Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 24 of 171
Found at i:11146443 original size:15 final size:15
Alignment explanation
Indices: 11146423--11146459 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
11146413 TTATATTAAA
11146423 TTATATTAAAATATT
1 TTATATTAAAATATT
11146438 TTATATTAAAATATT
1 TTATATTAAAATATT
11146453 TTATATT
1 TTATATT
11146460 TATATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:11146467 original size:13 final size:14
Alignment explanation
Indices: 11146405--11146459 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 14
11146395 ATTTTTAATA
11146405 TAAATATTTTATAT
1 TAAATATTTTATAT
11146419 T-AA-A--TTATAT
1 TAAATATTTTATAT
11146429 TAAAATATTTTATAT
1 T-AAATATTTTATAT
11146444 TAAAATATTTTATAT
1 T-AAATATTTTATAT
11146459 T
1 T
11146460 TATATTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.19
12 3 0.08
13 3 0.08
14 1 0.03
15 22 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATATTTTATAT
Found at i:11149466 original size:15 final size:16
Alignment explanation
Indices: 11149434--11149470 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11149424 CTAGATTAAA
*
11149434 TTTAAATTTAATTTAT
1 TTTAAATTTAATTCAT
11149450 TTTAAATTTAA-TCAT
1 TTTAAATTTAATTCAT
11149465 TTTAAA
1 TTTAAA
11149471 AAAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATTTAATTCAT
Found at i:11168525 original size:198 final size:197
Alignment explanation
Indices: 11168238--11168610 Score: 475
Period size: 198 Copynumber: 1.9 Consensus size: 197
11168228 GCCACTGTAC
* * * *
11168238 AAGGTCTCTTCTTTCTACCTATACTTCTATAGATTCTCTTTAATTGATTAAACATTAATTCACCA
1 AAGGTCTCTTCTTTCGACCTATACTTCTATAGATTCTCTTTAATTAATTAAACAATAATTCACAA
* * * * *
11168303 CAATAAAATAATTTAAAAAAAAAACGAATGAAAGAACTCATAACAATCAACAACATAATAACTTA
66 CAATAAAATAATTT-AAAAAAAAACAAACGAAAGAAATCATAACAATCAACAACACAAAAACTTA
**
11168368 ACAAACATGAACCTACA-ACATAAATTGAAAAAAATCTACAACAAACACAAAGCCTAACAAATAT
130 ACAAACAT-AAAATACATACATAAATTGAAAAAAATCTACAACAAACACAAAGCCTAACAAATAT
11168432 CGAA
194 CGAA
* * * * *
11168436 AAGGTCTTTTCTTTCGACTTAT-CTTTTTATATATTCTCCTTT-ATTAATTAAACAATGATTCAC
1 AAGGTCTCTTCTTTCGACCTATAC-TTCTATAGATTCT-CTTTAATTAATTAAACAATAATTCAC
* *
11168499 AACAATCAAGATAATATT-TAAAAAAACAAACGAAAGAAATCATAACAATCAACAACACAAAAAC
64 AACAAT-AAAATAAT-TTAAAAAAAAACAAACGAAAGAAATCATAACAATCAACAACACAAAAAC
* *
11168563 TTAACAAACATAAAATATATTACATAAATTGAAAAATATCTACAACAA
127 TTAACAAACATAAAATACA-TACATAAATTGAAAAAAATCTACAACAA
11168611 TAAACAACAC
Statistics
Matches: 149, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
197 6 0.04
198 104 0.70
199 37 0.25
200 2 0.01
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (197 bp):
AAGGTCTCTTCTTTCGACCTATACTTCTATAGATTCTCTTTAATTAATTAAACAATAATTCACAA
CAATAAAATAATTTAAAAAAAAACAAACGAAAGAAATCATAACAATCAACAACACAAAAACTTAA
CAAACATAAAATACATACATAAATTGAAAAAAATCTACAACAAACACAAAGCCTAACAAATATCG
AA
Found at i:11181355 original size:29 final size:30
Alignment explanation
Indices: 11181288--11181355 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
11181278 AATATCAAAA
* *
11181288 TTATACATGAACTATGGTTTAATGTGCAATT
1 TTATACATGAACTATGATTT-ATGTACAATT
* *
11181319 GTATACATGAACTTTGATTT-TGTACAATT
1 TTATACATGAACTATGATTTATGTACAATT
11181348 TTATACAT
1 TTATACAT
11181356 AAAATTTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (30 bp):
TTATACATGAACTATGATTTATGTACAATT
Found at i:11181595 original size:29 final size:31
Alignment explanation
Indices: 11181514--11181595 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 31
11181504 TAAATGAAAG
* *
11181514 TTAAACTTTCAAGTATACATTTGAACCACAA
1 TTAAAGTTTCAAGTATACAATTGAACCACAA
* * ** *
11181545 TTAGAGTTTCACGTATGTAATTGTACCA-AA
1 TTAAAGTTTCAAGTATACAATTGAACCACAA
*
11181575 TTAAAG-TTCATGTATACAATT
1 TTAAAGTTTCAAGTATACAATT
11181596 ACACATTAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 12 0.30
30 7 0.17
31 21 0.52
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (31 bp):
TTAAAGTTTCAAGTATACAATTGAACCACAA
Found at i:11186994 original size:3 final size:3
Alignment explanation
Indices: 11186986--11187012 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11186976 GTTGTTAGGC
11186986 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
11187013 ACAGGGAGGG
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11189037 original size:3 final size:3
Alignment explanation
Indices: 11189029--11189089 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
11189019 AATTTTAGTT
11189029 TTA TTA TTA TTA 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
11189077 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
11189090 AACAATTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11189726 original size:29 final size:28
Alignment explanation
Indices: 11189684--11189741 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
11189674 TTTTTAAATA
* *
11189684 TAATTTTTTTAATAATTTTAATGATTTT
1 TAATTTTTTAAATAATTTTAATAATTTT
* *
11189712 TAATTTTTTAAAATAGTTTTTATAATTTT
1 TAATTTTTT-AAATAATTTTAATAATTTT
11189741 T
1 T
11189742 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (28 bp):
TAATTTTTTAAATAATTTTAATAATTTT
Found at i:11191639 original size:63 final size:63
Alignment explanation
Indices: 11191540--11191667 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
11191530 TCTTGCTTAA
11191540 TTAACATTTTTACTACACACCATATCTATATGGAGATGCATACAGGTCTAGATATCTTACATT
1 TTAACATTTTTACTACACACCATATCTATATGGAGATGCATACAGGTCTAGATATCTTACATT
11191603 TTAACATTTTTACTACACACCATATCTATATGGAGATGCATACAGGTCTAGATATCTTACATT
1 TTAACATTTTTACTACACACCATATCTATATGGAGATGCATACAGGTCTAGATATCTTACATT
11191666 TT
1 TT
11191668 GCTTAATTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (63 bp):
TTAACATTTTTACTACACACCATATCTATATGGAGATGCATACAGGTCTAGATATCTTACATT
Found at i:11196582 original size:70 final size:67
Alignment explanation
Indices: 11196451--11196583 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
11196441 ATAAACAATA
* * * * *
11196451 TAATGGTTTTACCTTTTAACTTAATAGATAAACATTTATCAAAATGATGTAATTTTGCCTTTTAA
1 TAATGGTTTTAACTTTTAACTTAAAAGATAAACATTTATCAAAACGACGTAATTTTACCTTTTAA
11196516 TT
66 TT
* *
11196518 TAATGGTTTTAACTTTTAACTTTACAAAAGATAAACATTTATCAGAACGACGTAGTTTTACCTTT
1 TAATGGTTTTAACTTTTAAC-TT--AAAAGATAAACATTTATCAAAACGACGTAATTTTACCTTT
11196583 T
63 T
11196584 TCTTGTTCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 19 0.34
68 2 0.04
70 35 0.62
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (67 bp):
TAATGGTTTTAACTTTTAACTTAAAAGATAAACATTTATCAAAACGACGTAATTTTACCTTTTAA
TT
Found at i:11201208 original size:18 final size:18
Alignment explanation
Indices: 11201187--11201221 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11201177 TTGAAATTTA
11201187 TTTAAT-ATTTTTATAAAT
1 TTTAATAATTTTT-TAAAT
11201205 TTTAATAATTTTTTAAA
1 TTTAATAATTTTTTAAA
11201222 AATTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATAATTTTTTAAAT
Found at i:11210125 original size:16 final size:15
Alignment explanation
Indices: 11210104--11210133 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
11210094 TTGATTAGAA
11210104 TTTTTAATAAATTTAT
1 TTTTTAA-AAATTTAT
11210120 TTTTTAAAAATTTA
1 TTTTTAAAAATTTA
11210134 AAGGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAAAAATTTAT
Found at i:11211339 original size:24 final size:24
Alignment explanation
Indices: 11211271--11211341 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
11211261 AGAAATAATC
* * *
11211271 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
11211295 TTTCAAATAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
11211319 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
11211342 ATTTGAGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:11211354 original size:24 final size:24
Alignment explanation
Indices: 11211279--11211357 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
11211269 TCTTTCAGTT
* * *
11211279 AAACTTTGTTTAATTGTTTCAAAT-
1 AAACTCTGTTTATTTATTTC-AATC
* *
11211303 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTATTTCAATC
* *
11211327 AAACTCTGTTTATTTATTTGAGTC
1 AAACTCTGTTTATTTATTTCAATC
11211351 AAACTCT
1 AAACTCT
11211358 TATTAGTCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 3 0.06
24 45 0.94
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:11212337 original size:3 final size:3
Alignment explanation
Indices: 11212331--11212357 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11212321 CAAACTTTTA
11212331 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11212358 TTGAAAGTAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11215660 original size:3 final size:3
Alignment explanation
Indices: 11215652--11215678 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11215642 AACAGATGCG
11215652 GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT
11215679 TTTTTTAATT
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:11231560 original size:14 final size:14
Alignment explanation
Indices: 11231541--11231567 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11231531 TCAAAGCAGA
11231541 TCACTTTTGCAAAG
1 TCACTTTTGCAAAG
11231555 TCACTTTTGCAAA
1 TCACTTTTGCAAA
11231568 CAATGTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
TCACTTTTGCAAAG
Found at i:11259998 original size:3 final size:3
Alignment explanation
Indices: 11259990--11260022 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
11259980 TTCAAACTTA
11259990 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11260023 TACTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11266731 original size:59 final size:60
Alignment explanation
Indices: 11266661--11266799 Score: 149
Period size: 59 Copynumber: 2.3 Consensus size: 60
11266651 TTACAGATGT
* * * *
11266661 TTAAAAGTTAAAATTATTAAATTTTTAGAATTTAA-ATTTAGA-TTATAAATTA-ATAAATA
1 TTAAAAATTAAATTTATTAAATTTTTA-AATTTAAGA-TTAAATTTATAAAATATATAAATA
* * * *
11266720 TTAAAAATTAAATTTATCGAATTTTTTATATTTAAGATTAAATTTATAAAATATGTAAATA
1 TTAAAAATTAAATTTAT-TAAATTTTTAAATTTAAGATTAAATTTATAAAATATATAAATA
11266781 TTAAAAGATTAAATTTATT
1 TTAAAA-ATTAAATTTATT
11266800 GTTATATTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
59 25 0.38
60 18 0.27
61 12 0.18
62 11 0.17
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (60 bp):
TTAAAAATTAAATTTATTAAATTTTTAAATTTAAGATTAAATTTATAAAATATATAAATA
Found at i:11266751 original size:30 final size:31
Alignment explanation
Indices: 11266714--11266798 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
11266704 TATAAATTAA
** *
11266714 TAAATATTAAAAATTAAATTTATCGAAT-TT
1 TAAATATTAAAAATTAAATTTATAAAATATG
** * *
11266744 TTTATATTTAAGATTAAATTTATAAAATATG
1 TAAATATTAAAAATTAAATTTATAAAATATG
11266775 TAAATATTAAAAGATTAAATTTAT
1 TAAATATTAAAA-ATTAAATTTAT
11266799 TGTTATATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 22 0.52
31 9 0.21
32 11 0.26
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (31 bp):
TAAATATTAAAAATTAAATTTATAAAATATG
Found at i:11271698 original size:22 final size:22
Alignment explanation
Indices: 11271652--11271715 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
11271642 CTCAACTTGG
*
11271652 ATTTTAATTTAAGTTTGAATTA
1 ATTTTAATTTAAGTTTAAATTA
11271674 ATTTTAATTT-A-TTTAAATTTAA
1 ATTTTAATTTAAGTTTAAA-TT-A
** *
11271696 ATTTTGTTTTAAATTTAAAT
1 ATTTTAATTTAAGTTTAAAT
11271716 ACATTTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 5 0.14
21 3 0.09
22 19 0.54
23 2 0.06
24 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
ATTTTAATTTAAGTTTAAATTA
Found at i:11272571 original size:3 final size:3
Alignment explanation
Indices: 11272434--11272552 Score: 85
Period size: 3 Copynumber: 38.0 Consensus size: 3
11272424 TAAATGCTAC
* * * * *
11272434 TAA TAA TAA TAT TAT TAA TAA TTA TAA TAA TAAA TAA TAC CAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA
* ** * * *
11272481 TAT TAA CGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11272529 TAA TGAA CTTAT TAA TAA TAA TAA
1 TAA T-AA --TAA TAA TAA TAA TAA
11272553 ATGACGTAAT
Statistics
Matches: 89, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
3 79 0.89
4 8 0.09
5 1 0.01
6 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11273674 original size:29 final size:29
Alignment explanation
Indices: 11273636--11273849 Score: 127
Period size: 29 Copynumber: 7.4 Consensus size: 29
11273626 CAGAAATTAT
*
11273636 ATTTTTACCCCTAAACTTTCCAAAATCCC
1 ATTTTAACCCCTAAACTTTCCAAAATCCC
* *
11273665 ATTTTAACCCC--AA-TTTCACCAAAAATTACT
1 ATTTTAACCCCTAAACTTT--CC-AAAA-TCCC
11273695 ATTTT-A-CCCTCAAACTTTCCAAAATCCC
1 ATTTTAACCCCT-AAACTTTCCAAAATCCC
*
11273723 ATTTTTAA-CCCT-AA-TTTCACCAAAAATTACC
1 A-TTTTAACCCCTAAACTTT--CC-AAAA-TCCC
11273754 ATTTT-ACCCCTAAACTTTCCAAAATCCC
1 ATTTTAACCCCTAAACTTTCCAAAATCCC
*
11273782 ATTTTTAA-CCCT-AA-TTTCACCAAAAATTACC
1 A-TTTTAACCCCTAAACTTT--CC-AAAA-TCCC
11273813 A-TTT-ACCCC-AAACTTT-CAAAATCCC
1 ATTTTAACCCCTAAACTTTCCAAAATCCC
11273838 ATTTTTAACCCC
1 A-TTTTAACCCC
11273850 GATTTCACCA
Statistics
Matches: 147, Mismatches: 9, Indels: 59
0.68 0.04 0.27
Matches are distributed among these distances:
25 4 0.03
26 7 0.05
27 12 0.08
28 22 0.15
29 48 0.33
30 36 0.24
31 12 0.08
32 6 0.04
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTTTAACCCCTAAACTTTCCAAAATCCC
Found at i:11273717 original size:30 final size:30
Alignment explanation
Indices: 11273638--11273905 Score: 106
Period size: 29 Copynumber: 9.3 Consensus size: 30
11273628 GAAATTATAT
*
11273638 TTTTACCC-CTAAACTTTCC-AAAA-TCCCA
1 TTTTACCCTC-AAACTTTCCAAAAATTACCA
*
11273666 TTTTAACCC-C-AA-TTTCACCAAAAATTACTA
1 TTTT-ACCCTCAAACTTT--CCAAAAATTACCA
*
11273696 TTTTACCCTCAAACTTTCC-AAAA-TCCCA
1 TTTTACCCTCAAACTTTCCAAAAATTACCA
11273724 TTTTTAACCCT--AA-TTTCACCAAAAATTACCA
1 -TTTT-ACCCTCAAACTTT--CCAAAAATTACCA
*
11273755 TTTTACCC-CTAAACTTTCC-AAAA-TCCCA
1 TTTTACCCTC-AAACTTTCCAAAAATTACCA
11273783 TTTTTAACCCT--AA-TTTCACCAAAAATTACCA
1 -TTTT-ACCCTCAAACTTT--CCAAAAATTACCA
*
11273814 -TTTACCC-CAAACTTT-C-AAAA-TCCCA
1 TTTTACCCTCAAACTTTCCAAAAATTACCA
*
11273839 TTTTTAACCC-C-GA-TTTCACCAAAAATTACCA
1 -TTTT-ACCCTCAAACTTT--CCAAAAATTACCA
*
11273870 TTTTACCCTCGAAA--GT-CAAAAATTACCA
1 TTTTACCCTC-AAACTTTCCAAAAATTACCA
*
11273898 TTTCACCC
1 TTTTACCC
11273906 CTGGCATCCA
Statistics
Matches: 188, Mismatches: 13, Indels: 78
0.67 0.05 0.28
Matches are distributed among these distances:
25 4 0.02
26 10 0.05
27 13 0.07
28 45 0.24
29 47 0.25
30 45 0.24
31 17 0.09
32 7 0.04
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.32
Consensus pattern (30 bp):
TTTTACCCTCAAACTTTCCAAAAATTACCA
Found at i:11273739 original size:59 final size:59
Alignment explanation
Indices: 11273638--11273877 Score: 400
Period size: 59 Copynumber: 4.1 Consensus size: 59
11273628 GAAATTATAT
*
11273638 TTTTACCCCTAAACTTTCCAAAATCCCA-TTTTAACCCCAATTTCACCAAAAATTACTA
1 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
*
11273696 TTTTA-CCCTCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
1 TTTTACCCCT-AAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
*
11273755 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
*
11273814 -TTTACCCC-AAACTTT-CAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
11273870 TTTTACCC
1 TTTTACCC
11273878 TCGAAAGTCA
Statistics
Matches: 174, Mismatches: 4, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
56 39 0.22
57 18 0.10
58 31 0.18
59 82 0.47
60 4 0.02
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (59 bp):
TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:11273877 original size:29 final size:30
Alignment explanation
Indices: 11273663--11273874 Score: 143
Period size: 30 Copynumber: 7.3 Consensus size: 30
11273653 TTCCAAAATC
11273663 CCATTTTAACCCCAATTTCACCAAAAATTA
1 CCATTTTAACCCCAATTTCACCAAAAATTA
* *
11273693 CTATTTT-ACCCTCAAACTTT--CC-AAAA-TC
1 CCATTTTAACCC-C-AA-TTTCACCAAAAATTA
*
11273721 CCATTTTTAACCCTAATTTCACCAAAAATTA
1 CCA-TTTTAACCCCAATTTCACCAAAAATTA
*
11273752 CCATTTT-ACCCCTAAACTTT--CC-AAAA-TC
1 CCATTTTAACCCC--AA-TTTCACCAAAAATTA
*
11273780 CCATTTTTAACCCTAATTTCACCAAAAATTA
1 CCA-TTTTAACCCCAATTTCACCAAAAATTA
*
11273811 CCA-TTT-ACCCCAAACTTT---C-AAAA-TC
1 CCATTTTAACCCC-AA-TTTCACCAAAAATTA
*
11273836 CCATTTTTAACCCCGATTTCACCAAAAATTA
1 CCA-TTTTAACCCCAATTTCACCAAAAATTA
11273867 CCATTTTA
1 CCATTTTA
11273875 CCCTCGAAAG
Statistics
Matches: 141, Mismatches: 13, Indels: 56
0.67 0.06 0.27
Matches are distributed among these distances:
25 4 0.03
26 7 0.05
27 11 0.08
28 20 0.14
29 34 0.24
30 43 0.30
31 16 0.11
32 6 0.04
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (30 bp):
CCATTTTAACCCCAATTTCACCAAAAATTA
Found at i:11273899 original size:115 final size:117
Alignment explanation
Indices: 11273638--11273900 Score: 347
Period size: 115 Copynumber: 2.3 Consensus size: 117
11273628 GAAATTATAT
* * * * *
11273638 TTTTACCCCTAAACTTTCCAAAATCCCA-TTTTAACCCCAATTTCACCAAAAATTACTATTTTAC
1 TTTTACCCCGAAAC-GTCAAAAATACCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
*
11273702 CCTCAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA
65 CCTCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * * *
11273755 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCTAATTTCACCAAAAATTACCA-TTTAC
1 TTTTACCCCGAAAC-GTCAAAAATACCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
*
11273819 CC-CAAACTTT-CAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
65 CCTCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
11273870 TTTTACCCTCGAAA-GTCAAAAATTACCATTT
1 TTTTACCC-CGAAACGTCAAAAA-TACCATTT
11273901 CACCCCTGGC
Statistics
Matches: 135, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
114 6 0.04
115 54 0.40
116 12 0.09
117 35 0.26
118 28 0.21
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (117 bp):
TTTTACCCCGAAACGTCAAAAATACCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACC
CTCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:11275187 original size:2 final size:2
Alignment explanation
Indices: 11275180--11275204 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11275170 TTTTCATTTT
11275180 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11275205 TTATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11278142 original size:22 final size:22
Alignment explanation
Indices: 11278114--11278185 Score: 105
Period size: 22 Copynumber: 3.3 Consensus size: 22
11278104 TATATTATTA
11278114 TTTTGGTGCTATTTTTTTACTG
1 TTTTGGTGCTATTTTTTTACTG
11278136 TTTTGGTTGCTA-TTTTTTACTG
1 TTTTGG-TGCTATTTTTTTACTG
11278158 TTTTGGTG-T-TGTTTTTTACTG
1 TTTTGGTGCTAT-TTTTTTACTG
11278179 TTTTGGT
1 TTTTGGT
11278186 TGTTGTTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.02
21 19 0.40
22 22 0.47
23 5 0.11
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.65
Consensus pattern (22 bp):
TTTTGGTGCTATTTTTTTACTG
Found at i:11278189 original size:22 final size:22
Alignment explanation
Indices: 11278126--11278194 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
11278116 TTGGTGCTAT
* *
11278126 TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTTGTTG
11278148 TTTTTTACTGTTTTGG-TGTTG
1 TTTTTTACTGTTTTGGTTGTTG
11278169 TTTTTTACTGTTTTGGTTGTTG
1 TTTTTTACTGTTTTGGTTGTTG
11278191 TTTT
1 TTTT
11278195 GATTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.43
22 25 0.57
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (22 bp):
TTTTTTACTGTTTTGGTTGTTG
Found at i:11278238 original size:12 final size:12
Alignment explanation
Indices: 11278218--11278309 Score: 127
Period size: 12 Copynumber: 7.9 Consensus size: 12
11278208 ATTTTGATAC
11278218 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
11278230 TGTTGTTTTTAT
1 TGTTATTTTTGT
*
11278242 TGTTATTTTTGC
1 TGTTATTTTTGT
11278254 TGTTATTTTTGT
1 TGTTATTTTTGT
*
11278266 TGTTGTTTTTGT
1 TGTTATTTTTGT
11278278 TGTTA--TTT-T
1 TGTTATTTTTGT
11278287 TGTTATTTTTGT
1 TGTTATTTTTGT
11278299 TGTTATTTTTG
1 TGTTATTTTTG
11278310 CTGCTGTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
9 6 0.09
10 3 0.04
11 3 0.04
12 57 0.83
ACGTcount: A:0.08, C:0.01, G:0.17, T:0.74
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:11278239 original size:36 final size:35
Alignment explanation
Indices: 11278198--11278308 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
11278188 TTGTTTTGAT
11278198 TTTTTTTACTATTTTGATACTGTTATTTTTGTTGTTG
1 TTTTTTTACTATTTT--TACTGTTATTTTTGTTGTTG
** *
11278235 TTTTTATTGTTATTTTTGCTGTTATTTTTGTTGTTG
1 TTTTT-TTACTATTTTTACTGTTATTTTTGTTGTTG
** *
11278271 TTTTTGTTGTTA-TTTT--TGTTATTTTTGTTGTTA
1 TTTTT-TTACTATTTTTACTGTTATTTTTGTTGTTG
11278304 TTTTT
1 TTTTT
11278309 GCTGCTGTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 21 0.31
35 4 0.06
36 30 0.44
37 5 0.07
38 8 0.12
ACGTcount: A:0.10, C:0.03, G:0.14, T:0.73
Consensus pattern (35 bp):
TTTTTTTACTATTTTTACTGTTATTTTTGTTGTTG
Found at i:11278293 original size:45 final size:44
Alignment explanation
Indices: 11278229--11278362 Score: 157
Period size: 45 Copynumber: 3.0 Consensus size: 44
11278219 GTTATTTTTG
*
11278229 TTGTTGTT-TTTATTGTTATTTTTGCTGTTATTTTTGTTGTTGTTT
1 TTGTTGTTATTT-TTGTTATTTTTGATGTTATTTTTGTTG-TGTTT
* *
11278274 TTGTTGTTATTTTTGTTATTTTTGTTGTTATTTTTGCTGCTGTTT
1 TTGTTGTTATTTTTGTTATTTTTGATGTTATTTTTGTTG-TGTTT
* * * *
11278319 TGGTTATTATTTTGGTTA-TTTGGATGTTATTTTT-TTGTGTTT
1 TTGTTGTTATTTTTGTTATTTTTGATGTTATTTTTGTTGTGTTT
11278361 TT
1 TT
11278363 ATTATTGTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 6 0.08
43 2 0.03
44 14 0.18
45 53 0.68
46 3 0.04
ACGTcount: A:0.08, C:0.02, G:0.19, T:0.71
Consensus pattern (44 bp):
TTGTTGTTATTTTTGTTATTTTTGATGTTATTTTTGTTGTGTTT
Found at i:11278329 original size:36 final size:36
Alignment explanation
Indices: 11278220--11278331 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 36
11278210 TTTGATACTG
* * *
11278220 TTATTTTTGTTGTTGTTTTTATTGTTATTTTTGCTG
1 TTATTTTTGTTGTTGTTTTTGTTGTTATTTTTGTTA
11278256 TTATTTTTGTTGTTGTTTTTGTTGTTATTTTTG---
1 TTATTTTTGTTGTTGTTTTTGTTGTTATTTTTGTTA
* * * * *
11278289 TTATTTTTGTTGTTATTTTTGCTGCTGTTTTGGTTA
1 TTATTTTTGTTGTTGTTTTTGTTGTTATTTTTGTTA
11278325 TTATTTT
1 TTATTTT
11278332 GGTTATTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
33 28 0.42
36 39 0.58
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (36 bp):
TTATTTTTGTTGTTGTTTTTGTTGTTATTTTTGTTA
Found at i:11279910 original size:30 final size:28
Alignment explanation
Indices: 11279876--11279960 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
11279866 AAAATTTAAA
*
11279876 AAATATATATAAAAATGCATAAATATTTT
1 AAATATATATAAAAAT-AATAAATATTTT
*
11279905 CAAATATATATATATAATAATAAA-A-TTT
1 -AAATATATATA-AAAATAATAAATATTTT
11279933 AAA-ATATATAAAAATAATTAAATATTTT
1 AAATATATATAAAAATAA-TAAATATTTT
11279961 TAAAAATACA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.12
26 11 0.23
27 4 0.08
28 6 0.12
29 1 0.02
30 16 0.33
31 4 0.08
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (28 bp):
AAATATATATAAAAATAATAAATATTTT
Found at i:11280663 original size:19 final size:19
Alignment explanation
Indices: 11280639--11280677 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11280629 GGGGTTATTT
11280639 TTATTTAATATT-AATATAA
1 TTATTT-ATATTAAATATAA
*
11280658 TTATTTTTATTAAATATAA
1 TTATTTATATTAAATATAA
11280677 T
1 T
11280678 ATAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTTATATTAAATATAA
Found at i:11280667 original size:25 final size:24
Alignment explanation
Indices: 11280633--11280681 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
11280623 GGAGACGGGG
*
11280633 TTATTTTTATTTAATATTAATATAA
1 TTATTTTTATTAAATA-TAATATAA
11280658 TTATTTTTATTAAATATAATATAA
1 TTATTTTTATTAAATATAATATAA
11280682 AATTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTTATTAAATATAATATAA
Found at i:11290889 original size:25 final size:25
Alignment explanation
Indices: 11290857--11290914 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
11290847 AAAATAAATC
11290857 AATGCTAAACATATAACACTATTCT
1 AATGCTAAACATATAACACTATTCT
11290882 AATGCTAAACATATAACACTATTCT
1 AATGCTAAACATATAACACTATTCT
11290907 AATG-TAAA
1 AATGCTAAA
11290915 TATTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (25 bp):
AATGCTAAACATATAACACTATTCT
Found at i:11292254 original size:21 final size:21
Alignment explanation
Indices: 11292230--11292276 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11292220 CTATGATTGG
*
11292230 TCAATATCGGTCAATAGTCAA
1 TCAATATCGATCAATAGTCAA
* **
11292251 TCAACATTTATCAATAGTCAA
1 TCAATATCGATCAATAGTCAA
11292272 TCAAT
1 TCAAT
11292277 GATAAAAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
TCAATATCGATCAATAGTCAA
Found at i:11296060 original size:29 final size:31
Alignment explanation
Indices: 11295977--11296237 Score: 106
Period size: 29 Copynumber: 8.8 Consensus size: 31
11295967 TTTTCGAGGG
* *
11295977 ATTTAGGGGTCAAAAT-TGAAATTTTTGAAAA
1 ATTTAGAGGTCAAAATGTG-AATTTTTGGAAA
* * *
11296008 ATTT-G-GGATTAAAAT-AGAACTTTTGGAAA
1 ATTTAGAGG-TCAAAATGTGAATTTTTGGAAA
11296037 ATTTA-AGGTCGAAAATGT-AATTTTTGG-AA
1 ATTTAGAGGTC-AAAATGTGAATTTTTGGAAA
*
11296066 ATTTAGGGGTCAAAATGTG-ATTTTTGGAAA
1 ATTTAGAGGTCAAAATGTGAATTTTTGGAAA
* * * * *** *
11296096 GTTTGGGGGTTAAAA-CAAAATATTTGGAAA
1 ATTTAGAGGTCAAAATGTGAATTTTTGGAAA
* *
11296126 GTTT-GAGGGTC-AAATGT-AATTTTTAGAAA
1 ATTTAGA-GGTCAAAATGTGAATTTTTGGAAA
* ** * * *
11296155 GTTTAG-GGGGACAATGTGATTTTTTAG-AA
1 ATTTAGAGGTCAAAATGTGAATTTTTGGAAA
* * *
11296184 GTTTAGGGGTCAAAGTGT-AATTTTTGG-AA
1 ATTTAGAGGTCAAAATGTGAATTTTTGGAAA
* * * *
11296213 GTTTAGGGGTTAAAGTGTG-ATTTTT
1 ATTTAGAGGTCAAAATGTGAATTTTT
11296238 AGACAAAATA
Statistics
Matches: 182, Mismatches: 32, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 102 0.56
30 74 0.41
31 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (31 bp):
ATTTAGAGGTCAAAATGTGAATTTTTGGAAA
Found at i:11296207 original size:30 final size:28
Alignment explanation
Indices: 11296049--11296240 Score: 136
Period size: 29 Copynumber: 6.6 Consensus size: 28
11296039 TTAAGGTCGA
* *
11296049 AAATGTAATTTTTGGAAATTTAGGGGTC
1 AAATGTAATTTTTAGAAGTTTAGGGGTC
* * * *
11296077 AAAATGTGATTTTTGGAAAGTTTGGGGGTTA
1 -AAATGTAATTTTTAG-AAGTTTAGGGG-TC
*** * *
11296108 AAACAAAATATTTGGAAAGTTT-GAGGGTC
1 AAATGTAATTTTTAG-AAGTTTAG-GGGTC
*
11296137 AAATGTAATTTTTAGAAAGTTTAGGGG-G
1 AAATGTAATTTTTAG-AAGTTTAGGGGTC
*
11296165 ACAATGTGATTTTTTAGAAGTTTAGGGGTC
1 A-AATGT-AATTTTTAGAAGTTTAGGGGTC
* *
11296195 AAAGTGTAATTTTTGGAAGTTTAGGGGTT
1 AAA-TGTAATTTTTAGAAGTTTAGGGGTC
*
11296224 AAAGTGTGATTTTTAGA
1 AAA-TGTAATTTTTAGA
11296241 CAAAATAAGG
Statistics
Matches: 132, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
28 1 0.01
29 88 0.67
30 42 0.32
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.38
Consensus pattern (28 bp):
AAATGTAATTTTTAGAAGTTTAGGGGTC
Found at i:11296210 original size:88 final size:87
Alignment explanation
Indices: 11296049--11296240 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 87
11296039 TTAAGGTCGA
* * * *
11296049 AAATGTAATTTTTGGAAATTTAGGGGTCAAAATGTGATTTTTGGAAAGTTTGGGGGTTAAAACAA
1 AAATGTAATTTTTAGAAATTTAGGGGTCAAAATGTGATTTTTAGAAAGTTTAGGGGTCAAAACAA
11296114 AATATTTGGAAAGTTT-GAGGGTC
66 AATATTTGG-AAGTTTAG-GGGTC
* * **
11296137 AAATGTAATTTTTAGAAAGTTTAGGGG-GACAATGTGATTTTTTAG-AAGTTTAGGGGTCAAAGT
1 AAATGTAATTTTTAGAAA-TTTAGGGGTCAAAATGTGA-TTTTTAGAAAGTTTAGGGGTCAAAAC
** * *
11296200 GTAATTTTTGGAAGTTTAGGGGTT
64 AAAATATTTGGAAGTTTAGGGGTC
*
11296224 AAAGTGTGATTTTTAGA
1 AAA-TGTAATTTTTAGA
11296241 CAAAATAAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
87 13 0.15
88 60 0.69
89 14 0.16
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.38
Consensus pattern (87 bp):
AAATGTAATTTTTAGAAATTTAGGGGTCAAAATGTGATTTTTAGAAAGTTTAGGGGTCAAAACAA
AATATTTGGAAGTTTAGGGGTC
Found at i:11296236 original size:59 final size:57
Alignment explanation
Indices: 11296049--11296237 Score: 168
Period size: 59 Copynumber: 3.2 Consensus size: 57
11296039 TTAAGGTCGA
* * * *
11296049 AAATGT-AATTTTTGGAAATTTAGGGGTCAAAATGTGATTTTTGGAAAGTTTGGGGGTT
1 AAATGTGATTTTTTGGAAGTTTAGGGGTC-AAATGTAATTTTTGG-AAGTTTAGGGGTT
**** * * * *
11296107 AAAACAAAATATTTGGAAAGTTT-GAGGGTCAAATGTAATTTTTAGAAAGTTTAGGGG-G
1 AAATGTGATTTTTTGG-AAGTTTAG-GGGTCAAATGTAATTTTT-GGAAGTTTAGGGGTT
*
11296165 ACAATGTGATTTTTTAGAAGTTTAGGGGTCAAAGTGTAATTTTTGGAAGTTTAGGGGTT
1 A-AATGTGATTTTTTGGAAGTTTAGGGGTCAAA-TGTAATTTTTGGAAGTTTAGGGGTT
11296224 AAAGTGTGATTTTT
1 AAA-TGTGATTTTT
11296238 AGACAAAATA
Statistics
Matches: 104, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
58 32 0.31
59 61 0.59
60 11 0.11
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.38
Consensus pattern (57 bp):
AAATGTGATTTTTTGGAAGTTTAGGGGTCAAATGTAATTTTTGGAAGTTTAGGGGTT
Found at i:11297168 original size:4 final size:4
Alignment explanation
Indices: 11297161--11297198 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
11297151 TCAACTTTCT
*
11297161 TTTA TTTA TTTA TTAA TATTA TTTA -TTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TT
11297199 AAAACGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.80
5 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:11331257 original size:14 final size:15
Alignment explanation
Indices: 11331232--11331293 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
11331222 GTCTTGATTC
11331232 TTAAATTTTTAAAAA
1 TTAAATTTTTAAAAA
*
11331247 TTAAATTTTAAAAAAA
1 TTAAATTTT-TAAAAA
* * *
11331263 TAGAAATATTTAAATA
1 T-TAAATTTTTAAAAA
11331279 TT-AATTTTTGAAAAA
1 TTAAATTTTT-AAAAA
11331294 ATATATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
14 6 0.17
15 13 0.36
16 11 0.31
17 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTAAATTTTTAAAAA
Found at i:11331275 original size:32 final size:32
Alignment explanation
Indices: 11331234--11331296 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
11331224 CTTGATTCTT
*
11331234 AAATTTTTAAAAATTAAATTTTAAAAAAATAG
1 AAATATTTAAAAATTAAATTTTAAAAAAATAG
* * *
11331266 AAATATTTAAATATTAATTTTTGAAAAAATA
1 AAATATTTAAAAATTAAATTTTAAAAAAATA
11331297 TATATAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
AAATATTTAAAAATTAAATTTTAAAAAAATAG
Found at i:11332136 original size:30 final size:30
Alignment explanation
Indices: 11332101--11332198 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
11332091 CGAAGTGAGA
*
11332101 CTAAATTGATAGAATATGTAAAATTGAGGG
1 CTAAATTGATAGAATTTGTAAAATTGAGGG
* * * * *
11332131 TTAAATTTG-TTGAATTTTTAAAATT-AAGA
1 CTAAA-TTGATAGAATTTGTAAAATTGAGGG
*
11332160 CTAAATTGATAGAATTTGAAAACATTGGAGGG
1 CTAAATTGATAGAATTTGTAAA-ATT-GAGGG
11332192 CTAAATT
1 CTAAATT
11332199 TGTTATTATT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
28 3 0.06
29 16 0.31
30 20 0.39
31 3 0.06
32 9 0.18
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (30 bp):
CTAAATTGATAGAATTTGTAAAATTGAGGG
Found at i:11332167 original size:59 final size:62
Alignment explanation
Indices: 11332080--11332202 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 62
11332070 TAATTTTTTA
* * * *
11332080 TTGAATTTTTACGAAGTGAGACTAAATTGATAGAATATGTAAA-ATT-GAGGGTTAAATTTG
1 TTGAATTTTTACAAAGTAAGACTAAATTGATAGAATATGAAAACATTGGAGGGCTAAATTTG
* *
11332140 TTGAATTTTTA-AAATTAAGACTAAATTGATAGAATTTGAAAACATTGGAGGGCTAAATTTG
1 TTGAATTTTTACAAAGTAAGACTAAATTGATAGAATATGAAAACATTGGAGGGCTAAATTTG
11332201 TT
1 TT
11332203 ATTATTCTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 26 0.47
60 14 0.25
61 15 0.27
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (62 bp):
TTGAATTTTTACAAAGTAAGACTAAATTGATAGAATATGAAAACATTGGAGGGCTAAATTTG
Found at i:11332296 original size:30 final size:29
Alignment explanation
Indices: 11332261--11332318 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
11332251 CCAAAATATT
11332261 AAAATTTGAAACCGTTAG-TGACTAAAATAA
1 AAAATTT-AAACC-TTAGATGACTAAAATAA
* *
11332291 AAAATTTAAATCTTGGATGACTAAAATA
1 AAAATTTAAACCTTAGATGACTAAAATA
11332319 GAAATACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (29 bp):
AAAATTTAAACCTTAGATGACTAAAATAA
Found at i:11336769 original size:6 final size:6
Alignment explanation
Indices: 11336758--11336786 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11336748 CCCAACCAGG
11336758 TTTTAC TTTTAC TTTTAC TTTTAC TTTTA
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTTA
11336787 ACTCCTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAC
Found at i:11356962 original size:2 final size:2
Alignment explanation
Indices: 11356955--11356995 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11356945 TTCAATTGCT
11356955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11356996 TATTAAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11358961 original size:3 final size:3
Alignment explanation
Indices: 11358955--11358983 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11358945 ATGTTTACTA
11358955 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
11358984 ATTTGGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:11369095 original size:13 final size:13
Alignment explanation
Indices: 11369077--11369104 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11369067 GTTTTTCGAA
11369077 AAAGTCAACGGTC
1 AAAGTCAACGGTC
11369090 AAAGTCAACGGTC
1 AAAGTCAACGGTC
11369103 AA
1 AA
11369105 TCAACACCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:11369216 original size:15 final size:15
Alignment explanation
Indices: 11369196--11369225 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11369186 TGGTTCATTT
11369196 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
11369211 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
11369226 AATTTGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:11369239 original size:21 final size:21
Alignment explanation
Indices: 11369213--11369275 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
11369203 TTCAAATGGG
11369213 TTTGGTTTAAATGAATTTGGA
1 TTTGGTTTAAATGAATTTGGA
* *
11369234 TTTGGTTTAAATGAATGTGGG
1 TTTGGTTTAAATGAATTTGGA
*
11369255 TTTGGTTTAAATAGGATTTGG
1 TTTGGTTTAAAT-GAATTTGG
11369276 GCTTAATGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 31 0.84
22 6 0.16
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
TTTGGTTTAAATGAATTTGGA
Found at i:11369680 original size:11 final size:11
Alignment explanation
Indices: 11369647--11369721 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
11369637 AAGTGTGATT
*
11369647 AAAAGAGGAAG
1 AAAAGAGAAAG
*
11369658 AAAATAGAAAAG
1 AAAAGAG-AAAG
11369670 AAAAGAGAAAG
1 AAAAGAGAAAG
11369681 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
11369693 AATGAGAAAAAG
1 AA-AAGAGAAAG
11369705 AAAAGAGAAAG
1 AAAAGAGAAAG
*
11369716 GAAAGA
1 AAAAGA
11369722 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:11369689 original size:23 final size:23
Alignment explanation
Indices: 11369647--11369719 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
11369637 AAGTGTGATT
*
11369647 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
11369670 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
11369693 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
11369717 AAA
1 AAA
11369720 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:11370784 original size:4 final size:4
Alignment explanation
Indices: 11370769--11370803 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
11370759 GAACCATTGT
*
11370769 TTTA TATA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
11370804 CAAACTTATT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:11371438 original size:15 final size:15
Alignment explanation
Indices: 11371418--11371471 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
11371408 ATATTACAAA
11371418 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
11371433 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
11371450 GAATATTTATTATTAAA
1 --ATATTTATTATTAAT
11371467 ATATT
1 ATATT
11371472 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:11373127 original size:30 final size:29
Alignment explanation
Indices: 11373093--11373261 Score: 173
Period size: 29 Copynumber: 5.8 Consensus size: 29
11373083 ATCTCAGGGT
*
11373093 AAAATGGTAATTTTT-GAAAGTTTCGGGTCA
1 AAAAT-GTAATTTTTAG-AAGTTTGGGGTCA
* *
11373123 AAAATGGAATTTTTAGAAGTTTGGGGGCA
1 AAAATGTAATTTTTAGAAGTTTGGGGTCA
* *
11373152 AAAATGTAATTTTTGGGAGTTTTGGGGTC-
1 AAAATGTAATTTTTAGAAG-TTTGGGGTCA
*
11373181 AAAATATAATTTTTAGAAGTTTTAGGGGT-A
1 AAAATGTAATTTTTAGAAG-TTT-GGGGTCA
* * * *
11373211 AAAATGGAATTTTTGGAAGTTCGGGGACA
1 AAAATGTAATTTTTAGAAGTTTGGGGTCA
*
11373240 AAAATATAATTTTTAGAAGTTT
1 AAAATGTAATTTTTAGAAGTTT
11373262 TTGGGTTAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.03
29 76 0.66
30 35 0.30
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTGGGGTCA
Found at i:11373133 original size:58 final size:56
Alignment explanation
Indices: 11372950--11373135 Score: 180
Period size: 57 Copynumber: 3.2 Consensus size: 56
11372940 CCCGATGGGC
* * *
11372950 AAAATGGTAATTTTGGAC-TCTCGGGGTAAAATGATAATTTTGGAAAAATTTAGGGTAA
1 AAAATGG-AATTTTGGACATCTCGGGGTAAAATGATAATTTT--AGAAATTTCGGGTCA
* * **
11373008 AAAATGAAATTTTGGA-AT-TCGGGGGTAAAACGATAATGTTTAGAAAAATCGGGATCA
1 AAAATGGAATTTTGGACATCTC-GGGGTAAAATGATAAT-TTTAGAAATTTCGGG-TCA
* * * *
11373065 AAAATAGAATTTTGGGACATCTCAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTCA
1 AAAATGGAATTTT-GGACATCTCGGGGTAAAATGATAATTTTAGAAA-TTTCGGGTCA
11373123 AAAATGGAATTTT
1 AAAATGGAATTTT
11373136 TAGAAGTTTG
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
56 10 0.10
57 38 0.37
58 34 0.33
59 20 0.19
60 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (56 bp):
AAAATGGAATTTTGGACATCTCGGGGTAAAATGATAATTTTAGAAATTTCGGGTCA
Found at i:11373214 original size:59 final size:58
Alignment explanation
Indices: 11373089--11373291 Score: 216
Period size: 59 Copynumber: 3.5 Consensus size: 58
11373079 GGACATCTCA
* * *
11373089 GGGT-AAAATGGTAATTTTTGAAAGTTTCGGGTCAAAA-ATGGAATTTTTAGAAG-TTTGG
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTGGGGTCAAAATAT--AATTTTTAGAAGTTTTAG
* *
11373147 GGGCAAAAATGTAATTTTTGGGAGTTTTGGGGTCAAAATATAATTTTTAGAAGTTTTAG
1 GGGTAAAAATGTAATTTTTGGAAG-TTTGGGGTCAAAATATAATTTTTAGAAGTTTTAG
* * * *
11373206 GGGTAAAAATGGAATTTTTGGAAGTTCGGGGACAAAAATATAATTTTTAGAAGTTTT-T
1 GGGTAAAAATGTAATTTTTGGAAGTTTGGGGTC-AAAATATAATTTTTAGAAGTTTTAG
* * *
11373264 GGGTTAAAATATATTTTTTGGATAGTTT
1 GGGTAAAAATGTAATTTTTGGA-AGTTT
11373292 AGAGACCTTC
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
58 52 0.42
59 69 0.56
60 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTGGGGTCAAAATATAATTTTTAGAAGTTTTAG
Found at i:11373272 original size:29 final size:29
Alignment explanation
Indices: 11373100--11373291 Score: 156
Period size: 29 Copynumber: 6.6 Consensus size: 29
11373090 GGTAAAATGG
* * *
11373100 TAATTTTT-GAAAGTTTCGGGTCAAAAATG
1 TAATTTTTAG-AAGTTTTGGGGCAAAAATA
* * *
11373129 GAATTTTTAGAAGTTTGGGGGCAAAAATG
1 TAATTTTTAGAAGTTTTGGGGCAAAAATA
* *
11373158 TAATTTTTGGGAGTTTTGGGGTC-AAAATA
1 TAATTTTTAGAAGTTTTGGGG-CAAAAATA
* *
11373187 TAATTTTTAGAAGTTTTAGGGGTAAAAATG
1 TAATTTTTAGAAGTTTT-GGGGCAAAAATA
* * *
11373217 GAATTTTTGGAAG-TTCGGGGACAAAAATA
1 TAATTTTTAGAAGTTTTGGGG-CAAAAATA
* **
11373246 TAATTTTTAGAAGTTTTTGGGTTAAAATA
1 TAATTTTTAGAAGTTTTGGGGCAAAAATA
* *
11373275 TATTTTTTGGATAGTTT
1 TAATTTTTAGA-AGTTT
11373292 AGAGACCTTC
Statistics
Matches: 131, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
28 4 0.03
29 95 0.73
30 32 0.24
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (29 bp):
TAATTTTTAGAAGTTTTGGGGCAAAAATA
Found at i:11373274 original size:88 final size:90
Alignment explanation
Indices: 11373117--11373291 Score: 246
Period size: 88 Copynumber: 2.0 Consensus size: 90
11373107 TGAAAGTTTC
* * * * *
11373117 GGGTCAAAAATGGAATTTTTAGAAGTTTGGGGGCAAAAATGTAATTTTTGGGAGTTTTGGGGTCA
1 GGGTCAAAAATGGAATTTTTAGAAGTTCGGGGACAAAAATATAATTTTTAGAAGTTTTGGGGTCA
11373182 AAATATAATTTTTAGA-AGTTTTAG
66 AAATATAATTTTTAGATAGTTTTAG
* * *
11373206 GGGT-AAAAATGGAATTTTTGGAAGTTCGGGGACAAAAATATAATTTTTAGAAGTTTTTGGGTTA
1 GGGTCAAAAATGGAATTTTTAGAAGTTCGGGGACAAAAATATAATTTTTAGAAGTTTTGGGGTCA
* *
11373270 AAATATATTTTTTGGATAGTTT
66 AAATATAATTTTTAGATAGTTT
11373292 AGAGACCTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
88 66 0.88
89 9 0.12
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (90 bp):
GGGTCAAAAATGGAATTTTTAGAAGTTCGGGGACAAAAATATAATTTTTAGAAGTTTTGGGGTCA
AAATATAATTTTTAGATAGTTTTAG
Found at i:11374345 original size:3 final size:3
Alignment explanation
Indices: 11374337--11374372 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
11374327 TAGAAAATAT
11374337 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
11374373 ATGTTGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11375140 original size:17 final size:17
Alignment explanation
Indices: 11375096--11375189 Score: 61
Period size: 17 Copynumber: 5.7 Consensus size: 17
11375086 TAATTAAACT
11375096 TTTTAAATTT-AAAT--
1 TTTTAAATTTAAAATAA
*
11375110 TTTT-AATTCAAAAATAA
1 TTTTAAATT-TAAAATAA
11375127 TTTTAAATTTAAAATAA
1 TTTTAAATTTAAAATAA
* * *
11375144 ATTTAAACTTCAAATAA
1 TTTTAAATTTAAAATAA
** * *
11375161 GCTTAAACTTACAATAA
1 TTTTAAATTTAAAATAA
* *
11375178 ATTTAAAATTAA
1 TTTTAAATTTAA
11375190 GATTGAATTA
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
13 4 0.06
14 4 0.06
15 4 0.06
17 46 0.74
18 4 0.06
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTTAAATTTAAAATAA
Found at i:11380884 original size:15 final size:15
Alignment explanation
Indices: 11380861--11380923 Score: 74
Period size: 15 Copynumber: 4.1 Consensus size: 15
11380851 TTATATTAAA
11380861 TTATATTAAAATATT
1 TTATATTAAAATATT
*
11380876 TTATTTTAAATTATATT
1 TTATATTAAA--ATATT
*
11380893 TTGA-AATAAAATATT
1 TT-ATATTAAAATATT
11380908 TTATATTAAAATATT
1 TTATATTAAAATATT
11380923 T
1 T
11380924 CAAATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 27 0.68
17 11 0.28
18 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:11382372 original size:9 final size:9
Alignment explanation
Indices: 11382358--11382448 Score: 63
Period size: 9 Copynumber: 10.6 Consensus size: 9
11382348 GCAAATGATT
11382358 TTAAAATTA
1 TTAAAATTA
11382367 TTAAAATTA
1 TTAAAATTA
11382376 TT----TT-
1 TTAAAATTA
*
11382380 TTAAAAATA
1 TTAAAATTA
*
11382389 -TAAAATGTT
1 TTAAAAT-TA
*
11382398 TTAAATTATTT
1 TTAAA--ATTA
11382409 TTTAAAA-TA
1 T-TAAAATTA
11382418 -TAAAATTA
1 TTAAAATTA
11382426 TTAAAATTA
1 TTAAAATTA
11382435 TTAAAATTA
1 TTAAAATTA
11382444 TTAAA
1 TTAAA
11382449 TAATTTTAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 5 0.08
8 8 0.12
9 35 0.53
10 5 0.08
11 3 0.05
12 6 0.09
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:11382419 original size:29 final size:30
Alignment explanation
Indices: 11382359--11382436 Score: 124
Period size: 29 Copynumber: 2.6 Consensus size: 30
11382349 CAAATGATTT
11382359 TAAAATTATTAAAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAAATA
*
11382389 TAAAATGT-TTTAAATTATTTTTT-AAAATA
1 TAAAAT-TATTAAAATTATTTTTTAAAAATA
11382418 TAAAATTATTAAAATTATT
1 TAAAATTATTAAAATTATT
11382437 AAAATTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 20 0.45
31 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAAATA
Found at i:11383358 original size:40 final size:40
Alignment explanation
Indices: 11383314--11383412 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
11383304 GATGATGATT
11383314 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
* *
11383354 ATAATTTTAAATTATTTTTAATAATTTTATATTTTAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
*
11383394 ATACTTTT--AATAATTTTAA
1 ATAATTTTAAAATAATTTTAA
11383413 AATCATTTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 9 0.17
40 45 0.83
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (40 bp):
ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
Found at i:11383370 original size:10 final size:10
Alignment explanation
Indices: 11383314--11383413 Score: 61
Period size: 10 Copynumber: 10.1 Consensus size: 10
11383304 GATGATGATT
11383314 ATAATTTTAAA
1 ATAATTTT-AA
11383325 ATAATTTT-A
1 ATAATTTTAA
11383334 ATAATTTT--
1 ATAATTTTAA
11383342 AT-ATTTTAAAAA
1 ATAATTTT---AA
11383354 ATAATTTTAA
1 ATAATTTTAA
* *
11383364 ATTATTTTTA
1 ATAATTTTAA
11383374 ATAATTTT--
1 ATAATTTTAA
11383382 AT-ATTTTAA
1 ATAATTTTAA
* *
11383391 AAAATACTTTTA
1 ATAAT--TTTAA
11383403 ATAATTTTAA
1 ATAATTTTAA
11383413 A
1 A
11383414 ATCATTTACT
Statistics
Matches: 71, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
7 10 0.14
8 4 0.06
9 10 0.14
10 24 0.34
11 8 0.11
12 10 0.14
13 5 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:11386140 original size:80 final size:80
Alignment explanation
Indices: 11386007--11386362 Score: 405
Period size: 80 Copynumber: 4.5 Consensus size: 80
11385997 CTCGCGAAAT
* ** *
11386007 AACCGCGAAA-GTGAGCGCAGCTCTAGTTGGATT-AATCAACAAATATCCGTCAAATCCTAGCAC
1 AACCGC-AAATGTGAGCCCAGCTCTAGTCAG-TTAAACCAACAAATATCCGTCAAATCCTAGCAC
* * **
11386070 TCAATGCTTAGTGGATA
64 CCAGTGCTTAGCAGATA
* * * *
11386087 AACCGCAAATGTGAGCCCAGCTCTTGTCAGTTAAACCGACAAATATCCGTCAAATCTTAGTACCC
1 AACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAACAAATATCCGTCAAATCCTAGCACCC
11386152 AGTGCTTAGCAGATA
66 AGTGCTTAGCAGATA
* * * * *
11386167 AATCACAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAATAAATATCCTTCAAATCTTAGCACCC
1 AACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAACAAATATCCGTCAAATCCTAGCACCC
*
11386232 AGTGCTTAGTAGATA
66 AGTGCTTAGCAGATA
* * ** * *
11386247 AATCGCAAATGTGAGCTCAGCTCTAGTTGGTTAAACCAAAAAATATCCGTCAAAT-CTTGACACC
1 AACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAACAAATATCCGTCAAATCCTAG-CACC
*
11386311 CAGTGCCTAGC-GAATA
65 CAGTGCTTAGCAG-ATA
* *
11386327 AACCGCAATTGTGAGTCCAGCTCTAGTCAGTTAAAC
1 AACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAAC
11386363 TGACAACATG
Statistics
Matches: 236, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
79 8 0.03
80 228 0.97
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (80 bp):
AACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAACAAATATCCGTCAAATCCTAGCACCC
AGTGCTTAGCAGATA
Found at i:11386256 original size:160 final size:160
Alignment explanation
Indices: 11385984--11386362 Score: 453
Period size: 160 Copynumber: 2.4 Consensus size: 160
11385974 CCGACAATTA
* * * ** *
11385984 TGACACCCAGTGCCTCGCGAA-ATAACCGCGAAA-GTGAGCGCAGCTCTAGTTGGATT-AATCAA
1 TGACACCCAGTGCCTAGCGAATA-AACCAC-AAATGTGAGCCCAGCTCTAGTCAG-TTAAACCAA
* * *
11386046 CAAATATCCGTCAAATCCTAGCACTCAATGCTTAGTGGATAAACCGCAAATGTGAGCCCAGCTCT
63 TAAATATCCGTCAAATCCTAGCACCCAATGCTTAGTAGATAAACCGCAAATGTGAGCCCAGCTCT
* * *
11386111 TGTCAGTTAAACCGACAAATATCCGTCAAATCT
128 AGTCAGTTAAACCAAAAAATATCCGTCAAATCT
* * *
11386144 T-AGTACCCAGTGCTTAGC-AGATAAATCACAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAAT
1 TGA-CACCCAGTGCCTAGCGA-ATAAACCACAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAAT
* * * * *
11386207 AAATATCCTTCAAATCTTAGCACCCAGTGCTTAGTAGATAAATCGCAAATGTGAGCTCAGCTCTA
64 AAATATCCGTCAAATCCTAGCACCCAATGCTTAGTAGATAAACCGCAAATGTGAGCCCAGCTCTA
**
11386272 GTTGGTTAAACCAAAAAATATCCGTCAAATCT
129 GTCAGTTAAACCAAAAAATATCCGTCAAATCT
* * *
11386304 TGACACCCAGTGCCTAGCGAATAAACCGCAATTGTGAGTCCAGCTCTAGTCAGTTAAAC
1 TGACACCCAGTGCCTAGCGAATAAACCACAAATGTGAGCCCAGCTCTAGTCAGTTAAAC
11386363 TGACAACATG
Statistics
Matches: 184, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
159 7 0.04
160 174 0.95
161 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (160 bp):
TGACACCCAGTGCCTAGCGAATAAACCACAAATGTGAGCCCAGCTCTAGTCAGTTAAACCAATAA
ATATCCGTCAAATCCTAGCACCCAATGCTTAGTAGATAAACCGCAAATGTGAGCCCAGCTCTAGT
CAGTTAAACCAAAAAATATCCGTCAAATCT
Found at i:11386806 original size:24 final size:24
Alignment explanation
Indices: 11386779--11386863 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
11386769 CCTTTGCATT
11386779 ATTCATCTATATCACATATCTATG
1 ATTCATCTATATCACATATCTATG
* * * *
11386803 ATTCATTCCATAATCATAGATACTTTGCATT
1 ATTCA-TCTAT-ATC--ACATA-TCT--ATG
11386834 ATTCATCTATATCACATATCTATG
1 ATTCATCTATATCACATATCTATG
11386858 ATTCAT
1 ATTCAT
11386864 TCCATAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
24 13 0.28
25 4 0.09
26 5 0.11
27 4 0.09
28 4 0.09
29 5 0.11
30 4 0.09
31 7 0.15
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (24 bp):
ATTCATCTATATCACATATCTATG
Found at i:11386836 original size:55 final size:55
Alignment explanation
Indices: 11386751--11386879 Score: 224
Period size: 55 Copynumber: 2.4 Consensus size: 55
11386741 CATAAATACA
* * *
11386751 TCATTCCATAAT-TTAAATCCTTTGCATTATTCATCTATATCACATATCTATGAT
1 TCATTCCATAATCATAGATACTTTGCATTATTCATCTATATCACATATCTATGAT
11386805 TCATTCCATAATCATAGATACTTTGCATTATTCATCTATATCACATATCTATGAT
1 TCATTCCATAATCATAGATACTTTGCATTATTCATCTATATCACATATCTATGAT
11386860 TCATTCCATAATCATAGATA
1 TCATTCCATAATCATAGATA
11386880 TGTGATATAG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
54 12 0.17
55 59 0.83
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (55 bp):
TCATTCCATAATCATAGATACTTTGCATTATTCATCTATATCACATATCTATGAT
Found at i:11390561 original size:18 final size:19
Alignment explanation
Indices: 11390511--11390564 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
11390501 TGAACAAAAT
11390511 AATTCAAAATAAATTT-T-AA
1 AATTCAAAAT--ATTTATAAA
11390530 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
11390549 AATTCTAAA-ATTTATA
1 AATTCAAAATATTTATA
11390565 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.12
18 8 0.25
19 20 0.62
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:11390704 original size:3 final size:3
Alignment explanation
Indices: 11390696--11390730 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11390686 CTAAAGTATC
11390696 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
11390731 TTGCTTTGAA
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:11398243 original size:52 final size:50
Alignment explanation
Indices: 11398187--11398283 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 50
11398177 AATTAATAAA
*
11398187 AAAAAATTATA-TTTTGA-TCATCTTAAAAATAATAAAATTTAATTTAATCTTT
1 AAAAAATTATACTTTT-ACT-ATCATAAAAAT--TAAAATTTAATTTAATCTTT
*
11398239 AAAAAATTATACTTTTACTATCATAAAAATTATAATTTAATTTAA
1 AAAAAATTATACTTTTACTATCATAAAAATTAAAATTTAATTTAA
11398284 AACTCCCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 14 0.34
52 22 0.54
53 5 0.12
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (50 bp):
AAAAAATTATACTTTTACTATCATAAAAATTAAAATTTAATTTAATCTTT
Found at i:11405037 original size:6 final size:6
Alignment explanation
Indices: 11405028--11405057 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
11405018 GTAGGATGGA
11405028 TGGCAG TGGCAG TGGCAG TGGCAAG TGGCA
1 TGGCAG TGGCAG TGGCAG TGGC-AG TGGCA
11405058 TTTTATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.20, C:0.17, G:0.47, T:0.17
Consensus pattern (6 bp):
TGGCAG
Found at i:11406483 original size:21 final size:22
Alignment explanation
Indices: 11406442--11406483 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
11406432 TTATTATTAT
*
11406442 TATTTTTTCTATTTTTATATGC
1 TATTTTTTCTATATTTATATGC
11406464 TATTTTTATCT-TATTT-TATG
1 TATTTTT-TCTATATTTATATG
11406484 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (22 bp):
TATTTTTTCTATATTTATATGC
Found at i:11413253 original size:14 final size:14
Alignment explanation
Indices: 11413193--11413253 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
11413183 AGTTTAATAA
*
11413193 AATTATTTAACTTT
1 AATTAATTAACTTT
* *
11413207 AATTAATCAAAATTT
1 AATTAAT-TAACTTT
*
11413222 AAACTAATTAA-TTAT
1 -AATTAATTAACTT-T
11413237 AATTAATTAACTTT
1 AATTAATTAACTTT
11413251 AAT
1 AAT
11413254 CAAATTTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 21 0.57
15 10 0.27
16 6 0.16
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTAATTAACTTT
Found at i:11415798 original size:13 final size:13
Alignment explanation
Indices: 11415780--11415804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11415770 AAACGTAAAA
11415780 CCTTATTTCTTGT
1 CCTTATTTCTTGT
11415793 CCTTATTTCTTG
1 CCTTATTTCTTG
11415805 CTTTCTTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (13 bp):
CCTTATTTCTTGT
Found at i:11418835 original size:23 final size:21
Alignment explanation
Indices: 11418784--11418836 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 21
11418774 GTACTAGGGA
11418784 AACAGTAGGCACACACAGTGC
1 AACAGTAGGCACACACAGTGC
11418805 AATTCAGTAGGCACACACAGTGC
1 AA--CAGTAGGCACACACAGTGC
11418828 TGAACAGTA
1 --AACAGTA
11418837 AGCGCGCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.07
23 24 0.86
25 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAGTAGGCACACACAGTGC
Found at i:11422113 original size:30 final size:30
Alignment explanation
Indices: 11422079--11422137 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
11422069 AACCATAAAA
*
11422079 ATAAATAATA-ATAAATATATTTTTTAATAG
1 ATAAA-AATACATAAATATATTTTGTAATAG
* *
11422109 ATAAAATTACATATATATATTTTGTAATA
1 ATAAAAATACATAAATATATTTTGTAATA
11422138 AGGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (30 bp):
ATAAAAATACATAAATATATTTTGTAATAG
Found at i:11424476 original size:56 final size:56
Alignment explanation
Indices: 11424401--11424511 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
11424391 AAACTAACTG
11424401 GCAGAGTTTAGTTCGATTCATAGTGATGTCCAGGGTCGAAATTACCTAACAAGTAA
1 GCAGAGTTTAGTTCGATTCATAGTGATGTCCAGGGTCGAAATTACCTAACAAGTAA
11424457 GCAGAGTTTAGTTCGATTCATAGTGATGTCCAGGGTCGAAATTACCTAACAAGTA
1 GCAGAGTTTAGTTCGATTCATAGTGATGTCCAGGGTCGAAATTACCTAACAAGTA
11424512 TTCTATTAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (56 bp):
GCAGAGTTTAGTTCGATTCATAGTGATGTCCAGGGTCGAAATTACCTAACAAGTAA
Found at i:11430520 original size:29 final size:28
Alignment explanation
Indices: 11430488--11430562 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
11430478 CGTTTTTATT
11430488 TTTCCCTCAAAACTTTTACTCCTTCCCAA
1 TTTCCC-CAAAACTTTTACTCCTTCCCAA
* *
11430517 TTTCCCCCAAAACTTTTACTCCTTCTCAG
1 TTT-CCCCAAAACTTTTACTCCTTCCCAA
*
11430546 TTTCTCCAAAACTTTTA
1 TTTCCCCAAAACTTTTA
11430563 TTTTCCTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.31
29 26 0.62
30 3 0.07
ACGTcount: A:0.24, C:0.35, G:0.01, T:0.40
Consensus pattern (28 bp):
TTTCCCCAAAACTTTTACTCCTTCCCAA
Found at i:11435436 original size:6 final size:6
Alignment explanation
Indices: 11435425--11435453 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11435415 CAAAAGGGAA
11435425 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
11435454 AGAGAGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:11441787 original size:17 final size:18
Alignment explanation
Indices: 11441761--11441794 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11441751 AAGTGTTTAG
*
11441761 ATTTATTTTGA-TATTTT
1 ATTTAATTTGACTATTTT
11441778 ATTTAATTTGACTATTT
1 ATTTAATTTGACTATTT
11441795 GTCAAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
ATTTAATTTGACTATTTT
Found at i:11446138 original size:15 final size:15
Alignment explanation
Indices: 11446118--11446169 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
11446108 ACTACAAAAC
11446118 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
11446133 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
11446152 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
11446167 ATT
1 ATT
11446170 AATATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:11446167 original size:19 final size:20
Alignment explanation
Indices: 11446131--11446182 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
11446121 TATTATTAAT
* **
11446131 ATATTTATAATTGTAATA-A
1 ATATTTATTATTAAAATATA
11446150 ATATTTATTATTAAAATATTA
1 ATATTTATTATTAAAATA-TA
*
11446171 ATATTTAATATT
1 ATATTTATTATT
11446183 TTTAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTTATTATTAAAATATA
Found at i:11446277 original size:16 final size:16
Alignment explanation
Indices: 11446258--11446288 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11446248 AATTTATTAA
11446258 AATAATTAATTATATT
1 AATAATTAATTATATT
*
11446274 AATAATTTATTATAT
1 AATAATTAATTATAT
11446289 GACTAAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATTAATTATATT
Found at i:11446298 original size:26 final size:27
Alignment explanation
Indices: 11446237--11446306 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
11446227 AATAAAATTA
*
11446237 AAATATTAAATAATTTATTAAAATAATT
1 AAATATT-AATAATTTATTAAAATAACT
* *
11446265 AATTATATTAATAATTTATT-ATATGACT
1 AA--ATATTAATAATTTATTAAAATAACT
*
11446293 AAATATAAATAATT
1 AAATATTAATAATT
11446307 AAAATATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 11 0.31
28 9 0.25
29 11 0.31
30 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
AAATATTAATAATTTATTAAAATAACT
Found at i:11447635 original size:18 final size:17
Alignment explanation
Indices: 11447595--11447637 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
11447585 GACCATAATT
11447595 TTTTATAAATAAATATA
1 TTTTATAAATAAATATA
* * *
11447612 TATTATAACATAATTATC
1 TTTTATAA-ATAAATATA
11447630 TTTTATAA
1 TTTTATAA
11447638 TATGCAACAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTATAAATAAATATA
Found at i:11452812 original size:8 final size:9
Alignment explanation
Indices: 11452801--11452832 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
11452791 GGTCTTACAT
11452801 ATATATAT-
1 ATATATATC
11452809 ATATATATC
1 ATATATATC
11452818 ATAT-TATC
1 ATATATATC
11452826 ATATATA
1 ATATATA
11452833 CTTTTGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATATC
Found at i:11467622 original size:19 final size:18
Alignment explanation
Indices: 11467598--11467643 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
11467588 GACATGATTC
*
11467598 TATATAAAAAAATATAAAA
1 TATATAAAAAAA-AAAAAA
11467617 TATATATAAAAAAAAAAAA
1 TATATA-AAAAAAAAAAAA
*
11467636 TATGTAAA
1 TATATAAA
11467644 TACATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
20 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TATATAAAAAAAAAAAAA
Found at i:11467624 original size:21 final size:19
Alignment explanation
Indices: 11467598--11467638 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
11467588 GACATGATTC
11467598 TATATAAAAAAATATAAAATA
1 TATATAAAAAAA-A-AAAATA
11467619 TATATAAAAAAAAAAAATA
1 TATATAAAAAAAAAAAATA
11467638 T
1 T
11467639 GTAAATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TATATAAAAAAAAAAAATA
Found at i:11467633 original size:17 final size:17
Alignment explanation
Indices: 11467598--11467680 Score: 51
Period size: 19 Copynumber: 4.6 Consensus size: 17
11467588 GACATGATTC
*
11467598 TATATAAAAAAATATAAAA
1 TATATATAAAAA-A-AAAA
11467617 TATATATAAAAAAAAAA
1 TATATATAAAAAAAAAA
* * *
11467634 AATATGTAAATACATAAAA
1 TATATATAAA-A-AAAAAA
* *
11467653 TAT-TAATAAATAATAAA
1 TATAT-ATAAAAAAAAAA
11467670 TATTATATAAA
1 TA-TATATAAA
11467681 GATTGTTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
17 18 0.36
18 9 0.18
19 23 0.46
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (17 bp):
TATATATAAAAAAAAAA
Found at i:11467650 original size:25 final size:26
Alignment explanation
Indices: 11467603--11467652 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
11467593 GATTCTATAT
*
11467603 AAAAAAATATAAAATATATATAAAAA
1 AAAAAAATATAAAATATACATAAAAA
**
11467629 AAAAAAATATGTAA-ATACATAAAA
1 AAAAAAATATAAAATATACATAAAA
11467653 TATTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAAAATATAAAATATACATAAAAA
Found at i:11471676 original size:16 final size:16
Alignment explanation
Indices: 11471608--11471679 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
11471598 CGTTTGGTTC
*
11471608 GCTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
* *
11471624 GATGCAATGGAATAGA
1 GCTGTAATGGAATAGA
11471640 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
11471656 ACTGTAATGGAATA-A
1 GCTGTAATGGAATAGA
11471671 GGCTGTAAT
1 -GCTGTAAT
11471680 CAATAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 1 0.02
16 47 0.98
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:11477827 original size:75 final size:77
Alignment explanation
Indices: 11477745--11477926 Score: 287
Period size: 81 Copynumber: 2.3 Consensus size: 77
11477735 TAAAATCTGT
* *
11477745 TTAGAAATACAAAATAATTTTAAAAAGTTCC-AAAAAAAATAATGACAAAGAACTATTAATGC-A
1 TTAGAAATGCAAAAGAATTTTAAAAAGTTCCAAAAAAAAATAATGACAAAGAACTATTAATGCAA
11477808 ATATATATATAC
66 ATATATATATAC
11477820 TTAGAAATGCAAAAGAATTTTAAAAAGTTCCAAAAAAAAAATAATGACAAAGAACTATTAATGCA
1 TTAGAAATGCAAAAGAATTTTAAAAAGTTCC-AAAAAAAAATAATGACAAAGAACTATTAATGC-
11477885 AAAAATATATATATAC
64 --AAATATATATATAC
*
11477901 TTAGAAATGTAAAAGAATTTTAAAAA
1 TTAGAAATGCAAAAGAATTTTAAAAA
11477927 CTACTTAGTT
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
75 29 0.30
77 31 0.32
81 38 0.39
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (77 bp):
TTAGAAATGCAAAAGAATTTTAAAAAGTTCCAAAAAAAAATAATGACAAAGAACTATTAATGCAA
ATATATATATAC
Found at i:11478332 original size:15 final size:15
Alignment explanation
Indices: 11478287--11478332 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
11478277 TCATTTATAT
11478287 TTCTTATTTTATAAA
1 TTCTTATTTTATAAA
**
11478302 CTT-TT-TTTGGTAAA
1 -TTCTTATTTTATAAA
11478316 TTCTTATTTTATAAA
1 TTCTTATTTTATAAA
11478331 TT
1 TT
11478333 TTAGAGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (15 bp):
TTCTTATTTTATAAA
Found at i:11479110 original size:2 final size:2
Alignment explanation
Indices: 11479103--11479157 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
11479093 ACAATGGGAA
11479103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11479145 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
11479158 AATAGCAGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11484925 original size:22 final size:22
Alignment explanation
Indices: 11484897--11484940 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11484887 ACTAAAAATC
11484897 TTATCACATATGTGAAACCATA
1 TTATCACATATGTGAAACCATA
11484919 TTATCACATATGTGAAACCATA
1 TTATCACATATGTGAAACCATA
11484941 GATTTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
TTATCACATATGTGAAACCATA
Found at i:11501446 original size:54 final size:53
Alignment explanation
Indices: 11501341--11501446 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 53
11501331 CTACTTATAT
** * * *
11501341 TTTTGGGAGGGCCATAATGTAAATTTCAAAGGGCTAAATTGAAAAATTTTAAG
1 TTTTGGGAGAACCATAATGTAAATTACAAAGGACTAAATTGAAAAAATTTAAG
* *
11501394 TTTTGGGAGAACCATAGTGTAAACTTACAAAGGACTGAATTGAAAAAATTTAA
1 TTTTGGGAGAACCATAATGTAAA-TTACAAAGGACTAAATTGAAAAAATTTAA
11501447 ACTTTAGGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 20 0.44
54 25 0.56
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (53 bp):
TTTTGGGAGAACCATAATGTAAATTACAAAGGACTAAATTGAAAAAATTTAAG
Found at i:11508418 original size:2 final size:2
Alignment explanation
Indices: 11508411--11508462 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11508401 TTTTGCATTA
11508411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11508453 AT AT AT AT AT
1 AT AT AT AT AT
11508463 TCATTATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11508558 original size:21 final size:22
Alignment explanation
Indices: 11508534--11508582 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
11508524 TTATATATTT
11508534 TTAAATAAAAT-ATAACTTTAA
1 TTAAATAAAATCATAACTTTAA
* *
11508555 TT-AAT-AAATCATAATTTTTA
1 TTAAATAAAATCATAACTTTAA
11508575 TTAAATAA
1 TTAAATAA
11508583 CACACTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 5 0.22
22 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAATAAAATCATAACTTTAA
Found at i:11508882 original size:38 final size:38
Alignment explanation
Indices: 11508840--11508915 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
11508830 TACACGTTAC
11508840 ACCACGATTTTGAATCAGAAGAGAGATTTCAAGAAATG
1 ACCACGATTTTGAATCAGAAGAGAGATTTCAAGAAATG
11508878 ACCACGATTTTGAATCAGAAGAGAGATTTCAAGAAATG
1 ACCACGATTTTGAATCAGAAGAGAGATTTCAAGAAATG
11508916 GCAGATCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (38 bp):
ACCACGATTTTGAATCAGAAGAGAGATTTCAAGAAATG
Found at i:11509677 original size:24 final size:21
Alignment explanation
Indices: 11509650--11509717 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
11509640 ACAAAAAAGA
11509650 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCTAAGTCACTTC---TCTT
* *
11509674 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCTAAGTCACTTCTCTT
* *
11509695 TTTGTTTAACTCACTTC-CTT
1 TTTGTCTAAGTCACTTCTCTT
11509715 TTT
1 TTT
11509718 TCTTTGTGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
24 15 0.39
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTGTCTAAGTCACTTCTCTT
Found at i:11511693 original size:132 final size:132
Alignment explanation
Indices: 11511456--11511710 Score: 501
Period size: 132 Copynumber: 1.9 Consensus size: 132
11511446 TTTAATAATA
11511456 TAGAGATTAAAGTGATTCATTTAATAATAGAGTGACTAATTTGAATTTGCCTGTTATAAATCTAA
1 TAGAGATTAAAGTGATTCATTTAATAATAGAGTGACTAATTTGAATTTGCCTGTTATAAATCTAA
11511521 GTTGCTGGAGTTAGGCGAATATATAAACAATAATAGAGTGATTCATCACTCGAAAAATCTAAGTT
66 GTTGCTGGAGTTAGGCGAATATATAAACAATAATAGAGTGATTCATCACTCGAAAAATCTAAGTT
11511586 GC
131 GC
*
11511588 TAGAGATTAAAGTGATTCATTTAATAATAGAGTGACTAATTTGTATTTGCCTGTTATAAATCTAA
1 TAGAGATTAAAGTGATTCATTTAATAATAGAGTGACTAATTTGAATTTGCCTGTTATAAATCTAA
11511653 GTTGCTGGAGTTAGGCGAATATATAAACAATAATAGAGTGATTCATCACTCGAAAAAT
66 GTTGCTGGAGTTAGGCGAATATATAAACAATAATAGAGTGATTCATCACTCGAAAAAT
11511711 GCTGTATGAG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 122 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (132 bp):
TAGAGATTAAAGTGATTCATTTAATAATAGAGTGACTAATTTGAATTTGCCTGTTATAAATCTAA
GTTGCTGGAGTTAGGCGAATATATAAACAATAATAGAGTGATTCATCACTCGAAAAATCTAAGTT
GC
Found at i:11512368 original size:18 final size:18
Alignment explanation
Indices: 11512345--11512381 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11512335 AAGAACTGCA
11512345 GAAAGGACCAGTAAAAAT
1 GAAAGGACCAGTAAAAAT
11512363 GAAAGGACCAGTAAAAAT
1 GAAAGGACCAGTAAAAAT
11512381 G
1 G
11512382 CGGAATCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAGGACCAGTAAAAAT
Found at i:11520912 original size:17 final size:18
Alignment explanation
Indices: 11520890--11520930 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
11520880 TTTTAAATAT
11520890 TTTTTTACA-TCT-TTTAA
1 TTTTTTACAGT-TATTTAA
11520907 TTTTTT-CAGTTATTTAA
1 TTTTTTACAGTTATTTAA
11520924 TTTTTTA
1 TTTTTTA
11520931 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTTACAGTTATTTAA
Found at i:11523615 original size:2 final size:2
Alignment explanation
Indices: 11523608--11523632 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11523598 GATCAAGCAA
11523608 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
11523633 AACGGGGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11527883 original size:7 final size:7
Alignment explanation
Indices: 11527873--11527909 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
11527863 ATGGTAATGG
11527873 GTAAGGA
1 GTAAGGA
11527880 GTAAGGA
1 GTAAGGA
11527887 GTAAGGA
1 GTAAGGA
11527894 GTAAGGA
1 GTAAGGA
11527901 GTAAGGA
1 GTAAGGA
11527908 GT
1 GT
11527910 GCTGGTATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.43, T:0.16
Consensus pattern (7 bp):
GTAAGGA
Found at i:11532810 original size:17 final size:17
Alignment explanation
Indices: 11532788--11532823 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11532778 AAAGATATTA
11532788 TTCTTTAATTTGCACTT
1 TTCTTTAATTTGCACTT
**
11532805 TTCTTTTGTTTGCACTT
1 TTCTTTAATTTGCACTT
11532822 TT
1 TT
11532824 ATAAATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TTCTTTAATTTGCACTT
Found at i:11538362 original size:141 final size:141
Alignment explanation
Indices: 11538104--11538386 Score: 548
Period size: 141 Copynumber: 2.0 Consensus size: 141
11538094 CAGATTCCAA
*
11538104 AAGGTCTTGCAAGGTCAAGAAATTTTTGTAAGCCCTCCATGTAGAAGAGGTTCAACTGCAGATGA
1 AAGGTCTTGCAAGGTCAAGAAATTTTTGTAAGCCCTCCATGTAGAAGAGGTCCAACTGCAGATGA
*
11538169 CACTCGAGAAAGTGACAGTCCTGGTGCCTCTGATGTTGGTCAGTTGTTGGGAACTAGAAGTGGAT
66 CACTCGAGAAAGTGACAGTCCTGGTGCCTCTGATGTTGGTCAGTTGTCGGGAACTAGAAGTGGAT
11538234 GGTCTTCTTTG
131 GGTCTTCTTTG
11538245 AAGGTCTTGCAAGGTCAAGAAATTTTTGTAAGCCCTCCATGTAGAAGAGGTCCAACTGCAGATGA
1 AAGGTCTTGCAAGGTCAAGAAATTTTTGTAAGCCCTCCATGTAGAAGAGGTCCAACTGCAGATGA
11538310 CACTCGAGAAAGTGACAGTCCTGGTGCCTCTGATGTTGGTCAGTTGTCGGGAACTAGAAGTGGAT
66 CACTCGAGAAAGTGACAGTCCTGGTGCCTCTGATGTTGGTCAGTTGTCGGGAACTAGAAGTGGAT
11538375 GGTCTTCTTTG
131 GGTCTTCTTTG
11538386 A
1 A
11538387 TGCAGAGCTA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (141 bp):
AAGGTCTTGCAAGGTCAAGAAATTTTTGTAAGCCCTCCATGTAGAAGAGGTCCAACTGCAGATGA
CACTCGAGAAAGTGACAGTCCTGGTGCCTCTGATGTTGGTCAGTTGTCGGGAACTAGAAGTGGAT
GGTCTTCTTTG
Found at i:11541074 original size:18 final size:17
Alignment explanation
Indices: 11541051--11541084 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11541041 TTGTATAAAA
*
11541051 ATTTATGTATAGTTTAAT
1 ATTTATCTATA-TTTAAT
11541069 ATTTATCTATATTTAA
1 ATTTATCTATATTTAA
11541085 AATAATTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTATCTATATTTAAT
Found at i:11542070 original size:27 final size:27
Alignment explanation
Indices: 11542024--11542076 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
11542014 CTAACTTAAA
*
11542024 TAATTTTTTTTTAAATAATTTAATGAT
1 TAATTTTTTTTTAAATAATTAAATGAT
11542051 TAATCTTTTATTTT-AA-AATTAAATGA
1 TAAT-TTTT-TTTTAAATAATTAAATGA
11542077 AAGTATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 13 0.57
28 6 0.26
29 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
TAATTTTTTTTTAAATAATTAAATGAT
Found at i:11549226 original size:2 final size:2
Alignment explanation
Indices: 11549215--11549310 Score: 171
Period size: 2 Copynumber: 49.5 Consensus size: 2
11549205 GAAAACAAAA
11549215 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11549256 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11549296 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
11549311 AATAAGGTTA
Statistics
Matches: 91, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
1 3 0.03
2 88 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11552848 original size:33 final size:32
Alignment explanation
Indices: 11552778--11552850 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
11552768 TCCAAAAATT
*
11552778 TCAACTTTTAAGGGGCCCAAAATTTTTTTTAC
1 TCAACTTTTAAGGGACCCAAAATTTTTTTTAC
* *
11552810 T-AACTTTTAAGTGACCTACAAATTTTTTTT-C
1 TCAACTTTTAAGGGACCCA-AAATTTTTTTTAC
11552841 TCCAACTTTT
1 T-CAACTTTT
11552851 CTGAAACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 16 0.46
32 12 0.34
33 7 0.20
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (32 bp):
TCAACTTTTAAGGGACCCAAAATTTTTTTTAC
Done.