Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3103
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: 51002
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:7155 original size:46 final size:46
Alignment explanation
Indices: 7105--7280 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
7095 TGGTTGAGCA
7105 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
7151 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
7196 CATCCGAAGTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
7244 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
7281 GCGGGTTGCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 61 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:7261 original size:93 final size:93
Alignment explanation
Indices: 7102--7273 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
7092 GGATGGTTGA
*
7102 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
7167 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
7195 GCATCCGAAGTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGAG
7259 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
7274 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 74 0.99
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:8646 original size:27 final size:27
Alignment explanation
Indices: 8616--8901 Score: 331
Period size: 27 Copynumber: 10.6 Consensus size: 27
8606 TTAGTTTACC
8616 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *** *
8643 AAATTACTAAAATACTATTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
8670 AAATCACCAAAATA-TCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** **
8696 AAATTACCAAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
8723 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * * *
8750 AAATTACTAAAATACGCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
8777 AGATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
8804 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
8831 AAATTATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
8858 AAATTACCAAAATACCCTTGATTTATG
1 AAATTACCAAAATACCCCTGGTTTGTA
*
8885 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
8902 TCGACCTGTA
Statistics
Matches: 216, Mismatches: 42, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 22 0.10
27 194 0.90
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:8681 original size:54 final size:54
Alignment explanation
Indices: 8616--8901 Score: 385
Period size: 54 Copynumber: 5.3 Consensus size: 54
8606 TTAGTTTACC
* **
8616 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACTATTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
8670 AAATCACCAAAATA-TCCTGGTTTGTAAAATTACCAAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * *
8723 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACGCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
8777 AGATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * * *
8831 AAATTATCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGATTTATG
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
*
8885 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
8902 TCGACCTGTA
Statistics
Matches: 203, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 48 0.24
54 155 0.76
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
Found at i:8902 original size:27 final size:27
Alignment explanation
Indices: 8616--9012 Score: 316
Period size: 27 Copynumber: 14.7 Consensus size: 27
8606 TTAGTTTACC
* *
8616 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* ** * *
8643 AAATTACTAAAATACTATTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
* * *
8670 AAATCACCAAAATATCC-TGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* * **
8696 AAATTACCAAAATACCATTGGTTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
8723 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* * *
8750 AAATTACTAAAATACGCTTTG-TTTATA
1 AAATTACCAAAATAC-CCTTGATTTGTA
* *
8777 AGATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
8804 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*
8831 AAATTATCAAAATACCCTT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
8858 AAATTACCAAAATACCCTTGATTTATG
1 AAATTACCAAAATACCCTTGATTTGTA
* * **
8885 AAATTACTAAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*** * *
8912 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* **
8939 AAATTACCAAAGTACCCTTGATTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
* **** * *
8966 GAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
**
8993 AAATTACTGAAATACCCTTG
1 AAATTACCAAAATACCCTTG
9013 TAGGGTAGAA
Statistics
Matches: 296, Mismatches: 67, Indels: 14
0.79 0.18 0.04
Matches are distributed among these distances:
26 24 0.08
27 268 0.91
28 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGATTTGTA
Found at i:9031 original size:27 final size:27
Alignment explanation
Indices: 9001--9293 Score: 390
Period size: 27 Copynumber: 10.9 Consensus size: 27
8991 TAAAATTACT
* *
9001 GAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
9028 GAAATACCCTTGTAGGGTAGAAGTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
*
9055 AAAATACCCCTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAAATACC
*
9082 GAAATACCCCTATAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* *
9109 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
9136 AAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
9163 AAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAAATACC
*
9190 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* *
9217 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
*
9244 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* *
9271 GAGATACCCTTGTAGGGTA-AAAT
1 GAAATACCCCTGTAGGGTAGAAAT
9294 TACCATTTTA
Statistics
Matches: 240, Mismatches: 26, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
26 3 0.01
27 237 0.99
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAAATACC
Found at i:9308 original size:81 final size:81
Alignment explanation
Indices: 8994--9298 Score: 441
Period size: 81 Copynumber: 3.8 Consensus size: 81
8984 CGATTTATAA
* * * * *
8994 AATTACTGAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAGTACTAAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAAAATTACCAAAA
9059 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
* * * * * *
9075 AAATACCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACTAAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAAAATTACCAAAA
9140 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
* * * *
9156 AATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAA-TACCGAA
1 AATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTA-AAATTACCAAA
9220 ATACCCCTGTAGGGTAG
65 ATACCCCTGTAGGGTAG
* *
9237 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTAGGGTAAAATTACCA
1 AATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAAAATTACCA
9299 TTTTACCCCT
Statistics
Matches: 201, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
80 3 0.01
81 196 0.98
82 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (81 bp):
AATTACTGAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAAAATTACCAAAA
TACCCCTGTAGGGTAG
Found at i:9636 original size:67 final size:67
Alignment explanation
Indices: 9523--9678 Score: 240
Period size: 67 Copynumber: 2.3 Consensus size: 67
9513 GAGGAAGCGT
* * *
9523 TCTGGCAGACTCGCTGCAATCTGGTGGCCTCGCCACATATACCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATTTAGTGGCCTCGCCACATATACCTGTTCTGGTGACTTCGTCACAA
9588 TA
66 TA
* * *
9590 TCTGGCAGCCTTGCTGCAATTTAGTGGCTTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATTTAGTGGCCTCGCCACATATACCTGTTCTGGTGACTTCGTCACAA
9655 TA
66 TA
* *
9657 TCTAGCAGCGTCGCTGCAATTT
1 TCTGGCAGCCTCGCTGCAATTT
9679 CTGTGGTGTG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 80 1.00
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATTTAGTGGCCTCGCCACATATACCTGTTCTGGTGACTTCGTCACAA
TA
Found at i:9816 original size:6 final size:6
Alignment explanation
Indices: 9801--9872 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
9791 ATTCTGTTAC
* *
9801 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATAT -TGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGAT-T CTGATT CTGATT
*
9850 CTGATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGA-TT CTGAT
9873 AATGTTTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
5 4 0.07
6 44 0.81
7 4 0.07
8 1 0.02
9 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:9829 original size:31 final size:31
Alignment explanation
Indices: 9778--9855 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
9768 TTGCATTCAC
*
9778 ATTCTGATTTTTTATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
9810 ATTCTGATTTTGATTCTGTTACCTGATATTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
9841 ATTCTGATTCTGATT
1 ATTCTGATTTTGATT
9856 TTGATTCTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
31 36 0.84
32 7 0.16
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:14960 original size:40 final size:40
Alignment explanation
Indices: 14889--14998 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
14879 TACCAGCTCC
* * * *
14889 TAGCCTACGGGTCTCT-AGCCCGGATAGCATTCTAGCACGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCA-GA
*
14929 -AGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCAGA
14968 TAGCCTGCGGGTCTTTAAGCCCGGAT-ACATT
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATT
14999 TCCTCAAGTC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 19 0.30
40 44 0.70
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCAGA
Found at i:22553 original size:40 final size:41
Alignment explanation
Indices: 22469--22578 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 41
22459 TACCATCTCG
* * * *
22469 TAGCCTGCAGGTCTCT-AGCCCGGATAGCATTCTAGCACGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
* *
22509 -AGCCTGCGGGTCTTTAAGCCTGGATAACATTCCAGCA-TA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
*
22548 TAGCCTGCGGGTCTTTAAGCCCAGAT-ACATT
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATT
22579 TCCTCAAGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 19 0.32
40 41 0.68
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (41 bp):
TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCACGA
Found at i:25879 original size:13 final size:13
Alignment explanation
Indices: 25858--25888 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25848 AACATTTCAC
25858 ACATAATATATAT
1 ACATAATATATAT
*
25871 ACATTATATATAT
1 ACATAATATATAT
25884 ACATA
1 ACATA
25889 CATGCAAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (13 bp):
ACATAATATATAT
Found at i:26910 original size:38 final size:40
Alignment explanation
Indices: 26840--26917 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 40
26830 AAGCCTAGTA
*
26840 TAATACACCGGCACAGAGCCTGCTAGGTAATAAACCTGATT
1 TAATACACCGG-ACAGAGCCTGCTAGGCAATAAACCTGATT
*
26881 TAATACACCGG-CA-AGCCTGCTAGGCAATAAGCCTGAT
1 TAATACACCGGACAGAGCCTGCTAGGCAATAAACCTGAT
26918 AACATACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 22 0.63
39 2 0.06
41 11 0.31
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (40 bp):
TAATACACCGGACAGAGCCTGCTAGGCAATAAACCTGATT
Found at i:26925 original size:38 final size:39
Alignment explanation
Indices: 26841--26931 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
26831 AGCCTAGTAT
* *
26841 AATACACCGGCACAGAGCCTGCTAGGTAATAAACCTGATTT
1 AATACACCGG--CAGAGCCTGCTAGGCAATAAACCTGATTA
*
26882 AATACACCGGCA-AGCCTGCTAGGCAATAAGCCTGA-TA
1 AATACACCGGCAGAGCCTGCTAGGCAATAAACCTGATTA
*
26919 ACATACACTGGCA
1 A-ATACACCGGCA
26932 TCAAGGCCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
37 2 0.04
38 31 0.69
39 2 0.04
41 10 0.22
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATACACCGGCAGAGCCTGCTAGGCAATAAACCTGATTA
Found at i:28864 original size:43 final size:42
Alignment explanation
Indices: 28817--28915 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
28807 TCCTAGACGT
*
28817 GGTCTTACATGTAATCAAATATCAATGCC-ACTATCCCAGACAG
1 GGTCTTACACGTAATCAAATA-CAATGCCGA-TATCCCAGACAG
* * * *
28860 GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAATCAAATACAATGCCGATATCCCAGACAG
28902 GGTCTTACACGTAA
1 GGTCTTACACGTAA
28916 ATCTCAAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 29 0.59
43 20 0.41
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATACAATGCCGATATCCCAGACAG
Found at i:28900 original size:42 final size:41
Alignment explanation
Indices: 28817--28962 Score: 127
Period size: 42 Copynumber: 3.4 Consensus size: 41
28807 TCCTAGACGT
* * * *
28817 GGTCTTACATGTAATCAAATATCAATGCCACTATCCCAGACAG
1 GGTCTTACACGAAATCAAATA-CGATGCCA-TGTCCCAGACAG
*
28860 GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATACGATGCC-ATGTCCCAGACAG
*
28902 GGTCTTACACGTAAATCTCAAAT-CGATGCCAACGTCCCA-A-ATG
1 GGTCTTACACG-AAA--TCAAATACGATGCC-ATGTCCCAGACA-G
*
28945 TGGTCTTACACAAAATCA
1 -GGTCTTACACGAAATCA
28963 CATATCGGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
41 3 0.03
42 28 0.32
43 27 0.31
44 24 0.27
45 6 0.07
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (41 bp):
GGTCTTACACGAAATCAAATACGATGCCATGTCCCAGACAG
Found at i:28949 original size:44 final size:42
Alignment explanation
Indices: 28793--28962 Score: 137
Period size: 43 Copynumber: 4.0 Consensus size: 42
28783 CAAAAAGCTT
* * * * * *
28793 ATACAATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAACGTCCCAAACATGGTCTTACACGAAATCAA
* * * *
28835 ATATCAATGCC-ACTATCCCAGACAGGGTCTTACACGAAATCAA
1 ATA-CGATGCCAAC-GTCCCAAACATGGTCTTACACGAAATCAA
* * *
28878 ATACGATGCCGATGTCCCAGACATGGTCTTACACGTAAATCTCAA
1 ATACGATGCCAACGTCCCAAACATGGTCTTACACG-AAA--TCAA
** *
28923 AT-CGATGCCAACGTCCCAAATGTGGTCTTACACAAAATCA
1 ATACGATGCCAACGTCCCAAACATGGTCTTACACGAAATCA
28963 CATATCGGAA
Statistics
Matches: 106, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
41 3 0.03
42 31 0.29
43 40 0.38
44 26 0.25
45 6 0.06
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAAACATGGTCTTACACGAAATCAA
Found at i:35588 original size:15 final size:15
Alignment explanation
Indices: 35568--35597 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35558 GACTGAAAAG
35568 AATATTGAATCCGTA
1 AATATTGAATCCGTA
35583 AATATTGAATCCGTA
1 AATATTGAATCCGTA
35598 CCAGTTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AATATTGAATCCGTA
Found at i:37621 original size:46 final size:47
Alignment explanation
Indices: 37569--37660 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 47
37559 TTGAATTTAA
* *
37569 AGCTTGTTAAA-TTGCTCTTAATATTTCCGGATAAGTTACTTAGTTC
1 AGCTTGTTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTTC
* *
37615 AGCTTGTTAAATTTGCCCTTATTATTTCCAGATAAGTTATTTAGTT
1 AGCTTGTTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTT
37661 AAAGAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 11 0.27
47 30 0.73
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (47 bp):
AGCTTGTTAAATTTGCCCTTAATATTTCCAGATAAGTTACTTAGTTC
Found at i:39645 original size:41 final size:40
Alignment explanation
Indices: 39514--39648 Score: 128
Period size: 40 Copynumber: 3.4 Consensus size: 40
39504 GGCTTCGGGT
* * * * * *
39514 CTTAACCCAGATATGGTCACTAGCATAAATGCCTTCGGGA
1 CTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTTGGGA
* *
39554 CTTAGCCTGGATATAGTCGCTAGCACAAATGCC-TTCGGA
1 CTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTTGGGA
* * * *
39593 TCTTAGTCCGGATGTAGTTGCTTAGCACAAAAGCCTTTGGGA
1 -CTTAGCCCGGATATAGTCGC-TAGCACAAATGCCTTTGGGA
*
39635 CTTAACCCGGATAT
1 CTTAGCCCGGATAT
39649 CATTCGAGTA
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
39 4 0.05
40 43 0.57
41 23 0.31
42 5 0.07
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (40 bp):
CTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTTGGGA
Found at i:40045 original size:44 final size:38
Alignment explanation
Indices: 40001--40075 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
39991 CAAGAACTCC
40001 TTCCTCC-TCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
40038 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
40076 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 7 0.19
38 30 0.81
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:46735 original size:39 final size:40
Alignment explanation
Indices: 46690--46857 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
46680 CGGGGTTTAG
* * *
46690 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
46729 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
46769 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
46809 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
46850 CCGGATAT
1 CCGGATAT
46858 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:46840 original size:41 final size:40
Alignment explanation
Indices: 46713--46857 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
46703 CTCGCACAAG
* * * * *
46713 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
46753 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
46793 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
46834 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
46858 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:47256 original size:45 final size:38
Alignment explanation
Indices: 47210--47285 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
47200 CAAGAACTCC
*
47210 TTCCTCCCTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
47248 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
47286 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:48169 original size:45 final size:45
Alignment explanation
Indices: 48096--48357 Score: 325
Period size: 45 Copynumber: 5.9 Consensus size: 45
48086 CGCACAGTAT
* *
48096 TATTCGGGCCTTTGAGCCTAGCAGGCTGTAATGCCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
48141 TATTTAGGCCTTTGAGCCTAGCAAGCTGTAATGCCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * * *
48186 TATTCGGGTCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGAAAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
48231 TATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
48276 TATTCAGGCTTTTGAGCCTAGCAGGCTATAATACCGGTGAAATGA-
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* * * *
48321 TA-TC-GGGCTTCGAGCCTAGCAGGCGA-AATGTCGGTGA
1 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
48358 ATGAATTTAG
Statistics
Matches: 191, Mismatches: 25, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
42 9 0.05
43 18 0.09
44 2 0.01
45 161 0.84
46 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (45 bp):
TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Done.