Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011107.1 Kokia drynarioides strain JFW-HI SEQ_126080, 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: 112033
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:253 original size:16 final size:17
Alignment explanation
Indices: 232--301 Score: 85
Period size: 16 Copynumber: 4.4 Consensus size: 17
222 TGAATTAATG
232 ATTACAGTC-CTATTCC
1 ATTACAGTCTCTATTCC
248 ATTACAG-CTCTATTCC
1 ATTACAGTCTCTATTCC
* *
264 ATTACAAT-TTTATTCC
1 ATTACAGTCTCTATTCC
*
280 ATTACA-ACTCTATTCC
1 ATTACAGTCTCTATTCC
296 ATTACA
1 ATTACA
302 ACGAACCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (17 bp):
ATTACAGTCTCTATTCC
Found at i:278 original size:32 final size:32
Alignment explanation
Indices: 242--302 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
232 ATTACAGTCC
*
242 TATTCCATTACAGCTCTATTCCATTACAATTT
1 TATTCCATTACAACTCTATTCCATTACAATTT
274 TATTCCATTACAACTCTATTCCATTACAA
1 TATTCCATTACAACTCTATTCCATTACAA
303 CGAACCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.41
Consensus pattern (32 bp):
TATTCCATTACAACTCTATTCCATTACAATTT
Found at i:302 original size:16 final size:16
Alignment explanation
Indices: 241--303 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
231 GATTACAGTC
*
241 CTATTCCATTACAGCT
1 CTATTCCATTACAACT
*
257 CTATTCCATTACAATT
1 CTATTCCATTACAACT
*
273 TTATTCCATTACAACT
1 CTATTCCATTACAACT
289 CTATTCCATTACAAC
1 CTATTCCATTACAAC
304 GAACCAAACG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.30, C:0.29, G:0.02, T:0.40
Consensus pattern (16 bp):
CTATTCCATTACAACT
Found at i:8989 original size:115 final size:114
Alignment explanation
Indices: 8829--9058 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 114
8819 AACTTCTTCT
8829 CTCTCAATCTATTCTGATTGTATATTTCCTTTATTTTCTGTGCTTTGCCTACCAAGACAAAAAAT
1 CTCTCAATCTATTCTGATTGTATATTTCCTTTATTTTCTGTGCTTTGCCTACCAAGACAAAAAAT
8894 GGTTGTATTTTTGAACCACCTACCATCATCTTAATCTCGTCATTAAAGC
66 GGTTGTATTTTTGAACCACCTACCATCATCTTAATCTCGTCATTAAAGC
8943 NCTCTCAATCTATTCTGATTGTATATTTCCTTTATTTTCTGTGCTTTGCCTACCAAGACAAAAAA
1 -CTCTCAATCTATTCTGATTGTATATTTCCTTTATTTTCTGTGCTTTGCCTACCAAGACAAAAAA
*
9008 TTGTTGTATTTTTGAACCACCTACCATCATCTTAATCTCGTCATTAAAGC
65 TGGTTGTATTTTTGAACCACCTACCATCATCTTAATCTCGTCATTAAAGC
9058 C
1 C
9059 GTCCTTAAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
114 1 0.01
115 113 0.99
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.40
Consensus pattern (114 bp):
CTCTCAATCTATTCTGATTGTATATTTCCTTTATTTTCTGTGCTTTGCCTACCAAGACAAAAAAT
GGTTGTATTTTTGAACCACCTACCATCATCTTAATCTCGTCATTAAAGC
Found at i:11942 original size:30 final size:28
Alignment explanation
Indices: 11908--12136 Score: 133
Period size: 29 Copynumber: 7.8 Consensus size: 28
11898 CTTCCGGGAG
*
11908 TAAAATGGTAATTTTTAAAAGTTTCGAGGT
1 TAAAAT-G-AATTTTTAGAAGTTTCGAGGT
* *
11938 TAAAAATGAAATTTTAGGAAGTTT-GGGAGT
1 T-AAAATGAATTTTTA-GAAGTTTCGAG-GT
* *
11968 AAAAACGTAATTTTTAGAAGTTTCGAGGT
1 TAAAATG-AATTTTTAGAAGTTTCGAGGT
* *
11997 TAAAAATGGAATTTTTGGAAG-TTCGGGGGT
1 T-AAAAT-GAATTTTTAGAAGTTTC-GAGGT
* * * *
12027 AAAAATATAATTTTTGGAAGTTTCAAGGT
1 TAAAAT-GAATTTTTAGAAGTTTCGAGGT
*
12056 AAAAAATTGAATTTTTAGAAGTTT-GAGGGT
1 -TAAAA-TGAATTTTTAGAAGTTTCGA-GGT
* * *
12086 AAAAATGTAATTTTCAAAAGTTTC-ATGGT
1 TAAAATG-AATTTTTAGAAGTTTCGA-GGT
* *
12115 CAAAATGGAATTTTTGGAAGTT
1 TAAAAT-GAATTTTTAGAAGTT
12137 CGGGGTCAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 31
0.73 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 85 0.54
30 64 0.41
31 7 0.04
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (28 bp):
TAAAATGAATTTTTAGAAGTTTCGAGGT
Found at i:11970 original size:29 final size:28
Alignment explanation
Indices: 11938--12178 Score: 123
Period size: 29 Copynumber: 8.2 Consensus size: 28
11928 GTTTCGAGGT
11938 TAAAAATGAAATTTTAGGAAGTTTGGGAG
1 TAAAAATGAAATTTTAGGAAGTTTGGG-G
* * *
11967 TAAAAACGTAATTTTTA-GAAGTTTCGAGGT
1 TAAAAATG-AAATTTTAGGAAGTTT-G-GGG
* * *
11997 TAAAAATGGAATTTTTGGAAGTTCGGGGG
1 TAAAAATGAAATTTTAGGAAGTT-TGGGG
* **
12026 TAAAAAT-ATAATTTTTGGAAGTTTCAAGG
1 TAAAAATGA-AATTTTAGGAAGTTT-GGGG
*
12055 TAAAAAATTGAATTTTTA-GAAGTTTGAGGG
1 T-AAAAA-TGAAATTTTAGGAAGTTTG-GGG
* * **
12085 TAAAAATGTAATTTTCA-AAAGTTTCATGG
1 TAAAAATGAAATTTT-AGGAAGTTT-GGGG
* * * *
12114 TCAAAATGGAATTTTTGGAAGTTCGGGG
1 TAAAAATGAAATTTTAGGAAGTTTGGGG
*
12142 TCAAAAAT-ATAATTTTGGAGAAGTTTGAGGG
1 T-AAAAATGA-AATTTTAG-GAAGTTTG-GGG
12173 CTAAAA
1 -TAAAA
12179 TATAATTTTT
Statistics
Matches: 160, Mismatches: 33, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
28 10 0.06
29 89 0.56
30 44 0.28
31 15 0.09
32 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (28 bp):
TAAAAATGAAATTTTAGGAAGTTTGGGG
Found at i:11983 original size:59 final size:59
Alignment explanation
Indices: 11903--12157 Score: 261
Period size: 59 Copynumber: 4.3 Consensus size: 59
11893 TTGGACTTCC
11903 GGGAGT-AAAATGGTAATTTTTAAAAGTTTCGAGGTTAAAAATGAAATTTTAGGAAGTTT
1 GGGAGTAAAAAT-GTAATTTTTAAAAGTTTCGAGGTTAAAAATGAAATTTTAGGAAGTTT
* * * * *
11962 GGGAGTAAAAACGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTC
1 GGGAGTAAAAATGTAATTTTTAAAAGTTTCGAGGTTAAAAATGAAATTTTAGGAAGTTT
* * ** * * *
12021 GGGGGTAAAAATATAATTTTTGGAAGTTTCAAGGTAAAAAATTGAATTTTTA-GAAGTTT
1 GGGAGTAAAAATGTAATTTTTAAAAGTTTCGAGGTTAAAAA-TGAAATTTTAGGAAGTTT
* * * * *
12080 GAGG-GTAAAAATGTAATTTTCAAAAGTTTC-ATGG-TCAAAATGGAATTTTTGGAAGTTC
1 G-GGAGTAAAAATGTAATTTTTAAAAGTTTCGA-GGTTAAAAATGAAATTTTAGGAAGTTT
*
12138 GGG-GTCAAAAATATAATTTT
1 GGGAGT-AAAAATGTAATTTT
12158 GGAGAAGTTT
Statistics
Matches: 164, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
57 11 0.07
58 25 0.15
59 115 0.70
60 13 0.08
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
GGGAGTAAAAATGTAATTTTTAAAAGTTTCGAGGTTAAAAATGAAATTTTAGGAAGTTT
Found at i:12107 original size:88 final size:87
Alignment explanation
Indices: 11909--12188 Score: 273
Period size: 88 Copynumber: 3.2 Consensus size: 87
11899 TTCCGGGAGT
* *
11909 AAAATGGTAATTTTTAAAAGTTTCGAGGTTAAAAATGAAATTTTAGGAAGTTT-GGGAGTAAAAA
1 AAAAT-GTAATTTTTAAAAGTTTCGAGGGTAAAAAT-AAATTTTTGGAAGTTTCGGG-GTAAAAA
** *
11973 CGTAATTTTTAGAAGTTTCGAGGTTA
63 ATTAATTTTTAGAAGTTT-GAGGGTA
* ** * **
11999 AAAATGGAATTTTTGGAAG-TTCGGGGGTAAAAATATAATTTTTGGAAGTTTCAAGGTAAAAAAT
1 AAAATGTAATTTTTAAAAGTTTCGAGGGTAAAAATA-AATTTTTGGAAGTTTCGGGGTAAAAAAT
12063 TGAATTTTTAGAAGTTTGAGGGTA
65 T-AATTTTTAGAAGTTTGAGGGTA
* * * * *
12087 AAAATGTAATTTTCAAAAGTTTC-ATGGTCAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAAT
1 AAAATGTAATTTTTAAAAGTTTCGAGGGTAAAAAT-AAATTTTTGGAAGTTTCGGGGTAAAAAAT
*
12150 ATAATTTTGGAGAAGTTTGAGGGCT-
65 -TAATTTT-TAGAAGTTTGAGGG-TA
*
12175 AAAATATAATTTTT
1 AAAATGTAATTTTT
12189 GGACTGTTTA
Statistics
Matches: 157, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
87 19 0.12
88 102 0.65
89 31 0.20
90 5 0.03
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (87 bp):
AAAATGTAATTTTTAAAAGTTTCGAGGGTAAAAATAAATTTTTGGAAGTTTCGGGGTAAAAAATT
AATTTTTAGAAGTTTGAGGGTA
Found at i:12189 original size:59 final size:56
Alignment explanation
Indices: 11916--12191 Score: 220
Period size: 59 Copynumber: 4.7 Consensus size: 56
11906 AGTAAAATGG
* * * * **
11916 TAATTTTTAAAAGTTTCGAGGTTAAAA-ATGAAATTTTAGGAAGTTTGGGAGTAAAAACG
1 TAATTTTGAGAAGTTTC-AGG-TAAAATATG-AATTTTTGGAAGTTCGGG-GTAAAAATA
*
11975 TAATTTTTAGAAGTTTCGAGGTTAAAA-ATGGAATTTTTGGAAGTTCGGGGGTAAAAATA
1 TAATTTTGAGAAGTTTC-AGG-TAAAATAT-GAATTTTTGGAAGTTC-GGGGTAAAAATA
* * * *
12034 TAATTTTTG-GAAGTTTCAAGGTAAAAAATTGAATTTTTAGAAGTTTGAGGGTAAAAATG
1 TAA-TTTTGAGAAGTTTC-AGGTAAAATA-TGAATTTTTGGAAGTTCG-GGGTAAAAATA
* * *
12093 TAATTTTCAAAAGTTTCATGGTCAAAAT-GGAATTTTTGGAAGTTCGGGGTCAAAAATA
1 TAATTTTGAGAAGTTTCA-GGT-AAAATATGAATTTTTGGAAGTTCGGGGT-AAAAATA
*
12151 TAATTTTGGAGAAGTTTGAGGGCTAAAATAT-AATTTTTGGA
1 TAATTTT-GAGAAGTTTCA-GG-TAAAATATGAATTTTTGGA
12192 CTGTTTAGGG
Statistics
Matches: 182, Mismatches: 22, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
57 4 0.02
58 39 0.21
59 125 0.69
60 14 0.08
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (56 bp):
TAATTTTGAGAAGTTTCAGGTAAAATATGAATTTTTGGAAGTTCGGGGTAAAAATA
Found at i:13252 original size:3 final size:3
Alignment explanation
Indices: 13244--13312 Score: 57
Period size: 3 Copynumber: 21.7 Consensus size: 3
13234 TAATTAAAAA
* * * *
13244 TAT TAT TAT TAT ATATT TAT TAT TAC TAT TAT TAT TAA AAA TAGT TAT
1 TAT TAT TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
13292 TAT TAC TAT TAAT TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TA
13313 ATAACAAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
3 44 0.81
4 9 0.17
5 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:13265 original size:26 final size:26
Alignment explanation
Indices: 13231--13280 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
13221 TTAATGATTT
13231 TATTAATTAAAAATATTATTATTATA
1 TATTAATTAAAAATATTATTATTATA
* ** *
13257 TATTTATTATTACTATTATTATTA
1 TATTAATTAAAAATATTATTATTA
13281 AAAATAGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTAATTAAAAATATTATTATTATA
Found at i:13307 original size:16 final size:15
Alignment explanation
Indices: 13245--13312 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 15
13235 AATTAAAAAT
13245 ATTATTATTATA-TA
1 ATTATTATTATATTA
*
13259 TTTATTATTACTATT-
1 ATTATTATTA-TATTA
* *
13274 ATTATTA--AAAATA
1 ATTATTATTATATTA
*
13287 GTTATTATTACTATTA
1 ATTATTATTA-TATTA
13303 ATTATTATTA
1 ATTATTATTA
13313 ATAACAAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 2 0.05
13 7 0.17
14 9 0.22
15 9 0.22
16 13 0.32
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
ATTATTATTATATTA
Found at i:13590 original size:14 final size:15
Alignment explanation
Indices: 13567--13595 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13557 AATTTGGACA
13567 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
13582 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
13596 ATAATAATTT
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:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:13625 original size:12 final size:11
Alignment explanation
Indices: 13608--13680 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
13598 AATAATTTTT
13608 TAAATTTGAAAA
1 TAAATTT-AAAA
*
13620 TAAATTTAAAT
1 TAAATTTAAAA
13631 TAAA-TT----
1 TAAATTTAAAA
13637 TAAATTTAAAA
1 TAAATTTAAAA
* *
13648 TTAATTTAAAT
1 TAAATTTAAAA
13659 TCAAATTTAAAA
1 T-AAATTTAAAA
*
13671 TAAATCTAAA
1 TAAATTTAAA
13681 TTTAAAAGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
10 2 0.04
11 25 0.51
12 16 0.33
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:13631 original size:6 final size:6
Alignment explanation
Indices: 13606--13686 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
13596 ATAATAATTT
* *
13606 TTTAAA TTTGAAA -ATAAA TTTAAA -TTAAA TTTAAA TTTAAA ATT-AA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
13652 TTTAAA TTCAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
13687 AGGGGTCCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
5 16 0.26
6 42 0.69
7 3 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:13633 original size:23 final size:22
Alignment explanation
Indices: 13607--13687 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
13597 TAATAATTTT
13607 TTAAATTTGAAAATAAATTTAAA
1 TTAAATTT-AAAATAAATTTAAA
* * *
13630 TTAAATTTAAATTTAAAATTAAT
1 TTAAATTTAAA-ATAAATTTAAA
* * *
13653 TTAAATTCAAATTTAAA-ATAAA
1 TTAAATTTAAA-ATAAATTTAAA
13675 TCTAAATTTAAAA
1 T-TAAATTTAAAA
13688 GGGGTCCGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 7 0.15
23 41 0.85
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (22 bp):
TTAAATTTAAAATAAATTTAAA
Found at i:13642 original size:17 final size:17
Alignment explanation
Indices: 13606--13687 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
13596 ATAATAATTT
13606 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
13624 TTTAAA-TTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* **
13641 TTTAAAATTAATTTAAA
1 TTTAAATTTAAAATAAA
*
13658 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
13675 TCTAAATTTAAAA
1 TTTAAATTTAAAA
13688 GGGGTCCGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 3 0.06
17 41 0.76
18 10 0.19
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14380 original size:206 final size:206
Alignment explanation
Indices: 14016--14394 Score: 535
Period size: 206 Copynumber: 1.8 Consensus size: 206
14006 TTCTTCTCTT
** * * *
14016 ATCAGGAAGACGACCGCATCACTTGTTTTGACCCACTTCTCTGTGTTTCATCAGGAAGACGGATT
1 ATCAGGAAGACGACCGCATCACTTGTTTCAACCCACTTCTCTGTATCTCATCAGGAAGACGAATT
* * *
14081 TGGTTCAATTCTCCGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTACTTCTCAGTA
66 TGATCCAATTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTACTTCTCAGTA
* * * * * *
14146 TCTCATCAGAAAGTTGGGGTTTGAAGATTTGCTCACATTGAGCATGAGTTTGATTTGGTCTTCTT
131 TCCCATCAGAAAGCTAGGATTCGAAGATTTGCTCACATCGAGCATGAGTTTGATTTGGTCTTCTT
14211 CTCAGTATCTC
196 CTCAGTATCTC
* * * * *
14222 ATCAGGAAGATGACCGTATCGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATT
1 ATCAGGAAGACGACCGCATCACTTGTTTCAACCCACTTCTCTGTATCTCATCAGGAAGACGAATT
* * * *
14287 TGATCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTTGACCTGCTTCTCAGTA
66 TGATCCAATTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTACTTCTCAGTA
14352 TCCCATCA-AGAAGCTAGGATTCGAAGATTTGCTCACATCGAGC
131 TCCCATCAGA-AAGCTAGGATTCGAAGATTTGCTCACATCGAGC
14395 CCTGAATTGG
Statistics
Matches: 149, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
205 1 0.01
206 148 0.99
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (206 bp):
ATCAGGAAGACGACCGCATCACTTGTTTCAACCCACTTCTCTGTATCTCATCAGGAAGACGAATT
TGATCCAATTCTCAGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTACTTCTCAGTA
TCCCATCAGAAAGCTAGGATTCGAAGATTTGCTCACATCGAGCATGAGTTTGATTTGGTCTTCTT
CTCAGTATCTC
Found at i:17322 original size:43 final size:43
Alignment explanation
Indices: 17264--17349 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
17254 TGATCCCTCG
17264 ATCTATGACTACTTGAATCCCTATAATGTACGCTTCGTATTCT
1 ATCTATGACTACTTGAATCCCTATAATGTACGCTTCGTATTCT
17307 ATCTATGACTACTTGAATCCCTATAATGTACGCTTCGTATTCT
1 ATCTATGACTACTTGAATCCCTATAATGTACGCTTCGTATTCT
17350 GTCATATTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (43 bp):
ATCTATGACTACTTGAATCCCTATAATGTACGCTTCGTATTCT
Found at i:17330 original size:22 final size:22
Alignment explanation
Indices: 17264--17330 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
17254 TGATCCCTCG
17264 ATCTATGACTACTTGAATCCCT
1 ATCTATGACTACTTGAATCCCT
* * * *
17286 AT-AATGTAC-GCTTCGTAT-TCT
1 ATCTATG-ACTACTT-GAATCCCT
17307 ATCTATGACTACTTGAATCCCT
1 ATCTATGACTACTTGAATCCCT
17329 AT
1 AT
17331 AATGTACGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (22 bp):
ATCTATGACTACTTGAATCCCT
Found at i:17699 original size:48 final size:48
Alignment explanation
Indices: 17628--17721 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
17618 TTTGGCTTAT
17628 GTAGACTATGTCGAATTCTGACAGTAAGATTTGCCATCTAGCCATTAC
1 GTAGACTATGTCGAATTCTGACAGTAAGATTTGCCATCTAGCCATTAC
17676 GTAGACTATGTCGAATTCTGACAGTAAGATTTGCCATCTAGCCATT
1 GTAGACTATGTCGAATTCTGACAGTAAGATTTGCCATCTAGCCATT
17722 CTTCCGTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (48 bp):
GTAGACTATGTCGAATTCTGACAGTAAGATTTGCCATCTAGCCATTAC
Found at i:22487 original size:21 final size:21
Alignment explanation
Indices: 22449--22489 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22439 TCGCATCGAT
*
22449 TTTTTCCTCTAATCGTCTATA
1 TTTTTCCTCCAATCGTCTATA
* *
22470 TTTTTCCTCCATTTGTCTAT
1 TTTTTCCTCCAATCGTCTAT
22490 GGAAATCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTCCTCCAATCGTCTATA
Found at i:26529 original size:28 final size:27
Alignment explanation
Indices: 26430--26531 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 27
26420 ATACCAGAGA
* *
26430 GTAAAATGGTAATTTTAGACTCTTGAGGG
1 GTAAAATGATAATTTTAGAC-ATTGA-GG
* * * *
26459 GTAAATTGGTAATTTTAGGAAATTTAGG
1 GTAAAATGATAATTTTA-GACATTGAGG
26487 GTTAAAAATGA-AATTTTAGACATTCGAGG
1 G-T-AAAATGATAATTTTAGACATT-GAGG
26516 GTAAAATGATAATTTT
1 GTAAAATGATAATTTT
26532 TAAAAGTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 7 0.12
28 15 0.25
29 31 0.52
30 7 0.12
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (27 bp):
GTAAAATGATAATTTTAGACATTGAGG
Found at i:26533 original size:58 final size:58
Alignment explanation
Indices: 26440--26679 Score: 190
Period size: 58 Copynumber: 4.1 Consensus size: 58
26430 GTAAAATGGT
* * *
26440 AATTTTAGAC-TCTTGAGGGGTAAATTGGTAA-TTTTAGGAAA-TTTAGGGTTAAAAATGA
1 AATTTTAGACAT-TCGA-GGGTAAAATGATAATTTTTA-GAAAGTTTAGGGTTAAAAATGA
*
26498 AATTTTAGACATTCGAGGGTAAAATGATAATTTTTA-AAAGTTTTAGGGTCAAAAATGA
1 AATTTTAGACATTCGAGGGTAAAATGATAATTTTTAGAAAG-TTTAGGGTTAAAAATGA
* * * * *
26556 AATTTTTTGGATATTCGAGGGTAAAATCATAATTTTT-GAAAGTTTCAAGGTTAAAAATGG
1 AA--TTTTAGACATTCGAGGGTAAAATGATAATTTTTAGAAAGTTT-AGGGTTAAAAATGA
* ** * * * *
26616 AATTTTGGGA-AGTTTAAGGGTAAAAATG-TAATTTTT-GAAAGTTTCGGGATCAAAATGG
1 AATTTT-AGACA-TTCGAGGGT-AAAATGATAATTTTTAGAAAGTTTAGGGTTAAAAATGA
26674 AATTTT
1 AATTTT
26680 GGGACGTTTT
Statistics
Matches: 154, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
56 3 0.02
57 12 0.08
58 57 0.37
59 30 0.19
60 52 0.34
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (58 bp):
AATTTTAGACATTCGAGGGTAAAATGATAATTTTTAGAAAGTTTAGGGTTAAAAATGA
Found at i:26562 original size:30 final size:29
Alignment explanation
Indices: 26481--27007 Score: 195
Period size: 29 Copynumber: 18.0 Consensus size: 29
26471 TTTTAGGAAA
* *
26481 TTTAGGGTTAAAAATGAAATTTTAGACA-T
1 TTTAGGG-TAAAAATGAAATTTTTGAAAGT
** *
26510 TCGAGGGT-AAAATGATAATTTTTAAAAGT
1 TTTAGGGTAAAAATGA-AATTTTTGAAAGT
*
26539 TTTAGGGTCAAAAATGAAATTTTTTGGATA-T
1 TTTAGGGT-AAAAATGAAA-TTTTT-GAAAGT
** *
26570 TCGAGGGT-AAAATCATAATTTTTGAAAGT
1 TTTAGGGTAAAAATGA-AATTTTTGAAAGT
* * * * *
26599 TTCAAGGTTAAAAATGGAATTTTGGGAAGT
1 TT-TAGGGTAAAAATGAAATTTTTGAAAGT
* *
26629 TTAAGGGTAAAAATGTAATTTTTGAAAG-
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
* * * * * *
26657 TTTCGGGATCAAAATGGAATTTTGGGACGT
1 TTTAGGG-TAAAAATGAAATTTTTGAAAGT
26687 TTT-GGGTCAAAAAT-AGAATTTTT-AGAAGT
1 TTTAGGGT-AAAAATGA-AATTTTTGA-AAGT
** * *
26716 TCGAGGGTAAAAATGTAA-TTTTGGAAGT
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
** * *
26744 TTCGGGGTTAAAAATGGAA-TTTTGGAAGT
1 TTTAGGG-TAAAAATGAAATTTTTGAAAGT
** * ** *
26773 TCAAGGGTAAAATTTTAATTTTTGGAAG-
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
* *
26801 TTTCGAGGTAAAAAATGGAATTTTT-AGAAGT
1 TTTAG-GGT-AAAAATGAAATTTTTGA-AAGT
** * *
26832 TCGAGGGTAAAAATGTAA-TTTTGGAAGT
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
** * *
26860 TTCGGGGTTAAAAATGGAA-TTTTGGAAGT
1 TTTAGGG-TAAAAATGAAATTTTTGAAAGT
** * ** *
26889 TCAAGGGTAAAATTTTAATTTTTGGAAG-
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
* * *
26917 TTTCGAGGTAAAAAAATGGAATTTTTGGAAGT
1 TTTAG-GGT--AAAAATGAAATTTTTGAAAGT
** * *
26949 TCGA-GGTAAAAATGTAATTTTCGAAAGT
1 TTTAGGGTAAAAATGAAATTTTTGAAAGT
* * * *
26977 TTCGAGGTTAAAAATGGAATTTTTGGAAGT
1 TT-TAGGGTAAAAATGAAATTTTTGAAAGT
27007 T
1 T
27008 CGAGGTCAAA
Statistics
Matches: 376, Mismatches: 89, Indels: 65
0.71 0.17 0.12
Matches are distributed among these distances:
27 7 0.02
28 81 0.22
29 172 0.46
30 70 0.19
31 43 0.11
32 3 0.01
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
TTTAGGGTAAAAATGAAATTTTTGAAAGT
Found at i:26591 original size:60 final size:60
Alignment explanation
Indices: 26481--26621 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 60
26471 TTTTAGGAAA
*
26481 TTTAGGGTTAAAAATGAAA--TTTTAGACATTCGAGGGTAAAATGATAATTTTTAAAAGT
1 TTTAGGGTTAAAAATGAAATTTTTTAGACATTCGAGGGTAAAATCATAATTTTTAAAAGT
* * * *
26539 TTTAGGGTCAAAAATGAAATTTTTTGGATATTCGAGGGTAAAATCATAATTTTTGAAAGT
1 TTTAGGGTTAAAAATGAAATTTTTTAGACATTCGAGGGTAAAATCATAATTTTTAAAAGT
* * *
26599 TTCAAGGTTAAAAATGGAATTTT
1 TTTAGGGTTAAAAATGAAATTTT
26622 GGGAAGTTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 18 0.25
60 54 0.75
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (60 bp):
TTTAGGGTTAAAAATGAAATTTTTTAGACATTCGAGGGTAAAATCATAATTTTTAAAAGT
Found at i:26621 original size:29 final size:29
Alignment explanation
Indices: 26589--27031 Score: 384
Period size: 29 Copynumber: 15.2 Consensus size: 29
26579 AAATCATAAT
* *
26589 TTTTGAAAGTTTCAAGGTTAAAAATGGAA
1 TTTTGGAAGTTTCGAGGTTAAAAATGGAA
* * *
26618 TTTTGGGAAGTTT-AAGGGTAAAAATGTAA
1 TTTT-GGAAGTTTCGAGGTTAAAAATGGAA
* * *
26647 TTTTTGAAAGTTTCG-GGATCAAAATGGAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
* * * *
26676 TTTTGGGACGTTTTG-GGTCAAAAATAGAA
1 TTTT-GGAAGTTTCGAGGTTAAAAATGGAA
* * *
26705 TTTTTAGAAG-TTCGAGGGTAAAAATGTAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
*
26734 TTTTGGAAGTTTCGGGGTTAAAAATGGAA
1 TTTTGGAAGTTTCGAGGTTAAAAATGGAA
* * * **
26763 TTTTGGAAG-TTCAAGGGTAAAATTTTAA
1 TTTTGGAAGTTTCGAGGTTAAAAATGGAA
*
26791 TTTTTGGAAGTTTCGAGGTAAAAAATGGAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
* * *
26821 TTTTTAGAAG-TTCGAGGGTAAAAATGTAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
*
26850 TTTTGGAAGTTTCGGGGTTAAAAATGGAA
1 TTTTGGAAGTTTCGAGGTTAAAAATGGAA
* * * **
26879 TTTTGGAAG-TTCAAGGGTAAAATTTTAA
1 TTTTGGAAGTTTCGAGGTTAAAAATGGAA
*
26907 TTTTTGGAAGTTTCGAGGTAAAAAAATGGAA
1 -TTTTGGAAGTTTCGAGGT-TAAAAATGGAA
*
26938 TTTTTGGAAG-TTCGAGG-TAAAAATGTAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
*
26966 TTTTCGAAAGTTTCGAGGTTAAAAATGGAA
1 TTTT-GGAAGTTTCGAGGTTAAAAATGGAA
* **
26996 TTTTTGGAAG-TTCGAGGTCAAAAATATAA
1 -TTTTGGAAGTTTCGAGGTTAAAAATGGAA
27025 TTTTGGA
1 TTTTGGA
27032 GAAGTTTGGG
Statistics
Matches: 331, Mismatches: 66, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.01
28 69 0.21
29 173 0.52
30 64 0.19
31 21 0.06
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTCGAGGTTAAAAATGGAA
Found at i:26759 original size:116 final size:116
Alignment explanation
Indices: 26607--27038 Score: 529
Period size: 116 Copynumber: 3.7 Consensus size: 116
26597 GTTTCAAGGT
* * ** * *
26607 TAAAAATGGAATTTTGGGAAGTTTAAGGG-TAAAAATGTAATTTTTGAAAGTTTC-GGGATCAAA
1 TAAAAATGTAATTTTCGGAAGTTTCGGGGTTAAAAATGGAA-TTTTGGAAG-TTCAGGG-T-AAA
** * * *
26670 A-TGGAATTTTGGGACGTTTTG-GGTCAAAAATAGAATTTTTAGAAGTTCGAGGG
62 ATTTTAATTTTGGGAAGTTTCGAGGTAAAAAATAGAATTTTTAGAAGTTCGAGGG
26723 TAAAAATGTAATTTT-GGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTCAAGGGTAAAATT
1 TAAAAATGTAATTTTCGGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTC-AGGGTAAAATT
* *
26787 TTAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTAGAAGTTCGAGGG
65 TTAATTTTGGGAAGTTTCGAGGTAAAAAATAGAATTTTTAGAAGTTCGAGGG
26839 TAAAAATGTAATTTT-GGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTCAAGGGTAAAATT
1 TAAAAATGTAATTTTCGGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTC-AGGGTAAAATT
* * *
26903 TTAATTTTTGGAAGTTTCGAGGTAAAAAAATGGAATTTTTGGAAGTTCGA-GG
65 TTAATTTTGGGAAGTTTCGAGGT-AAAAAATAGAATTTTTAGAAGTTCGAGGG
* *
26955 TAAAAATGTAATTTTCGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTC-GAGGTCAAAA
1 TAAAAATGTAATTTTCGGAAGTTTCGGGGTTAAAAATGGAA-TTTTGGAAGTTCAG-GGT-AAAA
* *
27019 ATATAATTTTGGAGAAGTTT
63 TTTTAATTTTGG-GAAGTTT
27039 GGGGGCAAAA
Statistics
Matches: 287, Mismatches: 18, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
114 7 0.02
115 35 0.12
116 162 0.56
117 51 0.18
118 25 0.09
119 7 0.02
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (116 bp):
TAAAAATGTAATTTTCGGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTCAGGGTAAAATTT
TAATTTTGGGAAGTTTCGAGGTAAAAAATAGAATTTTTAGAAGTTCGAGGG
Found at i:28114 original size:16 final size:15
Alignment explanation
Indices: 28050--28151 Score: 86
Period size: 16 Copynumber: 6.9 Consensus size: 15
28040 TTCTCTTTTT
* *
28050 TTATTATTAATGATT
1 TTATTATTAATAATA
*
28065 TTATTAATTAAAAATA
1 TTATT-ATTAATAATA
*
28081 TTATTATT-ATTATA
1 TTATTATTAATAATA
28095 -TA-T-TTAATAATA
1 TTATTATTAATAATA
*
28107 TTATTATTAAAAATA
1 TTATTATTAATAATA
* *
28122 GTTATTATTACTATTAA
1 -TTATTATTAATAAT-A
28139 TTATTATTAATAA
1 TTATTATTAATAA
28152 CAAAGTGTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
11 2 0.03
12 6 0.09
13 4 0.06
14 5 0.07
15 16 0.24
16 34 0.50
17 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (15 bp):
TTATTATTAATAATA
Found at i:28889 original size:14 final size:15
Alignment explanation
Indices: 28866--28894 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28856 AAATTGGACA
28866 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
28881 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
28895 ATAATAATTT
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:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:28941 original size:17 final size:17
Alignment explanation
Indices: 28905--28986 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 17
28895 ATAATAATTT
*
28905 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATTAA
28923 TTTAAATTTAAAATTAA
1 TTTAAATTTAAAATTAA
* *
28940 TTTAAATTCAAATTTAA
1 TTTAAATTTAAAATTAA
** * *
28957 AATAAATCTAAATTTAA
1 TTTAAATTTAAAATTAA
**
28974 AATAAATTTAAAA
1 TTTAAATTTAAAA
28987 GTGGCCCGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
17 46 0.84
18 9 0.16
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:28947 original size:23 final size:23
Alignment explanation
Indices: 28919--28974 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
28909 AATTTGAAAA
* *
28919 TAAATTTAAATTTAAAATTAATT
1 TAAATTTAAATTTAAAATAAATC
*
28942 TAAATTCAAATTTAAAATAAATC
1 TAAATTTAAATTTAAAATAAATC
28965 TAAATTTAAA
1 TAAATTTAAA
28975 ATAAATTTAA
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:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATC
Found at i:28960 original size:40 final size:41
Alignment explanation
Indices: 28908--28985 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
28898 ATAATTTTTT
* *
28908 AAATTTGAAAATAAATTTAAATTTAAAATTAATTTAAATTC
1 AAATTTGAAAATAAATCTAAATTTAAAATAAATTTAAATTC
28949 AAATTT-AAAATAAATCTAAATTTAAAATAAATTTAAA
1 AAATTTGAAAATAAATCTAAATTTAAAATAAATTTAAA
28986 AGTGGCCCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (41 bp):
AAATTTGAAAATAAATCTAAATTTAAAATAAATTTAAATTC
Found at i:28976 original size:7 final size:6
Alignment explanation
Indices: 28905--28985 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
28895 ATAATAATTT
* * *
28905 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA ATT-AA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
28952 TTTAAA -ATAAA TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
28986 AGTGGCCCGG
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
5 15 0.25
6 41 0.69
7 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:28979 original size:11 final size:11
Alignment explanation
Indices: 28925--28986 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
28915 AAAATAAATT
28925 TAAATTTAAAA
1 TAAATTTAAAA
* *
28936 TTAATTTAAAT
1 TAAATTTAAAA
28947 TCAAATTTAAAA
1 T-AAATTTAAAA
*
28959 TAAA--T---C
1 TAAATTTAAAA
28965 TAAATTTAAAA
1 TAAATTTAAAA
28976 TAAATTTAAAA
1 TAAATTTAAAA
28987 GTGGCCCGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
6 4 0.10
8 1 0.03
9 1 0.03
11 24 0.62
12 9 0.23
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:30597 original size:16 final size:16
Alignment explanation
Indices: 30576--30613 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30566 AAAAAATCAT
30576 TAAAAAT-TCATAAAAA
1 TAAAAATATCA-AAAAA
*
30592 TAAAAATATTAAAAAA
1 TAAAAATATCAAAAAA
30608 TAAAAA
1 TAAAAA
30614 ATTGGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAATATCAAAAAA
Found at i:31726 original size:18 final size:18
Alignment explanation
Indices: 31695--31729 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31685 TCTGCCTCTT
**
31695 TTAATTTATTTTTTAAAA
1 TTAATTTAGCTTTTAAAA
31713 TTAATTTAGCTTTTAAA
1 TTAATTTAGCTTTTAAA
31730 TGAAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTAATTTAGCTTTTAAAA
Found at i:32028 original size:53 final size:55
Alignment explanation
Indices: 31970--32077 Score: 123
Period size: 56 Copynumber: 2.0 Consensus size: 55
31960 CCACCAAATA
* *
31970 TTGATGACGACTATTTAATTG-TCA-A-CAAAAAAAATAATTTTTTACTTAAAAAG
1 TTGATGACAACTA-TTAAATGATCAGACCAAAAAAAATAATTTTTTACTTAAAAAG
** * *
32023 TTGATGTTAACTATTAAATGATCAGTACCTAAAAAAATAATTTTTTATTTAAAAA
1 TTGATGACAACTATTAAATGATCAG-ACCAAAAAAAATAATTTTTTACTTAAAAA
32078 ATTGGTGCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
52 6 0.13
53 13 0.29
55 1 0.02
56 25 0.56
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (55 bp):
TTGATGACAACTATTAAATGATCAGACCAAAAAAAATAATTTTTTACTTAAAAAG
Found at i:36537 original size:16 final size:16
Alignment explanation
Indices: 36513--36547 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36503 TAATATTAAA
36513 ATACATAGAATTTGAG
1 ATACATAGAATTTGAG
* *
36529 ATACGTAGAATTTGTG
1 ATACATAGAATTTGAG
36545 ATA
1 ATA
36548 TTATGTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (16 bp):
ATACATAGAATTTGAG
Found at i:37199 original size:18 final size:18
Alignment explanation
Indices: 37176--37210 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37166 ATTTTTTTAT
* *
37176 ATATTATTTGTAATATTA
1 ATATTATATATAATATTA
37194 ATATTATATATAATATT
1 ATATTATATATAATATT
37211 CTACTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATATTATATATAATATTA
Found at i:47024 original size:43 final size:43
Alignment explanation
Indices: 46960--47068 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
46950 GTGGGAAAAT
* *
46960 GCCACTATAGAACATGATCTTTAGCAGCGCTTTTCCCACAAAC
1 GCCACTATAGAACATGGTCTTTAGCAGCGCTTTCCCCACAAAC
* *
47003 GCCACTATAGAACATGGTCTTTAGCGGTGCTTTCCCCACAAAC
1 GCCACTATAGAACATGGTCTTTAGCAGCGCTTTCCCCACAAAC
** * *
47046 GCTTCTATACAACATGGTTTTTA
1 GCCACTATAGAACATGGTCTTTA
47069 AAGGTGCTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (43 bp):
GCCACTATAGAACATGGTCTTTAGCAGCGCTTTCCCCACAAAC
Found at i:47075 original size:43 final size:43
Alignment explanation
Indices: 46960--47089 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 43
46950 GTGGGAAAAT
* * * *
46960 GCCACTATAGAACATGATCTTTAGCA-GCGCTTTTCCCACAAAC
1 GCCACTATACAACATGGTCTTTA-AAGGTGCTTTTCCCACAAAC
* ** *
47003 GCCACTATAGAACATGGTCTTTAGCGGTGCTTTCCCCACAAAC
1 GCCACTATACAACATGGTCTTTAAAGGTGCTTTTCCCACAAAC
** * *
47046 GCTTCTATACAACATGGTTTTTAAAGGTGCTTTTGCCACAAAC
1 GCCACTATACAACATGGTCTTTAAAGGTGCTTTTCCCACAAAC
47089 G
1 G
47090 TAGCTATAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
GCCACTATACAACATGGTCTTTAAAGGTGCTTTTCCCACAAAC
Found at i:52255 original size:42 final size:41
Alignment explanation
Indices: 52207--52360 Score: 127
Period size: 42 Copynumber: 3.7 Consensus size: 41
52197 GTGTTTTTAT
52207 CATAAACGCCGCTAATGCTCTTTACTTTTTGCGGCGTTTTCC
1 CATAAACGCCGCTAATGCTCTTTAC-TTTTGCGGCGTTTTCC
* * *
52249 CATAAACGCTGCT-ATAGCTTTTTGCCTTTTGCGGCG-TTTCTC
1 CATAAACGCCGCTAAT-GCTCTTT-ACTTTTGCGGCGTTTTC-C
* * * * *
52291 CAAAAACGCCGTTATTG--CTTTAGCTTTTGTGGAGTTTTCC
1 CATAAACGCCGCTAATGCTCTTTA-CTTTTGCGGCGTTTTCC
* * * *
52331 CATAAACACCGCTATTTCTCTTTACCTTTG
1 CATAAACGCCGCTAATGCTCTTTACTTTTG
52361 GCAGCAAAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
40 26 0.30
41 15 0.17
42 45 0.51
43 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (41 bp):
CATAAACGCCGCTAATGCTCTTTACTTTTGCGGCGTTTTCC
Found at i:55714 original size:51 final size:52
Alignment explanation
Indices: 55613--55953 Score: 343
Period size: 52 Copynumber: 6.6 Consensus size: 52
55603 TAAATGCAAA
* * * *
55613 AAGGTCTGATGACTATGTTTCATCGTGAGTATATGAATCCTTTACAGATTAT
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
55665 AAGGTTCGATGGCTGCATGTCATCGTGAGT-TATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
55716 GAGGTCCGATGACAACGTGTCATCGCGAGTATATGAATCTTTTACGGATTAT
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
55768 GAGGTCCGATGACTACGTGTCATCGCGAGTATATGAAT-CTTTACGGATTA-
1 AAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
** * * **
55818 AGAGGTCTAATGACTGCGTGTCATCATGAGTATATGAATCCTTTATAGATTA-
1 A-AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * * *
55870 ATAGGTCTGATGACTACGTATCATCGTGATTATATGAGTCC-TTATGGATTA-
1 A-AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * ** *
55921 AGAAGTCCGTTGACTATATGTCATCGTTAGTAT
1 A-AGGTCCGATGACTACGTGTCATCGTGAGTAT
55954 TAAAAGAAAA
Statistics
Matches: 243, Mismatches: 43, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
51 119 0.49
52 124 0.51
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:55810 original size:103 final size:102
Alignment explanation
Indices: 55614--55953 Score: 376
Period size: 103 Copynumber: 3.3 Consensus size: 102
55604 AAATGCAAAA
* * * * *
55614 AGGTCTGATGACTATGTTTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTTCGATGGCT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTAT-AGGTCCGATGACT
* * *
55679 GCATGTCATCGTGAGT-TATGAATCCTTTACGGATTATG
65 ACGTGTCATCGTGAGTATATGAAT-CTTTACGGATTAAG
* * * *
55717 AGGTCCGATGACAACGTGTCATCGCGAGTATATGAATCTTTTACGGATTATGAGGTCCGATGACT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTAT-AGGTCCGATGACT
*
55782 ACGTGTCATCGCGAGTATATGAATCTTTACGGATTAAG
65 ACGTGTCATCGTGAGTATATGAATCTTTACGGATTAAG
** * * * *
55820 AGGTCTAATGACTGCGTGTCATCATGAGTATATGAATCCTTTATAGATTAATAGGTCTGATGACT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATT-ATAGGTCCGATGACT
* * * * *
55885 ACGTATCATCGTGATTATATGAGTCCTTATGGATTAAG
65 ACGTGTCATCGTGAGTATATGAATCTTTACGGATTAAG
* * ** *
55923 AAGTCCGTTGACTATATGTCATCGTTAGTAT
1 AGGTCCGATGACTACGTGTCATCGTGAGTAT
55954 TAAAAGAAAA
Statistics
Matches: 196, Mismatches: 39, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
103 187 0.95
104 9 0.05
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (102 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAGGTCCGATGACTA
CGTGTCATCGTGAGTATATGAATCTTTACGGATTAAG
Found at i:62269 original size:21 final size:22
Alignment explanation
Indices: 62240--62281 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
62230 ATCAGTATTT
62240 TCATGACTTGTATCGGTAGAAA
1 TCATGACTTGTATCGGTAGAAA
62262 TCAT-ACTTGTATCGGTAGAA
1 TCATGACTTGTATCGGTAGAA
62282 CTAGTAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (22 bp):
TCATGACTTGTATCGGTAGAAA
Found at i:65227 original size:17 final size:17
Alignment explanation
Indices: 65205--65244 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
65195 AGCAAAATTT
65205 CAGCTTCCTGGGATTGG
1 CAGCTTCCTGGGATTGG
65222 CAGCTTCCTGGGATTGG
1 CAGCTTCCTGGGATTGG
*
65239 TAGCTT
1 CAGCTT
65245 GTTTTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.23, G:0.33, T:0.33
Consensus pattern (17 bp):
CAGCTTCCTGGGATTGG
Found at i:69378 original size:21 final size:22
Alignment explanation
Indices: 69354--69402 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
69344 CTTGCTTCAC
**
69354 TAGAAGTTA-CACTTGTATCGG
1 TAGAAGTTATCACAAGTATCGG
*
69375 TAGAA-CTATCACAAGTATCGG
1 TAGAAGTTATCACAAGTATCGG
69396 TAGAAGT
1 TAGAAGT
69403 CTGCACTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (22 bp):
TAGAAGTTATCACAAGTATCGG
Found at i:72605 original size:24 final size:24
Alignment explanation
Indices: 72545--72637 Score: 123
Period size: 24 Copynumber: 3.8 Consensus size: 24
72535 TTCCAGAAAT
* *
72545 TTAGCTCATACGAGCCCAGACAGAA
1 TTAGCTCATACGAGCCCAGATAG-G
*
72570 TTAGCTCATACGAGCCTAGATAGG
1 TTAGCTCATACGAGCCCAGATAGG
*
72594 TTAGCTCTTACGAGCCCAGATAGG
1 TTAGCTCATACGAGCCCAGATAGG
* *
72618 TTAGCTCTTACAAGCCCAGA
1 TTAGCTCATACGAGCCCAGA
72638 CAGAGTTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
24 41 0.66
25 21 0.34
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAGATAGG
Found at i:77316 original size:24 final size:24
Alignment explanation
Indices: 77252--77340 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
77242 TTCCAGAAAT
* *
77252 TTAGCTCATACGAGCCCAAACAGAA
1 TTAGCTCATACGAGCCCAAATAG-G
77277 TTAGCTCATACGAGCCCAAATAGG
1 TTAGCTCATACGAGCCCAAATAGG
* * * *
77301 TTAGCTCTTACAAGCCTAGATAGG
1 TTAGCTCATACGAGCCCAAATAGG
*
77325 TTAGCTCTTACGAGCC
1 TTAGCTCATACGAGCC
77341 TAGACAGAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
24 35 0.61
25 22 0.39
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAAATAGG
Found at i:80641 original size:9 final size:9
Alignment explanation
Indices: 80627--80668 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
80617 AAAACTTTTT
80627 AAAATTAAA
1 AAAATTAAA
80636 AAAATTAAA
1 AAAATTAAA
* *
80645 TAAATTATA
1 AAAATTAAA
80654 AAAATTCAAA
1 AAAATT-AAA
80664 AAAAT
1 AAAAT
80669 GTGTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATTAAA
Found at i:81311 original size:7 final size:7
Alignment explanation
Indices: 81299--81323 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
81289 ATACAGGGAC
81299 TAAATTT
1 TAAATTT
81306 TAAATTT
1 TAAATTT
81313 TAAATTT
1 TAAATTT
81320 TAAA
1 TAAA
81324 ATAGTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:81916 original size:20 final size:20
Alignment explanation
Indices: 81891--81929 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
81881 ACTATGGAAG
81891 GTGAGATGGAATTTTGCTTA
1 GTGAGATGGAATTTTGCTTA
81911 GTGAGATGGAATTTTGCTT
1 GTGAGATGGAATTTTGCTT
81930 CTTGCTATAC
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:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (20 bp):
GTGAGATGGAATTTTGCTTA
Found at i:85100 original size:16 final size:15
Alignment explanation
Indices: 85063--85101 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
85053 CGGTTAAATT
*
85063 ATTAAAATATTAATC
1 ATTAAAAAATTAATC
85078 ATATAAAAAATTAATC
1 AT-TAAAAAATTAATC
85094 ACTTAAAA
1 A-TTAAAA
85102 TTTACACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAAAAATTAATC
Found at i:85669 original size:8 final size:9
Alignment explanation
Indices: 85654--85684 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
85644 ATTCTAAATC
85654 TAAAAAAAA
1 TAAAAAAAA
85663 TAAAAAAAA
1 TAAAAAAAA
85672 TAAAAAAACA
1 TAAAAAAA-A
85682 TAA
1 TAA
85685 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:85884 original size:10 final size:11
Alignment explanation
Indices: 85858--85883 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
85848 ATGATTTCTG
85858 TTTTTCTTTTT
1 TTTTTCTTTTT
85869 TTTTTCTTTTT
1 TTTTTCTTTTT
85880 TTTT
1 TTTT
85884 CAATGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:86273 original size:20 final size:20
Alignment explanation
Indices: 86236--86272 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
86226 CTTTTATTTT
86236 ATTTAATATTAATATTTTAA
1 ATTTAATATTAATATTTTAA
*
86256 ATTTATTATT-ATATTTT
1 ATTTAATATTAATATTTT
86273 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATATTAATATTTTAA
Found at i:92739 original size:30 final size:32
Alignment explanation
Indices: 92705--92774 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 32
92695 AAATTTTAAT
92705 TCAGTCACTCAAC-TT-TCAAAAAATAACAAA
1 TCAGTCACTCAACGTTATCAAAAAATAACAAA
92735 TCAGT--CT-AACGTTATCAAAAAATAACAAA
1 TCAGTCACTCAACGTTATCAAAAAATAACAAA
*
92764 TTAGTCACTCA
1 TCAGTCACTCA
92775 TTCACATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
29 19 0.56
30 5 0.15
31 2 0.06
32 1 0.03
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (32 bp):
TCAGTCACTCAACGTTATCAAAAAATAACAAA
Found at i:92840 original size:172 final size:173
Alignment explanation
Indices: 92528--92853 Score: 420
Period size: 172 Copynumber: 1.9 Consensus size: 173
92518 ATCTGGTTTC
* * * ** * *
92528 AATTTAGTCACTCAACTTTCGAAAAATAATAAAACAATCACTAACGTTATTGAAAAGTGACAAAT
1 AATTCAGTCACTCAACTTTCAAAAAATAACAAAACAAT-ACTAACGTTATCAAAAAATAACAAAT
* * * *
92593 CAGTCAATCATTAACATTTTCTGTTATAGGCCTAACGAGACAAGTGACATGACCAGTTAACTAGC
65 CAGTCAATCATTAACATTTTCCGTTATAGCCCTAACGAGACAAGTGACATGACCAGTAAACTAAC
*
92658 TAACGTGGCCAGTCAACTTGCCACATTGGATAAATCAAAATTTT
130 TAACGTGGCCAGTCAACATGCCACATTGGATAAATCAAAATTTT
* * *
92702 AATTCAGTCACTCAACTTTCAAAAAATAACAAATCAGT-CTAACGTTATCAAAAAATAACAAATT
1 AATTCAGTCACTCAACTTTCAAAAAATAACAAAACAATACTAACGTTATCAAAAAATAACAAATC
* * * * * * *
92766 AGTCACTCATTCACATTTTCCGTTATAGCCCTAACGAGATAGGTGACGTGACTAGTAAATTAACT
66 AGTCAATCATTAACATTTTCCGTTATAGCCCTAACGAGACAAGTGACATGACCAGTAAACTAACT
* *
92831 AATGTGGCCAGTTAACATGCCAC
131 AACGTGGCCAGTCAACATGCCAC
92854 GTTAGACGAT
Statistics
Matches: 128, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
172 95 0.74
174 33 0.26
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (173 bp):
AATTCAGTCACTCAACTTTCAAAAAATAACAAAACAATACTAACGTTATCAAAAAATAACAAATC
AGTCAATCATTAACATTTTCCGTTATAGCCCTAACGAGACAAGTGACATGACCAGTAAACTAACT
AACGTGGCCAGTCAACATGCCACATTGGATAAATCAAAATTTT
Found at i:94548 original size:14 final size:14
Alignment explanation
Indices: 94521--94553 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
94511 AATAAATATG
*
94521 TTATT-CAAATTAA
1 TTATTACAAAATAA
94534 TTATTACAAAATAA
1 TTATTACAAAATAA
94548 TTATTA
1 TTATTA
94554 ATCTAGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATTACAAAATAA
Found at i:102758 original size:31 final size:31
Alignment explanation
Indices: 102694--102759 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
102684 AAAAAGAAAC
* * *
102694 AATTCGACTCTTTTTGAAAGATTGATGGATA
1 AATTCAACTCTTTTTAAAAGATTGAGGGATA
*
102725 AATTCAACTCTTTTTAAAATG-TTGAGGGCTA
1 AATTCAACTCTTTTTAAAA-GATTGAGGGATA
102756 AATT
1 AATT
102760 TAGCTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (31 bp):
AATTCAACTCTTTTTAAAAGATTGAGGGATA
Found at i:103617 original size:27 final size:27
Alignment explanation
Indices: 103585--103636 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
103575 GTAGAAAATA
* *
103585 TTTAAAAATTGTGAAAAATTAAAATTC
1 TTTAAAAATTGTAAAAAATAAAAATTC
*
103612 TTTAAAAATTTTAAAAAATAAAAAT
1 TTTAAAAATTGTAAAAAATAAAAAT
103637 ATATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
TTTAAAAATTGTAAAAAATAAAAATTC
Found at i:104408 original size:26 final size:26
Alignment explanation
Indices: 104379--104454 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 26
104369 AGAAATATAT
*
104379 ATTTTTCATATGTTTTTATTTTTAAA
1 ATTTTTAATATGTTTTTATTTTTAAA
* * *
104405 ATTTTTTAA-AGAGTTTTAAATTTTAAA
1 A-TTTTTAATA-TGTTTTTATTTTTAAA
* *
104432 ATATTTAAT-TGTTTATATTTTTA
1 ATTTTTAATATGTTTTTATTTTTA
104455 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
25 10 0.26
26 8 0.21
27 20 0.53
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTTTTAATATGTTTTTATTTTTAAA
Found at i:104697 original size:21 final size:22
Alignment explanation
Indices: 104672--104716 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
104662 TTTCTCAAAA
*
104672 TTAAAATATAAAAACTA-AATT
1 TTAAAATATAAAAAATACAATT
* *
104693 TTAAATTTTAAAAAATACAATT
1 TTAAAATATAAAAAATACAATT
104715 TT
1 TT
104717 CTTTTGACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATATAAAAAATACAATT
Found at i:112010 original size:2 final size:2
Alignment explanation
Indices: 112003--112033 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
111993 TAATATTAGT
112003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.