Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015106.1 Kokia drynarioides strain JFW-HI SEQ_130150, 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: 116210
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:5000 original size:15 final size:16
Alignment explanation
Indices: 4980--5011 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4970 ATTACAATAA
4980 TGTATTATA-AATTTT
1 TGTATTATATAATTTT
4995 TGTATTATATAATTTT
1 TGTATTATATAATTTT
5011 T
1 T
5012 ATAGATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TGTATTATATAATTTT
Found at i:5026 original size:25 final size:26
Alignment explanation
Indices: 4961--5029 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
4951 TCGTGAATAA
*
4961 AGATTTTGTATTACAATAATGTATTAT
1 AGATTTTGTATTA-TATAATGTATTAT
* *
4988 AAATTTTTGTATTATATAAT-TTTTAT
1 AGA-TTTTGTATTATATAATGTATTAT
5014 AGATTTTGTATTATAT
1 AGATTTTGTATTATAT
5030 CTTAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.35
26 7 0.19
27 7 0.19
28 10 0.27
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (26 bp):
AGATTTTGTATTATATAATGTATTAT
Found at i:13032 original size:20 final size:20
Alignment explanation
Indices: 13009--13047 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12999 ATTTTTTATG
*
13009 ATATGCTATCATTTAATTTT
1 ATATGCTATCAATTAATTTT
13029 ATATGCTATCAATTAATTT
1 ATATGCTATCAATTAATTT
13048 ATTGATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATGCTATCAATTAATTTT
Found at i:13472 original size:28 final size:29
Alignment explanation
Indices: 13433--13487 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
13423 TTTAGTTTAA
13433 TTTTAATGTTCAATAT-GATATTTAAATCT
1 TTTTAATGTTCAAT-TCGATATTTAAATCT
*
13462 TTTTAAT-TTCAATTCGGTATTTAAAT
1 TTTTAATGTTCAATTCGATATTTAAAT
13488 TTGTCTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 16 0.67
29 7 0.29
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (29 bp):
TTTTAATGTTCAATTCGATATTTAAATCT
Found at i:20585 original size:28 final size:29
Alignment explanation
Indices: 20518--20585 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
20508 TAAAATAATG
*
20518 TTAAAATGACTATATAAAAAATTTAAATAA
1 TTAAAAT-AATATATAAAAAATTTAAATAA
* *
20548 ATAAAA-AATATAT-AAAATTATTAAAT-A
1 TTAAAATAATATATAAAAAAT-TTAAATAA
20575 TTAAAATAATA
1 TTAAAATAATA
20586 CAATATAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 11 0.34
28 16 0.50
30 5 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
TTAAAATAATATATAAAAAATTTAAATAA
Found at i:27031 original size:17 final size:17
Alignment explanation
Indices: 27009--27106 Score: 60
Period size: 17 Copynumber: 5.7 Consensus size: 17
26999 AAACTCCCTT
27009 TAAATTTATTTTAAGAA
1 TAAATTTATTTTAAGAA
*
27026 TAAATTTA-TTTAAAAA
1 TAAATTTATTTTAAGAA
* *
27042 TTTAAATTTATATTAA-ATT
1 --TAAATTTATTTTAAGA-A
*
27061 TAAATTTA-TTT-CGAA
1 TAAATTTATTTTAAGAA
* **
27076 TTTAAATTTAATTTAAGTT
1 --TAAATTTATTTTAAGAA
27095 TAAATTTATTTT
1 TAAATTTATTTT
27107 CCAAATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
16 10 0.16
17 35 0.56
18 12 0.19
19 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTTAAGAA
Found at i:27046 original size:35 final size:34
Alignment explanation
Indices: 27007--27105 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
26997 CCAAACTCCC
*
27007 TTTAAATTTATTTTAAGAATAAATTTATTTAAAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTT-AAAA
* **
27042 TTTAAATTTATATTAA-ATTTAAATTTATTTCGAA
1 TTTAAATTTATTTTAAGA-TTAAATTTATTTAAAA
* *
27076 TTTAAATTTAATTTAAGTTTAAATTTATTT
1 TTTAAATTTATTTTAAGATTAAATTTATTT
27106 TCCAAATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 29 0.53
35 26 0.47
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTAAAA
Found at i:27050 original size:6 final size:6
Alignment explanation
Indices: 27039--27102 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
27029 ATTTATTTAA
* *
27039 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
27085 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
27103 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 9 0.19
6 31 0.65
7 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:27914 original size:18 final size:18
Alignment explanation
Indices: 27865--27921 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
27855 GGCGGTTTTC
27865 ATAATATTTATTAATAATA
1 ATAATA-TTATTAATAATA
* *
27884 A-ATATTTTCTTAATAATA
1 ATA-ATATTATTAATAATA
*
27902 ATAATATTATTAATATTA
1 ATAATATTATTAATAATA
27920 AT
1 AT
27922 GACAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATATTATTAATAATA
Found at i:29099 original size:29 final size:29
Alignment explanation
Indices: 29045--29335 Score: 290
Period size: 30 Copynumber: 9.9 Consensus size: 29
29035 CCTCGAGGGT
29045 CCCTAAACTGTCCAAAAATTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
29075 CCCTAAACTTCTAAAAA-TCCTATTTTTAA
1 CCCTAAACTTCCAAAAATTCC-ATTTTTAC
29104 CCCTAAAACTTCCAAAAATTCCA-TTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
*
29133 CCTTAAACTTCCAAAAATTCCATTTTTAGC
1 CCCTAAACTTCCAAAAATTCCATTTTTA-C
* *
29163 CCCAAAACTTCCAAGAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
29191 CCCTCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* *
29222 CTCGAAACTTCCAAAAATTCCATTTTTAGC
1 CCCTAAACTTCCAAAAATTCCATTTTTA-C
*
29252 CCC-GAACTTCCAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* **
29280 CACTAAAACTTTTAAAAATTACCA-TTTTAC
1 CCCT-AAACTTCCAAAAATT-CCATTTTTAC
** *
29310 CCCTGGA-TGTCCAAAAACTCCATTTT
1 CCCTAAACT-TCCAAAAATTCCATTTT
29336 CGACCTCGAA
Statistics
Matches: 217, Mismatches: 28, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
28 30 0.14
29 86 0.40
30 93 0.43
31 8 0.04
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:29323 original size:59 final size:57
Alignment explanation
Indices: 29049--29371 Score: 307
Period size: 59 Copynumber: 5.5 Consensus size: 57
29039 GAGGGTCCCT
* * *
29049 AAACTGTCCAAAAATTCCATTTTTACCCCTAAACTTCTAAAAA-TCCTATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCA-TTTTACCCCTGAACTTCCAAAAATTCC-ATTTTTGA-CCTA
* * * *
29109 AAACTTCCAAAAATTCCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTAGCCCCA
1 AAACTTCCAAAAATTCCATTTTACCCCTGAACTTCCAAAAATTCCATTTTT-GACCTA
* * *
29167 AAACTTCCAAGAATTCCATTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTACCCCT-GAACTTCCAAAAATTCCATTTTTGACCT-A
29226 AAACTTCCAAAAATTCCATTTTTAGCCCC-GAACTTCCAAAAATTCCATTTTTGACACTA
1 AAACTTCCAAAAATTCCA-TTTTA-CCCCTGAACTTCCAAAAATTCCATTTTTGAC-CTA
** * * * *
29285 AAACTTTTAAAAATTACCATTTTACCCCTGGA-TGTCCAAAAACTCCATTTTCGACCTCG
1 AAACTTCCAAAAATT-CCATTTTACCCCTGAACT-TCCAAAAATTCCATTTTTGACCT-A
*
29344 AAAC-TCTC-AAAATTACCCTTTTACCCCT
1 AAACTTC-CAAAAATT-CCATTTTACCCCT
29372 TAATGTTTAA
Statistics
Matches: 226, Mismatches: 24, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
58 80 0.35
59 133 0.59
60 10 0.04
61 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTA
Found at i:29390 original size:58 final size:59
Alignment explanation
Indices: 29294--29429 Score: 157
Period size: 58 Copynumber: 2.3 Consensus size: 59
29284 AAAACTTTTA
* * *
29294 AAAATTACCATTTTACCCCTGGATGTCCAAAAACTCCATTTTCGACCTCGAA-ACTCTC
1 AAAATTACCATTTTACCCCTGAATGTCCAAAAACTCCATTTTCAACATCGAATACTCTC
* * ** ** * **
29352 AAAATTACCCTTTTACCCCTTAATGTTTAAAATTTCCATTTTTAACATCGAATTTTCTC
1 AAAATTACCATTTTACCCCTGAATGTCCAAAAACTCCATTTTCAACATCGAATACTCTC
29411 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
29430 CGGCTATCCA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
58 42 0.66
59 22 0.34
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTGAATGTCCAAAAACTCCATTTTCAACATCGAATACTCTC
Found at i:44693 original size:8 final size:8
Alignment explanation
Indices: 44682--44728 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
44672 AAAAGTCATG
44682 ATTTTTTA
1 ATTTTTTA
44690 A-TTTTTA
1 ATTTTTTA
*
44697 ATTTTTAA
1 ATTTTTTA
*
44705 ATTTATATAA
1 ATTT-T-TTA
44715 ATTTTTTA
1 ATTTTTTA
44723 ATTTTT
1 ATTTTT
44729 ATGTGATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.21
8 18 0.53
9 2 0.06
10 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATTTTTTA
Found at i:45166 original size:16 final size:18
Alignment explanation
Indices: 45127--45160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45117 TAAGTTTATA
45127 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
45144 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
45161 AATTTAGAAC
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:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:51244 original size:28 final size:28
Alignment explanation
Indices: 51197--51275 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
51187 GAGCATCATT
* * *
51197 ACCTTTGGGTTAACATGGAGTAAGCATG
1 ACCTTTAGGTCAACAAGGAGTAAGCATG
*
51225 ACCTTTAGGTCAATAAGGAGTAAGCATG
1 ACCTTTAGGTCAACAAGGAGTAAGCATG
* *
51253 ACCTTTGGGTCAACAGGGAGTAA
1 ACCTTTAGGTCAACAAGGAGTAA
51276 ATCGGATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (28 bp):
ACCTTTAGGTCAACAAGGAGTAAGCATG
Found at i:59501 original size:12 final size:12
Alignment explanation
Indices: 59484--59523 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
59474 GGATTTGGGT
59484 TTTTTTTTTTAA
1 TTTTTTTTTTAA
59496 TTTTTTTTTTAA
1 TTTTTTTTTTAA
* **
59508 ATCATTTTTTAA
1 TTTTTTTTTTAA
59520 TTTT
1 TTTT
59524 AAAAAAGTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:60280 original size:24 final size:24
Alignment explanation
Indices: 60252--60310 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
60242 CATAAAATTT
60252 AAAAAATTATAATTTTT-AAAAAA
1 AAAAAATTATAATTTTTCAAAAAA
* *
60275 ATAAAAATCAT-ATTTTTCAATAAA
1 A-AAAAATTATAATTTTTCAAAAAA
*
60299 AAAAAACTATAA
1 AAAAAATTATAA
60311 AATTGAACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATTATAATTTTTCAAAAAA
Found at i:61246 original size:51 final size:51
Alignment explanation
Indices: 61140--61251 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
61130 TTGGTATAAT
* * * * *
61140 AACAAATTTAGACCTTAAAATTTACAAATTCTGTCATTTTGATCTTAATTT
1 AACAAATTTAGACCGTAAAATTTACAAATTCTGTCAATTTGATCATAAGTA
* * * * * *
61191 AACAAATTTAGCCCGTAACATTTACATATTCTTTTAATTTGGTCATAAGTA
1 AACAAATTTAGACCGTAAAATTTACAAATTCTGTCAATTTGATCATAAGTA
61242 AACAAATTTA
1 AACAAATTTA
61252 ACTTACATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (51 bp):
AACAAATTTAGACCGTAAAATTTACAAATTCTGTCAATTTGATCATAAGTA
Found at i:63888 original size:8 final size:8
Alignment explanation
Indices: 63875--63900 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
63865 ATTGAAAATG
63875 AATAAACA
1 AATAAACA
63883 AATAAACA
1 AATAAACA
63891 AATAAACA
1 AATAAACA
63899 AA
1 AA
63901 CTAGAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAACA
Found at i:64234 original size:14 final size:14
Alignment explanation
Indices: 64212--64243 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
64202 CTTTTTCATT
*
64212 TTTATTGCAAAAAA
1 TTTAATGCAAAAAA
64226 TTTAATGCAAAAAA
1 TTTAATGCAAAAAA
64240 TTTA
1 TTTA
64244 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (14 bp):
TTTAATGCAAAAAA
Found at i:65259 original size:13 final size:13
Alignment explanation
Indices: 65241--65271 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
65231 TATCATATGC
*
65241 ATATTATAATTTT
1 ATATTATAATATT
65254 ATATTATAATATT
1 ATATTATAATATT
65267 ATATT
1 ATATT
65272 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTATAATATT
Found at i:78709 original size:15 final size:15
Alignment explanation
Indices: 78689--78718 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
78679 CATTATTTTA
78689 ATAATTTATATATTT
1 ATAATTTATATATTT
*
78704 ATAATTTTTATATTT
1 ATAATTTATATATTT
78719 TAAAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATAATTTATATATTT
Found at i:86726 original size:17 final size:17
Alignment explanation
Indices: 86700--86732 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
86690 ATTCGTTTCG
86700 GAATTAAATAATTAATC
1 GAATTAAATAATTAATC
*
86717 GAATTTAATAATTAAT
1 GAATTAAATAATTAAT
86733 AATACAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
GAATTAAATAATTAATC
Found at i:88630 original size:80 final size:80
Alignment explanation
Indices: 88497--88658 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
88487 AGCACCCTTG
88497 GCATTTTCGTGTTGGATGCCGAAACAAAAGGACACACCGTCCTTGGACTTTGTTTCACCTCAATT
1 GCATTTTCGTGTTGGATGCCGAAACAAAAGGACACACCGTCCTTGGACTTTGTTTCACCTCAATT
88562 TCTTGGCTATTCCCC
66 TCTTGGCTATTCCCC
88577 GCATTTTCGTGTTGGATGCCGAAACAAAAGGACACACCGTCCTTGGACTTTGTTTCACCTCAATT
1 GCATTTTCGTGTTGGATGCCGAAACAAAAGGACACACCGTCCTTGGACTTTGTTTCACCTCAATT
88642 TCTTGGCTATTCCCC
66 TCTTGGCTATTCCCC
88657 GC
1 GC
88659 GTATTAGCAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (80 bp):
GCATTTTCGTGTTGGATGCCGAAACAAAAGGACACACCGTCCTTGGACTTTGTTTCACCTCAATT
TCTTGGCTATTCCCC
Found at i:90213 original size:101 final size:101
Alignment explanation
Indices: 90038--90245 Score: 310
Period size: 101 Copynumber: 2.1 Consensus size: 101
90028 GGAGGCAGCA
* *
90038 GCAACAACATCAATGCCAACTAAACTAACACTCAATCGGCAACCTTAATTAATTCTAAAAATGGA
1 GCAACAACACCAATGCCAACTAAACTAACACTCAATCAGCAACCTTAATTAATTCTAAAAATGGA
* *
90103 TGGAACTAAGAACTTTCTAATACA-ATCACAAAGATT
66 TGGAACTAAGAACTTACTAATA-ATATCACAAAGACT
* * * *
90139 GCAACACCACCAATGCCTACTAAATTAGCACTCAATCAGCAACCTTAATTAATTCTAAAAATGGA
1 GCAACAACACCAATGCCAACTAAACTAACACTCAATCAGCAACCTTAATTAATTCTAAAAATGGA
* *
90204 TGGGACTAAGAACTTACTAATAATATCACAGAGACT
66 TGGAACTAAGAACTTACTAATAATATCACAAAGACT
90240 GCAACA
1 GCAACA
90246 TCAATGCCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 95 0.99
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (101 bp):
GCAACAACACCAATGCCAACTAAACTAACACTCAATCAGCAACCTTAATTAATTCTAAAAATGGA
TGGAACTAAGAACTTACTAATAATATCACAAAGACT
Found at i:93345 original size:13 final size:12
Alignment explanation
Indices: 93322--93355 Score: 50
Period size: 12 Copynumber: 2.7 Consensus size: 12
93312 TTTTGACCCG
93322 TTATTTATTTATTT
1 TTATTT-TTTA-TT
93336 TTATTTTTTATT
1 TTATTTTTTATT
93348 TTATTTTT
1 TTATTTTT
93356 AAATCACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:95542 original size:42 final size:41
Alignment explanation
Indices: 95477--95604 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 41
95467 ATAAAATAAG
* *
95477 TTATTATTATTTATTATTGTCTTTGTCCAAATTGATATTGTTT
1 TTATTTTTA-TTATTATTGTCTTTATCC-AATTGATATTGTTT
* *
95520 TTATTTTTATTATTATTCTCTTTATCCAATTGATATTTTTTT
1 TTATTTTTATTATTATTGTCTTTATCCAATTGATA-TTGTTT
*
95562 TTATTTTTTTTATTATTGTC--TATCCAATTGATATTGTTT
1 TTATTTTTATTATTATTGTCTTTATCCAATTGATATTGTTT
95601 TTAT
1 TTAT
95605 AATATCCTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
39 9 0.12
40 13 0.17
41 8 0.10
42 39 0.51
43 8 0.10
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (41 bp):
TTATTTTTATTATTATTGTCTTTATCCAATTGATATTGTTT
Found at i:96066 original size:19 final size:20
Alignment explanation
Indices: 96030--96068 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
96020 TAATCCTTAC
*
96030 TCTTCAAAACATTTAAAAAT
1 TCTTCAAAACATTAAAAAAT
*
96050 TCTT-AAAAGATTAAAAAAT
1 TCTTCAAAACATTAAAAAAT
96069 AAAGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TCTTCAAAACATTAAAAAAT
Found at i:101031 original size:17 final size:17
Alignment explanation
Indices: 101009--101094 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
100999 GTCATTTTGG
*
101009 GTTTAAATTTGATTTAA
1 GTTTAAATTTAATTTAA
**
101026 GTTTAAACTTTTTTTTTTAAA
1 GTTTAAA---TTTAATTT-AA
* *
101047 GCTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
101064 GTTTAAATTTAAATTGAA
1 GTTTAAATTT-AATTTAA
*
101082 -TTTAAATTGAATT
1 GTTTAAATTTAATT
101095 AAAGAAGTCC
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.07
17 26 0.48
18 10 0.19
20 6 0.11
21 8 0.15
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.51
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:101058 original size:6 final size:6
Alignment explanation
Indices: 101049--101089 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
101039 TTTTTAAAGC
* *
101049 TTAAAT TTAAA- TTAAGT TTAAAT TTAAA- TTGAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
101090 GAATTAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:101090 original size:11 final size:11
Alignment explanation
Indices: 101069--101094 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
101059 ATTAAGTTTA
101069 AATTTAAATTG
1 AATTTAAATTG
101080 AATTTAAATTG
1 AATTTAAATTG
101091 AATT
1 AATT
101095 AAAGAAGTCC
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:103028 original size:29 final size:29
Alignment explanation
Indices: 102972--103134 Score: 116
Period size: 29 Copynumber: 5.5 Consensus size: 29
102962 CTAAACTGTC
** *
102972 CAAAAATTCCATTTTTAACATTGAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCAAACTTT
** * *
103002 CAAAAATTATATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTT
* *
103031 CAAAAACTCCATTTTTACCCTCAAAC-CT
1 CAAAAATTCCATTTTTACCCTCAAACTTT
* ** *
103059 CTAAAAATTCCATTTTTACCCCCGGA-TGTC
1 C-AAAAATTCCATTTTTACCCTCAAACT-TT
* *
103089 CAAAAACTCCATTTTTTACCC-CAAAACTCT
1 CAAAAATTCCA-TTTTTACCCTC-AAACTTT
103119 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
103135 AGGCCCGAAT
Statistics
Matches: 101, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
28 1 0.01
29 60 0.59
30 36 0.36
31 4 0.04
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCAAACTTT
Found at i:103091 original size:58 final size:58
Alignment explanation
Indices: 102968--103164 Score: 204
Period size: 59 Copynumber: 3.4 Consensus size: 58
102958 GTCCCTAAAC
* ** * * ** *
102968 TGTCCAAAAATTCCATTTTTAACATTGAAACTTTCAAAAATTATATTTTTACCCTCGAA
1 TGTCCAAAAACTCCATTTTT-ACCCTCAAACTCTCAAAAATTCCATTTTTACCCCCGAA
*
103027 CT-TCCAAAAACTCCATTTTTACCCTCAAAC-CTCTAAAAATTCCATTTTTACCCCCGGA
1 -TGTCCAAAAACTCCATTTTTACCCTCAAACTCTC-AAAAATTCCATTTTTACCCCCGAA
**
103085 TGTCCAAAAACTCCATTTTTTACCC-CAAAACTCTCAAAAATTACCA-TTTTAGGCCCGAA
1 TGTCCAAAAACTCCA-TTTTTACCCTC-AAACTCTCAAAAATT-CCATTTTTACCCCCGAA
*
103144 TGTCCAAAAATTCCATTTTTA
1 TGTCCAAAAACTCCATTTTTA
103165 TCCCATTTTC
Statistics
Matches: 118, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
57 3 0.03
58 47 0.40
59 61 0.52
60 7 0.06
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
TGTCCAAAAACTCCATTTTTACCCTCAAACTCTCAAAAATTCCATTTTTACCCCCGAA
Found at i:103135 original size:59 final size:58
Alignment explanation
Indices: 102968--103277 Score: 220
Period size: 58 Copynumber: 5.3 Consensus size: 58
102958 GTCCCTAAAC
**** * * * *
102968 TGTCCAAAAATTCCATTTTTAACATTGAAACTTTCAAAAATTA-TATTTTTACCCTCGAA
1 TGTCCAAAAATTCCATTTTT-ACCCCAAAACTCTCAAAAATTACCA-TTTTACCCCCGGA
* *
103027 CT-TCCAAAAACTCCATTTTTACCCTCAAACCTCT-AAAAATT-CCATTTTTACCCCCGGA
1 -TGTCCAAAAATTCCATTTTTACCC-CAAAACTCTCAAAAATTACCA-TTTTACCCCCGGA
* ** *
103085 TGTCCAAAAACTCCATTTTTTACCCCAAAACTCTCAAAAATTACCATTTTAGGCCCGAA
1 TGTCCAAAAATTCCA-TTTTTACCCCAAAACTCTCAAAAATTACCATTTTACCCCCGGA
* *** * *
103144 TGTCCAAAAATTCCATTTTTATCCC-ATTTTCT-AAAAATTACCGTTTTACCCTCGGA
1 TGTCCAAAAATTCCATTTTTACCCCAAAACTCTCAAAAATTACCATTTTACCCCCGGA
* * * * * * * * *
103200 TGT-CTAAAATTCGATTTTAAACCCAAAATTTCCCCAAAATTACCATTTTGCCCCCGGG
1 TGTCCAAAAATTCCATTTTTACCCCAAAA-CTCTCAAAAATTACCATTTTACCCCCGGA
* *
103258 TATCCAAAAAGTCTCATTTT
1 TGTCCAAAAATTC-CATTTT
103278 CAACTTCGAT
Statistics
Matches: 199, Mismatches: 40, Indels: 22
0.76 0.15 0.08
Matches are distributed among these distances:
55 17 0.09
56 23 0.12
57 8 0.04
58 73 0.37
59 69 0.35
60 9 0.05
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.34
Consensus pattern (58 bp):
TGTCCAAAAATTCCATTTTTACCCCAAAACTCTCAAAAATTACCATTTTACCCCCGGA
Found at i:103163 original size:29 final size:28
Alignment explanation
Indices: 103002--103164 Score: 123
Period size: 29 Copynumber: 5.6 Consensus size: 28
102992 TTGAAACTTT
**
103002 CAAAAATTATATTTTTACCCTCGAACT-TC
1 CAAAAATTCCATTTTTACCC-CGAA-TGTC
* * **
103031 CAAAAACTCCATTTTTACCCTCAAACCTC
1 CAAAAATTCCATTTTTACCC-CGAATGTC
* *
103060 TAAAAATTCCATTTTTACCCCCGGATGTC
1 CAAAAATTCCATTTTTA-CCCCGAATGTC
* * **
103089 CAAAAACTCCATTTTTTACCCCAAAACTC
1 CAAAAATTCCA-TTTTTACCCCGAATGTC
*
103118 TCAAAAATTACCA-TTTTAGGCCCGAATGTC
1 -CAAAAATT-CCATTTTTA-CCCCGAATGTC
103148 CAAAAATTCCATTTTTA
1 CAAAAATTCCATTTTTA
103165 TCCCATTTTC
Statistics
Matches: 105, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
28 3 0.03
29 76 0.72
30 23 0.22
31 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCCGAATGTC
Found at i:112952 original size:206 final size:206
Alignment explanation
Indices: 112340--113362 Score: 1537
Period size: 206 Copynumber: 5.0 Consensus size: 206
112330 CCAAATCAGG
* * * *
112340 GCTCGATATGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATATTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
112405 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
112470 CAGAGAAGCGAATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
*
112535 ATCAAACCGAC
196 ATCAAACCCAC
* * *
112546 GCTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATATTAAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * *
112611 ATAAAATGATTA-CTTCCTGATGAGTTACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
112675 CAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
112740 ATCAAACCCAC
196 ATCAAACCCAC
* * * *
112751 GCTCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCTAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
112816 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTTTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * ** * * *
112881 CAGAGAAGCGGATTGAAACAAACGATGTGATAATCTTCCCAATGAGATAATGATAAAAAGACCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
112946 ATCAAACCCAC
196 ATCAAACCCAC
* * * *
112957 ACTCGATGTGAGCAAATCTTCGAACCCCAGCTTTCTGATGAGATACTGAGAAGAAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
113022 ATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * *
113087 CAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAA
131 CAGAGAAGCGGATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
*
113152 ATCAAACCCAA
196 ATCAAACCCAC
113163 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * * * * * *
113228 ATAAAATGGTTAACTTCCTGATAATATACGGAGAAGTGAACCAAATCCGTCTTCTTGATGAAACA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * * * * *
113293 CAGAGAAGTGGA-TCAAGATAAGCGATACGATCATCTTCCTGATGAAATACTAAGAAGTAGACCA
131 CAGAGAAGCGGATTGAA-ACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCA
113357 AATCAA
195 AATCAA
113363 CGACACCAAA
Statistics
Matches: 739, Mismatches: 76, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
205 196 0.27
206 543 0.73
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (206 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGGATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
ATCAAACCCAC
Found at i:113214 original size:412 final size:411
Alignment explanation
Indices: 112340--113305 Score: 1509
Period size: 411 Copynumber: 2.3 Consensus size: 411
112330 CCAAATCAGG
* * * *
112340 GCTCGATATGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATATTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
112405 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * ** * *
112470 CAGAGAAGCGAATTGAAACAAGCGATGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAACAAACGATGCGATAATCTTCCCAATGAGATAATGAGAAAAAGACCAA
* * * *
112535 ATCAAACCGACGCTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATATTAAGAAGC
196 ATCAAACCCACACTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGA
* *
112600 AGGTCGAAGCAATAAAATGATTACTTCCTGATGAGTTACTGAGAAGTGGACCAAATTCGTCTTCC
261 AGGTCGAAGCAATAAAATGATTACTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCC
*
112665 TGATAAGATACAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGA
326 TGATAAGATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGA
*
112730 AGAAGACCAAATCAAACCCAC
391 AGAAGACCAAATCAAACCCAA
* * * *
112751 GCTCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCTAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
112816 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTTTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
112881 CAGAGAAGCGGATTGAAACAAACGATGTGATAATCTTCCCAATGAGATAATGATAAAAAGACCAA
131 CAGAGAAGCGGATTGAAACAAACGATGCGATAATCTTCCCAATGAGATAATGAGAAAAAGACCAA
* * * *
112946 ATCAAACCCACACTCGATGTGAGCAAATCTTCGAACCCCAGCTTTCTGATGAGATACTGAGAAGA
196 ATCAAACCCACACTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGA
* *
113011 AGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTC
261 AGGTCGAAGCAATAAAATGATTA-CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTC
*
113076 CTGATGAGATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAG
325 CTGATAAGATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAG
*
113141 AAGAAGATCAAATCAAACCCAA
390 AAGAAGACCAAATCAAACCCAA
113163 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * * * * * *
113228 ATAAAATGGTTAACTTCCTGATAATATACGGAGAAGTGAACCAAATCCGTCTTCTTGATGAAACA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
*
113293 CAGAGAAGTGGAT
131 CAGAGAAGCGGAT
113306 CAAGATAAGC
Statistics
Matches: 502, Mismatches: 52, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
411 254 0.51
412 248 0.49
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (411 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGGATTGAAACAAACGATGCGATAATCTTCCCAATGAGATAATGAGAAAAAGACCAA
ATCAAACCCACACTCAATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGA
AGGTCGAAGCAATAAAATGATTACTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCC
TGATAAGATACAGAGAAGCGAATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGA
AGAAGACCAAATCAAACCCAA
Found at i:113702 original size:17 final size:17
Alignment explanation
Indices: 113680--113761 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
113670 AGTCATTTTG
*
113680 AGTTTAAATTTGATTTA
1 AGTTTAAATTTAATTTA
**
113697 AGTTTAAACTTTTTTTTTTAA
1 AGTTTAAA---TTTAATTT-A
* *
113718 AGCTTAAATTTAAATTA
1 AGTTTAAATTTAATTTA
*
113735 AGTTTAAATTTTAATTGA
1 AGTTTAAA-TTTAATTTA
113753 A-TTTAAATT
1 AGTTTAAATT
113762 GAAGTAAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
16 2 0.04
17 22 0.43
18 13 0.25
20 6 0.12
21 8 0.16
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (17 bp):
AGTTTAAATTTAATTTA
Found at i:114404 original size:3 final size:3
Alignment explanation
Indices: 114398--114450 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
114388 TGATCATCAC
* * * * * *
114398 TAA TAA TAA TAA TAA TAT TAC TAA TAA CAC TAA TAA TAA AAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
114446 TAA TA
1 TAA TA
114451 TTAAGTAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:114421 original size:21 final size:21
Alignment explanation
Indices: 114396--114435 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
114386 AATGATCATC
*
114396 ACTAATAATAATAATAATATT
1 ACTAATAACAATAATAATATT
*
114417 ACTAATAACACTAATAATA
1 ACTAATAACAATAATAATA
114436 AAAATATTAA
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTAATAACAATAATAATATT
Found at i:114468 original size:36 final size:33
Alignment explanation
Indices: 114398--114472 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
114388 TGATCATCAC
* *
114398 TAATAATAATAATAATATTACTAATAACACTAA
1 TAATAAAAATAATAATAATACTAATAACACTAA
* * *
114431 TAATAAAAATATTAATAATATTAAGTAACACT-T
1 TAATAAAAATAATAATAATACTAA-TAACACTAA
114464 TAATAAAAA
1 TAATAAAAA
114473 AGGAAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 29 0.81
34 7 0.19
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (33 bp):
TAATAAAAATAATAATAATACTAATAACACTAA
Found at i:115685 original size:29 final size:29
Alignment explanation
Indices: 115596--115853 Score: 168
Period size: 29 Copynumber: 8.8 Consensus size: 29
115586 GAGGTCCTTA
* *
115596 AACTATCCAAAAATTCCATTTTTAACCTTG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
*** **
115626 AAACTTTTGAAAATTATATTTTTACCCCTCG
1 -AACTTCCAAAAATTCCATTTTTA-CCCTCG
*
115657 AACTTCCAAAAATTCCATTTTTGA-TCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
115686 AACTTCCAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* **
115715 AACCTCCAAAAATTCCATTTCAACCCT-G
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* ** * *
115743 AAAATTTTAAAAATTACATTTTTACTCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
115773 AA-TGTCCAAAAACTCCATTTTTGACCC-CG
1 AACT-TCCAAAAATTCCATTTTT-ACCCTCG
* * *
115802 AAAC-TCTCAAAAATTAC-TATTTTACCCCCA
1 -AACTTC-CAAAAATTCCAT-TTTTACCCTCG
* **
115832 AACGTAAAAAAATTCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
115854 TTATCCCTTT
Statistics
Matches: 175, Mismatches: 38, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.02
29 111 0.63
30 52 0.30
31 9 0.05
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:115731 original size:58 final size:59
Alignment explanation
Indices: 115601--115853 Score: 235
Period size: 59 Copynumber: 4.3 Consensus size: 59
115591 CCTTAAACTA
* ** *** * *
115601 TCCAAAAATTCCATTTTTAACCTTGAAACTTTTGAAAATTATATTTTTACCCCTCGAACT
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTA-CCCTCGAACG
* * *
115661 TCCAAAAATTCCATTTTTGATCTCG-AACTTCCAAAAATTACATTTTTACCCTCGAACC
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACG
** * * ** * *
115719 TCCAAAAATTCCA-TTTCAACCCTGAAAATTTTAAAAATTACATTTTTACTCTCGAATG
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACG
* * *
115777 TCCAAAAACTCCATTTTTGACCCCGAAAC-TCTCAAAAATTAC-TATTTTACCCCCAAACG
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTC-CAAAAATTACAT-TTTTACCCTCGAACG
**
115836 TAAAAAAATTCCATTTTT
1 TCCAAAAATTCCATTTTT
115854 TTATCCCTTT
Statistics
Matches: 156, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
57 6 0.04
58 63 0.40
59 65 0.42
60 22 0.14
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACG
Done.