Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005443.1 Hibiscus syriacus cultivar Beakdansim tig00012476_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 184502
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6967 original size:18 final size:17
Alignment explanation
Indices: 6931--6973 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
6921 AAAATCATCG
*
6931 TATCATAAAGTAAATCA
1 TATCATCAAGTAAATCA
6948 TATCATCAAGTAATATCA
1 TATCATCAAGTAA-ATCA
6966 TATCATCA
1 TATCATCA
6974 TTTTGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (17 bp):
TATCATCAAGTAAATCA
Found at i:9224 original size:2 final size:2
Alignment explanation
Indices: 9217--9250 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9207 GGTTACAAGA
9217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9251 TCATTCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12956 original size:18 final size:18
Alignment explanation
Indices: 12933--12968 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12923 CGGAGCTAAG
12933 TCCCCTGCACAATTAACC
1 TCCCCTGCACAATTAACC
12951 TCCCCTGCACAATTAACC
1 TCCCCTGCACAATTAACC
12969 ATTGACCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.06, T:0.22
Consensus pattern (18 bp):
TCCCCTGCACAATTAACC
Found at i:20429 original size:60 final size:59
Alignment explanation
Indices: 20361--20489 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
20351 TCTTTAAACA
* * *
20361 TTTT-AATATTATAATTTCAT-CCTCAAACTATAACTCTCATTATAGATTAGTTCTTAAAT
1 TTTTGAATATTATAATTCCATCCCT-AAACTATAACCCTCATTATA-ATTAGTCCTTAAAT
* * * * * *
20420 TTTTGAATATTCTAATTCCATCCCTAAATTATTACCCTCTTTCTAATTGGTCCTTAAAT
1 TTTTGAATATTATAATTCCATCCCTAAACTATAACCCTCATTATAATTAGTCCTTAAAT
20479 TTTTGAATATT
1 TTTTGAATATT
20490 CCAATTTATC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 27 0.46
60 29 0.49
61 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (59 bp):
TTTTGAATATTATAATTCCATCCCTAAACTATAACCCTCATTATAATTAGTCCTTAAAT
Found at i:22044 original size:7 final size:7
Alignment explanation
Indices: 22034--22067 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
22024 TTTGTTATTT
22034 GGTTTTG
1 GGTTTTG
22041 GGTTTTG
1 GGTTTTG
*
22048 GGTGTTG
1 GGTTTTG
22055 GGTTTTG
1 GGTTTTG
*
22062 CGTTTT
1 GGTTTT
22068 AGTTATTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.41, T:0.56
Consensus pattern (7 bp):
GGTTTTG
Found at i:22046 original size:21 final size:21
Alignment explanation
Indices: 22022--22075 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
22012 TGCGATTTTT
* * *
22022 TTTTTGTTATTTGGTTTTGGG
1 TTTTAGTTATTGGGTTTTGCG
* * *
22043 TTTTGGGTGTTGGGTTTTGCG
1 TTTTAGTTATTGGGTTTTGCG
22064 TTTTAGTTATTG
1 TTTTAGTTATTG
22076 TTTTAATAGA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.02, G:0.31, T:0.61
Consensus pattern (21 bp):
TTTTAGTTATTGGGTTTTGCG
Found at i:32058 original size:31 final size:30
Alignment explanation
Indices: 32023--32090 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
32013 CGATATGATA
32023 ATCAAAATTAATACAAA-ATATCATAAAATTT
1 ATCAAAATTAAT-CAAATA-ATCATAAAATTT
* * *
32054 ATCAAAAATTTATCAAATAATTATTAAATTT
1 ATC-AAAATTAATCAAATAATCATAAAATTT
32085 ATCAAA
1 ATCAAA
32091 CTTTTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.09
31 20 0.62
32 9 0.28
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (30 bp):
ATCAAAATTAATCAAATAATCATAAAATTT
Found at i:32075 original size:12 final size:11
Alignment explanation
Indices: 32041--32075 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
32031 TAATACAAAA
32041 TATCATAAAATT
1 TATCA-AAAATT
32053 TATCAAAAATT
1 TATCAAAAATT
32064 TATCAAATAATT
1 TATCAAA-AATT
32076 ATTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (11 bp):
TATCAAAAATT
Found at i:36842 original size:26 final size:25
Alignment explanation
Indices: 36813--36861 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
36803 CGAGCTATTA
36813 TTTATATAAAAAAATTTAAAAATACT
1 TTTATAT-AAAAAATTTAAAAATACT
* *
36839 TTTATATAACATATTTAAAAATA
1 TTTATATAAAAAATTTAAAAATA
36862 ATATGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATATAAAAAATTTAAAAATACT
Found at i:36952 original size:23 final size:23
Alignment explanation
Indices: 36908--36952 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
36898 TTATTAATTT
* *
36908 ATCATATAAATTATTATATAAAA
1 ATCATAAAAATTATGATATAAAA
36931 ATCATAAAAATTAATGAT-TAAA
1 ATCATAAAAATT-ATGATATAAA
36953 TTATCGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
ATCATAAAAATTATGATATAAAA
Found at i:47967 original size:22 final size:23
Alignment explanation
Indices: 47941--47994 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
47931 CAAACCCTAA
47941 ATTTTGATAAAAATT-AATAAAT
1 ATTTTGATAAAAATTCAATAAAT
* *
47963 ATTTTG-TAATAGTTCAATAAAT
1 ATTTTGATAAAAATTCAATAAAT
47985 -TTTATGATAA
1 ATTT-TGATAA
47995 TTTTACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.33
22 15 0.56
23 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
ATTTTGATAAAAATTCAATAAAT
Found at i:50159 original size:24 final size:24
Alignment explanation
Indices: 50126--50196 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
50116 ATCTCCTTTA
50126 CCATCGCCATCGTATTCACCATCT
1 CCATCGCCATCGTATTCACCATCT
* * * *
50150 CCATCTCCATCAGAAGT-GCCATCT
1 CCATCGCCATC-GTATTCACCATCT
*
50174 CCATCGCCATCGTATTCATCATC
1 CCATCGCCATCGTATTCACCATC
50197 CCCGACTCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
23 3 0.08
24 30 0.83
25 3 0.08
ACGTcount: A:0.23, C:0.39, G:0.10, T:0.28
Consensus pattern (24 bp):
CCATCGCCATCGTATTCACCATCT
Found at i:50255 original size:30 final size:30
Alignment explanation
Indices: 50221--50292 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
50211 CATCAGAAGT
50221 ACCATCTCCATCGCCATCAGTAGCACCTTC
1 ACCATCTCCATCGCCATCAGTAGCACCTTC
50251 ACCATCTCCATCGCCATCAGTAGCACCTTC
1 ACCATCTCCATCGCCATCAGTAGCACCTTC
50281 ACCATCTCCATC
1 ACCATCTCCATC
50293 AATTCCAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.24, C:0.44, G:0.08, T:0.24
Consensus pattern (30 bp):
ACCATCTCCATCGCCATCAGTAGCACCTTC
Found at i:50256 original size:48 final size:48
Alignment explanation
Indices: 50126--50262 Score: 159
Period size: 54 Copynumber: 2.7 Consensus size: 48
50116 ATCTCCTTTA
* *
50126 CCATCGCCATCGTATTCACCATCTCCATCTCCATCAGAAGTGCCATCT
1 CCATCGCCATCGTATTCACCATCACCATCTCCATCAGAAGTACCATCT
*
50174 CCATCGCCATCGTATTCATCATCCCCGACTCCATCTCCATCAGAAGTACCATCT
1 CCATCGCCATCGTATTCACCAT---C-A--CCATCTCCATCAGAAGTACCATCT
* *
50228 CCATCGCCATCAGTA-GCACCTTCACCATCTCCATC
1 CCATCGCCATC-GTATTCACCATCACCATCTCCATC
50263 GCCATCAGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
48 32 0.42
50 1 0.01
51 2 0.03
54 38 0.50
55 3 0.04
ACGTcount: A:0.23, C:0.42, G:0.09, T:0.26
Consensus pattern (48 bp):
CCATCGCCATCGTATTCACCATCACCATCTCCATCAGAAGTACCATCT
Found at i:50260 original size:54 final size:55
Alignment explanation
Indices: 50140--50293 Score: 179
Period size: 54 Copynumber: 2.8 Consensus size: 55
50130 CGCCATCGTA
* * *
50140 TTCACCATCTCCATCTCCATCAGAAGTGCCATCTCCATCGCCATC-GTATTCATC
1 TTCACCATCTCCATCTCCATCAGAAGTACCATCTCCATCGCCATCAGTATGCACC
* *
50194 ATCCCCGA-CTCCATCTCCATCAGAAGTACCATCTCCATCGCCATCAGTA-GCACC
1 TTCACC-ATCTCCATCTCCATCAGAAGTACCATCTCCATCGCCATCAGTATGCACC
* * * * * *
50248 TTCACCATCTCCATCGCCATCAGTAGCACCTTCACCATCTCCATCA
1 TTCACCATCTCCATCTCCATCAGAAGTACCATCTCCATCGCCATCA
50294 ATTCCAGAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
53 1 0.01
54 79 0.94
55 4 0.05
ACGTcount: A:0.24, C:0.42, G:0.09, T:0.25
Consensus pattern (55 bp):
TTCACCATCTCCATCTCCATCAGAAGTACCATCTCCATCGCCATCAGTATGCACC
Found at i:50277 original size:24 final size:24
Alignment explanation
Indices: 50126--50293 Score: 79
Period size: 24 Copynumber: 6.5 Consensus size: 24
50116 ATCTCCTTTA
*
50126 CCATCGCCATC-GTATTCACCATCT
1 CCATCGCCATCAGTA-GCACCATCT
* * **
50150 CCATCTCCATCAGAAGTGCCATCT
1 CCATCGCCATCAGTAGCACCATCT
* *
50174 CCATCGCCATC-GTATTCATCATCCCCGACT
1 CCATCGCCATCAGTA-GCACCAT------CT
* * *
50204 CCATCTCCATCAGAAGTACCATCT
1 CCATCGCCATCAGTAGCACCATCT
50228 CCATCGCCATCAGTAGCACCTTCACCATCT
1 CCATCGCCATCAGTAG------CACCATCT
* *
50258 CCATCGCCATCAGTAGCACCTTCA
1 CCATCGCCATCAGTAGCACCATCT
*
50282 CCATCTCCATCA
1 CCATCGCCATCA
50294 ATTCCAGAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
23 2 0.02
24 62 0.58
25 2 0.02
30 39 0.36
31 2 0.02
ACGTcount: A:0.24, C:0.42, G:0.10, T:0.25
Consensus pattern (24 bp):
CCATCGCCATCAGTAGCACCATCT
Found at i:52873 original size:24 final size:24
Alignment explanation
Indices: 52846--52901 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
52836 CCTTCACCAA
*
52846 CGCCATCATATTCACTATCACCGT
1 CGCCATCATATTCACCATCACCGT
** *
52870 CGCCATTGTATTCCCCATCACCGT
1 CGCCATCATATTCACCATCACCGT
*
52894 CACCATCA
1 CGCCATCA
52902 CTGTCGCTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.23, C:0.41, G:0.09, T:0.27
Consensus pattern (24 bp):
CGCCATCATATTCACCATCACCGT
Found at i:56363 original size:2 final size:2
Alignment explanation
Indices: 56358--56391 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
56348 CCCCCACCCC
56358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56392 ACAAAGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61824 original size:21 final size:21
Alignment explanation
Indices: 61798--61844 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
61788 GTTTCCAGAT
61798 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
61819 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
61840 TCGCA
1 TCGCA
61845 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:61849 original size:21 final size:21
Alignment explanation
Indices: 61805--61891 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
61795 GATTCGCAAC
*
61805 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCATT
61826 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCATT
*
61847 GCG-A-TT-TACATATTCGCATT
1 GCGAACTTCGAC-TA-TCGCATT
*
61867 GCG-ACAATCGACTATCGCATT
1 GCGAAC-TTCGACTATCGCATT
61888 GCGA
1 GCGA
61892 TTTACATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 4 0.07
20 12 0.21
21 33 0.59
22 3 0.05
23 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCATT
Found at i:61864 original size:41 final size:41
Alignment explanation
Indices: 61819--61907 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
61809 ACTTCGACTA
*
61819 TCGCAATGCGA-ACTTCGACTATCGCATTGCGATTTACATAT
1 TCGCAATGCGACA-ATCGACTATCGCATTGCGATTTACATAT
*
61860 TCGCATTGCGACAATCGACTATCGCATTGCGATTTACATAT
1 TCGCAATGCGACAATCGACTATCGCATTGCGATTTACATAT
61901 TCGCAAT
1 TCGCAAT
61908 ACCGTCGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 43 0.98
42 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (41 bp):
TCGCAATGCGACAATCGACTATCGCATTGCGATTTACATAT
Found at i:61865 original size:20 final size:20
Alignment explanation
Indices: 61840--61905 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
61830 ACTTCGACTA
61840 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
**
61860 TCGCATTGCGA-CAATCGACTA-
1 TCGCATTGCGATTTA-C-A-TAT
61881 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
61901 TCGCA
1 TCGCA
61906 ATACCGTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
19 3 0.08
20 18 0.49
21 13 0.35
22 3 0.08
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:61938 original size:21 final size:21
Alignment explanation
Indices: 61912--61964 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
61902 CGCAATACCG
*
61912 TCGTTGCGATTTATTCCAAGT
1 TCGTTGCGATATATTCCAAGT
61933 TCGTTGCGATATATTCCAAGT
1 TCGTTGCGATATATTCCAAGT
61954 TCGTTGCGATA
1 TCGTTGCGATA
61965 GTCCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TCGTTGCGATATATTCCAAGT
Found at i:62581 original size:6 final size:6
Alignment explanation
Indices: 62565--62614 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
62555 GTCCGTCTCG
62565 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
62612 GGT
1 GGT
62615 AATACGTGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:65076 original size:23 final size:23
Alignment explanation
Indices: 65050--65098 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
65040 TATATAAACG
* *
65050 AACATCTTCGCTAACATTAAATA
1 AACATCTTCGCGAACAATAAATA
*
65073 AACATGTTCGCGAACAATAAATA
1 AACATCTTCGCGAACAATAAATA
65096 AAC
1 AAC
65099 GAACACGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (23 bp):
AACATCTTCGCGAACAATAAATA
Found at i:69094 original size:10 final size:10
Alignment explanation
Indices: 69075--69161 Score: 75
Period size: 10 Copynumber: 8.1 Consensus size: 10
69065 TTTTTTGTGT
*
69075 TGTTCATTTA
1 TGTTCGTTTA
*
69085 TATTCGTTTA
1 TGTTCGTTTA
69095 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
69108 TGTTCGTTTT
1 TGTTCGTTTA
*
69118 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
69131 TGTTCGTTTG
1 TGTTCGTTTA
69141 TGTTCGTTTA
1 TGTTCGTTTA
69151 TGTTCGTTTA
1 TGTTCGTTTA
69161 T
1 T
69162 CATTTAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
10 44 0.71
11 1 0.02
12 1 0.02
13 16 0.26
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:69112 original size:33 final size:33
Alignment explanation
Indices: 69075--69161 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
69065 TTTTTTGTGT
* * *
69075 TGTTCATTTATATTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATGTTCGTTTATTATGTTCGTTTA
* * *
69108 TGTTCGTTTTTGTTCATTTATTATGTTCGTTTG
1 TGTTCGTTTATGTTCGTTTATTATGTTCGTTTA
69141 TGTTCGTTTATGTTCGTTTAT
1 TGTTCGTTTATGTTCGTTTAT
69162 CATTTAAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.62
Consensus pattern (33 bp):
TGTTCGTTTATGTTCGTTTATTATGTTCGTTTA
Found at i:69124 original size:43 final size:42
Alignment explanation
Indices: 69074--69159 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 42
69064 TTTTTTTGTG
69074 TTGTTCATTTA-TATTCGTT-TATTGTGTTCGTTTATGTTCGTTT
1 TTGTTCATTTATTA-T-GTTCT-TTGTGTTCGTTTATGTTCGTTT
69117 TTGTTCATTTATTATGTTCGTTTGTGTTCGTTTATGTTCGTTT
1 TTGTTCATTTATTATGTTC-TTTGTGTTCGTTTATGTTCGTTT
69160 ATCATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
42 3 0.08
43 34 0.85
44 3 0.08
ACGTcount: A:0.10, C:0.09, G:0.17, T:0.63
Consensus pattern (42 bp):
TTGTTCATTTATTATGTTCTTTGTGTTCGTTTATGTTCGTTT
Found at i:85764 original size:231 final size:230
Alignment explanation
Indices: 85050--85906 Score: 1201
Period size: 232 Copynumber: 3.7 Consensus size: 230
85040 ATCCTCATAA
* * * *
85050 TCATCTCTGTCACCTATATGTATTTTTTTTCAAATCCATAATTCATATAAATTTCAAATGATTTA
1 TCATCCCTGTCACCTATATGTA-TTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTT-
* * *
85115 AAAGCATAAATAAC-CA-ATACTAAAATATTAAGTG---AAAAATCAAAGATTGAGATAAACATA
64 AAAGCATAAATAACTAATATACCAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATA
85175 CCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTATCATC
129 CCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTATCATC
*
85240 TACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
194 CACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
* *
85277 TCATCTCTGTCACCTATATGAATTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTTAA
1 TCATCCCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTTAA
*
85342 AGCATAAATAACTAATAATACCAAAATATTAAGTGAAAAAAAAATCAAAGATTGAGATAAACATA
66 AGCATAAATAACTAAT-ATACCAAAATATTAAGCG-AAAAAAAATCAAAGATTGAGATAAACATA
*
85407 CCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATCGTTATCATC
129 CCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTATCATC
85472 CACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
194 CACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
* * **
85509 TCATCCCTGTCACCTATATGTATTTTTTTCAAACCCGTCATTCACATAAATTTCAAACGATTTAA
1 TCATCCCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTTAA
* *
85574 AGCATAAATAACTAATGATACCAAAATATTAAGCGAAAAAAAATCAAAGAATGCGATAAACATAC
66 AGCATAAATAACTAAT-ATACCAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATAC
* * * * * *
85639 CACGACATGGAGAATCGGGAAAGTGGGAGTCAAATTCATCTTCAATTGGAACTTTGTTATCATCC
130 CACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTATCATCC
* * *
85704 ACAGGAACTGTATCTAGTAGAAAGTTTAATTCATTA
195 ACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
* * * * * *
85740 TCA-CACCCGTCGCCTATGTGTATTTTTTTAAAACTCGA-AA-TCACATAATTTTCAAATAATTT
1 TCATC-CCTGTCACCTATATGTATTTTTTTCAAAC-CCATAATTCACATAAATTTCAAATAATTT
* * * *
85802 AAAGCATAAATAACAAATATGCTAAAATATTAAGCAAAAAAAAAATCAAAGATTGAGATAAACAT
64 AAAGCATAAATAACTAATATACCAAAATATTAAGC-GAAAAAAAATCAAAGATTGAGATAAACAT
* * * *
85867 ACCAGGAAAAA-GAGAATGGGGAAACTGGGAATCAAATTCA
128 ACCA-CAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCA
85907 AAGGGCTGGG
Statistics
Matches: 568, Mismatches: 51, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
225 14 0.02
226 39 0.07
227 21 0.04
228 17 0.03
229 15 0.03
230 93 0.16
231 150 0.26
232 219 0.39
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (230 bp):
TCATCCCTGTCACCTATATGTATTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTTAA
AGCATAAATAACTAATATACCAAAATATTAAGCGAAAAAAAATCAAAGATTGAGATAAACATACC
ACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTGTTATCATCCA
CAGGAACCGTATCTTGTAGAAAGTTTAATTCATTG
Found at i:85846 original size:463 final size:464
Alignment explanation
Indices: 84966--85906 Score: 1251
Period size: 463 Copynumber: 2.0 Consensus size: 464
84956 ACATTAGGTC
* * * *
84966 TCAAATTCATCCTCAGTTGAAACATTGTTATCATCTACAGGAACCGTATCTTGTAGAAGGTTTAA
1 TCAAATTCATCCTCAATTGAAACATCGTTATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAA
* *
85031 TTCAACATCATCCTCATAATCATCTCTGTCACCTATATGTATTTTTTTTCAAATCCATAATTCAT
66 TT--ACAT-ATCCTC--AATCA-CTCTGTCACCTATATGTATTTTTTTTCAAACCCATAATTCAC
* * * *
85096 ATAAATTTCAAATGATTTAAAAGCATAAATAACCAATACTAAAATATTAAGTGAAAAATCAAAGA
125 ATAAATTTCAAACGATTTAAAAGCATAAATAACAAATACCAAAATATTAAGCGAAAAATCAAAGA
*
85161 TTGAGATAAACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGA
190 ATGAGATAAACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGA
* * * * *
85226 ACATTGTTATCATCTACAGGAACCGTATCTTGTAGAAAGTTTAATTCATTGTCATCTCTGTCACC
255 ACATTGTTATCATCCACAGGAACCGTATCTAGTAGAAAGTTTAATTCATTATCATCCCCGTCACC
* *
85291 TATATGAATTTTTTTCAAACCCATAATTCACATAAATTTCAAATAATTTAAAGCATAAATAACTA
320 TATATGAATTTTTTTAAAACCCATAATTCACATAAATTTCAAATAATTTAAAGCATAAATAACAA
*
85356 ATAATACCAAAATATTAAGTGAAAAAAAAATCAAAGATTGAGATAAACATACCA-CAAAAAGGAG
385 ATAATACCAAAATATTAAG-AAAAAAAAAATCAAAGATTGAGATAAACATACCAGCAAAAA-GAG
*
85420 AATCGGGAAACTGAGAG
448 AATCGGGAAACTGAGAA
* *
85437 TCAAATTCATCTTCAATTGGAACATCGTTATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAA
1 TCAAATTCATCCTCAATTGAAACATCGTTATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAA
* * *
85502 TT-CAT-T-GTC-ATC-C-CTGTCACCTATATGTA-TTTTTTTCAAACCCGTCATTCACATAAAT
66 TTACATATCCTCAATCACTCTGTCACCTATATGTATTTTTTTTCAAACCCATAATTCACATAAAT
85560 TTCAAACGATTT-AAAGCATAAATAACTAATGATACCAAAATATTAAGCGAAAAAAAATCAAAGA
131 TTCAAACGATTTAAAAGCATAAATAAC-AA--ATACCAAAATATTAAGCG---AAAAATCAAAGA
* * * * * *
85624 ATGCGATAAACATACCACGACATGGAGAATCGGGAAAGTGGGAGTCAAATTCATCTTCAATTGGA
190 ATGAGATAAACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGA
* * *
85689 ACTTTGTTATCATCCACAGGAACTGTATCTAGTAGAAAGTTTAATTCATTATCA-CACCCGTCGC
255 ACATTGTTATCATCCACAGGAACCGTATCTAGTAGAAAGTTTAATTCATTATCATC-CCCGTCAC
* * * *
85753 CTATGTGTATTTTTTTAAAACTCGA-AA-TCACATAATTTTCAAATAATTTAAAGCATAAATAAC
319 CTATATGAATTTTTTTAAAAC-CCATAATTCACATAAATTTCAAATAATTTAAAGCATAAATAAC
* * *
85816 AAAT-ATGCTAAAATATTAAGCAAAAAAAAAATCAAAGATTGAGATAAACATACCAGGAAAAAGA
383 AAATAATACCAAAATATTAAG-AAAAAAAAAATCAAAGATTGAGATAAACATACCAGCAAAAAGA
* *
85880 GAATGGGGAAACTGGGAA
447 GAATCGGGAAACTGAGAA
85898 TCAAATTCA
1 TCAAATTCA
85907 AAGGGCTGGG
Statistics
Matches: 417, Mismatches: 44, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
457 14 0.03
458 37 0.09
459 16 0.04
460 17 0.04
461 73 0.18
462 47 0.11
463 144 0.35
464 2 0.00
465 2 0.00
466 1 0.00
468 3 0.01
471 61 0.15
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (464 bp):
TCAAATTCATCCTCAATTGAAACATCGTTATCATCCACAGGAACCGTATCTTGTAGAAAGTTTAA
TTACATATCCTCAATCACTCTGTCACCTATATGTATTTTTTTTCAAACCCATAATTCACATAAAT
TTCAAACGATTTAAAAGCATAAATAACAAATACCAAAATATTAAGCGAAAAATCAAAGAATGAGA
TAAACATACCACAAAAAGGAGAATCGGGAAACTGAGAGTCAAATTCATCTTCAATTGGAACATTG
TTATCATCCACAGGAACCGTATCTAGTAGAAAGTTTAATTCATTATCATCCCCGTCACCTATATG
AATTTTTTTAAAACCCATAATTCACATAAATTTCAAATAATTTAAAGCATAAATAACAAATAATA
CCAAAATATTAAGAAAAAAAAAATCAAAGATTGAGATAAACATACCAGCAAAAAGAGAATCGGGA
AACTGAGAA
Found at i:86397 original size:21 final size:21
Alignment explanation
Indices: 86368--86408 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
86358 ATTTACTCTA
*
86368 ATCAAATTAGTCAATTAATAT
1 ATCAAATTAGTCAATCAATAT
* *
86389 ATCACATTAGTTAATCAATA
1 ATCAAATTAGTCAATCAATA
86409 GATAGATCAA
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:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (21 bp):
ATCAAATTAGTCAATCAATAT
Found at i:100218 original size:76 final size:76
Alignment explanation
Indices: 100087--100244 Score: 282
Period size: 76 Copynumber: 2.1 Consensus size: 76
100077 GGCTAAGGCC
* *
100087 CTACCTGCCCCATTTAGATTCCCCCTTCGAGCTCATACCCATTTTGATTTAGTAAACAATGATGC
1 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATG-
100152 A-ATTTTGTCAT
65 ATATTTTGTCAT
100163 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
1 CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
100228 TATTTTGTCAT
66 TATTTTGTCAT
100239 CTACTT
1 CTACTT
100245 CTATGATTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
75 1 0.01
76 78 0.99
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.37
Consensus pattern (76 bp):
CTACTTGCCCCATTTAGATTCCCCCTTAGAGCTCATACCCATTTTGATTTAGTAAACAATGATGA
TATTTTGTCAT
Found at i:100343 original size:12 final size:12
Alignment explanation
Indices: 100328--100352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
100318 ATATTTTTGA
100328 TAAAATATTATT
1 TAAAATATTATT
100340 TAAAATATTATT
1 TAAAATATTATT
100352 T
1 T
100353 TTTACTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:101278 original size:18 final size:18
Alignment explanation
Indices: 101236--101295 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 18
101226 TTAAGGTATA
*
101236 AAACATTACTTTTTCAAAAT
1 AAACATTAC-TTTT-AAAGT
101256 AAACATTACTTTTAAAGT
1 AAACATTACTTTTAAAGT
*
101274 AAACATTACTTTTAAGGT
1 AAACATTACTTTTAAAGT
101292 AAAC
1 AAAC
101296 GTAAGTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 25 0.66
19 4 0.11
20 9 0.24
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (18 bp):
AAACATTACTTTTAAAGT
Found at i:102051 original size:31 final size:31
Alignment explanation
Indices: 102016--102112 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
102006 AGTAATGAAT
* *
102016 TTTGATAAGTTTAAGGACCATTTTTTAATAA
1 TTTGATAAGTTTAAAGACCATTTTATAATAA
* ** * *
102047 TTTGATAAGCTTAAAGATAATTTTCTAACAA
1 TTTGATAAGTTTAAAGACCATTTTATAATAA
* * * *
102078 TTTAATAAATGTTAATGACCATTTTATAATCA
1 TTTGATAAGT-TTAAAGACCATTTTATAATAA
102110 TTT
1 TTT
102113 AAAAAATTAA
Statistics
Matches: 50, Mismatches: 15, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
31 32 0.64
32 18 0.36
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (31 bp):
TTTGATAAGTTTAAAGACCATTTTATAATAA
Found at i:102494 original size:109 final size:109
Alignment explanation
Indices: 102371--102591 Score: 424
Period size: 109 Copynumber: 2.0 Consensus size: 109
102361 GTCCTTAGTG
*
102371 ATTTTATAATTTATGAGGACTCAGTCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCT
1 ATTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCT
*
102436 TTTTCGATATAAGATTAATGTCGTATACCTCTCCAAGACGTGAC
66 TTTTCGATATAAGATTAATGTCATATACCTCTCCAAGACGTGAC
102480 ATTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCT
1 ATTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCT
102545 TTTTCGATATAAGATTAATGTCATATACCTCTCCAAGACGTGAC
66 TTTTCGATATAAGATTAATGTCATATACCTCTCCAAGACGTGAC
102589 ATT
1 ATT
102592 CACCACTATA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (109 bp):
ATTTTATAATTTATGAGGACTCAATCAATATGTGTATAGTTATCATTTTCAAATTTTAGAATTCT
TTTTCGATATAAGATTAATGTCATATACCTCTCCAAGACGTGAC
Found at i:105685 original size:20 final size:20
Alignment explanation
Indices: 105591--105959 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
105581 GATTTTCCAT
* ** *
105591 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
105611 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
105631 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105651 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
105671 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
105691 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105711 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
105731 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105751 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
105771 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105791 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
105811 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105831 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
105851 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
105871 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
105891 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
105911 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
105931 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
105951 AATCACAAC
1 AATCGCAAC
105960 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:106681 original size:24 final size:24
Alignment explanation
Indices: 106642--106688 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
106632 AAATTTGGTC
106642 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
106666 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
106689 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:106880 original size:12 final size:12
Alignment explanation
Indices: 106863--106887 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
106853 ATATAATCCT
106863 GAAGAAGAAAAA
1 GAAGAAGAAAAA
106875 GAAGAAGAAAAA
1 GAAGAAGAAAAA
106887 G
1 G
106888 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:109185 original size:19 final size:19
Alignment explanation
Indices: 109163--109455 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
109153 CGGAAAATAC
*
109163 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
109182 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
109196 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
109216 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
109230 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109249 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
109268 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
109282 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
109301 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109320 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109339 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109358 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109377 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109396 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
109410 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109429 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109448 AATCGCAA
1 AATCGCAA
109456 CGAGATAATC
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 165 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:109278 original size:52 final size:55
Alignment explanation
Indices: 109191--109477 Score: 356
Period size: 52 Copynumber: 5.4 Consensus size: 55
109181 AAATCCCAAC
*
109191 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
109244 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
109296 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
109353 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
109408 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
109458 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
109478 TATAAACGCA
Statistics
Matches: 222, Mismatches: 2, Indels: 21
0.91 0.01 0.09
Matches are distributed among these distances:
50 2 0.01
52 127 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 64 0.29
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:109374 original size:128 final size:128
Alignment explanation
Indices: 109163--109477 Score: 462
Period size: 128 Copynumber: 2.6 Consensus size: 128
109153 CGGAAAATAC
* *
109163 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
109223 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
109282 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
109347 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
109410 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
109470 TGCGAAAT
66 TGCGAAAT
109478 TATAAACGCA
Statistics
Matches: 179, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
119 24 0.13
121 1 0.01
123 34 0.19
124 17 0.09
125 2 0.01
126 2 0.01
127 1 0.01
128 98 0.55
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:109593 original size:19 final size:19
Alignment explanation
Indices: 109484--109585 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
109474 AAATTATAAA
109484 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
109503 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
109523 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
109539 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
109556 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
109575 CGCATTGCGAT
1 CGCATTGCGAT
109586 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:109709 original size:14 final size:14
Alignment explanation
Indices: 109690--109726 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
109680 CATCAATTAC
109690 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
109704 ACAAATCATCTTTT
1 ACAAATCAACTTTT
109718 ACAAATCAA
1 ACAAATCAA
109727 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:111700 original size:14 final size:14
Alignment explanation
Indices: 111681--111737 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
111671 GCGAAATGAA
*
111681 AATCGCAACGACAG
1 AATCGCAACGAAAG
111695 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
111712 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
111728 AATCGCAACG
1 AATCGCAACG
111738 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:111708 original size:33 final size:33
Alignment explanation
Indices: 111662--111754 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
111652 GCGAAACCAA
*
111662 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
111695 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
111728 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
111755 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:111719 original size:19 final size:19
Alignment explanation
Indices: 111625--111759 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
111615 TAGTTTACTT
* *
111625 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
111645 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
111664 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
111683 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
111697 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
111716 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
111730 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
111749 TCGCAATGCGA
1 TCGCAACGCGA
111760 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:111777 original size:19 final size:19
Alignment explanation
Indices: 111755--111883 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
111745 AAAATCGCAA
111755 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
111774 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
111788 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
111807 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
111821 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
111840 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
111859 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
111879 TGCGA
1 TGCGA
111884 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:111797 original size:33 final size:33
Alignment explanation
Indices: 111755--111846 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
111745 AAAATCGCAA
111755 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
111788 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
111821 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
111847 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:112218 original size:93 final size:93
Alignment explanation
Indices: 111927--112397 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
111917 TTGAATGGAT
111927 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
111992 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
112020 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
112084 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
112112 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
112177 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
112205 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
112269 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
112297 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
112361 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
112389 AAATTTACT
1 AAATTTACT
112398 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 35 0.09
92 201 0.54
93 136 0.37
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:112239 original size:185 final size:185
Alignment explanation
Indices: 111927--112397 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
111917 TTGAATGGAT
111927 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
111992 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
112057 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
112112 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
112177 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
112242 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
112297 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
112361 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
112398 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 97 0.34
185 187 0.66
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:114140 original size:19 final size:19
Alignment explanation
Indices: 114116--114199 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
114106 ACAACGAGAG
* *
114116 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
114135 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
114154 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
114168 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
114187 AATCGCAATGCGA
1 AATCGCAACGCGA
114200 TTTGGTTTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:114156 original size:52 final size:52
Alignment explanation
Indices: 114094--114199 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
114084 TCTTTTGGTT
* *
114094 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
* *
114146 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
114198 GA
1 GA
114200 TTTGGTTTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:114229 original size:14 final size:14
Alignment explanation
Indices: 114210--114264 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
114200 TTTGGTTTCG
114210 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
114224 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
114243 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
114257 CGTTGCGA
1 CGTTGCGA
114265 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:114272 original size:33 final size:33
Alignment explanation
Indices: 114205--114286 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
114195 TGCGATTTGG
***
114205 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
114238 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
114271 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
114287 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:114291 original size:20 final size:20
Alignment explanation
Indices: 114217--114305 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
114207 TCGCGTTGCG
114217 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
114237 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
114250 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
114270 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
114290 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
114306 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:114426 original size:33 final size:33
Alignment explanation
Indices: 114384--114454 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
114374 AATACTAACT
*
114384 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
114417 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
114450 TGAAA
1 TGAAA
114455 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:114688 original size:22 final size:22
Alignment explanation
Indices: 114636--114690 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
114626 TGGTTGTGAG
**
114636 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
114658 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
114680 GGATTTCTTCG
1 GGATTTCTTCG
114691 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:114861 original size:20 final size:20
Alignment explanation
Indices: 114836--115028 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
114826 CTTTAAATAT
114836 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
114856 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
114878 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
114897 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
114917 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
114937 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
114957 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
114977 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
114997 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
115017 CGCGTTGCGATT
1 CGCGTTGCGATT
115029 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:115023 original size:60 final size:60
Alignment explanation
Indices: 114836--115028 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
114826 CTTTAAATAT
**
114836 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
114897 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
114957 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
115017 CGCGTTGCGATT
1 CGCGTTGCGATT
115029 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:115109 original size:20 final size:20
Alignment explanation
Indices: 115084--115135 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
115074 AAGAATCGCG
*
115084 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
115104 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
115124 TTGCGATTCTGG
1 TTGCGATTCTGG
115136 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:117744 original size:35 final size:39
Alignment explanation
Indices: 117674--117762 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 39
117664 TTTTTACCCT
117674 AAACCCGACCCGACCCGACCCGAACAGTGCATTTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACAGT-CATTTTTAAAA
**
117714 AAACCCGACCCGACCCGACCCG-A-A-TTTTTTTTAAAA
1 AAACCCGACCCGACCCGACCCGAACAGTCATTTTTAAAA
*
117750 AAATCCGACCCGA
1 AAACCCGACCCGA
117763 TCGGGTCGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 21 0.46
37 1 0.02
38 1 0.02
39 1 0.02
40 22 0.48
ACGTcount: A:0.35, C:0.35, G:0.13, T:0.17
Consensus pattern (39 bp):
AAACCCGACCCGACCCGACCCGAACAGTCATTTTTAAAA
Found at i:117891 original size:33 final size:31
Alignment explanation
Indices: 117843--117905 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
117833 GTTTGAACAT
117843 TTTATATTTATTAATG-TGATATAATGTTCTA
1 TTTATATTTATTAATGCTGAT-TAATGTTCTA
*
117874 TTTATATTAATATTAATGCTGATTAATTTTCT
1 TTTATATT--TATTAATGCTGATTAATGTTCT
117906 CTCATTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 8 0.29
33 16 0.57
34 4 0.14
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.56
Consensus pattern (31 bp):
TTTATATTTATTAATGCTGATTAATGTTCTA
Found at i:118081 original size:23 final size:22
Alignment explanation
Indices: 118055--118126 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
118045 TATGGAACAT
118055 TTTTCTCT-TCTTGTATGACACA
1 TTTTCTCTGTCTT-TATGACACA
118077 CTTTTCTCTGTCTTTATGACACA
1 -TTTTCTCTGTCTTTATGACACA
* *
118100 TTTTCTTCTGCCTTT-TGGCACA
1 TTTTC-TCTGTCTTTATGACACA
118122 TTTTC
1 TTTTC
118127 GGTCGTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
22 16 0.36
23 25 0.56
24 4 0.09
ACGTcount: A:0.14, C:0.25, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTTCTCTGTCTTTATGACACA
Found at i:119602 original size:2 final size:2
Alignment explanation
Indices: 119595--119647 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
119585 TTGTTTGTAT
* *
119595 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119632 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
119648 ATCGGGGCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:123132 original size:2 final size:2
Alignment explanation
Indices: 123125--123160 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
123115 AAACAAACTA
123125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123161 TAGAATCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129018 original size:88 final size:88
Alignment explanation
Indices: 128869--129044 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
128859 TGTCCGATTA
128869 TGTGGAAGTAAACTTCGGTGGTGTCGTTGCAGTCATTGCATAGGATCCAAACCTGCATTTCAATG
1 TGTGGAAGTAAACTTCGGTGGTGTCGTTGCAGTCATTGCATAGGATCCAAACCTGCATTTCAATG
128934 ATCAAATCAACTCGATATTCGAG
66 ATCAAATCAACTCGATATTCGAG
128957 TGTGGAAGTAAACTTCGGTGGTGTCGTTGCAGTCATTGCATAGGATCCAAACCTGCATTTCAATG
1 TGTGGAAGTAAACTTCGGTGGTGTCGTTGCAGTCATTGCATAGGATCCAAACCTGCATTTCAATG
129022 ATCAAATCAACTCGATATTCGAG
66 ATCAAATCAACTCGATATTCGAG
129045 AATAGAACAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (88 bp):
TGTGGAAGTAAACTTCGGTGGTGTCGTTGCAGTCATTGCATAGGATCCAAACCTGCATTTCAATG
ATCAAATCAACTCGATATTCGAG
Found at i:130728 original size:2 final size:2
Alignment explanation
Indices: 130723--130753 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
130713 GGGGAATCCA
130723 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
130754 AATACCACAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:146770 original size:45 final size:45
Alignment explanation
Indices: 146677--146767 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
146667 AAGATAATTT
* * ** * *
146677 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGA
146722 AATATATATATAATAATAATA-AAATAT-AGTAAAAAATCAAATGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAA-GA
146766 AA
1 AA
146768 ATAATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 12 0.31
44 8 0.21
45 19 0.49
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (45 bp):
AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGA
Found at i:146810 original size:17 final size:17
Alignment explanation
Indices: 146790--146831 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
146780 ATATATACAT
*
146790 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
146807 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
146824 ATAA-AATA
1 ATAATAATA
146832 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:148162 original size:105 final size:105
Alignment explanation
Indices: 147985--148602 Score: 964
Period size: 105 Copynumber: 6.0 Consensus size: 105
147975 CATTGTTCAG
* * **
147985 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
148045 AGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
** ** *
148085 AGAACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
148150 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
148190 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
148255 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
* * *
148295 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
148357 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
* * *
148397 AGTCTAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
148462 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
* *
148502 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
148567 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
148603 CCTCGAGTGC
Statistics
Matches: 480, Mismatches: 29, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 33 0.07
101 1 0.00
102 101 0.21
103 2 0.00
104 2 0.00
105 299 0.62
106 42 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
Found at i:148391 original size:312 final size:311
Alignment explanation
Indices: 147985--148641 Score: 998
Period size: 312 Copynumber: 2.1 Consensus size: 311
147975 CATTGTTCAG
* *
147985 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGG
1 AGTCCAATATCCTCCATCGTGAAGTTGAAATTGAATCTGAATGAAATGTTGTTGACAAGCAGCGG
* * *
148050 TCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTGGAGAAC-AATATCCTTCGTTGTGAAGTTGAA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAG-ACTAATATCCTTCATTGTGAAGTTGAA
** *
148114 ATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
130 ATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
148179 GCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-
195 GCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGT
* *
148243 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
260 TTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
* * ** *
148295 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-GTTGTTGACAGGCAG
1 AGTCCAATATCCTCCATCGTGAAGTTGAAATTGAATCTG-AA-TGA-AATGTTGTTGACAAGCAG
*
148359 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCTAATATCCTTCATTGTGAAGTTG
63 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGACTAATATCCTTCATTGTGAAGTTG
*
148424 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
128 AAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
148489 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTT
193 TTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTT
* * *
148554 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG-
258 GTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GA
* *
148608 AGTGCCACGATATCCTCCTTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCATCGTGAAGTTGAAAT
148642 CGCAGATGGC
Statistics
Matches: 312, Mismatches: 26, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
310 34 0.11
311 3 0.01
312 200 0.64
313 50 0.16
314 4 0.01
316 21 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (311 bp):
AGTCCAATATCCTCCATCGTGAAGTTGAAATTGAATCTGAATGAAATGTTGTTGACAAGCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGACTAATATCCTTCATTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTT
TGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
Found at i:148435 original size:207 final size:208
Alignment explanation
Indices: 147985--148602 Score: 951
Period size: 207 Copynumber: 3.0 Consensus size: 208
147975 CATTGTTCAG
* * **
147985 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* **
148045 AGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTGGAGAACAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
** *
148110 TGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
148175 ACTTGCGTTGTCTGA
194 ACTTGCGTTGTCTGA
148190 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
148255 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
148320 TGAAATTGGTTCTGAAATTGAGAA-GTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 TGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
148384 TTGCGTTGTCTGA
196 TTGCGTTGTCTGA
* * *
148397 AGTCTAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
148462 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
148527 TGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGAGAA--TG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
148592 AACTTGTGTTG
193 AACTTGCGTTG
148603 CCTCGAGTGC
Statistics
Matches: 378, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
205 35 0.09
206 2 0.01
207 202 0.53
208 2 0.01
209 2 0.01
210 93 0.25
211 42 0.11
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (208 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGA
Found at i:149380 original size:67 final size:66
Alignment explanation
Indices: 149245--149402 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 66
149235 AAGATATCTG
* * **
149245 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
149310 TT
65 TT
* * *
149312 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAA-TGTGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
149375 GTT
64 ATT
*
149378 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
149403 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 24 0.30
68 28 0.35
69 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:149429 original size:36 final size:36
Alignment explanation
Indices: 149378--149501 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
149368 TTCAAAGGTT
* *
149378 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
*
149414 TTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
* * *
149449 CTTAGTTCCAAGAGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
* *
149487 TTATTTCAAGGGAAA
1 TTGTTTCAAGAGAAA
149502 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 40 0.53
37 28 0.37
38 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAAA
Found at i:150493 original size:22 final size:22
Alignment explanation
Indices: 150468--150511 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
150458 CATTTTTGTT
150468 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
150490 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
150512 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:152344 original size:8 final size:8
Alignment explanation
Indices: 152328--152366 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
152318 ATTGTAGATG
152328 AAAATGCA
1 AAAATGCA
*
152336 AAAAGGCA
1 AAAATGCA
152344 AAAATGC-
1 AAAATGCA
152351 AAAATGCA
1 AAAATGCA
*
152359 AGAATGCA
1 AAAATGCA
152367 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:152354 original size:15 final size:15
Alignment explanation
Indices: 152328--152366 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
152318 ATTGTAGATG
152328 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
152344 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
152359 AGAATGCA
1 AAAATGCA
152367 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:155214 original size:18 final size:19
Alignment explanation
Indices: 155193--155237 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
155183 AATAATAATG
155193 AATAAAAAA-AATGA-AAAT
1 AATAAAAAATAAT-ATAAAT
155211 AATAAAAAATAATATAAAT
1 AATAAAAAATAATATAAAT
155230 ATATAAAA
1 A-ATAAAA
155238 TTATAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.42
19 8 0.33
20 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAAAATAATATAAAT
Found at i:155242 original size:10 final size:10
Alignment explanation
Indices: 155175--155238 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
155165 TTAAAAAAAT
155175 AATAATATAA
1 AATAATATAA
155185 TAATAATGAATAA
1 -AATAAT--ATAA
*
155198 AA-AAAATGAA
1 AATAATAT-AA
*
155208 AATAATAAAA
1 AATAATATAA
155218 AATAATAT-A
1 AATAATATAA
155227 AAT-ATATAA
1 AATAATATAA
155236 AAT
1 AAT
155239 TATAAGATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 4 0.09
9 10 0.23
10 13 0.30
11 11 0.25
12 2 0.05
13 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
AATAATATAA
Found at i:155460 original size:45 final size:45
Alignment explanation
Indices: 155367--155457 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
155357 AAGATAATTT
* * ** * *
155367 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGA
155412 AATATATATATAATAATAATA-AAATAT-AGTAAAAAATCAAATGA
1 AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAA-GA
155456 AA
1 AA
155458 ATAATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 12 0.31
44 8 0.21
45 19 0.49
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (45 bp):
AATATATATATAATAATAATAGAAATATAAGTAAAAAATCAAAGA
Found at i:155505 original size:18 final size:17
Alignment explanation
Indices: 155482--155524 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
155472 ATATATACAT
155482 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
155500 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
155517 ATAA-AATA
1 ATAATAATA
155525 TTCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:157303 original size:35 final size:33
Alignment explanation
Indices: 157228--157305 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 33
157218 TGGGTTGGGT
* * *
157228 ATGTAATTAAAGTATTTGGAGTTTGCGTTTAGA
1 ATGTAATTGAAGTATTTAGAATTTGCGTTTAGA
* *
157261 ATATAATTGAAGTATTTTAGAATTTAGGGTTTAGA
1 ATGTAATTGAAGTA-TTTAGAATTT-GCGTTTAGA
157296 ATGTAATTGA
1 ATGTAATTGA
157306 TAGTTGTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 12 0.32
34 8 0.22
35 17 0.46
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (33 bp):
ATGTAATTGAAGTATTTAGAATTTGCGTTTAGA
Found at i:157934 original size:2 final size:2
Alignment explanation
Indices: 157929--157960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
157919 TTGCAGATTT
157929 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
157961 AGAGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:158498 original size:39 final size:39
Alignment explanation
Indices: 158449--158548 Score: 155
Period size: 39 Copynumber: 2.6 Consensus size: 39
158439 GTAGTCTAAA
*
158449 GAAAGAAATAAGGGGTTTTGCTCCCCTTTATAATATGAG
1 GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
* * *
158488 GAAAAAAATAAGGGGTTTTGCTCTCTTTTACAATATGAG
1 GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
*
158527 GAAAGGAATAAGGGGTTTTGCT
1 GAAAGAAATAAGGGGTTTTGCT
158549 AAATATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (39 bp):
GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
Found at i:158858 original size:39 final size:39
Alignment explanation
Indices: 158799--158898 Score: 155
Period size: 39 Copynumber: 2.6 Consensus size: 39
158789 GTAGTCTAAA
*
158799 GAAAGAAATAAGGGGTTTTGCTCCCCTTTATAATATGAG
1 GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
* * *
158838 GAAAAAAATAAGGGGTTTTGCTCTCTTTTACAATATGAG
1 GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
*
158877 GAAAGGAATAAGGGGTTTTGCT
1 GAAAGAAATAAGGGGTTTTGCT
158899 AAATATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (39 bp):
GAAAGAAATAAGGGGTTTTGCTCCCCTTTACAATATGAG
Found at i:160249 original size:398 final size:398
Alignment explanation
Indices: 159513--160310 Score: 1587
Period size: 398 Copynumber: 2.0 Consensus size: 398
159503 AAGTGGGGAA
159513 CTCTGGTTTTGCTGTTGCTTTCCTCGTCTGCTTTGATCGTATCTTCAACGTTATATATATGTATC
1 CTCTGGTTTTGCTGTTGCTTTCCTCGTCTGCTTTGATCGTATCTTCAACGTTATATATATGTATC
159578 AAAGGGCGTGCAGATGATGGTGGAATCAATCTCTAAGCTGATGTTGAGCTTTCATGATACTCGTG
66 AAAGGGCGTGCAGATGATGGTGGAATCAATCTCTAAGCTGATGTTGAGCTTTCATGATACTCGTG
159643 TAGATAATTTTTTCTTTGTTTTGAACCTTCGTTTCAGAGTTGAGACATGCAGAAGGGTGTTCCAT
131 TAGATAATTTTTTCTTTGTTTTGAACCTTCGTTTCAGAGTTGAGACATGCAGAAGGGTGTTCCAT
159708 TAATTCCACACAAAAACCAAGTCGCTTTTGCATATCCCGCTTCCGTCCCTTTGAAACCCTTTGTT
196 TAATTCCACACAAAAACCAAGTCGCTTTTGCATATCCCGCTTCCGTCCCTTTGAAACCCTTTGTT
*
159773 GCATATCTTACAAATAAAACAAGCTAGTAGCGTACCTGGTTGATACATTTTGTCAATATCACCGC
261 GCATATCGTACAAATAAAACAAGCTAGTAGCGTACCTGGTTGATACATTTTGTCAATATCACCGC
159838 CTCGATTCTGAGGGCTTTCTTGACAGCTTTCCGCCAATATAATAAAACCCTACGACCTCTTCATC
326 CTCGATTCTGAGGGCTTTCTTGACAGCTTTCCGCCAATATAATAAAACCCTACGACCTCTTCATC
159903 ATCTGTAT
391 ATCTGTAT
159911 CTCTGGTTTTGCTGTTGCTTTCCTCGTCTGCTTTGATCGTATCTTCAACGTTATATATATGTATC
1 CTCTGGTTTTGCTGTTGCTTTCCTCGTCTGCTTTGATCGTATCTTCAACGTTATATATATGTATC
159976 AAAGGGCGTGCAGATGATGGTGGAATCAATCTCTAAGCTGATGTTGAGCTTTCATGATACTCGTG
66 AAAGGGCGTGCAGATGATGGTGGAATCAATCTCTAAGCTGATGTTGAGCTTTCATGATACTCGTG
160041 TAGATAATTTTTTCTTTGTTTTGAACCTTCGTTTCAGAGTTGAGACATGCAGAAGGGTGTTCCAT
131 TAGATAATTTTTTCTTTGTTTTGAACCTTCGTTTCAGAGTTGAGACATGCAGAAGGGTGTTCCAT
160106 TAATTCCACACAAAAACCAAGTCGCTTTTGCATATCCCGCTTCCGTCCCTTTGAAACCCTTTGTT
196 TAATTCCACACAAAAACCAAGTCGCTTTTGCATATCCCGCTTCCGTCCCTTTGAAACCCTTTGTT
160171 GCATATCGTACAAATAAAACAAGCTAGTAGCGTACCTGGTTGATACATTTTGTCAATATCACCGC
261 GCATATCGTACAAATAAAACAAGCTAGTAGCGTACCTGGTTGATACATTTTGTCAATATCACCGC
160236 CTCGATTCTGAGGGCTTTCTTGACAGCTTTCCGCCAATATAATAAAACCCTACGACCTCTTCATC
326 CTCGATTCTGAGGGCTTTCTTGACAGCTTTCCGCCAATATAATAAAACCCTACGACCTCTTCATC
160301 ATCTGTAT
391 ATCTGTAT
160309 CT
1 CT
160311 TTTGGATGGA
Statistics
Matches: 399, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
398 399 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (398 bp):
CTCTGGTTTTGCTGTTGCTTTCCTCGTCTGCTTTGATCGTATCTTCAACGTTATATATATGTATC
AAAGGGCGTGCAGATGATGGTGGAATCAATCTCTAAGCTGATGTTGAGCTTTCATGATACTCGTG
TAGATAATTTTTTCTTTGTTTTGAACCTTCGTTTCAGAGTTGAGACATGCAGAAGGGTGTTCCAT
TAATTCCACACAAAAACCAAGTCGCTTTTGCATATCCCGCTTCCGTCCCTTTGAAACCCTTTGTT
GCATATCGTACAAATAAAACAAGCTAGTAGCGTACCTGGTTGATACATTTTGTCAATATCACCGC
CTCGATTCTGAGGGCTTTCTTGACAGCTTTCCGCCAATATAATAAAACCCTACGACCTCTTCATC
ATCTGTAT
Found at i:163566 original size:18 final size:19
Alignment explanation
Indices: 163543--163579 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
163533 TCAGTAATCC
163543 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
163561 TATTCCTACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
163580 ACATTCCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:163585 original size:20 final size:20
Alignment explanation
Indices: 163549--163587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
163539 ATCCTATTCC
**
163549 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
163569 CTGGTAATCTTACATTCCT
1 CTGGTAATCTTACATTCCT
163588 TGAACCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:175077 original size:31 final size:31
Alignment explanation
Indices: 175035--175119 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
175025 TTAAATAATG
*
175035 ATAA-ATTTTGATAAGTTTAATGATT-ATTTT
1 ATAATATTTTGATAAATTTAATGATTCA-TTT
*
175065 ATAATATTTTGATAATTTTAATG-TTCATTT
1 ATAATATTTTGATAAATTTAATGATTCATTT
* *
175095 ATACTAATTTGATAGAATTTAATGA
1 ATAATATTTTGATA-AATTTAATGA
175120 CGATTTTGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (31 bp):
ATAATATTTTGATAAATTTAATGATTCATTT
Done.