Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 13 of 126
Found at i:3694347 original size:16 final size:16
Alignment explanation
Indices: 3694328--3694365 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
3694318 TTCAAAAAAA
3694328 ATCAATTTCATAACAC-
1 ATCAATTT-ATAACACT
3694344 ATC-ATTTATAACACT
1 ATCAATTTATAACACT
3694359 ATCAATT
1 ATCAATT
3694366 CTTATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (16 bp):
ATCAATTTATAACACT
Found at i:3695640 original size:9 final size:9
Alignment explanation
Indices: 3695626--3695651 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3695616 TCTTTTTCTA
3695626 TTTCATTTG
1 TTTCATTTG
3695635 TTTCATTTG
1 TTTCATTTG
3695644 TTTCATTT
1 TTTCATTT
3695652 TATGTTTATT
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:0.12, C:0.12, G:0.08, T:0.69
Consensus pattern (9 bp):
TTTCATTTG
Found at i:3695679 original size:16 final size:16
Alignment explanation
Indices: 3695658--3695696 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3695648 ATTTTATGTT
*
3695658 TATTATATTAATATAA
1 TATTATATTAACATAA
3695674 TATTATATTAACATAA
1 TATTATATTAACATAA
3695690 TAATTAT
1 T-ATTAT
3695697 TATTTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTATATTAACATAA
Found at i:3698911 original size:19 final size:18
Alignment explanation
Indices: 3698869--3699363 Score: 192
Period size: 17 Copynumber: 26.6 Consensus size: 18
3698859 ACAAAATAAT
3698869 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
3698887 GATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
3698904 AATTTTTTGAAAACACGAAA
1 AA-TTTTTGAAAACACG-AA
*** **
3698924 ACATAAATTTTTTTAACACGGG
1 A-AT---TTTTGAAAACACGAA
*
3698946 AATTTTTGAAAACACGAC
1 AATTTTTGAAAACACGAA
* * *
3698964 AGTTTTTG-AAACATGAG
1 AATTTTTGAAAACACGAA
*
3698981 AATTTTTTAAAACAC-AA
1 AATTTTTGAAAACACGAA
*
3698998 AATTTTATTTTGAAAACACAAA
1 AA---T-TTTTGAAAACACGAA
*
3699020 AATTTTGATAAATTATGAAACACGAGGA
1 AA-TTT--T---TGA--AAACACGA--A
** * *
3699048 TTTTTTTTTG-AAACGCGGA
1 --AATTTTTGAAAACACGAA
* * **
3699067 AATTTATG-AAACAAGGTC
1 AATTTTTGAAAAC-ACGAA
3699085 AATTTTTTGAAAACACGAA
1 AATT-TTTGAAAACACGAA
*
3699104 AATTTTTG-AAAGACGAGA
1 AATTTTTGAAAACACGA-A
* *
3699122 ATTTTTTGAAAACACGGA
1 AATTTTTGAAAACACGAA
* *
3699140 GATTTAT-AAAACACGAA
1 AATTTTTGAAAACACGAA
* *
3699157 AGTTTTTTTTTGAAAACAAGAA
1 A----ATTTTTGAAAACACGAA
* * *
3699179 AA-TTTTCAAAATACGAG
1 AATTTTTGAAAACACGAA
**
3699196 AATTTTTGAAAACATAAA
1 AATTTTTGAAAACACGAA
*
3699214 AATTTTTGAAAACATGAA
1 AATTTTTGAAAACACGAA
* *
3699232 AATTTTTG-AAACACTAG
1 AATTTTTGAAAACACGAA
3699249 AA-TTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* * * *
3699266 GATTTTTG-AGACATGAG
1 AATTTTTGAAAACACGAA
*
3699283 AATTTTTGAAAACACGAGG
1 AATTTTTGAAAACACGA-A
*
3699302 ATTTTTTGAAATACA--AA
1 AATTTTTGAAA-ACACGAA
* * *
3699319 CATTTTAG-AAACATGAA
1 AATTTTTGAAAACACGAA
*
3699336 AATTTTT-AAAACACGAC
1 AATTTTTGAAAACACGAA
3699353 AATTTTTGAAA
1 AATTTTTGAAA
3699364 CCTGATTTTT
Statistics
Matches: 351, Mismatches: 82, Indels: 88
0.67 0.16 0.17
Matches are distributed among these distances:
15 3 0.01
16 7 0.02
17 119 0.34
18 107 0.30
19 36 0.10
20 14 0.04
21 25 0.07
22 15 0.04
23 10 0.03
24 3 0.01
26 7 0.02
27 1 0.00
28 1 0.00
29 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:3699013 original size:21 final size:22
Alignment explanation
Indices: 3698984--3699025 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3698974 ACATGAGAAT
*
3698984 TTTTTAAAACAC-AAAATTTTA
1 TTTTGAAAACACAAAAATTTTA
3699005 TTTTGAAAACACAAAAATTTT
1 TTTTGAAAACACAAAAATTTT
3699026 GATAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTGAAAACACAAAAATTTTA
Found at i:3699226 original size:75 final size:75
Alignment explanation
Indices: 3699087--3699238 Score: 189
Period size: 75 Copynumber: 2.0 Consensus size: 75
3699077 ACAAGGTCAA
* ** ** *
3699087 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAATTTTTTGAAAACACGGAGATTTATAAAAC
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACACAAAAATTTATAAAAC
*
3699152 ACGAAAGTTT
66 ACGAAAATTT
* * *
3699162 TTTTTTGAAAACAAGAAAATTTTCAAAATACGAGAA-TTTTTGAAAACATAAAAATTTTTGAAAA
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACACAAAAATTTAT-AAAA
*
3699226 CATGAAAATTT
65 CACGAAAATTT
3699237 TT
1 TT
3699239 GAAACACTAG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 18 0.28
75 47 0.72
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (75 bp):
TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACACAAAAATTTATAAAAC
ACGAAAATTT
Found at i:3699306 original size:87 final size:87
Alignment explanation
Indices: 3699193--3699361 Score: 202
Period size: 87 Copynumber: 1.9 Consensus size: 87
3699183 TTCAAAATAC
* * *
3699193 GAGAATTTTTGAAAACATAAAAA-TTTTTGAAA-ACATGAAAATTTTTGAAACACT-AGAATTTT
1 GAGAATTTTTGAAAACACAAAAATTTTTTGAAATACA--AAAATTTTAGAAACA-TGAAAATTTT
3699255 GAAAACACGA-AGATTTTTGAGACAT
63 GAAAACACGACA-ATTTTTGAGACAT
* ** * *
3699280 GAGAATTTTTGAAAACACGAGGATTTTTTGAAATACAAACATTTTAGAAACATGAAAATTTTTAA
1 GAGAATTTTTGAAAACACAAAAATTTTTTGAAATACAAAAATTTTAGAAACATGAAAATTTTGAA
3699345 AACACGACAATTTTTGA
66 AACACGACAATTTTTGA
3699362 AACCTGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
86 1 0.01
87 56 0.80
88 10 0.14
89 3 0.04
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (87 bp):
GAGAATTTTTGAAAACACAAAAATTTTTTGAAATACAAAAATTTTAGAAACATGAAAATTTTGAA
AACACGACAATTTTTGAGACAT
Found at i:3699664 original size:16 final size:16
Alignment explanation
Indices: 3699643--3699680 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3699633 TTAAAATTAT
3699643 TTAAAA-TAAATTAAAA
1 TTAAAATTAAATT-AAA
*
3699659 TTAAAATTGAATTAAA
1 TTAAAATTAAATTAAA
3699675 TTAAAA
1 TTAAAA
3699681 ATATAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAAATTAAATTAAA
Found at i:3699853 original size:10 final size:10
Alignment explanation
Indices: 3699838--3699898 Score: 72
Period size: 10 Copynumber: 6.2 Consensus size: 10
3699828 AAATTAAAAC
*
3699838 CTTTTTTTTT
1 CTTTTTTCTT
3699848 CTTTTTTCTT
1 CTTTTTTCTT
*
3699858 CTTTTATCTT
1 CTTTTTTCTT
*
3699868 CTTTTTTCCT
1 CTTTTTTCTT
3699878 CTCTTTTT-TT
1 CT-TTTTTCTT
3699888 CTTTTTT-TT
1 CTTTTTTCTT
3699897 CT
1 CT
3699899 GGACTGGGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
9 9 0.20
10 31 0.69
11 5 0.11
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:3700051 original size:24 final size:23
Alignment explanation
Indices: 3700000--3700067 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
3699990 CTGCATTTGG
*
3700000 GCTGCTTCTTTC-TTCTTATTTTT
1 GCTGCTTCTTTCTTTCTT-TTTTC
*
3700023 TCTGCTTCTTTCTTTCTTTTTTCC
1 GCTGCTTCTTTCTTTCTTTTTT-C
*
3700047 GCTGCTTCTTT-TTTCTGTTTT
1 GCTGCTTCTTTCTTTCTTTTTT
3700068 GGTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 24 0.62
24 15 0.38
ACGTcount: A:0.01, C:0.24, G:0.09, T:0.66
Consensus pattern (23 bp):
GCTGCTTCTTTCTTTCTTTTTTC
Found at i:3700212 original size:14 final size:14
Alignment explanation
Indices: 3700193--3700249 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
3700183 GTGATATATT
3700193 TCTTTTTTTCTTTC
1 TCTTTTTTTCTTTC
3700207 TC--TTTTTC-TTC
1 TCTTTTTTTCTTTC
* *
3700218 TCTCTTTTTCCTTC
1 TCTTTTTTTCTTTC
*
3700232 T-TTCTTTTTCTTTT
1 TCTT-TTTTTCTTTC
3700246 TCTT
1 TCTT
3700250 CTTCTTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 7 0.20
14 15 0.43
15 2 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TCTTTTTTTCTTTC
Found at i:3700216 original size:6 final size:6
Alignment explanation
Indices: 3700197--3700255 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
3700187 TATATTTCTT
* *
3700197 TTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC TTTTTC
*
3700248 TTCTTC TT
1 TTTTTC TT
3700256 CTTCGGGCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 31 0.69
7 11 0.24
8 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:3701643 original size:3 final size:3
Alignment explanation
Indices: 3701635--3701667 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3701625 ACAAATTTCA
3701635 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3701668 ACTCTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3704483 original size:27 final size:27
Alignment explanation
Indices: 3704453--3704504 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3704443 TGATTCTTTG
*
3704453 ATTCTTTTCGATTTTCTTCCAAATTTT
1 ATTCTTTTAGATTTTCTTCCAAATTTT
3704480 ATTCTTTTAGATTTTCTTCCAAATT
1 ATTCTTTTAGATTTTCTTCCAAATT
3704505 AATTTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTCTTTTAGATTTTCTTCCAAATTTT
Found at i:3705238 original size:19 final size:17
Alignment explanation
Indices: 3705215--3705262 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3705205 GTTCAGACTC
*
3705215 AAAAAAAAAATTCAAAA
1 AAAAAAAAAAATCAAAA
*
3705232 AATAAAAAAATCATCAAAA
1 AA-AAAAAAA-AATCAAAA
3705251 AAAAAATAAAAA
1 AAAAAA-AAAAA
3705263 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.08
18 12 0.48
19 11 0.44
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAAATCAAAA
Found at i:3705240 original size:17 final size:17
Alignment explanation
Indices: 3705215--3705256 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
3705205 GTTCAGACTC
3705215 AAAAAAAAAAT-TCAAA
1 AAAAAAAAAATATCAAA
3705231 AAATAAAAAAATCATCAAA
1 AAA-AAAAAAAT-ATCAAA
3705250 AAAAAAA
1 AAAAAAA
3705257 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 4 0.17
19 8 0.35
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAATATCAAA
Found at i:3705272 original size:24 final size:23
Alignment explanation
Indices: 3705228--3705273 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3705218 AAAAAAATTC
**
3705228 AAAAAATAAAAAAATCATCAAAA
1 AAAAAATAAAAAAAAAATCAAAA
3705251 AAAAAATAAAAAAAAAAGTCAAA
1 AAAAAATAAAAAAAAAA-TCAAA
3705274 GTCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAAAATAAAAAAAAAATCAAAA
Found at i:3706144 original size:13 final size:12
Alignment explanation
Indices: 3706111--3706144 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
3706101 ACTTTGAGTC
3706111 AAAAAAAATGAA
1 AAAAAAAATGAA
3706123 ATAAAAAAATGAA
1 A-AAAAAAATGAA
3706136 AAAATAAAA
1 AAAA-AAAA
3706145 AAGTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:3707587 original size:86 final size:87
Alignment explanation
Indices: 3707374--3707969 Score: 695
Period size: 86 Copynumber: 7.0 Consensus size: 87
3707364 CAGATCAATG
* * * * * * *
3707374 AAGACATCAGATCTTACCTTCCTGCGTTAACAGTGAAGCATATCGAAAACAAATCCTTACCTCCA
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
* *
3707439 TCGGTTGCAGTGGAGCTGGTTG
66 TTGGTTGCAGTGGAGCTGGTTA
* * * *
3707461 AATATAGCAGATCCTT-CCTTCCTGCGTTAACAGTGAAGCAGATTGAAAACAAAGCCTTGCCTTC
1 AAGACAGCAGAT-CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTC
3707525 ATTGGTTGCAGTGGAGCTGGTTA
65 ATTGGTTGCAGTGGAGCTGGTTA
3707548 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
*
3707612 TTGGTTACAGTGGAGCTGGTTA
66 TTGGTTGCAGTGGAGCTGGTTA
*
3707634 AAGA-AGCAGATCTTGCCTTCCTGCG-T---AGTGAA-C--ATCGAAAACAAAGCCTTGCCTTCA
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
*
3707691 TTGGTTACAGTGGAGCTGGTTA
66 TTGGTTGCAGTGGAGCTGGTTA
3707713 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
*
3707777 TTGGTTGCAGTGGAGCTGGTTG
66 TTGGTTGCAGTGGAGCTGGTTA
** * * *
3707799 AAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTC
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCT-
* *
3707863 CCTCATTTG-TG-A-TGGAGCTGGTTG
63 --TCATTGGTTGCAGTGGAGCTGGTTA
* ** * * * * * *
3707887 AAGACAACAGATCTTGCCTTTTTGCATTGACAGCGAAGCAGGTCGAAGACGAA-CCTTACCTCTC
1 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT-TC
* *
3707951 -TCGGTTGTAGTGGAGCTGG
65 ATTGGTTGCAGTGGAGCTGG
3707970 CTGAAGAATT
Statistics
Matches: 459, Mismatches: 32, Indels: 37
0.87 0.06 0.07
Matches are distributed among these distances:
79 71 0.15
80 1 0.00
81 1 0.00
82 5 0.01
83 7 0.02
84 6 0.01
85 5 0.01
86 168 0.37
87 113 0.25
88 68 0.15
89 6 0.01
90 2 0.00
91 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (87 bp):
AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCA
TTGGTTGCAGTGGAGCTGGTTA
Found at i:3707721 original size:165 final size:170
Alignment explanation
Indices: 3707381--3707976 Score: 685
Period size: 165 Copynumber: 3.5 Consensus size: 170
3707371 ATGAAGACAT
* * * * * * *
3707381 CAGATCTTACCTTCCTGCGTTAACAGTGAAGCATATCGAAAACAAATCCTTACCTCCATCGGTTG
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG
* * *
3707446 CAGTGGAGCTGGTTGAATATAGCAGATCCTT-CCTTCCTGCGTTAACAGTGAAGCAGATTGAAAA
66 CAGTGGAGCTGGTTGAAGACAGCAGAT-CTTGCCTTCCTGCGTT-A-AGTGAAGCA-ATCGAAAA
*
3707510 CAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAG
127 CAAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAG
*
3707554 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTA
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG
*
3707619 CAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCG-T-AGTGAA-C-ATCGAAAACAAA
66 CAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCGTTAAGTGAAGCAATCGAAAACAAA
3707679 GCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAG
131 GCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAG
3707719 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG
** * * *
3707784 CAGTGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAC
66 CAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCGTT-A-AGTGAAGCA-ATCGAA-A-
* * * *
3707849 ACAAA-CCTTGCCTCCCTCATTTG-T-GA-TGGAGCTGGTTGAAGACAA
126 ACAAAGCCTTGCCT---TCATTGGTTACAGTGGAGCTGGTTAAAGA-AG
** * * * * * * *
3707894 CAGATCTTGCCTTTTTGCATTGACAGCGAAGCAGGTCGAAGACGAA-CCTTACCTCTC-TCGGTT
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT-TCATTGGTT
* *
3707957 GTAGTGGAGCTGGCTGAAGA
65 GCAGTGGAGCTGGTTGAAGA
3707977 ATTTCAGATC
Statistics
Matches: 373, Mismatches: 34, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
165 132 0.35
166 18 0.05
167 2 0.01
168 6 0.02
170 5 0.01
171 5 0.01
172 17 0.05
173 79 0.21
174 54 0.14
175 48 0.13
176 1 0.00
177 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (170 bp):
CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTG
CAGTGGAGCTGGTTGAAGACAGCAGATCTTGCCTTCCTGCGTTAAGTGAAGCAATCGAAAACAAA
GCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAG
Found at i:3707859 original size:44 final size:44
Alignment explanation
Indices: 3707724--3707936 Score: 143
Period size: 44 Copynumber: 4.9 Consensus size: 44
3707714 AGAAGCAGAT
* * *
3707724 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-C
* * * * * * * *
3707767 CTTGCCTTCATTG-GTTG-CAGTGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CTGCATTGACAGCGAAGCAGGTCGAAGACACAA-AC
3707811 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
* ** * * * *
3707855 CTTGCCTCCCT-CATTTGTGATG-G-AGCTGGTTGAAGACAACAGAT
1 CTTGCCTTCCTGCA-TTGACA-GCGAAGCAGGTCGAAGAC-ACAAAC
**
3707899 CTTGCCTTTTTGCATTGACAGCGAAGCAGGTCGAAGAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAC
3707937 GAACCTTACC
Statistics
Matches: 127, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
42 12 0.09
43 30 0.24
44 50 0.39
45 35 0.28
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:3707880 original size:88 final size:89
Alignment explanation
Indices: 3707674--3707936 Score: 360
Period size: 88 Copynumber: 3.0 Consensus size: 89
3707664 AACATCGAAA
* * * *
3707674 ACAAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCG
1 ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCA
* *
3707738 TTAACAGCGAAGCAGATCGAA-A-
66 TTGACAGCGAAGCAGGTCGAAGAC
*
3707760 ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCA
1 ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCA
3707825 TTGACAGCGAAGCAGGTCGAAGAC
66 TTGACAGCGAAGCAGGTCGAAGAC
* **
3707849 ACAAA-CCTTGCCTCCCTCATTTG-TG-A-TGGAGCTGGTTGAAGACAACAGATCTTGCCTTTTT
1 ACAAAGCCTTGCCT---TCATTGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCT
3707910 GCATTGACAGCGAAGCAGGTCGAAGAC
63 GCATTGACAGCGAAGCAGGTCGAAGAC
3707937 GAACCTTACC
Statistics
Matches: 160, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
86 41 0.26
87 37 0.23
88 68 0.43
89 6 0.04
90 2 0.01
91 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (89 bp):
ACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCA
TTGACAGCGAAGCAGGTCGAAGAC
Found at i:3708166 original size:46 final size:45
Alignment explanation
Indices: 3708070--3708488 Score: 383
Period size: 46 Copynumber: 9.6 Consensus size: 45
3708060 TTAAAATAAA
* * * * *
3708070 AGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCG--CAC--C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* * *
3708111 AGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGACTTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-TTC
*
3708157 AGATCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGA---C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* * * *
3708199 AGAATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G-CATC
1 AG-ATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* * *
3708241 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAGGACTTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-TTC
*
3708287 AGATCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGA---C
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* * * *
3708329 AGAATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G-CATC
1 AG-ATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* * *
3708371 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAGGACTTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-TTC
* * * *
3708417 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGACAT-
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
* *
3708461 A-ATCCTATCTCCCTGAAGTTACAGTGGA
1 AGATCTTATCTCCCTGAGGTTACAGTGGA
3708489 ACGGTTTAAA
Statistics
Matches: 311, Mismatches: 44, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
40 2 0.01
41 90 0.29
42 12 0.04
43 86 0.28
44 3 0.01
45 3 0.01
46 115 0.37
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (45 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACTTC
Found at i:3708222 original size:130 final size:130
Alignment explanation
Indices: 3708072--3708612 Score: 741
Period size: 130 Copynumber: 4.2 Consensus size: 130
3708062 AAAATAAAAG
*
3708072 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGT
1 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
* *
3708137 AGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGACAGA
66 AGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA
*
3708202 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
1 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
* *
3708267 GGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGACAGA
66 AGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA
*
3708332 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
1 ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
* * *
3708397 GGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGACATA
66 AGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA
* * * * * * *** * * * *
3708462 ATCCTATCTCCCTGAAGTTACAGTGGAACGGTTTAAAATAAAGGACCTTATCTCTCTGAAGTTAC
1 ATCTTATCTCTCTGAAGTTACAGTAGAGCAG-ATCGCAT-CAGG-TCTTATCTCCCTGAGGTTAC
* * * * *
3708527 AGTAGAGCAGATC--GCAC---CAGGTCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGAC
63 AGTAGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
*
3708587 ATA
128 AGA
* *
3708590 ATCCTATCTCCCTGAAGTTACAG
1 ATCTTATCTCTCTGAAGTTACAG
3708613 CGGAGCGGAT
Statistics
Matches: 382, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
128 68 0.18
130 278 0.73
131 6 0.02
132 3 0.01
133 27 0.07
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (130 bp):
ATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
AGAGTAGACCGAGGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGA
Found at i:3708618 original size:43 final size:43
Alignment explanation
Indices: 3708114--3708617 Score: 367
Period size: 43 Copynumber: 11.6 Consensus size: 43
3708104 TCGCACCAGG
* * *
3708114 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-AT-A-A
* *
3708160 TCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGACAGAA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * * * * **
3708203 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCA-GG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * *
3708244 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAGGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-AT-A-A
* *
3708290 TCTTATCTCCCTGAGGTTACAGCGGAGTAGATCGAAGACAGAA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * * * * **
3708333 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCA-GG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * *
3708374 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAGGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGAC-AT-A-A
* * *
3708420 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGACATAA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * * ** * * *
3708463 TCCTATCTCCCTGAAGTTACAGTGGA--ACGGTTTAAAATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTA-GATCGAAGACATA--A
* * * * * * * **
3708507 CCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCA-CCA-GG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * *
3708548 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGACATAA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
* * *
3708591 TCCTATCTCCCTGAAGTTACAGCGGAG
1 TCTTATCTCCCTGAGGTTACAGTGGAG
3708618 CGGATTAAAA
Statistics
Matches: 357, Mismatches: 84, Indels: 37
0.75 0.18 0.08
Matches are distributed among these distances:
41 90 0.25
42 16 0.04
43 113 0.32
44 27 0.08
45 4 0.01
46 107 0.30
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGAAGACATAA
Found at i:3709466 original size:20 final size:20
Alignment explanation
Indices: 3709430--3709473 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3709420 ACAAGTTCTA
*
3709430 TTTTCCTTTTTTATTTTTAC
1 TTTTCCTTTATTATTTTTAC
*
3709450 TTTTCTCTTTATT-TTTTTTC
1 TTTTC-CTTTATTATTTTTAC
3709470 TTTT
1 TTTT
3709474 TTTCGTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCCTTTATTATTTTTAC
Found at i:3711436 original size:29 final size:30
Alignment explanation
Indices: 3711386--3711472 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
3711376 GTTAAAGTGC
**
3711386 AATTTTAAGAAAATTTAAGGGTCAAAATGT-
1 AATTTT-AGAAAATTTTGGGGTCAAAATGTG
* *
3711416 ACTTTTAGAAAATTTTGGGGTTAAAATGTG
1 AATTTTAGAAAATTTTGGGGTCAAAATGTG
*
3711446 AATTTTA-AAAAGGTTTGGGGTCAAAAT
1 AATTTTAGAAAA-TTTTGGGGTCAAAAT
3711473 AGAAATTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 24 0.50
30 24 0.50
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (30 bp):
AATTTTAGAAAATTTTGGGGTCAAAATGTG
Found at i:3711463 original size:30 final size:28
Alignment explanation
Indices: 3711367--3711512 Score: 103
Period size: 30 Copynumber: 4.9 Consensus size: 28
3711357 ATTTCCTGAG
* * *
3711367 AGTTTAGGGGTTAAAGTGCAATTTTAAGAA
1 AGTTT-GGGGTCAAAATGTAATTTTAA-AA
* * *
3711397 AATTTAAGGGTCAAAATGTACTTTTAGAAA
1 AGTTT-GGGGTCAAAATGTAATTTTA-AAA
* *
3711427 ATTTTGGGGTTAAAATGTGAATTTTAAAA
1 AGTTTGGGGTCAAAATGT-AATTTTAAAA
* *
3711456 AGGTTTGGGGTCAAAATAGAAATTTCAAAA
1 A-GTTTGGGGTCAAAAT-GTAATTTTAAAA
* *
3711486 AGTATAGGGGTTAAAATGTAATCTTTA
1 AGT-TTGGGGTCAAAATGTAAT-TTTA
3711513 TTTTTTGCTT
Statistics
Matches: 92, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
29 21 0.23
30 69 0.75
31 2 0.02
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (28 bp):
AGTTTGGGGTCAAAATGTAATTTTAAAA
Found at i:3717078 original size:23 final size:22
Alignment explanation
Indices: 3717026--3717078 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
3717016 TCCACGTCTT
*
3717026 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
3717048 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
3717071 TTTCTTTT
1 TTTCTTTT
3717079 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:3723699 original size:32 final size:32
Alignment explanation
Indices: 3723637--3723700 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3723627 ATTATCTATT
* *
3723637 TTCATTGTTCAACTCTTTGATAACACGAAAAA
1 TTCATTATTCAACTCTTTGACAACACGAAAAA
* *
3723669 TTCATTATTCAACTCTTTGACAATATGAAAAA
1 TTCATTATTCAACTCTTTGACAACACGAAAAA
3723701 AGTCAAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (32 bp):
TTCATTATTCAACTCTTTGACAACACGAAAAA
Found at i:3725506 original size:88 final size:88
Alignment explanation
Indices: 3725357--3725533 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
3725347 TAACATAATC
*
3725357 ATTAACTGCATATACTGATTTCTATAGTACTTACTGTTCGCACTTCATCGGATCTATTTAAATAT
1 ATTAACTGCATATACTGATTTCTATAGTACTTACTGTTCGCACTTCATCGGATCCATTTAAATAT
3725422 AATTGTTCAAATACATATACCAA
66 AATTGTTCAAATACATATACCAA
*
3725445 ATTAACTGCATATACTGATTTCTATAGTACTTATTGTTCGCACTTCATCGGATCCATTTAAATAT
1 ATTAACTGCATATACTGATTTCTATAGTACTTACTGTTCGCACTTCATCGGATCCATTTAAATAT
3725510 AATTGTTCAAATACATATACCAA
66 AATTGTTCAAATACATATACCAA
3725533 A
1 A
3725534 AGCATAATTT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (88 bp):
ATTAACTGCATATACTGATTTCTATAGTACTTACTGTTCGCACTTCATCGGATCCATTTAAATAT
AATTGTTCAAATACATATACCAA
Found at i:3725910 original size:41 final size:41
Alignment explanation
Indices: 3725809--3725913 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
3725799 TTTAAACAGA
* * * ** *
3725809 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGCTAGGCCTATAGCCTAATTCAG
*
3725850 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTAATTCAG
3725891 TTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAG
3725914 ACGTATAGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 55 0.98
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTAATTCAG
Found at i:3725921 original size:41 final size:41
Alignment explanation
Indices: 3725844--3725926 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
3725834 TTATAGTTTA
* *
3725844 ATTCCGTTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTG
* *
3725885 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTG
3725926 A
1 A
3725927 ATAATTTCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTG
Found at i:3725936 original size:41 final size:41
Alignment explanation
Indices: 3725849--3725941 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
3725839 GTTTAATTCC
* * *
3725849 GTTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCA
1 GTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAA
* *
3725890 GTTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGAATAA
1 GTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAA
* *
3725931 TTTCACTGGCA
1 GTTCACCGGCA
3725942 ATAAATCCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
GTTCACCGGCACTTAGCCTGCTAGACCTATAGCCTGAATAA
Found at i:3726592 original size:37 final size:37
Alignment explanation
Indices: 3726547--3726624 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
3726537 CATACTTAAA
3726547 CAAA-ATTCAATCCATATACTTTCAATTTCAGCTCAC
1 CAAATATTCAATCCATATACTTTCAATTTCAGCTCAC
*
3726583 TAAATATTCAATCCATATACTTTCAATTTCAGCTCAC
1 CAAATATTCAATCCATATACTTTCAATTTCAGCTCAC
3726620 CAAAT
1 CAAAT
3726625 TACTATAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 3 0.08
37 36 0.92
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (37 bp):
CAAATATTCAATCCATATACTTTCAATTTCAGCTCAC
Found at i:3727636 original size:13 final size:13
Alignment explanation
Indices: 3727618--3727642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3727608 CAATCAAATG
3727618 CACACAAAATAAA
1 CACACAAAATAAA
3727631 CACACAAAATAA
1 CACACAAAATAA
3727643 TATTAATAAT
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:3734324 original size:2 final size:2
Alignment explanation
Indices: 3734317--3734351 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3734307 GCATCTCTTT
*
3734317 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG GG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3734352 ATATATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:3737779 original size:13 final size:13
Alignment explanation
Indices: 3737761--3737787 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3737751 CTTCAAAAAG
3737761 TTAATTTAACTAA
1 TTAATTTAACTAA
3737774 TTAATTTAACTAA
1 TTAATTTAACTAA
3737787 T
1 T
3737788 CTTTTGGTTA
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:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATTTAACTAA
Found at i:3738233 original size:16 final size:16
Alignment explanation
Indices: 3738194--3738234 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3738184 ATAATAAAAA
3738194 TATAATTTTATCATTT
1 TATAATTTTATCATTT
3738210 TA-ATATTTTAT-ATCTT
1 TATA-ATTTTATCAT-TT
3738226 TATAATTTT
1 TATAATTTT
3738235 TAAATGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATCATTT
Found at i:3741541 original size:42 final size:40
Alignment explanation
Indices: 3741468--3741546 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
3741458 GTGAATATAA
* *
3741468 ATTTTTTTGTAATTTTTATTTGTATAGATTTTTTTAAAAT
1 ATTTTTTTGTAATTTTTATTTGTATAAATTTTCTTAAAAT
*
3741508 ATTTTTTTCTTAATTTATTATTT-TAATAAATTTTCTTAA
1 ATTTTTTT-GTAATTT-TTATTTGT-ATAAATTTTCTTAA
3741547 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 8 0.24
41 7 0.21
42 18 0.55
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (40 bp):
ATTTTTTTGTAATTTTTATTTGTATAAATTTTCTTAAAAT
Found at i:3742986 original size:17 final size:17
Alignment explanation
Indices: 3742963--3743002 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
3742953 AATAAAACAT
3742963 AGAAAAACTACGTTGAAA
1 AGAAAAACTACGTTG-AA
3742981 AGAAAAACTACGTTGAA
1 AGAAAAACTACGTTGAA
3742998 AGAAA
1 AGAAA
3743003 TGGAGAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.15
Consensus pattern (17 bp):
AGAAAAACTACGTTGAA
Found at i:3743247 original size:31 final size:29
Alignment explanation
Indices: 3743209--3743285 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
3743199 CTAACGGCTC
*
3743209 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTGA-AACATA
* ** *
3743240 AGTGACTAAAACGTAACATTTTAAACATA
1 AGTGACTAAAATGTAACACGTGAAACATA
3743269 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
3743286 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTGAAACATA
Found at i:3745357 original size:21 final size:21
Alignment explanation
Indices: 3745333--3745372 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3745323 TCATATCAAG
*
3745333 TAGTTAACTGGCCACGTCAGT
1 TAGTTAACTAGCCACGTCAGT
*
3745354 TAGTTAACTAGCCATGTCA
1 TAGTTAACTAGCCACGTCA
3745373 ACTGTCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGTTAACTAGCCACGTCAGT
Found at i:3745923 original size:23 final size:24
Alignment explanation
Indices: 3745884--3745939 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3745874 GTAAAATTGT
*
3745884 TAATA-AAATTATATATAATTTTAA
1 TAATATAAA-TATATATAAGTTTAA
*
3745908 TAA-ATAAATATATATAAGTTTAC
1 TAATATAAATATATATAAGTTTAA
3745931 TAATATAAA
1 TAATATAAA
3745940 AAGTCTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TAATATAAATATATATAAGTTTAA
Found at i:3745980 original size:23 final size:23
Alignment explanation
Indices: 3745951--3745998 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3745941 AGTCTTCTAA
3745951 AAATGGCGAGTAACCAGCAAATT
1 AAATGGCGAGTAACCAGCAAATT
3745974 AAATGGCGAGTAACCAGCAAATT
1 AAATGGCGAGTAACCAGCAAATT
3745997 AA
1 AA
3745999 GTAGTTGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (23 bp):
AAATGGCGAGTAACCAGCAAATT
Found at i:3760246 original size:88 final size:87
Alignment explanation
Indices: 3760001--3760247 Score: 232
Period size: 90 Copynumber: 2.8 Consensus size: 87
3759991 TTCTTTTTTG
* * * * *
3760001 GGTTTGTTTTACCTATGATGATGCAGATAGTGTTTTTGTTTTGTCGGCATCTTTCATGTTTGTTT
1 GGTTTGTTTTTCCTAGGATGAT-CTGATAATGTTTTT-TTTTATCGGCATCTTTCATGTTTGTTT
* *
3760066 TACTACACATATTCTGGTTGTTTT
64 TATTACACATATTCTGGTTGCTTT
* * * * *
3760090 GGTTTGTTTTTCCCTATGATGATGCTGATAATAGTTTTTTCTAATCGGCATTTTTCATATTTGTT
1 GGTTTGTTTTT-CCTAGGATGAT-CTGATAAT-GTTTTTTTTTATCGGCATCTTTCATGTTTGTT
*
3760155 TTATTATC-TATATT-TGAGTTGCTTT
63 TTATTA-CACATATTCTG-GTTGCTTT
* **
3760180 GGTTTGTTTTT-TTAGGATGCCAT-TGATAATGTTTTTCTTTTATCGGCATCTTTCATGTCAGTT
1 GGTTTGTTTTTCCTAGGATG--ATCTGATAATGTTTTT-TTTTATCGGCATCTTTCATGTTTGTT
3760243 TTATT
63 TTATT
3760248 GTTCATGTTC
Statistics
Matches: 132, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
87 6 0.05
88 38 0.29
89 12 0.09
90 69 0.52
91 7 0.05
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (87 bp):
GGTTTGTTTTTCCTAGGATGATCTGATAATGTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTA
TTACACATATTCTGGTTGCTTT
Found at i:3770816 original size:21 final size:21
Alignment explanation
Indices: 3770790--3770830 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3770780 ATCTGCTCAA
* *
3770790 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3770811 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3770831 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3773966 original size:17 final size:17
Alignment explanation
Indices: 3773944--3773981 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3773934 TTAATTTATG
3773944 TATTTATATGATATGAT-
1 TATTTATA-GATATGATA
*
3773961 TATTTATAGATGTGATA
1 TATTTATAGATATGATA
3773978 TATT
1 TATT
3773982 AGGTAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (17 bp):
TATTTATAGATATGATA
Found at i:3783589 original size:27 final size:28
Alignment explanation
Indices: 3783538--3783599 Score: 117
Period size: 27 Copynumber: 2.2 Consensus size: 28
3783528 AAAAATAACT
3783538 AAAATATTATAATTTTTTTTTATTTACC
1 AAAATATTATAATTTTTTTTTATTTACC
3783566 AAAATATTATAA-TTTTTTTTATTTACC
1 AAAATATTATAATTTTTTTTTATTTACC
3783593 AAAATAT
1 AAAATAT
3783600 ACCGAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAATATTATAATTTTTTTTTATTTACC
Found at i:3783717 original size:27 final size:27
Alignment explanation
Indices: 3783653--3783729 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
3783643 GGCCAATCAC
3783653 ATTGGCGGCACTCAA-GGTGCCAAAGAG
1 ATTGGCGGCAC-CAATGGTGCCAAAGAG
* * *
3783680 -TTTGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
3783706 ATTGGCGGCACCAATGGTGCCAAA
1 ATTGGCGGCACCAATGGTGCCAAA
3783730 AGACTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 3 0.07
26 19 0.44
27 21 0.49
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:3784326 original size:19 final size:19
Alignment explanation
Indices: 3784302--3784360 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
3784292 TCTAATTAAG
*
3784302 TAATAAATCTATTTTAATT
1 TAATAAATCTATTTTCATT
*
3784321 TAATAAA-CTATTCTCATT
1 TAATAAATCTATTTTCATT
*
3784339 TAATAACTCTATTTTCATT
1 TAATAAATCTATTTTCATT
3784358 TAA
1 TAA
3784361 AATATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 15 0.43
19 20 0.57
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAAATCTATTTTCATT
Found at i:3784608 original size:29 final size:27
Alignment explanation
Indices: 3784576--3784641 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
3784566 AAAATAGTTT
*
3784576 AATTTAATAACTCTATTTTAATTTTAAAA
1 AATTTAATAA-ACTATTTTAATTTT-AAA
* *
3784605 AATTAAATTAAACTATTTTAATTTTATA
1 AATTTAA-TAAACTATTTTAATTTTAAA
3784633 AATTTAATA
1 AATTTAATA
3784642 TATTCCCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 8 0.25
29 19 0.59
30 3 0.09
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTAATAAACTATTTTAATTTTAAA
Found at i:3785089 original size:28 final size:27
Alignment explanation
Indices: 3785036--3785106 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 27
3785026 TTTGTTTTTT
3785036 TTTTAT-ATATTTTGGTAAATAAAAAA
1 TTTTATAATATTTTGGTAAATAAAAAA
3785062 TTTTATAATATTTTGGTAAATAAAAAAA
1 TTTTATAATATTTTGGTAAAT-AAAAAA
**
3785090 AGTTATAATATTTTGGT
1 TTTTATAATATTTTGGT
3785107 TATTTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 6 0.15
27 14 0.34
28 21 0.51
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (27 bp):
TTTTATAATATTTTGGTAAATAAAAAA
Found at i:3795291 original size:44 final size:43
Alignment explanation
Indices: 3795230--3795341 Score: 107
Period size: 45 Copynumber: 2.5 Consensus size: 43
3795220 TTGTACTAGT
*
3795230 AGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGTACTGAC
1 AGCGAAGCAGAT-GAAGACACCAACCTTGCCTCCCTGTACTGAC
* * ** * * *
3795274 AGCGGAGCAGACTGAAGATAGTAAATCTTGCCTTCCTGTACTGAT
1 AGCGAAGCAGA-TGAAGACA-CCAACCTTGCCTCCCTGTACTGAC
*
3795319 GGCGAAGCAGATTGAAGACACCA
1 AGCGAAGCAGA-TGAAGACACCA
3795342 TAGTTTGCAA
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
44 17 0.33
45 35 0.67
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (43 bp):
AGCGAAGCAGATGAAGACACCAACCTTGCCTCCCTGTACTGAC
Found at i:3795417 original size:50 final size:50
Alignment explanation
Indices: 3795359--3795940 Score: 433
Period size: 50 Copynumber: 11.7 Consensus size: 50
3795349 CAATTAAAAG
* * *
3795359 GATTGAAGCCACAATGGCGAATCTTACTTCTCTGGCGA-TGCAGTGGAACA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGC-ATTGCAGTGGAACA
* * * * * * * *
3795409 TATTGAAGCTACAACGGCAAATCTTGCTTCCCCGACATTGCAAT-TAAAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTGGAACA
* *
3795458 GATTGAAGCCACAACGGCGAATCTTACTTCTCTGGCGA-TGCAGTGGAACA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGC-ATTGCAGTGGAACA
* * * * * * *
3795508 GATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTGCAAT-TAAAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTGGAACA
* * *
3795557 GATTCAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACA
1 GATTGAAGCCACAACGGCGAATCTTAC-TTCCCCGGCATTGCAGTGGAACA
* ** *** * * *
3795608 GATTGAAGCTACAACGGCGAATCTCGCTTCCCTAACATTGCAAT-TAAAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTGGAACA
* * * * * *
3795657 GATTCAAGCCATAACGGCGAATCTTACTTTCCCAGGAAGTGCAATGGAACA
1 GATTGAAGCCACAACGGCGAATCTTAC-TTCCCCGGCATTGCAGTGGAACA
* * ** * * * * *
3795708 GATTGAAGCTACAACAGCGAATCTCGCTTCCCCGACATTGTAAT-TAAAA
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTGGAACA
* * * *
3795757 GATTGAAGCCACAACGGCGAATCTTACTTTTCCTGGCAGTGCTGTGGAACA
1 GATTGAAGCCACAACGGCGAATCTTAC-TTCCCCGGCATTGCAGTGGAACA
* * * * * * *
3795808 GATTGAAGCTACAACGGTGAATCTCT-CTTCCTCGACATTGCAAT-TAAAA
1 GATTGAAGCCACAACGGCGAATCT-TACTTCCCCGGCATTGCAGTGGAACA
* * ** ** * *
3795857 GATTGAGGCCACAACGGTGAATCTTACTTTCCCAAGCGGTGTAGTGGAATA
1 GATTGAAGCCACAACGGCGAATCTTAC-TTCCCCGGCATTGCAGTGGAACA
* *
3795908 GATTGAAGCTACGACGGCGAATCTTACTTCCCC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCC
3795941 AACATTGTAG
Statistics
Matches: 401, Mismatches: 117, Indels: 28
0.73 0.21 0.05
Matches are distributed among these distances:
48 1 0.00
49 142 0.35
50 155 0.39
51 102 0.25
52 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (50 bp):
GATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCATTGCAGTGGAACA
Found at i:3795874 original size:49 final size:48
Alignment explanation
Indices: 3795346--3795880 Score: 348
Period size: 49 Copynumber: 10.8 Consensus size: 48
3795336 ACACCATAGT
* * *
3795346 TTGCAATTAAAAGGATTGAAGCCACAATGGCGAATCT-TACTTCTCTGGCGA
1 TTGCAATTAAAA-GATTGAAGCCACAACGGCGAATCTCT-CTTC-CCGAC-A
* * * * * *
3795397 -TGCAGTGGAACATATTGAAGCTACAACGGCAAATCT-TGCTTCCCCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCT-CTT-CCCGACA
* *
3795446 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCT-TACTTCTCTGGCGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCT-CTTC-CCGAC-A
* * * * * *
3795496 -TGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTCACTTCCCCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCTCTT-CCCGACA
* *
3795545 TTGCAATTAAAAGATTCAAGCCACAACGGCGAATCT-TACTTTCCCAGGCA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCT-C-TTCCC-GACA
* * * * * * *
3795595 GTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCTAACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCTCTTCCC-GACA
* *
3795645 TTGCAATTAAAAGATTCAAGCCATAACGGCGAATCT-TACTTTCCCAGGA-A
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCT-C-TTCCC--GACA
* * * * * *
3795695 GTGCAATGGAACAGATTGAAGCTACAACAGCGAATCTCGCTTCCCCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCTCTT-CCCGACA
* * * *
3795745 TTGTAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTTCCTGGCA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATC-T-CTCTTCCCGACA
* ** * * * *
3795795 GTGCTGTGGAACAGATTGAAGCTACAACGGTGAATCTCTCTTCCTCGACA
1 TTGCAAT-TAAAAGATTGAAGCCACAACGGCGAATCTCTCTTCC-CGACA
* *
3795845 TTGCAATTAAAAGATTGAGGCCACAACGGTGAATCT
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCT
3795881 TACTTTCCCA
Statistics
Matches: 368, Mismatches: 91, Indels: 52
0.72 0.18 0.10
Matches are distributed among these distances:
48 1 0.00
49 148 0.40
50 133 0.36
51 86 0.23
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (48 bp):
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTCTCTTCCCGACA
Found at i:3795955 original size:100 final size:100
Alignment explanation
Indices: 3795346--3795947 Score: 834
Period size: 100 Copynumber: 6.0 Consensus size: 100
3795336 ACACCATAGT
* * *
3795346 TTGCAATTAAAAGGATTGAAGCCACAATGGCGAATCTTAC-TTCTCTGGC-GATGCAGTGGAACA
1 TTGCAATTAAAA-GATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAG-TGCAGTGGAACA
* * *
3795409 TATTGAAGCTACAACGGCAAATCTTGCTTCCCCGACA
64 GATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* *
3795446 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCTCTGGC-GATGCAGTGGAACAG
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAG-TGCAGTGGAACAG
* *
3795509 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
*
3795545 TTGCAATTAAAAGATTCAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
**
3795610 TTGAAGCTACAACGGCGAATCTCGCTTCCCTAACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * *
3795645 TTGCAATTAAAAGATTCAAGCCATAACGGCGAATCTTACTTTCCCAGGAAGTGCAATGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
*
3795710 TTGAAGCTACAACAGCGAATCTCGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * *
3795745 TTGTAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTTCCTGGCAGTGCTGTGGAACAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
* * *
3795810 TTGAAGCTACAACGGTGAATCTCTCTTCCTCGACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
* * * * * *
3795845 TTGCAATTAAAAGATTGAGGCCACAACGGTGAATCTTACTTTCCCAAGCGGTGTAGTGGAATAGA
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
* ** *
3795910 TTGAAGCTACGACGGCGAATCTTACTTCCCCAACA
66 TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
3795945 TTG
1 TTG
3795948 TAGTTAAACA
Statistics
Matches: 453, Mismatches: 47, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
99 119 0.26
100 333 0.74
101 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (100 bp):
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCAGTGCAGTGGAACAGA
TTGAAGCTACAACGGCGAATCTCGCTTCCCCGACA
Found at i:3796185 original size:126 final size:125
Alignment explanation
Indices: 3795959--3796375 Score: 517
Period size: 126 Copynumber: 3.4 Consensus size: 125
3795949 AGTTAAACAG
* *
3795959 ACATTGAATCCAGTAATTCTATCTCTCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATATTA
1 ACATTGAAGCCA-TAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATATTA
*
3796024 TCTCCCAAAGTGGAGTAGATCGAAGATGGAGGATTTTACCTCTA-TGTGACTACAGTGGAGT
65 TCTCCCAAAGTGGAGAAGATCGAAGATGGAGGATTTTACCTC-ACTGTGACTACAGTGGAGT
* *
3796085 ACATTGAAGCCGATAATTCTATCTCCCTGGTTGGCAGTGGAATAAATTGAAGATTTCAGATCTTA
1 ACATTGAAGCC-ATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATATTA
3796150 TCTCCCAAAGTGGAGAAGATCGAAGATGGCA-GATTTTACCTCACTGTGACTACAGTGGAGT
65 TCTCCCAAAGTGGAGAAGATCGAAGATGG-AGGATTTTACCTCACTGTGACTACAGTGGAGT
*
3796211 ACATTGAAGCCAATAATTCTATCTCCCTGGTTGGCAGTAGAATAGATTGAAGATTTCAG------
1 ACATTGAAGCC-ATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATATTA
* * * *
3796270 --------AGAGGAGCAGATCGAAGATGGCA-GATTTTACCTCCCTGTGATTACAGTGGAGT
65 TCTCCCAAAGTGGAGAAGATCGAAGATGG-AGGATTTTACCTCACTGTGACTACAGTGGAGT
* * * * *
3796323 ATATTGAAGCCAGTAATTCTATCTCCTTGGGTAGCAGTGGAATAGATCGAAGA
1 ACATTGAAGCCA-TAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGA
3796376 CCATAGATTC
Statistics
Matches: 269, Mismatches: 18, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
111 1 0.00
112 94 0.35
125 1 0.00
126 171 0.64
127 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (125 bp):
ACATTGAAGCCATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATATTAT
CTCCCAAAGTGGAGAAGATCGAAGATGGAGGATTTTACCTCACTGTGACTACAGTGGAGT
Found at i:3796366 original size:112 final size:112
Alignment explanation
Indices: 3796161--3796375 Score: 340
Period size: 112 Copynumber: 1.9 Consensus size: 112
3796151 CTCCCAAAGT
3796161 GGAGAAGATCGAAGATGGCAGATTTTACCTCACTGTGACTACAGTGGAGTACATTGAAGCCAATA
1 GGAGAAGATCGAAGATGGCAGATTTTACCTCACTGTGACTACAGTGGAGTACATTGAAGCCAATA
* * *
3796226 ATTCTATCTCCCTGGTTGGCAGTAGAATAGATTGAAGATTTCAGAGA
66 ATTCTATCTCCCTGGGTAGCAGTAGAATAGATCGAAGATTTCAGAGA
* * * * *
3796273 GGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGATTACAGTGGAGTATATTGAAGCCAGTA
1 GGAGAAGATCGAAGATGGCAGATTTTACCTCACTGTGACTACAGTGGAGTACATTGAAGCCAATA
* *
3796338 ATTCTATCTCCTTGGGTAGCAGTGGAATAGATCGAAGA
66 ATTCTATCTCCCTGGGTAGCAGTAGAATAGATCGAAGA
3796376 CCATAGATTC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 93 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (112 bp):
GGAGAAGATCGAAGATGGCAGATTTTACCTCACTGTGACTACAGTGGAGTACATTGAAGCCAATA
ATTCTATCTCCCTGGGTAGCAGTAGAATAGATCGAAGATTTCAGAGA
Found at i:3797811 original size:3 final size:3
Alignment explanation
Indices: 3797765--3797872 Score: 71
Period size: 3 Copynumber: 36.3 Consensus size: 3
3797755 TTCAACATTT
* * * *
3797765 TTA TTA TT- TTC TTCA TTA TT- TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * *
3797809 TTA CTA TTA TTA TTA TTA TTA -TA TTTA CTA TTA TTA TAA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
3797854 TTA TTA GTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA T
3797873 GTTTTTTTTA
Statistics
Matches: 80, Mismatches: 18, Indels: 14
0.71 0.16 0.12
Matches are distributed among these distances:
2 8 0.10
3 67 0.84
4 5 0.06
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3798107 original size:14 final size:15
Alignment explanation
Indices: 3798090--3798118 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3798080 ACGTATTAAA
3798090 ATATGTATAT-TTTT
1 ATATGTATATATTTT
3798104 ATATGTATATATTTT
1 ATATGTATATATTTT
3798119 TCATCTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
ATATGTATATATTTT
Found at i:3798488 original size:18 final size:18
Alignment explanation
Indices: 3798467--3798512 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3798457 TCATATGTCC
3798467 ATTTTTATGT-TTTAGTTT
1 ATTTTTATGTATTTA-TTT
*
3798485 ATTTTTATTTATTTATTT
1 ATTTTTATGTATTTATTT
3798503 ATTTGTTATG
1 ATTT-TTATG
3798513 ATATATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (18 bp):
ATTTTTATGTATTTATTT
Found at i:3798972 original size:108 final size:109
Alignment explanation
Indices: 3798630--3799051 Score: 568
Period size: 109 Copynumber: 3.9 Consensus size: 109
3798620 AAGGAAATTT
* * *
3798630 TTTCTAAATGAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGTCCC-AATATGCTGGGTT
1 TTTCAAAATAAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACGTG-CCCTAATATGCTGGGTT
*
3798694 TCGATTTTTCTCTCTCAACCAAATAGCCAAATATTCTTTCAAAAA
65 TCGATTTTTCTCGCTCAACCAAATAGCCAAATATTCTTTCAAAAA
* * *
3798739 TTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
** * * * *
3798804 CGATTTTTTCTCATTCAACCAAATAGCTAAGTATCCTTTTAAAAA
66 CGA-TTTTTCTCGCTCAACCAAATAGCCAAATATTCTTTCAAAAA
**
3798849 TTTCAAAATAAGGCAATG-AAAGCGTTTGGAAATTCGAGAAAACGTGTCCC-AATATGCTGGGTT
1 TTTCAAAATAAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACGTG-CCCTAATATGCTGGGTT
3798912 TCGATTTTTCTCGCTCAACCAAATAGCCAAATATTCTTTCAAAAA
65 TCGATTTTTCTCGCTCAACCAAATAGCCAAATATTCTTTCAAAAA
* * * * *
3798957 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAGCTTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
* * *
3799021 CGA--TTTCTCGTTTAACCAAATAGTCAAATAT
66 CGATTTTTCTCGCTCAACCAAATAGCCAAATAT
3799052 CCTCTTGAAT
Statistics
Matches: 275, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
106 25 0.09
107 3 0.01
108 76 0.28
109 115 0.42
110 56 0.20
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
CGATTTTTCTCGCTCAACCAAATAGCCAAATATTCTTTCAAAAA
Found at i:3800293 original size:3 final size:3
Alignment explanation
Indices: 3800287--3800315 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3800277 TGTACAAAAA
3800287 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3800316 AAAGCAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3807248 original size:117 final size:117
Alignment explanation
Indices: 3806949--3807254 Score: 413
Period size: 117 Copynumber: 2.6 Consensus size: 117
3806939 CACAGTACAA
* *
3806949 ATTTTTTT--TGTCAGAATCAAATATAAAAATACG-AAAAAATTTAAAAAAAAAAATTTTGGGTG
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTT-AAAAAAAAATTTTTGGGTG
* * *
3807011 CTTGCCTGTCAATGGCCGACACCCAGTACACAATACAAAAAAATTTGTTTTTTTTTTT
65 CTGGACTGTCAATGGCCGACACCCAGTACACAATACAAAAAAA-----TTTTTCTTTT
3807069 ATTTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAAATTTAAAAAAAAATTTTTGGGT
1 A-TTTTTTTCGTGTCAGAATCAGATATAAAAATACG-AAAAAAATTTAAAAAAAAATTTTTGGGT
* *
3807134 GCTGGACTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAA-TTTTCTTTT
64 GCTGGACTGTCAATGGCCGACACCCAGTACACAATACAAAAAAATTTTTCTTTT
* * *
3807187 ATTTTTTTCGTGTTAGAATCAGATATAAAAATACGAAAAATAATTTTAAAAAAATTTTTTGGGTG
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAA-AATTTAAAAAAAAATTTTTGGGTG
3807252 CTG
65 CTG
3807255 ATTTTTTTTC
Statistics
Matches: 170, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
116 5 0.03
117 58 0.34
118 9 0.05
120 1 0.01
121 7 0.04
123 24 0.14
124 57 0.34
125 9 0.05
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (117 bp):
ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTTAAAAAAAAATTTTTGGGTGC
TGGACTGTCAATGGCCGACACCCAGTACACAATACAAAAAAATTTTTCTTTT
Found at i:3807590 original size:64 final size:63
Alignment explanation
Indices: 3807462--3807581 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 63
3807452 TATATATATA
*
3807462 TTTTAATTTTTTCGTATTTTTATATCTGATTCTGACATGAAAAAAATAAAAAAAAAACAATTT
1 TTTTAATTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAAAAAAACAATTT
*
3807525 TTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAA
1 TTTTAA-TTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAAAAAA
3807582 TTTTTTTTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
63 6 0.11
64 48 0.89
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (63 bp):
TTTTAATTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAAAAAAACAATTT
Found at i:3807791 original size:115 final size:116
Alignment explanation
Indices: 3807522--3807802 Score: 548
Period size: 116 Copynumber: 2.4 Consensus size: 116
3807512 AAAAAAACAA
3807522 TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAATTTTT
1 TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAATTTTT
3807587 TTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
66 TTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
3807638 TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAATTTTT
1 TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAATTTTT
3807703 TTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
66 TTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
3807754 TTTTTTTAATTTTTTTCGTA-TTTTATATCTGATTCTGACAC-AAAAAAAT
1 TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAT
3807803 TTGTAAATTT
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
114 8 0.05
115 21 0.13
116 136 0.82
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (116 bp):
TTTTTTTAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAATAAAAGAAAATTTTT
TTTTGTACTGTGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
Found at i:3816352 original size:13 final size:15
Alignment explanation
Indices: 3816334--3816371 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
3816324 AAAACAGATT
3816334 CAACAAAAAA-TA-A
1 CAACAAAAAATTAGA
3816347 CAACAAAAAATTAGA
1 CAACAAAAAATTAGA
*
3816362 AAACAAAAAA
1 CAACAAAAAA
3816372 ACAAAACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 2 0.09
15 10 0.45
ACGTcount: A:0.76, C:0.13, G:0.03, T:0.08
Consensus pattern (15 bp):
CAACAAAAAATTAGA
Found at i:3817303 original size:13 final size:14
Alignment explanation
Indices: 3817285--3817313 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3817275 ATATTTTGTC
3817285 TTATTATAT-ATTA
1 TTATTATATAATTA
3817298 TTATTATATAATTA
1 TTATTATATAATTA
3817312 TT
1 TT
3817314 TATATCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATATAATTA
Found at i:3817500 original size:4 final size:4
Alignment explanation
Indices: 3817485--3817521 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3817475 TTTTACTTGA
3817485 TATT TA-T T-TT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
3817522 GTGTCCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.13
4 27 0.87
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:3821518 original size:41 final size:39
Alignment explanation
Indices: 3821471--3821604 Score: 153
Period size: 40 Copynumber: 3.3 Consensus size: 39
3821461 ATTATAATCC
* *
3821471 CGCACACTAAGTGCCTTACATAGCCGAAGCTATCTCAGTCT
1 CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCA-T-T
* * * *
3821512 CACACACTAAGTGCCA-AATATAGCCAAAGCTATTCCCAAT
1 CGCACACTAAGTGCCATAA-ATAGCCGAAGCTA-TCTCATT
*
3821552 CGCACACTAAGTGCCATAAATAGCCGAAGTTATCTCAATT
1 CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC-ATT
3821592 CGCACACTAAGTG
1 CGCACACTAAGTG
3821605 ATAAACACAG
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
39 3 0.04
40 43 0.55
41 28 0.36
42 4 0.05
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (39 bp):
CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCATT
Found at i:3824227 original size:44 final size:43
Alignment explanation
Indices: 3824179--3824286 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
3824169 TATAACAATG
* * *
3824179 TCGCACACTTAGTGCCATCACATTAAACCGAAGCTCTCTT-AGT
1 TCGCACACTTAGTGCCAT-ACATCAAACCGAAGCTATCTTGAAT
** * *
3824222 ATCGCACACTTAGTGCCATTTATCCAACTGAAGCTATCTTGAAT
1 -TCGCACACTTAGTGCCATACATCAAACCGAAGCTATCTTGAAT
3824266 TCGCACACTTAGTGCCATACA
1 TCGCACACTTAGTGCCATACA
3824287 CTTTTGAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
43 34 0.63
44 20 0.37
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (43 bp):
TCGCACACTTAGTGCCATACATCAAACCGAAGCTATCTTGAAT
Found at i:3830770 original size:83 final size:83
Alignment explanation
Indices: 3830631--3830797 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
3830621 GAAAAGGGAA
*
3830631 ACATGTTCTCTAAATCATCGTTTATGGTTGCAATGAGGATTGCACTATCAGAAAAGAAAAACAAA
1 ACATGTTCTCTAAATCATCATTTATGGTTGCAATGAGGATTGCACTATCAGAAAAGAAAAACAAA
3830696 CGAAAGAGAAGGGGCAGG
66 CGAAAGAGAAGGGGCAGG
3830714 ACATGTTCTCTAAATCATCATTTATGGTTGCAATGAGGATTGCACTATCAGAAAAGAAAAACAAA
1 ACATGTTCTCTAAATCATCATTTATGGTTGCAATGAGGATTGCACTATCAGAAAAGAAAAACAAA
3830779 CGAAAGAGAAGGGGCAGG
66 CGAAAGAGAAGGGGCAGG
3830797 A
1 A
3830798 GAATGACATT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (83 bp):
ACATGTTCTCTAAATCATCATTTATGGTTGCAATGAGGATTGCACTATCAGAAAAGAAAAACAAA
CGAAAGAGAAGGGGCAGG
Found at i:3835994 original size:13 final size:14
Alignment explanation
Indices: 3835961--3835994 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3835951 TGAATAAGAG
3835961 TTTTAAAAAATATA
1 TTTTAAAAAATATA
*
3835975 TTATAAAAAATA-A
1 TTTTAAAAAATATA
3835988 TTTTAAA
1 TTTTAAA
3835995 GTATTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAAATATA
Found at i:3836009 original size:17 final size:17
Alignment explanation
Indices: 3835984--3836023 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3835974 ATTATAAAAA
* *
3835984 ATAATTTTAAAGTATTT
1 ATAAATTTAAAATATTT
3836001 ATAAATTTAAAATATTT
1 ATAAATTTAAAATATTT
3836018 A-AAATT
1 ATAAATT
3836024 AATTGAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAAATTTAAAATATTT
Found at i:3837425 original size:23 final size:24
Alignment explanation
Indices: 3837381--3837426 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3837371 TTTCTCACAT
* **
3837381 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
3837405 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
3837427 AATTCACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:3837798 original size:11 final size:11
Alignment explanation
Indices: 3837784--3837809 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3837774 CTTTTTCTTC
3837784 TTTCTCCCCTG
1 TTTCTCCCCTG
3837795 TTTCTCCCCTG
1 TTTCTCCCCTG
3837806 TTTC
1 TTTC
3837810 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:3838191 original size:21 final size:21
Alignment explanation
Indices: 3838167--3838209 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3838157 AATAATAACT
3838167 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
3838188 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
3838209 A
1 A
3838210 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:3838797 original size:27 final size:28
Alignment explanation
Indices: 3838743--3838799 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3838733 AAAACATAGT
*
3838743 TTATTTTCATATTTAAAATGTTTATAAA
1 TTATTTTCATATTTAAAATATTTATAAA
*
3838771 TTATTTTTA-ATTTAAAAATATTT-TAAA
1 TTATTTTCATATTT-AAAATATTTATAAA
3838798 TT
1 TT
3838800 TCTTCTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTATTTTCATATTTAAAATATTTATAAA
Found at i:3846292 original size:20 final size:19
Alignment explanation
Indices: 3846267--3846305 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3846257 TATATACATT
*
3846267 TTTTTAGATTTTTTTTAAAA
1 TTTTTAGA-ATTTTTTAAAA
*
3846287 TTTTTATAATTTTTTAAAA
1 TTTTTAGAATTTTTTAAAA
3846306 AATAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTAGAATTTTTTAAAA
Found at i:3846307 original size:21 final size:22
Alignment explanation
Indices: 3846264--3846308 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3846254 TTCTATATAC
* **
3846264 ATTTTTTTAGATTTTTTTTAAA
1 ATTTTTATAGATTTTTTAAAAA
3846286 ATTTTTATA-ATTTTTTAAAAA
1 ATTTTTATAGATTTTTTAAAAA
3846307 AT
1 AT
3846309 AAAAATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTTTATAGATTTTTTAAAAA
Found at i:3855933 original size:31 final size:31
Alignment explanation
Indices: 3855897--3855965 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3855887 TTATAATTTG
* **
3855897 GTCACTAAATTATTTGAAAGTTTTCATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
* *
3855928 GTCACTAAACTATTCAAAATTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
3855959 GTCACTA
1 GTCACTA
3855966 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTCATTTAA
Found at i:3857590 original size:4 final size:4
Alignment explanation
Indices: 3857576--3857614 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
3857566 TATGACTTGT
3857576 ATTA ATT- ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
3857615 GTCCTTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
ATTA
Found at i:3860367 original size:3 final size:3
Alignment explanation
Indices: 3860359--3860385 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3860349 ACTTTTTTAC
3860359 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3860386 ATAGTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3861794 original size:43 final size:43
Alignment explanation
Indices: 3861695--3861864 Score: 218
Period size: 43 Copynumber: 4.0 Consensus size: 43
3861685 ACGGTATTTA
* **
3861695 TAGCAGCGTTTGTGATAAAAGCGTCGCTAAAGGTCATG-TCTT
1 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTT
*
3861737 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTT
* * * **
3861780 TAGCGGAGTTTGTGATAAAAGCAACGCTAAAGATCATGACCTT
1 TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTT
* *
3861823 TAGCGGCGTTTGTGGGT-AAAGCACCGCTAAATGTCATGTTCT
1 TAGCGGCGTTTGT-GATAAAAGCACCGCTAAAGGTCATGTTCT
3861865 ATAGTGGCAC
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 36 0.32
43 73 0.66
44 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTGATAAAAGCACCGCTAAAGGTCATGTTCTT
Found at i:3863567 original size:2 final size:2
Alignment explanation
Indices: 3863560--3863585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3863550 GTTATATTAA
3863560 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
3863586 GATTAGATAT
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):
AT
Found at i:3865745 original size:19 final size:20
Alignment explanation
Indices: 3865709--3865750 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3865699 TATTTTCTTG
*
3865709 ATATTTTCAAGACTAACA-A
1 ATATTTTCAAGACAAACACA
3865728 ATATATTTCAA-ACAAACACA
1 ATAT-TTTCAAGACAAACACA
3865748 ATA
1 ATA
3865751 ATAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATTTTCAAGACAAACACA
Found at i:3867267 original size:17 final size:16
Alignment explanation
Indices: 3867239--3867271 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3867229 TCGAATCGGA
3867239 TTTTATAATTTATAAT
1 TTTTATAATTTATAAT
3867255 TTTTATAAATTTATAAT
1 TTTTAT-AATTTATAAT
3867272 AATTTAATTA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATAATTTATAAT
Found at i:3891212 original size:19 final size:17
Alignment explanation
Indices: 3891184--3891236 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
3891174 TTTTAATAAA
*
3891184 TTATTTAATATTATAATT
1 TTATTTAATAATA-AATT
3891202 TTATATTAATAATAAATT
1 TTAT-TTAATAATAAATT
*
3891220 TTA-ATAATAATAAATT
1 TTATTTAATAATAAATT
3891236 T
1 T
3891237 AAATTTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 13 0.41
18 11 0.34
19 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTAATAATAAATT
Found at i:3891229 original size:16 final size:16
Alignment explanation
Indices: 3891177--3891236 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
3891167 TTTATTATTT
3891177 TAATAAATTATT--TAA
1 TAATAAATT-TTAATAA
*
3891192 TATTATAATTTTATATTAA
1 TAATA-AATTTTA-A-TAA
3891211 TAATAAATTTTAATAA
1 TAATAAATTTTAATAA
3891227 TAATAAATTT
1 TAATAAATTT
3891237 AAATTTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 6 0.16
16 17 0.45
17 1 0.03
18 7 0.18
19 7 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATAAATTTTAATAA
Found at i:3891973 original size:19 final size:19
Alignment explanation
Indices: 3891949--3892061 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
3891939 AATTTTTTAG
3891949 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
**
3891968 GATATACAATCCAAGATAT
1 GATATACAATCTTAGATAT
3891987 GATATATGCAATCTTAGATAT
1 GATATA--CAATCTTAGATAT
* * *
3892008 AATATGCAATATTAGATAT
1 GATATACAATCTTAGATAT
*
3892027 GATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
3892046 GATATGCAATCTTAGA
1 GATATACAATCTTAGA
3892062 ATATATGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 64 0.81
21 15 0.19
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:3892029 original size:59 final size:58
Alignment explanation
Indices: 3891950--3892066 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 58
3891940 ATTTTTTAGG
*
3891950 ATATACAATCTTAGATATGATATACAATCCAAGATATGATATATGCAATCTTAG-ATATA
1 ATATACAATATTAGATATGATATACAATCCAAGATATG--ATATGCAATCTTAGAATATA
* * **
3892009 ATATGCAATATTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAATATA
1 ATATACAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAATATA
3892067 TGATTTTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 14 0.27
58 5 0.10
59 33 0.63
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (58 bp):
ATATACAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAATATA
Found at i:3892061 original size:38 final size:38
Alignment explanation
Indices: 3891949--3892061 Score: 154
Period size: 40 Copynumber: 2.9 Consensus size: 38
3891939 AATTTTTTAG
* * **
3891949 GATATACAATCTTAGATATGATATACAATCCAAGATAT
1 GATATATAATCTTAGATATGATATGCAATCTTAGATAT
* *
3891987 GATATATGCAATCTTAGATATAATATGCAATATTAGATAT
1 GATATAT--AATCTTAGATATGATATGCAATCTTAGATAT
3892027 GATATATAATCTTAGATATGATATGCAATCTTAGA
1 GATATATAATCTTAGATATGATATGCAATCTTAGA
3892062 ATATATGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
38 32 0.49
40 33 0.51
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (38 bp):
GATATATAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:3892845 original size:25 final size:26
Alignment explanation
Indices: 3892812--3892861 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
3892802 TACATGTATA
3892812 TATATTTTTTAAAACGAATATTTTCC
1 TATATTTTTTAAAACGAATATTTTCC
* *
3892838 TATATTTTTT-TAATGAATATTTTC
1 TATATTTTTTAAAACGAATATTTTC
3892862 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (26 bp):
TATATTTTTTAAAACGAATATTTTCC
Found at i:3893652 original size:98 final size:98
Alignment explanation
Indices: 3893533--3893729 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
3893523 AAAAAAATCA
*
3893533 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
3893598 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTATTTTAAAG
* *
3893631 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
3893696 TTAAATCTTGGATGAGTGGATGTTATTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTATTTTAAAG
3893729 T
1 T
3893730 TTTATTGTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTATTTTAAAG
Found at i:3897631 original size:21 final size:19
Alignment explanation
Indices: 3897583--3897631 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 19
3897573 AGTTCAGATT
3897583 AAAAAAAACAAAAAAATAA
1 AAAAAAAACAAAAAAATAA
3897602 AAACAAAAACAAAAAAAATAA
1 AAA-AAAAAC-AAAAAAATAA
3897623 AAAATAAAA
1 AAAA-AAAA
3897632 GAGAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 17 0.63
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAACAAAAAAATAA
Found at i:3897638 original size:21 final size:21
Alignment explanation
Indices: 3897586--3897625 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3897576 TCAGATTAAA
3897586 AAAAAC-AAAAAAATAAAAAC
1 AAAAACAAAAAAAATAAAAAC
3897606 AAAAACAAAAAAAATAAAAA
1 AAAAACAAAAAAAATAAAAA
3897626 ATAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (21 bp):
AAAAACAAAAAAAATAAAAAC
Found at i:3899034 original size:132 final size:132
Alignment explanation
Indices: 3898797--3899671 Score: 1426
Period size: 132 Copynumber: 6.6 Consensus size: 132
3898787 TCAGTGAAAT
* *
3898797 TTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
*
3898862 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGAGGAGAAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
3898927 GA
131 GA
* *
3898929 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* * * * *
3898994 GATAGTGGGAAGCAGATTTAAGGCACCAAGCCTTGTCTCCCTGAGTAGTAGCGGAGAAAGTTAAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
*
3899059 AA
131 GA
* *
3899061 TTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* * *
3899126 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAGTGGAAAAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
3899191 GA
131 GA
* * *
3899193 TTATAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGACAGCAAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* *
3899258 GATAGTGGGAAACAGATTTAAGCCACCAAGCCTTTTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
3899323 GA
131 GA
*
3899325 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* * * **
3899390 GATAGTGGGAAGCAGATTTAAGCCAACAAGCTTTGTCTCCCTAAGCAATAGCGGAGAAGGTTGAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
3899455 GA
131 GA
*
3899457 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
* * * * * *
3899522 GATAGTGGGAAGCAGATTCAAGCCACCAAGTCTTCTTTCCCTGAGCAGCAGCGGAGTAGGTTAAA
66 GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
3899587 GA
131 GA
* *
3899589 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCATATCTTTCCAA
1 TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
3899654 GATAGTGGGAAGCAGATT
66 GATAGTGGGAAGCAGATT
3899672 AAAGTCGACA
Statistics
Matches: 686, Mismatches: 57, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 686 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
TTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAA
GATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAA
GA
Found at i:3899674 original size:88 final size:88
Alignment explanation
Indices: 3899321--3899675 Score: 198
Period size: 88 Copynumber: 4.0 Consensus size: 88
3899311 GAGAAGGTTG
**
3899321 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTAAATCTTATCTTT
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
*
3899386 CCAAGA-TAGTGGGAAGCAGATTT
66 CCAAGAGTAGTGGG-AGCAGATTA
*** * * * * * * * * * *
3899409 AAGCCA-ACAAGCT-TTGTCTCCCTAAGCAATAGCGGAGAAGGTTGAAGATTG-TAGATCTTATC
1 AAG--ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGACAAATCTTATC
* **
3899471 -TCCCTAAGCAGTAGT-GGAGCAGATCG
63 TTTCC-AAG-AGTAGTGGGAGCAGATTA
** * * * *
3899497 AAGACGGTAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTC-AAG-CCACCAAGTC-T-
1 AAGATTGTAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA-TCGAAGACGA-CAAATCTTA
** * * * *
3899555 TCTTTCCCTGAGCAGCAGCGGAGTAGGTTA
61 TCTTTCCAAGAGTAG-TG-GGAGCAGATTA
*
3899585 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCATATCTTT
1 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
3899650 CCAAGA-TAGTGGGAAGCAGATTA
66 CCAAGAGTAGTGGG-AGCAGATTA
3899673 AAG
1 AAG
3899676 TCGACAATCC
Statistics
Matches: 189, Mismatches: 52, Indels: 52
0.65 0.18 0.18
Matches are distributed among these distances:
85 4 0.02
86 7 0.04
87 19 0.10
88 122 0.65
89 19 0.10
90 18 0.10
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (88 bp):
AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTT
CCAAGAGTAGTGGGAGCAGATTA
Found at i:3899716 original size:44 final size:43
Alignment explanation
Indices: 3899668--3899752 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
3899658 GTGGGAAGCA
* *
3899668 GATTAAAGTCGACA-ATCCTATCT-TCCTGAAGTTGCAGTAGAGTG
1 GATTAAAATC-ACAGATCCTATCTCT-CTGAAGTTACAG-AGAGTG
*
3899712 GATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAG
1 GATTAAAATCACAGATCCTATCTCTCTGAAGTTACAGAGAG
3899753 CAGATCGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 7 0.19
44 28 0.78
45 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (43 bp):
GATTAAAATCACAGATCCTATCTCTCTGAAGTTACAGAGAGTG
Found at i:3899816 original size:44 final size:43
Alignment explanation
Indices: 3899765--3900099 Score: 238
Period size: 44 Copynumber: 7.7 Consensus size: 43
3899755 GATCGCATCT
*
3899765 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
3899809 AGTCTTATCCTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGACA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGA-GCAGACT-AAGAAG-CA
* * * * * **
3899854 AATCTTAACTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCGACA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CA
* * * * *
3899899 A-TCCTGT-TTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCA
1 AGTCTTATCTT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * *
3899940 CAGATCTTATC-TCTCTGAAGTTGCAG-AGAACAGA-TCA-CATCT
1 -AG-TCTTATCTTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
3899982 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAA-GAAGCA
* *
3900026 AGTCTTATCCTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATAGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* *
3900071 AGTCTTATCTCCCTGAAGTTACAGTGGAG
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAG
3900100 TAGATTGAAG
Statistics
Matches: 229, Mismatches: 43, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
40 19 0.08
41 11 0.05
42 8 0.03
43 13 0.06
44 107 0.47
45 67 0.29
46 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:3899915 original size:217 final size:217
Alignment explanation
Indices: 3899664--3900110 Score: 718
Period size: 217 Copynumber: 2.1 Consensus size: 217
3899654 GATAGTGGGA
* *
3899664 AGCAGATTAAAGTCGACAATCCTATCTTCCTGAAGTTGCAGTAGAGTGGATTAAAATCACAGATC
1 AGCAGATTAAAGCCGACAATCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATC
* * *
3899729 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTTCCTGAAGTTGCAGTGGAG
66 TTATCTCTCTGAAGTTACAGAGAACAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
* *
3899794 CAGACTAAGTAAGTAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGAT-GACAAATC
131 CAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAG-CAAATC
3899858 TTAACTCCCTGAAGTTACAGTGG
195 TTAACTCCCTGAAGTTACAGTGG
* *
3899881 AGCAGATTAAAGCCGACAATCCTGT-TTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGAT
1 AGCAGATTAAAGCCGACAATCCTATCTT-CCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGAT
*
3899945 CTTATCTCTCTGAAGTTGCAGAGAACAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
65 CTTATCTCTCTGAAGTTACAGAGAACAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
** *
3900010 GCAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATAGCAAGTC
130 GCAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAGCAAATC
*
3900075 TTATCTCCCTGAAGTTACAGTGG
195 TTAACTCCCTGAAGTTACAGTGG
* *
3900098 AGTAGATTGAAGC
1 AGCAGATTAAAGC
3900111 ACTAATTCCT
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
216 2 0.01
217 209 0.99
218 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (217 bp):
AGCAGATTAAAGCCGACAATCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATC
TTATCTCTCTGAAGTTACAGAGAACAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
CAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATAGCAAATCT
TAACTCCCTGAAGTTACAGTGG
Found at i:3900337 original size:19 final size:19
Alignment explanation
Indices: 3900313--3900425 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
3900303 AATTTTTTAG
3900313 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
3900332 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
3900351 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
3900372 GATATGCAATATTAGATAT
1 GATATGCAATCTTAGATAT
**
3900391 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3900410 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3900426 ATATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3900358 original size:40 final size:40
Alignment explanation
Indices: 3900314--3900420 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
3900304 ATTTTTTAGG
3900314 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
***
3900354 ATATGCAATCTTAGATATGATATGCAATATTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
3900394 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
3900421 TTAGAATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 22 0.35
40 41 0.65
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:3900380 original size:59 final size:56
Alignment explanation
Indices: 3900313--3900432 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 56
3900303 AATTTTTTAG
* *
3900313 GATATGCAATCTTAGATATGATATGCAATCCAAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATATTAGATATGATATACAATCCAAGATATG--ATATGCAATCTTAGA-AT
* **
3900372 GATATGCAATATTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
3900428 -ATATG
1 GATATG
3900433 ATTTTGTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 15 0.27
59 34 0.61
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (56 bp):
GATATGCAATATTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
Found at i:3900855 original size:25 final size:26
Alignment explanation
Indices: 3900822--3900871 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
3900812 TACATGTATA
3900822 TATATTTTTTAAAACGAATATTTTCC
1 TATATTTTTTAAAACGAATATTTTCC
* *
3900848 TATATTTTTT-TAATGAATATTTTC
1 TATATTTTTTAAAACGAATATTTTC
3900872 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (26 bp):
TATATTTTTTAAAACGAATATTTTCC
Found at i:3904210 original size:11 final size:11
Alignment explanation
Indices: 3904189--3904249 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
3904179 AGACTATAAA
3904189 AAAAGAAATTAT
1 AAAA-AAATTAT
3904201 AAAAAAATTAT
1 AAAAAAATTAT
* *
3904212 -TAATAATTAT
1 AAAAAAATTAT
**
3904222 TTAAAAATTAT
1 AAAAAAATTAT
3904233 AAAATTAAATTAT
1 AAAA--AAATTAT
3904246 AAAA
1 AAAA
3904250 TAAAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.20
11 18 0.44
12 4 0.10
13 11 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:3904220 original size:21 final size:19
Alignment explanation
Indices: 3904194--3904239 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
3904184 ATAAAAAAAG
3904194 AAATTATAAAAAAATTATTA
1 AAATTATAAAAAAATTA-TA
**
3904214 ATAATTATTTAAAAATTATA
1 A-AATTATAAAAAAATTATA
3904234 AAATTA
1 AAATTA
3904240 AATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTATAAAAAAATTATA
Found at i:3904244 original size:13 final size:13
Alignment explanation
Indices: 3904226--3904250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3904216 AATTATTTAA
3904226 AAATTATAAAATT
1 AAATTATAAAATT
3904239 AAATTATAAAAT
1 AAATTATAAAAT
3904251 AAAAAAATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTATAAAATT
Found at i:3904249 original size:21 final size:21
Alignment explanation
Indices: 3904203--3904250 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3904193 GAAATTATAA
*
3904203 AAAAATTATTAATAATTATTT
1 AAAAATTATTAATAATTAATT
3904224 AAAAATTA-TAA-AATTAAATT
1 AAAAATTATTAATAATT-AATT
3904244 ATAAAAT
1 A-AAAAT
3904251 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATTATTAATAATTAATT
Found at i:3906543 original size:9 final size:10
Alignment explanation
Indices: 3906515--3906550 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3906505 AGGGAGAAGC
* *
3906515 AGAAGAAAAT
1 AGAAAAAAAA
3906525 AGAAAAAAAA
1 AGAAAAAAAA
3906535 AGAAAAAAAA
1 AGAAAAAAAA
3906545 AGAAAA
1 AGAAAA
3906551 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:3906736 original size:28 final size:28
Alignment explanation
Indices: 3906705--3906780 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
3906695 TTTTTATGTA
*
3906705 AATTTTTTTTAACTTTTTTTACAATT-TT
1 AATTTTTTTTAA-TTTTTTTAAAATTATT
**
3906733 AATTTTTTAGAATTTTTTTAAAATTATT
1 AATTTTTTTTAATTTTTTTAAAATTATT
3906761 AATATTTGTTTATAATTTTT
1 AAT-TTT-TTT-TAATTTTT
3906781 AATATTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 12 0.31
28 15 0.38
29 3 0.08
30 2 0.05
31 7 0.18
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (28 bp):
AATTTTTTTTAATTTTTTTAAAATTATT
Found at i:3906738 original size:27 final size:29
Alignment explanation
Indices: 3906708--3906780 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
3906698 TTATGTAAAT
* *
3906708 TTTTTTTA-ACTTTTTTTACAATT-TTAA
1 TTTTTTTAGAATTTTTTTAAAATTATTAA
3906735 -TTTTTTAGAATTTTTTTAAAATTATTAA
1 TTTTTTTAGAATTTTTTTAAAATTATTAA
*
3906763 TATTTGTTTATAATTTTT
1 T-TTT-TTTAGAATTTTT
3906781 AATATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.18
27 13 0.34
28 4 0.11
30 3 0.08
31 11 0.29
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTTTTAGAATTTTTTTAAAATTATTAA
Found at i:3906799 original size:20 final size:20
Alignment explanation
Indices: 3906744--3906787 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3906734 ATTTTTTAGA
* * *
3906744 ATTTTTTTAAAATTATTAAT
1 ATTTGTTTATAATTTTTAAT
3906764 ATTTGTTTATAATTTTTAAT
1 ATTTGTTTATAATTTTTAAT
3906784 ATTT
1 ATTT
3906788 TTTCATAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTGTTTATAATTTTTAAT
Found at i:3910749 original size:23 final size:23
Alignment explanation
Indices: 3910719--3910787 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
3910709 AATAAAGCAT
3910719 GGGTTAAGAGACAATGACTGACA
1 GGGTTAAGAGACAATGACTGACA
3910742 GGGTTAAGAGACAATGACTGACA
1 GGGTTAAGAGACAATGACTGACA
3910765 GGGTTAAGAGACAATGACTGACA
1 GGGTTAAGAGACAATGACTGACA
3910788 ACGAGAGCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.17
Consensus pattern (23 bp):
GGGTTAAGAGACAATGACTGACA
Found at i:3912679 original size:29 final size:30
Alignment explanation
Indices: 3912647--3912726 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 30
3912637 TGCACTTTGA
* *
3912647 TGTTGTCTTGTTCTAAATACACT-CTTTAG
1 TGTTGTCTTGTTCTAAATACAATACTTCAG
* * *
3912676 TGTTGCCTTATTCTTAAAATA-AATACTTCGG
1 TGTTGTCTTGTTC-T-AAATACAATACTTCAG
*
3912707 TGTTGTCTTGTTCTGAATAC
1 TGTTGTCTTGTTCTAAATAC
3912727 GCGCTTCGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
29 15 0.38
30 4 0.10
31 20 0.51
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (30 bp):
TGTTGTCTTGTTCTAAATACAATACTTCAG
Found at i:3912856 original size:31 final size:31
Alignment explanation
Indices: 3912746--3912920 Score: 114
Period size: 31 Copynumber: 5.8 Consensus size: 31
3912736 TGCTATTTTA
* *
3912746 AAAATACACACTTTAAT-CTGTCCTGTTCTG
1 AAAATACACACTTTGATGTTGTCCTGTTCTG
* * *
3912776 AAAATACGCA-TTTCAGCGTTG-CCTTGTTCTG
1 AAAATACACACTTTGA-TGTTGTCC-TGTTCTG
** *
3912807 --AATATGCACTTTGGTGTTGTCCTGTTCTG
1 AAAATACACACTTTGATGTTGTCCTGTTCTG
*
3912836 AAAATACACACTTTGATGTTGTCTTGTTCTG
1 AAAATACACACTTTGATGTTGTCCTGTTCTG
** * * * *
3912867 --AATATGCAC-TTCAGTGCTGTCTTGTTATG
1 AAAATACACACTTTGA-TGTTGTCCTGTTCTG
* *
3912896 AAAATACACACTTCGGTGTTGTCCT
1 AAAATACACACTTTGATGTTGTCCT
3912921 ACGCATTTCG
Statistics
Matches: 110, Mismatches: 24, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
28 3 0.03
29 42 0.38
30 16 0.15
31 48 0.44
32 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (31 bp):
AAAATACACACTTTGATGTTGTCCTGTTCTG
Found at i:3912887 original size:29 final size:28
Alignment explanation
Indices: 3912793--3912897 Score: 93
Period size: 29 Copynumber: 3.6 Consensus size: 28
3912783 GCATTTCAGC
* *
3912793 GTTGCCTTGTTCTGAATATGCACTTTGGT
1 GTTGTCTTGTTCTGAATATGCAC-TTAGT
* ** *
3912822 GTTGTCCTGTTCTGAAAATACACACTTTGAT
1 GTTGTCTTGTTCTG--AATATGCACTTAG-T
3912853 GTTGTCTTGTTCTGAATATGCACTTCAGT
1 GTTGTCTTGTTCTGAATATGCACTT-AGT
* *
3912882 GCTGTCTTGTTATGAA
1 GTTGTCTTGTTCTGAA
3912898 AATACACACT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 36 0.59
30 4 0.07
31 21 0.34
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (28 bp):
GTTGTCTTGTTCTGAATATGCACTTAGT
Found at i:3912916 original size:60 final size:60
Alignment explanation
Indices: 3912763--3912918 Score: 204
Period size: 60 Copynumber: 2.6 Consensus size: 60
3912753 ACACTTTAAT
* * * * * **
3912763 CTGTCCTGTTCTGAAAATACGCATTTCAGCGTTGCCTTGTTCTGAATATGCACTTTGGTG
1 CTGTCCTGTTCTGAAAATACACACTTCGGTGTTGTCTTGTTCTGAATATGCACTTCAGTG
* * *
3912823 TTGTCCTGTTCTGAAAATACACACTTTGATGTTGTCTTGTTCTGAATATGCACTTCAGTG
1 CTGTCCTGTTCTGAAAATACACACTTCGGTGTTGTCTTGTTCTGAATATGCACTTCAGTG
* *
3912883 CTGTCTTGTTATGAAAATACACACTTCGGTGTTGTC
1 CTGTCCTGTTCTGAAAATACACACTTCGGTGTTGTC
3912919 CTACGCATTT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (60 bp):
CTGTCCTGTTCTGAAAATACACACTTCGGTGTTGTCTTGTTCTGAATATGCACTTCAGTG
Found at i:3913046 original size:31 final size:31
Alignment explanation
Indices: 3912924--3913048 Score: 119
Period size: 31 Copynumber: 4.1 Consensus size: 31
3912914 TTGTCCTACG
* * **
3912924 CATTTCGGTATTGTCTTGTTTTGAAAATATG
1 CATTTCGGTATTGTCCTGTTCTGAAAATACA
3912955 CATTTCGGTATTGTCCTGTTCTGAAAATACA
1 CATTTCGGTATTGTCCTGTTCTGAAAATACA
* ** * **
3912986 CCACTTCAATGTTGT-CT-TTCTCTAAATACA
1 -CATTTCGGTATTGTCCTGTTCTGAAAATACA
* *
3913016 CATTTCGGTGTTTTCCTGTTCTGAAAATACA
1 CATTTCGGTATTGTCCTGTTCTGAAAATACA
3913047 CA
1 CA
3913049 CTTGGCAAAG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
29 10 0.13
30 13 0.17
31 42 0.56
32 10 0.13
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (31 bp):
CATTTCGGTATTGTCCTGTTCTGAAAATACA
Done.