Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008660.1 Hibiscus syriacus cultivar Beakdansim tig00111657_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: 1057077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 5
Found at i:294525 original size:8 final size:8
Alignment explanation
Indices: 294514--294575 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
294504 TTTTTGGCTC
294514 TTTTTTTG
1 TTTTTTTG
294522 TTTTTTTG
1 TTTTTTTG
**
294530 CCCTTTTT-
1 -TTTTTTTG
294538 TTTTTTTG
1 TTTTTTTG
*
294546 CCTTTTTTG
1 -TTTTTTTG
294555 --TTTTT-
1 TTTTTTTG
294560 TTTTTTTG
1 TTTTTTTG
294568 TTTTTTTG
1 TTTTTTTG
294576 AAAAAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
6 5 0.12
7 10 0.23
8 16 0.37
9 12 0.28
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:294542 original size:15 final size:15
Alignment explanation
Indices: 294516--294560 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 15
294506 TTTGGCTCTT
294516 TTTTTGTTTTTTTGCCC
1 TTTTT-TTTTTTTG-CC
294533 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
294548 TTTTTTGTTTTTT
1 TTTTTT-TTTTTT
294561 TTTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:294551 original size:24 final size:22
Alignment explanation
Indices: 294533--294575 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
294523 TTTTTTGCCC
294533 TTTTTTTTTTTTGCCTTTTTTG
1 TTTTTTTTTTTTGCCTTTTTTG
*
294555 TTTTTTTTTTTTG-TTTTTTTG
1 TTTTTTTTTTTTGCCTTTTTTG
294576 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTTGCCTTTTTTG
Found at i:294561 original size:19 final size:18
Alignment explanation
Indices: 294503--294563 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
294493 AAATTTTGGC
* *
294503 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGC-CTTTTTTTT
*
294522 TTTTTTTGCC--CTTTTT
1 TTTTTTTGCCTTTTTTTT
294538 TTTTTTTGCCTTTTTTGTT
1 TTTTTTTGCCTTTTTT-TT
294557 TTTTTTT
1 TTTTTTT
294564 TTTGTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 14 0.40
18 4 0.11
19 17 0.49
ACGTcount: A:0.00, C:0.11, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTT
Found at i:294564 original size:13 final size:13
Alignment explanation
Indices: 294548--294574 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
294538 TTTTTTTGCC
294548 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
294561 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
294574 T
1 T
294575 GAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:294961 original size:16 final size:15
Alignment explanation
Indices: 294923--294961 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
294913 TAAGATTAGA
294923 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
294938 ATAAATAAACGGAAG
1 ATAAATAAACAAAAG
294953 ATGAAATAA
1 AT-AAATAA
294962 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Found at i:306221 original size:24 final size:24
Alignment explanation
Indices: 306181--306235 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
306171 CTTTTCTTTG
* *
306181 CTTTT-TTTTTTTTGAGTGCTTGA
1 CTTTTCTTCTTTTGGAGTGCTTGA
306204 CTTTTCTTCTTTTGGAGTGCTTGA
1 CTTTTCTTCTTTTGGAGTGCTTGA
306228 CTTTTCTT
1 CTTTTCTT
306236 TTCTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.07, C:0.15, G:0.16, T:0.62
Consensus pattern (24 bp):
CTTTTCTTCTTTTGGAGTGCTTGA
Found at i:307037 original size:23 final size:23
Alignment explanation
Indices: 307009--307060 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
306999 CAAATTGGAT
307009 GGGAGATGTTGCTTGGCCGAATA
1 GGGAGATGTTGCTTGGCCGAATA
307032 GGGAGATGTTGCTTGGCCGAATA
1 GGGAGATGTTGCTTGGCCGAATA
307055 GGGAGA
1 GGGAGA
307061 GGGCTCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.42, T:0.23
Consensus pattern (23 bp):
GGGAGATGTTGCTTGGCCGAATA
Found at i:313813 original size:12 final size:12
Alignment explanation
Indices: 313796--313820 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
313786 TATATTTGTT
313796 TTCCCTTCCTAC
1 TTCCCTTCCTAC
313808 TTCCCTTCCTAC
1 TTCCCTTCCTAC
313820 T
1 T
313821 AACCCATTTG
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:0.08, C:0.48, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCCCTTCCTAC
Found at i:319836 original size:13 final size:12
Alignment explanation
Indices: 319817--319881 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
319807 TTATTGGCGT
319817 GATATGGTGATG
1 GATATGGTGATG
319829 GAATATGGTGAT-
1 G-ATATGGTGATG
*
319841 GATATAGGCG-T-
1 GATAT-GGTGATG
319852 GATAATGGTGATG
1 GAT-ATGGTGATG
319865 GACTATGGTGAT-
1 GA-TATGGTGATG
319877 GATAT
1 GATAT
319882 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:319872 original size:36 final size:35
Alignment explanation
Indices: 319786--319912 Score: 163
Period size: 36 Copynumber: 3.7 Consensus size: 35
319776 ATGGTTATGA
* * * *
319786 AATGGTAATGGA-ATGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGGTGATGATATAGGCGTGAT
319820 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
319855 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
319891 AAT-G-GATGGATTATGGTGATGA
1 AATGGTGATGGA-TATGGTGATGA
319913 AAATAGTATC
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
33 9 0.11
34 18 0.21
35 21 0.25
36 36 0.43
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:320298 original size:19 final size:20
Alignment explanation
Indices: 320251--320301 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
320241 GAAACCCCTT
**
320251 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
320271 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
320290 TGAAGATACATG
1 TGAAAATACATG
320302 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:323939 original size:33 final size:33
Alignment explanation
Indices: 323897--323965 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
323887 GTTGATGAAT
*
323897 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
323930 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
323963 GAA
1 GAA
323966 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:323970 original size:13 final size:12
Alignment explanation
Indices: 323951--324047 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
323941 TTATTGGCGT
323951 GATATGGTGATG
1 GATATGGTGATG
323963 GAATATGGTGAT-
1 G-ATATGGTGATG
*
323975 GATATAGGCG-T-
1 GATAT-GGTGATG
323986 GATAATGGTGATG
1 GAT-ATGGTGATG
323999 GACTATGGTGAT-
1 GA-TATGGTGATG
*
324011 GATATAGGCG-T-
1 GATAT-GGTGATG
*
324022 GATAATGGAGATG
1 GAT-ATGGTGATG
324035 GATTATGGTGATG
1 GA-TATGGTGATG
324048 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:324006 original size:36 final size:36
Alignment explanation
Indices: 323936--324048 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
323926 AATGGAAGGA
* *
323936 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
323971 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
324007 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
324043 TGATGA
1 TGATGA
324049 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:324431 original size:19 final size:20
Alignment explanation
Indices: 324384--324434 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
324374 GAAACCCCTT
**
324384 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
324404 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
324423 TGAAGATACATG
1 TGAAAATACATG
324435 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:325769 original size:14 final size:13
Alignment explanation
Indices: 325750--325816 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
325740 TGCAAAAAAG
325750 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
325764 AAAG-AAGAGAAA
1 AAAGAAAAAGAAA
*
325776 AATCAGAAAAGGAAA
1 AA--AGAAAAAGAAA
325791 AGAAG-AAAAGAAGA
1 A-AAGAAAAAGAA-A
325805 AAAGAAAAAGAA
1 AAAGAAAAAGAA
325817 GTTCAAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 4 0.09
13 14 0.33
14 17 0.40
15 7 0.16
16 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:325799 original size:22 final size:22
Alignment explanation
Indices: 325762--325817 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
325752 AGAAAAAGAC
*
325762 AAAAAGAAGAGAAAAATCAGAAAAG
1 AAAAAGAAGA-AAAGA--AGAAAAG
*
325787 GAAAAGAAGAAAAGAAGAAAAG
1 AAAAAGAAGAAAAGAAGAAAAG
325809 AAAAAGAAG
1 AAAAAGAAG
325818 TTCAAAAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.54
24 4 0.14
25 9 0.32
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (22 bp):
AAAAAGAAGAAAAGAAGAAAAG
Found at i:331004 original size:19 final size:20
Alignment explanation
Indices: 330980--331018 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
330970 TATCCTTTCT
330980 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
330999 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
331019 AATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:331697 original size:18 final size:17
Alignment explanation
Indices: 331674--331708 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
331664 TAGGTTAGGG
331674 TAGAAAGAATAAAAGAAA
1 TAGAAAG-ATAAAAGAAA
*
331692 TAGAAAGATAGAAGAAA
1 TAGAAAGATAAAAGAAA
331709 GGATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAAAAGAAA
Found at i:331954 original size:20 final size:20
Alignment explanation
Indices: 331918--331955 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
331908 TCTTTTGAAT
*
331918 TTCTTTTTCTTTTTTTTTTA
1 TTCTTTTTCTTTCTTTTTTA
331938 TTCTTTTT-TTATCTTTTT
1 TTCTTTTTCTT-TCTTTTT
331956 CTTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
TTCTTTTTCTTTCTTTTTTA
Found at i:333850 original size:23 final size:23
Alignment explanation
Indices: 333824--333879 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
333814 AGAAGTTGTT
*
333824 AAATAAATGGATAATAAGAAA-GG
1 AAATAAATGGA-AAGAAGAAATGG
*
333847 AAATAGAAAGGAAAGAAGAAATGG
1 AAATA-AATGGAAAGAAGAAATGG
*
333871 AAAGAAATG
1 AAATAAATG
333880 TTATCAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (23 bp):
AAATAAATGGAAAGAAGAAATGG
Found at i:333874 original size:13 final size:12
Alignment explanation
Indices: 333839--333876 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
333829 AATGGATAAT
333839 AAGAAAGGAAA-
1 AAGAAAGGAAAG
*
333850 TAGAAAGGAAAG
1 AAGAAAGGAAAG
333862 AAGAAATGGAAAG
1 AAGAAA-GGAAAG
333875 AA
1 AA
333877 ATGTTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 5 0.22
13 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (12 bp):
AAGAAAGGAAAG
Found at i:334123 original size:36 final size:35
Alignment explanation
Indices: 334024--334134 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
334014 TTGGTGGTTA
* * * * *
334024 TATAGGTGTGAAATGGTGGTAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* * *
334059 TATAGGCGTGCAACGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
334094 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
334130 T-TAGG
1 TATAGG
334135 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:338854 original size:8 final size:8
Alignment explanation
Indices: 338824--338865 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
338814 TCTTTTTGAA
338824 CTTCTCTTT
1 CTTCT-TTT
338833 -TTCTTTT
1 CTTCTTTT
338840 CATTTCTTTT
1 C--TTCTTTT
338850 CTTCTTTT
1 CTTCTTTT
338858 CTTCTTTT
1 CTTCTTTT
338866 TTGATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.10
8 19 0.63
10 8 0.27
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (8 bp):
CTTCTTTT
Found at i:350918 original size:19 final size:20
Alignment explanation
Indices: 350894--350936 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
350884 AGCATTTATC
*
350894 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
350913 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
350933 TTCA
1 TTCA
350937 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:351355 original size:19 final size:20
Alignment explanation
Indices: 351331--351370 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
351321 TATTCTTTAT
351331 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
351350 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
351370 T
1 T
351371 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:351908 original size:22 final size:23
Alignment explanation
Indices: 351880--351926 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
351870 ATTTAGAAGT
351880 TGGTGAT-AATATAGGTG-TGATA
1 TGGTGATGAATATA-GTGATGATA
351902 TGGTGATGGAATATAGTGATGATA
1 TGGTGAT-GAATATAGTGATGATA
351926 T
1 T
351927 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 3 0.14
24 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (23 bp):
TGGTGATGAATATAGTGATGATA
Found at i:355930 original size:15 final size:15
Alignment explanation
Indices: 355906--355944 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
355896 TGTAGGAGTC
355906 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
*
355921 TTTTTGTTTTTTTTCT
1 TTTTTCTTTTTTTT-T
*
355937 TCTTTCTT
1 TTTTTCTT
355945 GTTGCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:356353 original size:22 final size:23
Alignment explanation
Indices: 356325--356371 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
356315 ATTTAGAAGT
356325 TGGTGAT-AATATAGGTG-TGATA
1 TGGTGATGAATATA-GTGATGATA
356347 TGGTGATGGAATATAGTGATGATA
1 TGGTGAT-GAATATAGTGATGATA
356371 T
1 T
356372 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 3 0.14
24 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (23 bp):
TGGTGATGAATATAGTGATGATA
Found at i:357126 original size:18 final size:18
Alignment explanation
Indices: 357083--357120 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
357073 GTGAAGTATG
*
357083 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
357101 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
357119 AA
1 AA
357121 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:363180 original size:19 final size:18
Alignment explanation
Indices: 363156--363191 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
363146 TACTCCCTCC
363156 CTTTTTAAACTTTTTTTTT
1 CTTTTT-AACTTTTTTTTT
*
363175 CTTTTTGACTTTTTTTT
1 CTTTTTAACTTTTTTTT
363192 GATTTTGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (18 bp):
CTTTTTAACTTTTTTTTT
Found at i:363542 original size:18 final size:18
Alignment explanation
Indices: 363499--363536 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
363489 GTGAAGTATG
*
363499 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
363517 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
363535 AA
1 AA
363537 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:365731 original size:11 final size:11
Alignment explanation
Indices: 365717--365782 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
365707 AAAGAAGTTC
365717 AAAAGAAAAAA
1 AAAAGAAAAAA
*
365728 AAAAGACAAAAG
1 AAAAGA-AAAAA
* *
365740 AAGAGAAAAATC
1 AAAAGAAAAA-A
* *
365752 AGAA-AAAAAG
1 AAAAGAAAAAA
*
365762 AAAAGAAAAGA
1 AAAAGAAAAAA
365773 AAAAGAAAAA
1 AAAAGAAAAA
365783 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
10 3 0.07
11 28 0.67
12 11 0.26
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:365738 original size:7 final size:6
Alignment explanation
Indices: 365717--365782 Score: 52
Period size: 5 Copynumber: 11.7 Consensus size: 6
365707 AAAGAAGTTC
* ** *
365717 AAAAGA AAAA-A AAAAGA CAAAAG- AAGAGA AAAATC AGAA-A AAAAG-
1 AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
365762 AAAAG- AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAA
365783 TTCAAAAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
5 22 0.46
6 21 0.44
7 5 0.10
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:365771 original size:32 final size:33
Alignment explanation
Indices: 365720--365783 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
365710 GAAGTTCAAA
*
365720 AGAAAAAAAAAAGACAAAAG-AAGAGAAAAATC
1 AGAAAAAAAAAAGACAAAAGAAAAAGAAAAATC
*
365752 AGAAAAAAAGAAA-AGAAAAGAAAAAGAAAAAT
1 AGAAAAAAA-AAAGACAAAAGAAAAAGAAAAAT
365784 TCAAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (33 bp):
AGAAAAAAAAAAGACAAAAGAAAAAGAAAAATC
Found at i:372113 original size:8 final size:8
Alignment explanation
Indices: 372100--372143 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
372090 GGAATCTTTT
372100 TTTTCTTC
1 TTTTCTTC
372108 TTTTCTTC
1 TTTTCTTC
372116 TTTTCTTC
1 TTTTCTTC
*
372124 TTTT-GTC
1 TTTTCTTC
372131 TTTTCTTTC
1 TTTTC-TTC
372140 TTTT
1 TTTT
372144 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 6 0.19
8 20 0.62
9 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:373769 original size:2 final size:2
Alignment explanation
Indices: 373758--373791 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
373748 TAACTATAGG
373758 TA TA -A TA 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 TA TA TA TA T
373792 GAAAATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:374351 original size:30 final size:31
Alignment explanation
Indices: 374315--374372 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
374305 TAGCTTTATC
**
374315 TTATGTTTACATATTTTTTAGAT-TCATTTA
1 TTATGTTTACATATCATTTAGATATCATTTA
*
374345 TTATGTTTGCATATCATTTAGATATCAT
1 TTATGTTTACATATCATTTAGATATCAT
374373 GGCAGCATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (31 bp):
TTATGTTTACATATCATTTAGATATCATTTA
Found at i:380811 original size:24 final size:21
Alignment explanation
Indices: 380769--380811 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
380759 AGCCATCTCT
380769 ATTCTTTTTTTATTTCATTTC
1 ATTCTTTTTTTATTTCATTTC
380790 ATTCTTATTATTTATTTTCATT
1 ATTCTT-TT-TTTA-TTTCATT
380812 ACTTATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 4 0.21
24 7 0.37
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTCTTTTTTTATTTCATTTC
Found at i:381834 original size:95 final size:95
Alignment explanation
Indices: 381671--381952 Score: 485
Period size: 95 Copynumber: 3.0 Consensus size: 95
381661 GGTATGGGTG
*
381671 ATGAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGCAAGAACCA-TTGCTAT
1 ATGAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGGAAGAACCAGTT-CTAT
381735 AGAGAGCAAAGACCTAGCCTTACAAATCCTC
65 AGAGAGCAAAGACCTAGCCTTACAAATCCTC
* *
381766 ATGAAACAATGGAATTTTGAATAAGATAGTATCTTAGAAATGACTAAGGAAGAACCAGTTCTATA
1 ATGAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGGAAGAACCAGTTCTATA
*
381831 GAGAGCAAAGACCCAGCCTTACAAATCCTC
66 GAGAGCAAAGACCTAGCCTTACAAATCCTC
* *
381861 ATAAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGGAAGAACCAGTGCTATA
1 ATGAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGGAAGAACCAGTTCTATA
*
381926 GAAAGCAAAGACCTAGCCTTACAAATC
66 GAGAGCAAAGACCTAGCCTTACAAATC
381953 ATTCTAAAGG
Statistics
Matches: 176, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
95 174 0.99
96 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (95 bp):
ATGAAACAATGGAATGTTGAATAAGATAGTATCTTAGAAATGACCAAGGAAGAACCAGTTCTATA
GAGAGCAAAGACCTAGCCTTACAAATCCTC
Found at i:382962 original size:13 final size:13
Alignment explanation
Indices: 382944--383076 Score: 63
Period size: 13 Copynumber: 10.9 Consensus size: 13
382934 TATAGGCGTG
382944 ATATGGTGATGAA
1 ATATGGTGATGAA
*
382957 ATATGGTGATGAT
1 ATATGGTGATGAA
*
382970 ATA-GGCG-TGATA
1 ATATGGTGATGA-A
*
382982 AT-T-GTGATGGA
1 ATATGGTGATGAA
*
382993 CTATGGTGATG--
1 ATATGGTGATGAA
* *
383004 ATAT-GTGCGTGAT
1 ATATGGTG-ATGAA
*
383017 A-ATGGTGATGGA
1 ATATGGTGATGAA
*
383029 ATATGGTGATGAT
1 ATATGGTGATGAA
* *
383042 ATA-GGCG-TGAT
1 ATATGGTGATGAA
*
383053 A-ATGGTGATGGA
1 ATATGGTGATGAA
*
383065 CTATGGTGATGA
1 ATATGGTGATGA
383077 TATAGGCGTG
Statistics
Matches: 88, Mismatches: 19, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
10 4 0.05
11 20 0.23
12 18 0.20
13 46 0.52
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:382998 original size:36 final size:36
Alignment explanation
Indices: 382925--383101 Score: 286
Period size: 36 Copynumber: 4.9 Consensus size: 36
382915 ATTTATAAGT
* * *
382925 TGGTGATAATATAGGCGTGAT-ATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
382960 TGGTGATGATATAGGCGTGATAATTGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
382996 TGGTGATGATAT-GTGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAG-GCGTGATAATGGTGATGGACTA
383032 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
383068 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
383102 AGATTGTATC
Statistics
Matches: 132, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
35 21 0.16
36 110 0.83
37 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:383058 original size:23 final size:23
Alignment explanation
Indices: 382959--383062 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
382949 GTGATGAAAT
382959 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
* *
382982 ATTGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
383006 AT-GTGCGTGATA-ATG-GTGATGGAA
1 ATGGTG-ATGATATAGGCGTGAT---A
383030 TATGGTGATGATATAGGCGTGATA
1 -ATGGTGATGATATAGGCGTGATA
383054 ATGGTGATG
1 ATGGTGATG
383063 GACTATGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 21 0.34
24 9 0.15
25 14 0.23
26 5 0.08
27 5 0.08
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:386948 original size:36 final size:36
Alignment explanation
Indices: 386896--387116 Score: 381
Period size: 36 Copynumber: 6.2 Consensus size: 36
386886 GATACTATTT
* * *
386896 TCATCACCATAATCCATCTCCATTATCACACCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
386932 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
386968 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
387004 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
387040 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
387076 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
387111 ACATCA
1 TCATCA
387117 TCCTTCCATT
Statistics
Matches: 179, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 17 0.09
36 162 0.91
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:387588 original size:14 final size:15
Alignment explanation
Indices: 387565--387613 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 15
387555 TTTGGAGTGC
387565 AAAAGAAAGAAAATA
1 AAAAGAAAGAAAATA
387580 AAAAG-AAGAAAATA
1 AAAAGAAAGAAAATA
387594 AAAAGTAAAAGAAAAGTA
1 AAAAG--AAAGAAAA-TA
387612 AA
1 AA
387614 GCAAGTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.47
15 5 0.17
17 7 0.23
18 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
AAAAGAAAGAAAATA
Found at i:391134 original size:36 final size:36
Alignment explanation
Indices: 391082--391302 Score: 381
Period size: 36 Copynumber: 6.2 Consensus size: 36
391072 GATACTATTT
* *
391082 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
391118 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
391154 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
391190 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
391226 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* * *
391262 TCATCACCATATTCCATCACCA-TATCAAGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
391297 ACATCA
1 TCATCA
391303 TCCTTCCATT
Statistics
Matches: 179, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 16 0.09
36 163 0.91
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.28
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:393234 original size:14 final size:15
Alignment explanation
Indices: 393201--393245 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
393191 CTTGCTTCAC
393201 TTTTCTTTTGCTTTTGA
1 TTTTC-TTT-CTTTTGA
*
393218 TTTTC-TTCTTTTTA
1 TTTTCTTTCTTTTGA
393232 TTTTCTTTCTTTTG
1 TTTTCTTTCTTTTG
393246 CACTCCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
17 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTCTTTCTTTTGA
Found at i:393732 original size:13 final size:12
Alignment explanation
Indices: 393714--393845 Score: 66
Period size: 13 Copynumber: 11.0 Consensus size: 12
393704 TATAGGCGAG
393714 ATATGGTGATGGA
1 ATATGGTGAT-GA
393727 ATATGGTGATGA
1 ATATGGTGATGA
*
393739 TATAGGCGTGAT-A
1 -ATATG-GTGATGA
393752 AT-T-GTGATGGA
1 ATATGGTGAT-GA
*
393763 CTATGGTGATGA
1 ATATGGTGATGA
* *
393775 AT-GGGCG-TG-
1 ATATGGTGATGA
393784 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
393798 ATATGGTGATG-
1 ATATGGTGATGA
*
393809 ATATAGGCG-TG-
1 ATAT-GGTGATGA
393820 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
*
393834 CTATGGTGATGA
1 ATATGGTGATGA
393846 TAGGCGTGAT
Statistics
Matches: 92, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
9 7 0.08
10 2 0.02
11 19 0.21
12 18 0.20
13 38 0.41
14 8 0.09
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:393768 original size:36 final size:36
Alignment explanation
Indices: 393695--393868 Score: 266
Period size: 36 Copynumber: 4.9 Consensus size: 36
393685 ATTTATAAGT
* * *
393695 TGGTGATAATATAGGCGAGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
393730 TGGTGATGATATAGGCGTGATAATTGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
393766 TGGTGATGA-ATGGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
393801 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
393837 TGGTGATG--ATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
393869 AGATTGTATC
Statistics
Matches: 128, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
34 24 0.19
35 51 0.40
36 53 0.41
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:393811 original size:71 final size:70
Alignment explanation
Indices: 393705--393867 Score: 283
Period size: 71 Copynumber: 2.3 Consensus size: 70
393695 TGGTGATAAT
* *
393705 ATAGGCGAGAT-ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATTGTGATGGACTATGG
1 ATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGG
393769 TGATG
66 TGATG
*
393774 AATGGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATG
1 -ATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATG
393839 GTGATG
65 GTGATG
393845 ATAGGCGTGATAATGGTGATGGA
1 ATAGGCGTGATAATGGTGATGGA
393868 CAGATTGTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
70 31 0.35
71 57 0.65
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.29
Consensus pattern (70 bp):
ATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGG
TGATG
Found at i:397812 original size:14 final size:15
Alignment explanation
Indices: 397779--397823 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
397769 CTTGCTTCAC
397779 TTTTCTTTTGCTTTTGA
1 TTTTC-TTT-CTTTTGA
*
397796 TTTTC-TTCTTTTTA
1 TTTTCTTTCTTTTGA
397810 TTTTCTTTCTTTTG
1 TTTTCTTTCTTTTG
397824 CACTCCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
17 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTCTTTCTTTTGA
Found at i:398308 original size:13 final size:12
Alignment explanation
Indices: 398290--398421 Score: 66
Period size: 13 Copynumber: 11.0 Consensus size: 12
398280 TATAGGCGAG
398290 ATATGGTGATGGA
1 ATATGGTGAT-GA
398303 ATATGGTGATGA
1 ATATGGTGATGA
*
398315 TATAGGCGTGAT-A
1 -ATATG-GTGATGA
398328 AT-T-GTGATGGA
1 ATATGGTGAT-GA
*
398339 CTATGGTGATGA
1 ATATGGTGATGA
* *
398351 AT-GGGCG-TG-
1 ATATGGTGATGA
398360 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
398374 ATATGGTGATG-
1 ATATGGTGATGA
*
398385 ATATAGGCG-TG-
1 ATAT-GGTGATGA
398396 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
*
398410 CTATGGTGATGA
1 ATATGGTGATGA
398422 TATAGGCGTG
Statistics
Matches: 92, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
9 7 0.08
10 2 0.02
11 19 0.21
12 18 0.20
13 38 0.41
14 8 0.09
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:398344 original size:36 final size:36
Alignment explanation
Indices: 398271--398446 Score: 284
Period size: 36 Copynumber: 4.9 Consensus size: 36
398261 ATTTATAAGT
* * *
398271 TGGTGATAATATAGGCGAGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
398306 TGGTGATGATATAGGCGTGATAATTGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
398342 TGGTGATGA-ATGGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
398377 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
398413 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
398447 AGATTGTATC
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
35 51 0.39
36 79 0.61
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:398387 original size:71 final size:72
Alignment explanation
Indices: 398271--398445 Score: 300
Period size: 71 Copynumber: 2.5 Consensus size: 72
398261 ATTTATAAGT
* * *
398271 TGGTGATAATATAGGCGAGAT-ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATTGTGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGA
398335 TGGACTA
66 TGGACTA
*
398342 TGGTGATGA-ATGGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGA
398406 TGGACTA
66 TGGACTA
398413 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
398446 CAGATTGTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
70 9 0.09
71 66 0.68
72 22 0.23
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.30
Consensus pattern (72 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGA
TGGACTA
Found at i:402889 original size:13 final size:12
Alignment explanation
Indices: 402871--403003 Score: 68
Period size: 13 Copynumber: 11.0 Consensus size: 12
402861 TATAGGCATG
402871 ATATGGTGATGGA
1 ATATGGTGAT-GA
402884 ATATGGTGATGA
1 ATATGGTGATGA
*
402896 TATAGGCGTGAT-A
1 -ATATG-GTGATGA
402909 AT-T-GTGATGGA
1 ATATGGTGAT-GA
* *
402920 CTTTGGTGATG-
1 ATATGGTGATGA
402931 ATATGG-GCATG-
1 ATATGGTG-ATGA
402942 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
402956 ATATGGTGATG-
1 ATATGGTGATGA
*
402967 ATATAGGCG-TG-
1 ATAT-GGTGATGA
402978 ATAATGGTGATGGA
1 AT-ATGGTGAT-GA
*
402992 CTATGGTGATGA
1 ATATGGTGATGA
403004 TATAGGCGTG
Statistics
Matches: 96, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
9 5 0.05
10 1 0.01
11 22 0.23
12 21 0.22
13 39 0.41
14 8 0.08
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:402927 original size:36 final size:36
Alignment explanation
Indices: 402854--403028 Score: 271
Period size: 36 Copynumber: 4.9 Consensus size: 36
402844 TTATAAGTTA
* * *
402854 GTGATAATATAGGCATGAT-ATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
* *
402889 GTGATGATATAGGCGTGATAATTGTGATGGACTTTG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
* * *
402925 GTGATGATATGGGCATGATAATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
402961 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
402997 GTGATGATATAGGCGTGATAATGGTGATGGAC
1 GTGATGATATAGGCGTGATAATGGTGATGGAC
403029 ATATTGTATC
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 17 0.13
36 109 0.87
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGACTATG
Found at i:402950 original size:23 final size:22
Alignment explanation
Indices: 402868--403025 Score: 99
Period size: 23 Copynumber: 6.6 Consensus size: 22
402858 TAATATAGGC
402868 ATGATATGGTGATGGAATATGGTG
1 ATGATATGGTGAT-G-ATATGGTG
* *
402892 ATGATATAGGCG-TGATAATTGTG
1 ATGATAT-GGTGATGAT-ATGGTG
*
402915 ATGGACTTTGGTGATGATATGG-G
1 AT-GA-TATGGTGATGATATGGTG
402938 CATGATAATGGTGATGGAATATGGTG
1 -ATGAT-ATGGTGAT-G-ATATGGTG
*
402964 ATGATATAGGCG-TGATAATGGTG
1 ATGATAT-GGTGATGAT-ATGGTG
*
402987 ATGGACTATGGTGATGATATAGGCG
1 AT-GA-TATGGTGATGATAT-GGTG
403012 -TGATAATGGTGATG
1 ATGAT-ATGGTGATG
403026 GACATATTGT
Statistics
Matches: 108, Mismatches: 9, Indels: 35
0.71 0.06 0.23
Matches are distributed among these distances:
22 6 0.06
23 38 0.35
24 30 0.28
25 33 0.31
26 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.32
Consensus pattern (22 bp):
ATGATATGGTGATGATATGGTG
Found at i:405032 original size:15 final size:16
Alignment explanation
Indices: 405012--405047 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
405002 AATATGGAAG
405012 AAGAAAGGAAAT-GAT
1 AAGAAAGGAAATAGAT
405027 AAGAAAGGAAATAGAT
1 AAGAAAGGAAATAGAT
405043 -AGAAA
1 AAGAAA
405048 TGTTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (16 bp):
AAGAAAGGAAATAGAT
Found at i:408694 original size:35 final size:36
Alignment explanation
Indices: 408629--408696 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
408619 ATACAATCTG
*
408629 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTAAATCATCACCATAT
* *
408665 TCCATCACCA-TATCTCGCCTAAATTATCACCA
1 TCCATCACCATTATCACGCCTAAATCATCACCA
408697 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTAAATCATCACCATAT
Found at i:409178 original size:14 final size:15
Alignment explanation
Indices: 409143--409171 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
409133 AATTTGGAGT
409143 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
409158 GAAAAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
409172 TCAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAAA
Found at i:412605 original size:13 final size:11
Alignment explanation
Indices: 412564--412648 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
412554 ACAATATGTC
412564 CATCACCATTAT
1 CATCACCA-TAT
*
412576 CA-CGCCTATAT
1 CATCACC-ATAT
412587 CATCACCATAGT
1 CATCACCATA-T
412599 CCATCACCATTAT
1 -CATCACCA-TAT
*
412612 CA-CGCCTATAT
1 CATCACC-ATAT
412623 CATCACCATATT
1 CATCACCATA-T
412635 CCATCACCATAT
1 -CATCACCATAT
412647 CA
1 CA
412649 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:412608 original size:36 final size:36
Alignment explanation
Indices: 412561--412665 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
412551 GATACAATAT
412561 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
412597 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
412633 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
412666 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:416612 original size:15 final size:16
Alignment explanation
Indices: 416569--416614 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
416559 TGGAAATATA
416569 GAAATGGAAGAAGAAAG
1 GAAATGG-AGAAGAAAG
*
416586 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
416601 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
416615 TGATATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 19 0.70
16 3 0.11
17 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:418156 original size:19 final size:18
Alignment explanation
Indices: 418134--418180 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
418124 AGTGAATAAT
418134 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
418153 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
418172 AATA-AAGAA
1 AATATAAGAA
418181 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:420042 original size:23 final size:22
Alignment explanation
Indices: 420004--420046 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
419994 CAATTCCTTT
420004 ATCTTTTATTTATCTTGTTTTA
1 ATCTTTTATTTATCTTGTTTTA
*
420026 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTATTTATCTTGTTT
420047 CCAGTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTATTTATCTTGTTTTA
Found at i:420428 original size:18 final size:18
Alignment explanation
Indices: 420390--420447 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
420380 TTCTATTTTT
*
420390 AAAAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAAGCC
420408 AAAAAAAAAACAAAAA-CC
1 AAAAAAAAAA-AAAAAGCC
***
420426 AAAAAAGCCAAAAAAGCC
1 AAAAAAAAAAAAAAAGCC
420444 AAAA
1 AAAA
420448 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.15
18 24 0.71
19 5 0.15
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGCC
Found at i:420431 original size:9 final size:9
Alignment explanation
Indices: 420419--420447 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
420409 AAAAAAAAAC
420419 AAAAA-CCA
1 AAAAAGCCA
420427 AAAAAGCCA
1 AAAAAGCCA
420436 AAAAAGCCA
1 AAAAAGCCA
420445 AAA
1 AAA
420448 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.72, C:0.21, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAGCCA
Found at i:423824 original size:19 final size:20
Alignment explanation
Indices: 423782--423833 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
423772 GAAACCCCTT
*
423782 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-TTTTTAA
423803 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
423822 TGAAGATACATG
1 TGAAAATACATG
423834 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:425577 original size:15 final size:16
Alignment explanation
Indices: 425546--425582 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
425536 CTTTATTATC
425546 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
425562 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
425577 TTATTT
1 TTATTT
425583 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:425947 original size:9 final size:9
Alignment explanation
Indices: 425933--425978 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
425923 CTATTTTTTT
425933 CAAAAAAAA
1 CAAAAAAAA
425942 CAAAAAAAA
1 CAAAAAAAA
425951 -AACAAAAAA
1 CAA-AAAAAA
425960 GGC-AAAAAAA
1 --CAAAAAAAA
425970 CAAAAAAAA
1 CAAAAAAAA
425979 AGCCAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 3 0.09
9 22 0.69
10 6 0.19
11 1 0.03
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:425979 original size:11 final size:11
Alignment explanation
Indices: 425934--425959 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
425924 TATTTTTTTC
425934 AAAAAAAACAA
1 AAAAAAAACAA
425945 AAAAAAAACAA
1 AAAAAAAACAA
425956 AAAA
1 AAAA
425960 GGCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:425980 original size:20 final size:18
Alignment explanation
Indices: 425934--425986 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
425924 TATTTTTTTC
425934 AAAAAAAA-CAAAAAAAA
1 AAAAAAAAGCAAAAAAAA
425951 AACAAAAAAGGCAAAAAAACA
1 AA-AAAAAA-GCAAAAAAA-A
425972 AAAAAAAAGCCAAAA
1 AAAAAAAAG-CAAAA
425987 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.06
18 6 0.19
19 1 0.03
20 19 0.61
21 3 0.10
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCAAAAAAAA
Found at i:425993 original size:28 final size:28
Alignment explanation
Indices: 425930--425996 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
425920 TTGCTATTTT
425930 TTTCAAAAAAAACAAAAAAAAAACAAAAA
1 TTTC-AAAAAAACAAAAAAAAAACAAAAA
*** * *
425959 AGGCAAAAAAACAAAAAAAAAGCCAAAA
1 TTTCAAAAAAACAAAAAAAAAACAAAAA
425987 TTTCAAAAAA
1 TTTCAAAAAA
425997 TTGCAAACGA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.75, C:0.12, G:0.04, T:0.09
Consensus pattern (28 bp):
TTTCAAAAAAACAAAAAAAAAACAAAAA
Found at i:430285 original size:15 final size:16
Alignment explanation
Indices: 430254--430290 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
430244 CTTTATTATC
430254 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
430270 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
430285 TTATTT
1 TTATTT
430291 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:432322 original size:20 final size:20
Alignment explanation
Indices: 432297--432352 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
432287 ATCTTCATTT
432297 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
432317 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
432337 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
432353 AAGGGATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:433227 original size:14 final size:14
Alignment explanation
Indices: 433204--433249 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
433194 TTTGGAGTGC
433204 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
*
433219 AAAAGAAGAATA-A
1 AAAAGAAGAAAAGA
*
433232 AAAA-AAGCAAAGA
1 AAAAGAAGAAAAGA
433245 AAAAG
1 AAAAG
433250 TGAAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:433259 original size:26 final size:27
Alignment explanation
Indices: 433202--433259 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
433192 AATTTGGAGT
*
433202 GCAAAAGAAAGAAAAGAAAAAGAAGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
* * *
433229 -TAAAAAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAAAAAGAAAAGAAAAAGAAGAA
433254 GCAAAA
1 GCAAAA
433260 TTGCAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.72, C:0.05, G:0.19, T:0.03
Consensus pattern (27 bp):
GCAAAAAAAAGAAAAGAAAAAGAAGAA
Found at i:436802 original size:33 final size:33
Alignment explanation
Indices: 436723--436826 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
436713 ATACAATCTG
* *
436723 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
436759 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
436792 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
436825 TC
1 TC
436827 ATTCATCAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:437735 original size:23 final size:24
Alignment explanation
Indices: 437709--437762 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
437699 AAATTCAGCA
*
437709 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
*
437732 AAGAAATTAAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
437756 AAGAAAA
1 AAGAAAA
437763 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:444332 original size:13 final size:12
Alignment explanation
Indices: 444313--444398 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
444303 ATATAGGCGT
444313 GATATGGTGATG
1 GATATGGTGATG
444325 GAATATGGTGAT-
1 G-ATATGGTGATG
*
444337 GATATAGGCG-T-
1 GATAT-GGTGATG
444348 GATAATGGTGATG
1 GAT-ATGGTGATG
444361 GACTATGGTGAT-
1 GA-TATGGTGATG
*
444373 GATATAGGCG-T-
1 GATAT-GGTGATG
444384 GATAATGGTGATG
1 GAT-ATGGTGATG
444397 GA
1 GA
444399 CAAATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:444368 original size:36 final size:36
Alignment explanation
Indices: 444295--444399 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
444285 ATTTATAAGT
* *
444295 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
444330 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
444366 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
444400 AAATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:453247 original size:23 final size:23
Alignment explanation
Indices: 453215--453259 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
453205 TAATATATAT
453215 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
*
453239 ATATG-AAATAAGTATCTATAA
1 ATATGAAAATAACTATCTATAA
453260 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:456686 original size:13 final size:12
Alignment explanation
Indices: 456667--456824 Score: 88
Period size: 13 Copynumber: 13.2 Consensus size: 12
456657 ATATAGGCGT
456667 GATATGGTGATG
1 GATATGGTGATG
456679 GAATATGGTGAT-
1 G-ATATGGTGATG
*
456691 GATATAGGCG-T-
1 GATAT-GGTGATG
456702 GATAATGGTGATG
1 GAT-ATGGTGATG
456715 GACTATGGTGAT-
1 GA-TATGGTGATG
*
456727 GATATGG-G-CG
1 GATATGGTGATG
456737 TGATAATGGTGATG
1 -GAT-ATGGTGATG
456751 GAATATGGTGAT-
1 G-ATATGGTGATG
*
456763 GATATAGGCG-T-
1 GATAT-GGTGATG
456774 GATAATGGTGATG
1 GAT-ATGGTGATG
456787 GACTATGGTGAT-
1 GA-TATGGTGATG
*
456799 GATATAGGCG-T-
1 GATAT-GGTGATG
456810 GATAATGGTGATG
1 GAT-ATGGTGATG
456823 GA
1 GA
456825 CAGATTGTAT
Statistics
Matches: 117, Mismatches: 8, Indels: 41
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.01
11 40 0.34
12 29 0.25
13 42 0.36
14 5 0.04
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:456722 original size:36 final size:36
Alignment explanation
Indices: 456649--456825 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
456639 ATTTATAAGT
* *
456649 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
456684 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
456720 TGGTGATGATATGGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
456756 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
456792 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
456826 AGATTGTATC
Statistics
Matches: 135, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.15
36 115 0.85
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:456818 original size:23 final size:24
Alignment explanation
Indices: 456649--456822 Score: 93
Period size: 23 Copynumber: 7.3 Consensus size: 24
456639 ATTTATAAGT
* *
456649 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATAGGGTGATGATA
*
456671 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
456695 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
*
456720 TGGTGATGATAT-GGGCG-TGATAA
1 TGGTGATGATATAGGGTGATGAT-A
*
456743 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
456767 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
456792 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
456815 TGGTGATG
1 TGGTGATG
456823 GACAGATTGT
Statistics
Matches: 121, Mismatches: 11, Indels: 39
0.71 0.06 0.23
Matches are distributed among these distances:
22 11 0.09
23 45 0.37
24 28 0.23
25 30 0.25
26 2 0.02
27 5 0.04
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (24 bp):
TGGTGATGATATAGGGTGATGATA
Found at i:460724 original size:13 final size:12
Alignment explanation
Indices: 460705--460862 Score: 88
Period size: 13 Copynumber: 13.2 Consensus size: 12
460695 ATATAGGCGT
460705 GATATGGTGATG
1 GATATGGTGATG
460717 GAATATGGTGAT-
1 G-ATATGGTGATG
*
460729 GATATAGG-CAT-
1 GATAT-GGTGATG
460740 GATAATGGTGATG
1 GAT-ATGGTGATG
460753 GACTATGGTGAT-
1 GA-TATGGTGATG
*
460765 GATATGG-G-CG
1 GATATGGTGATG
460775 TGATAATGGTGATG
1 -GAT-ATGGTGATG
460789 GAATATGGTGAT-
1 G-ATATGGTGATG
*
460801 GATATAGGCG-T-
1 GATAT-GGTGATG
460812 GATAATGGTGATG
1 GAT-ATGGTGATG
460825 GACTATGGTGAT-
1 GA-TATGGTGATG
*
460837 GATATCGGCG-T-
1 GATAT-GGTGATG
460848 GATAATGGTGATG
1 GAT-ATGGTGATG
460861 GA
1 GA
460863 CAGATTGTAT
Statistics
Matches: 117, Mismatches: 8, Indels: 41
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.01
11 40 0.34
12 29 0.25
13 42 0.36
14 5 0.04
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:460760 original size:36 final size:36
Alignment explanation
Indices: 460687--460863 Score: 293
Period size: 36 Copynumber: 4.9 Consensus size: 36
460677 ATTTATAAGT
* *
460687 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
460722 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
460758 TGGTGATGATATGGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
460794 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
460830 TGGTGATGATATCGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
460864 AGATTGTATC
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.14
36 113 0.86
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:460856 original size:23 final size:22
Alignment explanation
Indices: 460687--460860 Score: 97
Period size: 23 Copynumber: 7.4 Consensus size: 22
460677 ATTTATAAGT
*
460687 TGGTGATAATATAGGCG-TGATA
1 TGGTGATGATAT-GGCGATGATA
*
460709 TGGTGATGGAATATGGTGATGATA
1 TGGTGAT-G-ATATGGCGATGATA
* *
460733 TAGG-CATGATAATGGTGATGGACTA
1 T-GGTGATGAT-ATGGCGAT-GA-TA
460758 TGGTGATGATATGGGCG-TGATAA
1 TGGTGATGATAT-GGCGATGAT-A
*
460781 TGGTGATGGAATATGGTGATGATA
1 TGGTGAT-G-ATATGGCGATGATA
* *
460805 TAGGCG-TGATAATGGTGATGGACTA
1 T-GGTGATGAT-ATGGCGAT-GA-TA
460830 TGGTGATGATATCGGCG-TGATAA
1 TGGTGATGATAT-GGCGATGAT-A
460853 TGGTGATG
1 TGGTGATG
460861 GACAGATTGT
Statistics
Matches: 123, Mismatches: 9, Indels: 39
0.72 0.05 0.23
Matches are distributed among these distances:
22 13 0.11
23 42 0.34
24 34 0.28
25 34 0.28
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (22 bp):
TGGTGATGATATGGCGATGATA
Found at i:466677 original size:36 final size:36
Alignment explanation
Indices: 466637--466776 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
466627 ATACAATCTT
*
466637 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
466673 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
466709 TTCATCCCCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
466745 TCCACCACCA-TATCATGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
466777 AATTATAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
35 20 0.21
36 74 0.79
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:470794 original size:13 final size:11
Alignment explanation
Indices: 470774--470945 Score: 113
Period size: 13 Copynumber: 14.5 Consensus size: 11
470764 GTTATTGGCG
470774 TGATATGGTGA
1 TGATATGGTGA
470785 TGGAATATGGTGA
1 T-G-ATATGGTGA
470798 TGATATATGCGTGA
1 TG--ATATG-GTGA
470812 T-A-ATGGTGA
1 TGATATGGTGA
470821 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
470834 TGATATAGGCG-
1 TGATAT-GGTGA
470845 TGATAATGGTGA
1 TGAT-ATGGTGA
470857 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
470870 TGATATAGGCG-
1 TGATAT-GGTGA
470881 TGATAATGGTGA
1 TGAT-ATGGTGA
*
470893 TGGACTATGGTAA
1 T-GA-TATGGTGA
470906 TGATATAGGTG-
1 TGATAT-GGTGA
470917 TGAT-TGGTGA
1 TGATATGGTGA
470927 TGGACTATGGTGA
1 T-GA-TATGGTGA
470940 TGATAT
1 TGATAT
470946 ATGCGTGATA
Statistics
Matches: 131, Mismatches: 7, Indels: 46
0.71 0.04 0.25
Matches are distributed among these distances:
9 9 0.07
10 5 0.04
11 35 0.27
12 26 0.20
13 49 0.37
14 7 0.05
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:470819 original size:23 final size:24
Alignment explanation
Indices: 470776--470978 Score: 121
Period size: 23 Copynumber: 8.5 Consensus size: 24
470766 TATTGGCGTG
470776 ATATGGTGATGGAATATGGTGATGAT
1 ATATGGTGAT-G-ATATGGTGATGAT
470802 ATATGCGTGAT-A-ATGGTGATGGA-
1 ATATG-GTGATGATATGGTGAT-GAT
* *
470825 CTATGGTGATGATATAGGCG-TGAT
1 ATATGGTGATGATAT-GGTGATGAT
470849 A-ATGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
*
470874 ATA-GGCG-TGATAATGGTGATGGA-
1 ATATGGTGATGAT-ATGGTGAT-GAT
* *
470897 CTATGGTAATGATATAGGTG-TG--
1 ATATGGTGATGATAT-GGTGATGAT
470919 AT-TGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
*
470944 ATATGCGTGAT-A-ATGGAGATGGAT
1 ATATG-GTGATGATATGGTGAT-GAT
470968 -TATGGTGATGA
1 ATATGGTGATGA
470979 AAATAGTATC
Statistics
Matches: 142, Mismatches: 11, Indels: 51
0.70 0.05 0.25
Matches are distributed among these distances:
21 6 0.04
22 18 0.13
23 53 0.37
24 22 0.15
25 25 0.18
26 8 0.06
27 10 0.07
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (24 bp):
ATATGGTGATGATATGGTGATGAT
Found at i:470830 original size:36 final size:36
Alignment explanation
Indices: 470760--470978 Score: 336
Period size: 36 Copynumber: 6.2 Consensus size: 36
470750 AATGGAAGGA
* * *
470760 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
*
470795 TGATGATATATGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
470831 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
470867 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
* *
470903 TAATGATATAGGTGTGAT--TGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
* * *
470937 TGATGATATATGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
470973 TGATGA
1 TGATGA
470979 AAATAGTATC
Statistics
Matches: 169, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
34 31 0.18
35 15 0.09
36 123 0.73
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:470952 original size:106 final size:106
Alignment explanation
Indices: 470760--470978 Score: 332
Period size: 106 Copynumber: 2.1 Consensus size: 106
470750 AATGGAAGGA
* * * *
470760 TGATGTTATTGGCGTGATATGGTGATGGAATATGGTGATGATATATGCGTGATAATGGTGATGGA
1 TGATGATATAGGCGTGATATGGTGATGGAATATGGTAATGATATAGGCGTGAT-ATGGTGATGGA
*
470825 CTATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGG
65 CTATGGTGATGATATAGGCGTGATAATGGAGATGGACTATGG
* *
470867 TGATGATATAGGCGTGATAATGGTGATGGACTATGGTAATGATATAGGTGTGAT-TGGTGATGGA
1 TGATGATATAGGCGTGAT-ATGGTGATGGAATATGGTAATGATATAGGCGTGATATGGTGATGGA
* *
470931 CTATGGTGATGATATATGCGTGATAATGGAGATGGATTATGG
65 CTATGGTGATGATATAGGCGTGATAATGGAGATGGACTATGG
470973 TGATGA
1 TGATGA
470979 AAATAGTATC
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 55 0.54
107 16 0.16
108 31 0.30
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.33
Consensus pattern (106 bp):
TGATGATATAGGCGTGATATGGTGATGGAATATGGTAATGATATAGGCGTGATATGGTGATGGAC
TATGGTGATGATATAGGCGTGATAATGGAGATGGACTATGG
Found at i:471365 original size:19 final size:20
Alignment explanation
Indices: 471318--471368 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
471308 GAAACCCCTT
**
471318 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
471338 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
471357 TGAAGATACATG
1 TGAAAATACATG
471369 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:471853 original size:14 final size:15
Alignment explanation
Indices: 471819--471865 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
471809 AATTTGGAGT
471819 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
471834 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
471848 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
471865 G
1 G
471866 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:479945 original size:19 final size:21
Alignment explanation
Indices: 479921--479972 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
479911 CGGCCAAGAG
*
479921 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
479940 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
479961 CATGTATTTTCA
1 CATGTATTTTCA
479973 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:488405 original size:12 final size:10
Alignment explanation
Indices: 488383--488430 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
488373 TTTTGGCTTA
488383 TTTTGTTTTT
1 TTTTGTTTTT
488393 TTTTGCCTTTTT
1 TTTTG--TTTTT
488405 TTTTGTTTTT
1 TTTTGTTTTT
*
488415 TTTTTTTGTTT
1 TTTTGTT-TTT
488426 TTTTG
1 TTTTG
488431 AAAAAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 16 0.48
11 7 0.21
12 10 0.30
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:488419 original size:13 final size:13
Alignment explanation
Indices: 488400--488429 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
488390 TTTTTTTGCC
488400 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
488413 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
488426 TTTT
1 TTTT
488430 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:492140 original size:30 final size:31
Alignment explanation
Indices: 492088--492147 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
492078 CTTAGCTTCA
**
492088 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
492118 TATTATGTTTTCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
492148 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:493013 original size:19 final size:20
Alignment explanation
Indices: 492989--493039 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
492979 CGGCCAAGAG
* *
492989 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
493008 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
493028 CATGTATTTTCA
1 CATGTATTTTCA
493040 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:493796 original size:17 final size:18
Alignment explanation
Indices: 493747--493810 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 18
493737 AATTGGAGTG
* **
493747 CAAAAAGAACGAAAAAGA
1 CAAAAAGAAAGAAAAATT
493765 C-AAAAGAAGAGAAAAA-T
1 CAAAAAGAA-AGAAAAATT
493782 CAGAAAAGAAA-AAAAATT
1 CA-AAAAGAAAGAAAAATT
493800 CAAAAAGAAAG
1 CAAAAAGAAAG
493811 CAAGCCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 21 0.54
18 11 0.28
19 7 0.18
ACGTcount: A:0.72, C:0.08, G:0.16, T:0.05
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAATT
Found at i:496183 original size:30 final size:31
Alignment explanation
Indices: 496131--496190 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
496121 CTTAGCTTTA
**
496131 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
496161 TATTATGTTTTCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
496191 GACAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:497124 original size:19 final size:20
Alignment explanation
Indices: 497100--497150 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
497090 CGGCCAATAG
* *
497100 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
497119 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
497139 CATGTATTTTCA
1 CATGTATTTTCA
497151 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:512052 original size:13 final size:13
Alignment explanation
Indices: 512036--512060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
512026 TTTTTTTGCC
512036 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
512049 TTTTTTTGTTTT
1 TTTTTTTGTTTT
512061 TTTGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:527860 original size:18 final size:18
Alignment explanation
Indices: 527830--527882 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 18
527820 TTATTAAAAT
527830 GGAATATGA-AAGAGGAAA
1 GGAA-ATGATAAGAGGAAA
527848 GGAAATGATAAGAAAGAGGAAA
1 GGAAATGAT----AAGAGGAAA
527870 GGAAATGATAAGA
1 GGAAATGATAAGA
527883 AAGAAAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
22 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.32, T:0.11
Consensus pattern (18 bp):
GGAAATGATAAGAGGAAA
Found at i:527864 original size:22 final size:22
Alignment explanation
Indices: 527837--527886 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
527827 AATGGAATAT
527837 GAAAGAGGAAAGGAAATGATAA
1 GAAAGAGGAAAGGAAATGATAA
527859 GAAAGAGGAAAGGAAATGATAA
1 GAAAGAGGAAAGGAAATGATAA
527881 GAAAGA
1 GAAAGA
527887 AAATGGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (22 bp):
GAAAGAGGAAAGGAAATGATAA
Found at i:528076 original size:35 final size:35
Alignment explanation
Indices: 528036--528151 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
528026 TGGTAAGGTA
**
528036 ATGGTGATGATATAGGTTTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* *
528071 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* **
528106 ATGGTGATGTTATAGGCGTGAAAATGGTGATTTAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATAGAAG
528142 ATGGTGATGA
1 ATGGTGATGA
528152 ACATATATTG
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 50 0.70
36 21 0.30
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.30
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:528935 original size:35 final size:37
Alignment explanation
Indices: 528889--528968 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
528879 TTTGAGAATT
**
528889 TGGTGATGATATAGGCGTGAT-AT-GTTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
528924 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
528961 TGGTGATG
1 TGGTGATG
528969 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 2 0.05
37 17 0.44
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.34
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:532282 original size:15 final size:16
Alignment explanation
Indices: 532231--532283 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
532221 AGATAGTGAA
532231 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
532248 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
532265 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
532280 ATAA
1 ATAA
532284 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:532860 original size:11 final size:11
Alignment explanation
Indices: 532838--532884 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
532828 TTTGAGAATT
532838 TGGTGATGATA
1 TGGTGATGATA
532849 TAGGTG-TGATA
1 T-GGTGATGATA
532860 TGGTGATGGACTA
1 TGGTGAT-GA-TA
532873 TGGTGATGATA
1 TGGTGATGATA
532884 T
1 T
532885 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:532866 original size:22 final size:24
Alignment explanation
Indices: 532838--532884 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
532828 TTTGAGAATT
532838 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
532860 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
532884 T
1 T
532885 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:532884 original size:35 final size:37
Alignment explanation
Indices: 532838--532917 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
532828 TTTGAGAATT
* *
532838 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
532873 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
532910 TGGTGATG
1 TGGTGATG
532918 GAAATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:533303 original size:19 final size:20
Alignment explanation
Indices: 533256--533306 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
533246 GAAACCCCTT
**
533256 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
533276 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
533295 TGAAGATACATG
1 TGAAAATACATG
533307 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:537298 original size:36 final size:36
Alignment explanation
Indices: 537251--537355 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
537241 GATTGAATCT
* *
537251 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
537287 GTCCATCACCATTATCACGCCAATATTATCACCATA
1 GTCCATCACCATTATCACGCCTATATTATCACCATA
*
537323 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATTATCACCA
537356 ACTTATAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATTATCACCATA
Found at i:541049 original size:19 final size:20
Alignment explanation
Indices: 541025--541070 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
541015 CGGCCAAGAG
**
541025 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
541044 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
541064 CATGTAT
1 CATGTAT
541071 TTTTAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:542949 original size:17 final size:17
Alignment explanation
Indices: 542927--542976 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
542917 GTAGGAGTCT
542927 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
542944 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
* *
542962 TTTTTTTTTTGTTGT
1 TTTTCTTTTTCTTGT
542977 AGCACTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:543388 original size:36 final size:36
Alignment explanation
Indices: 543347--543495 Score: 210
Period size: 36 Copynumber: 4.1 Consensus size: 36
543337 ATTTATAAGT
* * *
543347 TGGTGATAATATAGGCGTGAAAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
543383 TGGTGATGATATAGGCGTGATAATGGAGAT-GAACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA-TA
* * *
543419 TAGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
543455 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
543491 TGGTG
1 TGGTG
543496 TTGGACAGAT
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
35 3 0.03
36 94 0.95
37 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:543408 original size:23 final size:22
Alignment explanation
Indices: 543382--543485 Score: 68
Period size: 25 Copynumber: 4.4 Consensus size: 22
543372 GTGGTGGAAT
543382 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGG-GTGATA
* *
543405 ATGGAGATGAACTATAGTGATGATA
1 ATGGTGATG-A-TATAG-GGTGATA
* * *
543430 AAGGCG-TGATA-ATGGTGATGGA
1 ATGGTGATGATATAGGGTGAT--A
543452 CTATGGTGATGATATAGGCGTGATA
1 --ATGGTGATGATATAGG-GTGATA
543477 ATGGTGATG
1 ATGGTGATG
543486 GAAGATGGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
20 5 0.08
21 1 0.02
22 3 0.05
23 18 0.29
24 7 0.11
25 20 0.32
26 3 0.05
27 5 0.08
ACGTcount: A:0.32, C:0.05, G:0.35, T:0.29
Consensus pattern (22 bp):
ATGGTGATGATATAGGGTGATA
Found at i:547741 original size:34 final size:32
Alignment explanation
Indices: 547688--547757 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
547678 CCTTACAAAC
*
547688 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
547720 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
547754 TCCC
1 TCCC
547758 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Done.