Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 131 of 279
Found at i:41936996 original size:15 final size:15
Alignment explanation
Indices: 41936976--41937005 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41936966 GTGATTCAGG
41936976 TCTCGAACACTAACC
1 TCTCGAACACTAACC
41936991 TCTCGAACACTAACC
1 TCTCGAACACTAACC
41937006 GTCAGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (15 bp):
TCTCGAACACTAACC
Found at i:41937890 original size:8 final size:8
Alignment explanation
Indices: 41937873--41937905 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41937863 ACGATATCAC
41937873 TCTT-CTT
1 TCTTCCTT
41937880 TCTTCCTT
1 TCTTCCTT
41937888 TCTTCCTT
1 TCTTCCTT
*
41937896 TCTTTCTT
1 TCTTCCTT
41937904 TC
1 TC
41937906 CTATTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TCTTCCTT
Found at i:41978857 original size:21 final size:21
Alignment explanation
Indices: 41978831--41978871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41978821 ATCTGCTCAA
* *
41978831 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
41978852 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
41978872 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:41994512 original size:15 final size:15
Alignment explanation
Indices: 41994492--41994521 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41994482 GGCGTGCCCT
41994492 TAAATACCATCTTTA
1 TAAATACCATCTTTA
41994507 TAAATACCATCTTTA
1 TAAATACCATCTTTA
41994522 CCATTGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATACCATCTTTA
Found at i:41999837 original size:32 final size:32
Alignment explanation
Indices: 41999796--41999860 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
41999786 CGATAACATA
41999796 ATATGATATTACACAAATCTGATGATCAAATT
1 ATATGATATTACACAAATCTGATGATCAAATT
*
41999828 ATATGATATTACACAGATCTGATGATCAAATT
1 ATATGATATTACACAAATCTGATGATCAAATT
41999860 A
1 A
41999861 AGTGTGGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (32 bp):
ATATGATATTACACAAATCTGATGATCAAATT
Found at i:42002767 original size:201 final size:198
Alignment explanation
Indices: 42002425--42002815 Score: 575
Period size: 201 Copynumber: 2.0 Consensus size: 198
42002415 CAAGGTAAGC
* * *
42002425 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAAAATGTTTATATCCTCAAGTGC
1 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAAAAAAAAGAAAATGTTTATATCCTCAAGAGC
* * ** *
42002490 CTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATTGAAAAGAAATTAATCACCT
66 CTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCACCT
* ** *
42002555 CGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAGAGTGGCAACCACTTTATAGTA
131 CGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTTTATAGTA
42002620 ACT
196 ACT
*
42002623 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATATCCTTAAGG
1 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAA-AAAA-AAGAAAATGTTTATATCCTCAA-G
* * * * *
42002688 AGCCTAGCAAGACCAGATATAATATTGGCAACAGGGAAAAGAGGTGATCCATAAGATATTGACCA
63 AGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCA
* *
42002753 CCTCGGCAAAGTTGCCCATCCTTCAAATTCCAGCCTACATCTTACAGAGTGACAACCACTTTA
128 CCTCGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTTTA
42002816 CGATAATTTG
Statistics
Matches: 170, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
198 34 0.20
199 3 0.02
200 21 0.12
201 112 0.66
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (198 bp):
TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAAAAAAAAGAAAATGTTTATATCCTCAAGAGC
CTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCACCT
CGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTTTATAGTA
ACT
Found at i:42003042 original size:486 final size:487
Alignment explanation
Indices: 42002139--42003103 Score: 1354
Period size: 486 Copynumber: 2.0 Consensus size: 487
42002129 TGGTAGTTTC
* *
42002139 TAAAGAAAATTTAGGTCCCATAGGCAATTGGAATAAAACAAGAAACTGTTTAACTCCTCAAGGAG
1 TAAAGAAAATTTAGGTCCCATAGGCAATTAGAATAAAACAAGAAAATGTTTAACTCCTCAAGGAG
* * *
42002204 CCTAGCATGACCAGACATAGTATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGATCACC
66 CCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGACCACC
** **
42002269 TCGGCAAAGTTGCCCAGCCTTCAAATTTTTATTCTACATCTTACATAGAGTGACAACCACTTCAC
131 TCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACA-AGAGTGACAACCACTTCAC
* * * * *
42002334 GATAGTTTGATAAAAACCAGCCCGAGGATAACTACTTTAGATCTAGTTTGATAAAAGTAATCATG
195 GATAATTTGATAAAAACAAGCCCGAGGATAACTACTCTAAATCTAGTTTGATAAAAGAAATCATG
* * *
42002399 AGGGTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAA
260 AGGCTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGGAAAAAA
* * *
42002464 AAGAAAATGTTTATATCCTCAAGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGA
325 AAGAAAATGTCTATATCCTCAAGAGCCTAGCATGACCAGACATAATATTGGCAACAGGGAAAAGA
* * *
42002529 GGAGATTGAAAAGAAATTAATCACCTCGGCAAAGTTGCCCAGCCTTC-AAATTCTATTCTACACC
390 GGAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCGAAATTCTATTCTACACC
42002593 TTAC-AGAGTGG-CAACCACTTTATAGTAACTTT
455 TTACAAGAG-GGACAACCACTTTATAGTAACTTT
* * *
42002625 TAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATA-TCCTTAAGGA
1 TAAAGAAAATTTAGGTCCCATAGGCAATTAGAATAAAACAAGAAAATGTTTA-ACTCCTCAAGGA
* * *
42002689 GCCTAGCAAGACCAGATATAATATTGGCAACAGGGAAAAGAGGTGATCC-ATAAGATATTGACCA
65 GCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGA-CCGATAAGAAATTGACCA
* *
42002753 CCTCGGCAAAGTTGCCCATCCTTCAAA-TTCCAGCCTACATCTTAC-AGAGTGACAACCACTTTA
129 CCTCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACAAGAGTGACAACCACTTCA
** * *
42002816 CGATAATTTGATAAAAACAATTCCGAGGGTAACTACTCTAAATCTTGTTTGATAAAAGAAATCAT
194 CGATAATTTGATAAAAACAAGCCCGAGGATAACTACTCTAAATCTAGTTTGATAAAAGAAATCAT
* *** *
42002881 GAGGCTAACAGCCACTT--AGTAGTATTTTTTAAATAAAATTTAGGTCCCTTAGGCAATTGGAAT
259 GAGGCTAACACCCACTTCAAG--GTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGGAA-
* * *
42002944 AAAACAAGAAAATGTCTATATCCTTAGGGAGCCTAGCATGACCAGACATAATTTTGGCAACAGGG
321 AAAA-AAGAAAATGTCTATATCCTCA-AGAGCCTAGCATGACCAGACATAATATTGGCAACAGGG
* * *
42003009 AAAAGAGGAGATCGATAAGAAATTGACCACCTCGGCAAAGTTGCCCAGCCATCGAATTTCTATTC
384 AAAAGAGGAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCGAAATTCTATTC
*
42003074 TACATCTTACATAGAGGGACAACCACTTTA
449 TACACCTTACA-AGAGGGACAACCACTTTA
42003104 CAATAGATTC
Statistics
Matches: 421, Mismatches: 47, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
481 2 0.00
483 124 0.29
484 3 0.01
485 33 0.08
486 220 0.52
487 22 0.05
488 2 0.00
489 15 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (487 bp):
TAAAGAAAATTTAGGTCCCATAGGCAATTAGAATAAAACAAGAAAATGTTTAACTCCTCAAGGAG
CCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGACCACC
TCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACAAGAGTGACAACCACTTCACG
ATAATTTGATAAAAACAAGCCCGAGGATAACTACTCTAAATCTAGTTTGATAAAAGAAATCATGA
GGCTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGGAAAAAAA
AGAAAATGTCTATATCCTCAAGAGCCTAGCATGACCAGACATAATATTGGCAACAGGGAAAAGAG
GAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCGAAATTCTATTCTACACCT
TACAAGAGGGACAACCACTTTATAGTAACTTT
Found at i:42008314 original size:44 final size:42
Alignment explanation
Indices: 42008259--42008583 Score: 234
Period size: 44 Copynumber: 7.6 Consensus size: 42
42008249 ATCTACTCTG
*
42008259 CTGTAA-CTTCAGGGAGATAAGATCCTTTATTTTAATCTGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCC-TTA-TTCAATCTGCTCCA
* ** * *
42008303 CTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCCT-TATTCAATCTGCTCCA
* ***
42008346 CTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGA-TCCT-TATTCAATCTGCTCCA
* * * *
42008390 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTAGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCCT--TATTC---AATCTGCTCCA
* ** * * *
42008436 CTGTAATCTCAGGGAAATAAGA-CCTGGTGCGATCTGCTCTA
1 CTGTAATCTCAGGGAGATAAGATCCTTATTCAATCTGCTCCA
* *
42008477 CTGTAA-CTTCAGAGAGATAAGATCC-T-TT-AATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCCTTATTCAATCTGCTCCA
* * *
42008516 CTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGA-TCCT-TATTCAATCTGCTCCA
42008560 CTGTAATCTCAGGGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATC
42008584 TGCAATTCTT
Statistics
Matches: 223, Mismatches: 42, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
39 26 0.12
40 5 0.02
41 25 0.11
42 5 0.02
43 38 0.17
44 93 0.42
46 31 0.14
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
CTGTAATCTCAGGGAGATAAGATCCTTATTCAATCTGCTCCA
Found at i:42008362 original size:87 final size:84
Alignment explanation
Indices: 42008259--42008578 Score: 256
Period size: 87 Copynumber: 3.7 Consensus size: 84
42008249 ATCTACTCTG
*
42008259 CTGTAA-CTTCAGGGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAG
1 CTGTAATC-TCAGGGAGATAAGATCCTTTA-TTCAATCTGCTCCACTGTAACTTCAGGGAGATA-
* *
42008323 GATAGTGTCTTCAATCTGCTCCG
63 GATA-TGTCTTTAATCTGCTCCA
* **** *
42008346 CTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAAG
1 CTGTAATCTCAGGGAGATAAGA-TCCTTTATTCAATCTGCTCCACTGTAACTTCAGGGAGAT-AG
* * *
42008411 ATCTGAAATTCTTTAGTCTGTTCCA
64 ATATG----TCTTTAATCTGCTCCA
* ** * * * * *
42008436 CTGTAATCTCAGGGAAATAAGA-CC-TGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATA-AG
1 CTGTAATCTCAGGGAGATAAGATCCTTTATTCAATCTGCTCCACTGTAACTTCAGGGAGATAGAT
* *
42008498 AT-CCTTTAATCCGCTCCA
66 ATGTCTTTAATCTGCTCCA
* * * *
42008516 CTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCTGTAA-TCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGA-TCCTTTATTCAATCTGCTCCACTGTAACT-TCAGGGAGATA
42008579 AGATCTGCAA
Statistics
Matches: 183, Mismatches: 39, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
80 32 0.17
82 2 0.01
83 26 0.14
85 2 0.01
86 3 0.02
87 79 0.43
88 6 0.03
90 33 0.18
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (84 bp):
CTGTAATCTCAGGGAGATAAGATCCTTTATTCAATCTGCTCCACTGTAACTTCAGGGAGATAGAT
ATGTCTTTAATCTGCTCCA
Found at i:42008448 original size:46 final size:44
Alignment explanation
Indices: 42008259--42008627 Score: 213
Period size: 44 Copynumber: 8.5 Consensus size: 44
42008249 ATCTACTCTG
*
42008259 CTGTAA-CTTCAGGGAGATAAGATCCT--TTATTTTAATCTGCTCCA
1 CTGTAATC-TCAGGGAGATAAGAT-CTGATT-CTTTAATCTGCTCCA
* * * *
42008303 CTGTAA-CTTCAGGGAGATAGGAT-AG-TGTCTTCAATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTGAT-TCTTTAATCTGCTCCA
* * *
42008346 CTGTAATCTCAGGGAGATAAGATTTCTG--GCCTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGA--TCTGATTCTTTAATCTGCTCCA
* * *
42008390 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTAGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCTG--ATTCTTTAATCTGCTCCA
* * * * * *
42008436 CTGTAATCTCAGGGAAATAAGACCTGGTGC---GATCTGCTCTA
1 CTGTAATCTCAGGGAGATAAGATCTGATTCTTTAATCTGCTCCA
* *
42008477 CTGTAA-CTTCAGAGAGATAAGATC-----CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTGATTCTTTAATCTGCTCCA
* * * *
42008516 CTGTAATCTCAGGGAGATAGGAT-T-ACTATATTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCTGA-T-TCTTTAATCTGCTCCA
** *
42008560 CTGTAATCTCAGGGAGATAAGATCTGCAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCTG--ATTCTTTAATCTGCTCCA
42008606 -TCGTAATCTCAGGG-GAATAAGA
1 CT-GTAATCTCAGGGAG-ATAAGA
42008628 CCTTTTATAA
Statistics
Matches: 254, Mismatches: 44, Indels: 52
0.73 0.13 0.15
Matches are distributed among these distances:
36 1 0.00
39 27 0.11
40 2 0.01
41 26 0.10
42 4 0.02
43 32 0.13
44 93 0.37
45 4 0.02
46 63 0.25
47 1 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATCTGATTCTTTAATCTGCTCCA
Found at i:42008553 original size:170 final size:173
Alignment explanation
Indices: 42008293--42008630 Score: 468
Period size: 170 Copynumber: 2.0 Consensus size: 173
42008283 CTTTATTTTA
* * * * *
42008293 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCGCTGTAATCTCAG
1 ATCTGCTCCACTGTAACTTCAGAGAGATA-GAGAGTGCCTTCAATCCGCTCCACTGTAATCTCAG
* * *
42008358 GGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCT
65 GGAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCT
42008423 TTAGTCTGTTCCA-CTGTAATCTCAGGGAAATAAGACCTGGTGCG
130 TTAGTCTGTTCCATC-GTAATCTCAGGGAAATAAGACCTGGTGCG
* *
42008467 ATCTGCTCTACTGTAACTTCAGAGAGATA-AGA-T-CCTTTAATCCGCTCCACTGTAATCTCAGG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAGAGAGTGCCTTCAATCCGCTCCACTGTAATCTCAGG
* * * * * *
42008529 GAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTT
66 GAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTT
* *
42008594 TGGTCTGTTCCATCGTAATCTCAGGGGAATAAGACCT
131 TAGTCTGTTCCATCGTAATCTCAGGGAAATAAGACCT
42008631 TTTATAATGA
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
170 114 0.79
171 2 0.01
172 2 0.01
174 27 0.19
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (173 bp):
ATCTGCTCCACTGTAACTTCAGAGAGATAGAGAGTGCCTTCAATCCGCTCCACTGTAATCTCAGG
GAGATAAGATTACTAGACTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTT
TAGTCTGTTCCATCGTAATCTCAGGGAAATAAGACCTGGTGCG
Found at i:42012516 original size:41 final size:41
Alignment explanation
Indices: 42012471--42012553 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
42012461 CAAGACCTGA
* * *
42012471 ACATGCTCTTCTTCCGCTCTTGACTTTGCTATCATATAGTC
1 ACATGCTCTTCTTCCGATCTAGACTTTGCGATCATATAGTC
*
42012512 ACATGCTCTTCTTCCGATCTAGACTTTGCGATCATATCGTC
1 ACATGCTCTTCTTCCGATCTAGACTTTGCGATCATATAGTC
42012553 A
1 A
42012554 ACATAGACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (41 bp):
ACATGCTCTTCTTCCGATCTAGACTTTGCGATCATATAGTC
Found at i:42026629 original size:15 final size:16
Alignment explanation
Indices: 42026596--42026629 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42026586 TCGATCATTT
*
42026596 TTGTTAAAAATTTATA
1 TTGTTAAAAATTTACA
42026612 TTGTTAAAAA-TTACA
1 TTGTTAAAAATTTACA
42026627 TTG
1 TTG
42026630 GCTGACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (16 bp):
TTGTTAAAAATTTACA
Found at i:42027770 original size:5 final size:5
Alignment explanation
Indices: 42027717--42027763 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
42027707 TGTTAAAATA
* *
42027717 TATAT ATATAT TAAAT TATTAT TATAT TATAG TATAT TATAT TATAT
1 TATAT -TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
42027764 ATTATATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 27 0.75
6 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:42028486 original size:18 final size:19
Alignment explanation
Indices: 42028463--42028501 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
42028453 ATATATAGAT
42028463 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
42028481 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
42028500 AT
1 AT
42028502 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:42028851 original size:39 final size:39
Alignment explanation
Indices: 42028741--42028875 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
42028731 GACCTCGAGT
* * * *
42028741 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
42028782 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
42028820 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
42028859 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
42028876 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:42029019 original size:18 final size:19
Alignment explanation
Indices: 42028998--42029038 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
42028988 AATGAAATGA
42028998 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
42029016 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
42029035 GAAA
1 GAAA
42029039 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:42036202 original size:102 final size:102
Alignment explanation
Indices: 42036066--42036688 Score: 537
Period size: 111 Copynumber: 5.8 Consensus size: 102
42036056 AATTCAATGG
* ** * ** * * **
42036066 CATTTCACCTGCAAG-ATCTCTTGCATCAGAGGGTGTTGGCATATTTGGCTCTTGCGTTCCAGGC
1 CATTTCACCTGC-AGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGC
42036130 ATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
65 ATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
42036168 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
42036233 TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
66 TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
* *
42036270 CATTTCATCTGCAGCATCTCTTACATCATCGGGTGCTGGAATATTCAGCTCTTGCCTTTCTTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* * *
42036335 TGCTACGGTTCATGTTTTGATGGACTTGATCGTCGGAGCTCGATGG
66 TGCTACGGTTCGTGTTTTGAT---C--GA---T-GGAACTCGATGC
* ** * **
42036381 CATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATATTCAGCTCTTGCCTTTCTTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* * * * *
42036446 TGCTACAGTTCATTTTTTGATGGGCTTGATCGTCGGAGCTCGATGG
66 TGCTACGGTTCGTGTTTTGAT---C--GA---T-GGAACTCGATGC
* * ** * ** *
42036492 CATTTCACCTGAAGCATCTCTTGCATCAAAGGATGTTGTCATATTCAGCTCTTGCCTTTCTTGCG
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* * * * *
42036557 TGCTACGATTCATGTTTTGATGGACTTGATCGTCGGAGCTAGATGG
66 TGCTACGGTTCGTGTTTTGAT---C--GA---T-GGAACTCGATGC
* ** * *** * *
42036603 CATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTATCATATTCAGCTCTTGCCTTCCCTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* *
42036668 TGCTACTGTTCATGTTTTGAT
66 TGCTACGGTTCGTGTTTTGAT
42036689 AAACTTGATT
Statistics
Matches: 471, Mismatches: 40, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
101 2 0.00
102 172 0.37
105 1 0.00
107 2 0.00
110 1 0.00
111 293 0.62
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (102 bp):
CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
Found at i:42036425 original size:111 final size:111
Alignment explanation
Indices: 42036249--42036796 Score: 679
Period size: 111 Copynumber: 4.9 Consensus size: 111
42036239 GGTTCGTGTT
* * * * ** * * **
42036249 TTGATCGAT-GGAACTCGATGCCATTTCATCTGCAGCATCTCTTACATCATCGGGTGCTGGAATA
1 TTGATCG-TCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATA
42036313 TTCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
65 TTCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
42036360 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
1 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
* * *
42036425 TCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATTTTTTGATGGGC
66 TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
*
42036471 TTGATCGTCGGAGCTCGATGGCATTTCACCTGAAGCATCTCTTGCATCAAAGGATGTTGTCATAT
1 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
* *
42036536 TCAGCTCTTGCCTTTCTTGCGTGCTACGATTCATGTTTTGATGGAC
66 TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
* *
42036582 TTGATCGTCGGAGCTAGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTATCATAT
1 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
* * * **
42036647 TCAGCTCTTGCCTTCCCTGCATGCTACTGTTCATGTTTTGATAAAC
66 TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
* * * ** * * * * * *
42036693 TTGATTTGT-GGAACTCAATGGCCGTACACCTACAGCATGTCTTGCATAAAAGGGTCTCTGT-AT
1 TTGA-TCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGT-TGTCAT
* * * * * * *
42036756 ATTCGGTTCTTGCCATCCCTGCATGCTTCGGCTCATGTTTT
64 ATTCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTT
42036797 CGTAAACTTG
Statistics
Matches: 386, Mismatches: 48, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
110 1 0.00
111 380 0.98
112 5 0.01
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (111 bp):
TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
Found at i:42036576 original size:222 final size:213
Alignment explanation
Indices: 42036147--42036688 Score: 726
Period size: 222 Copynumber: 2.5 Consensus size: 213
42036137 GGTTCGTGTT
* * * ** * **
42036147 TTGATCGAT-GGAACTCGATGCCATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATA
1 TTGATCG-TCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATA
* *
42036211 TTCAGCTCTTGCCTTTCTTGCATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGCCATTTC
65 TTCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATGTTTTGATCGATGGAACTCGATGCCATTTC
* * ** *
42036276 ATCTGCAGCATCTCTTACATCATCGGGTGCTGGAATATTCAGCTCTTGCCTTTCTTGCATGCTAC
130 ACCTGAAGCATCTCTTACATCAAAGGATGCTGGAATATTCAGCTCTTGCCTTTCTTGCATGCTAC
*
42036341 GGTTCATGTTTTGATGGAC
195 GATTCATGTTTTGATGGAC
42036360 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
1 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
* *
42036425 TCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATTTTTTGATGGGCTTGATCGTCGGAGCTCGAT
66 TCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATGTTTTGAT---C--GA---T-GGAACTCGAT
* * * **
42036490 GGCATTTCACCTGAAGCATCTCTTGCATCAAAGGATGTTGTCATATTCAGCTCTTGCCTTTCTTG
122 GCCATTTCACCTGAAGCATCTCTTACATCAAAGGATGCTGGAATATTCAGCTCTTGCCTTTCTTG
*
42036555 CGTGCTACGATTCATGTTTTGATGGAC
187 CATGCTACGATTCATGTTTTGATGGAC
* *
42036582 TTGATCGTCGGAGCTAGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTATCATAT
1 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
* * *
42036647 TCAGCTCTTGCCTTCCCTGCATGCTACTGTTCATGTTTTGAT
66 TCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATGTTTTGAT
42036689 AAACTTGATT
Statistics
Matches: 289, Mismatches: 30, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
212 1 0.00
213 94 0.33
216 1 0.00
218 2 0.01
221 1 0.00
222 190 0.66
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (213 bp):
TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
TCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATGTTTTGATCGATGGAACTCGATGCCATTTCA
CCTGAAGCATCTCTTACATCAAAGGATGCTGGAATATTCAGCTCTTGCCTTTCTTGCATGCTACG
ATTCATGTTTTGATGGAC
Found at i:42036781 original size:333 final size:324
Alignment explanation
Indices: 42036147--42036782 Score: 738
Period size: 333 Copynumber: 1.9 Consensus size: 324
42036137 GGTTCGTGTT
* ** *
42036147 TTGATCGATGGAACTCGATGCCATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATAT
1 TTGATCGATGGAACTCGATGCCATTTCACCTGAAGCATCTCTTACATCAAAGGATGTTGGAATAT
* * *
42036212 TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGCCATTTCA
66 TCAGCTCTTGCCTTTCTTGCATGCTACGATTCATGTTTTGATCGATGGAACTAGATGCCATTTCA
* ** * * * *
42036277 TCTGCAGCATCTCTTACATCATCGGGTGCTGGAATATTCAGCTCTTGCCTTTCTTGCATGCTACG
131 CCTGCAGCATCTCTTACATCAAAGGATGCTAGAATATTCAGCTCTTGCCTTCCCTGCATGCTACG
** * * * * *
42036342 GTTCATGTTTTGATGGACTTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCAT
196 GTTCATGTTTTGATAAACTTGATCGTCGGAACTCAATGGCAGTACACCTACAGCATCTCTTGCAT
* * * * *
42036407 CAAAGGATGTTGTCATATTCAGCTCTTGCCTTTCTTGCATGCTACAGTTCATTTTTTGATGGGC
261 AAAAGGATCTTGTCATATTCAGCTCTTGCCATCCCTGCATGCTACAGTTCATTTTTTGATGGGC
* * * **
42036471 TTGATCG-TCGGAGCTCGATGGCATTTCACCTGAAGCATCTCTTGCATCAAAGGATGTTGTCATA
1 TTGATCGAT-GGAACTCGATGCCATTTCACCTGAAGCATCTCTTACATCAAAGGATGTTGGAATA
* *
42036535 TTCAGCTCTTGCCTTTCTTGCGTGCTACGATTCATGTTTTGATGGACTTGATCGTCGGAGCTAGA
65 TTCAGCTCTTGCCTTTCTTGCATGCTACGATTCATGTTTTGAT---C--GA---T-GGAACTAGA
* * * **
42036600 TGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTATCATATTCAGCTCTTGCCTTCCCT
121 TGCCATTTCACCTGCAGCATCTCTTACATCAAAGGATGCTAGAATATTCAGCTCTTGCCTTCCCT
* * *
42036665 GCATGCTACTGTTCATGTTTTGATAAACTTGATTTGT-GGAACTCAATGGCCGTACACCTACAGC
186 GCATGCTACGGTTCATGTTTTGATAAACTTGA-TCGTCGGAACTCAATGGCAGTACACCTACAGC
* * * *
42036729 ATGTCTTGCATAAAAGGGTCTCTGT-ATATTCGGTTCTTGCCATCCCTGCATGCT
250 ATCTCTTGCATAAAAGGATCT-TGTCATATTCAGCTCTTGCCATCCCTGCATGCT
42036783 TCGGCTCATG
Statistics
Matches: 255, Mismatches: 45, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
323 1 0.00
324 93 0.36
327 1 0.00
329 2 0.01
332 1 0.00
333 151 0.59
334 6 0.02
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (324 bp):
TTGATCGATGGAACTCGATGCCATTTCACCTGAAGCATCTCTTACATCAAAGGATGTTGGAATAT
TCAGCTCTTGCCTTTCTTGCATGCTACGATTCATGTTTTGATCGATGGAACTAGATGCCATTTCA
CCTGCAGCATCTCTTACATCAAAGGATGCTAGAATATTCAGCTCTTGCCTTCCCTGCATGCTACG
GTTCATGTTTTGATAAACTTGATCGTCGGAACTCAATGGCAGTACACCTACAGCATCTCTTGCAT
AAAAGGATCTTGTCATATTCAGCTCTTGCCATCCCTGCATGCTACAGTTCATTTTTTGATGGGC
Found at i:42036803 original size:111 final size:110
Alignment explanation
Indices: 42036608--42036880 Score: 323
Period size: 111 Copynumber: 2.5 Consensus size: 110
42036598 GATGGCATTT
* * * * * * *
42036608 CACCTGCAGCATCTCTTGCATCAAAGGATGTTATCATATTCAGCTCTTGCCTTCCCTGCATGCTA
1 CACCTACAGCATCTCTTGCATAAAAGGGTCTTGT-ATATTCGGCTCTTGCCATCCCTGCATGCTA
* * ** **
42036673 CTGTTCATGTTTTGATAAACTTGATTTGTGGAACTCAATGGCCGTA
65 CGGCTCATGTTTTGATAAACTTGATTAATGGAAAACAATGGCCGTA
* * *
42036719 CACCTACAGCATGTCTTGCATAAAAGGGTCTCTGTATATTCGGTTCTTGCCATCCCTGCATGCTT
1 CACCTACAGCATCTCTTGCATAAAAGGGTCT-TGTATATTCGGCTCTTGCCATCCCTGCATGCTA
*
42036784 CGGCTCATGTTTTCG-TAAACTTGATTAATGGAAAACAATGGCTGTA
65 CGGCTCATGTTTT-GATAAACTTGATTAATGGAAAACAATGGCCGTA
* * *
42036830 CACCTACAGCACCTCTTCCATAAAAGGGTCTTTGAATATTCGGCTCTTGCC
1 CACCTACAGCATCTCTTGCATAAAAGGGTC-TTGTATATTCGGCTCTTGCC
42036881 TATATACTTG
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
111 133 0.97
112 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (110 bp):
CACCTACAGCATCTCTTGCATAAAAGGGTCTTGTATATTCGGCTCTTGCCATCCCTGCATGCTAC
GGCTCATGTTTTGATAAACTTGATTAATGGAAAACAATGGCCGTA
Found at i:42040135 original size:22 final size:22
Alignment explanation
Indices: 42040110--42040152 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42040100 TAATCAACTA
*
42040110 TTTTGCTACCATTTCGTTATTG
1 TTTTGCTACAATTTCGTTATTG
* *
42040132 TTTTGCTGCAATTTTGTTATT
1 TTTTGCTACAATTTCGTTATT
42040153 ATATTGTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (22 bp):
TTTTGCTACAATTTCGTTATTG
Found at i:42041777 original size:30 final size:30
Alignment explanation
Indices: 42041743--42041802 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42041733 TATTTTATTA
42041743 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
*
42041773 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
42041803 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:42045328 original size:30 final size:30
Alignment explanation
Indices: 42045282--42045488 Score: 378
Period size: 30 Copynumber: 6.9 Consensus size: 30
42045272 TTTTATTATG
* *
42045282 CCAATATCTCGATACCCATATCATTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
42045313 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
42045343 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
42045373 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
42045403 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
42045433 CCAATATTTGATACCCATATCTTTGACTGT
1 CCAATATTTGATACCCATATCTTTGACTTT
42045463 CCAATATTTGATACCCATATCTTTGA
1 CCAATATTTGATACCCATATCTTTGA
42045489 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
30 166 0.96
31 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:42048832 original size:30 final size:30
Alignment explanation
Indices: 42048786--42048879 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
42048776 TTTTATTATG
*
42048786 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
42048817 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
42048847 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
42048877 CCA
1 CCA
42048880 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:42048841 original size:15 final size:15
Alignment explanation
Indices: 42048796--42048873 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
42048786 CCAATATCTC
42048796 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
42048811 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
42048826 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
42048841 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
42048856 GATACCCATATCTTT
1 GATACCCATATCTTT
42048871 GAT
1 GAT
42048874 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:42054215 original size:11 final size:11
Alignment explanation
Indices: 42054199--42054228 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42054189 TAAATTATTA
42054199 TATTTTAATTT
1 TATTTTAATTT
42054210 TATTTTAATTT
1 TATTTTAATTT
*
42054221 TTTTTTAA
1 TATTTTAA
42054229 AAATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTAATTT
Found at i:42055814 original size:4 final size:4
Alignment explanation
Indices: 42055800--42055833 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
42055790 AAGGAAATTA
*
42055800 AAAT AAAAT AAAT AAAT AAAT AAAT CAAT AAAT A
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
42055834 TATATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:42057595 original size:15 final size:15
Alignment explanation
Indices: 42057575--42057604 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42057565 TTTAATCCTT
*
42057575 TATAAATTATAAAAA
1 TATAAACTATAAAAA
42057590 TATAAACTATAAAAA
1 TATAAACTATAAAAA
42057605 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:42057689 original size:5 final size:6
Alignment explanation
Indices: 42057675--42057699 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42057665 GAATTATCAC
42057675 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
42057700 TCAAAGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:42057988 original size:14 final size:13
Alignment explanation
Indices: 42057969--42058016 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
42057959 TTCTTTAAAC
42057969 TTTTCTTCTTCATT
1 TTTTCTT-TTCATT
*
42057983 TTTTCTTTTCTTT
1 TTTTCTTTTCATT
*
42057996 TTTTCATTTTCTTCT
1 TTTTC-TTTTCAT-T
42058011 TTTTCT
1 TTTTCT
42058017 CCATCTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.32
14 15 0.48
15 6 0.19
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTCATT
Found at i:42057990 original size:19 final size:21
Alignment explanation
Indices: 42057968--42058013 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42057958 GTTCTTTAAA
42057968 CTTTTC-TTCTTCATTTT-TT
1 CTTTTCTTTCTTCATTTTCTT
*
42057987 CTTTTCTTTTTTTCATTTTCTT
1 CTTTTC-TTTCTTCATTTTCTT
42058009 CTTTT
1 CTTTT
42058014 TCTCCATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
21 10 0.43
22 7 0.30
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
CTTTTCTTTCTTCATTTTCTT
Found at i:42058045 original size:20 final size:20
Alignment explanation
Indices: 42058020--42058059 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42058010 TTTTTCTCCA
42058020 TCTGTTTTCCTACATTTTCT
1 TCTGTTTTCCTACATTTTCT
*
42058040 TCTGTTTTCTTACATTTTCT
1 TCTGTTTTCCTACATTTTCT
42058060 ATTTCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (20 bp):
TCTGTTTTCCTACATTTTCT
Found at i:42058767 original size:26 final size:28
Alignment explanation
Indices: 42058724--42058776 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
42058714 ATAACAATCC
* *
42058724 ATTTTTGTTTAAT-TTTTTATGAATTTT
1 ATTTTTGTTGAATATTTTTATAAATTTT
42058751 ATTTTT-TTGAATATTTTTATAAATTT
1 ATTTTTGTTGAATATTTTTATAAATTT
42058777 CAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (28 bp):
ATTTTTGTTGAATATTTTTATAAATTTT
Found at i:42059344 original size:15 final size:15
Alignment explanation
Indices: 42059324--42059353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42059314 TTTAATCCTT
*
42059324 TATAAATTATAAAAA
1 TATAAACTATAAAAA
42059339 TATAAACTATAAAAA
1 TATAAACTATAAAAA
42059354 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:42059622 original size:29 final size:28
Alignment explanation
Indices: 42059576--42059633 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
42059566 AATATAATTT
* *
42059576 TTTTTAAAAAAATTTAAAATCAT-TAAAA
1 TTTTAAAAAAAAATTAAAAT-ATATAAAA
42059604 TTTTAAAAACAAAATTAAAATATATAAAA
1 TTTTAAAAA-AAAATTAAAATATATAAAA
42059633 T
1 T
42059634 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTTAAAAAAAAATTAAAATATATAAAA
Found at i:42069614 original size:16 final size:15
Alignment explanation
Indices: 42069593--42069645 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
42069583 GTTCTGAAAG
42069593 AAAATTGAAAAGATGA
1 AAAATT-AAAAGATGA
* *
42069609 AAAATTAAAGGGATAA
1 AAAATTAAA-AGATGA
*
42069625 AAAAATAGAAAGATGA
1 AAAATTA-AAAGATGA
42069641 AAAAT
1 AAAAT
42069646 ATAATTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.83
17 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
AAAATTAAAAGATGA
Found at i:42075004 original size:11 final size:11
Alignment explanation
Indices: 42074990--42075023 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
42074980 CGAAACAGGG
42074990 GAGAAAGAAAA
1 GAGAAAGAAAA
42075001 GAGAAAGAAAA
1 GAGAAAGAAAA
*
42075012 GAAAAAGGAAAA
1 GAGAAA-GAAAA
42075024 TTAGAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAGAAAGAAAA
Found at i:42075289 original size:8 final size:8
Alignment explanation
Indices: 42075276--42075304 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
42075266 AATAGGGACT
42075276 AAATTGTA
1 AAATTGTA
42075284 AAATTGTA
1 AAATTGTA
42075292 AAATTGTA
1 AAATTGTA
42075300 AAATT
1 AAATT
42075305 AGGGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (8 bp):
AAATTGTA
Found at i:42076793 original size:20 final size:20
Alignment explanation
Indices: 42076750--42076793 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42076740 ATTGATTTTT
*
42076750 TTGACATGTTTTAAAGATGT
1 TTGACATGTTTTAAAGATGG
*
42076770 TTGACTATGTTTTGAAG-TGG
1 TTGAC-ATGTTTTAAAGATGG
42076790 TTGA
1 TTGA
42076794 ACGATTGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGACATGTTTTAAAGATGG
Found at i:42077772 original size:15 final size:15
Alignment explanation
Indices: 42077752--42077782 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42077742 CACAACAACA
42077752 TATTTGCTCAATTCT
1 TATTTGCTCAATTCT
*
42077767 TATTTGTTCAATTCT
1 TATTTGCTCAATTCT
42077782 T
1 T
42077783 TTCATTTGCT
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:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (15 bp):
TATTTGCTCAATTCT
Found at i:42079217 original size:13 final size:13
Alignment explanation
Indices: 42079199--42079226 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42079189 CCTCTTTTTA
42079199 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
42079212 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
42079225 TT
1 TT
42079227 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:42082978 original size:5 final size:5
Alignment explanation
Indices: 42082968--42082995 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42082958 TTGTTTGCTC
42082968 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
42082996 TCACAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:42103041 original size:207 final size:207
Alignment explanation
Indices: 42102686--42103097 Score: 806
Period size: 207 Copynumber: 2.0 Consensus size: 207
42102676 TAGTTTACCT
42102686 AACAATAATATCAACACTCATATGATAAGAAATTTGGTGCATTTTAAGTAAAATTTTGGGCTCGA
1 AACAATAATATCAACACTCATATGATAAGAAATTTGGTGCATTTTAAGTAAAATTTTGGGCTCGA
*
42102751 GTTTTGTGGATAAAAGAAAACAACGATAAGAGAACTTTGCCCCTAATTTAAAAGGTGACTAGACT
66 GTTTTGTGGATAAAAGAAAACAACGATAAGAGAACTTTGCCCCCAATTTAAAAGGTGACTAGACT
*
42102816 TGACTCTAGATTTAGTTAAGATCCAATTTAGATTAAATTCTACTATGTATAGCCTCTCACTTTAA
131 TGACTCTAGATTTAGTTAAGATCCAATTTAGATTAAATTCTACTATGTATAGCCTCTCACCTTAA
42102881 ATTTCAATTTAC
196 ATTTCAATTTAC
42102893 AACAATAATATCAACACTCATATGATAAGAAATTTGGTGCATTTTAAGTAAAATTTTGGGCTCGA
1 AACAATAATATCAACACTCATATGATAAGAAATTTGGTGCATTTTAAGTAAAATTTTGGGCTCGA
42102958 GTTTTGTGGATAAAAGAAAACAACGATAAGAGAACTTTGCCCCCAATTTAAAAGGTGACTAGACT
66 GTTTTGTGGATAAAAGAAAACAACGATAAGAGAACTTTGCCCCCAATTTAAAAGGTGACTAGACT
42103023 TGACTCTAGATTTAGTTAAGATCCAATTTAGATTAAATTCTACTATGTATAGCCTCTCACCTTAA
131 TGACTCTAGATTTAGTTAAGATCCAATTTAGATTAAATTCTACTATGTATAGCCTCTCACCTTAA
42103088 ATTTCAATTT
196 ATTTCAATTT
42103098 GATTGTAATT
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
207 203 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (207 bp):
AACAATAATATCAACACTCATATGATAAGAAATTTGGTGCATTTTAAGTAAAATTTTGGGCTCGA
GTTTTGTGGATAAAAGAAAACAACGATAAGAGAACTTTGCCCCCAATTTAAAAGGTGACTAGACT
TGACTCTAGATTTAGTTAAGATCCAATTTAGATTAAATTCTACTATGTATAGCCTCTCACCTTAA
ATTTCAATTTAC
Found at i:42103882 original size:51 final size:51
Alignment explanation
Indices: 42103806--42103903 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
42103796 TACATTGTAA
*
42103806 GTTACCAATTTAGTCCTCCCCTAGACCCCTACTCTAATTTTATCATTCATC
1 GTTACCAATTTAGTCCTCCCCTAGACCCCTACTCTAATTTTACCATTCATC
42103857 GTTACCAATTTAGTCCTCCCCTAGACCCCTACTCTAATTTTACCATT
1 GTTACCAATTTAGTCCTCCCCTAGACCCCTACTCTAATTTTACCATT
42103904 TATCAGTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (51 bp):
GTTACCAATTTAGTCCTCCCCTAGACCCCTACTCTAATTTTACCATTCATC
Found at i:42106808 original size:29 final size:29
Alignment explanation
Indices: 42106769--42106826 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42106759 CTGTCATGCA
*
42106769 AATATGTCATCACGTATGAAACAATCAAT
1 AATATGTCATCACGTACGAAACAATCAAT
42106798 AATATGTCATCACGTACGAAACAATCAAT
1 AATATGTCATCACGTACGAAACAATCAAT
42106827 CATTTTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (29 bp):
AATATGTCATCACGTACGAAACAATCAAT
Found at i:42109248 original size:54 final size:54
Alignment explanation
Indices: 42109178--42109284 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
42109168 GGAGACATTG
* *
42109178 GTTTTATTGTTTGAGTTTGATTCAAATTCTAAGCCATTTCGAATTTAAACTAAA
1 GTTTTATGGTTCGAGTTTGATTCAAATTCTAAGCCATTTCGAATTTAAACTAAA
42109232 GTTTTATGGTTCGAGTTTGATTCAAATTCTAAGCCATTTCGAATTTAAACTAA
1 GTTTTATGGTTCGAGTTTGATTCAAATTCTAAGCCATTTCGAATTTAAACTAA
42109285 TGGATTTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (54 bp):
GTTTTATGGTTCGAGTTTGATTCAAATTCTAAGCCATTTCGAATTTAAACTAAA
Found at i:42111968 original size:45 final size:45
Alignment explanation
Indices: 42111903--42112000 Score: 178
Period size: 45 Copynumber: 2.2 Consensus size: 45
42111893 GTTTAAAAGA
*
42111903 GAAAGAGAAAACATCACGGGGAGAGAAATTCTAGATTAATAAACAT
1 GAAAGA-AAAACAACACGGGGAGAGAAATTCTAGATTAATAAACAT
42111949 GAAAGAAAAACAACACGGGGAGAGAAATTCTAGATTAATAAACAT
1 GAAAGAAAAACAACACGGGGAGAGAAATTCTAGATTAATAAACAT
42111994 GAAAGAA
1 GAAAGAA
42112001 CCTTCTTCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 45 0.88
46 6 0.12
ACGTcount: A:0.53, C:0.10, G:0.21, T:0.15
Consensus pattern (45 bp):
GAAAGAAAAACAACACGGGGAGAGAAATTCTAGATTAATAAACAT
Found at i:42122965 original size:287 final size:289
Alignment explanation
Indices: 42122414--42123081 Score: 986
Period size: 287 Copynumber: 2.3 Consensus size: 289
42122404 TGAATGCGAA
* * * * *
42122414 AACATAGCATCGAACTACAA-TTATGCTTATCATATACCATAATAAAAAAGATGCCATCCAGATC
1 AACATAGCATCAAACTACAAGCTATACTTATCATATACCATAATCAAAAAGATGCCATCCAAATC
* * * * ** * *
42122478 ATCATCAAACTAAGCTGAAAACCA-GAACCCATGAATGCTTAAATGATAACAAAAGAATAGGAAA
66 ATCATCAAACTATGTTGAAAA-TAGGAAACCACAAATGCTTAAACGATAACAAAAGAACAGGAAA
42122542 GTCGACTGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACATTTTTAAGTCAAAAAATG
130 GTCGA-TGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACATTTTTAAGTCAAAAAATG
* *
42122607 TAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCACTACCAATCACTACTTCCAAAT
194 TAGTAATATCACTTCCAAAGCACGTTATTATATCGGCTTTTCACTACCAATCACTACTTCCAAAC
42122672 AACTTCAAAGTTAAAAGCAAAAGAATAGGAC
259 AACTTCAAAGTTAAAAGCAAAAGAATAGGAC
* ** * *
42122703 AACATAGCATCAAACTACAAGCTATTCTTATCATATACCATAATCGGAAAGATGTCACCCAAATC
1 AACATAGCATCAAACTACAAGCTATACTTATCATATACCATAATCAAAAAGATGCCATCCAAATC
** *
42122768 ATCATCAAACTATGTTGAAAATAGGAAATTACAAATGCTTATACGA-AACCAAAAGAACAGGAAA
66 ATCATCAAACTATGTTGAAAATAGGAAACCACAAATGCTTAAACGATAA-CAAAAGAACAGGAAA
* * *
42122832 GTTG-TGTTCTTAAACCACTTGAAAGCATAA-TCAATGACTTCACATTTTTAAGTTAAAAAATGT
130 GTCGATGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACATTTTTAAGTCAAAAAATGT
*
42122895 AGTAATATCACTTCCAAAGCACGTTATTATATTGGCTTTTCACTACCAATCACTACTTCCAAACA
195 AGTAATATCACTTCCAAAGCACGTTATTATATCGGCTTTTCACTACCAATCACTACTTCCAAACA
*
42122960 ACTTCAAAGTTAAAAGCAAAAGAATAGGGC
260 ACTTCAAAGTTAAAAGCAAAAGAATAGGAC
* * *
42122990 AACATAGCATCAAACTACAAGCTATACTTACCATATTCCATAATCAAAAAGATGCCTTCCAAATC
1 AACATAGCATCAAACTACAAGCTATACTTATCATATACCATAATCAAAAAGATGCCATCCAAATC
*
42123055 ATCATCAAACTATGTTGAAGATAGGAA
66 ATCATCAAACTATGTTGAAAATAGGAA
42123082 GTGTTCTTAA
Statistics
Matches: 340, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
287 205 0.60
288 26 0.08
289 22 0.06
290 87 0.26
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (289 bp):
AACATAGCATCAAACTACAAGCTATACTTATCATATACCATAATCAAAAAGATGCCATCCAAATC
ATCATCAAACTATGTTGAAAATAGGAAACCACAAATGCTTAAACGATAACAAAAGAACAGGAAAG
TCGATGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACATTTTTAAGTCAAAAAATGTA
GTAATATCACTTCCAAAGCACGTTATTATATCGGCTTTTCACTACCAATCACTACTTCCAAACAA
CTTCAAAGTTAAAAGCAAAAGAATAGGAC
Found at i:42125118 original size:33 final size:33
Alignment explanation
Indices: 42125076--42125166 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
42125066 TTTCTTCTTG
*
42125076 ACATTCCAGCTACTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
42125109 ACATTCCAGCTCCCGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
42125142 ACATTCCAGCTCCTGTCCAGCAACC
1 ACATTCCAGCTCCTGTCCAGCAACC
42125167 TGAAACAGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.30, C:0.43, G:0.10, T:0.18
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:42128226 original size:13 final size:13
Alignment explanation
Indices: 42128210--42128237 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42128200 AATGTGACTA
42128210 GTTAATCTAGATG
1 GTTAATCTAGATG
42128223 GTTAATCTAGATG
1 GTTAATCTAGATG
42128236 GT
1 GT
42128238 GTACATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (13 bp):
GTTAATCTAGATG
Found at i:42137120 original size:5 final size:5
Alignment explanation
Indices: 42137094--42137151 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
42137084 ATGTGTTAAA
* *
42137094 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
42137143 ATATT ATAT
1 ATATT ATAT
42137152 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:42137130 original size:10 final size:9
Alignment explanation
Indices: 42137095--42137152 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
42137085 TGTGTTAAAA
42137095 TATATATAT
1 TATATATAT
*
42137104 TAAAT-TAT
1 TATATATAT
42137112 TAT-TATAT
1 TATATATAT
42137120 TATAGTATAT
1 TATA-TATAT
42137130 TATAT-TA-
1 TATATATAT
42137137 TATATTATAT
1 TATA-TATAT
42137147 TATATA
1 TATATA
42137153 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:42137142 original size:12 final size:12
Alignment explanation
Indices: 42137097--42137152 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
42137087 TGTTAAAATA
*
42137097 TATATATTAAAT
1 TATATATTATAT
42137109 TAT-TATTATATT
1 TATATATTATA-T
42137121 ATAGTATATTATAT
1 -TA-TATATTATAT
42137135 TATATATTATAT
1 TATATATTATAT
42137147 TATATA
1 TATATA
42137153 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:42137999 original size:18 final size:19
Alignment explanation
Indices: 42137976--42138014 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
42137966 ATATATAGAT
42137976 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
42137994 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
42138013 AT
1 AT
42138015 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:42138364 original size:39 final size:39
Alignment explanation
Indices: 42138254--42138388 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
42138244 GACCTCGAGT
* * * *
42138254 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
42138295 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
42138333 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
42138372 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
42138389 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:42138532 original size:18 final size:19
Alignment explanation
Indices: 42138511--42138551 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
42138501 AATGAAATGA
42138511 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
42138529 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
42138548 GAAA
1 GAAA
42138552 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:42142025 original size:36 final size:36
Alignment explanation
Indices: 42141966--42142043 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
42141956 GTAACAAGAC
* *
42141966 TAACAATAAAAGAAGAGTTATATAATATAC-AAATAA
1 TAACAACAAAAGAAGAGTAATATAATA-ACGAAATAA
42142002 TAACAACAAAA-AAGTAGTAATATAATAACGAAATAA
1 TAACAACAAAAGAAG-AGTAATATAATAACGAAATAA
*
42142038 CAACAA
1 TAACAA
42142044 AACAATGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
36 32 0.86
ACGTcount: A:0.63, C:0.09, G:0.08, T:0.21
Consensus pattern (36 bp):
TAACAACAAAAGAAGAGTAATATAATAACGAAATAA
Found at i:42146330 original size:50 final size:49
Alignment explanation
Indices: 42146251--42146351 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 49
42146241 CCTATATATT
* *
42146251 TTTCATTCGGTTATTTTTGTCACCATCTTCGCTATTCTTCTTCTTCTTC
1 TTTCATTCGGTTATTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
*
42146300 TTTCATTCGGTTGTTTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
1 TTTCATTCGGTT-ATTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
42146350 TT
1 TT
42146352 CTGCCGCTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 12 0.25
50 36 0.75
ACGTcount: A:0.10, C:0.27, G:0.08, T:0.55
Consensus pattern (49 bp):
TTTCATTCGGTTATTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
Found at i:42150375 original size:10 final size:10
Alignment explanation
Indices: 42150360--42150385 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42150350 TAAAACAGCT
42150360 TATATACATA
1 TATATACATA
42150370 TATATACATA
1 TATATACATA
42150380 TATATA
1 TATATA
42150386 TTCACTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATACATA
Found at i:42160942 original size:49 final size:49
Alignment explanation
Indices: 42160864--42161151 Score: 315
Period size: 49 Copynumber: 5.8 Consensus size: 49
42160854 GTAGCCGAAG
* * * * *
42160864 CTATCTGGTACGCATAGCAGCTTGGACTTAGTACTACACATGCGACCAG
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
*
42160913 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * * * *
42160962 TTATCCGGTACACGTAGTAGCCTGCATTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AA
* * * * * *
42161012 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* * * *
42161062 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGGCCAA
1 -CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
42161112 TTATCTAGTACACGTAGTAGCCTGTACTTAGTACTACACA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
42161152 CGTGACCTCA
Statistics
Matches: 204, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
49 120 0.59
50 47 0.23
51 37 0.18
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:42161091 original size:150 final size:148
Alignment explanation
Indices: 42160889--42161159 Score: 434
Period size: 150 Copynumber: 1.8 Consensus size: 148
42160879 AGCAGCTTGG
* * *
42160889 ACTTAGTACTACACATGCGACCAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACAT
1 ACTTAGTACTACACACGCGACAAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACAT
* *
42160954 GCGACCAATTATCCGGTACACGTAGTAGCCTGCATTTAGTACTACACACGTGACCTAACCATCTG
66 GCGACCAATTATCCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTG
42161019 ATACACGTAGTAGCCTGC
131 ATACACGTAGTAGCCTGC
* *
42161037 ACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACAC
1 ACTTAGTACTACACACGCGA-C-AAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACAC
* * *
42161102 ATGCGGCCAATTATCTAGTACACGTAGTAGCCTGTACTTAGTACTACACACGTGACCT
64 ATGCGACCAATTATCCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
42161160 CACAATAGCT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
148 18 0.16
149 1 0.01
150 92 0.83
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (148 bp):
ACTTAGTACTACACACGCGACAAGCTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACAT
GCGACCAATTATCCAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTG
ATACACGTAGTAGCCTGC
Found at i:42162232 original size:17 final size:17
Alignment explanation
Indices: 42162212--42162263 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 17
42162202 ATACTACTCC
42162212 AATGTAAATATTAAAAT
1 AATGTAAATATTAAAAT
*
42162229 AATGTTAATA-TAAAAT
1 AATGTAAATATTAAAAT
*
42162245 TAT-TAAATATTAAAAT
1 AATGTAAATATTAAAAT
42162261 AAT
1 AAT
42162264 ATAATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 16 0.53
17 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AATGTAAATATTAAAAT
Found at i:42162252 original size:32 final size:31
Alignment explanation
Indices: 42162216--42162298 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 31
42162206 TACTCCAATG
*
42162216 TAAATATTAAAATAATGTTAATATAAA-ATTAT
1 TAAATATTAAAATAAT-ATAATATAAATATT-T
42162248 TAAATATTAAAATAATATAATATAAATATTT
1 TAAATATTAAAATAATATAATATAAATATTT
*
42162279 TAAAAATTTTAAAATAATAT
1 T--AAATATTAAAATAATAT
42162299 GGGCGAGCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 11 0.24
32 19 0.41
33 16 0.35
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
TAAATATTAAAATAATATAATATAAATATTT
Found at i:42162269 original size:16 final size:15
Alignment explanation
Indices: 42162218--42162270 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
42162208 CTCCAATGTA
42162218 AATATTAAAATAATGTT
1 AATATTAAAATAA--TT
*
42162235 AATA-TAAAATTATT
1 AATATTAAAATAATT
42162249 AAATATTAAAATAATAT
1 -AATATTAAAATAAT-T
42162266 AATAT
1 AATAT
42162271 AAATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 20 0.65
17 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AATATTAAAATAATT
Found at i:42173694 original size:4 final size:4
Alignment explanation
Indices: 42173669--42173719 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
42173659 TTTGATTGCA
* * *
42173669 TATG TATG TGTG TGTG TGTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
42173717 TAT
1 TAT
42173720 ATGTGTTATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:42177615 original size:20 final size:21
Alignment explanation
Indices: 42177580--42177621 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42177570 AAAAGCCAAG
42177580 TAAAACTGATTTTTTTATTAC
1 TAAAACTGATTTTTTTATTAC
42177601 TAAAACTGATTTTTTT-TTAC
1 TAAAACTGATTTTTTTATTAC
42177621 T
1 T
42177622 TTTTTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
TAAAACTGATTTTTTTATTAC
Found at i:42180674 original size:31 final size:31
Alignment explanation
Indices: 42180636--42180706 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
42180626 TTTTAAATAT
42180636 AAGTGACTAAAACGTAACCTGAGATAAACAA
1 AAGTGACTAAAACGTAACCTGAGATAAACAA
* *
42180667 AAGTGACTAAAATGTAACTTGAGATAAACAA
1 AAGTGACTAAAACGTAACCTGAGATAAACAA
42180698 AAGTGACTA
1 AAGTGACTA
42180707 TTTTGACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.20
Consensus pattern (31 bp):
AAGTGACTAAAACGTAACCTGAGATAAACAA
Found at i:42181191 original size:21 final size:21
Alignment explanation
Indices: 42181165--42181207 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42181155 CCAGAAAAAA
* *
42181165 AAAAAAAACCCAAAGAGGGAG
1 AAAAAAAACACAAAGAGAGAG
*
42181186 AAAAAAAATACAAAGAGAGAG
1 AAAAAAAACACAAAGAGAGAG
42181207 A
1 A
42181208 GAGGGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.09, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAAAAAACACAAAGAGAGAG
Found at i:42189858 original size:24 final size:24
Alignment explanation
Indices: 42189823--42189870 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42189813 AAAATATCCA
*
42189823 TAAAATGTTAAAAACGAT-AAATG
1 TAAAATGTTAAAAACAATGAAATG
*
42189846 TAAAATTTATAAAAACAATGAAATG
1 TAAAATGT-TAAAAACAATGAAATG
42189871 AATGGTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.27
Consensus pattern (24 bp):
TAAAATGTTAAAAACAATGAAATG
Found at i:42195784 original size:118 final size:118
Alignment explanation
Indices: 42195639--42195869 Score: 403
Period size: 118 Copynumber: 2.0 Consensus size: 118
42195629 TTTCAACTTG
*
42195639 AAATAATTTCCTTTCGTACAAAGAGCTTTACTTGGTCTTCACTC-CTTTCTACTATGCTTGATCT
1 AAATAATTTCCTTTCGTACAAAAAGCTTTACTTGGTCTTCACTCTC-TTCTACTATGCTTGATCT
*
42195703 TCGTAGCACCACATCTATG-TTTGTTGTCGTAAACACCTCTTTTACGGTAGCTGA
65 TCGTAGCAACACATCTATGCTTT-TTGTCGTAAACACCTCTTTTACGGTAGCTGA
42195757 AAATAATTTCCTTTCGTACAAAAAGCTTTACTTGGTCTTCACTCTCTTCTACTATGCTTGATCTT
1 AAATAATTTCCTTTCGTACAAAAAGCTTTACTTGGTCTTCACTCTCTTCTACTATGCTTGATCTT
*
42195822 CGTAGCAACACATCTATGCTTTTTGTCGTAAACACCTCTTTTATGGTA
66 CGTAGCAACACATCTATGCTTTTTGTCGTAAACACCTCTTTTACGGTA
42195870 AAAATATTAT
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
118 104 0.96
119 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (118 bp):
AAATAATTTCCTTTCGTACAAAAAGCTTTACTTGGTCTTCACTCTCTTCTACTATGCTTGATCTT
CGTAGCAACACATCTATGCTTTTTGTCGTAAACACCTCTTTTACGGTAGCTGA
Found at i:42197048 original size:22 final size:21
Alignment explanation
Indices: 42196989--42197048 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
42196979 AATGGCATAG
*
42196989 AAATTAAAGAAATTGTAAATTA
1 AAATTAAA-AAATTATAAATTA
***
42197011 AAATTAAGAGGTTTATAAATTA
1 AAATTAA-AAAATTATAAATTA
42197033 AAATTATAAAAATTAT
1 AAATTA-AAAAATTAT
42197049 GGTACATATG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
AAATTAAAAAATTATAAATTA
Found at i:42205504 original size:18 final size:18
Alignment explanation
Indices: 42205477--42205569 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
42205467 TACGACCGTT
42205477 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
42205495 TACGGCACTATTTACGTA
1 TACGGTACTATTCACGTA
*
42205513 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
42205531 TATGGTACTATTGACGTA
1 TACGGTACTATTCACGTA
*
42205549 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
42205567 TAC
1 TAC
42205570 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:42208010 original size:284 final size:284
Alignment explanation
Indices: 42207500--42208067 Score: 1028
Period size: 284 Copynumber: 2.0 Consensus size: 284
42207490 CTGGTAAATC
*
42207500 TTTGGTTAACGATGATTCTTTGCATGTATTTGGTTCCACTGCATATTGTCATGTAAAAGAATCTA
1 TTTGGTTAACGATGATTCTTTGCATGTATTTGGTTCCACTGCATATTATCATGTAAAAGAATCTA
* *
42207565 AGTTAGACCCAAGAGCAAAGAAAGCATTATTCTTGGGTATAACTGATGAAGTAAAAGGATATCGT
66 AGTTAGACCCAAGAGCAAAGAAAGCATTATTCATGGGTATAACTGATGAAGTAAAAGGATACCGT
*
42207630 CTCTGGTGTCCTGATACAAGGAAGATTGTTTTCAGTAGAGATGTGACTTTTGATGAATCAACCAT
131 CTCTGGTGTCCTGATACAAGGAAGATTGTTTTCAGTAGAGATGTAACTTTTGATGAATCAACCAT
* *
42207695 GTTGAAGTACAAGGATTCACAAAAGGATGACAAAACCAGTAGTACTTTGCAGCAGGTGGAGCTTG
196 GATGAAGAACAAGGATTCACAAAAGGATGACAAAACCAGTAGTACTTTGCAGCAGGTGGAGCTTG
42207760 AAAAGGTTAACGATGATCCAGCTA
261 AAAAGGTTAACGATGATCCAGCTA
42207784 TTTGGTTAACGATGATTCTTTGCATGTATTTGGTTCCACTGCATATTATCATGTAAAAGAATCTA
1 TTTGGTTAACGATGATTCTTTGCATGTATTTGGTTCCACTGCATATTATCATGTAAAAGAATCTA
* **
42207849 AGTTAGACCCAAGAGCAAAGAAAGCATTATTCATGGGTATAACTGGTGGTGTAAAAGGATACCGT
66 AGTTAGACCCAAGAGCAAAGAAAGCATTATTCATGGGTATAACTGATGAAGTAAAAGGATACCGT
42207914 CTCTGGTGTCCTGATACAAGGAAGATTGTTTTCAGTAGAGATGTAACTTTTGATGAATCAACCAT
131 CTCTGGTGTCCTGATACAAGGAAGATTGTTTTCAGTAGAGATGTAACTTTTGATGAATCAACCAT
* *
42207979 GATGAAGAACGAGGATTCACAAAAGGATGACAAAACCAGTAGTACTTTGCAGCAGGTGGAGTTTG
196 GATGAAGAACAAGGATTCACAAAAGGATGACAAAACCAGTAGTACTTTGCAGCAGGTGGAGCTTG
*
42208044 AAAAGGTTAATGATGATCCAGCTA
261 AAAAGGTTAACGATGATCCAGCTA
42208068 ATATTGAAAG
Statistics
Matches: 272, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
284 272 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (284 bp):
TTTGGTTAACGATGATTCTTTGCATGTATTTGGTTCCACTGCATATTATCATGTAAAAGAATCTA
AGTTAGACCCAAGAGCAAAGAAAGCATTATTCATGGGTATAACTGATGAAGTAAAAGGATACCGT
CTCTGGTGTCCTGATACAAGGAAGATTGTTTTCAGTAGAGATGTAACTTTTGATGAATCAACCAT
GATGAAGAACAAGGATTCACAAAAGGATGACAAAACCAGTAGTACTTTGCAGCAGGTGGAGCTTG
AAAAGGTTAACGATGATCCAGCTA
Found at i:42218636 original size:17 final size:17
Alignment explanation
Indices: 42218614--42218647 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42218604 AAGGCCCTTT
42218614 CTCTAAACTGATATTCA
1 CTCTAAACTGATATTCA
42218631 CTCTAAACTGATATTCA
1 CTCTAAACTGATATTCA
42218648 AATTTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
CTCTAAACTGATATTCA
Found at i:42223591 original size:13 final size:13
Alignment explanation
Indices: 42223575--42223622 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
42223565 TAAATCAAAT
42223575 TTTTCAAAAACAC
1 TTTTCAAAAACAC
* *
42223588 TTTTCCACAACAC
1 TTTTCAAAAACAC
* *
42223601 TTTTTAAAAGCAC
1 TTTTCAAAAACAC
42223614 TTTTCAAAA
1 TTTTCAAAA
42223623 GTATTGCCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:42235812 original size:27 final size:28
Alignment explanation
Indices: 42235779--42235843 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
42235769 AATTTTGATG
*
42235779 TAAACTTAAAAATTCAATCCAATCAA-T
1 TAAACTTAAAAATTCAATACAATCAATT
*
42235806 TAAACTTAAAAATTCAATACGATCAATT
1 TAAACTTAAAAATTCAATACAATCAATT
*
42235834 TAAATTTAAA
1 TAAACTTAAA
42235844 GTAAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAACTTAAAAATTCAATACAATCAATT
Found at i:42239916 original size:31 final size:29
Alignment explanation
Indices: 42239866--42239923 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
42239856 TATATCTATG
42239866 AAATTTTGATTGCAGTTCAAATGTATACATA
1 AAATTTTGATTGCAGTTC-AAT-TATACATA
*
42239897 AAATTTTGATTTC-GATTCAATTATACA
1 AAATTTTGATTGCAG-TTCAATTATACA
42239924 CATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 4 0.16
31 15 0.60
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATTTTGATTGCAGTTCAATTATACATA
Found at i:42248183 original size:18 final size:18
Alignment explanation
Indices: 42248160--42248252 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
42248150 CCCAACTACT
*
42248160 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
42248178 GTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
*
42248196 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
42248214 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
42248232 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
42248250 GTA
1 GTA
42248253 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:42248205 original size:36 final size:36
Alignment explanation
Indices: 42248158--42248252 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
42248148 ATCCCAACTA
*
42248158 CTGTATACGTGAACAGTACCGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
*
42248194 CTGTATACGTGAATAGTACTGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
*
42248230 CCGTATACGTGAATAGTACCGTA
1 CTGTATACGTGAATAGTACCGTA
42248253 AACGGTCGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (36 bp):
CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
Found at i:42254810 original size:6 final size:6
Alignment explanation
Indices: 42254799--42254832 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42254789 AAAGTTGAAC
42254799 TATACA TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATA
42254833 TATACCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:42282808 original size:13 final size:13
Alignment explanation
Indices: 42282790--42282818 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42282780 TTAAATATAT
42282790 AATTTTGAAAAGC
1 AATTTTGAAAAGC
42282803 AATTTTGAAAAGC
1 AATTTTGAAAAGC
42282816 AAT
1 AAT
42282819 GAGAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (13 bp):
AATTTTGAAAAGC
Found at i:42285318 original size:33 final size:34
Alignment explanation
Indices: 42285275--42285341 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
42285265 TATAACACAC
*
42285275 TCTCACAGCTTTAGTCCCTTTC-CCCAAATCTTG
1 TCTCAAAGCTTTAGTCCCTTTCACCCAAATCTTG
*
42285308 TCTCAAAGCTTTAGTCCTTTTCACCCAAATCTTG
1 TCTCAAAGCTTTAGTCCCTTTCACCCAAATCTTG
42285342 GCAAAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (34 bp):
TCTCAAAGCTTTAGTCCCTTTCACCCAAATCTTG
Found at i:42286650 original size:12 final size:12
Alignment explanation
Indices: 42286633--42286657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42286623 TTCACATTAC
42286633 AAAAATGAGATA
1 AAAAATGAGATA
42286645 AAAAATGAGATA
1 AAAAATGAGATA
42286657 A
1 A
42286658 GTATAATTAT
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAAATGAGATA
Found at i:42298391 original size:15 final size:16
Alignment explanation
Indices: 42298371--42298408 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42298361 TAGTCCATAT
*
42298371 TTTTTAATT-GGATCA
1 TTTTTAATTCGGATAA
*
42298386 TTTTTAATTCGTATAA
1 TTTTTAATTCGGATAA
42298402 TTTTTAA
1 TTTTTAA
42298409 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (16 bp):
TTTTTAATTCGGATAA
Found at i:42302419 original size:20 final size:21
Alignment explanation
Indices: 42302390--42302430 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42302380 CTTTATAATC
42302390 TTTTTAGTAAATAAATATATA
1 TTTTTAGTAAATAAATATATA
* *
42302411 TTTTT-GTAACTTAATATATA
1 TTTTTAGTAAATAAATATATA
42302431 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTTAGTAAATAAATATATA
Found at i:42304519 original size:28 final size:29
Alignment explanation
Indices: 42304468--42304544 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 29
42304458 TAACCATGAC
*
42304468 CTTTGATTTAATGTACAATTTTATACA-AAA
1 CTTTGATTT--TGTTCAATTTTATACAGAAA
42304498 CTTTGATTTTGTTCAATTTTATACATGAAA
1 CTTTGATTTTGTTCAATTTTATACA-GAAA
42304528 -TTTGA-TTTGTTTCAATT
1 CTTTGATTTTG-TTCAATT
42304545 CTCACAAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 19 0.44
29 12 0.28
30 12 0.28
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (29 bp):
CTTTGATTTTGTTCAATTTTATACAGAAA
Found at i:42323332 original size:25 final size:25
Alignment explanation
Indices: 42323264--42323332 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
42323254 TTTAGCCCAT
* **
42323264 TTAAATATTTGACAAAAATAAAAAGT
1 TTAAATATTT-AAAAAAATAAAAAAA
**
42323290 TTAAGGA-TTAAAATAAATAAAAAAA
1 TTAAATATTTAAAA-AAATAAAAAAA
42323315 TTAAATATTTAAAAAAAT
1 TTAAATATTTAAAAAAAT
42323333 TATAAATTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
24 3 0.09
25 20 0.59
26 11 0.32
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.30
Consensus pattern (25 bp):
TTAAATATTTAAAAAAATAAAAAAA
Found at i:42323345 original size:17 final size:17
Alignment explanation
Indices: 42323308--42323346 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
42323298 TAAAATAAAT
*
42323308 AAAAAAATTAAATATTT
1 AAAAAAATTAAATATTC
42323325 AAAAAAATTATAA-ATTC
1 AAAAAAATTA-AATATTC
42323342 AAAAA
1 AAAAA
42323347 TTAAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAAATTAAATATTC
Found at i:42328653 original size:6 final size:6
Alignment explanation
Indices: 42328642--42328667 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42328632 CAAAAGGATT
42328642 TGCCAA TGCCAA TGCCAA TGCCAA TG
1 TGCCAA TGCCAA TGCCAA TGCCAA TG
42328668 GGATACTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (6 bp):
TGCCAA
Found at i:42338929 original size:4 final size:4
Alignment explanation
Indices: 42338920--42338960 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
42338910 CCACAAGACA
42338920 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
42338961 CACGTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:42341463 original size:51 final size:52
Alignment explanation
Indices: 42341403--42341503 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 52
42341393 CCGAACGTAT
*
42341403 TACGGTAGTCCTAGAATCGATTAAACCCT-GCTCTGAAACCAATAAAAATAC
1 TACGGTAGTCCTAGAATCGACTAAACCCTAGCTCTGAAACCAATAAAAATAC
* * *
42341454 TACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATTAAAAT
1 TACGGTAGTCCTAGAATCGACTAAACCCTAGCTCTGAAACCAATAAAAAT
42341504 GTAACACCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 27 0.60
52 18 0.40
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (52 bp):
TACGGTAGTCCTAGAATCGACTAAACCCTAGCTCTGAAACCAATAAAAATAC
Found at i:42345206 original size:8 final size:8
Alignment explanation
Indices: 42345193--42345236 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
42345183 CTTTTATATT
42345193 TTATTAAA
1 TTATTAAA
42345201 TTATTAAA
1 TTATTAAA
42345209 TTATTAAA
1 TTATTAAA
*
42345217 TTATTATA
1 TTATTAAA
*
42345225 TTATTATA
1 TTATTAAA
42345233 TTAT
1 TTAT
42345237 ATACTTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATTAAA
Found at i:42345793 original size:8 final size:8
Alignment explanation
Indices: 42345782--42345820 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
42345772 ATATATTAAT
42345782 TTATATTA
1 TTATATTA
42345790 TTATATTA
1 TTATATTA
42345798 TTATATTA
1 TTATATTA
*
42345806 TTACATTA
1 TTATATTA
42345814 TATATAT
1 T-TATAT
42345821 GTAAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 24 0.86
9 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATATTA
Found at i:42345883 original size:13 final size:15
Alignment explanation
Indices: 42345852--42345888 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
42345842 CAAAACGAAT
42345852 AGGAGAGAAAGAAAGA
1 AGGAGA-AAAGAAAGA
42345868 AGG-GAAAAGAAA-A
1 AGGAGAAAAGAAAGA
42345881 AGGAGAAA
1 AGGAGAAA
42345889 TTAGGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 2 0.10
16 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGGAGAAAAGAAAGA
Found at i:42348984 original size:58 final size:58
Alignment explanation
Indices: 42348894--42349003 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
42348884 AAGATAGTGA
* *
42348894 TTGGTAGCAATTTCCCATAAGTTGTGGGCTACCGTAGCTCTGTGTGAACATCAATGTG
1 TTGGTAGCAATTTCCCATAAGTTGTGGACTACCGTAGCTCTATGTGAACATCAATGTG
* *
42348952 TTGGTAGTAA-TTCCGCATAAGTTGTGGACTACCGTAGCTCTATGTGAGCATC
1 TTGGTAGCAATTTCC-CATAAGTTGTGGACTACCGTAGCTCTATGTGAACATC
42349004 GAAGTATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 4 0.09
58 43 0.91
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (58 bp):
TTGGTAGCAATTTCCCATAAGTTGTGGACTACCGTAGCTCTATGTGAACATCAATGTG
Found at i:42350465 original size:18 final size:18
Alignment explanation
Indices: 42350428--42350467 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
42350418 CAGTGAAGAA
42350428 AAATGGAGAAAGGAAAAGG
1 AAATGGAGAAA-GAAAAGG
42350447 AAATGGAGAAA-ATAAAGG
1 AAATGGAGAAAGA-AAAGG
42350465 AAA
1 AAA
42350468 ATATGTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 8 0.40
19 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (18 bp):
AAATGGAGAAAGAAAAGG
Found at i:42351969 original size:21 final size:20
Alignment explanation
Indices: 42351910--42351969 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
42351900 GCACATAAGT
* *
42351910 GTTGAGCGAAAACCCGTAAGG
1 GTTGAACGAAAACCCAT-AGG
* * *
42351931 GTTGAACGTAAGCTCATAGG
1 GTTGAACGAAAACCCATAGG
42351951 AGTTGAACGAAAACCCATA
1 -GTTGAACGAAAACCCATA
42351970 TAGGTTATTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (20 bp):
GTTGAACGAAAACCCATAGG
Found at i:42352307 original size:20 final size:20
Alignment explanation
Indices: 42352282--42352328 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
42352272 ATCATTTATC
42352282 ATTTAACATATAACATTAAA
1 ATTTAACATATAACATTAAA
42352302 ATTTAACATATAACATTAAA
1 ATTTAACATATAACATTAAA
42352322 ATTTAAC
1 ATTTAAC
42352329 CATACAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTAACATATAACATTAAA
Found at i:42355089 original size:6 final size:6
Alignment explanation
Indices: 42355078--42355106 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42355068 GTTGTTTGTT
42355078 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
42355107 CCCATGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (6 bp):
TTCTTG
Found at i:42358022 original size:17 final size:16
Alignment explanation
Indices: 42357994--42358046 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
42357984 TTTGGTTCGC
42357994 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42358010 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
42358027 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42358043 TGTA
1 TGTA
42358047 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:42358302 original size:16 final size:16
Alignment explanation
Indices: 42358262--42358303 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42358252 TTAATCATAT
*
42358262 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
42358278 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
42358293 TTAAAATATAT
1 TTAAAATATAT
42358304 AATTTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:42358554 original size:59 final size:59
Alignment explanation
Indices: 42358372--42358556 Score: 187
Period size: 59 Copynumber: 3.1 Consensus size: 59
42358362 TATGATACTG
* *
42358372 TAAAATATAAATTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAG
1 TAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
* * * * ** ** * * *
42358431 TAAAATTCTTAATATTAA-AT-ATTCTTATATGAATTTTCTAAAATCATAATATATAATACT-A
1 TAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATAATTTAATAAAAATATATAAT-TTAA
42358492 TAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
1 TAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
42358551 TAAAAT
1 TAAAAT
42358557 TCTTAATATT
Statistics
Matches: 94, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 5 0.05
59 38 0.40
60 16 0.17
61 30 0.32
62 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (59 bp):
TAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
Found at i:42358652 original size:120 final size:120
Alignment explanation
Indices: 42358265--42358605 Score: 567
Period size: 120 Copynumber: 2.8 Consensus size: 120
42358255 ATCATATTTA
* * * *
42358265 AACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATT-A
1 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAT-ATTAA
* * * * *
42358329 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAAATT
*
42358385 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAATATTAAA
1 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
*
42358450 TATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTT
66 TATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAAATT
42358505 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
1 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
42358570 TATTCTTATATGAATTTTCTAAAATCATAATATATA
66 TATTCTTATATGAATTTTCTAAAATCATAATATATA
42358606 TAATACTACA
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
119 3 0.01
120 205 0.99
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
TATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAAATT
Found at i:42358731 original size:14 final size:15
Alignment explanation
Indices: 42358712--42358744 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
42358702 CATTATTCTT
*
42358712 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
42358726 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
42358741 AAAA
1 AAAA
42358745 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:42359214 original size:58 final size:58
Alignment explanation
Indices: 42359091--42359240 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
42359081 AAAGTTGCTA
* **
42359091 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGGATTAAATT
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
* * * *
42359149 TGTTTTGGCACCAAAAGTAAACCACAAGTCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-CAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
*
42359208 TGTTTGGGCACTAAAAGCAACCGCAA-TCACAAG
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAG
42359241 CCACAAGTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 7 0.09
58 23 0.29
59 50 0.62
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
Found at i:42369409 original size:38 final size:38
Alignment explanation
Indices: 42369348--42369547 Score: 310
Period size: 38 Copynumber: 5.2 Consensus size: 38
42369338 ATTTGATGTG
* *
42369348 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
42369388 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* *
42369426 TATCCGGGTTAAAACCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
42369464 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* * *
42369502 TATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
*
42369540 TATTCGGG
1 TATCCGGG
42369548 CCTTCGTGCC
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
38 137 0.91
39 5 0.03
40 8 0.05
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
Found at i:42369664 original size:43 final size:43
Alignment explanation
Indices: 42369540--42369651 Score: 224
Period size: 43 Copynumber: 2.6 Consensus size: 43
42369530 GCTGGTATTA
42369540 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42369583 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
42369626 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
42369652 GTAATGCCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.10, C:0.27, G:0.34, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:42378100 original size:12 final size:12
Alignment explanation
Indices: 42378076--42378117 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
42378066 TTTCTTAATT
42378076 TTTTTTATATTAA
1 TTTTTTAT-TTAA
*
42378089 TTTTTTGTTTAA
1 TTTTTTATTTAA
42378101 TTTATTTATTT-A
1 TTT-TTTATTTAA
42378113 TTTTT
1 TTTTT
42378118 ACAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 11 0.42
13 13 0.50
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:42378670 original size:12 final size:12
Alignment explanation
Indices: 42378653--42378677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42378643 GGTGTTCATT
42378653 CGGTTAACCGAC
1 CGGTTAACCGAC
42378665 CGGTTAACCGAC
1 CGGTTAACCGAC
42378677 C
1 C
42378678 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:42378851 original size:9 final size:9
Alignment explanation
Indices: 42378837--42378897 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
42378827 TTTGGTTAAA
42378837 AATTACCCG
1 AATTACCCG
42378846 AATTACCCG
1 AATTACCCG
42378855 AATTACCCG
1 AATTACCCG
*
42378864 AATTAACCG
1 AATTACCCG
*
42378873 AATTAACCG
1 AATTACCCG
*
42378882 AATTAACCG
1 AATTACCCG
42378891 AATTACC
1 AATTACC
42378898 GAAAAATACC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.39, C:0.28, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:42379132 original size:12 final size:12
Alignment explanation
Indices: 42379115--42379140 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42379105 ATTTTTTCGG
42379115 TTAACCGAAAAT
1 TTAACCGAAAAT
42379127 TTAACCGAAAAT
1 TTAACCGAAAAT
42379139 TT
1 TT
42379141 TCGGTTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
TTAACCGAAAAT
Found at i:42379920 original size:6 final size:6
Alignment explanation
Indices: 42379909--42379942 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
42379899 TTCCCTATTC
*
42379909 ATATAA ATATAA ATATAA ATATAA ATACAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
42379943 CAAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:42387840 original size:15 final size:15
Alignment explanation
Indices: 42387822--42387852 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42387812 CTATTGAAGC
*
42387822 AAAAACGATTGCAGG
1 AAAAAAGATTGCAGG
42387837 AAAAAAGATTGCAGG
1 AAAAAAGATTGCAGG
42387852 A
1 A
42387853 CCTTGGTCGC
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:0.52, C:0.10, G:0.26, T:0.13
Consensus pattern (15 bp):
AAAAAAGATTGCAGG
Found at i:42394298 original size:43 final size:43
Alignment explanation
Indices: 42394245--42394334 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
42394235 TCAAAACAAC
*
42394245 ACTTGAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
1 ACTTAAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
*
42394288 ACTTAAATTTTGATCAAAAGTACAATTTAATATATGAATTTTG
1 ACTTAAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
42394331 ACTT
1 ACTT
42394335 GATATAGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (43 bp):
ACTTAAATTTTGATCAAAAGTACAATTTAATACATGAATTTTG
Found at i:42395477 original size:3 final size:3
Alignment explanation
Indices: 42395469--42395507 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42395459 TCTCTCCTGC
42395469 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42395508 CTCAGTTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42398074 original size:95 final size:95
Alignment explanation
Indices: 42397952--42398146 Score: 390
Period size: 95 Copynumber: 2.1 Consensus size: 95
42397942 AAGTCAAATG
42397952 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
1 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
42398017 TTATCTTGAACTTAACGTTAAATTTAACCT
66 TTATCTTGAACTTAACGTTAAATTTAACCT
42398047 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
1 CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
42398112 TTATCTTGAACTTAACGTTAAATTTAACCT
66 TTATCTTGAACTTAACGTTAAATTTAACCT
42398142 CAACA
1 CAACA
42398147 TTTATTCTCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (95 bp):
CAACAAATTTCTTGCATACATGATACATTGATTCAAGGCAAACATTCAAAAAAAATGGTTTTAAT
TTATCTTGAACTTAACGTTAAATTTAACCT
Found at i:42403051 original size:53 final size:52
Alignment explanation
Indices: 42402993--42403094 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 52
42402983 CACATATATT
* *
42402993 ACCGATGCCATATATCAGATATGGTCTTATACGGAAGCACATAATCACATTAC
1 ACCGATGCCATAGACCAGATATGGTCTTATACGGAAGCACAT-ATCACATTAC
* * * * *
42403046 ACCGATGTCATAGCCCTGCTATGTTCTTATACGGAAGCACATATCACAT
1 ACCGATGCCATAGACCAGATATGGTCTTATACGGAAGCACATATCACAT
42403095 GTTGCCATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 7 0.17
53 35 0.83
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (52 bp):
ACCGATGCCATAGACCAGATATGGTCTTATACGGAAGCACATATCACATTAC
Found at i:42404155 original size:12 final size:12
Alignment explanation
Indices: 42404140--42404165 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42404130 TAAAACTTAG
42404140 TAGGCAATATAA
1 TAGGCAATATAA
42404152 TAGGCAATATAA
1 TAGGCAATATAA
42404164 TA
1 TA
42404166 TGTTTTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TAGGCAATATAA
Done.