Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015229.1 Kokia drynarioides strain JFW-HI SEQ_130274, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 287973
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:12098 original size:55 final size:54
Alignment explanation
Indices: 12024--12128 Score: 201
Period size: 55 Copynumber: 1.9 Consensus size: 54
12014 GTGAGGATCT
12024 AAAAAAAAAAAAAATTCCTTTTTTTTTTACTAAAAGAAAAAGATTGATTANTTTA
1 AAAAAAAAAAAAAATTCCTTTTTTTTTTACTAAAAGAAAAAGATTGATTA-TTTA
12079 AAAAAAAAAAAAAATTCCTTTTTTTTTTACTAAAAGAAAAAGATTGATTA
1 AAAAAAAAAAAAAATTCCTTTTTTTTTTACTAAAAGAAAAAGATTGATTA
12129 GTCTTGTCGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (54 bp):
AAAAAAAAAAAAAATTCCTTTTTTTTTTACTAAAAGAAAAAGATTGATTATTTA
Found at i:13733 original size:38 final size:37
Alignment explanation
Indices: 13681--13798 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 37
13671 TTTCTCGAGA
13681 AAAAAACAACCTAGTTCACATTACCTCTTTTGTTTGCTT
1 AAAAAA-AACCTAGTTCACATT-CCTCTTTTGTTTGCTT
* *
13720 AAAAAAAACCTAGTTAAAATTGCCTCTTTTGTTTGCTT
1 AAAAAAAACCTAGTTCACATT-CCTCTTTTGTTTGCTT
* * *
13758 AAAAAGAA-CTCAATTCACATTGCTCTTTTGTTTGCTT
1 AAAAAAAACCT-AGTTCACATTCCTCTTTTGTTTGCTT
13795 AAAA
1 AAAA
13799 CGAACTCAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
37 21 0.30
38 43 0.61
39 6 0.09
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (37 bp):
AAAAAAAACCTAGTTCACATTCCTCTTTTGTTTGCTT
Found at i:17473 original size:20 final size:19
Alignment explanation
Indices: 17450--17494 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
17440 AAAAATAATT
17450 AAAAATGCATGAAATATTTC
1 AAAAATGCATGAAA-ATTTC
*
17470 AAAAGATTCATGAAAATTTC
1 AAAA-ATGCATGAAAATTTC
17490 AAAAA
1 AAAAA
17495 AAAAATTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 9 0.39
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (19 bp):
AAAAATGCATGAAAATTTC
Found at i:18209 original size:14 final size:15
Alignment explanation
Indices: 18192--18224 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
18182 TCCACAAAGA
18192 TTTCTTTTTCTT-TT
1 TTTCTTTTTCTTATT
18206 TTTCTTTTTCTTATT
1 TTTCTTTTTCTTATT
18221 TTTC
1 TTTC
18225 GGTTGTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTCTTATT
Found at i:20884 original size:6 final size:6
Alignment explanation
Indices: 20875--20902 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20865 AAATAAGAAT
20875 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT
20903 TCAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:21496 original size:19 final size:18
Alignment explanation
Indices: 21474--21519 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
21464 AAATAGGAAA
* *
21474 AAATAATTACAATAATATG
1 AAATAATTA-AAGAAGATG
21493 AAAT-ATTAAAGAAGATG
1 AAATAATTAAAGAAGATG
21510 AAA-AATTAAA
1 AAATAATTAAA
21520 AATCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 16 0.67
18 4 0.17
19 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATAATTAAAGAAGATG
Found at i:23396 original size:22 final size:21
Alignment explanation
Indices: 23371--23440 Score: 50
Period size: 22 Copynumber: 3.1 Consensus size: 21
23361 TCCTTTTTGT
23371 TTTACGAAAATTGAAATTTTAA
1 TTTAC-AAAATTGAAATTTTAA
* *
23393 TTTATCAAAATTCGATTATTTTAT
1 TTTA-CAAAATT-GA-AATTTTAA
* **
23417 TTTATTAAAATAAAAATTTTAA
1 TTTA-CAAAATTGAAATTTTAA
23439 TT
1 TT
23441 AAATTGTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 18 0.47
23 4 0.11
24 16 0.42
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTACAAAATTGAAATTTTAA
Found at i:24209 original size:11 final size:12
Alignment explanation
Indices: 24193--24222 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
24183 AAATTTACAA
24193 TTTTTCTTT-TT
1 TTTTTCTTTGTT
24204 TTTTTCTTTGTT
1 TTTTTCTTTGTT
24216 TTTTTCT
1 TTTTTCT
24223 CAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTGTT
Found at i:24817 original size:21 final size:19
Alignment explanation
Indices: 24784--24827 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
24774 CTAGAAAAAA
* *
24784 AGTTGTCGTTAATTTGTAAT
1 AGTTGTCATTAATTT-TAAC
24804 AGTTGATCATTAATTTTAAC
1 AGTTG-TCATTAATTTTAAC
24824 AGTT
1 AGTT
24828 AAAAGCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (19 bp):
AGTTGTCATTAATTTTAAC
Found at i:25906 original size:2 final size:2
Alignment explanation
Indices: 25901--25925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25891 AACCAAAACC
25901 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25926 GTATCGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57446 original size:2 final size:2
Alignment explanation
Indices: 57439--57464 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57429 TAGTTGCATT
57439 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
57465 CATGTGCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57977 original size:2 final size:2
Alignment explanation
Indices: 57970--57999 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57960 CTTACCCTAA
57970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58000 TGGTATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61333 original size:28 final size:27
Alignment explanation
Indices: 61271--61333 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
61261 CTTTTCAAAT
*
61271 TTTAAAATTTAATCTTTCATCTTTTAA
1 TTTAAAATTTAATCTCTCATCTTTTAA
* *
61298 TTTCAAAATTTTAATCTCT-ATTTGTTTGA
1 TTT-AAAA-TTTAATCTCTCATCT-TTTAA
61327 TTTAAAA
1 TTTAAAA
61334 ACTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 11 0.37
29 16 0.53
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (27 bp):
TTTAAAATTTAATCTCTCATCTTTTAA
Found at i:63383 original size:4 final size:4
Alignment explanation
Indices: 63374--63406 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
63364 GATTTAGCTT
63374 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
63407 GCAATGAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:66527 original size:16 final size:15
Alignment explanation
Indices: 66486--66532 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
66476 AATAAATTTA
*
66486 TGTTTATG-TTCATT
1 TGTTTATGTTTAATT
*
66500 TGTTTATTTTTAAATT
1 TGTTTATGTTT-AATT
*
66516 TGTTTGTGTTTAATT
1 TGTTTATGTTTAATT
66531 TG
1 TG
66533 AATCCATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 7 0.26
15 8 0.30
16 12 0.44
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (15 bp):
TGTTTATGTTTAATT
Found at i:71646 original size:23 final size:22
Alignment explanation
Indices: 71620--71664 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
71610 AACTTGGATT
*
71620 TAATTGAATATTTTAAAAT-TTTA
1 TAATT-AA-ATTTCAAAATATTTA
71643 TAATTAAATTTCAAAATATTTA
1 TAATTAAATTTCAAAATATTTA
71665 CTACAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTAAATTTCAAAATATTTA
Found at i:80094 original size:29 final size:29
Alignment explanation
Indices: 80059--80114 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
80049 ATTAGCAATA
*
80059 ATAAAATTATATTTTAAT-CTCCTAAAATG
1 ATAAAATTATAATTTAATCCT-CTAAAATG
*
80088 ATAAAATTTTAATTTAATCCTCTAAAA
1 ATAAAATTATAATTTAATCCTCTAAAA
80115 ATTATGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (29 bp):
ATAAAATTATAATTTAATCCTCTAAAATG
Found at i:82159 original size:29 final size:31
Alignment explanation
Indices: 82112--82174 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
82102 GTCCTTATAC
* * * *
82112 TTTTATTTGGTCACTTTTAGTCCCTGTACTT
1 TTTTATTTGGTCACATTTAATCCATATACTT
82143 TTTTATTT-GTCA-ATTTAATCCATATACTT
1 TTTTATTTGGTCACATTTAATCCATATACTT
82172 TTT
1 TTT
82175 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 4 0.14
31 8 0.29
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (31 bp):
TTTTATTTGGTCACATTTAATCCATATACTT
Found at i:84330 original size:6 final size:6
Alignment explanation
Indices: 84264--84316 Score: 97
Period size: 6 Copynumber: 8.7 Consensus size: 6
84254 CTTGGCTCCA
84264 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
84312 GAAAC
1 -AAAC
84317 AATCTAAACC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 42 0.91
7 4 0.09
ACGTcount: A:0.51, C:0.47, G:0.02, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:91479 original size:2 final size:2
Alignment explanation
Indices: 91472--91496 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91462 CCATTCTTTT
91472 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
91497 TCCGATAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:92833 original size:47 final size:47
Alignment explanation
Indices: 92774--92867 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
92764 TTGACGGTGC
92774 AAGTTTTTTTGACTTATAGATAACCCTTAAGAGCAATTGATTAAAAT
1 AAGTTTTTTTGACTTATAGATAACCCTTAAGAGCAATTGATTAAAAT
92821 AAGTTTTTTTGACTTATAGATAACCCTTAAGAGCAATTGATTAAAAT
1 AAGTTTTTTTGACTTATAGATAACCCTTAAGAGCAATTGATTAAAAT
92868 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (47 bp):
AAGTTTTTTTGACTTATAGATAACCCTTAAGAGCAATTGATTAAAAT
Found at i:101925 original size:12 final size:12
Alignment explanation
Indices: 101908--101937 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
101898 TGAGAAGAGT
101908 TTTTTTCTTTTC
1 TTTTTTCTTTTC
101920 TTTTTTCTTTTC
1 TTTTTTCTTTTC
101932 TCTTTT
1 T-TTTT
101938 GCTTCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:108861 original size:22 final size:22
Alignment explanation
Indices: 108833--108879 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
108823 TGGGAGTAAG
108833 CCTCTATTTATAGTTGAAGCCT
1 CCTCTATTTATAGTTGAAGCCT
108855 CCTCTATTTATAGTTGAAGCCT
1 CCTCTATTTATAGTTGAAGCCT
108877 CCT
1 CCT
108880 ACATCTAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (22 bp):
CCTCTATTTATAGTTGAAGCCT
Found at i:111003 original size:80 final size:80
Alignment explanation
Indices: 110870--111058 Score: 249
Period size: 80 Copynumber: 2.4 Consensus size: 80
110860 AATTAACATG
* * *
110870 AATCCCTACTACTTTTCGAA-ACCCACCGT-GTGACAATCAAGTTAAAAGAGATAAATTGTTCGA
1 AATCCCTACTACTTTTC-AAGGCCCACC-TCGTGACAATCAAGGTAAAAGAGATAAATTATTCGA
*
110933 TGTTTAAAAGATCTCTA
64 TATTTAAAAGATCTCTA
* * *
110950 AATCCC-ATCTTCTTTTTAAGGCCCACCTCGTGACATTCAAGGTAAAAGAGATAAATTATTCGAT
1 AATCCCTA-CTACTTTTCAAGGCCCACCTCGTGACAATCAAGGTAAAAGAGATAAATTATTCGAT
*
111014 ATTTAAAAGATCTTTA
65 ATTTAAAAGATCTCTA
*
111030 AATCCCTACTACTTTTCAAGGCTCACCTC
1 AATCCCTACTACTTTTCAAGGCCCACCTC
111059 CTGGCATCCA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
79 4 0.04
80 89 0.95
81 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (80 bp):
AATCCCTACTACTTTTCAAGGCCCACCTCGTGACAATCAAGGTAAAAGAGATAAATTATTCGATA
TTTAAAAGATCTCTA
Found at i:111084 original size:80 final size:80
Alignment explanation
Indices: 110912--111086 Score: 210
Period size: 80 Copynumber: 2.2 Consensus size: 80
110902 ACAATCAAGT
* * * *
110912 TAAAAGAGATAAATTGTTCGATGTTTAAAAGATCTCTAAATCCCATCTTCTTTTTAAGGCCCACC
1 TAAAAGAGATAAATTATTCGATATTTAAAAGATCTCTAAATCCCATCTACTTTTCAAGGCCCACC
* * **
110977 TCGTGACATTCAAGG
66 TCCTGACATCCAAAC
* *
110992 TAAAAGAGATAAATTATTCGATATTTAAAAGATCTTTAAATCCC-TACTACTTTTCAAGGCTCAC
1 TAAAAGAGATAAATTATTCGATATTTAAAAGATCTCTAAATCCCAT-CTACTTTTCAAGGCCCAC
*
111056 CTCCTGGCATCCAAAC
65 CTCCTGACATCCAAAC
*
111072 TGAAAA-ATATAAATT
1 T-AAAAGAGATAAATT
111087 GAACAACCAT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 76 0.94
81 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (80 bp):
TAAAAGAGATAAATTATTCGATATTTAAAAGATCTCTAAATCCCATCTACTTTTCAAGGCCCACC
TCCTGACATCCAAAC
Found at i:114284 original size:46 final size:46
Alignment explanation
Indices: 114234--114323 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
114224 CCGCGTGCAT
* * *
114234 CTTGGGATGGAAACAATGGGCTGGACCTAGTTTAAGTGGTTTTAGG
1 CTTGGGATGGAAACAATGGGCCGGACCTAGCTTAAATGGTTTTAGG
*
114280 CTTGGGATGGAAACAATGGGCCGGATCTAGCTTAAATGGTTTTA
1 CTTGGGATGGAAACAATGGGCCGGACCTAGCTTAAATGGTTTTA
114324 AACTTAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.30
Consensus pattern (46 bp):
CTTGGGATGGAAACAATGGGCCGGACCTAGCTTAAATGGTTTTAGG
Found at i:116665 original size:6 final size:7
Alignment explanation
Indices: 116644--116668 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
116634 TTCTCTCTTC
116644 AAAGAAA
1 AAAGAAA
116651 AAAGAAA
1 AAAGAAA
116658 AAAGAAA
1 AAAGAAA
116665 AAAG
1 AAAG
116669 TCTCTCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:121599 original size:61 final size:60
Alignment explanation
Indices: 121518--121657 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 60
121508 CCAAATTTGG
* *** * * * * *
121518 ATTTTTTGAAC-TTTTAGAATTAGGGTTAAAATGATAAATTTTGTAAATATTTAGGGTTAA
1 ATTTATTGAACTTTTTAGAATTAGAACTAAAA-GACAAATATTGTAAACATTAACGGTTAA
121578 ATTTATTGAACTTTTTAGAATTAGAACTAAAAGACAAATATTGTAAACATTAACGGTTAA
1 ATTTATTGAACTTTTTAGAATTAGAACTAAAAGACAAATATTGTAAACATTAACGGTTAA
*
121638 ATTTGTTGAA-TTTTTA-AATT
1 ATTTATTGAACTTTTTAGAATT
121658 TAAAATCAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 4 0.06
59 6 0.09
60 42 0.61
61 17 0.25
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (60 bp):
ATTTATTGAACTTTTTAGAATTAGAACTAAAAGACAAATATTGTAAACATTAACGGTTAA
Found at i:127981 original size:14 final size:15
Alignment explanation
Indices: 127962--127994 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
127952 AATTCTATAT
127962 GTTTCTCTTCT-GGA
1 GTTTCTCTTCTAGGA
*
127976 GTTTCTTTTCTAGGA
1 GTTTCTCTTCTAGGA
127991 GTTT
1 GTTT
127995 GTTTGTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.09, C:0.15, G:0.21, T:0.55
Consensus pattern (15 bp):
GTTTCTCTTCTAGGA
Found at i:136262 original size:14 final size:15
Alignment explanation
Indices: 136236--136264 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
136226 TTTAGTTATT
136236 TTATAACTAAAAAAA
1 TTATAACTAAAAAAA
136251 TTATAA-TAAAAAAA
1 TTATAACTAAAAAAA
136265 AATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
TTATAACTAAAAAAA
Found at i:144780 original size:31 final size:31
Alignment explanation
Indices: 144718--144780 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
144708 TTAGACATCT
**
144718 TTTAGATAATAATATTTATTTCAACTTTAAA
1 TTTAGATAATAATATTTAGATCAACTTTAAA
*
144749 TTTAGATAATAATATTTGGAT-AACTTATAAA
1 TTTAGATAATAATATTTAGATCAACTT-TAAA
144780 T
1 T
144781 AATAAATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTAGATAATAATATTTAGATCAACTTTAAA
Found at i:158412 original size:21 final size:21
Alignment explanation
Indices: 158397--158436 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
158387 TAATTGCTAC
158397 AATATGGATCACAATTATAAA
1 AATATGGATCACAATTATAAA
158418 AATATGGATCACAATTATA
1 AATATGGATCACAATTATA
158437 GTGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AATATGGATCACAATTATAAA
Found at i:167425 original size:18 final size:20
Alignment explanation
Indices: 167402--167440 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
167392 CTTACATTAT
167402 AATATTA-TATGT-TGTTAA
1 AATATTAGTATGTATGTTAA
*
167420 AATATTAGTTTGTATGTTAA
1 AATATTAGTATGTATGTTAA
167440 A
1 A
167441 GCCCATATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
AATATTAGTATGTATGTTAA
Found at i:167674 original size:27 final size:28
Alignment explanation
Indices: 167644--167697 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
167634 ATTTTTTTAT
*
167644 TTTTATAATATTACTAATTAGT-GAAAA
1 TTTTATAATATCACTAATTAGTCGAAAA
* *
167671 TTTTATAATGTCATTAATTAGTCGAAA
1 TTTTATAATATCACTAATTAGTCGAAA
167698 GACTATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (28 bp):
TTTTATAATATCACTAATTAGTCGAAAA
Found at i:168776 original size:32 final size:32
Alignment explanation
Indices: 168712--168782 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
168702 ACATTACAAT
* **
168712 TTTGGGTTGTTCTTATATTTTGTATATGCAAA
1 TTTGGGTTGATCTTATATTTTACATATGCAAA
168744 TTTGAGGTTGATCTTAT-TTTTACATATGCAAA
1 TTTG-GGTTGATCTTATATTTTACATATGCAAA
*
168776 TTCGGGT
1 TTTGGGT
168783 CGTTTGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.09
32 20 0.59
33 11 0.32
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.49
Consensus pattern (32 bp):
TTTGGGTTGATCTTATATTTTACATATGCAAA
Found at i:178768 original size:12 final size:12
Alignment explanation
Indices: 178751--178775 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
178741 TCCCCCACGC
178751 TTCTTCTTCTTG
1 TTCTTCTTCTTG
178763 TTCTTCTTCTTG
1 TTCTTCTTCTTG
178775 T
1 T
178776 CTTTTGCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCTTG
Found at i:181025 original size:14 final size:15
Alignment explanation
Indices: 181006--181034 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
180996 AAATTAAGTC
181006 TTATTATTTC-CAAA
1 TTATTATTTCGCAAA
181020 TTATTATTTCGCAAA
1 TTATTATTTCGCAAA
181035 CATTATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (15 bp):
TTATTATTTCGCAAA
Found at i:188464 original size:16 final size:17
Alignment explanation
Indices: 188445--188482 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
188435 GTATAAATAA
*
188445 ATATAGATT-ATAATTT
1 ATATAGATTAAAAATTT
*
188461 ATATTGATTAAAAATTT
1 ATATAGATTAAAAATTT
188478 ATATA
1 ATATA
188483 AAAATCAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATAGATTAAAAATTT
Found at i:194738 original size:21 final size:22
Alignment explanation
Indices: 194677--194740 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
194667 TTAGGATCGA
194677 AATTAAATTATAATTTTTATAAT
1 AATTAAATT-TAATTTTTATAAT
* * *
194700 AATAAAAATATAACTTTTA-AA-
1 AAT-TAAATTTAATTTTTATAAT
194721 AGATTAAATTTAATTTTTAT
1 A-ATTAAATTTAATTTTTAT
194741 CATTTAGTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
21 13 0.41
22 4 0.12
23 11 0.34
24 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTAAATTTAATTTTTATAAT
Found at i:202367 original size:15 final size:15
Alignment explanation
Indices: 202349--202429 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 15
202339 AATTTATATT
202349 TTAATAATAATTATA
1 TTAATAATAATTATA
*
202364 TTAAGAAT-ATTAT-
1 TTAATAATAATTATA
* *
202377 TAAATTATATATTAT-
1 TTAATAATA-ATTATA
* *
202392 TTTATTA-AATTATA
1 TTAATAATAATTATA
202406 TTTAATAATAATTATA
1 -TTAATAATAATTATA
202422 TTAA-AATA
1 TTAATAATA
202430 TGAATAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
13 10 0.19
14 10 0.19
15 26 0.49
16 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TTAATAATAATTATA
Found at i:202466 original size:60 final size:60
Alignment explanation
Indices: 202318--202471 Score: 206
Period size: 60 Copynumber: 2.5 Consensus size: 60
202308 TATTATGATG
* * * *
202318 TTATATATTATGATTTTTATTAATTTATATTTTAATAATAATTATATTAAGAATATTATTAAA
1 TTAT-TATTATTA-TTTTATTAAATTATA-TTTAATAATAATTATATTAAGAATATGAATAAA
202381 TTA-TA-TATTATTTTATTAAATTATATTTAATAATAATTATATTAA-AATATGAATAAA
1 TTATTATTATTATTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGAATAAA
*
202438 TTATTTATTATTATTTTATTAAAATATATTTAAT
1 TTA-TTATTATTATTTTATTAAATTATATTTAAT
202472 TTAAATGTTA
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
57 13 0.16
58 20 0.24
59 16 0.19
60 29 0.35
61 2 0.02
63 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (60 bp):
TTATTATTATTATTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGAATAAA
Found at i:205271 original size:31 final size:29
Alignment explanation
Indices: 205207--205275 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
205197 ATACTAACGT
** *
205207 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATAGCAAACAA
*
205236 AAGTGACTAAAATGTAACCTGAAGCAAACAA
1 AAGTGACTAAAATGTAACAT--AGCAAACAA
205267 AAGTGACTA
1 AAGTGACTA
205276 TTTTTGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATAGCAAACAA
Found at i:205444 original size:25 final size:24
Alignment explanation
Indices: 205407--205471 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
205397 AAGTTATTAC
* *
205407 TTAAATAAAATTATATTAATCTCA-T
1 TTAATTAATATTATATTAAT-T-ATT
*
205432 TTAATTAATATTAGAATTAATTATT
1 TTAATTAATATTA-TATTAATTATT
205457 TTAATTAATTATTAT
1 TTAATTAA-TATTAT
205472 TTTGAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.03
25 21 0.64
26 11 0.33
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAATTAATATTATATTAATTATT
Found at i:205462 original size:13 final size:13
Alignment explanation
Indices: 205431--205469 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
205421 ATTAATCTCA
205431 TTTAATTAA-TAT
1 TTTAATTAATTAT
**
205443 TAGAATTAATTAT
1 TTTAATTAATTAT
205456 TTTAATTAATTAT
1 TTTAATTAATTAT
205469 T
1 T
205470 ATTTTGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTAATTAATTAT
Found at i:205481 original size:29 final size:30
Alignment explanation
Indices: 205432--205490 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
205422 TTAATCTCAT
205432 TTAATTAATATTAGAATTAA-TTATTTTAA
1 TTAATTAATATTAGAATTAAGTTATTTTAA
* *
205461 TTAATTATTATTTTGAA-TAATGTTATTTTA
1 TTAATTAATA-TTAGAATTAA-GTTATTTTA
205491 GTTATGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 12 0.48
30 5 0.20
31 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
TTAATTAATATTAGAATTAAGTTATTTTAA
Found at i:207108 original size:30 final size:29
Alignment explanation
Indices: 207058--207352 Score: 241
Period size: 30 Copynumber: 9.9 Consensus size: 29
207048 TCGGATACTC
* *
207058 GGGGGTAAAAA-GGGTAATTTTGGGAAATTT
1 GGGGGTAAAAATGGG--ATTTTTGGAAGTTT
*
207088 TGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGT-AAAAATGGGATTTTTGGAAGTTT
** ** *
207118 AAGGGTAAATTTGTGATTTTTGGAAGTTTT
1 GGGGGTAAAAATGGGATTTTTGGAAG-TTT
* *
207148 GGGGTTAAAAATGAGATTTTTGGAAGTTT
1 GGGGGTAAAAATGGGATTTTTGGAAGTTT
* * *
207177 GGGGGTAAAAATTAGAATTTTTGAAAGTTT
1 GGGGGTAAAAA-TGGGATTTTTGGAAGTTT
**
207207 CAGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGT-AAAAATGGGATTTTTGGAAGTTT
* * ***
207237 GGGGGTAAAAATGGAAATTTCAAAAGTTT
1 GGGGGTAAAAATGGGATTTTTGGAAGTTT
* * * *
207266 CGGGGTTAAAAATGAGTTTTTTGGAAGTTC
1 -GGGGGTAAAAATGGGATTTTTGGAAGTTT
**** *
207296 GGGGGTAAAAACAAAATTTTTGAAAGTTT
1 GGGGGTAAAAATGGGATTTTTGGAAGTTT
*
207325 CGGGGTCAAAAATGGGATTTTTGGAAGT
1 GGGGGT-AAAAATGGGATTTTTGGAAGT
207353 CAAGGACCTC
Statistics
Matches: 205, Mismatches: 53, Indels: 14
0.75 0.19 0.05
Matches are distributed among these distances:
29 75 0.37
30 117 0.57
31 10 0.05
32 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGGGTAAAAATGGGATTTTTGGAAGTTT
Found at i:207158 original size:59 final size:58
Alignment explanation
Indices: 207058--207352 Score: 313
Period size: 59 Copynumber: 5.0 Consensus size: 58
207048 TCGGATACTC
* * *
207058 GGGGGTAAAAAGGGTAATTTTGGGAAA-TTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAAA-TG-AATTTT-TGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
** ** * * * * *
207118 AAGGGTAAATTTGTGATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTGGAAGTTT
1 GGGGGTAAAAATG-AATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
*
207177 GGGGGTAAAAATTAGAATTTTTGAAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGTAAAAA-T-GAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
* ** * * * *
207237 GGGGGTAAAAATGGAAATTTCAAAAGTTTCGGGGTTAAAAATGAGTTTTTTGGAAGTTC
1 GGGGGTAAAAAT-GAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
**
207296 GGGGGTAAAAACAAAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGT
1 GGGGGTAAAAA-TGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGT
207353 CAAGGACCTC
Statistics
Matches: 194, Mismatches: 37, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
58 3 0.02
59 132 0.68
60 58 0.30
61 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (58 bp):
GGGGGTAAAAATGAATTTTTGAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTT
Found at i:209099 original size:17 final size:18
Alignment explanation
Indices: 209079--209135 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 18
209069 TGAGCTTTAC
* *
209079 TTAAATTT-ATAATAATT
1 TTAAATTTGAAAATAAAT
209096 TTAAATTTGAAAATAAAT
1 TTAAATTTGAAAATAAAT
* *
209114 TTAAACTT-AAATTAAAT
1 TTAAATTTGAAAATAAAT
209131 TTAAA
1 TTAAA
209136 ATAAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAATTTGAAAATAAAT
Found at i:209123 original size:6 final size:6
Alignment explanation
Indices: 209095--209149 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
209085 TTATAATAAT
* * *
209095 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
209141 TTTAAA TTT
1 TTTAAA TTT
209150 TTAAACAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
5 12 0.30
6 25 0.62
7 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:209134 original size:11 final size:11
Alignment explanation
Indices: 209109--209148 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
209099 AATTTGAAAA
*
209109 TAAATTTAAACT
1 TAAA-TTAAATT
209121 TAAATTAAATT
1 TAAATTAAATT
*
209132 TAAAATAAATT
1 TAAATTAAATT
209143 TAAATT
1 TAAATT
209149 TTTAAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:209145 original size:17 final size:17
Alignment explanation
Indices: 209079--209182 Score: 76
Period size: 18 Copynumber: 6.3 Consensus size: 17
209069 TGAGCTTTAC
* *
209079 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
209096 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
*
209114 TTAAA-CT----TAAA-
1 TTAAATTTAAAATAAAT
209125 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
209142 TTAAATTTTTAAACAAAT
1 TTAAA-TTTAAAATAAAT
* *
209160 TTAATTTTTAACATAAAT
1 TTAA-ATTTAAAATAAAT
209178 TTAAA
1 TTAAA
209183 AGTAGTTTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.07
12 5 0.07
16 4 0.06
17 14 0.21
18 39 0.58
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:210816 original size:82 final size:82
Alignment explanation
Indices: 210721--210887 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
210711 AACTCCAGTA
210721 AACACATCACATAACCTAACACTTCTAATCCTAATCCCCTTCGAACCCTAGTATCACCAACTCGA
1 AACACATCACATAACCTAACACTTCTAATCCTAATCCCCTTCGAACCCTAGTATCACCAACTCGA
210786 TTCTTACCAAAACCCCC
66 TTCTTACCAAAACCCCC
210803 AACACATCACATAACCTAACACTTCTAATCCTAATCCCCTTCGAACCCTAGTATCACCAACTCGA
1 AACACATCACATAACCTAACACTTCTAATCCTAATCCCCTTCGAACCCTAGTATCACCAACTCGA
210868 TTCTTACCAAAACCCCC
66 TTCTTACCAAAACCCCC
210885 AAC
1 AAC
210888 CCCTCTCAAC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.35, C:0.39, G:0.04, T:0.23
Consensus pattern (82 bp):
AACACATCACATAACCTAACACTTCTAATCCTAATCCCCTTCGAACCCTAGTATCACCAACTCGA
TTCTTACCAAAACCCCC
Found at i:216003 original size:6 final size:6
Alignment explanation
Indices: 215985--216020 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
215975 ATTTTTAAAT
215985 TTTC-A TTTC-A TTTCAA TTT-AA TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTT
216021 GAACTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 14 0.48
6 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTCAA
Found at i:216030 original size:17 final size:17
Alignment explanation
Indices: 215994--216031 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
215984 TTTTCATTTC
*
215994 ATTTCAATTTAATTTCA
1 ATTTCAATTTAACTTCA
216011 ATTTCAATTTGAACTT-A
1 ATTTCAATTT-AACTTCA
216028 ATTT
1 ATTT
216032 TAAACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTCAATTTAACTTCA
Found at i:216205 original size:16 final size:16
Alignment explanation
Indices: 216184--216230 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
216174 AAATTAAATT
*
216184 TTAATTTTGAACTTTA
1 TTAATTTTAAACTTTA
216200 TTAATTTTAAACTTTA
1 TTAATTTTAAACTTTA
216216 -T-ATTATTAAACTTTA
1 TTAATT-TTAAACTTTA
216231 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 3 0.10
15 11 0.38
16 15 0.52
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (16 bp):
TTAATTTTAAACTTTA
Found at i:216275 original size:28 final size:28
Alignment explanation
Indices: 216234--216363 Score: 88
Period size: 28 Copynumber: 4.5 Consensus size: 28
216224 AACTTTAATT
*
216234 TTAAATTTCAATTTCATTCAAATTTGAA
1 TTAAATTTAAATTTCATTCAAATTTGAA
* *
216262 CTT-AATTTAAATTTCATTTAAATTTTAA
1 -TTAAATTTAAATTTCATTCAAATTTGAA
** *
216290 TTAAATTTTAAATTGAAAATT-AAATTTTAA
1 TTAAA-TTTAAATT--TCATTCAAATTTGAA
*
216320 TTTTAAA-TTAAATTTCATTTAAA-TTGAAAA
1 --TTAAATTTAAATTTCATTCAAATTTG--AA
*
216350 TTAAATTTTAATTT
1 TTAAATTTAAATTT
216364 TAAACTTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
27 2 0.02
28 34 0.41
29 20 0.24
30 18 0.22
31 3 0.04
32 5 0.06
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (28 bp):
TTAAATTTAAATTTCATTCAAATTTGAA
Found at i:216298 original size:11 final size:11
Alignment explanation
Indices: 216263--216362 Score: 65
Period size: 11 Copynumber: 8.5 Consensus size: 11
216253 AAATTTGAAC
216263 TTAATTTAAATT
1 TTAA-TTAAATT
* *
216275 TCATTTAAATT
1 TTAATTAAATT
216286 TTAATTAAATT
1 TTAATTAAATT
*
216297 TTAAATTGAAAAT
1 TT-AATT-AAATT
* *
216310 TAAATTTTAATT
1 TTAA-TTAAATT
216322 TTAAATTAAATT
1 TT-AATTAAATT
* *
216334 TCATTTAAATT
1 TTAATTAAATT
**
216345 GAAAATTAAATT
1 -TTAATTAAATT
216357 TTAATT
1 TTAATT
216363 TTAAACTTTA
Statistics
Matches: 66, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
11 30 0.45
12 27 0.41
13 9 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAATTAAATT
Found at i:216299 original size:18 final size:18
Alignment explanation
Indices: 216278--216334 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
216268 TTAAATTTCA
216278 TTTAAATTTTAATTAAAT
1 TTTAAATTTTAATTAAAT
**
216296 TTTAAATTGAAAATTAAAT
1 TTTAAATT-TTAATTAAAT
216315 TTT-AATTTTAAATTAAAT
1 TTTAAATTTT-AATTAAAT
216333 TT
1 TT
216335 CATTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 22 0.67
19 11 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTTAATTAAAT
Found at i:216313 original size:41 final size:40
Alignment explanation
Indices: 216268--216367 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 40
216258 TGAACTTAAT
* *
216268 TTAAATTTCA-TTTAAATTTTAATTAAATTTTAAATTGAAAA
1 TTAAATTTAATTTTAAA-TTAAATTAAA-TTTAAATTGAAAA
**
216309 TTAAATTTTAATTTTAAATTAAATTTCATTTAAATTGAAAA
1 TTAAA-TTTAATTTTAAATTAAATTAAATTTAAATTGAAAA
216350 TTAAATTTTAATTTTAAA
1 TTAAA-TTTAATTTTAAA
216368 CTTTATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 36 0.68
42 11 0.21
43 6 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (40 bp):
TTAAATTTAATTTTAAATTAAATTAAATTTAAATTGAAAA
Found at i:216357 original size:18 final size:18
Alignment explanation
Indices: 216288--216362 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
216278 TTTAAATTTT
216288 AATTAAATTTTAAATTGAA
1 AATTAAA-TTTAAATTGAA
* **
216307 AATTAAATTTTAATTTTA
1 AATTAAATTTAAATTGAA
216325 AATTAAATTTCATTTAAATTGAA
1 AATT-AA----ATTTAAATTGAA
*
216348 AATTAAATTTTAATT
1 AATTAAATTTAAATT
216363 TTAAACTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 20 0.45
19 9 0.20
22 2 0.05
23 13 0.30
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTAAATTTAAATTGAA
Found at i:216380 original size:28 final size:27
Alignment explanation
Indices: 216349--216403 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
216339 TAAATTGAAA
* *
216349 ATTAAATTTTAATTTTAAACTTTATATT
1 ATTAAACTTGAATTTTAAA-TTTATATT
*
216377 ATTAAACTTGAATTTTAAATTTCTATT
1 ATTAAACTTGAATTTTAAATTTATATT
216404 TCATTTACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTAAACTTGAATTTTAAATTTATATT
Found at i:216383 original size:15 final size:14
Alignment explanation
Indices: 216349--216395 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
216339 TAAATTGAAA
*
216349 ATTAAATTTTAATT
1 ATTAAACTTTAATT
216363 -TTAAACTTTATATT
1 ATTAAACTTTA-ATT
*
216377 ATTAAACTTGAATT
1 ATTAAACTTTAATT
216391 -TTAAA
1 ATTAAA
216396 TTTCTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 14 0.48
14 6 0.21
15 9 0.31
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTAAACTTTAATT
Found at i:216395 original size:41 final size:39
Alignment explanation
Indices: 216200--216398 Score: 119
Period size: 41 Copynumber: 5.0 Consensus size: 39
216190 TTGAACTTTA
* *
216200 TTAATTTTAAACTTTATATTATTAAACTTTAATTTTAAATT
1 TTAATTTTAAA-TTTA-ATTATTAAACTTGAAATTTAAATT
* * * * *
216241 TCAA-TTT-CATTCAAAT-TTGAACTT--AATTTAAA-T
1 TTAATTTTAAATTTAATTATTAAACTTGAAATTTAAATT
* *
216274 TTCA-TTTAAATTTTAATTAAATTTTAAA-TTGAAAATTAAATT
1 TTAATTTTAAA-TTTAATT--A--TTAAACTTGAAATTTAAATT
* *
216316 TTAATTTTAAATTAAATTTCATTTAAA-TTGAAAATTAAATT
1 TTAATTTTAAATTTAA-TT-A-TTAAACTTGAAATTTAAATT
*
216357 TTAATTTTAAACTTTATATTATTAAACTTGAATTTTAAATT
1 TTAATTTTAAA-TTTA-ATTATTAAACTTGAAATTTAAATT
216398 T
1 T
216399 CTATTTCATT
Statistics
Matches: 124, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
33 6 0.05
34 8 0.06
35 5 0.04
36 7 0.06
37 2 0.02
38 3 0.02
39 3 0.02
40 12 0.10
41 55 0.44
42 14 0.11
43 9 0.07
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (39 bp):
TTAATTTTAAATTTAATTATTAAACTTGAAATTTAAATT
Found at i:216496 original size:28 final size:27
Alignment explanation
Indices: 216401--216496 Score: 76
Period size: 28 Copynumber: 3.6 Consensus size: 27
216391 TTAAATTTCT
* * *
216401 ATTTCATTTACATTTGAACTTAACTTAA
1 ATTTCATTT-CATTTTAATTTAAATTAA
* * *
216429 ATTTCAATTTCATTTAAATTTTAAGTAA
1 ATTTC-ATTTCATTTTAATTTAAATTAA
216457 ATTT--TTT-A--TTAATTTAAAATTAA
1 ATTTCATTTCATTTTAATTT-AAATTAA
216480 ATTTCATTTCATTTTAA
1 ATTTCATTTCATTTTAA
216497 ACTTGTATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
22 6 0.11
23 9 0.17
24 1 0.02
25 6 0.11
26 1 0.02
28 26 0.49
29 4 0.08
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (27 bp):
ATTTCATTTCATTTTAATTTAAATTAA
Found at i:216524 original size:6 final size:6
Alignment explanation
Indices: 216505--216564 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
216495 AAACTTGTAT
* * * *
216505 TTTAAT TTTGAA TTTAAA TTTGAA TTACAAAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT--TAA-A TTTAAA TTTAAA TTTAAA
216556 TTTAAA TTT
1 TTTAAA TTT
216565 GTATGTATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 38 0.86
7 2 0.05
8 1 0.02
9 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:219577 original size:54 final size:54
Alignment explanation
Indices: 219453--219561 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
219443 TCAATAGTTT
* * * *
219453 TAAAACAAAAAAAAATTGAATACTGATAAATGTGATCCCGACCATTAATAGGGA
1 TAAAACAAAAAAAAATTGAATACTGAAAAAGGTGATCCCGACCATCAATAAGGA
* *
219507 TAAAACAAAAAAAAATTGAATACTGAAAAAGGTGATTCCGACGATCAATAAGGA
1 TAAAACAAAAAAAAATTGAATACTGAAAAAGGTGATCCCGACCATCAATAAGGA
219561 T
1 T
219562 GAAATCAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (54 bp):
TAAAACAAAAAAAAATTGAATACTGAAAAAGGTGATCCCGACCATCAATAAGGA
Found at i:219902 original size:19 final size:20
Alignment explanation
Indices: 219859--219895 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
219849 TTTGTTTTCA
219859 AATTAATTAATATATTATAT
1 AATTAATTAATATATTATAT
*
219879 AATTAA-TAATATTTTAT
1 AATTAATTAATATATTAT
219896 TATATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAATTAATATATTATAT
Found at i:225129 original size:3 final size:3
Alignment explanation
Indices: 225121--225145 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
225111 TAAAATTGAT
225121 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
225146 ATAGGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:233824 original size:31 final size:31
Alignment explanation
Indices: 233783--233847 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
233773 TACAATTTGA
* *
233783 TCATTGAACTATTCGAA-AATTTTCATTTAAG
1 TCATTAAACTATTCAAATAATTTT-ATTTAAG
*
233814 TCATTAAACTATTTAAATAATTTTATTTAAG
1 TCATTAAACTATTCAAATAATTTTATTTAAG
233845 TCA
1 TCA
233848 CTGGGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (31 bp):
TCATTAAACTATTCAAATAATTTTATTTAAG
Found at i:237091 original size:15 final size:16
Alignment explanation
Indices: 237062--237094 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
237052 TTTTAATTTT
*
237062 AAAATTTAAGTTTTCA
1 AAAATTTAAGATTTCA
237078 AAAATTTAA-ATTTCA
1 AAAATTTAAGATTTCA
237093 AA
1 AA
237095 TTTTTACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATTTAAGATTTCA
Found at i:237581 original size:12 final size:12
Alignment explanation
Indices: 237564--237610 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
237554 ATCATTAACA
237564 AATAAACGAGTC
1 AATAAACGAGTC
*
237576 AATAAATGAG-C
1 AATAAACGAGTC
* *
237587 TTATAAACGAGGC
1 -AATAAACGAGTC
237600 AATAAACGAGT
1 AATAAACGAGT
237611 TTGTTAGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:238058 original size:20 final size:19
Alignment explanation
Indices: 238026--238085 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 19
238016 TTTTAAAAAT
*
238026 AAAAAATTCAAAAAATATA
1 AAAAAATTAAAAAAATATA
*
238045 AAAAATATTAAAAAGAATTTA
1 AAAAA-ATTAAAAA-AATATA
* *
238066 AAAAGCATAAAAAAAATATA
1 AAAA-AATTAAAAAAATATA
238086 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 16 0.48
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAAATTAAAAAAATATA
Found at i:239821 original size:166 final size:166
Alignment explanation
Indices: 239357--239854 Score: 887
Period size: 166 Copynumber: 3.0 Consensus size: 166
239347 TTTTTTGCTG
*
239357 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATACTCAGTTTTATGGAAAAAGAG
1 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAGTTTTATGGAAAAAGAG
*
239422 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATCCGAGTTCCTTTG
66 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
*
239487 CTCCTTATATATTTCATAAAGGGGATGGTATCTTTC
131 CTCCTTATATAATTCATAAAGGGGATGGTATCTTTC
* *
239523 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAG-TTT-T--ACAGAGAG
1 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAGTTTTATGGAAAAAGAG
239584 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
66 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
**
239649 CTCCTTATATAATTCGCAAAGGGGATGGTATCTTTC
131 CTCCTTATATAATTCATAAAGGGGATGGTATCTTTC
239685 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAGTTTTATGGAAAAAGAG
1 CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAGTTTTATGGAAAAAGAG
239750 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
66 GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
* *
239815 CTCCTTACATAATTCATAAAGGGGATGGTATCCTTC
131 CTCCTTATATAATTCATAAAGGGGATGGTATCTTTC
239851 CCTT
1 CCTT
239855 CTTTTGAGCT
Statistics
Matches: 315, Mismatches: 13, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
162 152 0.48
163 3 0.01
164 2 0.01
165 3 0.01
166 155 0.49
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (166 bp):
CCTTGGTTATCTAAGTTTAACTTGAGAATGATACTATTTCAATTCTCAGTTTTATGGAAAAAGAG
GATCTCTTTTTGCTCATCTGCTTGCTTAGAAAACTTTCCAATTGTACATAATTCGAGTTCCTTTG
CTCCTTATATAATTCATAAAGGGGATGGTATCTTTC
Found at i:244955 original size:12 final size:12
Alignment explanation
Indices: 244940--244993 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
244930 TAATAATAAT
244940 AAAAACAACAGC
1 AAAAACAACAGC
*
244952 AAAAATAACAGC
1 AAAAACAACAGC
* *
244964 -AACACAACAAC
1 AAAAACAACAGC
* *
244975 AAAAATAATAGC
1 AAAAACAACAGC
244987 AAAAACA
1 AAAAACA
244994 TCAAAACAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.69, C:0.20, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAACAACAGC
Found at i:244977 original size:23 final size:23
Alignment explanation
Indices: 244944--244988 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
244934 AATAATAAAA
*
244944 ACAACAGCAAAAATAACAGCAAC
1 ACAACAACAAAAATAACAGCAAC
*
244967 ACAACAACAAAAATAATAGCAA
1 ACAACAACAAAAATAACAGCAA
244989 AAACATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.22, G:0.07, T:0.07
Consensus pattern (23 bp):
ACAACAACAAAAATAACAGCAAC
Found at i:244993 original size:26 final size:25
Alignment explanation
Indices: 244940--244990 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
244930 TAATAATAAT
*
244940 AAAA-ACAACAGCAAAAATAACAGC
1 AAAACACAACAACAAAAATAACAGC
*
244964 --AACACAACAACAAAAATAATAGC
1 AAAACACAACAACAAAAATAACAGC
244987 AAAA
1 AAAA
244991 ACATCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.09
23 18 0.82
25 2 0.09
ACGTcount: A:0.69, C:0.20, G:0.06, T:0.06
Consensus pattern (25 bp):
AAAACACAACAACAAAAATAACAGC
Found at i:246177 original size:44 final size:40
Alignment explanation
Indices: 246113--246198 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 40
246103 ATTTATGAGG
246113 ATATTTTTATATATAATAAATCAATAAAAATTTAATTATAATA
1 ATATTTTTATATATAATAAAT-AAT--AAATTTAATTATAATA
** * *
246156 ATATTTTTCATATATGTTAAATAATTAATTTTATTATAATA
1 ATATTTTT-ATATATAATAAATAATAAATTTAATTATAATA
246197 AT
1 AT
246199 CAAAGTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 16 0.42
43 11 0.29
44 11 0.29
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (40 bp):
ATATTTTTATATATAATAAATAATAAATTTAATTATAATA
Found at i:247204 original size:22 final size:22
Alignment explanation
Indices: 247179--247256 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 22
247169 ATCAAACCAG
*
247179 AAAATGGCAACTGAAATAGCAA
1 AAAAAGGCAACTGAAATAGCAA
* * * *
247201 AAAAAGACAAGTG--A-ACCAG
1 AAAAAGGCAACTGAAATAGCAA
*
247220 AAAAGGGCAACTGAAATAGCAA
1 AAAAAGGCAACTGAAATAGCAA
* *
247242 AAAAAGACAAGTGAA
1 AAAAAGGCAACTGAA
247257 CTTACACTCT
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
19 13 0.32
20 1 0.03
21 1 0.03
22 25 0.62
ACGTcount: A:0.58, C:0.13, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGGCAACTGAAATAGCAA
Found at i:247220 original size:41 final size:41
Alignment explanation
Indices: 247173--247257 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
247163 TAAGGCATCA
*
247173 AACCAGAAAATGGCAACTGAAATAGCAAAAAAAGACAAGTG
1 AACCAGAAAAGGGCAACTGAAATAGCAAAAAAAGACAAGTG
247214 AACCAGAAAAGGGCAACTGAAATAGCAAAAAAAGACAAGTG
1 AACCAGAAAAGGGCAACTGAAATAGCAAAAAAAGACAAGTG
247255 AAC
1 AAC
247258 TTACACTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.56, C:0.15, G:0.20, T:0.08
Consensus pattern (41 bp):
AACCAGAAAAGGGCAACTGAAATAGCAAAAAAAGACAAGTG
Found at i:251982 original size:6 final size:6
Alignment explanation
Indices: 251971--251999 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
251961 TGGTGAAATA
251971 GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
252000 AGAAAAATAA
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:0.17, C:0.00, G:0.69, T:0.14
Consensus pattern (6 bp):
GGAGGT
Found at i:253203 original size:19 final size:18
Alignment explanation
Indices: 253179--253242 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
253169 GTATAGTAAT
253179 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTAC-AA
* *
253198 TTTTAT-ATTTCTTTATAT
1 TTTTATAATTT-TTTACAA
253216 TTTTATAATTTTATTACAA
1 TTTTATAATTTT-TTACAA
*
253235 CTTTATAA
1 TTTTATAA
253243 AATTTTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 12 0.32
19 25 0.68
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTTTTACAA
Found at i:253250 original size:37 final size:37
Alignment explanation
Indices: 253177--253256 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
253167 TGGTATAGTA
* **
253177 ATTTTTATAATTTTTTACGAATTTTATATTTCTTTAT
1 ATTTTTATAATTTTTTACGAACTTTATAAATCTTTAT
253214 ATTTTTATAATTTTATTAC-AACTTTATAAAAT-TTTAT
1 ATTTTTATAATTTT-TTACGAACTTTAT-AAATCTTTAT
253251 ATTTTT
1 ATTTTT
253257 TTCTATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (37 bp):
ATTTTTATAATTTTTTACGAACTTTATAAATCTTTAT
Found at i:259706 original size:4 final size:4
Alignment explanation
Indices: 259697--259723 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
259687 TGGCCGAGCA
259697 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
259724 TGTCAAGGCT
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:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:262564 original size:14 final size:16
Alignment explanation
Indices: 262532--262565 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
262522 CGTTCACATA
262532 TTCAATTTCTATGTAT
1 TTCAATTTCTATGTAT
262548 TTCAA-TTCTAT-TAT
1 TTCAATTTCTATGTAT
262562 TTCA
1 TTCA
262566 TCCACATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (16 bp):
TTCAATTTCTATGTAT
Found at i:264657 original size:23 final size:24
Alignment explanation
Indices: 264616--264670 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
264606 TCTCCAAAAA
264616 AAAAAAATTAGAATCAGATTA-T-
1 AAAAAAATTAGAATCAGATTATTC
* *
264638 AAAAAAATTGATAATGAGATTATTC
1 AAAAAAATT-AGAATCAGATTATTC
264663 AAAAAAAT
1 AAAAAAAT
264671 GTATTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.32
23 10 0.36
24 1 0.04
25 8 0.29
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (24 bp):
AAAAAAATTAGAATCAGATTATTC
Found at i:267356 original size:16 final size:17
Alignment explanation
Indices: 267323--267367 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
267313 ACAATCTTTA
*
267323 TTTTTT-TACTAATAAT
1 TTTTTTATAATAATAAT
267339 TTTTCTTA-AATAAT-AT
1 TTTT-TTATAATAATAAT
267355 TTTTTTATAATAA
1 TTTTTTATAATAA
267368 AAAAAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 3 0.12
16 15 0.60
17 7 0.28
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTTATAATAATAAT
Found at i:276427 original size:25 final size:27
Alignment explanation
Indices: 276399--276454 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
276389 ATTCGAGTGA
*
276399 TTCTATTTGTT-TTTTTGAAG-TTCAG
1 TTCTATATGTTATTTTTGAAGTTTCAG
*
276424 TTCT-TATGTTATTTTTGTAGTTTCAG
1 TTCTATATGTTATTTTTGAAGTTTCAG
*
276450 ATCTA
1 TTCTA
276455 CTGTTTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 5 0.20
25 12 0.48
26 8 0.32
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (27 bp):
TTCTATATGTTATTTTTGAAGTTTCAG
Found at i:280595 original size:17 final size:18
Alignment explanation
Indices: 280562--280595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
280552 TAAGTTTTAA
280562 AATAAATATAGGCATAAT
1 AATAAATATAGGCATAAT
*
280580 AATAAATTTA-GCATAA
1 AATAAATATAGGCATAA
280596 CATTTACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (18 bp):
AATAAATATAGGCATAAT
Found at i:283397 original size:11 final size:13
Alignment explanation
Indices: 283380--283408 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
283370 TTATCACGTG
283380 TTTTTT-TTAATA
1 TTTTTTCTTAATA
283392 TTTTTTCTTAATA
1 TTTTTTCTTAATA
283405 TTTT
1 TTTT
283409 AGTATACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCTTAATA
Done.