Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_pilon, whole genome shotgun sequence
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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:394149 original size:20 final size:19
Alignment explanation
Indices: 394114--394180 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
394104 GAAACTTAAA
394114 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
394133 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
394153 ATCGCAATGTGAAATGAAA
1 ATCGCAACGCGAAATGACT
394172 ATCGCAACG
1 ATCGCAACG
394181 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:394188 original size:14 final size:14
Alignment explanation
Indices: 394169--394226 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
394159 ATGTGAAATG
394169 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
394183 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
394199 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
394215 AAAATCGCAACG
1 AAAATCGCAACG
394227 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:394211 original size:32 final size:33
Alignment explanation
Indices: 394153--394231 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
394143 GGAAATGGCT
* *
394153 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
394186 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
394218 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
394232 CACAAATCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 30 0.68
33 14 0.32
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:394265 original size:19 final size:19
Alignment explanation
Indices: 394243--394371 Score: 82
Period size: 19 Copynumber: 7.3 Consensus size: 19
394233 ACAAATCACA
394243 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
394262 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
394276 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
394294 TTGC-AATTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
394308 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
394327 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
394347 TTGCGATAGTCATTTCGTG
1 TTGCGATTTTCATTTCGCG
394366 TTGCGA
1 TTGCGA
394372 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
14 17 0.20
15 4 0.05
16 6 0.07
17 3 0.03
18 12 0.14
19 28 0.32
20 17 0.20
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:394279 original size:14 final size:14
Alignment explanation
Indices: 394260--394317 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
394250 TTTCATTTCG
394260 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
394274 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
394290 CGCGTTGCAATTTTGT
1 --CGTTGCGATTTTGT
394306 CGTTGCGATTTT
1 CGTTGCGATTTT
394318 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:394290 original size:32 final size:33
Alignment explanation
Indices: 394243--394333 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
394233 ACAAATCACA
394243 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
394276 TTGCGA-TTTCATTTCGCGTTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
394308 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
394334 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:394352 original size:20 final size:19
Alignment explanation
Indices: 394318--394371 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
394308 TTGCGATTTT
*
394318 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
394337 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
394357 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
394372 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:394863 original size:17 final size:18
Alignment explanation
Indices: 394838--394881 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
394828 GTCGATCAGA
*
394838 TGATGGCTCTGGGTG-GG
1 TGATGGCTCTGGGCGAGG
*
394855 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
394873 TGATGGCTC
1 TGATGGCTC
394882 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.11, C:0.16, G:0.45, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:396432 original size:22 final size:22
Alignment explanation
Indices: 396407--396450 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
396397 GATTTAGATA
396407 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
396429 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
396451 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:396731 original size:20 final size:20
Alignment explanation
Indices: 396618--396731 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
396608 CGCTTTGAAA
396618 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
396638 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
396658 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * *
396678 ATCTCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
396699 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
396719 ATCGCATTGCGAT
1 ATCGCATTGCGAT
396732 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 55 0.71
21 13 0.17
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:396749 original size:21 final size:21
Alignment explanation
Indices: 396720--396812 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
396710 ATAGTAAGTA
396720 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
396741 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
396761 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
396782 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
396802 TCGCATTGCGA
1 TCGCATTGCGA
396813 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:396750 original size:41 final size:41
Alignment explanation
Indices: 396659--396793 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 41
396649 AAAGTCAGTA
* * ** *
396659 TCGCGTTGCGAAAGTAAGTATCTCATTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
396699 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
396741 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
396782 TCGCGTTGCGAT
1 TCGCGTTGCGAT
396794 TTACTTATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 4 0.05
41 76 0.93
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:396794 original size:41 final size:41
Alignment explanation
Indices: 396720--396812 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
396710 ATAGTAAGTA
396720 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
396761 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
396802 TCGCATTGCGA
1 TCGCATTGCGA
396813 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:401164 original size:33 final size:33
Alignment explanation
Indices: 401110--401172 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
401100 TTACATCGAT
*
401110 AAATGTATCGAGATCAGAATG-AGAAAGAGGACC
1 AAATGGATCGAGATCAGAATGAAG-AAGAGGACC
*
401143 AAATGGATCGAGAT-TGCAATGAAGAAGAGG
1 AAATGGATCGAGATCAG-AATGAAGAAGAGG
401173 GTTAAAAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 23 0.88
34 2 0.08
ACGTcount: A:0.44, C:0.10, G:0.30, T:0.16
Consensus pattern (33 bp):
AAATGGATCGAGATCAGAATGAAGAAGAGGACC
Found at i:404089 original size:17 final size:15
Alignment explanation
Indices: 404066--404104 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
404056 ACCCGACATA
*
404066 CGGGTACCCGTAAAAT
1 CGGGTACCC-AAAAAT
404082 CTGGGTACCCAAAAAT
1 C-GGGTACCCAAAAAT
404098 CGGGTAC
1 CGGGTAC
404105 TCGAAACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (15 bp):
CGGGTACCCAAAAAT
Found at i:404098 original size:16 final size:16
Alignment explanation
Indices: 404050--404110 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
404040 AATCGGGTAT
* *
404050 TCGGGTACCCGACATA
1 TCGGGTACCCGAAAAA
*
404066 -CGGGTACCCGTAAAA
1 TCGGGTACCCGAAAAA
404081 TCTGGGTACCC-AAAAA
1 TC-GGGTACCCGAAAAA
*
404097 TCGGGTACTCGAAA
1 TCGGGTACCCGAAA
404111 CATCCAGGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 19 0.51
16 10 0.27
17 8 0.22
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (16 bp):
TCGGGTACCCGAAAAA
Found at i:417188 original size:59 final size:60
Alignment explanation
Indices: 417076--417188 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
417066 ATTATAGACG
* **
417076 TTATTTTATTGAATCTCTTAACTATTAAAAGTTACAAAATGATACTTCGACTATAGAATA
1 TTATTTTATTGAATCTCTAAACTATTAAAAGTTACAAAATGATACTTAAACTATAGAATA
* *
417136 TTATTTTGTTGAAT-TCTCAAACTATTGAAAGTT-CAAAATGAT-CATTAAACTAT
1 TTATTTTATTGAATCTCT-AAACTATTAAAAGTTACAAAATGATAC-TTAAACTAT
417189 TTATATGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 1 0.02
59 19 0.41
60 26 0.57
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (60 bp):
TTATTTTATTGAATCTCTAAACTATTAAAAGTTACAAAATGATACTTAAACTATAGAATA
Found at i:425875 original size:29 final size:30
Alignment explanation
Indices: 425843--425957 Score: 139
Period size: 29 Copynumber: 4.0 Consensus size: 30
425833 ATTGTCATTT
*
425843 TTTTTCACAAAAAATT-TCAGAATGTCACC
1 TTTTTCACAAAAAATTCCCAGAATGTCACC
* * * * *
425872 TTTTCCAAAAAAAATTCTCAGAATATCACA
1 TTTTTCACAAAAAATTCCCAGAATGTCACC
*
425902 TTTTTTAC--AAAATTCCCAGAATGTCACC
1 TTTTTCACAAAAAATTCCCAGAATGTCACC
425930 TTTTTCACAAAAAATT-CCAGAATGTCAC
1 TTTTTCACAAAAAATTCCCAGAATGTCAC
425958 TGGGTCGGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 24 0.33
29 26 0.36
30 22 0.31
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (30 bp):
TTTTTCACAAAAAATTCCCAGAATGTCACC
Found at i:428661 original size:24 final size:24
Alignment explanation
Indices: 428625--428670 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
428615 CCTATAACAC
428625 TAAACAGAGAGGAAAAAGATTTGA
1 TAAACAGAGAGGAAAAAGATTTGA
**
428649 TAAACAGTTAGGAAAAAGATTT
1 TAAACAGAGAGGAAAAAGATTT
428671 AATCTTCGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (24 bp):
TAAACAGAGAGGAAAAAGATTTGA
Found at i:430206 original size:20 final size:21
Alignment explanation
Indices: 430186--430225 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
430176 CGAAATATTT
* *
430186 GAAAAATGATCGATCCCTTTG
1 GAAAAAGGATCAATCCCTTTG
*
430207 GTAAAAGGATCAATCCCTT
1 GAAAAAGGATCAATCCCTT
430226 GTGCCTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
GAAAAAGGATCAATCCCTTTG
Found at i:432760 original size:59 final size:59
Alignment explanation
Indices: 432627--432760 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 59
432617 TTAAATTATG
* ** * *
432627 ACTCACATTCTAAATTAATATCTAATTTTTAAAATATTTTATATCAATCCTAAAACTATA
1 ACTCACATTCT-ATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTAAAACTATA
*
432687 ACTCACATTTTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCC-ATAAACTATCA
1 ACTCACATTCTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTA-AAACTAT-A
432747 A-T-ATCATTCTATTT
1 ACTCA-CATTCTATTT
432761 TTATTCTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
58 2 0.03
59 50 0.78
60 12 0.19
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (59 bp):
ACTCACATTCTATTTAATCCCTAAATTTTAAAACATTTTATATCAATCCTAAAACTATA
Found at i:441023 original size:19 final size:19
Alignment explanation
Indices: 441001--441040 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
440991 GTCCTTAATT
*
441001 TTTATAGTAAATTGTGATA
1 TTTATAGTAAACTGTGATA
441020 TTTATAGTAAACTGTGATA
1 TTTATAGTAAACTGTGATA
441039 TT
1 TT
441041 GATTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (19 bp):
TTTATAGTAAACTGTGATA
Found at i:445679 original size:39 final size:39
Alignment explanation
Indices: 445636--445762 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
445626 AATGGATGGA
445636 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
* ** * ** ** * * *
445675 TTTGGTTTAATCACCGATGGT-GATGGTGCTATGGACGGA
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTG-TGGG
* *
445714 TTTGGTTTAACCATTGTTGGTGGATTTTGAGGCTGTGGG
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
445753 TTTGGTTTAA
1 TTTGGTTTAA
445763 TCACTGGTGG
Statistics
Matches: 62, Mismatches: 24, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
38 8 0.13
39 48 0.77
40 6 0.10
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.43
Consensus pattern (39 bp):
TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
Found at i:445966 original size:18 final size:18
Alignment explanation
Indices: 445945--445999 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
445935 TGGTGGTGGC
445945 GACAACGGTGACGATGGT
1 GACAACGGTGACGATGGT
* *
445963 GACAATGGTGATGATGGT
1 GACAACGGTGACGATGGT
* *
445981 GACAACGGCGACGACGGT
1 GACAACGGTGACGATGGT
445999 G
1 G
446000 GTGGTGGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.40, T:0.16
Consensus pattern (18 bp):
GACAACGGTGACGATGGT
Found at i:446725 original size:15 final size:15
Alignment explanation
Indices: 446707--446740 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
446697 ATTTTAATTT
446707 TTTATTAAAATATAA
1 TTTATTAAAATATAA
* *
446722 TTTATTAAGATATTA
1 TTTATTAAAATATAA
446737 TTTA
1 TTTA
446741 AATTATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTATTAAAATATAA
Found at i:447578 original size:26 final size:26
Alignment explanation
Indices: 447542--447594 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
447532 CTGAGATAGG
447542 TATGAAAGGTCATGTTGCTTAGACCA
1 TATGAAAGGTCATGTTGCTTAGACCA
447568 TATGAAAGGTCATGTTGCTTAGACCA
1 TATGAAAGGTCATGTTGCTTAGACCA
447594 T
1 T
447595 CAGAGCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (26 bp):
TATGAAAGGTCATGTTGCTTAGACCA
Found at i:450585 original size:13 final size:13
Alignment explanation
Indices: 450545--450585 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
450535 CAATTAAGAG
450545 AATTATCTTTTGT
1 AATTATCTTTTGT
**
450558 AATT-T-TTAGGT
1 AATTATCTTTTGT
450569 AATTATCTTTTGT
1 AATTATCTTTTGT
450582 AATT
1 AATT
450586 TTTAGGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (13 bp):
AATTATCTTTTGT
Found at i:450595 original size:23 final size:23
Alignment explanation
Indices: 450544--450613 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 23
450534 ACAATTAAGA
450544 GAATTATCTTTTGTAATTTTTAG
1 GAATTATCTTTTGTAATTTTTAG
450567 GTAATTATCTTTTGTAATTTTTAG
1 G-AATTATCTTTTGTAATTTTTAG
**
450591 GAATTATCTTGAGT-ATTTTTAG
1 GAATTATCTTTTGTAATTTTTAG
450613 G
1 G
450614 GTTTTAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 9 0.20
23 12 0.27
24 23 0.52
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (23 bp):
GAATTATCTTTTGTAATTTTTAG
Found at i:451379 original size:13 final size:13
Alignment explanation
Indices: 451361--451385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
451351 TTCCTCTCCA
451361 TCTTCTTCATTTT
1 TCTTCTTCATTTT
451374 TCTTCTTCATTT
1 TCTTCTTCATTT
451386 CTTCCCTATC
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:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCATTTT
Found at i:458825 original size:19 final size:19
Alignment explanation
Indices: 458803--458842 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
458793 GTCCTTAATT
*
458803 TTTATAGTAAATTGTGATA
1 TTTATAGTAAACTGTGATA
458822 TTTATAGTAAACTGTGATA
1 TTTATAGTAAACTGTGATA
458841 TT
1 TT
458843 GATTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (19 bp):
TTTATAGTAAACTGTGATA
Found at i:468520 original size:39 final size:39
Alignment explanation
Indices: 468477--468603 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
468467 AATGGATGGA
468477 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
* ** * ** ** * * *
468516 TTTGGTTTAATCACCGATGGT-GATGGTGCTATGGACGGA
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTG-TGGG
* *
468555 TTTGGTTTAACCATTGTTGGTGGATTTTGAGGCTGTGGG
1 TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
468594 TTTGGTTTAA
1 TTTGGTTTAA
468604 TCACTGGTGG
Statistics
Matches: 62, Mismatches: 24, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
38 8 0.13
39 48 0.77
40 6 0.10
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.43
Consensus pattern (39 bp):
TTTGGTTTAACCATTGTTGGTGGATTTTGCGGTTGTGGG
Found at i:468807 original size:18 final size:18
Alignment explanation
Indices: 468786--468840 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
468776 TGGTGGTGGC
468786 GACAACGGTGACGATGGT
1 GACAACGGTGACGATGGT
* *
468804 GACAATGGTGATGATGGT
1 GACAACGGTGACGATGGT
* *
468822 GACAACGGCGACGACGGT
1 GACAACGGTGACGATGGT
468840 G
1 G
468841 GTGGTGGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.40, T:0.16
Consensus pattern (18 bp):
GACAACGGTGACGATGGT
Found at i:469569 original size:15 final size:15
Alignment explanation
Indices: 469549--469582 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
469539 ATTTTAATTT
469549 TTTATTAAAATATAA
1 TTTATTAAAATATAA
* *
469564 TTTATTAAGATATTA
1 TTTATTAAAATATAA
469579 TTTA
1 TTTA
469583 AATTATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTATTAAAATATAA
Found at i:470417 original size:26 final size:26
Alignment explanation
Indices: 470381--470433 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
470371 CTGAGATAGG
470381 TATGAAAGGTCATGTTGCTTAGACCA
1 TATGAAAGGTCATGTTGCTTAGACCA
470407 TATGAAAGGTCATGTTGCTTAGACCA
1 TATGAAAGGTCATGTTGCTTAGACCA
470433 T
1 T
470434 CAGAGCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (26 bp):
TATGAAAGGTCATGTTGCTTAGACCA
Found at i:471801 original size:18 final size:18
Alignment explanation
Indices: 471778--471812 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
471768 TACGTTTGTT
471778 CTTTATTTATTCTAAAAG
1 CTTTATTTATTCTAAAAG
*
471796 CTTTATTTATTTTAAAA
1 CTTTATTTATTCTAAAA
471813 ATGCTAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
CTTTATTTATTCTAAAAG
Found at i:473435 original size:13 final size:13
Alignment explanation
Indices: 473395--473435 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
473385 CAATTAAGAG
473395 AATTATCTTTTGT
1 AATTATCTTTTGT
**
473408 AATT-T-TTAGGT
1 AATTATCTTTTGT
473419 AATTATCTTTTGT
1 AATTATCTTTTGT
473432 AATT
1 AATT
473436 TTTAGGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (13 bp):
AATTATCTTTTGT
Found at i:473445 original size:23 final size:23
Alignment explanation
Indices: 473394--473463 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 23
473384 ACAATTAAGA
473394 GAATTATCTTTTGTAATTTTTAG
1 GAATTATCTTTTGTAATTTTTAG
473417 GTAATTATCTTTTGTAATTTTTAG
1 G-AATTATCTTTTGTAATTTTTAG
**
473441 GAATTATCTTGAGT-ATTTTTAG
1 GAATTATCTTTTGTAATTTTTAG
473463 G
1 G
473464 GTTTTAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 9 0.20
23 12 0.27
24 23 0.52
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (23 bp):
GAATTATCTTTTGTAATTTTTAG
Found at i:474228 original size:13 final size:13
Alignment explanation
Indices: 474210--474234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
474200 TTCCTCTCCA
474210 TCTTCTTCATTTT
1 TCTTCTTCATTTT
474223 TCTTCTTCATTT
1 TCTTCTTCATTT
474235 CTTCCCTATC
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:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCATTTT
Found at i:481396 original size:6 final size:6
Alignment explanation
Indices: 481385--481409 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
481375 TTTATTTAAA
481385 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
481410 TATTTTTACT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:481761 original size:91 final size:91
Alignment explanation
Indices: 481605--481773 Score: 241
Period size: 91 Copynumber: 1.9 Consensus size: 91
481595 GCAGGTCCAT
* * * * **
481605 ATGTTCCGTCACAAAATTTAAAGTTTTTTTATTTACCTGCTCATTTTCTCCAATTTCCTCAATTG
1 ATGTTCCGTCACAAAATTTAAAGTATTTTTACTTACCCGCCCATTACCTCCAATTTCCTCAATTG
481670 AAACATAAAATTTGTGACGGATTCAC
66 AAACATAAAATTTGTGACGGATTCAC
* * *
481696 ATGTTCCGTCACAAAATTTAGA-TATTTTTACTTACCCGCCCATTACCTTCAATTTCTCTCCATT
1 ATGTTCCGTCACAAAATTTAAAGTATTTTTACTTACCCGCCCATTACCTCCAATTTC-CTCAATT
481760 GAAACATAAAATTT
65 GAAACATAAAATTT
481774 CAAACATACC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 27 0.40
91 41 0.60
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (91 bp):
ATGTTCCGTCACAAAATTTAAAGTATTTTTACTTACCCGCCCATTACCTCCAATTTCCTCAATTG
AAACATAAAATTTGTGACGGATTCAC
Found at i:482631 original size:25 final size:26
Alignment explanation
Indices: 482580--482631 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
482570 ATTTTAAATG
**
482580 TTTCGTCAGTAAATTTACTGATGGAT
1 TTTCGTCAGTAAATTTACTGACAGAT
*
482606 TTTCGTCAGTACATTT-CTGACAGAT
1 TTTCGTCAGTAAATTTACTGACAGAT
482631 T
1 T
482632 AATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTCGTCAGTAAATTTACTGACAGAT
Found at i:486741 original size:30 final size:28
Alignment explanation
Indices: 486705--486763 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 28
486695 TTATTTAAAC
*
486705 ATAATTTATTAAGATATTATTTAAAAT-ATG
1 ATAATTT-TTAA-ATA-TATGTAAAATGATG
486735 ATAATTTTTAAATATATGTAAAATGATG
1 ATAATTTTTAAATATATGTAAAATGATG
486763 A
1 A
486764 CTAAGATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 4 0.15
30 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATAATTTTTAAATATATGTAAAATGATG
Found at i:490523 original size:18 final size:18
Alignment explanation
Indices: 490502--490536 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
490492 TACGTTTGTT
490502 CTTTATTTATTTTAAAAG
1 CTTTATTTATTTTAAAAG
490520 CTTTATTTATTTTAAAA
1 CTTTATTTATTTTAAAA
490537 ATGCTAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
CTTTATTTATTTTAAAAG
Found at i:492455 original size:18 final size:18
Alignment explanation
Indices: 492421--492455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
492411 TTCTTTCATT
*
492421 CTTTATTTATTTTAAAAG
1 CTTTATTTATTTAAAAAG
*
492439 CTTTCTTTATTTAAAAA
1 CTTTATTTATTTAAAAA
492456 TACTAAGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
CTTTATTTATTTAAAAAG
Found at i:500223 original size:6 final size:6
Alignment explanation
Indices: 500212--500236 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
500202 TTTATTTAAA
500212 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
500237 TATTTTTACT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:500579 original size:92 final size:92
Alignment explanation
Indices: 500433--500603 Score: 245
Period size: 92 Copynumber: 1.9 Consensus size: 92
500423 GCAGGTCCAT
* * * **
500433 ATGTTCCGTCACAAAATTTAAAGTTTTTTTATTTACCTGCTCATTTTCTCCAATTTCCCTCAATT
1 ATGTTCCGTCACAAAATTTAAAGTTTTTTTACTTACCCGCCCATTACCTCCAATTTCCCTCAATT
500498 GAAACATAAAATTTGTGACGGATTCAC
66 GAAACATAAAATTTGTGACGGATTCAC
* * * *
500525 ATGTTCCGTCACAAAATTTAGA-TATTTTTTACTTACCCGCCCATTACCTTCAATTTCTCTCCAT
1 ATGTTCCGTCACAAAATTTAAAGT-TTTTTTACTTACCCGCCCATTACCTCCAATTTCCCTCAAT
500589 TGAAACATAAAATTT
65 TGAAACATAAAATTT
500604 CAAACATACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
91 1 0.01
92 68 0.99
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (92 bp):
ATGTTCCGTCACAAAATTTAAAGTTTTTTTACTTACCCGCCCATTACCTCCAATTTCCCTCAATT
GAAACATAAAATTTGTGACGGATTCAC
Found at i:501465 original size:25 final size:26
Alignment explanation
Indices: 501414--501465 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
501404 ATTTTAAATG
**
501414 TTTCGTCAGTAAATTTACTGATGGAT
1 TTTCGTCAGTAAATTTACTGACAGAT
*
501440 TTTCGTCAGTACATTT-CTGACAGAT
1 TTTCGTCAGTAAATTTACTGACAGAT
501465 T
1 T
501466 AATTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTCGTCAGTAAATTTACTGACAGAT
Found at i:505578 original size:30 final size:28
Alignment explanation
Indices: 505542--505600 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 28
505532 TTATTTAAAC
*
505542 ATAATTTATTAAGATATTATTTAAAAT-ATG
1 ATAATTT-TTAA-ATA-TATGTAAAATGATG
505572 ATAATTTTTAAATATATGTAAAATGATG
1 ATAATTTTTAAATATATGTAAAATGATG
505600 A
1 A
505601 CTAAGATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 4 0.15
30 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (28 bp):
ATAATTTTTAAATATATGTAAAATGATG
Found at i:514061 original size:18 final size:18
Alignment explanation
Indices: 514038--514072 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
514028 TACGTTTGTT
514038 CTTTATTTATTTTAAAAG
1 CTTTATTTATTTTAAAAG
514056 CTTTATTTATTTTAAAA
1 CTTTATTTATTTTAAAA
514073 ATGCTAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
CTTTATTTATTTTAAAAG
Found at i:515855 original size:23 final size:23
Alignment explanation
Indices: 515804--515860 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 23
515794 ACAATTAAGA
*
515804 GAATTATCTTTTGTGATTTTTAG
1 GAATTATCTTTTGTAATTTTTAG
515827 GTAATTATCTTTTGTAATTTTTAG
1 G-AATTATCTTTTGTAATTTTTAG
515851 GAATTATCTT
1 GAATTATCTT
515861 GAGCATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (23 bp):
GAATTATCTTTTGTAATTTTTAG
Found at i:516023 original size:18 final size:18
Alignment explanation
Indices: 515989--516023 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
515979 TTCTTTCATT
*
515989 CTTTATTTATTTTAAAAG
1 CTTTATTTATTTAAAAAG
*
516007 CTTTCTTTATTTAAAAA
1 CTTTATTTATTTAAAAA
516024 ATACTAAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (18 bp):
CTTTATTTATTTAAAAAG
Found at i:524607 original size:45 final size:45
Alignment explanation
Indices: 524543--524634 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
524533 ACAATATGGG
524543 AACATTAGAATCTCTGCACTTTTCAAACAACCAACTCCCTGGTGC
1 AACATTAGAATCTCTGCACTTTTCAAACAACCAACTCCCTGGTGC
524588 AACATTAGAATCTCTGCACTTTTCAAACAACCAACTCCCTGGTGC
1 AACATTAGAATCTCTGCACTTTTCAAACAACCAACTCCCTGGTGC
524633 AA
1 AA
524635 TCCCTGGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (45 bp):
AACATTAGAATCTCTGCACTTTTCAAACAACCAACTCCCTGGTGC
Found at i:533612 original size:20 final size:20
Alignment explanation
Indices: 533587--533634 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
533577 TCATAATCTT
533587 TTTATTTCTTCAATTCGTCA
1 TTTATTTCTTCAATTCGTCA
533607 TTTATTTCTTCAATTCGTCA
1 TTTATTTCTTCAATTCGTCA
533627 TTTATTTC
1 TTTATTTC
533635 AAGTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTATTTCTTCAATTCGTCA
Found at i:533761 original size:178 final size:179
Alignment explanation
Indices: 533428--533791 Score: 529
Period size: 178 Copynumber: 2.0 Consensus size: 179
533418 TCTGATTCCA
* * * * *
533428 TTATTTTTTCAATTCCTCCTTCATTTTAAGTCCATTTTTTTTATCAAATTTGAACCACTTGTTCC
1 TTATTTCTTCAATTCCTCATTCATTTCAAGTCCATTTTTTTTACCAAATTTGAACCACTTGCTCC
533493 TAAACCATAGTAGAATACATGTGTACTTTCAATTATTTTTTTCGATAACAAATTTTTTATTTTTC
66 TAAACCATAGTAGAATACATGTGTACTTTCAATTATTTTTTTC-ATAACAAATTTTTTATTTTTC
* * *
533558 AATTTAGTCCTTCAATTTTTCATAATCTTTTTATTTCTTCAATTCGTCAT
130 AATTTAGTCCTTCAATTTTTCATAATCTTCTTATTCCTTCAATTCATCAT
* * **
533608 TTATTTCTTCAATTCGTCATTTATTTCAAGT-C-TTTTTTTTACCAAATTTGAGTCA-TATGCTC
1 TTATTTCTTCAATTCCTCATTCATTTCAAGTCCATTTTTTTTACCAAATTTGAACCACT-TGCTC
* *
533670 CTAAGCCATAGTAGAATACATGTGTACTTTCAATTCCTATTTTTT-ATAACAAATTTTTTATTTT
65 CTAAACCATAGTAGAATACATGTGTACTTTCAATT-AT-TTTTTTCATAACAAATTTTTTATTTT
*
533734 TCAATTTAGTCCTTCAATTTTTCATAATCTTCTTATTCCTTCAATTTATCAT
128 TCAATTTAGTCCTTCAATTTTTCATAATCTTCTTATTCCTTCAATTCATCAT
533786 TTATTT
1 TTATTT
533792 TATGTTCGTT
Statistics
Matches: 166, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
177 1 0.01
178 131 0.79
179 2 0.01
180 32 0.19
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (179 bp):
TTATTTCTTCAATTCCTCATTCATTTCAAGTCCATTTTTTTTACCAAATTTGAACCACTTGCTCC
TAAACCATAGTAGAATACATGTGTACTTTCAATTATTTTTTTCATAACAAATTTTTTATTTTTCA
ATTTAGTCCTTCAATTTTTCATAATCTTCTTATTCCTTCAATTCATCAT
Found at i:535567 original size:26 final size:26
Alignment explanation
Indices: 535537--535587 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
535527 TGCACCAGCT
*
535537 CCTGACATGTCGGTCGCCTGCCACCG
1 CCTGACACGTCGGTCGCCTGCCACCG
*
535563 CCTGACACGTCGGTCGCCTGTCACC
1 CCTGACACGTCGGTCGCCTGCCACC
535588 TCCATCTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.43, G:0.25, T:0.20
Consensus pattern (26 bp):
CCTGACACGTCGGTCGCCTGCCACCG
Found at i:536917 original size:29 final size:29
Alignment explanation
Indices: 536819--536937 Score: 109
Period size: 29 Copynumber: 4.1 Consensus size: 29
536809 TCCCTTAGGA
* * *
536819 TTAGTTTTTCACACTTATGTCCTTAGACT
1 TTAGTTTTTTACACTTAGGTCCCTAGACT
* * * * *
536848 TTAAATATTTTACACATAGG-CCCTACATT
1 TT-AGTTTTTTACACTTAGGTCCCTAGACT
*
536877 TTA-TTTTTTACACTTAGGTCTCTAGACT
1 TTAGTTTTTTACACTTAGGTCCCTAGACT
*
536905 TTAGTTTTTTACACTTTA-ATCCCTAGACT
1 TTAGTTTTTTACAC-TTAGGTCCCTAGACT
536934 TTAG
1 TTAG
536938 AGTTCTCATA
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
27 13 0.18
28 10 0.14
29 33 0.46
30 15 0.21
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.46
Consensus pattern (29 bp):
TTAGTTTTTTACACTTAGGTCCCTAGACT
Found at i:544842 original size:28 final size:28
Alignment explanation
Indices: 544783--544844 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
544773 CCAAAGAAAC
*
544783 CAACCTGAAACACATTACCTCCCCAAAT
1 CAACCTGAAACACATTACCTCCACAAAT
544811 CAACCTGAAACAC-TCTACCTCCACAAGA-
1 CAACCTGAAACACAT-TACCTCCACAA-AT
544839 CAACCT
1 CAACCT
544845 AAGCCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 1 0.03
28 29 0.94
29 1 0.03
ACGTcount: A:0.39, C:0.40, G:0.05, T:0.16
Consensus pattern (28 bp):
CAACCTGAAACACATTACCTCCACAAAT
Found at i:547943 original size:21 final size:21
Alignment explanation
Indices: 547917--547975 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
547907 ATTTACCGTG
*
547917 ATTACGGCCGTCACGGGCGCT
1 ATTACGGCCGTCGCGGGCGCT
* * *
547938 ATTACGACTGTCGCGGACGCT
1 ATTACGGCCGTCGCGGGCGCT
*
547959 ATTGCGGCCGTCGCGGG
1 ATTACGGCCGTCGCGGG
547976 TAACTCGGAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.20
Consensus pattern (21 bp):
ATTACGGCCGTCGCGGGCGCT
Found at i:548477 original size:20 final size:20
Alignment explanation
Indices: 548453--548740 Score: 167
Period size: 20 Copynumber: 14.4 Consensus size: 20
548443 AGTTTCCAAT
*
548453 TTCGCAACGCGAATTTGTAAA
1 TTCGCAACGCGAA-TAGTAAA
*
548474 -TCGCAACAC-AGA-AGTCAAA
1 TTCGCAACGCGA-ATAGT-AAA
548493 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGT-AAA
548513 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGT-AAA
548533 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGT-AAA
*
548553 TTCGCAACGCG-ATAGTTCAA
1 TTCGCAACGCGAATAG-TAAA
548573 TTCGCAACGCG-ATAGTTAAA
1 TTCGCAACGCGAATAG-TAAA
* *
548593 TTCGCAACACGAATCTGTAAA
1 TTCGCAACGCGAAT-AGTAAA
* *
548614 -TCGCAACGTGAATCTGTAAA
1 TTCGCAACGCGAAT-AGTAAA
*
548634 -TCGCAACAC-AGA-AGTCAAA
1 TTCGCAACGCGA-ATAGT-AAA
* * *
548653 TTCACAACAC-AAAAGTCAAA
1 TTCGCAACGCGAATAGT-AAA
* *
548673 TTCGCAACAC-AAAAGTCAAA
1 TTCGCAACGCGAATAGT-AAA
*
548693 TTCGCAACGCGGAAT-TTCAAA
1 TTCGCAACGC-GAATAGT-AAA
* * *
548714 TTCGCAACACGAAT-TTAAT
1 TTCGCAACGCGAATAGTAAA
548733 TTCGCAAC
1 TTCGCAAC
548741 AGGTTTTAGT
Statistics
Matches: 234, Mismatches: 19, Indels: 30
0.83 0.07 0.11
Matches are distributed among these distances:
18 4 0.02
19 20 0.09
20 186 0.79
21 21 0.09
22 3 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAATAGTAAA
Found at i:548497 original size:40 final size:39
Alignment explanation
Indices: 548453--548740 Score: 236
Period size: 40 Copynumber: 7.2 Consensus size: 39
548443 AGTTTCCAAT
*
548453 TTCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAA-TAGTAAATTCGCAACAC-GAAGTCAAA
*
548493 TTCGCAACGCG-ATAGTCAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAATAGT-AAATTCGCAACACGA-AGTCAAA
*
548533 TTCGCAACGCG-ATAGTCAAATTCGCAACGCGATAGTTC-AA
1 TTCGCAACGCGAATAGT-AAATTCGCAACACGA-AG-TCAAA
548573 TTCGCAACGCG-ATAGTTAAATTCGCAACACGAA-TCTGTAAA
1 TTCGCAACGCGAATAG-TAAATTCGCAACACGAAGTC---AAA
* *
548614 -TCGCAACGTGAATCTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAAT-AGTAAATTCGCAACAC-GAAGTCAAA
* * * *
548653 TTCACAACAC-AAAAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATAGT-AAATTCGCAACAC-GAAGTCAAA
* * * *
548693 TTCGCAACGCGGAAT-TTCAAATTCGCAACACGAATTTAAT
1 TTCGCAACGC-GAATAGT-AAATTCGCAACACGAAGTCAAA
548733 TTCGCAAC
1 TTCGCAAC
548741 AGGTTTTAGT
Statistics
Matches: 211, Mismatches: 19, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
37 2 0.01
38 5 0.02
39 15 0.07
40 155 0.73
41 29 0.14
42 5 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (39 bp):
TTCGCAACGCGAATAGTAAATTCGCAACACGAAGTCAAA
Found at i:548517 original size:60 final size:59
Alignment explanation
Indices: 548453--548740 Score: 229
Period size: 60 Copynumber: 4.8 Consensus size: 59
548443 AGTTTCCAAT
*
548453 TTCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAA-TAGTAAATTCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAA
*
548513 TTCGCAACGCG-ATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTTC-AA
1 TTCGCAACGCGAATAGT-AAATTCGCAACACGA-AGTCAAATTCGCAACGCGATAG-TCAAA
* *
548573 TTCGCAACGCG-ATAGTTAAATTCGCAACACGAA-TCTGTAAA-TCGCAACGTGAATCTGT-AAA
1 TTCGCAACGCGAATAG-TAAATTCGCAACACGAAGTC---AAATTCGCAACGCG-AT-AGTCAAA
* * * * * *
548634 -TCGCAACAC-AGA-AGTCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGA-ATAGT-AAATTCGCAACAC-GAAGTCAAATTCGCAACGCGATAGTCAAA
* * * *
548693 TTCGCAACGCGGAAT-TTCAAATTCGCAACACGAATTTAATTTCGCAAC
1 TTCGCAACGC-GAATAGT-AAATTCGCAACACGAAGTCAAATTCGCAAC
548741 AGGTTTTAGT
Statistics
Matches: 186, Mismatches: 20, Indels: 44
0.74 0.08 0.18
Matches are distributed among these distances:
58 7 0.04
59 15 0.08
60 131 0.70
61 29 0.16
62 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (59 bp):
TTCGCAACGCGAATAGTAAATTCGCAACACGAAGTCAAATTCGCAACGCGATAGTCAAA
Found at i:549548 original size:12 final size:12
Alignment explanation
Indices: 549527--549566 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
549517 ACCATATTTC
*
549527 CAATACCAAACA
1 CAATATCAAACA
549539 CAATATCAAACA
1 CAATATCAAACA
*
549551 CAATCTCAAACCA
1 CAATATCAAA-CA
549564 CAA
1 CAA
549567 CCTTTCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:549734 original size:24 final size:24
Alignment explanation
Indices: 549683--549736 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
549673 GTATTCAAAA
*
549683 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
549707 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
549731 TTTGAT
1 TTTGAT
549737 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:552009 original size:18 final size:18
Alignment explanation
Indices: 551986--552021 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
551976 AAGCAAAAGG
*
551986 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
552004 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
552022 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:552447 original size:20 final size:19
Alignment explanation
Indices: 552404--552459 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
552394 CAATGCTTAT
*
552404 TTCGCATTGCGAATTTTACA
1 TTCGCGTTGCGAA-TTTACA
* *
552424 TTCGTGTTGCGAATTTACCT
1 TTCGCGTTGCGAATTTA-CA
*
552444 TTCGCGTTGTGAATTT
1 TTCGCGTTGCGAATTT
552460 GTACCTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGAATTTACA
Found at i:552653 original size:64 final size:65
Alignment explanation
Indices: 552514--552687 Score: 253
Period size: 65 Copynumber: 2.6 Consensus size: 65
552504 AATTTAAAAC
552514 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACGCATCAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACGCATCAAATTA
* * *
552579 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTGTTTCCTCATC-AATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACGCATCAAATTA
552643 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
552688 AGTGTACCTC
Statistics
Matches: 100, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
64 16 0.16
65 58 0.58
68 4 0.04
69 22 0.22
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACGCATCAAATTA
Found at i:554075 original size:21 final size:21
Alignment explanation
Indices: 554015--554133 Score: 109
Period size: 21 Copynumber: 5.7 Consensus size: 21
554005 GTGAATCGGG
* *
554015 CTCTTGAACGGT-ATGAGGGAC
1 CTCTTGAACGATGA-GAGGGGC
*
554036 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
554057 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
554078 CTTTTCG-ATGATGAGAGGGGC
1 CTCTT-GAACGATGAGAGGGGC
*
554099 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
*
554120 CTCTTGAATGATGA
1 CTCTTGAACGATGA
554134 TAGGTGCATC
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 74 0.94
22 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:554075 original size:42 final size:41
Alignment explanation
Indices: 554015--554137 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 41
554005 GTGAATCGGG
* *
554015 CTCTTGAACGGTATGAGGGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTAGGAGGG-CCTCTTGAATGATGATAGGGGC
* * *
554057 CTCTTGAACGGTGGGAGGGGCCTTTTCG-ATGATGAGAGGGGC
1 CTCTTGAACGGTAGGA-GGGCCTCTT-GAATGATGATAGGGGC
*
554099 CTCTTGAACGATAGGAGGCGCCTCTTGAATGATGATAGG
1 CTCTTGAACGGTAGGAGG-GCCTCTTGAATGATGATAGG
554138 TGCATCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 3 0.04
42 61 0.90
43 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGCCTCTTGAATGATGATAGGGGC
Found at i:554587 original size:42 final size:41
Alignment explanation
Indices: 554491--554590 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
554481 TGTAAAAAAT
* * *
554491 CCACCTCACCACGTAAAGACCGAACCTCATCACGCCATGCA
1 CCACCTCATCACGTAAAGACCGAACCTCATCACGCAAAGCA
** * *
554532 CCATTATCTTCACGTAAAGTACCG-ACCTCATGACGCAAAGCA
1 CCA-CCTCATCACGTAAAG-ACCGAACCTCATCACGCAAAGCA
554574 CCGACCTCATCACGTAA
1 CC-ACCTCATCACGTAA
554591 CTCCCCTAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (41 bp):
CCACCTCATCACGTAAAGACCGAACCTCATCACGCAAAGCA
Found at i:556310 original size:20 final size:20
Alignment explanation
Indices: 556282--556364 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
556272 TTTTGAAACT
556282 AAAATTCGCAACACGAAAATG
1 AAAA-TCGCAACACGAAAATG
*
556303 AAAATCGCAACAC------C
1 AAAATCGCAACACGAAAATG
*
556317 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACACGAAAATG
* *
556337 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
556356 AAAATCGCA
1 AAAATCGCA
556365 CGAAACTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
14 12 0.23
19 9 0.17
20 27 0.52
21 4 0.08
ACGTcount: A:0.51, C:0.24, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:556326 original size:34 final size:35
Alignment explanation
Indices: 556282--556347 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 35
556272 TTTTGAAACT
556282 AAAATTCGCAACACGAAAATGAAAATCGCAACACC
1 AAAATTCGCAACACGAAAATGAAAATCGCAACACC
*
556317 AAAA-TCGCAACGCGAAAATGAAAATCGCAAC
1 AAAATTCGCAACACGAAAATGAAAATCGCAAC
556348 GCGAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.11
Consensus pattern (35 bp):
AAAATTCGCAACACGAAAATGAAAATCGCAACACC
Found at i:556353 original size:14 final size:14
Alignment explanation
Indices: 556302--556335 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
556292 ACACGAAAAT
556302 GAAAATCGCAACAC
1 GAAAATCGCAACAC
* *
556316 CAAAATCGCAACGC
1 GAAAATCGCAACAC
556330 GAAAAT
1 GAAAAT
556336 GAAAATCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:556370 original size:16 final size:16
Alignment explanation
Indices: 556349--556379 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
556339 AATCGCAACG
556349 CGAAACTAAAATCGCA
1 CGAAACTAAAATCGCA
556365 CGAAACTAAAATCGC
1 CGAAACTAAAATCGC
556380 GTTGCGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CGAAACTAAAATCGCA
Found at i:556431 original size:20 final size:20
Alignment explanation
Indices: 556392--556431 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
556382 TGCGATTTTG
* * *
556392 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
556412 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
556432 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:556778 original size:22 final size:22
Alignment explanation
Indices: 556753--556796 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
556743 GGGTTGCTCT
* *
556753 GAGATGGGGACGGATTTTGTCG
1 GAGATAGGGACGGATGTTGTCG
556775 GAGATAGGGACGGATGTTGTCG
1 GAGATAGGGACGGATGTTGTCG
556797 TAGAGAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.45, T:0.25
Consensus pattern (22 bp):
GAGATAGGGACGGATGTTGTCG
Found at i:556928 original size:20 final size:20
Alignment explanation
Indices: 556903--557065 Score: 182
Period size: 20 Copynumber: 8.1 Consensus size: 20
556893 TAATATTGTG
556903 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
556923 TTTCGCGTTTCGAATTCGAC
1 TTTCGCGTTGCGAATTTGAC
* *
556943 TATCACGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
556963 TATCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
556983 TTTTGTGTTGCGAATTTGAA
1 TTTCGCGTTGCGAATTTGAC
* *
557003 ATTCAGTGTTGCGAATTTGAC
1 TTTC-GCGTTGCGAATTTGAC
*
557024 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
557044 TTTTGTGTTGCGGATTTGAC
1 TTTCGCGTTGCGAATTTGAC
557064 TT
1 TT
557066 CTGTATTGCG
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
20 102 0.86
21 17 0.14
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:557013 original size:21 final size:21
Alignment explanation
Indices: 556970--557022 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
556960 GACTATCGCA
* **
556970 TTGCGAATTTG-ACTTTTGTG
1 TTGCGAATTTGAAATTCAGTG
556990 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
557011 TTGCGAATTTGA
1 TTGCGAATTTGA
557023 CTATCGCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCAGTG
Found at i:557023 original size:41 final size:40
Alignment explanation
Indices: 556970--557076 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 40
556960 GACTATCGCA
556970 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTG-AATTCAGTG
* * * * **
557011 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAATTCAGTG
* * *
557051 TTGCGGATTTGACTTCTGTATTGCGA
1 TTGCGAATTTGACTTTTGTGTTGCGA
557077 TTTACAGATT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 26 0.48
41 28 0.52
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (40 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGAATTCAGTG
Found at i:557035 original size:61 final size:61
Alignment explanation
Indices: 556905--557062 Score: 221
Period size: 61 Copynumber: 2.6 Consensus size: 61
556895 ATATTGTGTT
* * * * *
556905 TCGCGTTGCGAATTTGACTTTCGCGTTTCGAATTCG-ACTATCACGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATATCACGTTGCGAATTTGACTA
* *
556965 TCGCATTGCGAATTTGACTTTTGTGTTGCGAATTTGAAAT-TCAGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATATCA-CGTTGCGAATTTGACTA
*
557026 TCGCGTTGCGAATTTGACTTTTGTGTTGCGGATTTGA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGA
557063 CTTCTGTATT
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 34 0.39
61 53 0.61
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (61 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATATCACGTTGCGAATTTGACTA
Found at i:557088 original size:81 final size:80
Alignment explanation
Indices: 556910--557116 Score: 215
Period size: 81 Copynumber: 2.6 Consensus size: 80
556900 GTGTTTCGCG
** * * * *
556910 TTGCGAATTTGACTTTCGCGTTTCGAATTCGACTATCACGTTGCGAATTTGACTATCGCATTGCG
1 TTGCGAATTTGAAATTCACGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCATTGCG
* *
556975 AATTTGACTTTTGTG
66 AATTTGACTTCTGTA
* * * **
556990 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGC
1 TTGCGAATTTGAAATTCA-CGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCATTGC
*
557055 GGATTTGACTTCTGTA
65 GAATTTGACTTCTGTA
557071 TTGCG-ATTT-ACAGATTCACGTTGCG-ATTT-ACATATTCGCGTTGCGA
1 TTGCGAATTTGA-A-ATTCACGTTGCGAATTTGAC-TA-TCGCGTTGCGA
557117 TATTGGAAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.02
79 7 0.07
80 37 0.35
81 61 0.57
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (80 bp):
TTGCGAATTTGAAATTCACGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCATTGCG
AATTTGACTTCTGTA
Found at i:557094 original size:20 final size:20
Alignment explanation
Indices: 557071--557117 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
557061 GACTTCTGTA
557071 TTGCGATTTACAGATTCACG
1 TTGCGATTTACAGATTCACG
* *
557091 TTGCGATTTACATATTCGCG
1 TTGCGATTTACAGATTCACG
557111 TTGCGAT
1 TTGCGAT
557118 ATTGGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCACG
Found at i:559142 original size:34 final size:33
Alignment explanation
Indices: 559098--559173 Score: 125
Period size: 34 Copynumber: 2.3 Consensus size: 33
559088 CTCCTCCCCC
559098 ACCCCCTTTTTTCCACCATGTTTATCACCTCCTT
1 ACCCCCTTTTTTCCACCATGTTTATCACC-CCTT
* *
559132 ACCCCTTTTTTTCCACCATGTTTATCACCCTTT
1 ACCCCCTTTTTTCCACCATGTTTATCACCCCTT
559165 ACCCCCTTT
1 ACCCCCTTT
559174 GTACTTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 11 0.28
34 28 0.72
ACGTcount: A:0.14, C:0.41, G:0.03, T:0.42
Consensus pattern (33 bp):
ACCCCCTTTTTTCCACCATGTTTATCACCCCTT
Found at i:559421 original size:12 final size:12
Alignment explanation
Indices: 559404--559494 Score: 91
Period size: 12 Copynumber: 7.8 Consensus size: 12
559394 GACCAAATTC
559404 CTCATCATCAAA
1 CTCATCATCAAA
559416 CTCATCATC--A
1 CTCATCATCAAA
559426 -TCATCATCAAA
1 CTCATCATCAAA
*
559437 CTCATCATCGAA
1 CTCATCATCAAA
* * *
559449 TTCATCGTCGAA
1 CTCATCATCAAA
* *
559461 CTCGTCATCGAA
1 CTCATCATCAAA
559473 CTCATCATCATAA
1 CTCATCATCA-AA
559486 -TCATCATCA
1 CTCATCATCA
559495 CTCCCATCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
9 8 0.12
10 1 0.01
11 1 0.01
12 55 0.82
13 2 0.03
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (12 bp):
CTCATCATCAAA
Found at i:560848 original size:50 final size:50
Alignment explanation
Indices: 560737--560848 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
560727 CCCCTTACAT
** * * *
560737 CGCGCTATACGATGATTTGACGTCACGTAGGGTATAGCACGACCCTTGCA
1 CGCGCTATACGATGAGCTGACGCCACGTAGGATATAGCACGACCCCTGCA
* * * *
560787 CACCGCTATACGATGAGCTGGCGCCACGT-GGATATAGCGCGGCCCCTGCA
1 C-GCGCTATACGATGAGCTGACGCCACGTAGGATATAGCACGACCCCTGCA
560837 GCGCGCTATACG
1 -CGCGCTATACG
560849 CCACATAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
50 27 0.54
51 23 0.46
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.20
Consensus pattern (50 bp):
CGCGCTATACGATGAGCTGACGCCACGTAGGATATAGCACGACCCCTGCA
Found at i:564753 original size:12 final size:12
Alignment explanation
Indices: 564738--564768 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
564728 ATCACCGTCA
564738 TCGTCGTCATCG
1 TCGTCGTCATCG
564750 TCGTCGTCATCG
1 TCGTCGTCATCG
564762 TCGTCGT
1 TCGTCGT
564769 TATCTTACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.32, G:0.26, T:0.35
Consensus pattern (12 bp):
TCGTCGTCATCG
Found at i:565614 original size:160 final size:160
Alignment explanation
Indices: 565350--565670 Score: 610
Period size: 160 Copynumber: 2.0 Consensus size: 160
565340 CTCAGCATAC
565350 ATTAAGAGATCATCAAAAATGGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAACAC
1 ATTAAGAGATCATCAAAAATGGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAACAC
565415 GACCCACTCATGATGCCTAACCAGCCAATCTGTGGCTGTCTTGCCGCGTCTGTC-AAGCTATGCG
66 GACCCACTCATGATGCCTAACCAGCCAATCTGTGGCTGTCTTGCCGCGTCTGTCTAAGCTAT--G
565479 CAACTCG-CCATATTGCGAGGTGCTTCCGGCA
129 CAACTCGTCCATATTGCGAGGTGCTTCCGGCA
565510 ATTAAGAGATCATCAAAAATGGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAACAC
1 ATTAAGAGATCATCAAAAATGGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAACAC
565575 GACCCACTCATGATGCCTAACCAGCCAATCTGTGGCTGTCTTGCCGCGTCTGTCTAAGCTATGCA
66 GACCCACTCATGATGCCTAACCAGCCAATCTGTGGCTGTCTTGCCGCGTCTGTCTAAGCTATGCA
565640 ACTCGTCCATATTGCGAGGTGCTTCCGGCA
131 ACTCGTCCATATTGCGAGGTGCTTCCGGCA
565670 A
1 A
565671 CCAAACTGCC
Statistics
Matches: 159, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
159 8 0.05
160 144 0.91
161 7 0.04
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (160 bp):
ATTAAGAGATCATCAAAAATGGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAACAC
GACCCACTCATGATGCCTAACCAGCCAATCTGTGGCTGTCTTGCCGCGTCTGTCTAAGCTATGCA
ACTCGTCCATATTGCGAGGTGCTTCCGGCA
Found at i:567062 original size:20 final size:19
Alignment explanation
Indices: 567034--567072 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
567024 CCTTAAAAAG
*
567034 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
567054 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
567073 GGGGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:567291 original size:51 final size:50
Alignment explanation
Indices: 567185--567311 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 50
567175 AGATATACAG
* * * **
567185 GTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
* *
567235 TTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACC-CACGTGGCACCAAATCACC
*
567286 GTATAGCGCGGTGCAGGGAGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
567312 TTACTGCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 28 0.42
51 39 0.58
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
Found at i:567701 original size:30 final size:28
Alignment explanation
Indices: 567652--567707 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
567642 TATGATTTTA
567652 AAAATAAATAAAATTTAAATATTAAAAT
1 AAAATAAATAAAATTTAAATATTAAAAT
*
567680 AAAATAAATAATGATTTTAAATATTAAA
1 AAAATAAATAA--AATTTAAATATTAAA
567708 TGTGTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
30 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATAAATAAAATTTAAATATTAAAAT
Found at i:571975 original size:19 final size:20
Alignment explanation
Indices: 571930--571988 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
571920 TTCCCCTGTG
571930 GGGGGAATCGGTTCCCTTCAAA
1 GGGGGAATCGGTTCCC-TC-AA
571952 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
571971 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
571989 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 16 0.46
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:577779 original size:2 final size:2
Alignment explanation
Indices: 577728--577764 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
577718 AATATCAATA
577728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
577765 CTCTAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:578516 original size:23 final size:21
Alignment explanation
Indices: 578464--578516 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
578454 AATTCTACAT
578464 ATTTAA-TTATATTATTTTTA
1 ATTTAATTTATATTATTTTTA
*
578484 AATTATATTTATTATTATATTTTA
1 ATTTA-ATTTA-TATTAT-TTTTA
578508 ATTTAATTT
1 ATTTAATTT
578517 TAATTACGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 3 0.11
23 10 0.37
24 9 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTTATATTATTTTTA
Found at i:582639 original size:18 final size:18
Alignment explanation
Indices: 582616--582697 Score: 119
Period size: 18 Copynumber: 4.3 Consensus size: 18
582606 ACTGAATATT
582616 TATCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
582634 TATCCCGAAGGACCACTGTA
1 TATCCCGAAGGACCAC--TA
582654 TATGTCCCGAAGGACCACTA
1 TA--TCCCGAAGGACCACTA
*
582674 TGTCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
582692 TATCCC
1 TATCCC
582698 TCGACTCTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
18 37 0.64
20 7 0.12
22 14 0.24
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:587230 original size:17 final size:17
Alignment explanation
Indices: 587189--587245 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 17
587179 AAACTTAAAC
*
587189 TATTTTA-AATTTTGTTG
1 TATTTTATAATTTT-TTA
587206 TAATTTTATAATTTTTTA
1 T-ATTTTATAATTTTTTA
587224 TATTTTAT-A-TTTTTA
1 TATTTTATAATTTTTTA
587239 TATTTTA
1 TATTTTA
587246 ATTTTAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 13 0.35
16 1 0.03
17 8 0.22
18 9 0.24
19 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (17 bp):
TATTTTATAATTTTTTA
Found at i:587231 original size:7 final size:7
Alignment explanation
Indices: 587219--587251 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
587209 TTTTATAATT
587219 TTTTATA
1 TTTTATA
587226 TTTTATA
1 TTTTATA
587233 TTTTTATA
1 -TTTTATA
587241 TTTTA-A
1 TTTTATA
587247 TTTTA
1 TTTTA
587252 GATTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:587238 original size:15 final size:15
Alignment explanation
Indices: 587208--587250 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
587198 TTTTGTTGTA
587208 ATTTTATAATTTTTTAT
1 ATTTTAT-A-TTTTTAT
587225 ATTTTATATTTTTAT
1 ATTTTATATTTTTAT
587240 ATTTTA-ATTTT
1 ATTTTATATTTT
587251 AGATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 13 0.50
16 1 0.04
17 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTATATTTTTAT
Found at i:587322 original size:13 final size:13
Alignment explanation
Indices: 587272--587322 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
587262 TTTGAATATA
587272 TAAATTTTATGTT
1 TAAATTTTATGTT
**
587285 TATGTTATGTAT-TT
1 TAAATT-T-TATGTT
587299 TAAAGTTTTATGTT
1 TAAA-TTTTATGTT
587313 TAAATTTTAT
1 TAAATTTTAT
587323 TTTTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 13 0.43
14 12 0.40
15 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (13 bp):
TAAATTTTATGTT
Found at i:592469 original size:201 final size:206
Alignment explanation
Indices: 592248--592654 Score: 770
Period size: 205 Copynumber: 2.0 Consensus size: 206
592238 TAATACTTGA
592248 CACCCTTTTATATTTTTTATATTTCTTTTAATTTATTTTTTTAAAATTATACTATCATTAATTTT
1 CACCCTTTTATATTTTTTATATTTCTTTTAATTTATTTTTTTAAAATTATACTATCATTAATTTT
592313 CAAAACCCTTAAATTATCT-AAA-T-TTAATCTTAAATCTCTAAATC-AAAATCAACCACCATTG
66 CAAAACCCTTAAATTATCTAAAATTCTTAATCTTAAATCTCTAAATCTAAAATCAACCACCATTG
592374 ATCATCTCTTCTATCATCAGATTCTACACGATCGGTCGCCTCTAATTAATATTAATAAAAAATTA
131 ATCATCTCTTCTATCATCAGATTCTACACGATCGGTCGCCTCTAATTAATATTAATAAAAAATTA
592439 ATATCATATAT
196 ATATCATATAT
592450 CACCC-TTTATATTTTTTATATTTCTTTTAATTTATTTTTTTAAAATTATACTATCATTAATTTT
1 CACCCTTTTATATTTTTTATATTTCTTTTAATTTATTTTTTTAAAATTATACTATCATTAATTTT
592514 CAAAACCCTTAAATTATCTAAAATTCTTAATCTTAAATCTCTAAATCTAAAATCAACCACCATTG
66 CAAAACCCTTAAATTATCTAAAATTCTTAATCTTAAATCTCTAAATCTAAAATCAACCACCATTG
*
592579 ATCATCTCTTCTATCATCAGATTCTACACGATCGGTGGCCTCTAATTAATATTAATAAAAAATTA
131 ATCATCTCTTCTATCATCAGATTCTACACGATCGGTCGCCTCTAATTAATATTAATAAAAAATTA
592644 ATATCATATAT
196 ATATCATATAT
592655 GAATCAATAA
Statistics
Matches: 200, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
201 78 0.39
202 8 0.04
203 1 0.00
204 21 0.10
205 92 0.46
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (206 bp):
CACCCTTTTATATTTTTTATATTTCTTTTAATTTATTTTTTTAAAATTATACTATCATTAATTTT
CAAAACCCTTAAATTATCTAAAATTCTTAATCTTAAATCTCTAAATCTAAAATCAACCACCATTG
ATCATCTCTTCTATCATCAGATTCTACACGATCGGTCGCCTCTAATTAATATTAATAAAAAATTA
ATATCATATAT
Found at i:592560 original size:15 final size:15
Alignment explanation
Indices: 592529--592567 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
592519 CCCTTAAATT
*
592529 ATCTAAAAT-TCTTA
1 ATCTAAAATCTCTAA
*
592543 ATCTTAAATCTCTAA
1 ATCTAAAATCTCTAA
592558 ATCTAAAATC
1 ATCTAAAATC
592568 AACCACCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (15 bp):
ATCTAAAATCTCTAA
Found at i:593099 original size:20 final size:21
Alignment explanation
Indices: 593054--593100 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
593044 ATTTTAGCCA
*
593054 AACCAAAAGTAATCCGAATCT
1 AACCAAAAGTAACCCGAATCT
593075 AACCAAAA-TCAACCCGAAT-T
1 AACCAAAAGT-AACCCGAATCT
593095 AACCAA
1 AACCAA
593101 TCGAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.51, C:0.28, G:0.06, T:0.15
Consensus pattern (21 bp):
AACCAAAAGTAACCCGAATCT
Found at i:593198 original size:2 final size:2
Alignment explanation
Indices: 593193--593223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
593183 TATCAATAAT
593193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
593224 GATTTGACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:593699 original size:40 final size:38
Alignment explanation
Indices: 593617--593703 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 38
593607 AAAAAAATTC
* * * *
593617 TAATATTTTCGATTGAACTGAAAATGTTTTAAAGAATG
1 TAATATTTTCGATTGAACCGAAAATATTTGAAAGAATA
*
593655 TAATATTTTCGGTTGTCAACCGAAAATATTATGAAA-AATA
1 TAATATTTTCGATTG--AACCGAAAATATT-TGAAAGAATA
593695 TAATATTTT
1 TAATATTTT
593704 TAATTCAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 14 0.34
40 23 0.56
41 4 0.10
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (38 bp):
TAATATTTTCGATTGAACCGAAAATATTTGAAAGAATA
Found at i:595815 original size:60 final size:58
Alignment explanation
Indices: 595717--595830 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 58
595707 AATAGTCAAT
* * ** *
595717 GACTATTTTGTAACTTTTAATAGTTTAGAGACTCAATAAAATATCATCATATAATTAAGA
1 GACTATTTTATAACTTTTAATAATCGAGAGACTAAATAAAATA--ATCATATAATTAAGA
* *
595777 GACTGTTTTATAACTTTTAATAATCGAGATACTAAATAAAATAATCATATAATT
1 GACTATTTTATAACTTTTAATAATCGAGAGACTAAATAAAATAATCATATAATT
595831 GGAATACTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 11 0.23
60 36 0.77
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (58 bp):
GACTATTTTATAACTTTTAATAATCGAGAGACTAAATAAAATAATCATATAATTAAGA
Found at i:596889 original size:2 final size:2
Alignment explanation
Indices: 596884--596941 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
596874 TTCATATGTG
596884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
596926 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
596942 CATACACAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:598657 original size:3 final size:3
Alignment explanation
Indices: 598651--598701 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
598641 TTTCATTTTT
* * * * *
598651 TTA TTA TAA ATA TTA TTA TTA ATA TTA TTT TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
598699 TTA
1 TTA
598702 CAAACAGGCC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:598700 original size:15 final size:15
Alignment explanation
Indices: 598661--598701 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
598651 TTATTATAAA
598661 TATTATTATTAATAT
1 TATTATTATTAATAT
*
598676 TATTTTTATTAATAT
1 TATTATTATTAATAT
598691 TATTATTATTA
1 TATTATTATTA
598702 CAAACAGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTATTAATAT
Found at i:599170 original size:15 final size:17
Alignment explanation
Indices: 599150--599182 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
599140 CCAACAGGAG
599150 AAAAAA-AA-AGAAAAA
1 AAAAAACAAGAGAAAAA
599165 AAAAAACAAGAGAAAAA
1 AAAAAACAAGAGAAAAA
599182 A
1 A
599183 CGAACAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAACAAGAGAAAAA
Found at i:600448 original size:29 final size:30
Alignment explanation
Indices: 600415--600472 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
600405 ATATTTCTAA
600415 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTATTTCATAAATATAT
* * *
600444 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTATTTCATAAATATA
600473 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAAATAAATATTTTATTTCATAAATATAT
Found at i:602516 original size:15 final size:14
Alignment explanation
Indices: 602464--602517 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
602454 TTTACGTTTG
* *
602464 TATTTAAATTTACA
1 TATTTACATTTGCA
*
602478 TTTTTACATTTGCA
1 TATTTACATTTGCA
602492 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
602507 TCTTTGCATTT
1 TATTTACATTT
602518 TTTATGTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:606064 original size:9 final size:9
Alignment explanation
Indices: 606052--606085 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
606042 AAGGAGAAAG
606052 AAAAAAGAA
1 AAAAAAGAA
606061 AAAAAATGAA
1 AAAAAA-GAA
*
606071 AAAAATGAA
1 AAAAAAGAA
606080 AAAAAA
1 AAAAAA
606086 AGGAGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:611598 original size:20 final size:20
Alignment explanation
Indices: 611535--611598 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
611525 GCCAGGTAGA
611535 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
611555 G-TCAT-CTGAAGAAGAAGAA
1 GTTCATAATG-AGAAGAACTT
* *
611574 ATTCATAATGAGAAGAATTT
1 GTTCATAATGAGAAGAACTT
611594 GTTCA
1 GTTCA
611599 GCCTTTTGCT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.28
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:611719 original size:113 final size:112
Alignment explanation
Indices: 611385--612280 Score: 881
Period size: 112 Copynumber: 7.8 Consensus size: 112
611375 GCAAAGATTA
*
611385 AAATCCATCGCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
611450 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CT
* * * * * * *
611498 GAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTTGTCATCT
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAAC---TCATCT
*
611562 GAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAGCCTTTTGCT
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
611609 CAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 -AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* ** *
611674 GAAGGAAGAAGAAGTTCATAATGAGAAGAATGTGTTCAATATTTTGTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CT
* * * * * * * *
611723 GAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCAT-C
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC-TGA
* *
611786 TGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
* *
611834 CAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAA
1 -AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
611899 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG--
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
* * * * * * * *
611945 -AATTCATCATTTGCTGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAATAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* * **
612008 GAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-T
* * * * *
612057 AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCTGAGAAAGTTCATAATGAGAAGAA
1 AA----ATC-C---ATCA-CTTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* **
612122 CTCATCT---GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT
55 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-T
* * * * *
612177 AATTCTATCAC-AGAAGGATATAAATTAGCATCAAACTTTCCAGAGAAAGTTCATAATGAGAAGA
1 AAATCCATCACTTGATGG------ATCAGC-T-----TTTCCAGAGAAAGTTCATAATGAGAAGA
*
612241 ACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGA
54 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
612281 GCTTATTCAA
Statistics
Matches: 649, Mismatches: 84, Indels: 89
0.79 0.10 0.11
Matches are distributed among these distances:
108 1 0.00
109 106 0.16
110 7 0.01
111 4 0.01
112 176 0.27
113 172 0.27
114 8 0.01
115 5 0.01
116 14 0.02
117 2 0.00
118 1 0.00
120 81 0.12
121 6 0.01
122 2 0.00
123 4 0.01
124 59 0.09
125 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
Found at i:611776 original size:225 final size:222
Alignment explanation
Indices: 611385--612166 Score: 1114
Period size: 225 Copynumber: 3.5 Consensus size: 222
611375 GCAAAGATTA
*
611385 AAATCCATCGCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
611450 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-ATTTTGTTTGAATTCATCATTTGATG
611515 GATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTCATCTGAAGAAGAAGAAATTCAT
130 GATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAC-T-TCATCTGAAGAAGAAGAAATTCAT
*
611580 AATGAGAAGAATTTGTTCAGCCTTTTGCTC
193 AATGAGAAGAATTTGTTCAACCTTTTGCTC
611610 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
611675 AAGGAAGAAGAAGTTCATAATGAGAAGAATGTGTTCAATATTTTGTTTGAATTCATCATTTGATG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-ATTTTGTTTGAATTCATCATTTGATG
611740 GATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTCAT
130 GATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT--TCATCTGAAGAAGAAGAAATTCAT
611805 AATGAGAAGAATTTGTTCAACCTTTTGCTC
193 AATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
611835 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
** *
611900 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-AA-CCT-TTTGAATTCATCATTTGCTGG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTGTTTGAATTCATCATTTGATGG
*
611962 ATCAACATTGCCAGGTAGAGTTCATAATGAGAATAAC-TCATCTGAAGAAGAAAGAAGAAGTTCA
131 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTCATCTGAAGAAG-AAG-A-AA-TTCA
* **
612026 CAATGAGAAGAGCTTGTTCAACCTTTTGCAT-
192 TAATGAGAAGAATTTGTTCAACCTTTTGC-TC
* * * * *
612057 AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCTGAGAAAGTTCATAATGAGAAGAA
1 AA----ATC-C---ATCA-CTTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* **
612122 CTCATCT---GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAA
55 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
612167 CCTTTTGCAT
Statistics
Matches: 514, Mismatches: 25, Indels: 31
0.90 0.04 0.05
Matches are distributed among these distances:
218 13 0.03
219 3 0.01
220 1 0.00
221 58 0.11
222 33 0.06
223 2 0.00
224 2 0.00
225 315 0.61
226 3 0.01
227 1 0.00
229 30 0.06
230 7 0.01
231 3 0.01
232 1 0.00
233 42 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (222 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTGTTTGAATTCATCATTTGATGG
ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTCATCTGAAGAAGAAGAAATTCATAAT
GAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:612118 original size:124 final size:122
Alignment explanation
Indices: 611980--612385 Score: 554
Period size: 120 Copynumber: 3.3 Consensus size: 122
611970 TGCCAGGTAG
*
611980 AGTTCATAATGAGAATAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
* * *
612045 AACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCTGAGAA
66 AACCTTTTGCATAATTCTATCACAGAAGGAAATAGATTAGCATCA-C-TTTCCAGAGAA
612104 AGTTCATAATGAGAAGAACTCATCT---GAAG-AAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
* *
612165 AACCTTTTGCATAATTCTATCACAGAAGGATATAAATTAGCATCAAACTTTCCAGAGAA
66 AACCTTTTGCATAATTCTATCACAGAAGGAAATAGATTAGCATC--ACTTTCCAGAGAA
* *
612224 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
* * * * * * * * **
612289 AACCCTTTGAATGACTCTATCACATAAGGAAATAGGTCAACATCA-TCCCCAGAGAAA
66 AACCTTTTGCATAATTCTATCACAGAAGGAAATAGATTAGCATCACTTTCCAGAG-AA
*
612346 AGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
612386 TTTATTCAAC
Statistics
Matches: 255, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
120 108 0.42
121 20 0.08
122 35 0.14
123 4 0.02
124 88 0.35
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAGAGCTTGTTC
AACCTTTTGCATAATTCTATCACAGAAGGAAATAGATTAGCATCACTTTCCAGAGAA
Found at i:612562 original size:12 final size:13
Alignment explanation
Indices: 612517--612564 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
612507 TTTTATTTTT
612517 TTATTA-TAAATA
1 TTATTATTAAATA
612529 TTATTATTAATATTA
1 TTATTATTAA-A-TA
*
612544 TTTTTATTAAA-A
1 TTATTATTAAATA
612556 TTATTATTA
1 TTATTATTA
612565 TTACAAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 15 0.48
13 3 0.10
14 2 0.06
15 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATTATTAAATA
Found at i:612566 original size:15 final size:15
Alignment explanation
Indices: 612517--612567 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
612507 TTTTATTTTT
612517 TTATTATAAA-TATTA
1 TTATTA-AAATTATTA
* *
612532 TTATTAATATTATTT
1 TTATTAAAATTATTA
612547 TTATTAAAATTATTA
1 TTATTAAAATTATTA
612562 TTATTA
1 TTATTA
612568 CAAACAGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 2 0.06
15 29 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTAAAATTATTA
Found at i:613055 original size:16 final size:14
Alignment explanation
Indices: 613007--613048 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
612997 CACAGCAACC
*
613007 AACAGGAGAAAAAA
1 AACAAGAGAAAAAA
*
613021 AA-AGAAAGAAAAAA
1 AACA-AGAGAAAAAA
613035 AACAAGAGAAAAAA
1 AACAAGAGAAAAAA
613049 CGAACAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (14 bp):
AACAAGAGAAAAAA
Found at i:613344 original size:18 final size:18
Alignment explanation
Indices: 613323--613357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
613313 CGGGGTTACC
613323 GCCGGCGAACGGCTTCCG
1 GCCGGCGAACGGCTTCCG
* *
613341 GCCGGTGACCGGCTTCC
1 GCCGGCGAACGGCTTCC
613358 CTCCGATGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.40, G:0.37, T:0.14
Consensus pattern (18 bp):
GCCGGCGAACGGCTTCCG
Found at i:614023 original size:28 final size:27
Alignment explanation
Indices: 613949--614024 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
613939 GTTCTAATTG
** *
613949 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
613976 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
614005 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
614025 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:614326 original size:29 final size:30
Alignment explanation
Indices: 614293--614350 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
614283 ATATTTCTAA
614293 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTATTTCATAAATATAT
* * *
614322 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTATTTCATAAATATA
614351 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAAATAAATATTTTATTTCATAAATATAT
Done.