Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 14 of 132
Found at i:3992405 original size:106 final size:106
Alignment explanation
Indices: 3992216--3992648 Score: 661
Period size: 106 Copynumber: 4.0 Consensus size: 106
3992206 CTGCAGGTCT
* * *
3992216 CAACGTCATCCCCTCGAAATTGAAGTGGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
*
3992281 GAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAG
66 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG
3992322 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
3992387 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG
66 GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG
*
3992428 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
* *
3992493 GAGTGGATAACAGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAG
66 GAGTGGATAAC------------ACGTCTTCATCTCCGAAATTGAAGTAAGAG
3992546 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
*
3992611 GAGTGGATAACGCGTCTTCATC-CCTTGAAATTGAAGTA
66 GAGTGGATAACACGTCTTCATCTCC--GAAATTGAAGTA
3992649 GAGTGGATAA
Statistics
Matches: 302, Mismatches: 11, Indels: 27
0.89 0.03 0.08
Matches are distributed among these distances:
105 1 0.00
106 186 0.62
107 12 0.04
118 103 0.34
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (106 bp):
CAACGTCATCCCCTTGAAATTAAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
GAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAG
Found at i:3992449 original size:68 final size:67
Alignment explanation
Indices: 3992366--3992492 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 67
3992356 TAACACGTCT
3992366 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCC-GAAATTGAAGTAAGAGCA
1 TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATC-CCTGAAATTGAAGTAAGAGCA
3992430 ACG
65 ACG
3992433 TCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTA
1 TCAT-CCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCC-TGAAATTGAAGTA
3992493 GAGTGGATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
67 6 0.11
68 39 0.68
69 12 0.21
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (67 bp):
TCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCCCTGAAATTGAAGTAAGAGCAA
CG
Found at i:3992594 original size:118 final size:118
Alignment explanation
Indices: 3992386--3992621 Score: 436
Period size: 118 Copynumber: 2.0 Consensus size: 118
3992376 AAATTGAAGT
*
3992386 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGA
1 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
3992451 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC
66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC
* * *
3992504 AGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
1 AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
3992569 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC
66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC
3992622 GCGTCTTCAT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (118 bp):
AGAGTGGATAACACGTCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAAC
Found at i:3992708 original size:224 final size:221
Alignment explanation
Indices: 3992280--3992726 Score: 618
Period size: 224 Copynumber: 2.0 Consensus size: 221
3992270 AAATTGAAGT
3992280 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
1 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
3992345 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
* * *
3992410 CCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCA
131 CCGAAATTGAAGTAAGAGAAACGTCATCACCTTGAAATTGAAGTAGA--GGAGAACACG--TTCA
*
3992475 TCCCTTGAAATTGAAGTAGAG-TGGATAAC
192 TCCCTTGAAATTGAAGTAAAGTTGGATAAC
* * * *
3992504 AGAGTGGATAATACGTCTTGATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
1 AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
*
3992569 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACGCGTCTTCATC-
66 AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
* * * *
3992633 CCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTA-A-GAGCA-ACG
131 CC--GAAATTGAAGTA-A---GAGAA-ACGTCATCACCT-TGAAATTGAAGTAGAGGAGAACACG
3992695 -TCATCCTCTTGAAATTGAAGTAAAGTTGGATA
188 TTCATCC-CTTGAAATTGAAGTAAAGTTGGATA
3992727 GCAAAGTCTT
Statistics
Matches: 200, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
223 8 0.04
224 141 0.70
225 18 0.09
226 4 0.02
227 3 0.01
229 3 0.01
230 10 0.05
231 13 0.06
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (221 bp):
AGAGTGGATAACACATCTTCATCTCCGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTAA
AGTAGAGTGGATAACACGTCTTCATCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCT
CCGAAATTGAAGTAAGAGAAACGTCATCACCTTGAAATTGAAGTAGAGGAGAACACGTTCATCCC
TTGAAATTGAAGTAAAGTTGGATAAC
Found at i:3993049 original size:6 final size:6
Alignment explanation
Indices: 3993024--3993106 Score: 71
Period size: 6 Copynumber: 13.7 Consensus size: 6
3993014 TTAAATTTAG
* * *
3993024 TTAAAT TTAGAT TT-ATT TTAAAT TTAAAT ATCTAAAT TT-AAT TTGAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -T-TAAAT TTAAAT TTAAAT
** *
3993072 TTAAAT TTAAAT AAAAAT TAAAAT ATTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAA
3993107 CATTAAAAGT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
5 8 0.13
6 43 0.68
7 7 0.11
8 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:3993063 original size:31 final size:31
Alignment explanation
Indices: 3993025--3993084 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
3993015 TAAATTTAGT
*
3993025 TAAATTTAGATTT-ATTTTAAATTTAAATATC
1 TAAATTTA-ATTTGAATTTAAATTTAAATATC
3993056 TAAATTTAATTTGAATTTAAATTTAAATA
1 TAAATTTAATTTGAATTTAAATTTAAATA
3993085 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (31 bp):
TAAATTTAATTTGAATTTAAATTTAAATATC
Found at i:3993207 original size:13 final size:15
Alignment explanation
Indices: 3993190--3993226 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
3993180 ACCCATTTTT
3993190 TGGCCCAAATTA-AA
1 TGGCCCAAATTACAA
3993204 -GGCCC-AATTACAA
1 TGGCCCAAATTACAA
3993217 TGGCCCAAAT
1 TGGCCCAAAT
3993227 AGGCCCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 5 0.25
15 3 0.15
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (15 bp):
TGGCCCAAATTACAA
Found at i:3993304 original size:15 final size:15
Alignment explanation
Indices: 3993284--3993314 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3993274 GCCTATGCTG
3993284 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
3993299 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
3993314 C
1 C
3993315 CATCCACCAT
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:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:3995002 original size:30 final size:30
Alignment explanation
Indices: 3994962--3995148 Score: 269
Period size: 30 Copynumber: 6.4 Consensus size: 30
3994952 AAACAATTCG
* *
3994962 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
3994992 AAAATCACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
3995022 AAAATCATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
3995052 --AA--A-A-TTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
3995076 AAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
3995106 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
3995136 AAAATTACATTTT
1 AAAATTACATTTT
3995149 GATCCTAAAA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
24 19 0.13
25 1 0.01
26 3 0.02
28 3 0.02
29 1 0.01
30 117 0.81
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:3995063 original size:24 final size:24
Alignment explanation
Indices: 3995036--3995081 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3995026 TCATATTTTA
3995036 ACCCCAAAACTTTTCCAAAATTTG
1 ACCCCAAAACTTTTCCAAAATTTG
3995060 ACCCCAAAACTTTTCCAAAATT
1 ACCCCAAAACTTTTCCAAAATT
3995082 ATATTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.28
Consensus pattern (24 bp):
ACCCCAAAACTTTTCCAAAATTTG
Found at i:3995068 original size:54 final size:54
Alignment explanation
Indices: 3995006--3995111 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
3994996 TCACATTTTA
3995006 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG
1 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG
*
3995060 ACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATT
1 ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATT
3995112 ACATTTTAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32
Consensus pattern (54 bp):
ACCCCAAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTTTCCAAAATTTG
Found at i:3995118 original size:84 final size:84
Alignment explanation
Indices: 3994972--3995141 Score: 295
Period size: 84 Copynumber: 2.0 Consensus size: 84
3994962 AAAATTACAT
* *
3994972 TTTGACCCTAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTAA
1 TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA
3995037 CCCCAAAACTTTTCCAAAA
66 CCCCAAAACTTTTCCAAAA
* * *
3995056 TTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCCAAAATTACATTTTAA
1 TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA
3995121 CCCCAAAACTTTTCCAAAA
66 CCCCAAAACTTTTCCAAAA
3995140 TT
1 TT
3995142 ACATTTTGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34
Consensus pattern (84 bp):
TTTGACCCCAAAACTTTTCCAAAATCACATTTTAACCCCAAAACTTTTCCAAAATCACATTTTAA
CCCCAAAACTTTTCCAAAA
Found at i:3996626 original size:3 final size:3
Alignment explanation
Indices: 3996618--3996651 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3996608 GTATATTCAA
3996618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3996652 TGTTTTTTTG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3998359 original size:21 final size:21
Alignment explanation
Indices: 3998335--3998381 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3998325 GATTCCTTCC
*
3998335 GATACAAGTGACAGTTCTACA
1 GATACAAGTGACACTTCTACA
* *
3998356 GATACAAGTGACTCTTCTACC
1 GATACAAGTGACACTTCTACA
3998377 GATAC
1 GATAC
3998382 TAGTCTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (21 bp):
GATACAAGTGACACTTCTACA
Found at i:3998645 original size:114 final size:117
Alignment explanation
Indices: 3998432--3998661 Score: 297
Period size: 114 Copynumber: 2.0 Consensus size: 117
3998422 GAAATCTTAC
* ** * * *
3998432 CCTGTTACTTCTACCGATATATGTATGCGAACTACCTATATTTCTAAATACATGACTACCAATAA
1 CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA
* * *
3998497 TTGTTATTCATCTACTGATACAACCCAAGTCAGTGTACAA-CTTCTCTCCTAT
66 TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATC-TCTCTCCTAT
* ** *
3998549 CCTG-TACTTCTACCGATACAAATATGC-AAATATCGATACTTCTAAATACATGACTACTGATAC
1 CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA
*
3998612 TAGTTATT-ATCTACCGATACAACTCAAGTCAGTGAACAATCTCTCTCCTA
66 TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATCTCTCTCCTA
3998662 CTTTCTACTT
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
114 37 0.38
115 37 0.38
116 20 0.20
117 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (117 bp):
CCTGTTACTTCTACCGATACAAATATGCGAAATACCGATACTTCTAAATACATGACTACCAATAA
TAGTTATTCATCTACCGATACAACCCAAGTCAGTGAACAATCTCTCTCCTAT
Found at i:4001888 original size:28 final size:28
Alignment explanation
Indices: 4001783--4001889 Score: 101
Period size: 28 Copynumber: 3.8 Consensus size: 28
4001773 TTTTTGATGT
* **
4001783 TTGAGGATAAAATGGTAATTTTGGACTT
1 TTGAGGGTAAAATGGTAATTTTGGACAA
*
4001811 TTGAGGGTAAAATGGTAATTTTGGAAAAA
1 TTGAGGGTAAAATGGTAATTTTGG-ACAA
* *
4001840 TTTAGGGTTAAAAT-G-ACATTTTAGACAA
1 TTGAGGG-TAAAATGGTA-ATTTTGGACAA
* *
4001868 TCGAGGGTAAAATGGTGATTTT
1 TTGAGGGTAAAATGGTAATTTT
4001890 TAGAAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.09
28 38 0.59
29 14 0.22
30 6 0.09
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (28 bp):
TTGAGGGTAAAATGGTAATTTTGGACAA
Found at i:4001901 original size:146 final size:145
Alignment explanation
Indices: 4001645--4001921 Score: 403
Period size: 146 Copynumber: 1.9 Consensus size: 145
4001635 ACCCGAGGGC
4001645 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
1 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
*** * *
4001710 ACATTTTAGATGTTCGAGGGTAAAATGGTAATTTTTGGAAGAATCGGGATAAAAAACGAGACTTT
66 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGA-TTT
4001775 TTTGATGTTTGAGGAT
130 TTTGATGTTTGAGGAT
* * * * * *
4001791 AAAATGGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTA-AAATG
1 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
* * *
4001855 ACATTTTAGACAATCGAGGGTAAAATGGTGATTTTTAGAAAAAATCGGGATCAAAAATGAGATTT
66 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGGGATAAAAAACGAGATTT
4001920 TT
130 TT
4001922 GGAAGTTAAG
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
145 41 0.35
146 75 0.65
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (145 bp):
AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGATTTT
TTGATGTTTGAGGAT
Found at i:4001941 original size:146 final size:145
Alignment explanation
Indices: 4001645--4001978 Score: 399
Period size: 146 Copynumber: 2.3 Consensus size: 145
4001635 ACCCGAGGGC
* * * *
4001645 AAAATAGTAATTTTAGACTCTCGAGGGAAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
1 AAAAT-GTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
*** * *
4001710 ACATTTTAGATGTTCGAGGGTAAAATGGTAATTTTTGGAAGAATCGGGATAAAAAACGAGACTTT
65 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGACTTT
* * *
4001775 TTTGATGTTTGAGGAT
130 TTGGAAGTTAGAGGAT
*
4001791 AAAATGGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTA-AAATG
1 AAAAT-GTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAG
* * *
4001855 ACATTTTAGACAATCGAGGGTAAAATGGTGATTTTTAGAAAAAATCGGGATCAAAAATGAGA-TT
65 ACATTTTAGACAATCGAGGGTAAAATGGTAATTTTT-GAAAAAATCGGGATAAAAAACGAGACTT
*
4001919 TTTGGAAGTTA-AGGGGT
129 TTTGGAAGTTAGA-GGAT
*
4001936 AAAAATGTAATTTTGGGAAGTTTT-AGGGTCAAAATGG-AATTTT
1 -AAAATGTAATTTT-GG-ACTTTTGAGGGT-AAAATGGTAATTTT
4001979 AAGAAGTTTA
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
144 1 0.01
145 57 0.35
146 93 0.57
147 12 0.07
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (145 bp):
AAAATGTAATTTTGGACTTTTGAGGGTAAAATGGTAATTTTGGAAAAATTTAGGGTTATAAAAGA
CATTTTAGACAATCGAGGGTAAAATGGTAATTTTTGAAAAAATCGGGATAAAAAACGAGACTTTT
TGGAAGTTAGAGGAT
Found at i:4001985 original size:58 final size:57
Alignment explanation
Indices: 4001923--4002213 Score: 185
Period size: 59 Copynumber: 5.0 Consensus size: 57
4001913 GAGATTTTTG
4001923 GAAGTTAAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA
1 GAAGTT-AGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA
* * * * * * **
4001981 GAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTCAAGGTAAAAAATGGGATTTTTG
1 GAAG-TTAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGT-CAAAATGGAATTTTAA
* ** * **
4002040 GATA-TTCGAGGGTAAAAACATAATTTTGGGAAGTTTTGGGGTCAAAAATGGAATTTTTG
1 GA-AGTTAG-GGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTC-AAAATGGAATTTTAA
** * * * ** *
4002099 GAAGCTCGGGGGCAAGAATGTAAGTTTT-GGAAGTCTCGGGGTCAAAAATGTAATTTTTAA
1 GAAG-TTAGGGGTAAAAATGTAA-TTTTGGGAAGTTTTAGGGTC-AAAATGGAA-TTTTAA
** * * * * *
4002159 -AAGTTTTGTGTCAAAATGCAATTTTGGAGAAATTTT-GGGATCAAAATGTAATTTT
1 GAAGTTAGGGGTAAAAATGTAATTTTGG-GAAGTTTTAGGG-TCAAAATGGAATTTT
4002214 TAGATAATTT
Statistics
Matches: 181, Mismatches: 40, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
57 8 0.04
58 62 0.34
59 100 0.55
60 11 0.06
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (57 bp):
GAAGTTAGGGGTAAAAATGTAATTTTGGGAAGTTTTAGGGTCAAAATGGAATTTTAA
Found at i:4002109 original size:29 final size:30
Alignment explanation
Indices: 4001899--4002156 Score: 192
Period size: 29 Copynumber: 8.8 Consensus size: 30
4001889 TTAGAAAAAA
*
4001899 TCGGGATCAAAAAT-GAGATTTTTGGAAGTT
1 TCGGGGTCAAAAATGGA-ATTTTTGGAAGTT
** * *
4001929 AAGGGGT-AAAAATGTAATTTTGGGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT
** **
4001958 TTAGGGTC-AAAATGGAATTTTAAGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT
* *
4001987 TAGGGG-CAAAAATGTAATTTTTGGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT
** * *
4002016 TCAAGGTAAAAAATGGGATTTTTGG-A-TAT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGT-T
* *
4002045 TCGAGGGTAAAAACAT--AATTTTGGGAAGTT
1 TCG-GGGTCAAAA-ATGGAATTTTTGGAAGTT
* *
4002075 TTGGGGTCAAAAATGGAATTTTTGGAAG-C
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT
* * * * *
4002104 TCGGGGGCAAGAATGTAAGTTTTGGAAGTC
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTT
*
4002134 TCGGGGTCAAAAATGTAATTTTT
1 TCGGGGTCAAAAATGGAATTTTT
4002157 AAAAGTTTTG
Statistics
Matches: 178, Mismatches: 38, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
28 4 0.02
29 107 0.60
30 64 0.36
31 3 0.02
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
TCGGGGTCAAAAATGGAATTTTTGGAAGTT
Found at i:4002154 original size:59 final size:59
Alignment explanation
Indices: 4001899--4002156 Score: 247
Period size: 59 Copynumber: 4.4 Consensus size: 59
4001889 TTAGAAAAAA
* * *
4001899 TCGGGATCAAAAAT-GAGATTTTTGGAAGTTAAGGGGTAAAAATGTAATTTTGGGAAGTT
1 TCGGGGTCAAAAATGGA-ATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT
** ** * *
4001958 TTAGGGTC-AAAATGGAATTTTAAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT
** * * * **
4002016 TCAAGGTAAAAAATGGGATTTTTGGATA-TTC-GAGGGTAAAAACATAATTTTGGGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGTTCAG-GGGCAAAAATGTAATTTTGGGAAGTT
* * * * *
4002075 TTGGGGTCAAAAATGGAATTTTTGGAAGCTCGGGGGCAAGAATGTAAGTTTT-GGAAGTC
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAA-TTTTGGGAAGTT
*
4002134 TCGGGGTCAAAAATGTAATTTTT
1 TCGGGGTCAAAAATGGAATTTTT
4002157 AAAAGTTTTG
Statistics
Matches: 160, Mismatches: 32, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
58 49 0.31
59 105 0.66
60 6 0.04
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
TCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTGGGAAGTT
Found at i:4002223 original size:30 final size:29
Alignment explanation
Indices: 4002143--4002228 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
4002133 CTCGGGGTCA
*
4002143 AAAATGTAATTTTTA-AAAGTTTTGTG-TC
1 AAAATGTAATTTTTAGAAA-TTTTGGGATC
* *
4002171 AAAATGCAATTTTGGAGAAATTTTGGGATC
1 AAAATGTAATTTT-TAGAAATTTTGGGATC
*
4002201 AAAATGTAATTTTTAGATAATTTAGGGA
1 AAAATGTAATTTTTAGA-AATTTTGGGA
4002229 CCTCTAGGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.25
29 10 0.21
30 26 0.54
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAATTTTGGGATC
Found at i:4003900 original size:22 final size:22
Alignment explanation
Indices: 4003867--4003911 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4003857 TTTGCAGGTC
4003867 GGCTTGGAGGCTGATA-CAGTG
1 GGCTTGGAGGCTGATAGCAGTG
* *
4003888 GGCTATGGTGGCTTATAGCAGTG
1 GGCT-TGGAGGCTGATAGCAGTG
4003911 G
1 G
4003912 CGGTGCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.18, C:0.13, G:0.42, T:0.27
Consensus pattern (22 bp):
GGCTTGGAGGCTGATAGCAGTG
Found at i:4004220 original size:17 final size:17
Alignment explanation
Indices: 4004198--4004247 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
4004188 TAAAATTAAT
*
4004198 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
*
4004215 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
*
4004232 TTAATTTAAACTTTAA
1 TAAATTTAAA-TTTAA
4004248 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4004241 original size:23 final size:24
Alignment explanation
Indices: 4004197--4004247 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
4004187 TTAAAATTAA
* *
4004197 TTAAATTTAAATTTAAGATAAA-T
1 TTAAAATTAAAATTAAGATAAACT
**
4004220 TTAAAATTAAAATTAATTTAAACT
1 TTAAAATTAAAATTAAGATAAACT
4004244 TTAA
1 TTAA
4004248 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAAAATTAAAATTAAGATAAACT
Found at i:4004947 original size:19 final size:19
Alignment explanation
Indices: 4004916--4004953 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4004906 AAAAATCACA
*
4004916 TTTTTTACATTTAACATAT
1 TTTTTTACATTTAAAATAT
4004935 TTTTTTA-ATTTTAAAATAT
1 TTTTTTACA-TTTAAAATAT
4004954 ATGGTGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTACATTTAAAATAT
Found at i:4006057 original size:20 final size:21
Alignment explanation
Indices: 4006032--4006080 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
4006022 TTTAAGCGAA
4006032 ATAAAAATCATAAATTTTA-G
1 ATAAAAATCATAAATTTTATG
*
4006052 ATAAAATAT-TTAAATTTTATG
1 ATAAAA-ATCATAAATTTTATG
4006073 -TAAAAATC
1 ATAAAAATC
4006081 TATTGAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
ATAAAAATCATAAATTTTATG
Found at i:4008853 original size:20 final size:20
Alignment explanation
Indices: 4008828--4008893 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
4008818 AAAATCAATC
4008828 ATTATTTATATTTATTTATA
1 ATTATTTATATTTATTTATA
* *
4008848 ATTATTGATATTT-TTAAATA
1 ATTATTTATATTTATT-TATA
*
4008868 ATT-TTT-TATATATTTATA
1 ATTATTTATATTTATTTATA
4008886 ATTATTTA
1 ATTATTTA
4008894 AGAAACTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.27
19 9 0.24
20 18 0.49
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTATTTATATTTATTTATA
Found at i:4012855 original size:41 final size:41
Alignment explanation
Indices: 4012798--4012893 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
4012788 CCACTAATGG
4012798 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT
1 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT
*
4012839 TTTGCAGGTAAACTGGCAATAGCTATGGATACTCAACAAAT
1 TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT
*
4012880 TTTGCAGATAAACT
1 TTTGCAGGTAAACT
4012894 ACCGATACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (41 bp):
TTTGCAGGTAAACTGGCAATAGCTATGGATACACAACAAAT
Found at i:4013883 original size:28 final size:26
Alignment explanation
Indices: 4013844--4013901 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
4013834 TTAAGATGAC
*
4013844 TATATAAAAATTTAATAAATAAAA-AA
1 TATATAAAAATTAAAT-AATAAAATAA
*
4013870 TATATAAATTAATTAAATATTAAAATAA
1 TATATAAA--AATTAAATAATAAAATAA
4013898 TATA
1 TATA
4013902 ATATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 6 0.22
28 13 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TATATAAAAATTAAATAATAAAATAA
Found at i:4016972 original size:30 final size:30
Alignment explanation
Indices: 4016938--4016998 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4016928 AATATGAAGC
*
4016938 AATATAATAAGCAGAT-AAATAATATGCGAA
1 AATATAAGAAGCAGATCAAATAA-ATGCGAA
*
4016968 AATATAAGATGCAGATGCAAATAAATGCGAA
1 AATATAAGAAGCAGAT-CAAATAAATGCGAA
4016999 TATTGGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 14 0.52
31 7 0.26
32 6 0.22
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.21
Consensus pattern (30 bp):
AATATAAGAAGCAGATCAAATAAATGCGAA
Found at i:4019147 original size:11 final size:11
Alignment explanation
Indices: 4019133--4019226 Score: 64
Period size: 11 Copynumber: 8.2 Consensus size: 11
4019123 ATATTTTCAT
*
4019133 AATTTGATTTA
1 AATTTAATTTA
4019144 AATTTAAATTTA
1 AATTT-AATTTA
* *
4019156 AAATAAATTTA
1 AATTTAATTTA
4019167 AATAGTTGAATTTA
1 AAT--TT-AATTTA
**
4019181 AATTTAAAATA
1 AATTTAATTTA
4019192 AATTTAAATTTA
1 AATTT-AATTTA
* *
4019204 AA-TAAATTAA
1 AATTTAATTTA
*
4019214 AAATTAATTTA
1 AATTTAATTTA
4019225 AA
1 AA
4019227 AACATAAAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
10 7 0.11
11 31 0.48
12 16 0.25
13 1 0.02
14 9 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:4019150 original size:6 final size:6
Alignment explanation
Indices: 4019139--4019226 Score: 78
Period size: 6 Copynumber: 15.2 Consensus size: 6
4019129 TCATAATTTG
* *
4019139 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATAGTTGA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
* * *
4019188 A-ATAA ATTTAA ATTTAA A--TAA ATTAAA AATT-A ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
4019227 AACATAAAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.06
5 12 0.18
6 44 0.68
8 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:4019217 original size:17 final size:17
Alignment explanation
Indices: 4019175--4019220 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
4019165 TAAATAGTTG
*
4019175 AATTTAAATTTAAAATA
1 AATTAAAATTTAAAATA
*
4019192 AATTTAAATTT-AAATA
1 AATTAAAATTTAAAATA
*
4019208 AATTAAAAATTAA
1 AATTAAAATTTAA
4019221 TTTAAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAAAATTTAAAATA
Found at i:4020465 original size:6 final size:6
Alignment explanation
Indices: 4020454--4020487 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4020444 TTCCAGTGTG
4020454 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GAGT
1 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GAGT
4020488 TGACTCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (6 bp):
GAGTCT
Found at i:4021969 original size:14 final size:14
Alignment explanation
Indices: 4021952--4021979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4021942 ATTTTAAATT
4021952 TTTAATTAATTAAA
1 TTTAATTAATTAAA
4021966 TTTAATTAATTAAA
1 TTTAATTAATTAAA
4021980 AATGTATTCT
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:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:4021974 original size:18 final size:18
Alignment explanation
Indices: 4021936--4021978 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
4021926 TTTTCAGTTA
4021936 TAATTAATT--TTAAATT
1 TAATTAATTAATTAAATT
4021952 T--TTAATTAATTAAATT
1 TAATTAATTAATTAAATT
4021968 TAATTAATTAA
1 TAATTAATTAA
4021979 AAATGTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
16 9 0.39
18 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAATTAAATT
Found at i:4023624 original size:32 final size:32
Alignment explanation
Indices: 4023556--4023625 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
4023546 ACTTTTTCAT
4023556 ATTTTTT--TATTATTTAATAATATTTTAATA
1 ATTTTTTCATATTATTTAATAATATTTTAATA
*
4023586 ATTTTTTCATATTA-TTAATACATAATTTTGATA
1 ATTTTTTCATATTATTTAATA-AT-ATTTTAATA
4023619 ATTTTTT
1 ATTTTTT
4023626 ACTCCGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 7 0.20
31 6 0.17
32 7 0.20
33 15 0.43
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (32 bp):
ATTTTTTCATATTATTTAATAATATTTTAATA
Found at i:4023693 original size:33 final size:33
Alignment explanation
Indices: 4023648--4023726 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
4023638 AAACATTGAT
* * **
4023648 CTCGAATCTCAAATTTTGAATATGAATCCTGAAC
1 CTCGAA-CTCAAACTCTGAATAAAAATCCTGAAC
*
4023682 CTCGAACTCAAACTCTGAATAAAAATCTTGAAC
1 CTCGAACTCAAACTCTGAATAAAAATCCTGAAC
4023715 CTCGAAACTCAA
1 CTCG-AACTCAA
4023727 TCTTAAACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (33 bp):
CTCGAACTCAAACTCTGAATAAAAATCCTGAAC
Found at i:4023761 original size:28 final size:29
Alignment explanation
Indices: 4023729--4023797 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
4023719 AAACTCAATC
*
4023729 TTAAACCCTAAACTTT-AAATATT-GAACT
1 TTAAACCCTAAACTTTAAAAT-TTAAAACT
*
4023757 TTAAACCTTAAA-TTTAAAATTTAAAACT
1 TTAAACCCTAAACTTTAAAATTTAAAACT
*
4023785 CTAAACCCTAAAC
1 TTAAACCCTAAAC
4023798 ATAAAACTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.33
Consensus pattern (29 bp):
TTAAACCCTAAACTTTAAAATTTAAAACT
Found at i:4032203 original size:17 final size:17
Alignment explanation
Indices: 4032181--4032213 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4032171 CTTTCAACAA
4032181 AAAATACAA-AATAATTC
1 AAAATA-AATAATAATTC
4032198 AAAATAAATAATAATT
1 AAAATAAATAATAATT
4032214 TTGGGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAATAATAATTC
Found at i:4044163 original size:22 final size:22
Alignment explanation
Indices: 4044107--4044163 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4044097 ATATCCAAAC
*
4044107 AATAATAATAAAATAGTAGCAA
1 AATAATAATAAAATAGCAGCAA
* *
4044129 TATAATAGTAAAATTA-CAGCAA
1 AATAATAATAAAA-TAGCAGCAA
*
4044151 AATAATAACAAAA
1 AATAATAATAAAA
4044164 AAAATTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (22 bp):
AATAATAATAAAATAGCAGCAA
Found at i:4050013 original size:2 final size:2
Alignment explanation
Indices: 4050001--4050035 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4049991 AAGTACTTTT
*
4050001 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4050036 TTCAAGAACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4052952 original size:42 final size:43
Alignment explanation
Indices: 4052900--4053112 Score: 288
Period size: 43 Copynumber: 5.0 Consensus size: 43
4052890 TTTGTTAATA
* * * *
4052900 TTAGTGGCGTTTGTGGGAAAA-TGCCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
* * *
4052942 TTAGCGGCGTTTGCGGGAAAAGTGCCGCTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
*
4052985 TTAGCGGCGTTTGT-GGAATAAGCGCCGCTAAAGATCGTGTTCT
1 TTAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGATCATGTTCT
* * *
4053028 TTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAGATCGTGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
*
4053071 TTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
4053113 ATAACGGCAT
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 47 0.31
43 103 0.67
44 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCT
Found at i:4059154 original size:29 final size:29
Alignment explanation
Indices: 4059064--4059208 Score: 104
Period size: 30 Copynumber: 4.9 Consensus size: 29
4059054 GACACTTTAA
*
4059064 GGGTAAAATGGTAATTTTTAGAAA-ATTTG
1 GGGTAAAATGGTAATTTTT-GAAAGTTTTG
* * **
4059093 AGGTCAAAAATGGT-ATTTTTGGACA--TCCG
1 GGGT--AAAATGGTAATTTTT-GAAAGTTTTG
4059122 GGGTAAAATGGTAATTTTTGAAAGTTTTG
1 GGGTAAAATGGTAATTTTTGAAAGTTTTG
*
4059151 GGGTCAAAAAT-GTAATTTTTGAAAGTTTAG
1 GGGT--AAAATGGTAATTTTTGAAAGTTTTG
* *
4059181 GGGCAAAAAT-GTGATTTTTGAAAAGTTT
1 GGG-TAAAATGGTAATTTTTG-AAAGTTT
4059209 AGGTTTTCAA
Statistics
Matches: 95, Mismatches: 12, Indels: 17
0.77 0.10 0.14
Matches are distributed among these distances:
27 11 0.12
28 6 0.06
29 28 0.29
30 37 0.39
31 13 0.14
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGAAAGTTTTG
Found at i:4059168 original size:30 final size:29
Alignment explanation
Indices: 4059126--4059211 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 29
4059116 CATCCGGGGT
*
4059126 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAAT-GTAATTTTTGAAAGTTTAGGGG-CA
4059157 AAAATGTAATTTTTGAAAGTTTAGGGGCA
1 AAAATGTAATTTTTGAAAGTTTAGGGGCA
*
4059186 AAAATGTGATTTTTGAAAAGTTTAGG
1 AAAATGTAATTTTTG-AAAGTTTAGG
4059212 TTTTCAATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
29 16 0.31
30 31 0.60
31 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTAGGGGCA
Found at i:4059259 original size:30 final size:30
Alignment explanation
Indices: 4059135--4059259 Score: 91
Period size: 30 Copynumber: 4.2 Consensus size: 30
4059125 TAAAATGGTA
*
4059135 ATTTTTGAAA-GTTTTGGGGTCAAAA-ATG
1 ATTTTTGAAATGTTTAGGGGTCAAAATATG
*
4059163 TAATTTTTGAAA-GTTTAGGGG-CAAAAATGTG
1 --ATTTTTGAAATGTTTAGGGGTC-AAAATATG
* ** ***
4059194 ATTTTTGAAAAGTTTAGGTTTTC--AATGCA
1 ATTTTTGAAATGTTTAGG-GGTCAAAATATG
*
4059223 ATTTTTGAAATCTTTAGGGGTCAAAATATG
1 ATTTTTGAAATGTTTAGGGGTCAAAATATG
4059253 ATTTTTG
1 ATTTTTG
4059260 GATAGTCTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
28 2 0.03
29 31 0.41
30 39 0.52
31 2 0.03
32 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (30 bp):
ATTTTTGAAATGTTTAGGGGTCAAAATATG
Found at i:4061231 original size:433 final size:433
Alignment explanation
Indices: 4060425--4061279 Score: 1674
Period size: 433 Copynumber: 2.0 Consensus size: 433
4060415 TTACATAGTT
4060425 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT
1 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT
4060490 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA
66 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA
4060555 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT
131 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT
4060620 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT
196 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT
4060685 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT
261 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT
*
4060750 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTTTTCTTTT
326 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT
4060815 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA
391 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA
4060858 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT
1 ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT
*
4060923 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTTTAGAA
66 AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA
4060988 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT
131 CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT
4061053 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT
196 GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT
4061118 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT
261 GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT
4061183 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT
326 ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT
* *
4061248 TGCAGGTCGGCTTACAGTGGTGGCTGTGGCAG
391 TGCAGGTCGACTTACAGTGGTCGCTGTGGCAG
4061280 TGACGGTGCA
Statistics
Matches: 418, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
433 418 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (433 bp):
ATCATAAAATATTTAGAAATTAATAATAAATAATAATAACCGGTGACTGTATTAATATGCTAGTT
AATGCATATGAAACGTTGTAAACCTTAAACAAGAACTTAAACAAACAATGAATATACCTCTAGAA
CCAGTGTTGTTTGGTTGCTTGGATCTGTTGGGCTTTAATTCTTGACTTTGGATGCTCTTCCTTCT
GTATTTGAATTGAAACTATCCGATTAATTGCCAATAGTCTCTGTATCTAAAGAAAACTAGTAACT
GTGTATTGATTTTTGAATGTTCCAAAGGTCAGTAACCTCCTACAATTTATTTCAATTCTGGCTTT
ATAGCCATGTTTACAATCATCTTATTTTGTTTTCTTCTAACTAAATGCTTGTCTTCTCTTCTTTT
TGCAGGTCGACTTACAGTGGTCGCTGTGGCAGGTCGGTTTACA
Found at i:4061538 original size:23 final size:22
Alignment explanation
Indices: 4061498--4061540 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4061488 TTGGACATTA
*
4061498 TAAATTTAAATAATTTTAAACT
1 TAAATTTAAATAAATTTAAACT
4061520 TAAATTTATAATAAATTTAAA
1 TAAATTTA-AATAAATTTAAA
4061541 TTCTGTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTTAAATAAATTTAAACT
Found at i:4069013 original size:13 final size:13
Alignment explanation
Indices: 4068997--4069021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4068987 ATTAAAGACA
4068997 ATAATTTTTATTG
1 ATAATTTTTATTG
4069010 ATAATTTTTATT
1 ATAATTTTTATT
4069022 TAAAACATCA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATAATTTTTATTG
Found at i:4077810 original size:24 final size:24
Alignment explanation
Indices: 4077783--4077846 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
4077773 TAATCTAGAG
*
4077783 TAATAAGAGTTTGACTCAAACAAA
1 TAATAAGAGTTTAACTCAAACAAA
* * *
4077807 TAATTAGAGTTTAATTGAAACAAA
1 TAATAAGAGTTTAACTCAAACAAA
*
4077831 TAA-ACAAAGTTTAACT
1 TAATA-AGAGTTTAACT
4077847 GAAAGACTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (24 bp):
TAATAAGAGTTTAACTCAAACAAA
Found at i:4077849 original size:24 final size:24
Alignment explanation
Indices: 4077790--4077850 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4077780 GAGTAATAAG
* * ** *
4077790 AGTTTGACTCAAACAAATAATTAG
1 AGTTTAACTGAAACAAATAAACAA
*
4077814 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
4077838 AGTTTAACTGAAA
1 AGTTTAACTGAAA
4077851 GACTATTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:4089234 original size:185 final size:186
Alignment explanation
Indices: 4088921--4089356 Score: 732
Period size: 185 Copynumber: 2.3 Consensus size: 186
4088911 AAAGTTTCGA
* * * *
4088921 AGTATAGTGGTAAGAATTCCCACCTGTCACGCGGGTGACCCGGATTCGATCCCCGGCAACAGCGA
1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
*
4088986 CCGTGTATATTTGTTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT
66 CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT
** * **
4089051 TTATTTTGAATCAATCA-AGTTTTGTCAAATCCTCGTACTAACAACAAAGTCGTTGT
131 TTAGATTGAATCAATCATA-TCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT
4089107 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCG-
1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
*
4089171 CCGTGTTTATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT
66 CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT
* *
4089236 TTAGATTGAATCAATCATATCTTGTCAAATCCTTACACTAACATCAAAGTCGTTGT
131 TTAGATTGAATCAATCATATCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT
4089292 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
1 AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
4089357 TCTGTTTTTG
Statistics
Matches: 235, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
185 174 0.74
186 61 0.26
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (186 bp):
AGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
CCGTGTATATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATATCAGAT
TTAGATTGAATCAATCATATCTTGTCAAATCCTCACACTAACAACAAAGTCGTTGT
Found at i:4098159 original size:19 final size:20
Alignment explanation
Indices: 4098127--4098167 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
4098117 GGTTAATATG
*
4098127 ATTTTAATATATTATTTTTA
1 ATTTTAATATATTATTTATA
4098147 ATTTTAA-ATATTATTTATA
1 ATTTTAATATATTATTTATA
4098166 AT
1 AT
4098168 ATATATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTAATATATTATTTATA
Found at i:4099749 original size:9 final size:9
Alignment explanation
Indices: 4099735--4099762 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4099725 AAGACAACGG
4099735 TTCTTCCAA
1 TTCTTCCAA
4099744 TTCTTCCAA
1 TTCTTCCAA
4099753 TTCTTCCAA
1 TTCTTCCAA
4099762 T
1 T
4099763 CACATCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.46
Consensus pattern (9 bp):
TTCTTCCAA
Found at i:4105985 original size:21 final size:22
Alignment explanation
Indices: 4105959--4106006 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
4105949 TTATAAAATG
* *
4105959 ATTTTATTTTATGA-ATTTTAA
1 ATTTTATTTGATAATATTTTAA
4105980 ATTTTATTTGATAATATTTTAA
1 ATTTTATTTGATAATATTTTAA
*
4106002 GTTTT
1 ATTTT
4106007 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (22 bp):
ATTTTATTTGATAATATTTTAA
Found at i:4106600 original size:42 final size:42
Alignment explanation
Indices: 4106553--4106634 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
4106543 TTTACAAACA
4106553 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT
1 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT
4106595 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAA
1 TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAA
4106635 TTTAATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (42 bp):
TTCTGTAAATAGTTCTGGAAGTACATAAGTATTGGGATAACT
Found at i:4110285 original size:32 final size:32
Alignment explanation
Indices: 4110249--4110325 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
4110239 TAATAATTAA
*
4110249 AGAAACACAAGCAATATCATATAAGCCCTTGC
1 AGAAACACAAGCAAGATCATATAAGCCCTTGC
4110281 AGAAACACAAGCAAGATCATATAAGCCCTTGC
1 AGAAACACAAGCAAGATCATATAAGCCCTTGC
4110313 AGAAACACAAGCA
1 AGAAACACAAGCA
4110326 CAACACATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (32 bp):
AGAAACACAAGCAAGATCATATAAGCCCTTGC
Found at i:4115707 original size:30 final size:29
Alignment explanation
Indices: 4115673--4115796 Score: 167
Period size: 30 Copynumber: 4.1 Consensus size: 29
4115663 CATTCAAACA
4115673 GGGTTAAATTTGAATTTTTAAAAATTTTAG
1 GGGTTAAATTTGAATTTTTAAAAA-TTTAG
4115703 GGGTTAAATTTGAATTTTTGAAAAATTTAG
1 GGGTTAAATTTGAATTTTT-AAAAATTTAG
* *
4115733 GGGTGAAATTTGAATTTTTAGAAAATTTGG
1 GGGTTAAATTTGAATTTTTA-AAAATTTAG
* * *
4115763 GGGTCAAATTTGAATTTTTGAAAACTTTGG
1 GGGTTAAATTTGAATTTTT-AAAAATTTAG
4115793 GGGT
1 GGGT
4115797 CAAAAAATGA
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.01
30 80 0.92
31 6 0.07
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (29 bp):
GGGTTAAATTTGAATTTTTAAAAATTTAG
Found at i:4115772 original size:60 final size:60
Alignment explanation
Indices: 4115673--4115796 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
4115663 CATTCAAACA
* *
4115673 GGGTTAAATTTGAATTTTTAAAAATTTTAGGGGTTAAATTTGAATTTTTGAAAAATTTAG
1 GGGTGAAATTTGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG
* * *
4115733 GGGTGAAATTTGAATTTTTAGAAAA-TTTGGGGGTCAAATTTGAATTTTTGAAAACTTTGG
1 GGGTGAAATTTGAATTTTTA-AAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG
4115793 GGGT
1 GGGT
4115797 CAAAAAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 54 0.93
61 4 0.07
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (60 bp):
GGGTGAAATTTGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAG
Found at i:4115810 original size:29 final size:29
Alignment explanation
Indices: 4115683--4115810 Score: 105
Period size: 30 Copynumber: 4.3 Consensus size: 29
4115673 GGGTTAAATT
* * * **
4115683 TGAATTTTTAAAAATTTTAGGGGTTAAATT
1 TGAATTTTTGAAAA-TTTGGGGGTCAAAAA
* * **
4115713 TGAATTTTTGAAAAATTTAGGGGTGAAATT
1 TGAATTTTTG-AAAATTTGGGGGTCAAAAA
**
4115743 TGAATTTTTAGAAAATTTGGGGGTCAAATT
1 TGAATTTTT-GAAAATTTGGGGGTCAAAAA
4115773 TGAATTTTTGAAAACTTTGGGGGTCAAAAAA
1 TGAATTTTTGAAAA-TTTGGGGGTC-AAAAA
4115804 TG-ATTTT
1 TGAATTTT
4115811 AAAATAAATC
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.06
30 73 0.83
31 10 0.11
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.41
Consensus pattern (29 bp):
TGAATTTTTGAAAATTTGGGGGTCAAAAA
Found at i:4115810 original size:60 final size:60
Alignment explanation
Indices: 4115683--4115814 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
4115673 GGGTTAAATT
* * **
4115683 TGAATTTTTAAAAATTTTAGGGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTGAAATT
1 TGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGTAAAAAA
* * *
4115743 TGAATTTTTAGAAAA-TTTGGGGGTCAAATTTGAATTTTTGAAAACTTTGGGGGTCAAAAAA
1 TGAATTTTTA-AAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGT-AAAAAA
4115804 TG-A-TTTTAAAA
1 TGAATTTTTAAAA
4115815 TAAATCAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 3 0.05
59 5 0.08
60 46 0.73
61 9 0.14
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.40
Consensus pattern (60 bp):
TGAATTTTTAAAAATTTTAGGGGTCAAATTTGAATTTTTGAAAAATTTAGGGGTAAAAAA
Found at i:4116580 original size:11 final size:11
Alignment explanation
Indices: 4116564--4116588 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4116554 TTTATTTATT
4116564 TAATAAATAAA
1 TAATAAATAAA
4116575 TAATAAATAAA
1 TAATAAATAAA
4116586 TAA
1 TAA
4116589 AATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:4116732 original size:33 final size:33
Alignment explanation
Indices: 4116690--4116757 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
4116680 TCTCTTGTCG
4116690 TATTTGTGGTTATGAATAGAAAA-ATATATTGCA
1 TATTTGTGGTTATGAATA-AAAAGATATATTGCA
*
4116723 TATTTGTGGTTATGAATAAAAAGATATTTTGCA
1 TATTTGTGGTTATGAATAAAAAGATATATTGCA
4116756 TA
1 TA
4116758 GTTTAATAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (33 bp):
TATTTGTGGTTATGAATAAAAAGATATATTGCA
Found at i:4133141 original size:3 final size:3
Alignment explanation
Indices: 4133133--4133170 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4133123 ATTTATTGAT
4133133 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4133171 TTAAAGTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4135954 original size:18 final size:18
Alignment explanation
Indices: 4135917--4135951 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4135907 ATGTTATGTG
4135917 AAAAATATAAAAAAAATT
1 AAAAATATAAAAAAAATT
*
4135935 AAAAATA-AAAATAAATT
1 AAAAATATAAAAAAAATT
4135952 TAACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATAAAAAAAATT
Found at i:4145879 original size:25 final size:24
Alignment explanation
Indices: 4145836--4145900 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
4145826 ATCACTAATT
* *
4145836 ACCAAAAAAAAATACAAAAACAAAA
1 ACCAAAAAAAAAGAGAAAAA-AAAA
**
4145861 ACCAAAAAAAAAGAGAAAAAACCA
1 ACCAAAAAAAAAGAGAAAAAAAAA
4145885 A--AAAAAAAAAGAGAAA
1 ACCAAAAAAAAAGAGAAA
4145901 CCTAAGTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 15 0.42
24 3 0.08
25 18 0.50
ACGTcount: A:0.80, C:0.12, G:0.06, T:0.02
Consensus pattern (24 bp):
ACCAAAAAAAAAGAGAAAAAAAAA
Found at i:4145880 original size:26 final size:26
Alignment explanation
Indices: 4145836--4145888 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
4145826 ATCACTAATT
* *
4145836 ACCAAAAAAAAATACAAAAA-CAAAA
1 ACCAAAAAAAAAGAAAAAAACCAAAA
4145861 ACCAAAAAAAAAGAGAAAAAACCAAAA
1 ACCAAAAAAAAAGA-AAAAAACCAAAA
4145888 A
1 A
4145889 AAAAAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 5 0.21
27 6 0.25
ACGTcount: A:0.79, C:0.15, G:0.04, T:0.02
Consensus pattern (26 bp):
ACCAAAAAAAAAGAAAAAAACCAAAA
Found at i:4148857 original size:21 final size:21
Alignment explanation
Indices: 4148811--4148858 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4148801 TCAATCCTAA
* *
4148811 AATATATTATTATTTTATTTT
1 AATATATTATTACTTTATTAT
*
4148832 GATATATTATGTACTTTA-TAT
1 AATATATTAT-TACTTTATTAT
4148853 AATATA
1 AATATA
4148859 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATATTATTACTTTATTAT
Found at i:4150079 original size:20 final size:20
Alignment explanation
Indices: 4150054--4150093 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4150044 TAATTCAACG
4150054 CAGGGGTGTAATTAGGGGGC
1 CAGGGGTGTAATTAGGGGGC
4150074 CAGGGGTGTAATTAGGGGGC
1 CAGGGGTGTAATTAGGGGGC
4150094 TATCAGGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.50, T:0.20
Consensus pattern (20 bp):
CAGGGGTGTAATTAGGGGGC
Found at i:4150217 original size:31 final size:32
Alignment explanation
Indices: 4150141--4150217 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
4150131 CATTTAGGTT
* *
4150141 TTTTAAAATTT-TTAAAAATTGCATTTTGATC
1 TTTTAAAATTTATAAAAAATTGCATTTTAATC
* *
4150172 CTTTAAAA-TGATAAAAAATTTG-A-TTTAATC
1 TTTTAAAATTTATAAAAAA-TTGCATTTTAATC
4150202 TTTTAAAATTTATAAA
1 TTTTAAAATTTATAAA
4150218 GATATAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 14 0.38
31 20 0.54
32 3 0.08
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTTAAAATTTATAAAAAATTGCATTTTAATC
Found at i:4152905 original size:29 final size:30
Alignment explanation
Indices: 4152831--4152995 Score: 212
Period size: 30 Copynumber: 5.6 Consensus size: 30
4152821 CAAAAAATGA
* *
4152831 GGTCAAAAATGAAATTTTGG-AAAG-TTCGG
1 GGTC-AAAATGTAATTTTGGAAAAGTTTTGG
*
4152860 AGGT-AAAATATAATTTT-GAAAAGTTTTGG
1 -GGTCAAAATGTAATTTTGGAAAAGTTTTGG
4152889 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
4152919 GGTCAAAATGTAATTTTGGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
* * *
4152949 GGTTAAAATATAATTTTGGAAAAGTTTTAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTTGG
*
4152979 GATCAAAATGTAATTTT
1 GGTCAAAATGTAATTTT
4152996 TGGACAATTT
Statistics
Matches: 121, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
27 1 0.01
28 18 0.15
29 16 0.13
30 86 0.71
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTTGG
Found at i:4152907 original size:19 final size:19
Alignment explanation
Indices: 4152883--4152937 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
4152873 TTTTGAAAAG
4152883 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
4152902 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
4152913 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
4152932 TTTTGG
1 TTTTGG
4152938 AAAAGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:4155049 original size:6 final size:6
Alignment explanation
Indices: 4155040--4155150 Score: 106
Period size: 6 Copynumber: 18.8 Consensus size: 6
4155030 TTTTTTAATG
* ** *
4155040 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
4155088 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
4155135 TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
4155151 ATCAATTTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.05
5 12 0.14
6 60 0.69
7 5 0.06
8 6 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:4155075 original size:31 final size:30
Alignment explanation
Indices: 4155065--4155172 Score: 109
Period size: 31 Copynumber: 3.7 Consensus size: 30
4155055 TAATTTTTAT
*
4155065 TTAAATTTAAATTCAAATTAAATTTAAATAA
1 TTAAATTTAAATTTAAATTAAATTT-AATAA
* *
4155096 TTAAATTTAAATTTAAAATAAATTTAA-AT
1 TTAAATTTAAATTTAAATTAAATTTAATAA
*
4155125 TTAAA--TAAATTTAAAATAAATTTAA-AA
1 TTAAATTTAAATTTAAATTAAATTTAATAA
* * *
4155152 -TCAATTTAACTCTAAATTAAA
1 TTAAATTTAAATTTAAATTAAA
4155173 CGAAAAGTCC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
26 3 0.04
27 21 0.31
28 12 0.18
29 6 0.09
30 2 0.03
31 23 0.34
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAATTTAAATTTAAATTAAATTTAATAA
Found at i:4155083 original size:37 final size:36
Alignment explanation
Indices: 4155041--4155160 Score: 111
Period size: 37 Copynumber: 3.2 Consensus size: 36
4155031 TTTTTAATGT
* ** *
4155041 TAAATTTAATATTTTAAT-TTTTATTTAAATTTAAAT
1 TAAATTTAA-ATTTAAATATTAAATTTAAATTTAAAA
4155077 TCAAA-TTAAATTTAAATAATTAAATTTAAATTTAAAA
1 T-AAATTTAAATTTAAAT-ATTAAATTTAAATTTAAAA
*
4155114 TAAATTTAAATTTAAATAAATTTAAA-ATAAATTTAAAA
1 TAAATTTAAATTTAAAT--A-TTAAATTTAAATTTAAAA
*
4155152 TCAATTTAA
1 TAAATTTAA
4155161 CTCTAAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
35 7 0.10
36 8 0.11
37 31 0.43
38 21 0.29
39 5 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (36 bp):
TAAATTTAAATTTAAATATTAAATTTAAATTTAAAA
Found at i:4155085 original size:11 final size:11
Alignment explanation
Indices: 4155063--4155160 Score: 83
Period size: 11 Copynumber: 8.5 Consensus size: 11
4155053 TTTAATTTTT
4155063 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
4155075 ATTCAAATTAA
1 ATTTAAATTAA
4155086 ATTTAAATAATTAA
1 ATTT--A-AATTAA
4155100 ATTTAAATTTAA
1 ATTTAAA-TTAA
*
4155112 A-ATAAATTTAA
1 ATTTAAA-TTAA
4155123 ATTTAAA-TAA
1 ATTTAAATTAA
*
4155133 ATTTAAAATAA
1 ATTTAAATTAA
* *
4155144 ATTTAAAATCA
1 ATTTAAATTAA
4155155 ATTTAA
1 ATTTAA
4155161 CTCTAAATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.13
11 38 0.51
12 16 0.21
13 1 0.01
14 10 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:4155085 original size:17 final size:17
Alignment explanation
Indices: 4155065--4155139 Score: 104
Period size: 17 Copynumber: 4.6 Consensus size: 17
4155055 TAATTTTTAT
*
4155065 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTTAAA
4155082 TTAAATTTAAA--T-AA
1 TTAAATTTAAATTTAAA
4155096 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
4155113 ATAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
4155130 -TAAATTTAAA
1 TTAAATTTAAA
4155140 ATAAATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 13 0.25
16 11 0.21
17 29 0.55
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:4155553 original size:38 final size:36
Alignment explanation
Indices: 4155511--4156107 Score: 311
Period size: 31 Copynumber: 17.4 Consensus size: 36
4155501 ATCTTTCTCT
* *
4155511 TACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCC-ACTC
* * * * *
4155549 TACTTAAATTTCA-AGAGGATGAC-G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
4155580 TACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAGA-CTGTTATCC-ACTC
* * * *
4155618 TACTTCAATTTCA-AGAGGATGAC-G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4155649 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
** * * * *
4155686 TACTTCAATTTCA-AGGGGATGAC--AT-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4155717 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAAGTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCC-ACTC
* * * * * *
4155755 TACTTCGATTTCA-ATAGGATGAC-G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4155786 TACTTCAATTTCAGAGATGAAAACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
* * * * *
4155823 TACTTCAATTTCA-AGAGGATGAC--AT-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4155854 TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
* * ** * * *
4155891 AACTTTAATTTCA-AGCGGATGAC-G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4155922 TACTTCAATTTCAGAGATGAAAACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
* * * * *
4155959 AACTTCAATTTCA-AGAGGATGAC-ATT-T-CTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
* *
4155990 TACTTCAATTTCAAAGATGAAGACTTGTTATTCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
* * ** * * *
4156027 AACTTTAATTTC-GAGCGGATGAC-G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
*
4156058 TACTTCAATTTTAGAGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGAC-TGTTATCCACTC
4156095 TACTTCAATTTCA
1 TACTTCAATTTCA
4156108 AGCGGGTTGG
Statistics
Matches: 404, Mismatches: 105, Indels: 101
0.66 0.17 0.17
Matches are distributed among these distances:
31 95 0.24
32 80 0.20
33 12 0.03
34 14 0.03
35 11 0.03
36 61 0.15
37 94 0.23
38 37 0.09
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (36 bp):
TACTTCAATTTCAGAGATGAAGACTGTTATCCACTC
Found at i:4156112 original size:68 final size:68
Alignment explanation
Indices: 4155507--4156109 Score: 909
Period size: 68 Copynumber: 8.8 Consensus size: 68
4155497 AATGATCTTT
* * *
4155507 CTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTAAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
4155572 GTTG
65 GTTG
*
4155576 CTCTTACTTCAATTTCAGAGATGAAGACCTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
4155641 GTTG
65 GTTG
* * *
4155645 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACA
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
4155710 TTG
66 TTG
* * * *
4155713 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAAGTCTACTTCGATTTCAATAGGATGAC
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
4155778 GTTG
65 GTTG
* *
4155782 CTCTTACTTCAATTTCAGAGATGAAAACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACA
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
4155847 TTG
66 TTG
* * * * *
4155850 CTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCAACTTTAATTTCAAGCGGATGACG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
4155915 TTG
66 TTG
* * *
4155918 CTCTTACTTCAATTTCAGAGATGAAAACGTGTTATCCACTCAACTTCAATTTCAAGAGGATGACA
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
*
4155983 TTT
66 TTG
* * * * * * *
4155986 CTCTTACTTCAATTTCAAAGATGAAGACTTGTTATTCACTCAACTTTAATTTCGAGCGGATGACG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
4156051 TTG
66 TTG
*
4156054 CTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG
4156110 CGGGTTGGAA
Statistics
Matches: 482, Mismatches: 51, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
68 321 0.67
69 161 0.33
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (68 bp):
CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
TTG
Found at i:4167984 original size:28 final size:29
Alignment explanation
Indices: 4167953--4168105 Score: 148
Period size: 30 Copynumber: 5.2 Consensus size: 29
4167943 TCAAAAATGA
4167953 AATTTTGGAAAG-TTCGGAGG-CAAAATAT
1 AATTTTGGAAAGTTTCGG-GGTCAAAATAT
* * *
4167981 AATTTTGAAAAGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAGTTTCGGGGTCAAAATAT
* ** *
4168010 AATTTTGGCAAAATTTTAGGGTCAAAATGT
1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT
* **
4168040 AATTTTGGTAAATTTTTAGGGTCAAAATAT
1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT
* *
4168070 AATTTTGGAAAAGTTTTGGGGTTAAAATAT
1 AATTTTGG-AAAGTTTCGGGGTCAAAATAT
4168100 AATTTT
1 AATTTT
4168106 TGGACAATTT
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.12
29 18 0.17
30 78 0.72
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39
Consensus pattern (29 bp):
AATTTTGGAAAGTTTCGGGGTCAAAATAT
Found at i:4168034 original size:30 final size:30
Alignment explanation
Indices: 4167973--4168105 Score: 180
Period size: 30 Copynumber: 4.5 Consensus size: 30
4167963 AGTTCGGAGG
*
4167973 CAAAATATAATTTT-GAAAAGTTTTGGGGT
1 CAAAATATAATTTTGGAAAAGTTTTAGGGT
*
4168002 CAAAATGTAATTTTGGCAAAA-TTTTAGGGT
1 CAAAATATAATTTTGG-AAAAGTTTTAGGGT
* * *
4168032 CAAAATGTAATTTTGGTAAATTTTTAGGGT
1 CAAAATATAATTTTGGAAAAGTTTTAGGGT
*
4168062 CAAAATATAATTTTGGAAAAGTTTTGGGGT
1 CAAAATATAATTTTGGAAAAGTTTTAGGGT
*
4168092 TAAAATATAATTTT
1 CAAAATATAATTTT
4168106 TGGACAATTT
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
29 16 0.17
30 73 0.78
31 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (30 bp):
CAAAATATAATTTTGGAAAAGTTTTAGGGT
Found at i:4170159 original size:6 final size:6
Alignment explanation
Indices: 4170150--4170249 Score: 91
Period size: 6 Copynumber: 16.8 Consensus size: 6
4170140 TTTTTTAATG
* ** *
4170150 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
4170198 TTAAAT AATTACAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAA- -TAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
4170245 TTAAA
1 TTAAA
4170250 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 55 0.71
7 5 0.06
8 5 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:4170193 original size:37 final size:36
Alignment explanation
Indices: 4170151--4170241 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 36
4170141 TTTTTAATGT
* ** *
4170151 TAAATTTAATATTTTAAT-TTTTATTTAAATTTAAAT
1 TAAATTTAA-ATTTAAATATTACATTTAAATTTAAAA
4170187 TCAAA-TTAAATTTAAATAATTACATTTAAATTTAAAA
1 T-AAATTTAAATTTAAAT-ATTACATTTAAATTTAAAA
4170224 TAAATTTAAATTTAAATA
1 TAAATTTAAATTTAAATA
4170242 AATTTAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
35 7 0.15
36 9 0.19
37 31 0.66
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (36 bp):
TAAATTTAAATTTAAATATTACATTTAAATTTAAAA
Found at i:4170195 original size:17 final size:17
Alignment explanation
Indices: 4170175--4170259 Score: 88
Period size: 17 Copynumber: 5.2 Consensus size: 17
4170165 TAATTTTTAT
4170175 TTAAATTTAAATTCAAA
1 TTAAATTTAAATTCAAA
4170192 TTAAATTTAAA-T--AA
1 TTAAATTTAAATTCAAA
* *
4170206 TTACATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
4170223 ATAAATTTAAATTTAAA
1 TTAAATTTAAATTCAAA
* *
4170240 -TAAATTTAAAATCAAT
1 TTAAATTTAAATTCAAA
4170256 TTAA
1 TTAA
4170260 CTCTAAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 14 0.24
17 31 0.53
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAATTCAAA
Found at i:4170213 original size:14 final size:14
Alignment explanation
Indices: 4170175--4170242 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 14
4170165 TAATTTTTAT
4170175 TTAAATTTAAATTCAAA
1 TTAAATTTAAA-T--AA
4170192 TTAAATTTAAATAA
1 TTAAATTTAAATAA
*
4170206 TTACATTTAAAT--
1 TTAAATTTAAATAA
*
4170218 TTAAA-ATAAAT--
1 TTAAATTTAAATAA
4170229 TTAAATTTAAATAA
1 TTAAATTTAAATAA
4170243 ATTTAAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 10 0.23
12 9 0.20
14 13 0.30
16 1 0.02
17 11 0.25
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAATTTAAATAA
Found at i:4170266 original size:27 final size:27
Alignment explanation
Indices: 4170213--4170267 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4170203 TAATTACATT
*
4170213 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
4170240 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
4170267 T
1 T
4170268 TAAACGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:4171532 original size:3 final size:3
Alignment explanation
Indices: 4171524--4171557 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4171514 TCAGCCCCAT
4171524 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
4171558 TTCTTCGATA
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:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:4173526 original size:23 final size:25
Alignment explanation
Indices: 4173480--4173528 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
4173470 TTTTAATCAT
*
4173480 ACTAAAATATAGTAATCAAAATTTA
1 ACTAAAATATAATAATCAAAATTTA
4173505 ACTAAAA-ATAATAAT-AAAATTTA
1 ACTAAAATATAATAATCAAAATTTA
4173528 A
1 A
4173529 TTAGGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 7 0.30
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (25 bp):
ACTAAAATATAATAATCAAAATTTA
Found at i:4174179 original size:29 final size:30
Alignment explanation
Indices: 4174141--4174204 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
4174131 AGTTTATATC
*
4174141 TTTATAATTTTTAAAGA-TT-AAATCATAAT
1 TTTATAATTTTTAAAAAGTTAAAAT-ATAAT
*
4174170 TTTATTATTTTTAAAAAGTTAAAATATAAT
1 TTTATAATTTTTAAAAAGTTAAAATATAAT
4174200 TTTAT
1 TTTAT
4174205 CTTTATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 15 0.48
30 12 0.39
31 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAGTTAAAATATAAT
Found at i:4174806 original size:17 final size:18
Alignment explanation
Indices: 4174781--4174819 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4174771 TTTATTGATT
*
4174781 TATAAAAAAAAA-CTTAA
1 TATAAAAAAAAATCTAAA
*
4174798 TATAGAAAAAAATCTAAA
1 TATAAAAAAAAATCTAAA
4174816 TATA
1 TATA
4174820 TAGATTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (18 bp):
TATAAAAAAAAATCTAAA
Found at i:4174808 original size:18 final size:17
Alignment explanation
Indices: 4174781--4174819 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
4174771 TTTATTGATT
*
4174781 TATAAAAAAAAACTTAA
1 TATAAAAAAAAACTAAA
*
4174798 TATAGAAAAAAATCTAAA
1 TATA-AAAAAAAACTAAA
4174816 TATA
1 TATA
4174820 TAGATTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (17 bp):
TATAAAAAAAAACTAAA
Found at i:4177952 original size:25 final size:27
Alignment explanation
Indices: 4177934--4178007 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
4177924 GGTATTATGA
4177934 TATTTTT-TTTAATTTGGTATTTAAAT
1 TATTTTTGTTTAATTTGGTATTTAAAT
* *
4177960 TTTTTTTGTTTAATTTGGTATTTATACT
1 TATTTTTGTTTAATTTGGTATTTA-AAT
*
4177988 TGATTCTTGTTTTAATTTGG
1 T-ATTTTTG-TTTAATTTGG
4178008 CATCTAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 6 0.15
27 16 0.40
28 3 0.08
29 5 0.12
30 10 0.25
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (27 bp):
TATTTTTGTTTAATTTGGTATTTAAAT
Found at i:4178215 original size:14 final size:13
Alignment explanation
Indices: 4178186--4178219 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4178176 TCAATTACTT
*
4178186 TTAATTTTATTTA
1 TTAATTTCATTTA
4178199 TTAATTTCATGTTA
1 TTAATTTCAT-TTA
4178213 TTAATTT
1 TTAATTT
4178220 AAAATAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (13 bp):
TTAATTTCATTTA
Found at i:4188199 original size:23 final size:23
Alignment explanation
Indices: 4188181--4188224 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4188171 AAGGTTTAAG
*
4188181 GTTTGGGTTTGGGATGGTTCAAA
1 GTTTGGGTTTGAGATGGTTCAAA
4188204 GTTTGGGTTTGAGATGGTTCA
1 GTTTGGGTTTGAGATGGTTCA
4188225 TGGTTCATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.39, T:0.41
Consensus pattern (23 bp):
GTTTGGGTTTGAGATGGTTCAAA
Found at i:4188764 original size:16 final size:16
Alignment explanation
Indices: 4188739--4188785 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
4188729 ACCCGAGTCC
* **
4188739 AAAAAAATTCAAATTT
1 AAAAATATTCAAACCT
4188755 AAAAATATTCAAACCT
1 AAAAATATTCAAACCT
*
4188771 AAAAATATCCAAACC
1 AAAAATATTCAAACC
4188786 CGGATTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATATTCAAACCT
Found at i:4192617 original size:41 final size:41
Alignment explanation
Indices: 4192552--4192637 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
4192542 GATATTGCGT
* * * ** * *
4192552 TGTATATTATCATGCTTTGTGCCTAGTAGGCTTTGTGTCGG
1 TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG
*
4192593 TGTATATTATTAGGCCTTGGGCCTAACAAGCTTCGTGTCGG
1 TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG
4192634 TGTA
1 TGTA
4192638 ATAAATCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40
Consensus pattern (41 bp):
TGTATATTATCAGGCCTTGGGCCTAACAAGCTTCGTGTCGG
Found at i:4193815 original size:31 final size:32
Alignment explanation
Indices: 4193777--4193854 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
4193767 TTCATTTCAA
4193777 ATATATGAAAAATGTGAAAAATA-TTTATTAG
1 ATATATGAAAAATGTGAAAAATATTTTATTAG
* *
4193808 ATGTATGAAAAATGTGAATAATATTTTATTAG
1 ATATATGAAAAATGTGAAAAATATTTTATTAG
*
4193840 ATAAATGAAAAATGT
1 ATATATGAAAAATGT
4193855 AAAGAGGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 21 0.50
32 21 0.50
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (32 bp):
ATATATGAAAAATGTGAAAAATATTTTATTAG
Found at i:4194811 original size:114 final size:115
Alignment explanation
Indices: 4194645--4194872 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 115
4194635 ATGAAACAAG
*
4194645 TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGTTGTACTTTTTTTTGATGGAATA
1 TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGCTGTA-TTTTTTTT-ATGGAATA
*
4194710 GTATTTG-AAAAAAAA-AA-ATGAAATTGTGATTTCACGTCATTCATATCAA
64 GTATTTGAAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATCAA
*
4194759 TTATTAATGGTAGAAAAAC-TCTTATATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAG
1 TTATTAATGGTAGAAAAACTTC-TACATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAG
*
4194823 TATTTGAAAAAAAAAACAATATGAAATTATGATTTTACGTCATTCATATC
65 TATTTG-AAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATC
4194873 CATTTTCAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
112 15 0.14
113 10 0.10
114 50 0.48
115 2 0.02
116 28 0.27
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (115 bp):
TTATTAATGGTAGAAAAACTTCTACATAGGTCCTAGTAGTAGCTGTATTTTTTTTATGGAATAGT
ATTTGAAAAAAAAACAATATGAAATTATGATTTCACGTCATTCATATCAA
Found at i:4200536 original size:37 final size:36
Alignment explanation
Indices: 4200487--4200607 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 36
4200477 ATGTAATTCT
* * *
4200487 TTTTA-ATTTTAAATATAGTTTTAATTTTACCTTTAC
1 TTTTATATATTAAATGTAGTTTTAATTTTA-CTTTAA
* *
4200523 TTTTATATATTAAATGTAGTTTATACTTTTATTTTAA
1 TTTTATATATTAAATGTAGTTT-TAATTTTACTTTAA
* * * *
4200560 TTATATATCTTATATGTAGTTTTAATTTTAATGCTTAA
1 TTTTATATATTAAATGTAGTTTTAATTTTACT--TTAA
4200598 TTTT-TATATT
1 TTTTATATATT
4200608 TAATTATGTA
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
36 13 0.19
37 42 0.61
38 14 0.20
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (36 bp):
TTTTATATATTAAATGTAGTTTTAATTTTACTTTAA
Found at i:4200572 original size:26 final size:25
Alignment explanation
Indices: 4200543--4200622 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
4200533 TAAATGTAGT
4200543 TTATACTTTTATTTTAATTATATATC
1 TTATA-TTTTATTTTAATTATATATC
* *
4200569 TTATA-TGTAGTTTTAATTTTA-ATGC
1 TTATATTTTA-TTTTAATTATATAT-C
*
4200594 TTA-ATTTTTATATTTAATTATGTATC
1 TTATA-TTTTAT-TTTAATTATATATC
4200620 TTA
1 TTA
4200623 AATTGCTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
24 6 0.14
25 15 0.35
26 20 0.47
27 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (25 bp):
TTATATTTTATTTTAATTATATATC
Found at i:4200785 original size:7 final size:7
Alignment explanation
Indices: 4200775--4200799 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4200765 CATTAAAGTA
4200775 TAAATTT
1 TAAATTT
4200782 TAAATTT
1 TAAATTT
4200789 TAAATTT
1 TAAATTT
4200796 TAAA
1 TAAA
4200800 AAAATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:4201721 original size:22 final size:22
Alignment explanation
Indices: 4201673--4201724 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4201663 ATTAACAAAT
* *
4201673 TTAACATTAAAATAAATTATTA
1 TTAATATTAAAATAAATTAATA
*
4201695 TTAATATTATAATAAATTAATA
1 TTAATATTAAAATAAATTAATA
4201717 TTAATATT
1 TTAATATT
4201725 CATACATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATATTAAAATAAATTAATA
Found at i:4201770 original size:16 final size:16
Alignment explanation
Indices: 4201749--4201780 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4201739 TTTTGTGTTA
*
4201749 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
4201765 TTTTAAAATTAAATAT
1 TTTTAAAATTAAATAT
4201781 ATTAATATAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:4202295 original size:24 final size:25
Alignment explanation
Indices: 4202247--4202296 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4202237 AATTAATTTT
*
4202247 TAAAAATTTTAAAAACATTTTATAA
1 TAAAAATTTTAAAAACATTTAATAA
* *
4202272 TAAAAATTTTAATAA-GTTTAATAA
1 TAAAAATTTTAAAAACATTTAATAA
4202296 T
1 T
4202297 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAAATTTTAAAAACATTTAATAA
Found at i:4204009 original size:29 final size:29
Alignment explanation
Indices: 4203951--4204011 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4203941 TTAATTTAAT
*
4203951 AAATGGTAAAATTATACATTTAACTCTTA
1 AAATGATAAAATTATACATTTAACTCTTA
* *
4203980 AAATGATAAAATT-TTCATTTAATCTTTTA
1 AAATGATAAAATTATACATTTAA-CTCTTA
4204009 AAA
1 AAA
4204012 ATTATAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (29 bp):
AAATGATAAAATTATACATTTAACTCTTA
Found at i:4204290 original size:7 final size:8
Alignment explanation
Indices: 4204261--4204295 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
4204251 ATTAATCTTT
4204261 TAAAAATTA
1 TAAAAA-TA
4204270 TAAAAATA
1 TAAAAATA
4204278 TAAAAATA
1 TAAAAATA
*
4204286 TAAAATTA
1 TAAAAATA
4204294 TA
1 TA
4204296 TTTTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAAAATA
Found at i:4216586 original size:22 final size:21
Alignment explanation
Indices: 4216547--4216592 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
4216537 TAATAAATTG
* *
4216547 AATTCAAGATAATTAAATTCA
1 AATTCAAGAAAATCAAATTCA
4216568 AATTACAAGAAAATCAAATTCA
1 AATT-CAAGAAAATCAAATTCA
4216590 AAT
1 AAT
4216593 CGAAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (21 bp):
AATTCAAGAAAATCAAATTCA
Found at i:4222597 original size:29 final size:28
Alignment explanation
Indices: 4222532--4222597 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
4222522 CTTCACAAAG
4222532 TTAAAATTTAATCCCTATACTTTTAACT
1 TTAAAATTTAATCCCTATACTTTTAACT
* * * * *
4222560 TTAGGAATTTAATTCCTTTATTTTTAGATT
1 TTA-AAATTTAATCCCTATACTTTTA-ACT
4222590 TTAAAATT
1 TTAAAATT
4222598 CAGGTTCGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.10
29 22 0.73
30 5 0.17
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52
Consensus pattern (28 bp):
TTAAAATTTAATCCCTATACTTTTAACT
Found at i:4222870 original size:6 final size:6
Alignment explanation
Indices: 4222854--4222890 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
4222844 ATATATTTTA
4222854 ATATA- ATATAG ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
4222891 TTTATATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:4222882 original size:18 final size:17
Alignment explanation
Indices: 4222854--4222900 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
4222844 ATATATTTTA
4222854 ATATAATATAGATATAG
1 ATATAATATAGATATAG
4222871 ATATAGATATAGATATAG
1 ATATA-ATATAGATATAG
* *
4222889 ATTTTATATAGA
1 ATATAATATAGA
4222901 ATTGTAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (17 bp):
ATATAATATAGATATAG
Found at i:4225483 original size:21 final size:22
Alignment explanation
Indices: 4225457--4225507 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
4225447 TTTAATTCGA
*
4225457 TTAATTT-ATCGGTAGTT-AATT
1 TTAATTTGATCAG-AGTTAAATT
4225478 TTAATTTGATCAGAGTTAAATT
1 TTAATTTGATCAGAGTTAAATT
4225500 TATAATTT
1 T-TAATTT
4225508 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (22 bp):
TTAATTTGATCAGAGTTAAATT
Found at i:4228560 original size:21 final size:20
Alignment explanation
Indices: 4228518--4228560 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
4228508 ATAATATATC
* * *
4228518 AAATACACTTAAAAATATTA
1 AAATAAACTTAAAAAAAATA
4228538 AAATAAACATTAAAAAAAATA
1 AAATAAAC-TTAAAAAAAATA
4228559 AA
1 AA
4228561 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATAAACTTAAAAAAAATA
Found at i:4228765 original size:12 final size:12
Alignment explanation
Indices: 4228727--4228778 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
4228717 AAACAGCAAA
* *
4228727 AAAAATAATAGT
1 AAAAATAACAGC
* *
4228739 AAAAATAATAAC
1 AAAAATAACAGC
4228751 AAAAATAACAGC
1 AAAAATAACAGC
* *
4228763 AAAAGTAACACC
1 AAAAATAACAGC
4228775 AAAA
1 AAAA
4228779 TAGTAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAATAACAGC
Found at i:4228777 original size:24 final size:24
Alignment explanation
Indices: 4228727--4228778 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4228717 AAACAGCAAA
* * *
4228727 AAAAATAATAGTAAAAATAATAAC
1 AAAAATAACAGCAAAAATAACAAC
* *
4228751 AAAAATAACAGCAAAAGTAACACC
1 AAAAATAACAGCAAAAATAACAAC
4228775 AAAA
1 AAAA
4228779 TAGTAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAATAACAGCAAAAATAACAAC
Found at i:4229281 original size:21 final size:18
Alignment explanation
Indices: 4229238--4229273 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4229228 TATATTATTT
4229238 TATAAACATTAAAAAATA
1 TATAAACATTAAAAAATA
4229256 TATAATACATTAAAAAAT
1 TATAA-ACATTAAAAAAT
4229274 TAATATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAACATTAAAAAATA
Found at i:4229445 original size:8 final size:9
Alignment explanation
Indices: 4229416--4229448 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
4229406 ACAATATCCA
4229416 AATAATAAC
1 AATAATAAC
4229425 AATAA-AAC
1 AATAATAAC
4229433 AATAATAAC
1 AATAATAAC
4229442 -ATAATAA
1 AATAATAA
4229449 TGAAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAATAAC
Found at i:4229478 original size:19 final size:20
Alignment explanation
Indices: 4229456--4229499 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
4229446 TAATGAAATG
4229456 ATAGT-AAAACAATGAGAAA
1 ATAGTAAAAACAATGAGAAA
4229475 ATAGTAACAAAACAATGAGAAA
1 ATAGT-A-AAAACAATGAGAAA
4229497 ATA
1 ATA
4229500 ATAACAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
22 17 0.77
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (20 bp):
ATAGTAAAAACAATGAGAAA
Found at i:4229486 original size:22 final size:22
Alignment explanation
Indices: 4229461--4229512 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
4229451 AAATGATAGT
*
4229461 AAAACAATGAGAAAATAGTAAC
1 AAAACAATGAGAAAATAATAAC
4229483 AAAACAATGAGAAAATAATAAC
1 AAAACAATGAGAAAATAATAAC
*
4229505 AAATCAAT
1 AAAACAAT
4229513 TTTTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAACAATGAGAAAATAATAAC
Found at i:4232439 original size:18 final size:20
Alignment explanation
Indices: 4232398--4232439 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
4232388 ACAAAACCAT
*
4232398 CAAAATTTAAAAGACACAAA
1 CAAAATTTAAAAGACAAAAA
4232418 -AAAATTT-AAAGA-AAAAA
1 CAAAATTTAAAAGACAAAAA
4232435 CAAAA
1 CAAAA
4232440 CTAAACCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (20 bp):
CAAAATTTAAAAGACAAAAA
Done.