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 13 of 17
Found at i:2457897 original size:16 final size:16
Alignment explanation
Indices: 2457872--2457909 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2457862 ATTATAATAT
*
2457872 TTAAAAAAAATTTAAA
1 TTAAATAAAATTTAAA
2457888 TTAAATAAAATTTAAA
1 TTAAATAAAATTTAAA
*
2457904 ATAAAT
1 TTAAAT
2457910 TTCTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAATAAAATTTAAA
Found at i:2460687 original size:34 final size:35
Alignment explanation
Indices: 2460639--2460722 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 35
2460629 AAATCCAAGC
* * *
2460639 AAATTTCAAAATCAAGCGTCT-AAGACC-CTGAAGT
1 AAATTTCAAGATCAAG-GTCTCAAAACCTCTGAAGA
*
2460673 AAATTTCAAGATCAA-GTCTCAAAACCTTTGAAGA
1 AAATTTCAAGATCAAGGTCTCAAAACCTCTGAAGA
2460707 AAATTTCAAGATCAAG
1 AAATTTCAAGATCAAG
2460723 TCATCCAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
32 4 0.09
33 5 0.12
34 34 0.79
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (35 bp):
AAATTTCAAGATCAAGGTCTCAAAACCTCTGAAGA
Found at i:2464255 original size:3 final size:3
Alignment explanation
Indices: 2464247--2464280 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2464237 TAAAAAGATT
2464247 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2464281 ACATGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2464313 original size:22 final size:21
Alignment explanation
Indices: 2464288--2464328 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2464278 TATACATGAA
2464288 ATTTTGTATTAAAATAAAAAAG
1 ATTTTGTA-TAAAATAAAAAAG
* *
2464310 ATTTTTTATATAATAAAAA
1 ATTTTGTATAAAATAAAAA
2464329 TAGAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTTTGTATAAAATAAAAAAG
Found at i:2464748 original size:22 final size:22
Alignment explanation
Indices: 2464723--2464773 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2464713 TAATTATAAA
* *
2464723 ATTTTCTAATATGTTATTAATC
1 ATTTACTAATATCTTATTAATC
* *
2464745 ATTTACTATTATCTTATTCATC
1 ATTTACTAATATCTTATTAATC
*
2464767 AATTACT
1 ATTTACT
2464774 GTCTTTCTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTACTAATATCTTATTAATC
Found at i:2478954 original size:15 final size:15
Alignment explanation
Indices: 2478923--2478959 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2478913 AATAAAAATT
2478923 TAAAACA-TTTAAAA
1 TAAAACATTTTAAAA
*
2478937 TAAAACATTTTAACA
1 TAAAACATTTTAAAA
2478952 T-AAACATT
1 TAAAACATT
2478960 AACTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAACATTTTAAAA
Found at i:2482339 original size:15 final size:16
Alignment explanation
Indices: 2482307--2482339 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2482297 TATTTTTTCT
*
2482307 AATTCATTTTTTTAAA
1 AATTCATTTTTTAAAA
2482323 AATT-ATTTTTTAAAA
1 AATTCATTTTTTAAAA
2482338 AA
1 AA
2482340 ATTAATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTCATTTTTTAAAA
Found at i:2482483 original size:20 final size:21
Alignment explanation
Indices: 2482445--2482484 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2482435 ATATTTTTTA
*
2482445 TATAATAAAATATACTTAATT
1 TATAATAAAATAAACTTAATT
*
2482466 TATAA-AAAATAAATTTAAT
1 TATAATAAAATAAACTTAAT
2482485 ATATTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAATAAAATAAACTTAATT
Found at i:2482984 original size:20 final size:20
Alignment explanation
Indices: 2482959--2482997 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2482949 AATAATAATA
2482959 ATATTTAAATTTTTTAAATG
1 ATATTTAAATTTTTTAAATG
*
2482979 ATATTTTAATTTTTTAAAT
1 ATATTTAAATTTTTTAAAT
2482998 TTGTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATTTAAATTTTTTAAATG
Found at i:2483307 original size:20 final size:19
Alignment explanation
Indices: 2483268--2483307 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2483258 AGTTATGTTT
* *
2483268 ATTATTTTTATTAAATTTG
1 ATTATTGTTATTAAAATTG
2483287 ATTATTGTTATTTAAAATTG
1 ATTATTGTTA-TTAAAATTG
2483307 A
1 A
2483308 ATTCAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
ATTATTGTTATTAAAATTG
Found at i:2485004 original size:19 final size:19
Alignment explanation
Indices: 2484982--2485023 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2484972 ACCCAACTTA
2484982 TTTTTTAA-ATAAATTTAAT
1 TTTTTTAATATAAATTT-AT
*
2485001 TTTTTTAATTTAAATTTAT
1 TTTTTTAATATAAATTTAT
2485020 TTTT
1 TTTT
2485024 AACTTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAATATAAATTTAT
Found at i:2485358 original size:17 final size:18
Alignment explanation
Indices: 2485336--2485375 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2485326 ATGTATTATT
2485336 ATAATAT-TTTTTAAATA
1 ATAATATATTTTTAAATA
2485353 ATAATATAAATTTTTAAATA
1 ATAATAT--ATTTTTAAATA
2485373 ATA
1 ATA
2485376 TGACAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
20 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATATATTTTTAAATA
Found at i:2486016 original size:14 final size:14
Alignment explanation
Indices: 2485992--2486079 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 14
2485982 AATGATACAG
2485992 TTTAAATAATTAATA
1 TTTAAA-AATTAATA
2486007 TTTAAAAATTAATA
1 TTTAAAAATTAATA
**
2486021 TAAAAAAATTAA-A
1 TTTAAAAATTAATA
*
2486034 ATTATAAAA-TAATA
1 TTTA-AAAATTAATA
* *
2486048 TTCATAATATT-ATA
1 TTTA-AAAATTAATA
*
2486062 -TT-AAAATTACTA
1 TTTAAAAATTAATA
2486074 TTTAAA
1 TTTAAA
2486080 TTTCTAATTA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
11 5 0.09
12 2 0.04
13 8 0.14
14 34 0.61
15 7 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAAAAATTAATA
Found at i:2488720 original size:13 final size:12
Alignment explanation
Indices: 2488707--2488744 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
2488697 AAAGAAAAAT
2488707 TTTAAAATATAA
1 TTTAAAATATAA
2488719 TTTAAAAGTATAA
1 TTTAAAA-TATAA
*
2488732 ATTAAAATA-AA
1 TTTAAAATATAA
2488743 TT
1 TT
2488745 AATAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 9 0.39
13 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TTTAAAATATAA
Found at i:2489402 original size:6 final size:6
Alignment explanation
Indices: 2489383--2489434 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
2489373 ATGTTATATT
* * *
2489383 AATAAA AATGAA AATAAA AATAAA AATAATA AA-AATA TATAAA AATATA
1 AATAAA AATAAA AATAAA AATAAA AATAA-A AATAA-A AATAAA AATAAA
2489432 AAT
1 AAT
2489435 TATTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:2489412 original size:27 final size:25
Alignment explanation
Indices: 2489382--2489434 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
2489372 AATGTTATAT
2489382 TAATAAAAATGAAAATAAAAATAAAAA
1 TAATAAAAAT--AAATAAAAATAAAAA
* *
2489409 TAATAAAAATATATAAAAATATAAA
1 TAATAAAAATAAATAAAAATAAAAA
2489434 T
1 T
2489435 TATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (25 bp):
TAATAAAAATAAATAAAAATAAAAA
Found at i:2489424 original size:10 final size:10
Alignment explanation
Indices: 2489402--2489431 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2489392 GAAAATAAAA
2489402 ATAAAAATA-
1 ATAAAAATAT
2489411 ATAAAAATAT
1 ATAAAAATAT
2489421 ATAAAAATAT
1 ATAAAAATAT
2489431 A
1 A
2489432 AATTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:2489896 original size:5 final size:5
Alignment explanation
Indices: 2489886--2489926 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
2489876 TATTATTAAA
* *
2489886 AAATT AAATT AAATT AACTT AAATT -AATT -AATT AAAAT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
2489927 AATTAATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:2490164 original size:13 final size:12
Alignment explanation
Indices: 2490148--2490216 Score: 51
Period size: 13 Copynumber: 6.0 Consensus size: 12
2490138 AATTTAATAT
2490148 TTAAATATAAAAA
1 TTAAAT-TAAAAA
2490161 TTAAATT---AA
1 TTAAATTAAAAA
*
2490170 TTAATTTAAATAA
1 TTAAATTAAA-AA
2490183 TTAAATT---AA
1 TTAAATTAAAAA
2490192 TTAAATTAAAAA
1 TTAAATTAAAAA
*
2490204 TAAAAATTAAAAA
1 T-TAAATTAAAAA
2490217 ATTTTAACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
9 17 0.38
12 4 0.09
13 24 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAATTAAAAA
Found at i:2490168 original size:5 final size:5
Alignment explanation
Indices: 2490158--2490201 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
2490148 TTAAATATAA
*
2490158 AAATT AAATT -AATT AATTT AAA-T -AATT AAATT -AATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
2490202 AATAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
3 2 0.06
4 10 0.30
5 21 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AAATT
Found at i:2490173 original size:9 final size:9
Alignment explanation
Indices: 2490158--2490200 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
2490148 TTAAATATAA
2490158 AAATTAAATT
1 AAATT-AATT
2490168 -AATTAATTT
1 AAATTAA-TT
2490177 AAA-TAATT
1 AAATTAATT
2490185 AAATTAATT
1 AAATTAATT
2490194 AAATTAA
1 AAATTAA
2490201 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.23
9 21 0.70
10 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:2490184 original size:22 final size:21
Alignment explanation
Indices: 2490148--2490213 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
2490138 AATTTAATAT
2490148 TTAAATATAAAAATTAAATTAA
1 TTAAAT-TAAAAATTAAATTAA
*
2490170 TTAATTTAAATAATTAAATTAA
1 TTAAATTAAA-AATTAAATTAA
*
2490192 TTAAATTAAAAATAAAAATTAA
1 TTAAATTAAAAAT-TAAATTAA
2490214 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 7 0.18
22 32 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATTAAAAATTAAATTAA
Found at i:2491137 original size:17 final size:18
Alignment explanation
Indices: 2491110--2491157 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
2491100 ATATTTAAAT
*
2491110 TAATAAAAAATAAAATAA
1 TAATAATAAATAAAATAA
*
2491128 -AATAATAAAT-ATATAA
1 TAATAATAAATAAAATAA
*
2491144 TAATAATAATTAAA
1 TAATAATAAATAAA
2491158 CTTAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 5 0.21
17 18 0.75
18 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAATAATAAATAAAATAA
Found at i:2491147 original size:14 final size:13
Alignment explanation
Indices: 2491111--2491149 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
2491101 TATTTAAATT
2491111 AATAAAA-AATAA
1 AATAAAATAATAA
2491123 AATAAAATAATAA
1 AATAAAATAATAA
*
2491136 ATATATAATAATAA
1 A-ATAAAATAATAA
2491150 TAATTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 7 0.29
13 6 0.25
14 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAAATAATAA
Found at i:2491151 original size:20 final size:19
Alignment explanation
Indices: 2491110--2491153 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2491100 ATATTTAAAT
2491110 TAATAA-AAAATAAAATAA
1 TAATAATAAAATAAAATAA
*
2491128 -AATAATAAATATATAATAA
1 TAATAATAAA-ATAAAATAA
2491147 TAATAAT
1 TAATAAT
2491154 TAAACTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 3 0.14
19 8 0.36
20 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAATAAAATAAAATAA
Found at i:2491440 original size:3 final size:3
Alignment explanation
Indices: 2491434--2491485 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
2491424 CAGAAAAAAA
2491434 AAT AAT AAT AAT -AT AAT AAT -AT AAT AA- AA- AAT AAT AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
2491476 -AT ATT AAT AA
1 AAT AAT AAT AA
2491486 AATGAAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 10 0.24
3 29 0.69
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2491494 original size:29 final size:29
Alignment explanation
Indices: 2491430--2491493 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
2491420 TTCCCAGAAA
*
2491430 AAAAAATAATAATAATATAATAATATAAT
1 AAAAAATAATAATAATATAATAATAAAAT
*
2491459 AAAAAATAATAATGAATATATTAATAAAAT
1 AAAAAATAATAAT-AATATAATAATAAAAT
*
2491489 GAAAA
1 AAAAA
2491494 TGTTGTGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAAATAATAATAATATAATAATAAAAT
Found at i:2491643 original size:16 final size:16
Alignment explanation
Indices: 2491622--2491672 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
2491612 GGTCAAATTT
2491622 TTAATTTTTAATATAA
1 TTAATTTTTAATATAA
*
2491638 TTAATTTTT--TATAT
1 TTAATTTTTAATATAA
* * *
2491652 TTAATATTAAATATTA
1 TTAATTTTTAATATAA
2491668 TTAAT
1 TTAAT
2491673 AATAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTTTAATATAA
Found at i:2491756 original size:18 final size:18
Alignment explanation
Indices: 2491735--2491775 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2491725 TTTATTTATT
* *
2491735 ATAAAAATTTTTTAAAAA
1 ATAAAAATTATATAAAAA
*
2491753 ATAAAAATTATATATAAA
1 ATAAAAATTATATAAAAA
2491771 ATAAA
1 ATAAA
2491776 TTTAATTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATTATATAAAAA
Found at i:2498732 original size:19 final size:17
Alignment explanation
Indices: 2498708--2498746 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2498698 TATGATAAAA
2498708 ATTTAAAAAAATTAAATAT
1 ATTT-AAAAAA-TAAATAT
*
2498727 ATTTAAAACATAAATAT
1 ATTTAAAAAATAAATAT
2498744 ATT
1 ATT
2498747 CGACATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAAAAATAAATAT
Found at i:2500714 original size:16 final size:17
Alignment explanation
Indices: 2500674--2500715 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2500664 ATATCCTTTC
2500674 ATAAAAT-ATAAAAATA
1 ATAAAATAATAAAAATA
*
2500690 ATAAAATAATAATAA-A
1 ATAAAATAATAAAAATA
2500706 ATAAAATAAT
1 ATAAAATAAT
2500716 TAATTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAATAATAAAAATA
Found at i:2500723 original size:24 final size:24
Alignment explanation
Indices: 2500675--2500740 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
2500665 TATCCTTTCA
* *
2500675 TAAAATATAAAAATAATAAAATAA-
1 TAAAAAAT-AAAATAATTAAATAAT
*
2500699 TAATAAAATAAAATAATTAATTAAT
1 TAA-AAAATAAAATAATTAAATAAT
* *
2500724 TAAAAAATTAATTAATT
1 TAAAAAATAAAATAATT
2500741 TTACATATGC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 28 0.80
25 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAAATAAAATAATTAAATAAT
Found at i:2500732 original size:16 final size:17
Alignment explanation
Indices: 2500691--2500740 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
2500681 ATAAAAATAA
* *
2500691 TAAAATAA-TAATAAAA
1 TAAAATAATTAATTAAT
2500707 TAAAATAATTAATTAAT
1 TAAAATAATTAATTAAT
2500724 TAAAA-AATTAATTAAT
1 TAAAATAATTAATTAAT
2500740 T
1 T
2500741 TTACATATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATAATTAATTAAT
Found at i:2501772 original size:13 final size:14
Alignment explanation
Indices: 2501754--2501782 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2501744 CATTTTTAGT
2501754 AATTATA-TTTTAA
1 AATTATATTTTTAA
2501767 AATTATATTTTTAA
1 AATTATATTTTTAA
2501781 AA
1 AA
2501783 AGATTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTATATTTTTAA
Found at i:2502655 original size:6 final size:6
Alignment explanation
Indices: 2502626--2502674 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
2502616 GATATATTTA
*
2502626 ATAAAT AT-AA- A-AAAT ATAAA- ATAAAT ATAATAT ATATAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAA-AT ATAAAT ATAAAT
2502671 ATAA
1 ATAA
2502675 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
4 3 0.08
5 8 0.22
6 20 0.56
7 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:2503121 original size:34 final size:34
Alignment explanation
Indices: 2503083--2503152 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 34
2503073 GTAATTAAAA
* *
2503083 TTTTTATTAACATTTAAAAGTAAT-TAATATAAC
1 TTTTTTTTAACATTTAAAAGTAATGAAATATAAC
* * * *
2503116 TTTTTTTTTACCTTTCAAATTAATGAAATATAAC
1 TTTTTTTTAACATTTAAAAGTAATGAAATATAAC
2503150 TTT
1 TTT
2503153 GAAGATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (34 bp):
TTTTTTTTAACATTTAAAAGTAATGAAATATAAC
Found at i:2503350 original size:16 final size:17
Alignment explanation
Indices: 2503321--2503358 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2503311 TGAATGTATT
2503321 AAATTTTAATAATAA-A
1 AAATTTTAATAATAACA
2503337 AAATATTTAA-AATAACA
1 AAAT-TTTAATAATAACA
2503354 AAATT
1 AAATT
2503359 GGTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTTTAATAATAACA
Found at i:2503434 original size:20 final size:20
Alignment explanation
Indices: 2503407--2503456 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2503397 TATTTTATAT
2503407 ATATATATATATAAATATTTTA
1 ATATATATAT-TAAA-ATTTTA
* *
2503429 ATATATGTATTCAAATTTTA
1 ATATATATATTAAAATTTTA
*
2503449 TTATATAT
1 ATATATAT
2503457 TATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATATATTAAAATTTTA
Found at i:2505630 original size:2 final size:2
Alignment explanation
Indices: 2505623--2505664 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
2505613 CTCTGTCCAT
*
2505623 TA TA TA TA TA TA TA TA TA TT 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 TA TA TA TA TA T-A TA T
2505665 TCGAGATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2505755 original size:2 final size:2
Alignment explanation
Indices: 2505748--2505773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2505738 TCAACCTCAT
2505748 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
2505774 ATTTGAGCTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2506528 original size:23 final size:23
Alignment explanation
Indices: 2506498--2506551 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2506488 TTTAATATGT
*
2506498 TAAATATAAATATAAT-TATTTAA
1 TAAATATAAA-ATAATATATTAAA
2506521 TAAATATAAAATAATATATTAAA
1 TAAATATAAAATAATATATTAAA
2506544 TATAATAT
1 TA-AATAT
2506552 GATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.18
23 18 0.64
24 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATATAAAATAATATATTAAA
Found at i:2506545 original size:19 final size:20
Alignment explanation
Indices: 2506490--2506548 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
2506480 TAAAAATTTT
*
2506490 TAATATGTTAAATATAAATA
1 TAATATATTAAATATAAATA
*
2506510 TAATTATTTAATAAATATAAA-A
1 TAA-TA--TATTAAATATAAATA
2506532 TAATATATTAAATATAA
1 TAATATATTAAATATAA
2506549 TATGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 4 0.12
22 4 0.12
23 11 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATATATTAAATATAAATA
Found at i:2506556 original size:19 final size:19
Alignment explanation
Indices: 2506490--2506556 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
2506480 TAAAAATTTT
* *
2506490 TAATATGTTAAATATAAATA
1 TAATATGATATAT-TAAATA
* *
2506510 TAAT-T-ATTTAATAAATA
1 TAATATGATATATTAAATA
* *
2506527 TAAAATAATATATTAAATA
1 TAATATGATATATTAAATA
2506546 TAATATGATAT
1 TAATATGATAT
2506557 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 20 0.56
20 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAATATGATATATTAAATA
Found at i:2506580 original size:43 final size:43
Alignment explanation
Indices: 2506490--2506606 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 43
2506480 TAAAAATTTT
* *
2506490 TAATATGTTAAATATAA-ATATAATTATTTAAT-AAATATAAAA
1 TAATATATTAAATATAATATAT-ATTTTTTAATAAAATATAAAA
*
2506532 TAATATATTAAATATAATATGATATTTTTTAATAAAAT-TAATGA
1 TAATATATTAAATATAATAT-ATATTTTTTAATAAAATATAA-AA
*
2506576 -AATATATTTAATAT-ATATCATA-TTTTTAATA
1 TAATATATTAAATATAATAT-ATATTTTTTAATA
2506607 TATTTAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
41 9 0.14
42 23 0.35
43 27 0.41
44 7 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (43 bp):
TAATATATTAAATATAATATATATTTTTTAATAAAATATAAAA
Found at i:2506588 original size:9 final size:9
Alignment explanation
Indices: 2506576--2506620 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
2506566 AAATTAATGA
2506576 AATATATTT
1 AATATATTT
*
2506585 AATATATAT
1 AATATATTT
* *
2506594 CATATTTTT
1 AATATATTT
2506603 AATATATTT
1 AATATATTT
2506612 AATA-ATTT
1 AATATATTT
2506620 A
1 A
2506621 TATTTATAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
8 5 0.17
9 25 0.83
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATATTT
Found at i:2507205 original size:20 final size:19
Alignment explanation
Indices: 2507144--2507208 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
2507134 GATATATACA
*
2507144 TATATAAATATATCAAAATA
1 TATAT-AATATATCAAAATT
*
2507164 AATATAA-A-AT--AAA-T
1 TATATAATATATCAAAATT
2507178 TAT-TAATATATCAAAATT
1 TATATAATATATCAAAATT
2507196 TATATAAATATAT
1 TATAT-AATATAT
2507209 GATATATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 5 0.14
17 5 0.14
18 5 0.14
19 3 0.09
20 11 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAATATATCAAAATT
Found at i:2507572 original size:23 final size:21
Alignment explanation
Indices: 2507526--2507587 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
2507516 ACAATATCAC
*
2507526 ATTAT-TAAAAAAT-AT-TAA
1 ATTATATAAAAAATAATATGA
2507544 ATTATAATAAAAAATAATATGA
1 ATTAT-ATAAAAAATAATATGA
*
2507566 ATATATATAAAATATAAATATG
1 AT-TATATAAAAAAT-AATATG
2507588 TTAAAATCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 5 0.14
20 8 0.22
21 2 0.06
22 12 0.33
23 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTATATAAAAAATAATATGA
Found at i:2507707 original size:16 final size:17
Alignment explanation
Indices: 2507686--2507733 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
2507676 TATTTTAATG
2507686 TATAATTTTTAAAATA-
1 TATAATTTTTAAAATAT
2507702 TATAA-TTTT-AAATAT
1 TATAATTTTTAAAATAT
*
2507717 TTTATATTTTTAAAATA
1 TATA-ATTTTTAAAATA
2507734 ATTTTTTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 6 0.22
17 4 0.15
18 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAATTTTTAAAATAT
Found at i:2507727 original size:17 final size:15
Alignment explanation
Indices: 2507686--2507733 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
2507676 TATTTTAATG
2507686 TATA-ATTTTTAAAA
1 TATATATTTTTAAAA
*
2507700 TATATAATTTTAAATA
1 TATATATTTTTAAA-A
*
2507716 TTTTATATTTTTAAAA
1 -TATATATTTTTAAAA
2507732 TA
1 TA
2507734 ATTTTTTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 2 0.07
17 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATTTTTAAAA
Found at i:2508020 original size:20 final size:20
Alignment explanation
Indices: 2507995--2508032 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2507985 ATATTTTTAT
2507995 TAAAAT-TTAATTATAAAATA
1 TAAAATATTAA-TATAAAATA
2508015 TAAAATATTAATATAAAA
1 TAAAATATTAATATAAAA
2508033 ATTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATATTAATATAAAATA
Found at i:2510446 original size:59 final size:59
Alignment explanation
Indices: 2510354--2510474 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
2510344 CACATTTTAC
*
2510354 TTAAAAAATTGAGTATTTTGAAAATTAAAACCCCATGAGATTCATAAATAGAAAATGAA
1 TTAAAAAATTGAGAATTTTGAAAATTAAAACCCCATGAGATTCATAAATAGAAAATGAA
2510413 TTAAAAAATTGAGAATTTTGAAAATTAAAACCCCATGAGATTCATAAATAGAAAATGAA
1 TTAAAAAATTGAGAATTTTGAAAATTAAAACCCCATGAGATTCATAAATAGAAAATGAA
2510472 TTA
1 TTA
2510475 GTTAAAAGCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (59 bp):
TTAAAAAATTGAGAATTTTGAAAATTAAAACCCCATGAGATTCATAAATAGAAAATGAA
Found at i:2516732 original size:32 final size:33
Alignment explanation
Indices: 2516691--2516761 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
2516681 CAAAATTAGC
2516691 TTTTAATATATTAATAATT-TATTTT-ATATAAT
1 TTTTAATATATTAAT-ATTATATTTTCATATAAT
* *
2516723 TTTTGATATATTAATATTATATTTTCATATGAT
1 TTTTAATATATTAATATTATATTTTCATATAAT
2516756 ATTTTA
1 -TTTTA
2516762 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 20 0.61
33 6 0.18
34 4 0.12
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (33 bp):
TTTTAATATATTAATATTATATTTTCATATAAT
Found at i:2517099 original size:16 final size:17
Alignment explanation
Indices: 2517078--2517114 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2517068 TTCATTCCAC
2517078 GAATTTCTATTTA-TTT
1 GAATTTCTATTTATTTT
*
2517094 GAATTTTTATTTATTTT
1 GAATTTCTATTTATTTT
2517111 GAAT
1 GAAT
2517115 GGAGAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (17 bp):
GAATTTCTATTTATTTT
Found at i:2517299 original size:17 final size:17
Alignment explanation
Indices: 2517270--2517340 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
2517260 TTTTTAATAT
*
2517270 ATATTAGATATATATTA
1 ATATTATATATATATTA
*
2517287 A-AGTTGTATATATATTA
1 ATA-TTATATATATATTA
2517304 ATATTATATATATAATTATA
1 ATATTATATATAT-A-T-TA
* *
2517324 ATTTTATACATATATTA
1 ATATTATATATATATTA
2517341 TACATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 25 0.57
18 3 0.07
19 2 0.05
20 13 0.30
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
ATATTATATATATATTA
Found at i:2517330 original size:20 final size:19
Alignment explanation
Indices: 2517302--2517349 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2517292 GTATATATAT
*
2517302 TAATATTATATATATAATTA
1 TAATATTATACATAT-ATTA
*
2517322 TAATTTTATACATATATTA
1 TAATATTATACATATATTA
2517341 TACATATTA
1 TA-ATATTA
2517350 AATAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATATTATACATATATTA
Found at i:2517342 original size:31 final size:30
Alignment explanation
Indices: 2517304--2517361 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2517294 ATATATATTA
*
2517304 ATATTATATATA-TAATTATAATTTTATACAT
1 ATATTATACATATTAA--ATAATTTTATACAT
2517335 ATATTATACATATTAAATAATTTTATA
1 ATATTATACATATTAAATAATTTTATA
2517362 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 11 0.44
32 3 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
ATATTATACATATTAAATAATTTTATACAT
Found at i:2520043 original size:33 final size:32
Alignment explanation
Indices: 2520006--2520077 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
2519996 AAATTATTTT
*
2520006 TTAATATATTTTTTATT-TATTTATATTATTAAA
1 TTAATATATTTTTTATTAT-TTTA-ATAATTAAA
* *
2520039 TTAATTTATTTTTTATTATTTTAATAATTTAA
1 TTAATATATTTTTTATTATTTTAATAATTAAA
2520071 TTAATAT
1 TTAATAT
2520078 TCAATCAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.38
33 20 0.59
34 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTAATATATTTTTTATTATTTTAATAATTAAA
Found at i:2520066 original size:23 final size:26
Alignment explanation
Indices: 2520017--2520069 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2520007 TAATATATTT
2520017 TTTATTTATTTATATTATTAAATTAA
1 TTTATTTATTTATATTATTAAATTAA
2520043 TTTATTT-TTTATTATT-TT-AA-TAA
1 TTTATTTATTTA-TATTATTAAATTAA
2520066 TTTA
1 TTTA
2520070 ATTAATATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.27
24 2 0.08
25 6 0.23
26 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTATTTATTTATATTATTAAATTAA
Found at i:2520073 original size:32 final size:33
Alignment explanation
Indices: 2520006--2520077 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
2519996 AAATTATTTT
*
2520006 TTAATATATTTTTTATTTATTTATATTATTAAA
1 TTAATATATTTTTTATTTATTTATATAATTAAA
* *
2520039 TTAATTTATTTTTTA-TTATTT-TAATAATTTAA
1 TTAATATATTTTTTATTTATTTAT-ATAATTAAA
2520071 TTAATAT
1 TTAATAT
2520078 TCAATCAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 19 0.56
33 14 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (33 bp):
TTAATATATTTTTTATTTATTTATATAATTAAA
Found at i:2525903 original size:20 final size:20
Alignment explanation
Indices: 2525874--2525915 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2525864 ATTTTTATAA
*
2525874 TAAATCAATTCAACTTAAAT
1 TAAATCAATTCAAATTAAAT
* *
2525894 TAAATTAATTTAAATTAAAT
1 TAAATCAATTCAAATTAAAT
2525914 TA
1 TA
2525916 TTATTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATCAATTCAAATTAAAT
Found at i:2525906 original size:15 final size:16
Alignment explanation
Indices: 2525888--2525925 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2525878 TCAATTCAAC
2525888 TTAAATTAAATTA-AT
1 TTAAATTAAATTATAT
2525903 TTAAATTAAATTATTAT
1 TTAAATTAAATTA-TAT
2525920 TTAAAT
1 TTAAAT
2525926 ATTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTAAATTATAT
Found at i:2531356 original size:2 final size:2
Alignment explanation
Indices: 2531349--2531378 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2531339 TAACTTTGCA
2531349 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2531379 CCCCCTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2531919 original size:24 final size:23
Alignment explanation
Indices: 2531884--2531946 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
2531874 TAAATATTTA
*
2531884 AATT-TTATTTTTATTATTATATT
1 AATTATTATTTTTATTATT-TAAT
* *
2531907 AATTATTAATTTTATAATTTAAT
1 AATTATTATTTTTATTATTTAAT
2531930 AATATATT-TTTTTATTA
1 AAT-TATTATTTTTATTA
2531947 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
AATTATTATTTTTATTATTTAAT
Found at i:2531968 original size:18 final size:16
Alignment explanation
Indices: 2531942--2531986 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2531932 TATATTTTTT
2531942 TATTAATAAAATTATGA
1 TATTAATAAAATTAT-A
*
2531959 TATGTAAT-AATTTATA
1 TAT-TAATAAAATTATA
2531975 TATTAATAAAAT
1 TATTAATAAAAT
2531987 CATTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 9 0.38
18 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
TATTAATAAAATTATA
Found at i:2532025 original size:17 final size:17
Alignment explanation
Indices: 2532003--2532036 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2531993 AATATTTTAA
* *
2532003 AAAATTTTAAATTAAAT
1 AAAATTTAAAAATAAAT
2532020 AAAATTTAAAAATAAAT
1 AAAATTTAAAAATAAAT
2532037 TTCTTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTTAAAAATAAAT
Found at i:2539310 original size:21 final size:21
Alignment explanation
Indices: 2539285--2539324 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2539275 TATTTTTATT
2539285 TAAAT-TTAAATATAAAATATA
1 TAAATATT-AATATAAAATATA
2539306 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
2539325 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:2540781 original size:13 final size:13
Alignment explanation
Indices: 2540751--2540788 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2540741 ATGGTCGGTG
2540751 TAATAAAT-ATTA
1 TAATAAATAATTA
* *
2540763 TTATAATTAATTA
1 TAATAAATAATTA
2540776 TAATAAATAATTA
1 TAATAAATAATTA
2540789 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAAATAATTA
Found at i:2541230 original size:2 final size:2
Alignment explanation
Indices: 2541223--2541247 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2541213 ATTACTCATG
2541223 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2541248 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2546743 original size:29 final size:31
Alignment explanation
Indices: 2546700--2546770 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
2546690 TATATATTTA
*
2546700 AAAATTTTAATTATAAATATTAATATAA-AA-AT
1 AAAATTTTTA-TAT-AATATTAA-ATAATAATAT
* *
2546732 AAAATTTTTATATCATTTTAAATAATAATAT
1 AAAATTTTTATATAATATTAAATAATAATAT
2546763 AAAATTTT
1 AAAATTTT
2546771 AAATTATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 8 0.24
31 13 0.38
32 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
AAAATTTTTATATAATATTAAATAATAATAT
Found at i:2547947 original size:21 final size:20
Alignment explanation
Indices: 2547901--2547962 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
2547891 TATTTAATAT
2547901 AATATTAATAAATTATATTAG
1 AATA-TAATAAATTATATTAG
*
2547922 TATATAATAAATATATATTTA-
1 AATATAATAAAT-TATA-TTAG
*
2547943 AATATTATATAATTAATATT
1 AATATAATA-AATT-ATATT
2547963 GTTAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 8 0.24
21 17 0.50
22 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATATAATAAATTATATTAG
Found at i:2548122 original size:33 final size:35
Alignment explanation
Indices: 2548055--2548124 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
2548045 TATATCTTTA
*
2548055 TTATTATTTAATATAAAATATAAATTTACTATATTT
1 TTATTATTTAACATAAAATATAAATTTAC-ATATTT
* *
2548091 TTATTATTTAACGT-AAATATAATTTTA-ATATTT
1 TTATTATTTAACATAAAATATAAATTTACATATTT
2548124 T
1 T
2548125 ATAAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 7 0.23
35 12 0.39
36 12 0.39
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (35 bp):
TTATTATTTAACATAAAATATAAATTTACATATTT
Found at i:2548272 original size:21 final size:21
Alignment explanation
Indices: 2548246--2548292 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2548236 AATATTAATT
2548246 TTAATTTTATCTTTATAATAA
1 TTAATTTTATCTTTATAATAA
*
2548267 TTAATTTTATTTTTATAATAA
1 TTAATTTTATCTTTATAATAA
2548288 TTAAT
1 TTAAT
2548293 CCAATCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATTTTATCTTTATAATAA
Found at i:2549215 original size:16 final size:17
Alignment explanation
Indices: 2549194--2549227 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2549184 TAGGGTAACA
*
2549194 TTTTT-AAACAATTATT
1 TTTTTAAAAAAATTATT
2549210 TTTTTAAAAAAATTATT
1 TTTTTAAAAAAATTATT
2549227 T
1 T
2549228 ATAGGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAAAAAAATTATT
Found at i:2549641 original size:24 final size:27
Alignment explanation
Indices: 2549608--2549659 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
2549598 TTAAAATTAA
*
2549608 TTTAATAATAA-AATTATT-TAAAAAT
1 TTTAATAATAACAATAATTATAAAAAT
2549633 TTTAA-AATAACAATAATTATAAAAAT
1 TTTAATAATAACAATAATTATAAAAAT
2549659 T
1 T
2549660 AATCATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 11 0.46
26 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTAATAATAACAATAATTATAAAAAT
Found at i:2549743 original size:19 final size:20
Alignment explanation
Indices: 2549721--2549761 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2549711 ATAATAAAAA
2549721 TTCTTTAAAT-TTTATAATT
1 TTCTTTAAATATTTATAATT
*
2549740 TTCTTTAAGTATTTATAATT
1 TTCTTTAAATATTTATAATT
2549760 TT
1 TT
2549762 TTATTACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTCTTTAAATATTTATAATT
Found at i:2549843 original size:30 final size:29
Alignment explanation
Indices: 2549809--2549887 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 29
2549799 TATTCACCTG
2549809 AATTTTTATATTTTA-TTTTACTTTTAAATA
1 AATTTTTATATTTTATTTTTA--TTTAAATA
*
2549839 AA-TTTTAAATTTTAAATTTTTATTTAAATA
1 AATTTTTATATTTT--ATTTTTATTTAAATA
* *
2549869 AATTCTTAATATTTAATTT
1 AATT-TTTATATTTTATTT
2549888 ATTCTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
29 10 0.25
30 16 0.40
31 2 0.05
32 12 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
AATTTTTATATTTTATTTTTATTTAAATA
Found at i:2549883 original size:23 final size:24
Alignment explanation
Indices: 2549844--2549888 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2549834 AAATAAATTT
*
2549844 TAAATTTTAAAT-TTTTATTTAAA
1 TAAATTTTAAATATTTAATTTAAA
2549867 TAAATTCTT-AATATTTAATTTA
1 TAAATT-TTAAATATTTAATTTA
2549889 TTCTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATTTTAAATATTTAATTTAAA
Found at i:2549896 original size:30 final size:32
Alignment explanation
Indices: 2549832--2549908 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 32
2549822 TATTTTACTT
*
2549832 TTAAATAAATT-TTAA-ATTTTAAATTTTTAT
1 TTAAATAAATTCTTAATATTTTAAATTTTTAC
2549862 TTAAATAAATTCTTAATA-TTT-AATTTATT-C
1 TTAAATAAATTCTTAATATTTTAAATTT-TTAC
* *
2549892 TTAAAAAAATCCTTAAT
1 TTAAATAAATTCTTAAT
2549909 TTAAATCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 31 0.76
31 9 0.22
32 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAATAAATTCTTAATATTTTAAATTTTTAC
Found at i:2551095 original size:18 final size:17
Alignment explanation
Indices: 2551069--2551107 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2551059 ATATTATTTG
*
2551069 TATATAAAATTATAAAAA
1 TATACAAAATTA-AAAAA
*
2551087 TATACAAAATTAACAAA
1 TATACAAAATTAAAAAA
2551104 TATA
1 TATA
2551108 AGTGACTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
TATACAAAATTAAAAAA
Found at i:2551914 original size:23 final size:24
Alignment explanation
Indices: 2551887--2551937 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2551877 TCACTAAAAT
* *
2551887 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAAAAATATATTAATAAA
*
2551910 TTTAAATAAAAATATTTTAATAAA
1 TTTAAATAAAAATATATTAATAAA
2551934 TTTA
1 TTTA
2551938 TTTCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATAAAAATATATTAATAAA
Found at i:2552764 original size:7 final size:7
Alignment explanation
Indices: 2552752--2552802 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
2552742 AAATAATATC
2552752 ATAAAAT
1 ATAAAAT
2552759 ATAAAAT
1 ATAAAAT
2552766 ATAAAAT
1 ATAAAAT
2552773 ATAAAAT
1 ATAAAAT
* *
2552780 AT-TAAG
1 ATAAAAT
2552786 ATAAAAT
1 ATAAAAT
2552793 ATATAAAT
1 ATA-AAAT
2552801 AT
1 AT
2552803 TTAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 4 0.11
7 28 0.74
8 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
ATAAAAT
Found at i:2552811 original size:20 final size:21
Alignment explanation
Indices: 2552766--2552818 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2552756 AATATAAAAT
2552766 ATAAAATATA-AAATATTAAG
1 ATAAAATATATAAATATTAAG
2552786 ATAAAATATATAAATATTTAA-
1 ATAAAATATATAAATA-TTAAG
2552807 A-AAAAT-TATAAA
1 ATAAAATATATAAA
2552819 AAAAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.19
20 15 0.48
21 6 0.19
22 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAATATATAAATATTAAG
Found at i:2552853 original size:18 final size:17
Alignment explanation
Indices: 2552787--2552893 Score: 50
Period size: 17 Copynumber: 6.4 Consensus size: 17
2552777 AATATTAAGA
2552787 TAAAA-TATATAAATATT
1 TAAAATTATATAAATA-T
**
2552804 TAAAAAAATTATAAA-A-
1 TAAAATTA-TATAAATAT
*
2552820 -AAAATTAT-TATTATAT
1 TAAAATTATATA-AATAT
2552836 TAAAATTTATATAAATA-
1 TAAAA-TTATATAAATAT
*
2552853 TAAAA-TATACTATATA-
1 TAAAATTATA-TAAATAT
*
2552869 TAAAAATATAATAAATTAT
1 TAAAATTAT-ATAAA-TAT
2552888 TAAAAT
1 TAAAAT
2552894 ATAATAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
13 2 0.03
14 2 0.03
15 10 0.14
16 10 0.14
17 20 0.29
18 12 0.17
19 13 0.19
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTATATAAATAT
Found at i:2552894 original size:18 final size:17
Alignment explanation
Indices: 2552832--2552901 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
2552822 AATTATTATT
*
2552832 ATATTAAAATTTATATAA
1 ATATTAAAATATA-ATAA
* *
2552850 ATA-TAAAATATACTAT
1 ATATTAAAATATAATAA
*
2552866 ATATAAAAATATAATAA
1 ATATTAAAATATAATAA
2552883 ATTATTAAAATATAATAA
1 A-TATTAAAATATAATAA
2552901 A
1 A
2552902 ATATATACGC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 5 0.12
17 19 0.44
18 19 0.44
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTAAAATATAATAA
Found at i:2555820 original size:18 final size:18
Alignment explanation
Indices: 2555799--2555836 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2555789 ATTAGTACGC
2555799 ATTTTGATA-TTTAAATTA
1 ATTTTGATACTTT-AATTA
2555817 ATTTTGATACTTTAATTA
1 ATTTTGATACTTTAATTA
2555835 AT
1 AT
2555837 AAATATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTGATACTTTAATTA
Found at i:2555968 original size:7 final size:7
Alignment explanation
Indices: 2555956--2556002 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
2555946 CACATGACTC
2555956 AATATAA
1 AATATAA
2555963 AATAT-A
1 AATATAA
2555969 AATATAA
1 AATATAA
*
2555976 AGTATAA
1 AATATAA
2555983 AA-AT-A
1 AATATAA
2555988 AATAATAA
1 AAT-ATAA
2555996 AATATAA
1 AATATAA
2556003 CTCCAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 3 0.09
6 8 0.24
7 19 0.56
8 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
AATATAA
Found at i:2555974 original size:13 final size:13
Alignment explanation
Indices: 2555956--2556002 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
2555946 CACATGACTC
2555956 AATATAAA-ATATA
1 AATATAAATATA-A
2555969 AATATAAAGTATAA
1 AATATAAA-TATAA
2555983 AA-ATAAATAATAA
1 AATATAAAT-ATAA
2555996 AATATAA
1 AATATAA
2556003 CTCCAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 19 0.63
14 7 0.23
15 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:2555983 original size:20 final size:20
Alignment explanation
Indices: 2555956--2556002 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2555946 CACATGACTC
2555956 AATATAAAATATAAAT-ATAA
1 AATATAAAA-ATAAATAATAA
*
2555976 AGTATAAAAATAAATAATAA
1 AATATAAAAATAAATAATAA
2555996 AATATAA
1 AATATAA
2556003 CTCCAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AATATAAAAATAAATAATAA
Found at i:2556059 original size:28 final size:28
Alignment explanation
Indices: 2556025--2556079 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2556015 TTTTTTTTAG
2556025 TTTTTAC-AATATTAATAATATTTATATA
1 TTTTTACAAAT-TTAATAATATTTATATA
2556053 TTTTTACAAATTTAATAATATTTATAT
1 TTTTTACAAATTTAATAATATTTATAT
2556080 TACATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTTACAAATTTAATAATATTTATATA
Found at i:2559081 original size:22 final size:22
Alignment explanation
Indices: 2559028--2559069 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2559018 TAATATTTTT
2559028 AAATT-ATTTATTATTTAACAA
1 AAATTAATTTATTATTTAACAA
2559049 AAATTAATTTATTA-TTAACAA
1 AAATTAATTTATTATTTAACAA
2559070 GTACTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTAATTTATTATTTAACAA
Found at i:2559963 original size:19 final size:20
Alignment explanation
Indices: 2559888--2559964 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 20
2559878 GGTTTATTCG
*
2559888 ATTAT-TTATTAATTTATTT
1 ATTATATTAATAATTTATTT
*
2559907 ATATATAATTATATATTTTATTT
1 AT-TAT-ATTA-ATAATTTATTT
* *
2559930 -TTATATTCAT-GTTTATTT
1 ATTATATTAATAATTTATTT
2559948 ATTATA-TAATAATTTAT
1 ATTATATTAATAATTTAT
2559965 ATATAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
18 10 0.22
19 14 0.30
20 6 0.13
21 3 0.07
22 4 0.09
23 9 0.20
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (20 bp):
ATTATATTAATAATTTATTT
Found at i:2559991 original size:17 final size:17
Alignment explanation
Indices: 2559942--2559994 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
2559932 ATATTCATGT
2559942 TTATTTAT-TAT-ATAA
1 TTATTTATATATAATAA
*
2559957 TAATTTATATATAA-AA
1 TTATTTATATATAATAA
2559973 TTATTT-TATATAATTAA
1 TTATTTATATATAA-TAA
2559990 TTATT
1 TTATT
2559995 GAAGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.44
16 10 0.31
17 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTATATATAATAA
Found at i:2560465 original size:65 final size:66
Alignment explanation
Indices: 2560393--2560518 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 66
2560383 TTTTTATAAA
* **
2560393 TTAATTAAA-TTT-AAAAATTTAATAAATAATAATTTATTA-ATT-ATTATTTTTAATAAAAATA
1 TTAATTAAATTTTAAAAAATTT-AT-AATAATAAATTAAAATATTAATTATTTTTAA-AAAAATA
2560454 ATAT
63 ATAT
*
2560458 TTAATTAAATTTTAAAAAATTTATATTAATAAATTAAAATATTAATTATTTTTAAAAAAAT
1 TTAATTAAATTTTAAAAAATTTATAATAATAAATTAAAATATTAATTATTTTTAAAAAAAT
2560519 TAAATTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
65 20 0.38
66 14 0.26
67 19 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (66 bp):
TTAATTAAATTTTAAAAAATTTATAATAATAAATTAAAATATTAATTATTTTTAAAAAAATAATA
T
Found at i:2560479 original size:20 final size:20
Alignment explanation
Indices: 2560456--2560527 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
2560446 TAAAAATAAT
2560456 ATTTAATTAAATTTTAAAAA
1 ATTTAATTAAATTTTAAAAA
** *
2560476 ATTTATATTAATAAATTAAAAT
1 ATTTA-ATTAA-ATTTTAAAAA
*
2560498 A-TTAATT-ATTTTTAAAAAA
1 ATTTAATTAAATTTT-AAAAA
*
2560517 ATTAAATTAAA
1 ATTTAATTAAA
2560528 AAGGGTTTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.05
19 6 0.16
20 13 0.34
21 9 0.24
22 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAATTAAATTTTAAAAA
Found at i:2560486 original size:25 final size:26
Alignment explanation
Indices: 2560401--2560492 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
2560391 AATTAATTAA
2560401 ATTTAA-AAA-TTTAATAAATAATAAT
1 ATTTAATAAATTTTAATAAA-AATAAT
* *
2560426 TTATTAATTATTATTTTTAATAAAAATAAT
1 AT-TTAA-TA--AATTTTAATAAAAATAAT
* *
2560456 ATTTAATTAAATTTTAA-AAAATTTAT
1 ATTTAA-TAAATTTTAATAAAAATAAT
2560482 A-TTAATAAATT
1 ATTTAATAAATT
2560493 AAAATATTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
24 6 0.11
25 5 0.09
26 12 0.22
27 7 0.13
28 1 0.02
29 7 0.13
30 8 0.15
31 9 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTAATAAATTTTAATAAAAATAAT
Found at i:2560490 original size:24 final size:27
Alignment explanation
Indices: 2560410--2560492 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 27
2560400 AATTTAAAAA
* *
2560410 TTTAATAAATAATAATTTATTAATTATTATT
1 TTTAATAAA-AATAATAT-TTAATTA--AAT
2560441 TTTAATAAAAATAATATTTAATTAAAT
1 TTTAATAAAAATAATATTTAATTAAAT
* *
2560468 TTTAA-AAAATTTATA-TTAA-TAAAT
1 TTTAATAAAAATAATATTTAATTAAAT
2560492 T
1 T
2560493 AAAATATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.12
25 4 0.08
26 8 0.17
27 7 0.15
29 7 0.15
30 7 0.15
31 9 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAATAAAAATAATATTTAATTAAAT
Found at i:2560503 original size:41 final size:39
Alignment explanation
Indices: 2560441--2560619 Score: 121
Period size: 40 Copynumber: 4.7 Consensus size: 39
2560431 AATTATTATT
*
2560441 TTTAA-TAAAAA-TAATAT-TTAATTAAATTTTAAAAAA
1 TTTAATTAAAAATTAAAATATTAATTAAATTTTAAAAAA
*
2560477 TTTATATTAATAAATTAAAATATTAATT-ATTTTTAAAAAAA
1 TTTA-ATTAA-AAATTAAAATATTAATTAAATTTT-AAAAAA
* * * * * *
2560518 TTAAATTAAAAAGGGTT-TATTATT-ATT-ATTTTTTAATAA
1 TTTAATTAAAAA---TTAAAATATTAATTAAATTTTAAAAAA
*
2560557 ---AATTAAAAA-TAATAT-TTAATTAAATTTTAAAAAA
1 TTTAATTAAAAATTAAAATATTAATTAAATTTTAAAAAA
2560591 TTTACATTAATAAATTAAAATATTAATTA
1 TTTA-ATTAA-AAATTAAAATATTAATTA
2560620 TATGTTTTTA
Statistics
Matches: 110, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
32 3 0.03
33 4 0.04
34 9 0.08
36 13 0.12
37 2 0.02
38 8 0.07
39 13 0.12
40 29 0.26
41 27 0.25
42 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (39 bp):
TTTAATTAAAAATTAAAATATTAATTAAATTTTAAAAAA
Found at i:2560544 original size:114 final size:110
Alignment explanation
Indices: 2560444--2560717 Score: 378
Period size: 114 Copynumber: 2.5 Consensus size: 110
2560434 TATTATTTTT
*
2560444 AATAAAAATAATATTTAATTAAATTTTAAAAAATTTATATTAATAAATTAAAATATTAATTAT-T
1 AATAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATAT
* *
2560508 -TTTAAAAAAATTAAATTAAAAAGGGTTTATTATTATTATTTTTTAATAA
66 GTTT-AAAAAA--AAA-TAAAAAGGATTTATTATTATTA-ATTTTAATAA
2560557 AATTAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATA
1 AA-TAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATA
** * *
2560622 TGTTTTTATAAAAATAAAAAGTATTTATTATTATT-A-TTTAATAA
65 TGTTTAAAAAAAAATAAAAAGGATTTATTATTATTAATTTTAATAA
* *
2560666 AATAAAAATGATATTTAA-TAAATTTTAAAAAATTTACATTAACAAATTAAAA
1 AATAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAATAAATTAAAA
2560718 AAATAGTATT
Statistics
Matches: 149, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
107 33 0.22
108 15 0.10
109 10 0.07
112 19 0.13
113 5 0.03
114 60 0.40
115 4 0.03
116 3 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (110 bp):
AATAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAATAAATTAAAATATTAATTATAT
GTTTAAAAAAAAATAAAAAGGATTTATTATTATTAATTTTAATAA
Found at i:2561183 original size:120 final size:119
Alignment explanation
Indices: 2561034--2561384 Score: 387
Period size: 120 Copynumber: 2.9 Consensus size: 119
2561024 TAAAAATATT
*
2561034 ATTATAATAAAAAACTTTTTTTAATTTAAAAATTTTTATTTTTAAAAACATAATAATTAATATTT
1 ATTATAATAAAAAAC--TTCTT-ATTTAAAAATTTTTATTTTT-AAAA-ATAATAATTAATATTT
*
2561099 TAATTTGTTAATGTAAAATTTTAAACTTAATTGAATATTATTTTT-ATTTTATT-AAAA
61 TAATTTGTTAATGTAAAATTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
* * *
2561156 ATTATAATAAAAAACTTCTTCATTTAAAATTTTTTATTTTTATAAAGTATATGATTAATATTTTA
1 ATTATAATAAAAAACTTCTT-ATTTAAAAATTTTTATTTTTA-AAAATA-ATAATTAATATTTTA
** *
2561221 ATTTGTTAATGTAATTTTTTAAAATTTAATTAAATATTATTTTTAATTTTATTAAAAA
63 ATTTGTTAATGTAAAATTTT-AAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
* * * * *
2561279 ATAATAATAATAAGC-CCTT-TTTAATTTAATTTTTA--TTT-AAAA-AA-AATTAATATTTTAA
1 ATTATAATAAAAAACTTCTTATTTAA--AAATTTTTATTTTTAAAAATAATAATTAATATTTTAA
* *
2561337 TTTATTAATGTAAATATTTTAAAGTTAATTAAATATTATTTTTTAATT
64 TTTGTTAATGTAAA-ATTTTAAACTTAATTAAATATTA-TTTTTAATT
2561385 AAAAAATAAT
Statistics
Matches: 199, Mismatches: 21, Indels: 24
0.82 0.09 0.10
Matches are distributed among these distances:
115 42 0.21
116 14 0.07
117 1 0.01
118 3 0.02
119 3 0.02
120 66 0.33
121 21 0.11
122 33 0.17
123 16 0.08
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (119 bp):
ATTATAATAAAAAACTTCTTATTTAAAAATTTTTATTTTTAAAAATAATAATTAATATTTTAATT
TGTTAATGTAAAATTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
Found at i:2561432 original size:115 final size:116
Alignment explanation
Indices: 2561086--2561433 Score: 310
Period size: 115 Copynumber: 3.0 Consensus size: 116
2561076 TAAAAACATA
* *
2561086 ATAATTAATATTTTAATTTGTTAATGTAAA-ATTTTAAACTTAATTGAATATTATTTTTATTTTA
1 ATAATTAATATTTTAATTTGTTAATGTAAATATTTTAAACTTAATTAAATATTA--TTT-TTTAA
*
2561150 TTAAAAATTATAATAA-AA-AACTTCTTCATTTA--AAATTTTTTATTTTTATAAAGTAT
63 TTAAAAA--ATAATAATAATAACTTCTT-ATTTATTAAATTTTTTA-ATTTA-AAAG-AT
* * *
2561206 ATGATTAATATTTTAATTTGTTAATGT-AATTTTTTAAAATTTAATTAAATATTATTTTTAATTT
1 ATAATTAATATTTTAATTTGTTAATGTAAATATTTT-AAACTTAATTAAATATTA--TTT--TTT
* * *
2561270 TATTAAAAAATAATAATAATAAGC-CCTT-TTTAATTTAA-TTTTT-ATTTAAAA-A-
61 AATTAAAAAATAATAATAATAA-CTTCTTATTT-ATTAAATTTTTTAATTTAAAAGAT
* *
2561322 A-AATTAATATTTTAATTTATTAATGTAAATATTTTAAAGTTAATTAAATATTATTTTTTAATTA
1 ATAATTAATATTTTAATTTGTTAATGTAAATATTTTAAACTTAATTAAATATTATTTTTTAATTA
* *
2561386 AAAAATAATAATTACTATA-TTATTATTTATTAAATTTTTTAAATTTAA
66 AAAAATAATAA-TAATA-ACTTCTTATTTATTAAATTTTTT-AATTTAA
2561434 TTAATTTATT
Statistics
Matches: 195, Mismatches: 16, Indels: 39
0.78 0.06 0.16
Matches are distributed among these distances:
111 18 0.09
112 11 0.06
113 12 0.06
115 46 0.24
116 8 0.04
117 1 0.01
119 5 0.03
120 44 0.23
121 24 0.12
122 23 0.12
123 3 0.02
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (116 bp):
ATAATTAATATTTTAATTTGTTAATGTAAATATTTTAAACTTAATTAAATATTATTTTTTAATTA
AAAAATAATAATAATAACTTCTTATTTATTAAATTTTTTAATTTAAAAGAT
Found at i:2561730 original size:20 final size:21
Alignment explanation
Indices: 2561702--2561740 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2561692 TATTTTTAAA
*
2561702 ATTTTCATA-AAATATATTAT
1 ATTTACATATAAATATATTAT
2561722 ATTTACATATAAATATATT
1 ATTTACATATAAATATATT
2561741 TCAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTACATATAAATATATTAT
Found at i:2561740 original size:16 final size:16
Alignment explanation
Indices: 2561719--2561769 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2561709 TAAAATATAT
2561719 TATATTTACATATAAA
1 TATATTTACATATAAA
*
2561735 TATATTT-CA-ATTATA
1 TATATTTACATA-TAAA
* *
2561750 TATATTTAAATGTAAA
1 TATATTTACATATAAA
2561766 TATA
1 TATA
2561770 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 12 0.43
16 15 0.54
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (16 bp):
TATATTTACATATAAA
Found at i:2561752 original size:21 final size:21
Alignment explanation
Indices: 2561707--2561753 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2561697 TTAAAATTTT
*
2561707 CATA-AAATATATTATATTTA
1 CATATAAATATATTATAATTA
2561727 CATATAAATATATT-TCAATTA
1 CATATAAATATATTAT-AATTA
*
2561748 TATATA
1 CATATA
2561754 TTTAAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
CATATAAATATATTATAATTA
Found at i:2562869 original size:3 final size:3
Alignment explanation
Indices: 2562861--2562904 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2562851 CAGGGTTTTT
2562861 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2562905 TTTTTAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2565557 original size:12 final size:14
Alignment explanation
Indices: 2565526--2565558 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2565516 TAAATTTATA
2565526 AAAAAATATATTTT
1 AAAAAATATATTTT
2565540 AAAAAATAT-TTTT
1 AAAAAATATATTTT
2565553 CAAAAA
1 -AAAAA
2565559 GCAGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:2570296 original size:28 final size:28
Alignment explanation
Indices: 2570265--2570382 Score: 73
Period size: 28 Copynumber: 4.0 Consensus size: 28
2570255 CTCAATTTCC
*
2570265 TTTTTTTTTTTAATATTATATATTAAAA
1 TTTTTTTTTTAAATATTATATATTAAAA
* * *
2570293 TTTTATTATTCAATA-TATAATATTTAATTATTA
1 TTTTTTTTTTAAATATTAT-ATA-TTAA--A--A
2570326 TATTATTATTTTTAAATATTATATATTAAAA
1 T-TT-TT-TTTTTAAATATTATATATTAAAA
* *
2570357 --TTTTATTTAAA-AATATATATTAAAA
1 TTTTTTTTTTAAATATTATATATTAAAA
2570382 T
1 T
2570383 ACAATATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
25 13 0.18
26 7 0.10
27 5 0.07
28 16 0.23
29 4 0.06
31 2 0.03
33 3 0.04
34 2 0.03
35 5 0.07
36 11 0.15
37 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTTTTTTTAAATATTATATATTAAAA
Found at i:2570317 original size:22 final size:23
Alignment explanation
Indices: 2570282--2570324 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2570272 TTTTAATATT
*
2570282 ATATATTAAAATTTTATTATTCA
1 ATATATTAAAATTTAATTATTCA
*
2570305 ATATA-TAATATTTAATTATT
1 ATATATTAAAATTTAATTATT
2570325 ATATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATTAAAATTTAATTATTCA
Found at i:2573450 original size:34 final size:34
Alignment explanation
Indices: 2573402--2573487 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
2573392 TAAAGTAAAA
* *
2573402 AATACTTCAAAATCATCTT-AAAGTAATTCGATTT
1 AATATTTCAAAATCAT-TTCAAACTAATTCGATTT
*
2573436 AATATTTCAAAATCATTTCAATCTAATTCGATTT
1 AATATTTCAAAATCATTTCAAACTAATTCGATTT
*
2573470 AATAATTTTAAATATCAT
1 AAT-ATTTCAAA-ATCAT
2573488 ATAATTATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 2 0.04
34 31 0.69
35 7 0.16
36 5 0.11
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (34 bp):
AATATTTCAAAATCATTTCAAACTAATTCGATTT
Found at i:2573513 original size:11 final size:11
Alignment explanation
Indices: 2573478--2573549 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
2573468 TTAATAATTT
*
2573478 TAAATATCATA
1 TAAATATAATA
*
2573489 TAATTATATGATA
1 TAA--ATATAATA
2573502 TAAATATAATA
1 TAAATATAATA
*
2573513 TAAAAATAAT-
1 TAAATATAATA
2573523 TAAA-AT-ATA
1 TAAATATAATA
*
2573532 -AAAAATAATA
1 TAAATATAATA
2573542 TAAATATA
1 TAAATATA
2573550 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 5 0.10
9 4 0.08
10 7 0.14
11 25 0.49
13 10 0.20
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2573522 original size:30 final size:29
Alignment explanation
Indices: 2573499--2573556 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
2573489 TAATTATATG
*
2573499 ATAT-AAATATAATATAAAAATAATTAAA
1 ATATAAAAAATAATATAAAAATAATTAAA
*
2573527 ATATAAAAAATAATATAAATAT-ATTAAA
1 ATATAAAAAATAATATAAAAATAATTAAA
2573555 AT
1 AT
2573557 TTATATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATATAAAAAATAATATAAAAATAATTAAA
Found at i:2573537 original size:18 final size:19
Alignment explanation
Indices: 2573499--2573555 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 19
2573489 TAATTATATG
2573499 ATATAAATATAATATAAAAATA
1 ATATAAA-AT-ATA-AAAAATA
2573521 AT-TAAAATATAAAAAATA
1 ATATAAAATATAAAAAATA
2573539 ATATAAATATATTAAAA
1 ATATAAA-ATA-TAAAA
2573556 TTTATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 5 0.16
21 9 0.28
22 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAAATATAAAAAATA
Found at i:2573652 original size:18 final size:18
Alignment explanation
Indices: 2573629--2573664 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2573619 TATAAATCGT
*
2573629 AAAATTATATGAATATAA
1 AAAATTATACGAATATAA
2573647 AAAATTATACGAATATAA
1 AAAATTATACGAATATAA
2573665 TATAAATATA
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:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAATTATACGAATATAA
Found at i:2574294 original size:3 final size:3
Alignment explanation
Indices: 2574286--2574328 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2574276 ATAGAACGAC
2574286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2574329 GTGTATATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2574537 original size:18 final size:17
Alignment explanation
Indices: 2574490--2574544 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
2574480 ATATTTATTT
2574490 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
2574506 T-ATA-TTAT-TAAAATA
1 TAAAATTTATAT-AAATA
2574521 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
2574539 TAAAAT
1 TAAAAT
2574545 ATCTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 6 0.19
16 2 0.06
17 8 0.26
18 9 0.29
19 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2575096 original size:18 final size:18
Alignment explanation
Indices: 2575054--2575097 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2575044 GTAAAGAATT
* *
2575054 TTTATATTATTTATAATC
1 TTTATATTATATATAATA
*
2575072 TTAATATTATATATAATA
1 TTTATATTATATATAATA
2575090 TTTATATT
1 TTTATATT
2575098 TAATGTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATATTATATATAATA
Found at i:2596370 original size:3 final size:3
Alignment explanation
Indices: 2596359--2596388 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2596349 TGGTGGTACG
2596359 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA
2596389 CTTCGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2596675 original size:19 final size:19
Alignment explanation
Indices: 2596638--2596684 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2596628 TTTTATTTTG
*
2596638 TTATTTAA-TATTATAAAT
1 TTATTTAATTTTTATAAAT
*
2596656 TTATTTAATTTTTATTAAT
1 TTATTTAATTTTTATAAAT
2596675 TTA-TTAATTT
1 TTATTTAATTT
2596685 AATTGATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTAATTTTTATAAAT
Found at i:2597630 original size:19 final size:19
Alignment explanation
Indices: 2597606--2597650 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2597596 TAAATAAAAT
2597606 TAATTTTATTAGAT-ATAAG
1 TAATTTTATTA-ATAATAAG
*
2597625 TAATTTT-TTAATAATGAG
1 TAATTTTATTAATAATAAG
2597643 TAATTTTA
1 TAATTTTA
2597651 AATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
19 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (19 bp):
TAATTTTATTAATAATAAG
Found at i:2598342 original size:3 final size:3
Alignment explanation
Indices: 2598288--2598327 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2598278 CCTCTTAGAT
2598288 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2598328 ATTAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2598390 original size:3 final size:3
Alignment explanation
Indices: 2598382--2598426 Score: 56
Period size: 3 Copynumber: 14.3 Consensus size: 3
2598372 GTAAAATGCA
2598382 ATT ATT ATTT ATT ATAT ATT -TAT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT A-TT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT ATT A
2598427 AAATGTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 1 0.03
3 30 0.79
4 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.