Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2361
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: 31572
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:911 original size:13 final size:13
Alignment explanation
Indices: 893--918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
883 TACACAAAGT
893 ATGTATCGATACA
1 ATGTATCGATACA
906 ATGTATCGATACA
1 ATGTATCGATACA
919 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:916 original size:32 final size:34
Alignment explanation
Indices: 875--939 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
865 GTAGCCAACT
**
875 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAAATGTATCGATACAA
907 TGTATCGATACACCAAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAAATGTATCGATACA
940 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 1 0.03
34 16 0.55
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAAATGTATCGATACAA
Found at i:2978 original size:70 final size:69
Alignment explanation
Indices: 2829--2978 Score: 160
Period size: 70 Copynumber: 2.1 Consensus size: 69
2819 CTGAGGAGGT
* * * ***
2829 ACTCCAATCCCGTTTTTAAACTTGTCAATGTTTAAATCTTATTTTGACTTTAATTATCATCATCA
1 ACTCCAA-CCCCTTTTTAAACTTGTCAATGTTTAAATCTTAATTTCACCCAAATTATCATCATCA
*
2894 GAGAT
65 GAGAC
*
2899 ACTCTAACCCCTTTTTAGAACTTGTCAA-GATTTAAATCTTAATTTCACCCAAATTATCAT-ATT
1 ACTCCAACCCCTTTTTA-AACTTGTCAATG-TTTAAATCTTAATTTCACCCAAATTATCATCA-T
* *
2962 CGGGGAC
63 CAGAGAC
2969 ACTCCAACCC
1 ACTCCAACCC
2979 TATTTCTCCA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
69 11 0.17
70 55 0.83
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (69 bp):
ACTCCAACCCCTTTTTAAACTTGTCAATGTTTAAATCTTAATTTCACCCAAATTATCATCATCAG
AGAC
Found at i:3071 original size:52 final size:52
Alignment explanation
Indices: 2993--3092 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
2983 TCTCCAAAGG
*
2993 GATACTCCAACCCCGTTTTTAAACTTGTTAAGATTTAAATCTTAATTTTAGA
1 GATACTCCAACCCCGTTTTTAAACTTGTCAAGATTTAAATCTTAATTTTAGA
*
3045 GATACTCTAACCCC-TTTTTAGAACTTGTCAAGATTTAAATCTTAATTT
1 GATACTCCAACCCCGTTTTTA-AACTTGTCAAGATTTAAATCTTAATTT
3093 CACCCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 6 0.13
52 39 0.87
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (52 bp):
GATACTCCAACCCCGTTTTTAAACTTGTCAAGATTTAAATCTTAATTTTAGA
Found at i:3147 original size:149 final size:148
Alignment explanation
Indices: 2893--3189 Score: 567
Period size: 149 Copynumber: 2.0 Consensus size: 148
2883 TATCATCATC
2893 AGAGATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCA
1 AGAGATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCA
*
2958 TATTCGGGGACACTCCAACCCTATTTCTCCAAAGGGATACTCCAACCCCGTTTTTAAACTTGTTA
66 TATTCGGGGACACTCCAACCCTATTCCTCCAAAGGGATACTCCAACCCCGTTTTTAAACTTGTTA
3023 AGATTTAAATCTTAATTTT
131 AGATTTAAATCTT-ATTTT
3042 AGAGATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCA
1 AGAGATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCA
3107 TATTCGGGGACACTCCAACCCTATTCCTCCAAAGGGATACTCCAACCCCGTTTTTAAACTTGTTA
66 TATTCGGGGACACTCCAACCCTATTCCTCCAAAGGGATACTCCAACCCCGTTTTTAAACTTGTTA
*
3172 AGGTTTAAATCTTATTTT
131 AGATTTAAATCTTATTTT
3190 CGCTTAAGTT
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
148 5 0.03
149 141 0.97
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (148 bp):
AGAGATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCA
TATTCGGGGACACTCCAACCCTATTCCTCCAAAGGGATACTCCAACCCCGTTTTTAAACTTGTTA
AGATTTAAATCTTATTTT
Found at i:3213 original size:97 final size:97
Alignment explanation
Indices: 3045--3232 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 97
3035 TAATTTTAGA
* *
3045 GATACTCTAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCATAT
1 GATACTCCAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCATAG
* *
3110 TCGGGGACACTCCAACCCTATTCCTCCAAAGG
66 TAGGGGACACTCCAACCCCATTCCTCCAAAGG
* * * * ** * *
3142 GATACTCCAACCCCGTTTTTA-AACTTGTTAAGGTTTAAATCTTATTTTCGCTTAAGTTATCATC
1 GATACTCCAACCCC-TTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCATA
*
3206 GTAGGGGATACTCCAACCCCATTCCTC
65 GTAGGGGACACTCCAACCCCATTCCTC
3233 TGTGGGGACA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 71 0.92
98 6 0.08
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (97 bp):
GATACTCCAACCCCTTTTTAGAACTTGTCAAGATTTAAATCTTAATTTCACCCAAATTATCATAG
TAGGGGACACTCCAACCCCATTCCTCCAAAGG
Found at i:3846 original size:19 final size:18
Alignment explanation
Indices: 3821--3885 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
3811 ATTTCAACGA
3821 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3839 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3855 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3871 TTTTGTATCGATACA
1 -TTTGTATCGATACA
3886 ATGTACAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:3859 original size:32 final size:32
Alignment explanation
Indices: 3823--3890 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3813 TTCAACGATT
3823 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3855 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3887 TGTA
1 TGTA
3891 CAGTTACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3860 original size:13 final size:13
Alignment explanation
Indices: 3842--3866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3832 ACATAAGTGT
3842 TGTATCGATACAA
1 TGTATCGATACAA
3855 TGTATCGATACA
1 TGTATCGATACA
3867 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3956 original size:13 final size:13
Alignment explanation
Indices: 3938--3962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3928 ATTACTCAAA
3938 TGTATCGATACAT
1 TGTATCGATACAT
3951 TGTATCGATACA
1 TGTATCGATACA
3963 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13926 original size:32 final size:33
Alignment explanation
Indices: 13864--13927 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
13854 TACAAGCCAA
* *
13864 TGTATCGATACAATTATTTGTGTATTGATACAT
1 TGTATCGATACAATTATTGGTGTATCGATACAT
13897 TGTATCGATAC-A-TACTTGGTGTATCGATACA
1 TGTATCGATACAATTA-TTGGTGTATCGATACA
13928 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 2 0.07
32 15 0.54
33 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATTATTGGTGTATCGATACAT
Found at i:14569 original size:52 final size:49
Alignment explanation
Indices: 14356--14586 Score: 221
Period size: 49 Copynumber: 4.8 Consensus size: 49
14346 GCATCTTCTT
* * *
14356 TTAAGTCCAATATCGCTGGCCATGAATCAGCATATTGG------CA-CC
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGACCTTTCATCC
* * * *
14398 TTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATTGG-CATCTTCA-CC
1 -TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGACCT-TTCATCC
* *
14447 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC-TTCATCT
1 -TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG-ACCTTTCATCC
* *
14497 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCATCC
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG-ACC-TT-TCATCC
*
14549 TTAAGTGCAATGTCGCTGGCCTTGAATCAGCACATTGG
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG
14587 CATTTTTCTC
Statistics
Matches: 158, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
43 32 0.20
49 83 0.53
50 1 0.01
51 2 0.01
52 40 0.25
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (49 bp):
TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGACCTTTCATCC
Found at i:14599 original size:52 final size:49
Alignment explanation
Indices: 14356--14692 Score: 251
Period size: 52 Copynumber: 6.8 Consensus size: 49
14346 GCATCTTCTT
* * * *
14356 TTAAGTCCAATATCGCTGGCCATGAATCAGCATATTGGCA----C--CT
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCC
* * * *
14399 TTAAGTCTAATGTTGCTGGCCTTGAATCAACACATTGGCATCTTCA-CC
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCC
* ** *
14447 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1 -TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCC
* * *
14497 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCATCC
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG--CATTT-TCATCC
*
14549 TTAAGTGCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTTC-TCATC
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TTTTCATC--C
* * * * * *
14600 TTCAAGT-CTATGGTCGCTGACCGTGAATCAGCACATTGACATTCTTTATATCT
1 TT-AAGTCCAAT-GTCGCTGGCCTTGAATCAGCACATTGGCA-T-TTT-CATCC
** * * * *
14653 TTAAACCCAATATCACTGGTCTTGAATCAGCATATTGGCA
1 TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
14693 CCTTTCTCAC
Statistics
Matches: 237, Mismatches: 38, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
43 34 0.14
47 1 0.00
48 1 0.00
49 80 0.34
50 4 0.02
51 11 0.05
52 96 0.41
53 8 0.03
55 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (49 bp):
TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCC
Found at i:15275 original size:21 final size:21
Alignment explanation
Indices: 15251--15306 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
15241 TGTTTGTCCA
15251 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAG
15272 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAG
15293 AATGTATCGATACA
1 AATGTATCGATACA
15307 AGGTCCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTCTAG
Found at i:19398 original size:61 final size:60
Alignment explanation
Indices: 19264--19402 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 60
19254 GGTCAGCGAC
* * * *
19264 ATTAGACTTAAAGATGCAAAAAATGATAAAAATGCCAATATGCTGATTCACGGCCAATGAT
1 ATTAGGCTTAAAGATG-AAAAAATGATAAAAATGCCAATATGCTAATTCAAGGCCAATAAT
* * ** *
19325 A-TCGGGTCTAAAGATGAGAAAAATGATAAAGGTGCCAATATGCTAATTGAAGGCCAATAAT
1 ATTAGGCT-TAAAGATGA-AAAAATGATAAAAATGCCAATATGCTAATTCAAGGCCAATAAT
19386 ATTAGGCTTAAAGATGA
1 ATTAGGCTTAAAGATGA
19403 CAAAGGTGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
60 4 0.06
61 56 0.88
62 4 0.06
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.24
Consensus pattern (60 bp):
ATTAGGCTTAAAGATGAAAAAATGATAAAAATGCCAATATGCTAATTCAAGGCCAATAAT
Found at i:19430 original size:52 final size:52
Alignment explanation
Indices: 19347--20291 Score: 446
Period size: 52 Copynumber: 17.7 Consensus size: 52
19337 GATGAGAAAA
* * * ***
19347 ATGATAAAGGTGCCAATATGCTAATTGAAGGCCAATAATATTAGGCTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * *
19399 ATGACAAAGGTGCCAATGTGCTGATTCAAGGCCAACAACATT-GGACTTGAAGATGAGAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-C-T-----T-A-AAG
* * * * * *
19459 AATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGCTATCAGACTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * *
19512 ATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * * * * *
19564 ATGAGAATA-ATGCCAATGTGCTTATTCAAGGCTAGCGACATTAGGCTT-AGG
1 ATGACAA-AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
** * * * * *
19615 AATGTTAAAGATGCCAATATGCTAATTCAAGGCCAACGATA-TCGGACTTAAAT
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAG
* * * **
19668 ATG-CAAAGAATGATAAAAGTACCGATATGCTGATTCACGGCCAGTGATATCGGGCTTGAAGATG
1 ATGACAAAG---G-T----G--CCAATATGCTGATTCAAGGCCAGCGATATTAGGC-T-----T-
19732 AGAAG
49 A-AAG
* * * *
19737 AATGATAAAGGTGTCAATATGGTGATTCAAGGCTAGCGATATTAGGCTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * * * *
19790 ATGACAAATGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTGAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * * * * * * *
19842 ATGA-GAAGAATGCTAATGTACTGATTCAAGGCCAACAACATTGGGCTT-AAG
1 ATGACAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
** * * * **
19893 AATG-TTAAGGATGCCAATATGCTGATTTAAGGCTAGCGATATCATACTTAAAG
1 -ATGACAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * * * * *
19946 ATGACAAAAGTGCTAATATACTAATTCAAAGCCAGTGATATTAGACTT-AAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * * ** * *
19997 AAAGAAAAAGGTGCCAATGTATTGATTCAAGGCCAACGACATT-GGACTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAG
* *
20050 ATGACAAAGGCGCCAATATGCTGATTTAAGGCCAGCGATATT-GGACTT-AAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAG
* * * * ** * * *
20101 AAAGAAAAAGGTGCCAATGTGCTGATTTAAGGCCAATGACACTAGACTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
* * ** * *
20154 ATGA-TAAGGATGCCAATGTGCTGATTCAAGGTTAGCGACATT-GGACTTAGAG
1 ATGACAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAG
* ** * *
20206 ATGAAAAAAATGCTAATATGCTGATTCAAGGTCAGCGATATT-GGACTT-AAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTTAAAG
* * * *
20257 AAAGAAAAATGTGCCAATGTGCTGATTCAAGGCCA
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCA
20292 AAGACATTGG
Statistics
Matches: 682, Mismatches: 158, Indels: 106
0.72 0.17 0.11
Matches are distributed among these distances:
51 31 0.05
52 512 0.75
53 24 0.04
54 2 0.00
55 3 0.00
58 1 0.00
59 2 0.00
60 5 0.01
61 84 0.12
62 4 0.01
63 1 0.00
67 2 0.00
68 2 0.00
69 2 0.00
70 3 0.00
71 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (52 bp):
ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAAAG
Found at i:19509 original size:113 final size:113
Alignment explanation
Indices: 19333--19575 Score: 333
Period size: 113 Copynumber: 2.2 Consensus size: 113
19323 ATATCGGGTC
* * * * *
19333 TAAAGATGAGAAAAATGATAAAGGTGCCAATATGCTAATTGAAGGCCAATAATATTAGGCTTAAA
1 TAAAGATGAGAAAAATGATAAAGGTGCCAATATGCTAATTCAAAGCCAACAATATCAGACTTAAA
* * *
19398 GATGACAAAGGTGCCAATGTGCTGATTCAAGGCCAACAACATTGGACT
66 GATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACAACATTAGACT
* * * * * **
19446 TGAAGATGAGAAGAATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGCTATCAGACTTAAA
1 TAAAGATGAGAAAAATGATAAAGGTGCCAATATGCTAATTCAAAGCCAACAATATCAGACTTAAA
*
19511 GATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACT
66 GATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACAACATTAGACT
*
19559 TAAAGATGAGAATAATG
1 TAAAGATGAGAAAAATG
19576 CCAATGTGCT
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (113 bp):
TAAAGATGAGAAAAATGATAAAGGTGCCAATATGCTAATTCAAAGCCAACAATATCAGACTTAAA
GATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACAACATTAGACT
Found at i:19751 original size:278 final size:279
Alignment explanation
Indices: 19444--19953 Score: 752
Period size: 278 Copynumber: 1.8 Consensus size: 279
19434 CAACATTGGA
*
19444 CTTGAAGATGAGAAGAATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGCTATCAGACTTA
1 CTTGAAGATGAGAAGAATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGATATCAGACTTA
*
19509 AAGATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACTTAAAGATGAGAATAA
66 AAGATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACTTAAAGATGAGAAGAA
* * * * * *
19574 TGCCAATGTGCTTATTCAAGGCTAGCGACATTAGGCTTAGGAATGTTAAAGATGCCAATATGCTA
131 TGCCAATGTACTGATTCAAGGCCAACAACATTAGGCTTAAGAATGTTAAAGATGCCAATATGCTA
* *
19639 ATTCAAGGCCAACGATATCGGACTTAAATATG-CAAAGAATGATAAAAGTACCGATATGCTGATT
196 ATTCAAGGCCAACGATATCAGACTTAAAGATGACAAAGAATGATAAAAGTACCGATATGCTGATT
19703 CACGGCCAGTGATATCGGG
261 CACGGCCAGTGATATCGGG
* * * * *
19722 CTTGAAGATGAGAAGAATGATAAAGGTGTCAATATGGTGATTCAAGGCTAGCGATATTAGGCTTA
1 CTTGAAGATGAGAAGAATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGATATCAGACTTA
* * * * * *
19787 AAGATGACAAATGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTGAAGATGAGAAGAA
66 AAGATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACTTAAAGATGAGAAGAA
* * * *
19852 TGCTAATGTACTGATTCAAGGCCAACAACATTGGGCTTAAGAATGTTAAGGATGCCAATATGCTG
131 TGCCAATGTACTGATTCAAGGCCAACAACATTAGGCTTAAGAATGTTAAAGATGCCAATATGCTA
* * * *
19917 ATTTAAGGCTAGCGATATCATACTTAAAGATGACAAA
196 ATTCAAGGCCAACGATATCAGACTTAAAGATGACAAA
19954 AGTGCTAATA
Statistics
Matches: 202, Mismatches: 29, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
278 198 0.98
279 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (279 bp):
CTTGAAGATGAGAAGAATGATAAAGGTGTCAATATGCTGATTCAAAGCCAGCGATATCAGACTTA
AAGATGACAAAGGTGCCAATATGCTGATTCAAAGCCAACGACATTAGACTTAAAGATGAGAAGAA
TGCCAATGTACTGATTCAAGGCCAACAACATTAGGCTTAAGAATGTTAAAGATGCCAATATGCTA
ATTCAAGGCCAACGATATCAGACTTAAAGATGACAAAGAATGATAAAAGTACCGATATGCTGATT
CACGGCCAGTGATATCGGG
Found at i:19757 original size:61 final size:60
Alignment explanation
Indices: 19614--19793 Score: 189
Period size: 61 Copynumber: 3.0 Consensus size: 60
19604 TTAGGCTTAG
* * * * * *
19614 GAATGTTAAAGATGCCAATATGCTAATTCAAGGCCAACGATATCGGACTTAAATATGCAAA
1 GAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTTAAAGATG-AAA
* * * * * *
19675 GAATGATAAAAGTACCGATATGCTGATTCACGGCCAGTGATATCGGGCTTGAAGATGAGAA
1 GAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTTAAAGATGA-AA
* * * **
19736 GAATGATAAAGGTGTCAATATGGTGATTCAAGGCTAGCGATATTAGGCTTAAAGATGA
1 GAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTTAAAGATGA
19794 CAAATGTGCC
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 1 0.01
61 94 0.99
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (60 bp):
GAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGGCTTAAAGATGAAA
Found at i:19950 original size:156 final size:156
Alignment explanation
Indices: 19734--20291 Score: 569
Period size: 156 Copynumber: 3.6 Consensus size: 156
19724 TGAAGATGAG
* * * * *
19734 AAGA-ATGATAAAGGTGTCAATATGGTGATTCAAGGCTAGCGATATTAGGCTTAA-AGATGACAA
1 AAGAGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAAGA-AAGAAAA
* * *
19797 ATGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGACTTGAAGATGAGAAGAATGCTAATGTA
65 ATGTGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTT-AAGATGAGAAGAATGCCAATGTA
* *
19862 CTGATTCAAGGCCAACAACATTGGGCTT
129 CTGATTCAAGGCCAACGACATTGGACTT
* * * * *
19890 AAGA-ATG-TTAAGGATGCCAATATGCTGATTTAAGGCTAGCGATATCATACTTAA-AGATGACA
1 AAGAGATGATAAAGG-TGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAAGA-AAGA-A
* * * * * * * *
19952 AAA-GTGCTAATATACTAATTCAAAGCCAGTGATATTAGACTTAAGA-AAGAAAAAGGTGCCAAT
63 AAATGTGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAGATGAGAAGAA--TGCCAAT
*
20015 GTATTGATTCAAGGCCAACGACATTGGACTT
126 GTACTGATTCAAGGCCAACGACATTGGACTT
* * * * *
20046 AA-AGATGACAAAGGCGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAGAAAGAAAAA
1 AAGAGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAAGAAAGAAAAA
* * * * * * *
20110 GGTGCCAATGTGCTGATTTAAGGCCAATGACACTAGACTTAAAGATGATAAGGATGCCAATGTGC
66 TGTGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTT-AAGATGAGAAGAATGCCAATGTAC
** *
20175 TGATTCAAGGTTAGCGACATTGGACTT
130 TGATTCAAGGCCAACGACATTGGACTT
* ** * *
20202 -AGAGATGAAAAAAATGCTAATATGCTGATTCAAGG-TCAGCGATATTGGACTTAAGAAAGAAAA
1 AAGAGATGATAAAGGTGCCAATATGCTGATTCAAGGCT-AGCGATATTAGACTTAAGAAAGAAAA
20265 ATGTGCCAATGTGCTGATTCAAGGCCA
65 ATGTGCCAATGTGCTGATTCAAGGCCA
20292 AAGACATTGG
Statistics
Matches: 333, Mismatches: 57, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
154 6 0.02
155 15 0.05
156 296 0.89
157 12 0.04
158 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (156 bp):
AAGAGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAAGAAAGAAAAA
TGTGCCAATGTGCTGATTCAAGGCCAGTGACATTAGACTTAAGATGAGAAGAATGCCAATGTACT
GATTCAAGGCCAACGACATTGGACTT
Found at i:20380 original size:32 final size:32
Alignment explanation
Indices: 20303--20792 Score: 499
Period size: 32 Copynumber: 15.3 Consensus size: 32
20293 AGACATTGGG
* *
20303 TTAAGAAGGGTTGCTACTGACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
20335 TTAGAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTA-AGAAGGGTTGCCACCGACTTGTGTGGGCT
**
20368 TTAAGAAGGGTTGCCATTGACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
*** ** *
20400 TCCGGAAGGGTTGCCACTAACTTCTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
* *
20432 TTAAAGAAGGGTTGCTACCGACTTGTGGGGGCT
1 TT-AAGAAGGGTTGCCACCGACTTGTGTGGGCT
* *
20465 TTGAGAAAGGTTGCCACCGACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
* * * **
20497 TTGATAAAGGTTGCCACTAACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
* * ***
20529 TTAAGAAAGGTTGGCATTAACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
* *
20561 TTAA-AACGGGTTGCCAACGACTTATGTGGGCT
1 TTAAGAA-GGGTTGCCACCGACTTGTGTGGGCT
** * *
20593 TT-AGAAAAG--G--A-TGACTTATGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
* **
20619 TTGAGAAAGGGTTGCCACCGACTTGTGCAGGCT
1 TTAAG-AAGGGTTGCCACCGACTTGTGTGGGCT
*
20652 TTAAGAAAGGTTGCCACCGACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
20684 TTAGAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTA-AGAAGGGTTGCCACCGACTTGTGTGGGCT
* * * * *
20717 TTAGAGAAGGGTTCCCATCAACTTATATGGGCT
1 TTA-AGAAGGGTTGCCACCGACTTGTGTGGGCT
**
20750 TTAAGAAGGGTTGCCACTAACTTGTGTGGGCT
1 TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
*
20782 TTGAGAAGGGT
1 TTAAGAAGGGT
20793 AAGGTGCCAT
Statistics
Matches: 386, Mismatches: 60, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
26 16 0.04
27 3 0.01
28 3 0.01
29 1 0.00
30 1 0.00
31 4 0.01
32 229 0.59
33 129 0.33
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (32 bp):
TTAAGAAGGGTTGCCACCGACTTGTGTGGGCT
Found at i:20439 original size:65 final size:65
Alignment explanation
Indices: 20305--20783 Score: 455
Period size: 65 Copynumber: 7.5 Consensus size: 65
20295 ACATTGGGTT
* * * *
20305 AAGAAGGGTTGCTACTGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-GAAAGGTTGCCACTGACTTGTGTGGGCTTT
20370 -
65 A
** ** * * *
20370 AAGAAGGGTTGCCATTGACTTGTGTGGGCTTCCGGAAGGGTTGCCACTAACTTCTGTGGGCTTTA
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGAAAGGTTGCCACTGACTTGTGTGGGCTTTA
* * *
20435 AAGAAGGGTTGCTACCGACTTGTGGGGGCTTT-GAGAAAGGTTGCCACCGACTTGTGTGGGCTTT
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-GAAAGGTTGCCACTGACTTGTGTGGGCTTT
20499 GA
65 -A
* ** * * * *
20501 TA-AA-GGTTGCCACTAACTTGTGTGGGCTTTAAGAAAGGTTGGCATTAACTTGTGTGGGCTTTA
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGAAAGGTTGCCACTGACTTGTGTGGGCTTTA
* * * * *
20564 AA-ACGGGTTGCCAACGACTTATGTGGGCTTTA-GAAAAG--G--A-TGACTTATGTGGGCTTT-
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGAAAGGTTGCCACTGACTTGTGTGGGCTTTA
* ** * *
20621 GAGAAAGGGTTGCCACCGACTTGTGCAGGCTTTAAGAAAGGTTGCCACCGACTTGTGTGGGCTTT
1 AAG-AAGGGTTGCCACCGACTTGTGTGGGCTTTAGGAAAGGTTGCCACTGACTTGTGTGGGCTTT
20686 A
65 A
* * * * * *
20687 GAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTCCCA-TCAACTTATATGGGCTT
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-GAAAGGTTGCCACT-GACTTGTGTGGGCTT
20751 T-
64 TA
**
20752 AAGAAGGGTTGCCACTAACTTGTGTGGGCTTT
1 AAGAAGGGTTGCCACCGACTTGTGTGGGCTTT
20784 GAGAAGGGTA
Statistics
Matches: 342, Mismatches: 56, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
57 1 0.00
58 15 0.04
59 26 0.08
60 5 0.01
61 1 0.00
62 1 0.00
63 8 0.02
64 100 0.29
65 157 0.46
66 28 0.08
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (65 bp):
AAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGAAAGGTTGCCACTGACTTGTGTGGGCTTTA
Found at i:20870 original size:34 final size:33
Alignment explanation
Indices: 20817--20969 Score: 166
Period size: 32 Copynumber: 4.5 Consensus size: 33
20807 TTGTGGACTT
* *
20817 AAAAGGCTGTCACGGAGTTATGGACTTAAAAAAGA
1 AAAAGG-TGCCACAGAGTTATGGACTT-AAAAAGA
*
20852 AAAAGGTGCCACAGAGTTATGGAATTAAAAAGA
1 AAAAGGTGCCACAGAGTTATGGACTTAAAAAGA
* *
20885 AAAA-GTGCCATAGAGTTATGGACTTAAAAGGA
1 AAAAGGTGCCACAGAGTTATGGACTTAAAAAGA
* * * *
20917 AAAA-GTGCAACGGAGTTGTGGACTTTAGAAGAGA
1 AAAAGGTGCCACAGAGTTATGGAC-TTA-AAAAGA
20951 AAAGAGGTGCCACAGAGTT
1 AAA-AGGTGCCACAGAGTT
20970 GTGGGCTTTG
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
32 44 0.44
33 14 0.14
34 24 0.24
35 7 0.07
36 11 0.11
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.20
Consensus pattern (33 bp):
AAAAGGTGCCACAGAGTTATGGACTTAAAAAGA
Found at i:20952 original size:66 final size:68
Alignment explanation
Indices: 20831--20969 Score: 169
Period size: 66 Copynumber: 2.1 Consensus size: 68
20821 GGCTGTCACG
*
20831 GAGTTATGGACTTAAAAAAGAAAAAGGTGCCACAGAGTTATGGAATTAAAAAGAAAA-A-GTGCC
1 GAGTTATGGACTTAAAAAAGAAAAAGGTGCAACAGAGTTATGGAATTAAAAAGAAAAGAGGTGCC
*
20894 ATA
66 ACA
* * * * *
20897 GAGTTATGGACTT-AAAAGGAAAAA-GTGCAACGGAGTTGTGGACTTTAGAAGAGAAAAGAGGTG
1 GAGTTATGGACTTAAAAAAGAAAAAGGTGCAACAGAGTTATGGA-ATTA-AAAAGAAAAGAGGTG
20960 CCACA
64 CCACA
20965 GAGTT
1 GAGTT
20970 GTGGGCTTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
64 15 0.24
65 13 0.21
66 21 0.34
67 1 0.02
68 12 0.19
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (68 bp):
GAGTTATGGACTTAAAAAAGAAAAAGGTGCAACAGAGTTATGGAATTAAAAAGAAAAGAGGTGCC
ACA
Found at i:20983 original size:30 final size:29
Alignment explanation
Indices: 20949--21039 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 29
20939 CTTTAGAAGA
20949 GAAAAGAGGTGCCACAGAGTTGTGGGCTTT
1 GAAAAG-GGTGCCACAGAGTTGTGGGCTTT
*
20979 GAAAAGGGTTGCCATC-GACTTGTATGGGC-TT
1 GAAAAGGG-TGCCA-CAGAGTTG--TGGGCTTT
* * *
21010 CAGGAAGGGTGCCACAGAGTCGTGGGCTTT
1 GA-AAAGGGTGCCACAGAGTTGTGGGCTTT
21040 TGGAAAAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
29 7 0.14
30 19 0.39
31 13 0.27
32 10 0.20
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.24
Consensus pattern (29 bp):
GAAAAGGGTGCCACAGAGTTGTGGGCTTT
Found at i:22570 original size:55 final size:56
Alignment explanation
Indices: 22504--22616 Score: 210
Period size: 55 Copynumber: 2.0 Consensus size: 56
22494 GGTTTCAAAA
22504 GAATGATTTTGTTAGGCTCAAAGGGTGTGGAAAAGGA-TTTTTTTTGAGAGAAGAT
1 GAATGATTTTGTTAGGCTCAAAGGGTGTGGAAAAGGATTTTTTTTTGAGAGAAGAT
*
22559 GAATGATTTTGTTAGGCTCAAAGGGTGTGGAAAAGGATTTTTTTTTTAGAGAAGAT
1 GAATGATTTTGTTAGGCTCAAAGGGTGTGGAAAAGGATTTTTTTTTGAGAGAAGAT
22615 GA
1 GA
22617 TGAAAGAAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 37 0.66
56 19 0.34
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (56 bp):
GAATGATTTTGTTAGGCTCAAAGGGTGTGGAAAAGGATTTTTTTTTGAGAGAAGAT
Found at i:29373 original size:31 final size:31
Alignment explanation
Indices: 29253--29376 Score: 106
Period size: 31 Copynumber: 4.0 Consensus size: 31
29243 CTTAACTCGA
* * * * *
29253 ACTAAGGTGCCACCAGCTTGTGTGGGCTTTA
1 ACTAGGGTGCCACCAACTCGTGCGGGCTTTG
* * *
29284 ACTTA-GGTGCTACCAACTCGTACGGGCTTAG
1 AC-TAGGGTGCCACCAACTCGTGCGGGCTTTG
* * * **
29315 ACTCGGGTGCCGCCAGCTTATGCGGGCTTTG
1 ACTAGGGTGCCACCAACTCGTGCGGGCTTTG
*
29346 ACTAGGGTGCCACCAACTCGTGTGGGCTTTG
1 ACTAGGGTGCCACCAACTCGTGCGGGCTTTG
29377 GCATTCTAAG
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
30 1 0.01
31 67 0.96
32 2 0.03
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.27
Consensus pattern (31 bp):
ACTAGGGTGCCACCAACTCGTGCGGGCTTTG
Found at i:29384 original size:180 final size:179
Alignment explanation
Indices: 28992--29554 Score: 793
Period size: 180 Copynumber: 3.1 Consensus size: 179
28982 CTCAGACTTA
* * * * * *
28992 GGTGCCACCAGCTTGCGTGGGCTTTGACATTCTAAGTCTTGATCTCCTTAGACAGGTGCCAACTA
1 GGTGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTA
* * * **
29057 ATGTGGACTTGACTCGAACTTAGGTGCCACCAACTTGTGTGGACTTTGACTCAGGCACGCCAACT
66 ATATGGACTTGACTCGAACTTAGGTGCCACCAACTTGTGTGGGCTTTGACTTAGGTGCGCCAACT
** * * *
29122 CGTGTAGGCTTAGACTCAGGTGCCGTCAGCTTGTGTGGACTTTGATTAG
131 CGTGCGGGCTTAGACTCAGGTGCCGTCAGCTTGTGCGGGCTTTGACTAG
* *
29171 GGTGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTCAGATAGGTGCCAACTA
1 GGTGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTA
* * * * * *
29236 ATATGAACTTAACTCGAACTAAGGTGCCACCAGCTTGTGTGGGCTTTAACTTAGGTGCTACCAAC
66 ATATGGACTTGACTCGAACTTAGGTGCCACCAACTTGTGTGGGCTTTGACTTAGGTGC-GCCAAC
* * * *
29301 TCGTACGGGCTTAGACTCGGGTGCCGCCAGCTTATGCGGGCTTTGACTAG
130 TCGTGCGGGCTTAGACTCAGGTGCCGTCAGCTTGTGCGGGCTTTGACTAG
*
29351 GGTGCCACCAACTCGTGTGGGCTTTGGCATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTA
1 GGTGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTA
* * *
29416 ATTTGGGCTTGACTCTAACTTAGGTGCCACCAACTTGTGTGGGCTTTGACTTAGGTGCCGCCAAC
66 ATATGGACTTGACTCGAACTTAGGTGCCACCAACTTGTGTGGGCTTTGACTTAGGTG-CGCCAAC
* *
29481 TTGTGCGGGCTTAGACTCAGGTGCCGTTAGCTTGTGCGGGCTTTGACTAG
130 TCGTGCGGGCTTAGACTCAGGTGCCGTCAGCTTGTGCGGGCTTTGACTAG
*
29531 GGTGCCACCAACTCGTGCGGGCTT
1 GGTGCCACCAACTCGTGTGGGCTT
29555 AAAAAAGAGT
Statistics
Matches: 335, Mismatches: 47, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
179 105 0.31
180 229 0.68
181 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (179 bp):
GGTGCCACCAACTCGTGTGGGCTTTGACATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTA
ATATGGACTTGACTCGAACTTAGGTGCCACCAACTTGTGTGGGCTTTGACTTAGGTGCGCCAACT
CGTGCGGGCTTAGACTCAGGTGCCGTCAGCTTGTGCGGGCTTTGACTAG
Found at i:29456 original size:87 final size:87
Alignment explanation
Indices: 28933--29465 Score: 304
Period size: 87 Copynumber: 6.0 Consensus size: 87
28923 GGGTTTTGGT
* *
28933 ATTCTAAAGCTTGACCTCCTTAGATAGGTGCCAACTAATGTGGACTTGACTC-AGACTTAGGTGC
1 ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTCTA-ACTTAGGTGC
* *
28997 CACCAGCTTGCGTGGGCTTTGAC
65 CACCAACTTGTGTGGGCTTTGAC
* * * * *
29020 ATTCTAAGTCTTGATCTCCTTAGACAGGTGCCAACTAATGTGGACTTGACTCGAACTTAGGTGCC
1 ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTCTAACTTAGGTGCC
*
29085 ACCAACTTGTGTGGACTTTGAC
66 ACCAACTTGTGTGGGCTTTGAC
** * ** ** * *
29107 --TC--AGGCACGCCAACTCGTGTAGGCTTAGACTCAGGTGCCGTC-AGCTTGTG--TGGACTTT
1 ATTCTAAGGCTTG---AC-C---T--CCTTAGA-T-AGGTGCCAACTAATTTG-GACTTGACTCT
* *
29165 GA-TTAGGGTGCCACCAACTCGTGTGGGCTTTGAC
54 AACTTA-GGTGCCACCAACTTGTGTGGGCTTTGAC
* * * * * * *
29199 ATTCTAAGGCTTAACCTCCTCAGATAGGTGCCAACTAATATGAACTTAACTCGAACTAAGGTGCC
1 ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTCTAACTTAGGTGCC
* *
29264 ACCAGCTTGTGTGGGCTTTAAC
66 ACCAACTTGTGTGGGCTTTGAC
* * * *** * * * * * * * *
29286 TTAGGTGCTACCA-ACTCGTACGGGCTTAGACTCGGGTGCC-GCCAGCTTAT-G-C-GGGCTTTG
1 --A--TTCTA--AGGCTTG-ACCTCCTTAGA-T-AGGTGCCAACTA-ATT-TGGACTTGACTCTA
* *
29346 AC-TAGGGTGCCACCAACTCGTGTGGGCTTTGGC
55 ACTTA-GGTGCCACCAACTTGTGTGGGCTTTGAC
*
29379 ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGGCTTGACTCTAACTTAGGTGCC
1 ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTCTAACTTAGGTGCC
29444 ACCAACTTGTGTGGGCTTTGAC
66 ACCAACTTGTGTGGGCTTTGAC
29466 TTAGGTGCCG
Statistics
Matches: 321, Mismatches: 85, Indels: 80
0.66 0.17 0.16
Matches are distributed among these distances:
83 4 0.01
84 1 0.00
85 19 0.06
86 9 0.03
87 155 0.48
88 8 0.02
89 6 0.02
90 1 0.00
91 8 0.02
92 42 0.13
93 41 0.13
94 15 0.05
95 7 0.02
96 5 0.02
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (87 bp):
ATTCTAAGGCTTGACCTCCTTAGATAGGTGCCAACTAATTTGGACTTGACTCTAACTTAGGTGCC
ACCAACTTGTGTGGGCTTTGAC
Found at i:29471 original size:31 final size:31
Alignment explanation
Indices: 29433--29554 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 31
29423 CTTGACTCTA
*
29433 ACTTAGGTGCCACCAACTTGTGTGGGCTTTG
1 ACTTAGGTGCCACCAACTTGTGCGGGCTTTG
* *
29464 ACTTAGGTGCCGCCAACTTGTGCGGGCTTAG
1 ACTTAGGTGCCACCAACTTGTGCGGGCTTTG
* *** *
29495 ACTCAGGTGCCGTTAGCTTGTGCGGGCTTTG
1 ACTTAGGTGCCACCAACTTGTGCGGGCTTTG
*
29526 AC-TAGGGTGCCACCAACTCGTGCGGGCTT
1 ACTTA-GGTGCCACCAACTTGTGCGGGCTT
29555 AAAAAAGAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 1 0.01
31 75 0.99
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (31 bp):
ACTTAGGTGCCACCAACTTGTGCGGGCTTTG
Found at i:29662 original size:39 final size:40
Alignment explanation
Indices: 29580--29674 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 40
29570 CCATGCTATC
* *
29580 TGAGGATAAAGGAAAAGGAGAATGAAATGGGTCCTGCTCCT
1 TGAGGACAAAGG-AAAGGAGAATGAAATGAGTCCTGCTCCT
* * *
29621 TGAGGACAAAGGAAAGGAG-ATGAAGTGAGTCTTGCTTCT
1 TGAGGACAAAGGAAAGGAGAATGAAATGAGTCCTGCTCCT
*
29660 TGAGGACAAAAGAAA
1 TGAGGACAAAGGAAA
29675 ATAAGTGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 30 0.62
40 7 0.15
41 11 0.23
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.19
Consensus pattern (40 bp):
TGAGGACAAAGGAAAGGAGAATGAAATGAGTCCTGCTCCT
Found at i:30840 original size:16 final size:16
Alignment explanation
Indices: 30819--30857 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30809 ATTGGAACAC
** *
30819 TTTTTTTTTTATTTTG
1 TTTTTTTTAAATTTTA
30835 TTTTTTTTAAATTTTA
1 TTTTTTTTAAATTTTA
30851 TTTTTTT
1 TTTTTTT
30858 AAGGCATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTTTTAAATTTTA
Done.