Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 162 of 344
Found at i:54118493 original size:9 final size:9
Alignment explanation
Indices: 54118457--54118616 Score: 81
Period size: 9 Copynumber: 16.7 Consensus size: 9
54118447 GACATATGGA
54118457 AAAAATTAT
1 AAAAATTAT
54118466 AAAAA--AT
1 AAAAATTAT
*
54118473 AAAAATCAAT
1 AAAAAT-TAT
*
54118483 AAAAGTTAT
1 AAAAATTAT
54118492 AAAAATTATT
1 AAAAATTA-T
**
54118502 AAATTTTAAT
1 AAAAATT-AT
*
54118512 AAAAAATATTT
1 -AAAAAT-TAT
*
54118523 AAAATTTAT
1 AAAAATTAT
* *
54118532 TAAAATTAGAA
1 AAAAATT--AT
54118543 AAAAATTAT
1 AAAAATTAT
*
54118552 AAAAATCAT
1 AAAAATTAT
*
54118561 AAAAAATATAA
1 -AAAAAT-TAT
*
54118572 AAAAATTGT
1 AAAAATTAT
*
54118581 AGAATATTAT
1 A-AAAATTAT
*
54118591 AAAAATCAT
1 AAAAATTAT
54118600 AAACAAATTAT
1 -AA-AAATTAT
54118611 AAAAAT
1 AAAAAT
54118617 GCATAAAAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
7 7 0.06
9 42 0.38
10 42 0.38
11 20 0.18
12 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:54118518 original size:21 final size:21
Alignment explanation
Indices: 54118482--54118536 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
54118472 TAAAAATCAA
* *
54118482 TAAAAGTT-ATAAAAATTA-T
1 TAAAATTTAATAAAAAATATT
*
54118501 TAAATTTTAATAAAAAATATT
1 TAAAATTTAATAAAAAATATT
*
54118522 TAAAATTTATTAAAA
1 TAAAATTTAATAAAA
54118537 TTAGAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 6 0.21
20 9 0.31
21 14 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAATTTAATAAAAAATATT
Found at i:54118546 original size:20 final size:20
Alignment explanation
Indices: 54118523--54118626 Score: 61
Period size: 20 Copynumber: 5.2 Consensus size: 20
54118513 AAAAATATTT
* *
54118523 AAAATTTATTAAAATTAGAA
1 AAAATTTATAAAAATCAGAA
* *
54118543 AAAAATTATAAAAATCATAA
1 AAAATTTATAAAAATCAGAA
* * * *
54118563 AAAATATAAAAAAAT-TG-T
1 AAAATTTATAAAAATCAGAA
* *
54118581 AGAATATTATAAAAATCATAA
1 AAAAT-TTATAAAAATCAGAA
*
54118602 ACAAA-TTATAAAAATGCATAA
1 A-AAATTTATAAAAAT-CAGAA
54118623 AAAA
1 AAAA
54118627 AGGTCCTTTA
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
18 4 0.06
19 8 0.13
20 41 0.66
21 7 0.11
22 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATTTATAAAAATCAGAA
Found at i:54118557 original size:30 final size:30
Alignment explanation
Indices: 54118456--54118625 Score: 106
Period size: 30 Copynumber: 5.8 Consensus size: 30
54118446 TGACATATGG
*
54118456 AAAAAATTATAAAAA---ATAAAAATCA-A
1 AAAAAATTATAAAAATTTATAAAAATTATA
* * **
54118482 TAAAAGTTATAAAAA-TTATTAAATTTTAATA
1 AAAAAATTATAAAAATTTA-TAAAAATT-ATA
* *
54118513 AAAAATATT-T-AAAATTTATTAAAATTAGA
1 AAAAA-ATTATAAAAATTTATAAAAATTATA
* *
54118542 AAAAAATTATAAAAA-TCATAAAAAATATA
1 AAAAAATTATAAAAATTTATAAAAATTATA
* * *
54118571 AAAAAATTGT-AGAATATTATAAAAATCATA
1 AAAAAATTATAAAAAT-TTATAAAAATTATA
* **
54118601 AACAAATTATAAAAATGCATAAAAA
1 AAAAAATTATAAAAATTTATAAAAA
54118626 AAGGTCCTTT
Statistics
Matches: 107, Mismatches: 25, Indels: 20
0.70 0.16 0.13
Matches are distributed among these distances:
26 13 0.12
28 7 0.07
29 32 0.30
30 40 0.37
31 13 0.12
32 2 0.02
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAAATTATAAAAATTTATAAAAATTATA
Found at i:54118625 original size:11 final size:10
Alignment explanation
Indices: 54118542--54118626 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
54118532 TAAAATTAGA
*
54118542 AAAAAATTAT
1 AAAAAATCAT
54118552 -AAAAATCAT
1 AAAAAATCAT
54118561 AAAAAAT-AT
1 AAAAAATCAT
**
54118570 AAAAAAATTGT
1 -AAAAAATCAT
* * *
54118581 AGAATATTAT
1 AAAAAATCAT
54118591 -AAAAATCAT
1 AAAAAATCAT
*
54118600 AAACAAATTAT
1 AAA-AAATCAT
54118611 -AAAAATGCAT
1 AAAAAAT-CAT
54118621 AAAAAA
1 AAAAAA
54118627 AGGTCCTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
9 20 0.34
10 26 0.45
11 12 0.21
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.25
Consensus pattern (10 bp):
AAAAAATCAT
Found at i:54118842 original size:38 final size:36
Alignment explanation
Indices: 54118799--54118928 Score: 104
Period size: 38 Copynumber: 3.4 Consensus size: 36
54118789 TAGTATGATA
54118799 ATTTTTATATATTTTTTATGAATTTTATATTTCTTTAC
1 ATTTTTATATATTTTTTAT-AATTTTATATTT-TTTAC
* * *
54118837 ATTTTTTTATAATTTTCTTACAATTTTATAAATTTTTT-T
1 ATTTTTATAT-ATTTT-TTATAATTTTAT--ATTTTTTAC
* **
54118876 ATTTTT-TCTATATTACTATATATTTTATATTTTTTAC
1 ATTTTTATATAT-TTTTTATA-ATTTTATATTTTTTAC
54118913 GATTTTTATA-ATTTTT
1 -ATTTTTATATATTTTT
54118929 CCCCTTTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
36 7 0.10
37 7 0.10
38 28 0.39
39 20 0.28
40 6 0.08
41 4 0.06
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (36 bp):
ATTTTTATATATTTTTTATAATTTTATATTTTTTAC
Found at i:54118857 original size:21 final size:22
Alignment explanation
Indices: 54118821--54118876 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 22
54118811 TTTTTATGAA
*
54118821 TTTTAT-A-TTTCTTTACATTT
1 TTTTATAATTTTCTTTACAATT
54118841 TTTTATAATTTTC-TTACAATT
1 TTTTATAATTTTCTTTACAATT
*
54118862 TTATA-AATTTT-TTTA
1 TTTTATAATTTTCTTTA
54118877 TTTTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 15 0.48
21 12 0.39
22 4 0.13
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATAATTTTCTTTACAATT
Found at i:54119290 original size:91 final size:90
Alignment explanation
Indices: 54119137--54119429 Score: 327
Period size: 91 Copynumber: 3.2 Consensus size: 90
54119127 TTCAAATATT
*
54119137 CAATTGAGTGC-AAAAAAAAA-A-TAGAGGCTTAATTGCTTTGTTTGAAAAAGTTTGAA--GTTT
1 CAATTGAGTGCAAAAAAAAAAGAGTAGAGGCTTAATT-CTTTTTTTGAAAAAGTTT-AAGGGTTT
54119197 TTTTATACATTATGAAATCTAAAGTACC
64 TTTTATACATTATGAAAT-TAAAGTACC
*
54119225 CAATTGAGTGCAAAAAAAAAAGAGTAGGGGCTTAATTACTTTTTTTGAAAAAGTTTAAGGGTTTT
1 CAATTGAGTGCAAAAAAAAAAGAGTAGAGGCTTAATT-CTTTTTTTGAAAAAGTTTAAGGGTTTT
*
54119290 TTTGATACATTATGAAAATTAAAGTACT
65 TTT-ATACATTATG-AAATTAAAGTACC
* * *
54119318 CAATTGAGTG-AAAAAAAATAGAGGCTTA-ATGG-TT--TTTTTTTTTTGAAAAAGTTTGAGGGA
1 CAATTGAGTGCAAAAAAAAAAGA-G--TAGA-GGCTTAATTCTTTTTTTGAAAAAGTTTAAGGG-
54119378 TTTTTTTTATACATTATGAAAGTTAAAGTACC
61 -TTTTTTTATACATTATGAAA-TTAAAGTACC
**
54119410 CAATTGAGTATAAAAAAAAA
1 CAATTGAGTGCAAAAAAAAA
54119430 GATACTTTTT
Statistics
Matches: 179, Mismatches: 11, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
88 11 0.06
89 9 0.05
90 3 0.02
91 53 0.30
92 49 0.27
93 44 0.25
94 6 0.03
95 4 0.02
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (90 bp):
CAATTGAGTGCAAAAAAAAAAGAGTAGAGGCTTAATTCTTTTTTTGAAAAAGTTTAAGGGTTTTT
TTATACATTATGAAATTAAAGTACC
Found at i:54123225 original size:23 final size:23
Alignment explanation
Indices: 54123199--54123247 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
54123189 TTGGATTTGT
54123199 TTCCAACTTGATTTGTTTAAACA
1 TTCCAACTTGATTTGTTTAAACA
54123222 TTCCAACTTGATTTGTTTAAACA
1 TTCCAACTTGATTTGTTTAAACA
54123245 TTC
1 TTC
54123248 TTTTAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (23 bp):
TTCCAACTTGATTTGTTTAAACA
Found at i:54133061 original size:2 final size:2
Alignment explanation
Indices: 54133054--54133333 Score: 117
Period size: 2 Copynumber: 140.0 Consensus size: 2
54133044 TTAAAGAATG
* * *
54133054 AT AT AT AT CAT AT CT AT -T AT AT AT CT AT AT AT A- ACT TT CA-
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT
* * * *
54133094 AT A- AT AT AT AT AT CT AT CT AT AT AT AT GAC AT AT AT GAT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT
* *
54133137 AT AT AT AT AT AT GAT AT AT AT -T AT CT AT -T AT AT CAT AT CT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* * * *
54133179 AT AT AT AT -T AT -T GAA AGT -T AT AT AT AG AT AG AT AG AT AT AT
1 AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
54133220 AT -T AT -T GAA AGT -T AT AT AT AT GAT AT AT AT AT -T AT CT AT
1 AT AT AT AT -AT A-T AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
* *
54133259 -T AT AT AT CAT AT AT AT A- ACT TT CA- AT A- AT AT AT AT AT CT
1 AT AT AT AT -AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT
* *
54133298 AT AT AT AT AT AT GAC AT AT AT GAT CT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT
54133334 TGAAATGATG
Statistics
Matches: 206, Mismatches: 38, Indels: 68
0.66 0.12 0.22
Matches are distributed among these distances:
1 17 0.08
2 173 0.84
3 16 0.08
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:54133170 original size:9 final size:11
Alignment explanation
Indices: 54133057--54133184 Score: 60
Period size: 11 Copynumber: 11.9 Consensus size: 11
54133047 AAGAATGATA
54133057 TATATCATATC
1 TATATCATATC
54133068 TATTAT-ATATC
1 TA-TATCATATC
*
54133079 TATAT-ATAAC
1 TATATCATATC
* * *
54133089 TTTCAATAATATA
1 TAT--ATCATATC
54133102 TATATC-TATC
1 TATATCATATC
54133112 TATAT-ATATGAC
1 TATATCATAT--C
54133124 -ATAT-ATGATC
1 TATATCAT-ATC
*
54133134 TATAT-ATATA
1 TATATCATATC
* *
54133144 TATATGATATA
1 TATATCATATC
54133155 TATTATC-TAT-
1 TA-TATCATATC
54133165 TATATCATATC
1 TATATCATATC
54133176 TATAT-ATAT
1 TATATCATAT
54133185 ATTATTGAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 27
0.73 0.07 0.21
Matches are distributed among these distances:
9 4 0.04
10 37 0.39
11 38 0.40
12 11 0.12
13 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATCATATC
Found at i:54133262 original size:23 final size:23
Alignment explanation
Indices: 54133236--54133318 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
54133226 GAAAGTTATA
54133236 TATATGATATATATATTATCTAT
1 TATATGATATATATATTATCTAT
*
54133259 TATAT-ATCATATATA-TAACT-T
1 TATATGAT-ATATATATTATCTAT
* *
54133280 TCA-ATAATATATATATCTATATAT
1 T-ATATGATATATATAT-TATCTAT
*
54133304 ATATATGACATATAT
1 -TATATGATATATAT
54133319 GATCTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
21 11 0.23
22 9 0.19
23 15 0.32
24 2 0.04
25 10 0.21
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATGATATATATATTATCTAT
Found at i:54133295 original size:25 final size:26
Alignment explanation
Indices: 54133233--54133334 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 26
54133223 ATTGAAAGTT
* *
54133233 ATATATATGATATATATATTATCTATT
1 ATATATAT-ATATATATATTATCAATA
54133260 ATATATCATATATATA-ACTT-TCAATA
1 ATATAT-ATATATATATA-TTATCAATA
*
54133286 ATATATATATCTATATATATATATGACAT-
1 ATATATATA--TATATATAT-TATCA-ATA
*
54133315 ATATGATCTATATATATATT
1 ATAT-ATATATATATATATT
54133335 GAAATGATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
25 3 0.05
26 11 0.18
27 23 0.37
28 13 0.21
29 6 0.10
30 6 0.10
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (26 bp):
ATATATATATATATATATTATCAATA
Found at i:54133295 original size:94 final size:93
Alignment explanation
Indices: 54133051--54133333 Score: 271
Period size: 94 Copynumber: 3.0 Consensus size: 93
54133041 TTATTAAAGA
**
54133051 ATGATATATATCA-TATCTATTATATATC-TATATATAACTTTCAATAATATATATATCTATCTA
1 ATGATATATAT-ATTATCTATTATATATCATATATATAACTTTCAATAATATATATA--TATAGA
* *
54133114 TATATATGACATATATGATCTATATATATAT
63 TAGATATGACATATATGATCTAAATATATAT
* *
54133145 AT-ATGATATATATTATCTATTATATCAT-ATCTATATATA-TATT-ATTGAA-AGT-TATATAT
1 ATGAT-ATATATATTATCTATTATAT-ATCATATATATA-ACT-TTCAAT-AATA-TATATATAT
* *
54133204 AGATAGATA-GATATATATTAT-TGAAAGTTATATAT
60 AGATAGATATGACATATATGATCT-AAA--TATATAT
*
54133239 ATGATATATATATTATCTATTATATATCATATATATAACTTTCAATAATATATATATCTATATAT
1 ATGATATATATATTATCTATTATATATCATATATATAACTTTCAATAATATATATA--TATAGAT
* *
54133304 ATATATGACATATATGATCTATATATATAT
64 AGATATGACATATATGATCTAAATATATAT
54133334 TGAAATGATG
Statistics
Matches: 153, Mismatches: 15, Indels: 41
0.73 0.07 0.20
Matches are distributed among these distances:
91 1 0.01
92 12 0.08
93 20 0.13
94 65 0.42
95 26 0.17
96 16 0.10
97 12 0.08
98 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (93 bp):
ATGATATATATATTATCTATTATATATCATATATATAACTTTCAATAATATATATATATAGATAG
ATATGACATATATGATCTAAATATATAT
Found at i:54147548 original size:11 final size:11
Alignment explanation
Indices: 54147532--54147557 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54147522 GACCACACTC
54147532 ACACACAATTG
1 ACACACAATTG
54147543 ACACACAATTG
1 ACACACAATTG
54147554 ACAC
1 ACAC
54147558 TAATTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (11 bp):
ACACACAATTG
Found at i:54155465 original size:93 final size:93
Alignment explanation
Indices: 54155353--54155524 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
54155343 CGCCCATAAG
*
54155353 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
*
54155417 AATGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
54155446 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54155511 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54155525 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54155519 original size:46 final size:46
Alignment explanation
Indices: 54155346--54155521 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
54155336 TGTAACCCGC
* *
54155346 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * *
54155392 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
54155442 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54155485 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
54155522 TGCTCAATCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54163040 original size:93 final size:93
Alignment explanation
Indices: 54162928--54163099 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
54162918 CGCCCATGAG
*
54162928 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
54162992 AAAGAGTTCGGATGCCTAGTTACATCTCA
65 AAAGAGTTCGGATGCCTAGTTACATCTCA
*
54163021 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
54163086 ACGAGTTCGGATGC
66 AAGAGTTCGGATGC
54163100 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
AAGAGTTCGGATGCCTAGTTACATCTCA
Found at i:54163087 original size:46 final size:46
Alignment explanation
Indices: 54162929--54163096 Score: 193
Period size: 46 Copynumber: 3.6 Consensus size: 46
54162919 GCCCATGAGC
* *
54162929 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGT
* * * *
54162975 GAACTCGGACTCAACTCAAAGAGTTCGGATGCCTAGTT-ACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGT
54163022 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
54163068 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
54163097 TGCTCAATCA
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 53 0.52
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
Found at i:54170234 original size:68 final size:65
Alignment explanation
Indices: 54170022--54170272 Score: 201
Period size: 68 Copynumber: 3.8 Consensus size: 65
54170012 ATAGTTCGGT
* *
54170022 TCTCTTGTACACATGGTGAACACTCAGTACCACCCATGTGACCTAGC--CA-AT-TTATCTCGTA
1 TCTCTTGTACACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATATATT-TCTCGTA
54170083 GC
64 GC
* * * * *
54170085 TCTCTTGT-CTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATA--TCCC
1 TCTCTTGTAC-ACATGGTG---TACA-CTAGTACCACCCATGCGACCTAGCTACATATATTTCTC
54170147 GTAGC
61 GTAGC
** * *
54170152 TCTCTTGTTTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATATTGTCTTGT
1 TCTCTTGTACACATGGTGTACAC-TAGTACCACCCATGCGACCTAGCTACAT-ATATT-TCTCGT
54170217 AGC
63 AGC
* * * ** *
54170220 TCTCTTGTACACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 TCTCTTGTACACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATA
54170273 CTATCTGTAT
Statistics
Matches: 148, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
62 1 0.01
63 17 0.11
64 27 0.18
65 3 0.02
66 20 0.14
67 28 0.19
68 50 0.34
69 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (65 bp):
TCTCTTGTACACATGGTGTACACTAGTACCACCCATGCGACCTAGCTACATATATTTCTCGTAGC
Found at i:54172046 original size:15 final size:15
Alignment explanation
Indices: 54172026--54172056 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54172016 CAAATAGGGA
54172026 TTTTATTTGTTATTT
1 TTTTATTTGTTATTT
*
54172041 TTTTATTTTTTATTT
1 TTTTATTTGTTATTT
54172056 T
1 T
54172057 CTTTCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTATTTGTTATTT
Found at i:54179317 original size:40 final size:39
Alignment explanation
Indices: 54179280--54179449 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 39
54179270 GCTACTCGTT
* *
54179280 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
54179320 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
* *
54179360 CAAATGCCGTCGGGACTTAACCCTGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGTTTAGTAACTCGCA
* * * *
54179400 CCAATTCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
54179439 CAAATGCCTTC
1 CAAATGCCTTC
54179450 AGATCTTAGT
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 82 0.71
41 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:54179489 original size:79 final size:78
Alignment explanation
Indices: 54179306--54179504 Score: 184
Period size: 79 Copynumber: 2.5 Consensus size: 78
54179296 ATAGCCCGGT
* * *
54179306 TATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCGTC
1 TATAGTAACTAGCACAAA-GCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCGTC
* **
54179371 GGGACTTAACCCTGA
64 GAGACTTAACCCAAA
* * ** *
54179386 TTTAGTAACTCGCACCAATTCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-
1 TATAGTAACTAGCA-CAAAGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCGTCG
**
54179450 AGATCTTAGTCCAAA
65 AGA-CTTAACCCAAA
* * * *
54179465 TATGGTCACTTAGCACAAAGCCTTCGAGCCTTCGCCCGGA
1 TATAGTAAC-TAGCACAAAGCCTTCG-GGCTTAGCCCGGA
54179505 CATCATTCGA
Statistics
Matches: 96, Mismatches: 19, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
78 2 0.02
79 55 0.57
80 36 0.38
81 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (78 bp):
TATAGTAACTAGCACAAAGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCGTCGA
GACTTAACCCAAA
Found at i:54187692 original size:119 final size:120
Alignment explanation
Indices: 54187486--54187708 Score: 303
Period size: 119 Copynumber: 1.9 Consensus size: 120
54187476 TACTCGTTCA
*
54187486 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
54187551 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
**
54187606 AATGCCTTC-GGA-ATTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 AATGCCTTCGGGACA-TAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * *
54187667 GATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
63 GATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
54187709 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
118 5 0.05
119 69 0.76
120 17 0.19
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:54187708 original size:40 final size:40
Alignment explanation
Indices: 54187465--54187708 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
54187455 TGGAATTTAA
** *
54187465 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54187505 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54187545 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54187585 CCGGATTTAGTAACTCGCACCAATGCCTTC-GGAATTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54187624 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54187664 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54187704 CCGGA
1 CCGGA
54187709 CATCATTCGA
Statistics
Matches: 180, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
39 38 0.21
40 130 0.72
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54191427 original size:13 final size:13
Alignment explanation
Indices: 54191411--54191436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54191401 AATTAAAATT
54191411 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
54191424 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
54191437 CCTTACCGGA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:54191812 original size:13 final size:13
Alignment explanation
Indices: 54191790--54191841 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
54191780 TGTTTGACAA
*
54191790 ATTTCTTAAAAAT
1 ATTTCATAAAAAT
*
54191803 ATTTCATAAAAGTT
1 ATTTCATAAAA-AT
* *
54191817 GTTTTCTTAAAAAT
1 -ATTTCATAAAAAT
54191831 ATTTCATAAAA
1 ATTTCATAAAA
54191842 GTTGTTTTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 19 0.63
14 2 0.07
15 9 0.30
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (13 bp):
ATTTCATAAAAAT
Found at i:54191823 original size:28 final size:28
Alignment explanation
Indices: 54191791--54191850 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
54191781 GTTTGACAAA
54191791 TTTCTTAAAAATATTTCATAAAAGTTGT
1 TTTCTTAAAAATATTTCATAAAAGTTGT
54191819 TTTCTTAAAAATATTTCATAAAAGTTGT
1 TTTCTTAAAAATATTTCATAAAAGTTGT
54191847 TTTC
1 TTTC
54191851 AAGGAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTCTTAAAAATATTTCATAAAAGTTGT
Found at i:54191827 original size:15 final size:15
Alignment explanation
Indices: 54191804--54191851 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
54191794 CTTAAAAATA
54191804 TTTCATAAAAGTTGT
1 TTTCATAAAAGTTGT
* * *
54191819 TTTCTTAAAA-AT-A
1 TTTCATAAAAGTTGT
54191832 TTTCATAAAAGTTGT
1 TTTCATAAAAGTTGT
54191847 TTTCA
1 TTTCA
54191852 AGGAAACAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 9 0.36
14 2 0.08
15 14 0.56
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (15 bp):
TTTCATAAAAGTTGT
Found at i:54192287 original size:15 final size:14
Alignment explanation
Indices: 54192257--54192290 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
54192247 ACGTAAATAA
54192257 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
54192270 TATTATTTTAAAATT
1 TATTATTTTAAAA-T
54192285 TATTAT
1 TATTAT
54192291 CAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:54192370 original size:38 final size:35
Alignment explanation
Indices: 54192306--54192421 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 35
54192296 TAAAATTGAA
*
54192306 ATATTAAATAATTTATTAAAAT-AATAAATTATATTAATT
1 ATATT-AATAATTTATT-ATATGAATAAATTATA--AA-T
*
54192345 ATATTAATAGTTTATTATATGAATAAA-TATAAAT
1 ATATTAATAATTTATTATATGAATAAATTATAAAT
* *
54192379 A-ATTAATAATTTTTTATATGATTAAA-TATAAAT
1 ATATTAATAATTTATTATATGAATAAATTATAAAT
54192412 AT-TTAATAAT
1 ATATTAATAAT
54192422 ATAAATTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
33 38 0.54
34 2 0.03
35 2 0.03
37 7 0.10
38 16 0.23
39 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
ATATTAATAATTTATTATATGAATAAATTATAAAT
Found at i:54196573 original size:37 final size:37
Alignment explanation
Indices: 54196523--54196601 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54196513 TTATTACGAA
* * *
54196523 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54196560 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54196597 GTCTT
1 GTCTT
54196602 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54202161 original size:38 final size:38
Alignment explanation
Indices: 54202117--54202220 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 38
54202107 GGCTTAAAGA
* *
54202117 CCTGCAGGCTATATGCTAGAATTATATCCAGGTTAAAT
1 CCTGCAGGCTATGTGCTAGTATTATATCCAGGTTAAAT
* *
54202155 CTTGCAGGCT-TCGTGCTGGTATTATATCCAGGTTAAAT
1 CCTGCAGGCTAT-GTGCTAGTATTATATCCAGGTTAAAT
*
54202193 CCCGCAGGCCTA-GTGCTAGTATTATATC
1 CCTGCAGG-CTATGTGCTAGTATTATATC
54202221 TAACTTTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
37 1 0.02
38 53 0.95
39 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (38 bp):
CCTGCAGGCTATGTGCTAGTATTATATCCAGGTTAAAT
Found at i:54202249 original size:40 final size:38
Alignment explanation
Indices: 54202130--54202249 Score: 114
Period size: 38 Copynumber: 3.1 Consensus size: 38
54202120 GCAGGCTATA
* * * **
54202130 TGCTAGAATTATATCCAGGTTAAATCTTGCAGGCTTCG
1 TGCTAGTATTATATCAACGTTAAATCCCGCAGGCTTCG
* * * * *
54202168 TGCTGGTATTATATCCAGGTTAAATCCCGCAGGCCTAG
1 TGCTAGTATTATATCAACGTTAAATCCCGCAGGCTTCG
* *
54202206 TGCTAGTATTATATCTAACTTTAAAGTCCCGTAGGCTTCG
1 TGCTAGTATTATATC-AACGTTAAA-TCCCGCAGGCTTCG
54202246 TGCT
1 TGCT
54202250 GGTGTTATGT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 46 0.69
39 6 0.09
40 15 0.22
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (38 bp):
TGCTAGTATTATATCAACGTTAAATCCCGCAGGCTTCG
Found at i:54203534 original size:60 final size:60
Alignment explanation
Indices: 54203409--54203543 Score: 139
Period size: 60 Copynumber: 2.2 Consensus size: 60
54203399 GAGTTAACTG
* * * *
54203409 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATGAGAGTATACTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGTACGAGAGTATACTA
** * * *
54203470 GGCCTAGCCCATATCGGTATCAATTTGGGCCGTAGCCCTATTACAAGT-CGAGA-TATATTA
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTAC-AGTACGAGAGTATACTA
*
54203530 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
54203544 TAACACAGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
60 47 0.76
61 12 0.19
62 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (60 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGTACGAGAGTATACTA
Found at i:54203589 original size:19 final size:19
Alignment explanation
Indices: 54203548--54203590 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54203538 CCATATTAAC
* *
54203548 ACAGTTGGGCCCATTCAAT
1 ACAGTTGGGCCCATACAAA
54203567 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCAT-ACAAA
54203586 ACAGT
1 ACAGT
54203591 CTCATATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (19 bp):
ACAGTTGGGCCCATACAAA
Found at i:54207664 original size:18 final size:18
Alignment explanation
Indices: 54207643--54207686 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
54207633 TGCTCCACCG
*
54207643 CCTAAACCTCCTGG-TCCA
1 CCTAAACCTCC-GGCCCCA
54207661 CCTAAACCTCCGGCCCCA
1 CCTAAACCTCCGGCCCCA
54207679 CCTAAACC
1 CCTAAACC
54207687 GCCGAGACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.25, C:0.50, G:0.09, T:0.16
Consensus pattern (18 bp):
CCTAAACCTCCGGCCCCA
Found at i:54211599 original size:11 final size:11
Alignment explanation
Indices: 54211572--54211614 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
54211562 TTGCATTAAA
*
54211572 AAAATATATAC
1 AAAATATATAT
*
54211583 ATAATATATAT
1 AAAATATATAT
*
54211594 AAAATACATAT
1 AAAATATATAT
*
54211605 AACATATATA
1 AAAATATATA
54211615 CGTATTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATATATAT
Found at i:54212135 original size:12 final size:12
Alignment explanation
Indices: 54212099--54212140 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54212089 ATGTATATAT
54212099 AAAGAAAGAAAA
1 AAAGAAAGAAAA
* *
54212111 AAACAACACAAAA
1 AAAGAA-AGAAAA
54212124 AAAGAAAGAAAA
1 AAAGAAAGAAAA
54212136 AAAGA
1 AAAGA
54212141 TTCGAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:54213547 original size:74 final size:74
Alignment explanation
Indices: 54213246--54213675 Score: 530
Period size: 74 Copynumber: 5.7 Consensus size: 74
54213236 GTGATCTGAA
54213246 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
*
54213311 GCATGTGAAC-CGAG
63 GCATGT---CTTGAG
* *
54213325 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAACAGAAATTGAAAATACCTCAG
*
54213390 CGTGTCTTGAG
64 CATGTCTTGAG
** * * * * *
54213401 GCTCAACTCATTTCTCACAAT-TAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGCA
**
54213463 TGTCCCGAG
66 TGTCTTGAG
*
54213472 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
54213536 ATGTCTTGAG
65 ATGTCTTGAG
** * * *
54213546 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTACAACAGAAATTGAAATTACCTCAGCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGCA
54213611 TGT-TCTGAG
66 TGTCT-TGAG
* *
54213620 GCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAGAAATTGAAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAA
54213676 ACGGAAATTG
Statistics
Matches: 309, Mismatches: 35, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
71 55 0.18
72 7 0.02
73 9 0.03
74 121 0.39
75 29 0.09
76 21 0.07
78 25 0.08
79 42 0.14
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (74 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGCA
TGTCTTGAG
Found at i:54213641 original size:148 final size:149
Alignment explanation
Indices: 54213246--54213675 Score: 600
Period size: 148 Copynumber: 2.9 Consensus size: 149
54213236 GTGATCTGAA
** *
54213246 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTTT-AAA-ACAGAAATTGAAATTACCTCA
*
54213311 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAA-ACAGAAA
63 GCATGT--ACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAA
*
54213375 TTGAAAATACCTCAACGTGTCTTGAG
124 TTGAAAATACCTCAACATGTCTTGAG
* * * * *
54213401 GCTCAACTCATTTCTCACAAT-TAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCTCAGCA
* *
54213463 TGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAGACAAAAATTGAAAA
66 TGTACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAA
*
54213527 TACCTCAGCATGTCTTGAG
131 TACCTCAACATGTCTTGAG
*
54213546 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTACAACAGAAATTGAAATTACCTCAGCA
1 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCTCAGCA
* * * *
54213611 TGTTCTGAGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGGCAGAAATTGAAAA
66 TGTACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAA
54213676 ACGGAAATTG
Statistics
Matches: 246, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
144 10 0.04
145 50 0.20
146 7 0.03
147 34 0.14
148 65 0.26
149 48 0.20
150 3 0.01
151 4 0.02
154 7 0.03
155 18 0.07
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (149 bp):
GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCTCAGCA
TGTACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAA
TACCTCAACATGTCTTGAG
Found at i:54213887 original size:61 final size:63
Alignment explanation
Indices: 54213777--54213943 Score: 167
Period size: 68 Copynumber: 2.6 Consensus size: 63
54213767 CCTCAGTGTG
* *** ***
54213777 TCCTGAGGCTCAACTCACCTCTCGCAATATGTGTTGATTTTTTTAA-A-AATACCTCAGCGCA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAACATACAAATACAATACCTCAGCGCA
*
54213838 TCCTGAGGCTCAGCTCACCTCTCGCAATATGAGTTGAACATACAGAAAATTGACAATACCTCAGC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAACATAC---AAA-T-ACAATACCTCAGC
**
54213903 GTG
61 GCA
* *
54213906 TCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA
54213944 TTTTGAAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
61 36 0.42
64 2 0.02
67 1 0.01
68 47 0.55
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (63 bp):
TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAACATACAAATACAATACCTCAGCGCA
Found at i:54214291 original size:17 final size:18
Alignment explanation
Indices: 54214266--54214299 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54214256 ATATCACTCT
54214266 TTTGCCCTTG-GTTGAGC
1 TTTGCCCTTGCGTTGAGC
*
54214283 TTTGTCCTTGCGTTGAG
1 TTTGCCCTTGCGTTGAG
54214300 GCTCTTGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.21, G:0.29, T:0.44
Consensus pattern (18 bp):
TTTGCCCTTGCGTTGAGC
Found at i:54223831 original size:19 final size:19
Alignment explanation
Indices: 54223809--54223895 Score: 61
Period size: 19 Copynumber: 4.3 Consensus size: 19
54223799 TAATAATAAT
54223809 ATAAAATAATAATATGTAC
1 ATAAAATAATAATATGTAC
*
54223828 ATAAAAATACATATATATATGTGC
1 AT-AAAAT--A-ATA-ATATGTAC
*
54223852 ATATAATAA-AAGTATGTA-
1 ATAAAATAATAA-TATGTAC
*
54223870 ATAATAATAATAATATCTAC
1 ATAA-AATAATAATATGTAC
54223890 AATAAA
1 -ATAAA
54223896 TGAAATTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 19
0.69 0.06 0.25
Matches are distributed among these distances:
18 4 0.08
19 18 0.34
20 9 0.17
21 5 0.09
22 1 0.02
23 7 0.13
24 9 0.17
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
ATAAAATAATAATATGTAC
Found at i:54224208 original size:24 final size:23
Alignment explanation
Indices: 54224155--54224226 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
54224145 CATGGAATAG
*
54224155 TATAAGAAATATATAACTAAT-TGCA
1 TATAAAAAATATATAA-TAATAT--A
54224180 T-TAAAAAATATATACATAATATA
1 TATAAAAAATATATA-ATAATATA
* *
54224203 TATAAAATACATATAAT-ATATA
1 TATAAAAAATATATAATAATATA
54224225 TA
1 TA
54224227 CGTATTAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.17
23 4 0.10
24 27 0.66
25 3 0.07
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (23 bp):
TATAAAAAATATATAATAATATA
Found at i:54224211 original size:11 final size:11
Alignment explanation
Indices: 54224184--54224226 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
54224174 ATTGCATTAA
*
54224184 AAAATATATAC
1 AAAATATATAT
*
54224195 ATAATATATAT
1 AAAATATATAT
*
54224206 AAAATACATAT
1 AAAATATATAT
*
54224217 AATATATATA
1 AAAATATATA
54224227 CGTATTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATATATAT
Found at i:54224746 original size:12 final size:12
Alignment explanation
Indices: 54224710--54224751 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54224700 ATGTATATAT
54224710 AAAGAAAGAAAA
1 AAAGAAAGAAAA
* *
54224722 AAACAACACAAAA
1 AAAGAA-AGAAAA
54224735 AAAGAAAGAAAA
1 AAAGAAAGAAAA
54224747 AAAGA
1 AAAGA
54224752 TTCGAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:54231324 original size:21 final size:21
Alignment explanation
Indices: 54231286--54231325 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54231276 TTTGAAAACA
* *
54231286 TTAATAATTATTTTATAAATT
1 TTAATAATTATGTAATAAATT
*
54231307 TTAATAGTTATGTAATAAA
1 TTAATAATTATGTAATAAA
54231326 AAGAAAACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTAATAATTATGTAATAAATT
Found at i:54232994 original size:132 final size:132
Alignment explanation
Indices: 54232752--54232994 Score: 378
Period size: 132 Copynumber: 1.8 Consensus size: 132
54232742 TTGCCTCGCC
* * * *
54232752 TTAGAAAAGACGAATGAAATTCCAAAGGGATATTCGATTATTTTACGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCAATTATTTTACGCAAACGAGAAATTGCAAC
54232817 CCAGCACAATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATTTCATTCGTTTTAAAAAGT
66 CCAGCACAATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATTTCATTCGTTTTAAAAAGT
54232882 TT
131 TT
* * **
54232884 TTAGAAAACATGAATGAAATTCTAAAGAGACATTCAATTATTTTGGGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAATGAAATTCCAAAGAGACATTCAATTATTTTACGCAAACGAGAAATTGCAAC
* * * *
54232949 CCAGCACGATAGGGCACGATTCCCCGAATTGCTAAATATCGAACAT
66 CCAGCACAATAGGGCACGATTCCCCGAATTGCCAAACATCAAACAT
54232995 CGTCTCCGTT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 99 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (132 bp):
TTAGAAAACACGAATGAAATTCCAAAGAGACATTCAATTATTTTACGCAAACGAGAAATTGCAAC
CCAGCACAATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATTTCATTCGTTTTAAAAAGT
TT
Found at i:54240082 original size:26 final size:26
Alignment explanation
Indices: 54240053--54240110 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
54240043 TTCTATATAT
*
54240053 ACACACTAAAAGAGGACCTAAAGGGG
1 ACACACTAAAAGAGGACCTAAAGGGA
54240079 ACACACTAAAAGAGGACCTAAAGGGA
1 ACACACTAAAAGAGGACCTAAAGGGA
54240105 ACACAC
1 ACACAC
54240111 AGACTAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (26 bp):
ACACACTAAAAGAGGACCTAAAGGGA
Found at i:54241092 original size:11 final size:11
Alignment explanation
Indices: 54241059--54241101 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
54241049 TAATTTAGTC
54241059 ATTTTTATTTT
1 ATTTTTATTTT
**
54241070 A-TTGCATTTT
1 ATTTTTATTTT
*
54241080 ATTTTTGTTTT
1 ATTTTTATTTT
54241091 ATTTTTATTTT
1 ATTTTTATTTT
54241102 TTAATTACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:54242855 original size:6 final size:6
Alignment explanation
Indices: 54242824--54242945 Score: 79
Period size: 6 Copynumber: 19.8 Consensus size: 6
54242814 TATTAGAGCT
* * * *
54242824 AGAATC AAAATA AGAATC AGAGTC AGAATC AGAATC AG-GTGAC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* * * * * *
54242873 AGAATC AGAATT AGAATC ACAATT AG-GTGAC AGAATC AGGATC AGTATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
54242922 AAGTAA-C AGAATC AGAATC AGAAT
1 -AG-AATC AGAATC AGAATC AGAAT
54242946 GTGAATACAA
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
5 4 0.05
6 73 0.83
7 8 0.09
8 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:54242871 original size:19 final size:19
Alignment explanation
Indices: 54242847--54242917 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
54242837 GAATCAGAGT
54242847 CAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGGTGA
*
54242866 CAGAATCAGAATCA-G-AA
1 CAGAATCAGAATCAGGTGA
* * *
54242883 TTAGAATCACAATTAGGTGA
1 -CAGAATCAGAATCAGGTGA
*
54242903 CAGAATCAGGATCAG
1 CAGAATCAGAATCAG
54242918 TATCAAGTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.03
18 12 0.30
19 26 0.65
20 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTGA
Found at i:54242889 original size:37 final size:37
Alignment explanation
Indices: 54242836--54242922 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 37
54242826 AATCAAAATA
* *
54242836 AGAATCAGAGTCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCACAATCAGGTGACAGAATC
* *
54242873 AGAATCAGAATTAGAATCACAATTAGGTGACAGAATC
1 AGAATCAGAATCAGAATCACAATCAGGTGACAGAATC
* *
54242910 AGGATCAGTATCA
1 AGAATCAGAATCA
54242923 AGTAACAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCACAATCAGGTGACAGAATC
Found at i:54242941 original size:19 final size:19
Alignment explanation
Indices: 54242847--54242941 Score: 50
Period size: 19 Copynumber: 4.7 Consensus size: 19
54242837 GAATCAGAGT
* *
54242847 CAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAAGTAA
54242866 CAGAATCAGAATC-AG-AA
1 CAGAATCAGAATCAAGTAA
* * * * *
54242883 TTAGAATCACAATTAGGTGA
1 -CAGAATCAGAATCAAGTAA
54242903 CAGAATCAGGATCAGTATCAAGTAA
1 CAGAATCA-G---A--ATCAAGTAA
54242928 CAGAATCAGAATCA
1 CAGAATCAGAATCA
54242942 GAATGTGAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
17 1 0.02
18 11 0.20
19 25 0.45
20 1 0.02
21 1 0.02
23 1 0.02
24 1 0.02
25 14 0.25
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (19 bp):
CAGAATCAGAATCAAGTAA
Found at i:54243159 original size:27 final size:26
Alignment explanation
Indices: 54243063--54243156 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 26
54243053 AGCATGGCTG
* *
54243063 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
*
54243089 CCAGATGCAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
* *
54243116 CCAGAACAGGTATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGCCA
54243143 CCAGAACAGATATT
1 CCAGAACAGATATT
54243157 TGTAGAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.20
27 47 0.80
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:54243378 original size:22 final size:21
Alignment explanation
Indices: 54243344--54243407 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
54243334 GCAAATTCGT
*
54243344 TTGGCACACAGCCATAATCAGG
1 TTGGCA-AAAGCCATAATCAGG
*
54243366 TTGGCAAAGAGCCAT-ATGTAGG
1 TTGGCAAA-AGCCATAAT-CAGG
*
54243388 TTGGCGCAAAGCCATAATCA
1 TTGGC-AAAAGCCATAATCA
54243408 AAATAGGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.09
22 27 0.79
23 4 0.12
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (21 bp):
TTGGCAAAAGCCATAATCAGG
Found at i:54244227 original size:27 final size:27
Alignment explanation
Indices: 54243794--54244225 Score: 544
Period size: 27 Copynumber: 16.0 Consensus size: 27
54243784 GGGTAAAATG
* * * * *
54243794 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
54243821 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
54243848 CTATTTCTACCCTACAAGGGTA-TTCTG
1 GTAATTCTACCCTACAGGGGTATTTC-A
* * *
54243875 GTAATTATACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
54243902 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54243929 GTAATTCTACCTTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54243956 ATAATTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54243983 GTAATTCTACCTTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54244010 GTAATTCTACCCTACAAGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
54244036 GATAATTTTACCTTATAGGGGTATTTCG
1 G-TAATTCTACCCTACAGGGGTATTTCA
*
54244064 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54244091 ATAATTATACCGTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54244118 GTAATTCTACCTTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54244145 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
54244172 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54244199 ATAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
54244226 ATCATTTTGT
Statistics
Matches: 351, Mismatches: 50, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.01
27 344 0.98
28 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:54246322 original size:6 final size:6
Alignment explanation
Indices: 54246301--54246410 Score: 71
Period size: 6 Copynumber: 17.8 Consensus size: 6
54246291 TATTAGAACT
* * ** *
54246301 AGAATC AAAATG AGAATC AGAATC AGGTTAC AGAATC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AGAATC AGAAT-C AGAATC AGAATC AGAATC
* * * **
54246350 AGAATC AGAATT AGGTGAT- AGAAAC AGAATC AGTTTC AAGTAA-C AGAATC
1 AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC -AG-AATC AGAATC
54246400 AGAATC AGAAT
1 AGAATC AGAAT
54246411 GTGAATGCAA
Statistics
Matches: 78, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
5 3 0.04
6 64 0.82
7 9 0.12
8 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:54246337 original size:19 final size:18
Alignment explanation
Indices: 54246313--54246401 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
54246303 AATCAAAATG
54246313 AGAATCAGAATCAGGTTA
1 AGAATCAGAATCAGGTTA
*
54246331 CAGAATCAGAATCAGAATT-
1 -AGAATCAGAATCAG-GTTA
* *
54246350 AGAATCAGAATTAGGTGA
1 AGAATCAGAATCAGGTTA
* *
54246368 TAGAAACAGAATCAGTTTCA
1 -AGAATCAGAATCAGGTT-A
54246388 AGTAA-CAGAATCAG
1 AG-AATCAGAATCAG
54246402 AATCAGAATG
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.23
19 38 0.67
20 5 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (18 bp):
AGAATCAGAATCAGGTTA
Found at i:54246348 original size:31 final size:31
Alignment explanation
Indices: 54246301--54246410 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 31
54246291 TATTAGAACT
* *
54246301 AGAATCAAAATGAGAATCAGAATCAGGTTAC
1 AGAATCAGAATCAGAATCAGAATCAGGTTAC
* *
54246332 AGAATCAGAATCAGAATTAGAATCAGAATTA-
1 AGAATCAGAATCAGAATCAGAATCAG-GTTAC
* * * ** * *
54246363 GGTGAT-AGAAACAGAATCAGTTTCAAGTAAC
1 AG-AATCAGAATCAGAATCAGAATCAGGTTAC
54246394 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
54246411 GTGAATGCAA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
30 4 0.07
31 50 0.85
32 5 0.08
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTTAC
Found at i:54246354 original size:37 final size:37
Alignment explanation
Indices: 54246301--54246382 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
54246291 TATTAGAACT
* * *
54246301 AGAATCAAAATGAGAATCAGAATCAGGTTACAGAATC
1 AGAATCAGAATGAGAATCAGAATCAGGTGACAGAAAC
* * *
54246338 AGAATCAGAATTAGAATCAGAATTAGGTGATAGAAAC
1 AGAATCAGAATGAGAATCAGAATCAGGTGACAGAAAC
54246375 AGAATCAG
1 AGAATCAG
54246383 TTTCAAGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATGAGAATCAGAATCAGGTGACAGAAAC
Found at i:54246566 original size:27 final size:26
Alignment explanation
Indices: 54246528--54246662 Score: 126
Period size: 27 Copynumber: 5.0 Consensus size: 26
54246518 AGCATGGCTC
* * * *
54246528 CCAGAATAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCACAGCCA
54246554 CCAGATACAGATATTGTGGCACAGCCA
1 CCAGA-ACAGATATTGTGGCACAGCCA
* *
54246581 CCAGAACAGGTATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCACAGCCA
** *
54246608 CCAGAACAGATATTTGTGTTATAGCCA
1 CCAGAACAGATA-TTGTGGCACAGCCA
* * *
54246635 CCAGAAATAGATAATGTGGCAAAGCCA
1 CCAG-AACAGATATTGTGGCACAGCCA
54246662 C
1 C
54246663 TTAATAGAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
26 11 0.12
27 74 0.80
28 7 0.08
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCACAGCCA
Found at i:54246653 original size:54 final size:53
Alignment explanation
Indices: 54246528--54246662 Score: 146
Period size: 54 Copynumber: 2.5 Consensus size: 53
54246518 AGCATGGCTC
* * *
54246528 CCAGAATAGATATTGTGACAGAGTCACCAGATACAGATATTGTGGCACAGCCA
1 CCAGAATAGATATTGTGGCAAAGCCACCAGATACAGATATTGTGGCACAGCCA
* * * ** *
54246581 CCAGAACAGGTATTTGTGGCATAGCCACCAGA-ACAGATATTTGTGTTATAGCCA
1 CCAGAATAGATA-TTGTGGCAAAGCCACCAGATACAGATA-TTGTGGCACAGCCA
*
54246635 CCAGAAATAGATAATGTGGCAAAGCCAC
1 CCAG-AATAGATATTGTGGCAAAGCCAC
54246663 TTAATAGAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
53 17 0.25
54 44 0.66
55 6 0.09
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (53 bp):
CCAGAATAGATATTGTGGCAAAGCCACCAGATACAGATATTGTGGCACAGCCA
Found at i:54246857 original size:22 final size:23
Alignment explanation
Indices: 54246832--54246883 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
54246822 TGGCACACAA
*
54246832 CCATAATCT-GGTTGG-GACAGAG
1 CCATAATCTAGGTTGGCG-CAAAG
*
54246854 CCAT-ATGTAGGTTGGCGCAAAG
1 CCATAATCTAGGTTGGCGCAAAG
54246876 CCATAATC
1 CCATAATC
54246884 AGAATAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (23 bp):
CCATAATCTAGGTTGGCGCAAAG
Found at i:54247734 original size:27 final size:27
Alignment explanation
Indices: 54247274--54247732 Score: 537
Period size: 27 Copynumber: 17.0 Consensus size: 27
54247264 GGGCAAAATG
* * * * *
54247274 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54247301 GTAATTCTACCTTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54247328 GTATTTCTACCCTACAAGGGTA-TTCTG
1 GTAATTCTACCCTACAGGGGTATTTC-A
* *
54247355 GTAATTCTACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* **
54247382 GTAATTCTACCCTATAGGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54247409 GTAGTTCTACCCTACACGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54247436 GTAGTTCTACCTTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54247463 GTAATTCTACCTTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54247490 GTAATTCTACCTTACAAGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54247516 GATAATTCTACCCTACAAGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTCA
* * * *
54247544 GTAATTTTACCTTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
*
54247571 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
54247598 ATAATTATACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
54247625 GTAATTCTATCATACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
54247652 GTAATTCTACCCTACAGGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
54247678 GATAATTCTACCCTACAGGGGTATTTCA
1 G-TAATTCTACCCTACAGGGGTATTTCA
* *
54247706 ATAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
54247733 ATTATTTTGT
Statistics
Matches: 379, Mismatches: 47, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
26 5 0.01
27 371 0.98
28 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:54252298 original size:40 final size:40
Alignment explanation
Indices: 54252243--54252322 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
54252233 TTACGGTACT
54252243 TAGCATTTTTCCATTTGGTACAGTCGAGGTAAGTCATCCC
1 TAGCATTTTTCCATTTGGTACAGTCGAGGTAAGTCATCCC
*
54252283 TAGCATTTTTCCATTTGGTATAGTCGAGGTAAGTCATCCC
1 TAGCATTTTTCCATTTGGTACAGTCGAGGTAAGTCATCCC
54252323 AAGTTCGGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (40 bp):
TAGCATTTTTCCATTTGGTACAGTCGAGGTAAGTCATCCC
Found at i:54252767 original size:55 final size:55
Alignment explanation
Indices: 54252707--54252814 Score: 128
Period size: 55 Copynumber: 2.0 Consensus size: 55
54252697 CGGGTGTGTG
**
54252707 ACACGCCCGTGCCTTGA-AACCATGGGCAAAACTGTCAAATTAACACGAGCGTGCA
1 ACACGCCCGTGCC-AAACAACCATGGGCAAAACTGTCAAATTAACACGAGCGTGCA
* * * * * *
54252762 ACACGCTCGTGCCAAACAACCATGGTCGAACCTGTTAGATTAACACGAGCGTG
1 ACACGCCCGTGCCAAACAACCATGGGCAAAACTGTCAAATTAACACGAGCGTG
54252815 GGAGAAGCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 1 0.02
55 43 0.98
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (55 bp):
ACACGCCCGTGCCAAACAACCATGGGCAAAACTGTCAAATTAACACGAGCGTGCA
Found at i:54256550 original size:27 final size:27
Alignment explanation
Indices: 54256520--54256697 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
54256510 ATATTGAGTC
* * * *
54256520 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
54256547 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54256574 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54256602 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54256629 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54256656 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54256683 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54256698 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54256659 original size:82 final size:81
Alignment explanation
Indices: 54256541--54256696 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
54256531 TGCTATATAA
*
54256541 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54256606 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54256623 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54256687 CACTTAGTGC
65 CACTTAGTGC
54256697 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54266113 original size:6 final size:6
Alignment explanation
Indices: 54266104--54266183 Score: 117
Period size: 6 Copynumber: 13.2 Consensus size: 6
54266094 ATCTTTATGC
*
54266104 TTATTT TTATTT TTATTT TTATTT TTATCT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
54266152 TTATTT TTATGT TTATTT TGT-TTT TATATTT T
1 TTATTT TTATTT TTATTT T-TATTT T-TATTT T
54266184 GAACTTTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
6 62 0.93
7 5 0.07
ACGTcount: A:0.16, C:0.01, G:0.03, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:54293782 original size:38 final size:38
Alignment explanation
Indices: 54293739--54293996 Score: 313
Period size: 38 Copynumber: 6.8 Consensus size: 38
54293729 AAAGGCCCAA
* *
54293739 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCAGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGG
54293777 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCA-G
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAA-CCAGG
* * * * *
54293815 ATATATTATCAGCACAAAGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGG
** *
54293853 ATATAATACCAGTGCGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGG
* * *
54293891 ATATAATACCATCACAAAGCCTGTGGGATTTAACCCA-G
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAA-CCAGG
* * * **
54293929 ACATATTACCAGCACGAAGCCTGCAGGATTTAACCCTG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGG
*
54293967 ATATATTACCAGCACGAAGCCTGCGGGATT
1 ATATAATACCAGCACGAAGCCTGCGGGATT
54293997 CATACACAAC
Statistics
Matches: 188, Mismatches: 28, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
37 4 0.02
38 179 0.95
39 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGG
Found at i:54293844 original size:76 final size:76
Alignment explanation
Indices: 54293734--54293996 Score: 348
Period size: 76 Copynumber: 3.5 Consensus size: 76
54293724 GGCTCAAAGG
* * *
54293734 CCCAAATATAATACCAGCACTAGGCCTGCGGGATTTAACCAGGATATAATACCAGCACGAAGCCT
1 CCCAGATATAATACCAGCACAAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACGAAGCCT
54293799 GCGGGATTTAA
66 GCGGGATTTAA
* * * * **
54293810 CCCAGATATATTATCAGCACAAAGCCTGTGGGATTTAACCCGGATATAATACCAGTGCGAAGCCT
1 CCCAGATATAATACCAGCACAAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACGAAGCCT
54293875 GCGGGATTTAA
66 GCGGGATTTAA
* * * * *
54293886 CCCGGATATAATACCATCACAAAGCCTGTGGGATTTAACCCA-GACATATTACCAGCACGAAGCC
1 CCCAGATATAATACCAGCACAAAGCCTGCGGGATTTAA-CCAGGATATAATACCAGCACGAAGCC
*
54293950 TGCAGGATTTAA
65 TGCGGGATTTAA
* * *
54293962 CCCTGATATATTACCAGCACGAAGCCTGCGGGATT
1 CCCAGATATAATACCAGCACAAAGCCTGCGGGATT
54293997 CATACACAAC
Statistics
Matches: 162, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
76 160 0.99
77 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCAGATATAATACCAGCACAAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACGAAGCCT
GCGGGATTTAA
Found at i:54293942 original size:114 final size:114
Alignment explanation
Indices: 54293739--54293996 Score: 381
Period size: 114 Copynumber: 2.3 Consensus size: 114
54293729 AAAGGCCCAA
* * *
54293739 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCAGGATATAATACCAGCACGAAGCCTGCGGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACAAAGCCTGCGGG
* * **
54293804 ATTTAACCCAGATATATTATCAGCACAAAGCCTGTGGGATTTAACCCGG
66 ATTTAACCCAGACATATTACCAGCACAAAGCCTGCAGGATTTAACCCGG
** * * *
54293853 ATATAATACCAGTGCGAAGCCTGCGGGATTTAACCCGGATATAATACCATCACAAAGCCTGTGGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACAAAGCCTGCGGG
* *
54293918 ATTTAACCCAGACATATTACCAGCACGAAGCCTGCAGGATTTAACCCTG
66 ATTTAACCCAGACATATTACCAGCACAAAGCCTGCAGGATTTAACCCGG
*
54293967 ATATATTACCAGCACGAAGCCTGCGGGATT
1 ATATAATACCAGCACGAAGCCTGCGGGATT
54293997 CATACACAAC
Statistics
Matches: 127, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 127 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (114 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAGGATATAATACCAGCACAAAGCCTGCGGG
ATTTAACCCAGACATATTACCAGCACAAAGCCTGCAGGATTTAACCCGG
Found at i:54298989 original size:38 final size:38
Alignment explanation
Indices: 54298938--54299170 Score: 331
Period size: 38 Copynumber: 6.1 Consensus size: 38
54298928 AAAGGCCCAA
* * *
54298938 ATATAATACCAGCACTAGGCCTACGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
54298976 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
54299014 ATATAATACCAGCACGAAGCCTGTGGGATTTAACCTGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * * * *
54299052 ACATATTACCAGCATGAAGCCTGCGAGATTTAATCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
54299090 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
54299128 ATATAATACCAGCACAAAGCCTGCAGGATTTAACTCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
54299166 ATATA
1 ATATA
54299171 CATCAAATAT
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 173 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:54302146 original size:16 final size:16
Alignment explanation
Indices: 54302125--54302174 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
54302115 GTCAAGTGGT
*
54302125 TTTGGAAAATGAGGTA
1 TTTGGAAAATAAGGTA
54302141 TTTGGAAAATAAGGTA
1 TTTGGAAAATAAGGTA
54302157 TTTGGAAAATAAGGTA
1 TTTGGAAAATAAGGTA
54302173 TT
1 TT
54302175 GGGACCTCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (16 bp):
TTTGGAAAATAAGGTA
Found at i:54303357 original size:6 final size:6
Alignment explanation
Indices: 54303336--54303475 Score: 115
Period size: 6 Copynumber: 22.8 Consensus size: 6
54303326 TATTAGAACT
* * *
54303336 AGAATC AAAATG AGAATC AGAATC -GAAATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AG-AATC AGAAT--C AGAATC AGAATC
* *
54303385 AGAATC AGAATC AGAATC AGAACC AGAATC AGAATC AGGTAA-C AGAATT
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
* * * * *
54303434 AGAATC ATAATC AGTATC AGGTACC AGAATC AAAATC AGAAT
1 AGAATC AGAATC AGAATC A-GAATC AGAATC AGAATC AGAAT
54303476 GTGAATGCAA
Statistics
Matches: 107, Mismatches: 18, Indels: 18
0.75 0.13 0.13
Matches are distributed among these distances:
5 4 0.04
6 88 0.82
7 12 0.11
8 3 0.03
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:54303386 original size:31 final size:30
Alignment explanation
Indices: 54303348--54303475 Score: 126
Period size: 31 Copynumber: 4.4 Consensus size: 30
54303338 AATCAAAATG
54303348 AGAATCAGAATC-GAAATCAGGTGACAGAATC
1 AGAATCAGAATCAG-AATCAGGT-ACAGAATC
54303379 AGAATCAGAATCAG-A--A--T-CAGAATC
1 AGAATCAGAATCAGAATCAGGTACAGAATC
* *
54303403 AGAACCAGAATCAGAATCAGGTAACAGAATT
1 AGAATCAGAATCAGAATCAGGT-ACAGAATC
* *
54303434 AGAATCATAATCAGTATCAGGTACCAGAATC
1 AGAATCAGAATCAGAATCAGGTA-CAGAATC
*
54303465 AAAATCAGAAT
1 AGAATCAGAAT
54303476 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
24 20 0.25
25 1 0.01
26 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 2 0.03
31 52 0.65
32 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (30 bp):
AGAATCAGAATCAGAATCAGGTACAGAATC
Found at i:54303421 original size:55 final size:55
Alignment explanation
Indices: 54303336--54303453 Score: 157
Period size: 55 Copynumber: 2.1 Consensus size: 55
54303326 TATTAGAACT
* * * *
54303336 AGAATCAAAATGAGAATCAGAATCGAAATCAGGTGACAGAATCAGAATCAGAATC
1 AGAATCAGAATCAGAACCAGAATCGAAATCAGGTAACAGAATCAGAATCAGAATC
* *
54303391 AGAATCAGAATCAGAACCAGAATC-AGAATCAGGTAACAGAATTAGAATCATAATC
1 AGAATCAGAATCAGAACCAGAATCGA-AATCAGGTAACAGAATCAGAATCAGAATC
*
54303446 AGTATCAG
1 AGAATCAG
54303454 GTACCAGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.02
55 54 0.98
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (55 bp):
AGAATCAGAATCAGAACCAGAATCGAAATCAGGTAACAGAATCAGAATCAGAATC
Found at i:54303638 original size:27 final size:26
Alignment explanation
Indices: 54303590--54303649 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
54303580 GCAAGGCTGC
*
54303590 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
54303617 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
54303643 TAGATAT
1 CAGATAT
54303650 ATATATATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:54304006 original size:27 final size:27
Alignment explanation
Indices: 54303976--54304490 Score: 662
Period size: 27 Copynumber: 19.2 Consensus size: 27
54303966 AACACCCTAG
* *
54303976 GGGTAAAATGGTAATTTTGTAAATTGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304003 GGGTAAAACAATAATTTTGTAAATCGG
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
54304030 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304057 -GGTAAAACATTAATTTTGTAAATCAA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304083 GGGTAAAATGGTAATTTTGTCAATCAA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304110 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
54304137 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304164 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
54304191 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * *
54304218 GGGTAAAA-CGATAATTCTATAAATCGA
1 GGGTAAAATAG-TAATTTTGTAAATCGA
* *
54304245 GGGTAAAATAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
54304272 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
54304299 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
54304326 GGGTAAAATAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
54304353 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
** *
54304380 GGGTAAAACGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
54304407 GGGTAAAA-AGGTAATTTTGTAAATCGA
1 GGGTAAAATA-GTAATTTTGTAAATCGA
*
54304434 GGG--AAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
54304459 GGGTAAAATAGTAATTTTATAATTCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
54304486 GGGTA
1 GGGTA
54304491 CTTTAATAAT
Statistics
Matches: 434, Mismatches: 47, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.05
26 26 0.06
27 385 0.89
28 1 0.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (27 bp):
GGGTAAAATAGTAATTTTGTAAATCGA
Found at i:54304500 original size:27 final size:27
Alignment explanation
Indices: 54304470--54304530 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
54304460 GGTAAAATAG
* *
54304470 TAATTTTATAATTCGAGGGTACTTTAA
1 TAATTTTACAAGTCGAGGGTACTTTAA
* *
54304497 TAATTTTACAAGTCGAGGGTATTTTAG
1 TAATTTTACAAGTCGAGGGTACTTTAA
54304524 TAATTTT
1 TAATTTT
54304531 GCAAACTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGGTACTTTAA
Found at i:54304543 original size:54 final size:53
Alignment explanation
Indices: 54304485--54304636 Score: 146
Period size: 54 Copynumber: 2.8 Consensus size: 53
54304475 TTATAATTCG
** * * *
54304485 AGGGTACTTTAATAATTTTACAAGTCGAGGGTATTTTAGTAATTTTGCAAACTT
1 AGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAAC-T
* * ** *
54304539 AGGGTA-TTTCGGTAATTTTACAAATCGATGATATTTGGGTAATTTTATAAACT
1 AGGGTACTTT-GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACT
* * *
54304592 GGAGGTACTTTGGTAATTTTACAACT-GGGGGTATTTCAGTAATTT
1 AG-GGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTT
54304637 GGTAAACTAA
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
53 19 0.24
54 57 0.72
55 3 0.04
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (53 bp):
AGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACT
Found at i:54304633 original size:26 final size:26
Alignment explanation
Indices: 54304497--54304636 Score: 104
Period size: 27 Copynumber: 5.2 Consensus size: 26
54304487 GGTACTTTAA
* **
54304497 TAATTTTACAAGTCGAGGGTATTTTAG
1 TAATTTTACAACT-GAGGGTATTTCGG
* *
54304524 TAATTTTGCAAACTTAGGGTATTTCGG
1 TAATTTTAC-AACTGAGGGTATTTCGG
* * * *
54304551 TAATTTTACAAATCGATGATATTTGGG
1 TAATTTTACAACT-GAGGGTATTTCGG
*
54304578 TAATTTTATAAACTG-GAGGTACTTT-GG
1 TAATTTTA-CAACTGAG-GGTA-TTTCGG
* *
54304605 TAATTTTACAACTGGGGGTATTTCAG
1 TAATTTTACAACTGAGGGTATTTCGG
54304631 TAATTT
1 TAATTT
54304637 GGTAAACTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
25 3 0.03
26 19 0.21
27 58 0.65
28 9 0.10
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (26 bp):
TAATTTTACAACTGAGGGTATTTCGG
Found at i:54311769 original size:41 final size:41
Alignment explanation
Indices: 54311712--54311794 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
54311702 CAATGGATGC
*
54311712 ATAAAAAGTGATTAGAAAAGA-TGATGATGCGTTTTTAGCTT
1 ATAAAAAGTGATTAGAAAAGATTG-TGATGCATTTTTAGCTT
54311753 ATAAAAAGTGATTAGAAAAGATTGTGATGCATTTTTAGCTT
1 ATAAAAAGTGATTAGAAAAGATTGTGATGCATTTTTAGCTT
54311794 A
1 A
54311795 CATTCTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (41 bp):
ATAAAAAGTGATTAGAAAAGATTGTGATGCATTTTTAGCTT
Found at i:54314512 original size:33 final size:34
Alignment explanation
Indices: 54314469--54314540 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
54314459 AAGTTCTAGA
*
54314469 CTAAGACTCGAAACGTAAAATGACAATTAAAAAC
1 CTAAGACTCGAAACGTAAAATGAAAATTAAAAAC
54314503 CTAAG-CTCGAAACGTAAAATGAAAATTAAAAAC
1 CTAAGACTCGAAACGTAAAATGAAAATTAAAAAC
54314536 CTAAG
1 CTAAG
54314541 GCGAAGCCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.18
Consensus pattern (34 bp):
CTAAGACTCGAAACGTAAAATGAAAATTAAAAAC
Found at i:54315769 original size:21 final size:20
Alignment explanation
Indices: 54315743--54315814 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 20
54315733 ATCTTTCAGC
54315743 CATGATCTTACTCGTCTTTAT
1 CATGATCTTACTC-TCTTTAT
* *
54315764 CATGATGCCATAGCATCT-TTTAG
1 CATGAT--CTTA-C-TCTCTTTAT
54315787 CAATGATCTTACTCATCTTTAT
1 C-ATGATCTTACTC-TCTTTAT
54315809 CATGAT
1 CATGAT
54315815 GCCATAGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 8 0.20
23 8 0.20
24 7 0.17
25 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (20 bp):
CATGATCTTACTCTCTTTAT
Found at i:54315780 original size:45 final size:45
Alignment explanation
Indices: 54315719--54315851 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
54315709 GTCCCATTAC
* * * *
54315719 CATGATGTCATGGCATCTTTCAGCCATGATCTTACTCGTCTTTAT
1 CATGATGCCATAGCATCTTTCAGCAATGATCTTACTCATCTTTAT
*
54315764 CATGATGCCATAGCATCTTTTAGCAATGATCTTACTCATCTTTAT
1 CATGATGCCATAGCATCTTTCAGCAATGATCTTACTCATCTTTAT
* *
54315809 CATGATGCCATAGCATCTTTCAGCTATGTTCTTACTCAT-TTTA
1 CATGATGCCATAGCATCTTTCAGCAATGATCTTACTCATCTTTA
54315852 AGCGTATAGC
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 4 0.05
45 76 0.95
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (45 bp):
CATGATGCCATAGCATCTTTCAGCAATGATCTTACTCATCTTTAT
Found at i:54315825 original size:22 final size:22
Alignment explanation
Indices: 54315757--54315828 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
54315747 ATCTTACTCG
54315757 TCTTTATCATGATGCCATAGCA
1 TCTTTATCATGATGCCATAGCA
* * *
54315779 TCTTTTAGCAATGAT--CTTACTCA
1 TC-TTTATC-ATGATGCCATA-GCA
54315802 TCTTTATCATGATGCCATAGCA
1 TCTTTATCATGATGCCATAGCA
54315824 TCTTT
1 TCTTT
54315829 CAGCTATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
21 5 0.13
22 17 0.44
23 12 0.31
24 5 0.13
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (22 bp):
TCTTTATCATGATGCCATAGCA
Found at i:54330477 original size:71 final size:67
Alignment explanation
Indices: 54330337--54330477 Score: 158
Period size: 67 Copynumber: 2.0 Consensus size: 67
54330327 AGGAATTGTC
* * * * *
54330337 CTGGCATCCTCACTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCATCACAAT
1 CTGGCAGCCTCACTGCAATATGGTGGCCTCGCCACATATATCTATTCTGGTGACCTCACCACAAT
54330402 AT
66 AT
* * *
54330404 CTGGCAGCCTCCCTGCAATATGGTGGCTTCGCCACATATATATATCTATTCTGGTGGCCT-AGCC
1 CTGGCAGCCTCACTGCAATATGGTGGCCTCGCCAC----ATATATCTATTCTGGTGACCTCA-CC
54330468 ACAATAT
61 ACAATAT
54330475 CTG
1 CTG
54330478 TATCTGGTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
67 31 0.51
70 1 0.02
71 29 0.48
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.30
Consensus pattern (67 bp):
CTGGCAGCCTCACTGCAATATGGTGGCCTCGCCACATATATCTATTCTGGTGACCTCACCACAAT
AT
Found at i:54339085 original size:36 final size:36
Alignment explanation
Indices: 54339031--54339099 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
54339021 AGATAGCATA
54339031 GTAACCGCATCGAAGTTGAAAACACTGGCTGCTTTT
1 GTAACCGCATCGAAGTTGAAAACACTGGCTGCTTTT
* * *
54339067 GTAATCGCATCGAGGTTGAAAACATTGGCTGCT
1 GTAACCGCATCGAAGTTGAAAACACTGGCTGCT
54339100 ATCATCGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (36 bp):
GTAACCGCATCGAAGTTGAAAACACTGGCTGCTTTT
Found at i:54342068 original size:40 final size:38
Alignment explanation
Indices: 54342035--54342128 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 38
54342025 TATATTCAGA
54342035 ACTAAGTGTGCGATTTGAAATAACTTCGGCTATAAATAGC
1 ACTAAGTGTGCGATTTGAAATAACTTCGGCTAT--ATAGC
* * * *
54342075 ACTAAGTGTGCGAATTGGAATAGCTTTGGCTATATGAGGC
1 ACTAAGTGTGCGATTTGAAATAACTTCGGCTATAT-A-GC
54342115 ACTAAGTGTGCGAT
1 ACTAAGTGTGCGAT
54342129 ACTGAGATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 44 0.94
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (38 bp):
ACTAAGTGTGCGATTTGAAATAACTTCGGCTATATAGC
Found at i:54346970 original size:27 final size:27
Alignment explanation
Indices: 54346935--54347001 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
54346925 AGCATGGCTG
*
54346935 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGACAGAGCCA
*
54346961 CCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGACAGAGCCA
54346989 CCAGAACAGATAA
1 CCAGAACAGATAA
54347002 CACCAGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 5 0.14
27 16 0.43
28 16 0.43
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGACAGAGCCA
Found at i:54347174 original size:26 final size:27
Alignment explanation
Indices: 54347138--54347201 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
54347128 CAAAAGTAAC
** *
54347138 CCTAGGGGTATAATGGTAATTT-TATA
1 CCTAGGGGTATAACAGTAATTTCCATA
54347164 CCTAGGGGTATAACAGTAATTTCCATA
1 CCTAGGGGTATAACAGTAATTTCCATA
*
54347191 CATAGGGGTAT
1 CCTAGGGGTAT
54347202 TCAAGTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (27 bp):
CCTAGGGGTATAACAGTAATTTCCATA
Found at i:54347471 original size:16 final size:15
Alignment explanation
Indices: 54347450--54347480 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
54347440 CAAAATATCA
54347450 GCTTTTCGGCATTTTG
1 GCTTTTCGGC-TTTTG
54347466 GCTTTTCGGCTTTTG
1 GCTTTTCGGCTTTTG
54347481 CCGATCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.03, C:0.19, G:0.26, T:0.52
Consensus pattern (15 bp):
GCTTTTCGGCTTTTG
Found at i:54350775 original size:18 final size:18
Alignment explanation
Indices: 54350754--54350788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54350744 AAATAGTAAG
* *
54350754 CTTTCAATTGGCAGTATA
1 CTTTCAAATGGAAGTATA
54350772 CTTTCAAATGGAAGTAT
1 CTTTCAAATGGAAGTAT
54350789 GCTTATGTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (18 bp):
CTTTCAAATGGAAGTATA
Found at i:54353155 original size:21 final size:21
Alignment explanation
Indices: 54353131--54353183 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54353121 GTTTTTGATA
* *
54353131 AGGAAGTTGCTACTGCAGGAG
1 AGGAAGTTGCTACTGAAGAAG
* *
54353152 AGGAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
54353173 AAGAAGTTGCT
1 AGGAAGTTGCT
54353184 GAAAATAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.09, G:0.36, T:0.23
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:54356420 original size:47 final size:47
Alignment explanation
Indices: 54356353--54356591 Score: 338
Period size: 47 Copynumber: 5.0 Consensus size: 47
54356343 TTATCACAGT
* * *
54356353 TATACACTTCCAC-TTCCATCACATTGACCATTCGGTCTTATCATATA
1 TATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCATATA
* *
54356400 TATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATA
54356447 CT-TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATA
1 -TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT--CATATA
* * *
54356496 CATACACCTTCACATTCATCACATTGGCCATTTGGCCTTATCATATA
1 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATA
* *
54356543 TATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATA
54356590 TA
1 TA
54356592 CATATCTTGT
Statistics
Matches: 172, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
47 127 0.74
48 3 0.02
49 42 0.24
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.36
Consensus pattern (47 bp):
TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATA
Found at i:54356442 original size:22 final size:22
Alignment explanation
Indices: 54356417--54356492 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
54356407 TTTCACATTC
54356417 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
54356439 ATCACATACTTACACTTTC-ACATT
1 ATCACAT--TGGC-CATTCGGCCTT
54356463 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
54356486 ATCACAT
1 ATCACAT
54356493 ATACATACAC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:54356538 original size:96 final size:96
Alignment explanation
Indices: 54356342--54356595 Score: 365
Period size: 96 Copynumber: 2.7 Consensus size: 96
54356332 TCCTTCGGGA
* * * *
54356342 CTTATCACAGT-TATACACTTCCAC-TTCCATCACATTGACCATTCGGTCTTAT--CATATATAT
1 CTTATCACA-TATATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACATATACAT
* *
54356403 ATACTTTCACATTCATCACATTGGCCATTCGGC
64 ACACCTTCACATTCATCACATTGGCCATTCGGC
54356436 CTTATCACATACT-TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATA
1 CTTATCACATA-TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATA
*
54356500 CACCTTCACATTCATCACATTGGCCATTTGGC
65 CACCTTCACATTCATCACATTGGCCATTCGGC
* *
54356532 CTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATA
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATA
54356596 TCTTGTACAT
Statistics
Matches: 145, Mismatches: 9, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
93 1 0.01
94 42 0.29
95 4 0.03
96 98 0.68
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.35
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATAC
ACCTTCACATTCATCACATTGGCCATTCGGC
Found at i:54361126 original size:21 final size:21
Alignment explanation
Indices: 54361093--54361132 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54361083 TTTTCTAAAC
*
54361093 TTAAAAGTCAAAACTATTAAG
1 TTAAAAGTCAAAACAATTAAG
54361114 TTAAAAGGT-AAAACAATTA
1 TTAAAA-GTCAAAACAATTA
54361133 TATTGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (21 bp):
TTAAAAGTCAAAACAATTAAG
Found at i:54367679 original size:20 final size:19
Alignment explanation
Indices: 54367641--54367680 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
54367631 CATCAATGGA
* *
54367641 AACTTTCAAAATCTTTAAC
1 AACTTTCAAAATATGTAAC
54367660 AACTTTGCAAAATATGTAAC
1 AACTTT-CAAAATATGTAAC
54367680 A
1 A
54367681 CCCCTTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (19 bp):
AACTTTCAAAATATGTAAC
Found at i:54369374 original size:33 final size:33
Alignment explanation
Indices: 54369324--54369450 Score: 164
Period size: 33 Copynumber: 3.7 Consensus size: 33
54369314 AGTCATACCT
*
54369324 GGATTACCAGTCCAGGCTAAATCCAGTCGATTA
1 GGATTACCAGTCCAGGCTAAATCCAGTCAATTA
* * *
54369357 GGATTACTAGTCTAGGCTAAATCTAGTCAATTAGGA
1 GGATTACCAGTCCAGGCTAAATCCAGTCAATT---A
54369393 TGGATTACCAGTCCAGGCTAAATCCAGTCAATTA
1 -GGATTACCAGTCCAGGCTAAATCCAGTCAATTA
* *
54369427 GAATTACTAGTCCAGGCTAAATCC
1 GGATTACCAGTCCAGGCTAAATCC
54369451 GAATTGAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
33 50 0.62
34 1 0.01
36 1 0.01
37 29 0.36
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (33 bp):
GGATTACCAGTCCAGGCTAAATCCAGTCAATTA
Found at i:54381390 original size:40 final size:40
Alignment explanation
Indices: 54381287--54381507 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
54381277 TATTCGAATG
* *
54381287 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACT
* *
54381328 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACT
* ** * * *
54381368 ATATCCGGGCCAAAACCTGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
* * *
54381408 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
* * **
54381448 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
*
54381487 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
54381508 ATACTTGGGT
Statistics
Matches: 150, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
38 13 0.09
39 15 0.10
40 93 0.62
41 28 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACT
Found at i:54386750 original size:29 final size:29
Alignment explanation
Indices: 54386668--54386737 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
54386658 GTCATTTGGG
* * *
54386668 TTATC-AGACACTAGGTGTCAATGTTTATT
1 TTATCAAG-CACTATGTGTCGATGTTTATA
*
54386697 TTATCAAGCACTATGTGTCGGTGTTTATA
1 TTATCAAGCACTATGTGTCGATGTTTATA
54386726 TTATCAAGCACT
1 TTATCAAGCACT
54386738 TTGTACTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (29 bp):
TTATCAAGCACTATGTGTCGATGTTTATA
Found at i:54408468 original size:6 final size:6
Alignment explanation
Indices: 54408303--54408450 Score: 185
Period size: 6 Copynumber: 24.3 Consensus size: 6
54408293 AAGAAACATT
* *
54408303 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAAA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
54408352 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * *
54408400 ATCAGA ATCAGA ATTAGA ATCAGA ATTAG- GTGACAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
54408449 AT
1 AT
54408451 TAGGTGACAG
Statistics
Matches: 124, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
5 3 0.02
6 113 0.91
7 6 0.05
8 2 0.02
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:54408473 original size:25 final size:25
Alignment explanation
Indices: 54408360--54408475 Score: 132
Period size: 24 Copynumber: 4.7 Consensus size: 25
54408350 GAATCAGAAT
* *
54408360 CAGAATCAGAATCAGAATCA-G-AA
1 CAGAATCAGAATCAGAATTAGGTGA
* *
54408383 TCAGAATCAGAATCAGAATCA-G-AA
1 -CAGAATCAGAATCAGAATTAGGTGA
*
54408407 TCAGAATTAGAATCAGAATTAGGTGA
1 -CAGAATCAGAATCAGAATTAGGTGA
54408433 CAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATTAGGTGA
*
54408458 CAGAATCAGAACCAGAAT
1 CAGAATCAGAATCAGAAT
54408476 GTGAATGCAA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
24 42 0.49
25 42 0.49
26 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATTAGGTGA
Found at i:54409210 original size:27 final size:27
Alignment explanation
Indices: 54408869--54409197 Score: 424
Period size: 27 Copynumber: 12.2 Consensus size: 27
54408859 AACACCCTAG
* *
54408869 GGGTAAAATGATAATTTTATAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * *
54408896 GGGTAAAACGATAATTCTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*** * *
54408923 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * *
54408950 GGGTAAAATGGTAATTCTATAGATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*** *
54408977 GGGTAAAACATTAATTTTGTAAATTGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
54409004 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
54409031 GGGTAAAATGATAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * * *
54409058 GGGTAAAACGGTAATTCTATAAATCAA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
54409085 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
54409112 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* *
54409139 GGGTAAAATAGTAATTTTGTAAGTCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
54409166 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
54409193 GGGTA
1 GGGTA
54409198 CTTTGGTAAT
Statistics
Matches: 266, Mismatches: 36, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 266 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTGTAAATCGA
Found at i:54409257 original size:26 final size:27
Alignment explanation
Indices: 54409203--54409262 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
54409193 GGGTACTTTG
* *
54409203 GTAATTTTACAAGTTAAGGGTATTTCA
1 GTAATTTTACAAGTCAACGGTATTTCA
*
54409230 GTAATTTTACAA-TCGACGGTATTTCA
1 GTAATTTTACAAGTCAACGGTATTTCA
54409256 GTAATTT
1 GTAATTT
54409263 GATATTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (27 bp):
GTAATTTTACAAGTCAACGGTATTTCA
Found at i:54412257 original size:18 final size:18
Alignment explanation
Indices: 54412229--54412282 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
54412219 TGGCCCATTG
*
54412229 CAGTAACAGTAAACAGTA
1 CAGTAATAGTAAACAGTA
*
54412247 CAGTAGTAGTAAACAGTA
1 CAGTAATAGTAAACAGTA
54412265 CAGTAATAGTAAACAGTA
1 CAGTAATAGTAAACAGTA
54412283 TGCAAGTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (18 bp):
CAGTAATAGTAAACAGTA
Found at i:54412620 original size:26 final size:26
Alignment explanation
Indices: 54412590--54412804 Score: 162
Period size: 27 Copynumber: 8.0 Consensus size: 26
54412580 ATAAAAATAC
* *
54412590 ACCACATAGGGTAAAACAGTCATCTT
1 ACCACATAGGGCAAAACAGTCATTTT
* * *
54412616 ACCACAAAGGGCAAAACAATTATTTT
1 ACCACATAGGGCAAAACAGTCATTTT
* *
54412642 ACCATATAAGGGCAAAATAGTCATTTT
1 ACCACAT-AGGGCAAAACAGTCATTTT
* * * * *
54412669 ACCTCATAAGTGCGAAACAATTATTTT
1 ACCACAT-AGGGCAAAACAGTCATTTT
** *
54412696 ACCTTATAAGGGCAAAACAATCATTTT
1 ACCACAT-AGGGCAAAACAGTCATTTT
*
54412723 ACC-CTATAAAGGCAAAACAGTCATTTT
1 ACCAC-AT-AGGGCAAAACAGTCATTTT
* * *
54412750 ACCTCATAAGGGAAAAATAGTCATTTT
1 ACCACAT-AGGGCAAAACAGTCATTTT
* * *
54412777 ACCCCATAAGGGAAAAACAATCATTTT
1 ACCACAT-AGGGCAAAACAGTCATTTT
54412804 A
1 A
54412805 ACAATTTGGG
Statistics
Matches: 156, Mismatches: 30, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
26 26 0.17
27 129 0.83
28 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (26 bp):
ACCACATAGGGCAAAACAGTCATTTT
Found at i:54412667 original size:27 final size:26
Alignment explanation
Indices: 54412622--54412804 Score: 195
Period size: 27 Copynumber: 6.8 Consensus size: 26
54412612 TCTTACCACA
*
54412622 AAGGGCAAAACAATTATTTTACCATAT
1 AAGGGCAAAACAATCATTTTACC-TAT
* *
54412649 AAGGGCAAAATAGTCATTTTACCTCAT
1 AAGGGCAAAACAATCATTTTACCT-AT
* * *
54412676 AAGTGCGAAACAATTATTTTACCTTAT
1 AAGGGCAAAACAATCATTTTACC-TAT
54412703 AAGGGCAAAACAATCATTTTACCCTAT
1 AAGGGCAAAACAATCATTTTA-CCTAT
* *
54412730 AAAGGCAAAACAGTCATTTTACCTCAT
1 AAGGGCAAAACAATCATTTTACCT-AT
* * * *
54412757 AAGGGAAAAATAGTCATTTTACCCCAT
1 AAGGGCAAAACAATCATTTTA-CCTAT
*
54412784 AAGGGAAAAACAATCATTTTA
1 AAGGGCAAAACAATCATTTTA
54412805 ACAATTTGGG
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.03
27 123 0.93
28 5 0.04
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (26 bp):
AAGGGCAAAACAATCATTTTACCTAT
Found at i:54412693 original size:54 final size:52
Alignment explanation
Indices: 54412597--54412804 Score: 229
Period size: 54 Copynumber: 3.9 Consensus size: 52
54412587 TACACCACAT
* * *
54412597 AGGGTAAAACAGTCATCTTACCACA-AAGGGCAAAACAATTATTTTACCATATA
1 AGGGCAAAACAGTCATTTTACC-CATAAGGGCAAAACAATCATTTTACC-TATA
* * * *
54412650 AGGGCAAAATAGTCATTTTACCTCATAAGTGCGAAACAATTATTTTACCTTATA
1 AGGGCAAAACAGTCATTTTACC-CATAAGGGCAAAACAATCATTTTACC-TATA
* * *
54412704 AGGGCAAAACAATCATTTTACCCTATAAAGGCAAAACAGTCATTTTACCTCATA
1 AGGGCAAAACAGTCATTTTACCC-ATAAGGGCAAAACAATCATTTTACCT-ATA
* * *
54412758 AGGGAAAAATAGTCATTTTACCCCATAAGGGAAAAACAATCATTTTA
1 AGGGCAAAACAGTCATTTTA-CCCATAAGGGCAAAACAATCATTTTA
54412805 ACAATTTGGG
Statistics
Matches: 131, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
53 23 0.18
54 105 0.80
55 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (52 bp):
AGGGCAAAACAGTCATTTTACCCATAAGGGCAAAACAATCATTTTACCTATA
Found at i:54412722 original size:81 final size:80
Alignment explanation
Indices: 54412609--54412804 Score: 254
Period size: 81 Copynumber: 2.4 Consensus size: 80
54412599 GGTAAAACAG
* * * * *
54412609 TCATCTTACCACA-AAGGGCAAAACAATTATTTTACCATATAAGGGCAAAATAGTCATTTTACCT
1 TCATTTTACCCCATAAGGGCAAAACAATCATTTTACCATATAAAGGCAAAACAGTCATTTTACCT
54412673 CATAAGTGCGAAACAAT-
66 CATAAG-G-GAAA-AATA
** *
54412690 T-ATTTTACCTTATAAGGGCAAAACAATCATTTTACCCTATAAAGGCAAAACAGTCATTTTACCT
1 TCATTTTACCCCATAAGGGCAAAACAATCATTTTACCATATAAAGGCAAAACAGTCATTTTACCT
54412754 CATAAGGGAAAAATA
66 CATAAGGGAAAAATA
*
54412769 GTCATTTTACCCCATAAGGGAAAAACAATCATTTTA
1 -TCATTTTACCCCATAAGGGCAAAACAATCATTTTA
54412805 ACAATTTGGG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 4 0.04
80 10 0.10
81 84 0.83
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (80 bp):
TCATTTTACCCCATAAGGGCAAAACAATCATTTTACCATATAAAGGCAAAACAGTCATTTTACCT
CATAAGGGAAAAATA
Found at i:54416162 original size:18 final size:18
Alignment explanation
Indices: 54416136--54416172 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54416126 CTTGGCCCAT
54416136 TGCACTAACAGTAAACAG
1 TGCACTAACAGTAAACAG
*
54416154 TGCAGTAACAGTAAACAG
1 TGCACTAACAGTAAACAG
54416172 T
1 T
54416173 ATGCAAGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (18 bp):
TGCACTAACAGTAAACAG
Found at i:54416536 original size:27 final size:27
Alignment explanation
Indices: 54416506--54416698 Score: 136
Period size: 27 Copynumber: 7.1 Consensus size: 27
54416496 AACAGTTATC
*
54416506 TTACCATAAACGGGCAAAAAAATCATT
1 TTACCATAAAAGGGCAAAAAAATCATT
* * * * * *
54416533 TTACCACATAGGGGTAAAATAGTCATT
1 TTACCATAAAAGGGCAAAAAAATCATT
54416560 TTACCATAAAAGGGCAAAAAAATCATT
1 TTACCATAAAAGGGCAAAAAAATCATT
* * * * * *
54416587 TTACCACATAGGGGTAAAACAATCATC
1 TTACCATAAAAGGGCAAAAAAATCATT
* **
54416614 TTACCATAAAAAGGCAAAACGATCATT
1 TTACCATAAAAGGGCAAAAAAATCATT
** * * ** *
54416641 TTACCCCATAACGGCAAAACGACCATT
1 TTACCATAAAAGGGCAAAAAAATCATT
* * *
54416668 TTACC-TCATAAGGGCAAAATAGTCATT
1 TTACCAT-AAAAGGGCAAAAAAATCATT
54416695 TTAC
1 TTAC
54416699 ACCATAAGGG
Statistics
Matches: 129, Mismatches: 36, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
27 129 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (27 bp):
TTACCATAAAAGGGCAAAAAAATCATT
Found at i:54416704 original size:27 final size:26
Alignment explanation
Indices: 54416508--54416724 Score: 97
Period size: 27 Copynumber: 8.0 Consensus size: 26
54416498 CAGTTATCTT
*
54416508 ACCATAAACGGGCAAAAAAATCATTTTAC
1 ACCAT-AA-GGGC-AAAAAGTCATTTTAC
* *
54416537 -CACATAGGGGTAAAATAGTCATTTT--
1 AC-CATAAGGGCAAAA-AGTCATTTTAC
*
54416562 ACCATAAAAGGGCAAAAAAATCATTTTAC
1 ACCAT--AAGGGC-AAAAAGTCATTTTAC
* * * *
54416591 -CACATAGGGGTAAAACAATCATCTT--
1 AC-CATAAGGGCAAAA-AGTCATTTTAC
* *
54416616 ACCATAAAAAGGCAAAACGATCATTTTAC
1 ACCAT--AAGGGCAAAAAG-TCATTTTAC
* * * *
54416645 CCCATAACGGCAAAACGACCATTTTAC
1 ACCATAAGGGCAAAAAG-TCATTTTAC
54416672 -CTCATAAGGGCAAAATAGTCATTTTAC
1 AC-CATAAGGGCAAAA-AGTCATTTTAC
*
54416699 ACCATAAGGGAAAAACAGTCATTTTA
1 ACCATAAGGGCAAAA-AGTCATTTTA
54416725 ACAATTTAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
25 6 0.04
26 11 0.08
27 110 0.75
28 9 0.06
29 10 0.07
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (26 bp):
ACCATAAGGGCAAAAAGTCATTTTAC
Found at i:54416722 original size:54 final size:54
Alignment explanation
Indices: 54416483--54416724 Score: 249
Period size: 54 Copynumber: 4.5 Consensus size: 54
54416473 AAACATATAT
* * *
54416483 CACAT-AGTGGTAAAACAGTTATCTTACCATAAACGGGCAAAAAAATCATTTTAC
1 CACATAAG-GGTAAAACAGTCATTTTACCATAAAAGGGCAAAAAAATCATTTTAC
* *
54416537 CACATAGGGGTAAAATAGTCATTTTACCATAAAAGGGCAAAAAAATCATTTTAC
1 CACATAAGGGTAAAACAGTCATTTTACCATAAAAGGGCAAAAAAATCATTTTAC
* * * * **
54416591 CACATAGGGGTAAAACAATCATCTTACCATAAAAAGGCAAAACGATCATTTTAC
1 CACATAAGGGTAAAACAGTCATTTTACCATAAAAGGGCAAAAAAATCATTTTAC
* * * * * * *
54416645 CCCATAACGGCAAAAC-GACCATTTTACC-TCATAAGGGCAAAATAGTCATTTTA-
1 CACATAAGGGTAAAACAG-TCATTTTACCAT-AAAAGGGCAAAAAAATCATTTTAC
*
54416698 CACCATAAGGGAAAAACAGTCATTTTA
1 CA-CATAAGGGTAAAACAGTCATTTTA
54416725 ACAATTTAAG
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
53 2 0.01
54 152 0.97
55 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (54 bp):
CACATAAGGGTAAAACAGTCATTTTACCATAAAAGGGCAAAAAAATCATTTTAC
Found at i:54419194 original size:44 final size:45
Alignment explanation
Indices: 54419131--54419256 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 45
54419121 CACTAGGAAA
54419131 TAAGAAATCTGAACTTATTGAGTTGGT-CGAGTTCAT-GATATATG
1 TAAGAAATCTGAACTTATTGAGTTGGTCCGAGTTCATAG-TATATG
* *
54419175 TAAGAAATCCGAACTTATTGAGTTGGTCCAAGTTCATAGTATATG
1 TAAGAAATCTGAACTTATTGAGTTGGTCCGAGTTCATAGTATATG
* * * *
54419220 TGAAG-CATCTGAGCTCATTAAGTTGGTCCGAGTTCAT
1 T-AAGAAATCTGAACTTATTGAGTTGGTCCGAGTTCAT
54419257 TATGGATACG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 26 0.37
45 41 0.58
46 4 0.06
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (45 bp):
TAAGAAATCTGAACTTATTGAGTTGGTCCGAGTTCATAGTATATG
Found at i:54423620 original size:22 final size:22
Alignment explanation
Indices: 54423590--54423635 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
54423580 TTTTGAGTAA
*
54423590 AGGATAGATAGTCTGAATGAAG
1 AGGACAGATAGTCTGAATGAAG
54423612 AGGACAGATAGTCTGAATGAAG
1 AGGACAGATAGTCTGAATGAAG
54423634 AG
1 AG
54423636 TTTATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.20
Consensus pattern (22 bp):
AGGACAGATAGTCTGAATGAAG
Done.