Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013976.1 Kokia drynarioides strain JFW-HI SEQ_129007, 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: 219783
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:2685 original size:68 final size:68
Alignment explanation
Indices: 2574--2721 Score: 228
Period size: 68 Copynumber: 2.2 Consensus size: 68
2564 ATGGTACTGG
* * *
2574 GTTAAACCACCCGAGATCCAACCCGGCATAGCGAAACCTTTAACTCAAC-CTGTAAGGGCCAAGT
1 GTTAAACCACCCGAGATACAACCCGGCATAGCCAAACCCTTAACTCAACTC-GTAAGGGCCAAGT
2638 -TAGA
65 CT-GA
*
2642 GTTAAACCACCCGAGATACAACTCGGCATAGCCAAACCCTTAACTCAACTCGTAAGGGCCAAGTC
1 GTTAAACCACCCGAGATACAACCCGGCATAGCCAAACCCTTAACTCAACTCGTAAGGGCCAAGTC
2707 TGA
66 TGA
2710 GTTAAACCACCC
1 GTTAAACCACCC
2722 AAGAATCGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
68 72 0.97
69 2 0.03
ACGTcount: A:0.34, C:0.31, G:0.18, T:0.18
Consensus pattern (68 bp):
GTTAAACCACCCGAGATACAACCCGGCATAGCCAAACCCTTAACTCAACTCGTAAGGGCCAAGTC
TGA
Found at i:5110 original size:19 final size:20
Alignment explanation
Indices: 5064--5111 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5054 ATTGTTTTGT
*
5064 TGTTGTT-TTCTCACTATTT
1 TGTTGTTATTCTCACTATTA
* *
5083 TGCTATTATT-TCACTATTA
1 TGTTGTTATTCTCACTATTA
5102 TGTTGTTATT
1 TGTTGTTATT
5112 GTTTGGATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (20 bp):
TGTTGTTATTCTCACTATTA
Found at i:5232 original size:10 final size:10
Alignment explanation
Indices: 5217--5241 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5207 AATATACGTA
5217 TTTTTTTAAT
1 TTTTTTTAAT
5227 TTTTTTTAAT
1 TTTTTTTAAT
5237 TTTTT
1 TTTTT
5242 GAGAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:7117 original size:49 final size:49
Alignment explanation
Indices: 7042--7139 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
7032 CATGCAAACT
*
7042 TATTAACTGCTAATTAATGCGTACAATGGAGTGCGTTGCTGTAAATTAG
1 TATTAACTGCTAATTAATGCGCACAATGGAGTGCGTTGCTGTAAATTAG
* *
7091 TATTAACTGCTAATTAATGCGCACAATGGAGTGCTTTTCTGTAAATTAG
1 TATTAACTGCTAATTAATGCGCACAATGGAGTGCGTTGCTGTAAATTAG
7140 AAGGCAGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (49 bp):
TATTAACTGCTAATTAATGCGCACAATGGAGTGCGTTGCTGTAAATTAG
Found at i:14887 original size:14 final size:15
Alignment explanation
Indices: 14868--14897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14858 TTTTAGAGTG
14868 TGGA-TTAGGGTTTT
1 TGGATTTAGGGTTTT
14882 TGGATTTAGGGTTTT
1 TGGATTTAGGGTTTT
14897 T
1 T
14898 AATTGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
TGGATTTAGGGTTTT
Found at i:20827 original size:87 final size:87
Alignment explanation
Indices: 20681--20853 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 87
20671 CGCACTACAT
* *
20681 CTAAAGGGTGTTGCTTAAAGGAAAGTTTATCATTTGCTCCTTCAAAGGTTCGAATTCAGATAGGT
1 CTAAAGGGTGTTGCTTAAAAGAAAGTTTATCATTTGCTCCTTCAAAGGTTCGAACTCAGATAGGT
20746 TCTATGGATGAACAACCCTTAG
66 TCTATGGATGAACAACCCTTAG
*
20768 CTAAAGGGTGTTGCTTAAAAGAAGGTTTATCATTTGCTCCTTCAAAGGTTCGAACTCAGATAGGT
1 CTAAAGGGTGTTGCTTAAAAGAAAGTTTATCATTTGCTCCTTCAAAGGTTCGAACTCAGATAGGT
20833 TCTATGGATGAACAACCCTTA
66 TCTATGGATGAACAACCCTTA
20854 ACTAGACCTG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (87 bp):
CTAAAGGGTGTTGCTTAAAAGAAAGTTTATCATTTGCTCCTTCAAAGGTTCGAACTCAGATAGGT
TCTATGGATGAACAACCCTTAG
Found at i:28036 original size:29 final size:29
Alignment explanation
Indices: 27979--28036 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
27969 TATTTTATAC
* * *
27979 ATTTCTCTAATAAATTAATTTCATATATT
1 ATTTCTCAAATAAATAAATTTAATATATT
28008 ATTTCTCAAATAAATAAATTTTAAT-TATT
1 ATTTCTCAAATAAATAAA-TTTAATATATT
28037 TTAACAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTCTCAAATAAATAAATTTAATATATT
Found at i:39967 original size:4 final size:4
Alignment explanation
Indices: 39958--40006 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
39948 GCTAGAAGAG
39958 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
40006 G
1 G
40007 ATGGTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:40910 original size:2 final size:2
Alignment explanation
Indices: 40903--40927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40893 TTCCATTGAC
40903 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40928 ACTAGGACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45033 original size:18 final size:18
Alignment explanation
Indices: 45010--45044 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45000 CCGATATCTC
*
45010 TATCATATCTATCTAAAA
1 TATCATATCTATATAAAA
*
45028 TATCATGTCTATATAAA
1 TATCATATCTATATAAA
45045 TATAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (18 bp):
TATCATATCTATATAAAA
Found at i:48413 original size:20 final size:21
Alignment explanation
Indices: 48388--48433 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48378 CCAAACAATA
*
48388 TTAAAAAATTTA-TAAAAATT
1 TTAAAAAATATATTAAAAATT
*
48408 TTAAAATATATATTAAAAATT
1 TTAAAAAATATATTAAAAATT
*
48429 ATAAA
1 TTAAA
48434 TCATTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAAAAATATATTAAAAATT
Found at i:55040 original size:21 final size:21
Alignment explanation
Indices: 54998--55041 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54988 TTGCGGTTAA
* *
54998 AAATATTAACATTTATTATTT
1 AAATAATAACATTTACTATTT
* *
55019 AAATAATATCATTTACTGTTT
1 AAATAATAACATTTACTATTT
55040 AA
1 AA
55042 TAGAGTTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATAATAACATTTACTATTT
Found at i:55883 original size:19 final size:19
Alignment explanation
Indices: 55855--55892 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55845 GTTAAGAATG
* *
55855 TATTTTTATATTTTAATAA
1 TATTTATATATATTAATAA
55874 TATTTATATATATTAATAA
1 TATTTATATATATTAATAA
55893 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATATATATTAATAA
Found at i:57128 original size:20 final size:21
Alignment explanation
Indices: 57089--57128 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57079 AATATGTATG
* *
57089 GGTTTTGTTCGGATTCTTTTC
1 GGTTTTGTTCAGAATCTTTTC
57110 GGTTTTGTT-AGAATCTTTT
1 GGTTTTGTTCAGAATCTTTT
57129 TTATTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (21 bp):
GGTTTTGTTCAGAATCTTTTC
Found at i:64157 original size:24 final size:25
Alignment explanation
Indices: 64129--64203 Score: 102
Period size: 24 Copynumber: 3.1 Consensus size: 25
64119 AGAAATAATC
*
64129 TTTCAGTTAAACTCTGTTTAATTT-
1 TTTCAATTAAACTCTGTTTAATTTG
*
64153 TTTCAATTAAACTCTATTT-ATTTG
1 TTTCAATTAAACTCTGTTTAATTTG
*
64177 TTTTAATTAAACTCTGTTT-ATTTG
1 TTTCAATTAAACTCTGTTTAATTTG
64201 TTT
1 TTT
64204 GAGTCGAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (25 bp):
TTTCAATTAAACTCTGTTTAATTTG
Found at i:64213 original size:24 final size:24
Alignment explanation
Indices: 64137--64215 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
64127 TCTTTCAGTT
* * *
64137 AAACTCTGTTTAATTT-TTTCAATT
1 AAACTCTATTT-ATTTGTTTGAATC
* *
64161 AAACTCTATTTATTTGTTTTAATT
1 AAACTCTATTTATTTGTTTGAATC
* *
64185 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTGAATC
*
64209 GAACTCT
1 AAACTCT
64216 TATTAGTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.09
24 43 0.91
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.52
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTGAATC
Found at i:64991 original size:6 final size:6
Alignment explanation
Indices: 64980--65018 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
64970 GAATGGAGGG
64980 AAAAAT AAAAAT AAAAAGT AAAAAT -AAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAA-T AAAAAT AAAAAT AAAAAT AAAA
65019 TAACGTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.32
6 15 0.48
7 6 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:70463 original size:47 final size:47
Alignment explanation
Indices: 70394--70488 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
70384 TTTAAAACAC
* *
70394 TCTAATGTCACTTTTCACTTCGTTTAAACCTTTAATCACGATATTCA
1 TCTAATGTCACTTGTCACTTCGTTTAAACCTTTAATCACAATATTCA
70441 TCTAATGTCACTTGTCACTTCGTTTAAACCTTTAATCACAATATTCA
1 TCTAATGTCACTTGTCACTTCGTTTAAACCTTTAATCACAATATTCA
70488 T
1 T
70489 TCCACATATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.42
Consensus pattern (47 bp):
TCTAATGTCACTTGTCACTTCGTTTAAACCTTTAATCACAATATTCA
Found at i:79296 original size:52 final size:52
Alignment explanation
Indices: 79238--79344 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
79228 GTTCCGTACT
* *
79238 TTTTTTATGGAGTGTCCCATACATTTCATTAATTGCGAACTAACGCTATTAA
1 TTTTTTATGGAGTGTCCCATACATTTCATTAATTGCCAACCAACGCTATTAA
79290 TTTTTTATGGAGTGTCCCATACATTTCATTAATTGCCAACCAACGCTATTAA
1 TTTTTTATGGAGTGTCCCATACATTTCATTAATTGCCAACCAACGCTATTAA
79342 TTT
1 TTT
79345 ATAGTTAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (52 bp):
TTTTTTATGGAGTGTCCCATACATTTCATTAATTGCCAACCAACGCTATTAA
Found at i:102602 original size:16 final size:16
Alignment explanation
Indices: 102571--102604 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
102561 GAATATATAT
*
102571 TAAAAATATGTAAAAA
1 TAAAAATATATAAAAA
102587 TAAAAATATATTAAAAA
1 TAAAAATATA-TAAAAA
102604 T
1 T
102605 GAAATATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAATATATAAAAA
Found at i:102611 original size:16 final size:18
Alignment explanation
Indices: 102572--102604 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
102562 AATATATATT
102572 AAAA-ATATGTAAAAATA
1 AAAATATATGTAAAAATA
102589 AAAATATAT-TAAAAAT
1 AAAATATATGTAAAAAT
102605 GAAATATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATATATGTAAAAATA
Found at i:112058 original size:23 final size:25
Alignment explanation
Indices: 112026--112085 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
112016 TTGATCATTC
*
112026 TGTTATAAATTTCAACTA-TTTT-T
1 TGTTAAAAATTTCAACTATTTTTAT
*
112049 TGTTAAAAATTTCATCTATTTTTAT
1 TGTTAAAAATTTCAACTATTTTTAT
*
112074 TGGTAAAAATTT
1 TGTTAAAAATTT
112086 ATCTTTACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 16 0.50
24 4 0.12
25 12 0.38
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (25 bp):
TGTTAAAAATTTCAACTATTTTTAT
Found at i:112085 original size:25 final size:23
Alignment explanation
Indices: 112032--112089 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
112022 ATTCTGTTAT
* *
112032 AAATTTCAACTATTTTTTGTTAA
1 AAATTTCATCTATTTTTTGGTAA
112055 AAATTTCATCTATTTTTATTGGTAA
1 AAATTTCATCTA-TTTT-TTGGTAA
112080 AAATTT-ATCT
1 AAATTTCATCT
112090 TTACACGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 11 0.35
24 8 0.26
25 12 0.39
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (23 bp):
AAATTTCATCTATTTTTTGGTAA
Found at i:114438 original size:12 final size:13
Alignment explanation
Indices: 114421--114449 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
114411 TAAAGACTAA
114421 AAAAATAAAAA-T
1 AAAAATAAAAACT
114433 AAAAATAAAAACT
1 AAAAATAAAAACT
114446 AAAA
1 AAAA
114450 TAACTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAACT
Found at i:129562 original size:2 final size:2
Alignment explanation
Indices: 129557--129585 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
129547 AAGAACTTAG
129557 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
129586 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:135160 original size:6 final size:6
Alignment explanation
Indices: 135149--135191 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
135139 TACCTATTCG
135149 CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA C
1 CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA CTGAAA C
135192 GTAAAGCCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (6 bp):
CTGAAA
Found at i:140438 original size:24 final size:23
Alignment explanation
Indices: 140405--140453 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
140395 TTTTCTTTCT
* *
140405 TTCTTTTTTCACTTTTCTTTTCCA
1 TTCTTCTTTC-CTTTTATTTTCCA
*
140429 TTCTTCTTTCTTTTTATTTTCCA
1 TTCTTCTTTCCTTTTATTTTCCA
140452 TT
1 TT
140454 AAATCTGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTCTTTCCTTTTATTTTCCA
Found at i:140925 original size:33 final size:35
Alignment explanation
Indices: 140873--140944 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 35
140863 GAAAATTTTT
* *
140873 TATTTAGATTTTTTAAAAATTTTAAA-ATTTAATAC
1 TATTTAGATTTTTTAAAAATTATAAATATATAA-AC
140908 TATTT-GATTTTTT-AAAATTATAAATATATAAAC
1 TATTTAGATTTTTTAAAAATTATAAATATATAAAC
140941 TATT
1 TATT
140945 AAAATGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 16 0.47
34 13 0.38
35 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (35 bp):
TATTTAGATTTTTTAAAAATTATAAATATATAAAC
Found at i:142123 original size:10 final size:10
Alignment explanation
Indices: 142102--142135 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
142092 TTAATTTAAT
142102 AAATTAATAAA
1 AAATT-ATAAA
142113 AAATTATAAA
1 AAATTATAAA
142123 AAATT-TAAA
1 AAATTATAAA
142132 AAAT
1 AAAT
142136 AGAGAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
10 10 0.43
11 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTATAAA
Found at i:143125 original size:121 final size:120
Alignment explanation
Indices: 142984--143227 Score: 407
Period size: 121 Copynumber: 2.0 Consensus size: 120
142974 CATATTCACT
* * * *
142984 TTATATATATATATATATTATAAAAGTTTGCAATATAATTAGTTATTTGTTTTAGAAGATTAAAT
1 TTATATATATATATAAATTATAAAAGTTAGCAATATAATTAGTTATTTGTTTTAAAACATTAAAT
*
143049 TATAAAGATGCATAAAAAGGAAAAAAATTCAGAGAGGTAATAATAATAAAAAATAA
66 TATAAAGATGCATAAAAA-GAAAAAAATTCAGAGAAGTAATAATAATAAAAAATAA
* *
143105 TTATATATATTTTTAAATTATAAAAGTTAGCAATATAATTAGTTATTTGTTTTAAAACATTAAAT
1 TTATATATATATATAAATTATAAAAGTTAGCAATATAATTAGTTATTTGTTTTAAAACATTAAAT
*
143170 TATAAAGATGCATAAAAAGAAAAAAATTCTGAGAAGTAATAATAATAAAAAATAA
66 TATAAAGATGCATAAAAAGAAAAAAATTCAGAGAAGTAATAATAATAAAAAATAA
143225 TTA
1 TTA
143228 AATAATTAAT
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 38 0.33
121 77 0.67
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (120 bp):
TTATATATATATATAAATTATAAAAGTTAGCAATATAATTAGTTATTTGTTTTAAAACATTAAAT
TATAAAGATGCATAAAAAGAAAAAAATTCAGAGAAGTAATAATAATAAAAAATAA
Found at i:145773 original size:41 final size:41
Alignment explanation
Indices: 145549--145843 Score: 207
Period size: 41 Copynumber: 7.0 Consensus size: 41
145539 AAACGTCGCA
* * * *
145549 AAAGGT-AAAGCAATAGCTG-CGCTTATGGGAAAGAGCTGCT
1 AAAGGTCAGAGCAATAGC-GACGCTTATGGGCAAGCGCCGCT
* * * * *
145589 AAATGTCAAAGCAATAGCGGCGCTTATGGCCAAGCGTCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
* * * * ** * * * *
145630 GATGGTCATAGCAAAAATGACGATTTTGGGAAAGCGCCTCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
* * * ** **
145671 AAAGGTCAGAGCAGTAGCGAAGCTTTTGGAAAAGCATCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
145712 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
* * *
145753 AAAGGTTAGAGCAATAGCGACACTTATGGTCAGAGCATTAGCGACGCT
1 AAAGGTCAGAGCAATAGCGACGCTTAT-G---G-GCA--AGCGCCGCT
* * * *
145801 TATGGTCAGAGCATTAGCGACGCTTATGGTCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
145842 AA
1 AA
145844 TTTATTTAAA
Statistics
Matches: 195, Mismatches: 51, Indels: 17
0.74 0.19 0.06
Matches are distributed among these distances:
40 6 0.03
41 150 0.77
42 1 0.01
43 2 0.01
44 1 0.01
45 1 0.01
46 3 0.02
47 1 0.01
48 30 0.15
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCT
Found at i:145787 original size:24 final size:24
Alignment explanation
Indices: 145760--145832 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
145750 GCTAAAGGTT
* *
145760 AGAGCAATAGCGACACTTATGGTC
1 AGAGCATTAGCGACGCTTATGGTC
145784 AGAGCATTAGCGACGCTTATGGTC
1 AGAGCATTAGCGACGCTTATGGTC
145808 AGAGCATTAGCGACGCTTATGGTC
1 AGAGCATTAGCGACGCTTATGGTC
145832 A
1 A
145833 AGCGCCGCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (24 bp):
AGAGCATTAGCGACGCTTATGGTC
Found at i:147240 original size:42 final size:43
Alignment explanation
Indices: 147181--147261 Score: 139
Period size: 42 Copynumber: 1.9 Consensus size: 43
147171 TGGGAAATCA
147181 AAATAATATTTAAATAAAATAACTAA-ATA-ATAATAATAATTT
1 AAATAATATTTAAATAAAATAA-TAATATATATAATAATAATTT
147223 AAATAATATTTAAATAAAATAATAATATATATAATAATA
1 AAATAATATTTAAATAAAATAATAATATATATAATAATA
147262 GATACACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
41 3 0.08
42 25 0.68
43 9 0.24
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (43 bp):
AAATAATATTTAAATAAAATAATAATATATATAATAATAATTT
Found at i:147261 original size:31 final size:29
Alignment explanation
Indices: 147182--147258 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
147172 GGGAAATCAA
**
147182 AATAAT-ATTTAAATAAAATAACTAAATAAT
1 AATAATAATTTAAAT--AATATTTAAATAAT
147212 AATAATAATTTAAATAATATTTAAATAA-
1 AATAATAATTTAAATAATATTTAAATAAT
* *
147240 AATAATAATATATATAATA
1 AATAATAATTTAAATAATA
147259 ATAGATACAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.40
29 11 0.26
30 6 0.14
31 8 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
AATAATAATTTAAATAATATTTAAATAAT
Found at i:147380 original size:41 final size:41
Alignment explanation
Indices: 147322--147598 Score: 405
Period size: 41 Copynumber: 6.8 Consensus size: 41
147312 ACAGAAAACC
* * *
147322 CCGCAAAAGGT-AAAGCAATAGCGGCGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
*
147362 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGTG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
147403 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* *
147444 ACGCTAAAGGTCGGAGCAATAGCGGCGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* * * *
147485 CTGCTAAATGTCAGAGCAATAGCGGCGCTTATGTGCAAGAG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* *
147526 CCGCGAAAGGTCAGAGCAACAGCGGCGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
* *
147567 CCGCTAAAGATCA-AGGCATTAGCGGCGCTTAT
1 CCGCTAAAGGTCAGA-GCAATAGCGGCGCTTAT
147599 TTGAAAAACG
Statistics
Matches: 212, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
40 11 0.05
41 201 0.95
ACGTcount: A:0.29, C:0.23, G:0.33, T:0.16
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
Found at i:147390 original size:24 final size:24
Alignment explanation
Indices: 147358--147431 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
147348 CTTATGGGAA
*
147358 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGGCGCTAAAGGTCAGAGCAAT
* * *
147382 AGCGGCGCTTATGGGCA-AG---T
1 AGCGGCGCTAAAGGTCAGAGCAAT
147402 -GC--CGCTAAAGGTCAGAGCAAT
1 AGCGGCGCTAAAGGTCAGAGCAAT
147423 AGCGGCGCT
1 AGCGGCGCT
147432 TATGGGCAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
17 9 0.25
18 2 0.06
19 2 0.06
20 1 0.03
21 1 0.03
22 2 0.06
23 2 0.06
24 17 0.47
ACGTcount: A:0.27, C:0.24, G:0.34, T:0.15
Consensus pattern (24 bp):
AGCGGCGCTAAAGGTCAGAGCAAT
Found at i:150495 original size:26 final size:24
Alignment explanation
Indices: 150455--150502 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
150445 TCTACATGGG
150455 CATAATCTCTCATATTCATCATTTTT
1 CATAATCTCTCATA-TCA-CATTTTT
* *
150481 CATAATTTCTTATATCACATTT
1 CATAATCTCTCATATCACATTT
150503 ACATTTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 3 0.15
26 12 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (24 bp):
CATAATCTCTCATATCACATTTTT
Found at i:152418 original size:17 final size:17
Alignment explanation
Indices: 152396--152455 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
152386 TAACAATTAT
152396 TTAAAAACTTATATAAA
1 TTAAAAACTTATATAAA
* *
152413 TTAAAAAAAATTCTA-AAA
1 TT--AAAAACTTATATAAA
*
152431 TTTTAAAACTTATATAAA
1 -TTAAAAACTTATATAAA
*
152449 CTAAAAA
1 TTAAAAA
152456 AATTGGTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 15 0.47
18 6 0.19
19 11 0.34
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAACTTATATAAA
Found at i:152420 original size:19 final size:19
Alignment explanation
Indices: 152398--152457 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
152388 ACAATTATTT
152398 AAAAACTTATATAAATTAA
1 AAAAACTTATATAAATTAA
* * *
152417 AAAAAATTCTA-AAATT-T
1 AAAAACTTATATAAATTAA
* *
152434 TAAAACTTATATAAACTAA
1 AAAAACTTATATAAATTAA
152453 AAAAA
1 AAAAA
152458 TTGGTTTTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 8 0.27
18 9 0.30
19 13 0.43
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAACTTATATAAATTAA
Found at i:153140 original size:21 final size:21
Alignment explanation
Indices: 153116--153162 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
153106 GTTTATGATT
153116 CTTTTTGTTCTTGGTTTTTTA
1 CTTTTTGTTCTTGGTTTTTTA
153137 CTTTTTGTTCTTGGTTTTTTA
1 CTTTTTGTTCTTGGTTTTTTA
153158 CTTTT
1 CTTTT
153163 AATTCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.11, G:0.13, T:0.72
Consensus pattern (21 bp):
CTTTTTGTTCTTGGTTTTTTA
Found at i:153168 original size:21 final size:21
Alignment explanation
Indices: 153123--153168 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
153113 ATTCTTTTTG
**
153123 TTCTTGGTTTTTTACTTTTTG
1 TTCTTGGTTTTTTACTTTTAA
153144 TTCTTGGTTTTTTACTTTTAA
1 TTCTTGGTTTTTTACTTTTAA
153165 TTCT
1 TTCT
153169 AAAGAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.70
Consensus pattern (21 bp):
TTCTTGGTTTTTTACTTTTAA
Found at i:155245 original size:43 final size:43
Alignment explanation
Indices: 155178--155533 Score: 459
Period size: 43 Copynumber: 8.3 Consensus size: 43
155168 ATTTATTAAT
* *
155178 TTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
* *
155221 TTTAGTGGCGTTTGTTGGGA-AAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTG-TGGGAGAAGCGCCGCTAAAGACCATGTTC
* *
155264 TTTAGCGGCGTTTGTTGGTA-AAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTG-TGGGAGAAGCGCCGCTAAAGACCATGTTC
* *
155307 TTTAGCAGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
* * * *
155350 TTTAGCGGCGTTTATTGGAAAAGCGCCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
** *
155393 TTTAGCGGCGTTTGTGATATAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
*
155436 TTTAGCGGCGTTTGTGGG-GAAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAG-AAGCGCCGCTAAAGACCATGTTC
* * * *
155479 TTTAGTGGCGTTTGT-GGATAAGCGACGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
* *
155521 TATAGAGGCGTTT
1 TTTAGCGGCGTTT
155534 TTCCTCATAA
Statistics
Matches: 276, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
42 37 0.13
43 234 0.85
44 5 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGACCATGTTC
Found at i:155422 original size:129 final size:128
Alignment explanation
Indices: 155178--155533 Score: 511
Period size: 129 Copynumber: 2.8 Consensus size: 128
155168 ATTTATTAAT
* * * *
155178 TTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAAGACTATGTTCTTTAGTGGCGTTTGTTGGGAAA
1 TTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTT-TTGGAAAA
* * *
155243 GCGTCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTTGGTAAAGCACCGCTAAAGACCATGTTC
65 GCGACGCTAAAGACTATGTTCTTTAGCGGCGTTTGTTGATAAAGCACCGCTAAAGACCATGTTC
* *
155307 TTTAGCAGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTCTTTAGCGGCGTTTATTGGAAAA
1 TTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTT-TTGGAAAA
* *
155372 GCGCCGCTAAAGACTATGTTCTTTAGCGGCGTTTG-TGATATAAGCGCCGCTAAAGACCATGTTC
65 GCGACGCTAAAGACTATGTTCTTTAGCGGCGTTTGTTGATA-AAGCACCGCTAAAGACCATGTTC
* *
155436 TTTAGCGGCGTTTGTGGG-GAAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGATAA
1 TTTAGCGGCGTTTGTGGGAG-AAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTTTGGAAAA
* *
155500 GCGACGCTAAAGA-TCATGTTCTATAGAGGCGTTT
65 GCGACGCTAAAGACT-ATGTTCTTTAGCGGCGTTT
155534 TTCCTCATAA
Statistics
Matches: 206, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
127 1 0.00
128 40 0.19
129 165 0.80
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTCTTTAGTGGCGTTTTTGGAAAAG
CGACGCTAAAGACTATGTTCTTTAGCGGCGTTTGTTGATAAAGCACCGCTAAAGACCATGTTC
Found at i:155718 original size:22 final size:23
Alignment explanation
Indices: 155692--155737 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
155682 TTCTAAATCG
155692 AAATATATTAA-TATAAATATAA
1 AAATATATTAATTATAAATATAA
*
155714 AAATATATTAATTATTAATATAA
1 AAATATATTAATTATAAATATAA
155737 A
1 A
155738 TATAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATATTAATTATAAATATAA
Found at i:155733 original size:29 final size:29
Alignment explanation
Indices: 155697--155791 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
155687 AATCGAAATA
155697 TATTAATATAAATATAAAAATATATTAAT
1 TATTAATATAAATATAAAAATATATTAAT
*
155726 TATTAATATAAATATAAATAT-TATTAAT
1 TATTAATATAAATATAAAAATATATTAAT
* * *
155754 TACTTAATATTAATA-ACAAATAATATAAAT
1 TA-TTAATATAAATATAAAAAT-ATATTAAT
*
155784 TAATAATA
1 TATTAATA
155792 ATTGATAGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.23
29 36 0.63
30 8 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TATTAATATAAATATAAAAATATATTAAT
Found at i:155735 original size:15 final size:15
Alignment explanation
Indices: 155715--155763 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
155705 TAAATATAAA
155715 AATATATTAATTATT
1 AATATATTAATTATT
*
155730 AATATA--AA-TATA
1 AATATATTAATTATT
155742 AATATTATTAATTACTT
1 AATA-TATTAATTA-TT
155759 AATAT
1 AATAT
155764 TAATAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
15 8 0.30
16 3 0.11
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATTAATTATT
Found at i:156175 original size:21 final size:21
Alignment explanation
Indices: 156151--156200 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
156141 AAATTGTCTT
156151 CTTCTTCACGCACGCCCTTCC
1 CTTCTTCACGCACGCCCTTCC
*
156172 CTTCTTCACGCACGCCCTTCT
1 CTTCTTCACGCACGCCCTTCC
156193 CTTCTTCA
1 CTTCTTCA
156201 GTCTTATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.10, C:0.48, G:0.08, T:0.34
Consensus pattern (21 bp):
CTTCTTCACGCACGCCCTTCC
Found at i:156388 original size:18 final size:17
Alignment explanation
Indices: 156346--156389 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
156336 TTTAATCCTT
**
156346 TTTATTGTTTAATTTTG
1 TTTATTGTTTAATTTAA
156363 TTTAATTGTTTAATTTCAA
1 TTT-ATTGTTTAATTT-AA
156382 TTTATTGT
1 TTTATTGT
156390 AAACCTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (17 bp):
TTTATTGTTTAATTTAA
Found at i:157671 original size:24 final size:23
Alignment explanation
Indices: 157644--157690 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
157634 TCGAAATCGT
157644 AAGAAAACA-AATTAATTATAGAGA
1 AAGAAAA-AGAATTAA-TATAGAGA
*
157668 AAGAAAAAGAATTGATATAGAGA
1 AAGAAAAAGAATTAATATAGAGA
157691 GAAAATCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (23 bp):
AAGAAAAAGAATTAATATAGAGA
Found at i:178228 original size:151 final size:151
Alignment explanation
Indices: 177993--178295 Score: 414
Period size: 151 Copynumber: 2.0 Consensus size: 151
177983 GGGTTGTTTC
* ** * *
177993 CTTATTTTTCATGTAACCTAAGTCATGTATGGGATACTATGCTTTGTAATTTTGCTCTTTGAGAG
1 CTTATTTTTCAAGTAACCTAAGTCATACATGGGATACTATGCTTTGTAATTTTACTC-TTGAGAA
** *
178058 TTTTTACAAGATTTGATTCTTGTTCTTTCTTT-AAAAGCGGCAGCAACTCAATCTTCAAGATAGT
65 TTTTTACAAGATTCAATTCTTGTTCTTTCTTTGAAAA-CGGCAACAACTCAAT-TTCAAGATAGT
*
178122 GGTGTTTACTTCTTCACACTCCAA
128 GATGTTTACTTCTTCACACTCCAA
* *
178146 CTTATTTTTCAAGTAACTTAAGTCTATACATGGGATACTATTCTTTGTAA-TTTACTC-TGAGAA
1 CTTATTTTTCAAGTAACCTAAGTC-ATACATGGGATACTATGCTTTGTAATTTTACTCTTGAGAA
* * *
178209 TTTTTATAAGATTCAATTCTTGTTCTTTCTTTGAAAATGGCAACAACTCAATTTCAAGATTGTGA
65 TTTTTACAAGATTCAATTCTTGTTCTTTCTTTGAAAACGGCAACAACTCAATTTCAAGATAGTGA
*
178274 TGTTTACTTGTTCACACTCCAA
130 TGTTTACTTCTTCACACTCCAA
178296 TTAGCAAGAG
Statistics
Matches: 133, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
150 32 0.24
151 47 0.35
152 4 0.03
153 28 0.21
154 22 0.17
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (151 bp):
CTTATTTTTCAAGTAACCTAAGTCATACATGGGATACTATGCTTTGTAATTTTACTCTTGAGAAT
TTTTACAAGATTCAATTCTTGTTCTTTCTTTGAAAACGGCAACAACTCAATTTCAAGATAGTGAT
GTTTACTTCTTCACACTCCAA
Found at i:189302 original size:11 final size:11
Alignment explanation
Indices: 189288--189375 Score: 50
Period size: 11 Copynumber: 8.6 Consensus size: 11
189278 AAATACCTTT
189288 AAAATAATAAC
1 AAAATAATAAC
189299 AAAAT--TAAC
1 AAAATAATAAC
189308 --AATAA-AAC
1 AAAATAATAAC
*
189316 AAGAATTAT-AC
1 AA-AATAATAAC
*
189327 AACATACA-AAC
1 AAAATA-ATAAC
189338 --AATAATAAC
1 AAAATAATAAC
*
189347 AAAATAGTAAC
1 AAAATAATAAC
*
189358 AATATAATAAC
1 AAAATAATAAC
*
189369 GAAATAA
1 AAAATAA
189376 CATCAAAACA
Statistics
Matches: 57, Mismatches: 9, Indels: 22
0.65 0.10 0.25
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 10 0.18
10 2 0.04
11 38 0.67
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:189322 original size:18 final size:18
Alignment explanation
Indices: 189286--189328 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
189276 GCAAATACCT
189286 TTAA-AATAATAACAAAA
1 TTAACAATAATAACAAAA
189303 TTAACAATAA-AACAAGAA
1 TTAACAATAATAACAA-AA
189321 TTATACAA
1 TTA-ACAA
189329 CATACAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.39
18 10 0.43
19 4 0.17
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.23
Consensus pattern (18 bp):
TTAACAATAATAACAAAA
Found at i:192155 original size:26 final size:26
Alignment explanation
Indices: 192119--192174 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
192109 ATTTATTATG
*
192119 TTTAATATATGTTTTATTTATACTTA
1 TTTAATATATGTTTTATTTATACCTA
192145 TTTAATATATGTTTTATTTATACCTA
1 TTTAATATATGTTTTATTTATACCTA
192171 TTTA
1 TTTA
192175 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTAATATATGTTTTATTTATACCTA
Found at i:195248 original size:17 final size:18
Alignment explanation
Indices: 195228--195261 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
195218 ACCTTTATCA
*
195228 TTTCATCTTCTT-TAACC
1 TTTCATATTCTTGTAACC
195245 TTTCATATTCTTGTAAC
1 TTTCATATTCTTGTAAC
195262 TACTTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCATATTCTTGTAACC
Found at i:203830 original size:57 final size:57
Alignment explanation
Indices: 203754--203874 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 57
203744 GATAAAATTG
* * * *
203754 AATAGTTGAGTAATTATTTTGTAA-CTTTTT-ATAA-ATGAGTGACAAAAAAAAATTATT
1 AATAATTGAGTAATCATTTTATAATCTTTTTCATAATATG-GTGAC--AAAAAAACTATT
* * *
203811 AATAATTGAGTGATCATTTTATAATTTTTTTCATAATTTGGTGACAAAAAAACTATT
1 AATAATTGAGTAATCATTTTATAATCTTTTTCATAATATGGTGACAAAAAAACTATT
203868 AATAATT
1 AATAATT
203875 AGATGACTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
57 38 0.70
58 5 0.09
59 9 0.17
60 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (57 bp):
AATAATTGAGTAATCATTTTATAATCTTTTTCATAATATGGTGACAAAAAAACTATT
Found at i:215523 original size:19 final size:20
Alignment explanation
Indices: 215486--215530 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
215476 ATTCTAAATC
215486 CTAAACTTCGAATCTGAACT
1 CTAAACTTCGAATCTGAACT
*
215506 TTAAAC-TCGAA-CTCGAACT
1 CTAAACTTCGAATCT-GAACT
215525 CTAAAC
1 CTAAAC
215531 CCTAAACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 15 0.68
20 5 0.23
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.27
Consensus pattern (20 bp):
CTAAACTTCGAATCTGAACT
Found at i:219742 original size:2 final size:2
Alignment explanation
Indices: 219737--219783 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
219727 ACATGACTAA
219737 AT AT AT 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 AT AT AT
219779 AT AT A
1 AT AT A
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.