Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1515
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: 37748
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:2438 original size:13 final size:13
Alignment explanation
Indices: 2420--2491 Score: 84
Period size: 13 Copynumber: 6.0 Consensus size: 13
2410 AATGTTTTCT
*
2420 TTGTATCTATACA
1 TTGTATCGATACA
2433 TTGTATCGATACA
1 TTGTATCGATACA
*
2446 TT-T-T---T-CT
1 TTGTATCGATACA
2453 TTGTATCGATACA
1 TTGTATCGATACA
2466 TTGTATCGATACA
1 TTGTATCGATACA
2479 TTGTATCGATACA
1 TTGTATCGATACA
2492 GGGTGATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 1 0.02
11 1 0.02
12 2 0.04
13 41 0.82
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2456 original size:33 final size:33
Alignment explanation
Indices: 2367--2480 Score: 133
Period size: 33 Copynumber: 3.4 Consensus size: 33
2357 ATGTCCAAAA
* *
2367 TGTATCGATACATGTTTCTGTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
* * * *
2400 CTGGA--AATTCAATGTTTTCTTTGTATCTATACAT
1 -TGTATCGATAC-AT-TTTTCTTTGTATCGATACAT
2434 TGTATCGATACATTTTTCTTTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
2467 TGTATCGATACATT
1 TGTATCGATACATT
2481 GTATCGATAC
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
32 3 0.05
33 38 0.58
34 22 0.33
35 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTTTTCTTTGTATCGATACAT
Found at i:7812 original size:52 final size:52
Alignment explanation
Indices: 7734--7862 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
7724 CGAAATATGA
* * *
7734 AAATTTATCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGC
*
7786 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGC
*
7838 AAATTTGCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
7863 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGC
Found at i:7875 original size:52 final size:51
Alignment explanation
Indices: 7734--7882 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
7724 CGAAATATGA
* *
7734 AAATTTATCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGC
* *
7786 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGC
* *
7838 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
7883 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGAGC
Found at i:7889 original size:13 final size:13
Alignment explanation
Indices: 7871--7895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7861 CAAAGATCAG
7871 TGTATCGATACAA
1 TGTATCGATACAA
7884 TGTATCGATACA
1 TGTATCGATACA
7896 TGTGAGTAAT
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:7978 original size:13 final size:13
Alignment explanation
Indices: 7960--7984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7950 CAAAAAAATA
7960 TGTATCGATACAT
1 TGTATCGATACAT
7973 TGTATCGATACA
1 TGTATCGATACA
7985 ACATTTTATG
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:7984 original size:33 final size:33
Alignment explanation
Indices: 7938--8004 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
7928 AGTAGCTTAA
7938 ATTGGATCGATACAAAAAAATATGTATCGATAC
1 ATTGGATCGATACAAAAAAATATGTATCGATAC
* * ***
7971 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGGATCGATACAAAAAAATATGTATCGATAC
8004 A
1 A
8005 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTGGATCGATACAAAAAAATATGTATCGATAC
Found at i:8931 original size:171 final size:171
Alignment explanation
Indices: 8734--9128 Score: 682
Period size: 171 Copynumber: 2.3 Consensus size: 171
8724 TTTTAGAGAT
* *
8734 GATGAAGGTGCCAATATGCTGATTCAAGACCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
8799 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
8864 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * * *
8905 GATGAAGATGCCAATATGCTGATTCAAGGCGAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
8970 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
9035 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
9076 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
9129 GTGCCAATGT
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 167 0.80
172 4 0.02
174 39 0.19
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:9185 original size:49 final size:49
Alignment explanation
Indices: 9042--9921 Score: 1241
Period size: 49 Copynumber: 17.7 Consensus size: 49
9032 GGATGTCAAC
* * *
9042 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9094 ATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9137 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* * *
9186 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9235 GTGCTGAGTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9284 GTGCTGAGTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9333 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9385 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9434 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9486 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9535 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9587 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9636 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9688 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9737 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
9789 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
9838 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAAT
* *
9890 ATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCTGATTCAAGGCCAGCTATATTGGACTTA
9922 GAGGGGTTGC
Statistics
Matches: 753, Mismatches: 51, Indels: 48
0.88 0.06 0.06
Matches are distributed among these distances:
43 39 0.05
47 1 0.00
48 1 0.00
49 409 0.54
50 6 0.01
51 5 0.01
52 292 0.39
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (49 bp):
GTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
Found at i:9424 original size:101 final size:101
Alignment explanation
Indices: 8975--9921 Score: 1567
Period size: 101 Copynumber: 9.4 Consensus size: 101
8965 GAAAAGTGAT
* * * * * * *
8975 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * *
9040 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
60 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
9082 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
9141 TGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
9175 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* *
9239 TGAGTCAAGGCCAGCGATATTGGACTTAAAGAT-G-
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
9273 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9337 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
9373 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9438 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
9474 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9539 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
9575 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9640 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
9676 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9741 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
9777 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
9842 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
9878 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
9922 GAGGGGTTGC
Statistics
Matches: 804, Mismatches: 27, Indels: 24
0.94 0.03 0.03
Matches are distributed among these distances:
92 39 0.05
94 1 0.00
95 41 0.05
96 4 0.00
98 137 0.17
99 1 0.00
101 544 0.68
103 1 0.00
107 36 0.04
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (101 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:9958 original size:28 final size:28
Alignment explanation
Indices: 9924--10014 Score: 137
Period size: 28 Copynumber: 3.1 Consensus size: 28
9914 TGGGCTTAGA
9924 GGGGTTGCCACCGACTTGTGTGGGCTTT
1 GGGGTTGCCACCGACTTGTGTGGGCTTT
*
9952 GGGGTTGCCACCAACTTGTGTGGGCTTT
1 GGGGTTGCCACCGACTTGTGTGGGCTTT
9980 GGGAAGAGTTGCCACCGACTTGTGTGGGCTTT
1 -GG--G-GTTGCCACCGACTTGTGTGGGCTTT
10012 GGG
1 GGG
10015 AAGGAAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
28 27 0.47
29 3 0.05
31 3 0.05
32 24 0.42
ACGTcount: A:0.11, C:0.20, G:0.40, T:0.30
Consensus pattern (28 bp):
GGGGTTGCCACCGACTTGTGTGGGCTTT
Found at i:10001 original size:32 final size:31
Alignment explanation
Indices: 9926--10018 Score: 147
Period size: 32 Copynumber: 3.1 Consensus size: 31
9916 GGCTTAGAGG
9926 GGTTGCCACCGACTTGTGTGGGCTTT-GG--
1 GGTTGCCACCGACTTGTGTGGGCTTTGGGAA
*
9954 GGTTGCCACCAACTTGTGTGGGCTTTGGGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGGAA
9985 GAGTTGCCACCGACTTGTGTGGGCTTTGGGAA
1 G-GTTGCCACCGACTTGTGTGGGCTTTGGGAA
10017 GG
1 GG
10019 AAAAAAGATG
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
28 25 0.42
29 2 0.03
31 2 0.03
32 30 0.51
ACGTcount: A:0.13, C:0.19, G:0.39, T:0.29
Consensus pattern (31 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGGAA
Found at i:10091 original size:34 final size:35
Alignment explanation
Indices: 10015--10940 Score: 502
Period size: 35 Copynumber: 25.9 Consensus size: 35
10005 GGGCTTTGGG
*
10015 AAGGAAAAA-AGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
10049 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
10085 AA-GAAAAA-AGTGCCACAGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
10119 AAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
10155 ACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * ** * ***
10190 AAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGA
1 AA-GGAAAAAGAGTGCCACGGAGTTGT-GG-GCTTTA-A
** * ** * * **** **
10229 GTTGTGGGCTTTAAAAGA---AAAAGGTGCCACGGAG-TTGTGGGC
1 ----AAGG---AAAAAGAGTGCCACGGAGTTGTGG-GCTT-T--AA
*** * * *
10271 TTTGAAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--A
* * *
10310 AGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10343 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10379 AA-GAAAAA-AGTGCCACGGAGTTGTGGGC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10411 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10447 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * ** * ***
10481 AAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGA
1 AA-GGAAAAAGAGTGCCACGGAGTTGT-GG-GCTTTA-A
** * ** * * **** **
10520 GTTGTGGGCTTTAAAAGA---AAAAGGTGCCACGGAG-TTGTGGGC
1 ----AAGG---AAAAAGAGTGCCACGGAGTTGTGG-GCTT-T--AA
*** * * *
10562 TTTGAAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--A
* * *
10601 AGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10634 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10670 AA-GAAAAA-AGTGCCACGGAGTTGTGGGC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10702 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10738 AA-GAAAAA-AGTGCCACGGAGTTGTGGGC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10770 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
10806 ACA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 A-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
10841 AA-GAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAA
1 AAGGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
10876 AA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
10909 AAAGAAGAAG-GTGCCACGGAGTTGTGGACTTT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
10941 GAGACAAAAT
Statistics
Matches: 692, Mismatches: 117, Indels: 166
0.71 0.12 0.17
Matches are distributed among these distances:
32 18 0.03
33 134 0.19
34 153 0.22
35 163 0.24
36 92 0.13
37 48 0.07
38 30 0.04
39 20 0.03
40 8 0.01
41 6 0.01
42 10 0.01
45 10 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (35 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:10254 original size:33 final size:33
Alignment explanation
Indices: 10217--10481 Score: 290
Period size: 33 Copynumber: 7.8 Consensus size: 33
10207 ACAAAGTCGT
*
10217 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
10250 AGGTGCCACGGAGTTGTGGGCTTT----GAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* * * *
10279 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
1 AGG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AGAAAA
* *
10318 AGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAA
10352 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
10386 AAGTGCCACGGAGTTGTGGGC-TTAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAA
10420 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
10454 AAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA
10482 AGGGAAAGAG
Statistics
Matches: 197, Mismatches: 17, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
29 7 0.04
30 8 0.04
31 1 0.01
32 16 0.08
33 70 0.36
34 24 0.12
35 39 0.20
36 18 0.09
37 1 0.01
38 8 0.04
39 5 0.03
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (33 bp):
AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
Found at i:10393 original size:68 final size:68
Alignment explanation
Indices: 10219--10940 Score: 608
Period size: 68 Copynumber: 10.3 Consensus size: 68
10209 AAAGTCGTAG
* * * *
10219 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT-----TGAAGA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
10279 AG-
66 AGA
* * * * * *
10281 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAG
1 G-TGCCACGGA-GT-TGTGGGCTTTA--AAAGAAAAAAG-TGCCACGGAGTTGTGGGCTTAAAAG
10346 GGAAAAAGA
60 GGAAAAAGA
10355 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
10420 AGA
66 AGA
10423 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGGAA
*
10488 AGAGA
64 AAAGA
* ** * ******* *** * * ****
10493 GTACCACAAAGTCGTAGGTGCCACAGAGTTGTGGGCTTTAAAAG-AAAAAGGTGCCACGGAG-TT
1 GTGCCACGGAGTTGT-GG-G---C----TT-TAAAAGAAAAAAGTGCCACGGAGTTGTGG-GCTT
*** *
10556 -GTGGGCTTTGAAGAAG-
55 AAAAGG----GAAAAAGA
* * * * * *
10572 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAG
1 G-TGCCACGGA-GT-TGTGGGCTTTA--AAAGAAAAAAG-TGCCACGGAGTTGTGGGCTTAAAAG
10637 GGAAAAAGA
60 GGAAAAAGA
10646 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
10711 AGA
66 AGA
10714 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
10779 AGA
66 AGA
*
10782 GTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GA
1 GTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAAAGTGCCACGGAGTTGTGGGC-TT-AAAAGGGA
10845 AGAAAGA
63 A-AAAGA
* * * * *
10852 GTGCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAG
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAGGGAAA
10916 AAG-
65 AAGA
*
10919 GTGCCACGGAGTTGTGGACTTT
1 GTGCCACGGAGTTGTGGGCTTT
10941 GAGACAAAAT
Statistics
Matches: 536, Mismatches: 80, Indels: 83
0.77 0.11 0.12
Matches are distributed among these distances:
62 1 0.00
63 8 0.01
64 1 0.00
65 11 0.02
67 27 0.05
68 237 0.44
69 79 0.15
70 55 0.10
71 28 0.05
72 4 0.01
73 30 0.06
74 6 0.01
75 1 0.00
76 10 0.02
77 3 0.01
78 2 0.00
79 9 0.02
80 19 0.04
81 3 0.01
82 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (68 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
AGA
Found at i:10572 original size:291 final size:291
Alignment explanation
Indices: 9970--10788 Score: 1491
Period size: 291 Copynumber: 2.8 Consensus size: 291
9960 CACCAACTTG
* * * *
9970 TGTGGGCTTTG-GGAAGAGTTGCCACCGACTTGTGTGGGCTTTGGGAAGGAAAAAAGATGCCACG
1 TGTGGGCTTTGAAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACG
10034 GAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCC
65 GAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCC
* * *
10099 ACAGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAA
130 ACGGAGTTGTGGGC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAA
*
10164 GGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGA
192 AGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGA
10229 GTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
257 GTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
10264 TGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGG
1 TGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGG
10329 AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCA
66 AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCA
10394 CGGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTG
131 CGGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTG
10459 CCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGAGTTG
196 CCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGAGTTG
10524 TGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
261 TGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
10555 TGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGG
1 TGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGG
10620 AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCA
66 AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCA
10685 CGGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTG
131 CGGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTG
* *
10750 CCACGGAGTTGTGGGC-TT-AAAAGGGAAAAAGAGTGCCAC
196 CCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCAC
10789 GGAGTTGTGG
Statistics
Matches: 514, Mismatches: 10, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
289 19 0.04
290 2 0.00
291 316 0.61
292 38 0.07
293 2 0.00
294 133 0.26
295 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (291 bp):
TGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGG
AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCA
CGGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTG
CCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGAGTTG
TGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
Found at i:10645 original size:155 final size:151
Alignment explanation
Indices: 10355--10652 Score: 370
Period size: 155 Copynumber: 1.9 Consensus size: 151
10345 GGGAAAAAGA
*
10355 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAGGGAAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTT---A-GGAAAA
* *
10420 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
62 AGAGTGCCACCGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAAGG
10485 GAAAGAGAGTACCACAAAGTCGTAG
127 GAAAGAGAGTACCACAAAGTCGTAG
* * *
10510 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT-TGAAGAAG-G
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAGGAAAAAGAG
* * * *
10573 TTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAA
66 -TGCCACCGA-GT-TGTGGGCTTTA--AAAGAAAAAAG-TGCCACGGAGTTGTGGACTTTAAAAA
* *
10636 GGGAAAAAGAGTGCCAC
125 GGGAAAGAGAGTACCAC
10653 GGAGTTGTGG
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
149 1 0.01
150 14 0.11
151 1 0.01
152 11 0.09
153 19 0.15
154 10 0.08
155 69 0.55
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (151 bp):
GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAGGAAAAAGAG
TGCCACCGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAAGGGAAA
GAGAGTACCACAAAGTCGTAG
Found at i:10942 original size:103 final size:101
Alignment explanation
Indices: 10508--10940 Score: 533
Period size: 103 Copynumber: 4.2 Consensus size: 101
10498 ACAAAGTCGT
*
10508 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT----GAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* * * ** *
10568 GAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
66 AAAGG-TGCCACGGA-GT-TGTGGGCTTTA--AAAAGAAAA
* *
10609 AGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
10673 AAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAGGGAAAA
64 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAA
10711 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA-AGTGCCACGGAGTTGTGGGC-TTAAAAGG
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--
*
10774 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAA
63 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
*
10814 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAG
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
10879 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGA
64 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
*
10917 AGGTGCCACGGAGTTGTGGACTTT
1 AGGTGCCACGGAGTTGTGGGCTTT
10941 GAGACAAAAT
Statistics
Matches: 295, Mismatches: 19, Indels: 34
0.85 0.05 0.10
Matches are distributed among these distances:
100 12 0.04
101 40 0.14
102 48 0.16
103 128 0.43
104 27 0.09
105 20 0.07
106 14 0.05
107 6 0.02
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (101 bp):
AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
Found at i:11020 original size:31 final size:31
Alignment explanation
Indices: 10920--11158 Score: 292
Period size: 31 Copynumber: 7.7 Consensus size: 31
10910 AAGAAGAAGG
* * *
10920 TGCCACGGAGTTGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
*
10950 TGCCACTGAGTCGTGGACTTTAAAG-AGAAGGA-
1 TGCCACTGAGTCGTGGACTTT-GAGCAG-A-GAT
*
10982 TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
*
11013 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
*
11044 TGCCACTGAGTCGTGGACTTTAAAG-AGAAGGA-
1 TGCCACTGAGTCGTGGACTTT-GAGCAG-A-GAT
*
11076 TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
*
11107 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
11138 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
11159 TTTTTGACTT
Statistics
Matches: 185, Mismatches: 12, Indels: 23
0.84 0.05 0.10
Matches are distributed among these distances:
29 1 0.01
30 23 0.12
31 111 0.60
32 47 0.25
33 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
Found at i:11062 original size:94 final size:94
Alignment explanation
Indices: 10920--11158 Score: 428
Period size: 94 Copynumber: 2.6 Consensus size: 94
10910 AAGAAGAAGG
* * *
10920 TGCCACGGAGTTGTGGACTTTGAGACA-A-AATGCCACTGAGTCGTGGACTTTAAAGAGAAGGAT
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGATTGCCACTGAGTCGTGGACTTTAAAGAGAAGGAT
10983 GCCACTGCGTCGTGGACTTTGAGCAGAGAT
65 GCCACTGCGTCGTGGACTTTGAGCAGAGAT
11013 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTAAAGAGAAGGATG
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTAAAGAGAAGGATG
11078 CCACTGCGTCGTGGACTTTGAGCAGAGAT
66 CCACTGCGTCGTGGACTTTGAGCAGAGAT
11107 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT
11159 TTTTTGACTT
Statistics
Matches: 141, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
92 1 0.01
93 24 0.17
94 116 0.82
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (94 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTAAAGAGAAGGATG
CCACTGCGTCGTGGACTTTGAGCAGAGAT
Found at i:11080 original size:63 final size:62
Alignment explanation
Indices: 10920--11158 Score: 310
Period size: 63 Copynumber: 3.8 Consensus size: 62
10910 AAGAAGAAGG
* * *
10920 TGCCACGGAGTTGTGGACTTTGAGACA-A-AATGCCACTGAGTCGTGGACTTTAAAGAGAAG-GA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGATTGCCACTGAGTCGTGGACTTT---GAGAAGAGA
10982 -
62 T
* *
10982 TGCCACTGCGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
* *
11044 TGCCACTGAGTCGTGGACTTTAAAGAGAAG-GA-TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTT---GAGAAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
11107 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT
11159 TTTTTGACTT
Statistics
Matches: 158, Mismatches: 10, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
60 12 0.08
61 5 0.03
62 62 0.39
63 72 0.46
64 2 0.01
65 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:11182 original size:9 final size:9
Alignment explanation
Indices: 11170--11194 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11160 TTTTGACTTT
11170 TTTTTTTTA
1 TTTTTTTTA
11179 TTTTTTTTA
1 TTTTTTTTA
11188 TTTTTTT
1 TTTTTTT
11195 AAAAAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:12149 original size:1 final size:1
Alignment explanation
Indices: 12138--12176 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
12128 TGAAAAGGGG
* *
12138 TTTTTTCTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12177 GAAGAGTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.95
Consensus pattern (1 bp):
T
Found at i:12164 original size:21 final size:20
Alignment explanation
Indices: 12137--12177 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12127 GTGAAAAGGG
*
12137 GTTTTTTCTTTTTTTTTTTT
1 GTTTTTTTTTTTTTTTTTTT
12157 GTTTTTTTTTTTTTTTTTTT
1 GTTTTTTTTTTTTTTTTTTT
12177 G
1 G
12178 AAGAGTAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.90
Consensus pattern (20 bp):
GTTTTTTTTTTTTTTTTTTT
Found at i:22092 original size:13 final size:13
Alignment explanation
Indices: 22074--22099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22064 CAATTTTTTG
22074 TGTATCGATACAT
1 TGTATCGATACAT
22087 TGTATCGATACAT
1 TGTATCGATACAT
22100 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22164 original size:21 final size:21
Alignment explanation
Indices: 22138--22213 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
22128 CTGCCAAGAA
*
22138 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
22159 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
22179 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
22200 ATGTATCGATACAT
1 ATGTATCGATACAT
22214 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:22184 original size:20 final size:20
Alignment explanation
Indices: 22159--22231 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
22149 CATCTTTTTT
22159 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
22179 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
22200 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
22220 ATGTATCGATAC
1 ATGTATCGATAC
22232 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:22195 original size:41 final size:41
Alignment explanation
Indices: 22138--22231 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
22128 CTGCCAAGAA
*
22138 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
22179 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
22220 ATGTATCGATAC
1 ATGTATCGATAC
22232 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:22868 original size:16 final size:16
Alignment explanation
Indices: 22837--22899 Score: 99
Period size: 16 Copynumber: 3.8 Consensus size: 16
22827 CTCTCCTTTG
22837 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
22855 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
22871 TCTCCCCCTTAAAAAAA
1 TCTCCCCCTT-AAAAAA
22888 TCTCCCCCTTAA
1 TCTCCCCCTTAA
22900 TTAGTTCACG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
16 20 0.45
17 16 0.36
18 8 0.18
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:22869 original size:17 final size:17
Alignment explanation
Indices: 22837--22899 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
22827 CTCTCCTTTG
*
22837 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC-TTAAAAAAA
22855 TCTCCCCCTT-AAAAAA
1 TCTCCCCCTTAAAAAAA
22871 TCTCCCCCTTAAAAAAA
1 TCTCCCCCTTAAAAAAA
22888 TCTCCCCCTTAA
1 TCTCCCCCTTAA
22900 TTAGTTCACG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.36
17 20 0.45
18 8 0.18
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (17 bp):
TCTCCCCCTTAAAAAAA
Found at i:22955 original size:16 final size:16
Alignment explanation
Indices: 22924--22969 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
22914 CTCTCCTTTG
22924 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
22942 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
22958 TCTCCCCCTTAA
1 TCTCCCCCTTAA
22970 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:24793 original size:13 final size:13
Alignment explanation
Indices: 24775--24814 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
24765 ATAATCACCC
*
24775 TGTATCGATACAG
1 TGTATCGATACAA
24788 TGTATCGATACAA
1 TGTATCGATACAA
24801 TGTATCGATACAA
1 TGTATCGATACAA
24814 T
1 T
24815 AAAAAATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:30731 original size:20 final size:20
Alignment explanation
Indices: 30689--30761 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
30679 ACATGGTCCA
* *
30689 GTATCGATACATTTCAATCAT
1 GTATCGATACA-TTCACTTAT
30710 GTATCGATACATTCACTTAT
1 GTATCGATACATTCACTTAT
*
30730 GTATCAATACATTCACTTATT
1 GTATCGATACATTCACTTA-T
30751 GTATCGATACA
1 GTATCGATACA
30762 AATTGTAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 25 0.53
21 22 0.47
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (20 bp):
GTATCGATACATTCACTTAT
Found at i:31471 original size:20 final size:20
Alignment explanation
Indices: 31448--31520 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
31438 ACAACTCAAA
31448 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
31468 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
31489 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
31509 GTATCGATACAT
1 GTATCGATACAT
31521 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:31492 original size:21 final size:21
Alignment explanation
Indices: 31466--31541 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
31456 ACATGTTGCA
31466 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
31487 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
31507 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
31528 ATGTATCGATACAT
1 ATGTATCGATACAT
31542 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:31499 original size:41 final size:41
Alignment explanation
Indices: 31448--31541 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
31438 ACAACTCAAA
*
31448 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
31489 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
31530 GTATCGATACAT
1 GTATCGATACAT
31542 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:31598 original size:13 final size:13
Alignment explanation
Indices: 31580--31605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31570 TACAGCAAGT
31580 ATGTATCGATACA
1 ATGTATCGATACA
31593 ATGTATCGATACA
1 ATGTATCGATACA
31606 CAAAAAATTG
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:37528 original size:9 final size:9
Alignment explanation
Indices: 37514--37538 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
37504 TTTGATTAAA
37514 TTTTGTGAT
1 TTTTGTGAT
37523 TTTTGTGAT
1 TTTTGTGAT
37532 TTTTGTG
1 TTTTGTG
37539 TTGAATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (9 bp):
TTTTGTGAT
Done.