Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 66 of 295
Found at i:19967330 original size:13 final size:13
Alignment explanation
Indices: 19967291--19967331 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
19967281 TGAGTGAATG
19967291 TGTGATAATTATA
1 TGTGATAATTATA
**
19967304 TGTGGCAA--ATA
1 TGTGATAATTATA
19967315 TGTGATAATTATA
1 TGTGATAATTATA
19967328 TGTG
1 TGTG
19967332 GCAAATACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTGATAATTATA
Found at i:19972947 original size:7 final size:7
Alignment explanation
Indices: 19972935--19972964 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19972925 TGCCTCGCAC
19972935 TATTCTT
1 TATTCTT
19972942 TATTCTT
1 TATTCTT
19972949 TATTCTT
1 TATTCTT
*
19972956 TATGCTT
1 TATTCTT
19972963 TA
1 TA
19972965 ACATCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.03, T:0.67
Consensus pattern (7 bp):
TATTCTT
Found at i:19973483 original size:7 final size:7
Alignment explanation
Indices: 19973471--19973506 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
19973461 CATGATATCA
19973471 TTATTTT
1 TTATTTT
19973478 TTATTTT
1 TTATTTT
19973485 TTATTTT
1 TTATTTT
19973492 TTATTTT
1 TTATTTT
19973499 TTATTTT
1 TTATTTT
19973506 T
1 T
19973507 AAGCATCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTATTTT
Found at i:19975245 original size:14 final size:15
Alignment explanation
Indices: 19975226--19975254 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19975216 AGTTAGAAAG
19975226 ATAAAAA-AGTGACT
1 ATAAAAATAGTGACT
19975240 ATAAAAATAGTGACT
1 ATAAAAATAGTGACT
19975255 TTTATTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (15 bp):
ATAAAAATAGTGACT
Found at i:19975765 original size:7 final size:8
Alignment explanation
Indices: 19975736--19975765 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19975726 CATACATTGT
19975736 TTTGAAAA
1 TTTGAAAA
19975744 TTTGAAAA
1 TTTGAAAA
19975752 TTTGAAAA
1 TTTGAAAA
19975760 -TTGAAA
1 TTTGAAA
19975766 GAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (8 bp):
TTTGAAAA
Found at i:19976498 original size:18 final size:18
Alignment explanation
Indices: 19976475--19976526 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
19976465 ACGTTTGTCA
19976475 TTCATTTAT-ATTTTTTTT
1 TTCATTT-TCATTTTTTTT
**
19976493 TTCATTTTCATTTTCATT
1 TTCATTTTCATTTTTTTT
19976511 TTCATTTTCATTTTTT
1 TTCATTTTCATTTTTT
19976527 AAATATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 1 0.03
18 28 0.97
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (18 bp):
TTCATTTTCATTTTTTTT
Found at i:19976500 original size:6 final size:6
Alignment explanation
Indices: 19976491--19976524 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
19976481 TATATTTTTT
19976491 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
19976525 TTAAATATCA
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:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:19977264 original size:35 final size:35
Alignment explanation
Indices: 19977218--19977287 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
19977208 CATCTCCGGA
*
19977218 GCTTGGCAAATACGGAACG-TGATCTTCAAAGATAT
1 GCTTGGCAAATACGGAA-GAGGATCTTCAAAGATAT
*
19977253 GCTTGGCAAATATGGAAGAGGATCTTCAAAGATAT
1 GCTTGGCAAATACGGAAGAGGATCTTCAAAGATAT
19977288 ATGATCCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATACGGAAGAGGATCTTCAAAGATAT
Found at i:19978006 original size:33 final size:32
Alignment explanation
Indices: 19977964--19978031 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
19977954 GTTTAGAAGT
*
19977964 TGACTGTAGGGA-TGATGCCATCAAGGCTATGA
1 TGACTGTA-GGACTGATGCCATCAAGGCTATAA
**
19977996 TGACTAGTAGGACTGATGCCATTGAGGCTATAA
1 TGACT-GTAGGACTGATGCCATCAAGGCTATAA
19978029 TGA
1 TGA
19978032 TGACCTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 8 0.26
33 23 0.74
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (32 bp):
TGACTGTAGGACTGATGCCATCAAGGCTATAA
Found at i:19982422 original size:35 final size:35
Alignment explanation
Indices: 19982383--19982453 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
19982373 CATCTCCTAA
*
19982383 GCTTGGCAAATATGGAAAGTGATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGGATCTTCAAAGATAT
* *
19982418 GCTTGGCAAATATGGAAGGGGATCTTCAAATATAT
1 GCTTGGCAAATATGGAAAGGGATCTTCAAAGATAT
19982453 G
1 G
19982454 TGATCCTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGGATCTTCAAAGATAT
Found at i:19983019 original size:5 final size:5
Alignment explanation
Indices: 19983011--19983065 Score: 92
Period size: 5 Copynumber: 10.6 Consensus size: 5
19983001 GTTTTTATAT
19983011 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TTATTA TATATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TAT-TA
19983063 TAT
1 TAT
19983066 GACAAAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 38 0.79
6 10 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:19983131 original size:40 final size:40
Alignment explanation
Indices: 19983074--19983169 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
19983064 ATGACAAAGA
19983074 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
19983115 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
19983155 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
19983170 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:19983935 original size:29 final size:30
Alignment explanation
Indices: 19983876--19983933 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19983866 TCCGAGCCTT
*
19983876 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
19983906 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
19983934 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:19984378 original size:50 final size:50
Alignment explanation
Indices: 19984258--19984556 Score: 366
Period size: 50 Copynumber: 5.8 Consensus size: 50
19984248 ATTTGGGTAA
* *
19984258 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* * *
19984314 AGAGCTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
19984364 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
19984414 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
19984464 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GACG
** *
19984514 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19984557 TGTTATTATC
Statistics
Matches: 218, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.00
50 138 0.63
51 34 0.16
52 1 0.00
53 3 0.01
55 2 0.01
56 39 0.18
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:19986642 original size:22 final size:22
Alignment explanation
Indices: 19986608--19986661 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
19986598 CATCTCTACA
* *
19986608 AAAAAATTCAAAATA-ATTT-T
1 AAAAATTTCAAAAAATATTTAT
*
19986628 CAAAATTTCAAAAAATATTTAT
1 AAAAATTTCAAAAAATATTTAT
19986650 AAAAATTTCAAA
1 AAAAATTTCAAA
19986662 TTTATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATTTCAAAAAATATTTAT
Found at i:19986675 original size:23 final size:22
Alignment explanation
Indices: 19986617--19986677 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
19986607 AAAAAAATTC
* *
19986617 AAAATAATTTTCAAAATTTCAA
1 AAAATATTTTTAAAAATTTCAA
*
19986639 AAAATATTTATAAAAATTTCAA
1 AAAATATTTTTAAAAATTTCAA
**
19986661 ATTTATATTTTTAAAAA
1 A-AAATATTTTTAAAAA
19986678 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATTTTTAAAAATTTCAA
Found at i:19988417 original size:7 final size:7
Alignment explanation
Indices: 19988405--19988429 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19988395 TTGGGGCAAG
19988405 TGGTAAT
1 TGGTAAT
19988412 TGGTAAT
1 TGGTAAT
19988419 TGGTAAT
1 TGGTAAT
19988426 TGGT
1 TGGT
19988430 CCACCTGGAT
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:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (7 bp):
TGGTAAT
Found at i:19989193 original size:21 final size:21
Alignment explanation
Indices: 19989156--19989212 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
19989146 TTTTAATTTG
19989156 AATTA-AAATTTTATATAAT-
1 AATTATAAATTTTATATAATA
*
19989175 AATTCATAAATATTT-TATATTA
1 AATT-ATAAAT-TTTATATAATA
19989197 AATTATAAATTTTATA
1 AATTATAAATTTTATA
19989213 GGTCAAATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 17 0.53
22 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATAAATTTTATATAATA
Found at i:19989979 original size:36 final size:37
Alignment explanation
Indices: 19989900--19989981 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
19989890 TATTGAATTT
* *
19989900 TAATAAAAATATAAAAATATTTAATATTTATCAAAAA
1 TAATAAAAACATAAAAATATTAAATATTTATCAAAAA
*
19989937 TTATAAAAACCATAAAAATA-TAAAGT-TTTAT-AAAAA
1 TAATAAAAA-CATAAAAATATTAAA-TATTTATCAAAAA
19989973 TAATAAAAA
1 TAATAAAAA
19989982 ATTATAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 13 0.33
37 16 0.41
38 10 0.26
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (37 bp):
TAATAAAAACATAAAAATATTAAATATTTATCAAAAA
Found at i:19990241 original size:25 final size:25
Alignment explanation
Indices: 19990210--19990259 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19990200 AAATTTTATA
* * *
19990210 ATTTTTTTATATTTTTATATATTTT
1 ATTTTTTTACAATTTTATAAATTTT
19990235 ATTTTTTTACAATTTTATAAATTTT
1 ATTTTTTTACAATTTTATAAATTTT
19990260 TTTACGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTTTACAATTTTATAAATTTT
Found at i:19990249 original size:16 final size:17
Alignment explanation
Indices: 19990214--19990253 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19990204 TTTATAATTT
*
19990214 TTTTATATTTTTATATA
1 TTTTATATTTTTACATA
*
19990231 TTTTATTTTTTTACA-A
1 TTTTATATTTTTACATA
19990247 TTTTATA
1 TTTTATA
19990254 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATATTTTTACATA
Found at i:19990260 original size:20 final size:20
Alignment explanation
Indices: 19990203--19990279 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
19990193 CTTTATAAAA
* *
19990203 TTTTATAATTTTTTTATATT
1 TTTTATAATTTTTTTACAAT
19990223 TTTATATATTTTATTTTTTTACAA-
1 TTT-TATA----ATTTTTTTACAAT
*
19990247 TTTTATAAATTTTTTTACGAT
1 TTTTAT-AATTTTTTTACAAT
19990268 TTTTATAATTTT
1 TTTTATAATTTT
19990280 AATTCTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 20 0.43
21 10 0.21
23 3 0.06
24 4 0.09
25 10 0.21
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAT
Found at i:19990310 original size:10 final size:9
Alignment explanation
Indices: 19990203--19990302 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 9
19990193 CTTTATAAAA
19990203 TTTTATAAT
1 TTTTATAAT
*
19990212 TTTTTTATAT
1 TTTTATA-AT
19990222 TTTTAT-AT
1 TTTTATAAT
*
19990230 ATTTTAT-TT
1 -TTTTATAAT
*
19990239 TTTTACAA-
1 TTTTATAAT
19990247 TTTTATAAAT
1 TTTTAT-AAT
*
19990257 TTTTTTACGAT
1 TTTTATA--AT
19990268 TTTTATAAT
1 TTTTATAAT
* **
19990277 TTTAATTCTTT
1 TTTTA-T-AAT
19990288 TTTTATAAT
1 TTTTATAAT
19990297 TTTTAT
1 TTTTAT
19990303 CATCTTTTGC
Statistics
Matches: 68, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
8 12 0.18
9 29 0.43
10 14 0.21
11 13 0.19
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:19990843 original size:24 final size:24
Alignment explanation
Indices: 19990798--19990844 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19990788 TAAAAGAATT
*
19990798 TAGATTTTTAAAAATTTTTAAAAA
1 TAGATTTTTAAAAATTTATAAAAA
19990822 TAGATTTTTCAAAAA-TTATAAAA
1 TAGATTTTT-AAAAATTTATAAAA
19990845 TTATAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
TAGATTTTTAAAAATTTATAAAAA
Found at i:19992274 original size:21 final size:20
Alignment explanation
Indices: 19992250--19992288 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19992240 TTGGTATCGT
*
19992250 TTTTAATAAAAGTTTCGATTA
1 TTTTAA-AAAAGTATCGATTA
*
19992271 TTTTCAAAAAGTATCGAT
1 TTTTAAAAAAGTATCGAT
19992289 ACCAAAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTAAAAAAGTATCGATTA
Found at i:19993593 original size:27 final size:28
Alignment explanation
Indices: 19993543--19993603 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
19993533 TAAATTAATA
*
19993543 TTTTTAATTAATAAATATGTTTTTCAAG
1 TTTTTAATTAATAAACATGTTTTTCAAG
* *
19993571 TTTTTAATTAATATACATGTTTTT-ATG
1 TTTTTAATTAATAAACATGTTTTTCAAG
19993598 TTTTTA
1 TTTTTA
19993604 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTTAATTAATAAACATGTTTTTCAAG
Found at i:19993964 original size:18 final size:18
Alignment explanation
Indices: 19993942--19993994 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
19993932 CAAAAATTAA
* *
19993942 AAAAATCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
19993961 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
19993979 AAAAATT-AAAAT-TTTA
1 -AAAATTCAAAATATTTA
19993995 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 10 0.32
19 17 0.55
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:19993969 original size:19 final size:18
Alignment explanation
Indices: 19993942--19993994 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
19993932 CAAAAATTAA
*
19993942 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
*
19993961 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTAT
*
19993979 AAAAATTAAAAT-TTTA
1 AAAAATCAAAATATTTA
19993995 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 4 0.13
18 15 0.50
19 11 0.37
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:19993987 original size:25 final size:23
Alignment explanation
Indices: 19993959--19994008 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
19993949 AAAATAATTT
19993959 TTAAAATTCAAAATATTTATAAAAA
1 TTAAAATTCAAAA-ATTT-TAAAAA
**
19993984 TTAAAATTTTAAAATTTTAAAAA
1 TTAAAATTCAAAAATTTTAAAAA
19994007 TT
1 TT
19994009 CTAAAGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 4 0.17
25 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAATTCAAAAATTTTAAAAA
Found at i:19995054 original size:13 final size:13
Alignment explanation
Indices: 19995036--19995063 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19995026 AATGTTTATT
19995036 AATTAAAAATAAA
1 AATTAAAAATAAA
19995049 AATTAAAAATAAA
1 AATTAAAAATAAA
19995062 AA
1 AA
19995064 AAAGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATTAAAAATAAA
Found at i:20004088 original size:20 final size:20
Alignment explanation
Indices: 20004065--20004115 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
20004055 AACTCGATTT
20004065 AATTTGAAAAAATTAAAAAA
1 AATTTGAAAAAATTAAAAAA
** *
20004085 AATTTGAATAATTTTGAAAAA
1 AATTTGAA-AAAATTAAAAAA
20004106 AA-TTGAAAAA
1 AATTTGAAAAA
20004116 TTGAGTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 13 0.50
21 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AATTTGAAAAAATTAAAAAA
Found at i:20004130 original size:9 final size:9
Alignment explanation
Indices: 20004118--20004150 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
20004108 TTGAAAAATT
20004118 GAGTTATTC
1 GAGTTATTC
20004127 GAGTTATTC
1 GAGTTATTC
*
20004136 GAATTATTC
1 GAGTTATTC
20004145 GAGTTA
1 GAGTTA
20004151 ACTTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (9 bp):
GAGTTATTC
Found at i:20005444 original size:41 final size:41
Alignment explanation
Indices: 20005389--20005499 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
20005379 GCTAGAAGGA
*
20005389 AAACGCAGCAAAAAGTTGAGCAATAGTGGCGTTTTAGGT-CC
1 AAACGCAGCTAAAAGTTGAGCAATAGTGGCGTTTT-GGTCCC
* ** * *
20005430 AAACGCCGCTAAAAGTTGTTCAATACTGGCGTTTTTGTCCC
1 AAACGCAGCTAAAAGTTGAGCAATAGTGGCGTTTTGGTCCC
* * *
20005471 AAACACTGCTAAAATTTGAGCAATAGTGG
1 AAACGCAGCTAAAAGTTGAGCAATAGTGG
20005500 TCGCCGCTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.04
41 55 0.96
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (41 bp):
AAACGCAGCTAAAAGTTGAGCAATAGTGGCGTTTTGGTCCC
Found at i:20005542 original size:68 final size:68
Alignment explanation
Indices: 20005433--20005567 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
20005423 TAGGTCCAAA
** * *
20005433 CGCCGCTAAAAGTTGTTCAATACTGGCGTTTTTGTCCCAAACACTGCTAA-AATTTGAGCAATAG
1 CGCCGCTAAAAGTTGAGCAATAATGGCGTTTTTGTCCCAAACACCGCTAAGAA-TTGAGCAATAG
20005497 TGGT
65 TGGT
* * *
20005501 CGCCGCTAAAAGTTGAGCAGTAATGGCTTTTTTGTCCCAAACACCGCTAAGAATTGAGCAATTGT
1 CGCCGCTAAAAGTTGAGCAATAATGGCGTTTTTGTCCCAAACACCGCTAAGAATTGAGCAATAGT
20005566 GG
66 GG
20005568 CGTTTTAGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 57 0.97
69 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (68 bp):
CGCCGCTAAAAGTTGAGCAATAATGGCGTTTTTGTCCCAAACACCGCTAAGAATTGAGCAATAGT
GGT
Found at i:20005560 original size:41 final size:40
Alignment explanation
Indices: 20005501--20005696 Score: 189
Period size: 41 Copynumber: 4.8 Consensus size: 40
20005491 CAATAGTGGT
* **
20005501 CGCCGCTAAAAGTTGAGCAGTAATGGC-TTTTTTGTCCCAAA
1 CGCCGCTAAAA-TTGAGCAATAATGGCGTTTTAGGT-CCAAA
* **
20005542 CACCGCTAAGAATTGAGCAATTGTGGCGTTTTAGGTCCAAA
1 CGCCGCTAA-AATTGAGCAATAATGGCGTTTTAGGTCCAAA
* * *
20005583 CGCCGCTGAAAGTTGAGCAATAGTGGCGTTTT-TGTCCCAAA
1 CGCCGCT-AAAATTGAGCAATAATGGCGTTTTAGGT-CCAAA
* *
20005624 CGCTGCTAAAAATCGAGCAATAATGGCGTTTTAGGTCCAAA
1 CGCCGCT-AAAATTGAGCAATAATGGCGTTTTAGGTCCAAA
* * *
20005665 CGCCGCTAAAAGCTGATCAATAGTGGCGTTTT
1 CGCCGCTAAAA-TTGAGCAATAATGGCGTTTT
20005697 TGGTTAAAAC
Statistics
Matches: 128, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
40 6 0.05
41 110 0.86
42 12 0.09
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (40 bp):
CGCCGCTAAAATTGAGCAATAATGGCGTTTTAGGTCCAAA
Found at i:20005599 original size:109 final size:109
Alignment explanation
Indices: 20005399--20005608 Score: 246
Period size: 109 Copynumber: 1.9 Consensus size: 109
20005389 AAACGCAGCA
* * **
20005399 AAAAGTTGAGCAATAGTGGCGTTTTAGGTCCAAACGCCGCTAAAAGTTGTTCAATACTGGCGTTT
1 AAAAGTTGAGCAATAATGGCGTTTTAGGTCCAAACACCGCTAAAAGTTGAGCAATACTGGCGTTT
* * *
20005464 TTGTCCCAAACACTGCTAAAATTTGAGCAATAGTGGTCGCCGCT
66 TGGTCCCAAACACCGCTAAAAGTTGAGCAATAGTGGTCGCCGCT
* ** **
20005508 AAAAGTTGAGCAGTAATGGC-TTTTTTGTCCCAAACACCGCTAAGAA-TTGAGCAATTGTGGCGT
1 AAAAGTTGAGCAATAATGGCGTTTTAGGT-CCAAACACCGCTAA-AAGTTGAGCAATACTGGCGT
* *
20005571 TTTAGGT-CCAAACGCCGCTGAAAGTTGAGCAATAGTGG
64 TTT-GGTCCCAAACACCGCTAAAAGTTGAGCAATAGTGG
20005609 CGTTTTTGTC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
108 6 0.07
109 74 0.88
110 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (109 bp):
AAAAGTTGAGCAATAATGGCGTTTTAGGTCCAAACACCGCTAAAAGTTGAGCAATACTGGCGTTT
TGGTCCCAAACACCGCTAAAAGTTGAGCAATAGTGGTCGCCGCT
Found at i:20005642 original size:82 final size:82
Alignment explanation
Indices: 20005501--20005698 Score: 288
Period size: 82 Copynumber: 2.4 Consensus size: 82
20005491 CAATAGTGGT
* * * * * **
20005501 CGCCGCTAAAAGTTGAGCAGTAATGGCTTTTTTGTCCCAAACACCGCTAAGAATTGAGCAATTGT
1 CGCCGCTAAAAGTTGAGCAATAGTGGCGTTTTTGTCCCAAACACCGCTAAAAATCGAGCAATAAT
20005566 GGCGTTTTAGGTCCAAA
66 GGCGTTTTAGGTCCAAA
* * *
20005583 CGCCGCTGAAAGTTGAGCAATAGTGGCGTTTTTGTCCCAAACGCTGCTAAAAATCGAGCAATAAT
1 CGCCGCTAAAAGTTGAGCAATAGTGGCGTTTTTGTCCCAAACACCGCTAAAAATCGAGCAATAAT
20005648 GGCGTTTTAGGTCCAAA
66 GGCGTTTTAGGTCCAAA
* *
20005665 CGCCGCTAAAAGCTGATCAATAGTGGCGTTTTTG
1 CGCCGCTAAAAGTTGAGCAATAGTGGCGTTTTTG
20005699 GTTAAAACCC
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (82 bp):
CGCCGCTAAAAGTTGAGCAATAGTGGCGTTTTTGTCCCAAACACCGCTAAAAATCGAGCAATAAT
GGCGTTTTAGGTCCAAA
Found at i:20005721 original size:41 final size:41
Alignment explanation
Indices: 20005503--20005738 Score: 167
Period size: 41 Copynumber: 5.8 Consensus size: 41
20005493 ATAGTGGTCG
* * * * * *
20005503 CCGCTAAAAGTTGAGCAGTAATGGC-TTTTTTGTCCCAAACA
1 CCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGGT-CAAAACC
* * * * *
20005544 CCGCTAAGAA-TTGAGCAATTGTGGCGTTTTAGGTCCAAACG
1 CCGCTAA-AAGCTGAGCAATAGTGGCGTTTTTGGTCAAAACC
* * * *
20005585 CCGCTGAAAGTTGAGCAATAGTGGCGTTTTT-GTCCCAAACG
1 CCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGGT-CAAAACC
* * * * * *
20005626 CTGCTAAAA-ATCGAGCAATAATGGCGTTTTAGGTCCAAACG
1 CCGCTAAAAGCT-GAGCAATAGTGGCGTTTTTGGTCAAAACC
* *
20005667 CCGCTAAAAGCTGATCAATAGTGGCGTTTTTGGTTAAAACC
1 CCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGGTCAAAACC
**
20005708 CCGC-AAAAGGCTGAGCTCTAGTGGCGTTTTT
1 CCGCTAAAA-GCTGAGCAATAGTGGCGTTTTT
20005739 TATCCAAATG
Statistics
Matches: 162, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
40 9 0.06
41 142 0.88
42 11 0.07
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
CCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGGTCAAAACC
Found at i:20005733 original size:82 final size:82
Alignment explanation
Indices: 20005501--20005737 Score: 244
Period size: 82 Copynumber: 2.9 Consensus size: 82
20005491 CAATAGTGGT
* * * * * * * ** *
20005501 CGCCGCTAAAAGTTGAGCAGTAATGGCTTTTTTGTCCCAAACACCGCTAAGAATTGAGCAATTGT
1 CGCCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGTCCAAAACCCCGCTAAAAAGCGAGCAATAGT
20005566 GGCGTTTTAGGTCCAAA
66 GGCGTTTTAGGTCCAAA
* * * * * * *
20005583 CGCCGCTGAAAGTTGAGCAATAGTGGCGTTTTTGTCCCAAACGCTGCTAAAAATCGAGCAATAAT
1 CGCCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGTCCAAAACCCCGCTAAAAAGCGAGCAATAGT
20005648 GGCGTTTTAGGTCCAAA
66 GGCGTTTTAGGTCCAAA
* * * **
20005665 CGCCGCTAAAAGCTGATCAATAGTGGCGTTTTTGGT-TAAAACCCCGC-AAAAGGCTGAGCTCTA
1 CGCCGCTAAAAGCTGAGCAATAGTGGCGTTTTT-GTCCAAAACCCCGCTAAAAAGC-GAGCAATA
20005728 GTGGCGTTTT
64 GTGGCGTTTT
20005738 TTATCCAAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
81 5 0.04
82 124 0.95
83 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (82 bp):
CGCCGCTAAAAGCTGAGCAATAGTGGCGTTTTTGTCCAAAACCCCGCTAAAAAGCGAGCAATAGT
GGCGTTTTAGGTCCAAA
Found at i:20006341 original size:14 final size:14
Alignment explanation
Indices: 20006322--20006353 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
20006312 ACATAAATCA
*
20006322 TAAACCTTAATCCC
1 TAAACCTTAAACCC
20006336 TAAACCTTAAACCC
1 TAAACCTTAAACCC
20006350 TAAA
1 TAAA
20006354 TGACACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:20006419 original size:41 final size:41
Alignment explanation
Indices: 20006359--20006453 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
20006349 CTAAATGACA
* * *
20006359 CAAAAGGTCAAGTAGTAGCGGCGTTTGTAATAAAAACGCCG
1 CAAAAGGTCAAGCAATAGCGACGTTTGTAATAAAAACGCCG
* *
20006400 CAAAAGGTCAAGCAATAGCGACGTTTGTGATTAAAACGCCG
1 CAAAAGGTCAAGCAATAGCGACGTTTGTAATAAAAACGCCG
20006441 CTAAAA-GTCAAGC
1 C-AAAAGGTCAAGC
20006454 CATAAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (41 bp):
CAAAAGGTCAAGCAATAGCGACGTTTGTAATAAAAACGCCG
Found at i:20006530 original size:30 final size:28
Alignment explanation
Indices: 20006478--20006541 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
20006468 TTTTATTTTA
20006478 GGTTTAGGTTTTAAGATTTAAGGTCTAT
1 GGTTTAGGTTTTAAGATTTAAGGTCTAT
* *
20006506 GGTTTATGGTTTTAAGGTTTTAAGGTTTAT
1 GGTTTA-GGTTTTAA-GATTTAAGGTCTAT
*
20006536 GCTTTA
1 GGTTTA
20006542 ATGTTTAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.19
29 8 0.26
30 17 0.55
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.50
Consensus pattern (28 bp):
GGTTTAGGTTTTAAGATTTAAGGTCTAT
Found at i:20006592 original size:50 final size:50
Alignment explanation
Indices: 20006516--20006613 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
20006506 GGTTTATGGT
* *
20006516 TTTAAGGTTTTAAGGTTTATGCTTTAATGTTTAGTA-TATT-GGGTTTAGCG
1 TTTAAGGTTTTAAGGTTTAGGCTTTAAGGTTT-GTAGT-TTAGGGTTTAGCG
* *
20006566 TTTAATGTTTTAAGGTTTAGGGTTTAAGGTTTGTAGTTTAGGGTTTAG
1 TTTAAGGTTTTAAGGTTTAGGCTTTAAGGTTTGTAGTTTAGGGTTTAG
20006614 TGTATTATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 5 0.12
50 37 0.88
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.50
Consensus pattern (50 bp):
TTTAAGGTTTTAAGGTTTAGGCTTTAAGGTTTGTAGTTTAGGGTTTAGCG
Found at i:20006663 original size:22 final size:22
Alignment explanation
Indices: 20006638--20006680 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20006628 GGCCTTAGTA
20006638 ATTAAGGTTT-AGTGGTTAGGGT
1 ATTAAGGTTTAAG-GGTTAGGGT
*
20006660 ATTATGGTTTAAGGGTTAGGG
1 ATTAAGGTTTAAGGGTTAGGG
20006681 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (22 bp):
ATTAAGGTTTAAGGGTTAGGGT
Found at i:20006886 original size:21 final size:21
Alignment explanation
Indices: 20006862--20006902 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20006852 AAGGTTATGT
20006862 TTTAAAGTTTA-GGCTTTAGGC
1 TTTAAAGTTTATGG-TTTAGGC
*
20006883 TTTAAGGTTTATGGTTTAGG
1 TTTAAAGTTTATGGTTTAGG
20006903 GATTTAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.05, G:0.27, T:0.46
Consensus pattern (21 bp):
TTTAAAGTTTATGGTTTAGGC
Found at i:20007865 original size:18 final size:17
Alignment explanation
Indices: 20007842--20007889 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
20007832 CCCCCTAACA
20007842 AAATTTCCCCAATTCCCT
1 AAATTTCCCCAA-TCCCT
*
20007860 AAATTTCCCTTAATCCCT
1 AAATTTCCC-CAATCCCT
*
20007878 AAATTTTCCCAA
1 AAATTTCCCCAA
20007890 ATCAAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTCCCCAATCCCT
Found at i:20010463 original size:13 final size:13
Alignment explanation
Indices: 20010447--20010472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20010437 TAATTAAAGG
20010447 GTTAAAATTTAAA
1 GTTAAAATTTAAA
20010460 GTTAAAATTTAAA
1 GTTAAAATTTAAA
20010473 TATGCTAATC
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:20010496 original size:9 final size:9
Alignment explanation
Indices: 20010482--20010570 Score: 76
Period size: 9 Copynumber: 10.1 Consensus size: 9
20010472 ATATGCTAAT
20010482 CATAACTTA
1 CATAACTTA
20010491 CATAACTTA
1 CATAACTTA
*
20010500 CAT-A-GTA
1 CATAACTTA
*
20010507 CATAA-ATA
1 CATAACTTA
* * *
20010515 AATATCATA
1 CATAACTTA
20010524 TCATAACTTA
1 -CATAACTTA
*
20010534 AATAACTTA
1 CATAACTTA
*
20010543 CATAATTTA
1 CATAACTTA
*
20010552 CATTACTTA
1 CATAACTTA
20010561 CATAACTTA
1 CATAACTTA
20010570 C
1 C
20010571 GTAATACATA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
7 5 0.08
8 7 0.11
9 46 0.72
10 6 0.09
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:20016573 original size:42 final size:42
Alignment explanation
Indices: 20016527--20016780 Score: 312
Period size: 42 Copynumber: 6.0 Consensus size: 42
20016517 AGAACATGAC
* * *
20016527 CTTTAGCAGTTTTTTGAGAAAAGTGCCGCTAAAGGTCATGTT
1 CTTTAGCGGTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
* *
20016569 CTTTAGCGGCGTTTTGAGAAAAGCGCCGCTAAAGGTCATTTT
1 CTTTAGCGGTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
* *
20016611 CTTTAGCGGCGTTTTGAGAAAAGCGCCGCTAAAGGTCACGTT
1 CTTTAGCGGTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
* * **
20016653 CTTTAGCGGCGTTTTTTGAGAAAAACGATGCTAAAGGTCATGTT
1 CTTTAGC-G-GTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
* * **
20016697 CTTTAGCGGTGTTTTGAGAAAAGCACCGCTAAATGTCACATT
1 CTTTAGCGGTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
* *
20016739 CTTTAGCGGCG-TTTGTATGAAAAGCGCCGCTAAATGTCATGT
1 CTTTAGCGGTGTTTTG-A-GAAAAGCGCCGCTAAAGGTCATGT
20016781 CTCAAAAAAG
Statistics
Matches: 183, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
41 4 0.02
42 121 0.66
43 23 0.13
44 35 0.19
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGTGTTTTGAGAAAAGCGCCGCTAAAGGTCATGTT
Found at i:20016688 original size:128 final size:129
Alignment explanation
Indices: 20016535--20016777 Score: 373
Period size: 128 Copynumber: 1.9 Consensus size: 129
20016525 ACCTTTAGCA
** * *
20016535 GTTTTTTGAGAAAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCCGCTA
1 GTTTTTTGAGAAAAACGACGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCACCGCTA
**
20016600 AAGGTCATTTTCTTTAGCGGCGTTT-TGA-GAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGC
66 AAGGTCACATTCTTTAGCGGCGTTTGT-ATGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGC
* *
20016663 GTTTTTTGAGAAAAACGATGCTAAAGGTCATGTTCTTTAGCGGTGTTTTGAGAAAAGCACCGCTA
1 GTTTTTTGAGAAAAACGACGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCACCGCTA
* *
20016728 AATGTCACATTCTTTAGCGGCGTTTGTATGAAAAGCGCCGCTAAATGTCA
66 AAGGTCACATTCTTTAGCGGCGTTTGTATGAAAAGCGCCGCTAAAGGTCA
20016778 TGTCTCAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
128 82 0.80
129 21 0.20
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (129 bp):
GTTTTTTGAGAAAAACGACGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCACCGCTA
AAGGTCACATTCTTTAGCGGCGTTTGTATGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGC
Found at i:20016699 original size:86 final size:86
Alignment explanation
Indices: 20016538--20016752 Score: 326
Period size: 86 Copynumber: 2.5 Consensus size: 86
20016528 TTTAGCAGTT
* * * *
20016538 TTTTGAGAAAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCG--TTTTGAGAAAAGCGCCGCTAA
1 TTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTTTTGAGAAAAACGACGCTAA
*
20016601 AGGTCATTTTCTTTAGCGGCG
66 AGGTCATGTTCTTTAGCGGCG
*
20016622 TTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTTTTGAGAAAAACGATGCTAA
1 TTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTTTTGAGAAAAACGACGCTAA
*
20016687 AGGTCATGTTCTTTAGCGGTG
66 AGGTCATGTTCTTTAGCGGCG
* * *
20016708 TTTTGAGAAAAGCACCGCTAAATGTCACATTCTTTAGCGGCGTTT
1 TTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTT
20016753 GTATGAAAAG
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
84 40 0.34
86 79 0.66
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (86 bp):
TTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTTTTGAGAAAAACGACGCTAA
AGGTCATGTTCTTTAGCGGCG
Found at i:20016885 original size:42 final size:42
Alignment explanation
Indices: 20016793--20016976 Score: 235
Period size: 42 Copynumber: 4.3 Consensus size: 42
20016783 CAAAAAAGCT
* ** *
20016793 GCTAAAGGTTATGTTCTTTAGC-GTTTTTTGTATGAAAAGTGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTTG-A-GAAAAGCGCC
*
20016836 GCTAAAGGTCATGTTCTTTAGCAGCGTTTTGAGAAAAGCGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCC
* * *
20016878 ACTAAAGGTCACGTTTTTTAGCGGCGTTTTGAGAAAAGCGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCC
* * *
20016920 GCTAAAGGTCACGTTCTTTAGTGGCGTTTTTGAAAAAAGCGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCG-TTTTGAGAAAAGCGCC
20016963 GCTAAAGGTCATGT
1 GCTAAAGGTCATGT
20016977 CTCAAAACAC
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 70 0.56
43 50 0.40
44 6 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCC
Found at i:20016939 original size:196 final size:194
Alignment explanation
Indices: 20016594--20017008 Score: 557
Period size: 196 Copynumber: 2.1 Consensus size: 194
20016584 GAGAAAAGCG
*
20016594 CCGCTAAAGGTCATTTTCTTTAGCGGCGTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAG
* ** * *
20016659 CGGCGTTTTTTGAGAAAAACGATGCTAAAGGTCATGTTCTTTAGCGGTGTTTTGAGAAAAGCACC
66 CAGCG-TTTTTGAGAAAAACGACACTAAAGGTCACGTTCTTTAGCGGCGTTTTGAGAAAAGCACC
* *
20016724 GCTAAATGTCACATTCTTTAGCGGCGTTTGTATG-AAAAGCGCCGCTAAATGTCATGTCTCAAAA
130 GCTAAAGGTCACATTCTTTAGCGGCGTTT-T-TGAAAAAGCGCCGCTAAAGGTCATGTCTCAAAA
20016788 AA
193 AA
* * ** * *
20016790 GCTGCTAAAGGTTATGTTCTTTAGC-GTTTTTTGTATGAAAAGTGCCGCTAAAGGTCATGTTCTT
1 -CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTG-A-GAAAAGCGCCGCTAAAGGTCACGTTCTT
* * * *
20016854 TAGCAGCG-TTTTGAGAAAAGCGCCACTAAAGGTCACGTTTTTTAGCGGCGTTTTGAGAAAAGCG
63 TAGCAGCGTTTTTGAGAAAAACGACACTAAAGGTCACGTTCTTTAGCGGCGTTTTGAGAAAAGCA
* *
20016918 CCGCTAAAGGTCACGTTCTTTAGTGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGTCTCAAA
128 CCGCTAAAGGTCACATTCTTTAGCGGCGTTTTTG-AAAAAGCGCCGCTAAAGGTCATGTCTCAAA
*
20016983 ACA
192 AAA
20016986 CCGCTAAAGGTCATGTTCTTTAG
1 CCGCTAAAGGTCATGTTCTTTAG
20017009 TGGTGTTTCT
Statistics
Matches: 191, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
194 2 0.01
195 22 0.12
196 112 0.59
197 22 0.12
198 33 0.17
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (194 bp):
CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAG
CAGCGTTTTTGAGAAAAACGACACTAAAGGTCACGTTCTTTAGCGGCGTTTTGAGAAAAGCACCG
CTAAAGGTCACATTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAGGTCATGTCTCAAAAAA
Found at i:20017156 original size:143 final size:143
Alignment explanation
Indices: 20016980--20017268 Score: 524
Period size: 143 Copynumber: 2.0 Consensus size: 143
20016970 GTCATGTCTC
*
20016980 AAAACACCGCTAAAGGTCATGTTCTTTAGTGGTGTTTCTTACCTAAACGCCGTAAAATGTTAGCG
1 AAAACACCGCTAAAGGTCATGTTCTTTAGTGGTGTTTCTTACCTAAACGCCGCAAAATGTTAGCG
*
20017045 GTGTTATCTTTAGCGGCATTTTTTGCTCCCAAAAAAAGGCCACTAAAAACCTGTTTTGCTGTAGT
66 GTGTTATCTTTAGCGGAATTTTTTGCTCCCAAAAAAAGGCCACTAAAAACCTGTTTTGCTGTAGT
20017110 GTCCGTCATATAT
131 GTCCGTCATATAT
* *
20017123 AAAACACCGCTAACGGTCATGTTCTTTAGTGGTGTTTCTTACCTAAACGCCGCAAAATGTTAGTG
1 AAAACACCGCTAAAGGTCATGTTCTTTAGTGGTGTTTCTTACCTAAACGCCGCAAAATGTTAGCG
* *
20017188 GTGTTGTCTTTAGCGGAATTTTTTGCTCCCAAAAAAAGGCCGCTAAAAACCTGTTTTGCTGTAGT
66 GTGTTATCTTTAGCGGAATTTTTTGCTCCCAAAAAAAGGCCACTAAAAACCTGTTTTGCTGTAGT
20017253 GTCCGTCATATAT
131 GTCCGTCATATAT
20017266 AAA
1 AAA
20017269 CTTTGGTTTT
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (143 bp):
AAAACACCGCTAAAGGTCATGTTCTTTAGTGGTGTTTCTTACCTAAACGCCGCAAAATGTTAGCG
GTGTTATCTTTAGCGGAATTTTTTGCTCCCAAAAAAAGGCCACTAAAAACCTGTTTTGCTGTAGT
GTCCGTCATATAT
Found at i:20021349 original size:30 final size:30
Alignment explanation
Indices: 20021303--20021359 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
20021293 ATCCCGAGCC
20021303 TAGGGGCAAAAATGTAAATATGCAAAAGTT
1 TAGGGGCAAAAATGTAAATATGCAAAAGTT
* * * *
20021333 TAGGGGTAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAAATGTAAATATGCAAAA
20021360 TTTGAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATGCAAAAGTT
Found at i:20021831 original size:46 final size:46
Alignment explanation
Indices: 20021781--20021956 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
20021771 TGGTTGAGCA
20021781 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
20021827 TCCGAACTCGTAGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
20021872 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
20021920 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20021957 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 62 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20021937 original size:93 final size:93
Alignment explanation
Indices: 20021778--20021949 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
20021768 GGATGGTTGA
*
20021778 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTAGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTAGAGT
20021843 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
20021871 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTAGAG
20021935 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
20021950 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTAGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20029238 original size:46 final size:46
Alignment explanation
Indices: 20029188--20029363 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
20029178 TGGTTGAGCA
20029188 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20029234 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
20029279 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
20029327 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20029364 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:20029344 original size:93 final size:93
Alignment explanation
Indices: 20029185--20029356 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
20029175 GGATGGTTGA
* *
20029185 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20029250 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
20029278 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
20029343 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20029357 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20033241 original size:13 final size:13
Alignment explanation
Indices: 20033223--20033259 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20033213 TAATTTTCCT
20033223 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
20033236 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
* *
20033249 CTCCTTTCTTT
1 TTTCTTTCTTT
20033260 CCCATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:20036006 original size:15 final size:15
Alignment explanation
Indices: 20035944--20036017 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
20035934 AGATATATAT
20035944 AAATATTAATATAAA
1 AAATATTAATATAAA
*
20035959 AATATATTATTAGTTAAA
1 AA-ATATTAATA--TAAA
* * * *
20035977 AAACAATATTTTAAA
1 AAATATTAATATAAA
20035992 AAATATTAATATAAA
1 AAATATTAATATAAA
20036007 AAATATATAAT
1 AAATAT-TAAT
20036018 TTGTTATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 23 0.49
16 12 0.26
17 6 0.13
18 6 0.13
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (15 bp):
AAATATTAATATAAA
Found at i:20040865 original size:24 final size:22
Alignment explanation
Indices: 20040838--20040883 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
20040828 AAGAAAGAAA
*
20040838 AGGAAAAGTGCATATTTTAAAAAT
1 AGGAAAAG-GCA-ACTTTAAAAAT
20040862 AGGAAAAGGCAACTTTAAAAAT
1 AGGAAAAGGCAACTTTAAAAAT
20040884 TCAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 8 0.38
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (22 bp):
AGGAAAAGGCAACTTTAAAAAT
Found at i:20042929 original size:21 final size:20
Alignment explanation
Indices: 20042905--20042945 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20042895 TCATTTTGGG
20042905 AAGAAAGAAGGAGAAGAAGAA
1 AAGAAAGAA-GAGAAGAAGAA
*
20042926 AAGAAAGAAGAGAAGGAGAA
1 AAGAAAGAAGAGAAGAAGAA
20042946 GCAGGGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAGAGAAGAAGAA
Found at i:20043168 original size:21 final size:21
Alignment explanation
Indices: 20043144--20043186 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20043134 GATATTAAGG
*
20043144 TATGTTTGTATTTATTTTATA
1 TATGTATGTATTTATTTTATA
20043165 TATGTATGTATTTATTTTATA
1 TATGTATGTATTTATTTTATA
20043186 T
1 T
20043187 TTTCATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (21 bp):
TATGTATGTATTTATTTTATA
Found at i:20043388 original size:15 final size:15
Alignment explanation
Indices: 20043358--20043423 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
20043348 CTATTTTACG
*
20043358 AAAATAGTATAAAAAT
1 AAAATA-TAAAAAAAT
*
20043374 AAAATATTAAAAAAT
1 AAAATATAAAAAAAT
***
20043389 ATCTTACTAAAAAAAT
1 AAAATA-TAAAAAAAT
20043405 AAAATATGAAAAAAAT
1 AAAATAT-AAAAAAAT
20043421 AAA
1 AAA
20043424 TTTTGGGGGC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 11 0.28
16 28 0.72
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATATAAAAAAAT
Found at i:20043642 original size:151 final size:151
Alignment explanation
Indices: 20043460--20044131 Score: 1154
Period size: 151 Copynumber: 4.5 Consensus size: 151
20043450 GTTTTTTTTT
** *
20043460 TAAAATAATAT-AAAAATAAAGCACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAATTTTA
1 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
* * * *
20043524 AAAATATAAAAAAAGAGACAAAATTAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
66 AAAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
*
20043589 TACATTTGAAACATTATATAC
131 TACATTTGAAACATTATGTAC
20043610 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
1 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
* *
20043675 AAAATACAAACAAAGGGCCAAAATCAAGGTTATTTACTAAATTAATAT-AAAAACACTAAAATAA
66 AAAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
*
20043739 TACATTTGAACCATTATGTAC
131 TACATTTGAAACATTATGTAC
* *
20043760 TAAAATAATATAAAAAAATGAAATACGAAAATAGTATATTTTAAAAAATAAAATCTGAAAATTTT
1 TAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTT
20043825 AAAAATACAAACAAAGGG-CTAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAAT
65 AAAAATACAAACAAAGGGAC-AAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAAT
20043889 AATACATTTGAAACATTATGTAC
129 AATACATTTGAAACATTATGTAC
*
20043912 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCGAAAATTTTA
1 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
*
20043977 AAAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATAAAAAA-ACTAAAATAA
66 AAAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
20044041 TACATTTGAAACATTATGTAC
131 TACATTTGAAACATTATGTAC
*
20044062 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAGAATCCGAAAATTTTA
1 TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
20044127 AAAAT
66 AAAAT
20044132 TTTAAAAATA
Statistics
Matches: 496, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
150 157 0.32
151 291 0.59
152 48 0.10
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (151 bp):
TAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATTTTA
AAAATACAAACAAAGGGACAAAATCAGGGTTATTTACTAAATTAATATAAAAAACACTAAAATAA
TACATTTGAAACATTATGTAC
Found at i:20043941 original size:25 final size:27
Alignment explanation
Indices: 20043913--20043972 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
20043903 ATTATGTACT
20043913 AAAATA-ATA-TAAAAAATAAAATACG
1 AAAATAGATATTAAAAAATAAAATACG
*
20043938 AAAATAGTATATTTTAAAAAATAAAATTCG
1 AAAATAG-ATA--TTAAAAAATAAAATACG
20043968 AAAAT
1 AAAAT
20043973 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.21
27 3 0.10
30 20 0.69
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (27 bp):
AAAATAGATATTAAAAAATAAAATACG
Found at i:20050125 original size:16 final size:16
Alignment explanation
Indices: 20050104--20050136 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20050094 TAATTTGATG
20050104 GTCCCGTTCTATTAAT
1 GTCCCGTTCTATTAAT
20050120 GTCCCGTTCTATTAAT
1 GTCCCGTTCTATTAAT
20050136 G
1 G
20050137 CCCCTCTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.42
Consensus pattern (16 bp):
GTCCCGTTCTATTAAT
Found at i:20050702 original size:16 final size:16
Alignment explanation
Indices: 20050681--20050713 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20050671 TAGTTTTTTT
20050681 ACTAACAATAATAATA
1 ACTAACAATAATAATA
20050697 ACTAACAATAATAATA
1 ACTAACAATAATAATA
20050713 A
1 A
20050714 GGGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
ACTAACAATAATAATA
Found at i:20050712 original size:43 final size:42
Alignment explanation
Indices: 20050605--20050744 Score: 166
Period size: 43 Copynumber: 3.4 Consensus size: 42
20050595 AATATAAATC
* *
20050605 AACAATAATAATAACTAACAACAAT--T-AAGGTTTTTTACT
1 AACAATAATAATAACTAACAATAATAATAAAGTTTTTTTACT
* **
20050644 AAC---AATAATAACCAACAATCCTAATAATAGTTTTTTTACT
1 AACAATAATAATAACTAACAATAATAATAA-AGTTTTTTTACT
*
20050684 AACAATAATAATAACTAACAATAATAATAAGGGTTTTTTTACT
1 AACAATAATAATAACTAACAATAATAATAA-AGTTTTTTTACT
20050727 AACAATAATAATAACTAA
1 AACAATAATAATAACTAA
20050745 AAAAAAATCA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
36 15 0.18
38 1 0.01
39 4 0.05
40 14 0.17
43 50 0.60
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (42 bp):
AACAATAATAATAACTAACAATAATAATAAAGTTTTTTTACT
Found at i:20050867 original size:22 final size:22
Alignment explanation
Indices: 20050818--20050864 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
20050808 AAAAAATATA
* *
20050818 CTTTCTCTTTTCTATTTTTTTT
1 CTTTCTCCTTTCTATTCTTTTT
*
20050840 CCTTCTCCTTTCT-TTCTTTTT
1 CTTTCTCCTTTCTATTCTTTTT
20050861 CTTT
1 CTTT
20050865 TCTTCTCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (22 bp):
CTTTCTCCTTTCTATTCTTTTT
Found at i:20050869 original size:25 final size:26
Alignment explanation
Indices: 20050826--20050874 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
20050816 TACTTTCTCT
20050826 TTTCTATTTTTTTTCCTTCTCCTTTC
1 TTTCTATTTTTTTTCCTTCTCCTTTC
20050852 TTTCT-TTTTCTTTT-CTTCTCCTT
1 TTTCTATTTT-TTTTCCTTCTCCTT
20050875 GCTGCTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTCTATTTTTTTTCCTTCTCCTTTC
Found at i:20059969 original size:26 final size:23
Alignment explanation
Indices: 20059940--20059997 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
20059930 TTGTTTTCAT
20059940 ATTTTAAGTATATTATTTTATTTAAA
1 ATTTTAAGTATA-TA-TTTA-TTAAA
*
20059966 ATTTAGTAATTATATATTTATTAAA
1 ATTT--TAAGTATATATTTATTAAA
20059991 ATTTTAA
1 ATTTTAA
20059998 ATAGAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.10
25 9 0.31
26 8 0.28
27 2 0.07
28 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
ATTTTAAGTATATATTTATTAAA
Found at i:20064445 original size:20 final size:19
Alignment explanation
Indices: 20064422--20064490 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
20064412 AAATGGAAAT
20064422 AAATAAATAAAAATTTAGAA
1 AAATAAATAAAAATTTA-AA
* * *
20064442 AAATATAT-ATAATCT-AA
1 AAATAAATAAAAATTTAAA
*
20064459 AAA-AAATATAAATTATAAA
1 AAATAAATAAAAATT-TAAA
20064478 AAAT-AATAAAAAT
1 AAATAAATAAAAAT
20064491 AAATTTTACA
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
16 3 0.08
17 8 0.22
18 1 0.03
19 18 0.49
20 7 0.19
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
AAATAAATAAAAATTTAAA
Found at i:20064467 original size:16 final size:16
Alignment explanation
Indices: 20064426--20064487 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 16
20064416 GGAAATAAAT
*
20064426 AAATAAAAATTTAGAAAA
1 AAATATAAA-TTA-AAAA
*
20064444 ATATATATAATCTAAAAA
1 AAATATA-AAT-TAAAAA
*
20064462 AAATATAAATTATAAA
1 AAATATAAATTAAAAA
20064478 AAATAATAAA
1 AAAT-ATAAA
20064488 AATAAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.24
17 8 0.22
18 16 0.43
19 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AAATATAAATTAAAAA
Found at i:20064492 original size:23 final size:24
Alignment explanation
Indices: 20064457--20064508 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
20064447 TATATAATCT
20064457 AAAA-AAAATATAAATTATA-AAA
1 AAAATAAAATATAAATTATACAAA
*
20064479 AATAATAAAA-ATAAATTTTACAAA
1 AA-AATAAAATATAAATTATACAAA
20064503 AAAATA
1 AAAATA
20064509 CGGTAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 15 0.58
24 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATAAAATATAAATTATACAAA
Found at i:20064615 original size:23 final size:23
Alignment explanation
Indices: 20064589--20064642 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
20064579 AAAACTTTCT
*
20064589 TTTAAAAATATAT-TTTATAAAAA
1 TTTAAAAATATATAATTAT-AAAA
20064612 TTT-AAAATATATAATTATAAAA
1 TTTAAAAATATATAATTATAAAA
20064634 TTCTAAAAA
1 TT-TAAAAA
20064643 GGTATACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 15 0.56
23 8 0.30
24 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAAATATATAATTATAAAA
Found at i:20065193 original size:15 final size:14
Alignment explanation
Indices: 20065163--20065210 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
20065153 AAATATTAAT
*
20065163 ATAAAATTCATATA
1 ATAAAATCCATATA
*
20065177 ATAAAATCTATTATA
1 ATAAAATCCA-TATA
*
20065192 ATGAAATCCATATA
1 ATAAAATCCATATA
20065206 ATAAA
1 ATAAA
20065211 TGAATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAAATCCATATA
Found at i:20073077 original size:46 final size:45
Alignment explanation
Indices: 20072991--20073109 Score: 141
Period size: 46 Copynumber: 2.6 Consensus size: 45
20072981 ATTTCGTAGT
* * *
20072991 CGATGCTTGTCCCAAACATGTCTTACACAGGCTTACGTCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACAGACTTA-GTCTCGAGGC
* *
20073037 CGATGCATGTCCCAGACATGTCTTACATTAGCACTT-GTCTCGATGC
1 CGATGCATGTCCCAGACATGTCTTACA-CAG-ACTTAGTCTCGAGGC
20073083 CGATGCCATGTCCCAGACATGTTCTTA
1 CGATG-CATGTCCCAGACATG-TCTTA
20073110 TACTGGCTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 39 0.61
47 17 0.27
48 8 0.12
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACAGACTTAGTCTCGAGGC
Found at i:20075941 original size:45 final size:45
Alignment explanation
Indices: 20075882--20075969 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
20075872 GAACTATGTG
*
20075882 ATCTGAACTAATTGAGTTATGGTCTGAGTGCGTGATATATGTGGC
1 ATCTGAACTAATTGAGTTATGGTCTGAGTGCATGATATATGTGGC
* * *
20075927 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATGTATGTG
1 ATCTGAACTAATTGAGTTATGGTCTGAGTGCATGATATATGTG
20075970 ACACATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (45 bp):
ATCTGAACTAATTGAGTTATGGTCTGAGTGCATGATATATGTGGC
Found at i:20083793 original size:28 final size:28
Alignment explanation
Indices: 20083753--20083822 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
20083743 ATGAAAATTT
* * * *
20083753 CACTAAGCGTGCGAGTTTGGTTA-ACGAG
1 CACTAAGTGTGCGAGTTTGATTATA-AAA
20083781 CACTAAGTGTGCGAGTTTGATTATAAAA
1 CACTAAGTGTGCGAGTTTGATTATAAAA
20083809 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
20083823 AGGAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 36 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATAAAA
Found at i:20088560 original size:68 final size:64
Alignment explanation
Indices: 20088441--20088678 Score: 221
Period size: 68 Copynumber: 3.6 Consensus size: 64
20088431 CAGATGGTAT
* * * * *
20088441 GTAGCTAGGTCACATGTGTAATACGA-GATGTATACCATGT-GTACAAGAGAGCTACGAGACATT
1 GTAGCTAGGTCGCATGGGTGATACTATG-TGTACACCATGTAG-ACAAGAGAGCTACGAG--A-T
*
20088504 ATGAG
61 A-GAA
* *
20088509 GTAGTTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAGAT
1 GTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAGAA
* * * * * * *
20088573 GTAGCTAGGTTGCATGTGTGGTTCTAGGTGAAGGACACCATGTAAACAAGAGAGCTACGAGATA-
1 GTAGCTAGGTCGCATGGGTGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGATAG
20088637 AA
63 AA
* *
20088639 GTGGCTAGGTCACATGGGTGATACTATGTGTACACCATGT
1 GTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGT
20088679 GTACAAAAGA
Statistics
Matches: 141, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
63 10 0.07
64 25 0.18
65 2 0.01
66 24 0.17
67 30 0.21
68 48 0.34
69 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (64 bp):
GTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAGAA
Found at i:20094412 original size:14 final size:14
Alignment explanation
Indices: 20094393--20094428 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
20094383 ATGCCATGAA
20094393 GTGAGTGTAAGTAT
1 GTGAGTGTAAGTAT
20094407 GTGAGTGTAAGTAT
1 GTGAGTGTAAGTAT
20094421 GTGAGTGT
1 GTGAGTGT
20094429 TTAAGGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (14 bp):
GTGAGTGTAAGTAT
Found at i:20103938 original size:46 final size:46
Alignment explanation
Indices: 20103888--20104013 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
20103878 TGGTTGAGCA
*
20103888 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
20103934 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
20103980 CCCGAGCTCGTTGATTTGAGTTCGATTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
20104014 GGGGCGGGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20108148 original size:49 final size:49
Alignment explanation
Indices: 20108088--20108446 Score: 519
Period size: 47 Copynumber: 7.6 Consensus size: 49
20108078 GATAATTGTG
20108088 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
20108135 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
20108182 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
20108231 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
20108280 ATGTGAAA--GTATATATATGTGATCAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
20108327 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
20108374 ATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
20108421 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
20108447 TCCCGAAGGG
Statistics
Matches: 285, Mismatches: 17, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
46 2 0.01
47 183 0.64
48 5 0.02
49 95 0.33
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:20108158 original size:96 final size:94
Alignment explanation
Indices: 20108088--20108446 Score: 506
Period size: 96 Copynumber: 3.8 Consensus size: 94
20108078 GATAATTGTG
20108088 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
20108153 GTGATAAGGCCG-AATGGCCAATGTGATGA
66 GTGATAAGG-CGTAATGGCCAATGTGATGA
20108182 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
20108247 ACATGTGATAAGGCCTAATGGCCGATGTGATGA
64 --ATGTGATAAGGCGTAATGGCCAATGTGATGA
* * *
20108280 ATGTGAAAGTATATATATGTGATCAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* *
20108345 GTGATAAGGCCTAATGGCCGATGTGATGA
66 GTGATAAGGCGTAATGGCCAATGTGATGA
* * * * * * * * *
20108374 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAA
1 ATGTGAATGTATATATATGTGATAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
20108438 TGTGATAAG
65 TGTGATAAG
20108447 TCCCGAAGGG
Statistics
Matches: 246, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
93 3 0.01
94 97 0.39
95 2 0.01
96 109 0.44
97 3 0.01
98 32 0.13
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCGTAATGGCCAATGTGATGA
Found at i:20112464 original size:14 final size:14
Alignment explanation
Indices: 20112445--20112471 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20112435 ATATTTGGCT
20112445 TGTTCTTAATTATG
1 TGTTCTTAATTATG
20112459 TGTTCTTAATTAT
1 TGTTCTTAATTAT
20112472 TGTCTTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTATG
Found at i:20130013 original size:49 final size:49
Alignment explanation
Indices: 20129936--20130180 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 49
20129926 TAGCCGAAGC
* * * *
20129936 TATCTGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * * *
20129985 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTAAACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC-AAT
* * * *
20130035 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-T
* * * * *
20130086 TATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
20130135 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
20130181 TCATAATAGC
Statistics
Matches: 165, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:20130863 original size:30 final size:30
Alignment explanation
Indices: 20130827--20130887 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
20130817 CCTTTAATAC
20130827 AAACTTTGGAAAAATTAC-CATTTTGCCCCT
1 AAACTTTGGAAAAATTACAC-TTTTGCCCCT
* * *
20130857 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
20130887 A
1 A
20130888 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:20151482 original size:14 final size:15
Alignment explanation
Indices: 20151453--20151485 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20151443 GTTTAAATAC
20151453 TTATGTGTTGATGTT
1 TTATGTGTTGATGTT
*
20151468 TTATGT-TTTATGTT
1 TTATGTGTTGATGTT
20151482 TTAT
1 TTAT
20151486 ATATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.67
Consensus pattern (15 bp):
TTATGTGTTGATGTT
Found at i:20154698 original size:39 final size:39
Alignment explanation
Indices: 20154631--20154892 Score: 402
Period size: 39 Copynumber: 6.7 Consensus size: 39
20154621 ACAAAGCATG
* *
20154631 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTGT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCT-T
*
20154672 -GGGACTTTATCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
20154711 CGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
20154750 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
20154789 CGGGACTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
20154828 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
20154867 CGGGACTTAGCCCAGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
20154893 TTATAAAGTC
Statistics
Matches: 207, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 189 0.91
40 18 0.09
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:20155036 original size:28 final size:28
Alignment explanation
Indices: 20154965--20155037 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
20154955 ATTTAATCAT
* *
20154965 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACATTAAGTGTCATTC
*
20154993 TCAATATCTCGCACATTAAGTGTCATTC
1 TCAATATTTCGCACATTAAGTGTCATTC
*
20155021 TCAATATTTCGTACATT
1 TCAATATTTCGCACATT
20155038 GAGTACCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (28 bp):
TCAATATTTCGCACATTAAGTGTCATTC
Found at i:20164859 original size:57 final size:58
Alignment explanation
Indices: 20164798--20164911 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
20164788 CATTTCCAAA
* * * *
20164798 ATATGCTCACA-AGAGCTTA-ATCAGGATTACCCGTCCGGGCCAAATCCTATCTGTAAC
1 ATATGCTCA-AGAGAGCTTATATCAAGATTACCAGCCCAGGCCAAATCCTATCTGTAAC
* * *
20164855 ATATGCTCAAGAGGGCTTATATCAAGATTACCAGCCCAGGCTAAATCCTTTCTGTAA
1 ATATGCTCAAGAGAGCTTATATCAAGATTACCAGCCCAGGCCAAATCCTATCTGTAA
20164912 TAACGTCAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.02
57 16 0.33
58 31 0.65
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (58 bp):
ATATGCTCAAGAGAGCTTATATCAAGATTACCAGCCCAGGCCAAATCCTATCTGTAAC
Found at i:20182083 original size:21 final size:20
Alignment explanation
Indices: 20182055--20182094 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
20182045 GATCTATACG
20182055 AATAAATTT-AACATCAATTT
1 AATAAATTTAAAC-TCAATTT
20182075 AATACAATTTAAACTCAATT
1 AATA-AATTTAAACTCAATT
20182095 CAGTCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 11 0.61
22 3 0.17
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTTAAACTCAATTT
Found at i:20184548 original size:24 final size:23
Alignment explanation
Indices: 20184487--20184549 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
20184477 CGAACACACC
* *
20184487 ACAGCTCATATGAGCTTCCTGTT
1 ACAGCTCGTATGAGCTTCCAGTT
* *
20184510 ATTTAGCTCGCATGAGCTTCCAGCTT
1 A--CAGCTCGTATGAGCTTCCAG-TT
20184536 ACAGCTCGTATGAG
1 ACAGCTCGTATGAG
20184550 TATACAAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.03
24 11 0.35
25 16 0.52
26 3 0.10
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (23 bp):
ACAGCTCGTATGAGCTTCCAGTT
Found at i:20185615 original size:21 final size:21
Alignment explanation
Indices: 20185591--20185635 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20185581 AACACGTCCA
20185591 TGTGAAAGGACAACATGCCCG
1 TGTGAAAGGACAACATGCCCG
*
20185612 TGTGAAAGGGCAACATGCCCG
1 TGTGAAAGGACAACATGCCCG
20185633 TGT
1 TGT
20185636 AGTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.31, T:0.18
Consensus pattern (21 bp):
TGTGAAAGGACAACATGCCCG
Found at i:20189113 original size:9 final size:9
Alignment explanation
Indices: 20189099--20189126 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20189089 TGAATTGAGT
20189099 CTTCAACTC
1 CTTCAACTC
20189108 CTTCAACTC
1 CTTCAACTC
20189117 CTTCAACTC
1 CTTCAACTC
20189126 C
1 C
20189127 ATTAGAGGTA
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:0.46, G:0.00, T:0.32
Consensus pattern (9 bp):
CTTCAACTC
Found at i:20193643 original size:43 final size:43
Alignment explanation
Indices: 20193582--20193765 Score: 314
Period size: 43 Copynumber: 4.3 Consensus size: 43
20193572 GCTGGTATTA
* * *
20193582 TATTCGGGCCTTCGTGCCTATCATGCTTTGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
20193625 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
20193668 TATTCAGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
20193711 TATTCGAGCCTTCGTGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
20193754 TATTCGGGCCTT
1 TATTCGGGCCTT
20193766 TGAGCTGCTA
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 133 1.00
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.33
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:20195683 original size:13 final size:13
Alignment explanation
Indices: 20195662--20195693 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20195652 ACTTAAGGGT
20195662 CACACGGCCAAGG
1 CACACGGCCAAGG
*
20195675 CACATGGCCAAGG
1 CACACGGCCAAGG
20195688 CACACG
1 CACACG
20195694 CCCGTGTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.31, C:0.38, G:0.28, T:0.03
Consensus pattern (13 bp):
CACACGGCCAAGG
Found at i:20196749 original size:48 final size:47
Alignment explanation
Indices: 20196537--20196766 Score: 182
Period size: 48 Copynumber: 4.8 Consensus size: 47
20196527 GGTATAATAA
* * * *
20196537 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCATCC--ATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACAC-TCCATATC-AGG
* * * *
20196584 CGATGCCATGTCCCATACATGGTCTTACACTAACTA-TCGAAATCGAGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACTCCATATC-AGG
** * * *
20196632 CTGACACCATGTCCTAGACATGGTCTTACACT-AGCTCTCACATATCCGCG
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGA-CACTC-CATATCAG-G
* * *
20196682 CTGATGCCATCTCCCAGACATGGTCTTACACTGACAACTCTATA-CATGT
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGAC-ACTCCATATCA-GG
20196731 CGATGCCATGTCCCAGACATGGTCTTACACTGACAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACAC
20196767 ATCTCGTAGC
Statistics
Matches: 147, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
46 2 0.01
47 32 0.22
48 39 0.27
49 32 0.22
50 38 0.26
51 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACACTCCATATCAGG
Found at i:20196819 original size:40 final size:39
Alignment explanation
Indices: 20196746--20196825 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 39
20196736 CCATGTCCCA
*
20196746 GACATGGTCTTACACTGACACATCTCGTAGCCGATGCAT
1 GACATGGTCTTACACTGACACATCTCGAAGCCGATGCAT
*
20196785 GACAT-GTCTTACACTGTCTTACATCTC-AAGGCCGATGCAT
1 GACATGGTCTTACACTGAC--ACATCTCGAA-GCCGATGCAT
20196825 G
1 G
20196826 TCCCAGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
38 12 0.33
39 6 0.17
40 18 0.50
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (39 bp):
GACATGGTCTTACACTGACACATCTCGAAGCCGATGCAT
Found at i:20201547 original size:11 final size:11
Alignment explanation
Indices: 20201531--20201557 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20201521 ATCATTAAGA
20201531 AGACACAATGC
1 AGACACAATGC
20201542 AGACACAATGC
1 AGACACAATGC
20201553 AGACA
1 AGACA
20201558 ATAAGAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (11 bp):
AGACACAATGC
Found at i:20204611 original size:4 final size:4
Alignment explanation
Indices: 20204602--20204632 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
20204592 ATTTACAACA
20204602 AATT AATT AATT AATT AATT AATT AAATT AA
1 AATT AATT AATT AATT AATT AATT -AATT AA
20204633 ATTGTTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:20205110 original size:64 final size:64
Alignment explanation
Indices: 20205027--20205218 Score: 224
Period size: 64 Copynumber: 3.0 Consensus size: 64
20205017 ATTTTCATAA
* * * * * *
20205027 CACATTTAATTAGGTGCATTTGATTCATTTCGATCATAGCGGCCTAATTATTTGACATCAGCAT
1 CACATCTAATTAGGAGCATTTGATTCATTTTGATCATAGCAGCCTAATTATGTGACATAAGCAT
* * *
20205091 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATGTGTCATAAGCAT
1 CACATCTAATTAGGAGCATTTGATTCATTTTGATCATAGCAGCCTAATTATGTGACATAAGCAT
** * * * * *
20205155 CATGTCTAATTAGGAGTATTTGATTCATTTTGGTCATAGTATCCTAATTA-GTTGGCATAAGCAT
1 CACATCTAATTAGGAGCATTTGATTCATTTTGATCATAGCAGCCTAATTATG-TGACATAAGCAT
20205219 GATACATCAA
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 110 0.99
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (64 bp):
CACATCTAATTAGGAGCATTTGATTCATTTTGATCATAGCAGCCTAATTATGTGACATAAGCAT
Found at i:20208189 original size:45 final size:45
Alignment explanation
Indices: 20208134--20208351 Score: 151
Period size: 45 Copynumber: 4.9 Consensus size: 45
20208124 GATCATGAAA
* *
20208134 ATCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATCGAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCGAAG
** **
20208179 ATCTTATCTCCCTGAAGTTGCAGCAGAGCAGA-TCGAAGAT-GGTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATCGAAG
* * * * * * * * ** *
20208223 AATCTTATCTCCATGTA-TCGAAAATGAAGCAGATTTTACCA-C-CAG
1 -ATCTTATCTCCCTGAAGTTG-CAGTGGAGCAGA-CTGAAGATCGAAG
* * * *
20208268 -CCTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCGAAG
* *
20208312 ATCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
20208352 GGTGAATCTT
Statistics
Matches: 124, Mismatches: 39, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
42 3 0.02
43 19 0.15
44 9 0.07
45 90 0.73
46 2 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (45 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCGAAG
Found at i:20208361 original size:45 final size:45
Alignment explanation
Indices: 20208269--20208367 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
20208259 TACCACCAGC
* * * *
20208269 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAGAT
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGATTGAAGAT
20208314 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGATGGTG-A-AT
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGAT--TGAAGAT
20208359 CTTATCTCC
1 CTTATCTCC
20208368 ATGCATCAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 45 0.94
46 1 0.02
47 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGATTGAAGAT
Found at i:20208387 original size:133 final size:133
Alignment explanation
Indices: 20208136--20208435 Score: 487
Period size: 133 Copynumber: 2.3 Consensus size: 133
20208126 TCATGAAAAT
20208136 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATCGAAGATCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATCGAAGATCTTATCTCCCTGAAGTTGCA
* *
20208201 GCAGAGCAGATCGAAGATGGTGAATCTTATCTCCATGTATCGAAAATGAAGCAGATTTTACCACC
66 GCAGAGCAGACCGAAGATGGTGAATCTTATCTCCATGCATCGAAAATGAAGCAGATTTTACCACC
20208266 AGC
131 AGC
*
20208269 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATTGAAGATCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATCGAAGATCTTATCTCCCTGAAGTTGCA
* * * *
20208334 GCGGAGCAGACCGAAGATGGTGAATCTTATCTCCATGCATC-AGCAATGGAGCAGATTTTACCAT
66 GCAGAGCAGACCGAAGATGGTGAATCTTATCTCCATGCATCGA-AAATGAAGCAGATTTTACCAC
20208398 CAGC
130 CAGC
* * *
20208402 CTTATCTCTCT-AAGTTGCAGTGGAGTAGATTGAA
1 CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAA
20208436 AATGGCGAAT
Statistics
Matches: 156, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
132 22 0.14
133 134 0.86
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (133 bp):
CTTATCTCCCTGAGGTTGCAGTGGAGTAGACTGAAGATCGAAGATCTTATCTCCCTGAAGTTGCA
GCAGAGCAGACCGAAGATGGTGAATCTTATCTCCATGCATCGAAAATGAAGCAGATTTTACCACC
AGC
Found at i:20208446 original size:87 final size:89
Alignment explanation
Indices: 20208314--20208499 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 89
20208304 GATTGAAGAT
* * * *
20208314 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGATGGTGAATCTTATCTCCATGCATCA-GC
1 CTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAAATGGCGAATCTTATATCCATGCA-CAGGC
*
20208378 AATGGAGCAGATTTTA-CCA-TCAGC
65 AATGGAGCAAATTTTAGCCACT-AGC
* * ** *
20208402 CTTATCTCTCT-AAGTTGCAGTGGAGTAGATTGAAAATGGCGAATCTTATATCCATGTACAGGCA
1 CTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAAATGGCGAATCTTATATCCATGCACAGGCA
*
20208466 ATGGAGCAAATTTTAGCCACTGGC
66 ATGGAGCAAATTTTAGCCACTAGC
20208490 CTTATCTCTC
1 CTTATCTCTC
20208500 GGAGGAAGCA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 56 0.67
88 25 0.30
89 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (89 bp):
CTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAAATGGCGAATCTTATATCCATGCACAGGCA
ATGGAGCAAATTTTAGCCACTAGC
Found at i:20208878 original size:43 final size:45
Alignment explanation
Indices: 20208817--20208912 Score: 142
Period size: 43 Copynumber: 2.2 Consensus size: 45
20208807 AGCCCCAAAC
* **
20208817 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTG-AG-T
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
*
20208860 CTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
20208905 CTTATCTC
1 CTTATCTC
20208913 CCTTAGCCGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 36 0.78
44 2 0.04
45 8 0.17
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (45 bp):
CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
Found at i:20208892 original size:180 final size:175
Alignment explanation
Indices: 20208590--20209094 Score: 636
Period size: 180 Copynumber: 2.9 Consensus size: 175
20208580 GGAAAAGGCA
* * * * * *
20208590 AATCTTATCTCTATGTATCGGCAATGGAGCAAAATTAAGCCTCAAGCCTTATCTCTCTGAGGTAG
1 AATCTTATCTCCATGTATCAGTAATGGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTAG
* *
20208655 CAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAAAAAGCAGACTG-TGAATT
66 CAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAG-ATT
* ** *
20208719 GAAGATTTTATCTCCCTGAAGTTGCAGCGGAGTAGATCTTCATAGATGGC
130 GAAGATCTTATCTCCCT-AAGCCGCAGCGGAGCAGATC--CA-AGATGGC
* * * * *
20208769 TAATCTTATCTCCATTTATCAGTAATGGAGTAGATTTGAGCCCCAAACCTTATCTCTCTGAGGTA
1 -AATCTTATCTCCATGTATCAGTAATGGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTA
20208834 GCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATT
65 GCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATT
* * *
20208899 GAAGATCTTATCTCCCTTAGCCGTAGCGGAGCAGATCGAAGATGGC
130 GAAGATCTTATCTCCCTAAGCCGCAGCGGAGCAGATCCAAGATGGC
* * *
20208945 AAGTCTTATCTCCATGTATCAGTAATGGAGCAGATTTTAGCCACTAGCCTTATCCCTCTGAGGTA
1 AA-TCTTATCTCCATGTATCAGTAATGGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTA
** * * * *
20209010 GCAAGAGAGCAGGTTGGCGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTAAAGAT
65 GCAAGAGAGCAGGTTGAAGATTG-AGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGAT
* * *
20209075 TAAAAATC-TATTTCCCTAAG
129 TGAAGATCTTATCTCCCTAAG
20209095 TAGTTGTGGA
Statistics
Matches: 286, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
175 2 0.01
176 93 0.33
177 44 0.15
179 15 0.05
180 131 0.46
181 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (175 bp):
AATCTTATCTCCATGTATCAGTAATGGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAGGTAG
CAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATTG
AAGATCTTATCTCCCTAAGCCGCAGCGGAGCAGATCCAAGATGGC
Found at i:20210863 original size:14 final size:14
Alignment explanation
Indices: 20210846--20210874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20210836 TATACATAGA
20210846 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
20210860 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
20210874 A
1 A
20210875 AATCTACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:20210925 original size:30 final size:31
Alignment explanation
Indices: 20210867--20210925 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
20210857 TTTATTTTTA
* * *
20210867 TTTTTTTAAATCTACTTGTATACGTAATTAT
1 TTTTTTTAAATCTACTTGCAAACATAATTAT
*
20210898 TTTTTTTAAATCTA-TTGCAAATATAATT
1 TTTTTTTAAATCTACTTGCAAACATAATT
20210926 TATGATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (31 bp):
TTTTTTTAAATCTACTTGCAAACATAATTAT
Found at i:20212729 original size:20 final size:20
Alignment explanation
Indices: 20212696--20212750 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
20212686 TATTGAAGTA
*
20212696 TTTAATATTATAAATTTATATT
1 TTTAA-ATT-TAAATTTAAATT
20212718 TTTAAATTTAAATTTAAATT
1 TTTAAATTTAAATTTAAATT
* *
20212738 TTTTATTTTAAAT
1 TTTAAATTTAAAT
20212751 AAACCTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 22 0.73
21 3 0.10
22 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAATTTAAATTTAAATT
Found at i:20213729 original size:17 final size:17
Alignment explanation
Indices: 20213687--20213722 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20213677 ACTAGAGTTC
20213687 TATAAGCTAAAGGGATT
1 TATAAGCTAAAGGGATT
20213704 TATAAGCTAAAGGGATT
1 TATAAGCTAAAGGGATT
20213721 TA
1 TA
20213723 ATAGCTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (17 bp):
TATAAGCTAAAGGGATT
Found at i:20231634 original size:27 final size:27
Alignment explanation
Indices: 20231600--20231772 Score: 229
Period size: 27 Copynumber: 6.4 Consensus size: 27
20231590 TGGATAAGTT
* *
20231600 GTAGAATTACCGAAATATCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
20231627 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20231654 GTAGAATTACCGAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20231681 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
20231708 GTAGAAATACCAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
20231735 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
20231762 GTAAAATTACC
1 GTAGAATTACC
20231773 ATTTTGCCCC
Statistics
Matches: 128, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:20233546 original size:46 final size:48
Alignment explanation
Indices: 20233459--20233561 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
20233449 TACATGAATT
* *
20233459 ATTCCTGTCTCCAATGCCATATATATATAATATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
* * *
20233507 ATTCCTGTCTCCAAAGCCATATA-A-CTGATATGGACTTACATGGCTT
1 ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
*
20233553 ATTTCTGTC
1 ATTCCTGTC
20233562 CTGTCCTGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 26 0.53
47 1 0.02
48 22 0.45
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (48 bp):
ATTCCTGTCTCCAAAGCCATATATATATAATATGGACTTACATGGCTC
Found at i:20235151 original size:27 final size:26
Alignment explanation
Indices: 20235099--20235158 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
20235089 ATATATATAT
*
20235099 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
20235125 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
20235152 ATATCTG
1 ATATCTG
20235159 GCAGTCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:20248627 original size:23 final size:24
Alignment explanation
Indices: 20248586--20248630 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
20248576 AACATTTTCG
*
20248586 GGAATTTTGAGGGGGCGGAGGGAT
1 GGAATTGTGAGGGGGCGGAGGGAT
*
20248610 GGAATTGTG-GGGGTCGGAGGG
1 GGAATTGTGAGGGGGCGGAGGG
20248631 CAACAAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.18, C:0.04, G:0.58, T:0.20
Consensus pattern (24 bp):
GGAATTGTGAGGGGGCGGAGGGAT
Found at i:20254721 original size:17 final size:18
Alignment explanation
Indices: 20254699--20254733 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20254689 ATTTGGGCAG
*
20254699 TGTGGG-CCATATGGGTA
1 TGTGGGCCCACATGGGTA
20254716 TGTGGGCCCACATGGGTA
1 TGTGGGCCCACATGGGTA
20254734 GTCCACATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.26
Consensus pattern (18 bp):
TGTGGGCCCACATGGGTA
Found at i:20260835 original size:29 final size:30
Alignment explanation
Indices: 20260792--20260861 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
20260782 AAATTAAAAT
20260792 TTCATGTATAAAATTGCACA-AAATCAGAG
1 TTCATGTATAAAATTGCACATAAATCAGAG
* * *
20260821 TTCATGTATACAATTGTACATTAAATCATAG
1 TTCATGTATAAAATTGCACA-TAAATCAGAG
20260852 TTCATGTATA
1 TTCATGTATA
20260862 GTTTTGGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (30 bp):
TTCATGTATAAAATTGCACATAAATCAGAG
Done.