Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 138 of 279
Found at i:44602248 original size:19 final size:20
Alignment explanation
Indices: 44602210--44602249 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44602200 GTAATTTTAT
*
44602210 TTTTTAATTTAAATTTAATA
1 TTTTTAATTTAAATTAAATA
*
44602230 TTTTTATTTTAAA-TAAATA
1 TTTTTAATTTAAATTAAATA
44602249 T
1 T
44602250 AATTGTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAATTTAAATTAAATA
Found at i:44603868 original size:22 final size:22
Alignment explanation
Indices: 44603840--44603881 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
44603830 AATTTTTTTA
*
44603840 TTTTTTAATTTAAATGTAATAT
1 TTTTTTAATTTAAATCTAATAT
44603862 TTTTTTAATTTAAATCTAAT
1 TTTTTTAATTTAAATCTAAT
44603882 TGCCATGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTTAATTTAAATCTAATAT
Found at i:44627414 original size:5 final size:5
Alignment explanation
Indices: 44627397--44627429 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
44627387 AGAAACAGCA
*
44627397 AAAAT AAAA- AAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
44627430 GGAAATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:44657310 original size:19 final size:20
Alignment explanation
Indices: 44657265--44657313 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
44657255 CAGAATTGAT
44657265 TTAATTTT-AAA-TTATATA
1 TTAATTTTAAAATTTATATA
*
44657283 TTAA-ATTAAAATTTATATA
1 TTAATTTTAAAATTTATATA
44657302 -TAATTTTAAAAT
1 TTAATTTTAAAAT
44657314 ATATCCCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 10 0.38
19 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTTTAAAATTTATATA
Found at i:44657316 original size:17 final size:18
Alignment explanation
Indices: 44657265--44657317 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
44657255 CAGAATTGAT
*
44657265 TTAATTTTAAATTATATA
1 TTAATTTTAAAATATATA
* *
44657283 TTAA-ATTAAAATTTATA
1 TTAATTTTAAAATATATA
44657300 TATAATTTTAAAATATAT
1 T-TAATTTTAAAATATAT
44657318 CCCTTCCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.39
18 7 0.25
19 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTTTAAAATATATA
Found at i:44658015 original size:25 final size:23
Alignment explanation
Indices: 44657984--44658051 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 23
44657974 ATTTATAAAA
44657984 ATAAATACATCAATTAATTTTTAT
1 ATAAATACAT-AATTAATTTTTAT
44658008 ATTAAATAACTATAATT-ATTTTTAT
1 A-TAAAT-AC-ATAATTAATTTTTAT
*
44658033 ATAATTACATTAA-TAATTT
1 ATAAATACA-TAATTAATTT
44658052 ATAAAAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.05
23 9 0.24
24 5 0.13
25 14 0.37
26 6 0.16
27 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAATACATAATTAATTTTTAT
Found at i:44659193 original size:16 final size:17
Alignment explanation
Indices: 44659162--44659195 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44659152 TAATTTTTTT
*
44659162 TAAAAATTTATCAAATA
1 TAAAAATATATCAAATA
44659179 TAAAAATATAT-AAATA
1 TAAAAATATATCAAATA
44659195 T
1 T
44659196 CTCAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATATCAAATA
Found at i:44659398 original size:16 final size:19
Alignment explanation
Indices: 44659355--44659400 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
44659345 TTACATAAGA
44659355 AAATTATTAATGTGTATGT
1 AAATTATTAATGTGTATGT
**
44659374 AAAAAATTAAT-T-T-TGT
1 AAATTATTAATGTGTATGT
44659390 AAATTATTAAT
1 AAATTATTAAT
44659401 ATGTTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 1 0.04
19 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (19 bp):
AAATTATTAATGTGTATGT
Found at i:44659663 original size:8 final size:8
Alignment explanation
Indices: 44659652--44659685 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
44659642 TAAAATTTAA
*
44659652 AAATTTTC
1 AAATTCTC
44659660 AAATTCTC
1 AAATTCTC
44659668 AAATTCTC
1 AAATTCTC
44659676 AAATTTCTC
1 AAA-TTCTC
44659685 A
1 A
44659686 TTCAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (8 bp):
AAATTCTC
Found at i:44662517 original size:6 final size:7
Alignment explanation
Indices: 44662497--44662521 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44662487 TATAGGGTGT
44662497 AATAAAA
1 AATAAAA
44662504 AATAAAA
1 AATAAAA
44662511 AATAAAA
1 AATAAAA
44662518 AATA
1 AATA
44662522 TAAATATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:44667258 original size:13 final size:13
Alignment explanation
Indices: 44667240--44667282 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
44667230 TTTAATAATA
44667240 AAATAAAGAAATG
1 AAATAAAGAAATG
44667253 AAATAAAGAAAT-
1 AAATAAAGAAATG
* *
44667265 AAATGAAATAAAAG
1 AAAT-AAAGAAATG
44667279 AAAT
1 AAAT
44667283 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:44667270 original size:17 final size:18
Alignment explanation
Indices: 44667236--44667282 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
44667226 ATAGTTTAAT
* *
44667236 AATAAAATAAAGAAATGA
1 AATAAAAGAAATAAATGA
44667254 AAT-AAAGAAATAAATGA
1 AATAAAAGAAATAAATGA
44667271 AATAAAAGAAAT
1 AATAAAAGAAAT
44667283 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AATAAAAGAAATAAATGA
Found at i:44667274 original size:9 final size:9
Alignment explanation
Indices: 44667248--44667282 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
44667238 TAAAATAAAG
44667248 AAATGAAAT
1 AAATGAAAT
44667257 AAA-GAAAT
1 AAATGAAAT
44667265 AAATGAAAT
1 AAATGAAAT
*
44667274 AAAAGAAAT
1 AAATGAAAT
44667283 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (9 bp):
AAATGAAAT
Found at i:44667308 original size:22 final size:23
Alignment explanation
Indices: 44667275--44667320 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
44667265 AAATGAAATA
*
44667275 AAAGAAATGAAA-A-AGAAAAAC
1 AAAGAAACGAAACAGAGAAAAAC
44667296 AAAGCAAACGAAACAGAGAAAAAC
1 AAAG-AAACGAAACAGAGAAAAAC
44667320 A
1 A
44667321 GGGGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 1 0.05
24 9 0.43
ACGTcount: A:0.72, C:0.11, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAGAAACGAAACAGAGAAAAAC
Found at i:44668579 original size:15 final size:15
Alignment explanation
Indices: 44668559--44668603 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
44668549 CAATTTTATG
*
44668559 TTGATTGAAATCATT
1 TTGATTGAAATCATA
* *
44668574 TTGATTGAATTTATA
1 TTGATTGAAATCATA
44668589 TTGATTGAAAT-ATA
1 TTGATTGAAATCATA
44668603 T
1 T
44668604 ATTATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (15 bp):
TTGATTGAAATCATA
Found at i:44677164 original size:13 final size:14
Alignment explanation
Indices: 44677148--44677183 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
44677138 CAATCTCATA
44677148 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
44677161 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
44677174 TCTC-ATTTCA
1 TCTCAATTTCA
44677184 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:44677173 original size:18 final size:19
Alignment explanation
Indices: 44677135--44677175 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
44677125 TGGTTCATGT
44677135 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
44677154 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
44677172 TTTC
1 TTTC
44677176 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:44677365 original size:39 final size:38
Alignment explanation
Indices: 44677298--44677432 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
44677288 ACCAATATGG
* * *
44677298 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
44677337 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
44677375 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
44677416 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
44677433 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:44677698 original size:18 final size:19
Alignment explanation
Indices: 44677672--44677710 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
44677662 TTTCAATTCA
*
44677672 ATTCAAATAATCAATATAT
1 ATTCAAATAATAAATATAT
*
44677691 ATTC-AATATTAAATATAT
1 ATTCAAATAATAAATATAT
44677709 AT
1 AT
44677711 ATCTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATAAATATAT
Found at i:44678190 original size:121 final size:121
Alignment explanation
Indices: 44677976--44678216 Score: 419
Period size: 121 Copynumber: 2.0 Consensus size: 121
44677966 ATACAATTCA
* *
44677976 TAATCATTAATACATTACTAATTCATATCTTGAGTTATAGAATTCTAAATTAAGATCCGCTAATT
1 TAATCATTAATACATTACTAATTCATATCTTGAGTTACAGAACTCTAAATTAAGATCCGCTAATT
* * *
44678041 TTTCCTGAAACTAGACTCACAAATCTTCTTACTATAAAATTTTCAGAATTTTTGGG
66 TTTCCTGAAACTAGACTCACAAATCTTCTTACAATAAAATTTCCAGAAATTTTGGG
*
44678097 TAATCATTAATACATTACTAATTTATATCTTGAGTTACAGAACTCTAAATTAAGATCCGCTAATT
1 TAATCATTAATACATTACTAATTCATATCTTGAGTTACAGAACTCTAAATTAAGATCCGCTAATT
*
44678162 TTTTCTGAAACTAGACTCACAAATCTTCTTACAATAAAATTTCCAGAAATTTTGG
66 TTTCCTGAAACTAGACTCACAAATCTTCTTACAATAAAATTTCCAGAAATTTTGG
44678217 TTTAGCCATT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (121 bp):
TAATCATTAATACATTACTAATTCATATCTTGAGTTACAGAACTCTAAATTAAGATCCGCTAATT
TTTCCTGAAACTAGACTCACAAATCTTCTTACAATAAAATTTCCAGAAATTTTGGG
Found at i:44680838 original size:12 final size:12
Alignment explanation
Indices: 44680823--44680852 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44680813 ACAATAATAC
44680823 TATATATAAATG
1 TATATATAAATG
*
44680835 TATATATATATG
1 TATATATAAATG
44680847 TATATA
1 TATATA
44680853 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:44680958 original size:19 final size:17
Alignment explanation
Indices: 44680934--44680980 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
44680924 AATTAAAGTA
*
44680934 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
44680953 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
44680970 AT-AAAAATATA
1 ATAAAAAATATA
44680981 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:44680976 original size:18 final size:19
Alignment explanation
Indices: 44680937--44680985 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
44680927 TAAAGTAATA
*
44680937 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
44680955 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
44680972 AAAAATATACACTA
1 AAAAATATATACTA
44680986 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:44681215 original size:3 final size:3
Alignment explanation
Indices: 44681202--44681287 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
44681192 GAGGGCATAT
44681202 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
44681246 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44681288 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:44681228 original size:18 final size:18
Alignment explanation
Indices: 44681207--44681287 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
44681197 CATATATAAT
44681207 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
44681225 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
44681246 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
44681264 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
44681281 ATAATAA
1 ATAATAA
44681288 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:44681642 original size:21 final size:22
Alignment explanation
Indices: 44681618--44681716 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 22
44681608 CTTCTTTCCA
44681618 AAAAAACAAAAAAA-CACCTCC
1 AAAAAACAAAAAAACCACCTCC
*
44681639 AAAAAACAAAAAAACCTCCTCC
1 AAAAAACAAAAAAACCACCTCC
**
44681661 --AAAACAAAGAACAATCCTTCTCC
1 AAAAAACAAA-AA-AA-CCACCTCC
* * *
44681684 AAAAAACCAAAAACCCACATCCC
1 AAAAAACAAAAAAACCACCT-CC
*
44681707 TAAAAACAAA
1 AAAAAACAAA
44681717 GTCTTGAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 8 0.13
21 16 0.26
22 11 0.18
23 18 0.29
24 2 0.03
25 7 0.11
ACGTcount: A:0.60, C:0.30, G:0.01, T:0.09
Consensus pattern (22 bp):
AAAAAACAAAAAAACCACCTCC
Found at i:44681642 original size:22 final size:23
Alignment explanation
Indices: 44681614--44681664 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
44681604 TAACCTTCTT
44681614 TCCAAAAAAACAAAAAAA-CACC
1 TCCAAAAAAACAAAAAAACCACC
*
44681636 TCC-AAAAAACAAAAAAACCTCC
1 TCCAAAAAAACAAAAAAACCACC
44681658 TCCAAAA
1 TCCAAAA
44681665 CAAAGAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (23 bp):
TCCAAAAAAACAAAAAAACCACC
Found at i:44681687 original size:23 final size:20
Alignment explanation
Indices: 44681620--44681687 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
44681610 TCTTTCCAAA
*
44681620 AAAACAAAAAAA-CACCTCC
1 AAAACAAAAAAACCTCCTCC
44681639 AAAAAACAAAAAAACCTCCTCC
1 --AAAACAAAAAAACCTCCTCC
*
44681661 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAA-AA-AA-CCTCCTCC
44681684 AAAA
1 AAAA
44681688 AACCAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.20
21 14 0.34
22 8 0.20
23 11 0.27
ACGTcount: A:0.59, C:0.29, G:0.01, T:0.10
Consensus pattern (20 bp):
AAAACAAAAAAACCTCCTCC
Found at i:44683633 original size:6 final size:7
Alignment explanation
Indices: 44683610--44683642 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
44683600 TTTTTTTAAT
44683610 TCACACC
1 TCACACC
44683617 TCACACC
1 TCACACC
44683624 TCAC-CC
1 TCACACC
44683630 TCACACC
1 TCACACC
44683637 ATCACA
1 -TCACA
44683643 TGAAGATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 13 0.54
8 5 0.21
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
TCACACC
Found at i:44683633 original size:13 final size:15
Alignment explanation
Indices: 44683610--44683642 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
44683600 TTTTTTTAAT
44683610 TCACACCTCACACC-
1 TCACACCTCACACCA
44683624 TCAC-CCTCACACCA
1 TCACACCTCACACCA
44683638 TCACA
1 TCACA
44683643 TGAAGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (15 bp):
TCACACCTCACACCA
Found at i:44684143 original size:24 final size:24
Alignment explanation
Indices: 44684113--44684171 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
44684103 TTAAAATAAT
*
44684113 AAAATTACAATGTTTACTATCGTA
1 AAAATTACAATGTTTACTATCATA
44684137 AAAATTACAATGTTTACTATCATA
1 AAAATTACAATGTTTACTATCATA
44684161 AAAATTACAAT
1 AAAATTACAAT
44684172 TTAATTTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (24 bp):
AAAATTACAATGTTTACTATCATA
Found at i:44705622 original size:17 final size:16
Alignment explanation
Indices: 44705594--44705633 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
44705584 TTTTGACCTC
44705594 TTAAATTGATAAAATT
1 TTAAATTGATAAAATT
*
44705610 TTATAATTTATAAAATT
1 TTA-AATTGATAAAATT
44705627 TTAAATT
1 TTAAATT
44705634 ACTAATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATTGATAAAATT
Found at i:44707770 original size:95 final size:95
Alignment explanation
Indices: 44707607--44707784 Score: 277
Period size: 95 Copynumber: 1.9 Consensus size: 95
44707597 ATATATCTGA
* * *
44707607 TGAAGATGCGTTGCGTTTGCATTGAATTTATATTAAGAATAATTCGTTCTTTTGTCGTACTCGTG
1 TGAAGATGCGTTGCGTTTGCATTGAATTTAAATGAAGAATAATTCATTCTTTTGTCGTACTCGTG
*
44707672 AATGGGACCGAATGTGTTCTATGAATCTCC
66 AATGGCACCGAATGTGTTCTATGAATCTCC
* *
44707702 TGAAGATGCGTTGCGTTTGCATTGAATTTAAAATGAAGAATAATTCATTC-TTTGTTGTAGTCGT
1 TGAAGATGCGTTGCGTTTGCATTGAATTT-AAATGAAGAATAATTCATTCTTTTGTCGTACTCGT
*
44707766 GAATGGCACCGAGTGTGTT
65 GAATGGCACCGAATGTGTT
44707785 TATAAAAAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
95 58 0.77
96 17 0.23
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (95 bp):
TGAAGATGCGTTGCGTTTGCATTGAATTTAAATGAAGAATAATTCATTCTTTTGTCGTACTCGTG
AATGGCACCGAATGTGTTCTATGAATCTCC
Found at i:44711727 original size:16 final size:17
Alignment explanation
Indices: 44711699--44711733 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
44711689 TAAATTGAAT
44711699 TTTTTATATATTTTTTA
1 TTTTTATATATTTTTTA
44711716 TTTTTATA-ATTTTTTA
1 TTTTTATATATTTTTTA
44711732 TT
1 TT
44711734 GATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTATATATTTTTTA
Found at i:44711741 original size:16 final size:16
Alignment explanation
Indices: 44711702--44711743 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
44711692 ATTGAATTTT
*
44711702 TTATATATTTTTTATTT
1 TTATA-ATTTTTTATTA
44711719 TTATAATTTTTTATTGA
1 TTATAATTTTTTATT-A
44711736 TT-TAATTT
1 TTATAATTT
44711744 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATAATTTTTTATTA
Found at i:44711756 original size:9 final size:9
Alignment explanation
Indices: 44711731--44711764 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
44711721 ATAATTTTTT
*
44711731 ATTGATTTA
1 ATTGATTAA
*
44711740 ATTTATTAA
1 ATTGATTAA
44711749 ATTGATTAA
1 ATTGATTAA
44711758 ATTGATT
1 ATTGATT
44711765 GTATCATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (9 bp):
ATTGATTAA
Found at i:44712285 original size:24 final size:24
Alignment explanation
Indices: 44712257--44712309 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
44712247 AAAATTAAAC
*
44712257 ATTAAAATTAAATTTAAATACCAA
1 ATTAAAAATAAATTTAAATACCAA
* *
44712281 TTTAAAAATAAATTTAAATATCAA
1 ATTAAAAATAAATTTAAATACCAA
44712305 ATTAA
1 ATTAA
44712310 GCATTGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTAAAAATAAATTTAAATACCAA
Found at i:44712362 original size:35 final size:35
Alignment explanation
Indices: 44712320--44712395 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
44712310 GCATTGAAAT
44712320 CAATATCATATATTAAATATTATATTAGCCCAATA
1 CAATATCATATATTAAATATTATATTAGCCCAATA
44712355 CAATATCATATATTAAATATTATATTAGCCCAATA
1 CAATATCATATATTAAATATTATATTAGCCCAATA
44712390 CAATAT
1 CAATAT
44712396 ACACGAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (35 bp):
CAATATCATATATTAAATATTATATTAGCCCAATA
Found at i:44715781 original size:3 final size:3
Alignment explanation
Indices: 44715773--44715815 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
44715763 GTAGGAACAC
* * * *
44715773 ATT ATT ATT ATT ACT ATT ATT ATC ATC ATT ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
44715816 GGAAGTATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:44717837 original size:6 final size:6
Alignment explanation
Indices: 44717826--44717850 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44717816 AACTCCCTCC
44717826 ACCATA ACCATA ACCATA ACCATA A
1 ACCATA ACCATA ACCATA ACCATA A
44717851 TTAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCATA
Found at i:44719718 original size:3 final size:3
Alignment explanation
Indices: 44719710--44719736 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44719700 TACAAAATGT
44719710 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
44719737 GTGATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44720937 original size:20 final size:20
Alignment explanation
Indices: 44720891--44720938 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
44720881 CTAGGGTCCG
*
44720891 GTTAA-TAATTGAATCAAAC
1 GTTAATTAATTGAAACAAAC
*
44720910 -TATTATTAATTGAAACAAAC
1 GT-TAATTAATTGAAACAAAC
44720930 GTTAATTAA
1 GTTAATTAA
44720939 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 1 0.04
19 2 0.09
20 19 0.83
21 1 0.04
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
GTTAATTAATTGAAACAAAC
Found at i:44721983 original size:4 final size:4
Alignment explanation
Indices: 44721976--44722001 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
44721966 TATTCGTTGA
44721976 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
44722002 TTATTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:44745671 original size:6 final size:6
Alignment explanation
Indices: 44745660--44745685 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
44745650 ACATTTACAC
44745660 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
44745686 TTGCATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:44747757 original size:51 final size:51
Alignment explanation
Indices: 44747681--44747825 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 51
44747671 TATTGTGAGG
* *
44747681 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTAGA
* * * ** *
44747732 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAGCAGAT-GGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTAGA
44747782 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
44747826 GCTTTGGCTA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 43 0.52
51 39 0.48
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (51 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTAGA
Found at i:44755564 original size:31 final size:31
Alignment explanation
Indices: 44755529--44755737 Score: 301
Period size: 31 Copynumber: 6.7 Consensus size: 31
44755519 CTTGTCACTT
* *
44755529 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
44755560 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
44755591 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
44755622 GTAGCCGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
44755653 GTAGCAGAAGCTATCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
44755684 GTAGCGGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
44755715 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
44755738 GTTGTCATTT
Statistics
Matches: 159, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 159 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:44755821 original size:50 final size:50
Alignment explanation
Indices: 44755715--44755891 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
44755705 CACTGATCAG
* * * *
44755715 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
44755766 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
44755816 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
44755866 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
44755892 GTGTCCATGG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:44758489 original size:19 final size:19
Alignment explanation
Indices: 44758465--44758502 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44758455 TTGAACTATT
44758465 CGAAAGTTTTCATTTTAAG
1 CGAAAGTTTTCATTTTAAG
*
44758484 CGAAAGTTTTTATTTTAAG
1 CGAAAGTTTTCATTTTAAG
44758503 TCATTGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (19 bp):
CGAAAGTTTTCATTTTAAG
Found at i:44760264 original size:23 final size:23
Alignment explanation
Indices: 44760196--44760267 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 23
44760186 CCTGATCAGT
** *
44760196 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACGAGGTGCCTGAA
*
44760218 A-AAGACACACGAGGTGCCTG--
1 ATACGACACACGAGGTGCCTGAA
44760238 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
44760261 ATACGAC
1 ATACGAC
44760268 GCATAAAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 32 0.78
22 1 0.02
23 7 0.17
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (23 bp):
ATACGACACACGAGGTGCCTGAA
Found at i:44761402 original size:5 final size:5
Alignment explanation
Indices: 44761389--44761435 Score: 85
Period size: 5 Copynumber: 9.2 Consensus size: 5
44761379 TTCTTTAGTT
44761389 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
44761436 TAAAACATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:44761471 original size:8 final size:8
Alignment explanation
Indices: 44761458--44761486 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
44761448 TATCTTTATT
44761458 ATATAATA
1 ATATAATA
44761466 ATATAATA
1 ATATAATA
44761474 ATATAATA
1 ATATAATA
44761482 ATATA
1 ATATA
44761487 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:44771024 original size:40 final size:40
Alignment explanation
Indices: 44770969--44771049 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
44770959 TGACCATTCA
44770969 ATGATGCATGCTAGACAACTGAAGTTAATTTATTAATTGG
1 ATGATGCATGCTAGACAACTGAAGTTAATTTATTAATTGG
44771009 ATGATGCATGCTAGACAACTGAAGTTAATTTATTAATTGG
1 ATGATGCATGCTAGACAACTGAAGTTAATTTATTAATTGG
44771049 A
1 A
44771050 GGACCACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.35
Consensus pattern (40 bp):
ATGATGCATGCTAGACAACTGAAGTTAATTTATTAATTGG
Found at i:44773587 original size:37 final size:38
Alignment explanation
Indices: 44773497--44773587 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 38
44773487 AGAACTTATT
* * * *
44773497 AAATCACTAGTTTAACAACATATATACATTGCATACCAA
1 AAATCAATAGTTCAACAACATATATACA-TGCAAAACAA
* * * *
44773536 AAATCAACAATTCAACAACTTATATGCA-GCAAAACAA
1 AAATCAATAGTTCAACAACATATATACATGCAAAACAA
44773573 AAATCAATAGTTCAA
1 AAATCAATAGTTCAA
44773588 ATTCATGTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
37 20 0.48
39 22 0.52
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (38 bp):
AAATCAATAGTTCAACAACATATATACATGCAAAACAA
Found at i:44782722 original size:21 final size:19
Alignment explanation
Indices: 44782681--44782728 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
44782671 AAATAACACA
**
44782681 TTATATAATTTATATGTAT
1 TTATATAATTTATATAAAT
44782700 TTATATAATTTATAATCAAAT
1 TTATATAATTTAT-AT-AAAT
*
44782721 TTAAATAA
1 TTATATAA
44782729 AAATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTATATAATTTATATAAAT
Found at i:44783525 original size:22 final size:21
Alignment explanation
Indices: 44783481--44783526 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
44783471 AAGAATTTTA
**
44783481 AAAGTAAATTTATATATGTAT
1 AAAGTAAATTTATATATAAAT
*
44783502 AAAGTGAATTATATATATAAAT
1 AAAGTAAATT-TATATATAAAT
44783524 AAA
1 AAA
44783527 AATTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
AAAGTAAATTTATATATAAAT
Found at i:44800133 original size:17 final size:17
Alignment explanation
Indices: 44800113--44800146 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44800103 TTCGTATATT
*
44800113 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
44800130 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
44800147 GCGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:44801521 original size:32 final size:32
Alignment explanation
Indices: 44801480--44801543 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
44801470 CATTAAATGA
44801480 AAACCTCTCAAATCAAATGAAGATACAAGTAT
1 AAACCTCTCAAATCAAATGAAGATACAAGTAT
44801512 AAACCTCTCAAATCAAATGAAGATACAAGTAT
1 AAACCTCTCAAATCAAATGAAGATACAAGTAT
44801544 TCCCCTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (32 bp):
AAACCTCTCAAATCAAATGAAGATACAAGTAT
Found at i:44807244 original size:28 final size:27
Alignment explanation
Indices: 44807183--44807249 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
44807173 TCTAACAAAA
* *
44807183 TAAAAAATAAAATAAGATTGTTAAAATT
1 TAAAAAATAAAATAAGA-TGGTAAAATC
*
44807211 TTAAAAATAAAATAAAGA-GGTAATAATC
1 TAAAAAATAAAAT-AAGATGGTAA-AATC
44807239 TAAAAATATAA
1 TAAAAA-ATAA
44807250 TCTAATGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.12
28 20 0.62
29 8 0.25
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (27 bp):
TAAAAAATAAAATAAGATGGTAAAATC
Found at i:44811632 original size:17 final size:17
Alignment explanation
Indices: 44811612--44811653 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44811602 TATTTTTAAA
44811612 TTTATTTTATTTTT-TC
1 TTTATTTTATTTTTCTC
**
44811628 TTTTACGTTATTTTTCTC
1 -TTTATTTTATTTTTCTC
44811646 TTTATTTT
1 TTTATTTT
44811654 TTTCCTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTTTCTC
Found at i:44819954 original size:6 final size:6
Alignment explanation
Indices: 44819940--44819970 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
44819930 GAAGAGGGTT
*
44819940 CATCGG CATCAG CATCAG CATCAG CATCAG C
1 CATCAG CATCAG CATCAG CATCAG CATCAG C
44819971 TTCTGGTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATCAG
Found at i:44832845 original size:21 final size:21
Alignment explanation
Indices: 44832798--44832845 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
44832788 CTTGCATTTA
*
44832798 AAATATTTTATATTAATATTT
1 AAATATTTTATATTAATATAT
*
44832819 ATATATTTTATAATTAA-ATAT
1 AAATATTTTAT-ATTAATATAT
44832840 AAATAT
1 AAATAT
44832846 AAATAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATTTTATATTAATATAT
Found at i:44832845 original size:23 final size:21
Alignment explanation
Indices: 44832796--44832846 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
44832786 TTCTTGCATT
44832796 TAAA-ATATTTTATATTAATA
1 TAAATATATTTTATATTAATA
**
44832816 TTTATATATTTTATAATTAAATA
1 TAAATATATTTTAT-ATT-AATA
44832839 TAAATATA
1 TAAATATA
44832847 AATAATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 3 0.12
23 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATATATTTTATATTAATA
Found at i:44836020 original size:16 final size:17
Alignment explanation
Indices: 44835999--44836034 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
44835989 TTTGAAAATC
44835999 ATTATTTA-TTAAGTCT
1 ATTATTTATTTAAGTCT
44836015 ATTATTTATTTAAGTCT
1 ATTATTTATTTAAGTCT
44836032 ATT
1 ATT
44836035 TTGTTAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTATTTATTTAAGTCT
Found at i:44843681 original size:26 final size:26
Alignment explanation
Indices: 44843652--44843710 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
44843642 TTATTTAATA
* *
44843652 AATTCCAAAATTTTTACTATGGATTT
1 AATTACAAAATTTATACTATGGATTT
44843678 AATTACAAAATTTATACTATGGATTT
1 AATTACAAAATTTATACTATGGATTT
44843704 AATTACA
1 AATTACA
44843711 TTTTCCACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (26 bp):
AATTACAAAATTTATACTATGGATTT
Found at i:44850609 original size:21 final size:22
Alignment explanation
Indices: 44850580--44850626 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44850570 CAGAAGGAGT
*
44850580 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44850602 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44850623 GAGT
1 GAGT
44850627 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:44852852 original size:21 final size:21
Alignment explanation
Indices: 44852826--44852877 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
44852816 TCTTTCTTTT
*
44852826 GTTTGATTTGATTGATGTTGG
1 GTTTGATTTGATTGATGTTAG
44852847 GTTTGATTTGATTGATGTTAG
1 GTTTGATTTGATTGATGTTAG
44852868 GTATTGATTT
1 GT-TTGATTT
44852878 TTTTTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (21 bp):
GTTTGATTTGATTGATGTTAG
Found at i:44860490 original size:12 final size:12
Alignment explanation
Indices: 44860473--44860497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44860463 TCTATTTTAA
44860473 TCAAACTTAGGG
1 TCAAACTTAGGG
44860485 TCAAACTTAGGG
1 TCAAACTTAGGG
44860497 T
1 T
44860498 GGGAGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (12 bp):
TCAAACTTAGGG
Found at i:44861579 original size:156 final size:156
Alignment explanation
Indices: 44861295--44861606 Score: 624
Period size: 156 Copynumber: 2.0 Consensus size: 156
44861285 TGCGGAAGCG
44861295 ACGATAATATTAATAACAATATTATCAGAAATATTTAGATAATTATTATGCCAACAATTATACTA
1 ACGATAATATTAATAACAATATTATCAGAAATATTTAGATAATTATTATGCCAACAATTATACTA
44861360 AGAAAATTCCCAGTTAAATTGGAGGGGTCACAATGGTCCCGCTTAAAACCCAACAACTAGACAGA
66 AGAAAATTCCCAGTTAAATTGGAGGGGTCACAATGGTCCCGCTTAAAACCCAACAACTAGACAGA
44861425 ACTCACTTAGATATTTATAGCAATAA
131 ACTCACTTAGATATTTATAGCAATAA
44861451 ACGATAATATTAATAACAATATTATCAGAAATATTTAGATAATTATTATGCCAACAATTATACTA
1 ACGATAATATTAATAACAATATTATCAGAAATATTTAGATAATTATTATGCCAACAATTATACTA
44861516 AGAAAATTCCCAGTTAAATTGGAGGGGTCACAATGGTCCCGCTTAAAACCCAACAACTAGACAGA
66 AGAAAATTCCCAGTTAAATTGGAGGGGTCACAATGGTCCCGCTTAAAACCCAACAACTAGACAGA
44861581 ACTCACTTAGATATTTATAGCAATAA
131 ACTCACTTAGATATTTATAGCAATAA
44861607 TAACTAAATA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (156 bp):
ACGATAATATTAATAACAATATTATCAGAAATATTTAGATAATTATTATGCCAACAATTATACTA
AGAAAATTCCCAGTTAAATTGGAGGGGTCACAATGGTCCCGCTTAAAACCCAACAACTAGACAGA
ACTCACTTAGATATTTATAGCAATAA
Found at i:44862313 original size:21 final size:22
Alignment explanation
Indices: 44862287--44862333 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44862277 CTCTGCTCAA
*
44862287 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
44862308 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
44862330 ACTC
1 ACTC
44862334 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:44867584 original size:25 final size:24
Alignment explanation
Indices: 44867547--44867595 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
44867537 GAGGGGATTC
*
44867547 TTATTTTCTTTAATATTAATATAA
1 TTATTTTATTTAATATTAATATAA
*
44867571 TTATATTTATTTAATATTTATATAA
1 TTAT-TTTATTTAATATTAATATAA
44867596 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTTTATTTAATATTAATATAA
Found at i:44876927 original size:15 final size:15
Alignment explanation
Indices: 44876906--44876980 Score: 55
Period size: 15 Copynumber: 5.0 Consensus size: 15
44876896 ATTTATGGAA
44876906 AATCAAAGATATGGG
1 AATCAAAGATATGGG
* * * *
44876921 CATCAAATA-ATTGA
1 AATCAAAGATATGGG
44876935 AAGTCAAAGATATGGG
1 AA-TCAAAGATATGGG
* * *
44876951 TATCAAATAT-TGGA
1 AATCAAAGATATGGG
44876965 AAGTCAAAGATATGGG
1 AA-TCAAAGATATGGG
44876981 TATCGAGATA
Statistics
Matches: 42, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 27 0.64
16 7 0.17
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (15 bp):
AATCAAAGATATGGG
Found at i:44876944 original size:30 final size:30
Alignment explanation
Indices: 44876901--44876994 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
44876891 TCCATATTTA
*
44876901 TGGAAAATCAAAGATATGGGCATCAAATAAT
1 TGGAAAGTCAAAGATATGGGCATCAAAT-AT
*
44876932 T-GAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGCATCAAATAT
* *
44876961 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGCATC-AAATAT
44876992 TGG
1 TGG
44876995 CATAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 3 0.05
30 46 0.79
31 9 0.16
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGCATCAAATAT
Found at i:44881010 original size:29 final size:30
Alignment explanation
Indices: 44880951--44881008 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
44880941 TCCGAGCCTT
*
44880951 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
44880981 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
44881009 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:44881238 original size:13 final size:13
Alignment explanation
Indices: 44881220--44881251 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
44881210 TTTCCAGCAA
44881220 TTATGAATTTATT
1 TTATGAATTTATT
44881233 TTATGAATTTATT
1 TTATGAATTTATT
*
44881246 TGATGA
1 TTATGA
44881252 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:44881459 original size:50 final size:50
Alignment explanation
Indices: 44881346--44881587 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
44881336 ATTTGGGTAA
* * *
44881346 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
44881402 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
44881452 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
44881502 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
44881552 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
44881588 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:44881535 original size:100 final size:103
Alignment explanation
Indices: 44881346--44881595 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
44881336 ATTTGGGTAA
44881346 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
44881411 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
44881452 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
44881514 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
44881552 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
44881596 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:44885535 original size:15 final size:15
Alignment explanation
Indices: 44885515--44885622 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
44885505 TTTATGGAAA
44885515 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
44885530 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
44885544 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44885560 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44885574 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44885590 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44885604 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
44885620 ATC
1 ATC
44885623 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:44885544 original size:30 final size:30
Alignment explanation
Indices: 44885508--44885622 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
44885498 ATCCATATTT
*
44885508 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
44885538 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
44885568 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
44885598 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
44885623 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:44891811 original size:17 final size:17
Alignment explanation
Indices: 44891789--44891823 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
44891779 GAATAATGGA
*
44891789 AGAATAATTGAAGTACC
1 AGAATAATTGAAATACC
44891806 AGAATAATTGAAATACC
1 AGAATAATTGAAATACC
44891823 A
1 A
44891824 CTCATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (17 bp):
AGAATAATTGAAATACC
Found at i:44892540 original size:51 final size:51
Alignment explanation
Indices: 44892485--44892585 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
44892475 TTTTTTGAAG
* * * *
44892485 TTTTTAGAATTAAGATTAAATTGA-G-AATATTTATAAATTTTGAGAGTTAAT
1 TTTTTAAAATTAAGACTAAATTGATGTAATATGTA-AAA-GTTGAGAGTTAAT
*
44892536 TTTTTAAAATTATGACTAAATTGATGTAATATGTAAAAGTTGAGAGTTAA
1 TTTTTAAAATTAAGACTAAATTGATGTAATATGTAAAAGTTGAGAGTTAA
44892586 ATTTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
51 32 0.74
52 4 0.09
53 7 0.16
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.43
Consensus pattern (51 bp):
TTTTTAAAATTAAGACTAAATTGATGTAATATGTAAAAGTTGAGAGTTAAT
Found at i:44899805 original size:21 final size:21
Alignment explanation
Indices: 44899773--44899814 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
44899763 TTAAACAAAA
44899773 AAAAAGACAAGAT-ATTTTAC
1 AAAAAGACAAGATAATTTTAC
*
44899793 AAAAATACAAAGATAATTTTAC
1 AAAAAGAC-AAGATAATTTTAC
44899815 GTTGACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAAAGACAAGATAATTTTAC
Found at i:44900786 original size:25 final size:25
Alignment explanation
Indices: 44900752--44900803 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
44900742 GCATTACTGA
44900752 TTAAGATTAAAATAGTAAAGATTTG
1 TTAAGATTAAAATAGTAAAGATTTG
44900777 TTAAGATTAAAATAGTAAAGATTTG
1 TTAAGATTAAAATAGTAAAGATTTG
44900802 TT
1 TT
44900804 CGGATCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (25 bp):
TTAAGATTAAAATAGTAAAGATTTG
Found at i:44905289 original size:15 final size:15
Alignment explanation
Indices: 44905269--44905301 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
44905259 GCTTATCATG
44905269 CATGCACCAATGAAC
1 CATGCACCAATGAAC
44905284 CATGCACCAATGAAC
1 CATGCACCAATGAAC
44905299 CAT
1 CAT
44905302 TCAGGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.15
Consensus pattern (15 bp):
CATGCACCAATGAAC
Found at i:44912752 original size:25 final size:25
Alignment explanation
Indices: 44912718--44912768 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
44912708 TTCTATATTT
*
44912718 TTATCTCCAACAATTAAATAGTTAA
1 TTATCACCAACAATTAAATAGTTAA
*
44912743 TTATCACCAACAATTATATAGTTAA
1 TTATCACCAACAATTAAATAGTTAA
44912768 T
1 T
44912769 GAAAAGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (25 bp):
TTATCACCAACAATTAAATAGTTAA
Found at i:44916333 original size:39 final size:39
Alignment explanation
Indices: 44916279--44916385 Score: 205
Period size: 39 Copynumber: 2.7 Consensus size: 39
44916269 ATTATTATGT
*
44916279 AATCTATGACATCATCTTCCTGTTAACCATTAATTTTAA
1 AATCTATGACATCATCTTCCCGTTAACCATTAATTTTAA
44916318 AATCTATGACATCATCTTCCCGTTAACCATTAATTTTAA
1 AATCTATGACATCATCTTCCCGTTAACCATTAATTTTAA
44916357 AATCTATGACATCATCTTCCCGTTAACCA
1 AATCTATGACATCATCTTCCCGTTAACCA
44916386 ATCAATAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (39 bp):
AATCTATGACATCATCTTCCCGTTAACCATTAATTTTAA
Found at i:44921566 original size:40 final size:40
Alignment explanation
Indices: 44921511--44921587 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
44921501 ATCTCAACAA
44921511 GATTACTTGTTTGTTGTTTACCTAAATAAAGCCTTAGCAT
1 GATTACTTGTTTGTTGTTTACCTAAATAAAGCCTTAGCAT
44921551 GATTACTTGTTTGTTGTTTACCTAAATAAAGCCTTAG
1 GATTACTTGTTTGTTGTTTACCTAAATAAAGCCTTAG
44921588 AAAGAGTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (40 bp):
GATTACTTGTTTGTTGTTTACCTAAATAAAGCCTTAGCAT
Found at i:44943373 original size:18 final size:18
Alignment explanation
Indices: 44943333--44943379 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
44943323 TAACTGATTA
*
44943333 TTACCGGATAATTGACTG
1 TTACTGGATAATTGACTG
44943351 TTACTGGAT-ATTAGACTG
1 TTACTGGATAATT-GACTG
*
44943369 TTACTGAATAA
1 TTACTGGATAA
44943380 CTAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (18 bp):
TTACTGGATAATTGACTG
Found at i:44943420 original size:18 final size:17
Alignment explanation
Indices: 44943369--44943506 Score: 84
Period size: 18 Copynumber: 7.7 Consensus size: 17
44943359 TATTAGACTG
*
44943369 TTACTGAATAACTAAATA
1 TTACTGAATAACT-GATA
*
44943387 TTACTGAATAATTGATCA
1 TTACTGAATAACTGAT-A
44943405 TTACTGAATAACTGAT-
1 TTACTGAATAACTGATA
*
44943421 TGTCACTGAATGAA-TGACTG
1 T-T-ACTGAAT-AACTGA-TA
* *
44943441 CTACTGAATAACTTAATAA
1 TTACTGAATAAC-TGAT-A
* *
44943460 TTACTGCATATCTGAT-
1 TTACTGAATAACTGATA
* *
44943476 TTCACTGAATAATTGACTG
1 TT-ACTGAATAACTGA-TA
44943495 TTACTGAATAAC
1 TTACTGAATAAC
44943507 CGATCAATTG
Statistics
Matches: 94, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
16 3 0.03
17 15 0.16
18 59 0.63
19 17 0.18
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (17 bp):
TTACTGAATAACTGATA
Found at i:44943429 original size:54 final size:53
Alignment explanation
Indices: 44943387--44943506 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 53
44943377 TAACTAAATA
* *
44943387 TTACTGAATAA-TTGATCATTACTGAATAACTGATTGTCACTGAATGAATGACTG
1 TTACTGAATAACTTAATAATTACTGAATAACTGATT-TCACTGAAT-AATGACTG
* * *
44943441 CTACTGAATAACTTAATAATTACTGCATATCTGATTTCACTGAATAATTGACTG
1 TTACTGAATAACTTAATAATTACTGAATAACTGATTTCACTGAATAA-TGACTG
44943495 TTACTGAATAAC
1 TTACTGAATAAC
44943507 CGATCAATTG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 2 0.03
54 36 0.62
55 20 0.34
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (53 bp):
TTACTGAATAACTTAATAATTACTGAATAACTGATTTCACTGAATAATGACTG
Found at i:44943440 original size:72 final size:72
Alignment explanation
Indices: 44943364--44943503 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 72
44943354 CTGGATATTA
* *
44943364 GACTGTTACTGAATAACTAAAT-ATTACTGAATAAT-TGATCATT-ACTGAATAACTGATTGTCA
1 GACTGCTACTGAATAACTAAATAATTACTGAAT-ATCTGAT--TTCACTGAATAACTGACTGTCA
44943426 CTGAATGAAT
63 CTGAATGAAT
* * * *
44943436 GACTGCTACTGAATAACTTAATAATTACTGCATATCTGATTTCACTGAATAATTGACTGTTACTG
1 GACTGCTACTGAATAACTAAATAATTACTGAATATCTGATTTCACTGAATAACTGACTGTCACTG
44943501 AAT
66 AAT
44943504 AACCGATCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 2 0.03
72 44 0.75
73 13 0.22
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (72 bp):
GACTGCTACTGAATAACTAAATAATTACTGAATATCTGATTTCACTGAATAACTGACTGTCACTG
AATGAAT
Found at i:44943565 original size:18 final size:18
Alignment explanation
Indices: 44943544--44943585 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44943534 GGTTATTATT
* *
44943544 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
*
44943562 GAATAACTGACTGTTACT
1 GAATAACTGACTGTTACC
44943580 GAATAA
1 GAATAA
44943586 ATAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:44945978 original size:14 final size:14
Alignment explanation
Indices: 44945961--44945990 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44945951 TGGGGTATAA
44945961 CCACCCATGAGAAC
1 CCACCCATGAGAAC
44945975 CCACCCATGAGAAC
1 CCACCCATGAGAAC
44945989 CC
1 CC
44945991 TCCGGAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCACCCATGAGAAC
Found at i:44946592 original size:14 final size:15
Alignment explanation
Indices: 44946568--44946602 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
44946558 TATATTTATT
44946568 ACCATATAAATACTA
1 ACCATATAAATACTA
44946583 ACCATA-AAATACTA
1 ACCATATAAATACTA
44946597 ATCCAT
1 A-CCAT
44946603 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:44947298 original size:41 final size:41
Alignment explanation
Indices: 44947267--44947421 Score: 161
Period size: 41 Copynumber: 3.8 Consensus size: 41
44947257 CTATATAAAA
* * ** *
44947267 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGAT-TCATTT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCTAATAT-AATT
* *
44947308 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGAAT-TAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCT-AATATAATT
* * *
44947349 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCTAATATAATT
* * *
44947390 CACCGGCATCAAGCCTGCTAGGCATTAAGCCT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCT
44947422 GAAAATCTCA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
40 2 0.02
41 94 0.95
42 3 0.03
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGCCTAATATAATT
Found at i:44947658 original size:64 final size:63
Alignment explanation
Indices: 44947540--44947720 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
44947530 GCAAACAAAC
*
44947540 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
44947601 T
63 T
44947602 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
44947666 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
44947721 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:44953488 original size:14 final size:15
Alignment explanation
Indices: 44953464--44953498 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
44953454 TATATATATT
44953464 ACCATATAAATACTA
1 ACCATATAAATACTA
44953479 ACCATA-AAATACTA
1 ACCATATAAATACTA
44953493 ATCCAT
1 A-CCAT
44953499 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:44954208 original size:41 final size:40
Alignment explanation
Indices: 44954163--44954315 Score: 164
Period size: 41 Copynumber: 3.8 Consensus size: 40
44954153 CTATATAAAA
* * *
44954163 CACCGGCATAAAGCCTGCTAGGCACAAAGCTCGATTCATTT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCTCGATT-AATT
*
44954204 CACCGGCACAAAGCCTGCTAGACATAAAG-TCTGAATTAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCTC-G-ATTAATT
* ** *
44954245 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAG-CTCGATTAATT
* * *
44954286 CACCGGCATCAAGCCTGCTAGGCATTAAGC
1 CACCGGCATAAAGCCTGCTAGACATAAAGC
44954316 CTGAAAATCT
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.03
41 90 0.93
42 3 0.03
43 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGCTCGATTAATT
Found at i:44954554 original size:64 final size:63
Alignment explanation
Indices: 44954436--44954616 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
44954426 GCAAACAAAC
*
44954436 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
44954497 T
63 T
44954498 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
44954562 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
44954617 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:44957013 original size:58 final size:58
Alignment explanation
Indices: 44956923--44957038 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
44956913 TCCCATCTCT
44956923 CAAAGGCTTCAAATACCTTGATGAACAGAAATTAGCTTAGTGTTTGGCCCAACGCACC
1 CAAAGGCTTCAAATACCTTGATGAACAGAAATTAGCTTAGTGTTTGGCCCAACGCACC
*
44956981 CAAAGGCTTCAAATACCTTGATGAACAGAAATTAGCTTGGTGTTTGGCCCAACGCACC
1 CAAAGGCTTCAAATACCTTGATGAACAGAAATTAGCTTAGTGTTTGGCCCAACGCACC
44957039 ATAGTATCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (58 bp):
CAAAGGCTTCAAATACCTTGATGAACAGAAATTAGCTTAGTGTTTGGCCCAACGCACC
Found at i:44957716 original size:30 final size:29
Alignment explanation
Indices: 44957650--44957722 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
44957640 TTTTATAAAA
*
44957650 TTAAAATTTAATTCTTATACTTTTTATTT
1 TTAAAATTTAATTCTTATACTTTTTAATT
44957679 TTAAAAATTTAA-TCTCTATA-TTTTTCAGATT
1 TT-AAAATTTAATTCT-TATACTTTTT-A-ATT
*
44957710 TTAAAATTAAATT
1 TTAAAATTTAATT
44957723 GCACTGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 10 0.27
30 22 0.59
31 5 0.14
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAAAATTTAATTCTTATACTTTTTAATT
Found at i:44966207 original size:18 final size:18
Alignment explanation
Indices: 44966184--44966234 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
44966174 ATATTTTTAT
44966184 GAAAAATATTAAAAATTA
1 GAAAAATATTAAAAATTA
* * *
44966202 GAAAAAAAATAAACATTA
1 GAAAAATATTAAAAATTA
*
44966220 AAAATAATATTAAAA
1 GAAA-AATATTAAAA
44966235 TTGATATAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
GAAAAATATTAAAAATTA
Found at i:44966398 original size:19 final size:19
Alignment explanation
Indices: 44966376--44966436 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
44966366 ATTTAAATTT
* *
44966376 TTCTAAAAAAGTATTAGAA
1 TTCTAAAAAAATATTAAAA
44966395 TTCTTAAAAAAATATTAAAA
1 TTC-TAAAAAAATATTAAAA
44966415 TAT-TAAAAAAAATATTAAAA
1 T-TCT-AAAAAAATATTAAAA
44966435 TT
1 TT
44966437 GATATCAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 5 0.14
20 31 0.84
21 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (19 bp):
TTCTAAAAAAATATTAAAA
Found at i:44967028 original size:25 final size:28
Alignment explanation
Indices: 44966982--44967033 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
44966972 TTAAATAGTT
44966982 TAAATATGTTATATCAAATTTAATTTTG
1 TAAATATGTTATATCAAATTTAATTTTG
44967010 TAAATAT-TTA-AT-AAATTTAATTTT
1 TAAATATGTTATATCAAATTTAATTTT
44967034 TTCTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 2 0.08
27 3 0.12
28 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (28 bp):
TAAATATGTTATATCAAATTTAATTTTG
Found at i:44971195 original size:17 final size:19
Alignment explanation
Indices: 44971162--44971199 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
44971152 TTAATTGAAA
44971162 AATATTTTTTGATTAATTT
1 AATATTTTTTGATTAATTT
44971181 AATA-TTTTTGA-TAATTT
1 AATATTTTTTGATTAATTT
44971198 AA
1 AA
44971200 GATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
AATATTTTTTGATTAATTT
Found at i:44973433 original size:16 final size:16
Alignment explanation
Indices: 44973400--44973433 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44973390 AAAGAATGTT
* *
44973400 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
44973416 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
44973432 AA
1 AA
44973434 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:44976262 original size:21 final size:21
Alignment explanation
Indices: 44976236--44976276 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44976226 AGACGAGCAA
* *
44976236 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
44976257 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
44976277 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:44978215 original size:16 final size:16
Alignment explanation
Indices: 44978182--44978215 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44978172 GGAGATTGTT
* *
44978182 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
44978198 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
44978214 AA
1 AA
44978216 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:44982721 original size:20 final size:21
Alignment explanation
Indices: 44982698--44982741 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
44982688 AGTGTCGTGA
44982698 TAGGGC-TA-TGGATGTCAACC
1 TAGGGCATACTGGA-GTCAACC
44982718 TAGGGCATAGCTGGAGTCAACC
1 TAGGGCATA-CTGGAGTCAACC
44982740 TA
1 TA
44982742 AAGGGACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 9 0.43
23 4 0.19
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (21 bp):
TAGGGCATACTGGAGTCAACC
Found at i:44990905 original size:18 final size:19
Alignment explanation
Indices: 44990882--44990928 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
44990872 ATAATAATAT
*
44990882 ATATGTTATATA-TTTAAC
1 ATATGTTATATATTTTAAA
* *
44990900 ATATGTAATAAATTTTAAA
1 ATATGTTATATATTTTAAA
44990919 ATAT-TTATAT
1 ATATGTTATAT
44990929 TTAGGTATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
ATATGTTATATATTTTAAA
Found at i:44991717 original size:21 final size:21
Alignment explanation
Indices: 44991691--44991731 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
44991681 AACTTTATGA
44991691 TTAGTGAAAAATATCATATTT
1 TTAGTGAAAAATATCATATTT
44991712 TTAGTGAAAAATATCATATT
1 TTAGTGAAAAATATCATATT
44991732 CGTTCCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
TTAGTGAAAAATATCATATTT
Found at i:45005441 original size:4 final size:4
Alignment explanation
Indices: 45005425--45005459 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
45005415 CAAGATTTTG
*
45005425 ATTT ATTT GTTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
45005460 GGGTAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:45006450 original size:23 final size:21
Alignment explanation
Indices: 45006423--45006479 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
45006413 TTTTTTTTAC
45006423 TTTTATTTTTAAGAATTTAAATA
1 TTTTATTTTTAA-AATTTAAA-A
*
45006446 TTTTATTTTATAAATTTTAAAA
1 TTTTATTTT-TAAAATTTAAAA
*
45006468 TTTTAATTTTAA
1 TTTTATTTTTAA
45006480 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.10
22 9 0.29
23 16 0.52
24 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTATTTTTAAAATTTAAAA
Found at i:45006496 original size:30 final size:31
Alignment explanation
Indices: 45006429--45006501 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
45006419 TTACTTTTAT
* *
45006429 TTTTAAGAATTTAAATATTTTATTTTATAA-A
1 TTTTAA-AATTTTAATATTTAATTTTATAATA
45006460 TTTTAAAATTTTAAT-TTTAATTTT-TAATA
1 TTTTAAAATTTTAATATTTAATTTTATAATA
*
45006489 TTATTAAATTTTT
1 TT-TTAAAATTTT
45006502 TTGTTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 11 0.30
30 17 0.46
31 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTTAAAATTTTAATATTTAATTTTATAATA
Found at i:45019454 original size:30 final size:30
Alignment explanation
Indices: 45019427--45019485 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
45019417 TATAATTAGA
45019427 TTATAAAATTTGTAAATATTAAAAATTAAAT
1 TTATAAAATTTGTAAA-ATTAAAAATTAAAT
** *
45019458 TTATTGAATTTTTAAAATT-AAAATTAAA
1 TTATAAAATTTGTAAAATTAAAAATTAAA
45019486 ATGATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 3 0.12
31 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
TTATAAAATTTGTAAAATTAAAAATTAAAT
Found at i:45019456 original size:23 final size:24
Alignment explanation
Indices: 45019430--45019482 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
45019420 AATTAGATTA
45019430 TAAAATTT-GTAAATATTAAAAAT
1 TAAAATTTAGTAAATATTAAAAAT
* * * *
45019453 T-AAATTTATTGAATTTTTAAAAT
1 TAAAATTTAGTAAATATTAAAAAT
45019476 TAAAATT
1 TAAAATT
45019483 AAAATGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
TAAAATTTAGTAAATATTAAAAAT
Found at i:45026244 original size:37 final size:37
Alignment explanation
Indices: 45026194--45026268 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
45026184 TTGTTTAATA
45026194 TATTTCCTGATCGTTAATAAAGGTAAAACTTGGCAAC
1 TATTTCCTGATCGTTAATAAAGGTAAAACTTGGCAAC
45026231 TATTTCCTGATCGTTAATAAAGGTAAAACTTGGCAAC
1 TATTTCCTGATCGTTAATAAAGGTAAAACTTGGCAAC
45026268 T
1 T
45026269 TGAGATGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (37 bp):
TATTTCCTGATCGTTAATAAAGGTAAAACTTGGCAAC
Found at i:45031951 original size:46 final size:46
Alignment explanation
Indices: 45031777--45031953 Score: 230
Period size: 46 Copynumber: 3.8 Consensus size: 46
45031767 TTTGACATGA
* * * * ** *
45031777 TGCCATAGTGTCTCTCAACTATGGTCTTACTCATTTTTTATCATC-T
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCA-CGT
* *
45031823 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* *
45031869 TGCCATGGTATCTTTCAACCATGATCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
*
45031915 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
45031954 ATCAGAGAGC
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 115 0.99
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
Found at i:45034102 original size:11 final size:11
Alignment explanation
Indices: 45034086--45034133 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
45034076 CTTTATATAC
45034086 TAATAAAATAA
1 TAATAAAATAA
*
45034097 TAATAAAATATCT
1 TAATAAAATA--A
* *
45034110 TATTAAAATAT
1 TAATAAAATAA
45034121 TAATAAAATAA
1 TAATAAAATAA
45034132 TA
1 TA
45034134 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:45043803 original size:39 final size:39
Alignment explanation
Indices: 45043753--45043839 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
45043743 AATGTAATTA
*
45043753 TGGTTCAAAAAATAATGTTTGTTAGTCGAAATTGAATGG
1 TGGTTCAAAAAATAATGTTTGTTAGTCGAAATTGAACGG
45043792 TGGTTCAAAAAATAATGTTTGTTAGTCGAAATTGAACGG
1 TGGTTCAAAAAATAATGTTTGTTAGTCGAAATTGAACGG
45043831 T-GTT-AAAAA
1 TGGTTCAAAAA
45043840 CTACTTCCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 5 0.11
38 3 0.06
39 39 0.83
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (39 bp):
TGGTTCAAAAAATAATGTTTGTTAGTCGAAATTGAACGG
Found at i:45063214 original size:39 final size:40
Alignment explanation
Indices: 45063167--45063242 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
45063157 ATAGATGCGT
45063167 GTTTAAAAA-AATAACAT-ATAATAA-ATAATGAAATATATA
1 GTTTAAAAATAATAA-ATCATAATAATAT-ATGAAATATATA
*
45063206 GTTTAAAAATAATTAATCATAATAATATATGAAATAT
1 GTTTAAAAATAATAAATCATAATAATATATGAAATAT
45063243 GTATAATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 11 0.33
40 20 0.61
41 2 0.06
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (40 bp):
GTTTAAAAATAATAAATCATAATAATATATGAAATATATA
Done.