Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 107 of 198
Found at i:34248406 original size:2 final size:2
Alignment explanation
Indices: 34248399--34248444 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
34248389 ACAATAAAAG
34248399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34248440 AT AT A
1 AT AT A
34248445 CACTACAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34254199 original size:2 final size:2
Alignment explanation
Indices: 34254192--34254228 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34254182 GATAAGCCAT
34254192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34254229 TGTCAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34254984 original size:14 final size:14
Alignment explanation
Indices: 34254946--34254984 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
34254936 TAGTATTTAT
*
34254946 AAAAATTTAAAATA
1 AAAAATTTAATATA
* *
34254960 ATAAATTTAATCTA
1 AAAAATTTAATATA
34254974 AAAAATTTAAT
1 AAAAATTTAAT
34254985 TAATATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAATTTAATATA
Found at i:34255170 original size:19 final size:19
Alignment explanation
Indices: 34255139--34255191 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
34255129 CTAAAACACC
34255139 ATTAAAAACTAAAACACAAA
1 ATTAAAAA-TAAAACACAAA
* *
34255159 ATTAAAAATAAATCTCAAA
1 ATTAAAAATAAAACACAAA
* *
34255178 TTTAAAAAAAAAAC
1 ATTAAAAATAAAAC
34255192 TTAAAAAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (19 bp):
ATTAAAAATAAAACACAAA
Found at i:34257516 original size:20 final size:19
Alignment explanation
Indices: 34257491--34257532 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
34257481 GAGTTTTTTT
*
34257491 TTTCAATCGATTTAAAAATG
1 TTTCAATCGAGTTAAAAA-G
34257511 TTTCAATCGAGTTAAAAAG
1 TTTCAATCGAGTTAAAAAG
34257530 TTT
1 TTT
34257533 AAAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (19 bp):
TTTCAATCGAGTTAAAAAG
Found at i:34258267 original size:87 final size:87
Alignment explanation
Indices: 34258121--34258295 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
34258111 CCAAGACGCT
34258121 ACATTAAACCTCACAACTTCATACACATTCACATAGTCACATTTACGTACAACCATCATCACATT
1 ACATTAAACCTCACAACTTCATACACATTCACATAGTCACATTTACGTACAACCATCATCACATT
*
34258186 CAAACATTTATAGGATTATTGA
66 CAAACATTTATAGGAGTATTGA
34258208 ACATTAAACCTCACAACTTCATACACATTCACATAGTCACATTTACGTACAACCATCATCACATT
1 ACATTAAACCTCACAACTTCATACACATTCACATAGTCACATTTACGTACAACCATCATCACATT
34258273 CAAACATTTATAGGAGTATTGA
66 CAAACATTTATAGGAGTATTGA
34258295 A
1 A
34258296 GCTAAAACAC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.29
Consensus pattern (87 bp):
ACATTAAACCTCACAACTTCATACACATTCACATAGTCACATTTACGTACAACCATCATCACATT
CAAACATTTATAGGAGTATTGA
Found at i:34263065 original size:140 final size:141
Alignment explanation
Indices: 34262905--34263183 Score: 542
Period size: 140 Copynumber: 2.0 Consensus size: 141
34262895 GACGACACAA
34262905 AAAAAGGGTGAAAGGGTGTTTCTCTTTTCTCTTCTTTCACGTTAAAAATAGGGTGAAAGGGGGAA
1 AAAAAGGGTGAAAGGGTGTTTCTCTTTTCTCTTCTTTCACGTTAAAAATAGGGTGAAAGGGGGAA
34262970 AATATGGGCTAATTTTAAAACTTGGTGTAGTAGCTTTAAAGCTACCCTTAAGTTTAATATTTTTA
66 AATATGGGCTAATTTTAAAACTTGGTGTAGTAGCTTTAAAGCTACCCTTAAGTTTAATATTTTTA
34263035 CAAAACAGTAG
131 CAAAACAGTAG
34263046 AAAAA-GGTGAAAGGGTGTTTCTCTTTTCTCTTCTTTCACGTTAAAAATAGGGTGAAAGGGGGAA
1 AAAAAGGGTGAAAGGGTGTTTCTCTTTTCTCTTCTTTCACGTTAAAAATAGGGTGAAAGGGGGAA
*
34263110 AATATGGGCTAATTTTAAAACTTGGTGTGGTAGCTTTAAAGCTACCCTTAAGTTTAATATTTTTA
66 AATATGGGCTAATTTTAAAACTTGGTGTAGTAGCTTTAAAGCTACCCTTAAGTTTAATATTTTTA
34263175 CAAAACAGT
131 CAAAACAGT
34263184 CATCTTTTTA
Statistics
Matches: 137, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
140 132 0.96
141 5 0.04
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (141 bp):
AAAAAGGGTGAAAGGGTGTTTCTCTTTTCTCTTCTTTCACGTTAAAAATAGGGTGAAAGGGGGAA
AATATGGGCTAATTTTAAAACTTGGTGTAGTAGCTTTAAAGCTACCCTTAAGTTTAATATTTTTA
CAAAACAGTAG
Found at i:34265988 original size:18 final size:17
Alignment explanation
Indices: 34265955--34265993 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
34265945 TTTTATAAAT
34265955 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
34265973 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
34265990 TGTG
1 TGTG
34265994 GAAGTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:34266246 original size:23 final size:23
Alignment explanation
Indices: 34266219--34266294 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
34266209 AGGGTTTTTG
34266219 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
34266242 TTCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
34266265 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
34266288 ATCAGTG
1 ATCAGTG
34266295 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:34279519 original size:23 final size:22
Alignment explanation
Indices: 34279500--34279543 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34279490 TAAAATAAAT
34279500 AAATAATATTGAAAATAATATAA
1 AAATAATA-TGAAAATAATATAA
*
34279523 ATATAATATG-AAATACATATA
1 AAATAATATGAAAATA-ATATA
34279544 CTTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (22 bp):
AAATAATATGAAAATAATATAA
Found at i:34279954 original size:22 final size:23
Alignment explanation
Indices: 34279917--34279962 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
34279907 CCTAATTTGG
34279917 TACTTAATCTTTTTTGTTCAATT
1 TACTTAATCTTTTTTGTTCAATT
34279940 TACTTAAT-TTTTTTGTTCAATT
1 TACTTAATCTTTTTTGTTCAATT
34279962 T
1 T
34279963 GGTACTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (23 bp):
TACTTAATCTTTTTTGTTCAATT
Found at i:34280391 original size:31 final size:30
Alignment explanation
Indices: 34280349--34280506 Score: 100
Period size: 31 Copynumber: 5.4 Consensus size: 30
34280339 TAAAAAGCTT
*
34280349 AGGTACCAAATTAGGAAAAAATGCCAAGTTC
1 AGGTACTAAATTAGGAAAAAATG-CAAGTTC
* * *
34280380 AGGTACTAAATTGGGCCAAAAA---AA-TTT
1 AGGTACTAAATTAGG-AAAAAATGCAAGTTC
*
34280407 AGGTA-TCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACT-AAATTAGGAAAAAATG-CAAGTTC
* * * *
34280438 AGGTACCAAATTGGGCCAAAAA---AA-TTT
1 AGGTACTAAATTAGG-AAAAAATGCAAGTTC
34280465 AGGTACTAAATTAGGAAAAAATGTCAAGTTC
1 AGGTACTAAATTAGGAAAAAATG-CAAGTTC
* *
34280496 ATGTACAAAAT
1 AGGTACTAAAT
34280507 GTTATATTAA
Statistics
Matches: 94, Mismatches: 19, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
26 10 0.11
27 29 0.31
28 4 0.04
30 4 0.04
31 38 0.40
32 9 0.10
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (30 bp):
AGGTACTAAATTAGGAAAAAATGCAAGTTC
Found at i:34280419 original size:58 final size:57
Alignment explanation
Indices: 34280347--34280506 Score: 248
Period size: 58 Copynumber: 2.8 Consensus size: 57
34280337 AATAAAAAGC
* *
34280347 TTAGGTACCAAATTAGGAAAAAATGCCAAGTTCAGGTACTAAATTGGGCCAAAAAAAT
1 TTAGGTA-CAAATTAGGAAAAAATGTCAAGTTCAGGTACAAAATTGGGCCAAAAAAAT
* *
34280405 TTAGGTATCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTGGGCCAAAAAAAT
1 TTAGGTA-CAAATTAGGAAAAAATGTCAAGTTCAGGTACAAAATTGGGCCAAAAAAAT
*
34280463 TTAGGTACTAAATTAGGAAAAAATGTCAAGTTCATGTACAAAAT
1 TTAGGTAC-AAATTAGGAAAAAATGTCAAGTTCAGGTACAAAAT
34280507 GTTATATTAA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 1 0.01
58 93 0.99
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (57 bp):
TTAGGTACAAATTAGGAAAAAATGTCAAGTTCAGGTACAAAATTGGGCCAAAAAAAT
Found at i:34280476 original size:27 final size:27
Alignment explanation
Indices: 34280380--34280476 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
34280370 TGCCAAGTTC
34280380 AGGTACTAAATTGGGCCAAAAAAATTT
1 AGGTACTAAATTGGGCCAAAAAAATTT
* *
34280407 AGGTA-TCAAATTAGG--AAAAAGTGTCAAGTTC
1 AGGTACT-AAATTGGGCCAAAAA-----AA-TTT
*
34280438 AGGTACCAAATTGGGCCAAAAAAATTT
1 AGGTACTAAATTGGGCCAAAAAAATTT
34280465 AGGTACTAAATT
1 AGGTACTAAATT
34280477 AGGAAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
25 5 0.09
26 1 0.02
27 25 0.46
28 2 0.04
30 2 0.04
31 14 0.26
33 5 0.09
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (27 bp):
AGGTACTAAATTGGGCCAAAAAAATTT
Found at i:34280485 original size:27 final size:27
Alignment explanation
Indices: 34280347--34280485 Score: 73
Period size: 27 Copynumber: 4.9 Consensus size: 27
34280337 AATAAAAAGC
* *
34280347 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACTAAATTAGGAAAAAA----AAAT
* * **
34280378 TCAGGTACTAAATTGGGCCAAAAAAAT
1 TTAGGTACTAAATTAGGAAAAAAAAAT
* *
34280405 TTAGGTA-TCAAATTAGGAAAAAGTGTCAAGT
1 TTAGGTACT-AAATTAGGAAAAA----AAAAT
* * * **
34280436 TCAGGTACCAAATTGGGCCAAAAAAAT
1 TTAGGTACTAAATTAGGAAAAAAAAAT
34280463 TTAGGTACTAAATTAGGAAAAAA
1 TTAGGTACTAAATTAGGAAAAAA
34280486 TGTCAAGTTC
Statistics
Matches: 78, Mismatches: 24, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
26 1 0.01
27 40 0.51
31 37 0.47
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (27 bp):
TTAGGTACTAAATTAGGAAAAAAAAAT
Found at i:34280775 original size:21 final size:21
Alignment explanation
Indices: 34280751--34280800 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
34280741 TTAACTAATT
34280751 ATTTTTA-AAATTTAAAAATA
1 ATTTTTATAAATTTAAAAATA
* *
34280771 CA-TTTTATAATTTTTAAAATA
1 -ATTTTTATAAATTTAAAAATA
34280792 ATTTTTATA
1 ATTTTTATA
34280801 TATTATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTTTATAAATTTAAAAATA
Found at i:34289293 original size:20 final size:20
Alignment explanation
Indices: 34289270--34289307 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34289260 ATTTATAGAC
34289270 ATACATATATACATATATAT
1 ATACATATATACATATATAT
*
34289290 ATACATATTTACATATAT
1 ATACATATATACATATAT
34289308 CTTTGTTGTC
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:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
ATACATATATACATATATAT
Found at i:34289297 original size:12 final size:12
Alignment explanation
Indices: 34289263--34289297 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34289253 TTTTACAATT
* *
34289263 TATAGACATACA
1 TATATACATATA
34289275 TATATACATATA
1 TATATACATATA
34289287 TATATACATAT
1 TATATACATAT
34289298 TTACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (12 bp):
TATATACATATA
Found at i:34299266 original size:22 final size:22
Alignment explanation
Indices: 34299239--34299292 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
34299229 TCCAAAGAAT
34299239 AACAACAAAATGGCAACAAAAC
1 AACAACAAAATGGCAACAAAAC
* * * *
34299261 AGCAACGAAATGGTAGCAAAAC
1 AACAACAAAATGGCAACAAAAC
*
34299283 AATAACAAAA
1 AACAACAAAA
34299293 AGTTTAGGCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.61, C:0.19, G:0.13, T:0.07
Consensus pattern (22 bp):
AACAACAAAATGGCAACAAAAC
Found at i:34304066 original size:20 final size:17
Alignment explanation
Indices: 34304041--34304083 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 17
34304031 ATTAGAATGC
34304041 TTTAAAGTTTAGAGATCAAT
1 TTTAAA-TTT-GAG-TCAAT
34304061 TTTAAATTTGAGTCAA-
1 TTTAAATTTGAGTCAAT
34304077 TTTAAAT
1 TTTAAAT
34304084 GTATAAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 3 0.13
19 3 0.13
20 6 0.26
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTAAATTTGAGTCAAT
Found at i:34312629 original size:6 final size:6
Alignment explanation
Indices: 34312618--34312666 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
34312608 AAATAAGTTG
34312618 GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT
1 GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT GCCCAT
34312666 G
1 G
34312667 ACATTGACTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.49, G:0.18, T:0.16
Consensus pattern (6 bp):
GCCCAT
Found at i:34316023 original size:82 final size:81
Alignment explanation
Indices: 34315856--34316030 Score: 181
Period size: 82 Copynumber: 2.1 Consensus size: 81
34315846 CTTTTTGGCC
* ** * * * *** *
34315856 AAGTATCGATATTTTATGAATTATCGATACCCTTCTTAAAAGCGATACCAAAATGGCATTTTATT
1 AAGTATCGATATTTCAAAAAATATCGATACCCTTCTTAAAAACAATACCAAAACAACATTCTATT
* **
34315921 TTTCACAAACCCTATT
66 TCTCACAAACCCTACA
*
34315937 AAGTATCGATATTTCAAAAAATATCGATACCCCTTCTTAAAAACAATACTAAAACAACATTCTAT
1 AAGTATCGATATTTCAAAAAATATCGATA-CCCTTCTTAAAAACAATACCAAAACAACATTCTAT
*
34316002 TTCTCACAATA-CTTACA
65 TTCTCACAA-ACCCTACA
*
34316019 AAGTATCAATAT
1 AAGTATCGATAT
34316031 GGTATCGATA
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 25 0.33
82 50 0.66
83 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (81 bp):
AAGTATCGATATTTCAAAAAATATCGATACCCTTCTTAAAAACAATACCAAAACAACATTCTATT
TCTCACAAACCCTACA
Found at i:34322660 original size:42 final size:38
Alignment explanation
Indices: 34322576--34322692 Score: 216
Period size: 38 Copynumber: 3.1 Consensus size: 38
34322566 ATAAATTTTA
* *
34322576 TTTATCTATCTATTTTTCAAGATTGGCATTGGATGAAT
1 TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
34322614 TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
1 TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
34322652 TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
1 TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
34322690 TTT
1 TTT
34322693 TTAAAAAAAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (38 bp):
TTTATTTATCTATTTTTCAAGATTGGGATTGGATGAAT
Found at i:34324113 original size:42 final size:42
Alignment explanation
Indices: 34324048--34324153 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
34324038 TTCTGATAAA
34324048 TGTTTTCGTGTAAGACCACGTCTGGG-AGTTGGCATCGA-CTT
1 TGTTTTCGTGTAAGACCACGTCTGGGAAG-TGGCATCGATCTT
34324089 GTGTTTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATCTT
1 -TGTTTTCGTGTAAGACCAC-GTCTGGGA-AGTGGCATCGATCTT
* * *
34324133 TGTTTACATGTAAGACTACGT
1 TGTTTTCGTGTAAGACCACGT
34324154 TTGAGACATT
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
41 1 0.02
42 24 0.43
43 25 0.45
44 6 0.11
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (42 bp):
TGTTTTCGTGTAAGACCACGTCTGGGAAGTGGCATCGATCTT
Found at i:34324883 original size:2 final size:2
Alignment explanation
Indices: 34324876--34324917 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
34324866 CTTATAAGGA
34324876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34324917 A
1 A
34324918 ANNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34337948 original size:31 final size:31
Alignment explanation
Indices: 34337910--34337970 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
34337900 AAAGTAAGAA
34337910 AAGTTTTGTTGCCTAATAGTAAATACTCAAC
1 AAGTTTTGTTGCCTAATAGTAAATACTCAAC
34337941 AAGTTTTGTTGCCTAATAGTAAATACTCAA
1 AAGTTTTGTTGCCTAATAGTAAATACTCAA
34337971 AATTTGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
AAGTTTTGTTGCCTAATAGTAAATACTCAAC
Found at i:34342434 original size:41 final size:41
Alignment explanation
Indices: 34342333--34342438 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
34342323 TCAGGCTCTG
**
34342333 TGCCTAGCAGGCTTAATGCAAGTGAAATATTTCAGACTTTA
1 TGCCTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTA
* *
34342374 CGTCTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTA
1 TGCCTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTA
34342415 TGCCTAGCAGGCTTAATGCCGGTG
1 TGCCTAGCAGGCTTAATGCCGGTG
34342439 TTCTAAATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (41 bp):
TGCCTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTA
Found at i:34342461 original size:41 final size:41
Alignment explanation
Indices: 34342334--34342481 Score: 136
Period size: 41 Copynumber: 3.6 Consensus size: 41
34342324 CAGGCTCTGT
** ** * *
34342334 GCCTAGCAGGCTTAATGCAAGTGAAATATTTCAGACTTTAC
1 GCCTAGCAGGCTTAATGCCGGTGAAATAAATCAGACTTCAA
* ** * *
34342375 GTCTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTAT
1 GCCTAGCAGGCTTAATGCCGGTGAAATAAATCAGACTTCAA
*** *
34342416 GCCTAGCAGGCTTAATGCCGGTGTTCTAAATCAGGCTTCAA
1 GCCTAGCAGGCTTAATGCCGGTGAAATAAATCAGACTTCAA
*
34342457 GCCTAGCAGGC-TACATGCTGGTGAA
1 GCCTAGCAGGCTTA-ATGCCGGTGAA
34342482 TCATTTTAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 2 0.02
41 88 0.98
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
GCCTAGCAGGCTTAATGCCGGTGAAATAAATCAGACTTCAA
Found at i:34351424 original size:29 final size:27
Alignment explanation
Indices: 34351374--34351436 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
34351364 TTCTCCCTCC
* * *
34351374 AAAAATAACATATATCGATAAATATATAA
1 AAAAATAACACAAATCCATAAAT-T-TAA
*
34351403 AAAAATAACACAAATCCTTAAATTTAA
1 AAAAATAACACAAATCCATAAATTTAA
34351430 AAAAATA
1 AAAAATA
34351437 TGCATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.33
28 1 0.03
29 19 0.63
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAAATAACACAAATCCATAAATTTAA
Found at i:34353676 original size:6 final size:6
Alignment explanation
Indices: 34353667--34353740 Score: 61
Period size: 6 Copynumber: 13.2 Consensus size: 6
34353657 AATGACAAGC
* *
34353667 AAAAG- AAAA-A AAAAGA AAAAG- AAAAG- GAAAGA AAAAGA AATAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* *
34353710 -AAAGA AAAAGA AAAGGA AAAATGG AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA A
34353741 GGAGAATGAC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.05
5 17 0.31
6 30 0.55
7 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:34353688 original size:16 final size:16
Alignment explanation
Indices: 34353667--34353728 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
34353657 AATGACAAGC
*
34353667 AAAAGAAAAAAAAAGA
1 AAAAGAAAAAGAAAGA
*
34353683 AAAAGAAAAGGAAAGA
1 AAAAGAAAAAGAAAGA
*
34353699 AAAAGAAATAGAAAGA
1 AAAAGAAAAAGAAAGA
*
34353715 AAAAGAAAAGGAAA
1 AAAAGAAAAAGAAA
34353729 AATGGAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAGAAAGA
Found at i:34353704 original size:32 final size:32
Alignment explanation
Indices: 34353667--34353728 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
34353657 AATGACAAGC
34353667 AAAAGAAAAAAAAAGAAAAAGAAAAGGAAAGA
1 AAAAGAAAAAAAAAGAAAAAGAAAAGGAAAGA
* *
34353699 AAAAGAAATAGAAAGAAAAAGAAAAGGAAA
1 AAAAGAAAAAAAAAGAAAAAGAAAAGGAAA
34353729 AATGGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (32 bp):
AAAAGAAAAAAAAAGAAAAAGAAAAGGAAAGA
Found at i:34354158 original size:45 final size:47
Alignment explanation
Indices: 34354082--34354176 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 47
34354072 GGGGCGTTAC
* * * *
34354082 ACTAAATAATAGATTAAATTATATAATATTTATTA-TAATTTTTTAAT
1 ACTAAATAATAGACTAAATTACATAACATTTATTATTAATTGTTT-AT
*
34354129 ACTAAAT-ATA-ACTAAATTACATAGCATTTATTATTAATTGTTTAT
1 ACTAAATAATAGACTAAATTACATAACATTTATTATTAATTGTTTAT
34354174 ACT
1 ACT
34354177 TGGTTAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 24 0.57
46 11 0.26
47 7 0.17
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (47 bp):
ACTAAATAATAGACTAAATTACATAACATTTATTATTAATTGTTTAT
Found at i:34354748 original size:27 final size:27
Alignment explanation
Indices: 34354716--34354774 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
34354706 CTTAAATTTC
*
34354716 ATAAAAAATCAAAAAATA-GAA-AAATA
1 ATAAAAAA-CAAAAAATACAAATAAATA
*
34354742 ATAAAAAACAATAAATACAAATAAATA
1 ATAAAAAACAAAAAATACAAATAAATA
34354769 ATAAAA
1 ATAAAA
34354775 GGAACATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 10 0.34
27 11 0.38
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (27 bp):
ATAAAAAACAAAAAATACAAATAAATA
Found at i:34358139 original size:36 final size:36
Alignment explanation
Indices: 34358097--34358167 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
34358087 TCTTGATGGG
* *
34358097 CAAGACATTAGCAAAATGAAGTTCTGTGAGTACTAA
1 CAAGACATTAACAAAATGAAGTTCTGTGAGCACTAA
*
34358133 CAAGACATTAACAAAATGAAGTTTTGTGAGCACTA
1 CAAGACATTAACAAAATGAAGTTCTGTGAGCACTA
34358168 CATTTTTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (36 bp):
CAAGACATTAACAAAATGAAGTTCTGTGAGCACTAA
Found at i:34361365 original size:20 final size:20
Alignment explanation
Indices: 34361340--34361380 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
34361330 TCCAATTTAG
*
34361340 TCCCTAAACCGAGACGAATT
1 TCCCTAAACCGAGACAAATT
34361360 TCCCTAAACCGAGACAAATT
1 TCCCTAAACCGAGACAAATT
34361380 T
1 T
34361381 TATTCTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (20 bp):
TCCCTAAACCGAGACAAATT
Found at i:34361816 original size:3 final size:3
Alignment explanation
Indices: 34361808--34361851 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
34361798 GTTTTGTTTT
*
34361808 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34361852 TATTATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34361856 original size:3 final size:3
Alignment explanation
Indices: 34361850--34361893 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
34361840 GATAATAATA
* *
34361850 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATC ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
34361894 ATAATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:34388017 original size:27 final size:26
Alignment explanation
Indices: 34387960--34388019 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
34387950 GAATATATAT
* * * *
34387960 ATTTTTAAATTTTAAGTTTTTTTGCA
1 ATTTTTAAAATTTAAATATTTTTCCA
34387986 ATTTTCTAAAATTTAAATATTTTTCCA
1 ATTTT-TAAAATTTAAATATTTTTCCA
*
34388013 TTTTTTA
1 ATTTTTA
34388020 CAAAATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTTTTAAAATTTAAATATTTTTCCA
Found at i:34389562 original size:15 final size:15
Alignment explanation
Indices: 34389542--34389572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34389532 TATAAAAAGG
34389542 ATATAACCTAATATA
1 ATATAACCTAATATA
*
34389557 ATATAACCTATTATA
1 ATATAACCTAATATA
34389572 A
1 A
34389573 GTTTTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAACCTAATATA
Found at i:34390880 original size:11 final size:11
Alignment explanation
Indices: 34390864--34390905 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
34390854 CATATCTTTC
34390864 TTTTTTTTCTT
1 TTTTTTTTCTT
34390875 TTTTTTTTCTT
1 TTTTTTTTCTT
* *
34390886 TTCTTTATGCTT
1 TT-TTTTTTCTT
34390898 TTTTTTTT
1 TTTTTTTT
34390906 TGGATTTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:34390885 original size:20 final size:23
Alignment explanation
Indices: 34390860--34390905 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
34390850 GTGGCATATC
34390860 TTTCTTTT-TTT-T-CTTTTTTT
1 TTTCTTTTCTTTATGCTTTTTTT
34390880 TTTCTTTTCTTTATGCTTTTTTT
1 TTTCTTTTCTTTATGCTTTTTTT
34390903 TTT
1 TTT
34390906 TGGATTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 1 0.04
23 11 0.48
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.85
Consensus pattern (23 bp):
TTTCTTTTCTTTATGCTTTTTTT
Found at i:34397124 original size:44 final size:44
Alignment explanation
Indices: 34397060--34397805 Score: 704
Period size: 44 Copynumber: 17.0 Consensus size: 44
34397050 CTGCCACACT
**
34397060 ACCAATATAAAAAGACAAGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
34397104 GCCAATACATGAAGATAAGATATGCTTTCTTCGATCTACTTCGCC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
** *
34397149 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-C
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
34397191 TACCAATATAAGAAGACAGGATCTGTTATCTTCGATCTACTTCAC
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
34397236 GCCAATACATGAAGACGAGATCTACTTTCTTCGATCCACTTC-C
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
34397279 TACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCA-TTGC-C
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTT-CAC
* * * **
34397323 TACTAATATAGGAAGACAGGATCTGCTATCTTTTATCTACTTCAC
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
34397368 GCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
** * *
34397413 ACCAATATGGGAAGACAATATCTGC-ATCTTCGATCCACTTC-C
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
34397455 TACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCAC
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
34397500 GCCAATACATGAAGACGAGATCTACTTTCTTCGATCCACTTC-C
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * **
34397543 TACTAATATAGGAAGACAGGATCTGCTATCTTTTATCTACTTCAC
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* *
34397588 GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
34397632 GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* *
34397677 ACCAATAT-GGAAAGACAAGATCTGC-ATCTTCGATCCACTT-AC
1 ACCAATATATG-AAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
34397719 AACCAATATAGGAAAACAGGATCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
34397764 GCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTTC
1 ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC
34397806 GCCACGCATC
Statistics
Matches: 572, Mismatches: 110, Indels: 40
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.01
43 66 0.12
44 434 0.76
45 69 0.12
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (44 bp):
ACCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:34397310 original size:132 final size:132
Alignment explanation
Indices: 34397058--34397810 Score: 1075
Period size: 132 Copynumber: 5.7 Consensus size: 132
34397048 GTCTGCCACA
** * *
34397058 CTACCAATATAAAAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAG
1 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
* *
34397123 ATATGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACT
66 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCATCTTCGATCCACT
34397188 TC
131 TC
* * *
34397190 CTACCAATATAAGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAG
1 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
* * * * * *
34397255 ATCTACTTTCTTCGATCCACTTC-CTACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCA-
66 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGC-ATCTTCGATCCAC
34397318 TTGC
130 TT-C
* ** *
34397322 CTACTAATATAGGAAGACAGGATCTGCTATCTTTTATCTACTTCACGCCAATACATGAAGATAAG
1 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
* *
34397387 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAATATCTGCATCTTCGATCCACT
66 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCATCTTCGATCCACT
34397452 TC
131 TC
* *
34397454 CTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAG
1 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
* * * * * ** *
34397519 ATCTACTTTCTTCGATCCACTTC-CTACTAATATAGGAAGACAGGATCTGCTATCTTTTATCTAC
66 ATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGC-ATCTTCGATCCAC
34397583 TTC
130 TTC
* * * *
34397586 AC-GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 -CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
34397650 GATCTGCTTTCTTCGATCTACTTCGCCACCAATAT-GGAAAGACAAGATCTGCATCTTCGATCCA
65 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGG-AAGACAAGATCTGCATCTTCGATCCA
*
34397714 CTTA
129 CTTC
* *
34397718 CAACCAATATAGGAAAACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
*
34397783 ATCTGCTTTTTTCGATCTACTTCGCCAC
66 ATCTGCTTTCTTCGATCTACTTCGCCAC
34397811 GCATCTTTGA
Statistics
Matches: 547, Mismatches: 65, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
131 48 0.09
132 453 0.83
133 46 0.08
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (132 bp):
CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
ATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCATCTTCGATCCACT
TC
Found at i:34397553 original size:264 final size:264
Alignment explanation
Indices: 34397071--34397805 Score: 1231
Period size: 264 Copynumber: 2.8 Consensus size: 264
34397061 CCAATATAAA
*
34397071 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATATGCTTTCTTC
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTC
34397136 GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
66 GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
*
34397201 AGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
131 GGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
*
34397266 TCGATCCACTTCCTACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCA-TTGC-CTACTAA
196 TCGATCCACTTCCTACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCACTT-CAC-ACCAA
*
34397329 TATAGG
259 TACAGG
* **
34397335 AAGACAGGATCTGCTATCTTTTATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTC
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTC
*
34397400 GATCTACTTCGCCACCAATATGGGAAGACAATATCTGCATCTTCGATCCACTTCCTACCAATATA
66 GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
34397465 GGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
131 GGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
* * * *
34397530 TCGATCCACTTCCTACTAATATAGGAAGACAGGATCTGCTATCTTTTATCTACTTCACGCCAATA
196 TCGATCCACTTCCTACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCACTTCACACCAATA
*
34397595 CATG
261 CAGG
*
34397599 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
1 AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTC
* * *
34397664 GATCTACTTCGCCACCAATATGGAAAGACAAGATCTGCATCTTCGATCCACTTACAACCAATATA
66 GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
* * * * *
34397729 GGAAAACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTT
131 GGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
*
34397794 TCGATCTACTTC
196 TCGATCCACTTC
34397806 GCCACGCATC
Statistics
Matches: 442, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
264 439 0.99
265 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (264 bp):
AAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTC
GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
GGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACGAGATCTACTTTCT
TCGATCCACTTCCTACAAATATAGGAAGACAGGATCTGCTATCTTCTATCCACTTCACACCAATA
CAGG
Found at i:34398704 original size:25 final size:26
Alignment explanation
Indices: 34398676--34398724 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
34398666 GTGTCTTGAA
*
34398676 AAGAA-AAAGATATT-CAATAACAATG
1 AAGAATAAAG-TATTACAAGAACAATG
34398701 AAGAATAAAGTATTACAAGAACAA
1 AAGAATAAAGTATTACAAGAACAA
34398725 ACAAATTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.18
Consensus pattern (26 bp):
AAGAATAAAGTATTACAAGAACAATG
Found at i:34413561 original size:16 final size:17
Alignment explanation
Indices: 34413542--34413575 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
34413532 ATTAGTAAAT
34413542 AAAATTGAAAAT-ATAA
1 AAAATTGAAAATAATAA
34413558 AAAATTGAAAATAATAA
1 AAAATTGAAAATAATAA
34413575 A
1 A
34413576 TTTAATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAATTGAAAATAATAA
Found at i:34413682 original size:17 final size:16
Alignment explanation
Indices: 34413620--34413678 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
34413610 TTCAATCATA
* **
34413620 ATTTAAAAATATTTAA
1 ATTTGAAAATATTTTT
34413636 ATTATGAAAATATTTTT
1 ATT-TGAAAATATTTTT
34413653 ATTTGAAAATATTTTT
1 ATTTGAAAATATTTTT
*
34413669 ATTTTAAAAT
1 ATTTGAAAAT
34413679 TATTATAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTGAAAATATTTTT
Found at i:34417149 original size:2 final size:2
Alignment explanation
Indices: 34417105--34417129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34417095 TAAAACAGTG
34417105 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34417130 GAAAATAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34418785 original size:100 final size:100
Alignment explanation
Indices: 34418603--34419095 Score: 618
Period size: 100 Copynumber: 5.0 Consensus size: 100
34418593 AACTTGTAAT
** ** * * * *
34418603 TTTAATCCGTTTAACTATAATGTCGAGGAGGCAAGATTCGCTATTGTAGC-TTCAATCTGTTCCA
1 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCATTGTGGCGTT-AATCTGTTCCA
* * *
34418667 CTACACCGCCTG-GAAAGTAAGATTTGCTGTTATAGC
65 CTGCACCGCTTGAG-AAGTAAGATTCGCTGTTATAGC
* * * *
34418703 TTTAATATTTTTAAATGCAATGTCAAGGAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCCAC
1 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCATTGTGGCGTTAATCTGTTCCAC
*
34418768 TGCACCGCTTGAGAAGTAAGATTCGCTGTTGTAGC
66 TGCACCGCTTGAGAAGTAAGATTCGCTGTTATAGC
* **
34418803 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTTCCATTGTGGCGTTAATCTGTTCCAC
1 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCATTGTGGCGTTAATCTGTTCCAC
* *
34418868 TGCACCACTTGAGAAGTAAGATTCGCCGTTATAGC
66 TGCACCGCTTGAGAAGTAAGATTCGCTGTTATAGC
* * *
34418903 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAATATT-ACCAATGTGGCGTTAATCTGTTCTAC
1 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCATTGTGGCGTTAATCTGTTCCAC
* *
34418967 TGCACCGCTTGAGAAGTAAAATTCGC-GTTATAAC
66 TGCACCGCTTGAGAAGTAAGATTCGCTGTTATAGC
* *
34419001 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCCA
1 TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACC-ATTGTGGCGTTAATCTGTTCCA
* * * * * *
34419065 CTGAATCGCCTGGGGAGTAAGATTTGCTGTT
65 CTGCACCGCTTGAGAAGTAAGATTCGCTGTT
34419096 CTCAGTCTGC
Statistics
Matches: 343, Mismatches: 45, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
98 43 0.13
99 88 0.26
100 209 0.61
101 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (100 bp):
TTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCATTGTGGCGTTAATCTGTTCCAC
TGCACCGCTTGAGAAGTAAGATTCGCTGTTATAGC
Found at i:34418789 original size:50 final size:50
Alignment explanation
Indices: 34418730--34419067 Score: 191
Period size: 50 Copynumber: 6.8 Consensus size: 50
34418720 CAATGTCAAG
*
34418730 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCCACTGCACCGCTTGA
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCTTGA
* * * * * * * ** * *
34418780 GAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGG
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCT-TGA
** * * *
34418830 GAAGCAAGATTTTCCATTGTGGCGTTAATCTGTTCCACTGCACCACTTGA
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCTTGA
* * * * * * * ** *
34418880 GAAGTAAGATTCGCCGTTATAGCTTTAATCTTTTTAACTGCAATG-TCGA
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCTTGA
* ** *
34418929 GGAAGCAATATT-ACCAATGTGGCGTTAATCTGTTCTACTGCACCGCTTGA
1 -GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCTTGA
* * * * ** * * * ** * *
34418979 GAAGTAAAATTC-GCGTTATAACTTTAATCTTTTTAACTGCAATG-TCGGG
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCT-TGA
* * *
34419028 GAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTG
1 GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTG
34419068 AATCGCCTGG
Statistics
Matches: 200, Mismatches: 81, Indels: 14
0.68 0.27 0.05
Matches are distributed among these distances:
48 1 0.00
49 66 0.33
50 132 0.66
51 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
GAAGCAAGATTCACCGTTGTGGCGTTAATCTGTTCAACTGCACCGCTTGA
Found at i:34419158 original size:44 final size:45
Alignment explanation
Indices: 34419076--34419179 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 45
34419066 TGAATCGCCT
* *
34419076 GGGGAGTAAGATTTGCTGTTCTCAGTCTGCCCCACTGCAACTTCAG
1 GGGGA-TAAGACTTGCTGTACTCAGTCTGCCCCACTGCAACTTCAG
* * * *
34419122 GGGGATAAGACTTGCT-TACTCAGTTTGCTCCGCTGCAACTTTAG
1 GGGGATAAGACTTGCTGTACTCAGTCTGCCCCACTGCAACTTCAG
*
34419166 GGAGATAAGACTTG
1 GGGGATAAGACTTG
34419180 ATGCGATCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 36 0.71
45 10 0.20
46 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (45 bp):
GGGGATAAGACTTGCTGTACTCAGTCTGCCCCACTGCAACTTCAG
Found at i:34419283 original size:44 final size:45
Alignment explanation
Indices: 34419235--34419338 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
34419225 TTTAATCCGT
* * * *
34419235 TCCACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGC
1 TCCACTACAACCTCAGGAAGATAAGATATATCAGCTTCAATCTGC
* * **
34419279 TCCACTACATCCTCAGGAAGATAAGATATATCATCTTCGGTCTGC
1 TCCACTACAACCTCAGGAAGATAAGATATATCAGCTTCAATCTGC
*
34419324 CCCACTACAACCTCA
1 TCCACTACAACCTCA
34419339 AGGGGATAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
44 23 0.47
45 26 0.53
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (45 bp):
TCCACTACAACCTCAGGAAGATAAGATATATCAGCTTCAATCTGC
Found at i:34419709 original size:218 final size:218
Alignment explanation
Indices: 34419101--34419743 Score: 964
Period size: 217 Copynumber: 3.0 Consensus size: 218
34419091 CTGTTCTCAG
* * * * * *
34419101 TCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTTACTCAGTTTGCTCCGCTGCAACTTTAG
1 TCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
* * *
34419166 GGAGATAAGACTTGATGCGATCCACTCTACTACAACTTCAGAGAGATAAAATCTATTACTTTAAT
66 GGAGATAAGACTTGATGCGATCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
* * *
34419231 CCGTTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACATCCTCAGG
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGG
* * *
34419296 AAGATAAGATATATCATCTTCGG
196 GAGATAAGATTTATCATCTTCGA
* *
34419319 TCTGCCCCACTACAACCTCAAGGGGATAAGACCTGCTTACTCAGTCTGCT-CACTGCAACCTCAG
1 TCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
* * *
34419383 AGAGATAAGACCTGATGCGATCCACTCTATTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
66 GGAGATAAGACTTGATGCGATCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
* * * * * *
34419448 CCTCCCCACCACAACTTCAGGGAGATAGGATTATCGTCTTCAATCTACTCCACTGCAACCTTAGG
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGG
34419513 GAGATAAGATTTATCATCTTCGA
196 GAGATAAGATTTATCATCTTCGA
* *
34419536 TTTGCCCCACTGCAACCTCAGGGGGATAAGACCTGTTTACTCAGTCTGCTCCACTGCAACCTCAG
1 TCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
* * *
34419601 GGAGATAAGATTTGATGGGATCCACTCTACTGCAACTTTAGAGAGATAAGATCCATTACTTTAAT
66 GGAGATAAGACTTGATGCGATCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
* * *
34419666 TCGCTCCACTACAATTTCAGGGAGATAGGACTATCGGCTTCAATCTGCTCCACTGCAACCTCAGG
131 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGG
*
34419731 GAGATAATATTTA
196 GAGATAAGATTTA
34419744 ATAAGATCCA
Statistics
Matches: 378, Mismatches: 46, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
217 192 0.51
218 186 0.49
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (218 bp):
TCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
GGAGATAAGACTTGATGCGATCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGG
GAGATAAGATTTATCATCTTCGA
Found at i:34419715 original size:129 final size:129
Alignment explanation
Indices: 34419580--34419872 Score: 444
Period size: 129 Copynumber: 2.3 Consensus size: 129
34419570 GTTTACTCAG
** * *
34419580 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGATGGGATCCACTCTACTGCAACTTTAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGATAAGATCCACTCTACTACAACTTCAGAGA
* * *
34419645 GATAAGATCCATTACTTTAAT-TCGCTCCACTACAATTTCAGGGAGATAGGACTATCGGCTTCAA
66 GATAAGATCCATTACTTTAATCT-GCTCCACTACAACTGCAGGGAGATAGAACTATCGGCTTCAA
* *
34419709 TCTGCTCCACTGCAACCTCAGGGAGATAATATTTAATAAGATCCACTCTACTACAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGATAAGATCCACTCTACTACAACTTCAGAGA
* * *
34419774 GATAAGATCTATTACTTTAATCTGCTCCACTACAACTGCAGGGAGATAGAATTATCGGTTTCAA
66 GATAAGATCCATTACTTTAATCTGCTCCACTACAACTGCAGGGAGATAGAACTATCGGCTTCAA
* *
34419838 TCTGTTCCACTGCAACCTTAGGGAGATAAGATTTG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTG
34419873 CCATCTTCAA
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 146 0.99
130 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (129 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGATAAGATCCACTCTACTACAACTTCAGAGA
GATAAGATCCATTACTTTAATCTGCTCCACTACAACTGCAGGGAGATAGAACTATCGGCTTCAA
Found at i:34419783 original size:347 final size:346
Alignment explanation
Indices: 34419363--34420042 Score: 981
Period size: 347 Copynumber: 2.0 Consensus size: 346
34419353 GCTTACTCAG
* ** * * *
34419363 TCTGCTCACTGCAACCTCAGAGAGATAAGACCTGATGCGATCCACTCTATTGCAACTTTAGAGAG
1 TCTGCTCACTGCAACCTCAGAGAGATAAGACCTAATAAGATCCACTCTACTACAACTTCAGAGAG
* *
34419428 ATAAGATCTATTACTTTAATCCT-CCCCACCACAACTTCAGGGAGATAGGATTATC-GTCTTCAA
66 ATAAGATCTATTACTTTAAT-CTGCCCCACCACAACTGCAGGGAGATAGAATTATCGGT-TTCAA
* * *
34419491 TCTACTCCACTGCAACCTTAGGGAGATAAGATTTATCATCTTCGATTTGCCCCACTGCAACCTCA
129 TCTACTCCACTGCAACCTTAGGGAGATAAGATTTACCATCTTCAATCTGCCCCACTGCAACCTCA
* ** * *
34419556 GGGGGATAAGACCTGTTTACTCAGTCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGATGGGA
194 GGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTAATGCGA
* ** *
34419621 TCCACTCTACTGCAACTTTAGAGAGATAAGATCCATTACTTTAATTC-GCTCCACTACAA-TTTC
259 TCCACTCCACTAAAACTTCAGAGAGATAAGATCCATTACTTTAA-TCAGCTCCACTACAAGTTT-
34419684 AGGGAGATAGGACTATCGGCTTCAA
322 AGGGAGATAGGACTATCGGCTTCAA
* * **
34419709 TCTGCTCCACTGCAACCTCAGGGAGATAATATTTAATAAGATCCACTCTACTACAACTTCAGAGA
1 TCTGCT-CACTGCAACCTCAGAGAGATAAGACCTAATAAGATCCACTCTACTACAACTTCAGAGA
* *
34419774 GATAAGATCTATTACTTTAATCTGCTCCACTACAACTGCAGGGAGATAGAATTATCGGTTTCAAT
65 GATAAGATCTATTACTTTAATCTGCCCCACCACAACTGCAGGGAGATAGAATTATCGGTTTCAAT
** * * *
34419839 CTGTTCCACTGCAACCTTAGGGAGATAAGATTTGCCATCTTCAATCTGTCCCACTGCAACTTCAG
130 CTACTCCACTGCAACCTTAGGGAGATAAGATTTACCATCTTCAATCTGCCCCACTGCAACCTCAG
*
34419904 GGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGAT
195 GGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTAATGCGAT
* *
34419969 CCACTCCACTAAAACTTCAGAGAGATAAGATCTATTACTTTAATCATCTCCACTACAAGTTTAGG
260 CCACTCCACTAAAACTTCAGAGAGATAAGATCCATTACTTTAATCAGCTCCACTACAAGTTTAGG
34420034 GAGATAGGA
325 GAGATAGGA
34420043 TTTGTGGCTT
Statistics
Matches: 295, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
346 10 0.03
347 280 0.95
348 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (346 bp):
TCTGCTCACTGCAACCTCAGAGAGATAAGACCTAATAAGATCCACTCTACTACAACTTCAGAGAG
ATAAGATCTATTACTTTAATCTGCCCCACCACAACTGCAGGGAGATAGAATTATCGGTTTCAATC
TACTCCACTGCAACCTTAGGGAGATAAGATTTACCATCTTCAATCTGCCCCACTGCAACCTCAGG
GGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTAATGCGATC
CACTCCACTAAAACTTCAGAGAGATAAGATCCATTACTTTAATCAGCTCCACTACAAGTTTAGGG
AGATAGGACTATCGGCTTCAA
Found at i:34419808 original size:44 final size:44
Alignment explanation
Indices: 34419194--34420039 Score: 339
Period size: 44 Copynumber: 19.5 Consensus size: 44
34419184 GATCCACTCT
* * * * *
34419194 ACTACAACTTCAGAGAGATAAAATCTATTACTTTAATCCGTTCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
* **
34419238 ACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCC
1 ACTACAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCTCC
* * * * * ** *
34419282 ACTACATCCTCAGGAAGATAAGATATATCATCTTCGGTCTGCCCC
1 ACTACAACTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCTCC
* * * *
34419327 ACTACAACCTCAAGGG-GATAAGACCTGCTTAC-TCAGTCTGCT-C
1 ACTACAACTTC-AGGGAGATAAGATCT-ATTACTTCAATCTGCTCC
* * * * * * * ** *
34419370 ACTGCAACCTCAGAGAGATAAGA-C-CTGA-TGCGATCCACTCT
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
* * * * * *
34419411 ATTGCAACTTTAGAGAGATAAGATCTATTACTTTAATCCT-CCCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAAT-CTGCTCC
* * *
34419455 ACCACAACTTCAGGGAGATAGGAT-TATCGT-CTTCAATCTACTCC
1 ACTACAACTTCAGGGAGATAAGATCTAT--TACTTCAATCTGCTCC
* * * * * *
34419499 ACTGCAACCTT-AGGGAGATAAGATTTATCATCTTCGATTTGCCCC
1 ACTACAA-CTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCTCC
* * * * * *
34419544 ACTGCAACCTCAGGGGGATAAGACCTGTTTAC-TCAGTCTGCTCC
1 ACTACAACTTCAGGGAGATAAGATCT-ATTACTTCAATCTGCTCC
* * * *** ** *
34419588 ACTGCAACCTCAGGGAGATAAGAT-T-TGA-TGGGATCCACTCT
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
* * * * *
34419629 ACTGCAACTTTAGAGAGATAAGATCCATTACTTTAAT-TCGCTCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCT-GCTCC
* * **
34419673 ACTACAATTTCAGGGAGATAGGA-CTATCGGCTTCAATCTGCTCC
1 ACTACAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCTCC
* * * * * ** *
34419717 ACTGCAACCTCAGGGAGAT-A-ATAT-TTA-ATAAGATCCACTCT
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCA-ATCTGCTCC
* *
34419758 ACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCTGCTCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
* *** *
34419802 ACTACAACTGCAGGGAGAT-AGAAT-TATCGGTTTCAATCTGTTCC
1 ACTACAACTTCAGGGAGATAAG-ATCTAT-TACTTCAATCTGCTCC
* * ***
34419846 ACTGCAACCTT-AGGGAGATAAGATTTGCCATCTTCAATCTG-TCCC
1 ACTACAA-CTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCT-CC
* * * * *
34419891 ACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCTGCTCC
1 ACTACAACTTCAGGGAGATAAGATCT-ATTACTTCAATCTGCTCC
* * * * * * **
34419935 GCTGCAACCTCAGGGAGATAAGACCTA--A-TGCGATCCACTCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
* * *
34419976 ACTAAAACTTCAGAGAGATAAGATCTATTACTTTAATCAT-CTCC
1 ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATC-TGCTCC
* *
34420020 ACTACAAGTTTAGGGAGATA
1 ACTACAACTTCAGGGAGATA
34420040 GGATTTGTGG
Statistics
Matches: 587, Mismatches: 166, Indels: 98
0.69 0.20 0.12
Matches are distributed among these distances:
40 10 0.02
41 99 0.17
42 8 0.01
43 44 0.07
44 307 0.52
45 111 0.19
46 8 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
ACTACAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCTCC
Found at i:34420182 original size:129 final size:129
Alignment explanation
Indices: 34420031--34420433 Score: 662
Period size: 129 Copynumber: 3.1 Consensus size: 129
34420021 CTACAAGTTT
* * **
34420031 AGGGAGATAGGATTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGTCGTCTTCG
1 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
* *
34420096 ATCTGCTTCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCTAGCCTATTCCACTGCTGACC
66 ATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACC
* *
34420160 AGGGATATAGGACTTATGGCTTAAATCTACTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
1 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
* *
34420225 ATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTTCTAACATATTCCACTGCTGACC
66 ATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACC
34420289 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
1 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
* * * * * *
34420354 ATCTGCTCCGCTATTACTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCCATTGCTGACC
66 ATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACC
34420418 AGGGATATAGGACTTG
1 AGGGATATAGGACTTG
34420434 CAATCTTCAA
Statistics
Matches: 254, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 254 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (129 bp):
AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCG
ATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACC
Found at i:34420479 original size:44 final size:44
Alignment explanation
Indices: 34420431--34420521 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
34420421 GATATAGGAC
*
34420431 TTGCAATCTTCAACCTATTCCGCTGCTGGTCA-ATGAGCTAGGTT
1 TTGCAATCTTCAACCTATTCCACTGCTGGTCAGA-GAGCTAGGTT
34420475 TTGCAATCTTCAACCTATTCCACTGCTGGTCAGAGAGCTAGGTT
1 TTGCAATCTTCAACCTATTCCACTGCTGGTCAGAGAGCTAGGTT
34420519 TTG
1 TTG
34420522 TGATTTCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (44 bp):
TTGCAATCTTCAACCTATTCCACTGCTGGTCAGAGAGCTAGGTT
Found at i:34421825 original size:8 final size:7
Alignment explanation
Indices: 34421783--34421824 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
34421773 TACTCTTTCA
34421783 TCATTTT
1 TCATTTT
34421790 T-ATTTT
1 TCATTTT
34421796 TCA-TTT
1 TCATTTT
34421802 TCACTTTT
1 TCA-TTTT
34421810 TCATTTT
1 TCATTTT
34421817 TCATTTT
1 TCATTTT
34421824 T
1 T
34421825 TTTACTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.38
7 14 0.44
8 6 0.19
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
TCATTTT
Found at i:34422678 original size:6 final size:6
Alignment explanation
Indices: 34422653--34422728 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
34422643 CCTTCTCTCT
* * * * * *
34422653 ATTTTC ATTTTG ACTTTG ATTTTG ATTTTC CTTTTT CTTCTT- -TTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG ATTTTG
34422700 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
34422729 TTTTGGATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 55 0.90
7 2 0.03
ACGTcount: A:0.13, C:0.08, G:0.11, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:34422729 original size:41 final size:42
Alignment explanation
Indices: 34422645--34422729 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
34422635 CTTTTTTTCC
*
34422645 TTCTCTCTATTTTCATTTTGACTTTGATTTTGATTTTCCTTT
1 TTCTCTCTATTTTCATTTTGACTTTGATTTTGATTTTCATTT
* * * *
34422687 TTCT-TCTTTTTTGATTTTGATTTTGATTTTGATTTTGATTT
1 TTCTCTCTATTTTCATTTTGACTTTGATTTTGATTTTCATTT
34422728 TT
1 TT
34422730 TTTGGATTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.12, C:0.11, G:0.09, T:0.68
Consensus pattern (42 bp):
TTCTCTCTATTTTCATTTTGACTTTGATTTTGATTTTCATTT
Found at i:34422732 original size:35 final size:35
Alignment explanation
Indices: 34422660--34422733 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
34422650 TCTATTTTCA
* * **
34422660 TTTTGACTTTGATTTTGATTTTCCTTTTTCTTCTT
1 TTTTGATTTTGATTTTGATTTTCATTTTGATTCTT
*
34422695 TTTTGATTTTGATTTTGATTTTGATTTTGATT-TT
1 TTTTGATTTTGATTTTGATTTTCATTTTGATTCTT
34422729 TTTTG
1 TTTTG
34422734 GATTGGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.11, C:0.07, G:0.12, T:0.70
Consensus pattern (35 bp):
TTTTGATTTTGATTTTGATTTTCATTTTGATTCTT
Found at i:34426138 original size:71 final size:71
Alignment explanation
Indices: 34426022--34426173 Score: 304
Period size: 71 Copynumber: 2.1 Consensus size: 71
34426012 TGTCCCCAGT
34426022 GGAGTCGCCAAGCTGTCGAAACCATTTTTTATGTATTTGAAAAACGGGGATCGACTTTGAGAATG
1 GGAGTCGCCAAGCTGTCGAAACCATTTTTTATGTATTTGAAAAACGGGGATCGACTTTGAGAATG
34426087 AAAATG
66 AAAATG
34426093 GGAGTCGCCAAGCTGTCGAAACCATTTTTTATGTATTTGAAAAACGGGGATCGACTTTGAGAATG
1 GGAGTCGCCAAGCTGTCGAAACCATTTTTTATGTATTTGAAAAACGGGGATCGACTTTGAGAATG
34426158 AAAATG
66 AAAATG
34426164 GGAGTCGCCA
1 GGAGTCGCCA
34426174 CCGATCTTTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (71 bp):
GGAGTCGCCAAGCTGTCGAAACCATTTTTTATGTATTTGAAAAACGGGGATCGACTTTGAGAATG
AAAATG
Found at i:34427686 original size:2 final size:2
Alignment explanation
Indices: 34427630--34427666 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
34427620 AGTAAATAAG
*
34427630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34427667 GAAAATAAGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34433234 original size:20 final size:21
Alignment explanation
Indices: 34433208--34433250 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
34433198 CGGCAAAAGT
* *
34433208 TTTTTAAAATTGTATTATAAA
1 TTTTAAAAATTATATTATAAA
34433229 TTTTAAAAAATTATATTATAAA
1 TTTT-AAAAATTATATTATAAA
34433251 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAAAAATTATATTATAAA
Found at i:34433593 original size:16 final size:14
Alignment explanation
Indices: 34433572--34433605 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
34433562 ATCATTTTTT
34433572 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
34433588 TTATAAATTTTATA
1 TTATAAATTTTATA
34433602 TTAT
1 TTAT
34433606 TTTTACCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:34437861 original size:56 final size:59
Alignment explanation
Indices: 34437788--34437902 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 59
34437778 ACTATTCCAA
* * * *
34437788 AAATAATATTATTTTAATAGTTTTAATATTAAATTTAATTTAATATTTATCTTGTAGAT
1 AAATATTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGTAGAT
34437847 AAATATTCTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTG
1 AAATA-T-TATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTG
34437903 ACAAGTATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 5 0.10
61 45 0.90
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (59 bp):
AAATATTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGTAGAT
Found at i:34437945 original size:58 final size:60
Alignment explanation
Indices: 34437794--34437951 Score: 162
Period size: 61 Copynumber: 2.6 Consensus size: 60
34437784 CCAAAAATAA
* * * * *
34437794 TATTATTTTAATAGTTTTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTC
1 TATTAATTTAATA-ATTAAATATTAAATTTAATCTAATATTTATCTTGTAGACAAATATTC
* * *
34437855 TATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATC-T-T-GACAAGTATTG
1 TATTAATTTAATA-ATTAAATATTAAATTTAATCTAATATTTATCTTGTAGACAAATATTC
*
34437913 TATTAATTTAAT-ATTAAAGTGATTAAGTTTAATCATAAT
1 TATTAATTTAATAATTAAA-T-ATTAAATTTAATC-TAAT
34437952 TGAACTTTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
56 5 0.06
57 1 0.01
58 32 0.37
59 5 0.06
60 1 0.01
61 42 0.49
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (60 bp):
TATTAATTTAATAATTAAATATTAAATTTAATCTAATATTTATCTTGTAGACAAATATTC
Found at i:34441908 original size:61 final size:60
Alignment explanation
Indices: 34441833--34441957 Score: 214
Period size: 61 Copynumber: 2.1 Consensus size: 60
34441823 GGATGCGAAC
**
34441833 TATGATGAGTAAAATAGACGGATGACGTTTAGTGAAACAATGATGTTTAGTTTAAGAAAAA
1 TATGATGAGTAAAATAGACGGATGACGTTTAGTGAAACAATGAACTTTAGTTTAAG-AAAA
*
34441894 TATGATGAGTAAAATAGACGGGTGACGTTTAGTGAAACAATGAACTTTAGTTTAAGAAAA
1 TATGATGAGTAAAATAGACGGATGACGTTTAGTGAAACAATGAACTTTAGTTTAAGAAAA
34441954 TATG
1 TATG
34441958 GCAAACTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
60 8 0.13
61 53 0.87
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (60 bp):
TATGATGAGTAAAATAGACGGATGACGTTTAGTGAAACAATGAACTTTAGTTTAAGAAAA
Found at i:34445008 original size:30 final size:31
Alignment explanation
Indices: 34444974--34445044 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
34444964 TTGCCCAAGA
* *
34444974 GTAAATATTTAAAATTTGAGGGGTTAA-AGT
1 GTAAATATTTAAAATTTGAAGGATTAATAGT
** *
34445004 GTAAATATGAAAAATTTGAAGGATTAATTGT
1 GTAAATATTTAAAATTTGAAGGATTAATAGT
34445035 GTAAATATTT
1 GTAAATATTT
34445045 TAAGGGTGGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (31 bp):
GTAAATATTTAAAATTTGAAGGATTAATAGT
Found at i:34448475 original size:11 final size:11
Alignment explanation
Indices: 34448430--34448475 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
34448420 ACTATTCAAT
34448430 TTAATTTAATA
1 TTAATTTAATA
*
34448441 CTAATATTAATA
1 TTAAT-TTAATA
34448453 TT-ATTT--TA
1 TTAATTTAATA
34448461 TTAATTTAATA
1 TTAATTTAATA
34448472 TTAA
1 TTAA
34448476 AGTAATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 2 0.07
11 12 0.41
12 7 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:34448483 original size:20 final size:18
Alignment explanation
Indices: 34448422--34448509 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 18
34448412 ATATTTTTAC
34448422 TATTCAATTTAAT-TT-AA
1 TATT-AATTTAATATTAAA
* **
34448439 TACTAATATTAATATTATTT
1 TATTAAT-TTAATATTA-AA
34448459 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
34448477 GTAATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
34448497 T-TTAATTTAATAT
1 TATTAATTTAATAT
34448510 CTATCTTGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
16 3 0.05
17 17 0.30
18 4 0.07
19 13 0.23
20 20 0.35
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:34456689 original size:18 final size:18
Alignment explanation
Indices: 34456658--34456707 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
34456648 TAAAAAAAAC
*
34456658 ATTTTGAAATTGAATAAT
1 ATTTTGAAAATGAATAAT
*
34456676 GA-TTTGTAAATGAATAAT
1 -ATTTTGAAAATGAATAAT
34456694 ATTTTGAAAATGAA
1 ATTTTGAAAATGAA
34456708 CGACATGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
ATTTTGAAAATGAATAAT
Found at i:34464387 original size:21 final size:21
Alignment explanation
Indices: 34464362--34464437 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
34464352 TAAAAAGTTA
*
34464362 TATGTTATGTATGATCTGTG-T
1 TATGTTAAGTATGATCTG-GAT
* *
34464383 TATGTTAAATATGATCAGGAT
1 TATGTTAAGTATGATCTGGAT
* **
34464404 TATGTAAAGTATGATCTATAT
1 TATGTTAAGTATGATCTGGAT
*
34464425 TATGGTAAGTATG
1 TATGTTAAGTATG
34464438 TATGAATCTA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (21 bp):
TATGTTAAGTATGATCTGGAT
Found at i:34464689 original size:20 final size:20
Alignment explanation
Indices: 34464661--34464702 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
34464651 TAACAAAATC
*
34464661 TCAAAACTGTCACATA-GGTA
1 TCAAAACTGACAC-TAGGGTA
*
34464681 TCAATACTGACACTAGGGTA
1 TCAAAACTGACACTAGGGTA
34464701 TC
1 TC
34464703 GATATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
TCAAAACTGACACTAGGGTA
Found at i:34465610 original size:39 final size:38
Alignment explanation
Indices: 34465550--34465699 Score: 169
Period size: 39 Copynumber: 3.9 Consensus size: 38
34465540 AATATCAAGA
* *
34465550 ATATATGACAATACTC-AATAATCACATAACATCTAAGC
1 ATATATCACAATACTCGTATAATCACATAACAT-TAAGC
* * *
34465588 ATATATCACAATTCACGTATAAT-ATCATAACATTCAAAC
1 ATATATCACAATACTCGTATAATCA-CATAACATT-AAGC
* * *
34465627 ATATATAACAATACTCATATAATCGCATAACATTTAAGC
1 ATATATCACAATACTCGTATAATCACATAACA-TTAAGC
*
34465666 ATATATCACAATACTCGTTTAATCACATAACATT
1 ATATATCACAATACTCGTATAATCACATAACATT
34465700 CATAATTTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
38 17 0.18
39 73 0.79
40 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (38 bp):
ATATATCACAATACTCGTATAATCACATAACATTAAGC
Found at i:34465695 original size:78 final size:77
Alignment explanation
Indices: 34465550--34465701 Score: 225
Period size: 78 Copynumber: 2.0 Consensus size: 77
34465540 AATATCAAGA
* *
34465550 ATATATGACAATACTCAATAATCACATAACATCTAAGCATATATCACAATTCACGTATAATATCA
1 ATATATAACAATACTCAATAATCACATAACATCTAAGCATATATCACAATACACGTATAATATCA
34465615 TAACATTCAAAC
66 TAACATTCAAAC
* * * *
34465627 ATATATAACAATACTCATATAATCGCATAACATTTAAGCATATATCACAATACTCGTTTAATCA-
1 ATATATAACAATACTCA-ATAATCACATAACATCTAAGCATATATCACAATACACGTATAAT-AT
34465691 CATAACATTCA
64 CATAACATTCA
34465702 TAATTTAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 16 0.24
78 50 0.75
79 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.30
Consensus pattern (77 bp):
ATATATAACAATACTCAATAATCACATAACATCTAAGCATATATCACAATACACGTATAATATCA
TAACATTCAAAC
Found at i:34473530 original size:88 final size:87
Alignment explanation
Indices: 34473381--34473923 Score: 694
Period size: 88 Copynumber: 6.2 Consensus size: 87
34473371 TGGGGTCTTC
* * * *
34473381 GATCTGCTATTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* *
34473446 TCATTGTCAGTACAGGAAGGCAA
66 TCACTGTC-GTGCAGGAAGGCAA
* * *
34473469 GATCTGATATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGTTGGTATCTTCGATCTGCT
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* *
34473534 TCGCTGTCGATGCAAGAAGGCAA
66 TCACTGTCG-TGCAGGAAGGCAA
* * *
34473557 GATCTGCTATCTTTAACCTGCTCCACTGCAACTGAGGGAGGCAAGGCTGGTGTCTTCGATCTACT
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* *
34473622 TCACTATCGGTGCAAGAAGGCAA
66 TCACTGTC-GTGCAGGAAGGCAA
* * * * *
34473645 GATCTGCTATTTTTAACTTGCTCCACTGTAA-TCGAGGGAGGCAAGGCTGGTGTCTTTGATCTGC
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTC-AGGGAGGCAAGGCTGGTGTCTTCGATCTGC
*
34473709 TTCACTGTCAGTACAGGAAGGCAA
65 TTCACTGTC-GTGCAGGAAGGCAA
* * * *
34473733 GATCTGCTATCTTCAACCTCCTCCACTGCAACCCAGGGAGGCAAGGCTGATATCTTCGATCTGCT
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
**
34473798 TCGTTGTCGATGCAGGAAGGCAA
66 TCACTGTCG-TGCAGGAAGGCAA
* * * *
34473821 GATCTGCTATCTTCAACCTGCTCCACTGTAAC-CAAGGGAAGCAAGGCTAGTGTCTTCAATCTGC
1 GATCTGCTATCTTCAACCTGCTCCACTGCAACTC-AGGGAGGCAAGGCTGGTGTCTTCGATCTGC
*
34473885 TTCACTGTCGGTGCAGGAAAGCAA
65 TTCACTGTC-GTGCAGGAAGGCAA
*
34473909 GATATGCTATCTTCA
1 GATCTGCTATCTTCA
34473924 CTGATCTATT
Statistics
Matches: 396, Mismatches: 52, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
87 4 0.01
88 389 0.98
89 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (87 bp):
GATCTGCTATCTTCAACCTGCTCCACTGCAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
TCACTGTCGTGCAGGAAGGCAA
Found at i:34473867 original size:264 final size:264
Alignment explanation
Indices: 34473381--34473923 Score: 825
Period size: 264 Copynumber: 2.1 Consensus size: 264
34473371 TGGGGTCTTC
*
34473381 GATCTGCTATTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
1 GATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
* * *
34473446 TCATTGTCAGTACAGGAAGGCAAGATCTGATATCTTCAACCTGCTCCACTGCAACTCAGGGAGGC
66 TCACTGTCAGTACAGGAAGGCAAGATCTGATATCTTCAACCTCCTCCACTGCAACCCAGGGAGGC
* * *
34473511 AAGGTTGGTATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATCTTTAACCT
131 AAGGCTGATATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATCTTCAACCT
** * * * *
34473576 GCTCCACTGCAACTGAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTATCGGTGCAAGAAG
196 GCTCCACTGCAACCAAGGGAAGCAAGGCTAGTGTCTTCAATCTACTTCACTATCGGTGCAAGAAA
34473641 GCAA
261 GCAA
* * * * * * *
34473645 GATCTGCTATTTTTAACTTGCTCCACTGTAATCGAGGGAGGCAAGGCTGGTGTCTTTGATCTGCT
1 GATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
*
34473710 TCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTCCTCCACTGCAACCCAGGGAGGC
66 TCACTGTCAGTACAGGAAGGCAAGATCTGATATCTTCAACCTCCTCCACTGCAACCCAGGGAGGC
* *
34473775 AAGGCTGATATCTTCGATCTGCTTCGTTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCT
131 AAGGCTGATATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATCTTCAACCT
* * * *
34473840 GCTCCACTGTAACCAAGGGAAGCAAGGCTAGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAA
196 GCTCCACTGCAACCAAGGGAAGCAAGGCTAGTGTCTTCAATCTACTTCACTATCGGTGCAAGAAA
34473905 GCAA
261 GCAA
* *
34473909 GATATGCTATCTTCA
1 GATCTGCTATTTTCA
34473924 CTGATCTATT
Statistics
Matches: 249, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
264 249 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (264 bp):
GATCTGCTATTTTCAACCTGCTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
TCACTGTCAGTACAGGAAGGCAAGATCTGATATCTTCAACCTCCTCCACTGCAACCCAGGGAGGC
AAGGCTGATATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATCTTCAACCT
GCTCCACTGCAACCAAGGGAAGCAAGGCTAGTGTCTTCAATCTACTTCACTATCGGTGCAAGAAA
GCAA
Found at i:34475200 original size:15 final size:16
Alignment explanation
Indices: 34475176--34475207 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
34475166 GGCCTCTCCA
34475176 TTTTCTTTTTTCTTCT
1 TTTTCTTTTTTCTTCT
34475192 TTTTC-TTTTTCTTCT
1 TTTTCTTTTTTCTTCT
34475207 T
1 T
34475208 CATTATCTTT
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTTTTCTTCT
Found at i:34475224 original size:24 final size:24
Alignment explanation
Indices: 34475189--34475235 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34475179 TCTTTTTTCT
* *
34475189 TCTTTTTCTTTTTCTTCTTCATTA
1 TCTTTTTCTTTTTATTCATCATTA
34475213 TCTTTATT-TTTTTATTCATCATT
1 TCTTT-TTCTTTTTATTCATCATT
34475236 TTTTTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (24 bp):
TCTTTTTCTTTTTATTCATCATTA
Found at i:34486246 original size:21 final size:20
Alignment explanation
Indices: 34486222--34486287 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
34486212 AATAAGTTAG
*
34486222 ATGTTAAGTATGATCTGTGTT
1 ATGTTAAGTATGAT-TGTATT
*
34486243 ATGTTAAATATGATTAGTATT
1 ATGTTAAGTATGATT-GTATT
*
34486264 ATGTAAAGTATGATTTGTATT
1 ATGTTAAGTATGA-TTGTATT
34486285 ATG
1 ATG
34486288 GTAACTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.47
Consensus pattern (20 bp):
ATGTTAAGTATGATTGTATT
Found at i:34486296 original size:21 final size:21
Alignment explanation
Indices: 34486230--34486301 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
34486220 AGATGTTAAG
* * *
34486230 TATGATCTGTGTTATGTTAAA
1 TATGATTTGTATTATGGTAAA
*
34486251 TATGATTAGTATTAT-GTAAA
1 TATGATTTGTATTATGGTAAA
*
34486271 GTATGATTTGTATTATGGTAAC
1 -TATGATTTGTATTATGGTAAA
*
34486293 TATGTTTTG
1 TATGATTTG
34486302 AATCTGTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 4 0.10
21 34 0.81
22 4 0.10
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (21 bp):
TATGATTTGTATTATGGTAAA
Found at i:34488155 original size:13 final size:13
Alignment explanation
Indices: 34488137--34488161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34488127 AATAAACTCA
34488137 AATAATTATCTTT
1 AATAATTATCTTT
34488150 AATAATTATCTT
1 AATAATTATCTT
34488162 CGAAACACAA
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTATCTTT
Found at i:34489187 original size:18 final size:18
Alignment explanation
Indices: 34489166--34489207 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
34489156 TTAAGTAATA
34489166 AAAATTGGAA-TTTATTTT
1 AAAATT-GAATTTTATTTT
*
34489184 AAAACATGAATTTTATTTT
1 AAAA-TTGAATTTTATTTT
34489203 AAAAT
1 AAAAT
34489208 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (18 bp):
AAAATTGAATTTTATTTT
Found at i:34493662 original size:43 final size:43
Alignment explanation
Indices: 34493582--34493784 Score: 230
Period size: 43 Copynumber: 4.7 Consensus size: 43
34493572 AAAAAACACG
* **
34493582 GCTATAGAACATGACCTTTAGCGATGC-TTTACCTACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTA-CTACAAACGCC
* * *
34493625 GCTAAAGAACATGACCTTTAGCGGCACTTTTATTACAAATGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTACTACAAACGCC
34493668 GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCT-CAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTA-CTACAAACGCC
* * * ** **
34493711 ACTAAAAAACATGACCTTTAGCGGAGCTGCTACCGCAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTACTACAAACGCC
** *
34493754 GCTAAAGAGTATGATCTTTAGCGGCGCTTTT
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTT
34493785 TAAAACAAAT
Statistics
Matches: 134, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 128 0.96
44 5 0.04
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTTACTACAAACGCC
Found at i:34495469 original size:7 final size:7
Alignment explanation
Indices: 34495457--34495669 Score: 117
Period size: 7 Copynumber: 29.9 Consensus size: 7
34495447 ACTAATTAAT
34495457 CTAAACC
1 CTAAACC
34495464 CTAAACTC
1 CTAAAC-C
* **
34495472 ATATCCC
1 CTAAACC
34495479 CTAAACC
1 CTAAACC
*
34495486 CTAAATC
1 CTAAACC
* *
34495493 ATAAAAC
1 CTAAACC
*
34495500 ATAAACC
1 CTAAACC
34495507 CTAAACC
1 CTAAACC
34495514 CTAAACC
1 CTAAACC
34495521 CTAAACC
1 CTAAACC
34495528 TCTAAACC
1 -CTAAACC
34495536 CTAAACC
1 CTAAACC
*
34495543 TTAAACC
1 CTAAACC
*
34495550 C-CAACC
1 CTAAACC
34495556 CTTAAACC
1 C-TAAACC
*
34495564 ATAAACC
1 CTAAACC
* *
34495571 ATAATCC
1 CTAAACC
* **
34495578 ATAATTC
1 CTAAACC
34495585 CTAAACC
1 CTAAACC
*
34495592 CATAATCC
1 C-TAAACC
*
34495600 ATAAACC
1 CTAAACC
*
34495607 TTAAA--
1 CTAAACC
*
34495612 ATAGTAACTC
1 CTA--AAC-C
*
34495622 TTAAACC
1 CTAAACC
*
34495629 TTAAACC
1 CTAAACC
*
34495636 CTAAATC
1 CTAAACC
* *
34495643 ATATACC
1 CTAAACC
34495650 CTAAACC
1 CTAAACC
*
34495657 ATAAACC
1 CTAAACC
34495664 CTAAAC
1 CTAAAC
34495670 TATAATGATA
Statistics
Matches: 160, Mismatches: 36, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
5 2 0.01
6 5 0.03
7 128 0.80
8 23 0.14
10 2 0.01
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:34495511 original size:14 final size:14
Alignment explanation
Indices: 34495458--34495674 Score: 143
Period size: 14 Copynumber: 15.2 Consensus size: 14
34495448 CTAATTAATC
34495458 TAAACCCTAAACTCA
1 TAAACCCTAAAC-CA
** *
34495473 TATCCCCTAAACCC
1 TAAACCCTAAACCA
* * *
34495487 TAAATCATAAAACA
1 TAAACCCTAAACCA
*
34495501 TAAACCCTAAACCC
1 TAAACCCTAAACCA
*
34495515 TAAACCCTAAACCTC
1 TAAACCCTAAACC-A
*
34495530 TAAACCCTAAACCT
1 TAAACCCTAAACCA
* * *
34495544 TAAACCCCAACCCT
1 TAAACCCTAAACCA
*
34495558 TAAACCATAAACCA
1 TAAACCCTAAACCA
* * *
34495572 TAATCCATAATTCC-
1 TAAACCCTAA-ACCA
*
34495586 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
*
34495601 TAAACCTTAAA--A
1 TAAACCCTAAACCA
* *
34495613 TAGTAACTCTTAAACCT
1 TA--AAC-CCTAAACCA
*
34495630 TAAACCCTAAATCA
1 TAAACCCTAAACCA
*
34495644 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
34495658 TAAACCCTAAACTA
1 TAAACCCTAAACCA
34495672 TAA
1 TAA
34495675 TGATAATTAA
Statistics
Matches: 159, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
12 3 0.02
14 110 0.69
15 44 0.28
17 2 0.01
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:34495547 original size:29 final size:28
Alignment explanation
Indices: 34495502--34495570 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
34495492 CATAAAACAT
*
34495502 AAACCCTAAACCCTAAACCCTAAACCTCT
1 AAACCCTAAA-CCTAAACCCCAAACCTCT
*
34495531 AAACCCTAAACCTTAAACCCCAACCCT-T
1 AAACCCTAAACC-TAAACCCCAAACCTCT
*
34495559 AAACCATAAACC
1 AAACCCTAAACC
34495571 ATAATCCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (28 bp):
AAACCCTAAACCTAAACCCCAAACCTCT
Found at i:34495596 original size:15 final size:15
Alignment explanation
Indices: 34495558--34495606 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
34495548 CCCCAACCCT
*
34495558 TAAA-CCATAAACCA
1 TAAACCCATAATCCA
*
34495572 T-AATCCATAATTCC-
1 TAAACCCATAA-TCCA
34495586 TAAACCCATAATCCA
1 TAAACCCATAATCCA
34495601 TAAACC
1 TAAACC
34495607 TTAAAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 11 0.38
15 16 0.55
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:34496145 original size:40 final size:40
Alignment explanation
Indices: 34496085--34496175 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
34496075 TATAGGTAGC
*
34496085 GCCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAAAAGT
1 GCCGCTAATGCTCGACCTATAGCAGCGTTTTTCAAAAAGT
* * * *
34496125 GCCGGTAATGCTCGATCTATAGCTGCGTTTTTCAAAAAGC
1 GCCGCTAATGCTCGACCTATAGCAGCGTTTTTCAAAAAGT
*
34496165 GCCACTAATGC
1 GCCGCTAATGC
34496176 CATTAAAGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (40 bp):
GCCGCTAATGCTCGACCTATAGCAGCGTTTTTCAAAAAGT
Found at i:34496244 original size:106 final size:106
Alignment explanation
Indices: 34496109--34496386 Score: 396
Period size: 106 Copynumber: 2.6 Consensus size: 106
34496099 ACCTATAGCA
* * * *
34496109 GCGTTTTTCAAAAAGTGCCGGTAATGCTCGATCTATAGCTGCGTTTTTCAAAAAGCGCCACTAAT
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAAT
* *
34496174 GCCATTAAAGCTCAATATAAAACGTGCTTAATTTTTTTGTG
66 GCCACTAAAGCTCAATATAAAACGTGCTTAATTTTTTTGCG
* *
34496215 GCGTTTTTCAAGAAGCGCCGCTAATGCTCGATCTATAGCGGC-TTTTTCCAAAAAGCGACGCTAA
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTT-CAAAAAGCGCCGCTAA
*
34496279 TGCCACTAAAGCTTAATATAAAACGTGCTTAATTTTTTTGCG
65 TGCCACTAAAGCTCAATATAAAACGTGCTTAATTTTTTTGCG
* ** * * * *
34496321 GTGTTTTTCAAAAAGCATCGCTAATGGTCGACCTATAGCGGTGTTTTTCAAAAAGCACCGCTAAT
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAAT
34496386 G
66 G
34496387 GTCAACCTAT
Statistics
Matches: 152, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
105 5 0.03
106 142 0.93
107 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (106 bp):
GCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAAT
GCCACTAAAGCTCAATATAAAACGTGCTTAATTTTTTTGCG
Found at i:34496373 original size:40 final size:40
Alignment explanation
Indices: 34496318--34496416 Score: 171
Period size: 40 Copynumber: 2.5 Consensus size: 40
34496308 TAATTTTTTT
* *
34496318 GCGGTGTTTTTCAAAAAGCATCGCTAATGGTCGACCTATA
1 GCGGTGTTTTTCAAAAAGCACCGCTAATGGTCAACCTATA
34496358 GCGGTGTTTTTCAAAAAGCACCGCTAATGGTCAACCTATA
1 GCGGTGTTTTTCAAAAAGCACCGCTAATGGTCAACCTATA
*
34496398 GCGGCGTTTTTCAAAAAGC
1 GCGGTGTTTTTCAAAAAGC
34496417 CCTAAGCGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (40 bp):
GCGGTGTTTTTCAAAAAGCACCGCTAATGGTCAACCTATA
Found at i:34503931 original size:3 final size:3
Alignment explanation
Indices: 34503925--34503979 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
34503915 ATCATCGAAG
*
34503925 GTA GTA GTA GTA GTA GTA GTC GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
34503973 GTA GTA G
1 GTA GTA G
34503980 AAGTTGAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:34513433 original size:18 final size:18
Alignment explanation
Indices: 34513403--34513450 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
34513393 TGTCGTTCGT
34513403 TTTCAAAAT-ATTATTC-A
1 TTTC-AAATCATTATTCAA
34513420 TTTACAAATCATTATTCAA
1 TTT-CAAATCATTATTCAA
*
34513439 TTTCAAAACATT
1 TTTCAAATCATT
34513451 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTCAAATCATTATTCAA
Found at i:34514418 original size:17 final size:18
Alignment explanation
Indices: 34514386--34514420 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
34514376 CCATGATGTT
34514386 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGGCCCACA
*
34514404 CGCCCTTGT-GGCCCACA
1 CGCCCGTGTGGGCCCACA
34514421 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.46, G:0.29, T:0.14
Consensus pattern (18 bp):
CGCCCGTGTGGGCCCACA
Found at i:34522198 original size:28 final size:28
Alignment explanation
Indices: 34522167--34522262 Score: 156
Period size: 28 Copynumber: 3.4 Consensus size: 28
34522157 ATAAGTTCAG
* * * *
34522167 ACACTTAGTGCTTAATAATCAAACTCAC
1 ACACTTAGTGCTTTACAATTAAACTCGC
34522195 ACACTTAGTGCTTTACAATTAAACTCGC
1 ACACTTAGTGCTTTACAATTAAACTCGC
34522223 ACACTTAGTGCTTTACAATTAAACTCGC
1 ACACTTAGTGCTTTACAATTAAACTCGC
34522251 ACACTTAGTGCT
1 ACACTTAGTGCT
34522263 AATCTCATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (28 bp):
ACACTTAGTGCTTTACAATTAAACTCGC
Found at i:34524676 original size:14 final size:14
Alignment explanation
Indices: 34524657--34524686 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34524647 CATTTCACTA
*
34524657 TTATGTCTTTTTAT
1 TTATGTCTTTATAT
34524671 TTATGTCTTTATAT
1 TTATGTCTTTATAT
34524685 TT
1 TT
34524687 TGCATGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TTATGTCTTTATAT
Found at i:34526055 original size:19 final size:19
Alignment explanation
Indices: 34526013--34526055 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
34526003 ATTTTCTTAA
* **
34526013 AAATTAATTTGGAAAATCT
1 AAATTAATTTAGAAAAAAT
34526032 AAATTAATTTAGAAAAAAT
1 AAATTAATTTAGAAAAAAT
*
34526051 TAATT
1 AAATT
34526056 TTGATCAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (19 bp):
AAATTAATTTAGAAAAAAT
Found at i:34526537 original size:37 final size:36
Alignment explanation
Indices: 34526491--34526601 Score: 115
Period size: 37 Copynumber: 3.1 Consensus size: 36
34526481 ATTCCAAAAA
34526491 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
34526527 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
**
34526564 TAA-ATTTAATGATAA-A-TATTATATTAATTTAATAT
1 TAATA-TT-ATTTTAATAGTATTATATTAATTTAATAT
34526599 TAA
1 TAA
34526602 AGTCATTAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
35 21 0.32
36 17 0.26
37 26 0.39
38 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:34526564 original size:11 final size:11
Alignment explanation
Indices: 34526491--34526601 Score: 79
Period size: 12 Copynumber: 9.8 Consensus size: 11
34526481 ATTCCAAAAA
*
34526491 TAATATTATTT
1 TAATATTAATT
34526502 TAATAGTTTAATAT
1 TAATA--TTAAT-T
34526516 TAA-ATTTAATT
1 TAATA-TTAATT
*
34526527 TAATACTTATTT
1 TAATA-TTAATT
*
34526539 TAATAGT-ATT
1 TAATATTAATT
34526549 T--TATTAATT
1 TAATATTAATT
34526558 TAATATTAAATT
1 TAATATT-AATT
*
34526570 TAATGATAAATAT
1 TAAT-ATTAAT-T
34526583 T-ATATTAATT
1 TAATATTAATT
34526593 TAATATTAA
1 TAATATTAA
34526602 AGTCATTAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 5 0.06
11 26 0.32
12 30 0.37
13 9 0.11
14 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:34530367 original size:29 final size:28
Alignment explanation
Indices: 34530310--34530375 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
34530300 TACATAGTAC
*
34530310 ATATATATGTGCGGTTCTGCTATACATA
1 ATATATATGTGCGGTTCTACTATACATA
* * *
34530338 ATATATATGTGTGAGTTCTATTATATATA
1 ATATATATGTGCG-GTTCTACTATACATA
34530367 ATATATATG
1 ATATATATG
34530376 CGGTTATAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (28 bp):
ATATATATGTGCGGTTCTACTATACATA
Found at i:34542627 original size:22 final size:22
Alignment explanation
Indices: 34542585--34542651 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
34542575 AATCCAAATC
34542585 AATA-AAAATTTTA-AAACATA
1 AATATAAAATTTTATAAACATA
*
34542605 AA-ATAAAATTTTATAAATTATA
1 AATATAAAATTTTATAAA-CATA
34542627 AATTATAATACATTTTATAAACATA
1 AA-TATAA-A-ATTTTATAAACATA
34542652 TACATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 3 0.08
22 5 0.13
24 4 0.11
25 4 0.11
26 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAATTTTATAAACATA
Found at i:34547650 original size:14 final size:15
Alignment explanation
Indices: 34547618--34547651 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34547608 TTTCATCCGT
*
34547618 TTTGGGCCATTGTAA
1 TTTGGGCCACTGTAA
34547633 TTTGGGCCACTG-AA
1 TTTGGGCCACTGTAA
34547647 TTTGG
1 TTTGG
34547652 TTTTGGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (15 bp):
TTTGGGCCACTGTAA
Found at i:34548038 original size:44 final size:44
Alignment explanation
Indices: 34547946--34548574 Score: 212
Period size: 44 Copynumber: 14.3 Consensus size: 44
34547936 CTGCAACTTC
* * * * * **
34547946 AGGGAGATAGGA-TTGTCGGCTTTAATCTGCTCCACTGCAACTT
1 AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* *
34547989 CAGGGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* * ** * * * * * * *
34548034 AGGGAGATAAGATCTACAATTTTCAATTTTCTCCGCTGCTACTC
1 AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* ** ** *
34548078 AGGGAGACAAGGCTTGGTGGC-TCAAATCTGCTTCCCACTA-T-CTT
1 AGGGAGATAAGATTTGCCGTCTTC-AATCTGC-T-CCACTACTGCTT
* * *
34548122 -GGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
1 AGG-GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* **** * * * *
34548166 AGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTGCTGCTC
1 AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* ** ** *
34548210 AGGGAGACAAGGCTTGGTGGC-TCAAATCTGCTTCCCACTA-T-CTT
1 AGGGAGATAAGATTTGCCGTCTTC-AATCTGC-T-CCACTACTGCTT
* * * *
34548254 -GGAAAGATAAGATTCGCCGTCTTCGATCTGCTTCACTACTGCTT
1 AGG-GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* **** * * * *
34548298 AGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTGCTGCTC
1 AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* ** ** *
34548342 AGGGAGACAAGGCTTGGTGGC-TCAAATCTGCTTCCCACTA-T-C-T
1 AGGGAGATAAGATTTGCCGTCTTC-AATCTGC-T-CCACTACTGCTT
* * *
34548385 AGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
1 AGG-GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* **** * * * *
34548430 AGGGAGATAAGATCTATAATCTTCAACCTTCTCCACTGCTGCTC
1 AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
* ** ** *
34548474 AGGGAGACAAGGCTTGGTGGCTT-AGATCTGCTTCCCACTA-T-CTT
1 AGGGAGATAAGATTTGCCGTCTTCA-ATCTGC-T-CCACTACTGCTT
* * **
34548518 -GGAAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTT
1 AGG-GAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
*
34548562 AGGGAGACAAGAT
1 AGGGAGATAAGAT
34548575 CTATAATCTT
Statistics
Matches: 402, Mismatches: 150, Indels: 66
0.65 0.24 0.11
Matches are distributed among these distances:
42 23 0.06
43 24 0.06
44 289 0.72
45 47 0.12
46 19 0.05
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTT
Found at i:34548130 original size:132 final size:132
Alignment explanation
Indices: 34547994--34548624 Score: 1127
Period size: 132 Copynumber: 4.8 Consensus size: 132
34547984 AACTTCAGGG
* * * *
34547994 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
** * *
34548059 ATTTTCTCCGCTGCTACTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
34548124 AA
131 AA
34548126 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
34548191 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
34548256 AA
131 AA
*
34548258 AGATAAGATTCGCCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
*
34548323 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTAGG
66 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
34548388 AA
131 AA
34548390 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
* *
34548455 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAGATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
34548520 AA
131 AA
* *
34548522 AGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTATAATCTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
*
34548587 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTGGGTG
66 ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTG
34548625 TTTCACCAGT
Statistics
Matches: 482, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 482 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (132 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
ACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
AA
Found at i:34560170 original size:98 final size:98
Alignment explanation
Indices: 34560050--34560240 Score: 319
Period size: 98 Copynumber: 1.9 Consensus size: 98
34560040 AGAATAAAAC
* *
34560050 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTATGGCACGATCCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
*
34560115 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
66 TAGAATCCCAAACTCGGAACATTTCCTTTACTT
* * *
34560148 TAAAAGAACTTCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
*
34560213 TAGAATCTCAAACTCGGAACATTTCCTT
66 TAGAATCCCAAACTCGGAACATTTCCTT
34560241 CATGATTTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 86 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (98 bp):
TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCCTT
TAGAATCCCAAACTCGGAACATTTCCTTTACTT
Found at i:34562106 original size:14 final size:15
Alignment explanation
Indices: 34562074--34562107 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34562064 TTTCATCCGT
*
34562074 TTTGGGCCATTGTAA
1 TTTGGGCCACTGTAA
34562089 TTTGGGCCACTG-AA
1 TTTGGGCCACTGTAA
34562103 TTTGG
1 TTTGG
34562108 TTTTGGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (15 bp):
TTTGGGCCACTGTAA
Found at i:34562456 original size:44 final size:44
Alignment explanation
Indices: 34562359--34562479 Score: 127
Period size: 44 Copynumber: 2.8 Consensus size: 44
34562349 GGACTACTGG
* * * * *
34562359 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTCAT
1 CTTCAATCTACTCCACTACTGCTTAGGGAGATAAAATCTATAAT
** *
34562403 CTTTGATCTACTCCACTATTGCTTAGGGAGATAAAATCTATAAT
1 CTTCAATCTACTCCACTACTGCTTAGGGAGATAAAATCTATAAT
* * *
34562447 CTTCAATCTATTCCATTGCTGAC-TAGGGAGATA
1 CTTCAATCTACTCCACTACTG-CTTAGGGAGATA
34562480 GGACTACTGG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 61 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (44 bp):
CTTCAATCTACTCCACTACTGCTTAGGGAGATAAAATCTATAAT
Found at i:34562565 original size:131 final size:130
Alignment explanation
Indices: 34562227--34562567 Score: 400
Period size: 131 Copynumber: 2.6 Consensus size: 130
34562217 AAGATTCATC
*
34562227 GCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGACCTGCTCCACTACT
1 GCTTAAATCT-CTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACT
* ** * *
34562292 GTTTAGGGAGACCAGATCTGTAATTTCTAACCTATTCCACTGCTGACCAGGGAAATAGGACTACT
65 GCTTAGGGAGATAAAATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAAATAGGACTACT
34562357 G
130 G
* * * * * * *
34562358 GCTTCAATCTGC-TCCACTACTGCTTAGGG-AGATAAGATTTGTCATCTTTGATCTACTCCACTA
1 GCTTAAATCT-CTTCC-CTACT-CCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
* * * * *
34562421 TTGCTTAGGGAGATAAAATCTATAATCTTC-AATCTATTCCATTGCTGACTAGGGAGATAGGACT
63 CTGCTTAGGGAGATAAAATCTATAAT-TTCTAACCTATTCCACTGCTGACCAGGGAAATAGGACT
34562485 ACTG
127 ACTG
* * * *
34562489 GCTTAAATCTATTTCCCTACTCCTGGGGAATATAAGATTCGCCGTCTTCGATCTGCTCTACTACT
1 GCTTAAATCT-CTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACT
*
34562554 GCTTAGAGAGATAA
65 GCTTAGGGAGATAA
34562568 GATATGTACT
Statistics
Matches: 173, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
130 8 0.05
131 154 0.89
132 11 0.06
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (130 bp):
GCTTAAATCTCTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTG
CTTAGGGAGATAAAATCTATAATTTCTAACCTATTCCACTGCTGACCAGGGAAATAGGACTACTG
Found at i:34562724 original size:154 final size:154
Alignment explanation
Indices: 34562428--34562712 Score: 435
Period size: 154 Copynumber: 1.9 Consensus size: 154
34562418 CTATTGCTTA
* * *
34562428 GGGAGATAAAATCTATAATCTTCAATCTATTCCATTGCTGACTAGGGAGATAGGACTACTGGCTT
1 GGGAGATAAAATCTATAATCTTCAATCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTT
* *
34562493 AAATCTATTTCCCTACTCCTGGGGAATATAAGATTCGCCGTCTTCGATCTGCTCTACTACTGCTT
66 AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
34562558 AGAGAGATAAGATATGTACTATTC
131 AGAGAGATAAGATATGTACTATTC
* * * * * *
34562582 GGGAGATAAGATCTGTACTCTTCATTCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
1 GGGAGATAAAATCTATAATCTTCAATCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTT
* * * *
34562647 AAATCTATTTCCCTACTCTTGGGGAAGATGAGATTCGCCGTCTTTGATTTGCTCCACTACTGCTT
66 AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
34562712 A
131 A
34562713 AGGGGATAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
154 116 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (154 bp):
GGGAGATAAAATCTATAATCTTCAATCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTT
AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
AGAGAGATAAGATATGTACTATTC
Found at i:34562815 original size:285 final size:285
Alignment explanation
Indices: 34562323--34562860 Score: 785
Period size: 285 Copynumber: 1.9 Consensus size: 285
34562313 AATTTCTAAC
* *
34562323 CTATTCCACTGCTGACCAGGGAAATAGGACTACTGGCTTCAATCTGCTCCACTACTGCTTAGGGA
1 CTATTCCACTGCTGACCAGGGAAATAGAACTACTGGCTTAAATCTGCTCCACTACTGCTTAGGGA
* * *
34562388 GATAAGATTTGTCATCTTTGATCTACTCCACTATTGCTTAGGGAGATAAAATCTATAATCTTCAA
66 GATAAGATTCGCCATCTTTGATCTACTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAA
* * *
34562453 TCTATTCCATTGCTGACTAGGGAGATAGGACTACTGGCTTAAATCTATTTCCCTACTCCTGGGGA
131 TCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTTAAATCTATTTCCCTACTCCTGGGGA
* *
34562518 ATATAAGATTCGCCGTCTTCGATCTGCTCTACTACTGCTTAGAGAGATAAGATATGTACTATTCG
196 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATATGTACTATTCG
34562583 GGAGATAAGATCTGTACTCTTCATT
261 GGAGATAAGATCTGTACTCTTCATT
* * * ** *
34562608 CTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTAAATCTATTTCC-CTACT-CTTGGGG
1 CTATTCCACTGCTGACCAGGGAAATAGAACTACTGGCTTAAATCT-GCTCCACTACTGCTTAGGG
* * * * * *
34562671 AAGATGAGATTCGCCGTCTTTGATTTGCTCCACTACTGCTTAAGGG-GATAAGATCTATACTCTT
65 -AGATAAGATTCGCCATCTTTGATCTACTCCACTACTGCTT-AGGGAGATAAAATCTATAATCTT
* * *
34562735 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTAAATCTGTTTCCCTACTCCTGG
128 CAATCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTTAAATCTATTTCCCTACTCCTGG
* *
34562800 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
193 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATATGTA
34562861 ATCTTTAACT
Statistics
Matches: 223, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
284 6 0.03
285 210 0.94
286 7 0.03
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (285 bp):
CTATTCCACTGCTGACCAGGGAAATAGAACTACTGGCTTAAATCTGCTCCACTACTGCTTAGGGA
GATAAGATTCGCCATCTTTGATCTACTCCACTACTGCTTAGGGAGATAAAATCTATAATCTTCAA
TCTATTCCACTGCTGACCAGGGAGATAGAACTACTGGCTTAAATCTATTTCCCTACTCCTGGGGA
AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATATGTACTATTCG
GGAGATAAGATCTGTACTCTTCATT
Found at i:34562820 original size:131 final size:131
Alignment explanation
Indices: 34562582--34562857 Score: 473
Period size: 131 Copynumber: 2.1 Consensus size: 131
34562572 TGTACTATTC
* *
34562582 GGGAGATAAGATCTGTACTCTTCATTCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
1 GGGAGATAAGATCTATACTCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
* * * *
34562647 AAATCTATTTCCCTACTCTTGGGGAAGATGAGATTCGCCGTCTTTGATTTGCTCCACTACTGCTT
66 AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
34562712 AA
131 -A
34562714 GGG-GATAAGATCTATACTCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
1 GGGAGATAAGATCTATACTCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
*
34562778 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
66 AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
34562843 A
131 A
34562844 GGGAGATAAGATCT
1 GGGAGATAAGATCT
34562858 GTAATCTTTA
Statistics
Matches: 136, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
130 4 0.03
131 129 0.95
132 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (131 bp):
GGGAGATAAGATCTATACTCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTT
AAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
A
Found at i:34585081 original size:35 final size:35
Alignment explanation
Indices: 34584984--34585083 Score: 155
Period size: 35 Copynumber: 2.9 Consensus size: 35
34584974 TTTGTTTGGC
* * *
34584984 GTGTTACGGTTGGATTAGCTCTTATGAACATTGGT
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCAATGGT
*
34585019 GTGTTTCGGTTGAATTAGCTCTTATGAGCAATGGT
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCAATGGT
*
34585054 GTGTTTCGATTGGATTAGCTCTTATGAGCA
1 GTGTTTCGGTTGGATTAGCTCTTATGAGCA
34585084 TCAGCGTGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (35 bp):
GTGTTTCGGTTGGATTAGCTCTTATGAGCAATGGT
Found at i:34585093 original size:35 final size:34
Alignment explanation
Indices: 34584980--34585102 Score: 147
Period size: 35 Copynumber: 3.5 Consensus size: 34
34584970 ACTTTTTGTT
*
34584980 TGGCGTGTTACGGTTGGATTAGCTCTTATGAACA
1 TGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
* * *
34585014 TTGGTGTGTTTCGGTTGAATTAGCTCTTATGAGCAA
1 -TGGCGTGTTACGGTTGGATTAGCTCTTATGAGC-A
* * *
34585050 TGGTGTGTTTCGATTGGATTAGCTCTTATGAGCA
1 TGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
*
34585084 TCAGCGTGTTACGGTTGGA
1 T-GGCGTGTTACGGTTGGA
34585103 CTGACAATGT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
34 2 0.03
35 73 0.96
36 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (34 bp):
TGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
Found at i:34595865 original size:16 final size:16
Alignment explanation
Indices: 34595821--34595868 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
34595811 TTCCACTAAT
*
34595821 AAGATTAATTATAATTA
1 AAGATTAAAT-TAATTA
*
34595838 AAG--TAAACTAATTA
1 AAGATTAAATTAATTA
34595852 AAGATTAAATTAATTA
1 AAGATTAAATTAATTA
34595868 A
1 A
34595869 TTAAGGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.35
15 3 0.12
16 11 0.42
17 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (16 bp):
AAGATTAAATTAATTA
Found at i:34595869 original size:20 final size:20
Alignment explanation
Indices: 34595824--34595872 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
34595814 CACTAATAAG
*
34595824 ATTAATTATAATTAAAGTAA
1 ATTAATTAAAATTAAAGTAA
* *
34595844 ACTAATTAAAGATTAAA-TTA
1 ATTAATTAAA-ATTAAAGTAA
34595864 ATTAATTAA
1 ATTAATTAA
34595873 GGTATAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
ATTAATTAAAATTAAAGTAA
Found at i:34596228 original size:21 final size:22
Alignment explanation
Indices: 34596204--34596250 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
34596194 TTTATTATTG
* * *
34596204 TTTTGCTGTTG-TTTGCTGCCA
1 TTTTGATGTTGCTCTGCTACCA
34596225 TTTTGATGTTGCTCTGCTACCA
1 TTTTGATGTTGCTCTGCTACCA
34596247 TTTT
1 TTTT
34596251 TCTATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (22 bp):
TTTTGATGTTGCTCTGCTACCA
Found at i:34596264 original size:22 final size:22
Alignment explanation
Indices: 34596239--34596280 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
34596229 GATGTTGCTC
34596239 TGCTACCATTTT-TCTATTATAT
1 TGCTACCATTTTGT-TATTATAT
*
34596261 TGCTACTATTTTGTTATTAT
1 TGCTACCATTTTGTTATTAT
34596281 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (22 bp):
TGCTACCATTTTGTTATTATAT
Done.