Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013530.1 Kokia drynarioides strain JFW-HI SEQ_128556, 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: 335120
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 315 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:232932 original size:58 final size:58
Alignment explanation
Indices: 232765--233014 Score: 222
Period size: 58 Copynumber: 4.3 Consensus size: 58
232755 ACTCGAGGGC
* * * * *
232765 AAAATAGTAA-TTTTGGAAAAGTTAGGGGTCAAAAACGGAATTTTTAGACA-TTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATTA-GGGTCAAAAATGGAATTTTTGGA-AGTT-TGGGGT
* * * * *
232824 TAAATGGTACTTTTTGGAAGAATTGGGGTC-AAAATGGAGTTTTTGGAAGTTTGGGGT
1 AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGT
* ** *
232881 AAATTTTTAATTTTTGAAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTT-GGGGT
* * * * * *
232940 AAAATGGTAA-TTTTGGAAAAATCAAGGTCAAAAATGCAATTTTAGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTT-TGGGGT
*
232998 AAAAAT-ATAATTTTTGG
1 -AAAATGGTAATTTTTGG
233015 GAAGTTCGAG
Statistics
Matches: 154, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
57 28 0.18
58 80 0.52
59 35 0.23
60 11 0.07
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGT
Found at i:232990 original size:116 final size:118
Alignment explanation
Indices: 232775--233000 Score: 253
Period size: 116 Copynumber: 1.9 Consensus size: 118
232765 AAAATAGTAA
* * * * *
232775 TTTTGGAAAAGTTAGGGGTCAAAAACGGAATTTTTAGACATTCGGGGGTTAAATGGTACTTTTTG
1 TTTTGAAAAAATTAGGGGTCAAAAACGGAATTTTTAGACATTCAGGGGTAAAATGGTACATTTTG
* *** * * * * *
232840 GAAGAATTGGGGTCAAAATGGAGTTTTTGGAAGTT-TGGGGTAAATTTTTAAT
66 GAAAAATCAAGGTCAAAATGCAATTTTAGAAAGTTCGGGGGTAAATTTTTAAT
* * *
232892 TTTTGAAAAAATTA-GGGTCAAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAATGGTA-ATTTT
1 TTTTGAAAAAATTAGGGGTCAAAAACGGAATTTTTAGACA-TTCAGGGGTAAAATGGTACATTTT
232954 GGAAAAATCAAGGTCAAAAATGCAATTTTAGAAAGTTCGGGGGTAAA
65 GGAAAAATCAAGGTC-AAAATGCAATTTTAGAAAGTTCGGGGGTAAA
233001 AATATAATTT
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
115 16 0.18
116 53 0.60
117 20 0.22
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (118 bp):
TTTTGAAAAAATTAGGGGTCAAAAACGGAATTTTTAGACATTCAGGGGTAAAATGGTACATTTTG
GAAAAATCAAGGTCAAAATGCAATTTTAGAAAGTTCGGGGGTAAATTTTTAAT
Found at i:233032 original size:30 final size:30
Alignment explanation
Indices: 232964--233032 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
232954 GGAAAAATCA
*
232964 AGGTCAAAAATGCAATTTTAGAAAGTTCGG
1 AGGTCAAAAATACAATTTTAGAAAGTTCGG
* * * *
232994 GGGT-AAAAATATAATTTTTGGGAAGTTC-G
1 AGGTCAAAAATACAA-TTTTAGAAAGTTCGG
233023 AGGTCAAAAA
1 AGGTCAAAAA
233033 AGGAAGGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.28
Consensus pattern (30 bp):
AGGTCAAAAATACAATTTTAGAAAGTTCGG
Found at i:234292 original size:20 final size:20
Alignment explanation
Indices: 234267--234305 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
234257 TAATATTGCC
234267 AAAATATTTATTATTATTAA
1 AAAATATTTATTATTATTAA
234287 AAAATATTTATTATTATTA
1 AAAATATTTATTATTATTA
234306 TTATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATATTTATTATTATTAA
Found at i:234300 original size:3 final size:3
Alignment explanation
Indices: 234294--234326 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
234284 TAAAAAATAT
234294 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
234327 CATTCATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:235057 original size:17 final size:17
Alignment explanation
Indices: 235035--235143 Score: 71
Period size: 17 Copynumber: 6.4 Consensus size: 17
235025 GGACATTTAG
* *
235035 TTTAAATTTAAAACCAT
1 TTTAAATTTAAAACAAA
* *
235052 TTTAAATCT-AAGCTAAA
1 TTTAAATTTAAAAC-AAA
*
235069 TTTAAATTTAAAACAAG
1 TTTAAATTTAAAACAAA
*
235086 TTTAAATTTAAATTCAGAA
1 TTTAAATTTAAA-ACA-AA
* *
235105 -ATAAA-TTAAAATCAAT
1 TTTAAATTTAAAA-CAAA
* *
235121 TTTAAATTTAATATAAA
1 TTTAAATTTAAAACAAA
235138 TTTAAA
1 TTTAAA
235144 AGTTTGATCC
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.06
17 50 0.72
18 14 0.20
19 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAACAAA
Found at i:235113 original size:23 final size:23
Alignment explanation
Indices: 235065--235114 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
235055 AAATCTAAGC
* *
235065 TAAATTTAAATTTAAAACAAGTT
1 TAAATTTAAATTCAAAACAAGAT
*
235088 TAAATTTAAATTCAGAAATAA-AT
1 TAAATTTAAATTCA-AAACAAGAT
235111 TAAA
1 TAAA
235115 ATCAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
TAAATTTAAATTCAAAACAAGAT
Found at i:235309 original size:18 final size:18
Alignment explanation
Indices: 235286--235341 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
235276 TAATTGTGGC
235286 CTTAAATTGTGACAAAAG
1 CTTAAATTGTGACAAAAG
*
235304 CTTAAATTGTGGC---A-
1 CTTAAATTGTGACAAAAG
235318 -TTAAATTGTGACAAAAG
1 CTTAAATTGTGACAAAAG
235335 CTTAAAT
1 CTTAAAT
235342 AATGTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 11 0.35
15 1 0.03
16 1 0.03
18 18 0.58
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (18 bp):
CTTAAATTGTGACAAAAG
Found at i:235312 original size:31 final size:31
Alignment explanation
Indices: 235277--235341 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
235267 ATTTATTATT
*
235277 AATTGTGGCCTTAAATTGTGACAAAAGCTTA
1 AATTGTGGCATTAAATTGTGACAAAAGCTTA
235308 AATTGTGGCATTAAATTGTGACAAAAGCTTA
1 AATTGTGGCATTAAATTGTGACAAAAGCTTA
235339 AAT
1 AAT
235342 AATGTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (31 bp):
AATTGTGGCATTAAATTGTGACAAAAGCTTA
Found at i:238202 original size:57 final size:57
Alignment explanation
Indices: 238124--238302 Score: 190
Period size: 57 Copynumber: 3.2 Consensus size: 57
238114 GATTCAGTTA
* * * *
238124 AACATCAATATAAACAGCTTGAACAACCTTATTTCGGACAGCTTTATGACTCAATTT
1 AACATCAATACAAACAGCTTGAATAACCTTATTTCGGGCAACTTTATGACTCAATTT
* * * * *
238181 ATCATCAATACAAACAACTTGATTAACCTTGA-TTCGGGCAACATTT-TAACTC-ACTT
1 AACATCAATACAAACAGCTTGAATAACCTT-ATTTCGGGCAAC-TTTATGACTCAATTT
* *
238237 AAGCATCAATATAAATAGCTTGAATAACC-T-TTT-GGGCAACTTTATGACTCAATTT
1 AA-CATCAATACAAACAGCTTGAATAACCTTATTTCGGGCAACTTTATGACTCAATTT
238292 AACATCAATAC
1 AACATCAATAC
238303 GGACAACTCG
Statistics
Matches: 99, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
53 3 0.03
54 20 0.20
55 7 0.07
56 5 0.05
57 60 0.61
58 4 0.04
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (57 bp):
AACATCAATACAAACAGCTTGAATAACCTTATTTCGGGCAACTTTATGACTCAATTT
Found at i:238302 original size:111 final size:114
Alignment explanation
Indices: 238121--238340 Score: 311
Period size: 111 Copynumber: 2.0 Consensus size: 114
238111 TTTGATTCAG
* *
238121 TTAAACATCAATATAAACAGCTTGAACAACCTTATTTCGGACAGCTTTATGACTCAATTTATCAT
1 TTAAACATCAATATAAACAGCTTGAACAACCTTATTTCGGACAACTTTATGACTCAATTTAACAT
* * * *
238186 CAATACAAACAACTTGATTAACCTTGATTCGGGCAACATTTTAACTCAC
66 CAATACAAACAACTCGATTAACCTTGAATAGGACAACATTTTAACTCAC
* * * *
238235 TTAAGCATCAATATAAATAGCTTGAATAACC-T-TTT-GGGCAACTTTATGACTCAATTTAACAT
1 TTAAACATCAATATAAACAGCTTGAACAACCTTATTTCGGACAACTTTATGACTCAATTTAACAT
**
238297 CAATACGGACAACTCGATTAACCTTGAATAGGACAACATTTTAA
66 CAATACAAACAACTCGATTAACCTTGAATAGGACAACATTTTAA
238341 TCCAAATTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
111 62 0.66
112 3 0.03
113 1 0.01
114 28 0.30
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (114 bp):
TTAAACATCAATATAAACAGCTTGAACAACCTTATTTCGGACAACTTTATGACTCAATTTAACAT
CAATACAAACAACTCGATTAACCTTGAATAGGACAACATTTTAACTCAC
Found at i:239059 original size:14 final size:14
Alignment explanation
Indices: 239040--239068 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
239030 AGCCACCACG
239040 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
239054 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
239068 T
1 T
239069 ANNNNNNNNN
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:239062 original size:13 final size:13
Alignment explanation
Indices: 239044--239068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
239034 ACCACGTTCT
239044 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
239057 TTTTTTTTTTTT
1 TTTTTTTTTTTT
239069 ANNNNNNNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:239560 original size:23 final size:23
Alignment explanation
Indices: 239530--239587 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
239520 CTGACGTGGC
239530 GTCCAGTCAGCAGCTTCTAGAAG
1 GTCCAGTCAGCAGCTTCTAGAAG
239553 GTCCAGTCAGCAGCTTCTAGAAG
1 GTCCAGTCAGCAGCTTCTAGAAG
*
239576 GTCTAGTCAGCA
1 GTCCAGTCAGCA
239588 AGGATGGACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
GTCCAGTCAGCAGCTTCTAGAAG
Found at i:246177 original size:23 final size:23
Alignment explanation
Indices: 246147--246202 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
246137 CTGACGTGGC
246147 GTCCAGTCAGCAACTGCTAAAAG
1 GTCCAGTCAGCAACTGCTAAAAG
* * *
246170 GTCCAGTCAGCAGCTTCTAGAAG
1 GTCCAGTCAGCAACTGCTAAAAG
*
246193 GTCTAGTCAG
1 GTCCAGTCAG
246203 TAAGGATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
GTCCAGTCAGCAACTGCTAAAAG
Found at i:249908 original size:16 final size:17
Alignment explanation
Indices: 249872--249909 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
249862 TATATTATTC
*
249872 TTTAATTTTTTATACAA
1 TTTAATATTTTATACAA
249889 -TTAATATTTTA-ACAA
1 TTTAATATTTTATACAA
249904 TTTAAT
1 TTTAAT
249910 CATCGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATATTTTATACAA
Found at i:250105 original size:15 final size:16
Alignment explanation
Indices: 250080--250110 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
250070 AAAACACAGA
250080 TTTTACGGGAAAAACC
1 TTTTACGGGAAAAACC
250096 TTTT-CGGGAAAAACC
1 TTTTACGGGAAAAACC
250111 ATGGGCAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
TTTTACGGGAAAAACC
Found at i:251049 original size:20 final size:22
Alignment explanation
Indices: 251014--251059 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
251004 TGATTGAACC
*
251014 TATTTATAATATTTTAATTATT
1 TATTTATAATATTTTAATTAAT
251036 TATTTA-AA-ATTTTAATTAAT
1 TATTTATAATATTTTAATTAAT
251056 TATT
1 TATT
251060 ATTATATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 2 0.09
22 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATAATATTTTAATTAAT
Found at i:251267 original size:21 final size:20
Alignment explanation
Indices: 251229--251269 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
251219 TTTTCTTCTA
*
251229 TTTTATTATTATTGATTTTT
1 TTTTATTATTATTAATTTTT
*
251249 TTTTATTGTCTATTAATTTTT
1 TTTTATTAT-TATTAATTTTT
251270 AATATTCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTATTATTATTAATTTTT
Found at i:254550 original size:29 final size:29
Alignment explanation
Indices: 254460--254564 Score: 117
Period size: 28 Copynumber: 3.7 Consensus size: 29
254450 TTGGAAATTA
* * * *
254460 GAGGGCAAAATGGTAA-TTTTAGACGTTC
1 GAGGGTAAAATGGTAATTTTTGGATGTCC
* *
254488 GAGGGCAAAATGGGAA-TTTTGGATGTCC
1 GAGGGTAAAATGGTAATTTTTGGATGTCC
*
254516 GAGGGTAAAATGGTAATTTTTGGATGCTCT
1 GAGGGTAAAATGGTAATTTTTGGATG-TCC
254546 G-GGGTAAAATGGTAATTTT
1 GAGGGTAAAATGGTAATTTT
254565 GGAAAGTTCG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 38 0.56
29 27 0.40
30 3 0.04
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (29 bp):
GAGGGTAAAATGGTAATTTTTGGATGTCC
Found at i:254583 original size:29 final size:26
Alignment explanation
Indices: 254466--254640 Score: 91
Period size: 28 Copynumber: 6.2 Consensus size: 26
254456 ATTAGAGGGC
* * *
254466 AAAATGGTAATTTTAGACGTTCGAGGGC
1 AAAATGGTAATTTTGGAAGTTC--GGGT
* * *
254494 AAAATGGGAATTTTGGATGTCCGAGGGT
1 AAAATGGTAATTTTGGAAGTTC--GGGT
* *
254522 AAAATGGTAATTTTTGGATGCTCTGGGGT
1 AAAATGGTAA-TTTTGGAAG-T-TCGGGT
254551 AAAATGGTAATTTTGGAAAGTTCGGGAT
1 AAAATGGTAATTTTGG-AAGTTCGGG-T
* * *
254579 CAAAAAT-GCAATTTTGGAAATCCATGGGT
1 --AAAATGGTAATTTTGGAAGTTC--GGGT
*
254608 AAAATGGTAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAATTTT-GGAAGTTC--GGGT
254637 AAAA
1 AAAA
254641 ACATAATTTT
Statistics
Matches: 117, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
27 9 0.08
28 51 0.44
29 48 0.41
30 9 0.08
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.30
Consensus pattern (26 bp):
AAAATGGTAATTTTGGAAGTTCGGGT
Found at i:254620 original size:28 final size:26
Alignment explanation
Indices: 254494--254626 Score: 79
Period size: 29 Copynumber: 4.7 Consensus size: 26
254484 GTTCGAGGGC
* **
254494 AAAATGGGAATTTTGGATGTCCGAGGGT
1 AAAATGGTAATTTTGGAAATCC--GGGT
** *
254522 AAAATGGTAATTTTTGGATGCTCTGGGGT
1 AAAATGGTAA-TTTTGGA-AATC-CGGGT
*
254551 AAAATGGTAATTTTGGAAAGTTCGGGAT
1 AAAATGGTAATTTTGGAAA-TCCGGG-T
*
254579 CAAAAAT-GCAATTTTGGAAATCCATGGGT
1 --AAAATGGTAATTTTGGAAATCC--GGGT
*
254608 AAAATGGTAATTTTAGAAA
1 AAAATGGTAATTTTGGAAA
254627 GTTCGAGGGT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
27 8 0.10
28 31 0.37
29 34 0.41
30 10 0.12
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.32
Consensus pattern (26 bp):
AAAATGGTAATTTTGGAAATCCGGGT
Found at i:254647 original size:29 final size:29
Alignment explanation
Indices: 254615--254757 Score: 103
Period size: 29 Copynumber: 4.9 Consensus size: 29
254605 GGTAAAATGG
254615 TAATTTTAGAAAGTTCGAGGGTAAAAACA
1 TAATTTTAGAAAGTTCGAGGGTAAAAACA
* *
254644 TAATTTTTACAAAGTTCGAGGTTAAAAATGCA
1 TAA-TTTTAGAAAGTTCGAGGGTAAAAA--CA
* * ***
254676 -ATTTTTA-AAAGTTTGAGGGTAAAATGG
1 TAATTTTAGAAAGTTCGAGGGTAAAAACA
* * * *
254703 TAATTTTTG-ATGTTTGAGGGTAAAAACT
1 TAATTTTAGAAAGTTCGAGGGTAAAAACA
* * * *
254731 TAATTTTTGGAAGTTAGGGGGTAAAAA
1 TAATTTTAGAAAGTTCGAGGGTAAAAA
254758 ATGTGATTTT
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
28 29 0.32
29 32 0.35
30 27 0.30
31 1 0.01
32 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
TAATTTTAGAAAGTTCGAGGGTAAAAACA
Found at i:254734 original size:28 final size:29
Alignment explanation
Indices: 254618--254796 Score: 141
Period size: 30 Copynumber: 6.1 Consensus size: 29
254608 AAAATGGTAA
* *
254618 TTTTAGAAAGTTCGAGGGTAAAAACATAAT
1 TTTTAG-AAGTTTGAGGGTAAAAATATAAT
* * * **
254648 TTTTACAAAGTTCGAGGTTAAAAATGCAAT
1 TTTTA-GAAGTTTGAGGGTAAAAATATAAT
* *
254678 TTTTAAAAGTTTGAGGGT-AAAATGGTAAT
1 TTTTAGAAGTTTGAGGGTAAAAAT-ATAAT
*
254707 TTTT-GATGTTTGAGGGTAAAAACT-TAAT
1 TTTTAGAAGTTTGAGGGTAAAAA-TATAAT
* * * * *
254735 TTTTGGAAGTTAGGGGGTAAAAAATGTGAT
1 TTTTAGAAGTTTGAGGGT-AAAAATATAAT
254765 TTTTAGAAGTTT-AGGGGTAAAAATATAAT
1 TTTTAGAAGTTTGA-GGGTAAAAATATAAT
254794 TTT
1 TTT
254797 GGAATAGTTT
Statistics
Matches: 122, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
28 24 0.20
29 46 0.38
30 52 0.43
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.37
Consensus pattern (29 bp):
TTTTAGAAGTTTGAGGGTAAAAATATAAT
Found at i:254758 original size:87 final size:87
Alignment explanation
Indices: 254518--254786 Score: 235
Period size: 87 Copynumber: 3.1 Consensus size: 87
254508 GGATGTCCGA
* *** * *
254518 GGGTAAAATGGTAATTTTTGGATGCTCTG-GGGTAAAATGGTAA-TTTTGGAAAGTTCGGGATCA
1 GGGTAAAATGGTAATTTTT-GATG-TTTGAGGGTAAAAACATAATTTTTGG-AAGTTCGGGGTAA
** ** *
254581 AAAATGCAATTTTGGAAA--TCCAT
63 AAAATGCAATTTTTAAAAGTTTGAG
* * * ** * *
254604 GGGTAAAATGGTAATTTTAGAAAGTTCGAGGGTAAAAACATAATTTTTACAAAGTTCGAGGTTAA
1 GGGTAAAATGGTAATTTTTG-ATGTTTGAGGGTAAAAACATAATTTTT-GGAAGTTCGGGGTAAA
254669 AAATGCAATTTTTAAAAGTTTGA-
64 AAATGCAATTTTTAAAAGTTTGAG
* *
254692 GGGTAAAATGGTAATTTTTGATGTTTGAGGGTAAAAACTTAATTTTTGGAAGTTAGGGGGTAAAA
1 GGGTAAAATGGTAATTTTTGATGTTTGAGGGTAAAAACATAATTTTTGGAAGTT-CGGGGTAAAA
** *
254757 AATGTGATTTTTAGAAGTTT-AG
65 AATGCAATTTTTAAAAGTTTGAG
254779 GGGTAAAA
1 GGGTAAAA
254787 ATATAATTTT
Statistics
Matches: 147, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
85 3 0.02
86 37 0.25
87 86 0.59
88 19 0.13
89 2 0.01
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (87 bp):
GGGTAAAATGGTAATTTTTGATGTTTGAGGGTAAAAACATAATTTTTGGAAGTTCGGGGTAAAAA
ATGCAATTTTTAAAAGTTTGAG
Found at i:254767 original size:29 final size:29
Alignment explanation
Indices: 254703--254840 Score: 92
Period size: 30 Copynumber: 4.7 Consensus size: 29
254693 GGTAAAATGG
*
254703 TAATTTTT-GATGTTT-GAGGGTAAAAACT-
1 TAATTTTTGGAAGTTTAG-GGGTAAAAA-TA
*
254731 TAATTTTTGGAAG-TTAGGGGGTAAAAAATG
1 TAATTTTTGGAAGTTTA-GGGGT-AAAAATA
* *
254761 TGATTTTTAGAAGTTTAGGGGTAAAAATA
1 TAATTTTTGGAAGTTTAGGGGTAAAAATA
* *
254790 TAA-TTTTGGAATAGTTT-GGGCATCAAAATA
1 TAATTTTTGG-A-AGTTTAGGG-GTAAAAATA
254820 TGAA-TTTTGGATAGTTTAGGG
1 T-AATTTTTGGA-AGTTTAGGG
254841 ACCTTCTGAG
Statistics
Matches: 91, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
28 15 0.16
29 20 0.22
30 42 0.46
31 14 0.15
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTAGGGGTAAAAATA
Found at i:254782 original size:30 final size:29
Alignment explanation
Indices: 254618--254796 Score: 89
Period size: 29 Copynumber: 6.1 Consensus size: 29
254608 AAAATGGTAA
* *
254618 TTTTAGAAAGTTCGAGGGTAAAAACA-TAAT
1 TTTTAG-AAGTTAGGGGGTAAAAA-ATTAAT
* * * * *
254648 TTTTACAAAGTT-CGAGGTTAAAAATGCAAT
1 TTTTA-GAAGTTAGGGGGTAAAAAAT-TAAT
* * * ***
254678 TTTTAAAAGTTTGAGGGTAAAATGGTAAT
1 TTTTAGAAGTTAGGGGGTAAAAAATTAAT
* * * *
254707 TTTT-GATGTTTGAGGGTAAAAACTTAAT
1 TTTTAGAAGTTAGGGGGTAAAAAATTAAT
* *
254735 TTTTGGAAGTTAGGGGGTAAAAAATGTGAT
1 TTTTAGAAGTTAGGGGGTAAAAAAT-TAAT
254765 TTTTAGAAGTTTA-GGGGT-AAAAATATAAT
1 TTTTAGAAG-TTAGGGGGTAAAAAAT-TAAT
254794 TTT
1 TTT
254797 GGAATAGTTT
Statistics
Matches: 115, Mismatches: 27, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
28 24 0.21
29 48 0.42
30 40 0.35
31 3 0.03
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.37
Consensus pattern (29 bp):
TTTTAGAAGTTAGGGGGTAAAAAATTAAT
Found at i:256663 original size:18 final size:17
Alignment explanation
Indices: 256626--256738 Score: 145
Period size: 18 Copynumber: 6.5 Consensus size: 17
256616 GGACATTATT
**
256626 AATTTAAATTTATGATA
1 AATTTAAATTTAAAATA
256643 AATTTAAATTTAAGAATA
1 AATTTAAATTTAA-AATA
* *
256661 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
256678 AATTTAAATTTTAAAATA
1 AATTTAAA-TTTAAAATA
256696 AATTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
*
256714 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
256731 AATCTAAA
1 AATTTAAA
256739 ACAAAATGGG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
17 39 0.46
18 46 0.54
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:256667 original size:35 final size:33
Alignment explanation
Indices: 256626--256738 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 33
256616 GGACATTATT
*
256626 AATTTAAATTTATGATAAATTTAAATTTAAGAATA
1 AATTTAAATTTA-AATAAATTTAAATTTAA-AATA
*
256661 AATTTAAACTTAAATTAAATTTAAATTTTAAAATA
1 AATTTAAATTTAAA-TAAATTTAAA-TTTAAAATA
*
256696 AATTTAAATTTAAAAATAAATTTAAACTTAAAATA
1 AATTTAAATTT--AAATAAATTTAAATTTAAAATA
*
256731 AATCTAAA
1 AATTTAAA
256739 ACAAAATGGG
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
34 1 0.01
35 50 0.72
36 15 0.22
37 3 0.04
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (33 bp):
AATTTAAATTTAAATAAATTTAAATTTAAAATA
Found at i:256692 original size:7 final size:6
Alignment explanation
Indices: 256641--256727 Score: 81
Period size: 6 Copynumber: 14.7 Consensus size: 6
256631 AAATTTATGA
* *
256641 TAAATT TAAATT TAAGA-A TAAATT TAAACT TAAA-T TAAATT TAAATTT
1 TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT TAAATT TAAA-TT
* ** *
256689 TAAA-A TAAATT TAAATT TAAAAA TAAATT TAAACT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
256728 ATAAATCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
5 10 0.15
6 49 0.74
7 7 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:256703 original size:53 final size:52
Alignment explanation
Indices: 256626--256738 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 52
256616 GGACATTATT
** * *
256626 AATTTAAATTTATGATAAATTTAAATTTAAGAATAAATTTAAACTTAAATTA
1 AATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTTAAAATA
256678 AATTTAAATTTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTTAAAATA
1 AATTTAAA-TTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTTAAAATA
*
256731 AATCTAAA
1 AATTTAAA
256739 ACAAAATGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 8 0.15
53 47 0.85
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (52 bp):
AATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAACTTAAAATA
Found at i:257577 original size:210 final size:209
Alignment explanation
Indices: 257136--257724 Score: 698
Period size: 210 Copynumber: 2.8 Consensus size: 209
257126 TTTTACTAGA
* * * ** * * *
257136 AAGATGGATTTGGTTCACTTCTCTGCGTCTCGTCAGGAAGGTGACCACTTTATTACTTCGACCTA
1 AAGAAGGATTTTGTCCACTTCTCTGTATCTCATCAGGAAGGTGACCACTTTATTGCTTCGACCTG
** * * * * * *
257201 CTTCTCTGTATCTCATCAGGAAGATAAGGGTTTGAAGCTTCACTCGCATTTGAACTTTGTTTCAC
66 CTTCTCAATATCTCATCAGGAAGCT-AGGGTTCGAAGTTTCGCTCACA-TTGAGCTTTGTTTCA-
** * * *
257266 TTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCATTTGCTTCAATCCACTT
128 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCACTT
* *
257331 CTTTGTATCTCATTAGG
193 CTTTGTATCTCATCAAG
* * *
257348 AAGAAGGA-TTTGATCCACTTCTCTGTATCTCATCAGGAAGGTTACCATTTTATTGCTTCGACCC
1 AAGAAGGATTTTG-TCCACTTCTCTGTATCTCATCAGGAAGGTGACCACTTTATTGCTTCGACCT
* *
257412 GTTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCAT
65 GCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTT-GTTTCAT
* * * ** *
257477 TGTTTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCGCTTC
129 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCACTTC
257542 TTTGTATCTCATCAAG
194 TTTGTATCTCATCAAG
* ** * * *
257558 AAGACGGATTTTGTCCACTTCTCTGTATCTCATCAGGAAGACGATCGCTTTATTGCTTCAACCTG
1 AAGAAGGATTTTGTCCACTTCTCTGTATCTCATCAGGAAGGTGACCACTTTATTGCTTCGACCTG
* * *
257623 CTTCTCAATATCTCAT-AGGAAGCTGGGGTTCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTG
66 CTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
* *
257687 ATTTGGTATACTTCTCTA-TATCTCATTAGGAAGATGAC
131 ATTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGAC
257725 TGCCTCGTTT
Statistics
Matches: 321, Mismatches: 52, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
208 41 0.13
209 36 0.11
210 142 0.44
211 31 0.10
212 71 0.22
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
AAGAAGGATTTTGTCCACTTCTCTGTATCTCATCAGGAAGGTGACCACTTTATTGCTTCGACCTG
CTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTG
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGCTTCAATCCACTTCTT
TGTATCTCATCAAG
Found at i:257579 original size:37 final size:38
Alignment explanation
Indices: 257528--257600 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
257518 GCATCACTTG
* *
257528 TTTTGATCCGCTTCTTTGTATCTCATCAAGAAGACGGA
1 TTTTGATCCACTTCTCTGTATCTCATCAAGAAGACGGA
*
257566 TTTTG-TCCACTTCTCTGTATCTCATCAGGAAGACG
1 TTTTGATCCACTTCTCTGTATCTCATCAAGAAGACG
257601 ATCGCTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (38 bp):
TTTTGATCCACTTCTCTGTATCTCATCAAGAAGACGGA
Found at i:258202 original size:50 final size:49
Alignment explanation
Indices: 258083--259059 Score: 535
Period size: 49 Copynumber: 20.0 Consensus size: 49
258073 TGTTTTCTAA
* * * *
258083 GGTACCGGGTTCGCCATTGTGGCCTCCACCTTTCCCTTCATATCTTC-T
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* *
258131 --TA-AGAGGTTCGCCATTGCGACCTCAACCTTTTCCCTTAAAATCTTCAT
1 GGTACCG-GGTTCGCCATTGCGACCTCAACC-TTTCCCTTCAAATCTTCAT
* * *
258179 GGTACCGGGTTCGCCATTTCGACCTCAACCTTTCCCATCACAT-TTCAT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * * * * * * * *
258227 GGTATCGGATTCACCGTTGTGACCTCAATCTTTCCCATCACATCTT-TT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
** * * * *
258275 GAGGTACCGGGTTTACTATTGCGGCATCAACCTTTCCCTTCAAATCTTCTT
1 --GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
*** * * *
258326 AGGTACCGGGTTCGTTGTTGCAACATCAACATTTCCCTTCAAATCTTCAT
1 -GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * ** * * * * *
258376 GATACCGAGTTTTCCGTTGTGGCCTCAACCTTTCCCATCACAT-TTCAT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * * * *
258424 AGTACCGGATTCGCCATTGC-AGCCTCAATCTTTCCCATCACAT-TTC-T
1 GGTACCGGGTTCGCCATTGCGA-CCTCAACCTTTCCCTTCAAATCTTCAT
* * **
258471 GAGGTACCAGGTTCGCCATTGCGACATCAACCTTTCCCTTCAAATCTTTTT
1 --GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
** * *
258522 AGGTACCGGGTTCGCCATTGCGGTCTTAACCTTTCCCTTCAAATCTTTAT
1 -GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * * * * *
258572 GGTTCCAGGTTTGCCATTGC-AGTCTCAACCTTT-CCTATCATAT-TTCAC
1 GGTACCGGGTTCGCCATTGCGA-CCTCAACCTTTCCCT-TCAAATCTTCAT
* * * * * * * * * * *
258620 GGTATCGGATTCACCGTTGAGGCCTCAATCTTTCCCATCATATTTTTGA-
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCA-AATCTTCAT
** * * * * * *
258669 GGTACCATGTTCGTCGTTACGGCATCAACCTTTCCCTTCAAATCTTCTT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
** * * *
258718 AGGTATTGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTAAATTTTCAT
1 -GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
** * * * *
258768 GGTACCGGGTTTACCGTTGTGACCTCAACC-TT-CCATCATAT-TTCAT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
* * * * * * * * *
258814 GGTACCGGATTCGTCGTTGTGGCCTCAATCTTTCCCATCACAT-TTCTAA
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTC-AT
** * * **
258863 GGTACTAGGTTCGCCGTTGC-AGCATCAACCTTTTTCTTCAAATCTGT-AT
1 GGTACCGGGTTCGCCATTGCGA-CCTCAACCTTTCCCTTCAAATCT-TCAT
* *
258912 GGTACCGGGTTCGCCATTGCAACCTCAACCTTTCCCATT-ACAT-TTCAT
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCC-TTCAAATCTTCAT
* *** * * * * * * *
258960 GGCACCAAATTCGCCATTACGGCCTCAATCTTTCTCATCACATAT-TTTAA
1 GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCA-A-ATCTTCAT
* * *
259010 GGTACCGGGTTCGCCGTTG-TAGCCTCAACCTTTCTCTTCAAATCTTCAT
1 GGTACCGGGTTCGCCATTGCGA-CCTCAACCTTTCCCTTCAAATCTTCAT
259059 G
1 G
259060 TTTTTCTCAA
Statistics
Matches: 706, Mismatches: 185, Indels: 75
0.73 0.19 0.08
Matches are distributed among these distances:
45 1 0.00
46 51 0.07
47 26 0.04
48 163 0.23
49 233 0.33
50 227 0.32
51 5 0.01
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (49 bp):
GGTACCGGGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCAT
Found at i:258568 original size:196 final size:195
Alignment explanation
Indices: 258076--259043 Score: 963
Period size: 196 Copynumber: 5.0 Consensus size: 195
258066 TTCATCTTGT
* * * * * * *
258076 TTTCTAAGGTACCGGGTTCGCCATTGTGGCCTCCACCTTTCCCTTCATATCTTCTTAAG-A---G
1 TTTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGG
* * *
258137 GTTCGCCATTGCGACCTCAACCTTTTCCCTTAAAATCTTCATGGTACCGGGTTCGCCATT-TCGA
66 GTTCGCCATTGCGACCTCAACC-TTTCCCTTCAAATCTTCATGGTACCGAGTTTGCCATTGT-GA
* *
258201 CCTCAACCTTTCCCATCACATTTCATGGTATCGGATTCACCGTTGTGACCTCAATCTTTCCCATC
129 CCTCAACCTTTCCCATCACATTTCATGGTACCGGATTCACCGTTGAG-CCTCAATCTTTCCCATC
258266 ACA
193 ACA
* * ** *
258269 TCTTTTGAGGTACCGGGTTTACTATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCG
1 T-TTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCG
*** * * * * * * *
258334 GGTTCGTTGTTGCAACATCAACATTTCCCTTCAAATCTTCATGATACCGAGTTTTCCGTTGTGGC
65 GGTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAGTTTGCCATTGTGAC
* * *
258399 CTCAACCTTTCCCATCACATTTCATAGTACCGGATTCGCCATTGCAGCCTCAATCTTTCCCATCA
130 CTCAACCTTTCCCATCACATTTCATGGTACCGGATTCACCGTTG-AGCCTCAATCTTTCCCATCA
258464 CA
194 CA
* *
258466 TTTCTGAGGTACCAGGTTCGCCATTGCGACATCAACCTTTCCCTTCAAATCTTTTTAGGTACCGG
1 TTTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGG
** * * * *
258531 GTTCGCCATTGCGGTCTTAACCTTTCCCTTCAAATCTTTATGGTTCC-AGGTTTGCCATTG-CAG
66 GTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA-GTTTGCCATTGTGA-
* * * * *
258594 TCTCAACCTTTCCTATCATATTTCACGGTATCGGATTCACCGTTGAGGCCTCAATCTTTCCCATC
129 CCTCAACCTTTCCCATCACATTTCATGGTACCGGATTCACCGTTGA-GCCTCAATCTTTCCCATC
*
258659 ATA
193 ACA
* * * * * **
258662 TTTTTGAGGTACCATGTTCGTCGTTACGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTATTGG
1 TTTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGG
* * * * * *
258727 GTTCGCCGTTGCGACCTCAACCTTTCCCTTTAAATTTTCATGGTACCGGGTTTACCGTTGTGACC
66 GTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAGTTTGCCATTGTGACC
* ** *
258792 TCAACC-TT-CCATCATATTTCATGGTACCGGATTCGTCGTTGTGGCCTCAATCTTTCCCATCAC
131 TCAACCTTTCCCATCACATTTCATGGTACCGGATTCACCGTTG-AGCCTCAATCTTTCCCATCAC
258855 A
195 A
* * * * ** *
258856 TTTCTAAGGTACTAGGTTCGCCGTTGCAGCATCAACCTTTTTCTTCAAATC-T-GTATGGTACCG
1 TTTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTA-GGTACCG
* * * * * * ** *
258919 GGTTCGCCATTGCAACCTCAACCTTTCCCATT-ACAT-TTCATGGCACCAAATTCGCCATTACGG
65 GGTTCGCCATTGCGACCTCAACCTTTCCC-TTCAAATCTTCATGGTACCGAGTTTGCCATTGTGA
* * * * * * *
258982 CCTCAATCTTTCTCATCACATATTTTAAGGTACCGGGTTCGCCGTTGTAGCCTCAACCTTTC
129 CCTCAACCTTTCCCATCAC--ATTTCATGGTACCGGATTCACCGTTG-AGCCTCAATCTTTC
259044 TCTTCAAATC
Statistics
Matches: 633, Mismatches: 123, Indels: 35
0.80 0.16 0.04
Matches are distributed among these distances:
192 26 0.04
193 39 0.06
194 145 0.23
195 5 0.01
196 304 0.48
197 95 0.15
198 19 0.03
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (195 bp):
TTTCTGAGGTACCAGGTTCGCCATTGCGGCATCAACCTTTCCCTTCAAATCTTCTTAGGTACCGG
GTTCGCCATTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAGTTTGCCATTGTGACC
TCAACCTTTCCCATCACATTTCATGGTACCGGATTCACCGTTGAGCCTCAATCTTTCCCATCACA
Found at i:258832 original size:46 final size:48
Alignment explanation
Indices: 258762--258859 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 48
258752 CCCTTTAAAT
* * *
258762 TTTCATGGTACCGGGTTTACCGTTGTGACCTCAA-CCTT-CCATCATA
1 TTTCATGGTACCGGATTCACCGTTGTGACCTCAATCCTTCCCATCACA
** * *
258808 TTTCATGGTACCGGATTCGTCGTTGTGGCCTCAATCTTTCCCATCACA
1 TTTCATGGTACCGGATTCACCGTTGTGACCTCAATCCTTCCCATCACA
258856 TTTC
1 TTTC
258860 TAAGGTACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 29 0.67
47 3 0.07
48 11 0.26
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (48 bp):
TTTCATGGTACCGGATTCACCGTTGTGACCTCAATCCTTCCCATCACA
Found at i:260043 original size:24 final size:24
Alignment explanation
Indices: 259998--260074 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 24
259988 TGACCTCTCC
*
259998 TTTTCTTTTTCCTGTTTT-TTCTA
1 TTTTCTTTTTCCTTTTTTCTTCTA
*
260021 TTTTCTTTTTCCTTTTTTCTTCTT
1 TTTTCTTTTTCCTTTTTTCTTCTA
* *
260045 TTTTCTCCTTT--TTTTTTCTT-TC
1 TTTTCT-TTTTCCTTTTTTCTTCTA
260067 TTTTCTTT
1 TTTTCTTT
260075 ATTTTTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.02
22 7 0.15
23 26 0.55
24 10 0.21
25 3 0.06
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTCCTTTTTTCTTCTA
Found at i:260047 original size:10 final size:10
Alignment explanation
Indices: 260032--260074 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
260022 TTTCTTTTTC
260032 CTTTTTTCTT
1 CTTTTTTCTT
*
260042 CTTTTTTCTC
1 CTTTTTTCTT
*
260052 CTTTTTTTTT
1 CTTTTTTCTT
*
260062 CTTTCTT-TT
1 CTTTTTTCTT
260071 CTTT
1 CTTT
260075 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:260047 original size:31 final size:29
Alignment explanation
Indices: 259998--260093 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 29
259988 TGACCTCTCC
* *
259998 TTTT-CTTTTTCCTGTTTTTTCTATTTTCT
1 TTTTCCTTTTTTCTTTTTTTTCTATTTT-T
*
260027 TTTTCCTTTTTTCTTCTTTTTTCTCCTTTTT
1 TTTTCCTTTTTTCTT-TTTTTTCT-ATTTTT
*
260058 TTTTCTTTCTTTTCTTTATTTTT-TATTTATT
1 TTTTCCTT-TTTTCTTT-TTTTTCTATTT-TT
260089 TTTTC
1 TTTTC
260094 TTCATTGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.07
30 11 0.20
31 25 0.45
32 16 0.29
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTTCCTTTTTTCTTTTTTTTCTATTTTT
Found at i:260053 original size:20 final size:21
Alignment explanation
Indices: 260012--260069 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
260002 CTTTTTCCTG
*
260012 TTTTTTCTAT-TTTCTTTTTCC
1 TTTTTTCT-TCTTTCTTTCTCC
260033 TTTTTTCTTCTTT-TTTCTCC
1 TTTTTTCTTCTTTCTTTCTCC
*
260053 TTTTTTTTTCTTTCTTT
1 TTTTTTCTTCTTTCTTT
260070 TCTTTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTCTTTCTTTCTCC
Found at i:260079 original size:20 final size:20
Alignment explanation
Indices: 259999--260081 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
259989 GACCTCTCCT
259999 TTTCTTTTTCCTGTTTTTTCTAT-
1 TTTC-TTTTCCT-TTTTTT-T-TC
*
260022 TTTCTTTTTCCTTTTTTCTTC
1 TTTC-TTTTCCTTTTTTTTTC
260043 TTT-TTTCTCCTTTTTTTTTC
1 TTTCTTT-TCCTTTTTTTTTC
260063 TTTCTTTT-CTTTATTTTTT
1 TTTCTTTTCCTTT-TTTTTT
260082 ATTTATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.43
21 7 0.13
22 5 0.09
23 12 0.22
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCCTTTTTTTTTC
Found at i:260081 original size:11 final size:10
Alignment explanation
Indices: 259997--260095 Score: 65
Period size: 11 Copynumber: 9.3 Consensus size: 10
259987 TTGACCTCTC
259997 CTTTTCTTTTT
1 CTTTT-TTTTT
*
260008 CCTGTTTTTTCT
1 -CT-TTTTTTTT
*
260020 ATTTTCTTTTT
1 CTTTT-TTTTT
*
260031 CCTTTTTTCTT
1 -CTTTTTTTTT
* *
260042 CTTTTTTCTC
1 CTTTTTTTTT
260052 CTTTTTTTTT
1 CTTTTTTTTT
*
260062 C-TTTCTTTT
1 CTTTTTTTTT
260071 CTTTATTTTTT
1 CTTT-TTTTTT
*
260082 ATTTATTTTTT
1 CTTT-TTTTTT
260093 CTT
1 CTT
260096 CATTGAATCC
Statistics
Matches: 70, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
9 8 0.11
10 23 0.33
11 26 0.37
12 10 0.14
13 3 0.04
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:260090 original size:20 final size:19
Alignment explanation
Indices: 260052--260090 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
260042 CTTTTTTCTC
* *
260052 CTTTTTTTTTCTTTCTTTT
1 CTTTTTTTTTATTTATTTT
260071 CTTTATTTTTTATTTATTTT
1 CTTT-TTTTTTATTTATTTT
260091 TTCTTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (19 bp):
CTTTTTTTTTATTTATTTT
Found at i:260958 original size:17 final size:17
Alignment explanation
Indices: 260936--260968 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
260926 TTTGTCTTAA
260936 CTTT-CCTTTCTTTTTTC
1 CTTTCCCTTT-TTTTTTC
260953 CTTTCCCTTTTTTTTT
1 CTTTCCCTTTTTTTTT
260969 TGGCCTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTCCCTTTTTTTTTC
Found at i:265563 original size:57 final size:56
Alignment explanation
Indices: 265391--265653 Score: 180
Period size: 57 Copynumber: 4.6 Consensus size: 56
265381 TGTGTGATTT
* * * * *
265391 TTTTGGAAATTCGAGGGCAAAATGGTAATTTTAGACA-TCCGAGGGCAAAATGGT-AA
1 TTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGA-AGTTCGAGAGTAAAAT-GTAAA
*** * * * *
265447 TTTTGGATGCTCGGGGGTAAAATGGTAATTTTGGAAAGCTCGGGA-TCAAAA-ATACAA
1 TTTTGGAAATTCGAGGGTAAAATGGTAATTTTGG-AAGTTCGAGAGT-AAAATGTA-AA
265504 TTTTGGAAATTC-AGGGTAAAATGGTAATTTTTGGAAGTTCGAGAGTAAAATGGTAAA
1 TTTTGGAAATTCGAGGGTAAAATGGTAA-TTTTGGAAGTTCGAGAGTAAAAT-GTAAA
** *** * * *
265561 -TTTGGATGTTCGAGGGTAAAAACTTAATTTTTGGAAGTTCGAGGGTTAAAATGTGAT
1 TTTTGGAAATTCGAGGGTAAAATGGTAA-TTTTGGAAGTTCGAGAG-TAAAATGTAAA
* * *
265618 TTTTGGAAGTTTGAGGGTAAAAAT-GCAATTTTGGAA
1 TTTTGGAAATTCGAGGGT-AAAATGGTAATTTTGGAA
265654 TATTTTGGAA
Statistics
Matches: 162, Mismatches: 32, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
55 1 0.01
56 64 0.40
57 68 0.42
58 25 0.15
59 4 0.02
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (56 bp):
TTTTGGAAATTCGAGGGTAAAATGGTAATTTTGGAAGTTCGAGAGTAAAATGTAAA
Found at i:265582 original size:29 final size:28
Alignment explanation
Indices: 265391--265653 Score: 205
Period size: 28 Copynumber: 9.3 Consensus size: 28
265381 TGTGTGATTT
* *
265391 TTTTGGAAATTCGAGGGCAAAATGGTAA
1 TTTTGGAAGTTCGAGGGTAAAATGGTAA
* * *
265419 TTTTAGACA-TCCGAGGGCAAAATGGTAA
1 TTTTGGA-AGTTCGAGGGTAAAATGGTAA
* * *
265447 TTTTGGATGCTCGGGGGTAAAATGGTAA
1 TTTTGGAAGTTCGAGGGTAAAATGGTAA
* * **
265475 TTTTGGAAAGCTCG-GGATCAAAAAT-ACAA
1 TTTTGG-AAGTTCGAGGGT--AAAATGGTAA
*
265504 TTTTGGAAATTC-AGGGTAAAATGGTAA
1 TTTTGGAAGTTCGAGGGTAAAATGGTAA
*
265531 TTTTTGGAAGTTCGAGAGTAAAATGGTAA
1 -TTTTGGAAGTTCGAGGGTAAAATGGTAA
* * ***
265560 ATTTGGATGTTCGAGGGTAAAAACTTAA
1 TTTTGGAAGTTCGAGGGTAAAATGGTAA
*
265588 TTTTTGGAAGTTCGAGGGTTAAAAT-GTGAT
1 -TTTTGGAAGTTCGAGGG-TAAAATGGT-AA
* *
265618 TTTTGGAAGTTTGAGGGTAAAAAT-GCAA
1 TTTTGGAAGTTCGAGGGT-AAAATGGTAA
265646 TTTTGGAA
1 TTTTGGAA
265654 TATTTTGGAA
Statistics
Matches: 189, Mismatches: 33, Indels: 26
0.76 0.13 0.10
Matches are distributed among these distances:
26 5 0.03
27 2 0.01
28 104 0.55
29 67 0.35
30 11 0.06
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (28 bp):
TTTTGGAAGTTCGAGGGTAAAATGGTAA
Found at i:265589 original size:113 final size:114
Alignment explanation
Indices: 265391--265596 Score: 274
Period size: 113 Copynumber: 1.8 Consensus size: 114
265381 TGTGTGATTT
* *
265391 TTTTGGAAATTCGAGGGCAAAATGGTAATTTTAGACATCCGAGGGCAAAATGGTAATTTTGGATG
1 TTTTGGAAATTCGAGGGCAAAATGGTAATTTTAGACATCCGAGAGCAAAATGGTAAATTTGGATG
* **
265456 CTCGGGGGTAAAATGGTAA-TTTTGGAAAGCTCGGGATCAAAAATACAA
66 CTCGAGGGTAAAAACGTAATTTTTGGAAAGCTCGGGATCAAAAATACAA
* * * *
265504 TTTTGGAAATTC-AGGGTAAAATGGTAATTTTTGGA-AGTTCGAGAGTAAAATGGTAAATTTGGA
1 TTTTGGAAATTCGAGGGCAAAATGGTAA-TTTTAGACA-TCCGAGAGCAAAATGGTAAATTTGGA
* *
265567 TGTTCGAGGGTAAAAACTTAATTTTTGGAA
64 TGCTCGAGGGTAAAAACGTAATTTTTGGAA
265597 GTTCGAGGGT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
112 15 0.19
113 56 0.71
114 8 0.10
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (114 bp):
TTTTGGAAATTCGAGGGCAAAATGGTAATTTTAGACATCCGAGAGCAAAATGGTAAATTTGGATG
CTCGAGGGTAAAAACGTAATTTTTGGAAAGCTCGGGATCAAAAATACAA
Found at i:269665 original size:15 final size:17
Alignment explanation
Indices: 269645--269676 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
269635 TATGACAAAC
269645 ATAAAT-TA-AAAATAT
1 ATAAATATATAAAATAT
269660 ATAAATATATAAAATAT
1 ATAAATATATAAAATAT
269677 GTTTATCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAATATATAAAATAT
Found at i:278042 original size:87 final size:87
Alignment explanation
Indices: 277886--278045 Score: 225
Period size: 87 Copynumber: 1.8 Consensus size: 87
277876 TGCGCAAAGA
277886 TGAGTTTTTACTCTTAATGAATTCATAGCCCAGAGAATTTGGGTGATCCTATTGAGACGAACTTA
1 TGAGTTTTTACTCTTAATGAATTCATAGCCCAGAG-ATTTGGGTGATCCTATTGAGACGAACTTA
277951 ATGAATTTACTGACTTAAGAAGT
65 ATGAATTTACTGACTTAAGAAGT
* ** * *
277974 TGAGTTTATTACTCTTAATGAATTCATATCTTAGAG-TTTGGGTCG-TCCTATTGAGATGGACTT
1 TGAGTTT-TTACTCTTAATGAATTCATAGCCCAGAGATTTGGGT-GATCCTATTGAGACGAACTT
*
278037 GATGAATTT
64 AATGAATTT
278046 TTCGAACTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
87 31 0.48
88 8 0.12
89 25 0.39
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (87 bp):
TGAGTTTTTACTCTTAATGAATTCATAGCCCAGAGATTTGGGTGATCCTATTGAGACGAACTTAA
TGAATTTACTGACTTAAGAAGT
Found at i:278538 original size:22 final size:22
Alignment explanation
Indices: 278513--278569 Score: 53
Period size: 25 Copynumber: 2.5 Consensus size: 22
278503 ATTTAATTAT
278513 TTATATTTAATTATATAATAAA
1 TTATATTTAATTATATAATAAA
* **
278535 TTATTAATATAATTTATATAATTTA
1 TTA-T-ATTTAA-TTATATAATAAA
278560 TTAT-TTTAAT
1 TTATATTTAAT
278570 AAATTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
21 1 0.04
22 7 0.25
23 1 0.04
24 6 0.21
25 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATTTAATTATATAATAAA
Found at i:278575 original size:13 final size:12
Alignment explanation
Indices: 278507--278582 Score: 55
Period size: 12 Copynumber: 6.0 Consensus size: 12
278497 ATACATATTT
*
278507 AATTATTTATATTT
1 AATTATTTA-A-TA
*
278521 AATTATATAATA
1 AATTATTTAATA
278533 AATTA-TTAATA
1 AATTATTTAATA
* *
278544 TAATTTATATAATT
1 -AA-TTATTTAATA
*
278558 TATTATTTTAATA
1 AATTA-TTTAATA
278571 AATTATTTAATA
1 AATTATTTAATA
278583 GTTCAATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
11 5 0.10
12 18 0.37
13 14 0.29
14 12 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATTATTTAATA
Found at i:278609 original size:13 final size:13
Alignment explanation
Indices: 278593--278682 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 13
278583 GTTCAATTTT
278593 ATTTTAATAATAA
1 ATTTTAATAATAA
278606 ATTTTAGA-AATAATA
1 ATTTTA-ATAAT-A-A
278621 ATTTTAAATAAT-A
1 ATTTT-AATAATAA
* *
278634 TTTTTCACATGA-AA
1 ATTTT-A-ATAATAA
*
278648 ATATTTAATATTAA
1 AT-TTTAATAATAA
278662 TATTTTAATAATAA
1 -ATTTTAATAATAA
278676 ATATTTA
1 AT-TTTA
278683 TTACAATTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 21
0.68 0.08 0.24
Matches are distributed among these distances:
13 19 0.32
14 24 0.41
15 12 0.20
16 4 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (13 bp):
ATTTTAATAATAA
Found at i:278633 original size:16 final size:17
Alignment explanation
Indices: 278597--278633 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
278587 AATTTTATTT
*
278597 TAATAATAAATTTTAGA
1 TAATAATAAATTTTAAA
278614 -AATAAT-AATTTTAAA
1 TAATAATAAATTTTAAA
278629 TAATA
1 TAATA
278634 TTTTTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:278680 original size:15 final size:15
Alignment explanation
Indices: 278646--278716 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
278636 TTTCACATGA
278646 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
278659 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
278674 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
278693 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
278708 AAATGTTTT
1 AAATATTTT
278717 GCAATATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:282070 original size:19 final size:18
Alignment explanation
Indices: 282037--282072 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
282027 GTTTTTAAAC
282037 TGTTATATATATTATGTT
1 TGTTATATATATTATGTT
*
282055 TGTTATGTACTATTATGT
1 TGTTATATA-TATTATGT
282073 ATGTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (18 bp):
TGTTATATATATTATGTT
Found at i:282075 original size:23 final size:24
Alignment explanation
Indices: 282049--282104 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
282039 TTATATATAT
282049 TATGTTTGTTATG-TACTATTATG-
1 TATGTTT-TTATGTTACTATTATGA
*
282072 TATGTATTTTATGTTTACTGTTATGA
1 TATGT-TTTTATG-TTACTATTATGA
282098 TATGTTT
1 TATGTTT
282105 AATATTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 10 0.36
24 2 0.07
25 11 0.39
26 5 0.18
ACGTcount: A:0.21, C:0.04, G:0.16, T:0.59
Consensus pattern (24 bp):
TATGTTTTTATGTTACTATTATGA
Found at i:282118 original size:9 final size:9
Alignment explanation
Indices: 282106--282190 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
282096 GATATGTTTA
282106 ATATTATGT
1 ATATTATGT
*
282115 ATATTATAT
1 ATATTATGT
*
282124 ATGTTATGT
1 ATATTATGT
* * *
282133 TTACTGT-T
1 ATATTATGT
*
282141 ATGTT-TGT
1 ATATTATGT
282149 ATATTTGTATGT
1 ATA--T-TATGT
*
282161 ATGTTATGT
1 ATATTATGT
282170 ACTATTATGT
1 A-TATTATGT
282180 ATATTATGT
1 ATATTATGT
282189 AT
1 AT
282191 GTATAATTGT
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
7 1 0.02
8 6 0.11
9 34 0.60
10 10 0.18
11 1 0.02
12 5 0.09
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.56
Consensus pattern (9 bp):
ATATTATGT
Found at i:286132 original size:13 final size:13
Alignment explanation
Indices: 286114--286139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286104 TTTAAATAAT
286114 GTCCAATTACAAA
1 GTCCAATTACAAA
286127 GTCCAATTACAAA
1 GTCCAATTACAAA
286140 TCAGGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:286776 original size:15 final size:14
Alignment explanation
Indices: 286756--286809 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
286746 TAATTAATGT
*
286756 TAATAATAATGGTAA
1 TAATAATAAT-ATAA
* *
286771 TAATAAGTTATTTAA
1 TAATAA-TAATATAA
286786 TAATAATAAATATAA
1 TAATAAT-AATATAA
286801 TAATAATAA
1 TAATAATAA
286810 AAAAAGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 3 0.09
15 27 0.82
16 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:287922 original size:30 final size:29
Alignment explanation
Indices: 287866--288085 Score: 221
Period size: 30 Copynumber: 7.5 Consensus size: 29
287856 CTAATCTATT
* *
287866 CAAAAATTACATTTTTACCCCCAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
*
287895 CAAAAATTCCATTTTTAACCCCAAAACTTT
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
* **
287925 CAAAAATTCTA-TTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
*
287953 CAAAAATTCCATTTTTGACCCCGAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
*
287983 CAAAAATTCCATTTTTGACCCTAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
* ** *
288013 CAAAAATTCTA-TTTT-CCCCTTAACCTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * ** *
288040 CAAAATTTCCATTTTTAACCTCGGAACTTT
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
288070 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
288086 GCCCCAGGAT
Statistics
Matches: 159, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.11
28 24 0.15
29 27 0.17
30 84 0.53
31 7 0.04
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:287955 original size:58 final size:58
Alignment explanation
Indices: 287864--288027 Score: 222
Period size: 58 Copynumber: 2.8 Consensus size: 58
287854 CCCTAATCTA
287864 TTCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
1 TTCAAAAATT-CATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
* * *
287923 TTCAAAAATTC-TATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
1 TTCAAAAATTCAT-TTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
* ** *
287981 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCTATTTT
1 TTCAAAAATT-CATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTT
288028 CCCCTTAACC
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
57 1 0.01
58 52 0.56
59 15 0.16
60 25 0.27
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (58 bp):
TTCAAAAATTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
Found at i:288017 original size:88 final size:86
Alignment explanation
Indices: 287866--288085 Score: 296
Period size: 88 Copynumber: 2.5 Consensus size: 86
287856 CTAATCTATT
* * *
287866 CAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAAA
1 CAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAA
*
287931 TTCTATTTTACCCCCGAACTTC
66 TTCTATTTT-CCCCCGAACCTC
* *
287953 CAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAA
1 CAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAA
**
288018 ATTCTATTTTCCCCTTAACCTC
65 ATTCTATTTTCCCCCGAACCTC
* * * *
288040 CAAAATTTCCATTTTTAACCTCGGAACTTTCAAAAATTACCATTTT
1 CAAAAATTCCATTTTT-ACCCCGAAACTTCCAAAAATT-CCATTTT
288086 GCCCCAGGAT
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
87 57 0.48
88 61 0.52
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (86 bp):
CAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAA
TTCTATTTTCCCCCGAACCTC
Found at i:288068 original size:57 final size:59
Alignment explanation
Indices: 287866--288085 Score: 200
Period size: 58 Copynumber: 3.8 Consensus size: 59
287856 CTAATCTATT
* * * * * *
287866 CAAAAATTACATTTTTACCCCCA-AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTT
1 CAAAAATTCCATTTTTAACCCTAGAACTTCCAAAAATTCCATTTTT-ACCCCGAAACCTC
* ** *
287925 CAAAAATTCTA-TTTT-ACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
1 CAAAAATTCCATTTTTAACCCTAGAACTTCCAAAAATTCCATTTTT-ACCCCGAAACCTC
* * * **
287983 CAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCTA-TTTT-CCCCTTAACCTC
1 CAAAAATTCCATTTTTAACCCTAGAACTTCCAAAAATTCCATTTTTACCCCGAAACCTC
* * *
288040 CAAAATTTCCATTTTTAA-CCTCGGAACTTTCAAAAATTACCATTTT
1 CAAAAATTCCATTTTTAACCCT-AGAACTTCCAAAAATT-CCATTTT
288086 GCCCCAGGAT
Statistics
Matches: 134, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
56 3 0.02
57 42 0.31
58 49 0.37
59 20 0.15
60 20 0.15
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTCCATTTTTAACCCTAGAACTTCCAAAAATTCCATTTTTACCCCGAAACCTC
Found at i:288242 original size:27 final size:27
Alignment explanation
Indices: 288189--288245 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
288179 AATTTTCCCA
* * *
288189 AAATTACCATTTTTCCCCTGGGAATCC
1 AAATTACCATTTTGCCCCCGAGAATCC
**
288216 AAATTACCATTTTGCCCCCGATTATCC
1 AAATTACCATTTTGCCCCCGAGAATCC
288243 AAA
1 AAA
288246 GTCTCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCATTTTGCCCCCGAGAATCC
Found at i:296009 original size:2 final size:2
Alignment explanation
Indices: 295957--295989 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
295947 ATCAATTACC
295957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
295990 GGGTTTAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:303657 original size:25 final size:26
Alignment explanation
Indices: 303620--303673 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
303610 GTTTCGGTGC
303620 TTTTTTTTACTG-TTTTG-GTTGATTT
1 TTTTTTTTACTGTTTTTGAGTTG-TTT
*
303645 TTTTTTTTGCTGTTTTTGAGTTGTTT
1 TTTTTTTTACTGTTTTTGAGTTGTTT
303671 TTT
1 TTT
303674 ATAGTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.42
26 11 0.42
27 4 0.15
ACGTcount: A:0.06, C:0.04, G:0.17, T:0.74
Consensus pattern (26 bp):
TTTTTTTTACTGTTTTTGAGTTGTTT
Found at i:303663 original size:22 final size:24
Alignment explanation
Indices: 303620--303673 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
303610 GTTTCGGTGC
*
303620 TTTTTTTTACTGTTTTGGTTGATTT
1 TTTTTTTTACTGTTTT-GTTGAGTT
*
303645 TTTTTTTTGCTG-TTT-TTGAGTT
1 TTTTTTTTACTGTTTTGTTGAGTT
*
303667 GTTTTTT
1 TTTTTTT
303674 ATAGTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
24 3 0.12
25 11 0.42
ACGTcount: A:0.06, C:0.04, G:0.17, T:0.74
Consensus pattern (24 bp):
TTTTTTTTACTGTTTTGTTGAGTT
Found at i:303705 original size:12 final size:12
Alignment explanation
Indices: 303678--303791 Score: 94
Period size: 12 Copynumber: 9.8 Consensus size: 12
303668 TTTTTTATAG
*
303678 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
*
303691 TTTCG-TGTTAT
1 TTTTGTTGTTAT
*
303702 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
303714 TTTTGTTGCTAT
1 TTTTGTTGTTAT
303726 TTTTGTTGTTA-
1 TTTTGTTGTTAT
303737 TTTT-TT-TTA-
1 TTTTGTTGTTAT
**
303746 TTTTACTGTTAT
1 TTTTGTTGTTAT
* * *
303758 TTTTGCTGCTGT
1 TTTTGTTGTTAT
*
303770 TTTGGTTGTTAT
1 TTTTGTTGTTAT
303782 TTTTGTTGTT
1 TTTTGTTGTT
303792 TGGATGTTTA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
9 7 0.09
10 3 0.04
11 16 0.20
12 52 0.63
13 4 0.05
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:303757 original size:44 final size:44
Alignment explanation
Indices: 303702--303785 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
303692 TTCGTGTTAT
* * *
303702 TTTTGCTGTTATTTTTGTTGCTATTTTTGTTGTTATTTTTTTTA
1 TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTTTTTA
*
303746 TTTTACTGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTT
1 TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTT
303786 GTTGTTTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.08, C:0.06, G:0.15, T:0.70
Consensus pattern (44 bp):
TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTTTTTA
Found at i:303802 original size:56 final size:56
Alignment explanation
Indices: 303688--303805 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 56
303678 TTTTGATTGC
* * ** *
303688 TATTTTCGTGTTATTTTTGCTGTTATTTTTGTTGCTATTTTTGTTGTTATTTTTTT
1 TATTTTCGTGTTATTTTTGCTGCTATTTTGGTTGCTATTTTTGTTGTTATGATGTT
* *
303744 TATTTTAC-TGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTTGTTGTT-TGGATGTT
1 TATTTT-CGTGTTATTTTTGCTGCTATTTTGGTTGCTATTTTTGTTGTTAT-GATGTT
303800 TATTTT
1 TATTTT
303806 TTTTATGCGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 1 0.02
56 51 0.96
57 1 0.02
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (56 bp):
TATTTTCGTGTTATTTTTGCTGCTATTTTGGTTGCTATTTTTGTTGTTATGATGTT
Found at i:304007 original size:39 final size:38
Alignment explanation
Indices: 303922--304009 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
303912 TTAATATAAT
* * * *
303922 TTTTTTTAATGTATTTTGAATTTATTTATTTTTTATTG
1 TTTTTTTAATGTATTTTGAATGTATTTATATATTATTA
303960 TTTGTTTTAATGT-TTTT-AAGTGTATTTGATATATTATATA
1 TTT-TTTTAATGTATTTTGAA-TGTATTT-ATATATTAT-TA
304000 TTTTTTTAAT
1 TTTTTTTAAT
304010 TTGTTGTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
37 2 0.05
38 13 0.31
39 23 0.55
40 4 0.10
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (38 bp):
TTTTTTTAATGTATTTTGAATGTATTTATATATTATTA
Found at i:316388 original size:20 final size:20
Alignment explanation
Indices: 316363--316425 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
316353 TCCAGTGAGC
316363 CTTTTACCGGTAGAACTCAA
1 CTTTTACCGGTAGAACTCAA
*
316383 CTTTTACAGGTAGAACTCAA
1 CTTTTACCGGTAGAACTCAA
* * * *
316403 CTTCTACCGATACAACTCCA
1 CTTTTACCGGTAGAACTCAA
316423 CTT
1 CTT
316426 ATACTGTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (20 bp):
CTTTTACCGGTAGAACTCAA
Found at i:318312 original size:5 final size:5
Alignment explanation
Indices: 318302--318327 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
318292 ACAAAGAAGT
318302 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
318328 TTTACAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:321495 original size:6 final size:6
Alignment explanation
Indices: 321486--321514 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
321476 GTCATCAAAT
321486 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
321515 CTCCTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:321522 original size:18 final size:18
Alignment explanation
Indices: 321486--321523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
321476 GTCATCAAAT
*
321486 TCTTCATCTTCATCTTCA
1 TCTTCATCTTCATCCTCA
*
321504 TCTTCATCTTCCTCCTCA
1 TCTTCATCTTCATCCTCA
321522 TC
1 TC
321524 AGTATCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.39, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTCATCTTCATCCTCA
Found at i:322691 original size:14 final size:15
Alignment explanation
Indices: 322672--322700 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
322662 AAGGTTAGTT
322672 TGTAATTAT-TTTTA
1 TGTAATTATATTTTA
322686 TGTAATTATATTTTA
1 TGTAATTATATTTTA
322701 CTTTATATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TGTAATTATATTTTA
Found at i:331398 original size:28 final size:28
Alignment explanation
Indices: 331366--331451 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
331356 TTAGGAAAAT
331366 AACATAACAACTCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
* * *
331394 AACAT---AACTCAAAATT-AGGAGAAT-
1 AACATAACAACTCTAAATTCA-AATAATA
* *
331418 AACAAAACAAATCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
331446 AA-ATAA
1 AACATAA
331452 TGTTTTAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 13
0.66 0.14 0.20
Matches are distributed among these distances:
24 5 0.12
25 14 0.33
27 16 0.37
28 8 0.19
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.22
Consensus pattern (28 bp):
AACATAACAACTCTAAATTCAAATAATA
Found at i:331409 original size:52 final size:51
Alignment explanation
Indices: 331340--331451 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 51
331330 TAAAAGATAA
* *
331340 AATAAAA-AACTCAAAATTAGGAAAATAACATAACAACTCTAAATTCAAAT
1 AATAAAATAACTCAAAATTAGGAAAATAACAAAACAAATCTAAATTCAAAT
*
331390 AATAAACATAACTCAAAATTAGGAGAATAACAAAACAAATCTAAATTCAAAT
1 AATAAA-ATAACTCAAAATTAGGAAAATAACAAAACAAATCTAAATTCAAAT
331442 AATAAAATAA
1 AATAAAATAA
331452 TGTTTTAATC
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 6 0.11
51 5 0.09
52 46 0.81
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.21
Consensus pattern (51 bp):
AATAAAATAACTCAAAATTAGGAAAATAACAAAACAAATCTAAATTCAAAT
Found at i:331442 original size:24 final size:24
Alignment explanation
Indices: 331362--331448 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
331352 AAAATTAGGA
* *
331362 AAATAACATAACAACTCTAAATTC
1 AAATAACAAAACAAATCTAAATTC
* * *
331386 AAATAA-TAAACATAACTCAAAATTAGG
1 AAATAACAAAACA-AA-TCTAAATT--C
331413 AGAATAACAAAACAAATCTAAATTC
1 A-AATAACAAAACAAATCTAAATTC
*
331438 AAATAATAAAA
1 AAATAACAAAA
331449 TAATGTTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 4 0.08
24 16 0.33
25 8 0.17
27 8 0.17
28 7 0.15
29 5 0.10
ACGTcount: A:0.61, C:0.14, G:0.03, T:0.22
Consensus pattern (24 bp):
AAATAACAAAACAAATCTAAATTC
Found at i:331737 original size:3 final size:3
Alignment explanation
Indices: 331731--331768 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
331721 GTGTTGTTGT
* *
331731 TGG TGG TGG TGG TGG TGG TGG TGA TGG TGG TAG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
331769 TTGCTCTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.00, G:0.61, T:0.34
Consensus pattern (3 bp):
TGG
Done.