Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1928
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: 404355
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:298275 original size:13 final size:13
Alignment explanation
Indices: 298257--298314 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
298247 ACATAAGGGT
298257 TGTATCGATACAA
1 TGTATCGATACAA
298270 TGTATCGATACATAA
1 TGTATCGATAC--AA
298285 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
298302 TGTATCGCTACAA
1 TGTATCGATACAA
298315 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:298279 original size:32 final size:32
Alignment explanation
Indices: 298238--298313 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
298228 ACCGTTGGGT
298238 TGTATCGATACATAAGGGTTGTATCGATACAA
1 TGTATCGATACATAAGGGTTGTATCGATACAA
*
298270 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGGGTTGTATCGATACAA
*
298302 TGTATCGCTACA
1 TGTATCGATACA
298314 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATAAGGGTTGTATCGATACAA
Found at i:298370 original size:13 final size:13
Alignment explanation
Indices: 298352--298379 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
298342 CATTATTCAA
298352 TGTATCGATACAT
1 TGTATCGATACAT
298365 TGTATCGATACAT
1 TGTATCGATACAT
298378 TG
1 TG
298380 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298376 original size:33 final size:33
Alignment explanation
Indices: 298334--298397 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
298324 CAAGGAAATT
298334 TATCGATACATT-ATTCAATGTATCGATACATTG
1 TATCGATACATTGA-TCAATGTATCGATACATTG
**
298367 TATCGATACATTGATCTTTGTATCGATACAT
1 TATCGATACATTGATCAATGTATCGATACAT
298398 CTGGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (33 bp):
TATCGATACATTGATCAATGTATCGATACATTG
Found at i:305460 original size:52 final size:52
Alignment explanation
Indices: 305382--305529 Score: 217
Period size: 52 Copynumber: 2.8 Consensus size: 52
305372 TGAAATATGA
*
305382 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCT-GAGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAG-GC
* *
305434 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
*** *
305486 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATAC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATAC
305530 GATGTATCGA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 85 0.99
53 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
Found at i:306546 original size:67 final size:68
Alignment explanation
Indices: 306424--306550 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
306414 ATTGGGTTTT
* * *
306424 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
306489 AGA
66 AGA
* * * *
306492 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
306551 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:306600 original size:55 final size:52
Alignment explanation
Indices: 306500--306929 Score: 311
Period size: 49 Copynumber: 8.9 Consensus size: 52
306490 GAAAAGTGAT
* * * * * * **
306500 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-AG-A
* *
306554 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* * *
306607 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* * *
306650 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* *
306700 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* *
306742 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* * *
306792 -AAGGTTCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* * *
306834 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
* * * *
306884 -AAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAG
306930 GTGAAGATGA
Statistics
Matches: 312, Mismatches: 36, Indels: 61
0.76 0.09 0.15
Matches are distributed among these distances:
43 111 0.36
44 3 0.01
46 1 0.00
48 2 0.01
49 116 0.37
51 1 0.00
52 31 0.10
53 6 0.02
54 6 0.02
55 35 0.11
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGA
Found at i:306654 original size:22 final size:22
Alignment explanation
Indices: 306629--306696 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
306619 ATGTTGATTC
306629 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
306651 AAGGTGCCA-ATGTACT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
306672 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
306694 AAG
1 AAG
306697 AAGAAGGTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 9 0.28
23 5 0.16
24 4 0.12
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:306670 original size:43 final size:43
Alignment explanation
Indices: 306607--307339 Score: 426
Period size: 49 Copynumber: 16.1 Consensus size: 43
306597 TAAAGATAGA
*
306607 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
306650 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
306693 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
306742 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
306785 AAAGAAGAAGGTTCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
306834 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
306877 AAAGATGAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * * *
306926 AAAGGTG--AAGATG-AGA--AAAGTG--A--TAAAGATGAGA--A
1 AAAGGTGCCAATATGCTGATTCAAG-GCCAGCTATA-TTG-GACTT
* * * * * * *
306961 AAAGGATG--ATTCACGGCCAACGA-T-ATTGG---GCTTAAAGATGAGA--A
1 AAAGG-TGCCAAT-A-TG-C--TGATTCA-AGGCCAGC-TATA-TTG-GACTT
* * * * * *
307005 AAAGGATGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGAT
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
307055 GGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
307101 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
307144 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
307193 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCTAACTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
307242 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
307285 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATTTTGGGCTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
307334 AGAAGG
1 A-AAGG
307340 GTTGCCACCG
Statistics
Matches: 562, Mismatches: 65, Indels: 125
0.75 0.09 0.17
Matches are distributed among these distances:
35 7 0.01
36 5 0.01
37 4 0.01
38 4 0.01
39 1 0.00
40 2 0.00
41 5 0.01
42 7 0.01
43 207 0.37
44 33 0.06
45 3 0.01
46 3 0.01
47 1 0.00
48 4 0.01
49 240 0.43
51 1 0.00
52 30 0.05
53 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:306738 original size:92 final size:92
Alignment explanation
Indices: 306554--307323 Score: 723
Period size: 92 Copynumber: 8.4 Consensus size: 92
306544 AAGATGAGAA
* *
306554 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG--AAGGTGCCAAT
*
306619 ATGTTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
*
306650 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
306715 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
306742 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTTCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
306807 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
306834 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATAC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
306899 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * * * * * *
306926 AAAGGTG--AA-GATG-AGA--AAAGTG--A--TAAAGATGAGA--AAAAGGATGATTCACG-GC
1 AAAGGTGCCAATG-TGCTGATTCAAG-GCCAGCTACA-TTG-GACTTAAA-GAAGA---AGGTGC
* * * * * * **
306978 C-A-ACGAT-ATT--GGGCTTA--AAGA-TGAGA-AA
58 CAATATGCTGATTCAAGGC-CAGCTATATTG-GACTT
* * * * * * * *
307006 AAGGATGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATA
307071 TGCTGATTCAAGGCCAGCTATATTGGACTT
63 TGCTGATTCAAGGCCAGCTATATTGGACTT
307101 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
307166 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * * *
307193 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCTAACTATATTGGACTT-----A-AAGGTGCCA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCA
* *
307252 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
307285 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
307324 TTTTGGGCTT
Statistics
Matches: 570, Mismatches: 63, Indels: 86
0.79 0.09 0.12
Matches are distributed among these distances:
80 7 0.01
81 4 0.01
82 7 0.01
83 3 0.01
84 9 0.02
85 12 0.02
86 6 0.01
87 12 0.02
88 12 0.02
89 4 0.01
90 8 0.01
91 3 0.01
92 346 0.61
93 4 0.01
94 6 0.01
95 83 0.15
96 5 0.01
97 1 0.00
98 38 0.07
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:307054 original size:451 final size:446
Alignment explanation
Indices: 306430--307288 Score: 1407
Period size: 451 Copynumber: 1.9 Consensus size: 446
306420 TTTTAAAGAT
*
306430 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGGTGCCAATATACTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
* * * *
306495 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCAAAAAGGATGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
* * * *
306560 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAGAAAAGGTGCCAATATGTTG
131 TGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGATAGAAAAGGTGCCAATATGCTG
306625 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGA
196 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGA
*
306690 CTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A-AAGGTGCCAA
261 CTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAA
* * *
306753 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTTCCAATATGCTGATTCAAGGC
326 TATGCTGATTCAAGGCCAACTACATTGGACTT-----A-AAGGTGCCAATATGCTGATTCAAGGC
*
306818 CAGCTATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
385 CAGCTACATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* *
306880 GATGAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGATGAGAAAA
1 GATGAAGGTGCCAATATACTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
306945 GTGATAAAGATGAGAAAAAGGATGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
66 GTGATAAAGATG-CAAAAAGGATGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
*
307010 ATGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGATGGAAAAGGTGCCAATATGCT
130 ATGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGATAGAAAAGGTGCCAATATGCT
*
307075 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
195 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGG
307140 ACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGT
260 ACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT----AAGAAGGT
* * *
307205 GCCAATATGCTGATTCAAGGCTAACTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
321 GCCAATATGCTGATTCAAGGCCAACTACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCC
307270 AGCTACATTGGACTTAAAG
386 AGCTACATTGGACTTAAAG
307289 AAGAAGGTGC
Statistics
Matches: 380, Mismatches: 22, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
450 74 0.19
451 266 0.70
452 1 0.00
456 1 0.00
457 38 0.10
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (446 bp):
GATGAAGGTGCCAATATACTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCAAAAAGGATGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
TGTCAATGTGCTAATTCAAGACCAGCTACATTGAACGTAAAGATAGAAAAGGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGA
CTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAA
TATGCTGATTCAAGGCCAACTACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
CATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
Found at i:307557 original size:61 final size:63
Alignment explanation
Indices: 307375--307815 Score: 244
Period size: 69 Copynumber: 6.8 Consensus size: 63
307365 AAGAAGGGTG
* * *
307375 AAAGA-TGACACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCA-CGAAGTTGTGGACTTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAA--AAC--GGTGCCACCG-AGTTGTGGAC-TTAAAA
307438 GGGAA
60 -GGAA
* * * *
307443 AAAGAGTGCCATGGAGTTGTGGGCTTTGAAAAAACGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTT--AAAAACGGTGCCACCGAGTTGTGGACTTAAAAGGAA
* * *
307508 CAAG-GTGCCACGTG-GTTGTGGACTTT-AAAAGGGTGCCACCGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACG-GAGTTGTGGACTTTAAAAACGGTGCCACCGAGTTGTGGACTTAAAAGGAA
* * *
307569 AAAGAGTGCCACGGAGTTGTGGGCTTAAACGGATAAAAGAGTGCCA-CGAAGTTGTAGG-CTTAA
1 AAAGAGTGCCACGGAGTTGTGGACTT-TA---A-AAACG-GTGCCACCG-AGTTGT-GGACTTAA
*
307632 ACGGGTAA
58 A-AGG-AA
* * * * * * * *
307640 AAA-AATGTCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGAGTGCCACGGAGTTGTGGACTT--TA--AAAACG-GTGCCACCGAGTTGTGGACTTAAAAG
307704 GAA
61 GAA
* * * * * * * *
307707 AAAGAGTGCCACGGAGTCGTGAACTTAAAGAAAAGATGCCACTGAGTCGTGGACTT---TGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAA-AAACGGTGCCACCGAGTTGTGGACTTAAAAGGAA
* * * *
307768 AGAGA-TGCCACTGAGTTGTGGGC-TTAAAAA-GGTGCCACAGAGTTGTGG
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAACGGTGCCACCGAGTTGTGG
307816 GCTTTGAGAC
Statistics
Matches: 304, Mismatches: 46, Indels: 57
0.75 0.11 0.14
Matches are distributed among these distances:
57 15 0.05
58 3 0.01
59 3 0.01
60 14 0.05
61 43 0.14
62 18 0.06
64 37 0.12
65 13 0.04
66 8 0.03
67 22 0.07
68 32 0.11
69 59 0.19
70 27 0.09
71 10 0.03
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.20
Consensus pattern (63 bp):
AAAGAGTGCCACGGAGTTGTGGACTTTAAAAACGGTGCCACCGAGTTGTGGACTTAAAAGGAA
Found at i:307572 original size:34 final size:33
Alignment explanation
Indices: 307375--307795 Score: 315
Period size: 34 Copynumber: 12.9 Consensus size: 33
307365 AAGAAGGGTG
* *
307375 AAAGA-TGACACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTT-AAAGGAA
* *
307408 CAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TT-AAA-GGAA
* * *
307443 AAAGAGTGCCATGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAGGAA
* *
307475 AACG-GTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTT-AAAGGAA
* *
307508 CAAG-GTGCCACGTG-GTTGTGGACTT-----TA
1 AAAGAGTGCCACG-GAGTTGTGGACTTAAAGGAA
* *
307535 AAAGGGTGCCACCGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTA-AAGGAA
*
307569 AAAGAGTGCCACGGAGTTGTGGGCTTAAACGGATA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAA-GGA-A
*
307604 AAAGAGTGCCACGAAGTTGTAGG-CTTAAACGGGTAA
1 AAAGAGTGCCACGGAGTTGT-GGACTTAAA--GG-AA
* * * *
307640 AAA-AATGTCACGGAGTTATGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTA-AAGGAA
307673 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTA-AAGGAA
* *
307707 AAAGAGTGCCACGGAGTCGTGAACTTAAA-G-A
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAGGAA
* * *
307738 AAAGA-TGCCACTGAGTCGTGGACTT--TGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAGGAA
* * *
307768 AGAGA-TGCCACTGAGTTGTGGGCTTAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAA
307796 AAGGTGCCAC
Statistics
Matches: 319, Mismatches: 41, Indels: 57
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.02
28 18 0.06
29 1 0.00
30 43 0.13
31 24 0.08
32 6 0.02
33 51 0.16
34 90 0.28
35 51 0.16
36 29 0.09
37 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (33 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAAAGGAA
Found at i:307774 original size:30 final size:29
Alignment explanation
Indices: 307707--307881 Score: 126
Period size: 30 Copynumber: 6.0 Consensus size: 29
307697 TTAGAAGGAA
* * *
307707 AAAGAG-TGCCACGGAGTCGTGAACTTAAAG
1 AAAGAGATGCCACTGAGTCGTGGACTT--TG
307737 AAA-AGATGCCACTGAGTCGTGGACTTTGG
1 AAAGAGATGCCACTGAGTCGTGGACTTT-G
* *
307766 AAAGAGATGCCACTGAGTTGTGGGC-TT-
1 AAAGAGATGCCACTGAGTCGTGGACTTTG
* * * * *
307793 AAAAAGGTGCCACAGAGTTGTGGGCTTTG
1 AAAGAGATGCCACTGAGTCGTGGACTTTG
* * *
307822 AGACA-AAATGCCACTGAGTCGTGGGCATTG
1 A-A-AGAGATGCCACTGAGTCGTGGACTTTG
*
307852 AGAAGAGATTACCACTGAGTCGTGGACTTT
1 A-AAGAGA-TGCCACTGAGTCGTGGACTTT
307882 AAGAAGGTAT
Statistics
Matches: 119, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
27 22 0.18
28 2 0.02
29 10 0.08
30 66 0.55
31 19 0.16
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.23
Consensus pattern (29 bp):
AAAGAGATGCCACTGAGTCGTGGACTTTG
Found at i:307821 original size:57 final size:57
Alignment explanation
Indices: 307737--307881 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 57
307727 GAACTTAAAG
* *
307737 AAAAGATGCCACTGAGTCGTGGACTTTG-GA-AAGAGATGCCACTGAGTTGTGGGCTTA
1 AAAAGATGCCACAGAGTCGTGGACTTTGAGACAA-A-ATGCCACTGAGTCGTGGGCTTA
* * *
307794 AAAAGGTGCCACAGAGTTGTGGGCTTTGAGACAAAATGCCACTGAGTCGTGGGCATTGA
1 AAAAGATGCCACAGAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGGC-TT-A
* * *
307853 GAAGAGATTACCACTGAGTCGTGGACTTT
1 -AAAAGA-TGCCACAGAGTCGTGGACTTT
307882 AAGAAGGTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
57 42 0.59
58 5 0.07
59 3 0.04
60 4 0.06
61 17 0.24
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (57 bp):
AAAAGATGCCACAGAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGGCTTA
Found at i:308839 original size:1 final size:1
Alignment explanation
Indices: 308835--308872 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
308825 TTTTCCTTCC
* *
308835 TTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
308873 GTGAAGATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:316073 original size:52 final size:52
Alignment explanation
Indices: 315995--316123 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
315985 TGAAATATGA
* *
315995 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
316047 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
316099 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
316124 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:316136 original size:52 final size:51
Alignment explanation
Indices: 315995--316143 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
315985 TGAAATATGA
*
315995 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
316047 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
316099 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
316144 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:316150 original size:13 final size:13
Alignment explanation
Indices: 316132--316156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
316122 CAAAGATCAG
316132 TGTATCGATACAA
1 TGTATCGATACAA
316145 TGTATCGATACA
1 TGTATCGATACA
316157 TTTGAGTAAT
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:316234 original size:33 final size:33
Alignment explanation
Indices: 316197--316263 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
316187 AGTAGCTTAA
316197 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
316230 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
316263 A
1 A
316264 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:316237 original size:13 final size:13
Alignment explanation
Indices: 316219--316243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
316209 CAAAAAAATA
316219 TGTATCGATACAT
1 TGTATCGATACAT
316232 TGTATCGATACA
1 TGTATCGATACA
316244 ACACTTTATG
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:326620 original size:24 final size:23
Alignment explanation
Indices: 326588--326666 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 23
326578 AAGAAAGAAG
326588 AAAAA-AAAACAAACAAACAAAA
1 AAAAACAAAACAAACAAACAAAA
*
326610 AAATAACAAAAAAAACAAA-AAAA
1 AAA-AACAAAACAAACAAACAAAA
326633 ACCAAAACAAAACAAACAAAACAAAA
1 A--AAAACAAAACAAAC-AAACAAAA
326659 AAAAACAA
1 AAAAACAA
326667 CAAAAAGGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
22 3 0.06
23 7 0.14
24 29 0.59
25 5 0.10
26 5 0.10
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (23 bp):
AAAAACAAAACAAACAAACAAAA
Found at i:326626 original size:9 final size:9
Alignment explanation
Indices: 326589--326672 Score: 89
Period size: 9 Copynumber: 8.8 Consensus size: 9
326579 AGAAAGAAGA
326589 AAAAAAAAC
1 AAAAAAAAC
326598 AAACAAACAA-
1 AAA-AAA-AAC
*
326608 AAAAATAAC
1 AAAAAAAAC
326617 AAAAAAAAC
1 AAAAAAAAC
326626 AAAAAAAACC
1 AAAAAAAA-C
326636 AAAACAAAAC
1 AAAA-AAAAC
*
326646 AAACAAAAC
1 AAAAAAAAC
326655 AAAAAAAAAC
1 -AAAAAAAAC
326665 AACAAAAA
1 AA-AAAAA
326673 GGGTCCGGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
8 2 0.03
9 28 0.44
10 28 0.44
11 6 0.09
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:326634 original size:29 final size:28
Alignment explanation
Indices: 326589--326672 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
326579 AGAAAGAAGA
*
326589 AAAAAAAAC-AAACAAACAAAAAAATAAC
1 AAAAAAAACAAAAAAAACAAAAAAA-AAC
*
326617 AAAAAAAACAAAAAAAACCAAAACAAAAC
1 AAAAAAAACAAAAAAAA-CAAAAAAAAAC
* *
326646 AAACAAAACAAAAAAAAACAACAAAAA
1 AAAAAAAAC-AAAAAAAACAAAAAAAA
326673 GGGTCCGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.19
29 24 0.50
30 15 0.31
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.01
Consensus pattern (28 bp):
AAAAAAAACAAAAAAAACAAAAAAAAAC
Found at i:326672 original size:1 final size:1
Alignment explanation
Indices: 326570--326663 Score: 53
Period size: 1 Copynumber: 94.0 Consensus size: 1
326560 CATCCTCCGC
* * * * * * * * * *
326570 AAAAAAAAAAGAAAGAAGAAAAAAAAACAAACAAACAAAAAAATAACAAAAAAAACAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
326635 CAAAACAAAACAAACAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
326664 CAACAAAAAG
Statistics
Matches: 65, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:328129 original size:28 final size:28
Alignment explanation
Indices: 328096--328334 Score: 277
Period size: 28 Copynumber: 8.5 Consensus size: 28
328086 TCACCTTTTC
328096 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
328124 AAAGCCCACAAATCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
328153 AAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * * *
328181 AAAGCCCACAAGTTAGTGACATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
328210 AAAGCCCACAAGTCAGTGGCAATCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
328238 AAAGCCCACAAGTCAGTGGCACCCCTTTC-
1 AAAGCCCACAAGTCAGTGGCA-ACC-TTCA
* *
328267 -AAGCCCACAAGTCAGTGGTATCCTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
328294 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
328322 AAAGCACACAAGT
1 AAAGCCCACAAGT
328335 TGATGCAACC
Statistics
Matches: 179, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.05
28 121 0.68
29 46 0.26
30 3 0.02
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:328177 original size:57 final size:57
Alignment explanation
Indices: 328090--328314 Score: 323
Period size: 57 Copynumber: 4.0 Consensus size: 57
328080 CATTCCTCAC
*
328090 CTTTT-CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAT
* * *
328146 CTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGACAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAT
* *
328203 CTTTTCCAAAGCCCACAAGTCAGTGGCAATCTTCAAAAGCCCACAAGTCAGTGGCACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCA-T
* * *
328261 CCTTT-C-AAGCCCACAAGTCAGTGGTATCCTTTC-AAAGCCCACAAGTCAGTGGCA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCA
328315 ACCTTCAAAA
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
56 46 0.30
57 103 0.67
58 4 0.03
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.21
Consensus pattern (57 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAT
Found at i:328249 original size:85 final size:85
Alignment explanation
Indices: 328092--328358 Score: 307
Period size: 85 Copynumber: 3.2 Consensus size: 85
328082 TTCCTCACCT
* * * * *
328092 TTTC-AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAATCAGTGGC-ATCTTTTCCAA
1 TTTCAAAAGCCCACAAGTCAGTGGCATCTTTCCAAAGCCCACAAGTCAGTGGCAATC--TTCAAA
328155 AGCCCACAAGTTAGTGGCAACC
64 AGCCCACAAGTTAGTGGCAACC
* *
328177 -TTCAAAAGCCCACAAGTTAGTGACATCTTTTCCAAAGCCCACAAGTCAGTGGCAATCTTCAAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCATC-TTTCCAAAGCCCACAAGTCAGTGGCAATCTTCAAAA
* *
328241 GCCCACAAGTCAGTGGCACCCC
65 GCCCACAAGTTAGTGGCA-ACC
* *
328263 TTTC--AAGCCCACAAGTCAGTGGTATCCTTT-CAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCAT-CTTTCCAAAGCCCACAAGTCAGTGGCAATCTTCAAAA
*
328325 GCACACAAGTT-GAT-GCAACCC
65 GCCCACAAGTTAG-TGGCAA-CC
328346 TTTCAAAAGCCCA
1 TTTCAAAAGCCCA
328359 TACAAGTTGA
Statistics
Matches: 156, Mismatches: 16, Indels: 20
0.81 0.08 0.10
Matches are distributed among these distances:
83 10 0.06
84 44 0.28
85 71 0.46
86 25 0.16
87 6 0.04
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (85 bp):
TTTCAAAAGCCCACAAGTCAGTGGCATCTTTCCAAAGCCCACAAGTCAGTGGCAATCTTCAAAAG
CCCACAAGTTAGTGGCAACC
Found at i:328367 original size:31 final size:31
Alignment explanation
Indices: 328318--328398 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
328308 AGTGGCAACC
328318 TTCAAAAG--CACACAAGTTGATGCAACCCT
1 TTCAAAAGCCCACACAAGTTGATGCAACCCT
*
328347 TTCAAAAGCCCATACAAGTTGATGCAACCCT
1 TTCAAAAGCCCACACAAGTTGATGCAACCCT
*
328378 TTCCAAAGCCCACACAAGTTG
1 TTCAAAAGCCCACACAAGTTG
328399 GTGGCGTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 8 0.17
31 39 0.83
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.21
Consensus pattern (31 bp):
TTCAAAAGCCCACACAAGTTGATGCAACCCT
Found at i:328537 original size:48 final size:49
Alignment explanation
Indices: 328419--328875 Score: 354
Period size: 48 Copynumber: 9.8 Consensus size: 49
328409 CTTCTAAGTT
* * * *
328419 CAATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGA-C
* * * *
328469 CAATATCGCTGGCCTTGAATCAGCATACTGACA-CTTTGTCTTTAAGAC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * *
328517 CAATGTCGTTGGCCTTGAATCAACACATTGG---C---A----TAAG-C
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * * *
328555 CTAATATCGTTGGCCTTGAATCAGCATATTGGCA-CCTTGTCTTTAAGAC
1 C-AATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* *
328604 CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAG-T
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * ***
328652 CAAAGTCGTTGGCCTTGAATCAGCATATTGGCATCGACATCTTTAAGAC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * *
328701 CAATGTTGCTGGCCTTGAATCAGCACATTGG---C---A----TAAGCC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * * * * * *
328740 CAATATCGCTGGCTTTGAATCGGTATGTTGGCA-CCTTGTCTTTAAGAC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
* * *
328788 CAATGTCGCTAGCCTTGAATCAGCACATTGGCAT-TTTCATCTTTAAGTC
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTT-ATCTTTAAGAC
* * * *
328837 CGATATCGTTGGCATTGAATCAGCATATTGGCATCTTTA
1 CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTA
328876 ACATCCCTAA
Statistics
Matches: 323, Mismatches: 59, Indels: 51
0.75 0.14 0.12
Matches are distributed among these distances:
38 2 0.01
39 60 0.19
41 2 0.01
43 1 0.00
46 2 0.01
48 133 0.41
49 90 0.28
50 33 0.10
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (49 bp):
CAATGTCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGAC
Found at i:328617 original size:87 final size:87
Alignment explanation
Indices: 328470--328821 Score: 425
Period size: 87 Copynumber: 3.9 Consensus size: 87
328460 TTTAAAACCC
* * * *
328470 AATATCGCTGGCCTTGAATCAGCATACTGACACTTTGTCTTTAAGACCAATGTCGTTGGCCTTGA
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
*
328535 ATCAACACATTGGCATAAGCCT
66 ATCAGCACATTGGCATAAGCCT
*
328557 AATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
* * *
328622 ATCAGCACATTGGCATCTTTATCTTT
66 ATCAGCACATTGGCA---TAAGC-CT
* **** *
328648 AAGTCAAAGTCGTTGGCCTTGAATCAGCATATTGGCATCGACATCTTTAAGACCAATGTTGCTGG
1 AA-T---A-TCGCTGGCCTTGAATCAGCATATTGGCA-CCTTGTCTTTAAGACCAATGTCGCTGG
*
328713 CCTTGAATCAGCACATTGGCATAAGCCC
60 CCTTGAATCAGCACATTGGCATAAGCCT
* * * * *
328741 AATATCGCTGGCTTTGAATCGGTATGTTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTTGA
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
328806 ATCAGCACATTGGCAT
66 ATCAGCACATTGGCAT
328822 TTTCATCTTT
Statistics
Matches: 226, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
87 117 0.52
88 23 0.10
89 1 0.00
90 3 0.01
91 3 0.01
92 2 0.01
93 2 0.01
94 3 0.01
95 1 0.00
96 28 0.12
97 43 0.19
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (87 bp):
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGA
ATCAGCACATTGGCATAAGCCT
Found at i:328664 original size:135 final size:137
Alignment explanation
Indices: 328420--328685 Score: 385
Period size: 135 Copynumber: 2.0 Consensus size: 137
328410 TTCTAAGTTC
328420 AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT
1 AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT
* * *
328485 GAATCAGCATACTGACACTTTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCA
66 GAATCAGCACACTGACACTTTATCTTTAAGACCAAAGTCGTTGGCCTTGAATCAACACATTGGCA
328550 TAAGCCT
131 TAAGCCT
* * * * *
328557 AATATCGTTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGA-CCAATGTCGCTGGCCTT
1 AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT
* * * * *
328620 GAATCAGCACATTGGCATCTTTATCTTTAAG-TCAAAGTCGTTGGCCTTGAATCAGCATATTGGC
66 GAATCAGCACACTGACA-CTTTATCTTTAAGACCAAAGTCGTTGGCCTTGAATCAACACATTGGC
328684 AT
130 AT
328686 CGACATCTTT
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
135 61 0.53
136 22 0.19
137 32 0.28
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (137 bp):
AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT
GAATCAGCACACTGACACTTTATCTTTAAGACCAAAGTCGTTGGCCTTGAATCAACACATTGGCA
TAAGCCT
Found at i:328731 original size:49 final size:49
Alignment explanation
Indices: 328565--328965 Score: 278
Period size: 48 Copynumber: 8.4 Consensus size: 49
328555 CTAATATCGT
* *
328565 TGGCCTTGAATCAGCATATTGGCA-CCTTGTCTTTAAGACCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
* * * *
328613 TGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAG-TCAAAGTCGT
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
* *** *
328661 TGGCCTTGAATCAGCATATTGGCATCGACATCTTTAAGACCAATGTTGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
* *
328710 TGGCCTTGAATCAGCACATTGG----C--A----TAAGCCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
* * * ** *
328749 TGGCTTTGAATCGGTATGTTGGCA-CCTTGTCTTTAAGACCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
* * * * * *
328797 TAGCCTTGAATCAGCACATTGGCAT-TTTCATCTTTAAGTCCGATATCGT
1 TGGCCTTGAATCAGCACATTGGCATCCTT-ATCTTTAAGACCAATGTCGC
* * * ** * *
328846 TGGCATTGAATCAGCATATTGGCATCTTTAACATCCCTAAGCCCAATGTCAC
1 TGGCCTTGAATCAGCACATTGGCATCCTT---ATCTTTAAGACCAATGTCGC
** * * * *
328898 TGGCCTTGTCTCAGCACATTGACATTC-T-TCTTTAA-ATCTAATGTCGA
1 TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGA-CCAATGTCGC
* *
328945 TGGCCATGAATCAACACATTG
1 TGGCCTTGAATCAGCACATTG
328966 TCATTCTTCG
Statistics
Matches: 270, Mismatches: 66, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
39 29 0.11
42 1 0.00
43 1 0.00
47 29 0.11
48 97 0.36
49 75 0.28
50 3 0.01
51 1 0.00
52 34 0.13
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (49 bp):
TGGCCTTGAATCAGCACATTGGCATCCTTATCTTTAAGACCAATGTCGC
Found at i:328734 original size:184 final size:183
Alignment explanation
Indices: 328419--328871 Score: 604
Period size: 184 Copynumber: 2.4 Consensus size: 183
328409 CTTCTAAGTT
* * * * ** *
328419 CAATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCT
1 CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTT--AAGTCAA-ATCGTTGGCCT
* * **** *
328484 TGAATCAGCATACTGACA-CTTTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGG
63 TGAATCAGCATATTGGCATCGACATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGG
* *
328548 CATAAGCCTAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAC
128 CATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAC
328604 CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGTCAAAGTCGTTGGCCTTG
1 CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGTCAAA-TCGTTGGCCTTG
* *
328669 AATCAGCATATTGGCATCGACATCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
65 AATCAGCATATTGGCATCGACATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCA
* * * *
328734 TAAGCCCAATATCGCTGGCTTTGAATCGGTATGTTGGCACCTTGTCTTTAAGAC
130 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAC
* * *
328788 CAATGTCGCTAGCCTTGAATCAGCACATTGGCAT-TTTCATCTTTAAGTCCGATATCGTTGGCAT
1 CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTT-ATCTTTAAGT-C-AAATCGTTGGCCT
328852 TGAATCAGCATATTGGCATC
63 TGAATCAGCATATTGGCATC
328872 TTTAACATCC
Statistics
Matches: 238, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
182 1 0.00
183 33 0.14
184 132 0.55
185 70 0.29
186 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (183 bp):
CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAGTCAAATCGTTGGCCTTGA
ATCAGCATATTGGCATCGACATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCAT
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGAC
Found at i:328771 original size:136 final size:136
Alignment explanation
Indices: 328598--328870 Score: 314
Period size: 136 Copynumber: 2.0 Consensus size: 136
328588 ACCTTGTCTT
* * * *
328598 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCTTTAAG-TCAAAGTCGTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTTATCTTTAAGACCAAAGTCGCT
* * * * *
328662 GGCCTTGAATCAGCATATTGGCATCGACATCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCAC
65 AGCCTTGAATCAGCACATTGGCATCGACATCTTTAAGACCAATATCGCTGGCATTGAATCAGCAC
328727 ATTGGCA
130 ATTGGCA
* * * * ** * *
328734 TAAGCCCAATATCGCTGGCTTTGAATCGGTATGTTGGCACCTTGTCTTTAAGACCAATGTCGCTA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTATCTTTAAGACCAAAGTCGCTA
*** * * * *
328799 GCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGTCCGATATCGTTGGCATTGAATCAGCATA
66 GCCTTGAATCAGCACATTGGCATCGACATCTTTAAGACCAATATCGCTGGCATTGAATCAGCACA
328864 TTGGCA
131 TTGGCA
328870 T
1 T
328871 CTTTAACATC
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
135 11 0.10
136 101 0.90
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (136 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTATCTTTAAGACCAAAGTCGCTA
GCCTTGAATCAGCACATTGGCATCGACATCTTTAAGACCAATATCGCTGGCATTGAATCAGCACA
TTGGCA
Found at i:329744 original size:19 final size:19
Alignment explanation
Indices: 329720--329769 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
329710 AAACAGTAAA
329720 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
329739 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
329758 TGTATCGATACA
1 TGTATCGATACA
329770 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:329824 original size:20 final size:20
Alignment explanation
Indices: 329799--329853 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
329789 CTGCCAAGGA
329799 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
329819 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
329839 TTTGTATCGATACAT
1 AATGTATCGATACAT
329854 CTGGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:337372 original size:156 final size:155
Alignment explanation
Indices: 337022--337633 Score: 493
Period size: 156 Copynumber: 3.9 Consensus size: 155
337012 GTCTAGAAAT
* * * * * * * *
337022 AGGATGAATCTATCCAAAATGCCCACCTTCGGCATAAAAGCGGACCCAGAGATGACCTAGGACTT
1 AGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAACCCAGTGATAACCTAGGAGTT
* * * * * * * *
337087 GGTTCTAGAAAAATTACGAAAATGCTCTTAGGGGATACTTTTTGACATAAAAATACCCGATACCC
66 GGTTCTAAAAAAATTACAAAAATGC-CCTAGGGGATAC-CTTCGACGTGAAAGTACCCGATACCC
* *
337152 CTAAAGGACTTAAAGAGGACACATAAAA
129 CTAAAAGACTTAAAAAGGAC-CATAAAA
* * * * * *
337180 GGGATGAACCTATCCTAAATGCCCACCCTC-AGCATAAAAGTGAACCCGGTGATGACCTAGGAGT
1 AGGATGAACCTATCCTAAATACCCACCTTCGA-CATAAAAGCGAACCCAGTGATAACCTAGGAGT
* * *
337244 TGGTTCTAAAAAAATTACAAAAATGCCCTAGGGGATACTTTCGATGTGAAAGTACCCGATACCCT
65 TGGTTCTAAAAAAATTACAAAAATGCCCTAGGGGATACCTTCGACGTGAAAGTACCCGATACCCC
*
337309 TAAAAGACTTAAAAATGACCCATAAAA
130 TAAAAGACTTAAAAAGGA-CCATAAAA
* ** *
337336 AGGATGAACCTATCCTAAACACCCACCTTCGACATAAAA-ATAGACCCAGTGATAACCTAGGA-C
1 AGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGA-ACCCAGTGATAACCTAGGAGT
* * * * ** * * *
337399 TCG-ACTATGAAAAGTTATGAAAATACCCCTAGGGGATACCTTGGACGTGAAAGTATCCCGGTAC
65 TGGTTCTA-AAAAAATTACAAAAAT-GCCCTAGGGGATACCTTCGACGTGAAAGTA-CCCGATAC
* ** *
337463 CCCTAAAAGA-TTTAAAAGGA-TTTTAAA
127 CCCTAAAAGACTTAAAAAGGACCATAAAA
* * * * * * ** *
337490 ATGAGTGAACCTATCCTAAATATCCACCTTCGTCATAGAAGCGGA-CCTGATGGCAACCTAAGAG
1 AGGA-TGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAACCCAG-TGATAACCTAGGAG
* * ** * * * *
337554 TTGGTT-TTAGAAAATTACAAAAATATCTTAGGAGATACCTTCGACGTGAAAGTACCCGAAACTC
64 TTGGTTCTAAAAAAATTACAAAAATGCCCTAGGGGATACCTTCGACGTGAAAGTACCCGATACCC
**
337618 CTAAGGGACTTAAAAA
129 CTAAAAGACTTAAAAA
337634 AGACTATAGA
Statistics
Matches: 361, Mismatches: 80, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
153 13 0.04
154 44 0.12
155 68 0.19
156 130 0.36
157 29 0.08
158 77 0.21
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (155 bp):
AGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCGAACCCAGTGATAACCTAGGAGTT
GGTTCTAAAAAAATTACAAAAATGCCCTAGGGGATACCTTCGACGTGAAAGTACCCGATACCCCT
AAAAGACTTAAAAAGGACCATAAAA
Found at i:339672 original size:166 final size:164
Alignment explanation
Indices: 339484--340035 Score: 588
Period size: 171 Copynumber: 3.3 Consensus size: 164
339474 ATTAGATACA
* * * * * * * *
339484 TTTAAAAATTTTAAACCAAAAAAAAATCTCCTAG-AAATATTTATGGAATAGAAAACTTAGTTTT
1 TTTAAAAA-TTAAAAACAAAAAAAAATC-CCTAGAAAAAATTTACGGAGTAGAAAACATCGTATT
* * * *
339548 TCGAGAAAATGGGGATTTCAAAGCAAAAATTCAAAAACTCATGAAGATGAATGAATTTTTGAAAA
64 TCGAAAAAAT-GGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAA
* * *
339613 CTGAATTACTATAAAATAAATAATGATGTTTGACGAAT
128 CTGAATTAATATGAAATAAATAAT-ATGTTTGATGAAT
* * *
339651 TTCAAAAATTGAAAACAAAAAAAAATCCTCTCGAAAAAATTTACGGAGTAGAAAACATCGTATTT
1 TTTAAAAATTAAAAACAAAAAAAAATCC-CTAGAAAAAATTTACGGAGTAGAAAACATCGTATTT
* * * *
339716 CAGAAAAAAAAATGGAAGTTTTAAGGAAAAAAATT-AAAAACTCATGAAAATGAAAGAATTTCTG
65 C-G---AAAAAATGGAA-TTTCAAAG-AAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTG
*
339780 AAAACTGAATTAATATGAAATAAATGATATTGTTTGATGAAT
124 AAAACTGAATTAATATGAAATAAATAATA-TGTTTGATGAAT
* * * *
339822 TTTAAAAATTAAAAACCAAGAAAAATCCCCTTGAAAAAATTTACGGAGTAGAAAACACCGTATTT
1 TTTAAAAATTAAAAACAAAAAAAAAT-CCCTAGAAAAAATTTACGGAGTAGAAAACATCGTATTT
* * * * *
339887 CGAAAAAAAAGAAATTTCAAGGAAAAAA-TCAAAAGCTCATGAAAATGAATGAATTTTTAAAAAC
65 CG-AAAAAATGGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAAC
* *
339951 TGAATTAATATGAAATAAATAAAAATATTTGATGAAT
129 TGAATTAATATGAAATAAAT-AATATGTTTGATGAAT
** * * *
339988 TTTAAAAATTAAAAATTAAGAAAAATCCTCTCGAAAAAATTTAAGGAG
1 TTTAAAAATTAAAAACAAAAAAAAATCC-CTAGAAAAAATTTACGGAG
340036 GAACAAAATT
Statistics
Matches: 330, Mismatches: 42, Indels: 27
0.83 0.11 0.07
Matches are distributed among these distances:
165 4 0.01
166 128 0.39
167 42 0.13
168 11 0.03
170 5 0.02
171 131 0.40
172 9 0.03
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.27
Consensus pattern (164 bp):
TTTAAAAATTAAAAACAAAAAAAAATCCCTAGAAAAAATTTACGGAGTAGAAAACATCGTATTTC
GAAAAAATGGAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTG
AATTAATATGAAATAAATAATATGTTTGATGAAT
Found at i:339784 original size:171 final size:165
Alignment explanation
Indices: 339562--340035 Score: 633
Period size: 171 Copynumber: 2.8 Consensus size: 165
339552 GAAAATGGGG
* * * * *
339562 ATTTCAAAGCAAAAATTCAAAAACTCATGAAGATGAATGAATTTTTGAAAACTGAATTACTATAA
1 ATTTCAAGGAAAAAATT-AAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* * * *
339627 AATAAATAATGATGTTTGACGAATTTCAAAAATTGAAAACAAAAAAAAATCCTCTCGAAAAAATT
65 AATAAATAAT-ATGTTTGATGAATTTTAAAAATTAAAAACAAAGAAAAATCCTCTCGAAAAAATT
*
339692 TACGGAGTAGAAAACATCGTATTTCAGAAAAAAAAATGGAA
129 TACGGAGTAGAAAACACCGTATTTC-G-AAAAAAAA--GAA
* * * *
339733 GTTTTAAGGAAAAAAATTAAAAACTCATGAAAATGAAAGAATTTCTGAAAACTGAATTAATATGA
1 ATTTCAAGG-AAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGA
* * * *
339798 AATAAATGATATTGTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCTTGAAAAAATT
65 AATAAATAATA-TGTTTGATGAATTTTAAAAATTAAAAACAAAGAAAAATCCTCTCGAAAAAATT
339863 TACGGAGTAGAAAACACCGTATTTCGAAAAAAAAGAA
129 TACGGAGTAGAAAACACCGTATTTCGAAAAAAAAGAA
* * *
339900 ATTTCAAGGAAAAAATCAAAAGCTCATGAAAATGAATGAATTTTTAAAAACTGAATTAATATGAA
1 ATTTCAAGGAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAA
* * **
339965 ATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATCCTCTCGAAAAAATTT
66 ATAAAT-AATATGTTTGATGAATTTTAAAAATTAAAAACAAAGAAAAATCCTCTCGAAAAAATTT
*
340030 AAGGAG
130 ACGGAG
340036 GAACAAAATT
Statistics
Matches: 267, Mismatches: 33, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
166 111 0.42
167 12 0.04
169 8 0.03
170 2 0.01
171 127 0.48
172 7 0.03
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (165 bp):
ATTTCAAGGAAAAAATTAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAA
ATAAATAATATGTTTGATGAATTTTAAAAATTAAAAACAAAGAAAAATCCTCTCGAAAAAATTTA
CGGAGTAGAAAACACCGTATTTCGAAAAAAAAGAA
Found at i:341134 original size:26 final size:26
Alignment explanation
Indices: 341076--341134 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
341066 TACCTTATCT
**
341076 AATAAAATCTAAACATTTTTTCAACT
1 AATAAAATCTAAACATTTTTTCAAAA
*
341102 AA-AAAATCTAAATATTTTTT-AAAA
1 AATAAAATCTAAACATTTTTTCAAAA
341126 AATATAAAT
1 AATA-AAAT
341135 AACACTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 18 0.64
26 6 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCTAAACATTTTTTCAAAA
Found at i:341299 original size:14 final size:15
Alignment explanation
Indices: 341275--341303 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
341265 TTAATAAAAT
341275 TTAATTTAAAATTAA
1 TTAATTTAAAATTAA
341290 TTAA-TTAAAATTAA
1 TTAATTTAAAATTAA
341304 AAAACCAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATTTAAAATTAA
Found at i:341532 original size:20 final size:20
Alignment explanation
Indices: 341509--341571 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 20
341499 AATATTATTT
341509 TATAATAAAAATTATATAAA
1 TATAATAAAAATTATATAAA
341529 TATAAT--AAATTATATATAA
1 TATAATAAAAATTATATA-AA
*
341548 TAT-TTAAAAA--ATATAAA
1 TATAATAAAAATTATATAAA
*
341565 AATAATA
1 TATAATA
341572 TCAAAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
17 4 0.11
18 18 0.50
19 5 0.14
20 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAATAAAAATTATATAAA
Found at i:346042 original size:3 final size:3
Alignment explanation
Indices: 346034--346075 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
346024 ACCGCCACGG
* * *
346034 TCA TCA TCA TCA TCA CCA CCA TCA CCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
346076 CCACAACCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.26
Consensus pattern (3 bp):
TCA
Found at i:346048 original size:9 final size:9
Alignment explanation
Indices: 346034--346096 Score: 69
Period size: 9 Copynumber: 7.3 Consensus size: 9
346024 ACCGCCACGG
*
346034 TCATCATCA
1 TCATCACCA
346043 TCATCACCA
1 TCATCACCA
*
346052 CCATCACCA
1 TCATCACCA
*
346061 TCATCATCA
1 TCATCACCA
346070 TCATCACCA
1 TCATCACCA
346079 -CA--ACCA
1 TCATCACCA
*
346085 CCATCACCA
1 TCATCACCA
346094 TCA
1 TCA
346097 CCACAACCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.09
7 2 0.04
8 2 0.04
9 37 0.82
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (9 bp):
TCATCACCA
Found at i:346048 original size:24 final size:24
Alignment explanation
Indices: 346035--346100 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
346025 CCGCCACGGT
346035 CATCATCATCATCACCACCATCAC
1 CATCATCATCATCACCACCATCAC
*
346059 CATCATCATCATCATCACCA-CAAC
1 CATCATCATCATCACCACCATC-AC
* *
346083 CACCATCACCATCACCAC
1 CATCATCATCATCACCAC
346101 AACCACCACC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (24 bp):
CATCATCATCATCACCACCATCAC
Found at i:346064 original size:27 final size:27
Alignment explanation
Indices: 346034--346114 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
346024 ACCGCCACGG
*
346034 TCATCATCATCATCACCACCATCACCA
1 TCATCATCATCATCACCACCACCACCA
*
346061 TCATCATCATCATCACCACAACCACCA
1 TCATCATCATCATCACCACCACCACCA
* *
346088 TCACCATCACCA-CAACCACCACCACCA
1 TCATCATCATCATC-ACCACCACCACCA
346115 CCATAGTGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (27 bp):
TCATCATCATCATCACCACCACCACCA
Found at i:346087 original size:3 final size:3
Alignment explanation
Indices: 346074--346117 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
346064 TCATCATCAT
* * * *
346074 CAC CAC AAC CAC CAT CAC CAT CAC CAC AAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
346118 TAGTGCTGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.39, C:0.57, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:346089 original size:21 final size:21
Alignment explanation
Indices: 346038--346108 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 21
346028 CCACGGTCAT
346038 CATCATCATCACCACCATCACCATC
1 CATCATCATCACCA-CA--ACCA-C
346063 ATCATCATCATCACCACAACCAC
1 --CATCATCATCACCACAACCAC
*
346086 CATCACCATCACCACAACCAC
1 CATCATCATCACCACAACCAC
346107 CA
1 CA
346109 CCACCACCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 22 0.51
23 1 0.02
24 4 0.09
26 2 0.05
27 14 0.33
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.15
Consensus pattern (21 bp):
CATCATCATCACCACAACCAC
Found at i:346113 original size:21 final size:21
Alignment explanation
Indices: 346071--346114 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
346061 TCATCATCAT
*
346071 CATCACCACAACCACCATCAC
1 CATCACCACAACCACCACCAC
346092 CATCACCACAACCACCACCAC
1 CATCACCACAACCACCACCAC
346113 CA
1 CA
346115 CCATAGTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.55, G:0.00, T:0.07
Consensus pattern (21 bp):
CATCACCACAACCACCACCAC
Found at i:348469 original size:15 final size:16
Alignment explanation
Indices: 348449--348484 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
348439 TGTAATTTTA
*
348449 TTAAATTAATTAA-AT
1 TTAAATTAATAAATAT
348464 TTAAATTAATAAATAT
1 TTAAATTAATAAATAT
348480 TTAAA
1 TTAAA
348485 ATTAGAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTAATAAATAT
Found at i:348599 original size:97 final size:98
Alignment explanation
Indices: 348407--348666 Score: 308
Period size: 97 Copynumber: 2.6 Consensus size: 98
348397 TTTTTGAAAA
* *
348407 TTTAAAATTAATCAAAGTATTTTATTTAAATATGTAATTTTATTAAATTAATTAAATTTAAATTA
1 TTTAAAATTAAT-AAAATATTTTATTTATATATGTAATTTTATT-AA-T--TT--ATTTAAATTA
* * ** * *
348472 ATAAATATTTAAAATTAGAATTCATGTGATATTAATTTAC
59 ATAAATATTTAAAAATAAAATTCAAATGATATTAAATGAC
*
348512 TTTAAAATTAATAAAAAATTTTATTTATATATGTAA-TTTATTAATTTATTTAAATTAATAAATA
1 TTTAAAATTAATAAAATATTTTATTTATATATGTAATTTTATTAATTTATTTAAATTAATAAATA
348576 TTTAAAAATAAAATTCAAATGATATTAAATGAC
66 TTTAAAAATAAAATTCAAATGATATTAAATGAC
* * * *
348609 CTTAAAATTAATAAACTTTTCTTATTT-TAGTATGTAATTTTTTTAATTTATTTAAATT
1 TTTAAAATTAATAAAATATT-TTATTTATA-TATGTAATTTTATTAATTTATTTAAATT
348667 TAAATGAACT
Statistics
Matches: 138, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
97 62 0.45
98 13 0.09
99 21 0.15
101 1 0.01
102 2 0.01
103 6 0.04
104 21 0.15
105 12 0.09
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (98 bp):
TTTAAAATTAATAAAATATTTTATTTATATATGTAATTTTATTAATTTATTTAAATTAATAAATA
TTTAAAAATAAAATTCAAATGATATTAAATGAC
Found at i:348746 original size:24 final size:24
Alignment explanation
Indices: 348692--348757 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 24
348682 TTAACTATTT
*
348692 TAATTAAAGATAGAGTAGTTAGTA
1 TAATTAAAGATAGAGTATTTAGTA
348716 T--TT--AGATAGAGTATTTAGTA
1 TAATTAAAGATAGAGTATTTAGTA
*
348736 TAATTAAAGATAGAATATTTAG
1 TAATTAAAGATAGAGTATTTAG
348758 CATTGTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 17 0.47
22 4 0.11
24 15 0.42
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (24 bp):
TAATTAAAGATAGAGTATTTAGTA
Found at i:348858 original size:36 final size:36
Alignment explanation
Indices: 348818--348922 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 36
348808 CGACTTTGTC
*
348818 TTATTTAAATATATAATTTTTATTAATCTAATTAAA
1 TTATTTAAAAATATAATTTTTATTAATCTAATTAAA
** * *
348854 TTATTTAAAAATAGGA-TTATA-TAA---AATTAAC
1 TTATTTAAAAATATAATTTTTATTAATCTAATTAAA
* * *
348885 CTATTTTAACATATAATTTTTATTAATCTAATTAAA
1 TTATTTAAAAATATAATTTTTATTAATCTAATTAAA
348921 TT
1 TT
348923 TAAATCAATT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
31 17 0.33
32 4 0.08
33 3 0.06
34 3 0.06
35 4 0.08
36 20 0.39
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (36 bp):
TTATTTAAAAATATAATTTTTATTAATCTAATTAAA
Found at i:348942 original size:16 final size:16
Alignment explanation
Indices: 348909--348938 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
348899 AATTTTTATT
348909 AATCTAATTAAATTTA
1 AATCTAATTAAATTTA
348925 AATC-AATTAAATTT
1 AATCTAATTAAATTT
348939 TAAAAATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
AATCTAATTAAATTTA
Found at i:349302 original size:18 final size:20
Alignment explanation
Indices: 349258--349300 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
349248 AAAGTTAATG
*
349258 AAAAATTATGAAACTGTCTA
1 AAAAATTATGAAACTGTATA
349278 AAAAATTATGAAA-TGATATA
1 AAAAATTATGAAACTG-TATA
349298 AAA
1 AAA
349301 TTTAGTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAAATTATGAAACTGTATA
Found at i:349411 original size:63 final size:63
Alignment explanation
Indices: 349309--349435 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
349299 AATTTAGTAA
* * * **
349309 CACTAAGTTGCTAAATTTTGTTTATAATTTTCATTGAAGTTGTTGACAAAGGAGTTGTATGTC
1 CACTAAGTTACTAAATTTTGTTCATAATTTTCATAGAAGTTGTTGACAAAGGACATGTATGTC
* *
349372 CACTAAGTTACTAACTTTTGTTCATAATTTTTATAGAAGTTGTTGACAAAGGACATGTATGTC
1 CACTAAGTTACTAAATTTTGTTCATAATTTTCATAGAAGTTGTTGACAAAGGACATGTATGTC
349435 C
1 C
349436 CTTATTACAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (63 bp):
CACTAAGTTACTAAATTTTGTTCATAATTTTCATAGAAGTTGTTGACAAAGGACATGTATGTC
Found at i:349586 original size:105 final size:105
Alignment explanation
Indices: 349404--349659 Score: 467
Period size: 105 Copynumber: 2.4 Consensus size: 105
349394 CATAATTTTT
* *
349404 ATAGAAGTTGTTGACAAAGGACATGTATGTCCCTTATTACAACATAATGGATCAAAATTATCAAA
1 ATAGAAGTTGTTGACAAAGGACATGTATGTCCATTATTACAATATAATGGATCAAAATTATCAAA
349469 AATTATTTGCATATTAATATATTAAAAAAGTTATAGAAAA
66 AATTATTTGCATATTAATATATTAAAAAAGTTATAGAAAA
*
349509 ATAGAAGTCGTTGACAAAGGACATGTATGTCCATTATTACAATATAATGGATCAAAATTATCAAA
1 ATAGAAGTTGTTGACAAAGGACATGTATGTCCATTATTACAATATAATGGATCAAAATTATCAAA
* *
349574 AATTATTTGCATATTAATATATTGAAAAAGTTTTAGAAAA
66 AATTATTTGCATATTAATATATTAAAAAAGTTATAGAAAA
349614 ATAGAAGTTGTTGACAAAGGACATGTATGTCCATTATTACAATATA
1 ATAGAAGTTGTTGACAAAGGACATGTATGTCCATTATTACAATATA
349660 TTGAAAAAGT
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 145 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (105 bp):
ATAGAAGTTGTTGACAAAGGACATGTATGTCCATTATTACAATATAATGGATCAAAATTATCAAA
AATTATTTGCATATTAATATATTAAAAAAGTTATAGAAAA
Found at i:350203 original size:22 final size:22
Alignment explanation
Indices: 350170--350211 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
350160 ATCAGAGCAG
*
350170 ATAATTGATAACATAATAGTAA
1 ATAATTGATAACACAATAGTAA
350192 ATAATT-AGTAACACAATAGT
1 ATAATTGA-TAACACAATAGT
350212 TAATTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (22 bp):
ATAATTGATAACACAATAGTAA
Found at i:351792 original size:43 final size:42
Alignment explanation
Indices: 351660--351785 Score: 164
Period size: 43 Copynumber: 3.0 Consensus size: 42
351650 AAAGATTAAT
* * * * *
351660 AACATAGTAGTAACTAATTAATAACAT-GTATTAAATTTTGAC
1 AACATAGTACTAA-TTATTAATAACATATTAATAAATTATGAC
* *
351702 AACATAGTACTAATTATTAATAACAAATTAATAAATAATTGAC
1 AACATAGTACTAATTATTAATAACATATTAATAAATTA-TGAC
351745 AACATAGTACTAATTATTAATAACATATTAATAAATTATGA
1 AACATAGTACTAATTATTAATAACATATTAATAAATTATGA
351786 GTAACATTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 11 0.15
42 22 0.30
43 40 0.55
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (42 bp):
AACATAGTACTAATTATTAATAACATATTAATAAATTATGAC
Found at i:352984 original size:14 final size:15
Alignment explanation
Indices: 352955--352987 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
352945 AGTAATTAAT
352955 AAATAATATAATAGC
1 AAATAATATAATAGC
*
352970 AAATAAT-TGATAGC
1 AAATAATATAATAGC
352984 AAAT
1 AAAT
352988 TTTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (15 bp):
AAATAATATAATAGC
Found at i:353589 original size:22 final size:23
Alignment explanation
Indices: 353564--353613 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
353554 TAATCGATTA
* *
353564 ATAATAG-AGTAGTAAACACTTT
1 ATAATAGTAGTAATAAACAATTT
*
353586 ATAAT-GTAGTAATAAATAATTT
1 ATAATAGTAGTAATAAACAATTT
353608 ATAATA
1 ATAATA
353614 TATGAGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (23 bp):
ATAATAGTAGTAATAAACAATTT
Found at i:355391 original size:28 final size:30
Alignment explanation
Indices: 355354--355420 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 30
355344 ATTAAAAAGT
* *
355354 TAAAATTTTAAATTGACTTTTATTTT-TAA
1 TAAAATTTTAAATTGAATTTTATTTTAAAA
*
355383 T-AAATTTT-AATTTAATTTTATTTTAAAA
1 TAAAATTTTAAATTGAATTTTATTTTAAAA
355411 TAAAATTTTA
1 TAAAATTTTA
355421 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 14 0.44
28 10 0.31
29 8 0.25
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TAAAATTTTAAATTGAATTTTATTTTAAAA
Found at i:355419 original size:18 final size:19
Alignment explanation
Indices: 355396--355436 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
355386 ATTTTAATTT
355396 AATTTTATTTTAAAA-TAA
1 AATTTTATTTTAAAATTAA
355414 AATTTTATTTTAAAATTAA
1 AATTTTATTTTAAAATTAA
355433 AATT
1 AATT
355437 AATAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTATTTTAAAATTAA
Found at i:356594 original size:39 final size:39
Alignment explanation
Indices: 356527--356607 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
356517 GCTTACTCTT
* **
356527 TACTTCATTAAGAATGAGACAATTCTTGATCATAACACC
1 TACTTCATTAAGAAAGAGACAACCCTTGATCATAACACC
* *
356566 TACTTCATTAGGAAAGAGATAACCCTTGATCATAACACC
1 TACTTCATTAAGAAAGAGACAACCCTTGATCATAACACC
356605 TAC
1 TAC
356608 GGGTTTATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (39 bp):
TACTTCATTAAGAAAGAGACAACCCTTGATCATAACACC
Found at i:356949 original size:19 final size:18
Alignment explanation
Indices: 356924--356988 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
356914 ATTTCAACGA
356924 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
356942 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
356958 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
356974 TTTTGTATCGATACA
1 -TTTGTATCGATACA
356989 ATGTATCGCT
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:356962 original size:32 final size:32
Alignment explanation
Indices: 356926--356996 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
356916 TTCAACGATT
356926 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
356958 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
356990 TGTATCG
1 TGTATCG
356997 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:356963 original size:13 final size:13
Alignment explanation
Indices: 356945--356969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
356935 ACATAAGTGT
356945 TGTATCGATACAA
1 TGTATCGATACAA
356958 TGTATCGATACA
1 TGTATCGATACA
356970 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:357059 original size:13 final size:13
Alignment explanation
Indices: 357041--357065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
357031 ATTACTCAAA
357041 TGTATCGATACAT
1 TGTATCGATACAT
357054 TGTATCGATACA
1 TGTATCGATACA
357066 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:360460 original size:13 final size:13
Alignment explanation
Indices: 360442--360480 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
360432 ATAATCACCC
*
360442 TGTATCGATACAG
1 TGTATCGATACAA
360455 TGTATCGATACAA
1 TGTATCGATACAA
360468 TGTATCGATACAA
1 TGTATCGATACAA
360481 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:360491 original size:20 final size:20
Alignment explanation
Indices: 360466--360544 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
360456 GTATCGATAC
360466 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
360486 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
360511 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
360531 CATGTATCGATACA
1 AATGTATCGATACA
360545 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:362578 original size:15 final size:15
Alignment explanation
Indices: 362558--362588 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
362548 ATTTTGTTTG
*
362558 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
362573 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
362588 G
1 G
362589 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:364421 original size:21 final size:21
Alignment explanation
Indices: 364392--364436 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
364382 AAGTTTTCAT
*
364392 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
364412 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
364434 TTT
1 TTT
364437 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:366671 original size:13 final size:13
Alignment explanation
Indices: 366653--366678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
366643 CAATTTTTTG
366653 TGTATCGATACAT
1 TGTATCGATACAT
366666 TGTATCGATACAT
1 TGTATCGATACAT
366679 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:370365 original size:12 final size:12
Alignment explanation
Indices: 370348--370372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
370338 CATTGGTAGT
370348 AGCAAAAAAAAA
1 AGCAAAAAAAAA
370360 AGCAAAAAAAAA
1 AGCAAAAAAAAA
370372 A
1 A
370373 AAAAAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AGCAAAAAAAAA
Found at i:370382 original size:16 final size:17
Alignment explanation
Indices: 370351--370382 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
370341 TGGTAGTAGC
370351 AAAAAAAAAAGCAAAAA
1 AAAAAAAAAAGCAAAAA
370368 AAAAAAAAAAG-AAAA
1 AAAAAAAAAAGCAAAA
370383 GAAAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGCAAAAA
Found at i:370395 original size:24 final size:23
Alignment explanation
Indices: 370351--370425 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
370341 TGGTAGTAGC
* *
370351 AAAAAA-AAAAGCAAAA-AAAAA
1 AAAAAAGAAAAGGAAAAGGAAAA
370372 AAAAAAGAAAA-GAAAGAGAGAAAA
1 AAAAAAGAAAAGGAAA-AG-GAAAA
** *
370396 ATCAAAGAAAAGGAAAAGGAAGA
1 AAAAAAGAAAAGGAAAAGGAAAA
370419 AAAAAAG
1 AAAAAAG
370426 TTCATCCAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 9 0.21
22 5 0.12
23 9 0.21
24 15 0.36
25 4 0.10
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAAAGGAAAAGGAAAA
Found at i:371238 original size:59 final size:60
Alignment explanation
Indices: 371157--371326 Score: 184
Period size: 59 Copynumber: 2.9 Consensus size: 60
371147 ATCACTTTAT
* * * *
371157 TTATTTTCCATAATCTAAGGACCATTTAGTAATTTTCATACATTTTAAG-GTCATTTAGG
1 TTATTTTCCATAATCTAGGGACCATTTAGCAATTTTCATACATTTTAAGAGTCACTTAGA
* * * ** *
371216 TTATTTCCCATATTCTAGGGACCATTTAACAATTTTCAT-GTTTTTAAGAGTTACTTAGA
1 TTATTTTCCATAATCTAGGGACCATTTAGCAATTTTCATACATTTTAAGAGTCACTTAGA
* * * * *
371275 ATATTTTCCATAGTCTAGGGACCATTTAGCAACTTCCATACCTTTT-AGAGTC
1 TTATTTTCCATAATCTAGGGACCATTTAGCAATTTTCATACATTTTAAGAGTC
371327 TATTAAGGTT
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
58 7 0.08
59 79 0.88
60 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (60 bp):
TTATTTTCCATAATCTAGGGACCATTTAGCAATTTTCATACATTTTAAGAGTCACTTAGA
Found at i:375072 original size:83 final size:85
Alignment explanation
Indices: 374854--375136 Score: 235
Period size: 84 Copynumber: 3.4 Consensus size: 85
374844 GACCTAGGTT
* * * * *
374854 AAACCGACATGCCAACAAAGGATAAAAAGATTTACCCAGGACTAAGCCGATAAGTAAACAAGGGA
1 AAACCGACAAGTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGCCGACAAGTAAACAAGAGA
* *
374919 TGAAAGATTGACTGGGATTG
66 AGAAAGATTGACTGGGATTC
* * * * * * *
374939 AAA-CAATGAA-TCAATAACGGATAAAAAGATTTACTTAGGACTAGGTCGACAAGTAAACAAGAG
1 AAACCGA-CAAGTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGCCGACAAGTAAACAAGAG
375002 AAGAAAG-TTGA-TCGGGA-TC
65 AAGAAAGATTGACT-GGGATTC
* ** * * **
375021 AAACCGACAAGTCAACAAAGGATAGAAAGAAGTACCTAGGACCAAGCCGACAGGTGAATGAAG-G
1 AAACCGACAAGTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGCCGACAAGT-AAACAAGAG
* *
375085 -ATAAAG-TTGACTAGGATT-
65 AAGAAAGATTGACTGGGATTC
* * *
375103 AAACCGGCAAGTCAACGAGGGAT-AAAAGATTTAC
1 AAACCGACAAGTCAACAAAGGATAAAAAGATTTAC
375137 TTGGGATTGG
Statistics
Matches: 155, Mismatches: 36, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
81 8 0.05
82 39 0.25
83 47 0.30
84 57 0.37
85 4 0.03
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.17
Consensus pattern (85 bp):
AAACCGACAAGTCAACAAAGGATAAAAAGATTTACCTAGGACTAAGCCGACAAGTAAACAAGAGA
AGAAAGATTGACTGGGATTC
Found at i:375312 original size:84 final size:84
Alignment explanation
Indices: 375224--375679 Score: 562
Period size: 84 Copynumber: 5.4 Consensus size: 84
375214 GGAAGTACCT
** * * * * *
375224 AGGACTAAGCCGACAGGTGAATGAA-GGATAAAAGTTGATCGGAGATTGAGCTGACAAGTCACCA
1 AGGACTAAGCCGACAGGT-AAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCA
*
375288 TAAAGGTAATGGGCTTACTG
65 TAAAGGTAATGGGTTTACTG
*
375308 AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCAT
1 AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCAT
*
375373 AAAGGTAATGGATTTACTG
66 AAAGGTAATGGGTTTACTG
* * * * *
375392 AGGATTAAACCGATAGGTAAATAATGGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCAT
1 AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCAT
375457 AAAGGTAATGGGTTTA-TCG
66 AAAGGTAATGGGTTTACT-G
** *
375476 AGGACTAAGTTGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCAT
1 AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCAT
* *
375541 AAGGGTAATGGGTTTAC-C
66 AAAGGTAATGGGTTTACTG
* * * * * * *
375559 AGAGACTAAGTCAATAGGTAAACAATGGATGAAGGTTGACCGGAGATTAAGCTGGCAAGTCACCA
1 AG-GACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCA
375624 T-AAGGATAATGGGTTTA-TCG
65 TAAAGG-TAATGGGTTTACT-G
* **
375644 GGGACTAAGCTAACAGGTAAACAATGGATGAAGGTT
1 AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTT
375680 ATTTCCCAAG
Statistics
Matches: 324, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
83 10 0.03
84 313 0.97
85 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (84 bp):
AGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGACAGGTCACCAT
AAAGGTAATGGGTTTACTG
Found at i:375527 original size:168 final size:168
Alignment explanation
Indices: 375249--375679 Score: 634
Period size: 168 Copynumber: 2.6 Consensus size: 168
375239 GGTGAATGAA
* * *
375249 GGATAAAAGTTGATCGGAGATTGAGCTGACAAGTCACCATAAAGGTAATGGGCTTA-CTGAGGAC
1 GGATAAAGGTTGACCGGAGATTGAGCTGACAAGTCACCATAAAGGTAATGGGTTTATC-GAGGAC
*
375313 TAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCATAAAGG
65 TAAGCTGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCATAAAGG
* * * *
375378 TAATGGATTTA-CTGAGGATTAAACCGATAGGTAAATAAT
130 TAATGGATTTACCAGA-GACTAAACCAATAGGTAAACAAT
* *
375417 GGATAAAGGTTGACCGGAGACTGAGCTGACAGGTCACCATAAAGGTAATGGGTTTATCGAGGACT
1 GGATAAAGGTTGACCGGAGATTGAGCTGACAAGTCACCATAAAGGTAATGGGTTTATCGAGGACT
* *
375482 AAGTTGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCATAAGGGT
66 AAGCTGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCATAAAGGT
* **
375547 AATGGGTTTACCAGAGACTAAGTCAATAGGTAAACAAT
131 AATGGATTTACCAGAGACTAAACCAATAGGTAAACAAT
* * * *
375585 GGATGAAGGTTGACCGGAGATTAAGCTGGCAAGTCACCAT-AAGGATAATGGGTTTATCGGGGAC
1 GGATAAAGGTTGACCGGAGATTGAGCTGACAAGTCACCATAAAGG-TAATGGGTTTATCGAGGAC
*
375649 TAAGCTAACAGGTAAACAATGGATGAAGGTT
65 TAAGCTGACAGGTAAACAATGGATGAAGGTT
375680 ATTTCCCAAG
Statistics
Matches: 237, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
167 4 0.02
168 229 0.97
169 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (168 bp):
GGATAAAGGTTGACCGGAGATTGAGCTGACAAGTCACCATAAAGGTAATGGGTTTATCGAGGACT
AAGCTGACAGGTAAACAATGGATGAAGGTTGACCGGAGACTGAGCTGATAGGTCACCATAAAGGT
AATGGATTTACCAGAGACTAAACCAATAGGTAAACAAT
Found at i:375787 original size:42 final size:42
Alignment explanation
Indices: 375741--375990 Score: 184
Period size: 42 Copynumber: 5.9 Consensus size: 42
375731 GGTTTCCTGG
*
375741 GTCTAAGCTGATGGGCAGATAAAAGATGAAGAAGTCTCCCGA
1 GTCTAAGCCGATGGGCAGATAAAAGATGAAGAAGTCTCCCGA
*
375783 GTCTAAGCCGATGGGCAAATGAAAA-ATGAAGAAGTCTCCCGA
1 GTCTAAGCCGATGGGCAGAT-AAAAGATGAAGAAGTCTCCCGA
* ** **
375825 GTCTAAGCCGATGGGTAGACGATTGATGAAGAAGTCTCCC-A
1 GTCTAAGCCGATGGGCAGATAAAAGATGAAGAAGTCTCCCGA
* * *** * * ** * *
375866 GGTCTAAACCAACAAGCGGATGATTGATAAAGAAAGTCTTCCGA
1 -GTCTAAGCCGATGGGCAGATAAAAGATGAAG-AAGTCTCCCGA
* * * * *
375910 GACTAAGTCAACGGGCAG-TCAAAAAATGAAGAAGTCTCCC-A
1 GTCTAAGCCGATGGGCAGAT-AAAAGATGAAGAAGTCTCCCGA
* * *
375951 GGTCTAAGTCGATGGGCAAATGAAAGATGAAGGAAGTCTC
1 -GTCTAAGCCGATGGGCAGATAAAAGATGAA-GAAGTCTC
375991 TAGGGTCAAA
Statistics
Matches: 163, Mismatches: 36, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
41 3 0.02
42 120 0.74
43 39 0.24
44 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (42 bp):
GTCTAAGCCGATGGGCAGATAAAAGATGAAGAAGTCTCCCGA
Found at i:376012 original size:43 final size:42
Alignment explanation
Indices: 375929--376101 Score: 129
Period size: 42 Copynumber: 4.1 Consensus size: 42
375919 AACGGGCAGT
* * * *
375929 CAAAAAATGAAGAAGTCTCCCA-GGTCTAAGTCGATGGGCAAA
1 CAAAAGATGAAGAAGTCT-CTAGGGTCAAAGTCGATAGGCAAA
** *
375971 TGAAAGATGAAGGAAGTCTCTAGGGTCAAAGTTGATAGGCAAA
1 CAAAAGATGAA-GAAGTCTCTAGGGTCAAAGTCGATAGGCAAA
* * *
376014 CAAAAGATAAAGAAGTCTTCT-GGGTCAAAG-CTA-ACGGGCAGA
1 CAAAAGATGAAGAAGTC-TCTAGGGTCAAAGTCGATA--GGCAAA
* * * * * *
376056 CAAAGGACGTAGAAGTCTTTAGGGTCAAAGCCGATAGGCAGA
1 CAAAAGATGAAGAAGTCTCTAGGGTCAAAGTCGATAGGCAAA
376098 CAAA
1 CAAA
376102 GAAAGGGTAA
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 62 0.60
43 37 0.36
44 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.17
Consensus pattern (42 bp):
CAAAAGATGAAGAAGTCTCTAGGGTCAAAGTCGATAGGCAAA
Found at i:376092 original size:84 final size:90
Alignment explanation
Indices: 375983--376188 Score: 230
Period size: 90 Copynumber: 2.4 Consensus size: 90
375973 AAAGATGAAG
* ** *
375983 GAAGTCTCTAGGGTCAAAGTTGATAGGCA-A-ACA-AAA-GATAAAG-AAGTC-TTCTGGGTCAA
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGATAAAGAAAGTCTTTC-GGGTCAA
** *
376042 AG-CTAACGGGCAGAC-AAAGGACGTA
65 AGTC-AACAAGCAGACTAAAGGACGGA
*
376067 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGGTAAAGAAAGTCTTTCGGGTCAAA
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGATAAAGAAAGTCTTTCGGGTCAAA
* **
376132 GTCAACAAGCAGACTTAAGGGTGGA
66 GTCAACAAGCAGACTAAAGGACGGA
*
376157 GAAGTCTTTAGGGTCAAAACCGATAGGCAGAC
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGAC
376189 TTAAGATTAA
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
84 26 0.25
85 1 0.01
86 2 0.02
87 3 0.03
88 6 0.06
89 23 0.23
90 41 0.40
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (90 bp):
GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGATAAAGAAAGTCTTTCGGGTCAAA
GTCAACAAGCAGACTAAAGGACGGA
Found at i:376096 original size:42 final size:42
Alignment explanation
Indices: 375983--376188 Score: 135
Period size: 42 Copynumber: 4.8 Consensus size: 42
375973 AAAGATGAAG
* ** * * **
375983 GAAGTCTCTAGGGTCAAAGTTGATAGGCAAACAAAAGATAAA
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGGATGTA
** ** *
376025 GAAGTCTTCT-GGGTCAAAGCTAACGGGCAGACAAAGGACGTA
1 GAAGTCTT-TAGGGTCAAAGCCGATAGGCAGACAAAGGATGTA
* *
376067 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGGTAAA
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAG-GA-TGT--A
* * * * * * * *
376113 GAAAGTCTTTCGGGTCAAAGTCAACAAGCAGACTTAAGGGTGGA
1 G-AAGTCTTTAGGGTCAAAGCCGATAGGCAGAC-AAAGGATGTA
*
376157 GAAGTCTTTAGGGTCAAAACCGATAGGCAGAC
1 GAAGTCTTTAGGGTCAAAGCCGATAGGCAGAC
376189 TTAAGATTAA
Statistics
Matches: 124, Mismatches: 32, Indels: 15
0.73 0.19 0.09
Matches are distributed among these distances:
41 1 0.01
42 60 0.48
43 27 0.22
44 4 0.03
46 3 0.02
47 26 0.21
48 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (42 bp):
GAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGGATGTA
Found at i:376187 original size:43 final size:43
Alignment explanation
Indices: 376066--376193 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 43
376056 CAAAGGACGT
**
376066 AGAAGTCTTTAGGGTCAAAGCCGATAGGCAGACAAAGAAAGGGTAA
1 AGAAGTCTTTAGGGTCAAAGCCGATAGGCAGAC---TTAAGGGTAA
* * * * * **
376112 AGAAAGTCTTTCGGGTCAAAGTCAACAAGCAGACTTAAGGGTGG
1 AG-AAGTCTTTAGGGTCAAAGCCGATAGGCAGACTTAAGGGTAA
*
376156 AGAAGTCTTTAGGGTCAAAACCGATAGGCAGACTTAAG
1 AGAAGTCTTTAGGGTCAAAGCCGATAGGCAGACTTAAG
376194 ATTAAAGTAT
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
43 30 0.45
44 8 0.12
46 2 0.03
47 26 0.39
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.19
Consensus pattern (43 bp):
AGAAGTCTTTAGGGTCAAAGCCGATAGGCAGACTTAAGGGTAA
Found at i:376409 original size:44 final size:44
Alignment explanation
Indices: 376270--376412 Score: 137
Period size: 44 Copynumber: 3.2 Consensus size: 44
376260 AATGCAAATC
* *
376270 GTTTGACCAGGGTGGTAACCATACGTCAAACAAGAAAGAGGCAGA
1 GTTTGACTAGGGTGGTAACCATACGTCAAATAAGAAAGAGG-AGA
* * * * **
376315 -TTTGACTGGGGTGGTAACCATACATCAAAT-TGAAATAAAAAGA
1 GTTTGACTAGGGTGGTAACCATACGTCAAATAAGAAA-GAGGAGA
* * * * *
376358 ATCTGACTAGGGTGGTAACCATATGTCAGATAGGAAAGAGGAGA
1 GTTTGACTAGGGTGGTAACCATACGTCAAATAAGAAAGAGGAGA
376402 GTTTGACTAGG
1 GTTTGACTAGG
376413 CCCTAACACC
Statistics
Matches: 76, Mismatches: 19, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
43 7 0.09
44 65 0.86
45 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (44 bp):
GTTTGACTAGGGTGGTAACCATACGTCAAATAAGAAAGAGGAGA
Found at i:376910 original size:89 final size:90
Alignment explanation
Indices: 376785--377023 Score: 299
Period size: 90 Copynumber: 2.7 Consensus size: 90
376775 GTCAGGATGT
* * * * *
376785 CCTTGCCCCAAGGATATCAGGCTTTGTAATGCATCAATACCATCTAGTGGTT--GGATGAAGGGG
1 CCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTAAGAAAG-AGGGG
* *
376848 ATAT-ATTGGGAATGTGTGGGCTGCA
65 ATATGATTAGGAATGTGTGGCCTGCA
*
376873 CCTTGCCCCAAAGGAAATCAAGCTTTGTGATGCATCAATACCATTTAGTGGTTAAGAAAGAGGGG
1 CCTTGCCCC-AAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTAAGAAAGAGGGG
*
376938 ATATGATTAGGAGTGTGTGGCCTGCA
65 ATATGATTAGGAATGTGTGGCCTGCA
* * *
376964 CCTTGCCCTATGGAAAT-TAGACTTTGTGATGCATCAATACCATCTAG-GAGTTAAGAAAGA
1 CCTTGCCCCAAGGAAATCAAG-CTTTGTGATGCATCAATACCATCTAGTG-GTTAAGAAAGA
377024 AAAAATTACT
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
88 9 0.07
89 42 0.32
90 52 0.39
91 29 0.22
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (90 bp):
CCTTGCCCCAAGGAAATCAAGCTTTGTGATGCATCAATACCATCTAGTGGTTAAGAAAGAGGGGA
TATGATTAGGAATGTGTGGCCTGCA
Found at i:378162 original size:112 final size:112
Alignment explanation
Indices: 377988--378200 Score: 288
Period size: 112 Copynumber: 1.9 Consensus size: 112
377978 GAAATATAAG
* * **
377988 TTTCTTTAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAGATTTCAAAGCTGATAAGATACG
1 TTTCTTCAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAAAGATCAAAGCTGATAAGATACG
*
378053 TGCTC-TATTTCTTAGGCACAAATGGATCAAAATGTATGAAGTGTGAA
66 TGCCCAT-TTTCTTAGGCACAAATGGATCAAAATGTATGAAGTGTGAA
* *
378100 TTTCTTCAAAAATC-AAGCAAATTTGATGTTGTGGGGCTCAAAAAGATCGAAA-CTGATGAGATA
1 TTTCTTCAAAAATCTAA-CAAATTTGATGTTGCGGGGCTCAAAAAGATC-AAAGCTGATAAGATA
** *
378163 CGTGCCCATTTTCTTAGGCATTAATGGATCAAGATGTA
64 CGTGCCCATTTTCTTAGGCACAAATGGATCAAAATGTA
378201 GAAAACATGA
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
111 2 0.02
112 82 0.93
113 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (112 bp):
TTTCTTCAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAAAGATCAAAGCTGATAAGATACG
TGCCCATTTTCTTAGGCACAAATGGATCAAAATGTATGAAGTGTGAA
Found at i:378224 original size:112 final size:112
Alignment explanation
Indices: 377974--378241 Score: 287
Period size: 112 Copynumber: 2.4 Consensus size: 112
377964 GGGCCAGAAC
* * **
377974 GTATGAAATAT-AAGTTTCTTTAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAGATTTCAA
1 GTATGAAACATGAA-TTTCTTTAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAAAGATCAA
*
378038 AGCTGATAAGATACGTGCTCTATTTCTTAGGCACAAATGGATCAAAAT
65 AGCTGATAAGATACGTGCCCTATTTCTTAGGCACAAATGGATCAAAAT
*** * *
378086 GTATGAAGTGTGAATTTCTTCAAAAATC-AAGCAAATTTGATGTTGTGGGGCTCAAAAAGATCGA
1 GTATGAAACATGAATTTCTTTAAAAATCTAA-CAAATTTGATGTTGCGGGGCTCAAAAAGATC-A
* ** *
378150 AA-CTGATGAGATACGTGCCC-ATTTTCTTAGGCATTAATGGATCAAGAT
64 AAGCTGATAAGATACGTGCCCTA-TTTCTTAGGCACAAATGGATCAAAAT
* * *
378198 GTA-GAAAACATGAATTTCTTTGAAAAT-TAAACGAATTCGATGTT
1 GTATG-AAACATGAATTTCTTTAAAAATCT-AACAAATTTGATGTT
378242 CTTCCAAGTT
Statistics
Matches: 130, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
111 4 0.03
112 119 0.92
113 7 0.05
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (112 bp):
GTATGAAACATGAATTTCTTTAAAAATCTAACAAATTTGATGTTGCGGGGCTCAAAAAGATCAAA
GCTGATAAGATACGTGCCCTATTTCTTAGGCACAAATGGATCAAAAT
Found at i:381505 original size:235 final size:235
Alignment explanation
Indices: 381081--381548 Score: 731
Period size: 235 Copynumber: 2.0 Consensus size: 235
381071 TTTTTTAAAA
381081 AAAAAGTATCGAGGATGATAATTAAATATTAGTTGAAACCAAATTAATCAAAATTTATTTAACAC
1 AAAAAGTATCGAGGATGATAATTAAATATTAGTTGAAACCAAATTAATCAAAATTTATTTAACAC
* ** * * *
381146 GTAATCAATTTTAGGCCTGGGGCTCTAACTATCCCCAGTAGAGTCGCTAAGCTGCCACAACATGG
66 GTAATCAATTCTAGGCCTGCCGCTCTAACTATCCCCAGGAGAGTCGCCAAGCTGCCAAAACATGG
*
381211 CCCGGATGCGAATCCCGACCAAGCTCGACTTAAAATGGCCTTTAATTAAGTAAGTAATGAAGTTT
131 CCCGGATGCGAATCCCGACCAAGCTCGACTTAAAATGGCCCTTAATTAAGTAAGTAATGAAGTTT
381276 TGTTAGTTTTGATGACTCCTATTTTATGAGCCATATTAGT
196 TGTTAGTTTTGATGACTCCTATTTTATGAGCCATATTAGT
*
381316 AAAAAGTATCGGGGATGATAATTAAATATTAAG-TGAAACCAAATTAATCAAAATTTATTTAACA
1 AAAAAGTATCGAGGATGATAATTAAATATT-AGTTGAAACCAAATTAATCAAAATTTATTTAACA
* * * * * *
381380 CGTAATCAATTCTAGGCCTGCCTCTCTAACTGTCCCCAGGGGAGTCGCCAAGTTGTCAAAACGTG
65 CGTAATCAATTCTAGGCCTGCCGCTCTAACTATCCCCAGGAGAGTCGCCAAGCTGCCAAAACATG
* * * * *
381445 GCCCGGATGCGAATCCCGACCAAGCTTGACTTAAAATGTCCCTTGATTATGTAGGTAATGAAGTT
130 GCCCGGATGCGAATCCCGACCAAGCTCGACTTAAAATGGCCCTTAATTAAGTAAGTAATGAAGTT
* *
381510 TTGTTATTTTTGATGACTCTTATTTTATGAGCCATATTA
195 TTGTTAGTTTTGATGACTCCTATTTTATGAGCCATATTA
381549 ATAATGATAT
Statistics
Matches: 211, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
235 209 0.99
236 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (235 bp):
AAAAAGTATCGAGGATGATAATTAAATATTAGTTGAAACCAAATTAATCAAAATTTATTTAACAC
GTAATCAATTCTAGGCCTGCCGCTCTAACTATCCCCAGGAGAGTCGCCAAGCTGCCAAAACATGG
CCCGGATGCGAATCCCGACCAAGCTCGACTTAAAATGGCCCTTAATTAAGTAAGTAATGAAGTTT
TGTTAGTTTTGATGACTCCTATTTTATGAGCCATATTAGT
Found at i:383011 original size:157 final size:157
Alignment explanation
Indices: 382592--384077 Score: 1073
Period size: 157 Copynumber: 9.6 Consensus size: 157
382582 TAAGTTTAAG
* * ** * * ** * *
382592 AAAAATTACGAAAATGCCCTT-AGGGGATAATTTTGACGTAGAAGTACCT-GATACCCCTAAAAG
1 AAAAATTACGAAAATACCCTTAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAGG
* *
382655 ACTT-AAAAAGACTCATAAAAGGG-TGAACCTATCCTCAATGCCCACCTTCAGTATAAAAGCAGA
66 ACTTAAAAAAGACT-ATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAGA
* * * *
382718 CCCGATTATAACCTAAGA-TTCGGTTCTA
130 CCCGGTGATGACCTAGGACTT-GGTTCTA
* * * * * * * * * *
382746 AAAGATTATGAAAATACCCTACCCTTAGGGGATACCCTCGACGTGAAAGCATCTCGGTACCCCTA
1 AAAAATTACGAAAATACCCT----TAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTA
* ** * * *
382811 AAAGACTTAAAATGGCCTACAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGT
62 AAGGACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGC
*
382876 AGACCCGGTGATGACCTAGGAGTTGGTTCTA
127 AGACCCGGTGATGACCTAGGACTTGGTTCTA
* *
382907 AAAAATTACCAAAATATCCTTAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAGG
1 AAAAATTACGAAAATACCCTTAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAGG
** *
382972 ACGCAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTT-AGACATAAAAGC-GA
66 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAG-CATAAAAGCAG-
* * * *
383035 ACCCAGTGACGACCTAAGAGTTGGTTCTA
129 ACCCGGTGATGACCTAGGACTTGGTTCTA
* *
383064 AAAAATTACCG-AAATACCCCTAAGGGTATACCTTTGACATAAAAGTATCTCGGCAACCCTAAAG
1 AAAAATTA-CGAAAATACCCTTAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAG
* * * * ** *
383128 GACTT-AAAAAGACTCATACAAGGGATGAAACTATTCTAAATGCCCAACTTTGGTATAAAAGCAG
65 GACTTAAAAAAGACT-ATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAG
* * *
383192 ACTCGGTGACGACCTAGGA-TTCGGTTCTG
129 ACCCGGTGATGACCTAGGACTT-GGTTCTA
* * * *
383221 AAAAATTATGAAAATA-CCTCTAGGGGGTAT--CTTCGACG-----GTA------C--CTCTAAA
1 AAAAATTACGAAAATACCCT-TA-AGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAA
* ** * * *
383270 GGACTTAAAAAAGACTATAAAAGCGATGAACCTATCCTAAACACCCTCTTTTAGCATAAAAGCAG
64 GGACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAG
* ** * *
383335 ACCCGGTGATGACCTAAGACTTTATTTTG
129 ACCCGGTGATGACCTAGGACTTGGTTCTA
* * * * * * *
383364 AAAAATTACGAAAATACCCCT-AGAGGT-TACCTTCGATGTGAAAA-TATCTTGGTACCCCTAAC
1 AAAAATTACGAAAATACCCTTAAG-GGTATACCTTTGACGT-AAAAGTATCTCGGCAACCCTAAA
* * * * * * *
383426 GAACTTAAAAAAGACTATAAAAGGGGTGAACTTATCCTAAATACCCACCTTCGGCATAAAAACAA
64 GGACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAG
* *
383491 ACCCGGTGATGACCTAGGACTCGATTCTA
129 ACCCGGTGATGACCTAGGACTTGGTTCTA
* * * * * * * *
383520 AAAAATTATGAAAATACCCCT-AGGGGATACATTCT-ACATAAAAGTATCCCGGTACCCCTAAAG
1 AAAAATTACGAAAATACCCTTAAGGGTATACCTT-TGACGTAAAAGTATCTCGGCAACCCTAAAG
* * * * *
383583 GACCTAAAAAAGACTATAAAAGGGGTGAGCCTATCATAAATACCCACCTTCAGCATAAAAGC-GA
65 GACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAG-
* *
383647 ACTCGGTGATGACCTAGGA-TTCGGTTCTG
129 ACCCGGTGATGACCTAGGACTT-GGTTCTA
* * * * * **
383676 AAAAATTACGAAAATA-CCTCTAGGGGT-T--CTTTCAACATGAAAGTATCCCAAC-ACCTCTAA
1 AAAAATTACGAAAATACCCT-TAAGGGTATACCTTT-GACGTAAAAGTATCTCGGCAACC-CTAA
* * * * * *
383736 AGGACTTAAAAAAGACTATAAAAGAGG-TGAACCTGTCCTAAATACCCACTTTTAACATAAAAGT
63 AGGACTTAAAAAAGACTATAAAAG-GGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGC
* * ** * * *
383800 GGACCCGATGACAACCTACGACTCGATTCTA
127 AGACCCGGTGATGACCTAGGACTTGGTTCTA
* ** ** * * *
383831 GAAAATTATAAAAATACCCTTATA-GGTATACCTTCAATGTGAAAGTATCTCGGCAACTCTAAAG
1 AAAAATTACGAAAATACCCTTA-AGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAG
* * * * * *
383895 GACTT-AAAAAGATTAGAAATGATGATGAACCTATCCTAAATGCCCACC-TCTGGCATAAAAGTA
65 GACTTAAAAAAGACTATAAAAG-GGATGAACCTATCCTAAATGCCCACCTTC-AGCATAAAAGCA
* * * * *
383958 AACCCGGTGGTTATCTAGGACTCGGTTCTAA
128 GACCCGGTGATGACCTAGGACTTGGTTCT-A
* * * * * *
383989 AAAAATTACGAAAATACCCATAAGAG-ATA-CTTTCGACGTGAAAGTATC-CTAGTACCCCTAAA
1 AAAAATTACGAAAATACCCTTAAGGGTATACCTTT-GACGTAAAAGTATCTC-GGCAACCCTAAA
* * *
384051 GGACTTAAAAAGGACTAGAAATGGGAT
64 GGACTTAAAAAAGACTATAAAAGGGAT
384078 TCTACCCTAG
Statistics
Matches: 1067, Mismatches: 200, Indels: 127
0.77 0.14 0.09
Matches are distributed among these distances:
141 2 0.00
142 3 0.00
143 93 0.09
144 13 0.01
145 1 0.00
148 2 0.00
151 3 0.00
153 1 0.00
154 21 0.02
155 117 0.11
156 273 0.26
157 362 0.34
158 49 0.05
159 20 0.02
160 25 0.02
161 80 0.07
162 2 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (157 bp):
AAAAATTACGAAAATACCCTTAAGGGTATACCTTTGACGTAAAAGTATCTCGGCAACCCTAAAGG
ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATGCCCACCTTCAGCATAAAAGCAGAC
CCGGTGATGACCTAGGACTTGGTTCTA
Found at i:383524 original size:156 final size:156
Alignment explanation
Indices: 383257--384067 Score: 766
Period size: 156 Copynumber: 5.2 Consensus size: 156
383247 GTATCTTCGA
* * * * * * *
383257 CGGTACCTCTAAAGGACTTAAAAAAGACTATAAAAGCGATGAACCTATCCTAAACACCCTCTTTT
1 CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC
* * ** * *
383322 AGCATAAAAGCAGACCCGGTGATGACCTAAGACTTTATTTTGAAAAATTACGAAAATACCCCTAG
66 AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCCTAG
* * * *
383387 AGGTTACCTTCGATGTGAAAATATCT
131 AGGTTACCTTCAACGTGAAAGTATCC
* * * *
383413 TGGTACCCCTAACGAACTTAAAAAAGACTATAAAAGGGGTGAACTTATCCTAAATACCCACCTTC
1 CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC
* * *
383478 GGCATAAAAACAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTATGAAAATACCCCTAG
66 AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCCTAG
* * * * * *
383543 GGGATACATTCTACATAAAAGTATCC
131 AGGTTACCTTCAACGTGAAAGTATCC
* * *
383569 CGGTACCCCTAAAGGACCTAAAAAAGACTATAAAAGGGGTGAGCCTATCATAAATACCCACCTTC
1 CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC
* * * * * *
383634 AGCATAAAAGCGAACTCGGTGATGACCTAGGATTCGGTTCTGAAAAATTACGAAAATACCTCTAG
66 AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCCTAG
* * *
383699 GGGTT-CTTTCAACATGAAAGTATCC
131 AGGTTACCTTCAACGTGAAAGTATCC
*** * * * * *
383724 CAACACCTCTAAAGGACTTAAAAAAGACTATAAAAGAGGTGAACCTGTCCTAAATACCCACTTTT
1 CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC
* *** * ** * * ** * *
383789 AACATAAAAGTGGACCCGATGACAACCTACGACTCGATTCTAGAAAATTATAAAAATACCCTTAT
66 AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCCTAG
* *
383854 AGGTATACCTTCAATGTGAAAGTATCT
131 AGGT-TACCTTCAACGTGAAAGTATCC
* * * * * * * * *
383881 CGGCAACTCTAAAGGACTT-AAAAAGATTAGAAATGATGATGAACCTATCCTAAATGCCCACC-T
1 CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAG-GGGTGAACCTATCCTAAATACCCACCTT
* * * * * * *
383944 CTGGCATAAAAGTAAACCCGGTGGTTATCTAGGACTCGGTTCTAAAAAAATTACGAAAATACCCA
65 C-AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCT-AAAAAATTACGAAAATACCCC
* * *
384009 TA-AGAGATACTTTCGACGTGAAAGTATCC
128 TAGAG-GTTACCTTCAACGTGAAAGTATCC
** *
384038 TAGTACCCCTAAAGGACTTAAAAAGGACTA
1 CGGTACCCCTAAAGGACTTAAAAAAGACTA
384068 GAAATGGGAT
Statistics
Matches: 527, Mismatches: 121, Indels: 12
0.80 0.18 0.02
Matches are distributed among these distances:
155 122 0.23
156 260 0.49
157 117 0.22
158 28 0.05
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (156 bp):
CGGTACCCCTAAAGGACTTAAAAAAGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTC
AGCATAAAAGCAAACCCGGTGATGACCTAGGACTCGATTCTAAAAAATTACGAAAATACCCCTAG
AGGTTACCTTCAACGTGAAAGTATCC
Found at i:384445 original size:3 final size:3
Alignment explanation
Indices: 384437--384474 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
384427 ATTTATTTAT
384437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
384475 TTGATTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:394027 original size:28 final size:31
Alignment explanation
Indices: 393963--394040 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 31
393953 AAATAATGTT
*
393963 ATATTCACACAAAGTAAAGGAGGGACGATCGAA
1 ATATTCACACAAAGTAAAGGAGGCACGAT--AA
393996 ATATTCACACAAAGTAAAGGA-GCAC-AT-A
1 ATATTCACACAAAGTAAAGGAGGCACGATAA
394024 ATATTCACACAAAGTAA
1 ATATTCACACAAAGTAA
394041 CAATAAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 18 0.41
31 2 0.05
32 3 0.07
33 21 0.48
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.18
Consensus pattern (31 bp):
ATATTCACACAAAGTAAAGGAGGCACGATAA
Found at i:398116 original size:20 final size:20
Alignment explanation
Indices: 398091--398189 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
398081 TTTGCCTGCA
398091 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
398111 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATCAG
398124 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
398144 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATCAG
398157 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
398177 TGTATCGATACAA
1 TGTATCGATACAA
398190 TGTATCGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 2 0.03
17 2 0.03
19 2 0.03
20 35 0.54
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGATCAG
Found at i:398129 original size:13 final size:13
Alignment explanation
Indices: 398111--398201 Score: 80
Period size: 13 Copynumber: 7.9 Consensus size: 13
398101 CAAAGATCAG
398111 TGTATCGATACAA
1 TGTATCGATACAA
398124 TGTATCGATACAA
1 TGTATCGATACAA
*
398137 ---A--GAT-CAG
1 TGTATCGATACAA
398144 TGTATCGATACAA
1 TGTATCGATACAA
398157 TGTATCGATACAA
1 TGTATCGATACAA
*
398170 ---A--GAT-CAG
1 TGTATCGATACAA
398177 TGTATCGATACAA
1 TGTATCGATACAA
398190 TGTATCGATACA
1 TGTATCGATACA
398202 TTTGAGTAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
7 4 0.06
8 6 0.10
10 4 0.06
12 6 0.10
13 42 0.68
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:398132 original size:33 final size:33
Alignment explanation
Indices: 398090--398201 Score: 224
Period size: 33 Copynumber: 3.4 Consensus size: 33
398080 ATTTGCCTGC
398090 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
398123 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
398156 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
398189 ATGTATCGATACA
1 ATGTATCGATACA
398202 TTTGAGTAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAGTGTATCGATACA
Found at i:398285 original size:20 final size:19
Alignment explanation
Indices: 398244--398296 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
398234 TAGCTTAAAT
398244 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
**
398263 TGTATCGATACAATATTTTA
1 TGTATCGATACAA-AACTTA
398283 TGTATCGATACAAA
1 TGTATCGATACAAA
398297 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:399058 original size:105 final size:104
Alignment explanation
Indices: 398949--399256 Score: 286
Period size: 104 Copynumber: 3.0 Consensus size: 104
398939 ATGCAGCTAG
* * * * * ***
398949 CGATATTAGGCTCGAAGATGCGAAAAATGACAATGTGCTGATTCATGACCAGCGT-CATTGGGTT
1 CGATATTAGACTCAAAGATGCCAAAAATGACAATATGCTGATTCAAGACCAGC-TACATT-GAAC
*
399013 TTAAAGAT-GATGAAGGTGCCAATATGCTGATTCAAGGCCAA
64 TTAAAGATGGA-AAAGGTGCCAATATGCTGATTCAAGGCCAA
* * ** * *
399054 CGATATTAGACTTAAAGGTGCCAAAGGTGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTT
1 CGATATTAGACTCAAAGATGCCAAAAATGACAATATGCTGATTCAAGACCAGCTACATTGAACTT
*
399119 AAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
66 AAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAA
* * * * *** * * * * *
399158 CTATATTGGACTTAAAGGTGCCAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 CGATATTAGACTCAAAGATGCCAAAAATGACAATATGCTGATTCAAGACCAGCTACATTGAACTT
*
399223 AAAGAT-G--AA-GTGCCAATGTGCTGATTCAAGGCCA
66 AAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
399257 GCTACATTGG
Statistics
Matches: 178, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
100 24 0.13
101 2 0.01
103 1 0.01
104 103 0.58
105 48 0.27
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (104 bp):
CGATATTAGACTCAAAGATGCCAAAAATGACAATATGCTGATTCAAGACCAGCTACATTGAACTT
AAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAA
Found at i:399081 original size:52 final size:52
Alignment explanation
Indices: 399025--399321 Score: 394
Period size: 52 Copynumber: 5.9 Consensus size: 52
399015 AAAGATGATG
* * * *
399025 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGGTGCCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
* * * **
399077 AAGGTGTCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
*
399129 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
* * *
399181 AAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
* *
399230 AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---C-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
*
399277 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
399322 AGAAGACGCC
Statistics
Matches: 216, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
47 2 0.01
48 78 0.36
49 2 0.01
52 134 0.62
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (52 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGCCA
Found at i:399398 original size:28 final size:28
Alignment explanation
Indices: 399341--399479 Score: 165
Period size: 28 Copynumber: 4.9 Consensus size: 28
399331 CACCAACTTG
*
399341 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* *
399370 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
399398 TGTGGGCTTTTAAAGATTGCTACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
399426 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
399454 TGTGGGCTTTTGAAAAGGGTGCCACT
1 TGTGGGCTTTT--AAAGGTTGCCACT
399480 AATTCGTCCC
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.03
28 70 0.73
29 11 0.11
30 12 0.12
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:401134 original size:20 final size:20
Alignment explanation
Indices: 401109--401283 Score: 89
Period size: 20 Copynumber: 7.7 Consensus size: 20
401099 TTTTAACTAG
401109 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
401129 ATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACA--T---T---AA-A-A-A
* *
401160 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTAAAAA
* * *
401180 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTAAAAA
* *
401200 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTAAAAA
401220 ATGTATCGATACATCTGGGTAAAAGACAGA
1 ATGTATCGATACA--T---T--AA-A-A-A
*
401250 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTAAAAA
401270 ATGTATCGATACAT
1 ATGTATCGATACAT
401284 CTGGGTAAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
20 74 0.61
21 2 0.02
22 4 0.03
23 2 0.02
25 3 0.02
26 1 0.01
27 1 0.01
28 4 0.03
29 2 0.02
30 15 0.12
31 13 0.11
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:401281 original size:90 final size:91
Alignment explanation
Indices: 401109--401283 Score: 307
Period size: 90 Copynumber: 1.9 Consensus size: 91
401099 TTTTAACTAG
* *
401109 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATATAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
401174 TGAAAAATGTATCGATACATTCATAC
66 TGAAAAATGTATCGATACATTCATAC
* *
401200 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGT-AAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
401264 TGAAAAATGTATCGATACAT
66 TGAAAAATGTATCGATACAT
401284 CTGGGTAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 42 0.52
91 38 0.47
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
TGAAAAATGTATCGATACATTCATAC
Found at i:402430 original size:13 final size:13
Alignment explanation
Indices: 402412--402442 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
402402 ACAATTCATC
402412 ATGTATCGATACA
1 ATGTATCGATACA
402425 ATGTATCGATACA
1 ATGTATCGATACA
*
402438 TTGTA
1 ATGTA
402443 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:402430 original size:33 final size:33
Alignment explanation
Indices: 402391--402458 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
402381 CGTTACAAGA
*
402391 AATGTATCGATACAATT-CATCATGTATCGATAC
1 AATGTATCGATAC-ATTGCACCATGTATCGATAC
*
402424 AATGTATCGATACATTGTACCATGTATCGATAC
1 AATGTATCGATACATTGCACCATGTATCGATAC
402457 AA
1 AA
402459 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
AATGTATCGATACATTGCACCATGTATCGATAC
Found at i:402538 original size:19 final size:19
Alignment explanation
Indices: 402487--402542 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
402477 CTGCCAATTT
**
402487 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
402507 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
402526 CATTTATCGATACAATG
1 CATGTATCGATACAATG
402543 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:403149 original size:50 final size:50
Alignment explanation
Indices: 403074--403185 Score: 197
Period size: 50 Copynumber: 2.2 Consensus size: 50
403064 AGTTTTCGTT
* *
403074 TTTCTCTCCCTTAATTAATTAATGAGATTTTCTGATCCTAGATAAACATA
1 TTTCTCCCCCTTAATTAATTAATGAGATTTTCTCATCCTAGATAAACATA
*
403124 TTTCTCCCCCTTAATTGATTAATGAGATTTTCTCATCCTAGATAAACATA
1 TTTCTCCCCCTTAATTAATTAATGAGATTTTCTCATCCTAGATAAACATA
403174 TTTCTCCCCCTT
1 TTTCTCCCCCTT
403186 TATCAAAGCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (50 bp):
TTTCTCCCCCTTAATTAATTAATGAGATTTTCTCATCCTAGATAAACATA
Found at i:404024 original size:13 final size:13
Alignment explanation
Indices: 404006--404032 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
403996 ATAGTAACCC
404006 ATGTATCGATACA
1 ATGTATCGATACA
404019 ATGTATCGATACA
1 ATGTATCGATACA
404032 A
1 A
404033 GGAATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Done.