Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 6 of 295
Found at i:1767054 original size:15 final size:15
Alignment explanation
Indices: 1767036--1767070 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1767026 TTTCATTCAC
*
1767036 TTTGATTCGATTCGA
1 TTTGATTCGACTCGA
1767051 TTTGATTCGACTCGA
1 TTTGATTCGACTCGA
*
1767066 CTTGA
1 TTTGA
1767071 ATTTCATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (15 bp):
TTTGATTCGACTCGA
Found at i:1767370 original size:75 final size:75
Alignment explanation
Indices: 1767245--1767384 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 75
1767235 AGAAGGATCG
** * *** * *
1767245 CACATATCTGCTATAGTTTGCCTAATGGAGTTCGCATATATAACAATTTATGTAAGCATTCGCAC
1 CACATATCAACTACAGTTTGCCTAACAAAGTTCGCAGATATAACAATTTATATAAGCATTCGCAC
1767310 CTAGGGCTCT
66 CTAGGGCTCT
* * **
1767320 CACATATCAACTACAGTTTGCCTAACAAAGTTCGCAGGTATAACAGTTTATATAAGGGTTCGCAC
1 CACATATCAACTACAGTTTGCCTAACAAAGTTCGCAGATATAACAATTTATATAAGCATTCGCAC
1767385 TTATGGGGGT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 53 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (75 bp):
CACATATCAACTACAGTTTGCCTAACAAAGTTCGCAGATATAACAATTTATATAAGCATTCGCAC
CTAGGGCTCT
Found at i:1780573 original size:15 final size:15
Alignment explanation
Indices: 1780553--1780581 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1780543 TTCAAATAAT
1780553 ATTAAAAATTAAAAA
1 ATTAAAAATTAAAAA
1780568 ATTAAAAATTAAAA
1 ATTAAAAATTAAAA
1780582 TATTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAAATTAAAAA
Found at i:1780629 original size:17 final size:18
Alignment explanation
Indices: 1780603--1780637 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1780593 ATTCTAAAAT
1780603 TTAT-ATTTTTTAAATAA
1 TTATAATTTTTTAAATAA
1780620 TTATAATTTTTTAAATAA
1 TTATAATTTTTTAAATAA
1780638 ATTCTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAATTTTTTAAATAA
Found at i:1783776 original size:8 final size:8
Alignment explanation
Indices: 1783759--1783791 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1783749 AAGGCCACTG
1783759 TTTT-TTT
1 TTTTATTT
1783766 TTTTATTTT
1 TTTTA-TTT
1783775 TTTTATTT
1 TTTTATTT
1783783 TTTTATTT
1 TTTTATTT
1783791 T
1 T
1783792 GGCTCATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.17
8 12 0.50
9 8 0.33
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTATTT
Found at i:1783776 original size:9 final size:9
Alignment explanation
Indices: 1783762--1783791 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1783752 GCCACTGTTT
1783762 TTTTTTTTA
1 TTTTTTTTA
1783771 TTTTTTTTA
1 TTTTTTTTA
1783780 -TTTTTTTA
1 TTTTTTTTA
1783788 TTTT
1 TTTT
1783792 GGCTCATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1783785 original size:17 final size:16
Alignment explanation
Indices: 1783759--1783791 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1783749 AAGGCCACTG
1783759 TTTTTTTTTTTATTTT
1 TTTTTTTTTTTATTTT
1783775 TTTTATTTTTTTATTTT
1 TTTT-TTTTTTTATTTT
1783792 GGCTCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTATTTT
Found at i:1786195 original size:31 final size:31
Alignment explanation
Indices: 1786113--1786182 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
1786103 TTTATGTATC
*
1786113 ATTATATTAAATTATTTAAATATCATATATA
1 ATTATATTAAATTATTTAAATATAATATATA
* * *
1786144 ATTATACTAAATTATTTAAATATAATCTATT
1 ATTATATTAAATTATTTAAATATAATATATA
1786175 ATTATATT
1 ATTATATT
1786183 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATAATATATA
Found at i:1790123 original size:107 final size:108
Alignment explanation
Indices: 1789984--1790199 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 108
1789974 AAAAAACACG
1789984 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
1790049 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
1790092 TCAAAAATTTTAT-AGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
* *
1790156 AAAACTTATTCTAACTTTACATATCATTGTTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
1790199 T
1 T
1790200 TTTTTGTTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 93 0.88
108 13 0.12
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (108 bp):
TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
Found at i:1790441 original size:17 final size:17
Alignment explanation
Indices: 1790419--1790453 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1790409 GGTGTTGTGC
*
1790419 CTACCTGTCAGGCACGA
1 CTACCTGACAGGCACGA
*
1790436 CTACCTGACAGGCTCGA
1 CTACCTGACAGGCACGA
1790453 C
1 C
1790454 CCGTTTCGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (17 bp):
CTACCTGACAGGCACGA
Found at i:1795449 original size:14 final size:14
Alignment explanation
Indices: 1795430--1795457 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1795420 AAGTCGAAAC
1795430 TGGTTTATTCTCTA
1 TGGTTTATTCTCTA
1795444 TGGTTTATTCTCTA
1 TGGTTTATTCTCTA
1795458 AGGTAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TGGTTTATTCTCTA
Found at i:1807300 original size:17 final size:17
Alignment explanation
Indices: 1807278--1807311 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1807268 ATCCACTAAT
*
1807278 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1807295 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1807312 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1811938 original size:17 final size:17
Alignment explanation
Indices: 1811916--1811949 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1811906 ATCCACTAAT
*
1811916 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1811933 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1811950 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1816277 original size:15 final size:15
Alignment explanation
Indices: 1816257--1816291 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1816247 CTCAAGAGAC
1816257 TTAACCAGCATCACT
1 TTAACCAGCATCACT
1816272 TTAACCAGCATCACT
1 TTAACCAGCATCACT
1816287 TTAAC
1 TTAAC
1816292 AGAGCTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (15 bp):
TTAACCAGCATCACT
Found at i:1820807 original size:21 final size:20
Alignment explanation
Indices: 1820762--1820809 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1820752 GGAATTACCA
*
1820762 GAAAATTTTAAAATATATTT
1 GAAAATTATAAAATATATTT
*
1820782 AAAAATTCATAAAATAT-TTAT
1 GAAAATT-ATAAAATATATT-T
1820803 GAAAATT
1 GAAAATT
1820810 TCAATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
GAAAATTATAAAATATATTT
Found at i:1825004 original size:2 final size:2
Alignment explanation
Indices: 1824997--1825026 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1824987 CACAAAATTA
1824997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1825027 GAGCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1825338 original size:20 final size:20
Alignment explanation
Indices: 1825306--1825360 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1825296 TATTCTTAAT
*
1825306 TTAAATACCAAAAATATAAA
1 TTAAATACTAAAAATATAAA
1825326 -TATAATACTAAAACAT-TAAA
1 TTA-AATACTAAAA-ATATAAA
1825346 TTAAATA-TAAAAATA
1 TTAAATACTAAAAATA
1825361 AATTTATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 7 0.23
20 17 0.57
21 4 0.13
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAATACTAAAAATATAAA
Found at i:1832820 original size:8 final size:8
Alignment explanation
Indices: 1832807--1832832 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1832797 AGTTAGGCTC
1832807 ATCTATAT
1 ATCTATAT
1832815 ATCTATAT
1 ATCTATAT
1832823 ATCTATAT
1 ATCTATAT
1832831 AT
1 AT
1832833 ATTGTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATCTATAT
Found at i:1832959 original size:9 final size:9
Alignment explanation
Indices: 1832923--1832970 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
1832913 AAGATGATTC
*
1832923 TAAAATATA
1 TAAAATATT
1832932 TAAAAT-TT
1 TAAAATATT
*
1832940 T--AATTTT
1 TAAAATATT
1832947 TAAAATATT
1 TAAAATATT
1832956 TAAAATA-T
1 TAAAATATT
1832964 TAAAATA
1 TAAAATA
1832971 ACGCAATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
6 3 0.09
7 3 0.09
8 10 0.29
9 18 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAAATATT
Found at i:1832966 original size:17 final size:17
Alignment explanation
Indices: 1832908--1832970 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1832898 GGAATAAATT
*
1832908 ATATTAAGATGATTCTAAA
1 ATATTAAAAT-ATT-TAAA
1832927 ATATATAAAAT-TTT-AA
1 ATAT-TAAAATATTTAAA
* *
1832943 TTTTTAAAATATTTAAA
1 ATATTAAAATATTTAAA
1832960 ATATTAAAATA
1 ATATTAAAATA
1832971 ACGCAATACC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 6 0.17
16 7 0.19
17 12 0.33
18 2 0.06
19 4 0.11
20 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATTAAAATATTTAAA
Found at i:1835890 original size:190 final size:190
Alignment explanation
Indices: 1835567--1835950 Score: 768
Period size: 190 Copynumber: 2.0 Consensus size: 190
1835557 TCTTCAAGTC
1835567 TTTAGACAGAAGCTGCAGAACTAAAGTCAAGATAGGAAATGGTCATTTTATTCAAGCTGAAGGCA
1 TTTAGACAGAAGCTGCAGAACTAAAGTCAAGATAGGAAATGGTCATTTTATTCAAGCTGAAGGCA
1835632 AGGGTGATGTGCTGATATGCACCCCTACAGGTACCAAAGTGATTTCAAATGTGCTGTTGGTGCCT
66 AGGGTGATGTGCTGATATGCACCCCTACAGGTACCAAAGTGATTTCAAATGTGCTGTTGGTGCCT
1835697 GAAATTGACAGAAACCTGCTCAGCATAGCTCAGTTGCTGGAAAAAGGCTATACAGTTGTG
131 GAAATTGACAGAAACCTGCTCAGCATAGCTCAGTTGCTGGAAAAAGGCTATACAGTTGTG
1835757 TTTAGACAGAAGCTGCAGAACTAAAGTCAAGATAGGAAATGGTCATTTTATTCAAGCTGAAGGCA
1 TTTAGACAGAAGCTGCAGAACTAAAGTCAAGATAGGAAATGGTCATTTTATTCAAGCTGAAGGCA
1835822 AGGGTGATGTGCTGATATGCACCCCTACAGGTACCAAAGTGATTTCAAATGTGCTGTTGGTGCCT
66 AGGGTGATGTGCTGATATGCACCCCTACAGGTACCAAAGTGATTTCAAATGTGCTGTTGGTGCCT
1835887 GAAATTGACAGAAACCTGCTCAGCATAGCTCAGTTGCTGGAAAAAGGCTATACAGTTGTG
131 GAAATTGACAGAAACCTGCTCAGCATAGCTCAGTTGCTGGAAAAAGGCTATACAGTTGTG
1835947 TTTA
1 TTTA
1835951 AAGACCACCA
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 194 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (190 bp):
TTTAGACAGAAGCTGCAGAACTAAAGTCAAGATAGGAAATGGTCATTTTATTCAAGCTGAAGGCA
AGGGTGATGTGCTGATATGCACCCCTACAGGTACCAAAGTGATTTCAAATGTGCTGTTGGTGCCT
GAAATTGACAGAAACCTGCTCAGCATAGCTCAGTTGCTGGAAAAAGGCTATACAGTTGTG
Found at i:1844559 original size:22 final size:21
Alignment explanation
Indices: 1844524--1844599 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
1844514 AAAAGGTATC
* *
1844524 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1844545 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1844568 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
1844587 TGC-AATCATATCT
1 TACAAATCATATCT
1844600 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1844616 original size:35 final size:37
Alignment explanation
Indices: 1844553--1844650 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
1844543 ATTACAAAAT
1844553 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
1844589 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
1844624 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
1844651 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:1844658 original size:17 final size:19
Alignment explanation
Indices: 1844560--1844650 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
1844550 AATCATATCT
1844560 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1844579 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
1844597 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
1844614 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1844633 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
1844651 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1847228 original size:46 final size:46
Alignment explanation
Indices: 1847176--1847443 Score: 331
Period size: 46 Copynumber: 5.8 Consensus size: 46
1847166 AGTGTGCTCT
* *
1847176 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1847222 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
1847268 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
1847314 CTGACATGAAATGAGTAAGACCATTGTTGAAAGATACCTTGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** * *
1847360 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACGATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
1847407 ATGACA-GAAAACGAGTAAAATCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
1847444 TATGACATCA
Statistics
Matches: 199, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 160 0.80
47 39 0.20
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1848448 original size:45 final size:45
Alignment explanation
Indices: 1848395--1848739 Score: 255
Period size: 45 Copynumber: 7.9 Consensus size: 45
1848385 CGATATCTAC
* *
1848395 TATCTTTGATCTGCTTCCCGTCTAATACAGAGACGCCAAATCTGT
1 TATCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
1848440 TATCTTTGATCTGC-TCCTCGTCTAATACAGAGATGCCAAATTTGC
1 TATCTTCGATCTGCTTCC-CGTCTAATACAGAGATGCCAAATCTGT
* * * * *
1848485 T-TCTTCAATCTGCTCCCCTTCTAATAAAGAGATGCTAAATCTGT
1 TATCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCTGT
*
1848529 TATCTTCGATTTG-TTCCCTGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTCGATCTGCTTCCC-GTCTAATACAGAGATGCCAAATCTGT
* * * * * * *
1848574 CATCTTGGATCTGCTT--CGATGTAA-ACACATGAAGGTCAGATCTGCT
1 TATCTTCGATCTGCTTCCCG-TCTAATACAGA-G-ATGCCAAATCTG-T
* *
1848620 ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC---
1 -TATCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCTGT
*
1848663 -ATCTTGGATCTGC-T----TC-AATGA-AG-G-T-CC-AATCTGT
1 TATCTTCGATCTGCTTCCCGTCTAAT-ACAGAGATGCCAAATCTGT
*
1848697 TATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
1 TA--TCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAAT
1848740 TACATTGGAT
Statistics
Matches: 230, Mismatches: 39, Indels: 60
0.70 0.12 0.18
Matches are distributed among these distances:
31 4 0.02
32 2 0.01
33 1 0.00
34 1 0.00
35 6 0.03
36 3 0.01
37 11 0.05
41 11 0.05
42 3 0.01
43 10 0.04
44 47 0.20
45 93 0.40
46 5 0.02
47 22 0.10
48 5 0.02
49 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (45 bp):
TATCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCTGT
Found at i:1848516 original size:44 final size:45
Alignment explanation
Indices: 1848395--1848662 Score: 256
Period size: 45 Copynumber: 5.9 Consensus size: 45
1848385 CGATATCTAC
* * *
1848395 TATCTTTGATCTGCTTCCCGTCTAATACAGAGACGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * *
1848440 TATCTTTGATCTGCTCCTCGTCTAATACAGAGATGCCAAATTTGC
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * *
1848485 T-TCTTCAATCTGCTCCCCTTCTAATAAAGAGATGCTAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
1848529 TATCTTCGATTTGTTCCCTGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * * * * * *
1848574 CATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAGATCTGCT
1 TATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAAATCTG-T
*
1848620 ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1 -TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1848663 ATCTTGGATC
Statistics
Matches: 174, Mismatches: 40, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
43 5 0.03
44 41 0.24
45 97 0.56
46 1 0.01
47 19 0.11
48 5 0.03
49 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
Found at i:1848527 original size:89 final size:89
Alignment explanation
Indices: 1848403--1848569 Score: 246
Period size: 89 Copynumber: 1.9 Consensus size: 89
1848393 ACTATCTTTG
* * *
1848403 ATCTGCTTCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTTGATCTGCT-CCTCGTCTAATA
1 ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCT-GTCTAATA
1848467 CAGAGATGCCAAATTTGCTTCTTCA
65 CAGAGATGCCAAATTTGCTTCTTCA
* * * * *
1848492 ATCTGCTCCCCTTCTAATAAAGAGATGCTAAATCTGTTATCTTCGATTTGTTCCCTGTCTAATAC
1 ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCTGTCTAATAC
1848557 AGAGATGCCAAAT
66 AGAGATGCCAAAT
1848570 CTGTCATCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
89 66 0.96
90 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (89 bp):
ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCTGTCTAATAC
AGAGATGCCAAATTTGCTTCTTCA
Found at i:1848731 original size:78 final size:78
Alignment explanation
Indices: 1848602--1848974 Score: 615
Period size: 78 Copynumber: 4.8 Consensus size: 78
1848592 ATGTAAACAC
1848602 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1848667 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
1848680 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTA-C
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1848743 ATTGGATCTGCTTCA
65 -TTGGATCTGCTTCA
*
1848758 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1848823 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * *
1848836 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATAT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1848901 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * **
1848914 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1848975 TGTTTCTTCG
Statistics
Matches: 277, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
77 3 0.01
78 271 0.98
79 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:1851422 original size:25 final size:24
Alignment explanation
Indices: 1851390--1851441 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1851380 AACCCAAACC
1851390 AAAAAATAAAACAAAAAAAATATA
1 AAAAAATAAAACAAAAAAAATATA
* * *
1851414 AAAATAATAAAACCAAAATAATTTA
1 AAAA-AATAAAACAAAAAAAATATA
1851439 AAA
1 AAA
1851442 GTCCATTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAAAATAAAACAAAAAAAATATA
Found at i:1856163 original size:26 final size:27
Alignment explanation
Indices: 1856116--1856177 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1856106 AAATAATATA
*
1856116 ATAATAATATAAAAAGTGGATAA-AAT
1 ATAATAATATAAAAAGTAGATAAGAAT
*
1856142 ATAATGATATAAAAA-TAAGATAAGAAT
1 ATAATAATATAAAAAGT-AGATAAGAAT
1856169 A-AAGTAATA
1 ATAA-TAATA
1856178 GGTAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (27 bp):
ATAATAATATAAAAAGTAGATAAGAAT
Found at i:1862723 original size:47 final size:47
Alignment explanation
Indices: 1862617--1862806 Score: 193
Period size: 47 Copynumber: 3.9 Consensus size: 47
1862607 ATGTGATTTT
* * * *
1862617 CGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTC
1 CGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGCTAC
*
1862669 CGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTAC
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTAC
* * *
1862716 TGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-C
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTAC
* ** * *
1862762 CGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 CGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
1862807 ACTATGTGCA
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 26 0.22
47 55 0.46
48 11 0.09
50 1 0.01
51 1 0.01
52 26 0.22
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (47 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTAC
Found at i:1862794 original size:93 final size:97
Alignment explanation
Indices: 1862600--1862825 Score: 228
Period size: 93 Copynumber: 2.3 Consensus size: 97
1862590 CCATGGCAGC
* * * * *
1862600 ATGTGAAATGTGATTTTCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTG
1 ATGTGATATGTGACTAT-GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTG
* *
1862665 CTTCCGTATAAGACCATATCCGGGATATGGCATCGG
62 CATCCGTATAAGACCATAGCCGGGATATGGCATCGG
*
1862701 -TGTGATATGTG-CTACTGTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-AT
1 ATGTGATATGTGACTA-TGTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCAT
* * * * *
1862761 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGG
65 CCGTATAAGACCATAGCCGGGATATGGCATCGG
**
1862794 TATGTGATATGTGACTATGTGCAAGACCATAG
1 -ATGTGATATGTGACTATGTATAAGACCATAG
1862826 TTTTACTATG
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
93 28 0.27
94 11 0.10
95 23 0.22
96 3 0.03
97 2 0.02
99 27 0.26
100 11 0.10
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (97 bp):
ATGTGATATGTGACTATGTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATC
CGTATAAGACCATAGCCGGGATATGGCATCGG
Found at i:1866950 original size:18 final size:17
Alignment explanation
Indices: 1866915--1866947 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1866905 CTTTTTATTC
1866915 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
1866932 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
1866948 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:1867102 original size:31 final size:29
Alignment explanation
Indices: 1867067--1867140 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
1867057 TTCTTTTATT
1867067 TATTTAACAAATAAAAATCTTATAATATTAA
1 TATTTAACAAATAAAAATCTT-TAA-ATTAA
** * *
1867098 TATTTAATTAATAAATATCTTTAACTTAA
1 TATTTAACAAATAAAAATCTTTAAATTAA
*
1867127 AATTTAAGCAAATA
1 TATTTAA-CAAATA
1867141 CATAATTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 10 0.29
30 7 0.20
31 18 0.51
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (29 bp):
TATTTAACAAATAAAAATCTTTAAATTAA
Found at i:1870386 original size:22 final size:21
Alignment explanation
Indices: 1870351--1870426 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
1870341 AAAAGGTATC
* *
1870351 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1870372 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1870395 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
1870414 TGC-AATCATATCT
1 TACAAATCATATCT
1870427 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1870443 original size:35 final size:37
Alignment explanation
Indices: 1870380--1870458 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
1870370 ATTACAAAAT
1870380 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
1870416 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
1870451 CATATCAT
1 CATATCAT
1870459 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:1870456 original size:14 final size:15
Alignment explanation
Indices: 1870401--1870456 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
1870391 AGATTGCATA
1870401 TCATATCTAAGATTG
1 TCATATCTAAGATTG
1870416 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
1870434 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
1870451 -CATATC
1 TCATATC
1870457 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:1870466 original size:17 final size:19
Alignment explanation
Indices: 1870387--1870458 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
1870377 AATCATATCT
1870387 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1870406 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
1870424 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
1870441 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
1870459 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1876588 original size:12 final size:12
Alignment explanation
Indices: 1876571--1876596 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1876561 CATTCCTCAA
1876571 TTGTATAGTCAT
1 TTGTATAGTCAT
1876583 TTGTATAGTCAT
1 TTGTATAGTCAT
1876595 TT
1 TT
1876597 TACAATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGTATAGTCAT
Found at i:1877220 original size:17 final size:18
Alignment explanation
Indices: 1877198--1877231 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1877188 AGTTGAGTTA
1877198 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
1877215 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
1877232 AGGAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:1878768 original size:42 final size:43
Alignment explanation
Indices: 1878716--1878801 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
1878706 TAATAAAATC
* * *
1878716 AATTATAATTTGAATATTTATTTTTAAAA-ATATCAAGAGTAT
1 AATTACAATTTGAATAATTATTTTTAAAATATATCAAAAGTAT
*
1878758 AATTACAATTTGAATAATTATTTTTAAAATTTATCAAAAGTAT
1 AATTACAATTTGAATAATTATTTTTAAAATATATCAAAAGTAT
1878801 A
1 A
1878802 TATATAGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 27 0.69
43 12 0.31
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (43 bp):
AATTACAATTTGAATAATTATTTTTAAAATATATCAAAAGTAT
Found at i:1879315 original size:30 final size:30
Alignment explanation
Indices: 1879281--1879394 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 30
1879271 TAAATTTAAA
*
1879281 TTTAAAATTTAAAATATTATTTTTATAATT
1 TTTAAAATTTAAAATATAATTTTTATAATT
* * * *
1879311 TTTAAAAAATTAAATTA-AATTATTATTATT
1 TTT-AAAATTTAAAATATAATTTTTATAATT
* * *
1879341 TTAAAAAAGTAAAAATATAATTTTATCATAATT
1 TT-TAAAATTTAAAATATAATTTT-T-ATAATT
1879374 AATTTAAAATTTAAAATATAA
1 --TTTAAAATTTAAAATATAA
1879395 ACAATTTTTC
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
30 25 0.40
31 16 0.25
32 1 0.02
33 5 0.08
34 14 0.22
35 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
TTTAAAATTTAAAATATAATTTTTATAATT
Found at i:1883017 original size:31 final size:29
Alignment explanation
Indices: 1882982--1883067 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
1882972 TTTACAAGAA
*
1882982 TTACATCAAATTAAAACTTTATGTATGA-AAT
1 TTACAT-AAATTAAAA-TTAATGTAT-ATAAT
* *
1883013 TTACA-AAATTAAAATTCATATATATAAT
1 TTACATAAATTAAAATTAATGTATATAAT
1883041 TATACATTAAATTAAAATTAATGTATA
1 T-TACA-TAAATTAAAATTAATGTATA
1883068 ATTTTGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 11 0.23
29 13 0.28
31 22 0.47
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (29 bp):
TTACATAAATTAAAATTAATGTATATAAT
Found at i:1883068 original size:29 final size:27
Alignment explanation
Indices: 1882982--1883071 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
1882972 TTTACAAGAA
*
1882982 TTACATCAAATTAAAACTTTATGTATGAAAT
1 TTACAT-AAATTAAAA-TTAATGTAT--AAT
*
1883013 TTACA-AAATTAAAATTCATATATATAAT
1 TTACATAAATTAAAATT-A-ATGTATAAT
1883041 TATACATTAAATTAAAATTAATGTATAAT
1 T-TACA-TAAATTAAAATTAATGTATAAT
1883070 TT
1 TT
1883072 TGAAAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 7 0.14
29 22 0.43
30 6 0.12
31 16 0.31
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (27 bp):
TTACATAAATTAAAATTAATGTATAAT
Found at i:1892032 original size:22 final size:25
Alignment explanation
Indices: 1892007--1892052 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
1891997 TAGCGACCAA
1892007 AAATATATA-AT-TATA-AATAAAC
1 AAATATATATATATATATAATAAAC
*
1892029 AAATATTTATATATATATAATAAA
1 AAATATATATATATATATAATAAA
1892053 ATATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 4 0.20
25 6 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATATATATATATATATAATAAAC
Found at i:1904529 original size:18 final size:18
Alignment explanation
Indices: 1904506--1904598 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
1904496 CCCAACTACT
* *
1904506 GTATACGTAAACAGTACC
1 GTATACGTGAATAGTACC
*
1904524 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
** *
1904542 GTATATATGAATAGTATC
1 GTATACGTGAATAGTACC
* *
1904560 GTATATGTGAATAGTGCC
1 GTATACGTGAATAGTACC
1904578 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1904596 GTA
1 GTA
1904599 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1921742 original size:21 final size:21
Alignment explanation
Indices: 1921710--1921750 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1921700 GAACATTTGG
1921710 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
1921731 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
1921751 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:1927317 original size:43 final size:43
Alignment explanation
Indices: 1927267--1927449 Score: 213
Period size: 43 Copynumber: 4.3 Consensus size: 43
1927257 GTCTATTTTA
* * ** * *
1927267 TAGCGGCGTCTGTGAAAAAAATGCCACTAAAAGTCATAGTCTT
1 TAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAAGTCATGGTCTT
** *
1927310 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAAGTCATGGTCTT
* * ** * *
1927353 TAGCAGCCTTTAAGAGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAAGTCATGGTCTT
* *
1927396 TAGCAGCGTTTGCGAAAATAGCGCCGCTAAAAGTCATGGTCTT
1 TAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAAGTCATGGTCTT
1927439 TAGCGGCGTTT
1 TAGCGGCGTTT
1927450 TTTAAAATAA
Statistics
Matches: 119, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAAGTCATGGTCTT
Found at i:1927465 original size:43 final size:43
Alignment explanation
Indices: 1927280--1927470 Score: 154
Period size: 43 Copynumber: 4.4 Consensus size: 43
1927270 CGGCGTCTGT
* * *
1927280 GAAAA-AAATGCCACTAAAAGTCATAGTCTTTAGCGGCGTTTGC
1 GAAAATAAA-GCCGCTAAAAGTCATGGTCTTTAGCAGCGTTTGC
* ** * * **
1927323 GGGAAA-AGCGCCGCTAAAGGTCATGGTCTTTAGCAGCCTTTAA
1 -GAAAATAAAGCCGCTAAAAGTCATGGTCTTTAGCAGCGTTTGC
** *
1927366 GAGAAA-AGCGCCGCTAAAGGTCATGGTCTTTAGCAGCGTTTGC
1 GA-AAATAAAGCCGCTAAAAGTCATGGTCTTTAGCAGCGTTTGC
** * **
1927409 GAAAATAGCGCCGCTAAAAGTCATGGTCTTTAGCGGCGTTTTT
1 GAAAATAAAGCCGCTAAAAGTCATGGTCTTTAGCAGCGTTTGC
* *
1927452 TAAAATAAAGCCGCAAAAA
1 GAAAATAAAGCCGCTAAAA
1927471 TTTACGGCGT
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 4 0.03
43 114 0.93
44 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
GAAAATAAAGCCGCTAAAAGTCATGGTCTTTAGCAGCGTTTGC
Found at i:1927465 original size:86 final size:85
Alignment explanation
Indices: 1927267--1927470 Score: 221
Period size: 86 Copynumber: 2.4 Consensus size: 85
1927257 GTCTATTTTA
* * * * *
1927267 TAGCGGCGTCTGTGAAAAAAATGCCACTAAAAGTCATAGTCTTTAGCGGCGTTTGCGGGAAAAGC
1 TAGCGGCGTTTATGAAAAAAA-GCCGCTAAAAGTCATAGTCTTTAGCAGCGTTTGCGGAAAAAGC
*
1927332 GCCGCTAAAGGTCATGGTCTT
65 GCCGCTAAAAGTCATGGTCTT
* * * ** * *
1927353 TAGCAGCCTTTAAGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCAGCGTTTGC-GAAAATAG
1 TAGCGGCGTTTATGA-AAAAAAGCCGCTAAAAGTCATAGTCTTTAGCAGCGTTTGCGGAAAA-AG
1927417 CGCCGCTAAAAGTCATGGTCTT
64 CGCCGCTAAAAGTCATGGTCTT
* * *
1927439 TAGCGGCGTTTTTTAAAATAAAGCCGCAAAAA
1 TAGCGGCGTTTATGAAAA-AAAGCCGCTAAAA
1927471 TTTACGGCGT
Statistics
Matches: 93, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
85 7 0.08
86 82 0.88
87 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (85 bp):
TAGCGGCGTTTATGAAAAAAAGCCGCTAAAAGTCATAGTCTTTAGCAGCGTTTGCGGAAAAAGCG
CCGCTAAAAGTCATGGTCTT
Found at i:1927943 original size:32 final size:32
Alignment explanation
Indices: 1927895--1927962 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1927885 CAGCTCAGAC
1927895 AATG-ATTGTACAATTTTGTCTATAGGTTGTT
1 AATGTATTGTACAATTTTGTCTATAGGTTGTT
*
1927926 AATGTATTGTACTATTTTGTCTATAGGTTGTT
1 AATGTATTGTACAATTTTGTCTATAGGTTGTT
1927958 AATGT
1 AATGT
1927963 CATAATGGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (32 bp):
AATGTATTGTACAATTTTGTCTATAGGTTGTT
Found at i:1929876 original size:16 final size:15
Alignment explanation
Indices: 1929851--1929880 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1929841 CGGATGAAAT
1929851 TTTAATTTTTTATAG
1 TTTAATTTTTTATAG
1929866 TTTATATTTTTTATA
1 TTTA-ATTTTTTATA
1929881 ATTTGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTTATAG
Found at i:1934377 original size:17 final size:17
Alignment explanation
Indices: 1934355--1934388 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1934345 ATCCACTAAT
*
1934355 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1934372 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1934389 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1939015 original size:17 final size:17
Alignment explanation
Indices: 1938993--1939026 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1938983 ATCCACTAAT
*
1938993 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1939010 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1939027 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1959701 original size:30 final size:32
Alignment explanation
Indices: 1959649--1959711 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
1959639 AGCCTATATC
*
1959649 TTTATAATTTTTAAATGATTAAA-T-CAATTT
1 TTTATAATTTTTAAAGGATTAAAGTGCAATTT
* * *
1959679 TTTATCATTTTTAAGGGGTTAAAGTGCAATTT
1 TTTATAATTTTTAAAGGATTAAAGTGCAATTT
1959711 T
1 T
1959712 ACCTTTGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.70
31 1 0.04
32 7 0.26
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (32 bp):
TTTATAATTTTTAAAGGATTAAAGTGCAATTT
Found at i:1966889 original size:30 final size:30
Alignment explanation
Indices: 1966843--1966909 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1966833 ATCTTCGATT
* *
1966843 TGCTCTCCGCCCATACAGAGACGCCAAATC
1 TGCTATCCGCCAATACAGAGACGCCAAATC
1966873 TGCTATCCGCCAATACAGAGACGCCAAATC
1 TGCTATCCGCCAATACAGAGACGCCAAATC
*
1966903 TGTTATC
1 TGCTATC
1966910 TTCGATCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.21
Consensus pattern (30 bp):
TGCTATCCGCCAATACAGAGACGCCAAATC
Found at i:1966919 original size:44 final size:44
Alignment explanation
Indices: 1966870--1967214 Score: 528
Period size: 44 Copynumber: 7.8 Consensus size: 44
1966860 GAGACGCCAA
* * * *
1966870 ATCTGCTATCCGCCAATACAGAGACGCCAAATCTGTTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
**
1966914 ATCTGCTCTCTGTTAATACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
* * *
1966958 ATCTGCTCTCCGGCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
1967002 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
* *
1967046 ATCTGCTCTCTACCAATACAGAGATGCCAAATCTACTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
* * *
1967090 ATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGTTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
* * *
1967134 ATCTGTTCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCG
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
*
1967178 ATCTGCTCTCGGCCAATACAGAGATGCCAAATCTGCT
1 ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCT
1967215 GGATTCGCCA
Statistics
Matches: 271, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 271 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (44 bp):
ATCTGCTCTCTGCCAATACAGAGATGCCAAATCTGCTATCTTCG
Found at i:1966921 original size:74 final size:74
Alignment explanation
Indices: 1966796--1966953 Score: 201
Period size: 74 Copynumber: 2.1 Consensus size: 74
1966786 GTTATTTTTT
* * * * *
1966796 ATCTGCTTTCTGCCAACACAGAGATGCCAAATTCGCTATCTTCGATTTGCTCTCCGCCCATACAG
1 ATCTGCTATCCGCCAACACAGAGACGCCAAATTCGCTATCTTCGATCTGCTCTCCGCCAATACAG
1966861 AGACGCCAA
66 AGACGCCAA
* * * **
1966870 ATCTGCTATCCGCCAATACAGAGACGCCAAA-TCTGTTATCTTCGATCTGCTCTCTGTTAATACA
1 ATCTGCTATCCGCCAACACAGAGACGCCAAATTC-GCTATCTTCGATCTGCTCTCCGCCAATACA
*
1966934 GAGATGCCAA
65 GAGACGCCAA
1966944 ATCTGCTATC
1 ATCTGCTATC
1966954 TTCGATCTGC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 2 0.03
74 70 0.97
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (74 bp):
ATCTGCTATCCGCCAACACAGAGACGCCAAATTCGCTATCTTCGATCTGCTCTCCGCCAATACAG
AGACGCCAA
Found at i:1971055 original size:24 final size:24
Alignment explanation
Indices: 1971028--1971079 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1971018 TTAGTAAGTC
*
1971028 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1971052 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1971076 AAAT
1 AAAT
1971080 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1973023 original size:24 final size:24
Alignment explanation
Indices: 1972996--1973047 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1972986 TTAGTAAGTC
*
1972996 AAATAAATTATACTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
1973020 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
1973044 AAAT
1 AAAT
1973048 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:1976891 original size:60 final size:60
Alignment explanation
Indices: 1976804--1976922 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
1976794 ATATTAAACT
* * *
1976804 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
* *
1976864 AAACACAGAAAATTT-TAACATAGTCCTAAATTACTAACAAATTAATTTTAACATAATTA
1 AAACACA-AAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1976923 TAAAAAACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 47 0.89
61 6 0.11
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:1984453 original size:21 final size:21
Alignment explanation
Indices: 1984427--1984467 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1984417 AGACGAGCAA
* *
1984427 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1984448 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1984468 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1990884 original size:15 final size:14
Alignment explanation
Indices: 1990866--1990896 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1990856 TTAATTTATT
1990866 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
1990881 TAATAATAATCTAA
1 TAATAATAATCTAA
1990895 TA
1 TA
1990897 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:1990907 original size:21 final size:20
Alignment explanation
Indices: 1990883--1990951 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1990873 AATGCTAATA
1990883 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
1990904 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
1990923 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
1990944 ATAATAAT
1 ATAATAAT
1990952 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:1994085 original size:131 final size:131
Alignment explanation
Indices: 1993851--1994109 Score: 437
Period size: 131 Copynumber: 2.0 Consensus size: 131
1993841 TAATTATTCG
* * ** *
1993851 TTTAAAATTTCTTTAAAACGAAGGCGATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACAAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
* **
1993916 ATGCTGGGTTGCAATTTCCTGTTTGTTCAAAATAATCGAATATCCCTTTGGAATTTCACTCATAT
66 ATGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCATAT
1993981 C
131 C
1993982 TTTAAAAATTCTTTAAAACAAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACAAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
*
1994047 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCAT
66 ATGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCAT
1994110 GTTTTCTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 119 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACAAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
ATGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCATAT
C
Found at i:1996962 original size:8 final size:9
Alignment explanation
Indices: 1996939--1996964 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1996929 GTTCAATCAA
1996939 AATTTTTAT
1 AATTTTTAT
1996948 AATTTTTAT
1 AATTTTTAT
1996957 AATTTTTA
1 AATTTTTA
1996965 CAATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATTTTTAT
Found at i:2001086 original size:2 final size:2
Alignment explanation
Indices: 2001079--2001104 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2001069 TGCTTTCTTT
2001079 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2001105 GTTTAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2001188 original size:23 final size:23
Alignment explanation
Indices: 2001171--2001214 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2001161 TTATAGTTTA
2001171 ATTT-TTATTTTGTTTATAAATT
1 ATTTGTTATTTTGTTTATAAATT
* *
2001193 ATTTGTTATTTTGGTTAAAAAT
1 ATTTGTTATTTTGTTTATAAAT
2001215 AAATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
ATTTGTTATTTTGTTTATAAATT
Found at i:2002652 original size:15 final size:15
Alignment explanation
Indices: 2002628--2002661 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2002618 AACAATTACG
* *
2002628 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
2002643 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
2002658 ATAA
1 ATAA
2002662 CAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:2003670 original size:10 final size:9
Alignment explanation
Indices: 2003655--2003692 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2003645 TAGCTTCTAT
2003655 AAACAACAAA
1 AAACAA-AAA
2003665 AAACAAAAA
1 AAACAAAAA
2003674 AAA-ACAAAA
1 AAACA-AAAA
2003683 AAACAAAAA
1 AAACAAAAA
2003692 A
1 A
2003693 GTCCTCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.04
9 18 0.69
10 7 0.27
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:2004732 original size:40 final size:40
Alignment explanation
Indices: 2004673--2004821 Score: 158
Period size: 40 Copynumber: 3.7 Consensus size: 40
2004663 TGTTTTTAGC
* *
2004673 CTGCTCCACTACTATTTAGGAAGATAAGACTGGATGTGAT
1 CTGCTCCACTACTACTTAGGGAGATAAGACTGGATGTGAT
*
2004713 CTGCTCCACTACTACTTAGGGAGATAAGATCTATGG-TTTCG-T
1 CTGCTCCACTACTACTTAGGGAGATAAGA-C--TGGATGT-GAT
* * ** *
2004755 CTGCTCCGCTACTGCTTAGGGAGATAAGACTTAATGCGAT
1 CTGCTCCACTACTACTTAGGGAGATAAGACTGGATGTGAT
* *
2004795 CTACTCCACTACAACTTAGGGAGATAA
1 CTGCTCCACTACTACTTAGGGAGATAA
2004822 AATTGTAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
39 2 0.02
40 52 0.58
41 2 0.02
42 30 0.33
43 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (40 bp):
CTGCTCCACTACTACTTAGGGAGATAAGACTGGATGTGAT
Found at i:2005100 original size:44 final size:45
Alignment explanation
Indices: 2004912--2005504 Score: 484
Period size: 44 Copynumber: 13.5 Consensus size: 45
2004902 GGGAGGTAAA
* * ** * * *
2004912 ATCTGCCATCTTCGATCTGCTTCGTTGCCAAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGACAAG
* * * * * * *
2004958 ATCTGCAATCCTCAATCTA-TTCCACTGTCAAATACAGG--GATAAG
1 ATCTGCTATCTTCGATCTACTT-CACT-ACCAATATAGGAAGACAAG
* * * *
2005002 ATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
2005047 ATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
2005090 ACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * * *
2005134 ATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* *
2005179 ATCTG-TATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * *
2005222 ATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
2005266 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
2005311 ATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
2005354 ATATGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * * * *
2005398 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
* * *
2005443 ATCTGC-ATCTTCGATCCA-TT---T-CCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
*
2005482 ATCAGCTATCTTCGATCTACTTC
1 ATCTGCTATCTTCGATCTACTTC
2005505 TTGCCCCGGG
Statistics
Matches: 428, Mismatches: 102, Indels: 38
0.75 0.18 0.07
Matches are distributed among these distances:
39 20 0.05
40 11 0.03
41 2 0.00
43 72 0.17
44 219 0.51
45 78 0.18
46 25 0.06
47 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAG
Found at i:2005184 original size:132 final size:132
Alignment explanation
Indices: 2004999--2005504 Score: 858
Period size: 132 Copynumber: 3.9 Consensus size: 132
2004989 ATACAGGGAT
* * * * *
2004999 AAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCC
1 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* * *
2005064 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAG
2005129 AC
131 AC
* *
2005131 AAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTCGATCC
1 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
2005196 ACTTCCTACCAATATAGGAAGACAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAG
2005261 AC
131 AC
2005263 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
*
2005328 ACTTCCTACCAATATAGGAAGATAGGATATGCTACCTTCGATCTACTTCACGCCAATACATGAAG
66 ACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAG
2005393 AC
131 AC
2005395 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
1 AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
* *
2005460 A-TT--T-CCAATATAGGAAGATAGGATCAGCTATCTTCGATCTACTTC
66 ACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTC
2005505 TTGCCCCGGG
Statistics
Matches: 358, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
128 38 0.11
129 1 0.00
131 2 0.01
132 317 0.89
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (132 bp):
AAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCC
ACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAG
AC
Found at i:2005718 original size:134 final size:134
Alignment explanation
Indices: 2005512--2005985 Score: 768
Period size: 134 Copynumber: 3.5 Consensus size: 134
2005502 TTCTTGCCCC
** * * * * *
2005512 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
* * * * *
2005577 AACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCACTGCCGAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
2005642 TACA
131 TACA
*
2005646 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
*
2005711 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTTCACTGCCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
2005776 TACA
131 TACA
*
2005780 AGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
2005845 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
2005910 TACA
131 TACA
* * *
2005914 GGGAAATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCGCATGGAGGTAAAATCTGCCATCC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
2005979 TTGATCT
64 TTGATCT
2005986 TCAATCTATT
Statistics
Matches: 317, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 289 0.91
136 28 0.09
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (134 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACA
Found at i:2005772 original size:46 final size:46
Alignment explanation
Indices: 2005588--2005915 Score: 156
Period size: 46 Copynumber: 7.3 Consensus size: 46
2005578 ACCTGCTTTG
* *
2005588 CTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
* * ** * * ** *
2005634 CTGCCGAATACAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGCA-AGATCTGCAATCTTCAATCTACTCCA
*** * * * * ** * * *
2005679 CTG--TGGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCG
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
* *
2005722 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTTCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
** * * ** *
2005768 CTGCCAAATACAAGG-AGATAGAGTTAT-C-GGCTTCAATGTACTCCA
1 CTGCCAAATAC-AGGAAGGCA-AGATCTGCAATCTTCAATCTACTCCA
* * * * * * ** * * *
2005813 CTG--TAGT-CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCG
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
*
2005856 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
2005902 CTGCCAAATACAGG
1 CTGCCAAATACAGG
2005916 GAAATAGAGT
Statistics
Matches: 196, Mismatches: 72, Indels: 28
0.66 0.24 0.09
Matches are distributed among these distances:
41 9 0.05
42 16 0.08
43 27 0.14
45 34 0.17
46 99 0.51
47 11 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTCCA
Found at i:2006051 original size:97 final size:95
Alignment explanation
Indices: 2005885--2006080 Score: 322
Period size: 97 Copynumber: 2.0 Consensus size: 95
2005875 AAGATCTGCA
*
2005885 ATCTTCAATCTATTCCACTGCCAAATACAGGGAAATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAAATAGAATTATCGGCTTCAATGTACTCCACTG
*
2005950 TAGTCGCATGGAGGTAAAATCTGCCATCCTT-G
66 TAGT--CAGGGAGGTAAAATCTGCCAT-CTTCG
* *
2005982 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAAATAGAATTATCGGCTTCAATGTACTCCACTG
2006047 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
2006077 ATCT
1 ATCT
2006081 GCTTCGCTGC
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
94 3 0.03
95 25 0.27
97 66 0.70
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAAATAGAATTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCG
Found at i:2006205 original size:86 final size:86
Alignment explanation
Indices: 2006070--2006333 Score: 429
Period size: 86 Copynumber: 3.1 Consensus size: 86
2006060 AAAATCTGCC
* * * * * * *
2006070 ATCTTCGATCTGCTTCGCTGCCAAATACAGAAAAGCAAGATCTGATATCTTCAACCAGCTCTGCT
1 ATCTTCGATCTGCTTCGCTGTC-AGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACT
*
2006135 ACAAACGAGAGAGGCGAGGTTT
65 ACAAACGAGAGAGGCAAGGTTT
* *
2006157 GTCTTTGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTA
1 ATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTA
2006222 CAAACGAGAGAGGCAAGGTTT
66 CAAACGAGAGAGGCAAGGTTT
2006243 ATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTA
1 ATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTA
2006308 CAAACGAGAGAGGCAAGGTTT
66 CAAACGAGAGAGGCAAGGTTT
2006329 ATCTT
1 ATCTT
2006334 TAATTTTTAC
Statistics
Matches: 165, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
86 146 0.88
87 19 0.12
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (86 bp):
ATCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTA
CAAACGAGAGAGGCAAGGTTT
Found at i:2006248 original size:41 final size:41
Alignment explanation
Indices: 2006201--2006333 Score: 110
Period size: 41 Copynumber: 3.1 Consensus size: 41
2006191 CAAGATCTGC
2006201 TATCTTCAACCAGCTCTACTACAAACGAGAGAGGCAAGGTT
1 TATCTTCAACCAGCTCTACTACAAACGAGAGAGGCAAGGTT
* * * * * ** *
2006242 TATCTTCGATCTGCT-TCGCTGTC-AGTGCAG-GAAGGCAAGATCT
1 TATCTTCAACCAGCTCT-ACT-ACAAACG-AGAG-AGGCAAGGT-T
2006285 GCTATCTTCAACCAGCTCTACTACAAACGAGAGAGGCAAGGTT
1 --TATCTTCAACCAGCTCTACTACAAACGAGAGAGGCAAGGTT
2006328 TATCTT
1 TATCTT
2006334 TAATTTTTAC
Statistics
Matches: 66, Mismatches: 16, Indels: 20
0.65 0.16 0.20
Matches are distributed among these distances:
40 1 0.02
41 23 0.35
42 11 0.17
43 2 0.03
44 11 0.17
45 17 0.26
46 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
TATCTTCAACCAGCTCTACTACAAACGAGAGAGGCAAGGTT
Found at i:2006293 original size:45 final size:45
Alignment explanation
Indices: 2006158--2006293 Score: 115
Period size: 45 Copynumber: 3.1 Consensus size: 45
2006148 GCGAGGTTTG
*
2006158 TCTTTGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTA
* * * * * ** *
2006203 TCTTCAACCAGC-TCTACT-ACA-AAC-GAGAGAGGCAAGGT-T--TA
1 TCTTCGATCTGCTTC-GCTGTCAGTGCAG-GA-AGGCAAGATCTGCTA
2006244 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTA
2006289 TCTTC
1 TCTTC
2006294 AACCAGCTCT
Statistics
Matches: 64, Mismatches: 17, Indels: 20
0.63 0.17 0.20
Matches are distributed among these distances:
41 13 0.20
42 13 0.20
43 8 0.12
44 13 0.20
45 17 0.27
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTA
Found at i:2006324 original size:44 final size:44
Alignment explanation
Indices: 2006188--2006324 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
2006178 CAGTGCAGGA
2006188 AGGCAAGATCTGCTATCTTCAACCAGCTCTACTACAAACGAGAG
1 AGGCAAGATCTGCTATCTTCAACCAGCTCTACTACAAACGAGAG
* * * * * * **
2006232 AGGCAAGGT-T--TATCTTCGATCTGCT-TCGCTGTC-AGTGCAG-G
1 AGGCAAGATCTGCTATCTTCAACCAGCTCT-ACT-ACAAACG-AGAG
2006273 AAGGCAAGATCTGCTATCTTCAACCAGCTCTACTACAAACGAGAG
1 -AGGCAAGATCTGCTATCTTCAACCAGCTCTACTACAAACGAGAG
2006318 AGGCAAG
1 AGGCAAG
2006325 GTTTATCTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
40 1 0.01
41 17 0.25
42 11 0.16
43 2 0.03
44 18 0.27
45 17 0.25
46 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAACCAGCTCTACTACAAACGAGAG
Found at i:2007312 original size:16 final size:16
Alignment explanation
Indices: 2007291--2007337 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
2007281 TGGCCTCTCC
2007291 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
*
2007307 TTTTTCTTTTTC--AT
1 TTTTTCTTTTTCTTTT
2007321 TTTTTCATTTTTCTTTT
1 TTTTTC-TTTTTCTTTT
2007338 CGTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 12 0.46
17 1 0.04
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTT
Found at i:2007344 original size:7 final size:6
Alignment explanation
Indices: 2007290--2007337 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
2007280 TTGGCCTCTC
2007290 CTTTTT CTTTTT C-TTTT -TTTTT CTTTTT CATTTTTT CATTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C--TTTTT C-TTTTT CTTTT
2007338 CGTTTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
5 8 0.22
6 17 0.46
7 6 0.16
8 6 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:2007346 original size:21 final size:21
Alignment explanation
Indices: 2007307--2007345 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2007297 TTTTTCTTTT
2007307 TTTTTCTTTTTCATTTTTTCA
1 TTTTTCTTTTTCATTTTTTCA
*
2007328 TTTTTC-TTTTCGTTTTTT
1 TTTTTCTTTTTCATTTTTT
2007346 TAGTGAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTCATTTTTTCA
Found at i:2007799 original size:35 final size:34
Alignment explanation
Indices: 2007755--2007829 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 34
2007745 CCAGTAGAGG
2007755 TTTTTCTTTTATTTGGT-TTTTTTATTT-TCTCATT
1 TTTTTCTTTT-TTTGGTCTTTTTT-TTTGTCTCATT
* *
2007789 TTTTTACTTTTTTTTGTCCTTTTTTTTTGTCTCTTT
1 TTTTT-CTTTTTTTGGT-CTTTTTTTTTGTCTCATT
2007825 TTTTT
1 TTTTT
2007830 TTGCCTCCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 10 0.29
35 8 0.23
36 17 0.49
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.79
Consensus pattern (34 bp):
TTTTTCTTTTTTTGGTCTTTTTTTTTGTCTCATT
Found at i:2007803 original size:13 final size:12
Alignment explanation
Indices: 2007771--2007831 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
2007761 TTTTATTTGG
2007771 TTTTTTTATTTTC
1 TTTTTTT-TTTTC
** *
2007784 TCATTTTTTTAC
1 TTTTTTTTTTTC
* *
2007796 TTTTTTTTGTCC
1 TTTTTTTTTTTC
2007808 TTTTTTTTTGTCTC
1 TTTTTTTTT-T-TC
2007822 TTTTTTTTTT
1 TTTTTTTTTT
2007832 GCCTCCACTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
12 20 0.54
13 7 0.19
14 10 0.27
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:2007803 original size:21 final size:22
Alignment explanation
Indices: 2007774--2007814 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2007764 TATTTGGTTT
2007774 TTTTATTTTCTCATTTTTTTAC
1 TTTTATTTTCTCATTTTTTTAC
* *
2007796 TTTT-TTTTGTCCTTTTTTT
1 TTTTATTTTCTCATTTTTTT
2007815 TTGTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTTCTCATTTTTTTAC
Found at i:2007810 original size:12 final size:13
Alignment explanation
Indices: 2007795--2007829 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2007785 CATTTTTTTA
2007795 CTTTTTTTTGTC-
1 CTTTTTTTTGTCT
2007807 CTTTTTTTTTGTCT
1 C-TTTTTTTTGTCT
2007821 CTTTTTTTT
1 CTTTTTTTT
2007830 TTGCCTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTGTCT
Found at i:2011098 original size:15 final size:15
Alignment explanation
Indices: 2011074--2011107 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2011064 AACAATTACG
* *
2011074 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
2011089 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
2011104 ATAA
1 ATAA
2011108 CAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:2012131 original size:8 final size:8
Alignment explanation
Indices: 2012109--2012141 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2012099 TTCTATAAAC
2012109 AACAAAAA
1 AACAAAAA
2012117 CAA-AAAAA
1 -AACAAAAA
2012125 AACAAAAA
1 AACAAAAA
2012133 AACAAAAA
1 AACAAAAA
2012141 A
1 A
2012142 GTCCTCTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.09
8 19 0.83
9 2 0.09
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AACAAAAA
Found at i:2012135 original size:18 final size:19
Alignment explanation
Indices: 2012105--2012141 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2012095 TAGCTTCTAT
2012105 AAACAACAAAAACAAAAAA
1 AAACAACAAAAACAAAAAA
2012124 AAACAA-AAAAACAAAAAA
1 AAACAACAAAAACAAAAAA
2012142 GTCCTCTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (19 bp):
AAACAACAAAAACAAAAAA
Found at i:2015432 original size:374 final size:376
Alignment explanation
Indices: 2014739--2015494 Score: 1417
Period size: 374 Copynumber: 2.0 Consensus size: 376
2014729 TTAACAGGAC
2014739 AAAATTAAGTATGGAACAAAATGAAAGTGAGAACAAGTTTATTTAATGATTTATTTGAAGTAATT
1 AAAATTAAGTATGGAACAAAATGAAAGTGAGAACAAGTTTATTTAATGATTTATTTGAAGTAATT
2014804 AGCTATTACAGTGATTTGTTGATTGATTTAAGATTTTATAAATATGGTGAATTTTTTAAAATAAA
66 AGCTATTACAGTGATTTGTTGATTGATTTAAGATTTTATAAATATGGTGAATTTTTTAAAATAAA
2014869 AATATTTAAATAACTATTTTAATTATAGTTTTAAATTATTTTTTTATAAGTACAATTTGCATTTT
131 AATATTTAAATAACTATTTTAATTATAGTTTTAAATTATTTTTTTATAAGTACAATTTGCATTTT
2014934 GGAATTACAATTAGACTCAATGCGTACGATGTATAAACAAAATTACAGGGTAAATTGAATTAGTA
196 GGAATTACAATTAGACTCAATGCGTACGATGTATAAACAAAATTACAGGGTAAATTGAATTAGTA
*
2014999 CAGAGGTGTCTATTATATTAGAATGTGAAAAATGAAAATGGTTATCAGGTTATTATATTAGGAGG
261 CAGAGGTGTCTATTATATTAGAATGTGAAAAATGAAAATGGTTATCAGGTTACTATATTAGGAGG
* *
2015064 CCCCA-AAAT-TAGGTAGCACACGAGACAAAATCAGGTAGTAAAATGGTGT
326 CCCCAGAAATCCAGGTAGCACACCAGACAAAATCAGGTAGTAAAATGGTGT
2015113 AAAATTAAGTATGGAACAAAATGAAAGTGAGAACAAGTTTATTTAATGATTTATTTGAAGTAATT
1 AAAATTAAGTATGGAACAAAATGAAAGTGAGAACAAGTTTATTTAATGATTTATTTGAAGTAATT
2015178 AGCTATTACAGTGATTTGTTGATTGATTTAAGATTTTATAAATATGGTGAATTTTTTAAAATAAA
66 AGCTATTACAGTGATTTGTTGATTGATTTAAGATTTTATAAATATGGTGAATTTTTTAAAATAAA
2015243 AATATTTAAATAACTATTTTAATTATAGTTTTAAATTATTTTTTTATAAGTACAATTTGCATTTT
131 AATATTTAAATAACTATTTTAATTATAGTTTTAAATTATTTTTTTATAAGTACAATTTGCATTTT
2015308 GGAATTACAATTAGACTCAATGCGTACGATGTATAAACAAAATTACAGGGTAAATTGAATTAGTA
196 GGAATTACAATTAGACTCAATGCGTACGATGTATAAACAAAATTACAGGGTAAATTGAATTAGTA
* *
2015373 CAGAGGTGTCTATTATATTAGAATGTGAAAAATGAAAATGGTTTTCAGGTTACTATATTAGGAGT
261 CAGAGGTGTCTATTATATTAGAATGTGAAAAATGAAAATGGTTATCAGGTTACTATATTAGGAGG
* * *
2015438 CCCCAGGTACTCCAGGTAGCACACCAGACAAAATCAGGTAGTAAAGTGGTGT
326 CCCCA-GAAATCCAGGTAGCACACCAGACAAAATCAGGTAGTAAAATGGTGT
2015490 AAAAT
1 AAAAT
2015495 AAATACTATT
Statistics
Matches: 371, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
374 327 0.88
376 2 0.01
377 42 0.11
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (376 bp):
AAAATTAAGTATGGAACAAAATGAAAGTGAGAACAAGTTTATTTAATGATTTATTTGAAGTAATT
AGCTATTACAGTGATTTGTTGATTGATTTAAGATTTTATAAATATGGTGAATTTTTTAAAATAAA
AATATTTAAATAACTATTTTAATTATAGTTTTAAATTATTTTTTTATAAGTACAATTTGCATTTT
GGAATTACAATTAGACTCAATGCGTACGATGTATAAACAAAATTACAGGGTAAATTGAATTAGTA
CAGAGGTGTCTATTATATTAGAATGTGAAAAATGAAAATGGTTATCAGGTTACTATATTAGGAGG
CCCCAGAAATCCAGGTAGCACACCAGACAAAATCAGGTAGTAAAATGGTGT
Found at i:2016485 original size:44 final size:44
Alignment explanation
Indices: 2016436--2016524 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2016426 AAATCTCAAA
2016436 CCCCAAAATTCAAGGTTTAAATTTAGAGTACAAAGTTCAGTATT
1 CCCCAAAATTCAAGGTTTAAATTTAGAGTACAAAGTTCAGTATT
2016480 CCCCAAAATTCAAGGTTTAAATTTAGAGTACAAAGTTCAGTATT
1 CCCCAAAATTCAAGGTTTAAATTTAGAGTACAAAGTTCAGTATT
2016524 C
1 C
2016525 GAGTTTGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (44 bp):
CCCCAAAATTCAAGGTTTAAATTTAGAGTACAAAGTTCAGTATT
Found at i:2026478 original size:17 final size:18
Alignment explanation
Indices: 2026456--2026495 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2026446 AAAAAAAAAG
2026456 AAAATAATT-TAACA-ATA
1 AAAATAATTATAA-ATATA
2026473 AAAATAATTATAAATATA
1 AAAATAATTATAAATATA
2026491 AAAAT
1 AAAAT
2026496 TCAAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATTATAAATATA
Found at i:2027851 original size:8 final size:8
Alignment explanation
Indices: 2027827--2027883 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
2027817 TAATGATATG
2027827 AATAATAA
1 AATAATAA
2027835 AATATATAA
1 AATA-ATAA
2027844 AATAATAA
1 AATAATAA
*
2027852 AATATTAA
1 AATAATAA
2027860 AAT-ATCAA
1 AATAAT-AA
* *
2027868 AATATTAG
1 AATAATAA
2027876 AATAATAA
1 AATAATAA
2027884 TAATTAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
7 1 0.03
8 30 0.75
9 9 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (8 bp):
AATAATAA
Found at i:2027860 original size:16 final size:16
Alignment explanation
Indices: 2027827--2027883 Score: 80
Period size: 16 Copynumber: 3.5 Consensus size: 16
2027817 TAATGATATG
2027827 AATAATAAAATATATAA
1 AATAATAAAATAT-TAA
2027844 AATAATAAAATATTAA
1 AATAATAAAATATTAA
*
2027860 AAT-ATCAAAATATTAG
1 AATAAT-AAAATATTAA
2027876 AATAATAA
1 AATAATAA
2027884 TAATTAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 2 0.05
16 20 0.54
17 15 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AATAATAAAATATTAA
Found at i:2028085 original size:22 final size:23
Alignment explanation
Indices: 2028031--2028093 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 23
2028021 CGTGATAATA
*
2028031 TTAAAATATGTACATAATATAGTG
1 TTAAAATATATACATAATATAG-G
2028055 TTAAAATATATACATAATATA-G
1 TTAAAATATATACATAATATAGG
*
2028077 TTAAGATATATACATAA
1 TTAAAATATATACATAA
2028094 GATAACATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 17 0.46
24 20 0.54
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (23 bp):
TTAAAATATATACATAATATAGG
Found at i:2028122 original size:29 final size:29
Alignment explanation
Indices: 2028082--2028148 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
2028072 TATAGTTAAG
*
2028082 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* *
2028111 ATATATAAATAATATAATATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
*
2028140 ATAAATAAA
1 ATATATAAA
2028149 ATAGTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:2028139 original size:27 final size:27
Alignment explanation
Indices: 2028082--2028191 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 27
2028072 TATAGTTAAG
* * *
2028082 ATATATACATAAGATAACATGTAAAATAT
1 ATATATAAATAATATAATAT-T-AAATAT
*
2028111 ATATATAAATAATATAATATT-AA-AG
1 ATATATAAATAATATAATATTAAATAT
* * *
2028136 ATATATAAATAAAATAGTATAAAATAT
1 ATATATAAATAATATAATATTAAATAT
**
2028163 ATATATACGTAATATAGA-ATTAAA-AT
1 ATATATAAATAATATA-ATATTAAATAT
2028189 ATA
1 ATA
2028192 CCTAATATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
25 19 0.29
26 9 0.14
27 19 0.29
28 1 0.02
29 17 0.26
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (27 bp):
ATATATAAATAATATAATATTAAATAT
Found at i:2028148 original size:14 final size:13
Alignment explanation
Indices: 2028103--2028158 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
2028093 AGATAACATG
*
2028103 TAAAATATATATA
1 TAAAATATATAAA
2028116 T-AAATAATATAATA
1 TAAAAT-ATATAA-A
2028130 TTAAAGATATATAAA
1 -TAAA-ATATATAAA
2028145 TAAAATAGTATAAA
1 TAAAATA-TATAAA
2028159 ATATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
12 4 0.11
13 9 0.25
14 11 0.31
15 2 0.06
16 8 0.22
17 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (13 bp):
TAAAATATATAAA
Found at i:2028241 original size:23 final size:25
Alignment explanation
Indices: 2028198--2028243 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2028188 TATACCTAAT
2028198 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
2028223 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
2028244 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:2028864 original size:30 final size:28
Alignment explanation
Indices: 2028803--2028907 Score: 126
Period size: 30 Copynumber: 3.7 Consensus size: 28
2028793 GGCTAGTTGT
*
2028803 GTGGAAAGGTGTGGCTAGTGGAGTTGTG
1 GTGGAAAGGTGTGGCTAGTGGAGTGGTG
*
2028831 GTGGAAAAGGAGTGGC-AGTGTAGAGTGGTG
1 GTGG-AAAGGTGTGGCTAGTG--GAGTGGTG
2028861 GTGGAAA-G-GTGGCTAGTGGAGTTGGTG
1 GTGGAAAGGTGTGGCTAGTGGAG-TGGTG
2028888 GTGGAAAAGGTGTGGCTAGT
1 GTGG-AAAGGTGTGGCTAGT
2028908 TGAAAAGTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.04
27 14 0.21
28 16 0.24
29 14 0.21
30 20 0.30
ACGTcount: A:0.22, C:0.04, G:0.50, T:0.25
Consensus pattern (28 bp):
GTGGAAAGGTGTGGCTAGTGGAGTGGTG
Found at i:2028872 original size:27 final size:27
Alignment explanation
Indices: 2028803--2028899 Score: 108
Period size: 28 Copynumber: 3.4 Consensus size: 27
2028793 GGCTAGTTGT
* *
2028803 GTGGAAAGGTGTGGCTAGTGGAGTTGTG
1 GTGGAAAAG-GTGGCTAGTGGAGTGGTG
2028831 GTGGAAAAGGAGTGGC-AGTGTAGAGTGGTG
1 GTGGAAAA-G-GTGGCTAGTG--GAGTGGTG
2028861 GTGG-AAAGGTGGCTAGTGGAGTTGGTG
1 GTGGAAAAGGTGGCTAGTGGAG-TGGTG
2028888 GTGGAAAAGGTG
1 GTGGAAAAGGTG
2028900 TGGCTAGTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.05
27 14 0.23
28 23 0.38
29 9 0.15
30 11 0.18
ACGTcount: A:0.23, C:0.03, G:0.51, T:0.24
Consensus pattern (27 bp):
GTGGAAAAGGTGGCTAGTGGAGTGGTG
Found at i:2029792 original size:161 final size:161
Alignment explanation
Indices: 2029570--2030023 Score: 539
Period size: 166 Copynumber: 2.8 Consensus size: 161
2029560 TATCTGAAGC
* *
2029570 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG-AATTGAAAA-TAGCTCAGCGC
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTG-AA-ACAGAAATT-AAAATTA-CTCA--GC
* * *
2029633 GTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTGAAAGGTA-AAATTGA
60 GTG-TCC-AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGA
*
2029697 AAAACGGAAATTGAAAAT-C-CGGCGTGTGA-TGAGGCT
123 AAAACGAAAATTGAAAATACTCGGCGTGTGACTGAGGCT
* * *
2029733 CAACTCGCCGCTCGCAATACGAG-TGATTTTTTTGCAATAGAAATTAAAATTACCTCAGCGTGTC
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAACAGAAATTAAAATTA-CTCAGCGTGTC
*
2029797 CTGAGGCTCAACTCACCTCTCGAAAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAA
65 C--AGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAA
*
2029862 TGAAAATTGAAAATACCTCGGCGTGTGACCTGAGGCT
127 CGAAAATTGAAAATA-CTCGGCGTGTGA-CTGAGGCT
* * *
2029899 CAACTCGCCTCTCACAACACGAGTTGA-TTTTTTGAAAACAGAAATTGAAATTACTCAGCGTGTC
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTG-AAACAGAAATTAAAATTACTCAGCGTGTC
* **
2029963 CTGAGCTCAAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTGAAA
65 CAG-GCTC-AACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAA
2030024 TACCTTAGCA
Statistics
Matches: 254, Mismatches: 23, Indels: 27
0.84 0.08 0.09
Matches are distributed among these distances:
158 2 0.01
159 24 0.09
160 34 0.13
161 34 0.13
162 11 0.04
163 21 0.08
164 35 0.14
165 16 0.06
166 59 0.23
167 18 0.07
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (161 bp):
CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAACAGAAATTAAAATTACTCAGCGTGTCC
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGAA
AATTGAAAATACTCGGCGTGTGACTGAGGCT
Found at i:2029930 original size:92 final size:89
Alignment explanation
Indices: 2029773--2029948 Score: 223
Period size: 94 Copynumber: 1.9 Consensus size: 89
2029763 TTTGCAATAG
* *
2029773 AAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGAAAATATGAGTTGATTTTT
1 AAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGAAAACACGAGTTGA--TTT
*
2029838 TTTTGAAAGGCAGAAATTGAAAAATGA
64 TTTTGAAA-ACAGAAATTGAAAAATGA
* * *
2029865 AAATTGAAAA-TACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTC-ACAACACGAGTTGA-T
1 AAATT-AAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGAAAACACGAGTTGATT
2029927 TTTTTGAAAACAGAAATTGAAA
63 TTTTTGAAAACAGAAATTGAAA
2029949 TTACTCAGCG
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
89 12 0.16
90 10 0.13
92 17 0.23
93 15 0.20
94 21 0.28
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (89 bp):
AAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGAAAACACGAGTTGATTTTT
TTGAAAACAGAAATTGAAAAATGA
Found at i:2029960 original size:166 final size:162
Alignment explanation
Indices: 2029570--2030302 Score: 595
Period size: 149 Copynumber: 4.7 Consensus size: 162
2029560 TATCTGAAGC
* * * *
2029570 CAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG-AATTGAAAATAGCTCAGCGCG
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAA-ACAGAAATTGAAATTACCTCA--GCG
* * * *
2029634 TGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTGAAAGGTA-AAATTGA
63 TG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGA
*
2029697 AAAACGGAAATTGAAAATCCGGCGTGTGATGAGGCT
127 AAAACGAAAATTGAAAATCCGGCGTGTGATGAGGCT
* * * *
2029733 CAACTCGCCGCTCGCAATACGAG-TGATTTTTTTG-CAATAGAAATTAAAATTACCTCAGCGTGT
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
*
2029796 CCTGAGGCTCAACTCACCTCTCGAAAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAA
66 CCTGAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAA
*
2029861 ATGAAAATTGAAAATACCTCGGCGTGTGACCTGAGGCT
130 ACGAAAATTGAAAAT--C-CGGCGTGTGA--TGAGGCT
* *
2029899 CAACTCGCCTCTCACAACACGAGTTGA-TTTTTTGAAAACAGAAATTGAAATTA-CTCAGCGTGT
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
** *
2029962 CCTGA-GCTCAAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAATTGAAAT
66 CCTGAGGCTC-AACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAA
* * **
2030025 AC----CTT----A----GCATGTTTTGAGGCT
130 ACGAAAATTGAAAATCCGGCGTGTGATGAGGCT
*** * * * * *
2030046 CAACTCATTTCTCACAAAATGAGTTGATTTTTTTGAAAACAGAAATTTGAAAATACCTCAGCATG
1 CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAA-TTGAAATTACCTCAGCGTG
* ** * *
2030111 TCTTGAGGCT-AACTCATTTCTCACAATATGAGTTGATTTTTTTTTTG--A---A-AAATAG-AA
65 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTGAAAGGCAGAAATTGAAA
** ** * * **
2030168 ATTGAAAA-T--ACCT-CAGCATGTCTTGAGGC-
129 AACGAAAATTGAAAATCCGGCGTGTGATGAGGCT
*** * * * *
2030197 CAACTCATTTCGTCGC-ATATGAGTTGA--ATTTTGAAAATAGAAATTTAAATTACCTCAGCGTG
1 CAACTCGCCTC-TCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
**
2030259 TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTT
65 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
2030303 AACAACAGAA
Statistics
Matches: 484, Mismatches: 57, Indels: 73
0.79 0.09 0.12
Matches are distributed among these distances:
144 2 0.00
145 5 0.01
146 1 0.00
147 30 0.06
148 49 0.10
149 76 0.16
150 13 0.03
151 33 0.07
152 16 0.03
156 1 0.00
158 2 0.00
159 24 0.05
160 32 0.07
161 37 0.08
162 11 0.02
163 21 0.04
164 35 0.07
165 16 0.03
166 62 0.13
167 18 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (162 bp):
CAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAA
CGAAAATTGAAAATCCGGCGTGTGATGAGGCT
Found at i:2030128 original size:74 final size:74
Alignment explanation
Indices: 2029865--2030594 Score: 737
Period size: 74 Copynumber: 9.9 Consensus size: 74
2029855 TGAAAAATGA
* * *** * * *
2029865 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAACACGAGTTGA-TTT
1 AAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
2029929 TTTGAAAACAG
64 TTTGAAAACAG
* * **
2029940 AAATTGAAATTA-CTCAGCGTGTCCTGA-GCTCAAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTC-AACTCATTTCTCGCAATATGAGTTGA-TTTT
2030003 TTTGAAAAACAG
64 TTTG-AAAACAG
* * * * *
2030015 AAATTG-AAATACCTTAGCATGTTTTGAGGCTCAACTCATTTCTCACAAAATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
2030079 TGAAAACAG
66 TGAAAACAG
* *
2030088 AAATTTGAAAATACCTCAGCATGTCTTGAGGCT-AACTCATTTCTCACAATATGAGTTGATTTTT
1 AAA-TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA---TT
*
2030152 TTTTTGAAAAATAG
62 TTTTTG-AAAACAG
* *
2030166 AAATTGAAAATACCTCAGCATGTCTTGAGGC-CAACTCATTTCGTCGC-ATATGAGTTGA--ATT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTC-TCGCAATATGAGTTGATTTTT
*
2030227 TTGAAAATAG
65 TTGAAAACAG
* * *
2030237 AAATTTAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
2030302 T-AACAACAG
66 TGAA-AACAG
* * * *
2030311 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTT-TCGCAGTATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA-TTTT
*
2030375 TTTGAAAGA-AA
64 TTTGAAA-ACAG
* *
2030386 AGAATTGAAAATA-CTCAACGTGTCTTGAGGCTC-ACTCATTTCTCGCAATATGAGTTGA-ATTT
1 A-AATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
2030448 TTGAAAA-AG
65 TTGAAAACAG
* * *
2030457 -AATTGAAATTACCTCAACGTGTCTTGAGGCT-AACTCATTTTTGCGCAATAATGAGTTGA--TT
1 AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCT-CGCAAT-ATGAGTTGATTTT
*
2030518 TTTGAAAATAG
64 TTTGAAAACAG
* * ** *
2030529 AAATTGAAATTACCTCAGCTCAGGGTTCCCGAGGCTCAACTCA-TTCTAGCAATATGAGTTGATT
1 AAATTGAAAATACCTCAG--C-GTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT
2030593 TT
62 TT
2030595 GAAAACAAAT
Statistics
Matches: 571, Mismatches: 46, Indels: 74
0.83 0.07 0.11
Matches are distributed among these distances:
69 10 0.02
70 28 0.05
71 60 0.11
72 74 0.13
73 30 0.05
74 137 0.24
75 120 0.21
76 24 0.04
77 70 0.12
78 18 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (74 bp):
AAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTT
TGAAAACAG
Found at i:2030142 original size:149 final size:148
Alignment explanation
Indices: 2029865--2030594 Score: 751
Period size: 149 Copynumber: 4.9 Consensus size: 148
2029855 TGAAAAATGA
* * * * *** * * *
2029865 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCACAACACGAGTTGATTTT
1 AAATTGAAATTACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCGCAAAATGAGTTGATTTT
**
2029930 TTGAAAACAGAAATTGAAATTA-CTCAGCGTGTCCTGA-GCTCAAACTCACCTCTCGCAATATGA
64 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC-AACTCATTTCTCGCAATATGA
2029993 GTTGATTTTTTTTGAAAAACAG
128 GTTGA-TTTTTTTGAAAAACAG
* * *
2030015 AAATTGAAA-TACCTTAGCATGTTTTGAGGCTCAACTCATTTCTCACAAAATGAGTTGATTTTTT
1 AAATTGAAATTACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAAATGAGTTGA-TTTTT
* * * *
2030079 TGAAAACAGAAATTTGAAAATACCTCAGCATGTCTTGAGGCT-AACTCATTTCTCACAATATGAG
65 TGAAAACAGAAA-TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
*
2030143 TTGATTTTTTTTTTGAAAAATAG
129 TTGA---TTTTTTTGAAAAACAG
* * *
2030166 AAATTGAAAATACCTCAGCATGTCTTGAGGC-CAACTCATTTCGTCGC-ATATGAGTTGA-ATTT
1 AAATTGAAATTACCTCAGCATGTCTTGAGGCTCAACTCATTTC-TCGCAAAATGAGTTGATTTTT
* *
2030228 TGAAAATAGAAATTTAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
65 TGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGT
*
2030293 TGATTTTTTT-AACAACAG
130 TGATTTTTTTGAAAAACAG
* * * **
2030311 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTT-TCGCAGTATGAGTTGATTTTT
1 AAATTGAAATTACCTCAGCATGTCTTGAGGCTCAACTCA-TTTCTCGCAAAATGAGTTGA--TTT
* * * *
2030375 TTTGAAAGA-AAAGAATTGAAAATA-CTCAACGTGTCTTGAGGCTC-ACTCATTTCTCGCAATAT
63 TTTGAAA-ACAGA-AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT
*
2030437 GAGTTGA-ATTTTTG-AAAA-AG
126 GAGTTGATTTTTTTGAAAAACAG
* * *
2030457 -AATTGAAATTACCTCAACGTGTCTTGAGGCT-AACTCATTTTTGCGCAATAATGAGTTGA-TTT
1 AAATTGAAATTACCTCAGCATGTCTTGAGGCTCAACTCATTTCT-CGCAA-AATGAGTTGATTTT
* * * *
2030519 TTGAAAATAGAAATTGAAATTACCTCAGCTCAGGGTTCCCGAGGCTCAACTCA-TTCTAGCAATA
64 TTGAAAACAGAAATTGAAATTACCTCAG--C-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATA
2030583 TGAGTTGATTTT
125 TGAGTTGATTTT
2030595 GAAAACAAAT
Statistics
Matches: 495, Mismatches: 56, Indels: 60
0.81 0.09 0.10
Matches are distributed among these distances:
142 11 0.02
143 17 0.03
144 7 0.01
145 72 0.15
146 37 0.07
147 66 0.13
148 74 0.15
149 108 0.22
150 32 0.06
151 49 0.10
152 22 0.04
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (148 bp):
AAATTGAAATTACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAAAATGAGTTGATTTTTT
GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
GATTTTTTTGAAAAACAG
Found at i:2030414 original size:297 final size:291
Alignment explanation
Indices: 2029919--2030594 Score: 841
Period size: 297 Copynumber: 2.3 Consensus size: 291
2029909 CTCACAACAC
* *
2029919 GAGTTGATTTTTTGAAAACAGAAATTGAAATTA-CTCAGCGTGTCCTGA-GCTCAAACTCACCTC
1 GAGTTGA-TTTTTGAAAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC-AACTCA-TTC
* **
2029982 TCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAATACCTTAGCATGTTTTGAGGCTC
63 TCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAATACCTCAGCATGTCCTGAGGCTC
* * *
2030047 AACTCATTTCTCACAAAATGAGTTGATTTTTTTGAAAACAGAAATTTGAAAATACCTCAGCATGT
127 AACTCACTTCTCACAAAATGAGTTGATTTTTTTGAAAACAGAAAATTGAAAATACCTCAACATGT
*
2030112 CTTGAGGCTAACTCATTTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTGAAAAT
192 CTTGAGGCTAACTCATTTCTCACAATATGAGTTGA----ATTTTTG-AAAA-AG-AATTGAAAAT
*
2030177 ACCTCAGCATGTCTTGAGGCCAACTCATTTCGT-CGC-AT-AT
250 ACCTCAACATGTCTTGAGGCCAACTCATTT-GTGCGCAATAAT
* *
2030217 GAGTTGAATTTTGAAAATAGAAATTTAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTC
1 GAGTTGATTTTTGAAAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA-TTCTC
* *
2030282 GCAATATGAGTTGATTTTTTT-AACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAA
65 GCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAA-TACCTCAGCATGTCCTGAGGCTCAA
* ** *
2030346 CTCACCTT-TCGCAGTATGAGTTGATTTTTTTTGAAAGA-A-AAGAATTGAAAATA-CTCAACGT
129 CTCA-CTTCTCACAAAATGAGTTGA-TTTTTTTGAAA-ACAGAA-AATTGAAAATACCTCAACAT
* * *
2030407 GTCTTGAGGCTCACTCATTTCTCGCAATATGAGTTGAATTTTTGAAAAAGAATTGAAATTACCTC
190 GTCTTGAGGCTAACTCATTTCTCACAATATGAGTTGAATTTTTGAAAAAGAATTGAAAATACCTC
* * *
2030472 AACGTGTCTTGAGGCTAACTCATTTTTGCGCAATAAT
255 AACATGTCTTGAGGCCAACTCATTTGTGCGCAATAAT
* *
2030509 GAGTTGATTTTTGAAAATAGAAATTGAAATTACCTCAGCTCAGGGTTCCCGAGGCTCAACTCATT
1 GAGTTGATTTTTGAAAATAGAAATTGAAATTACCTCAG--C-GTG-TCCTGAGGCTCAACTCATT
*
2030574 CTAGCAATATGAGTTGATTTT
62 CTCGCAATATGAGTTGATTTT
2030595 GAAAACAAAT
Statistics
Matches: 334, Mismatches: 30, Indels: 31
0.85 0.08 0.08
Matches are distributed among these distances:
289 1 0.00
290 39 0.12
291 4 0.01
292 42 0.13
293 6 0.02
294 1 0.00
295 24 0.07
296 32 0.10
297 110 0.33
298 70 0.21
299 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (291 bp):
GAGTTGATTTTTGAAAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTCTCG
CAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAATACCTCAGCATGTCCTGAGGCTCAACT
CACTTCTCACAAAATGAGTTGATTTTTTTGAAAACAGAAAATTGAAAATACCTCAACATGTCTTG
AGGCTAACTCATTTCTCACAATATGAGTTGAATTTTTGAAAAAGAATTGAAAATACCTCAACATG
TCTTGAGGCCAACTCATTTGTGCGCAATAAT
Found at i:2039209 original size:16 final size:16
Alignment explanation
Indices: 2039190--2039234 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2039180 TGTGAATAAT
2039190 AAATATATAAAATAT-A
1 AAATAT-TAAAATATCA
2039206 AAATATTAAAATATCA
1 AAATATTAAAATATCA
*
2039222 AAATATTAGAATA
1 AAATATTAAAATA
2039235 ATAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
AAATATTAAAATATCA
Found at i:2039215 original size:8 final size:8
Alignment explanation
Indices: 2039190--2039234 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
2039180 TGTGAATAAT
2039190 AAATATATA
1 AAATAT-TA
2039199 AAATA-TA
1 AAATATTA
2039206 AAATATTA
1 AAATATTA
*
2039214 AAATATCA
1 AAATATTA
2039222 AAATATTA
1 AAATATTA
*
2039230 GAATA
1 AAATA
2039235 ATAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 7 0.22
8 20 0.62
9 5 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AAATATTA
Found at i:2039447 original size:22 final size:24
Alignment explanation
Indices: 2039384--2039448 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
2039374 CGTGATAATA
*
2039384 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
2039409 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
2039432 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
2039449 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:2039483 original size:15 final size:14
Alignment explanation
Indices: 2039461--2039525 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 14
2039451 TAACATGTAG
2039461 AAAATATATATATA
1 AAAATATATATATA
2039475 AATAATATATAT-TA
1 AA-AATATATATATA
* *
2039489 AAGATATATAAAT-
1 AAAATATATATATA
*
2039502 AAAATA-GTATA-A
1 AAAATATATATATA
*
2039514 AATATATATATA
1 AAAATATATATA
2039526 CGTAATATAG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
12 8 0.20
13 16 0.40
14 7 0.17
15 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:2039598 original size:23 final size:25
Alignment explanation
Indices: 2039555--2039600 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2039545 TATACCTAAT
2039555 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
2039580 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
2039601 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:2040018 original size:22 final size:23
Alignment explanation
Indices: 2039978--2040022 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2039968 TTCTCTCCCA
2039978 AAAACTCTCCAAAAAAAATCCCCC
1 AAAACTCTCC-AAAAAAATCCCCC
2040002 AAAACTCTCC-AAAAAATCCCC
1 AAAACTCTCCAAAAAAATCCCC
2040023 TCCTCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
24 10 0.48
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (23 bp):
AAAACTCTCCAAAAAAATCCCCC
Found at i:2040178 original size:30 final size:31
Alignment explanation
Indices: 2040106--2040252 Score: 171
Period size: 30 Copynumber: 4.9 Consensus size: 31
2040096 TGTAGGTACA
* * *
2040106 AGTT-GTGGTGGAGCAA-CTGTGGTTAGTGG
1 AGTTGGTGGTGGAGAAAGGTGTGGCTAGTGG
* ** *
2040135 AGTAGGTAATGGAGCAA-GTGTGGCTAGTGG
1 AGTTGGTGGTGGAGAAAGGTGTGGCTAGTGG
*
2040165 ATTTGGTGGTGGAG-AAGGTGTGGCTAGTGG
1 AGTTGGTGGTGGAGAAAGGTGTGGCTAGTGG
*
2040195 AGTTGGTGGTGGA-AAAGGAGTGGCTAGTGG
1 AGTTGGTGGTGGAGAAAGGTGTGGCTAGTGG
2040225 AGTTGGTGGTGGA-AAAGGTGTGGCTAGT
1 AGTTGGTGGTGGAGAAAGGTGTGGCTAGT
2040253 TGAGAAAAGT
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
29 5 0.05
30 98 0.95
ACGTcount: A:0.21, C:0.05, G:0.47, T:0.27
Consensus pattern (31 bp):
AGTTGGTGGTGGAGAAAGGTGTGGCTAGTGG
Found at i:2049239 original size:30 final size:31
Alignment explanation
Indices: 2049203--2049267 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
2049193 TCTTTATAGT
*
2049203 TTTTTAAA-GGATTAAATA-AAAATTGTATCA
1 TTTTTAAAGGGACTAAATAGAAAATT-TATCA
*
2049233 TTTTTAAAGGGACTAAATAGAAAATTTTTCA
1 TTTTTAAAGGGACTAAATAGAAAATTTATCA
2049264 TTTT
1 TTTT
2049268 AAGGGGTCGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 17 0.55
32 6 0.19
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (31 bp):
TTTTTAAAGGGACTAAATAGAAAATTTATCA
Found at i:2060609 original size:16 final size:16
Alignment explanation
Indices: 2060588--2060620 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2060578 TTCGCTGTAT
*
2060588 TGGAATAGAGGCGTAA
1 TGGAATAGACGCGTAA
2060604 TGGAATAGACGCGTAA
1 TGGAATAGACGCGTAA
2060620 T
1 T
2060621 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGACGCGTAA
Found at i:2071098 original size:24 final size:23
Alignment explanation
Indices: 2071055--2071100 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2071045 AGTGTTGTTA
*
2071055 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2071078 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2071101 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2071852 original size:16 final size:16
Alignment explanation
Indices: 2071831--2071863 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2071821 ATCTTTTTAA
2071831 AATTATT-TTATCAAAT
1 AATTATTATT-TCAAAT
2071847 AATTATTATTTCAAAT
1 AATTATTATTTCAAAT
2071863 A
1 A
2071864 GAATCTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATTATTTCAAAT
Done.