Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 91
Found at i:3341772 original size:33 final size:34
Alignment explanation
Indices: 3341732--3341841 Score: 93
Period size: 34 Copynumber: 3.3 Consensus size: 34
3341722 AAACAATTTA
**
3341732 TAACAAATATTA-ATTTTTCATTATAAAAAATTG
1 TAACAAATATTATATTTTTCACAATAAAAAATTG
* * * *
3341765 TGACAAATAATATTTTTTTCACAATAAACAATTG
1 TAACAAATATTATATTTTTCACAATAAAAAATTG
** * *
3341799 TAACAAA-ATTAT-TTAGTCACAGTAAAAAAGTTA
1 TAACAAATATTATATTTTTCACAATAAAAAA-TTG
3341832 TAA-AAATATT
1 TAACAAATATT
3341842 TAGTAACGAA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
32 16 0.26
33 22 0.36
34 23 0.38
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (34 bp):
TAACAAATATTATATTTTTCACAATAAAAAATTG
Found at i:3350621 original size:17 final size:17
Alignment explanation
Indices: 3350593--3350632 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
3350583 GTTAATACCT
3350593 AAAAATATATTTTTAGAA
1 AAAAATATATTTTTA-AA
3350611 AAAAATA-ATTTTTAAA
1 AAAAATATATTTTTAAA
3350627 AAAAAT
1 AAAAAT
3350633 TTAAATACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAAATATATTTTTAAA
Found at i:3351631 original size:3 final size:3
Alignment explanation
Indices: 3351623--3351691 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
3351613 GCATACATAT
3351623 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3351671 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
3351692 CAGAGACTGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3354371 original size:3 final size:3
Alignment explanation
Indices: 3354363--3354395 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3354353 CGTCCCAATA
3354363 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3354396 ATAATTAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3356515 original size:13 final size:13
Alignment explanation
Indices: 3356497--3356539 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
3356487 GTTATACTAA
3356497 TGTGATTCATTTT
1 TGTGATTCATTTT
3356510 TGTGATTCATTTT
1 TGTGATTCATTTT
3356523 TGTGATTCATTTT
1 TGTGATTCATTTT
3356536 TGTG
1 TGTG
3356540 TTTCGGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.60
Consensus pattern (13 bp):
TGTGATTCATTTT
Found at i:3358990 original size:20 final size:20
Alignment explanation
Indices: 3358967--3359027 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3358957 GCAAATGTTG
3358967 ATTTTGAAAATCAAAATAAA
1 ATTTTGAAAATCAAAATAAA
** *
3358987 ATTTTGAAACAT-AATTTAGA
1 ATTTTGAAA-ATCAAAATAAA
*
3359007 ATTTTCAAAAATCAAAATAAA
1 ATTTT-GAAAATCAAAATAAA
3359028 TGATTTAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATAAA
Found at i:3359707 original size:30 final size:30
Alignment explanation
Indices: 3359671--3359732 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3359661 ATAAATTTGA
3359671 ATGTTTATGCATGTGGTTTAAATGAAAATG
1 ATGTTTATGCATGTGGTTTAAATGAAAATG
3359701 ATGTTTATGCATGTGGTTTAAATGAAAATG
1 ATGTTTATGCATGTGGTTTAAATGAAAATG
3359731 AT
1 AT
3359733 ATCTCTCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40
Consensus pattern (30 bp):
ATGTTTATGCATGTGGTTTAAATGAAAATG
Found at i:3360194 original size:18 final size:18
Alignment explanation
Indices: 3360171--3360267 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 18
3360161 CAACAGTTGG
3360171 TAACAATATG-TATCTTTT
1 TAACAAT-TGATATCTTTT
* **
3360189 TAACAATTGATAAATAATTGG
1 TAACAATTGAT--AT-CTTTT
* *
3360210 TAACAATAGGTATCTTTT
1 TAACAATTGATATCTTTT
3360228 TAACAATTGATATCCATTTGT
1 TAACAATTGATAT-C-TTT-T
3360249 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
3360267 T
1 T
3360268 CATTAAACAT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
17 2 0.03
18 23 0.37
19 6 0.10
20 6 0.10
21 25 0.40
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:3360253 original size:39 final size:39
Alignment explanation
Indices: 3360162--3360267 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
3360152 TATATTTTCC
* *
3360162 AACAGTTGGTAACAATATGTATCTTTTTAACAATTGATA
1 AACAATTGGTAACAATAGGTATCTTTTTAACAATTGATA
*
3360201 AATAATTGGTAACAATAGGTATCTTTTTAACAATTGATA
1 AACAATTGGTAACAATAGGTATCTTTTTAACAATTGATA
** * * * *
3360240 TCCATTTGTTAACAATTGATATCTTTTT
1 AACAATTGGTAACAATAGGTATCTTTTT
3360268 CATTAAACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (39 bp):
AACAATTGGTAACAATAGGTATCTTTTTAACAATTGATA
Found at i:3360971 original size:21 final size:21
Alignment explanation
Indices: 3360945--3361000 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
3360935 TGAACAGTGT
3360945 TACAGTGCATCGATTCATTGC
1 TACAGTGCATCGATTCATTGC
3360966 TACAGTGCATCGATTCATTGC
1 TACAGTGCATCGATTCATTGC
3360987 TACAGTGCATCGAT
1 TACAGTGCATCGAT
3361001 GCACAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (21 bp):
TACAGTGCATCGATTCATTGC
Found at i:3361051 original size:21 final size:21
Alignment explanation
Indices: 3361025--3361068 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3361015 AATACAAATT
3361025 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
*
3361046 GTGCATCGATGCGCTGCTACA
1 GTGCATCGATGCACTGCTACA
3361067 GT
1 GT
3361069 ACTGCTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:3361394 original size:3 final size:3
Alignment explanation
Indices: 3361386--3361486 Score: 193
Period size: 3 Copynumber: 33.3 Consensus size: 3
3361376 TAACATATAT
3361386 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3361434 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
3361480 TAA TAA T
1 TAA TAA T
3361487 GCATTTCATA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 94 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3363730 original size:23 final size:23
Alignment explanation
Indices: 3363712--3363772 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3363702 CTCGTATAAA
3363712 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* **
3363735 TGTACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3363758 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3363773 TATAAACTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3364039 original size:31 final size:30
Alignment explanation
Indices: 3363995--3364054 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3363985 TATTGTATAG
*
3363995 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
3364025 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
3364055 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:3364492 original size:63 final size:64
Alignment explanation
Indices: 3364398--3364553 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 64
3364388 AATGAAGGTA
* ** *
3364398 TGCATCGATGCAC-CACACCATGCATCGATGCA-TAAATCTTATTCGATGTTTATA-TTT-AAGG
1 TGCATCGATGCACTC-CA-TATGCATCGATGCACT-AATCGCATTCGATGTTTATATTTTAAAAG
3364459 AGG
63 A-G
* * * *
3364462 TGCATCGATGCACTCCTTATGCATCGATGCACTGATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTCCATATGCATCGATGCACTAATCGCATTCGATGTTTATATTTTAAAAGAG
* *
3364526 TGCATCGATGCACTTCATGTGCATCGAT
1 TGCATCGATGCACTCCATATGCATCGAT
3364554 ACACCTTGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 28 0.36
64 44 0.57
65 5 0.06
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTCCATATGCATCGATGCACTAATCGCATTCGATGTTTATATTTTAAAAGAG
Found at i:3370687 original size:23 final size:23
Alignment explanation
Indices: 3370655--3370715 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
3370645 CTCGTATAAA
*
3370655 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3370678 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3370701 TGTACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
3370716 TATAAGCTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3370982 original size:31 final size:30
Alignment explanation
Indices: 3370938--3370997 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3370928 TATTGTATAG
*
3370938 ACATATAATTTCCATACCTT-TATCACATAA
1 ACATATAATTTCCAT-CATTGTATCACATAA
*
3370968 ACATATCATGTTCCATCATTGTATCACATA
1 ACATATAAT-TTCCATCATTGTATCACATA
3370998 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCATTGTATCACATAA
Found at i:3371433 original size:63 final size:64
Alignment explanation
Indices: 3371341--3371496 Score: 151
Period size: 64 Copynumber: 2.4 Consensus size: 64
3371331 AATGAAGGTA
* * *
3371341 TGCATCGATTCAC-CACACTATGCAACGATGCA-TAAAT-CCTATTCGATGTTTATA-TTT-AAG
1 TGCATCGATGCACTC-CA-TATGCATCGATGCACT-AATGCC-ATTCGATGTTTATATTTTAAAA
3371401 GAGG
62 GA-G
* * * *
3371405 TGCATCGATGCACTCCTTATGCATCGATGCACTGATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTCCATATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAG
* *
3371469 TGCATCGATGCACTTCATGTGCATCGAT
1 TGCATCGATGCACTCCATATGCATCGAT
3371497 ACACCTTGAA
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
63 28 0.36
64 44 0.57
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTCCATATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAG
Found at i:3380418 original size:189 final size:188
Alignment explanation
Indices: 3380062--3380453 Score: 601
Period size: 189 Copynumber: 2.1 Consensus size: 188
3380052 CAAGAAAGTT
* * *
3380062 ATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAGTCATTTGGGCCATCAGTAAG
1 ATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAGTCATTCGGGCCATCAATAAG
** * *
3380127 TATTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGTTAAGTC
66 TATTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGAAAGATGTTAAGTC
3380192 CTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAG-A
131 CTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAGCA
* *
3380249 GATTTCCAAAGTTTCTTACCGAGTAAACTATTTTCC-AAA-TTGATAAGTCATTCGGGCCATCAA
1 -ATTACCAAAGTTTCTTACCCAGTAAACTA-TTTCCAAAATTTG-T-AGTCATTCGGGCCATCAA
* * *
3380312 TAAGTCTTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGGGAAAGATGTTA
62 TAAGTATTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGAAAGATGTTA
* *
3380377 AGTCCTTCGGGCCATCCGTAAGATCTTCGGGTAGTATGCTTTCACATGAAAATGAGAAAGCA
127 AGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAGCA
3380439 ATTACCAAAGTTTCT
1 ATTACCAAAGTTTCT
3380454 CATTTAAATC
Statistics
Matches: 185, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
187 3 0.02
188 30 0.16
189 151 0.82
190 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (188 bp):
ATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTTGTAGTCATTCGGGCCATCAATAAG
TATTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGAAAGATGTTAAGTC
CTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAGCA
Found at i:3380604 original size:250 final size:250
Alignment explanation
Indices: 3380242--3381170 Score: 1403
Period size: 250 Copynumber: 3.7 Consensus size: 250
3380232 CATGAAAATG
* *
3380242 AGAAAGAGATTTCCAAAGTTTCTTACCGAGTAAACTATTTTCCAAATTGATAAGTCATTCGGGCC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCATTCGGGCC
* * * * *
3380307 ATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGGGAAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* *
3380372 TGTTAAGTCCTTCGGGCCATCCGTAAGATCTTCGGGTAGTATGCTTTCACATGAAAATGAGAAAG
131 TGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAG
* * * * *
3380437 CAATTACCAAAGTTTCTCATTTAAATCTTTTCTGAAAATGGAATTTTTTATAAGTA
196 CGATTACCAAAGTTTCTCATTT-AATATTTTCTGAAAATGAAATTTTTAAAAAGTA
* * * *
3380493 AGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTG-TAAGTCCTTCGGGCC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCATTCGGGCC
* *
3380557 ATCAGTAAGTCTTTCGAGCATGCTGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGTAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * *
3380622 TGTTAAGTCTTTCAGGCCATCCGTAAGACCTTTGGGTAGGATGCTTTCACATGAAAATGAGAAAG
131 TGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAG
* * * *
3380687 TGATTACCAAAGTTTCTCATTTAATGTTTTCTGAAAATGAAATTGTTAAAAAATA
196 CGATTACCAAAGTTTCTCATTTAATATTTTCTGAAAATGAAATTTTTAAAAAGTA
*
3380742 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCCTTCGGGCC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCATTCGGGCC
* * *
3380807 ATCAGTAAGTCTTTCGAGCATGACGCTTAAATCCTTCGGGTCATCTGTAAATCTTTTGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * **
3380872 TGTTAAGTCGTTCGAGCCATCCGTAAGACCTTTAGGTAGGATGCTTTCACATGAAAATGAGAAAG
131 TGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAG
* * *
3380937 CGATTACCAAAGTTTCCCATTTAATATTTTCAGAAAATGAAATTGTTGAAAAAGTA
196 CGATTACCAAAGTTTCTCATTTAATATTTTCTGAAAATGAAATT-TTTAAAAAGTA
*
3380993 AGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTG-TAAGTCATTCGGGCC
1 AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCATTCGGGCC
* * * * *
3381057 ATTAGTAAGTCTATCGAGCATGATGATTAAATCCTTCGGGTCACCTGTTAGTCTTTCGAGCAAGA
66 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
* * *
3381122 TGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCA
131 TGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCA
3381171 TTCTTTGTTA
Statistics
Matches: 615, Mismatches: 61, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
249 73 0.12
250 442 0.72
251 100 0.16
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (250 bp):
AGAAAGAGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTGATAAGTCATTCGGGCC
ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
TGTTAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGCTTTCACATGAAAATGAGAAAG
CGATTACCAAAGTTTCTCATTTAATATTTTCTGAAAATGAAATTTTTAAAAAGTA
Found at i:3381096 original size:42 final size:40
Alignment explanation
Indices: 3381049--3381141 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 40
3381039 TTGTAAGTCA
*
3381049 TTCGGGCCATTAGTAAGTCTATCGAGCATGATGATTAAATCC
1 TTCGGGCCATT-GTAAGTCTATCGAGCAAGATGA-TAAATCC
* * * * *
3381091 TTCGGGTCACCTGTTAGTCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCA-TTGTAAGTCTATCGAGCAAGATGATAAATCC
3381132 TTCGGGCCAT
1 TTCGGGCCAT
3381142 CCGTAAAACC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 14 0.33
42 27 0.64
43 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (40 bp):
TTCGGGCCATTGTAAGTCTATCGAGCAAGATGATAAATCC
Found at i:3381265 original size:38 final size:38
Alignment explanation
Indices: 3381167--3381257 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 38
3381157 GTAGGATGTT
* *
3381167 TTCATTCTTTGTTATTCTTGACTTCCTAGAGAAGAGAA
1 TTCAATCTTTGTTATACTTGACTTCCTAGAGAAGAGAA
* * * * *
3381205 GTCAGTCTTTCTTATACTTGACTTCCTCGTGAAGAGAA
1 TTCAATCTTTGTTATACTTGACTTCCTAGAGAAGAGAA
3381243 TTCAATCTTTGTTAT
1 TTCAATCTTTGTTAT
3381258 CCCTGACTCC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (38 bp):
TTCAATCTTTGTTATACTTGACTTCCTAGAGAAGAGAA
Found at i:3381438 original size:124 final size:124
Alignment explanation
Indices: 3381218--3381443 Score: 348
Period size: 124 Copynumber: 1.8 Consensus size: 124
3381208 AGTCTTTCTT
* * * *
3381218 ATACTTGACTTCCTCGTGAAGAGAATTCAATCTTTGTTATCCCTGACTCCCCTGTAGAGTCAATA
1 ATACTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATCCCTAACTCCCCAGTAGAATCAATA
3381283 CTTGACTTCCTCATGAAAAGAAGTCAATCTTTGTTATCACTGACTCCCTAGTAGAGTCA
66 CTTGACTTCCTCATGAAAAGAAGTCAATCTTTGTTATCACTGACTCCCTAGTAGAGTCA
* *
3381342 ATACTTGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCCTAACTCCCCAGTAGAATCAAT-
1 ATACTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATCCCTAACTCCCCAGTAGAATCAATA
* *
3381406 CATTGACTTCCTCGT-AAAGAGAAGTCAATCTTTTTTAT
66 C-TTGACTTCCTCATGAAA-AGAAGTCAATCTTTGTTAT
3381444 TTGATATTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
123 4 0.04
124 88 0.96
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (124 bp):
ATACTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATCCCTAACTCCCCAGTAGAATCAATA
CTTGACTTCCTCATGAAAAGAAGTCAATCTTTGTTATCACTGACTCCCTAGTAGAGTCA
Found at i:3381444 original size:62 final size:62
Alignment explanation
Indices: 3381218--3381444 Score: 307
Period size: 62 Copynumber: 3.7 Consensus size: 62
3381208 AGTCTTTCTT
* * * *
3381218 ATACTTGACTTCCTCGTGAAGAGAATTCAATCTTTGTTATCCCTGACTCCCCTGTAGAGTCA
1 ATACTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCCAGTAGAGTCA
* *
3381280 ATACTTGACTTCCTCATGAAA-AGAAGTCAATCTTTGTTA-TCACTGACTCCCTAGTAGAGTCA
1 ATACTTGACTTCCTCGT-AAAGAGAAGTCAATCTTTGTTATTC-CTGACTCCCCAGTAGAGTCA
* * * *
3381342 ATACTTGACTTCCTTGTGAAGAGAAGTCAATCTTTGTTATTCCTAACTCCCCAGTAGAATCA
1 ATACTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCCAGTAGAGTCA
*
3381404 AT-CATTGACTTCCTCGTAAAGAGAAGTCAATCTTTTTTATT
1 ATAC-TTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATT
3381445 TGATATTCAT
Statistics
Matches: 145, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
61 4 0.03
62 137 0.94
63 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (62 bp):
ATACTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCTGACTCCCCAGTAGAGTCA
Found at i:3382015 original size:3 final size:3
Alignment explanation
Indices: 3382007--3382050 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3381997 TTTTATGTAT
* *
3382007 ATA ATA ATA ATA ATA ATA ATT ATA ATA ATT AT- ATA ATTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT
3382051 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:3386259 original size:84 final size:84
Alignment explanation
Indices: 3386109--3386266 Score: 228
Period size: 84 Copynumber: 1.9 Consensus size: 84
3386099 ACACTAAAAA
* * * *
3386109 TATATTTTATGACCACCAATATTGTCACACTTAGTACTTTTTAGTGATCAAATGTTCGATACTAT
1 TATACTTTATGACCACCAATATTGGCACACTAAGTACTTTTTAGTGATCAAATGTTCGACACTAT
3386174 TATCAATAAAAATTGTGAC
66 TATCAATAAAAATTGTGAC
* * * *
3386193 TATACTTTGTGACCACCAATGTTGGCACACTAAGTATTATTTTAGTGA-CAAATGTTTGACACTA
1 TATACTTTATGACCACCAATATTGGCACACTAAGTACT-TTTTAGTGATCAAATGTTCGACACTA
3386257 TTATCAATAA
65 TTATCAATAA
3386267 CTCTGCACTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
84 56 0.86
85 9 0.14
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (84 bp):
TATACTTTATGACCACCAATATTGGCACACTAAGTACTTTTTAGTGATCAAATGTTCGACACTAT
TATCAATAAAAATTGTGAC
Found at i:3389617 original size:17 final size:17
Alignment explanation
Indices: 3389568--3389617 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3389558 TAGAGACTAA
3389568 TAACAAAATTTTACCTTT
1 TAACAAAATTTTA-CTTT
3389586 TAACAAATTATTTTA-TTT
1 TAACAAA--ATTTTACTTT
3389604 TAACAACAATTTTA
1 TAACAA-AATTTTA
3389618 ATTATTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.21
18 16 0.55
19 1 0.03
20 6 0.21
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (17 bp):
TAACAAAATTTTACTTT
Found at i:3393953 original size:19 final size:20
Alignment explanation
Indices: 3393919--3393958 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3393909 TTTTATGTAT
*
3393919 AATAATAAAAATAAAATTTA
1 AATAATAAAAATAAAAATTA
*
3393939 AATAA-AAATATAAAAATTA
1 AATAATAAAAATAAAAATTA
3393958 A
1 A
3393959 TTTGGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAATAAAAATAAAAATTA
Found at i:3395015 original size:230 final size:230
Alignment explanation
Indices: 3394612--3395072 Score: 832
Period size: 230 Copynumber: 2.0 Consensus size: 230
3394602 AGTTATTGAA
*
3394612 TGATTGATGGGTTTAATTTTGGTTGGAAAAGATGTGTTGATGTACCAAATTCATCGGCGAACCAA
1 TGATTGATGGGTTTAATTTTGGTTGGAAAAGATGTGTTGATGTACCAAATTCATCGGCCAACCAA
* * * *
3394677 ACTGCCCCTTTTCGCCGTCTCACGCACCGCTACGCACCATCGCTTGTACGTGGGGCTTCTTCCCC
66 ACTACCCCTTGTCGCCGTCTCACGCACCGCCACGCACCATCGCTTGCACGTGGGGCTTCTTCCCC
3394742 TTCTTTGGAAACATTCTAGAATCGGTCCAGTCGGTCTGGACTGGCCCGAACTGGGTCTGTTTGAA
131 TTCTTTGGAAACATTCTAGAATCGGTCCAGTCGGTCTGGACTGGCCCGAACTGGGTCTGTTTGAA
* *
3394807 CCAAATCGAGTTAACTTGACCTGACTCGTTGACTT
196 CCAAATCGAGTTAACTTGACCCGACCCGTTGACTT
*
3394842 TGATTGATGGGTTTAATTTTGGTTGGAAATGATGTGTTGATGTACCAAATTCATCGGCCAACCAA
1 TGATTGATGGGTTTAATTTTGGTTGGAAAAGATGTGTTGATGTACCAAATTCATCGGCCAACCAA
*
3394907 ACTACCCCTTGTCGCCGTCTCACGCACCGCCACGCACTATCGCTTGCACGTGGGGCTTCTTCCCC
66 ACTACCCCTTGTCGCCGTCTCACGCACCGCCACGCACCATCGCTTGCACGTGGGGCTTCTTCCCC
*
3394972 TTCTTTGGAAACCTTCTAGAATCGGTCCAGTCGGTCTGGACTGGCCCGAACTGGGTCTGTTTGAA
131 TTCTTTGGAAACATTCTAGAATCGGTCCAGTCGGTCTGGACTGGCCCGAACTGGGTCTGTTTGAA
3395037 CCAAATCGAGTTAACTTGACCCGACCCGTTGACTT
196 CCAAATCGAGTTAACTTGACCCGACCCGTTGACTT
3395072 T
1 T
3395073 AAGCCGGTCC
Statistics
Matches: 221, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
230 221 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (230 bp):
TGATTGATGGGTTTAATTTTGGTTGGAAAAGATGTGTTGATGTACCAAATTCATCGGCCAACCAA
ACTACCCCTTGTCGCCGTCTCACGCACCGCCACGCACCATCGCTTGCACGTGGGGCTTCTTCCCC
TTCTTTGGAAACATTCTAGAATCGGTCCAGTCGGTCTGGACTGGCCCGAACTGGGTCTGTTTGAA
CCAAATCGAGTTAACTTGACCCGACCCGTTGACTT
Found at i:3396672 original size:22 final size:22
Alignment explanation
Indices: 3396644--3396729 Score: 154
Period size: 22 Copynumber: 3.9 Consensus size: 22
3396634 TCAGTATTTG
3396644 TCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTGGATACA
*
3396666 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACA
3396688 TCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTGGATACA
*
3396710 TCCCAAAGGACCACTGGATA
1 TCCCGAAGGACCACTGGATA
3396730 TGTCCTGAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.14
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACA
Found at i:3401733 original size:24 final size:22
Alignment explanation
Indices: 3401695--3401763 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
3401685 AGTCGAGGGT
* *
3401695 TACATAGGTCATTCGGGACAAA
1 TACACAGGTCCTTCGGGACAAA
*
3401717 GTAACACAGGTCCTTCGGGACATA
1 -T-ACACAGGTCCTTCGGGACAAA
* *
3401741 TACAGAGGTCCTTCGGGATAAA
1 TACACAGGTCCTTCGGGACAAA
3401763 T
1 T
3401764 TTCACATGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
22 19 0.49
23 2 0.05
24 18 0.46
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (22 bp):
TACACAGGTCCTTCGGGACAAA
Found at i:3401752 original size:22 final size:23
Alignment explanation
Indices: 3401695--3401758 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 23
3401685 AGTCGAGGGT
* *
3401695 TACATAGGTCATTCGGGACAAAG
1 TACACAGGTCCTTCGGGACAAAG
*
3401718 TAACACAGGTCCTTCGGGACATA-
1 T-ACACAGGTCCTTCGGGACAAAG
*
3401741 TACAGAGGTCCTTCGGGA
1 TACACAGGTCCTTCGGGA
3401759 TAAATTTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 16 0.44
23 2 0.06
24 18 0.50
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (23 bp):
TACACAGGTCCTTCGGGACAAAG
Found at i:3407053 original size:24 final size:22
Alignment explanation
Indices: 3407021--3407075 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
3407011 AGGGTTATAT
3407021 AGGTCCTTCAGGAAATAGTAACAC
1 AGGTCCTTCAGGAAAT-GT-ACAC
* * *
3407045 AGGTCCTTCGGGACATGTACAG
1 AGGTCCTTCAGGAAATGTACAC
3407067 AGGTCCTTC
1 AGGTCCTTC
3407076 GGGACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 12 0.43
23 2 0.07
24 14 0.50
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (22 bp):
AGGTCCTTCAGGAAATGTACAC
Found at i:3407073 original size:22 final size:24
Alignment explanation
Indices: 3407021--3407081 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
3407011 AGGGTTATAT
* *
3407021 AGGTCCTTCAGGAAATAGTAACAC
1 AGGTCCTTCGGGACATAGTAACAC
*
3407045 AGGTCCTTCGGGACAT-GT-ACAG
1 AGGTCCTTCGGGACATAGTAACAC
3407067 AGGTCCTTCGGGACA
1 AGGTCCTTCGGGACA
3407082 AATTTCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 18 0.53
23 2 0.06
24 14 0.41
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (24 bp):
AGGTCCTTCGGGACATAGTAACAC
Found at i:3407794 original size:16 final size:17
Alignment explanation
Indices: 3407767--3407800 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3407757 AATTTTATTC
3407767 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
3407784 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
3407800 T
1 T
3407801 GACATCTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:3408979 original size:32 final size:32
Alignment explanation
Indices: 3408892--3408986 Score: 120
Period size: 31 Copynumber: 3.0 Consensus size: 32
3408882 ATAACATAAA
*
3408892 AACTCGTTAGTCTATATTGATAAGGAAATTAAG
1 AACTCGTTAGT-TATATTGATAAGAAAATTAAG
* * *
3408925 GATTCGTCAG-TATATTGATAAGAAAATTAAG
1 AACTCGTTAGTTATATTGATAAGAAAATTAAG
* *
3408956 AACTCGTTAGTTATATTGGTAAGAGAATTAA
1 AACTCGTTAGTTATATTGATAAGAAAATTAA
3408987 AGATTCGCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 27 0.52
32 18 0.35
33 7 0.13
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (32 bp):
AACTCGTTAGTTATATTGATAAGAAAATTAAG
Found at i:3413030 original size:37 final size:37
Alignment explanation
Indices: 3412930--3413031 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 37
3412920 TCTTTTCGTC
*
3412930 CTACTAGGATTCAAACTCTTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCTTAAAAATAGGATAGAATT
* * *
3412967 -T--TAGGATTCAAATTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCTTAAAAATAGGATAGAATT
* * *
3413001 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCTTAAAAATAGGAT
3413032 TCACAAGCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
34 29 0.55
35 1 0.02
36 1 0.02
37 22 0.42
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCTTAAAAATAGGATAGAATT
Found at i:3413442 original size:2 final size:2
Alignment explanation
Indices: 3413437--3413479 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3413427 TTAGTGTTAT
3413437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3413479 T
1 T
3413480 TTCCTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3413567 original size:20 final size:20
Alignment explanation
Indices: 3413542--3413579 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3413532 ATTATTATTA
3413542 TTTTACTTATATATATATGT
1 TTTTACTTATATATATATGT
* *
3413562 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3413580 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTACTTATATATATATGT
Found at i:3413608 original size:37 final size:36
Alignment explanation
Indices: 3413522--3413609 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 36
3413512 CTTTTGATTT
*
3413522 TCTTTTTA-TTATTATTATTATTTTACTTATATATATA
1 TCTTTTTACTT-TT-TTATTATTTTACTCATATATATA
* * *
3413559 TGTTTTTACTTTTTTATATATTTTACTCATTTATTTA
1 TCTTTTTACTTTTTTAT-TATTTTACTCATATATATA
3413596 TCTATTTT-CTTTTT
1 TCT-TTTTACTTTTT
3413610 ATCTTTATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 4 0.09
37 33 0.77
38 6 0.14
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (36 bp):
TCTTTTTACTTTTTTATTATTTTACTCATATATATA
Found at i:3416829 original size:17 final size:18
Alignment explanation
Indices: 3416807--3416850 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3416797 ATCCAATCAA
3416807 AAAC-AAAGAAAAAAGAG
1 AAACAAAAGAAAAAAGAG
*
3416824 AAACAAAAGAAAAAAGAA
1 AAACAAAAGAAAAAAGAG
3416842 AGAACAAAA
1 A-AACAAAA
3416851 TCAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (18 bp):
AAACAAAAGAAAAAAGAG
Found at i:3416847 original size:19 final size:18
Alignment explanation
Indices: 3416805--3416863 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 18
3416795 AGATCCAATC
3416805 AAAAAC-AAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
*
3416822 AGAAACAAAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
**
3416840 AAAGAACAAAATCAAAAAG
1 AAA-AACAAAAGAAAAAAG
3416859 AAAAA
1 AAAAA
3416864 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 5 0.14
18 15 0.42
19 16 0.44
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAAG
Found at i:3417493 original size:22 final size:22
Alignment explanation
Indices: 3417465--3417541 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
3417455 GCTACCCCAT
3417465 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
*
3417487 CAAACCTTTGAACATCAAAT-A
1 CAAACCTTTGAGCATCAAATGA
* *
3417508 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
3417531 CAAACCTTTGA
1 CAAACCTTTGA
3417542 CCAAACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:3418318 original size:37 final size:35
Alignment explanation
Indices: 3418275--3418408 Score: 142
Period size: 37 Copynumber: 3.7 Consensus size: 35
3418265 TTTCCAATAT
* *
3418275 AAATTTTGTCTCGCTTGAGACAGTCTCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTC-TTTGAAAC
* * * *
3418311 AAGATTTTATCTCGCTTGAGATAGTTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGACAG--TCTCTTTGAAAC
* * *
3418349 AAATTTCGTCTCCCTTGAGACAATCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTC-TCTTTGAAAC
3418385 AAATTTTGTCTCCCTTGAGACAGT
1 AAATTTTGTCTCCCTTGAGACAGT
3418409 TTCTCTCCAG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
35 1 0.01
36 33 0.41
37 35 0.43
38 9 0.11
39 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (35 bp):
AAATTTTGTCTCCCTTGAGACAGTCTCTTTGAAAC
Found at i:3418371 original size:21 final size:21
Alignment explanation
Indices: 3418342--3418402 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3418332 TAGTTTTTCT
3418342 TTGAAACAAATTTCGTCTCCC
1 TTGAAACAAATTTCGTCTCCC
*
3418363 TTGAGAC-AA--TC-T-T-CC
1 TTGAAACAAATTTCGTCTCCC
*
3418378 TTGAAACAAATTTTGTCTCCC
1 TTGAAACAAATTTCGTCTCCC
3418399 TTGA
1 TTGA
3418403 GACAGTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
15 8 0.26
16 3 0.10
17 1 0.03
18 3 0.10
19 1 0.03
20 3 0.10
21 12 0.39
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGAAACAAATTTCGTCTCCC
Found at i:3418602 original size:106 final size:106
Alignment explanation
Indices: 3418413--3420111 Score: 2740
Period size: 106 Copynumber: 16.0 Consensus size: 106
3418403 GACAGTTTCT
* * *
3418413 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3418478 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTTGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * * ** **
3418519 CTCAAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCTT
1 CTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
3418583 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTAGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
3418625 CTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3418690 ATTTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3418731 CTCCATG-CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 CTCCA-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3418795 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
3418837 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3418902 ATTTCAGAGCCAATTTCAACTTCATAGTGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3418943 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
3419008 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3419049 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
3419114 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
3419155 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTCTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3419220 ATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
3419261 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAAAAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3419326 ATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3419367 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
3419432 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3419473 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
* *
3419538 ATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * *
3419579 CTCCAGACAACCCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
3419644 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * *
3419685 CTCCAGACAACGCAAGTTCAACTTTACGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
3419750 ATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
3419791 CTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
3419856 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * ** *
3419897 CTCGAGACGACGCAAGTTCAACTTCAAAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
*
3419962 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * *
3420003 CTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAATAATTTCCC
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCC
* * *
3420067 GATTACAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGA
3420109 CTC
1 CTC
3420112 TGAACAATCC
Statistics
Matches: 1494, Mismatches: 93, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
105 5 0.00
106 1487 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
Found at i:3421437 original size:20 final size:20
Alignment explanation
Indices: 3421412--3421449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3421402 ATTATTATTA
3421412 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
3421432 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
3421450 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:3424756 original size:16 final size:17
Alignment explanation
Indices: 3424722--3424781 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
3424712 AGATATTAAG
3424722 AAAA-AAAATAATAGAA
1 AAAATAAAATAATAGAA
*
3424738 AAAATAAAATAA-AGTA
1 AAAATAAAATAATAGAA
* *
3424754 AAAATATAATATATATAA
1 AAAATAAAATA-ATAGAA
3424772 ATAAATAAAA
1 A-AAATAAAA
3424782 AAAAAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 17 0.49
17 8 0.23
18 3 0.09
19 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATAAAATAATAGAA
Found at i:3424790 original size:30 final size:30
Alignment explanation
Indices: 3424722--3424790 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
3424712 AGATATTAAG
3424722 AAAAAAA-ATAATAGAAAAAATAAAATAAA
1 AAAAAAATATAATAGAAAAAATAAAATAAA
** * *
3424751 GTAAAAATATAATATATATAAAT-AAATAAA
1 AAAAAAATATAATAGA-AAAAATAAAATAAA
3424781 AAAAAAATAT
1 AAAAAAATAT
3424791 TAAGAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 5 0.16
30 22 0.69
31 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (30 bp):
AAAAAAATATAATAGAAAAAATAAAATAAA
Found at i:3424798 original size:25 final size:25
Alignment explanation
Indices: 3424744--3424808 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
3424734 AGAAAAAATA
* * *
3424744 AAATAAAGTAAAAATATAATATATAT
1 AAATAAA-TAAAAAAAAAATATATAG
3424770 AAATAAATAAAAAAAAAATAT-TAAG
1 AAATAAATAAAAAAAAAATATAT-AG
* *
3424795 AAATATATATAAAA
1 AAATAAATAAAAAA
3424809 CGTATAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 1 0.03
25 25 0.76
26 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (25 bp):
AAATAAATAAAAAAAAAATATATAG
Found at i:3424801 original size:31 final size:30
Alignment explanation
Indices: 3424739--3424807 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
3424729 ATAATAGAAA
** * *
3424739 AAATAAAATAAAGTAAAAATATAATATATAT
1 AAAT-AAATAAAAAAAAAATATAAGAAATAT
3424770 AAATAAATAAAAAAAAAATATTAAGAAATAT
1 AAATAAATAAAAAAAAAATA-TAAGAAATAT
*
3424801 ATATAAA
1 AAATAAA
3424808 ACGTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATAAATAAAAAAAAAATATAAGAAATAT
Found at i:3424889 original size:2 final size:2
Alignment explanation
Indices: 3424882--3424933 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
3424872 ATACAAATAC
3424882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
3424923 AG AT AT AT AT A
1 AT AT AT AT AT A
3424934 ATAAAAATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3424937 original size:14 final size:14
Alignment explanation
Indices: 3424882--3424947 Score: 66
Period size: 14 Copynumber: 4.8 Consensus size: 14
3424872 ATACAAATAC
*
3424882 ATATATATATATAT
1 ATATATATATATAA
*
3424896 ATATATATATATAT
1 ATATATATATATAA
3424910 ATATA-ATGATATAA
1 ATATATAT-ATATAA
3424924 GATATATATA-ATAA
1 -ATATATATATATAA
*
3424938 AAATA-ATATA
1 ATATATATATA
3424948 ATATTAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
12 3 0.07
13 7 0.15
14 28 0.61
15 6 0.13
16 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:3424946 original size:25 final size:27
Alignment explanation
Indices: 3424898--3424948 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
3424888 ATATATATAT
* *
3424898 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
3424925 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
3424949 TATTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:3424956 original size:16 final size:17
Alignment explanation
Indices: 3424886--3424956 Score: 58
Period size: 19 Copynumber: 4.1 Consensus size: 17
3424876 AAATACATAT
*
3424886 ATATATATATATATATATAT
1 ATATATATA-ATAT-TA-AA
*
3424906 ATATATATAATGATATAAG
1 ATATATATAAT-AT-TAAA
3424925 ATATATATAATA--AAA
1 ATATATATAATATTAAA
3424940 ATA-ATATAATATTAAA
1 ATATATATAATATTAAA
3424956 A
1 A
3424957 AAATGGAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.17
15 5 0.11
16 4 0.09
18 1 0.02
19 14 0.30
20 14 0.30
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATATATAATATTAAA
Found at i:3426824 original size:19 final size:20
Alignment explanation
Indices: 3426800--3426847 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3426790 AACGATTTTC
*
3426800 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3426819 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3426839 TTTTGAAAA
1 TTTTGAAAA
3426848 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3428218 original size:18 final size:18
Alignment explanation
Indices: 3428195--3428248 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
3428185 ACCGGTCACA
3428195 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
3428213 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
3428231 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
3428249 TTGACCGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:3429596 original size:18 final size:18
Alignment explanation
Indices: 3429570--3429604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3429560 TCAAAAGGAC
*
3429570 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3429588 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3429605 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3430741 original size:12 final size:12
Alignment explanation
Indices: 3430726--3430764 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3430716 GATACGTTAC
3430726 CTGAATTCTGTT
1 CTGAATTCTGTT
*
3430738 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
3430749 CTGGATTCTGTT
1 CTGAATTCTGTT
3430761 CTGA
1 CTGA
3430765 TATCTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:3430746 original size:11 final size:11
Alignment explanation
Indices: 3430730--3430765 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3430720 CGTTACCTGA
3430730 ATTCTGTTCTG
1 ATTCTGTTCTG
*
3430741 ATTCTGATCTGG
1 ATTCTGTTCT-G
3430753 ATTCTGTTCTG
1 ATTCTGTTCTG
3430764 AT
1 AT
3430766 ATCTAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:3432964 original size:18 final size:18
Alignment explanation
Indices: 3432918--3432965 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3432908 GGTCACAACC
*
3432918 TGACCCGACCAGACCCGT
1 TGACCCGACCCGACCCGT
*
3432936 TGACCCGACCCGACCTGT
1 TGACCCGACCCGACCCGT
3432954 TGACCCGACCCG
1 TGACCCGACCCG
3432966 TTGATCGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:3433014 original size:12 final size:12
Alignment explanation
Indices: 3432993--3433022 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3432983 TTGACCACTG
*
3432993 TTGACCAAAACT
1 TTGACTAAAACT
3433005 TTGACTAAAACT
1 TTGACTAAAACT
3433017 TTGACT
1 TTGACT
3433023 GGCTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (12 bp):
TTGACTAAAACT
Found at i:3434325 original size:18 final size:18
Alignment explanation
Indices: 3434299--3434333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3434289 TCAAAAGAAC
*
3434299 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3434317 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3434334 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3435470 original size:12 final size:12
Alignment explanation
Indices: 3435432--3435523 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
3435422 ATTTTCGAAT
3435432 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3435444 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
3435456 TGAATTCTGTTC
1 TGAATTCTGTTC
*
3435468 TG-ATTCTGATC
1 TGAATTCTGTTC
* *
3435479 TGGATTCTGTTA
1 TGAATTCTGTTC
* *
3435491 TGATATT-TGATA
1 TGA-ATTCTGTTC
*
3435503 TGAATTCTGTTT
1 TGAATTCTGTTC
*
3435515 TGATTTCTG
1 TGAATTCTG
3435524 ATATCTCCGT
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
10 3 0.05
11 16 0.25
12 35 0.56
13 6 0.10
14 3 0.05
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:3435509 original size:24 final size:23
Alignment explanation
Indices: 3435456--3435527 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
3435446 ATACGTTACC
* * *
3435456 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTATGATTTTGATA
*
3435479 TGGATTCTGTTATGATATTTGATA
1 TGAATTCTGTTATGAT-TTTGATA
*
3435503 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTT-TGATA
3435527 T
1 T
3435528 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 16 0.39
24 25 0.61
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (23 bp):
TGAATTCTGTTATGATTTTGATA
Found at i:3437681 original size:18 final size:18
Alignment explanation
Indices: 3437654--3437700 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
3437644 AACCTGACCC
3437654 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* *
3437672 GACTCGACCCGACCTGTT
1 GACCCGACCCGACCCGTT
3437690 GACCCGACCCG
1 GACCCGACCCG
3437701 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:3437693 original size:13 final size:13
Alignment explanation
Indices: 3437677--3437706 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3437667 CCGTTGACTC
*
3437677 GACCCGACCTGTT
1 GACCCGACCCGTT
3437690 GACCCGACCCGTT
1 GACCCGACCCGTT
3437703 GACC
1 GACC
3437707 GTTGACTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3437749 original size:12 final size:12
Alignment explanation
Indices: 3437728--3437757 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3437718 TTGACCACTG
*
3437728 TTGACCAAAACT
1 TTGACTAAAACT
3437740 TTGACTAAAACT
1 TTGACTAAAACT
3437752 TTGACT
1 TTGACT
3437758 GGCTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (12 bp):
TTGACTAAAACT
Found at i:3439060 original size:18 final size:18
Alignment explanation
Indices: 3439034--3439068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3439024 TCAAAAGGAC
*
3439034 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3439052 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3439069 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3441877 original size:20 final size:20
Alignment explanation
Indices: 3441849--3441912 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
3441839 AATCAGATTG
*
3441849 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
3441869 CCCAAGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
3441889 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
3441909 CCCA
1 CCCA
3441913 CGCTCCAAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:3442234 original size:35 final size:33
Alignment explanation
Indices: 3442189--3442261 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
3442179 CCTTTTGTAA
* * *
3442189 AGGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
3442224 AGGGAAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
3442257 AGGGA
1 AGGGA
3442262 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 11 0.32
34 1 0.03
35 22 0.65
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (33 bp):
AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:3443931 original size:106 final size:106
Alignment explanation
Indices: 3443619--3443987 Score: 474
Period size: 106 Copynumber: 3.4 Consensus size: 106
3443609 TGTTTCCGAA
** * * *
3443619 TCCAATAT-CCTC-CGTCGTGAAGTTGAAATTGGCTCTGGAACTAGGAAATTGTTTGTTAACAGC
1 TCCAATATCCCTCGC-T-GTGAAGTTGAAATTGGCTCTAAAACTGGGAAAATATTTGTTAACAGC
* * *
3443682 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAG
64 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
* * * * * * * *
3443725 TTCATTATCCTTCGCTGTGAAGTTGAAATAGACTCTGAATAAAAT-TGAAAAGTTATTTGTTGAC
1 TCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCT--A-AAACTGGGAAAA--TATTTGTTAAC
**
3443789 AATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
61 AGCCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
3443835 TCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAAATATTTGTTAACAGCCA
1 TCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAAATATTTGTTAACAGCCA
3443900 GTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
66 GTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
* *
3443941 TTCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
1 TCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAA
3443988 GCCCCTTCGT
Statistics
Matches: 226, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
106 123 0.54
107 8 0.04
108 11 0.05
109 3 0.01
110 81 0.36
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
TCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAAATATTTGTTAACAGCCA
GTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAG
Found at i:3444826 original size:67 final size:65
Alignment explanation
Indices: 3444707--3445012 Score: 227
Period size: 65 Copynumber: 4.5 Consensus size: 65
3444697 TGTTCCATGA
* * **
3444707 AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAA
3444772 GAG
63 GAG
* *
3444775 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
* * * * ** * *
3444840 AAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ACTTAG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-ATTCAAAGATTTTG
* *
3444904 TTCCAAAAG
57 TTTCAAGAG
** * *** * * * * *
3444913 AAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
* * *
3444978 AAACTGTCTCGAGAGAGACAAAATTTGTTTCAAGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGG
3445013 AAAACTGTCT
Statistics
Matches: 189, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
64 5 0.03
65 83 0.44
66 4 0.02
67 25 0.13
68 21 0.11
70 1 0.01
72 1 0.01
73 44 0.23
74 5 0.03
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
Found at i:3444864 original size:65 final size:67
Alignment explanation
Indices: 3444707--3444878 Score: 231
Period size: 65 Copynumber: 2.6 Consensus size: 67
3444697 TGTTCCATGA
* * **
3444707 AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAA
3444772 GAG
65 GAG
*
3444775 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAG
*
3444838 GG
66 AG
* * * *
3444840 AAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAA
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
3444879 CTGTCTCAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
65 44 0.47
66 3 0.03
67 25 0.27
68 21 0.23
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (67 bp):
AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAG
AG
Found at i:3444879 original size:36 final size:35
Alignment explanation
Indices: 3444827--3445052 Score: 191
Period size: 36 Copynumber: 6.5 Consensus size: 35
3444817 ATTCAAAGAT
*
3444827 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGA-TAAA
*
3444863 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGA-TAAA
* * * *
3444899 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAT-AAA
* *
3444936 TTTGTTTCAA-ATAAAACATAT-TC---A-A-AT-AA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGATAAA
* * *
3444965 TTTGTTTCAAGGGAAACTGTCTCGAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGA-TAAA
3445001 TTTGTTTCAAG-GAAAACTGTCTCAAGAGAGATGAAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGAT-AAA
* *
3445037 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
3445053 TGTTTTCAAT
Statistics
Matches: 155, Mismatches: 19, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
31 2 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 2 0.01
36 94 0.61
37 33 0.21
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (35 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAA
Found at i:3444924 original size:37 final size:36
Alignment explanation
Indices: 3444839--3444930 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 36
3444829 TGTTTCAAGG
* * * *
3444839 GAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
3444875 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
3444912 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
3444931 TGAAATTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 23 0.46
37 27 0.54
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:3444930 original size:138 final size:138
Alignment explanation
Indices: 3444773--3445031 Score: 385
Period size: 138 Copynumber: 1.9 Consensus size: 138
3444763 GTGTTTCAAG
* ** * * *
3444773 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
3444838 GGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAACTT
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACTGTCTCAAGAGAGACAAAACTT
3444902 AGTTCCAAA
130 AGTTCCAAA
** * * *
3444911 AGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
3444976 GGAAACTGTCTCGAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGA
3445032 TGAAATTTAT
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 105 0.98
139 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:3445118 original size:101 final size:100
Alignment explanation
Indices: 3444861--3445118 Score: 293
Period size: 101 Copynumber: 2.5 Consensus size: 100
3444851 AGAGAGACTA
* *
3444861 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAA-AAACTGTCTCAAG
* * *
3444926 GGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
64 AGAGATGAAATTTATTTCAAAGAAAACATATTCAAAT
* * *
3444963 AATTTGTTTCAAGGGAAACTGTCTCGAGAGAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-AAAAACTGTCTCAAGA
* * ** *
3445028 GAGATGAAATTTATTTCAAGGGAAATGTTTTC-AAT
65 GAGATGAAATTTATTTCAAAGAAAACATATTCAAAT
** * * **
3445063 GTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAAC
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAA-AAAAC
3445119 ATATTCAAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
100 5 0.04
101 89 0.68
102 37 0.28
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (100 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAAACTGTCTCAAGAG
AGATGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:3445126 original size:65 final size:65
Alignment explanation
Indices: 3445003--3445148 Score: 152
Period size: 65 Copynumber: 2.2 Consensus size: 65
3444993 AGACAAAATT
* * ** *
3445003 TGTTTCAAGGAAAACTGTCTCAAGAGAGATGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGAAAACTGTCTCAAGAGAGATGAAATTTATTTCAAAGAAAACATATTCAATGTTTA
* * * * **
3445068 TGTTTCAA-GAGAAATTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAAT
1 TGTTTCAAGGA-AAACTGTCTCAAGAGAGATGAAATTTATTTCAAAGAAAACATATTC-AATGTT
3445132 T-
64 TA
*
3445133 TGTTTCAAGGGAAACT
1 TGTTTCAAGGAAAACT
3445149 TGGAAACTGT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
64 2 0.03
65 57 0.88
66 6 0.09
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (65 bp):
TGTTTCAAGGAAAACTGTCTCAAGAGAGATGAAATTTATTTCAAAGAAAACATATTCAATGTTTA
Found at i:3446030 original size:31 final size:32
Alignment explanation
Indices: 3445965--3446058 Score: 145
Period size: 31 Copynumber: 2.9 Consensus size: 32
3445955 ATTCCCAAAG
* *
3445965 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAATATTTGATGTTAAATCTCAAAAA
*
3445997 ATGCCCCAACATTTGATGTTAAATCT-AAAAA
1 ATGCCCCAATATTTGATGTTAAATCTCAAAAA
3446028 ATGCCCCAATATTTGATGTTAAATCTTCAAA
1 ATGCCCCAATATTTGATGTTAAATC-TCAAA
3446059 GATGCCCTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 29 0.52
32 24 0.43
33 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (32 bp):
ATGCCCCAATATTTGATGTTAAATCTCAAAAA
Found at i:3447092 original size:69 final size:69
Alignment explanation
Indices: 3446977--3447110 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 69
3446967 TGTCTCTCTC
3446977 TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAATAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAATAATTCAGAAATGATTGTGCTTGATCAATC
3447042 ACAT
66 ACAT
* * * * *
3447046 TTGATGCTCTATGATCTTCGAGT-GAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCCATGATCTTCGAGTAG-AGTGATGCAATAATTCAGAAATGATTGTGCTTGATCAAT
3447110 C
65 C
3447111 TCATAGTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTAGAGTGATGCAATAATTCAGAAATGATTGTGCTTGATCAATC
ACAT
Found at i:3450621 original size:16 final size:17
Alignment explanation
Indices: 3450589--3450627 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3450579 TATTAAGAAA
3450589 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
3450606 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
*
3450622 ATAATA
1 AAAATA
3450628 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:3450776 original size:21 final size:19
Alignment explanation
Indices: 3450768--3450817 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3450758 TACATATAAT
3450768 ATATATATATAATAATATA
1 ATATATATATAATAATATA
* *
3450787 AGATATATATAATAAAAATA
1 ATATATATATAAT-AATATA
3450807 ATATA-ATATAA
1 ATATATATATAA
3450818 ATAAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATATATATAATAATATA
Found at i:3450806 original size:25 final size:23
Alignment explanation
Indices: 3450766--3450812 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
3450756 CATACATATA
*
3450766 ATATATATATATAATAATATAAG
1 ATATATATATAAAATAATATAAG
3450789 ATATATATAATAAAAATAATATAA
1 ATATATAT-AT-AAAATAATATAA
3450813 TATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 2 0.10
25 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATATATATAAAATAATATAAG
Found at i:3450815 original size:19 final size:19
Alignment explanation
Indices: 3450763--3450824 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
3450753 ATACATACAT
3450763 ATAATAT-ATATATATAATAA
1 ATAATATAATATA-ATAA-AA
*
3450783 TATAAGATATATATAATAAAA
1 -ATAATATA-ATATAATAAAA
3450804 ATAATATAATATAAATAAAA
1 ATAATATAATAT-AATAAAA
3450824 A
1 A
3450825 AGAGGAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 4 0.11
20 15 0.42
21 8 0.22
22 4 0.11
23 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATATAATATAATAAAA
Found at i:3450815 original size:23 final size:23
Alignment explanation
Indices: 3450761--3450860 Score: 73
Period size: 23 Copynumber: 4.3 Consensus size: 23
3450751 CTATACATAC
*
3450761 ATATAATATATAT-AT-ATAATA
1 ATATAATATATATAATAAAAATA
3450782 ATATAAGATATATATAATAAAAATA
1 ATAT-A-ATATATATAATAAAAATA
* *
3450807 ATATAATATAAATAA-AAAAGAGGA
1 ATATAATATATATAATAAAA-A-TA
* * *
3450831 ATATAGTAAATA-AATAAATAAAA
1 ATATAATATATATAATAAA-AATA
3450854 ATATAAT
1 ATATAAT
3450861 TAAAAATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
21 4 0.06
22 5 0.08
23 27 0.43
24 17 0.27
25 10 0.16
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (23 bp):
ATATAATATATATAATAAAAATA
Found at i:3452831 original size:18 final size:18
Alignment explanation
Indices: 3452810--3452857 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
3452800 CAAATTATTC
*
3452810 TTAAAAATATAAAAATAT
1 TTAAAAATATAAAAAAAT
3452828 TT-AAAATATAAAAAAAT
1 TTAAAAATATAAAAAAAT
*
3452845 TTAAAAATTTAAA
1 TTAAAAATATAAA
3452858 GTAAACAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAATATAAAAAAAT
Found at i:3461079 original size:16 final size:17
Alignment explanation
Indices: 3461011--3461089 Score: 79
Period size: 18 Copynumber: 4.5 Consensus size: 17
3461001 TCGTCCCGTT
*
3461011 GGACCACTATGCCCCGAA
1 GGACCAC-ATGTCCCGAA
*
3461029 GTACCACTATGTCCCGAA
1 GGACCAC-ATGTCCCGAA
*
3461047 GGACCACTATATCCCGAA
1 GGACCAC-ATGTCCCGAA
*
3461065 TGACCAC-TGTCCCGAA
1 GGACCACATGTCCCGAA
*
3461081 GGTCCACAT
1 GGACCACAT
3461090 ATCACATATG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
16 13 0.25
17 1 0.02
18 38 0.73
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.18
Consensus pattern (17 bp):
GGACCACATGTCCCGAA
Found at i:3461081 original size:34 final size:35
Alignment explanation
Indices: 3461011--3461092 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
3461001 TCGTCCCGTT
**
3461011 GGACCACTATGCCCCGAAGTACCACTATGTCCCGAA
1 GGACCACTATATCCCGAAGTACCAC-ATGTCCCGAA
3461047 GGACCACTATATCCCGAA-TGACCAC-TGTCCCGAA
1 GGACCACTATATCCCGAAGT-ACCACATGTCCCGAA
*
3461081 GGTCCAC-ATATC
1 GGACCACTATATC
3461093 ACATATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 5 0.12
34 15 0.36
35 1 0.02
36 21 0.50
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.18
Consensus pattern (35 bp):
GGACCACTATATCCCGAAGTACCACATGTCCCGAA
Found at i:3462411 original size:17 final size:18
Alignment explanation
Indices: 3462380--3462413 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3462370 GATTTCACTT
*
3462380 ATTCCTCTCTTTTCTCTA
1 ATTCCTCTCTATTCTCTA
3462398 ATTCC-CTCTATTCTCT
1 ATTCCTCTCTATTCTCT
3462414 TCATCTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTCCTCTCTATTCTCTA
Found at i:3462867 original size:30 final size:30
Alignment explanation
Indices: 3462798--3462867 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3462788 TACAATTGCT
* *
3462798 ACAGTGACCACCATAGGTCTCCAGGAGCAC
1 ACAGTGACCTCCATAGGTCTCCAGGAGAAC
* * *
3462828 ACAGCGACCTCCATAGGTTTCTAGGAGAAC
1 ACAGTGACCTCCATAGGTCTCCAGGAGAAC
*
3462858 ACGGTGACCT
1 ACAGTGACCT
3462868 ATGGAGGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (30 bp):
ACAGTGACCTCCATAGGTCTCCAGGAGAAC
Found at i:3462878 original size:19 final size:19
Alignment explanation
Indices: 3462851--3462891 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3462841 TAGGTTTCTA
**
3462851 GGAGAACACGGTGACCTAT
1 GGAGAACACGACGACCTAT
*
3462870 GGAGGACACGACGACCTAT
1 GGAGAACACGACGACCTAT
3462889 GGA
1 GGA
3462892 ACACTTGGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.34, T:0.12
Consensus pattern (19 bp):
GGAGAACACGACGACCTAT
Found at i:3463207 original size:45 final size:45
Alignment explanation
Indices: 3463158--3463263 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 45
3463148 AGTAAGTTAT
* * * *
3463158 AACACTTTAGGTTAATATTTTGTTTAAACTTAAACATAAAATTTA
1 AACACTTTAGATTAATATTATGTTTAAACATAAACATAAAACTTA
** *
3463203 AACACTTTAGATTAATATTATGTTTAAACATAAATGTAAAACTTC
1 AACACTTTAGATTAATATTATGTTTAAACATAAACATAAAACTTA
*
3463248 AATACTTTAGATTAAT
1 AACACTTTAGATTAAT
3463264 TGACGAACAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (45 bp):
AACACTTTAGATTAATATTATGTTTAAACATAAACATAAAACTTA
Found at i:3475106 original size:21 final size:23
Alignment explanation
Indices: 3475060--3475107 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3475050 ATCAAGTACA
* *
3475060 ATAATATATTAGGTAGGGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
3475083 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
3475106 AT
1 AT
3475108 TAACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:3475817 original size:19 final size:19
Alignment explanation
Indices: 3475795--3475835 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3475785 TCGATACATT
3475795 TTTTATAAAGTATCGACAC
1 TTTTATAAAGTATCGACAC
3475814 TTTTATAAAGTATCGACAC
1 TTTTATAAAGTATCGACAC
3475833 TTT
1 TTT
3475836 ATTAGCACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (19 bp):
TTTTATAAAGTATCGACAC
Found at i:3476138 original size:182 final size:182
Alignment explanation
Indices: 3475814--3476382 Score: 917
Period size: 182 Copynumber: 3.1 Consensus size: 182
3475804 GTATCGACAC
*
3475814 TTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTTTCTTTTTAAATTCCAAAAGTGTC
1 TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTC-TTTTAAATTCCAAAAGTGTC
*
3475879 GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTT
65 GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTT
*
3475944 ATAGAACGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
130 ATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
*
3475997 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
1 TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
* * * * * **
3476062 ATACTTATAATAAAGTATTGATACTTTCAACATATCTGGTAGCTATTTA-CTGGTTTTGTCATTT
66 ATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCT-GTTTTGTCATTT
** *
3476126 CGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
130 ATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
* *
3476179 TTTTATAAAGTATCGACACTCTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
1 TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
*
3476244 ATACTTATAATAAAATATCGACACTATCAACATATCCAGTAGCGCTTTACCTGTTTTGTCATTTA
66 ATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTA
* *
3476309 TAGACCGATTTT-TCATTTTTTTTACCTTTTATATTGTTATGGATCGATACAT
131 TAGACCGGTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACAT
*
3476361 TTTTATAAAGTATCAACACTTT
1 TTTTATAAAGTATCGACACTTT
3476383 CAATATATCC
Statistics
Matches: 351, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
181 5 0.01
182 302 0.86
183 44 0.13
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
ATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTA
TAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
Found at i:3476419 original size:112 final size:112
Alignment explanation
Indices: 3476253--3476716 Score: 750
Period size: 112 Copynumber: 4.1 Consensus size: 112
3476243 GATACTTATA
* * * *
3476253 ATAAAATATCGACACTATCAACATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
3476318 TTT-TCATTTTTTTTACCTTTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* *
3476365 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
3476430 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
3476477 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
3476542 TTTGTCATTTTTTTACCTGTTATATTGTTATTGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* *
3476589 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
3476654 TTTGTCATTTTTTTTACTTGTTATATTGTTACGGATCAATATATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
3476702 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
3476717 AAACCGACAA
Statistics
Matches: 331, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
112 276 0.83
113 55 0.17
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:3479035 original size:26 final size:24
Alignment explanation
Indices: 3479013--3479079 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 24
3479003 TTATAAAATC
3479013 TTATAAAATAAATAAATTTTAAAA
1 TTATAAAATAAATAAATTTTAAAA
* *
3479037 GTTATAAAATTAAAATATATTTTTAAA
1 -TTATAAAA-T-AAATAAATTTTAAAA
3479064 TTATAAAA-AATATAAA
1 TTATAAAATAA-ATAAA
3479080 AAAAAACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.06
24 4 0.11
25 8 0.22
26 9 0.25
27 13 0.36
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
TTATAAAATAAATAAATTTTAAAA
Found at i:3479299 original size:23 final size:25
Alignment explanation
Indices: 3479273--3479326 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
3479263 AAATTAATTT
3479273 TATTTTTAATA-TTCAT-TTTTAAA
1 TATTTTTAATATTTCATATTTTAAA
*
3479296 TA-TTTT-ATATTTTATATTTTAAA
1 TATTTTTAATATTTCATATTTTAAA
3479319 TATTTTTA
1 TATTTTTA
3479327 TTTTGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.31
23 11 0.42
24 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTTAATATTTCATATTTTAAA
Found at i:3479312 original size:14 final size:15
Alignment explanation
Indices: 3479269--3479316 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
3479259 TAGCAAATTA
3479269 ATTTTAT-TTTTAAT
1 ATTTTATATTTTAAT
*
3479283 A-TTCAT-TTTTAAAT
1 ATTTTATATTTT-AAT
3479297 ATTTTATATTTT-AT
1 ATTTTATATTTTAAT
3479311 ATTTTA
1 ATTTTA
3479317 AATATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 8 0.28
14 13 0.45
15 4 0.14
16 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTATATTTTAAT
Found at i:3482186 original size:23 final size:23
Alignment explanation
Indices: 3482160--3482208 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3482150 CAAGCACATT
*
3482160 AAACATACATATACACTTATCAA
1 AAACATACATATACACTTATAAA
* *
3482183 AAACATGCATTTACACTTATAAA
1 AAACATACATATACACTTATAAA
3482206 AAA
1 AAA
3482209 TTAAACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (23 bp):
AAACATACATATACACTTATAAA
Found at i:3484131 original size:2 final size:2
Alignment explanation
Indices: 3484124--3484148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3484114 ATAGATATGA
3484124 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3484149 GGTAGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3486091 original size:21 final size:20
Alignment explanation
Indices: 3486061--3486099 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3486051 TCACTTTATT
*
3486061 TTATTTATTTATTTATTCTGG
1 TTATTAATTTATTT-TTCTGG
3486082 TTATTAATTTATTTTTCT
1 TTATTAATTTATTTTTCT
3486100 TTGATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TTATTAATTTATTTTTCTGG
Found at i:3487937 original size:29 final size:29
Alignment explanation
Indices: 3487895--3487957 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
3487885 TTAATTGGAA
3487895 AAGTTTGGATGAATTCTAAAAGAATTCAT
1 AAGTTTGGATGAATTCTAAAAGAATTCAT
3487924 AAGTTTGGATGAATTCTAAAAGAATTCAT
1 AAGTTTGGATGAATTCTAAAAGAATTCAT
3487953 AAGTT
1 AAGTT
3487958 GTGGTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (29 bp):
AAGTTTGGATGAATTCTAAAAGAATTCAT
Found at i:3487974 original size:29 final size:29
Alignment explanation
Indices: 3487895--3487973 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3487885 TTAATTGGAA
* *
3487895 AAGTTTGGATGAATTCTAAAAGAATTCAT
1 AAGTTTGGATAAAATCTAAAAGAATTCAT
* *
3487924 AAGTTTGGATGAATTCTAAAAGAATTCAT
1 AAGTTTGGATAAAATCTAAAAGAATTCAT
* *
3487953 AAGTTGTGGTTAAAATGTAAA
1 AAGTT-TGGATAAAATCTAAA
3487974 GTTTGTGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 34 0.76
30 11 0.24
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (29 bp):
AAGTTTGGATAAAATCTAAAAGAATTCAT
Found at i:3495184 original size:2 final size:2
Alignment explanation
Indices: 3495177--3495234 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3495167 TGTATCGTTA
3495177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3495219 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3495235 GCAGGTGTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3498636 original size:21 final size:21
Alignment explanation
Indices: 3498612--3498653 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3498602 ATGAAGAAAG
* *
3498612 GGAAGCAGAGAGAGTAGCAGC
1 GGAAGCACAGAGAGAAGCAGC
3498633 GGAAGCACAGAGAGAAGCAGC
1 GGAAGCACAGAGAGAAGCAGC
3498654 ATATCAGCAG
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:0.40, C:0.17, G:0.40, T:0.02
Consensus pattern (21 bp):
GGAAGCACAGAGAGAAGCAGC
Found at i:3499200 original size:43 final size:43
Alignment explanation
Indices: 3499153--3499282 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 43
3499143 ACGGCATTTA
* *
3499153 TGGGAAAAACACTTTTAAATCTCAACACCTATTGTGGCGTTTG
1 TGGGAAAAATACTTTTAAATATCAACACCTATTGTGGCGTTTG
* *
3499196 TGGGAAAAATGCTGTTAAATATCAACACCTATTGTGGCGTTTG
1 TGGGAAAAATACTTTTAAATATCAACACCTATTGTGGCGTTTG
* * * * *
3499239 TAGGAAAAATACCTCTAAATATCAACACCTATTGCGGTGTTTG
1 TGGGAAAAATACTTTTAAATATCAACACCTATTGTGGCGTTTG
3499282 T
1 T
3499283 CCCACAAACG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (43 bp):
TGGGAAAAATACTTTTAAATATCAACACCTATTGTGGCGTTTG
Found at i:3499333 original size:43 final size:42
Alignment explanation
Indices: 3499168--3499366 Score: 164
Period size: 43 Copynumber: 4.6 Consensus size: 42
3499158 AAAACACTTT
* * ** *
3499168 TAAATCTCAACACCTATTGTGGCGTTTGTGGGAAAAATGCTGT
1 TAAATATCAACACCTATTGCGGCGTTTGTACGAAAAATGC-GC
* * * *
3499211 TAAATATCAACACCTATTGTGGCGTTTGTAGGAAAAATACCTC
1 TAAATATCAACACCTATTGCGGCGTTTGTACGAAAAAT-GCGC
* * * * *
3499254 TAAATATCAACACCTATTGCGGTGTTTGTCCCACAAACGTCGC
1 TAAATATCAACACCTATTGCGGCGTTTGTACGAAAAATG-CGC
* * * *
3499297 TAAATCTCAACACCTATTGCGGCGTTTGTTCGACAAATGCCTC
1 TAAATATCAACACCTATTGCGGCGTTTGTACGAAAAATG-CGC
* ** *
3499340 TATATATCATTACCAATTGCGGCGTTT
1 TAAATATCAACACCTATTGCGGCGTTT
3499367 ATTGTTATCA
Statistics
Matches: 128, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
43 127 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
TAAATATCAACACCTATTGCGGCGTTTGTACGAAAAATGCGC
Found at i:3513482 original size:20 final size:20
Alignment explanation
Indices: 3513432--3513482 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3513422 GACACCTGAG
*
3513432 TCAAAGCTATCTTCAATTTC
1 TCAAAGCTCTCTTCAATTTC
*
3513452 TCAAAGTTCTCTTCAATTTC
1 TCAAAGCTCTCTTCAATTTC
3513472 TCAAAGCTCTC
1 TCAAAGCTCTC
3513483 ATGCTGAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.39
Consensus pattern (20 bp):
TCAAAGCTCTCTTCAATTTC
Found at i:3516399 original size:13 final size:14
Alignment explanation
Indices: 3516374--3516402 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3516364 CATGATATGT
3516374 ATGAATACATGTTA
1 ATGAATACATGTTA
3516388 ATGAAT-CATGTTA
1 ATGAATACATGTTA
3516401 AT
1 AT
3516403 AGATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
ATGAATACATGTTA
Found at i:3517946 original size:24 final size:21
Alignment explanation
Indices: 3517890--3517946 Score: 51
Period size: 24 Copynumber: 2.4 Consensus size: 21
3517880 TTGTAAACCA
3517890 TATATTTTATATAATAGAAAT
1 TATATTTTATATAATAGAAAT
*
3517911 TATTATGATTTATTATAAATGATAAAT
1 TA-TAT--TTTA-TAT-AAT-AGAAAT
3517938 TATATTTTA
1 TATATTTTA
3517947 GTGGTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
24 8 0.28
25 3 0.10
26 6 0.21
27 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TATATTTTATATAATAGAAAT
Found at i:3524704 original size:16 final size:16
Alignment explanation
Indices: 3524683--3524722 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3524673 TTTCACCCTA
3524683 AACCCGAATCCGACCC
1 AACCCGAATCCGACCC
*
3524699 AACCCGAATTCGACCC
1 AACCCGAATCCGACCC
3524715 AACCCGAA
1 AACCCGAA
3524723 CACATCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.45, G:0.12, T:0.07
Consensus pattern (16 bp):
AACCCGAATCCGACCC
Found at i:3528080 original size:6 final size:6
Alignment explanation
Indices: 3528069--3528099 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3528059 TAAGAGTTAC
3528069 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA G
1 GGGGGA GGGGGA GGGGGA GGGGGA GGGGGA G
3528100 AGAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (6 bp):
GGGGGA
Found at i:3546471 original size:33 final size:33
Alignment explanation
Indices: 3546433--3546540 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 33
3546423 CAAAATATAG
*
3546433 CAACCTCACAACAATGTCCTAAAAACCAAACAA
1 CAACCTCACAACAATGTCCTAAACACCAAACAA
* * * *
3546466 CAACCTCA-AAAAACTATCATAAACATCAAACAA
1 CAACCTCACAACAA-TGTCCTAAACACCAAACAA
* * *
3546499 CAACCTCAAAACACTGTCCTAAACACCGAACAA
1 CAACCTCACAACAATGTCCTAAACACCAAACAA
3546532 CAACCTCAC
1 CAACCTCAC
3546541 TTTCATGACC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
32 4 0.07
33 54 0.89
34 3 0.05
ACGTcount: A:0.50, C:0.34, G:0.03, T:0.13
Consensus pattern (33 bp):
CAACCTCACAACAATGTCCTAAACACCAAACAA
Found at i:3557460 original size:20 final size:20
Alignment explanation
Indices: 3557421--3557461 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3557411 TTAGACCTTT
* *
3557421 TATTTTCATCTTCATCTTTA
1 TATTTTAATCTTCATATTTA
*
3557441 TATTTTAATCTTTATATTTA
1 TATTTTAATCTTCATATTTA
3557461 T
1 T
3557462 CTGTTTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTAATCTTCATATTTA
Found at i:3559413 original size:2 final size:2
Alignment explanation
Indices: 3559406--3559430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3559396 TAAATCAAAC
3559406 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3559431 AACATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3561429 original size:23 final size:23
Alignment explanation
Indices: 3561395--3561453 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3561385 AATCTGTGGA
* **
3561395 GGGTATCAGTACCCATTCAACTG
1 GGGTATCGGTACCCATTCAAAGG
3561418 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCGGTACCCATTCAAAGG
*
3561441 GGGTATCGATACC
1 GGGTATCGGTACC
3561454 TCATGCGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
GGGTATCGGTACCCATTCAAAGG
Found at i:3565280 original size:21 final size:22
Alignment explanation
Indices: 3565254--3565294 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3565244 GATTATTTTC
3565254 ATTTTTCA-ATTTT-GAAATATA
1 ATTTTT-ATATTTTAGAAATATA
3565275 ATTTTTATATTTTAGAAATA
1 ATTTTTATATTTTAGAAATA
3565295 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
ATTTTTATATTTTAGAAATATA
Found at i:3568280 original size:36 final size:37
Alignment explanation
Indices: 3568239--3568314 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
3568229 GTGAATATCA
3568239 TTCGTAAAATAAATAATTAAT-AAAAAAAACTAAGAT
1 TTCGTAAAATAAATAATTAATCAAAAAAAACTAAGAT
*
3568275 TTCGTAAAATAAATAATTAATCAAAGAAAACTAAGAT
1 TTCGTAAAATAAATAATTAATCAAAAAAAACTAAGAT
3568312 TTC
1 TTC
3568315 AAGATAGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 21 0.55
37 17 0.45
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.29
Consensus pattern (37 bp):
TTCGTAAAATAAATAATTAATCAAAAAAAACTAAGAT
Done.