Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 65
Found at i:4482501 original size:22 final size:22
Alignment explanation
Indices: 4482470--4482524 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4482460 AGATTTTTTT
*
4482470 ATGAATAGTGATGAACAGTACC
1 ATGAACAGTGATGAACAGTACC
**
4482492 ATGAACAGTGATGAATTGTACC
1 ATGAACAGTGATGAACAGTACC
*
4482514 GTGAACAGTGA
1 ATGAACAGTGA
4482525 ACAATGCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (22 bp):
ATGAACAGTGATGAACAGTACC
Found at i:4482632 original size:30 final size:30
Alignment explanation
Indices: 4482596--4482691 Score: 156
Period size: 30 Copynumber: 3.2 Consensus size: 30
4482586 AATATTATGA
*
4482596 ATCGATACGCTATAGTAACTGATACAGTGC
1 ATCGATACGCTACAGTAACTGATACAGTGC
* *
4482626 ATCGATACGCTACAGTAACTCATACGGTGC
1 ATCGATACGCTACAGTAACTGATACAGTGC
*
4482656 ATCGATACGCTACAGTAACTGCTACAGTGC
1 ATCGATACGCTACAGTAACTGATACAGTGC
4482686 ATCGAT
1 ATCGAT
4482692 GCATAATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (30 bp):
ATCGATACGCTACAGTAACTGATACAGTGC
Found at i:4484025 original size:21 final size:22
Alignment explanation
Indices: 4483999--4484045 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
4483989 ACTGGTATAG
*
4483999 TTTACCTTTTA-TTTTAAATAA
1 TTTACCTTTAATTTTTAAATAA
*
4484020 TTTACCTTTAATTTTTAACTAA
1 TTTACCTTTAATTTTTAAATAA
4484042 TTTA
1 TTTA
4484046 TAATTATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTACCTTTAATTTTTAAATAA
Found at i:4493851 original size:17 final size:18
Alignment explanation
Indices: 4493813--4493848 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4493803 ATATAAGTAC
4493813 AATA-TTAAATAAATTAA
1 AATACTTAAATAAATTAA
4493830 AATACTTAAATAAATTAA
1 AATACTTAAATAAATTAA
4493848 A
1 A
4493849 TACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AATACTTAAATAAATTAA
Found at i:4501547 original size:20 final size:20
Alignment explanation
Indices: 4501530--4501592 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
4501520 GCCAACTCGA
4501530 ACCTGTCTGAGTCAACTCAG
1 ACCTGTCTGAGTCAACTCAG
* *
4501550 ACCTGTTTGAGTCAACTTAG
1 ACCTGTCTGAGTCAACTCAG
*
4501570 A-CTGGTCTGAGTCAACTTAG
1 ACCT-GTCTGAGTCAACTCAG
4501590 ACC
1 ACC
4501593 GAATTGAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.05
20 35 0.92
21 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (20 bp):
ACCTGTCTGAGTCAACTCAG
Found at i:4501600 original size:20 final size:19
Alignment explanation
Indices: 4501537--4501603 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
4501527 CGAACCTGTC
* *
4501537 TGAGTCAACTCAGACCTGTT
1 TGAGTCAACTTAGACC-GAT
* *
4501557 TGAGTCAACTTAGACTGGT
1 TGAGTCAACTTAGACCGAT
4501576 CTGAGTCAACTTAGACCGAAT
1 -TGAGTCAACTTAGACCG-AT
4501597 TGAGTCA
1 TGAGTCA
4501604 GCCCGAACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 37 0.93
21 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (19 bp):
TGAGTCAACTTAGACCGAT
Found at i:4504185 original size:25 final size:27
Alignment explanation
Indices: 4504157--4504209 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4504147 ATAAAAATCG
*
4504157 TTAACTC-T-ACTAACTCCAAATATTT
1 TTAACTCATCACTAACTCCAAAAATTT
4504182 TTAACTCATCGACTAACTCCAAAAATTT
1 TTAACTCATC-ACTAACTCCAAAAATTT
4504210 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 1 0.04
28 16 0.67
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAACTCATCACTAACTCCAAAAATTT
Found at i:4507100 original size:3 final size:3
Alignment explanation
Indices: 4507085--4507134 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
4507075 TTCTCCTTTG
*
4507085 TCT TCT GCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
4507133 TC
1 TC
4507135 CTCCTCCTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:4510161 original size:12 final size:12
Alignment explanation
Indices: 4510144--4510168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4510134 ATTAATGTTT
4510144 AAGAACTTTGAG
1 AAGAACTTTGAG
4510156 AAGAACTTTGAG
1 AAGAACTTTGAG
4510168 A
1 A
4510169 TTTTTAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
AAGAACTTTGAG
Found at i:4511997 original size:21 final size:20
Alignment explanation
Indices: 4511973--4512013 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4511963 TTGATAATAT
*
4511973 ATATATGGTATATATATTATA
1 ATATATAGTATAT-TATTATA
4511994 ATATATAGTATATTATTATA
1 ATATATAGTATATTATTATA
4512014 TAGTTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATATATAGTATATTATTATA
Found at i:4512005 original size:17 final size:16
Alignment explanation
Indices: 4511981--4512015 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4511971 ATATATATGG
4511981 TATATATATTATAATA
1 TATATATATTATAATA
*
4511997 TATAGTATATTATTATA
1 TATA-TATATTATAATA
4512014 TA
1 TA
4512016 GTTTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TATATATATTATAATA
Found at i:4512013 original size:25 final size:25
Alignment explanation
Indices: 4511966--4512015 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
4511956 ACGATTTTTG
*
4511966 ATAATATATATATGGTATATATATT
1 ATAATATATATATAGTATATATATT
*
4511991 ATAATATATAGTATATTATTATATA
1 ATAATATATA-TATAGTA-TATATA
4512016 GTTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 5 0.24
27 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (25 bp):
ATAATATATATATAGTATATATATT
Found at i:4512054 original size:11 final size:11
Alignment explanation
Indices: 4512033--4512066 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
4512023 AAATATATAT
4512033 TATTATTATTTG
1 TATT-TTATTTG
4512045 TATTTTATTTG
1 TATTTTATTTG
4512056 TATTTGTATTT
1 TATTT-TATTT
4512067 TTTATTTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (11 bp):
TATTTTATTTG
Found at i:4516824 original size:15 final size:16
Alignment explanation
Indices: 4516804--4516833 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4516794 GTTATTTTAA
4516804 TAATTTT-TTAAAATT
1 TAATTTTCTTAAAATT
4516819 TAATTTTCTTAAAAT
1 TAATTTTCTTAAAAT
4516834 AACAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTTCTTAAAATT
Found at i:4522423 original size:42 final size:42
Alignment explanation
Indices: 4522376--4522457 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
4522366 CATCCGGTTA
* *
4522376 GAAGAATATTTCACTTGACTTTCCCATGAAGGGGAGTCATTC
1 GAAGAATATCTCACTTGACTTTCCCACGAAGGGGAGTCATTC
* * *
4522418 GAAGAATATCTCACTTGGCTTTTCCGCGAAGGGGAGTCAT
1 GAAGAATATCTCACTTGACTTTCCCACGAAGGGGAGTCAT
4522458 CAAGAACTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (42 bp):
GAAGAATATCTCACTTGACTTTCCCACGAAGGGGAGTCATTC
Found at i:4523121 original size:224 final size:225
Alignment explanation
Indices: 4522533--4523128 Score: 604
Period size: 226 Copynumber: 2.6 Consensus size: 225
4522523 AAATCAATCT
* * *
4522533 CAATTCAGAATCGACTGCAGTCTAGCTTAACTCAGCAACGATGAGCTAGTTTCTAGTCAAAGTTT
1 CAATTCAGAATC-AATGCAGTCTAGCTTAACTCAGCAGCGAGGAGCTAGTTTCTAGTCAAAGTTT
* * * * * * * * *
4522598 TTAGGCCATGTCTCAACTTTATGACGGAGGATTCTTGACCCATAAACACATCCAGAACTGACCGT
65 TTATGCCAAGTATCAACTTCATGATGGAGGATTCTTGACCCAAAAACACATCCAGAACCGACTGC
* * *** * *
4522663 ATTTTGGATTAAATCAGCGGTGTGGAGCCATATTCTAGTTAAATTGTTTCGAAGTCAATCTCAAC
130 ATTTTGGCTTAACTCAGCGGCAAGGAGCCATATTCTAATCAAATTGTTTCGAAGTCAATCTCAAC
* ** *
4522728 TCCACGATGGAGGATATTGGGTTCGGAAAAA
195 TCAACGACAGAGGATATTGGGTTCAGAAAAA
* * * * *
4522759 CAATTCAGAATCAATTGCAGTCTAGCATAACTCAGCAGCGAGGAGATAGTTTCCAATCAAATTTT
1 CAATTCAGAATCAA-TGCAGTCTAGCTTAACTCAGCAGCGAGGAGCTAGTTTCTAGTCAAAGTTT
* * * * ** * *
4522824 TTATGGCAAGTATCAACTTCATGATAGAAGATTCTTGACACAAAAATGCATCTAGAACCGACTAC
65 TTATGCCAAGTATCAACTTCATGATGGAGGATTCTTGACCCAAAAACACATCCAGAACCGACTGC
* * * *
4522889 ATTTTGGCTTAACTCAGTGGCAAGGAGCCATCTT-TCAATCAATTTTTTTCGAAGTCAA-CTCAA
130 ATTTTGGCTTAACTCAGCGGCAAGGAGCCATATTCT-AATCAAATTGTTTCGAAGTCAATCTCAA
* *
4522952 CTCAACGACAGATGATA-TGGGTTCAGAAATA
194 CTCAACGACAGAGGATATTGGGTTCAGAAAAA
* * * *** * **
4522983 TAATTTAGAATCTAATGCAATCTAGCTTAACTCAATGGCGAGGAGCTAGTTTTTAGTTGAAGTTT
1 CAATTCAGAATC-AATGCAGTCTAGCTTAACTCAGCAGCGAGGAGCTAGTTTCTAGTCAAAGTTT
* * * ** * *
4523048 TTATGCCAAGTTTCAACTTCACGGTGGAGGATTCTTGACCCGGAAGCACATCCAGAACGGACTGC
65 TTATGCCAAGTATCAACTTCATGATGGAGGATTCTTGACCCAAAAACACATCCAGAACCGACTGC
*
4523113 AATTTGGCTTAACTCA
130 ATTTTGGCTTAACTCA
4523129 ACAAAAAGGA
Statistics
Matches: 295, Mismatches: 72, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
224 125 0.42
225 22 0.07
226 148 0.50
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (225 bp):
CAATTCAGAATCAATGCAGTCTAGCTTAACTCAGCAGCGAGGAGCTAGTTTCTAGTCAAAGTTTT
TATGCCAAGTATCAACTTCATGATGGAGGATTCTTGACCCAAAAACACATCCAGAACCGACTGCA
TTTTGGCTTAACTCAGCGGCAAGGAGCCATATTCTAATCAAATTGTTTCGAAGTCAATCTCAACT
CAACGACAGAGGATATTGGGTTCAGAAAAA
Found at i:4523391 original size:2 final size:2
Alignment explanation
Indices: 4523386--4523461 Score: 67
Period size: 2 Copynumber: 40.5 Consensus size: 2
4523376 ATATAAATGG
*
4523386 TA TA TA TA T- TA TA -A TA TA TA -A TA TA T- TA T- TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
4523424 TT TGA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4523462 GTTTATTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
1 7 0.11
2 55 0.87
3 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4523493 original size:12 final size:12
Alignment explanation
Indices: 4523476--4523501 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4523466 ATTATTAGTA
4523476 TTTTATTTTATT
1 TTTTATTTTATT
4523488 TTTTATTTTATT
1 TTTTATTTTATT
4523500 TT
1 TT
4523502 ATTGTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:4525974 original size:32 final size:32
Alignment explanation
Indices: 4525938--4526074 Score: 123
Period size: 32 Copynumber: 4.3 Consensus size: 32
4525928 ATCAACATTG
* ** *
4525938 CATTCAGATGATGTATAGTAAAGTTAGTATTA
1 CATTCAGATAATGTATAACAAAGTCAGTATTA
* *
4525970 CATTCAGATAATGCATAACAAAGTCAGTATTT
1 CATTCAGATAATGTATAACAAAGTCAGTATTA
* * *
4526002 CATTCAGATAATGTATAA-AAGAGACATTATTG
1 CATTCAGATAATGTATAACAA-AGTCAGTATTA
* * * * * *
4526034 CATTCAAATAATGCATAACAGAGTTAGTGTCA
1 CATTCAGATAATGTATAACAAAGTCAGTATTA
4526066 CATTCAGAT
1 CATTCAGAT
4526075 GATTCACAGA
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
31 2 0.02
32 80 0.96
33 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (32 bp):
CATTCAGATAATGTATAACAAAGTCAGTATTA
Found at i:4531190 original size:29 final size:27
Alignment explanation
Indices: 4531139--4531201 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 27
4531129 TATGATCCTA
4531139 TTATTT-TATAATTATGAAAAAAATAT
1 TTATTTATATAATTATGAAAAAAATAT
4531165 TTATTTATATATATT-TGTAAATAAAATAT
1 TTATTTATATA-ATTATG-AAA-AAAATAT
4531194 TTATTTAT
1 TTATTTAT
4531202 TTAGAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 6 0.18
27 6 0.18
28 6 0.18
29 15 0.45
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
TTATTTATATAATTATGAAAAAAATAT
Found at i:4531375 original size:20 final size:20
Alignment explanation
Indices: 4531340--4531379 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4531330 TAAATAAATA
*
4531340 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
4531361 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
4531380 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:4532815 original size:3 final size:3
Alignment explanation
Indices: 4532807--4532877 Score: 83
Period size: 3 Copynumber: 23.7 Consensus size: 3
4532797 AATTATTTTT
*
4532807 TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4532852 TAA TAA TTA TTA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TA
4532878 TTCAAATGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.85
4 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:4533275 original size:112 final size:112
Alignment explanation
Indices: 4533114--4533737 Score: 989
Period size: 112 Copynumber: 5.6 Consensus size: 112
4533104 TTGAATAATC
* * * ** *
4533114 TCTTCTCATTATAAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAG
1 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
* ** * * * * *
4533179 AAAAGTTGATCCAACAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
65 CACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* * * * * *
4533227 TATTCTCATTATGAACATCTTCTTCTTTTTTAGATGAGTTCTTTTCATTATGAACTCTAATTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
*
4533292 ACTGCTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
* *
4533339 TCTTCTCATTATGAACTTCTTCTTCTTCTTCACATGAGTTCTTCTCATTATAAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
*
4533404 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAATTGAACAAGT
66 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
4533451 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
4533516 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
66 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
4533563 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-AGTTCTTCTCATTATGAACTCTAACTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
*
4533627 ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAAGTTGAACACGT
66 ACTGCTGATCCACCGAGGGATGAATTTAAGC-AAAAAGTTGAACAAGT
*
4533675 TCTTCTCATTATGAACTTCTTTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
4533738 AAAATGTTGA
Statistics
Matches: 475, Mismatches: 34, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
111 60 0.13
112 368 0.77
113 47 0.10
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
ACTGCTGATCCACCGAGGGATGAATTTAAGCAAAAAGTTGAACAAGT
Found at i:4534928 original size:19 final size:17
Alignment explanation
Indices: 4534900--4534948 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
4534890 AAAAAAAAAG
*
4534900 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
4534919 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
4534935 AATAAATTGAATTT
1 AATAAATTGAATTT
4534949 AGATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:4535319 original size:9 final size:9
Alignment explanation
Indices: 4535301--4535399 Score: 89
Period size: 9 Copynumber: 10.9 Consensus size: 9
4535291 CTTGACCCCC
*
4535301 TCTTTTTTT
1 TCTTTCTTT
4535310 TCTTTCTTT
1 TCTTTCTTT
4535319 TCTTTCTTT
1 TCTTTCTTT
4535328 TCTTTCTTTT
1 TCTTTC-TTT
4535338 TCTTT-TTCT
1 TCTTTCTT-T
*
4535347 TTTTTCTTT
1 TCTTTCTTT
*
4535356 TTTTTCTTTT
1 TCTTTC-TTT
4535366 TCTTTTCTTCT
1 TC-TTTCTT-T
4535377 TC-TTCTTT
1 TCTTTCTTT
*
4535385 T-TTTCATT
1 TCTTTCTTT
4535393 T-TTTCTT
1 TCTTTCTT
4535400 CAAGCATAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
8 15 0.19
9 40 0.51
10 16 0.21
11 7 0.09
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (9 bp):
TCTTTCTTT
Found at i:4535342 original size:28 final size:29
Alignment explanation
Indices: 4535301--4535395 Score: 119
Period size: 28 Copynumber: 3.4 Consensus size: 29
4535291 CTTGACCCCC
4535301 TCTTT-TTTTTCTTTCTT-TTCTTTCTTT
1 TCTTTCTTTTTCTTTCTTCTTCTTTCTTT
*
4535328 TCTTTCTTTTTCTTT-TTCTTTTTTCTTT
1 TCTTTCTTTTTCTTTCTTCTTCTTTCTTT
*
4535356 TTTTTCTTTTTCTTTTCTTCTTC-TTCTTT
1 TCTTTCTTTTTC-TTTCTTCTTCTTTCTTT
4535385 T-TTTCATTTTT
1 TCTTTC-TTTTT
4535396 TCTTCAAGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.12
28 33 0.55
29 15 0.25
30 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (29 bp):
TCTTTCTTTTTCTTTCTTCTTCTTTCTTT
Found at i:4535398 original size:22 final size:21
Alignment explanation
Indices: 4535301--4535400 Score: 96
Period size: 22 Copynumber: 4.6 Consensus size: 21
4535291 CTTGACCCCC
4535301 TCTTTTTT-TTCTTTCTTTTCTT
1 TCTTTTTTCTTC-TTCTTTT-TT
* *
4535323 TCTTTTCT-TTCTTTTTCTTTT
1 TCTTTTTTCTTCTTCTT-TTTT
* *
4535344 TCTTTTTTCTTTTTTTTCTTTT
1 TCTTTTTTCTTCTTCTT-TTTT
4535366 TCTTTTCTTCTTCTTCTTTTTT
1 TCTTTT-TTCTTCTTCTTTTTT
4535388 TCATTTTTTCTTC
1 TC-TTTTTTCTTC
4535401 AAGCATAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.19
22 42 0.62
23 13 0.19
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (21 bp):
TCTTTTTTCTTCTTCTTTTTT
Found at i:4542723 original size:15 final size:15
Alignment explanation
Indices: 4542700--4542731 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4542690 TTCAATGAAT
4542700 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
4542715 AATGCATGTATGCAA
1 AATGAATGTATGCAA
4542730 AA
1 AA
4542732 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:4546560 original size:25 final size:29
Alignment explanation
Indices: 4546526--4546590 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
4546516 TTTATGATCC
*
4546526 TATTATTTTATA-AT-TATG-AAA-AAAA
1 TATTAATTTATATATATATGTAAATAAAA
*
4546551 TATTAATTTATATATATTTGTAAATAAAA
1 TATTAATTTATATATATATGTAAATAAAA
*
4546580 TATTTATTTAT
1 TATTAATTTAT
4546591 TTAGAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.33
26 2 0.06
27 3 0.09
28 3 0.09
29 14 0.42
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TATTAATTTATATATATATGTAAATAAAA
Found at i:4546685 original size:20 final size:19
Alignment explanation
Indices: 4546646--4546687 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
4546636 TTTCTTCGAT
4546646 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
4546665 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
4546685 ATT
1 ATT
4546688 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:4546798 original size:120 final size:117
Alignment explanation
Indices: 4546579--4546813 Score: 278
Period size: 120 Copynumber: 2.0 Consensus size: 117
4546569 TGTAAATAAA
* * * * * *
4546579 ATATTTATTTATTTAGAAATATCAGAAAAGAACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTCG
1 ATATTTATTTATTTAAAAATATCAGAAAAGAACATCCAGGTACCTTAAGACAGCTCATTTCTTCA
*
4546644 ATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATTTATAAAATAGG
66 ATATTAAAAAATAAATAAATAATTAAAACAATTAA-A-ATAAGTTA-AAAATAGG
* * ** *
4546699 ATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTATTTTAAGACTGC-CATTTCTT-
1 ATATTTATTTATTTAAAAATATCAGAAAA-GAACATCCAGGTACCTTAAGACAGCTCATTTCTTC
*
4546762 AATATTGAAAAATAAATAAAT-ATTAAAACAGGATTAAAATAAGTTAAAAATA
65 AATATTAAAAAATAAATAAATAATTAAAACA--ATTAAAATAAGTTAAAAATA
4546814 ATTAAATAAG
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
117 6 0.06
118 16 0.16
119 20 0.20
120 40 0.40
121 17 0.17
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (117 bp):
ATATTTATTTATTTAAAAATATCAGAAAAGAACATCCAGGTACCTTAAGACAGCTCATTTCTTCA
ATATTAAAAAATAAATAAATAATTAAAACAATTAAAATAAGTTAAAAATAGG
Found at i:4546888 original size:3 final size:3
Alignment explanation
Indices: 4546880--4546921 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
4546870 TTTATGGCTA
*
4546880 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4546922 TAAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4547822 original size:19 final size:21
Alignment explanation
Indices: 4547795--4547837 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
4547785 GCTCTCTGTA
4547795 TCTTCTTTT-CTTT-TCTTTT
1 TCTTCTTTTGCTTTCTCTTTT
* *
4547814 TCTTTTTTTGCTTTCTGTTTT
1 TCTTCTTTTGCTTTCTCTTTT
4547835 TCT
1 TCT
4547838 CTTGGGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTCTTTTGCTTTCTCTTTT
Found at i:4548280 original size:6 final size:6
Alignment explanation
Indices: 4548269--4548356 Score: 81
Period size: 6 Copynumber: 13.8 Consensus size: 6
4548259 AATTATTTTT
4548269 TAATAA TAATAA T-ATATA TAATAA TAATATA TATATATA TATATATA
1 TAATAA TAATAA TAATA-A TAATAA TAATA-A TA-ATA-A TA-ATA-A
* *
4548316 TAATAA TTATAA TAATAT TAATAA TAATAA T-ATAAA TAATA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAAT-AA TAATA
4548357 TTCAAATGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
5 5 0.07
6 41 0.57
7 11 0.15
8 15 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TAATAA
Found at i:4548285 original size:2 final size:2
Alignment explanation
Indices: 4548280--4548317 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4548270 AATAATAATA
4548280 AT AT AT AT A- AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4548318 ATAATTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4548291 original size:15 final size:15
Alignment explanation
Indices: 4548271--4548356 Score: 97
Period size: 15 Copynumber: 5.6 Consensus size: 15
4548261 TTATTTTTTA
4548271 ATAATAATAATATAT
1 ATAATAATAATATAT
4548286 ATAATAATAATATAT
1 ATAATAATAATATAT
4548301 AT-AT-ATATATATAT
1 ATAATAATA-ATATAT
*
4548315 ATAATAATTATAATAAT
1 ATAATAATAAT-AT-AT
4548332 ATTAATAATAATA-AT
1 A-TAATAATAATATAT
4548347 ATAAATAATA
1 AT-AATAATA
4548357 TTCAAATGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.05
14 11 0.18
15 31 0.50
16 4 0.06
17 4 0.06
18 9 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:4550761 original size:26 final size:25
Alignment explanation
Indices: 4550729--4550785 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
4550719 TTAATTGGAC
*
4550729 TAAAAGAACTAATAAATCTATTCTAA
1 TAAAAGAA-GAATAAATCTATTCTAA
* *
4550755 TAAAAG-AGAATAAATCTCTTTTAA
1 TAAAAGAAGAATAAATCTATTCTAA
4550779 TAAAAGA
1 TAAAAGA
4550786 GTAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 20 0.74
25 1 0.04
26 6 0.22
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAAGAAGAATAAATCTATTCTAA
Found at i:4550769 original size:24 final size:24
Alignment explanation
Indices: 4550739--4550786 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4550729 TAAAAGAACT
4550739 AATAAATCTATTCTAATAAAAGAG
1 AATAAATCTATTCTAATAAAAGAG
* *
4550763 AATAAATCTCTTTTAATAAAAGAG
1 AATAAATCTATTCTAATAAAAGAG
4550787 TAATTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
AATAAATCTATTCTAATAAAAGAG
Found at i:4551835 original size:29 final size:29
Alignment explanation
Indices: 4551801--4551859 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4551791 CCTAAATTAA
4551801 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4551830 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4551859 T
1 T
4551860 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:4556505 original size:29 final size:29
Alignment explanation
Indices: 4556471--4556529 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4556461 CCTAAATTAA
4556471 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4556500 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4556529 T
1 T
4556530 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:4558210 original size:24 final size:24
Alignment explanation
Indices: 4558148--4558211 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 24
4558138 AGATATTAAT
* * *
4558148 TATTAAAATATTTAA-AATATATT
1 TATTAATATTTTTAATAATATATA
*
4558171 TATTAATATTTCTAATAATATA-A
1 TATTAATATTTTTAATAATATATA
*
4558194 TATTATATTTTTTTAATA
1 TATTA-ATATTTTTAATA
4558212 TTACAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAATATTTTTAATAATATATA
Found at i:4558566 original size:28 final size:31
Alignment explanation
Indices: 4558508--4558595 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 31
4558498 TAAAATGCAC
* *
4558508 TAATCTTAATATTTTATTAATAAAATTATAAA
1 TAATC-TAATATTTTAATAATAAAATAATAAA
4558540 -AA-C-AATATTTTAATAAT-AAATAAATAAA
1 TAATCTAATATTTTAATAATAAAAT-AATAAA
*
4558568 TAATTCTAATATTTTAAAAATAATAATA
1 TAA-TCTAATATTTTAATAATAA-AATA
4558596 TTAAGTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
27 4 0.09
28 18 0.39
29 2 0.04
30 1 0.02
31 3 0.07
32 13 0.28
33 2 0.04
34 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATCTAATATTTTAATAATAAAATAATAAA
Found at i:4559763 original size:43 final size:43
Alignment explanation
Indices: 4559716--4559914 Score: 163
Period size: 43 Copynumber: 4.7 Consensus size: 43
4559706 TGACAACATA
* * *
4559716 TAGCGGCGTTTTTTCAACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGTTTTTCCAACAAACGCCGCAAAAGATGTTGATATT
** * * * *
4559759 TAGCGGCG-TTTGACAGAAAAACGCCGCAATAGGCT-TTGATGTT
1 TAGCGGCGTTTTTCCA-ACAAACGCCGCAA-AAGATGTTGATATT
* ** * *
4559802 TAGCGGCGTTTTCTTC-ACAAACGCCGCAGTAGATGTTTATTTT
1 TAGCGGCGTTTT-TCCAACAAACGCCGCAAAAGATGTTGATATT
** * * *
4559845 TCCCGGCGTTTTTCCTACAAACGTCGCAGAAGATGTTGATATT
1 TAGCGGCGTTTTTCCAACAAACGCCGCAAAAGATGTTGATATT
*
4559888 TAGCGGCG-TTTTCCTACAAACGCCGCA
1 TAGCGGCGTTTTTCCAACAAACGCCGCA
4559915 GAATATGTCT
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
42 27 0.22
43 91 0.73
44 6 0.05
45 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCAACAAACGCCGCAAAAGATGTTGATATT
Found at i:4559852 original size:86 final size:86
Alignment explanation
Indices: 4559716--4559917 Score: 196
Period size: 86 Copynumber: 2.4 Consensus size: 86
4559706 TGACAACATA
* * *
4559716 TAGCGGCGTTTT-TTCAACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTGACAGAAAAA
1 TAGCGGCGTTTTCTTC-ACAAACGCCGCAGAAGATATTGATATTTACCGGCGTTTGACAGAAAAA
* *
4559780 CGCCGCA-ATAGGCT-TTGATGTT
65 CGCCGCAGA-A-GATGTTGATATT
* * * * * ** ** *
4559802 TAGCGGCGTTTTCTTCACAAACGCCGCAGTAGATGTTTATTTTTCCCGGCGTTTTTCCTACAAAC
1 TAGCGGCGTTTTCTTCACAAACGCCGCAGAAGATATTGATATTTACCGGCGTTTGACAGAAAAAC
*
4559867 GTCGCAGAAGATGTTGATATT
66 GCCGCAGAAGATGTTGATATT
*
4559888 TAGCGGCGTTTTCCT-ACAAACGCCGCAGAA
1 TAGCGGCGTTTTCTTCACAAACGCCGCAGAA
4559918 TATGTCTTGA
Statistics
Matches: 95, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
85 16 0.17
86 75 0.79
87 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (86 bp):
TAGCGGCGTTTTCTTCACAAACGCCGCAGAAGATATTGATATTTACCGGCGTTTGACAGAAAAAC
GCCGCAGAAGATGTTGATATT
Found at i:4560366 original size:21 final size:21
Alignment explanation
Indices: 4560342--4560414 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
4560332 ATATATTACT
4560342 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTTCTGCCGCTGCC
* * *
4560363 TCTCTATGTGCTGCCACTGCTTC
1 TCTCTCTGTTCTGCCGCTGC--C
* *
4560386 TCTCTCTGCTTCCGCTGCTG-C
1 TCTCTCTG-TTCTGCCGCTGCC
4560407 TCTCTCTG
1 TCTCTCTG
4560415 CTTCCCTTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
21 26 0.63
23 8 0.20
24 7 0.17
ACGTcount: A:0.03, C:0.40, G:0.18, T:0.40
Consensus pattern (21 bp):
TCTCTCTGTTCTGCCGCTGCC
Found at i:4560425 original size:21 final size:21
Alignment explanation
Indices: 4560379--4560419 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4560369 TGTGCTGCCA
*
4560379 CTGCTTCTCTCTCTGCTTCCG
1 CTGCTGCTCTCTCTGCTTCCG
4560400 CTGCTGCTCTCTCTGCTTCC
1 CTGCTGCTCTCTCTGCTTCC
4560420 CTTGCTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.44, G:0.15, T:0.41
Consensus pattern (21 bp):
CTGCTGCTCTCTCTGCTTCCG
Found at i:4563153 original size:14 final size:14
Alignment explanation
Indices: 4563134--4563168 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
4563124 TCGTTATATC
4563134 AACTTATATTTGGG
1 AACTTATATTTGGG
4563148 AACTTATATTTGGG
1 AACTTATATTTGGG
4563162 AACTTAT
1 AACTTAT
4563169 GAAGTGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (14 bp):
AACTTATATTTGGG
Found at i:4564275 original size:42 final size:42
Alignment explanation
Indices: 4564188--4564315 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
4564178 AATGGCGGCA
* * *
4564188 TTTATTACCAAAACGCCCCTAAAACGCCAAACT-TATACGACG
1 TTTATTACAAAAACGCCCCTAAAACACAAAACTAT-TACGACG
**
4564230 TTTATTACAAAAACGCCCCTAAAACACAAAACTATTGA-GGTG
1 TTTATTACAAAAACGCCCCTAAAACACAAAACTATT-ACGACG
* ** *
4564272 TTTATTA-AAAAACGCCACTAAATGACAAAACTATTACGGCG
1 TTTATTACAAAAACGCCCCTAAAACACAAAACTATTACGACG
4564313 TTT
1 TTT
4564316 TTCCTATAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.01
41 31 0.42
42 40 0.54
43 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (42 bp):
TTTATTACAAAAACGCCCCTAAAACACAAAACTATTACGACG
Found at i:4564387 original size:41 final size:41
Alignment explanation
Indices: 4564342--4564458 Score: 144
Period size: 41 Copynumber: 2.9 Consensus size: 41
4564332 TAAATAACAT
* **
4564342 GGATATAACGGCGTTTGGTCACAAACGCCACTAAAGTATAA
1 GGATATTACGGCGTTTTCTCACAAACGCCACTAAAGTATAA
* * * *
4564383 GGATATTGCGGCGTTTTCTCAAAAACGCCACTAAAGTTTAT
1 GGATATTACGGCGTTTTCTCACAAACGCCACTAAAGTATAA
* * *
4564424 TGCTATTTCGGCGTTTTCTCACAAACGCCACTAAA
1 GGATATTACGGCGTTTTCTCACAAACGCCACTAAA
4564459 TTAATCATAT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (41 bp):
GGATATTACGGCGTTTTCTCACAAACGCCACTAAAGTATAA
Found at i:4564834 original size:18 final size:18
Alignment explanation
Indices: 4564813--4564851 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4564803 AAAATGTTTA
4564813 ATAAAAATACTAATCTAC
1 ATAAAAATACTAATCTAC
* *
4564831 ATAATAATCCTAATCTAC
1 ATAAAAATACTAATCTAC
4564849 ATA
1 ATA
4564852 TACTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATACTAATCTAC
Found at i:4565796 original size:22 final size:22
Alignment explanation
Indices: 4565756--4565797 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4565746 TTCAGAAGGT
*
4565756 ATTATTTTCCTGTTAGAAAGTA
1 ATTATTTTCCTATTAGAAAGTA
* *
4565778 ATTATTTTTCTATTCGAAAG
1 ATTATTTTCCTATTAGAAAG
4565798 CAAAAAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (22 bp):
ATTATTTTCCTATTAGAAAGTA
Found at i:4566424 original size:82 final size:82
Alignment explanation
Indices: 4566216--4566519 Score: 250
Period size: 82 Copynumber: 3.7 Consensus size: 82
4566206 CGTTTCTAAA
* * * * * * *
4566216 AAACGCCACGATAAACAACA-TATTGCGGCGTTTGTAGGAAAAACACCGCTAAATT-TTTACTAT
1 AAACGCCACTATAAACAACATTATTGCGACGTTTTTAGTATAAACGCCGCTAAATTACTT-CTAT
*
4566279 ATTGCGGCGCTTT-TTGTAC
65 A-TGCGGCG-TTTGTTGAAC
* ** * *
4566298 AAACGCCACTA-AAAAAACCCTATTGC-AGCGTTTCTTTG-ATAAACGCCACTAAATTACTTCTA
1 AAACGCCACTATAAACAACATTATTGCGA-CGTTT-TTAGTATAAACGCCGCTAAATTACTTCTA
*
4566360 TATAGCGTCGTTTGTTGAAC
64 TAT-GCGGCGTTTGTTGAAC
* * **
4566380 AAACGCCACTATAAACAACATTATTGCGACGTTTTTA-TACAAACGCCGCAAAATTAACAAACTA
1 AAACGCCACTATAAACAACATTATTGCGACGTTTTTAGTATAAACGCCGCTAAATT-AC-TTCTA
*
4566444 T-TGCGGCGTTTGTTGAAG
64 TATGCGGCGTTTGTTGAAC
* * *
4566462 AAACGTCACTATAAACAAC-TCTATTGTGGCG-TTTTAGTTATAAACGCCGCTAAATTAC
1 AAACGCCACTATAAACAACAT-TATTGCGACGTTTTTAG-TATAAACGCCGCTAAATTAC
4566520 CACTTTATTA
Statistics
Matches: 180, Mismatches: 28, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
81 16 0.09
82 119 0.66
83 40 0.22
84 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (82 bp):
AAACGCCACTATAAACAACATTATTGCGACGTTTTTAGTATAAACGCCGCTAAATTACTTCTATA
TGCGGCGTTTGTTGAAC
Found at i:4566486 original size:41 final size:41
Alignment explanation
Indices: 4566278--4566495 Score: 139
Period size: 40 Copynumber: 5.3 Consensus size: 41
4566268 ATTTTTACTA
* * *
4566278 TATTGCGGCGCTTT-TTGTACAAACGCCACTA-AAAAAACCC
1 TATTGCGGCG-TTTGTTGAACAAACGCCACTATAAACAACTC
* * * **
4566318 TATTGCAGCGTTTCTTTG-ATAAACGCCAC--TAAATTACTTC
1 TATTGCGGCGTTT-GTTGAACAAACGCCACTATAAACAAC-TC
*
4566358 TATATAGCGTCGTTTGTTGAACAAACGCCACTATAAACAACAT-
1 TAT-T-GCGGCGTTTGTTGAACAAACGCCACTATAAACAAC-TC
* ** * *
4566401 TATTGCGACGTTT-TT-ATACAAACGCCGCAAAATTAACAA-AC
1 TATTGCGGCGTTTGTTGA-ACAAACG-C-CACTATAAACAACTC
* *
4566442 TATTGCGGCGTTTGTTGAAGAAACGTCACTATAAACAACTC
1 TATTGCGGCGTTTGTTGAACAAACGCCACTATAAACAACTC
*
4566483 TATTGTGGCGTTT
1 TATTGCGGCGTTT
4566496 TAGTTATAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
39 9 0.07
40 41 0.30
41 41 0.30
42 35 0.26
43 4 0.03
44 7 0.05
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (41 bp):
TATTGCGGCGTTTGTTGAACAAACGCCACTATAAACAACTC
Found at i:4570167 original size:28 final size:28
Alignment explanation
Indices: 4570127--4570180 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4570117 ATTCCAACCC
* *
4570127 AATACTTAAAATT-TTTACAATAAAAATA
1 AATAATTAAAATTCTTTA-AAAAAAAATA
4570155 AATAATTAAAATTCTTTAAAAAAAAA
1 AATAATTAAAATTCTTTAAAAAAAAA
4570181 GCAGCCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (28 bp):
AATAATTAAAATTCTTTAAAAAAAAATA
Found at i:4572160 original size:3 final size:3
Alignment explanation
Indices: 4572141--4572189 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
4572131 ATTAATTATT
4572141 TAA TAA TTAA -AA T-A 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
4572185 TAA TA
1 TAA TA
4572190 TCAAACCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4572740 original size:15 final size:15
Alignment explanation
Indices: 4572713--4572754 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
4572703 AATCAAGTGA
4572713 AGAGAAGAGAAAGGAG
1 AGAGAA-AGAAAGGAG
4572729 AG-GAGAAGAAAGGAG
1 AGAGA-AAGAAAGGAG
4572744 AGAGAAAGAAA
1 AGAGAAAGAAA
4572755 CAAAGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AGAGAAAGAAAGGAG
Found at i:4573740 original size:32 final size:32
Alignment explanation
Indices: 4573703--4573813 Score: 101
Period size: 32 Copynumber: 3.7 Consensus size: 32
4573693 GTTTTAACTT
4573703 ATCACACTCATTCAAATAATATATGAAAATCA
1 ATCACACTCATTCAAATAATATATGAAAATCA
* *
4573735 ATCACACTCATTCAAA-AATAAAT--AGA-CA
1 ATCACACTCATTCAAATAATATATGAAAATCA
* * * * *
4573763 A--ACATTTATTCAAATAAAATGTGGAAATTC-
1 ATCACACTCATTCAAATAATATAT-GAAAATCA
4573793 ATCACACTCATTCAAATAATA
1 ATCACACTCATTCAAATAATA
4573814 AATGGGAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
26 11 0.18
27 4 0.07
28 3 0.05
29 2 0.03
30 2 0.03
31 7 0.12
32 31 0.52
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.28
Consensus pattern (32 bp):
ATCACACTCATTCAAATAATATATGAAAATCA
Found at i:4573797 original size:58 final size:59
Alignment explanation
Indices: 4573710--4573941 Score: 224
Period size: 58 Copynumber: 3.8 Consensus size: 59
4573700 CTTATCACAC
* *
4573710 TCATTCAAATAATATAT-GAAAATCAATCACACTCATTCAAAAATAAATAGACAAACAT
1 TCATTCAAATAAAATATGGAAATTCAATCACACTCATTCAAAAATAAATAGACAAACAT
* * *
4573768 TTATTCAAATAAAATGTGGAAATTC-ATCACACTCATTCAAATAATAAATGGGA-AAACAT
1 TCATTCAAATAAAATATGGAAATTCAATCACACTCATTCAAA-AATAAAT-AGACAAACAT
* *
4573827 TCATTCAAATAAAA-ATGGAAA-TCCATCACACTTATTCAAAAAAATAAATAGGAAAAATCAAAC
1 TCATTCAAATAAAATATGGAAATTCAATCACACTCATTC--AAAAATAAATA-G----A-CAAAC
4573890 AT
58 AT
* * * *
4573892 TCATTCAAATAAAATGTGGAAA-TCTATCACACTAATTAAAAAAATAAATA
1 TCATTCAAATAAAATATGGAAATTCAATCACACTCATT-CAAAAATAAATA
4573942 CAAAATCAAA
Statistics
Matches: 146, Mismatches: 13, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
57 2 0.01
58 48 0.33
59 40 0.27
60 5 0.03
63 1 0.01
65 31 0.21
66 19 0.13
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (59 bp):
TCATTCAAATAAAATATGGAAATTCAATCACACTCATTCAAAAATAAATAGACAAACAT
Found at i:4573893 original size:65 final size:63
Alignment explanation
Indices: 4573821--4573961 Score: 212
Period size: 65 Copynumber: 2.2 Consensus size: 63
4573811 ATAAATGGGA
*
4573821 AAACATTCATTCAAATAAAA-ATGGAAATCCATCACACTTATTCAAAAAAATAAATAGGAAAAAT
1 AAACATTCATTCAAATAAAATATGGAAATCCATCACACTAATT-AAAAAAATAAATA--AAAAAT
4573885 C
63 C
* * *
4573886 AAACATTCATTCAAATAAAATGTGGAAATCTATCACACTAATTAAAAAAATAAATACAAAATC
1 AAACATTCATTCAAATAAAATATGGAAATCCATCACACTAATTAAAAAAATAAATAAAAAATC
4573949 AAACATTCATTCA
1 AAACATTCATTCA
4573962 TTATTCATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
63 19 0.27
65 33 0.46
66 19 0.27
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.25
Consensus pattern (63 bp):
AAACATTCATTCAAATAAAATATGGAAATCCATCACACTAATTAAAAAAATAAATAAAAAATC
Found at i:4573906 original size:35 final size:35
Alignment explanation
Indices: 4573821--4573906 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 35
4573811 ATAAATGGGA
*
4573821 AAACATTCATTCAAAT--AA-AAATGGAAATCCATC
1 AAACATTCATTCAAATAAAATAAATGGAAA-CAATC
*
4573854 ACAC-TT-ATTCAAA-AAAATAAATAGGAAA-AATC
1 AAACATTCATTCAAATAAAATAAAT-GGAAACAATC
4573886 AAACATTCATTCAAATAAAAT
1 AAACATTCATTCAAATAAAAT
4573907 GTGGAAATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
31 7 0.16
32 10 0.23
33 9 0.21
34 12 0.28
35 5 0.12
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (35 bp):
AAACATTCATTCAAATAAAATAAATGGAAACAATC
Found at i:4573923 original size:124 final size:117
Alignment explanation
Indices: 4573710--4573940 Score: 295
Period size: 124 Copynumber: 1.9 Consensus size: 117
4573700 CTTATCACAC
* *
4573710 TCATTCAAATAATATATGAAAATCAATCACACTCATTCAAAAATAAATAGACAAACATTTATTCA
1 TCATTCAAATAATAAATGAAAATCAATCACACTCATTCAAAAATAAATAGACAAACATTCATTCA
* * *
4573775 AATAAAATGTGGAAATTCATCACACTCATTCAAATAATAAATGGGAAAACAT
66 AATAAAATGTGGAAATTCATCACACTAATTAAAAAAATAAATGGGAAAACAT
* * *
4573827 TCATTCAAATAA-AAATGGAAATCCATCACACTTATTCAAAAAAATAAATAGGAAAAATCAAACA
1 TCATTCAAATAATAAATGAAAATCAATCACACTCATTC--AAAAATAAATA-G----A-CAAACA
4573891 TTCATTCAAATAAAATGTGGAAA-TCTATCACACTAATTAAAAAAATAAAT
58 TTCATTCAAATAAAATGTGGAAATTC-ATCACACTAATTAAAAAAATAAAT
4573941 ACAAAATCAA
Statistics
Matches: 97, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
116 21 0.22
117 12 0.12
118 11 0.11
119 1 0.01
123 3 0.03
124 49 0.51
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.26
Consensus pattern (117 bp):
TCATTCAAATAATAAATGAAAATCAATCACACTCATTCAAAAATAAATAGACAAACATTCATTCA
AATAAAATGTGGAAATTCATCACACTAATTAAAAAAATAAATGGGAAAACAT
Found at i:4582382 original size:3 final size:3
Alignment explanation
Indices: 4582374--4582403 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4582364 TATATTAATT
*
4582374 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4582404 ATTGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4588728 original size:46 final size:46
Alignment explanation
Indices: 4588669--4588780 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
4588659 CATTTATCTT
4588669 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACC
* *
4588715 ATAAGCTCATAAGCTTAGTTTACCAATATACTTACCATTTAATACC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACC
* *
4588761 ATAAGTTCGCAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
4588781 GCATGCTTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (46 bp):
ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATACC
Found at i:4588934 original size:40 final size:40
Alignment explanation
Indices: 4588855--4588934 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
4588845 ATAGGAGTCA
* * * * * *
4588855 AATATTGCACCGAAGTGTTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCAAACTTTACCCACCT
*
4588895 AATAATGCACCGTAGTGCTGAGGTCAAACTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCAAACTTTACCCACCT
4588935 TGTACACCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCAAACTTTACCCACCT
Found at i:4590819 original size:97 final size:97
Alignment explanation
Indices: 4590648--4590850 Score: 325
Period size: 97 Copynumber: 2.1 Consensus size: 97
4590638 ACTTCAAATT
* * * *
4590648 TTTGTAAAATTCTAATTCGATCTGAAATTACCGATTCCTTATAGGCTTTAACCCTTTCTAATTTT
1 TTTGTAAAATTCCAATTCAATCTAAAATTACCGATTCCTTACAGGCTTTAACCCTTTCTAATTTT
*
4590713 TCTTTACTAAAATTATAAATCCAAAAATATGA
66 TCTTCACTAAAATTATAAATCCAAAAATATGA
*
4590745 TTTGTAAAATTCCAATTCAATCTAAAATTACCGATTCCTTACCGGCTTTAACCCTTTCTAATTTT
1 TTTGTAAAATTCCAATTCAATCTAAAATTACCGATTCCTTACAGGCTTTAACCCTTTCTAATTTT
* *
4590810 TCTTCACTAAAATTCTAAATTCAAAAATATGA
66 TCTTCACTAAAATTATAAATCCAAAAATATGA
*
4590842 TTTCTAAAA
1 TTTGTAAAA
4590851 AAAACTCCAC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (97 bp):
TTTGTAAAATTCCAATTCAATCTAAAATTACCGATTCCTTACAGGCTTTAACCCTTTCTAATTTT
TCTTCACTAAAATTATAAATCCAAAAATATGA
Found at i:4592907 original size:24 final size:23
Alignment explanation
Indices: 4592878--4592924 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
4592868 ATTTATCTTT
*
4592878 TAAATTTTATAAAGAAATTATATA
1 TAAATTTTATAAA-AAAGTATATA
*
4592902 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
4592925 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:4594102 original size:17 final size:16
Alignment explanation
Indices: 4594071--4594125 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
4594061 GGTATTACCC
*
4594071 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
4594087 GACCTGTTTTTAAACC-
1 GACCTGTTTTT-AACCT
* *
4594103 GACCTATTTTTAACAT
1 GACCTGTTTTTAACCT
4594119 GACCTGT
1 GACCTGT
4594126 AAATGATCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 26 0.79
17 4 0.12
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:4594404 original size:23 final size:23
Alignment explanation
Indices: 4594378--4594421 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4594368 AGGAAAATTA
*
4594378 ATATATTTTAATTTATATAAATC
1 ATATAGTTTAATTTATATAAATC
4594401 ATATAGTTTAATTTATATAAA
1 ATATAGTTTAATTTATATAAA
4594422 GAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATAGTTTAATTTATATAAATC
Found at i:4594440 original size:20 final size:20
Alignment explanation
Indices: 4594408--4594445 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4594398 ATCATATAGT
4594408 TTAATTTATATAAAGAAAAA
1 TTAATTTATATAAAGAAAAA
*
4594428 TTAATATTA-ATAATGAAA
1 TTAAT-TTATATAAAGAAA
4594446 GTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TTAATTTATATAAAGAAAAA
Found at i:4594601 original size:7 final size:7
Alignment explanation
Indices: 4594589--4594648 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
4594579 TTTACATTAG
4594589 GGTTTAT
1 GGTTTAT
4594596 GGTTTAT
1 GGTTTAT
*
4594603 TGTTTAT
1 GGTTTAT
*
4594610 TGTTTAT
1 GGTTTAT
*
4594617 TGTTTAT
1 GGTTTAT
*
4594624 GGTTTAA
1 GGTTTAT
*
4594631 GGTTTAG
1 GGTTTAT
4594638 GGTTTA-
1 GGTTTAT
4594644 GGTTT
1 GGTTT
4594649 CTATAAACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
6 5 0.10
7 44 0.90
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
GGTTTAT
Found at i:4595154 original size:20 final size:20
Alignment explanation
Indices: 4595116--4595169 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
4595106 TATATTAGGG
*
4595116 TTTAGTGTTTAGTGTTTAT-A
1 TTTAGGGTTTAG-GTTTATGA
*
4595136 GTTTATGGTTTAGGTTTATGA
1 -TTTAGGGTTTAGGTTTATGA
4595157 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
4595170 GTTTCTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.54
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTTATGA
Found at i:4595217 original size:469 final size:477
Alignment explanation
Indices: 4594718--4595701 Score: 1565
Period size: 480 Copynumber: 2.1 Consensus size: 477
4594708 ATAAGTAATT
*
4594718 TACTTTATATA-GTTTATATA-TATATATATACTATACATGGTTTATACATACATATTATAT-AA
1 TACTTTAT-TACG-TTATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAA
4594780 A-A-TTA-T-TTAATAAAATTA-TTAAATGT-AATTATATAAAACATGATTAATTAGGTGTTAAA
64 ATATTTAGTATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
4594839 TAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCA
129 TAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCA
4594904 TTTGCATAATTAGTATTTTAGTTGCATGTTAGATTAATTCACATTAATAGACCATTTATTTTGTT
194 TTTGCATAATTAGTATTTTAGTTGCATGTTAGATTAATTCACATTAATAGACCATTTATTTTGTT
*
4594969 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTTACA
259 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTACAATAGTGCTAGTCCATTTACA
**
4595034 TTAGTTTACATAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTA
324 TTAGTTTACATAGGCCCAATACATAAGCCCACAATTTTATTACAAATATATATGCATTAGTGCTA
* * * ** *
4595099 GTCTATTTATATTAGGGTTTAGTGTTTAGTGTTTATAGTTTATGGTTTA-GGTTTATGATTTAGG
389 GTCCATTTATATTAGGGTTTAGGGTTTAGTGTTTAGAGTTTAAAGTTTAGGGTTTATGATTTAAG
4595163 GTTTAGGGTTTCTATAAAACTATA
454 GTTTAGGGTTTCTATAAAACTATA
*
4595187 TACTTTATTACGTTATATAGTTTATATATACTATACTTGGTTTATACATACATATTATATAAAAT
1 TACTTTATTACGTTATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAA-
4595252 TATTTAGTAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTA
65 TATTTAGT---ATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTA
*
4595317 AATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTT
127 AATAATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTT
* * *
4595382 CATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGTCTATTTATTTTG
192 CATTTGCATAATTAGTATTTTAGTTGCATGTTAGATTAATTCACATTAATAGACCATTTATTTTG
* * *
4595447 TTGTTATGAATAAGTAATAATAAAACTCAGAAATAAGTCCATTTACATTAGTGCTAGTCCATTTA
257 TTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTACAATAGTGCTAGTCCATTTA
* * *
4595512 CATTAGTTTACATAGGCTCAATACATAAGCCCACAATTTTATTACAAATATATATGTATTAGTGT
322 CATTAGTTTACATAGGCCCAATACATAAGCCCACAATTTTATTACAAATATATATGCATTAGTGC
* *
4595577 TAGTCCATTTATATTAGGGTTTAGGGTTTAGTGTTTAGGGTTTAAATTTTAGGGTTTATGATTTA
387 TAGTCCATTTATATTAGGGTTTAGGGTTTAGTGTTTAGAGTTTAAAGTTTAGGGTTTATGATTTA
** * *
4595642 AGGTTTAGGGTTTCTATAAATTTTTT
452 AGGTTTAGGGTTTCTATAAAACTATA
* * **
4595668 TATTTTATTACTTTATATAGTTTATGCATACTAT
1 TACTTTATTACGTTATATAGTTTATATATACTAT
4595702 TTCTATAAAC
Statistics
Matches: 470, Mismatches: 31, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
468 9 0.02
469 47 0.10
470 3 0.01
472 1 0.00
473 3 0.01
474 1 0.00
478 12 0.03
479 8 0.02
480 322 0.69
481 64 0.14
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (477 bp):
TACTTTATTACGTTATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAAT
ATTTAGTATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
ATTAGTATGCCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATT
TGCATAATTAGTATTTTAGTTGCATGTTAGATTAATTCACATTAATAGACCATTTATTTTGTTGT
TATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTACAATAGTGCTAGTCCATTTACATT
AGTTTACATAGGCCCAATACATAAGCCCACAATTTTATTACAAATATATATGCATTAGTGCTAGT
CCATTTATATTAGGGTTTAGGGTTTAGTGTTTAGAGTTTAAAGTTTAGGGTTTATGATTTAAGGT
TTAGGGTTTCTATAAAACTATA
Found at i:4595602 original size:7 final size:7
Alignment explanation
Indices: 4595590--4595654 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
4595580 TCCATTTATA
4595590 TTAGGGT
1 TTAGGGT
4595597 TTAGGGT
1 TTAGGGT
*
4595604 TTAGTGT
1 TTAGGGT
4595611 TTAGGGT
1 TTAGGGT
***
4595618 TTAAATT
1 TTAGGGT
4595625 TTAGGGT
1 TTAGGGT
* *
4595632 TTATGAT
1 TTAGGGT
*
4595639 TTAAGGT
1 TTAGGGT
4595646 TTAGGGT
1 TTAGGGT
4595653 TT
1 TT
4595655 CTATAAATTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (7 bp):
TTAGGGT
Found at i:4596030 original size:139 final size:139
Alignment explanation
Indices: 4595730--4596019 Score: 562
Period size: 139 Copynumber: 2.1 Consensus size: 139
4595720 TAATTTACTT
* *
4595730 TATATAGTTTATATATATATATATATATATACTATACATGGTTTATACATACATGTACTATAAGT
1 TATATACTTTATATATATATATATAAATATACTATACATGGTTTATACATACATGTACTATAAGT
4595795 TACATATATAGTTCATGGGTTAGGGGTTAGGGTTTATGATTAAGGGTTTAGGGTTTAGGTTTTTT
66 TACATATATAGTTCATGGGTTAGGGGTTAGGGTTTATGATTAAGGGTTTAGGGTTTAGGTTTTTT
4595860 TTAATAAAC
131 TTAATAAAC
4595869 TATATACTTTATATATATATATATAAATATACTATACATGGTTTATACATACATGTACTATAAGT
1 TATATACTTTATATATATATATATAAATATACTATACATGGTTTATACATACATGTACTATAAGT
4595934 TACATATATAGTTCATGGGTTAGGGGTTAGGGTTTATGATTAAGGGTTTAGGGTTTAGGTTTTTT
66 TACATATATAGTTCATGGGTTAGGGGTTAGGGTTTATGATTAAGGGTTTAGGGTTTAGGTTTTTT
4595999 TTAATAAAC
131 TTAATAAAC
4596008 TATATACTTTAT
1 TATATACTTTAT
4596020 TACTTTATAT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 149 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (139 bp):
TATATACTTTATATATATATATATAAATATACTATACATGGTTTATACATACATGTACTATAAGT
TACATATATAGTTCATGGGTTAGGGGTTAGGGTTTATGATTAAGGGTTTAGGGTTTAGGTTTTTT
TTAATAAAC
Found at i:4596060 original size:2 final size:2
Alignment explanation
Indices: 4596049--4596217 Score: 63
Period size: 2 Copynumber: 87.0 Consensus size: 2
4596039 ATAGTGTTTC
*
4596049 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
4596089 GA T- TA CT- TA TA T- TA GT- TA TA CA TA CA TA TA TA TA CTA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
4596128 T- TA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * * * *
4596166 TA GTT TA TA CA TA TA TA GTT TA TA TA CA TA CA TA CA TA CA TA CA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
4596210 TA TA TA TA
1 TA TA TA TA
4596218 GAAAATTAAA
Statistics
Matches: 119, Mismatches: 31, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
1 11 0.09
2 101 0.85
3 7 0.06
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4596460 original size:20 final size:20
Alignment explanation
Indices: 4596409--4596465 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
4596399 ATATCAATTC
*
4596409 TCAATTTCCCTCCAAATTTT
1 TCAATTTCCCTCTAAATTTT
4596429 T--ATATTCCCTCTAAATTTT
1 TCAAT-TTCCCTCTAAATTTT
*
4596448 TCAATTTCACTCTAAATT
1 TCAATTTCCCTCTAAATT
4596466 CTCAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 13 0.41
21 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (20 bp):
TCAATTTCCCTCTAAATTTT
Found at i:4596603 original size:2 final size:2
Alignment explanation
Indices: 4596598--4596760 Score: 69
Period size: 2 Copynumber: 82.5 Consensus size: 2
4596588 TTTTATAATT
* * * *
4596598 TA TA TA CA TA TA TA GTT TA CA TA TA TA GTT TA TA TA TA TA GT-
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* *
4596640 TCA TA TA AA CA TA -A TA TA TA TA TA TA TA -A CT- TA TA -A TA -A
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
4596679 T- TA TA TA GTT TA TA -A TA TA AA TA TA GTT TA TA TA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
*
4596720 TA TA TA TA AA CT- TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4596760 T
1 T
4596761 TTTTTTCAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
1 11 0.09
2 102 0.85
3 7 0.06
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4596759 original size:13 final size:14
Alignment explanation
Indices: 4596600--4596760 Score: 104
Period size: 13 Copynumber: 11.4 Consensus size: 14
4596590 TTATAATTTA
*
4596600 TATACATATATAGT
1 TATATATATATAGT
*
4596614 T-TACATATATAGT
1 TATATATATATAGT
4596627 T-TATATATATAGT
1 TATATATATATAGT
* * *
4596640 TCATATAAACATAAT
1 T-ATATATATATAGT
*
4596655 ATATATATATATAACT
1 -TATATATATAT-AGT
4596671 TATAATAATTATATAGTT
1 TAT-AT-A-TATATAG-T
4596689 TATAATATAAATATAGT
1 TAT-ATAT--ATATAGT
4596706 T-TATATATATAGT
1 TATATATATATAGT
* *
4596719 T-TATATATAAACT
1 TATATATATATAGT
4596732 TATAT-TATATA--
1 TATATATATATAGT
4596743 TATATATATATA-T
1 TATATATATATAGT
4596756 TATAT
1 TATAT
4596761 TTTTTTCAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
11 5 0.04
12 6 0.05
13 54 0.44
14 4 0.03
15 24 0.20
16 7 0.06
17 5 0.04
18 18 0.15
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (14 bp):
TATATATATATAGT
Found at i:4598442 original size:2 final size:2
Alignment explanation
Indices: 4598435--4598498 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
4598425 TATAAATTTA
4598435 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
4598477 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4598499 TAATGATGTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4601398 original size:34 final size:35
Alignment explanation
Indices: 4601347--4601421 Score: 125
Period size: 34 Copynumber: 2.1 Consensus size: 35
4601337 GCTTGGCTAA
*
4601347 TGTATAACTCTATATTTTAATTATGAATCTTCAGTT
1 TGTATAAC-CTATATTTTAATTATGAATCTTCAATT
4601383 TGTATAA-CTATATTTTAATTATGAATCTTCAATT
1 TGTATAACCTATATTTTAATTATGAATCTTCAATT
4601417 TGTAT
1 TGTAT
4601422 TTCATTGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 31 0.82
36 7 0.18
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.51
Consensus pattern (35 bp):
TGTATAACCTATATTTTAATTATGAATCTTCAATT
Found at i:4606699 original size:60 final size:60
Alignment explanation
Indices: 4606584--4606701 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
4606574 GAACACTTTG
* * * * *
4606584 TAACTTTTAATAGTCGAGGGACTCAACGAAGCAACTCTCTATAGTTGAGAGATCATTTTT
1 TAACTTTTAATAGTCGAGGGACTCAACAAAGCAAATCTCTATAGGTAACAGATCATTTTT
* *
4606644 TAACTTTTAATAGTCTGA-GGACTCAATAAAGCAATATCT-TATAGGTAACATATCATTT
1 TAACTTTTAATAGTC-GAGGGACTCAACAAAGCAA-ATCTCTATAGGTAACAGATCATTT
4606702 GTGTACTTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
60 44 0.90
61 5 0.10
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (60 bp):
TAACTTTTAATAGTCGAGGGACTCAACAAAGCAAATCTCTATAGGTAACAGATCATTTTT
Found at i:4611424 original size:6 final size:6
Alignment explanation
Indices: 4611415--4611449 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4611405 ATCTCCATCC
*
4611415 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA ACCCA
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCA
4611450 GATGCTGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.14
Consensus pattern (6 bp):
TCCCAA
Found at i:4614487 original size:20 final size:20
Alignment explanation
Indices: 4614455--4614494 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4614445 CAGAGATTTT
4614455 ATCCCCAAACGGCTAGAAAAC
1 ATCCCCAAACGGCTA-AAAAC
4614476 ATCCCC-AACGGCTAAAAAC
1 ATCCCCAAACGGCTAAAAAC
4614495 GGTCATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.10
Consensus pattern (20 bp):
ATCCCCAAACGGCTAAAAAC
Found at i:4627212 original size:21 final size:19
Alignment explanation
Indices: 4627188--4627232 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4627178 TGACTAACTG
4627188 TTGACTTGACGAGAGTTGAAT
1 TTGACTTG--GAGAGTTGAAT
**
4627209 TTGACTTGGATCGTTGAAT
1 TTGACTTGGAGAGTTGAAT
4627228 TTGAC
1 TTGAC
4627233 CAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (19 bp):
TTGACTTGGAGAGTTGAAT
Found at i:4638531 original size:17 final size:17
Alignment explanation
Indices: 4638509--4638548 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4638499 ACTCAGGTTC
*
4638509 GGTCAACATTGGGCTTG
1 GGTCAACATCGGGCTTG
4638526 GGTCAACATCGGGCTTG
1 GGTCAACATCGGGCTTG
4638543 GGTCAA
1 GGTCAA
4638549 AATGACCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (17 bp):
GGTCAACATCGGGCTTG
Found at i:4647310 original size:25 final size:24
Alignment explanation
Indices: 4647232--4647328 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
4647222 GTTGATCATG
* * *
4647232 TATTAGTGCATTTGTGCACT-CTCA
1 TATTAGTACATTCGTGTACTCCT-A
*
4647256 TATTAGTACATTCGTGTACTCCCA
1 TATTAGTACATTCGTGTACTCCTA
4647280 TATTAGTACCATT-GTGTACTCCTA
1 TATTAGTA-CATTCGTGTACTCCTA
*
4647304 TATTTAGCACATTCGTGTACTCCTA
1 TA-TTAGTACATTCGTGTACTCCTA
4647329 GAAATATTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
24 42 0.67
25 21 0.33
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (24 bp):
TATTAGTACATTCGTGTACTCCTA
Found at i:4652957 original size:15 final size:15
Alignment explanation
Indices: 4652937--4652966 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4652927 ACTGTAAAAT
4652937 AGCTAGAAAAATATA
1 AGCTAGAAAAATATA
*
4652952 AGCTAGAAAAGTATA
1 AGCTAGAAAAATATA
4652967 GGAAAAATCA
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:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
AGCTAGAAAAATATA
Found at i:4664596 original size:20 final size:21
Alignment explanation
Indices: 4664569--4664613 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4664559 TACATCAAGG
*
4664569 CTTTTTTTGAAGCCATAAAAT
1 CTTTTTTCGAAGCCATAAAAT
*
4664590 CTTTTTTCGAGGCCATAAAAT
1 CTTTTTTCGAAGCCATAAAAT
4664611 CTT
1 CTT
4664614 GCAGTGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (21 bp):
CTTTTTTCGAAGCCATAAAAT
Found at i:4674154 original size:26 final size:26
Alignment explanation
Indices: 4674115--4674175 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
4674105 AGGCCATTTT
4674115 CTCTCACCTGAACTATCTCTCTCATA
1 CTCTCACCTGAACTATCTCTCTCATA
*
4674141 CTTTCACCTGAACTATCTCTCTCATA
1 CTCTCACCTGAACTATCTCTCTCATA
4674167 CTCTCACCT
1 CTCTCACCT
4674176 AGGACGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.39, G:0.03, T:0.36
Consensus pattern (26 bp):
CTCTCACCTGAACTATCTCTCTCATA
Found at i:4674804 original size:21 final size:21
Alignment explanation
Indices: 4674780--4674837 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
4674770 ATTTCTGTCG
*
4674780 AGGGATAGATCATTT-TCTCCA
1 AGGGATAGATCCTTTCTC-CCA
*
4674801 AGGGATCGATCCTTTCTCCCA
1 AGGGATAGATCCTTTCTCCCA
*
4674822 AGGGGATCGATCCTTT
1 A-GGGATAGATCCTTT
4674838 TAAAAATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (21 bp):
AGGGATAGATCCTTTCTCCCA
Found at i:4674818 original size:20 final size:22
Alignment explanation
Indices: 4674793--4674837 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4674783 GATAGATCAT
4674793 TTTCT-CCAA-GGGATCGATCC
1 TTTCTCCCAAGGGGATCGATCC
4674813 TTTCTCCCAAGGGGATCGATCC
1 TTTCTCCCAAGGGGATCGATCC
4674835 TTT
1 TTT
4674838 TAAAAATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (22 bp):
TTTCTCCCAAGGGGATCGATCC
Found at i:4676698 original size:2 final size:2
Alignment explanation
Indices: 4676691--4676721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4676681 TTTCATATTG
4676691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4676722 ATTTAGGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4680247 original size:14 final size:14
Alignment explanation
Indices: 4680228--4680262 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
4680218 TTGCCTAGAG
4680228 GATTAAGAAATCAT
1 GATTAAGAAATCAT
4680242 GATTAAGAAATCAT
1 GATTAAGAAATCAT
4680256 GATTAAG
1 GATTAAG
4680263 GATTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (14 bp):
GATTAAGAAATCAT
Found at i:4685428 original size:12 final size:12
Alignment explanation
Indices: 4685411--4685445 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4685401 GTAAGTACAC
4685411 ATGACATTGGAA
1 ATGACATTGGAA
*
4685423 ATGACATTGGAC
1 ATGACATTGGAA
*
4685435 ATGACGTTGGA
1 ATGACATTGGA
4685446 GAACCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (12 bp):
ATGACATTGGAA
Found at i:4686043 original size:39 final size:39
Alignment explanation
Indices: 4685999--4686084 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
4685989 GCATTTTTAA
*
4685999 ATGGTTTTATAAAGGAAGAATTGTATGTGGAACAACCTC
1 ATGGTTTTATAAAGAAAGAATTGTATGTGGAACAACCTC
* *
4686038 CTGGTTTTATAAAGAAAGAATTGTATGTGGAACAACCTT
1 ATGGTTTTATAAAGAAAGAATTGTATGTGGAACAACCTC
4686077 ATGGTTTT
1 ATGGTTTT
4686085 GAAGATTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (39 bp):
ATGGTTTTATAAAGAAAGAATTGTATGTGGAACAACCTC
Found at i:4687505 original size:21 final size:21
Alignment explanation
Indices: 4687459--4687535 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
4687449 TTTGTGCAAA
* *
4687459 GTGTATCGATACCCCCTTG-CT
1 GTGTATCGATA-CACCTTGAAT
*
4687480 ATGTATCGATACACCTTGAAT
1 GTGTATCGATACACCTTGAAT
* * * *
4687501 GTGTACCAATATATTCCTTCAAT
1 GTGTATCGATACA--CCTTGAAT
4687524 GTGTATCGATAC
1 GTGTATCGATAC
4687536 CCCTAGAGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 6 0.14
21 20 0.48
23 16 0.38
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (21 bp):
GTGTATCGATACACCTTGAAT
Found at i:4689861 original size:21 final size:21
Alignment explanation
Indices: 4689835--4689875 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4689825 GTCGAGGGTT
4689835 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
4689856 TCATAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
4689876 TAAAATGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:4689885 original size:21 final size:21
Alignment explanation
Indices: 4689839--4689896 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4689829 AGGGTTTCAT
* *
4689839 AGGTCCTTCGGGACAACTCAT
1 AGGTCCTTCGGGACAACTAAA
4689860 AGGTCCTTCGGGACAA-TAAA
1 AGGTCCTTCGGGACAACTAAA
*
4689880 ATGGTCCTTCAGGACAA
1 A-GGTCCTTCGGGACAA
4689897 ATTTCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTAAA
Found at i:4692469 original size:13 final size:13
Alignment explanation
Indices: 4692440--4692473 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
4692430 GGGGAGTAAT
*
4692440 TTTTCAAAATTGA
1 TTTTCAAAAATGA
4692453 -TTTCAAAAATGA
1 TTTTCAAAAATGA
4692465 TTTTCAAAA
1 TTTTCAAAA
4692474 CGAAAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:4697753 original size:22 final size:23
Alignment explanation
Indices: 4697728--4697772 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4697718 AATTATCATA
4697728 TATTT-TAGATAT-TTTTTATTTT
1 TATTTATA-ATATATTTTTATTTT
4697750 TATTTATAATATATTTTTATTTT
1 TATTTATAATATATTTTTATTTT
4697773 ATAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTATAATATATTTTTATTTT
Found at i:4699018 original size:70 final size:72
Alignment explanation
Indices: 4698944--4699076 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 72
4698934 GAGATTAAAG
** *
4698944 GTTTAATTTCATTAATTTTAAAATTC-A-AATGTCTTAAA-AATAATTAAACCAAACAAAATTTG
1 GTTTAATTTCATTAATTTTAAAAGCCGATAATATCTTAAATAATAATTAAACC-AACAAAATTTG
4699006 GGTCAAAT
65 GGTCAAAT
* * *
4699014 GTTTAATTTTATTAATTTTAAAAGCCGATAGTATCTTAAATAATAATTATACCAACAAAATTT
1 GTTTAATTTCATTAATTTTAAAAGCCGATAATATCTTAAATAATAATTAAACCAACAAAATTT
4699077 TGGAGGAGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
70 23 0.43
71 1 0.02
72 19 0.35
73 11 0.20
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (72 bp):
GTTTAATTTCATTAATTTTAAAAGCCGATAATATCTTAAATAATAATTAAACCAACAAAATTTGG
GTCAAAT
Found at i:4702883 original size:40 final size:40
Alignment explanation
Indices: 4702828--4702950 Score: 192
Period size: 40 Copynumber: 3.1 Consensus size: 40
4702818 TGCAAGTTTA
*
4702828 TAATACACGTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
4702868 TAATACACTTTGGTGTATATGGTGGGCACGGCTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
4702908 TAATACACTTCAGTGTATATAGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
4702948 TAA
1 TAA
4702951 CACTACGGTG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:4703532 original size:30 final size:30
Alignment explanation
Indices: 4703477--4703533 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4703467 GAAATTACTG
* ** *
4703477 TAGCAGTTACTGTAGTGTATTGATGCACTA
1 TAGCAGTTACTATAGCATATCGATGCACTA
4703507 TAGCAGTTACTATAGCATATCGATGCA
1 TAGCAGTTACTATAGCATATCGATGCA
4703534 TAATATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (30 bp):
TAGCAGTTACTATAGCATATCGATGCACTA
Found at i:4718065 original size:12 final size:12
Alignment explanation
Indices: 4718048--4718073 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4718038 GTTCTAATTC
4718048 GAAAAGAAAAAA
1 GAAAAGAAAAAA
4718060 GAAAAGAAAAAA
1 GAAAAGAAAAAA
4718072 GA
1 GA
4718074 GAAAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:4719001 original size:21 final size:20
Alignment explanation
Indices: 4718963--4719012 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4718953 CTCAAAGTGA
* *
4718963 TCAATTCACAAGGTAGGATT
1 TCAATTCACAACGAAGGATT
4718983 TCAACTTCACAACGAAGGATAT
1 TCAA-TTCACAACGAAGGAT-T
*
4719005 CCAATTCA
1 TCAATTCA
4719013 AAGCTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (20 bp):
TCAATTCACAACGAAGGATT
Found at i:4719952 original size:7 final size:7
Alignment explanation
Indices: 4719940--4719965 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4719930 CCCGATGGTA
4719940 ACCCGAG
1 ACCCGAG
4719947 ACCCGAG
1 ACCCGAG
4719954 ACCCGAG
1 ACCCGAG
4719961 ACCCG
1 ACCCG
4719966 GATCCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.46, G:0.27, T:0.00
Consensus pattern (7 bp):
ACCCGAG
Found at i:4721073 original size:11 final size:10
Alignment explanation
Indices: 4721053--4721262 Score: 60
Period size: 10 Copynumber: 19.1 Consensus size: 10
4721043 TAAATATATA
4721053 TTTTTTTATT
1 TTTTTTTATT
4721063 TTTTTTGTATT
1 TTTTTT-TATT
*
4721074 TTTTGTTTCTAT
1 TTTT-TTTAT-T
*
4721086 TTTTTCTATT
1 TTTTTTTATT
** **
4721096 TAATTCCATT
1 TTTTTTTATT
*
4721106 ACTTTTTTTCTT
1 --TTTTTTTATT
4721118 TTGTTTTTATTT
1 TT-TTTTTA-TT
4721130 TTTTTTTATT
1 TTTTTTTATT
** *
4721140 TAATTTTGTT
1 TTTTTTTATT
4721150 TATTTTATTCATT
1 T-TTTT-TT-ATT
*
4721163 TTGTTTTATT
1 TTTTTTTATT
*
4721173 TCATTTTTCATT
1 T--TTTTTTATT
**
4721185 TCATTTTATT
1 TTTTTTTATT
*
4721195 TTTATTCTTATCC
1 TTT-TT-TTAT-T
*
4721208 TTATTTTATT
1 TTTTTTTATT
**
4721218 CTTTTAATATTT
1 -TTTTTTTA-TT
*
4721230 TTCCTTTTTATC
1 TT--TTTTTATT
*
4721242 TTTTATTATT
1 TTTTTTTATT
*
4721252 TTATTTTATT
1 TTTTTTTATT
4721262 T
1 T
4721263 ATTTAGCTAA
Statistics
Matches: 142, Mismatches: 39, Indels: 38
0.65 0.18 0.17
Matches are distributed among these distances:
10 52 0.37
11 41 0.29
12 40 0.28
13 9 0.06
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:4721130 original size:5 final size:5
Alignment explanation
Indices: 4721122--4721217 Score: 52
Period size: 5 Copynumber: 18.4 Consensus size: 5
4721112 TTTCTTTTGT
* * * * *
4721122 TTTTA TTTTTT TTTTA TTTAA TTTT- GTTTA TTTTA -TTCA TTTTG TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
4721171 TTTCA TTTTTCA TTTCA TTTTA TTTTTA TTCTTA TCCTTA TTTTA TT
1 TTTTA -TTTT-A TTTTA TTTTA -TTTTA TT-TTA T-TTTA TTTTA TT
4721218 CTTTTAATAT
Statistics
Matches: 67, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
4 6 0.09
5 37 0.55
6 23 0.34
7 1 0.01
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:4721133 original size:22 final size:22
Alignment explanation
Indices: 4721108--4721197 Score: 58
Period size: 22 Copynumber: 4.1 Consensus size: 22
4721098 ATTCCATTAC
4721108 TTTTTTTCTTTTGTTTTTATTT
1 TTTTTTTCTTTTGTTTTTATTT
* ** *
4721130 TTTTTTTATTTAATTTTGT-TTA
1 TTTTTTTCTTTTGTTTT-TATTT
*
4721152 TTTTATTCATTTTG-TTTTATTT
1 TTTTTTTC-TTTTGTTTTTATTT
** * **
4721174 CATTTTTCATTTCATTTTATTT
1 TTTTTTTCTTTTGTTTTTATTT
4721196 TT
1 TT
4721198 ATTCTTATCC
Statistics
Matches: 48, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
21 4 0.08
22 40 0.83
23 4 0.08
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.78
Consensus pattern (22 bp):
TTTTTTTCTTTTGTTTTTATTT
Found at i:4721157 original size:19 final size:20
Alignment explanation
Indices: 4721128--4721178 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4721118 TTGTTTTTAT
*
4721128 TTTTTTTTTATTTAATTTTG
1 TTTTATTTTATTTAATTTTG
*
4721148 -TTTATTTTA-TTCATTTTG
1 TTTTATTTTATTTAATTTTG
*
4721166 TTTTATTTCATTT
1 TTTTATTTTATTT
4721179 TTCATTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.31
19 16 0.62
20 2 0.08
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTTAATTTTG
Found at i:4726960 original size:30 final size:28
Alignment explanation
Indices: 4726907--4726962 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
4726897 AAACACTCAA
4726907 AATATTATTATTTTATATATTTAATATT
1 AATATTATTATTTTATATATTTAATATT
4726935 AATA-TATTATTTTAGTATCACTTTAATA
1 AATATTATTATTTTA-TAT-A-TTTAATA
4726963 AAAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.40
28 7 0.28
29 1 0.04
30 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
AATATTATTATTTTATATATTTAATATT
Found at i:4726972 original size:30 final size:27
Alignment explanation
Indices: 4726912--4726973 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
4726902 CTCAAAATAT
** *
4726912 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAAAA
4726939 TATTATTTTAGTATCACTTTAATAAAAAAA
1 TATTATTTTA-TAT-A-TTTAATAAAAAAA
4726969 TATTA
1 TATTA
4726974 ATTATTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 10 0.34
28 3 0.10
29 1 0.03
30 15 0.52
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAAAA
Found at i:4727042 original size:14 final size:15
Alignment explanation
Indices: 4727023--4727063 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
4727013 TAGTATATTT
4727023 TATTATTATAAT-TA
1 TATTATTATAATATA
4727037 TATTATTATAATAATA
1 TATTATTATAAT-ATA
*
4727053 TAATATTATAA
1 TATTATTATAA
4727064 AATTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATTATAATATA
Found at i:4727295 original size:39 final size:40
Alignment explanation
Indices: 4727204--4727301 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 40
4727194 AATTTTTAAT
* * *
4727204 ATTT-TAATAATATTATTATTTTAATAAACAATTAATATA
1 ATTTATAATATTATTATTATTTTAAAAAACAATAAATATA
* * *
4727243 ATTAATAATA-TATTATTCTTTTTTAAAAAATAATAAATATA
1 ATTTATAATATTATTA-T-TATTTTAAAAAACAATAAATATA
*
4727284 ATTTATAATATTTTTATT
1 ATTTATAATATTATTATT
4727302 TTAAGAATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
39 8 0.17
40 7 0.15
41 29 0.60
42 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTTATAATATTATTATTATTTTAAAAAACAATAAATATA
Found at i:4727581 original size:2 final size:2
Alignment explanation
Indices: 4727574--4727599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4727564 AATGGACCCT
4727574 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
4727600 CGTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4729902 original size:25 final size:24
Alignment explanation
Indices: 4729874--4729933 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
4729864 ATTTTTTATT
*
4729874 AATTATTTAATTTTGCACC-CTCTAA
1 AATT-TTTAATTATGCACCTC-CTAA
*
4729899 AATTTTATAATTATGCATCTCCTAA
1 AATTTT-TAATTATGCACCTCCTAA
4729924 AATTTTTAAT
1 AATTTTTAAT
4729934 ATAACTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 24 0.77
26 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (24 bp):
AATTTTTAATTATGCACCTCCTAA
Found at i:4730461 original size:15 final size:15
Alignment explanation
Indices: 4730437--4730473 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4730427 AATCATTTTT
*
4730437 TTCAATTTCGAGTTA
1 TTCAAGTTCGAGTTA
*
4730452 TTCAAGTTCGTGTTA
1 TTCAAGTTCGAGTTA
4730467 TTCAAGT
1 TTCAAGT
4730474 ATTCAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (15 bp):
TTCAAGTTCGAGTTA
Found at i:4731468 original size:2 final size:2
Alignment explanation
Indices: 4731395--4731451 Score: 61
Period size: 2 Copynumber: 30.0 Consensus size: 2
4731385 TTTATTACAT
4731395 TA TA TA -A TA TA TA TGA TA -A TA TA TA TA -A TA -A T- TCA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A TA TA
4731434 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
4731452 GTTTTTGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
1 5 0.10
2 40 0.83
3 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4731479 original size:23 final size:21
Alignment explanation
Indices: 4731441--4731507 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 21
4731431 ATATATATAT
4731441 ATATATATATAGTTTTTGAAA
1 ATATATATATAGTTTTTGAAA
*
4731462 ATATATAGTATGATTTTTTGAAA
1 ATATATA-TAT-AGTTTTTGAAA
*
4731485 ACATATAATATAGTTTTT-AAA
1 ATATAT-ATATAGTTTTTGAAA
4731506 AT
1 AT
4731508 GGTTTTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 11 0.28
22 9 0.23
23 18 0.46
24 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (21 bp):
ATATATATATAGTTTTTGAAA
Found at i:4731634 original size:21 final size:20
Alignment explanation
Indices: 4731581--4731646 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
4731571 AAAAGTATAT
*
4731581 AATATATATAATTTTTGAAA
1 AATATATATAGTTTTTGAAA
*
4731601 ACATAT-TAGAGTTTTTGAAA
1 A-ATATATATAGTTTTTGAAA
4731621 AATATAATATAGTTTTT-AAA
1 AATAT-ATATAGTTTTTGAAA
*
4731641 TATATA
1 AATATA
4731647 GTGTACGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.13
20 21 0.54
21 13 0.33
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (20 bp):
AATATATATAGTTTTTGAAA
Done.