Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002659.1 Kokia drynarioides strain JFW-HI SEQ_114908, 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: 36389
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:2589 original size:33 final size:33
Alignment explanation
Indices: 2552--2619 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2542 CAATAAATAT
*
2552 TTGGATCTTGTTCTTAATTATGTGTGTTTAATC
1 TTGGATCTTGTTCTCAATTATGTGTGTTTAATC
2585 TTGGATCTTGTTCTCAATTATGTGTGTTTAATC
1 TTGGATCTTGTTCTCAATTATGTGTGTTTAATC
2618 TT
1 TT
2620 TGGTTTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (33 bp):
TTGGATCTTGTTCTCAATTATGTGTGTTTAATC
Found at i:4290 original size:24 final size:24
Alignment explanation
Indices: 4263--4308 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4253 ATATCATCAT
4263 AATA-ATATTAATTATAATTTTAAA
1 AATATATATT-ATTATAATTTTAAA
*
4287 AATATATATTTTTATAATTTTA
1 AATATATATTATTATAATTTTA
4309 TAATTGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATATATTATTATAATTTTAAA
Found at i:4467 original size:42 final size:42
Alignment explanation
Indices: 4408--4503 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
4398 TAAAACGGTG
4408 GAATCGAGCGATATTTGGGCGGATATTGACAGAGGCTAGCGA
1 GAATCGAGCGATATTTGGGCGGATATTGACAGAGGCTAGCGA
4450 GAATCGAGCGATATTTGGGCGGATATTGACAGAGGCTAGCGA
1 GAATCGAGCGATATTTGGGCGGATATTGACAGAGGCTAGCGA
*
4492 GAATCGATCGAT
1 GAATCGAGCGAT
4504 GAGAAGACTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GAATCGAGCGATATTTGGGCGGATATTGACAGAGGCTAGCGA
Found at i:11005 original size:30 final size:29
Alignment explanation
Indices: 10969--11248 Score: 153
Period size: 30 Copynumber: 9.5 Consensus size: 29
10959 TTGAATTGTC
* **
10969 CAAAAATCATATTTTGGCCCTTAAACTTAT
1 CAAAAATCACATTTTAACCCTTAAACTT-T
* *
10999 CAAAAATTACATTTTAACCCCTAAACTTT
1 CAAAAATCACATTTTAACCCTTAAACTTT
* *
11028 CCAAAAATTACATTTTAACCCTCAAACTTT
1 -CAAAAATCACATTTTAACCCTTAAACTTT
** * ** *
11058 TGAAAATCATATTTTAACCCTCGAAGTTT
1 CAAAAATCACATTTTAACCCTTAAACTTT
* *
11087 CCAAAAATTACATTTTTACCCTTAAACTTT
1 -CAAAAATCACATTTTAACCCTTAAACTTT
*** * *
11117 TTGAAATTACATCTTTGA-CCTTAAA-TTT
1 CAAAAATCACAT-TTTAACCCTTAAACTTT
* * **
11145 CTTAAAAATTACATTTTCACCCTCGAACTTT
1 C--AAAAATCACATTTTAACCCTTAAACTTT
11176 CAAAAATTC-CATTTTAACACC--AAA-TTT
1 CAAAAA-TCACATTTTAAC-CCTTAAACTTT
* * *
11203 CCTAAAAGTTACCATTTT-ACCCTTAAACTTC
1 -C-AAAAATCA-CATTTTAACCCTTAAACTTT
11234 CAAAAATTC-CATTTT
1 CAAAAA-TCACATTTT
11249 TGACCTCGAA
Statistics
Matches: 194, Mismatches: 39, Indels: 36
0.72 0.14 0.13
Matches are distributed among these distances:
27 3 0.02
28 15 0.08
29 67 0.35
30 103 0.53
31 6 0.03
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
CAAAAATCACATTTTAACCCTTAAACTTT
Found at i:11064 original size:29 final size:29
Alignment explanation
Indices: 10986--11284 Score: 209
Period size: 29 Copynumber: 10.2 Consensus size: 29
10976 CATATTTTGG
*
10986 CCCTTAAACTTATCAAAAATTACATTTTAA
1 CCCTCAAACTT-TCAAAAATTACATTTTAA
11016 CCC-CTAAACTTTCCAAAAATTACATTTTAA
1 CCCTC-AAACTTT-CAAAAATTACATTTTAA
** * *
11046 CCCTCAAACTTTTGAAAATCATATTTTAA
1 CCCTCAAACTTTCAAAAATTACATTTTAA
* * *
11075 CCCTCGAAGTTTCCAAAAATTACATTTTTA
1 CCCTCAAACTTT-CAAAAATTACATTTTAA
* *** *
11105 CCCTTAAACTTTTTGAAATTACATCTTTGA
1 CCCTCAAACTTTCAAAAATTACAT-TTTAA
* *
11135 -CCTTAAA-TTTCTTAAAAATTACATTTTCA
1 CCCTCAAACTTTC--AAAAATTACATTTTAA
* *
11164 CCCTCGAACTTTCAAAAATTCCATTTTAA
1 CCCTCAAACTTTCAAAAATTACATTTTAA
* *
11193 CAC-CAAA-TTTCCTAAAAGTTACCATTTT-A
1 CCCTCAAACTTT-C-AAAAATTA-CATTTTAA
* * * *
11222 CCCTTAAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTTCAAAAATTACA-TTTTAA
* *
11252 -CCTCGAACTTTCAAAAATTTCCATTTT-A
1 CCCTCAAACTTTCAAAAA-TTACATTTTAA
11280 CCCTC
1 CCCTC
11285 GAAAATCACA
Statistics
Matches: 212, Mismatches: 39, Indels: 37
0.74 0.14 0.13
Matches are distributed among these distances:
27 3 0.01
28 10 0.05
29 101 0.48
30 91 0.43
31 7 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTCAAACTTTCAAAAATTACATTTTAA
Found at i:11152 original size:59 final size:58
Alignment explanation
Indices: 10986--11248 Score: 228
Period size: 59 Copynumber: 4.5 Consensus size: 58
10976 CATATTTTGG
* *
10986 CCCTTAAACTTATCAAAAATTACATTTTAACCCCTAAACTTTCC-AAAAATTACATTTTAA
1 CCCTTAAACTT-TCAAAAATTACATTTTAACACC-AAA-TTTCCTAAAAATTACATTTTTA
* ** * * * *
11046 CCCTCAAACTTTTGAAAATCATATTTTAACCCTCGAAGTTTCC-AAAAATTACATTTTTA
1 CCCTTAAACTTTCAAAAATTACATTTTAACAC-C-AAATTTCCTAAAAATTACATTTTTA
*** * * * *
11105 CCCTTAAACTTTTTGAAATTACATCTTTGAC-CTTAAATTTCTTAAAAATTACATTTTCA
1 CCCTTAAACTTTCAAAAATTACAT-TTTAACAC-CAAATTTCCTAAAAATTACATTTTTA
** * *
11164 CCCTCGAACTTTCAAAAATTCCATTTTAACACCAAATTTCCTAAAAGTTACCA-TTTTA
1 CCCTTAAACTTTCAAAAATTACATTTTAACACCAAATTTCCTAAAAATTA-CATTTTTA
* *
11222 CCCTTAAACTTCCAAAAATTCCATTTT
1 CCCTTAAACTTTCAAAAATTACATTTT
11249 TGACCTCGAA
Statistics
Matches: 166, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
58 54 0.33
59 94 0.57
60 18 0.11
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (58 bp):
CCCTTAAACTTTCAAAAATTACATTTTAACACCAAATTTCCTAAAAATTACATTTTTA
Found at i:11276 original size:58 final size:59
Alignment explanation
Indices: 10986--11283 Score: 222
Period size: 59 Copynumber: 5.1 Consensus size: 59
10976 CATATTTTGG
* * * *
10986 CCCTTAAACTTATCAAAAATTACA-TTTTAACCCCTAAACTTTCC-AAAAATTACATTTTAA
1 CCCTTAAACTT-TCAAAAATTCCATTTTTGACCTCGAAA-TTTCCTAAAAATTACATTTT-A
* ** * *
11046 CCCTCAAACTTTTGAAAA-T-CATATTTTAACCCTCGAAGTTTCC-AAAAATTACATTTTTA
1 CCCTTAAACTTTCAAAAATTCCAT-TTTTGA-CCTCGAAATTTCCTAAAAATTACA-TTTTA
*** * * * *
11105 CCCTTAAACTTTTTGAAATTACATCTTTGACCT-TAAATTTCTTAAAAATTACATTTTCA
1 CCCTTAAACTTTCAAAAATTCCATTTTTGACCTCGAAATTTCCTAAAAATTACATTTT-A
** * *
11164 CCCTCGAACTTTCAAAAATTCCA-TTTTAACAC-C-AAATTTCCTAAAAGTTACCATTTTA
1 CCCTTAAACTTTCAAAAATTCCATTTTTGAC-CTCGAAATTTCCTAAAAATTA-CATTTTA
* * *
11222 CCCTTAAACTTCCAAAAATTCCATTTTTGACCTCGAACTTT-C-AAAAATTTCCATTTTA
1 CCCTTAAACTTTCAAAAATTCCATTTTTGACCTCGAAATTTCCTAAAAA-TTACATTTTA
11280 CCCT
1 CCCT
11284 CGAAAATCAC
Statistics
Matches: 192, Mismatches: 31, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
57 2 0.01
58 68 0.35
59 90 0.47
60 29 0.15
61 3 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (59 bp):
CCCTTAAACTTTCAAAAATTCCATTTTTGACCTCGAAATTTCCTAAAAATTACATTTTA
Found at i:11285 original size:29 final size:29
Alignment explanation
Indices: 11148--11373 Score: 119
Period size: 29 Copynumber: 7.8 Consensus size: 29
11138 TAAATTTCTT
*
11148 AAAAA-TTACATTTTCACCCTCGAACTTTC
1 AAAAATTTCCATTTT-ACCCTCGAACTTTC
* *
11177 AAAAA-TTCCATTTTAACAC-C-AAATTTCC
1 AAAAATTTCCATTTT-ACCCTCGAACTTT-C
* * ** *
11205 TAAAAGTTACCATTTTACCCTTAAACTTCC
1 -AAAAATTTCCATTTTACCCTCGAACTTTC
11235 AAAAA-TTCCATTTTTGA-CCTCGAACTTTC
1 AAAAATTTCCA-TTTT-ACCCTCGAACTTTC
**
11264 AAAAATTTCCATTTTACCCTCGAA-AATC
1 AAAAATTTCCATTTTACCCTCGAACTTTC
* * * * *
11292 ACAAAATTACCATTTT-CGCCCCTAAGTGTC
1 A-AAAATTTCCATTTTAC-CCTCGAACTTTC
* * * *
11322 CAAAATTAT-CGTTTTACCCTCGAACCTCC
1 AAAAATT-TCCATTTTACCCTCGAACTTTC
* *
11351 AAAAATTACCATTTTACCTTCGA
1 AAAAATTTCCATTTTACCCTCGA
11374 GTATCCAAAA
Statistics
Matches: 147, Mismatches: 35, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
27 5 0.03
28 11 0.07
29 109 0.74
30 18 0.12
31 4 0.03
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTTCCATTTTACCCTCGAACTTTC
Found at i:11327 original size:87 final size:88
Alignment explanation
Indices: 11148--11373 Score: 204
Period size: 87 Copynumber: 2.6 Consensus size: 88
11138 TAAATTTCTT
* *
11148 AAAAATTA-CATTTTCACCCTCGAACTTTCAAAAA-TTCCATTTTAACAC-C-AAATTTCCTAAA
1 AAAAATTATC-TTTT-ACCCTCGAACTTTCAAAAATTTCCATTTT-ACCCTCGAAATATCCTAAA
*
11209 AGTTACCATTTTACCCTTAAACTTCC
63 AGTTACCATTTTACCCCTAAACTTCC
11235 AAAAATTCCAT-TTTTGA-CCTCGAACTTTCAAAAATTTCCATTTTACCCTCGAAA-ATCAC-AA
1 AAAAATT--ATCTTTT-ACCCTCGAACTTTCAAAAATTTCCATTTTACCCTCGAAATATC-CTAA
* *
11296 AA-TTACCATTTTCGCCCCT-AAGTGTCC
62 AAGTTACCATTTT-ACCCCTAAACT-TCC
* * * *
11323 -AAAATTATCGTTTTACCCTCGAACCTCCAAAAATTACCATTTTACCTTCGA
1 AAAAATTATC-TTTTACCCTCGAACTTTCAAAAATTTCCATTTTACCCTCGA
11374 GTATCCAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
85 2 0.02
86 1 0.01
87 81 0.69
88 28 0.24
89 5 0.04
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (88 bp):
AAAAATTATCTTTTACCCTCGAACTTTCAAAAATTTCCATTTTACCCTCGAAATATCCTAAAAGT
TACCATTTTACCCCTAAACTTCC
Found at i:15249 original size:24 final size:23
Alignment explanation
Indices: 15201--15260 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
15191 AAAATCAATT
15201 CATTTTCTT-GCATTACATACATG
1 CATTTT-TTCGCATTACATACATG
*
15224 CATTTTATTCGCATTACAT-CTTTG
1 CATTTT-TTCGCATTACATAC-ATG
*
15248 CATATTTTCGCAT
1 CATTTTTTCGCAT
15261 AATTAATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.47
Consensus pattern (23 bp):
CATTTTTTCGCATTACATACATG
Found at i:19519 original size:20 final size:20
Alignment explanation
Indices: 19505--19711 Score: 243
Period size: 20 Copynumber: 10.3 Consensus size: 20
19495 TCACCAGCAC
*
19505 AAAGCCTGATACACCGACAT
1 AAAGCCTGATACACCGGCAT
* * *
19525 AAAGCCTGATTCACCTGCAC
1 AAAGCCTGATACACCGGCAT
19545 AAAGCCTGATACACCGGCAT
1 AAAGCCTGATACACCGGCAT
* *
19565 AAAGCCTGATTCACCGGCAC
1 AAAGCCTGATACACCGGCAT
* * *
19585 AAAGCTTGATACGCTGGCAT
1 AAAGCCTGATACACCGGCAT
* * ***
19605 AAAGCCTAATTCACATACAT
1 AAAGCCTGATACACCGGCAT
*
19625 AAAGCCTGATACACCGTCAT
1 AAAGCCTGATACACCGGCAT
* * *
19645 AAAGCCTAATTCACCAGCAT
1 AAAGCCTGATACACCGGCAT
19665 AAAGCCTGATACACCGGCAT
1 AAAGCCTGATACACCGGCAT
*
19685 AAAGCCTGATACACCGACAT
1 AAAGCCTGATACACCGGCAT
19705 AAAGCCT
1 AAAGCCT
19712 AGTACATAGA
Statistics
Matches: 153, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 153 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAGCCTGATACACCGGCAT
Found at i:19545 original size:40 final size:40
Alignment explanation
Indices: 19489--19699 Score: 280
Period size: 40 Copynumber: 5.3 Consensus size: 40
19479 TATATTAGTT
* *
19489 CCTGAATCACCAGCACAAAGCCTGATACACCGACATAAAG
1 CCTGATTCACCAGCACAAAGCCTGATACACCGGCATAAAG
*
19529 CCTGATTCACCTGCACAAAGCCTGATACACCGGCATAAAG
1 CCTGATTCACCAGCACAAAGCCTGATACACCGGCATAAAG
* * * *
19569 CCTGATTCACCGGCACAAAGCTTGATACGCTGGCATAAAG
1 CCTGATTCACCAGCACAAAGCCTGATACACCGGCATAAAG
* * * *
19609 CCTAATTCA-CATACATAAAGCCTGATACACCGTCATAAAG
1 CCTGATTCACCA-GCACAAAGCCTGATACACCGGCATAAAG
* *
19649 CCTAATTCACCAGCATAAAGCCTGATACACCGGCATAAAG
1 CCTGATTCACCAGCACAAAGCCTGATACACCGGCATAAAG
*
19689 CCTGATACACC
1 CCTGATTCACC
19700 GACATAAAGC
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 147 0.98
41 2 0.01
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.18
Consensus pattern (40 bp):
CCTGATTCACCAGCACAAAGCCTGATACACCGGCATAAAG
Found at i:21920 original size:8 final size:8
Alignment explanation
Indices: 21907--21941 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
21897 TTATAAAATT
21907 TAATTATA
1 TAATTATA
21915 TAATTATA
1 TAATTATA
*
21923 TATATTAAA
1 TA-ATTATA
21932 TAATTATA
1 TAATTATA
21940 TA
1 TA
21942 TATTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TAATTATA
Found at i:21926 original size:25 final size:24
Alignment explanation
Indices: 21898--21955 Score: 57
Period size: 25 Copynumber: 2.3 Consensus size: 24
21888 TATATTATGT
21898 TATAAAATTTAATTATATA-ATTATA
1 TATAAAA-TTAATTATATATATT-TA
21923 TATATTAAA-TAATTATATATATTTA
1 TATA--AAATTAATTATATATATTTA
*
21948 TATTAAAT
1 TATAAAAT
21956 CACTAACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
23 3 0.11
25 19 0.68
26 3 0.11
27 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAAAATTAATTATATATATTTA
Found at i:21934 original size:17 final size:17
Alignment explanation
Indices: 21909--21945 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21899 ATAAAATTTA
*
21909 ATTATATAATTATATAT
1 ATTAAATAATTATATAT
21926 ATTAAATAATTATATAT
1 ATTAAATAATTATATAT
21943 ATT
1 ATT
21946 TATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATAATTATATAT
Found at i:24001 original size:19 final size:20
Alignment explanation
Indices: 23960--24003 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23950 GTACCACAAC
* *
23960 TTTAAATTTTGAGATAGTTT
1 TTTAAATTTTAAAATAGTTT
23980 TTTAAATTTTAAAATA-TTT
1 TTTAAATTTTAAAATAGTTT
23999 TTTAA
1 TTTAA
24004 TTATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTAAATTTTAAAATAGTTT
Found at i:25122 original size:35 final size:35
Alignment explanation
Indices: 25034--25136 Score: 104
Period size: 35 Copynumber: 2.9 Consensus size: 35
25024 CATTTTATTA
*
25034 ATTATTTCT-TTAATATAAATATAA--TTAATAAAT
1 ATTATTT-TATTAATATAAATATAATTTTAATATAT
* * * *
25067 TTTAATTATTATCAAGATAAATATAATTTTGATATAT
1 ATT-ATT-TTATTAATATAAATATAATTTTAATATAT
*
25104 ATTATTTTATTAATATAAATAAAATTTTAATAT
1 ATTATTTTATTAATATAAATATAATTTTAATAT
25137 TTTTAATATT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
33 2 0.04
34 4 0.07
35 37 0.67
36 3 0.05
37 9 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
ATTATTTTATTAATATAAATATAATTTTAATATAT
Found at i:25154 original size:3 final size:3
Alignment explanation
Indices: 25146--25194 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
25136 TTTTTAATAT
25146 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25194 T
1 T
25195 ATAGTTTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27057 original size:58 final size:60
Alignment explanation
Indices: 26994--27145 Score: 193
Period size: 58 Copynumber: 2.6 Consensus size: 60
26984 ATTTTCTTTA
* **
26994 AAAATTATATTTTGATCCTCAAACTTTTTTAAAATCAAATTTTCACCCCT-AA-TTTTCC
1 AAAATTATATTTTGACCCTCAAACTTTTCCAAAATCAAATTTTCACCCCTAAACTTTTCC
* * * * *
27052 AAAATTATATTTTCACCCTTAAACTTTTCCAAACTTACATTTTCACCCCTAAACTTTTCC
1 AAAATTATATTTTGACCCTCAAACTTTTCCAAAATCAAATTTTCACCCCTAAACTTTTCC
* *
27112 AAAATTACATTTTGACCC-CAAAATTTTCCAAAAT
1 AAAATTATATTTTGACCCTCAAACTTTTCCAAAAT
27146 TTACCATTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 42 0.53
59 15 0.19
60 22 0.28
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (60 bp):
AAAATTATATTTTGACCCTCAAACTTTTCCAAAATCAAATTTTCACCCCTAAACTTTTCC
Found at i:27082 original size:30 final size:30
Alignment explanation
Indices: 27014--27162 Score: 164
Period size: 30 Copynumber: 5.1 Consensus size: 30
27004 TTTGATCCTC
** * *
27014 AAACTTTTTTAAAATCAAATTTTCACCCCT
1 AAACTTTTCCAAAATTACATTTTCACCCCT
* *
27044 -AA-TTTTCCAAAATTATATTTTCACCCTT
1 AAACTTTTCCAAAATTACATTTTCACCCCT
*
27072 AAACTTTTCCAAACTTACATTTTCACCCCT
1 AAACTTTTCCAAAATTACATTTTCACCCCT
*
27102 AAACTTTTCCAAAATTACATTTTGACCCC-
1 AAACTTTTCCAAAATTACATTTTCACCCCT
*
27131 AAAATTTTCCAAAATTTACCA-TTTC-CCCCT
1 AAACTTTTCCAAAA-TTA-CATTTTCACCCCT
27161 AA
1 AA
27163 CATCCAAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
28 21 0.21
29 21 0.21
30 58 0.57
31 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTCACCCCT
Found at i:27159 original size:29 final size:29
Alignment explanation
Indices: 27032--27230 Score: 137
Period size: 30 Copynumber: 6.9 Consensus size: 29
27022 TTAAAATCAA
*
27032 ATTTTCACCCCT--AATTTTCCAAAATTAT
1 ATTTTC-CCCCTAAAATTTTCCAAAATTAC
* * *
27060 ATTTTCACCCTTAAACTTTTCCAAACTTAC
1 ATTTTC-CCCCTAAAATTTTCCAAAATTAC
*
27090 ATTTTCACCCCTAAACTTTTCCAAAATTAC
1 ATTTTC-CCCCTAAAATTTTCCAAAATTAC
*
27120 ATTTTGACCCC-AAAATTTTCCAAAATTTACC
1 ATTTT-CCCCCTAAAATTTTCCAAAA-TTA-C
*
27151 A-TTTCCCCCTAACA---TCCAAAAATTAC
1 ATTTTCCCCCTAAAATTTTCC-AAAATTAC
* *
27177 TATTTT-GCCCTCAAA-TTTCCAAAAATTAC
1 -ATTTTCCCCCTAAAATTTTCC-AAAATTAC
*** *
27206 ATTTTTTACCTCAAATTTTCCAAAA
1 ATTTTCCCCCTAAAATTTTCCAAAA
27231 GTTCTATTTT
Statistics
Matches: 143, Mismatches: 15, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 13 0.09
28 23 0.16
29 40 0.28
30 64 0.45
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (29 bp):
ATTTTCCCCCTAAAATTTTCCAAAATTAC
Found at i:27240 original size:29 final size:30
Alignment explanation
Indices: 27044--27262 Score: 124
Period size: 30 Copynumber: 7.5 Consensus size: 30
27034 TTTCACCCCT
* *
27044 AATTTTCC-AAAATTA-TATTTTCACCCTTA
1 AATTTTCCAAAAATTACTATTTT-AACCTCA
* * *
27073 AACTTTTCC-AAACTTAC-ATTTTCACCCCTA
1 AA-TTTTCCAAAAATTACTATTTTAACCTC-A
* *
27103 AACTTTTCC-AAAATTAC-ATTTTGACCCCAA
1 AA-TTTTCCAAAAATTACTATTTTAACCTC-A
* * ***
27133 AATTTTCCAAAATTTACCATTTCCCCCT-A
1 AATTTTCCAAAAATTACTATTTTAACCTCA
**
27162 ACA---TCCAAAAATTACTATTTTGCCCTCA
1 A-ATTTTCCAAAAATTACTATTTTAACCTCA
*
27190 AA-TTTCCAAAAATTAC-ATTTTTTACCTCA
1 AATTTTCCAAAAATTACTA-TTTTAACCTCA
*
27219 AATTTTCCAAAAGTT-CTATTTTAATCCT-A
1 AATTTTCCAAAAATTACTATTTTAA-CCTCA
27248 AATTTTCCAAAAATT
1 AATTTTCCAAAAATT
27263 TCAATTTTGA
Statistics
Matches: 155, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
27 20 0.13
28 3 0.02
29 56 0.36
30 70 0.45
31 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (30 bp):
AATTTTCCAAAAATTACTATTTTAACCTCA
Found at i:30879 original size:18 final size:19
Alignment explanation
Indices: 30856--30891 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30846 CTTAAAGAGC
30856 TATTTT-ATAATGTGAAAA
1 TATTTTAATAATGTGAAAA
*
30874 TATTTTAATAATTTGAAA
1 TATTTTAATAATGTGAAA
30892 GTGTTCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
TATTTTAATAATGTGAAAA
Found at i:34019 original size:8 final size:8
Alignment explanation
Indices: 34006--34037 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
33996 TATATAAATG
34006 CGCACACA
1 CGCACACA
34014 CGCACACA
1 CGCACACA
34022 CGCACACA
1 CGCACACA
*
34030 CACACACA
1 CGCACACA
34038 GCTAATCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.50, G:0.09, T:0.00
Consensus pattern (8 bp):
CGCACACA
Found at i:34637 original size:13 final size:14
Alignment explanation
Indices: 34619--34647 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34609 ATATTTGAGG
34619 TTTAAGATTT-AAA
1 TTTAAGATTTGAAA
34632 TTTAAGATTTGAAA
1 TTTAAGATTTGAAA
34646 TT
1 TT
34648 CGAAATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTAAGATTTGAAA
Found at i:34833 original size:32 final size:32
Alignment explanation
Indices: 34796--34880 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
34786 CCATATATAA
* * * *
34796 TTTCTTTTATTATTTTTTGGAGCTTTCAATGG
1 TTTCTTTAATAATTTTTAGCAGCTTTCAATGG
* * *
34828 TTTCTTTAATGATTATTAGCAGCTTTTAATGG
1 TTTCTTTAATAATTTTTAGCAGCTTTCAATGG
34860 TTTCTTTAATAATTTTTAGCA
1 TTTCTTTAATAATTTTTAGCA
34881 TCCCATCACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.55
Consensus pattern (32 bp):
TTTCTTTAATAATTTTTAGCAGCTTTCAATGG
Done.