Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 17 of 25
Found at i:2765683 original size:21 final size:20
Alignment explanation
Indices: 2765639--2765681 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2765629 GACTTGCCAT
2765639 AAATGGCAATCTTTTTGAAA
1 AAATGGCAATCTTTTTGAAA
2765659 AAATGGCAATCTTTTTGAAA
1 AAATGGCAATCTTTTTGAAA
2765679 AAA
1 AAA
2765682 ATACGCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATGGCAATCTTTTTGAAA
Found at i:2768796 original size:97 final size:97
Alignment explanation
Indices: 2768644--2768819 Score: 280
Period size: 97 Copynumber: 1.8 Consensus size: 97
2768634 CCCAGCATTC
* * *
2768644 AAGTGGAATTCAGAAGTAATTCTCCTTCGTAAAGAAAATAGGTAATAATCCCTTGAATTTGAGAT
1 AAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAATTTCAGAT
2768709 GGAGCAGCCTTCGTCTAAATTTCTCAGCACTA
66 GGAGCAGCCTTCGTCTAAATTTCTCAGCACTA
* * * *
2768741 AAGTGGAATTCAGAAGTAATTCTCCTTTATAAAGAAATTCCGTAATAATCTCTTGAATTTCAGAT
1 AAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAATTTCAGAT
*
2768806 GGAGCATCCTTCGT
66 GGAGCAGCCTTCGT
2768820 AGAAAATGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (97 bp):
AAGTGGAATTCAGAAGTAATTCTCCTTCATAAAGAAAATACGTAATAATCCCTTGAATTTCAGAT
GGAGCAGCCTTCGTCTAAATTTCTCAGCACTA
Found at i:2772077 original size:11 final size:11
Alignment explanation
Indices: 2772038--2772108 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
2772028 ATAATTACAT
2772038 ATATAAATATA
1 ATATAAATATA
*
2772049 ATACAAA-A-A
1 ATATAAATATA
2772058 ATATAAATATA
1 ATATAAATATA
*
2772069 ATATTAATAT-
1 ATATAAATATA
2772079 ATA-AATATATCA
1 ATATAA-ATAT-A
**
2772091 A-ATTTATATA
1 ATATAAATATA
2772101 ATATAAAT
1 ATATAAAT
2772109 TTTTAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
9 8 0.18
10 11 0.24
11 25 0.56
12 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:2772099 original size:21 final size:19
Alignment explanation
Indices: 2772030--2772107 Score: 56
Period size: 19 Copynumber: 4.1 Consensus size: 19
2772020 AACAAAATAT
2772030 AATTACATATATAAATATAA
1 AATTA-ATATATAAATATAA
* *
2772050 TACA-AAAAATATAAATATAA
1 -A-ATTAATATATAAATATAA
*
2772070 TATTAATATATAAATATATCA
1 AATTAATATATAAATATA--A
2772091 AATT--TATAT-AATATAA
1 AATTAATATATAAATATAA
2772107 A
1 A
2772108 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
16 2 0.04
18 7 0.15
19 18 0.38
20 13 0.28
21 6 0.13
22 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAATATATAAATATAA
Found at i:2774820 original size:5 final size:5
Alignment explanation
Indices: 2774810--2774834 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2774800 TCATTTGAAT
2774810 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
2774835 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:2775108 original size:16 final size:16
Alignment explanation
Indices: 2775087--2775123 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2775077 TAATCGAAAC
*
2775087 TAAAATTAGTCAAATT
1 TAAAATGAGTCAAATT
*
2775103 TAAAATGATTCAAATT
1 TAAAATGAGTCAAATT
2775119 TAAAA
1 TAAAA
2775124 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (16 bp):
TAAAATGAGTCAAATT
Found at i:2776862 original size:27 final size:26
Alignment explanation
Indices: 2776824--2776875 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
2776814 TGCAACTTTT
2776824 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
2776851 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
2776876 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:2776876 original size:12 final size:13
Alignment explanation
Indices: 2776827--2776876 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
2776817 AACTTTTACT
2776827 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
2776839 ATTTCAAAATTAA
1 ATTTCAAAATTGA
2776852 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
2776866 A-TTCAAAATTG
1 ATTTCAAAATTG
2776877 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:2781637 original size:27 final size:26
Alignment explanation
Indices: 2781599--2781650 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
2781589 TGCAACTTTT
2781599 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
2781626 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
2781651 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:2781651 original size:12 final size:13
Alignment explanation
Indices: 2781602--2781651 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
2781592 AACTTTTACT
2781602 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
2781614 ATTTCAAAATTAA
1 ATTTCAAAATTGA
2781627 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
2781641 A-TTCAAAATTG
1 ATTTCAAAATTG
2781652 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:2788003 original size:23 final size:23
Alignment explanation
Indices: 2787962--2788017 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
2787952 ATTTTTTTAT
* *
2787962 ATATAATTTT-ATATTAAAAT-A
1 ATATATTTTTAATATAAAAATCA
2787983 ATTATATTTTTAATATAAAAATCA
1 A-TATATTTTTAATATAAAAATCA
2788007 A-ATATTTTTAA
1 ATATATTTTTAA
2788018 GTTACATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 18 0.60
23 9 0.30
24 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATTTTTAATATAAAAATCA
Found at i:2788359 original size:78 final size:77
Alignment explanation
Indices: 2788277--2788429 Score: 184
Period size: 78 Copynumber: 2.0 Consensus size: 77
2788267 TTTTCATTAT
* * * * *
2788277 TAATAATTATTTATTGTAATAAT-AGTAGATAA-AAATATTTTTAATTTATTGGTGTTAATTTTG
1 TAATAATTATTTACTATAATAATCA-TAAATAATAAATATTTTTAATTTAGT-G-GTTAATTTTA
*
2788340 TAATTCTTTCAAATC
63 TAATTCTTCCAAATC
* **
2788355 TAATAATTATTTACTATAATGATCATAAATAATAAATATTTTTTGTTTAGTGGTTAATTTTATAA
1 TAATAATTATTTACTATAATAATCATAAATAATAAATATTTTTAATTTAGTGGTTAATTTTATAA
2788420 TTCTTCCAAA
66 TTCTTCCAAA
2788430 AAATTTCTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
77 21 0.33
78 27 0.42
79 16 0.25
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (77 bp):
TAATAATTATTTACTATAATAATCATAAATAATAAATATTTTTAATTTAGTGGTTAATTTTATAA
TTCTTCCAAATC
Found at i:2788448 original size:2 final size:2
Alignment explanation
Indices: 2788443--2788467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2788433 TTTCTAACAC
2788443 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2788468 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2788472 original size:2 final size:2
Alignment explanation
Indices: 2788467--2788495 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2788457 ATATATATAT
2788467 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2788496 TTGAATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2793561 original size:186 final size:185
Alignment explanation
Indices: 2793215--2793597 Score: 588
Period size: 186 Copynumber: 2.1 Consensus size: 185
2793205 TTATAGTATC
2793215 AATT-AAAAGATAGTACATATTAATTTCATGTTATCTATATCTAAAAAAATAATTTTAACTTTAA
1 AATTCAAAAG-TAGTACATATTAATTTCATGTTATCTATATCTAAAAAAATAATTTTAACTTTAA
*
2793279 TATCTAAAATAATTCACTTAATGCATTTTACTAGAAACATTATTATATTTCTCGTAATGTCTTAT
65 TATCTAAAATAATTCACTTAATGCATTTCACTAGAAACATTATTATATTTCTCGTAATGTCTTAT
* * *
2793344 TATTTGAAAACTTTTGACATCGAAAACTTCATTTAAATTCCCAAACATTCAAGTGG
130 TATTTGAAAACTTTTAACATAGAAAACTTCATCTAAATTCCCAAACATTCAAGTGG
* * * * *
2793400 AATTCAAAAGTAGTATATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAATTTTAA
1 AATTCAAAAGTAGTACATATTAATTTCATGTTATCTATA-TCTAAAAAAATAATTTTAACTTTAA
* *
2793465 TATCTAAAATAATTCACTTAATGCATTTCATTAGAAACATTATTATATTTCTCGTAATGTCTTTT
65 TATCTAAAATAATTCACTTAATGCATTTCACTAGAAACATTATTATATTTCTCGTAATGTCTTAT
** * * *
2793530 TATTTGAAAGTTTTTAACGTAGAAGACTTCATCTAAATTCCCAAGCATTCAAGTGG
130 TATTTGAAAACTTTTAACATAGAAAACTTCATCTAAATTCCCAAACATTCAAGTGG
*
2793586 AATTCAGAAGTA
1 AATTCAAAAGTA
2793598 ATTCTCCCTT
Statistics
Matches: 179, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
185 31 0.17
186 148 0.83
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (185 bp):
AATTCAAAAGTAGTACATATTAATTTCATGTTATCTATATCTAAAAAAATAATTTTAACTTTAAT
ATCTAAAATAATTCACTTAATGCATTTCACTAGAAACATTATTATATTTCTCGTAATGTCTTATT
ATTTGAAAACTTTTAACATAGAAAACTTCATCTAAATTCCCAAACATTCAAGTGG
Found at i:2793731 original size:97 final size:97
Alignment explanation
Indices: 2793560--2793752 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 97
2793550 AGAAGACTTC
* * * *
2793560 ATCTAAATTCCCAAGCATTCAAGTGGAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTTCGTAA
1 ATCTAAATCCCCAAGCATTCAAATGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTTCATAA
2793625 CAATCCCTTGAATTTGAGATGGAGCACCCTTA
66 CAATCCCTTGAATTTGAGATGGAGCACCCTTA
* * * * * *
2793657 ATCTAAATCCCCCAGCGTTCAAATGAAATTCGGAAGTAATTCTCCTTTGTAAGGAAA-TTCTATA
1 ATCTAAATCCCCAAGCATTCAAATGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTTC-ATA
* * *
2793721 ATAATTCCTTGAATTTGAGATGGAGCATCCTT
65 ACAATCCCTTGAATTTGAGATGGAGCACCCTT
2793753 CGTAGGAATG
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 3 0.04
97 79 0.96
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (97 bp):
ATCTAAATCCCCAAGCATTCAAATGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTTCATAA
CAATCCCTTGAATTTGAGATGGAGCACCCTTA
Found at i:2794224 original size:22 final size:23
Alignment explanation
Indices: 2794169--2794220 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2794159 ATTTTATTTT
2794169 TATTTTTATTTAATTATAAAAATA
1 TATTTTTA-TTAATTATAAAAATA
**
2794193 TATTAATATTAA-TATAAAAATA
1 TATTTTTATTAATTATAAAAATA
2794215 -ATTTTT
1 TATTTTT
2794221 TATTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 4 0.17
24 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTTTATTAATTATAAAAATA
Found at i:2795685 original size:46 final size:47
Alignment explanation
Indices: 2795623--2795719 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 47
2795613 AATTTTAAGG
2795623 ATTTAAAAAAAAATTATGTATTTTAATTAATAATTGTTAAACAAATA
1 ATTTAAAAAAAAATTATGTATTTTAATTAATAATTGTTAAACAAATA
*
2795670 ATTT-AAAAAATATTATGTATTTTAATTAATAATTGTTAAACAAATA
1 ATTTAAAAAAAAATTATGTATTTTAATTAATAATTGTTAAACAAATA
2795716 ATTT
1 ATTT
2795720 TAAATTTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 45 0.92
47 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (47 bp):
ATTTAAAAAAAAATTATGTATTTTAATTAATAATTGTTAAACAAATA
Found at i:2800422 original size:13 final size:14
Alignment explanation
Indices: 2800392--2800427 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2800382 AGGAAATGAA
2800392 GAAAAA-AA-AAAG
1 GAAAAAGAAGAAAG
2800404 GAAAAAGAAGAAAG
1 GAAAAAGAAGAAAG
2800418 G-AAAAGAAGA
1 GAAAAAGAAGA
2800428 GAGAGAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 11 0.50
14 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAGAAAG
Found at i:2800574 original size:5 final size:5
Alignment explanation
Indices: 2800564--2800590 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2800554 TTCATTTAAA
2800564 ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT AT
2800591 TTTTGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:2806466 original size:6 final size:6
Alignment explanation
Indices: 2806455--2806492 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2806445 TTAAAATAAT
*
2806455 AATTTA AATTTA TAAATTA AA-TTA AATTTA AATTTA AA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AA
2806493 CAAAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:2806935 original size:35 final size:34
Alignment explanation
Indices: 2806878--2807000 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 34
2806868 AAAAAGCTAA
*
2806878 GTCTGCCTCTCAATCCCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCCCCCGTTCCACAAGTTAAT
*
2806912 GTCTACCAT-TCAATCCTCCCGTTCCACAAGTTGAT
1 GTCTACC-TCTCAATCC-CCCGTTCCACAAGTTAAT
* * * *
2806947 GTCTGCCTCGCAATCACACCCCATTCCACAAGGTAAT
1 GTCTACCTCTCAAT--C-CCCCGTTCCACAAGTTAAT
2806984 GTCTACCTCTCAATCCC
1 GTCTACCTCTCAATCCC
2807001 ACCCCATGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
34 16 0.22
35 29 0.39
37 28 0.38
38 1 0.01
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (34 bp):
GTCTACCTCTCAATCCCCCGTTCCACAAGTTAAT
Found at i:2806986 original size:37 final size:37
Alignment explanation
Indices: 2806893--2807007 Score: 110
Period size: 37 Copynumber: 3.2 Consensus size: 37
2806883 CCTCTCAATC
* * *
2806893 CCCCGTTCCACAAGTTAATGTCTACCAT-TCAATC-C-
1 CCCCATTCCACAAGGTAATGTCTACC-TCGCAATCACA
* * * * *
2806928 TCCCGTTCCACAAGTTGATGTCTGCCTCGCAATCACA
1 CCCCATTCCACAAGGTAATGTCTACCTCGCAATCACA
* *
2806965 CCCCATTCCACAAGGTAATGTCTACCTCTCAATCCCA
1 CCCCATTCCACAAGGTAATGTCTACCTCGCAATCACA
2807002 CCCCAT
1 CCCCAT
2807008 GTATAGTTGA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 28 0.42
36 1 0.02
37 36 0.55
ACGTcount: A:0.24, C:0.39, G:0.10, T:0.26
Consensus pattern (37 bp):
CCCCATTCCACAAGGTAATGTCTACCTCGCAATCACA
Found at i:2807219 original size:246 final size:246
Alignment explanation
Indices: 2806763--2807253 Score: 793
Period size: 246 Copynumber: 2.0 Consensus size: 246
2806753 TGGTGACTGA
* *
2806763 TATAGTTAATTTCTCAACTTTGGGGTAATCTATGCCTTCTTTGATTCTAGTCATTTTTTTAAATA
1 TATAGTTAACTTCTCAACTTTGGGGTAATCTATGCCTTCTTTGATTCGAGTCATTTTTTTAAATA
* * * * **
2806828 GAGGTTACCAAGGCGGTCCTCAGTTTCATGATTGACTTGCAAAAAGCTAAGTCTGCCTCTCAATC
66 GAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTAACTCTCAATC
* * *
2806893 CCCCGTTCCACAAGTTAATGTCTACCATTCAATCCTCCCGTTCCACAAGTTGATGTCTGCCTCGC
131 CCCCGTTCCACAAGTTAATGTCTACCACTCAATCCTCCCATTCCACAAGTTGATGTCTACCTCGC
2806958 AATCACACCCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCATG
196 AATCACACCCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCATG
* * * * *
2807009 TATAGTTGACTTCTCAACTTTGGGGTGATCTATGCCTTCTTTGATTCGATTCGTTTTTTTATATA
1 TATAGTTAACTTCTCAACTTTGGGGTAATCTATGCCTTCTTTGATTCGAGTCATTTTTTTAAATA
2807074 GAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTAACTCTCAATC
66 GAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTAACTCTCAATC
* * *
2807139 CCCCGTTCCACAAGTTAATGTCTACTACTCAATCCTCCTATTCCACAAGTTGATGTCTACCTCTC
131 CCCCGTTCCACAAGTTAATGTCTACCACTCAATCCTCCCATTCCACAAGTTGATGTCTACCTCGC
* *
2807204 AATCATACTCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCAT
196 AATCACACCCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCAT
2807254 TTCACAAGTT
Statistics
Matches: 224, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
246 224 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.33
Consensus pattern (246 bp):
TATAGTTAACTTCTCAACTTTGGGGTAATCTATGCCTTCTTTGATTCGAGTCATTTTTTTAAATA
GAGGTTACCAAGGCGATCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTAACTCTCAATC
CCCCGTTCCACAAGTTAATGTCTACCACTCAATCCTCCCATTCCACAAGTTGATGTCTACCTCGC
AATCACACCCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCATG
Found at i:2807232 original size:37 final size:35
Alignment explanation
Indices: 2807124--2807268 Score: 152
Period size: 37 Copynumber: 4.1 Consensus size: 35
2807114 AAAAAGCCAA
* * *
2807124 GTCTAACTCTCAATC-CCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCACTCCATTCCACAAGTTAAT
*
2807158 GTCTA-CTACTCAATC-CTCCTATTCCACAAGTTGAT
1 GTCTACCT-CTCAATCACTCC-ATTCCACAAGTTAAT
*
2807193 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAAT
1 GTCTACCTCTCAATC--ACTCCATTCCACAAGTTAAT
* *
2807230 GTCTACCTCTCAATCCCACCCCATTTCACAAGTTAAT
1 GTCTACCTCTCAAT--CACTCCATTCCACAAGTTAAT
2807267 GT
1 GT
2807269 ACGACACTTG
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.02
34 15 0.16
35 25 0.26
36 2 0.02
37 46 0.48
38 4 0.04
39 1 0.01
ACGTcount: A:0.27, C:0.34, G:0.08, T:0.31
Consensus pattern (35 bp):
GTCTACCTCTCAATCACTCCATTCCACAAGTTAAT
Found at i:2807783 original size:2 final size:2
Alignment explanation
Indices: 2807776--2807813 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2807766 CCATTCTTTA
*
2807776 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2807814 TGCAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2808695 original size:15 final size:15
Alignment explanation
Indices: 2808675--2808726 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2808665 AAATAATAAT
2808675 TTAATTAAAATTAAA
1 TTAATTAAAATTAAA
*
2808690 TTAATTTAAATTAAA
1 TTAATTAAAATTAAA
* *
2808705 -AAATTAATATTTAAA
1 TTAATTAA-AATTAAA
2808720 TCTAATT
1 T-TAATT
2808727 TATTTCTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.17
15 20 0.69
17 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATTAAAATTAAA
Found at i:2809256 original size:9 final size:8
Alignment explanation
Indices: 2809235--2809259 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2809225 ATATAAAAAT
2809235 ATTTTTTA
1 ATTTTTTA
2809243 ATTTTTTA
1 ATTTTTTA
2809251 ATTTTTTA
1 ATTTTTTA
2809259 A
1 A
2809260 AATAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTTA
Found at i:2810708 original size:16 final size:16
Alignment explanation
Indices: 2810687--2810718 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2810677 TGCTTTCTAA
2810687 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2810703 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2810719 TGTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AACACATACTAAGTTC
Found at i:2812218 original size:22 final size:22
Alignment explanation
Indices: 2812193--2812234 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2812183 TATTTTTATT
2812193 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2812215 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2812235 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2812452 original size:23 final size:23
Alignment explanation
Indices: 2812425--2812489 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
2812415 GCTTGAATTA
2812425 ATTAATAATAATAAATATTTAAAT
1 ATTAAT-ATAATAAATATTTAAAT
*
2812449 -TTAATTATAA-AAATATATAAAT
1 ATTAA-TATAATAAATATTTAAAT
*
2812471 ATTAATATAATAATTATTT
1 ATTAATATAATAAATATTT
2812490 TTAAAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 16 0.46
23 18 0.51
24 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATATAATAAATATTTAAAT
Found at i:2814254 original size:79 final size:79
Alignment explanation
Indices: 2814153--2814354 Score: 226
Period size: 79 Copynumber: 2.6 Consensus size: 79
2814143 AATAACGGAG
* * * * * * *
2814153 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
2814217 AAAAAAAAATCGGGA
65 AAAAAAAAACCGGGA
* * *
2814232 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
2814297 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* * *
2814311 TTGGAGTATCCCCTCGGAAGTAACGGGGTTAGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
2814355 GAAATAACAA
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 102 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:2814362 original size:28 final size:28
Alignment explanation
Indices: 2814306--2814377 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
2814296 GGAATAAAGC
** *
2814306 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
2814334 CGGGGTTAGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
2814362 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2814378 TCGACTGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2814497 original size:52 final size:50
Alignment explanation
Indices: 2814365--2814548 Score: 170
Period size: 52 Copynumber: 3.6 Consensus size: 50
2814355 GAAATAACAA
* * * * * *
2814365 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGG--TGTTTGAAAATAAAACCGG
* * *
2814417 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTT-GAAAATAAAACCGG
* * * *
2814469 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTGGTGTTTGA-AAATAAAACCGG
* * *
2814521 GATTGGAATATCTCCGATTATGAAAAAT
1 GGTTGGAGTATCCCCGATTATGAAAAAT
2814549 CAATATTTTG
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
51 12 0.11
52 87 0.81
53 9 0.08
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTGAAAATAAAACCGG
Found at i:2814609 original size:28 final size:28
Alignment explanation
Indices: 2814569--2814641 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
2814559 GAAATAAAGT
**
2814569 CGGGGTTAAAGTATCCCCTCGGA-AAT-AA
1 CGGGGTTGGAGTATCCCC-C-GATAATCAA
*
2814597 CGGGGTTGGAGTAT-CCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCCGATAATCAA
2814624 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
2814642 GATTGTGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 19 0.49
28 15 0.38
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGATAATCAA
Found at i:2814690 original size:54 final size:51
Alignment explanation
Indices: 2814628--2814758 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
2814618 GATCAACGGG
* * * *
2814628 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TCTTGAAAATAAAATCAGA
*
2814682 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTCTTGAAAATAAAATCAGA
*
2814733 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
2814759 TTGAGAAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
51 34 0.51
52 4 0.06
53 10 0.15
54 19 0.28
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTCTTGAAAATAAAATCAGA
Found at i:2814746 original size:263 final size:262
Alignment explanation
Indices: 2814255--2814755 Score: 738
Period size: 263 Copynumber: 1.9 Consensus size: 262
2814245 TCGAAAATAA
* * * * **
2814255 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTAAAGTAT
* *
2814320 CCCCTCGGAAGTAACGGGGTTAGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTG
66 CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTG
*
2814385 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
* * *
2814450 GTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 GTTTCGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
2814515 AAC
260 AAC
* * *
2814518 CGGGATTGGAATATCTCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTAAAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTAAAGTAT
* ** *
2814583 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTG
* *
2814647 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATTA
130 TGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTA
*
2814711 GTGTCTT-GAAAATAAAATCAGAGTTGGAATATCCCCGATTGTGGA
193 GTGT-TTCGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTGGA
2814756 GAATTGAGAA
Statistics
Matches: 212, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 143 0.67
264 42 0.20
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (262 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTAAAGTAT
CCCCTCGGAAATAACGGGGTTAGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTCGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
AC
Found at i:2817118 original size:20 final size:20
Alignment explanation
Indices: 2817091--2817145 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2817081 TAAAATTTCC
*
2817091 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
2817111 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
2817131 AAATGTATCGATACA
1 AAATGTATCGATACA
2817146 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:2817189 original size:19 final size:18
Alignment explanation
Indices: 2817165--2817264 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
2817155 CAGTAGCTAA
2817165 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2817184 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2817199 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2817216 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2817231 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2817248 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2817265 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2817205 original size:13 final size:13
Alignment explanation
Indices: 2817187--2817243 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2817177 ACAATACTTA
2817187 TGTATCGATACAT
1 TGTATCGATACAT
2817200 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
2817218 ATGTATCGATACAT
1 -TGTATCGATACAT
2817232 TGTATCGATACA
1 TGTATCGATACA
2817244 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2817209 original size:32 final size:32
Alignment explanation
Indices: 2817168--2817262 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
2817158 TAGCTAATTA
*
2817168 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2817200 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2817232 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2817263 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2817326 original size:21 final size:21
Alignment explanation
Indices: 2817300--2817377 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2817290 GTTGGGACCC
* **
2817300 TGTATCGATACATTTGTAGGA
1 TGTATCGATACATTTCTAAAA
* *
2817321 TGTATCGATACATTCCAAAAA
1 TGTATCGATACATTTCTAAAA
2817342 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTCTA-AAA
2817363 TGTATCGATACATTT
1 TGTATCGATACATTT
2817378 GGATAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 3 0.06
21 43 0.90
22 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTCTAAAA
Found at i:2818491 original size:28 final size:28
Alignment explanation
Indices: 2818460--2818546 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
2818450 TGAGGAGTAA
2818460 AAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAGTGCCACCAACTCGTGTGGGCTTTG
** ** *
2818488 AAAG-GCGTCCTGCTC-TTTGAGGAC--TG
1 AAAGTGCCACCAACTCGTGTG-GG-CTTTG
*
2818514 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAA-GTGCCACCAACTCGTGTGGGCTTTG
2818543 AAAG
1 AAAG
2818547 GTGTCCTGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
26 8 0.20
27 11 0.27
28 14 0.34
29 8 0.20
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (28 bp):
AAAGTGCCACCAACTCGTGTGGGCTTTG
Found at i:2818535 original size:55 final size:55
Alignment explanation
Indices: 2818440--2819061 Score: 918
Period size: 55 Copynumber: 11.3 Consensus size: 55
2818430 ATAAAGTGTA
* * * * * * *
2818440 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2818495 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2818550 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2818605 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2818660 TCCTGCTCTTTG-GGAATGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2818714 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
2818769 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2818824 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2818879 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2818934 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2818989 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2819044 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2819062 AAAAAGCGGA
Statistics
Matches: 524, Mismatches: 33, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
53 2 0.00
54 60 0.11
55 450 0.86
56 12 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2818570 original size:26 final size:26
Alignment explanation
Indices: 2818486--2818575 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
2818476 GTGTGGGCTT
* *
2818486 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
2818512 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
2818539 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
2818567 TGAAAGGTG
1 TGAAAGGTG
2818576 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 20 0.41
27 6 0.12
28 5 0.10
29 12 0.24
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:2818602 original size:29 final size:29
Alignment explanation
Indices: 2818512--2819043 Score: 105
Period size: 26 Copynumber: 19.3 Consensus size: 29
2818502 CTTTGAGGAC
2818512 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
2818541 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAAAGGTG-CCACCAACTTGTGTGGG-CTT
2818567 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** * * *
2818596 TAAAAGGTGTCCTGC-TCTT-TGAGGAC-T
1 TGAAAGGTG-CCACCAACTTGTGTGGGCTT
* * *
2818623 GGAAA-ATGCCACCAACTTGGGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** **
2818651 TGAAAGGTG--TCCTGCTCT-T-TGGGAAT
1 TGAAAGGTGCCACCAACT-TGTGTGGGCTT
* *
2818677 GGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
2818705 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
*
2818731 TGGAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
2818760 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
* **
2818786 TGGAAGACGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
2818815 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
2818841 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
2818870 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC-T
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
* * *
2818897 GGAAA-ATGCCACCAACTTGGGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
2818925 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAAAGGTG-CCACCAACTTGTGTGGG-CTT
*
2818951 TGAAAGGTGCCACCAACTTTTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
2818980 T-AAGAGGTGTCCTA-C-TCTT-TGAGGAC--
1 TGAA-AGGTG-CC-ACCAACTTGTGTGGGCTT
2819006 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
2819035 T-AAGAGGTG
1 TGAA-AGGTG
2819044 TCCTGCTCTT
Statistics
Matches: 338, Mismatches: 100, Indels: 130
0.60 0.18 0.23
Matches are distributed among these distances:
24 1 0.00
25 26 0.08
26 78 0.23
27 64 0.19
28 69 0.20
29 75 0.22
30 24 0.07
31 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:2820068 original size:12 final size:13
Alignment explanation
Indices: 2820045--2820104 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 13
2820035 CTTTTCTCTC
*
2820045 TTTTTCTTTG-TT
1 TTTTTTTTTGCTT
* *
2820057 TTGTTTTTTGTTT
1 TTTTTTTTTGCTT
2820070 TTTTTTTTTGC--
1 TTTTTTTTTGCTT
2820081 TTTTTTTTTGCTCT
1 TTTTTTTTTGCT-T
2820095 TTTTTTTTTG
1 TTTTTTTTTG
2820105 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 11 0.28
12 8 0.20
13 11 0.28
14 10 0.25
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTGCTT
Found at i:2820073 original size:25 final size:25
Alignment explanation
Indices: 2820029--2820104 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
2820019 TAAGCAGGTT
*
2820029 CTTTTTCTTTT-CTCTCTTTTTCTTTG
1 CTTTTT-TTTTGCTCT-TTTTTTTTTG
* *
2820055 TTTTGTTTTTTG-TTTTTTTTTTTTG
1 CTTT-TTTTTTGCTCTTTTTTTTTTG
2820080 CTTTTTTTTTGCTCTTTTTTTTTTG
1 CTTTTTTTTTGCTCTTTTTTTTTTG
2820105 AAGAGAAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 7 0.17
25 24 0.57
26 9 0.21
27 2 0.05
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (25 bp):
CTTTTTTTTTGCTCTTTTTTTTTTG
Found at i:2820076 original size:13 final size:13
Alignment explanation
Indices: 2820045--2820103 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
2820035 CTTTTCTCTC
*
2820045 TTTTTCTTTG-TT
1 TTTTTTTTTGTTT
*
2820057 TTGTTTTTTGTTT
1 TTTTTTTTTGTTT
2820070 TTTTTTTTTGCTTT
1 TTTTTTTTTG-TTT
** *
2820084 TTTTTTGCTCTTT
1 TTTTTTTTTGTTT
2820097 TTTTTTT
1 TTTTTTT
2820104 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 8 0.21
13 20 0.53
14 10 0.26
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:2830640 original size:79 final size:79
Alignment explanation
Indices: 2830534--2830731 Score: 218
Period size: 79 Copynumber: 2.5 Consensus size: 79
2830524 AATAACGGGG
* * * * ** * *
2830534 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTAG
*
2830598 AAAAAAAAATCGAGA
65 AAAAAAAAACCGAGA
* *
2830613 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
* * * * *
2830678 GAATAAAGCCGGGG
66 AAAAAAAACCGAGA
* *
2830692 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCC
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
2830732 GGATGAAATA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 99 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
AAAAAAAACCGAGA
Found at i:2830743 original size:28 final size:28
Alignment explanation
Indices: 2830687--2830758 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
2830677 GGAATAAAGC
** *
2830687 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
2830715 CGGGGTTGGAGTATCCCGGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
2830743 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2830759 TCGACTGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2830878 original size:52 final size:50
Alignment explanation
Indices: 2830746--2831131 Score: 161
Period size: 52 Copynumber: 7.4 Consensus size: 50
2830736 GAAATAACAA
* * * * * *
2830746 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGG--TGTTTGAAAATAAAACCGG
* * *
2830798 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTT-GAAAATAAAACCGG
* * * * *
2830850 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTGGTGTTTGA-AAATAAAACCGG
* * * *** * * **
2830902 GATTGAAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGT-GTTTGAAAATAAAACCGG
* *** * * ** *
2830953 GGTTGGAGTATCGCCTCGGA-AAT-AACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATC-CC-C-GATTATGAA--AAATTGGTGT-T---TGAAAATAAAACCGG
* *
2831008 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTGGTG---TTTGAAAATAAAACCGG
* * * * *
2831062 AGTTCGAGTATCCCCGATTAT-AGAAAATTAGTATTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTGGT-GTTTGAAAATAAAACCGG
* *
2831113 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
2831132 GTGGAGAATT
Statistics
Matches: 246, Mismatches: 65, Indels: 47
0.69 0.18 0.13
Matches are distributed among these distances:
51 66 0.27
52 98 0.40
53 31 0.13
54 30 0.12
55 16 0.07
56 2 0.01
57 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTGAAAATAAAACCGG
Found at i:2830985 original size:28 final size:27
Alignment explanation
Indices: 2830950--2831025 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
2830940 GAAATAAAGT
2830950 CGGGGTTGGAGTATCGCCTCGGA-AAT-AA
1 CGGGGTTGGAGTATC-CC-C-GATAATCAA
*
2830978 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAATCAA
2831005 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2831026 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 25 0.56
28 15 0.33
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAATCAA
Found at i:2831127 original size:263 final size:262
Alignment explanation
Indices: 2830647--2831136 Score: 732
Period size: 263 Copynumber: 1.9 Consensus size: 262
2830637 GGGGTTGGAG
* * *
2830647 TATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAG
1 TATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAA
* *
2830712 TAACGGGGTTGGAGTATCCCGGATGAAATAACAAGGTTGGAGTATCCTCGACTGTGAAAAATTGG
66 TAACGGGGTTGGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTGTGAAAAATTGG
* * * *
2830777 TATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAAT
130 TATTTTTGAAAATAAAATCGGAGTTCGAGTATCCCCGATTAAAGGAAAATTAGTATTTCGAAAAT
* *
2830842 AAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGATTG
195 AAAACCGGAGTTGGAATATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGATTG
2830907 AAA
260 AAA
* * *
2830910 TATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCGCCTCGGAAA
1 TATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAA
** *
2830975 TAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTG
66 TAACGGGGTTGGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACTGTGAA-AAATTG
* * *
2831039 GTGTTTTTTGAAAATAAAATCGGAGTTCGAGTATCCCCGATTATA-GAAAATTAGTATTTTGAAA
129 GT-ATTTTTGAAAATAAAATCGGAGTTCGAGTATCCCCGATTAAAGGAAAATTAGTATTTCGAAA
* *
2831103 ATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
193 ATAAAACCGGAGTTGGAATATCCCCAATTGTGGA
2831137 GAATTGAGAA
Statistics
Matches: 202, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 137 0.68
264 38 0.19
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (262 bp):
TATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAA
TAACGGGGTTGGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGTGAAAAATTGGT
ATTTTTGAAAATAAAATCGGAGTTCGAGTATCCCCGATTAAAGGAAAATTAGTATTTCGAAAATA
AAACCGGAGTTGGAATATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGATTGA
AA
Found at i:2833515 original size:13 final size:13
Alignment explanation
Indices: 2833497--2833522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2833487 ACAAAGATCC
2833497 ATGTATCGATACA
1 ATGTATCGATACA
2833510 ATGTATCGATACA
1 ATGTATCGATACA
2833523 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2833518 original size:33 final size:33
Alignment explanation
Indices: 2833476--2833542 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2833466 AAAATTTCCA
***
2833476 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2833509 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2833542 A
1 A
2833543 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2833586 original size:19 final size:18
Alignment explanation
Indices: 2833562--2833629 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2833552 CAGTAGCTAA
2833562 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2833581 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2833596 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2833613 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2833630 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2833602 original size:13 final size:13
Alignment explanation
Indices: 2833584--2833608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2833574 ACAATACTTA
2833584 TGTATCGATACAT
1 TGTATCGATACAT
2833597 TGTATCGATACA
1 TGTATCGATACA
2833609 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2833606 original size:32 final size:32
Alignment explanation
Indices: 2833565--2833627 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2833555 TAGCTAATTA
*
2833565 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2833597 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2833628 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2836277 original size:26 final size:26
Alignment explanation
Indices: 2836238--2836306 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
2836228 ACAACAAGCT
* *
2836238 ACCATTTTTTACAAACAAA-AATAACC
1 ACCATATTTGACAAACAAAGAA-AACC
*
2836264 ACCATATTTGACAAATACAAAGGAAACC
1 ACCATATTTGAC-AA-ACAAAGAAAACC
2836292 ACCATATTTGACAAA
1 ACCATATTTGACAAA
2836307 TATAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 11 0.30
27 4 0.11
28 21 0.57
29 1 0.03
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.23
Consensus pattern (26 bp):
ACCATATTTGACAAACAAAGAAAACC
Found at i:2836283 original size:28 final size:28
Alignment explanation
Indices: 2836252--2836308 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
2836242 TTTTTTACAA
2836252 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
2836280 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
2836308 A
1 A
2836309 TAAATTATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:2838025 original size:97 final size:97
Alignment explanation
Indices: 2837856--2838046 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 97
2837846 AAGACTTCAT
* * *
2837856 CTAAATTCCCAAGCATTCAAGTGGAATTCAGAAGTAATTCTCTCTTGAGAAGAAATTTCGTAACA
1 CTAAATCCCCAAGCATTCAAATGGAATTCAGAAGTAATTCTCTCTTGAGAAGAAATTTCATAACA
*
2837921 ATCCCTTGAATTTGAGATGGAGCACCCTTAAC
66 ATCCCTTGAATTTGAGATGAAGCACCCTTAAC
* *
2837953 CTAAATCCCCCAGCGTTCAAATGGAATTCAGAAGTAATTCTC-CTTTGTA-AAGAAA-TTCTATA
1 CTAAATCCCCAAGCATTCAAATGGAATTCAGAAGTAATTCTCTC-TTG-AGAAGAAATTTC-ATA
* * *
2838015 ATAATTCCTTGAATTTGAGATGAAGCATCCTT
63 ACAATCCCTTGAATTTGAGATGAAGCACCCTT
2838047 CGTAGAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
96 4 0.05
97 77 0.94
98 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (97 bp):
CTAAATCCCCAAGCATTCAAATGGAATTCAGAAGTAATTCTCTCTTGAGAAGAAATTTCATAACA
ATCCCTTGAATTTGAGATGAAGCACCCTTAAC
Found at i:2838697 original size:23 final size:23
Alignment explanation
Indices: 2838671--2838737 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
2838661 GAATAATTAG
2838671 TTAATAATAAAAAATATTTAAAT-
1 TTAAT-ATAAAAAATATTTAAATA
* *
2838694 TTAATGAT-AAAAATCTATAAATA
1 TTAAT-ATAAAAAATATTTAAATA
* *
2838717 TTAATATAATAATTATTTAAA
1 TTAATATAAAAAATATTTAAA
2838738 AAAAATCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (23 bp):
TTAATATAAAAAATATTTAAATA
Found at i:2838714 original size:22 final size:22
Alignment explanation
Indices: 2838675--2838725 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2838665 AATTAGTTAA
*
2838675 TAATA-AAAAATATTTAAAT-T
1 TAATATAAAAATATATAAATAT
*
2838695 TAATGATAAAAATCTATAAATAT
1 TAAT-ATAAAAATATATAAATAT
2838718 TAATATAA
1 TAATATAA
2838726 TAATTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 16 0.62
23 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATATAAAAATATATAAATAT
Found at i:2839374 original size:34 final size:34
Alignment explanation
Indices: 2839308--2839524 Score: 245
Period size: 34 Copynumber: 6.4 Consensus size: 34
2839298 GGTTTGGTAA
* * * *
2839308 AAACCACCACATCACCCATTTAATCAATAATGGC
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
* * *
2839342 AAACTATCAAATCTCCCATTTAGTTAACAATGGC
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
* *
2839376 AAACCACCAAATCACCCATTTAATCAACAATGGC
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
* * * * *
2839410 ACACTACCAAATCTCCCATTTAGTCAATAATTGT
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
* * *
2839444 AAACTACCAAATCACCCATTTAATCGACAATGGT
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
* * *
2839478 AAACTACCAAATCTCTCATTTAGTCAATAATGGC
1 AAACTACCAAATCTCCCATTTAATCAACAATGGC
*
2839512 AAACCACCAAATC
1 AAACTACCAAATC
2839525 AATGGTAAAT
Statistics
Matches: 151, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 151 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (34 bp):
AAACTACCAAATCTCCCATTTAATCAACAATGGC
Found at i:2839421 original size:68 final size:68
Alignment explanation
Indices: 2839308--2839525 Score: 328
Period size: 68 Copynumber: 3.2 Consensus size: 68
2839298 GGTTTGGTAA
* * * * *
2839308 AAACCACCACATCACCCATTTAATCAATAATGGCAAACTATCAAATCTCCCATTTAGTTAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
2839373 GGC
66 GGC
*
2839376 AAACCACCAAATCACCCATTTAATCAACAATGGCACACTACCAAATCTCCCATTTAGTCAATAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
* *
2839441 TGT
66 GGC
* * * *
2839444 AAACTACCAAATCACCCATTTAATCGACAATGGTAAACTACCAAATCTCTCATTTAGTCAATAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
2839509 GGC
66 GGC
2839512 AAACCACCAAATCA
1 AAACCACCAAATCA
2839526 ATGGTAAATT
Statistics
Matches: 134, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 134 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (68 bp):
AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
GGC
Found at i:2839462 original size:102 final size:102
Alignment explanation
Indices: 2839308--2839525 Score: 274
Period size: 102 Copynumber: 2.1 Consensus size: 102
2839298 GGTTTGGTAA
* * * * *
2839308 AAACCACCACATCACCCATTTAATCAATAATGGCAAACTATCAAATCTCCCATTTAGTTAACAAT
1 AAACCACCAAATCACCCATTTAATCAATAATGGCAAACTACCAAATCACCCATTTAATCAACAAT
2839373 GGCAAACCACCAAATCACCCATTTAATCAACAATGGC
66 GGCAAACCACCAAATCACCCATTTAATCAACAATGGC
* * * * * * *
2839410 ACACTACCAAATCTCCCATTTAGTCAATAATTGTAAACTACCAAATCACCCATTTAATCGACAAT
1 AAACCACCAAATCACCCATTTAATCAATAATGGCAAACTACCAAATCACCCATTTAATCAACAAT
* * * * * *
2839475 GGTAAACTACCAAATCTCTCATTTAGTCAATAATGGC
66 GGCAAACCACCAAATCACCCATTTAATCAACAATGGC
2839512 AAACCACCAAATCA
1 AAACCACCAAATCA
2839526 ATGGTAAATT
Statistics
Matches: 95, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (102 bp):
AAACCACCAAATCACCCATTTAATCAATAATGGCAAACTACCAAATCACCCATTTAATCAACAAT
GGCAAACCACCAAATCACCCATTTAATCAACAATGGC
Found at i:2843664 original size:19 final size:19
Alignment explanation
Indices: 2843616--2843672 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
2843606 TTACATGCAC
2843616 AATACC-GTATACGTGAAT
1 AATACCTGTATACGTGAAT
* * * *
2843634 AGTATCTATATATGTGAAT
1 AATACCTGTATACGTGAAT
*
2843653 AATACCTGTATACGTAAAT
1 AATACCTGTATACGTGAAT
2843672 A
1 A
2843673 GTTCCTCGAC
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (19 bp):
AATACCTGTATACGTGAAT
Found at i:2844039 original size:34 final size:34
Alignment explanation
Indices: 2843978--2844194 Score: 188
Period size: 34 Copynumber: 6.4 Consensus size: 34
2843968 GGTTTGGTAA
* * * *
2843978 AAACCACCACATCACCCATTTAATCAACAATAAC
1 AAACCACCAAATCTCCTATTTAATCAACAATGAC
* * *
2844012 AAACTACCAAATCTCCTATTTAGTCAACAATGGC
1 AAACCACCAAATCTCCTATTTAATCAACAATGAC
*
2844046 AAACCACCAAATC-ACTCATTTAATCAACAATGAC
1 AAACCACCAAATCTCCT-ATTTAATCAACAATGAC
* * ** * *
2844080 ATACTATTAAATCTCCTATTTAGTCAACAATTG-T
1 AAACCACCAAATCTCCTATTTAATCAACAA-TGAC
* * **
2844114 AAACCACCAAATCACCCATTTAATCAACAATGGT
1 AAACCACCAAATCTCCTATTTAATCAACAATGAC
** * *
2844148 AAATTACCAAATCT-CTCATTTAGTCAATAATGAC
1 AAACCACCAAATCTCCT-ATTTAATCAACAATGAC
2844182 AAACCACCAAATC
1 AAACCACCAAATC
2844195 AAAGATAAAT
Statistics
Matches: 143, Mismatches: 35, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
33 5 0.03
34 134 0.94
35 4 0.03
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (34 bp):
AAACCACCAAATCTCCTATTTAATCAACAATGAC
Found at i:2844060 original size:68 final size:68
Alignment explanation
Indices: 2843978--2844195 Score: 303
Period size: 68 Copynumber: 3.2 Consensus size: 68
2843968 GGTTTGGTAA
* *
2843978 AAACCACCACATCACCCATTTAATCAACAATAACAAACTACCAAATCTCCTATTTAGTCAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGACAAACTACCAAATCTCCTATTTAGTCAACAAT
2844043 GGC
66 GGC
* * **
2844046 AAACCACCAAATCACTCATTTAATCAACAATGACATACTATTAAATCTCCTATTTAGTCAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGACAAACTACCAAATCTCCTATTTAGTCAACAAT
* *
2844111 TGT
66 GGC
** * *
2844114 AAACCACCAAATCACCCATTTAATCAACAATGGTAAATTACCAAATCT-CTCATTTAGTCAATAA
1 AAACCACCAAATCACCCATTTAATCAACAATGACAAACTACCAAATCTCCT-ATTTAGTCAACAA
*
2844178 TGAC
65 TGGC
2844182 AAACCACCAAATCA
1 AAACCACCAAATCA
2844196 AAGATAAATT
Statistics
Matches: 130, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
67 2 0.02
68 128 0.98
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (68 bp):
AAACCACCAAATCACCCATTTAATCAACAATGACAAACTACCAAATCTCCTATTTAGTCAACAAT
GGC
Found at i:2844194 original size:102 final size:102
Alignment explanation
Indices: 2843978--2844195 Score: 247
Period size: 102 Copynumber: 2.1 Consensus size: 102
2843968 GGTTTGGTAA
* * * * *
2843978 AAACCACCACATCACCCATTTAATCAACAATAACAAACTACCAAATCTCCTATTTAGTCAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATAACAAACCACCAAATCACCCATTTAATCAACAAT
2844043 GGCAAACCACCAAATCACTCATTTAATCAACAATGAC
66 GGCAAACCACCAAATCACTCATTTAATCAACAATGAC
* * ** * * * ***
2844080 ATACTATTAAATCTCCTATTTAGTCAACAATTGTAAACCACCAAATCACCCATTTAATCAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATAACAAACCACCAAATCACCCATTTAATCAACAAT
* ** * * *
2844145 GGTAAATTACCAAATCTCTCATTTAGTCAATAATGAC
66 GGCAAACCACCAAATCACTCATTTAATCAACAATGAC
2844182 AAACCACCAAATCA
1 AAACCACCAAATCA
2844196 AAGATAAATT
Statistics
Matches: 90, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (102 bp):
AAACCACCAAATCACCCATTTAATCAACAATAACAAACCACCAAATCACCCATTTAATCAACAAT
GGCAAACCACCAAATCACTCATTTAATCAACAATGAC
Found at i:2845713 original size:13 final size:13
Alignment explanation
Indices: 2845695--2845720 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2845685 AATTTTTTGG
2845695 TGTATCGATACAT
1 TGTATCGATACAT
2845708 TGTATCGATACAT
1 TGTATCGATACAT
2845721 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2847841 original size:21 final size:20
Alignment explanation
Indices: 2847812--2847854 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2847802 GGCTAGTGTG
*
2847812 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
2847833 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
2847853 GG
1 GG
2847855 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:2848169 original size:21 final size:22
Alignment explanation
Indices: 2848135--2848175 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2848125 GCTGATTTTG
2848135 ATGAAAAACAAAGTAATTTGAA
1 ATGAAAAACAAAGTAATTTGAA
*
2848157 ATGAAAAAC-AAGTATTTTG
1 ATGAAAAACAAAGTAATTTG
2848176 CAAAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (22 bp):
ATGAAAAACAAAGTAATTTGAA
Found at i:2848319 original size:13 final size:13
Alignment explanation
Indices: 2848297--2848335 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2848287 ATAATCCCCT
* *
2848297 TGTATTGATACAG
1 TGTATCGATACAA
2848310 TGTATCGATACAA
1 TGTATCGATACAA
2848323 TGTATCGATACAA
1 TGTATCGATACAA
2848336 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2854538 original size:13 final size:13
Alignment explanation
Indices: 2854520--2854577 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
2854510 AATTTTTTGG
2854520 TGTATCGATACAT
1 TGTATCGATACAT
2854533 TGTATCGATACATACTT
1 TGTATCGATAC--A--T
2854550 GGTGTATCGATACAT
1 --TGTATCGATACAT
2854565 TGTATCGATACAT
1 TGTATCGATACAT
2854578 ACTTGGTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
15 2 0.05
17 2 0.05
19 11 0.28
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2854557 original size:32 final size:32
Alignment explanation
Indices: 2854516--2854595 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
2854506 ATACAATTTT
2854516 TTGGTGTATCGATACATTGTATCGATACATAC
1 TTGGTGTATCGATACATTGTATCGATACATAC
2854548 TTGGTGTATCGATACATTGTATCGATACATAC
1 TTGGTGTATCGATACATTGTATCGATACATAC
2854580 TTGGTGTATCGATACA
1 TTGGTGTATCGATACA
2854596 AGTTTGGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (32 bp):
TTGGTGTATCGATACATTGTATCGATACATAC
Found at i:2854602 original size:19 final size:19
Alignment explanation
Indices: 2854533--2854595 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
2854523 ATCGATACAT
2854533 TGTATCGATACATACTTGG
1 TGTATCGATACATACTTGG
2854552 TGTATCGATAC--A--T--
1 TGTATCGATACATACTTGG
2854565 TGTATCGATACATACTTGG
1 TGTATCGATACATACTTGG
2854584 TGTATCGATACA
1 TGTATCGATACA
2854596 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATACTTGG
Found at i:2859196 original size:14 final size:13
Alignment explanation
Indices: 2859179--2859233 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
2859169 TATCAACCCA
2859179 TTTAATTAAATTTT
1 TTTAATT-AATTTT
2859193 TTTAATTAATTTGT
1 TTTAATTAATTT-T
2859207 TTT-ATTAATTATT
1 TTTAATTAATT-TT
* *
2859220 TTTATTTTATTTT
1 TTTAATTAATTTT
2859233 T
1 T
2859234 AAAAAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 19 0.53
14 17 0.47
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTAATTAATTTT
Found at i:2861436 original size:21 final size:23
Alignment explanation
Indices: 2861400--2861446 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
2861390 TATTAATTTA
2861400 AATTATTAATACTTTAACAAAAT
1 AATTATTAATACTTTAACAAAAT
*
2861423 AATTATTAA-A-TTTAATAAAAT
1 AATTATTAATACTTTAACAAAAT
2861444 AAT
1 AAT
2861447 AATACACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 1 0.04
23 9 0.39
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTATTAATACTTTAACAAAAT
Found at i:2861634 original size:20 final size:20
Alignment explanation
Indices: 2861611--2861694 Score: 50
Period size: 20 Copynumber: 4.3 Consensus size: 20
2861601 TATTAAATAT
2861611 TAATATAATATAAAATATAA
1 TAATATAATATAAAATATAA
*
2861631 TAAT-TAA-ATTAAATA-AA
1 TAATATAATATAAAATATAA
* * * *
2861648 TATAAATTATATAAAAAATTA
1 TA-ATATAATATAAAATATAA
* ** *
2861669 TAAAATTTTATAAAATTTAA
1 TAATATAATATAAAATATAA
2861689 T-ATATA
1 TAATATA
2861695 TTGTGTAATC
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
17 4 0.08
18 8 0.17
19 8 0.17
20 25 0.52
21 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATATAATATAAAATATAA
Found at i:2861644 original size:18 final size:20
Alignment explanation
Indices: 2861600--2861649 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
2861590 TACATAATCT
2861600 ATATTAAATAT--TAATATA
1 ATATTAAATATAATAATATA
*
2861618 ATATAAAATATAATAAT-TA
1 ATATTAAATATAATAATATA
2861637 A-ATTAAATA-AATA
1 ATATTAAATATAATA
2861650 TAAATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 17 0.61
19 3 0.11
20 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTAAATATAATAATATA
Found at i:2861661 original size:15 final size:15
Alignment explanation
Indices: 2861613--2861662 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2861603 TTAAATATTA
*
2861613 ATAT-AATATAAAAT
1 ATATAAATATAAATT
2861627 ATA-ATAAT-TAAATT
1 ATATA-AATATAAATT
*
2861641 AAATAAATATAAATT
1 ATATAAATATAAATT
2861656 ATATAAA
1 ATATAAA
2861663 AAATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAATATAAATT
Found at i:2862571 original size:24 final size:24
Alignment explanation
Indices: 2862516--2862581 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2862506 TTTAAAAATA
* *
2862516 AATAATTATAATTATAT-ATTTTTT
1 AATAAATAT-ATTATATAATTTATT
2862540 AATAAATAATATTATATAATTTATT
1 AATAAAT-ATATTATATAATTTATT
*
2862565 -ATCAATATATTATATAA
1 AATAAATATATTATATAA
2862582 ATATTATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.30
24 18 0.49
25 8 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AATAAATATATTATATAATTTATT
Found at i:2862793 original size:35 final size:35
Alignment explanation
Indices: 2862754--2862827 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2862744 ATAAATTATA
*
2862754 AAAAAAATTATATATTT-TTATAATTAT-ATTTAAAT
1 AAAAAAATT-TATATTTATTA-AATAATAATTTAAAT
* *
2862789 AAAAATATTTTTATTTATTAAATAATAATTTAAAT
1 AAAAAAATTTATATTTATTAAATAATAATTTAAAT
2862824 AAAA
1 AAAA
2862828 TTAAATTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
AAAAAAATTTATATTTATTAAATAATAATTTAAAT
Found at i:2863448 original size:23 final size:23
Alignment explanation
Indices: 2863422--2863479 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
2863412 TTTATTTATA
* *
2863422 TAATAAAAAAATTTATTTAAA-AT
1 TAATATAAAAA-TTATATAAATAT
2863445 TAATTATAAAAA-TATATAAATAT
1 TAA-TATAAAAATTATATAAATAT
2863468 TAATATAAAAAT
1 TAATATAAAAAT
2863480 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 15 0.50
23 8 0.27
24 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATATAAAAATTATATAAATAT
Found at i:2863474 original size:22 final size:22
Alignment explanation
Indices: 2863439--2863480 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2863429 AAAATTTATT
2863439 TAAAATTAATTATAAAAATATA
1 TAAAATTAATTATAAAAATATA
2863461 TAAATATTAA-TATAAAAATA
1 TAAA-ATTAATTATAAAAATA
2863481 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATTAATTATAAAAATATA
Found at i:2863494 original size:26 final size:27
Alignment explanation
Indices: 2863424--2863494 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
2863414 TATTTATATA
2863424 ATAAAAA-AATTTATTTAAA-ATTAATT
1 ATAAAAATAATTT-TTTAAATATTAATT
*
2863450 ATAAAAAT-A---TATAAATATTAA-T
1 ATAAAAATAATTTTTTAAATATTAATT
2863472 ATAAAAATAATTTTTTAAATATT
1 ATAAAAATAATTTTTTAAATATT
2863495 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
22 14 0.38
23 6 0.16
26 17 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAAAATAATTTTTTAAATATTAATT
Found at i:2863512 original size:20 final size:20
Alignment explanation
Indices: 2863489--2863545 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2863479 TAATTTTTTA
* * *
2863489 AATATTTTAATTTTTTAAAT
1 AATAATTTAAATTTATAAAT
2863509 AATAATTTAAATTTATAAAT
1 AATAATTTAAATTTATAAAT
*
2863529 AAATTAAATTAAATTTA
1 -AA-TAATTTAAATTTA
2863546 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.55
21 2 0.06
22 12 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTAAATTTATAAAT
Found at i:2863547 original size:20 final size:20
Alignment explanation
Indices: 2863501--2863560 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2863491 TATTTTAATT
*
2863501 TTTTAAAT-AATAATTTAAA
1 TTTTAAATAAATAAATTAAA
2863520 TTTATAAATAAATTAAATTAAA
1 TTT-TAAATAAA-TAAATTAAA
2863542 -TTTAAATAAA-AATATTAAA
1 TTTTAAATAAATAA-ATTAAA
2863561 AATATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.06
19 9 0.25
20 13 0.36
21 4 0.11
22 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTAAATAAATAAATTAAA
Found at i:2863554 original size:17 final size:19
Alignment explanation
Indices: 2863501--2863560 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
2863491 TATTTTAATT
*
2863501 TTTTAAATAATAATTTAAA
1 TTTTAAATAATAAATTAAA
2863520 TTTATAAATAAATTAAATTAAA
1 TTT-TAAAT-AA-TAAATTAAA
*
2863542 -TTTAAATAAAAATATTAAA
1 TTTTAAATAATAA-ATTAAA
2863561 AATATTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 10 0.29
21 4 0.11
22 8 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAATAATAAATTAAA
Found at i:2864071 original size:10 final size:10
Alignment explanation
Indices: 2864057--2864129 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 10
2864047 AAAAATTAAC
2864057 AAAAAAATTAT
1 AAAAAAA-TAT
2864068 AAAAAAATAT
1 AAAAAAATAT
*
2864078 AATTACATAATAT
1 AA--A-AAAATAT
2864091 AAATAAAATAT
1 AAA-AAAATAT
2864102 AAAAATAAT-T
1 AAAAA-AATAT
2864112 AAAATAAAATAT
1 -AAA-AAAATAT
2864124 AAAAAA
1 AAAAAA
2864130 TTTAATATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
10 11 0.21
11 29 0.56
12 4 0.08
13 8 0.15
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:2864116 original size:22 final size:22
Alignment explanation
Indices: 2864057--2864159 Score: 90
Period size: 22 Copynumber: 4.7 Consensus size: 22
2864047 AAAAATTAAC
2864057 AAAAA-AATTATAAA-AAAATAT
1 AAAAATAATTA-AAATAAAATAT
*
2864078 AATTACATAA-TATAAATAAAATAT
1 AA--AAATAATTA-AAATAAAATAT
2864102 AAAAATAATTAAAATAAAATAT
1 AAAAATAATTAAAATAAAATAT
* *
2864124 AAAAA-ATTTAATAT-AAATAT
1 AAAAATAATTAAAATAAAATAT
*
2864144 ATAAATATATTAAAAT
1 AAAAATA-ATTAAAAT
2864160 TTATATTAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
20 10 0.15
21 10 0.15
22 27 0.40
23 10 0.15
24 11 0.16
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAATAATTAAAATAAAATAT
Found at i:2864128 original size:55 final size:57
Alignment explanation
Indices: 2864033--2864150 Score: 138
Period size: 55 Copynumber: 2.1 Consensus size: 57
2864023 GAAATGAACT
* *
2864033 TAAATAAACTTAATAAAAATTAACAAAAAAATTATAAAAAAATATAAT-TACATAATA
1 TAAATAAAATTAATAAAAATTAACAAAAAAATTATAAAAAAATATAATATAAAT-ATA
* *
2864090 TAAATAAAATATAA-AAATAATTAA-AATAAAA-TAT-AAAAAATTTAATATAAATATA
1 TAAATAAAAT-TAATAAA-AATTAACAAAAAAATTATAAAAAAATATAATATAAATATA
2864145 TAAATA
1 TAAATA
2864151 TATTAAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 20 0.37
56 7 0.13
57 18 0.33
58 9 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (57 bp):
TAAATAAAATTAATAAAAATTAACAAAAAAATTATAAAAAAATATAATATAAATATA
Found at i:2864136 original size:28 final size:28
Alignment explanation
Indices: 2864109--2864178 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
2864099 TATAAAAATA
2864109 ATTAAAATAAAATATA-AAAAATTTAAT
1 ATTAAAATAAAATATATAAAAATTTAAT
*
2864136 A-TAAATATATAAATATATTAAAATTT-AT
1 ATTAAA-ATA-AAATATATAAAAATTTAAT
2864164 ATTAATAAATAAAAT
1 ATT-A-AAATAAAAT
2864179 TTTAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 10 0.28
29 12 0.33
30 4 0.11
31 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATTAAAATAAAATATATAAAAATTTAAT
Found at i:2864147 original size:29 final size:29
Alignment explanation
Indices: 2864113--2864178 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
2864103 AAAATAATTA
2864113 AAATAAAATATA-AAAAATTTAATATAAAT
1 AAATAAAATATATAAAAATTT-ATATAAAT
* * *
2864142 ATAT-AAATATATTAAAATTTATATTAAT
1 AAATAAAATATATAAAAATTTATATAAAT
2864170 AAATAAAAT
1 AAATAAAAT
2864179 TTTAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAATAAAATATATAAAAATTTATATAAAT
Found at i:2864164 original size:18 final size:18
Alignment explanation
Indices: 2864127--2864190 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
2864117 AAAATATAAA
* *
2864127 AAATTTAATATAAATATAT
1 AAATATAATA-AAATTTAT
*
2864146 AAATATATTAAAATTTAT
1 AAATATAATAAAATTTAT
2864164 ATTAATA-AATAAAATTT-T
1 A--AATATAATAAAATTTAT
2864182 AAATATAAT
1 AAATATAAT
2864191 TATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.11
17 3 0.08
18 10 0.26
19 17 0.45
20 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATAATAAAATTTAT
Found at i:2864184 original size:12 final size:12
Alignment explanation
Indices: 2864060--2864210 Score: 78
Period size: 12 Copynumber: 13.1 Consensus size: 12
2864050 AATTAACAAA
2864060 AAAATTATAAA-
1 AAAATTATAAAT
*
2864071 AAAA-TATAATT
1 AAAATTATAAAT
2864082 ACATAA-TATAAAT
1 A-A-AATTATAAAT
2864095 AAAA-TATAAA-
1 AAAATTATAAAT
2864105 AATAATTA-AAAT
1 AA-AATTATAAAT
2864117 AAAA-TAT-AA-
1 AAAATTATAAAT
2864126 AAAATT-T-AAT
1 AAAATTATAAAT
2864136 ATAAATATATAAAT
1 A-AAAT-TATAAAT
*
2864150 -ATATTA-AAATT
1 AAAATTATAAA-T
* *
2864161 TATATTAATAAAT
1 AAAATT-ATAAAT
*
2864174 AAAATTTTAAAT
1 AAAATTATAAAT
*
2864186 ATAATTATAAA-
1 AAAATTATAAAT
2864197 AAAATATATAAAT
1 AAAAT-TATAAAT
2864210 A
1 A
2864211 TTATATTATA
Statistics
Matches: 112, Mismatches: 9, Indels: 36
0.71 0.06 0.23
Matches are distributed among these distances:
9 7 0.06
10 16 0.14
11 31 0.28
12 35 0.31
13 17 0.15
14 6 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATTATAAAT
Found at i:2864188 original size:24 final size:24
Alignment explanation
Indices: 2864168--2864220 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
2864158 ATTTATATTA
*
2864168 ATAAATAAAAT-TTTAAATATAATT
1 ATAAA-AAAATATATAAATATAATT
2864192 ATAAAAAAATATATAAATATTATATT
1 ATAAAAAAATATATAAATA-TA-ATT
2864218 ATA
1 ATA
2864221 TATATACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 12 0.48
25 2 0.08
26 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAAAAATATATAAATATAATT
Found at i:2864639 original size:17 final size:17
Alignment explanation
Indices: 2864600--2864660 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
2864590 AATAAGACAC
* *
2864600 ATATAATAAAAAATTAAA
1 ATATAATATAAAA-TATA
*
2864618 ATATAATTTAAAATATA
1 ATATAATATAAAATATA
2864635 ATATAATATAAAATA-A
1 ATATAATATAAAATATA
*
2864651 AAATAATATA
1 ATATAATATA
2864661 TGAATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
16 10 0.26
17 17 0.45
18 11 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAATATAAAATATA
Found at i:2864649 original size:12 final size:12
Alignment explanation
Indices: 2864614--2864660 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
2864604 AATAAAAAAT
*
2864614 TAAAATATAATT
1 TAAAATATAATA
2864626 TAAAATATAATA
1 TAAAATATAATA
*
2864638 T--AATATAAAA
1 TAAAATATAATA
2864648 TAAAA-ATAATA
1 TAAAATATAATA
2864659 TA
1 TA
2864661 TGAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 9 0.30
11 7 0.23
12 14 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:2864910 original size:18 final size:19
Alignment explanation
Indices: 2864887--2864925 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2864877 AAATTATATA
2864887 ATTAT-AATTTAAATTTTT
1 ATTATAAATTTAAATTTTT
2864905 ATTATAAATTTAAATTTTT
1 ATTATAAATTTAAATTTTT
2864924 AT
1 AT
2864926 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATAAATTTAAATTTTT
Found at i:2864927 original size:16 final size:16
Alignment explanation
Indices: 2864888--2865077 Score: 65
Period size: 16 Copynumber: 12.0 Consensus size: 16
2864878 AATTATATAA
2864888 TTAT-AATTTAAATTTTT
1 TTATAAATTTAAA--TTT
2864905 ATTATAAATTTAAATTT
1 -TTATAAATTTAAATTT
2864922 TTATAAATTTTAAA---
1 TTATAAA-TTTAAATTT
**
2864936 AAATAAATTTAAATTT
1 TTATAAATTTAAATTT
* *
2864952 ATCA-AAATTAAAATTT
1 -TTATAAATTTAAATTT
* **
2864968 TTAT-AATTTCAGATCA
1 TTATAAATTT-AAATTT
* * ** *
2864984 TGACAGTTTTAAATAT
1 TTATAAATTTAAATTT
*
2865000 TTCTAAATTTAAATTT
1 TTATAAATTTAAATTT
* *
2865016 TTTTATATTTAAATTCT
1 TTATAAATTTAAATT-T
* *
2865033 TT-TAATTTTTAATTT
1 TTATAAATTTAAATTT
** *
2865048 TTAT-TTTTTAAATTA
1 TTATAAATTTAAATTT
*
2865063 ATATAAA-TTAAATTT
1 TTATAAATTTAAATTT
2865078 AATCTAAATT
Statistics
Matches: 125, Mismatches: 35, Indels: 27
0.67 0.19 0.14
Matches are distributed among these distances:
13 6 0.05
14 5 0.04
15 27 0.22
16 59 0.47
17 16 0.13
18 4 0.03
19 8 0.06
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATAAATTTAAATTT
Found at i:2865085 original size:16 final size:15
Alignment explanation
Indices: 2865055--2865089 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2865045 TTTTTATTTT
2865055 TTAAATTAATATAAA
1 TTAAATTAATATAAA
*
2865070 TTAAATTTAATCTAAA
1 TTAAA-TTAATATAAA
2865086 TTAA
1 TTAA
2865090 TTCAAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTAATATAAA
Found at i:2865437 original size:16 final size:16
Alignment explanation
Indices: 2865411--2865455 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2865401 TTTATTTTTT
2865411 AAAAATT-TTTTTAAA
1 AAAAATTATTTTTAAA
2865426 AAAAATTATTTTTAAA
1 AAAAATTATTTTTAAA
*
2865442 ATTAAA-TATTTTTA
1 A-AAAATTATTTTTA
2865456 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.26
16 17 0.63
17 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATTATTTTTAAA
Found at i:2865641 original size:9 final size:10
Alignment explanation
Indices: 2865617--2865659 Score: 59
Period size: 10 Copynumber: 4.0 Consensus size: 10
2865607 TATGATATAT
2865617 TAAAAAATAA
1 TAAAAAATAA
2865627 TAAAAAATAA
1 TAAAAAATAA
2865637 TAAAAATTTATAA
1 TAAAAA---ATAA
2865650 TAAAAAATAA
1 TAAAAAATAA
2865660 GTGTATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 20 0.67
13 10 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:2865701 original size:19 final size:17
Alignment explanation
Indices: 2865663--2865695 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2865653 AAAATAAGTG
*
2865663 TATAATAAATATTTTAA
1 TATAATAAAAATTTTAA
2865680 TATAATAAAAATTTTA
1 TATAATAAAAATTTTA
2865696 TAATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAATAAAAATTTTAA
Found at i:2865715 original size:20 final size:19
Alignment explanation
Indices: 2865667--2865742 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
2865657 TAAGTGTATA
*
2865667 ATAAATATTTTAATA-TAAT
1 ATAAAT-TTATAATATTAAT
*
2865686 AAAAATTTTATAATATTAATT
1 ATAAA-TTTATAATATTAA-T
* *
2865707 ATTAATTTATAAATATTTAT
1 ATAAATTTAT-AATATTAAT
*
2865727 ATAAATATATAATATT
1 ATAAATTTATAATATT
2865743 TTAAATATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 17 0.37
20 18 0.39
21 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAAATTTATAATATTAAT
Found at i:2865745 original size:20 final size:20
Alignment explanation
Indices: 2865694--2865760 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2865684 ATAAAAATTT
* *
2865694 TATAATA-TTAATTATTAATT
1 TATAATATTTAAATA-TAATA
*
2865714 TATAAATATTTATATA-AATA
1 TAT-AATATTTAAATATAATA
2865734 TATAATATTTTAAATATAAT-
1 TATAATA-TTTAAATATAATA
2865754 TATAATA
1 TATAATA
2865761 AAAAATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.10
20 23 0.59
21 7 0.18
22 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATATTTAAATATAATA
Found at i:2865769 original size:30 final size:29
Alignment explanation
Indices: 2865711--2865771 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
2865701 TTAATTATTA
*
2865711 ATTTATAAATATTTATATAAATATATAAT
1 ATTTATAAATATTTATATAAATAAATAAT
2865740 ATTT-TAAATATAATTATAATAAA-AAATAAT
1 ATTTATAAATAT--TTAT-ATAAATAAATAAT
2865770 AT
1 AT
2865772 AAAAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.25
29 4 0.14
30 12 0.43
31 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTTATAAATATTTATATAAATAAATAAT
Found at i:2865775 original size:11 final size:11
Alignment explanation
Indices: 2865755--2865785 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2865745 AAATATAATT
2865755 ATAATA-AAAA
1 ATAATATAAAA
2865765 ATAATATAAAA
1 ATAATATAAAA
2865776 ATAATATAAA
1 ATAATATAAA
2865786 TACATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:2865787 original size:27 final size:27
Alignment explanation
Indices: 2865725--2865787 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2865715 ATAAATATTT
* * * * *
2865725 ATATAAATATATAATATTTTAAATATA
1 ATATAAATAAAAAATAATATAAAAATA
2865752 AT-TATAATAAAAAATAATATAAAAATA
1 ATATA-AATAAAAAATAATATAAAAATA
2865779 ATATAAATA
1 ATATAAATA
2865788 CATAAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 2 0.07
27 25 0.86
28 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAAATAAAAAATAATATAAAAATA
Found at i:2866367 original size:118 final size:117
Alignment explanation
Indices: 2866130--2866599 Score: 496
Period size: 117 Copynumber: 4.0 Consensus size: 117
2866120 TTAATTCAAT
* * * * *
2866130 ATTAAATAGTGAATATATGTTTTCTTGCCGTATAAACTCATAGAAGATGAAATTAATCGAGTAAA
1 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
** * * * * * *
2866195 ATATTTGGATACTTTACATTAGATTTATTTAATAAATAATTTTATCTGCTTA
66 ATATTTCAATATTTTACATTAGATCTATTCAATAATTAATTTTATTTACTTA
*
2866247 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTGATAGAA-AGTCAAAATTAATTGAGTA
1 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTCATAGAAGA-T-AAAATTAATTGAGTA
* * * *
2866311 AAATATTTCAATATTTTACGTTAGATCTATACAATGATTAATATTATTTACTTA
64 AAATATTTCAATATTTTACATTAGATCTATTCAATAATTAATTTTATTTACTTA
* * * *
2866365 ATTAAATAGTTAATATATATTTTCTTATCATATAAACTCATAGAAGATAAAATTAACTAAGTAAA
1 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
* * * * * *
2866430 ATATTTTATTATTTTATATTAGATCTATTCAATAATCAATTTTA-TCAGCTTG
66 ATATTTCAATATTTTACATTAGATCTATTCAATAATTAATTTTATTTA-CTTA
** * * *
2866482 ATTAAATACAGTATATATATTTTCTTACCATATAAACTTATAGAAGATGAAATTAATT-ATGTAA
1 ATTAAATAGTGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGA-GTAA
*** ** * * ** *
2866546 AATATTTTGTTATTTTATTTTAAATCTATTCAGTCGTAAATTTTATTTACTTA
65 AATATTTCAATATTTTACATTAGATCTATTCAATAATTAATTTTATTTACTTA
2866599 A
1 A
2866600 ATTTAAAAGT
Statistics
Matches: 297, Mismatches: 50, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
116 4 0.01
117 192 0.65
118 100 0.34
119 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (117 bp):
ATTAAATAGTGAATATATATTTTCTTACCATATAAACTCATAGAAGATAAAATTAATTGAGTAAA
ATATTTCAATATTTTACATTAGATCTATTCAATAATTAATTTTATTTACTTA
Found at i:2867953 original size:17 final size:16
Alignment explanation
Indices: 2867920--2867960 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2867910 AAAAGTTATA
2867920 TAATATTTAATTAAAT
1 TAATATTTAATTAAAT
*
2867936 TAATATTATAATTTAAT
1 TAATATT-TAATTAAAT
*
2867953 TAAAATTT
1 TAATATTT
2867961 TAAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTAATTAAAT
Found at i:2867980 original size:28 final size:29
Alignment explanation
Indices: 2867940--2867999 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
2867930 TTAAATTAAT
* *
2867940 ATTATAATTTAATTAAAATTTTAAAATTA
1 ATTATAATATAATAAAAATTTTAAAATTA
* *
2867969 ATTA-AATATAATAAAAATTTTATATTTA
1 ATTATAATATAATAAAAATTTTAAAATTA
2867997 ATT
1 ATT
2868000 TATTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTATAATATAATAAAAATTTTAAAATTA
Found at i:2868011 original size:18 final size:18
Alignment explanation
Indices: 2867990--2868024 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2867980 TAAAAATTTT
2867990 ATATTTAATTTAT-TAATA
1 ATATTT-ATTTATATAATA
2868008 ATATTTATTTATATAAT
1 ATATTTATTTATATAAT
2868025 TAGATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATTTATATAATA
Found at i:2868041 original size:23 final size:23
Alignment explanation
Indices: 2867984--2868042 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
2867974 ATATAATAAA
*
2867984 AATTTTATATTTA-ATTTATTAAT
1 AATTTTAT-TTTATATTAATTAAT
2868007 AATATTTA-TTTATA-TAATTAGAT
1 AAT-TTTATTTTATATTAATTA-AT
2868030 AATTTTATTTTAT
1 AATTTTATTTTAT
2868043 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
22 13 0.42
23 14 0.45
24 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
AATTTTATTTTATATTAATTAAT
Found at i:2868887 original size:22 final size:22
Alignment explanation
Indices: 2868862--2868907 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2868852 TCGTGCTTCG
* *
2868862 TTTTGAATTAATT-TTTATATAA
1 TTTTAAATT-ATTATTTATAAAA
2868884 TTTTAAATTATTATTTATAAAA
1 TTTTAAATTATTATTTATAAAA
2868906 TT
1 TT
2868908 AATTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAAATTATTATTTATAAAA
Found at i:2869291 original size:20 final size:18
Alignment explanation
Indices: 2869249--2869295 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 18
2869239 TGTTTGTATA
2869249 TTTTATATTTATATTATTT
1 TTTTATA-TTATATTATTT
2869268 TTTTATATTATATTATAATT
1 TTTTATATTATATTAT--TT
2869288 TTTTATAT
1 TTTTATAT
2869296 CGTATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.35
19 7 0.27
20 10 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATTATATTATTT
Found at i:2869676 original size:15 final size:15
Alignment explanation
Indices: 2869656--2869704 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2869646 TGATTATAAT
2869656 TTTTTTCTTTCTTTC
1 TTTTTTCTTTCTTTC
*
2869671 TTTTTTCTTTTTTTC
1 TTTTTTCTTTCTTTC
***
2869686 TCCCTTCTTTCTTT-
1 TTTTTTCTTTCTTTC
2869700 TTTTT
1 TTTTT
2869705 CAACTTATTG
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
14 2 0.08
15 24 0.92
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTCTTTC
Done.