Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold149
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: 533615
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.25
Warning! 129246 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:411377 original size:28 final size:28
Alignment explanation
Indices: 411341--411426 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 28
411331 TAATAAATAA
*
411341 ATATATTATATCAAATTTTAAATATTTTT
1 ATATATTATATCATA-TTTAAATATTTTT
*
411370 ATAT-TTATATCATATTTAATTTATTTTT
1 ATATATTATATCATATTTAA-ATATTTTT
411398 ATATATTATATCATATTTAAATTATTTTT
1 ATATATTATATCATATTTAAA-TATTTTT
411427 TATTTTACGT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.10
28 20 0.39
29 26 0.51
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATATTATATCATATTTAAATATTTTT
Found at i:411777 original size:9 final size:9
Alignment explanation
Indices: 411755--411788 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
411745 TTCTGAATTG
411755 AGTTAAAAA
1 AGTTAAAAA
411764 A-TTAAAAA
1 AGTTAAAAA
411772 AGTT-AAAA
1 AGTTAAAAA
411780 AGTTAAAAA
1 AGTTAAAAA
411789 TATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (9 bp):
AGTTAAAAA
Found at i:411777 original size:17 final size:17
Alignment explanation
Indices: 411755--411788 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
411745 TTCTGAATTG
411755 AGTTAAAAAATTAAAAA
1 AGTTAAAAAATTAAAAA
*
411772 AGTTAAAAAGTTAAAAA
1 AGTTAAAAAATTAAAAA
411789 TATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
AGTTAAAAAATTAAAAA
Found at i:412829 original size:31 final size:31
Alignment explanation
Indices: 412711--412825 Score: 149
Period size: 31 Copynumber: 3.7 Consensus size: 31
412701 GATTCATAAC
* * *
412711 AAAACTACTATTTTTATCCGGTAGCACAGCA
1 AAAACCACTATTCTTATCCGGTAGCACGGCA
* * *
412742 AAAACCATTATTCTTATCCGGTAGTACGGTA
1 AAAACCACTATTCTTATCCGGTAGCACGGCA
* *
412773 AAAACCACTATTCTTATCCAGTGGCACGGCA
1 AAAACCACTATTCTTATCCGGTAGCACGGCA
*
412804 AAAACCACTATTCTTAACCGGT
1 AAAACCACTATTCTTATCCGGT
412826 GGCATGGTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (31 bp):
AAAACCACTATTCTTATCCGGTAGCACGGCA
Found at i:417698 original size:21 final size:21
Alignment explanation
Indices: 417674--417717 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
417664 ATTAAAAAAA
417674 TATTTTAT-ATTAATATTTATT
1 TATTTTATAATTAA-ATTTATT
417695 TATTTTATAATTAAATTTATT
1 TATTTTATAATTAAATTTATT
417716 TA
1 TA
417718 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATT
Found at i:418262 original size:34 final size:34
Alignment explanation
Indices: 418202--418352 Score: 223
Period size: 34 Copynumber: 4.5 Consensus size: 34
418192 TTCCCTAACT
*
418202 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
*
418235 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
418269 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
418303 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
418337 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
418353 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 14 0.13
34 90 0.87
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:418715 original size:19 final size:19
Alignment explanation
Indices: 418659--418721 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
418649 TGGTTGTCGA
**
418659 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
418678 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
418697 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
418716 GTTACT
1 GGTACT
418722 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:422847 original size:34 final size:34
Alignment explanation
Indices: 422787--422937 Score: 223
Period size: 34 Copynumber: 4.5 Consensus size: 34
422777 AAGTGGGAGA
*
422787 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
*
422820 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
422854 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
422888 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
422922 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
422938 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 14 0.13
34 90 0.87
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:426227 original size:2 final size:2
Alignment explanation
Indices: 426218--426250 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
426208 AAAAAAGTTG
426218 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
426251 AACGTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:429450 original size:15 final size:15
Alignment explanation
Indices: 429416--429457 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
429406 TTGTAATAAT
429416 TTTAAAAATATAAAA
1 TTTAAAAATATAAAA
*
429431 GTTAAAAATACT-AAA
1 TTTAAAAATA-TAAAA
*
429446 TTTAATAATATA
1 TTTAAAAATATA
429458 TAAACTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TTTAAAAATATAAAA
Found at i:432432 original size:72 final size:70
Alignment explanation
Indices: 432218--432503 Score: 253
Period size: 71 Copynumber: 4.1 Consensus size: 70
432208 TATAAGTTTA
* * * * *
432218 TTTTTGGATATAATTTTACGAA-TTCAAATCTTTAAGATATTATTTATCTTTATTTTTAGAAGTT
1 TTTTTGG-TATAATTATAC-AAGTTTAAATTTTTAAGATA-TATTTATTTTTATTTATAGAAGTT
*
432282 T-AAGTT-
63 TAAATTTG
* * * * * * * *
432288 TTTTT-GTATGATTATATAAGTTTAAATTTTTTAAGCTATAATT-TTTTTATTTGTAAAAATATA
1 TTTTTGGTATAATTATACAAGTTTAAA-TTTTTAAGATATATTTATTTTTATTTATAGAAGTTTA
432351 AATTTG
65 AATTTG
* * *
432357 TTTTTGGGTATAATTATACGAGTTTAAATTTTGAATG-TATGATTTATTTTTATTTATAGAACTT
1 TTTTT-GGTATAATTATACAAGTTTAAATTTTTAA-GATAT-ATTTATTTTTATTTATAGAAGTT
432421 TAAATTTG
63 TAAATTTG
* * * *
432429 TTTTCTAGTTTGATTATACAAGTTTAAATTTTTAATG-TATTTTTATTTTTATTTATAGAAGTTT
1 TTTT-TGGTATAATTATACAAGTTTAAATTTTTAA-GATATATTTATTTTTATTTATAGAAGTTT
432493 AAATTTG
64 AAATTTG
432500 TTTT
1 TTTT
432504 ATATGAGTTT
Statistics
Matches: 177, Mismatches: 29, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
67 16 0.09
68 21 0.12
69 15 0.08
70 14 0.08
71 55 0.31
72 55 0.31
73 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (70 bp):
TTTTTGGTATAATTATACAAGTTTAAATTTTTAAGATATATTTATTTTTATTTATAGAAGTTTAA
ATTTG
Found at i:432472 original size:139 final size:138
Alignment explanation
Indices: 432207--432461 Score: 316
Period size: 139 Copynumber: 1.8 Consensus size: 138
432197 GGACCTGATT
* * *
432207 ATATAAGTTTATTTTTGGATATAATTTTACGAATTCAAATCTTTAAGATATTATTTATCTTTATT
1 ATATAAATTTATTTTTGGATATAATTATACGAATTCAAATCTTTAAGATATGATTTATCTTTATT
* * *
432272 TTTAGAAGTTTAAGTTTTTTTGTATGATTATATAAGTTTAAATTTTTTAAGCTATAATTTTTTTA
66 TATAGAACTTTAAGTTTTTTTGTATGATTATACAAGTTTAAATTTTTTAA-CTATAATTTTTTTA
432337 TTTGTAAAA
130 TTTGTAAAA
* * * * *
432346 ATATAAATTTGTTTTTGGGTATAATTATACGAGTTTAAAT-TTTGAATG-TATGATTTATTTTTA
1 ATATAAATTTATTTTTGGATATAATTATACGAATTCAAATCTTT-AA-GATATGATTTATCTTTA
* *
432409 TTTATAGAACTTTAAATTTGTTTTCTAGTTTGATTATACAAGTTTAAATTTTT
64 TTTATAGAACTTT-AAGTT-TTTT-T-GTATGATTATACAAGTTTAAATTTTT
432462 AATGTATTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
138 3 0.03
139 60 0.62
140 5 0.05
141 4 0.04
142 1 0.01
143 24 0.25
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (138 bp):
ATATAAATTTATTTTTGGATATAATTATACGAATTCAAATCTTTAAGATATGATTTATCTTTATT
TATAGAACTTTAAGTTTTTTTGTATGATTATACAAGTTTAAATTTTTTAACTATAATTTTTTTAT
TTGTAAAA
Found at i:432504 original size:21 final size:21
Alignment explanation
Indices: 432480--432519 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
432470 TTTATTTTTA
432480 TTTATA-GAAGTTTAAATTTGT
1 TTTATATG-AGTTTAAATTTGT
432501 TTTATATGAGTTTAAATTT
1 TTTATATGAGTTTAAATTT
432520 TTTAAGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTATATGAGTTTAAATTTGT
Found at i:438434 original size:98 final size:95
Alignment explanation
Indices: 438238--438484 Score: 243
Period size: 98 Copynumber: 2.6 Consensus size: 95
438228 AAGATTTCCT
* * * ** *
438238 TCATTGAGGATACTTCAACCCCATTATTCTGAGGGGATACTCCAATCATGTTTTTAAAAATTATT
1 TCATTG-GGATACTCCAACCCCATTATTCTGA-GGGATACTTCAACCCCGTTTTTAAAAATTATC
*
438303 AAGATTTAAACCTTAATTTTTCTTAAATTATCA
64 AAGA-TTAAACATTAATTTTTCTTAAATTATCA
* *
438336 TCATTGGGAATACTCCAACCCCATTATTCTGAGGGAATACTTCAACCCCGTTTTT-AAACTTGTC
1 TCATTGGG-ATACTCCAACCCCATTATTCTGAGGG-ATACTTCAACCCCGTTTTTAAAAATTATC
** *
438400 AAGA-TAATTATT-ATTTTTGCTTAAATTGTCA
64 AAGATTAAACATTAATTTTT-CTTAAATTATCA
* * *
438431 TCATCGGGATACTCCAACCCTATTCCTTC-GAAGGGATAC-TCTAACCCCGTTTTT
1 TCATTGGGATACTCCAACCCCATT-ATTCTG-AGGGATACTTC-AACCCCGTTTTT
438485 CAACCAAAAG
Statistics
Matches: 128, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
93 2 0.02
94 38 0.30
95 30 0.23
97 15 0.12
98 43 0.34
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (95 bp):
TCATTGGGATACTCCAACCCCATTATTCTGAGGGATACTTCAACCCCGTTTTTAAAAATTATCAA
GATTAAACATTAATTTTTCTTAAATTATCA
Found at i:442860 original size:29 final size:27
Alignment explanation
Indices: 442763--442880 Score: 94
Period size: 27 Copynumber: 4.2 Consensus size: 27
442753 AAAATATAAA
** *
442763 TATATTATATTTATATATTAAATTTATGT
1 TATATTATATTTA-A-ATTATTTTTATAT
* *
442792 TATATAAATTTTTAAA-TATTTTTATAT
1 TATAT-TATATTTAAATTATTTTTATAT
* **
442819 TATATTATTTTTATTTTATTTTTATAT
1 TATATTATATTTAAATTATTTTTATAT
*
442846 ATCATATTATATTTAAATTATTTTTTATTT
1 -T-ATATTATATTTAAATTA-TTTTTATAT
442876 TATAT
1 TATAT
442881 ATACATCTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
26 7 0.10
27 24 0.33
28 6 0.08
29 21 0.29
30 14 0.19
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.64
Consensus pattern (27 bp):
TATATTATATTTAAATTATTTTTATAT
Found at i:444760 original size:20 final size:20
Alignment explanation
Indices: 444719--444759 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
444709 TATTACTTTT
*
444719 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
*
444739 ATATTATATATTTTATATAAA
1 ATATTATA-ATTATATATAAA
444760 TTATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:444776 original size:18 final size:19
Alignment explanation
Indices: 444719--444777 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 19
444709 TATTACTTTT
444719 ATATTATAATTATATTTAA-A
1 ATATTATAATT-TA-TTAATA
444739 ATATTAT-ATATT-TTATATA
1 ATATTATAAT-TTATTA-ATA
444758 A-ATTATAATTTATTAATA
1 ATATTATAATTTATTAATA
444776 AT
1 AT
444778 TCGTAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 10 0.30
20 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTATAATTTATTAATA
Found at i:444856 original size:27 final size:28
Alignment explanation
Indices: 444791--444865 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
444781 TAATATATAA
**
444791 ATTTTAATATATTTTAATATTTATATCTTG
1 ATTTTAAT-TATTTTTTTA-TTATATCTTG
* *
444821 CTTGT-ATTATTTTTTTATTATATCTT-
1 ATTTTAATTATTTTTTTATTATATCTTG
444847 ATTTTAATTATTTTTTTAT
1 ATTTTAATTATTTTTTTAT
444866 ATTTTATTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 3 0.08
27 22 0.58
28 8 0.21
29 2 0.05
30 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (28 bp):
ATTTTAATTATTTTTTTATTATATCTTG
Found at i:446497 original size:15 final size:16
Alignment explanation
Indices: 446474--446503 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
446464 TCTTAATATT
446474 AAACATAATTAACTTG
1 AAACATAATTAACTTG
446490 AAAC-TAATTAACTT
1 AAACATAATTAACTT
446504 AACTGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (16 bp):
AAACATAATTAACTTG
Found at i:448683 original size:2 final size:2
Alignment explanation
Indices: 448676--448702 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
448666 TGTGAATAAC
448676 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 A
448703 CACACACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:451015 original size:111 final size:112
Alignment explanation
Indices: 450820--451039 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 112
450810 AACTCGAAAG
**
450820 CTCTAATACCAAGTTGGAAATAACAAAAGAGTGTTTGAAGAATTCATATTTCTTGTGTAAATAAT
1 CTCTAATACCAAGTTAAAAATAACAAAAGAGTGTTTGAAGAATTCATATTTCTTGTGTAAATAAT
* *
450885 AATGTATAAGCTAGTGATTGTTTATGTACATGGTCTTTCCTAGTATT
66 AATGTATAACCTAGTGATTGTTTATGTACATGGTCTTGCCTAGTATT
450932 CTCTAATACCAAGTTAAAAATAACAAAA-AGTGTTTGAAGAATTCATATTTCTTGTGTAAATAAT
1 CTCTAATACCAAGTTAAAAATAACAAAAGAGTGTTTGAAGAATTCATATTTCTTGTGTAAATAAT
450996 AATGTATAACCTAGTGATTGTTTATGTACATGGTCTTGCCTAGT
66 AATGTATAACCTAGTGATTGTTTATGTACATGGTCTTGCCTAGT
451040 TTGATTATTT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 78 0.75
112 26 0.25
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (112 bp):
CTCTAATACCAAGTTAAAAATAACAAAAGAGTGTTTGAAGAATTCATATTTCTTGTGTAAATAAT
AATGTATAACCTAGTGATTGTTTATGTACATGGTCTTGCCTAGTATT
Found at i:451413 original size:163 final size:157
Alignment explanation
Indices: 451141--451465 Score: 454
Period size: 163 Copynumber: 2.0 Consensus size: 157
451131 GAGCTTAAGA
* * *
451141 ATAATATTTTTGGAGATCAAATATGATCTTTTGGAGATCCAAAACCTCGAAAAATATCCTATAAT
1 ATAATATTTTTGGAGATCAAATATGATATTTAGGAGATCCAAAACCCCGAAAAATATCCTATAAT
* *
451206 TAATATTAGTTAACACATGCTGAGAATACTACTTACTATTTTCTTAAATTTGTTTTCCAGTTACA
66 TAATATTAGTTAACACATGCTAAGAATAATACTTACTATTTTCTTAAATTTGTTTTCC-G-----
* *
451271 GCTTCTATTTTGTAGTTTTGCCTTTTTTTCATT
125 GCTTCTATTTTGAAGTTTTGCCTTTTCTTCATT
* *
451304 ATAATATTTTTGGATATCAAATATGATATTTAGGAGAT-CAAGAACCCCGAAAAATGTCCTATAA
1 ATAATATTTTTGGAGATCAAATATGATATTTAGGAGATCCAA-AACCCCGAAAAATATCCTATAA
* * * *
451368 TTAATATTAGTTAATACATGCTAAGAATAATACTTACTCTTTTCTTAATTTTGTTTTCCGGCTTT
65 TTAATATTAGTTAACACATGCTAAGAATAATACTTACTATTTTCTTAAATTTGTTTTCCGGCTTC
*
451433 TATTTTGAAGTTTTGCCTTTTCTTCGTT
130 TATTTTGAAGTTTTGCCTTTTCTTCATT
451461 ATAAT
1 ATAAT
451466 TCGAGTGTTA
Statistics
Matches: 147, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
157 34 0.23
162 4 0.03
163 109 0.74
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (157 bp):
ATAATATTTTTGGAGATCAAATATGATATTTAGGAGATCCAAAACCCCGAAAAATATCCTATAAT
TAATATTAGTTAACACATGCTAAGAATAATACTTACTATTTTCTTAAATTTGTTTTCCGGCTTCT
ATTTTGAAGTTTTGCCTTTTCTTCATT
Found at i:452027 original size:21 final size:21
Alignment explanation
Indices: 451979--452027 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
451969 TTAAAGATAA
451979 TTAATAATTATTTTTAAAAGAT
1 TTAA-AATTATTTTTAAAAGAT
**
452001 AAAAAATTATTTTTAAAA-ATT
1 TTAAAATTATTTTTAAAAGA-T
452022 TTAAAA
1 TTAAAA
452028 ATAAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 19 0.86
22 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAAATTATTTTTAAAAGAT
Found at i:452049 original size:29 final size:30
Alignment explanation
Indices: 451990--452049 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
451980 TAATAATTAT
*
451990 TTTTAAAAGATAAAAAATTATTTTTAAAAA
1 TTTTAAAAGATAAAAAATTATTCTTAAAAA
452020 TTTTAAAA-ATAAAAAATTA-TCTTAACAAA
1 TTTTAAAAGATAAAAAATTATTCTTAA-AAA
452049 T
1 T
452050 AGAGACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.18
29 15 0.54
30 8 0.29
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAAAAGATAAAAAATTATTCTTAAAAA
Found at i:452234 original size:2 final size:2
Alignment explanation
Indices: 452227--452275 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
452217 CGTGTGCATC
*
452227 TA TA TA TA TA TA TA -A GT- TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
452268 TA TA TA TA
1 TA TA TA TA
452276 AGTTACCTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:454527 original size:20 final size:20
Alignment explanation
Indices: 454479--454527 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
454469 TTATAATTTG
*
454479 TATCGATACAAACTGTGAATC
1 TATCGATACAAAC-GTGAATA
*
454500 TATTGATACATAA-GTGAATA
1 TATCGATACA-AACGTGAATA
454520 TATCGATA
1 TATCGATA
454528 ATGTCTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.54
21 9 0.38
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATACAAACGTGAATA
Found at i:454656 original size:51 final size:52
Alignment explanation
Indices: 454592--454724 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 52
454582 AAGAAAATGT
* *
454592 ATCGATACATTTTTCATTGTATTGATACATTCTGAGTTTTAG-CCCAAATAT
1 ATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
* * * *
454643 ATC-AGTACATTTTTCATTTTATCGATACATTTTGGGTTTTTGACCCAAATAC
1 ATCGA-TACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
* *
454695 ATCGATACATTCTTCAATGTATCGATACAT
1 ATCGATACATTTTTCATTGTATCGATACAT
454725 GCAGGCTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.01
51 35 0.50
52 33 0.47
53 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.42
Consensus pattern (52 bp):
ATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTAGACCCAAATAC
Found at i:456664 original size:38 final size:38
Alignment explanation
Indices: 456622--456699 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
456612 CTTATAACTT
*
456622 ATAGGGTGAAGCTTTATTGACGGCCTGTTATATCCATA
1 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
456660 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
1 ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
456698 AT
1 AT
456700 GGAAGGTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (38 bp):
ATAGGGTGAAGCTTTATTAACGGCCTGTTATATCCATA
Found at i:458254 original size:1 final size:1
Alignment explanation
Indices: 458248--458272 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
458238 AAATGCTCAG
458248 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
458273 GAGTACCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:461178 original size:74 final size:73
Alignment explanation
Indices: 460871--461210 Score: 324
Period size: 72 Copynumber: 4.7 Consensus size: 73
460861 TTATTTTGCG
* * * * *
460871 AAACTTTTATAAATAAAAA-AAATTATAGCTTAAAAAATTTAAACTTATATGATTATATCCAAAA
1 AAACTTCTATAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATTATACCCAAAA
460935 AATAAATTT
65 AATAAATTT
* * *
460944 AAAC-TCGTACAAAT-AAAA-AAA-TAT-TTTAAAAAATTTAAACTCATATAATTA-AACCAGAA
1 AAACTTC-TATAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATTATACCCAAAA
* *
461003 AACAAATAT
65 AATAAATTT
* * * * ** *
461012 AAAGTTCAATAAATGAAAATAAATCATATATT-AAAAATTTAAA-TTTTATAATTATACTCAAAA
1 AAACTTCTATAAATAAAAATAAATTATAT-TTAAAAAATTTAAACTCATATAATTATACCCAAAA
461075 AATAAA-TT
65 AATAAATTT
* * * **
461083 AATACTTCTATAAATAGAAATAAATTATAGTTTAAAAAATTTAAACTCGTATACTCGTACCCAAA
1 AA-ACTTCTATAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATTATACCCAAA
*
461148 AAATAAGTTT
64 AAATAAATTT
* *
461158 AAACTTTTACAAATAAAAATAAATTATATTCT-AAAAATTTAAACTCATATAAT
1 AAACTTCTATAAATAAAAATAAATTATATT-TAAAAAATTTAAACTCATATAAT
461211 CATATTTAAA
Statistics
Matches: 216, Mismatches: 37, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
68 21 0.10
69 30 0.14
70 3 0.01
71 17 0.08
72 53 0.25
73 45 0.21
74 43 0.20
75 4 0.02
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (73 bp):
AAACTTCTATAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATTATACCCAAAAA
ATAAATTT
Found at i:461220 original size:60 final size:60
Alignment explanation
Indices: 461155--461280 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
461145 AAAAAATAAG
*
461155 TTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
* * *
461215 TTTAAACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
*
461275 TCTAAA
1 TTTAAA
461281 AACAAATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.39
Consensus pattern (60 bp):
TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
Found at i:461244 original size:134 final size:130
Alignment explanation
Indices: 461081--461338 Score: 322
Period size: 133 Copynumber: 2.0 Consensus size: 130
461071 AAAAAATAAA
* * * * *
461081 TTAATACTTCTATAAATAGAAATAAATTATAGTTTAAAAAATTTAAACTCGTATACTCGTACCCA
1 TTAATACTTCTACAAATAAAAATAAATTATA-TTTAAAAAATTTAAACTCATATAATCATACCCA
461146 AAAA-ATAAGTTTAAACTTTTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAA
65 AAAACA-AA-TTTAAACTTTTACAAAT-AAAA-AAATTAT-TTCTAAAAATTTAAACTCATATAA
461210 TCATAT
125 TCATAT
* * * * *
461216 TTAA-ACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAA
1 TTAATACTTCTACAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATCATACCCAA
* * * *
461280 AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTTTTAAAATTTAAATTCGTATAA
66 AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTCTAAAAATTTAAACTCATATAA
461339 CTATATAATT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
129 20 0.19
130 7 0.06
131 4 0.04
132 17 0.16
133 32 0.30
134 24 0.22
135 4 0.04
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (130 bp):
TTAATACTTCTACAAATAAAAATAAATTATATTTAAAAAATTTAAACTCATATAATCATACCCAA
AAACAAATTTAAACTTTTACAAATAAAAAAATTATTTCTAAAAATTTAAACTCATATAATCATAT
Found at i:464581 original size:28 final size:28
Alignment explanation
Indices: 464521--464598 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
464511 AAATGTCACC
*
464521 CTTTGTATTTGTCAAATATGGTGGTTTT
1 CTTTGTATTTGTCAAATATGGTAGTTTT
464549 CTTTGTATTTGTCAAATATGGTAGTTATT
1 CTTTGTATTTGTCAAATATGGTAGTT-TT
* *
464578 -TTTG--TTTGTAAAAAATGGTAG
1 CTTTGTATTTGTCAAATATGGTAG
464599 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 15 0.33
28 29 0.63
29 2 0.04
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (28 bp):
CTTTGTATTTGTCAAATATGGTAGTTTT
Found at i:464615 original size:24 final size:25
Alignment explanation
Indices: 464556--464620 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
464546 TTTCTTTGTA
* *
464556 TTTGTCAAATATGGTAGTTATTTTTG
1 TTTGTCAAAAATGGTAG-TATTGTTG
* *
464582 TTTGTAAAAAATGGTAG-CTTGTTG
1 TTTGTCAAAAATGGTAGTATTGTTG
*
464606 TTTGTCAAAATTGGT
1 TTTGTCAAAAATGGT
464621 GGCTAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 18 0.55
26 15 0.45
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.48
Consensus pattern (25 bp):
TTTGTCAAAAATGGTAGTATTGTTG
Found at i:465935 original size:59 final size:60
Alignment explanation
Indices: 465872--465996 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
465862 AAAAAATAAG
*
465872 TTTAAACTTTTACAAAT-AAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
* * *
465931 TTTAAACTTCTACAGATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATA
1 TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
*
465991 TCTAAA
1 TTTAAA
465997 AACAAATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
59 15 0.25
60 45 0.75
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (60 bp):
TTTAAACTTCTACAAATAAAAATAAATTATATTCTAAAAATTTAAACTCATATAATCATA
Found at i:466039 original size:130 final size:133
Alignment explanation
Indices: 465798--466054 Score: 326
Period size: 132 Copynumber: 2.0 Consensus size: 133
465788 AAAAAATAAA
* * * * *
465798 TTAATACTTCTATAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCGTATACTCGTACCCA
1 TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
*
465863 AAAAATAAGTTTAAACTTTTACAAATAAAATAAATTATATTCTAAAAATTTAAACTCATATAATC
66 AAAAATAAGTTTAAACTTTTACAAATAAAAAAAATTATATTCT-AAAATTTAAACTCATATAATC
465928 ATAT
130 ATAT
* * * * * *
465932 TTAA-ACTTCTACAGATAAAAATAAATTATA-TTTTAAAAATTTAAACTCATATAATTATATCTA
1 TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
* * *
465995 AAAACA-AA-TTTAAAC-TTTACAAATAAAAAAAATTATATTTTAAAATTTAAATTCGTATAA
66 AAAA-ATAAGTTTAAACTTTTACAAATAAAAAAAATTATATTCTAAAATTTAAACTCATATAA
466055 CTATATATTT
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
129 17 0.16
130 24 0.22
131 7 0.07
132 31 0.29
133 24 0.22
134 4 0.04
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (133 bp):
TTAATACTTCTACAAATAAAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATACCCA
AAAAATAAGTTTAAACTTTTACAAATAAAAAAAATTATATTCTAAAATTTAAACTCATATAATCA
TAT
Found at i:466089 original size:70 final size:71
Alignment explanation
Indices: 465946--466091 Score: 165
Period size: 70 Copynumber: 2.1 Consensus size: 71
465936 ACTTCTACAG
* *
465946 ATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAAAAACAAATTTAAACT
1 ATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAAAAACAAATATAAACA
*
466011 TTACAA
66 TTAAAA
* * * * *
466017 ATAAAAA-AAATTATATTTT-AAAATTTAAATTCGTATAACTATATATTTAAAAA-TACTAT-AA
1 ATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAA-T-TATATCTAAAAACAAATATAAA
466078 CAATTAAAA
64 C-ATTAAAA
466087 ATAAA
1 ATAAA
466092 TCATACCTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
69 20 0.31
70 26 0.41
71 18 0.28
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (71 bp):
ATAAAAATAAATTATATTTTAAAAATTTAAACTCATATAATTATATCTAAAAACAAATATAAACA
TTAAAA
Found at i:466597 original size:25 final size:26
Alignment explanation
Indices: 466555--466605 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
466545 ATCATACTCA
*
466555 AAAAATAAATTTAAACTTTTACAAAT
1 AAAAATAAATTTAAACTTTTAAAAAT
*
466581 AAAAATAAA-TTATACTTTTAAAAAT
1 AAAAATAAATTTAAACTTTTAAAAAT
466606 TTAAACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTTTAAAAAT
Found at i:466609 original size:74 final size:73
Alignment explanation
Indices: 466513--466705 Score: 286
Period size: 74 Copynumber: 2.7 Consensus size: 73
466503 TCAATAATAC
**
466513 TAAATTATA-TTTTAAAAATTTAAACTCGTATAATCATACTCAAAAAATAAATTTAAACTTTTAC
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
466577 AAATAAAAA
66 AAAT-AAAA
* *
466586 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACCCAAAAAATAAATTTAAATTTTTAC
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
466651 AAATAAAA
66 AAATAAAA
* * *
466659 -AAATTACAC-TTTAAAAATTTAAATTTATATAATCATA-TCTAAAAATA
1 TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATA
466706 CTTTAACAAC
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
70 8 0.07
71 27 0.24
72 8 0.07
73 13 0.12
74 55 0.50
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (73 bp):
TAAATTATACTTTTAAAAATTTAAACTTATATAATCATACTCAAAAAATAAATTTAAACTTTTAC
AAATAAAA
Found at i:467251 original size:74 final size:74
Alignment explanation
Indices: 467130--467320 Score: 171
Period size: 74 Copynumber: 2.6 Consensus size: 74
467120 TTTATAATAC
* * * *
467130 TAAATTATACATTTAAAAATTTTTAACTCATATAATTATACTCAAAAATAAATTTTAACTTCTAC
1 TAAATTATACATTTAAAAATTTTAAACTCATATAATCATACTAAAAAATAAATTTAAACTTCTAC
*
467195 AAGTAAAAA
66 AAATAAAAA
* * * * * *
467204 TAAATTATA-TTTTCAAAAA-TTTAAACTCGTATAATCATGCTTAAAAAATCAATTTAAATTTTT
1 TAAATTATACATTT-AAAAATTTTAAACTCATATAATCATAC-TAAAAAATAAATTTAAACTTCT
467267 ACAAAT--AAA
64 ACAAATAAAAA
* * * *
467276 -AAATTAT--ATTAAAAAAATTTAAATTTATATAATCATATCTAAAAA
1 TAAATTATACATTTAAAAATTTTAAACTCATATAATCATA-CTAAAAA
467321 CACATTAATA
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
69 5 0.05
70 24 0.25
71 8 0.08
72 3 0.03
73 20 0.21
74 36 0.38
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (74 bp):
TAAATTATACATTTAAAAATTTTAAACTCATATAATCATACTAAAAAATAAATTTAAACTTCTAC
AAATAAAAA
Found at i:467545 original size:50 final size:49
Alignment explanation
Indices: 467471--467569 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
467461 CCTCAATTAC
* * * *
467471 TTGGGGGTGGGGTATTCAGCGACTCCCCTAAATAATAATTGTACCCTAAA
1 TTGGGGGTAGGGTATCCAACGACTCCCAT-AATAATAATTGTACCCTAAA
* * *
467521 TTGGGGGTAGGGTATCCAATGACTCCCATATTAATAATTGTACCTTAAA
1 TTGGGGGTAGGGTATCCAACGACTCCCATAATAATAATTGTACCCTAAA
467570 CCCTATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 18 0.43
50 24 0.57
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (49 bp):
TTGGGGGTAGGGTATCCAACGACTCCCATAATAATAATTGTACCCTAAA
Found at i:470502 original size:18 final size:18
Alignment explanation
Indices: 470479--470534 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
470469 AGAGAATTAG
*
470479 TGCTTGGCAGCGATTACA
1 TGCTTGGCAGAGATTACA
*
470497 TGCTTGGCAGAGACTACA
1 TGCTTGGCAGAGATTACA
470515 TGCTTGGCAGAGATTACA
1 TGCTTGGCAGAGATTACA
470533 TG
1 TG
470535 ATGCTCCTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
TGCTTGGCAGAGATTACA
Found at i:471294 original size:117 final size:117
Alignment explanation
Indices: 471172--471382 Score: 266
Period size: 117 Copynumber: 1.8 Consensus size: 117
471162 TATATATATA
* * * * * * *
471172 TATATTCAATGAATTATATTCTTAATTTGTAATTTGTGACT-TTTTGTTA-TTCTTAAGGCTAAC
1 TATATTAAATGAATTACACTC-CAATCTGTAATTTGTGA-TATGTTGTTATTTATTAAGGCTAA-
471235 A-TACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
63 AGTACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
* *
471289 TATATTAAATGAATTACACTCCCATCTGTAATTTGTGATATGTTGTTATTTATTAAGGTTAAAGT
1 TATATTAAATGAATTACACTCCAATCTGTAATTTGTGATATGTTGTTATTTATTAAGGCTAAAGT
* * *
471354 ATTAAAGAAATCCTTGTATGTTTTAAAGT
66 ACTAAAGAAATCCTTATATATTTTAAAGT
471383 TACATTTATA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
115 1 0.01
116 22 0.28
117 56 0.71
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (117 bp):
TATATTAAATGAATTACACTCCAATCTGTAATTTGTGATATGTTGTTATTTATTAAGGCTAAAGT
ACTAAAGAAATCCTTATATATTTTAAAGTGAACTAAATTTTCACTACCTTTC
Found at i:473141 original size:5 final size:5
Alignment explanation
Indices: 473133--473173 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
473123 AAATATTTTA
* *
473133 TTAAT TTAAA TTAAT TTAAT TTAAT TTAAA TTAAT ATTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT -TTAAT
473174 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:473147 original size:10 final size:10
Alignment explanation
Indices: 473132--473172 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
473122 TAAATATTTT
473132 ATTAATTTAA
1 ATTAATTTAA
473142 ATTAATTTAA
1 ATTAATTTAA
*
473152 TTTAATTTAA
1 ATTAATTTAA
473162 ATTAATATTAA
1 ATTAAT-TTAA
473173 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 24 0.86
11 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:473158 original size:20 final size:21
Alignment explanation
Indices: 473133--473173 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
473123 AAATATTTTA
473133 TTAATTTAAATTAAT-TTAAT
1 TTAATTTAAATTAATATTAAT
473153 TTAATTTAAATTAATATTAAT
1 TTAATTTAAATTAATATTAAT
473174 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATTTAAATTAATATTAAT
Found at i:473238 original size:50 final size:51
Alignment explanation
Indices: 473145--473289 Score: 135
Period size: 50 Copynumber: 2.9 Consensus size: 51
473135 AATTTAAATT
**
473145 AATTTAATTTAATT-TAAAT--T-AATATTAATAATTAAAAAATATTTTTATATA
1 AATTTAA-TTAATTATAAATAATAAATATTAATAA-TAAAATTTATTTTT-TA-A
473196 AATTTAATT-A-TAT-AATATATAAATATTAAT-ATAAAATTTATTTTTTAA
1 AATTTAATTAATTATAAATA-ATAAATATTAATAATAAAATTTATTTTTTAA
* * *
473244 TATTTTATTAATTATAAATAATAAATATAAATAATATAAATTTATT
1 AATTTAATTAATTATAAATAATAAATATTAATAATA-AAATTTATT
473290 AAATCAAATC
Statistics
Matches: 79, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
48 12 0.15
49 5 0.06
50 28 0.35
51 16 0.20
52 18 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (51 bp):
AATTTAATTAATTATAAATAATAAATATTAATAATAAAATTTATTTTTTAA
Found at i:473933 original size:18 final size:17
Alignment explanation
Indices: 473892--473934 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
473882 AAAATTAAAT
*
473892 ATATTTTGTATATTTTA
1 ATATTTTGTATATATTA
*
473909 ATAATTTTTTATATGATTA
1 AT-ATTTTGTATAT-ATTA
473928 ATATTTT
1 ATATTTT
473935 AACAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 15 0.68
19 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
ATATTTTGTATATATTA
Found at i:474293 original size:23 final size:23
Alignment explanation
Indices: 474267--474313 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
474257 AATATTTTTA
*
474267 ATATAAAT-TTAATTATAAAATAT
1 ATATAAATATTAA-TAAAAAATAT
474290 ATATAAATATTAATAAAAAATAT
1 ATATAAATATTAATAAAAAATAT
474313 A
1 A
474314 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAATATTAATAAAAAATAT
Found at i:474397 original size:25 final size:24
Alignment explanation
Indices: 474347--474400 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
474337 TAATATGAAT
474347 AAAATAAATAAATCAAATCAAGTTA
1 AAAATAAATAAATCAAAT-AAGTTA
*
474372 AAAATAAAATAAAATCAAAT-ATTTA
1 AAAAT-AAAT-AAATCAAATAAGTTA
474397 AAAA
1 AAAA
474401 AATTTTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 13 0.50
26 4 0.15
27 9 0.35
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAATAAATCAAATAAGTTA
Found at i:475617 original size:29 final size:28
Alignment explanation
Indices: 475577--475653 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
475567 ACACATATAC
*
475577 ATAAAGTA-AAAAATAATTTAAATATATT
1 ATAAA-TATAAAAATAATTTAAATATAAT
* **
475605 ATGATATATAAAAATAA-AAAAATATAAT
1 AT-AAATATAAAAATAATTTAAATATAAT
475633 ATAAATATAAAAAT-ATTTAAA
1 ATAAATATAAAAATAATTTAAA
475654 ATTTTATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.03
27 14 0.36
28 14 0.36
29 10 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
ATAAATATAAAAATAATTTAAATATAAT
Found at i:475654 original size:28 final size:28
Alignment explanation
Indices: 475577--475664 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
475567 ACACATATAC
*
475577 ATAAAGTA-AAAAATAATTT-AAATATATT
1 ATAAA-TATAAAAAT-ATTTAAAATATAAT
* **
475605 ATGATATATAAAAATA-AAAAAATATAAT
1 AT-AAATATAAAAATATTTAAAATATAAT
* *
475633 ATAAATATAAAAATATTTAAAATTTTAT
1 ATAAATATAAAAATATTTAAAATATAAT
475661 ATAA
1 ATAA
475665 TACAAATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
27 12 0.26
28 27 0.57
29 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAAATATAAAAATATTTAAAATATAAT
Found at i:475699 original size:13 final size:13
Alignment explanation
Indices: 475673--475721 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
475663 AATACAAATT
**
475673 TAATATATAAATA
1 TAATATATTTATA
475686 TAATATATTTATA
1 TAATATATTTATA
*
475699 TATTATAATTTATA
1 TAATAT-ATTTATA
475713 TAAATATAT
1 T-AATATAT
475722 AACATTGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 10 0.33
15 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATATATTTATA
Found at i:475943 original size:92 final size:90
Alignment explanation
Indices: 475776--475946 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 90
475766 TTCAAAAAAA
* * * * *
475776 AGTAATAGCAAGTCGTTACCGTTACTAAGAAGTTAATTGCTTCAGTCTGTATTCTTATTCACCTA
1 AGTAATAGCAAGTCGTCACCGTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCACCTA
475841 CCCTCTACTAATGACTTTTTGAAGT
66 CCCTCTACTAATGACTTTTTGAAGT
* * * *
475866 AGTAATAGCAAGTCGTCACCGAAGTGAGTAAAAAGTCAATTGCTTCTGTC-GGATTGTTATTTAC
1 AGTAATAGCAAGTCGTCACC---GTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCAC
*
475930 CTACCCTTTACTAATGA
63 CTACCCTCTACTAATGA
475947 AAGTAAAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 19 0.28
92 27 0.40
93 22 0.32
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (90 bp):
AGTAATAGCAAGTCGTCACCGTGACTAAAAAGTCAATTGCTTCAGTCTGGATTCTTATTCACCTA
CCCTCTACTAATGACTTTTTGAAGT
Found at i:476264 original size:14 final size:14
Alignment explanation
Indices: 476245--476276 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
476235 TCATAGTTTG
476245 ATTTTATAATTGTT
1 ATTTTATAATTGTT
*
476259 ATTTTATAATTTTT
1 ATTTTATAATTGTT
476273 ATTT
1 ATTT
476277 ATTTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
ATTTTATAATTGTT
Found at i:480401 original size:6 final size:6
Alignment explanation
Indices: 480390--480418 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
480380 TAGAGGTCCT
480390 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
480419 TGTCTTTATA
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:481874 original size:21 final size:21
Alignment explanation
Indices: 481840--481906 Score: 91
Period size: 22 Copynumber: 3.2 Consensus size: 21
481830 TCCCTTTTTT
481840 TTAAATT-TTAATTAATTATA
1 TTAAATTATTAATTAATTATA
*
481860 TTAAATTAATAATTAATTATA
1 TTAAATTATTAATTAATTATA
* *
481881 TTAAAAATATTAAGTAATTATA
1 TT-AAATTATTAATTAATTATA
481903 TTAA
1 TTAA
481907 TAAATAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
20 7 0.17
21 16 0.39
22 18 0.44
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAAATTATTAATTAATTATA
Found at i:487696 original size:28 final size:29
Alignment explanation
Indices: 487633--487696 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
487623 ACACTAGTGG
*
487633 TCAATT-AAAATTTTATATATGATAAAAT
1 TCAATTAAAAATTTAATATATGATAAAAT
*
487661 TCATTTAAAAATTTAAT-TATG-TAAAAT
1 TCAATTAAAAATTTAATATATGATAAAAT
487688 TCTAATTAA
1 TC-AATTAA
487697 GAGACCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 14 0.45
29 9 0.29
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
TCAATTAAAAATTTAATATATGATAAAAT
Found at i:488661 original size:71 final size:71
Alignment explanation
Indices: 488571--488703 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 71
488561 AAAATATTAT
* * *
488571 ACCTAAGGATTATCTTTTACTTAAACT-TAGAGATAGCATATTTTTTAACTTGTAAAATTGGTAC
1 ACCTAAGGATTATCTTTTACTTAAA-TGCAGAGATAGCATATTTTCTAACTTGCAAAATTGGTAC
488635 TTATTGA
65 TTATTGA
* *
488642 ACCTAAGTATTAT-TCTTTACTTAAATGCAGAGATAGCATATTTTCTCACTTGCAAAATTGGT
1 ACCTAAGGATTATCT-TTTACTTAAATGCAGAGATAGCATATTTTCTAACTTGCAAAATTGGT
488704 TGCTACTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 2 0.04
71 53 0.96
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (71 bp):
ACCTAAGGATTATCTTTTACTTAAATGCAGAGATAGCATATTTTCTAACTTGCAAAATTGGTACT
TATTGA
Found at i:493101 original size:25 final size:24
Alignment explanation
Indices: 493066--493146 Score: 89
Period size: 25 Copynumber: 3.5 Consensus size: 24
493056 GATTTTTTCA
*
493066 ATTTTAGATATATTTTATTAAATGT
1 ATTTTAAATATATTTTATTAAAT-T
*
493091 ATTTTAAATATGTTTTATTAAA-T
1 ATTTTAAATATATTTTATTAAATT
*
493114 ATATT---TATATTTTATTAAATAT
1 ATTTTAAATATATTTTATTAAAT-T
493136 ATTTTAAATAT
1 ATTTTAAATAT
493147 TAATTTGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 13 0.28
22 5 0.11
23 5 0.11
25 23 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTTAAATATATTTTATTAAATT
Found at i:493128 original size:20 final size:20
Alignment explanation
Indices: 493074--493139 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 20
493064 CAATTTTAGA
*
493074 TATATTTTATTAAATGTATTT
1 TATATTTTATTAAATATA-TT
493095 TAAATATGTTTTATTAAATATATT
1 T--ATA--TTTTATTAAATATATT
493119 TATATTTTATTAAATATATT
1 TATATTTTATTAAATATATT
493139 T
1 T
493140 TAAATATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 17 0.43
21 1 0.03
22 3 0.08
23 3 0.08
24 3 0.08
25 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATTTTATTAAATATATT
Found at i:493141 original size:14 final size:14
Alignment explanation
Indices: 493073--493124 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
493063 TCAATTTTAG
493073 ATATATTTTATTAA
1 ATATATTTTATTAA
*
493087 ATGTA--TT-TTAA
1 ATATATTTTATTAA
*
493098 ATATGTTTTATTAA
1 ATATATTTTATTAA
493112 ATATATTTATATT
1 ATATATTT-TATT
493125 TTATTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 7 0.23
12 2 0.07
13 2 0.07
14 15 0.50
15 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
ATATATTTTATTAA
Found at i:494839 original size:11 final size:10
Alignment explanation
Indices: 494832--494861 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
494822 GAAAAAATAC
494832 AAAAAAAAGA
1 AAAAAAAAGA
494842 AAAAAAGAAGA
1 AAAAAA-AAGA
494853 AAAAAAAAG
1 AAAAAAAAG
494862 GGGTGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:495267 original size:20 final size:20
Alignment explanation
Indices: 495242--495340 Score: 108
Period size: 20 Copynumber: 4.8 Consensus size: 20
495232 TTTTTACCCA
* *
495242 AATGTATCGAGACATTTTTC
1 AATGTATCGATACATTCTTC
*** *
495262 AATGTATCGATACATGGATG
1 AATGTATCGATACATTCTTC
495282 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
495302 AATGTATCGATACATTCTACCC
1 AATGTATCGATACATTCT--TC
495324 AGATGTATCGATACATT
1 A-ATGTATCGATACATT
495341 GTTCGGGCCA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
20 49 0.74
22 2 0.03
23 15 0.23
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:500757 original size:19 final size:19
Alignment explanation
Indices: 500732--500815 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
500722 ATTTCAACGA
*
500732 TTTGTATCGATACATTAGT
1 TTTGTATCGATACATAAGT
*
500751 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
500766 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
500783 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
500802 TTTGTATCGATACA
1 TTTGTATCGATACA
500816 ATGTACTACT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 1 0.02
19 43 0.75
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:500770 original size:32 final size:32
Alignment explanation
Indices: 500734--500796 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
500724 TTCAACGATT
*
500734 TGTATCGATACATTAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
500766 TGTATCGATACATAAGTTTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
500797 TAAGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:500771 original size:13 final size:13
Alignment explanation
Indices: 500753--500777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500743 ACATTAGTGT
500753 TGTATCGATACAA
1 TGTATCGATACAA
500766 TGTATCGATACA
1 TGTATCGATACA
500778 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:500886 original size:13 final size:13
Alignment explanation
Indices: 500868--500892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500858 ATTACTCAAA
500868 TGTATCGATACAT
1 TGTATCGATACAT
500881 TGTATCGATACA
1 TGTATCGATACA
500893 CTGCTCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:504553 original size:13 final size:13
Alignment explanation
Indices: 504535--504560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
504525 TACACCAAGT
504535 ATGTATCGATACA
1 ATGTATCGATACA
504548 ATGTATCGATACA
1 ATGTATCGATACA
504561 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:504558 original size:32 final size:33
Alignment explanation
Indices: 504517--504580 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
504507 TAGCCAAACT
**
504517 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
504549 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
504581 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:510764 original size:13 final size:13
Alignment explanation
Indices: 510746--510784 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
510736 ACATTTTTCT
510746 TTGTATCGATACA
1 TTGTATCGATACA
510759 TTGTATCGATACA
1 TTGTATCGATACA
*
510772 CTGTATCGATACA
1 TTGTATCGATACA
510785 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:510949 original size:20 final size:20
Alignment explanation
Indices: 510906--510952 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
510896 AAATCTTTTG
510906 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
510927 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
510947 CAAAAT
1 CAAAAT
510953 CAGATTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:511077 original size:13 final size:13
Alignment explanation
Indices: 511059--511083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
511049 TTAGAAAGTG
511059 TTTTTGAACCAAA
1 TTTTTGAACCAAA
511072 TTTTTGAACCAA
1 TTTTTGAACCAA
511084 TCCTTTCCCA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTTGAACCAAA
Found at i:513337 original size:13 final size:13
Alignment explanation
Indices: 513319--513344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
513309 TACACCAAGT
513319 ATGTATCGATACA
1 ATGTATCGATACA
513332 ATGTATCGATACA
1 ATGTATCGATACA
513345 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:513363 original size:34 final size:32
Alignment explanation
Indices: 513301--513365 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
513291 TAGCCAAACT
**
513301 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
513333 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
513366 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:519830 original size:33 final size:33
Alignment explanation
Indices: 519788--519850 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
519778 AGGAGATAAT
519788 AGTCACGTTCATCAACACCCTGTGAGCTCCAAC
1 AGTCACGTTCATCAACACCCTGTGAGCTCCAAC
519821 AGTCACGTTCATCAACACCCTGTGAGCTCC
1 AGTCACGTTCATCAACACCCTGTGAGCTCC
519851 TTATTATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (33 bp):
AGTCACGTTCATCAACACCCTGTGAGCTCCAAC
Found at i:523421 original size:28 final size:28
Alignment explanation
Indices: 522810--523742 Score: 835
Period size: 27 Copynumber: 33.6 Consensus size: 28
522800 TCACTGGCAT
* *
522810 CTTTTTAAGTCCACAACTCAGTGGCATTCC
1 CTTTTAAAGTCCACAACTCCGTGGCA--CC
*
522840 CTTTT-AAGTCCACAACTCTGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
522866 CTTTTTAAGTCCACAACACTGTGACA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
522893 CTTTTTAAGTCCATAACTCCATGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
522920 ATTTTTAAGTCCACAACTCCGTGGAATTC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
* *
522949 CTTTTAAAGTCCATAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
522977 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523005 CTTTT-AAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
523032 CTTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523059 CTTTT-AAGTCTACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
523086 CTTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523113 CTTTT-AAGTCGACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
523140 CTTTT-AAGTCCACAACTCCGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
523166 CTTTTTAAGTCCACAACTCAGAGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523193 CTTTTTAAGTCCACAACTCCGTGGCATTCC
1 CTTTTAAAGTCCACAACTCCGTGGCA--CC
* * *
523223 CTTGTAAA-TCCACAACTCTGTGGCACA
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
523250 CTTTAAAAGTCCACAACTTCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523278 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
523306 CTTTTAAAGTCCACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523334 CTTTT-AAGTCCATAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
523361 TTTTTAAAGTCCATAACACTGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523389 TTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
523417 CTTTT----T-CACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
**
523440 CTTTTAAAGTCCGTAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
**
523468 CTTTT-AAGTCCACAACTTTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
523495 CTTTTTAAGTCCACAAGTCAGTGGCATTCC
1 CTTTTAAAGTCCACAACTCCGTGGCA--CC
* * * **
523525 CTTTTAAAGCCCATAAGTTAGTGGCACCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
* * * * *
523554 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
523582 TTTTTCAAAGTCCACACAAATCGGTGGCAACT
1 CTTTT-AAAGT-C-CACAACTCCGTGGC-ACC
* * ** *
523614 CTTTTCAAAGCCCACAAGTCAATGGCATC
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
* * * ** *
523643 CTTTCAAAGCCCACAAGTCAATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * * *
523671 ATTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
523699 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
523727 ATTTCAAAGCCCACAA
1 CTTTTAAAGTCCACAA
523743 GTTAGTGGCA
Statistics
Matches: 792, Mismatches: 90, Indels: 44
0.86 0.10 0.05
Matches are distributed among these distances:
23 21 0.03
24 1 0.00
26 12 0.02
27 310 0.39
28 283 0.36
29 92 0.12
30 48 0.06
31 13 0.02
32 12 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:523430 original size:23 final size:23
Alignment explanation
Indices: 523400--523444 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
523390 TTTTAAAGTC
*
523400 CACAACTCCGTGGCACCCTTTTT
1 CACAACTCCATGGCACCCTTTTT
523423 CACAACTCCATGGCACCCTTTT
1 CACAACTCCATGGCACCCTTTT
523445 AAAGTCCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.40, G:0.11, T:0.29
Consensus pattern (23 bp):
CACAACTCCATGGCACCCTTTTT
Found at i:523743 original size:28 final size:28
Alignment explanation
Indices: 523505--524536 Score: 1161
Period size: 28 Copynumber: 36.2 Consensus size: 28
523495 CTTTTTAAGT
* *
523505 CCACAAGTCAGTGGCATTCCCTTTTAAAGC
1 CCACAAGTCAGTGGCA-T-CATTTCAAAGC
* * * *
523535 CCATAAGTTAGTGGCACCCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCATTTCAAAGC
**
523564 CCACAAGTCAGTGGCACTTTTTTCAAAGTC
1 CCACAAGTCAGTGGCA-TCATTTCAAAG-C
* * *
523594 CACACAAATCGGTGGCAACTCTTTTCAAAGC
1 C-CACAAGTCAGTGGC-A-TCATTTCAAAGC
* *
523625 CCACAAGTCAATGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
523653 CCACAAGTCAATGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
523681 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
523709 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523737 CCACAAGTTAGTGGCAGCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
** * *
523765 CCACAAGTCAGTGGTGTCCTTTCATAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523793 CCATAAGTTAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523821 TCACAAGTTAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
523849 CCACAAGTTAGTGCCATCATTTCAAAAC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523877 CCAGAAGTCAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523905 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
523933 CCACAAGGCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
523961 CCACAAGTCAGTGGCATCCTTTCAAAGCC
1 CCACAAGTCAGTGGCATCATTTCAAAG-C
*
523990 CATAAGTCAGCAAGTCAGTGGCATCCTTTCAAAGC
1 C------CA-CAAGTCAGTGGCATCATTTCAAAGC
* *
524025 CCACAAGTTAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
524053 CCACAAGTCAATGGCACCATTTTAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
524081 CCACAAGTTAGTAGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524109 CCACAAGTCAGTGGCAACATTTCGAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524137 CTACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
524165 TCACAAGTCAGTGGCATCCTTTCGAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
524193 CCACAAGTCAGTGGCATCATTTGAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
524221 CCACAAGTCAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
524249 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524277 CCACAAGTCAATGGCATC-CTT-AAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
524303 CCACAAGTTAGTGGCATCCTTT-AAAAC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
*
524330 CCACAAGTCAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524358 CCACAACTCAGTGGCACCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524386 CCACAAGTTAGTGGCCTCATTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* *
524414 CCATAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * * *
524442 CCATAAGTCAGTGGCACCATCTCAAAAC
1 CCACAAGTCAGTGGCATCATTTCAAAGC
* * *
524470 CCACAAGTCAATGGCTTACCCTTTCAAAGCC
1 CCACAAGTCAGTGGC--ATCATTTCAAAG-C
* * *
524501 CACACAAGTCGGTGGGAACTCTTTTCAAAGC
1 C-CACAAGTCAGT-GGCA-TCATTTCAAAGC
524532 CCACA
1 CCACA
524537 CAAGTTAGTG
Statistics
Matches: 869, Mismatches: 114, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
26 21 0.02
27 27 0.03
28 664 0.76
29 38 0.04
30 40 0.05
31 19 0.02
32 30 0.03
33 2 0.00
35 4 0.00
36 24 0.03
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCATTTCAAAGC
Found at i:524011 original size:36 final size:36
Alignment explanation
Indices: 523964--524032 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
523954 TCAAAGCCCA
*
523964 CAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAG
1 CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAG
524000 CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGT
1 CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGT
524033 TAGTGGCACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (36 bp):
CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAG
Found at i:532120 original size:38 final size:38
Alignment explanation
Indices: 531940--532120 Score: 114
Period size: 38 Copynumber: 4.7 Consensus size: 38
531930 CAAGCTATGA
* * * * **
531940 ACAAAAACCATTATTTTAAACCGGTGATACAGTTCGAA-
1 ACAAAAATCACTATTCTAAACCGGTGGTATGGTTC-AAT
* * * *
531978 ACAAAAACCACTATTCTAAACCAGCGGTAAGGTTCGAA-
1 ACAAAAATCACTATTCTAAACCGGTGGTATGGTTC-AAT
** * * * *
532016 ATGAAAATTACTATTCTAAAACCGATAGCATGGTTCAAT
1 ACAAAAATCACTATTCT-AAACCGGTGGTATGGTTCAAT
* * * * *
532055 ACAAAAAATTACTATTTTTATCTGGTGGTATGGTTCAAT
1 AC-AAAAATCACTATTCTAAACCGGTGGTATGGTTCAAT
*
532094 ACAAAAATCACTATTCTTAACCGGTGG
1 ACAAAAATCACTATTCTAAACCGGTGG
532121 CACGGTTTGA
Statistics
Matches: 110, Mismatches: 30, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
38 67 0.61
39 30 0.27
40 13 0.12
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (38 bp):
ACAAAAATCACTATTCTAAACCGGTGGTATGGTTCAAT
Done.