Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 54
Found at i:5244832 original size:14 final size:14
Alignment explanation
Indices: 5244813--5244839 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5244803 TTTTCTTATT
5244813 TTTCTTATTTCTTA
1 TTTCTTATTTCTTA
5244827 TTTCTTATTTCTT
1 TTTCTTATTTCTT
5244840 TCTTTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTATTTCTTA
Found at i:5246754 original size:19 final size:19
Alignment explanation
Indices: 5246714--5246755 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5246704 AATAAGAAAT
*
5246714 TAAAGAATGTAAAGAATGA
1 TAAAGAATATAAAGAATGA
*
5246733 TAAAGAATATGAA-AATGTA
1 TAAAGAATATAAAGAATG-A
5246752 TAAA
1 TAAA
5246756 ATGATTGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.24
Consensus pattern (19 bp):
TAAAGAATATAAAGAATGA
Found at i:5247265 original size:58 final size:60
Alignment explanation
Indices: 5247197--5247314 Score: 197
Period size: 58 Copynumber: 2.0 Consensus size: 60
5247187 GGGAATTGGG
*
5247197 CCCAAATTTTGATCCAAAACAATTTTCTTTC-AGATTGATAGTC-T-GTTTGGTTTTGAAA
1 CCCAAATTTTGATCCAAAACAATTTTCTTTCAAGA-TGATAGTCTTGGTTGGGTTTTGAAA
5247255 CCCAAATTTTGATCCAAAACAATTTTCTTTCAAGATGATAGTCTTGGTTGGGTTTTGAAA
1 CCCAAATTTTGATCCAAAACAATTTTCTTTCAAGATGATAGTCTTGGTTGGGTTTTGAAA
5247315 AATAGTTGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
58 39 0.70
59 4 0.07
60 13 0.23
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (60 bp):
CCCAAATTTTGATCCAAAACAATTTTCTTTCAAGATGATAGTCTTGGTTGGGTTTTGAAA
Found at i:5257892 original size:22 final size:24
Alignment explanation
Indices: 5257867--5257916 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
5257857 GTTTTTATTA
5257867 TTATTTAA-AATT-AATTAAATAT
1 TTATTTAATAATTAAATTAAATAT
5257889 TTATTTAATTAATTGAAATTAAATAT
1 TTATTTAA-TAATT-AAATTAAATAT
5257915 TT
1 TT
5257917 GGGATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
24 4 0.17
26 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTTAATAATTAAATTAAATAT
Found at i:5259391 original size:21 final size:23
Alignment explanation
Indices: 5259367--5259425 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
5259357 TATAAATTAA
*
5259367 AATAAAATATAAATAACTAT-G-
1 AATAAAATATAAAAAACTATAGT
5259388 AATAAAATA-AATAAAACTATAGT
1 AATAAAATATAA-AAAACTATAGT
*
5259411 ATTAAAATATAAAAA
1 AATAAAATATAAAAA
5259426 GTAATAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.50
22 1 0.03
23 11 0.34
24 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (23 bp):
AATAAAATATAAAAAACTATAGT
Found at i:5260133 original size:139 final size:140
Alignment explanation
Indices: 5259883--5260163 Score: 555
Period size: 139 Copynumber: 2.0 Consensus size: 140
5259873 ACACCCCTCA
5259883 CTGAAATGTCATCGTTTTGGTGAGGGTATAAATACCCCTTTAAACCGGCCATAAGGCCATTTTTA
1 CTGAAATGTCATCGTTTTGGTGAGGGTATAAATACCCCTTTAAACCGGCCATAAGGCCATTTTTA
5259948 TCTCATTTTTCCATTTCTTTTCTCTCTCTAGAAGAGGGAGATGAAATAAATCTCTCTCCCTCTCT
66 TCTCATTTTTCCATTTCTTTTCTCTCTCTAGAAGAGGGAGATGAAATAAATCTCTCTCCCTCTCT
5260013 CTAAAA-CCT
131 CTAAAATCCT
5260022 CTGAAATGTCATCGTTTTGGTGAGGGTATAAATACCCCTTTAAACCGGCCATAAGGCCATTTTTA
1 CTGAAATGTCATCGTTTTGGTGAGGGTATAAATACCCCTTTAAACCGGCCATAAGGCCATTTTTA
5260087 TCTCATTTTTCCATTTCTTTTCTCTCTCTAGAAGAGGGAGATGAAATAAATCTCTCTCCCTCTCT
66 TCTCATTTTTCCATTTCTTTTCTCTCTCTAGAAGAGGGAGATGAAATAAATCTCTCTCCCTCTCT
5260152 CTAAAATCCT
131 CTAAAATCCT
5260162 CT
1 CT
5260164 ATCCAGAGGG
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 136 0.96
140 5 0.04
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (140 bp):
CTGAAATGTCATCGTTTTGGTGAGGGTATAAATACCCCTTTAAACCGGCCATAAGGCCATTTTTA
TCTCATTTTTCCATTTCTTTTCTCTCTCTAGAAGAGGGAGATGAAATAAATCTCTCTCCCTCTCT
CTAAAATCCT
Found at i:5260920 original size:3 final size:3
Alignment explanation
Indices: 5260912--5260999 Score: 99
Period size: 3 Copynumber: 28.7 Consensus size: 3
5260902 AAATTTTATT
5260912 TAA TAA TAA TAA TATA TAA T-A TATA TATA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA
* * *
5260960 TAA TAA TAA TAA TAG TAA -AA TAA AAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5261000 GAATGAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.05
3 57 0.76
4 14 0.19
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5261008 original size:23 final size:23
Alignment explanation
Indices: 5260913--5261010 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 23
5260903 AATTTTATTT
* * *
5260913 AATAATAAT-AATATATAATATA
1 AATAATAATAAAAATAAAATAAA
* * *
5260935 TATATATATATAATAATAATAATAAT
1 AATA-ATA-ATAAAAATAA-AATAAA
* *
5260961 AATAATAATAATAGTAAAATAAA
1 AATAATAATAAAAATAAAATAAA
*
5260984 AATAATAATAAAAATAGAATGAAA
1 AATAATAATAAAAATAAAAT-AAA
5261008 AAT
1 AAT
5261011 TAGTGTTTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
22 3 0.05
23 25 0.42
24 17 0.29
25 7 0.12
26 7 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AATAATAATAAAAATAAAATAAA
Found at i:5261233 original size:45 final size:45
Alignment explanation
Indices: 5261167--5261575 Score: 667
Period size: 45 Copynumber: 9.1 Consensus size: 45
5261157 AAGGTCTTAT
* * *
5261167 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
5261212 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
**
5261257 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGACTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
5261302 CATCATGCACTGAAGGGCTTACAGATGACCCGAAAGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
5261347 CATCATGCACTGAAGGGCTTACAGATTACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* * * *
5261392 CATCATGCATTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
** *
5261437 CATCATGCACTGAAGGGCTTACAGATGACCTAAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
5261482 CATCATGCACTGAAGGGCTTACAGATGACCCGAATGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
5261527 CATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
5261571 CATCA
1 CATCA
5261576 AAAAGCTCTC
Statistics
Matches: 340, Mismatches: 24, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
44 19 0.06
45 321 0.94
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:5261456 original size:26 final size:26
Alignment explanation
Indices: 5261426--5261501 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
5261416 ATGACCCAAA
5261426 GGCTTTGAAAACATCATGCACTGAAG
1 GGCTTTGAAAACATCATGCACTGAAG
* *
5261452 GGC-TT----ACA-GATG-ACCT-AAA
1 GGCTTTGAAAACATCATGCA-CTGAAG
5261471 GGCTTTGAAAACATCATGCACTGAAG
1 GGCTTTGAAAACATCATGCACTGAAG
5261497 GGCTT
1 GGCTT
5261502 ACAGATGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 6 0.16
20 7 0.19
21 3 0.08
24 3 0.08
25 7 0.19
26 11 0.30
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (26 bp):
GGCTTTGAAAACATCATGCACTGAAG
Found at i:5262365 original size:22 final size:22
Alignment explanation
Indices: 5262340--5262381 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5262330 TGAAAAGAGA
5262340 ATCTATCATCTTTCAAGAATAT
1 ATCTATCATCTTTCAAGAATAT
* *
5262362 ATCTATCATTTTTGAAGAAT
1 ATCTATCATCTTTCAAGAAT
5262382 GTAGATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (22 bp):
ATCTATCATCTTTCAAGAATAT
Found at i:5262908 original size:54 final size:54
Alignment explanation
Indices: 5262747--5262908 Score: 229
Period size: 54 Copynumber: 3.0 Consensus size: 54
5262737 ATAATCACTG
* *
5262747 GTTCGTAAAACATTTGACAACACGTTCATTCTTTCCTGTGGTTTCTGTC-CAGAG
1 GTTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGTTTCTG-CACAGAT
* *
5262801 GTTCATAAAATATTTGACAACACATTCA-TCATTTCCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTC-TTTCCTGTGGTTTCTGCACAGAT
* * *
5262855 GTTCGTAAAACATTTGATAACACATTCATTCTTTCCTATGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGTTTCTGCACAGAT
5262909 TTCTGGTCAG
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
53 3 0.03
54 91 0.95
55 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATTCTTTCCTGTGGTTTCTGCACAGAT
Found at i:5267489 original size:14 final size:14
Alignment explanation
Indices: 5267470--5267496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5267460 CTTGATTCAA
5267470 TTTTTCCTTTTTTC
1 TTTTTCCTTTTTTC
5267484 TTTTTCCTTTTTT
1 TTTTTCCTTTTTT
5267497 TAGTATAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCCTTTTTTC
Found at i:5267780 original size:2 final size:2
Alignment explanation
Indices: 5267773--5267830 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5267763 ACAACAAGGG
5267773 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
5267815 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5267831 TTGAAAGGAT
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:5272356 original size:27 final size:29
Alignment explanation
Indices: 5272326--5272386 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
5272316 AAATAAAAAT
*
5272326 AAAAATAAT-A-TACATATAAATATTATG
1 AAAAATAATAAGTACATATAAAAATTATG
* *
5272353 AAAAATAATAAGTATATATAAAAATTTTG
1 AAAAATAATAAGTACATATAAAAATTATG
5272382 AAAAA
1 AAAAA
5272387 CAAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 9 0.31
28 1 0.03
29 19 0.66
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATAATAAGTACATATAAAAATTATG
Found at i:5272397 original size:29 final size:29
Alignment explanation
Indices: 5272339--5272397 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5272329 AATAATATAC
* * *
5272339 ATATAAATATTATGAAAAATAATAAGTAT
1 ATATAAAAATTATGAAAAACAAAAAGTAT
* *
5272368 ATATAAAAATTTTGAAAAACAAAAATTAT
1 ATATAAAAATTATGAAAAACAAAAAGTAT
5272397 A
1 A
5272398 AATTAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
ATATAAAAATTATGAAAAACAAAAAGTAT
Found at i:5272953 original size:23 final size:21
Alignment explanation
Indices: 5272911--5272954 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5272901 ATATATATAT
*
5272911 ATATATTTAATTTTATAAATA
1 ATATATTTAATTTTAGAAATA
*
5272932 ATATATTTATTTACTTAGAAATA
1 ATATATTTAATT--TTAGAAATA
5272955 TCAGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATATTTAATTTTAGAAATA
Found at i:5273314 original size:17 final size:17
Alignment explanation
Indices: 5273285--5273357 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 17
5273275 ATGACTACAT
*
5273285 AATA-ATAATAATAATTA
1 AATATATAA-AATAAATA
5273302 AATATATAAAATAAATA
1 AATATATAAAATAAATA
5273319 AA-ATATAAATATAAATA
1 AATATATAAA-ATAAATA
*
5273336 AACAATGAATAAAATAAATA
1 AA-TAT--ATAAAATAAATA
5273356 AA
1 AA
5273358 ATTAAAACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
16 7 0.14
17 22 0.45
18 4 0.08
19 2 0.04
20 9 0.18
21 5 0.10
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (17 bp):
AATATATAAAATAAATA
Found at i:5273318 original size:24 final size:24
Alignment explanation
Indices: 5273283--5273336 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5273273 ATATGACTAC
5273283 ATAATAATAATAATAAT-TAAATAT
1 ATAATAATAATAA-AATATAAATAT
5273307 ATAA-AATAAATAAAATATAAATAT
1 ATAATAAT-AATAAAATATAAATAT
5273331 A-AATAA
1 ATAATAA
5273337 ACAATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
ATAATAATAATAAAATATAAATAT
Found at i:5273336 original size:26 final size:25
Alignment explanation
Indices: 5273301--5273351 Score: 57
Period size: 28 Copynumber: 1.9 Consensus size: 25
5273291 AATAATAATT
*
5273301 AAATATATAAAATAAATAAAATATA
1 AAATAAATAAAATAAATAAAATATA
*
5273326 AATATAAATAAACAATGAATAAAATA
1 AA-ATAAAT-AA-AATAAATAAAATA
5273352 AATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
25 2 0.10
26 5 0.24
27 2 0.10
28 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (25 bp):
AAATAAATAAAATAAATAAAATATA
Found at i:5274746 original size:3 final size:3
Alignment explanation
Indices: 5274738--5274800 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
5274728 AACTTTTATT
5274738 TAA TAA TAA TATA TAA T-A TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
5274784 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
5274801 GAATGAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 50 0.88
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5275412 original size:35 final size:35
Alignment explanation
Indices: 5275373--5275513 Score: 122
Period size: 35 Copynumber: 4.0 Consensus size: 35
5275363 ACGAAGTCTC
* *
5275373 TATAGGTTTAGCTAGATCAAATTGGTAATTCCTTA
1 TATAGGTTCAGCTCGATCAAATTGGTAATTCCTTA
* * * *
5275408 TATAGTTTCAAGC-CGATCGAACTGTTAATTCCTTA
1 TATAGGTTC-AGCTCGATCAAATTGGTAATTCCTTA
* * * * *
5275443 CGACAGGTTCAGCTCGGTTAAATTGGTAATTTCTTA
1 -TATAGGTTCAGCTCGATCAAATTGGTAATTCCTTA
* * * *
5275479 TATAGATTCAGATCGATCGAGTTGGTAATTCCTTA
1 TATAGGTTCAGCTCGATCAAATTGGTAATTCCTTA
5275514 CGGATCTAAG
Statistics
Matches: 79, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
35 54 0.68
36 25 0.32
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (35 bp):
TATAGGTTCAGCTCGATCAAATTGGTAATTCCTTA
Found at i:5278635 original size:20 final size:20
Alignment explanation
Indices: 5278602--5278639 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5278592 GGGCAGATTG
5278602 CCCAGAGGGAACCGATTCAC
1 CCCAGAGGGAACCGATTCAC
* *
5278622 CCCAGGGGGTACCGATTC
1 CCCAGAGGGAACCGATTC
5278640 CCCTTGAATA
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:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (20 bp):
CCCAGAGGGAACCGATTCAC
Found at i:5284562 original size:13 final size:13
Alignment explanation
Indices: 5284544--5284576 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5284534 GTATATTGAC
5284544 TTTCAAACCTT-GT
1 TTTCAAA-CTTAGT
5284557 TTTCAAACTTAGT
1 TTTCAAACTTAGT
5284570 TTTCAAA
1 TTTCAAA
5284577 ATTTCCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTCAAACTTAGT
Found at i:5294804 original size:53 final size:53
Alignment explanation
Indices: 5294746--5294856 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
5294736 CTTTGTGTAC
* * *
5294746 TTTCGACACTATGTGTGCATCCATGGTATTCATAATGAATTTGTGGATTACCA
1 TTTCGACACTATGTGTGCACCCATGGTATTCATAATGAATTCGTGAATTACCA
*
5294799 TTTCGACACTATGTGTGCACCCATGGTATTCATAATGAGTTCGTGAATTACCA
1 TTTCGACACTATGTGTGCACCCATGGTATTCATAATGAATTCGTGAATTACCA
5294852 TTTCG
1 TTTCG
5294857 TTACCTTAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (53 bp):
TTTCGACACTATGTGTGCACCCATGGTATTCATAATGAATTCGTGAATTACCA
Found at i:5295501 original size:2 final size:2
Alignment explanation
Indices: 5295494--5295520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5295484 TTAACATTAT
5295494 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5295521 TTAAAGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5295723 original size:11 final size:12
Alignment explanation
Indices: 5295697--5295730 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
5295687 TTTTTTAAAA
5295697 TAAAATATTATTT
1 TAAAATA-TATTT
5295710 TAAAATAT-TTT
1 TAAAATATATTT
5295721 TAAAATATAT
1 TAAAATATAT
5295731 GAACCTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 2 0.10
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAAATATATTT
Found at i:5296179 original size:13 final size:14
Alignment explanation
Indices: 5296149--5296183 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
5296139 TTAAATTATA
5296149 AATTATGAAAAGTAT
1 AATTAT-AAAAGTAT
5296164 AATTATAAAA-TAT
1 AATTATAAAAGTAT
5296177 AATTATA
1 AATTATA
5296184 GTAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
AATTATAAAAGTAT
Found at i:5296626 original size:27 final size:26
Alignment explanation
Indices: 5296570--5296628 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
5296560 CTCAAAATAT
*
5296570 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATA-TAAAA
5296597 TATTATTTTAGTATATTTGAATA-AAAA
1 TATTATTTTA-TATATTT-AATATAAAA
5296624 TATTA
1 TATTA
5296629 ATTACTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 18 0.62
28 7 0.24
29 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
TATTATTTTATATATTTAATATAAAA
Found at i:5296884 original size:30 final size:30
Alignment explanation
Indices: 5296849--5296911 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5296839 TCCTATTTTA
*
5296849 ATATTATTATTATTTTAATAAGTAAATAAT
1 ATATTATTATTATTTTAATAAATAAATAAT
* *
5296879 ATATTATTCTTATTTTAATAAATAATTAAT
1 ATATTATTATTATTTTAATAAATAAATAAT
5296909 ATA
1 ATA
5296912 ATTTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
ATATTATTATTATTTTAATAAATAAATAAT
Found at i:5298053 original size:177 final size:177
Alignment explanation
Indices: 5297843--5298198 Score: 712
Period size: 177 Copynumber: 2.0 Consensus size: 177
5297833 ATTTCTTAAA
5297843 TTATTCCACATTAACATTATAAATTATTTTTTTAATTTTTTTTATTAATTTAATGTAAGTACAAG
1 TTATTCCACATTAACATTATAAATTATTTTTTTAATTTTTTTTATTAATTTAATGTAAGTACAAG
5297908 GCATTATCTGTTCAAAAATAAGTCTCAACCTTTTGATATTGAACGCTCACACCCCTGATGTGACT
66 GCATTATCTGTTCAAAAATAAGTCTCAACCTTTTGATATTGAACGCTCACACCCCTGATGTGACT
5297973 TATTTAATATAAGATCTCATCAACGATCCAAACATATTCTTAGGCGC
131 TATTTAATATAAGATCTCATCAACGATCCAAACATATTCTTAGGCGC
5298020 TTATTCCACATTAACATTATAAATTATTTTTTTAATTTTTTTTATTAATTTAATGTAAGTACAAG
1 TTATTCCACATTAACATTATAAATTATTTTTTTAATTTTTTTTATTAATTTAATGTAAGTACAAG
5298085 GCATTATCTGTTCAAAAATAAGTCTCAACCTTTTGATATTGAACGCTCACACCCCTGATGTGACT
66 GCATTATCTGTTCAAAAATAAGTCTCAACCTTTTGATATTGAACGCTCACACCCCTGATGTGACT
5298150 TATTTAATATAAGATCTCATCAACGATCCAAACATATTCTTAGGCGC
131 TATTTAATATAAGATCTCATCAACGATCCAAACATATTCTTAGGCGC
5298197 TT
1 TT
5298199 TCATCTCATT
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 179 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (177 bp):
TTATTCCACATTAACATTATAAATTATTTTTTTAATTTTTTTTATTAATTTAATGTAAGTACAAG
GCATTATCTGTTCAAAAATAAGTCTCAACCTTTTGATATTGAACGCTCACACCCCTGATGTGACT
TATTTAATATAAGATCTCATCAACGATCCAAACATATTCTTAGGCGC
Found at i:5305267 original size:3 final size:3
Alignment explanation
Indices: 5305259--5305323 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
5305249 TAATGGCCTG
5305259 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
*
5305307 TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TA
5305324 GTGGGACGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5311263 original size:18 final size:19
Alignment explanation
Indices: 5311240--5311288 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
5311230 ATCAAAAATA
5311240 TTATTATTTTTATCA-ATT
1 TTATTATTTTTATCACATT
* *
5311258 TTATTATTATTA-GACATT
1 TTATTATTTTTATCACATT
*
5311276 TTATTAATTTTAT
1 TTATTATTTTTAT
5311289 TAATAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATTATTTTTATCACATT
Found at i:5312025 original size:12 final size:12
Alignment explanation
Indices: 5312010--5312040 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5312000 GTTATTTAAA
5312010 CGGGTATCGGGC
1 CGGGTATCGGGC
5312022 CGGGTATCGGGC
1 CGGGTATCGGGC
*
5312034 CGAGTAT
1 CGGGTAT
5312041 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:5312132 original size:39 final size:39
Alignment explanation
Indices: 5312038--5312143 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 39
5312028 TCGGGCCGAG
* *
5312038 TATATAT-ATTTAAATTAAATATATAAATATTAATTATA
1 TATATATAATTTAAATTAAATTTATTAATATTAATTATA
* * *
5312076 TTTTTTTAATTTAAATTAAATTTATTAATATT-ATATATA
1 TATATATAATTTAAATTAAATTTATTAATATTAAT-TATA
5312115 TATATATAATATT-AATT--ATTT-TTAATATT
1 TATATATAAT-TTAAATTAAATTTATTAATATT
5312144 TATCGGGCCG
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
36 8 0.14
37 4 0.07
38 6 0.11
39 37 0.65
40 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TATATATAATTTAAATTAAATTTATTAATATTAATTATA
Found at i:5315418 original size:23 final size:23
Alignment explanation
Indices: 5315388--5315448 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
5315378 TGACCCTTGA
*
5315388 CGGTGGTTCATCTACGGCCTCAC
1 CGGTGGTTCATCGACGGCCTCAC
5315411 CGGTGGTTCATCGACGGCCTCAC
1 CGGTGGTTCATCGACGGCCTCAC
5315434 CGGTGGTTCATCGAC
1 CGGTGGTTCATCGAC
5315449 AATGTGATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.13, C:0.33, G:0.30, T:0.25
Consensus pattern (23 bp):
CGGTGGTTCATCGACGGCCTCAC
Found at i:5324242 original size:2 final size:2
Alignment explanation
Indices: 5324237--5324285 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5324227 AATATATTTG
5324237 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
5324279 AT AT AT A
1 AT AT AT A
5324286 GGTTACCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5325056 original size:426 final size:427
Alignment explanation
Indices: 5323914--5325213 Score: 1960
Period size: 426 Copynumber: 3.0 Consensus size: 427
5323904 CGTTTGGGTC
* *
5323914 ATTGGATCTCATCATATCCAACGATGGACCCATGGGTGCATATGCTTCCTTTCTTAGGGTTATAA
1 ATTGGATCTCATCATATCCAACGGTGGACCCATGGATGCATATGCTTCCTTTCTTAGGGTTATAA
* * * * *
5323979 GAACCTTAATCTAAAGTCTTGATATGGACCGTCAGATTGGTTAACAGATATGAC-GACTCTAGGC
66 GAACCCTAATCTAAAGTCTTGATATGGACCATCAGATTGGTTAACAAATCTGACTG-CTCTAGGA
* * * * * * *
5324043 TTCTGGCGACACTAGACAAAAGAATGGAAAGGCTAGAGTTTCTTCCGAGACTTAATCTATTGGGC
130 TTCTGGCGGCACTGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCTTAATCTACTGGGT
* ** *
5324108 CTGCTTCAGTTTGGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTTATTAGGGCCT
195 CTGCTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTAGGGCCT
* *
5324173 GCAAATAGCATTAATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTGA
260 GCAAATAACATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTG-
*
5324238 TATATATATATATATATATATATATATATATATATATATATATATATAGGTTACCTATTCCATAA
324 ---AT-T-TA-ATATATATATATATATATATATATA-ATGT-TATATA--TT--C----CCATAA
5324303 TAATAATATATATGGCCACACCCATAAATAATTATTGGTAAGTAG-CCCTATATA
373 TAATAATATATATGGCCACACCCATAAATAATTATTGGTAAGTAGCCCCTATATA
* * * *
5324357 ATTGGATCTCGTCATATCCAACGGTGGACCCATGGCTGGATATGCTTTCTTTCTTAGGGTTATAA
1 ATTGGATCTCATCATATCCAACGGTGGACCCATGGATGCATATGCTTCCTTTCTTAGGGTTATAA
* * *
5324422 GAACACTAATCTAAAGTCTTCATCTGGACCATCAGATTGGTTAACAAATCTGACTGCTCTAGGAT
66 GAACCCTAATCTAAAGTCTTGATATGGACCATCAGATTGGTTAACAAATCTGACTGCTCTAGGAT
*
5324487 TCTGGCGGCAATGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCTTAATCTACTGGGTC
131 TCTGGCGGCACTGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCTTAATCTACTGGGTC
*
5324552 TACTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTAGGGCCTG
196 TGCTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTAGGGCCTG
* *
5324617 TAAATACCATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTGAT
261 CAAATAACATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTGAT
5324682 TTAAT-TATATATATATATATATATATAATGTTATATATTCCCATAATAATAATATATATGGCCA
326 TTAATATATATATATATATATATATATAATGTTATATATTCCCATAATAATAATATATATGGCCA
5324746 CACCCATAAATAATTATTGGTAAGTAGCCCCTATATA
391 CACCCATAAATAATTATTGGTAAGTAGCCCCTATATA
* * * *
5324783 ATTGGATCTCATCCTATCCAATGGTGGACCCATAGATGCATATGCTTCCTTTATTAGGGTTATAA
1 ATTGGATCTCATCATATCCAACGGTGGACCCATGGATGCATATGCTTCCTTTCTTAGGGTTATAA
* *
5324848 GAACCCTAATATAAAGTCTTGA-ATTGGACCATCAGATTGGTTAATAAATCTGACTGCTCTAGGA
66 GAACCCTAATCTAAAGTCTTGATA-TGGACCATCAGATTGGTTAACAAATCTGACTGCTCTAGGA
* *
5324912 TTCTGGCGGCACTGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCGTAATCTACTAGGT
130 TTCTGGCGGCACTGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCTTAATCTACTGGGT
* *
5324977 CTGCTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTTGGGCCC
195 CTGCTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTAGGGCCT
*
5325042 GCAAATAACATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAACATATTTGA
260 GCAAATAACATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTGA
* **
5325107 TTTAATTATATATATATATATATATATATAAGGTTACCTATTCCCATAATAATAATATATATGGC
325 TTTAA-TATATATATATATATATATATATAATGTTATATATTCCCATAATAATAATATATATGGC
* *
5325172 CACACCCATAAATAATTATTGATAAGTAGCCCCTACATA
389 CACACCCATAAATAATTATTGGTAAGTAGCCCCTATATA
5325211 ATT
1 ATT
5325214 TTAAACACAC
Statistics
Matches: 795, Mismatches: 57, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
425 51 0.06
426 315 0.40
427 1 0.00
428 94 0.12
429 1 0.00
431 2 0.00
433 6 0.01
434 3 0.00
435 22 0.03
436 2 0.00
437 2 0.00
438 1 0.00
439 2 0.00
443 292 0.37
444 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (427 bp):
ATTGGATCTCATCATATCCAACGGTGGACCCATGGATGCATATGCTTCCTTTCTTAGGGTTATAA
GAACCCTAATCTAAAGTCTTGATATGGACCATCAGATTGGTTAACAAATCTGACTGCTCTAGGAT
TCTGGCGGCACTGGACAAAAGAATGGAAAGGCTAGAGTTTCCTCCGGGCCTTAATCTACTGGGTC
TGCTTCAGCTCAGGTTTGGCTACTGTTTGGGCCACTCTTGTTTTTGGTTTTGTAATTAGGGCCTG
CAAATAACATTGATAAAGATTAGTGCATTTTAAATTAGTATTTTATGTACATAAATATATTTGAT
TTAATATATATATATATATATATATATAATGTTATATATTCCCATAATAATAATATATATGGCCA
CACCCATAAATAATTATTGGTAAGTAGCCCCTATATA
Found at i:5326837 original size:54 final size:54
Alignment explanation
Indices: 5326691--5326848 Score: 201
Period size: 54 Copynumber: 2.9 Consensus size: 54
5326681 TTACATCAAT
* *
5326691 ACTAAGTGTGAAACCCACGAAATTCATAATGTGTTTATGAACGACCATATCTGA
1 ACTAAGTGTGAAACCCACGGAATTCATAATGTGTTTATGAACGACCGTATCTGA
* **
5326745 ACTAAGTGTGCAACCCATAGAATTCATAATGTGTTTATGAACGACCGTATC-GA
1 ACTAAGTGTGAAACCCACGGAATTCATAATGTGTTTATGAACGACCGTATCTGA
* * *** *
5326798 CACTAAGAGTGTAACCCACGGAATTCATAATGACCTTATGAATGACCGTAT
1 -ACTAAGTGTGAAACCCACGGAATTCATAATGTGTTTATGAACGACCGTAT
5326849 TGGCACTACG
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.02
54 88 0.98
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
ACTAAGTGTGAAACCCACGGAATTCATAATGTGTTTATGAACGACCGTATCTGA
Found at i:5329031 original size:54 final size:54
Alignment explanation
Indices: 5328949--5329128 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 54
5328939 GTTACATCAG
5328949 CACTAAGTGTGCAACCCAC-ATAATTCATAATGTGTTTATGAACGACCGTATCGA
1 CACTAAGTGTGCAACCCACGA-AATTCATAATGTGTTTATGAACGACCGTATCGA
* * * *
5329003 CACTAAGTGTGCAACCCATGGAATTCATAATGTGTTTATGAACGACCGTGTCGT
1 CACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCGA
* * * * * *
5329057 CATTAAGTGTGCAACCAACGAAATTCATAATGAGCTTATGAATGACCGTATCGG
1 CACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCGA
* *
5329111 CACTACGTGTGCACCCCA
1 CACTAAGTGTGCAACCCA
5329129 AAGAACTTAT
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCGTATCGA
Found at i:5332012 original size:60 final size:60
Alignment explanation
Indices: 5331948--5332130 Score: 199
Period size: 60 Copynumber: 3.0 Consensus size: 60
5331938 TTTATATGAA
* ** *
5331948 TTTGAGGAGGAAATTAGAAGATTCAAAAGTTTGGGGATCAATTTAGAATGAGAGTCATAG
1 TTTGAGGATGAAATTAGAAGATTCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATAG
* * * *
5332008 TTTGAGGATGAAATTAGAATGCTT-AAAAGTTTAAGGA-CTAATTTAAAATAATAGTCATAA
1 TTTGAGGATGAAATTAGAA-GATTCAAAAGTTTAAGGATC-AATTTAAAATGAGAGTCATAG
* * * * * * *
5332068 TTTGGGGATGAAATTAAAATATCCAAAAGTTTAAAGATCAATTTAAAATGAGGGCCATAG
1 TTTGAGGATGAAATTAGAAGATTCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATAG
5332128 TTT
1 TTT
5332131 AGGGATACAT
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 94 0.94
61 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (60 bp):
TTTGAGGATGAAATTAGAAGATTCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATAG
Found at i:5335092 original size:14 final size:15
Alignment explanation
Indices: 5335061--5335092 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5335051 ACTACCTTTT
5335061 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
5335076 AAAATAATTTTAA-A
1 AAAATAATTTTAAGA
5335090 AAA
1 AAA
5335093 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:5337484 original size:257 final size:257
Alignment explanation
Indices: 5337013--5338449 Score: 1510
Period size: 258 Copynumber: 5.4 Consensus size: 257
5337003 GTGAGACCGA
* *
5337013 CAGATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
* * ** *
5337078 ATTTTTGGAAATAGTTTACTGTGTAAGAAACTTTGGAAATAACTTTCCTACTTTTCAAAAATTTC
66 A-TTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTC
* * * * * *
5337143 ATTTTCT-AAAATCATTAAATGAGAAACTTTGGAAATCACATTCTCATTTTTCGAATTCATGTGA
130 ATTTTCTAAAAAT-ACTAAATGAGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTGA
* * * *
5337207 AAATATCCTACCCGAAGGTCTTACGGATGGCCTGAATGACTTATCATCTCT-CTCGAAAGTCTGT
194 AAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCT-TACTCGAAAGACTGT
* * * *
5337271 CAGATGACCCAAAGGATTTAATCATCATGATCGAAAGACTTACTAATGGCTCGAAGGACTTACCA
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
* * *
5337336 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTTGAAATTGCTTTCTTACTTTACAAAAATTTCA
66 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA
*
5337401 TTTTCTGAAAATACTAAATGAGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTGAAA
131 TTTTCTAAAAATACTAAATGAGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTGAAA
** * * *
5337466 ACATCCTACCTAAAGGTCTTACGGATTGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGA
196 ACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGACTGT
* * * * * * * * *
5337528 CAGATGACCCGAAGAATTTAATCATCACGCTCGCAAGACTGACAGATGACCTGAAGGATTTAATC
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT-ACC
* * * * * * * *
5337593 -ATCATGCTCGAAAGA-CTTACTGATGGCCCGAAGGACTTACAAATTTTTGAAATAG-TTTACTG
65 AAT-TTG--GGAAATAGTTTACTG--GG---TAA-G------AAACTTTGGAAATCGCTTT-CT-
*
5337655 GTAAGAAAC-TTTGAAAATCATTTTCTTACTTTTCAAAAATATCATTTTCTGAAAATACTAAATG
113 -T-----ACTTTTCAAAA--A-TTTC--A-TTTTC-------T-A-------AAAATACTAAATG
* *
5337719 AGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTAAAAACATCCTACCAGAAGGTCTT
151 AGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTT
*
5337784 ACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAAACTGT
216 ACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGACTGT
* *
5337826 CAGATGACCCGAAGGATTTAATCATTATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCA
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
** * *
5337891 ATTTGGGAAATAGTTTACTATGTAA-AAATCATTGGAAATCGCCTTCTTACTTTTCAAAAATTTC
66 ATTTGGGAAATAGTTTACTGGGTAAGAAA-CTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTC
* * * * * *
5337955 ATTTTCAAAAAACATTAAATGAGAAACTTTGGATA-TCGCTTTCTCATTTTTAAAAAATCATGTG
130 ATTTTCTAAAAATACTAAATGAGAAACTTTGGA-AGTCGCTTTCTCACTTTT-CAAATTCATGTG
* * * ** * *
5338019 AAAACATCCTACCCGAGGGTCTTACGAATGACCCGAAGGACTTATCATCTTGGTCGAAAGAGTGA
193 AAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGACTGT
* * * *
5338084 CAGATGACTCGAAGGATTTAATCATCATGCTAGGAAGACTTACTGATGGCCTGAAGGACTTACCA
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
* *
5338149 ATTTGGGAAATAGTTTACTGGGTAAGAAACATTGGAAATCGCTTTCTTACTTTTCAAAATTTTCA
66 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA
* * *
5338214 TTTTCTGAAAATACTAAGTGAGAAACTTTGGAAG-CTGCTTTCTCACTTTTCAAATTCATATGAA
131 TTTTCTAAAAATACTAAATGAGAAACTTTGGAAGTC-GCTTTCTCACTTTTCAAATTCATGTGAA
* * * * * *
5338278 AA-AACCTACCCGAA-GTACTTACAGATGGCCCTAAGGACTTATCATTTTACTTGAAAGACTAT
195 AACATCCTACCCGAAGGT-CTTACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGACTGT
* * * *
5338340 CAAATGACCTGAAGGATTTAATCATCGTACTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
1 CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
*
5338405 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTTGAAATCGCTTT
66 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTT
5338450 TTGATTTTTT
Statistics
Matches: 982, Mismatches: 139, Indels: 118
0.79 0.11 0.10
Matches are distributed among these distances:
255 2 0.00
256 145 0.15
257 266 0.27
258 291 0.30
259 9 0.01
260 5 0.01
261 2 0.00
264 3 0.00
265 1 0.00
270 3 0.00
271 15 0.02
272 5 0.01
273 2 0.00
275 4 0.00
276 1 0.00
277 8 0.01
278 9 0.01
279 1 0.00
280 4 0.00
282 2 0.00
283 8 0.01
284 10 0.01
285 2 0.00
290 1 0.00
291 2 0.00
294 1 0.00
295 5 0.01
296 5 0.01
297 4 0.00
298 166 0.17
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (257 bp):
CAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCA
ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA
TTTTCTAAAAATACTAAATGAGAAACTTTGGAAGTCGCTTTCTCACTTTTCAAATTCATGTGAAA
ACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGACTGT
Found at i:5337626 original size:42 final size:42
Alignment explanation
Indices: 5337494--5337627 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
5337484 TTACGGATTG
* *
5337494 CCCGAAGGACTT-ATCATCTTGCTCGAAAGACTGACAGATGA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTGACAGATGA
* * *
5337535 CCCGAAGAATTTAATCATCACGCTCGCAAGACTGACAGATGA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTGACAGATGA
* * * *
5337577 CCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTGACAGATGA
5337619 CCCGAAGGA
1 CCCGAAGGA
5337628 CTTACAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 10 0.13
42 69 0.87
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTGACAGATGA
Found at i:5337879 original size:42 final size:41
Alignment explanation
Indices: 5337781--5337887 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
5337771 ACCAGAAGGT
*
5337781 CTTACGGATGGCCCGAAGGACTTATCATCTTACTCGAAAAA
1 CTTACAGATGGCCCGAAGGACTTATCATCTTACTCGAAAAA
* * * *
5337822 CTGT-CAGATGACCCGAAGGATTTAATCAT-TATGCTCGAAAGA
1 CT-TACAGATGGCCCGAAGGACTT-ATCATCT-TACTCGAAAAA
* *
5337864 CTTACTGATGGCCCGAATGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
5337888 CCAATTTGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCTTACTCGAAAAA
Found at i:5338106 original size:258 final size:254
Alignment explanation
Indices: 5337557--5338449 Score: 1202
Period size: 256 Copynumber: 3.5 Consensus size: 254
5337547 AATCATCACG
*
5337557 CTCGCAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 CTCGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
* ** * * **
5337622 GAAGGACTTACAAATTTTTGAAATAGTTTACTGGTAAGAAACTTTGAAAATCATTTTCTTACTTT
66 GAAGGACTTACCAATTTGGGAAATAGTTTACTGGTAAGAAACATTGGAAATCGCTTTCTTACTTT
*
5337687 TCAAAAATATCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAGTCGCTTTCTCACTTTTCAA
131 TCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAA-TCGCTTTCTCACTTTTCAA
* * *
5337752 ATTCATGTAAAAACATCCTACCAGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTA
195 ATTCATGTGAAAACATCCTACCCG-AGGTCTTACGAATGGCCCGAAGGACTTATCATCTTA
* * * *
5337813 CTCGAAAAACTGTCAGATGACCCGAAGGATTTAATCATTATGCTCGAAAGACTTACTGATGGCCC
1 CTCGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
* * *
5337878 GAATGACTTACCAATTTGGGAAATAGTTTACTATGTAA-AAATCATTGGAAATCGCCTTCTTACT
66 GAAGGACTTACCAATTTGGGAAATAGTTTACT-GGTAAGAAA-CATTGGAAATCGCTTTCTTACT
** * * *
5337942 TTTCAAAAATTTCATTTTCAAAAAACATTAAATGAGAAACTTTGGATATCGCTTTCTCATTTTTA
129 TTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGA-ATCGCTTTCTCACTTTT-
* * * *
5338007 AAAAATCATGTGAAAACATCCTACCCGAGGGTCTTACGAATGACCCGAAGGACTTATCATCTTG
192 CAAATTCATGTGAAAACATCCTACCCGA-GGTCTTACGAATGGCCCGAAGGACTTATCATCTTA
* * * *
5338071 GTCGAAAGAGTGACAGATGA-CTCGAAGGATTTAATCATCATGCTAGGAAGACTTACTGATGGCC
1 CTCGAAAGACTGACAGATGACCT-GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCC
*
5338135 TGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACATTGGAAATCGCTTTCTTACT
65 CGAAGGACTTACCAATTTGGGAAATAGTTTACT-GGTAAGAAACATTGGAAATCGCTTTCTTACT
* * *
5338200 TTTCAAAATTTTCATTTTCTGAAAATACTAAGTGAGAAACTTTGGAAGCTGCTTTCTCACTTTTC
129 TTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAATC-GCTTTCTCACTTTTC
* * * * *
5338265 AAATTCATATGAAAA-AACCTACCCGAAGTACTTAC-AGATGGCCCTAAGGACTTATCATTTTA
193 AAATTCATGTGAAAACATCCTACCCGAGGT-CTTACGA-ATGGCCCGAAGGACTTATCATCTTA
* * * *
5338327 CTTGAAAGACT-ATCAAATGACCTGAAGGATTTAATCATCGTACTCGAAAGACTTACTGATGGCC
1 CTCGAAAGACTGA-CAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCC
* *
5338391 CGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTTGAAATCGCTTT
65 CGAAGGACTTACCAATTTGGGAAATAGTTTACT-GGTAAGAAACATTGGAAATCGCTTT
5338450 TTGATTTTTT
Statistics
Matches: 556, Mismatches: 69, Indels: 24
0.86 0.11 0.04
Matches are distributed among these distances:
255 4 0.01
256 234 0.42
257 96 0.17
258 219 0.39
259 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (254 bp):
CTCGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
GAAGGACTTACCAATTTGGGAAATAGTTTACTGGTAAGAAACATTGGAAATCGCTTTCTTACTTT
TCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAATCGCTTTCTCACTTTTCAAA
TTCATGTGAAAACATCCTACCCGAGGTCTTACGAATGGCCCGAAGGACTTATCATCTTA
Found at i:5338574 original size:42 final size:42
Alignment explanation
Indices: 5338515--5338594 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
5338505 CGAATAACTT
*
5338515 ATCATCTTGCTCGAAAGACTGACAAATGACTCGAAGGATTTA
1 ATCATCATGCTCGAAAGACTGACAAATGACTCGAAGGATTTA
* ** *
5338557 ATCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGA
1 ATCATCATGCTCGAAAGACTGACAAATGACTCGAAGGA
5338595 CTTACAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTGACAAATGACTCGAAGGATTTA
Found at i:5348180 original size:21 final size:21
Alignment explanation
Indices: 5348156--5348195 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5348146 ATATAATGAA
*
5348156 AATAAAAATAATATTAATAGT
1 AATAAAAATAATAATAATAGT
*
5348177 AATATAAATAATAATAATA
1 AATAAAAATAATAATAATA
5348196 ATACTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAAAAATAATAATAATAGT
Found at i:5348191 original size:3 final size:3
Alignment explanation
Indices: 5348124--5348198 Score: 50
Period size: 3 Copynumber: 25.3 Consensus size: 3
5348114 AAGCCTGCAA
* * *
5348124 AAT AAT AAA AAT AAA AAT -AT ACAT -AT AAT GAA- AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AAT AAT
* *
5348168 ATT AAT AGT AAT -AT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
5348199 CTATTATTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
2 8 0.15
3 41 0.75
4 6 0.11
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5349302 original size:21 final size:21
Alignment explanation
Indices: 5349276--5349315 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5349266 GTTAGGAGTG
5349276 TAGGTGTATAAGTACACTCTC
1 TAGGTGTATAAGTACACTCTC
*
5349297 TAGGTGTATCAGTACACTC
1 TAGGTGTATAAGTACACTC
5349316 AGTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
TAGGTGTATAAGTACACTCTC
Found at i:5349862 original size:17 final size:17
Alignment explanation
Indices: 5349840--5349878 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
5349830 AAATTACTCC
5349840 CCCTTACTTTATTCTCA
1 CCCTTACTTTATTCTCA
*
5349857 CCCTTACTTTATTCTCC
1 CCCTTACTTTATTCTCA
5349874 CCCTT
1 CCCTT
5349879 TTTGTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (17 bp):
CCCTTACTTTATTCTCA
Found at i:5351592 original size:12 final size:14
Alignment explanation
Indices: 5351565--5351598 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5351555 AATGGGCAAC
5351565 TTTGAAAACTATTG
1 TTTGAAAACTATTG
5351579 -TTGAAAAC-ATTG
1 TTTGAAAACTATTG
5351591 TTTGAAAA
1 TTTGAAAA
5351599 AAATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (14 bp):
TTTGAAAACTATTG
Found at i:5352140 original size:21 final size:21
Alignment explanation
Indices: 5352069--5352146 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 21
5352059 AAACCCGAAG
* * *
5352069 AGTGTATCGAAACAC-TCCTT
1 AGTGTATCGATACACATTCAT
* *
5352089 AGTGTATCAATACACATTCAA
1 AGTGTATCGATACACATTCAT
*
5352110 AGAATGTATCGGTACACATTCAT
1 AG--TGTATCGATACACATTCAT
5352133 AGTGTATCGATACA
1 AGTGTATCGATACA
5352147 TAGAGAGGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.28
21 15 0.33
23 18 0.39
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (21 bp):
AGTGTATCGATACACATTCAT
Found at i:5354575 original size:20 final size:20
Alignment explanation
Indices: 5354550--5354592 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5354540 TCTAAGAGCT
5354550 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
5354570 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
5354590 CAT
1 CAT
5354593 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:5358275 original size:20 final size:20
Alignment explanation
Indices: 5358250--5358292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5358240 TCTAAGAGCT
5358250 CATTTAGGACCACATAGATG
1 CATTTAGGACCACATAGATG
* * *
5358270 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCACATAGATG
5358290 CAT
1 CAT
5358293 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (20 bp):
CATTTAGGACCACATAGATG
Found at i:5361578 original size:22 final size:23
Alignment explanation
Indices: 5361530--5361578 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
5361520 TTTCAAATCG
*
5361530 AAATTTTCTTTTTCAAAGCTTTC
1 AAATTTTATTTTTCAAAGCTTTC
* *
5361553 AAATTTTATTTTTGAGAGCTTT-
1 AAATTTTATTTTTCAAAGCTTTC
5361575 AAAT
1 AAAT
5361579 CCTTCTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (23 bp):
AAATTTTATTTTTCAAAGCTTTC
Found at i:5361736 original size:117 final size:118
Alignment explanation
Indices: 5361530--5361742 Score: 295
Period size: 117 Copynumber: 1.8 Consensus size: 118
5361520 TTTCAAATCG
* * * * *
5361530 AAATTTTCTTTTTCAAAGCTTTCAAATTTTATTTTTGAGAGCTTTAAATCCTTCTTCAATATTTC
1 AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAAAATTTC
5361595 ATTTTGATTTTCAAAACCCATTTTA-GTTTCTTGAAGAAGTTTGTTTAATTCA
66 ATTTTGATTTTCAAAACCCATTTTAGGTTTCTTGAAGAAGTTTGTTTAATTCA
* * *
5361647 AAATTTTCTTTTTCAAAGTTTTCATATTTCATTTTTAAAAGCTCTAACA-CCTTTTTCAAAATTT
1 AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTAAAAGCTCTAA-ATCCTTCTTCAAAATTT
* ** *
5361711 CATTTTGATTTTCCAAGTCTATTTTAGGTTTC
65 CATTTTGATTTTCAAAACCCATTTTAGGTTTC
5361743 AAAAGAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
117 76 0.93
118 6 0.07
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.50
Consensus pattern (118 bp):
AAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAAAATTTC
ATTTTGATTTTCAAAACCCATTTTAGGTTTCTTGAAGAAGTTTGTTTAATTCA
Found at i:5363073 original size:45 final size:45
Alignment explanation
Indices: 5363022--5363124 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
5363012 GCTTGACCTA
* *
5363022 GTGTATCGGTACACTAATTACATTCGATGTTTCTCGGAGTCAGGG
1 GTGTATCGGTACACTAATTACATTCGATGTTTCTCGGAGCCAAGG
5363067 GTGTATCGGTACACTAATTACATTCGATGTTTCTCGGAGCCAAGG
1 GTGTATCGGTACACTAATTACATTCGATGTTTCTCGGAGCCAAGG
5363112 GTGTATCGGTACA
1 GTGTATCGGTACA
5363125 TCAGCAGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (45 bp):
GTGTATCGGTACACTAATTACATTCGATGTTTCTCGGAGCCAAGG
Found at i:5363846 original size:229 final size:229
Alignment explanation
Indices: 5363445--5363899 Score: 856
Period size: 229 Copynumber: 2.0 Consensus size: 229
5363435 TTTTCAACAA
5363445 AATTTATTGGGGTTTTACAGAAGGTGTGAACATTGGATATGTGGTAAGTAGTTCTTTGAGTTTGT
1 AATTTATTGGGGTTTTACAGAAGGTGTGAACATTGGATATGTGGTAAGTAGTTCTTTGAGTTTGT
* *
5363510 ATTTGAAATGGGATTAATAGATGTTGGGTATCAAGGGAAAAAATACACTTGGGGTAGATGCTCAT
66 ATTTCAAATGGGATTAATAGATGTTGGGTATAAAGGGAAAAAATACACTTGGGGTAGATGCTCAT
5363575 TACATCAATGCCTTAATCGCTATTTGTATAAAGAAGTGAACCGTTCGGTAGGAATTTTGTTTATT
131 TACATCAATGCCTTAATCGCTATTTGTATAAAGAAGTGAACCGTTCGGTAGGAATTTTGTTTATT
5363640 TATTAAACGAATGAACATGAACAAGATTTTACAT
196 TATTAAACGAATGAACATGAACAAGATTTTACAT
5363674 AATTTATTGGGGTTTTACAGAAGGTGTGAACATTGGATATGTGGTAAGTAGTTCTTTGAGTTTGT
1 AATTTATTGGGGTTTTACAGAAGGTGTGAACATTGGATATGTGGTAAGTAGTTCTTTGAGTTTGT
* * *
5363739 ATTTCACATGGGATTAATAGATGTTGGGTTTAAAGGGATAAAATACACTTGGGGTAGATGCTCAT
66 ATTTCAAATGGGATTAATAGATGTTGGGTATAAAGGGAAAAAATACACTTGGGGTAGATGCTCAT
*
5363804 TACATCAATGCTTTAATCGCTATTTGTATAAAGAAGTGAACCGTTCGGTAGGAATTTTGTTTATT
131 TACATCAATGCCTTAATCGCTATTTGTATAAAGAAGTGAACCGTTCGGTAGGAATTTTGTTTATT
5363869 TATTAAACGAATGAACATGAACAAGATTTTA
196 TATTAAACGAATGAACATGAACAAGATTTTA
5363900 TGTTTGTTTA
Statistics
Matches: 220, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 220 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (229 bp):
AATTTATTGGGGTTTTACAGAAGGTGTGAACATTGGATATGTGGTAAGTAGTTCTTTGAGTTTGT
ATTTCAAATGGGATTAATAGATGTTGGGTATAAAGGGAAAAAATACACTTGGGGTAGATGCTCAT
TACATCAATGCCTTAATCGCTATTTGTATAAAGAAGTGAACCGTTCGGTAGGAATTTTGTTTATT
TATTAAACGAATGAACATGAACAAGATTTTACAT
Found at i:5364033 original size:14 final size:14
Alignment explanation
Indices: 5364016--5364075 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
5364006 TTTATACTCA
5364016 TTCATTTATGTTTG
1 TTCATTTATGTTTG
5364030 TTCATTTATGTCCATGTATG
1 TTCATTTATG----T-T-TG
*
5364050 TTCAATTATGTTTG
1 TTCATTTATGTTTG
5364064 TTCATTTATGTT
1 TTCATTTATGTT
5364076 CGTATATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
18 1 0.03
19 1 0.03
20 11 0.29
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.58
Consensus pattern (14 bp):
TTCATTTATGTTTG
Found at i:5364051 original size:20 final size:20
Alignment explanation
Indices: 5364023--5364060 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5364013 TCATTCATTT
* *
5364023 ATGTTTGTTCATTTATGTCC
1 ATGTATGTTCAATTATGTCC
5364043 ATGTATGTTCAATTATGT
1 ATGTATGTTCAATTATGT
5364061 TTGTTCATTT
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:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (20 bp):
ATGTATGTTCAATTATGTCC
Found at i:5364076 original size:10 final size:10
Alignment explanation
Indices: 5363995--5364061 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
5363985 ATGTTATTTT
5363995 ATTTATGTTC
1 ATTTATGTTC
**
5364005 ATTTATACTC
1 ATTTATGTTC
*
5364015 ATTCAT-TT-
1 ATTTATGTTC
5364023 ATGTT-TGTTC
1 AT-TTATGTTC
*
5364033 ATTTATGTCC
1 ATTTATGTTC
*
5364043 ATGTATGTTC
1 ATTTATGTTC
*
5364053 AATTATGTT
1 ATTTATGTT
5364062 TGTTCATTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
8 3 0.07
9 6 0.14
10 34 0.79
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.55
Consensus pattern (10 bp):
ATTTATGTTC
Found at i:5364093 original size:34 final size:34
Alignment explanation
Indices: 5364018--5364095 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
5364008 TATACTCATT
* *
5364018 CATTTATGTTTGTTCATTTATGTCCATGTATGTT
1 CATTTATGTTTGTTCATTTATGTCCATATATGTC
* * *
5364052 CAATTATGTTTGTTCATTTATGTTCGTATATGTC
1 CATTTATGTTTGTTCATTTATGTCCATATATGTC
*
5364086 CGTTTATGTT
1 CATTTATGTT
5364096 CGTTTGTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.55
Consensus pattern (34 bp):
CATTTATGTTTGTTCATTTATGTCCATATATGTC
Found at i:5364099 original size:10 final size:10
Alignment explanation
Indices: 5364062--5364100 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5364052 CAATTATGTT
*
5364062 TGTTCATTTA
1 TGTTCGTTTA
*
5364072 TGTTCGTATA
1 TGTTCGTTTA
*
5364082 TGTCCGTTTA
1 TGTTCGTTTA
5364092 TGTTCGTTT
1 TGTTCGTTT
5364101 GTTTATATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:5370639 original size:78 final size:78
Alignment explanation
Indices: 5370509--5370663 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 78
5370499 TTATTTCTAT
* *
5370509 ATTTCCCTTATTCTACACTTTTATTCTCACCCTCTCTTATTATTCCTGAAACTAGAGTATTAGAA
1 ATTTCCCTTATTCTACACTTTCATTCTCACCCTCTCTTATTATTCCTAAAACTAGAGTATTAGAA
5370574 TCATATTATCTCG
66 TCATATTATCTCG
* * * * * * *
5370587 ATTTCCCTTCTTCTCCCCTTTCATTGTCATCCTCT-TCTATTCTTCCTAAAACTAGAGTTTTAGA
1 ATTTCCCTTATTCTACACTTTCATTCTCACCCTCTCT-TATTATTCCTAAAACTAGAGTATTAGA
5370651 ATCATATTATCTC
65 ATCATATTATCTC
5370664 TTTATATTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
77 1 0.01
78 66 0.99
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (78 bp):
ATTTCCCTTATTCTACACTTTCATTCTCACCCTCTCTTATTATTCCTAAAACTAGAGTATTAGAA
TCATATTATCTCG
Found at i:5371636 original size:18 final size:18
Alignment explanation
Indices: 5371613--5371647 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5371603 ACATTTAAAC
5371613 CAATTTAACTTACATAAT
1 CAATTTAACTTACATAAT
*
5371631 CAATTTAACTTGCATAA
1 CAATTTAACTTACATAA
5371648 AAAATATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (18 bp):
CAATTTAACTTACATAAT
Found at i:5373122 original size:23 final size:23
Alignment explanation
Indices: 5373096--5373146 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5373086 GAGTCGAGGG
* *
5373096 TTCTATGCGGTCGTTTGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
* *
5373119 TTCTATGTGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCGGGACAA
5373142 TTCTA
1 TTCTA
5373147 CGTTGTCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAA
Found at i:5373154 original size:23 final size:23
Alignment explanation
Indices: 5373112--5373157 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5373102 GCGGTCGTTT
*
5373112 GGGACAATTCTATGTGGTCCTTC
1 GGGACAATTCTACGTGGTCCTTC
* *
5373135 GGGACATTTCTACGTTGTCCTTC
1 GGGACAATTCTACGTGGTCCTTC
5373158 TGGAATTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (23 bp):
GGGACAATTCTACGTGGTCCTTC
Found at i:5380305 original size:23 final size:23
Alignment explanation
Indices: 5380237--5380305 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
5380227 GAGTCGACGG
* *
5380237 TTCTACGAGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
* * *
5380260 GTCTACATGGTCTTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
5380283 TTCTACGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
5380306 ATATGTGGTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:5385872 original size:22 final size:22
Alignment explanation
Indices: 5385827--5385868 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5385817 TTAAACCAAG
5385827 TTTTAAAATATTTACTTTAATA
1 TTTTAAAATATTTACTTTAATA
5385849 TTTT-AAATATATTA-TTTAAT
1 TTTTAAAATAT-TTACTTTAAT
5385869 TATTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATATTTACTTTAATA
Found at i:5387639 original size:22 final size:22
Alignment explanation
Indices: 5387586--5387639 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5387576 TTCAGCTGTT
* *
5387586 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* *
5387608 GTAA-TCCCTGGAATTAAATCAA
1 ATAACT-CCTGAAATTAAATCAA
5387630 ATAACTCCTG
1 ATAACTCCTG
5387640 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:5387927 original size:6 final size:6
Alignment explanation
Indices: 5387916--5387964 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
5387906 GACACGTATT
*
5387916 ACCACG ACCACG ACCACG ACCACG ACCATG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5387964 A
1 A
5387965 GCCAAGCCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.35, C:0.47, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:5393570 original size:22 final size:22
Alignment explanation
Indices: 5393517--5393570 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
5393507 TTTAGCTGTT
* *
5393517 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
** * *
5393539 GCAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
5393561 ATAACTCCTG
1 ATAACTCCTG
5393571 TAACTCCTGA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:5394326 original size:14 final size:14
Alignment explanation
Indices: 5394307--5394336 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5394297 TATGTTGTTG
5394307 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5394321 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5394335 AC
1 AC
5394337 AATAAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:5397773 original size:112 final size:112
Alignment explanation
Indices: 5397648--5397860 Score: 347
Period size: 112 Copynumber: 1.9 Consensus size: 112
5397638 ATTTTGATAA
* * *
5397648 AAAAATATCAATTTAATTTATGACGGGACAATGATTCCGTCGGAAATTGTGTTCAAATTTAAATA
1 AAAAATATCAATTTAATTTATGACGGGACAATGATTCCATCGAAAATTGTATTCAAATTTAAATA
5397713 AAATATA-CTAATTTAATTTGTGATGGAATAATCATTCCGTCAGAAAT
66 AAATATATC-AATTTAATTTGTGATGGAATAATCATTCCGTCAGAAAT
* * *
5397760 AAAAATATCAATTTAATTTATGACGGGACAATGATTCCATCGAAAATTTTATTCAACTTTAATTA
1 AAAAATATCAATTTAATTTATGACGGGACAATGATTCCATCGAAAATTGTATTCAAATTTAAATA
*
5397825 AAATATATCAATTTAATTTGTGATGGAATAGTCATT
66 AAATATATCAATTTAATTTGTGATGGAATAATCATT
5397861 ATGTAGGAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
112 92 0.99
113 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (112 bp):
AAAAATATCAATTTAATTTATGACGGGACAATGATTCCATCGAAAATTGTATTCAAATTTAAATA
AAATATATCAATTTAATTTGTGATGGAATAATCATTCCGTCAGAAAT
Found at i:5400800 original size:17 final size:16
Alignment explanation
Indices: 5400764--5400815 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
5400754 ATAAGGAAAG
5400764 TAATAAAAATAAAGTAAA
1 TAAT-AAAATAAA-TAAA
5400782 T-ATGAAAATAAATAGAA
1 TAAT-AAAATAAATA-AA
5400799 TACATAAAATAAATAAA
1 TA-ATAAAATAAATAAA
5400816 ATGAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 15 0.50
18 11 0.37
19 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (16 bp):
TAATAAAATAAATAAA
Found at i:5401060 original size:2 final size:2
Alignment explanation
Indices: 5401053--5401089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5401043 AAATAAATAA
5401053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5401090 GGAAGTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5401145 original size:35 final size:37
Alignment explanation
Indices: 5401106--5401194 Score: 128
Period size: 35 Copynumber: 2.5 Consensus size: 37
5401096 AAAATAGGAA
*
5401106 ATATAAATATATATATAATAACACTAATGG-AATA-T
1 ATATAAATATATATATAATAACACTAATGGAAAAACT
* *
5401141 ATATATATATATATATAATAATACTAATGGAAAAACT
1 ATATAAATATATATATAATAACACTAATGGAAAAACT
*
5401178 ATATACATATATATATA
1 ATATAAATATATATATA
5401195 TATATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 28 0.58
36 3 0.06
37 17 0.35
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (37 bp):
ATATAAATATATATATAATAACACTAATGGAAAAACT
Found at i:5403417 original size:100 final size:103
Alignment explanation
Indices: 5403228--5403476 Score: 306
Period size: 100 Copynumber: 2.4 Consensus size: 103
5403218 AGTATTGTTC
* * *
5403228 CGAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT--AAAT-GGAAATTGTTTGTTGACA
* * * * *
5403293 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
63 ATCAGCCACCCCTTCGCCGTGAAGTTGAACTTATGTTGTCT
* * *
5403334 CGAGTCTAATATCCTTCGTTGTGAATTTGAAATTGACTCTAAAT-GAAA-T-TTTGTTGACAATC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATGGAAATTGTTTGTTGACAATC
5403396 AGCCACCCCTTCGCCGTGAAGTTGAACTTATGTTGTCT
66 AGCCACCCCTTCGCCGTGAAGTTGAACTTATGTTGTCT
* * * * *
5403434 TGGGTCCAATATTCTTCGCTATGAAGTTGAAATTGGCTCTAAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAA
5403477 ATTGGGAAGG
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 81 0.65
101 1 0.01
102 4 0.03
104 3 0.02
106 35 0.28
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATGGAAATTGTTTGTTGACAATC
AGCCACCCCTTCGCCGTGAAGTTGAACTTATGTTGTCT
Found at i:5404621 original size:16 final size:15
Alignment explanation
Indices: 5404580--5404622 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5404570 ACCCACCTTA
*
5404580 TTTTTCTTTTACTTT
1 TTTTTCTTTTTCTTT
5404595 TTTGTTCTTTTTCTCTT
1 TTT-TTCTTTTTCT-TT
*
5404612 TTTTTATTTTT
1 TTTTTCTTTTT
5404623 TTCAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 5 0.21
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:5404687 original size:24 final size:24
Alignment explanation
Indices: 5404660--5404708 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5404650 TCACCCTAAA
** *
5404660 TATTTTTTCCTTTTTTCCTTTTTT
1 TATTTTTTATTTTTTCCCTTTTTT
5404684 TATTTTTTATTTTTTCCCTTTTTT
1 TATTTTTTATTTTTTCCCTTTTTT
5404708 T
1 T
5404709 GACTTAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (24 bp):
TATTTTTTATTTTTTCCCTTTTTT
Found at i:5409416 original size:17 final size:18
Alignment explanation
Indices: 5409396--5409431 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
5409386 CCTTGCAATA
5409396 CGTAGTAAT-ATGCAGTG
1 CGTAGTAATAATGCAGTG
5409413 CGTAGTAATAATGCAGTG
1 CGTAGTAATAATGCAGTG
5409431 C
1 C
5409432 ATTTGTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (18 bp):
CGTAGTAATAATGCAGTG
Found at i:5413761 original size:20 final size:18
Alignment explanation
Indices: 5413745--5413779 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5413735 CGTGCATTCC
5413745 GTAGCACTTCAGTGCATT
1 GTAGCACTTCAGTGCATT
* *
5413763 GTGGCACTTCGGTGCAT
1 GTAGCACTTCAGTGCAT
5413780 CGTGTATCAC
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:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (18 bp):
GTAGCACTTCAGTGCATT
Found at i:5414375 original size:3 final size:3
Alignment explanation
Indices: 5414367--5414403 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5414357 GTGTCCTTTC
5414367 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5414404 AGTCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5418995 original size:30 final size:29
Alignment explanation
Indices: 5418959--5419016 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 29
5418949 TTTTATGTGA
5418959 TTGTATTTTT-TCATTTATTTTATATTTTCT
1 TTGTATTTTTCTCA-TTATTTT-TATTTTCT
5418989 TTGTATTTTTCCTCATTATTTTTATTTT
1 TTGTATTTTT-CTCATTATTTTTATTTT
5419017 TGTTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 16 0.62
31 7 0.27
32 3 0.12
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (29 bp):
TTGTATTTTTCTCATTATTTTTATTTTCT
Found at i:5430779 original size:98 final size:98
Alignment explanation
Indices: 5430602--5430791 Score: 272
Period size: 98 Copynumber: 1.9 Consensus size: 98
5430592 ATATCGTGTT
* * *
5430602 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGTGAAGG
1 AATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGTGAAGG
* *
5430667 GACGGTTGATTGTCAACAAAAAATTTCAGAGTC
66 GACGGCTGACTGTCAACAAAAAATTTCAGAGTC
* * *
5430700 AATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACGGTGAAGG
1 AATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGTGAAGG
** * *
5430765 GGTGGCTGGCTGTCAACAAACAATTTC
66 GACGGCTGACTGTCAACAAAAAATTTC
5430792 CCAGTTCCAG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (98 bp):
AATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGTGAAGG
GACGGCTGACTGTCAACAAAAAATTTCAGAGTC
Found at i:5431028 original size:280 final size:272
Alignment explanation
Indices: 5430631--5431182 Score: 854
Period size: 280 Copynumber: 2.0 Consensus size: 272
5430621 AGGATATTGG
* ** *
5430631 ACTCGAGACAACACAAGTTCAACTTCACAGTGAAGGGACGGTTGATTGTCAACAAAAAATTTCAG
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAAATTTCAG
* *
5430696 AGTCAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCAC-GGT
66 AGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGG-
* * *
5430760 GAAGGGGTGGCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACGACGG
130 GAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAGACAATTTCAACTTCACGACGG
*
5430825 AGGATATTAGACTCGGAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAAT
195 AGGATATTAGACTCGAAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAAT
5430890 TACCAGGCTCAAC
260 TACCAGGCTCAAC
*
5430903 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-AA------
* *
5430968 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACT
58 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACT
5431033 TCACAGGGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAGACAATTTCAACTTC
123 TCACAGGGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAGACAATTTCAACTTC
* * * *
5431098 ACGATGGAGGATATTGGACTCGAAGCGATACAACTTACTTGGATTTCAACTTCACGATGAAGGAT
188 ACGACGGAGGATATTAGACTCGAAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGAT
*
5431163 ATTCAATTACCAGGCTCAAC
253 ATCCAATTACCAGGCTCAAC
5431183 TTCACGACAG
Statistics
Matches: 253, Mismatches: 18, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
272 48 0.19
273 2 0.01
274 2 0.01
280 199 0.79
281 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (272 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAAATTTCAG
AGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGGG
AAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAGACAATTTCAACTTCACGACGGA
GGATATTAGACTCGAAGCAATACAACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATT
ACCAGGCTCAAC
Found at i:5431032 original size:106 final size:106
Alignment explanation
Indices: 5430903--5431120 Score: 296
Period size: 106 Copynumber: 2.1 Consensus size: 106
5430893 CAGGCTCAAC
* * **
5430903 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* *
5430968 AATTTCAGAGTCAATTTCAACTTCAC-A-GCGAAGGATATTAG
66 AATTCCAGAGACAATTTCAACTTCACGATG-G-AGGATATTAG
** * *
5431009 ACTCGAGACAACACAAGCTCAACTTCACAGGGAAGGGGCGGCTGACTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* *
5431074 AGTTCCAGAGACAATTTCAACTTCACGATGGAGGATATTGG
66 AATTCCAGAGACAATTTCAACTTCACGATGGAGGATATTAG
5431115 ACTCGA
1 ACTCGA
5431121 AGCGATACAA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
106 95 0.97
107 2 0.02
108 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
AATTCCAGAGACAATTTCAACTTCACGATGGAGGATATTAG
Found at i:5434851 original size:22 final size:20
Alignment explanation
Indices: 5434826--5434867 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
5434816 TTATTCTTGA
*
5434826 TATTTGTTTATCTATATTATTT
1 TATTTATTTAT-T-TATTATTT
5434848 TATTTATTTATTTATTATTT
1 TATTTATTTATTTATTATTT
5434868 CTTACTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTATTTATTTATTATTT
Found at i:5440667 original size:25 final size:25
Alignment explanation
Indices: 5440637--5440692 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
5440627 TATAACTGAA
*
5440637 AATAATGACAAGATAACCACATGAT
1 AATAATGACAACATAACCACATGAT
*
5440662 AATAATGACAACATAATCACATGAT
1 AATAATGACAACATAACCACATGAT
*
5440687 AGTAAT
1 AATAAT
5440693 AGTATATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (25 bp):
AATAATGACAACATAACCACATGAT
Found at i:5445352 original size:18 final size:18
Alignment explanation
Indices: 5445329--5445363 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5445319 TATTTTATTG
5445329 AATAAAAATAATATTTTA
1 AATAAAAATAATATTTTA
*
5445347 AATAAAAATATTATTTT
1 AATAAAAATAATATTTT
5445364 GGGTCCAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAAAATAATATTTTA
Found at i:5449415 original size:28 final size:28
Alignment explanation
Indices: 5449383--5449514 Score: 138
Period size: 28 Copynumber: 4.7 Consensus size: 28
5449373 AATGGATCGT
* * *
5449383 GGAACACATCCCATACAAAATAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
** * *
5449411 GGAACAAATCTTACACAGAATAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
* ** * *
5449439 GAAATGAATCCCATATAGAACCGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
*
5449467 GGAACAAATCCCATACATAACAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
*
5449495 GGAACAAATCCCATATAGAA
1 GGAACAAATCCCATACAGAA
5449515 TTAGGATGGG
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 82 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (28 bp):
GGAACAAATCCCATACAGAACAGAGCGG
Found at i:5449573 original size:28 final size:29
Alignment explanation
Indices: 5449541--5449606 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
5449531 GCTCATTTAG
*
5449541 AATCAGTA-CGGGATATAATCCCATGCAA
1 AATCAGGATCGGGATATAATCCCATGCAA
* *
5449569 AATCAGGATGGGGATATAATTCCATGCAA
1 AATCAGGATCGGGATATAATCCCATGCAA
5449598 AATCAGGAT
1 AATCAGGAT
5449607 GAAGGGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (29 bp):
AATCAGGATCGGGATATAATCCCATGCAA
Found at i:5449584 original size:29 final size:29
Alignment explanation
Indices: 5449550--5449607 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5449540 GAATCAGTAC
5449550 GGGATATAATCCCATGCAAAATCAGGATG
1 GGGATATAATCCCATGCAAAATCAGGATG
*
5449579 GGGATATAATTCCATGCAAAATCAGGATG
1 GGGATATAATCCCATGCAAAATCAGGATG
5449608 AAGGGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (29 bp):
GGGATATAATCCCATGCAAAATCAGGATG
Found at i:5451250 original size:22 final size:24
Alignment explanation
Indices: 5451223--5451269 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5451213 CTTTACCCTT
5451223 TCTC-TCTAGCTTTTCTAAGCTGTC
1 TCTCATCTAGCTTTTCTAAGCTG-C
5451247 TCTCATTCTAGCTTTTCTAAGCT
1 TCTCA-TCTAGCTTTTCTAAGCT
5451270 TTTACTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 4 0.19
26 17 0.81
ACGTcount: A:0.15, C:0.28, G:0.11, T:0.47
Consensus pattern (24 bp):
TCTCATCTAGCTTTTCTAAGCTGC
Found at i:5454048 original size:60 final size:60
Alignment explanation
Indices: 5453940--5454057 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
5453930 TTCGAGGATA
* * ** *
5453940 AAATTAGAAGATTTAAATGTTTGGGGACCAATTTAAAATAAAAATCATAATTTGAGAATG
1 AAATTAGAAGATTTAAAAGTTTAGAAACCAATTTAAAATAAAAATCATAATTTAAGAATG
* *
5454000 AAATTAG-AGTATTTAAAAGTTTAGAAACCAATTTAAAA-AGAAATTCATACTTTAAGAA
1 AAATTAGAAG-ATTTAAAAGTTTAGAAACCAATTTAAAATA-AAAATCATAATTTAAGAA
5454058 CATATAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 46 0.94
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (60 bp):
AAATTAGAAGATTTAAAAGTTTAGAAACCAATTTAAAATAAAAATCATAATTTAAGAATG
Found at i:5455263 original size:3 final size:3
Alignment explanation
Indices: 5455255--5455280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5455245 AAAGACTATA
5455255 ACT ACT ACT ACT ACT ACT ACT ACT AC
1 ACT ACT ACT ACT ACT ACT ACT ACT AC
5455281 AAGTAGTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
ACT
Found at i:5456731 original size:12 final size:12
Alignment explanation
Indices: 5456714--5456765 Score: 88
Period size: 12 Copynumber: 4.4 Consensus size: 12
5456704 ACATCAATTT
5456714 AGTTAGGTGAAG
1 AGTTAGGTGAAG
5456726 AGTTAGGTGAAG
1 AGTTAGGTGAAG
*
5456738 AATTAGGTGAAG
1 AGTTAGGTGAAG
5456750 AGTTAGGTG-AG
1 AGTTAGGTGAAG
5456761 AGTTA
1 AGTTA
5456766 AGTATTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
11 7 0.18
12 31 0.82
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:5457174 original size:19 final size:19
Alignment explanation
Indices: 5457150--5457200 Score: 93
Period size: 19 Copynumber: 2.6 Consensus size: 19
5457140 AGTTAACTCA
5457150 CCGAGTTGAGCCAACTAAG
1 CCGAGTTGAGCCAACTAAG
5457169 CCGAGTTGAGCCAACTAAG
1 CCGAGTTGAGCCAACTAAG
5457188 CCGAGTTGGAGCC
1 CCGAGTT-GAGCC
5457201 CCTTGACTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.16
Consensus pattern (19 bp):
CCGAGTTGAGCCAACTAAG
Found at i:5461756 original size:12 final size:12
Alignment explanation
Indices: 5461739--5461815 Score: 111
Period size: 12 Copynumber: 6.5 Consensus size: 12
5461729 ATCAATTTAG
5461739 TTAGGTGAAGAA
1 TTAGGTGAAGAA
*
5461751 TTAGGTGAAGAG
1 TTAGGTGAAGAA
5461763 TTAGGTGAAGAA
1 TTAGGTGAAGAA
5461775 TTAGGTGAAGAA
1 TTAGGTGAAGAA
*
5461787 TTAGGTGAAGAG
1 TTAGGTGAAGAA
* *
5461799 TTAAGTG-AGAG
1 TTAGGTGAAGAA
5461810 TTAGGT
1 TTAGGT
5461816 ATTTGTATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
11 9 0.15
12 51 0.85
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (12 bp):
TTAGGTGAAGAA
Found at i:5461769 original size:24 final size:24
Alignment explanation
Indices: 5461737--5461815 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
5461727 ACATCAATTT
5461737 AGTTAGGTGAAGAATTAGGTGAAG
1 AGTTAGGTGAAGAATTAGGTGAAG
5461761 AGTTAGGTGAAGAATTAGGTGAAG
1 AGTTAGGTGAAGAATTAGGTGAAG
* * *
5461785 AATTAGGTGAAGAGTTAAGTG-AG
1 AGTTAGGTGAAGAATTAGGTGAAG
5461808 AGTTAGGT
1 AGTTAGGT
5461816 ATTTGTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 9 0.18
24 42 0.82
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (24 bp):
AGTTAGGTGAAGAATTAGGTGAAG
Found at i:5461786 original size:36 final size:35
Alignment explanation
Indices: 5461739--5461815 Score: 127
Period size: 36 Copynumber: 2.2 Consensus size: 35
5461729 ATCAATTTAG
*
5461739 TTAGGTGAAGAATTAGGTGAAGAGTTAGGTGAAGAA
1 TTAGGTGAAGAATTAGGTGAAGAGTTAAGTG-AGAA
*
5461775 TTAGGTGAAGAATTAGGTGAAGAGTTAAGTGAGAG
1 TTAGGTGAAGAATTAGGTGAAGAGTTAAGTGAGAA
5461810 TTAGGT
1 TTAGGT
5461816 ATTTGTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (35 bp):
TTAGGTGAAGAATTAGGTGAAGAGTTAAGTGAGAA
Found at i:5466961 original size:55 final size:56
Alignment explanation
Indices: 5466902--5467015 Score: 212
Period size: 55 Copynumber: 2.1 Consensus size: 56
5466892 AGGTAGGTCG
5466902 AATACCTAAAAATTATATTTTAAAAGAGTCTTT-AAAAAACATCAGTTAAAAGATA
1 AATACCTAAAAATTATATTTTAAAAGAGTCTTTAAAAAAACATCAGTTAAAAGATA
*
5466957 AATACCTAAAAATTATATTTTAAAAGAGTTTTTAAAAAAACATCAGTTAAAAGATA
1 AATACCTAAAAATTATATTTTAAAAGAGTCTTTAAAAAAACATCAGTTAAAAGATA
5467013 AAT
1 AAT
5467016 TGGTATGCGT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 32 0.56
56 25 0.44
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.32
Consensus pattern (56 bp):
AATACCTAAAAATTATATTTTAAAAGAGTCTTTAAAAAAACATCAGTTAAAAGATA
Found at i:5467702 original size:24 final size:22
Alignment explanation
Indices: 5467647--5467704 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
5467637 AAACTATATA
5467647 TTTAAAATATAAAAAAAATAAAG
1 TTTAAAAT-TAAAAAAAATAAAG
* *
5467670 TTTATAATTAAAAAAAATGAAG
1 TTTAAAATTAAAAAAAATAAAG
5467692 ATATTAAAATTAA
1 -T-TTAAAATTAA
5467705 TGACTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.43
23 8 0.27
24 9 0.30
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
TTTAAAATTAAAAAAAATAAAG
Found at i:5468944 original size:30 final size:30
Alignment explanation
Indices: 5468908--5468975 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
5468898 TGTTGGTGGC
5468908 TAGGGTTGAGATATAAACCCTAAATAGGTT
1 TAGGGTTGAGATATAAACCCTAAATAGGTT
*
5468938 TAGGGTTGAGATATAAACCCTAAATGGGTT
1 TAGGGTTGAGATATAAACCCTAAATAGGTT
*
5468968 TAAGGTTG
1 TAGGGTTG
5468976 TCATTTAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (30 bp):
TAGGGTTGAGATATAAACCCTAAATAGGTT
Found at i:5469151 original size:3 final size:3
Alignment explanation
Indices: 5469089--5469135 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
5469079 ATTTATTATT
*
5469089 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5469136 ATCAAATGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5469734 original size:113 final size:112
Alignment explanation
Indices: 5469586--5469919 Score: 404
Period size: 113 Copynumber: 3.1 Consensus size: 112
5469576 TATCTCCTTC
* *
5469586 AGTGATAGAA-TCAAAC-AACGATTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
1 AGTGAT-GAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
*
5469649 GATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCTATCG
65 GATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
*
5469697 AGTGATGAATTCAAACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
1 AGTGATGAATTCAAACAAAAGG-TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCA
* * * * * *
5469762 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGCTGATCCATCA
65 GATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATCCATCG
* * *
5469810 AGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAA------C-T--TCTTCAG
1 AGTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAG
* ** *
5469866 ATAAGTTCTTCTCATTATGAACATTCTCTAAAAAAGTTGATCCATTG
66 ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
5469913 AGTGATG
1 AGTGATG
5469920 GGTATGAATC
Statistics
Matches: 194, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
102 2 0.01
103 48 0.25
105 1 0.01
106 1 0.01
110 3 0.02
111 12 0.06
112 26 0.13
113 99 0.51
114 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (112 bp):
AGTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAG
ATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCG
Found at i:5471495 original size:12 final size:12
Alignment explanation
Indices: 5471474--5471507 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5471464 TCTATTTTTT
5471474 TTTTATTTTTTCA
1 TTTTA-TTTTTCA
5471487 TTTTATTTTTCA
1 TTTTATTTTTCA
5471499 TTTTATTTT
1 TTTTATTTT
5471508 CTTTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:5471495 original size:20 final size:20
Alignment explanation
Indices: 5471461--5471502 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5471451 TTGACCCTCA
*
5471461 TTTTCTATTTTTTTTTTATT
1 TTTTCTATTTTTTTTTCATT
5471481 TTTTC-ATTTTATTTTTCATT
1 TTTTCTATTTT-TTTTTCATT
5471501 TT
1 TT
5471503 ATTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTCTATTTTTTTTTCATT
Found at i:5471514 original size:12 final size:11
Alignment explanation
Indices: 5471461--5471514 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
5471451 TTGACCCTCA
*
5471461 TTTTCTATTTT
1 TTTTTTATTTT
5471472 TTTTTTATTTT
1 TTTTTTATTTT
5471483 TTCATTTTATTTT
1 TT--TTTTATTTT
*
5471496 TCATTTTATTTT
1 T-TTTTTATTTT
5471508 CTTTTTT
1 -TTTTTT
5471515 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 12 0.33
12 13 0.36
13 11 0.31
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:5482987 original size:30 final size:30
Alignment explanation
Indices: 5482925--5482997 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
5482915 AAATGATGAC
* *
5482925 TAAAATAAAT-AAAACTAAAACTATATATT
1 TAAAATAAATAAAAAATAAAACTATATACT
* * *
5482954 TAAAATATATAAAAAATAAAAGTTTATACT
1 TAAAATAAATAAAAAATAAAACTATATACT
5482984 TAAAAATAAATAAA
1 T-AAAATAAATAAA
5482998 TATATTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 9 0.25
30 16 0.44
31 11 0.31
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (30 bp):
TAAAATAAATAAAAAATAAAACTATATACT
Found at i:5483005 original size:19 final size:18
Alignment explanation
Indices: 5482955--5483007 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
5482945 CTATATATTT
*
5482955 AAAATATATAAAAAATAA
1 AAAATATATTAAAAATAA
**
5482973 AAGTTTATACTTAAAAATAA
1 AA-AATATA-TTAAAAATAA
5482993 ATAAATATATTAAAA
1 A-AAATATATTAAAA
5483008 TTAATGACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.37
20 14 0.52
21 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATATATTAAAAATAA
Found at i:5484448 original size:3 final size:3
Alignment explanation
Indices: 5484387--5484432 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
5484377 ATTTATTATT
*
5484387 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA -AA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5484433 ATCAAATGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5484448 original size:22 final size:22
Alignment explanation
Indices: 5484387--5484448 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5484377 ATTTATTATT
5484387 TAATAATAATAATAATAATAATA
1 TAATAA-AATAATAATAATAATA
*
5484410 TAATAAAATAATTATAATAATA
1 TAATAAAATAATAATAATAATA
* *
5484432 -AATCAAATGGATAATAA
1 TAATAAAAT-AATAATAA
5484449 AAAACTAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.21
22 21 0.62
23 6 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (22 bp):
TAATAAAATAATAATAATAATA
Found at i:5485554 original size:24 final size:25
Alignment explanation
Indices: 5485522--5485573 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
5485512 ATAATCATAA
* *
5485522 AAATCAAAAGAGAGGAA-AATAAAT
1 AAATAAAAAGAGAGGAACAAAAAAT
* *
5485546 AAATAAAAATATAGGAACAAAAAAT
1 AAATAAAAAGAGAGGAACAAAAAAT
5485571 AAA
1 AAA
5485574 AATAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.13
Consensus pattern (25 bp):
AAATAAAAAGAGAGGAACAAAAAAT
Found at i:5486852 original size:7 final size:7
Alignment explanation
Indices: 5486837--5486927 Score: 68
Period size: 6 Copynumber: 13.4 Consensus size: 7
5486827 ACGAGAAAAA
5486837 AAATAAT
1 AAATAAT
*
5486844 AAGTAAT
1 AAATAAT
5486851 AAATAAT
1 AAATAAT
5486858 AAAATAAT
1 -AAATAAT
5486866 AAA-AAT
1 AAATAAT
*
5486872 -AATAAA
1 AAATAAT
*
5486878 AAAGGTAAA
1 AAA--TAAT
5486887 AAATAAT
1 AAATAAT
5486894 -AATAAT
1 AAATAAT
5486900 -AATAAT
1 AAATAAT
*
5486906 -AATAGT
1 AAATAAT
5486912 AAATAA-
1 AAATAAT
*
5486918 ATATAAT
1 AAATAAT
5486925 AAA
1 AAA
5486928 AAACATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
5 2 0.03
6 27 0.39
7 26 0.38
8 7 0.10
9 7 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (7 bp):
AAATAAT
Found at i:5486872 original size:9 final size:9
Alignment explanation
Indices: 5486841--5486929 Score: 65
Period size: 9 Copynumber: 9.2 Consensus size: 9
5486831 GAAAAAAAAT
5486841 AATAAGTAATA
1 AATAA-TAA-A
5486852 AATAAT-AA
1 AATAATAAA
5486860 AATAATAAA
1 AATAATAAA
5486869 AATAATAAA
1 AATAATAAA
*
5486878 AA-AGGTAAAA
1 AATA-AT-AAA
*
5486888 AATAATAAT
1 AATAATAAA
5486897 AATAATAATA
1 AATAATAA-A
5486907 ATAGTAAATAAA
1 A-A-T-AATAAA
*
5486919 TATAATAAA
1 AATAATAAA
5486928 AA
1 AA
5486930 ACATTTTTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
8 8 0.12
9 32 0.50
10 9 0.14
11 8 0.12
12 2 0.03
13 5 0.08
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (9 bp):
AATAATAAA
Found at i:5486873 original size:31 final size:30
Alignment explanation
Indices: 5486835--5486929 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 30
5486825 AAACGAGAAA
*
5486835 AAAAATAATAAGTAATAAATAATAAAATAAT
1 AAAAATAATAA-TAATAAGTAATAAAATAAT
5486866 AAAAATAATAA-AA-AAGGTAA-AAAATAAT
1 AAAAATAATAATAATAA-GTAATAAAATAAT
*
5486894 AATAATAATAATAAT-AGTAAATAAATATAAT
1 AAAAATAATAATAATAAGT-AATAAA-ATAAT
5486925 AAAAA
1 AAAAA
5486930 ACATTTTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
28 22 0.40
29 10 0.18
30 3 0.05
31 20 0.36
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (30 bp):
AAAAATAATAATAATAAGTAATAAAATAAT
Found at i:5486926 original size:3 final size:3
Alignment explanation
Indices: 5486838--5486909 Score: 64
Period size: 3 Copynumber: 24.3 Consensus size: 3
5486828 CGAGAAAAAA
*
5486838 AAT AAT AAGT AAT AAAT AAT AA- AAT AAT AAA AAT AAT AA- AA- AAGGT
1 AAT AAT AA-T AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T
5486884 AA- AA- AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5486910 GTAAATAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 10 0.17
3 42 0.70
4 6 0.10
5 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:5487068 original size:40 final size:38
Alignment explanation
Indices: 5486981--5487426 Score: 483
Period size: 40 Copynumber: 11.3 Consensus size: 38
5486971 TTTCAAAACT
5486981 ATATAATATATATTTTCAAAAATTGTTTTAAAAACTTATATA
1 ATAT-ATATATATTTTC-AAAA-TGTTTTAAAAAC-TATATA
* * *
5487023 TTATATATATA-TTTCAAAAACGTTTTAAAAATTATATAATATATA
1 ATATATATATATTTTC-AAAATGTTTT---AA--A-A-ACTATATA
*
5487068 TATATATATATATGTTTTTAAAATGTTTTAAAAACTATATA
1 -ATATATATATA--TTTTCAAAATGTTTTAAAAACTATATA
*
5487109 ATATATATATGTTTTCAAAATGTTTTAAAAACTATAATA
1 ATATATATATATTTTCAAAATGTTTTAAAAACTAT-ATA
*
5487148 TATATATATATGTTTTCAAAATGTTTTAAAAACTATAATA
1 -ATATATATATATTTTCAAAATGTTTTAAAAACTAT-ATA
* *
5487188 TATATATATATATATTCAAAATGTTTTAAAAACTATATG
1 -ATATATATATATTTTCAAAATGTTTTAAAAACTATATA
* * *
5487227 ATATATACATTTTTTAAAAATGTTTTAAAAACTATAT-
1 ATATATATATATTTTCAAAATGTTTTAAAAACTATATA
5487264 AT-TATATATATTTTCAAAATGTTTTTAAAAACTATAT-
1 ATATATATATATTTTCAAAATG-TTTTAAAAACTATATA
*
5487301 AT-TATACATATTTTCAAAATGTTTTAAAAACTATATA
1 ATATATATATATTTTCAAAATGTTTTAAAAACTATATA
*
5487338 ATATATATATGTTTTCAAAAATGTTTTTAAAAACT-TAT-
1 ATATATATATATTTTC-AAAATG-TTTTAAAAACTATATA
* * *
5487376 ATATCATATATATTTTCAAAATGATTTCAAAATTATATA
1 ATAT-ATATATATTTTCAAAATGTTTTAAAAACTATATA
*
5487415 ATATATACATAT
1 ATATATATATAT
5487427 ATATATATAT
Statistics
Matches: 356, Mismatches: 27, Indels: 46
0.83 0.06 0.11
Matches are distributed among these distances:
36 31 0.09
37 47 0.13
38 87 0.24
39 34 0.10
40 103 0.29
41 14 0.04
42 6 0.02
43 1 0.00
44 1 0.00
45 9 0.03
46 11 0.03
48 9 0.03
49 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (38 bp):
ATATATATATATTTTCAAAATGTTTTAAAAACTATATA
Done.