Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 19 of 56
Found at i:3442620 original size:15 final size:15
Alignment explanation
Indices: 3442573--3442622 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
3442563 TTAAGAAATA
3442573 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
* * *
3442588 TATTAAATTTAATA-
1 TTTTAATTTTTATAT
*
3442602 TTTTAGTTTTTATAT
1 TTTTAATTTTTATAT
3442617 TTTTAA
1 TTTTAA
3442623 AATATTAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTAATTTTTATAT
Found at i:3442649 original size:18 final size:18
Alignment explanation
Indices: 3442621--3442661 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3442611 TTATATTTTT
3442621 AAAATATTAATAA-ATAA
1 AAAATATTAATAATATAA
*
3442638 AAAATAATTAATAATATTA
1 AAAAT-ATTAATAATATAA
3442657 AAAAT
1 AAAAT
3442662 TATTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATTAATAATATAA
Found at i:3442684 original size:11 final size:10
Alignment explanation
Indices: 3442622--3442686 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
3442612 TATATTTTTA
3442622 AAATATTAAT
1 AAATATTAAT
3442632 AAATA--AA-
1 AAATATTAAT
3442639 AAATAATTAAT
1 AAAT-ATTAAT
3442650 -AATATTAA-
1 AAATATTAAT
3442658 AAATTATT--T
1 AAA-TATTAAT
3442667 AAATATTAAT
1 AAATATTAAT
3442677 AAATTATTAA
1 AAA-TATTAA
3442687 CGTATTATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 19
0.70 0.00 0.30
Matches are distributed among these distances:
7 4 0.09
8 7 0.16
9 10 0.22
10 18 0.40
11 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATTAAT
Found at i:3442883 original size:14 final size:14
Alignment explanation
Indices: 3442866--3442917 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3442856 TATTATAATT
3442866 TTAAAATATAAAAA
1 TTAAAATATAAAAA
* *
3442880 TTAAAATATTAAAT
1 TTAAAATATAAAAA
3442894 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
*
3442909 ATAAAATAT
1 TTAAAATAT
3442918 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:3442895 original size:29 final size:30
Alignment explanation
Indices: 3442856--3442918 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
3442846 TTTATTTATT
*
3442856 TATTATAATTTTAA-AATATAAAAATTAAAA
1 TATTATAA-TTTAATAATATAAAAAATAAAA
3442886 TATTA-AATTTAATAATATAAAAAATAAAA
1 TATTATAATTTAATAATATAAAAAATAAAA
3442915 TATT
1 TATT
3442919 TTTTTTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 5 0.16
29 21 0.68
30 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TATTATAATTTAATAATATAAAAAATAAAA
Found at i:3443412 original size:18 final size:18
Alignment explanation
Indices: 3443375--3443413 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3443365 AAATTTAATA
* *
3443375 TAATTATATTTAATTTTT
1 TAATTATATTTAAGTATT
*
3443393 TAATTATTTTTAAGTATT
1 TAATTATATTTAAGTATT
3443411 TAA
1 TAA
3443414 AAAATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATTATATTTAAGTATT
Found at i:3444933 original size:55 final size:55
Alignment explanation
Indices: 3444867--3444979 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
3444857 CAAGATTTTG
*
3444867 TAAAAGTTAAACATTATCGTGGACAAAGTTTTAAAAATATAAATTAAATCTAATC
1 TAAAAGTTAAACATTATCATGGACAAAGTTTTAAAAATATAAATTAAATCTAATC
*
3444922 TAAAAGTTAAACATTATCATGGACAAAGTTTTAAAAATATAAATTAAATTTAATC
1 TAAAAGTTAAACATTATCATGGACAAAGTTTTAAAAATATAAATTAAATCTAATC
3444977 TAA
1 TAA
3444980 CTCGATCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (55 bp):
TAAAAGTTAAACATTATCATGGACAAAGTTTTAAAAATATAAATTAAATCTAATC
Found at i:3448244 original size:2 final size:2
Alignment explanation
Indices: 3448237--3448276 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3448227 GTTTAAAGGA
3448237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3448277 CCAGCTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3448919 original size:19 final size:19
Alignment explanation
Indices: 3448897--3448944 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3448887 TTTTTTATTA
3448897 TTTAA-AATATATTAAATAT
1 TTTAATAATAT-TTAAATAT
*
3448916 TTTAATTAATATTTATATAT
1 TTTAA-TAATATTTAAATAT
*
3448936 TTTTATAAT
1 TTTAATAAT
3448945 TAAAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.36
20 11 0.44
21 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATAATATTTAAATAT
Found at i:3450107 original size:5 final size:5
Alignment explanation
Indices: 3450099--3450123 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3450089 TAATTAAAGT
3450099 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
3450124 ACAGCTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:3450633 original size:2 final size:2
Alignment explanation
Indices: 3450626--3450672 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
3450616 ACATACATAC
* * *
3450626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3450668 AT AT A
1 AT AT A
3450673 CACACACGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3451779 original size:6 final size:6
Alignment explanation
Indices: 3451761--3451790 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3451751 TCATTTAAAA
3451761 AAATTT AAAATTT AAATTT AAATTT AAATT
1 AAATTT -AAATTT AAATTT AAATTT AAATT
3451791 CAACCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:3451890 original size:21 final size:20
Alignment explanation
Indices: 3451865--3451913 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3451855 TTGTAATTAA
*
3451865 AATTAAATAAAAATATTATTT
1 AATTAAATAAAAA-ATTATTC
*
3451886 AATTAAATAAATAATTATTC
1 AATTAAATAAAAAATTATTC
*
3451906 AAATAAAT
1 AATTAAAT
3451914 TAAATCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAATAAAAAATTATTC
Found at i:3452988 original size:16 final size:17
Alignment explanation
Indices: 3452967--3453003 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
3452957 ATCTCCAAAT
3452967 TATCAAATATATATA-A
1 TATCAAATATATATATA
3452983 TATCAAATATATATATA
1 TATCAAATATATATATA
3453000 TATC
1 TATC
3453004 TGTAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TATCAAATATATATATA
Found at i:3457114 original size:2 final size:2
Alignment explanation
Indices: 3457107--3457148 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3457097 ATCATATTAA
*
3457107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3457149 GAAATCTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3466837 original size:16 final size:16
Alignment explanation
Indices: 3466803--3466841 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3466793 ACCTTTATCT
3466803 TTCAATAATTAATTATA
1 TTCAA-AATTAATTATA
* *
3466820 TTCAAAATTTATTCTA
1 TTCAAAATTAATTATA
3466836 TTCAAA
1 TTCAAA
3466842 TATGTAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (16 bp):
TTCAAAATTAATTATA
Found at i:3467459 original size:4 final size:4
Alignment explanation
Indices: 3467450--3467511 Score: 76
Period size: 4 Copynumber: 15.8 Consensus size: 4
3467440 GTGCCATTGC
*
3467450 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT -AAT -AAT AAAAC AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
3467496 AAAT AAAT AAAAT AAA
1 AAAT AAAT -AAAT AAA
3467512 AATCTTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 9 0.17
4 38 0.72
5 6 0.11
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3470814 original size:6 final size:6
Alignment explanation
Indices: 3470804--3470874 Score: 124
Period size: 6 Copynumber: 11.8 Consensus size: 6
3470794 TTATATATTT
* *
3470804 ATATAC GTATAC GTATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
3470852 ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATA
3470875 TTCTCAATTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:3476968 original size:19 final size:20
Alignment explanation
Indices: 3476928--3476968 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3476918 ATTTTATTAG
* *
3476928 AATTTTTTTTTTTTTCGTGA
1 AATTTTATTTTTTTTCGCGA
3476948 AATTTTATTTTTTTTC-CGA
1 AATTTTATTTTTTTTCGCGA
3476967 AA
1 AA
3476969 ATCATTCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (20 bp):
AATTTTATTTTTTTTCGCGA
Found at i:3477203 original size:21 final size:22
Alignment explanation
Indices: 3477170--3477227 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
3477160 TATATTAATA
3477170 ATTTATATATTTATATCATA-TTT
1 ATTTAT-T-TTTATATCATATTTT
*
3477193 ATTTATTTTTAT-TTATATTTT
1 ATTTATTTTTATATCATATTTT
*
3477214 AATTATTTTTATAT
1 ATTTATTTTTATAT
3477228 TTTATTCGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 2 0.06
23 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATTTTTATATCATATTTT
Found at i:3477205 original size:10 final size:10
Alignment explanation
Indices: 3477190--3477225 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3477180 TTATATCATA
3477190 TTTATTTATT
1 TTTATTTATT
3477200 TTTATTTATAT
1 TTTATTTAT-T
*
3477211 TTTAATTATT
1 TTTATTTATT
3477221 TTTAT
1 TTTAT
3477226 ATTTTATTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTATTTATT
Found at i:3477220 original size:29 final size:32
Alignment explanation
Indices: 3477170--3477230 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 32
3477160 TATATTAATA
3477170 ATTTATATATTTATATCATATTTATT-TATTTTT
1 ATTTATATATTTATAT-ATATTT-TTATATTTTT
3477203 ATTTATAT-TTTA-AT-TATTTTTATATTTT
1 ATTTATATATTTATATATATTTTTATATTTT
3477231 ATTCGTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 2 0.07
29 11 0.41
31 2 0.07
32 4 0.15
33 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (32 bp):
ATTTATATATTTATATATATTTTTATATTTTT
Found at i:3480947 original size:21 final size:21
Alignment explanation
Indices: 3480909--3480952 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3480899 TGATAAATTA
* *
3480909 AATTAAATTAAAATTATTATTT
1 AATTAAATAAAAAATATT-TTT
3480931 AATT-AATAAAAAATATTTTT
1 AATTAAATAAAAAATATTTTT
3480951 AA
1 AA
3480953 AATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAAATAAAAAATATTTTT
Found at i:3480998 original size:22 final size:21
Alignment explanation
Indices: 3480932--3481000 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
3480922 TTATTATTTA
* *
3480932 ATTAATAAAAAATATTTTTAAA
1 ATTAATATAAAA-ATTTTTAAT
* *
3480954 ATTTAATTTAAAAATATATTAAT
1 A-TTAATATAAAAAT-TTTTAAT
3480977 ATTAATATAAATAATTTTTAAT
1 ATTAATATAAA-AATTTTTAAT
3480999 AT
1 AT
3481001 ATTTTAAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 20 0.53
23 18 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAATATAAAAATTTTTAAT
Found at i:3481525 original size:29 final size:28
Alignment explanation
Indices: 3481493--3481548 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
3481483 TTTATAATTT
* *
3481493 TATTTAAATAAATTTTTATATTTTTATTA
1 TATTCAAATAAATCTTT-TATTTTTATTA
3481522 TATTCAAATAAATCTTTTATTTTTATT
1 TATTCAAATAAATCTTTTATTTTTATT
3481549 TTTCATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTCAAATAAATCTTTTATTTTTATTA
Found at i:3481689 original size:29 final size:30
Alignment explanation
Indices: 3481646--3481724 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 30
3481636 ATATTTTATT
* *
3481646 AAATTTAAAAATTATTTAAATATAAATAAA
1 AAATATAAAATTTATTTAAATATAAATAAA
*
3481676 AAATAT-AAATTTATTT-GAT-T--ATAAA
1 AAATATAAAATTTATTTAAATATAAATAAA
3481701 AAATATAAAATTT-TTTAAA-ATAAA
1 AAATATAAAATTTATTTAAATATAAA
3481725 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
25 14 0.35
26 8 0.20
27 1 0.03
28 3 0.08
29 9 0.22
30 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATATAAAATTTATTTAAATATAAATAAA
Found at i:3492308 original size:12 final size:12
Alignment explanation
Indices: 3492281--3492323 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3492271 TACAATCGCT
*
3492281 TTCCTCCGTCAT
1 TTCCTCCGTCAC
*
3492293 TTCCTCCGTCCC
1 TTCCTCCGTCAC
* *
3492305 TTCCTCCCTCTC
1 TTCCTCCGTCAC
3492317 TTCCTCC
1 TTCCTCC
3492324 CCAAACCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.02, C:0.53, G:0.05, T:0.40
Consensus pattern (12 bp):
TTCCTCCGTCAC
Found at i:3493425 original size:18 final size:18
Alignment explanation
Indices: 3493393--3493539 Score: 80
Period size: 18 Copynumber: 8.3 Consensus size: 18
3493383 TAATTTCATG
*
3493393 TATTTATATTGTATTTATA
1 TATTT-TATTATATTTATA
3493412 TATTTTATTATA-TTATA
1 TATTTTATTATATTTATA
* *
3493429 -A--TTA-TAT-TTAAAA
1 TATTTTATTATATTTATA
3493442 TATTTTA-TATATTTATA
1 TATTTTATTATATTTATA
*
3493459 TATTTT-TTAATAAGTTA-A
1 TATTTTATT-AT-ATTTATA
*
3493477 TAATTTATATTATATATATA
1 T-ATTT-TATTATATTTATA
* **
3493497 AATTTTAAAATATTTATA
1 TATTTTATTATATTTATA
*
3493515 AATTTATATTAT-TTTATAA
1 TATTT-TATTATATTTAT-A
3493534 TATTTT
1 TATTTT
3493540 TTAAATCATA
Statistics
Matches: 99, Mismatches: 15, Indels: 29
0.69 0.10 0.20
Matches are distributed among these distances:
13 6 0.06
14 4 0.04
16 7 0.07
17 16 0.16
18 31 0.31
19 29 0.29
20 4 0.04
21 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (18 bp):
TATTTTATTATATTTATA
Found at i:3493425 original size:29 final size:29
Alignment explanation
Indices: 3493393--3493539 Score: 90
Period size: 29 Copynumber: 4.9 Consensus size: 29
3493383 TAATTTCATG
* *
3493393 TATTTATATTGTATTT-ATATATTTTAT-
1 TATTTATATTATATTTAAAATATTTTATA
3493420 TATATTATAATTATATTTAAAATATTTTATA
1 TAT-TTAT-ATTATATTTAAAATATTTTATA
*
3493451 TATTTATA-TATTTTTTAATAAGTTAATAATTTATA
1 TATTTATATTA-TATTTAA-AA--T-AT--TTTATA
* *
3493486 T-TATATATATAAATTTTAAAATA-TTTATA
1 TATTTATAT-TATA-TTTAAAATATTTTATA
* *
3493515 AATTTATATTAT-TTTATAATATTTT
1 TATTTATATTATATTTAAAATATTTT
3493540 TTAAATCATA
Statistics
Matches: 94, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
27 11 0.12
28 9 0.10
29 23 0.24
30 22 0.23
31 3 0.03
32 2 0.02
33 3 0.03
34 5 0.05
35 9 0.10
36 7 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
TATTTATATTATATTTAAAATATTTTATA
Found at i:3493505 original size:65 final size:65
Alignment explanation
Indices: 3493413--3493535 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 65
3493403 GTATTTATAT
* *
3493413 ATTTTATTATATTATAATTATATTTAAAATATTTTATATATTTATA-TATTTTTTAATAAGTTAA
1 ATTTTATTATATTATAA-TATATTTAAAATA-TTTATAAATTTATATTATTTTATAATAAGTTAA
3493477 TA
64 TA
3493479 ATTTATATTATATATATAA-AT-TTTAAAATATTTATAAATTTATATTATTTTATAATA
1 ATTT-TATTATAT-TATAATATATTTAAAATATTTATAAATTTATATTATTTTATAATA
3493536 TTTTTTAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
64 13 0.25
65 20 0.38
66 6 0.12
67 8 0.15
68 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (65 bp):
ATTTTATTATATTATAATATATTTAAAATATTTATAAATTTATATTATTTTATAATAAGTTAATA
Found at i:3493530 original size:10 final size:10
Alignment explanation
Indices: 3493406--3493539 Score: 67
Period size: 8 Copynumber: 14.3 Consensus size: 10
3493396 TTATATTGTA
3493406 TTTAT-ATAT
1 TTTATAATAT
3493415 TTTAT--TAT
1 TTTATAATAT
*
3493423 ATTATAATTAT
1 TTTATAA-TAT
*
3493434 ATTTAAAATAT
1 -TTTATAATAT
3493445 TTTAT-ATA-
1 TTTATAATAT
3493453 TTTAT-ATAT
1 TTTATAATAT
*
3493462 TTTTTAATA-
1 TTTATAATAT
** *
3493471 AGT-TAATAA
1 TTTATAATAT
*
3493480 TTTATATTAT
1 TTTATAATAT
*
3493490 ATATATAA-AT
1 -TTTATAATAT
*
3493500 TTTAAAATA-
1 TTTATAATAT
3493509 TTTATAA-A-
1 TTTATAATAT
*
3493517 TTTATATTAT
1 TTTATAATAT
3493527 TTTATAATAT
1 TTTATAATAT
3493537 TTT
1 TTT
3493540 TTAAATCATA
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
8 27 0.28
9 26 0.27
10 26 0.27
11 11 0.12
12 5 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTATAATAT
Found at i:3493535 original size:27 final size:26
Alignment explanation
Indices: 3493498--3493569 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
3493488 ATATATATAA
*
3493498 ATTTTAAAATATTTATAAATTTATATT
1 ATTTT-AAATATTTATAAATTCATATT
*
3493525 ATTTTATAATATTTTTTAAA-TCATATT
1 ATTTTA-AATA-TTTATAAATTCATATT
*
3493552 ATGTTAAATA-TTATAAAT
1 ATTTTAAATATTTATAAAT
3493570 CTAAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 6 0.16
26 5 0.13
27 20 0.53
28 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
ATTTTAAATATTTATAAATTCATATT
Found at i:3493553 original size:64 final size:66
Alignment explanation
Indices: 3493417--3493562 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 66
3493407 TTATATATTT
* * *
3493417 TATTATATTATAATTATATTTAAAATATTTTATATATTTATATATTTTTTAATAAGTTAATAATT
1 TATTATATTATAA-TATATTTAAAATATTTTATAAATTTATATATTTTATAATAAGTTAATAAAT
*
3493482 TA
65 CA
* **
3493484 TATTATATATATAA-AT-TTTAAAATA-TTTATAAATTTATATTATTTTATAAT-ATTTTTTAAA
1 TATTATAT-TATAATATATTTAAAATATTTTATAAATTTATA-TATTTTATAATAAGTTAATAAA
3493545 TCA
64 TCA
*
3493548 TATTATGTTA-AATAT
1 TATTATATTATAATAT
3493563 TATAAATCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
62 2 0.03
63 4 0.06
64 28 0.41
65 19 0.28
66 2 0.03
67 8 0.12
68 5 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (66 bp):
TATTATATTATAATATATTTAAAATATTTTATAAATTTATATATTTTATAATAAGTTAATAAATC
A
Found at i:3494111 original size:19 final size:18
Alignment explanation
Indices: 3494089--3494139 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
3494079 AGAGTTAGTG
3494089 ATTTATATATTCATATTAT
1 ATTTATATATT-ATATTAT
*
3494108 ATTTATATATTTTATTAT
1 ATTTATATATTATATTAT
*
3494126 A-TCATA-ATTATATT
1 ATTTATATATTATATT
3494140 TAATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.24
17 4 0.14
18 7 0.24
19 11 0.38
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATATATTATATTAT
Found at i:3494187 original size:18 final size:18
Alignment explanation
Indices: 3494154--3494188 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3494144 ATATTTTAAA
3494154 TTTATATAATTTTATTAC
1 TTTATATAATTTTATTAC
3494172 TTTA-ATAATTTATATTA
1 TTTATATAATTT-TATTA
3494189 TATAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATAATTTTATTAC
Found at i:3495434 original size:22 final size:21
Alignment explanation
Indices: 3495369--3495435 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
3495359 TTTTTTAAAA
* *
3495369 AAATTAAATTAATATAATTAA
1 AAATTTAATTAATATAATTAT
* * *
3495390 AAATTTGATAAACAGTAATTAT
1 AAATTTAATTAATA-TAATTAT
*
3495412 AAATTTAATTAATATTAAATAT
1 AAATTTAATTAATA-TAATTAT
3495434 AA
1 AA
3495436 TTATTCAGTA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 10 0.29
22 25 0.71
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (21 bp):
AAATTTAATTAATATAATTAT
Found at i:3507064 original size:2 final size:2
Alignment explanation
Indices: 3507057--3507090 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3507047 TTCCCTTCTT
3507057 TC TC 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 TC TC
3507091 GGCAATCTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3507737 original size:51 final size:53
Alignment explanation
Indices: 3507643--3507743 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 53
3507633 AAATTTTATA
*
3507643 TTAATAATAATAATAATATAAATTTAAAAATATTATAATCTTTTA-ATAATTT
1 TTAATAATAATAATAATAAAAATTTAAAAATATTATAATCTTTTATATAATTT
*
3507695 TTAA-AATAATTAATAA-AAAAATATTAAAAA-ATTAT-TTACTTTTATATAA
1 TTAATAATAA-TAATAATAAAAAT-TTAAAAATATTATAAT-CTTTTATATAA
3507744 AAAGTTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
50 1 0.02
51 21 0.49
52 21 0.49
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (53 bp):
TTAATAATAATAATAATAAAAATTTAAAAATATTATAATCTTTTATATAATTT
Found at i:3507941 original size:18 final size:19
Alignment explanation
Indices: 3507910--3507955 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3507900 AATGTTATAG
3507910 AATTAAAGATAATTATTT-TT
1 AATTAAA-A-AATTATTTATT
*
3507930 ATTTAAAAAATTATTTATT
1 AATTAAAAAATTATTTATT
3507949 AATTAAA
1 AATTAAA
3507956 TTTTTAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTAAAAAATTATTTATT
Found at i:3508096 original size:12 final size:13
Alignment explanation
Indices: 3508073--3508097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3508063 ATAGTAGAGA
3508073 AGTAATTTTTTTG
1 AGTAATTTTTTTG
3508086 AGTAATTTTTTT
1 AGTAATTTTTTT
3508098 AAGGGTAGTT
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
AGTAATTTTTTTG
Found at i:3508403 original size:18 final size:18
Alignment explanation
Indices: 3508380--3508414 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3508370 GTGACATGAG
3508380 TGAGTAATTTTTAAAATT
1 TGAGTAATTTTTAAAATT
* *
3508398 TGAGTAGTTTTTTAAAT
1 TGAGTAATTTTTAAAAT
3508415 ATAAAAATAT
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:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
TGAGTAATTTTTAAAATT
Found at i:3508527 original size:14 final size:14
Alignment explanation
Indices: 3508508--3508541 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3508498 TTAATATTAG
3508508 TCTATAATTTATAA
1 TCTATAATTTATAA
3508522 TCTATAATTTATAA
1 TCTATAATTTATAA
*
3508536 TATATA
1 TCTATA
3508542 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TCTATAATTTATAA
Found at i:3509687 original size:3 final size:3
Alignment explanation
Indices: 3509679--3509706 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3509669 TAGCGAACCC
3509679 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3509707 GGCATGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3510719 original size:15 final size:15
Alignment explanation
Indices: 3510699--3510732 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3510689 TTCGAGTTTG
*
3510699 ATTTAAATTGAATTA
1 ATTTAAATTAAATTA
3510714 ATTTAAATTAAATTA
1 ATTTAAATTAAATTA
3510729 ATTT
1 ATTT
3510733 TGATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAAATTA
Found at i:3511184 original size:4 final size:4
Alignment explanation
Indices: 3511177--3511229 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
3511167 TCGGCAGGAG
* * *
3511177 AGAA AGAA AGAA AGAA A-AA AAAA AGAA A-AA A-AA AGAA AGGA GGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
3511222 A-AA AGAA A
1 AGAA AGAA A
3511230 AAAAAGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
3 12 0.29
4 29 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3511212 original size:25 final size:24
Alignment explanation
Indices: 3511183--3511243 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
3511173 GGAGAGAAAG
3511183 AAAGAAAGAAAAAAAAAAGAAAAAA
1 AAAGAAAGAAAAAAAAAAG-AAAAA
* **
3511208 AAAGAAAGGAGGAAAAAAGAAAAA
1 AAAGAAAGAAAAAAAAAAGAAAAA
3511232 AAAGAAA-AAAAA
1 AAAGAAAGAAAAA
3511244 TATTTGTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.07
24 12 0.40
25 16 0.53
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAAAGAAAAAAAAAAGAAAAA
Found at i:3511231 original size:8 final size:8
Alignment explanation
Indices: 3511177--3511242 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
3511167 TCGGCAGGAG
*
3511177 AGAAAGAA
1 AGAAAAAA
*
3511185 AGAAAGAA
1 AGAAAAAA
3511193 A-AAAAAA
1 AGAAAAAA
3511200 AGAAAAAA
1 AGAAAAAA
*
3511208 A-AAGAAAGG
1 AGAA-AAA-A
*
3511217 AGGAAAAA
1 AGAAAAAA
3511225 AGAAAAAAA
1 AG-AAAAAA
3511234 AGAAAAAA
1 AGAAAAAA
3511242 A
1 A
3511243 ATATTTGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
7 8 0.17
8 28 0.58
9 11 0.23
10 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:3511231 original size:33 final size:34
Alignment explanation
Indices: 3511177--3511243 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
3511167 TCGGCAGGAG
3511177 AGAAAGAAAGAAAG-AAAAAAAAAAGAAAAAAAA
1 AGAAAGAAAGAAAGAAAAAAAAAAAGAAAAAAAA
* *
3511210 AGAAAGGAGGAAA-AAAGAAAAAAAAGAAAAAAAA
1 AGAAAGAAAGAAAGAAA-AAAAAAAAGAAAAAAAA
3511244 TATTTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (34 bp):
AGAAAGAAAGAAAGAAAAAAAAAAAGAAAAAAAA
Found at i:3511303 original size:31 final size:31
Alignment explanation
Indices: 3511253--3511343 Score: 155
Period size: 31 Copynumber: 2.9 Consensus size: 31
3511243 ATATTTGTAT
*
3511253 TTATATTTATGTTATTTTTTATATGTAAAATA
1 TTATATTTTTG-TATTTTTTATATGTAAAATA
3511285 TTATATTTTTGTATTTTTTATATGTAAAATA
1 TTATATTTTTGTATTTTTTATATGTAAAATA
*
3511316 TTATATTTTTGTATTTTTTATATATAAA
1 TTATATTTTTGTATTTTTTATATGTAAA
3511344 TAATTCGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 47 0.82
32 10 0.18
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (31 bp):
TTATATTTTTGTATTTTTTATATGTAAAATA
Found at i:3512387 original size:58 final size:59
Alignment explanation
Indices: 3512278--3512390 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 59
3512268 TATCATATTC
* * * *
3512278 GTATCGTATCTCCATTCATGACATATTTTACATAATTTTTTTTAATAATTTAATTTAAT
1 GTATCATATCTCAATTCATGACATATTTTACATAATTTGTTATAATAATTTAATTTAAT
* * * *
3512337 GTATCATATCTCAATTCGTGATAT-TTTTTCATAATTTGTTATAATGATTTAATT
1 GTATCATATCTCAATTCATGACATATTTTACATAATTTGTTATAATAATTTAATT
3512391 AAAAAAATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 26 0.57
59 20 0.43
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (59 bp):
GTATCATATCTCAATTCATGACATATTTTACATAATTTGTTATAATAATTTAATTTAAT
Found at i:3512535 original size:10 final size:10
Alignment explanation
Indices: 3512520--3512563 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
3512510 TTGTCAAGAG
3512520 AAAAAGAAAA
1 AAAAAGAAAA
*
3512530 AAAAAGATAGA
1 AAAAAGA-AAA
* *
3512541 AAAAAGGAGA
1 AAAAAGAAAA
3512551 AAAAAGAAAA
1 AAAAAGAAAA
3512561 AAA
1 AAA
3512564 TTATGTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3513568 original size:28 final size:27
Alignment explanation
Indices: 3513536--3513625 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
3513526 TTTATCTTAT
3513536 ATTTTATATAAATTTTTTATATAATTAA
1 ATTTTATATAAATTTTTTAT-TAATTAA
* *
3513564 ATTTTAATTTAAAATTTATTTATTAAAT-A
1 ATTTT-ATAT-AAATTT-TTTATTAATTAA
* *
3513593 TTTTTAAATAAA--TTTTATTAATTATA
1 ATTTTATATAAATTTTTTATTAATTA-A
3513619 ATTTTAT
1 ATTTTAT
3513626 TTAATTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 9 0.18
25 1 0.02
26 6 0.12
27 3 0.06
28 7 0.14
29 8 0.16
30 10 0.20
31 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATAAATTTTTTATTAATTAA
Found at i:3513585 original size:16 final size:15
Alignment explanation
Indices: 3513566--3513635 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 15
3513556 ATAATTAAAT
3513566 TTTAATTTAAAATTTA
1 TTTAA-TTAAAATTTA
3513582 TTT-ATT-AAATATT-
1 TTTAATTAAAAT-TTA
* *
3513595 TTTAAATAAATTTTA
1 TTTAATTAAAATTTA
*
3513610 -TTAATTATAATTTTA
1 TTTAATTA-AAATTTA
3513625 TTTAATTAAAA
1 TTTAATTAAAA
3513636 ATTTTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.16
14 14 0.32
15 13 0.30
16 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATTAAAATTTA
Found at i:3515184 original size:2 final size:2
Alignment explanation
Indices: 3515177--3515219 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3515167 ACCACTTTGG
*
3515177 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3515219 A
1 A
3515220 CATAACCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3526928 original size:17 final size:16
Alignment explanation
Indices: 3526891--3526931 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
3526881 GTGGAGGGAA
3526891 AAGGAGGGAA-GAGGG
1 AAGGAGGGAATGAGGG
3526906 --GGAGGGAATGTAGGG
1 AAGGAGGGAATG-AGGG
3526921 AAGGAGGGAAT
1 AAGGAGGGAAT
3526932 TAAGAGGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.36
14 1 0.05
15 4 0.18
17 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.56, T:0.07
Consensus pattern (16 bp):
AAGGAGGGAATGAGGG
Found at i:3532560 original size:17 final size:17
Alignment explanation
Indices: 3532540--3532576 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3532530 AATATTAATC
3532540 ATAT-ATTAATAAAAATA
1 ATATAATTAATAAAAA-A
3532557 ATATAATTAATAAAAAA
1 ATATAATTAATAAAAAA
3532574 ATA
1 ATA
3532577 AAAATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAATTAATAAAAAA
Found at i:3532576 original size:26 final size:26
Alignment explanation
Indices: 3532547--3532600 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
3532537 ATCATATATT
3532547 AATAAAAATAATATAATTAATAAAAA
1 AATAAAAATAATATAATTAATAAAAA
* * * *
3532573 AATAAAAATAGTTTAATTGATAAGAA
1 AATAAAAATAATATAATTAATAAAAA
3532599 AA
1 AA
3532601 GAATTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (26 bp):
AATAAAAATAATATAATTAATAAAAA
Found at i:3533403 original size:29 final size:29
Alignment explanation
Indices: 3533356--3533448 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
3533346 AGATACTCAG
*
3533356 TTTTAAAATTTTATAAAAAATATATTTATTT
1 TTTTAATA-TTTA-AAAAAATATATTTATTT
*
3533387 TTTTAATATTTAAAAAATATTTATTTA-TT
1 TTTTAATATTTAAAAAA-ATATATTTATTT
*
3533416 TTTT-ATATTTAATACAAAATATATTTGTTT
1 TTTTAATATTTAA-A-AAAATATATTTATTT
3533446 TTT
1 TTT
3533449 ATAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.15
29 19 0.35
30 20 0.37
31 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTAATATTTAAAAAAATATATTTATTT
Found at i:3533408 original size:26 final size:29
Alignment explanation
Indices: 3533371--3533427 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
3533361 AAATTTTATA
3533371 AAAAATATATTTA-TT-TTTTTAATATTT
1 AAAAATATATTTATTTATTTTTAATATTT
*
3533398 AAAAA-ATATTTATTTATTTTTTATATTT
1 AAAAATATATTTATTTATTTTTAATATTT
3533426 AA
1 AA
3533428 TACAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
28 13 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AAAAATATATTTATTTATTTTTAATATTT
Found at i:3533414 original size:30 final size:26
Alignment explanation
Indices: 3533369--3533461 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 26
3533359 TAAAATTTTA
3533369 TAAAAAATATATTTATTTTTTTAATATT
1 TAAAAAATATATTTA-TTTTTT-ATATT
3533397 TAAAAAATATTTATTTATTTTTTATATT
1 TAAAAAATA--TATTTATTTTTTATATT
* **
3533425 TAATACAAAATATATTTGTTTTTTATAAA
1 T-A-A-AAAATATATTTATTTTTTATATT
3533454 TAAAAAAT
1 TAAAAAAT
3533462 TATCTAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
26 5 0.09
27 1 0.02
28 16 0.28
29 22 0.39
30 7 0.12
31 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TAAAAAATATATTTATTTTTTATATT
Found at i:3533447 original size:28 final size:26
Alignment explanation
Indices: 3533369--3533461 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 26
3533359 TAAAATTTTA
*
3533369 TAAAAAATATATTTATTTTTTTAATATT
1 TAAAAAATATA--TATTTTTTTTATATT
*
3533397 TAAAAAATATTTATTTATTTTTTATATT
1 TAAAAAATATATA-TT-TTTTTTATATT
**
3533425 TAATACAAA-ATATATTTGTTTTTTATAAA
1 TAA-A-AAATATATA-TT-TTTTTTATATT
3533454 TAAAAAAT
1 TAAAAAAT
3533462 TATCTAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.04
27 5 0.09
28 24 0.44
29 20 0.37
30 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TAAAAAATATATATTTTTTTTATATT
Found at i:3533450 original size:29 final size:28
Alignment explanation
Indices: 3533371--3533451 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 28
3533361 AAATTTTATA
3533371 AAAAATATATTTATTTTTTTAATATTTAA-
1 AAAAATATATTTA-TTTTTT-ATATTTAAT
*
3533400 AAAATATTTATTTATTTTTTATATTTAAT
1 AAAA-ATATATTTATTTTTTATATTTAAT
*
3533429 ACAAAATATATTTGTTTTTTATA
1 A-AAAATATATTTATTTTTTATA
3533452 AATAAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.17
29 27 0.59
30 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
AAAAATATATTTATTTTTTATATTTAAT
Found at i:3533691 original size:29 final size:27
Alignment explanation
Indices: 3533659--3533729 Score: 63
Period size: 29 Copynumber: 2.5 Consensus size: 27
3533649 TTTTTATTTC
3533659 AAATTAATTTAAAATAATATTTTTAAAA
1 AAATTAATTTAAAATAA-ATTTTTAAAA
* *
3533687 TAAA-TACATTTTATATTAAATTTTTAAAA
1 -AAATTA-A-TTTAAAATAAATTTTTAAAA
*
3533716 AAATATTATTTAAA
1 AAAT-TAATTTAAA
3533730 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
28 10 0.29
29 15 0.44
30 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATTAATTTAAAATAAATTTTTAAAA
Found at i:3533751 original size:28 final size:26
Alignment explanation
Indices: 3533677--3533754 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 26
3533667 TTAAAATAAT
*
3533677 ATTTTTAAAATAAATACATTTTATATTAA
1 ATTTTTAAAATAAATA-A-ATTAT-TTAA
3533706 ATTTTTAAAA-AAAT--ATTATTTAA
1 ATTTTTAAAATAAATAAATTATTTAA
3533729 ATTTTTAAAAATAAATAAAATTATTT
1 ATTTTT-AAAATAAAT-AAATTATTT
3533755 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 10 0.23
24 8 0.19
25 4 0.09
28 11 0.26
29 10 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTTAAAATAAATAAATTATTTAA
Found at i:3533786 original size:30 final size:30
Alignment explanation
Indices: 3533713--3533790 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
3533703 TAAATTTTTA
* *
3533713 AAAAAATATTATTTAAATTTTTAAAAATAAAT
1 AAAATATATTTTTTAAA--TTTAAAAATAAAT
3533745 AAAAT-TA-TTTTTAAATTTAAAAGAT-AAT
1 AAAATATATTTTTTAAATTTAAAA-ATAAAT
*
3533773 AATATATATTTTTTAAAT
1 AAAATATATTTTTTAAAT
3533791 AAAATTCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 16 0.40
31 2 0.05
32 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATATATTTTTTAAATTTAAAAATAAAT
Found at i:3534988 original size:16 final size:16
Alignment explanation
Indices: 3534967--3534997 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3534957 TATTAAAAAA
*
3534967 AAAAGCTTAAGTTAAG
1 AAAAGCTCAAGTTAAG
3534983 AAAAGCTCAAGTTAA
1 AAAAGCTCAAGTTAA
3534998 ATAAGTATCT
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:0.52, C:0.10, G:0.16, T:0.23
Consensus pattern (16 bp):
AAAAGCTCAAGTTAAG
Found at i:3535596 original size:23 final size:25
Alignment explanation
Indices: 3535570--3535624 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
3535560 TTATAATAAA
*
3535570 AATTATAA-CTTAAAATTTAAAT-T
1 AATTATAATATTAAAATTTAAATAT
* *
3535593 AATTA-AATATTACATTTTAAATAT
1 AATTATAATATTAAAATTTAAATAT
3535617 AATTATAA
1 AATTATAA
3535625 AAAATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 6 0.23
25 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTATAATATTAAAATTTAAATAT
Found at i:3535691 original size:13 final size:13
Alignment explanation
Indices: 3535673--3535699 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3535663 AAAATTACAT
3535673 TAAATTTAAATTA
1 TAAATTTAAATTA
3535686 TAAATTTAAATTA
1 TAAATTTAAATTA
3535699 T
1 T
3535700 TATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTAAATTA
Found at i:3537918 original size:18 final size:18
Alignment explanation
Indices: 3537876--3537925 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3537866 CATGAAAAAA
*
3537876 ATTTAAAATTTTAATCAT
1 ATTTAAAATATTAATCAT
**
3537894 AAATAAAATATTAATCAT
1 ATTTAAAATATTAATCAT
*
3537912 GTTTAAATATATTA
1 ATTTAAA-ATATTA
3537926 TATTATTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTTAAAATATTAATCAT
Found at i:3537940 original size:14 final size:14
Alignment explanation
Indices: 3537921--3537951 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3537911 TGTTTAAATA
3537921 TATTATATTATTTT
1 TATTATATTATTTT
3537935 TATTATATTATTTT
1 TATTATATTATTTT
3537949 TAT
1 TAT
3537952 ATTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATATTATTTT
Found at i:3538208 original size:13 final size:13
Alignment explanation
Indices: 3538190--3538214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3538180 TTGAATCTGT
3538190 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
3538203 TTTTTTTTTTTT
1 TTTTTTTTTTTT
3538215 AGTTTGCTTT
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:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:3538384 original size:17 final size:17
Alignment explanation
Indices: 3538362--3538398 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3538352 GAATCTTAAA
3538362 TTTCTTTCTTC-TTTTCT
1 TTTCTTT-TTCTTTTTCT
3538379 TTTCTTTTTCTTTTTCT
1 TTTCTTTTTCTTTTTCT
3538396 TTT
1 TTT
3538399 TCTTGGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTCT
Found at i:3538389 original size:6 final size:6
Alignment explanation
Indices: 3538362--3538402 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
3538352 GAATCTTAAA
3538362 TTTCTT TCTTC-T TTTC-T TTTCTT TTTCTT TTTCTT TTTCTT
1 TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
3538403 GGATGCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 8 0.24
6 22 0.67
7 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:3539035 original size:13 final size:13
Alignment explanation
Indices: 3539017--3539044 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3539007 TCACTATATT
3539017 ATATGAATCAATA
1 ATATGAATCAATA
3539030 ATATGAATCAATA
1 ATATGAATCAATA
3539043 AT
1 AT
3539045 GATTTTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
ATATGAATCAATA
Found at i:3545919 original size:16 final size:16
Alignment explanation
Indices: 3545864--3545938 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
3545854 TTTTTCATAT
*
3545864 TTTAATTATATTTAAAA
1 TTTAA-TATATATAAAA
* *
3545881 TATTATTTATTTATATAAA
1 T-TTA-ATATATATA-AAA
3545900 TTTAATATAT-TAATAA
1 TTTAATATATATAA-AA
* *
3545916 TTTATTTTATATAAAA
1 TTTAATATATATAAAA
3545932 TTTAATA
1 TTTAATA
3545939 AATTCGTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
15 1 0.02
16 19 0.43
17 8 0.18
18 12 0.27
19 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATATATATAAAA
Found at i:3545954 original size:32 final size:31
Alignment explanation
Indices: 3545879--3545955 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
3545869 TTATATTTAA
* *
3545879 AATATTATTTATTTATATAAATTTAATATATT
1 AATATTATAT-TTTATATAAATTTAATAAATT
3545911 AATAATT-TATTTTATATAAAATTTAATAAATT
1 AAT-ATTATATTTTATAT-AAATTTAATAAATT
**
3545943 CGTATTATATTTT
1 AATATTATATTTT
3545956 GTGATGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 10 0.26
32 25 0.66
33 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
AATATTATATTTTATATAAATTTAATAAATT
Found at i:3546652 original size:16 final size:15
Alignment explanation
Indices: 3546633--3546662 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3546623 TTTTTTTATT
3546633 TAAATTTAACTCAATA
1 TAAATTTAA-TCAATA
3546649 TAAATTTAATCAAT
1 TAAATTTAATCAAT
3546663 CAAGTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTTAATCAATA
Found at i:3550289 original size:12 final size:13
Alignment explanation
Indices: 3550270--3550302 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3550260 TTAATTTTTG
3550270 TATTTTAATTTAA
1 TATTTTAATTTAA
*
3550283 T-TTTTAATTTGA
1 TATTTTAATTTAA
3550295 TATTTTAA
1 TATTTTAA
3550303 GAAAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TATTTTAATTTAA
Found at i:3550299 original size:19 final size:20
Alignment explanation
Indices: 3550257--3550299 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3550247 ATTAAATATT
* *
3550257 TATTTAATTTTTGTATTTTA
1 TATTTAATTTTTGAATTTGA
3550277 -ATTTAATTTTT-AATTTGA
1 TATTTAATTTTTGAATTTGA
3550295 TATTT
1 TATTT
3550300 TAAGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TATTTAATTTTTGAATTTGA
Found at i:3550457 original size:8 final size:9
Alignment explanation
Indices: 3550444--3550479 Score: 58
Period size: 8 Copynumber: 4.2 Consensus size: 9
3550434 AAAAACTTTT
3550444 AAAAA-TAA
1 AAAAATTAA
3550452 AAAAATT-A
1 AAAAATTAA
3550460 AAAAATTAA
1 AAAAATTAA
3550469 AAAAATTAA
1 AAAAATTAA
3550478 AA
1 AA
3550480 TTATTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATTAA
Found at i:3550464 original size:17 final size:17
Alignment explanation
Indices: 3550444--3550479 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3550434 AAAAACTTTT
3550444 AAAAATAAAAAAATTAA
1 AAAAATAAAAAAATTAA
*
3550461 AAAATTAAAAAAATTAA
1 AAAAATAAAAAAATTAA
3550478 AA
1 AA
3550480 TTATTTTATA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATAAAAAAATTAA
Found at i:3551292 original size:17 final size:18
Alignment explanation
Indices: 3551254--3551295 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3551244 AATTAACTTT
3551254 TTTTCTTTTAAAAATATAA
1 TTTT-TTTTAAAAATATAA
3551273 TTTTTTTTAAATAA-AT-A
1 TTTTTTTTAAA-AATATAA
3551290 TTTTTT
1 TTTTTT
3551296 ATCCATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTTTTAAAAATATAA
Found at i:3551385 original size:2 final size:2
Alignment explanation
Indices: 3551325--3551366 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3551315 TAAATTTTAG
3551325 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
3551367 GTTTCTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3551746 original size:22 final size:22
Alignment explanation
Indices: 3551724--3551778 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
3551714 AGATAGATAT
3551724 TTTAAAAA-ATTTTATTAATTA
1 TTTAAAAATATTTTATTAATTA
3551745 TTTAAAAATATTTTATTAAACTTA
1 TTTAAAAATATTTTATT-AA-TTA
*
3551769 TTAAAAAATA
1 TTTAAAAATA
3551779 ATAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.27
22 8 0.27
23 2 0.07
24 12 0.40
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAAAATATTTTATTAATTA
Found at i:3553298 original size:3 final size:3
Alignment explanation
Indices: 3553290--3553332 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3553280 TAGTTTTAAC
3553290 ATA 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 ATA A
3553333 AAGAATGTTT
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):
ATA
Found at i:3555840 original size:65 final size:65
Alignment explanation
Indices: 3555732--3555866 Score: 263
Period size: 65 Copynumber: 2.1 Consensus size: 65
3555722 TACTTAAAAT
3555732 TGTT-ATTTCATTATTCCTTGTCAAACCATGTCTTTATTTTGGTTAATTTTTCACTAATTAAACA
1 TGTTCATTTCATTATTCCTTGTCAAACCATGTCTTTATTTTGGTTAATTTTTCACTAATTAAACA
3555796 TGTTCATTTCATTATTCCTTGTCAAACCATGTCTTTATTTTGGTTAATTTTTCACTAATTAAACA
1 TGTTCATTTCATTATTCCTTGTCAAACCATGTCTTTATTTTGGTTAATTTTTCACTAATTAAACA
3555861 TGTTCA
1 TGTTCA
3555867 ACTACTTTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 4 0.06
65 66 0.94
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (65 bp):
TGTTCATTTCATTATTCCTTGTCAAACCATGTCTTTATTTTGGTTAATTTTTCACTAATTAAACA
Found at i:3556142 original size:2 final size:2
Alignment explanation
Indices: 3556131--3556165 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3556121 TGATACGATG
3556131 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3556166 GTAGACCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3558831 original size:11 final size:10
Alignment explanation
Indices: 3558813--3558853 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
3558803 CGTACGATAT
3558813 AATAATATAA
1 AATAATATAA
3558823 AATTAATATAA
1 AA-TAATATAA
*
3558834 TATAATA-AA
1 AATAATATAA
3558843 AATAATATAA
1 AATAATATAA
3558853 A
1 A
3558854 TATGATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.30
10 10 0.37
11 9 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAATATAA
Found at i:3558833 original size:19 final size:19
Alignment explanation
Indices: 3558809--3558900 Score: 70
Period size: 19 Copynumber: 4.9 Consensus size: 19
3558799 TAGACGTACG
3558809 ATATAATAATATAAAATTA
1 ATATAATAATATAAAATTA
*
3558828 ATATAAT-ATAATAAAAATA
1 ATATAATAAT-ATAAAATTA
* *
3558847 ATAT-A-AATATGATATTA
1 ATATAATAATATAAAATTA
*
3558864 ATATATAAATATATTAAAATT-
1 ATATA-ATA-ATA-TAAAATTA
3558885 -TAT-ATAATATAAAATT
1 ATATAATAATATAAAATT
3558901 TTAATTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
16 7 0.12
17 13 0.22
18 7 0.12
19 20 0.34
20 4 0.07
21 3 0.05
22 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
ATATAATAATATAAAATTA
Found at i:3558835 original size:16 final size:16
Alignment explanation
Indices: 3558814--3558900 Score: 57
Period size: 16 Copynumber: 5.8 Consensus size: 16
3558804 GTACGATATA
3558814 ATAATATAAAATTAAT
1 ATAATATAAAATTAAT
3558830 ATAATATAATAA--AA-
1 ATAATATAA-AATTAAT
*
3558844 ATAATAT-AAATATGAT
1 ATAATATAAAAT-TAAT
*
3558860 ATTAATAT---ATAAAT
1 A-TAATATAAAATTAAT
*
3558874 AT-AT-TAAAATTTAT
1 ATAATATAAAATTAAT
3558888 ATAATATAAAATT
1 ATAATATAAAATT
3558901 TTAATTATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
11 1 0.02
12 4 0.07
13 2 0.04
14 16 0.29
15 7 0.13
16 17 0.31
17 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAATATAAAATTAAT
Found at i:3558889 original size:28 final size:27
Alignment explanation
Indices: 3558809--3558942 Score: 87
Period size: 27 Copynumber: 4.9 Consensus size: 27
3558799 TAGACGTACG
* *
3558809 ATATAATAATA-TAAAATTAATATAAT
1 ATATAAAAATATTAAAATTTATATAAT
* *
3558835 ATAATAAAAATAATATAAATATGATATTAAT
1 AT-ATAAAAATATTA-AAAT-TTATA-TAAT
*
3558866 ATATAAATATATTAAAATTTATATAAT
1 ATATAAAAATATTAAAATTTATATAAT
** * *
3558893 ATA-AAATTTTAATTATAATTTAT-T-TT
1 ATATAAA-AAT-ATTAAAATTTATATAAT
*
3558919 ATATAAAAATATTATAAATATATA
1 ATATAAAAATATTA-AAATTTATA
3558943 AATTATCGTG
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.05
26 16 0.19
27 21 0.24
28 17 0.20
29 8 0.09
30 14 0.16
31 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATAAAAATATTAAAATTTATATAAT
Found at i:3558942 original size:19 final size:19
Alignment explanation
Indices: 3558817--3558944 Score: 59
Period size: 19 Copynumber: 7.4 Consensus size: 19
3558807 CGATATAATA
* *
3558817 ATATAAAATTAATAT-AAT
1 ATATAAAAATATTATAAAT
*
3558835 ATAATAAAAATAATATAAAT
1 AT-ATAAAAATATTATAAAT
**
3558855 ATGATATTAATA-TATAAAT
1 AT-ATAAAAATATTATAAAT
* *
3558874 ATATTAAAAT-TTATATA-
1 ATATAAAAATATTATAAAT
3558891 ATAT-AAAAT-TT-T-AAT
1 ATATAAAAATATTATAAAT
**
3558906 -TAT---AAT-TTAT-TTT
1 ATATAAAAATATTATAAAT
3558919 ATATAAAAATATTATAAAT
1 ATATAAAAATATTATAAAT
3558938 ATATAAA
1 ATATAAA
3558945 TTATCGTGAC
Statistics
Matches: 86, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 7 0.08
15 1 0.01
16 7 0.08
17 7 0.08
18 16 0.19
19 29 0.34
20 12 0.14
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
ATATAAAAATATTATAAAT
Found at i:3562678 original size:21 final size:21
Alignment explanation
Indices: 3562649--3562694 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3562639 AAAATTTTAA
* * *
3562649 AAATTTTATTTAATTTGATTC
1 AAATCTTATTAAATTTAATTC
*
3562670 AAATCTTATTAAATTTAATTT
1 AAATCTTATTAAATTTAATTC
3562691 AAAT
1 AAAT
3562695 ATATAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AAATCTTATTAAATTTAATTC
Found at i:3562827 original size:12 final size:11
Alignment explanation
Indices: 3562790--3562841 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
3562780 ATTAAATAAT
3562790 AAATTATATT-
1 AAATTATATTA
**
3562800 AAATTATAAAA
1 AAATTATATTA
3562811 AAATTATATTTA
1 AAATTATA-TTA
*
3562823 AAATTTAAATTA
1 AAA-TTATATTA
3562835 AAATTAT
1 AAATTAT
3562842 TAAACTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.24
11 11 0.33
12 10 0.30
13 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTATATTA
Found at i:3564787 original size:13 final size:13
Alignment explanation
Indices: 3564769--3564793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3564759 AAGTATAATG
3564769 AAAAAAACAAAAA
1 AAAAAAACAAAAA
3564782 AAAAAAACAAAA
1 AAAAAAACAAAA
3564794 TTTTATTCAT
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:3565245 original size:31 final size:33
Alignment explanation
Indices: 3565210--3565279 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
3565200 TTTATTAGAT
*
3565210 TTATATAAA-TTTAATACATTAAT-CATTTATA
1 TTATATAAATTTTAAAACATTAATACATTTATA
* *
3565241 TTATATAAATTTTAAAATATTAATATATTTATA
1 TTATATAAATTTTAAAACATTAATACATTTATA
3565274 TTATAT
1 TTATAT
3565280 TTATATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 9 0.26
32 12 0.35
33 13 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTATATAAATTTTAAAACATTAATACATTTATA
Found at i:3565273 original size:6 final size:6
Alignment explanation
Indices: 3565264--3565317 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
3565254 AAAATATTAA
* *
3565264 TATATT TATA-T TATATT TATATT AATATT TCATA-T TAT-TG TATATAT
1 TATATT TATATT TATATT TATATT TATATT T-ATATT TATATT TATAT-T
3565311 TATATT T
1 TATATT T
3565318 TTTATATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
5 10 0.26
6 21 0.54
7 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (6 bp):
TATATT
Found at i:3565330 original size:38 final size:42
Alignment explanation
Indices: 3565263--3565340 Score: 110
Period size: 38 Copynumber: 2.0 Consensus size: 42
3565253 TAAAATATTA
*
3565263 ATATATTTATATTATATTTATATTAATATTTCATATTATTGT
1 ATATATTTATATTATATTTATATTAATATTTAATATTATTGT
*
3565305 ATATA-TTATATT-T-TTTATA-TCATATTTAATATTATT
1 ATATATTTATATTATATTTATATTAATATTTAATATTATT
3565341 AAGTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 15 0.44
39 6 0.18
40 1 0.03
41 7 0.21
42 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (42 bp):
ATATATTTATATTATATTTATATTAATATTTAATATTATTGT
Found at i:3565625 original size:22 final size:22
Alignment explanation
Indices: 3565582--3565622 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3565572 AAAAATATAA
*
3565582 TTTAATTTAAATAATTATAATT
1 TTTAATTTAAATAATTAAAATT
3565604 TTTAATTTAAA-AATTAAAA
1 TTTAATTTAAATAATTAAAA
3565623 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATTTAAATAATTAAAATT
Found at i:3570032 original size:32 final size:33
Alignment explanation
Indices: 3569974--3570035 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
3569964 AGTTTTCATA
3569974 AATTTAATAAAATATTAAATAAAATTATTCGTT
1 AATTTAATAAAATATTAAATAAAATTATTCGTT
* **
3570007 AATTTAAT-AAATATTTAATTTAATTATTC
1 AATTTAATAAAATATTAAATAAAATTATTC
3570036 ATAAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (33 bp):
AATTTAATAAAATATTAAATAAAATTATTCGTT
Found at i:3570218 original size:27 final size:26
Alignment explanation
Indices: 3570166--3570228 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
3570156 TATTTATTTC
***
3570166 ATATTTAAAAATATTTTTTATATAAT
1 ATATTTAAAAATATTTAAAATATAAT
*
3570192 ATATATTAAAAATATTTAAAATTTAAT
1 ATAT-TTAAAAATATTTAAAATATAAT
*
3570219 AAATTTAAAA
1 ATATTTAAAA
3570229 TGATATAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTAAAAATATTTAAAATATAAT
Found at i:3570450 original size:9 final size:9
Alignment explanation
Indices: 3570436--3570461 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3570426 AAATTAACCT
3570436 AGTTGTAGA
1 AGTTGTAGA
3570445 AGTTGTAGA
1 AGTTGTAGA
3570454 AGTTGTAG
1 AGTTGTAG
3570462 GACCACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (9 bp):
AGTTGTAGA
Found at i:3572242 original size:22 final size:22
Alignment explanation
Indices: 3572216--3572285 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
3572206 TTAAATTTAA
3572216 ATAAAATTTAATTATAAAATAT
1 ATAAAATTTAATTATAAAATAT
*
3572238 ATAAAGA-ATAATTATAAAATATT
1 ATAAA-ATTTAATTATAAAATA-T
* * *
3572261 TTAATATTTAAATAGTAAAATAT
1 ATAAAATTTAATTA-TAAAATAT
3572284 AT
1 AT
3572286 TTTTTTAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 19 0.50
23 12 0.32
24 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
ATAAAATTTAATTATAAAATAT
Found at i:3573310 original size:16 final size:18
Alignment explanation
Indices: 3573289--3573326 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3573279 AGTGTTCTTG
* *
3573289 TAAAAAAATTAAAAT-TA
1 TAAAAATATAAAAATATA
3573306 TAAAAATATAAAAATATA
1 TAAAAATATAAAAATATA
3573324 TAA
1 TAA
3573327 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATATAAAAATATA
Found at i:3573508 original size:25 final size:27
Alignment explanation
Indices: 3573480--3573545 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
3573470 AAAAAATAAA
3573480 AAATATTTTAATATTT-ATT-TATTAT
1 AAATATTTTAATATTTAATTATATTAT
* *
3573505 AAAT-TTTTTATTTTTAAATTATATTAT
1 AAATATTTTAATATTT-AATTATATTAT
3573532 AAATA--TTAATATTT
1 AAATATTTTAATATTT
3573546 TTAATCGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
24 9 0.27
25 4 0.12
26 10 0.30
27 10 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
AAATATTTTAATATTTAATTATATTAT
Found at i:3573522 original size:15 final size:15
Alignment explanation
Indices: 3573483--3573529 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
3573473 AAATAAAAAA
3573483 TATTTTAATATTTATT
1 TATTTTAA-ATTTATT
*
3573499 TATTATAAATTT-TT
1 TATTTTAAATTTATT
3573513 TATTTTTAAATTATATT
1 TA-TTTTAAATT-TATT
3573530 ATAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 12 0.46
16 8 0.31
17 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTAAATTTATT
Found at i:3573726 original size:22 final size:22
Alignment explanation
Indices: 3573659--3573730 Score: 94
Period size: 24 Copynumber: 3.3 Consensus size: 22
3573649 ATCATAAAAA
*
3573659 TATAAAAAATTAA-TTTAATTT
1 TATAAAAAATTAATTTTTATTT
*
3573680 TATAAAAATATTATTTTATTATTT
1 TATAAAAA-ATTAATTT-TTATTT
3573704 TATAAAAAATTAATTTTTATTT
1 TATAAAAAATTAATTTTTATTT
3573726 T-TAAA
1 TATAAA
3573731 TTAATTCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.27
22 11 0.24
23 9 0.20
24 13 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAAAAAATTAATTTTTATTT
Found at i:3573736 original size:22 final size:23
Alignment explanation
Indices: 3573659--3573730 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 23
3573649 ATCATAAAAA
3573659 TATAAAAAATTAATTTA--ATTT
1 TATAAAAAATTAATTTATTATTT
*
3573680 TATAAAAATATTATTTTATTATTT
1 TATAAAAA-ATTAATTTATTATTT
3573704 TATAAAAAATTAATTT-TTATTT
1 TATAAAAAATTAATTTATTATTT
3573726 T-TAAA
1 TATAAA
3573731 TTAATTCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.26
22 15 0.33
23 7 0.15
24 12 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATAAAAAATTAATTTATTATTT
Found at i:3573923 original size:7 final size:6
Alignment explanation
Indices: 3573907--3573956 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
3573897 TCCTTGGTCA
* * *
3573907 AAAAAG AAAAGG AAAAAG AAAAAG AAAAA- AAAACAC AAAAAG AAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG
3573955 AA
1 AA
3573957 GTCGGCGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 30 0.79
7 4 0.11
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3585594 original size:36 final size:37
Alignment explanation
Indices: 3585535--3585612 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 37
3585525 TTTGGATTAA
*
3585535 TTTTATTAAAATTATTATTTAAATAATAA-A-AAATAT
1 TTTTATTAAAATTATAATTTAAATAATAATATAAAT-T
* *
3585571 TTTTATTTAAATT-TAATTGTAAATATTAATATAAATT
1 TTTTATTAAAATTATAATT-TAAATAATAATATAAATT
3585608 TTTTA
1 TTTTA
3585613 AAAATTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 4 0.11
36 21 0.58
37 7 0.19
38 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (37 bp):
TTTTATTAAAATTATAATTTAAATAATAATATAAATT
Found at i:3590799 original size:16 final size:13
Alignment explanation
Indices: 3590764--3590816 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
3590754 TAATACCATA
3590764 TTTATATTATTTT
1 TTTATATTATTTT
*
3590777 TTTATATTATATT
1 TTTATATTATTTT
* **
3590790 TTTATAATA-TAC
1 TTTATATTATTTT
3590802 TTTA-ATTATTTT
1 TTTATATTATTTT
3590814 TTT
1 TTT
3590817 CAATATCATA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
11 3 0.10
12 8 0.26
13 20 0.65
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTATTTT
Found at i:3593149 original size:10 final size:11
Alignment explanation
Indices: 3593129--3593153 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3593119 GTTGCAAATC
3593129 AAAAACAAAAA
1 AAAAACAAAAA
3593140 AAAAACAAAAA
1 AAAAACAAAAA
3593151 AAA
1 AAA
3593154 CAGAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:3598361 original size:100 final size:100
Alignment explanation
Indices: 3598240--3598512 Score: 311
Period size: 100 Copynumber: 2.9 Consensus size: 100
3598230 TTTTTTTCTG
* * *
3598240 TTACCTATTTGAGATATCCAAACAAGGAAATG-AATATTTATTTTTCCTTTATTTTCCTTTAAAA
1 TTACCTATTTGAAATATCCAAACAAGGAAATGAAATATTTA-CTTTCCTTTATATTCCTTTAAAA
3598304 ACCATTAATTTCCTTTCTTTTCCTTTCCACCTTTTT
65 ACCATTAATTTCCTTTCTTTTCCTTTCCACCTTTTT
*
3598340 TTACCTATTTTAAATATCCAAACAAGGAAATGAAATATTTACTTTCCTTTATATTCCTTTAAAAA
1 TTACCTATTTGAAATATCCAAACAAGGAAATGAAATATTTACTTTCCTTTATATTCCTTTAAAAA
* * *
3598405 TCATTTATTTCCTTTTTTTTCCTTT--A-C-----
66 CCATTAATTTCCTTTCTTTTCCTTTCCACCTTTTT
* * * * *
3598432 TTA--T-TTT-AAATATTCAAACAAGGAAGTAAAATATTTACTTTCCTTTTTTTTCCTTTAAAAA
1 TTACCTATTTGAAATATCCAAACAAGGAAATGAAATATTTACTTTCCTTTATATTCCTTTAAAAA
* * *
3598493 CTATTTATTTCCTTTTTTTT
66 CCATTAATTTCCTTTCTTTT
3598513 TTCTTTCCTT
Statistics
Matches: 158, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
88 67 0.42
89 3 0.02
90 1 0.01
92 3 0.02
97 1 0.01
98 1 0.01
100 74 0.47
101 8 0.05
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (100 bp):
TTACCTATTTGAAATATCCAAACAAGGAAATGAAATATTTACTTTCCTTTATATTCCTTTAAAAA
CCATTAATTTCCTTTCTTTTCCTTTCCACCTTTTT
Found at i:3598416 original size:30 final size:30
Alignment explanation
Indices: 3598372--3598430 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3598362 CAAGGAAATG
3598372 AAATATTTACTTTCCTTTATATTCCTTTAA
1 AAATATTTACTTTCCTTTATATTCCTTTAA
* *
3598402 AAATCATTTA-TTTCCTTTTTTTTCCTTTA
1 AAAT-ATTTACTTTCCTTTATATTCCTTTA
3598431 CTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (30 bp):
AAATATTTACTTTCCTTTATATTCCTTTAA
Found at i:3598444 original size:88 final size:88
Alignment explanation
Indices: 3598339--3598512 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 88
3598329 TCCACCTTTT
*
3598339 TTTACCTATTTTAAATATCCAAACAAGGAAATGAAATATTTACTTTCCTTTATATTCCTTTAAAA
1 TTTACCTATTTTAAATATCCAAACAAGGAAATAAAATATTTACTTTCCTTTATATTCCTTTAAAA
3598404 A-TCATTTATTTCCTTTTTTTTCC
66 ACT-ATTTATTTCCTTTTTTTTCC
* * * * *
3598427 TTTACTTATTTTAAATATTCAAACAAGGAAGTAAAATATTTACTTTCCTTTTTTTTCCTTTAAAA
1 TTTACCTATTTTAAATATCCAAACAAGGAAATAAAATATTTACTTTCCTTTATATTCCTTTAAAA
3598492 ACTATTTATTTCCTTTTTTTT
66 ACTATTTATTTCCTTTTTTTT
3598513 TTCTTTCCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 78 0.99
89 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (88 bp):
TTTACCTATTTTAAATATCCAAACAAGGAAATAAAATATTTACTTTCCTTTATATTCCTTTAAAA
ACTATTTATTTCCTTTTTTTTCC
Found at i:3598698 original size:19 final size:19
Alignment explanation
Indices: 3598674--3598767 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 19
3598664 ATGATAAAAT
3598674 TTAAAATTTAAAATTTAAA
1 TTAAAATTTAAAATTTAAA
* * **
3598693 TTAAAAATATACATATTTTTA
1 TT-AAAATTTA-AAATTTAAA
* *
3598714 TTAAAATATCAAATTTATAA
1 TTAAAATTTAAAATTTA-AA
* *
3598734 TTTAATATTT-TAATTT-AA
1 -TTAAAATTTAAAATTTAAA
3598752 TTAAAATATTAAAATT
1 TTAAAAT-TTAAAATT
3598768 ACATAATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
17 6 0.11
18 4 0.07
19 11 0.20
20 20 0.36
21 15 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATTTAAAATTTAAA
Found at i:3598700 original size:7 final size:7
Alignment explanation
Indices: 3598668--3598692 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3598658 TCTAACATGA
3598668 TAAAATT
1 TAAAATT
3598675 TAAAATT
1 TAAAATT
3598682 TAAAATT
1 TAAAATT
3598689 TAAA
1 TAAA
3598693 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:3598861 original size:16 final size:17
Alignment explanation
Indices: 3598840--3598872 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3598830 AACACCAAAA
3598840 AATATA-TAAATTTATT
1 AATATATTAAATTTATT
3598856 AATATATTAAATTTATT
1 AATATATTAAATTTATT
3598873 CACCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATATATTAAATTTATT
Found at i:3604643 original size:23 final size:23
Alignment explanation
Indices: 3604616--3604660 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3604606 ACCTTTTAAT
3604616 AATTTAAATAGTATTTAAATAAA
1 AATTTAAATAGTATTTAAATAAA
* *
3604639 AATTTAATTATTATTTAAATAA
1 AATTTAAATAGTATTTAAATAA
3604661 TAAAATATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTTAAATAGTATTTAAATAAA
Found at i:3604899 original size:27 final size:28
Alignment explanation
Indices: 3604842--3604900 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
3604832 ATTTAACTGG
*
3604842 TTTCATTCAATTCTCTTTAAGAGGAAAA
1 TTTCATTCAATTCTCTTGAAGAGGAAAA
* *
3604870 TTTCATTCACTTCTC-TGAAGAGGAAGA
1 TTTCATTCAATTCTCTTGAAGAGGAAAA
3604897 TTTC
1 TTTC
3604901 GGCAGAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (28 bp):
TTTCATTCAATTCTCTTGAAGAGGAAAA
Done.