Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397282.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_25.0, 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: 1368273
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 33278 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:5583 original size:24 final size:24
Alignment explanation
Indices: 5556--5601 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5546 TAAATAATTT
* *
5556 TGAATTAATCTAAATTTTAATTGC
1 TGAATTAACCTAAATCTTAATTGC
*
5580 TGAATTACCCTAAATCTTAATT
1 TGAATTAACCTAAATCTTAATT
5602 AAGTTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (24 bp):
TGAATTAACCTAAATCTTAATTGC
Found at i:11195 original size:68 final size:68
Alignment explanation
Indices: 11039--11288 Score: 299
Period size: 68 Copynumber: 3.7 Consensus size: 68
11029 CGTTACCTCT
* * * * * *
11039 TATAGTATGTAGAAA-AAAATCATATACATATCATCATAGAATATATCTCA-CCTTATTCTTATC
1 TATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATATATCTCATGCTTATTCTTATC
*
11102 TTA
66 TCA
* *
11105 TGTAGTATGTGAAAACAACATCACATACATGTCATCATAGCATATATCTCATGCTTATTCTTATC
1 TATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATATATCTCATGCTTATTCTTATC
11170 TCA
66 TCA
* * * * *
11173 TATAGCATGTGGAAATAACATCACATACATGTCATCATAACATATGTCTCATGCTTGTTCTTATC
1 TATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATATATCTCATGCTTATTCTTATC
11238 TCA
66 TCA
* * * * *
11241 TATAGTATGT-GAAAGCCACATCACATACTTGGCATAATAGCATTTATC
1 TATAGTATGTGGAAA-CAACATCACATACATGTCATCATAGCATATATC
11289 ATGTGTTCAT
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
66 12 0.08
67 35 0.22
68 109 0.70
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (68 bp):
TATAGTATGTGGAAACAACATCACATACATGTCATCATAGCATATATCTCATGCTTATTCTTATC
TCA
Found at i:11249 original size:136 final size:134
Alignment explanation
Indices: 11039--11321 Score: 322
Period size: 136 Copynumber: 2.1 Consensus size: 134
11029 CGTTACCTCT
* * * *
11039 TATAGTATGTAGAAAAAAATCATATACATATCATCATAGAATATATCTCACCTTATTCTTATCTT
1 TATAGCATGTGGAAAAAAATCACATACATATCATCATAGAATATATCTCACCTTATTCTTATCTC
* * * *
11104 ATGTAGTATGTGAAAACAACATCACATACATGTCATCATAGCATATATCTCATG-CTT-ATTCTT
66 ATATAGTATGTGAAAACAACATCACATACATGGCATAATAGCAT-T-TATCATGTCTTCATTCTT
11167 ATCTCA
129 ATCTCA
* * * * *
11173 TATAGCATGTGGAAATAACATCACATACATGTCATCATA-ACATATGTCTCATGCTTGTTCTTAT
1 TATAGCATGTGGAAA-AAAATCACATACATATCATCATAGA-ATATATCTCA-CCTTATTCTTAT
* * * *
11237 CTCATATAGTATGTGAAAGCCACATCACATACTTGGCATAATAGCATTTATCATGTGTTCATTCT
63 CTCATATAGTATGTGAAAACAACATCACATACATGGCATAATAGCATTTATCATGTCTTCATTCT
*
11302 TATTTCA
128 TATCTCA
*
11309 -AGAGCATGTGGAA
1 TATAGCATGTGGAA
11322 CAGCATCACA
Statistics
Matches: 125, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
134 20 0.16
135 44 0.35
136 61 0.49
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (134 bp):
TATAGCATGTGGAAAAAAATCACATACATATCATCATAGAATATATCTCACCTTATTCTTATCTC
ATATAGTATGTGAAAACAACATCACATACATGGCATAATAGCATTTATCATGTCTTCATTCTTAT
CTCA
Found at i:12068 original size:21 final size:21
Alignment explanation
Indices: 12042--12091 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
12032 CTAAAGGAGG
12042 GTTTGGAGAGTGAAAGAGAAT
1 GTTTGGAGAGTGAAAGAGAAT
12063 GTTTGGAGAGTGAAAGAGAAT
1 GTTTGGAGAGTGAAAGAGAAT
12084 GTTTGGAG
1 GTTTGGAG
12092 GCTAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (21 bp):
GTTTGGAGAGTGAAAGAGAAT
Found at i:12099 original size:21 final size:21
Alignment explanation
Indices: 12042--12100 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
12032 CTAAAGGAGG
*
12042 GTTTGGAGAGTGAAAGAGAAT
1 GTTTGGAGAGTAAAAGAGAAT
*
12063 GTTTGGAGAGTGAAAGAGAAT
1 GTTTGGAGAGTAAAAGAGAAT
12084 GTTTGGAG-GCTAAAAGA
1 GTTTGGAGAG-TAAAAGA
12101 AAAATCACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (21 bp):
GTTTGGAGAGTAAAAGAGAAT
Found at i:17092 original size:206 final size:205
Alignment explanation
Indices: 16635--17228 Score: 757
Period size: 206 Copynumber: 2.9 Consensus size: 205
16625 TTAATAATAA
* * * *
16635 CTTAATTAAATAGTGTAATCAGTAAAATAAAATAAATGTATTAGAAAAAAAATTAAAT-AATAA-
1 CTTAATTAAATAGTGTAATTAGTAAAATAAAAT-AATGTATTAG-TAAACAATTAATTAAATAAG
* * * * * * *
16698 TTATAATATTTAATTTAAAAGTAATTAATTTAGTTAATGCATTAATAACTTATTTAAATAGTTTA
64 TAATAATATTTAATTAAAAAATAATTAAATTAGTTAATGTATTAATAACATACTTAAATAGTTTA
* * * * ** * *
16763 ATAGATTAAATAAAATTTAAATAAATAAGTAATATTATTTACATTT-AAAAATTTAAATTAATTT
129 ATTGATTAAATAAAATGTAATTAAATAAGTAACATTATTTAGTTTTCAAAAAATTAAATTAATTA
*
16827 CTGTACTCATAT
194 ATGTACTCATAT
* * *
16839 CCTAATTAAAT-GCAGTAATTAGTAAAATAAAATAATGTATTAGTAAACTATTAATTAAATAAGT
1 CTTAATTAAATAG-TGTAATTAGTAAAATAAAATAATGTATTAGTAAACAATTAATTAAATAAGT
* *
16903 AATAATATTTAATTGAAAAAATAATTAAATTAGTTAATTTATTAATAACATACGTAAATAGTTTA
65 AATAATATTTAATT-AAAAAATAATTAAATTAGTTAATGTATTAATAACATACTTAAATAGTTTA
*
16968 ATTGATTAAATAAAATGTAATTAAATAACTAACATTATTTAGTTTTCAAAAAATTAAATTAATTA
129 ATTGATTAAATAAAATGTAATTAAATAAGTAACATTATTTAGTTTTCAAAAAATTAAATTAATTA
*
17033 ATTTACTCATAT
194 ATGTACTCATAT
* ** *
17045 CTTAATTAAGTAGTGTAATTTCTAACATAAAATAATGTATTAGTAAACAATTAATTAAATAAGTA
1 CTTAATTAAATAGTGTAATTAGTAAAATAAAATAATGTATTAGTAAACAATTAATTAAATAAGTA
* *
17110 ATAATATTTAATTTAAAAAAGAATTCAATTAGTTAATGTATTAATAACATACTTAAATAGTTTAA
66 ATAATATTTAA-TTAAAAAATAATTAAATTAGTTAATGTATTAATAACATACTTAAATAGTTTAA
* * * * *
17175 TTGATTAGATAAAATGTAATAAAATAAGT-ACTTCTTTTTAGTTTACAAAAAATT
130 TTGATTAAATAAAATGTAATTAAATAAGTAACAT-TATTTAGTTTTCAAAAAATT
17229 GTATAAATCA
Statistics
Matches: 338, Mismatches: 44, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
202 9 0.03
203 16 0.05
204 42 0.12
205 84 0.25
206 184 0.54
207 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (205 bp):
CTTAATTAAATAGTGTAATTAGTAAAATAAAATAATGTATTAGTAAACAATTAATTAAATAAGTA
ATAATATTTAATTAAAAAATAATTAAATTAGTTAATGTATTAATAACATACTTAAATAGTTTAAT
TGATTAAATAAAATGTAATTAAATAAGTAACATTATTTAGTTTTCAAAAAATTAAATTAATTAAT
GTACTCATAT
Found at i:23530 original size:34 final size:34
Alignment explanation
Indices: 23490--23558 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
23480 AGGAAAAGGG
23490 CTAAAATCATCAAATAATACATGAGTAGATTCTT
1 CTAAAATCATCAAATAATACATGAGTAGATTCTT
23524 CTAAAATCATCAAATAATACATGAGTAGATTCTT
1 CTAAAATCATCAAATAATACATGAGTAGATTCTT
23558 C
1 C
23559 AACAACTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (34 bp):
CTAAAATCATCAAATAATACATGAGTAGATTCTT
Found at i:33921 original size:15 final size:17
Alignment explanation
Indices: 33883--33923 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
33873 ATATTTTTTA
33883 ATTTTAAAAGGGTTGAAT
1 ATTTTAAAA-GGTTGAAT
*
33901 AATTTAAAA-GTT-AAT
1 ATTTTAAAAGGTTGAAT
33916 ATTTTAAA
1 ATTTTAAA
33924 TTGAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
18 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
ATTTTAAAAGGTTGAAT
Found at i:33951 original size:14 final size:15
Alignment explanation
Indices: 33913--33951 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
33903 TTTAAAAGTT
33913 AATATTTTAAATTGAA
1 AATATTTTAAATT-AA
33929 AATTATTTTAAATT-A
1 AA-TATTTTAAATTAA
33944 AATATTTT
1 AATATTTT
33952 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 3 0.14
16 2 0.09
17 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
AATATTTTAAATTAA
Found at i:36459 original size:2 final size:2
Alignment explanation
Indices: 36452--36480 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36442 CTATAATCTC
36452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36481 AAATCGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41201 original size:2 final size:2
Alignment explanation
Indices: 41194--41242 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
41184 CAACCAACCT
41194 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41235 TC TC TC TC
1 TC TC TC TC
41243 AACACACACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41263 original size:13 final size:13
Alignment explanation
Indices: 41245--41269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41235 TCTCTCTCAA
41245 CACACACACACAC
1 CACACACACACAC
41258 CACACACACACA
1 CACACACACACA
41270 GACATAAAGA
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (13 bp):
CACACACACACAC
Found at i:44200 original size:81 final size:81
Alignment explanation
Indices: 44057--44219 Score: 238
Period size: 81 Copynumber: 2.0 Consensus size: 81
44047 AATCAGAGTA
* * * *
44057 ACATACAAGATCACCAACTAGACAAATTACATATGCCACCTCTTACTTCTAAGGAAATAATTTTA
1 ACATACAAGATCACCAAATAAACAAATTACATAGGCCACCTCTTACTTCTAAGGAAACAATTTTA
*
44122 GGTTGTTATACATTGC
66 GGTTGTTAAACATTGC
* *
44138 ACATACAAGATCACCAAATAAACACATTACATAGGCCACCTTTTACTTCTACA-GAAACAATTTT
1 ACATACAAGATCACCAAATAAACAAATTACATAGGCCACCTCTTACTTCTA-AGGAAACAATTTT
*
44202 TGGTTGTTAAACATTGC
65 AGGTTGTTAAACATTGC
44219 A
1 A
44220 TTCTACAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 72 0.99
82 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (81 bp):
ACATACAAGATCACCAAATAAACAAATTACATAGGCCACCTCTTACTTCTAAGGAAACAATTTTA
GGTTGTTAAACATTGC
Found at i:46374 original size:48 final size:48
Alignment explanation
Indices: 46312--46408 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
46302 ACAAAGAATT
46312 ATGCAAATTACTTTCTCCTACCCACTTCAATGGTCTAGCAAACAGAGC
1 ATGCAAATTACTTTCTCCTACCCACTTCAATGGTCTAGCAAACAGAGC
46360 ATGCAAATTACTTTCTCCTACCCACTTCAATGGTCTAGCAAACAGAGC
1 ATGCAAATTACTTTCTCCTACCCACTTCAATGGTCTAGCAAACAGAGC
46408 A
1 A
46409 CCCGAGAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (48 bp):
ATGCAAATTACTTTCTCCTACCCACTTCAATGGTCTAGCAAACAGAGC
Found at i:48658 original size:15 final size:16
Alignment explanation
Indices: 48624--48658 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48614 TACTACAATC
48624 AGAAAACCACAGATTA
1 AGAAAACCACAGATTA
*
48640 AGAAAACCCCAGA-TA
1 AGAAAACCACAGATTA
48655 AGAA
1 AGAA
48659 CATTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (16 bp):
AGAAAACCACAGATTA
Found at i:56979 original size:15 final size:15
Alignment explanation
Indices: 56959--56987 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56949 TTTTAAATTG
56959 AAGGAGTATGGATTC
1 AAGGAGTATGGATTC
56974 AAGGAGTATGGATT
1 AAGGAGTATGGATT
56988 TGTTAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.28
Consensus pattern (15 bp):
AAGGAGTATGGATTC
Found at i:58888 original size:21 final size:22
Alignment explanation
Indices: 58864--58905 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
58854 ATAAATTTAA
*
58864 AAAATTATTTATTATT-TTTTC
1 AAAAGTATTTATTATTGTTTTC
*
58885 AAAAGTATTTTTTATTGTTTT
1 AAAAGTATTTATTATTGTTTT
58906 ATGTCAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (22 bp):
AAAAGTATTTATTATTGTTTTC
Found at i:62390 original size:28 final size:28
Alignment explanation
Indices: 62351--62404 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
62341 TATTGAAACT
*
62351 TTATTTACATTTGATGTAATTTATTTAC
1 TTATTTACATTTAATGTAATTTATTTAC
*
62379 TTATTTATATTTAATGTAATTTATTT
1 TTATTTACATTTAATGTAATTTATTT
62405 TTATCATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (28 bp):
TTATTTACATTTAATGTAATTTATTTAC
Found at i:64628 original size:2 final size:2
Alignment explanation
Indices: 64621--64647 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64611 GCATTGCCTG
64621 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
64648 GTGTGTGTGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:64851 original size:47 final size:47
Alignment explanation
Indices: 64798--64936 Score: 253
Period size: 46 Copynumber: 3.0 Consensus size: 47
64788 CTTATAAGAG
*
64798 CATTATGACATTATAAAAAGCCCTATGCAATATGATTGAAAATAGCC
1 CATTATGACATTATAAAATGCCCTATGCAATATGATTGAAAATAGCC
64845 CATTATGACATTATAAAATG-CCTATGCAATATGATTGAAAATAGCC
1 CATTATGACATTATAAAATGCCCTATGCAATATGATTGAAAATAGCC
*
64891 CATTATGACATTATAAAATGCCTTATGCAATATGATTGAAAATAGC
1 CATTATGACATTATAAAATGCCCTATGCAATATGATTGAAAATAGC
64937 TTAAGGGTTG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
46 46 0.52
47 43 0.48
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (47 bp):
CATTATGACATTATAAAATGCCCTATGCAATATGATTGAAAATAGCC
Found at i:71969 original size:17 final size:17
Alignment explanation
Indices: 71937--71969 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
71927 TACACCACAA
71937 CAAAATAACAAGAACAT
1 CAAAATAACAAGAACAT
71954 CAAATATAACAA-AACA
1 CAAA-ATAACAAGAACA
71970 AAATTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.67, C:0.18, G:0.03, T:0.12
Consensus pattern (17 bp):
CAAAATAACAAGAACAT
Found at i:81365 original size:3 final size:3
Alignment explanation
Indices: 81359--81391 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
81349 ATTGTTGTTG
81359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81392 CTGCCCCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:90657 original size:25 final size:25
Alignment explanation
Indices: 90620--90696 Score: 127
Period size: 25 Copynumber: 3.1 Consensus size: 25
90610 TTCTTACAAC
*
90620 TATGATGATTCCCAATCCCTATAAT
1 TATGGTGATTCCCAATCCCTATAAT
* *
90645 TATGGTGAATCCCAATCCCCATAAT
1 TATGGTGATTCCCAATCCCTATAAT
90670 TATGGTGATTCCCAATCCCTATAAT
1 TATGGTGATTCCCAATCCCTATAAT
90695 TA
1 TA
90697 CATTTATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (25 bp):
TATGGTGATTCCCAATCCCTATAAT
Found at i:95028 original size:9 final size:9
Alignment explanation
Indices: 95011--95040 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
95001 TTATTTTTAT
95011 TTAATCGTG
1 TTAATCGTG
*
95020 TTAAACGTG
1 TTAATCGTG
95029 TTAATCGTG
1 TTAATCGTG
95038 TTA
1 TTA
95041 TTAATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TTAATCGTG
Found at i:98566 original size:7 final size:7
Alignment explanation
Indices: 98556--98596 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
98546 AGCTCTTCTC
*
98556 TCTCTTA
1 TCTCCTA
98563 TCTCCTA
1 TCTCCTA
98570 TCTCCTA
1 TCTCCTA
98577 TCTCCTA
1 TCTCCTA
*
98584 TTTCCTA
1 TCTCCTA
98591 TCTCCT
1 TCTCCT
98597 CATTTCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.12, C:0.39, G:0.00, T:0.49
Consensus pattern (7 bp):
TCTCCTA
Found at i:98580 original size:21 final size:21
Alignment explanation
Indices: 98556--98605 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
98546 AGCTCTTCTC
*
98556 TCTCTTATCTCCTATCTCCTA
1 TCTCCTATCTCCTATCTCCTA
*
98577 TCTCCTATTTCCTATCTCCTCA
1 TCTCCTATCTCCTATCTCCT-A
*
98599 TTTCCTA
1 TCTCCTA
98606 CTTGCCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.48
Consensus pattern (21 bp):
TCTCCTATCTCCTATCTCCTA
Found at i:104462 original size:2 final size:2
Alignment explanation
Indices: 104449--104482 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
104439 AGTTGTTCAC
*
104449 AT AT AC 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
104483 TAAAAGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:106299 original size:2 final size:2
Alignment explanation
Indices: 106292--106329 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
106282 AGGCAATGCT
106292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106330 GGAATAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107140 original size:24 final size:21
Alignment explanation
Indices: 107108--107151 Score: 52
Period size: 24 Copynumber: 2.0 Consensus size: 21
107098 TATTTATATA
107108 TATGATAACTATAGTTTATAGAGT
1 TATGATAAC-ATA-TTT-TAGAGT
*
107132 TATGTTAACATATTTTAGAG
1 TATGATAACATATTTTAGAG
107152 ACTTAAGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 3 0.16
24 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (21 bp):
TATGATAACATATTTTAGAGT
Found at i:110476 original size:31 final size:31
Alignment explanation
Indices: 110438--110595 Score: 172
Period size: 31 Copynumber: 5.1 Consensus size: 31
110428 TATTTAAAAT
110438 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
1 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
* *
110469 TTGGAACCTTAGTGGAAGAATTCTTAAGATT
1 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
* * * * * *
110500 TTGGAAACTCAATAGAGAAATTATTAAGATA
1 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
* * **
110531 TTAGAGCCTCGGTGGAGGAATTCTTAAGATA
1 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
* * * *
110562 TTGAAACCTTTGTGGAGGAATTCATATGATA
1 TTGGAACCTTAGTGGAGGAATTCTTAAGATA
110593 TTG
1 TTG
110596 AAGCCTCGAT
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (31 bp):
TTGGAACCTTAGTGGAGGAATTCTTAAGATA
Found at i:110593 original size:62 final size:62
Alignment explanation
Indices: 110438--110614 Score: 173
Period size: 62 Copynumber: 2.9 Consensus size: 62
110428 TATTTAAAAT
* * ** * *
110438 TTGG-AACCTTAGTGGAGGAATTCTTAAGATATTGGAACCTTAGTGGAAGAATTCTTAAGATT
1 TTGGAAACCTTAGTGGAGGAATTCATAAGATATT-GAGCCTCGGTGGAGGAATTCTTAAGATA
* * * *
110500 TTGGAAA-CTCAATAGAGAAATT-ATTAAGATATTAGAGCCTCGGTGGAGGAATTCTTAAGATA
1 TTGGAAACCTTAGTGGAGGAATTCA-TAAGATATT-GAGCCTCGGTGGAGGAATTCTTAAGATA
* * *
110562 TT-GAAACCTTTGTGGAGGAATTCATATGATATTGAAGCCTCGATGGAGGAATT
1 TTGGAAACCTTAGTGGAGGAATTCATAAGATATTG-AGCCTCGGTGGAGGAATT
110615 TGAGGCTTTG
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
61 5 0.05
62 84 0.91
63 3 0.03
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (62 bp):
TTGGAAACCTTAGTGGAGGAATTCATAAGATATTGAGCCTCGGTGGAGGAATTCTTAAGATA
Found at i:110596 original size:31 final size:30
Alignment explanation
Indices: 110449--110614 Score: 113
Period size: 31 Copynumber: 5.4 Consensus size: 30
110439 TGGAACCTTA
* * *
110449 GTGGAGGAATTCTTAAGATATTGGAACCTTA
1 GTGGAGGAATTCATAAGATATTGAAACC-TC
* * *
110480 GTGGAAGAATTCTTAAGATTTTGGAAA-CTC
1 GTGGAGGAATTCATAAGATATT-GAAACCTC
* * * *
110510 AATAGAGAAATT-ATTAAGATATT-AGAGCCTC
1 -GTGGAGGAATTCA-TAAGATATTGA-AACCTC
* *
110541 GGTGGAGGAATTCTTAAGATATTGAAACCTTT
1 -GTGGAGGAATTCATAAGATATTGAAACC-TC
* *
110573 GTGGAGGAATTCATATGATATTGAAGCCTC
1 GTGGAGGAATTCATAAGATATTGAAACCTC
110603 GATGGAGGAATT
1 G-TGGAGGAATT
110615 TGAGGCTTTG
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
29 1 0.01
30 4 0.04
31 94 0.90
32 5 0.05
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (30 bp):
GTGGAGGAATTCATAAGATATTGAAACCTC
Found at i:115230 original size:15 final size:15
Alignment explanation
Indices: 115200--115266 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
115190 CGTTTGGTAC
*
115200 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
115216 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
**
115231 ATTGTAAGTAATGTG
1 ATTACAAGTAATGTG
* *
115246 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
115261 ATTACA
1 ATTACA
115267 GGGAAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 37 0.86
16 6 0.14
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:115487 original size:29 final size:27
Alignment explanation
Indices: 115412--115934 Score: 223
Period size: 30 Copynumber: 18.6 Consensus size: 27
115402 AAAATATAAG
* *
115412 TTTATATATTTATATTTTTTATTATTAATT
1 TTTA-ATATATATATTTTTAATTA-T-ATT
*
115442 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
* *
115471 TTTAATATCATATA-TTTTATTTTTATT
1 TTTAATAT-ATATATTTTTAATTATATT
* * *
115498 TATTATTATAAATATTTTTATATTTTTATT
1 T-TTAATATATATATTTTTA-A-TTATATT
115528 TTTAATATATTATATTTTT-ATTATTAATT
1 TTTAATATA-TATATTTTTAATTA-T-ATT
*
115557 TTT-ATATAATATCATTTCTTAAAT-TATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
*
115585 TTTAATGTCATATA-TTTT-ATT-TATT
1 TTTAATAT-ATATATTTTTAATTATATT
* *
115610 TATTATTATA-ATA-TTTTATATT-T-TA
1 T-TTAATATATATATTTTTA-ATTATATT
115635 TTTAATATATTTATATTTTT-ATTATTAATT
1 TTTAATATA--TATATTTTTAATTA-T-ATT
* *
115665 TTT-CTATAATATCATTTCTTAAATATATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
* *
115694 TTTAATGTCATATA-TTTT-ATTTTATT
1 TTTAATAT-ATATATTTTTAATTATATT
* *
115720 TATTATTATA-ATA-TTTTATATTTTATT
1 T-TTAATATATATATTTTTA-ATTATATT
115747 TTTAATATATTTATATTTTT-ATTATTAATT
1 TTTAATATA--TATATTTTTAATTA-T-ATT
*
115777 TTT-ATATAATATCATTTCTTAAATATATT
1 TTTAATAT-ATAT-ATTT-TTAATTATATT
* *
115806 TTTAATGTCATATATTTTT-ATTTTA-T
1 TTTAATAT-ATATATTTTTAATTATATT
* *
115832 TTTATTATA-ATA-TTTTATATTTTATT
1 TTTAATATATATATTTTTA-ATTATATT
* *
115858 TTTAATATATTTATATTTATATTATTAATT
1 TTTAATATATATATTTTTA-ATTA-T-ATT
*
115888 TTT-ATATAATATCATATTTTAAATATATT
1 TTTAATAT-ATAT-AT-TTTTAATTATATT
*
115917 TTAAATATCATATATTTT
1 TTTAATAT-ATATATTTT
115935 ATTTTTATTT
Statistics
Matches: 387, Mismatches: 49, Indels: 116
0.70 0.09 0.21
Matches are distributed among these distances:
23 4 0.01
24 17 0.04
25 24 0.06
26 45 0.12
27 42 0.11
28 62 0.16
29 84 0.22
30 87 0.22
31 18 0.05
32 4 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTAATATATATATTTTTAATTATATT
Found at i:115529 original size:14 final size:14
Alignment explanation
Indices: 115510--115563 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
115500 TTATTATAAA
115510 TATTTTTATATTTT
1 TATTTTTATATTTT
*
115524 TATTTTTAATATATTA
1 TATTTTT-ATAT-TTT
*
115540 TATTTTTAT-TATT
1 TATTTTTATATTTT
*
115553 AATTTTTATAT
1 TATTTTTATAT
115564 AATATCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.27
14 9 0.27
15 6 0.18
16 9 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTATATTTT
Found at i:115624 original size:19 final size:18
Alignment explanation
Indices: 115602--115653 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
115592 TCATATATTT
115602 TATTTAT-TTATTATTATAA
1 TATTTATATT-TTATT-TAA
115621 TATTTTATATTTTATTTAATA
1 TA-TTTATATTTTATTT-A-A
115642 TATTTATATTTT
1 TATTTATATTTT
115654 TATTATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 21 0.72
21 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATATTTTATTTAA
Found at i:115756 original size:23 final size:22
Alignment explanation
Indices: 115508--115894 Score: 131
Period size: 23 Copynumber: 17.6 Consensus size: 22
115498 TATTATTATA
*
115508 AATATTTTTATATTTTTATTTTT
1 AATATATTTATA-TTTTATTTTT
*
115531 AATATA-TTATATTTTTATTATT
1 AATATATTTATA-TTTTATTTTT
** *
115553 AAT-T-TTTATATAATATCATTT
1 AATATATTTATATTTTAT-TTTT
** * * *
115574 CTTA-AATTAT-TTTTA-ATGT
1 AATATATTTATATTTTATTTTT
* *
115593 CATATATTTTATTTATTTATTATTAT
1 AATATA-TTTATAT-TTTATT-TT-T
115619 AATAT-TTTATATTTTA--TTT
1 AATATATTTATATTTTATTTTT
*
115638 AATATATTTATATTTTTATTATT
1 AATATATTTATA-TTTTATTTTT
* * *
115661 AAT-TTTTCTATAATATCATTTCTT
1 AATATATT-TAT-ATTTTATTT-TT
* *
115685 AA-ATA--TAT-TTTTA-ATGT
1 AATATATTTATATTTTATTTTT
*
115702 CATATATTT-TATTTTATTTATT
1 AATATATTTATATTTTATTT-TT
115724 ATTATAATATTTTATATTTTATTTTT
1 A--AT-ATA-TTTATATTTTATTTTT
*
115750 AATATATTTATATTTTTATTATT
1 AATATATTTATA-TTTTATTTTT
*
115773 AAT-T-TTTATATAATATCATTTCTT
1 AATATATTTATAT--T-TTATTT-TT
* *
115797 AA-ATA--TAT-TTTTA-ATGT
1 AATATATTTATATTTTATTTTT
* *
115814 CATATATTTTTATTTTATTTTAT
1 AATATATTTATATTTTATTTT-T
*
115837 TATAATATTTTATATTTTATTTTT
1 AAT-ATA-TTTATATTTTATTTTT
*
115861 AATATATTTATATTTATATTATT
1 AATATATTTATATTT-TATTTTT
115884 AAT-T-TTTATAT
1 AATATATTTATAT
115895 AATATCATAT
Statistics
Matches: 272, Mismatches: 46, Indels: 94
0.66 0.11 0.23
Matches are distributed among these distances:
17 4 0.01
18 8 0.03
19 18 0.07
20 23 0.08
21 43 0.16
22 47 0.17
23 63 0.23
24 27 0.10
25 18 0.07
26 11 0.04
27 10 0.04
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (22 bp):
AATATATTTATATTTTATTTTT
Found at i:115833 original size:223 final size:219
Alignment explanation
Indices: 115415--115974 Score: 939
Period size: 223 Copynumber: 2.5 Consensus size: 219
115405 ATATAAGTTT
115415 ATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATC
1 ATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATC
115480 ATATATTTTATTTTTATTTATTATTATAAATATTTTTATATTTTTATTTTTAATATATTATATTT
65 ATATATTTTATTTTTATTTATTATTAT-AATA-TTTTATA-TTTTATTTTTAATATATTATATTT
115545 TTATTATTAATTTTTATATAATATCATTTCTTAAATTATTTTTAATGTCATATATTTTATTTATT
127 TTATTATTAATTTTTATATAATATCATTTCTTAAATTATTTTTAATGTCATATATTTTATTTA-T
115610 TATTATTATAATATTTTATATTTTA-TTTA
191 T-TTATTATAATATTTTATATTTTATTTTA
* *
115639 ATATATTTATATTTTTATTATTAATTTTTCTATAATATCATTTCTTAAATATATTTTTAATGTCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCA
115704 TATATTTTA-TTTTATTTATTATTATAATATTTTATATTTTATTTTTAATATATTTATATTTTTA
66 TATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTAATATA-TTATATTTTTA
115768 TTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTTATTTTATT
130 TTATTAATTTTTATATAATATCATTTCTTAAAT-TATTTTTAATGTCATATA-TTTTA-TTTATT
115833 TTATTATAATATTTTATATTTTATTTTTA
192 TTATTATAATATTTTATATTTTA-TTTTA
* *
115862 ATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTAAATATC
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAATATC
115926 ATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATTTTTA
65 ATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATTTTTA
115975 TTTTTTAATA
Statistics
Matches: 321, Mismatches: 6, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
219 16 0.05
220 51 0.16
221 45 0.14
222 23 0.07
223 139 0.43
224 47 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (219 bp):
ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCA
TATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTAATATATTATATTTTTAT
TATTAATTTTTATATAATATCATTTCTTAAATTATTTTTAATGTCATATATTTTATTTATTTTAT
TATAATATTTTATATTTTATTTTA
Found at i:115891 original size:111 final size:112
Alignment explanation
Indices: 115415--115974 Score: 931
Period size: 111 Copynumber: 5.0 Consensus size: 112
115405 ATATAAGTTT
*
115415 ATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATC
1 ATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTC
115480 ATATATTTTATTTTTATTTATTATTATAAATATTTTTATATTTTTATTTTTA
65 ATATATTTTA-TTTTATTTATTATTAT-AATA-TTTTATA-TTTTATTTTTA
115532 ATATA-TTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAAT-TATTTTTAATGTCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
115595 TATATTTTA-TTTATTTATTATTATAATATTTTATATTTTA--TTTA
66 TATATTTTATTTTATTTATTATTATAATATTTTATATTTTATTTTTA
*
115639 ATATATTTATATTTTTATTATTAATTTTTCTATAATATCATTTCTTAAATATATTTTTAATGTCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
115704 TATATTTTATTTTATTTATTATTATAATATTTTATATTTTATTTTTA
66 TATATTTTATTTTATTTATTATTATAATATTTTATATTTTATTTTTA
115751 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
115816 TATATTTTTATTTTA-TT-TTATTATAATATTTTATATTTTATTTTTA
66 TATA-TTTTATTTTATTTATTATTATAATATTTTATATTTTATTTTTA
* * *
115862 ATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTAAATATC
1 ATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAATGTC
115926 ATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATTTTTA
65 ATATATTTTA-TTTTATTTATTATTATAATATTT-TATATTTTATTTTTA
115975 TTTTTTAATA
Statistics
Matches: 426, Mismatches: 6, Indels: 26
0.93 0.01 0.06
Matches are distributed among these distances:
107 9 0.02
108 43 0.10
109 28 0.07
110 43 0.10
111 101 0.24
112 96 0.23
113 35 0.08
114 22 0.05
115 39 0.09
116 5 0.01
117 5 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (112 bp):
ATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
TATATTTTATTTTATTTATTATTATAATATTTTATATTTTATTTTTA
Found at i:115942 original size:6 final size:6
Alignment explanation
Indices: 115931--115979 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
115921 ATATCATATA
* *
115931 TTTTAT TTTTAT TTATTAT TATAAT TTTATAT ATTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTT
115980 TAATATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 23 0.64
7 10 0.28
8 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:115975 original size:39 final size:38
Alignment explanation
Indices: 115902--116016 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 38
115892 TATAATATCA
* * *
115902 TATTTTAAATATATTTTAAATATCATATATTTTATTTT
1 TATTTTTAATATATTTTTAATATTATATATTTTATTTT
* *
115940 TA--TTT-AT-TA-TTATAATTTTATATATTTTATTTT
1 TATTTTTAATATATTTTTAATATTATATATTTTATTTT
*
115973 TATTTTTTAATATATTTTTTATATTATATATTTTATTTT
1 TA-TTTTTAATATATTTTTAATATTATATATTTTATTTT
*
116012 AATTT
1 TATTT
116017 GTTTTACCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
33 22 0.35
34 2 0.03
35 2 0.03
36 5 0.08
37 2 0.03
38 7 0.11
39 22 0.35
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (38 bp):
TATTTTTAATATATTTTTAATATTATATATTTTATTTT
Found at i:115977 original size:60 final size:59
Alignment explanation
Indices: 115834--115999 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 59
115824 TATTTTATTT
* * *
115834 TATTATAATATTTTATATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATA
1 TATTATAATATTTTAT-TTTTATTTTAAATATATATATATTTATATTATTAATTATTATA
* * ** * * *
115894 TAATATCATATTTTAAATATATTTTAAATATCATATAT-TTTATTTTTATTTATTATTATA
1 TATTATAATATTTTATTTTTATTTTAAATAT-ATATATATTTA-TATTATTAATTATTATA
* *
115954 -ATTTTATATATTTTATTTTTATTTTTTAATATAT-T-T-TTTATATTAT
1 TATTATA-ATATTTTATTTTTA-TTTTAAATATATATATATTTATATTAT
116000 ATATTTTATT
Statistics
Matches: 84, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
57 5 0.06
58 5 0.06
59 20 0.24
60 45 0.54
61 9 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (59 bp):
TATTATAATATTTTATTTTTATTTTAAATATATATATATTTATATTATTAATTATTATA
Found at i:116053 original size:54 final size:52
Alignment explanation
Indices: 115989--116118 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 52
115979 TTAATATATT
115989 TTTTATATTATATATTTTATTTTAATTTGTT-TTACCTATATTATATAAATGTTAA
1 TTTT-TATTATATATTTTATTTTAATTT-TTATT-CCTATATTATATAAAT-TTAA
* * * *
116044 TTTTTATTATTTTATTTTATTTTAATTTTTATTCTTATATTATATATATTTTA
1 TTTTTATTA-TATATTTTATTTTAATTTTTATTCCTATATTATATAAATTTAA
116097 -TTTTA--ATAT-TTTTATTTTAATT
1 TTTTTATTATATATTTTATTTTAATT
116119 ATAATATTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
48 13 0.19
49 2 0.03
50 1 0.01
52 5 0.07
53 3 0.04
54 21 0.31
55 23 0.34
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (52 bp):
TTTTTATTATATATTTTATTTTAATTTTTATTCCTATATTATATAAATTTAA
Found at i:116081 original size:6 final size:5
Alignment explanation
Indices: 116050--116115 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
116040 TTAATTTTTA
* *
116050 TTATT TTATT TTATT TTAATTT TTATT CTTATA TTATAT ATATT TTATT
1 TTATT TTATT TTATT TT-A-TT TTATT -TTATT TTAT-T TTATT TTATT
* *
116099 TTAAT AT-TT TTATT TTA
1 TTATT TTATT TTATT TTA
116116 ATTATAATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.04
5 33 0.69
6 9 0.19
7 4 0.08
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (5 bp):
TTATT
Found at i:116109 original size:14 final size:14
Alignment explanation
Indices: 116061--116117 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
116051 TATTTTATTT
*
116061 TATTTTAATTTT--
1 TATTTTTATTTTAA
* *
116073 TATTCTTATATTATA
1 TATTTTTATTTTA-A
116088 TATATTTTATTTTAA
1 TAT-TTTTATTTTAA
116103 TATTTTTATTTTAA
1 TATTTTTATTTTAA
116117 T
1 T
116118 TATAATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 9 0.25
14 12 0.33
15 7 0.19
16 8 0.22
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTATTTTAA
Found at i:123745 original size:30 final size:28
Alignment explanation
Indices: 123689--123751 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
123679 CAAATCAATA
* *
123689 TTTATTTTTTATTATATTTAATTAAGTT
1 TTTATTTTTTATTATAGTTAAATAAGTT
*
123717 TTTATATTTTTATTTTAAGTTAAATAAGTT
1 TTTAT-TTTTTATTAT-AGTTAAATAAGTT
*
123747 CTTAT
1 TTTAT
123752 GCATGAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 9 0.31
30 15 0.52
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTATTTTTTATTATAGTTAAATAAGTT
Found at i:125880 original size:24 final size:25
Alignment explanation
Indices: 125833--125895 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
125823 AATGAGAAAA
**
125833 AAGG-GAAAAAGGCAAGGTGAGAAG
1 AAGGAGAAAAAGGCAAGAAGAGAAG
125857 AAGGAGAAAAAGGCAAGAAG-GAAG
1 AAGGAGAAAAAGGCAAGAAGAGAAG
*
125881 AAAGA-AAAGAAGGCA
1 AAGGAGAAA-AAGGCA
125896 GAANNNNNNN
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.09
24 18 0.53
25 13 0.38
ACGTcount: A:0.57, C:0.05, G:0.37, T:0.02
Consensus pattern (25 bp):
AAGGAGAAAAAGGCAAGAAGAGAAG
Found at i:132141 original size:22 final size:22
Alignment explanation
Indices: 132116--132190 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 22
132106 TTATTTTTAT
132116 TTTATTTATTAAATATTAATAA
1 TTTATTTATTAAATATTAATAA
132138 TTTATAATGTAATTAAAATATTAATAA
1 TTTAT--T-T-ATT-AAATATTAATAA
* *
132165 TTTA-TAATTTAAATATTAATAT
1 TTTATTTA-TTAAATATTAATAA
132187 TTTA
1 TTTA
132191 GTATAGTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
22 21 0.47
23 2 0.04
24 2 0.04
25 1 0.02
26 3 0.07
27 16 0.36
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TTTATTTATTAAATATTAATAA
Found at i:132221 original size:15 final size:15
Alignment explanation
Indices: 132153--132227 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
132143 AATGTAATTA
*
132153 AAATATTAATAATTT
1 AAATATTAATATTTT
*
132168 ATAAT-TTAA-ATATT
1 A-AATATTAATATTTT
* *
132182 AATATTTTAGTATAGTTT
1 AA-ATATTA--ATATTTT
*
132200 AATTATTAATATTTT
1 AAATATTAATATTTT
132215 AAATATTAATATT
1 AAATATTAATATT
132228 GTATTTATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
13 1 0.02
14 6 0.13
15 26 0.57
16 3 0.07
17 5 0.11
18 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
AAATATTAATATTTT
Found at i:132247 original size:40 final size:39
Alignment explanation
Indices: 132158--132267 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
132148 AATTAAAATA
* * *
132158 TTAATAATTTATAATTTAAATATTAATATTTTAGTATAGT
1 TTAAT-ATTAATATTTTAAATATTAATATTGTAGTATAGT
*
132198 TTAATTATTAATATTTTAAATATTAATATTGTA-TTTATGAT
1 TTAA-TATTAATATTTTAAATATTAATATTGTAGTATA-G-T
* *
132239 TTAATATTATTATGATTAAAATATTAATA
1 TTAATATTAATAT--TTTAAATATTAATA
132268 ATTTTTAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 3 0.05
40 37 0.63
41 6 0.10
42 13 0.22
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.53
Consensus pattern (39 bp):
TTAATATTAATATTTTAAATATTAATATTGTAGTATAGT
Found at i:132411 original size:15 final size:15
Alignment explanation
Indices: 132333--132411 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 15
132323 AAGAAAACAA
*
132333 TAATATTTTAAAATAT
1 TAATATTAT-AAATAT
* *
132349 TAATATTTTACTCATAT
1 TAATATTATA--AATAT
132366 TAATATTA-ATAATATT
1 TAATATTATA-AATA-T
132382 TATATTATATATAAATAT
1 TA-A-TAT-TATAAATAT
132400 TAATATTATAAA
1 TAATATTATAAA
132412 ATTTATAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
15 11 0.21
16 16 0.30
17 13 0.25
18 6 0.11
19 6 0.11
20 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTATAAATAT
Found at i:133583 original size:14 final size:14
Alignment explanation
Indices: 133554--133582 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
133544 GCCCAGGGAG
133554 AAGAAGAAAAGAAA
1 AAGAAGAAAAGAAA
133568 AAGAA-AAAAGAAA
1 AAGAAGAAAAGAAA
133581 AA
1 AA
133583 ATTAGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAGAAA
Found at i:133619 original size:27 final size:26
Alignment explanation
Indices: 133588--133668 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
133578 AAAAAATTAG
133588 TTATA-AATTTTAAAATATTAATATT
1 TTATATAATTTTAAAATATTAATATT
*
133613 TTATATATTATTTAAAATTTATTAATA-T
1 TTATATAAT-TTTAAAA--TATTAATATT
* * *
133641 TAATATGA--TTAAAATATTAATTTT
1 TTATATAATTTTAAAATATTAATATT
133665 TTAT
1 TTAT
133669 TAAATTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
23 7 0.16
24 4 0.09
25 11 0.24
26 2 0.04
27 7 0.16
28 6 0.13
29 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TTATATAATTTTAAAATATTAATATT
Found at i:133651 original size:29 final size:27
Alignment explanation
Indices: 133596--133651 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
133586 AGTTATAAAT
*
133596 TTTAAAATATTAATATTTTATATATTA
1 TTTAAAATATTAATATTTAATATATTA
133623 TTTAAAATTTATTAATA-TTAATATGATTA
1 TTTAAAA--TATTAATATTTAATAT-ATTA
133652 AAATATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTAATATTTAATATATTA
Found at i:133660 original size:23 final size:26
Alignment explanation
Indices: 133596--133661 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
133586 AGTTATAAAT
*
133596 TTTAAAATATTAATATTTTATATATTA
1 TTTAAAATATTAATA-TTTATATATGA
133623 TTTAAAATTTATTAATA-TTA-ATATGA
1 TTTAAAA--TATTAATATTTATATATGA
133649 -TTAAAATATTAAT
1 TTTAAAATATTAAT
133662 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 7 0.19
25 6 0.17
26 5 0.14
27 10 0.28
29 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAAATATTAATATTTATATATGA
Found at i:133672 original size:19 final size:19
Alignment explanation
Indices: 133636--133687 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
133626 AAAATTTATT
*
133636 AATATTAA-TA-TGATTAA
1 AATATTAATTATTTATTAA
*
133653 AATATTAATTTTTTATTAA
1 AATATTAATTATTTATTAA
*
133672 ATTATTAATTATTTAT
1 AATATTAATTATTTAT
133688 ATTTAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 8 0.28
18 1 0.03
19 20 0.69
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATATTAATTATTTATTAA
Found at i:136533 original size:50 final size:49
Alignment explanation
Indices: 136438--136542 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 49
136428 ACAGTAAATC
136438 AAAA-GGCATTAAGATCAAATGACAAAAAAAGACTAAATCTCTATTATT
1 AAAAGGGCATTAAGATCAAATGACAAAAAAAGACTAAATCTCTATTATT
136486 AAAAGGGCATTAAGATCAAATGA-AAAGAACAAGACTAAATCTCTATTATT
1 AAAAGGGCATTAAGATCAAATGACAAA-AA-AAGACTAAATCTCTATTATT
136536 AAAAGGG
1 AAAAGGG
136543 TAAGACAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
48 7 0.13
49 20 0.37
50 27 0.50
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (49 bp):
AAAAGGGCATTAAGATCAAATGACAAAAAAAGACTAAATCTCTATTATT
Found at i:141851 original size:22 final size:21
Alignment explanation
Indices: 141804--141855 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
141794 GAACATGGTG
* *
141804 TGTAACAATTTTTGAACTTGCG
1 TGTAAC-ATTTTTGAACTGGCA
*
141826 TGTAACATTTTTGAGCATGGCA
1 TGTAACATTTTTGAAC-TGGCA
141848 TGTAACAT
1 TGTAACAT
141856 AGTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (21 bp):
TGTAACATTTTTGAACTGGCA
Found at i:142790 original size:15 final size:15
Alignment explanation
Indices: 142772--142801 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
142762 GGAGGTGTTG
142772 ATGTAGGAGATGTAT
1 ATGTAGGAGATGTAT
142787 ATGTAGGAGATGTAT
1 ATGTAGGAGATGTAT
142802 GGTGTGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (15 bp):
ATGTAGGAGATGTAT
Found at i:145450 original size:23 final size:23
Alignment explanation
Indices: 145422--145847 Score: 323
Period size: 23 Copynumber: 18.1 Consensus size: 23
145412 CAAAAGTGTT
* *
145422 ACGCCATGCCCAAATGTGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* *
145445 ATGCCATGCCCCAATGCAGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * *
145468 ACGCCATACCCTAGTG-GGCTGAC
1 ACGCCATGCCCCAATGCGG-TGAC
* * *
145491 AAGCCATGCCCGAATGTGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
*
145514 ACGCCATGCCCGAATGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
** *
145537 ACGCCATGCCTTAGTGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * * *
145560 AAGCCATGCCCCAGTGGGGTGAT
1 ACGCCATGCCCCAATGCGGTGAC
**
145583 ACGCCATGCCCCAATGTAGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * * *
145606 AAGCCATGCCCTAGTGGGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
*
145629 AAGCTATGCCATGCCCCAATGCAGTGAC
1 -A-C---GCCATGCCCCAATGCGGTGAC
* * *
145657 AAGCCATGCCCCAGTGGGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * *
145680 AAGCTATGCCATGCCCTAGTGCAGTGAC
1 -A-C---GCCATGCCCCAATGCGGTGAC
* ** *
145708 AAGCCATGCCCCAGCGGGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * *
145731 ACGTCATGCCCGAATACGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
**
145754 ACGCTGTGCCCCAATGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
*
145777 ACGCCGTGCCCCAATGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* *
145800 ACGCCGTGCACCAATGCGGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
* * * *
145823 ATGCCATGCCCTAATCCAGTGAC
1 ACGCCATGCCCCAATGCGGTGAC
145846 AC
1 AC
145848 ACCGCGTGGT
Statistics
Matches: 319, Mismatches: 72, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
22 1 0.00
23 277 0.87
24 4 0.01
27 2 0.01
28 35 0.11
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (23 bp):
ACGCCATGCCCCAATGCGGTGAC
Found at i:145536 original size:69 final size:69
Alignment explanation
Indices: 145424--145835 Score: 394
Period size: 69 Copynumber: 5.8 Consensus size: 69
145414 AAAGTGTTAC
* * * * *
145424 GCCATGCCCAAATGTGGTGACATGCCATGCCCCAATGCAGTGACACGCCATACCCTAGTG-GGCT
1 GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTAGTGCGG-T
145488 GACAA
65 GACAA
* * * *
145493 GCCATGCCCGAATGTGGTGACACGCCATGCCCGAATGCGGTGACACGCCATGCCTTAGTGCGGTG
1 GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTAGTGCGGTG
145558 ACAA
66 ACAA
* * * ** * *
145562 GCCATGCCCCAGTGGGGTGATACGCCATGCCCCAATGTAGTGACAAGCCATGCCCTAGTGGGGTG
1 GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTAGTGCGGTG
145627 ACAAGCTA
66 AC-A---A
* * * *
145635 TGCCATGCCCCAATGCAGTGACAAGCCATGCCCCAGTGGGGTGACAAGCTATGCCATGCCCTAGT
1 -GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGAC-A-C---GCCATGCCCTAGT
*
145700 GCAGTGACAA
60 GCGGTGACAA
** * * * * ** * *
145710 GCCATGCCCCAGCGGGGTGACACGTCATGCCCGAATACGGTGACACGCTGTGCCCCAATGCGGTG
1 GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTAGTGCGGTG
*
145775 ACAC
66 ACAA
* * * *
145779 GCCGTGCCCCAATGCGGTGACACGCCGTGCACCAATGCGGTGACATGCCATGCCCTA
1 GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTA
145836 ATCCAGTGAC
Statistics
Matches: 276, Mismatches: 56, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
69 178 0.64
70 3 0.01
72 1 0.00
73 2 0.01
74 70 0.25
75 2 0.01
78 1 0.00
79 19 0.07
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (69 bp):
GCCATGCCCCAATGCGGTGACACGCCATGCCCCAATGCGGTGACACGCCATGCCCTAGTGCGGTG
ACAA
Found at i:145655 original size:28 final size:28
Alignment explanation
Indices: 145608--145717 Score: 113
Period size: 28 Copynumber: 4.1 Consensus size: 28
145598 GTAGTGACAA
* **
145608 GCCATGCCCTAGTGGGGTGACAAGCTAT
1 GCCATGCCCCAGTGCAGTGACAAGCTAT
*
145636 GCCATGCCCCAATGCAGTGAC-A---A-
1 GCCATGCCCCAGTGCAGTGACAAGCTAT
**
145659 GCCATGCCCCAGTGGGGTGACAAGCTAT
1 GCCATGCCCCAGTGCAGTGACAAGCTAT
* *
145687 GCCATGCCCTAGTGCAGTGACAAGCCAT
1 GCCATGCCCCAGTGCAGTGACAAGCTAT
145715 GCC
1 GCC
145718 CCAGCGGGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
23 18 0.27
24 2 0.03
27 2 0.03
28 44 0.67
ACGTcount: A:0.24, C:0.31, G:0.28, T:0.17
Consensus pattern (28 bp):
GCCATGCCCCAGTGCAGTGACAAGCTAT
Found at i:145847 original size:46 final size:46
Alignment explanation
Indices: 145422--145847 Score: 357
Period size: 46 Copynumber: 9.0 Consensus size: 46
145412 CAAAAGTGTT
* * * *
145422 ACGCCATGCCCAAATGTGGTGACATGCCATGCCCCAATGCAGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
* * * * * **
145468 ACGCCATACCCTAGTGGGCTGACAAGCCATGCCCGAATGTGGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
* * * ** * *
145514 ACGCCATGCCCGAATGCGGTGACACGCCATGCCTTAGTGCGGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
* * *
145560 AAGCCATGCCCCAGTGGGGTGATACGCCATGCCCCAATGTAGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
* *
145606 AAGCCATGCCCTAGTGGGGTGACAAGCTATGCCATGCCCCAATGCAGTGAC
1 ACGCCATGCCCCAGTGGGGTGAC-A-C---GCCATGCCCCAATGCAGTGAC
* * *
145657 AAGCCATGCCCCAGTGGGGTGACAAGCTATGCCATGCCCTAGTGCAGTGAC
1 ACGCCATGCCCCAGTGGGGTGAC-A-C---GCCATGCCCCAATGCAGTGAC
* * * * * *
145708 AAGCCATGCCCCAGCGGGGTGACACGTCATGCCCGAATACGGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
** * * * *
145754 ACGCTGTGCCCCAATGCGGTGACACGCCGTGCCCCAATGCGGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
* * * * * * *
145800 ACGCCGTGCACCAATGCGGTGACATGCCATGCCCTAATCCAGTGAC
1 ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
145846 AC
1 AC
145848 ACCGCGTGGT
Statistics
Matches: 317, Mismatches: 58, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
46 223 0.70
47 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 90 0.28
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (46 bp):
ACGCCATGCCCCAGTGGGGTGACACGCCATGCCCCAATGCAGTGAC
Found at i:149591 original size:31 final size:31
Alignment explanation
Indices: 149556--149840 Score: 336
Period size: 31 Copynumber: 9.2 Consensus size: 31
149546 AACATAGCAC
* *
149556 AAATGTGGTTACATGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* * *
149587 AAATGTGGTTACACGCTATGCATTACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* * * *
149618 AAAGGTCGTCACACGCCATGCATAATAAATA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* *
149649 AAATGTGATCACATGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
*
149680 AAAGGTGGTCACACGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* *
149711 AAATGTTGTCACCCGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* *
149742 AAATGTTGTCACTCGCCATGCATAACAAGTA
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* * * * * *
149773 AATTGTTGTTACACGCCAGGCATATCAAGTC
1 AAATGTGGTCACACGCCATGCATAACAAGTA
* * * *
149804 AAATGTCGTGACACGTCATGCATAACAAGTC
1 AAATGTGGTCACACGCCATGCATAACAAGTA
149835 AAATGT
1 AAATGT
149841 TGTAACATGC
Statistics
Matches: 219, Mismatches: 35, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 219 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (31 bp):
AAATGTGGTCACACGCCATGCATAACAAGTA
Found at i:150582 original size:22 final size:24
Alignment explanation
Indices: 150543--150600 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
150533 TGAACGCTGT
*
150543 CGTGTCACAAATCTTGAATGTTAG
1 CGTGTCACAAATCTTGAATCTTAG
* *
150567 CGTGTCA-AACTC-TGAATCTTGG
1 CGTGTCACAAATCTTGAATCTTAG
150589 CGTGTCACAAAT
1 CGTGTCACAAAT
150601 TTCCTCCATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 7 0.24
24 7 0.24
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
CGTGTCACAAATCTTGAATCTTAG
Found at i:150674 original size:92 final size:92
Alignment explanation
Indices: 150572--150988 Score: 473
Period size: 92 Copynumber: 4.5 Consensus size: 92
150562 GTTAGCGTGT
* * * * *
150572 CAAACTCTGAATCTTGGCGTGTCACAAATTTCCTCCATGGCGTGTCAAACTCTGAACACTGACGT
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAACTCTGACGT
* **
150637 GTCACAGATTCCCTTAATGGTGTGTCA
66 GTCACAAATTCCCTCCATGGTGTGTCA
* * * * * * *
150664 CAAACTCTGAATCCTGGCATCTCACAGATTCCCTCCATGGCATGTCACAAATCCTGAACCCTGCC
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA-AACT-CTGAACTCTGAC
* * *
150729 ATGTCACAGATTCCCTCCATGGCGTGTCA
64 GTGTCACAAATTCCCTCCATGGTGTGTCA
* * * *
150758 CAAACTCTGAATACTAACGTGTCACAGATTCCCTTCATGGCGTGTCAAACTCTGAACTCTAACGT
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAACTCTGACGT
* *
150823 GTCACAAATTCCGTCCATGCTGTGTCA
66 GTCACAAATTCCCTCCATGGTGTGTCA
* *
150850 CAAACTCTGAA-CACTGACGTGTCACAGATTCCTTCCATGGCGTGTCAAACTCTGAACTCT-AGT
1 CAAACTCTGAATC-CTGACGTGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAACTCTGA-C
*
150913 GTGTCACAAATTCCCTCCATAGTGTGTCA
64 GTGTCACAAATTCCCTCCATGGTGTGTCA
* * * *
150942 CAAACTTTGAA-CTCTAGA-GTGTTATAGATTCCCTCCATGGCATGTCA
1 CAAACTCTGAATC-CT-GACGTGTCACAGATTCCCTCCATGGCGTGTCA
150989 CAAATTTTGA
Statistics
Matches: 277, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
91 1 0.00
92 193 0.70
93 8 0.03
94 75 0.27
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (92 bp):
CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAACTCTGACGT
GTCACAAATTCCCTCCATGGTGTGTCA
Found at i:150689 original size:47 final size:47
Alignment explanation
Indices: 150572--151015 Score: 396
Period size: 47 Copynumber: 9.6 Consensus size: 47
150562 GTTAGCGTGT
* * * *
150572 CAAACTCTGAATCTTGGCGTGTCACAAATTTCCTCCATGGCGTGT--
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
** *
150617 CAAACTCTGAA-CACTGACGTGTCACAGATTCCCTTAATGGTGTGTCA
1 CAAACTCTGAATC-CTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * * *
150664 CAAACTCTGAATCCTGGCATCTCACAGATTCCCTCCATGGCATGTCA
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * *
150711 CAAA-TCCTGAACCCTGCCATGTCACAGATTCCCTCCATGGCGTGTCA
1 CAAACT-CTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * *
150758 CAAACTCTGAATACTAACGTGTCACAGATTCCCTTCATGGCGTGT--
1 CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * *
150803 CAAACTCTGAA-CTCTAACGTGTCACAAATTCCGTCCAT-GCTGTGTCA
1 CAAACTCTGAATC-CTGACGTGTCACAGATTCCCTCCATGGC-GTGTCA
*
150850 CAAACTCTGAA-CACTGACGTGTCACAGATTCCTTCCATGGCGTGT--
1 CAAACTCTGAATC-CTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * * *
150895 CAAACTCTGAA-CTCT-AGTGTGTCACAAATTCCCTCCATAGTGTGTCA
1 CAAACTCTGAATC-CTGA-CGTGTCACAGATTCCCTCCATGGCGTGTCA
* * * *
150942 CAAACTTTGAA-CTCTAGA-GTGTTATAGATTCCCTCCATGGCATGTCA
1 CAAACTCTGAATC-CT-GACGTGTCACAGATTCCCTCCATGGCGTGTCA
* * * * *
150989 CAAATTTTGAACCCTGCCTTGTCACAG
1 CAAACTCTGAATCCTGACGTGTCACAG
151016 CCCTATCACA
Statistics
Matches: 331, Mismatches: 50, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
44 4 0.01
45 110 0.33
46 2 0.01
47 209 0.63
48 5 0.02
49 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (47 bp):
CAAACTCTGAATCCTGACGTGTCACAGATTCCCTCCATGGCGTGTCA
Found at i:150705 original size:23 final size:23
Alignment explanation
Indices: 150678--150759 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 23
150668 CTCTGAATCC
*
150678 TGGCATCTCACAGATTCCCTCCA
1 TGGCATGTCACAGATTCCCTCCA
* *
150701 TGGCATGTCACA-AAT-CCTGAACCC
1 TGGCATGTCACAGATTCCCT---CCA
*
150725 TGCCATGTCACAGATTCCCTCCA
1 TGGCATGTCACAGATTCCCTCCA
*
150748 TGGCGTGTCACA
1 TGGCATGTCACA
150760 AACTCTGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 3 0.07
22 2 0.04
23 23 0.50
24 13 0.28
25 2 0.04
26 3 0.07
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.24
Consensus pattern (23 bp):
TGGCATGTCACAGATTCCCTCCA
Found at i:150828 original size:139 final size:138
Alignment explanation
Indices: 150591--151015 Score: 475
Period size: 139 Copynumber: 3.1 Consensus size: 138
150581 AATCTTGGCG
* * * * *
150591 TGTCACAAATTTCCTCCATGGCGTGTCAAACTCTGAACACTGACGTGTCACAGATTCCCTTAATG
1 TGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAATACTAACGTGTCACAGATTCCCTTCATG
** * *
150656 GTGTGTCACAAACTCTGAA-TCCTGGCATCTCACAGATTCCCTCCATGGCATGTCACAAATCCTG
66 GTGTGT-ACAAACTCTGAACT-CTAACGTGTCACAGATTCCCTCCATGGCATGTCACAAATCCTG
150720 AACCCTGCCA
129 AACCCTGCCA
150730 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAATACTAACGTGTCACAGATTCCCTTCA
1 TGTCACAGATTCCCTCCATGGCGTGT--CAAACTCTGAATACTAACGTGTCACAGATTCCCTTCA
* * * *
150795 TGGCGTGT-CAAACTCTGAACTCTAACGTGTCACAAATTCCGTCCAT-GCTGTGTCACAAA-CTC
64 TGGTGTGTACAAACTCTGAACTCTAACGTGTCACAGATTCCCTCCATGGC-ATGTCACAAATC-C
* * *
150857 TGAACACTGACG
127 TGAACCCTGCCA
* ** * *
150869 TGTCACAGATTCCTTCCATGGCGTGTCAAACTCTGAACT-CTAGTGTGTCACAAATTCCCTCCAT
1 TGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAA-TACTAACGTGTCACAGATTCCCTTCAT
* * * * **
150933 AGTGTGTCACAAACTTTGAACTCTAGA-GTGTTATAGATTCCCTCCATGGCATGTCACAAATTTT
65 GGTGTGT-ACAAACTCTGAACTCTA-ACGTGTCACAGATTCCCTCCATGGCATGTCACAAATCCT
*
150997 GAACCCTGCCT
128 GAACCCTGCCA
151008 TGTCACAG
1 TGTCACAG
151016 CCCTATCACA
Statistics
Matches: 241, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
137 37 0.15
138 4 0.02
139 155 0.64
140 4 0.02
141 41 0.17
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (138 bp):
TGTCACAGATTCCCTCCATGGCGTGTCAAACTCTGAATACTAACGTGTCACAGATTCCCTTCATG
GTGTGTACAAACTCTGAACTCTAACGTGTCACAGATTCCCTCCATGGCATGTCACAAATCCTGAA
CCCTGCCA
Found at i:162448 original size:29 final size:28
Alignment explanation
Indices: 162398--162535 Score: 141
Period size: 28 Copynumber: 4.8 Consensus size: 28
162388 TGGCAGCTTT
162398 AACATGTTTGTCTTAATTTAGAAAAGAA
1 AACATGTTTGTCTTAATTTAGAAAAGAA
* *
162426 AACATGTTTGGTTTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGAAAAGAA
* * *
162455 AATATGTTTATCTTAATTTAAAACAAGAAA
1 AACATGTTTGTCTTAATTTAGAA-AAG-AA
* * * * *
162485 AATATTTTTTGTCATAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGAAAAGAA
*
162514 AACATATTTGTCTTAATTTAGA
1 AACATGTTTGTCTTAATTTAGA
162536 CTAGATAAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
28 34 0.38
29 33 0.37
30 9 0.10
31 13 0.15
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGAAAAGAA
Found at i:162528 original size:59 final size:59
Alignment explanation
Indices: 162398--162552 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 59
162388 TGGCAGCTTT
* * * ** *
162398 AACATGTTTGTCTTAATTTAGAA-AAG-AAAACATGTTTGGTTTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAAAACAAGAAAAATATTTTTGGTCATAATCTAGACAAGAA
* * *
162455 AATATGTTTATCTTAATTTAAAACAAGAAAAATATTTTTTGTCATAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTTAAAACAAGAAAAATATTTTTGGTCATAATCTAGACAAGAA
* * *
162514 AACATATTTGTCTTAATTT-AGACTAGATAAAATATTTTT
1 AACATGTTTGTCTTAATTTAAAACAAGA-AAAATATTTTT
162553 ATCTTAATTA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 20 0.25
58 9 0.11
59 52 0.64
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (59 bp):
AACATGTTTGTCTTAATTTAAAACAAGAAAAATATTTTTGGTCATAATCTAGACAAGAA
Found at i:162735 original size:17 final size:17
Alignment explanation
Indices: 162713--162745 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
162703 ATAATAATAA
162713 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
162730 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
162746 TTCTCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:163592 original size:16 final size:16
Alignment explanation
Indices: 163564--163612 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
163554 CGTTGTCTTT
*
163564 TGATGAAAA-ATAATAA
1 TGAT-AAAAGATAAAAA
163580 TGATAAAAGATAAAAA
1 TGATAAAAGATAAAAA
*
163596 TAATAAAAG-TAAAAA
1 TGATAAAAGATAAAAA
163611 TG
1 TG
163613 TAGATAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.22
Consensus pattern (16 bp):
TGATAAAAGATAAAAA
Found at i:169448 original size:23 final size:22
Alignment explanation
Indices: 169400--169448 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
169390 ATATTATTGT
* * *
169400 TATTTTTATTTATTTATTTATT
1 TATTTTTATTTATTTACTCATA
169422 TATTTTTATTCTATTTACTCATA
1 TATTTTTATT-TATTTACTCATA
169445 TATT
1 TATT
169449 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTTATTTATTTACTCATA
Found at i:182390 original size:41 final size:41
Alignment explanation
Indices: 182345--182427 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
182335 GATACCACTA
182345 GCCATCAGGAATTTTTAAGATGATCAGGGGTCACTGCCATT
1 GCCATCAGGAATTTTTAAGATGATCAGGGGTCACTGCCATT
*
182386 GCCATCAGGAATTTTTAAGATGATCAGGGGTCACTGCTATT
1 GCCATCAGGAATTTTTAAGATGATCAGGGGTCACTGCCATT
182427 G
1 G
182428 GACCTGCAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (41 bp):
GCCATCAGGAATTTTTAAGATGATCAGGGGTCACTGCCATT
Found at i:183814 original size:21 final size:21
Alignment explanation
Indices: 183783--183822 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
183773 CCCCCAAAAT
183783 TTTTAAAATTTTTTTCATAATA
1 TTTTAAAATTTTTTT-ATAATA
183805 TTTT-AAATTTTTTTATAA
1 TTTTAAAATTTTTTTATAA
183823 ATTCTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAAATTTTTTTATAATA
Found at i:183958 original size:18 final size:18
Alignment explanation
Indices: 183935--183980 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
183925 TTTTCTTTCA
183935 ATTTATATTA-TTATTTTT
1 ATTTAT-TTATTTATTTTT
183953 ATTTATTTATTTATTTTT
1 ATTTATTTATTTATTTTT
183971 ATTCTATTTA
1 ATT-TATTTA
183981 ATTGTATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTATTTATTTATTTTT
Found at i:184137 original size:15 final size:16
Alignment explanation
Indices: 184117--184147 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
184107 TCTGTCATAT
184117 TGATTTT-ATTTTCAA
1 TGATTTTAATTTTCAA
184132 TGATTTTAATTTTCAA
1 TGATTTTAATTTTCAA
184148 AAATTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TGATTTTAATTTTCAA
Found at i:184392 original size:16 final size:16
Alignment explanation
Indices: 184371--184402 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
184361 TGACCCTTAA
*
184371 AATAATTTTTTTATTT
1 AATAATTATTTTATTT
184387 AATAATTATTTTATTT
1 AATAATTATTTTATTT
184403 CTCAAACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATAATTATTTTATTT
Found at i:186637 original size:4 final size:4
Alignment explanation
Indices: 186628--186659 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
186618 CACAATGTAG
186628 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
186660 TATCAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:186919 original size:17 final size:18
Alignment explanation
Indices: 186897--186954 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
186887 AAAACTCATA
186897 TTTTATCTTTTT-TTCCT
1 TTTTATCTTTTTCTTCCT
*
186914 TTTTATGATTTTTTCTTCCT
1 TTTTAT--CTTTTTCTTCCT
* * *
186934 CTTTATCTTTCTCTTTCT
1 TTTTATCTTTTTCTTCCT
186952 TTT
1 TTT
186955 ACTAATGACC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 6 0.19
18 11 0.34
19 5 0.16
20 10 0.31
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTATCTTTTTCTTCCT
Found at i:189454 original size:21 final size:21
Alignment explanation
Indices: 189428--189483 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
189418 GATTGATTAA
189428 GGTCAACTATGTTTAGTCCAG
1 GGTCAACTATGTTTAGTCCAG
* * *
189449 GGTCAACTATGCTTGGTCTAG
1 GGTCAACTATGTTTAGTCCAG
*
189470 GGTTAACTATGTTT
1 GGTCAACTATGTTT
189484 GTTCAAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (21 bp):
GGTCAACTATGTTTAGTCCAG
Found at i:191536 original size:25 final size:24
Alignment explanation
Indices: 191465--191540 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
191455 CCTAACATGT
* * *
191465 TTTGAACTTACATGTCTCACCACG
1 TTTGAACTTACGTGCCTCACCACA
* **
191489 TTTGAAAC-CACGTGCCTTGCCACA
1 TTTG-AACTTACGTGCCTCACCACA
191513 TGTTGAACTTACGTGCCTCACCACA
1 T-TTGAACTTACGTGCCTCACCACA
191538 TTT
1 TTT
191541 TGGATGTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (24 bp):
TTTGAACTTACGTGCCTCACCACA
Found at i:202970 original size:20 final size:20
Alignment explanation
Indices: 202947--202997 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
202937 TAGAAAATTT
**
202947 TATCAATAGATCATATTATC
1 TATCAATAGATCATACGATC
*
202967 TATCAATAGATTATACGATC
1 TATCAATAGATCATACGATC
*
202987 TATCGATAGAT
1 TATCAATAGAT
202998 AGATAGAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCAATAGATCATACGATC
Found at i:203445 original size:47 final size:48
Alignment explanation
Indices: 203343--203443 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 48
203333 GACAATATGA
* *
203343 AAAAAGAGAAGAAGGCAAGGAGAAAAGAAGGAGAAAAAGGTAAAAAGG
1 AAAAAGAGAAGAAGACAAGGAGAAAAGAAAGAGAAAAAGGTAAAAAGG
* * *
203391 AAGAAAGAGACGAAGAC-AGGA-AAAAGAAAGTGAAGAAGGTAAGAAAGAG
1 AA-AAAGAGAAGAAGACAAGGAGAAAAGAAAGAGAAAAAGGTAA-AAAG-G
203440 AAAA
1 AAAA
203444 GAAGGTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
47 18 0.40
48 12 0.27
49 15 0.33
ACGTcount: A:0.62, C:0.03, G:0.32, T:0.03
Consensus pattern (48 bp):
AAAAAGAGAAGAAGACAAGGAGAAAAGAAAGAGAAAAAGGTAAAAAGG
Found at i:209612 original size:50 final size:50
Alignment explanation
Indices: 209533--209671 Score: 126
Period size: 50 Copynumber: 2.8 Consensus size: 50
209523 CAAAGATAGT
** *
209533 AATAACCTTACAAAATCCACAACGGGATTCTTG-TTTTTCATGAGATCGAGC
1 AATAACCTTAC-AAATCCACAACAAGATTCTTGCTTTTT-ACGAGATCGAGC
* *
209584 AATAACCTTTAC-AATCCACAACAAGATTCTTGCTTTTTACGAGATCAAGT
1 AATAACC-TTACAAATCCACAACAAGATTCTTGCTTTTTACGAGATCGAGC
* * *
209634 AGTAACC-CACATAATCCACAA-AGGGA-TCTTGCTTTTTA
1 AATAACCTTACA-AATCCACAACA-AGATTCTTGCTTTTTA
209672 ATAGAAAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
48 2 0.03
49 13 0.17
50 44 0.59
51 12 0.16
52 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (50 bp):
AATAACCTTACAAATCCACAACAAGATTCTTGCTTTTTACGAGATCGAGC
Found at i:211634 original size:22 final size:23
Alignment explanation
Indices: 211592--211637 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
211582 ATTGCTTATA
211592 AAGGTGAGTCTATTCAGAATGAAAG
1 AAGGTGAGTCTATT-A-AATGAAAG
211617 AAGGTGAGTCTATT-AATGAAA
1 AAGGTGAGTCTATTAAATGAAA
211638 TGTTTGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
25 14 0.67
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (23 bp):
AAGGTGAGTCTATTAAATGAAAG
Found at i:211975 original size:45 final size:45
Alignment explanation
Indices: 211924--212015 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
211914 TCGAAGAGGA
211924 TAAGAGAAACATCAAAAGTAAGATTGAAAATGAAAAAGATTTGAC
1 TAAGAGAAACATCAAAAGTAAGATTGAAAATGAAAAAGATTTGAC
*
211969 TAAGAGAAACATCAAAAGTAAGATTGAAAATGAAAGAGATTTGAC
1 TAAGAGAAACATCAAAAGTAAGATTGAAAATGAAAAAGATTTGAC
212014 TA
1 TA
212016 TGTTAACAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (45 bp):
TAAGAGAAACATCAAAAGTAAGATTGAAAATGAAAAAGATTTGAC
Found at i:215991 original size:16 final size:16
Alignment explanation
Indices: 215970--216001 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
215960 AAAAGTTTGA
215970 CATAAAAAAGGAGTCG
1 CATAAAAAAGGAGTCG
215986 CATAAAAAAGGAGTCG
1 CATAAAAAAGGAGTCG
216002 TTATCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (16 bp):
CATAAAAAAGGAGTCG
Found at i:216473 original size:13 final size:12
Alignment explanation
Indices: 216417--216473 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
216407 TTATTGGAGA
*
216417 ATTTATTTATTTA
1 ATTT-TTTATTTT
216430 ATTTTTTAGTTTT
1 ATTTTTTA-TTTT
* *
216443 ATCTTTTAATTT
1 ATTTTTTATTTT
216455 ACTTTTCTTATTTT
1 A-TTTT-TTATTTT
216469 ATTTT
1 ATTTT
216474 ATTAGTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 8 0.22
13 21 0.58
14 7 0.19
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:216877 original size:14 final size:16
Alignment explanation
Indices: 216858--216890 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
216848 GAAAGATCAA
216858 AAAAATAAA-T-AAAT
1 AAAAATAAAGTAAAAT
216872 AAAAATAAAGTAAAAT
1 AAAAATAAAGTAAAAT
216888 AAA
1 AAA
216891 TCATTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAGTAAAAT
Found at i:217914 original size:34 final size:34
Alignment explanation
Indices: 217869--217959 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 34
217859 AAAGCTTTTC
*
217869 ATCTGGAATGAGTTTACGTAACTTAAAACTCCTT
1 ATCTTGAATGAGTTTACGTAACTTAAAACTCCTT
* * **
217903 ATCTTGAATGAGGTTT-TGTAACTTTAAACTTTTT
1 ATCTTGAATGA-GTTTACGTAACTTAAAACTCCTT
* **
217937 ATCTTGAATAAGGCTACGTAACT
1 ATCTTGAATGAGTTTACGTAACT
217960 CCTCATCTCG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
33 2 0.04
34 40 0.87
35 4 0.09
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (34 bp):
ATCTTGAATGAGTTTACGTAACTTAAAACTCCTT
Found at i:218043 original size:27 final size:27
Alignment explanation
Indices: 217993--218047 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
217983 AACTTAAAAT
217993 TCCTCATATAGAAGGAGACGACGTAAC
1 TCCTCATATAGAAGGAGACGACGTAAC
* * * *
218020 TCCTCATATCGAATGAGGCTACGTAAC
1 TCCTCATATAGAAGGAGACGACGTAAC
218047 T
1 T
218048 TAAAACTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (27 bp):
TCCTCATATAGAAGGAGACGACGTAAC
Found at i:218154 original size:43 final size:44
Alignment explanation
Indices: 218087--218185 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
218077 ACAATTTTTT
* *
218087 TTAAAT-GGAATAAACTCCTTATCTTGAATAAGGCT-CATAACC
1 TTAAATAGGAATAAACTCATCATCTTGAATAAGGCTACATAACC
* * * *
218129 TTAAATAGGAATCAACTCATCATCTTGAATGAGGCTACGTAACT
1 TTAAATAGGAATAAACTCATCATCTTGAATAAGGCTACATAACC
218173 TTAAA-AGGAATAA
1 TTAAATAGGAATAA
218186 GCATATGATG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 6 0.12
43 32 0.67
44 10 0.21
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (44 bp):
TTAAATAGGAATAAACTCATCATCTTGAATAAGGCTACATAACC
Found at i:224810 original size:35 final size:35
Alignment explanation
Indices: 224764--224840 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
224754 ATTCGATTAG
* *
224764 TTGGGTTCTCTAGTATTGTTTGGTCGGGCAATGGA
1 TTGGGTTCTCTAGTATTGTTTGGTCGAGCAACGGA
*
224799 TTGGGTTCTCTAGTATTGTTTGGTCGAGTAACGGA
1 TTGGGTTCTCTAGTATTGTTTGGTCGAGCAACGGA
224834 TTGGGTT
1 TTGGGTT
224841 GGTGGTGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.42
Consensus pattern (35 bp):
TTGGGTTCTCTAGTATTGTTTGGTCGAGCAACGGA
Found at i:246698 original size:14 final size:13
Alignment explanation
Indices: 246663--246697 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
246653 GTAATTGGTT
246663 TAAAAAAAATCAA
1 TAAAAAAAATCAA
246676 TAAAAAAAATCAA
1 TAAAAAAAATCAA
246689 TAAAAAAAA
1 TAAAAAAAA
246698 AGTGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (13 bp):
TAAAAAAAATCAA
Found at i:248122 original size:15 final size:15
Alignment explanation
Indices: 248104--248134 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
248094 GTAATTACAG
248104 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
248119 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
248134 G
1 G
248135 CAATACGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:248407 original size:41 final size:40
Alignment explanation
Indices: 248340--248426 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
248330 TAATATCATC
* * *
248340 TCTTAAATATATTTTTAATGTCATATATTTTATTTTTATT
1 TCTTTAATATATTTTTAATATCATATATTTTATTTTAATT
* *
248380 TCTTTAATATAATTTTTTATATTATATATTTTATTTTAATT
1 TCTTTAATAT-ATTTTTAATATCATATATTTTATTTTAATT
*
248421 TTTTTA
1 TCTTTA
248427 CCTATATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (40 bp):
TCTTTAATATATTTTTAATATCATATATTTTATTTTAATT
Found at i:248480 original size:25 final size:26
Alignment explanation
Indices: 248389--248503 Score: 83
Period size: 25 Copynumber: 4.3 Consensus size: 26
248379 TTCTTTAATA
**
248389 TAATTTTTTATATTATATATTTTATTT
1 TAATTTTTTATA-CCTATATTTTATTT
248416 TAATTTTTT-TACCTATATTATATAAATTT
1 TAATTTTTTATACCTATATT-T-T--ATTT
* **
248445 TAATTTCTTATAGGT-TATTTTATTT
1 TAATTTTTTATACCTATATTTTATTT
* *
248470 TAATTTTTTATTCTTATATTATATATTT
1 TAATTTTTTATACCTATATT-T-TATTT
248498 T-ATTTT
1 TAATTTT
248504 AATATTTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
25 21 0.30
26 7 0.10
27 17 0.24
28 7 0.10
29 16 0.23
30 3 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (26 bp):
TAATTTTTTATACCTATATTTTATTT
Found at i:248497 original size:33 final size:33
Alignment explanation
Indices: 248460--248525 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
248450 TCTTATAGGT
248460 TATTTTATTTT-A-ATTTTTTATTCTTATATTATA
1 TATTTTATTTTAATATTTTTTATT-TTA-ATTATA
248493 TATTTTATTTTAATATTTTTTATTTTAATTATA
1 TATTTTATTTTAATATTTTTTATTTTAATTATA
248526 ACATTACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 17 0.55
34 4 0.13
35 10 0.32
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
TATTTTATTTTAATATTTTTTATTTTAATTATA
Found at i:248498 original size:21 final size:18
Alignment explanation
Indices: 248459--248523 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 18
248449 TTCTTATAGG
*
248459 TTATTTTATTTTAATTTT
1 TTATTTTATATTAATTTT
*
248477 TTATTCTTATATTATATATT
1 TTATT-TTATATTA-ATTTT
248497 TTATTTTA-A-T-ATTTT
1 TTATTTTATATTAATTTT
248512 TTATTTTA-ATTA
1 TTATTTTATATTA
248524 TAACATTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.32
16 1 0.03
17 1 0.03
18 6 0.15
19 10 0.25
20 9 0.22
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTATATTAATTTT
Found at i:248500 original size:20 final size:20
Alignment explanation
Indices: 248475--248519 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
248465 TATTTTAATT
248475 TTTTATTCTT-ATATTATATA
1 TTTTATT-TTAATATTATATA
* *
248495 TTTTATTTTAATATTTTTTA
1 TTTTATTTTAATATTATATA
248515 TTTTA
1 TTTTA
248520 ATTATAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTTTAATATTATATA
Found at i:248519 original size:53 final size:53
Alignment explanation
Indices: 248406--248508 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
248396 TTATATTATA
**
248406 TATTTTATTTTAATTTTTTTACCTATATTATATAAATTTTAATTTCTTATAGGT
1 TATTTTATTTTAATTTTTTTACCTATATTATAT-AATTTTAATTTAATATAGGT
* * *
248460 TATTTTATTTTAATTTTTTATTCTTATATTATAT-ATTTTATTTTAATAT
1 TATTTTATTTTAATTTTTT-TACCTATATTATATAATTTTAATTTAATAT
248509 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 12 0.28
54 19 0.44
55 12 0.28
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (53 bp):
TATTTTATTTTAATTTTTTTACCTATATTATATAATTTTAATTTAATATAGGT
Found at i:250116 original size:3 final size:3
Alignment explanation
Indices: 250108--250144 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
250098 CGAAGTGAAT
*
250108 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
250145 GTGAAAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:264069 original size:15 final size:16
Alignment explanation
Indices: 264037--264079 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
264027 CTCTCTAGAG
*
264037 TTTTCTTTAAACTCTT
1 TTTTTTTTAAACTCTT
* *
264053 TTTTTTTTAAATTTTT
1 TTTTTTTTAAACTCTT
264069 TTTTTTTTAAA
1 TTTTTTTTAAA
264080 AAAAGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTTAAACTCTT
Found at i:264799 original size:14 final size:14
Alignment explanation
Indices: 264780--264807 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
264770 AAAAATGAAA
264780 TTCACAAAGACAAT
1 TTCACAAAGACAAT
264794 TTCACAAAGACAAT
1 TTCACAAAGACAAT
264808 CAAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
TTCACAAAGACAAT
Found at i:267417 original size:4 final size:4
Alignment explanation
Indices: 267403--267441 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
267393 TATATGCTAT
*
267403 TTTG GTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
267442 TTAATTGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
TTTG
Found at i:275625 original size:32 final size:33
Alignment explanation
Indices: 275558--275625 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
275548 TTTGATGTAT
* * *
275558 TGAGTTGTTGGAAATTTTAGTTTTCCCTCCCAAA
1 TGAGCTGTTGGAAATTTTAG-TCTCACTCCCAAA
275592 TGAGCTGTTGGAAATTTTAG-CTCACTCCCAAA
1 TGAGCTGTTGGAAATTTTAGTCTCACTCCCAAA
275624 TG
1 TG
275626 TTTTGGAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 12 0.39
34 19 0.61
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (33 bp):
TGAGCTGTTGGAAATTTTAGTCTCACTCCCAAA
Found at i:281215 original size:4 final size:4
Alignment explanation
Indices: 281206--281230 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
281196 GTTAGTGCTA
281206 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
281231 TGTGTGTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:284735 original size:141 final size:142
Alignment explanation
Indices: 284585--284863 Score: 461
Period size: 141 Copynumber: 2.0 Consensus size: 142
284575 CTTTTTAGTG
* *
284585 ATTTTATATTCTCTAATGTGTATGTTTTGACTTATATTATGACTTTCTGATTAGGTTCTTTTGAG
1 ATTTTATATTCTCTAATATGTATGTTTTGACTTATATTATGACTTTCTGATGAGGTTCTTTTGAG
* ** * *
284650 TTAAAAGTGAGATGTATA-AAAAAAGGTAGGCCAAAAAGTGCCATGATGGTTAAGAGTTAGAGAG
66 TCAAAAGTGAGATGTATACAAAAAAAATAGGCCAAAAAGTGCCATGATGGTTAAGAATTAAAGAG
284714 CTTAGCTTAGCA
131 CTTAGCTTAGCA
*
284726 ATTTTATATTCTCTAATATGTATGTTTTGACTTATATTATGACTTTGTGATGAGGTTCTTTTGAG
1 ATTTTATATTCTCTAATATGTATGTTTTGACTTATATTATGACTTTCTGATGAGGTTCTTTTGAG
* *
284791 TCAAAAGTGAGATGTATACAAAAAAAATGGGCCCAAAAGTGCCATGATGGTTAAGAATTAAAGAG
66 TCAAAAGTGAGATGTATACAAAAAAAATAGGCCAAAAAGTGCCATGATGGTTAAGAATTAAAGAG
284856 CTTAGCTT
131 CTTAGCTT
284864 GATTTTGAAG
Statistics
Matches: 127, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
141 79 0.62
142 48 0.38
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (142 bp):
ATTTTATATTCTCTAATATGTATGTTTTGACTTATATTATGACTTTCTGATGAGGTTCTTTTGAG
TCAAAAGTGAGATGTATACAAAAAAAATAGGCCAAAAAGTGCCATGATGGTTAAGAATTAAAGAG
CTTAGCTTAGCA
Found at i:294436 original size:21 final size:21
Alignment explanation
Indices: 294410--294498 Score: 101
Period size: 21 Copynumber: 4.2 Consensus size: 21
294400 TATGTATGCA
*
294410 TTTTAAAACCTGCAGG-TACAT
1 TTTTAAAACCT-CCGGATACAT
*
294431 TTTTAAAACCTCTGGATACAT
1 TTTTAAAACCTCCGGATACAT
* *
294452 TCTCAAAACCTCCGGATACAT
1 TTTTAAAACCTCCGGATACAT
*
294473 TCTTAAAACCTCC-GAGTACAT
1 TTTTAAAACCTCCGGA-TACAT
294494 TTTTA
1 TTTTA
294499 TGAAACTTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 5 0.08
21 55 0.92
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.34
Consensus pattern (21 bp):
TTTTAAAACCTCCGGATACAT
Found at i:294623 original size:21 final size:21
Alignment explanation
Indices: 294574--294618 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
294564 AGCAACATTT
*
294574 TTCAAAACTTCTAGGTATGTC
1 TTCAAAACTTCTAGGTATCTC
294595 TTCAAAACTTCTAAGTGTATCTC
1 TTCAAAACTTCT-AG-GTATCTC
294618 T
1 T
294619 AAAACCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 2 0.10
23 7 0.33
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (21 bp):
TTCAAAACTTCTAGGTATCTC
Found at i:295402 original size:59 final size:59
Alignment explanation
Indices: 295337--295740 Score: 406
Period size: 58 Copynumber: 6.9 Consensus size: 59
295327 TCAAGTTTTT
* ** * *
295337 AAATTGAACTTGTTGCAAGATAGGTAGAGCGTAAATTAAGTCTAGGAGTTCAAAATATC
1 AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
* * * * **
295396 AAATTG-ATTTGTTTTAAGATACGTAGAGCGTAAATTAAGTCTAAGAGAGCAAAATATC
1 AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
* *
295454 AAATTG-ATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTC-AAATATC
1 AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
** * * *
295511 AAATCAAATTTGTTTTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAGTTTAAAATATC
1 AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
* * * * * * * *
295570 AAATCGAATCTGTTTTGAGATAAGTTA-AGCCTAAATTAAGTCTAGGAGTTTCAAACTTTTT
1 AAATTGAATTTGTTTTAAGAT-AGGTAGAGCCTAGATTAAGTCTAGGAG-TTCAAA-ATATC
* ** * * *
295631 AAATT-AAGCTTGTCGCTAA-ATAGGTCGAGCCTAGATTGAGTTTAGGAGTTCAAAATATC
1 AAATTGAA-TTTGT-TTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
* * *
295690 AAATTGAATTTATTTTAAGATAGGTTGAGCCTAGATTAAGTCTAAGAGTTC
1 AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTC
295741 CAAACCTTTT
Statistics
Matches: 283, Mismatches: 52, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
57 11 0.04
58 130 0.46
59 90 0.32
60 21 0.07
61 29 0.10
62 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (59 bp):
AAATTGAATTTGTTTTAAGATAGGTAGAGCCTAGATTAAGTCTAGGAGTTCAAAATATC
Found at i:295782 original size:120 final size:116
Alignment explanation
Indices: 295337--295797 Score: 383
Period size: 120 Copynumber: 3.9 Consensus size: 116
295327 TCAAGTTTTT
* ** * * * * * * **
295337 AAATTGAACTTGTTGCAAGATAGGTAGAGCGTAAATTAAGTCTAGGAGTTCAAAATATCAAATTG
1 AAATTGAATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAGTTCAAACTTTTAAATCA
* * * * * * **
295402 A--TTTGTTTTAAGATACGTAGAGCGTAAATTAAGTCTAAGAGAGCAAAATATC
66 ACCTTTG--TT-AGATAGGTCGAGCCTAGATTAAGTTTAGGAGTTCAAAATATC
* * *
295454 AAATTG-ATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAATTCAAA-TATCAAATCA
1 AAATTGAATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAGTTCAAACTTTTAAATCA
* * *
295517 A-ATTTGTTTTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAGTTTAAAATATC
66 ACCTTTG--TT-AGATAGGTCGAGCCTAGATTAAGTTTAGGAGTTCAAAATATC
* * * * * *
295570 AAATCGAATCTGTTTTGAGATAAGTTAAGCCTAAATTAAGTCTAGGAGTTTCAAACTTTTTAAAT
1 AAATTGAATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAG-TTCAAAC-TTTTAAAT
* * * * *
295635 TAAGCTTGTCGCTAAATAGGTCGAGCCTAGATTGAGTTTAGGAGTTCAAAATATC
64 CAACCTT-T-GTTAGATAGGTCGAGCCTAGATTAAGTTTAGGAGTTCAAAATATC
* * *
295690 AAATTGAATTTATTTTAAGATAGGTTGAGCCTAGATTAAGTCTAAGAGTTCCAAACCTTTTATAT
1 AAATTGAATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAGTT-CAAA-CTTTTAAAT
* **
295755 CACACCTATTGTTAGATAGATTAAGCCTAGATTAAGTTTAGGA
64 CA-ACCT-TTGTTAGATAGGTCGAGCCTAGATTAAGTTTAGGA
295798 ACTTTTACTT
Statistics
Matches: 281, Mismatches: 51, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
115 9 0.03
116 87 0.31
117 41 0.15
118 6 0.02
119 2 0.01
120 125 0.44
121 8 0.03
122 2 0.01
123 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (116 bp):
AAATTGAATTTGTTTTAAGATAGGTTGAGCCTAGATTAAGTCTAGGAGTTCAAACTTTTAAATCA
ACCTTTGTTAGATAGGTCGAGCCTAGATTAAGTTTAGGAGTTCAAAATATC
Found at i:297415 original size:23 final size:25
Alignment explanation
Indices: 297387--297434 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
297377 ATTTAGGTAT
297387 AGAG-AAATAAAAT-TAAATACATA
1 AGAGAAAATAAAATATAAATACATA
* *
297410 AGAGAAAATGAAATATATATACATA
1 AGAGAAAATAAAATATAAATACATA
297435 TGTTTAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 8 0.38
25 9 0.43
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23
Consensus pattern (25 bp):
AGAGAAAATAAAATATAAATACATA
Found at i:300098 original size:18 final size:17
Alignment explanation
Indices: 300061--300093 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
300051 TATTTTGTGT
300061 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
300078 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
300093 T
1 T
300094 TATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:315043 original size:17 final size:19
Alignment explanation
Indices: 315023--315057 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
315013 ATACAAACAA
315023 AAAAT-AATA-TAAAATAT
1 AAAATAAATATTAAAATAT
315040 AAAATAAATATTAAAATA
1 AAAATAAATATTAAAATA
315058 CTCATTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAAATATTAAAATAT
Found at i:316198 original size:17 final size:17
Alignment explanation
Indices: 316166--316198 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
316156 TTGGTTTAGG
316166 TTTCAAATTTTCATAAA
1 TTTCAAATTTTCATAAA
316183 TTTCATAATTTT-ATAA
1 TTTCA-AATTTTCATAA
316199 TAATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTCAAATTTTCATAAA
Found at i:316898 original size:11 final size:11
Alignment explanation
Indices: 316882--316911 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
316872 TGTACTTGAG
316882 GACTTTGATGA
1 GACTTTGATGA
316893 GACTTTGATGA
1 GACTTTGATGA
*
316904 TACTTTGA
1 GACTTTGA
316912 ATAAACTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (11 bp):
GACTTTGATGA
Found at i:319861 original size:25 final size:25
Alignment explanation
Indices: 319802--319861 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
319792 TGAGCCATGT
*
319802 ATTTATATATATATATATATATATA
1 ATTTATATATATATAAATATATATA
319827 ATTT-TGATATATAATAAA-AT-TATTA
1 ATTTAT-ATATAT-ATAAATATATA-TA
319852 ATTTATATAT
1 ATTTATATAT
319862 CAAATGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
24 3 0.10
25 22 0.73
26 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTATATATATATAAATATATATA
Done.