Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2234.1
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: 276128
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.32
Warning! 12491 characters in sequence are not A, C, G, or T
Found at i:2516 original size:12 final size:12
Alignment explanation
Indices: 2493--2533 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
2483 TGGAGGTAAA
2493 AAAAAGCAAAAAC
1 AAAAAGC-AAAAC
2506 AAAAAGCAAAAC
1 AAAAAGCAAAAC
*
2518 AAAAAACAAAAC
1 AAAAAGCAAAAC
2530 AAAA
1 AAAA
2534 CAAACCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 20 0.74
13 7 0.26
ACGTcount: A:0.80, C:0.15, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAGCAAAAC
Found at i:2521 original size:17 final size:17
Alignment explanation
Indices: 2500--2570 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 17
2490 AAAAAAAAGC
2500 AAAAACAAAAAGCAAAACA
1 AAAAAC-AAAA-CAAAACA
2519 AAAAACAAAACAAAAC-
1 AAAAACAAAACAAAACA
**
2535 AAACCCAAAA-AAAACA
1 AAAAACAAAACAAAACA
* *
2551 AGAAA-ATAA-AAAACA
1 AAAAACAAAACAAAACA
2566 AAAAA
1 AAAAA
2571 ACTCTACCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 18 0.41
16 10 0.23
17 6 0.14
18 4 0.09
19 6 0.14
ACGTcount: A:0.80, C:0.15, G:0.03, T:0.01
Consensus pattern (17 bp):
AAAAACAAAACAAAACA
Found at i:3406 original size:45 final size:46
Alignment explanation
Indices: 3331--3418 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
3321 TTTATTTATT
*
3331 TTTTGTATTTTTGACAAAATACGCCATCTTGATTAATTTATTCTCA
1 TTTTGTATTTCTGACAAAATACGCCATCTTGATTAATTTATTCTCA
** *
3377 TTTTGTA-TTCTGACAAAATTTGCTATCTTGATTAATTTATTC
1 TTTTGTATTTCTGACAAAATACGCCATCTTGATTAATTTATTC
3419 ATTTCGAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 31 0.82
46 7 0.18
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (46 bp):
TTTTGTATTTCTGACAAAATACGCCATCTTGATTAATTTATTCTCA
Found at i:3976 original size:44 final size:44
Alignment explanation
Indices: 3909--4116 Score: 120
Period size: 44 Copynumber: 4.6 Consensus size: 44
3899 AAACTACAAG
* * * *
3909 TCTTATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGCAGTGGAGTAGATTGAAGATAGTAGA
* * * * **
3953 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGGCGAA
1 TCTTATCTCCCTAAGCAGCAGTGGAGTAGATTGAAGATAGTAG-A
* * * * *
3997 TCTTATCTTCCC-AAG-A-TAGTAGGAAGAAGATTTAAGCTACCAGCTACCA
1 TCTTATC-TCCCTAAGCAGCAGT-GG-AGTAGATTGAAG--A-TAG-TA-GA
* *
4046 GT-TCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATGGTAGA
1 -TCT-TATCTCCCTAAGCAGCAGTGGAGTAGATTGAAGATAGTAGA
*
4091 TCTTATCTCCCTAAGCAGAAGTGGAG
1 TCTTATCTCCCTAAGCAGCAGTGGAG
4117 CGGATCAAAG
Statistics
Matches: 124, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
42 4 0.03
43 5 0.04
44 74 0.60
45 6 0.05
46 3 0.02
47 1 0.01
48 2 0.02
49 6 0.05
50 17 0.14
51 3 0.02
52 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGCAGTGGAGTAGATTGAAGATAGTAGA
Found at i:4160 original size:138 final size:131
Alignment explanation
Indices: 3907--4234 Score: 494
Period size: 138 Copynumber: 2.5 Consensus size: 131
3897 TGAAACTACA
* * *
3907 AGTCTTATCTCCCTGAGAAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGA
* *
3972 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGATAGTAGGAAGAAGATTTAAGCTAC
66 AGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGATAGTAGGAAGAAGATTTAAG----
4037 CAGCTACC
127 C--C-ACC
* * *
4045 AGTTCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATGGTAGATCTTATCTCCCTAAGCAGA
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGA
* * *
4110 AGTGGAGCGGATCAAAGACGACGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGATAGTAGGAAGAAGATTTAAGCCAC
4175 C
131 C
4176 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTA
1 AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTA
4235 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
131 59 0.34
132 1 0.01
134 1 0.01
138 115 0.65
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (131 bp):
AGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGA
AGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCAAGATAGTAGGAAGAAGATTTAAGCCAC
C
Found at i:35872 original size:304 final size:304
Alignment explanation
Indices: 35374--35982 Score: 1218
Period size: 304 Copynumber: 2.0 Consensus size: 304
35364 AACAATAATT
35374 GGTGGTCTGTGTGTGTACTTATTTTACTACAATCATTTTAAATTACCCCCTTTTTTTCTTACAGC
1 GGTGGTCTGTGTGTGTACTTATTTTACTACAATCATTTTAAATTACCCCCTTTTTTTCTTACAGC
35439 AATTCCTTAATTGTCGGCTAAATTCCTTTGCTTTGTTTTTTTTTTTTTGTAAATTTTTAAAAACT
66 AATTCCTTAATTGTCGGCTAAATTCCTTTGCTTTGTTTTTTTTTTTTTGTAAATTTTTAAAAACT
35504 ATTTTAACAAAATTTCGCCCCTAGTTATCCATATTTTCCGACCATATTTTTTTTAGTTATATTTA
131 ATTTTAACAAAATTTCGCCCCTAGTTATCCATATTTTCCGACCATATTTTTTTTAGTTATATTTA
35569 TTAAATAATTTTATATTTGATTCTCATACCTCATCCAAAGAAACGGAGTTTAAGTTGATAAAACT
196 TTAAATAATTTTATATTTGATTCTCATACCTCATCCAAAGAAACGGAGTTTAAGTTGATAAAACT
35634 CGAATTACTTTATAGAGTTTATATTAATGTGTTTGGAATAGCGA
261 CGAATTACTTTATAGAGTTTATATTAATGTGTTTGGAATAGCGA
35678 GGTGGTCTGTGTGTGTACTTATTTTACTACAATCATTTTAAATTACCCCCTTTTTTTCTTACAGC
1 GGTGGTCTGTGTGTGTACTTATTTTACTACAATCATTTTAAATTACCCCCTTTTTTTCTTACAGC
35743 AATTCCTTAATTGTCGGCTAAATTCCTTTGCTTTGTTTTTTTTTTTTTGTAAATTTTTAAAAACT
66 AATTCCTTAATTGTCGGCTAAATTCCTTTGCTTTGTTTTTTTTTTTTTGTAAATTTTTAAAAACT
35808 ATTTTAACAAAATTTCGCCCCTAGTTATCCATATTTTCCGACCATATTTTTTTTAGTTATATTTA
131 ATTTTAACAAAATTTCGCCCCTAGTTATCCATATTTTCCGACCATATTTTTTTTAGTTATATTTA
35873 TTAAATAATTTTATATTTGATTCTCATACCTCATCCAAAGAAACGGAGTTTAAGTTGATAAAACT
196 TTAAATAATTTTATATTTGATTCTCATACCTCATCCAAAGAAACGGAGTTTAAGTTGATAAAACT
35938 CGAATTACTTTATAGAGTTTATATTAATGTGTTTGGAATAGCGA
261 CGAATTACTTTATAGAGTTTATATTAATGTGTTTGGAATAGCGA
35982 G
1 G
35983 AGCCTTAAAA
Statistics
Matches: 305, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
304 305 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.46
Consensus pattern (304 bp):
GGTGGTCTGTGTGTGTACTTATTTTACTACAATCATTTTAAATTACCCCCTTTTTTTCTTACAGC
AATTCCTTAATTGTCGGCTAAATTCCTTTGCTTTGTTTTTTTTTTTTTGTAAATTTTTAAAAACT
ATTTTAACAAAATTTCGCCCCTAGTTATCCATATTTTCCGACCATATTTTTTTTAGTTATATTTA
TTAAATAATTTTATATTTGATTCTCATACCTCATCCAAAGAAACGGAGTTTAAGTTGATAAAACT
CGAATTACTTTATAGAGTTTATATTAATGTGTTTGGAATAGCGA
Found at i:37457 original size:57 final size:57
Alignment explanation
Indices: 37389--37504 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
37379 TTCATTTTTA
37389 ATATTTTTTATGAATTTTAAATTATTTATTGACGTAACATATAAGACAAATAATAAC
1 ATATTTTTTATGAATTTTAAATTATTTATTGACGTAACATATAAGACAAATAATAAC
* * *
37446 ATATTTTTTATGATTTTTAAATTATTTATTGACGTGACATATAAGACAAATAATGAC
1 ATATTTTTTATGAATTTTAAATTATTTATTGACGTAACATATAAGACAAATAATAAC
37503 AT
1 AT
37505 GCAGGTTGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (57 bp):
ATATTTTTTATGAATTTTAAATTATTTATTGACGTAACATATAAGACAAATAATAAC
Found at i:49549 original size:116 final size:116
Alignment explanation
Indices: 49362--49577 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 116
49352 CTGTCGATGC
* * * * *
49362 AGGAAGGCAAGATCTGTTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
* *
49427 CGATCTGCTTCGCTGTTGACGCAGGAAAGCAAGATGCTTCGCTATTAACAT
66 CGATCTGCTTCGCTATTAACGCAGGAAAGCAAGATGCTTCGCTATTAACAT
*
49478 AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
* * *
49543 TGATCTGCTTTGCTATTAACGCAGGAAGGCAAGAT
66 CGATCTGCTTCGCTATTAACGCAGGAAAGCAAGAT
49578 CTGCTATCTT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (116 bp):
AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTTT
CGATCTGCTTCGCTATTAACGCAGGAAAGCAAGATGCTTCGCTATTAACAT
Found at i:49607 original size:87 final size:87
Alignment explanation
Indices: 49461--49635 Score: 269
Period size: 87 Copynumber: 2.0 Consensus size: 87
49451 GAAAGCAAGA
* * *
49461 TGCTTCGCTATTAACATAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGG
1 TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
*
49526 AGGCAAGGCTTCGTTTTTGATC
66 AGGCAAGGCTTCGTTTTTCATC
* * * *
49548 TGCTTTGCTATTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGA
1 TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
*
49613 AGGCAAGGCTTTGTTTTTCATC
66 AGGCAAGGCTTCGTTTTTCATC
49635 T
1 T
49636 TCACTGATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
AGGCAAGGCTTCGTTTTTCATC
Found at i:50870 original size:7 final size:7
Alignment explanation
Indices: 50858--50890 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
50848 TAGCCTCTCT
50858 ATTTTTC
1 ATTTTTC
50865 ATTTTTC
1 ATTTTTC
*
50872 A-TTCTC
1 ATTTTTC
50878 ATTTTTC
1 ATTTTTC
50885 ATTTTT
1 ATTTTT
50891 TTTGAAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTC
Found at i:50881 original size:13 final size:13
Alignment explanation
Indices: 50863--50887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50853 TCTCTATTTT
50863 TCATTTTTCATTC
1 TCATTTTTCATTC
50876 TCATTTTTCATT
1 TCATTTTTCATT
50888 TTTTTTGAAA
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:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATTTTTCATTC
Found at i:51302 original size:29 final size:28
Alignment explanation
Indices: 51259--51344 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
51249 TCTTTTCATA
*
51259 TTTTATTTTAACTTTGATTGATTT-CTTT
1 TTTTATTTTGACTTTGATT-ATTTACTTT
* *
51287 TTTTACTTTTGACTTTGATTTTTTATTTT
1 TTTTA-TTTTGACTTTGATTATTTACTTT
* *
51316 TTTTATTTTGATTTTGATTTTTTTACTTT
1 TTTTATTTTGACTTTGA-TTATTTACTTT
51345 GATTTTTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 19 0.38
29 31 0.62
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (28 bp):
TTTTATTTTGACTTTGATTATTTACTTT
Found at i:51316 original size:20 final size:19
Alignment explanation
Indices: 51285--51357 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
51275 ATTGATTTCT
*
51285 TTTTTTACTTTTGACTTTGA
1 TTTTTTA-TTTTTACTTTGA
*
51305 TTTTTTATTTTTTTTATTTTGA
1 TTTTTTA---TTTTTACTTTGA
51327 TTTTGATT-TTTTTACTTTGA
1 TTTT--TTATTTTTACTTTGA
*
51347 TTTTTTCTTTT
1 TTTTTTATTTT
51358 CTTTTTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
18 2 0.05
19 4 0.09
20 22 0.50
22 14 0.32
24 2 0.05
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTTATTTTTACTTTGA
Found at i:51376 original size:46 final size:42
Alignment explanation
Indices: 51293--51385 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 42
51283 CTTTTTTTAC
*
51293 TTTTGACTTTGATTTTTTATTTTTTTTATTTTGATTTTGATT
1 TTTTTACTTTGATTTTTTATTTTTTTTATTTTGATTTTGATT
* *
51335 TTTTTACTTTGATTTTTTCTTTTCTTTTTTGTTTTTGATTTTGATT
1 TTTTTACTTTGA-TTTTT-TATT-TTTTTT-ATTTTGATTTTGATT
51381 TTTTT
1 TTTTT
51386 TTGAATTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 11 0.25
43 5 0.11
44 3 0.07
45 6 0.14
46 19 0.43
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.76
Consensus pattern (42 bp):
TTTTTACTTTGATTTTTTATTTTTTTTATTTTGATTTTGATT
Found at i:54091 original size:6 final size:6
Alignment explanation
Indices: 54069--54103 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
54059 TTCCAAATGA
54069 TTTCAT TTCTCCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TT-T-CAT TTTCAT TTTCAT TTTCAT TTT
54104 TATATTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCAT
Found at i:63511 original size:18 final size:18
Alignment explanation
Indices: 63488--63522 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
63478 AATCATCTTC
63488 GTATTGAAGAAGAGTATA
1 GTATTGAAGAAGAGTATA
63506 GTATTGAAGAAGAGTAT
1 GTATTGAAGAAGAGTAT
63523 CGAAAACAAG
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:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (18 bp):
GTATTGAAGAAGAGTATA
Found at i:69407 original size:30 final size:30
Alignment explanation
Indices: 69373--69443 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
69363 TGAAGGAGAA
* * *
69373 GTAAAAATATGATGGGTTGAAATAAGTTAT
1 GTAAAAATATAATGGGATGAAATAAATTAT
69403 GTAAAAATATAATGGGATGAAATAAATTAT
1 GTAAAAATATAATGGGATGAAATAAATTAT
69433 GTAAAAATATA
1 GTAAAAATATA
69444 TTTGTAATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (30 bp):
GTAAAAATATAATGGGATGAAATAAATTAT
Found at i:71429 original size:19 final size:20
Alignment explanation
Indices: 71405--71447 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
71395 TTGAAATTTT
71405 AAAAAATATAT-ATAA-TATA
1 AAAAAATATATGA-AAGTATA
71424 AAAAAATATATGAAAGTATA
1 AAAAAATATATGAAAGTATA
71444 AAAA
1 AAAA
71448 TTTACAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAAATATATGAAAGTATA
Found at i:76612 original size:17 final size:17
Alignment explanation
Indices: 76590--76625 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
76580 ATTCTTTTTA
76590 AAATCACAAAATTCACT
1 AAATCACAAAATTCACT
76607 AAATCACAAAATTCACT
1 AAATCACAAAATTCACT
76624 AA
1 AA
76626 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATCACAAAATTCACT
Found at i:76634 original size:17 final size:17
Alignment explanation
Indices: 76590--76634 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
76580 ATTCTTTTTA
*
76590 AAATCACAAAATTCACT
1 AAATCAAAAAATTCACT
*
76607 AAATCACAAAATTCACT
1 AAATCAAAAAATTCACT
*
76624 AATTCAAAAAA
1 AAATCAAAAAA
76635 ATTCTTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.58, C:0.20, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATCAAAAAATTCACT
Found at i:87668 original size:9 final size:9
Alignment explanation
Indices: 87654--87687 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
87644 TGTATTATTA
87654 TTGTTTCTT
1 TTGTTTCTT
*
87663 TTGTTTATT
1 TTGTTTCTT
87672 ATTGTTTCTT
1 -TTGTTTCTT
87682 TTGTTT
1 TTGTTT
87688 TATAAGAGAT
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:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (9 bp):
TTGTTTCTT
Found at i:87672 original size:19 final size:19
Alignment explanation
Indices: 87648--87687 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
87638 TCTCAGTGTA
87648 TTATTATTGTTTCTTTTGT
1 TTATTATTGTTTCTTTTGT
87667 TTATTATTGTTTCTTTTGT
1 TTATTATTGTTTCTTTTGT
87686 TT
1 TT
87688 TATAAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.05, G:0.10, T:0.75
Consensus pattern (19 bp):
TTATTATTGTTTCTTTTGT
Found at i:104121 original size:17 final size:17
Alignment explanation
Indices: 104099--104132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
104089 CATGTTAGAG
104099 CATATAAATCTGAAAAA
1 CATATAAATCTGAAAAA
* *
104116 CATATATATTTGAAAAA
1 CATATAAATCTGAAAAA
104133 AATTTCAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (17 bp):
CATATAAATCTGAAAAA
Found at i:114046 original size:43 final size:43
Alignment explanation
Indices: 113985--114070 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
113975 ATTGAGAAGG
*
113985 GGATCACAAGGTTTAAAGTTAAGCAAAATTTAGGAAAGCAGGA
1 GGATCACAAGGTTTAAAGTTAAGCAAAATTTAGGAAAACAGGA
114028 GGATCACAAGGTTTAAAGTTAAGCAAAATTTAGGAAAACAGGA
1 GGATCACAAGGTTTAAAGTTAAGCAAAATTTAGGAAAACAGGA
114071 ATGGGTGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (43 bp):
GGATCACAAGGTTTAAAGTTAAGCAAAATTTAGGAAAACAGGA
Found at i:115532 original size:2 final size:2
Alignment explanation
Indices: 115525--115551 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115515 AAGTTGCAGG
115525 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
115552 ATGTATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:122608 original size:29 final size:27
Alignment explanation
Indices: 122576--122669 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 27
122566 ATATATATAT
122576 ATATGGAAATTAAAAATATGTATACAAGG
1 ATATGGAAATTAAAAATATGTATA-AA-G
* * *
122605 ATATATGGATAAATAAAATATAAAGTATATAG
1 --ATATGGA-AATTAAAA-AT-ATGTATAAAG
122637 ATATGGAAATTAAAAATATGTATATAAAG
1 ATATGGAAATTAAAAATATG--TATAAAG
122666 ATAT
1 ATAT
122670 ATAAATAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 17 0.33
30 7 0.13
31 7 0.13
32 8 0.15
33 3 0.06
34 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.14, T:0.31
Consensus pattern (27 bp):
ATATGGAAATTAAAAATATGTATAAAG
Found at i:122688 original size:55 final size:58
Alignment explanation
Indices: 122569--122694 Score: 161
Period size: 61 Copynumber: 2.2 Consensus size: 58
122559 AGCATGTATA
* *
122569 TATATATATATGGAAATTAAAAATATGTATACAAGGATATATGGATAAATAAAATATAAAG
1 TATATAGATATGGAAATTAAAAATATGTATACAA-GAGATAT-GATAAAT-AAATATAAAG
* *
122630 TATATAGATATGGAAATTAAAAATATGTATATAA-AGATAT-ATAAAT-AATATAAGG
1 TATATAGATATGGAAATTAAAAATATGTATACAAGAGATATGATAAATAAATATAAAG
122685 TATA-AGATAT
1 TATATAGATAT
122695 AAAGTATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
54 6 0.10
55 12 0.20
57 6 0.10
59 5 0.08
61 32 0.52
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.33
Consensus pattern (58 bp):
TATATAGATATGGAAATTAAAAATATGTATACAAGAGATATGATAAATAAATATAAAG
Found at i:122970 original size:20 final size:20
Alignment explanation
Indices: 122945--122987 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
122935 ATTAAAATAT
122945 ATATATGTAAAGA-TACATAA
1 ATATATGTAAAGATTACA-AA
*
122965 ATATATGTATAGATTACAAA
1 ATATATGTAAAGATTACAAA
122985 ATA
1 ATA
122988 CCAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (20 bp):
ATATATGTAAAGATTACAAA
Found at i:124154 original size:4 final size:4
Alignment explanation
Indices: 124145--124182 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
124135 TAACGGACAT
124145 ATAA ATAA ATAA ATAA ATAA ATGAA GA-AA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA AT-AA -ATAA ATAA ATAA A
124183 AGATATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 27 0.87
5 2 0.06
6 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:124583 original size:3 final size:3
Alignment explanation
Indices: 124569--124651 Score: 64
Period size: 3 Copynumber: 27.0 Consensus size: 3
124559 CAAATAAAAC
* * *
124569 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAC TAA TAA TTCAA AAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA -T-AA TAA TAA
*
124617 TAA T-A TGA T-A TAA TAA T-A TAA TAA TGAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A TAA
124652 GTGTAAAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
2 6 0.09
3 48 0.73
4 10 0.15
5 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:124593 original size:19 final size:19
Alignment explanation
Indices: 124569--124651 Score: 73
Period size: 19 Copynumber: 4.3 Consensus size: 19
124559 CAAATAAAAC
* *
124569 TAATAATGATAATAATTAA
1 TAATAATAATAATAATGAA
*
124588 TAATAATAATACTAAT-AA
1 TAATAATAATAATAATGAA
*
124606 TTCAAAAATAATAAT-ATGATA
1 -T-AATAATAATAATAATGA-A
124627 TAATAAT-ATAATAATGAA
1 TAATAATAATAATAATGAA
124645 TAGATAA
1 TA-ATAA
124652 GTGTAAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
18 10 0.19
19 30 0.57
20 12 0.23
21 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (19 bp):
TAATAATAATAATAATGAA
Found at i:128818 original size:16 final size:17
Alignment explanation
Indices: 128797--128829 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
128787 AGAAAAGGGT
128797 GGGAAAAT-AGAGGAAA
1 GGGAAAATGAGAGGAAA
128813 GGGAAAATGAGAGGAAA
1 GGGAAAATGAGAGGAAA
128830 AAAAAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (17 bp):
GGGAAAATGAGAGGAAA
Found at i:129776 original size:63 final size:63
Alignment explanation
Indices: 129698--129875 Score: 261
Period size: 63 Copynumber: 2.8 Consensus size: 63
129688 GAGAAAGGAG
* *
129698 GAGATGAAGGGCTGAGATTTGTAATGACATTCTATTGGAGCTCAAATAGAAAGATG-AGATGAA
1 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAGAAAGA-GAAGATGAA
* * *
129761 GAGATGAAGGGCTGAGATTTATATTGACCTTCTATTGGAGCTCCAATAGAAGGAGAAGATGAA
1 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAGAAAGAGAAGATGAA
* * *
129824 AAGATGAAGGGCTAAGATTTGTAATGACCTTCTATTGAAGCTCCAATA-AAAG
1 GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAGAAAG
129876 GAGTAGACGA
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
62 4 0.04
63 99 0.96
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (63 bp):
GAGATGAAGGGCTGAGATTTGTAATGACCTTCTATTGGAGCTCCAATAGAAAGAGAAGATGAA
Found at i:134117 original size:4 final size:4
Alignment explanation
Indices: 134108--134134 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
134098 TCACAGTAAG
134108 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
134135 GATGCATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:137221 original size:14 final size:15
Alignment explanation
Indices: 137199--137275 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
137189 CAATCAAACA
137199 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
137213 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
137228 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
137248 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
137262 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
137276 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:137232 original size:29 final size:28
Alignment explanation
Indices: 137200--137302 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 28
137190 AATCAAACAC
137200 CAGAAAATATTTTCCAGTAAATCATTTTA
1 CAGAAAATATTTTCCAG-AAATCATTTTA
137229 CAGAAAAGTAAAACATTTTCCAGAAATCATTTTA
1 CAGAAAA-T-----ATTTTCCAGAAATCATTTTA
* ** *
137263 CGGAAAATATTTTACTGGCAATCATTTTA
1 CAGAAAATATTTT-CCAGAAATCATTTTA
*
137292 CGGAAAATATT
1 CAGAAAATATT
137303 ATCAGTTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
28 5 0.08
29 30 0.48
30 1 0.02
33 1 0.02
34 17 0.27
35 9 0.14
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (28 bp):
CAGAAAATATTTTCCAGAAATCATTTTA
Found at i:137240 original size:20 final size:20
Alignment explanation
Indices: 137215--137254 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
137205 AATATTTTCC
*
137215 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
137235 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
137255 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:137260 original size:34 final size:35
Alignment explanation
Indices: 137203--137269 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
137193 CAAACACCAG
*
137203 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
137238 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
137270 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:137289 original size:15 final size:15
Alignment explanation
Indices: 137252--137299 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
137242 CATTTTCCAG
137252 AAATCATTTTACGGA
1 AAATCATTTTACGGA
137267 AAAT-ATTTTACTGG-
1 AAATCATTTTAC-GGA
*
137281 CAATCATTTTACGGA
1 AAATCATTTTACGGA
137296 AAAT
1 AAAT
137300 ATTATCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (15 bp):
AAATCATTTTACGGA
Found at i:138664 original size:21 final size:19
Alignment explanation
Indices: 138639--138688 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 19
138629 TTATATTGAT
138639 TTTTAAAAATTCAAAAAAA
1 TTTTAAAAATTCAAAAAAA
138658 TAATTTAAAAA-T--AAAAAA
1 T--TTTAAAAATTCAAAAAAA
138676 TTTTAAAAATTCA
1 TTTTAAAAATTCA
138689 TTTTTCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 7 0.27
19 1 0.04
20 1 0.04
21 8 0.31
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
TTTTAAAAATTCAAAAAAA
Found at i:139367 original size:26 final size:25
Alignment explanation
Indices: 139330--139381 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
139320 ATAATATATA
139330 ATTTTTATTTTTTTAATTTTAAAAT
1 ATTTTTATTTTTTTAATTTTAAAAT
* *
139355 ATTTTTTTCTTTTTTATTTTTAAAAT
1 ATTTTTAT-TTTTTTAATTTTAAAAT
139381 A
1 A
139382 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTTTATTTTTTTAATTTTAAAAT
Found at i:139388 original size:27 final size:27
Alignment explanation
Indices: 139329--139389 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
139319 TATAATATAT
*
139329 AATTTTTATTTTTTTAATTTTAAAAT-
1 AATTTTTACTTTTTTAATTTTAAAATA
* * *
139355 ATTTTTTTCTTTTTTATTTTTAAAATAA
1 AATTTTTACTTTTTTAATTTTAAAAT-A
139383 AATTTTT
1 AATTTTT
139390 GTGTTTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 22 0.79
28 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
AATTTTTACTTTTTTAATTTTAAAATA
Found at i:141564 original size:36 final size:36
Alignment explanation
Indices: 141517--141588 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
141507 TTTTTAAAAA
*
141517 AATCTAAGCTCAGATTTAGCTTGACCCTGAAACACC
1 AATCTAAGCTCAGATTTAGCTTGACCCTCAAACACC
141553 AATCTAAGCTCAGATTTAGCTTGACCCTCAAACACC
1 AATCTAAGCTCAGATTTAGCTTGACCCTCAAACACC
141589 GACACCAACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25
Consensus pattern (36 bp):
AATCTAAGCTCAGATTTAGCTTGACCCTCAAACACC
Found at i:142182 original size:21 final size:21
Alignment explanation
Indices: 142144--142184 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
142134 CCAAACCTCA
**
142144 AGATTTAAGGTTTGATGTTCG
1 AGATTTAAGGTTCAATGTTCG
*
142165 AGATTTGAGGTTCAATGTTC
1 AGATTTAAGGTTCAATGTTC
142185 AGGGTTCGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.41
Consensus pattern (21 bp):
AGATTTAAGGTTCAATGTTCG
Found at i:143804 original size:24 final size:24
Alignment explanation
Indices: 143776--143829 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
143766 GCCTATAACA
143776 GGTAGCTCCGAAGAGCAATCAACG
1 GGTAGCTCCGAAGAGCAATCAACG
* *
143800 GGTAGCTTCGAAGAGCAATTAACG
1 GGTAGCTCCGAAGAGCAATCAACG
143824 GGTAGC
1 GGTAGC
143830 ATCAGATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.17
Consensus pattern (24 bp):
GGTAGCTCCGAAGAGCAATCAACG
Found at i:143931 original size:26 final size:25
Alignment explanation
Indices: 143867--143932 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
143857 AAACACACAC
*
143867 TAACGGGAAGCTCACAATGAGCCTT
1 TAACGGGAAGCTCACAATGAGCCTA
*
143892 TAATCGAGAAGCTCACGAA-GAGCCATA
1 TAA-CGGGAAGCTCAC-AATGAGCC-TA
*
143919 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
143933 TAAGAGCTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.09
26 25 0.74
27 6 0.18
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (25 bp):
TAACGGGAAGCTCACAATGAGCCTA
Found at i:144416 original size:21 final size:21
Alignment explanation
Indices: 144392--144433 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
144382 AATTTTAGCA
* *
144392 TCAATTTAATATAATTTACAT
1 TCAATTCAATATAATTCACAT
*
144413 TCAATTCAATCTAATTCACAT
1 TCAATTCAATATAATTCACAT
144434 CCTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (21 bp):
TCAATTCAATATAATTCACAT
Found at i:144615 original size:20 final size:20
Alignment explanation
Indices: 144574--144617 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
144564 AACCCATTAA
* *
144574 TTTCATGAAATTTCAGAATT
1 TTTCATGAAATTTAACAATT
*
144594 TTTCATG-AATTTAACAACT
1 TTTCATGAAATTTAACAATT
144613 TTTCA
1 TTTCA
144618 ATTTAATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTCATGAAATTTAACAATT
Found at i:145349 original size:17 final size:17
Alignment explanation
Indices: 145327--145360 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
145317 CAAAAATCTT
145327 TTAAAAACCACATTTGG
1 TTAAAAACCACATTTGG
*
145344 TTAAAAACGACATTTGG
1 TTAAAAACCACATTTGG
145361 CTCGTAAATG
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:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (17 bp):
TTAAAAACCACATTTGG
Found at i:160877 original size:3 final size:3
Alignment explanation
Indices: 160871--160897 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
160861 TTTTGTCATA
160871 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
160898 TCTTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:165731 original size:31 final size:31
Alignment explanation
Indices: 165693--165758 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
165683 CGTAATACAA
165693 AAAATTCGAGTTCTAATATTTTCGTGTATTT
1 AAAATTCGAGTTCTAATATTTTCGTGTATTT
165724 AAAATTCGAGTTCTAATATTTTCGTGTATTT
1 AAAATTCGAGTTCTAATATTTTCGTGTATTT
165755 AAAA
1 AAAA
165759 GATCATATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
AAAATTCGAGTTCTAATATTTTCGTGTATTT
Found at i:173762 original size:67 final size:70
Alignment explanation
Indices: 173617--173751 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 70
173607 TATCGTTGTT
*
173617 TTTAAATATTTTTCTTATATATATATATATATTAACAATCTAATTTTTAGTTTATTGATAAATTA
1 TTTAAATATTTTTC-TATATATATATATATATTAAC-A-CTAATTTTTAGTTTATTAATAAATTA
173682 TATGTACA
63 TATGTACA
* * *
173690 TTTAAATATTTTTC-ATATATATATATTTA-TAGC-CTAATTTTTAGTTTCTTAATAAATTATAT
1 TTTAAATATTTTTCTATATATATATATATATTAACACTAATTTTTAGTTTATTAATAAATTATAT
173752 ATTAGTTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 27 0.47
70 3 0.05
71 14 0.24
73 14 0.24
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (70 bp):
TTTAAATATTTTTCTATATATATATATATATTAACACTAATTTTTAGTTTATTAATAAATTATAT
GTACA
Found at i:173793 original size:23 final size:23
Alignment explanation
Indices: 173763--173834 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
173753 TTAGTTTAAA
*
173763 AAATATATATTATATATACATAT
1 AAATATATATTATATATAAATAT
** * *
173786 AAATATATCAAAAT-TACATATAT
1 AAATATAT-ATTATATATAAATAT
*
173809 AAATATAT-TTATATGTAAATAT
1 AAATATATATTATATATAAATAT
173831 AAAT
1 AAAT
173835 TTTAATAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 2 0.05
22 10 0.26
23 23 0.61
24 3 0.08
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (23 bp):
AAATATATATTATATATAAATAT
Found at i:174342 original size:29 final size:32
Alignment explanation
Indices: 174305--174363 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 32
174295 CTATATCTTT
174305 ATAATTTTTAAAGGATTAAA-T-AAATTTTTA
1 ATAATTTTTAAAGGATTAAAGTGAAATTTTTA
**
174335 ATAA-TTTTAGGGGATTAAAGTGAAATTTT
1 ATAATTTTTAAAGGATTAAAGTGAAATTTT
174364 ATTTTTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 5 0.20
31 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (32 bp):
ATAATTTTTAAAGGATTAAAGTGAAATTTTTA
Found at i:175981 original size:13 final size:13
Alignment explanation
Indices: 175963--175987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175953 AGAGAGAGTT
175963 ATCGGTTTAATTG
1 ATCGGTTTAATTG
175976 ATCGGTTTAATT
1 ATCGGTTTAATT
175988 TATTCTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
ATCGGTTTAATTG
Found at i:182504 original size:24 final size:24
Alignment explanation
Indices: 182477--182525 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
182467 CTAATGTCAA
182477 TCAAAATAAATATAGCGACAAATT
1 TCAAAATAAATATAGCGACAAATT
* ** *
182501 TCAATATCCATATAGTGACAAATT
1 TCAAAATAAATATAGCGACAAATT
182525 T
1 T
182526 ACACTATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (24 bp):
TCAAAATAAATATAGCGACAAATT
Found at i:183276 original size:14 final size:14
Alignment explanation
Indices: 183253--183282 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
183243 GAAAAGTTAA
183253 AAGGACTAAATTAT
1 AAGGACTAAATTAT
*
183267 AAGGATTAAATTAT
1 AAGGACTAAATTAT
183281 AA
1 AA
183283 ATTTATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (14 bp):
AAGGACTAAATTAT
Found at i:183412 original size:25 final size:25
Alignment explanation
Indices: 183384--183466 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
183374 ATTAATAACA
183384 AAATTTATAATAAATTATAAGGACT
1 AAATTTATAATAAATTATAAGGACT
* * *
183409 AAATTAATAACAAAGATTA-AA--AAT
1 AAATTTATAA-TAA-ATTATAAGGACT
*
183433 AAA--TAAAAT-AATATATAAGGACT
1 AAATTTATAATAAAT-TATAAGGACT
183456 AAATTTATAAT
1 AAATTTATAAT
183467 TTATACATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 2 0.05
22 3 0.07
23 5 0.12
24 5 0.12
25 14 0.33
26 4 0.10
27 4 0.10
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATTTATAATAAATTATAAGGACT
Found at i:184327 original size:90 final size:90
Alignment explanation
Indices: 184001--184385 Score: 379
Period size: 89 Copynumber: 4.2 Consensus size: 90
183991 TTTCTCTTTC
* *
184001 ATGTTTGAATTATAGAGGTTTAATTTAGCTTTGTAATTTTGCAGAT-AAGTTTTGTAAGTGATTC
1 ATGTTTGAATTATAGAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAA-TTTTGTAAGTGATCC
* ***
184065 AGTTCGCATATTTGAA-TTAAAAAAA
65 AGTTCACATATTTGAATTTTTTAAAA
* * * * * * *
184090 ATGTTTGTATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTCGTAAGTGGTTCC
1 ATGTTTGAATTATAGAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAATTTTGTAAGT-GATCC
*
184155 -GTTCACGTATTTGAATTTTTGTAAAAAAAA
65 AGTTCACATATTTGAATTTTT-T----AAAA
* * *
184185 AAGTTTGAA-T-T-GAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAGTCTTGTAAGTGATCCA
1 ATGTTTGAATTATAGAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAATTTTGTAAGTGATCCA
* * **
184247 CTTCGCATATTTGAATTTTTTTTAA
66 GTTCACATATTTGAATTTTTTAAAA
* * * *
184272 ATGTTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGCAGATGAATTTTGTAAGTGATTCA
1 ATGTTTGAATTATAGAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAATTTTGTAAGTGATCCA
*
184337 GTTCAAATATTTGAATTTTTTTTTTAAAA
66 GTTCACATATTTGAA----TTTTTTAAAA
*
184366 A-GTTTGAATTCTAGAGTTTT
1 ATGTTTGAATTATAGAGTTTT
184386 TTTTTTTTTT
Statistics
Matches: 240, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
87 9 0.04
88 1 0.00
89 64 0.27
90 64 0.27
91 5 0.02
92 58 0.24
93 18 0.08
94 10 0.04
95 11 0.05
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (90 bp):
ATGTTTGAATTATAGAGTTTTAATTTAGCTTTGTAATTTTGCAGATGAATTTTGTAAGTGATCCA
GTTCACATATTTGAATTTTTTAAAA
Found at i:184350 original size:182 final size:181
Alignment explanation
Indices: 184019--184356 Score: 487
Period size: 182 Copynumber: 1.9 Consensus size: 181
184009 ATTATAGAGG
* * *
184019 TTTAATTTAGCTTTGTAATTTTGCAGATAAGTTTTGTAAGTGATTCAGTTCGCATATTTGAATTA
1 TTTAATTTAGCTTTGTAATTTTGCAGATAAGTCTTGTAAGTGATCCACTTCGCATATTTGAATTA
** * * * *
184084 AAAAAAATGTTTGTATTCTAGAGTTTTTATTTGGCTTTGTAATTTTGCAGATGAGTTTCGTAAGT
66 AAAAAAATGTTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGCAGATGAATTTCGTAAGT
* * **
184149 GGTTCCGTTCACGTATTTGAATTTTTGTAAAAAAAAAAGTTTGAATTGAGT
131 GATTCAGTTCAAATATTTGAATTTTTGTAAAAAAAAAAGTTTGAATTGAGT
*
184200 TTTAATTTAGCTTTGTAATTTTGCAGATGAGTCTTGTAAGTGATCCACTTCGCATATTTGAATTT
1 TTTAATTTAGCTTTGTAATTTTGCAGATAAGTCTTGTAAGTGATCCACTTCGCATATTTGAA-TT
***** *
184265 TTTTTAAATGTTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGCAGATGAATTTTGTAAG
65 AAAAAAAATGTTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGCAGATGAATTTCGTAAG
184330 TGATTCAGTTCAAATATTTGAATTTTT
130 TGATTCAGTTCAAATATTTGAATTTTT
184357 TTTTTAAAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
181 58 0.43
182 78 0.57
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (181 bp):
TTTAATTTAGCTTTGTAATTTTGCAGATAAGTCTTGTAAGTGATCCACTTCGCATATTTGAATTA
AAAAAAATGTTTAAATTATAGAGTTTTAATTTGGCTTTGTAATTATGCAGATGAATTTCGTAAGT
GATTCAGTTCAAATATTTGAATTTTTGTAAAAAAAAAAGTTTGAATTGAGT
Found at i:192499 original size:41 final size:41
Alignment explanation
Indices: 192439--192519 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
192429 CTATTGCCAT
*
192439 CCCTAGTTACACTATTTTTTA-CATTACATTGAACTAAAGGG
1 CCCTAGTTACACTAGTTTTTAGC-TTACATTGAACTAAAGGG
192480 CCCTAGTTACACTAGTTTTTAGCTTACATTGAACTAAAGG
1 CCCTAGTTACACTAGTTTTTAGCTTACATTGAACTAAAGG
192520 ACCCAGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (41 bp):
CCCTAGTTACACTAGTTTTTAGCTTACATTGAACTAAAGGG
Found at i:197431 original size:30 final size:30
Alignment explanation
Indices: 197390--197473 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
197380 TACAATTTTA
*
197390 AAAATTGAAAAATATAAGGACTAAAAATGAT
1 AAAATT-AAAAATATAAGTACTAAAAATGAT
* * *
197421 -CAATTCAAAAAGTGTAA-TACTAAAATTGAT
1 AAAATT-AAAAA-TATAAGTACTAAAAATGAT
197451 AAAATT-AAAATATAAGTACTAAA
1 AAAATTAAAAATATAAGTACTAAA
197474 TTCATAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.09
29 11 0.26
30 20 0.47
31 8 0.19
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (30 bp):
AAAATTAAAAATATAAGTACTAAAAATGAT
Found at i:215118 original size:60 final size:60
Alignment explanation
Indices: 215054--215802 Score: 725
Period size: 60 Copynumber: 12.6 Consensus size: 60
215044 TTGGAGAAGA
* * *
215054 CTTAATGCTAGGA-TTTAAGCTAACAACAAATTAACATCATGTGGAGCACGTTATGAAAGG
1 CTTAATGCT-GGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
** * * * * * * *
215114 CTTAATGCAAGACTTTAAGTTAACAACAAACTAATGA-CACGCGGAGCACATCA-GAAAGG
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAA-CATCACGTGGAACACGTTACGAAAGG
* * *
215173 TTTAATGCTGGGA-TTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGG
1 CTTAATGCT-GGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
* ** * * *
215233 CTTAAGGCTGGACTTTAAGCTAACGGCAAATTAACCTCACGTGGAGCACGTTACAAAAGG
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
* * * * *
215293 CTTAAGGCTGGACTTTAAGCTAACAACAAATTAATATCACGTGGAACATGTCATGAAAGG
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
* * * * *
215353 CTTAATGCTGGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGCGAACA--
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAA-AGG
* * * *
215412 TTTAATGCAGGGA-TTTAAGCTAACAACAAATTAACATCACATGGAACACGTTATGAAAGG
1 CTTAATGC-TGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
** * * * * * * *
215472 CTTAATGCAAGACTTTAAGTTAACAACAAACTAATGA-CACGCGGAGCACATCA-GAAAGG
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAA-CATCACGTGGAACACGTTACGAAAGG
* * *
215531 TTTAATGCTGGGA-TTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGG
1 CTTAATGCT-GGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
* * * * *
215591 CTTAAGGCTGGACTTTAAGCTAACAACAAATTAATATCACGTGGAACATGTCATGAAAGG
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
* * * * *
215651 CTTAATGCTGGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGCGAACA--
1 CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAA-AGG
* * * * ** *
215710 TTTAATGCAGGGA-TTTAAGCTAACAACAAATTAACATCACATGGAACTCAATACAAAAGG
1 CTTAATGC-TGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
*
215770 CTTAATGCTGGGA-TTTAAGCTAACGACAAATTA
1 CTTAATGCT-GGACTTTAAGCTAACAACAAATTA
215803 TTACCTTGAG
Statistics
Matches: 558, Mismatches: 110, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
58 4 0.01
59 183 0.33
60 367 0.66
61 4 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (60 bp):
CTTAATGCTGGACTTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACGAAAGG
Found at i:215279 original size:119 final size:120
Alignment explanation
Indices: 215054--215802 Score: 779
Period size: 119 Copynumber: 6.3 Consensus size: 120
215044 TTGGAGAAGA
* * * **
215054 CTTAATGCTAGGATTTAAGCTAACAACAAATTAACATCATGTGGAGCACGTTATGAAAGGCTTAA
1 CTTAATGCTGGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
** * * ** *
215119 TGCAAGACTTTAAGTTAACAACAAACTAATGACACGCGGAGCACAT-CAGAAAGG
66 TGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCACATACAGAAAGG
* *
215173 TTTAATGCTGGGATTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
1 CTTAATGCTGGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
* ** ** *
215238 GGCTGGACTTTAAGCTAACGGCAAATTAACCTCACGTGGAGCACGTTACA-AAAGG
66 TGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCAC-ATACAGAAAGG
* * * * **
215293 CTTAAGGCT-GGACTTTAAGCTAACAACAAATTAATATCACGTGGAACATGTCATGAAAGGCTTA
1 CTTAATGCTGGGA-TTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTA
* *
215357 ATGCTGGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGC-GAACA--
65 ATGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCACA-TACAGAA-AGG
* * * **
215412 TTTAATGCAGGGATTTAAGCTAACAACAAATTAACATCACATGGAACACGTTATGAAAGGCTTAA
1 CTTAATGCTGGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
** * * ** *
215477 TGCAAGACTTTAAGTTAACAACAAACTAATGACACGCGGAGCACAT-CAGAAAGG
66 TGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCACATACAGAAAGG
* *
215531 TTTAATGCTGGGATTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
1 CTTAATGCTGGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
* * * *
215596 GGCTGGACTTTAAGCTAACAACAAATTAATATCACGTGGA--ACATGTCATGAAAGG
66 TGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCACAT-ACA-GAAAGG
* * * * * * *
215651 CTTAATGCT-GGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGCGAACA--TTT
1 CTTAATGCTGGGA-TTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTAC-AAAAGGCTT
* * * * *
215713 AATGCAGGGA-TTTAAGCTAACAACAAATTAACATCACATGGAACTCAATACA-AAAGG
64 AATGC-TGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCAC-ATACAGAAAGG
*
215770 CTTAATGCTGGGATTTAAGCTAACGACAAATTA
1 CTTAATGCTGGGATTTAAGCTAACAACAAATTA
215803 TTACCTTGAG
Statistics
Matches: 530, Mismatches: 80, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
117 6 0.01
118 4 0.01
119 350 0.66
120 159 0.30
121 9 0.02
122 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (120 bp):
CTTAATGCTGGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTACAAAAGGCTTAA
TGCTGGACTTTAAGCTAACAACAAATTAACAACACGTGGAGCACATACAGAAAGG
Found at i:215699 original size:179 final size:178
Alignment explanation
Indices: 215054--215802 Score: 907
Period size: 179 Copynumber: 4.2 Consensus size: 178
215044 TTGGAGAAGA
* *
215054 CTTAATGCTAGGATTTAAGCTAACAACAAATTAACATCATGTGGAGCACGTTATGAAAGGCTTAA
1 CTTAATGCT-GGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTATGAAAGGCTTAA
* *
215119 TGCAAGACTTTAAGTTAACAACAAACTAATGACACGCGGAGCACATCAGAAAGGTTTAATGCTGG
65 TGCAAGACTTTAAGCTAACAACAAACTAATAACACGCGGAGCACATCAGAAAGGTTTAATGCTGG
*
215184 GATTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGG
130 GATTTAAGCAAACAACAAATTAACATCACGTGGAACACATTACAAAAGG
* ** * * **
215233 CTTAAGGCTGGACTTTAAGCTAACGGCAAATTAACCTCACGTGGAGCACGTTACAAAAGGCTTAA
1 CTTAATGCTGGA-TTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTATGAAAGGCTTAA
* ** * * * * ** *
215298 GGCTGGACTTTAAGCTAACAACAAATTAATATCACGTGGAACATGTCATGAAAGGCTTAATGCT-
65 TGCAAGACTTTAAGCTAACAACAAACTAATAACACGCGGAGCACATCA-GAAAGGTTTAATGCTG
* * * * * *
215362 GGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGCGAACA--
129 GGA-TTTAAGCAAACAACAAATTAACATCACGTGGAACACATTAC-AAAAGG
* * *
215412 TTTAATGCAGGGATTTAAGCTAACAACAAATTAACATCACATGGAACACGTTATGAAAGGCTTAA
1 CTTAATGC-TGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTATGAAAGGCTTAA
* *
215477 TGCAAGACTTTAAGTTAACAACAAACTAATGACACGCGGAGCACATCAGAAAGGTTTAATGCTGG
65 TGCAAGACTTTAAGCTAACAACAAACTAATAACACGCGGAGCACATCAGAAAGGTTTAATGCTGG
*
215542 GATTTAAGCAAACAACAAATTAACATCACGTGGAACACGTTACAAAAGG
130 GATTTAAGCAAACAACAAATTAACATCACGTGGAACACATTACAAAAGG
* * * *
215591 CTTAAGGCTGGACTTTAAGCTAACAACAAATTAATATCACGTGGAACATGTCATGAAAGGCTTAA
1 CTTAATGCTGGA-TTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTATGAAAGGCTTAA
** * * * *
215656 TGCTGGACTTTAAGCTAACAAGAAATTAACAACACGTGGAGCACATTGC-GAACA--TTTAATGC
65 TGCAAGACTTTAAGCTAACAACAAACTAATAACACGCGGAGCACA-T-CAGAA-AGGTTTAATGC
* * * * *
215718 AGGGATTTAAGCTAACAACAAATTAACATCACATGGAACTCAATACAAAAGG
127 TGGGATTTAAGCAAACAACAAATTAACATCACGTGGAACACATTACAAAAGG
*
215770 CTTAATGCTGGGATTTAAGCTAACGACAAATTA
1 CTTAATGCT-GGATTTAAGCTAACAACAAATTA
215803 TTACCTTGAG
Statistics
Matches: 479, Mismatches: 78, Indels: 26
0.82 0.13 0.04
Matches are distributed among these distances:
177 3 0.01
178 55 0.11
179 357 0.75
180 59 0.12
181 5 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (178 bp):
CTTAATGCTGGATTTAAGCTAACAACAAATTAACATCACGTGGAACACGTTATGAAAGGCTTAAT
GCAAGACTTTAAGCTAACAACAAACTAATAACACGCGGAGCACATCAGAAAGGTTTAATGCTGGG
ATTTAAGCAAACAACAAATTAACATCACGTGGAACACATTACAAAAGG
Found at i:227554 original size:59 final size:60
Alignment explanation
Indices: 227474--227650 Score: 217
Period size: 59 Copynumber: 3.1 Consensus size: 60
227464 GAAATAATTG
*
227474 AATAATTGAGTGA-CTATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAATAAATTTACT
1 AATAATTGAGTGATC-ATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAATAAATTTACT
* *
227534 AATAATT-AGTGATCATTTTGTAGCTTTTCATGGTTGGGTGACC--AAAA-AAA--TACT
1 AATAATTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAATAAATTTACT
* * * * *
227588 AATAATTGGGTAACCATCTTGTAACTTTTCATAATTGGGTGACCAAAAAAT-AATTTACT
1 AATAATTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAATAAATTTACT
227647 AATA
1 AATA
227651 GTTAGATGAT
Statistics
Matches: 100, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
54 11 0.11
55 29 0.29
56 3 0.03
57 10 0.10
59 39 0.39
60 8 0.08
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (60 bp):
AATAATTGAGTGATCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAATAAATTTACT
Found at i:227626 original size:55 final size:56
Alignment explanation
Indices: 227474--227637 Score: 197
Period size: 55 Copynumber: 2.9 Consensus size: 56
227464 GAAATAATTG
* *
227474 AATAATTGAGTGACTATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAATAAATTTACT
1 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTGGGTGACC--AAAA-AAA-TTACT
* * *
227534 AATAATT-AGTGATCATTTTGTAGCTTTTCATGGTTGGGTGACCAAAAAAA-TACT
1 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAAATTACT
* * * *
227588 AATAATTGGGTAACCATCTTGTAACTTTTCATAATTGGGTGACCAAAAAA
1 AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAA
227638 TAATTTACTA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
54 11 0.12
55 35 0.38
56 3 0.03
57 4 0.04
59 31 0.34
60 7 0.08
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (56 bp):
AATAATTGAGTGACCATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAAATTACT
Found at i:236596 original size:13 final size:13
Alignment explanation
Indices: 236578--236602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
236568 TATGGAAGGT
236578 TTCTAGTTTATAC
1 TTCTAGTTTATAC
236591 TTCTAGTTTATA
1 TTCTAGTTTATA
236603 AGGGCTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
TTCTAGTTTATAC
Found at i:237614 original size:21 final size:21
Alignment explanation
Indices: 237588--237634 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
237578 CGCATTCCTT
237588 AATTTTTATATCCCTTTATAA
1 AATTTTTATATCCCTTTATAA
237609 AATTTTTATATCCCTTTATAA
1 AATTTTTATATCCCTTTATAA
237630 AATTT
1 AATTT
237635 AAATTCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTTATATCCCTTTATAA
Found at i:248355 original size:15 final size:15
Alignment explanation
Indices: 248335--248365 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
248325 TATTATGGGC
248335 GTTGTGAATAAAAAA
1 GTTGTGAATAAAAAA
248350 GTTGTGAATAAAAAA
1 GTTGTGAATAAAAAA
248365 G
1 G
248366 CTGTTTGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (15 bp):
GTTGTGAATAAAAAA
Found at i:255566 original size:214 final size:217
Alignment explanation
Indices: 255169--255606 Score: 648
Period size: 214 Copynumber: 2.0 Consensus size: 217
255159 GAAATGATTC
255169 ATATCATGCAACTCTGTTATAGGGCTCAGATCGGAACATACATTGGAAAGTACGAGATTTCCTTA
1 ATATCATGCAACTCTGTTATAGGGCT---ATCGGAACATACATTGGAAAGTACGAGATTTCCTTA
* * * *
255234 GAAGGGTTTATATGGACCTAGACTTTCACACCCTAATATCTAGCTTTTTGGGTATGGTTCTCCGA
63 GAAAGGTTTATATGGACCTACACTCTCACACCCTAATATCTAGCTTTTCGGGTATGGTTCTCCGA
255299 AGATCCATATCAATTAGTATCGAAACTTCACATCATAGGTAAAATCAGTATTGTAGCATTGCAAA
128 AGATCCATATCAATTAGTATCGAAACTTCACATCATAGGTAAAATCAGTATTGTAGCATTGCAAA
255364 CCTAGACCACATAACATAGCTGGTG
193 CCTAGACCACATAACATAGCTGGTG
* * * * *
255389 ATATCATGCTACTCTGTTATAGGGCT-T-GGATCCTACATTGGAAAGTAGGGGATTTCCTTA-AA
1 ATATCATGCAACTCTGTTATAGGGCTATCGGAACATACATTGGAAAGTACGAGATTTCCTTAGAA
* * *
255451 AGGTTTATATGGACCTACTCTCTCTCACCCTAATATCTAGCTTTTCGGGTATGGTTCTCCGGAGA
66 AGGTTTATATGGACCTACACTCTCACACCCTAATATCTAGCTTTTCGGGTATGGTTCTCCGAAGA
* * * * * * **
255516 TCCATATCAATTGGTATCGAAGCTTCCCGTCATTGGTGAAATTGGTATTGTAGCATTGCAAACCT
131 TCCATATCAATTAGTATCGAAACTTCACATCATAGGTAAAATCAGTATTGTAGCATTGCAAACCT
255581 AGACCACATAACATAGCTGGTG
196 AGACCACATAACATAGCTGGTG
255603 ATAT
1 ATAT
255607 AGGTAATATA
Statistics
Matches: 198, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
214 143 0.72
215 29 0.15
216 1 0.01
220 25 0.13
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (217 bp):
ATATCATGCAACTCTGTTATAGGGCTATCGGAACATACATTGGAAAGTACGAGATTTCCTTAGAA
AGGTTTATATGGACCTACACTCTCACACCCTAATATCTAGCTTTTCGGGTATGGTTCTCCGAAGA
TCCATATCAATTAGTATCGAAACTTCACATCATAGGTAAAATCAGTATTGTAGCATTGCAAACCT
AGACCACATAACATAGCTGGTG
Found at i:256602 original size:31 final size:31
Alignment explanation
Indices: 256567--256628 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
256557 ATAATCACTG
* * *
256567 AACTATTTATAAATTTTTATTTAAGTTACTA
1 AACTATATAAAAATTTTCATTTAAGTTACTA
256598 AACTATATAAAAATTTTCATTTAAGTTACTA
1 AACTATATAAAAATTTTCATTTAAGTTACTA
256629 GATTGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (31 bp):
AACTATATAAAAATTTTCATTTAAGTTACTA
Found at i:259694 original size:3 final size:3
Alignment explanation
Indices: 259686--259712 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
259676 CTCAAATAAC
259686 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
259713 TAATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:265252 original size:298 final size:298
Alignment explanation
Indices: 264678--265435 Score: 854
Period size: 298 Copynumber: 2.6 Consensus size: 298
264668 GTCTCCGAAT
* * * * *
264678 TCCA-AAAAGAAAACAAAAAATATCAAAAATC-TTTTCATAAGTAATCACACTTTACTCAAAATA
1 TCCAGAAAACAAAA-AAAAAAAATCGAATATCATTTTCATAAGCAATCACACTTTACTCAAAATA
* * * *** * * *
264741 AATCAATTCAAATCATTCAAATATACAGGATCCATCATCGAACGTGATAACTACAAGTATAAT--
65 AATCAATTCAAATCATTGAAATACACAGGATCCATCATTGAAAACGATAAATACAAGCACAATAA
* * * * * * * * *
264804 GATCCAGTCAAACTGTTTGACCAAAACTTCTAGAATCTTCTTTTCCTATCACTACAGTTAGACCC
130 GCTACAGTCAAACTGTTTGACCAAAACTTCCAGAATCTTATTTTCCTATCAATACACTAAAAACC
* * *
264869 CTCTATGTTTAATTTAGCTACAAATGTTCCTTCACTAAATTCTAAAAGAAGAAAATATAAATTTC
195 CTCTATGTTTAATTTAACTACAAATGTTCCTTCACTAAATCCTAAAAGAAGAAAAGATAAATTTC
* ** * * *
264934 TTTACTGGTTTGCTAAGAACAAATT-AATCCAAAAATAC
260 TTGACTACTCTGCAAAGAACAAATTAAATCCAAAAACAC
* *
264972 TCTAG-AAACAAAAAATGAAAAATCGAATATCATTTTTCATAAGCAATCACACTTTACTCAAAAT
1 TCCAGAAAACAAAAAA-AAAAAATCGAATATCA-TTTTCATAAGCAATCACACTTTACTCAAAAT
* * *
265036 AAATAAATACAAATCATTGAAATACATAGGATCCATCATTGAAAACGATAAATACAAGCACAATA
64 AAATCAATTCAAATCATTGAAATACACAGGATCCATCATTGAAAACGATAAATACAAGCACAATA
* * *
265101 AGCTACAGTCAAACTATTTGACCAAAATTTCCAGATTCTTATTTTCCTATCAATAC-CTCAAAAA
129 AGCTACAGTCAAACTGTTTGACCAAAACTTCCAGAATCTTATTTTCCTATCAATACACT-AAAAA
* * ** * * *
265165 TCCTTTATGTTTGGTTTAACTACAAACTTTTCGTT-ACTAAATCCTAAAAGAATGGAACAGA-AA
193 CCCTCTATGTTTAATTTAACTACAAA-TGTTCCTTCACTAAATCCTAAAAGAA--GAAAAGATAA
* * * *
265228 CTTT-TTGGCTACTCTGCAAAGAACAAATTAAATCCAAAAGCAT
255 ATTTCTTGACTACTCTGCAAAGAACAAATTAAATCCAAAAACAC
* *
265271 TCCAGAAAACAAAAAAAAAAAATTGAATATCATTTTCATAAGCAATCACACTTCACTCAAAATAA
1 TCCAGAAAACAAAAAAAAAAAATCGAATATCATTTTCATAAGCAATCACACTTTACTCAAAATAA
* * *
265336 ATCAATTCCAATCATTGAAATACACAGGATCCATCATTGAAAACGATAATTAAAAGCACAATACA
66 ATCAATTCAAATCATTGAAATACACAGGATCCATCATTGAAAACGATAAATACAAGCACAATA-A
265401 -CTACAGTCAAACTGTTTGACCAAAAACTTCCAGAA
130 GCTACAGTCAAACTGTTTGACC-AAAACTTCCAGAA
265436 CCTTCTTCTT
Statistics
Matches: 386, Mismatches: 64, Indels: 23
0.82 0.14 0.05
Matches are distributed among these distances:
293 2 0.01
294 21 0.05
296 82 0.21
297 1 0.00
298 214 0.55
299 51 0.13
300 15 0.04
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (298 bp):
TCCAGAAAACAAAAAAAAAAAATCGAATATCATTTTCATAAGCAATCACACTTTACTCAAAATAA
ATCAATTCAAATCATTGAAATACACAGGATCCATCATTGAAAACGATAAATACAAGCACAATAAG
CTACAGTCAAACTGTTTGACCAAAACTTCCAGAATCTTATTTTCCTATCAATACACTAAAAACCC
TCTATGTTTAATTTAACTACAAATGTTCCTTCACTAAATCCTAAAAGAAGAAAAGATAAATTTCT
TGACTACTCTGCAAAGAACAAATTAAATCCAAAAACAC
Found at i:267509 original size:23 final size:23
Alignment explanation
Indices: 267479--267525 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
267469 TGATCAACAA
267479 AGACAAATTCGATTAGTTTAGTG
1 AGACAAATTCGATTAGTTTAGTG
267502 AGACAAATTCGATTAGTTTAGTG
1 AGACAAATTCGATTAGTTTAGTG
267525 A
1 A
267526 CTATCTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (23 bp):
AGACAAATTCGATTAGTTTAGTG
Found at i:268281 original size:21 final size:22
Alignment explanation
Indices: 268257--268300 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
268247 CAAAATTTAA
*
268257 AAATTATTAG-AATATATTTTT
1 AAATTAATAGTAATATATTTTT
*
268278 AAATTAATAGTTATATATTTTT
1 AAATTAATAGTAATATATTTTT
268300 A
1 A
268301 TAATCGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
AAATTAATAGTAATATATTTTT
Found at i:269610 original size:21 final size:20
Alignment explanation
Indices: 269586--269629 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
269576 TTTAATTATT
269586 ATATATGTTA-AAATATTTTTA
1 ATAT-TGTTATAAATA-TTTTA
*
269607 ATATTGTTATGAATATTTTA
1 ATATTGTTATAAATATTTTA
269627 ATA
1 ATA
269630 CTTAGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATATTGTTATAAATATTTTA
Found at i:271563 original size:17 final size:18
Alignment explanation
Indices: 271534--271568 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
271524 AATCCCCAAT
271534 TTTCCCTTTCTTCTTTTC
1 TTTCCCTTTCTTCTTTTC
271552 TTTCCC-TTCTTCTTTTC
1 TTTCCCTTTCTTCTTTTC
271569 CGCCGTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCCTTTCTTCTTTTC
Done.