Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008351.1 Kokia drynarioides strain JFW-HI SEQ_123018, 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: 284908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:5123 original size:18 final size:18
Alignment explanation
Indices: 5102--5138 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5092 ACTTATTAGG
*
5102 ATAAATTAAAGTATAAGA
1 ATAAATTAAAGGATAAGA
5120 ATAAATTAAAGGATAAGA
1 ATAAATTAAAGGATAAGA
5138 A
1 A
5139 GGCGGAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (18 bp):
ATAAATTAAAGGATAAGA
Found at i:5880 original size:43 final size:43
Alignment explanation
Indices: 5828--5949 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
5818 ATTTTAGCTA
* * *
5828 CGTTTGTGTGGAAAGCCCCGCTAAAGATCATGTTTTTTAACGG
1 CGTTTGTGTGAAAAGCCCCGCTAAAGATCATGTTCTTTAACAG
* * * * * *
5871 GGTTTGTGTGTAAAGCCTCGCTAAAAACCATGTTCTTTACCAG
1 CGTTTGTGTGAAAAGCCCCGCTAAAGATCATGTTCTTTAACAG
* *
5914 CGTTTGT-TAGAAAAGCGCCACTAAAGATCATGTTCT
1 CGTTTGTGT-GAAAAGCCCCGCTAAAGATCATGTTCT
5950 CTACCGATGT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (43 bp):
CGTTTGTGTGAAAAGCCCCGCTAAAGATCATGTTCTTTAACAG
Found at i:18560 original size:29 final size:29
Alignment explanation
Indices: 18528--18584 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
18518 TTCCACAGCT
* *
18528 TGTGTGATATTATTTTGTGTTATGTTATC
1 TGTGTGATATTAATCTGTGTTATGTTATC
* *
18557 TGTGTGATTTTAATCTGTGTTGTGTTAT
1 TGTGTGATATTAATCTGTGTTATGTTAT
18585 AGCATGTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.23, T:0.58
Consensus pattern (29 bp):
TGTGTGATATTAATCTGTGTTATGTTATC
Found at i:21816 original size:20 final size:20
Alignment explanation
Indices: 21791--21835 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21781 GACCCGAACT
21791 GTTGACCTAAACCATTGACC
1 GTTGACCTAAACCATTGACC
* **
21811 GTTGACTTTGACCATTGACC
1 GTTGACCTAAACCATTGACC
*
21831 TTTGA
1 GTTGA
21836 TCGTTGACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
GTTGACCTAAACCATTGACC
Found at i:21821 original size:13 final size:13
Alignment explanation
Indices: 21805--21859 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
21795 ACCTAAACCA
*
21805 TTGACCGTTGACT
1 TTGACCATTGACT
21818 TTGACCATTGACCT
1 TTGACCATTGA-CT
* *
21832 TTGATCGTTGACT
1 TTGACCATTGACT
*
21845 TTGATCATTGACT
1 TTGACCATTGACT
21858 TT
1 TT
21860 TTCGAACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 26 0.70
14 11 0.30
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (13 bp):
TTGACCATTGACT
Found at i:21840 original size:27 final size:27
Alignment explanation
Indices: 21805--21856 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
21795 ACCTAAACCA
21805 TTGACCGTTGACTTTGACCATTGACCT
1 TTGACCGTTGACTTTGACCATTGACCT
* *
21832 TTGATCGTTGACTTTGATCATTGAC
1 TTGACCGTTGACTTTGACCATTGAC
21857 TTTTTCGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (27 bp):
TTGACCGTTGACTTTGACCATTGACCT
Found at i:22274 original size:29 final size:29
Alignment explanation
Indices: 22242--22298 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
22232 TTCCATATCT
*
22242 TGTGTGATATT-ATTTCGTGTTGTGTTATG
1 TGTGTGATATTAATAT-GTGTTGTGTTATG
*
22271 TGTGTGATTTTAATATGTGTTGTGTTAT
1 TGTGTGATATTAATATGTGTTGTGTTAT
22299 TGCATGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.16, C:0.02, G:0.26, T:0.56
Consensus pattern (29 bp):
TGTGTGATATTAATATGTGTTGTGTTATG
Found at i:34756 original size:22 final size:22
Alignment explanation
Indices: 34730--34775 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34720 ATAGAGTTAG
34730 TATGTTAGTATCTATATAAGTA
1 TATGTTAGTATCTATATAAGTA
34752 TATGTTAGTATCTATATAAGTA
1 TATGTTAGTATCTATATAAGTA
34774 TA
1 TA
34776 AAAATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (22 bp):
TATGTTAGTATCTATATAAGTA
Found at i:36234 original size:40 final size:40
Alignment explanation
Indices: 36190--36292 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
36180 TAGTATTATA
36190 AGGATCGTACCCAAAGGAGGCTTAAGGAAATAGTATTCCG
1 AGGATCGTACCCAAAGGAGGCTTAAGGAAATAGTATTCCG
* * * *
36230 AGGATCATACCCAAAGGAGACTTAAGGTAATAGTATTTCG
1 AGGATCGTACCCAAAGGAGGCTTAAGGAAATAGTATTCCG
*
36270 AGGATCGTAGCCAAAGGAGGCTT
1 AGGATCGTACCCAAAGGAGGCTT
36293 GAGGCTTAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (40 bp):
AGGATCGTACCCAAAGGAGGCTTAAGGAAATAGTATTCCG
Found at i:36802 original size:15 final size:15
Alignment explanation
Indices: 36779--36808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36769 GTAAAATAAA
36779 TATTCTGGATACTTT
1 TATTCTGGATACTTT
*
36794 TATTTTGGATACTTT
1 TATTCTGGATACTTT
36809 GAGGAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (15 bp):
TATTCTGGATACTTT
Found at i:37177 original size:24 final size:24
Alignment explanation
Indices: 37140--37232 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
37130 TTAAACTCTT
**
37140 TCTGGGCTTGTAAGAGCTAACCTA
1 TCTGGGCTCATAAGAGCTAACCTA
* *
37164 TCTAGGCTCATAAGGGCTAACCTA
1 TCTGGGCTCATAAGAGCTAACCTA
* * * *
37188 TCTGGGTTCGTAAGAGCTAATTCTG
1 TCTGGGCTCATAAGAGCTAA-CCTA
*
37213 TCTGGGCTCATATGAGCTAA
1 TCTGGGCTCATAAGAGCTAA
37233 ATTCCTGGAA
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
24 36 0.65
25 19 0.35
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (24 bp):
TCTGGGCTCATAAGAGCTAACCTA
Found at i:39229 original size:16 final size:16
Alignment explanation
Indices: 39204--39238 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39194 TAAAATCGGC
39204 GACAACGGCGTGTGAT
1 GACAACGGCGTGTGAT
*
39220 GACAATGGCGTGTGAT
1 GACAACGGCGTGTGAT
39236 GAC
1 GAC
39239 GATGACGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GACAACGGCGTGTGAT
Found at i:39645 original size:6 final size:6
Alignment explanation
Indices: 39631--39680 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
39621 TATTAAACAT
* * *
39631 AAATT- AAATTA AAATTA AAATTA AAA-AA ACAATAA AAATGA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA A-AATTA AAATTA AAATTA
39678 AAA
1 AAA
39681 ATTTCAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
5 7 0.18
6 29 0.74
7 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (6 bp):
AAATTA
Found at i:44201 original size:3 final size:3
Alignment explanation
Indices: 44193--44221 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44183 TTTATTTTGT
44193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
44222 TAGGCTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45318 original size:63 final size:63
Alignment explanation
Indices: 45219--45360 Score: 266
Period size: 63 Copynumber: 2.3 Consensus size: 63
45209 GATTCAAGCC
45219 TACACTTTCTAACCATTAAAATAGAGCTTAAACCAATCATTAATGAGAGTGTAGAAGAGCCAA
1 TACACTTTCTAACCATTAAAATAGAGCTTAAACCAATCATTAATGAGAGTGTAGAAGAGCCAA
*
45282 TACACTTTCTAACCATTAAAATAGAGCTTAAACCAATCGTTAATGAGAGTGTAGAAGAGCCAA
1 TACACTTTCTAACCATTAAAATAGAGCTTAAACCAATCATTAATGAGAGTGTAGAAGAGCCAA
*
45345 TACACTTTCTAGCCAT
1 TACACTTTCTAACCAT
45361 AATAGAGAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (63 bp):
TACACTTTCTAACCATTAAAATAGAGCTTAAACCAATCATTAATGAGAGTGTAGAAGAGCCAA
Found at i:54728 original size:18 final size:18
Alignment explanation
Indices: 54705--54741 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54695 ACAAGTGCAT
54705 TGTCATTGTATTTCCATG
1 TGTCATTGTATTTCCATG
54723 TGTCATTGTATTTCCATG
1 TGTCATTGTATTTCCATG
54741 T
1 T
54742 CAGCGTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (18 bp):
TGTCATTGTATTTCCATG
Found at i:55294 original size:10 final size:11
Alignment explanation
Indices: 55279--55321 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
55269 CAGTCACATG
55279 AAAAAAAGAAA
1 AAAAAAAGAAA
55290 AAAAAAAGAAA
1 AAAAAAAGAAA
*
55301 AAGGGAAAAGAAGA
1 AA--AAAAAGAA-A
55315 AAAAAAA
1 AAAAAAA
55322 TATTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 13 0.48
12 4 0.15
13 7 0.26
14 3 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:55331 original size:2 final size:2
Alignment explanation
Indices: 55321--55365 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
55311 AAGAAAAAAA
*
55321 AT AT TT AT AT AT AT AT AT AT AT AT -T 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
55362 AT AT
1 AT AT
55366 TATTGTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:57819 original size:22 final size:21
Alignment explanation
Indices: 57780--57821 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
57770 TCCTTAAGCA
**
57780 ATAAAAACTAAGTTAAAATAT
1 ATAAAAACTAAGGGAAAATAT
57801 ATAAAAACATAAGGGAAAATA
1 ATAAAAAC-TAAGGGAAAATA
57822 CTAGATTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (21 bp):
ATAAAAACTAAGGGAAAATAT
Found at i:60282 original size:231 final size:231
Alignment explanation
Indices: 59879--60340 Score: 888
Period size: 231 Copynumber: 2.0 Consensus size: 231
59869 ACCTAATCAT
59879 GCCATCAAGCTTCATGTCAATGCTTCCTTTGGTTTTTGCCCCATTCCTTGATTTGTCTTTTCTCT
1 GCCATCAAGCTTCATGTCAATGCTTCCTTTGGTTTTTGCCCCATTCCTTGATTTGTCTTTTCTCT
59944 TCATTGATGCCGATACATCCATTTTTTCCTTCCTCCTTTGATTCCACTCCTTGATTTGTTTTCTC
66 TCATTGATGCCGATACATCCATTTTTTCCTTCCTCCTTTGATTCCACTCCTTGATTTGTTTTCTC
60009 TAAAGCTCAACATATTGTTTGTATAATGAATCTTCTATGATGCTTCGAGTTGACTTTAGGAATTA
131 TAAAGCTCAACATATTGTTTGTATAATGAATCTTCTATGATGCTTCGAGTTGACTTTAGGAATTA
*
60074 TTCATTTTCTTGCATTAGTACATCCGTCTTTTTGCA
196 TTCATTTTCTTCCATTAGTACATCCGTCTTTTTGCA
**
60110 GCCATCAAGCTTCATGTCAATGCTTCCTTTGGTTTTTGCCCTGTTCCTTGATTTGTCTTTTCTCT
1 GCCATCAAGCTTCATGTCAATGCTTCCTTTGGTTTTTGCCCCATTCCTTGATTTGTCTTTTCTCT
*
60175 TCATTGATGCCGGTACATCCATTTTTTCCTTCCTCCTTTGATTCCACTCCTTGATTTGTTTTCTC
66 TCATTGATGCCGATACATCCATTTTTTCCTTCCTCCTTTGATTCCACTCCTTGATTTGTTTTCTC
60240 TAAAGCTCAACATATTGTTTGTATAATGAATCTTCTATGATGCTTCGAGTTGACTTTAGGAATTA
131 TAAAGCTCAACATATTGTTTGTATAATGAATCTTCTATGATGCTTCGAGTTGACTTTAGGAATTA
60305 TTCATTTTCTTCCATTAGTACATCCGTCTTTTTGCA
196 TTCATTTTCTTCCATTAGTACATCCGTCTTTTTGCA
60341 CAAGGTCGTT
Statistics
Matches: 227, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 227 1.00
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.46
Consensus pattern (231 bp):
GCCATCAAGCTTCATGTCAATGCTTCCTTTGGTTTTTGCCCCATTCCTTGATTTGTCTTTTCTCT
TCATTGATGCCGATACATCCATTTTTTCCTTCCTCCTTTGATTCCACTCCTTGATTTGTTTTCTC
TAAAGCTCAACATATTGTTTGTATAATGAATCTTCTATGATGCTTCGAGTTGACTTTAGGAATTA
TTCATTTTCTTCCATTAGTACATCCGTCTTTTTGCA
Found at i:67653 original size:19 final size:19
Alignment explanation
Indices: 67616--67655 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
67606 TGGCCTTGAA
* *
67616 AGCAATAAAATATCCTTTT
1 AGCAATAAAATAACATTTT
67635 AGCAATAAAATAACATTTT
1 AGCAATAAAATAACATTTT
67654 AG
1 AG
67656 ACAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (19 bp):
AGCAATAAAATAACATTTT
Found at i:87277 original size:28 final size:28
Alignment explanation
Indices: 87227--87280 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
87217 TACTTTTAAT
*
87227 AATTAGATGTCATTTTTGTAAATATTGA
1 AATTAGATGTCATTTTTGCAAATATTGA
*
87255 AATTAGCTGTC-TTTTCTGCAAATATT
1 AATTAGATGTCATTTT-TGCAAATATT
87281 TTAAAATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (28 bp):
AATTAGATGTCATTTTTGCAAATATTGA
Found at i:97927 original size:15 final size:14
Alignment explanation
Indices: 97907--97937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
97897 TCCTCAAACC
97907 AAGGGAGTTATAGAT
1 AAGGGAGTTATA-AT
97922 AAGGGAGTTATAAT
1 AAGGGAGTTATAAT
97936 AA
1 AA
97938 CCATCAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
AAGGGAGTTATAAT
Found at i:113499 original size:36 final size:36
Alignment explanation
Indices: 113454--113522 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
113444 TCAAACCAAC
*
113454 TATTTTTAAGAAAAGTATGTTGTGTGGTTATGACTA
1 TATTTTTAAGAAAAGTATGTTATGTGGTTATGACTA
113490 TATTTTTAAGAAAAGTATGTTATGTGGTTATGA
1 TATTTTTAAGAAAAGTATGTTATGTGGTTATGA
113523 TTATCACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (36 bp):
TATTTTTAAGAAAAGTATGTTATGTGGTTATGACTA
Found at i:113903 original size:43 final size:43
Alignment explanation
Indices: 113812--113962 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 43
113802 CTTCTCTGTA
* * * *
113812 AATTTGGTGGCTTTGTCCACAACCTACACGACAACTTGTTTGCA
1 AATTTGGTGG-TTTATCCACAACCTACATGACAGCTTGTTTGCG
* ** * *
113856 AATTTGGTGGTTTATCCATAACCTGTATGGCAGCTTGTATGCG
1 AATTTGGTGGTTTATCCACAACCTACATGACAGCTTGTTTGCG
*
113899 AATTTGGTGGTTTATCCACAATCTACATGACAGCTTGTTTGCG
1 AATTTGGTGGTTTATCCACAACCTACATGACAGCTTGTTTGCG
* *
113942 AATTTGATGGCTTCATCCACA
1 AATTTGGTGG-TTTATCCACA
113963 TATATGTCGG
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 70 0.79
44 19 0.21
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
AATTTGGTGGTTTATCCACAACCTACATGACAGCTTGTTTGCG
Found at i:114146 original size:19 final size:20
Alignment explanation
Indices: 114098--114146 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
114088 GCATCTTGCA
* *
114098 ATATGTGAAATTATGTTGTT
1 ATATATGAAATTATGTTATT
114118 ATATAT-AAATTATGTTATT
1 ATATATGAAATTATGTTATT
*
114137 -TTTATGAAAT
1 ATATATGAAAT
114147 GTACGTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
ATATATGAAATTATGTTATT
Found at i:121218 original size:32 final size:32
Alignment explanation
Indices: 121173--121239 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
121163 ATCGTGGCAA
*
121173 AATCCATTGGAATCTAATTATATACAATATGG
1 AATCCATTGGAATCTAATTATATACAATAAGG
*
121205 AATCCATTTGAATCTAATTATATACAATAAGG
1 AATCCATTGGAATCTAATTATATACAATAAGG
121237 AAT
1 AAT
121240 ATGAATGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (32 bp):
AATCCATTGGAATCTAATTATATACAATAAGG
Found at i:126521 original size:22 final size:21
Alignment explanation
Indices: 126481--126522 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
126471 TAAAATCATT
* *
126481 TTTAAAAAAATATATAAATTA
1 TTTAAAAAAATAAAAAAATTA
126502 TTTAAAAAGAATAAAAAAATT
1 TTTAAAAA-AATAAAAAAATT
126523 CACATCAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TTTAAAAAAATAAAAAAATTA
Found at i:126642 original size:8 final size:8
Alignment explanation
Indices: 126631--126656 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
126621 AAAATTAAAT
126631 AATTTATA
1 AATTTATA
126639 AATTTATA
1 AATTTATA
126647 AATTTATA
1 AATTTATA
126655 AA
1 AA
126657 CACATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTATA
Found at i:126756 original size:15 final size:15
Alignment explanation
Indices: 126738--126779 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
126728 TTATTAAAAT
126738 ATATTTTATAAATAC
1 ATATTTTATAAATAC
*
126753 ATATTTCTAT-AATAT
1 ATATTT-TATAAATAC
126768 ATA-TTTATAAAT
1 ATATTTTATAAAT
126780 TTTTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.12
14 5 0.21
15 13 0.54
16 3 0.12
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTATAAATAC
Found at i:126803 original size:13 final size:13
Alignment explanation
Indices: 126721--126813 Score: 66
Period size: 13 Copynumber: 7.0 Consensus size: 13
126711 ATAAAAGCTT
*
126721 TATAAATTTATTAA
1 TATATATTT-TTAA
*
126735 AATATATTTTATAAA
1 TATATATTTT-T-AA
*
126750 TACATATTTCTATAA
1 TATATATTT-T-TAA
*
126765 TATATATTTATAA
1 TATATATTTTTAA
*
126778 -AT-T-TTTATAA
1 TATATATTTTTAA
*
126788 TATGTATTTTTAA
1 TATATATTTTTAA
126801 TATATATTTTTAA
1 TATATATTTTTAA
126814 AAATTTATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.11
11 3 0.05
12 3 0.05
13 22 0.34
14 8 0.12
15 19 0.29
16 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (13 bp):
TATATATTTTTAA
Found at i:127285 original size:22 final size:21
Alignment explanation
Indices: 127262--127310 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
127252 AATGATATCA
127262 AAACAACATCAAAATGACAAC
1 AAACAACATCAAAATGACAAC
* **
127283 AAACAACAATAAAAAAAACAAC
1 AAACAAC-ATCAAAATGACAAC
127305 AAACAA
1 AAACAA
127311 TAGTGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.06
Consensus pattern (21 bp):
AAACAACATCAAAATGACAAC
Found at i:128810 original size:4 final size:4
Alignment explanation
Indices: 128801--128825 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
128791 TTAGAGATCG
128801 CCAA CCAA CCAA CCAA CCAA CCAA C
1 CCAA CCAA CCAA CCAA CCAA CCAA C
128826 AAACAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (4 bp):
CCAA
Found at i:130552 original size:18 final size:18
Alignment explanation
Indices: 130529--130574 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
130519 CTATTTATAT
*
130529 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
130547 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
130566 AATTGAATT
1 TATTGAATT
130575 ATTAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Found at i:138371 original size:17 final size:17
Alignment explanation
Indices: 138351--138383 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
138341 TTCCTTTTCC
138351 TTTTAT-TTTCTATTTTG
1 TTTTATCTTT-TATTTTG
138368 TTTTATCTTTTATTTT
1 TTTTATCTTTTATTTT
138384 ATCTCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATCTTTTATTTTG
Found at i:165384 original size:3 final size:3
Alignment explanation
Indices: 165365--165401 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
165355 GAAGGTCAAG
*
165365 AGA AGT AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
165402 GCATGAGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:165814 original size:21 final size:21
Alignment explanation
Indices: 165788--165848 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 21
165778 GCAGCCTCGG
165788 TATTGTCATTGCATACATTTT
1 TATTGTCATTGCATACATTTT
*
165809 TATTGTAGTTAGATTGCATACATTTT
1 TA-T-T-G-T-CATTGCATACATTTT
165835 TATTGTCATTGCAT
1 TATTGTCATTGCAT
165849 TTTATTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 9 0.27
22 2 0.06
23 2 0.06
24 2 0.06
25 2 0.06
26 16 0.48
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (21 bp):
TATTGTCATTGCATACATTTT
Found at i:169450 original size:20 final size:21
Alignment explanation
Indices: 169412--169450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
169402 TAAATCGAGC
*
169412 GTCACTGAGTTAGAAAATGTA
1 GTCACTAAGTTAGAAAATGTA
169433 GTCACTAAGTTA-AAAATG
1 GTCACTAAGTTAGAAAATG
169451 CTAAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (21 bp):
GTCACTAAGTTAGAAAATGTA
Found at i:177002 original size:33 final size:33
Alignment explanation
Indices: 176943--177071 Score: 132
Period size: 33 Copynumber: 3.9 Consensus size: 33
176933 ATGACATGTA
* * * *
176943 AGTACACAGTATGCTCATAAGAGCTAATCAATC
1 AGTACACTGTACGCTCGTAAGAGCTAACCAATC
* **
176976 TGTACTTTGTACGCTCGTAAGAGCTAACCAATC
1 AGTACACTGTACGCTCGTAAGAGCTAACCAATC
* *
177009 AGTACACTGTATGCTCGTAAGAGCTAACCAATT
1 AGTACACTGTACGCTCGTAAGAGCTAACCAATC
* * * * *
177042 ACTACACTATATGCTCATAAGAGTTAACCA
1 AGTACACTGTACGCTCGTAAGAGCTAACCA
177072 GCGAACACAC
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (33 bp):
AGTACACTGTACGCTCGTAAGAGCTAACCAATC
Found at i:177063 original size:66 final size:66
Alignment explanation
Indices: 176943--177071 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
176933 ATGACATGTA
* * ** * *
176943 AGTACACAGTATGCTCATAAGAGCTAATCAATCTGTACTTTGTACGCTCGTAAGAGCTAACCAAT
1 AGTACACAGTATGCTCATAAGAGCTAACCAATCTCTACACTATACGCTCATAAGAGCTAACCAAT
177008 C
66 C
* * * *
177009 AGTACACTGTATGCTCGTAAGAGCTAACCAAT-TACTACACTATATGCTCATAAGAGTTAACCA
1 AGTACACAGTATGCTCATAAGAGCTAACCAATCT-CTACACTATACGCTCATAAGAGCTAACCA
177072 GCGAACACAC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 1 0.02
66 51 0.98
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (66 bp):
AGTACACAGTATGCTCATAAGAGCTAACCAATCTCTACACTATACGCTCATAAGAGCTAACCAAT
C
Found at i:180383 original size:25 final size:25
Alignment explanation
Indices: 180355--180406 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
180345 TTACAAAAAT
* *
180355 TTAGCTCATACGAGCCTAGATAGAG
1 TTAGCTCATACGAGCCCAGATAAAG
*
180380 TTAGCTCTTACGAGCCCAGATAAAG
1 TTAGCTCATACGAGCCCAGATAAAG
180405 TT
1 TT
180407 TAAATAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
TTAGCTCATACGAGCCCAGATAAAG
Found at i:183742 original size:12 final size:12
Alignment explanation
Indices: 183725--183760 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
183715 TTTTGAGAGC
183725 ATAAAATAAAAG
1 ATAAAATAAAAG
*
183737 ATAAAATAAAAT
1 ATAAAATAAAAG
*
183749 AGAAAATAAAAG
1 ATAAAATAAAAG
183761 CGAAAGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:183747 original size:17 final size:17
Alignment explanation
Indices: 183725--183759 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
183715 TTTTGAGAGC
183725 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
183742 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
183759 A
1 A
183760 GCGAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:183765 original size:12 final size:12
Alignment explanation
Indices: 183727--183765 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
183717 TTGAGAGCAT
*
183727 AAAATAAAAGAT
1 AAAATAAAAGAG
*
183739 AAAATAAAATAG
1 AAAATAAAAGAG
*
183751 AAAATAAAAGCG
1 AAAATAAAAGAG
183763 AAA
1 AAA
183766 GTTTGAGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:217593 original size:73 final size:73
Alignment explanation
Indices: 217516--217662 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
217506 ACTAATCCTA
217516 ATTAAGTAAATCAATTAACTCAAATTAAGGTTTGCCATATAACTCTTTTCAAGAGTTATCAGGAG
1 ATTAAGTAAATCAATTAACTCAAATTAAGGTTTGCCATATAACTCTTTTCAAGAGTTATCAGGAG
217581 GCAACGTC
66 GCAACGTC
217589 ATTAAGTAAATCAATTAACTCAAATTAAGGTTTGCCATATAACTCTTTTCAAGAGTTATCAGGAG
1 ATTAAGTAAATCAATTAACTCAAATTAAGGTTTGCCATATAACTCTTTTCAAGAGTTATCAGGAG
217654 GCAACGTC
66 GCAACGTC
217662 A
1 A
217663 CTAGTTTGGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (73 bp):
ATTAAGTAAATCAATTAACTCAAATTAAGGTTTGCCATATAACTCTTTTCAAGAGTTATCAGGAG
GCAACGTC
Found at i:239030 original size:51 final size:50
Alignment explanation
Indices: 238905--239097 Score: 251
Period size: 51 Copynumber: 3.8 Consensus size: 50
238895 CTGTATAGGA
* * * **
238905 ATTCATGTACTCACGATGACACTAAGTCATTGGACCTCACAATCATTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCT-TTAATCA-TAAAGG
* *
238957 ATTCATTTACTCACGATAACACTTAGTCATCGGACCTTTAATCCATAGAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAAT-CATAAAGG
* * *
239008 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTAAATTCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAA-TCATAAAGG
*
239059 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
239098 TTATTTACGG
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
51 88 0.71
52 36 0.29
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (50 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCATAAAGG
Found at i:239086 original size:102 final size:103
Alignment explanation
Indices: 238905--239097 Score: 291
Period size: 102 Copynumber: 1.9 Consensus size: 103
238895 CTGTATAGGA
* *
238905 ATTCATGTACTCACGATGACACTAAGTCATTGGACCTCACAATCATTAAAGGATTCATTTACTCA
1 ATTCATGTACTCACGATGACACTAAGTCATCGGACCTCACAATCAGTAAAGGATTCATTTACTCA
*
238970 CGATAACACTTAGTCATCGGACCTTTAATCCATAGAGG
66 CGATAACACTTAGTCATCAGACCTTTAATCCATAGAGG
* * * *
239008 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTA-AATTC-GTAAAGGATTCATTTACTC
1 ATTCATGTACTCACGATGACACTAAGTCATCGGACCTCACAA-TCAGTAAAGGATTCATTTACTC
*
239071 ACGATGACACTTAGTCATCAGACCTTT
65 ACGATAACACTTAGTCATCAGACCTTT
239098 TTATTTACGG
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 45 0.56
103 36 0.44
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (103 bp):
ATTCATGTACTCACGATGACACTAAGTCATCGGACCTCACAATCAGTAAAGGATTCATTTACTCA
CGATAACACTTAGTCATCAGACCTTTAATCCATAGAGG
Found at i:239988 original size:22 final size:21
Alignment explanation
Indices: 239937--239988 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
239927 TTAGACTTTC
*
239937 ATTATTAACTTAATTAATCAT
1 ATTATTAACTTAATAAATCAT
* *
239958 ATCTTTTAACCTTAATAAATCCT
1 AT-TATTAA-CTTAATAAATCAT
239981 ATTATTAA
1 ATTATTAA
239989 TCAATATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 10 0.40
23 13 0.52
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAACTTAATAAATCAT
Found at i:246014 original size:51 final size:51
Alignment explanation
Indices: 245912--246096 Score: 212
Period size: 51 Copynumber: 3.6 Consensus size: 51
245902 TTTCATTTAA
* * * * *
245912 TACTCACGATGACA-TATTGTTATCGGACCTCACAATCCGTAAAAGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTA-AATCCATAAAGGATTCATT
* * * *
245964 TACTTACGATAACACTTAGTCATCGGACCGTT-AATCCTTATAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACC-TTAAATCCATAAAGGATTCATT
* * * *
246015 TACTCATGATGACACTTAGTCGTTGGACCTTAAATCCATAAAGGATCCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTAAATCCATAAAGGATTCATT
246066 TACTCACGATGACACTTAGTCATCGGACCTT
1 TACTCACGATGACACTTAGTCATCGGACCTT
246097 TTTGTTTATA
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 2 0.02
51 84 0.76
52 23 0.21
53 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTAAATCCATAAAGGATTCATT
Found at i:246724 original size:11 final size:11
Alignment explanation
Indices: 246708--246734 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
246698 TTAAATCAAG
246708 TATTTTCATAA
1 TATTTTCATAA
246719 TATTTTCATAA
1 TATTTTCATAA
246730 TATTT
1 TATTT
246735 AGTTAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTCATAA
Found at i:259566 original size:30 final size:30
Alignment explanation
Indices: 259464--259569 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
259454 TTACCAAAAA
*
259464 GTGGAAGCCTTTATGGCTATTCTCTGATAT
1 GTGGAAGCCTTTTTGGCTATTCTCTGATAT
* * * *
259494 GTGGAAGCCTTTGTGGTTATTCTTTAATAT
1 GTGGAAGCCTTTTTGGCTATTCTCTGATAT
* * *
259524 GTGAAAGCCTTTTTAGCTGTTCTCTGATAT
1 GTGGAAGCCTTTTTGGCTATTCTCTGATAT
*
259554 TTGGAAGCCTTTTTGG
1 GTGGAAGCCTTTTTGG
259570 TAGAACCTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (30 bp):
GTGGAAGCCTTTTTGGCTATTCTCTGATAT
Found at i:259773 original size:29 final size:29
Alignment explanation
Indices: 259742--259799 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
259732 TTTGGACACC
* *
259742 TTTGTTGCTATCTAATGTTAAGTGGATGCT
1 TTTGTGGCTAGCTAA-GTTAAGTGGATGCT
*
259772 TTTGTGGCTAGCTAAGTTATGTGGATGC
1 TTTGTGGCTAGCTAAGTTAAGTGGATGC
259800 CTTCATGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (29 bp):
TTTGTGGCTAGCTAAGTTAAGTGGATGCT
Found at i:262707 original size:21 final size:22
Alignment explanation
Indices: 262668--262710 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
262658 AAAAAAAAAA
*
262668 TTAGAGAAAATAAATTAATTTT
1 TTAGAAAAAATAAATTAATTTT
*
262690 TTAGAAAAAATATA-TAATTTT
1 TTAGAAAAAATAAATTAATTTT
262711 GAATTAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TTAGAAAAAATAAATTAATTTT
Found at i:263697 original size:19 final size:17
Alignment explanation
Indices: 263662--263709 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
263652 TATGTCACGT
*
263662 TAAAAAATAATTTAAAAA
1 TAAAAAAT-ATTCAAAAA
263680 TTATAAAAATATTCAAAAA
1 -TA-AAAAATATTCAAAAA
263699 TAAAAAATATT
1 TAAAAAATATT
263710 TATAAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
19 10 0.37
20 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATATTCAAAAA
Found at i:263716 original size:19 final size:18
Alignment explanation
Indices: 263662--263717 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
263652 TATGTCACGT
*
263662 TAAAAAATAATTTAAAAAT
1 TAAAAAAT-ATTTAAAAAA
*
263681 TATAAAAATA-TTCAAAAA
1 TA-AAAAATATTTAAAAAA
263699 TAAAAAATATTTATAAAAA
1 TAAAAAATATTTA-AAAAA
263718 GTTGATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.23
18 10 0.32
19 8 0.26
20 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATATTTAAAAAA
Found at i:265235 original size:14 final size:14
Alignment explanation
Indices: 265216--265243 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
265206 ATTTAAAATT
265216 TTTATTTAATTAAA
1 TTTATTTAATTAAA
265230 TTTATTTAATTAAA
1 TTTATTTAATTAAA
265244 AACCTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTTAATTAAA
Found at i:279646 original size:34 final size:34
Alignment explanation
Indices: 279592--279659 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
279582 TTCTTTCCCT
* *
279592 TTACATCCCACTGCATCTCACCTCCTTATTTCTC
1 TTACATCCCACTCCACCTCACCTCCTTATTTCTC
* *
279626 TTACATCTCACTCCACCTCACCTCTTTATTTCTC
1 TTACATCCCACTCCACCTCACCTCCTTATTTCTC
279660 ATTCTCTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.18, C:0.41, G:0.01, T:0.40
Consensus pattern (34 bp):
TTACATCCCACTCCACCTCACCTCCTTATTTCTC
Done.