGA
3928 ATCGAGCT
129 ATCGAGCT
* * * *
3936 AAGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATCAGATGA-TTTTTCTCATTAT
* *
4001 GAACTCTCCACCGGAAATTT-AT--CCCTAGTGAGGGGTC-ACAGATTCAACTCCATATGCGATG
65 GAACT-TCCACCGGAAATTTGATCCCCCAAGTGAGGGGTCGA-TGATTCAACTCCATATGCGATG
*
4062 AATTGAGC
128 AATCGAGC
4070 AAAATAAATT
Statistics
Matches: 237, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
134 1 0.00
135 39 0.16
137 12 0.05
138 148 0.62
139 37 0.16
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATCAGATGATTTTTCTCATTATG
AACTTCCACCGGAAATTTGATCCCCCAAGTGAGGGGTCGATGATTCAACTCCATATGCGATGAAT
CGAGCT
Found at i:4203 original size:36 final size:36
Alignment explanation
Indices: 4090--4271 Score: 172
Period size: 36 Copynumber: 5.0 Consensus size: 36
4080 GTTTTAAGAA
* * *
4090 AAACTATCTCAAGAGAGATAAATTTTATTTCGAGTG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGTG
* * * * **
4126 AAAGCTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAA
1 AAA-CTATCTCAAGCGAGATAAATTTTGTTTCAAGTG
* *
4163 AAACTATCTCGAGTGAGATAAATTTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGTG
*
4199 AAACTATCTCAAGCGAGACAAAGTTTT-TTT-AAG-G
1 AAACTATCTCAAGCGAGATAAA-TTTTGTTTCAAGTG
** *
4233 AAAACTATCTTGAGTGAGATAAATTTCTGTTTCAAGTG
1 -AAACTATCTCAAGCGAGATAAATTT-TGTTTCAAGTG
4271 A
1 A
4272 GATAAATCTT
Statistics
Matches: 115, Mismatches: 24, Indels: 13
0.76 0.16 0.09
Matches are distributed among these distances:
34 4 0.03
35 22 0.19
36 53 0.46
37 35 0.30
38 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (36 bp):
AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGTG
Found at i:4264 original size:72 final size:73
Alignment explanation
Indices: 4078--4271 Score: 302
Period size: 73 Copynumber: 2.7 Consensus size: 73
4068 GCAAAATAAA
* * * * *
4078 TTGTTTTAAGAAAAACTATCTCAAGAGAGATAAATTTTATTTCGAGTGAAAGCTGTCTCAAGCGA
1 TTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTTGTTTCAAGTGAAAGCTATCTCAAGCGA
4143 GACAAAGT
66 GACAAAGT
4151 TTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTTGTTTCAAGTGAAA-CTATCTCAAGCGA
1 TTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTTGTTTCAAGTGAAAGCTATCTCAAGCGA
4215 GACAAAGT
66 GACAAAGT
* *
4223 TT-TTTTAAGGAAAACTATCTTGAGTGAGATAAATTTCTGTTTCAAGTGA
1 TTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTT-TGTTTCAAGTGA
4272 GATAAATCTT
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
71 32 0.28
72 34 0.30
73 47 0.42
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (73 bp):
TTGTTTTAAGAAAAACTATCTCGAGTGAGATAAATTTTGTTTCAAGTGAAAGCTATCTCAAGCGA
GACAAAGT
Found at i:5717 original size:17 final size:17
Alignment explanation
Indices: 5690--5753 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
5680 CTTCTTGTCA
5690 TCTTTTTCTTTG-TTTT
1 TCTTTTTCTTTGCTTTT
5706 TCTTTCTTCTTTGCTTTT
1 TCTTT-TTCTTTGCTTTT
*
5724 TCTCTTTT-TTTCTCTTTT
1 TCT-TTTTCTTT-GCTTTT
*
5742 TTTCTTTTCTTT
1 TCT-TTTTCTTT
5754 TATCCCCGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.12
17 10 0.24
18 21 0.51
19 5 0.12
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTTGCTTTT
Found at i:6417 original size:27 final size:27
Alignment explanation
Indices: 6387--6450 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
6377 GTTCATTAGT
6387 AATCTATAATACTTGAAGAATTAAAAG
1 AATCTATAATACTTGAAGAATTAAAAG
*
6414 AATCTATAATACTTGAAGAATTAAGAG
1 AATCTATAATACTTGAAGAATTAAAAG
6441 AATCTATAAT
1 AATCTATAAT
6451 TCATTTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (27 bp):
AATCTATAATACTTGAAGAATTAAAAG
Found at i:8975 original size:14 final size:14
Alignment explanation
Indices: 8958--8999 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
8948 TGACTAAAAT
8958 GAAATAAATAAAGA
1 GAAATAAATAAAGA
8972 GAAATAAAATAAAGA
1 GAAAT-AAATAAAGA
* *
8987 TAAATAATTAAAG
1 GAAATAAATAAAG
9000 TACTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (14 bp):
GAAATAAATAAAGA
Found at i:9214 original size:18 final size:19
Alignment explanation
Indices: 9183--9219 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
9173 ATTGAAATAA
9183 AAAAATATGACTAAACTAT
1 AAAAATATGACTAAACTAT
*
9202 AAAAA-ATGCCTAAACTAT
1 AAAAATATGACTAAACTAT
9220 GAGGACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATATGACTAAACTAT
Found at i:10934 original size:139 final size:138
Alignment explanation
Indices: 10758--11167 Score: 538
Period size: 138 Copynumber: 3.0 Consensus size: 138
10748 ATTCGAGCAA
* *
10758 AAGGTTGAACAAGTTATTCTTGTTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTAT
* * *
10823 -AAGCTCTCTACTAGAAATGTGGATCCATCGAGTGAGGGGTCACTGATTCAACTCCATATGTGAT
66 GAA-CTCTCTACTAGAAATGTTGATCC-TCGAGTGAGGGGTCAATGATTCAACTCCATATGCGAT
10887 GAATCGAGCT
129 GAATCGAGCT
* * * * *
10897 AAGGTTGAACACGTTCTTCTTATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTAT
* ** ** *
10962 GAACT-TCT-TTAGGAAATGTTGATCCCTCGACCGAGGGGTCGTTGATTCAGCTCCATATGCGAT
66 GAACTCTCTACTA-GAAATGTTGAT-CCTCGAGTGAGGGGTCAATGATTCAACTCCATATGCGAT
11025 GAATCGAGCT
129 GAATCGAGCT
** *
11035 AAGGTTGAACAAGTTCTTCTCCTTATGAACTTCTTCTGCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTAT
* * * * *
11100 GAACTCTCTACTGGAAATGTTAATCTCTCGAGTGAGGGTTCAATGATTCAACTCCATATACAATG
66 GAACTCTCTACTAGAAATGTTGATC-CTCGAGTGAGGGGTCAATGATTCAACTCCATATGCGATG
11165 AAT
130 AAT
11168 TTGAGTGAAA
Statistics
Matches: 231, Mismatches: 34, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
137 2 0.01
138 117 0.51
139 109 0.47
140 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (138 bp):
AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCTACTAGAAATGTTGATCCTCGAGTGAGGGGTCAATGATTCAACTCCATATGCGATGA
ATCGAGCT
Found at i:11342 original size:73 final size:73
Alignment explanation
Indices: 11183--11377 Score: 257
Period size: 73 Copynumber: 2.6 Consensus size: 73
11173 TGAAATTAAA
* * * * *
11183 TTTGTTTTAAGAAAAACTATCTCATGTGAGATAAAATTTTGTTTCGAGTGAAAATTGTCTCAAGC
1 TTTGTTTTAAGAAAAACTATCTCAAGTGAGAT-AAATTTTGTTTCAAGTGAAAACTATCGCAAGC
*
11248 GATACAAAG
65 GAAACAAAG
* * *
11257 TTTGTTTTAAGAAAAACTATCCCAAGTGAGATAAATTTCTATTTCAAGTG-AAACTATCGCAAGT
1 TTTGTTTTAAGAAAAACTATCTCAAGTGAGATAAATTT-TGTTTCAAGTGAAAACTATCGCAAGC
11321 GAAACAAAG
65 GAAACAAAG
* *
11330 TTTGTTTTAAGAAAAACTATCTCGAGTGACATAAATTTTTGTTTCAAG
1 TTTGTTTTAAGAAAAACTATCTCAAGTGAGATAAA-TTTTGTTTCAAG
11378 CGAGATAAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
73 64 0.60
74 42 0.40
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (73 bp):
TTTGTTTTAAGAAAAACTATCTCAAGTGAGATAAATTTTGTTTCAAGTGAAAACTATCGCAAGCG
AAACAAAG
Found at i:11358 original size:36 final size:35
Alignment explanation
Indices: 11171--11367 Score: 135
Period size: 36 Copynumber: 5.4 Consensus size: 35
11161 AATGAATTTG
*
11171 AGTGAAATTAAATTTGTTTTAAGAAAAACTATCTCA
1 AGTGAAA-CAAATTTGTTTTAAGAAAAACTATCTCA
* ** * * *
11207 TGTGAGATA-AAATTTTGTTTCGAGTGAAAATTGTCTCA
1 AGTGA-A-ACAAA-TTTGTTTTAAG-AAAAACTATCTCA
* * *
11245 AGCGATACAAAGTTTGTTTTAAGAAAAACTATCCCA
1 AGTGAAACAAA-TTTGTTTTAAGAAAAACTATCTCA
* * * ** *
11281 AGTGAGATAAATTTCTATTTCAAGTGAAACTATCGCA
1 AGTGAAACAAATTTGT-TTT-AAGAAAAACTATCTCA
*
11318 AGTGAAACAAAGTTTGTTTTAAGAAAAACTATCTCG
1 AGTGAAACAAA-TTTGTTTTAAGAAAAACTATCTCA
* *
11354 AGTGACATAAATTT
1 AGTGAAACAAATTT
11368 TTGTTTCAAG
Statistics
Matches: 121, Mismatches: 32, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
35 7 0.06
36 49 0.40
37 47 0.39
38 18 0.15
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (35 bp):
AGTGAAACAAATTTGTTTTAAGAAAAACTATCTCA
Found at i:12919 original size:11 final size:10
Alignment explanation
Indices: 12900--12991 Score: 78
Period size: 11 Copynumber: 8.4 Consensus size: 10
12890 TCTTGTCCTC
12900 TTTTTCTTTT
1 TTTTTCTTTT
12910 TTTTTCCTTTT
1 TTTTT-CTTTT
12921 CTTTTTCTTTGT
1 -TTTTTCTTT-T
12933 TTTTTCTTTCT
1 TTTTTCTTT-T
*
12944 TCTTTGCTTTT
1 T-TTTTCTTTT
*
12955 TCTTTCTTTT
1 TTTTTCTTTT
12965 TTGTTT-TTTT
1 TT-TTTCTTTT
12975 ATTTTGTCTTTT
1 -TTTT-TCTTTT
12987 CTTTT
1 -TTTT
12992 ATCCTCGCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
10 19 0.28
11 28 0.41
12 21 0.31
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:12923 original size:22 final size:21
Alignment explanation
Indices: 12898--12991 Score: 95
Period size: 22 Copynumber: 4.3 Consensus size: 21
12888 CTTCTTGTCC
12898 TCTTTTTCTTTTTTTTTCCTTT
1 TCTTTTTCTTTTTTTTT-CTTT
12920 TCTTTTTCTTTGTTTTTTC-TT
1 TCTTTTTCTTT-TTTTTTCTTT
*
12941 TCTTCTTTGCTTTTTCTTTCTTT
1 TCTT-TTT-CTTTTTTTTTCTTT
12964 T-TTGTTT-TTTTATTTTGTCTTT
1 TCTT-TTTCTTTT-TTTT-TCTTT
12986 TCTTTT
1 TCTTTT
12992 ATCCTCGCCT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.06
21 9 0.15
22 34 0.55
23 15 0.24
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.80
Consensus pattern (21 bp):
TCTTTTTCTTTTTTTTTCTTT
Found at i:12948 original size:18 final size:18
Alignment explanation
Indices: 12917--12973 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
12907 TTTTTTTTCC
12917 TTTTCTTT-TTCTTTGTT
1 TTTTCTTTCTTCTTTGTT
*
12934 TTTTCTTTCTTCTTTGCT
1 TTTTCTTTCTTCTTTGTT
*
12952 TTTTCTTTCTTTTTTGTT
1 TTTTCTTTCTTCTTTGTT
12970 TTTT
1 TTTT
12974 TATTTTGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
17 8 0.22
18 28 0.78
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTCTTTCTTCTTTGTT
Found at i:12991 original size:18 final size:17
Alignment explanation
Indices: 12901--12991 Score: 68
Period size: 18 Copynumber: 5.5 Consensus size: 17
12891 CTTGTCCTCT
*
12901 TTTTCTTTTTTTTT-CC
1 TTTTCTTTTTTTTTGTC
* *
12917 TTTTCTTTTTCTTTGTT
1 TTTTCTTTTTTTTTGTC
*
12934 TTTTCTTTCTTCTTTG-C
1 TTTTCTTT-TTTTTTGTC
12951 TTTTTCTTTCTTTTTTG--
1 -TTTTCTTT-TTTTTTGTC
*
12968 -TTT-TTTTATTTTGTC
1 TTTTCTTTTTTTTTGTC
12983 TTTTCTTTT
1 TTTTCTTTT
12992 ATCCTCGCCT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
13 6 0.10
14 3 0.05
15 3 0.05
16 16 0.26
17 12 0.19
18 22 0.35
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTTTTTGTC
Found at i:14695 original size:149 final size:149
Alignment explanation
Indices: 14412--14683 Score: 375
Period size: 149 Copynumber: 1.8 Consensus size: 149
14402 CTCTTACTTT
* * * * *
14412 CAGAAGTCTTTCGAGCTGGTTCATGATCTTCAACTGTTGGCTTTGGCATAGAATTGTCTCGAGTC
1 CAGAAATCTTTCAAGCTAGTTCATGATCTTCAACTGCTGGCTTTAGCATAGAATTGTCTCGAGTC
* * *
14477 TAACTTGTTACCTCAGCATGAAAATGTCTGGATCGTCTCCTTTGTAGATAGACTCCCTCTAGCTC
66 CAACTTGTTACCTCAGCAGGAAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCTAGCTC
14542 CTACTTCATCTCTCATTTC
131 CTACTTCATCTCTCATTTC
**
14561 CAGAAATCTTTCAAGCTAGTTCATGATCTTCAACTGCTGGCTTTAGTGTCA-AATTGTCTCGAGT
1 CAGAAATCTTTCAAGCTAGTTCATGATCTTCAACTGCTGGCTTTAGCAT-AGAATTGTCTCGAGT
* * * * * * *
14625 CCAACTTGTTACCTCAGTAGGCAGATGTCTGGTTGGTCTCCTTGGTAGGTAGGCTCCCT
65 CCAACTTGTTACCTCAGCAGGAAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCT
14684 TTTGACGCTA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
149 104 0.99
150 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (149 bp):
CAGAAATCTTTCAAGCTAGTTCATGATCTTCAACTGCTGGCTTTAGCATAGAATTGTCTCGAGTC
CAACTTGTTACCTCAGCAGGAAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCTAGCTC
CTACTTCATCTCTCATTTC
Found at i:17438 original size:12 final size:12
Alignment explanation
Indices: 17421--17457 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
17411 TACATTAAAG
*
17421 ATAATTAACCTA
1 ATAATTAGCCTA
17433 ATAATTAGCCTA
1 ATAATTAGCCTA
*
17445 ACAATTAGCCTA
1 ATAATTAGCCTA
17457 A
1 A
17458 GAAACTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (12 bp):
ATAATTAGCCTA
Found at i:22025 original size:22 final size:22
Alignment explanation
Indices: 21997--22044 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
21987 GTTAAGAAAA
*
21997 ATATATAGAAATAAAAGTATAT
1 ATATATAGAAACAAAAGTATAT
* *
22019 ATATATATAAACAAACGTATAT
1 ATATATAGAAACAAAAGTATAT
22041 ATAT
1 ATAT
22045 GTATACAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (22 bp):
ATATATAGAAACAAAAGTATAT
Found at i:32545 original size:48 final size:48
Alignment explanation
Indices: 32482--32586 Score: 183
Period size: 48 Copynumber: 2.2 Consensus size: 48
32472 AAAATGCACT
*
32482 GTTAGGCATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAAACACA
1 GTTAGGCATCTAACTTGCATTAATGGAACCTTTCTGCCAAAAAACACA
* *
32530 GTTAGGCATCTAACTTGCATTAATGGAACCTTTCTGCCGAAAAGCACA
1 GTTAGGCATCTAACTTGCATTAATGGAACCTTTCTGCCAAAAAACACA
32578 GTTAGGCAT
1 GTTAGGCAT
32587 TTATTCTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (48 bp):
GTTAGGCATCTAACTTGCATTAATGGAACCTTTCTGCCAAAAAACACA
Found at i:33226 original size:56 final size:55
Alignment explanation
Indices: 32826--33436 Score: 904
Period size: 55 Copynumber: 11.1 Consensus size: 55
32816 CCTAATGTCA
* * * *
32826 ATACAGAAATTCATAAACTTATTATAAATTTCTTAG-GTTGCACACACACTGCCA
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
*
32880 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTTCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* * * *
32935 ATACGGAAGTTCATAAACTTATTATGAGTTTCTTAGTTTTGCACACACAATGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* ** * *
32990 GTATGGAAATTCATAAACTTATTATAAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
33045 ATACAGAAATTTATAAACTTATTATGAATTTCTTAGTTTTGCACACACCGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* * * *
33100 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTCGCACACACAATGCAC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
33155 ATACAGAAATTCATAAACTTATTATTAATTTCTTAGTTTTTGCACACATAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
*
33211 ATACATAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
* *
33267 ATACAGAAATTCATAAACTTACTATAAATTTCTTAGTTTTTGCACACACAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
33323 ATAC-GAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACAG-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
** *
33378 A-ATGGGAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
33433 ATAC
1 ATAC
33437 GGTAATAACT
Statistics
Matches: 504, Mismatches: 47, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
54 65 0.13
55 285 0.57
56 154 0.31
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (55 bp):
ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:36212 original size:30 final size:30
Alignment explanation
Indices: 36178--36254 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
36168 TGTTTCAAAA
36178 GTTACAAATCGGTCACTAACGTTATCGTTT
1 GTTACAAATCGGTCACTAACGTTATCGTTT
36208 GTTACAAATCGGTCACTAACGTTATCGTTT
1 GTTACAAATCGGTCACTAACGTTATCGTTT
36238 GTTACAAATCGGTCACT
1 GTTACAAATCGGTCACT
36255 CGCCGTTAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (30 bp):
GTTACAAATCGGTCACTAACGTTATCGTTT
Found at i:38784 original size:2 final size:2
Alignment explanation
Indices: 38777--38827 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
38767 CCATAAAAAC
38777 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
38819 TA TA TA TA T
1 TA TA TA TA T
38828 CTTTCTGACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40633 original size:45 final size:46
Alignment explanation
Indices: 40566--40653 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
40556 TTATTCGTTC
* * *
40566 TTTTCATTTATGGCATCATTTCATGCTGATAATGCACCGTTATGCA
1 TTTTCATTTATGGCATCATTTCATACCGATAATACACCGTTATGCA
* *
40612 TTTT-ATTTATGGCATCCTTTCATACCGGTAATACACCGTTAT
1 TTTTCATTTATGGCATCATTTCATACCGATAATACACCGTTAT
40654 TCATCTAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 33 0.89
46 4 0.11
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (46 bp):
TTTTCATTTATGGCATCATTTCATACCGATAATACACCGTTATGCA
Found at i:40712 original size:49 final size:49
Alignment explanation
Indices: 40655--40802 Score: 194
Period size: 48 Copynumber: 3.1 Consensus size: 49
40645 CACCGTTATT
* * *
40655 CATCTAACTTACATTAGTGGCACATTTCTGCCAAAAATGCACTGTTAGG
1 CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACTGTTAGG
* * *
40704 CATCTAACTTGCATTAATGTCACCTTTCTACCAAAAA-GCACAGTTAGG
1 CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACTGTTAGG
* *
40752 CACCTAACTTGTATTAATGGCACCTTTCTGCC-AAAATGCA-TGGTTAGG
1 CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACT-GTTAGG
40800 CAT
1 CAT
40803 TTATTCTTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
47 4 0.05
48 49 0.58
49 32 0.38
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (49 bp):
CATCTAACTTGCATTAATGGCACCTTTCTGCCAAAAATGCACTGTTAGG
Found at i:41232 original size:55 final size:55
Alignment explanation
Indices: 41047--41544 Score: 705
Period size: 56 Copynumber: 9.0 Consensus size: 55
41037 TGTCAATATA
* * * ** * * * *
41047 GAAATTCATAAACTCATTATCAATTCCAGAG-GTTGCACACACATTGCCAATACA
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
* * * *
41101 AAAATTCATAATCCTATTATGAATTTCTTAGTTTTGCACACGCAGTG-CCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
*
41155 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAGAGTGCCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
41210 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
41265 GAAATTCATAAACTTATTATGAATTTCTTAGTTTATGCACACACAGTGCCCATATC-
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTT-TGCACACACAGTGCCCATA-CG
* * *
41321 AAAATTCATAAACTTGTTATGAATTTCTTAGTTTTTGCACACACAGTGCCTATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCCATACG
* * *
41377 AAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATGCA
1 GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCCATACG
* *
41433 GAAATTCATAAACATATTATGAATTTCTTAGTTTTGCACACACAGTGTCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
* * *
41488 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGGACACACAATACCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCCATACG
41544 G
1 G
41545 TAATCACCAT
Statistics
Matches: 401, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
54 70 0.17
55 159 0.40
56 168 0.42
57 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (55 bp):
GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACG
Found at i:41341 original size:111 final size:111
Alignment explanation
Indices: 41079--41542 Score: 718
Period size: 111 Copynumber: 4.2 Consensus size: 111
41069 ATTCCAGAGG
* * * * *
41079 TTGCACACACATTGCCAATACAAAAATTCATAATCCTATTATGAATTTCTTAGTTTTGCACACGC
1 TTGCACACACAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
41144 AGTG-CCATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TT
66 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
* **
41188 TTGCACACAGAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
1 TTGCACACACAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
41253 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
66 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
* *
41299 ATGCACACACAGTGCCCATATC-AAAATTCATAAACTTGTTATGAATTTCTTAGTTTTTGCACAC
1 TTGCACACACAGTGCCCATA-CAAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACAC
* *
41363 ACAGTGCCTATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTT
64 ACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
* * *
41411 TTGCACACACAGTGCCCATGCAGAAATTCATAAACATATTATGAATTTCTTAGTTTTGCACACAC
1 TTGCACACACAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
*
41476 AGTGTCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
66 AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
* * *
41522 TTGGACACACAATACCCATAC
1 TTGCACACACAGTGCCCATAC
41543 GGTAATCACC
Statistics
Matches: 324, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
109 61 0.19
110 38 0.12
111 122 0.38
112 103 0.32
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (111 bp):
TTGCACACACAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC
AGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT
Found at i:50573 original size:2 final size:2
Alignment explanation
Indices: 50566--50592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50556 AAGACAATAA
50566 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
50593 ACGAAATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53284 original size:11 final size:11
Alignment explanation
Indices: 53268--53335 Score: 58
Period size: 9 Copynumber: 6.6 Consensus size: 11
53258 AACTGGTTTT
53268 GCCGGTTTTCA
1 GCCGGTTTTCA
53279 GCCGG--TTCA
1 GCCGGTTTTCA
*
53288 CCCCGGTTTT-A
1 -GCCGGTTTTCA
*
53299 -CCGGTTTTTA
1 GCCGGTTTTCA
*
53309 GCCGGTTCT-A
1 GCCGGTTTTCA
53319 -CCGGTTTTCA
1 GCCGGTTTTCA
53329 GCCGGTT
1 GCCGGTT
53336 CATTGCCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 19 0.40
10 7 0.15
11 19 0.40
12 2 0.04
ACGTcount: A:0.09, C:0.29, G:0.26, T:0.35
Consensus pattern (11 bp):
GCCGGTTTTCA
Found at i:53315 original size:20 final size:20
Alignment explanation
Indices: 53290--53336 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
53280 CCGGTTCACC
* *
53290 CCGGTTTTACCGGTTTTTAG
1 CCGGTTCTACCGGTTTTCAG
53310 CCGGTTCTACCGGTTTTCAG
1 CCGGTTCTACCGGTTTTCAG
53330 CCGGTTC
1 CCGGTTC
53337 ATTGCCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.09, C:0.28, G:0.26, T:0.38
Consensus pattern (20 bp):
CCGGTTCTACCGGTTTTCAG
Found at i:57267 original size:21 final size:21
Alignment explanation
Indices: 57227--57269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57217 ATGAGTTAAC
*
57227 ATTTTAGAATTTAAGGGTTAT
1 ATTTTAGAATTTAAAGGTTAT
* *
57248 ATTTTAGAGTTTAAATGTTAT
1 ATTTTAGAATTTAAAGGTTAT
57269 A
1 A
57270 GATTGGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (21 bp):
ATTTTAGAATTTAAAGGTTAT
Found at i:58035 original size:21 final size:21
Alignment explanation
Indices: 58006--58051 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
57996 GTTTACCGTG
* * *
58006 ATTGTGGCCGTCGCGGACGCT
1 ATTGCGGCCATCGCGGACACT
58027 ATTGCGGCCATCGCGGACACT
1 ATTGCGGCCATCGCGGACACT
58048 ATTG
1 ATTG
58052 GGCGCTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.24
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGACACT
Found at i:58861 original size:50 final size:50
Alignment explanation
Indices: 58682--58863 Score: 213
Period size: 50 Copynumber: 3.6 Consensus size: 50
58672 TTCATACTAC
* * * *
58682 AAAAAGTGTAACACTTAACACATACTTACTCCGATGTAGAGAATAAAATA
1 AAAAAGTATAATACTTAACACATACTTACACCGATGTAGTGAATAAAATA
* * * *
58732 AAAAAGTATAACACTTAACACTTACTTATATCGATGTAGTGAATAAAATA
1 AAAAAGTATAATACTTAACACATACTTACACCGATGTAGTGAATAAAATA
* * * * *
58782 AAAAAGTGTAGTACTTAACACATTCTTACACCGGTATAAGTGAATAAAATA
1 AAAAAGTATAATACTTAACACATACTTACACCGATGT-AGTGAATAAAATA
* *
58833 AAAAA-TATAATAGTTAACACGTACTTACACC
1 AAAAAGTATAATACTTAACACATACTTACACC
58864 AGTGTAAATG
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 93 0.84
51 18 0.16
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (50 bp):
AAAAAGTATAATACTTAACACATACTTACACCGATGTAGTGAATAAAATA
Found at i:58929 original size:60 final size:58
Alignment explanation
Indices: 58818--58937 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 58
58808 TACACCGGTA
* * * *
58818 TAAGTGAATAAAATAAAAAATATAATAGTTAACACGTACTTACACCAGTGTAAATGTG
1 TAAGTGAATAAAATAAAAAATATAACACTTAACACATACTTACACCAGTGTAAATATG
* * * *
58876 TAAGTGAATAAAATAAAAAAATTGTGACACTTAATACATACTTACACCGGTGTAAATATG
1 TAAGTGAATAAAAT-AAAAAA-TATAACACTTAACACATACTTACACCAGTGTAAATATG
58936 TA
1 TA
58938 CATCTCACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 14 0.27
59 6 0.12
60 32 0.62
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (58 bp):
TAAGTGAATAAAATAAAAAATATAACACTTAACACATACTTACACCAGTGTAAATATG
Found at i:59494 original size:15 final size:14
Alignment explanation
Indices: 59474--59516 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
59464 TTTAAAATTC
59474 TTTTATATTTTAAT
1 TTTTATATTTTAAT
*
59488 ATTTTATATATTAAT
1 -TTTTATATTTTAAT
59503 TATTTATAATTTTA
1 T-TTTAT-ATTTTA
59517 TGAGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATATTTTAAT
Found at i:60595 original size:11 final size:11
Alignment explanation
Indices: 60575--60623 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
60565 ATTGTTAGAG
*
60575 TGTTACTAGTT
1 TGTTATTAGTT
60586 TGTTATTAGTT
1 TGTTATTAGTT
*
60597 TGTTATGA-TT
1 TGTTATTAGTT
60607 TGTTATTAGTT
1 TGTTATTAGTT
60618 TGTTAT
1 TGTTAT
60624 GGTTTGTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:60610 original size:10 final size:11
Alignment explanation
Indices: 60582--60631 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
60572 GAGTGTTACT
*
60582 AGTTTGTTATT
1 AGTTTGTTATG
60593 AGTTTGTTATG
1 AGTTTGTTATG
*
60604 A-TTTGTTATT
1 AGTTTGTTATG
60614 AGTTTGTTATG
1 AGTTTGTTATG
60625 -GTTTGTT
1 AGTTTGTT
60632 GGTTACTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 16 0.46
11 19 0.54
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (11 bp):
AGTTTGTTATG
Found at i:60610 original size:21 final size:21
Alignment explanation
Indices: 60584--60631 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
60574 GTGTTACTAG
60584 TTTGTTATTAGTTTGTTATGA
1 TTTGTTATTAGTTTGTTATGA
*
60605 TTTGTTATTAGTTTGTTATGG
1 TTTGTTATTAGTTTGTTATGA
60626 TTTGTT
1 TTTGTT
60632 GGTTACTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (21 bp):
TTTGTTATTAGTTTGTTATGA
Found at i:62134 original size:14 final size:14
Alignment explanation
Indices: 62115--62143 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62105 TATTAGCTTG
62115 TTATTAGTTTGTTA
1 TTATTAGTTTGTTA
62129 TTATTAGTTTGTTA
1 TTATTAGTTTGTTA
62143 T
1 T
62144 GGTTTGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TTATTAGTTTGTTA
Found at i:62143 original size:11 final size:11
Alignment explanation
Indices: 62070--62131 Score: 90
Period size: 11 Copynumber: 5.7 Consensus size: 11
62060 AATGTTAGAG
*
62070 TGTTACTAGTT
1 TGTTATTAGTT
62081 TGTTATTAGTT
1 TGTTATTAGTT
*
62092 TGTTA-TGGTT
1 TGTTATTAGTT
*
62102 TGTTATTAGCT
1 TGTTATTAGTT
62113 TGTTATTAGTT
1 TGTTATTAGTT
62124 TGTTATTA
1 TGTTATTA
62132 TTAGTTTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
10 9 0.20
11 36 0.80
ACGTcount: A:0.18, C:0.03, G:0.19, T:0.60
Consensus pattern (11 bp):
TGTTATTAGTT
Found at i:62367 original size:23 final size:21
Alignment explanation
Indices: 62339--62385 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
62329 TTCATTTTAG
62339 ATATTATGTTATAAATTGAAAAT
1 ATATTAT-TTA-AAATTGAAAAT
**
62362 ATATTATTTAAGGTTGAAAAT
1 ATATTATTTAAAATTGAAAAT
62383 ATA
1 ATA
62386 ATTTCACCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 3 0.14
23 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (21 bp):
ATATTATTTAAAATTGAAAAT
Found at i:68241 original size:2 final size:2
Alignment explanation
Indices: 68198--68223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68188 TGTGTGTGTG
68198 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
68224 GTTCAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73632 original size:89 final size:87
Alignment explanation
Indices: 73516--73707 Score: 287
Period size: 89 Copynumber: 2.2 Consensus size: 87
73506 ATTCTGTAAT
** *
73516 AATATTAATAAATAAATATGTCGGTAATGCATGTGAAAATCGGTTCAAATGTTAATAACGCTCAA
1 AATATTAA-AAATAAATATGTCGGTAATGCATGCAAAAATCGATTCAAAT-TTAATAACGCTCAA
* *
73581 TGTCGCAAATACAAGCAATAAAAAT
64 TGTCGCAAACACAAGCAAT-AAAAG
*
73606 AAT-TCTAAAAATAAATATGTCGGTAATGCATGCAAAAATCGATTCAAATTTAATAACGTTCAAT
1 AATAT-TAAAAATAAATATGTCGGTAATGCATGCAAAAATCGATTCAAATTTAATAACGCTCAAT
73670 GTCGCAAACACAAGCAATAAAAG
65 GTCGCAAACACAAGCAATAAAAG
73693 AATATTAAAAATAAA
1 AATATTAAAAATAAA
73708 CAGTGTCTTA
Statistics
Matches: 94, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
87 17 0.18
88 32 0.34
89 39 0.41
90 6 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (87 bp):
AATATTAAAAATAAATATGTCGGTAATGCATGCAAAAATCGATTCAAATTTAATAACGCTCAATG
TCGCAAACACAAGCAATAAAAG
Found at i:78309 original size:10 final size:10
Alignment explanation
Indices: 78294--78334 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
78284 TTCATCACAC
78294 CAAATTCTCT
1 CAAATTCTCT
*
78304 CAAATTTTCT
1 CAAATTCTCT
*
78314 CAATTTCTCT
1 CAAATTCTCT
*
78324 CAAATACTCT
1 CAAATTCTCT
78334 C
1 C
78335 TGTTTAAGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:78411 original size:17 final size:18
Alignment explanation
Indices: 78374--78414 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
78364 ATATTATGTA
*
78374 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
78392 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
78409 TTTACT
1 TTTACT
78415 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:80743 original size:30 final size:29
Alignment explanation
Indices: 80707--80779 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
80697 GTATTTCAGT
80707 TAATTTGTTTATTACCATTTAATA-TCATTG
1 TAATTTGTTTATT--CATTTAATACTCATTG
* *
80737 TAATTTGGTTA-TCATTTAATACTTATTG
1 TAATTTGTTTATTCATTTAATACTCATTG
80765 TAAGTTTGTTGTATT
1 TAA-TTTGTT-TATT
80780 TAAATTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 9 0.25
28 8 0.22
29 6 0.17
30 12 0.33
31 1 0.03
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (29 bp):
TAATTTGTTTATTCATTTAATACTCATTG
Done.