Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005899.1 Hibiscus syriacus cultivar Beakdansim tig00013857_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: 72961
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3488 original size:73 final size:73
Alignment explanation
Indices: 3240--3657 Score: 435
Period size: 75 Copynumber: 5.8 Consensus size: 73
3230 TTCAACATAT
* * **
3240 CCGGTAGGTAGTTTAATGTATTAGGTAGCG-C-A-TAATTTACCGTTTACATTATTAGCAA-CTT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAATCTT
* *
3301 TCAAACAA
66 TAAAAAAA
*
3309 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTACCGTTTACATTATTAACAATCTT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAATCTT
*
3373 AAAAAAAA
66 TAAAAAAA
* * * * *
3381 GCGGTAGGTATTTTAATG---TAGGTAGCGCCTATTTTATTTATCATTTACATTATCA-CAATAT
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT-TTTACCGTTTACATTATTAGCAATCT
*
3442 TTAAACAAA
65 TTAAAAAAA
* *
3451 CCGATAGCTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTTACCGTTTACATTATTAGCAA
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA----TTTTTTTACCGTTTACATTATTAGCAA
* *
3516 -CCTT-CAAAAA
62 TCTTTAAAAAAA
** * * * * * *
3526 CCGGTATATAATTTAATATAATAGGTAACACCTATTTTTTTTTACCGTTTACATCATTAGCAACC
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA--TTTTTTTACCGTTTACATTATTAGCAATC
*
3591 TTCAAAAAAA
64 TTTAAAAAAA
* *
3601 CCGGTAGGTACTTTAATGTAATAGGTAGCGCCTATTTTTTTACTGTTTACATTATTA
1 CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTA
3658 ACCATTTTTA
Statistics
Matches: 290, Mismatches: 44, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
69 41 0.14
70 31 0.11
71 40 0.14
72 25 0.09
73 62 0.21
74 2 0.01
75 64 0.22
76 18 0.06
77 7 0.02
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (73 bp):
CCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAATCTT
TAAAAAAA
Found at i:3548 original size:75 final size:73
Alignment explanation
Indices: 3275--3657 Score: 390
Period size: 73 Copynumber: 5.3 Consensus size: 73
3265 TAGCGCATAA
* *
3275 TTTACCGTTTACATTATTAGCAACTTTCAAACAACCGGTAGGTATTTTAATGTAATAGGTAGCGC
1 TTTACCGTTTACATTATTAGCAACCTTCAAA-AACCGGTAGGTAATTTAATGTAATAGGTAGCGC
3340 CTA---TTT
65 CTATTTTTT
* * * * *
3346 TTTACCGTTTACATTATTAACAATCTTAAAAAAAAGCGGTAGGTATTTTAATG---TAGGTAGCG
1 TTTACCGTTTACATTATTAGCAACCTT--CAAAAACCGGTAGGTAATTTAATGTAATAGGTAGCG
*
3408 CCTA-TTTTA
64 CCTATTTTTT
* * * ** * * * *
3417 TTTATCATTTACATTATCA-CAATATTTAAACAAACCGATAGCTATTTTAATGTAATAGGTAGCG
1 TTTACCGTTTACATTATTAGCAA-CCTTCAA-AAACCGGTAGGTAATTTAATGTAATAGGTAGCG
3481 CCTATTTTTTTT
64 CCTA--TTTTTT
** * * *
3493 TTTACCGTTTACATTATTAGCAACCTTCAAAAACCGGTATATAATTTAATATAATAGGTAACACC
1 TTTACCGTTTACATTATTAGCAACCTTCAAAAACCGGTAGGTAATTTAATGTAATAGGTAGCGCC
3558 TATTTTTT
66 TATTTTTT
* *
3566 TTTACCGTTTACATCATTAGCAACCTTCAAAAAAACCGGTAGGTACTTTAATGTAATAGGTAGCG
1 TTTACCGTTTACATTATTAGCAACCTTC--AAAAACCGGTAGGTAATTTAATGTAATAGGTAGCG
3631 CCTA--TTTT
64 CCTATTTTTT
*
3639 TTTACTGTTTACATTATTA
1 TTTACCGTTTACATTATTA
3658 ACCATTTTTA
Statistics
Matches: 260, Mismatches: 37, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
69 16 0.06
70 21 0.08
71 44 0.17
72 19 0.07
73 70 0.27
75 63 0.24
76 24 0.09
77 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (73 bp):
TTTACCGTTTACATTATTAGCAACCTTCAAAAACCGGTAGGTAATTTAATGTAATAGGTAGCGCC
TATTTTTT
Found at i:3632 original size:150 final size:147
Alignment explanation
Indices: 3274--3641 Score: 419
Period size: 142 Copynumber: 2.5 Consensus size: 147
3264 GTAGCGCATA
* *
3274 ATTTACCGTTTACATTATTAGCAACTTTC-AAACAACCGGTAGGTATTTTAATGTAATAGGTAGC
1 ATTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGC
* * * *
3338 GCCTA-----TTTTTTACCGTTTACATTATTAACAATCTTAAAAAAAAGCGGTAGGTATTTTAAT
66 GCCTATTTTTTTTTTTACCGTTTACATTATTAACAACCTT-AAAAAAACCGGTAGATATTTAAAT
* * *
3398 GTAGGTAGCGCCTATTTT
130 ATAGGTAACACCTATTTT
* * * * * * * *
3416 ATTTATCATTTACATTATCA-CAATATTTAAACAAACCGATAGCTATTTTAATGTAATAGGTAGC
1 ATTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGC
* * *
3480 GCCTATTTTTTTTTTTACCGTTTACATTATTAGCAACCTT-CAAAAACCGGTATATAATTTAATA
66 GCCTATTTTTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACCGGTAGAT-ATTTAA-A
3544 TAATAGGTAACACCTATTTTT
129 T-ATAGGTAACACCTA-TTTT
* * * *
3565 TTTTACCGTTTACATCATTAGCAACCTTCAAAAAAACCGGTAGGTACTTTAATGTAATAGGTAGC
1 ATTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGC
3630 GCCTATTTTTTT
66 GCCTATTTTTTT
3642 ACTGTTTACA
Statistics
Matches: 183, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
141 5 0.03
142 53 0.29
145 11 0.06
146 5 0.03
147 30 0.16
148 11 0.06
149 19 0.10
150 49 0.27
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (147 bp):
ATTTACCGTTTACATTATTAGCAACATTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGC
GCCTATTTTTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACCGGTAGATATTTAAATA
TAGGTAACACCTATTTT
Found at i:9390 original size:41 final size:41
Alignment explanation
Indices: 9341--9419 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
9331 GCAATGCGAT
* *
9341 TTTGAAAAATATGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAACATGTTGCGATAGTTAAAAAGTGTTGCGAGAG
*
9382 TTTGAAAAACGTGTTGCGATAGTTAAAAAGTGTTGCGA
1 TTTGAAAAACATGTTGCGATAGTTAAAAAGTGTTGCGA
9420 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTGAAAAACATGTTGCGATAGTTAAAAAGTGTTGCGAGAG
Found at i:9395 original size:22 final size:20
Alignment explanation
Indices: 9345--9430 Score: 104
Period size: 19 Copynumber: 4.3 Consensus size: 20
9335 TGCGATTTTG
*
9345 AAAAATATGTTGCGATAGTT
1 AAAAATGTGTTGCGATAGTT
*
9365 -AAAATGTGTTGCGAGAGTTT
1 AAAAATGTGTTGCGATAG-TT
*
9385 GAAAAACGTGTTGCGATAGTT
1 -AAAAATGTGTTGCGATAGTT
*
9406 AAAAA-GTGTTGCGATAGTG
1 AAAAATGTGTTGCGATAGTT
9425 AAAAAT
1 AAAAAT
9431 CCAAAATAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
19 33 0.58
20 7 0.12
21 2 0.04
22 15 0.26
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTT
Found at i:9514 original size:94 final size:93
Alignment explanation
Indices: 9406--9580 Score: 341
Period size: 94 Copynumber: 1.9 Consensus size: 93
9396 TGCGATAGTT
9406 AAAAAGTGTTGCGATAGTGAAAAATCCAAAATAAGTTTACATTTTAACTATTCCAAATTCACGTG
1 AAAAAGTGTTGCGATAGTGAAAAATCCAAAATAAGTTTACATTTTAACTATTCCAAATTCACGTG
9471 GAGTTTGAAACAATAATGCGAGAGTTTG
66 GAGTTTGAAACAATAATGCGAGAGTTTG
9499 AAAAACGTGTTGCGATAGTGAAAAATCCAAAATAAGTTTACATTTTAACTATTCCAAATTCACGT
1 AAAAA-GTGTTGCGATAGTGAAAAATCCAAAATAAGTTTACATTTTAACTATTCCAAATTCACGT
9564 GGAGTTTGAAACAATAA
65 GGAGTTTGAAACAATAA
9581 AGAATGTGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 5 0.06
94 76 0.94
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (93 bp):
AAAAAGTGTTGCGATAGTGAAAAATCCAAAATAAGTTTACATTTTAACTATTCCAAATTCACGTG
GAGTTTGAAACAATAATGCGAGAGTTTG
Found at i:9877 original size:21 final size:21
Alignment explanation
Indices: 9843--9963 Score: 112
Period size: 21 Copynumber: 6.0 Consensus size: 21
9833 ACCAGTCGTT
*
9843 GCGATTTTGG-AAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
9863 GCGGATTTGGAAAAT----AC
1 GCGAATTTGGAAAATCGCAAC
9880 GCGAATTTGG-AAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
9900 GTGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
* *
9921 GCGAACTT-GAACTATCGCAAC
1 GCGAATTTGGAA-AATCGCAAC
* **
9942 GCGAACTTGGACTATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
9963 G
1 G
9964 AATTTGAACT
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.05
17 11 0.13
20 22 0.26
21 46 0.54
22 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:9898 original size:37 final size:37
Alignment explanation
Indices: 9843--9914 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
9833 ACCAGTCGTT
* *
9843 GCGATTTTGGAAATCGCAACGCGGATTTGGAAAATAC
1 GCGAATTTGGAAATCGCAACGCGAATTTGGAAAATAC
*
9880 GCGAATTTGGAAATCGCAACGTGAATTTGGAAAAT
1 GCGAATTTGGAAATCGCAACGCGAATTTGGAAAAT
9915 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (37 bp):
GCGAATTTGGAAATCGCAACGCGAATTTGGAAAATAC
Found at i:10039 original size:20 final size:20
Alignment explanation
Indices: 10014--10062 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
10004 TTGTATTATT
10014 GCGTTGCGATAGTCAAAATC
1 GCGTTGCGATAGTCAAAATC
*
10034 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAAAATC
10054 GCGTTGCGA
1 GCGTTGCGA
10063 ATCTGAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAAATC
Found at i:10100 original size:20 final size:19
Alignment explanation
Indices: 10077--10122 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
10067 GAAAACTGAT
* *
10077 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
10097 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
10116 TTGCGAT
1 TTGCGAT
10123 TTTGTTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:10112 original size:19 final size:19
Alignment explanation
Indices: 10088--10124 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10078 TGCGATACTG
*
10088 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
10107 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
10125 TGTTAGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:12275 original size:25 final size:25
Alignment explanation
Indices: 12241--12297 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
12231 CAGGAAACAA
12241 AAACTTCAGATAGATATAAGTCTTG
1 AAACTTCAGATAGATATAAGTCTTG
12266 AAACTTCAGATAGATATAAGTCTTG
1 AAACTTCAGATAGATATAAGTCTTG
12291 AAACTTC
1 AAACTTC
12298 GTAGTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (25 bp):
AAACTTCAGATAGATATAAGTCTTG
Found at i:16860 original size:4 final size:4
Alignment explanation
Indices: 16846--16876 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16836 AGCCTCAATT
16846 ACAA A-AA ACAA ACAA ACAA ACAA ACAA ACAA
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA
16877 GAAGATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:18873 original size:33 final size:34
Alignment explanation
Indices: 18812--18878 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
18802 CGATAGGTAA
*
18812 AAATTTTAAATCCACCCCGCCCATATGTGTATAT
1 AAATTTTAAATCCACCCCACCCATATGTGTATAT
*
18846 AAATTTTAAATTCA-CCCACCCATATGTGTATAT
1 AAATTTTAAATCCACCCCACCCATATGTGTATAT
18879 TCTCAAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (34 bp):
AAATTTTAAATCCACCCCACCCATATGTGTATAT
Found at i:19605 original size:2 final size:2
Alignment explanation
Indices: 19600--19624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19590 TTTTTTGGAA
19600 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19625 GTAATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20217 original size:33 final size:36
Alignment explanation
Indices: 20180--20252 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
20170 ACCGTCACGT
*
20180 TTTAACCATGC-AA-ATAC-GTGACTGATTCAGTAC
1 TTTAACCATGCAAACATACAGTGACTGATTCAGAAC
20213 TTTAACCATGCAAACATACATGTGACTGATTCAGAAC
1 TTTAACCATGCAAACATACA-GTGACTGATTCAGAAC
20250 TTT
1 TTT
20253 TTAAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 11 0.31
34 2 0.06
35 4 0.11
37 18 0.51
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (36 bp):
TTTAACCATGCAAACATACAGTGACTGATTCAGAAC
Found at i:20648 original size:17 final size:17
Alignment explanation
Indices: 20626--20670 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
20616 ACGATCATAT
20626 AAAGTTTAAAATATTAA
1 AAAGTTTAAAATATTAA
20643 AAAGTTTAAAATATTAA
1 AAAGTTTAAAATATTAA
*
20660 AAAGTTGAAAA
1 AAAGTTTAAAA
20671 AACCCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (17 bp):
AAAGTTTAAAATATTAA
Found at i:25212 original size:20 final size:20
Alignment explanation
Indices: 25163--25251 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
25153 GATTTTCCGG
*
25163 CTATCGCAATGCGAATATGTA
1 CTATCGCAATGCGATTATG-A
* *
25184 -AATCACAATGCGATTATGA
1 CTATCGCAATGCGATTATGA
25203 CTATCGCAATGCGATTATGA
1 CTATCGCAATGCGATTATGA
*
25223 CTATCGCAACGCGATTATGA
1 CTATCGCAATGCGATTATGA
*
25243 CTGTCGCAA
1 CTATCGCAA
25252 CACTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
CTATCGCAATGCGATTATGA
Found at i:26105 original size:24 final size:24
Alignment explanation
Indices: 26073--26126 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
26063 GTATTCGAAA
26073 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
26097 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
26121 TTTGAT
1 TTTGAT
26127 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:26317 original size:5 final size:6
Alignment explanation
Indices: 26301--26327 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26291 ATATAACCCT
26301 GAAAAA GAAAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAA
26328 GAAATCCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:26340 original size:12 final size:13
Alignment explanation
Indices: 26325--26357 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
26315 AAAAGAAAAA
26325 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
26337 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
26351 GAAGAAA
1 GAAGAAA
26358 ATGCCACGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:26351 original size:14 final size:14
Alignment explanation
Indices: 26332--26358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26322 AAAGAAGAAA
26332 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
26346 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
26359 TGCCACGCGA
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:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:28425 original size:18 final size:18
Alignment explanation
Indices: 28391--28427 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28381 CAAGAAAAAG
**
28391 AAAATCAAAATTGCAATC
1 AAAATCAAAATCCCAATC
28409 AAAATCAAAATCCCAATC
1 AAAATCAAAATCCCAATC
28427 A
1 A
28428 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAAATCAAAATCCCAATC
Found at i:28739 original size:140 final size:140
Alignment explanation
Indices: 28487--28756 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
28477 AAACGTTGTA
**
28487 TTATGTGTAAACTTTTAACATTTTCAGTTAGGTATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
28552 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
28617 TATGTGTATT
131 TATGTGTATT
28627 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
28692 TGATATGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
28757 CGCAACGCGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:28752 original size:20 final size:20
Alignment explanation
Indices: 28727--28897 Score: 192
Period size: 20 Copynumber: 8.8 Consensus size: 20
28717 TTACATATTC
*
28727 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
28747 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
28767 ATTTGATTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
28787 ATTTGACTATCGCTACGTGA
1 ATTTGACTATCGCAACGCGA
* *
28807 ATTTGTCTATGGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
28826 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
28841 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* * *
28861 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
28881 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
28898 AGAAAATCAC
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.07
15 2 0.02
19 3 0.02
20 112 0.89
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:28852 original size:74 final size:74
Alignment explanation
Indices: 28755--28935 Score: 222
Period size: 74 Copynumber: 2.4 Consensus size: 74
28745 GAATTTGACT
* * * * * *
28755 ATCGCAACGCGAATTTGATTATCGCAACGTGAATTTGACTATCGCTACGTGAATTTGTCTATGGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGC
28820 AACGCA-AAA
66 AACG-AGAAA
* * *
28829 ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGC
28894 AACGAGAAA
66 AACGAGAAA
* * *
28903 ATCACAAAGC-ATATTAGACTATCGCAACGCGAA
1 ATCGCAACGCGA-ATTTGACTATCGCAACGCGAA
28936 AGTCAATTCG
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 2 0.02
74 90 0.98
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGC
AACGAGAAA
Found at i:28935 original size:94 final size:94
Alignment explanation
Indices: 28732--28913 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 94
28722 TATTCATTTG
*
28732 AATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGTGAATTTGACTAT
1 AATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTAT
* * ** ** **
28797 CGCTACGTGAATTTGTCTATGGCAACGCA
66 CGCAACGAGAAAATCACTAAAGCAACGCA
* * *
28826 AAAATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATCGCAACGGGTATTTGACTAT
1 AATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTAT
28891 CGCAACGAGAAAATCAC-AAAGCA
66 CGCAACGAGAAAATCACTAAAGCA
28914 TATTAGACTA
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
93 4 0.05
94 72 0.95
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (94 bp):
AATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTAT
CGCAACGAGAAAATCACTAAAGCAACGCA
Found at i:31165 original size:18 final size:19
Alignment explanation
Indices: 31142--31187 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
31132 GAAACTTAAA
31142 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
31160 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
31180 ATCGCAAC
1 ATCGCAAC
31188 GAGAGAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:31259 original size:20 final size:20
Alignment explanation
Indices: 31231--31298 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
31221 GCGATTCTTT
* **
31231 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
31251 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCATTTTCG
31271 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
31291 CGTTGCGA
1 CGTTGCGA
31299 AAGTAAACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:31473 original size:18 final size:18
Alignment explanation
Indices: 31446--31495 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
31436 TTTACTAAGC
31446 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
31464 AATTTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
31482 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
31496 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:33309 original size:19 final size:20
Alignment explanation
Indices: 33226--33301 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
33216 TCTGAAACTT
*
33226 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
33246 AAAATCGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
33266 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
33285 AAAATCGCAACACGAAA
1 AAAATCGCAACACGAAA
33302 CTAAAATCAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.51, C:0.20, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:33971 original size:20 final size:20
Alignment explanation
Indices: 33935--34051 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
33925 GATTGTCACC
* *
33935 ATCGCGTTGCAACAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
33955 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
33975 ATCTCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* * *
33995 ATCTCTTTGCGATAGTCATA
1 ATCGCGTTGCGATAGTCAGA
* *
34015 ATCGTGTTGCGATAGTCATA
1 ATCGCGTTGCGATAGTCAGA
* *
34035 CTCGCATTGCGATAGTC
1 ATCGCGTTGCGATAGTC
34052 GGAAAATCGC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:33983 original size:40 final size:41
Alignment explanation
Indices: 33914--34051 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 41
33904 GCGCTTTGAA
* * ** * *
33914 AATCGCATTACGATTGTCACCATCG-CGTTGCAACAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGTCGTTGCGATAGTCAG
*
33954 AATCGCGTTGCGATAGTCAGAATC-TCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGTCGTTGCGATAGTCAG
* * * *
33994 AATCTCTTTGCGATAGTCATAATCGT-GTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAGAATCGTCGTTGCGATAGTCAG
*
34034 ACTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
34052 GGAAAATCGC
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 81 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
AATCGCATTGCGATAGTCAGAATCGTCGTTGCGATAGTCAG
Found at i:36568 original size:14 final size:14
Alignment explanation
Indices: 36551--36583 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
36541 ATTTCTATGT
*
36551 AGGGAATTATTTGC
1 AGGGAATTATTTAC
36565 AGGGAATTATTTAC
1 AGGGAATTATTTAC
36579 AGGGA
1 AGGGA
36584 TTACTCCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:38010 original size:20 final size:22
Alignment explanation
Indices: 37969--38010 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
37959 CAATGAGGAA
37969 AAGGAAAGTTCTGTATGCTTTG
1 AAGGAAAGTTCTGTATGCTTTG
*
37991 AAGGAAA-TTCT-TATGGTTTG
1 AAGGAAAGTTCTGTATGCTTTG
38011 TGGGGAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.38
Consensus pattern (22 bp):
AAGGAAAGTTCTGTATGCTTTG
Found at i:38449 original size:22 final size:22
Alignment explanation
Indices: 38405--38445 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
38395 TGTCCCCAAC
*
38405 TTTGGTTAAGTAAATGAAATCA
1 TTTGGTTAAGTAAATAAAATCA
*
38427 TTTGGTTCAGTAAA-AAAAT
1 TTTGGTTAAGTAAATAAAAT
38446 TCATATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (22 bp):
TTTGGTTAAGTAAATAAAATCA
Found at i:50434 original size:20 final size:22
Alignment explanation
Indices: 50409--50452 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
50399 CACCCTCAGC
50409 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
50429 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
50451 AT
1 AT
50453 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:50446 original size:2 final size:2
Alignment explanation
Indices: 50441--50511 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
50431 CCATCCATCC
50441 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
*
50483 -T AT AT AC AT AT -T AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50512 TAAAAAAATA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.05
2 61 0.95
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:50827 original size:18 final size:17
Alignment explanation
Indices: 50808--50888 Score: 61
Period size: 17 Copynumber: 5.1 Consensus size: 17
50798 TTGTTCATGT
50808 TTTGGTTTCTAAGAATG
1 TTTGGTTTCTAAGAATG
*
50825 TTTGAGTATC----AATG
1 TTTG-GTTTCTAAGAATG
50839 TTTGGTTTCTAAGAATG
1 TTTGGTTTCTAAGAATG
*
50856 TTTGAGTATC----AATG
1 TTTG-GTTTCTAAGAATG
*
50870 TTTGGTTTCTATGAATG
1 TTTGGTTTCTAAGAATG
50887 TT
1 TT
50889 AGAAGAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
13 8 0.16
14 16 0.32
17 18 0.36
18 8 0.16
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (17 bp):
TTTGGTTTCTAAGAATG
Found at i:50840 original size:14 final size:14
Alignment explanation
Indices: 50821--50873 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
50811 GGTTTCTAAG
50821 AATGTTTGAGTATC
1 AATGTTTGAGTATC
*
50835 AATGTTTG-GTTTC
1 AATGTTTGAGTATC
50848 TAAGAATGTTTGAGTATC
1 ----AATGTTTGAGTATC
50866 AATGTTTG
1 AATGTTTG
50874 GTTTCTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 16 0.50
17 8 0.25
18 4 0.12
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (14 bp):
AATGTTTGAGTATC
Found at i:50844 original size:31 final size:31
Alignment explanation
Indices: 50808--50888 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
50798 TTGTTCATGT
50808 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
1 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
50839 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
1 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
*
50870 TTTGGTTTCTATGAATGTT
1 TTTGGTTTCTAAGAATGTT
50889 AGAAGAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (31 bp):
TTTGGTTTCTAAGAATGTTTGAGTATCAATG
Found at i:51936 original size:21 final size:22
Alignment explanation
Indices: 51892--51937 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
51882 ACTAAAAATT
* * *
51892 AAATAATATTTGGTAAATTGAA
1 AAATAAGATTTGGTAAAATAAA
51914 AAATAAGATTT-GTAAAATAAA
1 AAATAAGATTTGGTAAAATAAA
51935 AAA
1 AAA
51938 AGAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (22 bp):
AAATAAGATTTGGTAAAATAAA
Found at i:52148 original size:21 final size:22
Alignment explanation
Indices: 52117--52191 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
52107 TGAGATTAAA
*
52117 AAAACTTAAGAATATCAATTAT
1 AAAACTTAAGAAAATCAATTAT
* *
52139 AAAA-TTAAGAAAATGATATTGAA
1 AAAACTTAAGAAAATCA-ATT-AT
*
52162 AAAACTTAA-AAACATCCATTAT
1 AAAACTTAAGAAA-ATCAATTAT
52184 AAAA-TTAA
1 AAAACTTAA
52192 AAGTGAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
21 14 0.33
22 12 0.28
23 11 0.26
24 6 0.14
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAACTTAAGAAAATCAATTAT
Found at i:52166 original size:45 final size:45
Alignment explanation
Indices: 52087--52207 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 45
52077 AATAGAGACC
* * *
52087 TCAATTA-AAAAGTT-AGAAAGTGAGATTAAAAAAACTTAAGAATA
1 TCAATTATAAAA-TTAAGAAAATGAGATTAAAAAAACTTAAAAACA
* *
52131 TCAATTATAAAATTAAGAAAATGATATTGAAAAAACTTAAAAACA
1 TCAATTATAAAATTAAGAAAATGAGATTAAAAAAACTTAAAAACA
* * *
52176 TCCATTATAAAATT-A-AAAGTGAGATTACAAAA
1 TCAATTATAAAATTAAGAAAATGAGATTAAAAAA
52208 TTAGGGGTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 13 0.20
44 10 0.15
45 42 0.65
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (45 bp):
TCAATTATAAAATTAAGAAAATGAGATTAAAAAAACTTAAAAACA
Found at i:52234 original size:41 final size:43
Alignment explanation
Indices: 52046--52335 Score: 182
Period size: 43 Copynumber: 6.7 Consensus size: 43
52036 TAAAGACCTT
* * * *
52046 AATTATAAAGATAGAAATTGAAATTGAAAAAAATAGAGACCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
* * * *
52089 AATTAAAAAGTTAGAAAGTGAGATT-AAAAAAACTTA-AGAATATC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAA--TAGAG-ATCTC
* * * * *
52133 AATTATAAA-ATTAAGAAAATGATATTGAAAAAACTTA-AAAACATC
1 AATTATAAAGA-TAA-AAAGTGAGATTGAAAAAA-ATAGAGATC-TC
* * * * * *
52178 CATTATAAA-ATTAAAAGTGAGATT-ACAAAATTAGGGGTCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
* *
52219 AATTATAAAGATAAAAAATG-GATTGAAAAAAATAGAGATTTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
* * * * * *
52261 AATTATAAAGATAAAAAGTTAGATTGAATAATATTA-AAACCTT
1 AATTATAAAGATAAAAAGTGAGATTGAA-AAAAATAGAGATCTC
* * *
52304 AATTATAAAGCTAAAAAATAAGATTGAAAAAA
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAA
52336 TTAAGGACCT
Statistics
Matches: 190, Mismatches: 44, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
41 17 0.09
42 54 0.28
43 67 0.35
44 23 0.12
45 23 0.12
46 6 0.03
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.27
Consensus pattern (43 bp):
AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
Found at i:52287 original size:43 final size:43
Alignment explanation
Indices: 52046--52288 Score: 174
Period size: 42 Copynumber: 5.7 Consensus size: 43
52036 TAAAGACCTT
* * * **
52046 AATTATAAAGATAGAAATTGAAATTGAAAAAAATAGAGACCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATATC
* * *
52089 AATTAAAAAGTTAGAAAGTGAGATT-AAAAAAACTTA-AGAATATC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAA--TAGAG-ATATC
* * * * * *
52133 AATTATAAA-ATTAAGAAAATGATATTGAAAAAACTTAAAAACATC
1 AATTATAAAGA-TAA-AAAGTGAGATTGAAAAAA-ATAGAGATATC
* * * * * * *
52178 CATTATAAA-ATTAAAAGTGAGATT-ACAAAATTAGGGGTCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATATC
* *
52219 AATTATAAAGATAAAAAATG-GATTGAAAAAAATAGAGATTTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATATC
*
52261 AATTATAAAGATAAAAAGTTAGATTGAA
1 AATTATAAAGATAAAAAGTGAGATTGAA
52289 TAATATTAAA
Statistics
Matches: 154, Mismatches: 35, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
41 17 0.11
42 50 0.32
43 39 0.25
44 17 0.11
45 24 0.16
46 7 0.05
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (43 bp):
AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATATC
Found at i:52308 original size:43 final size:42
Alignment explanation
Indices: 52029--52365 Score: 152
Period size: 43 Copynumber: 7.8 Consensus size: 42
52019 ATAAAATTTT
* *
52029 AAAAAATTAA-AGACCTTAATTATAAAGATAGAAATTGAA-ATTG
1 AAAAAATTAAGA-ACC-TAATTATAAAGATAAAAAAT-AAGATTG
* * * * * * *
52072 AAAAAAAT-AGAGACCTCAATTAAAAAGTTAGAAAGTGAGATTA
1 AAAAAATTAAGA-ACCT-AATTATAAAGATAAAAAATAAGATTG
** * *
52115 AAAAAACTTAAGAATATCAATTATAAA-ATTAAGAAAATGATATTG
1 AAAAAA-TTAAGAACCT-AATTATAAAGA-TAA-AAAATAAGATTG
* * * * * *
52160 AAAAAACTTAAAAACATCCATTATAAA-ATTAAAAGTGAGATT-
1 AAAAAA-TTAAGAACCT-AATTATAAAGATAAAAAATAAGATTG
* * *** *
52202 ACAAAATTAGGGGTCTCAATTATAAAGATAAAAAAT-GGATTG
1 AAAAAATTAAGAACCT-AATTATAAAGATAAAAAATAAGATTG
* ** * *
52244 AAAAAAAT-AGAGATTTCAATTATAAAGATAAAAAGTTAGATTG
1 AAAAAATTAAGA-ACCT-AATTATAAAGATAAAAAATAAGATTG
* *
52287 AATAATATTAA-AACCTTAATTATAAAGCTAAAAAATAAGATTG
1 AA-AAAATTAAGAACC-TAATTATAAAGATAAAAAATAAGATTG
* *
52330 AAAAAATTAAGGACCTAAATATAAAGATGAAAAAAT
1 AAAAAATTAAGAACCTAATTATAAAGAT-AAAAAAT
52366 GGGGACCCCA
Statistics
Matches: 227, Mismatches: 51, Indels: 32
0.73 0.16 0.10
Matches are distributed among these distances:
41 18 0.08
42 60 0.26
43 89 0.39
44 22 0.10
45 38 0.17
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (42 bp):
AAAAAATTAAGAACCTAATTATAAAGATAAAAAATAAGATTG
Found at i:54221 original size:17 final size:15
Alignment explanation
Indices: 54185--54215 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54175 AAATTCTAAA
54185 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
54200 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
54215 T
1 T
54216 TTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:58056 original size:24 final size:25
Alignment explanation
Indices: 58029--58122 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 25
58019 CACCACAGCT
58029 CGTATA-AATTGCACCGAAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
* *
58053 CGTAGA-AATTGTC-CCGAAG-GAC-
1 CGTATAGAATTG-CACCGAAGTGCCA
* *
58075 CGTGTAGAAATGCACCGAAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
*
58100 C--ATAGAATTGCACCGTAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
58123 TATAAGATTG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
22 5 0.09
23 31 0.55
24 18 0.32
25 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (25 bp):
CGTATAGAATTGCACCGAAGTGCCA
Found at i:61347 original size:2 final size:2
Alignment explanation
Indices: 61340--61366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61330 TTTACATTAT
61340 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
61367 TAATGACCTA
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:62343 original size:125 final size:125
Alignment explanation
Indices: 62107--62357 Score: 457
Period size: 125 Copynumber: 2.0 Consensus size: 125
62097 GTTGTTTTAG
*
62107 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACGCAATCTCCATC
1 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
* * *
62172 ATTTGCAGTTGTAAAATAAGAATTGTGGCGATATGCGTCTTCTTTCGCATTGGTAAACGA
66 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
62232 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
1 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
*
62297 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTTTTTCGCATTGGTAAACGA
66 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
62357 G
1 G
62358 CCATAACTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (125 bp):
GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
Found at i:63738 original size:44 final size:43
Alignment explanation
Indices: 63690--63845 Score: 131
Period size: 45 Copynumber: 3.6 Consensus size: 43
63680 AGACCTATCG
63690 AAAAATCTTAGAGACCTCAATTA-AAAAGTTAGAAAGTGAGATTA
1 AAAAATCTTA-AGACCTCAATTATAAAA-TTAGAAAGTGAGATTA
* * *
63734 AAAAAACTTAAGAGCCTCAATTATAAAATTAAGAAAATGATATTGA
1 AAAAATCTTAAGA-CCTCAATTATAAAATT-AGAAAGTGAGATT-A
* * * *
63780 ATAAA-CTTAAAAACATCCATTATAAAATTA-AAAGTGAGATTA
1 AAAAATCTT-AAGACCTCAATTATAAAATTAGAAAGTGAGATTA
* * **
63822 CAAAAT-TAAAGGTCTCAATTATAA
1 AAAAATCTTAAGACCTCAATTATAA
63846 GATAAAAATG
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
41 11 0.12
42 5 0.06
43 12 0.13
44 21 0.24
45 32 0.36
46 8 0.09
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.27
Consensus pattern (43 bp):
AAAAATCTTAAGACCTCAATTATAAAATTAGAAAGTGAGATTA
Found at i:63739 original size:45 final size:43
Alignment explanation
Indices: 63690--63826 Score: 134
Period size: 45 Copynumber: 3.1 Consensus size: 43
63680 AGACCTATCG
*
63690 AAAAATCTTAGAGACCTCAATTA-AAAAGTTAGAAAGTGAGATTA
1 AAAAAACTTA-AGACCTCAATTATAAAA-TTAGAAAGTGAGATTA
* * *
63734 AAAAAACTTAAGAGCCTCAATTATAAAATTAAGAAAATGATATTG
1 AAAAAACTTAAGA-CCTCAATTATAAAATT-AGAAAGTGAGATTA
* * * *
63779 AATAAACTTAAAAACATCCATTATAAAATTA-AAAGTGAGATTA
1 AAAAAACTT-AAGACCTCAATTATAAAATTAGAAAGTGAGATTA
*
63822 CAAAA
1 AAAAA
63827 TTAAAGGTCT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
43 15 0.20
44 21 0.28
45 37 0.49
46 3 0.04
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (43 bp):
AAAAAACTTAAGACCTCAATTATAAAATTAGAAAGTGAGATTA
Found at i:63979 original size:29 final size:29
Alignment explanation
Indices: 63940--64010 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
63930 GATAAAAAAT
*
63940 AAGATTGAAAAAATTAAGGA-CCTAATTATA
1 AAGA-TGAAAAAA-TAAGGACCCTAATTACA
**
63970 AAGATGAAAAAATGGGGACCCTAATTACA
1 AAGATGAAAAAATAAGGACCCTAATTACA
*
63999 AGGATGAAAAAA
1 AAGATGAAAAAA
64011 ATGGGGGCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 28 0.78
30 4 0.11
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20
Consensus pattern (29 bp):
AAGATGAAAAAATAAGGACCCTAATTACA
Found at i:63980 original size:42 final size:43
Alignment explanation
Indices: 63697--63980 Score: 160
Period size: 43 Copynumber: 6.6 Consensus size: 43
63687 TCGAAAAATC
* * * * *
63697 TTAGAGACCTCAATTAAAAAGTTAGAAAGTGAGATT-AAAAAAA
1 TTAGA-ACCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
* * * * *
63740 CTTAAGAGCCTCAATTATAAA-ATTAAGAAAATGATATTGAATAAAC
1 -TT-AGAACCTCAATTATAAAGA-TAA-AAAGTAAGATTGAATAAAA
* * * * * *
63786 TTAAAAACATCCATTATAAA-ATTAAAAGTGAGATT--ACAAAA
1 TT-AGAACCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
* *
63827 TTA-AAGGTCTCAATTAT-AAGATAAAAA-T-GGATTGAA-AAAA
1 TTAGAA--CCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
* ** * *
63867 ATAGATATTTCAATTATAAAGATAAAAAGTTAGATTGAATAATA
1 TTAGA-ACCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
*
63911 TTAGAACCTCAATTATAAAGATAAAAAATAAGATTGAA-AAAA
1 TTAGAACCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
*
63953 TTAAGGACCT-AATTATAAAGATGAAAAA
1 TT-AGAACCTCAATTATAAAGAT-AAAAA
63981 ATGGGGACCC
Statistics
Matches: 190, Mismatches: 33, Indels: 35
0.74 0.13 0.14
Matches are distributed among these distances:
39 6 0.03
40 19 0.10
41 31 0.16
42 19 0.10
43 56 0.29
44 25 0.13
45 29 0.15
46 5 0.03
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (43 bp):
TTAGAACCTCAATTATAAAGATAAAAAGTAAGATTGAATAAAA
Found at i:63988 original size:28 final size:30
Alignment explanation
Indices: 63960--64016 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
63950 AAATTAAGGA
*
63960 CCTAATTATAAAGATG-AAAAAATGGGGAC
1 CCTAATTACAAAGATGAAAAAAATGGGGAC
*
63989 CCTAATTACAAGGATGAAAAAAATGGGG
1 CCTAATTACAAAGATGAAAAAAATGGGG
64017 GCCATGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (30 bp):
CCTAATTACAAAGATGAAAAAAATGGGGAC
Found at i:66664 original size:22 final size:22
Alignment explanation
Indices: 66617--66664 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
66607 TCATATATAA
* **
66617 ATTTTAAAATTTTTATCTTCAG
1 ATTTTAAAATTTATATAATCAG
66639 ATTTTAAAA-TTATATAATCAG
1 ATTTTAAAATTTATATAATCAG
66660 CATTT
1 -ATTT
66665 AATTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTAAAATTTATATAATCAG
Found at i:72150 original size:3 final size:3
Alignment explanation
Indices: 72127--72188 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
72117 TTTGGGCTTG
**
72127 TAA TATA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA
1 TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
72173 TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA T
72189 TTTAATGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:72670 original size:76 final size:75
Alignment explanation
Indices: 72346--72948 Score: 877
Period size: 76 Copynumber: 8.4 Consensus size: 75
72336 AGGTCTTATG
* *
72346 AACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCTCCCGAA
72411 GGCTTTTTGGA
65 GGCTTTTTGGA
72422 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
72487 GCTTTTTGGA
66 GCTTTTTGGA
*
72497 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAA-A--AAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
72559 GCTTTTTGGA
66 GCTTTTTGGA
* *
72569 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCTCCCGAA
72634 GGCTTTTTGGA
65 GGCTTTTTGGA
* *
72645 AACATCATGCACTGAAGGGCTTACAGATG----T--GG----GAAACATCAAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
72700 GCTTTTTGGA
66 GCTTTTTGGA
*
72710 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCTCCCGAA
72775 GGC-TTTTGGA
65 GGCTTTTTGGA
*
72785 AACATCATGCACTGAAGG-CTTACAGATG----T---G----GAAACATCAAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
72838 GCTTTTTGG-
66 GCTTTTTGGA
*
72847 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAACATCAAAAAGCTCCCGAA-
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
72911 GC-TTTTGGA
66 GCTTTTTGGA
*
72920 AACATCATGCACTGAAGGGCTTACAGATG
1 AACATCATGCACTGAAGGACTTACAGATG
72949 TGGGAAACAT
Statistics
Matches: 484, Mismatches: 14, Indels: 61
0.87 0.03 0.11
Matches are distributed among these distances:
62 41 0.08
63 17 0.04
65 58 0.12
66 1 0.00
67 2 0.00
69 1 0.00
70 4 0.01
71 2 0.00
72 72 0.15
73 33 0.07
74 33 0.07
75 104 0.21
76 116 0.24
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (75 bp):
AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAACATCAAAAAGCTCCCGAAG
GCTTTTTGGA
Found at i:72721 original size:65 final size:65
Alignment explanation
Indices: 72617--72961 Score: 423
Period size: 65 Copynumber: 5.1 Consensus size: 65
72607 CTTTGAAAAT
72617 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
* *
72682 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG----T--G
72747 GTTTTGAAAAC
60 G----G-AAAC
72758 ATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAA-GGCTTACAGATGT-GGAAAC
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
* *
72820 ATCAAAAAGATCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG----T--G
72884 GTTTTGAAAC
60 G----GAAAC
72894 ATCAAAAAGCTCCCGAA-GC-TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
72957 ATCAA
1 ATCAA
Statistics
Matches: 247, Mismatches: 8, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
62 39 0.16
63 28 0.11
65 55 0.22
67 4 0.02
69 2 0.01
70 2 0.01
71 2 0.01
72 6 0.02
73 30 0.12
74 32 0.13
75 24 0.10
76 23 0.09
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (65 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
Found at i:72851 original size:62 final size:63
Alignment explanation
Indices: 72754--72961 Score: 260
Period size: 62 Copynumber: 3.1 Consensus size: 63
72744 AAGGTTTTGA
72754 AAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGCTTACAGATGT-GG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGCTTACAGATGTAGG
*
72816 AAACATCAAAAAGATCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGG-CTTACAGATG----
72880 TAAGGTTTTG
60 T-A-G----G
*
72890 AAACATCAAAAAGCTCCCGAA-GCTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAA-GGCTTACAGATGTAGG
72953 AAACATCAA
1 AAACATCAA
Statistics
Matches: 128, Mismatches: 3, Indels: 29
0.80 0.02 0.18
Matches are distributed among these distances:
62 41 0.32
63 26 0.20
67 2 0.02
69 1 0.01
70 1 0.01
72 6 0.05
73 28 0.22
74 23 0.18
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (63 bp):
AAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGCTTACAGATGTAGG
Found at i:72883 original size:137 final size:140
Alignment explanation
Indices: 72390--72961 Score: 919
Period size: 141 Copynumber: 4.1 Consensus size: 140
72380 AAGGTTTTGA
*
72390 AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
* *
72455 TAAGGCTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGGCTT
72519 ACAGATGACCCTAAGGCTTTG
130 ACAGATG----T--GG----G
72540 AAA-A--AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
* * *
72602 GAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGGCTT
72667 ACAGATGTGGG
130 ACAGATGTGGG
72678 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
72743 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAA-GGCTTA
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGGCTTA
72807 CAGATGT-GG
131 CAGATGTGGG
72816 AAACATCAAAAAGATCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
72880 TAAGGTTTTG-AAACATCAAAAAGCTCCCGAA-GCTTTTGGAAACATCATGCACTGAAGGGCTTA
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGGCTTA
72943 CAGATGTGGG
131 CAGATGTGGG
72953 AAACATCAA
1 AAACATCAA
Statistics
Matches: 409, Mismatches: 7, Indels: 25
0.93 0.02 0.06
Matches are distributed among these distances:
135 25 0.06
136 34 0.08
137 54 0.13
138 37 0.09
139 14 0.03
140 23 0.06
141 90 0.22
142 2 0.00
144 1 0.00
147 66 0.16
148 59 0.14
149 1 0.00
150 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (140 bp):
AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGGCTTA
CAGATGTGGG
Done.