Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015989.1 Corchorus capsularis cultivar CVL-1 contig16010, 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: 61409
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:821 original size:110 final size:110
Alignment explanation
Indices: 628--848 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 110
618 TGTGAGGTGA
628 AATGTAATGAGATGCTAGGAATGATGTAATGAAGGTTGCCATGTATGCTTATATTCTAATGTGAA
1 AATGTAATGAGATGCTAGGAATGATGTAATGAAGGTTGCCATGTATGCTTATATTCTAATGTGAA
*
693 GATGCTAAATTGTGGATGCTATATGCTAACTAAATTCTAAATATG
66 AATGCTAAATTGTGGATGCTATATGCTAACTAAATTCTAAATATG
738 AATGTAATGAGATGCTAGGAATGATGTAATGAAGGTTGCCATGTATGCTTATATTCTAATGTGAA
1 AATGTAATGAGATGCTAGGAATGATGTAATGAAGGTTGCCATGTATGCTTATATTCTAATGTGAA
803 AATGCTAAATTGTGGATGCTATATGCTAACTAAATTCTAAATATG
66 AATGCTAAATTGTGGATGCTATATGCTAACTAAATTCTAAATATG
848 A
1 A
849 TCAATAGTGC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (110 bp):
AATGTAATGAGATGCTAGGAATGATGTAATGAAGGTTGCCATGTATGCTTATATTCTAATGTGAA
AATGCTAAATTGTGGATGCTATATGCTAACTAAATTCTAAATATG
Found at i:3242 original size:18 final size:17
Alignment explanation
Indices: 3219--3254 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3209 CTCAACCTAA
*
3219 AACTAGAAGAAAAACTAG
1 AACTAGAA-AAAAAATAG
3237 AACTAGAAAAAAAATAG
1 AACTAGAAAAAAAATAG
3254 A
1 A
3255 TGAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.08, G:0.14, T:0.11
Consensus pattern (17 bp):
AACTAGAAAAAAAATAG
Found at i:4350 original size:4 final size:4
Alignment explanation
Indices: 4343--4434 Score: 93
Period size: 4 Copynumber: 23.2 Consensus size: 4
4333 TTTTTTTTTC
* * * *
4343 TCTT TC-T TCTT CCTTT TCTT T-TT CTTTT TCTT T--T TCTT TTTCT TCCT
1 TCTT TCTT TCTT TC-TT TCTT TCTT -TCTT TCTT TCTT TCTT TCT-T TCTT
4390 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
4435 TTTTTTCACT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.03
3 5 0.07
4 60 0.81
5 7 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:4354 original size:24 final size:24
Alignment explanation
Indices: 4325--4436 Score: 90
Period size: 24 Copynumber: 4.7 Consensus size: 24
4315 CGTCGCAATA
4325 TTCTTCCATTTT-TTTTTCTCTTTC
1 TTCTTCC-TTTTCTTTTTCTCTTTC
*
4349 TTCTTCCTTTTCTTTTTCTTTTTC
1 TTCTTCCTTTTCTTTTTCTCTTTC
* * **
4373 TTTTTCTTTTTCTTCCT-TCTTTC
1 TTCTTCCTTTTCTTTTTCTCTTTC
*
4396 TTTCTTTC-TTTCTTTCTT-TCTTTC
1 -TTCTTCCTTTTCTTT-TTCTCTTTC
*
4420 TTTCTTTC-TTTCTTTTT
1 -TTCTTCCTTTTCTTTTT
4437 TTTTCACTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
23 17 0.23
24 57 0.77
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (24 bp):
TTCTTCCTTTTCTTTTTCTCTTTC
Found at i:4365 original size:6 final size:6
Alignment explanation
Indices: 4333--4386 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
4323 TATTCTTCCA
* * *
4333 TTTT-T TTTTCT CTTTCT TCTTCC TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
4380 TTTTCT T
1 TTTTCT T
4387 CCTTCTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:5149 original size:2 final size:2
Alignment explanation
Indices: 5142--5174 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5132 ATAATAGAGA
5142 AT AT AT 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 AT AT AT A
5175 CAAGAGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8920 original size:36 final size:36
Alignment explanation
Indices: 8879--9135 Score: 167
Period size: 36 Copynumber: 7.2 Consensus size: 36
8869 CTCTTTTTAG
8879 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
* * ** * ** *
8915 ATTAAG-CCTTTTATTG-TTTTATTTAATCT-CTTTTTA
1 ATTAAGTTC-TTTATTGACTCCACTTAAT-TAC-CCTGA
8951 GATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 -ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
* * ** ** *
8988 ATTAAGCGT-TTTATTG-TTTTACTTAATCT-CTTTTTA
1 ATTAAG-TTCTTTATTGACTCCACTTAAT-TAC-CCTGA
9024 GATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 -ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
* *
9061 ATTAAG-TCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTTC-TTTATTGACTCCACTTAATTACCCTGA
** **
9097 ATTAAG-TCCCTA---ACTTGACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
9129 ATTAAGT
1 ATTAAGT
9136 CCCTAACTTG
Statistics
Matches: 168, Mismatches: 37, Indels: 35
0.70 0.15 0.15
Matches are distributed among these distances:
32 23 0.14
35 22 0.13
36 72 0.43
37 33 0.20
38 18 0.11
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.46
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
Found at i:8934 original size:73 final size:73
Alignment explanation
Indices: 8848--9076 Score: 413
Period size: 73 Copynumber: 3.1 Consensus size: 73
8838 TAAATCAAGC
* *
8848 CCTTTTACTGTTTTGCTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
1 CCTTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
8913 GAATTAAG
66 GAATTAAG
*
8921 CCTTTTATTGTTTTATTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
1 CCTTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
8986 GAATTAAG
66 GAATTAAG
*
8994 CGTTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
1 CCTTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
9059 GAATTAAG
66 GAATTAAG
*
9067 TCTTTTATTG
1 CCTTTTATTG
9077 ACGCTACTTA
Statistics
Matches: 149, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 149 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (73 bp):
CCTTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCT
GAATTAAG
Found at i:8965 original size:37 final size:37
Alignment explanation
Indices: 8851--9040 Score: 117
Period size: 37 Copynumber: 5.2 Consensus size: 37
8841 ATCAAGCCCT
* *
8851 TTTACTGTTTTGCTTAATCTCTTTTTAGATTAAGTTC
1 TTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTC
* ** ** * *
8888 TTTATTGACTCCACTTAAT-TAC-CCTGA-ATTAAG-CC
1 TTTATTG-TTTTACTTAATCT-CTTTTTAGATTAAGTTC
*
8923 TTTTATTGTTTTATTTAATCTCTTTTTAGATTAAGTTC
1 -TTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTC
* ** ** * *
8961 TTTATTGACTCCACTTAAT-TAC-CCTGA-ATTAAGCGT-
1 TTTATTG-TTTTACTTAATCT-CTTTTTAGATTAAG-TTC
8997 TTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTC
1 TTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTC
9034 TTTATTG
1 TTTATTG
9041 ACTCCACTTA
Statistics
Matches: 107, Mismatches: 32, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
35 18 0.17
36 33 0.31
37 39 0.36
38 17 0.16
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.52
Consensus pattern (37 bp):
TTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTC
Found at i:9115 original size:73 final size:74
Alignment explanation
Indices: 8863--9136 Score: 210
Period size: 73 Copynumber: 3.8 Consensus size: 74
8853 TACTGTTTTG
** * * * * *
8863 CTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGAATTAAG-CCTTTT
1 CTTAATCTCTCCTGAGATTAAGTCCCTAATTGACTCCACTTAATTACCCTGAATTAAGTCGTTTT
***
8927 ATTGTTTTA
66 ATTGCGCTA
* ** * * * *
8936 TTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGAATTAAG-CGTTTT
1 CTTAATCTCTCCTGAGATTAAGTCCCTAATTGACTCCACTTAATTACCCTGAATTAAGTCGTTTT
***
9000 ATTGTTTTA
66 ATTGCGCTA
** * * * *
9009 CTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGAATTAAGTC-TTTT
1 CTTAATCTCTCCTGAGATTAAGTCCCTAATTGACTCCACTTAATTACCCTGAATTAAGTCGTTTT
9073 ATTGACGCTA
66 ATTG-CGCTA
9083 CTTAAT-TAC-CCTGA-ATTAAGTCCCTAACTTG-----ACTTAATTACCCTGAATTAAGTC
1 CTTAATCT-CTCCTGAGATTAAGTCCCTAA-TTGACTCCACTTAATTACCCTGAATTAAGTC
9137 CCTAACTTGA
Statistics
Matches: 185, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
68 23 0.12
72 10 0.05
73 142 0.77
74 10 0.05
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (74 bp):
CTTAATCTCTCCTGAGATTAAGTCCCTAATTGACTCCACTTAATTACCCTGAATTAAGTCGTTTT
ATTGCGCTA
Found at i:9115 original size:146 final size:141
Alignment explanation
Indices: 8850--9134 Score: 360
Period size: 146 Copynumber: 2.0 Consensus size: 141
8840 AATCAAGCCC
*
8850 TTTTACTGTTTTGCTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 TTTTACTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
*** * ** * * * *
8915 ATTAAGCCTTTTATTGTTTTATTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAAT
66 ATTAAGCCTTTTATTGCGCTACTTAATCTCTCCTGAGATTAAGTCCCTAATTG-----ACTTAAT
8980 TACCCTGAATTAAGCG
126 TACCCTGAATTAAGCG
*
8996 TTTTATTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
1 TTTTACTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
*
9061 ATTAAGTCTTTTATTGACGCTACTTAAT-TAC-CCTGA-ATTAAGTCCCTAACTTGACTTAATTA
66 ATTAAGCCTTTTATTG-CGCTACTTAATCT-CTCCTGAGATTAAGTCCCTAA-TTGACTTAATTA
9123 CCCTGAATTAAG
128 CCCTGAATTAAG
9135 TCCCTAACTT
Statistics
Matches: 123, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
141 21 0.17
145 10 0.08
146 84 0.68
147 8 0.07
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (141 bp):
TTTTACTGTTTTACTTAATCTCTTTTTAGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
ATTAAGCCTTTTATTGCGCTACTTAATCTCTCCTGAGATTAAGTCCCTAATTGACTTAATTACCC
TGAATTAAGCG
Found at i:9123 original size:32 final size:32
Alignment explanation
Indices: 9082--9153 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
9072 TATTGACGCT
9082 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
1 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
9114 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
1 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
9146 ACTTAATT
1 ACTTAATT
9154 TCCTTCCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCCCTAACTTG
Found at i:9180 original size:37 final size:37
Alignment explanation
Indices: 9128--9315 Score: 244
Period size: 37 Copynumber: 5.2 Consensus size: 37
9118 AATTACCCTG
*
9128 AATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTTAACTCT-ACTTAATTTCCTTCCTTGA
* *
9165 AATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
*
9202 AATCAAGT-C----CTCTACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
* * * * *
9234 AATTAAGCCCTTTACTCTACTTAATTCCCTTTCTTGG
1 AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
9271 AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
1 AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
9308 AATTAAGT
1 AATTAAGT
9316 TCTCTGTCTG
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
32 27 0.21
33 1 0.01
36 1 0.01
37 99 0.77
38 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.41
Consensus pattern (37 bp):
AATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGA
Found at i:9187 original size:69 final size:70
Alignment explanation
Indices: 9096--9315 Score: 256
Period size: 69 Copynumber: 3.1 Consensus size: 70
9086 AATTACCCTG
* *
9096 AATTAAGTCCCTAACT-TGACTTAATTACCC-T-GAATTAAGTCCCTAACTTGACTTAATTTCCT
1 AATTAAGTCCTTAACTCT-ACTTAATTCCCCTTGGAATTAAGTCCCTAACTT-ACTTAATTTCCT
9158 TCCTTGA
64 TCCTTGA
*
9165 AATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGT-CCT--C-TACTTAATTTCC
1 AATTAAGTCCTTAACTCTACTTAATT-CC--CCTTGGAATTAAGTCCCTAACTTACTTAATTTCC
9226 TTCCTTGA
63 TTCCTTGA
* * *
9234 AATTAAGCCCTTTACTCTACTTAATTCCCTTTCTTGGAATTAAGTCCTTAACTCTACTTAATTTC
1 AATTAAGTCCTTAACTCTACTTAATTCCC---CTTGGAATTAAGTCCCTAACT-TACTTAATTTC
9299 CTTCCTTGA
62 CTTCCTTGA
9308 AATTAAGT
1 AATTAAGT
9316 TCTCTGTCTG
Statistics
Matches: 129, Mismatches: 8, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
66 1 0.01
68 2 0.02
69 78 0.60
70 5 0.04
71 1 0.01
72 3 0.02
73 4 0.03
74 35 0.27
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (70 bp):
AATTAAGTCCTTAACTCTACTTAATTCCCCTTGGAATTAAGTCCCTAACTTACTTAATTTCCTTC
CTTGA
Found at i:9462 original size:41 final size:41
Alignment explanation
Indices: 9417--9625 Score: 343
Period size: 41 Copynumber: 5.1 Consensus size: 41
9407 AATTATCCTG
*
9417 AATTAAGTCTGTGCTTGCTTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTTACCTAATTTCCTTCCTTGA
9458 AATTAAGTCTGTGCTTA-TCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACT-TTTACCTAATTTCCTTCCTTGA
9499 AATTAAGTCTGTGCTTAC-TTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTTACCTAATTTCCTTCCTTGA
9539 AATTAAGTCTGTGCTTACTTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTACTTTTACCTAATTTCCTTCCTTGA
* * *
9580 AATTAAGTCAGTGCTTTAC-TTTACCTAATTTACTGCCTTGA
1 AATTAAGTCTGTGC-TTACTTTTACCTAATTTCCTTCCTTGA
9621 AATTA
1 AATTA
9626 GTCCTTTAAC
Statistics
Matches: 160, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
40 41 0.26
41 115 0.72
42 4 0.03
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (41 bp):
AATTAAGTCTGTGCTTACTTTTACCTAATTTCCTTCCTTGA
Found at i:9532 original size:81 final size:81
Alignment explanation
Indices: 9417--9625 Score: 348
Period size: 81 Copynumber: 2.6 Consensus size: 81
9407 AATTATCCTG
*
9417 AATTAAGTCTGTGCTTGCTTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTA-TCTTTA
1 AATTAAGTCTGTGCTTAC-TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACT-TTTA
9481 CCTAATTTCCTTCCTTGA
64 CCTAATTTCCTTCCTTGA
9499 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTTACC
1 AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTTACC
9564 TAATTTCCTTCCTTGA
66 TAATTTCCTTCCTTGA
* * *
9580 AATTAAGTCAGTGCTTTACTTTACCTAATTTACTGCCTTGAAATTA
1 AATTAAGTCTGTGC-TTACTTTACCTAATTTCCTTCCTTGAAATTA
9626 GTCCTTTAAC
Statistics
Matches: 121, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
81 74 0.61
82 47 0.39
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (81 bp):
AATTAAGTCTGTGCTTACTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTTACC
TAATTTCCTTCCTTGA
Found at i:9685 original size:37 final size:37
Alignment explanation
Indices: 9640--9809 Score: 196
Period size: 37 Copynumber: 4.6 Consensus size: 37
9630 TTTAACTGCT
* *
9640 TTTACTTAATTTTCCTGAATTAAGCTCTTTGACTGTG
1 TTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGTG
* *
9677 TTTACTTAATTACCCTGAATTAAGTTCTTTCACTGTG
1 TTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGTG
* * * *
9714 TTTACTTAATTACCCAGAATTATGTCCTTTGACTGTG
1 TTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGTG
* * ** * *
9751 TTTACTTAATTCCCCAGAATTAAGCCCTTTAACTGTC
1 TTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGTG
* *
9788 TTTACTTAATTGCCATGAATTA
1 TTTACTTAATTTCCCTGAATTA
9810 CTTAATTACC
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 117 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGTG
Found at i:9723 original size:74 final size:74
Alignment explanation
Indices: 9628--10314 Score: 271
Period size: 74 Copynumber: 9.0 Consensus size: 74
9618 TGAAATTAGT
** *
9628 CCTTTAACTG-CTTTTACTTAATTTTCCTGAATTAAG-CTCTTTGACTGTGTTTACTTAATTACC
1 CCTTTAACTGTC-TTTACTTAATTACCCAGAATTAAGTC-CTTTGACTGTGTTTACTTAATTACC
* *
9691 CTGAATTAAGT
64 CAGAATTAAGC
* * * * *
9702 TCTTTCACTGTGTTTACTTAATTACCCAGAATTATGTCCTTTGACTGTGTTTACTTAATTCCCCA
1 CCTTTAACTGTCTTTACTTAATTACCCAGAATTAAGTCCTTTGACTGTGTTTACTTAATTACCCA
9767 GAATTAAGC
66 GAATTAAGC
* ** ** *** * ** * *
9776 CCTTTAACTGTCTTTACTTAATT-GCCATGAATTACTTAATTACCCAGAATTAAGTCCTTTAACT
1 CCTTTAACTGTCTTTACTTAATTACCCA-GAATTAAGTCCTTTGACTGTGTT---TAC-TTAATT
* **** * *
9840 GCTTTTACTTAATTTC
61 ACCCAGAATTAA--GC
* * * * *
9856 CCTAAATTAAGTTCTTTGACTGTGTTTACTTAATTACCCTGAATTAAGTTCTTTAACCTGTGATT
1 CCT---TTAA---CTGT--C----TTTACTTAATTACCCAGAATTAAGTCCTTTGA-CTGTGTTT
* ** *
9921 ACTTAATTTCCTTGAATTAAGT
53 ACTTAATTACCCAGAATTAAGC
* * * * * * * * * *
9943 TCTCTGACTATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGGTTTACTTAATTACCCT
1 CCTTTAACTGTCTTTACTTAATTACCCAGAATTAAGTCCTTTGACTGTGTTTACTTAATTACCCA
*
10008 GAATTAAGT
66 GAATTAAGC
* * * * * * *
10017 TCTCTGACTGTGTTTACTTAATT-TCCATGAATTAAGTCATTTTACTGCT-TTTACTTAATTACC
1 CCTTTAACTGTCTTTACTTAATTACCCA-GAATTAAGTCCTTTGACTG-TGTTTACTTAATTACC
*
10080 CTGAATTAAGC
64 CAGAATTAAGC
* * *
10091 CCTTTTACT-TCTTTTACTTAATTACCCTA-AATTAAGTCCTTTAACTGTTGTGTTTAGTTAATT
1 CCTTTAACTGTC-TTTACTTAATTACCC-AGAATTAAGTCCTTTGAC---TGTGTTTACTTAATT
** * *
10154 TTCCTGAATTAAGT
61 ACCCAGAATTAAGC
* ** * ** * *
10168 TCTTTGTCTG-CTTCTACTTAATTTCCTTGAATAAAGTTCTTTGACTGCT-TTTACTTAATTACC
1 CCTTTAACTGTCTT-TACTTAATTACCCAGAATTAAGTCCTTTGACTG-TGTTTACTTAATTACC
* *
10231 CTGAATTAAGT
64 CAGAATTAAGC
* ** * *
10242 ACTTTAACTG-CTTTTACTTAATTACCTTGAATTAAGTACTTTAACTGCT-TTTACTTAATTACC
1 CCTTTAACTGTC-TTTACTTAATTACCCAGAATTAAGTCCTTTGACTG-TGTTTACTTAATTACC
*
10305 CTGAATTAAG
64 CAGAATTAAG
10315 TTCTTAATTG
Statistics
Matches: 472, Mismatches: 104, Indels: 74
0.73 0.16 0.11
Matches are distributed among these distances:
73 6 0.01
74 300 0.64
75 36 0.08
76 4 0.01
77 56 0.12
78 11 0.02
80 4 0.01
81 3 0.01
83 4 0.01
84 2 0.00
86 3 0.01
87 2 0.00
88 1 0.00
89 13 0.03
90 2 0.00
92 20 0.04
93 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (74 bp):
CCTTTAACTGTCTTTACTTAATTACCCAGAATTAAGTCCTTTGACTGTGTTTACTTAATTACCCA
GAATTAAGC
Found at i:9825 original size:18 final size:18
Alignment explanation
Indices: 9789--9827 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9779 TTAACTGTCT
*
9789 TTACTTAATTGCCATGAA
1 TTACTTAATTCCCATGAA
9807 TTACTTAATTACCCA-GAA
1 TTACTTAATT-CCCATGAA
9825 TTA
1 TTA
9828 AGTCCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (18 bp):
TTACTTAATTCCCATGAA
Found at i:9864 original size:37 final size:37
Alignment explanation
Indices: 9807--10336 Score: 559
Period size: 37 Copynumber: 14.2 Consensus size: 37
9797 TTGCCATGAA
* *
9807 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* * *
9844 TTACTTAATTTCCCTAAATTAAGTTCTTTGACTG-TGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCT-T
*
9881 TTACTTAATTACCCTGAATTAAGTTCTTTAACCTG-TGA
1 TTACTTAATTACCCTGAATTAAGTTCTTTAA-CTGCT-T
* * * * *
9919 TTACTTAATTTCCTTGAATTAAGTTCTCTGACT-ATGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCT-T
* * **
9956 TTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* *
9993 TTACTTAATTACCCTGAATTAAGTTCTCTGACTG-TGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCT-T
* * *
10030 TTACTTAATTTCCATGAATTAAG-TCATTTTACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTC-TTTAACTGCTT
** * *
10067 TTACTTAATTACCCTGAATTAAGCCCTTTTACTTCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* * *
10104 TTACTTAATTACCCTAAATTAAGTCCTTTAACTGTTGTGT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTG--CT-T
* ** **
10144 TTAGTTAATTTTCCTGAATTAAGTTCTTTGTCTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* * * * *
10181 CTACTTAATTTCCTTGAATAAAGTTCTTTGACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
*
10218 TTACTTAATTACCCTGAATTAAGTACTTTAACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* *
10255 TTACTTAATTACCTTGAATTAAGTACTTTAACTGCTT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
* *
10292 TTACTTAATTACCCTGAATTAAGTTC-TTAATTGATT
1 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
10328 TTACTTAAT
1 TTACTTAAT
10337 AATCTTGAAT
Statistics
Matches: 423, Mismatches: 59, Indels: 23
0.84 0.12 0.05
Matches are distributed among these distances:
36 20 0.05
37 339 0.80
38 35 0.08
39 1 0.00
40 28 0.07
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (37 bp):
TTACTTAATTACCCTGAATTAAGTTCTTTAACTGCTT
Found at i:9864 original size:55 final size:55
Alignment explanation
Indices: 9752--9864 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 55
9742 TTGACTGTGT
* *
9752 TTACTTAATTCCCCAGAATTAAGCCCTTTAACTGTCTTTACTTAATTGCCATGAA
1 TTACTTAATTACCCAGAATTAAGCCCTTTAACTGTCTTTACTTAATTGCCATAAA
* * *
9807 TTACTTAATTACCCAGAATTAAGTCCTTTAACTG-CTTTTACTTAATTTCCCTAAA
1 TTACTTAATTACCCAGAATTAAGCCCTTTAACTGTC-TTTACTTAATTGCCATAAA
9862 TTA
1 TTA
9865 AGTTCTTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (55 bp):
TTACTTAATTACCCAGAATTAAGCCCTTTAACTGTCTTTACTTAATTGCCATAAA
Found at i:9878 original size:92 final size:92
Alignment explanation
Indices: 9715--9901 Score: 261
Period size: 92 Copynumber: 2.0 Consensus size: 92
9705 TTCACTGTGT
* *
9715 TTACTTAATTACCCAGAATTATGTCCTTTGACTGTGTTTACTTAATTCCCCAGAATTAAGCCCTT
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTCCCCAGAATTAAGCCCTT
*
9780 TAACTGTCTTTACTTAATTGCCATGAA
66 TAACTGTCTTTACTTAATTACCATGAA
* **
9807 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCT-TTTACTTAATTTCCCTA-AATTAAGTTC
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTG-TGTTTACTTAA-TTCCCCAGAATTAAGCCC
* * *
9870 TTTGACTGTGTTTACTTAATTACCCTGAA
64 TTTAACTGTCTTTACTTAATTACCATGAA
9899 TTA
1 TTA
9902 AGTTCTTTAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 77 0.92
93 7 0.08
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (92 bp):
TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTCCCCAGAATTAAGCCCTT
TAACTGTCTTTACTTAATTACCATGAA
Found at i:9910 original size:129 final size:130
Alignment explanation
Indices: 9678--9939 Score: 359
Period size: 129 Copynumber: 2.0 Consensus size: 130
9668 TTGACTGTGT
* * * *
9678 TTACTTAATTACCCTGAATTAAGTTCTTTCACTGTGTTTACTTAATTACCCAGAATTATGTCCTT
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTACCCAGAATTAAGTCCTT
* *
9743 TGACTGTGTTTACTTAATTCCCCAGAATTAAGCCCTTTAA-CTGTCTTTACTTAATTGCCATGAA
66 TGACTGTGTTTACTTAATTACCCAGAATTAAGCCCTTTAACCTGTCATTACTTAATTGCCATGAA
* *
9807 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCT-TTTACTTAATTTCCCTA-AATTAAGTTC
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTG-TGTTTACTTAATTACCC-AGAATTAAGTCC
* ** * * *
9870 TTTGACTGTGTTTACTTAATTACCCTGAATTAAGTTCTTTAACCTGTGATTACTTAATTTCCTTG
64 TTTGACTGTGTTTACTTAATTACCCAGAATTAAGCCCTTTAACCTGTCATTACTTAATTGCCATG
9935 AA
129 AA
9937 TTA
1 TTA
9940 AGTTCTCTGA
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 91 0.78
130 25 0.22
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (130 bp):
TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTACCCAGAATTAAGTCCTT
TGACTGTGTTTACTTAATTACCCAGAATTAAGCCCTTTAACCTGTCATTACTTAATTGCCATGAA
Found at i:10223 original size:188 final size:185
Alignment explanation
Indices: 9807--10336 Score: 615
Period size: 188 Copynumber: 2.8 Consensus size: 185
9797 TTGCCATGAA
* * * *
9807 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCCTAAATTAAGTTC-T
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTTTTACTTAATTTCCCTGAATTAAG-TCAT
* * * * * * *
9871 TTGACTG-TGTTTACTTAATTACCCTGAATTAAGTTCTTTAACCTGTGATTACTTAATTTCCTTG
65 TTAACTGCT-TTTACTTAATTACCCTGAATTAAGTACTTTAACTTCT-TTTACTTAATTACCCTG
* * *
9935 AATTAAGTTCTCTGACTATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGGT
128 AATTAAGTCCTCTAACTATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGCT
* *
9993 TTACTTAATTACCCTGAATTAAGTTCTCTGACTG-TGTTTACTTAATTTCCATGAATTAAGTCAT
1 TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCT-TTTACTTAATTTCCCTGAATTAAGTCAT
* ** * *
10057 TTTACTGCTTTTACTTAATTACCCTGAATTAAGCCCTTTTACTTCTTTTACTTAATTACCCTAAA
65 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTACTTTAACTTCTTTTACTTAATTACCCTGAA
* * * * *
10122 TTAAGTCCTTTAACTGTTGTGTTTAGTTAATTTTCCTGAATTAAGTTCTTTGTCT-GCT
130 TTAAGTCCTCTAAC---TATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGCT
* * * *
10180 TCTACTTAATTTCCTTGAATAAAGTTCTTTGACTGCTTTTACTTAATTACCCTGAATTAAGT-AC
1 T-TACTTAATTACCCTGAATTAAGTTCTTTGACTGCTTTTACTTAATTTCCCTGAATTAAGTCA-
* *
10244 TTTAACTGCTTTTACTTAATTACCTTGAATTAAGTACTTTAACTGCTTTTACTTAATTACCCTGA
64 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTACTTTAACTTCTTTTACTTAATTACCCTGA
* *
10309 ATTAAGTTCT-TAATTGAT-TTTACTTAAT
129 ATTAAGTCCTCTAACT-ATGTTTACTTAAT
10337 AATCTTGAAT
Statistics
Matches: 293, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
184 10 0.03
185 30 0.10
186 91 0.31
187 8 0.03
188 153 0.52
189 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (185 bp):
TTACTTAATTACCCTGAATTAAGTTCTTTGACTGCTTTTACTTAATTTCCCTGAATTAAGTCATT
TAACTGCTTTTACTTAATTACCCTGAATTAAGTACTTTAACTTCTTTTACTTAATTACCCTGAAT
TAAGTCCTCTAACTATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGCT
Found at i:10260 original size:225 final size:222
Alignment explanation
Indices: 9807--10314 Score: 668
Period size: 225 Copynumber: 2.3 Consensus size: 222
9797 TTGCCATGAA
* * * **
9807 TTACTTAATTACCCA-GAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCCTAAATTAAGTTCT
1 TTACTTAATTA-CCATGAATTAAGTCATTTAACTGCTTTTACTTAATTACCCTGAATTAAGCCCT
* *
9871 TTGACTGTGTTTACTTAATTACCCTGAATTAAGTTCTTTAACCTGTGATTACTTAATTTCCTTGA
65 TTGACTGTGTTTACTTAATTACCCTAAATTAAGTCCTTTAACCTGTGATTACTTAATTTCCTTGA
* *
9936 ATTAAGTTCTCTGACTATGTTTACTTAATTTCCCTGAATTAAGTTCTTTGACTGGGTTTACTTAA
130 ATTAAGTTCTCTGA-TATGTTTACTTAATTTCCCTGAATAAAGTTCTTTGACTGCGTTTACTTAA
* *
10001 TTACCCTGAATTAAGTTCTCTGACTGTGT
194 TTACCCTGAATTAAGTACTCTAACTGTGT
* *
10030 TTACTTAATTTCCATGAATTAAGTCATTTTACTGCTTTTACTTAATTACCCTGAATTAAGCCCTT
1 TTACTTAATTACCATGAATTAAGTCATTTAACTGCTTTTACTTAATTACCCTGAATTAAGCCCTT
* * * * *
10095 TTACT-TCTTTTACTTAATTACCCTAAATTAAGTCCTTTAACTGTTGTGTTTAGTTAATTTTCC-
66 TGACTGT-GTTTACTTAATTACCCTAAATTAAGTCCTTTAAC--CTGTGATTACTTAA-TTTCCT
* * * *
10158 TGAATTAAGTTCTTTG-TCTGCTTCTACTTAATTTCCTTGAATAAAGTTCTTTGACTGCTTTTAC
127 TGAATTAAGTTCTCTGATATG-TT-TACTTAATTTCCCTGAATAAAGTTCTTTGACTGCGTTTAC
*
10222 TTAATTACCCTGAATTAAGTACTTTAACTGCT-T
190 TTAATTACCCTGAATTAAGTACTCTAACTG-TGT
*
10255 TTACTTAATTACCTTGAATTAAGT-ACTTTAACTGCTTTTACTTAATTACCCTGAATTAAG
1 TTACTTAATTACCATGAATTAAGTCA-TTTAACTGCTTTTACTTAATTACCCTGAATTAAG
10315 TTCTTAATTG
Statistics
Matches: 250, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
222 4 0.02
223 92 0.37
224 3 0.01
225 145 0.58
226 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (222 bp):
TTACTTAATTACCATGAATTAAGTCATTTAACTGCTTTTACTTAATTACCCTGAATTAAGCCCTT
TGACTGTGTTTACTTAATTACCCTAAATTAAGTCCTTTAACCTGTGATTACTTAATTTCCTTGAA
TTAAGTTCTCTGATATGTTTACTTAATTTCCCTGAATAAAGTTCTTTGACTGCGTTTACTTAATT
ACCCTGAATTAAGTACTCTAACTGTGT
Found at i:16002 original size:2 final size:2
Alignment explanation
Indices: 15995--16027 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15985 TGCAATTTAA
15995 AT AT AT 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 AT AT AT A
16028 ATGTCTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24853 original size:78 final size:78
Alignment explanation
Indices: 24746--24981 Score: 463
Period size: 78 Copynumber: 3.0 Consensus size: 78
24736 CAAAATGTAG
24746 CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
1 CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
24811 ATCACTAGAAATA
66 ATCACTAGAAATA
24824 CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
1 CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
24889 ATCACTAGAAATA
66 ATCACTAGAAATA
*
24902 CATGCTCCTTCTATCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
1 CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
24967 ATCACTAGAAATA
66 ATCACTAGAAATA
24980 CA
1 CA
24982 ACATAATAAA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 157 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (78 bp):
CATGCTCCTTCTGTCAACTAAATTAATTAAATAAAAATCTTAATAAACTCCTTGATAAATATGTA
ATCACTAGAAATA
Found at i:33945 original size:14 final size:13
Alignment explanation
Indices: 33926--33956 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
33916 TGTTTTTTAG
33926 GATCCCATTAAGA
1 GATCCCATTAAGA
33939 TGATCCCATTAAGA
1 -GATCCCATTAAGA
33953 GATC
1 GATC
33957 AAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (13 bp):
GATCCCATTAAGA
Found at i:35794 original size:19 final size:18
Alignment explanation
Indices: 35770--35807 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
35760 TTGAAGATTT
35770 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAA-TTGAAGA
*
35789 ATTGAAGATCATTGAAGA
1 ATTGAAGATAATTGAAGA
35807 A
1 A
35808 ATATTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (18 bp):
ATTGAAGATAATTGAAGA
Found at i:35819 original size:30 final size:30
Alignment explanation
Indices: 35750--35819 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
35740 TGGAGATTCG
* * *
35750 AATTTCATG-ATTGAAGATTTATTGAAGAT
1 AATTTCAAGAATTGAAGATTCATTGAAGAA
*
35779 AATTTGAAGAATTGAAGA-TCATTGAAGAA
1 AATTTCAAGAATTGAAGATTCATTGAAGAA
35808 ATATTTCAAGAA
1 A-ATTTCAAGAA
35820 GCAAGAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.34
Consensus pattern (30 bp):
AATTTCAAGAATTGAAGATTCATTGAAGAA
Found at i:38559 original size:21 final size:21
Alignment explanation
Indices: 38535--38574 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38525 GCGACATGGA
38535 GATTCCAAACAAAAGCAAGGC
1 GATTCCAAACAAAAGCAAGGC
* * *
38556 GATTTCAACCAAGAGCAAG
1 GATTCCAAACAAAAGCAAG
38575 AAAGATCAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (21 bp):
GATTCCAAACAAAAGCAAGGC
Found at i:40058 original size:25 final size:25
Alignment explanation
Indices: 40030--40077 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40020 AAAACCGATC
* *
40030 ATCACCATGCCACCACCGGTCACCT
1 ATCAACATGCCACCACCAGTCACCT
* *
40055 ATCAACGTGCCATCACCAGTCAC
1 ATCAACATGCCACCACCAGTCAC
40078 ATCCGAGCCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (25 bp):
ATCAACATGCCACCACCAGTCACCT
Found at i:40184 original size:16 final size:16
Alignment explanation
Indices: 40163--40194 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40153 TTTCCCTTGC
40163 ATTGCTTTGAGTGATT
1 ATTGCTTTGAGTGATT
*
40179 ATTGCTTTGATTGATT
1 ATTGCTTTGAGTGATT
40195 GTCTATTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.53
Consensus pattern (16 bp):
ATTGCTTTGAGTGATT
Found at i:40450 original size:70 final size:70
Alignment explanation
Indices: 40337--40479 Score: 286
Period size: 70 Copynumber: 2.0 Consensus size: 70
40327 TGGATGCATA
40337 CTTTCTTTGTGAGTCAAGTATTTCATTAGCACATTCATTTATTTTTAAAACCACACTTATCACAC
1 CTTTCTTTGTGAGTCAAGTATTTCATTAGCACATTCATTTATTTTTAAAACCACACTTATCACAC
40402 ATGTG
66 ATGTG
40407 CTTTCTTTGTGAGTCAAGTATTTCATTAGCACATTCATTTATTTTTAAAACCACACTTATCACAC
1 CTTTCTTTGTGAGTCAAGTATTTCATTAGCACATTCATTTATTTTTAAAACCACACTTATCACAC
40472 ATGTG
66 ATGTG
40477 CTT
1 CTT
40480 AAATTCACAC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (70 bp):
CTTTCTTTGTGAGTCAAGTATTTCATTAGCACATTCATTTATTTTTAAAACCACACTTATCACAC
ATGTG
Found at i:42002 original size:19 final size:18
Alignment explanation
Indices: 41978--42015 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
41968 TTGAAGATTT
41978 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAA-TTGAAGA
*
41997 ATTGAAGATCATTGAAGA
1 ATTGAAGATAATTGAAGA
42015 A
1 A
42016 ATATTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (18 bp):
ATTGAAGATAATTGAAGA
Found at i:42027 original size:30 final size:30
Alignment explanation
Indices: 41967--42027 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41957 GAAGTTCGTG
* * *
41967 ATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTCATTGAAGAAAATTTCAAGA
41997 ATTGAAGA-TCATTGAAGAAATATTTCAAGA
1 ATTGAAGATTCATTGAAGAAA-ATTTCAAGA
42027 A
1 A
42028 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (30 bp):
ATTGAAGATTCATTGAAGAAAATTTCAAGA
Found at i:47782 original size:37 final size:37
Alignment explanation
Indices: 47727--47809 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
47717 TAAGACTACT
*
47727 CTTAATTGGACTATTGGTTTTAGAAGTAGCCCATTTG
1 CTTATTTGGACTATTGGTTTTAGAAGTAGCCCATTTG
47764 CTTATTTGGACTATTGGTTTTAGAAGTAGCCCATTTG
1 CTTATTTGGACTATTGGTTTTAGAAGTAGCCCATTTG
47801 CTTATTTGG
1 CTTATTTGG
47810 TTCATGTTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (37 bp):
CTTATTTGGACTATTGGTTTTAGAAGTAGCCCATTTG
Found at i:51123 original size:22 final size:22
Alignment explanation
Indices: 51093--51180 Score: 94
Period size: 22 Copynumber: 4.2 Consensus size: 22
51083 TAAAAGAGTG
51093 AAAGTAAAAGAAGTAATCAGTA
1 AAAGTAAAAGAAGTAATCAGTA
* * **
51115 GAAGAAAAAGAA--AAAGAGTA
1 AAAGTAAAAGAAGTAATCAGTA
*
51135 AAAGTAAAAGGAGTAATCAGTA
1 AAAGTAAAAGAAGTAATCAGTA
*
51157 AAAGTAAAAG-AGTAA-AAGTA
1 AAAGTAAAAGAAGTAATCAGTA
51177 AAAG
1 AAAG
51181 AAGTAACTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 23 0.43
21 5 0.09
22 26 0.48
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.14
Consensus pattern (22 bp):
AAAGTAAAAGAAGTAATCAGTA
Found at i:51231 original size:22 final size:21
Alignment explanation
Indices: 51203--51243 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
51193 GAAGTGAAAG
51203 AGTAGAAGAAAAAGGAGTAATC
1 AGTAGAAGAAAAA-GAGTAATC
*
51225 AGTAGAAGTAAAAGAGTAA
1 AGTAGAAGAAAAAGAGTAA
51244 AAGTAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (21 bp):
AGTAGAAGAAAAAGAGTAATC
Found at i:51300 original size:36 final size:37
Alignment explanation
Indices: 51064--51697 Score: 284
Period size: 36 Copynumber: 17.3 Consensus size: 37
51054 AAATAAAAAG
* *
51064 AAGA-AGTAATCAGTAGAATTAAAAGAGTGAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
*
51100 AAGA-AGTAATCAGTAGAAGAAAAAGAAAAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGT---AG---AAGTAAAAGAGTAAAAGTAA
*
51142 AAG-GAGTAATCAGTAAAAGTAAAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* * *
51178 AAGA-AGTAA-CTAGTAGAAGTGAAAGAGTAGAAGAAA
1 AAGAGAGTAATC-AGTAGAAGTAAAAGAGTAAAAGTAA
51214 AAG-GAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
**
51250 AAGA-AGTAGCCAGTAGAAGTAAAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* * *
51286 AAGAGA-AAATCAGT--AAGT---TG-GTGAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* * ***
51316 AAGA-AATAAGCAGAATATTGGTAAAAAGAAGTAAAAGTAA
1 AAGAGAGTAATCAG--TAGAAGT-AAAAG-AGTAAAAGTAA
* * *
51356 AAGA-AATAATCAGCAGAA-T--GA-AGTAAAAGT-A
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* ** * ** *
51387 AAGCAGTAGAAAAGAGTAAAAGTAAAAGGAGTACTCAGTAG
1 AAG-AG-AGTAATCAGTAGAAGTAAAA-GAGTA-AAAGTAA
* * * * * *
51428 AAGGGAGTAAAAGTAAAAGAAGTAATTAGTATAAAGGAGTAGAGGTGA
1 AAGAGAGT--AA-T--CAGTAG--A--AGTA-AAA-GAGTAAAAGTAA
*
51476 AAGA-AGTAATCAG-AAAATTGGTAATTAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAA---GTAA--AAGAGTAAAAGTAA
51516 AAG-GAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
*
51552 AAGA-AG---T-AGTAGAAGTGAAAGAGTAAAAG-AA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* * *
51583 AAAAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAA
1 AAGA-GAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
** * *
51621 AAGA-AACAATCAGCAGAA-T--GA-AGTAAAAGTAA
1 AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* **
51653 AAGTAAGAG-AATTA--ATCAGTAAAAGAGTAAAAGTAA
1 AAG--AGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
51689 AAGA-AGTAA
1 AAGAGAGTAA
51698 GCAGAAAATT
Statistics
Matches: 455, Mismatches: 76, Indels: 136
0.68 0.11 0.20
Matches are distributed among these distances:
29 1 0.00
30 18 0.04
31 10 0.02
32 48 0.11
33 7 0.02
34 23 0.05
35 5 0.01
36 177 0.39
37 24 0.05
38 11 0.02
39 11 0.02
40 49 0.11
41 11 0.02
42 32 0.07
44 4 0.01
45 2 0.00
46 1 0.00
47 3 0.01
48 9 0.02
49 9 0.02
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.16
Consensus pattern (37 bp):
AAGAGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
Found at i:51410 original size:16 final size:16
Alignment explanation
Indices: 51391--51468 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 16
51381 AAAGTAAAGC
*
51391 AGTAGAAAAGAGTAAA
1 AGTAGAAAGGAGTAAA
**
51407 AGTA-AAAGGAGTACTC
1 AGTAGAAAGGAGTA-AA
*
51423 AGTAGAAGGGAGTAAA
1 AGTAGAAAGGAGTAAA
* *
51439 AGTA-AAAGAAGTAATT
1 AGTAGAAAGGAGTAA-A
*
51455 AGTATAAAGGAGTA
1 AGTAGAAAGGAGTA
51469 GAGGTGAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 16 0.33
16 16 0.33
17 16 0.33
ACGTcount: A:0.53, C:0.03, G:0.27, T:0.18
Consensus pattern (16 bp):
AGTAGAAAGGAGTAAA
Found at i:51436 original size:32 final size:32
Alignment explanation
Indices: 51390--51696 Score: 125
Period size: 32 Copynumber: 8.9 Consensus size: 32
51380 AAAAGTAAAG
*
51390 CAGTAGAAAAGAGTAAAAGTAAAAGGAGTACT
1 CAGTAGAAAAGAGTAAAAGTAAAAGAAGTACT
** *
51422 CAGTAGAAGGGAGTAAAAGTAAAAGAAGTAAT
1 CAGTAGAAAAGAGTAAAAGTAAAAGAAGTACT
* * * * * * *
51454 TAGTATAAAGGAGTAGAGGTGAAAGAAGTAAT
1 CAGTAGAAAAGAGTAAAAGTAAAAGAAGTACT
* * *
51486 CAGAAAATTGGTAATTAAGAGTAAAAGTAAAAGGAGTAAT
1 CAG-----TAG-AA--AAGAGTAAAAGTAAAAGAAGTACT
*
51526 CAGTAGAAGTAAAAGAGTAAAAGTAAAAGAAGTAGT
1 CAGT---AG-AAAAGAGTAAAAGTAAAAGAAGTACT
* * * * *
51562 -AGAAGTGAAAGAGTAAAAGAAAAAAGGAGTAAT
1 CAGTAG-AAAAGAGTAAAAG-TAAAAGAAGTACT
* ** *
51595 CAATCGAAGTAAAAGAGTAAAAGTAAAAGAAACAAT
1 C-A--GTAG-AAAAGAGTAAAAGTAAAAGAAGTACT
* * * *
51631 CAGCAGAATGAAGTAAAAGTAAAAGTAAGAGAATTAAT
1 CAGTAGAA--AAG----AGTAAAAGTAAAAGAAGTACT
51669 CAGT--AAAAGAGTAAAAGTAAAAGAAGTA
1 CAGTAGAAAAGAGTAAAAGTAAAAGAAGTA
51697 AGCAGAAAAT
Statistics
Matches: 215, Mismatches: 38, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
30 17 0.08
32 73 0.34
33 13 0.06
34 6 0.03
35 5 0.02
36 34 0.16
37 18 0.08
38 27 0.13
40 22 0.10
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.17
Consensus pattern (32 bp):
CAGTAGAAAAGAGTAAAAGTAAAAGAAGTACT
Found at i:51535 original size:22 final size:21
Alignment explanation
Indices: 51505--51554 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
51495 GGTAATTAAG
51505 AGTAAAAGTAAAAGGAGTAATC
1 AGTAAAAGTAAAA-GAGTAATC
* *
51527 AGTAGAAGTAAAAGAGTAA-A
1 AGTAAAAGTAAAAGAGTAATC
51547 AGTAAAAG
1 AGTAAAAG
51555 AAGTAGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 6 0.24
22 12 0.48
ACGTcount: A:0.58, C:0.02, G:0.24, T:0.16
Consensus pattern (21 bp):
AGTAAAAGTAAAAGAGTAATC
Found at i:51549 original size:14 final size:14
Alignment explanation
Indices: 51527--51584 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
51517 AGGAGTAATC
*
51527 AGTAGAAGTAAAAG
1 AGTAAAAGTAAAAG
51541 AGTAAAAGTAAAAG
1 AGTAAAAGTAAAAG
*
51555 AAGTAGTAGAAGTGAAAG
1 -AGTA--A-AAGTAAAAG
51573 AGTAAAAG-AAAA
1 AGTAAAAGTAAAA
51585 AAGGAGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.08
14 16 0.43
15 5 0.14
17 5 0.14
18 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (14 bp):
AGTAAAAGTAAAAG
Found at i:51646 original size:69 final size:68
Alignment explanation
Indices: 51502--51693 Score: 207
Period size: 69 Copynumber: 2.8 Consensus size: 68
51492 ATTGGTAATT
* * * ** *
51502 AAGAGTAAAAG-TAAAAGGAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAAAAGAAGTAGTAGAA
1 AAGAGTAAAAGAAAAAAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAAAAGAAACAATAGAA
51566 GTGA
66 G-GA
*
51570 AAGAGTAAAAGAAAAAAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAAAAGAAACAATCAGC
1 AAGAGTAAAAGAAAAAAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAAAAGAAACAAT-AGA
51635 A-GA
65 AGGA
* *
51638 ATGAAGTAAAAGTAAAAGTAA-GAG-AATTAATC--AGTAAAAGAGTAAAAGTAAAAGAA
1 AAG-AGTAAAAG-AAAA--AAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAAAAGAA
51694 GTAAGCAGAA
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
68 39 0.36
69 51 0.47
70 14 0.13
71 3 0.03
72 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (68 bp):
AAGAGTAAAAGAAAAAAGGAGTAATCAATCGAAGTAAAAGAGTAAAAGTAAAAGAAACAATAGAA
GGA
Found at i:51657 original size:38 final size:37
Alignment explanation
Indices: 51600--51691 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 37
51590 GTAATCAATC
*
51600 GAAGTAAAAGAGTAAAAGTAAAAGAAACAATCAGCAGAAT
1 GAAGT-AAA-AGTAAAAGTAAAAGAAACAATCAGCA-AAA
* ** *
51640 GAAGTAAAAGTAAAAGTAAGAGAATTAATCAGTAAAA
1 GAAGTAAAAGTAAAAGTAAAAGAAACAATCAGCAAAA
51677 G-AGTAAAAGTAAAAG
1 GAAGTAAAAGTAAAAG
51692 AAGTAAGCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 14 0.30
37 3 0.06
38 22 0.47
39 3 0.06
40 5 0.11
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.15
Consensus pattern (37 bp):
GAAGTAAAAGTAAAAGTAAAAGAAACAATCAGCAAAA
Found at i:51689 original size:14 final size:15
Alignment explanation
Indices: 51647--51697 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
51637 AATGAAGTAA
*
51647 AAGTAAAAGTAAGAG
1 AAGTAAAAGTAAAAG
* *
51662 AATTAATCAGTAAAAG
1 AAGTAA-AAGTAAAAG
51678 -AGTAAAAGTAAAAG
1 AAGTAAAAGTAAAAG
51692 AAGTAA
1 AAGTAA
51698 GCAGAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.28
15 14 0.48
16 7 0.24
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.18
Consensus pattern (15 bp):
AAGTAAAAGTAAAAG
Found at i:51715 original size:30 final size:30
Alignment explanation
Indices: 51648--51705 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
51638 ATGAAGTAAA
* * *
51648 AGTAAAAGTAAGAGAATTAATCAGTAAAAG
1 AGTAAAAGTAAAAGAAGTAAGCAGTAAAAG
51678 AGTAAAAGTAAAAGAAGTAAGCAG-AAAA
1 AGTAAAAGTAAAAGAAGTAAGCAGTAAAA
51706 TTGGTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.60, C:0.03, G:0.21, T:0.16
Consensus pattern (30 bp):
AGTAAAAGTAAAAGAAGTAAGCAGTAAAAG
Found at i:51764 original size:15 final size:15
Alignment explanation
Indices: 51709--51766 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
51699 CAGAAAATTG
*
51709 GTAAAAGGGAGTAAAA
1 GTAAAA-GGAGTAATA
*
51725 G-AAGAAGAAGTAATCA
1 GTAA-AAGGAGTAAT-A
51741 GTAAAAAGGAGTAATA
1 GT-AAAAGGAGTAATA
51757 GTAAAAGGAG
1 GTAAAAGGAG
51767 AAACAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 16 0.46
16 8 0.23
17 9 0.26
18 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (15 bp):
GTAAAAGGAGTAATA
Found at i:55891 original size:15 final size:15
Alignment explanation
Indices: 55830--55883 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
55820 CATTTTCGGC
* *
55830 AATAAAAAAATTAAA
1 AATAAGAAAATAAAA
*
55845 AATTA-AAAA-AAAA
1 AATAAGAAAATAAAA
*
55858 CATAAGAAAATAAAA
1 AATAAGAAAATAAAA
55873 AATAAGAAAAT
1 AATAAGAAAAT
55884 GACAAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.17
Consensus pattern (15 bp):
AATAAGAAAATAAAA
Found at i:58363 original size:22 final size:22
Alignment explanation
Indices: 58323--58415 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 22
58313 CTGATTATTC
58323 TTTACT-TTGTACTGATTACTAT
1 TTTACTCTTGTA-TGATTACTAT
58345 TTTACTCTTGT-TGATTTACCT-T
1 TTTACTCTTGTATGA-TTA-CTAT
* *
58367 CTTACT-TTTTAGTGATTACTAT
1 TTTACTCTTGTA-TGATTACTAT
* *
58389 TTTACTCTT-TACTAATTACCAT
1 TTTACTCTTGTA-TGATTACTAT
58411 TTTAC
1 TTTAC
58416 CCTTTCAGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
21 8 0.14
22 39 0.67
23 11 0.19
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTACTCTTGTATGATTACTAT
Found at i:58700 original size:16 final size:16
Alignment explanation
Indices: 58679--58740 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
58669 GACTCTTTAA
58679 TTACTGATTACTCAAT
1 TTACTGATTACTCAAT
**
58695 TTACTGATTACTATCTTT
1 TTACTGATTAC--TCAAT
*
58713 TTACCTGATTACT-GAT
1 TTA-CTGATTACTCAAT
58729 TTACTGATTACT
1 TTACTGATTACT
58741 ATTACCTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.23
16 15 0.38
17 1 0.03
18 6 0.15
19 8 0.21
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (16 bp):
TTACTGATTACTCAAT
Found at i:58751 original size:15 final size:16
Alignment explanation
Indices: 58712--58752 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
58702 TTACTATCTT
58712 TTTACCTGATTACTGA
1 TTTACCTGATTACTGA
58728 TTTA-CTGATTACT-A
1 TTTACCTGATTACTGA
58742 -TTACCTTGATT
1 TTTACC-TGATT
58753 CGTAATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 2 0.09
15 14 0.61
16 4 0.17
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (16 bp):
TTTACCTGATTACTGA
Found at i:58775 original size:71 final size:72
Alignment explanation
Indices: 58685--58821 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 72
58675 TTAATTACTG
* * * * *
58685 ATTACTCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTG
1 ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
58750 ATTCGTA
66 ATTCGTA
* *
58757 ATTA-TCAATTTACCGATTAATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACCTTG
1 ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
58821 A
66 A
58822 CTCTGATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
71 54 0.93
72 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (72 bp):
ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
ATTCGTA
Found at i:58832 original size:55 final size:54
Alignment explanation
Indices: 58771--59138 Score: 574
Period size: 55 Copynumber: 6.7 Consensus size: 54
58761 TCAATTTACC
58771 GATTAATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
1 GATTAATCTCTT-TTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
* *
58826 GATTAATCTCTTCTTACTTGACTACTGATTTACTGATTACTATTACTTTGACTCT
1 GATTAATCTCTT-TTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
* *
58881 GATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACTCT
1 GATTAATCTCTTTT-ACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
* * *
58936 GATTAATCTCGTTTTACTTAATTACTGATTTATTGATTACTATTACCTTGACTTT
1 GATTAATCTC-TTTTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
*
58991 GATTAATCTCTTTTTACTTGACTACTGATTTACTGATTACTATTACCTTGACTCT
1 GATTAATCTC-TTTTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
*
59046 GATTAATCTCTTCTTACTTGACTACTGATTTACTGATTACTATTACCTTGACTCT
1 GATTAATCTCTT-TTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
* *
59101 GATTAATCTCTTTTCACTTAATTACTAATTTACTGATT
1 GATTAATCTCTTTT-ACTTAACTACTGATTTACTGATT
59139 GTTCGGATTG
Statistics
Matches: 294, Mismatches: 15, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
54 6 0.02
55 284 0.97
56 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (54 bp):
GATTAATCTCTTTTACTTAACTACTGATTTACTGATTACTATTACCTTGACTCT
Found at i:60117 original size:49 final size:49
Alignment explanation
Indices: 59995--60130 Score: 152
Period size: 49 Copynumber: 2.8 Consensus size: 49
59985 ACTAATTACT
** * * *
59995 CTAAAAA-TCAATCTTTTGCTCTAAGGTGACATCTTTACTTACTAATCA
1 CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA
** *
60043 CTAAAGTTTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATTA
1 CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA
*
60092 CTAAAAATTCAATC-TTCTA-TCCAAAGATGGCATTTTTAC
1 CTAAAAATTCAATCTTTC-ACT-CAAAGATGACATTTTTAC
60131 AAAAAGCTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 9 0.12
49 65 0.88
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (49 bp):
CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA
Found at i:60917 original size:16 final size:16
Alignment explanation
Indices: 60896--60939 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
60886 TGCTTTTTTT
60896 AAAACCCTAGTTTTCA
1 AAAACCCTAGTTTTCA
* *
60912 AGAACCCTAGATTTCA
1 AAAACCCTAGTTTTCA
60928 AAAACCCTAGTT
1 AAAACCCTAGTT
60940 GCCCTCTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (16 bp):
AAAACCCTAGTTTTCA
Done.