Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 1 of 26
Found at i:6335 original size:14 final size:14
Alignment explanation
Indices: 6316--6364 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
6306 TTAACATTTT
6316 AAATATAAAAATTA
1 AAATATAAAAATTA
* *
6330 AAATATTAAATTTA
1 AAATATAAAAATTA
6344 ATAATATAAAAATTA
1 A-AATATAAAAATTA
6359 AAATAT
1 AAATAT
6365 TTTTATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATAAAAATTA
Found at i:6349 original size:29 final size:29
Alignment explanation
Indices: 6304--6365 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
6294 TTTTTATATT
*
6304 TATTAACATTTTAAATATAAAAATTAAAA
1 TATTAACATTTAAAATATAAAAATTAAAA
6333 TATTAA-ATTTAATAATATAAAAATTAAAA
1 TATTAACATTTAA-AATATAAAAATTAAAA
6362 TATT
1 TATT
6366 TTTATTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TATTAACATTTAAAATATAAAAATTAAAA
Found at i:6358 original size:21 final size:21
Alignment explanation
Indices: 6305--6360 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
6295 TTTTATATTT
* *
6305 ATTAACATTTTAAATATAAAA
1 ATTAAAATATTAAATATAAAA
* *
6326 ATTAAAATATTAAATTTAATA
1 ATTAAAATATTAAATATAAAA
6347 ATATAAAA-ATTAAA
1 AT-TAAAATATTAAA
6361 ATATTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAAATATTAAATATAAAA
Found at i:6384 original size:29 final size:27
Alignment explanation
Indices: 6317--6383 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
6307 TAACATTTTA
6317 AATATAAAAATTAAAATATTAAATTTAAT
1 AATATAAAAATTAAAATATT--ATTTAAT
6346 AATATAAAAATTAAAATATT-TTTATTAT
1 AATATAAAAATTAAAATATTATTTA--AT
6374 AATATAAAAA
1 AATATAAAAA
6384 AATTTAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.11
28 12 0.33
29 20 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATATAAAAATTAAAATATTATTTAAT
Found at i:6387 original size:30 final size:29
Alignment explanation
Indices: 6304--6387 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
6294 TTTTTATATT
* *
6304 TATTAACATTTTA-AATATAAAAATTAAAA
1 TATTAA-ATTTAATAATAAAAAAATTAAAA
*
6333 TATTAAATTTAATAATATAAAAATTAAAA
1 TATTAAATTTAATAATAAAAAAATTAAAA
**
6362 TATTTTTATTATAAT-ATAAAAAAATT
1 TA-TTAAATT-TAATAATAAAAAAATT
6388 TAACAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.10
29 24 0.50
30 15 0.31
31 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
TATTAAATTTAATAATAAAAAAATTAAAA
Found at i:9086 original size:2 final size:2
Alignment explanation
Indices: 9081--9112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9071 GTCAAATCAA
9081 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
9113 CCGGTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10625 original size:2 final size:2
Alignment explanation
Indices: 10620--10649 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10610 CTAAAACTAA
10620 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10650 AAAACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11306 original size:2 final size:2
Alignment explanation
Indices: 11299--11340 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
11289 AATATCTTAT
* *
11299 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TC TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11340 T
1 T
11341 GTCCATATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11383 original size:2 final size:2
Alignment explanation
Indices: 11376--11413 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11366 TCAGAAACCA
11376 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
11414 TTCTAACTTA
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):
AT
Found at i:12716 original size:6 final size:6
Alignment explanation
Indices: 12709--12743 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
12699 TTTCATTTTA
* *
12709 AAAATA AAAATT AAAATT AAAATT AAAATT GAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
12744 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:12749 original size:2 final size:2
Alignment explanation
Indices: 12742--12776 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12732 TAAAATTGAA
*
12742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12777 AAGAGAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12783 original size:2 final size:2
Alignment explanation
Indices: 12778--12804 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12768 ATATCTATAA
12778 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
12805 TGGGGTTGGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17411 original size:31 final size:31
Alignment explanation
Indices: 17376--17437 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
17366 AGAGAGAGAG
*
17376 CAAAGGAAATCAACCCATATGTAGCAGAAGC
1 CAAAGGAAATCAAACCATATGTAGCAGAAGC
17407 CAAAGGAAATCAAACCATATGTAGCAGAAGC
1 CAAAGGAAATCAAACCATATGTAGCAGAAGC
17438 AGCAGCGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (31 bp):
CAAAGGAAATCAAACCATATGTAGCAGAAGC
Found at i:17748 original size:2 final size:2
Alignment explanation
Indices: 17741--17773 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17731 TAGAAACAGC
17741 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
17774 TTTTTAGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17922 original size:16 final size:16
Alignment explanation
Indices: 17898--17959 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
17888 AAATTTTAAA
17898 ATTTAAATTATTTTAG
1 ATTTAAATTATTTTAG
* *
17914 ATTTGAATTATTTTAA
1 ATTTAAATTATTTTAG
17930 ATTTAAATTATTTTAG
1 ATTTAAATTATTTTAG
*
17946 ATTTAAGTTATTTT
1 ATTTAAATTATTTT
17960 GAATTTAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTAAATTATTTTAG
Found at i:17936 original size:32 final size:32
Alignment explanation
Indices: 17890--17966 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
17880 ATTATTTTAA
17890 ATTTTAAAATTTAAATTATTTTAGATTTGAA-TT
1 ATTTT-AAATTTAAATTATTTTAGATTT-AAGTT
17923 ATTTTAAATTTAAATTATTTTAGATTTAAGTT
1 ATTTTAAATTTAAATTATTTTAGATTTAAGTT
*
17955 ATTTTGAATTTA
1 ATTTTAAATTTA
17967 GATCATTTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 2 0.05
32 35 0.83
33 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (32 bp):
ATTTTAAATTTAAATTATTTTAGATTTAAGTT
Found at i:17965 original size:16 final size:15
Alignment explanation
Indices: 17897--17966 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 15
17887 TAAATTTTAA
17897 AATTTAAATTATTTT
1 AATTTAAATTATTTT
*
17912 AGATTTGAATTATTTT
1 A-ATTTAAATTATTTT
17928 AAATTTAAATTATTTT
1 -AATTTAAATTATTTT
*
17944 AGATTTAAGTTATTTT
1 A-ATTTAAATTATTTT
17960 GAATTTA
1 -AATTTA
17967 GATCATTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
15 2 0.04
16 44 0.92
17 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (15 bp):
AATTTAAATTATTTT
Found at i:17981 original size:32 final size:32
Alignment explanation
Indices: 17890--17987 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 32
17880 ATTATTTTAA
* *
17890 ATTTTAAAATTTAAATTATTTTAGATTTGAATT
1 ATTTT-AAATTTAAATCATTTCAGATTTGAATT
* *
17923 ATTTTAAATTTAAATTATTTTAGATTT-AAGTT
1 ATTTTAAATTTAAATCATTTCAGATTTGAA-TT
* * * *
17955 ATTTTGAATTTAGATCATTTCGGATTTTAATT
1 ATTTTAAATTTAAATCATTTCAGATTTGAATT
17987 A
1 A
17988 ATCAAGCTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.03
32 49 0.84
33 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (32 bp):
ATTTTAAATTTAAATCATTTCAGATTTGAATT
Found at i:18800 original size:16 final size:16
Alignment explanation
Indices: 18791--18836 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
18781 TCATTTTGAG
*
18791 TTCGGATCATTTTGGA
1 TTCGGATCATTTCGGA
*
18807 TTCGAATCATTTCGGA
1 TTCGGATCATTTCGGA
*
18823 TTTGGATCATTTCG
1 TTCGGATCATTTCG
18837 AGTTCAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (16 bp):
TTCGGATCATTTCGGA
Found at i:21530 original size:3 final size:3
Alignment explanation
Indices: 21524--21552 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21514 TGTCACCACT
21524 CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
21553 TAATTCAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:22723 original size:2 final size:2
Alignment explanation
Indices: 22718--22754 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
22708 CAATCTACAC
*
22718 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22755 CATTTTCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35926 original size:27 final size:26
Alignment explanation
Indices: 35889--35985 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 26
35879 TAGGTAGGAG
35889 ATATTTATTTTTAATTTTATAAAAAT
1 ATATTTATTTTTAATTTTATAAAAAT
*
35915 ATATTTAGTTTTTAATGTTGA-AAAAAT
1 ATATTTA-TTTTTAAT-TTTATAAAAAT
*
35942 AT-TTATAATTTTTTAAGTTTTAGTTAAAAT
1 ATATT-T-A-TTTTTAA-TTTTA-TAAAAAT
35972 ATATTTATTTTTAA
1 ATATTTATTTTTAA
35986 GTTATTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
26 9 0.15
27 17 0.29
28 21 0.36
29 2 0.03
30 8 0.14
31 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (26 bp):
ATATTTATTTTTAATTTTATAAAAAT
Found at i:35988 original size:28 final size:28
Alignment explanation
Indices: 35889--35985 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 28
35879 TAGGTAGGAG
35889 ATATTTA-TTTTTAATTTTA-TAAAAAT
1 ATATTTAGTTTTTAATTTTAGTAAAAAT
* *
35915 ATATTTAGTTTTTAATGTT-GAAAAAAT
1 ATATTTAGTTTTTAATTTTAGTAAAAAT
* *
35942 AT-TTATAATTTTTTAAGTTTTAGTTAAAAT
1 ATATT-T-AGTTTTTAA-TTTTAGTAAAAAT
35972 ATATTTA-TTTTTAA
1 ATATTTAGTTTTTAA
35986 GTTATTATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 9 0.16
27 19 0.33
28 15 0.26
29 4 0.07
30 9 0.16
31 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
ATATTTAGTTTTTAATTTTAGTAAAAAT
Found at i:36071 original size:16 final size:17
Alignment explanation
Indices: 36052--36083 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
36042 TTAATTATTA
36052 TTTTTATT-TAAAATAT
1 TTTTTATTATAAAATAT
36068 TTTTTATTATAAAATA
1 TTTTTATTATAAAATA
36084 ATAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTATTATAAAATAT
Found at i:36116 original size:21 final size:22
Alignment explanation
Indices: 36092--36140 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
36082 TAATAAAAAA
36092 TTAATTAATT-TAAAATTAT-TT
1 TTAATT-ATTGTAAAATTATATT
*
36113 TTAATTATTGTTAAATTATATT
1 TTAATTATTGTAAAATTATATT
36135 TTAATT
1 TTAATT
36141 TAAATGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTAATTATTGTAAAATTATATT
Found at i:36450 original size:18 final size:18
Alignment explanation
Indices: 36409--36445 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
36399 TTAAAAATAT
*
36409 AATTTTTTTATTTTAATC
1 AATTTTTTTATTTTAAAC
36427 AATTTTTTTATTTTTAAAC
1 AATTTTTTTA-TTTTAAAC
36446 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTTTTTTATTTTAAAC
Found at i:36648 original size:22 final size:21
Alignment explanation
Indices: 36623--36670 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
36613 CTGAGAATAG
*
36623 AATTTAATTCTATTTTAATCAT
1 AATTTAATTATATTTTAA-CAT
36645 AATTTAATTATATTTTAACAT
1 AATTTAATTATATTTTAACAT
36666 -ATTTA
1 AATTTA
36671 TTTAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.20
21 3 0.12
22 17 0.68
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTAATTATATTTTAACAT
Found at i:37468 original size:2 final size:2
Alignment explanation
Indices: 37461--37485 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37451 CAACTGTAAT
37461 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 T
37486 TCAAAAGTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38241 original size:6 final size:6
Alignment explanation
Indices: 38222--38262 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
38212 TATAATAAAA
* * *
38222 TTAGAA TTAAAC TTAGAC TTGGAC TTAGAC TTAGAC TTAGA
1 TTAGAC TTAGAC TTAGAC TTAGAC TTAGAC TTAGAC TTAGA
38263 GCGGTAGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (6 bp):
TTAGAC
Found at i:39094 original size:6 final size:6
Alignment explanation
Indices: 39083--39116 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
39073 AATGCGATGG
* *
39083 TTCCTC TTCCTC TTCCTC TTCCTT TTCCTT TTCC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCC
39117 ATGCTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCCTC
Found at i:39215 original size:13 final size:14
Alignment explanation
Indices: 39192--39254 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 14
39182 AAAGTAACTT
*
39192 TATTTTTAAAATAA
1 TATTATTAAAATAA
39206 -ATTATTAAAATAA
1 TATTATTAAAATAA
*
39219 TATTATTTTAAAATTA
1 TATTA--TTAAAATAA
* *
39235 T-TTATTAAAGTAT
1 TATTATTAAAATAA
39248 TATTATT
1 TATTATT
39255 TTACTTGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
13 19 0.47
14 9 0.22
15 3 0.08
16 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTATTAAAATAA
Found at i:39232 original size:29 final size:29
Alignment explanation
Indices: 39195--39257 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
39185 GTAACTTTAT
39195 TTTTAAAATAAATTATTAAAATAATATTA
1 TTTTAAAATAAATTATTAAAATAATATTA
* * * *
39224 TTTTAAAATTATTTATTAAAGTATTATTA
1 TTTTAAAATAAATTATTAAAATAATATTA
39253 TTTTA
1 TTTTA
39258 CTTGTATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTAAAATAAATTATTAAAATAATATTA
Found at i:39356 original size:15 final size:15
Alignment explanation
Indices: 39336--39365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39326 ACACTTTATA
39336 AGTTTTATTTTTTTT
1 AGTTTTATTTTTTTT
*
39351 AGTTTTGTTTTTTTT
1 AGTTTTATTTTTTTT
39366 TTAAGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (15 bp):
AGTTTTATTTTTTTT
Found at i:39365 original size:17 final size:16
Alignment explanation
Indices: 39338--39389 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
39328 ACTTTATAAG
*
39338 TTTTATTTTTTTTAGT
1 TTTTTTTTTTTTTAGT
39354 TTTGTTTTTTTTTTAAGT
1 TTT-TTTTTTTTTT-AGT
*
39372 TTTTTTCATTTTTTAGT
1 TTTTTT-TTTTTTTAGT
39389 T
1 T
39390 AATTAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.10
17 16 0.52
18 12 0.39
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTTTTAGT
Found at i:39366 original size:18 final size:17
Alignment explanation
Indices: 39338--39389 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
39328 ACTTTATAAG
*
39338 TTTTATTTTTTTTAGTT
1 TTTTTTTTTTTTTAGTT
*
39355 TTGTTTTTTTTTTAAGTT
1 TT-TTTTTTTTTTTAGTT
**
39373 TTTTTCATTTTTTAGTT
1 TTTTTTTTTTTTTAGTT
39390 AATTAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTTTTAGTT
Found at i:39491 original size:17 final size:18
Alignment explanation
Indices: 39471--39504 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39461 TTTAAAAAAT
*
39471 AAATTTTTAT-TTTTAAA
1 AAATTATTATATTTTAAA
39488 AAATTATTATATTTTAA
1 AAATTATTATATTTTAA
39505 TACGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTATTATATTTTAAA
Found at i:39984 original size:17 final size:18
Alignment explanation
Indices: 39952--39986 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39942 TGATAATTTT
*
39952 ATATATTTTAATAATAAA
1 ATATATTTTAAAAATAAA
39970 ATATA-TTTAAAAATAAA
1 ATATATTTTAAAAATAAA
39987 TTAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATTTTAAAAATAAA
Found at i:40044 original size:22 final size:23
Alignment explanation
Indices: 40019--40061 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40009 ACAAAACTTT
*
40019 AAAAAAACAAAA-TTGAAAAGAA
1 AAAAAAACAAAACTTAAAAAGAA
*
40041 AAAACAACAAAACTTAAAAAG
1 AAAAAAACAAAACTTAAAAAG
40062 GACGAGGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAAAACAAAACTTAAAAAGAA
Found at i:40152 original size:16 final size:16
Alignment explanation
Indices: 40133--40181 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
40123 TTTAAAATAA
40133 TATTATTTTGATAATT
1 TATTATTTTGATAATT
***
40149 TATT-TTAAAATAA--
1 TATTATTTTGATAATT
40162 TATTATTTTGATAATT
1 TATTATTTTGATAATT
40178 TATT
1 TATT
40182 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 6 0.25
16 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
TATTATTTTGATAATT
Found at i:40153 original size:13 final size:14
Alignment explanation
Indices: 40129--40183 Score: 69
Period size: 13 Copynumber: 3.9 Consensus size: 14
40119 TAATTTTAAA
40129 ATAATATTATTTTG
1 ATAATATTATTTTG
*
40143 ATAAT-TTATTTTAAA
1 ATAATATTATTTT--G
40158 ATAATATTATTTTG
1 ATAATATTATTTTG
40172 ATAAT-TTATTTT
1 ATAATATTATTTT
40184 AAAATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 14 0.39
14 10 0.28
15 5 0.14
16 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
ATAATATTATTTTG
Found at i:40199 original size:30 final size:29
Alignment explanation
Indices: 40097--40203 Score: 160
Period size: 29 Copynumber: 3.7 Consensus size: 29
40087 CTCTCGAAAC
* * * *
40097 AAAATAATAATATTTTAATAAATAATTTT
1 AAAATAATATTATTTTGATAATTTATTTT
40126 AAAATAATATTATTTTGATAATTTATTTT
1 AAAATAATATTATTTTGATAATTTATTTT
40155 AAAATAATATTATTTTGATAATTTATTTT
1 AAAATAATATTATTTTGATAATTTATTTT
*
40184 AAAATTAAGATTATTTTGAT
1 AAAA-TAATATTATTTTGAT
40204 TAATCTATCA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
29 58 0.81
30 14 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
AAAATAATATTATTTTGATAATTTATTTT
Found at i:40399 original size:5 final size:5
Alignment explanation
Indices: 40389--40428 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
40379 CACTAGAGGG
40389 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
40429 AAGAAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:41219 original size:8 final size:8
Alignment explanation
Indices: 41206--41265 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
41196 ATAAAATTAA
*
41206 TTATATTT
1 TTATATAT
41214 TTATATAT
1 TTATATAT
*
41222 TTATTAAAT
1 TTA-TATAT
*
41231 ATATCATAT
1 TTAT-ATAT
41240 TTATATAT
1 TTATATAT
41248 TTA-ATAT
1 TTATATAT
* *
41255 TAATAAAT
1 TTATATAT
41263 TTA
1 TTA
41266 ACTGAGCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 6 0.15
8 23 0.56
9 12 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATATAT
Found at i:41259 original size:28 final size:27
Alignment explanation
Indices: 41192--41259 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
41182 TGCATTAAAA
* * *
41192 ATATATAAAATTAAT-TATATTTTTAT
1 ATATTTAATATTAATATATATATTTAT
*
41218 ATATTT-AT-TAAATATATCATATTTAT
1 ATATTTAATATTAATATAT-ATATTTAT
41244 ATATTTAATATTAATA
1 ATATTTAATATTAATA
41260 AATTTAACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 4 0.12
25 4 0.12
26 18 0.55
27 2 0.06
28 5 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATTTAATATTAATATATATATTTAT
Found at i:41740 original size:2 final size:2
Alignment explanation
Indices: 41733--41762 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41723 TAAATGAATT
41733 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
41763 AAACCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47870 original size:2 final size:2
Alignment explanation
Indices: 47863--47897 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
47853 TTATCTCTAA
*
47863 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
47898 TCCATCCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:59163 original size:84 final size:84
Alignment explanation
Indices: 59018--59186 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
59008 TAAGCTTGTA
*
59018 TATGGATGATCTAATTTACACAGGGAATGATGATAAGTTAATGATGGAGTTCAAGAGGTCCATGA
1 TATGGATGATCTAATTTACACAGGGAATGATGATAAGTTAATGATGGAGTTCAAGAAGTCCATGA
59083 AGCTAGAATTCGCGATGAC
66 AGCTAGAATTCGCGATGAC
*
59102 TATGGATGATCTAATTTACATAGGGAATGATGATAAGTTAATGATGGAGTTCAAGAAGTCCATGA
1 TATGGATGATCTAATTTACACAGGGAATGATGATAAGTTAATGATGGAGTTCAAGAAGTCCATGA
*
59167 AGCTAGAATTTGCGATGAC
66 AGCTAGAATTCGCGATGAC
59186 T
1 T
59187 GACATAGGAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (84 bp):
TATGGATGATCTAATTTACACAGGGAATGATGATAAGTTAATGATGGAGTTCAAGAAGTCCATGA
AGCTAGAATTCGCGATGAC
Found at i:62618 original size:26 final size:26
Alignment explanation
Indices: 62562--62611 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
62552 TTAGACTAAC
*
62562 AACATAATAGAACAAAATTTAAAGAT
1 AACATAATAGAACAAAATTTAAAAAT
62588 AACATAATA-AA-AAAATTTAAAAAT
1 AACATAATAGAACAAAATTTAAAAAT
62612 CTAACATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 2 0.09
26 9 0.39
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (26 bp):
AACATAATAGAACAAAATTTAAAAAT
Found at i:66285 original size:14 final size:16
Alignment explanation
Indices: 66256--66288 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
66246 AATATAGATT
66256 TTAATAAATAAACATA
1 TTAATAAATAAACATA
66272 TTAA-AAAT-AACATA
1 TTAATAAATAAACATA
66286 TTA
1 TTA
66289 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAATAAATAAACATA
Found at i:66467 original size:31 final size:32
Alignment explanation
Indices: 66432--66492 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
66422 GAACTCGAAT
*
66432 TCAAATTCG-AAAAATCTGAACTCGAAAAGGC
1 TCAAATTCGAAAAAATCTGAACTCAAAAAGGC
*
66463 TCAAATTCGAAAAAATTTGAACTCAAAAAG
1 TCAAATTCGAAAAAATCTGAACTCAAAAAG
66493 ACTCGAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (32 bp):
TCAAATTCGAAAAAATCTGAACTCAAAAAGGC
Found at i:66505 original size:32 final size:32
Alignment explanation
Indices: 66432--66505 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
66422 GAACTCGAAT
* * *
66432 TCAAATTCG-AAAAATCTGAACTCGAAAAGGC
1 TCAAACTCGAAAAAATCTGAACTCAAAAAGAC
* *
66463 TCAAATTCGAAAAAATTTGAACTCAAAAAGAC
1 TCAAACTCGAAAAAATCTGAACTCAAAAAGAC
*
66495 TCGAACTCGAA
1 TCAAACTCGAA
66506 TAGACCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 9 0.24
32 28 0.76
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (32 bp):
TCAAACTCGAAAAAATCTGAACTCAAAAAGAC
Found at i:66584 original size:16 final size:16
Alignment explanation
Indices: 66560--66591 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66550 CAAAAACTTT
*
66560 AAATCTAAAATAATCC
1 AAATATAAAATAATCC
66576 AAATATAAAATAATCC
1 AAATATAAAATAATCC
66592 GATCCAAACC
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:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATATAAAATAATCC
Found at i:66919 original size:16 final size:15
Alignment explanation
Indices: 66898--66936 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
66888 TTGATAAATA
66898 ATTTTAAAATAATATT
1 ATTTTAAAATAAT-TT
66914 ATTTT--AATAATTT
1 ATTTTAAAATAATTT
66927 ATTTTAAAAT
1 ATTTTAAAAT
66937 TAAGAGTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 3 0.14
16 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTAAAATAATTT
Found at i:74987 original size:2 final size:2
Alignment explanation
Indices: 74980--75005 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74970 AAATCCACCC
74980 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
75006 GATTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:75880 original size:2 final size:2
Alignment explanation
Indices: 75873--75914 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
75863 AAATATGTAC
75873 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
75915 GTTTAACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77706 original size:2 final size:2
Alignment explanation
Indices: 77699--77746 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
77689 ATGCTGTAAT
77699 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 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
77741 TC TC TC
1 TC TC TC
77747 CTGATAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:80046 original size:2 final size:2
Alignment explanation
Indices: 80039--80069 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80029 ACTAAATCAT
80039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80070 CATCCCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87055 original size:2 final size:2
Alignment explanation
Indices: 87043--87073 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
87033 CTAGTACTAT
87043 TA TA T- 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
87074 ATACCGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87556 original size:4 final size:4
Alignment explanation
Indices: 87547--87578 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
87537 TTGCTTTGGT
87547 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
87579 AAATGAATTA
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:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:88141 original size:26 final size:26
Alignment explanation
Indices: 88112--88164 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
88102 GTTATGTTGA
88112 TATTATAAA-TTAAAAAAAATTATTAT
1 TATTATAAATTTAAAAAAAATT-TTAT
* *
88138 TATTTTAAATTTAAAAATAATTTTAT
1 TATTATAAATTTAAAAAAAATTTTAT
88164 T
1 T
88165 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTATAAATTTAAAAAAAATTTTAT
Found at i:88159 original size:27 final size:26
Alignment explanation
Indices: 88112--88170 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
88102 GTTATGTTGA
*
88112 TATTATAAATTAAAAAAAATTATTA-T
1 TATTTTAAATTAAAAAAAATT-TTATT
*
88138 TATTTTAAATTTAAAAATAATTTTATT
1 TATTTTAAA-TTAAAAAAAATTTTATT
88165 TATTTT
1 TATTTT
88171 TAAAGTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TATTTTAAATTAAAAAAAATTTTATT
Found at i:88943 original size:16 final size:16
Alignment explanation
Indices: 88906--88951 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
88896 TTTAACATGC
*
88906 ATTTAATTAA-AATATA
1 ATTTAA-TAATAATTTA
*
88922 ACTTAATAATAATTTA
1 ATTTAATAATAATTTA
88938 ATTTAATAATAATT
1 ATTTAATAATAATT
88952 AAAGATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAATAATAATTTA
Found at i:89170 original size:29 final size:29
Alignment explanation
Indices: 89128--89198 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
89118 CCTTATGAGA
*
89128 TAAGTAGATATTTTT-T-AAATATTAAGAGGG
1 TAAGTATAT-TTTTTATAAAATATTAAGA--G
*
89158 TAAGTATATTTTTTATAAAATTTTAAGAG
1 TAAGTATATTTTTTATAAAATATTAAGAG
*
89187 TAAGTATCTTTT
1 TAAGTATATTTT
89199 ACCCTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 17 0.47
30 9 0.25
31 10 0.28
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.46
Consensus pattern (29 bp):
TAAGTATATTTTTTATAAAATATTAAGAG
Found at i:89338 original size:14 final size:15
Alignment explanation
Indices: 89304--89333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89294 ATTATCTTTT
*
89304 AATAATTTTTAATAA
1 AATAATTTTAAATAA
89319 AATAATTTTAAATAA
1 AATAATTTTAAATAA
89334 TTAATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATTTTAAATAA
Found at i:89340 original size:22 final size:19
Alignment explanation
Indices: 89312--89354 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 19
89302 TTAATAATTT
89312 TTAATAAAATAATTTTAAATAA
1 TTAATAAAA-AA-TTTAAA-AA
89334 TTAATAAAAAATTTAAAAA
1 TTAATAAAAAATTTAAAAA
89353 TT
1 TT
89355 TACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 2 0.10
22 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAAAAAATTTAAAAA
Found at i:89873 original size:17 final size:14
Alignment explanation
Indices: 89828--89867 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
89818 TCATAAATTT
* *
89828 TTTATTTTATCAAA
1 TTTATATTATTAAA
89842 -TTATATTATTAAA
1 TTTATATTATTAAA
89855 TTTATATTATTAA
1 TTTATATTATTAA
89868 TTAATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATATTATTAAA
Found at i:92467 original size:22 final size:22
Alignment explanation
Indices: 92439--92494 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
92429 ATTAGTTTTG
92439 AATTATTTTTTT-TAAAAATGAAT
1 AATTATTTTTTTGTAAAAA--AAT
92462 AA-TATTTTTCTTGTAAAAAAAT
1 AATTATTTTT-TTGTAAAAAAAT
92484 AATTATTTTTT
1 AATTATTTTTT
92495 ACTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 13 0.43
23 11 0.37
24 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
AATTATTTTTTTGTAAAAAAAT
Found at i:92494 original size:25 final size:26
Alignment explanation
Indices: 92452--92504 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
92442 TATTTTTTTT
*
92452 AAAAATGAATAATATTTTTCTTGTAA
1 AAAAATGAATAATATTTTACTTGTAA
* * *
92478 AAAAAT-AATTATTTTTTACTTTTAA
1 AAAAATGAATAATATTTTACTTGTAA
92503 AA
1 AA
92505 TGCATGGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
AAAAATGAATAATATTTTACTTGTAA
Found at i:92586 original size:20 final size:19
Alignment explanation
Indices: 92552--92600 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
92542 TTTAATTTAA
92552 TTTTAATT-T-TTAATAATT
1 TTTTAATTATATTAAT-ATT
92570 TTTTAATTATATTAATATT
1 TTTTAATTATATTAATATT
*
92589 ATTTAACTTATA
1 TTTTAA-TTATA
92601 ACATTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 8 0.30
19 9 0.33
20 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAATTATATTAATATT
Found at i:100218 original size:17 final size:17
Alignment explanation
Indices: 100196--100229 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
100186 TTAAATTTTA
100196 TTTA-TTTATTTAATTAT
1 TTTATTTTATTT-ATTAT
100213 TTTATTTTATTTATTAT
1 TTTATTTTATTTATTAT
100230 ATATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTATTTATTAT
Found at i:103092 original size:17 final size:17
Alignment explanation
Indices: 103060--103094 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
103050 GTTTAAGTTA
*
103060 TTATGTTTTTAATATTT
1 TTATGTTTTGAATATTT
*
103077 TTATGTTTTGATTATTT
1 TTATGTTTTGAATATTT
103094 T
1 T
103095 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (17 bp):
TTATGTTTTGAATATTT
Found at i:103940 original size:15 final size:13
Alignment explanation
Indices: 103906--103960 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
103896 ATCATTAAAC
103906 TAATAATTTTTAA
1 TAATAATTTTTAA
**
103919 TCGTAATATTTTAAA
1 TAATAAT-TTTT-AA
103934 TAATAATTTTTAA
1 TAATAATTTTTAA
*
103947 TAATAATATTTAA
1 TAATAATTTTTAA
103960 T
1 T
103961 GTTAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 20 0.57
14 8 0.23
15 7 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
TAATAATTTTTAA
Found at i:103942 original size:28 final size:29
Alignment explanation
Indices: 103900--103957 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
103890 TTATTTATCA
**
103900 TTAAACTAATAATTTTTAATCGTAATATT
1 TTAAACTAATAATTTTTAATAATAATATT
103929 TTAAA-TAATAATTTTTAATAATAATATT
1 TTAAACTAATAATTTTTAATAATAATATT
103957 T
1 T
103958 AATGTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAAACTAATAATTTTTAATAATAATATT
Found at i:103965 original size:19 final size:19
Alignment explanation
Indices: 103943--103985 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
103933 ATAATAATTT
*
103943 TTAATAATAATAT-TTAATG
1 TTAA-AATAATATATTAATA
*
103962 TTAAAATATTATATTAATA
1 TTAAAATAATATATTAATA
103981 TTAAA
1 TTAAA
103986 TACTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAAAATAATATATTAATA
Found at i:104059 original size:29 final size:30
Alignment explanation
Indices: 104027--104094 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
104017 ATAACTATAT
* *
104027 AAATATTTT-AAATATTATAATTATTACTA
1 AAATATTTTCAAATAATATAATTACTACTA
* *
104056 AAATATTATTTCAATTAATATAATTACTATTA
1 AAATA-T-TTTCAAATAATATAATTACTACTA
104088 AAATATT
1 AAATATT
104095 ATTTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.16
30 2 0.06
31 4 0.12
32 21 0.66
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (30 bp):
AAATATTTTCAAATAATATAATTACTACTA
Found at i:104133 original size:23 final size:21
Alignment explanation
Indices: 104083--104151 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 21
104073 ATATAATTAC
*
104083 TATTAAAATATTATTTTTAC-AA
1 TATT-AAATAATA-TTTTACTAA
*
104105 TTTTAAATAGAATATTATTA-TAA
1 TATTAAAT--AATATT-TTACTAA
104128 TATTAAATAATATTTTACTAA
1 TATTAAATAATATTTTACTAA
104149 TAT
1 TAT
104152 GTTACCACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
20 3 0.08
21 16 0.41
22 5 0.13
23 15 0.38
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
TATTAAATAATATTTTACTAA
Found at i:104226 original size:30 final size:30
Alignment explanation
Indices: 104174--104247 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
104164 CATTAAAATA
*
104174 AAAAATGAAATTAATCTTTATTA-ATTATTATT
1 AAAAAT-AAA-TAATATTTATTATA-TATTATT
104206 -AAAATAAATAATATTATATTATATATTATT
1 AAAAATAAATAATATT-TATTATATATTATT
104236 AGAAAATAAATA
1 A-AAAATAAATA
104248 TGTATGTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
29 6 0.16
30 15 0.41
31 6 0.16
32 10 0.27
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAAATAAATAATATTTATTATATATTATT
Found at i:108169 original size:2 final size:2
Alignment explanation
Indices: 108162--108190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
108152 ATGGTCTTCT
108162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
108191 TAGTATTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109377 original size:54 final size:54
Alignment explanation
Indices: 109319--109539 Score: 363
Period size: 54 Copynumber: 4.1 Consensus size: 54
109309 TAACAGCCAC
* * * * *
109319 TCTTGTAGTGGTTGCAGCAGTGGGTCTAGGTCATGTAAAGGGTGTGGCAGCTCT
1 TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
109373 TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
1 TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
109427 TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
1 TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
* *
109481 TCTTGTAGCGGATGCAGCAGTT-GTACTGGGTCATGTAAAGGGTGTGGCAGCTCT
1 TCTTGTAGCGGATGCAGCAGTTGGT-CTTGGTCATGTAAAGGGTGCGGCAGCTCT
109535 TCTTG
1 TCTTG
109540 CAACGGCCGA
Statistics
Matches: 159, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
53 2 0.01
54 157 0.99
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.31
Consensus pattern (54 bp):
TCTTGTAGCGGATGCAGCAGTTGGTCTTGGTCATGTAAAGGGTGCGGCAGCTCT
Found at i:109431 original size:30 final size:30
Alignment explanation
Indices: 109397--109485 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 30
109387 CAGCAGTTGG
109397 TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
1 TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
* * * * **
109427 TCTT-GT-A-G---CGGATGCAGCAGTTGG
1 TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
109451 TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
1 TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
109481 TCTTG
1 TCTTG
109486 TAGCGGATGC
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
24 14 0.34
25 2 0.05
26 1 0.02
27 2 0.05
28 1 0.02
29 2 0.05
30 19 0.46
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (30 bp):
TCTTGGTCATGTAAAGGGTGCGGCAGCTCT
Found at i:109500 original size:24 final size:24
Alignment explanation
Indices: 109365--109500 Score: 56
Period size: 24 Copynumber: 5.2 Consensus size: 24
109355 AAAGGGTGTG
109365 GCAGCTCTTCTTGTAGCGGATGCA
1 GCAGCTCTTCTTGTAGCGGATGCA
* * ** * *
109389 GCAGTTGGTCTTGGTCATGTAAAGGGTGCG
1 GCA---GCTC-T--TCTTGTAGCGGATGCA
109419 GCAGCTCTTCTTGTAGCGGATGCA
1 GCAGCTCTTCTTGTAGCGGATGCA
* * ** * *
109443 GCAGTTGGTCTTGGTCATGTAAAGGGTGCG
1 GCA---GCTC-T--TCTTGTAGCGGATGCA
109473 GCAGCTCTTCTTGTAGCGGATGCA
1 GCAGCTCTTCTTGTAGCGGATGCA
109497 GCAG
1 GCAG
109501 TTGTACTGGG
Statistics
Matches: 76, Mismatches: 24, Indels: 24
0.61 0.19 0.19
Matches are distributed among these distances:
24 32 0.42
26 2 0.03
27 12 0.16
28 2 0.03
30 28 0.37
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.29
Consensus pattern (24 bp):
GCAGCTCTTCTTGTAGCGGATGCA
Found at i:110754 original size:2 final size:2
Alignment explanation
Indices: 110747--110775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
110737 TTTATCTATC
110747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110776 CTGTATGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112362 original size:6 final size:6
Alignment explanation
Indices: 112356--112615 Score: 88
Period size: 6 Copynumber: 43.3 Consensus size: 6
112346 ACCGGCACCA
* * * * * * * *
112356 GCTCCA GCTCCA GCACCG GCACCG GCTCCT GCTCCA GCGCCG GCACCG
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG
* * * * * * * *
112404 GCTCCA GCACCG GCTCCG ACACCT GCTCCG GCACCT GCTCCG GCTCCA
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG
* * * * * * * * * *
112452 GCTCCG GCACCT GCACCT GCACCT GCTCCA GCACCG GCTCCA GCACCG
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG
* * * * * * * * * * *
112500 GCACCT GCACCT GCACCG GCTCCA GCACCG GCACCT GCACCG GCTCCA
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG
* * * * * * * * *
112548 GCACCG GCACCT GCACCG GCTCCA GCACCG GCTCCG GCACCT GCACCG
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG
* *
112596 GCTCCA GCACCG GCTCCG GC
1 GCTCCG GCTCCG GCTCCG GC
112616 ACCATCGCCA
Statistics
Matches: 192, Mismatches: 62, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 192 1.00
ACGTcount: A:0.14, C:0.50, G:0.25, T:0.11
Consensus pattern (6 bp):
GCTCCG
Found at i:112368 original size:12 final size:12
Alignment explanation
Indices: 112341--112619 Score: 162
Period size: 12 Copynumber: 23.2 Consensus size: 12
112331 AGTAGCCGCG
*
112341 CCAGCACCGGCA
1 CCAGCTCCGGCA
* *
112353 CCAGCTCCAGCT
1 CCAGCTCCGGCA
*
112365 CCAGCACCGGCA
1 CCAGCTCCGGCA
* * *
112377 CCGGCTCCTGCT
1 CCAGCTCCGGCA
*
112389 CCAGCGCCGGCA
1 CCAGCTCCGGCA
* *
112401 CCGGCTCCAGCA
1 CCAGCTCCGGCA
* *
112413 CCGGCTCCGACA
1 CCAGCTCCGGCA
*
112425 CCTGCTCCGGCA
1 CCAGCTCCGGCA
* *
112437 CCTGCTCCGGCT
1 CCAGCTCCGGCA
112449 CCAGCTCCGGCA
1 CCAGCTCCGGCA
* * *
112461 CCTGCACCTGCA
1 CCAGCTCCGGCA
* *
112473 CCTGCTCCAGCA
1 CCAGCTCCGGCA
* *
112485 CCGGCTCCAGCA
1 CCAGCTCCGGCA
* * *
112497 CCGGCACCTGCA
1 CCAGCTCCGGCA
* * *
112509 CCTGCACCGGCT
1 CCAGCTCCGGCA
*
112521 CCAGCACCGGCA
1 CCAGCTCCGGCA
* * *
112533 CCTGCACCGGCT
1 CCAGCTCCGGCA
*
112545 CCAGCACCGGCA
1 CCAGCTCCGGCA
* * *
112557 CCTGCACCGGCT
1 CCAGCTCCGGCA
* *
112569 CCAGCACCGGCT
1 CCAGCTCCGGCA
* * *
112581 CCGGCACCTGCA
1 CCAGCTCCGGCA
* *
112593 CCGGCTCCAGCA
1 CCAGCTCCGGCA
*
112605 CCGGCTCCGGCA
1 CCAGCTCCGGCA
112617 CCA
1 CCA
112620 TCGCCAGCGC
Statistics
Matches: 216, Mismatches: 51, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 216 1.00
ACGTcount: A:0.15, C:0.50, G:0.24, T:0.10
Consensus pattern (12 bp):
CCAGCTCCGGCA
Found at i:112380 original size:30 final size:30
Alignment explanation
Indices: 112344--112618 Score: 255
Period size: 30 Copynumber: 9.2 Consensus size: 30
112334 AGCCGCGCCA
* * * *
112344 GCACCGGCACCAGCTCCAGCTCCAGCACCG
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
* * * *
112374 GCACCGGCTCCTGCTCCAGCGCCGGCACCG
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
* * *
112404 GCTCCAGCACCGGCTCC-GACACCTGCTCCG
1 GCACCGGCACCGGCTCCAG-CACCGGCTCCG
* * * * *
112434 GCACCTGCTCCGGCTCCAGCTCCGGCACCT
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
* * *
112464 GCACCTGCACCTGCTCCAGCACCGGCTCCA
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
* * * *
112494 GCACCGGCACCTGCACCTGCACCGGCTCCA
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
* * * * * *
112524 GCACCGGCACCTGCACCGGCTCCAGCACCG
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
*
112554 GCACCTGCACCGGCTCCAGCACCGGCTCCG
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
*
112584 GCACCTGCACCGGCTCCAGCACCGGCTCCG
1 GCACCGGCACCGGCTCCAGCACCGGCTCCG
112614 GCACC
1 GCACC
112619 ATCGCCAGCG
Statistics
Matches: 205, Mismatches: 38, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.00
30 203 0.99
31 1 0.00
ACGTcount: A:0.15, C:0.50, G:0.25, T:0.11
Consensus pattern (30 bp):
GCACCGGCACCGGCTCCAGCACCGGCTCCG
Found at i:112627 original size:24 final size:24
Alignment explanation
Indices: 112344--112618 Score: 204
Period size: 24 Copynumber: 11.5 Consensus size: 24
112334 AGCCGCGCCA
* * * *
112344 GCACCGGCACCAGCTCCAGCTCCA
1 GCACCTGCACCGGCTCCAGCACCG
* * * *
112368 GCACCGGCACCGGCTCCTGCTCCA
1 GCACCTGCACCGGCTCCAGCACCG
* *
112392 GCGCCGGCACCGGCTCCAGCACCG
1 GCACCTGCACCGGCTCCAGCACCG
* * * *
112416 GCTCC-GACACCTGCTCCGGCACCT
1 GCACCTG-CACCGGCTCCAGCACCG
* * * * * *
112440 GCTCCGGCTCCAGCTCCGGCACCT
1 GCACCTGCACCGGCTCCAGCACCG
*
112464 GCACCTGCACCTGCTCCAGCACCG
1 GCACCTGCACCGGCTCCAGCACCG
* * *
112488 GCTCCAGCACC-G-----GCACCT
1 GCACCTGCACCGGCTCCAGCACCG
112506 GCACCTGCACCGGCTCCAGCACCG
1 GCACCTGCACCGGCTCCAGCACCG
112530 GCACCTGCACCGGCTCCAGCACCG
1 GCACCTGCACCGGCTCCAGCACCG
112554 GCACCTGCACCGGCTCCAGCACCGGCTCCG
1 GCACCTGCACCGGCTCCAGCA------CCG
112584 GCACCTGCACCGGCTCCAGCACCG
1 GCACCTGCACCGGCTCCAGCACCG
* *
112608 GCTCCGGCACC
1 GCACCTGCACC
112619 ATCGCCAGCG
Statistics
Matches: 211, Mismatches: 26, Indels: 28
0.80 0.10 0.11
Matches are distributed among these distances:
18 14 0.07
19 1 0.00
23 2 0.01
24 169 0.80
25 1 0.00
30 24 0.11
ACGTcount: A:0.15, C:0.50, G:0.25, T:0.11
Consensus pattern (24 bp):
GCACCTGCACCGGCTCCAGCACCG
Found at i:114378 original size:20 final size:19
Alignment explanation
Indices: 114340--114378 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
114330 ACATACAATT
**
114340 AAATTTAATTAAATTTTAA
1 AAATTTAATTAAAAATTAA
114359 AAATTTATATTAAAAATTAA
1 AAATTTA-ATTAAAAATTAA
114379 TACATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTAATTAAAAATTAA
Found at i:115990 original size:14 final size:16
Alignment explanation
Indices: 115970--116038 Score: 76
Period size: 15 Copynumber: 4.5 Consensus size: 16
115960 AAAAAATAAA
115970 TTATTAAA-ATATTAT
1 TTATTAAATATATTAT
*
115985 TT-TTAAATAAATT-T
1 TTATTAAATATATTAT
115999 TTATTATAATATATTA-
1 TTATTA-AATATATTAT
116015 TT-TTAAATATATTTAT
1 TTATTAAATATA-TTAT
116031 TTATTAAA
1 TTATTAAA
116039 ATCTATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
14 14 0.31
15 15 0.33
16 11 0.24
17 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTAAATATATTAT
Found at i:115992 original size:26 final size:28
Alignment explanation
Indices: 115963--116031 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
115953 TATACTTAAA
115963 AAATAAA-TTATTA-AA-ATATTATTTTT
1 AAATAAATTTATTATAATATATTA-TTTT
115989 AAATAAATTTTTATTATAATATATTATTTT
1 AAATAAA--TTTATTATAATATATTATTTT
*
116019 AAATATATTTATT
1 AAATAAATTTATT
116032 TATTAAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 7 0.19
28 6 0.16
29 6 0.16
30 12 0.32
31 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATAAATTTATTATAATATATTATTTT
Found at i:116016 original size:31 final size:28
Alignment explanation
Indices: 115970--116040 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 28
115960 AAAAAATAAA
115970 TTATTAAAATATTATTTTTAAATAAATTT
1 TTATTAAAATATTA-TTTTAAATAAATTT
*
115999 TTATTATAATATATTATTTTAAATATATTTAT
1 TTATTA-AA-ATATTATTTTAAATA-AATT-T
116031 TTATTAAAAT
1 TTATTAAAAT
116041 CTATATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 6 0.16
30 13 0.35
31 11 0.30
32 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTAAAATATTATTTTAAATAAATTT
Found at i:116142 original size:66 final size:66
Alignment explanation
Indices: 116015--116147 Score: 150
Period size: 66 Copynumber: 2.0 Consensus size: 66
116005 TAATATATTA
* *
116015 TTTTAAATATATTTATTTATTAAAATCTATATTTATATATATAATTAATCTGTTATATAAAATTA
1 TTTTAAATATATTTATTTATTAAAATCTATATTTATAGATATAATTAATCTGATATATAAAA-TA
116080 AT
65 AT
* *
116082 TTTTAAATA-ATTTA-TTATTACAATAT-TGTATATTATAGAT-TAATTATAT-TGATATTTAAA
1 TTTTAAATATATTTATTTATTA-AA-ATCTATAT-TTATAGATATAATTA-ATCTGATATATAAA
116142 ATAAT
62 ATAAT
116147 T
1 T
116148 GACACATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
65 11 0.19
66 27 0.47
67 20 0.34
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (66 bp):
TTTTAAATATATTTATTTATTAAAATCTATATTTATAGATATAATTAATCTGATATATAAAATAA
T
Found at i:117859 original size:4 final size:4
Alignment explanation
Indices: 117846--117875 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
117836 ATCTCAAGCA
117846 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
117876 GGTACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:118657 original size:14 final size:14
Alignment explanation
Indices: 118640--118684 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
118630 TTTTCTTTCA
118640 TTTTTTATTTTACT
1 TTTTTTATTTTACT
* *
118654 TTTTTTCTTTTCCT
1 TTTTTTATTTTACT
* *
118668 TTTTTTTTTTTGCT
1 TTTTTTATTTTACT
118682 TTT
1 TTT
118685 CATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTTACT
Found at i:118670 original size:20 final size:19
Alignment explanation
Indices: 118641--118700 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
118631 TTTCTTTCAT
*
118641 TTTTTATTTTACTTTTTTTC
1 TTTTCATTTTA-TTTTTTTC
* *
118661 TTTTCCTTTTTTTTTTTTGC
1 TTTTCATTTTATTTTTTT-C
118681 TTTTCATATTTATTTTTTTC
1 TTTTCAT-TTTATTTTTTTC
118701 ATTATTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 7 0.21
20 16 0.48
21 10 0.30
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTCATTTTATTTTTTTC
Found at i:118712 original size:20 final size:18
Alignment explanation
Indices: 118642--118712 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 18
118632 TTCTTTCATT
*
118642 TTTTATTTTACTTTTTTTC
1 TTTTCTTTTA-TTTTTTTC
*
118661 TTTTCCTTTTTTTTTTTTGC
1 TTTT-CTTTTATTTTTTT-C
118681 TTTTCATATTTATTTTTTTC
1 TTTTC-T-TTTATTTTTTTC
118701 ATTATTCTTTTA
1 -TT-TTCTTTTA
118713 AATTTTCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
19 12 0.28
20 15 0.35
21 13 0.30
22 3 0.07
ACGTcount: A:0.11, C:0.11, G:0.01, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTATTTTTTTC
Found at i:129504 original size:2 final size:2
Alignment explanation
Indices: 129499--129524 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
129489 ATATATATAT
129499 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
129525 TTTTGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:129770 original size:4 final size:4
Alignment explanation
Indices: 129761--129794 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
129751 CATCCAATAA
129761 AAAT AAAT AAAT AAAT AAA- AAAT AAA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
129795 CTATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:129774 original size:8 final size:8
Alignment explanation
Indices: 129761--129794 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
129751 CATCCAATAA
129761 AAATAAAT
1 AAATAAAT
129769 AAATAAAT
1 AAATAAAT
129777 AAA-AAAT
1 AAATAAAT
129784 AAA-AAAT
1 AAATAAAT
129791 AAAT
1 AAAT
129795 CTATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATAAAT
Found at i:129779 original size:18 final size:18
Alignment explanation
Indices: 129759--129794 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
129749 AACATCCAAT
129759 AAAAATAAATAAATAAATA
1 AAAAATAAA-AAATAAATA
129778 AAAAATAAAAAATAAAT
1 AAAAATAAAAAATAAAT
129795 CTATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAATAAAAAATAAATA
Found at i:129804 original size:22 final size:22
Alignment explanation
Indices: 129765--129811 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
129755 CAATAAAAAT
*
129765 AAATAAATAAATAAAAAATAAA
1 AAATAAATAAATAAAAAAGAAA
** *
129787 AAATAAATCTATATAAAAGAAA
1 AAATAAATAAATAAAAAAGAAA
129809 AAA
1 AAA
129812 GAATGACTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAATAAATAAAAAAGAAA
Found at i:130767 original size:5 final size:5
Alignment explanation
Indices: 130757--130787 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
130747 CAGCAATGCA
130757 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC T
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCTCC T
130788 ACATACATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
TCTCC
Found at i:134636 original size:3 final size:3
Alignment explanation
Indices: 134628--134661 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
134618 TTTACTAGTG
134628 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
134662 CTTTACGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:135294 original size:2 final size:2
Alignment explanation
Indices: 135287--135312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
135277 TTAATAATAC
135287 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
135313 CTTAGCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:140752 original size:4 final size:4
Alignment explanation
Indices: 140743--140776 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
140733 CTCGTCACAT
140743 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
140777 ATACTTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:141587 original size:2 final size:2
Alignment explanation
Indices: 141582--141620 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
141572 TAAAAAACAA
141582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
141621 AACTTTGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:142245 original size:39 final size:39
Alignment explanation
Indices: 142191--142276 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
142181 TCTCCTTGGT
142191 CTTCAGCTTCTTTTCTGTAAGTATCTTCTGATTCTTCTC
1 CTTCAGCTTCTTTTCTGTAAGTATCTTCTGATTCTTCTC
*
142230 CTTCAGCTTCTTTTCTGTAAGTATCTTCTGGTTCTTCTC
1 CTTCAGCTTCTTTTCTGTAAGTATCTTCTGATTCTTCTC
142269 CTTCAGCT
1 CTTCAGCT
142277 ACTCGGGGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.50
Consensus pattern (39 bp):
CTTCAGCTTCTTTTCTGTAAGTATCTTCTGATTCTTCTC
Found at i:143693 original size:2 final size:2
Alignment explanation
Indices: 143686--143714 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
143676 TCTACACGTG
143686 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143715 GGATATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:143744 original size:2 final size:2
Alignment explanation
Indices: 143739--143763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143729 TGCTGGTGTG
143739 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 T
143764 GAGATTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144228 original size:2 final size:2
Alignment explanation
Indices: 144221--144254 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
144211 AATAGAGATG
144221 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
144255 ATTATTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:145104 original size:23 final size:23
Alignment explanation
Indices: 145071--145118 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
145061 TTCAAATTAA
145071 TAATTAACATTGATTGCTTTGAG
1 TAATTAACATTGATTGCTTTGAG
*
145094 TAATTAGCATTGATTGCTTTGAG
1 TAATTAACATTGATTGCTTTGAG
145117 TA
1 TA
145119 TGACTACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (23 bp):
TAATTAACATTGATTGCTTTGAG
Found at i:145389 original size:2 final size:2
Alignment explanation
Indices: 145377--145411 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
145367 TACTAGCTAC
* *
145377 TA TA TA CA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
145412 GCTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:145683 original size:16 final size:17
Alignment explanation
Indices: 145658--145689 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
145648 AAATTTTTAA
145658 TTTATATTTAAATAAAT
1 TTTATATTTAAATAAAT
145675 TTTAT-TTTAAATAAA
1 TTTATATTTAAATAAA
145690 ATATTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATTTAAATAAAT
Found at i:145980 original size:2 final size:2
Alignment explanation
Indices: 145973--145998 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
145963 ATAGCACTGC
145973 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
145999 AAGAAGGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151485 original size:2 final size:2
Alignment explanation
Indices: 151478--151512 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
151468 ACCTGCATTC
151478 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
151513 ATCCCCAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:151583 original size:2 final size:2
Alignment explanation
Indices: 151576--151605 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
151566 TATATTGTAG
151576 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
151606 GTATCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153829 original size:2 final size:2
Alignment explanation
Indices: 153822--153864 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
153812 TTCTTCAGTT
153822 TA TA 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 TA TA
153864 T
1 T
153865 GACAATCTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:155542 original size:5 final size:5
Alignment explanation
Indices: 155531--155571 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
155521 TCTTCCTCAG
* * *
155531 CTCCT TTCCT TTCCT TTCCT CTCCT CTCCT CTCCT CTCCT C
1 CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT CTCCT C
155572 AAGCCATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (5 bp):
CTCCT
Found at i:155880 original size:16 final size:18
Alignment explanation
Indices: 155859--155891 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
155849 CACAAGGAGC
155859 AGGCAT-CA-AAATAAAA
1 AGGCATGCAGAAATAAAA
155875 AGGCATGCAGAAATAAA
1 AGGCATGCAGAAATAAA
155892 GCGTACATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (18 bp):
AGGCATGCAGAAATAAAA
Found at i:161046 original size:15 final size:15
Alignment explanation
Indices: 161026--161058 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
161016 AATTTTTTTA
161026 TAATTTTTAATATTT
1 TAATTTTTAATATTT
*
161041 TAATTTTTAATTTTT
1 TAATTTTTAATATTT
161056 TAA
1 TAA
161059 ATATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTAATATTT
Found at i:161048 original size:7 final size:7
Alignment explanation
Indices: 161021--161055 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
161011 ATATTAATTT
161021 TTTTATAA
1 TTTT-TAA
161029 TTTTTAA
1 TTTTTAA
161036 TATTTTAA
1 T-TTTTAA
161044 TTTTTAA
1 TTTTTAA
161051 TTTTT
1 TTTTT
161056 TAAATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.58
8 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Done.