Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 99 of 208
Found at i:29634037 original size:20 final size:21
Alignment explanation
Indices: 29633996--29634039 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
29633986 GAGTTGAAAT
*
29633996 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
29634017 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
29634037 TAA
1 TAA
29634040 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:29634045 original size:60 final size:61
Alignment explanation
Indices: 29633960--29634079 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
29633950 ATGGATAAGT
* * *
29633960 AGTTCGAATGTAAGATTTAATTTC-TTGAGTTGAA-ATTAA-AGTTATGAATTATATATATAA
1 AGTTCGAATGTAAGATATAAGTTCTTTGAGCTGAACA-TAATA-TTATGAATTATATATATAA
* *
29634020 AGTTTGAATGTATGATATAAGTTCTTTGAGCTGAACATAATATTATGAATTATATATATA
1 AGTTCGAATGTAAGATATAAGTTCTTTGAGCTGAACATAATATTATGAATTATATATATA
29634080 TATATGCACA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 20 0.38
61 30 0.58
62 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.42
Consensus pattern (61 bp):
AGTTCGAATGTAAGATATAAGTTCTTTGAGCTGAACATAATATTATGAATTATATATATAA
Found at i:29634259 original size:64 final size:63
Alignment explanation
Indices: 29634119--29634300 Score: 239
Period size: 64 Copynumber: 2.9 Consensus size: 63
29634109 TATATATATA
* * *
29634119 TATAAAGTTC-TTGAGCTGTATTTAATGTATGAATTTATATACATATGTGGTTCAAATATAGGT
1 TATAAAGTTCTTTGAGCTGAATTTAATGTATGAATTTA-ATACATATGTGGTTCGAACATAGGT
*
29634182 TACAAAGTT-TTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAACATAGGT
1 TATAAAGTTCTTTGAGCTGAATTTAATGTATGAA-TTTA-ATACATATGTGGTTCGAACATAGGT
*
29634246 TATAAA-TTCTTTGAGCTGAATTTTAATGT-TGTAAATT-ATACATATGTGGTTCGAA
1 TATAAAGTTCTTTGAGCTGAA-TTTAATGTATG-AATTTAATACATATGTGGTTCGAA
29634301 TGTTTGTTTG
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
62 18 0.17
63 32 0.30
64 47 0.44
65 10 0.09
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (63 bp):
TATAAAGTTCTTTGAGCTGAATTTAATGTATGAATTTAATACATATGTGGTTCGAACATAGGT
Found at i:29634904 original size:2 final size:2
Alignment explanation
Indices: 29634897--29634937 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29634887 TAAGTATTAG
29634897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29634938 GAATTTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29639317 original size:23 final size:26
Alignment explanation
Indices: 29639291--29639339 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 26
29639281 TGTAAATAAG
29639291 AAAAGAATTTC-T-AGA-AATTTTCT
1 AAAAGAATTTCTTCAGAGAATTTTCT
*
29639314 AAAATAATTTCTTCAGAGAATTTTCT
1 AAAAGAATTTCTTCAGAGAATTTTCT
29639340 CTCTACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 1 0.05
25 3 0.14
26 8 0.36
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (26 bp):
AAAAGAATTTCTTCAGAGAATTTTCT
Found at i:29639598 original size:59 final size:61
Alignment explanation
Indices: 29639466--29639626 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 61
29639456 TTAATATAAT
** ** * *
29639466 ATTATTAGGTTAAATTTAATATTAAATCTTATTAAATTAATAGAATATTTATCTACAAGATA
1 ATTATTAAATTAAATTTAATATTAAATAATATTAAATTAATAAAATATCTATCTA-AAGATA
** *
29639528 AACATTAAATTAAATTTAATATTAAGGTAATATTAAATTAATAAAATA-CTAT-T-AAGATA
1 ATTATTAAATTAAATTTAATATTAA-ATAATATTAAATTAATAAAATATCTATCTAAAGATA
* *
29639587 ATTATTAAATTAAATTTAATATTAAAT-CTATTAAAATAAT
1 ATTATTAAATTAAATTTAATATTAAATAATATTAAATTAAT
29639627 GTTATTTTTG
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
57 11 0.13
58 1 0.01
59 29 0.35
61 1 0.01
62 24 0.29
63 18 0.21
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (61 bp):
ATTATTAAATTAAATTTAATATTAAATAATATTAAATTAATAAAATATCTATCTAAAGATA
Found at i:29642313 original size:31 final size:32
Alignment explanation
Indices: 29642276--29642350 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
29642266 GAAAGGAAAA
*
29642276 CCTTTGTGGCAAGTACTGAATG-AAAATGATG
1 CCTTTGTGGCAAGTACTGAATGAAAAAAGATG
** *
29642307 CCTTTGTGGTGAGTATTGAATGAAAAAAGATG
1 CCTTTGTGGCAAGTACTGAATGAAAAAAGATG
29642339 CCTTTGTGGCAA
1 CCTTTGTGGCAA
29642351 ACCACTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 19 0.51
32 18 0.49
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (32 bp):
CCTTTGTGGCAAGTACTGAATGAAAAAAGATG
Found at i:29646907 original size:23 final size:23
Alignment explanation
Indices: 29646881--29646925 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29646871 ATATTTTAAT
29646881 GACTCTAATGACTTAGTAAATAC
1 GACTCTAATGACTTAGTAAATAC
*
29646904 GACTCTAATGACTTCGTAAATA
1 GACTCTAATGACTTAGTAAATA
29646926 TTCTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
GACTCTAATGACTTAGTAAATAC
Found at i:29655740 original size:15 final size:15
Alignment explanation
Indices: 29655720--29655800 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 15
29655710 TCTCTTTCAA
*
29655720 TTTCTTTTTTCACTT
1 TTTCTTTTTTCAATT
29655735 TTTC-TTTTTCAATT
1 TTTCTTTTTTCAATT
*
29655749 TTTTTTTCATTCTCAA--
1 TTTCTTT--TT-TCAATT
29655765 TTTC-TTTTTCAA-T
1 TTTCTTTTTTCAATT
29655778 TTTCTTTTCTTC-A-T
1 TTTCTTTT-TTCAATT
29655792 TTTCTTTTT
1 TTTCTTTTT
29655801 CTCTCACTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 25 0.45
15 11 0.20
16 3 0.05
17 2 0.04
18 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTTTTCAATT
Found at i:29655744 original size:14 final size:14
Alignment explanation
Indices: 29655714--29655785 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 14
29655704 TCAAGCTCTC
*
29655714 TTTCAATTTCT-TT
1 TTTCAATTTTTCTT
*
29655727 TTTCACTTTTTCTT
1 TTTCAATTTTTCTT
29655741 TTTCAA-TTTT-TT
1 TTTCAATTTTTCTT
*
29655753 TTTCATTCTCAATTTCTT
1 TTTCAAT-T---TTTCTT
29655771 TTTCAA-TTTTCTT
1 TTTCAATTTTTCTT
29655784 TT
1 TT
29655786 CTTCATTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
12 7 0.15
13 21 0.45
14 8 0.17
16 1 0.02
17 3 0.06
18 7 0.15
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCAATTTTTCTT
Found at i:29655771 original size:30 final size:27
Alignment explanation
Indices: 29655714--29655801 Score: 90
Period size: 30 Copynumber: 3.1 Consensus size: 27
29655704 TCAAGCTCTC
*
29655714 TTTCAA-TTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTTCTTTTCTTCA--ATTTCTT
*
29655741 TTTCAATTTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTTCTTTTC--T-TCAATTTCTT
*
29655771 TTTCAATTTTCTTTTCTTCATTTTCTT
1 TTTCAATTTTCTTTTCTTCAATTTCTT
29655798 TTTC
1 TTTC
29655802 TCTCACTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 19 0.37
28 8 0.15
30 21 0.40
31 1 0.02
32 3 0.06
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCAATTTTCTTTTCTTCAATTTCTT
Found at i:29655785 original size:12 final size:12
Alignment explanation
Indices: 29655696--29655897 Score: 58
Period size: 12 Copynumber: 17.7 Consensus size: 12
29655686 TTTTCACTTG
29655696 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
29655707 AGCTCTCTTTCA
1 ATTTCTTTTTCA
29655719 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
29655732 CTTTTTCTTTTTCA
1 --ATTTCTTTTTCA
*
29655746 ATTTTTTTTTC-
1 ATTTCTTTTTCA
29655757 A-TTC----TCA
1 ATTTCTTTTTCA
29655764 ATTTCTTTTTCA
1 ATTTCTTTTTCA
29655776 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
29655791 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** **
29655803 CTCACTTTTTTG
1 ATTTCTTTTTCA
29655815 A-TT-TTTTT--
1 ATTTCTTTTTCA
*
29655823 --TTCTTTTGCA
1 ATTTCTTTTTCA
*
29655833 ATTTCTTTTTCT
1 ATTTCTTTTTCA
* *
29655845 TTTTCTTTTTCG
1 ATTTCTTTTTCA
*
29655857 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
29655867 GTTT-TCTTTCA
1 ATTTCTTTTTCA
29655878 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
29655890 ATCTCTTT
1 ATTTCTTT
29655898 CTCCTTTTCT
Statistics
Matches: 140, Mismatches: 30, Indels: 41
0.66 0.14 0.19
Matches are distributed among these distances:
6 2 0.01
7 3 0.02
8 7 0.05
9 4 0.03
10 10 0.07
11 7 0.05
12 72 0.51
13 13 0.09
14 14 0.10
15 8 0.06
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.68
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:29655888 original size:6 final size:6
Alignment explanation
Indices: 29655732--29655875 Score: 71
Period size: 6 Copynumber: 23.7 Consensus size: 6
29655722 TCTTTTTTCA
* * * ** *
29655732 CTTTTT CTTTTT CAATTTT -TTTTT CATTCT CAATTT CTTTTT CAATTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* * ** *
29655781 CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT -TGATTTT -TTTTT CTTTTG
1 C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CT--TTTT CTTTTT CTTTTT
** * *
29655831 CAATTT CTTTTT CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
29655876 CAATTTCTTT
Statistics
Matches: 101, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
5 13 0.13
6 67 0.66
7 18 0.18
8 3 0.03
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:29658647 original size:20 final size:20
Alignment explanation
Indices: 29658624--29658688 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
29658614 AAGCTCAAAC
29658624 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
29658644 GAGCTCAAACG--AGCTAAATT
1 GAGCT-AAA-GTAAGCTAAATT
* * * *
29658664 AAGCTCATGTAAGCTAAATC
1 GAGCTAAAGTAAGCTAAATT
29658684 GAGCT
1 GAGCT
29658689 GGGAAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:29658687 original size:30 final size:29
Alignment explanation
Indices: 29658614--29658688 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
29658604 AACTTAAGCC
29658614 AAGCTCAAACGAGCTAAAGTAAGCTAAATT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAATT
* * *
29658644 GAGCTCAAACGAGCTAAATTAAGCT-CATGT
1 AAGCT-AAACGAGCTAAAGTAAGCTAAAT-T
29658674 AAGCTAAATCGAGCT
1 AAGCTAAA-CGAGCT
29658689 GGGAAAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 34 0.87
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (29 bp):
AAGCTAAACGAGCTAAAGTAAGCTAAATT
Found at i:29665209 original size:19 final size:19
Alignment explanation
Indices: 29665183--29665228 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
29665173 TTAATAATCT
* *
29665183 TGAATGCATATG-ATGACA
1 TGAATGCAGATGCATGAAA
29665201 TGTAATGCAGATGCATGAAA
1 TG-AATGCAGATGCATGAAA
29665221 TGAATGCA
1 TGAATGCA
29665229 AAAAGGAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (19 bp):
TGAATGCAGATGCATGAAA
Found at i:29666213 original size:36 final size:36
Alignment explanation
Indices: 29666166--29666237 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
29666156 TCCTTTTACG
29666166 TCACCACTCACCGTACTCTGGAGTTGTCATCGAACC
1 TCACCACTCACCGTACTCTGGAGTTGTCATCGAACC
29666202 TCACCACTCACCGTACTCTGGAGTTGTCATCGAACC
1 TCACCACTCACCGTACTCTGGAGTTGTCATCGAACC
29666238 CACAGCTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (36 bp):
TCACCACTCACCGTACTCTGGAGTTGTCATCGAACC
Found at i:29668823 original size:27 final size:26
Alignment explanation
Indices: 29668793--29668843 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
29668783 ATGAAATTCT
*
29668793 TACAAA-CAATATGATCGATTAACAATA
1 TACAAAGCAA-ATGAT-GAATAACAATA
29668820 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
29668844 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:29669245 original size:21 final size:20
Alignment explanation
Indices: 29669198--29669245 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
29669188 AATCTTAAAC
* *
29669198 AAAATTAAAATAATAGTATAT
1 AAAA-TAAAATAATAGAAAAT
29669219 AAAATAAAATAAATAGAAAAT
1 AAAATAAAAT-AATAGAAAAT
*
29669240 ACAATA
1 AAAATA
29669246 GACTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAAAATAATAGAAAAT
Found at i:29671740 original size:20 final size:20
Alignment explanation
Indices: 29671712--29671751 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29671702 TCTTAATTAG
*
29671712 AATCTCTAAAAATTAGCTAT
1 AATCCCTAAAAATTAGCTAT
**
29671732 AATCCCTAAAGGTTAGCTAT
1 AATCCCTAAAAATTAGCTAT
29671752 TCAGTGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (20 bp):
AATCCCTAAAAATTAGCTAT
Found at i:29675602 original size:20 final size:20
Alignment explanation
Indices: 29675569--29675613 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29675559 TAAATTCACA
29675569 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
29675589 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
29675609 TAATT
1 TAATT
29675614 CGGTTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:29676773 original size:248 final size:248
Alignment explanation
Indices: 29676330--29676821 Score: 867
Period size: 248 Copynumber: 2.0 Consensus size: 248
29676320 CGATACATTT
29676330 ATTAAGTACCCGTTCATCTCATCTTTTCGATGTTTCCTAGAGAACTTTCCCAATATTTTCTCTTC
1 ATTAAGTACCCGTTCATCTCATCTTTTCGATGTTTCCTAGAGAACTTTCCCAATATTTTCTCTTC
* * *
29676395 CAGACTTCCTAATATCTCATTACATAAGAAACTACTATACGTAATTGAGCTAATATAAAAATTTC
66 CAGACTTCCTAATATCTCATTACATAAGAAACCACTATACATAATTAAGCTAATATAAAAATTTC
29676460 ATATTTGCTAATTTACAAATCATATTCAGGAATGATCATTAGGAAGTACATCCTAAAGCTCCTAT
131 ATATTTGCTAATTTACAAATCATATTCAGGAATGATCATTAGGAAGTACATCCTAAAGCTCCTAT
* *
29676525 TATCATAGTGAAACATCTTGAAGGGATCAACAAAAAGGCAGTAAAAATATCTC
196 TAACATAGTGAAACATCTTGAAGGGATCAACAAAAAGGCAATAAAAATATCTC
* *
29676578 ATTAGGTACCCGTTCATCTCATCTTTTTGATGTTTCCTAGAGAACTTTCCCAATATTTTCTCTTC
1 ATTAAGTACCCGTTCATCTCATCTTTTCGATGTTTCCTAGAGAACTTTCCCAATATTTTCTCTTC
* **
29676643 TAGACTTCCTAATATCTCATTACATAAGAAACCACTATACATAATTAAGCTAATATAAATTTTTC
66 CAGACTTCCTAATATCTCATTACATAAGAAACCACTATACATAATTAAGCTAATATAAAAATTTC
* *
29676708 ATCTTTGCTAATTTACAAATCATATTCAGGAATGATCATTAGGAAGTACATCCTGAAGCTCCTAT
131 ATATTTGCTAATTTACAAATCATATTCAGGAATGATCATTAGGAAGTACATCCTAAAGCTCCTAT
*
29676773 TAACATAGTGAAACATCTTGAAGGGATCAATAAAAAGGCAATAAAAATA
196 TAACATAGTGAAACATCTTGAAGGGATCAACAAAAAGGCAATAAAAATA
29676822 ATAAATTTCT
Statistics
Matches: 231, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
248 231 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (248 bp):
ATTAAGTACCCGTTCATCTCATCTTTTCGATGTTTCCTAGAGAACTTTCCCAATATTTTCTCTTC
CAGACTTCCTAATATCTCATTACATAAGAAACCACTATACATAATTAAGCTAATATAAAAATTTC
ATATTTGCTAATTTACAAATCATATTCAGGAATGATCATTAGGAAGTACATCCTAAAGCTCCTAT
TAACATAGTGAAACATCTTGAAGGGATCAACAAAAAGGCAATAAAAATATCTC
Found at i:29681182 original size:203 final size:203
Alignment explanation
Indices: 29680833--29681227 Score: 700
Period size: 203 Copynumber: 1.9 Consensus size: 203
29680823 TATACGAGTG
* *
29680833 TGATCTGGTTCTAGGTGTTCAATGGCGCCTTTCTTTGGGAACCATTGTGTGGAGTTTCAGCTCAT
1 TGATCTGGTTCTAGGTGTTCAATAGCGCCTTTCTTTGGGAACAATTGTGTGGAGTTTCAGCTCAT
*
29680898 TGACCATGCAGTTCACTCTTGATTTCCATCATTGTGTGCTACAAAGCATTGAACCAAGCACCAGT
66 TGACCATGCAGTTCACTCTTGATTTCCATCATTGTGTGCTACAAAGCATTAAACCAAGCACCAGT
29680963 CAACTAGTTGAGAAGCCTCAATCCACTAAGTGCATCTCCCTTATAGATCAGTTAATAGGGCCTTG
131 CAACTAGTTGAGAAGCCTCAATCCACTAAGTGCATCTCCCTTATAGATCAGTTAATAGGGCCTTG
29681028 TTGTTGGT
196 TTGTTGGT
29681036 TGATCTGGTTCTAGGTGTTCAATAGCGCCTTTCTTTGGGAACAATTGTGTGGAGTTTCAGCTCAT
1 TGATCTGGTTCTAGGTGTTCAATAGCGCCTTTCTTTGGGAACAATTGTGTGGAGTTTCAGCTCAT
* * * *
29681101 TGACCATGCAGTTCACTCTTGATTTCCATCCTTGTGTGCTGCAAAGCATTAAACTAAGCACCATT
66 TGACCATGCAGTTCACTCTTGATTTCCATCATTGTGTGCTACAAAGCATTAAACCAAGCACCAGT
* **
29681166 CAGCTAGTTGAGAAGCCTCAATCCACTAAGTGTTTCTCCCTTATAGATCAGTTAATAGGGCC
131 CAACTAGTTGAGAAGCCTCAATCCACTAAGTGCATCTCCCTTATAGATCAGTTAATAGGGCC
29681228 ATGTGCCTTG
Statistics
Matches: 182, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 182 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (203 bp):
TGATCTGGTTCTAGGTGTTCAATAGCGCCTTTCTTTGGGAACAATTGTGTGGAGTTTCAGCTCAT
TGACCATGCAGTTCACTCTTGATTTCCATCATTGTGTGCTACAAAGCATTAAACCAAGCACCAGT
CAACTAGTTGAGAAGCCTCAATCCACTAAGTGCATCTCCCTTATAGATCAGTTAATAGGGCCTTG
TTGTTGGT
Found at i:29685358 original size:108 final size:107
Alignment explanation
Indices: 29685229--29685435 Score: 328
Period size: 108 Copynumber: 1.9 Consensus size: 107
29685219 AAATTTTGCT
*
29685229 TTTTAACCCCCCAGAAAACTTTCAACTGTTGTTTAGTTTTTTTTAATAAACTA-AAAAATAGTCA
1 TTTTAACCCCCCAAAAAACTTTCAACTGTTGTTTAG-TTTTTTTAATAAACTATAAAAATAGTCA
*
29685293 TATATCTTTTTT-AGTCATTAATGTTTTAATTCTTACAATTAGG
65 TATATCTTTTTTCA-TCACTAATGTTTTAATTCTTACAATTAGG
* *
29685336 TTTTAACCCCCCAAAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATACAAATTGTCA
1 TTTTAACCCCCC-AAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATAAAAATAGTCA
*
29685401 TATATCTTTTTTCATCACTAATTTTTTAATTCTTA
65 TATATCTTTTTTCATCACTAATGTTTTAATTCTTA
29685436 AAGTCAATTG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
107 28 0.30
108 63 0.68
109 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (107 bp):
TTTTAACCCCCCAAAAAACTTTCAACTGTTGTTTAGTTTTTTTAATAAACTATAAAAATAGTCAT
ATATCTTTTTTCATCACTAATGTTTTAATTCTTACAATTAGG
Found at i:29687941 original size:26 final size:26
Alignment explanation
Indices: 29687888--29687939 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
29687878 TTATTATATT
* * *
29687888 TAAATATATATATTAAAAATTATAAA
1 TAAATATAAATATAAAAAATAATAAA
29687914 TAAATATAAATCATAAAAAATAATAA
1 TAAATATAAAT-ATAAAAAATAATAA
29687940 TATTTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAATATAAATATAAAAAATAATAAA
Found at i:29687950 original size:8 final size:8
Alignment explanation
Indices: 29687937--29687961 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29687927 TAAAAAATAA
29687937 TAATATTT
1 TAATATTT
29687945 TAATATTT
1 TAATATTT
29687953 TAATATTT
1 TAATATTT
29687961 T
1 T
29687962 TATTAAAATT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATATTT
Found at i:29687992 original size:19 final size:19
Alignment explanation
Indices: 29687949--29688003 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
29687939 ATATTTTAAT
29687949 ATTTTAA-TATTTTTATTAA
1 ATTTTAATTATTTTTA-TAA
*
29687968 AATTTAATTATTTTTATAA
1 ATTTTAATTATTTTTATAA
*
29687987 CTTTT-ATTGATTTTTAT
1 ATTTTAATT-ATTTTTAT
29688004 TTTTGGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 20 0.65
20 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTAATTATTTTTATAA
Found at i:29688261 original size:89 final size:82
Alignment explanation
Indices: 29688100--29688268 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 82
29688090 TCAAAGGGCC
* * * * *
29688100 TTTTTGATTCATTTTGACAGTTCAAGTACTCAATTAAGTAAAAAAATGGGATTAATTGCTTTTTT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTAAAAAAATGGGATTAAATACTTTTTT
29688165 TAAAAAGTTTGAGGGTA
66 TAAAAAGTTTGAGGGTA
* *
29688182 TTTTTGATGCATTTTGAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGATTAAATA
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGT----AAAAAAA-T--GGGATTAAATA
**
29688247 CTTTTTTTTTAAAGTTTGAGGG
59 CTTTTTTTAAAAAGTTTGAGGG
29688269 CTTTTTACAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
82 34 0.48
86 7 0.10
87 1 0.01
89 29 0.41
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (82 bp):
TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTAAGTAAAAAAATGGGATTAAATACTTTTTT
TAAAAAGTTTGAGGGTA
Found at i:29690989 original size:49 final size:50
Alignment explanation
Indices: 29690884--29690990 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
29690874 AGTTGAGATG
* * *
29690884 CCAGAAACAAAATATTGTGGTCGAGCCACCAAATAATTGCAAATATACTA
1 CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
* * *
29690934 CCAGATACAAAATATTATGGTCAAGCCATCAGA-AATTGCAAATATACTG
1 CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
*
29690983 CTAGATAC
1 CCAGATAC
29690991 TTCCTCCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 22 0.44
50 28 0.56
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (50 bp):
CCAGATACAAAATATTATGGTCAAGCCACCAAATAATTGCAAATATACTA
Found at i:29704715 original size:15 final size:15
Alignment explanation
Indices: 29704669--29704715 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
29704659 GTTTTCAAAA
*
29704669 AAAAATAAAAAAATCG
1 AAAAA-AAAAAAATTG
29704685 AAAAGAAAAAAAATTG
1 AAAA-AAAAAAAATTG
*
29704701 AAAAAAAAAATATTG
1 AAAAAAAAAAAATTG
29704716 CATACGGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 17 0.61
17 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (15 bp):
AAAAAAAAAAAATTG
Found at i:29711353 original size:16 final size:15
Alignment explanation
Indices: 29711324--29711356 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29711314 AAAAAAATCA
29711324 AAAAAAATCGAAAAG
1 AAAAAAATCGAAAAG
*
29711339 AAAAAAATTGAAAA-
1 AAAAAAATCGAAAAG
29711353 AAAA
1 AAAA
29711357 TATTGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAAAAATCGAAAAG
Found at i:29718166 original size:22 final size:22
Alignment explanation
Indices: 29718119--29718168 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
29718109 ACCACCATAT
*
29718119 CACCACCATACAACCATTATAG
1 CACCACCATACAACCATTATAC
29718141 CACCACCACT-CAACCACTT-TAC
1 CACCACCA-TACAACCA-TTATAC
29718163 CACCAC
1 CACCAC
29718169 TACACCACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.16
Consensus pattern (22 bp):
CACCACCATACAACCATTATAC
Found at i:29724044 original size:20 final size:20
Alignment explanation
Indices: 29724019--29724065 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29724009 AGCTCGTTTC
29724019 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
29724039 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
29724059 CAGCTCA
1 CAGCTCA
29724066 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:29732804 original size:20 final size:20
Alignment explanation
Indices: 29732776--29732819 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29732766 TGAAGTCTAT
*
29732776 TTGTTTGCGAAACTATACTA
1 TTGTATGCGAAACTATACTA
* *
29732796 TTGTATGCGAACCTATGCTA
1 TTGTATGCGAAACTATACTA
29732816 TTGT
1 TTGT
29732820 GTGAACTAGT
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:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGTATGCGAAACTATACTA
Found at i:29753551 original size:51 final size:50
Alignment explanation
Indices: 29753476--29753607 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 50
29753466 ATGAATACGT
* *
29753476 GTGTAGTAGTACTATGTGAAGGCTACTATGTGCACCG-AAAAGCTTTGGTCAC
1 GTGT-GTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAA-C-TTGATCAC
* * *
29753528 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGTAAAACTTGATTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAACTTGATCAC
*
29753578 G-GTGTAGTACTATGTGAAGGCTAATACGTG
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG
29753608 TATCGAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
49 28 0.38
50 7 0.10
51 30 0.41
52 8 0.11
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGCACCGTAAAACTTGATCAC
Found at i:29753606 original size:49 final size:51
Alignment explanation
Indices: 29753476--29753614 Score: 176
Period size: 49 Copynumber: 2.7 Consensus size: 51
29753466 ATGAATACGT
* * *
29753476 GTGTAGTAGTACTATGTGAAGGCTACTATGTGCACCGAAAAGCTTTGGTCAC
1 GTGT-GTAGTACTATGTGAAGGCTACTACGTGCATCGAAAAGCTTTGATCAC
* *
29753528 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGTAAAA-C-TTGATTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCG-AAAAGCTTTGATCAC
* *
29753578 G-GTGTAGTACTATGTGAAGGCTAATACGTGTATCGAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCGAA
29753615 TGATAATAGT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
48 2 0.03
49 32 0.41
50 7 0.09
51 30 0.38
52 8 0.10
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (51 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGCATCGAAAAGCTTTGATCAC
Found at i:29757533 original size:20 final size:19
Alignment explanation
Indices: 29757498--29757535 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29757488 AGCTAATAAC
29757498 GAGCTCAATGAACTGAATT
1 GAGCTCAATGAACTGAATT
*
29757517 GAGCTCGAATGACCTGAAT
1 GAGCTC-AATGAACTGAAT
29757536 CAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAACTGAATT
Found at i:29757638 original size:12 final size:11
Alignment explanation
Indices: 29757607--29757651 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
29757597 AAAAAACAAA
*
29757607 CAAAAAAAACT
1 CAAAAAAAATT
29757618 C-AAAAAAATT
1 CAAAAAAAATT
29757628 CAAAAACAAATT
1 CAAAAA-AAATT
29757640 CGAAAAAAAATT
1 C-AAAAAAAATT
29757652 AGTTTCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.30
11 5 0.17
12 11 0.37
13 5 0.17
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:29757704 original size:12 final size:12
Alignment explanation
Indices: 29757687--29757724 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
29757677 GGATATCAAG
29757687 TTGTGAAAAAAA
1 TTGTGAAAAAAA
29757699 TTGTGAAAAAGAAA
1 TTGTG-AAAA-AAA
29757713 TTGTGAAAAAAA
1 TTGTGAAAAAAA
29757725 AAAACTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (12 bp):
TTGTGAAAAAAA
Found at i:29757715 original size:14 final size:13
Alignment explanation
Indices: 29757687--29757725 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
29757677 GGATATCAAG
29757687 TTGTG-AAAAAAA
1 TTGTGAAAAAAAA
29757699 TTGTGAAAAAGAAA
1 TTGTGAAAAA-AAA
29757713 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
29757726 AAACTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:29758805 original size:19 final size:18
Alignment explanation
Indices: 29758777--29758822 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29758767 GAGTTTTTCA
* *
29758777 AAAAACAAAGAGATTGTGG
1 AAAAAGAAAGAGA-AGTGG
*
29758796 AAAAAGAAAGAGAAGTTG
1 AAAAAGAAAGAGAAGTGG
29758814 AAAAAGAAA
1 AAAAAGAAA
29758823 CGAGTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAGAGAAGTGG
Found at i:29759022 original size:9 final size:9
Alignment explanation
Indices: 29759008--29759033 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29758998 CAAGAGCTTA
29759008 AAGGTAAGC
1 AAGGTAAGC
29759017 AAGGTAAGC
1 AAGGTAAGC
29759026 AAGGTAAG
1 AAGGTAAG
29759034 GAGTTTTTAG
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:0.46, C:0.08, G:0.35, T:0.12
Consensus pattern (9 bp):
AAGGTAAGC
Found at i:29761686 original size:14 final size:13
Alignment explanation
Indices: 29761659--29761698 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
29761649 GGATATCAAG
29761659 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
29761672 TTGTGAAAAAGAAA
1 TTGTGAAAAA-AAA
29761686 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
29761699 AAAACTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:29783724 original size:14 final size:13
Alignment explanation
Indices: 29783705--29783756 Score: 86
Period size: 14 Copynumber: 3.8 Consensus size: 13
29783695 CTAGCTCTCT
29783705 TTTTTTTTTCAGAA
1 TTTTTTTTTCA-AA
29783719 TTTTTTTTTCAAAA
1 TTTTTTTTTC-AAA
29783733 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
29783746 TTTTTTTTTCA
1 TTTTTTTTTCA
29783757 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 14 0.38
14 22 0.59
15 1 0.03
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:29783814 original size:11 final size:11
Alignment explanation
Indices: 29783798--29783827 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29783788 GGAAACTAGT
*
29783798 TTTTTTTTTAA
1 TTTTTTTTGAA
29783809 TTTTTTTTGAA
1 TTTTTTTTGAA
29783820 TTTTTTTT
1 TTTTTTTT
29783828 CGAGAACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:29787116 original size:51 final size:51
Alignment explanation
Indices: 29787056--29787276 Score: 193
Period size: 51 Copynumber: 4.4 Consensus size: 51
29787046 GATGAACACG
*
29787056 TGTGTAGTACTATGTGAAGGCTACTACGTATATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
* * * * * *
29787107 TGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCAAAAAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA--TAATGGTCACA
* * * * * *
29787158 TGTGTAGTACTATGTGAAGGCTACTACGTGGACCG-TAAA-ACTTGATTACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACA
* * *
29787208 TGTGTAGTACTATGTGAAGGCTATTACGTGTATC-A-AATGATAATAGTAACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA--ATAATGGTCACA
* *
29787259 TGGGTGGTACTATGTGAA
1 TGTGTAGTACTATGTGAA
29787277 AACCCCCAAA
Statistics
Matches: 137, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
49 2 0.01
50 43 0.31
51 89 0.65
52 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
Found at i:29793346 original size:10 final size:9
Alignment explanation
Indices: 29793320--29793354 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
29793310 CAAAAAATTC
29793320 AGTCAAAAA
1 AGTCAAAAA
29793329 AGTCAAAAA
1 AGTCAAAAA
*
29793338 ATTCAAAAA
1 AGTCAAAAA
*
29793347 AGACAAAA
1 AGTCAAAA
29793355 TCGAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.11, G:0.09, T:0.11
Consensus pattern (9 bp):
AGTCAAAAA
Found at i:29802100 original size:22 final size:23
Alignment explanation
Indices: 29802052--29802101 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
29802042 TTATTCTTTA
*
29802052 AAAAAGAAAAAACAACAAAAAAG
1 AAAAAGAAAAAACAACAAAAAAC
* *
29802075 AAAAAGAAAAAGC-ACAAAACAC
1 AAAAAGAAAAAACAACAAAAAAC
29802097 AAAAA
1 AAAAA
29802102 AAACCACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAACAACAAAAAAC
Found at i:29802101 original size:23 final size:22
Alignment explanation
Indices: 29802051--29802118 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 22
29802041 CTTATTCTTT
29802051 AAAAAAGAAAAAACAACAAAAA
1 AAAAAAGAAAAAACAACAAAAA
*
29802073 AGAAAAAGAAAAAGC-AC-AAAA
1 A-AAAAAGAAAAAACAACAAAAA
* * * *
29802094 CACAAA-AAAAACCACCAAAAA
1 AAAAAAGAAAAAACAACAAAAA
29802115 AAAA
1 AAAA
29802119 GTTGCCTACC
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 6 0.17
20 5 0.14
21 10 0.28
22 3 0.08
23 12 0.33
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAACAACAAAAA
Found at i:29807816 original size:22 final size:22
Alignment explanation
Indices: 29807785--29807849 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
29807775 ACCTTTTTGA
*
29807785 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
29807808 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
29807830 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
29807850 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:29810767 original size:20 final size:20
Alignment explanation
Indices: 29810716--29810769 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
29810706 TAATTCATGT
*
29810716 TTTAATTTAAGACATACTTAA
1 TTTAA-TTAAGACACACTTAA
** * *
29810737 TAAAATCAAGACACATTTAA
1 TTTAATTAAGACACACTTAA
29810757 TTTAATTAAGACA
1 TTTAATTAAGACA
29810770 AGACAAATTA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAATTAAGACACACTTAA
Found at i:29814098 original size:32 final size:31
Alignment explanation
Indices: 29814061--29814122 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
29814051 CCAGATATGT
29814061 AACTTTGCAA-CACTTTTTTTTCTTTTTTTAAC
1 AACTTTG-AATCA-TTTTTTTTCTTTTTTTAAC
*
29814093 AACTTTGAATTATTTTTTTTCTTTTTTTAA
1 AACTTTGAATCATTTTTTTTCTTTTTTTAA
29814123 TTACAAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (31 bp):
AACTTTGAATCATTTTTTTTCTTTTTTTAAC
Found at i:29819064 original size:11 final size:10
Alignment explanation
Indices: 29819039--29819099 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
29819029 ACCAATAAAA
29819039 TAAA-TGAGC
1 TAAATTGAGC
*
29819048 TGAATTGTAGC
1 TAAATTG-AGC
29819059 TAAATTGAGC
1 TAAATTGAGC
**
29819069 TCGATTGAGC
1 TAAATTGAGC
29819079 TGAAA-TGAGC
1 T-AAATTGAGC
*
29819089 TCAATTGAGC
1 TAAATTGAGC
29819099 T
1 T
29819100 GGTCGGAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:29819100 original size:20 final size:20
Alignment explanation
Indices: 29819040--29819100 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
29819030 CCAATAAAAT
*
29819040 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
29819060 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
29819081 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
29819101 GTCGGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:29819109 original size:30 final size:30
Alignment explanation
Indices: 29819044--29819120 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
29819034 TAAAATAAAT
* *
29819044 GAGCTGAATTGTAGCTAAATTGAGCTCGATT
1 GAGCTGAAATG-AGCTAAATTGAGCTCGATG
* *
29819075 GAGCTGAAATGAGCTCAATTGAGCT-GGTCG
1 GAGCTGAAATGAGCTAAATTGAGCTCGAT-G
*
29819105 GAGCTGAAACGAGCTA
1 GAGCTGAAATGAGCTA
29819121 GAAAAGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.05
30 27 0.69
31 10 0.26
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (30 bp):
GAGCTGAAATGAGCTAAATTGAGCTCGATG
Found at i:29822517 original size:15 final size:15
Alignment explanation
Indices: 29822480--29822518 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
29822470 ACAACCTCTT
29822480 TTTTTTTATGCACGAA
1 TTTTTTT-TGCACGAA
*
29822496 TTTTTTTTGCATGAA
1 TTTTTTTTGCACGAA
29822511 TTTTTTTT
1 TTTTTTTT
29822519 TTAATTCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.64
Consensus pattern (15 bp):
TTTTTTTTGCACGAA
Found at i:29823786 original size:11 final size:10
Alignment explanation
Indices: 29823761--29823821 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
29823751 ACAAATAAAA
29823761 TAAA-TGAGC
1 TAAATTGAGC
*
29823770 TGAATTGTAGC
1 TAAATTG-AGC
29823781 TAAATTGAGC
1 TAAATTGAGC
**
29823791 TCGATTGAGC
1 TAAATTGAGC
29823801 TGAAA-TGAGC
1 T-AAATTGAGC
*
29823811 TCAATTGAGC
1 TAAATTGAGC
29823821 T
1 T
29823822 GGTCGGAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:29823822 original size:20 final size:20
Alignment explanation
Indices: 29823762--29823822 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
29823752 CAAATAAAAT
*
29823762 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
29823782 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
29823803 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
29823823 GTCGGAACTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:29826708 original size:17 final size:17
Alignment explanation
Indices: 29826683--29826720 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
29826673 ATGCACTAAC
*
29826683 TTGTGTATTTGGTGATG
1 TTGTCTATTTGGTGATG
29826700 TTGTCTATTTGGTGATG
1 TTGTCTATTTGGTGATG
29826717 TTGT
1 TTGT
29826721 ATAGGCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.55
Consensus pattern (17 bp):
TTGTCTATTTGGTGATG
Found at i:29829944 original size:22 final size:22
Alignment explanation
Indices: 29829916--29830068 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
29829906 TTTATTGTTC
*
29829916 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29829938 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
29829960 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
29829982 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
29830004 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
29830026 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29830048 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
29830069 ACTGGCTAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:29831931 original size:25 final size:24
Alignment explanation
Indices: 29831884--29831970 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 24
29831874 CTACTCATAT
**
29831884 GAGCTTATTGATTTCAGCTCGTAA
1 GAGCTTACCGATTTCAGCTCGTAA
*
29831908 GAGCTTACCGATTCTCAGCTCGTAT
1 GAGCTTACCGATT-TCAGCTCGTAA
** *
29831933 GAGCTTACCGATTTCCAGCTTATGA
1 GAGCTTACCGATTT-CAGCTCGTAA
*
29831958 GAGCATACCGATT
1 GAGCTTACCGATT
29831971 CATAGCTCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 12 0.23
25 41 0.77
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (24 bp):
GAGCTTACCGATTTCAGCTCGTAA
Found at i:29831968 original size:50 final size:49
Alignment explanation
Indices: 29831881--29831982 Score: 125
Period size: 50 Copynumber: 2.1 Consensus size: 49
29831871 CCACTACTCA
** * *
29831881 TATGAGCTTATTGATTTCAGCTCGTAAGAGCTTACCGATTC-TCAGCTCG
1 TATGAGCTTACCGATTTCAGCTCATAAGAGCATACCGATTCAT-AGCTCG
* *
29831930 TATGAGCTTACCGATTTCCAGCTTATGAGAGCATACCGATTCATAGCTCG
1 TATGAGCTTACCGATTT-CAGCTCATAAGAGCATACCGATTCATAGCTCG
29831980 TAT
1 TAT
29831983 AAGCATACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 15 0.33
50 29 0.64
51 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (49 bp):
TATGAGCTTACCGATTTCAGCTCATAAGAGCATACCGATTCATAGCTCG
Found at i:29831987 original size:25 final size:25
Alignment explanation
Indices: 29831899--29831990 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 25
29831889 TATTGATTTC
*
29831899 AGCTCGTA-AGAGCTTACCGATTCT
1 AGCTCGTATAGAGCATACCGATTCT
* *
29831923 CAGCTCGTAT-GAGCTTACCGATTTCC
1 -AGCTCGTATAGAGCATACCGA-TTCT
29831949 AGCT--TATGAGAGCATACCGATTCAT
1 AGCTCGTAT-AGAGCATACCGATTC-T
29831974 AGCTCGTATA-AGCATAC
1 AGCTCGTATAGAGCATAC
29831991 ATGTACAGGA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
23 3 0.05
24 3 0.05
25 44 0.77
26 4 0.07
27 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCTCGTATAGAGCATACCGATTCT
Found at i:29834495 original size:46 final size:46
Alignment explanation
Indices: 29834444--29834537 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
29834434 ATAGTGTGGC
29834444 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
* *
29834490 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
29834536 GT
1 GT
29834538 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGAGTCGAG
Found at i:29847409 original size:50 final size:50
Alignment explanation
Indices: 29847304--29847432 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 50
29847294 AAGGTGGAAG
*
29847304 CAGTGGTAGTATATCTACAAATCAATGGTGGCTTATCCACAAAATTATAT
1 CAGTGGCAGTATATCTACAAATCAATGGTGGCTTATCCACAAAATTATAT
* * * * *
29847354 TAGTGGCAGTATATCTTCAATTCAATGGTGGCTTGTCCACAAAGTGT-TAT
1 CAGTGGCAGTATATCTACAAATCAATGGTGGCTTATCCACAAAAT-TATAT
* * * * *
29847404 CAGTGGTAGTTTATTTGCAAATCAGTGGT
1 CAGTGGCAGTATATCTACAAATCAATGGT
29847433 AGTTTATCTA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 64 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (50 bp):
CAGTGGCAGTATATCTACAAATCAATGGTGGCTTATCCACAAAATTATAT
Found at i:29847453 original size:21 final size:22
Alignment explanation
Indices: 29847402--29847468 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
29847392 ACAAAGTGTT
* *
29847402 ATCAGTGGTAGTTTATTTGCAA
1 ATCAGTGGTAGTTTATCTACAA
29847424 ATCAGTGGTAGTTTATCTAC-A
1 ATCAGTGGTAGTTTATCTACAA
* * * *
29847445 ATTAGTGGTGGCTTATCCACAA
1 ATCAGTGGTAGTTTATCTACAA
29847467 AT
1 AT
29847469 GGTGTTTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (22 bp):
ATCAGTGGTAGTTTATCTACAA
Found at i:29848208 original size:21 final size:21
Alignment explanation
Indices: 29848182--29848227 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
29848172 CCGTAATGTC
29848182 TAGGCCTGGTTTGAGGGGTTA
1 TAGGCCTGGTTTGAGGGGTTA
29848203 TAGGCCTGGTTTGAGGGGTTA
1 TAGGCCTGGTTTGAGGGGTTA
29848224 TAGG
1 TAGG
29848228 ACCAATACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.43, T:0.33
Consensus pattern (21 bp):
TAGGCCTGGTTTGAGGGGTTA
Found at i:29851209 original size:24 final size:24
Alignment explanation
Indices: 29851176--29851223 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29851166 TTTCCTATGT
*
29851176 GGAGAGATAAGGAAGGTGAG-AGAA
1 GGAGAAATAAGG-AGGTGAGTAGAA
29851200 GGAGAAATAAGGAGGTGAGTAGAA
1 GGAGAAATAAGGAGGTGAGTAGAA
29851224 AAGGGTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.44, T:0.10
Consensus pattern (24 bp):
GGAGAAATAAGGAGGTGAGTAGAA
Found at i:29852313 original size:33 final size:33
Alignment explanation
Indices: 29852276--29852377 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
29852266 TTTCTTTAGA
29852276 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
* * * * *
29852309 TTTAG-TTT-ATTTGTTTGTT--GTTTATAGA-
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
29852337 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
1 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
29852370 TTTAGTTT
1 TTTAGTTT
29852378 ATTTGTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
28 5 0.09
29 10 0.19
30 8 0.15
31 8 0.15
32 10 0.19
33 13 0.24
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.65
Consensus pattern (33 bp):
TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAG
Found at i:29852316 original size:28 final size:28
Alignment explanation
Indices: 29852279--29852377 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
29852269 CTTTAGATTT
*
29852279 AGTTTTGTTTTCTTTTTTAGGTTTCTAA
1 AGTTTAGTTTTCTTTTTTAGGTTTCTAA
* *
29852307 AGTTTAGTTTAT-TTGTTTGT-TGTTTATAGA
1 AGTTTAGTTT-TCTT-TTT-TAGGTTTCTA-A
*
29852337 TTTAGTTTTGTTTTCTTTTTTAGGTTTCTAA
1 ---AGTTTAGTTTTCTTTTTTAGGTTTCTAA
29852368 AGTTTAGTTT
1 AGTTTAGTTT
29852378 ATTTGTTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
28 20 0.36
29 10 0.18
30 2 0.04
31 2 0.04
32 10 0.18
33 11 0.20
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (28 bp):
AGTTTAGTTTTCTTTTTTAGGTTTCTAA
Found at i:29852367 original size:61 final size:61
Alignment explanation
Indices: 29852272--29852392 Score: 242
Period size: 61 Copynumber: 2.0 Consensus size: 61
29852262 TTTCTTTCTT
29852272 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
1 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
29852333 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTT
1 TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTT
29852393 TCTTTTAAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.16, C:0.03, G:0.17, T:0.64
Consensus pattern (61 bp):
TAGATTTAGTTTTGTTTTCTTTTTTAGGTTTCTAAAGTTTAGTTTATTTGTTTGTTGTTTA
Found at i:29854719 original size:11 final size:11
Alignment explanation
Indices: 29854703--29854727 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29854693 TAACATGTCC
29854703 CATAAGTGTAG
1 CATAAGTGTAG
29854714 CATAAGTGTAG
1 CATAAGTGTAG
29854725 CAT
1 CAT
29854728 TAGGCTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (11 bp):
CATAAGTGTAG
Found at i:29860132 original size:137 final size:137
Alignment explanation
Indices: 29859886--29860133 Score: 365
Period size: 137 Copynumber: 1.8 Consensus size: 137
29859876 GAGCCATAAA
*
29859886 TGGGTCTACTCACACAAGCTAACGGTTGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
1 TGGGTCTACTCACACAAGCTAACGGTAGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
* * * *
29859951 AGTATCCACAAAAAATGTCGGAACTCAGCCATCGGTAGGACATTCAGGATCAGCACTTGAAACAT
66 AGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCAGGATCAGCACTTGAAACAT
29860016 GGTAACC
131 GGTAACC
* * * *
29860023 TGGGTCTACTCACACAAGCTGATGGTCAG-AATGTAAGCTGCACGATGCTACTCACACAAGCTGA
1 TGGGTCTACTCACACAAGCTAACGGT-AGAAATGT-AGCTGCACGATGCCACTCACACAAGCTAA
* *
29860087 TGAGTATCCAC-AAAAATGCCAGATCTCAGCCATCAGTAGAACATTCA
64 CGAGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCA
29860134 AGACCAACAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
137 60 0.61
138 38 0.39
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (137 bp):
TGGGTCTACTCACACAAGCTAACGGTAGAAATGTAGCTGCACGATGCCACTCACACAAGCTAACG
AGTATCCACAAAAAATGCCAGAACTCAGCCATCAGTAGAACATTCAGGATCAGCACTTGAAACAT
GGTAACC
Found at i:29864184 original size:11 final size:11
Alignment explanation
Indices: 29864164--29864280 Score: 67
Period size: 11 Copynumber: 11.3 Consensus size: 11
29864154 TAAAAATTAA
29864164 AAAAAGTATTTT
1 AAAAA-TATTTT
29864176 AAAAATATTTT
1 AAAAATATTTT
29864187 --AAA-A--TT
1 AAAAATATTTT
* *
29864193 AAAAAAATTTA
1 AAAAATATTTT
29864204 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
29864216 AAAAAAATTTA
1 AAAAATATTTT
*
29864227 AAAAAAATTTT
1 AAAAATATTTT
29864238 --AAA-A--TT
1 AAAAATATTTT
29864244 AAAAA-ATTTT
1 AAAAATATTTT
29864254 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
29864267 AAAAGTATTTT
1 AAAAATATTTT
29864278 AAA
1 AAA
29864281 GTTAAAAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 27
0.71 0.06 0.23
Matches are distributed among these distances:
6 4 0.05
8 9 0.11
9 7 0.08
10 2 0.02
11 40 0.47
12 18 0.21
13 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:29864204 original size:10 final size:10
Alignment explanation
Indices: 29864187--29864259 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
29864177 AAAATATTTT
29864187 AAAA-TTAAA
1 AAAATTTAAA
29864196 AAAATTTAAA
1 AAAATTTAAA
29864206 AAAGTATTTTAAA
1 AAA--A-TTTAAA
29864219 AAAATTTAAAA
1 AAAATTT-AAA
*
29864230 AAAATTT--T
1 AAAATTTAAA
29864238 AAAA-TTAAA
1 AAAATTTAAA
*
29864247 AAATTTTAAA
1 AAAATTTAAA
29864257 AAA
1 AAA
29864260 GTATTTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 7 0.13
10 19 0.36
11 11 0.21
12 1 0.02
13 9 0.17
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:29864207 original size:40 final size:42
Alignment explanation
Indices: 29864137--29864270 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 42
29864127 ACCAAAAATT
29864137 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAATAAAAATTAAAAAAAGTATTTTAAAAA
*
29864181 TATTTTAAAATT-AA-AAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAATAAAAATTAAAAAAAGTATTTTAAAAA
* * * *
29864221 -AATTTAAAA-AAAATTTTAAAATT-AAAAAA-T-TTTAAAAAA
1 TATTTTAAAATTAAA--TAAAAATTAAAAAAAGTATTTTAAAAA
29864260 GTATTTTAAAA
1 -TATTTTAAAA
29864271 GTATTTTAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
39 18 0.23
40 26 0.33
41 16 0.21
42 6 0.08
43 6 0.08
44 6 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (42 bp):
TATTTTAAAATTAAATAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:29864237 original size:51 final size:51
Alignment explanation
Indices: 29864171--29864270 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
29864161 TAAAAAAAGT
* *
29864171 ATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAA
1 ATTTAAAAAAAATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAA
*
29864222 ATTTAAAAAAAATTTTAAAATTAAAAAATTTTAAAAAAGTATTTTAAAA
1 ATTTAAAAAAAATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAA
29864271 GTATTTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (51 bp):
ATTTAAAAAAAATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAA
Found at i:29864277 original size:40 final size:38
Alignment explanation
Indices: 29864211--29864290 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 38
29864201 TTAAAAAAGT
29864211 ATTTTAAAAAAATTTAAAAAAAATTTTAAAATTAAAAA
1 ATTTTAAAAAAATTTAAAAAAAATTTTAAAATTAAAAA
* ** *
29864249 ATTTTAAAAAAGTATTTTAAAAGTATTTTAAAGTTAAAAA
1 ATTTTAAAAAA--ATTTAAAAAAAATTTTAAAATTAAAAA
29864289 AT
1 AT
29864291 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 11 0.31
40 25 0.69
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (38 bp):
ATTTTAAAAAAATTTAAAAAAAATTTTAAAATTAAAAA
Found at i:29864336 original size:11 final size:11
Alignment explanation
Indices: 29864320--29864347 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29864310 ATTTATTATT
29864320 CGGGCCGGGCC
1 CGGGCCGGGCC
29864331 CGGGCCGGGCC
1 CGGGCCGGGCC
29864342 CGGGCC
1 CGGGCC
29864348 AAAAAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.46, G:0.54, T:0.00
Consensus pattern (11 bp):
CGGGCCGGGCC
Found at i:29865755 original size:22 final size:22
Alignment explanation
Indices: 29865728--29865773 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29865718 TAAATAACTA
29865728 TTAGTCTATTTTCCTAAATATT
1 TTAGTCTATTTTCCTAAATATT
29865750 TTAGTCTATTTTCCTAAATATT
1 TTAGTCTATTTTCCTAAATATT
29865772 TT
1 TT
29865774 TAATTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (22 bp):
TTAGTCTATTTTCCTAAATATT
Found at i:29869951 original size:8 final size:8
Alignment explanation
Indices: 29869938--29869988 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
29869928 TATAACACCA
29869938 ATTATTAT
1 ATTATTAT
*
29869946 ATTATTAA
1 ATTATTAT
*
29869954 ATTAATAT
1 ATTATTAT
29869962 ATTA-TAT
1 ATTATTAT
29869969 CATTA-TAT
1 -ATTATTAT
29869977 ATT-TTAT
1 ATTATTAT
29869984 ATTAT
1 ATTAT
29869989 CATTAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 12 0.32
8 25 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTATTAT
Found at i:29875163 original size:22 final size:22
Alignment explanation
Indices: 29875135--29875176 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29875125 AAGGACAAAT
* *
29875135 AGAATAAGATAAGATACATAAC
1 AGAATAACATAAAATACATAAC
29875157 AGAATAACATAAAATACATA
1 AGAATAACATAAAATACATA
29875177 CCTCGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.19
Consensus pattern (22 bp):
AGAATAACATAAAATACATAAC
Found at i:29877710 original size:18 final size:19
Alignment explanation
Indices: 29877673--29877714 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29877663 CCTTTCATAA
29877673 TTAAAATAATTTATATTAT
1 TTAAAATAATTTATATTAT
29877692 TTAAATATAATTTAATATT-T
1 TTAAA-ATAATTT-ATATTAT
29877712 TTA
1 TTA
29877715 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAAATAATTTATATTAT
Found at i:29888037 original size:20 final size:20
Alignment explanation
Indices: 29888014--29888053 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29888004 AATGTGTAAT
29888014 CAGAGGCACCAAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
**
29888034 CAGAGGCACTGAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAA
29888054 TCCCGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAA
Found at i:29893489 original size:19 final size:19
Alignment explanation
Indices: 29893465--29893503 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29893455 ATAAATTATC
*
29893465 ATTAGAACTTGCCAAACAT
1 ATTAGAACTTCCCAAACAT
29893484 ATTAGAACTTCCCAAACAT
1 ATTAGAACTTCCCAAACAT
29893503 A
1 A
29893504 CTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (19 bp):
ATTAGAACTTCCCAAACAT
Found at i:29897049 original size:26 final size:26
Alignment explanation
Indices: 29897020--29897085 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
29897010 TTCGACCCAT
* **
29897020 AGCTCATGTGAGCAGGCCCATTTCAC
1 AGCTCGTGTGAGCAGAACCATTTCAC
*
29897046 AGCTCGTGTGAGCAGAATCATTTCAC
1 AGCTCGTGTGAGCAGAACCATTTCAC
29897072 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
29897086 ATGATGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGAACCATTTCAC
Found at i:29908344 original size:25 final size:26
Alignment explanation
Indices: 29908315--29908370 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
29908305 TTAATTAGTA
*
29908315 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
29908339 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
29908365 TAAAAT
1 TAAAAT
29908371 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:29909076 original size:22 final size:19
Alignment explanation
Indices: 29909037--29909078 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
29909027 TGTAAAGTTG
29909037 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
29909056 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
29909078 A
1 A
29909079 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:29926269 original size:40 final size:40
Alignment explanation
Indices: 29926224--29926407 Score: 226
Period size: 40 Copynumber: 4.6 Consensus size: 40
29926214 ATGTGTTTTT
**
29926224 AGGGGTACCGAAGTACAAACAGGGGCATGTGTGTGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
* * *
29926264 AGGGGTACTGAAGTACAAACAGAGGCATGTAAATGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
* * *
29926304 AGGGGTGCCAAAGTACAAAACA-GGGCATGTATGTGCATTC
1 AGGGGTACCGAAGTAC-AAACAGGGGCATGTAAGTGCATTC
* * * * *
29926344 AGGGATATCAAAGTACAAACAGGGGAACGTAAGTGCATTC
1 AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
*
29926384 AGGGGTATCGAAGTACAAACAGGG
1 AGGGGTACCGAAGTACAAACAGGG
29926408 CACATATGTG
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 5 0.04
40 113 0.92
41 5 0.04
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (40 bp):
AGGGGTACCGAAGTACAAACAGGGGCATGTAAGTGCATTC
Found at i:29926358 original size:80 final size:79
Alignment explanation
Indices: 29926224--29926423 Score: 258
Period size: 80 Copynumber: 2.5 Consensus size: 79
29926214 ATGTGTTTTT
* * *
29926224 AGGGGTACCGAAGTACAAACAGGGGCATGTGTGTGCATTCAGGGGTACTGAAGTACAAACAGAGG
1 AGGGGTACCGAAGTACAAACA-GGGCATGTATGTGCATTCAGGGATACTAAAGTACAAACAGAGG
* *
29926289 CATGTAAATGCATTC
65 AACGTAAATGCATTC
* * *
29926304 AGGGGTGCCAAAGTACAAAACAGGGCATGTATGTGCATTCAGGGATA-TCAAAGTACAAACAGGG
1 AGGGGTACCGAAGTAC-AAACAGGGCATGTATGTGCATTCAGGGATACT-AAAGTACAAACAGAG
*
29926368 GAACGTAAGTGCATTC
64 GAACGTAAATGCATTC
* **
29926384 AGGGGTATCGAAGTACAAACAGGGCACATATGTGCATTCA
1 AGGGGTACCGAAGTACAAACAGGGCATGTATGTGCATTCA
29926424 ACAATAATTA
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 23 0.22
80 76 0.73
81 5 0.05
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (79 bp):
AGGGGTACCGAAGTACAAACAGGGCATGTATGTGCATTCAGGGATACTAAAGTACAAACAGAGGA
ACGTAAATGCATTC
Found at i:29926377 original size:20 final size:20
Alignment explanation
Indices: 29926354--29926407 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
29926344 AGGGATATCA
29926354 AAGTACAAACAGGGG-AACG
1 AAGTACAAACAGGGGTAACG
* ** *
29926373 TAAGTGCATTCAGGGGTATCG
1 -AAGTACAAACAGGGGTAACG
29926394 AAGTACAAACAGGG
1 AAGTACAAACAGGG
29926408 CACATATGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.39, C:0.15, G:0.31, T:0.15
Consensus pattern (20 bp):
AAGTACAAACAGGGGTAACG
Found at i:29929604 original size:25 final size:25
Alignment explanation
Indices: 29929576--29929624 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29929566 AGTTAATAAT
29929576 AATT-CTCATTGAGTTT-TTCTTAAAG
1 AATTGCTC-TTGAGTTTCTT-TTAAAG
29929601 AATTGCTCTTGAGTTTCTTTTAAA
1 AATTGCTCTTGAGTTTCTTTTAAA
29929625 AGCTGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (25 bp):
AATTGCTCTTGAGTTTCTTTTAAAG
Found at i:29930896 original size:28 final size:28
Alignment explanation
Indices: 29930833--29930896 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
29930823 CGTGTGCTAA
** *
29930833 GCCGTGTGGTAGCTGTGTGTGACACATG
1 GCCGTGTGGTAGCCATGTGTGACACACG
* *
29930861 ACCATGTGGTAGCCATGTGTGACACACG
1 GCCGTGTGGTAGCCATGTGTGACACACG
29930889 GCCGTGTG
1 GCCGTGTG
29930897 ACAAGTCGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (28 bp):
GCCGTGTGGTAGCCATGTGTGACACACG
Found at i:29941697 original size:13 final size:13
Alignment explanation
Indices: 29941679--29941705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29941669 TTCAAGCACT
29941679 CAGAGAGATGCAG
1 CAGAGAGATGCAG
29941692 CAGAGAGATGCAG
1 CAGAGAGATGCAG
29941705 C
1 C
29941706 CTGACTCTGG
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:0.37, C:0.19, G:0.37, T:0.07
Consensus pattern (13 bp):
CAGAGAGATGCAG
Found at i:29942101 original size:19 final size:18
Alignment explanation
Indices: 29942060--29942103 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
29942050 AAACCTATAA
* *
29942060 AAAATAAATACATTAAGT
1 AAAATAAAAACACTAAGT
*
29942078 TAAATAAAAACTACTAAGT
1 AAAATAAAAAC-ACTAAGT
29942097 AAAATAA
1 AAAATAA
29942104 CCAAAACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATAAAAACACTAAGT
Found at i:29945580 original size:30 final size:30
Alignment explanation
Indices: 29945505--29945701 Score: 127
Period size: 30 Copynumber: 6.6 Consensus size: 30
29945495 GATAGCTTCA
* *
29945505 ACTATCG-ATTATGAAAAGGGATGGTGACG
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* *
29945534 ACCATC-AACAATGAAAAGAGATGGTGACG
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* *
29945563 ACTATCGAACTATGAAAAAAGATGGCT-TCG
1 ACTATCGAACTATGAAAAGAGATGG-TGACG
* * * *
29945593 ACTATTGATCTATGAAAA-AGGATAGCT-TCG
1 ACTATCGAACTATGAAAAGA-GAT-GGTGACG
* * * *
29945623 GCTATC-AATTTATGAAAAGGGATGGTGATG
1 ACTATCGAA-CTATGAAAAGAGATGGTGACG
* * * *
29945653 ACCATCGAACAATGAAAAGAGATCGTGACA
1 ACTATCGAACTATGAAAAGAGATGGTGACG
* * *
29945683 ACCATCAAATTATGAAAAG
1 ACTATCGAACTATGAAAAG
29945702 GGATAGCTTC
Statistics
Matches: 129, Mismatches: 30, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
29 33 0.26
30 92 0.71
31 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (30 bp):
ACTATCGAACTATGAAAAGAGATGGTGACG
Found at i:29945668 original size:60 final size:59
Alignment explanation
Indices: 29945494--29945670 Score: 148
Period size: 60 Copynumber: 3.0 Consensus size: 59
29945484 ATACAGAAAG
* * *
29945494 GGATAGCTTCAACTATCGATTATGAAAAGGGATGGTGACGACCATC-AACAATG-AAAA
1 GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAA
* * * ** * * * *
29945551 GAGAT-GGTGACGACTATCGAACTATGAAAAAAGATGGCT--TCGACTATTGATCTATGAAAAA
1 G-GATAGCT-TCGACTATC-AATTATGAAAAGGGATGG-TGAT-GACCATCGAACAATGAAAAA
*
29945612 GGATAGCTTCGGCTATCAATTTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAA
1 GGATAGCTTCGACTATCAA-TTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAA
29945671 GAGATCGTGA
Statistics
Matches: 87, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
57 3 0.03
58 10 0.11
59 22 0.25
60 44 0.51
61 8 0.09
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (59 bp):
GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAA
Found at i:29945711 original size:120 final size:118
Alignment explanation
Indices: 29945466--29945766 Score: 336
Period size: 120 Copynumber: 2.5 Consensus size: 118
29945456 AATGGAAAGG
* * * ** *
29945466 GATAGCTTCAGCTATCGAA-TA-CAGAAAGGGATAGCTTCAACTATCGATTATGAAAAGGGATGG
1 GATAGCTTCAACTATCGAACTATGA-AAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATGG
* * * *
29945529 TGACGACCATCAACAATGAAAAGAGATGGTGACGACTATCGAACTATGAAAAAA
65 TGACGACCATCAACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
* * * *
29945583 GATGGCTTCGACTATTGATCTATGAAAAAGGATAGCTTCGGCTATCAATTTATGAAAAGGGATGG
1 GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAA-TTATGAAAAGGGATGG
* * **
29945648 TGATGACCATCGAACAATGAAAAGAGATCGTGACAACCATCAAATTATGAAAAGG
65 TGACGACCATC-AACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
* * * * **
29945703 GATAGCTTCAACTGTCGAACTATGAAAAGGGATAACTTCGGTTATCAAATTACAAAAAGGGATG
1 GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATC-AATTATGAAAAGGGATG
29945767 TGTCAAGCAT
Statistics
Matches: 151, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
117 14 0.09
118 21 0.14
119 27 0.18
120 87 0.58
121 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (118 bp):
GATAGCTTCAACTATCGAACTATGAAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATGGT
GACGACCATCAACAATGAAAAGAGATCGTGACAACCATCAAACTATGAAAAAA
Found at i:29955556 original size:42 final size:42
Alignment explanation
Indices: 29955496--29955577 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
29955486 GACTGTTGAC
*
29955496 GCCACACGGCTAAGGACATAGGCGTGTGCCCAAGCCGTGTGA
1 GCCACACGGCTAAAGACATAGGCGTGTGCCCAAGCCGTGTGA
* *
29955538 GCCACACGGGC-AAAGACATAGGCGTGTGTCCAGGCCGTGT
1 GCCACAC-GGCTAAAGACATAGGCGTGTGCCCAAGCCGTGT
29955578 AACTCACTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (42 bp):
GCCACACGGCTAAAGACATAGGCGTGTGCCCAAGCCGTGTGA
Found at i:29960649 original size:17 final size:17
Alignment explanation
Indices: 29960606--29960656 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
29960596 TTGGTAGAGT
*
29960606 GGATAGGAAAATTGGAAA
1 GGATAGAAAAATT-GAAA
29960624 -GAT-GAAAAATTGAAA
1 GGATAGAAAAATTGAAA
*
29960639 GGATAGAAAAATAGAAA
1 GGATAGAAAAATTGAAA
29960656 G
1 G
29960657 AAGGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (17 bp):
GGATAGAAAAATTGAAA
Found at i:29961766 original size:17 final size:18
Alignment explanation
Indices: 29961746--29961796 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
29961736 CCATATTAAA
29961746 TTTTTTAT-ATTATTTAT
1 TTTTTTATAATTATTTAT
*
29961763 TTTTAATATAATTA-TTAT
1 TTTT-TTATAATTATTTAT
*
29961781 TCTTTTATAATTATTT
1 TTTTTTATAATTATTT
29961797 TTTAAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 12 0.43
18 12 0.43
19 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTATAATTATTTAT
Found at i:29976473 original size:21 final size:21
Alignment explanation
Indices: 29976426--29976470 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
29976416 ATATTAGAAC
29976426 ATAAA-TATCGATACCCAACT
1 ATAAATTATCGATACCCAACT
29976446 ATAAATTATCGATA-CCAACT
1 ATAAATTATCGATACCCAACT
*
29976466 TTAAA
1 ATAAA
29976471 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAAATTATCGATACCCAACT
Found at i:29978060 original size:131 final size:131
Alignment explanation
Indices: 29977826--29978389 Score: 738
Period size: 131 Copynumber: 4.3 Consensus size: 131
29977816 AGCGATTGGA
* * * *
29977826 AAATCAACTAACACAAATGAGATTGTTCATGATATTAAATCGAATGAACTTAGGTTGTGATATTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
29977891 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
66 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
29977956 T
131 T
* *
29977957 AAATCAACTAACTCAAATAAGATTGTTCATGATGTTAAATCAAATGAACTTAGTTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
* * * * *
29978022 AATTAGTGAACCTTAACGATATC-ACTTGTGATCTTAAATCATCGAGATGTTTGGAGTAGCGGTA
66 AATCAGTGAACCTTAACGATATCAAC-TGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATC
29978086 TT
130 TT
** ** *
29978088 AAATCAA-TGAACTCAAATAAGATTGTTCACAATATTAAATTGAATGAACTTAGGTTGTAATCTT
1 AAATCAACT-AACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTT
*** ** * *
29978152 AAATCAGTGAACCTTAACGATATTGGCTGCAATCTTAAATCAACAAATTGTTTGGAGTAGC-ACT
65 AAATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGA-T
29978216 CTT
129 CTT
* * * *
29978219 AAATCAGCTAACTAAAATAATATTGTTCATGATATTAAATCAAATGAGCTTAGGTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
* * * * * * * *
29978284 AATCAGCGAATCTCAATGATATCAACTGTGATATTAAATCAGCGAGCTATTTGGAGTAGCGATCT
66 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
29978349 T
131 T
* *
29978350 AAATCAGCTAACTCAAATAAGATTTTTCATGATATATAAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATAT-TAAA
29978390 GTAAACAATA
Statistics
Matches: 370, Mismatches: 56, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
130 3 0.01
131 360 0.97
132 7 0.02
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (131 bp):
AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGGTTGTGATCTTA
AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
T
Found at i:29983892 original size:11 final size:13
Alignment explanation
Indices: 29983872--29983903 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29983862 AATAAATTAA
29983872 TAAAATATCAT-T
1 TAAAATATCATAT
29983884 TAAAA-ATCATAT
1 TAAAATATCATAT
29983896 TAAAATAT
1 TAAAATAT
29983904 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:29992198 original size:72 final size:72
Alignment explanation
Indices: 29992073--29992262 Score: 274
Period size: 72 Copynumber: 2.6 Consensus size: 72
29992063 GTTGAATAAT
* * * * *
29992073 CAGCTTAGAAAAATGCAACAGCAACCTCCTCTCTT-AATGCCGTCCTAAATCCCATGCACACATT
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCT-TTAAATGTCGTCCCAAATCCCATGCACACATT
29992137 AAATTCGG
65 AAATTCGG
* *
29992145 CAGCTTGGAAAAAGGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAGTCCCATGCACACATTA
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAATCCCATGCACACATTA
* *
29992210 CATTTGG
66 AATTCGG
29992217 CAGCTTGGAAAAATGCAGCAGCAACCTTTCTCTTTAAATGTCGTCC
1 CAGCTTGGAAAAATGCAGCAGCAACC-TTCTCTTTAAATGTCGTCC
29992263 ATGTACCTGC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.02
72 85 0.80
73 19 0.18
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (72 bp):
CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGTCGTCCCAAATCCCATGCACACATTA
AATTCGG
Found at i:29996832 original size:14 final size:14
Alignment explanation
Indices: 29996813--29996839 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29996803 ATTCATCTCC
29996813 CATGCATGAATCTA
1 CATGCATGAATCTA
29996827 CATGCATGAATCT
1 CATGCATGAATCT
29996840 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:29997497 original size:33 final size:33
Alignment explanation
Indices: 29997459--29997530 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
29997449 GATTACTCTC
29997459 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
29997492 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
29997525 TCCACT
1 TTCACT
29997531 TTTGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:29999929 original size:72 final size:73
Alignment explanation
Indices: 29999847--29999996 Score: 239
Period size: 72 Copynumber: 2.1 Consensus size: 73
29999837 CTCCTCCCTT
* *
29999847 AATGCCATCCCAAATCCCATGCACACATTAAATTTGGCAGCTTGGAAAAAGGCAACAGCAAC-CT
1 AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
29999911 TCTCTTTA
66 TCTCTTTA
* * * *
29999919 AATGCCATCCCAAGTCCCATGCACACATTAAATTCGGCAGCTTGAAAAAATGCAACAGGAACTTT
1 AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
29999984 TCTCTTTA
66 TCTCTTTA
29999992 AATGC
1 AATGC
29999997 TGTCCATGTA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 57 0.80
73 14 0.20
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (73 bp):
AATGCCATCCCAAATCCCATGCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
TCTCTTTA
Found at i:30005195 original size:74 final size:74
Alignment explanation
Indices: 30005051--30005188 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 74
30005041 AAATTGACAA
* * * *
30005051 AATTTGCACCCAGCGCTAGTCGGATAAACTGATGAATAATTAGTGAGCCCAGCTCTAGTTGGATA
1 AATTTGCACCCAACACTAGTCGGATAAACTGATGAATAATTAATAAGCCCAGCTCTAGTTGGATA
30005116 TACCAATGG
66 TACCAATGG
* * * *
30005125 AATTTGCGCCCAACACTAGTTGGATGAACTGATGAATTAA-TAATAAGCCTAGCTCTAGTTGGAT
1 AATTTGCACCCAACACTAGTCGGATAAACTGATGAA-TAATTAATAAGCCCAGCTCTAGTTGGAT
30005189 TAACCAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 52 0.95
75 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (74 bp):
AATTTGCACCCAACACTAGTCGGATAAACTGATGAATAATTAATAAGCCCAGCTCTAGTTGGATA
TACCAATGG
Found at i:30005453 original size:22 final size:22
Alignment explanation
Indices: 30005425--30005483 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
30005415 TTTATTGTTC
30005425 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
30005447 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
30005469 AGCCATGAGAGCTTA
1 AAACATGAGAGCTTA
30005484 CCATTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:30009447 original size:58 final size:58
Alignment explanation
Indices: 30009332--30009447 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
30009322 TGTGGCGTTT
* * * * *
30009332 GCTATACCTTTGGTTCTTATCTCGTTAGATAGTGGGTCAAGGTTTATTTGTTGATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
30009390 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
1 GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
30009448 ACGTTTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (58 bp):
GCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGCTAATTTC
Found at i:30012558 original size:26 final size:24
Alignment explanation
Indices: 30012488--30012560 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 24
30012478 AAGTTTAAGC
30012488 GAGCC-ATATCGGGAAGCTCATGA
1 GAGCCAATATCGGGAAGCTCATGA
*
30012511 GAGCCAATTAATCAGGAAGCTCATGAA
1 GAGCCAA-T-ATCGGGAAGCTCATG-A
*
30012538 GAGCCATATATCGGGACGCTCAT
1 GAGCCA-ATATCGGGAAGCTCAT
30012561 AAAAGCTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 5 0.12
24 1 0.02
25 1 0.02
26 26 0.62
27 8 0.19
28 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCATGA
Found at i:30013026 original size:21 final size:21
Alignment explanation
Indices: 30013000--30013041 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30012990 TAAATTTAAC
30013000 TCAATTCAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
30013021 TCAATTTAATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
30013042 CTTAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:30014873 original size:21 final size:22
Alignment explanation
Indices: 30014849--30014909 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
30014839 TCGATTTTAC
30014849 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
30014870 CTCACTCTTTT-TTTTCTTTTTT
1 CTCACTCTTTTCTTTT-TGTTTT
30014892 CT-A-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
30014910 CTTTTGCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 9 0.26
21 15 0.43
22 11 0.31
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:30014898 original size:20 final size:22
Alignment explanation
Indices: 30014849--30014909 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
30014839 TCGATTTTAC
*
30014849 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTTTTTTTGTTTT
30014870 CTCACTCTTTTTTTTCTT-TTTT
1 CTCACTCTTTTTTTT-TTGTTTT
*
30014892 CT-A-TCTTTTCTTTTTGTT
1 CTCACTCTTTTTTTTTTGTT
30014910 CTTTTGCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 7 0.20
22 13 0.37
23 2 0.06
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (22 bp):
CTCACTCTTTTTTTTTTGTTTT
Found at i:30014906 original size:22 final size:20
Alignment explanation
Indices: 30014849--30014906 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
30014839 TCGATTTTAC
*
30014849 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTCTTTT
30014870 CTCACTCTTT-TTTTTCTTTT
1 CTCACT-TTTCTTTTTCTTTT
*
30014890 TTCTATCTTTTCTTTTT
1 CTC-A-CTTTTCTTTTT
30014907 GTTCTTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 12 0.39
21 12 0.39
22 7 0.23
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (20 bp):
CTCACTTTTCTTTTTCTTTT
Found at i:30016141 original size:12 final size:13
Alignment explanation
Indices: 30016124--30016156 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
30016114 TTAAACTAAG
30016124 TAAATAAATAA-A
1 TAAATAAATAATA
30016136 TAAATAAATAATA
1 TAAATAAATAATA
*
30016149 AAAATAAA
1 TAAATAAA
30016157 ACTTTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAATA
Found at i:30016702 original size:23 final size:22
Alignment explanation
Indices: 30016651--30016702 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
30016641 CCTCGTCTTT
*
30016651 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
30016673 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
30016696 TTCTTTT
1 TTCTTTT
30016703 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:30026028 original size:18 final size:20
Alignment explanation
Indices: 30025991--30026033 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
30025981 ACATGTATAA
30025991 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
30026011 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
30026029 GTATG
1 GTATG
30026034 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:30027696 original size:50 final size:46
Alignment explanation
Indices: 30027623--30027786 Score: 174
Period size: 44 Copynumber: 3.6 Consensus size: 46
30027613 TTTTAGCCTA
* * *
30027623 CTCCACTGCAACTTCAAGTAGATAAAACTTGTCATGGTAAATTTAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGA--T-T-ATGGTAAATTCAATCTG
* * **
30027673 CTCCACTGCAACTTCAGGGAGATAGGATTA--GTAGCTTCAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
* * *
30027717 CTCCACTGCAACTTCAGGGAGATAAGA-T-TGGTATATTCAACCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
30027761 CTCCACTGCAACTTCAAGGAGATAAG
1 CTCCACTGCAACTTCAAGGAGATAAG
30027787 GTTTGATATG
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 73 0.73
46 1 0.01
47 1 0.01
48 1 0.01
50 23 0.23
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (46 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTATGGTAAATTCAATCTG
Done.