Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 98 of 202
Found at i:29885397 original size:19 final size:19
Alignment explanation
Indices: 29885344--29885407 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
29885334 AAATTTCCAA
*
29885344 ATTTTTTAATAAATGTTTTAT
1 ATTTTTT-AT-AATTTTTTAT
*
29885365 ATATTTTTAT-ATTTTTTGT
1 AT-TTTTTATAATTTTTTAT
*
29885384 ATTTTTTATAATTTTATA-
1 ATTTTTTATAATTTTTTAT
29885402 ATTTTT
1 ATTTTT
29885408 GCAAGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 13 0.35
19 15 0.41
21 4 0.11
22 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
ATTTTTTATAATTTTTTAT
Found at i:29885397 original size:27 final size:28
Alignment explanation
Indices: 29885359--29885435 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
29885349 TTAATAAATG
* * *
29885359 TTTTATATATTTTTATATTTTTTG-TATT
1 TTTTATA-ATTTTTATAATTTTTGCAAGT
29885387 TTTTATAA-TTTTATAATTTTTGCAAGT
1 TTTTATAATTTTTATAATTTTTGCAAGT
* * *
29885414 ATTTATAATTTTAATACTTTTT
1 TTTTATAATTTTTATAATTTTT
29885436 AAATAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 13 0.32
27 10 0.24
28 18 0.44
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTTATAATTTTTATAATTTTTGCAAGT
Found at i:29895262 original size:31 final size:31
Alignment explanation
Indices: 29895220--29895285 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
29895210 CTTAAATATA
* *
29895220 ATAAATTATATTTATATAATTTAATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
*
29895251 ATAAATGATATTTAAATAATTTGATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
29895282 ATAA
1 ATAA
29895286 TTTAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (31 bp):
ATAAATGATATTTAAATAATTTAATATAATG
Found at i:29895285 original size:16 final size:16
Alignment explanation
Indices: 29895235--29895293 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
29895225 TTATATTTAT
29895235 ATAATTTAATATAATG
1 ATAATTTAATATAATG
* * *
29895251 ATAAATGATATTTAA--
1 ATAATTTA-ATATAATG
*
29895266 ATAATTTGATATAATG
1 ATAATTTAATATAATG
29895282 ATAATTTAATAT
1 ATAATTTAATAT
29895294 TTTTTAGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 17 0.53
17 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
ATAATTTAATATAATG
Found at i:29896139 original size:39 final size:39
Alignment explanation
Indices: 29896096--29896173 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
29896086 TAGTTATAAT
29896096 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
1 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
*
29896135 CACGATATGAGTGGTTTCATATAAAATTAATATCTAAAC
1 CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
29896174 ATCATTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (39 bp):
CACGATATGAGTGGTTTCATATAAAATCAATATCTAAAC
Found at i:29896547 original size:17 final size:17
Alignment explanation
Indices: 29896525--29896557 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29896515 ATAATTTATT
*
29896525 TTTCTTTTTATAAAATA
1 TTTCTTTTTAAAAAATA
29896542 TTTCTTTTTAAAAAAT
1 TTTCTTTTTAAAAAAT
29896558 CGTGGCTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCTTTTTAAAAAATA
Found at i:29901726 original size:96 final size:96
Alignment explanation
Indices: 29901623--29901936 Score: 471
Period size: 96 Copynumber: 3.3 Consensus size: 96
29901613 AACAGCTACC
* *
29901623 TTTATTTGA-TTTTTCCTTAAAAACCCTAAATACTAAA-CCTCAAACTAATTTTTTTAAAATTTA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCT-AATCTAA-TTTTTTAAAATTTA
29901686 TAATTAATTTACTCAAGTAACCCTAAACCCTAA
64 TAATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
29901719 TTTATTTGATTTTTTTCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
29901784 ATTAATTTACTCAAGTAACCCTAAACCCTAA
66 ATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
29901815 TTTATTTGATTTTTTCCTTAAAAACCATAAACGCTAAACCCTAATCTAATTTTTTAAAATTTATA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
* * *
29901880 ATTAATTTAATTAAGAAACCCTAAACCC---
66 ATTAATTTACTCAAGTAACCCTAAACCCTAA
*
29901908 -TTATTTAATTTTTTCCTT-AAAACCCTAAA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAA
29901937 ATCTAAAAAC
Statistics
Matches: 203, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
91 10 0.05
92 17 0.08
96 142 0.70
97 31 0.15
98 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (96 bp):
TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
ATTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:29902445 original size:61 final size:60
Alignment explanation
Indices: 29902373--29902540 Score: 154
Period size: 57 Copynumber: 2.8 Consensus size: 60
29902363 AATATGATAT
29902373 TAAATTGATTATAACTAATAATTTTATAATATAATTAAAAAGTTGATGATAAGTAATATTA
1 TAAATTGATTATAACTAATAATTTTATAATATAA-TAAAAAGTTGATGATAAGTAATATTA
** * *
29902434 TAAATTGATTATTCCTTAA-AATTATTA-AA-ATAAAAAGAAAATTGA--A-AAGTAATATTA
1 TAAATTGATTATAAC-TAATAATT-TTATAATATAATAA-AAAGTTGATGATAAGTAATATTA
* * * *
29902491 TAACATGGA--ATAAATAATAAGTCTATAATATAAGTAAAAAGTTGATGATA
1 TAA-ATTGATTATAACTAATAATTTTATAATATAA-TAAAAAGTTGATGATA
29902541 TCATTGTTCC
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
55 5 0.06
56 7 0.08
57 25 0.30
58 7 0.08
59 3 0.04
60 12 0.14
61 19 0.23
62 6 0.07
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (60 bp):
TAAATTGATTATAACTAATAATTTTATAATATAATAAAAAGTTGATGATAAGTAATATTA
Found at i:29903513 original size:22 final size:22
Alignment explanation
Indices: 29903471--29903514 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29903461 TTATTTAATC
*
29903471 AATTACTCTAATTAATTAAATT
1 AATTACTCTAATTAATAAAATT
*
29903493 AATTTCTC-AATTAAATAAAATT
1 AATTACTCTAATT-AATAAAATT
29903515 TTCAACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTACTCTAATTAATAAAATT
Found at i:29904055 original size:15 final size:15
Alignment explanation
Indices: 29904035--29904086 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
29904025 ACTACAAAAC
29904035 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
29904050 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
29904069 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
29904084 ATT
1 ATT
29904087 AATATTGAAT
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:29904152 original size:16 final size:17
Alignment explanation
Indices: 29904119--29904158 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
29904109 ATGTGATTAA
*
29904119 TATTATTTATTTAAATT
1 TATTATTTATTAAAATT
29904136 TATTATTT-TTAAAATT
1 TATTATTTATTAAAATT
29904152 TATTATT
1 TATTATT
29904159 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTTATTAAAATT
Found at i:29904198 original size:16 final size:18
Alignment explanation
Indices: 29904173--29904231 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 18
29904163 TAAAATTGAA
29904173 ATATTAAATAATTTATTAT
1 ATATT-AATAATTTATTAT
29904192 -T-TTAATAAATTATATTTAGT
1 ATATTAAT-AATT-TA-TTA-T
29904212 ATATTAATAATTTATTAT
1 ATATTAATAATTTATTAT
29904230 AT
1 AT
29904232 GACTACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 6 0.18
19 6 0.18
20 3 0.09
21 5 0.15
22 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTAATAATTTATTAT
Found at i:29904209 original size:22 final size:22
Alignment explanation
Indices: 29904183--29904226 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29904173 ATATTAAATA
* *
29904183 ATTTATTATTTTAATAAATTAT
1 ATTTAGTATATTAATAAATTAT
*
29904205 ATTTAGTATATTAATAATTTAT
1 ATTTAGTATATTAATAAATTAT
29904227 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTAGTATATTAATAAATTAT
Found at i:29906962 original size:13 final size:13
Alignment explanation
Indices: 29906944--29906969 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29906934 ATCAGGCTTG
29906944 TAATTAATTTTAA
1 TAATTAATTTTAA
29906957 TAATTAATTTTAA
1 TAATTAATTTTAA
29906970 CCCAATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTAATTTTAA
Found at i:29908703 original size:43 final size:43
Alignment explanation
Indices: 29908600--29908695 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
29908590 AAACCTACAG
29908600 GGGACACACGGCCGTGTCGCATAGCCGTGTGTCACACATGGCT
1 GGGACACACGGCCGTGTCGCATAGCCGTGTGTCACACATGGCT
** * * * *
29908643 AAGACACACGGCCGTGTCGCATGGCTGTGTGTCATATATGGCT
1 GGGACACACGGCCGTGTCGCATAGCCGTGTGTCACACATGGCT
29908686 GGGACACACG
1 GGGACACACG
29908696 ATCGTGTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.20
Consensus pattern (43 bp):
GGGACACACGGCCGTGTCGCATAGCCGTGTGTCACACATGGCT
Found at i:29909691 original size:30 final size:29
Alignment explanation
Indices: 29909652--29909934 Score: 146
Period size: 30 Copynumber: 9.5 Consensus size: 29
29909642 AATGGTTGTC
*
29909652 ACCATCCCTTTTCATAGTTCGATAGCCGA
1 ACCATCCCTTTTCATAGTTCGATAGTCGA
* * * *
29909681 AGCTATCCCTTTTCATATTTCGATGGTCGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTCG-A
* *
29909712 TCCATCCCTTTTCATTGTT-GATAGTC-A
1 ACCATCCCTTTTCATAGTTCGATAGTCGA
** *
29909739 TCACCATCTGTTTTCATAATTCGATAG-CTGA
1 --ACCATCCCTTTTCATAGTTCGATAGTC-GA
* * ** *
29909770 AGCTATCCCTTTTCATATTTAAATGGTC-A
1 A-CCATCCCTTTTCATAGTTCGATAGTCGA
* * * *
29909799 TTACCATCCTTTTTCATAATTCGATAGCCAA
1 --ACCATCCCTTTTCATAGTTCGATAGTCGA
* * *
29909830 AGCTATCCCTTTTCATAGTTCGATGGTCGTC
1 A-CCATCCCTTTTCATAGTTCGATAGTCG-A
* * * *
29909861 ACCATCCTTTTTCATGGTT-GATGGTCGTC
1 ACCATCCCTTTTCATAGTTCGATAGTCG-A
* *
29909890 ACCATCCCTTTTCATATTTTGATAG-CTGA
1 ACCATCCCTTTTCATAGTTCGATAGTC-GA
*
29909919 AGCTATCCCTTTTCAT
1 A-CCATCCCTTTTCAT
29909935 TGGTCGATGA
Statistics
Matches: 191, Mismatches: 46, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
29 53 0.28
30 133 0.70
31 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (29 bp):
ACCATCCCTTTTCATAGTTCGATAGTCGA
Found at i:29909806 original size:89 final size:89
Alignment explanation
Indices: 29909650--29909815 Score: 244
Period size: 89 Copynumber: 1.9 Consensus size: 89
29909640 ACAATGGTTG
* ** *
29909650 TCACCATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCTCC
1 TCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTAAATGGTCATCTCC
29909715 ATCCCTTTTCATTGTTGATAGTCA
66 ATCCCTTTTCATTGTTGATAGTCA
** *
29909739 TCACCATCTGTTTTCATAATTCGATAGCTGAAGCTATCCCTTTTCATATTTAAATGGTCAT-TAC
1 TCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTAAATGGTCATCT-C
*
29909803 CATCCTTTTTCAT
65 CATCCCTTTTCAT
29909816 AATTCGATAG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 1 0.01
89 67 0.99
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (89 bp):
TCACCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTAAATGGTCATCTCC
ATCCCTTTTCATTGTTGATAGTCA
Found at i:29909815 original size:60 final size:60
Alignment explanation
Indices: 29909715--29909875 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 60
29909705 GGTCGTCTCC
* * * **
29909715 ATCCCTTTTCATTGTT-GATAGTCATCACCAT-CTGTTTTCATAATTCGATAGCTGAAGCT
1 ATCCCTTTTCATAGTTAAATGGTCATCACCATCCT-TTTTCATAATTCGATAGCCAAAGCT
* *
29909774 ATCCCTTTTCATATTTAAATGGTCATTACCATCCTTTTTCATAATTCGATAGCCAAAGCT
1 ATCCCTTTTCATAGTTAAATGGTCATCACCATCCTTTTTCATAATTCGATAGCCAAAGCT
** *
29909834 ATCCCTTTTCATAGTTCGATGGTCGTCACCATCCTTTTTCAT
1 ATCCCTTTTCATAGTTAAATGGTCATCACCATCCTTTTTCAT
29909876 GGTTGATGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 14 0.16
60 72 0.82
61 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (60 bp):
ATCCCTTTTCATAGTTAAATGGTCATCACCATCCTTTTTCATAATTCGATAGCCAAAGCT
Found at i:29909870 original size:89 final size:89
Alignment explanation
Indices: 29909774--29909943 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 89
29909764 AGCTGAAGCT
* * * *
29909774 ATCCCTTTTCATATTTAAATGGTCATTACCATCCTTTTTCATAATTCGATAGCCAAAGCTATCCC
1 ATCCTTTTTCATAGTT-AATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCC
*
29909839 TTTTCATAGTTCGATGGTCGTCACC
65 TTTTCATAGGTCGATGGTCGTCACC
* * * * * **
29909864 ATCCTTTTTCATGGTTGATGGTCGTCACCATCCCTTTTCATATTTTGATAGCTGAAGCTATCCCT
1 ATCCTTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCT
*
29909929 TTTCATTGGTCGATG
66 TTTCATAGGTCGATG
29909944 ATTGTCGATA
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
89 54 0.81
90 13 0.19
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (89 bp):
ATCCTTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCT
TTTCATAGGTCGATGGTCGTCACC
Found at i:29909883 original size:29 final size:30
Alignment explanation
Indices: 29909643--29909905 Score: 178
Period size: 30 Copynumber: 8.8 Consensus size: 30
29909633 TAAAATTACA
*
29909643 ATGGTTGTCACCATCCCTTTTCATAGTTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTTCG
* * * * *
29909673 ATAGCCG-AAGCTATCCCTTTTCATATTTCG
1 ATGGTCGTCA-CCATCCCTTTTCATAGTTCG
* *
29909703 ATGGTCGTCTCCATCCCTTTTCATTGTT-G
1 ATGGTCGTCACCATCCCTTTTCATAGTTCG
* * ** *
29909732 ATAGTCATCACCATCTGTTTTCATAATTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTTCG
* * * * **
29909762 ATAG-C-TGAAGCTATCCCTTTTCATATTTAA
1 ATGGTCGT-CA-CCATCCCTTTTCATAGTTCG
* * * *
29909792 ATGGTCATTACCATCCTTTTTCATAATTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTTCG
* *** *
29909822 ATAG-CCAAAGCTATCCCTTTTCATAGTTCG
1 ATGGTCGTCA-CCATCCCTTTTCATAGTTCG
* *
29909852 ATGGTCGTCACCATCCTTTTTCATGGTT-G
1 ATGGTCGTCACCATCCCTTTTCATAGTTCG
29909881 ATGGTCGTCACCATCCCTTTTCATA
1 ATGGTCGTCACCATCCCTTTTCATA
29909906 TTTTGATAGC
Statistics
Matches: 174, Mismatches: 50, Indels: 19
0.72 0.21 0.08
Matches are distributed among these distances:
28 1 0.01
29 51 0.29
30 117 0.67
31 4 0.02
32 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (30 bp):
ATGGTCGTCACCATCCCTTTTCATAGTTCG
Found at i:29909914 original size:149 final size:149
Alignment explanation
Indices: 29909652--29909934 Score: 449
Period size: 149 Copynumber: 1.9 Consensus size: 149
29909642 AATGGTTGTC
* * * *
29909652 ACCATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCTCCAT
1 ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAGTTCGATGGTCGTCACCAT
* **
29909717 CCCTTTTCATTGTTGATAGTCATCACCATCTGTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
66 CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
29909782 TCATATTTAAATGGTCATT
131 TCATATTTAAATGGTCATT
*
29909801 ACCATCCTTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAGTTCGATGGTCGTCACCAT
1 ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAGTTCGATGGTCGTCACCAT
* * * * *
29909866 CCTTTTTCATGGTTGATGGTCGTCACCATCCCTTTTCATATTTTGATAGCTGAAGCTATCCCTTT
66 CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
29909931 TCAT
131 TCAT
29909935 TGGTCGATGA
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
149 121 1.00
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (149 bp):
ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAGTTCGATGGTCGTCACCAT
CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
TCATATTTAAATGGTCATT
Found at i:29919228 original size:29 final size:29
Alignment explanation
Indices: 29919169--29919336 Score: 87
Period size: 29 Copynumber: 5.7 Consensus size: 29
29919159 AGTCGAAGCT
* *
29919169 ATCCCTTTTCATATTTCGATGGTCGTTACC
1 ATCCC-TTTCATATTTCGATGGTCATCACC
*
29919199 ATCCCTTT-ATATTGTTGATGGTCATCACC
1 ATCCCTTTCATATT-TCGATGGTCATCACC
* *** *
29919228 ATCCCTTTTTATAATTT-GATAACCGA--AGCT
1 ATCCC-TTTCAT-ATTTCGATGGTC-ATCA-CC
* *
29919258 ATCCCTTTCCATGTTTCGATGGTCGTCACC
1 ATCCCTTT-CATATTTCGATGGTCATCACC
**
29919288 ATCCCTTTTCATGGTT-GATGGTCATCA-C
1 ATCCC-TTTCATATTTCGATGGTCATCACC
*
29919316 AGTCCCATTTCATAATTCGAT
1 A-TCCC-TTTCATATTTCGAT
29919337 AGCCGAAGCT
Statistics
Matches: 106, Mismatches: 19, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
28 7 0.07
29 49 0.46
30 39 0.37
31 8 0.08
32 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (29 bp):
ATCCCTTTCATATTTCGATGGTCATCACC
Found at i:29919278 original size:89 final size:88
Alignment explanation
Indices: 29919134--29919401 Score: 360
Period size: 89 Copynumber: 3.0 Consensus size: 88
29919124 ACAATGGTTG
* * * *
29919134 TCACCATCCCTTTTTATAGTTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCGTTACC
1 TCACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATGTTTCGATGGTCGTCACC
*
29919199 ATCCCTTTATATTGTTGATGGTCA
66 ATCCCTTT-TATGGTTGATGGTCA
* * *
29919223 TCACCATCCCTTTTTATAATTTGATAACCGAAGCTATCCCTTTCCATGTTTCGATGGTCGTCACC
1 TCACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATGTTTCGATGGTCGTCACC
29919288 ATCCCTTTTCATGGTTGATGGTCA
66 ATCCCTTTT-ATGGTTGATGGTCA
* * * *
29919312 TCA-CAGTCCCATTTCATAATTCGATAGCCGAAGCTTTCCTTTTTCATAG-TTCGATGGTCGTCA
1 TCACCA-TCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCAT-GTTTCGATGGTCGTCA
*
29919375 CCATCCCTTTCCATGGTTGATGGTCA
64 CCATCCCTTT-TATGGTTGATGGTCA
29919401 T
1 T
29919402 TACCGTCTAT
Statistics
Matches: 159, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
88 3 0.02
89 155 0.97
90 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (88 bp):
TCACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATGTTTCGATGGTCGTCACC
ATCCCTTTTATGGTTGATGGTCA
Found at i:29919396 original size:29 final size:30
Alignment explanation
Indices: 29919127--29919428 Score: 145
Period size: 30 Copynumber: 10.2 Consensus size: 30
29919117 TAAAATAACA
* * *
29919127 ATGGTTGTCACCATCCCTTTTTATAGTTCG
1 ATGGTCGTCACCATCCCTTTTCATGGTTCG
* * * **
29919157 ATAGTCG-AAGCTATCCCTTTTCATATTTCG
1 ATGGTCGTCA-CCATCCCTTTTCATGGTTCG
* *
29919187 ATGGTCGTTACCATCCCTTTAT-ATTGTT-G
1 ATGGTCGTCACCATCCCTTT-TCATGGTTCG
* * ** *
29919216 ATGGTCATCACCATCCCTTTTTATAATTTG
1 ATGGTCGTCACCATCCCTTTTCATGGTTCG
*** * * * *
29919246 ATAACCG-AAGCTATCCCTTTCCATGTTTCG
1 ATGGTCGTCA-CCATCCCTTTTCATGGTTCG
29919276 ATGGTCGTCACCATCCCTTTTCATGGTT-G
1 ATGGTCGTCACCATCCCTTTTCATGGTTCG
* * **
29919305 ATGGTCATCA-CAGTCCCATTTCATAATTCG
1 ATGGTCGTCACCA-TCCCTTTTCATGGTTCG
* * * ** * *
29919335 ATAGCCG-AAGCTTTCCTTTTTCATAGTTCG
1 ATGGTCGTCA-CCATCCCTTTTCATGGTTCG
*
29919365 ATGGTCGTCACCATCCCTTTCCATGGTT-G
1 ATGGTCGTCACCATCCCTTTTCATGGTTCG
* * * **
29919394 ATGGTCATTACCGTCTATTTTCATGGTT-G
1 ATGGTCGTCACCATCCCTTTTCATGGTTCG
29919423 ATGGTC
1 ATGGTC
29919429 ATCCCTTTTC
Statistics
Matches: 200, Mismatches: 60, Indels: 25
0.70 0.21 0.09
Matches are distributed among these distances:
28 3 0.01
29 78 0.39
30 115 0.57
31 4 0.02
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.39
Consensus pattern (30 bp):
ATGGTCGTCACCATCCCTTTTCATGGTTCG
Found at i:29919438 original size:23 final size:23
Alignment explanation
Indices: 29919376--29919451 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 23
29919366 TGGTCGTCAC
*
29919376 CATCCCTTTCCATGGTTGATGGT
1 CATCCCTTTTCATGGTTGATGGT
29919399 CATTACCGTCTATTTTCATGGTTGATGGT
1 CA-T-CC--C--TTTTCATGGTTGATGGT
*
29919428 CATCCCTTTTCATTGTTGATGGT
1 CATCCCTTTTCATGGTTGATGGT
29919451 C
1 C
29919452 GATACGCCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
23 19 0.42
24 1 0.02
25 3 0.07
27 3 0.07
28 1 0.02
29 18 0.40
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (23 bp):
CATCCCTTTTCATGGTTGATGGT
Found at i:29926179 original size:23 final size:23
Alignment explanation
Indices: 29926149--29926201 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
29926139 TTATGGAGGC
29926149 TGAATTGTTCGATGTTTGGGGTA
1 TGAATTGTTCGATGTTTGGGGTA
29926172 TGAATTGTTCGATGTTTGGGGTA
1 TGAATTGTTCGATGTTTGGGGTA
*
29926195 TGGATTG
1 TGAATTG
29926202 AAGCTGTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.04, G:0.36, T:0.43
Consensus pattern (23 bp):
TGAATTGTTCGATGTTTGGGGTA
Found at i:29929523 original size:17 final size:17
Alignment explanation
Indices: 29929501--29929543 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
29929491 CACATTATCG
*
29929501 TTGCATTTTTATTTTCA
1 TTGCATTTTTATTGTCA
29929518 TTGCATTTTTATTGTCA
1 TTGCATTTTTATTGTCA
29929535 TTGCATTTT
1 TTGCATTTT
29929544 AATGTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (17 bp):
TTGCATTTTTATTGTCA
Found at i:29933132 original size:19 final size:19
Alignment explanation
Indices: 29933105--29933141 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29933095 TGCACGCACG
* *
29933105 ATTCTACTAATCAAACACA
1 ATTCCACTAATAAAACACA
29933124 ATTCCACTAATAAAACAC
1 ATTCCACTAATAAAACAC
29933142 CATTAACGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (19 bp):
ATTCCACTAATAAAACACA
Found at i:29944804 original size:12 final size:12
Alignment explanation
Indices: 29944787--29944812 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29944777 CACTGTGACA
29944787 CCCAAGACAATG
1 CCCAAGACAATG
29944799 CCCAAGACAATG
1 CCCAAGACAATG
29944811 CC
1 CC
29944813 TTCACGGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (12 bp):
CCCAAGACAATG
Found at i:29949987 original size:42 final size:42
Alignment explanation
Indices: 29949926--29950034 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
29949916 ACGACCAAGC
*
29949926 CACACACCCATGTGCCAAGCTGTGTAACACTCGAAATGGCCT
1 CACACACCCATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
* *
29949968 CACACACCCGTGTGTCAAGCCGTGTAACACTCGAAATGGCCT
1 CACACACCCATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
* * *
29950010 CACACATCCACGTGCCAGGCCGTGT
1 CACACACCCATGTGCCAAGCCGTGT
29950035 GCTAGGCCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (42 bp):
CACACACCCATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
Found at i:29951523 original size:50 final size:50
Alignment explanation
Indices: 29951459--29951637 Score: 184
Period size: 50 Copynumber: 3.6 Consensus size: 50
29951449 AGAGGTACAT
* * ** *
29951459 GTAAGACCAAGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * *
29951509 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * * * *
29951559 GTAAGACCATATCTGGGATATGGCATTGGCA--GTACA-GAAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC-TCCCAC
* *
29951608 GTAAGACCATGTCAGGGACATGGCTTTGGC
1 GTAAGACCATGTCTGGGACATGGCATTGGC
29951638 TTGTTATTAT
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
48 6 0.05
49 34 0.31
50 70 0.64
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
Found at i:29956463 original size:43 final size:44
Alignment explanation
Indices: 29956402--29956517 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 44
29956392 TTTGAGTACT
29956402 TCTGATCAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
29956445 TCTGATCGGTGACAAGTGACAAGTAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTG---A-TAAGTGGTAGCTTTAGCTACACTTA
* * *
29956493 TCTGATTAGTGATAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
29956518 ACAAGTGATA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
43 17 0.27
44 5 0.08
45 1 0.02
46 1 0.02
47 11 0.17
48 28 0.44
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:29956541 original size:58 final size:58
Alignment explanation
Indices: 29956453--29956589 Score: 217
Period size: 58 Copynumber: 2.4 Consensus size: 58
29956443 TATCTGATCG
* *
29956453 GTGACAAGTGACAA--G-TAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGATAA
1 GTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
29956508 GTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
1 GTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
* *
29956566 GTGACAAGTAACAAGTGACAAGTG
1 GTGACAAGTGACAAGTGATAAGTG
29956590 ACAAGTGATA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
55 14 0.19
57 1 0.01
58 60 0.80
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (58 bp):
GTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAA
Found at i:29956570 original size:7 final size:7
Alignment explanation
Indices: 29956558--29956597 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
29956548 TTATCTGATC
29956558 AGTGACA
1 AGTGACA
29956565 AGTGACA
1 AGTGACA
*
29956572 AGTAACA
1 AGTGACA
29956579 AGTGACA
1 AGTGACA
29956586 AGTGACA
1 AGTGACA
29956593 AGTGA
1 AGTGA
29956598 TAAATGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.28, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:29962247 original size:50 final size:50
Alignment explanation
Indices: 29962172--29962412 Score: 229
Period size: 50 Copynumber: 4.9 Consensus size: 50
29962162 CATTTGGGTA
* *
29962172 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
1 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGAT
* *
29962222 AAGAGGTCCTATGTAAGACCATGTCTAGGACATGGCGTTGGCAGC-GAGAT
1 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCA-CTGAGAT
* ** * * *
29962272 GAGAGGTCCTCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGAT
* ** * * * * *
29962322 GAGAACTCTTATGTAAGA-CATATCTGGGATATGGCATTGGCAGTACAGA-
1 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACT-GAGAT
** * * *
29962371 AA-ACATCCCATGTAAGACCATGTGTGGGACATGGCTTTGGCA
1 AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCA
29962413 TGTTATTATC
Statistics
Matches: 157, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 11 0.07
49 43 0.27
50 102 0.65
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (50 bp):
AAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGAT
Found at i:29967734 original size:50 final size:53
Alignment explanation
Indices: 29967680--29967811 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 53
29967670 ATGGGTGCCC
* * **
29967680 ATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCAT-CTCGGT-A-CCA
1 ATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATACTCAATAAGCCA
*
29967730 ATGCCATGTCCCAGACATGGTCTTACGTGAGACCTCTCATAACCTCAATAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCAT-A-CTCAATAA-GCCA
29967786 ATGCCATGTCCCAGACATGGTCTTAC
1 ATGCCATGTCCCAGACATGGTCTTAC
29967812 ATGGGGTCTC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
50 37 0.52
53 4 0.06
54 1 0.01
56 29 0.41
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (53 bp):
ATGCCATGTCCCAGACATGGTCTTACGGGAGACCTCTCATACTCAATAAGCCA
Found at i:29971640 original size:9 final size:9
Alignment explanation
Indices: 29971626--29971674 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
29971616 AAGCACCGGG
29971626 CTTTCAATT
1 CTTTCAATT
29971635 CTTTCAATT
1 CTTTCAATT
* *
29971644 CTTGCAACTCAG
1 CTTTCAA-T--T
29971656 CTTTCAATT
1 CTTTCAATT
29971665 CTTTCAATT
1 CTTTCAATT
29971674 C
1 C
29971675 CAACGGGGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 25 0.76
10 1 0.03
11 1 0.03
12 6 0.18
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (9 bp):
CTTTCAATT
Found at i:29975319 original size:50 final size:49
Alignment explanation
Indices: 29975198--29975323 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 49
29975188 AATAACATGC
* * *
29975198 CAAA-GCCATGTCCCAGACATGGTCTCACATGAGATGTTTCCTGTACTG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATATACTG
* *
29975246 CAAATGCCATATCCCAGATATGGTCTTACATGAGA-GTTCTCATAT-CGGTG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCATATAC--TG
**
29975296 CCCATGCCATGTCCCAGACATGGTCTTA
1 CAAATGCCATGTCCCAGACATGGTCTTA
29975324 TGGGGGACCT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
48 8 0.12
49 31 0.48
50 26 0.40
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (49 bp):
CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATATACTG
Found at i:29983858 original size:51 final size:54
Alignment explanation
Indices: 29983766--29983909 Score: 156
Period size: 56 Copynumber: 2.7 Consensus size: 54
29983756 AAAATAACAT
* * **
29983766 GCCAAA-GCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCAT-CTCGGT-A
1 GCCAAATGCCATGTCCCAGACATGGTCTTACATGGG-ATCTCTCATACTCAATAA
*
29983817 -CCAAATGCCATGTCCCAGACATGATCTTACATGGGATCTCTCATAAACTCAATAA
1 GCCAAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCAT--ACTCAATAA
*
29983872 TGCC-AATGCCATGTCCCAGACTTGGTCTTACATGGGAT
1 -GCCAAATGCCATGTCCCAGACATGGTCTTACATGGGAT
29983910 TTCATTTCCC
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
50 5 0.06
51 31 0.40
52 3 0.04
54 4 0.05
55 1 0.01
56 32 0.41
57 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (54 bp):
GCCAAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATACTCAATAA
Found at i:29985691 original size:645 final size:635
Alignment explanation
Indices: 29984471--29985750 Score: 1665
Period size: 645 Copynumber: 2.0 Consensus size: 635
29984461 AATCGCCTAG
29984471 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
1 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
* * * *
29984536 CAACTATGGGTGTTTTTCCAAATATGAACCTTAACATGAATTAATGGTTGAATAAGCTAAATCGA
66 CAACTATGGGTATTTTTCCAAATATGAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCGA
* * * *
29984601 GCTACAAGGACTCCAAAAACATAAAAAAACATTAAAAATGGGGCTTGTATGTACTTACAATCAAG
131 GCTACAAGGACTCCAAAAACATAAAAAAACATTAAAAACGGGGATTGGATGCACTTACAATCAAG
* * *
29984666 CTTGAAAGTGGCCAAAACCCTAGCCATGGAGAACTTGTAAGTTTCCACTATGGTGGAAGAAATAT
196 CTTGAAAGTGGCAAAAACCCTAGCCATGGAGAACTTGTAAGTTTCCACTATGATGGAAGAAAGAT
* * *
29984731 GAGCACATTTTGGCTTTATTTTCCCTTTTAATTCATTTAATTACCAAATGACAAAAATGCCCCTA
261 GAGCACATGTTGCCTCTATTTTCCCTTTTAATTCATTTAATTACCAAATGACAAAAATGCCCCTA
* * * *
29984796 ACTTAAAAATATCCTATTTCACCTATCTCTTGTCCATTTTTGTCTATGAAAATCTAATGGTCTAA
326 ACTTAAAAATATCCTATTTCACCTATCGCATGCCCATTTTTGTCCATGAAAATCTAATGGTCTAA
*
29984861 TTACCATTTAAGGACCTCTACTTCAATTAAATATTTTATCATCTAAAACTCATATTTACGCACTT
391 TTACCATTTAAGGACCTCTACTTCAATTAAATATTTTATCATCTAAAACTCATATTTACCCACTT
** *
29984926 TTGCAATTAAACCCTAATATGCAATTCAGACATGCAATTTCTAAAATTTCTTATCGGTATTCTAA
456 TTGCAATTAAACCCTAATATGCAATTCAGACATGCAATCGCTAAAATTTCTTATCGATATTCTAA
* * *
29984991 CACATGCATCCAATCAATTGGTAAATAATAAAAATTAATCACAATAAACTTTTCTATCTCAAAAT
521 CACATGCATCCAATAAATCGATAAATAATAAAAATTAATCACAATAAACTTTTCTATCTCAAAAT
* * *
29985056 CGTGGTTTCGCAACCACTATTTTGTTTAGGCCCTATTTCGGGATGTTACA
586 CATGGTTTCGCAACCACTATTTCGTTTAGGCCCTATTTCGAGATGTTACA
** **
29985106 CAAAAGTTTTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATTAAAATAAACACATTT
1 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
*
29985171 C-ACTTTTGGGTATTTTTCCAAATATGAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCG
66 CAAC-TATGGGTATTTTTCCAAATATGAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCG
* * * *
29985235 AGCTACGAA-GACTCGAAAAAC-TTAAAAAA-ATTAAAAACGGGGATTGGATGCACTTACTAT-G
130 AGCTAC-AAGGACTCCAAAAACATAAAAAAACATTAAAAACGGGGATTGGATGCACTTACAATCA
* **
29985296 AGCTTGAGAAAGT-G-AAGAAACCCTAGCTATGGAGTCCTT-TAAAGTTTTGGCC-CT-T-ATGG
194 AGCTT--GAAAGTGGCAA-AAACCCTAGCCATGGAGAACTTGT-AAG-TTT--CCACTATGATGG
* *
29985355 AAG-AAGATGAGCACATGTTGCCATCT-TTTTCCCTTTTAATT-ATTTTTATTACCAAATGACTA
252 AAGAAAGATGAGCACATGTTGCC-TCTATTTTCCCTTTTAATTCA-TTTAATTACCAAATGACAA
* * * * * * ** * *
29985417 TAATGCTCTTCA-TTAAAACTTTAGTTATTTTTATCTAT-GCATGCCCATTTTTGTCCATGAAAA
315 AAATGCCCCTAACTTAAAAATAT-CCTA-TTTCACCTATCGCATGCCCATTTTTGTCCATGAAAA
* *
29985480 TCTACTGGTCTAATTATCATTTAAGGACCTCTACTTCAATTACGCACTTCAATTAAATCCTTTAT
378 TCTAATGGTCTAATTACCATTTAAGGACCTCTACTTCAATT----A----AA-T--AT--TTTAT
*
29985545 CATCTAAAACTCATATTTACCCACTTTTGTAATTAAACCCTAATATGCAATTCAGACATGCAATC
430 CATCTAAAACTCATATTTACCCACTTTTGCAATTAAACCCTAATATGCAATTCAGACATGCAATC
* * *
29985610 GCTAAAATTTCTTATCGATATTCTAACATATGCATCTAATAAATCGATAAATTATAAAAATTAAT
495 GCTAAAATTTCTTATCGATATTCTAACACATGCATCCAATAAATCGATAAATAATAAAAATTAAT
* *
29985675 CACAATAAACTTTTCTATCTCAAATTCATGGTTTCGCAACCACTGTTTCGTTTAGGCCCTATTTC
560 CACAATAAACTTTTCTATCTCAAAATCATGGTTTCGCAACCACTATTTCGTTTAGGCCCTATTTC
*
29985740 GAGATTTTACA
625 GAGATGTTACA
29985751 TTACCGTAAA
Statistics
Matches: 558, Mismatches: 61, Indels: 42
0.84 0.09 0.06
Matches are distributed among these distances:
631 9 0.02
632 125 0.22
633 65 0.12
634 19 0.03
635 136 0.24
636 5 0.01
640 2 0.00
641 1 0.00
643 2 0.00
645 194 0.35
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (635 bp):
CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
CAACTATGGGTATTTTTCCAAATATGAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCGA
GCTACAAGGACTCCAAAAACATAAAAAAACATTAAAAACGGGGATTGGATGCACTTACAATCAAG
CTTGAAAGTGGCAAAAACCCTAGCCATGGAGAACTTGTAAGTTTCCACTATGATGGAAGAAAGAT
GAGCACATGTTGCCTCTATTTTCCCTTTTAATTCATTTAATTACCAAATGACAAAAATGCCCCTA
ACTTAAAAATATCCTATTTCACCTATCGCATGCCCATTTTTGTCCATGAAAATCTAATGGTCTAA
TTACCATTTAAGGACCTCTACTTCAATTAAATATTTTATCATCTAAAACTCATATTTACCCACTT
TTGCAATTAAACCCTAATATGCAATTCAGACATGCAATCGCTAAAATTTCTTATCGATATTCTAA
CACATGCATCCAATAAATCGATAAATAATAAAAATTAATCACAATAAACTTTTCTATCTCAAAAT
CATGGTTTCGCAACCACTATTTCGTTTAGGCCCTATTTCGAGATGTTACA
Found at i:29989721 original size:35 final size:35
Alignment explanation
Indices: 29989662--29989730 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
29989652 TTGGTTGGAT
*
29989662 AAATAATCTACTGGCACTACGTAGTGGCATCATGA
1 AAATAATCTACTGGCACTAAGTAGTGGCATCATGA
* * *
29989697 AAATAGTCTATTGGCTCTAAGTAGTGGCATCATG
1 AAATAATCTACTGGCACTAAGTAGTGGCATCATG
29989731 GAGTGATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (35 bp):
AAATAATCTACTGGCACTAAGTAGTGGCATCATGA
Found at i:29990282 original size:27 final size:28
Alignment explanation
Indices: 29990250--29990313 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
29990240 TATACCAAGG
29990250 ACTATCTTATGATGGAA-GTCT-CCAAAA
1 ACTATCTTATG-TGGAATGTCTGCCAAAA
**
29990277 ACTATCTTATGTGGAATGTCTGCCAAGG
1 ACTATCTTATGTGGAATGTCTGCCAAAA
29990305 ACTATCTTA
1 ACTATCTTA
29990314 AAGACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 5 0.15
27 15 0.45
28 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (28 bp):
ACTATCTTATGTGGAATGTCTGCCAAAA
Found at i:29990311 original size:28 final size:27
Alignment explanation
Indices: 29990218--29990313 Score: 104
Period size: 28 Copynumber: 3.5 Consensus size: 27
29990208 GAAGCCTACT
* ** *
29990218 AAGGACTATCTTATGCGGGCTGTATACC
1 AAGGACTATCTTATGTGGAATGTCT-CC
29990246 AAGGACTATCTTATGATGGAA-GTCTCC
1 AAGGACTATCTTATG-TGGAATGTCTCC
**
29990273 AAAAACTATCTTATGTGGAATGTCTGCC
1 AAGGACTATCTTATGTGGAATGTCT-CC
29990301 AAGGACTATCTTA
1 AAGGACTATCTTA
29990314 AAGACAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
26 5 0.09
27 19 0.33
28 31 0.54
29 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (27 bp):
AAGGACTATCTTATGTGGAATGTCTCC
Found at i:29992296 original size:27 final size:28
Alignment explanation
Indices: 29992225--29992299 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
29992215 AATCAAGGTA
* *
29992225 TGCCACAAAGGCA-GTCTATTTAGAGTT
1 TGCCACAAAGGCATTTCTATTCAGAGTT
* **
29992252 TTCCACAAA-GTTTATTCT-TTCAGAGTT
1 TGCCACAAAGGCAT-TTCTATTCAGAGTT
29992279 TGCCACAAAGGCATTTCTATT
1 TGCCACAAAGGCATTTCTATT
29992300 GTCAGGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
26 1 0.03
27 28 0.78
28 7 0.19
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (28 bp):
TGCCACAAAGGCATTTCTATTCAGAGTT
Found at i:29999057 original size:5 final size:5
Alignment explanation
Indices: 29999047--29999072 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29999037 TGAGCATTCG
29999047 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
29999073 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:30000110 original size:9 final size:9
Alignment explanation
Indices: 30000096--30000132 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30000086 TATAGTTTGA
30000096 TATTCGAAT
1 TATTCGAAT
30000105 TATTCGAAT
1 TATTCGAAT
*
30000114 TATTCGAGT
1 TATTCGAAT
30000123 TATTCGAAT
1 TATTCGAAT
30000132 T
1 T
30000133 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30000202 original size:9 final size:9
Alignment explanation
Indices: 30000185--30000215 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30000175 TCGAGTTGAT
30000185 TCGAATAAC
1 TCGAATAAC
*
30000194 TCGATTAAC
1 TCGAATAAC
30000203 TCGAATAAC
1 TCGAATAAC
30000212 TCGA
1 TCGA
30000216 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:30006317 original size:27 final size:27
Alignment explanation
Indices: 30006120--30006313 Score: 289
Period size: 27 Copynumber: 7.2 Consensus size: 27
30006110 ATATGCCACG
* *
30006120 AATGGCCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
* * *
30006147 AATAATCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
*
30006174 AATGACCAAAATACCCTCAAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
*
30006201 AATGACCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
30006228 AATGACCGAAATACCCTCAAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
*
30006255 AATGACCGAAATACCCTCAAAGGGTTA
1 AATGACCGAAATACCCTCAAAGGGTAA
* * *
30006282 AATAATCGAAATACCCTCCAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAA
30006309 AATGA
1 AATGA
30006314 TCGATTTGCT
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.16
Consensus pattern (27 bp):
AATGACCGAAATACCCTCAAAGGGTAA
Found at i:30006471 original size:27 final size:27
Alignment explanation
Indices: 30006426--30006499 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
30006416 ATAGGGGAAG
**
30006426 TATACTG-TACTGGTGGCTTTGCCACA
1 TATACTGTTACTGGCAGCTTTGCCACA
* **
30006452 TATACTGTTACTGGCAGCTTCGCTGCA
1 TATACTGTTACTGGCAGCTTTGCCACA
* *
30006479 -ATACTATTACTGGCAGATTTG
1 TATACTGTTACTGGCAGCTTTG
30006500 TTGCGATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
TATACTGTTACTGGCAGCTTTGCCACA
Found at i:30009816 original size:412 final size:405
Alignment explanation
Indices: 30008858--30009978 Score: 1176
Period size: 412 Copynumber: 2.7 Consensus size: 405
30008848 CTATCTTAGA
* * * ** ** *
30008858 AAAAAAACATATCGACTAGTTGGAGTTGAGATTCTTCATGGGTTGGTCTTTTCAAAACTTGTACC
1 AAAAAAACATATAGATTAGTTGGAGCTGAGATTCTTGGT-GGTTGGTCTTTTTGAAACTTGTAAC
* * * * * *
30008923 CAAGCAAGATAATGTTTGGGCTAAAACTCTTTCTCAAAAGGTTGGGAGGAG-TCATCATAAGTGG
65 CACGTAGGATAATGTTTGGGCT-AAACTCTCTATCAAAAGGCTGGGAGGAGCT-ATCATAAGTGG
* * * * * * * *
30008987 TTGGGTTGACTCAAGAATAGAGGTGCCAACAATTGTAAAGTTAGGTTTAATTGAGGAAGAATCC-
128 TTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATCGAGGGAGAA-CCT
* * * ** * *
30009051 ATGGCTTTTTAGTTTAGTATTCTCCCAGATTGTGCCAATTGTTGATGTCTCTTTCACTGGGCTTG
192 ATGGC-TTTTAGTTTAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTATTGGGCTTG
* * * * * *
30009116 GAGATTGGTTTAGCTAAACTTTATAGCTAGAAAATCTACAAAGTGTACTAGCAATATGGGTAGTC
256 GAGACTAGTTGAGCT-AACTTTATAGC-AGAAAATCGACAAAGTATACTAGCAATATGGATAGTC
* * *
30009181 ATGGTTGATGGTAGATATGATTGTGAGAACTTGTACTCAATATTTGGTAATGATCGTATGGCAAC
319 ATGGTTGATGGTAAAGATGATTGTGAGAACTTGTACTCAATATTTGGTAATGATCGTATGGAAAC
*
30009246 CAATTATTATTAGAAGTATCTT
384 CAATTACTATTAGAAGTATCTT
* * * * * * * * *
30009268 AGAAAAACATACAAATTTGTTGGAGCTGAGATTATTGGTGGACTGGTCTTTCTGGAACTTGTCAC
1 AAAAAAACATATAGATTAGTTGGAGCTGAGATTCTTGGTGG-TTGGTCTTTTTGAAACTTGTAAC
* * * ** ** *
30009333 CACGTAGGAAAATGTTTCGGCTCAAACTCTCAATCAAAA-GCTTAAGAACAGCCATCATAAGTGG
65 CACGTAGGATAATGTTTGGGCT-AAACTCTCTATCAAAAGGC-TGGGAGGAGCTATCATAAGTGG
* * *
30009397 TTGGGCTAACTCAAGAACAGGGGTGTTAGCAATTGTAAAGTTAGCTTGAATCGAGGGAGAACCTA
128 TTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATCGAGGGAGAACCTA
* * * *
30009462 -GAGCTTTTAGTTTAATATTCTCATAAACAGTGCCACTTGTTGATGACTCTTTTATTGGGCTTAG
193 TG-GCTTTTAGTTTAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTATTGGGCTTGG
* * *
30009526 AGACTAGTTGAGCTACACTTTATAGCCGAACAATCGGCAAAGTATTCTAGCAATATGGATAGTCA
257 AGACTAGTTGAGCTA-ACTTTATAGCAGAA-AATCGACAAAGTATACTAGCAATATGGATAGTCA
*
30009591 TGGTTGATGGTAAAGATGGTTGTGAAGAACTTGTACTCAAAATATTTTGGTAATGATCGTATGGA
320 TGGTTGATGGTAAAGATGATTGTG-AGAACTTGTACTC--AATA-TTTGGTAATGATCGTATGGA
**
30009656 AACTGATTACTATT-GAAAGTATC-T
381 AACCAATTACTATTAG-AAGTATCTT
* * *
30009680 AAAAAAACATATTGATTGGTTGGAGCTGAGATTCTAGGTAGGTTGGTCTTTTTGAAACTTGTAAC
1 AAAAAAACATATAGATTAGTTGGAGCTGAGATTCTTGGT-GGTTGGTCTTTTTGAAACTTGTAAC
* * * * * *
30009745 CACGTAGGGTAATGTTTGGGCTAGTACTCTCTATCAAAAGGCTGGGAGGAGCTGTCGTAAGTAGA
65 CACGTAGGATAATGTTTGGGCTA-AACTCTCTATCAAAAGGCTGGGAGGAGCTATCATAAGTGGT
* * ** * * *
30009810 TGGGCTAATTAAAGAACAGGGGTGTCAATTACTATAAAGTTAGGTTGAATCGAGAGAGAACCTAT
129 TGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATCGAGGGAGAACCTAT
* * *
30009875 GGCTTTTAGTTCAATATTCTCACAAACAGTGCCAATTATTGATGTCTCTTTTGTTGGGCTTGGAT
194 GGCTTTTAGTTTAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTATTGGGCTTGGA-
* *
30009940 G-CTAGTTGAGCTAAGCTTTATAGCTGAAAAATCTACAAA
258 GACTAGTTGAGCTAA-CTTTATAGCAG-AAAATCGACAAA
30009979 AAAAGGATAA
Statistics
Matches: 577, Mismatches: 115, Indels: 36
0.79 0.16 0.05
Matches are distributed among these distances:
408 4 0.01
409 126 0.22
410 157 0.27
411 2 0.00
412 243 0.42
413 45 0.08
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (405 bp):
AAAAAAACATATAGATTAGTTGGAGCTGAGATTCTTGGTGGTTGGTCTTTTTGAAACTTGTAACC
ACGTAGGATAATGTTTGGGCTAAACTCTCTATCAAAAGGCTGGGAGGAGCTATCATAAGTGGTTG
GGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATCGAGGGAGAACCTATGG
CTTTTAGTTTAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTTTATTGGGCTTGGAGAC
TAGTTGAGCTAACTTTATAGCAGAAAATCGACAAAGTATACTAGCAATATGGATAGTCATGGTTG
ATGGTAAAGATGATTGTGAGAACTTGTACTCAATATTTGGTAATGATCGTATGGAAACCAATTAC
TATTAGAAGTATCTT
Found at i:30011907 original size:21 final size:21
Alignment explanation
Indices: 30011881--30011952 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
30011871 TCATATGAGT
30011881 TTTCGTTCAGCTCTTACGAGC
1 TTTCGTTCAGCTCTTACGAGC
* * * *
30011902 TTTCGTTCAACCCTTATG-GG
1 TTTCGTTCAGCTCTTACGAGC
30011922 TTTCCGTTCAGCTCTTACGAGC
1 TTT-CGTTCAGCTCTTACGAGC
*
30011944 TTCCGTTCA
1 TTTCGTTCA
30011953 ACCCTTATGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.10
21 33 0.82
22 3 0.08
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTCGTTCAGCTCTTACGAGC
Found at i:30011967 original size:42 final size:42
Alignment explanation
Indices: 30011842--30011967 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
30011832 GTTTACTTTT
* * ** * * * * *
30011842 CGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAGTTTT
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
*
30011884 CGTTCAGCTCTTACGAGCTTTCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
30011926 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
30011968 TGTTTAGTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
Found at i:30011986 original size:42 final size:42
Alignment explanation
Indices: 30011842--30011986 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 42
30011832 GTTTACTTTT
* ** * * * * *
30011842 CGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAGTTTT
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* *
30011884 CGTTCAGCTCTTACGAGCTTTCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
*
30011926 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* * * *
30011968 TGTTTAGTTCTCATGAGCT
1 CGTTCAGCTCTCACGAGCT
30011987 ACTATTCAGG
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.40
Consensus pattern (42 bp):
CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
Found at i:30015652 original size:42 final size:43
Alignment explanation
Indices: 30015590--30015746 Score: 144
Period size: 42 Copynumber: 3.7 Consensus size: 43
30015580 TCGTGTTTAC
* * * *
30015590 TTTTCGTTTAGCTCTCACGAGCTTCT-ATTTAACTCATATGAG
1 TTTTCGTTCAGCTCTTACGAGCTTCTCATTCAACCCATATGAG
* * *
30015632 TTTTCGTTCAGCTCTTACGAGCTT-TCGTTCAACCCTTATGGG
1 TTTTCGTTCAGCTCTTACGAGCTTCTCATTCAACCCATATGAG
* * *
30015674 TTTCCGTTCAGCTCTTACGAGCTTC-CGTTCAACCCTTATG-G
1 TTTTCGTTCAGCTCTTACGAGCTTCTCATTCAACCCATATGAG
* * * *
30015715 GTTTCTGTTTAGCTCTCATGAGCTTCT-ATTCA
1 TTTTC-GTTCAGCTCTTACGAGCTTCTCATTCA
30015747 GCCTTCGGGC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
41 5 0.05
42 92 0.95
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (43 bp):
TTTTCGTTCAGCTCTTACGAGCTTCTCATTCAACCCATATGAG
Found at i:30015659 original size:21 final size:21
Alignment explanation
Indices: 30015633--30015704 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
30015623 TCATATGAGT
30015633 TTTCGTTCAGCTCTTACGAGC
1 TTTCGTTCAGCTCTTACGAGC
* * * *
30015654 TTTCGTTCAACCCTTATG-GG
1 TTTCGTTCAGCTCTTACGAGC
30015674 TTTCCGTTCAGCTCTTACGAGC
1 TTT-CGTTCAGCTCTTACGAGC
*
30015696 TTCCGTTCA
1 TTTCGTTCA
30015705 ACCCTTATGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.10
21 33 0.82
22 3 0.08
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTCGTTCAGCTCTTACGAGC
Found at i:30017361 original size:3 final size:3
Alignment explanation
Indices: 30017353--30017406 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
30017343 TGATTCATCT
30017353 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30017401 ATA ATA
1 ATA ATA
30017407 TAAGCACAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30017563 original size:44 final size:47
Alignment explanation
Indices: 30017499--30017593 Score: 142
Period size: 44 Copynumber: 2.1 Consensus size: 47
30017489 TTAGTTAAAA
* *
30017499 AATTTAAGTAAAATAGTTGTGATAATTATACATTTAAAAATAATTAT
1 AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
*
30017546 AATTTAA-T-AAA-AGTTGTGATAATTACACGTTTAAAAATAATTAG
1 AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
30017590 AATT
1 AATT
30017594 CAAATTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 34 0.76
45 3 0.07
46 1 0.02
47 7 0.16
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (47 bp):
AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
Found at i:30025119 original size:2 final size:2
Alignment explanation
Indices: 30025112--30025140 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30025102 AACACAGCTT
30025112 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30025141 GTAGAGAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30025297 original size:2 final size:2
Alignment explanation
Indices: 30025290--30025325 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30025280 TTGATTCCTT
30025290 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
30025326 CCCAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30027008 original size:98 final size:96
Alignment explanation
Indices: 30026896--30027075 Score: 254
Period size: 98 Copynumber: 1.9 Consensus size: 96
30026886 TTAAAAAATA
* * *
30026896 AAATATATTTAACATAACGATAAATGTAAAAATAATTTT-ATTATATAATTGCATATTTATATTA
1 AAATATATTTAACATAACAATAAATATAAAAAT-ATTTTCATTATATAATTACATA-TT-TATTA
30026960 ATTTATTTATATAAATAAATGAGTTACTAATTAC
63 ATTTATTTATATAAATAAATGAGTTACTAATTAC
* * * * *
30026994 AAATATTTTTAACATAATAATATATATAAATATATTTTCATTATATAATTACATATTTATTATTT
1 AAATATATTTAACATAACAATAAATATAAAAATATTTTCATTATATAATTACATATTTATTAATT
30027059 TATTTATATAAATAAAT
66 TATTTATATAAATAAAT
30027076 AAAATTATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
96 24 0.33
97 7 0.10
98 42 0.58
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (96 bp):
AAATATATTTAACATAACAATAAATATAAAAATATTTTCATTATATAATTACATATTTATTAATT
TATTTATATAAATAAATGAGTTACTAATTAC
Found at i:30027394 original size:15 final size:15
Alignment explanation
Indices: 30027354--30027394 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
30027344 TTTGCTCCAC
*
30027354 AAAAATAATTTTTAG
1 AAAAATAAATTTTAG
*
30027369 AAAAA-AGATTTTAG
1 AAAAATAAATTTTAG
30027383 AAAAATAAATTT
1 AAAAATAAATTT
30027395 ATTTTTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAAATAAATTTTAG
Found at i:30032780 original size:39 final size:39
Alignment explanation
Indices: 30032759--30032875 Score: 180
Period size: 39 Copynumber: 3.0 Consensus size: 39
30032749 CCATATTACA
* *
30032759 CATATAACCACATAACCTTTAAGCATATATCACAATACT
1 CATATAATCACATAACATTTAAGCATATATCACAATACT
* *
30032798 CATATAATTACATAACATTCAAGCATATATCACAATACT
1 CATATAATCACATAACATTTAAGCATATATCACAATACT
* *
30032837 CATATAATCACATAACATTCAAGCATACATCACAATACT
1 CATATAATCACATAACATTTAAGCATATATCACAATACT
30032876 AAAAAACATG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.28
Consensus pattern (39 bp):
CATATAATCACATAACATTTAAGCATATATCACAATACT
Found at i:30043201 original size:16 final size:16
Alignment explanation
Indices: 30043180--30043211 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30043170 GTTTTGTTGC
*
30043180 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
30043196 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
30043212 CTTCCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:30043392 original size:46 final size:43
Alignment explanation
Indices: 30043349--30043433 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
30043339 CATGGTGGAT
*
30043349 TCAGCACACAGCAACCACCCTTTGTAATCAATGATATCCGGTGGGA
1 TCAGCACACAGCAACCA-CC-TTATAATCAATGATA-CCGGTGGGA
* *
30043395 TCAGCACATAGCAACCACCTTATAATTAATGATACCGGT
1 TCAGCACACAGCAACCACCTTATAATCAATGATACCGGT
30043434 TCACATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 13 0.36
45 2 0.06
46 16 0.44
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
TCAGCACACAGCAACCACCTTATAATCAATGATACCGGTGGGA
Found at i:30043493 original size:51 final size:51
Alignment explanation
Indices: 30043435--30043629 Score: 236
Period size: 51 Copynumber: 3.8 Consensus size: 51
30043425 GATACCGGTT
*
30043435 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
* * *
30043486 CACATAGTAGCCTGCACATAGTAGTACACACGTGA--TTGAAGCTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT-CA-CTATCCGATA
* * * * * *
30043537 CGCATAGTAGCTTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGATA
*
30043587 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
30043630 TTCACTTTCA
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
49 5 0.04
50 39 0.32
51 74 0.62
53 1 0.01
54 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
Found at i:30043606 original size:101 final size:102
Alignment explanation
Indices: 30043437--30043621 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
30043427 TACCGGTTCA
*
30043437 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCTGCA
*
30043502 CATAGTAGTACACACGTGATTGAAGCTATCCGATACG
66 CATAGTACTACACACGTGATTGAAGCTATCCGATACG
* * * *
30043539 CATAGTAGCTTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACATAGTAGCCTGC
30043602 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
30043622 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCTGCA
CATAGTACTACACACGTGATTGAAGCTATCCGATACG
Found at i:30050673 original size:17 final size:17
Alignment explanation
Indices: 30050651--30050684 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30050641 CACTCACATG
*
30050651 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
30050668 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
30050685 TATACTTACC
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:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:30051178 original size:21 final size:20
Alignment explanation
Indices: 30051133--30051199 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 20
30051123 TTTTTCTTTT
* *
30051133 TCAGCAACCACTTCCTCTTC
1 TCAGCAACAACTTCATCTTC
30051153 T--GCAACAACTTCATCTTC
1 TCAGCAACAACTTCATCTTC
*
30051171 TACAGCAACAAATTC--CTTC
1 T-CAGCAACAACTTCATCTTC
*
30051190 TCAACAACAA
1 TCAGCAACAA
30051200 TGTCCTCTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 24 0.60
19 5 0.12
20 1 0.03
21 10 0.25
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (20 bp):
TCAGCAACAACTTCATCTTC
Found at i:30070359 original size:29 final size:29
Alignment explanation
Indices: 30070317--30070376 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
30070307 GAAAATTTGG
30070317 ACTGTAGGGGTCACACGGCTGAGACACAC
1 ACTGTAGGGGTCACACGGCTGAGACACAC
30070346 ACTGTAGGGGTCACACGGCTGAGACACAC
1 ACTGTAGGGGTCACACGGCTGAGACACAC
30070375 AC
1 AC
30070377 CCGTGTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.13
Consensus pattern (29 bp):
ACTGTAGGGGTCACACGGCTGAGACACAC
Found at i:30074487 original size:28 final size:28
Alignment explanation
Indices: 30074449--30074503 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
30074439 TTACCCTTGT
*
30074449 TCTCCGGTCCTCACTTCTCTTTCCAATC
1 TCTCCAGTCCTCACTTCTCTTTCCAATC
30074477 TCTCCAGTCCTCACTTCTCTTTCCAAT
1 TCTCCAGTCCTCACTTCTCTTTCCAAT
30074504 ATCAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.13, C:0.42, G:0.05, T:0.40
Consensus pattern (28 bp):
TCTCCAGTCCTCACTTCTCTTTCCAATC
Found at i:30090501 original size:176 final size:176
Alignment explanation
Indices: 30090207--30090564 Score: 565
Period size: 176 Copynumber: 2.0 Consensus size: 176
30090197 ATCTAGATTG
* * *
30090207 GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAACTAACATTGACCAAAACACTAAGAGATTTAG
1 GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGAGATTTAG
* * *
30090272 AAACTAACCAAAGATGTTGATTGAGTCTTAACTCAATTGGCATCAGCATTGTTGCCAGTGCAAGA
66 AAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAGA
*
30090337 GGACATGGGTTTGAGTGTGCTGAAGCACATTATCCTCTTATTTAAA
131 GGACATGGGTTTGAGCGTGCTGAAGCACATTATCCTCTTATTTAAA
* * *
30090383 GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAATTAACACTAACCACAACAATAGGATG-TTTA
1 GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGA-GATTTA
* *
30090447 GAAACTAACCAAATATATTGATTGAGTCTTAGCTCAATTGGCATCAACATTGTTGCCAATGCAAG
65 GAAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAG
* * *
30090512 AGGACGTGGGTTTGAGCGTGCTGAAGCGCATTATCCTCTTATTTAAG
130 AGGACATGGGTTTGAGCGTGCTGAAGCACATTATCCTCTTATTTAAA
30090559 GGTTGG
1 GGTTGG
30090565 AAAGGGGTTG
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 165 0.99
177 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (176 bp):
GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGAGATTTAG
AAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAGA
GGACATGGGTTTGAGCGTGCTGAAGCACATTATCCTCTTATTTAAA
Found at i:30091139 original size:13 final size:13
Alignment explanation
Indices: 30091123--30091147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30091113 TTATTTTCAT
30091123 TTTTTAAAAATTA
1 TTTTTAAAAATTA
30091136 TTTTTAAAAATT
1 TTTTTAAAAATT
30091148 TTAACTGAGT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAAATTA
Found at i:30092972 original size:89 final size:89
Alignment explanation
Indices: 30092869--30093048 Score: 324
Period size: 89 Copynumber: 2.0 Consensus size: 89
30092859 AGTTAGAAAT
30092869 TTTGGTAAACATTAGACATTTTGGTATTGGTATAACGTCATAAATTTTAGTATAAAGTTAAAAAA
1 TTTGGTAAACATTAGACATTTTGGTATTGGTATAACGTCATAAATTTTAGTATAAAGTTAAAAAA
30092934 ATTTATATGTCTATAAGCGCATAG
66 ATTTATATGTCTATAAGCGCATAG
* **
30092958 TTTGGTAAACATTAGACATTTTGGTATTGGTATAGCGTCATAAATTTTAGTATAAAGTTAAAATT
1 TTTGGTAAACATTAGACATTTTGGTATTGGTATAACGTCATAAATTTTAGTATAAAGTTAAAAAA
*
30093023 TTTTATATGTCTATAAGCGCATAG
66 ATTTATATGTCTATAAGCGCATAG
30093047 TT
1 TT
30093049 GAAACCCCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (89 bp):
TTTGGTAAACATTAGACATTTTGGTATTGGTATAACGTCATAAATTTTAGTATAAAGTTAAAAAA
ATTTATATGTCTATAAGCGCATAG
Found at i:30095296 original size:92 final size:92
Alignment explanation
Indices: 30095187--30095370 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
30095177 TATATATTTT
30095187 TTAAATTATTAAAAATCATATATATCTAATATATATCATTCATATATATTCTAAGTTAGTTTAAG
1 TTAAATTATTAAAAATCATATATATCTAATATATATCATTCATATATATTCTAAGTTAGTTTAAG
30095252 TTTTAATATATATTTAATTCTATTTAA
66 TTTTAATATATATTTAATTCTATTTAA
30095279 TTAAATTATTAAAAATCATATATATCTAATATATATCATTCATATATATTCTAAGTTAGTTTAAG
1 TTAAATTATTAAAAATCATATATATCTAATATATATCATTCATATATATTCTAAGTTAGTTTAAG
30095344 TTTTAATATATATTTAATTCTATTTAA
66 TTTTAATATATATTTAATTCTATTTAA
30095371 AATTGATCCC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (92 bp):
TTAAATTATTAAAAATCATATATATCTAATATATATCATTCATATATATTCTAAGTTAGTTTAAG
TTTTAATATATATTTAATTCTATTTAA
Found at i:30098125 original size:124 final size:123
Alignment explanation
Indices: 30097934--30098279 Score: 559
Period size: 123 Copynumber: 2.8 Consensus size: 123
30097924 TTTCGAGTTG
* *
30097934 ACGTTTCTAATCAAATAGTATAAAATCGCTTTTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
30097999 TCGCGCCCTCGTGGACGCGCTTTTGCTA-AGTAGGTCATGGAAGAAATAATTTTTTTTTC
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAAT--TTTTTTTTTC
* * *
30098058 ACGTTTCTGAGGAAATAGTATAAAATCGCTTCTAGTTGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* *
30098123 TCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAGAAATTTTTTTTTTG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATTTTTTTTTTC
* **
30098181 ACGTTTCTAAGCAAATAGTATAAAATGGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* *
30098246 TCGTGCCCTTGTGGACGCGCTTTTGCTACAGTAG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
30098280 CATGTTTGGG
Statistics
Matches: 205, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
123 99 0.48
124 88 0.43
125 18 0.09
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (123 bp):
ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATTTTTTTTTTC
Found at i:30102866 original size:22 final size:22
Alignment explanation
Indices: 30102838--30102890 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
30102828 TAAGAGGGGA
*
30102838 TAAAATATAAATTTTATGTGGC
1 TAAAATATAAATATTATGTGGC
* *
30102860 TAAAATACAAAATATTATGTGGT
1 TAAAATA-TAAATATTATGTGGC
*
30102883 TGAAATAT
1 TAAAATAT
30102891 GAAAATGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (22 bp):
TAAAATATAAATATTATGTGGC
Found at i:30102889 original size:23 final size:23
Alignment explanation
Indices: 30102838--30102881 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30102828 TAAGAGGGGA
* *
30102838 TAAAATA-TAAATTTTATGTGGC
1 TAAAATACAAAATATTATGTGGC
30102860 TAAAATACAAAATATTATGTGG
1 TAAAATACAAAATATTATGTGG
30102882 TTGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (23 bp):
TAAAATACAAAATATTATGTGGC
Found at i:30104265 original size:27 final size:27
Alignment explanation
Indices: 30104227--30104282 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
30104217 ATTGCTAAAC
30104227 TGCGAACTGTCCCATAGACACCTATAT
1 TGCGAACTGTCCCATAGACACCTATAT
* ** *
30104254 TGCGGACTGTCCTGTGGACACCTATAT
1 TGCGAACTGTCCCATAGACACCTATAT
30104281 TG
1 TG
30104283 TGGAAGGTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (27 bp):
TGCGAACTGTCCCATAGACACCTATAT
Found at i:30104302 original size:27 final size:27
Alignment explanation
Indices: 30104242--30104346 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 27
30104232 ACTGTCCCAT
** ** *
30104242 AGACACCTATATTGCGGACTGTCCTGT
1 AGACACCTATATTGTAGAAGGTCCTGC
* * *
30104269 GGACACCTATATTGTGGAAGGTCTTGC
1 AGACACCTATATTGTAGAAGGTCCTGC
* * *
30104296 A-ATCACCTATGTTGCAGAATGTCCTGC
1 AGA-CACCTATATTGTAGAAGGTCCTGC
*
30104323 AGACACCTATATTGTAGAATGTCC
1 AGACACCTATATTGTAGAAGGTCC
30104347 CATAGACATT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
26 1 0.02
27 60 0.97
28 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (27 bp):
AGACACCTATATTGTAGAAGGTCCTGC
Found at i:30104353 original size:27 final size:27
Alignment explanation
Indices: 30104234--30104354 Score: 75
Period size: 27 Copynumber: 4.5 Consensus size: 27
30104224 AACTGCGAAC
* *
30104234 TGTCCCATAGACACCTATATTGCGGAC
1 TGTCCCATAGACACCTATATTGCAGAA
** * **
30104261 TGTCCTGTGGACACCTATATTGTGGAA
1 TGTCCCATAGACACCTATATTGCAGAA
* * * *
30104288 GGTCTTGCA-A-TCACCTATGTTGCAGAA
1 TGTC--CCATAGACACCTATATTGCAGAA
*** *
30104315 TGTCCTGCAGACACCTATATTGTAGAA
1 TGTCCCATAGACACCTATATTGCAGAA
30104342 TGTCCCATAGACA
1 TGTCCCATAGACA
30104355 TTTAACCATG
Statistics
Matches: 66, Mismatches: 24, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
26 1 0.02
27 65 0.98
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (27 bp):
TGTCCCATAGACACCTATATTGCAGAA
Found at i:30123496 original size:27 final size:27
Alignment explanation
Indices: 30123454--30123507 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
30123444 ATTGTAAAGA
* *
30123454 AAGGAAAACTTTTTTCTTTTCCTCTCT
1 AAGGAAAAATTCTTTCTTTTCCTCTCT
30123481 AAGGAAAAATTCTTTCTTTTCCTCTCT
1 AAGGAAAAATTCTTTCTTTTCCTCTCT
30123508 TCTCACATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (27 bp):
AAGGAAAAATTCTTTCTTTTCCTCTCT
Found at i:30124696 original size:13 final size:14
Alignment explanation
Indices: 30124678--30124706 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30124668 AAAATTGCTT
30124678 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
30124691 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
30124705 AA
1 AA
30124707 GCCACTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:30125125 original size:12 final size:12
Alignment explanation
Indices: 30125108--30125135 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30125098 TCTTTTTTCT
30125108 TGTTTACAACAA
1 TGTTTACAACAA
30125120 TGTTTACAACAA
1 TGTTTACAACAA
30125132 TGTT
1 TGTT
30125136 AGCTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (12 bp):
TGTTTACAACAA
Found at i:30127095 original size:20 final size:20
Alignment explanation
Indices: 30127066--30127104 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30127056 ATTAAAATGC
*
30127066 TAACAGAGGCACCGAAGTGT
1 TAACAGAGGCACCAAAGTGT
*
30127086 TAACATAGGCACCAAAGTG
1 TAACAGAGGCACCAAAGTG
30127105 CAATCCCGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (20 bp):
TAACAGAGGCACCAAAGTGT
Found at i:30132165 original size:17 final size:15
Alignment explanation
Indices: 30132123--30132189 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 15
30132113 GTAAGTAATC
30132123 TAGATGTGAAAA-TA
1 TAGATGTGAAAACTA
*
30132137 TAGATTTGAAAACTA
1 TAGATGTGAAAACTA
*
30132152 TAGAACTGTGAAAAACTC
1 TAG-A-TGTG-AAAACTA
*
30132170 TAGATTGTGAAAACAA
1 TAGA-TGTGAAAACTA
30132186 TAGA
1 TAGA
30132190 AACTTTAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.26
15 5 0.12
16 10 0.23
17 8 0.19
18 9 0.21
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (15 bp):
TAGATGTGAAAACTA
Found at i:30135944 original size:126 final size:126
Alignment explanation
Indices: 30135719--30135972 Score: 472
Period size: 126 Copynumber: 2.0 Consensus size: 126
30135709 GCCGGGATTG
*
30135719 AAACGTGATGTGACAGAGTTTGTGGCAAGATGCTTGATGTGCCAACAAGTCAAGGCTGGACATCA
1 AAACGTGATGTGACAGAGTTTGTGGCAAGATGCTTGATGTGCCAACAAGTCAAGGCTGAACATCA
*
30135784 ATTTCCTTTAGGTTTGCTTTAGCAAATTCAAGTTCTTTAGTGGAAATGGGAACATATCACC
66 ATTTCCTTCAGGTTTGCTTTAGCAAATTCAAGTTCTTTAGTGGAAATGGGAACATATCACC
30135845 AAACGTGATGTGACAGAGTTTGTGGCAAGATGCTTGATGTGCCAACAAGTCAAGGCTGAACATCA
1 AAACGTGATGTGACAGAGTTTGTGGCAAGATGCTTGATGTGCCAACAAGTCAAGGCTGAACATCA
**
30135910 ATTTCCTTCAGGTTTGCTTTAGCCTATTCAAGTTCTTTAGTGGAAATGGGAACATATCACC
66 ATTTCCTTCAGGTTTGCTTTAGCAAATTCAAGTTCTTTAGTGGAAATGGGAACATATCACC
30135971 AA
1 AA
30135973 GGATTTTGTT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (126 bp):
AAACGTGATGTGACAGAGTTTGTGGCAAGATGCTTGATGTGCCAACAAGTCAAGGCTGAACATCA
ATTTCCTTCAGGTTTGCTTTAGCAAATTCAAGTTCTTTAGTGGAAATGGGAACATATCACC
Found at i:30147179 original size:23 final size:22
Alignment explanation
Indices: 30147127--30147180 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
30147117 GATTTATCAG
*
30147127 TATGGATATGTGTGGTATTGAAT
1 TATGG-TATGTCTGGTATTGAAT
*
30147150 TAAGGTATGTCTGAGTA-TGAATT
1 TATGGTATGTCTG-GTATTGAA-T
30147173 TATGGTAT
1 TATGGTAT
30147181 TATATTCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.43
Consensus pattern (22 bp):
TATGGTATGTCTGGTATTGAAT
Found at i:30148870 original size:50 final size:50
Alignment explanation
Indices: 30148767--30148959 Score: 206
Period size: 50 Copynumber: 3.7 Consensus size: 50
30148757 GGGAATGAGA
* *
30148767 TCCCATGTAAGACCAAGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
30148823 TCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*** * * **
30148873 TCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
30148923 TCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30148960 GTACAGAAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 79 0.68
53 3 0.03
55 1 0.01
56 34 0.29
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:30149225 original size:12 final size:12
Alignment explanation
Indices: 30149208--30149246 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30149198 ATGAGTTATT
30149208 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
30149220 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
30149232 TAAGTGAGTAAG
1 TAAGTAAGCAAG
30149244 TAA
1 TAA
30149247 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:30155565 original size:25 final size:25
Alignment explanation
Indices: 30155537--30155627 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
30155527 TCATGTACAT
*
30155537 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACGAGCTATGAATCG
* *
30155562 GTATGCTCACT-CAAGCTAT-AGATCA
1 GTATGCTCA-TACGAGCTATGA-ATCG
*
30155587 GTATGCTC-TCACGAGCTATAAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
*
30155612 GTATGCT-ACACGAGCT
1 GTATGCTCATACGAGCT
30155628 GTGGGTCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.02
24 8 0.15
25 43 0.80
26 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:30182429 original size:13 final size:13
Alignment explanation
Indices: 30182411--30182435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30182401 GTCATTATAT
30182411 CAATTCACTCTCA
1 CAATTCACTCTCA
30182424 CAATTCACTCTC
1 CAATTCACTCTC
30182436 CCAGTGTTTA
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
CAATTCACTCTCA
Found at i:30196866 original size:7 final size:7
Alignment explanation
Indices: 30196854--30196887 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
30196844 ATCAAATCAA
30196854 ATATTTT
1 ATATTTT
30196861 ATATTTT
1 ATATTTT
30196868 ATATTTT
1 ATATTTT
30196875 ATATTTT
1 ATATTTT
30196882 ATATTT
1 ATATTT
30196888 GGATGAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATATTTT
Found at i:30197014 original size:21 final size:21
Alignment explanation
Indices: 30196977--30197033 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
30196967 TTAATTTTTT
* *
30196977 TTATTTTTTATTATTTAATTAAG
1 TTATATTTTA-TATTT-ATAAAG
*
30197000 TT-TATTTTATATTTATAAAT
1 TTATATTTTATATTTATAAAG
30197020 TTATATTTTATATT
1 TTATATTTTATATT
30197034 ATTCTTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.20
21 16 0.53
22 6 0.20
23 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATATTTTATATTTATAAAG
Found at i:30197304 original size:22 final size:24
Alignment explanation
Indices: 30197270--30197321 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
30197260 GAGCTAAGCA
*
30197270 TTATTTAAATAAA-TACTCATA-T
1 TTATATAAATAAAGTACTCATATT
* *
30197292 TTATATAATTAAAGTATTCATATT
1 TTATATAAATAAAGTACTCATATT
30197316 TTATAT
1 TTATAT
30197322 CAAGCTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATATAAATAAAGTACTCATATT
Found at i:30197725 original size:19 final size:19
Alignment explanation
Indices: 30197701--30197746 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
30197691 ACTACAAAAC
30197701 ATTTATTA-T-TAATTAATAT
1 ATTTATTATTGTAA-TAA-AT
*
30197720 ATTTATAATTGTAATAAAT
1 ATTTATTATTGTAATAAAT
30197739 ATTTATTA
1 ATTTATTA
30197747 AAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 16 0.70
20 4 0.17
21 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTATTATTGTAATAAAT
Found at i:30197864 original size:16 final size:14
Alignment explanation
Indices: 30197838--30197882 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
30197828 AATATTGAAA
30197838 TATTAAATAATTTAT
1 TATT-AATAATTTAT
30197853 TAAATTAATAATTTA-
1 T--ATTAATAATTTAT
30197868 TATTAATAATTTAT
1 TATTAATAATTTAT
30197882 T
1 T
30197883 TTCTGATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 12 0.44
14 1 0.04
15 2 0.07
16 9 0.33
17 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTAATAATTTAT
Found at i:30199057 original size:22 final size:22
Alignment explanation
Indices: 30199032--30199075 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30199022 GTCACAACAT
30199032 TATGCACAGTTTATCAACTAAG
1 TATGCACAGTTTATCAACTAAG
30199054 TATGCACAGTTTATCAACTAAG
1 TATGCACAGTTTATCAACTAAG
30199076 GAGCGAACCT
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:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
TATGCACAGTTTATCAACTAAG
Found at i:30199663 original size:30 final size:31
Alignment explanation
Indices: 30199618--30199681 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
30199608 GATGAAAAAT
* * *
30199618 TAAAATATAAACTAAT-TAAATTAATTATCC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
* *
30199648 TAAAAAATAACCTAATGGAATTTAATTAACC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
30199679 TAA
1 TAA
30199682 GATATCCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (31 bp):
TAAAAAATAAACTAATGGAAATTAATTAACC
Found at i:30207413 original size:35 final size:35
Alignment explanation
Indices: 30207374--30207442 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
30207364 TTAAAGGTTG
30207374 TTGTTCCCTTTCTCTCTAAAGATATATCATATTTT
1 TTGTTCCCTTTCTCTCTAAAGATATATCATATTTT
*
30207409 TTGTTCCTTTTCTCTCTAAAGATATATCATATTT
1 TTGTTCCCTTTCTCTCTAAAGATATATCATATTT
30207443 ATTTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (35 bp):
TTGTTCCCTTTCTCTCTAAAGATATATCATATTTT
Found at i:30207587 original size:18 final size:18
Alignment explanation
Indices: 30207561--30207595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30207551 GCAAAAAATC
* *
30207561 ATTATAATTAGGATAATG
1 ATTAAAATTAAGATAATG
30207579 ATTAAAATTAAGATAAT
1 ATTAAAATTAAGATAAT
30207596 CCGCCAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
ATTAAAATTAAGATAATG
Found at i:30216762 original size:17 final size:17
Alignment explanation
Indices: 30216740--30216775 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
30216730 TATCTAACAT
*
30216740 CCTTCTTTTACGAATAC
1 CCTTCTTTTACGAAAAC
30216757 CCTTCTTTTACGAAAAC
1 CCTTCTTTTACGAAAAC
30216774 CC
1 CC
30216776 ATTTACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (17 bp):
CCTTCTTTTACGAAAAC
Found at i:30217682 original size:35 final size:35
Alignment explanation
Indices: 30217643--30217712 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
30217633 AACTTGCAAG
* *
30217643 CCATTTACATGGTGTCATTCCGAAGAGCCTGTAGA
1 CCATTTACATGGTGCCACTCCGAAGAGCCTGTAGA
* *
30217678 CCATTTACATGGTGCCGCTCCGAAGAGCTTGTAGA
1 CCATTTACATGGTGCCACTCCGAAGAGCCTGTAGA
30217713 TAACATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (35 bp):
CCATTTACATGGTGCCACTCCGAAGAGCCTGTAGA
Found at i:30220514 original size:50 final size:49
Alignment explanation
Indices: 30220439--30220540 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 49
30220429 AAACTTGGTA
* * *
30220439 GTTATCATTCTTTTTGGAAAGAATATAACGTTTTTTAATACTTTCCATAT
1 GTTATAATTATTTTTGGAAAGAATATAACG-TGTTTAATACTTTCCATAT
* *
30220489 GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTTCATGT
1 GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
30220538 GTT
1 GTT
30220541 CTCTATAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 19 0.40
50 28 0.60
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (49 bp):
GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
Found at i:30221833 original size:71 final size:71
Alignment explanation
Indices: 30221700--30221834 Score: 162
Period size: 71 Copynumber: 1.9 Consensus size: 71
30221690 TCATGACTTT
* ** * *
30221700 GATGGCAATATGCTCCCCCTTTGGACTCAAAGTTGGATGTTGCGAATTTAGCTTATGGATGTCGT
1 GATGGCAATATGCTCCCCCTTTGGAATCAAAGTTGGATGTCACGAATTTAGCTTAAGAATGTCGT
30221765 GACATC
66 GACATC
* ** ** * *
30221771 GATGGCAGTATGCTCTTCCTTTGGAATCAAAGTTGGATGTCACGGCTTTGGTTTAAGAATGTCG
1 GATGGCAATATGCTCCCCCTTTGGAATCAAAGTTGGATGTCACGAATTTAGCTTAAGAATGTCG
30221835 CAACATTATC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (71 bp):
GATGGCAATATGCTCCCCCTTTGGAATCAAAGTTGGATGTCACGAATTTAGCTTAAGAATGTCGT
GACATC
Found at i:30224535 original size:18 final size:18
Alignment explanation
Indices: 30224514--30224549 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30224504 TCTTCTCTTT
30224514 CTTTCTCTTCTTCAACAA
1 CTTTCTCTTCTTCAACAA
*
30224532 CTTTTTCTTCTTCAACAA
1 CTTTCTCTTCTTCAACAA
30224550 TGATTTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTTCTCTTCTTCAACAA
Found at i:30224556 original size:18 final size:18
Alignment explanation
Indices: 30224519--30224562 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
30224509 TCTTTCTTTC
*
30224519 TCTTCTTCAACAACTTTT
1 TCTTCTTCAACAACTATT
30224537 TCTTCTTCAACAA-TGATT
1 TCTTCTTCAACAACT-ATT
*
30224555 TCCTCTTC
1 TCTTCTTC
30224563 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (18 bp):
TCTTCTTCAACAACTATT
Found at i:30237646 original size:50 final size:53
Alignment explanation
Indices: 30237568--30237706 Score: 167
Period size: 56 Copynumber: 2.6 Consensus size: 53
30237558 CTACCAATGA
** *
30237568 CATGTCCCAGACATGGTCTTACGGGGGACCTCTC-ATCTC-GG-TGCCAACAC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATACCAACAC
***
30237618 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATACCAATGT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCA--ATCTC-AGGATACCAACAC
*
30237674 CATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
30237707 TTACCCAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
50 32 0.42
53 5 0.07
55 2 0.03
56 37 0.49
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (53 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATACCAACAC
Found at i:30237679 original size:56 final size:50
Alignment explanation
Indices: 30237519--30237706 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 50
30237509 ATGCCAAAGC
* ** * *
30237519 CATGTCCCAGACATGGTCTTACATGAGATGTTTCATGTAC--TACCAATGA
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTACCAATGA
** * *
30237568 CATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAA-CA
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTACCAATGA
*
30237617 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATACCAATGT
1 -CATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TACCAATGA
*
30237674 CATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
30237707 TTACCCAAAT
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
48 1 0.01
49 32 0.28
50 37 0.32
53 5 0.04
55 2 0.02
56 37 0.32
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTACCAATGA
Found at i:30241688 original size:18 final size:19
Alignment explanation
Indices: 30241661--30241696 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30241651 TAAAAATAAA
30241661 ATATACTTTTAT-ATTAAT
1 ATATACTTTTATAATTAAT
*
30241679 ATATATTTTTATAATTAA
1 ATATACTTTTATAATTAA
30241697 ATTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATACTTTTATAATTAAT
Found at i:30245819 original size:2 final size:2
Alignment explanation
Indices: 30245814--30245839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30245804 CATATATATC
30245814 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
30245840 CAAAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:30248569 original size:278 final size:279
Alignment explanation
Indices: 30248035--30248587 Score: 779
Period size: 278 Copynumber: 2.0 Consensus size: 279
30248025 AAAAATCTCA
* *
30248035 GTTTGAAAATAGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAATCGACCCGGTTTGTAATA
1 GTTTGAAAATAGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAACCAACCCGGTTTGTAATA
** * ** * *
30248100 TTTATAGCAATAAACCTTAATTGAATTCGTACATGTGTTTTTGACTTAGTGGACGTTCGTTGTTC
66 TTTATAGCAATAAACCTTAACCGAATTCGTACATATGTTTTCAACTTAGTGGACATTCATTGTTC
* * * * * *
30248165 TTGACTTTCAACCAAACGATCTTCTCCGCTTTTCTCGTACCACGAACTGCTTCGAGTGTAGGCTC
131 TCGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGTGTAGGCCC
* * *
30248230 GAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCTCTATTTTGGGTGAAAACGAAAA
196 AAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCCCTATTTGGGGTGAAAACGAAAA
30248295 TT-TTGTCTTTTTAATCCCG
261 TTCTT-TCTTTTTAATCCCG
* * * * * *
30248314 GTTTGAAAATGGTTTTCTTGCACAGCGAAAATTTAAAATTTTGAAAACCAACCTGGTTTGTGATA
1 GTTTGAAAATAGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAACCAACCCGGTTTGTAATA
*
30248379 TTTATAGCAATAAACCTTAACCGAATTCGTACTTATGTTTTCAACTTAGTGGACATTCATTGTTC
66 TTTATAGCAATAAACCTTAACCGAATTCGTACATATGTTTTCAACTTAGTGGACATTCATTGTTC
* * *
30248444 -CGAATTTCAACCAAACGATCTTCTCTGCTATTCTCATACTACGAACTACTTCGAGTGTGGGCCC
131 TCGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGTGTAGGCCC
* * * *
30248508 AAACCAATTGAATCGAAACACAGAACTAGAAAAAGTTTTCTCCCCT-TTTGGGGTGAAAACGAAA
196 AAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCT-CCCTATTTGGGGTGAAAACGAAA
30248572 ATTCTTTCTTTTTAAT
260 ATTCTTTCTTTTTAAT
30248588 AGAAATCGAT
Statistics
Matches: 240, Mismatches: 32, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
278 121 0.50
279 119 0.50
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (279 bp):
GTTTGAAAATAGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAACCAACCCGGTTTGTAATA
TTTATAGCAATAAACCTTAACCGAATTCGTACATATGTTTTCAACTTAGTGGACATTCATTGTTC
TCGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGTGTAGGCCC
AAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCCCTATTTGGGGTGAAAACGAAAA
TTCTTTCTTTTTAATCCCG
Found at i:30250129 original size:2 final size:2
Alignment explanation
Indices: 30250122--30250150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30250112 AATAAGCATG
30250122 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 T
30250151 GTAAATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30250278 original size:14 final size:14
Alignment explanation
Indices: 30250259--30250296 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
30250249 AAGGTATAAG
*
30250259 TATGTATATATGTA
1 TATGTATATATATA
30250273 TATGTATATATATA
1 TATGTATATATATA
30250287 TATGTATATA
1 TATGTATATA
30250297 ATGCTCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:30250279 original size:18 final size:18
Alignment explanation
Indices: 30250252--30250287 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30250242 TTAGATAAAG
*
30250252 GTATAAGTATGTATATAT
1 GTATAAGTATATATATAT
*
30250270 GTATATGTATATATATAT
1 GTATAAGTATATATATAT
30250288 ATGTATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (18 bp):
GTATAAGTATATATATAT
Found at i:30250656 original size:75 final size:75
Alignment explanation
Indices: 30250575--30250715 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
30250565 GCTTACATAT
* * * * * *
30250575 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATGTG-AGATTCGATTA
1 ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTATATAAGTATATG-GAAGATTCGATTA
30250639 TGCAGGTATAC
65 TGCAGGTATAC
* * *
30250650 ATGTATATGTTCTTGTAATAAATTTAAGTATGAAATTTATATATGTATATGGAAGATTCGATTAT
1 ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTATATAAGTATATGGAAGATTCGATTAT
30250715 G
66 G
30250716 TATATATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 1 0.02
75 55 0.98
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTATATAAGTATATGGAAGATTCGATTAT
GCAGGTATAC
Found at i:30250874 original size:41 final size:41
Alignment explanation
Indices: 30250797--30250876 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
30250787 TGATCGAATG
* * * **
30250797 TTTCAGACTTTATGTCTAGCAGGTTTGATATTGGTGAAATA
1 TTTCAGACTTTATATCTAGCAGGCTTAATACCGGTGAAATA
*
30250838 TTTCAGACTTTATATCTAGCAGGCTTAATGCCGGTGAAA
1 TTTCAGACTTTATATCTAGCAGGCTTAATACCGGTGAAA
30250877 CAATTCGGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (41 bp):
TTTCAGACTTTATATCTAGCAGGCTTAATACCGGTGAAATA
Found at i:30251111 original size:33 final size:34
Alignment explanation
Indices: 30251064--30251137 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
30251054 GATAGGCATA
** *
30251064 TGTATATATGCATTCAGCTATTCGTG-TTTAAAG
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
* *
30251097 TGTATATACACATTCGGCTATTCATGTTTTAAAT
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
30251131 TGTATAT
1 TGTATAT
30251138 GCATTCGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATATACACATTCAGCTATTCATGTTTTAAAG
Found at i:30257882 original size:10 final size:10
Alignment explanation
Indices: 30257867--30257891 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30257857 TCAAATAAGC
30257867 ATGTATATAT
1 ATGTATATAT
30257877 ATGTATATAT
1 ATGTATATAT
30257887 ATGTA
1 ATGTA
30257892 AATTTCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (10 bp):
ATGTATATAT
Found at i:30258006 original size:6 final size:6
Alignment explanation
Indices: 30257995--30258058 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
30257985 AAAGTTATGA
30257995 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
30258043 GTATAT GTATAT GTAT
1 GTATAT GTATAT GTAT
30258059 TTAACGCTCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:30258468 original size:75 final size:75
Alignment explanation
Indices: 30258336--30258476 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 75
30258326 TCTTACATAT
* * * * * *
30258336 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGATTCAATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGAAAATTTATATAAGTGTATATGAGATTCAATTAT
30258401 GCAGGTATAC
66 GCAGGTATAC
* * *
30258411 ATGTATATGTTCTTGTAATGAATTTAAGTATAAAATTTATAT-A-TGTATATGGAAGATTCGATT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGAAAATTTATATAAGTGTATAT-G-AGATTCAATT
30258474 ATG
64 ATG
30258477 TATATATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 2 0.04
75 47 0.85
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAAGAAAATTTATATAAGTGTATATGAGATTCAATTAT
GCAGGTATAC
Done.