Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 100 of 204
Found at i:30439731 original size:32 final size:32
Alignment explanation
Indices: 30439690--30439751 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
30439680 CACACGTTAG
*
30439690 ATTTTTGGCCCCAAAACTACTATTCTGACAAT
1 ATTTTTGGCCCCAAAACTACTATTCCGACAAT
*
30439722 ATTTTTGGCCCTAAAACTACTATTCCGACA
1 ATTTTTGGCCCCAAAACTACTATTCCGACA
30439752 CTTTAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.34
Consensus pattern (32 bp):
ATTTTTGGCCCCAAAACTACTATTCCGACAAT
Found at i:30445874 original size:5 final size:6
Alignment explanation
Indices: 30445853--30445890 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
30445843 AAATTACAAT
30445853 TAAAAA TAAAAGGA T-AAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAA--A TAAAAA TAAAAA TAAAAA TAAAAA T
30445891 TATTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 2 0.07
6 22 0.76
7 3 0.10
8 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:30446198 original size:21 final size:21
Alignment explanation
Indices: 30446172--30446213 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30446162 ACATACGAGG
30446172 ATGGGTATGCTTATCATGCCA
1 ATGGGTATGCTTATCATGCCA
*
30446193 ATGGGTGTGCTTATCATGCCA
1 ATGGGTATGCTTATCATGCCA
30446214 TCTTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
ATGGGTATGCTTATCATGCCA
Found at i:30448632 original size:51 final size:50
Alignment explanation
Indices: 30448497--30448685 Score: 229
Period size: 51 Copynumber: 3.7 Consensus size: 50
30448487 ACTATTATCA
* * *
30448497 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTT
* * *
30448546 TTACGGTCCACGTAGTAACCTTCACATAGTGCTACACATGTGACCAAAGCTT
1 TT-CGGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAG-TT
* * * *
30448598 TTCGGTACACATGGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TT
1 TTCGGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCA-AAGTT
*
30448648 TGTCGATACACGTAGTAGCCTTCACATAGTACTACACA
1 T-TCGGTACACGTAGTAGCCTTCACATAGTACTACACA
30448686 CGTGTTCATC
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 72 0.61
52 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTT
Found at i:30462595 original size:20 final size:20
Alignment explanation
Indices: 30462570--30462611 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
30462560 TCAAAATGCT
30462570 AATAGAGGCACTAAAGTGCA
1 AATAGAGGCACTAAAGTGCA
*
30462590 AATAGAGGCATTAAAGTGCA
1 AATAGAGGCACTAAAGTGCA
30462610 AA
1 AA
30462612 CCCATACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.17
Consensus pattern (20 bp):
AATAGAGGCACTAAAGTGCA
Found at i:30463878 original size:5 final size:5
Alignment explanation
Indices: 30463868--30463908 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
30463858 TTGTGCCGAA
* *
30463868 TCTTC TCTTC TCTTC TCTTC TCATC TCTT- T-TTC TCCTC TCT
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCT
30463909 ATTTTTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 26 0.87
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (5 bp):
TCTTC
Found at i:30464623 original size:27 final size:28
Alignment explanation
Indices: 30464579--30464911 Score: 341
Period size: 27 Copynumber: 12.3 Consensus size: 28
30464569 TGCGATTCGT
* *
30464579 GGGTAAAATTACT-GAAATACCCCCAAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* * *
30464606 GGGTAAAATT-CTCAAAATGCCCTTGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
*
30464633 GGGTAAAATTACT-GAAATACCCTTGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* * *
30464660 AGGTAAAATTAC-CAAAATACCC-CTAAA
1 GGGTAAAATTACTCGAAATACCCTC-GAA
* *
30464687 GGGTAAAATTAC-CAAAATACCCTCAAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* *
30464714 GGGTAAAATTACT-AAAATACCCTCGAT
1 GGGTAAAATTACTCGAAATACCCTCGAA
*
30464741 GGGTAAAATTA-TCGAAATACCCTCGAT
1 GGGTAAAATTACTCGAAATACCCTCGAA
* *
30464768 GAGTAAAATTA-TCGAAATACCCTTGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* *
30464795 GGGTAAAACTACT-GAAACACCCTCGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* * *
30464822 GGGTAAAATTAC-CAAAACACGCTCGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
* * *
30464849 AGGTAAAATTAC-CGAAATTCCCCCGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
*
30464876 GGGTAAAATTAC-CGAAATACCCCCGAA
1 GGGTAAAATTACTCGAAATACCCTCGAA
30464903 GGGTAAAAT
1 GGGTAAAAT
30464912 AACATTTATA
Statistics
Matches: 264, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.01
27 257 0.97
28 4 0.02
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (28 bp):
GGGTAAAATTACTCGAAATACCCTCGAA
Found at i:30465208 original size:26 final size:26
Alignment explanation
Indices: 30465113--30465204 Score: 130
Period size: 26 Copynumber: 3.5 Consensus size: 26
30465103 CAAATATTGT
* *
30465113 TACTGGTAGCTTTGCAGCGATACTGA
1 TACTGGCAGCTTTGCTGCGATACTGA
*
30465139 TACTGGCAGCTTTGCTGCGATACTGT
1 TACTGGCAGCTTTGCTGCGATACTGA
* * *
30465165 TACTGGCAGTTTTGTTGCGTTACTGA
1 TACTGGCAGCTTTGCTGCGATACTGA
30465191 TACTGGCAGCTTTG
1 TACTGGCAGCTTTG
30465205 TTGCAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTGA
Found at i:30465393 original size:30 final size:30
Alignment explanation
Indices: 30465320--30465461 Score: 128
Period size: 30 Copynumber: 4.8 Consensus size: 30
30465310 ATTTGTACTG
* *
30465320 ATTACTGTTTTGGGCTAAGGCCCAC-A-CT
1 ATTACTATATTGGGCTAAGGCCCACAATCT
* * * *
30465348 GTTACTGTATAGGGCTATGGCCCACAATCT
1 ATTACTATATTGGGCTAAGGCCCACAATCT
* *
30465378 ATTACTATTTTGGGCTAAGGCCCACACTCT
1 ATTACTATATTGGGCTAAGGCCCACAATCT
* *
30465408 GTTACTATATTGGGCTATGGCCCACACA-CT
1 ATTACTATATTGGGCTAAGGCCCACA-ATCT
** * *
30465438 GCTACTATATAGGGCTCAGGCCCA
1 ATTACTATATTGGGCTAAGGCCCA
30465462 GACTGATTCT
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 21 0.23
29 1 0.01
30 71 0.76
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (30 bp):
ATTACTATATTGGGCTAAGGCCCACAATCT
Found at i:30465444 original size:60 final size:58
Alignment explanation
Indices: 30465322--30465466 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 58
30465312 TTGTACTGAT
* * *
30465322 TACTGTTTTGGGCTAAGGCCCACACTGTTACTGTATAGGGCTATGGCCCACAATCTAT
1 TACTATTTTGGGCTAAGGCCCACACTGTTACTATATAGGGCTATGGCCCACAATCTAC
* *
30465380 TACTATTTTGGGCTAAGGCCCACACTCTGTTACTATATTGGGCTATGGCCCACACA-CTGC
1 TACTATTTTGGGCTAAGGCCCACA--CTGTTACTATATAGGGCTATGGCCCACA-ATCTAC
* * * *
30465440 TACTATATAGGGCTCAGGCCCAGACTG
1 TACTATTTTGGGCTAAGGCCCACACTG
30465467 ATTCTGCATG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
58 26 0.35
60 48 0.64
61 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (58 bp):
TACTATTTTGGGCTAAGGCCCACACTGTTACTATATAGGGCTATGGCCCACAATCTAC
Found at i:30467802 original size:21 final size:21
Alignment explanation
Indices: 30467776--30467895 Score: 77
Period size: 21 Copynumber: 5.8 Consensus size: 21
30467766 CAACCCAACT
30467776 AGAAGGGTGTTGTACCTCTTG
1 AGAAGGGTGTTGTACCTCTTG
* **
30467797 AGAAGGGAGTTGTACCTGGGTG
1 AGAAGGGTGTTGTACCT-CTTG
**
30467819 -GAAGGGTGTTGTA-C-CTAA
1 AGAAGGGTGTTGTACCTCTTG
** ***
30467837 ATTATCTTGTTGTACCTCTTG
1 AGAAGGGTGTTGTACCTCTTG
* **
30467858 AGAAGGGAGTTGTACCTGGGTG
1 AGAAGGGTGTTGTACCT-CTTG
30467880 -GAAGGGTGTTGTACCT
1 AGAAGGGTGTTGTACCT
30467896 AAATTATCTT
Statistics
Matches: 70, Mismatches: 24, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
19 8 0.11
20 2 0.03
21 56 0.80
22 4 0.06
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (21 bp):
AGAAGGGTGTTGTACCTCTTG
Found at i:30467878 original size:61 final size:61
Alignment explanation
Indices: 30467783--30467905 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
30467773 ACTAGAAGGG
30467783 TGTTGTACCTCTTGAGAAGGGAGTTGTACCTGGGTGGAAGGGTGTTGTACCTAAATTATCT
1 TGTTGTACCTCTTGAGAAGGGAGTTGTACCTGGGTGGAAGGGTGTTGTACCTAAATTATCT
30467844 TGTTGTACCTCTTGAGAAGGGAGTTGTACCTGGGTGGAAGGGTGTTGTACCTAAATTATCT
1 TGTTGTACCTCTTGAGAAGGGAGTTGTACCTGGGTGGAAGGGTGTTGTACCTAAATTATCT
30467905 T
1 T
30467906 AATCTACACG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (61 bp):
TGTTGTACCTCTTGAGAAGGGAGTTGTACCTGGGTGGAAGGGTGTTGTACCTAAATTATCT
Found at i:30470625 original size:24 final size:24
Alignment explanation
Indices: 30470563--30470614 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30470553 TTTCTAGAAG
* **
30470563 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAACATAATAT
30470587 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
30470611 ATTT
1 ATTT
30470615 GACTTTGATT
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:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:30475519 original size:24 final size:24
Alignment explanation
Indices: 30475470--30475523 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
30475460 TCTTTCTAGA
* * *
30475470 ATATTTAGTATTTATAAGTATGAT
1 ATATTTAGCATTTATAAGCATAAT
30475494 ATATTTAGCATTTATTAA-CATAAT
1 ATATTTAGCATTTA-TAAGCATAAT
30475518 ATATTT
1 ATATTT
30475524 GACTTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATTTAGCATTTATAAGCATAAT
Found at i:30475970 original size:16 final size:16
Alignment explanation
Indices: 30475928--30475983 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
30475918 ATATTTTTAA
*
30475928 ATTTT-TATTCTTTTTA
1 ATTTTATATT-TTTTTC
* *
30475944 ATTTCACATTTTTTTC
1 ATTTTATATTTTTTTC
*
30475960 ATTTTATATTTTTATC
1 ATTTTATATTTTTTTC
30475976 ATATTTAT
1 AT-TTTAT
30475984 TATATTAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTATATTTTTTTC
Found at i:30476345 original size:7 final size:7
Alignment explanation
Indices: 30476333--30476357 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30476323 CACTCATTAT
30476333 ATTTTAA
1 ATTTTAA
30476340 ATTTTAA
1 ATTTTAA
30476347 ATTTTAA
1 ATTTTAA
30476354 ATTT
1 ATTT
30476358 AATATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:30488415 original size:23 final size:23
Alignment explanation
Indices: 30488364--30488415 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
30488354 AAGGGGTGTT
*
30488364 ACAT-AAATAAATAAAATTAAGTG
1 ACATAAAATAAATAAAAATAAG-G
30488387 AC-TAAAATAAATAAGAAATAA-G
1 ACATAAAATAAATAA-AAATAAGG
30488409 ACATAAA
1 ACATAAA
30488416 TTGAGTGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (23 bp):
ACATAAAATAAATAAAAATAAGG
Found at i:30489979 original size:34 final size:35
Alignment explanation
Indices: 30489903--30489979 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 35
30489893 TTACTAAGTT
* **
30489903 GATCTGTTATAAGCATATTATTTGCTACTGTATTG
1 GATCTGTTATAAGCATATTATTTACTACCATATTG
30489938 GAT-TGTTATAAGCATATTGA-TTACTACCATATT-
1 GATCTGTTATAAGCATATT-ATTTACTACCATATTG
*
30489971 GTTCTGTTA
1 GATCTGTTA
30489980 AAAGTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.06
34 30 0.83
35 4 0.11
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (35 bp):
GATCTGTTATAAGCATATTATTTACTACCATATTG
Found at i:30497797 original size:20 final size:21
Alignment explanation
Indices: 30497758--30497799 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30497748 TATGAAATAT
**
30497758 TAAGTGAAAAATGTATTTAAA
1 TAAGTGAAAAACATATTTAAA
30497779 TAAGTGAAAAACATA-TTAAA
1 TAAGTGAAAAACATATTTAAA
30497799 T
1 T
30497800 TTTTTTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (21 bp):
TAAGTGAAAAACATATTTAAA
Found at i:30499438 original size:68 final size:68
Alignment explanation
Indices: 30499329--30499459 Score: 244
Period size: 68 Copynumber: 1.9 Consensus size: 68
30499319 GATTGTGTTA
30499329 GTTCGGAGGTGAAAATGCTTTAAATTTCGATCAGGATTGGATTGGATGTTTGATAGACAAATGAT
1 GTTCGGAGGTGAAAATGCTTTAAATTTCGATCAGGATTGGATTGGATGTTTGATAGACAAATGAT
30499394 ATT
66 ATT
* *
30499397 GTTCGGAGGTGAAAATGCTTTCAATTTCGATCAGGATTGGATTGGATGTTTGATAGATAAATG
1 GTTCGGAGGTGAAAATGCTTTAAATTTCGATCAGGATTGGATTGGATGTTTGATAGACAAATG
30499460 GTATAGTTAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (68 bp):
GTTCGGAGGTGAAAATGCTTTAAATTTCGATCAGGATTGGATTGGATGTTTGATAGACAAATGAT
ATT
Found at i:30505165 original size:18 final size:18
Alignment explanation
Indices: 30505142--30505176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30505132 CAAGAACAGG
*
30505142 AAGCATCAAAATGGTTTC
1 AAGCATCAAAATAGTTTC
*
30505160 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
30505177 GCCACATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:30521409 original size:7 final size:6
Alignment explanation
Indices: 30521374--30521406 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30521364 TAAACATAAA
*
30521374 AAAATT -AAATT GAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
30521407 ATTCTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:30525699 original size:21 final size:20
Alignment explanation
Indices: 30525673--30525716 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
30525663 TAAACAGCTG
30525673 AAAAATAAATCACAAAA-AAAT
1 AAAAATAAAT-A-AAAATAAAT
30525694 AAAAATAAATAAAAATAAAT
1 AAAAATAAATAAAAATAAAT
30525714 AAA
1 AAA
30525717 CCAATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 8 0.36
21 10 0.45
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAATAAATAAAAATAAAT
Found at i:30525705 original size:10 final size:10
Alignment explanation
Indices: 30525673--30525716 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
30525663 TAAACAGCTG
30525673 AAAAATAAAT
1 AAAAATAAAT
30525683 CACAAAA-AAAT
1 -A-AAAATAAAT
30525694 AAAAATAAAT
1 AAAAATAAAT
30525704 AAAAATAAAT
1 AAAAATAAAT
30525714 AAA
1 AAA
30525717 CCAATTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.13
10 18 0.58
11 5 0.16
12 4 0.13
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:30531395 original size:6 final size:6
Alignment explanation
Indices: 30531384--30531417 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
30531374 TAAAATATAT
30531384 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTGC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C TTT
30531418 GAAAAGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:30531569 original size:26 final size:26
Alignment explanation
Indices: 30531517--30531570 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
30531507 TAACTCGAAT
* *
30531517 AATTTCACTTGATTCAACTTGACTCG
1 AATTTCACTTCATTCAACTCGACTCG
* * *
30531543 AATTTCATTTCATTCGACTCGATTCG
1 AATTTCACTTCATTCAACTCGACTCG
30531569 AA
1 AA
30531571 AAAAATTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (26 bp):
AATTTCACTTCATTCAACTCGACTCG
Found at i:30532038 original size:21 final size:21
Alignment explanation
Indices: 30532011--30532061 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
30532001 TTTTTAAAAT
*
30532011 TAAAAAAATACAAATAATATAA
1 TAAAAATATA-AAATAATATAA
* *
30532033 TAAAAATTTAAAATAATATAT
1 TAAAAATATAAAATAATATAA
30532054 TAAAAATA
1 TAAAAATA
30532062 GTCAGAGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATATAAAATAATATAA
Found at i:30532166 original size:18 final size:18
Alignment explanation
Indices: 30532143--30532183 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
30532133 AGTTAAAAGC
*
30532143 AAATTTTCATTATAAAAA
1 AAATTTACATTATAAAAA
* *
30532161 AAATTTACATTTTATAAA
1 AAATTTACATTATAAAAA
30532179 AAATT
1 AAATT
30532184 CTACTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTACATTATAAAAA
Found at i:30532550 original size:16 final size:16
Alignment explanation
Indices: 30532531--30532582 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
30532521 ATTGGAAATG
*
30532531 AAATGATTATAACTTG
1 AAATGATTATAACTTA
* *
30532547 AAATAACTT-TTACTTA
1 AAATGA-TTATAACTTA
*
30532563 AAATGATTAAAACTTA
1 AAATGATTATAACTTA
30532579 AAAT
1 AAAT
30532583 AATTTAAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (16 bp):
AAATGATTATAACTTA
Found at i:30532597 original size:32 final size:33
Alignment explanation
Indices: 30532531--30532602 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
30532521 ATTGGAAATG
* * * *
30532531 AAATGATTATAACTTGAAATAACTTTTACTT-A
1 AAATGATTAAAACTTAAAATAACTTTAAATTAA
30532563 AAATGATTAAAACTTAAAATAA-TTTAAATCTAA
1 AAATGATTAAAACTTAAAATAACTTTAAAT-TAA
30532596 AAATGAT
1 AAATGAT
30532603 CTGAACACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.15
32 21 0.62
33 8 0.24
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (33 bp):
AAATGATTAAAACTTAAAATAACTTTAAATTAA
Found at i:30532615 original size:33 final size:32
Alignment explanation
Indices: 30532578--30532650 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
30532568 ATTAAAACTT
30532578 AAAATAATTTAAATCTAAAAATGATCTGAACAC
1 AAAATAATTTAAATCTAAAAATGATC-GAACAC
* * * * *
30532611 AAAATAACTTAAATTTGAAATTGATCGAACTC
1 AAAATAATTTAAATCTAAAAATGATCGAACAC
30532643 AAAATAAT
1 AAAATAAT
30532651 AATAAAGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (32 bp):
AAAATAATTTAAATCTAAAAATGATCGAACAC
Found at i:30547206 original size:20 final size:18
Alignment explanation
Indices: 30547181--30547222 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
30547171 ATGTTTAAGT
*
30547181 TTAATTAATTAAGGATTATA
1 TTAATTAATAAAGG-TTA-A
30547201 TTAATTAATAAAGGTTAA
1 TTAATTAATAAAGGTTAA
30547219 TTAA
1 TTAA
30547223 GTTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (18 bp):
TTAATTAATAAAGGTTAA
Found at i:30548363 original size:22 final size:22
Alignment explanation
Indices: 30548256--30548387 Score: 115
Period size: 22 Copynumber: 6.0 Consensus size: 22
30548246 TACTCTTTGT
* *
30548256 TTAGCACTTCGATGCTCTCT-A
1 TTAGCACTTTGGTGCTCTCTGA
*
30548277 TTTAGCACTTTGATGCTCTCTGA
1 -TTAGCACTTTGGTGCTCTCTGA
* * *
30548300 TCAACACTTTGGCGCTCTCTGA
1 TTAGCACTTTGGTGCTCTCTGA
* * * *
30548322 TCAACAC-TTGGTGCTATCTGC
1 TTAGCACTTTGGTGCTCTCTGA
* *
30548343 TTAGCACTTTAGTGCTCTCTGT
1 TTAGCACTTTGGTGCTCTCTGA
* *
30548365 TTAGCACTATGGTGTTCTCTGA
1 TTAGCACTTTGGTGCTCTCTGA
30548387 T
1 T
30548388 GTGGTGTAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
21 16 0.18
22 74 0.81
23 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (22 bp):
TTAGCACTTTGGTGCTCTCTGA
Found at i:30550030 original size:23 final size:22
Alignment explanation
Indices: 30549994--30550037 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
30549984 TTTAATTGAG
30549994 AAATTAATGTATTAAATTAAATT
1 AAATTAATGTATTAAA-TAAATT
30550017 AAATTAAATG-ATTAAATAAAT
1 AAATT-AATGTATTAAATAAAT
30550038 AATATTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTAATGTATTAAATAAATT
Found at i:30551147 original size:9 final size:9
Alignment explanation
Indices: 30551133--30551158 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30551123 TTTATTTTTA
30551133 AAAATATTT
1 AAAATATTT
30551142 AAAATATTT
1 AAAATATTT
30551151 AAAATATT
1 AAAATATT
30551159 ATATTTTAAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:30551281 original size:19 final size:18
Alignment explanation
Indices: 30551209--30551294 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 18
30551199 ATTTAGTCAT
* *
30551209 ATAATAAATTATTAATATA
1 ATAATAAATT-TTATTTTA
30551228 ATTAATATAATTTATTATTTT-
1 A-TAATA-AA-TT-TTATTTTA
30551249 -TAATAAA--TTA-TTTA
1 ATAATAAATTTTATTTTA
*
30551263 ATATTTAAATTTTATTTTA
1 ATA-ATAAATTTTATTTTA
30551282 ATAATAAATTTTA
1 ATAATAAATTTTA
30551295 AAAATAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 2 0.04
16 4 0.07
18 14 0.26
19 13 0.24
20 5 0.09
21 2 0.04
22 8 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATAAATTTTATTTTA
Found at i:30551292 original size:13 final size:14
Alignment explanation
Indices: 30551276--30551317 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
30551266 TTTAAATTTT
30551276 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
30551289 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
30551304 ATTTTAAATAATAT
1 ATTTT-AATAATAT
30551318 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:30551302 original size:16 final size:16
Alignment explanation
Indices: 30551280--30551316 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
30551270 AATTTTATTT
30551280 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
30551297 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
30551312 TAATA
1 TAATA
30551317 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:30551738 original size:14 final size:14
Alignment explanation
Indices: 30551719--30551745 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30551709 GAAAAGTAAG
30551719 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
30551733 TCATTTTCCAGAA
1 TCATTTTCCAGAA
30551746 GCCATTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:30551751 original size:14 final size:14
Alignment explanation
Indices: 30551720--30551754 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
30551710 AAAAGTAAGT
*
30551720 CATTTTCCAGAAAT
1 CATTTTCCAGAAAC
*
30551734 CATTTTCCAGAAGC
1 CATTTTCCAGAAAC
30551748 CATTTTC
1 CATTTTC
30551755 AGTTAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (14 bp):
CATTTTCCAGAAAC
Found at i:30552558 original size:25 final size:27
Alignment explanation
Indices: 30552530--30552587 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
30552520 AAATTTAAAA
*
30552530 TTTTTAAAAATAAAA-TAA-AATCAAT
1 TTTTTAAAAATAAAAGAAATAATCAAT
*
30552555 TTTTTAAAAATAAAAGAAATAATTAAT
1 TTTTTAAAAATAAAAGAAATAATCAAT
30552582 TTTTTA
1 TTTTTA
30552588 CTAGAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 15 0.52
26 2 0.07
27 12 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTTTAAAAATAAAAGAAATAATCAAT
Found at i:30552714 original size:10 final size:9
Alignment explanation
Indices: 30552671--30552717 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
30552661 AAAAACTAAT
30552671 ATTTTTAAA
1 ATTTTTAAA
30552680 A-TTTTAAA
1 ATTTTTAAA
30552688 ATTTTTTAAA
1 A-TTTTTAAA
30552698 ATGTTATTAAA
1 AT-TT-TTAAA
*
30552709 ATTTATAAA
1 ATTTTTAAA
30552718 TATAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 8 0.24
9 6 0.18
10 12 0.36
11 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:30552737 original size:9 final size:9
Alignment explanation
Indices: 30552725--30552749 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30552715 AAATATAATA
30552725 AAAAAATTC
1 AAAAAATTC
30552734 AAAAAATTC
1 AAAAAATTC
30552743 AAAAAAT
1 AAAAAAT
30552750 ATATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTC
Found at i:30553426 original size:19 final size:18
Alignment explanation
Indices: 30553385--30553429 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
30553375 TTTTTTTGTT
30553385 AATTTTTAATTTTTTGAA
1 AATTTTTAATTTTTTGAA
*
30553403 AATTTTTAATTTTATTTAA
1 AATTTTTAATTTT-TTGAA
*
30553422 TATTTTTA
1 AATTTTTA
30553430 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
AATTTTTAATTTTTTGAA
Found at i:30553438 original size:18 final size:20
Alignment explanation
Indices: 30553417--30553456 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30553407 TTTAATTTTA
*
30553417 TTTAATA-T-TTTTATAAAT
1 TTTAATAGTATTTTACAAAT
30553435 TTTAATAGTATTTTACAAAT
1 TTTAATAGTATTTTACAAAT
30553455 TT
1 TT
30553457 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTAATAGTATTTTACAAAT
Found at i:30553446 original size:28 final size:28
Alignment explanation
Indices: 30553389--30553447 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
30553379 TTTGTTAATT
**
30553389 TTTAATTTTTTGAAAATTTTTAATTTTA
1 TTTAATTTTTTGAAAATTTTTAATAGTA
30553417 TTTAATATTTTT-ATAAA-TTTTAATAGTA
1 TTTAAT-TTTTTGA-AAATTTTTAATAGTA
30553445 TTT
1 TTT
30553448 TACAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTAATTTTTTGAAAATTTTTAATAGTA
Found at i:30553589 original size:10 final size:9
Alignment explanation
Indices: 30553573--30553605 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
30553563 TAATGTTTTT
30553573 ATTTTTTAA
1 ATTTTTTAA
30553582 ACTTTTTTAA
1 A-TTTTTTAA
30553592 ATTTTTT-A
1 ATTTTTTAA
30553600 ATTTTT
1 ATTTTT
30553606 GCTAACGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 7 0.30
10 9 0.39
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:30553925 original size:29 final size:30
Alignment explanation
Indices: 30553893--30553960 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
30553883 TGCTTAAACG
*
30553893 AAGGGTAAACTTT-AC-AAAATGGTCAAAT
1 AAGGGTAAACTTTCACAAAAATGCTCAAAT
* *
30553921 AAAGGCCT-AACTTTCTCAAAAATGCTCAAAT
1 -AAGG-GTAAACTTTCACAAAAATGCTCAAAT
30553952 AAGGGTAAA
1 AAGGGTAAA
30553961 ATATTTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
29 11 0.35
30 8 0.26
31 12 0.39
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.24
Consensus pattern (30 bp):
AAGGGTAAACTTTCACAAAAATGCTCAAAT
Found at i:30554499 original size:27 final size:29
Alignment explanation
Indices: 30554468--30554522 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
30554458 TACTATTTAA
*
30554468 ATATTTAAA-T-ATTTTTTATCATAAGTG
1 ATATTTAAATTAATATTTTATCATAAGTG
*
30554495 ATATTTAAATTAATATTTTATCTTAAGT
1 ATATTTAAATTAATATTTTATCATAAGT
30554523 TGGTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 1 0.04
29 14 0.58
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (29 bp):
ATATTTAAATTAATATTTTATCATAAGTG
Found at i:30557281 original size:19 final size:17
Alignment explanation
Indices: 30557257--30557300 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
30557247 CAATGCATCT
*
30557257 AATAATTATACATATTACC
1 AATAATAATACAT-TT-CC
*
30557276 AATAATAATTCATTTCC
1 AATAATAATACATTTCC
30557293 AATAATAA
1 AATAATAA
30557301 AACACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATACATTTCC
Found at i:30561225 original size:90 final size:88
Alignment explanation
Indices: 30561025--30561228 Score: 221
Period size: 90 Copynumber: 2.3 Consensus size: 88
30561015 TAAACAGCAA
* * *** *
30561025 GAATAAATTCCGAAACAGATTTTA-TTCAATTTGATTTCTCATTTTTGGAAATAAAATTAAAAAA
1 GAATAAATCCCGAAACAGATTTTATTTCAATTTAAAAACTCATTTTTGGAAATAAAATCAAAAAA
* *
30561089 GAATAAAATCCGCTGAATGACGG
66 GAATAAAATCCGCTGAACGACAG
* * * * *
30561112 GAAGAAATCCCTAAGCAGGTTTTATTTTAATTTAAAAAACTCATTTTTGGAAATAAAATCAAAAT
1 GAATAAATCCCGAAACAGATTTTATTTCAATTT-AAAAACTCATTTTTGGAAATAAAATCAAAA-
** * * *
30561177 TGGAATAAAATCTGTTGAACGGCAG
64 AAGAATAAAATCCGCTGAACGACAG
30561202 GAATAAATCCCGAAACAGATTTTATTT
1 GAATAAATCCCGAAACAGATTTTATTT
30561229 ACTTTTTTTA
Statistics
Matches: 92, Mismatches: 22, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
87 19 0.21
88 7 0.08
89 25 0.27
90 41 0.45
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (88 bp):
GAATAAATCCCGAAACAGATTTTATTTCAATTTAAAAACTCATTTTTGGAAATAAAATCAAAAAA
GAATAAAATCCGCTGAACGACAG
Found at i:30561960 original size:15 final size:14
Alignment explanation
Indices: 30561926--30561960 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
30561916 TTTTATCCAC
30561926 TTTTTTAAAAAAAT
1 TTTTTTAAAAAAAT
*
30561940 TATTTTAAAAAAGAT
1 TTTTTTAAAAAA-AT
30561955 TTTTTT
1 TTTTTT
30561961 TTCTTTTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTTTAAAAAAAT
Found at i:30562643 original size:697 final size:694
Alignment explanation
Indices: 30561162--30562622 Score: 2169
Period size: 697 Copynumber: 2.1 Consensus size: 694
30561152 TCATTTTTGG
* *
30561162 AAATAAAATCAAAATTGGAATAAAA-TCTGTTGAACGGCAGGAATAAATCCCGAAACAGATTTTA
1 AAATAAAATCAAAATTGGAATAAAATTC-GTTGAACGGCGGGAATAAATCCCGAAACAAATTTTA
** * * *
30561226 TTTACTTTTTTTAAAATAATTTTAAAAATGATTTTTGTTTCTTTTTGCCTTGGTGTTTCATTTGT
65 TCCACTTTTTTT-AAATTATTTTAAAAAAGATTTTTGTTTCTTTTCGCCTTGGTGTTTCATTTGT
* * *
30561291 CTCGAATTAGAAGATTGTAAAAATAATAAGGATCTATCTTAAAGTTGTTAGACAAAACACATTAG
129 CTCGAATTAGAAGATTGCAAAAATAACAAGGATCTATCTTAAAGTTATTAGACAAAACACATTAG
* *
30561356 CGAACAAAATAAATTAAATATAAATAAACACATATAAAATAAGAATATAATCGTTTATTTTTAAT
194 CGAACAAAATAAATTAAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATTTTTAAT
** * * *
30561421 TTATCGAATACGAAGAACAATTAAAATTGAAATAAAATAAAATTTTAAATTAGAAGGAAGAATAG
259 TTATAAAATACGAAAAACAATGAAAATTGAAATAAAATAAAAGTTTAAATTAGAAGGAAGAATAG
* * * * *
30561486 GGATTTTACGAAACGTTGAGGCCTGTGAAACACAGTTTCCTTAAGACAGATTCAACCGCTCCTAC
324 GGATTTTACGAAACGTTGAGGCCTATGAAACACAATTCCCTTAAGACAGATTCAACCACCCCTAC
* ** *
30561551 GGTACTTGGAGAAACGTTGGTTGAATGTCTCCCAGGATACAACAACAACAGTAATCAAAGTAGGA
389 GGTACTTGGAGAAACATTGGTCAAATGTCTCCCAGGATACAACAACAACAATAATCAAAGTAGGA
* * *
30561616 GCACCTCTACAACGATCAACGAACGAACTTTGCCTTTTTCTATCACCGGAAAGTTTGAAAAATAC
454 ACACCTCTACAACGATCAACGAACAAACTTTGCCTTTTTCTATCACCGAAAAGTTTGAAAAATAC
* * *
30561681 GAAGAGGAAAAGGAAGAATTTTAAGAGCTATAGAATTTCGGTATAAGAAAAATATCAAAGTGTTG
519 AAAGAGGAAAAGGAAGAATTTTAAGAGCAACAGAATTTCGGTATAAGAAAAATATCAAAGTGTTG
30561746 GCTTAATACTACAGAAAACACAACATTTTATAGGCATGTAGGATGGTGGAAAATTTGGAAATAAC
584 GCTTAATACTACAGAAAACACAACATTTTATAGGCATGTAGGATGGTGGAAAATTTGGAAATAAC
* *
30561811 CACAAAATTTGCCATTAAAGAGCAAAAAAAAATCCGTACTGGGCTA
649 CACAAAATCTACCATTAAAGAGCAAAAAAAAATCCGTACTGGGCTA
* * * *
30561857 AAATAAAATCAAAATTGGAATGAAATTCGTTGAACGACGGGAATAAATCCCAAAACATATTTTAT
1 AAATAAAATCAAAATTGGAATAAAATTCGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
* * *
30561922 CCACTTTTTTAAAAAAATTATTTTAAAAAAGATTTTTTTTTCTTTTCGCCTTGGTGTTTCGTTTG
66 CCACTTTTTT---TAAATTATTTTAAAAAAGATTTTTGTTTCTTTTCGCCTTGGTGTTTCATTTG
* * *
30561987 TCTCGGATTAG-AGAATTGCAAAAATAACAGGGATCTATCTT-AAGATTATTAGACAAAACACGT
128 TCTCGAATTAGAAG-ATTGCAAAAATAACAAGGATCTATCTTAAAG-TTATTAGACAAAACACAT
* *
30562050 TAGTGAACAAAATAAATTAAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTGTTTTT
191 TAGCGAACAAAATAAATTAAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATTTTT
* *
30562115 AATTTATAAAATACGAAAAACAATGAAAATT-AAAGTCAAATAAAAGTTTAAATTAGAAGGACGA
256 AATTTATAAAATACGAAAAACAATGAAAATTGAAA-TAAAATAAAAGTTTAAATTAGAAGGAAGA
*
30562179 ATAGGGATTTTACGAAACGTTGAGGCCTATGAAACACAATTCCCTTAAGACAGATTCGACCACCC
320 ATAGGGATTTTACGAAACGTTGAGGCCTATGAAACACAATTCCCTTAAGACAGATTCAACCACCC
*** *
30562244 CTACGGTACTTGGAGAAACATTGGTCAAATGTCTTTTAGGATACAACAACAACAATGATCAAAGT
385 CTACGGTACTTGGAGAAACATTGGTCAAATGTCTCCCAGGATACAACAACAACAATAATCAAAGT
* *
30562309 AGTAACACCTCTACAACGATCAACGAACAAACTTTGCCTTTTTTTATCACCGAAAAGTTTGAAAA
450 AGGAACACCTCTACAACGATCAACGAACAAACTTTGCCTTTTTCTATCACCGAAAAGTTTGAAAA
*
30562374 ATACAAAGAGGAAAAGGAAGAATTTTGAA-AGCAACAGAATTTCGGTATAAGAAAAATATCAGAG
515 ATACAAAGAGGAAAAGGAAGAATTTT-AAGAGCAACAGAATTTCGGTATAAGAAAAATATCAAAG
* * * *
30562438 TGTTGGTTTAAT-CTTATAGAAAACACAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTGGA
579 TGTTGGCTTAATAC-TACAGAAAACACAACATTTTATAGGCATGTAGGATGGTGGAAAATTTGGA
* * * * **
30562502 AATAACTACAAAATCTACCATTAATGAGCTAAAAATAAATTCGTGTTGGGCTA
643 AATAACCACAAAATCTACCATTAAAGAGC-AAAAAAAAATCCGTACTGGGCTA
* *
30562555 AAATAAAATCAAAATTGGAATAAAATTCGTTGAACGGTGGGAATAAATCTCGAAACAAATTTTAT
1 AAATAAAATCAAAATTGGAATAAAATTCGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
30562620 CCA
66 CCA
30562623 TGTTTATCTT
Statistics
Matches: 685, Mismatches: 71, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
695 65 0.09
696 11 0.02
697 526 0.77
698 83 0.12
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (694 bp):
AAATAAAATCAAAATTGGAATAAAATTCGTTGAACGGCGGGAATAAATCCCGAAACAAATTTTAT
CCACTTTTTTTAAATTATTTTAAAAAAGATTTTTGTTTCTTTTCGCCTTGGTGTTTCATTTGTCT
CGAATTAGAAGATTGCAAAAATAACAAGGATCTATCTTAAAGTTATTAGACAAAACACATTAGCG
AACAAAATAAATTAAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATTTTTAATTT
ATAAAATACGAAAAACAATGAAAATTGAAATAAAATAAAAGTTTAAATTAGAAGGAAGAATAGGG
ATTTTACGAAACGTTGAGGCCTATGAAACACAATTCCCTTAAGACAGATTCAACCACCCCTACGG
TACTTGGAGAAACATTGGTCAAATGTCTCCCAGGATACAACAACAACAATAATCAAAGTAGGAAC
ACCTCTACAACGATCAACGAACAAACTTTGCCTTTTTCTATCACCGAAAAGTTTGAAAAATACAA
AGAGGAAAAGGAAGAATTTTAAGAGCAACAGAATTTCGGTATAAGAAAAATATCAAAGTGTTGGC
TTAATACTACAGAAAACACAACATTTTATAGGCATGTAGGATGGTGGAAAATTTGGAAATAACCA
CAAAATCTACCATTAAAGAGCAAAAAAAAATCCGTACTGGGCTA
Found at i:30572566 original size:20 final size:20
Alignment explanation
Indices: 30572541--30572581 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
30572531 TATTCTCTGA
30572541 AAAGTTTCAATTATGTAATG
1 AAAGTTTCAATTATGTAATG
30572561 AAAGTTTCAATTATGTAATG
1 AAAGTTTCAATTATGTAATG
30572581 A
1 A
30572582 TGTAAGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (20 bp):
AAAGTTTCAATTATGTAATG
Found at i:30572729 original size:17 final size:17
Alignment explanation
Indices: 30572703--30572754 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
30572693 CAAAACTCGA
*
30572703 TTCTCAAAATTTTAAGT
1 TTCTCCAAATTTTAAGT
30572720 TTCTCCAAATTTTTAAGT
1 TTCTCCAAA-TTTTAAGT
*
30572738 TT-T-CAAAATTTAAGT
1 TTCTCCAAATTTTAAGT
30572753 TT
1 TT
30572755 TAAATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 9 0.28
16 4 0.12
17 9 0.28
18 10 0.31
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTCCAAATTTTAAGT
Found at i:30574150 original size:16 final size:15
Alignment explanation
Indices: 30574116--30574148 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30574106 TTTTATCCAC
30574116 TTTTAAAAAAAATTA
1 TTTTAAAAAAAATTA
*
30574131 TTTTAAAAATAATT-
1 TTTTAAAAAAAATTA
30574145 TTTT
1 TTTT
30574149 TTTCTTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTAAAAAAAATTA
Found at i:30574719 original size:694 final size:694
Alignment explanation
Indices: 30572864--30575096 Score: 3324
Period size: 694 Copynumber: 3.2 Consensus size: 694
30572854 GATAATCTGG
* *
30572864 AAATATAAATAAATACATATAAAATAAGAATAAAATAGTTTATATTTAATTTATCAAATACGAAA
1 AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
30572929 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAGAAGGAAGAATAGGGATTTTACGAAAC
66 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATT---AGGAAGAATA-GGATTTTACGAAAC
* *
30572994 GTT-AGGGCCTGTGAAACACAGTTTCCTTAAGACAGATTCGACCGCTCCTACGGTACTTGGAGAA
127 GTTGA-GGACTGTGAAACACAATTTCCTTAAGACAGATTCGACCGCTCCTACGGTACTTGGAGAA
* * * *
30573058 ATGTTAGTCGAATGTCTCCCA--A-AATACAACAAAAGTGATCAAAGTAGTAGCACCTCTACAAC
191 ACGTTGGTCGAATGTCTCCCAGGATACTACAACAACAGTGATCAAAGTAGTAGCACCTCTACAAC
* ** *
30573120 AATCAACGGACGAACTTTGTC-TTTCTATCACCGGAAAGTTTGAAAAATAAGAAGAGGAAAAGGA
256 GATCAACGGACGAACTTTACCTTTTCTATCACCGGAAAGTTTGAAAAATACGAAGAGGAAAAGGA
*
30573184 AGTATTTTGAGAGCAACAGAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAG
321 AGAATTTTGAGAGCAACAGAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAG
*
30573249 AAAACATAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCA
386 AAAATATAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCA
* * *
30573314 TTAAGGAGCCAAAAATAAATTCGTGCTGGGTAAAAATAAAATCAAAATTGGAATAAAA-TCTGCT
451 TTAAGGAGCCAAAAATAAATTCGTGTTGGGCAAAAATAAAATCAAAATTGGAATAAAATTC-GTT
* * * *
30573378 GAACGGA-GGGAATAAATCTCGAAATAGATTTTACCCACTTTTTTAAAATAATTATTTTAAAAAT
515 GAAC-GACGGGAATAAATCTCGAAACAGATTTTATCCACTTTTTAAAAAAAATTATTTTAAAAAT
* * *
30573442 GATGTTTTTTTTTCTTTTCGCCTTGGTGTTTCGTTCGTCTTGGATTAGAGAATTGCAAAAATAAT
579 -A-ATTTTTTTTTCTTTTCGCCTTGGTGTTTCGTTTGTCTTGGATTAGAGAATTGCAAAAATAAC
* * * *
30573507 AAGGATCTGCCTTAAGATTGTTAAACAAAACACGTTAGTA-AACAAAATAAATG
642 AAGGATCTGTCTTAAGATTGTTAGACAAAACAAGTTAG-AGAACAAAATAAATT
* * *
30573560 AAATATAAATAAACACACATAAAATAAGAATAGAATAGTTTATATTTAGTTTATAAAATAC-AAA
1 AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
*
30573624 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAGAAGAAAGAATAGAGATTTTATGAAAC
66 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAG--G-AAGAATAG-GATTTTACGAAAC
* * *
30573689 ATTGAGGACTATGAAACACAATTTCCTTAAGACAGATTCGGCCGCTCCTACGGTACTTGGAGAAA
127 GTTGAGGACTGTGAAACACAATTTCCTTAAGACAGATTCGACCGCTCCTACGGTACTTGGAGAAA
* * *
30573754 CGTTGGTCGAATGTCTCTCAGGATACAACAACAACAGTGGTCAAAGTAGTAGCACCTCTACAACG
192 CGTTGGTCGAATGTCTCCCAGGATACTACAACAACAGTGATCAAAGTAGTAGCACCTCTACAACG
* * *
30573819 ATCAACGGACGAACTTTGTCTTTTTCTATCACCGGAAAGTTTGAAAAATACGAAGAGGAAATGGA
257 ATCAACGGACGAACTTT-ACCTTTTCTATCACCGGAAAGTTTGAAAAATACGAAGAGGAAAAGGA
* *
30573884 AGAATTTTGAGAGCTACAGAATTTTGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAG
321 AGAATTTTGAGAGCAACAGAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAG
* * * *
30573949 AAAATATAGCCTTTTATAGGCATGCAGGATGGTGGAAAATTTGGACATAACCACAAAATCTGTCA
386 AAAATATAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCA
*
30574014 TTAAGGAGCCAAAAATAAATTCGTATTGGGCAAAAATAAAATCAAAATTGGAATAAAATTCGTTG
451 TTAAGGAGCCAAAAATAAATTCGTGTTGGGCAAAAATAAAATCAAAATTGGAATAAAATTCGTTG
**
30574079 AATAACGGGAATAAATCTCGAAACAGATTTTATCCAC-TTTTAAAAAAAATTATTTTAAAAATAA
516 AACGACGGGAATAAATCTCGAAACAGATTTTATCCACTTTTTAAAAAAAATTATTTTAAAAATAA
* *
30574143 TTTTTTTTTCTTTTCGCCTTAGTGTTTCGTTTGTCTTTGATTAGAGAATTGCAAAAATAACAAGG
581 TTTTTTTTTCTTTTCGCCTTGGTGTTTCGTTTGTCTTGGATTAGAGAATTGCAAAAATAACAAGG
* * * *
30574208 ATCTGTCTTAACATTGTTAGACAAAACATGTTAGCGGACAAAATAAATT
646 ATCTGTCTTAAGATTGTTAGACAAAACAAGTTAGAGAACAAAATAAATT
*
30574257 AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGTAA
1 AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
* * * * * *
30574322 AAATAATCAAAATTAAAATCAAATCAAATTTTATATTAGGAGGAATATGGATTTTACAAAACGTT
66 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAGGAAGAATA-GGATTTTACGAAACGTT
* * *
30574387 GA-GACTTGTGAAACACAATTTTCTTAAGACAGATTCGACTGCTCCTACAGTACTTGGAGAAACG
130 GAGGAC-TGTGAAACACAATTTCCTTAAGACAGATTCGACCGCTCCTACGGTACTTGGAGAAACG
* * *
30574451 TTGGTTGAATGTCCCCCAGGATACTACAACAACAGTGATCAAAGTAGTAGCACCTCTACAATGAT
194 TTGGTCGAATGTCTCCCAGGATACTACAACAACAGTGATCAAAGTAGTAGCACCTCTACAACGAT
* * *
30574516 CAACGAACGAACTTTACCTTTTCTATCACCGAAAAGTTTGAAAAATACGAATAGGAAAAGGAAGA
259 CAACGGACGAACTTTACCTTTTCTATCACCGGAAAGTTTGAAAAATACGAAGAGGAAAAGGAAGA
* *
30574581 ATTTTGAGAGCAACAAAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTATAGAAA
324 ATTTTGAGAGCAACAGAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAGAAA
*
30574646 ATATAGCCTTTTATAGGCATGTAGAATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCATTA
389 ATATAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCATTA
* * * * * *
30574711 AAGAGCCAAAAAGAAATTCGTGTTGGGCTAAAATAAAATTAATATTGGAATAAAATCCGTTGAAC
454 AGGAGCCAAAAATAAATTCGTGTTGGGCAAAAATAAAATCAAAATTGGAATAAAATTCGTTGAAC
* *
30574776 GGCGAGAATAAATCTCGAAACAGATTTTATCCACTTTTTAAAAAAAATTATTTTAAAAATAA-TT
519 GACGGGAATAAATCTCGAAACAGATTTTATCCACTTTTTAAAAAAAATTATTTTAAAAATAATTT
* *
30574840 TTTTTTCTATTCGCCTTGGTGTTTCGTTTGTCTCGGATTAGAGAATTGCAAAAATAACAAGGATC
584 TTTTTTCTTTTCGCCTTGGTGTTTCGTTTGTCTTGGATTAGAGAATTGCAAAAATAACAAGGATC
30574905 TGTCTTAAGATTGTTAGAC--AACAAGTTAGAGAACAAAATAAATT
649 TGTCTTAAGATTGTTAGACAAAACAAGTTAGAGAACAAAATAAATT
**
30574949 AAATATAAATAAACACATATAAAGCAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
1 AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
* * * * * *
30575014 AAATAATCAAAATAAAAATCAAATAAAAGTTTAAACTAGAAAGGAAAATAGATATTTTACGAAAT
66 AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAGGAA-G--AATAG-GATTTTACGAAAC
* *
30575079 GTTAAGGCCTGTGAAACA
127 GTTGAGGACTGTGAAACA
30575097 TAGTGTGCAC
Statistics
Matches: 1389, Mismatches: 126, Indels: 45
0.89 0.08 0.03
Matches are distributed among these distances:
692 121 0.09
693 1 0.00
694 341 0.25
695 335 0.24
696 61 0.04
697 161 0.12
698 91 0.07
699 24 0.02
700 252 0.18
701 2 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (694 bp):
AAATATAAATAAACACATATAAAATAAGAATAGAATAGTTTATATTTAATTTATCAAATACGAAA
AAACAATCAAAATTAAAATCAAATAAAAGTTTAAATTAGGAAGAATAGGATTTTACGAAACGTTG
AGGACTGTGAAACACAATTTCCTTAAGACAGATTCGACCGCTCCTACGGTACTTGGAGAAACGTT
GGTCGAATGTCTCCCAGGATACTACAACAACAGTGATCAAAGTAGTAGCACCTCTACAACGATCA
ACGGACGAACTTTACCTTTTCTATCACCGGAAAGTTTGAAAAATACGAAGAGGAAAAGGAAGAAT
TTTGAGAGCAACAGAATTTCGGTATAAGAAAAATATCAGAGTGTTGGTTTAATCCTACAGAAAAT
ATAGCCTTTTATAGGCATGTAGGATGGTGGAAAATTTAGAAATAACCACAAAATCTGCCATTAAG
GAGCCAAAAATAAATTCGTGTTGGGCAAAAATAAAATCAAAATTGGAATAAAATTCGTTGAACGA
CGGGAATAAATCTCGAAACAGATTTTATCCACTTTTTAAAAAAAATTATTTTAAAAATAATTTTT
TTTTCTTTTCGCCTTGGTGTTTCGTTTGTCTTGGATTAGAGAATTGCAAAAATAACAAGGATCTG
TCTTAAGATTGTTAGACAAAACAAGTTAGAGAACAAAATAAATT
Found at i:30574844 original size:15 final size:15
Alignment explanation
Indices: 30574810--30574844 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30574800 TTTTATCCAC
30574810 TTTTTAAAAAAAATT
1 TTTTTAAAAAAAATT
* *
30574825 ATTTTAAAAATAATT
1 TTTTTAAAAAAAATT
30574840 TTTTT
1 TTTTT
30574845 TCTATTCGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTTAAAAAAAATT
Found at i:30579352 original size:29 final size:30
Alignment explanation
Indices: 30579286--30579360 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 30
30579276 TTTATATCTT
*
30579286 TATAATTTTTTATAATTTTTAAAGGATTAAAT
1 TATAA-TTTTTATAATTTTTAAA-GATTAAAG
*
30579318 TA-AATTTTTATATTTTTTAAA-ATTAAAG
1 TATAATTTTTATAATTTTTAAAGATTAAAG
30579346 TATAA-TTTTATAATT
1 TATAATTTTTATAATT
30579361 ACTAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 17 0.44
29 2 0.05
30 16 0.41
31 2 0.05
32 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
TATAATTTTTATAATTTTTAAAGATTAAAG
Found at i:30580459 original size:2 final size:2
Alignment explanation
Indices: 30580454--30580487 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30580444 ATGATAGAAA
30580454 AT AT 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 AT AT
30580488 TTCTTTCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30586922 original size:25 final size:25
Alignment explanation
Indices: 30586894--30586949 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
30586884 AAAAACCTTT
30586894 TTAAATCATATTTGATTCATAAATA
1 TTAAATCATATTTGATTCATAAATA
30586919 TTAAATCATATTTGATTCATAAATA
1 TTAAATCATATTTGATTCATAAATA
30586944 TTAAAT
1 TTAAAT
30586950 AATAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (25 bp):
TTAAATCATATTTGATTCATAAATA
Found at i:30591143 original size:92 final size:92
Alignment explanation
Indices: 30591027--30591220 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 92
30591017 TTGATTTTAG
*
30591027 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAAAACATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* * *
30591092 ATTTAAT-ATTAATTATTTTAAATTGTA
66 ATGTAATAATT-AGTATTTTAAATTATA
* * *
30591119 TAAATTCATATAAGAAA-ATTTTATTATCACGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAA-AAACATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
30591183 TATGTAATAATTAGTATTTTAAATTATA
65 TATGTAATAATTAGTATTTTAAATTATA
*
30591211 CAAATTCATA
1 TAAATTCATA
30591221 AAATATAATT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
92 86 0.93
93 6 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (92 bp):
TAAATTCATATAAAAACATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTAGTATTTTAAATTATA
Found at i:30591375 original size:120 final size:120
Alignment explanation
Indices: 30591251--30591666 Score: 735
Period size: 120 Copynumber: 3.5 Consensus size: 120
30591241 AATTATTTTA
* * * * *
30591251 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTT-TAATTTATATTT
*
30591315 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
30591371 AATTTTATTAAATTATATATTTTAATTATAACATATTTAATAATAATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
30591436 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
30591491 AAATTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
30591556 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
30591611 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT-TTTAA
30591667 ATATGATTAA
Statistics
Matches: 284, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
119 5 0.02
120 274 0.96
121 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:30591531 original size:15 final size:15
Alignment explanation
Indices: 30591496--30591547 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
30591486 TTAAGAAATT
*
30591496 TATTAAATTAT-ATA
1 TATTTAATTATAATA
30591510 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
30591524 TATTTAATAATAAT-
1 TATTTAATTATAATA
30591538 TATTTTAATT
1 TA-TTTAATT
30591548 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 7 0.22
15 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:30591544 original size:30 final size:30
Alignment explanation
Indices: 30591388--30591547 Score: 84
Period size: 30 Copynumber: 5.3 Consensus size: 30
30591378 TTAAATTATA
*
30591388 TATTTTAATTATAACATATTTAATAATAAT
1 TATTTTAATTATAATATATTTAATAATAAT
*
30591418 TATTTTAATT-T-ATAT-TTTACAGT-ATCAT
1 TATTTTAATTATAATATATTTA-A-TAATAAT
* * * * * *
30591446 ATATTATGATT-TGAGTAAATTCATATAAGAA-
1 -TATTTTAATTAT-AATATATTTA-ATAATAAT
* * * *
30591477 TA--TTAATTATTAAGAAATTTATTAAATTAT
1 TATTTTAATTA-TAATATATTTAAT-AATAAT
30591507 ATATTTTAATTATAATATATTTAATAATAAT
1 -TATTTTAATTATAATATATTTAATAATAAT
30591538 TATTTTAATT
1 TATTTTAATT
30591548 TATATTTTAC
Statistics
Matches: 94, Mismatches: 22, Indels: 28
0.65 0.15 0.19
Matches are distributed among these distances:
27 4 0.04
28 13 0.14
29 21 0.22
30 23 0.24
31 10 0.11
32 16 0.17
33 7 0.07
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
TATTTTAATTATAATATATTTAATAATAAT
Found at i:30591646 original size:16 final size:16
Alignment explanation
Indices: 30591625--30591666 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30591615 TTATTAAATT
*
30591625 ATATATTTTAATTATA
1 ATATATTTTAATAATA
30591641 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
30591656 AT-TATGTTTAA
1 ATATAT-TTTAA
30591667 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:30591651 original size:15 final size:15
Alignment explanation
Indices: 30591616--30591657 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30591606 TTAAGAATTT
*
30591616 TATTAAATTAT-ATA
1 TATTTAATTATAATA
30591630 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
30591644 TATTTAATAATAAT
1 TATTTAATTATAAT
30591658 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:30591901 original size:16 final size:16
Alignment explanation
Indices: 30591880--30591917 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30591870 TTGATTTGTT
*
30591880 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
30591896 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
30591912 AATACA
1 ATTACA
30591918 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:30597497 original size:14 final size:15
Alignment explanation
Indices: 30597468--30597497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30597458 ACCTTACGAA
30597468 ATTCCTCCATTCGAC
1 ATTCCTCCATTCGAC
30597483 ATTCCTCCA-TCGAC
1 ATTCCTCCATTCGAC
30597497 A
1 A
30597498 CACCTCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.40, G:0.07, T:0.30
Consensus pattern (15 bp):
ATTCCTCCATTCGAC
Found at i:30605703 original size:18 final size:17
Alignment explanation
Indices: 30605664--30605705 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30605654 TTTTAGTGCT
*
30605664 AATAAATTTTTATAATA
1 AATAAATTTTTATAAAA
30605681 AATAATATTTTT-TAAAA
1 AATAA-ATTTTTATAAAA
30605698 ATATAAAT
1 A-ATAAAT
30605706 CATATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAATTTTTATAAAA
Found at i:30608500 original size:18 final size:18
Alignment explanation
Indices: 30608465--30608514 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
30608455 TATAATTTTA
* *
30608465 AATTATAAAAATACTAAT
1 AATTATAAAATTATTAAT
*
30608483 TATTATAAAATTATTAAT
1 AATTATAAAATTATTAAT
*
30608501 AATAAT-AAATTATT
1 AATTATAAAATTATT
30608515 TAAATAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATAAAATTATTAAT
Found at i:30609450 original size:24 final size:23
Alignment explanation
Indices: 30609418--30609464 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
30609408 TATGCGTCAA
*
30609418 TTAATATTTGGTTTTAATTATTAT
1 TTAAAATTTGGTTTTAATT-TTAT
30609442 TTAAAATTTGGTTTTAATTTTAT
1 TTAAAATTTGGTTTTAATTTTAT
30609465 ACATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
TTAAAATTTGGTTTTAATTTTAT
Found at i:30609472 original size:24 final size:24
Alignment explanation
Indices: 30609423--30609472 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30609413 GTCAATTAAT
**
30609423 ATTTGGTTTTAATTATTATTTAAA
1 ATTTGGTTTTAATTATTATACAAA
30609447 ATTTGGTTTTAATT-TTATACATAA
1 ATTTGGTTTTAATTATTATACA-AA
30609471 AT
1 AT
30609473 AACAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTGGTTTTAATTATTATACAAA
Found at i:30620613 original size:30 final size:30
Alignment explanation
Indices: 30620574--30620637 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
30620564 ATTTACTTAA
* **
30620574 CCAATTTGAAGTATGTTTCTGTCTTCACTG
1 CCAAATTGAAGTATGTTTCCATCTTCACTG
30620604 CCAAATTGAAGTATGTTTCCATCTTCACTG
1 CCAAATTGAAGTATGTTTCCATCTTCACTG
30620634 CCAA
1 CCAA
30620638 CTTCCAATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (30 bp):
CCAAATTGAAGTATGTTTCCATCTTCACTG
Found at i:30625227 original size:16 final size:16
Alignment explanation
Indices: 30625206--30625237 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30625196 ATTTTGTTGC
*
30625206 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
30625222 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
30625238 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:30625620 original size:51 final size:51
Alignment explanation
Indices: 30625460--30625604 Score: 213
Period size: 51 Copynumber: 2.8 Consensus size: 51
30625450 GATACCGGTT
*
30625460 CACATAGTAGCCTGCACATAGTACTACACAAGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
* * *
30625511 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATA
*
30625562 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
30625605 TTCACTTTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
50 3 0.04
51 77 0.93
52 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
Found at i:30626867 original size:70 final size:70
Alignment explanation
Indices: 30626752--30626884 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
30626742 TATCAAAACT
* * *
30626752 TTGAGGACTTCTACCGAAGCAAGTCAAGTCGGTAGCCAAATTTCAGCATCTCC-TGCACTTCTAT
1 TTGAGGACTTCTACCGAAGCAAGTAAAGTCAGTAGCCAAAGTTCAGCATC-CCTTGCACTTCTAT
30626816 TGATAC
65 TGATAC
* * *
30626822 TTGAGGATTTCTACTGAAAG-AAGTAAAGTTAGTAGCCAAAGTTCAGCATCCCTTGCACTTCTA
1 TTGAGGACTTCTACCG-AAGCAAGTAAAGTCAGTAGCCAAAGTTCAGCATCCCTTGCACTTCTA
30626885 CCTATACTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
69 2 0.04
70 50 0.91
71 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (70 bp):
TTGAGGACTTCTACCGAAGCAAGTAAAGTCAGTAGCCAAAGTTCAGCATCCCTTGCACTTCTATT
GATAC
Found at i:30634358 original size:22 final size:22
Alignment explanation
Indices: 30634304--30634360 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 22
30634294 TTAAATTAAA
*
30634304 ATTTAAGCATATATCACATTAC
1 ATTTAAGCATATATCACATAAC
*
30634326 A---CAG-ATA-ATCACATAAC
1 ATTTAAGCATATATCACATAAC
30634343 ATTTAAGCATATATCACA
1 ATTTAAGCATATATCACA
30634361 ATACTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
17 10 0.37
18 3 0.11
19 2 0.07
20 2 0.07
21 3 0.11
22 7 0.26
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (22 bp):
ATTTAAGCATATATCACATAAC
Found at i:30650237 original size:50 final size:50
Alignment explanation
Indices: 30650150--30650255 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
30650140 CATTGAGATT
* ** *
30650150 ATGAGAGGTCCAATGTAAGACCATGTCTGGGTTATGGCGTTG-GCACCGAG
1 ATGAGAGGTCCAAGGTAAGACCATGTCTGGGACATGGC-ATGAGCACCGAG
** * *
30650200 ATGAGAGGTCCCCGGTAAGACCATGTCTTGGACATGGCATGAGCACCGAT
1 ATGAGAGGTCCAAGGTAAGACCATGTCTGGGACATGGCATGAGCACCGAG
30650250 ATGAGA
1 ATGAGA
30650256 ACTCCCATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.04
50 45 0.96
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCAAGGTAAGACCATGTCTGGGACATGGCATGAGCACCGAG
Found at i:30651226 original size:21 final size:20
Alignment explanation
Indices: 30651188--30651226 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30651178 CCCCTGTTCT
* *
30651188 AATTTTAGAAAATCATTAAA
1 AATTTTAAAAAATAATTAAA
30651208 AATTTTAAAAAAATAATTA
1 AATTTT-AAAAAATAATTA
30651227 TGAGTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
AATTTTAAAAAATAATTAAA
Found at i:30669760 original size:51 final size:49
Alignment explanation
Indices: 30669699--30669885 Score: 189
Period size: 51 Copynumber: 3.7 Consensus size: 49
30669689 CCGGTTCACA
* *
30669699 TAGTATCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT-ACTATCCG-TACACG
* * *
30669750 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCTGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATA-CTATCC-GTACACG
* * ** * *
30669801 TATTAGCCTGCACATTGTACTACACATTTGACCTATAAT-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATACTATC-CGTACACG
*
30669851 TAGTAGCTTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
30669886 CACTTTTAGT
Statistics
Matches: 111, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
49 2 0.02
50 37 0.33
51 68 0.61
52 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACTATCCGTACACG
Found at i:30677980 original size:86 final size:86
Alignment explanation
Indices: 30677829--30677998 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 86
30677819 AAATAGCAAT
* * **
30677829 AATTATCAGCAAAAGAGCCCTCCCTTGCCTAGCCTCACATGTGGCAAGTTTGATAGTTTTGACTT
1 AATTATCAGCAAAAGAGCCCTCCCTTGCCTAGCCTCACATATGGCAAGGTTGATAGTTTCAACTT
*
30677894 TGCTAATTTAGGCTTGGGGAA
66 TGCTAAGTTAGGCTTGGGGAA
* *
30677915 AATTATCAGCCAAAGAGCCCTCCCTTGGCC-GGCCTCACATATGGCAAGGTTGATAGTTTCAACT
1 AATTATCAGCAAAAGAGCCCTCCCTT-GCCTAGCCTCACATATGGCAAGGTTGATAGTTTCAACT
30677979 TTGCTAAGTTAGGCTTGGGG
65 TTGCTAAGTTAGGCTTGGGG
30677999 CAATTCTATA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
86 73 0.96
87 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (86 bp):
AATTATCAGCAAAAGAGCCCTCCCTTGCCTAGCCTCACATATGGCAAGGTTGATAGTTTCAACTT
TGCTAAGTTAGGCTTGGGGAA
Found at i:30679028 original size:9 final size:9
Alignment explanation
Indices: 30679014--30679045 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
30679004 TCCATTTCTA
30679014 TTCATTTTG
1 TTCATTTTG
30679023 TTCATTTTG
1 TTCATTTTG
30679032 TTCATTTTG
1 TTCATTTTG
30679041 ATTCA
1 -TTCA
30679046 ACACGTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (9 bp):
TTCATTTTG
Found at i:30684543 original size:29 final size:29
Alignment explanation
Indices: 30684507--30684562 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
30684497 ATTCCATTAA
* *
30684507 GTTATTTTA-GACTAATTAATTTCATTTAG
1 GTTATTTTAGGA-TAACTAATTTAATTTAG
30684536 GTTATTTTAGGATAACTAATTTAATTT
1 GTTATTTTAGGATAACTAATTTAATTT
30684563 GTTTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (29 bp):
GTTATTTTAGGATAACTAATTTAATTTAG
Found at i:30686685 original size:11 final size:11
Alignment explanation
Indices: 30686666--30686696 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
30686656 AAATAGGAAA
30686666 AAAACCTAAGAG
1 AAAA-CTAAGAG
30686678 AAAACTAAGAG
1 AAAACTAAGAG
30686689 AAAACTAA
1 AAAACTAA
30686697 ACTAGTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.10
Consensus pattern (11 bp):
AAAACTAAGAG
Found at i:30692339 original size:54 final size:54
Alignment explanation
Indices: 30692213--30692324 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
30692203 TATGTGCCAT
* * *
30692213 ACACGGTCTA-ACACATGGTCTGCGACATAGCCATGTGTATCAAGTCAGTGAGTC
1 ACACGGTCTAGA-ACACGGTCTGCGACACAGCCATGTGTATCAAGTAAGTGAGTC
* *
30692267 ACACGGTCTAGAACACGGTCTGCGACACAGTCATGTGATAT-AAGTAAGTGAGTT
1 ACACGGTCTAGAACACGGTCTGCGACACAGCCATGTG-TATCAAGTAAGTGAGTC
30692321 ACAC
1 ACAC
30692325 TGGCTGGGAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 47 0.92
55 4 0.08
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (54 bp):
ACACGGTCTAGAACACGGTCTGCGACACAGCCATGTGTATCAAGTAAGTGAGTC
Found at i:30695741 original size:3 final size:3
Alignment explanation
Indices: 30695735--30695764 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30695725 CTGCTATTAC
*
30695735 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30695765 CATTGATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30697168 original size:44 final size:44
Alignment explanation
Indices: 30697120--30697641 Score: 633
Period size: 44 Copynumber: 11.9 Consensus size: 44
30697110 CATAGAAACT
* **
30697120 AATCTTTC-ACCTATTCCACTGTTGGTTAGGGAGATAGGACTTGT
1 AATC-TTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* *
30697164 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* * * *
30697208 AATCTTCAACCTATTCCAATGCTAGTCAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* * *
30697252 AATCTTCAACCTATTCCACTGCTGGTCAAGGAGATAAGG-CTTTC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGAT-AGGACTTAC
* * *
30697296 AATCCTCAACCTATTCCACCGCT-GTTCAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTAC
*
30697340 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTGC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* *
30697384 AATCTTCAACCTATTCCACTGCTGGCTAGGGAGATAGGGCTTAC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* * * * * *
30697428 AATCTTCCACCTACTCCGCTGCTGGTCAGGGGGATATGACTTAC
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* *
30697472 AATCTTTC-ACCTATTCCACTACTAGTTAGGGAGATAGGACTTAC
1 AATC-TTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
* * **
30697516 AATCTTCCACCTATTCAACTGCT-GTTCAGGGATCTAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTAC
* * *
30697560 AATCTTCCACCTATTCCACTGAT-GTTCAGGGAGCTAGGACTTAC
1 AATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTAC
* *
30697604 AATCTTCAACCTATTCCACTGTTGGTCAGGGAGATAGG
1 AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGG
30697642 GCTTTGTGAT
Statistics
Matches: 424, Mismatches: 45, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
43 14 0.03
44 399 0.94
45 11 0.03
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTAC
Found at i:30712418 original size:20 final size:20
Alignment explanation
Indices: 30712393--30712437 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
30712383 GTAATATTTT
30712393 TTTTTAGACA-TGGTCAAATC
1 TTTTTA-ACATTGGTCAAATC
30712413 TTTTT-ACATTGGTCAAATC
1 TTTTTAACATTGGTCAAATC
30712432 TTTTTA
1 TTTTTA
30712438 CGTGAACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTTTAACATTGGTCAAATC
Found at i:30716426 original size:16 final size:16
Alignment explanation
Indices: 30716405--30716435 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30716395 TTTAAGTACA
*
30716405 AATAAGATTGAGCTTG
1 AATAAGAATGAGCTTG
30716421 AATAAGAATGAGCTT
1 AATAAGAATGAGCTT
30716436 AATCGAGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (16 bp):
AATAAGAATGAGCTTG
Found at i:30717093 original size:12 final size:14
Alignment explanation
Indices: 30717074--30717109 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
30717064 TATTTTTCAT
30717074 ATTA-TTTTAT-AA
1 ATTATTTTTATGAA
30717086 ATT-TTTTTATGAA
1 ATTATTTTTATGAA
30717099 ATTATTTTTAT
1 ATTATTTTTAT
30717110 TTTATATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
13 5 0.24
14 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
ATTATTTTTATGAA
Found at i:30717598 original size:9 final size:9
Alignment explanation
Indices: 30717584--30717614 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30717574 GTTAAACGAA
30717584 TCGAGTTAT
1 TCGAGTTAT
*
30717593 TCGAGTTAA
1 TCGAGTTAT
30717602 TCGAGTTAT
1 TCGAGTTAT
30717611 TCGA
1 TCGA
30717615 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30717685 original size:9 final size:9
Alignment explanation
Indices: 30717668--30717704 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30717658 TAAATTTTCG
30717668 AATTCGAAT
1 AATTCGAAT
*
30717677 AACTCGAAT
1 AATTCGAAT
30717686 AATTCGAAT
1 AATTCGAAT
30717695 AATTCGAAT
1 AATTCGAAT
30717704 A
1 A
30717705 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:30718904 original size:9 final size:9
Alignment explanation
Indices: 30718890--30718946 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
30718880 ATTATATATT
*
30718890 TAAATTTTG
1 TAAATTATG
30718899 TAAATTATG
1 TAAATTATG
30718908 --AATTATG
1 TAAATTATG
30718915 TAAATTATG
1 TAAATTATG
* *
30718924 TAAAATACG
1 TAAATTATG
*
30718933 TAAGTTATG
1 TAAATTATG
30718942 -AAATT
1 TAAATT
30718947 TGAACTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.18
8 4 0.10
9 28 0.72
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (9 bp):
TAAATTATG
Found at i:30718916 original size:16 final size:16
Alignment explanation
Indices: 30718892--30718923 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30718882 TATATATTTA
*
30718892 AATTTTGTAAATTATG
1 AATTATGTAAATTATG
30718908 AATTATGTAAATTATG
1 AATTATGTAAATTATG
30718924 TAAAATACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AATTATGTAAATTATG
Found at i:30721661 original size:5 final size:5
Alignment explanation
Indices: 30721651--30721676 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30721641 TGAGCATTCG
30721651 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
30721677 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:30721776 original size:5 final size:5
Alignment explanation
Indices: 30721766--30721791 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30721756 GAGATGGAAT
30721766 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
30721792 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:30725045 original size:46 final size:46
Alignment explanation
Indices: 30724978--30725065 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
30724968 CCAGTATAAG
* *
30724978 TGCAGACGAGCTGCCAGTAGTGTGGACAAGCCACCAATAATGGTAA
1 TGCAGACGAACTGCCAATAGTGTGGACAAGCCACCAATAATGGTAA
* * *
30725024 TGCAGATGAACTGCCAATAGTGTGGGCGAGCCACCAATAATG
1 TGCAGACGAACTGCCAATAGTGTGGACAAGCCACCAATAATG
30725066 CAGACAATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (46 bp):
TGCAGACGAACTGCCAATAGTGTGGACAAGCCACCAATAATGGTAA
Found at i:30729905 original size:12 final size:13
Alignment explanation
Indices: 30729884--30729912 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30729874 TTAAAAATTA
30729884 AAAAATATATTTT
1 AAAAATATATTTT
30729897 AAAAA-ATATTTT
1 AAAAATATATTTT
30729909 AAAA
1 AAAA
30729913 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:30729949 original size:37 final size:37
Alignment explanation
Indices: 30729863--30729993 Score: 171
Period size: 37 Copynumber: 3.5 Consensus size: 37
30729853 CAGCCCATTT
30729863 TATTTTAAAATTT-AAAAATTAAAAAATATATTTTAAAAAA
1 TATTTTAAAATTTAAAAAATT-AAAAA-ATATTTT--AAAA
*
30729903 TATTTTAAAATTTAAAAAATTAAAAAGTATTTTAAAA
1 TATTTTAAAATTTAAAAAATTAAAAAATATTTTAAAA
* *
30729940 TATTTTAAAATTTAAAAAATTAAAAAATATGTAAAAA
1 TATTTTAAAATTTAAAAAATTAAAAAATATTTTAAAA
30729977 TA-TTT-AAA-TTAAAAAAT
1 TATTTTAAAATTTAAAAAAT
30729994 AAATATATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
34 9 0.10
35 3 0.03
36 3 0.03
37 40 0.47
39 6 0.07
40 18 0.21
41 7 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (37 bp):
TATTTTAAAATTTAAAAAATTAAAAAATATTTTAAAA
Found at i:30732932 original size:2 final size:2
Alignment explanation
Indices: 30732885--30732917 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30732875 TCTTTCCTTT
30732885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30732918 TACACTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30733816 original size:9 final size:9
Alignment explanation
Indices: 30733797--30733878 Score: 53
Period size: 9 Copynumber: 8.9 Consensus size: 9
30733787 AACAAAACAT
30733797 TAAAA-TTA
1 TAAAATTTA
30733805 TAAAATTTA
1 TAAAATTTA
30733814 TAAAATTTA
1 TAAAATTTA
*
30733823 TTTAAAAATT-
1 --TAAAATTTA
*
30733833 TAAAATTGA
1 TAAAATTTA
*
30733842 TATAAACTTA
1 TA-AAATTTA
*
30733852 TAAAA-ATA
1 TAAAATTTA
*
30733860 TAATAAATTA
1 TAA-AATTTA
30733870 TAATAATTT
1 TAA-AATTT
30733879 TTTATAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
8 16 0.27
9 19 0.32
10 17 0.29
11 7 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (9 bp):
TAAAATTTA
Found at i:30733831 original size:21 final size:21
Alignment explanation
Indices: 30733806--30733917 Score: 62
Period size: 21 Copynumber: 5.6 Consensus size: 21
30733796 TTAAAATTAT
30733806 AAAATTTATAAAATTTATTTA
1 AAAATTTATAAAATTTATTTA
*
30733827 AAAA-TT-TAAAATTGA--TA
1 AAAATTTATAAAATTTATTTA
* * *
30733844 TAAACTTATAAAA---ATATA
1 AAAATTTATAAAATTTATTTA
30733862 ATAAA-TTATAATAATTT-TTTA
1 A-AAATTTATAA-AATTTATTTA
* **
30733883 TAAAATTAATAAAACATATTTA
1 -AAAATTTATAAAATTTATTTA
*
30733905 AAATTTTATAAAA
1 AAAATTTATAAAA
30733918 ACAAATAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
16 1 0.01
17 5 0.07
18 10 0.14
19 18 0.26
20 2 0.03
21 24 0.34
22 10 0.14
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (21 bp):
AAAATTTATAAAATTTATTTA
Found at i:30733847 original size:19 final size:20
Alignment explanation
Indices: 30733803--30733877 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 20
30733793 ACATTAAAAT
* *
30733803 TATAAAATTTATAAAATTTA
1 TATAAAAATTATAAAATTGA
*
30733823 TTTAAAAATT-TAAAATTGA
1 TATAAAAATTATAAAATTGA
*
30733842 TAT-AAACTTATAAAA---A
1 TATAAAAATTATAAAATTGA
30733858 TATAATAAATTATAATAATT
1 TATAA-AAATTATAA-AATT
30733878 TTTTATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
16 4 0.09
17 1 0.02
18 13 0.30
19 17 0.40
20 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (20 bp):
TATAAAAATTATAAAATTGA
Found at i:30733912 original size:30 final size:29
Alignment explanation
Indices: 30733849--30733984 Score: 93
Period size: 30 Copynumber: 4.6 Consensus size: 29
30733839 TGATATAAAC
*
30733849 TTATAAAAA-TATAATAAAT-TATAATAATT
1 TTATAAAAATTATAA-AAATATTTAA-AATT
*
30733878 TTTTATAAAATTAATAAAACATATTTAAAATT
1 TTATA-AAAATT-ATAAAA-ATATTTAAAATT
** **
30733910 TTATAAAAACAAATAAAAAT-TCTTAAAAAC
1 TTATAAAAA-TTATAAAAATAT-TTAAAATT
30733940 TTATAAAAACTTATAAAAATATTT-AAA-T
1 TTATAAAAA-TTATAAAAATATTTAAAATT
*
30733968 TGATATAAAATTATAAA
1 TTATA-AAAATTATAAA
30733985 CAATCATAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
28 11 0.13
29 12 0.14
30 32 0.37
31 14 0.16
32 14 0.16
33 4 0.05
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (29 bp):
TTATAAAAATTATAAAAATATTTAAAATT
Found at i:30733926 original size:20 final size:20
Alignment explanation
Indices: 30733903--30733958 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
30733893 AAAACATATT
30733903 TAAAATTTTATAAAAACAAA
1 TAAAATTTTATAAAAACAAA
* **
30733923 TAAAAATTCT-TAAAAACTTA
1 T-AAAATTTTATAAAAACAAA
**
30733943 TAAAAACTTATAAAAA
1 TAAAATTTTATAAAAA
30733959 TATTTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 5 0.18
20 16 0.57
21 7 0.25
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATTTTATAAAAACAAA
Found at i:30733946 original size:10 final size:10
Alignment explanation
Indices: 30733910--30733958 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
30733900 ATTTAAAATT
30733910 TTATAAAAAC
1 TTATAAAAAC
**
30733920 AAATAAAAA-
1 TTATAAAAAC
*
30733929 TTCTTAAAAAC
1 TT-ATAAAAAC
30733940 TTATAAAAAC
1 TTATAAAAAC
30733950 TTATAAAAA
1 TTATAAAAA
30733959 TATTTAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 29 0.94
11 2 0.06
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (10 bp):
TTATAAAAAC
Found at i:30733966 original size:20 final size:20
Alignment explanation
Indices: 30733845--30733966 Score: 58
Period size: 21 Copynumber: 6.0 Consensus size: 20
30733835 AAATTGATAT
30733845 AAACTTATAAAAATA--TAA
1 AAACTTATAAAAATATTTAA
* *
30733863 TAAA-TTATAATAATTTTTTATA
1 -AAACTTATAA-AAATATTTA-A
30733885 AAA-TTAATAAAACATATTTAA
1 AAACTT-ATAAAA-ATATTTAA
** * **
30733906 AATTTTATAAAAACAAATAA
1 AAACTTATAAAAATATTTAA
* *
30733926 AAATTCTTA-AAAACT-TATAA
1 AAA--CTTATAAAAATATTTAA
30733946 AAACTTATAAAAATATTTAA
1 AAACTTATAAAAATATTTAA
30733966 A
1 A
30733967 TTGATATAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
18 10 0.13
19 11 0.14
20 19 0.25
21 22 0.29
22 15 0.19
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAACTTATAAAAATATTTAA
Found at i:30734508 original size:9 final size:9
Alignment explanation
Indices: 30734486--30734610 Score: 117
Period size: 10 Copynumber: 13.0 Consensus size: 9
30734476 TATGACTTTT
30734486 TTTTTATAA
1 TTTTTATAA
*
30734495 GTTTTAATAA
1 -TTTTTATAA
*
30734505 -TTTTATAT
1 TTTTTATAA
30734513 TTTTTATAA
1 TTTTTATAA
30734522 TTTTTATAA
1 TTTTTATAA
30734531 GTTTTTATAA
1 -TTTTTATAA
*
30734541 TATTTTAAATA
1 T-TTTTATA-A
30734552 TATTTTATAAA
1 T-TTTTAT-AA
30734563 TTTTTATAA
1 TTTTTATAA
*
30734572 TCTTTATAA
1 TTTTTATAA
30734581 GTTTTTATAA
1 -TTTTTATAA
*
30734591 TTTTTTTATGA
1 --TTTTTATAA
30734602 TTTTTATAA
1 TTTTTATAA
30734611 GTTTATCTCA
Statistics
Matches: 97, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.06
9 35 0.36
10 37 0.38
11 18 0.19
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:30734537 original size:19 final size:19
Alignment explanation
Indices: 30734486--30734614 Score: 122
Period size: 19 Copynumber: 6.7 Consensus size: 19
30734476 TATGACTTTT
*
30734486 TTTTTATAAGTTTTAATAA
1 TTTTTATAAGTTTTTATAA
*
30734505 -TTTTAT-ATTTTTTATAA
1 TTTTTATAAGTTTTTATAA
30734522 TTTTTATAAGTTTTTATAA
1 TTTTTATAAGTTTTTATAA
*
30734541 TATTTTA-AATATATTTTATAAA
1 T-TTTTATAA-GT-TTTTAT-AA
*
30734563 TTTTTATAA-TCTTTATAA
1 TTTTTATAAGTTTTTATAA
* *
30734581 GTTTTTATAATTTTTTTATGA
1 -TTTTTATAA-GTTTTTATAA
30734602 TTTTTATAAGTTT
1 TTTTTATAAGTTT
30734615 ATCTCAATTC
Statistics
Matches: 92, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.10
18 14 0.15
19 30 0.33
20 16 0.17
21 18 0.20
22 5 0.05
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATAAGTTTTTATAA
Found at i:30740311 original size:48 final size:48
Alignment explanation
Indices: 30740236--30740399 Score: 274
Period size: 48 Copynumber: 3.4 Consensus size: 48
30740226 TTTAATTTGA
* * * *
30740236 AAATAATGGTGGTTCATCCATATTTTTTACTACTCGCAGTTTATCTGC
1 AAATACTGGTGGTTCATCCATAATTTTTACTACTGGCAATTTATCTGC
30740284 AAATACTGGTGGTTCATCCATAATTTTTACTACTGGCAATTTATCTGC
1 AAATACTGGTGGTTCATCCATAATTTTTACTACTGGCAATTTATCTGC
* *
30740332 AAATACTGGTGGTTCTTCCACAATTTTTACTACTGGCAATTTATCTGC
1 AAATACTGGTGGTTCATCCATAATTTTTACTACTGGCAATTTATCTGC
30740380 AAATACTGGTGGTTCATCCA
1 AAATACTGGTGGTTCATCCA
30740400 CAAACTTGAG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 109 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (48 bp):
AAATACTGGTGGTTCATCCATAATTTTTACTACTGGCAATTTATCTGC
Found at i:30743687 original size:25 final size:25
Alignment explanation
Indices: 30743639--30743689 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
30743629 TTTAAAAATA
*
30743639 TTTAAAATTATTAAAATATTATATT
1 TTTAAAATTATTAAAATATCATATT
*
30743664 TTTAATATTATTAAACATA-CATATT
1 TTTAAAATTATTAAA-ATATCATATT
30743689 T
1 T
30743690 AATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAAAATTATTAAAATATCATATT
Found at i:30743721 original size:16 final size:16
Alignment explanation
Indices: 30743700--30743734 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
30743690 AATTATTTAT
*
30743700 AATTATTCATATAATA
1 AATTATTAATATAATA
30743716 AATTATTAATATAATA
1 AATTATTAATATAATA
30743732 AAT
1 AAT
30743735 ATAATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATTAATATAATA
Found at i:30743738 original size:22 final size:22
Alignment explanation
Indices: 30743713--30743756 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30743703 TATTCATATA
*
30743713 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAAAATAATAAAT
*
30743735 ATAATTTATTAAAATAATAAAT
1 ATAAATTATTAAAATAATAAAT
30743757 TATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATTATTAAAATAATAAAT
Found at i:30743745 original size:25 final size:22
Alignment explanation
Indices: 30743708--30743764 Score: 53
Period size: 25 Copynumber: 2.5 Consensus size: 22
30743698 ATAATTATTC
30743708 ATATAATAAATTATTAATATAATAA
1 ATATAATAAATTA--AA-ATAATAA
**
30743733 ATATAATTTATTAAAATAATAA
1 ATATAATAAATTAAAATAATAA
*
30743755 AT-TATTAAAT
1 ATATAATAAAT
30743765 ATTTCAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.19
22 9 0.33
23 2 0.07
25 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAATAAATTAAAATAATAA
Found at i:30743759 original size:16 final size:16
Alignment explanation
Indices: 30743700--30743763 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 16
30743690 AATTATTTAT
* *
30743700 AATTATTCATATAATA
1 AATTATTAAAATAATA
30743716 AATTATTAATATAATAAATA
1 AATTATT-A-A-AAT-AATA
30743736 TAATTTATTAAAATAATA
1 -AA-TTATTAAAATAATA
30743754 AATTATTAAA
1 AATTATTAAA
30743764 TATTTCAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 15 0.38
17 2 0.05
18 5 0.12
19 5 0.12
20 5 0.12
21 3 0.08
22 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTATTAAAATAATA
Found at i:30743869 original size:15 final size:15
Alignment explanation
Indices: 30743835--30743905 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 15
30743825 ATATTATTGA
30743835 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
30743848 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
30743863 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
30743882 AAATATATTAATAAT
1 AAATATTTTAATAAT
30743897 AAATATTTT
1 AAATATTTT
30743906 GTAGTATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 19 0.41
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:30744382 original size:14 final size:14
Alignment explanation
Indices: 30744363--30744401 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30744353 CCTGAAAAGT
30744363 AAATCATTTTCCAG
1 AAATCATTTTCCAG
**
30744377 AAATCATTTTCTGG
1 AAATCATTTTCCAG
*
30744391 AAGTCATTTTC
1 AAATCATTTTC
30744402 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:30762185 original size:36 final size:36
Alignment explanation
Indices: 30762138--30762208 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
30762128 GATTATGTAA
30762138 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* * *
30762174 TCTTAGAGTTCTAATTGTATATAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
30762209 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:30762187 original size:19 final size:19
Alignment explanation
Indices: 30762137--30762193 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
30762127 TGATTATGTA
30762137 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
30762156 ATAC--A-ACTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
30762173 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
30762192 AT
1 AT
30762194 ATAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 2 0.07
19 14 0.47
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Done.