Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008894.1 Kokia drynarioides strain JFW-HI SEQ_123582, 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: 239623
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2234 original size:7 final size:8
Alignment explanation
Indices: 2218--2245 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2208 AATAAAGGAG
2218 AAAAGAAA
1 AAAAGAAA
2226 AAAAGAAA
1 AAAAGAAA
2234 AAAAGAAA
1 AAAAGAAA
2242 AAAA
1 AAAA
2246 TGTTTGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:4580 original size:17 final size:17
Alignment explanation
Indices: 4558--4591 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4548 CATCATCCTC
*
4558 TTCTCACTTGAAACCAA
1 TTCTCACCTGAAACCAA
4575 TTCTCACCTGAAACCAA
1 TTCTCACCTGAAACCAA
4592 CCAATCACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26
Consensus pattern (17 bp):
TTCTCACCTGAAACCAA
Found at i:7890 original size:12 final size:12
Alignment explanation
Indices: 7873--7918 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
7863 CCTCAGCAGA
7873 TTCTTTTCTTCT
1 TTCTTTTCTTCT
7885 TTCTTTTCTTCCT
1 TTCTTTTCTT-CT
7898 TTC-TTTCTTC-
1 TTCTTTTCTTCT
7908 TTCTTCTTCTT
1 TTCTT-TTCTT
7919 GGTCCTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.10
11 2 0.06
12 21 0.68
13 5 0.16
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:8292 original size:35 final size:36
Alignment explanation
Indices: 8232--8301 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
8222 TTCATTGGGC
* *
8232 GATAGATTGATAGGAAGGTTTGGAAGTTTGGTAATG
1 GATAGATTGATAGGAAGGTTGGGAAGTCTGGTAATG
*
8268 GATAGATTGAT-TGAAGGTTGGGAAGTCTGGTAAT
1 GATAGATTGATAGGAAGGTTGGGAAGTCTGGTAAT
8302 AGAGTCTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.30, C:0.01, G:0.36, T:0.33
Consensus pattern (36 bp):
GATAGATTGATAGGAAGGTTGGGAAGTCTGGTAATG
Found at i:16249 original size:30 final size:30
Alignment explanation
Indices: 16215--16277 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
16205 AAGATGCGAG
* * *
16215 CACTGGTGTTATGAGCACTCATGCTACGAA
1 CACTGGAGTTACGAACACTCATGCTACGAA
* * *
16245 CACTGGAGTTGCGAACACTCATGTTCCGAA
1 CACTGGAGTTACGAACACTCATGCTACGAA
16275 CAC
1 CAC
16278 ACACAATGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (30 bp):
CACTGGAGTTACGAACACTCATGCTACGAA
Found at i:18640 original size:111 final size:117
Alignment explanation
Indices: 18440--19024 Score: 639
Period size: 123 Copynumber: 4.9 Consensus size: 117
18430 TTAAAACATG
* * * *
18440 AAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTTCATATATTTCTTTGAATG
1 AAAG-TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGG
* *
18505 AATACTTCCATTTTAATATGAGATATTATATAAAATGAAATTGAATATT-AA-
65 AATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATTAAAC
* * * *
18556 AAA-T-AT-T-CATTTGGAAAGAATATAATGTTTTAATAAACCTCCCATATATTTCTTTAAAGGA
1 AAAGTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGA
* *
18617 ATATTTACATTTTAATATGAGATATTATATAAAAGAAAATTGAATATTAAAAAC
66 ATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATT--AAAC
*
18671 ATGGAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAACAAACCTTCCATATATTTCTTTAA
1 A---AAG-TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAA
*
18736 GGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATTAAAAAC
62 AGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATT--AAAC
* * * *
18794 ATGAAAGTTAATATCCTTTTGGAAATGATATAATATTTTAATAAATCTTCCATATATTTCTCT-G
1 ---AAAG-TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAA
** * *
18858 AGAGAATATTTTTATTTTAATATAAGATATTATATAAAAGGAATTTGAATATTAAAAAC
62 AG-GAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATT--AAAC
* * *
18917 ATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAACCTTCCA-ATATTTC-TCAG
1 A---AAG-TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTA-
* ** * * *
18980 AAGAAATATTTTTATTTTAATATAAGATATTAAATAAAAAGAAAT
61 AAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAAT
19025 GATAGCATAT
Statistics
Matches: 410, Mismatches: 38, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
111 92 0.22
112 1 0.00
113 2 0.00
114 3 0.01
115 1 0.00
116 3 0.01
118 2 0.00
120 2 0.00
121 2 0.00
122 47 0.11
123 254 0.62
126 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (117 bp):
AAAGTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGA
ATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATTAAAC
Found at i:18780 original size:123 final size:123
Alignment explanation
Indices: 18565--19024 Score: 665
Period size: 123 Copynumber: 3.7 Consensus size: 123
18555 AAAATATTCA
* * * *
18565 TTTGGAAAGAATATAATGTTTTAATAAACCTCCCATATATTTCTTTAAAGGAATATTTACATTTT
1 TTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGAATATTTTCATTTT
* *
18630 AATATGAGATATTATATAAAAGAAAATTGAATATTAAAAACATGGAAGTTAATATCCT
66 AATATAAGATATTATATAAAAGGAAATTGAATATTAAAAACATGGAAGTTAATATCCT
* * *
18688 TTTGGAAAGGATATAATATTTTAACAAACCTTCCATATATTTCTTTAAGGGAATATTTCCATTTT
1 TTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGAATATTTTCATTTT
* *
18753 AATATGAGATATTATATAAAAGGAAATTGAATATTAAAAACATGAAAGTTAATATCCT
66 AATATAAGATATTATATAAAAGGAAATTGAATATTAAAAACATGGAAGTTAATATCCT
* * * * *
18811 TTTGGAAATGATATAATATTTTAATAAATCTTCCATATATTTCTCT-GAGAGAATATTTTTATTT
1 TTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAG-GAATATTTTCATTT
*
18875 TAATATAAGATATTATATAAAAGGAATTTGAATATTAAAAACATGGAAGTTAATATCCT
65 TAATATAAGATATTATATAAAAGGAAATTGAATATTAAAAACATGGAAGTTAATATCCT
* * * * *
18934 TTTGGAAAAGATATAATGTTTTAATAAACCTTCCA-ATATTTC-TCAGAAGAAATATTTTTATTT
1 TTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTA-AAGGAATATTTTCATTT
* *
18997 TAATATAAGATATTAAATAAAAAGAAAT
65 TAATATAAGATATTATATAAAAGGAAAT
19025 GATAGCATAT
Statistics
Matches: 305, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
122 46 0.15
123 259 0.85
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (123 bp):
TTTGGAAAGGATATAATATTTTAATAAACCTTCCATATATTTCTTTAAAGGAATATTTTCATTTT
AATATAAGATATTATATAAAAGGAAATTGAATATTAAAAACATGGAAGTTAATATCCT
Found at i:30309 original size:10 final size:10
Alignment explanation
Indices: 30291--30327 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
30281 CATGATAGAT
*
30291 ATCTATTGTA
1 ATCTTTTGTA
30301 ATCTTTTGTA
1 ATCTTTTGTA
30311 ATCTTTTGTA
1 ATCTTTTGTA
30321 ATCTTTT
1 ATCTTTT
30328 ACTTTAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (10 bp):
ATCTTTTGTA
Found at i:41987 original size:21 final size:21
Alignment explanation
Indices: 41961--42000 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41951 ACTTACAGAG
* *
41961 CTTTGGGTTGTGATACCTAGC
1 CTTTGGGGTGCGATACCTAGC
41982 CTTTGGGGTGCGATACCTA
1 CTTTGGGGTGCGATACCTA
42001 ATCTGTCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.35
Consensus pattern (21 bp):
CTTTGGGGTGCGATACCTAGC
Found at i:43988 original size:64 final size:64
Alignment explanation
Indices: 43882--44011 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 64
43872 AATAGATATG
* * * * * *
43882 AAAAGTAAGCATATATGAAATTCAATAAATAAATCTAAGACTTATAAATGTCATGCATTTAAAC
1 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTACAAATGTAATGCATTTAAAC
* *
43946 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTACAGATTTAATGCATTTAAAC
1 AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTACAAATGTAATGCATTTAAAC
44010 AA
1 AA
44012 TGTGTAACAT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (64 bp):
AAAAATAAGCATACATGAAATCCAATAAATAAATCCAAGACTTACAAATGTAATGCATTTAAAC
Found at i:45251 original size:38 final size:38
Alignment explanation
Indices: 45209--45316 Score: 135
Period size: 38 Copynumber: 2.8 Consensus size: 38
45199 AACCGAATAT
* * *
45209 ATGTTAAGCATGCCTACTGCTACTGTTGAATTAAGTAC
1 ATGTTAAACATGTCTACTGCTAGTGTTGAATTAAGTAC
** * **
45247 ATGTTAAACATGTCTACTATTAGTGATGAATTGTGTAC
1 ATGTTAAACATGTCTACTGCTAGTGTTGAATTAAGTAC
*
45285 ATGCTAAACATGTCTACTGCTAGTGTTGAATT
1 ATGTTAAACATGTCTACTGCTAGTGTTGAATT
45317 GTTCTATTAC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (38 bp):
ATGTTAAACATGTCTACTGCTAGTGTTGAATTAAGTAC
Found at i:56326 original size:36 final size:36
Alignment explanation
Indices: 56232--56371 Score: 172
Period size: 36 Copynumber: 3.9 Consensus size: 36
56222 TGAAATGACC
** * * * *
56232 TTATGCTCTAACTAAGACATAAGTAGTTACTTAGCA
1 TTATGCTCTAACCGAGACGTAAGCACTTCCTTAGCA
** * *
56268 TTACACTTTAACCGAGATGTAAGCACTTCCTTAGCA
1 TTATGCTCTAACCGAGACGTAAGCACTTCCTTAGCA
*
56304 TTATGCTCTAACTGAGACGTAAGCACTTCCTTAGCA
1 TTATGCTCTAACCGAGACGTAAGCACTTCCTTAGCA
*
56340 TTATGCTCTAACCGAGATGTAAGCACTTCCTT
1 TTATGCTCTAACCGAGACGTAAGCACTTCCTT
56372 TGAAGTAATC
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 87 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (36 bp):
TTATGCTCTAACCGAGACGTAAGCACTTCCTTAGCA
Found at i:56352 original size:72 final size:72
Alignment explanation
Indices: 56232--56371 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
56222 TGAAATGACC
* * *
56232 TTATGCTCTAACTAAGACATAAGTAGTTACTTAGCATTACACTTTAACCGAGATGTAAGCACTTC
1 TTATGCTCTAACTAAGACATAAGCACTTACTTAGCATTACACTCTAACCGAGATGTAAGCACTTC
56297 CTTAGCA
66 CTTAGCA
* * * **
56304 TTATGCTCTAACTGAGACGTAAGCACTTCCTTAGCATTATGCTCTAACCGAGATGTAAGCACTTC
1 TTATGCTCTAACTAAGACATAAGCACTTACTTAGCATTACACTCTAACCGAGATGTAAGCACTTC
56369 CTT
66 CTT
56372 TGAAGTAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (72 bp):
TTATGCTCTAACTAAGACATAAGCACTTACTTAGCATTACACTCTAACCGAGATGTAAGCACTTC
CTTAGCA
Found at i:57695 original size:12 final size:13
Alignment explanation
Indices: 57678--57706 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
57668 CAATTCTTTC
57678 CTTTTATTTT-TT
1 CTTTTATTTTATT
57690 CTTTTATTTTATT
1 CTTTTATTTTATT
57703 CTTT
1 CTTT
57707 ATAAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTATTTTATT
Found at i:61022 original size:19 final size:21
Alignment explanation
Indices: 60998--61037 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
60988 GATGATGATC
*
60998 CGATCTTC-AAACAA-AAAAA
1 CGATCTACAAAACAACAAAAA
61017 CGATCTACAAAACAACAAAAA
1 CGATCTACAAAACAACAAAAA
61038 TAACTGTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (21 bp):
CGATCTACAAAACAACAAAAA
Found at i:69869 original size:23 final size:23
Alignment explanation
Indices: 69826--69870 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
69816 TAACAGAAAC
*
69826 AAAATGAAATCACTAAGCCTAAG
1 AAAATGAAATCACTAAACCTAAG
*
69849 AAAA-GAAATGACTTAAACCTAA
1 AAAATGAAATCAC-TAAACCTAA
69871 ATTACAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAATGAAATCACTAAACCTAAG
Found at i:72881 original size:52 final size:52
Alignment explanation
Indices: 72765--73004 Score: 266
Period size: 52 Copynumber: 4.6 Consensus size: 52
72755 TAAATGAAAA
* * * * * *
72765 AGGTCTGATGACTCTATGTCATCGTGAGTATATAAATCCTTT-ACGAATTATGAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGAA-CA--AG
* * ** *
72819 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGAACAAG
* * *
72871 AGGTCCGATGACTATGTGTCATTGTGAGTGTATGATTCCTTTAAGGAACAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGAACAAG
* * *
72923 AGGTCCGATGACTATGTGTCATCATGAGTGTATGATTCCTTTAAGGAACAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGAACAAG
* * *
72975 AGGTCCAATTATTATGTGTCATCGTGAGTA
1 AGGTCCGATGACTATGTGTCATCGTGAGTA
73005 CTAAAGGAAA
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
52 120 0.74
54 41 0.25
55 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAAGGAACAAG
Found at i:74867 original size:18 final size:17
Alignment explanation
Indices: 74841--74874 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
74831 GTAGTTGTAA
*
74841 TTAATTTTACTTAACTT
1 TTAATTTTACTAAACTT
74858 TTAATCTTTACTAAACT
1 TTAAT-TTTACTAAACT
74875 GTTGTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATTTTACTAAACTT
Found at i:82028 original size:17 final size:18
Alignment explanation
Indices: 82006--82046 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
81996 TTAGCTTTCA
82006 TGCATTCTT-ATTGT-ACC
1 TGCATTCTTAATTGTCA-C
82023 TGCATT-TTAATTGTCAC
1 TGCATTCTTAATTGTCAC
82040 TGCATTC
1 TGCATTC
82047 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (18 bp):
TGCATTCTTAATTGTCAC
Found at i:87152 original size:21 final size:21
Alignment explanation
Indices: 87111--87157 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
87101 TGTGATGGTT
* *
87111 CTACCAATACCAGTATGACTA
1 CTACCAATACAAATATGACTA
87132 CTACCAATACAAATCAT-ACTA
1 CTACCAATACAAAT-ATGACTA
87153 CTACC
1 CTACC
87158 GGTACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.23
Consensus pattern (21 bp):
CTACCAATACAAATATGACTA
Found at i:94043 original size:36 final size:36
Alignment explanation
Indices: 93983--94082 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
93973 TAGTAATAGG
*
93983 CATGACCTTTGGGTTAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
94019 CATGACCTTTAGGTCAACATGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
94055 CATGACCTTTGGGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
94083 TCGGATATCG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:96890 original size:17 final size:17
Alignment explanation
Indices: 96860--96892 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
96850 TAGTTGCAAT
96860 TAATTTTACTTAATTTC
1 TAATTTTACTTAATTTC
96877 TAATCTTTAC-TAATTT
1 TAAT-TTTACTTAATTT
96893 GTTTACTTTT
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:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTTACTTAATTTC
Found at i:102999 original size:15 final size:16
Alignment explanation
Indices: 102970--103006 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
102960 GATAACCAGT
*
102970 AGAAGGAGAAGGAAGA
1 AGAAGGAGAAAGAAGA
102986 AGAA-GAGAAAGAAGA
1 AGAAGGAGAAAGAAGA
103001 A-AAGGA
1 AGAAGGA
103007 TGAATGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 13 0.68
16 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAGGAGAAAGAAGA
Found at i:104094 original size:22 final size:22
Alignment explanation
Indices: 104066--104109 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
104056 TCAGTCACTT
*
104066 GAAAAAGGAAAATA-AAAAGAAA
1 GAAAAA-GAAAAGAGAAAAGAAA
104088 GAAAAAGAAAAGAGAAAAGAAA
1 GAAAAAGAAAAGAGAAAAGAAA
104110 AGAAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (22 bp):
GAAAAAGAAAAGAGAAAAGAAA
Found at i:104107 original size:12 final size:12
Alignment explanation
Indices: 104080--104117 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
104070 AAGGAAAATA
104080 AAAAG-AAAGA-
1 AAAAGAAAAGAG
104090 AAAAGAAAAGAG
1 AAAAGAAAAGAG
104102 AAAAGAAAAGAAG
1 AAAAGAAAAG-AG
104115 AAA
1 AAA
104118 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 10 0.40
13 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:127421 original size:26 final size:26
Alignment explanation
Indices: 127390--127484 Score: 111
Period size: 26 Copynumber: 3.7 Consensus size: 26
127380 GTCTTCCAAA
*
127390 AATTTAGCTCATACGAGCCCAGACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
*
127416 AGTTTAGCTCTTACGAGCCCAGACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* * *
127442 AATATCGCTCTTACGAG-CCAGTCAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* * *
127467 AATATCGCTCTTATGAGC
1 AATTTAGCTCTTACGAGC
127485 TAGATAGAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 23 0.38
26 38 0.62
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (26 bp):
AATTTAGCTCTTACGAGCCCAGACAG
Found at i:127468 original size:25 final size:25
Alignment explanation
Indices: 127422--127733 Score: 232
Period size: 25 Copynumber: 12.2 Consensus size: 25
127412 ACAGAGTTTA
*
127422 GCTCTTACGAGCCCAGACAGAATATC
1 GCTCTTACGAG-CCAGTCAGAATATC
127448 GCTCTTACGAGCCAGTCAGAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* * *
127473 GCTCTTATGAGCTAGAT-AGAATATT
1 GCTCTTACGAGCCAG-TCAGAATATC
* * *
127498 GCTCTCATGAGCTAGAT-AGAATATC
1 GCTCTTACGAGCCAG-TCAGAATATC
* * *
127523 ACTCTTTCGAGCCAGAATCAAAATATC
1 GCTCTTACGAGCCAG--TCAGAATATC
* *
127550 ACTCTTTCGAGCCAGAATCAGAATATC
1 GCTCTTACGAGCCAG--TCAGAATATC
* * * *
127577 GCTCTCACGAGCTAGACAAAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* * ** *
127602 ACTCCTATAAGCCAGTTAGAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* * *
127627 ACTCTTACGAGCCCGGCAGAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* * *
127652 GCTCTCATGAGCCAGACAGAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* * *
127677 GCTCTTATGAGCTAGACAGAATATC
1 GCTCTTACGAGCCAGTCAGAATATC
* *
127702 GCTCTTTCGAGCCAAAATCAGAATATC
1 GCTCTTACGAGCC--AGTCAGAATATC
*
127729 ACTCT
1 GCTCT
127734 CATGAGCTAG
Statistics
Matches: 234, Mismatches: 47, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
25 162 0.69
26 14 0.06
27 58 0.25
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
GCTCTTACGAGCCAGTCAGAATATC
Found at i:127502 original size:50 final size:50
Alignment explanation
Indices: 127422--127782 Score: 267
Period size: 50 Copynumber: 7.1 Consensus size: 50
127412 ACAGAGTTTA
* *
127422 GCTCTTACGAGCCCAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
1 GCTCTTATGAG-CTAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
* * * * *
127473 GCTCTTATGAGCTAGATAGAATATTGCTCTCATGAGCTAGAT-AGAATATC
1 GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCCAG-TCAGAATATC
* * * * *
127523 ACTCTT-TCGAGCCAGAATCAAAATATCACTCTTTCGAGCCAGAATCAGAATATC
1 GCTCTTAT-GAGCTAG-A-CAGAATATCGCTCTTACGAGCCAG--TCAGAATATC
* * * * * ** *
127577 GCTCTCACGAGCTAGACAAAATATCACTCCTATAAGCCAGTTAGAATATC
1 GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
* * ** * * * *
127627 ACTCTTACGAGCCCGGCAGAATATCGCTCTCATGAGCCAGACAGAATATC
1 GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
* *
127677 GCTCTTATGAGCTAGACAGAATATCGCTCTTTCGAGCCAAAATCAGAATATC
1 GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCC--AGTCAGAATATC
* * * * * * * ** *
127729 ACTCTCATGAGCTAGATAAAATACCGTTCCTATAAGCCAGTCAGAATAAC
1 GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
127779 GCTC
1 GCTC
127783 CTTCGAGCCA
Statistics
Matches: 240, Mismatches: 61, Indels: 19
0.75 0.19 0.06
Matches are distributed among these distances:
49 1 0.00
50 132 0.55
51 12 0.05
52 74 0.31
53 3 0.01
54 18 0.08
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (50 bp):
GCTCTTATGAGCTAGACAGAATATCGCTCTTACGAGCCAGTCAGAATATC
Found at i:127551 original size:27 final size:27
Alignment explanation
Indices: 127517--127605 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
127507 AGCTAGATAG
127517 AATATCACTCTTTCGAGCCAGAATCAA
1 AATATCACTCTTTCGAGCCAGAATCAA
*
127544 AATATCACTCTTTCGAGCCAGAATCAG
1 AATATCACTCTTTCGAGCCAGAATCAA
* ** *
127571 AATATCGCTCTCACGAGCTAG-A-CAA
1 AATATCACTCTTTCGAGCCAGAATCAA
127596 AATATCACTC
1 AATATCACTC
127606 CTATAAGCCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
25 11 0.20
26 1 0.02
27 43 0.78
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (27 bp):
AATATCACTCTTTCGAGCCAGAATCAA
Found at i:127774 original size:77 final size:77
Alignment explanation
Indices: 127457--127800 Score: 322
Period size: 77 Copynumber: 4.5 Consensus size: 77
127447 CGCTCTTACG
* * * * *
127457 AGCCAGTCAGAATATCGCTCTTAT-GAG-CTAGAT-AGAATATTGCTCTCATGAGCTAGATAGAA
1 AGCCAGTCAGAATATCGCTCTT-TCGAGCCAAAATCAGAATATCGCTCTCATGAGCTAGACAAAA
* *
127519 TATCACT-CTTTCG
65 TATCACTCCTAT-A
* * * *
127532 AGCCAGAATCAAAATATCACTCTTTCGAGCCAGAATCAGAATATCGCTCTCACGAGCTAGACAAA
1 AGCCAG--TCAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCGCTCTCATGAGCTAGACAAA
127597 ATATCACTCCTATA
64 ATATCACTCCTATA
* * * *** * *
127611 AGCCAGTTAGAATATCACTCTTACGAGCC--CGGCAGAATATCGCTCTCATGAGCCAGACAGAAT
1 AGCCAGTCAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCGCTCTCATGAGCTAGACAAAAT
* * *
127674 ATCGCTCTTATG
66 ATCACTCCTATA
* * * *
127686 AGCTAGACAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCACTCTCATGAGCTAGATAAAAT
1 AGCCAGTCAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCGCTCTCATGAGCTAGACAAAAT
* **
127751 ACCGTTCCTATA
66 ATCACTCCTATA
* * *
127763 AGCCAGTCAGAATAACGCTCCTTCGAGCCAGAATCAGA
1 AGCCAGTCAGAATATCGCTCTTTCGAGCCAAAATCAGA
127801 TTACTCCTCA
Statistics
Matches: 217, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
75 67 0.31
76 1 0.00
77 105 0.48
78 3 0.01
79 38 0.18
80 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (77 bp):
AGCCAGTCAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCGCTCTCATGAGCTAGACAAAAT
ATCACTCCTATA
Found at i:127790 original size:152 final size:154
Alignment explanation
Indices: 127457--127791 Score: 408
Period size: 152 Copynumber: 2.2 Consensus size: 154
127447 CGCTCTTACG
* * * ** ** * * *
127457 AGCCAGTCAGAATATCGCTCTTATGAGCTAGATAGAATATTGCTCTCATGAGCTAGATAGAATAT
1 AGCCAGTCAGAATAACACTCTTACGAGCCCGGCAGAATATCGCTCTCATGAGCCAGACAGAATAT
* *
127522 CACTCTTTCGAGCCAGAATCAAAATATCACTCTTTCGAGCCAGAATCAGAATATCGCTCTCACGA
66 CACTCTTTCGAGCCAGAATCAAAATATCACTCTTTCGAGCCAAAATCAGAATATCACTCTCACGA
*
127587 GCTAGACAAAATATCACTCCTATA
131 GCTAGACAAAATACCACTCCTATA
* *
127611 AGCCAGTTAGAATATCACTCTTACGAGCCCGGCAGAATATCGCTCTCATGAGCCAGACAGAATAT
1 AGCCAGTCAGAATAACACTCTTACGAGCCCGGCAGAATATCGCTCTCATGAGCCAGACAGAATAT
* * * * *
127676 CGCTCTTAT-GAGCTAG-A-CAGAATATCGCTCTTTCGAGCCAAAATCAGAATATCACTCTCATG
66 CACTCTT-TCGAGCCAGAATCAAAATATCACTCTTTCGAGCCAAAATCAGAATATCACTCTCACG
* **
127738 AGCTAGATAAAATACCGTTCCTATA
130 AGCTAGACAAAATACCACTCCTATA
*
127763 AGCCAGTCAGAATAACGCTCCTT-CGAGCC
1 AGCCAGTCAGAATAACACT-CTTACGAGCC
127792 AGAATCAGAT
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
152 83 0.54
153 4 0.03
154 67 0.43
155 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (154 bp):
AGCCAGTCAGAATAACACTCTTACGAGCCCGGCAGAATATCGCTCTCATGAGCCAGACAGAATAT
CACTCTTTCGAGCCAGAATCAAAATATCACTCTTTCGAGCCAAAATCAGAATATCACTCTCACGA
GCTAGACAAAATACCACTCCTATA
Found at i:143631 original size:15 final size:15
Alignment explanation
Indices: 143613--143674 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
143603 CCTTCATCCA
143613 TGTTCGCAACATCAG
1 TGTTCGCAACATCAG
*
143628 TGTTCGCAGC-TCCAG
1 TGTTCGCAACAT-CAG
*
143643 TGTTCGCAACATGAG
1 TGTTCGCAACATCAG
* * *
143658 TGCTCGTAACACCAG
1 TGTTCGCAACATCAG
143673 TG
1 TG
143675 CTCACATCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (15 bp):
TGTTCGCAACATCAG
Found at i:143673 original size:30 final size:30
Alignment explanation
Indices: 143613--143674 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
143603 CCTTCATCCA
* * *
143613 TGTTCGCAACATCAGTGTTCGCAGCTCCAG
1 TGTTCGCAACATCAGTGCTCGCAACACCAG
* *
143643 TGTTCGCAACATGAGTGCTCGTAACACCAG
1 TGTTCGCAACATCAGTGCTCGCAACACCAG
143673 TG
1 TG
143675 CTCACATCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (30 bp):
TGTTCGCAACATCAGTGCTCGCAACACCAG
Found at i:147208 original size:54 final size:54
Alignment explanation
Indices: 147145--147254 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
147135 ATGCAAGTGT
*
147145 TAGAAAAAGTAATCTAG-TCAAAGGCTATCACTGGAAGAGTGTGTGTCAGCGCAA
1 TAGAAAAAGTAATCTAGCT-AAAGGCTATCACTGCAAGAGTGTGTGTCAGCGCAA
* *
147199 TAGAAAAAGTAATCTAGCTAAAGGCTGTCACTGCAAGAGTGTGTGTCAGTGCAA
1 TAGAAAAAGTAATCTAGCTAAAGGCTATCACTGCAAGAGTGTGTGTCAGCGCAA
147253 TA
1 TA
147255 ACATACTCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (54 bp):
TAGAAAAAGTAATCTAGCTAAAGGCTATCACTGCAAGAGTGTGTGTCAGCGCAA
Found at i:149617 original size:46 final size:46
Alignment explanation
Indices: 149305--150202 Score: 953
Period size: 45 Copynumber: 19.8 Consensus size: 46
149295 CACCAAATCA
* * *
149305 AATCTTTTACCCCT-AATCCAGAGGTGCAGATTGAAGCCTCCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
149350 AGTCTTTTA-CCCTTAATCTAGAGGGGCAGATTGAAGCTACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
149395 AATCTTCTACCCC-AAATCTAGAGGGCCAGTTTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * *
149440 AATCTTTCACCCCT-AATCCAGAGAGGCAAATTGAA-CCTACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCC-ACCATCC
* * * * *
149485 AATCTTTTACTCCT-AATCTAAAGAGGCAAATTGAACCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
*
149530 AATCTTTTACCCCT-AATCTAGAGGGGCAGATTGAAGTCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * *
149575 AATATGTTACCCCTAAATCCAGAGGGGTAGATTGAAGCCACCATTC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * * * *
149621 AATCTTTTACCCCTAAATCCAAAAGGGAAAATT-AAGGTCACCATGC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAA-GCCACCATCC
* *
149667 AATCTTTTACCCCT-AATCTAGAGGGGTAGATTGAAGCCACCATCT
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* ** * * *
149712 AATCTTTTA-CCCTTAATCTAGAGGACCAAATCGAAGCAACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * *
149757 AATCTTTTACCCCTAAATCCAAAGAGGCATATTAAAGCCACCAT-C
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
** * *
149802 AATCTTTTACCTATAAATCCAGAGGGACAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * *
149848 AATCTTATACCCCTAAATCTGGAGGGACATATTGAAGCCAGCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * * *
149894 AATCTATTACCCC-AAATCCAAAGTGACAAATTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
149939 AATCTTTTACCCCT-AATCTGGA-GGGTAGAGTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * *
149983 AATCTTTTACCCCT-AATCTGGAGGCGTAGAGTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
150028 AATCTTTTACCTCTAAATCTAGAGGGACAGATTGAAGTCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * * * *
150074 AATCTTTTACCCTTAAATCCAGAGAGCCAGATTGAAGTCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
150120 AATCTTTTACCCCTAAATCTAAAAGGGCAGAGTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
* * *
150166 AATCTTATACCCTTAAATCTAGAGGGCCAGATTGAAG
1 AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAG
150203 TTACAATACC
Statistics
Matches: 714, Mismatches: 125, Indels: 27
0.82 0.14 0.03
Matches are distributed among these distances:
44 49 0.07
45 372 0.52
46 293 0.41
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (46 bp):
AATCTTTTACCCCTAAATCTAGAGGGGCAGATTGAAGCCACCATCC
Found at i:149807 original size:272 final size:273
Alignment explanation
Indices: 149305--150184 Score: 996
Period size: 272 Copynumber: 3.2 Consensus size: 273
149295 CACCAAATCA
* * * *
149305 AATCTTTTACCCCT-AATCCAGAGGTGCAGATTGAAGCCTCCATCCAGTCTTTTA-CCCTTAATC
1 AATC-TTTACCCCTAAATCCAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATC
* * * * * * * * ** *
149368 TAGAGGGGCAGATTGAAGCT-ACCATCCAATCTTCTACCCCAAATCTAGAGGGCCAGTTTGAAGC
65 CAAAAGGGAAAATTGAAGGTCACCATCCAATCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGC
* * * * * *
149432 CACCATCCAATCTTTCACCCCTAATCCAGA-GAGGCAAATTGAACCTACCATCCAATCTTTTACT
130 CACCATCCAATCTTTTACCCCTAATCTAGAGGA-CCAAA-TGAAGCAACCATCCAATCTTTTACC
* * * *
149496 CCT-AATCTAAAGAGGCAAATTGAACCCACCATCCAATCTTTTACCCCT-AATCTAGAGGGGCAG
193 CCTAAATCTAAAGAGGCAAATTGAAGCCACCATCCAATCTTTTACCCATAAATCCAGAGGGACAG
149559 ATTGAAGTCACCATCC
258 ATTGAAGTCACCATCC
* * *
149575 AATATGTTACCCCTAAATCCAGAGGGGTAGATTGAAGCCACCATTCAATCTTTTACCCCTAAATC
1 AATCT-TTACCCCTAAATCCAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATC
*
149640 CAAAAGGGAAAATT-AAGGTCACCATGCAATCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGC
65 CAAAAGGGAAAATTGAAGGTCACCATCCAATCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGC
* *
149704 CACCATCTAATCTTTTACCCTTAATCTAGAGGACCAAATCGAAGCAACCATCCAATCTTTTACCC
130 CACCATCCAATCTTTTACCCCTAATCTAGAGGACCAAAT-GAAGCAACCATCCAATCTTTTACCC
* * * *
149769 CTAAATCCAAAGAGGCATATTAAAGCCACCAT-CAATCTTTTACCTATAAATCCAGAGGGACAGA
194 CTAAATCTAAAGAGGCAAATTGAAGCCACCATCCAATCTTTTACCCATAAATCCAGAGGGACAGA
*
149833 TTGAAGCCACCATCC
259 TTGAAGTCACCATCC
** * * * *
149848 AATCTTATACCCCTAAATCTGGAGGGACATATTGAAGCCAGCATCCAATCTATTACCCC-AAATC
1 AATCTT-TACCCCTAAATCCAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATC
* * * *
149912 C-AAAGTGACAAATTGAA-GCCACCATCCAATCTTTTACCCCTAATCTGGA-GGGTAGAGTGAAG
65 CAAAAGGGA-AAATTGAAGGTCACCATCCAATCTTTTACCCCTAATCTAGAGGGGTAGATTGAAG
* * * *
149974 CCACCATCCAATCTTTTACCCCTAATCTGGAGG-CGTAGAGTGAAGCCACCATCCAATCTTTTAC
129 CCACCATCCAATCTTTTACCCCTAATCTAGAGGAC-CA-AATGAAGCAACCATCCAATCTTTTAC
* * * * * * *
150038 CTCTAAATCTAGAG-GGACAGATTGAAGTCACCATCCAATCTTTTACCCTTAAATCCAGAGAGCC
192 CCCTAAATCTAAAGAGG-CAAATTGAAGCCACCATCCAATCTTTTACCCATAAATCCAGAGGGAC
150102 AGATTGAAGTCACCATCC
256 AGATTGAAGTCACCATCC
* * * * * *
150120 AATCTTTTACCCCTAAATCTAAAAGGGCAGAGTGAAGCCACCATCCAATCTTATACCCTTAAATC
1 AATC-TTTACCCCTAAATCCAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATC
150185 TAGAGGGCCA
Statistics
Matches: 516, Mismatches: 77, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
269 1 0.00
270 14 0.03
271 136 0.26
272 253 0.49
273 112 0.22
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (273 bp):
AATCTTTACCCCTAAATCCAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCC
AAAAGGGAAAATTGAAGGTCACCATCCAATCTTTTACCCCTAATCTAGAGGGGTAGATTGAAGCC
ACCATCCAATCTTTTACCCCTAATCTAGAGGACCAAATGAAGCAACCATCCAATCTTTTACCCCT
AAATCTAAAGAGGCAAATTGAAGCCACCATCCAATCTTTTACCCATAAATCCAGAGGGACAGATT
GAAGTCACCATCC
Found at i:151113 original size:26 final size:25
Alignment explanation
Indices: 151074--151157 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 25
151064 CTTATTATTA
151074 TTATTATTATTATTTATATTTAGTTAT
1 TTATT-TTA-TATTTATATTTAGTTAT
151101 TTATTTTGATATTTA-ATTTA-TTGAT
1 TTATTTT-ATATTTATATTTAGTT-AT
* *
151126 TT-TTTTTTATTTATTTATTT-GTCAT
1 TTATTTTATATTTA--TATTTAGTTAT
151151 TTATTTT
1 TTATTTT
151158 CATGCCTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
23 6 0.12
24 6 0.12
25 13 0.27
26 17 0.35
27 6 0.12
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (25 bp):
TTATTTTATATTTATATTTAGTTAT
Found at i:151211 original size:4 final size:4
Alignment explanation
Indices: 151195--151245 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
151185 TTTATTTTAG
* * * *
151195 TATT TATT T-TT TATT TATT TTTT TGTT TATT TATA TA-G TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
151241 TATT T
1 TATT T
151246 TCAAGCCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 5 0.13
4 34 0.87
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:151216 original size:12 final size:12
Alignment explanation
Indices: 151173--151226 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
151163 CTAATCCTAA
*
151173 TTATTTTTATTGT
1 TTATTTTT-TTAT
**
151186 TTATTTTAGTAT
1 TTATTTTTTTAT
151198 TTA-TTTTTTAT
1 TTATTTTTTTAT
*
151209 TTATTTTTTTGT
1 TTATTTTTTTAT
151221 TTATTT
1 TTATTT
151227 ATATAGTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.26
12 18 0.53
13 7 0.21
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:151243 original size:35 final size:36
Alignment explanation
Indices: 151173--151245 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 36
151163 CTAATCCTAA
*
151173 TTATTTTTATTGTTTATTTTAGTATTTATTTTTTAT
1 TTATTTTTATTGTTTATTTTAGTATGTATTTTTTAT
151209 TTATTTTT-TTGTTTA-TTTA-TATAGTATTTATTTAT
1 TTATTTTTATTGTTTATTTTAGTAT-GTATTT-TTTAT
151244 TT
1 TT
151246 TCAAGCCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 3 0.09
34 9 0.26
35 14 0.41
36 8 0.24
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (36 bp):
TTATTTTTATTGTTTATTTTAGTATGTATTTTTTAT
Found at i:151518 original size:21 final size:22
Alignment explanation
Indices: 151483--151529 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
151473 ACATTCTTTC
*
151483 TTTTATTTAATTTTATTTATTG
1 TTTTATGTAATTTTATTTATTG
151505 TTTTATGT-ATTTTATTTATTG
1 TTTTATGTAATTTTATTTATTG
151526 TTTT
1 TTTT
151530 TTATGCTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (22 bp):
TTTTATGTAATTTTATTTATTG
Found at i:151770 original size:26 final size:23
Alignment explanation
Indices: 151733--151782 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 23
151723 TTGTCATCTA
151733 TTACTATGATTATATTGTTATTTTAT
1 TTACTATGA-T-TATT-TTATTTTAT
151759 TTACTACT-ATTATTTTATTTTAT
1 TTACTA-TGATTATTTTATTTTAT
151782 T
1 T
151783 GTTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 10 0.43
24 4 0.17
25 1 0.04
26 7 0.30
27 1 0.04
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (23 bp):
TTACTATGATTATTTTATTTTAT
Found at i:161857 original size:12 final size:12
Alignment explanation
Indices: 161840--161882 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
161830 AAGGAGCAAG
*
161840 AGAAGAACAGAA
1 AGAAGAACAGGA
*
161852 AGAAGAAAAGGA
1 AGAAGAACAGGA
161864 AGAA-AACAAGGA
1 AGAAGAAC-AGGA
161876 AGAAGAA
1 AGAAGAA
161883 GAAAGCATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (12 bp):
AGAAGAACAGGA
Found at i:162316 original size:17 final size:17
Alignment explanation
Indices: 162274--162323 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
162264 TAGTTGCATG
162274 CATT-TATTTTAATTGT
1 CATTGTATTTTAATTGT
* *
162290 CATTGCATTTTTATTGT
1 CATTGTATTTTAATTGT
*
162307 C-TCTGTATTTTATTTGT
1 CAT-TGTATTTTAATTGT
162324 TTCAGCATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (17 bp):
CATTGTATTTTAATTGT
Found at i:171492 original size:141 final size:142
Alignment explanation
Indices: 171324--171754 Score: 591
Period size: 141 Copynumber: 3.0 Consensus size: 142
171314 TTTTTTTAAA
171324 AAAATGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTA
1 AAAAT-AAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTA
* *
171389 AATGTTTAAACAAA-TTTTAATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAG
65 AATTTTTAAACAAAGTTTTAATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGAAAAG
171453 TAGTGTTTTTTTT
130 TAGTGTTTTTTTT
* * **
171466 AAAATAAAGTTTAGATTTTTATAAATAAAAGTATGTTTTTTAGTCATTTTAAAGGAAAACTTTTT
1 AAAATAAAGTTTAGATTTTTAAAAATAAAAATATG-TTTTTAGTCATTTTAAAGGAAAA--AGTT
* * * * * *
171531 TAATTTTTTAAACAAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAGGCTTTGATATTTAATA
63 TAAATTTTTAAACAAAGTTTT-A-ATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGA
*
171596 AAAGTAGTG-ATTTTTT
126 AAAGTAGTGTTTTTTTT
* *
171612 AAAAAAAAGTTTAGGTTTTTAAAAATATAAAATATGTTTTTAGTCATTTTAAA-GAAAAAGTTTA
1 AAAATAAAGTTTAGATTTTTAAAAATA-AAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTA
* *
171676 AATTTTTAAAACAAAGTTTT-ATTTTTTAACCATTTCGAAATAAAAACTTTGATTTTTAAGAAAA
65 AATTTTT-AAACAAAGTTTTAATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGAAAA
*
171740 ATAGTGATTTTTTTT
129 GTAGTG-TTTTTTTT
171755 TTTTTTTAAA
Statistics
Matches: 250, Mismatches: 29, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
141 70 0.28
142 28 0.11
143 16 0.06
144 28 0.11
145 9 0.04
146 48 0.19
147 51 0.20
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (142 bp):
AAAATAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTAA
ATTTTTAAACAAAGTTTTAATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGAAAAGT
AGTGTTTTTTTT
Found at i:171506 original size:22 final size:20
Alignment explanation
Indices: 171440--171506 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
171430 AAAGTTTTGA
*
171440 TTTTTAAGAAAAGTAGTGTTT
1 TTTTTAAAAAAAGTA-TGTTT
* *
171461 TTTTTAAAATAAAGTTTAGATT
1 TTTTTAAAA-AAAGTAT-GTTT
*
171483 TTTATAAATAAAAGTATGTTT
1 TTTTTAAA-AAAAGTATGTTT
171504 TTT
1 TTT
171507 AGTCATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 15 0.41
22 21 0.57
23 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAAAAGTATGTTT
Found at i:171691 original size:20 final size:21
Alignment explanation
Indices: 171658--171704 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
171648 TTTTTAGTCA
171658 TTTTAAAGAAAAAGTTTAAAT
1 TTTTAAAGAAAAAGTTTAAAT
* * *
171679 TTTTAAA-ACAAAGTTTTATT
1 TTTTAAAGAAAAAGTTTAAAT
171699 TTTTAA
1 TTTTAA
171705 CCATTTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTTAAAGAAAAAGTTTAAAT
Found at i:172333 original size:21 final size:21
Alignment explanation
Indices: 172308--172360 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
172298 CTTGTATAAT
172308 TTTTATTTATCATTATTTC-A
1 TTTTATTTATCATTATTTCTA
**
172328 TCTTTATTTATTTTTATTTCTA
1 T-TTTATTTATCATTATTTCTA
172350 TTTATATTTAT
1 TTT-TATTTAT
172361 GTTTTTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
22 9 0.32
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTTATCATTATTTCTA
Found at i:172451 original size:3 final size:3
Alignment explanation
Indices: 172445--172486 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
172435 GAATAAGGTG
172445 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
172487 GTCAATGTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:176429 original size:21 final size:21
Alignment explanation
Indices: 176403--176456 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
176393 AAGGTGTTAC
*
176403 AATTTTACCCTCTTTAAATGA
1 AATTTTAGCCTCTTTAAATGA
176424 AATTTTAGCCTCTTTAAATGA
1 AATTTTAGCCTCTTTAAATGA
176445 AATTTTAGCCTC
1 AATTTTAGCCTC
176457 GAAATTTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (21 bp):
AATTTTAGCCTCTTTAAATGA
Found at i:186791 original size:24 final size:24
Alignment explanation
Indices: 186763--186810 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
186753 AAATTCGTAA
**
186763 GTTAAATAAATTATGCTAATAAAT
1 GTTAAATAAATTATAATAATAAAT
*
186787 GTTAAATATATTATAATAATAAAT
1 GTTAAATAAATTATAATAATAAAT
186811 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (24 bp):
GTTAAATAAATTATAATAATAAAT
Found at i:186816 original size:24 final size:24
Alignment explanation
Indices: 186765--186817 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
186755 ATTCGTAAGT
** **
186765 TAAATAAATTATGCTAATAAATGT
1 TAAATAAATTATAATAATAAATAC
*
186789 TAAATATATTATAATAATAAATAC
1 TAAATAAATTATAATAATAAATAC
186813 TAAAT
1 TAAAT
186818 CTTTTAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATAAATTATAATAATAAATAC
Found at i:194567 original size:22 final size:22
Alignment explanation
Indices: 194540--194583 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
194530 TATGTGAGTG
194540 CTCTCTCGATTTTATATTATAT
1 CTCTCTCGATTTTATATTATAT
194562 CTCTCTCGATTTTATATTATAT
1 CTCTCTCGATTTTATATTATAT
194584 TTAAGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.55
Consensus pattern (22 bp):
CTCTCTCGATTTTATATTATAT
Found at i:195122 original size:29 final size:29
Alignment explanation
Indices: 195070--195125 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
195060 TAATATCATT
* *
195070 TTATATTTATATATTACAATAATAAATAA
1 TTATATTTATATAATACAAAAATAAATAA
* *
195099 TTATATTTATTTAATATAAAAATAAAT
1 TTATATTTATATAATACAAAAATAAAT
195126 TGATGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATATTTATATAATACAAAAATAAATAA
Found at i:198316 original size:14 final size:14
Alignment explanation
Indices: 198297--198334 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
198287 GTTTAAATAT
*
198297 AAAAAATTTGAA-A
1 AAAAAAATTGAAGA
198310 AAAAAAATTGAAGA
1 AAAAAAATTGAAGA
*
198324 AAAAACATTGA
1 AAAAAAATTGA
198335 CCCGCTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.18
Consensus pattern (14 bp):
AAAAAAATTGAAGA
Found at i:201849 original size:31 final size:31
Alignment explanation
Indices: 201814--201887 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
201804 CACCAGTATG
* * *
201814 TAGTACCTTATATAATATGGTCA-TCGGTACT
1 TAGTACCTGATATAATATAGTCACT-GGTACA
201845 TAGTACCTGATATAATATAGTCACTGGTACA
1 TAGTACCTGATATAATATAGTCACTGGTACA
*
201876 TAGTACTTGATA
1 TAGTACCTGATA
201888 CTTTCAAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (31 bp):
TAGTACCTGATATAATATAGTCACTGGTACA
Found at i:205548 original size:35 final size:35
Alignment explanation
Indices: 205505--205592 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
205495 TTACAATGTT
* * *
205505 TCTAGTGTGTTGGATGGTACTGGCTCCTACAAGCA
1 TCTAGTGTGCTAGATGGTACTAGCTCCTACAAGCA
* * **
205540 TCTGGTGTGCTAGATGGTACTAGCTCTTATGAGCA
1 TCTAGTGTGCTAGATGGTACTAGCTCCTACAAGCA
205575 TCTAGTGTGCTAGATGGT
1 TCTAGTGTGCTAGATGGT
205593 TAACTGTGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (35 bp):
TCTAGTGTGCTAGATGGTACTAGCTCCTACAAGCA
Found at i:210833 original size:16 final size:15
Alignment explanation
Indices: 210810--210848 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
210800 AAAAGTACTG
210810 AAAATAAACAAAAAT
1 AAAATAAACAAAAAT
* *
210825 AATAATAAATAAAGAT
1 AA-AATAAACAAAAAT
210841 AAAATAAA
1 AAAATAAA
210849 TAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAAACAAAAAT
Found at i:210842 original size:26 final size:26
Alignment explanation
Indices: 210810--210881 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
210800 AAAAGTACTG
210810 AAAATAAACAAAAATAAT-AATAAAT
1 AAAATAAACAAAAATAATAAATAAAT
*
210835 AAAGATAAA-ATAAATAAATAAATAAAT
1 AAA-ATAAACAAAAAT-AATAAATAAAT
210862 AAAATACAAACAAACAATAA
1 AAAAT--AAACAAA-AATAA
210882 AAGAGACTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 8 0.21
26 10 0.26
27 10 0.26
28 3 0.08
29 4 0.11
30 3 0.08
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.18
Consensus pattern (26 bp):
AAAATAAACAAAAATAATAAATAAAT
Found at i:211066 original size:4 final size:4
Alignment explanation
Indices: 211057--211108 Score: 52
Period size: 4 Copynumber: 12.2 Consensus size: 4
211047 ATATATAACA
*
211057 AAAT AAAT AAAT AAAAT AAAT AAAT AAA- AATAA AAAT AAAAT AAAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT -AAAT
211104 AAAT A
1 AAAT A
211109 TGCAAAGGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
3 2 0.05
4 26 0.60
5 15 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:211072 original size:13 final size:13
Alignment explanation
Indices: 211056--211108 Score: 74
Period size: 13 Copynumber: 4.1 Consensus size: 13
211046 AATATATAAC
211056 AAAATAAATAAAT
1 AAAATAAATAAAT
211069 AAAATAAATAAAT
1 AAAATAAATAAAT
211082 AAAA-ATAA-AAAT
1 AAAATA-AATAAAT
211094 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
211108 A
1 A
211109 TGCAAAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.25
13 21 0.58
14 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:211075 original size:5 final size:5
Alignment explanation
Indices: 211056--211106 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
211046 AATATATAAC
211056 AAAAT -AAAT -AAAT AAAAT -AAAT -AAAT AAAAAT AAAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT
211104 AAA
1 AAA
211107 TATGCAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 16 0.37
5 17 0.40
6 10 0.23
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:213172 original size:50 final size:50
Alignment explanation
Indices: 213118--213224 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
213108 GACCCATTGC
* *
213118 AACTTTAGGGGTATAGGATTTGGTATTGTAGCCTCATCTTGCTCTACTAA
1 AACTTCAGGGGTATAGGATTTGGTATTGTAGCCTCATCTTACTCTACTAA
* * **
213168 AACTTCAGTGGTATAGGATTTGGTATTGTAGCTTCATCTTACTCTACTGT
1 AACTTCAGGGGTATAGGATTTGGTATTGTAGCCTCATCTTACTCTACTAA
213218 AACTTCA
1 AACTTCA
213225 AAGAGATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (50 bp):
AACTTCAGGGGTATAGGATTTGGTATTGTAGCCTCATCTTACTCTACTAA
Found at i:218933 original size:81 final size:81
Alignment explanation
Indices: 218833--219001 Score: 302
Period size: 81 Copynumber: 2.1 Consensus size: 81
218823 TCGGACCTTC
218833 TTCTTAATGTTCTCACCTCTATATGCAAACTCACATTGGGCCAAACAATGTGTCGCGAGAATAAA
1 TTCTTAATGTTCTCACCTCTATATGCAAACTCACATTGGGCCAAACAATGTGTCGCGAGAATAAA
218898 CTGCCTCGATCTATAT
66 CTGCCTCGATCTATAT
* *
218914 TTCTTATTGTTCTCACCTCTATATGCAAACTCACTTTGGGCCAAACAATGTGTCGCGAGAATAAA
1 TTCTTAATGTTCTCACCTCTATATGCAAACTCACATTGGGCCAAACAATGTGTCGCGAGAATAAA
*
218979 TTGCCTCGATCTATAT
66 CTGCCTCGATCTATAT
218995 TGTCTTA
1 T-TCTTA
219002 GCACAAGTAG
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
81 79 0.94
82 5 0.06
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (81 bp):
TTCTTAATGTTCTCACCTCTATATGCAAACTCACATTGGGCCAAACAATGTGTCGCGAGAATAAA
CTGCCTCGATCTATAT
Found at i:228091 original size:26 final size:24
Alignment explanation
Indices: 228033--228092 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
228023 AATTCTTTTC
*
228033 TAATTTTTAATTTATTTAAATTGT
1 TAATTTTTAATTTATTTAAATTAT
228057 TAACTTTTTAATTTATTTTAAATTAT
1 TAA-TTTTTAATTTA-TTTAAATTAT
228083 TAATATTTTA
1 TAAT-TTTTA
228093 TACTAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 17 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:232422 original size:19 final size:19
Alignment explanation
Indices: 232398--232440 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
232388 GTCACTTTAT
232398 TACTTAATACAATTGTGTA
1 TACTTAATACAATTGTGTA
232417 TACTTAATACAATTGTGTA
1 TACTTAATACAATTGTGTA
*
232436 CACTT
1 TACTT
232441 GCACATTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (19 bp):
TACTTAATACAATTGTGTA
Done.