Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008272.1 Kokia drynarioides strain JFW-HI SEQ_122937, 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: 78331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:287 original size:6 final size:6
Alignment explanation
Indices: 271--301 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
261 GTGAATGGCA
271 GTGGAAG GTGGAG GTGGAG GTGGAG GTGGAG
1 GTGG-AG GTGGAG GTGGAG GTGGAG GTGGAG
302 AGACAAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.19, C:0.00, G:0.65, T:0.16
Consensus pattern (6 bp):
GTGGAG
Found at i:4812 original size:21 final size:21
Alignment explanation
Indices: 4786--4826 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4776 GTTGCTGCTG
4786 CTGCTGCTGATGATATTGATA
1 CTGCTGCTGATGATATTGATA
*
4807 CTGCTGCTGCTGATATTGAT
1 CTGCTGCTGATGATATTGAT
4827 GATGATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (21 bp):
CTGCTGCTGATGATATTGATA
Found at i:11922 original size:10 final size:11
Alignment explanation
Indices: 11906--11936 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
11896 TTGCTGTGAT
11906 TTTTGTTGTTA
1 TTTTGTTGTTA
11917 -TTTGTTGTTA
1 TTTTGTTGTTA
11927 TTTTGTTGTT
1 TTTTGTTGTT
11937 TGGATGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.74
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:12107 original size:38 final size:38
Alignment explanation
Indices: 12067--12138 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
12057 AATATAAATT
*
12067 TTTTTAA-TGTATTTTGA-AT-TTATTTATTTTTTAATG
1 TTTTTAAGTGTA-TTTGATATATTATATATTTTTTAATG
12103 TTTTTAAGTGTATTTGATATATTATATATTTTTTAA
1 TTTTTAAGTGTATTTGATATATTATATATTTTTTAA
12139 ATTTGTTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.38
37 6 0.19
38 14 0.44
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (38 bp):
TTTTTAAGTGTATTTGATATATTATATATTTTTTAATG
Found at i:14269 original size:34 final size:34
Alignment explanation
Indices: 14231--14296 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
14221 AAAAATTGTA
*
14231 TTTTTATAGCTTTTTA-TTTTGATAACAATATTTT
1 TTTTTATAACTTTTTACTTTTGATAA-AATATTTT
* *
14265 TTTTTATAATTTTTTACTTTTTATAAAATATT
1 TTTTTATAACTTTTTACTTTTGATAAAATATT
14297 ATAAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.64
Consensus pattern (34 bp):
TTTTTATAACTTTTTACTTTTGATAAAATATTTT
Found at i:14730 original size:18 final size:17
Alignment explanation
Indices: 14688--14730 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
14678 GTTTTAAGTT
*
14688 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
14705 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
14723 TATAATTT
1 TATAATTT
14731 AAAACACACT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:14839 original size:14 final size:14
Alignment explanation
Indices: 14820--14857 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
14810 TATATAAAAA
14820 ATTTCAATAAATAT
1 ATTTCAATAAATAT
14834 ATTTCAA-AAA-AT
1 ATTTCAATAAATAT
14846 -TTTCAATAAATA
1 ATTTCAATAAATA
14858 GAAATTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 4 0.18
14 7 0.32
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTCAATAAATAT
Found at i:17663 original size:17 final size:19
Alignment explanation
Indices: 17637--17674 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17627 ATATTATATC
17637 AAATTACATA-TTAAATTT
1 AAATTACATACTTAAATTT
*
17655 AAATT-CATACTTAATTTT
1 AAATTACATACTTAAATTT
17673 AA
1 AA
17675 TACTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTACATACTTAAATTT
Found at i:18549 original size:21 final size:20
Alignment explanation
Indices: 18516--18559 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18506 ATGGCACGTC
*
18516 AATAAAAAATATTTTTTTAAA
1 AATAAAAAATA-TTTTATAAA
**
18537 AATAAAATTTATTTTATAAA
1 AATAAAAAATATTTTATAAA
18557 AAT
1 AAT
18560 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAAAAAATATTTTATAAA
Found at i:18927 original size:29 final size:31
Alignment explanation
Indices: 18865--18934 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 31
18855 TTTACGTTAT
18865 TTTTTTTACAATTAAAAACTTAATTAAATATAA
1 TTTTTTTACAA-TAAAAAC-TAATTAAATATAA
* *
18898 TTTTTTTACAA-AAAAAC-AATTAATTTTAA
1 TTTTTTTACAATAAAAACTAATTAAATATAA
18927 TTGTTTTT
1 TT-TTTTT
18935 TTCTAGAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 12 0.35
30 5 0.15
31 6 0.18
33 11 0.32
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (31 bp):
TTTTTTTACAATAAAAACTAATTAAATATAA
Found at i:19380 original size:17 final size:18
Alignment explanation
Indices: 19349--19408 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 18
19339 ATCAATAAAT
*
19349 AATTTAAAAATATTCAAA
1 AATTCAAAAATATTCAAA
19367 AATTCAAAAA-ATTC-AA
1 AATTCAAAAATATTCAAA
* *
19383 AATTTAAAAATACTATAAAA
1 AATTCAAAAATA-T-TCAAA
19403 AATTCA
1 AATTCA
19409 TAGAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 11 0.32
17 5 0.15
18 10 0.29
19 1 0.03
20 7 0.21
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTCAAAAATATTCAAA
Found at i:24208 original size:26 final size:26
Alignment explanation
Indices: 24179--24236 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
24169 GTCACGTGAC
*
24179 GAAAATGATAAAATTGA-ATAAATATA
1 GAAAATGATAAAATT-ATAAAAATATA
*
24205 GAAAATTATAAAATTATAAAAATATA
1 GAAAATGATAAAATTATAAAAATATA
24231 GAAAAT
1 GAAAAT
24237 ATTTAAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (26 bp):
GAAAATGATAAAATTATAAAAATATA
Found at i:24235 original size:18 final size:18
Alignment explanation
Indices: 24198--24300 Score: 61
Period size: 19 Copynumber: 5.7 Consensus size: 18
24188 AAAATTGAAT
*
24198 AAATATAGAAAATTAT-A
1 AAATATATAAAATTATAA
*
24215 AAAT-TATAAAAATATAGA
1 AAATATATAAAATTATA-A
* * *
24233 AAATATTTAAATCTTATTA
1 AAATATATAAA-ATTATAA
* *
24252 AAAT-TTTAAAATTTTAA
1 AAATATATAAAATTATAA
*
24269 AAA-AGTATAGAAAATATTAA
1 AAATA-TATA-AAATTA-TAA
24289 AAATATATAAAA
1 AAATATATAAAA
24301 ACTAATAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
16 9 0.14
17 11 0.17
18 14 0.22
19 17 0.26
20 13 0.20
21 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (18 bp):
AAATATATAAAATTATAA
Found at i:24297 original size:20 final size:19
Alignment explanation
Indices: 24200--24314 Score: 57
Period size: 19 Copynumber: 6.2 Consensus size: 19
24190 AATTGAATAA
*
24200 ATATAGAAA-ATTATAAAAT
1 ATATAAAAATATTA-AAAAT
24219 -TATAAAAATA-TAGAAAAT
1 ATATAAAAATATTA-AAAAT
* **
24237 ATTTAAATCTTATT-AAAAT
1 ATATAAA-AATATTAAAAAT
* *
24256 -T-TTAAAATTTTAAAAA-
1 ATATAAAAATATTAAAAAT
24272 AGTATAGAAAATATTAAAAAT
1 A-TATA-AAAATATTAAAAAT
*
24293 ATATAAAAACTAAT-AAAAT
1 ATATAAAAA-TATTAAAAAT
24312 ATA
1 ATA
24315 CAAATATAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
16 3 0.04
17 7 0.10
18 16 0.22
19 24 0.33
20 21 0.29
21 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATAAAAATATTAAAAAT
Found at i:24923 original size:20 final size:18
Alignment explanation
Indices: 24875--24943 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 18
24865 TTTAACAATT
*
24875 TTTTAT-ATGTTT-TATA
1 TTTTATAATTTTTCTATA
*
24891 TTTTATAACTTTTCTATA
1 TTTTATAATTTTTCTATA
*
24909 CTTTTAATAATTTTTCTAAA
1 -TTTT-ATAATTTTTCTATA
24929 GTTTTGATAATTTTT
1 -TTTT-ATAATTTTT
24944 AATGTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.14
17 4 0.09
18 4 0.09
19 4 0.09
20 25 0.58
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTCTATA
Found at i:37369 original size:78 final size:79
Alignment explanation
Indices: 37263--37419 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 79
37253 GTGTAACACC
37263 TTTGAAAGCCTTTTGATCGTAACAATATTATTTTGAGCAATTACAAGAT-AATTTTTTTAAAAAT
1 TTTGAAAGCCTTTTGATCGTAACAATATTATTTTGAGCAATTACAAGATAAATTTTTTTAAAAAT
*
37327 AAATGAATTGTGAT
66 AAATAAATTGTGAT
* *
37341 TTTGAAAGCCTTTTGATCGTAACGATATTATTTTGAGCAATTACAAGATAAATTTTTTTCAAAAT
1 TTTGAAAGCCTTTTGATCGTAACAATATTATTTTGAGCAATTACAAGATAAATTTTTTTAAAAAT
37406 AAATAAATTGTGAT
66 AAATAAATTGTGAT
37420 CTATAAGTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 48 0.64
79 27 0.36
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (79 bp):
TTTGAAAGCCTTTTGATCGTAACAATATTATTTTGAGCAATTACAAGATAAATTTTTTTAAAAAT
AAATAAATTGTGAT
Found at i:38555 original size:56 final size:58
Alignment explanation
Indices: 38463--38580 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 58
38453 CATTTACGTG
* *
38463 TCATTTTCATTTCAGAAAAAAACCACATTTATTTTCAAATGATTTC-A-TTTTTCATTT
1 TCATTTTCATTTCAGAAAAAAACCACAATGATTTTCAAATG-TTTCTATTTTTTCATTT
* * *
38520 TCATTTTCATTTCA-TAGAAAACCATAATGATTTTCAAATGTTTCTTATTTTTTCATTT
1 TCATTTTCATTTCAGAAAAAAACCACAATGATTTTCAAATGTTTC-TATTTTTTCATTT
38578 TCA
1 TCA
38581 CCATTTCTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
55 4 0.08
56 21 0.40
57 15 0.28
58 13 0.25
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.49
Consensus pattern (58 bp):
TCATTTTCATTTCAGAAAAAAACCACAATGATTTTCAAATGTTTCTATTTTTTCATTT
Found at i:47376 original size:44 final size:44
Alignment explanation
Indices: 47326--47413 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
47316 CCTGGTGGTT
*
47326 ACTTGCAAGTAAATGGTTATGAAAGCTGAAGCGTGAAGTTGCTA
1 ACTTGCAAGTAAATGGTTATGAAAGCTGAAGAGTGAAGTTGCTA
*
47370 ACTTGCATGTAAATGGTTATGAAAGCTGAAGAGTGAAGTTGCTA
1 ACTTGCAAGTAAATGGTTATGAAAGCTGAAGAGTGAAGTTGCTA
47414 TCATTATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.28
Consensus pattern (44 bp):
ACTTGCAAGTAAATGGTTATGAAAGCTGAAGAGTGAAGTTGCTA
Found at i:65868 original size:15 final size:15
Alignment explanation
Indices: 65850--65879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
65840 AAAAAGTAAG
65850 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
*
65865 AAAAGAAGAAGAAGA
1 AAAAGAAGAAAAAGA
65880 TGGAGATGCC
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:72727 original size:59 final size:59
Alignment explanation
Indices: 72659--73336 Score: 533
Period size: 60 Copynumber: 11.3 Consensus size: 59
72649 GATGTTGACT
* * *
72659 ATTGCATGACCGACACCCTCTTTTTTTCAAATAAAAAATTCAAA-TTTTTGGTGTTTGTC
1 ATTGCATGACCGACACCC-CTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
* * *
72718 ATTGCATGACCGACACTCCTTTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGGCC
1 ATTGCATGACCGACAC-CCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
* * * *
72778 ATTACAT-AGCCGAAACCCCTTTTTATCAGATAAAAAATT-TAATTTTTTTGTGTTGGTC
1 ATTGCATGA-CCGACACCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
* * ***
72836 A-TGCCAT-AGCCGACACGCCTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTAACC
1 ATTG-CATGA-CCGACACCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
*** * * * * * *
72895 A-TGACATGGTTGACACCCCCTTTTTATCTGACAAAAAATTCAATTTTTTTTTGTGTAGGCC
1 ATTG-CATGACCGACA-CCCCTTTTTATCAGATAAAAAATTCAA-ATTTTTTGGTGTTGGTC
* * * ** *
72956 ATTGCATGGCCGACACCTCTTTTTTGTCAGAT-AAAAATTTGAATTTTTTTGTGTTGGTC
1 ATTGCATGACCGACACC-CCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
* * * *
73015 A-TGCCATGATCGACATCACCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGG-C
1 ATTG-CATGACCGACA-CCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
* * *
73074 -TATGCCATGACCGACACCCCCTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGATC
1 AT-TG-CATGACCGACA-CCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
** * *
73135 A-TGCCATGGTCGACACCACCTTTTTAT-ATGATAAAAAAAAATCAAATTTTTTGGTGTT-GAC
1 ATTG-CATGACCGACACC-CCTTTTTATCA-GAT--AAAAAATTCAAATTTTTTGGTGTTGGTC
** * * *
73196 TATTGCATGGTCGACACCACCTTTTTATCTGATAAAAAAATTAAAATTTTTTTGTGTTGGTC
1 -ATTGCATGACCGACACC-CCTTTTTATCAGAT-AAAAAATTCAAATTTTTTGGTGTTGGTC
* * * **
73258 ATCT-CATAACCGACACCACCTTTTTAT-ATGACAACAAATAATCAAATTTTTTGGTGTTGACC
1 AT-TGCATGACCGACACC-CCTTTTTATCA-GATAA-AAA-ATTCAAATTTTTTGGTGTTGGTC
73320 ATTGCAT-AGCCGACACC
1 ATTGCATGA-CCGACACC
73337 ACTATTGATT
Statistics
Matches: 511, Mismatches: 77, Indels: 59
0.79 0.12 0.09
Matches are distributed among these distances:
57 1 0.00
58 51 0.10
59 122 0.24
60 163 0.32
61 85 0.17
62 87 0.17
63 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (59 bp):
ATTGCATGACCGACACCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGGTGTTGGTC
Found at i:73010 original size:120 final size:120
Alignment explanation
Indices: 72689--73336 Score: 610
Period size: 120 Copynumber: 5.4 Consensus size: 120
72679 TTTTTTTCAA
* * * * * *
72689 ATAAAAAATTCAAA-TTTTTGGTGTTTGTCATTGCATGACCGACA-CTCCTTTTTTGTCAGATAA
1 ATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCTCC-TTTTTATCTGATAA
* * * * * *
72752 AAAATTCAAATTTTTTGGTGTTGGCCATTACATAGCCGAAACC-CCTTTTTATCAG
65 AAAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
** * * * *
72807 AT-AAAAAATTTAATTTTTTTGTGTTGGTCA-TGCCATAGCCGACA-CGCCTTTTTATCTGATAA
1 ATAAAAAAATCAAATTTTTTGGTGTTGGCCATTG-CATGGCCGACACCTCCTTTTTATCTGATAA
* * *
72869 AAAATTCAAATTTTTTGGTGTTAACCATGACATGGTTGACACCCCCTTTTTATCTG
65 AAAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
* * * * * * * *
72925 ACAAAAAATTCAATTTTTTTTTGTGTAGGCCATTGCATGGCCGACACCTCTTTTTTGTCAGAT-A
1 ATAAAAAAATCAA-ATTTTTTGGTGTTGGCCATTGCATGGCCGACACCTCCTTTTTATCTGATAA
** * ** * * *
72989 AAAATTTGAATTTTTTTGTGTTGGTCATGCCATGATCGACATCACCTTTTTATCTG
65 AAAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
* * *
73045 ATAAAAAAATCAAATTTTTTGGTGTTGGCTA-TGCCATGACCGACACCCCCTTTTTATCTGATAA
1 ATAAAAAAATCAAATTTTTTGGTGTTGGCCATTG-CATGGCCGACACCTCCTTTTTATCTGATAA
* * * *
73109 AAAAATCAAATTTTTTGGTGTTGATCATGCCATGGTCGACACCACCTTTTTATATG
65 AAAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
* * * *
73165 ATAAAAAAAAATCAAATTTTTTGGTGTTGACTATTGCATGGTCGACACCACCTTTTTATCTGATA
1 AT--AAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCTCCTTTTTATCTGAT-
* * ** ** *** *
73230 AAAAAATTAAAATTTTTTTGTGTTGGTCATCTCATAACCGACACCACCTTTTTATATG
63 AAAAAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
* * *
73288 ACAACAAATAATCAAATTTTTTGGTGTTGACCATTGCATAGCCGACACC
1 ATAA-AAA-AATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACC
73337 ACTATTGATT
Statistics
Matches: 438, Mismatches: 77, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
117 58 0.13
118 42 0.10
119 44 0.10
120 133 0.30
121 16 0.04
122 56 0.13
123 89 0.20
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (120 bp):
ATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACCTCCTTTTTATCTGATAAA
AAATTCAAATTTTTTGGTGTTGACCATGACATGGTCGACACCACCTTTTTATCTG
Found at i:74251 original size:19 final size:19
Alignment explanation
Indices: 74204--74251 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
74194 AAATGTTAAG
*
74204 AAATAATTA-TTATCGAAA
1 AAATAATAATTTATCGAAA
* * *
74222 AATTAAAAATTTATTGAAA
1 AAATAATAATTTATCGAAA
74241 AAATAATAATT
1 AAATAATAATT
74252 AAAATTAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATAATAATTTATCGAAA
Found at i:76549 original size:60 final size:59
Alignment explanation
Indices: 76367--76990 Score: 505
Period size: 60 Copynumber: 10.4 Consensus size: 59
76357 ACAAAAATCC
* * * *
76367 GCAATGGTCAACACCAAAAAAATTT-ATTTTTTAATCAGATAATAAGGTGGTGTCGCCCAT
1 GCAATGGCCAACACC-AAAAAATTTAATTTTTTTATCAGATAAAAAGG-GGTGTCGACCAT
* * * *
76427 GCAATGACCAACACCAAAAAATTTGATTATTTTTTATCATATAAAAAGGTGGTGTCGGCCAT
1 GCAATGGCCAACACCAAAAAATTT-AAT-TTTTTTATCAGATAAAAAGG-GGTGTCGACCAT
*
76489 G-ATATGGCTAACACCAAAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCAT
1 GCA-ATGGCCAACACCAAAAAATTTAATTTTTTTATCAGATAAAAAGG-GGTGTCGACCAT
* * * * * * * * * *
76549 GCAACGGTCAATATCAAAAAATTTGATTATTTTT-TTAAATAAAAAGATGCTGTCGTCCAT
1 GCAATGGCCAACACCAAAAAATTTAATT-TTTTTATCAGATAAAAAG-GGGTGTCGACCAT
* ** ** * *
76609 GGC-ATGACCAACATAAAAAAATTTGAA-TTTTTTATTTGACAAAAAAGGGGTGTCGATCAT
1 -GCAATGGCCAACACCAAAAAATTT-AATTTTTTTATCAGA-TAAAAAGGGGTGTCGACCAT
* * * * * *
76669 GCAATGACAAACACAAAAAAAAATTTAAATTTTTTGTCAAATAAAAAGAGGGTGTCGACCAT
1 GCAATGGCCAACAC--CAAAAAATTTAATTTTTTTATCAGATAAAAAG-GGGTGTCGACCAT
76731 GGC-ATGGCCAACA-CAAAAAATTTTGAA-TTTTTTATCAGATAAAAAAGGGGTGTCGACCAT
1 -GCAATGGCCAACACCAAAAAA-TTT-AATTTTTTTATCAGAT-AAAAAGGGGTGTCGACCAT
* * * * *
76791 GGC-ATGGTCAACACCAAAAAATTTGAA-TTTTTTATCTGACAAAAAAGAGGTGTCGATCAT
1 -GCAATGGCCAACACCAAAAAATTT-AATTTTTTTATCAGA-TAAAAAGGGGTGTCGACCAT
* * * * *
76851 GCAATGGCCAACACCAAAAAAATTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCAT
1 GCAATGGCCAACACCAAAAAATTTAATTTTTTTATCAGATAAAAAGGGGTGTCGACCAT
* * * * * * *
76910 GCAATGACAAACACC-AAAAATTTAAATTTTCTATCTGACAAAAAGGGGGTGTCAACCAT
1 GCAATGGCCAACACCAAAAAATTTAATTTTTTTATCAGATAAAAA-GGGGTGTCGACCAT
*
76969 TCAATGGCCAACACCTAAAAAA
1 GCAATGGCCAACACC-AAAAAA
76991 AAAAATTTAT
Statistics
Matches: 470, Mismatches: 67, Indels: 53
0.80 0.11 0.09
Matches are distributed among these distances:
58 27 0.06
59 81 0.17
60 226 0.48
61 47 0.10
62 87 0.19
63 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (59 bp):
GCAATGGCCAACACCAAAAAATTTAATTTTTTTATCAGATAAAAAGGGGTGTCGACCAT
Found at i:76641 original size:122 final size:120
Alignment explanation
Indices: 76370--76929 Score: 527
Period size: 122 Copynumber: 4.6 Consensus size: 120
76360 AAAATCCGCA
* * * * *
76370 ATGGTCAACACCAAAAAAATTT-ATTTTTTAATCAGATAATAAGGTGGTGTCGCCCATGCAATGA
1 ATGGCCAACA-CAAAAAAATTTAATTTTTTTATCAGATAAAAAGG-GGTGTCGACCATGCAATGG
* * * * **
76434 CCAACACCAAAAAATTTGATTATTTTTTATCATATAAAAAGGTGGTGTCGGCCATGAT
64 TCAACACCAAAAAATTTGA-TATTTTTTATCAAATAAAAAGATGGTGTCGACCATGGC
* * *
76492 ATGGCTAACACCAAAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAACGGT
1 ATGGCCAACACAAAAAAATTTAATTTTTTTATCAGATAAAAAGG-GGTGTCGACCATGCAATGGT
* * * *
76557 CAATATCAAAAAATTTGATTATTTTTT-T-AAATAAAAAGATGCTGTCGTCCATGGC
65 CAACACCAAAAAATTTGA-TATTTTTTATCAAATAAAAAGATGGTGTCGACCATGGC
* * ** * *
76612 ATGACCAACATAAAAAAATTTGAA-TTTTTTATTTGACAAAAAAGGGGTGTCGATCATGCAAT-G
1 ATGGCCAACACAAAAAAATTT-AATTTTTTTATCAGA-TAAAAAGGGGTGTCGACCATGCAATGG
* * * * *
76675 ACAAACACAAAAAAAAATTT-AAATTTTTTGTCAAATAAAAAGAGGGTGTCGACCATGGC
64 TC-AACAC--CAAAAAATTTGATATTTTTTATCAAATAAAAAGATGGTGTCGACCATGGC
*
76734 ATGGCCAACACAAAAAATTTTGAA-TTTTTTATCAGATAAAAAAGGGGTGTCGACCATGGC-ATG
1 ATGGCCAACACAAAAAAATTT-AATTTTTTTATCAGAT-AAAAAGGGGTGTCGACCAT-GCAATG
* *
76797 GTCAACACCAAAAAATTTGA-ATTTTTTATCTGACA-AAAAAGA-GGTGTCGATCAT-GC
63 GTCAACACCAAAAAATTTGATATTTTTTATC--AAATAAAAAGATGGTGTCGACCATGGC
* * * *
76853 AATGGCCAACACCAAAAAAA-TTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCATGCAAT-G
1 -ATGGCCAACA-CAAAAAAATTTAATTTTTTTATCAGATAAAAAGGGGTGTCGACCATGCAATGG
*
76916 ACAAACACCAAAAA
64 TC-AACACCAAAAA
76930 TTTAAATTTT
Statistics
Matches: 368, Mismatches: 51, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
118 4 0.01
119 37 0.10
120 125 0.34
121 37 0.10
122 161 0.44
123 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (120 bp):
ATGGCCAACACAAAAAAATTTAATTTTTTTATCAGATAAAAAGGGGTGTCGACCATGCAATGGTC
AACACCAAAAAATTTGATATTTTTTATCAAATAAAAAGATGGTGTCGACCATGGC
Found at i:76692 original size:182 final size:180
Alignment explanation
Indices: 76375--76932 Score: 521
Period size: 182 Copynumber: 3.1 Consensus size: 180
76365 CCGCAATGGT
* * * * *
76375 CAACACCAAAAAAATTT--ATTTTTTAATCAGAT-AATAAGGTGGTGTCGCCCAT-GCAATGACC
1 CAACA-CAAAAAATTTTGAATTTTTT-ATCAAATAAAAAAGG-GCTGTCGACCATGGC-ATGACC
* * * * ** * *
76436 AACACCAAAAAATTTGATTATTTTTTATCAT-ATAAAAAGGTGGTGTCGGCCATG-ATATGGCTA
62 AACACAAAAAAATTTGA--ATTTTTTATC-TGACAAAAAAGAGGTGTCGATCATGCA-ATGACAA
* * *
76499 ACAC-CAAAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAACGGT
123 ACACAAAAAAAATTTAAATTTTTTATCAGATAAAAAGG-GGTGTCGACCATGCAACGGC
* * *
76557 CAATATCAAAAAA-TTTGATTATTTTTT-T-AAAT-AAAAAGATGCTGTCGTCCATGGCATGACC
1 CAACA-CAAAAAATTTTGA--ATTTTTTATCAAATAAAAAAG-GGCTGTCGACCATGGCATGACC
* * *
76618 AACATAAAAAAATTTGAATTTTTTATTTGACAAAAAAGGGGTGTCGATCATGCAATGACAAACAC
62 AACACAAAAAAATTTGAATTTTTTATCTGACAAAAAAGAGGTGTCGATCATGCAATGACAAACAC
* * *
76683 AAAAAAAAATTTAAATTTTTTGTCAAATAAAAAGAGGGTGTCGACCATGGC-ATGGC
127 -AAAAAAAATTTAAATTTTTTATCAGATAAAAAG-GGGTGTCGACCAT-GCAACGGC
* * **
76739 CAACACAAAAAATTTTGAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATGGCATGGTCAACA
1 CAACACAAAAAATTTTGAATTTTTTATCAAATAAAAAAGGGCTGTCGACCATGGCATGACCAACA
* * * *
76804 CCAAAAAATTTGAATTTTTTATCTGACAAAAAAGAGGTGTCGATCATGCAATGGCCAACACCAAA
66 CAAAAAAATTTGAATTTTTTATCTGACAAAAAAGAGGTGTCGATCATGCAATGACAAACACAAAA
* * * * *
76869 AAAA-TTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCATGCAATGAC
131 AAAATTTAAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGCAACGGC
* *
76918 AAACACCAAAAATTT
1 CAACACAAAAAATTT
76933 AAATTTTCTA
Statistics
Matches: 314, Mismatches: 45, Indels: 37
0.79 0.11 0.09
Matches are distributed among these distances:
178 2 0.01
179 30 0.10
180 63 0.20
181 19 0.06
182 181 0.58
183 12 0.04
185 7 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (180 bp):
CAACACAAAAAATTTTGAATTTTTTATCAAATAAAAAAGGGCTGTCGACCATGGCATGACCAACA
CAAAAAAATTTGAATTTTTTATCTGACAAAAAAGAGGTGTCGATCATGCAATGACAAACACAAAA
AAAATTTAAATTTTTTATCAGATAAAAAGGGGTGTCGACCATGCAACGGC
Found at i:76811 original size:242 final size:242
Alignment explanation
Indices: 76375--76990 Score: 642
Period size: 242 Copynumber: 2.6 Consensus size: 242
76365 CCGCAATGGT
* * * * ** *
76375 CAACACCAAAAAAATT-TATTTTTTAATCAGATAATAAGGTGGTGTCGCCCATGCAATGACCAAC
1 CAACACCAAAAAAATTAAATTTTTT-ATCTGACAAAAAGG-GGTGTCGATCATGCAATGACAAAC
* * * * * *
76439 AC-CAAAAAATTTGATTATTTTTTATCATATAAAAAGGTGGTGTCGGCCATGATATGGCTAACAC
64 ACAAAAAAAATTTGATAATTTTTTATCAAATAAAAAGGTGGTGTCGACCATGACATGGCCAACAC
* *
76503 CAAAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAACGGTCAATATCAAAA
129 CAAAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAACGGTCAACACCAAAA
*
76568 AATTTG-ATTATTTT-T-TTAAATAAAAAGATGCTGTCG-TCCATGGC-ATGAC
194 AATTTGAATT-TTTTATCTGAAA-AAAAAGA-GCTGTCGAT-CAT-GCAATGAC
* * *
76617 CAACA-TAAAAAAATTTGAATTTTTTATTTGACAAAAAAGGGGTGTCGATCATGCAATGACAAAC
1 CAACACCAAAAAAA-TTAAATTTTTTATCTGAC-AAAAAGGGGTGTCGATCATGCAATGACAAAC
* *
76681 ACAAAAAAAAATTT-A-AATTTTTTGTCAAATAAAAAGAG-GGTGTCGACCATGGCATGGCCAAC
64 AC-AAAAAAAATTTGATAATTTTTTATCAAATAAAAAG-GTGGTGTCGACCATGACATGGCCAAC
*
76743 A-CAAAAAATTTTGAA-TTTTTTATCAGATAAAAAAGG-GGTGTCGACCATGGC-ATGGTCAACA
127 ACCAAAAAA-TTT-AATTTTTTTATCAGAT-AAAAAGGTGGTGTCGACCAT-GCAACGGTCAACA
* * *
76804 CCAAAAAATTTGAATTTTTTATCTGACAAAAAAGAGGTGTCGATCATGCAATGGC
188 CCAAAAAATTTGAATTTTTTATCTGAAAAAAAAGAGCTGTCGATCATGCAATGAC
76859 CAACACCAAAAAAATTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCATGCAATGACAAACAC
1 CAACACCAAAAAAATTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCATGCAATGACAAACAC
* * ** * * * *
76924 --CAAAAATTT-A-AATTTTCTATCTGACAAAAAGGGGGTGTCAACCAT-TCAATGGCCAACACC
66 AAAAAAAATTTGATAATTTTTTATCAAATAAAAAGGTGGTGTCGACCATGAC-ATGGCCAACACC
76984 TAAAAAA
130 -AAAAAA
76991 AAAAATTTAT
Statistics
Matches: 319, Mismatches: 35, Indels: 42
0.81 0.09 0.11
Matches are distributed among these distances:
237 2 0.01
238 46 0.14
239 1 0.00
240 6 0.02
241 49 0.15
242 158 0.50
243 45 0.14
244 12 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (242 bp):
CAACACCAAAAAAATTAAATTTTTTATCTGACAAAAAGGGGTGTCGATCATGCAATGACAAACAC
AAAAAAAATTTGATAATTTTTTATCAAATAAAAAGGTGGTGTCGACCATGACATGGCCAACACCA
AAAAATTTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAACGGTCAACACCAAAAAA
TTTGAATTTTTTATCTGAAAAAAAAGAGCTGTCGATCATGCAATGAC
Found at i:77011 original size:58 final size:55
Alignment explanation
Indices: 76852--77098 Score: 169
Period size: 58 Copynumber: 4.3 Consensus size: 55
76842 GTCGATCATG
* * * *
76852 CAATGGCCAACACCAAAAAAATTAAATTTTTTATCTGACAAAAA-GGGGTGTC-GATCATG
1 CAATGGCCAACACCAAAAAAA--AAA---TTTATTTGAAAAAAAGGGGGTGTCAG-CCATT
* * ** * * *
76911 CAATGACAAACACCAAAAATTTAAATTTTCTATCTGACAAAAAGGGGGTGTCAACCATT
1 CAATGGCCAACACCAAAAA---AAAAATT-TATTTGAAAAAAAGGGGGTGTCAGCCATT
*
76970 CAATGGCCAACACCTAAAAAAAAAAATTTATTTGAAAAAAAAAGGGGTGT-AGGCCATT
1 CAATGGCCAACACC--AAAAAAAAAATTTATTTG-AAAAAAAGGGGGTGTCA-GCCATT
* * * * * *
77028 -ACATAGCCAACACCAGAAAAAAATTTTATTTGACAAAAAGGTGGTGTCAGCCATG
1 CA-ATGGCCAACACCAAAAAAAAAATTTATTTGAAAAAAAGGGGGTGTCAGCCATT
77083 CAATGGCCAACACCAA
1 CAATGGCCAACACCAA
77099 TTTTTTTTCA
Statistics
Matches: 151, Mismatches: 24, Indels: 30
0.74 0.12 0.15
Matches are distributed among these distances:
55 29 0.19
56 18 0.12
57 9 0.06
58 47 0.31
59 40 0.26
60 1 0.01
61 5 0.03
62 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (55 bp):
CAATGGCCAACACCAAAAAAAAAATTTATTTGAAAAAAAGGGGGTGTCAGCCATT
Done.