Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 16 of 17
Found at i:2892666 original size:20 final size:20
Alignment explanation
Indices: 2892643--2892681 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2892633 ATAAATATAT
2892643 AATA-TTCAAAATATTTAAAA
1 AATATTTCAAAA-ATTTAAAA
*
2892663 AATATTTTAAAAATTTAAA
1 AATATTTCAAAAATTTAAA
2892682 TATACTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATTTCAAAAATTTAAAA
Found at i:2895941 original size:13 final size:13
Alignment explanation
Indices: 2895925--2895949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2895915 ATAATTATAA
2895925 TAAATATTAATTC
1 TAAATATTAATTC
2895938 TAAATATTAATT
1 TAAATATTAATT
2895950 AAAAAATTAA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTAATTC
Found at i:2896598 original size:22 final size:21
Alignment explanation
Indices: 2896573--2896622 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2896563 TTTCAAATTG
2896573 ATATATAAAATTTATTAATTAT
1 ATATATAAAATTTA-TAATTAT
** *
2896595 ATATAT-ATTTTTATAATTTT
1 ATATATAAAATTTATAATTAT
2896615 ATATATAA
1 ATATATAA
2896623 CTAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 6 0.25
22 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATAAAATTTATAATTAT
Found at i:2896611 original size:20 final size:21
Alignment explanation
Indices: 2896583--2896621 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2896573 ATATATAAAA
2896583 TTTATTAATTATATATATATT
1 TTTATTAATTATATATATATT
*
2896604 TTTA-TAATTTTATATATA
1 TTTATTAATTATATATATA
2896622 ACTAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTAATTATATATATATT
Found at i:2901091 original size:32 final size:33
Alignment explanation
Indices: 2901051--2901123 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
2901041 AAAATATTAA
*
2901051 TTAT-TTATATAAATTTTAATATATTAATA-AT
1 TTATATTATATAAATTTTAATACATTAATATAT
* * *
2901082 TTATATTATATAAATTTTGATACGTTCATATAT
1 TTATATTATATAAATTTTAATACATTAATATAT
2901115 TTATATTAT
1 TTATATTAT
2901124 TTTTATGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 4 0.11
32 21 0.58
33 11 0.31
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (33 bp):
TTATATTATATAAATTTTAATACATTAATATAT
Found at i:2901134 original size:11 final size:11
Alignment explanation
Indices: 2901114--2901163 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2901104 CGTTCATATA
2901114 TTTATATTATT
1 TTTATATTATT
*
2901125 TTTATGTTATTAT
1 TTTATATTA-T-T
2901138 TTTATATTATAT
1 TTTATATTAT-T
2901150 TTTA-ATT-TT
1 TTTATATTATT
2901159 TTTAT
1 TTTAT
2901164 TAAATTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
9 5 0.15
10 1 0.03
11 11 0.32
12 8 0.24
13 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2901142 original size:13 final size:13
Alignment explanation
Indices: 2901114--2901153 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2901104 CGTTCATATA
2901114 TTTATATTA-T-T
1 TTTATATTATTAT
*
2901125 TTTATGTTATTAT
1 TTTATATTATTAT
2901138 TTTATATTA-TAT
1 TTTATATTATTAT
2901150 TTTA
1 TTTA
2901154 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.32
12 8 0.32
13 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTATATTATTAT
Found at i:2905265 original size:209 final size:209
Alignment explanation
Indices: 2904898--2905306 Score: 631
Period size: 209 Copynumber: 2.0 Consensus size: 209
2904888 GTCAAACTAA
*
2904898 TACATTCGCCAATATTTTCAGGTGAAACAAAATTAAGTGCAACATTTATGCAAGACTGTTGAGCA
1 TACATTCGCCAATATTTTCAGGTGAAACAAAATTAAGTGCAACATTTATGCAAGACTCTTGAGCA
* * *
2904963 TTGAGACAATAACATCAAAACAGTATAAGCCTAACCATATTGACTGGTACACCAACAGAAATCAA
66 CTGAGACAACAACATCAAAACAGTATAAGCCTAACCATATTGACTGGTACACCAACAGAAACCAA
* * * * *
2905028 ATTCATTCATAACAACAAGCTAGAAAATCACAGCATTTATCATTTCGTTCGAAGCAACTATTTTT
131 ATTCATCCATAACAACAAGATAGAAAATCACAGCATTTATCACTTCATTCGAAACAACTATTTTT
2905093 GATGGCAGGCAAAG
196 GATGGCAGGCAAAG
*
2905107 TACATTCGCCAATATTTTCAGGTGAATCAAAATTAAGTGCAACATTTATGCAAGACTCTTGAGCA
1 TACATTCGCCAATATTTTCAGGTGAAACAAAATTAAGTGCAACATTTATGCAAGACTCTTGAGCA
* * *
2905172 CTGAGACAACAGCATCGGAAA-AGTATAAGCCTAACCATATTGACTGGTTCACCAACAGAAACCA
66 CTGAGACAACAACATC-AAAACAGTATAAGCCTAACCATATTGACTGGTACACCAACAGAAACCA
** * * * *
2905236 AATTCATCCATTGCAACTAGATGGAAAATCACAGCCTTTATCACTTCATTCGAAACAACTGTTTT
130 AATTCATCCATAACAACAAGATAGAAAATCACAGCATTTATCACTTCATTCGAAACAACTATTTT
2905301 TGATGG
195 TGATGG
2905307 GCATAGTACA
Statistics
Matches: 180, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
209 177 0.98
210 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (209 bp):
TACATTCGCCAATATTTTCAGGTGAAACAAAATTAAGTGCAACATTTATGCAAGACTCTTGAGCA
CTGAGACAACAACATCAAAACAGTATAAGCCTAACCATATTGACTGGTACACCAACAGAAACCAA
ATTCATCCATAACAACAAGATAGAAAATCACAGCATTTATCACTTCATTCGAAACAACTATTTTT
GATGGCAGGCAAAG
Found at i:2906899 original size:3 final size:3
Alignment explanation
Indices: 2906891--2906943 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
2906881 TTCATCCTCG
*
2906891 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2906939 TCT TC
1 TCT TC
2906944 ATGTTTCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:2908105 original size:25 final size:25
Alignment explanation
Indices: 2908054--2908103 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2908044 AAAAATTTAA
*
2908054 AAATATTTTTATAATATTTATATTT
1 AAATATTTTTATAATATTAATATTT
2908079 AAATATTTTT-TAATTATTAAATATT
1 AAATATTTTTATAA-TATT-AATATT
2908104 AATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATATTTTTATAATATTAATATTT
Found at i:2909421 original size:21 final size:21
Alignment explanation
Indices: 2909397--2909437 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2909387 TTTTTTTGTT
2909397 AATTGT-CTTCTTTTAAAAAAA
1 AATTGTGCTT-TTTTAAAAAAA
*
2909418 AATTGTGCTTTTTTACAAAA
1 AATTGTGCTTTTTTAAAAAA
2909438 TAGTAACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTGTGCTTTTTTAAAAAAA
Found at i:2915384 original size:13 final size:13
Alignment explanation
Indices: 2915347--2915402 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
2915337 ATTTTAAACT
*
2915347 AAATTT-TATTAA
1 AAATTTATATTTA
2915359 ATAATTTATTATTTA
1 A-AATTTA-TATTTA
2915374 AAATTTATATTTA
1 AAATTTATATTTA
* *
2915387 TAATTGAT-TTTA
1 AAATTTATATTTA
2915399 AAAT
1 AAAT
2915403 AAATTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 8 0.22
13 17 0.46
14 6 0.16
15 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
AAATTTATATTTA
Found at i:2915527 original size:12 final size:12
Alignment explanation
Indices: 2915510--2915572 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
2915500 ATTGACATAA
2915510 AATATATAAATT
1 AATATATAAATT
*
2915522 AATATATAGATT
1 AATATATAAATT
* *
2915534 AATTTTTAAA-T
1 AATATATAAATT
*
2915545 AACTCATTTAAATT
1 AA-T-ATATAAATT
2915559 AA-A-ATAAATT
1 AATATATAAATT
2915569 AATA
1 AATA
2915573 AAATAAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.20
11 5 0.12
12 19 0.46
13 6 0.15
14 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (12 bp):
AATATATAAATT
Found at i:2917840 original size:22 final size:21
Alignment explanation
Indices: 2917813--2917854 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2917803 TATGAGATTT
*
2917813 ATTTAACTTATAAAAATAAAAA
1 ATTTAAATT-TAAAAATAAAAA
*
2917835 ATTTAAATTTATAAATAAAA
1 ATTTAAATTTAAAAATAAAA
2917855 GTTTCTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAATTTAAAAATAAAAA
Found at i:2918308 original size:22 final size:21
Alignment explanation
Indices: 2918270--2918315 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
2918260 AGTAATGTCG
*
2918270 AAATTATAGTTTAATAATTAT
1 AAATTATAGTTTAATAATAAT
2918291 AAATTA-AGTTATAGATAATAAT
1 AAATTATAGTT-TA-ATAATAAT
2918313 AAA
1 AAA
2918316 AAATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATTATAGTTTAATAATAAT
Found at i:2919359 original size:30 final size:28
Alignment explanation
Indices: 2919315--2919370 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
2919305 TCTTTCATTT
*
2919315 TCTTTTCGTTTCTTTTTTCTTTATTTTTA
1 TCTTTTCGTTTCTTTCTTC-TTATTTTTA
*
2919344 TCTTTGTCTTTTCTTTCTTCTTATTTT
1 TCTTT-TCGTTTCTTTCTTCTTATTTT
2919371 CTTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (28 bp):
TCTTTTCGTTTCTTTCTTCTTATTTTTA
Found at i:2919375 original size:5 final size:5
Alignment explanation
Indices: 2919272--2919388 Score: 55
Period size: 5 Copynumber: 22.4 Consensus size: 5
2919262 TTTTCTCATC
* **
2919272 TTTC- TTTCT TTTCT GTTT-T TTTTT TTTAG TTTCT CTTTCAT TTTCT
1 TTTCT TTTCT TTTCT -TTTCT TTTCT TTTCT TTTCT -TTTC-T TTTCT
* * *
2919318 TTTCGT TTCTTT TTTCT TTATTT TTATCT TTGTCT TTTC- TTTCT TCTTAT
1 TTTC-T TT-TCT TTTCT TT-TCT TT-TCT TT-TCT TTTCT TTTCT T-TTCT
2919368 TTTCT TTT-T TTT-T ATTTCT TT
1 TTTCT TTTCT TTTCT -TTTCT TT
2919389 ATATATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 23
0.73 0.09 0.19
Matches are distributed among these distances:
4 16 0.18
5 36 0.40
6 36 0.40
7 2 0.02
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:2919390 original size:23 final size:23
Alignment explanation
Indices: 2919290--2919411 Score: 59
Period size: 27 Copynumber: 4.7 Consensus size: 23
2919280 TTTTCTGTTT
2919290 TTTTTTTTTAGTTTCTCTTTCATTTTC
1 TTTTTTTTTA--TT-TCTTT-ATTTTC
*
2919317 TTTTCGTTTCTTTTTTCTTTATTTTTATC
1 TTTT--TTT-TTATTTCTTTA--TTT-TC
* *
2919346 TTTGTCTTTTCTTTCTTCTTATTTTC
1 TTT-TTTTTTATTTC-T-TTATTTTC
2919372 TTTTTTTTTATTTCTTTATATATT-
1 TTTTTTTTTATTTCTTTAT-T-TTC
*
2919396 TTTTTCTTT-TTTCTTT
1 TTTTTTTTTATTTCTTT
2919412 CTATAATAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
23 11 0.14
24 10 0.13
25 11 0.14
26 6 0.08
27 18 0.23
28 8 0.10
29 11 0.14
30 3 0.04
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTTTTTTATTTCTTTATTTTC
Found at i:2919416 original size:23 final size:22
Alignment explanation
Indices: 2919372--2919416 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2919362 TCTTATTTTC
2919372 TTTTTTTTTATTTCTTTATATA
1 TTTTTTTTTATTTCTTTATATA
* *
2919394 TTTTTTTCTTTTTTCTTTCTATA
1 TTTTTTT-TTATTTCTTTATATA
2919417 ATAAAATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTTTATTTCTTTATATA
Found at i:2919416 original size:25 final size:25
Alignment explanation
Indices: 2919311--2919416 Score: 63
Period size: 27 Copynumber: 4.0 Consensus size: 25
2919301 TTTCTCTTTC
* *
2919311 ATTTTCTTTTCGTTTCTTTTTTCTTTAT
1 ATTTTCTTTT--TTT-TTCTTTCTATAT
* * *
2919339 TTTTATCTTTGTCTTTTCTTTCT-TCTT
1 ATTT-TCTTT-TTTTTTCTTTCTAT-AT
*
2919366 ATTTTCTTTTTTTTTATTTCTTTATAT
1 ATTTTCTTTTTTTTTCTTTC--TATAT
2919393 ATTTT-TTTCTTTTTTCTTTCTATA
1 ATTTTCTTT-TTTTTTCTTTCTATA
2919417 ATAAAATGAG
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
25 13 0.21
26 9 0.15
27 28 0.45
28 6 0.10
29 5 0.08
30 1 0.02
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.75
Consensus pattern (25 bp):
ATTTTCTTTTTTTTTCTTTCTATAT
Found at i:2921151 original size:6 final size:6
Alignment explanation
Indices: 2921113--2921142 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2921103 TTTATAAATG
*
2921113 AATTTA AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
2921143 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:2921246 original size:24 final size:24
Alignment explanation
Indices: 2921198--2921244 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2921188 AAATATTAAA
2921198 ATATTATATTTCATATTAATATTT
1 ATATTATATTTCATATTAATATTT
*
2921222 ATATTATTTTTACA-ATTAA-ATTT
1 ATATTATATTT-CATATTAATATTT
2921245 TAAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 15 0.71
25 2 0.10
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTATATTTCATATTAATATTT
Found at i:2922199 original size:18 final size:18
Alignment explanation
Indices: 2922185--2922219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2922175 AAAAATATAT
2922185 AAATAAATTTTAATATTA
1 AAATAAATTTTAATATTA
* *
2922203 AAATAATTTTTAGTATT
1 AAATAAATTTTAATATT
2922220 TTTTAAACAA
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATAAATTTTAATATTA
Found at i:2926410 original size:2 final size:2
Alignment explanation
Indices: 2926403--2926436 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2926393 CTAGCATGTG
2926403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2926437 AGACAAATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2926903 original size:4 final size:4
Alignment explanation
Indices: 2926894--2926918 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2926884 TATTATGTCC
2926894 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
2926919 GATTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2927913 original size:8 final size:8
Alignment explanation
Indices: 2927900--2927933 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
2927890 TGTGAATAAG
2927900 TTTTATAT
1 TTTTATAT
2927908 TTTTATA-
1 TTTTATAT
2927915 TTTTATAT
1 TTTTATAT
2927923 TTTT-TAT
1 TTTTATAT
2927930 TTTT
1 TTTT
2927934 GATTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATAT
Found at i:2927933 original size:15 final size:15
Alignment explanation
Indices: 2927900--2927932 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2927890 TGTGAATAAG
2927900 TTTTATATTTTTATA
1 TTTTATATTTTTATA
2927915 TTTTATATTTTT-TA
1 TTTTATATTTTTATA
2927929 TTTT
1 TTTT
2927933 TGATTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTTATA
Found at i:2928286 original size:17 final size:17
Alignment explanation
Indices: 2928266--2928301 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2928256 ATTAAAAAAG
2928266 AAAAAAAATTGAAAATT
1 AAAAAAAATTGAAAATT
*
2928283 AAAAATAATTGAAAATT
1 AAAAAAAATTGAAAATT
2928300 AA
1 AA
2928302 CAACAAATAA
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:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAAAAAATTGAAAATT
Found at i:2928588 original size:16 final size:18
Alignment explanation
Indices: 2928553--2928590 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2928543 CATATTTTTT
2928553 AAATATATTTAAAAATAA
1 AAATATATTTAAAAATAA
*
2928571 AAAT-TATTTATAAA-AA
1 AAATATATTTAAAAATAA
2928587 AAAT
1 AAAT
2928591 GTGGTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATATTTAAAAATAA
Found at i:2932551 original size:17 final size:16
Alignment explanation
Indices: 2932529--2932563 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2932519 GGGTAATTTT
2932529 TTAAAAACATATAAATA
1 TTAAAAA-ATATAAATA
*
2932546 TTAAAAAGTATAAATA
1 TTAAAAAATATAAATA
2932562 TT
1 TT
2932564 TTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAAAAATATAAATA
Found at i:2933843 original size:19 final size:19
Alignment explanation
Indices: 2933821--2933865 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2933811 TAATAATGTT
*
2933821 TTAAAAAATTA-TCTACTTC
1 TTAAAAAAATACTC-ACTTC
*
2933840 TTAAAAAAATACTCATTTC
1 TTAAAAAAATACTCACTTC
2933859 TTAAAAA
1 TTAAAAA
2933866 CTACTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAAAATACTCACTTC
Found at i:2936117 original size:2 final size:2
Alignment explanation
Indices: 2936110--2936141 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2936100 GTTGTTACAT
2936110 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2936142 GCAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2940402 original size:16 final size:15
Alignment explanation
Indices: 2940381--2940415 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
2940371 TAAATTCACT
2940381 AATATTATTTTTTAAA
1 AATATT-TTTTTTAAA
2940397 AATA-TTTTTTTAAA
1 AATATTTTTTTTAAA
2940411 AATAT
1 AATAT
2940416 AATCTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 13 0.72
15 1 0.06
16 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTTTTTTTAAA
Found at i:2940407 original size:14 final size:14
Alignment explanation
Indices: 2940388--2940415 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2940378 ACTAATATTA
2940388 TTTTTTAAAAATAT
1 TTTTTTAAAAATAT
2940402 TTTTTTAAAAATAT
1 TTTTTTAAAAATAT
2940416 AATCTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTTAAAAATAT
Found at i:2940540 original size:20 final size:22
Alignment explanation
Indices: 2940494--2940543 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
2940484 TTACATTGTG
* *
2940494 ATATTATATATATTTATTCTTT
1 ATATGATATATATGTATTCTTT
*
2940516 GTATGATATATATGTA-T-TTT
1 ATATGATATATATGTATTCTTT
2940536 ATATGATA
1 ATATGATA
2940544 AAAATAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (22 bp):
ATATGATATATATGTATTCTTT
Found at i:2940577 original size:21 final size:20
Alignment explanation
Indices: 2940535--2940583 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2940525 ATATGTATTT
*
2940535 TATATGATAAAAATAATATAA
1 TATAT-ATAAAAATAAAATAA
*
2940556 TATATATAAATATAAAACTAA
1 TATATATAAAAATAAAA-TAA
2940577 TATATAT
1 TATATAT
2940584 TATATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TATATATAAAAATAAAATAA
Found at i:2940577 original size:26 final size:26
Alignment explanation
Indices: 2940541--2940598 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2940531 ATTTTATATG
2940541 ATAAAAATAATATA-ATATATATAAAT
1 ATAAAAATAATATATAT-TATATAAAT
*
2940567 ATAAAACTAATATATATTATAT-AAT
1 ATAAAAATAATATATATTATATAAAT
2940592 -TAAAAAT
1 ATAAAAAT
2940599 GAGCTAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.21
25 3 0.10
26 18 0.62
27 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAAAAATAATATATATTATATAAAT
Found at i:2941131 original size:32 final size:30
Alignment explanation
Indices: 2941095--2941199 Score: 81
Period size: 29 Copynumber: 3.5 Consensus size: 30
2941085 AAATATACCG
2941095 TAAAAA-ATAATTAAAAATATAATATTAAAATA
1 TAAAAATATAATT-AAAAT-TAATA-TAAAATA
* *
2941127 TAAAAATTTTAATTAAAATTAATATAAAATT
1 TAAAAA-TATAATTAAAATTAATATAAAATA
** * * *
2941158 TATCAATAT-ATCAAAATTTATATATAATA
1 TAAAAATATAATTAAAATTAATATAAAATA
*
2941187 T-TAAATATAATTA
1 TAAAAATATAATTA
2941200 TAATAAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.10
29 20 0.34
30 2 0.03
31 10 0.17
32 11 0.19
33 5 0.08
34 5 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAAAATATAATTAAAATTAATATAAAATA
Found at i:2941596 original size:9 final size:9
Alignment explanation
Indices: 2941582--2941627 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
2941572 AAGGCTTCAG
2941582 AGAAAATAA
1 AGAAAATAA
2941591 AGAAAATAA
1 AGAAAATAA
2941600 AGGAAAA-AA
1 A-GAAAATAA
* *
2941609 CGAATA-AA
1 AGAAAATAA
2941617 AGAAAATAA
1 AGAAAATAA
2941626 AG
1 AG
2941628 GAACAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 10 0.32
9 16 0.52
10 5 0.16
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (9 bp):
AGAAAATAA
Found at i:2943005 original size:15 final size:16
Alignment explanation
Indices: 2942972--2943002 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2942962 TAGAGTCATT
*
2942972 TAAATCAATTTAAAAA
1 TAAATCAAGTTAAAAA
2942988 TAAATCAAGTTAAAA
1 TAAATCAAGTTAAAA
2943003 TAATAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAATCAAGTTAAAAA
Found at i:2943009 original size:18 final size:16
Alignment explanation
Indices: 2942972--2943010 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2942962 TAGAGTCATT
*
2942972 TAAATCAATTTAAAAA
1 TAAATCAATTAAAAAA
2942988 TAAATCAAGTTAAAATAA
1 TAAATCAA-TTAAAA-AA
2943006 TAAAT
1 TAAAT
2943011 AGTAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 5 0.25
18 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAATCAATTAAAAAA
Found at i:2943124 original size:23 final size:25
Alignment explanation
Indices: 2943098--2943144 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2943088 TAAAAGATAA
*
2943098 ATTATTTA-ATGTGGATAA-CTTAT
1 ATTATTTACATATGGATAATCTTAT
2943121 ATTATTTACATATGGATAATCTTA
1 ATTATTTACATATGGATAATCTTA
2943145 AAAAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 9 0.43
25 4 0.19
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (25 bp):
ATTATTTACATATGGATAATCTTAT
Found at i:2945163 original size:12 final size:11
Alignment explanation
Indices: 2945142--2945176 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2945132 CAGTTCATCG
2945142 AAATATTTTTT
1 AAATATTTTTT
2945153 AAATGATTTTTT
1 AAAT-ATTTTTT
*
2945165 ATATATTTTTT
1 AAATATTTTTT
2945176 A
1 A
2945177 TTTAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:2945448 original size:23 final size:23
Alignment explanation
Indices: 2945414--2945460 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
2945404 AATTAAAACT
2945414 ATTTAAAAATTAAATA-AATATA
1 ATTTAAAAATTAAATATAATATA
2945436 ATTTAAAAAATTAAATATAATATA
1 ATTT-AAAAATTAAATATAATATA
2945460 A
1 A
2945461 ACCGATACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTAAAAATTAAATATAATATA
Found at i:2946929 original size:16 final size:16
Alignment explanation
Indices: 2946890--2946931 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
2946880 TCATTAATAC
* *
2946890 TTTTAAATTATTATTT
1 TTTTAAAATATAATTT
2946906 TTTCTAAAATATAATTT
1 TTT-TAAAATATAATTT
2946923 TTTTAAAAT
1 TTTTAAAAT
2946932 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAAAATATAATTT
Found at i:2946939 original size:16 final size:15
Alignment explanation
Indices: 2946890--2946942 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2946880 TCATTAATAC
*
2946890 TTTTAAATTATTATTT
1 TTTTAAAATATT-TTT
*
2946906 TTTCTAAAATATAATTT
1 TTT-TAAAATAT-TTTT
2946923 TTTTAAAATCATTTTT
1 TTTTAAAAT-ATTTTT
2946939 TTTT
1 TTTT
2946943 TGCATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAAATATTTTT
Found at i:2946940 original size:17 final size:16
Alignment explanation
Indices: 2946890--2946943 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2946880 TCATTAATAC
*
2946890 TTTTAAATTATTATTTT
1 TTTTAAAATATT-TTTT
* **
2946907 TTCTAAAATATAATTT
1 TTTTAAAATATTTTTT
2946923 TTTTAAAATCATTTTTT
1 TTTTAAAAT-ATTTTTT
2946940 TTTT
1 TTTT
2946944 GCATTTTATG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAAATATTTTTT
Found at i:2947553 original size:36 final size:37
Alignment explanation
Indices: 2947487--2947559 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
2947477 ATAAATATGT
* * *
2947487 TTATTAGTTTTAATTTTAAAATAATAAAACATAAATA
1 TTATTAGTTATAATTATAAAATAATAAAACAAAAATA
2947524 TTATTAGTTAT-ATTAT-AAATAAATAAAACAAAAATA
1 TTATTAGTTATAATTATAAAAT-AATAAAACAAAAATA
2947560 ATAATATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 4 0.12
36 18 0.56
37 10 0.31
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (37 bp):
TTATTAGTTATAATTATAAAATAATAAAACAAAAATA
Found at i:2948927 original size:39 final size:38
Alignment explanation
Indices: 2948865--2948953 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 38
2948855 ATATTCTATC
2948865 AATGAATCAGATATATCACCTAATTAAAAGATTTTAAA
1 AATGAATCAGATATATCACCTAATTAAAAGATTTTAAA
2948903 AATGAATCAGATGATATCACCTAATTAAAAGATTTTAAA
1 AATGAATCAGAT-ATATCACCTAATTAAAAGATTTTAAA
*
2948942 AATAAATACAGA
1 AATGAAT-CAGA
2948954 ATCGAGACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 12 0.25
39 32 0.67
40 4 0.08
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (38 bp):
AATGAATCAGATATATCACCTAATTAAAAGATTTTAAA
Found at i:2950008 original size:538 final size:538
Alignment explanation
Indices: 2948991--2950065 Score: 2150
Period size: 538 Copynumber: 2.0 Consensus size: 538
2948981 AAAAACTCAT
2948991 GTCATATACGAGAAAATAAAGAACAAAAACATGATCAAAACACTCAGTTTATGTCTACACTAACC
1 GTCATATACGAGAAAATAAAGAACAAAAACATGATCAAAACACTCAGTTTATGTCTACACTAACC
2949056 ACAGTTCTAAATAGCGGTCTCGGATTTTGCAGCAGATGTGATTGGGGTGTCTAACCCTCAATACC
66 ACAGTTCTAAATAGCGGTCTCGGATTTTGCAGCAGATGTGATTGGGGTGTCTAACCCTCAATACC
2949121 TAAGGCACCTGAATTTAGCTCCATCTCCTTTTATCCTCCTCCTCGTCCACAGGAGTATACCACGA
131 TAAGGCACCTGAATTTAGCTCCATCTCCTTTTATCCTCCTCCTCGTCCACAGGAGTATACCACGA
2949186 TGGTCTTCGCTTTGAGTTGCTTAACCTGTAGTTCAACAGCACTTCTTCATTACAAAGTGCTGTAG
196 TGGTCTTCGCTTTGAGTTGCTTAACCTGTAGTTCAACAGCACTTCTTCATTACAAAGTGCTGTAG
2949251 TAGCCACCAAAACAAGAGTCTTTAATACAGGACCATCTGACCCACCATTTCTTGAGCCCCATCTG
261 TAGCCACCAAAACAAGAGTCTTTAATACAGGACCATCTGACCCACCATTTCTTGAGCCCCATCTG
2949316 AACCAAAAGCTGCCAAATCTCCTCATGTTTACTTCTTCGGCATTTCCAAATGATATATTTGGAAT
326 AACCAAAAGCTGCCAAATCTCCTCATGTTTACTTCTTCGGCATTTCCAAATGATATATTTGGAAT
2949381 ATAAGCTCTCATCTCTTTTTCATTCAGTGGGAAGTCATAAGGGCAAACCATCACGTTTGGCACCA
391 ATAAGCTCTCATCTCTTTTTCATTCAGTGGGAAGTCATAAGGGCAAACCATCACGTTTGGCACCA
2949446 TTTCTTTAGCCGGGTGATTGGCGAAATGGGCCAAAGCTAAAGGGTTCCTGCGTTCCAAAATTTCA
456 TTTCTTTAGCCGGGTGATTGGCGAAATGGGCCAAAGCTAAAGGGTTCCTGCGTTCCAAAATTTCA
2949511 CCACCACTCCCCACTCGA
521 CCACCACTCCCCACTCGA
2949529 GTCATATACGAGAAAATAAAGAACAAAAACATGATCAAAACACTCAGTTTATGTCTACACTAACC
1 GTCATATACGAGAAAATAAAGAACAAAAACATGATCAAAACACTCAGTTTATGTCTACACTAACC
2949594 ACAGTTCTAAATAGCGGTCTCGGATTTTGCAGCAGATGTGATTGGGGTGTCTAACCCTCAATACC
66 ACAGTTCTAAATAGCGGTCTCGGATTTTGCAGCAGATGTGATTGGGGTGTCTAACCCTCAATACC
2949659 TAAGGCACCTGAATTTAGCTCCATCTCCTTTTATCCTCCTCCTCGTCCACAGGAGTATACCACGA
131 TAAGGCACCTGAATTTAGCTCCATCTCCTTTTATCCTCCTCCTCGTCCACAGGAGTATACCACGA
2949724 TGGTCTTCGCTTTGAGTTGCTTAACCTGTAGTTCAACAGCACTTCTTCATTACAAAGTGCTGTAG
196 TGGTCTTCGCTTTGAGTTGCTTAACCTGTAGTTCAACAGCACTTCTTCATTACAAAGTGCTGTAG
2949789 TAGCCACCAAAACAAGAGTCTTTAATACAGGACCATCTGACCCACCATTTCTTGAGCCCCATCTG
261 TAGCCACCAAAACAAGAGTCTTTAATACAGGACCATCTGACCCACCATTTCTTGAGCCCCATCTG
2949854 AACCAAAAGCTGCCAAATCTCCTCATGTTTACTTCTTCGGCATTTCCAAATGATATATTTGGAAT
326 AACCAAAAGCTGCCAAATCTCCTCATGTTTACTTCTTCGGCATTTCCAAATGATATATTTGGAAT
2949919 ATAAGCTCTCATCTCTTTTTCATTCAGTGGGAAGTCATAAGGGCAAACCATCACGTTTGGCACCA
391 ATAAGCTCTCATCTCTTTTTCATTCAGTGGGAAGTCATAAGGGCAAACCATCACGTTTGGCACCA
2949984 TTTCTTTAGCCGGGTGATTGGCGAAATGGGCCAAAGCTAAAGGGTTCCTGCGTTCCAAAATTTCA
456 TTTCTTTAGCCGGGTGATTGGCGAAATGGGCCAAAGCTAAAGGGTTCCTGCGTTCCAAAATTTCA
2950049 CCACCACTCCCCACTCG
521 CCACCACTCCCCACTCG
2950066 TGAGTTTTCT
Statistics
Matches: 537, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
538 537 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (538 bp):
GTCATATACGAGAAAATAAAGAACAAAAACATGATCAAAACACTCAGTTTATGTCTACACTAACC
ACAGTTCTAAATAGCGGTCTCGGATTTTGCAGCAGATGTGATTGGGGTGTCTAACCCTCAATACC
TAAGGCACCTGAATTTAGCTCCATCTCCTTTTATCCTCCTCCTCGTCCACAGGAGTATACCACGA
TGGTCTTCGCTTTGAGTTGCTTAACCTGTAGTTCAACAGCACTTCTTCATTACAAAGTGCTGTAG
TAGCCACCAAAACAAGAGTCTTTAATACAGGACCATCTGACCCACCATTTCTTGAGCCCCATCTG
AACCAAAAGCTGCCAAATCTCCTCATGTTTACTTCTTCGGCATTTCCAAATGATATATTTGGAAT
ATAAGCTCTCATCTCTTTTTCATTCAGTGGGAAGTCATAAGGGCAAACCATCACGTTTGGCACCA
TTTCTTTAGCCGGGTGATTGGCGAAATGGGCCAAAGCTAAAGGGTTCCTGCGTTCCAAAATTTCA
CCACCACTCCCCACTCGA
Found at i:2950715 original size:100 final size:100
Alignment explanation
Indices: 2950542--2950742 Score: 312
Period size: 100 Copynumber: 2.0 Consensus size: 100
2950532 GCAGGGCCTT
* * * *
2950542 CCATTTATCTCTACTATTACTGGTACAAAATAGAAACTAGAGAGCAAAGGCACATATGATCAAAT
1 CCATTTATCTCTACTATTACCGGTACAAAAGAGAAAATAGAGAGCAAAGGCACATATGATCAAAG
*
2950607 TCAAACAACGGATCAAATGATTCATATTCCAAATA
66 TCAAACAACGGATCAAAAGATTCATATTCCAAATA
* * * *
2950642 CCATTTATCTCTGCTATTACCGGTACAAGAGAGAAAATAGAGAGCAATGGCATATATGATCAAAG
1 CCATTTATCTCTACTATTACCGGTACAAAAGAGAAAATAGAGAGCAAAGGCACATATGATCAAAG
*
2950707 TCAAACAACGGATCAAAAGATTCATATTCCGAATA
66 TCAAACAACGGATCAAAAGATTCATATTCCAAATA
2950742 C
1 C
2950743 TTGTTGCTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (100 bp):
CCATTTATCTCTACTATTACCGGTACAAAAGAGAAAATAGAGAGCAAAGGCACATATGATCAAAG
TCAAACAACGGATCAAAAGATTCATATTCCAAATA
Found at i:2953468 original size:12 final size:13
Alignment explanation
Indices: 2953451--2953479 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2953441 CGATTTTTTA
2953451 AAATAAAT-AAAT
1 AAATAAATAAAAT
2953463 AAATAAATAAAAT
1 AAATAAATAAAAT
2953476 AAAT
1 AAAT
2953480 GCAACGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:2953952 original size:18 final size:18
Alignment explanation
Indices: 2953916--2953952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2953906 TTATAAATTA
* *
2953916 AAAATATTTAATTTGAAT
1 AAAATATTTAAATTAAAT
2953934 AAAATATTTAAATTAAAT
1 AAAATATTTAAATTAAAT
2953952 A
1 A
2953953 TTAATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAAATATTTAAATTAAAT
Found at i:2956684 original size:15 final size:16
Alignment explanation
Indices: 2956666--2956700 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2956656 TATCATATTA
*
2956666 TAATAAAG-CATACAT
1 TAATAAAGACATAAAT
2956681 TAATAAAGACATAAAT
1 TAATAAAGACATAAAT
2956697 TAAT
1 TAAT
2956701 CTTTTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (16 bp):
TAATAAAGACATAAAT
Found at i:2963823 original size:2 final size:2
Alignment explanation
Indices: 2963812--2963847 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2963802 GCATTATTGT
*
2963812 TA TA TA -A TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2963848 GTATGTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2963848 original size:10 final size:10
Alignment explanation
Indices: 2963819--2963851 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2963809 TGTTATATAA
*
2963819 TATATATATA
1 TATATATATG
2963829 TATATATATG
1 TATATATATG
2963839 TATATATATG
1 TATATATATG
2963849 TAT
1 TAT
2963852 GTATGTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:2966724 original size:21 final size:21
Alignment explanation
Indices: 2966700--2966741 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2966690 ATTAATTATT
2966700 ATAAA-TACTTTAAATATTAAA
1 ATAAATTA-TTTAAATATTAAA
*
2966721 ATAAATTATTTTAATATTAAA
1 ATAAATTATTTAAATATTAAA
2966742 TAAGTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTATTTAAATATTAAA
Found at i:2967303 original size:26 final size:27
Alignment explanation
Indices: 2967273--2967332 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
2967263 AAAAATTTTG
2967273 AATAATGTAAATA-TTAGTTAA-TATAA
1 AATAAT-TAAATATTTAGTTAATTATAA
* *
2967299 TATAA-TAAATATTTATTTAATTATAA
1 AATAATTAAATATTTAGTTAATTATAA
2967325 AATAATTA
1 AATAATTA
2967333 GTTAACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 6 0.21
25 7 0.25
26 13 0.46
27 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
AATAATTAAATATTTAGTTAATTATAA
Found at i:2967987 original size:3 final size:3
Alignment explanation
Indices: 2967979--2968057 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
2967969 ATGCCCTGTT
2967979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2968027 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2968058 CTTTTTGAGC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2968858 original size:36 final size:37
Alignment explanation
Indices: 2968816--2968888 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
2968806 ACTAAATAAT
* * * * *
2968816 TATAAATTATATTTATATTTATGTTAGATAA-TAAAA
1 TATAAATTAAAATGATATTTATATTAAATAACTAAAA
2968852 TATAAATTAAAATGATATTTATATTAAATAACTAAAA
1 TATAAATTAAAATGATATTTATATTAAATAACTAAAA
2968889 ATTATGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAAATTAAAATGATATTTATATTAAATAACTAAAA
Found at i:2968904 original size:75 final size:76
Alignment explanation
Indices: 2968806--2968962 Score: 180
Period size: 75 Copynumber: 2.1 Consensus size: 76
2968796 AAATTTGTAT
*** *
2968806 ACTAAATAATTATAAATTATA-TTTAT-ATTTATGTTAGATAATAAAATATAAATTAAAATGATA
1 ACTAAATAATTATAAATTATATTTTATAATTTAAAATAAATAATAAAA-A-AAATTAAAATGATA
* *
2968869 TTTATATTAAATA
64 TTTAGATAAAATA
* *
2968882 ACTAAA-AATTATGAAATT-TATTTTATAATTTAAAATAAATAATTAAAAAAATTAAAATTATAT
1 ACTAAATAATTAT-AAATTATATTTTATAATTTAAAATAAATAATAAAAAAAATTAAAATGATAT
2968945 TTAGATAAAATA
65 TTAGATAAAATA
2968957 A-TAAAT
1 ACTAAAT
2968963 TATATATTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
74 4 0.06
75 33 0.48
76 17 0.25
77 15 0.22
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (76 bp):
ACTAAATAATTATAAATTATATTTTATAATTTAAAATAAATAATAAAAAAAATTAAAATGATATT
TAGATAAAATA
Found at i:2968954 original size:23 final size:24
Alignment explanation
Indices: 2968928--2968986 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2968918 AAATAATTAA
* *
2968928 AAAAATTAAAATTATAT-TTAGAT
1 AAAAATAAAAATTATATATTAAAT
2968951 -AAAATAATAAATTATATATTAAAT
1 AAAAATAA-AAATTATATATTAAAT
*
2968975 AATAATAAAAAT
1 AAAAATAAAAAT
2968987 GACAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 9 0.30
25 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATAAAAATTATATATTAAAT
Found at i:2968986 original size:24 final size:23
Alignment explanation
Indices: 2968923--2968986 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
2968913 AAAATAAATA
*
2968923 ATTAAA-AAAATTAAAATTATAT
1 ATTAAATAAAATAAAAATTATAT
*
2968945 -TTAGATAAAATAATAAATTATAT
1 ATTAAATAAAATAA-AAATTATAT
2968968 ATTAAATAATAATAAAAAT
1 ATTAAATAA-AATAAAAAT
2968987 GACAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 9 0.26
24 11 0.31
25 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTAAATAAAATAAAAATTATAT
Found at i:2979768 original size:2 final size:2
Alignment explanation
Indices: 2979761--2979787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2979751 AATTTACGTG
2979761 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 T
2979788 TTATCTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2981087 original size:12 final size:12
Alignment explanation
Indices: 2981070--2981102 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2981060 AAAAATTAAT
2981070 ATAATATAAAAA
1 ATAATATAAAAA
*
2981082 ATAATAT-AAAG
1 ATAATATAAAAA
2981093 ATAATATAAA
1 ATAATATAAA
2981103 TATATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:2981096 original size:18 final size:18
Alignment explanation
Indices: 2981059--2981096 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2981049 TATCAACGTA
*
2981059 AAAAAATTAATATAATAT
1 AAAAAATTAATATAAGAT
2981077 AAAAAA-TAATATAAAGAT
1 AAAAAATTAATAT-AAGAT
2981095 AA
1 AA
2981097 TATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAAATTAATATAAGAT
Found at i:2988837 original size:12 final size:12
Alignment explanation
Indices: 2988806--2988851 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
2988796 ACCAAATCGA
*
2988806 CCACCCCCAC-G
1 CCACCACCACGG
*
2988817 CCTACCACCCCGG
1 CC-ACCACCACGG
2988830 CCACCACCACGG
1 CCACCACCACGG
2988842 CCACCACCAC
1 CCACCACCAC
2988852 CTCTTCCACG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 25 0.83
13 3 0.10
ACGTcount: A:0.22, C:0.65, G:0.11, T:0.02
Consensus pattern (12 bp):
CCACCACCACGG
Found at i:2990973 original size:71 final size:71
Alignment explanation
Indices: 2990826--2991018 Score: 212
Period size: 71 Copynumber: 2.7 Consensus size: 71
2990816 CTTTCCCATG
* ** * * * * *
2990826 TTCTTCTCCACCCATTTTCAAAATAAGTAGCGACTCTCCGGTCCCCATCTCATCATTCCCCCCCC
1 TTCTTCTACA-CCATTTTCAAAATGGGCAGCGACTCCCCGGTCCCCATCTCTTAATACCCCCCCC
*
2990891 CCCTGTT
65 CACTGTT
* * * **
2990898 TTCTTCTTCACCATTTTCAAAATGGGCAGCGACTCCCCAGTCTCCATCTCTTAATACCCTTCCCC
1 TTCTTCTACACCATTTTCAAAATGGGCAGCGACTCCCCGGTCCCCATCTCTTAATACCCCCCCCC
2990963 ACT-TT
66 ACTGTT
*
2990968 CTTCTTC-AC-CCATTTTCAAAATGGGCAGCAACTCCCCGGTCCCCATCTCTT
1 -TTCTTCTACACCATTTTCAAAATGGGCAGCGACTCCCCGGTCCCCATCTCTT
2991019 CATCCCCATT
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
69 39 0.38
70 3 0.03
71 52 0.50
72 9 0.09
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.32
Consensus pattern (71 bp):
TTCTTCTACACCATTTTCAAAATGGGCAGCGACTCCCCGGTCCCCATCTCTTAATACCCCCCCCC
ACTGTT
Found at i:2992674 original size:25 final size:25
Alignment explanation
Indices: 2992656--2992707 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
2992646 AGCCTGCAGT
*
2992656 GTGATATTAATGCAGAGCCAAATTA
1 GTGATATTAATGCAGAGCCAAAGTA
*
2992681 GTGATATTAATGCAGAGCCAAATTA
1 GTGATATTAATGCAGAGCCAAAGTA
2992706 GT
1 GT
2992708 ACAAGTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (25 bp):
GTGATATTAATGCAGAGCCAAAGTA
Found at i:2992856 original size:2 final size:2
Alignment explanation
Indices: 2992849--2992879 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2992839 AGTGTACAAA
2992849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2992880 ATTAACAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2993233 original size:12 final size:12
Alignment explanation
Indices: 2993216--2993241 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2993206 AAAGATGAAA
2993216 ACACACACGCAC
1 ACACACACGCAC
2993228 ACACACACGCAC
1 ACACACACGCAC
2993240 AC
1 AC
2993242 CCCAAAAGGA
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:0.42, C:0.50, G:0.08, T:0.00
Consensus pattern (12 bp):
ACACACACGCAC
Found at i:2993296 original size:2 final size:2
Alignment explanation
Indices: 2993289--2993325 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2993279 TCTTGAACAT
2993289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2993326 CACACCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2994286 original size:13 final size:13
Alignment explanation
Indices: 2994268--2994310 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
2994258 AATTAATATT
2994268 TATATTTTATTAA
1 TATATTTTATTAA
*
2994281 TATATTTTAATATAT
1 TATATTTT-AT-TAA
2994296 TAATATTTTATTAA
1 T-ATATTTTATTAA
2994310 T
1 T
2994311 TATAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 8 0.32
14 5 0.20
15 5 0.20
16 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTTATTAA
Found at i:2994301 original size:29 final size:28
Alignment explanation
Indices: 2994241--2994315 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 28
2994231 TTAATTTTCA
2994241 ATTAA-ATTTTATTAA-ATAATTAATAT
1 ATTAATATTTTATTAATATAATTAATAT
*
2994267 -TT-ATATTTTATTAATATATTTTAATAT
1 ATTAATATTTTATTAATATA-ATTAATAT
2994294 ATTAATATTTTATTAATTATAA
1 ATTAATATTTTATTAA-TATAA
2994316 AATTTTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 1 0.02
25 12 0.29
26 3 0.07
27 7 0.17
28 2 0.05
29 12 0.29
30 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTAATATTTTATTAATATAATTAATAT
Found at i:2996670 original size:22 final size:23
Alignment explanation
Indices: 2996631--2996675 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2996621 TATTTTTAAA
* *
2996631 TTTAATATTTTTATCTAAATTTT
1 TTTAATATTTTAAACTAAATTTT
*
2996654 TTTAA-ATTTTAAACTAACTTTT
1 TTTAATATTTTAAACTAAATTTT
2996676 AAATTTAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAATATTTTAAACTAAATTTT
Found at i:2997259 original size:30 final size:29
Alignment explanation
Indices: 2997215--2997295 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
2997205 TAAAATTTTA
*
2997215 TAAAAAAATATATTTATTTTTTTAATATT
1 TAAAAAAATATATTTATTTTTTTAAAATT
* *
2997244 TAAAAAATATTTATTTA-TCTTTTAAAATT
1 TAAAAAA-ATATATTTATTTTTTTAAAATT
2997273 TAATAAAAAATATATTTATTTTT
1 T-A-AAAAAATATATTTATTTTT
2997296 AAATTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 18 0.42
30 17 0.40
31 8 0.19
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAAAAAATATATTTATTTTTTTAAAATT
Found at i:2997316 original size:34 final size:32
Alignment explanation
Indices: 2997208--2997321 Score: 91
Period size: 30 Copynumber: 3.6 Consensus size: 32
2997198 ACTTTCTTAA
2997208 AATTTTATAA-AAAAATATATTTATTTTT--TT
1 AATTTTA-AATAAAAATATATTTATTTTTAATT
* *
2997238 AATATTTAAA-AAATATTTATTTATCTTTTAA--
1 AAT-TTTAAATAAAAATATATTTAT-TTTTAATT
2997269 AA-TTT-AATAAAAAATATATTTATTTTTAAATT
1 AATTTTAAAT-AAAAATATATTTATTTTT-AATT
*
2997301 AATTTTAAATTAAAAACATAT
1 AATTTTAAA-TAAAAATATAT
2997322 ATACTCTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
28 2 0.03
29 7 0.10
30 31 0.46
31 10 0.15
32 2 0.03
33 3 0.04
34 11 0.16
35 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
AATTTTAAATAAAAATATATTTATTTTTAATT
Found at i:2997511 original size:37 final size:39
Alignment explanation
Indices: 2997419--2997513 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 39
2997409 TAAAACTATC
*
2997419 TTTAA-TT-ATTATAAATTAAATTATTGTTAAGTTATAT
1 TTTAATTTAATTATATATTAAATTATTGTTAAGTTATAT
* * * * *
2997456 TCTAATTCAAATACATATTAAA-TATT-TTAAATT-TATT
1 TTTAATTTAATTATATATTAAATTATTGTTAAGTTATA-T
2997493 TTTAATTTAATTATATATTAA
1 TTTAATTTAATTATATATTAA
2997514 CTTTAAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
36 2 0.04
37 28 0.62
38 5 0.11
39 10 0.22
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (39 bp):
TTTAATTTAATTATATATTAAATTATTGTTAAGTTATAT
Found at i:2999082 original size:24 final size:25
Alignment explanation
Indices: 2999054--2999133 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 25
2999044 TTTGAAATTA
2999054 AATTTTATTATTATAAAATAAATAT
1 AATTTTATTATTATAAAATAAATAT
*
2999079 -ATTTTATT-TTATATAATAATATAT
1 AATTTTATTATTATAAAATAA-ATAT
* * *
2999103 AAAATTTATTATTATGAAATTAATAT
1 -AATTTTATTATTATAAAATAAATAT
2999129 GAATT
1 -AATT
2999134 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
23 10 0.23
24 12 0.27
26 14 0.32
27 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATTTTATTATTATAAAATAAATAT
Found at i:2999230 original size:16 final size:16
Alignment explanation
Indices: 2999197--2999237 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2999187 TGATATATTT
*
2999197 TTATTAA-T-ATTTAA
1 TTATTAATTAATTAAA
2999211 TTATTAATTAATTAAA
1 TTATTAATTAATTAAA
*
2999227 TTATTAGTTAA
1 TTATTAATTAA
2999238 CATAAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 7 0.30
15 1 0.04
16 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATTAATTAATTAAA
Found at i:2999280 original size:35 final size:33
Alignment explanation
Indices: 2999229--2999340 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 33
2999219 TAATTAAATT
* *
2999229 ATTAGTTAACATAAATATCATTTTAATAACTTTTA
1 ATTATTTAAAATAAATAT-ATTTTAATAA-TTTTA
*
2999264 ATTATTTAAAATAAATAATATTTTATTTATATTTT-
1 ATTATTTAAAATAAAT-ATATTTTA-ATA-ATTTTA
** *
2999299 ATTATTTAATTTAAACATAATTTTAAT-ATTATTA
1 ATTATTTAAAATAAATAT-ATTTTAATAATT-TTA
2999333 ATTATTTA
1 ATTATTTA
2999341 TTAAATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
32 3 0.05
33 2 0.03
34 11 0.17
35 39 0.61
36 8 0.12
37 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.53
Consensus pattern (33 bp):
ATTATTTAAAATAAATATATTTTAATAATTTTA
Found at i:3003511 original size:52 final size:52
Alignment explanation
Indices: 3003426--3003550 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
3003416 ATATGAAAAG
* *
3003426 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
3003478 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
3003530 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3003551 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:3003563 original size:52 final size:51
Alignment explanation
Indices: 3003426--3003570 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
3003416 ATATGAAAAG
*
3003426 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
3003478 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
3003530 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3003571 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:3003577 original size:13 final size:13
Alignment explanation
Indices: 3003559--3003583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3003549 CAAAGATCAG
3003559 TGTATCGATACAA
1 TGTATCGATACAA
3003572 TGTATCGATACA
1 TGTATCGATACA
3003584 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3003666 original size:33 final size:33
Alignment explanation
Indices: 3003624--3003693 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
3003614 GGCAGTAGCT
3003624 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
3003657 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
3003690 TACA
1 TACA
3003694 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:3003667 original size:13 final size:13
Alignment explanation
Indices: 3003649--3003673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3003639 CAAAAAAATA
3003649 TGTATCGATACAT
1 TGTATCGATACAT
3003662 TGTATCGATACA
1 TGTATCGATACA
3003674 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3004147 original size:3 final size:3
Alignment explanation
Indices: 3004139--3004171 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3004129 ATATATACAA
3004139 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3004172 GATATTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3006651 original size:13 final size:13
Alignment explanation
Indices: 3006633--3006657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3006623 CATAAAGTGT
3006633 TGTATCGATACAA
1 TGTATCGATACAA
3006646 TGTATCGATACA
1 TGTATCGATACA
3006658 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3006673 original size:32 final size:33
Alignment explanation
Indices: 3006613--3006678 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
3006603 TTCAACGAGT
3006613 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
3006646 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3006678 T
1 T
3006679 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3006789 original size:52 final size:52
Alignment explanation
Indices: 3006731--3006859 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
3006721 CACTGATCTT
3006731 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
* * *
3006783 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
3006835 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3006860 TCATATTTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
Found at i:3013719 original size:15 final size:16
Alignment explanation
Indices: 3013695--3013733 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3013685 ATTGAAGCTC
*
3013695 AATTTCAAATTTAT-A
1 AATTTTAAATTTATCA
3013710 AATTTTAAATTTATCA
1 AATTTTAAATTTATCA
3013726 AATATTTA
1 AAT-TTTA
3013734 TCTTTTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTTAAATTTATCA
Found at i:3016862 original size:19 final size:19
Alignment explanation
Indices: 3016840--3016879 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3016830 TAATTTTTAA
3016840 AAAATAAATATATTTAAAT
1 AAAATAAATATATTTAAAT
* * *
3016859 AAAATATATATTTTTATAT
1 AAAATAAATATATTTAAAT
3016878 AA
1 AA
3016880 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAATATATTTAAAT
Found at i:3016954 original size:20 final size:18
Alignment explanation
Indices: 3016915--3016958 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
3016905 ATTTAATAAT
3016915 TTATATATTTGTATCATA
1 TTATATATTTGTATCATA
*
3016933 TTATATATTT-TATCATG
1 TTATATATTTGTATCATA
3016950 TTAT-TATTT
1 TTATATATTT
3016959 AAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
TTATATATTTGTATCATA
Found at i:3017045 original size:12 final size:11
Alignment explanation
Indices: 3017024--3017057 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3017014 TTTTAACATA
3017024 TATATTTATAT
1 TATATTTATAT
*
3017035 TTTATTTTATAT
1 TATA-TTTATAT
3017047 TATATTTATAT
1 TATATTTATAT
3017058 AATTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3017075 original size:12 final size:14
Alignment explanation
Indices: 3017024--3017068 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
3017014 TTTTAACATA
3017024 TATATTTATAT--T
1 TATATTTATATAAT
3017036 T-TATTT-TAT-AT
1 TATATTTATATAAT
3017047 TATATTTATATAAT
1 TATATTTATATAAT
3017061 TATATTTA
1 TATATTTA
3017069 AAATTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.10
11 7 0.24
12 6 0.21
13 3 0.10
14 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTATATAAT
Found at i:3031280 original size:58 final size:58
Alignment explanation
Indices: 3031191--3031348 Score: 174
Period size: 58 Copynumber: 2.7 Consensus size: 58
3031181 AAAAAAAGTT
* * * * *
3031191 ATCATAGAAAAATTATTTGAATAACATCAAAATGCATGAAATTACA-CCAAAGTCTCTAG
1 ATCATA-AAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCCAAA-TCCCTAA
* * * * * * *
3031250 ATTATGATAAATGTTCTAAATGACATCAAAATTCATAAAATTACATCCAAATCCCTAA
1 ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCCAAATCCCTAA
*
3031308 ATCATAAAAAATGATGTAAATAACATCAAAATGCATGAAAT
1 ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAAT
3031349 GATATTAAAG
Statistics
Matches: 78, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
58 69 0.88
59 9 0.12
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (58 bp):
ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCCAAATCCCTAA
Found at i:3031370 original size:58 final size:57
Alignment explanation
Indices: 3031191--3031379 Score: 155
Period size: 58 Copynumber: 3.2 Consensus size: 57
3031181 AAAAAAAGTT
* * * *
3031191 ATCATAGAAAAATTATTTGAATAACATCAAAATGCATGAAATTACACCAAAGTCTCTAG
1 ATCATA-AAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCAAAGT-TCTAG
* * * * * * * * *
3031250 ATTATGATAAATGTTCTAAATGACATCAAAATTCATAAAATTACATCCAAA-TCCCTAA
1 ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAATTACAT-CAAAGT-TCTAG
* * * *
3031308 ATCATAAAAAATGATGTAAATAACATCAAAATGCATGAAATGATATTAAAGTTACTAG
1 ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCAAAGTT-CTAG
**
3031366 ATCATGTAAAATGA
1 ATCATAAAAAATGA
3031380 CCTATATGGT
Statistics
Matches: 99, Mismatches: 28, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
57 3 0.03
58 88 0.89
59 8 0.08
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (57 bp):
ATCATAAAAAATGATCTAAATAACATCAAAATGCATGAAATTACATCAAAGTTCTAG
Found at i:3032347 original size:15 final size:15
Alignment explanation
Indices: 3032327--3032355 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3032317 GAAAAAACTC
3032327 TCTCTCTTTTTTTTT
1 TCTCTCTTTTTTTTT
3032342 TCTCTCTTTTTTTT
1 TCTCTCTTTTTTTT
3032356 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTCTCTTTTTTTTT
Found at i:3032351 original size:13 final size:12
Alignment explanation
Indices: 3032329--3032378 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
3032319 AAAAACTCTC
3032329 TCTCTTTTTTTTT
1 TCTC-TTTTTTTT
3032342 TCTCTCTTTTTTT
1 TCTCT-TTTTTTT
3032355 TCT-TTTTTTTT
1 TCTCTTTTTTTT
*
3032366 T-T-TTATTTTT
1 TCTCTTTTTTTT
3032376 TCT
1 TCT
3032379 ATTGAGAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 9 0.26
11 9 0.26
12 2 0.06
13 14 0.41
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTCTTTTTTTT
Found at i:3034197 original size:2 final size:2
Alignment explanation
Indices: 3034190--3034226 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3034180 AGTAGACATA
3034190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3034227 AAAGGAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3034280 original size:8 final size:10
Alignment explanation
Indices: 3034259--3034295 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
3034249 ATAAAGTTAG
3034259 TTTTATATAT
1 TTTTATATAT
3034269 TTTTATA-A-
1 TTTTATATAT
3034277 TTTTATATAT
1 TTTTATATAT
3034287 ATTTTATAT
1 -TTTTATAT
3034296 TTTAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.29
9 2 0.08
10 7 0.29
11 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3034287 original size:20 final size:18
Alignment explanation
Indices: 3034259--3034299 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3034249 ATAAAGTTAG
3034259 TTTTATATAT-TTTTATAA
1 TTTTATATATATTTTAT-A
3034277 TTTTATATATATTTTATA
1 TTTTATATATATTTTATA
3034295 TTTTA
1 TTTTA
3034300 ACAAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATATATTTTATA
Found at i:3034294 original size:9 final size:9
Alignment explanation
Indices: 3034259--3034299 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3034249 ATAAAGTTAG
3034259 TTTTATATA
1 TTTTATATA
3034268 TTTT-TATAA
1 TTTTATAT-A
3034277 TTTTATATA
1 TTTTATATA
3034286 TATTT-TATA
1 T-TTTATATA
3034295 TTTTA
1 TTTTA
3034300 ACAAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 6 0.21
9 16 0.57
10 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTATATA
Found at i:3035313 original size:44 final size:45
Alignment explanation
Indices: 3035259--3035353 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
3035249 CAATAGCTCA
*
3035259 AATTATTATTT-TA-ATATTAATAAAAAAATTTAAAAAATATTTTAT
1 AATTAATATTTATATAT-TTAATAAAAAAATTTAAAAAAT-TTTTAT
* ** *
3035304 -ATTAATATTTATATATTTTATAATTAAATTTAAATAATTTTTAT
1 AATTAATATTTATATATTTAATAAAAAAATTTAAAAAATTTTTAT
3035348 AATTAA
1 AATTAA
3035354 ATCATGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
44 15 0.36
45 25 0.60
46 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
AATTAATATTTATATATTTAATAAAAAAATTTAAAAAATTTTTAT
Found at i:3035321 original size:21 final size:21
Alignment explanation
Indices: 3035293--3035355 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
3035283 AAAATTTAAA
3035293 AAATATTTTAT-ATTAATATTT
1 AAATATTTTATAATTAA-ATTT
*
3035314 ATATATTTTATAATTAAATTT
1 AAATATTTTATAATTAAATTT
3035335 AAATAATTTTTATAATTAAAT
1 AAAT-A-TTTTATAATTAAAT
3035356 CATGTTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.46
22 6 0.16
23 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTTTATAATTAAATTT
Found at i:3035349 original size:23 final size:23
Alignment explanation
Indices: 3035284--3035355 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
3035274 ATTAATAAAA
*
3035284 AAATTTAAAAAATATTTTAT-ATT
1 AAATTTAAATAAT-TTTTATAATT
*
3035307 AATATTTATAT-A-TTTTATAATT
1 AA-ATTTAAATAATTTTTATAATT
3035329 AAATTTAAATAATTTTTATAATT
1 AAATTTAAATAATTTTTATAATT
3035352 AAAT
1 AAAT
3035356 CATGTTTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 13 0.31
22 6 0.14
23 17 0.40
24 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATAATTTTTATAATT
Found at i:3036466 original size:5 final size:5
Alignment explanation
Indices: 3036451--3036493 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
3036441 TAAATAATAT
* *
3036451 ATTTAA ATTTA ATTTA ATTTA ATTTTA AGTAA ATTTA ATTTA A
1 ATTT-A ATTTA ATTTA ATTTA A-TTTA ATTTA ATTTA ATTTA A
3036494 AATAATCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (5 bp):
ATTTA
Found at i:3036472 original size:16 final size:16
Alignment explanation
Indices: 3036451--3036493 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3036441 TAAATAATAT
* *
3036451 ATTTAAATTTAATTTA
1 ATTTAAATTTAAGTAA
*
3036467 ATTTAATTTTAAGTAA
1 ATTTAAATTTAAGTAA
3036483 ATTT-AATTTAA
1 ATTTAAATTTAA
3036494 AATAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAAATTTAAGTAA
Found at i:3037487 original size:26 final size:25
Alignment explanation
Indices: 3037458--3037515 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
3037448 GAGTTATTAA
*
3037458 GAAAAAATAAGAAAAGGAAAGGAAAG
1 GAAAAAAGAAGAAAAGG-AAGGAAAG
* * *
3037484 GAAAACAGAAGGAAAGGAAGGGAAG
1 GAAAAAAGAAGAAAAGGAAGGAAAG
3037509 GAAAAAA
1 GAAAAAA
3037516 ATTTGTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.02
Consensus pattern (25 bp):
GAAAAAAGAAGAAAAGGAAGGAAAG
Found at i:3037969 original size:12 final size:11
Alignment explanation
Indices: 3037947--3037994 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
3037937 TTATTTCATA
3037947 TTTTAATTATT
1 TTTTAATTATT
3037958 TTTTATATTATT
1 TTTTA-ATTATT
* * *
3037970 TTTGAGTTATA
1 TTTTAATTATT
3037981 TTTTAATTTATT
1 TTTTAA-TTATT
3037993 TT
1 TT
3037995 ATATTTTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 13 0.45
12 16 0.55
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTAATTATT
Found at i:3038726 original size:12 final size:12
Alignment explanation
Indices: 3038699--3038732 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3038689 ATATCATTTC
3038699 ATTTTTA-ATT-
1 ATTTTTATATTA
3038709 ATTTTTATATTA
1 ATTTTTATATTA
3038721 ATTTTTATATTA
1 ATTTTTATATTA
3038733 TACCTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 3 0.14
12 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTATATTA
Found at i:3038762 original size:22 final size:20
Alignment explanation
Indices: 3038707--3038767 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
3038697 TCATTTTTAA
*
3038707 TTAT-TTTTATATTAA-TTT
1 TTATATTTTACATTAATTTT
* *
3038725 TTATATTATACCTTAATTTAT
1 TTATATTTTACATTAATTT-T
3038746 TTCATATTTTACATTAATTTT
1 TT-ATATTTTACATTAATTTT
3038767 T
1 T
3038768 ACTTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 2 0.06
21 5 0.15
22 15 0.44
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATTTTACATTAATTTT
Found at i:3038945 original size:22 final size:21
Alignment explanation
Indices: 3038920--3038964 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
3038910 ATAAAATAAC
3038920 AATAAACTCCAACAAGAAAAAA
1 AATAAACTCCAACAA-AAAAAA
3038942 AATAAACTCCAACAAAAAAAA
1 AATAAACTCCAACAAAAAAAA
3038963 AA
1 AA
3038965 GAAAATAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.71, C:0.18, G:0.02, T:0.09
Consensus pattern (21 bp):
AATAAACTCCAACAAAAAAAA
Found at i:3042747 original size:2 final size:2
Alignment explanation
Indices: 3042740--3042784 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3042730 TAAGTTTGAT
3042740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3042782 TA T
1 TA T
3042785 GAGGAATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3042954 original size:24 final size:24
Alignment explanation
Indices: 3042927--3042979 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3042917 TAATTTAATT
3042927 TAATACTTTTATCATATCAATTGA
1 TAATACTTTTATCATATCAATTGA
3042951 TAATACTTTTATCATATCAATTGA
1 TAATACTTTTATCATATCAATTGA
3042975 TAATA
1 TAATA
3042980 TTATTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (24 bp):
TAATACTTTTATCATATCAATTGA
Found at i:3043673 original size:22 final size:22
Alignment explanation
Indices: 3043635--3043683 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3043625 AGAATGTACT
*
3043635 TTTAGGTTTGATTTTATATATAA
1 TTTATGTTTGATTTTATATAT-A
*
3043658 TTTATGTTT-ATTTTATTTATA
1 TTTATGTTTGATTTTATATATA
3043679 TTTAT
1 TTTAT
3043684 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 10 0.42
23 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTATGTTTGATTTTATATATA
Found at i:3044244 original size:15 final size:15
Alignment explanation
Indices: 3044215--3044256 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3044205 AAAAAAATAT
3044215 ATATTT-AATTTATC
1 ATATTTAAATTTATC
*
3044229 ATATTTAAAATTATC
1 ATATTTAAATTTATC
3044244 AT-TTTAAATTTAT
1 ATATTTAAATTTAT
3044257 TATAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTAAATTTATC
Found at i:3045432 original size:23 final size:21
Alignment explanation
Indices: 3045393--3045437 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
3045383 ATTTTAGATA
3045393 AAAATAATTTTTAAAATAATT
1 AAAATAATTTTTAAAATAATT
*
3045414 AAAATAATATTTTATAAATTATT
1 AAAATAAT-TTTTA-AAATAATT
3045437 A
1 A
3045438 TAATTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAATTTTTAAAATAATT
Found at i:3046782 original size:50 final size:50
Alignment explanation
Indices: 3046705--3046975 Score: 321
Period size: 50 Copynumber: 5.4 Consensus size: 50
3046695 TAGGTGCAAA
* * ***
3046705 AGAGGTGATCGTAATTGTTGACTATTTTTCATCATTTTTTGACAATCGAG
1 AGAGGTGACCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
* * *
3046755 AAAGGTGACCGTAATTGTTGACTATTTTTCACCAATCATTGACAATCGAG
1 AGAGGTGACCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
* **
3046805 AGAGGT-AGCCGTAATTGTTAACTATTCCTCACCAACCTTTGACAATCGAG
1 AGAGGTGA-CCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
* * * *
3046855 AGATGTGACCGTAATTGTTGACTATTTCTCATCAACCTTTGGCAATCGAG
1 AGAGGTGACCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
* * * * *
3046905 AGAGGTGATCGTAATTATTGACTATTCTTCACTAACCTTTGACAATAGAG
1 AGAGGTGACCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
*
3046955 A-ACGATGACCGTAATTGTTGA
1 AGA-GGTGACCGTAATTGTTGA
3046976 TTTAAGCATC
Statistics
Matches: 189, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 2 0.01
50 186 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (50 bp):
AGAGGTGACCGTAATTGTTGACTATTTTTCACCAACCTTTGACAATCGAG
Found at i:3051418 original size:50 final size:50
Alignment explanation
Indices: 3051349--3051514 Score: 199
Period size: 50 Copynumber: 3.3 Consensus size: 50
3051339 GCAAAAGAGA
* * * *
3051349 TGGTTGTAATTGTTAACTATTCTTCACCAATCTTTGACAATTGAGAGAGG
1 TGGTCGTAATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAAAGG
* *
3051399 TGGTCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCA-AGAAAGG
1 TGGTCGTAATTGTTAACTATTCTTCACCAACCTTTGACAAT-AGAGAAAGG
** * *
3051449 TGACCGTAATTGTTAACTATTTTTCACAAACCTTTGACAATAGAGAAAGG
1 TGGTCGTAATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAAAGG
***
3051499 TAACCGTAATTGTTAA
1 TGGTCGTAATTGTTAA
3051515 TTCTAAGCAT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
49 1 0.01
50 100 0.99
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (50 bp):
TGGTCGTAATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAAAGG
Done.