Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold129
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: 3652842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 48564 characters in sequence are not A, C, G, or T
File 2 of 23
Found at i:181861 original size:53 final size:53
Alignment explanation
Indices: 181787--181923 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
181777 CTACTTCCAA
*
181787 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGGTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
181840 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
181893 TGTATCGATACATATTTTTGTGTATCGATAC
1 TGTATCGATACATA-TTTTGTGTATCGATAC
181924 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.81
54 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:181918 original size:20 final size:20
Alignment explanation
Indices: 181893--181963 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
181883 GCCAATGTCT
181893 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTTTTG
**
181913 TGTATCGATAC-TATGCAATT-
1 TGTATCGATACATAT--TTTTG
*
181933 TGTATCGATACAT-TTATATG
1 TGTATCGATACATATT-TTTG
181953 TGTATCGATAC
1 TGTATCGATAC
181964 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.10
20 34 0.83
21 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:182029 original size:21 final size:21
Alignment explanation
Indices: 182003--182043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
181993 GTCAACCTTG
182003 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
182024 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
182044 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:182678 original size:31 final size:31
Alignment explanation
Indices: 182631--182691 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
182621 ACCAATATTC
* *
182631 TTCAATGTTTTTAGTTTCTTCCTTTATAACT
1 TTCAATATTTTCAGTTTCTTCCTTTATAACT
182662 TTCAATATTTTCAGTTTCTTCCTTTATAAC
1 TTCAATATTTTCAGTTTCTTCCTTTATAAC
182692 AAATAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (31 bp):
TTCAATATTTTCAGTTTCTTCCTTTATAACT
Found at i:183702 original size:13 final size:13
Alignment explanation
Indices: 183684--183708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183674 ACTGAAGCAA
183684 TGTATCGATACAT
1 TGTATCGATACAT
183697 TGTATCGATACA
1 TGTATCGATACA
183709 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:187350 original size:13 final size:13
Alignment explanation
Indices: 187332--187357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187322 CTATTTATGA
187332 TGTATCGATACAC
1 TGTATCGATACAC
187345 TGTATCGATACAC
1 TGTATCGATACAC
187358 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:187495 original size:22 final size:22
Alignment explanation
Indices: 187440--187495 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
187430 ACAGTGATCT
187440 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
187462 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
187483 ATGAACAGTGATG
1 ATGAACAGTGATG
187496 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:187502 original size:10 final size:10
Alignment explanation
Indices: 187483--187513 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
187473 GTATCGATAC
187483 ATGAACAGTG
1 ATGAACAGTG
*
187493 ATGAATAGTG
1 ATGAACAGTG
187503 ATGAACAGTG
1 ATGAACAGTG
187513 A
1 A
187514 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:187611 original size:53 final size:53
Alignment explanation
Indices: 187537--187673 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
187527 CTACTTCCAA
*
187537 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGGTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
187590 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
187643 TGTATCGATACATATTTTTGTGTATCGATAC
1 TGTATCGATACATA-TTTTGTGTATCGATAC
187674 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 63 0.81
54 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:187668 original size:20 final size:20
Alignment explanation
Indices: 187643--187713 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
187633 GCCAATGTCT
187643 TGTATCGATACATATTTTTG
1 TGTATCGATACATATTTTTG
**
187663 TGTATCGATAC-TATGCAATT-
1 TGTATCGATACATAT--TTTTG
*
187683 TGTATCGATACAT-TTATATG
1 TGTATCGATACATATT-TTTG
187703 TGTATCGATAC
1 TGTATCGATAC
187714 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.10
20 34 0.83
21 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:187779 original size:21 final size:21
Alignment explanation
Indices: 187753--187793 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
187743 GTCAACCTTG
187753 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
187774 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
187794 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:189252 original size:52 final size:50
Alignment explanation
Indices: 189127--189522 Score: 222
Period size: 52 Copynumber: 7.6 Consensus size: 50
189117 TTAAGTTTCT
* * * * * **
189127 CAATTGTTCATAATCGGGGATAATCCAACCTCGGTTTTATTTTTAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACC-CGATTTTATTTCCAAAACAC
* **
189178 CAATTTTCCTTTAATC-AGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGA-GGATACTCCAAC-CCGATTTTATTTCC-AAAACAC
* * ******* *
189231 CAATTTTTCACAATCGAGGATACTTCAACCTCGTTATTTCATCGGGGCTACTC
1 CAATTTTTCACAATCGAGGATACTCCAACC-CG--ATTTTATTTCCAAAACAC
* * * * * * *
189284 CAACCCTGTT-AC-CTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATAT
1 CAA--TTTTTCACAAT-CGA--GGATACTCCAACCCGA-TTTTATTTCCAAAACAC
* * * * * * *
189338 TAATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTTTTTCTAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACC-CGATTTTATTTCCAAAACAC
* * * * *
189389 TAATTTTCCACAATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCGA-TTTTATTTCCAAAACAC
* **
189440 CAATTTTCCTTTAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGAGGATACTCCAAC-CCGATTTTATTTCC-AAAACAC
189493 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTTCACAATCGAGGATACTCCAACC
189523 TCGTTATTTC
Statistics
Matches: 255, Mismatches: 69, Indels: 42
0.70 0.19 0.11
Matches are distributed among these distances:
50 1 0.00
51 83 0.33
52 90 0.35
53 46 0.18
54 19 0.07
55 4 0.02
56 12 0.05
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.33
Consensus pattern (50 bp):
CAATTTTTCACAATCGAGGATACTCCAACCCGATTTTATTTCCAAAACAC
Found at i:189364 original size:51 final size:51
Alignment explanation
Indices: 189302--189522 Score: 239
Period size: 51 Copynumber: 4.3 Consensus size: 51
189292 TTACCTCCGA
* * ** *
189302 GGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTAA-TTTCTCATAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTC-CACAATC
* * * * *
189353 GGGGATACTCCAACCTCGGTTTTTTTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATC
* **
189404 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCC-ACAATC
* * *
189456 GAGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCAG-TTTTATTTCC-AAAACACCAATTTTCCACAATC
*
189508 GAGGATACTCCAACC
1 GGGGATACTCCAACC
189523 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
51 78 0.55
52 50 0.35
53 15 0.10
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:189429 original size:102 final size:104
Alignment explanation
Indices: 189302--189522 Score: 279
Period size: 104 Copynumber: 2.1 Consensus size: 104
189292 TTACCTCCGA
* ** *
189302 GGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTAA-TTT-CTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCAATTTTCCT-ATAATCGAGGATACTCCA
* * * *
189365 AC-CTCGGTTTT-TTTTCTAAAACACTAATTTTCCACAATC
65 ACTC-CGATTTTATTTCCAAAAACACCAATTTTCCACAATC
* * *
189404 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCAATTTTCCTATAATCGAGGATACTCCAA
*
189469 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATC
66 CTCCGATTTTATTTCCAAAAACACCAATTTTCCACAATC
*
189508 GAGGATACTCCAACC
1 GGGGATACTCCAACC
189523 TCGTTATTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
102 34 0.33
103 27 0.26
104 41 0.40
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (104 bp):
GGGGATACTCCAACCCCAGCTTTATTTCCAAAACACCAATTTTCCTATAATCGAGGATACTCCAA
CTCCGATTTTATTTCCAAAAACACCAATTTTCCACAATC
Found at i:189608 original size:262 final size:262
Alignment explanation
Indices: 189138--189629 Score: 860
Period size: 262 Copynumber: 1.9 Consensus size: 262
189128 AATTGTTCAT
* * *
189138 AATCGGGGATAATCCAACCTCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATCAGGGATACT
1 AATCGGGGATAATCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
*
189203 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTTCAACCTCGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
* *
189268 TTCATCGGGGCTACTCCAACCCTGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
131 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
189333 AATATTAATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTTTTTCTAAAACACTAATTTTCC
196 AATATTAATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTTTTTCTAAAACACTAATTTTCC
189398 AC
261 AC
*
189400 AATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC-GAGGATAC
1 AATCGGGGATAATCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATCAG-GGATAC
189464 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
65 TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
* * *
189529 TTTCATCGGGGATGCTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCCCGGCTTTATTTCCA
130 TTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCA
* *
189594 AAATATTGATTTCTCATAATTGGGGATACTCCAACC
195 AAATATTAATTTCTCATAATCGGGGATACTCCAACC
189630 CCGTTATTTC
Statistics
Matches: 217, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
261 1 0.00
262 216 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (262 bp):
AATCGGGGATAATCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
AATATTAATTTCTCATAATCGGGGATACTCCAACCTCGGTTTTTTTTCTAAAACACTAATTTTCC
AC
Found at i:189667 original size:79 final size:79
Alignment explanation
Indices: 189535--189716 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 79
189525 GTTATTTCAT
* ** * **
189535 CGGGGATGCTCCAACCCCGTTACCTCCGAGGGGATACTCTAACCCCGGCTTTATTTCCAAAAT-A
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTTCC-AAATCA
** * *
189599 TTGATTTCTCATAAT
65 TCAATTTCTCACAAC
* * * * *
189614 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCTCAATTTTATTTCCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTTCCAAATCAT
*
189679 CAATTTTTCACAAC
66 CAATTTCTCACAAC
189693 CGGGGATACTCCAACCCCGTTATT
1 CGGGGATACTCCAACCCCGTTATT
189717 ATCTCCAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 3 0.04
79 82 0.96
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTTCCAAATCAT
CAATTTCTCACAAC
Found at i:192221 original size:52 final size:53
Alignment explanation
Indices: 192152--192489 Score: 256
Period size: 51 Copynumber: 6.6 Consensus size: 53
192142 TTAAGTTTCT
* * * *
192152 CAATTTTTCATAATCGGGGATACTCCAACCT-CGGTTTTATTT-TTAAAACAC
1 CAATTTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
* * * *
192203 CAATTTTCCTTTAATCGGGGATACT-CAAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
* * * ***** *
192256 CAATTTTTCACAATCGAGGATACTTCAACCT-CG---TTATTTCATCGGGGCTC
1 CAATTTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTC-TAAAAACAC
* * **
192306 CAACCTGTTACC-T--CCGAGGATACTCCAA-CTCCGATTTTATTT-TTGAAACAC
1 CAA--T-TTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
* * *
192357 CAATTTTCCACAATCGAGGATACTCCAACC-CCGGTTTTATTT-TCAAAACAC
1 CAATTTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
* * *
192408 AAATTTTCTATAATCGAGGATACTCCAA-CTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
* * *
192460 CAATTTTTCACAATCGGGGATACTCCAACC
1 CAATTTTCCATAATCGAGGATACTCCAACC
192490 CCGTTAATCA
Statistics
Matches: 223, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
48 4 0.02
49 10 0.04
50 21 0.09
51 88 0.39
52 70 0.31
53 30 0.13
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (53 bp):
CAATTTTCCATAATCGAGGATACTCCAACCTCCGATTTTATTTCTAAAAACAC
Found at i:193064 original size:79 final size:79
Alignment explanation
Indices: 192499--193020 Score: 803
Period size: 79 Copynumber: 6.6 Consensus size: 79
192489 CCCGTTAATC
* * *
192499 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCAGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
192564 ATTGATTTCTCATA
66 ATTGATTTCTCACA
* * *
192578 ATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
192643 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* *
192657 ATCGGGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
192722 ATTGATTTCTCACA
66 ATTGATTTCTCACA
*
192736 ATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
192801 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* * * *
192815 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATGCTCCAACCTCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
192880 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* * * * *
192894 ATCGGGGATACTCTAACCCCATTATTTCCGTGGGG-TACTCTAACCACGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
192958 ATTGATTTCTCATA
66 ATTGATTTCTCACA
** * ** *
192972 ATTAGGGATACTCCCACCCTATTATTTCCAAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
193021 ATTTTATTTC
Statistics
Matches: 406, Mismatches: 36, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
78 66 0.16
79 340 0.84
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
ATTGATTTCTCACA
Found at i:204871 original size:10 final size:10
Alignment explanation
Indices: 204858--204907 Score: 64
Period size: 11 Copynumber: 4.7 Consensus size: 10
204848 AAAAAGAGAC
204858 AAAAAAAACA
1 AAAAAAAACA
*
204868 AAAAACAAAAA
1 AAAAA-AAACA
204879 AAACAAAAACA
1 AAA-AAAAACA
204890 AAAAAAAACA
1 AAAAAAAACA
204900 ACAAAAAA
1 A-AAAAAA
204908 GGGTCCGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 13 0.37
11 20 0.57
12 2 0.06
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:204898 original size:25 final size:25
Alignment explanation
Indices: 204843--204907 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
204833 CGTCCTCCGT
* *
204843 AAAAAA-AAAAGAGACAAAAAAAAC
1 AAAAAACAAAAAAAACAAAAAAAAC
204867 AAAAAACAAAAAAAACAAAAACAAA-
1 AAAAAACAAAAAAAACAAAAA-AAAC
204892 AAAAAACAACAAAAAA
1 AAAAAACAA-AAAAAA
204908 GGGTCCGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 6 0.17
25 21 0.58
26 9 0.25
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (25 bp):
AAAAAACAAAAAAAACAAAAAAAAC
Found at i:204900 original size:16 final size:16
Alignment explanation
Indices: 204843--204896 Score: 76
Period size: 15 Copynumber: 3.5 Consensus size: 16
204833 CGTCCTCCGT
* *
204843 AAAAAAAA-AAGAGAC
1 AAAAAAAACAAAAAAC
204858 AAAAAAAACAAAAAAC
1 AAAAAAAACAAAAAAC
204874 AAAAAAAAC-AAAAAC
1 AAAAAAAACAAAAAAC
204889 AAAAAAAA
1 AAAAAAAA
204897 ACAACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 22 0.61
16 14 0.39
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:206386 original size:28 final size:28
Alignment explanation
Indices: 206339--206549 Score: 136
Period size: 33 Copynumber: 7.1 Consensus size: 28
206329 CATTCCTCAC
* *
206339 CCTTTTCAAAGCCCATAAGTCAGTGGTA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
206367 CCTTTTCGAAGGCCACAAGTTAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
206395 TCTTTTCAAAGCCCACAAGTCGGTGGCACCA
1 CCTTTTCAAAGCCCACAAGTCAGTGG---CA
* * *
206426 CCCCTTTCAAAAGCCCATAAGTCGGTGGCACCA
1 -CCTTTTC-AAAGCCCACAAGTCAGTGG---CA
* *
206459 CCTCTTTCAAAAGCCCATAAGTCGGTGGCA
1 CCT-TTTC-AAAGCCCACAAGTCAGTGGCA
* ** * *
206489 CCCCTTTCAAAGAACACAGGTTAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
206518 -CTTTTCAAAGCCCACAAGACAATGGCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGC-A
206546 CCTT
1 CCTT
206550 CAAAAACCCA
Statistics
Matches: 146, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
27 19 0.13
28 45 0.31
29 18 0.12
30 6 0.04
31 4 0.03
32 7 0.05
33 47 0.32
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (28 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:206441 original size:33 final size:33
Alignment explanation
Indices: 206398--206490 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
206388 AGTGGCATCT
*
206398 TTTC-AAAGCCCACAAGTCGGTGGCACCACCCC
1 TTTCAAAAGCCCATAAGTCGGTGGCACCACCCC
*
206430 TTTCAAAAGCCCATAAGTCGGTGGCACCACCTC
1 TTTCAAAAGCCCATAAGTCGGTGGCACCACCCC
206463 TTTCAAAAGCCCATAAGTCGGTGGCACC
1 TTTCAAAAGCCCATAAGTCGGTGGCACC
206491 CCTTTCAAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 4 0.07
33 54 0.93
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (33 bp):
TTTCAAAAGCCCATAAGTCGGTGGCACCACCCC
Found at i:206655 original size:49 final size:49
Alignment explanation
Indices: 206598--206871 Score: 176
Period size: 49 Copynumber: 5.8 Consensus size: 49
206588 TGATATCACT
* *
206598 GGCCTTGAATCAGCACATTGACACCTTTATCTTTAAGACCAATGTGGCC
1 GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTCGCC
* * * * * *
206647 GGCCTTGAATTAGCACATTGGCACCTTCATCTTTAAGTCCAATATTGCT
1 GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTCGCC
* * * * * * * *
206696 AGCCTTGAATCAGCATATTGGCGCTTTCATCATCTTTAAAACTAAGGTCGTC
1 GGCCTTGAATCAGCACATTGGCACCTT--T-ATCTTTAAGACCAATGTCGCC
* * * *
206748 GGCCTTGAATCAGCACATTGG---C---A----TAAGCCCAATATTGCT
1 GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTCGCC
* * * * * *
206787 AGCCTTGAATCATCATATTGGCACC-TTGTCTTTAAGACCAATGTCACT
1 GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTCGCC
* *
206835 GGCCTTAAATCAGCATATTGGCA-CTTTCATCTTTAAG
1 GGCCTTGAATCAGCACATTGGCACCTTT-ATCTTTAAG
206872 TCTGATATAG
Statistics
Matches: 167, Mismatches: 44, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
39 26 0.16
42 1 0.01
43 1 0.01
47 1 0.01
48 34 0.20
49 72 0.43
52 32 0.19
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (49 bp):
GGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTCGCC
Found at i:206951 original size:188 final size:189
Alignment explanation
Indices: 206599--206959 Score: 431
Period size: 188 Copynumber: 1.9 Consensus size: 189
206589 GATATCACTG
** * *
206599 GCCTTGAATCAGCACATTGACACCTTTATCTTTAAGACCAATGTGGCCGGCCTTGAATTAGCACA
1 GCCTTGAATCAGCACATTGACACCTTTATCTTTAAGACCAATGTCACCGGCCTTAAATCAGCACA
* * **
206664 TTGGCACCTTCATCTTTAAGTCCAATATTGCTAGCCTTGAATCAGCATATTGGCGCTTTCATCAT
66 TTGGCACCTTCATCTTTAAGTCCAATATAGCTAGCCTTGAATAAGCATATTGGCGCTTTCAAAAT
* *
206729 CTTTAAAACTAAGGTCGTCGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTA
131 CTCTAAAACCAAGGTCGTCGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTA
* * * * * *
206788 GCCTTGAATCATCATATTGGCACC-TTGTCTTTAAGACCAATGTCACTGGCCTTAAATCAGCATA
1 GCCTTGAATCAGCACATTGACACCTTTATCTTTAAGACCAATGTCACCGGCCTTAAATCAGCACA
* ** * * *
206852 TTGGCACTTTCATCTTTAAGTCTGATATAGTTGGCCTTGAATAAGCATATTGGCATCTTT-AAAA
66 TTGGCACCTTCATCTTTAAGTCCAATATAGCTAGCCTTGAATAAGCATATTGGC-GCTTTCAAAA
** * * **
206916 T-TCCTAAGCCCAAGGTTGTTGGCCTTGTCTCAGCACATTGGCAT
130 TCT-CTAAAACCAAGGTCGTCGGCCTTGAATCAGCACATTGGCAT
206960 TATTCTTCAA
Statistics
Matches: 142, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
187 1 0.01
188 116 0.82
189 25 0.18
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (189 bp):
GCCTTGAATCAGCACATTGACACCTTTATCTTTAAGACCAATGTCACCGGCCTTAAATCAGCACA
TTGGCACCTTCATCTTTAAGTCCAATATAGCTAGCCTTGAATAAGCATATTGGCGCTTTCAAAAT
CTCTAAAACCAAGGTCGTCGGCCTTGAATCAGCACATTGGCATAAGCCCAATATTGCTA
Found at i:207914 original size:20 final size:20
Alignment explanation
Indices: 207889--208014 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
207879 TTTTAACAAG
207889 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
207909 ATGTATCGATACATCTAGGTAAAAAGACAAA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
207940 ATGTATCGATACCTTGAAGA
1 ATGTATCGATACATTGAAAA
* *
207960 ATGTATCGATACATTCATACA
1 ATGTATCGATACATTGA-AAA
*
207981 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTGAAAA
208001 ATGTATCGATACAT
1 ATGTATCGATACAT
208015 CTAGGTACTT
Statistics
Matches: 87, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
20 46 0.53
21 19 0.22
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 14 0.16
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:207947 original size:51 final size:46
Alignment explanation
Indices: 207882--208021 Score: 148
Period size: 51 Copynumber: 3.0 Consensus size: 46
207872 TGTTTAATTT
*
207882 TAACAAGATGTATCGATACATTGAAAAATGTATCGATACATCTAGG
1 TAACAAAATGTATCGATACATTGAAAAATGTATCGATACATCTAGG
* *
207928 TAAAAAGACAAAATGTATCGATACCTTGAAGAATGTATCGATACAT-TCA--
1 T----A-ACAAAATGTATCGATACATTGAAAAATGTATCGATACATCT-AGG
*
207977 T-AC--AATGTATCGATACATTAAAAAATGTATCGATACATCTAGG
1 TAACAAAATGTATCGATACATTGAAAAATGTATCGATACATCTAGG
208020 TA
1 TA
208022 CTTTTCCATA
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
41 33 0.42
42 1 0.01
43 3 0.04
46 1 0.01
49 1 0.01
50 2 0.03
51 37 0.47
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (46 bp):
TAACAAAATGTATCGATACATTGAAAAATGTATCGATACATCTAGG
Found at i:209013 original size:28 final size:28
Alignment explanation
Indices: 208979--209612 Score: 729
Period size: 28 Copynumber: 22.4 Consensus size: 28
208969 CACTAGCTTA
208979 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
209007 TGAGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
209035 TGGGCTTTGAAAAGATGCCGCTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
209063 TGGGCTTTGAAAAGAGTGCCATTGACTTG
1 TGGGCTTTGAAAGGA-TGCCACTGACTTG
* * *
209092 TGGGATTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
209120 TGAGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAGGA-TGCCACTGACTTG
*
209149 TGGGCTTTGAAAGGGTGCCACTGACTTGCG
1 TGGGCTTTGAAAGGATGCCACTGACTT--G
*
209179 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
209207 TGGGCTTTGAAAGGATGCCACTAACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
**
209235 TGGGCTTTGAAAAAAGTGCCACTGACTTG
1 TGGGCTTTGAAAGGA-TGCCACTGACTTG
*
209264 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
209292 TGGGCTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
209320 TGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
209348 TGGGCTTTGAAAAGG-TGCCACTAACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTG
* * *
209376 TGAGCTTTGAAAGGGTGCCACT-AGCTTC
1 TGGGCTTTGAAAGGATGCCACTGA-CTTG
* * *
209404 TAGGCTTTGAAAAGATGCCATTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * **
209432 TGGGCTTTGAAAAGAGTTGCCAATGACTCA
1 TGGGCTTTG-AAAG-GATGCCACTGACTTG
* *
209462 TGGGCTTTGAAAGGATGCCATTGAGTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
209490 TGGGCTTTGAAA-TAGTGCAACTAACTTA
1 TGGGCTTTGAAAGGA-TGCCACTGACTTG
* *
209518 TGGGCTTTGAAAGGGTGCTACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
209546 TGGGCTTT-AAATGGATGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
* * *
209574 TGGGCTTTAAAAAGG-TACCACTAACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
209602 TGGGCTTTGAA
1 TGGGCTTTGAA
209613 GAAATAAACG
Statistics
Matches: 517, Mismatches: 73, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
27 12 0.02
28 369 0.71
29 85 0.16
30 51 0.10
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:210879 original size:20 final size:20
Alignment explanation
Indices: 210826--210879 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
210816 TCTGGAGCCC
*
210826 TTTTTATTT-TTTTTGCTAT
1 TTTTTTTTTGTTTTTGCTAT
* * * *
210845 TTTTTTCTTGGTTTTGTTGT
1 TTTTTTTTTGTTTTTGCTAT
210865 TTTTTTTTTGTTTTT
1 TTTTTTTTTGTTTTT
210880 TTGGGTATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.04, C:0.04, G:0.11, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTGTTTTTGCTAT
Found at i:218937 original size:13 final size:13
Alignment explanation
Indices: 218919--218943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218909 CATAAAATGT
218919 TGTATCGATACAA
1 TGTATCGATACAA
218932 TGTATCGATACA
1 TGTATCGATACA
218944 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:218941 original size:33 final size:33
Alignment explanation
Indices: 218899--218968 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
218889 TTCAACGATT
218899 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
218932 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
218965 TGTA
1 TGTA
218969 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:219026 original size:13 final size:13
Alignment explanation
Indices: 219008--219032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218998 ATTACTCACA
219008 TGTATCGATACAT
1 TGTATCGATACAT
219021 TGTATCGATACA
1 TGTATCGATACA
219033 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:219097 original size:52 final size:52
Alignment explanation
Indices: 219041--219160 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
219031 CACTGATCTT
*
219041 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
* *
219093 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
219145 TGTATCGATACATGCA
1 TGTATCGATACATGCA
219161 AGAAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
Found at i:226059 original size:15 final size:13
Alignment explanation
Indices: 226041--226122 Score: 76
Period size: 13 Copynumber: 5.9 Consensus size: 13
226031 AGAAGTGATG
*
226041 AAAAAAAAAACAC
1 AAAAAAAAAAAAC
*
226054 ACAAAAAAAAAAC
1 AAAAAAAAAAAAC
226067 AAAAAACACAAAAA-
1 AAAAAA-A-AAAAAC
*
226081 ACAAAAAAACAAAC
1 A-AAAAAAAAAAAC
226095 AAAACAAAAAACAAC
1 AAAA-AAAAAA-AAC
226110 AAACAAAAAAAAA
1 AAA-AAAAAAAAA
226123 AGGTGCAAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
13 23 0.40
14 11 0.19
15 22 0.39
16 1 0.02
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:226063 original size:19 final size:19
Alignment explanation
Indices: 226041--226123 Score: 105
Period size: 19 Copynumber: 4.3 Consensus size: 19
226031 AGAAGTGATG
*
226041 AAAAAAAAAACACACAAAA
1 AAAAAAAAAACAAACAAAA
226060 AAAAAACAAAA-AACACAAAA
1 AAAAAA-AAAACAA-ACAAAA
*
226080 AACAAAAAAACAAACAAAA
1 AAAAAAAAAACAAACAAAA
* *
226099 CAAAAAACAACAAACAAAA
1 AAAAAAAAAACAAACAAAA
226118 AAAAAA
1 AAAAAA
226124 GGTGCAAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
19 38 0.69
20 17 0.31
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAACAAACAAAA
Found at i:226086 original size:24 final size:24
Alignment explanation
Indices: 226041--226119 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
226031 AGAAGTGATG
*
226041 AAAA-AAAAAACAC-ACAAA-AAA
1 AAAACAAAAAACACAAAAAACAAA
226062 AAAACAAAAAACACAAAAAACAAA
1 AAAACAAAAAACACAAAAAACAAA
226086 AAAACAAACAAA-ACAAAAAAC-AA
1 AAAACAAA-AAACACAAAAAACAAA
*
226109 CAAACAAAAAA
1 AAAACAAAAAA
226120 AAAAGGTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
21 4 0.08
22 12 0.23
23 13 0.25
24 20 0.38
25 3 0.06
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAACAAAAAACACAAAAAACAAA
Found at i:226104 original size:40 final size:39
Alignment explanation
Indices: 226044--226121 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
226034 AGTGATGAAA
* *
226044 AAAAAAACACACAAAAAAAAAACAAAAAACACAAAAAAC
1 AAAAAAACAAACAAAAAAAAAACAAAAAACAAAAAAAAC
*
226083 AAAAAAACAAACAAAACAAAAAACAACAAACAAAAAAAA
1 AAAAAAACAAACAAAA-AAAAAACAAAAAACAAAAAAAA
226122 AAGGTGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 15 0.43
40 20 0.57
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (39 bp):
AAAAAAACAAACAAAAAAAAAACAAAAAACAAAAAAAAC
Found at i:226393 original size:16 final size:16
Alignment explanation
Indices: 226362--226393 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
226352 TGTTCTTTTC
*
226362 CAAAAAAGAAACAAAA
1 CAAAAAAGAAAAAAAA
226378 CAAAAAAGAAAAAAAA
1 CAAAAAAGAAAAAAAA
226394 GAGAGGAAAA
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:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAAAAAAA
Found at i:227378 original size:31 final size:31
Alignment explanation
Indices: 227340--227422 Score: 157
Period size: 31 Copynumber: 2.7 Consensus size: 31
227330 ATACCTTTTT
*
227340 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
227371 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
227402 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
227423 TCTTTTCCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:227478 original size:34 final size:33
Alignment explanation
Indices: 227402--227698 Score: 357
Period size: 34 Copynumber: 8.7 Consensus size: 33
227392 ATCTCTGCTC
* * * * *
227402 AAAGTCCACGACTCAGTGGCATC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
227434 AAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTT
*
227469 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTT
227502 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--C-TTTT
*
227539 AAAGCCCACAACTCCGTGGCACCTTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACC-T-TTTT-CTTTT
* *
227575 -AAGCCCACAACTCCGTGGCACCTTCTTCTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTT-T
*
227608 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
227641 CAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
227675 AAAGCCCACAACTCTGTGGCACCT
1 AAAGCCCACAACTCCGTGGCACCT
227699 ACAACTCTGT
Statistics
Matches: 236, Mismatches: 17, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
32 21 0.09
33 34 0.14
34 111 0.47
35 31 0.13
36 4 0.02
37 31 0.13
38 4 0.02
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:227517 original size:68 final size:67
Alignment explanation
Indices: 227431--227822 Score: 367
Period size: 68 Copynumber: 5.4 Consensus size: 67
227421 CATCTTTTCC
* *
227431 TTTAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACCTTTT
227495 TCTT
64 TCTT
227499 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C-TTTTAAAGCCCACAACTCCGTGGCACC-T
*
227564 CTTTTCCT
61 -TTTTCTT
* * * *
227572 TCT-AAGCCCACAACTCCGTGGCACCTTCTTCTTTCCAAAGCCCACAACTCCGTGGCACCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTT-TAAAGCCCACAACTCCGTGGCACCTTTTT
227636 CTT
65 CTT
* *
227639 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCTACAAC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCT-----
227704 TCTGTGGCACTCTT
61 T-T-T-----TCTT
*
227718 TTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCA
1 TTT--------AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCA
*
227783 CTCTTTTTCCCT
58 C-CTTTTT-CTT
* *
227795 TTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT
227823 CTCCATTCCT
Statistics
Matches: 272, Mismatches: 22, Indels: 60
0.77 0.06 0.17
Matches are distributed among these distances:
67 29 0.11
68 81 0.30
69 29 0.11
70 3 0.01
71 28 0.10
72 23 0.08
73 8 0.03
74 1 0.00
76 1 0.00
77 5 0.02
79 6 0.02
81 1 0.00
82 1 0.00
83 1 0.00
87 53 0.19
88 2 0.01
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (67 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
TT
Found at i:227742 original size:54 final size:50
Alignment explanation
Indices: 227649--227750 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 50
227639 TTCAAAGCCC
*
227649 ACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACCT
1 ACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCT
*
227699 ACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 ACAACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCAC
227751 TTTTTTCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.30
51 6 0.13
53 5 0.11
54 21 0.46
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (50 bp):
ACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCT
Found at i:227758 original size:87 final size:84
Alignment explanation
Indices: 227615--227783 Score: 275
Period size: 87 Copynumber: 2.0 Consensus size: 84
227605 TCCAAAGCCC
227615 ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGC
1 ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGC
*
227680 CCACAACTCTGTGGCACCT
66 CCACAACTCCGTGGCACCT
* * *
227699 ACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAA
1 ACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAA
227764 AGCCCACAACTCCGTGGCAC
63 AGCCCACAACTCCGTGGCAC
227784 TCTTTTTCCC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
84 14 0.18
85 5 0.06
87 59 0.76
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (84 bp):
ACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGC
CCACAACTCCGTGGCACCT
Found at i:227771 original size:33 final size:35
Alignment explanation
Indices: 227699--227842 Score: 179
Period size: 33 Copynumber: 4.1 Consensus size: 35
227689 TGTGGCACCT
*
227699 ACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 ACAACTCCGTGGCACTCTTTTT-CCTTTT-AAAGCCC
227736 ACAACTCCGTGGCACT-TTTTT-CTTTTAAAGCCC
1 ACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCC
*
227769 ACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCC
1 ACAACTCCGTGGCACTCTTTTT-CCTTTTAAAGCCC
* *
227804 ACAACTCCGTGGCA-TCTTTCTCCATTCCTAAAGCCC
1 ACAACTCCGTGGCACTCTTTTTCC-TT-TTAAAGCCC
227840 ACA
1 ACA
227843 CAAGTCGGTG
Statistics
Matches: 96, Mismatches: 5, Indels: 13
0.84 0.04 0.11
Matches are distributed among these distances:
33 25 0.26
34 18 0.19
35 20 0.21
36 18 0.19
37 15 0.16
ACGTcount: A:0.21, C:0.35, G:0.11, T:0.33
Consensus pattern (35 bp):
ACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCC
Found at i:227789 original size:35 final size:35
Alignment explanation
Indices: 227699--227842 Score: 177
Period size: 35 Copynumber: 4.1 Consensus size: 35
227689 TGTGGCACCT
*
227699 ACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCC
1 ACAACTCCGTGGCA-TCTTTTTCCCTTTT-AAAGCCC
*
227736 ACAACTCCGTGGCA-CTTTTT-TCTTTTAAAGCCC
1 ACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCC
*
227769 ACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCC
1 ACAACTCCGTGGCA-TCTTTTTCCCTTTTAAAGCCC
* * *
227804 ACAACTCCGTGGCATCTTTCTCCATTCCTAAAGCCC
1 ACAACTCCGTGGCATCTTTTTCCCTT-TTAAAGCCC
227840 ACA
1 ACA
227843 CAAGTCGGTG
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
33 21 0.22
34 15 0.16
35 32 0.34
36 13 0.14
37 13 0.14
ACGTcount: A:0.21, C:0.35, G:0.11, T:0.33
Consensus pattern (35 bp):
ACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCC
Found at i:227870 original size:33 final size:35
Alignment explanation
Indices: 227828--227896 Score: 124
Period size: 33 Copynumber: 2.0 Consensus size: 35
227818 TCTTTCTCCA
227828 TTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTTC
1 TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
227862 TTCC-AAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
227896 T
1 T
227897 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 24 0.71
34 10 0.29
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.20
Consensus pattern (35 bp):
TTCCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:228005 original size:43 final size:43
Alignment explanation
Indices: 227943--228259 Score: 391
Period size: 43 Copynumber: 7.1 Consensus size: 43
227933 CACCTTCATC
*
227943 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
* * * *
227986 TTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCCTCTTCAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG---C-AC-T
* * *
228034 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
* *
228078 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C-T
* *
228126 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
1 -TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
*
228170 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
*
228213 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CT
228257 TTT
1 TTT
228260 CCATCTTTAA
Statistics
Matches: 237, Mismatches: 24, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
43 154 0.65
44 4 0.02
45 2 0.01
46 2 0.01
47 2 0.01
48 1 0.00
49 72 0.30
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACT
Found at i:228058 original size:92 final size:91
Alignment explanation
Indices: 227891--228258 Score: 566
Period size: 92 Copynumber: 4.1 Consensus size: 91
227881 CGGTGGCAAC
*
227891 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC-CCTTCATCTTTAAGTCCAATG
227956 TAGCTGGCCTTGAATCAGCACATTGGCA
64 TAGCTGGCCTTGAATCAGCACATTGGCA
* * *
227984 CTTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCCTCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCC-CTTCATCTTTAAGTCCAATGT
*
228049 AGCTGGCCTTGACTCAGCACATTGGCA
65 AGCTGGCCTTGAATCAGCACATTGGCA
* *
228076 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC-CCTTCATCTTTAAGTCCAATGT
228141 AGCTGGCCTTGAATCAGCACATTGGCA
65 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
228168 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CACCTTTAAGTCCAATATA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCCCTTCATCTTTAAGTCCAATGTA
*
228228 GCTGGCCTTGAATCAGCATATTGGCA
66 GCTGGCCTTGAATCAGCACATTGGCA
228254 CCTTT
1 CCTTT
228259 TCCATCTTTA
Statistics
Matches: 259, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
86 47 0.18
91 1 0.00
92 208 0.80
93 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (91 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCCCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCA
Found at i:228171 original size:21 final size:21
Alignment explanation
Indices: 228147--228214 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
228137 ATGTAGCTGG
228147 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
228168 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
228190 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
228211 CCTT
1 CCTT
228215 TAAGTCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:228190 original size:24 final size:24
Alignment explanation
Indices: 228163--228233 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
228153 ATCAGCACAT
228163 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
* ** * *
228187 TGG--CCTTGAA-T-CAGCACA-T
1 TGGCACCTTTAAGTCCAATATAGC
228206 TGGCACCTTTAAGTCCAATATAGC
1 TGGCACCTTTAAGTCCAATATAGC
228230 TGGC
1 TGGC
228234 CTTGAATCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 7 0.22
23 4 0.12
24 7 0.22
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (24 bp):
TGGCACCTTTAAGTCCAATATAGC
Found at i:228193 original size:22 final size:22
Alignment explanation
Indices: 228168--228236 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
228158 CACATTGGCA
228168 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
228190 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
228211 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
228233 CCTT
1 CCTT
228237 GAATCAGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:228290 original size:52 final size:53
Alignment explanation
Indices: 228212--228365 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
228202 ACATTGGCAC
228212 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
228264 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
228319 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
228366 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 36 0.42
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:229215 original size:13 final size:13
Alignment explanation
Indices: 229197--229221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229187 CATAAAATGT
229197 TGTATCGATACAA
1 TGTATCGATACAA
229210 TGTATCGATACA
1 TGTATCGATACA
229222 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:229219 original size:33 final size:33
Alignment explanation
Indices: 229177--229246 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
229167 TTCAACGATT
229177 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
229210 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
229243 TGTA
1 TGTA
229247 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:229304 original size:13 final size:13
Alignment explanation
Indices: 229286--229310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229276 ATTACTCACA
229286 TGTATCGATACAT
1 TGTATCGATACAT
229299 TGTATCGATACA
1 TGTATCGATACA
229311 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:229375 original size:52 final size:52
Alignment explanation
Indices: 229319--229443 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
229309 CACTGATCTT
*
229319 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
229371 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
229423 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
229444 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:238663 original size:20 final size:20
Alignment explanation
Indices: 238638--238763 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 20
238628 TTTTAACTAG
238638 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
238658 ATGTATCGATACATCTAGGCAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
*
238689 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* *
238709 ATGTATCGATACATTCG-TAC
1 ATGTATCGATACATT-GAAAA
* * **
238729 TTGTTTCCTTACATTGAAAA
1 ATGTATCGATACATTGAAAA
238749 ATGTATCGATACATT
1 ATGTATCGATACATT
238764 TGGGTACTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 26
0.66 0.12 0.22
Matches are distributed among these distances:
19 1 0.01
20 53 0.67
21 2 0.03
22 1 0.01
23 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 15 0.19
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:240660 original size:20 final size:22
Alignment explanation
Indices: 240618--240662 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
240608 GTAGTGGGTG
* *
240618 TGGGAGCTGCCCGATTGCGACC
1 TGGGAGCTGCCCGATCGCAACC
240640 TGGGAG-TG-CCGATCGCAACC
1 TGGGAGCTGCCCGATCGCAACC
240660 TGG
1 TGG
240663 AGGTGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.16, C:0.29, G:0.38, T:0.18
Consensus pattern (22 bp):
TGGGAGCTGCCCGATCGCAACC
Found at i:246078 original size:19 final size:20
Alignment explanation
Indices: 246054--246104 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
246044 TACAAGCCAA
**
246054 TGTATCGATACAATTTTTG-
1 TGTATCGATACAATACTTGC
246073 TGTATCGATAC-ATACTTGC
1 TGTATCGATACAATACTTGC
246092 TGTATCGATACAA
1 TGTATCGATACAA
246105 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 22 0.79
20 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAATACTTGC
Found at i:246807 original size:36 final size:36
Alignment explanation
Indices: 246764--246836 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
246754 ATAAGGTAAT
246764 TCACGCATTCTCTCCTTTATCTCCCCCATTTATTAA
1 TCACGCATTCTCTCCTTTATCTCCCCCATTTATTAA
*
246800 TCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAA
1 TCACGCATTCTCTCCTTTATCTCCCCCATTTATTAA
246836 T
1 T
246837 AAATCTCCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (36 bp):
TCACGCATTCTCTCCTTTATCTCCCCCATTTATTAA
Found at i:248520 original size:21 final size:21
Alignment explanation
Indices: 248496--248542 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
248486 TTTGATGCTG
248496 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
248516 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
248537 ATTTTG
1 ATTTTG
248543 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:250775 original size:15 final size:15
Alignment explanation
Indices: 250755--250785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
250745 ATTTCGTTTG
*
250755 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
250770 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
250785 G
1 G
250786 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:252619 original size:21 final size:21
Alignment explanation
Indices: 252590--252634 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
252580 AAGTTTTCAT
*
252590 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
252610 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
252632 TTT
1 TTT
252635 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:258037 original size:51 final size:52
Alignment explanation
Indices: 257941--258060 Score: 224
Period size: 51 Copynumber: 2.3 Consensus size: 52
257931 TGAAAAGTTA
*
257941 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
257993 CTGCATGTATCGATACATTT-ATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
258044 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
258061 AAAATCAGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 47 0.70
52 20 0.30
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:258087 original size:13 final size:13
Alignment explanation
Indices: 258069--258093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
258059 CAAAAATCAG
258069 TGTATCGATACAA
1 TGTATCGATACAA
258082 TGTATCGATACA
1 TGTATCGATACA
258094 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:258165 original size:20 final size:20
Alignment explanation
Indices: 258136--258193 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
258126 GCAGTAGCTT
258136 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
258155 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
258175 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
258194 TCATTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:258270 original size:21 final size:21
Alignment explanation
Indices: 258229--258270 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
258219 GTTGGGACCT
*
258229 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
258250 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
258271 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:259243 original size:20 final size:20
Alignment explanation
Indices: 259218--259271 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
259208 GTTACAAACA
* *
259218 ATGTATCGATATAAT-TCATC
1 ATGTATCGATACAATGT-ACC
259238 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
259258 ATGTATCGATACAA
1 ATGTATCGATACAA
259272 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:259344 original size:19 final size:18
Alignment explanation
Indices: 259299--259356 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
259289 GCTTCCAGTT
259299 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
259318 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
259337 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
259356 T
1 T
259357 ATCGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:259358 original size:13 final size:13
Alignment explanation
Indices: 259340--259366 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
259330 TACAATGATC
259340 ATGTATCGATACA
1 ATGTATCGATACA
259353 ATGTATCGATACA
1 ATGTATCGATACA
259366 A
1 A
259367 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:259382 original size:33 final size:32
Alignment explanation
Indices: 259321--259384 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
259311 ACAATTGTCC
* *
259321 ATGTATCGATACAATGATCATGTATCGATACA
1 ATGTATCGATACAAAGATAATGTATCGATACA
259353 ATGTATCGATACAAAGCATAATGTATCGATAC
1 ATGTATCGATACAAAG-ATAATGTATCGATAC
259385 TTCTGGGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATGTATCGATACA
Found at i:265147 original size:17 final size:17
Alignment explanation
Indices: 265125--265158 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
265115 ACTTTCATTC
265125 TCAACTTATATCCCCTT
1 TCAACTTATATCCCCTT
*
265142 TCAACTTCTATCCCCTT
1 TCAACTTATATCCCCTT
265159 AAACCCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (17 bp):
TCAACTTATATCCCCTT
Found at i:269044 original size:158 final size:157
Alignment explanation
Indices: 268873--269209 Score: 385
Period size: 157 Copynumber: 2.1 Consensus size: 157
268863 TTTTGGAGAA
* * **
268873 AAAAT-GGGATTGGAGTATCCCCTCGAAAATAACAAGGTT-GAAGTA-CCTCCGGTGGTGGAAAA
1 AAAATCGGGATTGGAGTATCCCCTCAAAAATAACAAGGTTAG-AGTATCC-CCGATGGTAAAAAA
* *
268935 TCGATGCTTTGA-AAATTAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGACGTTAGAGTATC
64 TCGATG-TTTGAGAAATAAAACCGGGGTTGGAGTAT-CCCTCAAAAATAACAACGTTAGAGTATC
268999 CCCGATAGTGAAAAATCAATGTTTTAAAAAT
127 CCCGATAGTGAAAAATCAATGTTTTAAAAAT
* ** *
269030 AAAATCGGGATTGGAGTATACCCTCAAAAATAACGGGGTTAGAGTATCCCTGATGGTAAAAAATC
1 AAAATCGGGATTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCCGATGGTAAAAAATC
* * * ** * * * *
269095 GGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCTCGGAAATAATAAGGTTGGAGTATCCTCG
66 GATGTTTGAGAAATAAAACCGGGGTTGGAGTATCCCTCAAAAATAACAACGTTAGAGTATCCCCG
* * * *
269160 ATTGTGAAAAATTAGTGTTTTAGAAAT
131 ATAGTGAAAAATCAATGTTTTAAAAAT
* *
269187 AAAATCGGGGTTAGAGTATCCCC
1 AAAATCGGGATTGGAGTATCCCC
269210 GATTGTGAAA
Statistics
Matches: 150, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
157 77 0.51
158 70 0.47
159 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (157 bp):
AAAATCGGGATTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCCGATGGTAAAAAATC
GATGTTTGAGAAATAAAACCGGGGTTGGAGTATCCCTCAAAAATAACAACGTTAGAGTATCCCCG
ATAGTGAAAAATCAATGTTTTAAAAAT
Found at i:269179 original size:78 final size:79
Alignment explanation
Indices: 268873--269209 Score: 346
Period size: 79 Copynumber: 4.3 Consensus size: 79
268863 TTTTGGAGAA
* * * *
268873 AAAAT-GGGATTGGAGTATCCCCTCGAAAATAACAAGGTT-GAAGTA-CCTCCGGTGGTGGAAAA
1 AAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAG-AGTATCCT-CGATGGTGAAAAA
*
268935 TC-GATGCTTT-GAAAAT
64 TCAG-TGTTTTAG-AAAT
* * * * * *
268951 TAAACCGGGGTTGGAGTATCCCCTCAAAAATAACGACGTTAGAGTATCCCCGATAGTGAAAAATC
1 AAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCTCGATGGTGAAAAATC
* *
269016 AATGTTTTAAAAAT
66 AGTGTTTTAGAAAT
* * ** *
269030 AAAATCGGGATTGGAGTATACCCTCAAAAATAACGGGGTTAGAGTATCC-CTGATGGTAAAAAAT
1 AAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCTC-GATGGTGAAAAAT
*
269094 CGGTGTTTTAGAAAT
65 CAGTGTTTTAGAAAT
** * * * *
269109 AAAATCGGGGTTGGAGTAT-CCCTCGGAAATAATAAGGTTGGAGTATCCTCGATTGTGAAAAATT
1 AAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCTCGATGGTGAAAAATC
269173 AGTGTTTTAGAAAT
66 AGTGTTTTAGAAAT
*
269187 AAAATCGGGGTTAGAGTATCCCC
1 AAAATCGGGGTTGGAGTATCCCC
269210 GATTGTGAAA
Statistics
Matches: 215, Mismatches: 36, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
78 69 0.32
79 143 0.67
80 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (79 bp):
AAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCTCGATGGTGAAAAATC
AGTGTTTTAGAAAT
Found at i:269207 original size:51 final size:51
Alignment explanation
Indices: 269143--269256 Score: 151
Period size: 51 Copynumber: 2.2 Consensus size: 51
269133 GGAAATAATA
* * *
269143 AGGTTGGAGTATCCTCGATTGTG-AAAAATT-AGTGTTTTAGAAATAAAATCG
1 AGGTTGGAGTATCCCCGATTGTGAAAAAATTGA-TGTTTGA-AAATAAAACCG
* *
269194 GGGTTAGAGTATCCCCGATTGTGAAAAAATTGATGTTTGAAAATAAAACCG
1 AGGTTGGAGTATCCCCGATTGTGAAAAAATTGATGTTTGAAAATAAAACCG
269245 AGGTTGGAGTAT
1 AGGTTGGAGTAT
269257 TCCCTCAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 40 0.74
52 13 0.24
53 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATTGTGAAAAAATTGATGTTTGAAAATAAAACCG
Found at i:269298 original size:130 final size:129
Alignment explanation
Indices: 269063--269339 Score: 360
Period size: 130 Copynumber: 2.1 Consensus size: 129
269053 TCAAAAATAA
* * * * *
269063 CGGGGTTAGAGTATCCCTGATGGTAAAAAATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTAT
1 CGGGGTTAGAGTATCCCCGATGGTAAAAAATCGATGTTTGAGAAATAAAACCGAGGTTGGAGTAT
* * * * ** * *
269128 CCCTCGGAAATAATAAGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAT
66 CCCTCAGAAATAACAAGGTTGGAGTATCCTCGATTATGAAAAATCAACGTTTTAAAAATAAAAC
* *
269192 CGGGGTTAGAGTATCCCCGATTGTGAAAAAATTGATGTTTGA-AAATAAAACCGAGGTTGGAGTA
1 CGGGGTTAGAGTATCCCCGATGGT-AAAAAATCGATGTTTGAGAAATAAAACCGAGGTTGGAGTA
*
269256 TTCCCTCAGAAATAACGAGGTTGGAGTATCAC-CGATTATGAAAAATCAACGTTTTAAAAATAAA
65 -TCCCTCAGAAATAACAAGGTTGGAGTATC-CTCGATTATGAAAAATCAACGTTTTAAAAATAAA
269320 AC
128 AC
*
269322 CGGAGTTAGAGTATCCCC
1 CGGGGTTAGAGTATCCCC
269340 TCAGAAATAA
Statistics
Matches: 128, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
129 42 0.33
130 85 0.66
131 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (129 bp):
CGGGGTTAGAGTATCCCCGATGGTAAAAAATCGATGTTTGAGAAATAAAACCGAGGTTGGAGTAT
CCCTCAGAAATAACAAGGTTGGAGTATCCTCGATTATGAAAAATCAACGTTTTAAAAATAAAAC
Found at i:269445 original size:80 final size:80
Alignment explanation
Indices: 269195--269459 Score: 365
Period size: 79 Copynumber: 3.3 Consensus size: 80
269185 ATAAAATCGG
* *
269195 GGTTAGAGTATCCCCGATTGTGAAAAA-ATTGATGTTTGAAAATAAAACCGAGGTTGGAGTATTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATATTGATGTTTGAAAATAAAACCGGGGTTGGAGTATTC
269259 CCTCAGAAATAACGA
66 CCTCAGAAATAACGA
* * ** * * * *
269274 GGTTGGAGTATCACCGATTATGAAAAATCAACG-T-TTTAAAAATAAAACCGGAGTTAGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAAT-ATTGATGTTTGAAAATAAAACCGGGGTTGGAGTATT
269337 CCCTCAGAAATAACGA
65 CCCTCAGAAATAACGA
* *
269353 GGTTGGAATATCCCCGATTGTGAAAAATATTGATGTTTGGAAATAAAACCGGGGTTGGAGTATTC
1 GGTTGGAGTATCCCCGATTGTGAAAAATATTGATGTTTGAAAATAAAACCGGGGTTGGAGTATTC
*
269418 CCTCGGAAATAACGA
66 CCTCAGAAATAACGA
*
269433 GGATGGAGTATCCCCGATTGTAGAAAA
1 GGTTGGAGTATCCCCGATTGT-GAAAA
269460 TCGGTATTTT
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
78 2 0.01
79 90 0.57
80 59 0.37
81 7 0.04
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (80 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATATTGATGTTTGAAAATAAAACCGGGGTTGGAGTATTC
CCTCAGAAATAACGA
Found at i:277261 original size:22 final size:23
Alignment explanation
Indices: 277223--277267 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
277213 TTTAAATAAA
277223 TTAAAATTTTTATTAT-ATTAGT
1 TTAAAATTTTTATTATAATTAGT
277245 TTAAAATTTTTGA-TATAATTAGT
1 TTAAAATTTTT-ATTATAATTAGT
277268 GATAGTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
TTAAAATTTTTATTATAATTAGT
Found at i:277732 original size:15 final size:15
Alignment explanation
Indices: 277712--277741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
277702 TAAATTTTTA
277712 TTTAAAATTTTAAAT
1 TTTAAAATTTTAAAT
*
277727 TTTAAATTTTTAAAT
1 TTTAAAATTTTAAAT
277742 GTTTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAAATTTTAAAT
Found at i:278298 original size:11 final size:10
Alignment explanation
Indices: 278275--278344 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
278265 TTAATGTATA
278275 AATA-TTTTT
1 AATATTTTTT
278284 AATATTTTGTT
1 AATATTTT-TT
278295 AATAAATATTTTT
1 AAT--AT-TTTTT
278308 AATATTTTATT
1 AATATTTT-TT
** *
278319 AATAAATATT
1 AATATTTTTT
278329 -ATATTTTTT
1 AATATTTTTT
278338 AATATTT
1 AATATTT
278345 ATATTAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
9 10 0.21
10 14 0.29
11 14 0.29
13 7 0.15
14 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (10 bp):
AATATTTTTT
Found at i:278300 original size:24 final size:24
Alignment explanation
Indices: 278272--278328 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
278262 GGCTTAATGT
*
278272 ATAAATATTTTTAATATTTTGTTA
1 ATAAATATTTTTAATATTTTATTA
278296 ATAAATATTTTTAATATTTTATTA
1 ATAAATATTTTTAATATTTTATTA
278320 ATAAATATT
1 ATAAATATT
278329 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATAAATATTTTTAATATTTTATTA
Found at i:278328 original size:15 final size:15
Alignment explanation
Indices: 278308--278355 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
278298 AAATATTTTT
278308 AATATTTTATTAATA
1 AATATTTTATTAATA
* ** *
278323 AATATTATATTTTTT
1 AATATTTTATTAATA
278338 AATATTTATATTAATA
1 AATATTT-TATTAATA
278354 AA
1 AA
278356 ATAATATTCT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTTTATTAATA
Found at i:278339 original size:30 final size:30
Alignment explanation
Indices: 278299--278363 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
278289 TTTGTTAATA
278299 AATA-TTTTTAATATTT-TATTAATAAATAT
1 AATATTTTTTAATATTTATATTAATAAA-AT
*
278328 TATATTTTTTAATATTTATATTAATAAAAT
1 AATATTTTTTAATATTTATATTAATAAAAT
278358 AATATT
1 AATATT
278364 CTACAAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 19 0.59
31 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATATTTTTTAATATTTATATTAATAAAAT
Found at i:278353 original size:31 final size:29
Alignment explanation
Indices: 278275--278363 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 29
278265 TTAATGTATA
*
278275 AATA-TTTTTAATATTTTGTTAAT---A-
1 AATATTTTTTAATATTTTATTAATAAAAT
278299 AATA-TTTTTAATATTTTATTAATAAATAT
1 AATATTTTTTAATATTTTATTAATAAA-AT
*
278328 TATATTTTTTAATATTTATATTAATAAAAT
1 AATATTTTTTAATATTT-TATTAATAAAAT
278358 AATATT
1 AATATT
278364 CTACAAGTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 22 0.40
28 1 0.02
29 3 0.05
30 19 0.35
31 10 0.18
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
AATATTTTTTAATATTTTATTAATAAAAT
Found at i:278892 original size:16 final size:16
Alignment explanation
Indices: 278842--278895 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
278832 CCTGAACTTG
*
278842 AAAAAATTTAAATTCG
1 AAAAAATTTAAATTCA
* *
278858 AAAAGATTTAAACTCA
1 AAAAAATTTAAATTCA
*
278874 AAAAAATTTAAATTTA
1 AAAAAATTTAAATTCA
278890 AAAAAA
1 AAAAAA
278896 CTCAACATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAAAATTTAAATTCA
Found at i:281755 original size:15 final size:15
Alignment explanation
Indices: 281711--281755 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
281701 TAATCTTGTC
*
281711 CATCTACCACCTATT
1 CATCTACCACCTGTT
* *
281726 CATCCATCACCTGTT
1 CATCTACCACCTGTT
*
281741 CATCTACCACTTGTT
1 CATCTACCACCTGTT
281756 TACCCAGCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.38, G:0.04, T:0.36
Consensus pattern (15 bp):
CATCTACCACCTGTT
Found at i:282387 original size:18 final size:18
Alignment explanation
Indices: 282346--282390 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
282336 ATAGCATTAT
*
282346 AAATTAAT-AAGAATACA
1 AAATTAATAAAAAATACA
* *
282363 AATTTAATAAAAAATATA
1 AAATTAATAAAAAATACA
282381 AAATTAATAA
1 AAATTAATAA
282391 GTATATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATTAATAAAAAATACA
Found at i:282431 original size:25 final size:26
Alignment explanation
Indices: 282403--282460 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
282393 ATATATTTTT
*
282403 TAAAAATATAATAGC-TAATAATAAA
1 TAAAAATATAATAACATAATAATAAA
* * *
282428 TAAAAA-ATTATAACATTATAATAAT
1 TAAAAATATAATAACATAATAATAAA
282453 TAAAAATA
1 TAAAAATA
282461 AATTCCAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.22
25 20 0.74
26 1 0.04
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAAAATATAATAACATAATAATAAA
Found at i:282671 original size:14 final size:16
Alignment explanation
Indices: 282652--282686 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
282642 TCATATTTTT
282652 TAATTAATTA-TA-TA
1 TAATTAATTATTAGTA
282666 TAATTAATTATTAGTA
1 TAATTAATTATTAGTA
282682 TAATT
1 TAATT
282687 GGTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 2 0.11
16 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TAATTAATTATTAGTA
Found at i:288140 original size:18 final size:18
Alignment explanation
Indices: 288119--288154 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
288109 AATTTATTTA
288119 ATAAACTAATTTTATATC
1 ATAAACTAATTTTATATC
* *
288137 ATAAATTATTTTTATATC
1 ATAAACTAATTTTATATC
288155 TTTTTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAAACTAATTTTATATC
Found at i:290357 original size:13 final size:13
Alignment explanation
Indices: 290341--290365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290331 TACATTGTTC
290341 ATTGTATCGATAT
1 ATTGTATCGATAT
290354 ATTGTATCGATA
1 ATTGTATCGATA
290366 CATTCTGCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:290425 original size:20 final size:20
Alignment explanation
Indices: 290402--290439 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
290392 ATATATTTTG
290402 CATTGTATCGACACATTGCT
1 CATTGTATCGACACATTGCT
*
290422 CATTGTATCGATACATTG
1 CATTGTATCGACACATTG
290440 TATCGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTGTATCGACACATTGCT
Found at i:290438 original size:13 final size:13
Alignment explanation
Indices: 290422--290451 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
290412 ACACATTGCT
290422 CATTGTATCGATA
1 CATTGTATCGATA
290435 CATTGTATCGATA
1 CATTGTATCGATA
290448 CATT
1 CATT
290452 TAGGCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:292784 original size:51 final size:51
Alignment explanation
Indices: 292729--292911 Score: 294
Period size: 51 Copynumber: 3.6 Consensus size: 51
292719 TAAGTTTCTC
* *
292729 AATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
1 AATTTTTCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACT
*
292780 AATTTTTTACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACT
1 AATTTTTCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACT
* * *
292831 AATTTTTCACAATCGGGGATACTCCAACCCTGATTTTATTTCCAAAAACACC
1 AATTTTTCACAATCGGGGATACTCCAACCCTGGTTTTATTT-CTAAAACACT
*
292883 AATTTTTCATAATCGGGGATACTCCAACC
1 AATTTTTCACAATCGGGGATACTCCAACC
292912 TCGTTATTTC
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 87 0.71
52 36 0.29
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
AATTTTTCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACT
Found at i:293012 original size:79 final size:78
Alignment explanation
Indices: 292846--293130 Score: 238
Period size: 79 Copynumber: 3.6 Consensus size: 78
292836 TTCACAATCG
* * * *** *
292846 GGGATACTCCAACCCTGATTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGA-TTTATTTTC-AAAATATTGATTTCTCATAATCGGGGATACTCCAAC
292911 CTCGTTATTTCATCG--
64 CTCGTTATTTC--CGAA
* * *
292926 GGAATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCC-GATTTATTTTCAAAATATTGATTTCTCATAATCGGGGATACTCCAACC
292991 TCGTTATTTCCGAA
65 TCGTTATTTCCGAA
* ** * * *
293005 GGGATACTCCAATCCCGATTT-TATTTCCTAATCATCGATTTTTC-TCAACCGGGGATACTCCAA
1 GGGATACTCCAACCCCGATTTAT-TTTCAAAAT-ATTGATTTCTCAT-AATCGGGGATACTCCAA
* *
293068 CCCCGTTATTTTC-AA
63 CCTCGTTATTTCCGAA
* * * *
293083 GGGGATACTCCAACCCCGTTATTATCTCCAAAATATTAAATTTCTCAT
1 -GGGATACTCCAACCCCGAT-TTATTTTCAAAATATT-GATTTCTCAT
293131 CGGGAAATAT
Statistics
Matches: 164, Mismatches: 30, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
77 3 0.02
78 14 0.09
79 109 0.66
80 35 0.21
81 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (78 bp):
GGGATACTCCAACCCCGATTTATTTTCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCT
CGTTATTTCCGAA
Found at i:293535 original size:51 final size:51
Alignment explanation
Indices: 293480--293662 Score: 276
Period size: 51 Copynumber: 3.6 Consensus size: 51
293470 TAAGTTTCTC
*
293480 AATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
* **
293531 AATTTTTCACAATCGAGGATACTCCAACCTTGGTTTTATTTCTAAAACACT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
* * * *
293582 AATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAATACC
1 AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACT
*
293634 AATTTTTCATAATCGGGGATACTCCAACC
1 AATTTTTCACAATCGGGGATACTCCAACC
293663 TCGTTATTTC
Statistics
Matches: 119, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 84 0.71
52 35 0.29
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
Found at i:293747 original size:79 final size:77
Alignment explanation
Indices: 293595--293881 Score: 301
Period size: 79 Copynumber: 3.6 Consensus size: 77
293585 TTTTCACAAT
* * *
293595 CGGGGATACTCCAACCCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCA
1 CGGGGATACTCCAACCCCG-TTTTATTTCC-AAAATATCAATTTCTCATAATTGGGGATACTCCA
*
293660 ACCTCGTTATTTCA
64 ACCCCGTTATTTCA
* * **
293674 TCGGGGATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGATACTCCA
1 -CGGGGATACTCCAACCCC-GTTTTATTTCCAAAATATCAATTTCTCATAATTGGGGATACTCCA
293739 ACCCCGTTATTTC-
64 ACCCCGTTATTTCA
* * * * *
293752 CGAAGGGATACTCCAATCCCGATTTTATTTCC-TAATCATCGATTTTTC-TCAACTGGGGATACT
1 CG--GGGATACTCCAACCCCG-TTTTATTTCCAAAAT-ATCAATTTCTCAT-AATTGGGGATACT
293815 CCAACCCCGTTATTTTCA
61 CCAACCCCGTTA-TTTCA
* * *
293833 AGGGGATACTCCAACCCCGTTATTATCTCCAAAATATTAAATTTCTCAT
1 CGGGGATACTCCAACCCCGTT-TTATTTCCAAAATA-TCAATTTCTCAT
293882 CGGGAAATAT
Statistics
Matches: 173, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
77 2 0.01
78 7 0.04
79 121 0.70
80 40 0.23
81 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (77 bp):
CGGGGATACTCCAACCCCGTTTTATTTCCAAAATATCAATTTCTCATAATTGGGGATACTCCAAC
CCCGTTATTTCA
Found at i:294007 original size:751 final size:751
Alignment explanation
Indices: 292528--294412 Score: 3481
Period size: 751 Copynumber: 2.5 Consensus size: 751
292518 TTTCCAACGG
* * *
292528 TATCTCATTCCCCCTGTGAAACCTCCAAATCAACCCAAA-AAAATTCGAAAAGGAGGACAGCGCG
1 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
292592 ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
66 ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
*
292657 TTCGGACGTCTCCTTGTAAT-CCCCTAGGCTCGGACAAAGGCTAAACCCAAAAGTATTTTTGTTA
131 TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
292721 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
196 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
*
292786 TTACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
261 TCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
*
292851 ACTCCAACCCTGATTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGT
326 ACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGT
292916 TATTTCATCGGGAATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGA
391 TATTTCATCGGGAATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGA
*
292981 TACTCCAACCTCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
456 TACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
293046 TTCTCAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTC
521 TTCTCAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTC
293111 CAAAATATTAAATTTCTCATCGGGAAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTT
586 CAAAATATTAAATTTCTCATCGGGAAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTT
*
293176 TTTTTCTTTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTCG
651 TTTTTCATTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTCG
293241 AAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
716 AAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
*
293277 TATCTCATTCCCCCTGTGAAACCTCCAAATTAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
1 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
* * *
293342 ATGTTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCTCAAGACA
66 ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
293407 TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
131 TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
293472 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
196 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
* *
293537 TCACAATCGAGGATACTCCAACCTTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
261 TCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
*
293602 ACTCCAACCCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGGGGATACTCCAACCTCGT
326 ACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGT
*
293667 TATTTCATCGGGGATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGA
391 TATTTCATCGGGAATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGA
293732 TACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
456 TACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
*
293797 TTCTCAACTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTC
521 TTCTCAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTC
*
293862 CAAAATATTAAATTTCTCATCGGGAAATATATTCCAACCGCGTCCTCGAAGGAATATTTCAACTT
586 CAAAATATTAAATTTCTCATCGGGAAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTT
293927 TTTTTCATTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTCG
651 TTTTTCATTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTCG
293992 AAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
716 AAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
294028 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
1 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
294093 ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
66 ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
294158 TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
131 TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
*
294223 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTT
196 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
* * * * *
294288 CCACAATCGGGGATACTTCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAATTGGGGAT
261 TCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
* * * *
294353 ACTCCAACCCC-AGTTTTATTT-CTAAAACACTAATTTTCCACAATCGGGGATACTCCAACC
326 ACTCCAACCCCGA-TTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
294413 CCGATTTTAT
Statistics
Matches: 1098, Mismatches: 35, Indels: 5
0.96 0.03 0.00
Matches are distributed among these distances:
749 37 0.03
750 140 0.13
751 921 0.84
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (751 bp):
TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
ATGCTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACA
TTCGGACGTCTCCTTGTAATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTT
TCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTAATTTTTCACAATCGGGGAT
ACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGT
TATTTCATCGGGAATACTCCAACCCCAGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGGA
TACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
TTCTCAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTC
CAAAATATTAAATTTCTCATCGGGAAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTT
TTTTTCATTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTCG
AAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
Found at i:294286 original size:51 final size:51
Alignment explanation
Indices: 294231--294464 Score: 378
Period size: 51 Copynumber: 4.6 Consensus size: 51
294221 TAAGTTTCTC
* * *
294231 AATTTTTCATAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
*
294282 AATTTTCCACAATCGGGGATACTTCAACCCCGGTTTTATTTCTAAAACACT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
* *
294333 AATTTTCCACAATTGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
* *
294384 AATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACT
1 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACACT
*
294436 AATTTTTCACAATCGGGGATACTCCAACC
1 AATTTTCCACAATCGGGGATACTCCAACC
294465 TCGTTATTTC
Statistics
Matches: 170, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
51 133 0.78
52 37 0.22
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT
Found at i:294503 original size:80 final size:77
Alignment explanation
Indices: 294395--294631 Score: 235
Period size: 79 Copynumber: 3.0 Consensus size: 77
294385 ATTTTCCACA
* * *
294395 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACTAATTTTTCACAATCGGGGATACTC
1 ATCGAGGATACTCCAACTCCGATTTTATTTCC-AAAACA-TGATTTTTCACAATCGGGGATACTC
*
294460 CAACCTCGTTATTT
64 CAACCCCGTTATTT
** ** * * * *
294474 CATCGAGGATACTCCAACTCCGGCTTTATTTTTAAAATATTGATTTCTCATAATTGGGGATACTC
1 -ATCGAGGATACTCCAACTCCGATTTTATTTCCAAAACA-TGATTTTTCACAATCGGGGATACTC
294539 CAACCCCGTTATTT
64 CAACCCCGTTATTT
* * * * *
294553 -TTGAGGGAATACTCCAA-TCCCGATTTTATTTCCTAATCATCGATTTTTCTCAACCGGGGATAC
1 ATCGA-GG-ATACTCCAACT-CCGATTTTATTTCCAAAACAT-GATTTTTCACAATCGGGGATAC
294616 TCCAACCCCGTTATTT
62 TCCAACCCCGTTATTT
294632 TCAAGGGGAT
Statistics
Matches: 127, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
77 3 0.02
78 4 0.03
79 94 0.74
80 26 0.20
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (77 bp):
ATCGAGGATACTCCAACTCCGATTTTATTTCCAAAACATGATTTTTCACAATCGGGGATACTCCA
ACCCCGTTATTT
Found at i:294581 original size:79 final size:77
Alignment explanation
Indices: 294400--294672 Score: 234
Period size: 79 Copynumber: 3.5 Consensus size: 77
294390 CCACAATCGG
* * * * *
294400 GGATACTCCAACCCCGATTTTATTTCCAAAAACACTAATTTTTCACAATCGGGGATACTCCAACC
1 GGATACTCCAA-CCCGATTTTATTTCCTAAAATATTGATTTTTCATAATCGGGGATACTCCAACC
*
294465 TCGTTATTTCATCGA
65 CCGTTATTT--TCGA
** * * *
294480 GGATACTCCAACTCCGGCTTTATTT-TTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
1 GGATACTCCAAC-CCGATTTTATTTCCTAAAATATTGATTTTTCATAATCGGGGATACTCCAACC
*
294544 CCGTTATTTTTGA
65 CCGTTATTTTCGA
* *
294557 GGGAATACTCCAATCCCGATTTTATTTCCT--AATCATCGATTTTTC-TCAACCGGGGATACTCC
1 -GG-ATACTCCAA-CCCGATTTTATTTCCTAAAAT-ATTGATTTTTCAT-AATCGGGGATACTCC
*
294619 AACCCCGTTATTTTCAAGG
61 AACCCCGTTATTTTC--GA
* *
294638 GGATTCTCCAACCCCG-TTATTATCTCC-AAAATATT
1 GGATACTCCAA-CCCGATT-TTATTTCCTAAAATATT
294673 AAATTTCTCA
Statistics
Matches: 156, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
77 3 0.02
78 8 0.05
79 116 0.74
80 28 0.18
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (77 bp):
GGATACTCCAACCCGATTTTATTTCCTAAAATATTGATTTTTCATAATCGGGGATACTCCAACCC
CGTTATTTTCGA
Found at i:299073 original size:13 final size:13
Alignment explanation
Indices: 299033--299118 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
299023 CCGTTACAAG
299033 CAATGTATCGATA
1 CAATGTATCGATA
299046 CAA--T-TC-AT-
1 CAATGTATCGATA
299054 C-ATGTATCGATA
1 CAATGTATCGATA
299066 CAATGTATCGATA
1 CAATGTATCGATA
299079 C-A--T-T-G-TA
1 CAATGTATCGATA
*
299086 CCATGTATCGATA
1 CAATGTATCGATA
299099 CAATGTATCGATA
1 CAATGTATCGATA
*
299112 CATTGTA
1 CAATGTA
299119 CCATGTATCG
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 4 0.07
10 6 0.10
11 4 0.07
12 3 0.05
13 35 0.59
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:299073 original size:33 final size:33
Alignment explanation
Indices: 299033--299134 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
299023 CCGTTACAAG
* *
299033 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGTACCATGTATCGATA
299066 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
299099 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
299132 CAA
1 CAA
299135 ACAGTGGCAG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 3 0.05
33 63 0.95
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:299093 original size:20 final size:20
Alignment explanation
Indices: 299068--299133 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
299058 TATCGATACA
299068 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
299088 ATGTATCGATAC-----A--
1 ATGTATCGATACATTGTACC
299101 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
299121 ATGTATCGATACA
1 ATGTATCGATACA
299134 AACAGTGGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
15 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:299211 original size:19 final size:20
Alignment explanation
Indices: 299167--299219 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
299157 CTGCCAATCT
**
299167 CATGTATCGATACAATTGCC
1 CATGTATCGATACAATTGAA
*
299187 CATGTATCAATACAA-TGAA
1 CATGTATCGATACAATTGAA
299206 CATGTATCGATACA
1 CATGTATCGATACA
299220 TTCAAGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:299303 original size:71 final size:71
Alignment explanation
Indices: 299207--299360 Score: 274
Period size: 71 Copynumber: 2.2 Consensus size: 71
299197 TACAATGAAC
299207 ATGTATCGATACATTCAAGGGTTTTGACCTTTGTACCCTAAGTCAACCATAATGTATCGATACAA
1 ATGTATCGATACATTCAAGGGTTTTGACCTTTGTACCCTAAGTCAACCATAATGTATCGATACAA
*
299272 AGCA-TA
66 A-CACCA
299278 ATGTATCGATACATTCAAGGGTTTTGACCTTTGTACCCTAAGTCAACCATAATGTATCGATACAA
1 ATGTATCGATACATTCAAGGGTTTTGACCTTTGTACCCTAAGTCAACCATAATGTATCGATACAA
*
299343 ATACCA
66 ACACCA
299349 ATGTATCGATAC
1 ATGTATCGATAC
299361 TTTGAAGTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
70 1 0.01
71 79 0.99
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (71 bp):
ATGTATCGATACATTCAAGGGTTTTGACCTTTGTACCCTAAGTCAACCATAATGTATCGATACAA
ACACCA
Found at i:299875 original size:20 final size:22
Alignment explanation
Indices: 299798--299892 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
299788 GTTTTCGTTT
299798 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAGAA
299820 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATTAAAGAA
* * *
299842 TTTATCCCCTTTAA-TCAA-AA
1 TTTCTCCCCCTTAATTAAAGAA
* * * *
299862 TTTCTCCTCCTTAATCAACGCA
1 TTTCTCCCCCTTAATTAAAGAA
299884 TTTCTCCCC
1 TTTCTCCCC
299893 TTTGTCAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.22
21 4 0.07
22 43 0.72
ACGTcount: A:0.27, C:0.32, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTCTCCCCCTTAATTAAAGAA
Found at i:303363 original size:17 final size:17
Alignment explanation
Indices: 303338--303371 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
303328 AATAATTGAA
* *
303338 CAAATTAAAATTAAAAT
1 CAAAATAAAAGTAAAAT
303355 CAAAATAAAAGTAAAAT
1 CAAAATAAAAGTAAAAT
303372 TAAGGCCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (17 bp):
CAAAATAAAAGTAAAAT
Found at i:305225 original size:13 final size:13
Alignment explanation
Indices: 305207--305231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305197 TACATTGTTC
305207 ATTGTATCGATAT
1 ATTGTATCGATAT
305220 ATTGTATCGATA
1 ATTGTATCGATA
305232 CATTCTGCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:305291 original size:20 final size:20
Alignment explanation
Indices: 305268--305305 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
305258 ATATATTTTG
305268 CATTGTATCGACACATTGCT
1 CATTGTATCGACACATTGCT
*
305288 CATTGTATCGATACATTG
1 CATTGTATCGACACATTG
305306 TATCGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CATTGTATCGACACATTGCT
Found at i:305304 original size:13 final size:13
Alignment explanation
Indices: 305288--305317 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
305278 ACACATTGCT
305288 CATTGTATCGATA
1 CATTGTATCGATA
305301 CATTGTATCGATA
1 CATTGTATCGATA
305314 CATT
1 CATT
305318 CAGGCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:307680 original size:52 final size:51
Alignment explanation
Indices: 307559--307738 Score: 235
Period size: 52 Copynumber: 3.5 Consensus size: 51
307549 AGTTTCTCAA
*
307559 TTTTTCATAATC-GGGATACTCCAACCCCGGTTTTATTTCAAAACACTAAT
1 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCAAAACACTAAT
*
307609 TTTTT-AC-ATCCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACCACTAAT
1 TTTTTCACAAT-CGGGGATACTCCAACCCCGGTTTTATTTC-AAAA-CACTAAT
* *
307661 TTTTTCACAATC-GGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAT
1 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTT-C-AAAACACTAAT
*
307713 TTTTTCA-TATCGGGGATACTCCAACC
1 TTTTTCACAATCGGGGATACTCCAACC
307739 TCGTTATTTC
Statistics
Matches: 115, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
48 2 0.02
49 2 0.02
50 31 0.27
51 7 0.06
52 63 0.55
53 8 0.07
54 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCAAAACACTAAT
Found at i:307763 original size:79 final size:78
Alignment explanation
Indices: 307670--307901 Score: 244
Period size: 79 Copynumber: 3.0 Consensus size: 78
307660 TTTTTTCACA
* *
307670 ATCGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTTCATATCGGGGATACTCC
1 ATCGGGATACTCCAACCCCGATTTTATTTCC-AAAACATCGATTTTTTCATATCGGGGATACTCC
307735 AACCTCGTTATTTC
65 AACCTCGTTATTTC
* * * * * *
307749 ATCGGGA-ATCTCCAACCCCG-CTTTATTTTCAAAATATTGA-TTTCTCATAAT-TGGGATACTC
1 ATCGGGATA-CTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTTCAT-ATCGGGGATACTC
307810 CAACCTCGTTATTTCC
64 CAACCTCGTTATTT-C
* * * * *
307826 GA-AGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTTTTCTCA-ACCGGGGATACTC
1 -ATCGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTT-TCATATCGGGGATACTC
307889 CAACC-CGTTATTT
64 CAACCTCGTTATTT
307902 TCAGGGGTAC
Statistics
Matches: 125, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
76 30 0.24
77 23 0.18
78 34 0.27
79 35 0.28
80 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.34
Consensus pattern (78 bp):
ATCGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTTCATATCGGGGATACTCCA
ACCTCGTTATTTC
Found at i:308406 original size:51 final size:50
Alignment explanation
Indices: 308298--308475 Score: 254
Period size: 50 Copynumber: 3.6 Consensus size: 50
308288 AAGTTTCTCA
*
308298 ATTTTTCATAATCGGGGATACTCCAACCCCGG-TTTATTTTCTAAAAACAC
1 ATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAAACAC
* *
308348 ATTTTTCACAATCGAGGATACTCCAACCCTGGTTTTATTTCTAAAAACAC
1 ATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAAACAC
* *
308398 TATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAATACA-
1 -ATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAA-ACAC
*
308449 ATTTTTCATAATCGGGGA-ACTCCAACC
1 ATTTTTCACAATCGGGGATACTCCAACC
308476 TCGTTATTTC
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
49 9 0.08
50 59 0.50
51 46 0.39
52 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (50 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAAACAC
Found at i:308498 original size:76 final size:77
Alignment explanation
Indices: 308413--308594 Score: 221
Period size: 76 Copynumber: 2.4 Consensus size: 77
308403 TTCACAATCG
*
308413 GGGATACTCCAACCCCGATTTTATTTCCAAAATA-CAATTTTTCATAATCGGGGA-ACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAATATCAATTTCTCATAATCGGGGATACTCCAACC
*
308476 TCG-TTATTTCATC
66 CCGCTTATTTC--C
* ** *
308489 GGGATACTCCAACCCCAGCTTTT-TTT-CAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGATACTCCAACCCC-GATTTTATTTCCAAAATATCAATTTCTCATAATCGGGGATACTCCAAC
308552 CCCGCTTATTTCC
65 CCCGCTTATTTCC
*
308565 GAAGGATACTCCAATCCCGATTTTATTTCC
1 G--GGATACTCCAACCCCGATTTTATTTCC
308595 TAATCCTCGA
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
75 7 0.08
76 37 0.41
77 21 0.23
78 24 0.27
79 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.34
Consensus pattern (77 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAATATCAATTTCTCATAATCGGGGATACTCCAACC
CCGCTTATTTCC
Found at i:308856 original size:740 final size:735
Alignment explanation
Indices: 307358--309213 Score: 2806
Period size: 740 Copynumber: 2.5 Consensus size: 735
307348 TTTCCAACGG
* * * *
307358 TATCTCATTCCCCCTGTGAAACCTCCAAATCA-ACCAAAAAAAATTCGAAAAGGAGGACAGCGCG
1 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
307422 ATGCT-TCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCC-ACTCTCATCCCGAGAC
66 ATG-TGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACT-TCATCCCGAGAC
*
307485 ATTCGGACGTCTCCTTGTAATCCCCTAGGCTCGGACAAAGGCTAAACCCAAAA-TATTTTTGTTA
129 ATTCGGACG-CTCCTTGTAATCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTA
307549 AGTTTCTCAATTTTTCATAATC-GGGATACTCCAACCCCGGTTTTATTTC-AAAACACTAATTTT
193 AGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTT-TTTCTAAAACAC-AATTTT
* *
307612 TTAC-ATCCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACCACTAATTTTTTCACAATC-GG
256 TCACAAT-CGGGGATACTCCAACCCTGGTTTTATTTCTAAAAACACT-A-TTTTTCACAATCGGG
307675 GATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTTCAT-ATCGGGGATACTCCAACC
318 GATACTCCAACCCCGATTTTATTTCC-AAAACA-CAA-TTTTTCATAATCGGGGATACTCCAACC
307739 TCGTTATTTCATCGGGAATCTCCAACCCCGCTTTATTTTCAAAATATTGATTTCTCATAATTGGG
380 TCGTTATTTCATCGGGAATCTCCAACCCCGCTTTATTTTCAAAATATTGATTTCTCATAATTGGG
*
307804 ATACTCCAACCTCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATT
445 ATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATT
307869 TTTCTCAACCGGGGATACTCCAACCCGTTATTTTCAGGGGTACTCCAAACCCGTATTACTCCAAA
510 TTTCTCAACCGGGGATACTCCAACCCGTTATTTTCAGGGGTACTCCAAACCCGTATTACTCCAAA
307934 ATATTAAATTTCTCATCGGGAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTTTTTTT
575 ATATTAAATTTCTCATCGGGAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTTTTTTT
307999 CTTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTTCGAAAAC
640 CTTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTTCGAAAAC
308064 CTCACAGAATCCAATCAAGTCTCAACATTGT
705 CTCACAGAATCCAATCAAGTCTCAACATTGT
*
308095 TATCTCATTCCCCCTTGTGAAACCTCCAAATTAGCCCAAACCAAAATTCAAAAAGGAGGATAGCG
1 TATCTCATTCCCCC-TGTGAAACCTCCAAATCAGCCCAAA-CAAAATTCAAAAAGGAGGATAGCG
* *
308160 CGATGTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTT-TTCCCAACTTCATCTCAAGAC
64 CGATGTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGA-
308224 CATTCGGACGCTCCTTGT-ATCCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTT
128 CATTCGGACGCTCCTTGTAAT-CCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTT
308288 AAGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTATTTTCTAAAA-ACACATTT
192 AAGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTT-TTTTCTAAAACACA-ATTT
*
308352 TTCACAATCGAGGATACTCCAACCCTGGTTTTATTTCTAAAAACACTATTTTTCACAATCGGGGA
255 TTCACAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAAACACTATTTTTCACAATCGGGGA
*
308417 TACTCCAACCCCGATTTTATTTCCAAAATACAATTTTTCATAATCGGGGA-ACTCCAACCTCGTT
320 TACTCCAACCCCGATTTTATTTCCAAAACACAATTTTTCATAATCGGGGATACTCCAACCTCGTT
308481 ATTTCATCGGG-ATACTCCAACCCCAGCTTT-TTTTCAAAATATTGATTTCTCATAATTGGGGAT
385 ATTTCATCGGGAAT-CTCCAACCCC-GCTTTATTTTCAAAATATTGATTTCTCATAATT-GGGAT
*
308544 ACTCCAACCCCGCTTATTTCCGAA-GGATACTCCAATCCCGATTTTATTTCCTAATCCTCGA-TT
447 ACTCCAACCCCG-TTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTT
* * *
308607 TTCTCAACTGGGGAT-CTCCAACCCGTTATTTTCAAGGGGATACTCCCACCCCGTTATTATCTCC
511 TTCTCAACCGGGGATACTCCAACCCGTTATTTTC-AGGGG-TACTCCAAACCCG-TATTA-CTCC
*
308671 AAAAATATTAAATTTCTCATCGGGAAATATATTCCAACACCGCGTCCTCGAAGGAATATTTCAAC
572 -AAAATATTAAATTTCTCATCGGG-AATATATTCC-A-ACCGCATCCTCGAAGGAATATTTCAAC
*
308736 TTTTTTCTCTTTTGAATTTCCCTTAAATTCCCAACTTTTCTCTAGAGCACCCCTAGACCA-TTTT
633 TTTTTT-TCTTTTGAATTTCCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTT
* *
308800 TCGAAAACCTCACCGAATCCAATCAAGTCTCAACCTTGT
697 TCGAAAACCTCACAGAATCCAATCAAGTCTCAACATTGT
*
308839 TAT-TC-TT-CCCCTGTGAAACCTCCCAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
1 TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGC-
* *
308901 GGATGCGT-CCCTG-TTTGGTCATGAAAAAAAGTTAAAAGCCGTTCTTCCCAACTTCATCCCGAG
65 -GATGTGTCCCCTGTTTTGGTCATGAACAAAAGTT--AAGCCGTTCTTCCCAACTTCATCCCGAG
*
308964 ACATTCGGACGTTCTCTCTGTAATCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTG
127 ACATTCGGACGCTC-CT-TGTAATCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTG
* * *
309029 TT-AGTTTCTCAATTTTTCATAATCGGGG-TACTCCAA-CCTGGTTTTATTCTTAAACACTAATT
190 TTAAGTTTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTTTTCTAAAACAC-AATT
* * * *
309091 TTCCACCAATCGGGGTATACTTCAACCCCGGTTTTATTTCTAAAAACAC-A-TTTTCACAATTGG
254 TTTCA-CAATCGGGG-ATACTCCAACCCTGGTTTTATTTCTAAAAACACTATTTTTCACAATCGG
* * *
309154 GGATAC-CC-ACCCCAGTTTTTATTTCTAAAACACAATTTTTCACAA-C-GGGATACTCCAACC
317 GGATACTCCAACCCC-GATTTTATTTCCAAAACACAATTTTTCATAATCGGGGATACTCCAACC
309214 CCGATTTTAT
Statistics
Matches: 1037, Mismatches: 40, Indels: 83
0.89 0.03 0.07
Matches are distributed among these distances:
736 20 0.02
737 109 0.11
738 113 0.11
739 173 0.17
740 204 0.20
741 143 0.14
742 96 0.09
743 49 0.05
744 78 0.08
745 52 0.05
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (735 bp):
TATCTCATTCCCCCTGTGAAACCTCCAAATCAGCCCAAACAAAATTCAAAAAGGAGGATAGCGCG
ATGTGTCCCCTGTTTTGGTCATGAACAAAAGTTAAGCCGTTCTTCCCAACTTCATCCCGAGACAT
TCGGACGCTCCTTGTAATCCCCTAGGCTCGGACCAAGGCTAAACCCAAAAGTATTTTTGTTAAGT
TTCTCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTTTTCTAAAACACAATTTTTCACA
ATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAAACACTATTTTTCACAATCGGGGATACTCC
AACCCCGATTTTATTTCCAAAACACAATTTTTCATAATCGGGGATACTCCAACCTCGTTATTTCA
TCGGGAATCTCCAACCCCGCTTTATTTTCAAAATATTGATTTCTCATAATTGGGATACTCCAACC
CCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTATTTCCTAATCATCGATTTTTCTCAACCG
GGGATACTCCAACCCGTTATTTTCAGGGGTACTCCAAACCCGTATTACTCCAAAATATTAAATTT
CTCATCGGGAATATATTCCAACCGCATCCTCGAAGGAATATTTCAACTTTTTTTCTTTTGAATTT
CCCTTAAATTCCAAACTTTTCTCTAGAGCACCCCTAGACCATTTTTTCGAAAACCTCACAGAATC
CAATCAAGTCTCAACATTGT
Found at i:309215 original size:49 final size:49
Alignment explanation
Indices: 309038--309266 Score: 211
Period size: 48 Copynumber: 4.6 Consensus size: 49
309028 GTTAGTTTCT
* * * *
309038 CAATTTTTCATAATCGGGGTACTCCAA-CCTGGTTTTA-TTCTTAAACA
1 CAATTTTTCACAATCGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
* *
309085 CTAATTTTCCACCAATCGGGGTATACTTCAACCCCGGTTTTATTTCTAAAA-A
1 C-AATTTTTCA-CAATC-GGG-ATACTCCAACCCCGGTTTTATTTCTAAAACA
* *
309137 CACA-TTTTCACAATTGGGGATAC-CC-ACCCCAGTTTTTATTTCTAAAACA
1 CA-ATTTTTCACAA-TCGGGATACTCCAACCCC-GGTTTTATTTCTAAAACA
* *
309186 CAATTTTTCACAA-CGGGATACTCCAACCCCGATTTTATTTCCAAAAAACA
1 CAATTTTTCACAATCGGGATACTCCAACCCCGGTTTTATTT-C-TAAAACA
*
309236 CTAATTTTTCCCAATCGGGGATACTCCAACC
1 C-AATTTTTCACAATC-GGGATACTCCAACC
309267 TCGTTATTTC
Statistics
Matches: 150, Mismatches: 14, Indels: 30
0.77 0.07 0.15
Matches are distributed among these distances:
47 13 0.09
48 36 0.24
49 26 0.17
50 16 0.11
51 25 0.17
52 13 0.09
53 21 0.14
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (49 bp):
CAATTTTTCACAATCGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
Found at i:309412 original size:78 final size:77
Alignment explanation
Indices: 309201--309431 Score: 220
Period size: 78 Copynumber: 2.9 Consensus size: 77
309191 TTTCACAACG
* * * *
309201 GGATACTCCAACCCCGATTTTATTTCCAAAAAACACTAATTTTTCCCAATCGGGGATACTCCAAC
1 GGATACTCCAATCCCGATTTTATTTCC--TAAACA-T-ATTTTTCTCAAACGGGGATACTCCAAC
*
309266 CTCGTTATTTCATCGA
62 CCCGTTATTTCATCGA
** * * *
309282 GGATACTCCAACTCTGGCTTTT-TTT--TAAAAATATTGATTTCTCATAATGGGGATACTCCAAC
1 GGATACTCCAA-TCCCGATTTTATTTCCTAAACATATT--TTTCTCA-AACGGGGATACTCCAAC
309344 CCCGTTATTTC-T-GA
62 CCCGTTATTTCATCGA
* *
309358 GGCAATACTCCAATCCCGATTTTATTTCCTAATCATCATTTTTCTCAACCGGGGATACTCCAACC
1 GG--ATACTCCAATCCCGATTTTATTTCCTAAACAT-ATTTTTCTCAAACGGGGATACTCCAACC
309423 CCGTTATTT
63 CCGTTATTT
309432 TCAAGGGGAT
Statistics
Matches: 123, Mismatches: 17, Indels: 23
0.75 0.10 0.14
Matches are distributed among these distances:
75 3 0.02
76 5 0.04
77 18 0.15
78 62 0.50
79 7 0.06
80 5 0.04
81 17 0.14
82 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (77 bp):
GGATACTCCAATCCCGATTTTATTTCCTAAACATATTTTTCTCAAACGGGGATACTCCAACCCCG
TTATTTCATCGA
Found at i:310467 original size:17 final size:17
Alignment explanation
Indices: 310442--310478 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
310432 TTACTAGTTG
310442 TTTTTTTTTTT-AT-TT
1 TTTTTTTTTTTAATGTT
310457 TTTTTTCTTTTTAATGTT
1 TTTTTT-TTTTTAATGTT
310475 TTTT
1 TTTT
310479 CATTTTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 2 0.11
18 6 0.32
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTTAATGTT
Found at i:310484 original size:17 final size:16
Alignment explanation
Indices: 310440--310484 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
310430 ACTTACTAGT
*
310440 TGTTTTTT-TTTTTAT
1 TGTTTTTTCTTTTTAA
*
310455 TTTTTTTTCTTTTTAA
1 TGTTTTTTCTTTTTAA
*
310471 TGTTTTTTCATTTT
1 TGTTTTTTCTTTTT
310485 GTGGAGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.82
Consensus pattern (16 bp):
TGTTTTTTCTTTTTAA
Done.