Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 58 of 193
Found at i:18284103 original size:198 final size:198
Alignment explanation
Indices: 18283765--18284148 Score: 563
Period size: 198 Copynumber: 1.9 Consensus size: 198
18283755 TTGAGTTAGC
* ** * * *
18283765 CTAGTTTCGTTTAGAACAAACGAAGATTGATTTTGATTTTTAGTTTAAAATATATAAATTTTTTA
1 CTAGTTTCGTTTAGAAAAAACGAAGATTGATTTCAATTTGTAGCTTAAAATATATAAATTTTTGA
* * *
18283830 GTCTTGAAAGGTCATAAAGATCTGGCAGCAGAATTCTTATAAAACAGATTTAGTAGTGAATTCGA
66 GTCTTGAAAGATCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGAATTCGA
*
18283895 AAAATCACCAAAAATTGCACAAGATAAAATAGAAAATGAGTC-TTATATCCCTATAACTATACGG
131 AAAATCACCAAAAATTGCAAAAGATAAAATAGAAAATGA-TCTTTATATCCCTATAACTATACGG
18283959 AAGT
195 AAGT
* * * * * *
18283963 CTAGTTTCTTTTAGAAAAAATGGAGATTGATTTCAATTTGTAGCTTAACATATATTAATTTTTGG
1 CTAGTTTCGTTTAGAAAAAACGAAGATTGATTTCAATTTGTAGCTTAAAATATATAAATTTTTGA
* * *
18284028 GTGTTGAAAGATCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGACTTTGA
66 GTCTTGAAAGATCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGAATTCGA
* *
18284093 AAAATCACCAAAAATTGCAAAAGATAAAATAGGAAATTATCTTTATATCCCTATAA
131 AAAATCACCAAAAATTGCAAAAGATAAAATAGAAAATGATCTTTATATCCCTATAA
18284149 TCATACAAAA
Statistics
Matches: 164, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
197 2 0.01
198 162 0.99
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (198 bp):
CTAGTTTCGTTTAGAAAAAACGAAGATTGATTTCAATTTGTAGCTTAAAATATATAAATTTTTGA
GTCTTGAAAGATCATAAAAATCTGGCAGCAGAATTCTTATAAAACAGATTTAGCAGTGAATTCGA
AAAATCACCAAAAATTGCAAAAGATAAAATAGAAAATGATCTTTATATCCCTATAACTATACGGA
AGT
Found at i:18292524 original size:57 final size:57
Alignment explanation
Indices: 18292447--18292605 Score: 189
Period size: 57 Copynumber: 2.8 Consensus size: 57
18292437 ATATTCTAAC
* * * * * *
18292447 ATCAATCCATAAGATTATACCAATTGCA-ATTAACTCATTTCAATGGCATATCCCA-TT
1 ATCAATCGATAAGGTTATACCAATTACACA-TAATTCATTTCAATGACATAT-CAAGTT
* *
18292504 ATCAATCTA-AATGGTTATACCATTTACACATAATTCATTTCAATGACATATCAAGTT
1 ATCAATCGATAA-GGTTATACCAATTACACATAATTCATTTCAATGACATATCAAGTT
*
18292561 ATCAATCGATAAGGTTATACTAATTACACATAATTCATTTCAATG
1 ATCAATCGATAAGGTTATACCAATTACACATAATTCATTTCAATG
18292606 CATGTGAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.05
57 81 0.92
58 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (57 bp):
ATCAATCGATAAGGTTATACCAATTACACATAATTCATTTCAATGACATATCAAGTT
Found at i:18294515 original size:15 final size:16
Alignment explanation
Indices: 18294491--18294522 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18294481 TGAAAATTTA
18294491 AAAAATTATAAAATAT
1 AAAAATTATAAAATAT
18294507 AAAAA-TATAAAATAT
1 AAAAATTATAAAATAT
18294522 A
1 A
18294523 TTTTAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATTATAAAATAT
Found at i:18295192 original size:22 final size:21
Alignment explanation
Indices: 18295167--18295220 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
18295157 ACAAATATAA
*
18295167 AATATAAAATTATTAAATGTTT
1 AATATAAAAATATTAAAT-TTT
*
18295189 AATATAAAAATATTATATTTT
1 AATATAAAAATATTAAATTTT
18295210 AA-A-AAAAATAT
1 AATATAAAAATAT
18295221 AGATAAGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 1 0.03
21 5 0.17
22 16 0.53
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATAAAAATATTAAATTTT
Found at i:18302344 original size:29 final size:30
Alignment explanation
Indices: 18302298--18302356 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
18302288 GAATTGGATC
*
18302298 AAATCAAAATTTTATGTATA-AAGTTGCACA
1 AAATCAAAATTTCATGTATACAA-TTGCACA
18302328 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATACAATTGCACA
18302357 TTAAACCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATACAATTGCACA
Found at i:18307050 original size:20 final size:18
Alignment explanation
Indices: 18307026--18307074 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
18307016 AATAGTATTT
18307026 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
18307044 GTAATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
18307064 T-TTAATTTAAT
1 TATTAATTTAAT
18307075 GTTTATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 4 0.15
20 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:18307068 original size:51 final size:48
Alignment explanation
Indices: 18306967--18307069 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
18306957 ATTCCAAAAA
* * * *
18306967 TAATATTATTTTAATAATTTAATATTAAATTTATTTTAATACTGATTT
1 TAATAGTATTTTAATAATTTAATATTAAATTTATCTTAATACTAAATT
* *
18307015 TAATAGTATTTTATTAATTTAATATTAAAGTAATTATCTTAATATTAAATT
1 TAATAGTATTTTAATAATTTAATATTAAA-T--TTATCTTAATACTAAATT
18307066 TAAT
1 TAAT
18307070 TTAATGTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 27 0.59
49 1 0.02
51 18 0.39
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (48 bp):
TAATAGTATTTTAATAATTTAATATTAAATTTATCTTAATACTAAATT
Found at i:18307938 original size:18 final size:20
Alignment explanation
Indices: 18307897--18307943 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
18307887 ACTTAGGTAT
* *
18307897 CGATACCAATTCTTCAAAAT
1 CGATACCAATCCTTCAAAAA
18307917 CGATACCAA-CCTT-AAAAA
1 CGATACCAATCCTTCAAAAA
18307935 CGATACCAA
1 CGATACCAA
18307944 AACCACATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.52
19 3 0.12
20 9 0.36
ACGTcount: A:0.45, C:0.28, G:0.06, T:0.21
Consensus pattern (20 bp):
CGATACCAATCCTTCAAAAA
Found at i:18308726 original size:22 final size:22
Alignment explanation
Indices: 18308698--18308761 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
18308688 CTAATGGACA
* *
18308698 GAGAGCACTAAGGTGTTATACG
1 GAGAGCACTAAGGTGCTAAACG
*
18308720 GAGAGCA-TGAATGTGCTAAACG
1 GAGAGCACT-AAGGTGCTAAACG
*
18308742 GAGAGCACTAATTGTGCTAA
1 GAGAGCACTAA-GGTGCTAA
18308762 TAAACGGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.03
22 26 0.72
23 9 0.25
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (22 bp):
GAGAGCACTAAGGTGCTAAACG
Found at i:18314426 original size:25 final size:26
Alignment explanation
Indices: 18314368--18314427 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
18314358 TGATCTGGCC
18314368 TTGTGGCATAATCTGTATGATGCCTG
1 TTGTGGCATAATCTGTATGATGCCTG
* * * *
18314394 TT-TAGCATACTTTGTATGTTGCCT-
1 TTGTGGCATAATCTGTATGATGCCTG
18314418 TTGTGGCATA
1 TTGTGGCATA
18314428 TTCTAAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 2 0.07
25 24 0.86
26 2 0.07
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.43
Consensus pattern (26 bp):
TTGTGGCATAATCTGTATGATGCCTG
Found at i:18317588 original size:24 final size:24
Alignment explanation
Indices: 18317561--18317713 Score: 162
Period size: 24 Copynumber: 6.4 Consensus size: 24
18317551 ACAATTTCAT
* *
18317561 TACGTTTACGCTCGCCAGGTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
18317585 TACGTTTATGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* * **
18317609 TACGTTTACACTCGTCAACTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* *
18317633 CATGTTTACGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
* **
18317657 TATGTTTACGCTCGTCAGCTTGCA
1 TACGTTTACGCTCGTCAGCTTATA
* * *
18317681 CACATTTGCGCTCGTCAGCTTATA
1 TACGTTTACGCTCGTCAGCTTATA
*
18317705 TACATTTAC
1 TACGTTTAC
18317714 ACTATTATGA
Statistics
Matches: 104, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 104 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCTTATA
Found at i:18317640 original size:48 final size:48
Alignment explanation
Indices: 18317586--18317716 Score: 190
Period size: 48 Copynumber: 2.7 Consensus size: 48
18317576 CAGGTTATAT
*
18317586 ACGTTTATGCTCGTCAGCTTATATACGTTTACACTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAACTTGCAC
* * * *
18317634 ATGTTTACGCTCGTCAGCTTATATATGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAACTTGCAC
* * *
18317682 ACATTTGCGCTCGTCAGCTTATATACATTTACACT
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACT
18317717 ATTATGAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (48 bp):
ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAACTTGCAC
Found at i:18325261 original size:24 final size:24
Alignment explanation
Indices: 18325229--18325451 Score: 230
Period size: 24 Copynumber: 9.3 Consensus size: 24
18325219 CAATTTTATT
*
18325229 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
* *
18325253 ACGTTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
* *
18325277 ACGTTTACACTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
18325301 ACGTTTACACTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
18325325 ACGTTTACGCTCATCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
18325349 ACGTTTATGCTCATCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
18325373 ACATTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
** * *
18325397 GTGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
18325421 ACATTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
18325445 ACGTTTA
1 ACGTTTA
18325452 TGCTATTATG
Statistics
Matches: 162, Mismatches: 37, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 162 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTACAC
Found at i:18325346 original size:72 final size:72
Alignment explanation
Indices: 18325229--18325440 Score: 280
Period size: 72 Copynumber: 2.9 Consensus size: 72
18325219 CAATTTTATT
** * *
18325229 ACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAG
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAG
18325294 CTTGCAC
66 CTTGCAC
* * * *
18325301 ACGTTTACACTCGTCAGCTTATATACGTTTACGCTCATCAGCTTATATACGTTTATGCTCATCAG
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAG
18325366 CTTGCAC
66 CTTGCAC
* ** * ** * *
18325373 ACATTTACGCTCGTCAGCTTATATGTGTTTACGCTCGTCAACTTGCACACATTTACGCTCGTCAG
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAG
18325438 CTT
66 CTT
18325441 ATATACGTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 120 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (72 bp):
ACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAG
CTTGCAC
Found at i:18329433 original size:29 final size:26
Alignment explanation
Indices: 18329390--18329447 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
18329380 GTATTTGAAA
*
18329390 TAATTAAAAATATTATTTAAATTATTATT
1 TAATTAAAAACATTATTT---TTATTATT
18329419 TAATTAAAAACATTATTTTTATTATT
1 TAATTAAAAACATTATTTTTATTATT
18329445 TAA
1 TAA
18329448 ATAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 11 0.39
29 17 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTAAAAACATTATTTTTATTATT
Found at i:18329671 original size:20 final size:21
Alignment explanation
Indices: 18329638--18329677 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18329628 GGCTTATATA
*
18329638 TTTTTATAATTTTTGTAATTC
1 TTTTTATAATTTTTATAATTC
*
18329659 TTTTTTTAA-TTTTATAATT
1 TTTTTATAATTTTTATAATT
18329678 TTCGCAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTATAATTTTTATAATTC
Found at i:18329727 original size:21 final size:23
Alignment explanation
Indices: 18329694--18329737 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
18329684 AGTATTTAAA
18329694 ATTTTAATAATTTT-TAA-ATTT
1 ATTTTAATAATTTTATAAGATTT
18329715 ATTTTAA-AGATTTTATAAGATTT
1 ATTTTAATA-ATTTTATAAGATTT
18329738 TTTCTAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.05
21 12 0.60
22 3 0.15
23 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
ATTTTAATAATTTTATAAGATTT
Found at i:18334444 original size:15 final size:16
Alignment explanation
Indices: 18334417--18334448 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18334407 TTATCACATC
18334417 ATTAAATAATTTTAAA
1 ATTAAATAATTTTAAA
18334433 ATTAAA-AATTTTAAA
1 ATTAAATAATTTTAAA
18334448 A
1 A
18334449 ATTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATAATTTTAAA
Found at i:18337929 original size:20 final size:19
Alignment explanation
Indices: 18337904--18337940 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18337894 TGTATGGAGG
18337904 TTTTTTTT-TTATATTTTAA
1 TTTTTTTTCTTAT-TTTTAA
18337923 TTTTTTTTCTTATTTTTA
1 TTTTTTTTCTTATTTTTA
18337941 TTCTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTTCTTATTTTTAA
Found at i:18339666 original size:30 final size:30
Alignment explanation
Indices: 18339632--18339934 Score: 229
Period size: 30 Copynumber: 10.2 Consensus size: 30
18339622 TCAAAATGCC
* ***
18339632 ATTTTGGAGAAGTTTGGGGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* *
18339662 ATTTTAAAGAAG-TTCAAGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* * ***
18339691 AGTTTAGAAAAGTTTGGGGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* * ** * *
18339721 AGTTTAGAGAAATTTAGGGGTCAAAATTTA
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* * ** *
18339751 ATTTTGGAAAAGTTTTGAGGTTAAAATGTG
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* *
18339781 ATTTT-GGGAAAGTTTAAAGGTCAAAATGTA
1 ATTTTAGAG-AAGTTTAAAGGTTAAAATGTA
* * *
18339811 ATTTTAAAGAAATTT-AAGGATCAAAATGTA
1 ATTTTAGAGAAGTTTAAAGG-TTAAAATGTA
**
18339841 ATTTTAGAGAAGTTTGGAGGTTAAAATGTA
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
* * *
18339871 ATTTTTTGAGAAATTT-AAGGTTAAAATGTG
1 A-TTTTAGAGAAGTTTAAAGGTTAAAATGTA
* * *
18339901 ATTTTAG-GAAGTTTAAGGGTCAAAATGTG
1 ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
18339930 ATTTT
1 ATTTT
18339935 TAAAGAAAAT
Statistics
Matches: 220, Mismatches: 46, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
28 6 0.03
29 50 0.23
30 148 0.67
31 16 0.07
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
ATTTTAGAGAAGTTTAAAGGTTAAAATGTA
Found at i:18339776 original size:60 final size:60
Alignment explanation
Indices: 18339622--18339934 Score: 255
Period size: 60 Copynumber: 5.2 Consensus size: 60
18339612 GAATTCGAGA
** * * * * *
18339622 TCAAAATGCCATTTTGGAGAAGTTTGGGGGTTAAAATGTAATTTTAAAGAAGTTCAA-GG
1 TCAAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTAGAGAAGTTTAAGGG
* * * * * * * *
18339681 TTAAAATGTAAGTTTAGAAAAGTTTGGGGGTTAAAATGTAAGTTTAGAGAAATTTAGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTAGAGAAGTTTAAGGG
* * * *
18339741 TCAAAATTTAATTTTGGAAAAGTTTTGAGGTTAAAATGTGATTTT-GGGAAAGTTTAAAGG
1 TCAAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTAGAG-AAGTTTAAGGG
** * * *
18339801 TCAAAATGTAATTTT--AAAGAAATTTAAGGATCAAAATGTAATTTTAGAGAAGTTT-GGAGG
1 TCAAAATGTAATTTTGGAAA-AGTTTTGAGG-TTAAAATGTAATTTTAGAGAAGTTTAAG-GG
* * * *
18339861 TTAAAATGTAATTTTTTGAGAAA--TTTAAGGTTAAAATGTGATTTTAG-GAAGTTTAAGGG
1 TCAAAATGTAA-TTTTGGA-AAAGTTTTGAGGTTAAAATGTAATTTTAGAGAAGTTTAAGGG
*
18339920 TCAAAATGTGATTTT
1 TCAAAATGTAATTTT
18339935 TAAAGAAAAT
Statistics
Matches: 205, Mismatches: 38, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
58 7 0.03
59 73 0.36
60 108 0.53
61 13 0.06
63 2 0.01
64 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (60 bp):
TCAAAATGTAATTTTGGAAAAGTTTTGAGGTTAAAATGTAATTTTAGAGAAGTTTAAGGG
Found at i:18339936 original size:90 final size:89
Alignment explanation
Indices: 18339649--18339934 Score: 301
Period size: 90 Copynumber: 3.2 Consensus size: 89
18339639 AGAAGTTTGG
* * ** * ***
18339649 GGGTTAAAATGTAATTTTAAAGAAG-TTCAAGGTTAAAATGTAAGTTT-AGAAAAGTTTGGGGGT
1 GGGTCAAAATGTAATTTTAGAGAAGTTTGGAGGTTAAAATGTAATTTTGAG-AAAGTTTAAAGGT
* *
18339712 TAAAATGTAAGTTTAGAGAAATTTAG
65 TAAAATGTAATTTTAG-GAAATTTAA
* * * * * * *
18339738 GGGTCAAAATTTAATTTTGGAAAAGTTTTGAGGTTAAAATGTGATTTTGGGAAAGTTTAAAGGTC
1 GGGTCAAAATGTAATTTTAGAGAAGTTTGGAGGTTAAAATGTAATTTTGAGAAAGTTTAAAGGTT
*
18339803 AAAATGTAATTTTAAAGAAATTTAA
66 AAAATGTAATTTT-AGGAAATTTAA
*
18339828 GGATCAAAATGTAATTTTAGAGAAGTTTGGAGGTTAAAATGTAATTTTTTGAGAAA-TTT-AAGG
1 GGGTCAAAATGTAATTTTAGAGAAGTTTGGAGGTTAAAATGTAA--TTTTGAGAAAGTTTAAAGG
* *
18339891 TTAAAATGTGATTTTAGGAAGTTTAA
64 TTAAAATGTAATTTTAGGAAATTTAA
*
18339917 GGGTCAAAATGTGATTTT
1 GGGTCAAAATGTAATTTT
18339935 TAAAGAAAAT
Statistics
Matches: 162, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
89 45 0.28
90 103 0.64
91 5 0.03
92 9 0.06
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (89 bp):
GGGTCAAAATGTAATTTTAGAGAAGTTTGGAGGTTAAAATGTAATTTTGAGAAAGTTTAAAGGTT
AAAATGTAATTTTAGGAAATTTAA
Found at i:18345081 original size:3 final size:3
Alignment explanation
Indices: 18345073--18345102 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
18345063 TACCATTGCC
18345073 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18345103 TGACAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18362145 original size:10 final size:10
Alignment explanation
Indices: 18362105--18362137 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18362095 TAAGGGAGAG
18362105 AAGAGAAGAA
1 AAGAGAAGAA
*
18362115 ATG-GAAGAA
1 AAGAGAAGAA
18362124 AAGAGAAGAA
1 AAGAGAAGAA
18362134 AAGA
1 AAGA
18362138 TGAGAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (10 bp):
AAGAGAAGAA
Found at i:18366483 original size:12 final size:12
Alignment explanation
Indices: 18366466--18366490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18366456 ATTAAATAAT
18366466 TAATAGCATTCA
1 TAATAGCATTCA
18366478 TAATAGCATTCA
1 TAATAGCATTCA
18366490 T
1 T
18366491 CATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:18366739 original size:14 final size:12
Alignment explanation
Indices: 18366708--18366741 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
18366698 AATGGAAAAG
18366708 CTAGAGAGAACA
1 CTAGAGAGAACA
18366720 CTAGAGAGAACA
1 CTAGAGAGAACA
*
18366732 CTAAAGAGAA
1 CTAGAGAGAA
18366742 AGAAGAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.24, T:0.09
Consensus pattern (12 bp):
CTAGAGAGAACA
Found at i:18367867 original size:12 final size:12
Alignment explanation
Indices: 18367852--18367876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18367842 ATTAAAAAAT
18367852 TAATAGCATTCA
1 TAATAGCATTCA
18367864 TAATAGCATTCA
1 TAATAGCATTCA
18367876 T
1 T
18367877 CTTGTTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:18373662 original size:35 final size:35
Alignment explanation
Indices: 18373616--18373687 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
18373606 TCCATCAGCG
18373616 TAAAAGAAGGATTAAAGAATACAATCGAAGCTTAC
1 TAAAAGAAGGATTAAAGAATACAATCGAAGCTTAC
18373651 TAAAAGAAGGATTAAAGAATACAATCGAAGCTTAC
1 TAAAAGAAGGATTAAAGAATACAATCGAAGCTTAC
18373686 TA
1 TA
18373688 TCTCTAGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (35 bp):
TAAAAGAAGGATTAAAGAATACAATCGAAGCTTAC
Found at i:18388924 original size:22 final size:22
Alignment explanation
Indices: 18388870--18388917 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
18388860 TGTTCTTAAC
18388870 TAAACAAAAATTAACAAAGTCA
1 TAAACAAAAATTAACAAAGTCA
18388892 TAAACAAAAATTAACAAAGTCA
1 TAAACAAAAATTAACAAAGTCA
18388914 TAAA
1 TAAA
18388918 TAGAAATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.65, C:0.12, G:0.04, T:0.19
Consensus pattern (22 bp):
TAAACAAAAATTAACAAAGTCA
Found at i:18389130 original size:6 final size:5
Alignment explanation
Indices: 18389113--18389159 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
18389103 TATCAAATTT
18389113 TTTTC TTTTC TTTCTC TTTCTC TTTTC TTATTAC TTTT- TTTTC TTTT
1 TTTTC TTTTC TTT-TC TTT-TC TTTTC TT-TT-C TTTTC TTTTC TTTT
18389160 TTCAAATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.11
5 16 0.42
6 15 0.39
7 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:18396644 original size:79 final size:79
Alignment explanation
Indices: 18396513--18396671 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
18396503 CCATATCTAA
*
18396513 ACGTGGAAGTATTTTGATTTCCCCAAGGTTGTTGAGATCGGTTATTTTATGAGTTACCAAATGAA
1 ACGTGGAAGTATTTTGATTTCCCCAAGGTTGTTGAGATCAGTTATTTTATGAGTTACCAAATGAA
18396578 CTTCCTCTGATGTT
66 CTTCCTCTGATGTT
*
18396592 ACGTGGAAGTATTTTGATTTCCCCAAGGTTGTTGAGATCAGTTATTTTATGAGTTACCTAATGAA
1 ACGTGGAAGTATTTTGATTTCCCCAAGGTTGTTGAGATCAGTTATTTTATGAGTTACCAAATGAA
18396657 CTTCCTCTGATGTT
66 CTTCCTCTGATGTT
18396671 A
1 A
18396672 TTGACGTAGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (79 bp):
ACGTGGAAGTATTTTGATTTCCCCAAGGTTGTTGAGATCAGTTATTTTATGAGTTACCAAATGAA
CTTCCTCTGATGTT
Found at i:18402845 original size:21 final size:20
Alignment explanation
Indices: 18402821--18402896 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
18402811 ACATTCACCG
18402821 GTTTTGGTTCTGGTGAAACTT
1 GTTTTGGTTCTGGT-AAACTT
* *
18402842 GTTTAGGTTCTGGTAAAGTT
1 GTTTTGGTTCTGGTAAACTT
* * * *
18402862 AGTTCTGATTCCGGTAAAACTA
1 -GTTTTGGTTCTGGT-AAACTT
*
18402884 GTTATGGTTCTGG
1 GTTTTGGTTCTGG
18402897 AAAAGTTGGA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.12
21 33 0.79
22 4 0.10
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.42
Consensus pattern (20 bp):
GTTTTGGTTCTGGTAAACTT
Found at i:18404688 original size:16 final size:15
Alignment explanation
Indices: 18404655--18404697 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
18404645 CTAAAGTATT
*
18404655 CTAAACTAAATTAAA
1 CTAAATTAAATTAAA
*
18404670 CTAAGTTAAATTAAAA
1 CTAAATTAAATT-AAA
18404686 CTAAATTAAATT
1 CTAAATTAAATT
18404698 CCTATGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (15 bp):
CTAAATTAAATTAAA
Found at i:18415201 original size:13 final size:12
Alignment explanation
Indices: 18415181--18415215 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
18415171 ACAAACATAA
18415181 TTTTTTTCTTAT
1 TTTTTTTCTTAT
*
18415193 TTCTTTTTCTCAT
1 TT-TTTTTCTTAT
18415206 TTTTTTTCTT
1 TTTTTTTCTT
18415216 TTTAAGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTTAT
Found at i:18415834 original size:17 final size:17
Alignment explanation
Indices: 18415792--18415840 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
18415782 ACTAAATTAA
18415792 ACAA-AAAAATGCAATG
1 ACAATAAAAATGCAATG
18415808 ACAAAATAAAAATGCAATG
1 AC--AATAAAAATGCAATG
*
18415827 ACAATAAAGATGCA
1 ACAATAAAAATGCA
18415841 TGCAAACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.07
17 11 0.38
18 2 0.07
19 14 0.48
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.14
Consensus pattern (17 bp):
ACAATAAAAATGCAATG
Found at i:18428867 original size:14 final size:14
Alignment explanation
Indices: 18428848--18428877 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18428838 TCTGCAAATT
18428848 TATAAAGATCACAC
1 TATAAAGATCACAC
18428862 TATAAAGATCACAC
1 TATAAAGATCACAC
18428876 TA
1 TA
18428878 GATCTGCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (14 bp):
TATAAAGATCACAC
Found at i:18430778 original size:17 final size:17
Alignment explanation
Indices: 18430756--18430799 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
18430746 ATTGTGGGCG
*
18430756 CAATAAATTTGCGACCA
1 CAATAAATTTACGACCA
18430773 CAATAAATTTACGACCA
1 CAATAAATTTACGACCA
*
18430790 CAAGAAATTT
1 CAATAAATTT
18430800 TATCGGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.25
Consensus pattern (17 bp):
CAATAAATTTACGACCA
Found at i:18439623 original size:14 final size:15
Alignment explanation
Indices: 18439604--18439637 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
18439594 CCCAATTTTA
*
18439604 TTTTTATTTTTA-TT
1 TTTTTAGTTTTAGTT
18439618 TTTTTAGTTTTAGTT
1 TTTTTAGTTTTAGTT
18439633 TTTTT
1 TTTTT
18439638 TTTGCACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTAGTTTTAGTT
Found at i:18439628 original size:20 final size:20
Alignment explanation
Indices: 18439599--18439640 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18439589 AGCAACCCAA
*
18439599 TTTTATTTTTA-TTTTTATTT
1 TTTTAGTTTTAGTTTTT-TTT
18439619 TTTTAGTTTTAGTTTTTTTT
1 TTTTAGTTTTAGTTTTTTTT
18439639 TT
1 TT
18439641 GCACTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (20 bp):
TTTTAGTTTTAGTTTTTTTT
Found at i:18439883 original size:17 final size:16
Alignment explanation
Indices: 18439835--18439884 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
18439825 TATTTTTATC
18439835 TGTTGTTTT-TGTTGT
1 TGTTGTTTTATGTTGT
*
18439850 TG-TGTGTTCACTGTTGT
1 TGTTGT-TTTA-TGTTGT
18439867 TGTTGTTTTATGCTTGT
1 TGTTGTTTTATG-TTGT
18439884 T
1 T
18439885 TTGCTGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.11
15 4 0.14
16 2 0.07
17 16 0.57
18 3 0.11
ACGTcount: A:0.04, C:0.06, G:0.26, T:0.64
Consensus pattern (16 bp):
TGTTGTTTTATGTTGT
Found at i:18442758 original size:106 final size:106
Alignment explanation
Indices: 18442639--18442852 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 106
18442629 TAAAGTCGCC
*
18442639 ACCAATCTTTTTATATGGTGTGATTGGATCACCACAAAATGTTTAAAATCCGTTTTGAAAAATAT
1 ACCAATCTTTTTATATGGTGTGATTGGATCACCACAAAATGTTTAAAATCCGTTTTGAAAAACAT
18442704 TTTGGTCTTCAAAATTCAAAAAATGGGTTCGGGAGTCGGTT
66 TTTGGTCTTCAAAATTCAAAAAATGGGTTCGGGAGTCGGTT
18442745 ACCAATCTTTTTATATGGTGTGATTGGATCACCACAAAATGTTTAAAATCCGTTTTGAAAAACAT
1 ACCAATCTTTTTATATGGTGTGATTGGATCACCACAAAATGTTTAAAATCCGTTTTGAAAAACAT
18442810 TTTGGTCTTCAAAATTCAAAAAATGGGTTCGGGAGTCGGTT
66 TTTGGTCTTCAAAATTCAAAAAATGGGTTCGGGAGTCGGTT
18442851 AC
1 AC
18442853 GTATGAGGAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (106 bp):
ACCAATCTTTTTATATGGTGTGATTGGATCACCACAAAATGTTTAAAATCCGTTTTGAAAAACAT
TTTGGTCTTCAAAATTCAAAAAATGGGTTCGGGAGTCGGTT
Found at i:18443822 original size:28 final size:30
Alignment explanation
Indices: 18443760--18443824 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
18443750 ATTTTTGAGG
18443760 AATTTGGGGATCAAAATCTAAAGTTTTGGAA
1 AATTT-GGGATCAAAATCTAAAGTTTTGGAA
* *
18443791 AATTTGGGATTAAAATC-GAAG-TTTGGAA
1 AATTTGGGATCAAAATCTAAAGTTTTGGAA
18443819 AATTTG
1 AATTTG
18443825 AGGTTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 13 0.41
29 3 0.09
30 11 0.34
31 5 0.16
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
AATTTGGGATCAAAATCTAAAGTTTTGGAA
Found at i:18443915 original size:29 final size:28
Alignment explanation
Indices: 18443831--18443989 Score: 133
Period size: 29 Copynumber: 5.5 Consensus size: 28
18443821 TTTGAGGTTG
* * *
18443831 AAAATGTGATTTTTGGATGTTTATGGAC
1 AAAATGTAATTTTTGGATGTTTAGGGGC
18443859 AAAATGGTAATTTTTGGATGTTTAGGGGC
1 AAAAT-GTAATTTTTGGATGTTTAGGGGC
** *
18443888 AAAATGGTAATTTTTGGATGTTCGGGGGT
1 AAAAT-GTAATTTTTGGATGTTTAGGGGC
* *
18443917 AAAATGTAA-TTTTGGAAAAGTTT-GGGGTG
1 AAAATGTAATTTTTGG--ATGTTTAGGGG-C
* * * **
18443946 AAAATGTGATTTTTGGAAGTTCAAGGGTA
1 AAAATGTAATTTTTGGATGTT-TAGGGGC
18443975 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
18443990 AGAAGTTCGA
Statistics
Matches: 110, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
27 6 0.05
28 18 0.16
29 77 0.70
30 9 0.08
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTTGGATGTTTAGGGGC
Found at i:18444007 original size:29 final size:29
Alignment explanation
Indices: 18443859--18444017 Score: 146
Period size: 29 Copynumber: 5.4 Consensus size: 29
18443849 GTTTATGGAC
* * **
18443859 AAAATGGTAATTTTTGGATGTT-TAGGGGC
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTA
* *
18443888 AAAATGGTAATTTTTGGATGTTCGGGGGT-
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTA
* *
18443917 AAAATGTAA-TTTTGGAAAAGTTTG-GGGTG
1 AAAATGTAATTTTTGG--AAGTTCGAGGGTA
* *
18443946 AAAATGTGATTTTTGGAAGTTCAAGGGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGTA
*
18443975 AAAATGTAATTTTTGAGAAGTTCGAGAGTA
1 AAAATGTAATTTTTG-GAAGTTCGAGGGTA
18444005 AAAATGTAATTTT
1 AAAATGTAATTTT
18444018 AGAAAATTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
27 6 0.05
28 13 0.12
29 58 0.52
30 34 0.31
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTA
Found at i:18444045 original size:60 final size:60
Alignment explanation
Indices: 18443962--18444118 Score: 165
Period size: 60 Copynumber: 2.6 Consensus size: 60
18443952 TGATTTTTGG
* * *
18443962 AAGTTCAAGGGTAAAAATGTAATTTTTGAGAAGTTCGAGAGTAAAAATGTAATTTTAGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAGAAGTTCAAGAGTAAAAATGTAATTTTAGAA
* * * * * * *
18444022 AATTTTAAGGGTCAAAATGTAA-TTTTGAAAATTTTTAAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAGAA-GTTCAAGAGTAAAAATGTAATTTTAGAA
* * *
18444082 AAGTTTAGGGGTCAAAATATGATTTTT-AGAAAGTTCA
1 AAGTTTAAGGGTCAAAATGTAATTTTTGAG-AAGTTCA
18444119 GGGACCTTCT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
59 8 0.10
60 63 0.82
61 6 0.08
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (60 bp):
AAGTTTAAGGGTCAAAATGTAATTTTTGAGAAGTTCAAGAGTAAAAATGTAATTTTAGAA
Found at i:18444107 original size:30 final size:30
Alignment explanation
Indices: 18443878--18444099 Score: 174
Period size: 30 Copynumber: 7.5 Consensus size: 30
18443868 ATTTTTGGAT
*
18443878 GTTTAGGGG-CAAAATGGTAATTTTTGG--AT
1 GTTTAGGGGTCAAAAT-GTAA-TTTTGGAAAA
**
18443907 GTTCGGGGGT-AAAATGTAATTTTGGAAAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* *
18443936 GTTT-GGGGTGAAAATGTGATTTTTGG--AA
1 GTTTAGGGGTCAAAATGT-AATTTTGGAAAA
* * * * *
18443964 GTTCAAGGGTAAAAATGTAATTTTTGAGAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* * * *
18443994 G-TTCGAGAGTAAAAATGTAATTTTAGAAAA
1 GTTTAG-GGGTCAAAATGTAATTTTGGAAAA
* *
18444024 TTTTAAGGGTCAAAATGTAATTTT-GAAAA
1 GTTTAGGGGTCAAAATGTAATTTTGGAAAA
* *
18444053 TTTTTAAGGGTCAAAATGTAATTTTGGAAAA
1 -GTTTAGGGGTCAAAATGTAATTTTGGAAAA
18444084 GTTTAGGGGTCAAAAT
1 GTTTAGGGGTCAAAAT
18444100 ATGATTTTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 23
0.77 0.11 0.11
Matches are distributed among these distances:
27 6 0.04
28 20 0.13
29 40 0.25
30 85 0.54
31 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
GTTTAGGGGTCAAAATGTAATTTTGGAAAA
Found at i:18445868 original size:16 final size:16
Alignment explanation
Indices: 18445825--18445868 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
18445815 TGGACATTAG
* *
18445825 TAAATTTAAACAACTT
1 TAAATTTAAATAAATT
*
18445841 TAAACTTAAAATAAATT
1 TAAA-TTTAAATAAATT
18445858 TAAATTTAAAT
1 TAAATTTAAAT
18445869 TCTGTTTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATAAATT
Found at i:18446486 original size:39 final size:39
Alignment explanation
Indices: 18446427--18446722 Score: 205
Period size: 39 Copynumber: 7.7 Consensus size: 39
18446417 AATGACTGCA
* *
18446427 ATCTGCCCTAGGCTTAGGGTAAGAGATTTG-CTGACGGTG
1 ATCTGCCCCAGGCTCAGGGTAAGAGA-TTGACTGACGGTG
* * * * * * **
18446466 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGACGGTG
* *
18446505 ATCTGCCCCAAGCTC-GAGGTAAGAGATTTACTGACGGTG
1 ATCTGCCCCAGGCTCAG-GGTAAGAGATTGACTGACGGTG
* * * * * * ** *
18446544 ATCTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTGTA
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGACGGTG
* * * *
18446583 ATCTGCCCCAGGATTAAGGTAAGAGATTGACT-A-GTTG
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGACGGTG
* * *
18446620 ATCTGCCCCAGGCTC-GAGGTAAGAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCAG-GGTAAGAGATTGACTGACGGTG
* *
18446657 CAATCTACCCCAGGCTCAGGGTAAGAGATTGACTG--GTTG
1 --ATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGACGGTG
*
18446696 ATCTGCCCCAGGCTCAGGGTAAAAGAT
1 ATCTGCCCCAGGCTCAGGGTAAGAGAT
18446723 CGAATCTTCG
Statistics
Matches: 200, Mismatches: 49, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
37 56 0.28
38 4 0.02
39 138 0.69
40 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCAGGGTAAGAGATTGACTGACGGTG
Found at i:18446662 original size:76 final size:78
Alignment explanation
Indices: 18446367--18446727 Score: 403
Period size: 78 Copynumber: 4.7 Consensus size: 78
18446357 CATGATCGAA
* * * * *
18446367 GTAAGAGACTGGCTGATGGT-AGTCTACCCCAGGATCGAGGTAAAAGATCGAATGACTGCAATCT
1 GTAAGAGATTGACTGACGGTGA-TCTGCCCCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCT
* * *
18446431 GCCCTAGGCTTAGG
65 GCCCCAGGCTCAAG
* *
18446445 GTAAGAGATTTG-CTGACGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTGCAATCT
1 GTAAGAGA-TTGACTGACGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCT
* *
18446509 GCCCCAAGCTCGAG
65 GCCCCAGGCTCAAG
* * * * * *
18446523 GTAAGAGATTTACTGACGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTGTAATCTG
1 GTAAGAGATTGACTGACGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCTG
* *
18446588 CCCCAGGATTAAG
66 CCCCAGGCTCAAG
* * ** *
18446601 GTAAGAGATTGACT-A-GTTGATCTGCCCCAGGCTCGAGGTAAGAGATCGAATGGTTGCAATCTA
1 GTAAGAGATTGACTGACGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCTG
*
18446664 CCCCAGGCTCAGG
66 CCCCAGGCTCAAG
*
18446677 GTAAGAGATTGACTG--GTTGATCTGCCCCAGGCTC-AGGGTAAAAGATCGAAT
1 GTAAGAGATTGACTGACGGTGATCTGCCCCAGGCTCGA-GGTAAAAGATCGAAT
18446728 CTTCGATCTG
Statistics
Matches: 244, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
75 1 0.00
76 97 0.40
77 3 0.01
78 140 0.57
79 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (78 bp):
GTAAGAGATTGACTGACGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCGAATGACTGCAATCTG
CCCCAGGCTCAAG
Found at i:18472975 original size:100 final size:100
Alignment explanation
Indices: 18472826--18473024 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
18472816 CCAAAGCAAT
18472826 GTATGGTTTCATTTCATCAACTATCGTCTCCTGCCATCCACCCACAGTACATCTACAACGCTGGA
1 GTATGGTTTCATTTCATCAACTATCGTCTCCTGCCATCCACCCACAGTACATCTACAACGCTGGA
18472891 CAGAATGTGCTTGCTGCATTCTATACTCAAGGGAG
66 CAGAATGTGCTTGCTGCATTCTATACTCAAGGGAG
* *
18472926 GTATGGTTTCATTTCATCAACTATCGTCTCCTGCCATCCACCCATAGTACATCTACAATGCTGGA
1 GTATGGTTTCATTTCATCAACTATCGTCTCCTGCCATCCACCCACAGTACATCTACAACGCTGGA
18472991 CAGAATGTGCTTGCTGCATTCTATACTCAAGGGA
66 CAGAATGTGCTTGCTGCATTCTATACTCAAGGGA
18473025 CAACGAATTG
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (100 bp):
GTATGGTTTCATTTCATCAACTATCGTCTCCTGCCATCCACCCACAGTACATCTACAACGCTGGA
CAGAATGTGCTTGCTGCATTCTATACTCAAGGGAG
Found at i:18473720 original size:5 final size:5
Alignment explanation
Indices: 18473706--18473743 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
18473696 ATTGAAGTAG
*
18473706 AAGAA GAGAA AAGAA AAG-- AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
18473744 GGAAGGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
5 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:18473727 original size:18 final size:18
Alignment explanation
Indices: 18473704--18473757 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
18473694 GTATTGAAGT
18473704 AGAAGAAGAGAAAAGAAA
1 AGAAGAAGAGAAAAGAAA
*
18473722 AGAAGAAAAGAAAAGAAA
1 AGAAGAAGAGAAAAGAAA
18473740 AGAAGGAAG-GAAGAAGAA
1 AGAA-GAAGAGAA-AAGAA
18473758 GAAAATGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 24 0.75
19 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAGAAAAGAAA
Found at i:18473728 original size:13 final size:14
Alignment explanation
Indices: 18473706--18473762 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 14
18473696 ATTGAAGTAG
*
18473706 AAGAAGAGAAAAGAA
1 AAGAAGA-AGAAGAA
18473721 AAGAAGAA-AAGAA
1 AAGAAGAAGAAGAA
*
18473734 AAGAA-AAGAAGGA
1 AAGAAGAAGAAGAA
*
18473747 AGGAAGAAGAAGAA
1 AAGAAGAAGAAGAA
18473761 AA
1 AA
18473763 TGTTGCCCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 2 0.06
13 18 0.50
14 9 0.25
15 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAGAA
Found at i:18479578 original size:20 final size:20
Alignment explanation
Indices: 18479553--18479590 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18479543 AGATTCATTG
18479553 TATGATGTGATAAATATTAT
1 TATGATGTGATAAATATTAT
*
18479573 TATGATTTGATAAATATT
1 TATGATGTGATAAATATT
18479591 TTTGTAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (20 bp):
TATGATGTGATAAATATTAT
Found at i:18481766 original size:21 final size:20
Alignment explanation
Indices: 18481702--18481767 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
18481692 TTATGAAACA
* *
18481702 AAATGAAAGAAAAGTAAAGG
1 AAATGAGAGAAAAGAAAAGG
* *
18481722 AGATTGAGAGAAGAA-AAAAAG
1 A-AATGAGAGAA-AAGAAAAGG
18481743 AAATGAGAGAAAAGGAAAAGG
1 AAATGAGAGAAAA-GAAAAGG
18481764 AAAT
1 AAAT
18481768 AAAAAGAGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 22 0.61
22 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (20 bp):
AAATGAGAGAAAAGAAAAGG
Found at i:18481875 original size:21 final size:21
Alignment explanation
Indices: 18481851--18481892 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18481841 AAAAGAGTGC
18481851 AAGAGAGAAGAAA-AAGAAAGT
1 AAGAGAGAA-AAAGAAGAAAGT
**
18481872 AAGATTGAAAAAGAAGAAAGT
1 AAGAGAGAAAAAGAAGAAAGT
18481893 GATCAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (21 bp):
AAGAGAGAAAAAGAAGAAAGT
Found at i:18482777 original size:222 final size:223
Alignment explanation
Indices: 18482230--18483106 Score: 882
Period size: 222 Copynumber: 4.0 Consensus size: 223
18482220 TTCACAAAAC
* * * *** *
18482230 GACAAGCCTCAACTATTTAGACCAAATGATGCGACTTTATGAGCATGGAATGTTTGAAAAATTGC
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTTCCAAGCATGAAATGTTTGAAAAATTGC
* * * * * *
18482295 TCGAAAGAATGGA-TCGTCATGAATACATTAAGGAACATAAGTTATAAAATAACTCGTAAAAGTT
66 TCGAAGGAATGGATTCGGCTTGAATACTTTAAGGAACAGAAGTTATAAAAAAACTCGTAAAAGTT
* * ** * * * *
18482359 TGATAAATTTGAAAGTTCGGTCAAGAACCTATAGAGAAATACTTCTCA-AGTAAATAA-ATATTT
131 TGACAAGTTCAAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACA-TAAATAAGAT-TTT
18482422 AATTCAAAGACCAAAAGTTG--T---T--T
194 AATTCAAAGACCAAAAGTTGTTTACATAAT
* * *
18482445 -ACAAGCTTAAACTATTTAGACCAAACGATGCAATCTCTT--AAGCATGAAATGTTTGGAAAATT
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGAT-T-TTCCAAGCATGAAATGTTTGAAAAATT
** * * * *
18482507 GCTCGAAGGAATGGATT-ATCTTGAATACTTTATGGAACTGATGTTATAAAAAAATTCGTAAAAG
64 GCTCGAAGGAATGGATTCGGCTTGAATACTTTAAGGAACAGAAGTTATAAAAAAACTCGTAAAAG
* *
18482571 TTTGACAACTTCAAAAGTTCAGTCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGATTTT
129 TTTGACAAGTTCAAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGATTTT
* *
18482636 AATTCAAAAACCAAAAGTTATTTACATAAT
194 AATTCAAAGACCAAAAGTTGTTTACATAAT
* *
18482666 GACAAGCTTAAAATATTTAGACCAAATGATGCGATTTTCCAAGCATGAAATGTTTGAAAAATTGG
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTTCCAAGCATGAAATGTTTGAAAAATTGC
* * **
18482731 TCGAAGGTAT-GATTCGGCTGGAATACTTTAAGGAA-ACGAAGTTATAAATGAACTCGTAAAAGT
66 TCGAAGGAATGGATTCGGCTTGAATACTTTAAGGAACA-GAAGTTATAAAAAAACTCGTAAAAGT
* * * * * *
18482794 TTGACAAGTTTAGAAGTTCGATTAAGAACTAAGAGAGAAACAATTCCCACATAAATAAG-TTTCT
130 TTGACAAGTTCAAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGATTT-T
* *
18482858 AATTCAAAGACAAAAAGTTGTTTACAAAAT
194 AATTCAAAGACCAAAAGTTGTTTACATAAT
* * * * * *
18482888 GACAAGCTTAAACCATTTAGAACAAATGATGCGATTTCCCGAGCATGGAATGCTTTG-AAAATTA
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTTCCAAGCATGAAATG-TTTGAAAAATTG
* * * *
18482952 CTTGAAGGCATGG-GTCATG-TTGAATACTTTTAAGGAATC-GAAGTTA-AAAAAGAACTCGTAA
65 CTCGAAGGAATGGATTC-GGCTTGAATAC-TTTAAGGAA-CAGAAGTTATAAAAA-AACTCGTAA
* * * * * * ** *
18483013 AATTTTGATAAGTTCAGAAGTTTGGT-AAAAACCCAAGAGAGAAACAATTCTAATGTAAATAAGT
126 AAGTTTGACAAGTTCAAAAGTTCGGTCAAGAA-CCAAGAGAGAAACAATTCTCACATAAATAAGA
18483077 TTTTAATTCAAAGACCAAAAGTTGTTTACA
190 TTTTAATTCAAAGACCAAAAGTTGTTTACA
18483107 AAAGTTTGTT
Statistics
Matches: 552, Mismatches: 83, Indels: 46
0.81 0.12 0.07
Matches are distributed among these distances:
214 170 0.31
215 5 0.01
216 3 0.01
219 1 0.00
220 2 0.00
221 9 0.02
222 255 0.46
223 104 0.19
224 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (223 bp):
GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTTCCAAGCATGAAATGTTTGAAAAATTGC
TCGAAGGAATGGATTCGGCTTGAATACTTTAAGGAACAGAAGTTATAAAAAAACTCGTAAAAGTT
TGACAAGTTCAAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGATTTTAA
TTCAAAGACCAAAAGTTGTTTACATAAT
Found at i:18484299 original size:36 final size:36
Alignment explanation
Indices: 18484252--18484329 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
18484242 AAGATAATCA
* *
18484252 GTCACATGGCATGAAAAACATAGCCACATATTTACT
1 GTCACATGGCATGAAAAACATACCCACATATTCACT
* *
18484288 GTCACATGGCATGAATAACATACCCTCATATTCACT
1 GTCACATGGCATGAAAAACATACCCACATATTCACT
*
18484324 TTCACA
1 GTCACA
18484330 ACAGTCCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (36 bp):
GTCACATGGCATGAAAAACATACCCACATATTCACT
Found at i:18488658 original size:20 final size:21
Alignment explanation
Indices: 18488621--18488659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18488611 AAACTGAGCA
*
18488621 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
18488642 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
18488660 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:18489916 original size:29 final size:29
Alignment explanation
Indices: 18489843--18489918 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
18489833 AAAAATAAAG
*
18489843 TTTTGGAGAATTTTGGGGGTCAAAACGTAAT
1 TTTTGGAAAATTTT--GGGTCAAAACGTAAT
* * * * *
18489874 TTTAGTAAAGTTTTGGGTTAAAACTTAAT
1 TTTTGGAAAATTTTGGGTCAAAACGTAAT
18489903 TTTTGGAAAATTTTGG
1 TTTTGGAAAATTTTGG
18489919 AATGTTTAGG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 26 0.72
31 10 0.28
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (29 bp):
TTTTGGAAAATTTTGGGTCAAAACGTAAT
Found at i:18490045 original size:59 final size:61
Alignment explanation
Indices: 18489979--18490115 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 61
18489969 TAGTTTTGGG
* * * * * *
18489979 AAGTTCGAGGGTCAAATC-AAATTTTT-AGGAAGTTTGGGGGTGAAATCTGAATTTCTT-GA
1 AAGTTCGAGGGTCAAAACTAAATTTTTGA-AAAGTTCGAGGGTCAAATCTAAATTTCTTAGA
* * *
18490038 ATGTTCGA-GGTCAAAACTTAATTTTTGAAAAGTTCGAGGGTCAAATCTAAATTTTTTAGA
1 AAGTTCGAGGGTCAAAACTAAATTTTTGAAAAGTTCGAGGGTCAAATCTAAATTTCTTAGA
18490098 AAGTTCGAGGGTCAAAAC
1 AAGTTCGAGGGTCAAAAC
18490116 ATAAGGACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
58 8 0.12
59 37 0.58
60 10 0.16
61 9 0.14
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (61 bp):
AAGTTCGAGGGTCAAAACTAAATTTTTGAAAAGTTCGAGGGTCAAATCTAAATTTCTTAGA
Found at i:18490082 original size:30 final size:31
Alignment explanation
Indices: 18489979--18490113 Score: 138
Period size: 29 Copynumber: 4.5 Consensus size: 31
18489969 TAGTTTTGGG
*
18489979 AAGTTCGAGGGTCAAATC-AAATTTTT-AGG
1 AAGTTCGAGGGTCAAATCTAAATTTTTGAGA
* * * *
18490008 AAGTTTGGGGGTGAAATCTGAATTTCTT--GA
1 AAGTTCGAGGGTCAAATCTAAATTT-TTGAGA
* * *
18490038 ATGTTCGA-GGTCAAAACTTAATTTTTGA-A
1 AAGTTCGAGGGTCAAATCTAAATTTTTGAGA
*
18490067 AAGTTCGAGGGTCAAATCTAAATTTTTTAGA
1 AAGTTCGAGGGTCAAATCTAAATTTTTGAGA
18490098 AAGTTCGAGGGTCAAA
1 AAGTTCGAGGGTCAAA
18490114 ACATAAGGAC
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.02
29 36 0.42
30 28 0.33
31 19 0.22
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (31 bp):
AAGTTCGAGGGTCAAATCTAAATTTTTGAGA
Found at i:18503388 original size:13 final size:13
Alignment explanation
Indices: 18503370--18503394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18503360 CCTATTTTAT
18503370 CATTTTTAGCATG
1 CATTTTTAGCATG
18503383 CATTTTTAGCAT
1 CATTTTTAGCAT
18503395 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:18503429 original size:21 final size:20
Alignment explanation
Indices: 18503391--18503430 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18503381 TGCATTTTTA
*
18503391 GCATTTTTAACTTAGTGATT
1 GCATTTTTAACTCAGTGATT
*
18503411 GCATTTTCTAACTCGGTGAT
1 GCATTTT-TAACTCAGTGAT
18503431 GCTCAGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (20 bp):
GCATTTTTAACTCAGTGATT
Found at i:18505111 original size:50 final size:50
Alignment explanation
Indices: 18505043--18505143 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
18505033 TATATAGAAA
*
18505043 TATAATTTATGGACTTATATAATATAATTTCAAAACTTTTAAAAGAAATT
1 TATAATTTATGGACTTATATAATATAATTTAAAAACTTTTAAAAGAAATT
18505093 TATAATTTATGGACTTATATAATATAATTTAAAAACTTTTAAAAGAAATT
1 TATAATTTATGGACTTATATAATATAATTTAAAAACTTTTAAAAGAAATT
18505143 T
1 T
18505144 GGCTTATGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (50 bp):
TATAATTTATGGACTTATATAATATAATTTAAAAACTTTTAAAAGAAATT
Found at i:18507674 original size:9 final size:9
Alignment explanation
Indices: 18507646--18507675 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
18507636 AGCAACCATG
18507646 TTTTTTTCT
1 TTTTTTTCT
*
18507655 TCTTTTTCT
1 TTTTTTTCT
18507664 TTTTTTTCT
1 TTTTTTTCT
18507673 TTT
1 TTT
18507676 CGAACCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:18518071 original size:21 final size:21
Alignment explanation
Indices: 18518046--18518098 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18518036 GTTGTGAGTG
*
18518046 ATCTACCGATACAACCCTGCA
1 ATCTATCGATACAACCCTGCA
* *
18518067 CTCTATCGATACAATCCTGCA
1 ATCTATCGATACAACCCTGCA
18518088 ATCTATCGATA
1 ATCTATCGATA
18518099 TAACATATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.26
Consensus pattern (21 bp):
ATCTATCGATACAACCCTGCA
Found at i:18520610 original size:30 final size:30
Alignment explanation
Indices: 18520574--18520640 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
18520564 TGTTCCTAGT
18520574 CCAAGAATACAAATTATGGTCTTCTTTTCA
1 CCAAGAATACAAATTATGGTCTTCTTTTCA
* * *
18520604 CCAAGAATACCACTTATGGTCTTCTTTTGA
1 CCAAGAATACAAATTATGGTCTTCTTTTCA
18520634 CCAAGAA
1 CCAAGAA
18520641 GATCCATGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (30 bp):
CCAAGAATACAAATTATGGTCTTCTTTTCA
Found at i:18521843 original size:41 final size:41
Alignment explanation
Indices: 18521785--18521896 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
18521775 CCAAAGCCAA
* * *
18521785 ATGATTAATATACATTGAGAGTGAGAGATTAGATGAAGACT
1 ATGATTAATATATATTGAGAGTGAGAGAGTAGATAAAGACT
* *
18521826 ATGATTAATACATATTGAGAGTGAGAGAGTAGATAAAGAGT
1 ATGATTAATATATATTGAGAGTGAGAGAGTAGATAAAGACT
* * * *
18521867 ACGACTAATATATATGGAGAGTTAGAGAGT
1 ATGATTAATATATATTGAGAGTGAGAGAGT
18521897 GAAAGATTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.42, C:0.04, G:0.26, T:0.28
Consensus pattern (41 bp):
ATGATTAATATATATTGAGAGTGAGAGAGTAGATAAAGACT
Found at i:18523159 original size:49 final size:49
Alignment explanation
Indices: 18523087--18523187 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
18523077 AATATATATG
* * *
18523087 GAGAGTGTGAGATTAGAAGAAGACTATGATTAATATATATTGAGAGTGA
1 GAGAGTCTGAGATTAGAAGAAGACTATAATTAATATATATGGAGAGTGA
**
18523136 GAGAGTCTGAGATTAGATTAAGACTATAATTAATATATATGGAGAGTGA
1 GAGAGTCTGAGATTAGAAGAAGACTATAATTAATATATATGGAGAGTGA
18523185 GAG
1 GAG
18523188 GGTGAAAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.29
Consensus pattern (49 bp):
GAGAGTCTGAGATTAGAAGAAGACTATAATTAATATATATGGAGAGTGA
Found at i:18523198 original size:49 final size:49
Alignment explanation
Indices: 18523096--18523210 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
18523086 GGAGAGTGTG
* * * **
18523096 AGATTAGAAGAAGACTATGATTAATATATATTGAGAGTGAGAGAGTCTG
1 AGATTAGATGAAGACTATAATTAATATATATGGAGAGTGAGAGAGTCAA
* * *
18523145 AGATTAGATTAAGACTATAATTAATATATATGGAGAGTGAGAGGGTGAA
1 AGATTAGATGAAGACTATAATTAATATATATGGAGAGTGAGAGAGTCAA
*
18523194 AGATTAGATGAATACTA
1 AGATTAGATGAAGACTA
18523211 GAAAAAACAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.29
Consensus pattern (49 bp):
AGATTAGATGAAGACTATAATTAATATATATGGAGAGTGAGAGAGTCAA
Found at i:18528017 original size:27 final size:27
Alignment explanation
Indices: 18527987--18528038 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
18527977 GACCCTTATC
*
18527987 ATGTTTGATATCGTAGTTGTTCACATA
1 ATGTCTGATATCGTAGTTGTTCACATA
18528014 ATGTCTGATATCGTAGTTGTTCACA
1 ATGTCTGATATCGTAGTTGTTCACA
18528039 GTTTCTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
ATGTCTGATATCGTAGTTGTTCACATA
Found at i:18529878 original size:26 final size:26
Alignment explanation
Indices: 18529841--18529893 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18529831 TTCATTAGAC
*
18529841 ATAGTTTCCTTTTTTTTCTTTATGTT
1 ATAGTTTACTTTTTTTTCTTTATGTT
18529867 ATAGTTTACTTTTTTTTCTTTATGTT
1 ATAGTTTACTTTTTTTTCTTTATGTT
18529893 A
1 A
18529894 CCATTAGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.08, T:0.68
Consensus pattern (26 bp):
ATAGTTTACTTTTTTTTCTTTATGTT
Found at i:18532539 original size:69 final size:69
Alignment explanation
Indices: 18532335--18532542 Score: 301
Period size: 69 Copynumber: 3.0 Consensus size: 69
18532325 TGTATCTATA
* * *
18532335 CTTATATATTATTATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATGTTAATTTGATT
1 CTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATTTGATT
*
18532400 TATG
66 TGTG
*
18532404 CTTAAATATT-ATAGTGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATGTGAT
1 CTTAAATATTAATA-TGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATTTGAT
*
18532468 TTGTT
65 TTGTG
* * * * *
18532473 CTTAAATATTAATATGATTTGTTCTTAAATATTAATGTGATTTGTGCTTAAATATTAATTTGATT
1 CTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATTTGATT
18532538 TGTG
66 TGTG
18532542 C
1 C
18532543 ATAAGCTTAT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
68 2 0.02
69 119 0.96
70 3 0.02
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.50
Consensus pattern (69 bp):
CTTAAATATTAATATGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATATTAATTTGATT
TGTG
Found at i:18532542 original size:23 final size:23
Alignment explanation
Indices: 18532335--18532538 Score: 266
Period size: 23 Copynumber: 8.9 Consensus size: 23
18532325 TGTATCTATA
* *
18532335 CTTATATATTATTATGATTTATG
1 CTTAAATATTAATATGATTTATG
*
18532358 CTTAAATGTTAATATGATTTATG
1 CTTAAATATTAATATGATTTATG
* *
18532381 CTTAAATGTTAATTTGATTTATG
1 CTTAAATATTAATATGATTTATG
18532404 CTTAAATATT-ATAGTGATTTATG
1 CTTAAATATTAATA-TGATTTATG
*
18532427 CTTAAATGTTAATATGATTTATG
1 CTTAAATATTAATATGATTTATG
* * *
18532450 CTTAAATATTAATGTGATTTGTT
1 CTTAAATATTAATATGATTTATG
* *
18532473 CTTAAATATTAATATGATTTGTT
1 CTTAAATATTAATATGATTTATG
* *
18532496 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATATGATTTATG
*
18532519 CTTAAATATTAATTTGATTT
1 CTTAAATATTAATATGATTT
18532539 GTGCATAAGC
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
22 2 0.01
23 159 0.97
24 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (23 bp):
CTTAAATATTAATATGATTTATG
Found at i:18533685 original size:25 final size:23
Alignment explanation
Indices: 18533644--18533689 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
18533634 CCAATTAGGG
18533644 AATTATTGTTTAGATTTAATTAT
1 AATTATTGTTTAGATTTAATTAT
*
18533667 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
18533690 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTAT
Found at i:18535919 original size:4 final size:4
Alignment explanation
Indices: 18535910--18535960 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
18535900 GAAAGGGAGT
* * *
18535910 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA AAGA AAGA GAAA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
18535958 GAG
1 GAG
18535961 GGAGGGAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:18535921 original size:6 final size:6
Alignment explanation
Indices: 18535910--18535960 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
18535900 GAAAGGGAGT
* * *
18535910 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA AAGAAA GAGAAA
1 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
18535958 GAG
1 GAG
18535961 GGAGGGAGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
GAGAGA
Found at i:18535925 original size:10 final size:10
Alignment explanation
Indices: 18535910--18535960 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
18535900 GAAAGGGAGT
18535910 GAGAGAGAGA
1 GAGAGAGAGA
18535920 GAGAGAGAGA
1 GAGAGAGAGA
18535930 GAGAGAGAGA
1 GAGAGAGAGA
*
18535940 GAGAGAAAGA
1 GAGAGAGAGA
* *
18535950 AAGAGAAAGA
1 GAGAGAGAGA
18535960 G
1 G
18535961 GGAGGGAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGA
Found at i:18537624 original size:24 final size:23
Alignment explanation
Indices: 18537564--18537624 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
18537554 AGGTGTTCTA
18537564 TTATATATTTTTATAGTTTCTTT
1 TTATATATTTTTATAGTTTCTTT
* * *
18537587 TATTTAAATATTTAT-GATTTCATTT
1 T-TATATATTTTTATAG-TTTC-TTT
18537612 TTATATATTTTTA
1 TTATATATTTTTA
18537625 AATCAAACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 2 0.07
24 23 0.79
25 4 0.14
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (23 bp):
TTATATATTTTTATAGTTTCTTT
Found at i:18539043 original size:8 final size:8
Alignment explanation
Indices: 18539030--18539120 Score: 60
Period size: 8 Copynumber: 11.2 Consensus size: 8
18539020 TGAGACTGAA
18539030 AGAGGGAG
1 AGAGGGAG
18539038 AGAGGGGGAG
1 AGA--GGGAG
18539048 AGAGGGAG
1 AGAGGGAG
* *
18539056 GGATGGAG
1 AGAGGGAG
18539064 -GAGGGAG
1 AGAGGGAG
* *
18539071 GGAGGAAG
1 AGAGGGAG
*
18539079 GGTA-GGAG
1 AG-AGGGAG
*
18539087 AGAGAGAG
1 AGAGGGAG
**
18539095 AGACAGAG
1 AGAGGGAG
*
18539103 AGAGAGAG
1 AGAGGGAG
18539111 AGAGGGAG
1 AGAGGGAG
18539119 AG
1 AG
18539121 GGAGAGGGAG
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
7 7 0.10
8 52 0.76
9 1 0.01
10 8 0.12
ACGTcount: A:0.37, C:0.01, G:0.59, T:0.02
Consensus pattern (8 bp):
AGAGGGAG
Found at i:18539058 original size:12 final size:12
Alignment explanation
Indices: 18539031--18539130 Score: 66
Period size: 12 Copynumber: 8.2 Consensus size: 12
18539021 GAGACTGAAA
18539031 GAGGGAGAGA-G
1 GAGGGAGAGAGG
18539042 G-GGGAGAGAGG
1 GAGGGAGAGAGG
18539053 GAGGGATGGAGGAGG
1 GAGGGA--GA-GAGG
18539068 GAGGGAG-GAAGG
1 GAGGGAGAG-AGG
*
18539080 GTA-GGAGAGAGA
1 G-AGGGAGAGAGG
* * *
18539092 GAGAGACAGAGA
1 GAGGGAGAGAGG
*
18539104 GAGAGAGAGAGG
1 GAGGGAGAGAGG
18539116 GAGAGG-GAGAGG
1 GAG-GGAGAGAGG
18539128 GAG
1 GAG
18539131 AGGGAAGGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 19
0.74 0.06 0.19
Matches are distributed among these distances:
10 8 0.11
11 5 0.07
12 44 0.60
13 4 0.05
14 2 0.03
15 10 0.14
ACGTcount: A:0.36, C:0.01, G:0.61, T:0.02
Consensus pattern (12 bp):
GAGGGAGAGAGG
Found at i:18539069 original size:15 final size:16
Alignment explanation
Indices: 18539044--18539073 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18539034 GGAGAGAGGG
18539044 GGAGAGAGGGAGGGAT
1 GGAGAGAGGGAGGGAT
18539060 GGAG-GAGGGAGGGA
1 GGAGAGAGGGAGGGA
18539074 GGAAGGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.67, T:0.03
Consensus pattern (16 bp):
GGAGAGAGGGAGGGAT
Found at i:18539091 original size:2 final size:2
Alignment explanation
Indices: 18539084--18539132 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
18539074 GGAAGGGTAG
* * *
18539084 GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA GG GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
18539126 GG GA GA G
1 GA GA GA G
18539133 GGAAGGAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.02, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18539133 original size:18 final size:18
Alignment explanation
Indices: 18539030--18539135 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 18
18539020 TGAGACTGAA
* *
18539030 AGAGGGAGAGAGGGGGAG
1 AGAGAGAGAGAGGGAGAG
* * *
18539048 AGAGGGAGGGATGGAG-G
1 AGAGAGAGAGAGGGAGAG
* *
18539065 AGGGAGGGAGGAAGGGTAG-G
1 AGAGAGAGA-G-AGGG-AGAG
**
18539085 AGAGAGAGAGAGACAGAG
1 AGAGAGAGAGAGGGAGAG
18539103 AGAGAGAGAGAGGGAGAG
1 AGAGAGAGAGAGGGAGAG
* *
18539121 GGAGAGGGAGAGGGA
1 AGAGAGAGAGAGGGA
18539136 AGGAGATTAG
Statistics
Matches: 68, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
17 8 0.12
18 46 0.68
19 4 0.06
20 10 0.15
ACGTcount: A:0.37, C:0.01, G:0.60, T:0.02
Consensus pattern (18 bp):
AGAGAGAGAGAGGGAGAG
Found at i:18543874 original size:19 final size:18
Alignment explanation
Indices: 18543822--18543878 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
18543812 AGGTGTTCTA
* *
18543822 TTATATATTTTTATAGTT
1 TTATTTATTTTTATATTT
* **
18543840 TCATTTATTTAAATATTT
1 TTATTTATTTTTATATTT
18543858 TTATTTCATTTTTATATTT
1 TTATTT-ATTTTTATATTT
18543877 TT
1 TT
18543879 TAAAATCAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTTATTTTTATATTT
Found at i:18548084 original size:41 final size:41
Alignment explanation
Indices: 18548027--18548106 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
18548017 CAAAGGCAAA
*
18548027 GGTTAATATATATGGAGAGTGAGAGATTAGATGAAGATTCT
1 GGTTAATATATATGGAGAGGGAGAGATTAGATGAAGATTCT
18548068 GGTTAATATATATGGAGAGGGAGAGATTAGATGAAGATT
1 GGTTAATATATATGGAGAGGGAGAGATTAGATGAAGATT
18548107 AGATAAACCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.38, C:0.01, G:0.31, T:0.30
Consensus pattern (41 bp):
GGTTAATATATATGGAGAGGGAGAGATTAGATGAAGATTCT
Found at i:18548120 original size:41 final size:41
Alignment explanation
Indices: 18548034--18548121 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
18548024 AAAGGTTAAT
* * * * *
18548034 ATATATGGAGAGTGAGAGATTAGATGAAGATTCTGGTTAAT
1 ATATATGGAGAGGGAGAGATTAGATGAAGATTCAGATAAAC
18548075 ATATATGGAGAGGGAGAGATTAGATGAAGATT-AGATAAACC
1 ATATATGGAGAGGGAGAGATTAGATGAAGATTCAGATAAA-C
18548116 ATATAT
1 ATATAT
18548122 TACACTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.28
Consensus pattern (41 bp):
ATATATGGAGAGGGAGAGATTAGATGAAGATTCAGATAAAC
Found at i:18549637 original size:49 final size:49
Alignment explanation
Indices: 18549535--18549638 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
18549525 AAGGGATAAT
* * * ** *
18549535 ATATATGGAAAGTGAAAGAGTGAGAGATTAGATGAAGGCTATGATTAAT
1 ATATATGGAAAGTGAAAGAGCGAGAGATTACATGAAGACTATGAAAAAA
* *
18549584 ATATATGGAGAGTGAGAGAGCGAGAGATTACATGAAGACTA-GAAAAACA
1 ATATATGGAAAGTGAAAGAGCGAGAGATTACATGAAGACTATGAAAAA-A
18549633 ATATAT
1 ATATAT
18549639 AATGGAGACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.09
49 42 0.91
ACGTcount: A:0.45, C:0.05, G:0.27, T:0.23
Consensus pattern (49 bp):
ATATATGGAAAGTGAAAGAGCGAGAGATTACATGAAGACTATGAAAAAA
Found at i:18550553 original size:43 final size:41
Alignment explanation
Indices: 18550504--18550587 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
18550494 CAATGAGAGG
* * * *
18550504 GTGAGAGATTAGATGAATACTATGATTAATATATATGGAGA
1 GTGAGAGAGTAGATGAAAACTATGACTAATATATATGAAGA
* *
18550545 GTGAGAGAGTAGATGAAAACTATTACTAGTATATATGAAGA
1 GTGAGAGAGTAGATGAAAACTATGACTAATATATATGAAGA
18550586 GT
1 GT
18550588 CATAGAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.30
Consensus pattern (41 bp):
GTGAGAGAGTAGATGAAAACTATGACTAATATATATGAAGA
Found at i:18555310 original size:49 final size:49
Alignment explanation
Indices: 18555172--18555295 Score: 203
Period size: 49 Copynumber: 2.5 Consensus size: 49
18555162 AGTATATATG
* *
18555172 GAGAGTGAGAGATTAGAAGAAGACTATGATTAATATATATGGAGAGTGA
1 GAGAGTGAGAGATTAGATGAAGACTATGATTAATATATATAGAGAGTGA
* *
18555221 GAGAGTGTGAGATTAAATGAAGACTATGATTAATATATATAGAGAGTGA
1 GAGAGTGAGAGATTAGATGAAGACTATGATTAATATATATAGAGAGTGA
*
18555270 GAGGGTGAGAGATTAGATGAAGACTA
1 GAGAGTGAGAGATTAGATGAAGACTA
18555296 GAAAAAACAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.25
Consensus pattern (49 bp):
GAGAGTGAGAGATTAGATGAAGACTATGATTAATATATATAGAGAGTGA
Found at i:18556852 original size:3 final size:3
Alignment explanation
Indices: 18556844--18556869 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18556834 TAGTTGTTCA
18556844 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
18556870 ATGAGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:18558925 original size:24 final size:24
Alignment explanation
Indices: 18558897--18559007 Score: 188
Period size: 24 Copynumber: 4.6 Consensus size: 24
18558887 GTATACTAGT
*
18558897 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
18558921 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
18558945 TAACCATTCTGGGCT-AGTAAGAGC
1 TAACCATTCTGGGCTCA-TAAGAGC
18558969 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
18558993 TAACCATTCTAGGCT
1 TAACCATTCTGGGCT
18559008 TATGTGAGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:18573748 original size:31 final size:30
Alignment explanation
Indices: 18573703--18573762 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
18573693 CCTAGTCCAA
* *
18573703 GAATACCAATTATGGTCTTGTTTTCACCAG
1 GAATACAAATTATGGTCTTCTTTTCACCAG
*
18573733 GAATACAAACTTATGGTTTTCTTTTCACCA
1 GAATACAAA-TTATGGTCTTCTTTTCACCA
18573763 AGAAGATCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (30 bp):
GAATACAAATTATGGTCTTCTTTTCACCAG
Found at i:18575938 original size:26 final size:26
Alignment explanation
Indices: 18575885--18575938 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
18575875 ATTTTGGGAG
*
18575885 CAATTCTGGACACATTCATGTAGCGA
1 CAATTCTGGACACATTCATGCAGCGA
* ** *
18575911 CAATTTTGGACATGTTCATGCAGTGA
1 CAATTCTGGACACATTCATGCAGCGA
18575937 CA
1 CA
18575939 TTCCTAGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (26 bp):
CAATTCTGGACACATTCATGCAGCGA
Found at i:18580178 original size:37 final size:37
Alignment explanation
Indices: 18580137--18580216 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
18580127 CCGAAAATAT
*
18580137 TCATGCGACGATAGTTTTGGGTGCAATC-ACGAAGTGC
1 TCATGCGACGATAGTTTTGGGCGCAATCTA-GAAGTGC
* *
18580174 TCATGTGGCGATAGTTTTGGGCGCAATCTAGAAGTGC
1 TCATGCGACGATAGTTTTGGGCGCAATCTAGAAGTGC
*
18580211 TTATGC
1 TCATGC
18580217 AGCGACATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (37 bp):
TCATGCGACGATAGTTTTGGGCGCAATCTAGAAGTGC
Found at i:18580681 original size:41 final size:41
Alignment explanation
Indices: 18580636--18580731 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
18580626 GAGATAGTGA
* * * *
18580636 GAGAGTGAGAGATTAGATGAAGACTATGATTAATATATATG
1 GAGAGTCAGAGAGTAGATGAAGACTAGGACTAATATATATG
* * *
18580677 GAGAGTTAGAGAGTAGATGAAGTCTAGGACTAATATATGTG
1 GAGAGTCAGAGAGTAGATGAAGACTAGGACTAATATATATG
18580718 GAGAGTCAGAGAGT
1 GAGAGTCAGAGAGT
18580732 GAATGATTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.26
Consensus pattern (41 bp):
GAGAGTCAGAGAGTAGATGAAGACTAGGACTAATATATATG
Found at i:18581969 original size:49 final size:48
Alignment explanation
Indices: 18581897--18582106 Score: 251
Period size: 49 Copynumber: 4.5 Consensus size: 48
18581887 ATATATATTG
* *
18581897 AGAGTGAGAGATTAGAAT-AAGACTATGATTAATATATATGAAGAGTGAA
1 AGAGTGTGAGATTAG-ATGAAGACTATGATTAATATATATGGAGAG-GAA
18581946 AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAGG--
1 AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAGGAA
* *
18581992 AGAGGGTGAG---AGAT-TAG---ATGATTAATATATATGGAGAGTGAA
1 AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAG-GAA
*
18582034 AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAGGAG
1 AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAGGAA
* * *
18582082 CGGGTGAGAGATTAGATGAAGACTA
1 AGAGTGTGAGATTAGATGAAGACTA
18582107 GAAAAAACAT
Statistics
Matches: 140, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
39 21 0.15
40 1 0.01
42 11 0.08
43 4 0.03
45 4 0.03
46 11 0.08
48 27 0.19
49 61 0.44
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.26
Consensus pattern (48 bp):
AGAGTGTGAGATTAGATGAAGACTATGATTAATATATATGGAGAGGAA
Found at i:18582024 original size:39 final size:39
Alignment explanation
Indices: 18581970--18582100 Score: 145
Period size: 39 Copynumber: 3.1 Consensus size: 39
18581960 GATGAAGACT
18581970 ATGATTAATATATATGGAGAGGAGAGGGTGAGAGATTAG
1 ATGATTAATATATATGGAGAGGAGAGGGTGAGAGATTAG
* *
18582009 ATGATTAATATATATGGAGAGTGAAAGAGTGTGAGATTAGATGAAG
1 ATGATTAATATATATGGAGAG-G--AGAGGGTGAG---AGAT-TAG
*
18582055 ACTATGATTAATATATATGGAGAGGAGCGGGTGAGAGATTAG
1 ---ATGATTAATATATATGGAGAGGAGAGGGTGAGAGATTAG
18582097 ATGA
1 ATGA
18582101 AGACTAGAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
39 25 0.32
40 1 0.01
42 11 0.14
43 4 0.05
45 4 0.05
46 10 0.13
48 1 0.01
49 21 0.27
ACGTcount: A:0.39, C:0.02, G:0.33, T:0.27
Consensus pattern (39 bp):
ATGATTAATATATATGGAGAGGAGAGGGTGAGAGATTAG
Found at i:18582034 original size:88 final size:88
Alignment explanation
Indices: 18581921--18582100 Score: 342
Period size: 88 Copynumber: 2.0 Consensus size: 88
18581911 GAATAAGACT
18581921 ATGATTAATATATATGAAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAATATATATG
1 ATGATTAATATATATGAAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAATATATATG
18581986 GAGAGGAGAGGGTGAGAGATTAG
66 GAGAGGAGAGGGTGAGAGATTAG
*
18582009 ATGATTAATATATATGGAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAATATATATG
1 ATGATTAATATATATGAAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAATATATATG
*
18582074 GAGAGGAGCGGGTGAGAGATTAG
66 GAGAGGAGAGGGTGAGAGATTAG
18582097 ATGA
1 ATGA
18582101 AGACTAGAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27
Consensus pattern (88 bp):
ATGATTAATATATATGAAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAATATATATG
GAGAGGAGAGGGTGAGAGATTAG
Found at i:18582119 original size:48 final size:49
Alignment explanation
Indices: 18582018--18582120 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
18582008 GATGATTAAT
* ** *
18582018 ATATATGGAGAGTGAAAGAGTGTGAGATTAGATGAAGACTATGATTAAT
1 ATATATGGAGAGTGAAAGAGTGAGAGATTAGATGAAGACTATGAAAAAC
** *
18582067 ATATATGGAGAG-GAGCGGGTGAGAGATTAGATGAAGACTA-GAAAAAAC
1 ATATATGGAGAGTGAAAGAGTGAGAGATTAGATGAAGACTATG-AAAAAC
18582115 ATATAT
1 ATATAT
18582121 AATGGAGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 1 0.02
48 33 0.72
49 12 0.26
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (49 bp):
ATATATGGAGAGTGAAAGAGTGAGAGATTAGATGAAGACTATGAAAAAC
Found at i:18583638 original size:3 final size:3
Alignment explanation
Indices: 18583630--18583677 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
18583620 GTTGTTCACA
* * * * *
18583630 TCT TCT TCT TCT TAT TAT TTT TCT TCT CCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
18583678 ATGGGAGTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:18583676 original size:15 final size:15
Alignment explanation
Indices: 18583630--18583677 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
18583620 GTTGTTCACA
* *
18583630 TCTTCTTCTTCTTAT
1 TCTTTTTCTTCTTCT
* *
18583645 TATTTTTCTTCTCCT
1 TCTTTTTCTTCTTCT
18583660 TCTTTTTCTTCTTCT
1 TCTTTTTCTTCTTCT
18583675 TCT
1 TCT
18583678 ATGGGAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTTTTCTTCTTCT
Found at i:18594486 original size:16 final size:16
Alignment explanation
Indices: 18594465--18594495 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18594455 AGAATGTGAA
18594465 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
18594481 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
18594496 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:18595378 original size:37 final size:38
Alignment explanation
Indices: 18595337--18595430 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
18595327 ATGTTCATGT
18595337 AGCGATATTCTTGGGTGCAA-TTGAAAAATACTTATGC
1 AGCGATATTCTTGGGTGCAATTTGAAAAATACTTATGC
* * *
18595374 AGCGATAGTTC-TGGATGCAATTTGAAGAATATTTATGC
1 AGCGATA-TTCTTGGGTGCAATTTGAAAAATACTTATGC
* *
18595412 AGCGACAGTCTTGGGTGCA
1 AGCGATATTCTTGGGTGCA
18595431 TTTCAGAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 17 0.35
38 31 0.65
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (38 bp):
AGCGATATTCTTGGGTGCAATTTGAAAAATACTTATGC
Found at i:18595489 original size:37 final size:37
Alignment explanation
Indices: 18595448--18595522 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
18595438 AATATTCCTA
* *
18595448 CGGCGACAATTTTGGGTGCAATCTAGAAGTGCTGATG
1 CGGCGACAATTTTGGGCGCAATCTAGAAGTGCTCATG
*
18595485 CGGCGACAGTTTTGGGCGCAATCTAGAAGTGCTCATG
1 CGGCGACAATTTTGGGCGCAATCTAGAAGTGCTCATG
18595522 C
1 C
18595523 AGAGACATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
CGGCGACAATTTTGGGCGCAATCTAGAAGTGCTCATG
Found at i:18599567 original size:26 final size:26
Alignment explanation
Indices: 18599525--18599575 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
18599515 ATTCTAGGCA
18599525 CAATTTTGGACACGTTTACGTAGCAG
1 CAATTTTGGACACGTTTACGTAGCAG
* * *
18599551 CAATTTTGTACATGTTTATGTAGCA
1 CAATTTTGGACACGTTTACGTAGCA
18599576 ACATTCTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (26 bp):
CAATTTTGGACACGTTTACGTAGCAG
Found at i:18608319 original size:22 final size:23
Alignment explanation
Indices: 18608293--18608336 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
18608283 AAATAGTCAA
18608293 AATTGTCAATGAAA-TAAAAGTT
1 AATTGTCAATGAAACTAAAAGTT
*
18608315 AATTGTCACTGAAACTAAAAGT
1 AATTGTCAATGAAACTAAAAGT
18608337 AAATCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (23 bp):
AATTGTCAATGAAACTAAAAGTT
Found at i:18626535 original size:24 final size:24
Alignment explanation
Indices: 18626501--18626580 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
18626491 ATAATCTTTT
*
18626501 AATTAAGCTCTGTTTATTTGTTTC
1 AATTAAACTCTGTTTATTTGTTTC
*
18626525 AATTAAACTCTATTTATTTGTTTC
1 AATTAAACTCTGTTTATTTGTTTC
* *
18626549 AATTAAACTCTGTGTATTTGTTTG
1 AATTAAACTCTGTTTATTTGTTTC
*
18626573 AGTTAAAC
1 AATTAAAC
18626581 ACTTATTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (24 bp):
AATTAAACTCTGTTTATTTGTTTC
Found at i:18633526 original size:50 final size:50
Alignment explanation
Indices: 18633394--18633586 Score: 246
Period size: 49 Copynumber: 3.9 Consensus size: 50
18633384 TCAGAACTTG
* * * *
18633394 TTTATCTAAATTGTTTTGTTCAGATCTAGTGTTTTGTATAAAAATAAATA
1 TTTATTTAAATTTTTTTGTTCAGATCTAGTGTTTTATATAAATATAAATA
*
18633444 TTTATTT-AATTTTTTTGTTCGGATCTAGTGTTTTATATAAATATAAATA
1 TTTATTTAAATTTTTTTGTTCAGATCTAGTGTTTTATATAAATATAAATA
* * *
18633493 TTTATTTAAATTTTTTTGTTTAGATCTGGTGTTTTACATAAATATAAATA
1 TTTATTTAAATTTTTTTGTTCAGATCTAGTGTTTTATATAAATATAAATA
* * * * * *
18633543 TTTATTTATATTATTTT-TTCATATCTTGTATTTTATGTAAATAT
1 TTTATTTAAATTTTTTTGTTCAGATCTAGTGTTTTATATAAATAT
18633587 TTTATATTTA
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
49 66 0.53
50 59 0.47
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (50 bp):
TTTATTTAAATTTTTTTGTTCAGATCTAGTGTTTTATATAAATATAAATA
Found at i:18633546 original size:99 final size:99
Alignment explanation
Indices: 18633394--18633586 Score: 253
Period size: 99 Copynumber: 1.9 Consensus size: 99
18633384 TCAGAACTTG
** *
18633394 TTTATCTAAATTGTTTTGTTCAGATCTAGTGTTTTGTATAAAAATAAATATTTATTTA-ATTTTT
1 TTTATCTAAATTGTTTTGTTCAGATCTAGTGTTTTACATAAAAATAAATATTTATTTATATTATT
* *
18633458 TTGTTCGGATCTAGTGTTTTATATAAATATAAATA
66 TT-TTCAGATCTAGTATTTTATATAAATATAAATA
* * * * *
18633493 TTTATTTAAATTTTTTTGTTTAGATCTGGTGTTTTACATAAATATAAATATTTATTTATATTATT
1 TTTATCTAAATTGTTTTGTTCAGATCTAGTGTTTTACATAAAAATAAATATTTATTTATATTATT
* * *
18633558 TTTTCATATCTTGTATTTTATGTAAATAT
66 TTTTCAGATCTAGTATTTTATATAAATAT
18633587 TTTATATTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 73 0.91
100 7 0.09
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (99 bp):
TTTATCTAAATTGTTTTGTTCAGATCTAGTGTTTTACATAAAAATAAATATTTATTTATATTATT
TTTTCAGATCTAGTATTTTATATAAATATAAATA
Found at i:18634204 original size:82 final size:82
Alignment explanation
Indices: 18633998--18634606 Score: 543
Period size: 82 Copynumber: 7.5 Consensus size: 82
18633988 ATTATGTTTG
* *** * * *
18633998 TGAATAAATTC-GTTTCAGGATTTATTCCCATTGTTCAATAGATTTTATTCTATTGTGATTTTGT
1 TGAAT-AATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGT
18634062 TTCCAAA-AAGGATTAAT
65 TTCCAAACAAGGATTAAT
* * *** * * *
18634079 TTAATAAATCTGTTTCGGGATTTATTCCCATCGTTCAAAAAATTTTATTCTATTTTGATTTTGGT
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
18634144 TCCAAACAAGGATTAAT
66 TCCAAACAAGGATTAAT
* * * * * * * *
18634161 TGAGTAATTATGTTCCGAGATTTATTCTTGGCATTCAACAAATTTTATTCTGTTTTGATTTTGTT
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
*
18634226 CCCAAACAAGGATTAAT
66 TCCAAACAAGGATTAAT
* * * *
18634243 TGAATAATTCTGTTTCGGGAGTTAATCTCT-CCGTTCAACAGATTTTATTCTATTTTAATTTTGT
1 TGAATAATTCTGTTTCGGGATTTATTCT-TGTCGTTCAACAGATTTTATTCTATTTTGATTTTGT
* **
18634307 TTCCAAACAACGATTAGC
65 TTCCAAACAAGGATTAAT
* * * * * ***
18634325 TGAATAATTCTGTTTTGGGATTTATTCCTGTCGTACAATAGATTTCATTCTA-TACAATTTTGTT
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
*
18634389 TCCAAACAAGAATTAAT
66 TCCAAACAAGGATTAAT
* * * * ** * *
18634406 AGAATAATTCTTTTTTGGGATTTATTCTCGTTATTCAATAGATTTTATTCTATTCTGATTTTGTT
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
** *
18634471 TCCGTACAAGAATTAAT
66 TCCAAACAAGGATTAAT
* * * * * * * *
18634488 TGAATAATTCTATTTCGAGATTTGTTCCTATCGTTGAATAGA----ATT-GATTTTGATTTTGTT
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
*
18634548 TCCAAACAAGAATTAAT
66 TCCAAACAAGGATTAAT
* *** * *
18634565 TAAATAATTCTGTTTCATTATTTATTCCTGTCATTCAACAGA
1 TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGA
18634607 ATTGATTTTG
Statistics
Matches: 433, Mismatches: 90, Indels: 14
0.81 0.17 0.03
Matches are distributed among these distances:
77 60 0.14
78 3 0.01
80 4 0.01
81 126 0.29
82 239 0.55
83 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (82 bp):
TGAATAATTCTGTTTCGGGATTTATTCTTGTCGTTCAACAGATTTTATTCTATTTTGATTTTGTT
TCCAAACAAGGATTAAT
Found at i:18634430 original size:245 final size:245
Alignment explanation
Indices: 18634030--18634504 Score: 583
Period size: 245 Copynumber: 1.9 Consensus size: 245
18634020 TATTCCCATT
* * * * *
18634030 GTTCAATAGATTTTATTCTATTGTGATTTTGTTTCCAAAAAGGATTAATTTAATAAATCTGTTTC
1 GTTCAACAGATTTTATTCTATTGTAATTTTGTTTCCAAAAACGATTAACTGAATAAATCTGTTTC
* * *** *
18634095 GGGATTTATTCCCATCGTTCAAAAAATTTTATTCTATTTTGATTTTGGTTCCAAACAAGGATTAA
66 GGGATTTATTCCCATCGTACAAAAAATTTCATTCTATTACAATTTTGGTTCCAAACAAGAATTAA
* * * * *
18634160 TTGAGTAATTATGTTCCGAGATTTATTCTTGGCATTCAACAAATTTTATTCTGTTTTGATTTTGT
131 TAGAATAATTATGTTCCGAGATTTATTCTCGGCATTCAACAAATTTTATTCTATTCTGATTTTGT
* *
18634225 TCCCAAACAAGGATTAATTGAATAATTCTGTTTCGGGAGTTAATCTCTCC
196 TCCCAAACAAGAATTAATTGAATAATTCTATTTCGGGAGTTAATCTCTCC
* * *
18634275 GTTCAACAGATTTTATTCTATTTTAATTTTGTTTCCAAACAACGATTAGCTGAATAATTCTGTTT
1 GTTCAACAGATTTTATTCTATTGTAATTTTGTTTCCAAA-AACGATTAACTGAATAAATCTGTTT
* ** * * *
18634340 TGGGATTTATTCCTGTCGTACAATAGATTTCATTCTA-TACAATTTTGTTTCCAAACAAGAATTA
65 CGGGATTTATTCCCATCGTACAAAAAATTTCATTCTATTACAATTTTGGTTCCAAACAAGAATTA
* * ** * ** * *
18634404 ATAGAATAATTCTTTTTTGGGATTTATTCTCGTTATTCAATAGATTTTATTCTATTCTGATTTTG
130 ATAGAATAATTATGTTCCGAGATTTATTCTCGGCATTCAACAAATTTTATTCTATTCTGATTTTG
* **
18634469 TTTCCGTACAAGAATTAATTGAATAATTCTATTTCG
195 TTCCCAAACAAGAATTAATTGAATAATTCTATTTCG
18634505 AGATTTGTTC
Statistics
Matches: 190, Mismatches: 39, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
245 140 0.74
246 50 0.26
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (245 bp):
GTTCAACAGATTTTATTCTATTGTAATTTTGTTTCCAAAAACGATTAACTGAATAAATCTGTTTC
GGGATTTATTCCCATCGTACAAAAAATTTCATTCTATTACAATTTTGGTTCCAAACAAGAATTAA
TAGAATAATTATGTTCCGAGATTTATTCTCGGCATTCAACAAATTTTATTCTATTCTGATTTTGT
TCCCAAACAAGAATTAATTGAATAATTCTATTTCGGGAGTTAATCTCTCC
Found at i:18634451 original size:163 final size:158
Alignment explanation
Indices: 18633998--18634580 Score: 528
Period size: 163 Copynumber: 3.6 Consensus size: 158
18633988 ATTATGTTTG
** * *
18633998 TGAATAAATTC-GTTTC-AGGATTTATTCCCATTGTTCAATAGATTTTATTCTATTGTGATTTTG
1 TGAAT-AATTCTGTTTCGA-GATTTATTCCTGTCGTTCAATAGATTTCATTC---T-TGATTTTG
* ** * * *
18634061 TTTCCAAA-AAGGATTAATTTAATAAATCTGTTTCGGGATTTATTCCCATCGTTCAAAAAATTTT
60 TTTCCAAACAAGAATTAATAGAATAATTCTGTTTCGGGATTTATTCTC-TCGTTCAAAAGATTTT
*
18634125 ATTCTATTTTGATTTTGGTTCCAAACAAGGATTAAT
124 ATTCTATTTTGATTTTGTTTCCAAACAA-GATTAAT
* * * * * * * * *
18634161 TGAGTAATTATGTTCCGAGATTTATTCTTGGCATTCAACAAATTTTATTCTGTTTTGATTTTGTT
1 TGAATAATTCTGTTTCGAGATTTATTCCTGTCGTTCAATAGATTTCATTC----TTGATTTTGTT
* * * * * *
18634226 CCCAAACAAGGATTAATTGAATAATTCTGTTTCGGGAGTTAATCTCTCCGTTCAACAGATTTTAT
62 TCCAAACAAGAATTAATAGAATAATTCTGTTTCGGGATTTATTCTCT-CGTTCAAAAGATTTTAT
* **
18634291 TCTATTTTAATTTTGTTTCCAAACAACGATTAGC
126 TCTATTTTGATTTTGTTTCCAAACAA-GATTAAT
* * * *
18634325 TGAATAATTCTGTTTTGGGATTTATTCCTGTCGTACAATAGATTTCATTCTATACAATTTTGTTT
1 TGAATAATTCTGTTTCGAGATTTATTCCTGTCGTTCAATAGATTTCATTCT-T--GATTTTGTTT
* * ** *
18634390 CCAAACAAGAATTAATAGAATAATTCTTTTTTGGGATTTATTCTCGTTATTCAATAGATTTTATT
63 CCAAACAAGAATTAATAGAATAATTCTGTTTCGGGATTTATTCTC-TCGTTCAAAAGATTTTATT
* **
18634455 CTATTCTGATTTTGTTTCCGTACAAGAATTAAT
127 CTATTTTGATTTTGTTTCCAAACAAG-ATTAAT
* * * * * *
18634488 TGAATAATTCTATTTCGAGATTTGTTCCTATCGTTGAATAGAATTGATT-TTGATTTTGTTTCCA
1 TGAATAATTCTGTTTCGAGATTTATTCCTGTCGTTCAATAGATTTCATTCTTGATTTTGTTTCCA
18634552 AACAAGAATTAATTA-AATAATTCTGTTTC
66 AACAAGAATTAA-TAGAATAATTCTGTTTC
18634581 ATTATTTATT
Statistics
Matches: 342, Mismatches: 67, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
159 36 0.11
160 3 0.01
161 2 0.01
162 6 0.02
163 175 0.51
164 120 0.35
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (158 bp):
TGAATAATTCTGTTTCGAGATTTATTCCTGTCGTTCAATAGATTTCATTCTTGATTTTGTTTCCA
AACAAGAATTAATAGAATAATTCTGTTTCGGGATTTATTCTCTCGTTCAAAAGATTTTATTCTAT
TTTGATTTTGTTTCCAAACAAGATTAAT
Found at i:18634546 original size:77 final size:77
Alignment explanation
Indices: 18634381--18634627 Score: 214
Period size: 77 Copynumber: 3.1 Consensus size: 77
18634371 ATTCTATACA
* ***
18634381 ATTTTGTTTCCAAACAAGAATTAA-TAGAATAATTCTTTTTTGGGATTTATTCTCGT-T-ATTCA
1 ATTTTGTTTCCAAACAAGAATTAATTA-AATAATTCTATTTCATGATTTATTC-C-TATCATTCA
* * *
18634443 ATAGATTTTATTCTATTCTG
63 ACAGA----ATT-GATTTTG
** * * * * *
18634463 ATTTTGTTTCCGTACAAGAATTAATTGAATAATTCTATTTCGA-GATTTGTTCCTATCGTTGAAT
1 ATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC-ATGATTTATTCCTATCATTCAAC
18634527 AGAATTGATTTTG
65 AGAATTGATTTTG
* * *
18634540 ATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTGTTTCATTATTTATTCCTGTCATTCAACA
1 ATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCATGATTTATTCCTATCATTCAACA
18634605 GAATTGATTTTG
66 GAATTGATTTTG
18634617 TCATTTTGTTT
1 --ATTTTGTTT
18634628 TAGAATTTTA
Statistics
Matches: 137, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
76 1 0.01
77 70 0.51
78 3 0.02
79 9 0.07
80 1 0.01
81 2 0.01
82 50 0.36
83 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (77 bp):
ATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTCATGATTTATTCCTATCATTCAACA
GAATTGATTTTG
Found at i:18637257 original size:28 final size:28
Alignment explanation
Indices: 18637204--18637257 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
18637194 GTTCTGGGTT
* *
18637204 TTGTTTTTTCAGAACTTGTTTATTTAAA
1 TTGTTTTTTCAGAACTAGTGTATTTAAA
*
18637232 TTGTTTTCTTCAGATCTAGTGT-TTTA
1 TTGTTTT-TTCAGAACTAGTGTATTTA
18637258 TATAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.57
Consensus pattern (28 bp):
TTGTTTTTTCAGAACTAGTGTATTTAAA
Found at i:18637283 original size:50 final size:50
Alignment explanation
Indices: 18637222--18637417 Score: 268
Period size: 50 Copynumber: 3.9 Consensus size: 50
18637212 TCAGAACTTG
* * * *
18637222 TTTATTTAAATTGTTTTCTTCAGATCTAGTGTTTTATATAAAAATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTATATAAATATAAATA
* *
18637272 TTTATTTAAATTATTTTTTGTCCAGATATGGTGTTTTATATAAATATAAATA
1 TTTATTTAAA-T-TGTTTTGTTCAGATATGGTGTTTTATATAAATATAAATA
*
18637324 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTACATAAATATAAATA
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTATATAAATATAAATA
* * * *
18637374 TTTATTTATATTG-TTTGTTCAGATATTGTATTTTACATAAATAT
1 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTATATAAATAT
18637418 TTTATATTTA
Statistics
Matches: 132, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
49 29 0.22
50 58 0.44
51 2 0.02
52 43 0.33
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (50 bp):
TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTATATAAATATAAATA
Found at i:18637377 original size:102 final size:99
Alignment explanation
Indices: 18637222--18637417 Score: 275
Period size: 102 Copynumber: 1.9 Consensus size: 99
18637212 TCAGAACTTG
* *
18637222 TTTATTTAAATTGTTTTCTTCAGATCTAGTGTTTTATATAAAAATAAATATTTATTTAAATTATT
1 TTTATTTAAATTGTTTTCTTCAGATATAGTGTTTTACATAAAAATAAATATTTATTT--A-TATT
* * *
18637287 TTTTGTCCAGATATGGTGTTTTATATAAATATAAATA
63 GTTTGTCCAGATATGGTATTTTACATAAATATAAATA
* * *
18637324 TTTATTTAAATTGTTTTGTTCAGATATGGTGTTTTACATAAATATAAATATTTATTTATATTGTT
1 TTTATTTAAATTGTTTTCTTCAGATATAGTGTTTTACATAAAAATAAATATTTATTTATATTGTT
* *
18637389 TGTTCAGATATTGTATTTTACATAAATAT
66 TGTCCAGATATGGTATTTTACATAAATAT
18637418 TTTATATTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
99 31 0.37
100 1 0.01
102 52 0.62
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (99 bp):
TTTATTTAAATTGTTTTCTTCAGATATAGTGTTTTACATAAAAATAAATATTTATTTATATTGTT
TGTCCAGATATGGTATTTTACATAAATATAAATA
Found at i:18638318 original size:13 final size:13
Alignment explanation
Indices: 18638300--18638324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18638290 TCTCACAACT
18638300 GCTTGAATTGGAA
1 GCTTGAATTGGAA
18638313 GCTTGAATTGGA
1 GCTTGAATTGGA
18638325 GCAGCAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (13 bp):
GCTTGAATTGGAA
Found at i:18640785 original size:23 final size:23
Alignment explanation
Indices: 18640718--18640831 Score: 88
Period size: 23 Copynumber: 5.0 Consensus size: 23
18640708 TAAGTGCTGG
* **
18640718 GGAAA-CAATAAGCACACACACA
1 GGAAATCAGTAAGCACACACAGT
* * * **
18640740 GCAAATCAGTAGGTACATGCAGT
1 GGAAATCAGTAAGCACACACAGT
* *
18640763 GGAAAACAGTAATCACACACAGT
1 GGAAATCAGTAAGCACACACAGT
* * *
18640786 GCAAATCAGTAAGCACATATAGT
1 GGAAATCAGTAAGCACACACAGT
18640809 GCG-AATCAGTAAGCACACACAGT
1 G-GAAATCAGTAAGCACACACAGT
18640832 ACTGAACAAT
Statistics
Matches: 67, Mismatches: 23, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
22 4 0.06
23 63 0.94
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (23 bp):
GGAAATCAGTAAGCACACACAGT
Done.