Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004804.1 Hibiscus syriacus cultivar Beakdansim tig00010822_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 107396
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1476 original size:2 final size:2
Alignment explanation
Indices: 1469--1499 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1459 GAACTAGAAG
1469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1500 TCTATGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9109 original size:272 final size:266
Alignment explanation
Indices: 8494--9199 Score: 956
Period size: 272 Copynumber: 2.6 Consensus size: 266
8484 TTGTTGTTAA
* *
8494 AAACCCTAAACCCTAAGCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAATAAATATGT-ACC
1 AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATATGTAACC
* * *
8558 ACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTGCCCTCAACATACCATAAATTTATA
66 ACCATCATGATAGATATCTCCAT-CTCTACCCCTTTCATTGCCCTCAACATACCATGAATTTATA
* *
8623 AAGGTTTTCAGCAATAACTAAATATTTTAGGGTTTAGGGTTCCAAAATTAATATACAACAAATAA
130 AAGGTTTTCAGTAATAACAAAATATTTTAGGGTTTAGGGTTCCAAAATTAATATACAACAAATAA
* *
8688 TAAGCAACTATTATTTTTTAAACCCTAAACCCTAAAATTTTTTAGTTATTATTGAAAACCCTAAA
195 TAAGCAACTATTATTTTGTAAACCCTAAA--C-AAAATTTTTGAGTTATTATTGAAAACCCTAAA
8753 CCTAAATCAT
257 CCTAAATCAT
* * * * *
8763 AAACCATAAATCCTGACCATTCTCTCTCCAATCAATTTCTTCTTATAAAAAACAAATCTGTAACC
1 AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATATGTAACC
8828 ACCATCATGATAGATATCTCCATACTCTACCCCTTTCATTGCCCTCAACATACCATGAATTTATA
66 ACCATCATGATAGATATCTCCAT-CTCTACCCCTTTCATTGCCCTCAACATACCATGAATTTATA
* *
8893 AAGGCTTTCAGTAATAATCAAAATATTTTAGGGTTTAGGGTTCCAAAATTAATATATAACAAATA
130 AAGGTTTTCAGTAATAA-CAAAATATTTTAGGGTTTAGGGTTCCAAAATTAATATACAACAAAT-
* * * *
8958 ATATAAGTAACTATTGATTTTGTAAACCCT-AA-AATA-TTTTGA-TTGTTATTGAAAACCTTAA
193 A-ATAAGCAACTATT-ATTTTGTAAACCCTAAACAAAATTTTTGAGTTATTATTGAAAACCCTAA
*
9019 ACTCTAACCCTATCTT
256 AC-CTAA----ATCAT
* * *
9035 AAACCCTAAACCCTCACCATTCTCCCTCCAATCAATTTATTCTTATAAAAAAGAAATATGTAACC
1 AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATATGTAACC
**
9100 ACCATCATGATAGATAT-TACCATCATCTACCCCTTTCATTGCCCTCAACATACTGTGAATTTAT
66 ACCATCATGATAGATATCT-CCATC-TCTACCCCTTTCATTGCCCTCAACATACCATGAATTTAT
* * *
9164 AAAGGTTTTTAGTAACAACCAAAAGATTTTAGGGTT
129 AAAGGTTTTCAGTAATAA-CAAAATATTTTAGGGTT
9200 AGTGGCGATC
Statistics
Matches: 389, Mismatches: 36, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
267 19 0.05
268 9 0.02
269 57 0.15
270 79 0.20
271 46 0.12
272 152 0.39
273 14 0.04
274 13 0.03
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (266 bp):
AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATATGTAACC
ACCATCATGATAGATATCTCCATCTCTACCCCTTTCATTGCCCTCAACATACCATGAATTTATAA
AGGTTTTCAGTAATAACAAAATATTTTAGGGTTTAGGGTTCCAAAATTAATATACAACAAATAAT
AAGCAACTATTATTTTGTAAACCCTAAACAAAATTTTTGAGTTATTATTGAAAACCCTAAACCTA
AATCAT
Found at i:10206 original size:59 final size:58
Alignment explanation
Indices: 10081--10230 Score: 239
Period size: 59 Copynumber: 2.6 Consensus size: 58
10071 ATTGATAAAA
* **
10081 TAAATCATATCGATCATATGTTAATTAATCAAATAAAAAGTTCGTTGAAATTATCAAT
1 TAAATCATATCGAACATACATTAATTAATCAAATAAAAAGTTCGTTGAAATTATCAAT
*
10139 TAAATCATATCGAACATACATTAATTAATCAAATAAAAAAGTTCTTTGAAATTATCAAT
1 TAAATCATATCGAACATACATTAATTAATCAAAT-AAAAAGTTCGTTGAAATTATCAAT
10198 TAAATCATATC-AGACATACATTAATTAATCAAA
1 TAAATCATATCGA-ACATACATTAATTAATCAAA
10231 AGTTGAAAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
58 32 0.37
59 54 0.63
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (58 bp):
TAAATCATATCGAACATACATTAATTAATCAAATAAAAAGTTCGTTGAAATTATCAAT
Found at i:19833 original size:29 final size:31
Alignment explanation
Indices: 19769--19833 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
19759 TTTGAAAAAT
*
19769 CATTTTTGTCCCTAAACTTTTACAAAATTTA
1 CATTTTTGTCCCTAAACTTTTACAAAATGTA
*
19800 TATTTTTG-CCACTAAAC-TTT-CAAAATGTA
1 CATTTTTGTCC-CTAAACTTTTACAAAATGTA
19829 CATTT
1 CATTT
19834 AGTAACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 12 0.40
30 5 0.17
31 13 0.43
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (31 bp):
CATTTTTGTCCCTAAACTTTTACAAAATGTA
Found at i:31512 original size:2 final size:2
Alignment explanation
Indices: 31499--31538 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
31489 CTAAAAATAC
31499 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31539 TTTGAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31691 original size:17 final size:18
Alignment explanation
Indices: 31669--31705 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31659 AACTAAATCA
31669 AAATAAT-ATAAAATTAT
1 AAATAATCATAAAATTAT
*
31686 AAATAATCATTAAATTAT
1 AAATAATCATAAAATTAT
31704 AA
1 AA
31706 TAAAATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAATCATAAAATTAT
Found at i:32887 original size:21 final size:21
Alignment explanation
Indices: 32863--32906 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
32853 TGATAAAATA
* *
32863 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATCAATATTT
32884 TTATTTAAAATATCAATATTT
1 TTATTTAAAATATCAATATTT
32905 TT
1 TT
32907 TAATATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAAATATCAATATTT
Found at i:39927 original size:32 final size:32
Alignment explanation
Indices: 39876--39954 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
39866 TATTTTGTTA
39876 GGGTCGGGTC-GGTTTTTTAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTC
39907 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAGTGTGATATTC
39939 GGGTCGGGTCGGGTTT
1 GGGTCGGGTCGGGTTT
39955 AGGGTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 10 0.21
32 37 0.79
ACGTcount: A:0.10, C:0.10, G:0.41, T:0.39
Consensus pattern (32 bp):
GGGTCGGGTCGGGTTTTTTAAGTGTGATATTC
Found at i:44627 original size:7 final size:7
Alignment explanation
Indices: 44615--44640 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44605 AATATTCCTT
44615 CATGTTA
1 CATGTTA
44622 CATGTTA
1 CATGTTA
44629 CATGTTA
1 CATGTTA
44636 CATGT
1 CATGT
44641 GTAACCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (7 bp):
CATGTTA
Found at i:46312 original size:23 final size:23
Alignment explanation
Indices: 46285--46362 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
46275 CAGGGTTATT
46285 TTGTTAAGTAATACTTAATCTTA
1 TTGTTAAGTAATACTTAATCTTA
***
46308 TTGTTAAG-AA-A-TTAGGGTTA
1 TTGTTAAGTAATACTTAATCTTA
*
46328 TTTTGTTAAAGTAGTACTTAAATCTTA
1 --TTGTT-AAGTAATACTT-AATCTTA
46355 TTGTTAAG
1 TTGTTAAG
46363 AAATTTGGGA
Statistics
Matches: 41, Mismatches: 7, Indels: 13
0.67 0.11 0.21
Matches are distributed among these distances:
20 6 0.15
21 1 0.02
22 7 0.17
23 11 0.27
24 4 0.10
25 6 0.15
26 2 0.05
27 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TTGTTAAGTAATACTTAATCTTA
Found at i:46363 original size:47 final size:45
Alignment explanation
Indices: 46276--46367 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 45
46266 GACTAAGTTC
46276 AGGGTTATTTTGTTAAGTAATACTTAATCTTATTGTTAAGAAATT
1 AGGGTTATTTTGTTAAGTAATACTTAATCTTATTGTTAAGAAATT
*
46321 AGGGTTATTTTGTTAAAGTAGTACTTAAATCTTATTGTTAAGAAATT
1 AGGGTTATTTTGTT-AAGTAATACTT-AATCTTATTGTTAAGAAATT
46368 TGGGATTAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 14 0.32
46 10 0.23
47 20 0.45
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (45 bp):
AGGGTTATTTTGTTAAGTAATACTTAATCTTATTGTTAAGAAATT
Found at i:46382 original size:46 final size:45
Alignment explanation
Indices: 46290--46382 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 45
46280 TTATTTTGTT
**
46290 AAGTAATACTTAATCTTATTGTTAAGAAATTAGGGTTATTTTGTTA
1 AAGTAATACTTAATCTTATTGTTAAGAAATTAGGGTTA-TGGGTTA
* *
46336 AAGTAGTACTTAAATCTTATTGTTAAGAAATTTGGGATTA-GGGTTA
1 AAGTAATACTT-AATCTTATTGTTAAGAAATTAGGG-TTATGGGTTA
46382 A
1 A
46383 CTCAGTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 15 0.37
47 23 0.56
48 3 0.07
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.42
Consensus pattern (45 bp):
AAGTAATACTTAATCTTATTGTTAAGAAATTAGGGTTATGGGTTA
Found at i:46807 original size:20 final size:20
Alignment explanation
Indices: 46782--46823 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
46772 TTGAATTTAA
46782 ATTCCTTAGATATAGTTTTG
1 ATTCCTTAGATATAGTTTTG
46802 ATTCCTTAGATATAGTTTTG
1 ATTCCTTAGATATAGTTTTG
46822 AT
1 AT
46824 AAGGTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (20 bp):
ATTCCTTAGATATAGTTTTG
Found at i:57905 original size:24 final size:24
Alignment explanation
Indices: 57876--57922 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
57866 ATAAAATATA
57876 TATTTTTATTATAATTATATTTTT
1 TATTTTTATTATAATTATATTTTT
* *
57900 TATTTTTATTTTTATTATATTTT
1 TATTTTTATTATAATTATATTTT
57923 ATTACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (24 bp):
TATTTTTATTATAATTATATTTTT
Found at i:57908 original size:15 final size:16
Alignment explanation
Indices: 57876--57925 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
57866 ATAAAATATA
*
57876 TATTTTTATTATA-AT
1 TATTTTTATTATATTT
57891 TATATTTT-TTAT-TTT
1 TAT-TTTTATTATATTT
57906 TATTTTTATTATATTT
1 TATTTTTATTATATTT
57922 TATT
1 TATT
57926 ACAATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.13
15 15 0.50
16 11 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATTATATTT
Found at i:59402 original size:21 final size:21
Alignment explanation
Indices: 59378--59440 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
59368 AGTTTATTTT
*
59378 TAAACGTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
59399 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
59420 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
59441 AACTTGGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:59481 original size:33 final size:33
Alignment explanation
Indices: 59429--59501 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
59419 GTAAACTTTG
* *
59429 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTACCGAACTTGGAAGTATTTAAGTA
*
59461 TTTGAATTTACCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTACCGAACTTGGAAGTATTTAAGTA
59494 TTTCAATT
1 TTTCAATT
59502 AGGGATGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (33 bp):
TTTCAATTTACCGAACTTGGAAGTATTTAAGTA
Found at i:59887 original size:35 final size:35
Alignment explanation
Indices: 59841--59908 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
59831 ACCAAACCCG
59841 TCCCCGTTTAGCATAAACGGTTTTCCCCATCCTCT
1 TCCCCGTTTAGCATAAACGGTTTTCCCCATCCTCT
* *
59876 TCCCCGTTTAGCATAAACGGTTTTTCCCGTCCT
1 TCCCCGTTTAGCATAAACGGTTTTCCCCATCCT
59909 TGTTTAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.13, T:0.35
Consensus pattern (35 bp):
TCCCCGTTTAGCATAAACGGTTTTCCCCATCCTCT
Found at i:60247 original size:19 final size:19
Alignment explanation
Indices: 60223--60261 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
60213 GCAAGAAATG
60223 GTGATGAATGTGCTTTGAT
1 GTGATGAATGTGCTTTGAT
60242 GTGATGAATGTGCTTTGAT
1 GTGATGAATGTGCTTTGAT
60261 G
1 G
60262 AGAGTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (19 bp):
GTGATGAATGTGCTTTGAT
Found at i:61849 original size:31 final size:30
Alignment explanation
Indices: 61814--61891 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
61804 CGTCCCCAAC
*
61814 AGGTCGCCATGCATTCCCCA-ACACCCTTACA
1 AGGTCGCCATGCACTCCCCAGACA-CC-TACA
* **
61845 AGGTCGCCAAGCACT-CCCAGTGACCTACA
1 AGGTCGCCATGCACTCCCCAGACACCTACA
61874 AGGTCGCCATGCACTCCC
1 AGGTCGCCATGCACTCCC
61892 AGCGACCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 18 0.45
30 8 0.20
31 14 0.35
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.17
Consensus pattern (30 bp):
AGGTCGCCATGCACTCCCCAGACACCTACA
Found at i:61878 original size:29 final size:29
Alignment explanation
Indices: 61841--61956 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 29
61831 CCAACACCCT
* *
61841 TACAAGGTCGCCAAGCACTCCCAGTGACC
1 TACAAGGTCGCCAAGCAATCCCAGCGACC
* *
61870 TACAAGGTCGCCATGCACTCCCAGCGACC
1 TACAAGGTCGCCAAGCAATCCCAGCGACC
*** *
61899 TTGTAGGTCGCCAAGCAATCCCGGCGACC
1 TACAAGGTCGCCAAGCAATCCCAGCGACC
***
61928 TTGTAGGTCGCCAAGCAATCCCAGCGACC
1 TACAAGGTCGCCAAGCAATCCCAGCGACC
61957 AAGCCTCGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.24, C:0.37, G:0.23, T:0.16
Consensus pattern (29 bp):
TACAAGGTCGCCAAGCAATCCCAGCGACC
Found at i:61915 original size:58 final size:58
Alignment explanation
Indices: 61845--61956 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
61835 CACCCTTACA
* * * *
61845 AGGTCGCCAAGCACTCCCAGTGACCTACAAGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCAAGCAATCCCAGCGACCTACAAGGTCGCCAAGCAATCCCAGCGACCTTGT
* ***
61903 AGGTCGCCAAGCAATCCCGGCGACCTTGTAGGTCGCCAAGCAATCCCAGCGACC
1 AGGTCGCCAAGCAATCCCAGCGACCTACAAGGTCGCCAAGCAATCCCAGCGACC
61957 AAGCCTCGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (58 bp):
AGGTCGCCAAGCAATCCCAGCGACCTACAAGGTCGCCAAGCAATCCCAGCGACCTTGT
Found at i:62036 original size:32 final size:32
Alignment explanation
Indices: 61995--62059 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
61985 ACTTAACCCT
61995 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
62027 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
62059 G
1 G
62060 GAGATTCCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.28
Consensus pattern (32 bp):
GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
Found at i:62075 original size:23 final size:23
Alignment explanation
Indices: 62045--62088 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
62035 GTGCATGGGT
62045 TGCATCCATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
62068 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
62089 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:62528 original size:28 final size:29
Alignment explanation
Indices: 62497--62572 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
62487 TAGGGTAAAA
62497 TTAAAATT-TAGTTA-ATTAGTTTGTTAGT
1 TTAAAATTATA-TTATATTAGTTTGTTAGT
*
62525 TT-AAGTTATATTATATTAGTTTGTTAGT
1 TTAAAATTATATTATATTAGTTTGTTAGT
**
62553 TTAAGTTATATATTATATTA
1 TTAAAAT-TATATTATATTA
62573 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.17
28 20 0.49
29 2 0.05
30 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (29 bp):
TTAAAATTATATTATATTAGTTTGTTAGT
Found at i:62893 original size:20 final size:22
Alignment explanation
Indices: 62859--62899 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
62849 TTAAAAAAAA
62859 TGTTGTGTTTAAAAATATTTAG
1 TGTTGTGTTTAAAAATATTTAG
62881 TGTTGT-TTTAAAAATATTT
1 TGTTGTGTTTAAAAATATTT
62900 TGTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (22 bp):
TGTTGTGTTTAAAAATATTTAG
Found at i:62910 original size:20 final size:21
Alignment explanation
Indices: 62866--62910 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
62856 AAATGTTGTG
**
62866 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
62887 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
62907 TTTA
1 TTTA
62911 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:66064 original size:60 final size:60
Alignment explanation
Indices: 65991--66677 Score: 740
Period size: 60 Copynumber: 12.2 Consensus size: 60
65981 GTATTTATAA
* *
65991 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAATAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
66051 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
66111 GATTTAATAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
66171 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
*
66220 GA-TTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
66279 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
66339 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTT-A--A--CGAT--T--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
66390 GA--TAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
66448 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
* *
66497 GA-TTAGTAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
66556 GATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
66615 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTAATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
66663 GATTTAGTAATGATT
1 GATTTAGTAATGATT
66678 TGATAGTAAT
Statistics
Matches: 536, Mismatches: 44, Indels: 99
0.79 0.06 0.15
Matches are distributed among these distances:
48 31 0.06
49 76 0.14
50 5 0.01
51 23 0.04
52 23 0.04
53 8 0.01
54 12 0.02
55 10 0.02
56 20 0.04
57 13 0.02
58 11 0.02
59 68 0.13
60 236 0.44
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:66176 original size:49 final size:49
Alignment explanation
Indices: 66106--66673 Score: 507
Period size: 49 Copynumber: 10.6 Consensus size: 49
66096 TGATTTGATA
66106 TTAATGATTT-A-A-TAATGATTAGTAATAATGAAATTATTATTAATTT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
66152 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
66201 TTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATGAAATTATTATTAATATT
1 TTAATGATTTGATAGTAATGA-T--T-A-G-----TAATAATGAAATTATTATTAAT-TT
* *
66261 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATT
1 T--T-A-ATGAT--T--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * *
66321 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATAT
1 T--T-A-ATGAT--T--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTT
* *
66380 TTAACGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTATTTT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
66429 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
66478 TTAATGATTTGATAGTAATGATTAGTAATTATTAGTAATAATGAAATTATTATTAATATT
1 TTAATGATTTGATAGT-A--A-T-G-----ATTAGTAATAATGAAATTATTATTAAT-TT
*
66538 TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATG-AATTATTATTAATTT
1 T--T-A-ATG--ATT--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTT
* *
66596 TTAATGATTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATAT
1 TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
* *
66644 TTAATGATTTAATATTAATGATTTAGTAAT
1 TTAATGATTTGATAGTAATGA-TTAGTAAT
66674 GATTTGATAG
Statistics
Matches: 459, Mismatches: 16, Indels: 91
0.81 0.03 0.16
Matches are distributed among these distances:
46 10 0.02
47 1 0.00
48 53 0.12
49 160 0.35
50 5 0.01
51 3 0.01
52 5 0.01
53 3 0.01
54 4 0.01
55 4 0.01
56 2 0.00
57 1 0.00
58 3 0.01
59 64 0.14
60 100 0.22
62 2 0.00
63 2 0.00
64 6 0.01
65 2 0.00
66 6 0.01
67 2 0.00
68 6 0.01
69 2 0.00
70 13 0.03
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:66180 original size:24 final size:24
Alignment explanation
Indices: 66153--66233 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
66143 TATTAATTTT
66153 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* *** * * * **
66177 TAATAATGAAATTATTATTAATTTT
1 TAATGATTTGA-TAGTAATGATTAG
66202 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
66226 TAATGATT
1 TAATGATT
66234 AATAATAATG
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:66278 original size:21 final size:19
Alignment explanation
Indices: 66254--66398 Score: 69
Period size: 21 Copynumber: 7.2 Consensus size: 19
66244 AAATTATTAT
66254 TAATATTTAATGATTTGATAG
1 TAATATTTAAT-A-TTGATAG
* *
66275 TAATGATTTAGTAATGATTAG
1 TAAT-ATTTAATATTGA-TAG
* * * *
66296 TAATAATGAA-ATTGTTAT
1 TAATATTTAATATTGATAG
66314 TAATATTTAATGATTTGATAG
1 TAATATTTAAT-A-TTGATAG
* *
66335 TAATGATTTAGTAATGATTAG
1 TAAT-ATTTAATATTGA-TAG
* * * *
66356 TAATAATGAA-ATTGTTAT
1 TAATATTTAATATTGATAG
*
66374 TAATATTTAACGATTTGATAG
1 TAATATTTAA-TA-TTGATAG
66395 TAAT
1 TAAT
66399 GATTAGTAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
18 20 0.22
19 6 0.07
20 14 0.16
21 38 0.42
22 12 0.13
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (19 bp):
TAATATTTAATATTGATAG
Found at i:66391 original size:228 final size:227
Alignment explanation
Indices: 65994--66677 Score: 1122
Period size: 228 Copynumber: 3.1 Consensus size: 227
65984 TTTATAAGAT
* *
65994 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAGT
1 TTAGTAATGATTA-TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
*
66059 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATGA
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGA
66124 TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
130 TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
66189 TATTATTAATTTTTAATGATTTGATAGTAATGA
195 TATTATTAATTTTTAATGATTTGATAGTAATGA
66222 TTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
1 TTAGTAATGATT-ATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
* *
66287 AATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGA
* * *
66352 TTAGTAATAATGAAATTGTTATTAATATTTAACGATTTGATAGTAATGATTAGTAATAATGAAAT
130 TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
66417 TATTATTATTTTTTAATGATTTGATAGTAATGA
195 TATTATTAATTTTTAATGATTTGATAGTAATGA
*
66450 -T--T-A-G----TAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
1 TTAGTAATGATTATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
66505 ATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
*
66570 TAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT-AATTT
131 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
* * *
66633 ATTATTAATATTTAATGATTTAATATTAATGA
196 ATTATTAATTTTTAATGATTTGATAGTAATGA
66665 TTTAGTAATGATT
1 -TTAGTAATGATT
66678 TGATAGTAAT
Statistics
Matches: 425, Mismatches: 21, Indels: 24
0.90 0.04 0.05
Matches are distributed among these distances:
215 32 0.08
216 44 0.10
217 80 0.19
218 44 0.10
219 1 0.00
220 1 0.00
221 1 0.00
223 1 0.00
224 1 0.00
225 1 0.00
227 1 0.00
228 217 0.51
229 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (227 bp):
TTAGTAATGATTATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
ATTATTAATTTTTAATGATTTGATAGTAATGA
Found at i:66489 original size:277 final size:275
Alignment explanation
Indices: 66118--66624 Score: 942
Period size: 277 Copynumber: 1.8 Consensus size: 275
66108 AATGATTTAA
66118 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
1 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
66183 TGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATGAAAT
66 TGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATGAAAT
*
66248 TATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTGTTA
131 TATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG-AATTATTA
66313 TTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAAT
195 TTAATATTTAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTGTTATTAAT
66378 ATTTAACGATTTGATAG
259 ATTTAACGATTTGATAG
*
66395 TAATGATTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAA
1 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
* *
66460 TGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATTATTAGTAATAATGAAAT
66 TGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATGAAAT
*
66525 TATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAATTATTAT
131 TATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTAT
*
66590 TAATTTTTAATGATTTGATAGTAATGATTAGTAAT
196 TAATATTTAATGATTTGATAGTAATGATTAGTAAT
66625 AATAATTTAT
Statistics
Matches: 224, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
275 8 0.04
276 34 0.15
277 182 0.81
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (275 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
TGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAATAATAATGAAAT
TATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTAT
TAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATAT
TTAACGATTTGATAG
Found at i:66504 original size:59 final size:59
Alignment explanation
Indices: 66441--66624 Score: 325
Period size: 59 Copynumber: 3.1 Consensus size: 59
66431 AATGATTTGA
66441 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
* * *
66500 TAGTAATTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-T
66560 TAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
66618 TAGTAAT
1 TAGTAAT
66625 AATAATTTAT
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
58 8 0.07
59 89 0.75
60 21 0.18
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
Found at i:66526 original size:108 final size:114
Alignment explanation
Indices: 65994--66624 Score: 627
Period size: 109 Copynumber: 5.6 Consensus size: 114
65984 TTTATAAGAT
* * *
65994 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAGT
1 TTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGT
*
66059 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
64 AATGATTAGTAATAATGAAATTATTATTAATATTT-ATGATATGA-ATT-ATGA
*
66113 TTTAATAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA-TAGT
1 -TTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
* * * *
66168 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
64 AATGATTAGTAATAATGAAATTATTATTAA-TATTTATGATATGA-A-TTATGA
* *
66222 TTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
1 TTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGT
* * *
66287 AATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
64 AATGATTAGTAATAATGAAATTATTATTAATATTT-ATGATATGA-A-TTATGA
* * *
66341 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTT-A--A--CGAT--T--TGA-TAGT
1 -TTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
* * * *
66396 AATGATTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGA
64 AATGATTAGTAATAATGAAATTATTATTAATATTT-ATGATATGA-A-TTATGA
*
66450 TTAG---T-A--A-TAATGA--AATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* *
66506 TTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
66 TGATTAGTAATAATGAAATTATTATTAATATTT-ATGATATGA-ATT-ATGA
66558 TTTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTA
1 -TTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTA
66623 AT
65 AT
66625 AATAATTTAT
Statistics
Matches: 448, Mismatches: 27, Indels: 74
0.82 0.05 0.13
Matches are distributed among these distances:
98 15 0.03
99 1 0.00
101 6 0.01
102 1 0.00
103 3 0.01
104 1 0.00
105 2 0.00
107 4 0.01
108 93 0.21
109 109 0.24
110 4 0.01
111 7 0.02
112 1 0.00
113 7 0.02
115 9 0.02
116 5 0.01
117 5 0.01
118 47 0.10
119 53 0.12
120 75 0.17
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (114 bp):
TTAGTAATGATTAGTAATAATGAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
TGATTAGTAATAATGAAATTATTATTAATATTTATGATATGAATTATGA
Found at i:66617 original size:48 final size:48
Alignment explanation
Indices: 66560--66673 Score: 176
Period size: 48 Copynumber: 2.4 Consensus size: 48
66550 ATTAATGATT
* *
66560 TAGTAATGATTAGTAATAATGAA-TTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTAA
66608 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTAA
1 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTAA
*
66656 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
66674 GATTTGATAG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
47 2 0.03
48 51 0.84
49 8 0.13
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTAA
Found at i:66648 original size:21 final size:22
Alignment explanation
Indices: 66624--66673 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
66614 TGATTAGTAA
*
66624 TAATAATTTATTATTAAT-ATT
1 TAATAATTTAATATTAATGATT
*
66645 TAATGATTTAATATTAATGATT
1 TAATAATTTAATATTAATGATT
*
66667 TAGTAAT
1 TAATAAT
66674 GATTTGATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TAATAATTTAATATTAATGATT
Found at i:66661 original size:14 final size:14
Alignment explanation
Indices: 66530--66693 Score: 61
Period size: 14 Copynumber: 11.2 Consensus size: 14
66520 GAAATTATTA
66530 TTAATATTTAATGAT
1 TTAATA-TTAATGAT
*
66545 TTGATATTAATGA-
1 TTAATATTAATGAT
*
66558 TT--TAGTAATGAT
1 TTAATATTAATGAT
* *
66570 TAGTAATAATGAATTATT
1 T--TAAT-ATTAATGA-T
*
66588 ATTAATTTTTAATGAT
1 -TTAA-TATTAATGAT
* *
66604 TTGATAGTAATGAT
1 TTAATATTAATGAT
* *
66618 TAGTAATAATAATTTATT
1 T--TAATATTAA-TGA-T
66636 ATTAATATTTAATGAT
1 -TTAATA-TTAATGAT
66652 TTAATATTAATGA-
1 TTAATATTAATGAT
*
66665 TT--TAGTAATGAT
1 TTAATATTAATGAT
* *
66677 TTGATAGTAATGAT
1 TTAATATTAATGAT
66691 TTA
1 TTA
66694 CGACTTGAAC
Statistics
Matches: 113, Mismatches: 18, Indels: 37
0.67 0.11 0.22
Matches are distributed among these distances:
11 16 0.14
12 3 0.03
13 4 0.04
14 36 0.32
15 14 0.12
16 10 0.09
17 22 0.19
18 6 0.05
19 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (14 bp):
TTAATATTAATGAT
Found at i:66674 original size:118 final size:118
Alignment explanation
Indices: 66441--66678 Score: 331
Period size: 118 Copynumber: 2.0 Consensus size: 118
66431 AATGATTTGA
66441 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * * *
66506 TTATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
66 TAATAAGTAATAATGAAATTATGATTAATATTTAATGATTT-ATAGTAATGATT
66560 TAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
* * * *
66624 TAATAATTTATTATTAATATTTAATGATTTAATA-TTAATGA-TT-TAGTAATGATT
66 TAATAAGTAATAATGAA-A-TT-ATGA-TTAATATTTAATGATTTATAGTAATGATT
66678 T
1 T
66679 GATAGTAATG
Statistics
Matches: 107, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
118 65 0.61
119 22 0.21
120 4 0.04
121 10 0.09
122 6 0.06
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (118 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
TAATAAGTAATAATGAAATTATGATTAATATTTAATGATTTATAGTAATGATT
Found at i:67711 original size:23 final size:23
Alignment explanation
Indices: 67685--67729 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
67675 AAAATTACAA
*
67685 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
67708 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
67730 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:69422 original size:13 final size:13
Alignment explanation
Indices: 69383--69429 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
69373 CTCACAAGAG
69383 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
69397 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
69411 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
69424 -CTTTCT
1 CCTTTCT
69430 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:69474 original size:26 final size:26
Alignment explanation
Indices: 69436--69485 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
69426 TTCTTTCTCG
*
69436 GCTGCAATTTCTTCTCCATTTCTTCT
1 GCTGCAATCTCTTCTCCATTTCTTCT
*
69462 GCTGCAATCTCTTCTCCCTTTCTT
1 GCTGCAATCTCTTCTCCATTTCTT
69486 TCTTTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.10, C:0.34, G:0.08, T:0.48
Consensus pattern (26 bp):
GCTGCAATCTCTTCTCCATTTCTTCT
Found at i:69565 original size:23 final size:23
Alignment explanation
Indices: 69538--69581 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
69528 AGGTGTCACC
69538 GGCTGCCTCAATTATTTCACCCA
1 GGCTGCCTCAATTATTTCACCCA
69561 GGCTGCCTCAATTATTTCACC
1 GGCTGCCTCAATTATTTCACC
69582 AATAATTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (23 bp):
GGCTGCCTCAATTATTTCACCCA
Found at i:69823 original size:29 final size:29
Alignment explanation
Indices: 69747--69828 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
69737 CTTGGTCGTC
* ***
69747 GGGACTGCTTGGCGACCTACAAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
*
69776 GGGAGTGCATGGCGACCTTGTAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
69805 GGGAGTGCTTGGCGACCTTGTAGG
1 GGGAGTGCTTGGCGACCTTGTAGG
69829 GGTGTTGGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (29 bp):
GGGAGTGCTTGGCGACCTTGTAGGTCGCT
Found at i:71412 original size:17 final size:17
Alignment explanation
Indices: 71390--71424 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
71380 TTTATTTTAA
71390 TATATATAATATTAATTAT
1 TATA-ATAAT-TTAATTAT
71409 TATAATAATTTAATTA
1 TATAATAATTTAATTA
71425 AATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATAATTTAATTAT
Found at i:79374 original size:341 final size:342
Alignment explanation
Indices: 78751--79436 Score: 1324
Period size: 341 Copynumber: 2.0 Consensus size: 342
78741 TTCAAAATAA
78751 ATTAAGTGCAAAACCAACCTACAGCATAGAAATCAACCAGACAAAAACAAACCTTTAACTGAGAA
1 ATTAAGTGCAAAACCAACCTACAGCATAGAAATCAACCAGACAAAAACAAACCTTTAACTGAGAA
78816 AGGCTTCTTTCAGCTCTTTTCTTATTAACTGAGACTCCGCCTGGTAATGTCTCCTTGCTGTCAAG
66 AGGCTTCTTTCAGCTCTTTTCTTATTAACTGAGACTCCGCCTGGTAATGTCTCCTTGCTGTCAAG
78881 AATTACTGCAGTTAGGCAAAGATGGATTCCACTAGCGTTATCAAAGGTAATATAAAGTAGTTCAG
131 AATTACTGCAGTTAGGCAAAGATGGATTCCACTAGCGTTATCAAAGGTAATATAAAGTAGTTCAG
78946 CTCTGTGTTGCCACTTTTTCGAACATGGATGAATCACCATTTCACCACAGGGTTAATTCAAATGA
196 CTCTGTGTTGCCACTTTTTCGAACATGGATGAATCACCATTTCACCACAGGGTTAATTCAAATGA
79011 AAAATAAAACTTAAAACTGCAAGGAAAAATGTAG-A-GGGATTTTAAAAGACAACACAATTTTTT
261 AAAATAAAACTTAAAACTGCAAGGAAAAATGTAGAATGGGATTTTAAAAGACAACACAA-TTTTT
79074 TGCAGTTCAAAGTACGAG
325 TGCAGTTCAAAGTACGAG
79092 ATTAAGTGCAAAACCAACCTACAGCATAGAAATCAACCAGACAAAAACAAACCTTTAACTGAGAA
1 ATTAAGTGCAAAACCAACCTACAGCATAGAAATCAACCAGACAAAAACAAACCTTTAACTGAGAA
79157 AGGCTTCTTTCAGCTCTTTTCTTATTAACTGAGACTCCGCCTGGTAATGTCTCCTTGCTGTCAAG
66 AGGCTTCTTTCAGCTCTTTTCTTATTAACTGAGACTCCGCCTGGTAATGTCTCCTTGCTGTCAAG
79222 AAATTACTGCAGTTAGGCAAAGATGGATTCCACTAGCGTTATCAAAGGTAATATAAAGTAGTTCA
131 -AATTACTGCAGTTAGGCAAAGATGGATTCCACTAGCGTTATCAAAGGTAATATAAAGTAGTTCA
79287 GCTCTGTGTTGCCACTTTTTCGAACATGGATGAATCACCATTTCACCACAGGGTTAATTCAAATG
195 GCTCTGTGTTGCCACTTTTTCGAACATGGATGAATCACCATTTCACCACAGGGTTAATTCAAATG
79352 AAAAATAAAACTT-AAACTGCAAGGAAAAATGTAGAAATGGGATTTTAAAAGACAACACAATTTT
260 AAAAATAAAACTTAAAACTGCAAGGAAAAATGTAG-AATGGGATTTTAAAAGACAACACAATTTT
79416 TTGCAGTTCAAAGTACGAG
324 TTGCAGTTCAAAGTACGAG
79435 AT
1 AT
79437 CCAGAAAGCA
Statistics
Matches: 341, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
341 151 0.44
342 142 0.42
343 26 0.08
344 22 0.06
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (342 bp):
ATTAAGTGCAAAACCAACCTACAGCATAGAAATCAACCAGACAAAAACAAACCTTTAACTGAGAA
AGGCTTCTTTCAGCTCTTTTCTTATTAACTGAGACTCCGCCTGGTAATGTCTCCTTGCTGTCAAG
AATTACTGCAGTTAGGCAAAGATGGATTCCACTAGCGTTATCAAAGGTAATATAAAGTAGTTCAG
CTCTGTGTTGCCACTTTTTCGAACATGGATGAATCACCATTTCACCACAGGGTTAATTCAAATGA
AAAATAAAACTTAAAACTGCAAGGAAAAATGTAGAATGGGATTTTAAAAGACAACACAATTTTTT
GCAGTTCAAAGTACGAG
Found at i:81224 original size:12 final size:12
Alignment explanation
Indices: 81194--81226 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
81184 ATATTTAGTC
81194 TATTTAATCTGG
1 TATTTAATCTGG
81206 TATTTTAATCTGG
1 TA-TTTAATCTGG
81219 TATTTAAT
1 TATTTAAT
81227 TAGGGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (12 bp):
TATTTAATCTGG
Found at i:82127 original size:19 final size:19
Alignment explanation
Indices: 82103--82154 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
82093 CCTCTATACA
*
82103 TGGTTTCAAAACCGCTGAC
1 TGGTTTCAAAACCACTGAC
* *
82122 TGGTTTCTAAACCCACTGTC
1 TGGTTTC-AAAACCACTGAC
*
82142 TAGTTTCAAAACC
1 TGGTTTCAAAACC
82155 TCATATTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (19 bp):
TGGTTTCAAAACCACTGAC
Found at i:83151 original size:3 final size:3
Alignment explanation
Indices: 83129--83203 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
83119 TGATTACTTT
* *
83129 GAA GAA AAA TAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
83175 GAA -ACA GAA G-A GGA GAA AAA GAA AAA GAA
1 GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA
83204 AAAAAAACCA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.05
3 53 0.88
4 4 0.07
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:83651 original size:31 final size:31
Alignment explanation
Indices: 83595--83658 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
83585 AACATAGTTG
* *
83595 AGGGAATAAAATCGAATAGACCGATAATGTT
1 AGGGAATAAAATCGAACAGACCGATAACGTT
* * *
83626 AGGGATTAAAATCGAACGGATCGATAACGTT
1 AGGGAATAAAATCGAACAGACCGATAACGTT
83657 AG
1 AG
83659 AGATCATTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (31 bp):
AGGGAATAAAATCGAACAGACCGATAACGTT
Found at i:84000 original size:20 final size:19
Alignment explanation
Indices: 83968--84005 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
83958 ATGATATTTG
83968 TTTTATATTAATTTTTAAT
1 TTTTATATTAATTTTTAAT
83987 TTTTATATTTAATTTTTAA
1 TTTTATA-TTAATTTTTAA
84006 AGTATTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATTAATTTTTAAT
Found at i:84424 original size:20 final size:20
Alignment explanation
Indices: 84399--84495 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
84389 ATTCGCGTTG
*
84399 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
**
84419 CATTTCGCGTTATGATTTTC
1 CATTTCGCGTTGCGATTTTC
** * **
84439 CAGCTCGCATTGCGATAGTTGA
1 CATTTCGCGTTGCGAT--TTTC
* *
84461 AAATT-GCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
84480 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
84496 AGTCTACAGT
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
19 5 0.09
20 38 0.68
21 9 0.16
22 4 0.07
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:84477 original size:41 final size:42
Alignment explanation
Indices: 84432--84520 Score: 110
Period size: 41 Copynumber: 2.1 Consensus size: 42
84422 TTCGCGTTAT
84432 GATTTTCCAGCTCGCATTGCGATAGT-TGAAAATTG-CGTTGC
1 GATTTTCCAGCTCGCATTGCGATAGTCT-AAAATTGTCGTTGC
** * * *
84473 GATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGC
1 GATTTTCCAGCTCGCATTGCGATAGTCTAAAATTGTCGTTGC
84515 GATTTT
1 GATTTT
84521 TCAAATTCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 28 0.68
42 13 0.32
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (42 bp):
GATTTTCCAGCTCGCATTGCGATAGTCTAAAATTGTCGTTGC
Found at i:84513 original size:22 final size:22
Alignment explanation
Indices: 84487--84550 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
84477 TTCCATTTCG
84487 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
84509 CGTTGCGAT--TTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
84528 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
84550 C
1 C
84551 AAAATTCTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
19 10 0.32
20 5 0.16
21 5 0.16
22 11 0.35
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:84644 original size:6 final size:6
Alignment explanation
Indices: 84633--84671 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
84623 GACACGTATT
84633 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
84672 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:85327 original size:22 final size:22
Alignment explanation
Indices: 85299--85351 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
85289 AATTTGGAAA
*
85299 ATCGCAACGACAACTGTAGATT
1 ATCGCAACGACAACTGTAGACT
*
85321 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
85343 ATCGCAACG
1 ATCGCAACG
85352 CGAAATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:85368 original size:20 final size:20
Alignment explanation
Indices: 85343--85413 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
85333 ACTGTAGACT
85343 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* * **
85363 ATCGCAACGCG-ATTCAACT
1 ATCGCAACGCGAAATGAAAA
* *
85382 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
85402 ATCGCAACGCGA
1 ATCGCAACGCGA
85414 TTTTCAACTG
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:85386 original size:39 final size:40
Alignment explanation
Indices: 85340--85438 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 40
85330 ACAACTGTAG
85340 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGA-TTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTCA
* *
85379 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGA-TTTCA
*
85420 ACTGTCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
85439 CAACGCGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 33 0.61
41 21 0.39
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTCA
Found at i:93309 original size:19 final size:19
Alignment explanation
Indices: 93285--93334 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
93275 TAACCGTACT
*
93285 AAATTTATTAAACATTTTA
1 AAATTTATTAAAAATTTTA
93304 AAATTTA-TAATAAATTTTA
1 AAATTTATTAA-AAATTTTA
*
93323 AAATTAATTAAA
1 AAATTTATTAAA
93335 TTAGTCGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTATTAAAAATTTTA
Found at i:93390 original size:23 final size:24
Alignment explanation
Indices: 93348--93392 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
93338 GTCGAACTTT
*
93348 ATTATTTTTATTTAAAAATTAAAA
1 ATTAATTTTATTTAAAAATTAAAA
*
93372 ATTAATTTTA-TTAATAATTAA
1 ATTAATTTTATTTAAAAATTAA
93393 CTTTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTAATTTTATTTAAAAATTAAAA
Found at i:106315 original size:24 final size:24
Alignment explanation
Indices: 106278--106324 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
106268 CAATAGAATC
*
106278 AACAATAGTACTAGAGTCAGATTT
1 AACAATAGTACTAGAATCAGATTT
* *
106302 AACAATTGTGCTAGAATCAGATT
1 AACAATAGTACTAGAATCAGATT
106325 CTTTACTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (24 bp):
AACAATAGTACTAGAATCAGATTT
Done.