Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000546.1 Hibiscus syriacus cultivar Beakdansim tig00001057_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: 159753
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Found at i:3685 original size:18 final size:18
Alignment explanation
Indices: 3662--3698 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3652 CACTTGCATA
*
3662 TCAAATTGGCCAAGCTTG
1 TCAAATTGGCCAAACTTG
*
3680 TCAAATTGGTCAAACTTG
1 TCAAATTGGCCAAACTTG
3698 T
1 T
3699 TAGGATGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (18 bp):
TCAAATTGGCCAAACTTG
Found at i:3828 original size:55 final size:55
Alignment explanation
Indices: 3769--3915 Score: 179
Period size: 55 Copynumber: 2.7 Consensus size: 55
3759 CTAATTTAAC
* *
3769 AAATCTCGGGTGTCTGAATTGTTTCCCGAGCGCCACACATGGTCGCTAGTCAAAT
1 AAATCTCGGGTGTCTGAATTGTTTCCCGAGCGCCACACATGGCCACTAGTCAAAT
** * * **
3824 AAATCTCATGTGTCCGAATTGTTTCTCGAGTACCACACATGGCCACTAGTCAAAT
1 AAATCTCGGGTGTCTGAATTGTTTCCCGAGCGCCACACATGGCCACTAGTCAAAT
* * *
3879 -AATCTCGGGTGTCTGAATTATTTTTCCAAGCGCCACA
1 AAATCTCGGGTGTCTGAATT-GTTTCCCGAGCGCCACA
3916 GAAGACCGCT
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
54 16 0.22
55 58 0.78
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (55 bp):
AAATCTCGGGTGTCTGAATTGTTTCCCGAGCGCCACACATGGCCACTAGTCAAAT
Found at i:5373 original size:7 final size:7
Alignment explanation
Indices: 5361--5387 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5351 GCTCAAAAGG
5361 AAAAGAA
1 AAAAGAA
5368 AAAAGAA
1 AAAAGAA
5375 AAAAGAA
1 AAAAGAA
5382 AAAAGA
1 AAAAGA
5388 GGGATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:8946 original size:161 final size:160
Alignment explanation
Indices: 8765--9205 Score: 695
Period size: 161 Copynumber: 2.7 Consensus size: 160
8755 TTTCATTTGA
*
8765 CTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACA
1 CTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACA
* * *
8830 AAAGATTTTATCTCACTCATGATTATTTTTCCTTTAAACAGAAGATTTTATCTCACTCAAGATTG
66 AAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTG
*
8895 TTTTTCCTTGAAACAGAAGATTTTATCTCA-
131 TTTTTCCTTGAAACAGAAGATTTTATC-AAG
* * * *
8925 CTCGAGATTGTTTTTTCCTTGAAACATAAGATTTTATCCCATTCAAGATTATTTTTCCTTGAAAC
1 CTCAAGATTG-TTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* *
8990 AAAAGATTTTATTTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCATTCAAGATT
65 AAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATT
9055 GTTTTTCCTTGAAACAGAAGATTTTATCAAG
130 GTTTTTCCTTGAAACAGAAGATTTTATCAAG
**
9086 CTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTTCCTTGAAAC
1 CTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTG-TTTTTCCTTGAAAC
* * * *
9151 AGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATCTC
65 AAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTC
9206 GCTTGAGATA
Statistics
Matches: 256, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
160 44 0.17
161 212 0.83
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (160 bp):
CTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACA
AAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTG
TTTTTCCTTGAAACAGAAGATTTTATCAAG
Found at i:8996 original size:23 final size:23
Alignment explanation
Indices: 8969--9037 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
8959 TATCCCATTC
8969 AAGATTATTTTTCCTTGAAACAA
1 AAGATTATTTTTCCTTGAAACAA
8992 AAGATT-TTATTTCAC-T----C--
1 AAGATTATT-TTTC-CTTGAAACAA
9009 AAGATTATTTTTCCTTGAAACAA
1 AAGATTATTTTTCCTTGAAACAA
9032 AAGATT
1 AAGATT
9038 TTATCTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 20
0.64 0.00 0.36
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 17 0.47
24 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (23 bp):
AAGATTATTTTTCCTTGAAACAA
Found at i:8998 original size:20 final size:20
Alignment explanation
Indices: 8975--9039 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
8965 ATTCAAGATT
8975 ATTTTTCCTTGAAACAAAAG
1 ATTTTTCCTTGAAACAAAAG
* ** **
8995 ATTTTAT--TTCACTCAAGATT
1 ATTTT-TCCTTGAAACAA-AAG
9015 ATTTTTCCTTGAAACAAAAG
1 ATTTTTCCTTGAAACAAAAG
9035 ATTTT
1 ATTTT
9040 ATCTCATTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 7 0.23
20 17 0.55
21 7 0.23
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
ATTTTTCCTTGAAACAAAAG
Found at i:9075 original size:23 final size:23
Alignment explanation
Indices: 9049--9117 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
9039 TATCTCATTC
9049 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
9072 AAGA-T-TTTAT-C---AAGCTC
1 AAGATTGTTTTTCCTTGAAACAG
9089 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
9112 AAGATT
1 AAGATT
9118 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 7 0.22
18 1 0.03
19 4 0.12
20 2 0.06
21 4 0.12
22 1 0.03
23 13 0.41
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:9092 original size:201 final size:201
Alignment explanation
Indices: 8764--9232 Score: 717
Period size: 201 Copynumber: 2.3 Consensus size: 201
8754 ATTTCATTTG
* * *
8764 ACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 ACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAAC
* * *
8829 AAAAGATTTTATCTCACTCATGATTATTTTTCCTTTAAACAGAAGATTTTATCTCACTCAAGATT
66 AAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTAACTCAAGATT
* *
8894 GTTTTTCCTTGAAACAGAAGATTTTATCTCACTCGAGATTGTTTTTTCCTTGAAACATAAGATTT
131 GTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTTCCTTGAAACAGAAGATTT
8959 TATCCC
196 TATCCC
* *
8965 ATTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATTTCACTCAAGATTATTTTTCCTTGAAAC
1 ACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAAC
* *
9030 AAAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATC-AAGCTCAAGAT
66 AAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTAA-CTCAAGAT
*
9094 TGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTTCCTTGAAACAGAAGATT
130 TGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTTCCTTGAAACAGAAGATT
*
9159 TTATCTC
195 TTATCCC
* * * * ** * *
9166 GCTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATCTCGCTTGAGA-TAGTTTCCCTTGAAAC
1 ACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAAC
9230 AAA
66 AAA
9233 TTTTTTCTCT
Statistics
Matches: 243, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
200 18 0.07
201 225 0.93
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (201 bp):
ACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAAC
AAAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTAACTCAAGATT
GTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTTCCTTGAAACAGAAGATTT
TATCCC
Found at i:9208 original size:40 final size:40
Alignment explanation
Indices: 8764--9205 Score: 670
Period size: 40 Copynumber: 11.0 Consensus size: 40
8754 ATTTCATTTG
*
8764 ACTCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
8804 ATTCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
8844 ACTCATGATTATTTTTCCTTTAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
8884 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
8924 ACTCGAGATTGTTTTTTCCTTGAAACATAAGATTTTATCCC
1 ACTCAAGATTG-TTTTTCCTTGAAACAGAAGATTTTATCTC
* * * *
8965 ATTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATTTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
9005 ACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
9045 ATTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATC-A
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
9084 AGCTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 A-CTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
*
9125 GCTCAAGATTGTTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTG-TTTTTCCTTGAAACAGAAGATTTTATCTC
* *
9166 GCTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
9206 GCTTGAGATA
Statistics
Matches: 368, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.00
40 292 0.79
41 75 0.20
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (40 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:9247 original size:36 final size:36
Alignment explanation
Indices: 9182--9298 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
9172 GATTGTTTTT
* *
9182 CCTTGAAACATAAGATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAAC--AA-ATTTTATCTCTCTTGAGACAGTTTC
*
9221 CCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTC
* * *
9257 CCTCGAAACAAGTTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTC
9293 CCTTGA
1 CCTTGA
9299 GACAGTTCCC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
36 60 0.85
37 2 0.03
39 9 0.13
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
CCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTC
Found at i:9299 original size:15 final size:15
Alignment explanation
Indices: 9279--9310 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9269 TTTTGTCTCT
*
9279 CTTGAGACAGTTTCC
1 CTTGAGACAGTTCCC
9294 CTTGAGACAGTTCCC
1 CTTGAGACAGTTCCC
9309 CT
1 CT
9311 GTCTCCCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (15 bp):
CTTGAGACAGTTCCC
Found at i:9314 original size:38 final size:36
Alignment explanation
Indices: 9202--9344 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
9192 TAAGATTTTA
* * * * *
9202 TCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTCTG
* *
9238 TCTCTCTTGAGACAGTTTCCCTCGAAACAAGTTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTCTG
*
9274 TCTCTCTTGAGACAGTTTCCCTTGAGAC-AGTTCCCCTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTT---CTG
* * *
9312 TCTCCCTTGAGATAGTTTCTCTTGAAACAAGTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTT
9345 TTGATACAGT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.04
36 57 0.63
38 26 0.29
39 4 0.04
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (36 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTCTG
Found at i:9421 original size:36 final size:36
Alignment explanation
Indices: 9376--9550 Score: 100
Period size: 37 Copynumber: 4.8 Consensus size: 36
9366 CAAAGTTTTG
* *
9376 TCTCCCTTGAGATGGGTTTTCCTAAAACCAAGTTCA
1 TCTCACTTGAGATGGGTTTTCCTAAAACCAAATTCA
** * * * * **
9412 TCTCACTTGAGACAGCTTTCCCTTGAAACAAAATGAA
1 TCTCACTTGAGATGGGTTTTCC-TAAAACCAAATTCA
* * * * *
9449 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
1 TCTCACTTGAGATGGGTTTTCCTAAAACCAAATTCA
** ** * ** *
9485 TCTGGCTTGAGA-CAGTTTTCCTTTGAAATAAAATTTA
1 TCTCACTTGAGATGGGTTTTCC--TAAAACCAAATTCA
*
9522 TCTCACTTGAGATGGGTTTTCTTAAAACC
1 TCTCACTTGAGATGGGTTTTCCTAAAACC
9551 TACTTCGTCT
Statistics
Matches: 92, Mismatches: 43, Indels: 8
0.64 0.30 0.06
Matches are distributed among these distances:
35 5 0.05
36 38 0.41
37 43 0.47
38 6 0.07
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGATGGGTTTTCCTAAAACCAAATTCA
Found at i:9494 original size:73 final size:73
Alignment explanation
Indices: 9359--9606 Score: 300
Period size: 73 Copynumber: 3.4 Consensus size: 73
9349 TACAGTTTAT
* * * * * * * *
9359 CTTGAAACAAAGTTTTGTCTCCCTTGAGATGGGTTTTCCTAAAACCAAGTTCATCTCACTTGAGA
1 CTTGAAACAAA-ATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCGCTTGAGA
*
9424 CAGCTTTCC
65 CAGATTTCC
** * *
9433 CTTGAAACAAAATGAATCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTGGCTTGAGAC
1 CTTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCGCTTGAGAC
*
9498 AGTTTTCC
66 AGATTTCC
* * *
9506 TTTGAAATAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTTGCTTGAGAC
1 CTTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCGCTTGAGAC
*
9571 A-ATTTTC
66 AGATTTCC
*
9578 CTTCGGAACAAAATTTATCTCACTTGAGA
1 CTT-GAAACAAAATTTATCTCACTTGAGA
9607 GTATTTCTCT
Statistics
Matches: 149, Mismatches: 24, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
72 6 0.04
73 132 0.89
74 11 0.07
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (73 bp):
CTTGAAACAAAATTTATCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCGTCTCGCTTGAGAC
AGATTTCC
Found at i:9569 original size:36 final size:36
Alignment explanation
Indices: 9449--9569 Score: 91
Period size: 36 Copynumber: 3.3 Consensus size: 36
9439 ACAAAATGAA
* *
9449 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
1 TCTCGCTTGAGATGGGTTTTCTTAAAACCTACTTCG
* ** * *** * **
9485 TCTGGCTTGAGA-CAGTTTTCCTTTGAAATAAAATTTA
1 TCTCGCTTGAGATGGGTTTT-C-TTAAAACCTACTTCG
*
9522 TCTCACTTGAGATGGGTTTTCTTAAAACCTACTTCG
1 TCTCGCTTGAGATGGGTTTTCTTAAAACCTACTTCG
*
9558 TCTTGCTTGAGA
1 TCTCGCTTGAGA
9570 CAATTTTCCT
Statistics
Matches: 57, Mismatches: 25, Indels: 6
0.65 0.28 0.07
Matches are distributed among these distances:
35 4 0.07
36 29 0.51
37 19 0.33
38 5 0.09
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (36 bp):
TCTCGCTTGAGATGGGTTTTCTTAAAACCTACTTCG
Found at i:10848 original size:68 final size:70
Alignment explanation
Indices: 10702--10845 Score: 206
Period size: 68 Copynumber: 2.1 Consensus size: 70
10692 CAACAGGTAA
* * *
10702 AGGAGAGAACATCAGCAAAATAGAGGGCAATTTCAGGAAAATCCGTTCGAACAGGGGAAAGAAAT
1 AGGAGAGAACATCAGCAAAATACAGGACAATTTCAGGAAAATCCATTCGAACAGGGGAAAGAAAT
*
10767 ACCAG
66 AACAG
*
10772 AGGAGAGAACATCAGC-AAA-ACAGGACAATTTCAGGAAAATCTATTCGAACAGGGG-AAGAAA-
1 AGGAGAGAACATCAGCAAAATACAGGACAATTTCAGGAAAATCCATTCGAACAGGGGAAAGAAAT
10833 AACAG
66 AACAG
*
10838 AGAAGAGA
1 AGGAGAGA
10846 GAATGAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 11 0.16
67 6 0.09
68 32 0.47
69 3 0.04
70 16 0.24
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.12
Consensus pattern (70 bp):
AGGAGAGAACATCAGCAAAATACAGGACAATTTCAGGAAAATCCATTCGAACAGGGGAAAGAAAT
AACAG
Found at i:20199 original size:28 final size:28
Alignment explanation
Indices: 20159--20221 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
20149 AGGAGTGTTG
20159 TTGTAAAACATGTTAGTAGAATTGTCAA
1 TTGTAAAACATGTTAGTAGAATTGTCAA
20187 TTGTAAAACATGTTAGTAGAATTGTCAA
1 TTGTAAAACATGTTAGTAGAATTGTCAA
20215 TTGTAAA
1 TTGTAAA
20222 GCGGATGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (28 bp):
TTGTAAAACATGTTAGTAGAATTGTCAA
Found at i:27333 original size:16 final size:17
Alignment explanation
Indices: 27302--27334 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27292 GCTGATTCGA
*
27302 GAATTGATGTGTTGGTG
1 GAATTGAAGTGTTGGTG
27319 GAATTGAAG-GTTGGTG
1 GAATTGAAGTGTTGGTG
27335 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.36
Consensus pattern (17 bp):
GAATTGAAGTGTTGGTG
Found at i:34792 original size:7 final size:7
Alignment explanation
Indices: 34770--34811 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
34760 TAACAGAAAA
34770 AAAAAC-
1 AAAAACG
34776 AAAGAACG
1 AAA-AACG
34784 AAAAACG
1 AAAAACG
34791 AAAAACG
1 AAAAACG
34798 AAAAACG
1 AAAAACG
34805 AAAAACG
1 AAAAACG
34812 TCTATAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 3 0.09
7 28 0.82
8 3 0.09
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAACG
Found at i:37102 original size:22 final size:22
Alignment explanation
Indices: 37077--37125 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
37067 AGATCCTTGG
*
37077 GAACCTAGCATTTAAAGGAAAC
1 GAACCTAACATTTAAAGGAAAC
37099 GAACCTAACATTTAAAGGAAAC
1 GAACCTAACATTTAAAGGAAAC
37121 GAACC
1 GAACC
37126 CAACCAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (22 bp):
GAACCTAACATTTAAAGGAAAC
Found at i:41979 original size:22 final size:22
Alignment explanation
Indices: 41954--42048 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 22
41944 TCCCACAACT
41954 CACATAATTTG-CACCGAAGTG-C
1 CACATAATTTGTC-CCGAAG-GAC
41976 CACAT-ATTTGTCCCGAAGGAC
1 CACATAATTTGTCCCGAAGGAC
* *
41997 CACATAGGTTTGTCCCGAAAGAC
1 CACATA-ATTTGTCCCGAAGGAC
42020 CACATAATTTTGTCCC-AGAGGAC
1 CACATAA-TTTGTCCCGA-AGGAC
42043 CACATA
1 CACATA
42049 GAACTCTCGA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.27
22 7 0.11
23 38 0.60
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (22 bp):
CACATAATTTGTCCCGAAGGAC
Found at i:45808 original size:21 final size:21
Alignment explanation
Indices: 45779--45829 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
45769 GCACCGAAGT
*
45779 ACCAAATAATTATCCCAAAGA
1 ACCACATAATTATCCCAAAGA
* *
45800 ACCACATAATTATCCCGAAGG
1 ACCACATAATTATCCCAAAGA
45821 ACCACATAA
1 ACCACATAA
45830 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.27, G:0.08, T:0.18
Consensus pattern (21 bp):
ACCACATAATTATCCCAAAGA
Found at i:51809 original size:2 final size:2
Alignment explanation
Indices: 51802--51833 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
51792 AACATAGATG
51802 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
51834 AGAATAAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52188 original size:63 final size:62
Alignment explanation
Indices: 52082--52205 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 62
52072 GTCGAGGGTT
* *
52082 TACCTATGTTCTACGGAACACATAGACAGAATTACCTATTTCTTTCGGGACATATGGACAGTG
1 TACCTATGTTCTAAGGAACACATAGACAGAATTACCTAGTTCTTT-GGGACATATGGACAGTG
* * * * *
52145 TACCTATGTTCTAAGGAATATATGGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACACATAGACAGAATTACCTA-GTTCTTTGGGACATATGGACAGT
52206 TGCCGAGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 22 0.42
63 31 0.58
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACACATAGACAGAATTACCTAGTTCTTTGGGACATATGGACAGTG
Found at i:52200 original size:31 final size:30
Alignment explanation
Indices: 52113--52206 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
52103 ATAGACAGAA
*
52113 TTACCTATTTCTTTCGGGACATATGGACAGT
1 TTACCTAGTTCTTT-GGGACATATGGACAGT
* ** * *
52144 GTACCTATGTTCTAAGGAATATATGGACAGT
1 TTACCTA-GTTCTTTGGGACATATGGACAGT
*
52175 TTACCTAGGTTCTTTGGGACCTATGGACAGT
1 TTACCTA-GTTCTTTGGGACATATGGACAGT
52206 T
1 T
52207 GCCGAGGTTC
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 45 0.92
32 4 0.08
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (30 bp):
TTACCTAGTTCTTTGGGACATATGGACAGT
Found at i:52226 original size:30 final size:31
Alignment explanation
Indices: 52165--52231 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
52155 CTAAGGAATA
* * *
52165 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTGTAGGACC
* *
52196 TATGGACAG-TTGCCGAGGTTCTGTATGACC
1 TATGGACAGTTTACCGAGGTTCTGTAGGACC
*
52226 TCTGGA
1 TATGGA
52232 TAGGTCATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTGTAGGACC
Found at i:65159 original size:13 final size:13
Alignment explanation
Indices: 65141--65176 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
65131 TCGCTTGAAG
65141 AAGAAATAAA-AAA
1 AAGAAA-AAAGAAA
65154 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
65167 AAGAAAAAAG
1 AAGAAAAAAG
65177 GAGGAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:65223 original size:19 final size:17
Alignment explanation
Indices: 65183--65260 Score: 95
Period size: 17 Copynumber: 4.4 Consensus size: 17
65173 AAAGGAGGAG
*
65183 GAAAAATGAAAGAAAAT
1 GAAAAATGAAAAAAAAT
65200 GAAAAATGAGAAAAAAAT
1 GAAAAATGA-AAAAAAAT
65218 GAAAAATGGTGAAAAAAAA-
1 GAAAAA---TGAAAAAAAAT
*
65237 GAAAAATGAAGAAAAAT
1 GAAAAATGAAAAAAAAT
65254 GAAAAAT
1 GAAAAAT
65261 ATAAAACGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.17
17 16 0.30
18 13 0.24
19 6 0.11
20 7 0.13
21 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (17 bp):
GAAAAATGAAAAAAAAT
Found at i:66640 original size:37 final size:36
Alignment explanation
Indices: 66586--66657 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
66576 AAATAAGTCA
66586 ATCTTAAGCCTTCATGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCATGGAAGAGTAGTGAAGCAAACC
*
66622 ATCTGTAAGCCTTCATGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCATGGAAGAGTAGTGAAGCAAAC
66658 TCATTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCATGGAAGAGTAGTGAAGCAAACC
Found at i:66800 original size:55 final size:55
Alignment explanation
Indices: 66672--67146 Score: 517
Period size: 55 Copynumber: 8.7 Consensus size: 55
66662 TTTATGAAGA
* * * * * *
66672 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGTGGACAC-GTTTGTTAAAGA---T
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC-CTGTTTATTGAAGATTGT
* * *
66724 T-GAATCCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATT-T
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTGT
*
66777 TCTGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGT
1 TC-GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTG-TTTATTGAAGATTGT
* *
66834 TCGAGTTCTATACTTTCTGAAGGAATAGAGAGCGGA-CTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCT-GTTTATTGAAGATTGT
* * * *
66889 TTGAGTTCCATACTCTATGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTG-TTTATTGAAGATTGT
* *
66945 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CTCGTTTGTTGAATATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCT-GTTTATTGAAGATTGT
* * * *
67000 TCGAGTTCCATGCTCTCTGAAGGAATAGAGAGCGAACCCAT-TTTA-TGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CC-TGTTTATTGAAGATTGT
* *
67055 TCGAGTTCTATACTCTCTGAAAGAATAGAGAGCGGACCCAT-TTTA-TGAAAATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CC-TGTTTATTGAAGATTGT
* * *
67110 TCGAGTTCTATACTCCCTG-AGCGGATAGGGAGCGGAC
1 TCGAGTTCTATACTCTCTGAAG-GAATAGAGAGCGGAC
67147 TTATCATTTG
Statistics
Matches: 368, Mismatches: 40, Indels: 28
0.84 0.09 0.06
Matches are distributed among these distances:
50 1 0.00
51 42 0.11
52 1 0.00
53 2 0.01
54 2 0.01
55 216 0.59
56 99 0.27
57 4 0.01
58 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTGT
Found at i:66868 original size:111 final size:111
Alignment explanation
Indices: 66730--67146 Score: 583
Period size: 111 Copynumber: 3.8 Consensus size: 111
66720 AGATTGAATC
* *
66730 CTATACTCTCTGAAGGAATAGGGAGCGGAC-CTGTTTATTGAAGATT-TTCTGAGTTCTATACTC
1 CTATACTCTCTGAAGGAATAGAGAGCGGACTC-GTTTATTGAAGATTGTTC-GAGTTCCATACTC
66793 TCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
64 TCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
* * * *
66841 CTATACTTTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAAGATTGTTTGAGTTCCATACTCTA
1 CTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTGTTCGAGTTCCATACTCTC
66906 TGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
66 TGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
* * *
66952 CTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAATATTGTTCGAGTTCCATGCTCTC
1 CTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTGTTCGAGTTCCATACTCTC
* * *
67017 TGAAGGAATAGAGAGCGAACCCATTTTA-TGAAGATTATTCGAGTT
66 TGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
* * * * * *
67062 CTATACTCTCTGAAAGAATAGAGAGCGGACCCATTT-TATGAAAATTGTTCGAGTTCTATACTCC
1 CTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTAT-TGAAGATTGTTCGAGTTCCATACTCT
* *
67126 CTG-AGCGGATAGGGAGCGGAC
65 CTGAAG-GAATAGAGAGCGGAC
67147 TTATCATTTG
Statistics
Matches: 278, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
109 3 0.01
110 86 0.31
111 186 0.67
112 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (111 bp):
CTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTATTGAAGATTGTTCGAGTTCCATACTCTC
TGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTT
Found at i:66924 original size:166 final size:165
Alignment explanation
Indices: 66672--67146 Score: 565
Period size: 166 Copynumber: 2.9 Consensus size: 165
66662 TTTATGAAGA
* * * * * *
66672 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGTGGACACGTTTGTT-AA-A--GATTGA-ATCCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGTTTGAGTTCC-
*
66732 ATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATT-TTCTGAGTTCTATACTCTCT
65 ATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTC-GAGTTCTATACTCTCT
66796 GAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGT
129 GAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGT
* *
66834 TCGAGTTCTATACTTTCTGAAGGAATAGAGAGCGGACTCGTTTGTTGAAGATTGTTTGAGTTCCA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGTTTGAGTTCCA
* *
66899 TACTCTATGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCGAGTTCTATACTCTCTG
66 TACTCTCTGAAGGAATAGAGAGCGGACCTG-TTTATTGAAGATTGTTCGAGTTCTATACTCTCTG
* * *
66964 AAGGAATAGAGAGCGGACTCGTTTGTTGAATATTGT
130 AAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGT
* * * * * * * *
67000 TCGAGTTCCATGCTCTCTGAAGGAATAGAGAGCGAACCCATTT-TATGAAGATTATTCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGT-TGAAGATTGTTTGAGTTCC
* * *
67064 ATACTCTCTGAAAGAATAGAGAGCGGACCCAT-TTTA-TGAAAATTGTTCGAGTTCTATACTCCC
65 ATACTCTCTGAAGGAATAGAGAGCGGA-CC-TGTTTATTGAAGATTGTTCGAGTTCTATACTCTC
* *
67127 TG-AGCGGATAGGGAGCGGAC
128 TGAAG-GAATAGAGAGCGGAC
67147 TTATCATTTG
Statistics
Matches: 272, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
162 40 0.15
163 2 0.01
164 3 0.01
165 41 0.15
166 128 0.47
167 55 0.20
168 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (165 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGTTTGAGTTCCA
TACTCTCTGAAGGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTCTATACTCTCTGA
AGGAATAGAGAGCGGACCCGTTTATTGAAGATTGT
Found at i:70740 original size:31 final size:30
Alignment explanation
Indices: 70700--70795 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 30
70690 AAGAGTTGAG
70700 GGTTACCTATGTCTTTCGAGACATATGGATA
1 GGTTACCTATGTCTTTCG-GACATATGGATA
* *
70731 GTTTACCTATGTCTTTCGGGACATATGGACA
1 GGTTACCTATGTCTTTC-GGACATATGGATA
70762 GGTTACCTATGT-TCTTCGGAACATATGGATA
1 GGTTACCTATGTCT-TTCGG-ACATATGGATA
70793 GGT
1 GGT
70796 CATTCGGGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 3 0.05
31 54 0.93
32 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (30 bp):
GGTTACCTATGTCTTTCGGACATATGGATA
Found at i:73058 original size:22 final size:22
Alignment explanation
Indices: 72993--73052 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
72983 AGAAAATGGA
* *
72993 TCCACTATACGTTTGCCCATGC
1 TCCACTACACTTTTGCCCATGC
*
73015 TCCACTACACTATTGCCCATGC
1 TCCACTACACTTTTGCCCATGC
73037 TCCACTACACTTTTGC
1 TCCACTACACTTTTGC
73053 AAATGCCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.38, G:0.10, T:0.32
Consensus pattern (22 bp):
TCCACTACACTTTTGCCCATGC
Found at i:74458 original size:23 final size:23
Alignment explanation
Indices: 74431--74482 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
74421 TACAAAGGAA
74431 GAATTGTGATACCAGACAATGAG
1 GAATTGTGATACCAGACAATGAG
*
74454 GAATTGTGTTACCAGACAATGAG
1 GAATTGTGATACCAGACAATGAG
74477 GAATTG
1 GAATTG
74483 AAGAAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.25
Consensus pattern (23 bp):
GAATTGTGATACCAGACAATGAG
Found at i:78014 original size:103 final size:103
Alignment explanation
Indices: 77843--78163 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
77833 TAATGTCCAT
* **
77843 AAGGACCACATATCATTACTTAAGAATCATATACATATGGCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
77908 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
77946 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
78011 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
78049 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
78114 GACCTCACACATGTTCCAAAGAATACATATATGTCCCA
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
78152 AAGGACCACATA
1 AAGGACCACATA
78164 GACCCTCTAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:79594 original size:21 final size:20
Alignment explanation
Indices: 79568--79627 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
79558 CATATATGTA
79568 TCCTTTGGAACATGTATGAGG
1 TCCTTTGGAACATGTAT-AGG
*
79589 TCCTTTGGGAAACATG-ATTGG
1 TCCTTT-GG-AACATGTATAGG
*
79610 TCCTTTGGAATATGTATA
1 TCCTTTGGAACATGTATA
79628 TAGTTCTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 14 0.42
22 4 0.12
23 6 0.18
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (20 bp):
TCCTTTGGAACATGTATAGG
Found at i:79928 original size:2 final size:2
Alignment explanation
Indices: 79921--79988 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
79911 AGAATTATTA
79921 AT AT AT AT AT 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 AT AT AT AT AT
79963 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
79989 TATGCCTCAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82692 original size:20 final size:21
Alignment explanation
Indices: 82667--82707 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
82657 GTACATGTAT
*
82667 ATGTG-ATGATCTATGTGAAC
1 ATGTGAATAATCTATGTGAAC
82687 ATGTGATATAATCTATGTGAA
1 ATGTGA-ATAATCTATGTGAA
82708 TAATTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (21 bp):
ATGTGAATAATCTATGTGAAC
Found at i:82858 original size:23 final size:23
Alignment explanation
Indices: 82826--82903 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
82816 GATATATACG
*
82826 TGGTCTTTCGGGACAATTCTACA
1 TGGTCCTTCGGGACAATTCTACA
*
82849 TGGTCCTTCGGGACAATTCTACG
1 TGGTCCTTCGGGACAATTCTACA
* *
82872 TGGTCCTTTGGGAC-ATTTTACA
1 TGGTCCTTCGGGACAATTCTACA
82894 TGGTCCTTCG
1 TGGTCCTTCG
82904 AAACATTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 15 0.31
23 34 0.69
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (23 bp):
TGGTCCTTCGGGACAATTCTACA
Found at i:82909 original size:22 final size:22
Alignment explanation
Indices: 82826--82913 Score: 104
Period size: 23 Copynumber: 3.9 Consensus size: 22
82816 GATATATACG
*
82826 TGGTCTTTCGGGACAATTCTACA
1 TGGTCCTTCGGGAC-ATTCTACA
*
82849 TGGTCCTTCGGGACAATTCTACG
1 TGGTCCTTCGGGAC-ATTCTACA
* *
82872 TGGTCCTTTGGGACATTTTACA
1 TGGTCCTTCGGGACATTCTACA
**
82894 TGGTCCTTCGAAACATTCTA
1 TGGTCCTTCGGGACATTCTA
82914 TGTGGCACTT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
22 22 0.39
23 34 0.61
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (22 bp):
TGGTCCTTCGGGACATTCTACA
Found at i:84859 original size:16 final size:16
Alignment explanation
Indices: 84832--84870 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
84822 TAGGCCTATA
84832 AACGAACCGAACGTTC
1 AACGAACCGAACGTTC
* *
84848 AATGAACTGAACGTTC
1 AACGAACCGAACGTTC
84864 AACGAAC
1 AACGAAC
84871 AGTTTGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (16 bp):
AACGAACCGAACGTTC
Found at i:85218 original size:10 final size:10
Alignment explanation
Indices: 85205--85239 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
85195 AAATTGTTGG
85205 TTTATGTTCA
1 TTTATGTTCA
**
85215 TTTATGTTTG
1 TTTATGTTCA
85225 TTTATGTTCA
1 TTTATGTTCA
85235 TTTAT
1 TTTAT
85240 TGTGTTCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:85227 original size:20 final size:20
Alignment explanation
Indices: 85199--85239 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
85189 ATCCTAAAAT
85199 TGTTGGTTTATGTTCATTTA
1 TGTTGGTTTATGTTCATTTA
*
85219 TGTTTGTTTATGTTCATTTA
1 TGTTGGTTTATGTTCATTTA
85239 T
1 T
85240 TGTGTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.17, T:0.63
Consensus pattern (20 bp):
TGTTGGTTTATGTTCATTTA
Found at i:85286 original size:47 final size:47
Alignment explanation
Indices: 85209--85323 Score: 158
Period size: 47 Copynumber: 2.4 Consensus size: 47
85199 TGTTGGTTTA
* * * * *
85209 TGTTCATTTATGTTTGTTTATGTTCATTTATTGTGTTCATTTACTTT
1 TGTTCGTTTGTGTTCGTTTATATTCATTTATTGTGTTCATTTACGTT
* *
85256 TGTTCGTTTGTGTTCGTTTATATTCGTTTATTGTGTTCGTTTACGTT
1 TGTTCGTTTGTGTTCGTTTATATTCATTTATTGTGTTCATTTACGTT
*
85303 TGTTCGTTTGTGTTCATTTAT
1 TGTTCGTTTGTGTTCGTTTAT
85324 TCTGTTCGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.11, C:0.10, G:0.17, T:0.62
Consensus pattern (47 bp):
TGTTCGTTTGTGTTCGTTTATATTCATTTATTGTGTTCATTTACGTT
Found at i:85333 original size:23 final size:22
Alignment explanation
Indices: 85239--85357 Score: 116
Period size: 23 Copynumber: 5.1 Consensus size: 22
85229 TGTTCATTTA
85239 TTGTGTTCATTTACTTTTGTTCGT
1 TTGTGTTCATTTA--TTTGTTCGT
*
85263 TTGTGTTCGTTTATATTCGTT--T
1 TTGTGTTCATTTAT-TT-GTTCGT
*
85285 ATTGTGTTCGTTTACGTTTGTTCGT
1 -TTGTGTTCATTTA--TTTGTTCGT
85310 TTGTGTTCATTTATTCTGTTCGT
1 TTGTGTTCATTTATT-TGTTCGT
*
85333 TTATGTTCATTTATTGTGTTCGT
1 TTGTGTTCATTTATT-TGTTCGT
85356 TT
1 TT
85358 ATCATTTATA
Statistics
Matches: 83, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
22 4 0.05
23 48 0.58
24 29 0.35
25 2 0.02
ACGTcount: A:0.09, C:0.11, G:0.18, T:0.61
Consensus pattern (22 bp):
TTGTGTTCATTTATTTGTTCGT
Found at i:85340 original size:47 final size:46
Alignment explanation
Indices: 85225--85357 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 46
85215 TTTATGTTTG
* * * *
85225 TTTATGTTCATTTATTGTGTTCATTTACTTTTGTTCGTTTGTGTTCG
1 TTTATATTCGTTTATTATGTTCATTTAC-TTTGTTCGTTTGTGTTCA
* *
85272 TTTATATTCGTTTATTGTGTTCGTTTACGTTTGTTCGTTTGTGTTCA
1 TTTATATTCGTTTATTATGTTCATTTAC-TTTGTTCGTTTGTGTTCA
85319 -TT-TATTCTGTTCGT-TTATGTTCATTTA-TTGTGTTCGTTT
1 TTTATATTC-GTT--TATTATGTTCATTTACTT-TGTTCGTTT
85358 ATCATTTATA
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
45 7 0.09
46 14 0.19
47 53 0.71
48 1 0.01
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.62
Consensus pattern (46 bp):
TTTATATTCGTTTATTATGTTCATTTACTTTGTTCGTTTGTGTTCA
Found at i:86064 original size:45 final size:45
Alignment explanation
Indices: 86015--86226 Score: 286
Period size: 45 Copynumber: 4.7 Consensus size: 45
86005 TTCATTAATA
* *
86015 GCATCCATTCATGCTTATAATGCA-CCATTATGCATTTCAATTATG
1 GCATCCTTTCATGCTGATAATGCACCCA-TATGCATTTCAATTATG
* *
86060 GCATCCTTTCATG-TCAATAATGCACCCATATGCATTTTAATTATG
1 GCATCCTTTCATGCT-GATAATGCACCCATATGCATTTCAATTATG
* * * *
86105 ACATCCTTTTATGCCGATAATACACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCTGATAATGCACCCATATGCATTTCAATTATG
*
86150 GCATCCTTTCATG-TCCATAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCT-GATAATGCACCCATATGCATTTCAATTATG
*
86195 GCATCCTTTCATGCCGATAATGCACCCATATG
1 GCATCCTTTCATGCTGATAATGCACCCATATG
86227 AATTATATTT
Statistics
Matches: 146, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
44 1 0.01
45 142 0.97
46 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (45 bp):
GCATCCTTTCATGCTGATAATGCACCCATATGCATTTCAATTATG
Found at i:86170 original size:90 final size:90
Alignment explanation
Indices: 86016--86226 Score: 325
Period size: 90 Copynumber: 2.3 Consensus size: 90
86006 TCATTAATAG
* ** *
86016 CATCCATTCATGCTTATAATGCA-CCATTATGCATTTCAATTATGGCATCCTTTCATGTCAATAA
1 CATCCTTTCATGCCGATAATACACCCA-TATGCATTTCAATTATGGCATCCTTTCATGTCAATAA
*
86080 TGCACCCATATGCATTTTAATTATGA
65 TGCACCCATATGCATTTCAATTATGA
* *
86106 CATCCTTTTATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGTCCATAAT
1 CATCCTTTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGTCAATAAT
*
86171 GCACCCATATGCATTTCAATTATGG
66 GCACCCATATGCATTTCAATTATGA
*
86196 CATCCTTTCATGCCGATAATGCACCCATATG
1 CATCCTTTCATGCCGATAATACACCCATATG
86227 AATTATATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
90 107 0.97
91 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (90 bp):
CATCCTTTCATGCCGATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGTCAATAAT
GCACCCATATGCATTTCAATTATGA
Found at i:86714 original size:19 final size:22
Alignment explanation
Indices: 86663--86716 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 22
86653 TACCCCTACC
86663 ATGGTATCGATACTACTATTCT
1 ATGGTATCGATACTACTATTCT
* *
86685 AAGGTACCGATAC-ACTA-T-T
1 ATGGTATCGATACTACTATTCT
86704 ATGGTATCGATAC
1 ATGGTATCGATAC
86717 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 12 0.43
20 1 0.04
21 4 0.14
22 11 0.39
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGGTATCGATACTACTATTCT
Found at i:86764 original size:20 final size:21
Alignment explanation
Indices: 86739--86790 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
86729 CTGTTTTGAA
86739 TGGTATCGATACCTT-CCATT
1 TGGTATCGATACCTTCCCATT
* *
86759 TGGTATTGATA-CTTCCCCTT
1 TGGTATCGATACCTTCCCATT
*
86779 CGGTATCGATAC
1 TGGTATCGATAC
86791 TGATTGTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TGGTATCGATACCTTCCCATT
Found at i:91720 original size:26 final size:26
Alignment explanation
Indices: 91685--91740 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
91675 GAATACTGAT
91685 ATATATATCAATGTATAATTATGTAG
1 ATATATATCAATGTATAATTATGTAG
91711 ATATATATCAATGTATAATTATGTAG
1 ATATATATCAATGTATAATTATGTAG
91737 ATAT
1 ATAT
91741 TGAACGTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (26 bp):
ATATATATCAATGTATAATTATGTAG
Found at i:94384 original size:18 final size:18
Alignment explanation
Indices: 94361--94395 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
94351 AGGGATTATC
*
94361 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
94379 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
94396 AATATTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:107622 original size:18 final size:18
Alignment explanation
Indices: 107599--107659 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
107589 AGGGATTATC
107599 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGAGACAT
* *
107617 AGTGGTTCTTC-AGAATAATT
1 AGTGGTCCTTCGAG-A-CA-T
* *
107637 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
107655 AGTGG
1 AGTGG
107660 ACGTTCGGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.06
18 17 0.52
19 2 0.06
20 11 0.33
21 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:114546 original size:18 final size:18
Alignment explanation
Indices: 114523--114583 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
114513 AGGGATTATC
114523 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGAGACAT
* *
114541 AGTGGTTCTTC-AGAATAATT
1 AGTGGTCCTTCGAG-A-CA-T
*
114561 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
114579 AGTGG
1 AGTGG
114584 ACGTTCGGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.06
18 17 0.50
19 2 0.06
20 12 0.35
21 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:121175 original size:18 final size:18
Alignment explanation
Indices: 121152--121222 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
121142 AGGGCTTATC
121152 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
121170 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
121189 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
121208 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
121223 TAAATATTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 28 0.61
19 4 0.09
20 14 0.30
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:122845 original size:31 final size:30
Alignment explanation
Indices: 122792--122899 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
122782 ATTCTATGGA
* *
122792 ACATATGGACAGAATTACCTATGTCTTTCGGG
1 ACATATGGACAGTA-TACCTATGT-TTTAGGG
* **
122824 ACATATGGACAGTATACCTATGTTCTAAGAA
1 ACATATGGACAGTATACCTATGTT-TTAGGG
* * *
122855 ACATATGGACAGTTTACCTAGGTTATTTTGGG
1 ACATATGGACAGTATACCTATG-T-TTTAGGG
*
122887 ACCTATGGACAGT
1 ACATATGGACAGT
122900 TGTCGAGGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.02
31 31 0.51
32 28 0.46
33 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (30 bp):
ACATATGGACAGTATACCTATGTTTTAGGG
Found at i:122888 original size:63 final size:63
Alignment explanation
Indices: 122775--122899 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
122765 GTCGAGAGTT
* * * *
122775 TACCTATATTCTATGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAGTA
1 TACCTATATTCTAAGAAACATATGGACAGAATTACCTAGGTATTTCGGGACATATGGACAGTA
* * * *
122838 TACCTATGTTCTAAGAAACATATGGACAG-TTTACCTAGGTTATTTTGGGACCTATGGACAGT
1 TACCTATATTCTAAGAAACATATGGACAGAATTACCTAGG-TATTTCGGGACATATGGACAGT
122900 TGTCGAGGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 8 0.15
63 45 0.85
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (63 bp):
TACCTATATTCTAAGAAACATATGGACAGAATTACCTAGGTATTTCGGGACATATGGACAGTA
Found at i:123705 original size:11 final size:11
Alignment explanation
Indices: 123691--123716 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
123681 ACTATAACAA
123691 TATTATAGCAG
1 TATTATAGCAG
123702 TATTATAGCAG
1 TATTATAGCAG
123713 TATT
1 TATT
123717 GTAGAAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (11 bp):
TATTATAGCAG
Found at i:123877 original size:19 final size:21
Alignment explanation
Indices: 123829--123877 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
123819 GTTCACGGTT
*
123829 CTGTTCATACGGTATTGTTCA
1 CTGTTCATACCGTATTGTTCA
*
123850 CTATTCATACCGTATT-TT-A
1 CTGTTCATACCGTATTGTTCA
123869 CTGTTCATA
1 CTGTTCATA
123878 AAACCTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.45
Consensus pattern (21 bp):
CTGTTCATACCGTATTGTTCA
Found at i:126478 original size:13 final size:13
Alignment explanation
Indices: 126462--126487 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
126452 TGGAAGAAAA
126462 GATAAAGTGAGTT
1 GATAAAGTGAGTT
126475 GATAAAGTGAGTT
1 GATAAAGTGAGTT
126488 AATCAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
GATAAAGTGAGTT
Found at i:128076 original size:19 final size:20
Alignment explanation
Indices: 128052--128091 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
128042 CAGATTACGA
128052 AGGGGGTA-CAGATTCC-CCT
1 AGGGGGTATC-GATTCCGCCT
128071 AGGGGGTATCGATTCCGCCT
1 AGGGGGTATCGATTCCGCCT
128091 A
1 A
128092 AAGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (20 bp):
AGGGGGTATCGATTCCGCCT
Found at i:128987 original size:31 final size:30
Alignment explanation
Indices: 128901--129006 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
128891 GTCGAGGGTT
* *
128901 TACCTATGTTCTACGGGACATATGGACAGAA
1 TACCTATGTTCTA-AGGACATATGGACAGTA
** *
128932 TTACCTATG-TCTTTTGCGATATATGGACAGTA
1 -TACCTATGTTC-TAAG-GACATATGGACAGTA
*
128964 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGG-ACATATGGACAGTA
*
128995 TACCTAGGTTCT
1 TACCTATGTTCT
129007 TTTGGGACCT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 36 0.59
32 24 0.39
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (30 bp):
TACCTATGTTCTAAGGACATATGGACAGTA
Found at i:129008 original size:63 final size:63
Alignment explanation
Indices: 128901--129025 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
128891 GTCGAGGGTT
* * * *
128901 TACCTATGTTCTACGGGACATATGGACAGAATTACCTATGTCTTTTGCGATATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTTGCGACATATGGACAGTA
* * *
128964 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTTGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGG-TCTTTTGCGACATATGGACAGT
129026 TGTCGAGGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 8 0.15
63 46 0.85
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (63 bp):
TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTTGCGACATATGGACAGTA
Found at i:129025 original size:32 final size:31
Alignment explanation
Indices: 128898--129026 Score: 125
Period size: 32 Copynumber: 4.1 Consensus size: 31
128888 AGAGTCGAGG
*
128898 GTTTACCTATGTTCTACGGGACATATGGACA
1 GTTTACCTATGTTCTATGGGACATATGGACA
* * * *
128929 GAATTACCTATG-TCTTTTGCGATATATGGACA
1 G-TTTACCTATGTTC-TATGGGACATATGGACA
* * *
128961 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTATGGGACATATGGACA
* * *
128992 GTTTACCTAGGTTCTTTTGGGACCTATGGACA
1 GTTTACCTATGTTC-TATGGGACATATGGACA
129024 GTT
1 GTT
129027 GTCGAGGTTC
Statistics
Matches: 76, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
31 35 0.46
32 41 0.54
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGGACATATGGACA
Found at i:129457 original size:20 final size:20
Alignment explanation
Indices: 129432--129483 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
129422 AATACATTAT
129432 ATATGATATG-TATATTGGTA
1 ATATGATATGTTATA-TGGTA
* *
129452 ATATGAAATGTTATATGGTT
1 ATATGATATGTTATATGGTA
*
129472 ATATAATATGTT
1 ATATGATATGTT
129484 TTATATGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (20 bp):
ATATGATATGTTATATGGTA
Found at i:129815 original size:11 final size:11
Alignment explanation
Indices: 129801--129846 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
129791 ATTTTATGAA
129801 AGTATTGTAGC
1 AGTATTGTAGC
* *
129812 AGTATTTTAGT
1 AGTATTGTAGC
*
129823 AGTATTGTATC
1 AGTATTGTAGC
*
129834 AGTACTGTAGC
1 AGTATTGTAGC
129845 AG
1 AG
129847 GGAATCAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (11 bp):
AGTATTGTAGC
Found at i:129853 original size:19 final size:21
Alignment explanation
Indices: 129831--129873 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
129821 GTAGTATTGT
*
129831 ATCAGTAC-TGTAGCA-GGGA
1 ATCAATACATGTAGCAGGGGA
*
129850 ATCAATACATGTAGTAGGGGA
1 ATCAATACATGTAGCAGGGGA
129871 ATC
1 ATC
129874 GGTTCCCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 6 0.30
21 7 0.35
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (21 bp):
ATCAATACATGTAGCAGGGGA
Found at i:129931 original size:12 final size:12
Alignment explanation
Indices: 129914--129958 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
129904 AATATTCGGC
129914 ACTGTTCACGGT
1 ACTGTTCACGGT
**
129926 ACTGTTCATAGT
1 ACTGTTCACGGT
*
129938 ATTGTTCACGGT
1 ACTGTTCACGGT
*
129950 ACTATTCAC
1 ACTGTTCAC
129959 TATTGTTCAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (12 bp):
ACTGTTCACGGT
Found at i:129965 original size:22 final size:23
Alignment explanation
Indices: 129916--129967 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
129906 TATTCGGCAC
* *
129916 TGTTCACGGTACTGTTCATAGTAT
1 TGTTCACGGTACTATTCA-ACTAT
129940 TGTTCACGGTACTATTC-ACTAT
1 TGTTCACGGTACTATTCAACTAT
129962 TGTTCA
1 TGTTCA
129968 TACGATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 10 0.38
24 16 0.62
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
TGTTCACGGTACTATTCAACTAT
Found at i:129997 original size:21 final size:19
Alignment explanation
Indices: 129962--130009 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
129952 TATTCACTAT
129962 TGTTCATACGATATTGTTCAC
1 TGTTCATACGATATT-TT-AC
129983 TGTTCATACTG-TATTTTAC
1 TGTTCATAC-GATATTTTAC
*
130002 TATTCATA
1 TGTTCATA
130010 AAACGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 13 0.52
22 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (19 bp):
TGTTCATACGATATTTTAC
Found at i:130488 original size:31 final size:31
Alignment explanation
Indices: 130408--130503 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
130398 AAGAGTTGAG
* * *
130408 GGTTACCTATGTCTTTCGAGACATATGGATA
1 GGTTACCTATGTCATTCGGGACATATGGACA
* *
130439 GTTTACCTATGTCATTCGGGATATATGGACA
1 GGTTACCTATGTCATTCGGGACATATGGACA
* * *
130470 GGTTACCTATGTTC-TTCGGAACATAAGGATA
1 GGTTACCTATG-TCATTCGGGACATATGGACA
130501 GGT
1 GGT
130504 CCTTCGGGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 52 0.96
32 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTCATTCGGGACATATGGACA
Found at i:135928 original size:21 final size:20
Alignment explanation
Indices: 135902--135961 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
135892 CATATATGTA
135902 TCCTTTGGAACATGTATGAGG
1 TCCTTTGGAACATGTAT-AGG
*
135923 TCCTTTGGGACACATG-ATTGG
1 TCCTTT-GGA-ACATGTATAGG
*
135944 TCCTTTGGAATATGTATA
1 TCCTTTGGAACATGTATA
135962 TAGTTCTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 14 0.42
22 5 0.15
23 5 0.15
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (20 bp):
TCCTTTGGAACATGTATAGG
Found at i:139191 original size:23 final size:23
Alignment explanation
Indices: 139139--139245 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
139129 GAGTTTCGGG
*
139139 TTCTACGTGGTCCTTCGGGA-TA
1 TTCTACGTGGTCCTTCGGGACAA
*
139161 -TCTACGTGGTTCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
139183 TTCTACGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
**
139206 TTCTGTGTGGTCCTTCGGGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
*
139228 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
139246 TGCAATTTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.26
22 16 0.22
23 37 0.51
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:141571 original size:23 final size:24
Alignment explanation
Indices: 141545--141605 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 24
141535 TGTTAATTTA
*
141545 TTGTGTTCATTTACGTTTG-TCGT
1 TTGTGTTCGTTTACGTTTGTTCGT
141568 TTGTGTTCGTTTACGTTTGTTCGT
1 TTGTGTTCGTTTACGTTTGTTCGT
*
141592 TTTTGTTCGTTTAC
1 TTGTGTTCGTTTAC
141606 ATTCGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.07, C:0.13, G:0.21, T:0.59
Consensus pattern (24 bp):
TTGTGTTCGTTTACGTTTGTTCGT
Found at i:141612 original size:20 final size:20
Alignment explanation
Indices: 141587--141624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
141577 TTTACGTTTG
*
141587 TTCGTTTTTGTTCGTTTACA
1 TTCGTTTATGTTCGTTTACA
*
141607 TTCGTTTATGTTTGTTTA
1 TTCGTTTATGTTCGTTTA
141625 AATCTATTCA
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:0.11, C:0.11, G:0.16, T:0.63
Consensus pattern (20 bp):
TTCGTTTATGTTCGTTTACA
Found at i:142393 original size:45 final size:45
Alignment explanation
Indices: 142337--142548 Score: 280
Period size: 45 Copynumber: 4.7 Consensus size: 45
142327 TTCATTAATA
* ** * * *
142337 GCATCCATTCATGCTTATAATTCACCAATATGCATTTTAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* *
142382 GCATCCTTTCATGTCAATAATGCACCCATATGCATTTTAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* * * *
142427 ACATCCTTTTATGCCGATAATACACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
*
142472 GCATTCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* * *
142517 GCATCCTTTTATACCGATAATGCACCCATATG
1 GCATCCTTTCATGCCAATAATGCACCCATATG
142549 AATTATATTT
Statistics
Matches: 146, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (45 bp):
GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
Found at i:142491 original size:90 final size:90
Alignment explanation
Indices: 142353--142548 Score: 311
Period size: 90 Copynumber: 2.2 Consensus size: 90
142343 ATTCATGCTT
* * * *
142353 ATAATTCACCAATATGCATTTTAATTATGGCATCCTTTCATGTCAATAATGCACCCATATGCATT
1 ATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
* *
142418 TTAATTATGACATCCTTTTATGCCG
66 TCAATTATGACATCCTTTTATACCG
*
142443 ATAATACACCCATATGCATTTCAATTATGGCATTCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
*
142508 TCAATTATGGCATCCTTTTATACCG
66 TCAATTATGACATCCTTTTATACCG
*
142533 ATAATGCACCCATATG
1 ATAATACACCCATATG
142549 AATTATATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 97 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (90 bp):
ATAATACACCCATATGCATTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
TCAATTATGACATCCTTTTATACCG
Found at i:143029 original size:19 final size:21
Alignment explanation
Indices: 142986--143037 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
142976 CCCCTATCAT
142986 GGTATCGATACTACTATACTAA
1 GGTATCGATACTACTATA-TAA
*
143008 GGTACCGATAC-ACTAT-TAA
1 GGTATCGATACTACTATATAA
143027 GGTATCGATAC
1 GGTATCGATAC
143038 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.46
21 5 0.18
22 10 0.36
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (21 bp):
GGTATCGATACTACTATATAA
Found at i:143085 original size:20 final size:21
Alignment explanation
Indices: 143060--143111 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
143050 ATGTTTTGAA
143060 TGGTATCGATACCTTCC-CTT
1 TGGTATCGATACCTTCCTCTT
143080 TGGTATCGATA-CTTCCTCTT
1 TGGTATCGATACCTTCCTCTT
*
143100 CGGTATCGATAC
1 TGGTATCGATAC
143112 TGATTGCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.38
Consensus pattern (21 bp):
TGGTATCGATACCTTCCTCTT
Found at i:144152 original size:22 final size:22
Alignment explanation
Indices: 144108--144167 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
144098 ATATGAAATT
* *
144108 TGTCCCGAAGGACCT-CATATA
1 TGTCCCGAATGACCTATATATA
144129 TGTCCCGAATGACCTATATATA
1 TGTCCCGAATGACCTATATATA
144151 TGTCCCGAATGACCTAT
1 TGTCCCGAATGACCTAT
144168 GTAACCCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 14 0.39
22 22 0.61
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (22 bp):
TGTCCCGAATGACCTATATATA
Found at i:145676 original size:20 final size:21
Alignment explanation
Indices: 145651--145690 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
145641 CTCAGCTTAC
*
145651 TTAACATAT-CTTATATTCAT
1 TTAACACATCCTTATATTCAT
*
145671 TTAACACATCCTTATCTTCA
1 TTAACACATCCTTATATTCA
145691 ATATTTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAACACATCCTTATATTCAT
Done.