Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007841.1 Hibiscus syriacus cultivar Beakdansim tig00110195_pilon, whole genome shotgun sequence
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: 1873963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1700587 original size:48 final size:48
Alignment explanation
Indices: 1700515--1700611 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
1700505 ACAATATAGA
*
1700515 GCAACTTCCCACTCTTGGGGTGCAATCAAGATGGATCGAGGAACGGAT
1 GCAACTTCCCACTCTTGGGATGCAATCAAGATGGATCGAGGAACGGAT
* * *
1700563 GCAACTTCCCACTCTTGGGATGCAATTAGGATGGATCGATGAACGGAT
1 GCAACTTCCCACTCTTGGGATGCAATCAAGATGGATCGAGGAACGGAT
1700611 G
1 G
1700612 AAGGACAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (48 bp):
GCAACTTCCCACTCTTGGGATGCAATCAAGATGGATCGAGGAACGGAT
Found at i:1701824 original size:27 final size:27
Alignment explanation
Indices: 1701786--1701837 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1701776 TATAAATAAA
**
1701786 TAATATTTTAAATGTGGTCATGACATT
1 TAATATTTTAAATGTCATCATGACATT
1701813 TAATATTTTAAATGTCATCATGACA
1 TAATATTTTAAATGTCATCATGACA
1701838 AGCATCCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (27 bp):
TAATATTTTAAATGTCATCATGACATT
Found at i:1704140 original size:33 final size:33
Alignment explanation
Indices: 1704103--1704171 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1704093 GATAGAGGGG
*
1704103 ATGACGACAATGTGAATAAATCCGAGATAATTA
1 ATGACAACAATGTGAATAAATCCGAGATAATTA
* *
1704136 ATGACAACAATGTGAGTAGATCCGAGATAATTA
1 ATGACAACAATGTGAATAAATCCGAGATAATTA
1704169 ATG
1 ATG
1704172 TCTGAGGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (33 bp):
ATGACAACAATGTGAATAAATCCGAGATAATTA
Found at i:1705672 original size:30 final size:30
Alignment explanation
Indices: 1705637--1705702 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
1705627 AAGCAGATCG
* *
1705637 TTCTTTTATTTTGAGA-AAAAATATTCAATA
1 TTCTTTT-TTTTGAAATAAAAATATTAAATA
1705667 TTC-TTTTTTTGAAATAAAAATATTAAATA
1 TTCTTTTTTTTGAAATAAAAATATTAAATA
1705696 TTCTTTT
1 TTCTTTT
1705703 CCTTATACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.22
29 19 0.59
30 6 0.19
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (30 bp):
TTCTTTTTTTTGAAATAAAAATATTAAATA
Found at i:1712541 original size:2 final size:2
Alignment explanation
Indices: 1712534--1712595 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1712524 ATGAAAATGA
1712534 AT AT AT AT 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 AT AT AT AT
1712576 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1712596 CATAGGTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712783 original size:39 final size:39
Alignment explanation
Indices: 1712721--1712808 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
1712711 AGTGCTCAAC
* * *
1712721 GCGTCTTCAAGCTAAATATGAAGACTCCACGACTGCATG
1 GCGTCTTCAGGCTAAATAAGAAGACCCCACGACTGCATG
1712760 GCGTCTTCAGGC-AAATGAAGAAGACCCCACGACTGCATG
1 GCGTCTTCAGGCTAAAT-AAGAAGACCCCACGACTGCATG
* *
1712799 ACGTTTTCAG
1 GCGTCTTCAG
1712809 ATAAATAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 4 0.09
39 39 0.91
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (39 bp):
GCGTCTTCAGGCTAAATAAGAAGACCCCACGACTGCATG
Found at i:1726489 original size:3 final size:3
Alignment explanation
Indices: 1726481--1726514 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1726471 GCTATTGGAA
1726481 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1726515 CCGAACAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1726961 original size:19 final size:19
Alignment explanation
Indices: 1726937--1726999 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1726927 TCGATGATTT
1726937 CATATGAATCTAAACTAAA
1 CATATGAATCTAAACTAAA
* * * * **
1726956 CATATG-TTTTTATCTTATT
1 CATATGAATCTAAAC-TAAA
1726975 CATATGAATCTAAACTAAA
1 CATATGAATCTAAACTAAA
1726994 CATATG
1 CATATG
1727000 TTAGAAATGT
Statistics
Matches: 30, Mismatches: 12, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.38
Consensus pattern (19 bp):
CATATGAATCTAAACTAAA
Found at i:1728439 original size:20 final size:20
Alignment explanation
Indices: 1728410--1728449 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1728400 ATTTAAATGA
* *
1728410 TAAACAAACATAAATGAACG
1 TAAACAAACACAAACGAACG
*
1728430 TAAACGAACACAAACGAACG
1 TAAACAAACACAAACGAACG
1728450 AACATAAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
TAAACAAACACAAACGAACG
Found at i:1728451 original size:14 final size:14
Alignment explanation
Indices: 1728432--1728471 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1728422 AATGAACGTA
1728432 AACGAACACAAACG
1 AACGAACACAAACG
*
1728446 AACGAACATAAACG
1 AACGAACACAAACG
1728460 AAC-AACACAAAC
1 AACGAACACAAAC
1728472 ACAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.60, C:0.28, G:0.10, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1728743 original size:14 final size:16
Alignment explanation
Indices: 1728724--1728755 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1728714 GCCCTCTGTT
1728724 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
1728738 CGAACATATAATCGAA
1 CGAACATATAATCGAA
1728754 CG
1 CG
1728756 TTACGAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:1728860 original size:16 final size:17
Alignment explanation
Indices: 1728839--1728872 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1728829 CATGTTCGTT
*
1728839 CATTTAAT-TAAACGAA
1 CATTTAATAAAAACGAA
1728855 CATTTAATAAAAACGAA
1 CATTTAATAAAAACGAA
1728872 C
1 C
1728873 TTCCCACTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (17 bp):
CATTTAATAAAAACGAA
Found at i:1740425 original size:2 final size:2
Alignment explanation
Indices: 1740418--1740460 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1740408 TATTTACAAT
1740418 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
1740460 T
1 T
1740461 TGGTTATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1742578 original size:17 final size:18
Alignment explanation
Indices: 1742545--1742578 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1742535 CCATAGTTTT
1742545 GAAAATAAATATTTATAC
1 GAAAATAAATATTTATAC
*
1742563 GAAAATTAAT-TTTATA
1 GAAAATAAATATTTATA
1742579 AAAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
GAAAATAAATATTTATAC
Found at i:1743511 original size:31 final size:30
Alignment explanation
Indices: 1743476--1743563 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 30
1743466 CACTATTCTA
1743476 AGCTTTGCTAAGCTTTACTCAATTCTCTCAT
1 AGCTTTGCTAAGCTTTACTCAATTCTCTC-T
* *
1743507 AGCTTTGCTAAGCTAT-CTCAAATTTTCTCT
1 AGCTTTGCTAAGCTTTACTC-AATTCTCTCT
*
1743537 AGCTTTTCTAAGCTTTCACTCATATTC
1 AGCTTTGCTAAGCTTT-ACTCA-ATTC
1743564 CATCTCATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 18 0.38
31 24 0.50
32 6 0.12
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (30 bp):
AGCTTTGCTAAGCTTTACTCAATTCTCTCT
Found at i:1746537 original size:34 final size:34
Alignment explanation
Indices: 1746499--1746611 Score: 97
Period size: 34 Copynumber: 3.3 Consensus size: 34
1746489 GTTGTATTTT
1746499 GTGTTTGGTTGATTTAGCAGGAATAAAGATTATC
1 GTGTTTGGTTGATTTAGCAGGAATAAAGATTATC
* * * * *
1746533 GTGTTT-GTCGTATTTGGTTAAGGAATAAATATT-TT
1 GTGTTTGGTTG-ATTTAG--CAGGAATAAAGATTATC
* * *
1746568 GTGTTTGGTTG-GTTAACAGGAATATAAGATTACC
1 GTGTTTGGTTGATTTAGCAGGAATA-AAGATTATC
1746602 GTGTTTGGTT
1 GTGTTTGGTT
1746612 AAGGAATAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
32 7 0.12
33 8 0.13
34 23 0.38
35 7 0.12
36 15 0.25
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (34 bp):
GTGTTTGGTTGATTTAGCAGGAATAAAGATTATC
Found at i:1746736 original size:2 final size:2
Alignment explanation
Indices: 1746729--1746759 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1746719 TCATAAAATT
1746729 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 T
1746760 TTACAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1750699 original size:23 final size:21
Alignment explanation
Indices: 1750664--1750713 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
1750654 ATTGGGATTC
* *
1750664 CCATAAGCTGCACCTGCAGGGCA
1 CCATAACCAGCACCTGCA--GCA
1750687 CCATAACCAGCACCTGCAGCA
1 CCATAACCAGCACCTGCAGCA
1750708 CCATAA
1 CCATAA
1750714 TTGCCATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
23 16 0.64
ACGTcount: A:0.32, C:0.38, G:0.18, T:0.12
Consensus pattern (21 bp):
CCATAACCAGCACCTGCAGCA
Found at i:1756295 original size:164 final size:165
Alignment explanation
Indices: 1756002--1756332 Score: 614
Period size: 164 Copynumber: 2.0 Consensus size: 165
1755992 GCTACCCAGA
1756002 AAGCAAAAGGAGATGAATGATCAAACCCTAACCTCAAATTCAGAATTTATTTTTATTCTGGGTTT
1 AAGCAAAAGGAGATGAATGATCAAACCCTAACCTCAAATTCAGAATTTATTTTTATTCTGGGTTT
1756067 TTCAATATGTGGAAAGTCGAATCCTTCAATCTGATAAATCCGATAAGAAAGTCAACCCTTTGTTT
66 TTCAATATGTGGAAAGTCGAATCCTTCAATCTGATAAATCCGATAAGAAAGTCAACCCTTTGTTT
1756132 TTGACACCATAAAGAAAACCATGAAATGCAAATCC
131 TTGACACCATAAAGAAAACCATGAAATGCAAATCC
1756167 AAGCAAAAGGAGATGAATGATCAAACCCTAACCTCAAATTCAAGAA-TT-TTTTTATTCTGGG-T
1 AAGCAAAAGGAGATGAATGATCAAACCCTAACCTCAAATTC-AGAATTTATTTTTATTCTGGGTT
1756229 TTTCAATATGTGGAAAGTCGAATCCTTCAATCTGATAAATCCCGATAAGAAAGTCAACCCTTTGT
65 TTTCAATATGTGGAAAGTCGAATCCTTCAATCTGATAAAT-CCGATAAGAAAGTCAACCCTTTGT
*
1756294 TTTTGACACCATAATGAAAACCATGAAATGCAAATCC
129 TTTTGACACCATAAAGAAAACCATGAAATGCAAATCC
1756331 AA
1 AA
1756333 TTTCCAAGTG
Statistics
Matches: 163, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
163 41 0.25
164 75 0.46
165 43 0.26
166 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (165 bp):
AAGCAAAAGGAGATGAATGATCAAACCCTAACCTCAAATTCAGAATTTATTTTTATTCTGGGTTT
TTCAATATGTGGAAAGTCGAATCCTTCAATCTGATAAATCCGATAAGAAAGTCAACCCTTTGTTT
TTGACACCATAAAGAAAACCATGAAATGCAAATCC
Found at i:1756401 original size:20 final size:21
Alignment explanation
Indices: 1756376--1756422 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1756366 TTTATATTTC
1756376 TATTATT-ATAATTTATTTAT
1 TATTATTAATAATTTATTTAT
*
1756396 TATTATTAATAATTTCTTTAT
1 TATTATTAATAATTTATTTAT
1756417 T-TTATT
1 TATTATT
1756423 TTTTGTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTAATAATTTATTTAT
Found at i:1760158 original size:15 final size:15
Alignment explanation
Indices: 1760138--1760189 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
1760128 ATATTTAGCT
*
1760138 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGAG
1760153 GGGCGGGCGGATGAG
1 GGGCGGGCGGATGAG
*
1760168 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGAG
1760183 GGGCGGG
1 GGGCGGG
1760190 TAATGTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.08, C:0.15, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGAG
Found at i:1760905 original size:29 final size:29
Alignment explanation
Indices: 1760821--1760908 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
1760811 TGTGTATTTA
*
1760821 ATAAACACAAAAATAATATAATAAATATT
1 ATAAACACAAAAATAATATAATGAATATT
** *
1760850 A-AAA-A-AATTATCATGATAATGAAAATATT
1 ATAAACACAAAAATAAT-ATAATG--AATATT
1760879 ATAAACACAAAAATAATATAATGAATATT
1 ATAAACACAAAAATAATATAATGAATATT
1760908 A
1 A
1760909 AAAAAAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 6 0.13
27 6 0.13
28 3 0.07
29 15 0.33
30 3 0.07
31 7 0.15
32 6 0.13
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAACACAAAAATAATATAATGAATATT
Found at i:1761928 original size:17 final size:18
Alignment explanation
Indices: 1761891--1761928 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1761881 ATATTATGTA
1761891 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
1761909 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
1761926 TTT
1 TTT
1761929 GCTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:1765348 original size:27 final size:26
Alignment explanation
Indices: 1765309--1765369 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 26
1765299 AAAAGATGAG
1765309 GAAAAAAAAGAACAAGTGGCGGGTTA
1 GAAAAAAAAGAACAAGTGGCGGGTTA
1765335 GAAAAAAAAGGAACAAGTGGCGGGTTA
1 GAAAAAAAA-GAACAAGTGGCGGGTTA
1765362 GAAAAAAA
1 GAAAAAAA
1765370 GGACGGCGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.54, C:0.07, G:0.30, T:0.10
Consensus pattern (26 bp):
GAAAAAAAAGAACAAGTGGCGGGTTA
Found at i:1765587 original size:20 final size:17
Alignment explanation
Indices: 1765560--1765603 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1765550 TTTTATAATA
* *
1765560 ATTATATATATATATAT
1 ATTATTTATATATTTAT
1765577 GATTATTTATATATTTAT
1 -ATTATTTATATATTTAT
1765595 ATTATTTAT
1 ATTATTTAT
1765604 GTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTTATATATTTAT
Found at i:1774721 original size:18 final size:18
Alignment explanation
Indices: 1774698--1774744 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1774688 CAAAGAAAGT
* *
1774698 ATACATGTATACATATAC
1 ATACATATATACATACAC
1774716 ATACATACT-TACATACAC
1 ATACATA-TATACATACAC
1774734 ATACATATATA
1 ATACATATATA
1774745 AGGAAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (18 bp):
ATACATATATACATACAC
Found at i:1777855 original size:23 final size:23
Alignment explanation
Indices: 1777829--1777881 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1777819 TATATATTAC
**
1777829 ATTTTAAT-TTAATATTTTAAATA
1 ATTTTAATATTAA-ATTAAAAATA
*
1777852 ATTTGAATATTAAATTAAAAATA
1 ATTTTAATATTAAATTAAAAATA
*
1777875 AATTTAA
1 ATTTTAA
1777882 AATCAGATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTAATATTAAATTAAAAATA
Found at i:1779129 original size:21 final size:21
Alignment explanation
Indices: 1779012--1779129 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
1779002 ACGCGAAATA
**
1779012 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1779032 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1779052 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
1779073 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
1779094 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
1779115 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1779130 ACACATAAAT
Statistics
Matches: 72, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.33
21 45 0.62
22 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:1779161 original size:20 final size:20
Alignment explanation
Indices: 1779116--1779345 Score: 216
Period size: 20 Copynumber: 11.5 Consensus size: 20
1779106 CGATTTTCCA
* *
1779116 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
1779136 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
1779156 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
1779176 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * * *
1779196 ATATCGCAACGCGTATCTGT
1 AAATCGCAACGTGAATCCGT
1779216 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
1779236 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
1779256 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
1779276 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
1779296 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
1779316 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
1779336 AAATCACAAC
1 AAATCGCAAC
1779346 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 25, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
20 177 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:1779166 original size:40 final size:39
Alignment explanation
Indices: 1779116--1779345 Score: 250
Period size: 40 Copynumber: 5.7 Consensus size: 39
1779106 CGATTTTCCA
** *
1779116 AAATCGCAACGCGAACACATAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGCGAAC-TGTAAATCGCAACGAT-AATCCGT
* * *
1779156 ATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGCG-AACTGTAAATCGCAA--CGATAATCCGT
* *
1779196 ATATCGCAACGCGTATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCG-AACTGTAAATCGCAACGATAATCCGT
*
1779236 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAA-CTGTAAATCGCAACGATAATCCGT
*
1779276 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAA-CTGTAAATCGCAACGATAATCCGT
* *
1779316 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGAA-CTGTAAATCGCAAC
1779346 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 167 0.95
41 2 0.01
42 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (39 bp):
AAATCGCAACGCGAACTGTAAATCGCAACGATAATCCGT
Found at i:1780066 original size:24 final size:24
Alignment explanation
Indices: 1780027--1780073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1780017 AAATTTGGTC
1780027 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1780051 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1780074 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1782640 original size:19 final size:19
Alignment explanation
Indices: 1782600--1782697 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1782590 GATTCTCTCG
1782600 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1782620 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1782639 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1782653 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1782672 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1782691 TTACGAT
1 TTGCGAT
1782698 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1782648 original size:53 final size:52
Alignment explanation
Indices: 1782581--1782697 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 52
1782571 GAAATGAAAA
1782581 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1782634 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
1782686 TCGCATTACGAT
1 TCGCATTGCGAT
1782698 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1782780 original size:19 final size:19
Alignment explanation
Indices: 1782756--1782832 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 19
1782746 CCATTACATT
1782756 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1782775 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
1782789 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1782808 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1782827 TCGCAA
1 TCGCAA
1782833 CGAGAGAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 35 0.69
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:1782864 original size:52 final size:52
Alignment explanation
Indices: 1782752--1782870 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 52
1782742 TCAACCATTA
1782752 CATTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 CATTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
* ** ** *
1782804 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGATTTT
1 CATTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
1782856 CATTTCGCATTGCGA
1 CATTTCGCAATGCGA
1782871 TTCTCTCGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (52 bp):
CATTTCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
Found at i:1782869 original size:19 final size:19
Alignment explanation
Indices: 1782841--1782976 Score: 139
Period size: 19 Copynumber: 7.6 Consensus size: 19
1782831 AACGAGAGAA
*
1782841 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1782860 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
* *
1782876 TCG--TTGCGATTGTAATT
1 TCGCATTGCGATTTTCATT
**
1782893 TCCGTGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
1782913 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1782929 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1782946 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1782965 TCGCATTGCGAT
1 TCGCATTGCGAT
1782977 AGTCAATTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
14 17 0.18
16 8 0.08
17 8 0.08
18 2 0.02
19 49 0.51
20 13 0.13
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1782909 original size:53 final size:52
Alignment explanation
Indices: 1782841--1782976 Score: 209
Period size: 53 Copynumber: 2.6 Consensus size: 52
1782831 AACGAGAGAA
*
1782841 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATT
** * * *
1782893 TCCGTGTTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATT
1782946 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1782977 AGTCAATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
52 29 0.39
53 46 0.61
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATT
Found at i:1782938 original size:33 final size:33
Alignment explanation
Indices: 1782898--1782961 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1782888 TAATTTCCGT
1782898 GTTGCGATTTTCATTTCGCATTGCGATTTTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTTTCTC
1782931 GTTGCGATTTTCATTTCGCATTGCGATTTTC
1 GTTGCGATTTTCATTTCGCATTGCGATTTTC
1782962 ATTTCGCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTTTCTC
Found at i:1783102 original size:14 final size:14
Alignment explanation
Indices: 1783083--1783119 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1783073 CATCAATTAC
1783083 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1783097 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1783111 ACAAATCAA
1 ACAAATCAA
1783120 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1785084 original size:19 final size:19
Alignment explanation
Indices: 1785044--1785172 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
1785034 TAGTTTACTT
* *
1785044 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1785064 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1785083 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1785102 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
* **
1785116 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1785135 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
1785149 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1785168 TCGCA
1 TCGCA
1785173 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 18 0.20
15 1 0.01
16 6 0.07
17 6 0.07
18 1 0.01
19 44 0.49
20 13 0.15
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1785119 original size:14 final size:14
Alignment explanation
Indices: 1785100--1785156 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1785090 GCGAAATGAA
*
1785100 AATCGCAACGACAG
1 AATCGCAACGAAAG
1785114 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1785131 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1785147 AATCGCAACG
1 AATCGCAACG
1785157 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1785127 original size:33 final size:33
Alignment explanation
Indices: 1785081--1785172 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
1785071 GCGAAACCAA
*
1785081 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1785114 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
1785147 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
1785173 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1785190 original size:19 final size:19
Alignment explanation
Indices: 1785168--1785302 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1785158 GAAACCAAAA
*
1785168 TCGCATTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
1785187 TCGCGTTGCGATCTT-G--
1 TCGCGTTGCGATTTTGGTT
1785203 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
1785220 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTGGTT
**
1785236 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGGTT
1785253 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
1785272 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-GGTT
*
1785292 TCGTGTTGCGA
1 TCGCGTTGCGA
1785303 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 53 0.56
20 13 0.14
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTGGTT
Found at i:1785215 original size:33 final size:33
Alignment explanation
Indices: 1785173--1785265 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1785163 CAAAATCGCA
1785173 TTGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTC-TGTCG
1785206 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
**
1785239 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTGGTTTCGCGTTGCGATT
1785266 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 55 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
Found at i:1785509 original size:92 final size:93
Alignment explanation
Indices: 1785346--1785722 Score: 708
Period size: 92 Copynumber: 4.1 Consensus size: 93
1785336 TTGAATGGAT
1785346 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1785411 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1785439 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1785503 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1785531 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT--CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1785594 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1785622 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1785686 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1785714 AAATTTACT
1 AAATTTACT
1785723 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
90 10 0.04
91 79 0.28
92 145 0.52
93 44 0.16
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1785656 original size:183 final size:184
Alignment explanation
Indices: 1785346--1785722 Score: 720
Period size: 183 Copynumber: 2.0 Consensus size: 184
1785336 TTGAATGGAT
1785346 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-ACAGTGTTAAAGAATACAC
1785411 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
*
1785476 ACTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1785531 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT-CAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACAGTGTTAAAGAATACACA
1785595 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATA
*
1785660 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1785714 AAATTTACT
1 AAATTTACT
1785723 AAGCAATCTA
Statistics
Matches: 190, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
183 145 0.76
185 45 0.24
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1787443 original size:14 final size:14
Alignment explanation
Indices: 1787424--1787513 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1787414 TTGAAATGAA
1787424 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1787438 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1787455 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1787471 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1787490 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1787504 AATCGCAACG
1 AATCGCAACG
1787514 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1787461 original size:33 final size:33
Alignment explanation
Indices: 1787416--1787530 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1787406 TCTTTTGGTT
1787416 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1787449 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1787482 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1787515 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1787531 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1787462 original size:19 final size:18
Alignment explanation
Indices: 1787423--1787535 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1787413 GTTGAAATGA
1787423 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1787438 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1787455 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1787471 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1787488 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1787504 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1787521 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1787536 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1787566 original size:14 final size:14
Alignment explanation
Indices: 1787547--1787600 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1787537 TTTGGTTTCG
1787547 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1787561 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1787580 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1787594 CGTTGCG
1 CGTTGCG
1787601 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1787579 original size:33 final size:33
Alignment explanation
Indices: 1787531--1787611 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1787521 AAAATCGCAA
**
1787531 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1787564 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1787597 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
1787612 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1787647 original size:41 final size:41
Alignment explanation
Indices: 1787587--1787664 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1787577 TCGCGTTGCG
* *
1787587 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1787628 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1787665 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1787663 original size:21 final size:21
Alignment explanation
Indices: 1787588--1787663 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1787578 CGCGTTGCGA
*
1787588 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1787609 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1787629 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1787650 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1787664 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1787790 original size:33 final size:33
Alignment explanation
Indices: 1787743--1787813 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1787733 AATACTAACT
* *
1787743 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1787776 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1787809 TGAAA
1 TGAAA
1787814 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1788047 original size:22 final size:22
Alignment explanation
Indices: 1787995--1788049 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1787985 TGGTTGTGAG
**
1787995 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1788017 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1788039 GGATTTCTTCG
1 GGATTTCTTCG
1788050 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1788220 original size:20 final size:20
Alignment explanation
Indices: 1788195--1788348 Score: 202
Period size: 20 Copynumber: 7.7 Consensus size: 20
1788185 CTTTAAATAT
1788195 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1788215 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
1788237 -TCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
*
1788256 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1788276 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1788296 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1788316 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1788336 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1788349 TCATATTCGC
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 96 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1788360 original size:60 final size:60
Alignment explanation
Indices: 1788197--1788365 Score: 223
Period size: 60 Copynumber: 2.8 Consensus size: 60
1788187 TTAAATATCG
** *
1788197 CGTTGCGATTTACGGATACGCGTTGCGATTTT-ATGTATTATCGTTGCGATTTACGAATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTCA--TATTCGCGTTGCGATTTACGAATACA
* * * ** * *
1788258 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTCATATTCGCGTTGCGATTTACGAATACA
1788318 CGTTGCGATTTACGGATACGCGTTGCGATTTTCATATTCGCGTTGCGA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTCATATTCGCGTTGCGA
1788366 ATTTGTACTA
Statistics
Matches: 91, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
60 62 0.68
61 29 0.32
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTCATATTCGCGTTGCGATTTACGAATACA
Found at i:1788362 original size:40 final size:40
Alignment explanation
Indices: 1788194--1788365 Score: 184
Period size: 40 Copynumber: 4.3 Consensus size: 40
1788184 GCTTTAAATA
*
1788194 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTA-TGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACAG-AT
** * * *
1788235 TATCGTTGCGATTTACGAATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
* * ** *
1788275 ACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
* * * *
1788315 ACACGTTGCGATTTACGGATACGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
1788355 TCGCGTTGCGA
1 TCGCGTTGCGA
1788366 ATTTGTACTA
Statistics
Matches: 109, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
40 80 0.73
41 29 0.27
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
Found at i:1788379 original size:21 final size:21
Alignment explanation
Indices: 1788355--1788407 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1788345 ATTTTCATAT
*
1788355 TCGCGTTGCGAATTTGTACTA
1 TCGCATTGCGAATTTGTACTA
*
1788376 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGAATTTGTACTA
1788397 TCGCATTGCGA
1 TCGCATTGCGA
1788408 TTTTCAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGAATTTGTACTA
Found at i:1791580 original size:16 final size:16
Alignment explanation
Indices: 1791559--1791589 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1791549 TGATGTTGTG
1791559 TATATGCATATGTATA
1 TATATGCATATGTATA
*
1791575 TATATGTATATGTAT
1 TATATGCATATGTAT
1791590 GAGAGATACC
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:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (16 bp):
TATATGCATATGTATA
Found at i:1794104 original size:2 final size:2
Alignment explanation
Indices: 1794097--1794122 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1794087 ATAAATTACA
1794097 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
1794123 TTTTATTGAA
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):
AT
Found at i:1797209 original size:38 final size:37
Alignment explanation
Indices: 1797158--1797236 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 37
1797148 AAACCCGAAT
1797158 CCGACCCGACCCGAATATCACACTTAAAAGAACCTGAC
1 CCGACCCGACCCGAATATCACACTTAAAA-AACCTGAC
*
1797196 CCGACTCGACCCGAATATCACACTTAAAAAACCTGAC
1 CCGACCCGACCCGAATATCACACTTAAAAAACCTGAC
1797233 CCGA
1 CCGA
1797237 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 12 0.30
38 28 0.70
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Consensus pattern (37 bp):
CCGACCCGACCCGAATATCACACTTAAAAAACCTGAC
Found at i:1797924 original size:29 final size:29
Alignment explanation
Indices: 1797882--1797948 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
1797872 TTTGACGTAT
*
1797882 GTCGCCATGCTATCCGGGCGACCTACTAG
1 GTCGCCATGCTATCCGGCCGACCTACTAG
1797911 GTCGCCATGCTATCCGGCCGACCTACTAG
1 GTCGCCATGCTATCCGGCCGACCTACTAG
1797940 GTCGCCATG
1 GTCGCCATG
1797949 TCTTCCCGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.21
Consensus pattern (29 bp):
GTCGCCATGCTATCCGGCCGACCTACTAG
Found at i:1798091 original size:29 final size:29
Alignment explanation
Indices: 1798058--1798162 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
1798048 GGAGCAGGAG
* *
1798058 GGAGTGCATGACGACCTACAAGGTTGTCA
1 GGAGTGCATGACGACCTACAAGGTCGCCA
* *
1798087 GGAGTGCATGGCGACCTACAAGGTCGCCT
1 GGAGTGCATGACGACCTACAAGGTCGCCA
* * * *
1798116 GGAATGCATGACGACTTACAAGGTCACCC
1 GGAGTGCATGACGACCTACAAGGTCGCCA
*
1798145 GGAAG-GCATGGCGACCTA
1 GG-AGTGCATGACGACCTA
1798163 TGCTTGGGGA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
29 62 0.98
30 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.31, T:0.17
Consensus pattern (29 bp):
GGAGTGCATGACGACCTACAAGGTCGCCA
Found at i:1801137 original size:10 final size:10
Alignment explanation
Indices: 1801124--1801175 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
1801114 AACACAAATG
1801124 AACGAACATA
1 AACGAACATA
1801134 AACGAACATAATA
1 AACGAAC---ATA
*
1801147 AATGAACATA
1 AACGAACATA
1801157 AACGAACATA
1 AACGAACATA
1801167 TAACGAACA
1 -AACGAACA
1801176 ACACAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 19 0.53
11 8 0.22
13 9 0.25
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:1801157 original size:23 final size:23
Alignment explanation
Indices: 1801107--1801175 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1801097 CATTTAAATG
* *
1801107 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACA-TAATAAACGAAC
*
1801131 ATAAACGAACATAATAAATGAAC
1 ATAAACGAACATAATAAACGAAC
1801154 ATAAACGAACAT-AT-AACGAAC
1 ATAAACGAACATAATAAACGAAC
1801175 A
1 A
1801176 ACACAAACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
21 7 0.17
22 2 0.05
23 21 0.51
24 11 0.27
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.13
Consensus pattern (23 bp):
ATAAACGAACATAATAAACGAAC
Found at i:1806130 original size:2 final size:2
Alignment explanation
Indices: 1806125--1806152 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1806115 CTTCAAACGA
1806125 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
1806153 TGTAAATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1807554 original size:11 final size:12
Alignment explanation
Indices: 1807524--1807552 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1807514 ATATTAAAAT
1807524 TTAAAAAT-ATA
1 TTAAAAATAATA
1807535 TTAAAAATAATA
1 TTAAAAATAATA
1807547 TTAAAA
1 TTAAAA
1807553 TAGAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAAATAATA
Found at i:1813661 original size:30 final size:29
Alignment explanation
Indices: 1813627--1813690 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1813617 GCTTGTATAT
*
1813627 TTTTATTTTTGGTATAATTAGATACTCAAC
1 TTTTA-TTTTAGTATAATTAGATACTCAAC
* *
1813657 TTTTA-TTTAGTGTAATTAGATACTTAAC
1 TTTTATTTTAGTATAATTAGATACTCAAC
*
1813685 ATTTAT
1 TTTTAT
1813691 ACATACATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 24 0.83
30 5 0.17
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTATTTTAGTATAATTAGATACTCAAC
Found at i:1813704 original size:2 final size:2
Alignment explanation
Indices: 1813697--1813772 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1813687 TTATACATAC
1813697 AT AT AT AT 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 AT AT AT AT
1813739 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
1813773 GATACGTTCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1815609 original size:30 final size:30
Alignment explanation
Indices: 1815573--1815644 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1815563 CCCGCAGGAC
*
1815573 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1815603 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
1815633 CTGTCCATAGGT
1 CTATCCAGAGGT
1815645 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:1815669 original size:31 final size:30
Alignment explanation
Indices: 1815631--1815755 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 30
1815621 GATCCTCGGC
*
1815631 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATAGGTTCCGAAGAACATAGGT
* **
1815661 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATAGGTTCCGAAGAACATAGGT
* *
1815692 ATACTGTCCATATG-TCTCGAA-AGACAGAGGT
1 A-ACTGTCCATAGGTTC-CGAAGA-ACATAGGT
* *
1815723 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATAGGTTCCGAAGAACATAGGT
1815755 A
1 A
1815756 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 5 0.06
31 48 0.62
32 22 0.28
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (30 bp):
AACTGTCCATAGGTTCCGAAGAACATAGGT
Found at i:1816543 original size:21 final size:21
Alignment explanation
Indices: 1816517--1816560 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1816507 ATTTTATTCG
* *
1816517 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1816538 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1816559 CT
1 CT
1816561 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1820835 original size:30 final size:30
Alignment explanation
Indices: 1820799--1820870 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
1820789 CCCGCAGGAC
1820799 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1820829 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1820859 CTGTCCATAGGT
1 CTATCCAGAGGT
1820871 TCCGAAGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1820895 original size:31 final size:30
Alignment explanation
Indices: 1820854--1820981 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 30
1820844 AAAGATCCTC
* *
1820854 GGTAACTGTCCATAGGTTCCGAAGAACCTA
1 GGTAACTGTCCATATGTTCCGAAGAACATA
**
1820884 GGTGAACTGTCCATATGTTCCTTAGAACATA
1 GGT-AACTGTCCATATGTTCCGAAGAACATA
1820915 GGTATACTGTCCATATG-TCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTTC-CGAAGA-ACATA
*
1820946 GGTAATTCTGTCCATATGTTCCGTAGAACATA
1 GGTAA--CTGTCCATATGTTCCGAAGAACATA
1820978 GGTA
1 GGTA
1820982 CCCTCGACTC
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
30 8 0.10
31 49 0.59
32 23 0.28
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCGAAGAACATA
Found at i:1821771 original size:21 final size:21
Alignment explanation
Indices: 1821745--1821788 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1821735 ATTTTATTCG
* *
1821745 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1821766 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1821787 CT
1 CT
1821789 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1828013 original size:18 final size:18
Alignment explanation
Indices: 1827971--1828014 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1827961 AAAATCATCG
*
1827971 TATCATAAAGTAATATCA
1 TATCATCAAGTAATATCA
1827989 TATCATCAAGTAATATCA
1 TATCATCAAGTAATATCA
1828007 TATCATCA
1 TATCATCA
1828015 TTTTGTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (18 bp):
TATCATCAAGTAATATCA
Found at i:1830278 original size:2 final size:2
Alignment explanation
Indices: 1830271--1830308 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1830261 GGTTACAAGA
1830271 AT AT 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 AT AT
1830309 TCATTCTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1834859 original size:26 final size:26
Alignment explanation
Indices: 1834830--1834882 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1834820 GAGGACTTAC
1834830 ATGTAATATCATGTGACACGACCAAT
1 ATGTAATATCATGTGACACGACCAAT
*
1834856 ATGTAATATCATGTGACACGTCCAAT
1 ATGTAATATCATGTGACACGACCAAT
1834882 A
1 A
1834883 AACCTTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (26 bp):
ATGTAATATCATGTGACACGACCAAT
Found at i:1841527 original size:59 final size:60
Alignment explanation
Indices: 1841400--1841546 Score: 167
Period size: 59 Copynumber: 2.5 Consensus size: 60
1841390 TCTTTAAACA
* * * *
1841400 TTTT-AATATTATAATTTCAT-CCTCAAACTATAACTCTCATTATAGATTAGTTCTTAAAT
1 TTTTGAATATTCTAATTTCATCCCT-AAATTATAACCCTCATTATAGATTAGTCCTTAAAT
* * * *
1841459 TTTTGAATATTCTAATTTCATCCCTAAATTATTACCCTCTTTCTA-ATTGGTCCTTAAAT
1 TTTTGAATATTCTAATTTCATCCCTAAATTATAACCCTCATTATAGATTAGTCCTTAAAT
* *
1841518 TTTTGAATATTCCAATTT-ATCCCCAAATT
1 TTTTGAATATTCTAATTTCATCCCTAAATT
1841547 CATCCAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 10 0.13
59 33 0.43
60 30 0.39
61 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.46
Consensus pattern (60 bp):
TTTTGAATATTCTAATTTCATCCCTAAATTATAACCCTCATTATAGATTAGTCCTTAAAT
Found at i:1843033 original size:7 final size:7
Alignment explanation
Indices: 1843023--1843056 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1843013 TTTGTTATTT
1843023 GGTTTTG
1 GGTTTTG
1843030 GGTTTTG
1 GGTTTTG
1843037 GGTTTTG
1 GGTTTTG
1843044 GGTTTTG
1 GGTTTTG
*
1843051 CGTTTT
1 GGTTTT
1843057 AGTTATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.38, T:0.59
Consensus pattern (7 bp):
GGTTTTG
Found at i:1847559 original size:2 final size:2
Alignment explanation
Indices: 1847552--1847582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1847542 ACCAAAAAGG
1847552 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 T
1847583 TGTTGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1852517 original size:21 final size:22
Alignment explanation
Indices: 1852493--1852545 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1852483 TAAGGAAGCA
1852493 ATAAAATAAAGAT-AACAGTGT
1 ATAAAATAAAGATAAACAGTGT
*
1852514 ATAAAATGAAGATAAACAGTGT
1 ATAAAATAAAGATAAACAGTGT
*
1852536 ACAAAATAAA
1 ATAAAATAAA
1852546 AATGAAGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (22 bp):
ATAAAATAAAGATAAACAGTGT
Found at i:1854579 original size:105 final size:105
Alignment explanation
Indices: 1854413--1855393 Score: 1845
Period size: 105 Copynumber: 9.3 Consensus size: 105
1854403 TGTTTCGAAC
** * * *
1854413 CCAATATCCTTCGTTGTGAAGCAGCAATTGGCTCTGAAATTAAGAAATGTTCGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
1854478 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
1854518 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTAGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1854583 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1854623 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
1854688 GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1854728 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
1854793 GGTCCCTTCGTCGTGAAGTTGAACTCGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1854833 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
1854898 GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1854938 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1855003 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1855043 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
1855108 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1855148 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1855213 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1855253 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1855318 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1855358 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1855394 GGTAAAACCT
Statistics
Matches: 859, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 859 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:1864358 original size:12 final size:12
Alignment explanation
Indices: 1864341--1864366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1864331 TCCTCCACGA
1864341 TTCGGCTGCCTC
1 TTCGGCTGCCTC
1864353 TTCGGCTGCCTC
1 TTCGGCTGCCTC
1864365 TT
1 TT
1864367 TGATCATCTT
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:0.00, C:0.38, G:0.23, T:0.38
Consensus pattern (12 bp):
TTCGGCTGCCTC
Found at i:1868997 original size:12 final size:11
Alignment explanation
Indices: 1868963--1868997 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
1868953 TATTACAAAA
1868963 TATCATAAAATT
1 TATCA-AAAATT
1868975 TATCAAAAATT
1 TATCAAAAATT
1868986 TATCAAATAATT
1 TATCAAA-AATT
1868998 ATTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (11 bp):
TATCAAAAATT
Done.