Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold464
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: 258458
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:117424 original size:49 final size:48
Alignment explanation
Indices: 117221--117756 Score: 620
Period size: 43 Copynumber: 11.5 Consensus size: 48
117211 ATGTCAATGC
* ** *
117221 GCTGATTCAAGGCTAGCTACATTAAACTTAAAGATGGAAAATGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAGAT-G--AAGGTGCCAATAT
* *
117273 GCTGATTCAAGGCCAGCTATATTGGACTT---A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
**
117316 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATGC
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGGTGCCAATAT
117364 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGGTGCCAATAT
*
117413 GCTGATTCAAGGCCAGCTATATTGGACTTAATGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAA-GATGAAGGTGCCAATAT
* * *
117462 GCTGATTCAAGGCCAGCGATATTGGACTT---A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
*
117505 GCTGATTCAAGGCCAGCTACACTGGACTT---A--AAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
* * *
117548 GCTGATTCAAGGCCAGCGATATTGGACTT---A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
117591 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGGTGCCAATAT
* * *
117640 GCTGATTCAAGGCCAGCGATATTGGACTT---A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
117683 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGGTGCCAATAT
* *
117732 GCTAATTCAAGGCCAGCTATATTGG
1 GCTGATTCAAGGCCAGCTACATTGG
117757 GGTTAGAAGG
Statistics
Matches: 432, Mismatches: 32, Indels: 43
0.85 0.06 0.08
Matches are distributed among these distances:
43 195 0.45
45 2 0.00
47 3 0.01
48 50 0.12
49 157 0.36
52 25 0.06
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (48 bp):
GCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGGTGCCAATAT
Found at i:117473 original size:21 final size:21
Alignment explanation
Indices: 117449--117559 Score: 54
Period size: 21 Copynumber: 5.2 Consensus size: 21
117439 CTTAATGATG
117449 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
117470 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
*
117492 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
117513 AA-G-GCCAGCTACACTGGACTTA
1 AAGGTGCCA-ATATGCT-GA-TTC
117535 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
117556 AAGG
1 AAGG
117560 CCAGCGATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 28
0.62 0.12 0.27
Matches are distributed among these distances:
19 8 0.12
20 6 0.09
21 19 0.30
22 16 0.25
23 7 0.11
24 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:117535 original size:92 final size:92
Alignment explanation
Indices: 117206--117756 Score: 810
Period size: 92 Copynumber: 6.0 Consensus size: 92
117196 ATGATGAGAA
* * * ** *
117206 AAAGGATGTCAATGCGCTGATTCAAGGCTAGCTACATTAAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
117271 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
**
117302 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATGCGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
117366 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
117393 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGATGAAGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
117458 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
117491 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACACTGGACTT----A--AAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
117550 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
117577 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
117642 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
117669 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
117734 TAATTCAAGGCCAGCTATATTGG
66 TGATTCAAGGCCAGCGATATTGG
117757 GGTTAGAAGG
Statistics
Matches: 420, Mismatches: 22, Indels: 30
0.89 0.05 0.06
Matches are distributed among these distances:
86 84 0.20
88 1 0.00
90 1 0.00
91 37 0.09
92 167 0.40
94 2 0.00
95 40 0.10
96 5 0.01
97 46 0.11
98 37 0.09
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:117844 original size:34 final size:33
Alignment explanation
Indices: 117761--117866 Score: 185
Period size: 33 Copynumber: 3.2 Consensus size: 33
117751 TATTGGGGTT
117761 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
117794 AGAATGGTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
117827 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
117861 AGAAGG
1 AGAAGG
117867 TTGAAAGATG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
33 37 0.54
34 31 0.46
ACGTcount: A:0.19, C:0.17, G:0.37, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:117981 original size:34 final size:35
Alignment explanation
Indices: 117870--118581 Score: 816
Period size: 34 Copynumber: 20.8 Consensus size: 35
117860 GAGAAGGTTG
* * *
117870 AAAGA-TGCCACGAAGTTGTGGAC-TTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
117903 CAAG-GTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGG--AA
*
117940 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
117974 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118008 AAAGAGTGCCACGGAGTTGTAGGC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
118042 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
118075 AAAGAGTGCCACGTAGTTGTGGGCTTT-AAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118108 AAAGAGTGCCACGGAGTCGTGGAC-TTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
118139 ---G-GTGCCACGGAGTTGTGGGC-TTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
118168 AAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 AAAG-A-GTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
* *
118207 AAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
118242 AAAG-GTGCCACGGAGTTGTGGGCTTGGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTT-TAAAA-GGAA
* *
118278 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118313 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
118347 AAA-TGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
*
118383 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118418 AAAGTGTGCCACAGAGTTGTGGGCTTTAAACA-GAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGGAA
*
118453 AAAG-GTGCCATGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
*
118489 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118524 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGG--
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
118557 -AAG-GTGCCACGGAGTCGTGGACTTT
1 AAAGAGTGCCACGGAGTTGTGGGCTTT
118582 GAGCAGAGAT
Statistics
Matches: 604, Mismatches: 43, Indels: 66
0.85 0.06 0.09
Matches are distributed among these distances:
27 22 0.04
28 2 0.00
31 19 0.03
32 7 0.01
33 93 0.15
34 155 0.26
35 142 0.24
36 44 0.07
37 94 0.16
38 21 0.03
39 5 0.01
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (35 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:118145 original size:27 final size:27
Alignment explanation
Indices: 118107--118166 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
118097 GCTTTAAAGG
*
118107 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
118134 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
118161 AGAAGG
1 AAAAGG
118167 AAAAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:118185 original size:35 final size:35
Alignment explanation
Indices: 118134--118581 Score: 549
Period size: 35 Copynumber: 12.8 Consensus size: 35
118124 TCGTGGACTT
* *
118134 AAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAGG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
118167 AAAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 AAAAG-A-GTGCCACGGAGTTGTGGGCTTT-AAAA-GGA
* *
118206 AAAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
*
118241 AAAAG-GTGCCACGGAGTTGTGGGCTTGGAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-TAAAA-GGA
* *
118277 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
* *
118312 AAAAGTGTGCCACAGAGTTGTGGGCTTTAAAA-GA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
*
118346 AAAA-TGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGA
*
118382 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
* *
118417 AAAAGTGTGCCACAGAGTTGTGGGCTTTAAACA-GA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGGA
*
118452 AAAAG-GTGCCATGGAGTTGTGGGCTTTGAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGA
*
118488 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
* *
118523 AAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
* *
118557 --AAG-GTGCCACGGAGTCGTGGACTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
118582 GAGCAGAGAT
Statistics
Matches: 371, Mismatches: 26, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
31 19 0.05
32 3 0.01
33 27 0.07
34 51 0.14
35 137 0.37
36 39 0.11
37 87 0.23
38 3 0.01
39 5 0.01
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.21
Consensus pattern (35 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
Found at i:118261 original size:106 final size:105
Alignment explanation
Indices: 117870--118583 Score: 875
Period size: 106 Copynumber: 6.9 Consensus size: 105
117860 GAGAAGGTTG
* * *
117870 AAAGA-TGCCACGAAGTTGTGGAC-TTAAAAAGAACAAG-GTGCCACAGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTT-AA
*
117932 AAGGAAAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA-GGAA
65 AA-G--AAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
* * * * *
117974 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTAGGC-TTAGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTA-A
* *
118037 AGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA-GG-A
65 AAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
* * * * * *
118075 AAAGAGTGCCACGTAGTTGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGTCGTGGAC-TTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
* *
118137 AG-----GGTGCCACGGAGTTGTGGGC-TT-AGAAGGAAA
66 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
* * *
118170 AGAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTACCACGGAGTTGTGGGCTTT
1 A-AAGAGTGCCACGGAGTTGTGGGCTTTAAAAA--GAAAAAGTGTGCCACAGAGTTGTGGGCTTT
*
118234 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTGGAAAAGGGAA
63 -AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
*
118278 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
* *
118343 AGAAAAATGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
66 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
118383 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
*
118448 CAGAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAA
66 -AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
118489 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
* * *
118554 AG--GAAGGTGCCACGGAGTCGTGGACTTTGA
66 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
118584 GCAGAGATTG
Statistics
Matches: 549, Mismatches: 39, Indels: 45
0.87 0.06 0.07
Matches are distributed among these distances:
93 25 0.05
94 2 0.00
95 23 0.04
96 3 0.01
97 3 0.01
99 26 0.05
100 30 0.05
101 29 0.05
102 36 0.07
103 24 0.04
104 7 0.01
105 137 0.25
106 166 0.30
107 4 0.01
108 34 0.06
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (105 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAA
AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
Found at i:118633 original size:32 final size:30
Alignment explanation
Indices: 118557--118680 Score: 149
Period size: 31 Copynumber: 4.0 Consensus size: 30
118547 CTTTAAAAGG
*
118557 AAGGTGCCACGGAGTCGTGGACTTTGAGCA
1 AAGGTGCCACGGAGTCGTGGACTTTGAGAA
* * *
118587 GAGATTGCCACTGAGTCGTGGACTTTGAAGAA
1 AAG-GTGCCACGGAGTCGTGGACTTTG-AGAA
*
118619 AAGGATGCCACTGAGTCGTGGACTTTGAGAA
1 AAGG-TGCCACGGAGTCGTGGACTTTGAGAA
* *
118650 GAAGGTGCCACGGAGTCATGGACTTTAAGAA
1 -AAGGTGCCACGGAGTCGTGGACTTTGAGAA
118681 GGTACTTGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.02
31 48 0.59
32 31 0.38
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (30 bp):
AAGGTGCCACGGAGTCGTGGACTTTGAGAA
Found at i:118637 original size:63 final size:61
Alignment explanation
Indices: 118557--118680 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 61
118547 CTTTAAAAGG
* * * *
118557 AAGGTGCCACGGAGTCGTGGACTTTGAGCAG-AGATTGCCACTGAGTCGTGGACTTTGAAGAA
1 AAGGTGCCACGGAGTCGTGGACTTTGAGAAGAAG-GTGCCACGGAGTCATGGACTTT-AAGAA
*
118619 AAGGATGCCACTGAGTCGTGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
1 AAGG-TGCCACGGAGTCGTGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
118681 GGTACTTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 9 0.16
63 44 0.80
64 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (61 bp):
AAGGTGCCACGGAGTCGTGGACTTTGAGAAGAAGGTGCCACGGAGTCATGGACTTTAAGAA
Found at i:119642 original size:11 final size:10
Alignment explanation
Indices: 119617--119641 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
119607 TGAAAAGGGG
119617 TTTTTCTTTT
1 TTTTTCTTTT
119627 TTTTTCTTTT
1 TTTTTCTTTT
119637 TTTTT
1 TTTTT
119642 TTTGCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:119999 original size:16 final size:14
Alignment explanation
Indices: 119979--120070 Score: 114
Period size: 14 Copynumber: 6.4 Consensus size: 14
119969 TGCCTTTGCA
*
119979 TTTTTTTTTTGTGT
1 TTTTTTTTTTTTGT
*
119993 TTGTTTTTTTTTGT
1 TTTTTTTTTTTTGT
*
120007 TTTTGTTTTTTTGT
1 TTTTTTTTTTTTGT
*
120021 TTTTTTTTTGTGTGT
1 TTTTTTTTT-TTTGT
120036 TTTTTTGTTTGTTTGT
1 TTTTTT-TTT-TTTGT
120052 TTTTTTTTTTTT-T
1 TTTTTTTTTTTTGT
120065 TTTTTT
1 TTTTTT
120071 CATCACCTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
13 7 0.10
14 35 0.51
15 13 0.19
16 14 0.20
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTTGT
Found at i:120004 original size:41 final size:39
Alignment explanation
Indices: 119959--120041 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 39
119949 TGATGTTCCC
119959 TTTTTGATTTTGCCTTTGCATTTTTTTTTTGTGTTTGTTTT
1 TTTTTGATTTTGCCTTTGCATTTTTTTTTTGTG--TGTTTT
* ** ***
120000 TTTTTGTTTTTGTTTTTTTGTTTTTTTTTTGTGTGTTTT
1 TTTTTGATTTTGCCTTTGCATTTTTTTTTTGTGTGTTTT
120039 TTT
1 TTT
120042 GTTTGTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
39 9 0.25
41 27 0.75
ACGTcount: A:0.02, C:0.04, G:0.14, T:0.80
Consensus pattern (39 bp):
TTTTTGATTTTGCCTTTGCATTTTTTTTTTGTGTGTTTT
Found at i:120047 original size:41 final size:41
Alignment explanation
Indices: 119979--120070 Score: 134
Period size: 41 Copynumber: 2.2 Consensus size: 41
119969 TGCCTTTGCA
*
119979 TTTTTTTTTTGTGTTTGTTTTTTTTTGTTT-TTGTTTTTTTG
1 TTTTTTTTTTGTGTTTGTTTTTGTTTGTTTGTT-TTTTTTTG
*
120020 TTTTTTTTTTGTGTGTT-TTTTTGTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTGTGT-TTGTTTTTGTTTGTTTGTTTTTTTTTG
120061 TTTTTTTTTT
1 TTTTTTTTTT
120071 CATCACCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 43 0.91
42 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (41 bp):
TTTTTTTTTTGTGTTTGTTTTTGTTTGTTTGTTTTTTTTTG
Found at i:120067 original size:39 final size:39
Alignment explanation
Indices: 119979--120068 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
119969 TGCCTTTGCA
* * *
119979 TTTTTTTTTTGTGTTTGTTTTTTTTTGTTTTTGTTTTTT
1 TTTTTTTTTTTTGTGTGTTTTTTTTTGTGTTTGTTTTTT
*
120018 TGTTTTTTTTTTGTGTGTTTTTTTGTT-TGTTTGTTTTTT
1 TTTTTTTTTTTTGTGTGTTTTTTT-TTGTGTTTGTTTTTT
120057 TTTTTTTTTTTT
1 TTTTTTTTTTTT
120069 TTCATCACCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 43 0.96
40 2 0.04
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (39 bp):
TTTTTTTTTTTTGTGTGTTTTTTTTTGTGTTTGTTTTTT
Found at i:120083 original size:1 final size:1
Alignment explanation
Indices: 119979--120070 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
119969 TGCCTTTGCA
* * * * * * * * * *
119979 TTTTTTTTTTGTGTTTGTTTTTTTTTGTTTTTGTTTTTTTGTTTTTTTTTTGTGTGTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
120044 TTGTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
120071 CATCACCTTT
Statistics
Matches: 67, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:128076 original size:52 final size:52
Alignment explanation
Indices: 127998--128126 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
127988 CGAAATATGA
*
127998 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
128050 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
128102 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
128127 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:128137 original size:52 final size:51
Alignment explanation
Indices: 127998--128146 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
127988 CGAAATATGA
*
127998 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
128050 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
128102 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
128147 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:128153 original size:13 final size:13
Alignment explanation
Indices: 128135--128159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128125 CAAAGATCAG
128135 TGTATCGATACAA
1 TGTATCGATACAA
128148 TGTATCGATACA
1 TGTATCGATACA
128160 TTTGGGTAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:128226 original size:19 final size:18
Alignment explanation
Indices: 128202--128299 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
128192 TAGCTTACAT
128202 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
128221 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
128234 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
128253 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
128266 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
128286 TGTATCGATACAAA
1 TGTATCGATACAAA
128300 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:128238 original size:32 final size:32
Alignment explanation
Indices: 128197--128297 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
128187 GGCAGTAGCT
*
128197 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
128229 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
128261 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
128294 TACA
1 TACA
128298 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:128239 original size:13 final size:13
Alignment explanation
Indices: 128221--128277 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
128211 ACAAAACTTA
128221 TGTATCGATACAT
1 TGTATCGATACAT
128234 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
128252 ATGTATCGATACAT
1 -TGTATCGATACAT
128266 TGTATCGATACA
1 TGTATCGATACA
128278 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:128904 original size:11 final size:11
Alignment explanation
Indices: 128888--128917 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
128878 TTAAATTTCT
128888 AATCAAATTTG
1 AATCAAATTTG
128899 AATCAAATTTG
1 AATCAAATTTG
128910 AATCAAAT
1 AATCAAAT
128918 GTAAAGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (11 bp):
AATCAAATTTG
Found at i:130048 original size:14 final size:14
Alignment explanation
Indices: 130029--130056 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
130019 ATGAGCTTAA
130029 AGTTTTTTACTAAG
1 AGTTTTTTACTAAG
130043 AGTTTTTTACTAAG
1 AGTTTTTTACTAAG
130057 CAAATATTGC
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:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
AGTTTTTTACTAAG
Found at i:131377 original size:97 final size:97
Alignment explanation
Indices: 131166--131385 Score: 219
Period size: 97 Copynumber: 2.3 Consensus size: 97
131156 TTTTCCGAGA
* ** * * ** * *
131166 GGATACTCCAACCCTGTTTTTGAACTTGTCAAGATTTAAATCTTATTTTTGATTAAATTTTTATC
1 GGATACTCTAACCCCATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTCACCAAATTCTCATC
* * *
131231 ATCAGGGATACTCCAACCACATTCTTTCAAAG
66 ATCAGGGACACTCCAACCACATTCCTCCAAAG
* *
131263 GGATA-TTTCAACTCCATTTTTAAACTTGTCAAGATTTAAATCTTA-TTTTCACCCAAATTCTCA
1 GGATACTCT-AACCCCATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTCA-CCAAATTCTCA
** * * * *
131326 TTGTTAGGGACACTCCAATCTCCTTCCTCCAAAG
64 TCATCAGGGACACTCCAACCACATTCCTCCAAAG
*
131360 GGATACTCTAACCCCATTTTTCAACT
1 GGATACTCTAACCCCATTTTTAAACT
131386 AAAAAATTGA
Statistics
Matches: 97, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
96 6 0.06
97 89 0.92
98 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (97 bp):
GGATACTCTAACCCCATTTTTAAACTTGTCAAGATTTAAATCTTATTTTTCACCAAATTCTCATC
ATCAGGGACACTCCAACCACATTCCTCCAAAG
Found at i:133839 original size:25 final size:25
Alignment explanation
Indices: 133811--133861 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
133801 TAATTGTAGC
133811 TCTAATGATGGTATGGTTTCTATCA
1 TCTAATGATGGTATGGTTTCTATCA
* *
133836 TCTAATGATGGTATGTTTTCTCTCA
1 TCTAATGATGGTATGGTTTCTATCA
133861 T
1 T
133862 AGTAGATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.47
Consensus pattern (25 bp):
TCTAATGATGGTATGGTTTCTATCA
Found at i:137048 original size:2 final size:2
Alignment explanation
Indices: 137043--137070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
137033 GAGAGCAATA
137043 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
137071 TAAGATGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137762 original size:65 final size:65
Alignment explanation
Indices: 137682--137807 Score: 234
Period size: 65 Copynumber: 1.9 Consensus size: 65
137672 ATAATTATTC
*
137682 ATTTTGCTTATCACGAATTTGATTATTCATAATTATTCGCTTTTCTCTTTATAAATTTAGAGTGA
1 ATTTTGCTTATCACGAATTTGATTATTCATAATTATTCACTTTTCTCTTTATAAATTTAGAGTGA
*
137747 ATTTTGCTTATCACGAATTTGGTTATTCATAATTATTCACTTTTCTCTTTATAAATTTAGA
1 ATTTTGCTTATCACGAATTTGATTATTCATAATTATTCACTTTTCTCTTTATAAATTTAGA
137808 ATGGATGTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (65 bp):
ATTTTGCTTATCACGAATTTGATTATTCATAATTATTCACTTTTCTCTTTATAAATTTAGAGTGA
Found at i:139130 original size:24 final size:23
Alignment explanation
Indices: 139103--139170 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
139093 AATTATTAAA
139103 ATAATATTATATTTATATTTTTAT
1 ATAATATTATA-TTATATTTTTAT
* *
139127 ATAATATTTTAAT-TATTTTTAT
1 ATAATATTATATTATATTTTTAT
139149 ATCATATAATTATATTATATTT
1 AT-A-AT-ATTATATTATATTT
139171 AAGGTTGTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 11 0.31
23 2 0.06
24 12 0.33
25 6 0.17
26 5 0.14
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
ATAATATTATATTATATTTTTAT
Found at i:140438 original size:20 final size:20
Alignment explanation
Indices: 140402--140447 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
140392 CTTTTATATA
*
140402 TTATA-ATTATATTTAAAATT
1 TTATATATTATATGT-AAATT
140422 TTATATATT-TATGTAAATT
1 TTATATATTATATGTAAATT
140441 TTGATAT
1 TT-ATAT
140448 GTTAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 13 0.57
21 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATATATTATATGTAAATT
Found at i:140441 original size:19 final size:19
Alignment explanation
Indices: 140417--140506 Score: 68
Period size: 17 Copynumber: 5.0 Consensus size: 19
140407 ATTATATTTA
*
140417 AAATTTTATATATTTATGT
1 AAATTTTATATATTTATAT
* *
140436 AAATTTTGATATGTTAATAT
1 AAATTTT-ATATATTTATAT
140456 -AA--TT-TAT-TTTATAT
1 AAATTTTATATATTTATAT
*
140470 AAATTTTA-ATATTT-TTT
1 AAATTTTATATATTTATAT
*
140487 ATATTTTATCATATTTATAT
1 AAATTTTAT-ATATTTATAT
140507 TATTTTTTCG
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
14 6 0.11
15 5 0.09
17 15 0.27
18 3 0.05
19 15 0.27
20 11 0.20
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (19 bp):
AAATTTTATATATTTATAT
Found at i:140487 original size:26 final size:27
Alignment explanation
Indices: 140460--140514 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
140450 TAATATAATT
*
140460 TATTTTATATAAATTTTAATATTTTTTA
1 TATTTTAT-CAAATTTTAATATTTTTTA
* *
140488 TATTTTATCATATTTATATTATTTTTT
1 TATTTTATCAAATTT-TAATATTTTTT
140515 CGTATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTATCAAATTTTAATATTTTTTA
Found at i:140510 original size:19 final size:17
Alignment explanation
Indices: 140484--140556 Score: 60
Period size: 19 Copynumber: 4.1 Consensus size: 17
140474 TTTAATATTT
*
140484 TTTATA-TTTTATCATA
1 TTTATATTTTTTTCATA
*
140500 TTTATATTATTTTTTCGTA
1 TTTATA-T-TTTTTTCATA
*
140519 -TTATATTTTATGTCATA
1 TTTATATTTT-TTTCATA
140536 TTTTATGATTTTTTTCATA
1 -TTTAT-ATTTTTTTCATA
140555 TT
1 TT
140557 ATGTTCAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 9 0.20
17 6 0.13
18 7 0.16
19 18 0.40
20 5 0.11
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (17 bp):
TTTATATTTTTTTCATA
Found at i:140525 original size:34 final size:35
Alignment explanation
Indices: 140485--140558 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
140475 TTAATATTTT
* *
140485 TTATATTTTA-TCATATTTATATTA-TTTTTTCGTA
1 TTATATTTTAGTCATATTT-TATGATTTTTTTCATA
140519 TTATATTTTATGTCATATTTTATGATTTTTTTCATA
1 TTATATTTTA-GTCATATTTTATGATTTTTTTCATA
140555 TTAT
1 TTAT
140559 GTTCAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 10 0.29
35 4 0.11
36 21 0.60
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (35 bp):
TTATATTTTAGTCATATTTTATGATTTTTTTCATA
Found at i:144336 original size:19 final size:19
Alignment explanation
Indices: 144310--144348 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
144300 ATTCAATGAG
*
144310 ATGCTG-AACATATTAAAA
1 ATGCTGAAACATAATAAAA
144328 ATGCATGAAACATAATAAAA
1 ATGC-TGAAACATAATAAAA
144348 A
1 A
144349 AAATGCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 2 0.11
20 12 0.67
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (19 bp):
ATGCTGAAACATAATAAAA
Found at i:145290 original size:20 final size:20
Alignment explanation
Indices: 145265--145302 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
145255 GTAAAAAGAC
*
145265 AGAATATATTGATACATTGA
1 AGAATATATCGATACATTGA
145285 AGAATATATCGATACATT
1 AGAATATATCGATACATT
145303 CATACATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
AGAATATATCGATACATTGA
Found at i:145314 original size:20 final size:20
Alignment explanation
Indices: 145275--145341 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
145265 AGAATATATT
* * *
145275 GATACATTGAAGAATATATC
1 GATACATTCAAAAATGTATC
* *
145295 GATACATTCATACATGTATC
1 GATACATTCAAAAATGTATC
* *
145315 GATATATTGAAAAATGTATC
1 GATACATTCAAAAATGTATC
*
145335 AATACAT
1 GATACAT
145342 CTGGGTAAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
GATACATTCAAAAATGTATC
Found at i:145643 original size:17 final size:17
Alignment explanation
Indices: 145601--145643 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
145591 ATATCACGTA
145601 TTTTTTTATAATATTTG
1 TTTTTTTATAATATTTG
**
145618 TTTAATTATAAT-TTTG
1 TTTTTTTATAATATTTG
145634 TTATTTTTAT
1 TT-TTTTTAT
145644 TATAAGTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTTTTATAATATTTG
Found at i:145864 original size:17 final size:17
Alignment explanation
Indices: 145835--145867 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
145825 GTTAGTTGTT
145835 AATTATAAATAATTTTG
1 AATTATAAATAATTTTG
145852 AATTA-AAATTAATTTT
1 AATTATAAA-TAATTTT
145868 TATTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTATAAATAATTTTG
Found at i:146213 original size:25 final size:24
Alignment explanation
Indices: 146156--146217 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
146146 ATATAGAATG
*
146156 AAAATATATATTTATTATAATTTA
1 AAAATTTATATTTATTATAATTTA
** *
146180 ATATTTTTATATTTTTTATATATTTA
1 A-AAATTTATATTTATTATA-ATTTA
146206 AAAATTTATATT
1 AAAATTTATATT
146218 ATATAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 1 0.03
25 23 0.77
26 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAAATTTATATTTATTATAATTTA
Found at i:146932 original size:21 final size:23
Alignment explanation
Indices: 146894--146935 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
146884 ATTCATATAT
*
146894 TTATATCATATTTGTATATTTTG
1 TTATATCATATATGTATATTTTG
146917 TTATATCATA-AT-TATATTT
1 TTATATCATATATGTATATTT
146936 AAGTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (23 bp):
TTATATCATATATGTATATTTTG
Found at i:147590 original size:29 final size:29
Alignment explanation
Indices: 147554--147613 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
147544 TAAAAAATAA
*
147554 ATTATTAATATATTAAAATTTATATAAAT
1 ATTATTAACATATTAAAATTTATATAAAT
147583 ATTATTAACATATTAAAATTTATATAAAT
1 ATTATTAACATATTAAAATTTATATAAAT
147612 AT
1 AT
147614 ATAATACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTATTAACATATTAAAATTTATATAAAT
Found at i:148348 original size:15 final size:16
Alignment explanation
Indices: 148324--148355 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
148314 TAAATATATT
148324 TTAAATAAATTAAAAA
1 TTAAATAAATTAAAAA
148340 TTAAA-AAATTAAAAA
1 TTAAATAAATTAAAAA
148355 T
1 T
148356 ATTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TTAAATAAATTAAAAA
Found at i:148727 original size:20 final size:17
Alignment explanation
Indices: 148698--148750 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
148688 ATTAAAATTT
*
148698 AATAAATATAATATATTAA
1 AATAATTATAATATA--AA
148717 ACATAATTATAATATAAA
1 A-ATAATTATAATATAAA
*
148735 AATAATTAAAATATAA
1 AATAATTATAATATAA
148751 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 14 0.45
18 3 0.10
19 1 0.03
20 13 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATTATAATATAAA
Found at i:148734 original size:17 final size:17
Alignment explanation
Indices: 148688--148750 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
148678 TTATTTATTT
*
148688 ATTAAAATTTAATAAAT-
1 ATTAAAATATAA-AAATA
* *
148705 A-TAATATATTAAACATA
1 ATTAAAATA-TAAAAATA
*
148722 ATTATAATATAAAAATA
1 ATTAAAATATAAAAATA
148739 ATTAAAATATAA
1 ATTAAAATATAA
148751 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
16 8 0.22
17 23 0.64
18 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAATATAAAAATA
Found at i:149938 original size:2 final size:2
Alignment explanation
Indices: 149931--149977 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
149921 TTTAACCAAC
*
149931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149973 AT AT A
1 AT AT A
149978 AAATAAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:150949 original size:23 final size:24
Alignment explanation
Indices: 150923--150991 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
150913 AAATGATATA
150923 TATTTTTAAATATATTTA-AAAAT
1 TATTTTTAAATATATTTATAAAAT
** *
150946 TATTTAAAAATAAATTTATAATAAT
1 TATTTTTAAATATATTTATAA-AAT
*
150971 T-TTTTT-AATTTATTTATAAAA
1 TATTTTTAAATATATTTATAAAA
150992 GTAAAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 2 0.05
23 26 0.70
24 5 0.14
25 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTTAAATATATTTATAAAAT
Found at i:150954 original size:10 final size:12
Alignment explanation
Indices: 150920--150963 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
150910 ATAAAATGAT
**
150920 ATATATTTTTAA
1 ATATATTTAAAA
150932 ATATATTTAAAA
1 ATATATTTAAAA
150944 AT-TATTTAAAA
1 ATATATTTAAAA
*
150955 ATAAATTTA
1 ATATATTTA
150964 TAATAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTTAAAA
Found at i:151517 original size:11 final size:11
Alignment explanation
Indices: 151488--151524 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
151478 CATAGTAAAA
151488 TTTTCTTTAA-
1 TTTTCTTTAAT
151498 TTTTCTTTAAT
1 TTTTCTTTAAT
*
151509 TTTTTTTTAAT
1 TTTTCTTTAAT
151520 TTTTC
1 TTTTC
151525 AATTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTAAT
Found at i:151532 original size:10 final size:9
Alignment explanation
Indices: 151486--151536 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
151476 TACATAGTAA
151486 AATTTTCTTT
1 AATTTT-TTT
151496 AATTTTCTTT
1 AATTTT-TTT
151506 AATTTTTTTTT
1 AA--TTTTTTT
*
151517 AA-TTTTTC
1 AATTTTTTT
151525 AATTTTTTT
1 AATTTTTTT
151534 AAT
1 AAT
151537 AAAATTTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 12 0.33
11 5 0.14
12 4 0.11
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (9 bp):
AATTTTTTT
Found at i:151533 original size:11 final size:10
Alignment explanation
Indices: 151486--151522 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
151476 TACATAGTAA
151486 AATTTTCTTT
1 AATTTTCTTT
151496 AATTTTCTTT
1 AATTTTCTTT
*
151506 AATTTTTTTTT
1 AA-TTTTCTTT
151517 AATTTT
1 AATTTT
151523 TCAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (10 bp):
AATTTTCTTT
Found at i:152656 original size:13 final size:13
Alignment explanation
Indices: 152638--152663 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152628 ATTCTTTTTG
152638 AAATATATAATAA
1 AAATATATAATAA
152651 AAATATATAATAA
1 AAATATATAATAA
152664 TTTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATATAATAA
Found at i:153817 original size:20 final size:20
Alignment explanation
Indices: 153792--153861 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 20
153782 AATTTTAATA
153792 TTTTATAATATTTATATATT
1 TTTTATAATATTTATATATT
* *
153812 TTTTATTATATTTATGTAATT
1 TTTTATAATATTTATAT-ATT
*
153833 TTTATATTATATTT-TAATTATT
1 TTT-TATAATATTTAT-A-TATT
153855 TTTTATA
1 TTTTATA
153862 TTATATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.36
21 10 0.24
22 16 0.38
23 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTATAATATTTATATATT
Found at i:153857 original size:23 final size:23
Alignment explanation
Indices: 153809--153867 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
153799 ATATTTATAT
153809 ATTTTT-TATTATA-TTTATGTA
1 ATTTTTATATTATATTTTATGTA
153830 ATTTTTATATTATATTTTAAT-TA
1 ATTTTTATATTATATTTT-ATGTA
*
153853 TTTTTTATATTATAT
1 ATTTTTATATTATAT
153868 ATAATCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
23 19 0.56
24 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTTTTATATTATATTTTATGTA
Found at i:153862 original size:18 final size:19
Alignment explanation
Indices: 153783--153868 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 19
153773 TTATATGTAA
* *
153783 ATTT-TAATATTTTATAAT
1 ATTTATAATTTTTTATTAT
153801 ATTTATATATTTTTTATTAT
1 ATTTATA-ATTTTTTATTAT
153821 ATTTATGTAATTTTTATATTAT
1 ATTTA--TAATTTTT-TATTAT
153843 ATTT-TAATTATTTT-TTAT
1 ATTTATAATT-TTTTATTAT
153861 ATTATATA
1 ATT-TATA
153869 TAATCATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
18 11 0.19
19 9 0.16
20 20 0.34
21 6 0.10
22 12 0.21
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (19 bp):
ATTTATAATTTTTTATTAT
Found at i:153872 original size:22 final size:21
Alignment explanation
Indices: 153810--153878 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
153800 TATTTATATA
* *
153810 TTTTT-TATTATATTTATGTAA
1 TTTTTATATTATATTAAT-TAT
153831 TTTTTATATTATATTTTAATTAT
1 TTTTTATATTATA--TTAATTAT
*
153854 TTTTTATATTATATATAATCAT
1 TTTTTATATTATAT-TAATTAT
153876 TTT
1 TTT
153879 CGTATCAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.15
22 16 0.39
23 15 0.37
24 4 0.10
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTTTATATTATATTAATTAT
Found at i:155397 original size:22 final size:22
Alignment explanation
Indices: 155346--155392 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
155336 ATATTAAAAA
155346 AATATATT-TATAATTTTATATT
1 AATAT-TTATATAATTTTATATT
*
155368 AATATTTATATATTTTTATAATT
1 AATATTTATATAATTTTAT-ATT
155391 AA
1 AA
155393 GTTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 15 0.68
23 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATATTTATATAATTTTATATT
Found at i:159230 original size:3 final size:3
Alignment explanation
Indices: 159222--159247 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
159212 ACTGCATAAT
159222 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
159248 TTCTAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:159679 original size:17 final size:17
Alignment explanation
Indices: 159657--159693 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
159647 GTTACTTATT
159657 TACTCATGTGATTTGGG
1 TACTCATGTGATTTGGG
159674 TACTCATGTGATTTGGG
1 TACTCATGTGATTTGGG
159691 TAC
1 TAC
159694 AAAGTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.41
Consensus pattern (17 bp):
TACTCATGTGATTTGGG
Found at i:161656 original size:22 final size:22
Alignment explanation
Indices: 161629--161693 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
161619 GAATAAAATT
*
161629 AATGTACATATGACTATAACTA
1 AATGTACATATGACTTTAACTA
* * * *
161651 ATTGTATATATAACTTTAATTA
1 AATGTACATATGACTTTAACTA
*
161673 AATGTAGATATGACTTTAACT
1 AATGTACATATGACTTTAACT
161694 GAATATATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
AATGTACATATGACTTTAACTA
Found at i:161687 original size:44 final size:43
Alignment explanation
Indices: 161625--161712 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
161615 CTCCGAATAA
*
161625 AATTAATGTACATATGACTATAACT-AATTGTATATATAACTTT
1 AATTAATGTACATATGACTATAACTGAA-TATATATATAACTTT
* * *
161668 AATTAAATGTAGATATGACTTTAACTGAATATATATGTAACTTT
1 AATT-AATGTACATATGACTATAACTGAATATATATATAACTTT
161712 A
1 A
161713 GTTGAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 4 0.10
44 33 0.85
45 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (43 bp):
AATTAATGTACATATGACTATAACTGAATATATATATAACTTT
Found at i:161883 original size:46 final size:46
Alignment explanation
Indices: 161773--161887 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 46
161763 CCCAATACAT
161773 ATATAAAATAT-TTTTTAATTTTTA--AAAAATAATACAGAATTTA
1 ATATAAAATATATTTTTAATTTTTATTAAAAATAATACAGAATTTA
* *** *
161816 ATA-CAAA-ATATTTTTAATTTTTATTAATGGTAATTCA-AGATTTA
1 ATATAAAATATATTTTTAATTTTTATTAAAAATAATACAGA-ATTTA
161860 ATATAAAATATATTTTTAATTTTTATTA
1 ATATAAAATATATTTTTAATTTTTATTA
161888 TTTTTAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
41 2 0.03
42 16 0.27
43 4 0.07
44 16 0.27
45 3 0.05
46 19 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (46 bp):
ATATAAAATATATTTTTAATTTTTATTAAAAATAATACAGAATTTA
Found at i:161950 original size:52 final size:51
Alignment explanation
Indices: 161853--162425 Score: 305
Period size: 51 Copynumber: 11.3 Consensus size: 51
161843 TGGTAATTCA
161853 AGATTTAATATAAAATATATTTTTAATTTTTATTATTTTTAAAATAGTAATTTG
1 AGATTTAATAT-AAA-ATATTTTTAATTTTTATTATTTTT-AAATAGTAATTTG
* *
161907 AGATTGAATATAAAATATTTTTAATTTTGTATTATTTTTAAATAGT-ATTTT
1 AGATTTAATATAAAATATTTTTAATTTT-TATTATTTTTAAATAGTAATTTG
* *
161958 AGGTTTAAAGTAATTCAAAAT-TTAATATAAATTTTT-TTATTTTTAAATAGTAATTTG
1 AGATTT-AA-T-A-T-AAAATATT--T-TTAATTTTTATTATTTTTAAATAGTAATTTG
* **
162015 AGATTTAATATAAAATATTTTTAATCTATTATTATTTTTAAATAGTAATTAA
1 AGATTTAATATAAAATATTTTTAAT-TTTTATTATTTTTAAATAGTAATTTG
* *
162067 AAATTTAATATAAAATATATAAAATATTTTTAATTTTTTATTATTTTTACATAGTGAA-TTG
1 AGA--T--T-T---A-ATATAAAATATTTTTAA-TTTTTATTATTTTTAAATAGT-AATTTG
* *
162128 AG-TTTTATAT-ATATATTTTTTAATTTTTTATTATTTTT-AA-A-TAA---G
1 AGATTTAATATAAAATA-TTTTTAA-TTTTTATTATTTTTAAATAGTAATTTG
* * * * * *
162173 A-ATTT-ATA-AAAACATTTTTTATTTTTTATTA-TTTTAAAAAATAAATAG
1 AGATTTAATATAAAATA-TTTTTAATTTTTATTATTTTTAAATAGTAATTTG
* * * *
162221 AGATTTTATATAAAA-A-TTTGAATTTTTATTATTTTTCAAAGAGTAA-TTC
1 AGATTTAATATAAAATATTTTTAATTTTTATTATTTTT-AAATAGTAATTTG
* * *** * * *
162270 AGTATTTGATATAAAATA-TATT-A--TTTA--A-AAGTAATTTGAAATTT-
1 AG-ATTTAATATAAAATATTTTTAATTTTTATTATTTTTAAATAGTAATTTG
* *
162314 A-A--T-A--TAAAATATTTTTAAATTTTTTATTATTTTTAAATATTAATTTA
1 AGATTTAATATAAAATATTTTT-AA-TTTTTATTATTTTTAAATAGTAATTTG
* * **
162361 AGATTTAAAATAAAATATTTTT-ATTTTTATTAGTTTTTAAATAATAATTCA
1 AGATTTAATATAAAATATTTTTAATTTTTATTA-TTTTTAAATAGTAATTTG
162412 AGATTTAATATAAA
1 AGATTTAATATAAA
162426 GTTTTTAATT
Statistics
Matches: 411, Mismatches: 50, Indels: 119
0.71 0.09 0.21
Matches are distributed among these distances:
37 7 0.02
38 3 0.01
39 1 0.00
40 2 0.00
42 5 0.01
43 15 0.04
44 20 0.05
45 12 0.03
46 10 0.02
47 3 0.01
48 21 0.05
49 12 0.03
50 43 0.10
51 76 0.18
52 49 0.12
53 29 0.07
54 13 0.03
55 5 0.01
56 24 0.06
57 12 0.03
58 8 0.02
60 1 0.00
61 37 0.09
62 3 0.01
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (51 bp):
AGATTTAATATAAAATATTTTTAATTTTTATTATTTTTAAATAGTAATTTG
Found at i:162093 original size:108 final size:109
Alignment explanation
Indices: 161877--162170 Score: 309
Period size: 108 Copynumber: 2.7 Consensus size: 109
161867 ATATATTTTT
*
161877 AATTTTTATTATTTTTAAAATAGTAATTTGAGATTGAATATAAAATATTTTTAATTTTGTATTAT
1 AATTTTTATTATTTTT-AAATAGTAATTTGAGATTTAATATAAAATATTTTTAATTTT-TATTAT
** **
161942 TTTTAAATAGTATTTTAGGTTTAAAGTAATTCAAAATTTAATA-TA
64 TTTTAAATAGTATTAAAAATTTAAAGTAATTCAAAATTTAATATTA
*
161987 AATTTTT-TTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTAATCTATTATTATT
1 AATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTAAT-TTTTATTATT
*
162051 TTTAAATAGTAATTAAAAATTTAATA-TAAAATATATAAAATATT--T-TTA
65 TTTAAATAGT-ATTAAAAATTTAA-AGT--AAT-T-CAAAAT-TTAATATTA
* * * *
162099 ATTTTTTATTATTTTTACATAGTGAA-TTGAG-TTTTATAT-ATATATTTTTTAATTTTTTATTA
1 AATTTTTATTATTTTTAAATAGT-AATTTGAGATTTAATATAAAATA-TTTTTAA-TTTTTATTA
162161 TTTTTAAATA
63 TTTTTAAATA
162171 AGAATTTATA
Statistics
Matches: 159, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
108 54 0.34
109 20 0.13
110 8 0.05
111 7 0.04
112 41 0.26
113 25 0.16
114 4 0.03
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (109 bp):
AATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTAATTTTTATTATTT
TTAAATAGTATTAAAAATTTAAAGTAATTCAAAATTTAATATTA
Found at i:162228 original size:94 final size:90
Alignment explanation
Indices: 162070--162256 Score: 207
Period size: 94 Copynumber: 2.0 Consensus size: 90
162060 TAATTAAAAA
* * * * * *
162070 TTTAATATAAAATATATAAAATATTTTTAATTTTTTATTATTTTTACATAGTGAATTGAGTTTTA
1 TTTAATATAAAATATATAAAACATTTTTAATTTTTTATTATTTTTAAAAAATAAATAGAGTTTTA
** *
162135 TATATATATTTTTTAATTTTTTATTATT
66 TATA-A-AAATTTGAA-TTTTTATTATT
* *
162163 TTTAA-ATAAGAATTTATAAAAACATTTTTTATTTTTTATTA-TTTTAAAAAATAAATAGAGATT
1 TTTAATATAA-AATATAT-AAAACATTTTTAATTTTTTATTATTTTTAAAAAATAAATAGAG-TT
162226 TTATATAAAAATTTGAATTTTTATTATT
63 TTATATAAAAATTTGAATTTTTATTATT
162254 TTT
1 TTT
162257 CAAAGAGTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
91 14 0.17
92 10 0.12
93 26 0.32
94 30 0.38
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (90 bp):
TTTAATATAAAATATATAAAACATTTTTAATTTTTTATTATTTTTAAAAAATAAATAGAGTTTTA
TATAAAAATTTGAATTTTTATTATT
Found at i:163155 original size:15 final size:15
Alignment explanation
Indices: 163137--163206 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
163127 ATTAAATTAC
163137 AAATTATTATTTAAA
1 AAATTATTATTTAAA
** *
163152 AAATTAAAAATTAAA
1 AAATTATTATTTAAA
*
163167 AAATATTTTATATTAAATCTA
1 AAAT-TATTAT-TT-AA---A
163188 AAATTATTATTTAAA
1 AAATTATTATTTAAA
163203 AAAT
1 AAAT
163207 AATAAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
15 21 0.51
16 2 0.05
17 2 0.05
18 4 0.10
19 2 0.05
20 5 0.12
21 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTATTATTTAAA
Found at i:163193 original size:51 final size:53
Alignment explanation
Indices: 163112--163231 Score: 174
Period size: 51 Copynumber: 2.3 Consensus size: 53
163102 TGCAAATAAC
*
163112 TAAAGAATATTTTATATTAAATTACAAATTATTATTTAAAAAAT-T-AAAAAT
1 TAAAAAATATTTTATATTAAATTACAAATTATTATTTAAAAAATATAAAAAAT
163163 TAAAAAATATTTTATATTAAATCTA-AAATTATTATTTAAAAAATAATAAAAAAT
1 TAAAAAATATTTTATATTAAAT-TACAAATTATTATTTAAAAAAT-ATAAAAAAT
*
163217 TAAAAAGGTATTTTA
1 TAAAAA-ATATTTTA
163232 CATTCACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
51 40 0.65
52 2 0.03
53 1 0.02
54 12 0.19
55 7 0.11
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (53 bp):
TAAAAAATATTTTATATTAAATTACAAATTATTATTTAAAAAATATAAAAAAT
Found at i:163400 original size:22 final size:21
Alignment explanation
Indices: 163374--163421 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
163364 ATATTAGACC
*
163374 TATATTTAAAAAATAATAAATA
1 TATATTCAAAAAATAA-AAATA
*
163396 TATA-TCAAATAATAAAAATA
1 TATATTCAAAAAATAAAAATA
163416 TATATT
1 TATATT
163422 GAAACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 10 0.43
22 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATATTCAAAAAATAAAAATA
Found at i:163405 original size:18 final size:18
Alignment explanation
Indices: 163384--163418 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
163374 TATATTTAAA
*
163384 AAATAATAAATATATATC
1 AAATAATAAAAATATATC
163402 AAATAATAAAAATATAT
1 AAATAATAAAAATATAT
163419 ATTGAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAATAAAAATATATC
Found at i:163596 original size:48 final size:44
Alignment explanation
Indices: 163544--163662 Score: 123
Period size: 46 Copynumber: 2.6 Consensus size: 44
163534 ATATAAAAAT
* *
163544 AATAAAAAATTAAATATATTTTATATTAAATTTTGAATTACTATTAAA
1 AATAAAAAA-TAAATATATTTTATATTAAATCTTGAATTA-TAGT--A
* *
163592 AATAAAAAATAAA-AAATATTATATTAAATCTTGAATTATAGTA
1 AATAAAAAATAAATATATTTTATATTAAATCTTGAATTATAGTA
*
163635 AATAAAATACTAATTATATATTTTATAT
1 AATAAAA-AATAA--ATATATTTTATAT
163663 ATATTGAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
43 8 0.13
44 4 0.07
45 3 0.05
46 23 0.38
47 13 0.22
48 9 0.15
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (44 bp):
AATAAAAAATAAATATATTTTATATTAAATCTTGAATTATAGTA
Found at i:163890 original size:105 final size:105
Alignment explanation
Indices: 163800--164008 Score: 257
Period size: 105 Copynumber: 2.0 Consensus size: 105
163790 TATATATATT
* * * *
163800 AAAAATACTACTTAAAATTAATAAAAGA-ATAAAAATATTTTATATTAGATC-TAGAATTATTAT
1 AAAAATA-TACTTAAAAATAACAAAA-ATATAAAAATATTTTATATTAAATCTTA-AATTACTAT
*
163863 TTAAAAATAAT-AAAAATTAAAAAAATATTTTATATTAAATCC
63 TTAAAAATAATAAAAAATTAAAAAAATATATTATATTAAATCC
* * * *
163905 CAAATTATATTTAAAAATAACAAAAATTTTAAAAATATTTTATATTAAATCTTAAATTACTATTT
1 AAAAATATACTTAAAAATAACAAAAA-TATAAAAATATTTTATATTAAATCTTAAATTACTATTT
*
163970 AAAAATAATAAAAAATT--AAAAATATTTTATATTAAATCC
65 AAAAATAATAAAAAATTAAAAAAATATATTATATTAAATCC
164009 CAGAATTAGA
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
103 1 0.01
104 37 0.40
105 45 0.49
106 9 0.10
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (105 bp):
AAAAATATACTTAAAAATAACAAAAATATAAAAATATTTTATATTAAATCTTAAATTACTATTTA
AAAATAATAAAAAATTAAAAAAATATATTATATTAAATCC
Found at i:163893 original size:53 final size:50
Alignment explanation
Indices: 163811--164034 Score: 261
Period size: 52 Copynumber: 4.3 Consensus size: 50
163801 AAAATACTAC
* * * *
163811 TTAAAATTAATAAAAGAATAAAAATATTTTATATTAGAT-CTAGAATTATTAT
1 TTAAAAATAATAAAA-ATTAAAAATATTTTATATTAAATCCCA-AATTA-TAT
163863 TTAAAAATAATAAAAATTAAAAAAATATTTTATATTAAATCCCAAATTATAT
1 TTAAAAATAATAAAAATT--AAAAATATTTTATATTAAATCCCAAATTATAT
* **
163915 TTAAAAATAACAAAAATTTTAAAAATATTTTATATTAAATCTTAAATTACTAT
1 TTAAAAATAATAAAAA--TTAAAAATATTTTATATTAAATCCCAAATTA-TAT
*
163968 TTAAAAATAATAAAAAATTAAAAATATTTTATATTAAATCCCAGAATTAGAAT
1 TTAAAAATAAT-AAAAATTAAAAATATTTTATATTAAATCCCA-AATTA-TAT
164021 TTAAAAAATAATAA
1 TT-AAAAATAATAA
164035 TTTTTTACTA
Statistics
Matches: 151, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
51 2 0.01
52 83 0.55
53 48 0.32
54 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (50 bp):
TTAAAAATAATAAAAATTAAAAATATTTTATATTAAATCCCAAATTATAT
Found at i:164016 original size:105 final size:105
Alignment explanation
Indices: 163829--164027 Score: 314
Period size: 105 Copynumber: 1.9 Consensus size: 105
163819 AATAAAAGAA
* *
163829 TAAAAATATTTTATATTAGATCTAGAATTATTATTTAAAAATAATAAAAATTAAAAAAATATTTT
1 TAAAAATATTTTATATTAAATCTAGAATTACTATTTAAAAATAATAAAAATT-AAAAAATATTTT
*
163894 ATATTAAATCCCAAATTA-TATTTAAAAATAACAAAAATTT
65 ATATTAAATCCCAAATTAGAATTTAAAAATAACAAAAATTT
163934 TAAAAATATTTTATATTAAATCTTA-AATTACTATTTAAAAATAATAAAAAATT-AAAAATATTT
1 TAAAAATATTTTATATTAAATC-TAGAATTACTATTTAAAAATAAT-AAAAATTAAAAAATATTT
163997 TATATTAAATCCCAGAATTAGAATTTAAAAA
64 TATATTAAATCCCA-AATTAGAATTTAAAAA
164028 ATAATAATTT
Statistics
Matches: 87, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
104 24 0.28
105 45 0.52
106 18 0.21
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (105 bp):
TAAAAATATTTTATATTAAATCTAGAATTACTATTTAAAAATAATAAAAATTAAAAAATATTTTA
TATTAAATCCCAAATTAGAATTTAAAAATAACAAAAATTT
Found at i:164168 original size:22 final size:22
Alignment explanation
Indices: 164133--164175 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
164123 GAGGTTGGTT
** *
164133 CAATTAAATTTATATTTACATC
1 CAATTAAAACTATATATACATC
164155 CAATTAAAACTATATATACAT
1 CAATTAAAACTATATATACAT
164176 ATTATTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (22 bp):
CAATTAAAACTATATATACATC
Found at i:164568 original size:17 final size:17
Alignment explanation
Indices: 164546--164580 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
164536 AGATTGATTC
164546 TTTCGAATAAAATTGAA
1 TTTCGAATAAAATTGAA
164563 TTTCGAATAAAATTGAA
1 TTTCGAATAAAATTGAA
164580 T
1 T
164581 GTACATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (17 bp):
TTTCGAATAAAATTGAA
Found at i:164626 original size:22 final size:21
Alignment explanation
Indices: 164578--164632 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
164568 AATAAAATTG
164578 AATGTACATATGACTATAATA
1 AATGTACATATGACTATAATA
* *
164599 ATATGTACATATGATTTTAACTA
1 A-ATGTACATATGACTATAA-TA
*
164622 AATGTAAATAT
1 AATGTACATAT
164633 AGTAAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 25 0.86
23 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (21 bp):
AATGTACATATGACTATAATA
Found at i:164790 original size:22 final size:22
Alignment explanation
Indices: 164753--164814 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
164743 TTTTGAATAA
* * * *
164753 AATTAAATTTATATATGACTAT
1 AATTAAATGTACATATAACAAT
164775 AATTAAATGTACATATAACAAT
1 AATTAAATGTACATATAACAAT
*
164797 AA-TAGTATGTACATATAA
1 AATTA-AATGTACATATAA
164815 TTTTAACTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.37
Consensus pattern (22 bp):
AATTAAATGTACATATAACAAT
Found at i:165108 original size:2 final size:2
Alignment explanation
Indices: 165101--165144 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
165091 ACATGTTCCA
* *
165101 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT -T AT TT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
165143 AT
1 AT
165145 TCATTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:165150 original size:18 final size:18
Alignment explanation
Indices: 165101--165153 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
165091 ACATGTTCCA
*
165101 ATATATATATATTTATAT-
1 ATATATATATA-TTATTTG
165119 ATATATATATATTATTTG
1 ATATATATATATTATTTG
165137 ATATATAT-TCATTATTT
1 ATATATATAT-ATTATTT
165154 TTTAAATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATATATATATTATTTG
Found at i:168913 original size:13 final size:13
Alignment explanation
Indices: 168895--168920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168885 ACAAAGATCC
168895 ATGTATCGATACA
1 ATGTATCGATACA
168908 ATGTATCGATACA
1 ATGTATCGATACA
168921 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:168932 original size:33 final size:31
Alignment explanation
Indices: 168874--168962 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 31
168864 AAAATTTCCA
* ***
168874 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACACAGAAAAATGTAT--ATAC
168907 AATGTATCGATACACAGAAAAATG--TATAC
1 AATGTATCGATACACAGAAAAATGTATATAC
168936 AATGTATCGATACACAG-AAAATGTATA
1 AATGTATCGATACACAGAAAAATGTATA
168963 CATTTCCTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.12
29 21 0.42
30 2 0.04
31 1 0.02
33 20 0.40
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (31 bp):
AATGTATCGATACACAGAAAAATGTATATAC
Found at i:168945 original size:29 final size:28
Alignment explanation
Indices: 168903--168964 Score: 115
Period size: 29 Copynumber: 2.2 Consensus size: 28
168893 CCATGTATCG
168903 ATACAATGTATCGATACACAGAAAAATGT
1 ATACAATGTATCGATACACAG-AAAATGT
168932 ATACAATGTATCGATACACAGAAAATGT
1 ATACAATGTATCGATACACAGAAAATGT
168960 ATACA
1 ATACA
168965 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (28 bp):
ATACAATGTATCGATACACAGAAAATGT
Found at i:169008 original size:19 final size:18
Alignment explanation
Indices: 168984--169051 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
168974 CAGTAGCTAA
168984 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
169003 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
169018 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
169035 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
169052 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:169023 original size:32 final size:32
Alignment explanation
Indices: 168987--169049 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
168977 TAGCTAATTA
*
168987 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
169019 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
169050 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:169024 original size:13 final size:13
Alignment explanation
Indices: 169006--169030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168996 ACAATACTTA
169006 TGTATCGATACAT
1 TGTATCGATACAT
169019 TGTATCGATACA
1 TGTATCGATACA
169031 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:169131 original size:21 final size:19
Alignment explanation
Indices: 169107--169152 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
169097 CATTTGTAGG
169107 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATT-CAC-A
169128 ATGTATCGATACATTCACA
1 ATGTATCGATACATTCACA
169147 ATGTAT
1 ATGTAT
169153 ACATTTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.28
20 3 0.12
21 15 0.60
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACATTCACA
Found at i:170802 original size:21 final size:21
Alignment explanation
Indices: 170778--170818 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
170768 GATGATGGAA
*
170778 AATTAAAATATTTCAAGGGAT
1 AATTAAAATATTGCAAGGGAT
* *
170799 AATTGAATTATTGCAAGGGA
1 AATTAAAATATTGCAAGGGA
170819 AAATATGGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (21 bp):
AATTAAAATATTGCAAGGGAT
Found at i:171954 original size:21 final size:21
Alignment explanation
Indices: 171942--171999 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
171932 AAGTTGCTTT
171942 TTTCATCCAAAAAATGCATTC
1 TTTCATCCAAAAAATGCATTC
**
171963 TTTCATCCAACCAATGCA-TC
1 TTTCATCCAAAAAATGCATTC
171983 ATTTCATCCAAATAAAT
1 -TTTCATCCAAA-AAAT
172000 CTTTTCATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATTC
Found at i:181547 original size:18 final size:19
Alignment explanation
Indices: 181526--181563 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
181516 AAATTAAGTT
181526 ATTTAT-TTAAATTTAAAA
1 ATTTATCTTAAATTTAAAA
*
181544 ATTTATCTTATATTTAAAA
1 ATTTATCTTAAATTTAAAA
181563 A
1 A
181564 GATTTGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATCTTAAATTTAAAA
Found at i:187362 original size:16 final size:15
Alignment explanation
Indices: 187337--187370 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
187327 ACAAAATTTT
*
187337 TTTTATTTAAATTTAA
1 TTTTAATTAAA-TTAA
187353 TTTTAATTAAATTAA
1 TTTTAATTAAATTAA
187368 TTT
1 TTT
187371 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATTAAATTAA
Found at i:192589 original size:20 final size:20
Alignment explanation
Indices: 192551--192596 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
192541 TTTAAATTTT
*
192551 ATAAATAAAATTAAAATATA
1 ATAAATAAAATAAAAATATA
*
192571 TTAAAT-AAATAAAACATATA
1 ATAAATAAAATAAAA-ATATA
192591 ATAAAT
1 ATAAAT
192597 TTTTAATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAATAAAATAAAAATATA
Found at i:193356 original size:10 final size:10
Alignment explanation
Indices: 193341--193366 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
193331 AATATTTTTT
193341 TTAATTCAGA
1 TTAATTCAGA
193351 TTAATTCAGA
1 TTAATTCAGA
193361 TTAATT
1 TTAATT
193367 TGAATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (10 bp):
TTAATTCAGA
Found at i:193425 original size:22 final size:19
Alignment explanation
Indices: 193394--193435 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
193384 ATATTTTATT
193394 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
193415 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
193435 T
1 T
193436 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:194641 original size:3 final size:3
Alignment explanation
Indices: 194633--194659 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
194623 TTTCAGCTTT
194633 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
194660 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:194705 original size:21 final size:22
Alignment explanation
Indices: 194681--194729 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
194671 TTACAGTTTG
194681 AAAATA-AAAAATTATAAATAT
1 AAAATATAAAAATTATAAATAT
**
194702 AAAA-ATTTAAATTATAAATAT
1 AAAATATAAAAATTATAAATAT
*
194723 ATAATAT
1 AAAATAT
194730 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATATAAAAATTATAAATAT
Found at i:194707 original size:15 final size:14
Alignment explanation
Indices: 194682--194719 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
194672 TACAGTTTGA
194682 AAATA-AAAAATTAT
1 AAATATAAAAATT-T
194696 AAATATAAAAATTT
1 AAATATAAAAATTT
194710 AAATTATAAA
1 AAA-TATAAA
194720 TATATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATATAAAAATTT
Found at i:195004 original size:12 final size:12
Alignment explanation
Indices: 194989--195052 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
194979 TTTATTTTAT
194989 TATTTAAAATAA
1 TATTTAAAATAA
*
195001 TATTAAAAATAA
1 TATTTAAAATAA
**
195013 T-TTTTTAATAA
1 TATTTAAAATAA
195024 TATTTATAAATAA
1 TATTTA-AAATAA
195037 -ATTT-AAATAA
1 TATTTAAAATAA
*
195047 AATTTA
1 TATTTA
195053 TTTATTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 6 0.14
11 12 0.29
12 19 0.45
13 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:195045 original size:23 final size:24
Alignment explanation
Indices: 194989--195053 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
194979 TTTATTTTAT
*
194989 TATTTAAAATAATA-TTAAAAATAA
1 TATTT-AAATAATATTTATAAATAA
* *
195013 TTTTTTAATAATATTTATAAATAA
1 TATTTAAATAATATTTATAAATAA
*
195037 -ATTTAAATAAAATTTAT
1 TATTTAAATAATATTTAT
195054 TTATTATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTTAAATAATATTTATAAATAA
Found at i:196118 original size:24 final size:22
Alignment explanation
Indices: 196091--196135 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
196081 AGATCAGAAT
196091 TTAAAATTAAAAAATTATAAATTG
1 TTAAAATT-AAAAATT-TAAATTG
*
196115 TTAAAATTTAAAATTTAAATT
1 TTAAAATTAAAAATTTAAATT
196136 TATAAGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAAATTAAAAATTTAAATTG
Found at i:196872 original size:2 final size:2
Alignment explanation
Indices: 196865--196901 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
196855 TTCTAAAAGT
*
196865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196902 TCAAAATTAT
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:197110 original size:23 final size:24
Alignment explanation
Indices: 197079--197128 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
197069 ACATAAAACA
* * *
197079 TATATTAAACATATTTTATTA-AT
1 TATACTAAAAATATTATATTATAT
197102 TATACTAAAAATATTATATTATAT
1 TATACTAAAAATATTATATTATAT
197126 TAT
1 TAT
197129 TTTTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TATACTAAAAATATTATATTATAT
Found at i:199661 original size:11 final size:11
Alignment explanation
Indices: 199645--199669 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
199635 ATATATGACC
199645 AAAAAAAGACA
1 AAAAAAAGACA
199656 AAAAAAAGACA
1 AAAAAAAGACA
199667 AAA
1 AAA
199670 CGAACTTGAA
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:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGACA
Found at i:199914 original size:19 final size:19
Alignment explanation
Indices: 199883--199943 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
199873 TTTTATTAAT
*
199883 TATAAAATA-TAAATATAA
1 TATAAATTATTAAATATAA
*
199901 TATAAATTATTAAATATAT
1 TATAAATTATTAAATATAA
*
199920 TA-AAATT-TTAAAAATATA
1 TATAAATTATTAAATATA-A
199938 TATAAA
1 TATAAA
199944 ATATATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.22
18 15 0.42
19 13 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATAAATTATTAAATATAA
Found at i:199923 original size:17 final size:18
Alignment explanation
Indices: 199883--199945 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
199873 TTTTATTAAT
*
199883 TATAAAA-TATAAATATA
1 TATAAAATTTTAAATATA
199900 -ATATAAATTATTAAATATA
1 TATA-AAATT-TTAAATATA
199919 T-TAAAATTTTAAAAATATA
1 TATAAAATTTT--AAATATA
199938 TATAAAAT
1 TATAAAAT
199946 ATATTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.08
17 5 0.13
18 6 0.16
19 18 0.47
20 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAAAATTTTAAATATA
Found at i:199946 original size:11 final size:11
Alignment explanation
Indices: 199883--199949 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
199873 TTTTATTAAT
199883 TATAAAATATAAA
1 TATAAAATAT--A
* *
199896 TATAATATAAA
1 TATAAAATATA
*
199907 TTATTAAATATA
1 -TATAAAATATA
*
199919 T-TAAAAT-TT
1 TATAAAATATA
199928 TA-AAAATATA
1 TATAAAATATA
199938 TATAAAATATA
1 TATAAAATATA
199949 T
1 T
199950 TTTATTTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
9 7 0.17
10 8 0.19
11 11 0.26
12 8 0.19
13 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAAAATATA
Found at i:208638 original size:127 final size:126
Alignment explanation
Indices: 208295--208655 Score: 496
Period size: 124 Copynumber: 2.9 Consensus size: 126
208285 ATTTTTTAAT
*
208295 AAAAATAATAGTTAATTAAGTTTTAAAAAATTTACATTAACAAATTAAAATATT-A--A-T-TAT
1 AAAAATAATATTTAATTAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATAT
*
208355 TTTTT-AAAATAAAAAATTTAAATAAAAATAAAAAAGGTTATTATTATTAT--TTTTTAATAAAA
66 TTTTTAAAAAT-AAAAATTT---T-AAAATAAAAAAGGTT-TTTTTATTATAATTTTTAATAAAA
208417 TA
125 TA
* *
208419 AAAAATAATATTTAATTAAGTTTTAAAAAAATTACATTAACAAATT--AATATTAATTATTATGT
1 AAAAATAATATTTAATTAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATAT
208482 TTTTATAAAAATAAAAATTTTAAAATAAAAAAGGTTTTTTTATTTATAATTTTTAATAAAATA
66 TTTT-TAAAAATAAAAATTTTAAAATAAAAAAGGTTTTTTTA-TTATAATTTTTAATAAAATA
*
208545 AAAAATAATATTTAATTAAG-TTTAAAAAATTTACAATAACAAATTAAAATATTAATTATTTATA
1 AAAAATAATATTTAATTAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTA-TTATA
*
208609 TTTTTTAAAAATAAAAATTTTAAATTAAAAAA-G-TTTTTTATTATAAT
65 TTTTTTAAAAATAAAAATTTTAAAATAAAAAAGGTTTTTTTATTATAAT
208656 AATATTTTTT
Statistics
Matches: 216, Mismatches: 8, Indels: 26
0.86 0.03 0.10
Matches are distributed among these distances:
122 6 0.03
123 6 0.03
124 70 0.32
125 32 0.15
126 36 0.17
127 43 0.20
128 18 0.08
129 5 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (126 bp):
AAAAATAATATTTAATTAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATAT
TTTTTAAAAATAAAAATTTTAAAATAAAAAAGGTTTTTTTATTATAATTTTTAATAAAATA
Found at i:209577 original size:91 final size:90
Alignment explanation
Indices: 209392--210001 Score: 550
Period size: 91 Copynumber: 6.8 Consensus size: 90
209382 TGTCAGATTA
* **
209392 CAAATATTAGACTAATGCATGAATTATATCTA-AGAATC-GAATTCTTTTTTATAGAAAAAAAGA
1 CAAAGATTAGACTAATGCATGAATTATATC-AGAGAATCAG-ATT-TTTTTT-TTTAAAAAAAGA
* * * * *
209455 AAAATTGATTGATTGTAAATATTAGTCTG
62 AAAGTTGATTGAGTATAAATGTTAGACTG
*
209484 CAAAGATTAGACTAATGCATGAATTATATCAGAGAGTCA-ATTTTTTTTTTTAAAAAAAAAGAAA
1 CAAAGATTAGACTAATGCATGAATTATATCAGAGAATCAGATTTTTTTTTTT--AAAAAAAGAAA
209548 AGTTGATTGAGTATAAATGTTAGACTG
64 AGTTGATTGAGTATAAATGTTAGACTG
* * * * * * * *
209575 CAATGATTAGACTAATCCATAAATTATATCAGAGAATGAGA--TTCTTTTTTATAGAAA-AATAG
1 CAAAGATTAGACTAATGCATGAATTATATCAGAGAATCAGATTTTTTTTTTTAAAAAAAGAAAAG
* * *
209637 TTGATTGATTATAAATGTCAAACT-
66 TTGATTGAGTATAAATGTTAGACTG
** * * *
209661 -ATAAGAATTAGACTAATATATGAATTGTATCTGAGAATCAGA--TTTTTTATTAAAAAAAGAAA
1 CA-AAG-ATTAGACTAATGCATGAATTATATCAGAGAATCAGATTTTTTTTTTTAAAAAAAGAAA
* * *
209723 AGTTGATTAAGTGTAAATGTTAAACTG
64 AGTTGATTGAGTATAAATGTTAGACTG
* * * *
209750 CAATGATTAGACTAATGCATGAATTATATTAGAGAATCAGATTCTTTTTTATAGAAAAAAGAAAA
1 CAAAGATTAGACTAATGCATGAATTATATCAGAGAATCAGATTTTTTTTTTTA-AAAAAAGAAAA
*
209815 ATTGATTGAGTATAAATGTTAGACTG
65 GTTGATTGAGTATAAATGTTAGACTG
* ** * * *
209841 CAATGATTAGACTAATGCATGGGTTATATTTA-AGAATCAGA--TTCTTTTTTATAAAAA-AAAA
1 CAAAGATTAGACTAATGCATGAATTATA-TCAGAGAATCAGATTTTTTTTTTTAAAAAAAGAAAA
* * * *
209902 -TTGATTGATTGTAAATGTCAGACTA
65 GTTGATTGAGTATAAATGTTAGACTG
** * * * *
209927 CAAAGATTAGACTAATGCAT-AGATTATATTTGAGAATTAGATTTCTTTTTATAGAAAAGCAGAA
1 CAAAGATTAGACTAATGCATGA-ATTATATCAGAGAATCAGATTTTTTTTTTTA-AAAA-AAGAA
209991 AAGTTGATTGA
63 AAGTTGATTGA
210002 TTTTACATGT
Statistics
Matches: 426, Mismatches: 70, Indels: 44
0.79 0.13 0.08
Matches are distributed among these distances:
85 3 0.01
86 55 0.13
87 71 0.17
88 72 0.17
89 13 0.03
90 23 0.05
91 143 0.34
92 46 0.11
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (90 bp):
CAAAGATTAGACTAATGCATGAATTATATCAGAGAATCAGATTTTTTTTTTTAAAAAAAGAAAAG
TTGATTGAGTATAAATGTTAGACTG
Found at i:209752 original size:175 final size:172
Alignment explanation
Indices: 209397--209984 Score: 596
Period size: 175 Copynumber: 3.3 Consensus size: 172
209387 GATTACAAAT
*
209397 ATTAGACTAATGCATGAATTATATCTA-AGAATCGA-ATTCTTTTTTATAGAAAAAAAGAAAAAT
1 ATTAGACTAATGCATAAATTATATC-AGAGAAT-GAGATTCTTTTTTATAG-AAAAAAG----AT
* * * * *
209460 TGATTGATTGTAAATATTAGTCTGCAAAGATTAGACTAATGCATGAATTATATCAGAGAGTCA-A
59 TGATTGATTATAAATGTTAGACT--AAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGA
*
209524 TTTTTTTTTTTAAAAAAAAAGAAAAGTTGATTGAGTATAAATGTTAGACTGCAATG
122 ---TTTTTTTT--AAAAAAAGAAAAGTTGATTGAGTGTAAATGTTAGACTGCAATG
*
209580 ATTAGACTAATCCATAAATTATATCAGAGAATGAGATTCTTTTTTATAGAAAAATAG-TTGATTG
1 ATTAGACTAATGCATAAATTATATCAGAGAATGAGATTCTTTTTTATAGAAAAA-AGATTGATTG
* * ** *
209644 ATTATAAATGTCAAACTATAAGAATTAGACTAATATATGAATTGTATCTGAGAATCAGATTTTTT
65 ATTATAAATGTTAGACTA-AAG-ATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTT
* *
209709 ATTAAAAAAAGAAAAGTTGATTAAGTGTAAATGTTAAACTGCAATG
128 -TTAAAAAAAGAAAAGTTGATTGAGTGTAAATGTTAGACTGCAATG
* * *
209755 ATTAGACTAATGCATGAATTATATTAGAGAATCAGATTCTTTTTTATAGAAAAAAGAAAAATTGA
1 ATTAGACTAATGCATAAATTATATCAGAGAATGAGATTCTTTTTTATAGAAAAAAG----ATTGA
* * ** * *
209820 TTGAGTATAAATGTTAGACTGCAATGATTAGACTAATGCATGGGTTATATTTAAGAATCAGATTC
62 TTGATTATAAATGTTAGACT--AAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-
* * * * *
209885 TTTTTTATAAAAA-AAAA-TTGATTGATTGTAAATGTCAGACTACAAAG
124 TTTTTTAAAAAAAGAAAAGTTGATTGAGTGTAAATGTTAGACTGCAATG
* ** *
209932 ATTAGACTAATGCATAGATTATATTTGAGAATTAGATT-TCTTTTTATAGAAAA
1 ATTAGACTAATGCATAAATTATATCAGAGAATGAGATTCT-TTTTTATAGAAAA
209985 GCAGAAAAGT
Statistics
Matches: 348, Mismatches: 41, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
174 2 0.01
175 90 0.26
176 8 0.02
177 76 0.22
178 52 0.15
179 61 0.18
180 6 0.02
181 1 0.00
182 8 0.02
183 44 0.13
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (172 bp):
ATTAGACTAATGCATAAATTATATCAGAGAATGAGATTCTTTTTTATAGAAAAAAGATTGATTGA
TTATAAATGTTAGACTAAAGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTTTTA
AAAAAAGAAAAGTTGATTGAGTGTAAATGTTAGACTGCAATG
Found at i:209760 original size:266 final size:264
Alignment explanation
Indices: 209380--209999 Score: 732
Period size: 266 Copynumber: 2.3 Consensus size: 264
209370 ATAGATTGTT
* * * *
209380 AATGTCAGATTACAAATATTAGACTAATGCAT-GAATTATATCTAAGAATC-GAATTCTTTTTTA
1 AATGTCAAACTACAAAGATTAGACTAAT-CATAG-ATTATATCTGAGAATCAG-A---TTTTTTA
* * * * **
209443 TAGAAAAAAAGAAAAATTGATTGATTGTAAATATTAGTCTGCAAAGATTAGACTAATGCATGAAT
60 T-TAAAAAAAGAAAAGTTGATTAAGTGTAAATATTAAACTGCAAAGATTAGACTAATGCATGAAT
* * * *
209508 TATATCAGAGAGTCA-ATTTTTTTTTTTAAAAAAAAAGAAAAGTTGATTGAGTATAAATGTTAGA
124 TATATCAGAGAATCAGATTCTTTTTTAT-AAAAAAAAGAAAAATTGATTGAGTATAAATGTTAGA
* *
209572 CTGCAATGATTAGACTAATCCATAAATTATA-TCAGAGAATGAGATTCTTTTTTATAGAAAAATA
188 CTGCAATGATTAGACTAATCCATAAATTATATTCA-AGAATCAGATTCTTTTTTATA-AAAAAAA
*
209636 GTTGATTGATTATA
251 ATTGATTGATTATA
* *
209650 AATGTCAAACTA-TAAGAATTAGACTAAT-ATATGAATTGTATCTGAGAATCAGATTTTTTATTA
1 AATGTCAAACTACAAAG-ATTAGACTAATCATA-G-ATTATATCTGAGAATCAGATTTTTTATTA
* *
209713 AAAAAAGAAAAGTTGATTAAGTGTAAATGTTAAACTGCAATGATTAGACTAATGCATGAATTATA
63 AAAAAAGAAAAGTTGATTAAGTGTAAATATTAAACTGCAAAGATTAGACTAATGCATGAATTATA
* *
209778 TTAGAGAATCAGATTCTTTTTTATAGAAAAAAGAAAAATTGATTGAGTATAAATGTTAGACTGCA
128 TCAGAGAATCAGATTCTTTTTTATAAAAAAAAGAAAAATTGATTGAGTATAAATGTTAGACTGCA
* *** *
209843 ATGATTAGACTAATGCATGGGTTATATTTAAGAATCAGATTCTTTTTTATAAAAAAAAATTGATT
193 ATGATTAGACTAATCCATAAATTATATTCAAGAATCAGATTCTTTTTTATAAAAAAAAATTGATT
*
209908 GATTGTA
258 GATTATA
* * *
209915 AATGTCAGACTACAAAGATTAGACTAATGCATAGATTATATTTGAGAATTAGATTTCTTT-TTAT
1 AATGTCAAACTACAAAGATTAGACTAAT-CATAGATTATATCTGAGAATCAGATTT-TTTATTA-
209979 AGAAAAGCAGAAAAGTTGATT
63 A-AAAA--AGAAAAGTTGATT
210000 GATTTTACAT
Statistics
Matches: 302, Mismatches: 34, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
265 62 0.21
266 157 0.52
267 27 0.09
268 2 0.01
269 15 0.05
270 38 0.13
271 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (264 bp):
AATGTCAAACTACAAAGATTAGACTAATCATAGATTATATCTGAGAATCAGATTTTTTATTAAAA
AAAGAAAAGTTGATTAAGTGTAAATATTAAACTGCAAAGATTAGACTAATGCATGAATTATATCA
GAGAATCAGATTCTTTTTTATAAAAAAAAGAAAAATTGATTGAGTATAAATGTTAGACTGCAATG
ATTAGACTAATCCATAAATTATATTCAAGAATCAGATTCTTTTTTATAAAAAAAAATTGATTGAT
TATA
Found at i:213425 original size:16 final size:17
Alignment explanation
Indices: 213396--213428 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
213386 TAATTTTCAA
213396 AAAGTCATTAAAATTTG
1 AAAGTCATTAAAATTTG
213413 AAAGTCA-TAAAATTTG
1 AAAGTCATTAAAATTTG
213429 TGGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
AAAGTCATTAAAATTTG
Found at i:214211 original size:21 final size:22
Alignment explanation
Indices: 214164--214212 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
214154 AATGATAATT
* *
214164 TTTTTTAATTTCTTAAATGTTA
1 TTTTTTAATTACTTAAATGTAA
* *
214186 CTTTTTAATTAGTT-AATGTAA
1 TTTTTTAATTACTTAAATGTAA
214207 TTTTTT
1 TTTTTT
214213 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTTTAATTACTTAAATGTAA
Found at i:214250 original size:34 final size:34
Alignment explanation
Indices: 214206--214480 Score: 94
Period size: 34 Copynumber: 7.6 Consensus size: 34
214196 AGTTAATGTA
*
214206 ATTTTTTTAAAAATTTAATTAAATATTATTTTTT
1 ATTTTATTAAAAATTTAATTAAATATTATTTTTT
*
214240 ATTTTATTAAAAATAATAATGATAAATA--A-TTTTT
1 ATTTTATTAAAAAT-TTAAT--TAAATATTATTTTTT
* *
214274 ATTTT-TTAAAAAATATAATAATTAATATTTTAATTTGTTA
1 ATTTTATT-AAAAAT-T--TAATTAA-ATATT-ATTT-TTT
* * ** *
214314 ATGTAAATTTTTTAAACTTAATTAAATATTA-TTTTT
1 AT-T--TTATTAAAAATTTAATTAAATATTATTTTTT
* * ***
214350 ATTTTATTAAAAATTATAATAAAAAAGCCTTTTTT
1 ATTTTATTAAAAATT-TAATTAAATATTATTTTTT
* * * *
214385 ATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTA
1 A-TTTTATTAAAA-AT-TTAATTAA-ATATT-ATTT-TTT
* ** *
214425 ATGTAATTTTTTTAAACTTAATTAAATATTA-TTTTT
1 AT-T--TTATTAAAAATTTAATTAAATATTATTTTTT
214461 ATTTTATTAAAAATTATAAT
1 ATTTTATTAAAAATT-TAAT
214481 AAAAAAAGCC
Statistics
Matches: 171, Mismatches: 42, Indels: 56
0.64 0.16 0.21
Matches are distributed among these distances:
33 17 0.10
34 45 0.26
35 15 0.09
36 22 0.13
37 18 0.11
38 4 0.02
39 14 0.08
40 22 0.13
41 2 0.01
42 6 0.04
43 4 0.02
44 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
ATTTTATTAAAAATTTAATTAAATATTATTTTTT
Found at i:214279 original size:112 final size:112
Alignment explanation
Indices: 214188--214685 Score: 639
Period size: 111 Copynumber: 4.5 Consensus size: 112
214178 AAATGTTACT
* * *
214188 TTTTAATTAGTTAATGTAATTTTTTTAAAAATTTAATTAAATATTATTTTTTATTTTATTAAAAA
1 TTTTAATTTGTTAATGTAAATTTTTT--AAACTTAATTAAATATTA-TTTTTATTTTATTAAAAA
*
214253 TAATAATGATAAATAA-TTTTTA-TTTTTTAAAAA-ATATAATAATTAATA
63 TAATAATAATAAATAACTTTTTATTTTTTTAAAAACATA-AATAATTAATA
*
214301 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATTA
1 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
* *
214366 TAATAA-AAA-AGCCTTTTTTATTTTTATAAAAACAT-AATAATTAATA
66 TAATAATAAATA-AC-TTTTTATTTTTTTAAAAACATAAATAATTAATA
* *
214412 TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATTA
1 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
*
214477 TAATAA-AAA-AAGCCTTTTTTATTTTTATAAAAACAT-AATAATTAATA
66 TAATAATAAATAA--C-TTTTTATTTTTTTAAAAACATAAATAATTAATA
214524 TTTTAATTTGTTAATGT-AATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAA-AA
1 TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
*** *
214587 TAATAAT-AATAACCCTTTTTATTTTTTATTTTAA-A-AAATAGTTAATA
66 TAATAATAAATAA--CTTTTTATTTTTT-TAAAAACATAAATAATTAATA
*
214634 TTTTAATTTATTAATGTAAAATTTTTT-AACTTAATTAAATATTATTTTTATT
1 TTTTAATTTGTTAATGT-AAATTTTTTAAACTTAATTAAATATTATTTTTATT
214686 AAAAATAATA
Statistics
Matches: 354, Mismatches: 18, Indels: 28
0.88 0.05 0.07
Matches are distributed among these distances:
108 1 0.00
109 3 0.01
110 72 0.20
111 183 0.52
112 69 0.19
113 26 0.07
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (112 bp):
TTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
TAATAATAAATAACTTTTTATTTTTTTAAAAACATAAATAATTAATA
Found at i:214564 original size:222 final size:221
Alignment explanation
Indices: 214188--214685 Score: 708
Period size: 222 Copynumber: 2.2 Consensus size: 221
214178 AAATGTTACT
* *
214188 TTTTAATTAGTTAATGTAATTTTTTTAAAAATTTAATTAAATATTATTTTTTATTTTATTAAAAA
1 TTTTAATTTGTTAATGTAATTTTTTT--AAACTTAATTAAATATTA-TTTTTATTTTATTAAAAA
* *
214253 TAATAATGATAAATAATTTTTATTTTTTAAAAAATATAATAATTAATATTTTAATTTGTTAATGT
63 TAATAATGATAAAAAATTTTTATTTTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGT
* *
214318 AAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATTATAATAA-AA-AAGCCTT
128 AAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAA-AATAATAATAATAACCCTT
214381 TTT-TATTTTTA-TAAAAACATAATAATTAATA
192 TTTAT-TTTTTATTAAAAA-A-AATAATTAATA
*
214412 TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATTA
1 TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
214477 TAAT-A-AAAAAAGCCTTTTT-TATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAAT
66 TAATGATAAAAAA---TTTTTAT-TTTTTA-AAAAACATAATAATTAATATTTTAATTTGTTAAT
214539 GT-AATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAAATAATAATAATAACCCT
126 GTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAAATAATAATAATAACCCT
** *
214603 TTTTATTTTTTATTTTAAAAAATAGTTAATA
191 TTTTATTTTTTATTAAAAAAAATAATTAATA
* *
214634 TTTTAATTTATTAATGTAAAATTTTTT-AACTTAATTAAATATTATTTTTATT
1 TTTTAATTTGTTAATGT-AATTTTTTTAAACTTAATTAAATATTATTTTTATT
214686 AAAAATAATA
Statistics
Matches: 252, Mismatches: 12, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
219 5 0.02
220 1 0.00
221 32 0.13
222 125 0.50
223 59 0.23
224 30 0.12
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (221 bp):
TTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATAA
TAATGATAAAAAATTTTTATTTTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAA
TTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAAATAATAATAATAACCCTTTTTA
TTTTTTATTAAAAAAAATAATTAATA
Found at i:214687 original size:20 final size:19
Alignment explanation
Indices: 214640--214687 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
214630 AATATTTTAA
214640 TTTATTAATGTAAAATTTT
1 TTTATTAATGTAAAATTTT
*
214659 TTAACTTAAT-TAAATATTATT
1 TTTA-TTAATGTAAA-ATT-TT
214680 TTTATTAA
1 TTTATTAA
214688 AAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 7 0.29
20 12 0.50
21 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTATTAATGTAAAATTTT
Found at i:215350 original size:11 final size:12
Alignment explanation
Indices: 215318--215342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
215308 AATTATTATA
215318 TAAAATTAAAAT
1 TAAAATTAAAAT
215330 TAAAATTAAAAT
1 TAAAATTAAAAT
215342 T
1 T
215343 TAATTAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:215793 original size:36 final size:37
Alignment explanation
Indices: 215741--215831 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
215731 TAACATTCTG
* *
215741 ATAA-ATTTAAAATTTAATTTAATTAATTA-TTTTAGA
1 ATAATATTT-AAATTTAATTTAAATAATTATTTTTAAA
*
215777 ATAATATTTAAATTTAAATTAAATAATTATTTTTAAA
1 ATAATATTTAAATTTAATTTAAATAATTATTTTTAAA
*
215814 AAAATA-TTAATATTTAAT
1 ATAATATTTAA-ATTTAAT
215832 AAATTTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 26 0.55
37 21 0.45
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (37 bp):
ATAATATTTAAATTTAATTTAAATAATTATTTTTAAA
Found at i:221681 original size:23 final size:25
Alignment explanation
Indices: 221629--221674 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
221619 AGCAGTGTCT
*
221629 TACAGCAAAACTAAAGAGAACTTCA
1 TACAACAAAACTAAAGAGAACTTCA
*
221654 AACAACAAAAC-AAAGA-AACTT
1 TACAACAAAACTAAAGAGAACTT
221675 AGTACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 5 0.26
25 9 0.47
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.13
Consensus pattern (25 bp):
TACAACAAAACTAAAGAGAACTTCA
Found at i:222457 original size:20 final size:20
Alignment explanation
Indices: 222424--222462 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
222414 TAAGATGATA
* *
222424 AATTTATACGAAATTTAAAG
1 AATTTATACAAAATATAAAG
*
222444 AATTTATATAAAATATAAA
1 AATTTATACAAAATATAAA
222463 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
AATTTATACAAAATATAAAG
Found at i:222499 original size:22 final size:20
Alignment explanation
Indices: 222469--222509 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
222459 TAAATTTTAA
222469 AAATAAATTTAAGTAAAATATT
1 AAATAAATTTAA--AAAATATT
*
222491 AAATTAATTTAAAAAATAT
1 AAATAAATTTAAAAAATAT
222510 GTTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATAAATTTAAAAAATATT
Done.