Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 60 of 203
Found at i:19296598 original size:133 final size:133
Alignment explanation
Indices: 19296237--19297166 Score: 689
Period size: 133 Copynumber: 6.8 Consensus size: 133
19296227 TCTCCTTTAG
* * * ** * *
19296237 GTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCT--CTGAAGTTGCAGTACAACAAATTGA
1 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * * * *
19296300 AGTTACAAATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTGAAGATAACAAATCTTATCTCTC
66 AGCTACAAATCTTATC-CTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCC
19296365 TGAA
130 TGAA
* * * **
19296369 GTTGCAGTAGAGCAAATTGAAGTCACTGTAGTGAATCTTATC-CACCTGAAGTTGCAGTGGAGCA
1 GTTGCAGTGGAACAGATTGAAG--A---TAGCAAATCTTATCTC-CCTGAAGTTGCAGTGGAGCA
* * * * * *
19296433 GATTAAAGCCACAAATCTTATCTTCCTGAAGTTGTAGTGGAGCAAATTGAAGTTA-CAAATCTTA
60 GATTGAAGCTACAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTA
19296497 TCTCCCTGAA
124 TCTCCCTGAA
* * * *
19296507 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTAAAGTTACAGTAGAGTAGATTGA
1 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * * * *
19296572 AGCGACAAATCATATACCTCTGAAGTTGCAGTGG-GTCAGATTAAATCTATCGTAATGAGTCTTA
66 AGCTACAAATCTTAT-CCTCTGAAGTTGCAGTGGAG-CAGATTGAA--GATAGCAA--A-TCTTA
* *
19296636 TTTCCTTGAA
124 TCTCCCTGAA
* * * * * * * *
19296646 G-TGCAGCGGAATAGATTAAAGCTACAAGTTACAAACCTTATCTCTCTGAAGTTACAATGGAGCA
1 GTTGCAGTGGAACAGATTGAAG--A-TAG---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
** * * * * *
19296710 GATTGAATATGCGAATCTTATTTCC-CTGAATTTGCAGTGGAGCAGATTGAAGATAGAAAATATT
60 GATTGAAGCTACAAATCTTA--TCCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTT
* **
19296774 ATTTCCCCAAA
123 ATCTCCCTGAA
* * * *
19296785 GTTGTAGTGGAACAGATTAAAGCTACAAGTTACAAATCTCATCTCCCTGAAGTTGCAGTGGAGCA
1 GTTGCAGTGGAACAGATTGAAG--A-TAG---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * ** * *
19296850 GGTT-AGAGCTACAAATCTTATCTTCCTGAAGTTGCGGTGGAATAGATTGAAGATAGCGAATCTC
60 GATTGA-AGCTACAAATCTTATCCT-CTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTT
19296914 ATCTCCCTGAA
123 ATCTCCCTGAA
* * * * * * *
19296925 GTTGCCGTGGAGCAGATTGAAGCTA-CAAATCTCATCTTCCTAAAGTTGTAGTGGAGCAGATTGA
1 GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * *
19296989 AGCTACAAATCTTATTTCC-CTGAAGTTACAGTGGAGCAAATTGAAGATAGCAAATCTTATCTCT
66 AGCTACAAATCTTA--TCCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCC
19297053 CTGAA
129 CTGAA
* * * * * *
19297058 GCTGCAGT-AAACCTGATTGAAGCTA-CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
1 GTTGCAGTGGAA-CAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * *
19297121 AAGCTACAAATCTTATGTCC-CTAAAGTTGCAGTGGAGTAGGTTGAA
65 AAGCTACAAATCTTA--TCCTCTGAAGTTGCAGTGGAGCAGATTGAA
19297167 ATTACATTTC
Statistics
Matches: 636, Mismatches: 127, Indels: 69
0.76 0.15 0.08
Matches are distributed among these distances:
132 21 0.03
133 246 0.39
134 5 0.01
135 3 0.00
136 3 0.00
137 12 0.02
138 58 0.09
139 87 0.14
140 127 0.20
141 2 0.00
142 5 0.01
144 63 0.10
145 3 0.00
146 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (133 bp):
GTTGCAGTGGAACAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
AGCTACAAATCTTATCCTCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCT
GAA
Found at i:19301541 original size:18 final size:17
Alignment explanation
Indices: 19301513--19301548 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
19301503 TATTTAATAG
*
19301513 TTTAATATTAATTTTAA
1 TTTAATATTAATCTTAA
19301530 TTTAATACTTAATCTTAA
1 TTTAATA-TTAATCTTAA
19301548 T
1 T
19301549 AGTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATATTAATCTTAA
Found at i:19306348 original size:16 final size:16
Alignment explanation
Indices: 19306296--19306349 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
19306286 ATAACATAGA
*
19306296 GTAATTAAATGAAAAT
1 GTAATTAAATGAAAGT
* *
19306312 GTAACT-ACT-AAAGT
1 GTAATTAAATGAAAGT
19306326 AGTAATTAAATGAAAGT
1 -GTAATTAAATGAAAGT
19306343 GTAATTA
1 GTAATTA
19306350 CTACTATTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 14 0.47
17 5 0.17
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (16 bp):
GTAATTAAATGAAAGT
Found at i:19311095 original size:3 final size:3
Alignment explanation
Indices: 19311087--19311139 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
19311077 AAATACATAC
19311087 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19311135 TAT TA
1 TAT TA
19311140 CATTCAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19313963 original size:3 final size:3
Alignment explanation
Indices: 19313955--19313989 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19313945 ATCACATGTT
19313955 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19313990 TGGATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19314107 original size:72 final size:72
Alignment explanation
Indices: 19313990--19314245 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
19313980 TATTATTATT
19313990 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
19314055 TTTTAAG
66 TTTTAAG
19314062 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
19314127 TTTTAAG
66 TTTTAAG
19314134 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
19314199 TTTTAAG
66 TTTTAAG
*
19314206 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
19314246 GTCAAGTTGT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGGGGTGATTTA
TTTTAAG
Found at i:19318471 original size:3 final size:3
Alignment explanation
Indices: 19318463--19318515 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
19318453 ATCACATGTT
*
19318463 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19318511 TTA TT
1 TTA TT
19318516 TGGATGTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19318593 original size:72 final size:72
Alignment explanation
Indices: 19318516--19318771 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
19318506 TATTATTATT
19318516 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
19318581 TTTTAAG
66 TTTTAAG
19318588 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
19318653 TTTTAAG
66 TTTTAAG
19318660 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
19318725 TTTTAAG
66 TTTTAAG
*
19318732 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
19318772 GTCAAGTTGT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:19321910 original size:30 final size:30
Alignment explanation
Indices: 19321875--19321936 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19321865 CATATTCTCC
19321875 AAGAATC-GAATTCTCTGAGATTCAAACATT
1 AAGAATCAG-ATTCTCTGAGATTCAAACATT
19321905 AAGAATCAGATTCTCTGAGATTCAAACATT
1 AAGAATCAGATTCTCTGAGATTCAAACATT
19321935 AA
1 AA
19321937 AAAAAGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (30 bp):
AAGAATCAGATTCTCTGAGATTCAAACATT
Found at i:19324385 original size:16 final size:15
Alignment explanation
Indices: 19324364--19324408 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19324354 AAAATGCCAG
*
19324364 AAATAATAAAATAATA
1 AAATAAAAAAATAA-A
* *
19324380 AAATAACAAAATAAC
1 AAATAAAAAAATAAA
19324395 AAATAAAAAAATAA
1 AAATAAAAAAATAA
19324409 GTAGGCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:19324400 original size:7 final size:8
Alignment explanation
Indices: 19324364--19324408 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
19324354 AAAATGCCAG
*
19324364 AAATAATA
1 AAATAACA
*
19324372 AAATAATA
1 AAATAACA
19324380 AAATAACA
1 AAATAACA
19324388 AAATAAC-
1 AAATAACA
*
19324395 AAATAAAA
1 AAATAACA
19324403 AAATAA
1 AAATAA
19324409 GTAGGCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (8 bp):
AAATAACA
Found at i:19332419 original size:44 final size:44
Alignment explanation
Indices: 19332359--19332572 Score: 225
Period size: 44 Copynumber: 4.9 Consensus size: 44
19332349 GATATGCTAT
* *
19332359 CTTCAGTCTAATCCACTGCAACTTCAGGGGGATAAGACTT-GTAA
1 CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGA-TTAGTAA
* ** * *
19332403 CTTCAATCTACTCCACTGCAACCTCAGGAAGATAGGATTAGTTAT
1 CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGATTAG-TAA
* * * * * *
19332448 CCTCAATCTGCTCCACTGCAACTTCAGGGAGACAAAATTTGTAA
1 CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGATTAGTAA
* * **
19332492 CTTTAATCTACCCCACTGCAACTTCAGGGGG-TAAGATTAGTGG
1 CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGATTAGTAA
* *
19332535 CTTTAATCTGCTCCACTGCAACTTCAGGGGGATAAGAT
1 CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGAT
19332573 CCGCCATAAA
Statistics
Matches: 139, Mismatches: 28, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
43 38 0.27
44 66 0.47
45 35 0.25
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGCAACTTCAGGGGGATAAGATTAGTAA
Found at i:19332490 original size:89 final size:87
Alignment explanation
Indices: 19332370--19332563 Score: 244
Period size: 89 Copynumber: 2.2 Consensus size: 87
19332360 TTCAGTCTAA
* * * *
19332370 TCCACTGCAACTTCAGGGGGATAAGACTTGTAACTTCAATCTACTCCACTGCAACCTCAGGAAGA
1 TCCACTGCAACTTCAGGGAGACAAAACTTGTAACTTCAATCTACCCCACTGCAACCTCAGG-AGA
* *
19332435 TAGGATTAGTTATCCTCAATCTGC
65 TAAGATTAG-TAGCCTCAATCTGC
* * * * *
19332459 TCCACTGCAACTTCAGGGAGACAAAATTTGTAACTTTAATCTACCCCACTGCAACTTCAGGGGGT
1 TCCACTGCAACTTCAGGGAGACAAAACTTGTAACTTCAATCTACCCCACTGCAACCTCAGGAGAT
* * *
19332524 AAGATTAGTGGCTTTAATCTGC
66 AAGATTAGTAGCCTCAATCTGC
19332546 TCCACTGCAACTTCAGGG
1 TCCACTGCAACTTCAGGG
19332564 GGATAAGATC
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 28 0.31
88 9 0.10
89 54 0.59
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (87 bp):
TCCACTGCAACTTCAGGGAGACAAAACTTGTAACTTCAATCTACCCCACTGCAACCTCAGGAGAT
AAGATTAGTAGCCTCAATCTGC
Found at i:19333944 original size:49 final size:48
Alignment explanation
Indices: 19333803--19333971 Score: 191
Period size: 49 Copynumber: 3.5 Consensus size: 48
19333793 CTCAAGGCTC
* * * *
19333803 CCTTTACGGGTTTTCACATTGGCCTCTCCTTTTTTTAGGACTCAAAGCG
1 CCTTTACGGGTTTTCGCCTTGGTCT-TTCTTTTTTTAGGACTCAAAGCG
* * ***
19333852 CCATTTGCGAGTTTTCTATTTGGTC--T-TTTTTTTAGGACTCAAAGCG
1 CC-TTTACGGGTTTTCGCCTTGGTCTTTCTTTTTTTAGGACTCAAAGCG
19333898 CTCTTTACGGGTTTTCGCCTTGGTCTTTCTTTTTTTAGGACTCAAAGCG
1 C-CTTTACGGGTTTTCGCCTTGGTCTTTCTTTTTTTAGGACTCAAAGCG
*
19333947 CCCTTTGCGGGTTTTCGCCTTGGTC
1 -CCTTTACGGGTTTTCGCCTTGGTC
19333972 CCTTTTCCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
46 38 0.38
47 1 0.01
48 1 0.01
49 44 0.44
50 17 0.17
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (48 bp):
CCTTTACGGGTTTTCGCCTTGGTCTTTCTTTTTTTAGGACTCAAAGCG
Found at i:19342034 original size:7 final size:7
Alignment explanation
Indices: 19342022--19342077 Score: 57
Period size: 6 Copynumber: 8.4 Consensus size: 7
19342012 TAGATATATA
19342022 AAAAAAT
1 AAAAAAT
19342029 AAAAAA-
1 AAAAAAT
*
19342035 AACAAA-
1 AAAAAAT
19342041 AAAAAAT
1 AAAAAAT
*
19342048 GAAAAAT
1 AAAAAAT
19342055 GAAAAAAT
1 -AAAAAAT
19342063 -AAAAAT
1 AAAAAAT
19342069 -AAAAAT
1 AAAAAAT
19342075 AAA
1 AAA
19342078 TTTAAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
6 22 0.52
7 14 0.33
8 6 0.14
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:19348679 original size:18 final size:18
Alignment explanation
Indices: 19348631--19348679 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
19348621 TTACTTGAAA
*
19348631 TTTAAATATTTTTAAATT
1 TTTATATATTTTTAAATT
* *
19348649 TTTATA-ACATTTTCAATT
1 TTTATATA-TTTTTAAATT
19348667 TTTATATATTTTT
1 TTTATATATTTTT
19348680 TTGATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATATTTTTAAATT
Found at i:19364271 original size:3 final size:3
Alignment explanation
Indices: 19364263--19364295 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
19364253 ATAAGAAGTA
*
19364263 GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
19364296 TTTAGCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:19371057 original size:61 final size:61
Alignment explanation
Indices: 19370944--19371069 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 61
19370934 TTTTTGGATA
* * * * * *
19370944 TTTTTAGGATTAGAATTAAATTGAAAAATTTTGTAAATATTGAAGGTCAAATTTATTGAAT
1 TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAACATTGAAGCTCAAATTTATTGAAC
* *
19371005 TTTTTAGAATTTGAACTAAAATGAAAAATTTTGTAAACATTGAAGACT-AAATTTGTTGAAC
1 TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAACATTGAAG-CTCAAATTTATTGAAC
19371066 TTTT
1 TTTT
19371070 CATATTTAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 55 0.98
62 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAACATTGAAGCTCAAATTTATTGAAC
Found at i:19373976 original size:9 final size:9
Alignment explanation
Indices: 19373962--19374000 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
19373952 TAAAGTATCT
19373962 ATTAAACTA
1 ATTAAACTA
*
19373971 ATTAAATTA
1 ATTAAACTA
*
19373980 ATTAACCTAA
1 ATTAAACT-A
19373990 ATTAAACTA
1 ATTAAACTA
19373999 AT
1 AT
19374001 AGAATTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTAAACTA
Found at i:19380561 original size:37 final size:36
Alignment explanation
Indices: 19380455--19380597 Score: 151
Period size: 37 Copynumber: 3.9 Consensus size: 36
19380445 TTCTACTCGT
* * *
19380455 TTGAGCTTCACTCAGTATTACAGTAGAATTTGCTCTA
1 TTGAGCTTCATTCAGTATAACAGTA-AATTTGCTCAA
* * * *
19380492 TTGAACATCATTCAGTATAATAGTAAGGTTTGCTCAA
1 TTGAGCTTCATTCAGTATAACAGTAA-ATTTGCTCAA
* *
19380529 TTGAGCTTCATTCAGTATAACGGTATAATTTGCTCGA
1 TTGAGCTTCATTCAGTATAACAGTA-AATTTGCTCAA
* *
19380566 TTGAGCTTTATTCAGTATAACGGTAAGATTTG
1 TTGAGCTTCATTCAGTATAACAGTAA-ATTTG
19380598 GCTCGATAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
36 2 0.02
37 86 0.97
38 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (36 bp):
TTGAGCTTCATTCAGTATAACAGTAAATTTGCTCAA
Found at i:19380592 original size:74 final size:74
Alignment explanation
Indices: 19380455--19380597 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
19380445 TTCTACTCGT
* * * *
19380455 TTGAGCTTCACTCAGTATTACAGTAGAATTTGCTCTATTGAACATCATTCAGTATAATAGTAAGG
1 TTGAGCTTCACTCAGTATAACAGTAGAATTTGCTCGATTGAACATCATTCAGTATAACAGTAAGA
19380520 TTTGCTCAA
66 TTTGCTCAA
* * * * * * *
19380529 TTGAGCTTCATTCAGTATAACGGTATAATTTGCTCGATTGAGCTTTATTCAGTATAACGGTAAGA
1 TTGAGCTTCACTCAGTATAACAGTAGAATTTGCTCGATTGAACATCATTCAGTATAACAGTAAGA
19380594 TTTG
66 TTTG
19380598 GCTCGATAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (74 bp):
TTGAGCTTCACTCAGTATAACAGTAGAATTTGCTCGATTGAACATCATTCAGTATAACAGTAAGA
TTTGCTCAA
Found at i:19387886 original size:20 final size:20
Alignment explanation
Indices: 19387842--19387888 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
19387832 GATGTATGGG
19387842 TAGAAGTGGACTTATATCGA
1 TAGAAGTGGACTTATATCGA
*
19387862 CAGAAGTGGACTTATAAT-GA
1 TAGAAGTGGACTTAT-ATCGA
19387882 TAGAAGT
1 TAGAAGT
19387889 CCTTCTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (20 bp):
TAGAAGTGGACTTATATCGA
Found at i:19392135 original size:18 final size:18
Alignment explanation
Indices: 19392108--19392146 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19392098 TTTTTTAATC
*
19392108 TTTATTTCA-TTGTTTCT
1 TTTATTTCATTTCTTTCT
19392125 TTTATTTTCATTTCTTTCT
1 TTTA-TTTCATTTCTTTCT
19392144 TTT
1 TTT
19392147 GTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTCATTTCTTTCT
Found at i:19392199 original size:23 final size:23
Alignment explanation
Indices: 19392173--19392226 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
19392163 TATAATATAT
19392173 AAATGTATACATATATTAATTAC
1 AAATGTATACATATATTAATTAC
*
19392196 AAATGTATACATATATTTATTAC
1 AAATGTATACATATATTAATTAC
*
19392219 ACATGTAT
1 AAATGTAT
19392227 TTATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATGTATACATATATTAATTAC
Found at i:19396445 original size:3 final size:3
Alignment explanation
Indices: 19396437--19396462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19396427 CTGGTTTGGG
19396437 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
19396463 GATGTACTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19397459 original size:22 final size:23
Alignment explanation
Indices: 19397423--19397473 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
19397413 TTTTAAAATC
19397423 AATTTTTTTGGA-TTTAAGATTTT
1 AATTTTTTTGGATTTTAA-ATTTT
* *
19397446 AATTTTTTT-TATTTTAATTTTT
1 AATTTTTTTGGATTTTAAATTTT
19397468 AATTTT
1 AATTTT
19397474 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (23 bp):
AATTTTTTTGGATTTTAAATTTT
Found at i:19397460 original size:6 final size:6
Alignment explanation
Indices: 19397451--19397503 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
19397441 ATTTTAATTT
* * *
19397451 TTTTTA TTTTAA TTTTTA ATTTTA ATTTT- TTTTTA TTTTTTA TTTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA -TTTTTA
19397500 TTTT
1 TTTT
19397504 GTTTTGAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 4 0.10
6 24 0.59
7 13 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:19397466 original size:13 final size:13
Alignment explanation
Indices: 19397450--19397496 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
19397440 GATTTTAATT
19397450 TTTTTTATTTTAA
1 TTTTTTATTTTAA
*
19397463 TTTTTAATTTTAA
1 TTTTTTATTTTAA
19397476 -TTTTT-TTTT-A
1 TTTTTTATTTTAA
19397486 TTTTTTATTTT
1 TTTTTTATTTT
19397497 TTATTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 1 0.03
11 9 0.30
12 8 0.27
13 12 0.40
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTATTTTAA
Found at i:19397482 original size:30 final size:29
Alignment explanation
Indices: 19397441--19397503 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
19397431 TGGATTTAAG
19397441 ATTTTAATTTTTTTTA-TTTTAATTTTTA
1 ATTTTAATTTTTTTTATTTTTAATTTTTA
* *
19397469 ATTTTAATTTTTTTTTATTTTTTATTTTTT
1 ATTTTAA-TTTTTTTTATTTTTAATTTTTA
19397499 ATTTT
1 ATTTT
19397504 GTTTTGAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 7 0.23
29 9 0.29
30 15 0.48
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (29 bp):
ATTTTAATTTTTTTTATTTTTAATTTTTA
Found at i:19397489 original size:7 final size:7
Alignment explanation
Indices: 19397450--19397503 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
19397440 GATTTTAATT
19397450 TTTTTTA
1 TTTTTTA
*
19397457 -TTTTAA
1 TTTTTTA
*
19397463 TTTTTAA
1 TTTTTTA
*
19397470 TTTTAATTT
1 TTTT--TTA
19397479 TTTTTTA
1 TTTTTTA
19397486 TTTTTTA
1 TTTTTTA
19397493 TTTTTTA
1 TTTTTTA
19397500 TTTT
1 TTTT
19397504 GTTTTGAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 5 0.12
7 30 0.75
9 5 0.12
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:19398358 original size:9 final size:9
Alignment explanation
Indices: 19398329--19398379 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
19398319 TATGCTAAAA
19398329 TAATAATTT
1 TAATAATTT
19398338 TAATATATTTT
1 TAATA-A-TTT
19398349 TAATAATTT
1 TAATAATTT
*
19398358 TAATACTTT
1 TAATAATTT
*
19398367 ATAATTATTT
1 -TAATAATTT
19398377 TAA
1 TAA
19398380 AGATTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 19 0.53
10 9 0.25
11 8 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TAATAATTT
Found at i:19399040 original size:31 final size:31
Alignment explanation
Indices: 19399002--19399060 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
19398992 CACAAAAAAA
*
19399002 TATTTTAAAAATAAAAAAAATATTTTTAATG
1 TATTTTAAAAATAAAAAAAATATATTTAATG
* *
19399033 TATTTTAAAATTAAAAAATATATATTTA
1 TATTTTAAAAATAAAAAAAATATATTTA
19399061 TTATATTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTTTAAAAATAAAAAAAATATATTTAATG
Found at i:19399369 original size:27 final size:28
Alignment explanation
Indices: 19399314--19399378 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 28
19399304 ATAAAAAATA
*
19399314 ACTAAAATATTATAACTTTTTTTTATTT
1 ACTAAAATATTATAACATTTTTTTATTT
19399342 ACTAAAATATTATAA-ATTTTTTTATTT
1 ACTAAAATATTATAACATTTTTTTATTT
*
19399369 ACCAAAATAT
1 ACTAAAATAT
19399379 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (28 bp):
ACTAAAATATTATAACATTTTTTTATTT
Found at i:19399481 original size:27 final size:26
Alignment explanation
Indices: 19399451--19399524 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
19399441 CCCTGGTCAG
19399451 GCCAAGGTGATTGGCGGCACCAAAAGT
1 GCCAA-GTGATTGGCGGCACCAAAAGT
** **
19399478 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCC-AAGTGATTGGCGGCACCAAAAGT
*
19399505 GCCATACTGATTGGCGGCAC
1 GCCA-AGTGATTGGCGGCAC
19399525 TACTCGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 35 0.92
28 2 0.05
ACGTcount: A:0.26, C:0.27, G:0.31, T:0.16
Consensus pattern (26 bp):
GCCAAGTGATTGGCGGCACCAAAAGT
Found at i:19399693 original size:19 final size:21
Alignment explanation
Indices: 19399655--19399693 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19399645 AATAATTGAT
*
19399655 TATATTGTTGTTATTGTTTTG
1 TATATTGTTGTTATTATTTTG
19399676 TATATT-TTG-TATTATTTT
1 TATATTGTTGTTATTATTTT
19399694 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (21 bp):
TATATTGTTGTTATTATTTTG
Found at i:19399763 original size:3 final size:3
Alignment explanation
Indices: 19399757--19399791 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19399747 AGTATTATTA
19399757 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
19399792 AGTATTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:19400692 original size:18 final size:18
Alignment explanation
Indices: 19400648--19400692 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19400638 TTGATATGGT
*
19400648 TGGTAGTGAAGAAGAAGG
1 TGGTAGCGAAGAAGAAGG
* *
19400666 TGCTGGCGAAGAAGAAGG
1 TGGTAGCGAAGAAGAAGG
19400684 TGGTAGCGA
1 TGGTAGCGA
19400693 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.44, T:0.16
Consensus pattern (18 bp):
TGGTAGCGAAGAAGAAGG
Found at i:19402083 original size:37 final size:37
Alignment explanation
Indices: 19402022--19402167 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
19402012 TACGTATGAT
* *
19402022 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
19402057 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
19402094 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
19402131 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
19402168 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:19402184 original size:46 final size:46
Alignment explanation
Indices: 19402131--19402399 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
19402121 TAAGTGTAGC
* **
19402131 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
19402177 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
19402223 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
19402275 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
19402321 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
19402373 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
19402400 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:19402250 original size:52 final size:52
Alignment explanation
Indices: 19402174--19402393 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
19402164 TAGCTAAAGC
* *
19402174 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19402227 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19402279 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
19402325 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
19402377 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
19402394 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:19402296 original size:98 final size:98
Alignment explanation
Indices: 19402131--19402399 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
19402121 TAAGTGTAGC
* * *
19402131 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
19402196 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
19402230 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
19402295 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
19402328 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
19402393 GATCAGA
66 GATCAGA
19402400 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:19404573 original size:42 final size:42
Alignment explanation
Indices: 19404526--19404609 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
19404516 GTTCTGGACG
19404526 TTTGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTT
1 TTTGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTT
19404568 TTTGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTT
1 TTTGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTT
19404610 GTGCAGGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (42 bp):
TTTGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTT
Found at i:19408403 original size:159 final size:156
Alignment explanation
Indices: 19407924--19408392 Score: 395
Period size: 159 Copynumber: 3.0 Consensus size: 156
19407914 CAAGTTGAAA
* * * * *
19407924 AAAAAGTTAGTAAA-AACTCTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCCGCATTTTATTCT
1 AAAAAGTAAGAAAATAACTCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCAGCATTTTATTAT
** * *
19407987 TTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTT-AAAT
66 TTTAAAAAATATCATAATTAGT-ATTTTATAATTTTATATTATTTCAGTACATAATGTTTGAAAT
*
19408051 TTATTAATTTAGTGTGTT-ATTTAAATT
130 TTATTAATTTAGTGTGTTGAATTAAA-T
* * * * ** *
19408078 AATTTGATGTAAGAAAATAACTCTTA-TCCCTGCCCTTTACTCGTATTATTTTCTCA--ATTTTT
1 AA---AAAGTAAGAAAATAACTCTTACTTCC-GCCATTTGTTCGTATTTTTTTCTCAGCA-TTTT
* * * * **
19408140 ATTACTTTCAATAAAAATAT-ATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTT
61 ATTA-TTT-TA-AAAAATATCA-TA-ATTAGTATTTTATAATTTTATATTATTTCAGTACATAAT
* * * **
19408204 CTTTGAAATATTTTGTATAATT-GT-T-TCTGAATTTTAT
121 GTTTGAAAT-TTAT-TA-ATTTAGTGTGT-TGAATTAAAT
* * *
19408241 AAAAAGTTA-ATACTACACTCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCAGCATTTTATTA
1 AAAAAGTAAGAAAATA-ACTCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCAGCATTTTATTA
*
19408305 TTTTAAAAAATATCATAAACTTAGTCTTTTATAATTTTATATTATTTCAGTACATAATGTTTGAA
65 TTTTAAAAAATATCAT-AA-TTAGTATTTTATAATTTTATATTATTTCAGTACATAATGTTTGAA
19408370 ATTTATTAATTTAGTGTGTTGAA
128 ATTTATTAATTTAGTGTGTTGAA
19408393 GGGGAATAAA
Statistics
Matches: 240, Mismatches: 47, Indels: 52
0.71 0.14 0.15
Matches are distributed among these distances:
154 2 0.01
156 3 0.01
157 15 0.06
158 43 0.18
159 60 0.25
160 37 0.15
161 52 0.22
162 9 0.04
163 8 0.03
164 8 0.03
165 3 0.01
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (156 bp):
AAAAAGTAAGAAAATAACTCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCAGCATTTTATTAT
TTTAAAAAATATCATAATTAGTATTTTATAATTTTATATTATTTCAGTACATAATGTTTGAAATT
TATTAATTTAGTGTGTTGAATTAAAT
Found at i:19409269 original size:43 final size:42
Alignment explanation
Indices: 19409221--19409389 Score: 185
Period size: 41 Copynumber: 4.2 Consensus size: 42
19409211 TTCCTTCCCG
*
19409221 CTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTT-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
19409264 CTTCTTTTTCTTTCTTTTTTC-C-TCTCCTTTCCTCTTC-TT-
1 CTTCTTTTTCTTT-TTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
19409303 CTTC--TTTCTTTTTTTTTCTTTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* * *
19409343 CTTCTTTTTC-TTTCTTTGCTCTCCTTCC-TTCC-TTTCTTTC
1 CTTCTTTTTCTTTTTTTTTCTCTTC-TCCTTTCCTTTTCTTTC
*
19409383 TTTCTTT
1 CTTCTTT
19409390 CCCTCTCCTT
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
36 7 0.06
37 7 0.06
38 14 0.13
39 6 0.06
40 20 0.18
41 28 0.26
42 9 0.08
43 18 0.17
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (42 bp):
CTTCTTTTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:19409277 original size:4 final size:4
Alignment explanation
Indices: 19409256--19409390 Score: 56
Period size: 4 Copynumber: 34.0 Consensus size: 4
19409246 CTCCTTTCCT
* *
19409256 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTCC TCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTT-C T-TTC
* *
19409301 -TTC -TTC TTTC TTT- TTT- TTTC TTT- TCTCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTT-C -TTTC TTTC TTTC
* * *
19409347 -TT- TTTC TTTC TTTGC TCTCC TTCC TTCC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
19409391 CCTCTCCTTC
Statistics
Matches: 106, Mismatches: 8, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
3 24 0.23
4 62 0.58
5 13 0.12
6 7 0.07
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:19409337 original size:79 final size:75
Alignment explanation
Indices: 19409193--19409374 Score: 258
Period size: 79 Copynumber: 2.3 Consensus size: 75
19409183 AAAAATTATA
19409193 TTTTT-TTTCTTTTTTTCCTTCCTTCCCGCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTT
1 TTTTTCTTTC-TTTTTTCCTTCCTTCCCGCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTT
19409257 TTCTTTCCTTC
65 TTCTTTCCTTC
* * *
19409268 TTTTTCTTTCTTTTTTCCTCTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCCTTTC
1 TTTTTCTTTCTTTTTTCCT-TCCTTCCCGCTTCTTCTTC-TTC--TTTTTTTCTCTTCTCCTTTC
19409333 CTTTTCTTTCCTTC
62 CTTTTCTTTCCTTC
*
19409347 TTTTTCTTTCTTTGCTCTCCTTCCTTCC
1 TTTTTCTTTCTTT--TTTCCTTCCTTCC
19409375 TTTCTTTCTT
Statistics
Matches: 95, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
75 14 0.15
76 21 0.22
77 3 0.03
79 46 0.48
80 6 0.06
81 5 0.05
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (75 bp):
TTTTTCTTTCTTTTTTCCTTCCTTCCCGCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTT
TCTTTCCTTC
Found at i:19409359 original size:10 final size:10
Alignment explanation
Indices: 19409225--19409355 Score: 61
Period size: 10 Copynumber: 12.6 Consensus size: 10
19409215 TTCCCGCTTC
*
19409225 TTCTTCTTCT
1 TTCTTTTTCT
19409235 TT-TTTTCTCT
1 TTCTTTT-TCT
* *
19409245 TCTCCTTTCCT
1 T-TCTTTTTCT
* *
19409256 TT-TCTTTCC
1 TTCTTTTTCT
19409265 TTCTTTTTCT
1 TTCTTTTTCT
19409275 TTCTTTTTTCCT
1 TTC-TTTTT-CT
* * *
19409287 CTCCTTTCCT
1 TTCTTTTTCT
*
19409297 CTTCTTCTTCT
1 -TTCTTTTTCT
*
19409308 TTCTTTTTTT
1 TTCTTTTTCT
19409318 TTCTTTTCTCCT
1 TTCTTTT-T-CT
*
19409330 TTCCTTTTCT
1 TTCTTTTTCT
*
19409340 TTCCTTCTT-T
1 TT-CTTTTTCT
19409350 TTCTTT
1 TTCTTT
19409356 CTTTGCTCTC
Statistics
Matches: 88, Mismatches: 23, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
9 11 0.12
10 39 0.44
11 24 0.27
12 14 0.16
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:19409375 original size:31 final size:31
Alignment explanation
Indices: 19409340--19409400 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
19409330 TTCCTTTTCT
* *
19409340 TTCCTTCTTTTTCTTTCTTT-GCTCTCCTTCC
1 TTCCTT-TCTTTCTTTCTTTCCCTCTCCTTCC
19409371 TTCCTTTCTTTCTTTCTTTCCCTCTCCTTC
1 TTCCTTTCTTTCTTTCTTTCCCTCTCCTTC
19409401 TCCCCCCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.61
Consensus pattern (31 bp):
TTCCTTTCTTTCTTTCTTTCCCTCTCCTTCC
Found at i:19409378 original size:36 final size:37
Alignment explanation
Indices: 19409227--19409385 Score: 146
Period size: 36 Copynumber: 4.2 Consensus size: 37
19409217 CCCGCTTCTT
* * *
19409227 CTTCTTCTTTTTTTCTCT-TCTCCTTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTCTTTCTCTCCTTTCCTTTCCTTTC
*
19409264 CTTCTTTTTCTTTCTTTTTTCCTCTCCTTTCCTCTTCTTCTTC
1 CTTCTTTTTCTTTC---TTT-CTCTCCTTTCCT-TTCCT-TTC
* * *
19409307 TTTCTTTTTTTTTCTTT-TCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTCTCTCCTTTCCTTTCCTTTC
19409343 CTTCTTTTTCTTTCTTTGCTCTCC-TTCC-TTCCTTTC
1 CTTCTTTTTCTTTCTTT-CTCTCCTTTCCTTTCCTTTC
*
19409379 TTTCTTT
1 CTTCTTT
19409386 CTTTCCCTCT
Statistics
Matches: 101, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
36 38 0.38
37 13 0.13
38 16 0.16
39 2 0.02
40 3 0.03
41 11 0.11
42 3 0.03
43 15 0.15
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (37 bp):
CTTCTTTTTCTTTCTTTCTCTCCTTTCCTTTCCTTTC
Found at i:19409589 original size:29 final size:28
Alignment explanation
Indices: 19409530--19409596 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
19409520 TTTTTTTTGT
* * *
19409530 ATATTTTAGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAAAAAAAAAAAGTTATA
19409558 ATATTTTGGTAAAAAAATAAAAAGTTATA
1 ATATTTTGGTAAAAAAA-AAAAAGTTATA
19409587 ATATTTTGGT
1 ATATTTTGGT
19409597 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 15 0.43
29 20 0.57
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAAAAAAAAAAAGTTATA
Found at i:19410241 original size:5 final size:5
Alignment explanation
Indices: 19410231--19410259 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19410221 TTAAAAAATA
19410231 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
19410260 ATACTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:19412707 original size:19 final size:19
Alignment explanation
Indices: 19412683--19412720 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
19412673 TAATTTGCGA
19412683 CCCCTA-AGTAGTGCGAACC
1 CCCCTACAGTA-TGCGAACC
19412702 CCCCTACAGTATGCGAACC
1 CCCCTACAGTATGCGAACC
19412721 TCAGACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.39, G:0.18, T:0.16
Consensus pattern (19 bp):
CCCCTACAGTATGCGAACC
Found at i:19415125 original size:27 final size:28
Alignment explanation
Indices: 19415082--19415159 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
19415072 AAGGTGTGAC
* *
19415082 CCCCTAGATGCGAACCCTAATGTACGAA
1 CCCCTAGGTGCAAACCCTAATGTACGAA
* **
19415110 CCCC-AGGTGCAAACCCTAACGTGTGAA
1 CCCCTAGGTGCAAACCCTAATGTACGAA
*
19415137 CCCCTAGGTGCGAACCCTAATGT
1 CCCCTAGGTGCAAACCCTAATGT
19415160 GAGAAACTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (28 bp):
CCCCTAGGTGCAAACCCTAATGTACGAA
Found at i:19415151 original size:14 final size:14
Alignment explanation
Indices: 19415082--19415153 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
19415072 AAGGTGTGAC
*
19415082 CCCCTAGATGCGAA
1 CCCCTAGGTGCGAA
* *
19415096 -CCCTAATGTACGAA
1 CCCCT-AGGTGCGAA
19415110 CCCC-AGGTGC-AA
1 CCCCTAGGTGCGAA
* * *
19415122 ACCCTAACGTGTGAA
1 CCCCT-AGGTGCGAA
19415137 CCCCTAGGTGCGAA
1 CCCCTAGGTGCGAA
19415151 CCC
1 CCC
19415154 TAATGTGAGA
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
12 5 0.12
13 8 0.19
14 20 0.48
15 9 0.21
ACGTcount: A:0.28, C:0.36, G:0.21, T:0.15
Consensus pattern (14 bp):
CCCCTAGGTGCGAA
Found at i:19415184 original size:15 final size:14
Alignment explanation
Indices: 19415090--19415197 Score: 76
Period size: 14 Copynumber: 7.6 Consensus size: 14
19415080 ACCCCCTAGA
*
19415090 TGCGAACCCTAATG
1 TGCGAACCCTAAGG
* *
19415104 TACGAACCC-CAGG
1 TGCGAACCCTAAGG
* *
19415117 TGCAAACCCTAACG
1 TGCGAACCCTAAGG
*
19415131 TGTGAACCCCT-AGG
1 TGCGAA-CCCTAAGG
*
19415145 TGCGAACCCTAATG
1 TGCGAACCCTAAGG
* *
19415159 TGAGAAACTCTAAGG
1 TGCG-AACCCTAAGG
*
19415174 TGCGAACCTCTAAAG
1 TGCGAACC-CTAAGG
*
19415189 TGTGAACCC
1 TGCGAACCC
19415198 ATATGTATAA
Statistics
Matches: 70, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.19
14 30 0.43
15 27 0.39
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (14 bp):
TGCGAACCCTAAGG
Found at i:19415227 original size:15 final size:15
Alignment explanation
Indices: 19415123--19415229 Score: 76
Period size: 15 Copynumber: 7.3 Consensus size: 15
19415113 CAGGTGCAAA
*
19415123 CCCTAACGTGTGAAC
1 CCCTAAGGTGTGAAC
*
19415138 CCCT-AGGTGCGAA-
1 CCCTAAGGTGTGAAC
* * *
19415151 CCCTAATGTGAGAAA
1 CCCTAAGGTGTGAAC
* *
19415166 CTCTAAGGTGCGAAC
1 CCCTAAGGTGTGAAC
* *
19415181 CTCTAAAGTGTGAAC
1 CCCTAAGGTGTGAAC
* * * *
19415196 CCAT-ATGTATAAAC
1 CCCTAAGGTGTGAAC
19415210 CCCTAAGGTGTGAAC
1 CCCTAAGGTGTGAAC
19415225 CCCTA
1 CCCTA
19415230 TGTGCAACCT
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
13 4 0.06
14 24 0.34
15 42 0.60
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (15 bp):
CCCTAAGGTGTGAAC
Found at i:19420612 original size:29 final size:29
Alignment explanation
Indices: 19420558--19420613 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
19420548 AACGTAAGTG
* **
19420558 ACTAAATTGTAACATTTCAAACATAAATA
1 ACTAAAATGTAACATGACAAACATAAATA
19420587 ACTAAAATGTAACATGACACAA-ATAAA
1 ACTAAAATGTAACATGACA-AACATAAA
19420614 AATATCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.25
Consensus pattern (29 bp):
ACTAAAATGTAACATGACAAACATAAATA
Found at i:19425116 original size:23 final size:22
Alignment explanation
Indices: 19425082--19425126 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
19425072 CCTATTGAAT
19425082 AAAAAAAACAAAAATTTCAAAG
1 AAAAAAAACAAAAATTTCAAAG
* *
19425104 AAAAAAGACCAAAAATTTGAAAG
1 AAAAAA-AACAAAAATTTCAAAG
19425127 GTGATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (22 bp):
AAAAAAAACAAAAATTTCAAAG
Found at i:19425855 original size:18 final size:18
Alignment explanation
Indices: 19425834--19425868 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19425824 TTTATCATTA
19425834 TTATTA-TTATTATTAGTG
1 TTATTATTTA-TATTAGTG
19425852 TTATTATTTATATTAGT
1 TTATTATTTATATTAGT
19425869 TCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (18 bp):
TTATTATTTATATTAGTG
Found at i:19425901 original size:16 final size:16
Alignment explanation
Indices: 19425876--19425922 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
19425866 AGTTCATATA
19425876 TTTATCTATATAATT-T
1 TTTAT-TATATAATTAT
*
19425892 TTTATGTATATGCATTAT
1 TTTAT-TATAT-AATTAT
19425910 TTTATTATATAAT
1 TTTATTATATAAT
19425923 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTATTATATAATTAT
Found at i:19426140 original size:16 final size:16
Alignment explanation
Indices: 19426116--19426157 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
19426106 TTCAACTTTA
19426116 ATATATTATTATGTAT
1 ATATATTATTATGTAT
* *
19426132 ATATGTTATTATTTAT
1 ATATATTATTATGTAT
19426148 AT-TATTATTA
1 ATATATTATTA
19426158 AATCTTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
ATATATTATTATGTAT
Found at i:19426152 original size:12 final size:13
Alignment explanation
Indices: 19426116--19426157 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
19426106 TTCAACTTTA
19426116 ATATATTATTATGT
1 ATATATTATTAT-T
19426130 ATATATGTTATTATT
1 ATATA--TTATTATT
19426145 -TATATTATTATT
1 ATATATTATTATT
19426157 A
1 A
19426158 AATCTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
14 9 0.36
15 1 0.04
16 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
ATATATTATTATT
Found at i:19426245 original size:21 final size:21
Alignment explanation
Indices: 19426202--19426254 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
19426192 TAATATATGT
**
19426202 ATATAAT-TTTATGTATTTTG
1 ATATAATATTTATGTATTGGG
*
19426222 ATATAATATTTATTTATTGGG
1 ATATAATATTTATGTATTGGG
*
19426243 ATACTATTATTT
1 ATA-TAATATTT
19426255 TATGAAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 13 0.48
22 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
ATATAATATTTATGTATTGGG
Found at i:19427989 original size:12 final size:12
Alignment explanation
Indices: 19427972--19427997 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19427962 GTTTCAACCC
19427972 TTCATCTATTAA
1 TTCATCTATTAA
19427984 TTCATCTATTAA
1 TTCATCTATTAA
19427996 TT
1 TT
19427998 GCAACATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (12 bp):
TTCATCTATTAA
Found at i:19433438 original size:15 final size:14
Alignment explanation
Indices: 19433409--19433447 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
19433399 AGGTGAATCG
19433409 TTTTTTTTATTTTTTA
1 TTTTTTTTA--TTTTA
19433425 TTTTATTTTATTTTA
1 TTTT-TTTTATTTTA
19433440 TTTTTTTT
1 TTTTTTTT
19433448 CATCTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:19434740 original size:22 final size:22
Alignment explanation
Indices: 19434698--19434754 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19434688 GTGAATCGTT
*
19434698 TTTTTATTTTTTTATTTTATT-
1 TTTTTATTTTTTTATTCTATTC
19434719 TATTTTATTTTTTTCA-TCTATTC
1 T-TTTTATTTTTTT-ATTCTATTC
*
19434742 TTTTGATTTTTTT
1 TTTTTATTTTTTT
19434755 TGTTTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTTTATTCTATTC
Found at i:19435953 original size:18 final size:19
Alignment explanation
Indices: 19435921--19435956 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19435911 TTCATCAAAG
*
19435921 TTTTTTTGATTTAAAAGTT
1 TTTTTTTGATATAAAAGTT
19435940 TTTTTTTGA-ATAAAAGT
1 TTTTTTTGATATAAAAGT
19435957 ATTATTTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTTTTTGATATAAAAGTT
Found at i:19436554 original size:22 final size:22
Alignment explanation
Indices: 19436526--19436568 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19436516 GGTTTCAACA
19436526 GCTTGGCGACTCCACTGGGGAT
1 GCTTGGCGACTCCACTGGGGAT
19436548 GCTTGGCGACTCCACTGGGGA
1 GCTTGGCGACTCCACTGGGGA
19436569 CACTTGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
GCTTGGCGACTCCACTGGGGAT
Found at i:19436574 original size:22 final size:22
Alignment explanation
Indices: 19436527--19436574 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
19436517 GTTTCAACAG
**
19436527 CTTGGCGACTCCACTGGGGATG
1 CTTGGCGACTCCACTGGGGACA
19436549 CTTGGCGACTCCACTGGGGACA
1 CTTGGCGACTCCACTGGGGACA
19436571 CTTG
1 CTTG
19436575 AGAGTCGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.23
Consensus pattern (22 bp):
CTTGGCGACTCCACTGGGGACA
Found at i:19439264 original size:20 final size:20
Alignment explanation
Indices: 19439239--19439278 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19439229 TTCACCCCAT
19439239 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
*
19439259 GCATCGCATCCTATGCATTA
1 GCATCGCATCATATGCATTA
19439279 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:19447120 original size:50 final size:50
Alignment explanation
Indices: 19447066--19447337 Score: 199
Period size: 50 Copynumber: 5.4 Consensus size: 50
19447056 GCAGCGGAAC
** *
19447066 AGATTGAAGCTATGACGGCGGATCTGGTTTCCCTGATATTGTAATTAAAA
1 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * * *** * * * * ** *
19447116 AGATTGAAGCCACAATGGTGGATCTTACTT-CCTTAGCAGTGCAGTGGAAT
1 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGA-TATTGCAATTAAAA
19447166 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
1 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
* * * *** * * * * *
19447216 GGATTGAAGCCACAACGGCAGATCTTACTT-CCTTAGCAGTGC-AGTAGAAC
1 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGA-TATTGCAATTA-AAA
* * * *
19447266 AGATTGAAGCTACGACGGCGAATCTGGTTTCCCTAATATTGTAATTAAAAA
1 AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATT-AAAA
*
19447317 AGATTGAAGCCACAACGGCGG
1 AGATTGAAGCTACAACGGCGG
19447338 GGTCTNNNNN
Statistics
Matches: 158, Mismatches: 57, Indels: 13
0.69 0.25 0.06
Matches are distributed among these distances:
49 11 0.07
50 116 0.73
51 30 0.19
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
Found at i:19447184 original size:100 final size:100
Alignment explanation
Indices: 19447011--19447337 Score: 528
Period size: 100 Copynumber: 3.3 Consensus size: 100
19447001 GGTTGAAAAG
* *
19447011 TAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCGGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
*
19447076 TATGACGGCGGATCTGGTTTCCCTGATATTGTAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGTAAT
* * *
19447111 TAAAAAGATTGAAGCCACAATGGTGGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
19447176 TACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGTAAT
* * *
19447211 TAAAAGGATTGAAGCCACAACGGCAGATCTTACTTCCTTAGCAGTGCAGTAGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
* *
19447276 TACGACGGCGAATCTGGTTTCCCTAATATTGTAAT
66 TACGACGGCGGATCTGGTTTCCCTGATATTGTAAT
19447311 TAAAAAAGATTGAAGCCACAACGGCGG
1 T-AAAAAGATTGAAGCCACAACGGCGG
19447338 GGTCTNNNNN
Statistics
Matches: 206, Mismatches: 20, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
100 183 0.89
101 23 0.11
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
TACGACGGCGGATCTGGTTTCCCTGATATTGTAAT
Found at i:19449159 original size:100 final size:100
Alignment explanation
Indices: 19448986--19449222 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 100
19448976 GGTTGAAAAG
* *
19448986 TAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCTTTGCAGTGCAGCAGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCAGAACAGATTGAAGC
** *
19449051 TATGACGGCGAATCTGGTTTCCCTGATATTGTAAT
66 TACAACGGCGAATCTGGTTTCCCTGATATTGCAAT
* * ** *
19449086 TAAAAAGATTGAAGCCACAATGGTGGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCAGAACAGATTGAAGC
*
19449151 TACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
66 TACAACGGCGAATCTGGTTTCCCTGATATTGCAAT
* *
19449186 TAAAAGGATTGAAGCCACAACGGCAGATCTTACTTCC
1 TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCC
19449223 CTGATGGTGT
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 122 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (100 bp):
TAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGCAGAACAGATTGAAGC
TACAACGGCGAATCTGGTTTCCCTGATATTGCAAT
Found at i:19449223 original size:50 final size:49
Alignment explanation
Indices: 19448988--19449227 Score: 153
Period size: 50 Copynumber: 4.8 Consensus size: 49
19448978 TTGAAAAGTA
* * * * *
19448988 AAAAGATTAAAGCCACAACGGCGGATCTTACTTCCTTTG-CAGTGCAGCA-G
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCC-CTGATATTGCA--ATT
* * ** * *** *
19449038 AACAGATTGAAGCTATGACGGCGAATCTGGTTTCCCTGATATTGTAATT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGATATTGCAATT
* * * * * * *
19449087 AAAAAGATTGAAGCCACAATGGTGGATCTTACTT-CCTTAGCAGTGCAGTGG
1 -AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA-TATTGCAAT-T
* * ***
19449138 AATAGATTGAAGCTACAACGGCGGATCTGGTTTCCCTGATATTGCAATT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGATATTGCAATT
*
19449187 AAAAGGATTGAAGCCACAACGGCAGATCTTACTTCCCTGAT
1 AAAA-GATTGAAGCCACAACGGCGGATCTTACTTCCCTGAT
19449228 GGTGTGGTGG
Statistics
Matches: 135, Mismatches: 48, Indels: 14
0.69 0.24 0.07
Matches are distributed among these distances:
48 1 0.01
49 9 0.07
50 121 0.90
51 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (49 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGATATTGCAATT
Found at i:19449238 original size:100 final size:99
Alignment explanation
Indices: 19448986--19449299 Score: 344
Period size: 100 Copynumber: 3.1 Consensus size: 99
19448976 GGTTGAAAAG
* * ** **
19448986 TAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCTTTGCAGTGCAGCAGAACAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTGAG-AGTGCAGTGGAACAGATTGAAGC
* * *
19449051 TATGACGGCGAATCTGGTTTCCCTGATATTGTAAT
65 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
* ** * *
19449086 TAAAAAGATTGAAGCCACAATGGTGGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGC
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTGAG-AGTGCAGTGGAACAGATTGAAGC
*
19449151 TACAACGGCGGATCTGGTTTCCCTGATATTGCAAT
65 TACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
* ** *
19449186 TAAAAGGATTGAAGCCACAACGGCAGATCTTACTTCCCTGATG-GTGTGGTGGAACAGATTAAAG
1 TAAAAAGATTGAAGCCACAACGGCAGATCTTACTT-CCTGA-GAGTGCAGTGGAACAGATTGAAG
* * * * * *
19449250 CTACGACAGCGGATCTAGTTTCCCCGACATTGTAGT
64 CTACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
19449286 TGAAAAA-ATTGAAG
1 T-AAAAAGATTGAAG
19449300 ATTACAGATC
Statistics
Matches: 183, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
100 174 0.95
101 8 0.04
102 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (99 bp):
TAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTGAGAGTGCAGTGGAACAGATTGAAGCT
ACGACGGCGGATCTGGTTTCCCTGATATTGCAAT
Found at i:19450348 original size:22 final size:22
Alignment explanation
Indices: 19450306--19450362 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19450296 GTGAATCGTT
*
19450306 TTTTTATTTTTTTATTTTATT-
1 TTTTTATTTTTTTATTCTATTC
19450327 TATTTTATTTTTTTCA-TCTATTC
1 T-TTTTATTTTTTT-ATTCTATTC
*
19450350 TTTTGATTTTTTT
1 TTTTTATTTTTTT
19450363 TGTTTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTTTATTCTATTC
Found at i:19451529 original size:18 final size:19
Alignment explanation
Indices: 19451497--19451532 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19451487 TTCATCAAAG
*
19451497 TTTTTTTGATTTAAAAGTT
1 TTTTTTTGATATAAAAGTT
19451516 TTTTTTTGA-ATAAAAGT
1 TTTTTTTGATATAAAAGT
19451533 ATTATTTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTTTTTGATATAAAAGTT
Found at i:19452443 original size:13 final size:12
Alignment explanation
Indices: 19452378--19452445 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
19452368 AATATATATT
19452378 TATTA-TTAAAA
1 TATTATTTAAAA
*
19452389 TATTA-ATATAAA
1 TATTATTTA-AAA
*
19452401 TATTTTTTAATAA
1 TATTATTTAA-AA
*
19452414 TA-TATTTAGAA
1 TATTATTTAAAA
19452425 TATTATTTAAAA
1 TATTATTTAAAA
19452437 TTATTATTT
1 -TATTATTT
19452446 TTAATTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 11 0.24
12 21 0.46
13 14 0.30
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:19452513 original size:33 final size:31
Alignment explanation
Indices: 19452453--19452515 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
19452443 TTTTTAATTT
*
19452453 TTTATTAAAATAAAATTGTAATATTAAATAA
1 TTTATTAAAATAAAATTATAATATTAAATAA
* *
19452484 TTTATTAAAATAACAAATTATATTCTTAAATA
1 TTTATTAAAAT-A-AAATTATAATATTAAATA
19452516 TAAATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
32 1 0.04
33 15 0.56
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTATTAAAATAAAATTATAATATTAAATAA
Found at i:19454584 original size:18 final size:17
Alignment explanation
Indices: 19454539--19454616 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 17
19454529 ACATACTTGA
*
19454539 TTATAATTTTTATAATATAT
1 TTATAA-TTTT-TAAT-TTT
*
19454559 TTAGAATTTTTAATTTT
1 TTATAATTTTTAATTTT
*
19454576 TTATAAATTTCTAATTGTT
1 TTAT-AATTTTTAATT-TT
*
19454595 TTGTAATTTTTAATATTT
1 TTATAATTTTTAAT-TTT
19454613 TTAT
1 TTAT
19454617 TTAATTTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.10
18 28 0.58
19 10 0.21
20 5 0.10
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (17 bp):
TTATAATTTTTAATTTT
Found at i:19455603 original size:21 final size:21
Alignment explanation
Indices: 19455577--19455632 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
19455567 AACAGCGGTG
* *
19455577 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTATA
*
19455598 GCGGTGAGATTGGATACTATA
1 GCGGTGAGATTAGATACTATA
*
19455619 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
19455633 AACAGCGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:19458573 original size:25 final size:24
Alignment explanation
Indices: 19458515--19458574 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
19458505 GAATATGCTG
19458515 AGAAGAGAA-G-ATGAAGAACGGA
1 AGAAGAGAAGGAATGAAGAACGGA
*
19458537 AGAAGAAAAAGGAATGAAGAACGGA
1 AGAAG-AGAAGGAATGAAGAACGGA
19458562 AGAAAGAGAAGGA
1 AG-AAGAGAAGGA
19458575 GCCTTACCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 5 0.16
23 3 0.09
24 1 0.03
25 20 0.62
26 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.35, T:0.03
Consensus pattern (24 bp):
AGAAGAGAAGGAATGAAGAACGGA
Found at i:19468826 original size:6 final size:6
Alignment explanation
Indices: 19468810--19468867 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
19468800 GTAATTTCAA
** * *
19468810 AATTA- AATTAT AATTAT TTTTA- AATAAT AATTTT AAATTA- AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT -AATTAT AATTAT
19468856 AATTAT AATTAT
1 AATTAT AATTAT
19468868 CACAATATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
5 12 0.29
6 25 0.61
7 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:19469020 original size:23 final size:20
Alignment explanation
Indices: 19468965--19469032 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 20
19468955 AAATTTTTGT
*
19468965 AATTA-ATAATTGTAAATTA
1 AATTATATAATTTTAAATTA
*
19468984 AATTATAAATATTTTAAATTGA
1 AATTATATA-ATTTTAAATT-A
*
19469006 TAATTATCATAATTTT-TATTA
1 -AATTAT-ATAATTTTAAATTA
19469027 AATTAT
1 AATTAT
19469033 GATTTTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.12
20 8 0.20
21 10 0.25
22 4 0.10
23 11 0.28
24 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (20 bp):
AATTATATAATTTTAAATTA
Found at i:19471137 original size:18 final size:18
Alignment explanation
Indices: 19471106--19471150 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
19471096 TGGGCCAGGC
19471106 CATGTGGG-CCACATGAG
1 CATGTGGGCCCACATGAG
19471123 CATGTGGGCCCACATGAG
1 CATGTGGGCCCACATGAG
* *
19471141 AATATGGGCC
1 CATGTGGGCC
19471151 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (18 bp):
CATGTGGGCCCACATGAG
Found at i:19477327 original size:21 final size:21
Alignment explanation
Indices: 19477301--19477349 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
19477291 AAGTATATGG
*
19477301 AATGGTATGGATTGAGTCAGA
1 AATGGTATGGAGTGAGTCAGA
19477322 AATGGTATGGAGTGAGTCAGA
1 AATGGTATGGAGTGAGTCAGA
19477343 AATGGTA
1 AATGGTA
19477350 ACTTGATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.27
Consensus pattern (21 bp):
AATGGTATGGAGTGAGTCAGA
Found at i:19485519 original size:34 final size:33
Alignment explanation
Indices: 19485414--19485525 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 33
19485404 TGTATTATCA
* * * *
19485414 GAAACATATTTCAGATCATAATGTCATATTTCTG
1 GAAACATATATCAGATTAGAATGTCATTTTTC-G
* * * * **
19485448 G-AACATATTTCGGATTGGAATATCATATTTTTA
1 GAAACATATATCAGATTAGAATGTCAT-TTTTCG
19485481 GAAACATATATCAGATTAGAATGTCATGTTTTCG
1 GAAACATATATCAGATTAGAATGTCAT-TTTTCG
*
19485515 GAAACACATAT
1 GAAACATATAT
19485526 ATCATATCGA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 21 0.35
34 39 0.65
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (33 bp):
GAAACATATATCAGATTAGAATGTCATTTTTCG
Found at i:19486230 original size:30 final size:31
Alignment explanation
Indices: 19486173--19486235 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
19486163 TGGCCCAAAA
* *
19486173 GGTCCACACGGCCCAAAAAGCTAGCTCGTGT
1 GGTCCACACGGCCCAAAAAGATAGCTCGCGT
19486204 GGTCCACACGGCCCAAAAA-ATAGCTCGCGT
1 GGTCCACACGGCCCAAAAAGATAGCTCGCGT
19486234 GG
1 GG
19486236 ACTACCCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (31 bp):
GGTCCACACGGCCCAAAAAGATAGCTCGCGT
Found at i:19494690 original size:41 final size:41
Alignment explanation
Indices: 19494657--19494763 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
19494647 CACCGGCACA
19494657 AAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGACATC
1 AAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGACATC
* *
19494698 AAGCTTGCTAGACATAAAGTCTAAAGTAATTCACCGACATC
1 AAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGACATC
* * *
19494739 AAGCCTGCTAGGCATTAAGCCTGAA
1 AAGCCTGCTAGACATAAAGTCTGAA
19494764 AATCTCATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGACATC
Found at i:19494997 original size:64 final size:63
Alignment explanation
Indices: 19494879--19495059 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
19494869 GCAAACAAAC
*
19494879 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
19494940 T
63 T
19494941 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
19495005 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
19495060 AAATATATAT
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
62 17 0.15
63 6 0.05
64 77 0.70
65 10 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:19495183 original size:61 final size:60
Alignment explanation
Indices: 19495088--19495207 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 60
19495078 CATATGTGCA
** * * *
19495088 TATATATATAATTCATAATATTATGTTCAGCTCAAAGAACTTATATCATACATTCAAACTT
1 TATATATATAATTCATAATATTAAATTCAACTC-AAGAAATTAAATCATACATTCAAACTT
* *
19495149 TATATATATAATTCATAACT-TTAAATTCAACTCAAGAAATTAAATCTTACATTCGAACT
1 TATATATATAATTCATAA-TATTAAATTCAACTCAAGAAATTAAATCATACATTCAAACT
19495208 ACATATCCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 22 0.43
61 28 0.55
62 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (60 bp):
TATATATATAATTCATAATATTAAATTCAACTCAAGAAATTAAATCATACATTCAAACTT
Found at i:19496509 original size:258 final size:261
Alignment explanation
Indices: 19496048--19496567 Score: 1010
Period size: 258 Copynumber: 2.0 Consensus size: 261
19496038 ATGTAGCTAG
19496048 GTTCTTCTTTCTTTTTCTTTTGTTTAGTTTCGGTCATAAAGATGAAGAAAGAAAAAAATGAAATG
1 GTTCTTCTTTCTTTTTCTTTTGTTTAGTTTCGGTCATAAAGATGAAG-AAGAAAAAAATGAAATG
19496113 ATAATGGCTTATAATATTTTTATTATAACATAATAATATAATATACATAATTATAACCTTTATAA
65 ATAATGGCTTATAATATTTTTATTATAACATAATAATATAATATACATAATTATAACCTTTATAA
19496178 TTAATATTAATAATATAAAAACTATATACTATCACTTAATGCCGTCCACTAGCATTTAAATGGAT
130 TTAATATTAATAATATAAAAACTATATACTATCACTTAATGCCGTCCACTAGCATTTAAATGGAT
19496243 TAATTGCCACATAAAACCTCCATATTAAAAGAACATTCACTATTCAGCCCTTCTTAAAATAACCA
195 TAATTGCCACATAAAACCTCCATATTAAAAGAACATTCACTATTCAGCCCTTCTTAAAATAACCA
19496308 CA
260 CA
19496310 GTTCTTCTTTCTTTTTCTTTTGTTTAGTTTCGGTCATAAAGATGAAG-A-AAAAAAATGAAATGA
1 GTTCTTCTTTCTTTTTCTTTTGTTTAGTTTCGGTCATAAAGATGAAGAAGAAAAAAATGAAATGA
19496373 TAATGGCTTATAATATTTTT-TTATAACATAATAATATAATATACATAATTATAACCTTTATAAT
66 TAATGGCTTATAATATTTTTATTATAACATAATAATATAATATACATAATTATAACCTTTATAAT
19496437 TAATATTAATAATATAAAAACTATATACTATCACTTAATGCCGTCCACTAGCATTTAAATGGATT
131 TAATATTAATAATATAAAAACTATATACTATCACTTAATGCCGTCCACTAGCATTTAAATGGATT
19496502 AATTGCCACATAAAACCTCCATATTAAAAGAACATTCACTATTCAGCCCTTCTTAAAATAACCAC
196 AATTGCCACATAAAACCTCCATATTAAAAGAACATTCACTATTCAGCCCTTCTTAAAATAACCAC
19496567 A
261 A
19496568 AAATTTTTAT
Statistics
Matches: 258, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
258 175 0.68
259 35 0.14
260 1 0.00
262 47 0.18
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (261 bp):
GTTCTTCTTTCTTTTTCTTTTGTTTAGTTTCGGTCATAAAGATGAAGAAGAAAAAAATGAAATGA
TAATGGCTTATAATATTTTTATTATAACATAATAATATAATATACATAATTATAACCTTTATAAT
TAATATTAATAATATAAAAACTATATACTATCACTTAATGCCGTCCACTAGCATTTAAATGGATT
AATTGCCACATAAAACCTCCATATTAAAAGAACATTCACTATTCAGCCCTTCTTAAAATAACCAC
A
Found at i:19496889 original size:67 final size:67
Alignment explanation
Indices: 19496781--19496914 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
19496771 GCATGTCATC
* * *
19496781 TATATCTGACTTAGCCCGAAACAATTAATAGGGTCTCATTTCACTTTTCAATACATCAAATCTCC
1 TATATCCGACTTAGCCCGAAACAATTAATAGAGTCTCATTTCAATTTTCAATACATCAAATCTCC
19496846 CA
66 CA
* * *
19496848 TATATCCGACTTAGCTCGAAACAGTTAATAGAGTCTCATTTCAATTTTCAATACATCAAATGTCC
1 TATATCCGACTTAGCCCGAAACAATTAATAGAGTCTCATTTCAATTTTCAATACATCAAATCTCC
19496913 CA
66 CA
19496915 ATCTCATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.33
Consensus pattern (67 bp):
TATATCCGACTTAGCCCGAAACAATTAATAGAGTCTCATTTCAATTTTCAATACATCAAATCTCC
CA
Found at i:19501219 original size:12 final size:12
Alignment explanation
Indices: 19501204--19501232 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19501194 ATCCATCCCC
19501204 CCATTCCCATTT
1 CCATTCCCATTT
19501216 CCATTCCCATTT
1 CCATTCCCATTT
19501228 CCATT
1 CCATT
19501233 GTTCCAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.41, G:0.00, T:0.41
Consensus pattern (12 bp):
CCATTCCCATTT
Found at i:19502031 original size:10 final size:10
Alignment explanation
Indices: 19501987--19502033 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19501977 ATTAATATTA
*
19501987 AAAATATGGT
1 AAAATGTGGT
*
19501997 AAAATATGGT
1 AAAATGTGGT
*
19502007 AAAATGGGAGT
1 AAAATGTG-GT
19502018 -AAATGTGGT
1 AAAATGTGGT
19502027 AAAATGT
1 AAAATGT
19502034 TATTAGTAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 2 0.06
10 28 0.88
11 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.28
Consensus pattern (10 bp):
AAAATGTGGT
Found at i:19502300 original size:28 final size:28
Alignment explanation
Indices: 19502268--19502343 Score: 152
Period size: 28 Copynumber: 2.7 Consensus size: 28
19502258 TTTTTTACTT
19502268 TTCCCCCAAAACTTTTACTCATTCTCAC
1 TTCCCCCAAAACTTTTACTCATTCTCAC
19502296 TTCCCCCAAAACTTTTACTCATTCTCAC
1 TTCCCCCAAAACTTTTACTCATTCTCAC
19502324 TTCCCCCAAAACTTTTACTC
1 TTCCCCCAAAACTTTTACTC
19502344 CCCTCCCCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.36
Consensus pattern (28 bp):
TTCCCCCAAAACTTTTACTCATTCTCAC
Found at i:19502611 original size:190 final size:188
Alignment explanation
Indices: 19502296--19502643 Score: 443
Period size: 190 Copynumber: 1.8 Consensus size: 188
19502286 TCATTCTCAC
* *
19502296 TTCCCCCAAAACTTTTACTCATTCTCACTTCCCCCAAAACTTTTACTCCCCTCCCCTCCCAACCC
1 TTCCCCCAAAACTTTTACTCACTCTCACTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCC
** ** *
19502361 CCCATCTATCCCAAATTCATTTCCCACCAAAATTTTCTTTTAATATTTTTCCTCCAAAATTTTAC
66 CCCATCTATCCCAAACCCATCCCCCACCAAAATTTTCTTTAAATATTTTTCCTCCAAAATTTTAC
* * * *
19502426 TTCCTC-ATTTACTTTTCCTTAAAATTTTACTCCCAAAAACCCTCAAAATTTTTTATT
131 TCCCCCTATTTACTTTCCCTCAAAATTTTACTCCCAAAAACCCTCAAAATTTTTTATT
* * ** * *
19502483 TTCCCCCAAAAGTTTTACTCCCTCTCACTTTTCCCTTAAAACTTTTACTTCTCTCCCATCCC-AC
1 TTCCCCCAAAACTTTTACTCACTCTCAC--TTCCCCCAAAACTTTTACTCCCCTCCCATCCCAAC
**
19502547 CCCCCATCTA-CCACAAACCCATCCCCCCATCTCCCAATTTT-TTTAAATATTTTTCCTCCAAAA
64 CCCCCATCTATCC-CAAACCCAT-CCCCCA-C-CAAAATTTTCTTTAAATATTTTTCCTCCAAAA
19502610 TTTTACTCCCCCTATTTACTTTCCCTCAAAATTT
125 TTTTACTCCCCCTATTTACTTTCCCTCAAAATTT
19502644 CCCTCCCCAC
Statistics
Matches: 135, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
187 27 0.20
188 19 0.14
189 31 0.23
190 32 0.24
191 26 0.19
ACGTcount: A:0.25, C:0.37, G:0.00, T:0.38
Consensus pattern (188 bp):
TTCCCCCAAAACTTTTACTCACTCTCACTTCCCCCAAAACTTTTACTCCCCTCCCATCCCAACCC
CCCATCTATCCCAAACCCATCCCCCACCAAAATTTTCTTTAAATATTTTTCCTCCAAAATTTTAC
TCCCCCTATTTACTTTCCCTCAAAATTTTACTCCCAAAAACCCTCAAAATTTTTTATT
Found at i:19505897 original size:20 final size:20
Alignment explanation
Indices: 19505868--19505940 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
19505858 CAAAATTATA
*
19505868 AAAAAGTTCAAAATAATTTT
1 AAAAATTTCAAAATAATTTT
*
19505888 CAAAATTTCAAAATAATTTT
1 AAAAATTTCAAAATAATTTT
* *
19505908 TAAAA-TTC-AAATTATTTAT
1 AAAAATTTCAAAATAATTT-T
*
19505927 AAAAATTCCAAAAT
1 AAAAATTTCAAAAT
19505941 TTATATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 8 0.18
19 8 0.18
20 24 0.55
21 4 0.09
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAATTTCAAAATAATTTT
Found at i:19505965 original size:26 final size:27
Alignment explanation
Indices: 19505920--19505970 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19505910 AAATTCAAAT
*
19505920 TATTTATAAAAATT-CCAAAATTTATA
1 TATTTATAAAAATTACAAAAATTTATA
* *
19505946 TATTTTTAAAAATTATAAAAATTTA
1 TATTTATAAAAATTACAAAAATTTA
19505971 AAAAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTTATAAAAATTACAAAAATTTATA
Found at i:19505966 original size:10 final size:10
Alignment explanation
Indices: 19505953--19505993 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
19505943 ATATATTTTT
19505953 AAAAATTAT-
1 AAAAATTATA
19505962 AAAAATT-TA
1 AAAAATTATA
19505971 AAAAATTATA
1 AAAAATTATA
*
19505981 AAGAATATATA
1 AAAAAT-TATA
19505992 AA
1 AA
19505994 GAAAGTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 14 0.50
10 7 0.25
11 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:19505974 original size:18 final size:18
Alignment explanation
Indices: 19505859--19505982 Score: 70
Period size: 18 Copynumber: 6.6 Consensus size: 18
19505849 TTTCTTAACC
19505859 AAAATTATAAAAAAGTTCAA
1 AAAATTAT-AAAAA-TTCAA
* *
19505879 AATAATTTTCAAAATTTCAA
1 AA-AATTAT-AAAAATTCAA
* *
19505899 AATAATTTTTAAAATTCAA
1 AA-AATTATAAAAATTCAA
* * *
19505918 ATTATTTATAAAAATTCCA
1 A-AAATTATAAAAATTCAA
* * * **
19505937 AAATTTAT-ATATTTTTA
1 AAAATTATAAAAATTCAA
*
19505954 AAAATTATAAAAATTTAA
1 AAAATTATAAAAATTCAA
19505972 AAAATTATAAA
1 AAAATTATAAA
19505983 GAATATATAA
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
17 12 0.15
18 23 0.28
19 22 0.27
20 16 0.20
21 9 0.11
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.39
Consensus pattern (18 bp):
AAAATTATAAAAATTCAA
Found at i:19506129 original size:16 final size:16
Alignment explanation
Indices: 19506110--19506140 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19506100 TCAAAAAAGT
19506110 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
19506126 TTTCAAATTTATATG
1 TTTCAAATATATATG
19506141 CTTTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:19506447 original size:22 final size:20
Alignment explanation
Indices: 19506420--19506472 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
19506410 ACATGTGTCA
19506420 TAAAAATAAAAAAATATCATT
1 TAAAAATAAAAAAA-ATCATT
*
19506441 TCAAAAATTAAAAAAAATCCTT
1 T-AAAAA-TAAAAAAAATCATT
*
19506463 TAAAAGTAAA
1 TAAAAATAAA
19506473 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 11 0.39
23 8 0.29
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAATAAAAAAAATCATT
Found at i:19507045 original size:47 final size:44
Alignment explanation
Indices: 19506993--19507111 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 44
19506983 ATAATCATTA
*
19506993 TTATTATTTAAAATCTAGAATAAAAATTAAATTTATGTTAAAATGAT
1 TTATTACTTAAAA-CT--AATAAAAATTAAATTTATGTTAAAATGAT
*
19507040 TTATTACTT--AAGTAATAAAAATTAAATTTATGTTAAAATGAT
1 TTATTACTTAAAACTAATAAAAATTAAATTTATGTTAAAATGAT
*
19507082 TTATTACTT--AAGTAATAAAAATTAAATTTA
1 TTATTACTTAAAACTAATAAAAATTAAATTTA
19507112 AAAATCTTGA
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 59 0.84
44 1 0.01
45 2 0.03
47 8 0.11
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (44 bp):
TTATTACTTAAAACTAATAAAAATTAAATTTATGTTAAAATGAT
Found at i:19507057 original size:42 final size:42
Alignment explanation
Indices: 19507011--19507111 Score: 202
Period size: 42 Copynumber: 2.4 Consensus size: 42
19507001 TAAAATCTAG
19507011 AATAAAAATTAAATTTATGTTAAAATGATTTATTACTTAAGT
1 AATAAAAATTAAATTTATGTTAAAATGATTTATTACTTAAGT
19507053 AATAAAAATTAAATTTATGTTAAAATGATTTATTACTTAAGT
1 AATAAAAATTAAATTTATGTTAAAATGATTTATTACTTAAGT
19507095 AATAAAAATTAAATTTA
1 AATAAAAATTAAATTTA
19507112 AAAATCTTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (42 bp):
AATAAAAATTAAATTTATGTTAAAATGATTTATTACTTAAGT
Found at i:19507058 original size:24 final size:24
Alignment explanation
Indices: 19507031--19507101 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
19507021 AAATTTATGT
19507031 TAAAATGATTTATTACTTAAGTAA
1 TAAAATGATTTATTACTTAAGTAA
* * *
19507055 TAAAA--A-TTA-AATTTATGT--
1 TAAAATGATTTATTACTTAAGTAA
19507073 TAAAATGATTTATTACTTAAGTAA
1 TAAAATGATTTATTACTTAAGTAA
19507097 TAAAA
1 TAAAA
19507102 ATTAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 5 0.14
20 7 0.20
21 6 0.17
22 7 0.20
24 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (24 bp):
TAAAATGATTTATTACTTAAGTAA
Found at i:19516472 original size:16 final size:17
Alignment explanation
Indices: 19516441--19516478 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19516431 ACAAAATCTA
19516441 AATTTATTTCCCAATTT
1 AATTTATTTCCCAATTT
19516458 AATTTATTT-CCAATTT
1 AATTTATTTCCCAATTT
19516474 -ATTTA
1 AATTTA
19516479 ATTGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTATTTCCCAATTT
Found at i:19528798 original size:21 final size:21
Alignment explanation
Indices: 19528774--19528815 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19528764 TAACCGACCG
19528774 GTTAATTGAATTAATTCAGTT
1 GTTAATTGAATTAATTCAGTT
19528795 GTTAATTGAATTAATTCAGTT
1 GTTAATTGAATTAATTCAGTT
19528816 CAGTCAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
GTTAATTGAATTAATTCAGTT
Found at i:19529344 original size:301 final size:301
Alignment explanation
Indices: 19528802--19529400 Score: 1180
Period size: 301 Copynumber: 2.0 Consensus size: 301
19528792 GTTGTTAATT
19528802 GAATTAATTCAGTTCAGTCAGTTAAATCAGTTTTACCCGAAATTTACACACCCCTACATGTTGTT
1 GAATTAATTCAGTTCAGTCAGTTAAATCAGTTTTACCCGAAATTTACACACCCCTACATGTTGTT
19528867 GAAGCCAAAGTTGAAGTTCCACAGTTTGGTTGTCTTTATCTATTGCATTTCCTTCTTCATTTTTT
66 GAAGCCAAAGTTGAAGTTCCACAGTTTGGTTGTCTTTATCTATTGCATTTCCTTCTTCATTTTTT
19528932 TAAGGTGTCTCATTATCTTAATCCTCAAATAAATTATTAGGGAGTATACTTGAAGGTGCCCATGC
131 TAAGGTGTCTCATTATCTTAATCCTCAAATAAATTATTAGGGAGTATACTTGAAGGTGCCCATGC
*
19528997 TTTGTGGCGAGTGTCAACTATCTAGTGAATATTTGGTCCAACTTTCCTTTTAATTCAAGATCAAT
196 TTTGTGACGAGTGTCAACTATCTAGTGAATATTTGGTCCAACTTTCCTTTTAATTCAAGATCAAT
19529062 GCCTGTAATTTTAATTTCTAAGCTTCGAGAACAAATTAACC
261 GCCTGTAATTTTAATTTCTAAGCTTCGAGAACAAATTAACC
19529103 GAATTAATTCAGTTCAGTCAGTTAAATCAGTTTTACCCGAAATTTACACACCCCTACATGTTGTT
1 GAATTAATTCAGTTCAGTCAGTTAAATCAGTTTTACCCGAAATTTACACACCCCTACATGTTGTT
*
19529168 GAAGCCAAAGTTGAAGTTCTACAGTTTGGTTGTCTTTATCTATTGCATTTCCTTCTTCATTTTTT
66 GAAGCCAAAGTTGAAGTTCCACAGTTTGGTTGTCTTTATCTATTGCATTTCCTTCTTCATTTTTT
19529233 TAAGGTGTCTCATTATCTTAATCCTCAAATAAATTATTAGGGAGTATACTTGAAGGTGCCCATGC
131 TAAGGTGTCTCATTATCTTAATCCTCAAATAAATTATTAGGGAGTATACTTGAAGGTGCCCATGC
19529298 TTTGTGACGAGTGTCAACTATCTAGTGAATATTTGGTCCAACTTTCCTTTTAATTCAAGATCAAT
196 TTTGTGACGAGTGTCAACTATCTAGTGAATATTTGGTCCAACTTTCCTTTTAATTCAAGATCAAT
19529363 GCCTGTAATTTTAATTTCTAAGCTTCGAGAACAAATTA
261 GCCTGTAATTTTAATTTCTAAGCTTCGAGAACAAATTA
19529401 TCTATAAAAT
Statistics
Matches: 296, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
301 296 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (301 bp):
GAATTAATTCAGTTCAGTCAGTTAAATCAGTTTTACCCGAAATTTACACACCCCTACATGTTGTT
GAAGCCAAAGTTGAAGTTCCACAGTTTGGTTGTCTTTATCTATTGCATTTCCTTCTTCATTTTTT
TAAGGTGTCTCATTATCTTAATCCTCAAATAAATTATTAGGGAGTATACTTGAAGGTGCCCATGC
TTTGTGACGAGTGTCAACTATCTAGTGAATATTTGGTCCAACTTTCCTTTTAATTCAAGATCAAT
GCCTGTAATTTTAATTTCTAAGCTTCGAGAACAAATTAACC
Found at i:19536826 original size:17 final size:18
Alignment explanation
Indices: 19536796--19536833 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
19536786 AAATTTTATT
19536796 AATAAATTAATTTAATAC
1 AATAAATTAATTTAATAC
*
19536814 AATAAA-TATTTTAATAC
1 AATAAATTAATTTAATAC
19536831 AAT
1 AAT
19536834 TGGCATGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATTAATTTAATAC
Found at i:19543688 original size:25 final size:25
Alignment explanation
Indices: 19543650--19543756 Score: 87
Period size: 25 Copynumber: 4.3 Consensus size: 25
19543640 ATTATTAGGG
19543650 TTACCAAT-TCTCAGCTCG-AGAGAGC
1 TTACCAATAT-TCAGCTCGCA-AGAGC
* *
19543675 TTACCGATATTCAGCTCGCATGAGC
1 TTACCAATATTCAGCTCGCAAGAGC
* * *
19543700 TTACCAATATTCAGCTTGTATGAGC
1 TTACCAATATTCAGCTCGCAAGAGC
* *
19543725 TTACC-AT-TTACAGCTAGTAAGAGC
1 TTACCAATATT-CAGCTCGCAAGAGC
*
19543749 ATACCAAT
1 TTACCAAT
19543757 TCAAAGCTCG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.03
24 18 0.26
25 48 0.69
26 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (25 bp):
TTACCAATATTCAGCTCGCAAGAGC
Found at i:19543748 original size:24 final size:25
Alignment explanation
Indices: 19543670--19543756 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
19543660 TCAGCTCGAG
* * *
19543670 AGAGCTTACCGATATTCAGCTCGCA
1 AGAGCTTACCAATATTCAGCTAGTA
* *
19543695 TGAGCTTACCAATATTCAGCTTGTA
1 AGAGCTTACCAATATTCAGCTAGTA
*
19543720 TGAGCTTACC-AT-TTACAGCTAGTA
1 AGAGCTTACCAATATT-CAGCTAGTA
*
19543744 AGAGCATACCAAT
1 AGAGCTTACCAAT
19543757 TCAAAGCTCG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.04
24 18 0.34
25 33 0.62
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (25 bp):
AGAGCTTACCAATATTCAGCTAGTA
Found at i:19543773 original size:25 final size:24
Alignment explanation
Indices: 19543683--19543777 Score: 70
Period size: 25 Copynumber: 3.9 Consensus size: 24
19543673 GCTTACCGAT
* *
19543683 ATTC-AGCTCGCATGAGCTTACCAA
1 ATTCAAGCTCGTATGAGCATACC-A
* *
19543707 TATTC-AGCTTGTATGAGCTTACC-
1 -ATTCAAGCTCGTATGAGCATACCA
* * *
19543730 ATTTACAGCTAGTAAGAGCATACCA
1 ATTCA-AGCTCGTATGAGCATACCA
19543755 ATTCAAAGCTCGTATGAGCATAC
1 ATTC-AAGCTCGTATGAGCATAC
19543778 ATGTATAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 3 0.05
24 15 0.26
25 38 0.67
26 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (24 bp):
ATTCAAGCTCGTATGAGCATACCA
Found at i:19550931 original size:105 final size:105
Alignment explanation
Indices: 19550745--19550955 Score: 368
Period size: 105 Copynumber: 2.0 Consensus size: 105
19550735 CTTGAAGAGA
* * *
19550745 GATATTAGCATAATTTAGGGATTTCTACGGATCAAGATATTAGGTGAATAAATTGTTTAATTCAG
1 GATATTAGCATAATTTAGGGATTTCTACGAATCAAGATATTAGGTGAATAAACTATTTAATTCAG
19550810 ATTGATAATGAAAGATGCAGTCTAGGCGGATTCTTTCCTG
66 ATTGATAATGAAAGATGCAGTCTAGGCGGATTCTTTCCTG
*
19550850 GATATTAGCATAATTTAGGGATTTCTATGAATCAAGATATTAGGTGAATAAACTATTTAATTCAG
1 GATATTAGCATAATTTAGGGATTTCTACGAATCAAGATATTAGGTGAATAAACTATTTAATTCAG
* *
19550915 GTTGATAATGACAGATGCAGTCTAGGCGGATTCTTTCCTG
66 ATTGATAATGAAAGATGCAGTCTAGGCGGATTCTTTCCTG
19550955 G
1 G
19550956 GTACTGTTTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (105 bp):
GATATTAGCATAATTTAGGGATTTCTACGAATCAAGATATTAGGTGAATAAACTATTTAATTCAG
ATTGATAATGAAAGATGCAGTCTAGGCGGATTCTTTCCTG
Found at i:19555865 original size:47 final size:47
Alignment explanation
Indices: 19555796--19555889 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
19555786 TCACTTTGAG
19555796 TTAATAAATTTATTTTTTGAGTTTTCTTTTAGAAAAGTTTTAACAAT
1 TTAATAAATTTATTTTTTGAGTTTTCTTTTAGAAAAGTTTTAACAAT
19555843 TTAATAAATTTATTTTTTGAGTTTTCTTTTAGAAAAGTTTTAACAAT
1 TTAATAAATTTATTTTTTGAGTTTTCTTTTAGAAAAGTTTTAACAAT
19555890 CTTTTCAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (47 bp):
TTAATAAATTTATTTTTTGAGTTTTCTTTTAGAAAAGTTTTAACAAT
Found at i:19557408 original size:27 final size:27
Alignment explanation
Indices: 19557365--19557485 Score: 95
Period size: 27 Copynumber: 4.5 Consensus size: 27
19557355 GTGTCAAGAT
**
19557365 AGTAAACATGGAATAGTCTGCTGGGAC
1 AGTAAACATGGGGTAGTCTGCTGGGAC
19557392 AGTAAACATGGGGTAGTC--CATCGGGAC
1 AGTAAACATGGGGTAGTCTGC-T-GGGAC
* * *
19557419 AATAAACATGGGGTAGTCTACAGGGAC
1 AGTAAACATGGGGTAGTCTGCTGGGAC
* ** * * *
19557446 AATAAACACAGGGTAATTTGCTAGGAC
1 AGTAAACATGGGGTAGTCTGCTGGGAC
19557473 -GTAAAACATGGGG
1 AGT-AAACATGGGG
19557486 ATCATAGTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 71 0.95
29 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (27 bp):
AGTAAACATGGGGTAGTCTGCTGGGAC
Found at i:19559405 original size:29 final size:30
Alignment explanation
Indices: 19559373--19559429 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
19559363 GTATATTTTC
19559373 TTAAATT-TTA-AGTAAAATATATTTATTAA
1 TTAAATTATTATAGTAAAATAT-TTTATTAA
*
19559402 TTAAATTATTATATTAAAATATTTTATT
1 TTAAATTATTATAGTAAAATATTTTATT
19559430 TATTTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTAAATTATTATAGTAAAATATTTTATTAA
Found at i:19559802 original size:17 final size:16
Alignment explanation
Indices: 19559780--19559813 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19559770 ATTATATAAT
19559780 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
19559797 TAATGATATTATATTA
1 TAATGATATTAAATTA
19559813 T
1 T
19559814 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:19560092 original size:533 final size:533
Alignment explanation
Indices: 19559086--19560154 Score: 2093
Period size: 533 Copynumber: 2.0 Consensus size: 533
19559076 AGTTTAATTT
19559086 AAAGTAATTAGGAAAAAGGATCAAATTGAATAAAGAGCGAAAGTCTAATTATAGATTAAAAGAAA
1 AAAGTAATTAGGAAAAAGGATCAAATTGAATAAAGAGCGAAAGTCTAATTATAGATTAAAAGAAA
19559151 TTAAAAAAGGCTAAAATGGCAATTAAGCCATTTGGCATAGTTGAGGCGGCATAAAGGGAATAAAA
66 TTAAAAAAGGCTAAAATGGCAATTAAGCCATTTGGCATAGTTGAGGCGGCATAAAGGGAATAAAA
19559216 TCTAAGATTTTATTCGTTTTAATTATATAATTAATGATAATTAAATTATAATGATATTATAATAT
131 TCTAAGATTTTATTCGTTTTAATTATATAATTAATGATAATTAAATTATAATGATATTATAATAT
19559281 TAAATAAATCAAAATATGCCAATTGTATGGATATGATAAAATACATGTGTAATATATGTATTTGT
196 TAAATAAATCAAAATATGCCAATTGTATGGATATGATAAAATACATGTGTAATATATGTATTTGT
*
19559346 ACATTTGTAATATAATTGTATATTTTCTTAAATTTTAAGTAAAATATATTTATTAATTAAATTAT
261 ACATTTGTAATATAATTGTATATTTTCTTAAATTTTAAGTAAAAGATATTTATTAATTAAATTAT
* *
19559411 TATATTAAAATATTTTATTTATTTGATAAATTAGTTAGATTAAGACAAATGTAAGGTTATGATAT
326 TATATTAAAAGATTTTATTTATTTGATAAATTAGTTAGATTAAGACAAATATAAGGTTATGATAT
*
19559476 AGCACAAATGTATTAATTATATTTGTTATTCAAATAGATATTTTATAATTATTAATTAACTTAAA
391 AGCACAAATGTATTAATTATATTTGTTATTAAAATAGATATTTTATAATTATTAATTAACTTAAA
19559541 TATAAAATAAAGCAAATGAAATAAAAGAAAGAAAGAAACAGAACATTAAGCAGGAACGAAACAGA
456 TATAAAATAAAGCAAATGAAATAAAAGAAAGAAAGAAACAGAACATTAAGCAGGAACGAAACAGA
19559606 GAAAGGAGAGAAC
521 GAAAGGAGAGAAC
19559619 AAAGTAATTAGGAAAAAGGATCAAATTGAATAAAGAGCGAAAGTCTAATTATAGATTAAAAGAAA
1 AAAGTAATTAGGAAAAAGGATCAAATTGAATAAAGAGCGAAAGTCTAATTATAGATTAAAAGAAA
19559684 TTAAAAAAGGCTAAAATGGCAATTAAGCCATTTGGCATAGTTGAGGCGGCATAAAGGGAATAAAA
66 TTAAAAAAGGCTAAAATGGCAATTAAGCCATTTGGCATAGTTGAGGCGGCATAAAGGGAATAAAA
*
19559749 TCTAAGATTTTATTCGTTTTAATTATATAATTAATGATAATTAAATTATAATGATATTATATTAT
131 TCTAAGATTTTATTCGTTTTAATTATATAATTAATGATAATTAAATTATAATGATATTATAATAT
19559814 TAAATAAATCAAAATATGCCAATTGTATGGATATGATAAAATACATGTGTAATATATGTATTTGT
196 TAAATAAATCAAAATATGCCAATTGTATGGATATGATAAAATACATGTGTAATATATGTATTTGT
19559879 ACATTTGTAATATAATTGTATATTTTCTTAAATTTTAAGTAAAAGATATTTATTAATTAAATTAT
261 ACATTTGTAATATAATTGTATATTTTCTTAAATTTTAAGTAAAAGATATTTATTAATTAAATTAT
19559944 TATATTAAAAGATTTTATTTATTTGATAAATTAGTTAGATTAAGACAAATATAAGGTTATGATAT
326 TATATTAAAAGATTTTATTTATTTGATAAATTAGTTAGATTAAGACAAATATAAGGTTATGATAT
19560009 AGCACAAATGTATTAATTATATTTGTTATTAAAATAGATATTTTATAATTATTAATTAACTTAAA
391 AGCACAAATGTATTAATTATATTTGTTATTAAAATAGATATTTTATAATTATTAATTAACTTAAA
19560074 TATAAAATAAAGCAAATGAAATAAAAGAAAGAAAGAAACAGAACATTAAGCAGGAACGAAACAGA
456 TATAAAATAAAGCAAATGAAATAAAAGAAAGAAAGAAACAGAACATTAAGCAGGAACGAAACAGA
19560139 GAAAGGAGAGAAC
521 GAAAGGAGAGAAC
19560152 AAA
1 AAA
19560155 AAAAAAGGAA
Statistics
Matches: 531, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
533 531 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.34
Consensus pattern (533 bp):
AAAGTAATTAGGAAAAAGGATCAAATTGAATAAAGAGCGAAAGTCTAATTATAGATTAAAAGAAA
TTAAAAAAGGCTAAAATGGCAATTAAGCCATTTGGCATAGTTGAGGCGGCATAAAGGGAATAAAA
TCTAAGATTTTATTCGTTTTAATTATATAATTAATGATAATTAAATTATAATGATATTATAATAT
TAAATAAATCAAAATATGCCAATTGTATGGATATGATAAAATACATGTGTAATATATGTATTTGT
ACATTTGTAATATAATTGTATATTTTCTTAAATTTTAAGTAAAAGATATTTATTAATTAAATTAT
TATATTAAAAGATTTTATTTATTTGATAAATTAGTTAGATTAAGACAAATATAAGGTTATGATAT
AGCACAAATGTATTAATTATATTTGTTATTAAAATAGATATTTTATAATTATTAATTAACTTAAA
TATAAAATAAAGCAAATGAAATAAAAGAAAGAAAGAAACAGAACATTAAGCAGGAACGAAACAGA
GAAAGGAGAGAAC
Found at i:19561272 original size:45 final size:45
Alignment explanation
Indices: 19561166--19561272 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
19561156 ATATGCCGAC
* *
19561166 TACTGTTACTGTTACCGATTCGACATTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
* *
19561211 TACCGTTACTATTACAGATTC-AGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGA-CACTTTGTGTGTTGAATACTGT
*
19561256 TACTGTTACTGCTACAG
1 TACTGTTACTGTTACAG
19561273 TTACTAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTGTGTGTTGAATACTGT
Done.